From d97e486fb43db64a601b5cd3d0c7c17c2199a279 Mon Sep 17 00:00:00 2001
From: Cheryl Foil <cheryl.foil@gmail.com>
Date: Tue, 1 Jul 2008 21:02:36 +0000
Subject: [PATCH 001/314] Small modifications to place comments into the parse
 tree (Fairly inflexible at the moment)

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2008-cherylfoil@10620 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Source/CParse/cscanner.c | 10 ++++++++++
 Source/CParse/parser.y   | 33 ++++++++++++++++++++++++++++++++-
 2 files changed, 42 insertions(+), 1 deletion(-)

diff --git a/Source/CParse/cscanner.c b/Source/CParse/cscanner.c
index 2a0d341b5..140b7fedd 100644
--- a/Source/CParse/cscanner.c
+++ b/Source/CParse/cscanner.c
@@ -426,6 +426,14 @@ int yylook(void) {
 	if ((strncmp(loc,"/*@SWIG@",6) == 0) && (loc[Len(cmt)-3] == '@')) {
 	  scanner_locator(cmt);
 	}
+	
+	if (strncmp(loc, "/**", 3) == 0 || strncmp(loc, "///", 3) == 0||strncmp(loc, "/*!", 3) == 0||strncmp(loc, "//!", 3) == 0) {
+	  printf("Doxygen Comment: %s lines %d-%d [%s]\n", Char(Scanner_file(scan)), Scanner_start_line(scan), Scanner_line(scan), loc);
+	  yylval.str =  NewString(loc);
+	  return DOXYGENSTRING;
+	}
+
+
       }
       break;
     case SWIG_TOKEN_ENDLINE:
@@ -897,6 +905,8 @@ int yylex(void) {
     return (ID);
   case POUND:
     return yylex();
+  case SWIG_TOKEN_COMMENT:
+	  return yylex();
   default:
     return (l);
   }
diff --git a/Source/CParse/parser.y b/Source/CParse/parser.y
index 4fe8b47ed..6a835c7f3 100644
--- a/Source/CParse/parser.y
+++ b/Source/CParse/parser.y
@@ -55,6 +55,14 @@ static int      max_class_levels = 0;
 static int      class_level = 0;
 static Node   **class_decl = NULL;
 
+/* -----------------------------------------------------------------------------
+ *                            Doxygen Comment Globals
+ * ----------------------------------------------------------------------------- */
+
+int isComment = 0; /* boolean for parsing Doxygen Comments */
+String *currentComment = 0; /* Location of the stored Doxygen Comment */
+static String *sideDoxComments = 0;
+
 /* -----------------------------------------------------------------------------
  *                            Assist Functions
  * ----------------------------------------------------------------------------- */
@@ -71,6 +79,12 @@ static Node *new_node(const String_or_char *tag) {
   set_nodeType(n,tag);
   Setfile(n,cparse_file);
   Setline(n,cparse_line);
+  /* Sets Comment if a Comment is Availible */
+  if(isComment){
+    String *copyComment = Copy(currentComment);
+    Setattr(n,"comment",copyComment);
+    isComment = 0;
+  }	 
   return n;
 }
 
@@ -1440,6 +1454,7 @@ static void tag_nodes(Node *n, const String_or_char *attrname, DOH *value) {
 %token <str> OPERATOR
 %token <str> COPERATOR
 %token PARSETYPE PARSEPARM PARSEPARMS
+%token <str> DOXYGENSTRING 
 
 %left  CAST
 %left  QUESTIONMARK
@@ -1511,6 +1526,7 @@ static void tag_nodes(Node *n, const String_or_char *attrname, DOH *value) {
 %type <ptype>    type_specifier primitive_type_list ;
 %type <node>     fname stringtype;
 %type <node>     featattr;
+%type <str>	 doxygen_comment;
 
 %%
 
@@ -1568,6 +1584,7 @@ interface      : interface declaration {
 declaration    : swig_directive { $$ = $1; }
                | c_declaration { $$ = $1; } 
                | cpp_declaration { $$ = $1; }
+               | doxygen_comment { $$ = $1; }
                | SEMI { $$ = 0; }
                | error {
                   $$ = 0;
@@ -2811,6 +2828,7 @@ warn_directive : WARN string {
                }
                ;
 
+
 /* ======================================================================
  *                              C Parsing
  * ====================================================================== */
@@ -3132,6 +3150,20 @@ c_constructor_decl : storage_class type LPAREN parms RPAREN ctor_end {
                 }
                 ;
 
+/* ------------------------------------------------------------
+   A Doxygen Comment (a string in Doxygen Format)
+   ------------------------------------------------------------ */
+
+doxygen_comment : DOXYGENSTRING 
+	{
+		currentComment = NewString($1);
+		isComment = 1;
+		$$ = 0;
+	}
+	;
+
+
+
 /* ======================================================================
  *                       C++ Support
  * ====================================================================== */
@@ -5977,4 +6009,3 @@ ParmList *Swig_cparse_parms(String *s) {
    /*   Printf(stdout,"typeparse: '%s' ---> '%s'\n", s, top); */
    return top;
 }
-

From 848e1b55fc8edb487e9b654b6cf7d3a55f1937ee Mon Sep 17 00:00:00 2001
From: Cheryl Foil <cheryl.foil@gmail.com>
Date: Tue, 1 Jul 2008 22:06:28 +0000
Subject: [PATCH 002/314] Adding the Translator Module, which handles blobs of
 Doxygen Comments. Being heavily reworked at the moment.

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2008-cherylfoil@10622 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Source/DoxygenTranslator/DoxygenEntity.cpp    |   84 ++
 Source/DoxygenTranslator/DoxygenEntity.h      |   23 +
 .../DoxygenTranslator/DoxygenTranslator.cpp   |  630 ++++++++++
 Source/DoxygenTranslator/Skeleton             | 1070 +++++++++++++++++
 Source/DoxygenTranslator/example.i            |   19 +
 5 files changed, 1826 insertions(+)
 create mode 100644 Source/DoxygenTranslator/DoxygenEntity.cpp
 create mode 100644 Source/DoxygenTranslator/DoxygenEntity.h
 create mode 100644 Source/DoxygenTranslator/DoxygenTranslator.cpp
 create mode 100755 Source/DoxygenTranslator/Skeleton
 create mode 100644 Source/DoxygenTranslator/example.i

diff --git a/Source/DoxygenTranslator/DoxygenEntity.cpp b/Source/DoxygenTranslator/DoxygenEntity.cpp
new file mode 100644
index 000000000..9b02ade12
--- /dev/null
+++ b/Source/DoxygenTranslator/DoxygenEntity.cpp
@@ -0,0 +1,84 @@
+#include "DoxygenEntity.h"
+#include <string>
+
+/* Little data class for Doxygen Commands */
+
+
+/* Basic node for commands that have
+ * nothing after them
+ * example: \n
+ */
+string commandArray2[] = {"a", "addindex", "addtogroup", "anchor", "arg", "attention",
+		"author", "b", "brief", "bug", "c", "callgraph", "callergraph", "category",
+		"class", "code", "cond", "copybrief", "copydetails", "copydoc", "date", "def",
+		"defgroup", "deprecated", "details", "dir", "dontinclude", "dot", "dotfile", "e",
+		"else", "elseif", "em", "endcode", "endcond", "enddot", "endhtmlonly", "endif",
+		"endlatexonly", "endlink", "endmanonly", "endmsc", "endverbatim", "endxmlonly",
+		"enum", "example", "exception", "f$", "f[", "f]", "f{", "f}", "file", "fn", "headerfile",
+		"hideinitializer", "htmlinclude", "htmlonly", "if", "ifnot", "image", "include",
+		"includelineno", "ingroup", "internal", "invariant", "interface", "latexonly", "li",
+		"line", "link", "mainpage", "manonly", "msc", "n", "name", "namespace", "nosubgrouping",
+		"note", "overload", "p", "package", "page", "par", "paragraph", "param", "post", "pre",
+		"private", "privatesection", "property", "protected", "protectedsection", "protocol",
+		"public", "publicsection", "ref", "relates", "relatesalso", "remarks", "return", "retval",
+		"sa", "section", "see", "showinitializer", "since", "skip", "skipline", "struct", "subpage",
+		"subsection", "subsubsection", "test", "throw", "todo", "tparam", "typedef", "union", "until",
+		"var", "verbatim", "verbinclude", "version", "warning", "weakgroup", "xmlonly", "xrefitem",
+		"$", "@", string(1, 92), string(1, '&'), "~", "<", ">", string(1, '#'), "%"};
+
+string findCommand(int commandNum){
+
+	int arraySize = sizeof(commandArray2)/sizeof(*commandArray2);
+	if (commandNum - 101 >= 0 && commandNum - 101 < arraySize){
+		return commandArray2[commandNum];
+	}
+
+	return "" ;
+}
+
+DoxygenEntity::DoxygenEntity(int typeEnt){
+    typeOfEntity = typeEnt;
+    data = "";
+    isLeaf = 1;
+}
+
+/* Basic node for commands that have
+ * only 1 thing after them
+ * example: \b word
+ * OR holding a string
+ */
+DoxygenEntity::DoxygenEntity(int typeEnt, string param1){
+    typeOfEntity = typeEnt;
+    data = param1;
+    isLeaf = 1;
+}
+
+/* Nonterminal node
+ * contains
+ */
+DoxygenEntity::DoxygenEntity(int typeEnt, list <DoxygenEntity> entList){
+    typeOfEntity = typeEnt;
+    data = "";
+    isLeaf = 0;
+    entityList = entList;
+}
+
+
+void DoxygenEntity::printEntity(){
+	if (isLeaf) {
+		cout << "Node Command: " << findCommand(typeOfEntity);
+		if (data.compare("") != 0) cout << "Node Data: " << data;
+		cout << endl;
+	}
+	else{
+		list<DoxygenEntity>::iterator p = entityList.begin();
+		while (p != entityList.end()){
+			(*p).printEntity();
+			p++;
+		}
+	}
+}
+
+DoxygenEntity::~DoxygenEntity()
+{
+}
diff --git a/Source/DoxygenTranslator/DoxygenEntity.h b/Source/DoxygenTranslator/DoxygenEntity.h
new file mode 100644
index 000000000..8330e4507
--- /dev/null
+++ b/Source/DoxygenTranslator/DoxygenEntity.h
@@ -0,0 +1,23 @@
+
+#include <cstdlib>
+#include <iostream>
+#include <string>
+#include <list>
+
+using namespace std;
+
+class DoxygenEntity{
+
+public:
+	DoxygenEntity(int typeEnt);
+	DoxygenEntity(int typeEnt, string param1);
+	DoxygenEntity(int typeEnt, list <DoxygenEntity> entList);
+	virtual ~DoxygenEntity();
+	void printEntity();
+    int typeOfEntity;
+    list <DoxygenEntity> entityList;
+    string data;
+    int isLeaf;
+};
+
+
diff --git a/Source/DoxygenTranslator/DoxygenTranslator.cpp b/Source/DoxygenTranslator/DoxygenTranslator.cpp
new file mode 100644
index 000000000..dadea41b5
--- /dev/null
+++ b/Source/DoxygenTranslator/DoxygenTranslator.cpp
@@ -0,0 +1,630 @@
+/* The main class for translating blobs of Doxygen for SWIG
+ * by Cheryl Foil, mentor Olly Betts, for Google's Summer of Code Program
+ * Currently the spacing/format on this is a bit goofy in places, due to shuffling code
+ * between 2 editors! Apologies for anyone combing through it :)
+ */
+//TODO DOH instead of STL?
+//TODO Most commands are not fully implemented
+
+#include <cstdlib>
+#include <iostream>
+#include <fstream>
+#include <string>
+#include <list>
+#include "DoxygenEntity.h"
+
+using namespace std;
+
+
+//////////////////////////////////////////
+/*Set these to pick what internal functions
+to test. */
+
+//int testCommandParsingFunctions = 1;// not implemented
+
+int testCodeCrawlingFunctions = 1;
+int demonstrateParsing = 0;
+
+//////////////////////////////////////////
+
+
+
+/* Globals*/
+
+
+// An array of all the commands and my generic description tag, plaindescription
+
+string commandArray[] = {"a", "addindex", "addtogroup", "anchor", "arg", "attention",
+		"author", "b", "brief", "bug", "c", "callgraph", "callergraph", "category",
+		"class", "code", "cond", "copybrief", "copydetails", "copydoc", "date", "def",
+		"defgroup", "deprecated", "details", "dir", "dontinclude", "dot", "dotfile", "e",
+		"else", "elseif", "em", "endcode", "endcond", "enddot", "endhtmlonly", "endif",
+		"endlatexonly", "endlink", "endmanonly", "endmsc", "endverbatim", "endxmlonly",
+		"enum", "example", "exception", "f$", "f[", "f]", "f{", "f}", "file", "fn", "headerfile",
+		"hideinitializer", "htmlinclude", "htmlonly", "if", "ifnot", "image", "include",
+		"includelineno", "ingroup", "internal", "invariant", "interface", "latexonly", "li",
+		"line", "link", "mainpage", "manonly", "msc", "n", "name", "namespace", "nosubgrouping",
+		"note", "overload", "p", "package", "page", "par", "paragraph", "param", "post", "pre",
+		"private", "privatesection", "property", "protected", "protectedsection", "protocol",
+		"public", "publicsection", "ref", "relates", "relatesalso", "remarks", "return", "retval",
+		"sa", "section", "see", "showinitializer", "since", "skip", "skipline", "struct", "subpage",
+		"subsection", "subsubsection", "test", "throw", "todo", "tparam", "typedef", "union", "until",
+		"var", "verbatim", "verbinclude", "version", "warning", "weakgroup", "xmlonly", "xrefitem",
+		"$", "@", string(1, 92), string(1, '&'), "~", "<", ">", string(1, '#'), "%", "plaindescription"};
+
+
+string sectionIndicators[] = { "attention", "author", "brief", "bug", "cond", "date", "deprecated", "details",
+		"else", "elseif", "endcond", "endif", "exception", "if", "ifnot", "invariant", "note", "par", "param",
+		"tparam", "post" , "pre", "remarks", "return", "retval", "sa", "see", "since", "test", "throw", "todo",
+		"version", "warning", "xrefitem" };
+
+
+ int startIndex = 0;
+ int endIndex = 0;
+ int isNewLine = 0;
+
+ string doxygenString = "";
+ int briefDescExists = 0;
+
+ /* Entity list is the root list.
+  * it is arranged this way to help documentation modules,
+  * such as the javaDoc one, "sort" entities where they need to.
+  */
+
+ list <DoxygenEntity> rootList;
+
+/* General (untested) assist methods */
+
+ string StringToLower(string stringToConvert)
+
+ {//change each element of the string to lower case
+
+    for(unsigned int i=0;i<stringToConvert.length();i++)
+    {
+    stringToConvert[i] = tolower(stringToConvert[i]);
+    }
+    return stringToConvert;//return the converted string
+ }
+
+ int findCommand(string smallString){
+
+ 	smallString = StringToLower(smallString);
+ 	int a;
+ 	for (int i = 0; i < sizeof(commandArray)/sizeof(*commandArray); i++){
+ 		if( (a = smallString.compare(commandArray[i])) == 0){
+ 			return 101 + i;
+ 		}
+
+
+ 	}
+ 	return -1;
+ }
+
+ /* isSectionIndicator returns a boolean if the command is a section indicator
+  * This is a helper method for finding the end of a paragraph
+  * by Doxygen's terms
+  */
+ int isSectionIndicator(string smallString){
+ 	smallString = StringToLower(smallString);
+
+ 	for (int i = 0; i < sizeof(commandArray)/sizeof(*commandArray); i++){
+ 		if( smallString.compare(commandArray[i]) == 0){
+ 			return 1;
+ 		}
+ 	}
+ 	return 0;
+ }
+
+
+ /* HELPER METHODS
+  * To test these, change the flags at the top of this class
+  */
+
+ /* Tiny method to compartmentalise the removal of all optional comment fluff such as ///
+  * or **** that often occurs before commment blobs.
+  */
+ int clearFluff(int startInd){
+	int startIndex = startInd;
+ 	int amountRemoved = 0;
+
+ 	while(doxygenString[startIndex] == '/'|| doxygenString[startIndex] == '!' || doxygenString[startIndex] == '*'
+ 			|| doxygenString[startIndex] == '\n' || doxygenString[startIndex] == ' '){
+ 		startIndex++;
+ 		amountRemoved++;
+ 		}
+
+ 	return startIndex;
+ }
+
+ /* Returns the next word ON THE CURRENT LINE ONLY
+  * if a new line is encountered, returns a blank string.
+  * Updates the index it is given after completion.
+  */
+
+ string getNextWord(int &startInd){
+	int startIndex = startInd;
+ 	string nextWord = "";
+ 	while (doxygenString[startIndex] == '/'|| doxygenString[startIndex] == ' '
+ 		|| doxygenString[startIndex] == '*' || doxygenString[startIndex]== '\n'
+		|| doxygenString[startIndex] == '!'){
+ 		if(doxygenString[startIndex]== '\n') return nextWord;
+ 		startIndex++;
+ 		//cout << "Start Index" << startIndex << endl;
+ 		}
+ 	//cout << doxygenString[startIndex] << endl;
+ 	int endIndex = startIndex;
+
+ 	while (doxygenString[endIndex]!= '\n' && doxygenString[endIndex]!= ' '){
+ 		endIndex++;
+ 		//cout << "End Index " << endIndex << endl;
+ 		}
+ 	nextWord = doxygenString.substr(startIndex, endIndex - startIndex);
+ 	startInd = endIndex;
+ 	//cout << "Next Word :" << nextWord << ":" << endl;
+ 	return nextWord;
+ }
+
+ /* Returns the string remaining on a line
+  * and moved the index to the NEXT line
+  * returns "" if nothing on the current line.
+  */
+ string getOneLine(int &startInd){
+	int startIndex = startInd;
+ 	while (doxygenString[startIndex] == '/'|| doxygenString[startIndex] == ' '
+ 		|| doxygenString[startIndex] == '*' || doxygenString[startIndex]== '\n'
+		|| doxygenString[startIndex] == '!'){
+ 		if(doxygenString[startIndex]== '\n') return "";
+ 		startIndex++;
+ 		}
+
+	int endIndex = startIndex;
+ 	while ((endIndex != doxygenString.length())&& (doxygenString[endIndex] != '\n')){
+ 		endIndex++;
+ 		//cout << doxygenString[endIndex] << "End Index: " << endIndex << endl;
+ 		}
+ 	string returnedLine = doxygenString.substr(startIndex, endIndex - startIndex);
+ 	if (doxygenString[endIndex] == '\n' && (endIndex < doxygenString.length())) endIndex++;
+ 	startInd = endIndex;
+ 	return returnedLine;
+ }
+
+/* Returns a Paragraph- defined in Doxygen to be a paragraph of text
+ * seperate by either a structural command or a blank line
+ * This method is VERY messy currently
+ */
+ //TODO fix getStringTilEndOfParagraph to be more forgiving, work on ' ' characters
+ string getStringTilEndOfParagraph(int &startInd){
+	 if (startInd >= doxygenString.length()) return "";
+	int startIndex = startInd;
+	int endIndex = startInd;
+ 	string description = "";
+ 	/* Find the End of the description */
+ 	int keepLooping = 1;
+ 	int spareIndex = 0;
+ 	int counter;
+ 	int finalIndex;
+ 	while(keepLooping && endIndex < doxygenString.length()){
+		if (doxygenString[endIndex] == '\n'){
+			//cout << "1 ";
+			counter = endIndex;
+			if ( keepLooping && endIndex < doxygenString.length()-1) {
+				counter++;
+				//cout << "Counter :" << counter << endl;
+				while(keepLooping && endIndex < doxygenString.length() && (doxygenString[counter] == ' ' ||
+				               doxygenString[counter] == '*'|| doxygenString[counter] == '\n'|| doxygenString[counter] == '/'
+				            	   || doxygenString[counter] == '!') ){
+									if(doxygenString[counter] == '\n') {
+										//cout << "Blank line found" << endl;
+										keepLooping = 0;
+										finalIndex = counter;}
+									else{ counter++;}
+									}
+
+			}
+			//endIndex = counter;
+		}
+ 		else if (doxygenString[endIndex] == 92 || doxygenString[endIndex] == '@'){
+ 			//cout << "2 ";
+			spareIndex = endIndex;
+ 			if (isSectionIndicator(getNextWord(spareIndex))) keepLooping = 0;
+ 			}
+		else if(endIndex < doxygenString.length() - 1
+				&& string("*/").compare(doxygenString.substr(endIndex , endIndex  + 1)) == 0){
+			//cout << "3 ";
+			keepLooping = 0;
+		}
+ 		if(keepLooping){
+ 			//cout << "4 ";
+ 			endIndex++;
+ 		}
+ 	}
+ 	//cout << "Done with EndIndex" << endl;
+ 	while(doxygenString[startIndex] == '!' || doxygenString[startIndex] == ' '
+ 		|| doxygenString[startIndex] == '/' || doxygenString[startIndex] == '*') startIndex++;
+
+ 	for (int i = startIndex; i < endIndex; i++){
+
+ 		if (doxygenString[i] == '\n') {
+
+ 			while ((doxygenString[i] == '\n' || doxygenString[i] == ' '
+ 				|| doxygenString[i] == '*' || doxygenString[i] == '/')&& endIndex < doxygenString.length() - 1){
+ 				i++;
+ 				}
+ 			description.append(" ");
+ 		}
+ 		description.push_back(doxygenString[i]);
+ 		//cout << doxygenString[i];
+ 	}
+ 	startInd = finalIndex;
+ 	return description;
+ }
+
+ /* This method is for a specific form of doxygen command
+  * that begins with a \command and ends in \endcommand
+  * such as \code and \endcode. The proper usage is
+  * progressTilEndCommand("endcode", index)
+  * currently this method does NOT process what is in between the two commands
+  */
+ //TODO Make progressTilCommand return a formatted string
+ int progressTilEndCommand(string theCommand, int &startInd){
+ 	endIndex = startInd;
+ 	while (endIndex < doxygenString.length()){
+ 		if (doxygenString[endIndex] == 92 || doxygenString[endIndex] == '@'){
+ 			//cout << doxygenString.substr(endIndex + 1 , theCommand.length())<< endl;
+ 			if (theCommand.compare(doxygenString.substr(endIndex + 1 , theCommand.length())) == 0){
+ 				startInd = endIndex + theCommand.length() + 1;
+ 				return 1;
+ 			}
+ 		}
+ 		endIndex++;
+ 	}
+ 	//End command not found
+ 	return 0;
+ }
+
+ string getStringTilAnyCommand(string theCommand, int &startInd){
+	 endIndex = startInd;
+	 startIndex = startInd;
+	 int keepLooping = 1;
+	 while (keepLooping && endIndex < doxygenString.length()){
+	  		if (doxygenString[endIndex] == 92 || doxygenString[endIndex] == '@'){
+	  			startInd = endIndex;
+	  			keepLooping = 0;
+	  			}
+	 endIndex++;
+	 }
+	 string description = "";
+	 for (int i = startIndex; i < endIndex; i++){
+
+	  		if (doxygenString[i] == '\n') {
+
+	  			while ((doxygenString[i] == '\n' || doxygenString[i] == ' '
+	  				|| doxygenString[i] == '*' || doxygenString[i] == '/')&& endIndex < doxygenString.length() - 1){
+	  				i++;
+	  				}
+	  			description.append(" ");
+	  		}
+	  		description.push_back(doxygenString[i]);
+	  		//cout << doxygenString[i];
+	  	}
+	  	startInd = endIndex;
+	  	return description;
+	 return 0;
+ }
+ ///////////////TEST CLASSES AND MAIN BELOW/////////////////
+
+
+ /*  Testing clearFluff(), a method to scan past all excess / * ! from beginning of
+  * a comment blob. Compartmentalised simply because this is a comment habit that
+  * differs wildly */
+
+ int testClearFluff(){
+
+  string cases[] = {"/** WORD", "/*! WORD", "/******* WORD", "///// WORD", "//! WORD", "//! WORD", "///WORD",
+ 		 "/**\nWORD", "/**\n*WORD", "/** \n WORD"};
+  int testPassed = 1;
+  int casesSize = sizeof(cases)/sizeof(*cases);
+  for (int i = 0; i < casesSize; i++){
+	  doxygenString = cases[i];
+	  if(cases[i][clearFluff(0)] != 'W'){
+		  cout << "ClearFluff failed for string :" << doxygenString << "\t Displayed :" << cases[i][clearFluff(0)] << ": Instead." << endl;
+		  testPassed = 0;
+	  }
+  }
+  if(testPassed) cout << "+++ClearFluff passed for all tests+++\n" << endl;
+  else cout << "+++ClearFluff FAILED.+++" << endl;
+  return testPassed;
+
+  };
+
+ int testGetNextWord(){
+	  string cases[] = {"/** WORD ", " * WORD ", "///!WORD ", " WORD ", "//! WORD ", " * WORD ", "*WORD "};
+	  int testPassed = 1;
+	  string testWord = "";
+	  int placement = 0;
+	  int casesSize = sizeof(cases)/sizeof(*cases);
+	  for (int i = 0; i < casesSize; i++){
+		  doxygenString = cases[i];
+		  placement = 0;
+		  testWord = getNextWord(placement);
+		  if(testWord.compare("WORD") != 0){
+			  cout << "GetNextWord failed for string :" << doxygenString << "\t Displayed :" << testWord << ": Instead." << endl;
+			  testPassed = 0;
+		  }
+		 //else cout << "GetNextWord passed for string :" << doxygenString << endl;
+	  }
+	    placement = 0;
+		doxygenString = " * @WORD ";
+		testWord = getNextWord(placement);
+		if(testWord.compare("@WORD") != 0){
+			cout << "GetNextWord failed for string :"
+			<< doxygenString << "\t Displayed :" << testWord << ": Instead." << endl;
+			testPassed = 0;}
+		 //else cout << "GetNextWord passed for string :" << doxygenString << endl;
+		testWord = " * ";
+		testWord.push_back(92);
+		testWord = testWord + "WORD ";
+		string commandWord = "";
+		commandWord.push_back(92);
+		commandWord = commandWord + "WORD";
+		doxygenString = testWord;
+		placement = 0;
+		testWord = getNextWord(placement);
+		if(testWord.compare(commandWord) != 0){
+			cout << "GetNextWord failed for string :" << doxygenString
+			<< "\t Displayed :" << testWord << ": Instead." << endl;
+			testPassed = 0;}
+		  //else cout << "GetNextWord passed for string :" << doxygenString << endl;
+		doxygenString = "WORD ANOTHER WORD1 WORD2 \n";
+		placement = 0;
+		testWord = getNextWord(placement);
+		if(testWord.compare("WORD") != 0){
+			cout << "GetNextWord failed for string :" << doxygenString
+			<< "\t Displayed :" << testWord << ": Instead." << endl;
+			testPassed = 0;}
+		  //else cout << "GetNextWord passed for string :" << doxygenString << endl;
+		testWord = getNextWord(placement);
+		if(testWord.compare("ANOTHER") != 0){
+			cout << "GetNextWord failed for string :" << doxygenString
+			<< "\t Displayed :" << testWord << ": Instead." << endl;
+			testPassed = 0;}
+		 //else cout << "GetNextWord passed for string :" << doxygenString << endl;
+		testWord = getNextWord(placement);
+		if(testWord.compare("WORD1") != 0){
+			cout << "GetNextWord failed for string :" << doxygenString
+			<< "\t Displayed :" << testWord << ": Instead." << endl;
+			testPassed = 0;}
+		  //else cout << "GetNextWord passed for string :" << doxygenString << endl;
+		testWord = getNextWord(placement);
+		if(testWord.compare("WORD2") != 0){
+			cout << "GetNextWord failed for string :"
+			<< doxygenString << "\t Displayed :" << testWord
+			<< ": Instead." << endl;
+			testPassed = 0;}
+		  //else cout << "GetNextWord passed for string :" << doxygenString << endl;
+		testWord = getNextWord(placement);
+		if(testWord.compare("") != 0){
+			cout << "GetNextWord failed for string :" << doxygenString
+			<< "\t Displayed :" << testWord << ": Instead." << endl;
+			testPassed = 0;}
+		  //else cout << "GetNextWord passed for string :" << doxygenString << endl;
+		testWord = getNextWord(placement);
+		if(testWord.compare("") != 0){
+			cout << "GetNextWord failed for string :" << doxygenString <<
+			"\t Displayed :" << testWord << ": Instead." << endl;
+			testPassed = 0;}
+		  //else cout << "GetNextWord passed for string :" << doxygenString << endl;
+		  if(testPassed) cout << "+++NextWord passed for all tests+++\n" << endl;
+		 else cout << "+++NextWord FAILED+++\n" << endl;
+		  return testPassed;
+ }
+
+ int testGetOneLine(){
+	  string cases[] = {" * Crop this sentence after this period.\n",
+			  " * Crop this sentence after this period.\n",
+			  "Crop this sentence after this period.\n",
+			  "//! Crop this sentence after this period.\n",
+			  " Crop this sentence after this period.\n"
+			  };
+	  int testPassed = 1;
+	  string testWord = "";
+		int placement = 0;
+	  int casesSize = sizeof(cases)/sizeof(*cases);
+	  for (int i = 0; i < casesSize; i++){
+		  doxygenString = cases[i];
+		  placement = 0;
+		  testWord = getOneLine(placement);
+		  if(testWord.compare("Crop this sentence after this period.") != 0){
+			  cout << "GetOneLine failed for string :" << doxygenString << "\t Displayed :" << testWord << ": Instead." << endl;
+			  testPassed = 0;
+		  }
+	  }
+	  doxygenString = ("Get this line.\n * Now get this line.");
+	  placement = 0;
+	  testWord = getOneLine(placement);
+	  if(testWord.compare("Get this line.") != 0){
+	  		cout << "GetOneLine failed for string :" << doxygenString << "\t Displayed :" << testWord << ": Instead." << endl;
+	  		testPassed = 0;
+	  		  }
+	  testWord = getOneLine(placement);
+	  if(testWord.compare("Now get this line.") != 0){
+	  		cout << "GetOneLine failed for string :" << doxygenString << "\t Displayed :" << testWord << ": Instead." << endl;
+	  		testPassed = 0;
+	  		  }
+	  testWord = getOneLine(placement);
+	  if(testWord.compare("") != 0){
+	  		cout << "GetOneLine failed for string :" << doxygenString << "\t Displayed :" << testWord << ": Instead." << endl;
+	  		testPassed = 0;
+	  		  }
+
+	  if(testPassed) cout << "+++GetOneLine passed for all tests+++\n" << endl;
+	 else cout << "+++GetOneLine FAILED+++\n" << endl;
+	  return testPassed;
+ }
+//TODO Flesh testGetStringTilEndOfParagraph out, fix weird spacing problems
+ int testGetStringTilEndOfParagraph(){
+	int placement = 0;
+	int testPassed = 1;
+	string testParagraph;
+	doxygenString = ("/* This is a description,\n * thus it continues on\n * for several lines.\n\n This Shouldn't be included.\n\n **/");
+	testParagraph = getStringTilEndOfParagraph(placement);
+	if( testParagraph.compare("This is a description, thus it continues on for several lines.") != 0){
+  		cout << "GetOneLine failed for string :" << doxygenString << "\t Displayed :" << testParagraph << ": Instead." << endl;
+  		testPassed = 0;
+  	}
+	//cout << "Curr Placement: " << placement<< endl;
+	testParagraph = getStringTilEndOfParagraph(placement);
+	//cout << "Curr Placement: " << placement<< endl;
+	if( testParagraph.compare(" This Shouldn't be included.") != 0){
+  		cout << "GetOneLine failed for string :" << doxygenString << "\t Displayed :" << testParagraph << ": Instead." << endl;
+  		testPassed = 0;
+  	}
+
+	//cout << "Curr Placement: " << placement<< endl;
+	//cout << "String Length: " << doxygenString.length() << endl;
+
+	doxygenString = "/* This is a description,\n * thus it continues on\n * for several lines.\n * \n * ";
+	doxygenString.push_back(92);
+	doxygenString += "author cheryl foil \n\n **/";
+	placement = 0;
+	testParagraph = getStringTilEndOfParagraph(placement);
+	if( testParagraph.compare("This is a description, thus it continues on for several lines.") != 0){
+  		cout << "GetOneLine failed for string :" << doxygenString << "\t Displayed :" << testParagraph << ": Instead." << endl;
+  		testPassed = 0;
+  	}
+
+	if(testPassed) cout << "+++GetDescription passed for all tests+++\n" << endl;
+	else cout << "+++GetDescription FAILED+++\n" << endl;
+	return testPassed;
+ }
+
+ int testProgressTilEndCommand(){
+		int placement = 0;
+		int testPassed = 1;
+		string testParagraph;
+		doxygenString = "Let's pretend this \n * is a bunch of code to be ended in ";
+		doxygenString.push_back(92);
+		doxygenString += "endcodeSTOP";
+		progressTilEndCommand("endcode", placement);
+		//cout << "Placement : " << placement << endl;
+		if( doxygenString[placement] != 'S'){
+	  		cout << "GetOneLine failed for string :" << doxygenString << "\n\t Displayed :" << testParagraph << ": Instead." << endl;
+	  		testPassed = 0;
+	  	}
+		if(testPassed) cout << "+++ProgressTilEndCommand passed for all tests+++\n" << endl;
+		else cout << "+++ProgressTilEndCommand FAILED+++\n" << endl;
+	 return testPassed;
+ }
+
+ int testCCF(){
+	cout << "TESTING COMMAND PARSING FUNCTIONS" << endl;
+	cout << "Testing clearFluff" << endl;
+	testClearFluff();
+
+ 	cout << "Testing getNextWord" << endl;
+ 	testGetNextWord();
+ 	cout << "Testing getOneLine"<< endl;
+ 	testGetOneLine();
+
+ 	cout << "Testing getStringTilEndOfParagraph" << endl;
+ 	testGetStringTilEndOfParagraph();
+
+ 	cout << "Testing progressTilEndCommand" << endl;
+ 	testProgressTilEndCommand();
+
+ 	return 1;
+ }
+
+ /* prints the parse tree
+  *
+  */
+ void printTree(){
+
+		list<DoxygenEntity>::iterator p = rootList.begin();
+		while (p != rootList.end()){
+			(*p).printEntity();
+			p++;
+		}
+
+ }
+ /* The actual "meat" of the doxygen parser. This is not yet fully implemented
+  * with my current design- however the skeletal outline is contained in
+  * the file Skeleton
+  */
+
+ int addCommand(int commentNum, int &startInd, list <DoxygenEntity> &doxyList){
+	    startIndex = startInd;
+	 	string name;
+	 	string nextWordInLine = "";
+	 	string restOfLine = "";
+	 	string restOfParagraph = "";
+	 	string headerfile ="";
+	 	string headername = "";
+	 	switch(commentNum){
+
+
+		/* \b */
+		case 108:
+			name = getNextWord(startIndex);
+			if (!name.empty()) doxyList.push_back( DoxygenEntity(108, name));
+			else cout << "No word followed b command. Not added" << endl;
+			break;
+		/* \brief */
+		case 109:
+			restOfParagraph = getStringTilEndOfParagraph(startIndex);
+			if(!restOfParagraph.empty()) doxyList.push_back( DoxygenEntity(109, restOfLine));
+			else cout << "Nothing followed brief command. Not added" <<endl;
+			break;
+
+	 	/* plain description */
+	 	case 238:
+	 		//doxyList.push_back(DoxygenEntity(238, parse(startIndex, new list<DoxygenEntity> entityList() )));
+
+	 		break;
+
+	 	default:
+			cout << "Command " << commentNum << " not supported yet" << endl;
+			break;
+	 	}
+	 	startInd = startIndex;
+ }
+
+ /* Returns the parse tree */
+
+list<DoxygenEntity> parse(int startInd, int endInd, list<DoxygenEntity> &doxyList){
+	string currWord = "";
+	int startIndex = startInd;
+	int savedIndex;
+	int currCommand;
+	while (startIndex < endIndex){
+		savedIndex = startIndex;
+		currWord = getNextWord(startIndex);
+
+		if(currWord[0] == 92 || currWord[0] == '@'){
+			currWord = doxygenString.substr(startIndex+1, currWord.length() - 1);
+			currCommand = findCommand(currWord);
+			if (currCommand < 0 ){ cout << "BAD COMMAND: " << currWord << endl; exit(1);}
+				//cout << "Command: " << currWord << " " << currCommand << endl;
+			addCommand(currCommand, startIndex, doxyList);
+		}
+		else{
+			startIndex = savedIndex;
+			addCommand(238, startIndex, doxyList);
+
+		}
+	}
+
+
+}
+
+
+ int main(int argc, char *argv[]){
+ 	if(testCodeCrawlingFunctions) testCCF();
+ 	if (demonstrateParsing){
+ 		int placement = 0;
+ 		clearFluff(0);
+ 		parse(0, doxygenString.length(), rootList);
+ 		printTree();
+ 	}
+ 	return 1;
+ }
diff --git a/Source/DoxygenTranslator/Skeleton b/Source/DoxygenTranslator/Skeleton
new file mode 100755
index 000000000..099b94393
--- /dev/null
+++ b/Source/DoxygenTranslator/Skeleton
@@ -0,0 +1,1070 @@
+/** NOT A WORKING FILE- NOTES/SCRAPS
+ * A result of the initial implementation,
+ * stopped early because I changed my design. This is currently
+ * being reworked in the actual DoxygenTranslator class
+ */
+
+
+
+
+/* The Very Large and Unelegant Solution for dealing with Doxygen commands such as
+ * " \param".
+ * This is implemented this way because a LARGE number of potential Doxygen commands
+ * are not needed (such as PHP only or calling call graphs) and thus are simply
+ * thrown out. The more useful functions
+ * maybe be compartmentalised into their own method later on.
+ */
+
+int addComment(int commentNum){
+	
+	startIndex = endIndex;
+	string name;
+	string nextWordInLine = "";
+	string restOfLine = "";
+	string restOfParagraph = "";
+	string headerfile ="";
+	string headername = "";
+	switch(commentNum){
+	
+
+	/* \a */
+	case 101:
+		nextWordInLine = getNextWord();
+		if((nextWordInLine).empty()){
+			cout << "Error: No word after tag a "<< endl;
+		}
+		else entityList.push_back( DoxygenEntity(101, "", nextWordInLine));
+		startIndex = endIndex;
+		break;
+		
+		/* \addindex */
+	case 102:
+		cout << "Add Index May not be Supported."<< endl;
+		restOfLine = getOneLineSentence();
+		if((restOfLine).empty()){
+			cout << "Error: No word after tag a "<< endl;
+		}
+		else entityList.push_back( DoxygenEntity(102, "", restOfLine));
+		startIndex = endIndex;
+		break;
+	
+	/* \addtogroup */
+	case 103:
+
+	
+		name = getNextWord();
+		if (anythingLeftOnLine()){
+			restOfLine = getOneLineSentence();
+			entityList.push_back( DoxygenEntity(103, "", restOfLine));
+		}
+		else 	cout << "AddtoGroup only supported for <name> [(title)]. Command not added" << endl;
+		break;
+		
+	/* \anchor */
+	case 104 :
+		getNextWord();
+		cout << "Anchor is not supported. Command not added." << endl;
+		break;
+		
+	/* \arg */	
+	case 105:
+
+		break;
+		
+	/* \attention */	
+	case 106:
+		restOfParagraph = stringTilEndOfParagraph(endIndex);
+		if(!restOfParagraph.empty()) entityList.push_back( DoxygenEntity(106, "", restOfLine));
+		else cout << "Nothing followed attention command. Not added" <<endl;
+		break;
+		
+	/* \author */
+	case 107:
+		restOfParagraph = stringTilEndOfParagraph(endIndex);
+		entityList.push_back( DoxygenEntity(107, "", restOfLine));
+		break;
+	
+	/* \b */
+	case 108:
+		name = getNextWord();
+		if (!name.empty()) entityList.push_back( DoxygenEntity(108, "", restOfLine)); 
+		else cout << "No word followed b command. Not added" <<endl;
+		break;
+		
+	/* \brief */
+	case 109:
+		restOfParagraph = stringTilEndOfParagraph(endIndex);
+		if(!restOfParagraph.empty()) entityList.push_back( DoxygenEntity(109, "", restOfLine));
+		else cout << "Nothing followed brief command. Not added" <<endl;
+		break;
+		
+	/* \bug */
+	case 110:
+		restOfParagraph = stringTilEndOfParagraph(endIndex);
+		if(!restOfParagraph.empty()) entityList.push_back( DoxygenEntity(110, "", restOfLine));
+		else cout << "Nothing followed bug command. Not added" <<endl;
+		break;
+	
+	/* \c */
+	case 111:
+		name = getNextWord();
+		if (!name.empty()) entityList.push_back( DoxygenEntity(111, "", restOfLine)); 
+		else cout << "No word followed c command. Not added" <<endl;
+		break;
+
+	/* \callgraph */
+	case 112:
+		cout << "Callgraph is not supported. Command not added." << endl;
+		break;
+	
+	/* \callergraph */
+	case 113:
+		cout << "Callergraph is not supported. Command not added." << endl;
+		break;
+	
+		/* \category */
+	case 114:
+		cout << "Category is a command for Objective C only. Command not added." << endl;
+		break;
+		
+	/* \class <name> [<header-file>] [<header-name>] */
+	case 115:
+		name = getNextWord();
+		if (name.empty()) cout << "No word followed class command. Not added" <<endl;
+		headerfile = getNextWord();
+		headername = getNextWord();
+		entityList.push_back( DoxygenEntity(115, headerfile, headername));
+		break;
+	
+	/* \code */
+	case 116:
+		cout << "Code is not supported. Command not added." << endl;
+		if (progressTilEndCommand("endcode") < 1) cout << "No endcode for command code found" << endl;	
+		break;
+		
+	/* \cond [<section-label>] */
+	case 117:
+		cout << "cond is not supported. Command not added." << endl;
+		if (progressTilEndCommand("endcond") < 1) cout << "No endcode for command code found" << endl;	
+		break;
+		
+	/* \copybrief <link-object> */
+	case 118:
+		getNextWord();
+		cout << "copybrief is not yet implemented. Command not added." << endl;
+		break;
+		
+	/* \copydetails  <link-object> */
+	case 119:
+		getNextWord();
+		cout << "copydetails is not yet implemented. Command not added." << endl;
+		break;
+		
+	/* \copydoc <link-object> */
+	case 120:
+		getNextWord();
+		cout << "copydoc is not yet implemented. Command not added." << endl;
+		break;
+	
+		/* \date { date description } */
+	case 121:
+		restOfParagraph = stringTilEndOfParagraph(endIndex);
+		if(!restOfParagraph.empty()) entityList.push_back( DoxygenEntity(121, "", restOfLine));
+		else cout << "Nothing followed date command. Not added" << endl;
+		break;
+	
+	/* \def <name> */
+	case 122:
+		name = getNextWord();
+		if (!name.empty()) entityList.push_back( DoxygenEntity(122, name, "")); 
+		else cout << "No word followed def command. Not added" << endl;
+		break;
+	
+	/* \defgroup <name> (group title) */
+	case 123:
+		name = getNextWord();
+		if (name.empty())cout << "No word followed def command. Not added" << endl; 
+		else {
+			restOfLine = getOneLineSentence();
+			if((restOfLine).empty()){
+			cout << "Error: No word after tag a "<< endl;
+			}
+			else entityList.push_back( DoxygenEntity(123, name, restOfLine));
+		}
+		break;
+		
+	/* \deprecated { description } */
+	case 124:
+		restOfParagraph = stringTilEndOfParagraph(endIndex);
+		if(!restOfParagraph.empty()) entityList.push_back( DoxygenEntity(124, "", restOfLine));
+		else cout << "Nothing followed deprecated command. Not added" << endl;
+		break;
+		
+	/* \details {detailed decription} */
+	case 125:
+		restOfParagraph = stringTilEndOfParagraph(endIndex);
+		if(!restOfParagraph.empty()) entityList.push_back( DoxygenEntity(125, "", restOfLine));
+		else cout << "Nothing followed details command. Not added" << endl;
+		break;
+	
+	/* \dir [<path fragment>] */
+	case 126:
+		restOfLine = getOneLineSentence();
+		entityList.push_back( DoxygenEntity(126, restOfLine , ""));
+		break;
+		
+	/* \dontinclude <file-name> */
+	case 127:
+		getNextWord();
+		cout << "dontinclude is not implemented. Command not added." << endl;
+		break;
+	
+	/* \dot */
+	case 128:
+		cout << "dot is not implemented. Command not added." << endl;
+		break;
+		
+	/* \dotfile <file> ["caption"] */
+	case 129:
+		getOneLineSentence();
+		cout << "dotfile is not implemented. Command not added." << endl;
+		break;
+		
+	/* \e <word> */
+	case 130:
+		name = getNextWord();
+		if (!name.empty()) entityList.push_back( DoxygenEntity(130, name, "")); 
+		else cout << "No word followed e command. Not added" <<endl;
+	break;
+		   
+	/* \else */
+	case 131:
+		cout << "else not yet implemented." << endl;
+	break;
+		   
+	/* \elseif <section-label> */
+	case 132:
+		getNextWord();
+		cout << "elseif is not implemented. Command not added." << endl;
+	break;
+		   
+	/* \em <word> */
+	/* Identical to e, so calls e */
+	case 133:
+		addComment(130);
+	break;
+		   
+	/* \endcode */
+	case 134:
+		cout << "endcode is not implemented. Command not added." << endl;
+	break;
+		   
+	/* \endcond */
+	case 135:
+		cout << "endcond is not implemented. Command not added." << endl;
+	break;
+		   
+	/* \enddot */
+	case 136:
+		cout << "enddot is not implemented. Command not added." << endl;
+	break;
+		   
+	/* \endhtmlonly */
+	case 137:
+		cout << "endhtmlonly is not implemented. Command not added." << endl;
+	break;
+		   
+	/* \endif */
+	case 138:
+		cout << "endif is not implemented. Command not added." << endl;
+	break;
+		   
+	/* \endlatexonly */
+	case 139:
+		cout << "endlatexonly is not implemented. Command not added." << endl;
+	break;
+		   
+	/* \endlink */
+	case 140:
+		cout << "endlink is not implemented. Command not added." << endl;
+	break;
+		   
+	/* \endmanonly */
+	case 141:
+		cout << "endmanonly is not implemented. Command not added." << endl;
+	break;
+		   
+	/* \endmsc */
+	case 142:
+		cout << "endmsc is not implemented. Command not added." << endl;
+	 break;
+		   
+	/* \endverbatim */
+	case 143:
+		cout << "endmsc is not implemented. Command not added." << endl;
+	break;
+		   
+	/* \endxmlonly */
+	case 144:
+		cout << "endxmlonly is not implemented. Command not added." << endl;
+	break;
+		   
+	/* \enum <name> */
+	case 145:
+		name = getNextWord();
+		if (!name.empty()) entityList.push_back( DoxygenEntity(145, name, "")); 
+		else cout << "No word followed enum command. Not added" <<endl;
+	break;
+		   
+	/* \example <file-name> */
+	case 146:
+		name = getNextWord();
+		if (!name.empty()) entityList.push_back( DoxygenEntity(146, name, "")); 
+		else cout << "No word followed example command. Not added" <<endl;
+	break;
+		   
+	/* \exception <exception-object> { exception description } */
+	case 147:
+		name = getNextWord();
+		if (name.empty()) cout << "No word followed exception command. Not added" <<endl;
+		else {
+			restOfParagraph = stringTilEndOfParagraph(endIndex);
+			if(!restOfParagraph.empty()) entityList.push_back( DoxygenEntity(147, name, restOfParagraph));
+			else cout << "Nothing followed exception <word> command. Not added" << endl;
+		}
+	break;
+		   
+	/* \f$ */
+	case 148:
+		cout << "f$ is not supported. Command not added." << endl;
+		if (progressTilEndCommand("f$") < 1) cout << "No endcode for command f$ found" << endl;	
+	break;
+		   
+	/* \f[ */
+	case 149:
+		cout << "f$ is not supported. Command not added." << endl;
+		if (progressTilEndCommand("f]") < 1) cout << "No endcode for command f] found" << endl;	
+	break;
+		   
+	/* \f] */
+	case 150:
+		cout << "f] is not implemented. Command not added." << endl;
+	break;
+		   
+	/* \f{environment}{ */
+	case 151:
+		cout << "f{environment}{ is not implemented. This may cause abnormal behaviour." << endl;
+	break;
+		   
+	/* \f} */
+	case 152:
+		cout << "f} is not implemented. This may cause abnormal behaviour." << endl;
+	break;
+		   
+	/* \file [<name>] */
+	case 153:
+		name = getNextWord();
+				if (!name.empty()) entityList.push_back( DoxygenEntity(153, name, "")); 
+				else entityList.push_back( DoxygenEntity(153, "", "")); 
+	break;
+		   
+	/* \fn (function declaration) */
+	 case 154:
+			restOfLine = getOneLineSentence();
+			if((restOfLine).empty()){
+			cout << "Error: No word after tag fn "<< endl;
+			}
+			else entityList.push_back( DoxygenEntity(154, restOfLine, ""));
+		 break;
+		   
+	/* \headerfile <header-file> [<header-name>] */
+	case 155:
+		name = getNextWord();
+		if (name.empty())cout << "No word followed headerfile command. Not added" << endl; 
+		else {
+			restOfLine = getNextWord();
+			entityList.push_back( DoxygenEntity(155, name, restOfLine));
+		}
+	break;
+		   
+	/* \hideinitializer */
+	case 156:
+	cout << "hideinitializer is not implemented." << endl;	
+	break;
+		   
+	/* \htmlinclude <file-name>*/
+	case 157:
+		name = getNextWord();
+			if (name.empty())cout << "No word followed htmlinclude command. Not added" << endl; 
+			else {
+				entityList.push_back( DoxygenEntity(157, name,""));
+			}
+	break;
+		   
+	/* \htmlonly */
+	case 158:
+		cout << "htmlonly will be implemented later. For now the html is ignored." << endl;
+		if (progressTilEndCommand("endhtmlonly") < 1) cout << "No endcode for command code found" << endl;
+	break;
+		   
+	/* \if <section-label> */
+	case 159:
+		cout << "if command is not implemented." << endl;
+	break;
+		   
+	/* \ifnot <section-label> */
+	case 160:
+		cout << "ifnot command is not implemented." << endl;
+		break;
+		   
+	/* \image <format> <file> ["caption"] [<sizeindication>=<size>] */
+	case 161:
+		cout << "Image unsupported. Program may behave strangely if command is over one line." << endl;
+		getOneLineSentence();
+		 break;
+		   
+	/* \include <file-name> */
+	case 162:
+		name = getNextWord();
+			if (name.empty())cout << "No word followed include command. Not added" << endl; 
+			else {
+				entityList.push_back( DoxygenEntity(162, name,""));
+			}
+		break;
+		   
+	/* \includelineno <file-name> */
+	case 163:
+		name = getNextWord();
+					if (name.empty())cout << "No word followed includelineno command. Not added" << endl; 
+					else {
+						entityList.push_back( DoxygenEntity(163, name,""));
+					}
+	 break;
+		   
+	/* \ingroup (<groupname> [<groupname> <groupname>]) */
+	case 164:
+		name = getNextWord();
+					if (name.empty())cout << "No word followed ingroup command. Not added" << endl; 
+					else {
+						string groupnames = getOneLineSentence();
+						entityList.push_back( DoxygenEntity(164, name,groupnames));
+					}
+	break;
+		   
+	/* \internal */
+	case 165:
+		entityList.push_back( DoxygenEntity(165, "",""));
+		break;
+		   
+	/* \invariant { description of invariant } */
+	case 166:
+		restOfParagraph = stringTilEndOfParagraph(endIndex);
+		if(!restOfParagraph.empty()) entityList.push_back( DoxygenEntity(166, restOfLine,"" ));
+		else cout << "Nothing followed invariant command. Not added" << endl;
+		 break;
+		   
+	/* \interface <name> [<header-file>] [<header-name>] */
+	case 167:
+		name = getNextWord();
+					if (name.empty())cout << "No word followed ingroup command. Not added" << endl; 
+					else {
+						string groupnames = getOneLineSentence();
+						entityList.push_back( DoxygenEntity(167, name, groupnames));
+					}
+	break;
+		   
+	/* \latexonly */
+	case 168:
+		cout << "latex only is not implemented" << endl;
+		if (progressTilEndCommand("endlatexonly") < 1) cout << "No endcode for command latexonly found" << endl;
+		break;
+		   
+	/* \li { item-description } */
+		//REDO
+	case 169:
+		addComment(105);
+		break;
+		   
+	/* \line ( pattern ) */
+	case 170:
+		restOfLine = getOneLineSentence();
+		if((restOfLine).empty()){
+		cout << "Error: No word after tag line "<< endl;
+		}
+		else entityList.push_back( DoxygenEntity(170, restOfLine, ""));
+	 break;
+		   
+	/* \link <link-object> */
+	case 171:
+		name = getNextWord();
+			if (name.empty())cout << "No word followed link command. Not added" << endl; 
+			else {
+				entityList.push_back( DoxygenEntity(171, name,""));
+			}
+		break;
+		   
+	/* \mainpage [(title)] */
+	case 172:
+		restOfLine = getOneLineSentence();
+		entityList.push_back( DoxygenEntity(172, restOfLine, ""));
+		break;
+		   
+	/* \manonly */
+	case 173:
+		cout << "manonly is not implemented" << endl;
+		if (progressTilEndCommand("endmanonly") < 1) cout << "No endcode for command manonly found" << endl;
+		break;
+		   
+	/* \msc */
+	case 174:
+		cout << "msc is not implemented" << endl;
+		if (progressTilEndCommand("endmanonly") < 1) cout << "No endcode for command mscfound" << endl;
+		break;
+		   
+	/* \n */
+	case 175:
+		entityList.push_back( DoxygenEntity(175, "",""));
+	break;
+		   
+	/* \name (header) */
+	case 176:
+		restOfLine = getOneLineSentence();
+		if((restOfLine).empty()){
+		cout << "Error: No word after header line "<< endl;
+		}
+		else entityList.push_back( DoxygenEntity(176, restOfLine, ""));
+		break;
+		   
+	/* \namespace <name> */
+	case 177:
+		name = getNextWord();
+					if (name.empty())cout << "No word followed namespace command. Not added" << endl; 
+					else {
+						entityList.push_back( DoxygenEntity(177, name,""));
+					}
+		break;
+		   
+	/* \nosubgrouping */
+		case 178:
+			cout << "Nosubgrouping not implemented "<< endl;
+		   break;
+		   
+	 /* \note { text } */
+	case 179:
+		restOfParagraph = stringTilEndOfParagraph(endIndex);
+		if(!restOfParagraph.empty()) entityList.push_back( DoxygenEntity(179, restOfLine,"" ));
+		else cout << "Nothing followed note command. Not added" << endl;
+		break;
+		   
+	/* \overload [(function declaration)] */
+	case 180:
+		restOfLine = getOneLineSentence();
+		entityList.push_back( DoxygenEntity(172, restOfLine, ""));
+		break;
+		   
+	/* \p <word> */
+	case 181:
+		name = getNextWord();
+					if (name.empty())cout << "No word followed p command. Not added" << endl; 
+					else {
+						entityList.push_back( DoxygenEntity(181, name,""));
+					}
+		break;
+		   
+	/* \package <name> */
+	case 182:
+		name = getNextWord();
+					if (name.empty())cout << "No word followed package command. Not added" << endl; 
+					else {
+						entityList.push_back( DoxygenEntity(182, name,""));
+					}
+		 break;
+		   
+	/* \page <name> (title) */
+	case 183:
+		name = getNextWord();
+		if (name.empty())cout << "No word followed page command. Not added" << endl; 
+		else {
+			restOfLine = getOneLineSentence();
+			if((restOfLine).empty()){
+			cout << "Error: No word after tag page "<< endl;
+			}
+			else entityList.push_back( DoxygenEntity(183, name, restOfLine));
+		}
+		break;
+		   
+	/* \par [(paragraph title)] { paragraph } */
+	case 184:
+		name = getOneLineSentence();
+		restOfParagraph = stringTilEndOfParagraph(endIndex);
+		if(!restOfParagraph.empty()) entityList.push_back( DoxygenEntity(184, name, restOfParagraph ));
+				else cout << "Nothing followed par command. Not added" << endl;
+		break;
+		   
+	/* \paragraph <paragraph-name> (paragraph title) */
+	case 185:
+		name = getNextWord();
+		if (name.empty())cout << "No word followed paragraph command. Not added" << endl; 
+		else {
+			restOfLine = getOneLineSentence();
+			if((restOfLine).empty()){
+			cout << "Error: No word after tag paragraph "<< endl;
+			}
+			else entityList.push_back( DoxygenEntity(185, name, restOfLine));
+		}
+		break;
+		   
+	/* \param <parameter-name> { parameter description } */
+	case 186:
+		name = getNextWord();
+		if (name.empty())cout << "No word followed parameter command. Not added" << endl; 
+		else {
+			restOfParagraph = stringTilEndOfParagraph(endIndex);
+			if(!restOfParagraph.empty()) entityList.push_back( DoxygenEntity(186, name, restOfParagraph ));
+				else cout << "Nothing followed parameter command. Not added" << endl;
+		}
+		break;
+		   
+	/* \post { description of the postcondition } */
+	case 187:
+		restOfParagraph = stringTilEndOfParagraph(endIndex);
+		if(!restOfParagraph.empty()) entityList.push_back( DoxygenEntity(187, name, restOfParagraph ));
+			else cout << "Nothing followed post command. Not added" << endl;
+		break;
+		   
+	/* \pre { description of the precondition } */
+	case 188:
+		restOfParagraph = stringTilEndOfParagraph(endIndex);
+		if(!restOfParagraph.empty()) entityList.push_back( DoxygenEntity(187, name, restOfParagraph ));
+			else cout << "Nothing followed post command. Not added" << endl;
+		 break;
+		   
+		    /* \private (PHP only) */
+		    case 189:
+		    	cout << "Private is a PHP Only Command." << endl;
+		        break;
+		   
+		     /* \privatesection (PHP only) */
+		    case 190:
+		    	cout << "Privatesection is a PHP Only Command." << endl;
+		        break;
+		   
+		    /* \property (qualified property name) */
+		    case 191:
+				restOfLine = getOneLineSentence();
+				if(!restOfLine.empty()) entityList.push_back( DoxygenEntity(191, restOfLine, ""));
+				else cout << "Nothing followed property command. Not added" << endl;
+		        break;
+		   
+		    /* \protected (PHP only) */
+		    case 192:
+		    	cout << "Protected is a PHP Only Command." << endl;
+		        break;
+		   
+		    /* \protectedsection (PHP only) */
+		    case 193:
+		    	cout << "Protectedsection is a PHP Only Command." << endl;
+		        break;
+		   
+		    /* \protocol <name> [<header-file>] [<header-name>] */
+		    case 194:
+		        break;
+		   
+		    /* \public (PHP only) */
+		    case 195:
+		    	cout << "Public is a PHP Only Command." << endl;
+		        break;
+		   
+		    /* \publicsection (PHP only) */
+		    case 196:
+		    	cout << "Public Section is a PHP Only Command." << endl;
+		        break;
+		   
+	/* \ref <name> ["(text)"] */
+	 case 197:
+			name = getNextWord();
+			getOneLineSentence();
+			cout << "Ref is currently not supported." << endl;
+		break;
+		   
+	/* \relates <name> */
+	case 198:
+		name = getNextWord();
+					if (name.empty())cout << "No word followed relates command. Not added" << endl; 
+					else {
+						entityList.push_back( DoxygenEntity(198, name,""));
+					}
+		break;
+		   
+	/* \relatesalso <name> */
+	case 199:
+		name = getNextWord();
+					if (name.empty())cout << "No word followed relatesalso command. Not added" << endl; 
+					else {
+						entityList.push_back( DoxygenEntity(199, name,""));
+					}
+		break;
+		   
+	 /* \remarks { remark text } */
+	case 200:
+		restOfParagraph = stringTilEndOfParagraph(endIndex);
+		if(!restOfParagraph.empty()) entityList.push_back( DoxygenEntity(200, restOfParagraph, "" ));
+			else cout << "Nothing followed remarks command. Not added" << endl;
+		break;
+		   
+	/* \return { description of the return value } */
+	case 201:
+		restOfParagraph = stringTilEndOfParagraph(endIndex);
+		if(!restOfParagraph.empty()) entityList.push_back( DoxygenEntity(200, restOfParagraph, "" ));
+			else cout << "Nothing followed return command. Not added" << endl;
+		 break;
+		   
+	/* \retval <return value> { description } */
+	case 202:
+		name = getNextWord();
+		if (name.empty())cout << "No word followed retval command. Not added" << endl; 
+		else {
+			restOfParagraph = stringTilEndOfParagraph(endIndex);
+			if(!restOfParagraph.empty()) entityList.push_back( DoxygenEntity(202, name, restOfParagraph ));
+				else cout << "Nothing followed retval command. Not added" << endl;
+		}
+		break;
+		   
+	/* \sa { references } */
+	case 203:
+		restOfParagraph = stringTilEndOfParagraph(endIndex);
+		if(!restOfParagraph.empty()) entityList.push_back( DoxygenEntity(203, restOfParagraph, "" ));
+			else cout << "Nothing followed sa command. Not added" << endl;
+		break;
+		   
+	/* \section <section-name> (section title) */
+	case 204:
+		name = getNextWord();
+		if (name.empty())cout << "No word followed section command. Not added" << endl; 
+		else {
+			restOfLine = getOneLineSentence();
+			if((restOfLine).empty()){
+			cout << "Error: No word after section paragraph "<< endl;
+			}
+			else entityList.push_back( DoxygenEntity(204, name, restOfLine));
+		}
+		 break;
+		   
+	/* \see { references } */
+	case 205:
+		restOfParagraph = stringTilEndOfParagraph(endIndex);
+		if(!restOfParagraph.empty()) entityList.push_back( DoxygenEntity(205, restOfParagraph, "" ));
+		else cout << "Nothing followed see command. Not added" << endl;
+		break;
+		   
+	/* \showinitializer */
+	case 206:
+		cout << "Showerinitializer command unsupported"<< endl;
+		break;
+		   
+	/* \since { text } */
+	case 207:
+		restOfParagraph = stringTilEndOfParagraph(endIndex);
+		if(!restOfParagraph.empty()) entityList.push_back( DoxygenEntity(207, restOfParagraph, "" ));
+		else cout << "Nothing followed since command. Not added" << endl;
+		 break;
+		   
+	/* \skip ( pattern ) */
+	case 208:
+		getOneLineSentence();
+		cout << "Skip command unsupported"<< endl;
+		break;
+		   
+	/* \skipline ( pattern ) */
+	case 209:
+		getOneLineSentence();
+		cout << "Skipline command unsupported"<< endl;
+		break;
+		   
+	/* \struct <name> [<header-file>] [<header-name>] */
+	case 210:
+		name = getNextWord();
+					if (name.empty())cout << "No word followed struct command. Not added" << endl; 
+					else {
+						string groupnames = getOneLineSentence();
+						entityList.push_back( DoxygenEntity(210, name, groupnames));
+					}
+		break;
+		   
+	/* \subpage <name> ["(text)"] */
+	case 211:
+		getOneLineSentence();
+		cout << "subpag command unsupported"<< endl;
+		break;
+		   
+	/* \subsection <subsection-name> (subsection title) */
+	 case 212:
+			getOneLineSentence();
+		 cout << "subsection command unsupported"<< endl;
+		 break;
+		   
+	/* \subsubsection <subsubsection-name> (subsubsection title) */
+	case 213:
+		getOneLineSentence();
+		cout << "subsubsection  command unsupported"<< endl;
+		break;
+		   
+	/* \test { paragraph describing a test case } */
+	case 214:
+		restOfParagraph = stringTilEndOfParagraph(endIndex);
+		if(!restOfParagraph.empty()) entityList.push_back( DoxygenEntity(214, restOfParagraph, "" ));
+		else cout << "Nothing followed test command. Not added" << endl;
+		break;
+		   
+	/* \throw <exception-object> { exception description } */
+	case 215:
+		name = getNextWord();
+		if (name.empty())cout << "No word followed throw command. Not added" << endl; 
+		else {
+			restOfParagraph = stringTilEndOfParagraph(endIndex);
+			if(!restOfParagraph.empty()) entityList.push_back( DoxygenEntity(215, name, restOfParagraph ));
+				else cout << "Nothing followed throw command. Not added" << endl;  
+			}
+		 break;
+		   
+	/* \todo { paragraph describing what is to be done } */
+	case 216:
+		restOfParagraph = stringTilEndOfParagraph(endIndex);
+		if(!restOfParagraph.empty()) entityList.push_back( DoxygenEntity(216, restOfParagraph, "" ));
+		else cout << "Nothing followed todo command. Not added" << endl;
+		break;
+		   
+	/* \tparam <template-parameter-name> { description } */
+	case 217:
+		name = getNextWord();
+		if (name.empty())cout << "No word followed tparam command. Not added" << endl; 
+		else {
+			restOfParagraph = stringTilEndOfParagraph(endIndex);
+			if(!restOfParagraph.empty()) entityList.push_back( DoxygenEntity(217, name, restOfParagraph ));
+				else cout << "Nothing followed tparam command. Not added" << endl;
+		}
+		   break;
+		   
+	/* \typedef (typedef declaration) */
+	case 218:
+		restOfLine = getOneLineSentence();
+		if(!restOfLine.empty()) entityList.push_back( DoxygenEntity(218, restOfLine, ""));
+		else cout << "Nothing followed typedef command. Not added" << endl;
+		break;
+		   
+	/* \union <name> [<header-file>] [<header-name>] */
+	case 219:
+		name = getNextWord();
+					if (name.empty())cout << "No word followed union command. Not added" << endl; 
+					else {
+						string groupnames = getOneLineSentence();
+						entityList.push_back( DoxygenEntity(219, name, groupnames));
+					}
+		break;
+		   
+	/* \until ( pattern ) */
+	 case 220:
+		restOfLine = getOneLineSentence();
+		if(!restOfLine.empty()) entityList.push_back( DoxygenEntity(220, restOfLine, ""));
+		else cout << "Nothing followed until command. Not added" << endl;
+		break;  
+		   
+		    /* \var (variable declaration) */
+	case 221:
+		restOfLine = getOneLineSentence();
+		if(!restOfLine.empty()) entityList.push_back( DoxygenEntity(221, restOfLine, ""));
+		else cout << "Nothing followed var command. Not added" << endl;
+		break;
+		   
+	/* \verbatim */
+	case 222:
+		cout << "Verbatim is not supported. Command not added." << endl;
+		if (progressTilEndCommand("endverbatim") < 1) cout << "No endcode for command verbatim found" << endl;	
+		break;
+		   
+	/* \verbinclude <file-name> */
+	case 223:
+		name = getNextWord();
+					if (name.empty())cout << "No word followed verbinclude command. Not added" << endl; 
+					else {
+						entityList.push_back( DoxygenEntity(223, name,""));
+					}
+		break;
+		   
+	/* \version { version number } */
+	case 224:
+		restOfParagraph = stringTilEndOfParagraph(endIndex);
+		if(!restOfParagraph.empty()) entityList.push_back( DoxygenEntity(224, restOfParagraph, "" ));
+		else cout << "Nothing followed version command. Not added" << endl;
+		break;
+		   
+	/* \warning { warning message } */
+	case 225:
+		restOfParagraph = stringTilEndOfParagraph(endIndex);
+		if(!restOfParagraph.empty()) entityList.push_back( DoxygenEntity(225, restOfParagraph, "" ));
+		else cout << "Nothing followed warning command. Not added" << endl;
+		break;
+		   
+	/* \weakgroup <name> [(title)] */
+	case 226:
+		name = getNextWord();
+		if (name.empty())cout << "No word followed weakgroup command. Not added" << endl; 
+		else {
+			string groupnames = getOneLineSentence();
+			entityList.push_back( DoxygenEntity(226, name,groupnames));
+			}
+		break;
+		   
+	/* \xmlonly */
+	case 227:
+		cout << "XML is not supported. Command not added." << endl;
+		if (progressTilEndCommand("endxmlonly") < 1) cout << "No endcode for command xmlonly found" << endl;	
+		break;
+		   
+	/* \xrefitem <key> "(heading)" "(list title)" {text} */
+	case 228:
+		//NEED TO IMPLEMENT
+		cout << "xrefitem is not supported yet. Command not added." << endl;
+		break;
+		   
+	/* \$ */
+	case 229:
+		entityList.push_back(229);
+		break;
+		   
+	/* \@ */
+	case 230:
+		entityList.push_back(230);
+		break;
+		   
+	/* \\ */
+	case 231:
+		entityList.push_back(231);
+		break;
+		   
+	/* \& */
+	case 232:
+		entityList.push_back(232);
+		break;
+		   
+	 /* \~[LanguageId] */
+	case 233:
+		break;
+		   
+	/* \< */
+	case 234:
+		entityList.push_back(234);
+		break;
+		   
+	/* \> */
+	case 235:
+		entityList.push_back(235);
+		break;
+		   
+	/* \# */
+	case 236:
+		entityList.push_back(236);
+		break;
+		   
+	/* \%  */
+	case 237:
+		entityList.push_back(237);
+		break;		
+
+		
+}
+		
+		}
+		
+int parse(string commentBlob){
+ //NO error checking since this is only for my personal testing
+ // usage for now is "program -DocStyle filename
+ 
+	/*
+ string java = "-java";
+
+ 
+ if ((argc < 3)||(java.compare(StringToLower(argv[1])))!= 0 ) {cout << "Incorrect Usage. -Docstyle filename only." << endl; exit(1);}
+ string line;
+ ifstream doxCommentFile(argv[2], ios::in);
+ doxCommentFile >> doxygenString;
+ while(getline(doxCommentFile, line)){
+ doxygenString += line + "\n";}
+ doxCommentFile.close();
+ */
+	doxygenString = commentBlob;
+ cout << doxygenString;
+
+
+if(doxygenString.compare(0, 3, "/**")!= 0 && doxygenString.compare(0, 3, "/*!")!= 0 
+		&& doxygenString.compare(0, 3, "///")!= 0 && doxygenString.compare(0, 3, "//!")!= 0 ){
+	
+	cout << "String Is not in proper Doxygen format." << endl;
+	exit(1);
+	}
+
+ 
+if(doxygenString[3] == '<'){
+	cout << "Support for side comments not yet implemented"<<endl;
+	exit(1);
+}
+
+// Plows through the initial fluff
+
+string currWord = "";
+string nextWord = "";
+string currComment = "";
+int currCommand = 0;
+int scanIndex = 0;
+
+
+
+while( clearFluff() > 0){}
+
+while(endIndex < doxygenString.length() && startIndex < doxygenString.length()){
+currWord = getNextWord();
+
+//while((currWord = nextWord()).compare("") == 0 ){ nextLine();}
+
+if(currWord[0] == 92 || currWord[0] == '@'){
+	currWord = doxygenString.substr(startIndex+1, endIndex - startIndex - 1);
+	currCommand = findCommand(currWord);
+	if (currCommand < 0 ){ cout << "BAD COMMAND: " << currWord << endl; exit(1);}
+	cout << "Command: " << currWord << " " << currCommand << endl;
+	startIndex = endIndex;
+}
+
+else if (briefDescriptions && !briefDescExists ){
+	currComment = getOneLineSentence();
+	if (!currComment.empty()){
+	briefDescExists = 1;
+	cout << "Brief Description Found : " << currComment << endl << "-----" << endl;
+	entityList.push_back( DoxygenEntity(99, "", currComment));
+	startIndex = endIndex;
+	}
+	else cout << "Error: Brief comment extends more than 1 line." << endl;
+}
+
+else{ 
+	currComment = getDescription();
+	cout << "Long Description Found : " << currComment << endl << "-----" << endl;
+	entityList.push_back( DoxygenEntity(100, "", currComment));
+	startIndex = endIndex;
+}
+
+}
+
+cout << "Entity List : "<< endl;
+list<DoxygenEntity>::iterator p = entityList.begin();
+while (p != entityList.end()){
+	(*p).printEntity();
+	p++;
+}
+
+		
+ return 0;
+}
+
+
+}
+
diff --git a/Source/DoxygenTranslator/example.i b/Source/DoxygenTranslator/example.i
new file mode 100644
index 000000000..20f2488cb
--- /dev/null
+++ b/Source/DoxygenTranslator/example.i
@@ -0,0 +1,19 @@
+/** File example. This is the Simple Test File!
+ */
+
+%module example
+
+%inline %{
+
+/**   Function for Greater Common Divisor
+ * Compute the greatest common divisor of positive integers 
+ * @param x an integer argument.
+ * @param y another integer argument.
+ * @return the GCD
+ */
+extern int    gcd(int x, int y);
+
+/** Global Variable Foo. Foo is the value of Foo. 
+ */
+extern double Foo;
+%}

From af125cd25151eaca3f96098c418326edf7a957c6 Mon Sep 17 00:00:00 2001
From: Cheryl Foil <cheryl.foil@gmail.com>
Date: Mon, 7 Jul 2008 02:59:22 +0000
Subject: [PATCH 003/314] Major overhaul to the basic structure of this parser,
 currently still sensitive and buggy.

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2008-cherylfoil@10654 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Source/DoxygenTranslator/DoxygenEntity.cpp    |  17 +-
 Source/DoxygenTranslator/DoxygenEntity.h      |  10 +-
 .../DoxygenTranslator/DoxygenTranslator.cpp   | 665 +++++++++++++++---
 3 files changed, 573 insertions(+), 119 deletions(-)

diff --git a/Source/DoxygenTranslator/DoxygenEntity.cpp b/Source/DoxygenTranslator/DoxygenEntity.cpp
index 9b02ade12..cd192601e 100644
--- a/Source/DoxygenTranslator/DoxygenEntity.cpp
+++ b/Source/DoxygenTranslator/DoxygenEntity.cpp
@@ -30,13 +30,13 @@ string findCommand(int commandNum){
 
 	int arraySize = sizeof(commandArray2)/sizeof(*commandArray2);
 	if (commandNum - 101 >= 0 && commandNum - 101 < arraySize){
-		return commandArray2[commandNum];
+		return commandArray2[commandNum - 101];
 	}
 
 	return "" ;
 }
 
-DoxygenEntity::DoxygenEntity(int typeEnt){
+DoxygenEntity::DoxygenEntity(string typeEnt){
     typeOfEntity = typeEnt;
     data = "";
     isLeaf = 1;
@@ -47,7 +47,7 @@ DoxygenEntity::DoxygenEntity(int typeEnt){
  * example: \b word
  * OR holding a string
  */
-DoxygenEntity::DoxygenEntity(int typeEnt, string param1){
+DoxygenEntity::DoxygenEntity(string typeEnt, string param1){
     typeOfEntity = typeEnt;
     data = param1;
     isLeaf = 1;
@@ -56,7 +56,7 @@ DoxygenEntity::DoxygenEntity(int typeEnt, string param1){
 /* Nonterminal node
  * contains
  */
-DoxygenEntity::DoxygenEntity(int typeEnt, list <DoxygenEntity> entList){
+DoxygenEntity::DoxygenEntity(string typeEnt, list <DoxygenEntity> entList){
     typeOfEntity = typeEnt;
     data = "";
     isLeaf = 0;
@@ -64,16 +64,19 @@ DoxygenEntity::DoxygenEntity(int typeEnt, list <DoxygenEntity> entList){
 }
 
 
-void DoxygenEntity::printEntity(){
+void DoxygenEntity::printEntity(int level){
 	if (isLeaf) {
-		cout << "Node Command: " << findCommand(typeOfEntity);
+		for (int i = 0; i < level; i++) {cout << "\t";}
+		cout << "Node Command: " << typeOfEntity << " ";
 		if (data.compare("") != 0) cout << "Node Data: " << data;
 		cout << endl;
 	}
 	else{
+		cout << "Node Command : " << typeOfEntity << endl;
 		list<DoxygenEntity>::iterator p = entityList.begin();
+		level++;
 		while (p != entityList.end()){
-			(*p).printEntity();
+			(*p).printEntity(level);
 			p++;
 		}
 	}
diff --git a/Source/DoxygenTranslator/DoxygenEntity.h b/Source/DoxygenTranslator/DoxygenEntity.h
index 8330e4507..a0a99ed70 100644
--- a/Source/DoxygenTranslator/DoxygenEntity.h
+++ b/Source/DoxygenTranslator/DoxygenEntity.h
@@ -9,12 +9,12 @@ using namespace std;
 class DoxygenEntity{
 
 public:
-	DoxygenEntity(int typeEnt);
-	DoxygenEntity(int typeEnt, string param1);
-	DoxygenEntity(int typeEnt, list <DoxygenEntity> entList);
+	DoxygenEntity(string typeEnt);
+	DoxygenEntity(string typeEnt, string param1);
+	DoxygenEntity(string typeEnt, list <DoxygenEntity> entList);
 	virtual ~DoxygenEntity();
-	void printEntity();
-    int typeOfEntity;
+	void printEntity(int level);
+    string typeOfEntity;
     list <DoxygenEntity> entityList;
     string data;
     int isLeaf;
diff --git a/Source/DoxygenTranslator/DoxygenTranslator.cpp b/Source/DoxygenTranslator/DoxygenTranslator.cpp
index dadea41b5..e2fdaef8a 100644
--- a/Source/DoxygenTranslator/DoxygenTranslator.cpp
+++ b/Source/DoxygenTranslator/DoxygenTranslator.cpp
@@ -22,9 +22,10 @@ to test. */
 
 //int testCommandParsingFunctions = 1;// not implemented
 
-int testCodeCrawlingFunctions = 1;
-int demonstrateParsing = 0;
-
+int testCodeCrawlingFunctions = 0;
+int demonstrateParsing = 1;
+int noisy = 1; // set this to 1 for extra chatter from the parsing stage.
+int addCommand(string commandName, int &startInd, list <DoxygenEntity> &doxyList, string doxygenString);
 //////////////////////////////////////////
 
 
@@ -50,7 +51,7 @@ string commandArray[] = {"a", "addindex", "addtogroup", "anchor", "arg", "attent
 		"sa", "section", "see", "showinitializer", "since", "skip", "skipline", "struct", "subpage",
 		"subsection", "subsubsection", "test", "throw", "todo", "tparam", "typedef", "union", "until",
 		"var", "verbatim", "verbinclude", "version", "warning", "weakgroup", "xmlonly", "xrefitem",
-		"$", "@", string(1, 92), string(1, '&'), "~", "<", ">", string(1, '#'), "%", "plaindescription"};
+		"$", "@", string(1, 92), string(1, '&'), "~", "<", ">", string(1, '#'), "%"};
 
 
 string sectionIndicators[] = { "attention", "author", "brief", "bug", "cond", "date", "deprecated", "details",
@@ -58,12 +59,35 @@ string sectionIndicators[] = { "attention", "author", "brief", "bug", "cond", "d
 		"tparam", "post" , "pre", "remarks", "return", "retval", "sa", "see", "since", "test", "throw", "todo",
 		"version", "warning", "xrefitem" };
 
+/* All of the doxygen commands divided up by how they are parsed */
+string simpleCommands[] = {"n", "$", "@", string(1, 92), string(1, '&'), "~", "<", ">", string(1, '#'), "%"};
+string ignoredSimpleCommands[] = {"nothing at the moment"};
+string commandWords[] = {"a", "b", "c", "e", "em", "p", "def", "enum", "example", "package", 
+		"relates", "namespace", "relatesalso","anchor", "dontinclude", "include", "includelineno"};
+string ignoredCommandWords[] = {"copydoc", "copybrief", "copydetails", "verbinclude", "htmlinclude"};
+string commandLines[] = {"addindex", "fn", "name", "line", "var", "skipline", "typedef", "skip", "until", "property"};
+string ignoreCommandLines[] = {"nothing at the moment"};
+string commandParagraph[] = {"return", "remarks", "since", "test", "sa", "see", "pre", "post", "details", "invariant", 
+		    "deprecated", "date", "note", "warning", "version", "todo", "bug", "attention", "brief", "arg", "author"};
+string ignoreCommandParagraphs[] = {"nothing at the moment"};
+string commandEndCommands[] = {"code", "dot", "msc", "f$", "f[", "f{environment}{", "htmlonly", "latexonly", "manonly", 
+		   "verbatim", "xmlonly", "cond", "if", "ifnot", "link"};
+string commandWordParagraphs[] = {"param", "tparam", "throw", "retval", "exception"};
+string commandWordLines[] = {"page", "subsection", "subsubsection", "section", "paragraph", "defgroup"};
+string commandWordOWordOWords [] = {"category", "class", "protocol", "interface", "struct", "union"};
+string commandOWords[] = {"dir", "file", "cond"};
+string commandErrorThrowings[] = {"annotatedclasslist", "classhierarchy", "define", "functionindex", "header",
+		"headerfilelist", "inherit", "l", "postheader", "private", "privatesection", "protected", 
+		"protectedsection", "public", "publicsection", "endcode", "enddot", "endmsc", "endhtmlonly", 
+		"endlatexonly", "endmanonly", "endlink", "endverbatim", "endxmlonly", "f]", "f}", "endcond", 
+		"endif"};
+string commandUniques[] = {"xrefitem", "ingroup", "par", "headerfile", "overload", "weakgroup", "ref",
+		"subpage", "dotfile", "image", "addtogroup", "li"};
 
  int startIndex = 0;
  int endIndex = 0;
  int isNewLine = 0;
-
- string doxygenString = "";
+ //string doxygenString = "";
  int briefDescExists = 0;
 
  /* Entity list is the root list.
@@ -99,6 +123,61 @@ string sectionIndicators[] = { "attention", "author", "brief", "bug", "cond", "d
  	}
  	return -1;
  }
+ 
+ int commandBelongs(string theCommand){
+	 string smallString = StringToLower(theCommand );
+	 //cout << " Looking for command " << theCommand << endl;
+	 int i = 0;
+	 for ( i = 0; i < sizeof(simpleCommands)/sizeof(*simpleCommands); i++){
+	 	if(smallString.compare(simpleCommands[i]) == 0){return 1;}
+	 	}
+	 for ( i = 0; i < sizeof(ignoredSimpleCommands)/sizeof(*ignoredSimpleCommands); i++){
+	 	if(smallString.compare(ignoredSimpleCommands[i]) == 0){return 2;}
+	 	} 
+	 for ( i = 0; i < sizeof(commandWords)/sizeof(*commandWords); i++){
+	 	if(smallString.compare( commandWords[i]) == 0){return 3;}
+	 	} 
+	 for ( i = 0; i < sizeof(ignoredCommandWords)/sizeof(*ignoredCommandWords); i++){
+	 	if(smallString.compare( ignoredCommandWords[i]) == 0){return 4;}
+	 	} 
+	 for ( i = 0; i < sizeof(commandLines)/sizeof(*commandLines); i++){
+	 	if(smallString.compare( commandLines[i]) == 0){return 5;}
+	 	} 
+	 for ( i = 0; i < sizeof(ignoreCommandLines)/sizeof(*ignoreCommandLines); i++){
+	 	if(smallString.compare( ignoreCommandLines[i]) == 0){return 6;}
+	 	} 
+	 for ( i = 0; i <  sizeof(commandParagraph)/sizeof(*commandParagraph); i++){
+	 	if(smallString.compare( commandParagraph[i]) == 0){return 7;}
+	 	} 
+	 /* IgnoreCommandParagraph */
+	 for ( i = 0; i < sizeof(ignoreCommandParagraphs)/sizeof(*ignoreCommandParagraphs); i++){
+	 	if(smallString.compare( ignoreCommandParagraphs[i]) == 0){return 8;}
+	 	} 
+	 for ( i = 0; i < sizeof(commandEndCommands)/sizeof(*commandEndCommands); i++){
+	 	if(smallString.compare( commandEndCommands[i]) == 0){return 9;}
+	 	} 
+	 for ( i = 0; i < sizeof(commandWordParagraphs)/sizeof(*commandWordParagraphs); i++){
+	 	if(smallString.compare( commandWordParagraphs[i]) == 0){return 10;}
+	 	} 
+	 for ( i = 0; i < sizeof(commandWordLines)/sizeof(*commandWordLines); i++){
+	 	if(smallString.compare( commandWordLines[i]) == 0){return 11;}
+	 	} 
+	 for ( i = 0; i < sizeof(commandWordOWordOWords)/sizeof(*commandWordOWordOWords); i++){
+	 	if(smallString.compare( commandWordOWordOWords[i]) == 0){return 12;}
+	 	} 
+	 for ( i = 0; i < sizeof(commandOWords)/sizeof(*commandOWords); i++){
+	 	if(smallString.compare( commandOWords[i]) == 0){return 13;}
+	 	} 
+	 for ( i = 0; i < sizeof(commandErrorThrowings)/sizeof(*commandErrorThrowings); i++){
+	 	if(smallString.compare( commandErrorThrowings[i]) == 0){return 14;}
+	 	} 
+	 for ( i = 0; i < sizeof(commandUniques)/sizeof(*commandUniques); i++){
+	 	if(smallString.compare( commandUniques[i]) == 0){return 15;}
+	 	} 
+
+	 	return 0;
+	 
+ }
 
  /* isSectionIndicator returns a boolean if the command is a section indicator
   * This is a helper method for finding the end of a paragraph
@@ -123,7 +202,7 @@ string sectionIndicators[] = { "attention", "author", "brief", "bug", "cond", "d
  /* Tiny method to compartmentalise the removal of all optional comment fluff such as ///
   * or **** that often occurs before commment blobs.
   */
- int clearFluff(int startInd){
+ int clearFluff(int &startInd, string doxygenString){
 	int startIndex = startInd;
  	int amountRemoved = 0;
 
@@ -132,7 +211,7 @@ string sectionIndicators[] = { "attention", "author", "brief", "bug", "cond", "d
  		startIndex++;
  		amountRemoved++;
  		}
-
+ 	startInd = startIndex;
  	return startIndex;
  }
 
@@ -141,13 +220,13 @@ string sectionIndicators[] = { "attention", "author", "brief", "bug", "cond", "d
   * Updates the index it is given after completion.
   */
 
- string getNextWord(int &startInd){
+ string getNextWord(int &startInd, string doxygenString){
 	int startIndex = startInd;
  	string nextWord = "";
- 	while (doxygenString[startIndex] == '/'|| doxygenString[startIndex] == ' '
+ 	while (startIndex < doxygenString.length() && (doxygenString[startIndex] == '/'|| doxygenString[startIndex] == ' '
  		|| doxygenString[startIndex] == '*' || doxygenString[startIndex]== '\n'
-		|| doxygenString[startIndex] == '!'){
- 		if(doxygenString[startIndex]== '\n') return nextWord;
+		|| doxygenString[startIndex] == '!')){
+ 		if(doxygenString[startIndex]== '\n'){ startInd = startIndex; return nextWord;}
  		startIndex++;
  		//cout << "Start Index" << startIndex << endl;
  		}
@@ -168,7 +247,7 @@ string sectionIndicators[] = { "attention", "author", "brief", "bug", "cond", "d
   * and moved the index to the NEXT line
   * returns "" if nothing on the current line.
   */
- string getOneLine(int &startInd){
+ string getOneLine(int &startInd, string doxygenString){
 	int startIndex = startInd;
  	while (doxygenString[startIndex] == '/'|| doxygenString[startIndex] == ' '
  		|| doxygenString[startIndex] == '*' || doxygenString[startIndex]== '\n'
@@ -187,13 +266,11 @@ string sectionIndicators[] = { "attention", "author", "brief", "bug", "cond", "d
  	startInd = endIndex;
  	return returnedLine;
  }
-
-/* Returns a Paragraph- defined in Doxygen to be a paragraph of text
- * seperate by either a structural command or a blank line
- * This method is VERY messy currently
+/* Returns a properly formatted (all doxygen *, //! etc removed)
+ * up til ANY command or end of paragraph is encountered. Has all the same issues as
+ * getStringTilEndOfParagraph formatting wise.
  */
- //TODO fix getStringTilEndOfParagraph to be more forgiving, work on ' ' characters
- string getStringTilEndOfParagraph(int &startInd){
+string getStringTilCommand(int &startInd, string doxygenString){
 	 if (startInd >= doxygenString.length()) return "";
 	int startIndex = startInd;
 	int endIndex = startInd;
@@ -203,8 +280,89 @@ string sectionIndicators[] = { "attention", "author", "brief", "bug", "cond", "d
  	int spareIndex = 0;
  	int counter;
  	int finalIndex;
- 	while(keepLooping && endIndex < doxygenString.length()){
-		if (doxygenString[endIndex] == '\n'){
+ 	while(keepLooping){
+ 	 	if(endIndex >= doxygenString.length()){
+ 	 			finalIndex = endIndex;
+ 	 			keepLooping = 0;
+ 	 		}
+ 	 	else if (doxygenString[endIndex] == '\n'){
+			//cout << "1 ";
+			counter = endIndex;
+			if ( keepLooping && endIndex < doxygenString.length()-1) {
+				counter++;
+				//cout << "Counter :" << counter << endl;
+				while(keepLooping && endIndex < doxygenString.length() && (doxygenString[counter] == ' ' ||
+				               doxygenString[counter] == '*'|| doxygenString[counter] == '\n'|| doxygenString[counter] == '/'
+				            	   || doxygenString[counter] == '!') ){
+									if(doxygenString[counter] == '\n') {
+										//cout << "Blank line found" << endl;
+										keepLooping = 0;
+										finalIndex = counter;}
+									else{ counter++;}
+									}
+
+			}
+			//endIndex = counter;
+		}
+ 		else if (doxygenString[endIndex] == 92 || doxygenString[endIndex] == '@'){
+ 			finalIndex = endIndex;
+ 			keepLooping = 0;
+ 			}
+		else if(endIndex < doxygenString.length() -2
+				&& string("**/").compare(doxygenString.substr(endIndex , endIndex  + 2)) == 0){
+			finalIndex = endIndex;
+			//cout << "3 ";
+			keepLooping = 0;
+		}
+ 		if(keepLooping){
+ 			//cout << "4 ";
+ 			endIndex++;
+ 		}
+ 	}
+ 	//cout << "Done with EndIndex" << endl;
+ 	while(doxygenString[startIndex] == '!' || doxygenString[startIndex] == ' '
+ 		|| doxygenString[startIndex] == '/' || doxygenString[startIndex] == '*') startIndex++;
+
+ 	for (int i = startIndex; i < endIndex; i++){
+
+ 		if (doxygenString[i] == '\n') {
+
+ 			while ((doxygenString[i] == '\n' || doxygenString[i] == ' '
+ 				|| doxygenString[i] == '*' || doxygenString[i] == '/')&& endIndex < doxygenString.length() - 1){
+ 				i++;
+ 				}
+ 			description.append(" ");
+ 		}
+ 		description.push_back(doxygenString[i]);
+ 		//cout << doxygenString[i];
+ 	}
+ 	//if(noisy) cout << "Final Index is: " << finalIndex << endl;
+ 	startInd = finalIndex;
+ 	return description;
+ }
+ 
+ 
+/* Returns a Paragraph- defined in Doxygen to be a paragraph of text
+ * seperate by either a structural command or a blank line
+ * This method is VERY messy currently
+ */
+ //TODO fix getStringTilEndOfParagraph to be more forgiving, work on ' ' characters
+ string getStringTilEndOfParagraph(int &startInd, string doxygenString){
+	 if (startInd >= doxygenString.length()) return "";
+	int startIndex = startInd;
+	int endIndex = startInd;
+ 	string description = "";
+ 	/* Find the End of the description */
+ 	int keepLooping = 1;
+ 	int spareIndex = 0;
+ 	int counter;
+ 	int finalIndex;
+ 	while(keepLooping){
+ 		if(endIndex >= doxygenString.length()){
+ 			finalIndex = endIndex;
+ 			keepLooping = 0;
+ 		}
+ 		else if (doxygenString[endIndex] == '\n'){
 			//cout << "1 ";
 			counter = endIndex;
 			if ( keepLooping && endIndex < doxygenString.length()-1) {
@@ -226,7 +384,7 @@ string sectionIndicators[] = { "attention", "author", "brief", "bug", "cond", "d
  		else if (doxygenString[endIndex] == 92 || doxygenString[endIndex] == '@'){
  			//cout << "2 ";
 			spareIndex = endIndex;
- 			if (isSectionIndicator(getNextWord(spareIndex))) keepLooping = 0;
+ 			if (isSectionIndicator(getNextWord(spareIndex, doxygenString))) keepLooping = 0;
  			}
 		else if(endIndex < doxygenString.length() - 1
 				&& string("*/").compare(doxygenString.substr(endIndex , endIndex  + 1)) == 0){
@@ -266,7 +424,7 @@ string sectionIndicators[] = { "attention", "author", "brief", "bug", "cond", "d
   * currently this method does NOT process what is in between the two commands
   */
  //TODO Make progressTilCommand return a formatted string
- int progressTilEndCommand(string theCommand, int &startInd){
+ int progressTilEndCommand(string theCommand, int &startInd, string doxygenString){
  	endIndex = startInd;
  	while (endIndex < doxygenString.length()){
  		if (doxygenString[endIndex] == 92 || doxygenString[endIndex] == '@'){
@@ -282,7 +440,7 @@ string sectionIndicators[] = { "attention", "author", "brief", "bug", "cond", "d
  	return 0;
  }
 
- string getStringTilAnyCommand(string theCommand, int &startInd){
+ string getStringTilAnyCommand(string theCommand, int &startInd, string doxygenString){
 	 endIndex = startInd;
 	 startIndex = startInd;
 	 int keepLooping = 1;
@@ -319,15 +477,17 @@ string sectionIndicators[] = { "attention", "author", "brief", "bug", "cond", "d
   * differs wildly */
 
  int testClearFluff(){
-
+  string doxygenString = "";
   string cases[] = {"/** WORD", "/*! WORD", "/******* WORD", "///// WORD", "//! WORD", "//! WORD", "///WORD",
  		 "/**\nWORD", "/**\n*WORD", "/** \n WORD"};
   int testPassed = 1;
+  int placement = 0;
   int casesSize = sizeof(cases)/sizeof(*cases);
   for (int i = 0; i < casesSize; i++){
+	  placement = 0;
 	  doxygenString = cases[i];
-	  if(cases[i][clearFluff(0)] != 'W'){
-		  cout << "ClearFluff failed for string :" << doxygenString << "\t Displayed :" << cases[i][clearFluff(0)] << ": Instead." << endl;
+	  if(cases[i][clearFluff(placement, doxygenString)] != 'W'){
+		  cout << "ClearFluff failed for string :" << doxygenString << "\t Displayed :" << cases[i][clearFluff(placement = 0, doxygenString)] << ": Instead." << endl;
 		  testPassed = 0;
 	  }
   }
@@ -338,6 +498,7 @@ string sectionIndicators[] = { "attention", "author", "brief", "bug", "cond", "d
   };
 
  int testGetNextWord(){
+	  string doxygenString = "";
 	  string cases[] = {"/** WORD ", " * WORD ", "///!WORD ", " WORD ", "//! WORD ", " * WORD ", "*WORD "};
 	  int testPassed = 1;
 	  string testWord = "";
@@ -346,7 +507,7 @@ string sectionIndicators[] = { "attention", "author", "brief", "bug", "cond", "d
 	  for (int i = 0; i < casesSize; i++){
 		  doxygenString = cases[i];
 		  placement = 0;
-		  testWord = getNextWord(placement);
+		  testWord = getNextWord(placement, doxygenString);
 		  if(testWord.compare("WORD") != 0){
 			  cout << "GetNextWord failed for string :" << doxygenString << "\t Displayed :" << testWord << ": Instead." << endl;
 			  testPassed = 0;
@@ -355,7 +516,7 @@ string sectionIndicators[] = { "attention", "author", "brief", "bug", "cond", "d
 	  }
 	    placement = 0;
 		doxygenString = " * @WORD ";
-		testWord = getNextWord(placement);
+		testWord = getNextWord(placement, doxygenString);
 		if(testWord.compare("@WORD") != 0){
 			cout << "GetNextWord failed for string :"
 			<< doxygenString << "\t Displayed :" << testWord << ": Instead." << endl;
@@ -369,7 +530,7 @@ string sectionIndicators[] = { "attention", "author", "brief", "bug", "cond", "d
 		commandWord = commandWord + "WORD";
 		doxygenString = testWord;
 		placement = 0;
-		testWord = getNextWord(placement);
+		testWord = getNextWord(placement, doxygenString);
 		if(testWord.compare(commandWord) != 0){
 			cout << "GetNextWord failed for string :" << doxygenString
 			<< "\t Displayed :" << testWord << ": Instead." << endl;
@@ -377,38 +538,38 @@ string sectionIndicators[] = { "attention", "author", "brief", "bug", "cond", "d
 		  //else cout << "GetNextWord passed for string :" << doxygenString << endl;
 		doxygenString = "WORD ANOTHER WORD1 WORD2 \n";
 		placement = 0;
-		testWord = getNextWord(placement);
+		testWord = getNextWord(placement, doxygenString);
 		if(testWord.compare("WORD") != 0){
 			cout << "GetNextWord failed for string :" << doxygenString
 			<< "\t Displayed :" << testWord << ": Instead." << endl;
 			testPassed = 0;}
 		  //else cout << "GetNextWord passed for string :" << doxygenString << endl;
-		testWord = getNextWord(placement);
+		testWord = getNextWord(placement, doxygenString);
 		if(testWord.compare("ANOTHER") != 0){
 			cout << "GetNextWord failed for string :" << doxygenString
 			<< "\t Displayed :" << testWord << ": Instead." << endl;
 			testPassed = 0;}
 		 //else cout << "GetNextWord passed for string :" << doxygenString << endl;
-		testWord = getNextWord(placement);
+		testWord = getNextWord(placement, doxygenString);
 		if(testWord.compare("WORD1") != 0){
 			cout << "GetNextWord failed for string :" << doxygenString
 			<< "\t Displayed :" << testWord << ": Instead." << endl;
 			testPassed = 0;}
 		  //else cout << "GetNextWord passed for string :" << doxygenString << endl;
-		testWord = getNextWord(placement);
+		testWord = getNextWord(placement, doxygenString);
 		if(testWord.compare("WORD2") != 0){
 			cout << "GetNextWord failed for string :"
 			<< doxygenString << "\t Displayed :" << testWord
 			<< ": Instead." << endl;
 			testPassed = 0;}
 		  //else cout << "GetNextWord passed for string :" << doxygenString << endl;
-		testWord = getNextWord(placement);
+		testWord = getNextWord(placement, doxygenString);
 		if(testWord.compare("") != 0){
 			cout << "GetNextWord failed for string :" << doxygenString
 			<< "\t Displayed :" << testWord << ": Instead." << endl;
 			testPassed = 0;}
 		  //else cout << "GetNextWord passed for string :" << doxygenString << endl;
-		testWord = getNextWord(placement);
+		testWord = getNextWord(placement, doxygenString);
 		if(testWord.compare("") != 0){
 			cout << "GetNextWord failed for string :" << doxygenString <<
 			"\t Displayed :" << testWord << ": Instead." << endl;
@@ -420,6 +581,7 @@ string sectionIndicators[] = { "attention", "author", "brief", "bug", "cond", "d
  }
 
  int testGetOneLine(){
+	  string doxygenString = "";
 	  string cases[] = {" * Crop this sentence after this period.\n",
 			  " * Crop this sentence after this period.\n",
 			  "Crop this sentence after this period.\n",
@@ -433,7 +595,7 @@ string sectionIndicators[] = { "attention", "author", "brief", "bug", "cond", "d
 	  for (int i = 0; i < casesSize; i++){
 		  doxygenString = cases[i];
 		  placement = 0;
-		  testWord = getOneLine(placement);
+		  testWord = getOneLine(placement, doxygenString);
 		  if(testWord.compare("Crop this sentence after this period.") != 0){
 			  cout << "GetOneLine failed for string :" << doxygenString << "\t Displayed :" << testWord << ": Instead." << endl;
 			  testPassed = 0;
@@ -441,17 +603,17 @@ string sectionIndicators[] = { "attention", "author", "brief", "bug", "cond", "d
 	  }
 	  doxygenString = ("Get this line.\n * Now get this line.");
 	  placement = 0;
-	  testWord = getOneLine(placement);
+	  testWord = getOneLine(placement, doxygenString);
 	  if(testWord.compare("Get this line.") != 0){
 	  		cout << "GetOneLine failed for string :" << doxygenString << "\t Displayed :" << testWord << ": Instead." << endl;
 	  		testPassed = 0;
 	  		  }
-	  testWord = getOneLine(placement);
+	  testWord = getOneLine(placement, doxygenString);
 	  if(testWord.compare("Now get this line.") != 0){
 	  		cout << "GetOneLine failed for string :" << doxygenString << "\t Displayed :" << testWord << ": Instead." << endl;
 	  		testPassed = 0;
 	  		  }
-	  testWord = getOneLine(placement);
+	  testWord = getOneLine(placement, doxygenString);
 	  if(testWord.compare("") != 0){
 	  		cout << "GetOneLine failed for string :" << doxygenString << "\t Displayed :" << testWord << ": Instead." << endl;
 	  		testPassed = 0;
@@ -463,17 +625,18 @@ string sectionIndicators[] = { "attention", "author", "brief", "bug", "cond", "d
  }
 //TODO Flesh testGetStringTilEndOfParagraph out, fix weird spacing problems
  int testGetStringTilEndOfParagraph(){
+	string doxygenString = "";
 	int placement = 0;
 	int testPassed = 1;
 	string testParagraph;
 	doxygenString = ("/* This is a description,\n * thus it continues on\n * for several lines.\n\n This Shouldn't be included.\n\n **/");
-	testParagraph = getStringTilEndOfParagraph(placement);
+	testParagraph = getStringTilEndOfParagraph(placement, doxygenString);
 	if( testParagraph.compare("This is a description, thus it continues on for several lines.") != 0){
   		cout << "GetOneLine failed for string :" << doxygenString << "\t Displayed :" << testParagraph << ": Instead." << endl;
   		testPassed = 0;
   	}
 	//cout << "Curr Placement: " << placement<< endl;
-	testParagraph = getStringTilEndOfParagraph(placement);
+	testParagraph = getStringTilEndOfParagraph(placement, doxygenString);
 	//cout << "Curr Placement: " << placement<< endl;
 	if( testParagraph.compare(" This Shouldn't be included.") != 0){
   		cout << "GetOneLine failed for string :" << doxygenString << "\t Displayed :" << testParagraph << ": Instead." << endl;
@@ -487,25 +650,42 @@ string sectionIndicators[] = { "attention", "author", "brief", "bug", "cond", "d
 	doxygenString.push_back(92);
 	doxygenString += "author cheryl foil \n\n **/";
 	placement = 0;
-	testParagraph = getStringTilEndOfParagraph(placement);
+	testParagraph = getStringTilEndOfParagraph(placement, doxygenString);
 	if( testParagraph.compare("This is a description, thus it continues on for several lines.") != 0){
   		cout << "GetOneLine failed for string :" << doxygenString << "\t Displayed :" << testParagraph << ": Instead." << endl;
   		testPassed = 0;
   	}
 
-	if(testPassed) cout << "+++GetDescription passed for all tests+++\n" << endl;
-	else cout << "+++GetDescription FAILED+++\n" << endl;
+	if(testPassed) cout << "+++GetGetStringTilEndOfParagraph passed for all tests+++\n" << endl;
+	else cout << "+++GetGetStringTilEndOfParagraphFAILED+++\n" << endl;
 	return testPassed;
  }
 
+ int testGetStringTilCommand(){
+		string doxygenString = "";
+		int placement = 0;
+		int testPassed = 1;
+		string testParagraph;
+		doxygenString = ("/* This is a description,\n * thus it continues on\n * for several @b lines.\n\n This Shouldn't be included.\n\n **/");
+		testParagraph = getStringTilCommand(placement, doxygenString);
+		if( testParagraph.compare("This is a description, thus it continues on for several ") != 0){
+	  		cout << "GetOneLine failed for string :" << doxygenString << "\t Displayed :" << testParagraph << ": Instead." << endl;
+	  		testPassed = 0;
+	  	}
+		if(testPassed) cout << "+++GetStringTilCommand passed for all tests+++\n" << endl;
+		else cout << "+++GetStringTilCommand FAILED+++\n" << endl;
+		return testPassed;
+	 
+ }
  int testProgressTilEndCommand(){
+	    string doxygenString = "";
 		int placement = 0;
 		int testPassed = 1;
 		string testParagraph;
 		doxygenString = "Let's pretend this \n * is a bunch of code to be ended in ";
 		doxygenString.push_back(92);
 		doxygenString += "endcodeSTOP";
-		progressTilEndCommand("endcode", placement);
+		progressTilEndCommand("endcode", placement, doxygenString);
 		//cout << "Placement : " << placement << endl;
 		if( doxygenString[placement] != 'S'){
 	  		cout << "GetOneLine failed for string :" << doxygenString << "\n\t Displayed :" << testParagraph << ": Instead." << endl;
@@ -532,6 +712,8 @@ string sectionIndicators[] = { "attention", "author", "brief", "bug", "cond", "d
  	cout << "Testing progressTilEndCommand" << endl;
  	testProgressTilEndCommand();
 
+ 	cout << "Testing GetStringTilCommand" << endl;
+ 	testGetStringTilCommand();
  	return 1;
  }
 
@@ -542,88 +724,357 @@ string sectionIndicators[] = { "attention", "author", "brief", "bug", "cond", "d
 
 		list<DoxygenEntity>::iterator p = rootList.begin();
 		while (p != rootList.end()){
-			(*p).printEntity();
+			(*p).printEntity(0);
 			p++;
 		}
 
  }
+ 
+ 
+ 
+ list<DoxygenEntity> parse(int startInd, string doxygenString){
+ 	string currWord = "";
+ 	int startIndex = startInd;
+ 	int savedIndex;
+ 	list <DoxygenEntity> aNewList;
+ 	endIndex = doxygenString.length();
+ 	int currCommand;
+ 	while (startIndex < endIndex){
+ 		savedIndex = startIndex;
+ 		currWord = getNextWord(startIndex, doxygenString);
+ 		if(noisy) cout << "Parsing for phrase starting in:" << currWord << endl;
+ 		if(currWord == ""){
+ 			if (startIndex < endIndex) startIndex++;
+ 		}
+ 		else if(currWord[0] == 92 || currWord[0] == '@'){
+ 			currWord = currWord.substr(1, currWord.length() - 1);
+ 			currCommand = findCommand(currWord);
+ 			if (currCommand < 0 ){ cout << "BAD COMMAND: " << currWord << endl; exit(1);}
+ 				//cout << "Command: " << currWord << " " << currCommand << endl;
+ 			addCommand(currWord, startIndex, aNewList, doxygenString);
+ 		}
+ 		else{
+ 			startIndex = savedIndex;
+			addCommand(string("plainstring"), startIndex, aNewList, doxygenString);
+
+ 		}
+ 	}
+
+ 	return aNewList;
+ }
+ 
+ /*  Method for Adding a Simple Command
+  * Format: @command
+  * Plain commands, such as newline etc, they contain no other data
+  *  \n \\ \@ \& \$ \# \< \> \%
+  */
+  int addSimpleCommand(string theCommand, int &startInd, list <DoxygenEntity> &doxyList, string doxygenString){
+	 
+		if (noisy) cout << "Parsing " << theCommand << endl;
+		doxyList.push_back(DoxygenEntity(theCommand));
+		return 1;
+ }
+  
+  /* NOT INCLUDED Simple Commands
+   * Format: @command
+   * Plain commands, such as newline etc, they contain no other data
+   */
+  int ignoreSimpleCommand(string theCommand, int &startInd, list <DoxygenEntity> &doxyList, string doxygenString){
+	 
+		if (noisy) cout << "Not Adding " << theCommand << endl;
+		return 1;
+		//doxyList.push_back(DoxygenEntity(108));
+ }
+  
+  /* CommandWord
+   * Format: @command <word>
+   * Commands with a single WORD after then such as @b
+   * "a", "b", "c", "e", "em", "p", "def", "enum", "example", "package", 
+   * "relates", "namespace", "relatesalso","anchor", "dontinclude", "include", "includelineno"
+   */
+  int addCommandWord(string theCommand, int &startInd, list <DoxygenEntity> &doxyList, string doxygenString){
+	if (noisy) cout << "Parsing " << theCommand << endl;
+	string name = getNextWord(startInd, doxygenString);
+	if (!name.empty()){ 
+		doxyList.push_back(DoxygenEntity(theCommand, name));
+		return 1;
+	}
+	else cout << "No word followed " << theCommand <<  " command. Not added" << endl;
+	return 0;
+ }
+  /* NOT INCLUDED CommandWord
+   * Format: @command <word>
+   * Commands with a single WORD after then such as @b
+   * "copydoc", "copybrief", "copydetails", "verbinclude", "htmlinclude"
+   */
+  int ignoreCommandWord(string theCommand, int &startInd, list <DoxygenEntity> &doxyList, string doxygenString){
+	if (noisy) cout << "Not Adding " << theCommand << endl;
+	string name = getNextWord(startInd, doxygenString);
+	if (!name.empty()){ 
+		return 1;
+	}
+	else cout << "WARNING: No word followed " << theCommand <<  " command." << endl;
+	return 0;
+ }
+  
+  /* CommandLine
+   * Format: @command (line)
+   * Commands with a single LINE after then such as @var
+   * "addindex", "fn", "name", "line", "var", "skipline", "typedef", "skip", "until", "property"
+   */
+  int addCommandLine(string theCommand, int &startInd, list <DoxygenEntity> &doxyList, string doxygenString){
+	if (noisy) cout << "Parsing " << theCommand << endl;
+	string line = getOneLine(startInd, doxygenString);
+	if(!line.empty()){
+		int placement = 0;
+		list <DoxygenEntity> aNewList;
+		aNewList =  parse(placement, line);
+		doxyList.push_back( DoxygenEntity(theCommand, aNewList));
+		return 1;
+		}
+	else cout << "No line followed " << theCommand <<  " command. Not added" << endl;
+	return 0;
+ }
+  
+  /* NOT INCLUDED CommandLine
+   * Format: @command (line)
+   * Commands with a single LINE after then such as @var
+   * 
+   */
+  int ignoreCommandLine(string theCommand, int &startInd, list <DoxygenEntity> &doxyList, string doxygenString){
+	if (noisy) cout << "Not Adding " << theCommand << endl;
+	string line = getOneLine(startInd, doxygenString);
+	if(!line.empty()){
+		return 1;
+		}
+	else cout << "WARNING: No line followed " << theCommand <<  " command." << endl;
+	return 0;
+ }
+  
+  /* CommandParagraph
+   * Format: @command {paragraph}
+   * Commands with a single paragraph after then such as @return
+   * "return", "remarks", "since", "test", "sa", "see", "pre", "post", "details", "invariant", 
+   * "deprecated", "date", "note", "warning", "version", "todo", "bug", "attention", "brief", "arg", "author"
+   */
+  int addCommandParagraph(string theCommand, int &startInd, list <DoxygenEntity> &doxyList, string doxygenString){
+	if (noisy) cout << "Parsing " << theCommand << endl;
+	string restOfParagraph = getStringTilEndOfParagraph(startInd, doxygenString);
+	if(!restOfParagraph.empty()){
+		int placement = 0;
+		list <DoxygenEntity> aNewList;
+		aNewList =  parse(placement, restOfParagraph);
+		doxyList.push_back( DoxygenEntity(theCommand, aNewList));
+		return 1;
+		}
+	else cout << "No line followed " << theCommand <<  " command. Not added" << endl;
+	return 0;
+ }
+  /* CommandParagraph
+   * Format: @command {paragraph}
+   * Commands with a single LINE after then such as @var
+   * 
+   */
+  int ignoreCommandParagraph(string theCommand, int &startInd, list <DoxygenEntity> &doxyList, string doxygenString){
+	if (noisy) cout << "Not Adding " << theCommand << endl;
+	string restOfParagraph = getStringTilEndOfParagraph(startInd, doxygenString);
+	if(!restOfParagraph.empty()){
+		return 1;
+		}
+	else cout << "WARNING: No line followed " << theCommand <<  " command." << endl;
+	return 0;
+ }
+  /* Command EndCommand
+   * Format: @command and ends at @endcommand
+   * Commands that take in a block of text such as @code
+   * "code", "dot", "msc", "f$", "f[", "f{environment}{", "htmlonly", "latexonly", "manonly", 
+   * "verbatim", "xmlonly", "cond", "if", "ifnot", "link"
+   * Returns 1 if success, 0 if the endcommand is never encountered.
+   */
+  
+  int ignoreCommandEndCommand(string theCommand, int &startInd, list <DoxygenEntity> &doxyList, string doxygenString){
+	  if (noisy) cout << "Not Adding " << theCommand << endl;
+	  return progressTilEndCommand( "end" + theCommand, startInd, doxygenString);
+	  
+  }
+  
+  /* CommandWordParagraph
+   * Format: @command <word> {paragraph}
+   * Commands such as param
+   * "param", "tparam", "throw", "retval", "exception"
+   */
+  int addCommandWordParagraph(string theCommand, int &startInd, list <DoxygenEntity> &doxyList, string doxygenString){
+	if (noisy) cout << "Parsing " << theCommand << endl;
+	string name = getNextWord(startInd, doxygenString);
+	if (name.empty()){ 
+		cout << "No word followed " << theCommand <<  " command. Not added" << endl;
+		return 0;
+		}
+	string restOfParagraph = getStringTilEndOfParagraph(startInd, doxygenString);
+	int placement = 0;
+	if(!restOfParagraph.empty()){
+		list <DoxygenEntity> aNewList;
+		aNewList =  parse(placement, restOfParagraph);
+		aNewList.push_front(DoxygenEntity("plainstring", name));
+		doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+		return 1;
+		}
+	else cout << "No paragraph followed " << theCommand <<  " command. Not added" << endl;
+	return 0;
+  }
+  /* CommandWordLine
+   * Format: @command <word> (line)
+   * Commands such as param
+   * "page", "subsection", "subsubsection", "section", "paragraph", "defgroup"
+   */
+  int addCommandWordLine(string theCommand, int &startInd, list <DoxygenEntity> &doxyList, string doxygenString){
+	if (noisy) cout << "Parsing " << theCommand << endl;
+	string name = getNextWord(startInd, doxygenString);
+	if (name.empty()){ 
+		cout << "No word followed " << theCommand <<  " command. Not added" << endl;
+		return 0;
+		}
+	string restOfLine = getStringTilEndOfParagraph(startInd, doxygenString);
+	int placement = 0;
+	if(!restOfLine.empty()){
+		list <DoxygenEntity> aNewList;
+		aNewList =  parse(placement, restOfLine);
+		aNewList.push_front(DoxygenEntity("plainstring", name));
+		doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+		return 1;
+		}
+	else cout << "No line followed " << theCommand <<  " command. Not added" << endl;
+	return 0;
+  }
+  
+  /* Command Word Optional Word Optional Word
+   * Format: @command <word> [<header-file>] [<header-name>]
+   * Commands such as class
+   * "category", "class", "protocol", "interface", "struct", "union"
+   */
+  int addCommandWordOWordOWord(string theCommand, int &startInd, list <DoxygenEntity> &doxyList, string doxygenString){
+	if (noisy) cout << "Parsing " << theCommand << endl;
+	string name = getNextWord(startInd, doxygenString);
+	if (name.empty()){ 
+			cout << "No word followed " << theCommand <<  " command. Not added" << endl;
+			return 0;
+			}
+	string headerfile = getNextWord(startInd, doxygenString);
+	string headername = getNextWord(startInd, doxygenString);
+	list <DoxygenEntity> aNewList;
+	aNewList.push_back(DoxygenEntity("plainstring", name));
+	if (!headerfile.empty()) aNewList.push_back(DoxygenEntity("plainstring", headerfile));
+	if (!headername.empty()) aNewList.push_back(DoxygenEntity("plainstring", headername));
+	doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+	return 1;
+  }
+  
+  /* Command Optional Word
+   * Format: @command [<word>]
+   * Commands such as dir
+   * "dir", "file", "cond"
+   */
+  int addCommandOWord(string theCommand, int &startInd, list <DoxygenEntity> &doxyList, string doxygenString){
+	if (noisy) cout << "Parsing " << theCommand << endl;
+	string name = getNextWord(startInd, doxygenString);
+	doxyList.push_back(DoxygenEntity(theCommand, name));
+	return 1; 
+  }
+  
  /* The actual "meat" of the doxygen parser. This is not yet fully implemented
   * with my current design- however the skeletal outline is contained in
   * the file Skeleton
   */
 
- int addCommand(int commentNum, int &startInd, list <DoxygenEntity> &doxyList){
-	    startIndex = startInd;
-	 	string name;
-	 	string nextWordInLine = "";
-	 	string restOfLine = "";
-	 	string restOfParagraph = "";
-	 	string headerfile ="";
-	 	string headername = "";
-	 	switch(commentNum){
 
+ int addCommand(string commandString, int &startInd, list <DoxygenEntity> &doxyList, string doxygenString){
+	 string theCommand = StringToLower(commandString);
+	 string voidArray[] = {""};
+	 	/* @command */
 
-		/* \b */
-		case 108:
-			name = getNextWord(startIndex);
-			if (!name.empty()) doxyList.push_back( DoxygenEntity(108, name));
-			else cout << "No word followed b command. Not added" << endl;
-			break;
-		/* \brief */
-		case 109:
-			restOfParagraph = getStringTilEndOfParagraph(startIndex);
-			if(!restOfParagraph.empty()) doxyList.push_back( DoxygenEntity(109, restOfLine));
-			else cout << "Nothing followed brief command. Not added" <<endl;
-			break;
-
-	 	/* plain description */
-	 	case 238:
-	 		//doxyList.push_back(DoxygenEntity(238, parse(startIndex, new list<DoxygenEntity> entityList() )));
-
-	 		break;
-
-	 	default:
-			cout << "Command " << commentNum << " not supported yet" << endl;
-			break;
+	 
+	 if (theCommand.compare("plainstring") == 0){
+	 		string nextPhrase = getStringTilCommand(startInd, doxygenString);
+	 		if (noisy) cout << "Parsing plain string :" << nextPhrase << endl;
+	 		doxyList.push_back(DoxygenEntity("plainstring", nextPhrase ));
+	 		return 1;
+	 }
+	 int commandNumber = commandBelongs(theCommand);
+	 if (commandNumber == 1){
+	 	return addSimpleCommand(theCommand, startInd,doxyList, doxygenString);
 	 	}
-	 	startInd = startIndex;
+	 if (commandNumber == 2){
+	 	return ignoreSimpleCommand(theCommand, startInd,doxyList, doxygenString);
+	 	}
+	 if (commandNumber == 3){
+	 	return addCommandWord(theCommand, startInd,doxyList, doxygenString);
+	 	}
+	 if (commandNumber == 4){
+	 	return ignoreCommandWord(theCommand, startInd,doxyList, doxygenString);
+	 	}
+	 if (commandNumber == 5){
+	 	return addCommandLine(theCommand, startInd,doxyList, doxygenString);
+	 	}
+	 if (commandNumber == 6){
+	 	return ignoreCommandLine(theCommand, startInd,doxyList, doxygenString);
+	 	}
+	 if (commandNumber == 7){
+	 	return addCommandParagraph(theCommand, startInd,doxyList, doxygenString);
+	 	}
+	 if (commandNumber == 8){
+	 	return ignoreCommandParagraph(theCommand, startInd,doxyList, doxygenString);
+	 	}
+	 if (commandNumber == 9){
+	 	return ignoreCommandEndCommand(theCommand, startInd,doxyList, doxygenString);
+	 	}
+	 if (commandNumber == 10){
+	 	return addCommandWordParagraph(theCommand, startInd,doxyList, doxygenString);
+	 	}
+	 if (commandNumber == 11){
+	 	return addCommandWordLine(theCommand, startInd,doxyList, doxygenString);
+	 	}
+	 if (commandNumber == 12){
+	 	return addCommandWordOWordOWord(theCommand, startInd,doxyList, doxygenString);
+	 	}
+	 if (commandNumber == 13){
+	 	return addCommandOWord(theCommand, startInd,doxyList, doxygenString);
+	 	}
+	 if (commandNumber == 14){
+	 	return 0;
+	 	}
+	 if (commandNumber == 15){
+	 	return 0;
+	 	}
+	 	
+	 	return 0;
+ }
+ 
+ int weirdTest(){
+	 string doxygenString = "this is a test.";
+	 string restOfParagraph = "";
+	 int startIndex = 0;
+	 restOfParagraph = getStringTilEndOfParagraph(startIndex , doxygenString);
+	 cout << restOfParagraph<< " " << startIndex << endl;
+	 
+	 startIndex = 0;
+	 restOfParagraph = getStringTilCommand(startIndex, doxygenString);
+	 cout << restOfParagraph<< " " << startIndex << endl;
  }
 
- /* Returns the parse tree */
+ /* Returns a parse tree for a string */
 
-list<DoxygenEntity> parse(int startInd, int endInd, list<DoxygenEntity> &doxyList){
-	string currWord = "";
-	int startIndex = startInd;
-	int savedIndex;
-	int currCommand;
-	while (startIndex < endIndex){
-		savedIndex = startIndex;
-		currWord = getNextWord(startIndex);
-
-		if(currWord[0] == 92 || currWord[0] == '@'){
-			currWord = doxygenString.substr(startIndex+1, currWord.length() - 1);
-			currCommand = findCommand(currWord);
-			if (currCommand < 0 ){ cout << "BAD COMMAND: " << currWord << endl; exit(1);}
-				//cout << "Command: " << currWord << " " << currCommand << endl;
-			addCommand(currCommand, startIndex, doxyList);
-		}
-		else{
-			startIndex = savedIndex;
-			addCommand(238, startIndex, doxyList);
-
-		}
-	}
-
-
-}
 
 
  int main(int argc, char *argv[]){
+	//weirdTest();
  	if(testCodeCrawlingFunctions) testCCF();
  	if (demonstrateParsing){
+ 		string doxygenString = " This is a small sentence.\n *\n This is a line with a @b bold letter \n * \n  @brief small @b description. **/";
+ 		//string doxygenString = "This is a description.\n\n * @param x this is a parameter.";
  		int placement = 0;
- 		clearFluff(0);
- 		parse(0, doxygenString.length(), rootList);
+ 		clearFluff(placement, doxygenString);
+ 		rootList = parse(placement, doxygenString);
+ 		cout << "---THE TREE---" << endl;
  		printTree();
  	}
  	return 1;

From c727877cf9dd9f32cb47449a96c5012dfe45f10c Mon Sep 17 00:00:00 2001
From: Cheryl Foil <cheryl.foil@gmail.com>
Date: Thu, 10 Jul 2008 04:18:22 +0000
Subject: [PATCH 004/314] Functionality fixes, small tweaks to make
 DoxygenTranslator more robust and the beginnings of a doxygen example
 collection

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2008-cherylfoil@10656 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Source/DoxygenTranslator/DoxygenEntity.cpp    |  12 +-
 Source/DoxygenTranslator/DoxygenEntity.h      |   2 +-
 .../DoxygenTranslator/DoxygenTranslator.cpp   | 230 ++++++++++++------
 Source/DoxygenTranslator/Examples/Example1    |   6 +
 Source/DoxygenTranslator/Examples/Example2    |   7 +
 Source/DoxygenTranslator/Examples/Example3    |  10 +
 Source/DoxygenTranslator/Examples/Example4    |   5 +
 7 files changed, 186 insertions(+), 86 deletions(-)
 create mode 100644 Source/DoxygenTranslator/Examples/Example1
 create mode 100644 Source/DoxygenTranslator/Examples/Example2
 create mode 100644 Source/DoxygenTranslator/Examples/Example3
 create mode 100644 Source/DoxygenTranslator/Examples/Example4

diff --git a/Source/DoxygenTranslator/DoxygenEntity.cpp b/Source/DoxygenTranslator/DoxygenEntity.cpp
index cd192601e..6b8755592 100644
--- a/Source/DoxygenTranslator/DoxygenEntity.cpp
+++ b/Source/DoxygenTranslator/DoxygenEntity.cpp
@@ -24,7 +24,7 @@ string commandArray2[] = {"a", "addindex", "addtogroup", "anchor", "arg", "atten
 		"sa", "section", "see", "showinitializer", "since", "skip", "skipline", "struct", "subpage",
 		"subsection", "subsubsection", "test", "throw", "todo", "tparam", "typedef", "union", "until",
 		"var", "verbatim", "verbinclude", "version", "warning", "weakgroup", "xmlonly", "xrefitem",
-		"$", "@", string(1, 92), string(1, '&'), "~", "<", ">", string(1, '#'), "%"};
+		"$", "@", string(1, 92), "&", "~", "<", ">", "#", "%"};
 
 string findCommand(int commandNum){
 
@@ -56,7 +56,7 @@ DoxygenEntity::DoxygenEntity(string typeEnt, string param1){
 /* Nonterminal node
  * contains
  */
-DoxygenEntity::DoxygenEntity(string typeEnt, list <DoxygenEntity> entList){
+DoxygenEntity::DoxygenEntity(string typeEnt, list <DoxygenEntity> &entList ){
     typeOfEntity = typeEnt;
     data = "";
     isLeaf = 0;
@@ -65,18 +65,20 @@ DoxygenEntity::DoxygenEntity(string typeEnt, list <DoxygenEntity> entList){
 
 
 void DoxygenEntity::printEntity(int level){
+	int thisLevel = level;
 	if (isLeaf) {
-		for (int i = 0; i < level; i++) {cout << "\t";}
+		for (int i = 0; i < thisLevel; i++) {cout << "\t";}
 		cout << "Node Command: " << typeOfEntity << " ";
 		if (data.compare("") != 0) cout << "Node Data: " << data;
 		cout << endl;
 	}
 	else{
+		for (int i = 0; i < thisLevel; i++) {cout << "\t";}
 		cout << "Node Command : " << typeOfEntity << endl;
 		list<DoxygenEntity>::iterator p = entityList.begin();
-		level++;
+		thisLevel++;
 		while (p != entityList.end()){
-			(*p).printEntity(level);
+			(*p).printEntity(thisLevel);
 			p++;
 		}
 	}
diff --git a/Source/DoxygenTranslator/DoxygenEntity.h b/Source/DoxygenTranslator/DoxygenEntity.h
index a0a99ed70..734d09c8e 100644
--- a/Source/DoxygenTranslator/DoxygenEntity.h
+++ b/Source/DoxygenTranslator/DoxygenEntity.h
@@ -11,7 +11,7 @@ class DoxygenEntity{
 public:
 	DoxygenEntity(string typeEnt);
 	DoxygenEntity(string typeEnt, string param1);
-	DoxygenEntity(string typeEnt, list <DoxygenEntity> entList);
+	DoxygenEntity(string typeEnt, list <DoxygenEntity> &entList );
 	virtual ~DoxygenEntity();
 	void printEntity(int level);
     string typeOfEntity;
diff --git a/Source/DoxygenTranslator/DoxygenTranslator.cpp b/Source/DoxygenTranslator/DoxygenTranslator.cpp
index e2fdaef8a..13a3c56fe 100644
--- a/Source/DoxygenTranslator/DoxygenTranslator.cpp
+++ b/Source/DoxygenTranslator/DoxygenTranslator.cpp
@@ -24,7 +24,8 @@ to test. */
 
 int testCodeCrawlingFunctions = 0;
 int demonstrateParsing = 1;
-int noisy = 1; // set this to 1 for extra chatter from the parsing stage.
+int runExamples = 1;
+int noisy = 0; // set this to 1 for extra chatter from the parsing stage.
 int addCommand(string commandName, int &startInd, list <DoxygenEntity> &doxyList, string doxygenString);
 //////////////////////////////////////////
 
@@ -51,7 +52,7 @@ string commandArray[] = {"a", "addindex", "addtogroup", "anchor", "arg", "attent
 		"sa", "section", "see", "showinitializer", "since", "skip", "skipline", "struct", "subpage",
 		"subsection", "subsubsection", "test", "throw", "todo", "tparam", "typedef", "union", "until",
 		"var", "verbatim", "verbinclude", "version", "warning", "weakgroup", "xmlonly", "xrefitem",
-		"$", "@", string(1, 92), string(1, '&'), "~", "<", ">", string(1, '#'), "%"};
+		"$", "@", "//","&", "~", "<", ">", "#", "%"};
 
 
 string sectionIndicators[] = { "attention", "author", "brief", "bug", "cond", "date", "deprecated", "details",
@@ -60,7 +61,7 @@ string sectionIndicators[] = { "attention", "author", "brief", "bug", "cond", "d
 		"version", "warning", "xrefitem" };
 
 /* All of the doxygen commands divided up by how they are parsed */
-string simpleCommands[] = {"n", "$", "@", string(1, 92), string(1, '&'), "~", "<", ">", string(1, '#'), "%"};
+string simpleCommands[] = {"n", "$", "@", "//", "&", "~", "<", ">", "#", "%"};
 string ignoredSimpleCommands[] = {"nothing at the moment"};
 string commandWords[] = {"a", "b", "c", "e", "em", "p", "def", "enum", "example", "package", 
 		"relates", "namespace", "relatesalso","anchor", "dontinclude", "include", "includelineno"};
@@ -84,10 +85,8 @@ string commandErrorThrowings[] = {"annotatedclasslist", "classhierarchy", "defin
 string commandUniques[] = {"xrefitem", "ingroup", "par", "headerfile", "overload", "weakgroup", "ref",
 		"subpage", "dotfile", "image", "addtogroup", "li"};
 
- int startIndex = 0;
- int endIndex = 0;
+ //int startIndex = 0;
  int isNewLine = 0;
- //string doxygenString = "";
  int briefDescExists = 0;
 
  /* Entity list is the root list.
@@ -186,8 +185,8 @@ string commandUniques[] = {"xrefitem", "ingroup", "par", "headerfile", "overload
  int isSectionIndicator(string smallString){
  	smallString = StringToLower(smallString);
 
- 	for (int i = 0; i < sizeof(commandArray)/sizeof(*commandArray); i++){
- 		if( smallString.compare(commandArray[i]) == 0){
+ 	for (int i = 0; i < sizeof( sectionIndicators)/sizeof(* sectionIndicators); i++){
+ 		if( smallString.compare( sectionIndicators[i]) == 0){
  			return 1;
  		}
  	}
@@ -207,7 +206,7 @@ string commandUniques[] = {"xrefitem", "ingroup", "par", "headerfile", "overload
  	int amountRemoved = 0;
 
  	while(doxygenString[startIndex] == '/'|| doxygenString[startIndex] == '!' || doxygenString[startIndex] == '*'
- 			|| doxygenString[startIndex] == '\n' || doxygenString[startIndex] == ' '){
+ 			|| doxygenString[startIndex] == '\n' || doxygenString[startIndex] == ' '|| doxygenString[startIndex] == '\t'){
  		startIndex++;
  		amountRemoved++;
  		}
@@ -222,9 +221,9 @@ string commandUniques[] = {"xrefitem", "ingroup", "par", "headerfile", "overload
 
  string getNextWord(int &startInd, string doxygenString){
 	int startIndex = startInd;
- 	string nextWord = "";
+ 	string nextWord;
  	while (startIndex < doxygenString.length() && (doxygenString[startIndex] == '/'|| doxygenString[startIndex] == ' '
- 		|| doxygenString[startIndex] == '*' || doxygenString[startIndex]== '\n'
+ 		|| doxygenString[startIndex] == '*' || doxygenString[startIndex]== '\n' || doxygenString[startIndex] == '\t'
 		|| doxygenString[startIndex] == '!')){
  		if(doxygenString[startIndex]== '\n'){ startInd = startIndex; return nextWord;}
  		startIndex++;
@@ -233,7 +232,7 @@ string commandUniques[] = {"xrefitem", "ingroup", "par", "headerfile", "overload
  	//cout << doxygenString[startIndex] << endl;
  	int endIndex = startIndex;
 
- 	while (doxygenString[endIndex]!= '\n' && doxygenString[endIndex]!= ' '){
+ 	while (endIndex < doxygenString.length() && (doxygenString[endIndex]!= '\n' && doxygenString[endIndex]!= ' ')){
  		endIndex++;
  		//cout << "End Index " << endIndex << endl;
  		}
@@ -251,7 +250,7 @@ string commandUniques[] = {"xrefitem", "ingroup", "par", "headerfile", "overload
 	int startIndex = startInd;
  	while (doxygenString[startIndex] == '/'|| doxygenString[startIndex] == ' '
  		|| doxygenString[startIndex] == '*' || doxygenString[startIndex]== '\n'
-		|| doxygenString[startIndex] == '!'){
+		|| doxygenString[startIndex] == '!' || doxygenString[startIndex] == '\t'){
  		if(doxygenString[startIndex]== '\n') return "";
  		startIndex++;
  		}
@@ -274,7 +273,7 @@ string getStringTilCommand(int &startInd, string doxygenString){
 	 if (startInd >= doxygenString.length()) return "";
 	int startIndex = startInd;
 	int endIndex = startInd;
- 	string description = "";
+ 	string description;
  	/* Find the End of the description */
  	int keepLooping = 1;
  	int spareIndex = 0;
@@ -293,7 +292,7 @@ string getStringTilCommand(int &startInd, string doxygenString){
 				//cout << "Counter :" << counter << endl;
 				while(keepLooping && endIndex < doxygenString.length() && (doxygenString[counter] == ' ' ||
 				               doxygenString[counter] == '*'|| doxygenString[counter] == '\n'|| doxygenString[counter] == '/'
-				            	   || doxygenString[counter] == '!') ){
+				            	   || doxygenString[counter] == '!' || doxygenString[startIndex] == '\t') ){
 									if(doxygenString[counter] == '\n') {
 										//cout << "Blank line found" << endl;
 										keepLooping = 0;
@@ -304,7 +303,7 @@ string getStringTilCommand(int &startInd, string doxygenString){
 			}
 			//endIndex = counter;
 		}
- 		else if (doxygenString[endIndex] == 92 || doxygenString[endIndex] == '@'){
+ 		else if (doxygenString[endIndex] == '\\' || doxygenString[endIndex] == '@'){
  			finalIndex = endIndex;
  			keepLooping = 0;
  			}
@@ -321,13 +320,13 @@ string getStringTilCommand(int &startInd, string doxygenString){
  	}
  	//cout << "Done with EndIndex" << endl;
  	while(doxygenString[startIndex] == '!' || doxygenString[startIndex] == ' '
- 		|| doxygenString[startIndex] == '/' || doxygenString[startIndex] == '*') startIndex++;
+ 		|| doxygenString[startIndex] == '/' || doxygenString[startIndex] == '*' || doxygenString[startIndex] == '\t') startIndex++;
 
  	for (int i = startIndex; i < endIndex; i++){
 
  		if (doxygenString[i] == '\n') {
 
- 			while ((doxygenString[i] == '\n' || doxygenString[i] == ' '
+ 			while ((doxygenString[i] == '\n' || doxygenString[startIndex] == '\t'|| doxygenString[i] == ' '
  				|| doxygenString[i] == '*' || doxygenString[i] == '/')&& endIndex < doxygenString.length() - 1){
  				i++;
  				}
@@ -351,7 +350,7 @@ string getStringTilCommand(int &startInd, string doxygenString){
 	 if (startInd >= doxygenString.length()) return "";
 	int startIndex = startInd;
 	int endIndex = startInd;
- 	string description = "";
+ 	string description;
  	/* Find the End of the description */
  	int keepLooping = 1;
  	int spareIndex = 0;
@@ -369,7 +368,7 @@ string getStringTilCommand(int &startInd, string doxygenString){
 				counter++;
 				//cout << "Counter :" << counter << endl;
 				while(keepLooping && endIndex < doxygenString.length() && (doxygenString[counter] == ' ' ||
-				               doxygenString[counter] == '*'|| doxygenString[counter] == '\n'|| doxygenString[counter] == '/'
+				               doxygenString[counter] == '*'|| doxygenString[startIndex] == '\t' || doxygenString[counter] == '\n'|| doxygenString[counter] == '/'
 				            	   || doxygenString[counter] == '!') ){
 									if(doxygenString[counter] == '\n') {
 										//cout << "Blank line found" << endl;
@@ -381,30 +380,32 @@ string getStringTilCommand(int &startInd, string doxygenString){
 			}
 			//endIndex = counter;
 		}
- 		else if (doxygenString[endIndex] == 92 || doxygenString[endIndex] == '@'){
- 			//cout << "2 ";
-			spareIndex = endIndex;
- 			if (isSectionIndicator(getNextWord(spareIndex, doxygenString))) keepLooping = 0;
+ 		//todo this fix for not immediately exciting while parsing a paragraph seems somewhat cheap
+ 		else if (endIndex != startInd && doxygenString[endIndex] == '\\' || doxygenString[endIndex] == '@'){
+			spareIndex = endIndex +1;
+			
+ 			if (isSectionIndicator(getNextWord(spareIndex, doxygenString))) {
+ 				keepLooping = 0;
+ 				finalIndex = endIndex;}
  			}
 		else if(endIndex < doxygenString.length() - 1
 				&& string("*/").compare(doxygenString.substr(endIndex , endIndex  + 1)) == 0){
-			//cout << "3 ";
 			keepLooping = 0;
+			finalIndex = endIndex;
 		}
  		if(keepLooping){
- 			//cout << "4 ";
  			endIndex++;
  		}
  	}
  	//cout << "Done with EndIndex" << endl;
- 	while(doxygenString[startIndex] == '!' || doxygenString[startIndex] == ' '
+ 	while(doxygenString[startIndex] == '!' || doxygenString[startIndex] == ' ' || doxygenString[startIndex] == '\t'
  		|| doxygenString[startIndex] == '/' || doxygenString[startIndex] == '*') startIndex++;
 
  	for (int i = startIndex; i < endIndex; i++){
 
  		if (doxygenString[i] == '\n') {
 
- 			while ((doxygenString[i] == '\n' || doxygenString[i] == ' '
+ 			while ((doxygenString[i] == '\n' || doxygenString[startIndex] == '\t' || doxygenString[i] == ' ' ||doxygenString[startIndex] == '!'
  				|| doxygenString[i] == '*' || doxygenString[i] == '/')&& endIndex < doxygenString.length() - 1){
  				i++;
  				}
@@ -425,9 +426,9 @@ string getStringTilCommand(int &startInd, string doxygenString){
   */
  //TODO Make progressTilCommand return a formatted string
  int progressTilEndCommand(string theCommand, int &startInd, string doxygenString){
- 	endIndex = startInd;
+ 	int endIndex = startInd;
  	while (endIndex < doxygenString.length()){
- 		if (doxygenString[endIndex] == 92 || doxygenString[endIndex] == '@'){
+ 		if (doxygenString[endIndex] == '\\' || doxygenString[endIndex] == '@'){
  			//cout << doxygenString.substr(endIndex + 1 , theCommand.length())<< endl;
  			if (theCommand.compare(doxygenString.substr(endIndex + 1 , theCommand.length())) == 0){
  				startInd = endIndex + theCommand.length() + 1;
@@ -440,34 +441,78 @@ string getStringTilCommand(int &startInd, string doxygenString){
  	return 0;
  }
 
+ /* A specialty method for commands such as \arg that end at the end of a paragraph OR when another \arg is encountered
+  */
+ 
  string getStringTilAnyCommand(string theCommand, int &startInd, string doxygenString){
-	 endIndex = startInd;
-	 startIndex = startInd;
-	 int keepLooping = 1;
-	 while (keepLooping && endIndex < doxygenString.length()){
-	  		if (doxygenString[endIndex] == 92 || doxygenString[endIndex] == '@'){
-	  			startInd = endIndex;
-	  			keepLooping = 0;
-	  			}
-	 endIndex++;
-	 }
-	 string description = "";
-	 for (int i = startIndex; i < endIndex; i++){
+	 if (startInd >= doxygenString.length()) return "";
+		int startIndex = startInd;
+		int endIndex = startInd;
+	 	string description;
+	 	/* Find the End of the description */
+	 	int keepLooping = 1;
+	 	int spareIndex = 0;
+	 	int counter;
+	 	int finalIndex;
+	 	while(keepLooping){
+	 		if(endIndex >= theCommand.length()){
+	 			finalIndex = endIndex;
+	 			keepLooping = 0;
+	 		}
+	 		else if (doxygenString[endIndex] == '\n'){
+				//cout << "1 ";
+				counter = endIndex;
+				if ( keepLooping && endIndex < doxygenString.length()-1) {
+					counter++;
+					//cout << "Counter :" << counter << endl;
+					while(keepLooping && endIndex < doxygenString.length() && (doxygenString[counter] == ' ' ||
+					               doxygenString[counter] == '*'|| doxygenString[counter] == '\n'|| doxygenString[counter] == '/'
+					            	   || doxygenString[counter] == '!' || doxygenString[startIndex] == '\t') ){
+										if(doxygenString[counter] == '\n') {
+											//cout << "Blank line found" << endl;
+											keepLooping = 0;
+											finalIndex = counter;}
+										else{ counter++;}
+										}
 
-	  		if (doxygenString[i] == '\n') {
+				}
+				//endIndex = counter;
+			}
+	 		else if (doxygenString[endIndex] == '\\' || doxygenString[endIndex] == '@'){
+	 			//cout << "2 ";
+				spareIndex = endIndex;
+	 			if (endIndex + theCommand.length() < theCommand.length() 
+	 					&& theCommand.compare(doxygenString.substr(endIndex, theCommand.length())) == 0) keepLooping = 0;
+	 			}
+			else if(endIndex < doxygenString.length() - 1
+					&& string("*/").compare(doxygenString.substr(endIndex , endIndex  + 1)) == 0){
+				//cout << "3 ";
+				keepLooping = 0;
+			}
+	 		if(keepLooping){
+	 			//cout << "4 ";
+	 			endIndex++;
+	 		}
+	 	}
+	 	//cout << "Done with EndIndex" << endl;
+	 	while(doxygenString[startIndex] == '!' || doxygenString[startIndex] == ' '
+	 		|| doxygenString[startIndex] == '/' || doxygenString[startIndex] == '*' || doxygenString[startIndex] == '\t') startIndex++;
 
-	  			while ((doxygenString[i] == '\n' || doxygenString[i] == ' '
-	  				|| doxygenString[i] == '*' || doxygenString[i] == '/')&& endIndex < doxygenString.length() - 1){
-	  				i++;
-	  				}
-	  			description.append(" ");
-	  		}
-	  		description.push_back(doxygenString[i]);
-	  		//cout << doxygenString[i];
-	  	}
-	  	startInd = endIndex;
-	  	return description;
-	 return 0;
+	 	for (int i = startIndex; i < endIndex; i++){
+
+	 		if (doxygenString[i] == '\n') {
+
+	 			while ((doxygenString[i] == '\n' || doxygenString[i] == ' ' || doxygenString[startIndex] == '\t'
+	 				|| doxygenString[i] == '*' || doxygenString[i] == '/')&& endIndex < doxygenString.length() - 1){
+	 				i++;
+	 				}
+	 			description.append(" ");
+	 		}
+	 		description.push_back(doxygenString[i]);
+	 		//cout << doxygenString[i];
+	 	}
+	 	startInd = finalIndex;
+	 	return description;
  }
  ///////////////TEST CLASSES AND MAIN BELOW/////////////////
 
@@ -477,7 +522,7 @@ string getStringTilCommand(int &startInd, string doxygenString){
   * differs wildly */
 
  int testClearFluff(){
-  string doxygenString = "";
+  string doxygenString;
   string cases[] = {"/** WORD", "/*! WORD", "/******* WORD", "///// WORD", "//! WORD", "//! WORD", "///WORD",
  		 "/**\nWORD", "/**\n*WORD", "/** \n WORD"};
   int testPassed = 1;
@@ -498,10 +543,10 @@ string getStringTilCommand(int &startInd, string doxygenString){
   };
 
  int testGetNextWord(){
-	  string doxygenString = "";
+	  string doxygenString;
 	  string cases[] = {"/** WORD ", " * WORD ", "///!WORD ", " WORD ", "//! WORD ", " * WORD ", "*WORD "};
 	  int testPassed = 1;
-	  string testWord = "";
+	  string testWord;
 	  int placement = 0;
 	  int casesSize = sizeof(cases)/sizeof(*cases);
 	  for (int i = 0; i < casesSize; i++){
@@ -523,10 +568,10 @@ string getStringTilCommand(int &startInd, string doxygenString){
 			testPassed = 0;}
 		 //else cout << "GetNextWord passed for string :" << doxygenString << endl;
 		testWord = " * ";
-		testWord.push_back(92);
+		testWord.push_back('\\');
 		testWord = testWord + "WORD ";
-		string commandWord = "";
-		commandWord.push_back(92);
+		string commandWord;
+		commandWord.push_back('\\');
 		commandWord = commandWord + "WORD";
 		doxygenString = testWord;
 		placement = 0;
@@ -581,7 +626,7 @@ string getStringTilCommand(int &startInd, string doxygenString){
  }
 
  int testGetOneLine(){
-	  string doxygenString = "";
+	  string doxygenString;
 	  string cases[] = {" * Crop this sentence after this period.\n",
 			  " * Crop this sentence after this period.\n",
 			  "Crop this sentence after this period.\n",
@@ -589,7 +634,7 @@ string getStringTilCommand(int &startInd, string doxygenString){
 			  " Crop this sentence after this period.\n"
 			  };
 	  int testPassed = 1;
-	  string testWord = "";
+	  string testWord;
 		int placement = 0;
 	  int casesSize = sizeof(cases)/sizeof(*cases);
 	  for (int i = 0; i < casesSize; i++){
@@ -625,7 +670,7 @@ string getStringTilCommand(int &startInd, string doxygenString){
  }
 //TODO Flesh testGetStringTilEndOfParagraph out, fix weird spacing problems
  int testGetStringTilEndOfParagraph(){
-	string doxygenString = "";
+	string doxygenString;
 	int placement = 0;
 	int testPassed = 1;
 	string testParagraph;
@@ -647,7 +692,7 @@ string getStringTilCommand(int &startInd, string doxygenString){
 	//cout << "String Length: " << doxygenString.length() << endl;
 
 	doxygenString = "/* This is a description,\n * thus it continues on\n * for several lines.\n * \n * ";
-	doxygenString.push_back(92);
+	doxygenString.push_back('//');
 	doxygenString += "author cheryl foil \n\n **/";
 	placement = 0;
 	testParagraph = getStringTilEndOfParagraph(placement, doxygenString);
@@ -662,7 +707,7 @@ string getStringTilCommand(int &startInd, string doxygenString){
  }
 
  int testGetStringTilCommand(){
-		string doxygenString = "";
+		string doxygenString;
 		int placement = 0;
 		int testPassed = 1;
 		string testParagraph;
@@ -678,12 +723,12 @@ string getStringTilCommand(int &startInd, string doxygenString){
 	 
  }
  int testProgressTilEndCommand(){
-	    string doxygenString = "";
+	    string doxygenString ;
 		int placement = 0;
 		int testPassed = 1;
 		string testParagraph;
 		doxygenString = "Let's pretend this \n * is a bunch of code to be ended in ";
-		doxygenString.push_back(92);
+		doxygenString.push_back('\\');
 		doxygenString += "endcodeSTOP";
 		progressTilEndCommand("endcode", placement, doxygenString);
 		//cout << "Placement : " << placement << endl;
@@ -733,11 +778,11 @@ string getStringTilCommand(int &startInd, string doxygenString){
  
  
  list<DoxygenEntity> parse(int startInd, string doxygenString){
- 	string currWord = "";
+ 	string currWord;
  	int startIndex = startInd;
  	int savedIndex;
  	list <DoxygenEntity> aNewList;
- 	endIndex = doxygenString.length();
+ 	int endIndex = doxygenString.length();
  	int currCommand;
  	while (startIndex < endIndex){
  		savedIndex = startIndex;
@@ -746,12 +791,12 @@ string getStringTilCommand(int &startInd, string doxygenString){
  		if(currWord == ""){
  			if (startIndex < endIndex) startIndex++;
  		}
- 		else if(currWord[0] == 92 || currWord[0] == '@'){
+ 		else if(currWord[0] == '\\' || currWord[0] == '@'){
  			currWord = currWord.substr(1, currWord.length() - 1);
  			currCommand = findCommand(currWord);
- 			if (currCommand < 0 ){ cout << "BAD COMMAND: " << currWord << endl; exit(1);}
+ 			if (currCommand < 0 ){ if(noisy) cout << "BAD COMMAND: " << currWord << endl;}
  				//cout << "Command: " << currWord << " " << currCommand << endl;
- 			addCommand(currWord, startIndex, aNewList, doxygenString);
+ 			else addCommand(currWord, startIndex, aNewList, doxygenString);
  		}
  		else{
  			startIndex = savedIndex;
@@ -783,7 +828,6 @@ string getStringTilCommand(int &startInd, string doxygenString){
 	 
 		if (noisy) cout << "Not Adding " << theCommand << endl;
 		return 1;
-		//doxyList.push_back(DoxygenEntity(108));
  }
   
   /* CommandWord
@@ -1051,7 +1095,7 @@ string getStringTilCommand(int &startInd, string doxygenString){
  
  int weirdTest(){
 	 string doxygenString = "this is a test.";
-	 string restOfParagraph = "";
+	 string restOfParagraph;
 	 int startIndex = 0;
 	 restOfParagraph = getStringTilEndOfParagraph(startIndex , doxygenString);
 	 cout << restOfParagraph<< " " << startIndex << endl;
@@ -1061,16 +1105,42 @@ string getStringTilCommand(int &startInd, string doxygenString){
 	 cout << restOfParagraph<< " " << startIndex << endl;
  }
 
+ 
+
+ int doRunExamples(){
+	 string line;
+	 string filename;
+	 string exampleNames[] = {"Examples/Example1","Examples/Example2", "Examples/Example3", "Examples/Example4", "Examples/Example5"};
+	 int placement;
+	 string doxygenString;
+	 ifstream doxCommentFile;
+	 for (int i = 0; i < 5; i++){
+	   doxCommentFile.open(exampleNames[i].c_str());
+	   doxCommentFile >> doxygenString;
+	   while(getline(doxCommentFile, line)){
+	   doxygenString += line + "\n";}
+	   doxCommentFile.close();
+	   placement = 0;
+	   cout << "---RAW CODE---" << endl << doxygenString << endl<<endl;
+	   clearFluff(placement, doxygenString);
+	   rootList = parse(placement, doxygenString);
+
+	   cout << "---THE TREE---" << endl;
+	   printTree();
+	 }
+	return 1; 
+ }
+ 
+ 
  /* Returns a parse tree for a string */
-
-
-
  int main(int argc, char *argv[]){
 	//weirdTest();
  	if(testCodeCrawlingFunctions) testCCF();
+ 	if(runExamples) doRunExamples();
  	if (demonstrateParsing){
- 		string doxygenString = " This is a small sentence.\n *\n This is a line with a @b bold letter \n * \n  @brief small @b description. **/";
- 		//string doxygenString = "This is a description.\n\n * @param x this is a parameter.";
+ 		string doxygenString = "//! A normal member taking two arguments and returning an integer value.\n/*!\n \\param a an integer argument. \\param s a constant character pointer\n \\return The test results\n  \\sa Test(), ~Test(), testMeToo() and publicVar()\n */";
+ 		//string doxygenString = " /** This is a small sentence.\n *\n@param x this is a parameter. \n \n This is a line with a @b bold letter \n * \n  @brief small @b description. \n\n * **/";
+ 		//string doxygenString = "This is a description.";
  		int placement = 0;
  		clearFluff(placement, doxygenString);
  		rootList = parse(placement, doxygenString);
diff --git a/Source/DoxygenTranslator/Examples/Example1 b/Source/DoxygenTranslator/Examples/Example1
new file mode 100644
index 000000000..03aac4921
--- /dev/null
+++ b/Source/DoxygenTranslator/Examples/Example1
@@ -0,0 +1,6 @@
+/*! \brief Brief description.
+ *         Brief description continued.
+ *
+ *  Detailed description starts here.
+ */
+
diff --git a/Source/DoxygenTranslator/Examples/Example2 b/Source/DoxygenTranslator/Examples/Example2
new file mode 100644
index 000000000..27f915e4a
--- /dev/null
+++ b/Source/DoxygenTranslator/Examples/Example2
@@ -0,0 +1,7 @@
+//! A normal member taking two arguments and returning an integer value.
+/*!
+ \param a an integer argument.
+ \param s a constant character pointer.
+ \return The test results
+ \sa Test(), ~Test(), testMeToo() and publicVar()
+ */
diff --git a/Source/DoxygenTranslator/Examples/Example3 b/Source/DoxygenTranslator/Examples/Example3
new file mode 100644
index 000000000..8e24ba005
--- /dev/null
+++ b/Source/DoxygenTranslator/Examples/Example3
@@ -0,0 +1,10 @@
+      /**
+       * a normal member taking two arguments and returning an integer value.
+       * @param a an integer argument.
+       * @param s a constant character pointer.
+       * @see Test()
+       * @see ~Test()
+       * @see testMeToo()
+       * @see publicVar()
+       * @return The test results
+       */
diff --git a/Source/DoxygenTranslator/Examples/Example4 b/Source/DoxygenTranslator/Examples/Example4
new file mode 100644
index 000000000..55b68da18
--- /dev/null
+++ b/Source/DoxygenTranslator/Examples/Example4
@@ -0,0 +1,5 @@
+//! Brief descripion.
+
+//! Detailed description 
+//! starts here.
+

From da4e3cd374f50f1a4bbecbdf5f6b41239c70ce95 Mon Sep 17 00:00:00 2001
From: Cheryl Foil <cheryl.foil@gmail.com>
Date: Sun, 13 Jul 2008 04:51:51 +0000
Subject: [PATCH 005/314] Small tokenizer-related classes

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2008-cherylfoil@10659 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Source/DoxygenTranslator/Token.cpp     |  32 ++++++++
 Source/DoxygenTranslator/Token.h       |  21 +++++
 Source/DoxygenTranslator/TokenList.cpp | 103 +++++++++++++++++++++++++
 Source/DoxygenTranslator/TokenList.h   |  24 ++++++
 4 files changed, 180 insertions(+)
 create mode 100644 Source/DoxygenTranslator/Token.cpp
 create mode 100644 Source/DoxygenTranslator/Token.h
 create mode 100644 Source/DoxygenTranslator/TokenList.cpp
 create mode 100644 Source/DoxygenTranslator/TokenList.h

diff --git a/Source/DoxygenTranslator/Token.cpp b/Source/DoxygenTranslator/Token.cpp
new file mode 100644
index 000000000..e85799546
--- /dev/null
+++ b/Source/DoxygenTranslator/Token.cpp
@@ -0,0 +1,32 @@
+#include "Token.h"
+#include <cstdlib>
+#include <iostream>
+#include <string>
+#include <list>
+using namespace std;
+
+
+Token::Token(int tType, string tString)
+{	
+	tokenType = tType;
+	tokenString = tString;
+}
+
+string Token::toString()
+{
+	if (tokenType == END_LINE){
+		return "{END OF LINE}";
+	}
+	if (tokenType == PARAGRAPH_END){
+		return "{END OF PARAGRAPH}";
+	}
+	if (tokenType == PLAINSTRING){
+		return tokenString;
+	}
+	if (tokenType == COMMAND){
+		return "{COMMAND : " + tokenString+ "}";
+	}
+	return "";
+}
+
+Token::	~Token(){}
diff --git a/Source/DoxygenTranslator/Token.h b/Source/DoxygenTranslator/Token.h
new file mode 100644
index 000000000..d569f5f7b
--- /dev/null
+++ b/Source/DoxygenTranslator/Token.h
@@ -0,0 +1,21 @@
+#ifndef TOKEN_H_
+#define TOKEN_H_
+#include <string>
+
+#define  END_LINE 101
+#define PARAGRAPH_END 102
+#define  PLAINSTRING 103
+#define  COMMAND  104
+using namespace std;
+
+class Token
+{
+public:
+	Token(int tType, string tString);
+	~Token();
+	int tokenType;
+	string tokenString;
+	string toString();
+};
+
+#endif /*TOKEN_H_*/
diff --git a/Source/DoxygenTranslator/TokenList.cpp b/Source/DoxygenTranslator/TokenList.cpp
new file mode 100644
index 000000000..6122328c4
--- /dev/null
+++ b/Source/DoxygenTranslator/TokenList.cpp
@@ -0,0 +1,103 @@
+#include "TokenList.h"
+#include <cstdlib>
+#include <iostream>
+#include <string>
+#include <list>
+#include "Token.h"
+#define TOKENSPERLINE 8; //change this to change the printing behaviour of the token list
+#define  END_LINE 101
+#define PARAGRAPH_END 102 //not used at the moment 
+#define  PLAINSTRING 103
+#define  COMMAND  104
+using namespace std;
+
+
+list <Token> tokenList;
+list<Token>::iterator tokenListIterator;
+int noisy2 = 0;
+/* The tokenizer*/
+
+TokenList::TokenList(string doxygenString){
+	int currentIndex = 0;
+	//Regex whitespace("[ \t]+");
+	//Regex newLine("[\n]");
+	//Regex command("[@|\\]{1}[^ \t \n]+"); //the cheap solution 
+	//Regex doxygenFluff("[/*!]+");
+	int nextIndex = 0;
+	int isFluff = 0;
+	string currentWord;
+	while (currentIndex < doxygenString.length()){	
+		if(doxygenString[currentIndex] == '\n'){
+			tokenList.push_back(Token(END_LINE, currentWord));
+			currentIndex++;
+		}
+		while(currentIndex < doxygenString.length() && (doxygenString[currentIndex] == ' ' 
+			|| doxygenString[currentIndex]== '\t')) currentIndex ++;
+		if (currentIndex == doxygenString.length()) {} //do nothing since end of string was reached
+		else {nextIndex = currentIndex;
+		while (nextIndex  < doxygenString.length() && (doxygenString[nextIndex] != ' ' 
+			&& doxygenString[nextIndex]!= '\t' && doxygenString[nextIndex]!= '\n')) nextIndex++;
+		currentWord = doxygenString.substr(currentIndex, nextIndex-currentIndex);
+		if(noisy2) cout << "Current Word: " << currentWord << endl;
+		if (currentWord[0] == '@' || currentWord[0] == '\\'){
+			currentWord = currentWord.substr(1, currentWord.length()-1);
+			tokenList.push_back(Token(COMMAND, currentWord));
+		}
+		else if (currentWord[0] == '\n'){
+			//if ((tokenList.back()).tokenType == END_LINE){}
+			tokenList.push_back(Token(END_LINE, currentWord));
+			
+		}
+		else if (currentWord[0] == '*' || currentWord[0] == '/' ||currentWord[0] == '!'){
+			if (currentWord.length() == 1) {isFluff = 1;}	
+			else { isFluff = 1;
+				for(int i = 1; i < currentWord.length(); i++){
+					if (currentWord[0] != '*' && currentWord[0] != '/' && currentWord[0] != '!') isFluff = 0;
+				}
+				
+			}
+			if(!isFluff) tokenList.push_back(Token(PLAINSTRING, currentWord));
+		}
+		
+		else tokenList.push_back(Token(PLAINSTRING, currentWord));
+		currentIndex = nextIndex;
+	}
+	}
+	tokenListIterator = tokenList.begin(); 
+}
+
+Token TokenList::peek(){
+	list<Token>::iterator p = tokenList.begin();
+	if(p != tokenList.end()){
+		p++;
+		Token returnedToken = (*p);
+		p--;
+		return returnedToken;
+	}
+	else
+		return Token(0, "");
+} 
+
+Token TokenList::next(){
+	list<Token>::iterator p = tokenList.begin();
+	if(p != tokenList.end()){
+		p++;
+		return (*p);
+	}
+	else
+		return Token(0, "");
+} 	
+
+void TokenList::printList(){
+	list<Token>::iterator p = tokenList.begin();
+			int i = 1;
+			int b = 0;
+			while (p != tokenList.end()){
+				cout << (*p).toString() << " ";
+				b = i%TOKENSPERLINE;
+				if (b == 0) cout << endl;
+				p++; i++;
+			}
+}
+
+TokenList::	~TokenList(){}
\ No newline at end of file
diff --git a/Source/DoxygenTranslator/TokenList.h b/Source/DoxygenTranslator/TokenList.h
new file mode 100644
index 000000000..153c69163
--- /dev/null
+++ b/Source/DoxygenTranslator/TokenList.h
@@ -0,0 +1,24 @@
+#ifndef TOKENLIST_H_
+#define TOKENLIST_H_
+#include <cstdlib>
+#include <iostream>
+#include <string>
+#include <list>
+#include "Token.h"
+using namespace std;
+
+/* a small class used to represent the sequence of tokens
+ * that can be derived from a formatted doxygen string
+ */
+
+class TokenList{
+public:
+	/* constructor takes a blob of Doxygen comment */
+	TokenList(string doxygenString);
+	~TokenList();
+	Token peek(); 	/* returns next token without advancing */
+	Token next(); 	/* returns next token and advances */
+	void printList(); /* prints out the sequence of tokens */
+};
+
+#endif /*TOKENLIST_H_*/

From cc6db6eab60d0226ea47bb3caa16e915ce84a6ca Mon Sep 17 00:00:00 2001
From: Cheryl Foil <cheryl.foil@gmail.com>
Date: Wed, 16 Jul 2008 22:23:45 +0000
Subject: [PATCH 006/314] Reworking of DoxygenTranslator with the Tokenizer,
 more Doxygen commands implemented, beginning of the javaDoc convertor

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2008-cherylfoil@10670 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Source/DoxygenTranslator/DoxygenEntity.h      |    5 +-
 .../DoxygenTranslator/DoxygenTranslator.cpp   | 1470 +++++++----------
 Source/DoxygenTranslator/JavaDocConverter.cpp |  104 ++
 Source/DoxygenTranslator/JavaDocConverter.h   |   17 +
 Source/DoxygenTranslator/Token.h              |    4 +-
 Source/DoxygenTranslator/TokenList.cpp        |   31 +-
 Source/DoxygenTranslator/TokenList.h          |    7 +-
 7 files changed, 716 insertions(+), 922 deletions(-)
 create mode 100644 Source/DoxygenTranslator/JavaDocConverter.cpp
 create mode 100644 Source/DoxygenTranslator/JavaDocConverter.h

diff --git a/Source/DoxygenTranslator/DoxygenEntity.h b/Source/DoxygenTranslator/DoxygenEntity.h
index 734d09c8e..0605b1cc9 100644
--- a/Source/DoxygenTranslator/DoxygenEntity.h
+++ b/Source/DoxygenTranslator/DoxygenEntity.h
@@ -1,3 +1,5 @@
+#ifndef DOXYGENENTITY_H_
+#define DOXYGENENTITY_H_
 
 #include <cstdlib>
 #include <iostream>
@@ -12,7 +14,7 @@ public:
 	DoxygenEntity(string typeEnt);
 	DoxygenEntity(string typeEnt, string param1);
 	DoxygenEntity(string typeEnt, list <DoxygenEntity> &entList );
-	virtual ~DoxygenEntity();
+   ~DoxygenEntity();
 	void printEntity(int level);
     string typeOfEntity;
     list <DoxygenEntity> entityList;
@@ -21,3 +23,4 @@ public:
 };
 
 
+#endif /*TOKENLIST_H_*/
diff --git a/Source/DoxygenTranslator/DoxygenTranslator.cpp b/Source/DoxygenTranslator/DoxygenTranslator.cpp
index 13a3c56fe..d6129cda0 100644
--- a/Source/DoxygenTranslator/DoxygenTranslator.cpp
+++ b/Source/DoxygenTranslator/DoxygenTranslator.cpp
@@ -1,106 +1,112 @@
-/* The main class for translating blobs of Doxygen for SWIG
- * by Cheryl Foil, mentor Olly Betts, for Google's Summer of Code Program
- * Currently the spacing/format on this is a bit goofy in places, due to shuffling code
- * between 2 editors! Apologies for anyone combing through it :)
- */
-//TODO DOH instead of STL?
-//TODO Most commands are not fully implemented
 
-#include <cstdlib>
-#include <iostream>
-#include <fstream>
-#include <string>
-#include <list>
-#include "DoxygenEntity.h"
+ 
+ //THE TOKENIZER REWORK
 
-using namespace std;
-
-
-//////////////////////////////////////////
-/*Set these to pick what internal functions
-to test. */
-
-//int testCommandParsingFunctions = 1;// not implemented
-
-int testCodeCrawlingFunctions = 0;
-int demonstrateParsing = 1;
-int runExamples = 1;
-int noisy = 0; // set this to 1 for extra chatter from the parsing stage.
-int addCommand(string commandName, int &startInd, list <DoxygenEntity> &doxyList, string doxygenString);
-//////////////////////////////////////////
-
-
-
-/* Globals*/
-
-
-// An array of all the commands and my generic description tag, plaindescription
-
-string commandArray[] = {"a", "addindex", "addtogroup", "anchor", "arg", "attention",
-		"author", "b", "brief", "bug", "c", "callgraph", "callergraph", "category",
-		"class", "code", "cond", "copybrief", "copydetails", "copydoc", "date", "def",
-		"defgroup", "deprecated", "details", "dir", "dontinclude", "dot", "dotfile", "e",
-		"else", "elseif", "em", "endcode", "endcond", "enddot", "endhtmlonly", "endif",
-		"endlatexonly", "endlink", "endmanonly", "endmsc", "endverbatim", "endxmlonly",
-		"enum", "example", "exception", "f$", "f[", "f]", "f{", "f}", "file", "fn", "headerfile",
-		"hideinitializer", "htmlinclude", "htmlonly", "if", "ifnot", "image", "include",
-		"includelineno", "ingroup", "internal", "invariant", "interface", "latexonly", "li",
-		"line", "link", "mainpage", "manonly", "msc", "n", "name", "namespace", "nosubgrouping",
-		"note", "overload", "p", "package", "page", "par", "paragraph", "param", "post", "pre",
-		"private", "privatesection", "property", "protected", "protectedsection", "protocol",
-		"public", "publicsection", "ref", "relates", "relatesalso", "remarks", "return", "retval",
-		"sa", "section", "see", "showinitializer", "since", "skip", "skipline", "struct", "subpage",
-		"subsection", "subsubsection", "test", "throw", "todo", "tparam", "typedef", "union", "until",
-		"var", "verbatim", "verbinclude", "version", "warning", "weakgroup", "xmlonly", "xrefitem",
-		"$", "@", "//","&", "~", "<", ">", "#", "%"};
-
-
-string sectionIndicators[] = { "attention", "author", "brief", "bug", "cond", "date", "deprecated", "details",
-		"else", "elseif", "endcond", "endif", "exception", "if", "ifnot", "invariant", "note", "par", "param",
-		"tparam", "post" , "pre", "remarks", "return", "retval", "sa", "see", "since", "test", "throw", "todo",
-		"version", "warning", "xrefitem" };
-
-/* All of the doxygen commands divided up by how they are parsed */
-string simpleCommands[] = {"n", "$", "@", "//", "&", "~", "<", ">", "#", "%"};
-string ignoredSimpleCommands[] = {"nothing at the moment"};
-string commandWords[] = {"a", "b", "c", "e", "em", "p", "def", "enum", "example", "package", 
-		"relates", "namespace", "relatesalso","anchor", "dontinclude", "include", "includelineno"};
-string ignoredCommandWords[] = {"copydoc", "copybrief", "copydetails", "verbinclude", "htmlinclude"};
-string commandLines[] = {"addindex", "fn", "name", "line", "var", "skipline", "typedef", "skip", "until", "property"};
-string ignoreCommandLines[] = {"nothing at the moment"};
-string commandParagraph[] = {"return", "remarks", "since", "test", "sa", "see", "pre", "post", "details", "invariant", 
-		    "deprecated", "date", "note", "warning", "version", "todo", "bug", "attention", "brief", "arg", "author"};
-string ignoreCommandParagraphs[] = {"nothing at the moment"};
-string commandEndCommands[] = {"code", "dot", "msc", "f$", "f[", "f{environment}{", "htmlonly", "latexonly", "manonly", 
-		   "verbatim", "xmlonly", "cond", "if", "ifnot", "link"};
-string commandWordParagraphs[] = {"param", "tparam", "throw", "retval", "exception"};
-string commandWordLines[] = {"page", "subsection", "subsubsection", "section", "paragraph", "defgroup"};
-string commandWordOWordOWords [] = {"category", "class", "protocol", "interface", "struct", "union"};
-string commandOWords[] = {"dir", "file", "cond"};
-string commandErrorThrowings[] = {"annotatedclasslist", "classhierarchy", "define", "functionindex", "header",
-		"headerfilelist", "inherit", "l", "postheader", "private", "privatesection", "protected", 
-		"protectedsection", "public", "publicsection", "endcode", "enddot", "endmsc", "endhtmlonly", 
-		"endlatexonly", "endmanonly", "endlink", "endverbatim", "endxmlonly", "f]", "f}", "endcond", 
-		"endif"};
-string commandUniques[] = {"xrefitem", "ingroup", "par", "headerfile", "overload", "weakgroup", "ref",
-		"subpage", "dotfile", "image", "addtogroup", "li"};
-
- //int startIndex = 0;
- int isNewLine = 0;
- int briefDescExists = 0;
-
- /* Entity list is the root list.
-  * it is arranged this way to help documentation modules,
-  * such as the javaDoc one, "sort" entities where they need to.
+ /* The main class for translating blobs of Doxygen for SWIG
+  * by Cheryl Foil, mentor Olly Betts, for Google's Summer of Code Program
+  * Currently the spacing/format on this is a bit goofy in places, due to shuffling code
+  * between 2 editors! Apologies for anyone combing through it :)
   */
+ //TODO DOH instead of STL?
+//TODO work in Brief descriptions, detailed descriptions for autobrief
 
- list <DoxygenEntity> rootList;
+ #include <cstdlib>
+ #include <iostream>
+ #include <fstream>
+ #include <string>
+ #include <list>
+ #include "DoxygenEntity.h"
+ #include "TokenList.h"
+ #include "JavaDocConverter.h"
+ #define SIMPLECOMMAND 1
+ #define IGNOREDSIMPLECOMMAND 2
+ #define COMMANDWORD 3
+ #define IGNOREDCOMMANDWORD 4
+ #define COMMANDLINE 5
+ #define IGNOREDCOMMANDLINE 6
+ #define COMMANDPARAGRAPH 7
+ #define IGNORECOMMANDPARAGRAPH 8
+ #define COMMANDENDCOMMAND 9
+ #define COMMANDWORDPARAGRAPH 10
+ #define COMMANDWORDLINE 11
+ #define COMMANDWORDOWORDWORD 12
+ #define COMMANDOWORD 13
+ #define COMMANDERRORTHROW 14
+ #define COMMANDUNIQUE 15
+#define  END_LINE 101
+#define PARAGRAPH_END 102
+#define  PLAINSTRING 103
+#define  COMMAND  104
+ using namespace std;
 
-/* General (untested) assist methods */
+ //////////////////////////////////////////
+ /*Set these to pick what internal functions
+ to test. */
 
+ //int testCommandParsingFunctions = 1;// not implemented
+
+
+ int noisy = 0; // set this to 1 for extra chatter from the parsing stage.
+ int addCommand(string currCommand, TokenList &tokList,  list <DoxygenEntity> &aNewList);
+ list <DoxygenEntity> parse(list<Token>::iterator endParsingIndex, TokenList &tokList);
+
+ //////////////////////////////////////////
+
+
+ string commandArray[] = {"a", "addindex", "addtogroup", "anchor", "arg", "attention",
+ 		"author", "b", "brief", "bug", "c", "callgraph", "callergraph", "category",
+ 		"class", "code", "cond", "copybrief", "copydetails", "copydoc", "date", "def",
+ 		"defgroup", "deprecated", "details", "dir", "dontinclude", "dot", "dotfile", "e",
+ 		"else", "elseif", "em", "endcode", "endcond", "enddot", "endhtmlonly", "endif",
+ 		"endlatexonly", "endlink", "endmanonly", "endmsc", "endverbatim", "endxmlonly",
+ 		"enum", "example", "exception", "f$", "f[", "f]", "f{", "f}", "file", "fn", "headerfile",
+ 		"hideinitializer", "htmlinclude", "htmlonly", "if", "ifnot", "image", "include",
+ 		"includelineno", "ingroup", "internal", "invariant", "interface", "latexonly", "li",
+ 		"line", "link", "mainpage", "manonly", "msc", "n", "name", "namespace", "nosubgrouping",
+ 		"note", "overload", "p", "package", "page", "par", "paragraph", "param", "post", "pre",
+ 		"private", "privatesection", "property", "protected", "protectedsection", "protocol",
+ 		"public", "publicsection", "ref", "relates", "relatesalso", "remarks", "return", "retval",
+ 		"sa", "section", "see", "showinitializer", "since", "skip", "skipline", "struct", "subpage",
+ 		"subsection", "subsubsection", "test", "throw", "todo", "tparam", "typedef", "union", "until",
+ 		"var", "verbatim", "verbinclude", "version", "warning", "weakgroup", "xmlonly", "xrefitem",
+ 		"$", "@", "//","&", "~", "<", ">", "#", "%"};
+
+
+ string sectionIndicators[] = { "attention", "author", "brief", "bug", "cond", "date", "deprecated", "details",
+ 		"else", "elseif", "endcond", "endif", "exception", "if", "ifnot", "invariant", "note", "par", "param",
+ 		"tparam", "post" , "pre", "remarks", "return", "retval", "sa", "see", "since", "test", "throw", "todo",
+ 		"version", "warning", "xrefitem" };
+
+ /* All of the doxygen commands divided up by how they are parsed */
+ string simpleCommands[] = {"n", "$", "@", "//", "&", "~", "<", ">", "#", "%"};
+ string ignoredSimpleCommands[] = {"nothing at the moment"};
+ string commandWords[] = {"a", "b", "c", "e", "em", "p", "def", "enum", "example", "package", 
+ 		"relates", "namespace", "relatesalso","anchor", "dontinclude", "include", "includelineno"};
+ string ignoredCommandWords[] = {"copydoc", "copybrief", "copydetails", "verbinclude", "htmlinclude"};
+ string commandLines[] = {"addindex", "fn", "name", "line", "var", "skipline", "typedef", "skip", "until", "property"};
+ string ignoreCommandLines[] = {"nothing at the moment"};
+ string commandParagraph[] = {"return", "remarks", "since", "test", "sa", "see", "pre", "post", "details", "invariant", 
+ 		    "deprecated", "date", "note", "warning", "version", "todo", "bug", "attention", "brief", "author"};
+ string ignoreCommandParagraphs[] = {"nothing at the moment"};
+ string commandEndCommands[] = {"code", "dot", "msc", "f$", "f[", "f{environment}{", "htmlonly", "latexonly", "manonly", 
+ 		   "verbatim", "xmlonly", "cond", "if", "ifnot", "link"};
+ string commandWordParagraphs[] = {"param", "tparam", "throw", "retval", "exception"};
+ string commandWordLines[] = {"page", "subsection", "subsubsection", "section", "paragraph", "defgroup"};
+ string commandWordOWordOWords [] = {"category", "class", "protocol", "interface", "struct", "union"};
+ string commandOWords[] = {"dir", "file", "cond"};
+ string commandErrorThrowings[] = {"annotatedclasslist", "classhierarchy", "define", "functionindex", "header",
+ 		"headerfilelist", "inherit", "l", "postheader", "private", "privatesection", "protected", 
+ 		"protectedsection", "public", "publicsection", "endcode", "enddot", "endmsc", "endhtmlonly", 
+ 		"endlatexonly", "endmanonly", "endlink", "endverbatim", "endxmlonly", "f]", "f}", "endcond", 
+ 		"endif"};
+ string commandUniques[] = {"xrefitem", "arg", "ingroup", "par", "headerfile", "overload", "weakgroup", "ref",
+ 		"subpage", "dotfile", "image", "addtogroup", "li"};
+
+
+ /* Changes a string to all lower case*/
  string StringToLower(string stringToConvert)
 
- {//change each element of the string to lower case
+ {
 
     for(unsigned int i=0;i<stringToConvert.length();i++)
     {
@@ -109,6 +115,9 @@ string commandUniques[] = {"xrefitem", "ingroup", "par", "headerfile", "overload
     return stringToConvert;//return the converted string
  }
 
+ /* finds out if a command exists (is a possible command)
+  * from the string array commandArray
+  * returns -1 if no match is found */
  int findCommand(string smallString){
 
  	smallString = StringToLower(smallString);
@@ -122,61 +131,6 @@ string commandUniques[] = {"xrefitem", "ingroup", "par", "headerfile", "overload
  	}
  	return -1;
  }
- 
- int commandBelongs(string theCommand){
-	 string smallString = StringToLower(theCommand );
-	 //cout << " Looking for command " << theCommand << endl;
-	 int i = 0;
-	 for ( i = 0; i < sizeof(simpleCommands)/sizeof(*simpleCommands); i++){
-	 	if(smallString.compare(simpleCommands[i]) == 0){return 1;}
-	 	}
-	 for ( i = 0; i < sizeof(ignoredSimpleCommands)/sizeof(*ignoredSimpleCommands); i++){
-	 	if(smallString.compare(ignoredSimpleCommands[i]) == 0){return 2;}
-	 	} 
-	 for ( i = 0; i < sizeof(commandWords)/sizeof(*commandWords); i++){
-	 	if(smallString.compare( commandWords[i]) == 0){return 3;}
-	 	} 
-	 for ( i = 0; i < sizeof(ignoredCommandWords)/sizeof(*ignoredCommandWords); i++){
-	 	if(smallString.compare( ignoredCommandWords[i]) == 0){return 4;}
-	 	} 
-	 for ( i = 0; i < sizeof(commandLines)/sizeof(*commandLines); i++){
-	 	if(smallString.compare( commandLines[i]) == 0){return 5;}
-	 	} 
-	 for ( i = 0; i < sizeof(ignoreCommandLines)/sizeof(*ignoreCommandLines); i++){
-	 	if(smallString.compare( ignoreCommandLines[i]) == 0){return 6;}
-	 	} 
-	 for ( i = 0; i <  sizeof(commandParagraph)/sizeof(*commandParagraph); i++){
-	 	if(smallString.compare( commandParagraph[i]) == 0){return 7;}
-	 	} 
-	 /* IgnoreCommandParagraph */
-	 for ( i = 0; i < sizeof(ignoreCommandParagraphs)/sizeof(*ignoreCommandParagraphs); i++){
-	 	if(smallString.compare( ignoreCommandParagraphs[i]) == 0){return 8;}
-	 	} 
-	 for ( i = 0; i < sizeof(commandEndCommands)/sizeof(*commandEndCommands); i++){
-	 	if(smallString.compare( commandEndCommands[i]) == 0){return 9;}
-	 	} 
-	 for ( i = 0; i < sizeof(commandWordParagraphs)/sizeof(*commandWordParagraphs); i++){
-	 	if(smallString.compare( commandWordParagraphs[i]) == 0){return 10;}
-	 	} 
-	 for ( i = 0; i < sizeof(commandWordLines)/sizeof(*commandWordLines); i++){
-	 	if(smallString.compare( commandWordLines[i]) == 0){return 11;}
-	 	} 
-	 for ( i = 0; i < sizeof(commandWordOWordOWords)/sizeof(*commandWordOWordOWords); i++){
-	 	if(smallString.compare( commandWordOWordOWords[i]) == 0){return 12;}
-	 	} 
-	 for ( i = 0; i < sizeof(commandOWords)/sizeof(*commandOWords); i++){
-	 	if(smallString.compare( commandOWords[i]) == 0){return 13;}
-	 	} 
-	 for ( i = 0; i < sizeof(commandErrorThrowings)/sizeof(*commandErrorThrowings); i++){
-	 	if(smallString.compare( commandErrorThrowings[i]) == 0){return 14;}
-	 	} 
-	 for ( i = 0; i < sizeof(commandUniques)/sizeof(*commandUniques); i++){
-	 	if(smallString.compare( commandUniques[i]) == 0){return 15;}
-	 	} 
-
-	 	return 0;
-	 
- }
 
  /* isSectionIndicator returns a boolean if the command is a section indicator
   * This is a helper method for finding the end of a paragraph
@@ -192,580 +146,11 @@ string commandUniques[] = {"xrefitem", "ingroup", "par", "headerfile", "overload
  	}
  	return 0;
  }
-
-
- /* HELPER METHODS
-  * To test these, change the flags at the top of this class
-  */
-
- /* Tiny method to compartmentalise the removal of all optional comment fluff such as ///
-  * or **** that often occurs before commment blobs.
-  */
- int clearFluff(int &startInd, string doxygenString){
-	int startIndex = startInd;
- 	int amountRemoved = 0;
-
- 	while(doxygenString[startIndex] == '/'|| doxygenString[startIndex] == '!' || doxygenString[startIndex] == '*'
- 			|| doxygenString[startIndex] == '\n' || doxygenString[startIndex] == ' '|| doxygenString[startIndex] == '\t'){
- 		startIndex++;
- 		amountRemoved++;
- 		}
- 	startInd = startIndex;
- 	return startIndex;
- }
-
- /* Returns the next word ON THE CURRENT LINE ONLY
-  * if a new line is encountered, returns a blank string.
-  * Updates the index it is given after completion.
-  */
-
- string getNextWord(int &startInd, string doxygenString){
-	int startIndex = startInd;
- 	string nextWord;
- 	while (startIndex < doxygenString.length() && (doxygenString[startIndex] == '/'|| doxygenString[startIndex] == ' '
- 		|| doxygenString[startIndex] == '*' || doxygenString[startIndex]== '\n' || doxygenString[startIndex] == '\t'
-		|| doxygenString[startIndex] == '!')){
- 		if(doxygenString[startIndex]== '\n'){ startInd = startIndex; return nextWord;}
- 		startIndex++;
- 		//cout << "Start Index" << startIndex << endl;
- 		}
- 	//cout << doxygenString[startIndex] << endl;
- 	int endIndex = startIndex;
-
- 	while (endIndex < doxygenString.length() && (doxygenString[endIndex]!= '\n' && doxygenString[endIndex]!= ' ')){
- 		endIndex++;
- 		//cout << "End Index " << endIndex << endl;
- 		}
- 	nextWord = doxygenString.substr(startIndex, endIndex - startIndex);
- 	startInd = endIndex;
- 	//cout << "Next Word :" << nextWord << ":" << endl;
- 	return nextWord;
- }
-
- /* Returns the string remaining on a line
-  * and moved the index to the NEXT line
-  * returns "" if nothing on the current line.
-  */
- string getOneLine(int &startInd, string doxygenString){
-	int startIndex = startInd;
- 	while (doxygenString[startIndex] == '/'|| doxygenString[startIndex] == ' '
- 		|| doxygenString[startIndex] == '*' || doxygenString[startIndex]== '\n'
-		|| doxygenString[startIndex] == '!' || doxygenString[startIndex] == '\t'){
- 		if(doxygenString[startIndex]== '\n') return "";
- 		startIndex++;
- 		}
-
-	int endIndex = startIndex;
- 	while ((endIndex != doxygenString.length())&& (doxygenString[endIndex] != '\n')){
- 		endIndex++;
- 		//cout << doxygenString[endIndex] << "End Index: " << endIndex << endl;
- 		}
- 	string returnedLine = doxygenString.substr(startIndex, endIndex - startIndex);
- 	if (doxygenString[endIndex] == '\n' && (endIndex < doxygenString.length())) endIndex++;
- 	startInd = endIndex;
- 	return returnedLine;
- }
-/* Returns a properly formatted (all doxygen *, //! etc removed)
- * up til ANY command or end of paragraph is encountered. Has all the same issues as
- * getStringTilEndOfParagraph formatting wise.
- */
-string getStringTilCommand(int &startInd, string doxygenString){
-	 if (startInd >= doxygenString.length()) return "";
-	int startIndex = startInd;
-	int endIndex = startInd;
- 	string description;
- 	/* Find the End of the description */
- 	int keepLooping = 1;
- 	int spareIndex = 0;
- 	int counter;
- 	int finalIndex;
- 	while(keepLooping){
- 	 	if(endIndex >= doxygenString.length()){
- 	 			finalIndex = endIndex;
- 	 			keepLooping = 0;
- 	 		}
- 	 	else if (doxygenString[endIndex] == '\n'){
-			//cout << "1 ";
-			counter = endIndex;
-			if ( keepLooping && endIndex < doxygenString.length()-1) {
-				counter++;
-				//cout << "Counter :" << counter << endl;
-				while(keepLooping && endIndex < doxygenString.length() && (doxygenString[counter] == ' ' ||
-				               doxygenString[counter] == '*'|| doxygenString[counter] == '\n'|| doxygenString[counter] == '/'
-				            	   || doxygenString[counter] == '!' || doxygenString[startIndex] == '\t') ){
-									if(doxygenString[counter] == '\n') {
-										//cout << "Blank line found" << endl;
-										keepLooping = 0;
-										finalIndex = counter;}
-									else{ counter++;}
-									}
-
-			}
-			//endIndex = counter;
-		}
- 		else if (doxygenString[endIndex] == '\\' || doxygenString[endIndex] == '@'){
- 			finalIndex = endIndex;
- 			keepLooping = 0;
- 			}
-		else if(endIndex < doxygenString.length() -2
-				&& string("**/").compare(doxygenString.substr(endIndex , endIndex  + 2)) == 0){
-			finalIndex = endIndex;
-			//cout << "3 ";
-			keepLooping = 0;
-		}
- 		if(keepLooping){
- 			//cout << "4 ";
- 			endIndex++;
- 		}
- 	}
- 	//cout << "Done with EndIndex" << endl;
- 	while(doxygenString[startIndex] == '!' || doxygenString[startIndex] == ' '
- 		|| doxygenString[startIndex] == '/' || doxygenString[startIndex] == '*' || doxygenString[startIndex] == '\t') startIndex++;
-
- 	for (int i = startIndex; i < endIndex; i++){
-
- 		if (doxygenString[i] == '\n') {
-
- 			while ((doxygenString[i] == '\n' || doxygenString[startIndex] == '\t'|| doxygenString[i] == ' '
- 				|| doxygenString[i] == '*' || doxygenString[i] == '/')&& endIndex < doxygenString.length() - 1){
- 				i++;
- 				}
- 			description.append(" ");
- 		}
- 		description.push_back(doxygenString[i]);
- 		//cout << doxygenString[i];
- 	}
- 	//if(noisy) cout << "Final Index is: " << finalIndex << endl;
- 	startInd = finalIndex;
- 	return description;
- }
  
- 
-/* Returns a Paragraph- defined in Doxygen to be a paragraph of text
- * seperate by either a structural command or a blank line
- * This method is VERY messy currently
- */
- //TODO fix getStringTilEndOfParagraph to be more forgiving, work on ' ' characters
- string getStringTilEndOfParagraph(int &startInd, string doxygenString){
-	 if (startInd >= doxygenString.length()) return "";
-	int startIndex = startInd;
-	int endIndex = startInd;
- 	string description;
- 	/* Find the End of the description */
- 	int keepLooping = 1;
- 	int spareIndex = 0;
- 	int counter;
- 	int finalIndex;
- 	while(keepLooping){
- 		if(endIndex >= doxygenString.length()){
- 			finalIndex = endIndex;
- 			keepLooping = 0;
- 		}
- 		else if (doxygenString[endIndex] == '\n'){
-			//cout << "1 ";
-			counter = endIndex;
-			if ( keepLooping && endIndex < doxygenString.length()-1) {
-				counter++;
-				//cout << "Counter :" << counter << endl;
-				while(keepLooping && endIndex < doxygenString.length() && (doxygenString[counter] == ' ' ||
-				               doxygenString[counter] == '*'|| doxygenString[startIndex] == '\t' || doxygenString[counter] == '\n'|| doxygenString[counter] == '/'
-				            	   || doxygenString[counter] == '!') ){
-									if(doxygenString[counter] == '\n') {
-										//cout << "Blank line found" << endl;
-										keepLooping = 0;
-										finalIndex = counter;}
-									else{ counter++;}
-									}
-
-			}
-			//endIndex = counter;
-		}
- 		//todo this fix for not immediately exciting while parsing a paragraph seems somewhat cheap
- 		else if (endIndex != startInd && doxygenString[endIndex] == '\\' || doxygenString[endIndex] == '@'){
-			spareIndex = endIndex +1;
-			
- 			if (isSectionIndicator(getNextWord(spareIndex, doxygenString))) {
- 				keepLooping = 0;
- 				finalIndex = endIndex;}
- 			}
-		else if(endIndex < doxygenString.length() - 1
-				&& string("*/").compare(doxygenString.substr(endIndex , endIndex  + 1)) == 0){
-			keepLooping = 0;
-			finalIndex = endIndex;
-		}
- 		if(keepLooping){
- 			endIndex++;
- 		}
- 	}
- 	//cout << "Done with EndIndex" << endl;
- 	while(doxygenString[startIndex] == '!' || doxygenString[startIndex] == ' ' || doxygenString[startIndex] == '\t'
- 		|| doxygenString[startIndex] == '/' || doxygenString[startIndex] == '*') startIndex++;
-
- 	for (int i = startIndex; i < endIndex; i++){
-
- 		if (doxygenString[i] == '\n') {
-
- 			while ((doxygenString[i] == '\n' || doxygenString[startIndex] == '\t' || doxygenString[i] == ' ' ||doxygenString[startIndex] == '!'
- 				|| doxygenString[i] == '*' || doxygenString[i] == '/')&& endIndex < doxygenString.length() - 1){
- 				i++;
- 				}
- 			description.append(" ");
- 		}
- 		description.push_back(doxygenString[i]);
- 		//cout << doxygenString[i];
- 	}
- 	startInd = finalIndex;
- 	return description;
- }
-
- /* This method is for a specific form of doxygen command
-  * that begins with a \command and ends in \endcommand
-  * such as \code and \endcode. The proper usage is
-  * progressTilEndCommand("endcode", index)
-  * currently this method does NOT process what is in between the two commands
-  */
- //TODO Make progressTilCommand return a formatted string
- int progressTilEndCommand(string theCommand, int &startInd, string doxygenString){
- 	int endIndex = startInd;
- 	while (endIndex < doxygenString.length()){
- 		if (doxygenString[endIndex] == '\\' || doxygenString[endIndex] == '@'){
- 			//cout << doxygenString.substr(endIndex + 1 , theCommand.length())<< endl;
- 			if (theCommand.compare(doxygenString.substr(endIndex + 1 , theCommand.length())) == 0){
- 				startInd = endIndex + theCommand.length() + 1;
- 				return 1;
- 			}
- 		}
- 		endIndex++;
- 	}
- 	//End command not found
- 	return 0;
- }
-
- /* A specialty method for commands such as \arg that end at the end of a paragraph OR when another \arg is encountered
-  */
- 
- string getStringTilAnyCommand(string theCommand, int &startInd, string doxygenString){
-	 if (startInd >= doxygenString.length()) return "";
-		int startIndex = startInd;
-		int endIndex = startInd;
-	 	string description;
-	 	/* Find the End of the description */
-	 	int keepLooping = 1;
-	 	int spareIndex = 0;
-	 	int counter;
-	 	int finalIndex;
-	 	while(keepLooping){
-	 		if(endIndex >= theCommand.length()){
-	 			finalIndex = endIndex;
-	 			keepLooping = 0;
-	 		}
-	 		else if (doxygenString[endIndex] == '\n'){
-				//cout << "1 ";
-				counter = endIndex;
-				if ( keepLooping && endIndex < doxygenString.length()-1) {
-					counter++;
-					//cout << "Counter :" << counter << endl;
-					while(keepLooping && endIndex < doxygenString.length() && (doxygenString[counter] == ' ' ||
-					               doxygenString[counter] == '*'|| doxygenString[counter] == '\n'|| doxygenString[counter] == '/'
-					            	   || doxygenString[counter] == '!' || doxygenString[startIndex] == '\t') ){
-										if(doxygenString[counter] == '\n') {
-											//cout << "Blank line found" << endl;
-											keepLooping = 0;
-											finalIndex = counter;}
-										else{ counter++;}
-										}
-
-				}
-				//endIndex = counter;
-			}
-	 		else if (doxygenString[endIndex] == '\\' || doxygenString[endIndex] == '@'){
-	 			//cout << "2 ";
-				spareIndex = endIndex;
-	 			if (endIndex + theCommand.length() < theCommand.length() 
-	 					&& theCommand.compare(doxygenString.substr(endIndex, theCommand.length())) == 0) keepLooping = 0;
-	 			}
-			else if(endIndex < doxygenString.length() - 1
-					&& string("*/").compare(doxygenString.substr(endIndex , endIndex  + 1)) == 0){
-				//cout << "3 ";
-				keepLooping = 0;
-			}
-	 		if(keepLooping){
-	 			//cout << "4 ";
-	 			endIndex++;
-	 		}
-	 	}
-	 	//cout << "Done with EndIndex" << endl;
-	 	while(doxygenString[startIndex] == '!' || doxygenString[startIndex] == ' '
-	 		|| doxygenString[startIndex] == '/' || doxygenString[startIndex] == '*' || doxygenString[startIndex] == '\t') startIndex++;
-
-	 	for (int i = startIndex; i < endIndex; i++){
-
-	 		if (doxygenString[i] == '\n') {
-
-	 			while ((doxygenString[i] == '\n' || doxygenString[i] == ' ' || doxygenString[startIndex] == '\t'
-	 				|| doxygenString[i] == '*' || doxygenString[i] == '/')&& endIndex < doxygenString.length() - 1){
-	 				i++;
-	 				}
-	 			description.append(" ");
-	 		}
-	 		description.push_back(doxygenString[i]);
-	 		//cout << doxygenString[i];
-	 	}
-	 	startInd = finalIndex;
-	 	return description;
- }
- ///////////////TEST CLASSES AND MAIN BELOW/////////////////
-
-
- /*  Testing clearFluff(), a method to scan past all excess / * ! from beginning of
-  * a comment blob. Compartmentalised simply because this is a comment habit that
-  * differs wildly */
-
- int testClearFluff(){
-  string doxygenString;
-  string cases[] = {"/** WORD", "/*! WORD", "/******* WORD", "///// WORD", "//! WORD", "//! WORD", "///WORD",
- 		 "/**\nWORD", "/**\n*WORD", "/** \n WORD"};
-  int testPassed = 1;
-  int placement = 0;
-  int casesSize = sizeof(cases)/sizeof(*cases);
-  for (int i = 0; i < casesSize; i++){
-	  placement = 0;
-	  doxygenString = cases[i];
-	  if(cases[i][clearFluff(placement, doxygenString)] != 'W'){
-		  cout << "ClearFluff failed for string :" << doxygenString << "\t Displayed :" << cases[i][clearFluff(placement = 0, doxygenString)] << ": Instead." << endl;
-		  testPassed = 0;
-	  }
-  }
-  if(testPassed) cout << "+++ClearFluff passed for all tests+++\n" << endl;
-  else cout << "+++ClearFluff FAILED.+++" << endl;
-  return testPassed;
-
-  };
-
- int testGetNextWord(){
-	  string doxygenString;
-	  string cases[] = {"/** WORD ", " * WORD ", "///!WORD ", " WORD ", "//! WORD ", " * WORD ", "*WORD "};
-	  int testPassed = 1;
-	  string testWord;
-	  int placement = 0;
-	  int casesSize = sizeof(cases)/sizeof(*cases);
-	  for (int i = 0; i < casesSize; i++){
-		  doxygenString = cases[i];
-		  placement = 0;
-		  testWord = getNextWord(placement, doxygenString);
-		  if(testWord.compare("WORD") != 0){
-			  cout << "GetNextWord failed for string :" << doxygenString << "\t Displayed :" << testWord << ": Instead." << endl;
-			  testPassed = 0;
-		  }
-		 //else cout << "GetNextWord passed for string :" << doxygenString << endl;
-	  }
-	    placement = 0;
-		doxygenString = " * @WORD ";
-		testWord = getNextWord(placement, doxygenString);
-		if(testWord.compare("@WORD") != 0){
-			cout << "GetNextWord failed for string :"
-			<< doxygenString << "\t Displayed :" << testWord << ": Instead." << endl;
-			testPassed = 0;}
-		 //else cout << "GetNextWord passed for string :" << doxygenString << endl;
-		testWord = " * ";
-		testWord.push_back('\\');
-		testWord = testWord + "WORD ";
-		string commandWord;
-		commandWord.push_back('\\');
-		commandWord = commandWord + "WORD";
-		doxygenString = testWord;
-		placement = 0;
-		testWord = getNextWord(placement, doxygenString);
-		if(testWord.compare(commandWord) != 0){
-			cout << "GetNextWord failed for string :" << doxygenString
-			<< "\t Displayed :" << testWord << ": Instead." << endl;
-			testPassed = 0;}
-		  //else cout << "GetNextWord passed for string :" << doxygenString << endl;
-		doxygenString = "WORD ANOTHER WORD1 WORD2 \n";
-		placement = 0;
-		testWord = getNextWord(placement, doxygenString);
-		if(testWord.compare("WORD") != 0){
-			cout << "GetNextWord failed for string :" << doxygenString
-			<< "\t Displayed :" << testWord << ": Instead." << endl;
-			testPassed = 0;}
-		  //else cout << "GetNextWord passed for string :" << doxygenString << endl;
-		testWord = getNextWord(placement, doxygenString);
-		if(testWord.compare("ANOTHER") != 0){
-			cout << "GetNextWord failed for string :" << doxygenString
-			<< "\t Displayed :" << testWord << ": Instead." << endl;
-			testPassed = 0;}
-		 //else cout << "GetNextWord passed for string :" << doxygenString << endl;
-		testWord = getNextWord(placement, doxygenString);
-		if(testWord.compare("WORD1") != 0){
-			cout << "GetNextWord failed for string :" << doxygenString
-			<< "\t Displayed :" << testWord << ": Instead." << endl;
-			testPassed = 0;}
-		  //else cout << "GetNextWord passed for string :" << doxygenString << endl;
-		testWord = getNextWord(placement, doxygenString);
-		if(testWord.compare("WORD2") != 0){
-			cout << "GetNextWord failed for string :"
-			<< doxygenString << "\t Displayed :" << testWord
-			<< ": Instead." << endl;
-			testPassed = 0;}
-		  //else cout << "GetNextWord passed for string :" << doxygenString << endl;
-		testWord = getNextWord(placement, doxygenString);
-		if(testWord.compare("") != 0){
-			cout << "GetNextWord failed for string :" << doxygenString
-			<< "\t Displayed :" << testWord << ": Instead." << endl;
-			testPassed = 0;}
-		  //else cout << "GetNextWord passed for string :" << doxygenString << endl;
-		testWord = getNextWord(placement, doxygenString);
-		if(testWord.compare("") != 0){
-			cout << "GetNextWord failed for string :" << doxygenString <<
-			"\t Displayed :" << testWord << ": Instead." << endl;
-			testPassed = 0;}
-		  //else cout << "GetNextWord passed for string :" << doxygenString << endl;
-		  if(testPassed) cout << "+++NextWord passed for all tests+++\n" << endl;
-		 else cout << "+++NextWord FAILED+++\n" << endl;
-		  return testPassed;
- }
-
- int testGetOneLine(){
-	  string doxygenString;
-	  string cases[] = {" * Crop this sentence after this period.\n",
-			  " * Crop this sentence after this period.\n",
-			  "Crop this sentence after this period.\n",
-			  "//! Crop this sentence after this period.\n",
-			  " Crop this sentence after this period.\n"
-			  };
-	  int testPassed = 1;
-	  string testWord;
-		int placement = 0;
-	  int casesSize = sizeof(cases)/sizeof(*cases);
-	  for (int i = 0; i < casesSize; i++){
-		  doxygenString = cases[i];
-		  placement = 0;
-		  testWord = getOneLine(placement, doxygenString);
-		  if(testWord.compare("Crop this sentence after this period.") != 0){
-			  cout << "GetOneLine failed for string :" << doxygenString << "\t Displayed :" << testWord << ": Instead." << endl;
-			  testPassed = 0;
-		  }
-	  }
-	  doxygenString = ("Get this line.\n * Now get this line.");
-	  placement = 0;
-	  testWord = getOneLine(placement, doxygenString);
-	  if(testWord.compare("Get this line.") != 0){
-	  		cout << "GetOneLine failed for string :" << doxygenString << "\t Displayed :" << testWord << ": Instead." << endl;
-	  		testPassed = 0;
-	  		  }
-	  testWord = getOneLine(placement, doxygenString);
-	  if(testWord.compare("Now get this line.") != 0){
-	  		cout << "GetOneLine failed for string :" << doxygenString << "\t Displayed :" << testWord << ": Instead." << endl;
-	  		testPassed = 0;
-	  		  }
-	  testWord = getOneLine(placement, doxygenString);
-	  if(testWord.compare("") != 0){
-	  		cout << "GetOneLine failed for string :" << doxygenString << "\t Displayed :" << testWord << ": Instead." << endl;
-	  		testPassed = 0;
-	  		  }
-
-	  if(testPassed) cout << "+++GetOneLine passed for all tests+++\n" << endl;
-	 else cout << "+++GetOneLine FAILED+++\n" << endl;
-	  return testPassed;
- }
-//TODO Flesh testGetStringTilEndOfParagraph out, fix weird spacing problems
- int testGetStringTilEndOfParagraph(){
-	string doxygenString;
-	int placement = 0;
-	int testPassed = 1;
-	string testParagraph;
-	doxygenString = ("/* This is a description,\n * thus it continues on\n * for several lines.\n\n This Shouldn't be included.\n\n **/");
-	testParagraph = getStringTilEndOfParagraph(placement, doxygenString);
-	if( testParagraph.compare("This is a description, thus it continues on for several lines.") != 0){
-  		cout << "GetOneLine failed for string :" << doxygenString << "\t Displayed :" << testParagraph << ": Instead." << endl;
-  		testPassed = 0;
-  	}
-	//cout << "Curr Placement: " << placement<< endl;
-	testParagraph = getStringTilEndOfParagraph(placement, doxygenString);
-	//cout << "Curr Placement: " << placement<< endl;
-	if( testParagraph.compare(" This Shouldn't be included.") != 0){
-  		cout << "GetOneLine failed for string :" << doxygenString << "\t Displayed :" << testParagraph << ": Instead." << endl;
-  		testPassed = 0;
-  	}
-
-	//cout << "Curr Placement: " << placement<< endl;
-	//cout << "String Length: " << doxygenString.length() << endl;
-
-	doxygenString = "/* This is a description,\n * thus it continues on\n * for several lines.\n * \n * ";
-	doxygenString.push_back('//');
-	doxygenString += "author cheryl foil \n\n **/";
-	placement = 0;
-	testParagraph = getStringTilEndOfParagraph(placement, doxygenString);
-	if( testParagraph.compare("This is a description, thus it continues on for several lines.") != 0){
-  		cout << "GetOneLine failed for string :" << doxygenString << "\t Displayed :" << testParagraph << ": Instead." << endl;
-  		testPassed = 0;
-  	}
-
-	if(testPassed) cout << "+++GetGetStringTilEndOfParagraph passed for all tests+++\n" << endl;
-	else cout << "+++GetGetStringTilEndOfParagraphFAILED+++\n" << endl;
-	return testPassed;
- }
-
- int testGetStringTilCommand(){
-		string doxygenString;
-		int placement = 0;
-		int testPassed = 1;
-		string testParagraph;
-		doxygenString = ("/* This is a description,\n * thus it continues on\n * for several @b lines.\n\n This Shouldn't be included.\n\n **/");
-		testParagraph = getStringTilCommand(placement, doxygenString);
-		if( testParagraph.compare("This is a description, thus it continues on for several ") != 0){
-	  		cout << "GetOneLine failed for string :" << doxygenString << "\t Displayed :" << testParagraph << ": Instead." << endl;
-	  		testPassed = 0;
-	  	}
-		if(testPassed) cout << "+++GetStringTilCommand passed for all tests+++\n" << endl;
-		else cout << "+++GetStringTilCommand FAILED+++\n" << endl;
-		return testPassed;
-	 
- }
- int testProgressTilEndCommand(){
-	    string doxygenString ;
-		int placement = 0;
-		int testPassed = 1;
-		string testParagraph;
-		doxygenString = "Let's pretend this \n * is a bunch of code to be ended in ";
-		doxygenString.push_back('\\');
-		doxygenString += "endcodeSTOP";
-		progressTilEndCommand("endcode", placement, doxygenString);
-		//cout << "Placement : " << placement << endl;
-		if( doxygenString[placement] != 'S'){
-	  		cout << "GetOneLine failed for string :" << doxygenString << "\n\t Displayed :" << testParagraph << ": Instead." << endl;
-	  		testPassed = 0;
-	  	}
-		if(testPassed) cout << "+++ProgressTilEndCommand passed for all tests+++\n" << endl;
-		else cout << "+++ProgressTilEndCommand FAILED+++\n" << endl;
-	 return testPassed;
- }
-
- int testCCF(){
-	cout << "TESTING COMMAND PARSING FUNCTIONS" << endl;
-	cout << "Testing clearFluff" << endl;
-	testClearFluff();
-
- 	cout << "Testing getNextWord" << endl;
- 	testGetNextWord();
- 	cout << "Testing getOneLine"<< endl;
- 	testGetOneLine();
-
- 	cout << "Testing getStringTilEndOfParagraph" << endl;
- 	testGetStringTilEndOfParagraph();
-
- 	cout << "Testing progressTilEndCommand" << endl;
- 	testProgressTilEndCommand();
-
- 	cout << "Testing GetStringTilCommand" << endl;
- 	testGetStringTilCommand();
- 	return 1;
- }
-
  /* prints the parse tree
   *
   */
- void printTree(){
+ void printTree( list <DoxygenEntity> &rootList){
 
 		list<DoxygenEntity>::iterator p = rootList.begin();
 		while (p != rootList.end()){
@@ -775,45 +160,217 @@ string getStringTilCommand(int &startInd, string doxygenString){
 
  }
  
- 
- 
- list<DoxygenEntity> parse(int startInd, string doxygenString){
- 	string currWord;
- 	int startIndex = startInd;
- 	int savedIndex;
- 	list <DoxygenEntity> aNewList;
- 	int endIndex = doxygenString.length();
- 	int currCommand;
- 	while (startIndex < endIndex){
- 		savedIndex = startIndex;
- 		currWord = getNextWord(startIndex, doxygenString);
- 		if(noisy) cout << "Parsing for phrase starting in:" << currWord << endl;
- 		if(currWord == ""){
- 			if (startIndex < endIndex) startIndex++;
- 		}
- 		else if(currWord[0] == '\\' || currWord[0] == '@'){
- 			currWord = currWord.substr(1, currWord.length() - 1);
- 			currCommand = findCommand(currWord);
- 			if (currCommand < 0 ){ if(noisy) cout << "BAD COMMAND: " << currWord << endl;}
- 				//cout << "Command: " << currWord << " " << currCommand << endl;
- 			else addCommand(currWord, startIndex, aNewList, doxygenString);
- 		}
- 		else{
- 			startIndex = savedIndex;
-			addCommand(string("plainstring"), startIndex, aNewList, doxygenString);
+ /* Determines how a command should be handled (what group it belongs to
+  * for parsing rules
+  */
 
+ int commandBelongs(string theCommand){
+	 string smallString = StringToLower(theCommand );
+	 //cout << " Looking for command " << theCommand << endl;
+	 int i = 0;
+	 for ( i = 0; i < sizeof(simpleCommands)/sizeof(*simpleCommands); i++){
+	 	if(smallString.compare(simpleCommands[i]) == 0){return SIMPLECOMMAND ;}
+	 	}
+	 for ( i = 0; i < sizeof(ignoredSimpleCommands)/sizeof(*ignoredSimpleCommands); i++){
+	 	if(smallString.compare(ignoredSimpleCommands[i]) == 0){return IGNOREDSIMPLECOMMAND;}
+	 	} 
+	 for ( i = 0; i < sizeof(commandWords)/sizeof(*commandWords); i++){
+	 	if(smallString.compare( commandWords[i]) == 0){return COMMANDWORD;}
+	 	} 
+	 for ( i = 0; i < sizeof(ignoredCommandWords)/sizeof(*ignoredCommandWords); i++){
+	 	if(smallString.compare( ignoredCommandWords[i]) == 0){return IGNOREDCOMMANDWORD;}
+	 	} 
+	 for ( i = 0; i < sizeof(commandLines)/sizeof(*commandLines); i++){
+	 	if(smallString.compare( commandLines[i]) == 0){return COMMANDLINE;}
+	 	} 
+	 for ( i = 0; i < sizeof(ignoreCommandLines)/sizeof(*ignoreCommandLines); i++){
+	 	if(smallString.compare( ignoreCommandLines[i]) == 0){return IGNOREDCOMMANDLINE;}
+	 	} 
+	 for ( i = 0; i <  sizeof(commandParagraph)/sizeof(*commandParagraph); i++){
+	 	if(smallString.compare( commandParagraph[i]) == 0){return COMMANDPARAGRAPH;}
+	 	} 
+	 /* IgnoreCommandParagraph */
+	 for ( i = 0; i < sizeof(ignoreCommandParagraphs)/sizeof(*ignoreCommandParagraphs); i++){
+	 	if(smallString.compare( ignoreCommandParagraphs[i]) == 0){return IGNORECOMMANDPARAGRAPH;}
+	 	} 
+	 for ( i = 0; i < sizeof(commandEndCommands)/sizeof(*commandEndCommands); i++){
+	 	if(smallString.compare( commandEndCommands[i]) == 0){return COMMANDENDCOMMAND ;}
+	 	} 
+	 for ( i = 0; i < sizeof(commandWordParagraphs)/sizeof(*commandWordParagraphs); i++){
+	 	if(smallString.compare( commandWordParagraphs[i]) == 0){return COMMANDWORDPARAGRAPH;}
+	 	} 
+	 for ( i = 0; i < sizeof(commandWordLines)/sizeof(*commandWordLines); i++){
+	 	if(smallString.compare( commandWordLines[i]) == 0){return COMMANDWORDLINE ;}
+	 	} 
+	 for ( i = 0; i < sizeof(commandWordOWordOWords)/sizeof(*commandWordOWordOWords); i++){
+	 	if(smallString.compare( commandWordOWordOWords[i]) == 0){return COMMANDWORDOWORDWORD;}
+	 	} 
+	 for ( i = 0; i < sizeof(commandOWords)/sizeof(*commandOWords); i++){
+	 	if(smallString.compare( commandOWords[i]) == 0){return COMMANDOWORD;}
+	 	} 
+	 for ( i = 0; i < sizeof(commandErrorThrowings)/sizeof(*commandErrorThrowings); i++){
+	 	if(smallString.compare( commandErrorThrowings[i]) == 0){return COMMANDERRORTHROW;}
+	 	} 
+	 for ( i = 0; i < sizeof(commandUniques)/sizeof(*commandUniques); i++){
+	 	if(smallString.compare( commandUniques[i]) == 0){return COMMANDUNIQUE;}
+	 	} 
+
+	 	return 0;
+	 
+ }
+ /* Returns the next word ON THE CURRENT LINE ONLY
+  * if a new line is encountered, returns a blank string.
+  * Updates the index it is given if success.
+  */
+
+ string getNextWord(TokenList &tokList){
+	 Token nextToken = tokList.peek();
+	 if (nextToken.tokenType == PLAINSTRING ){
+		 nextToken = tokList.next();
+		 return nextToken.tokenString;
+	 }
+ 	return "";
+ }
+
+ /* Returns the location of the end of the line as
+  * an iterator.
+  */
+ list<Token>::iterator getOneLine(TokenList &tokList){
+	 list<Token>::iterator endOfParagraph = tokList.iteratorCopy();
+	 while(endOfParagraph != tokList.end()){
+		 if ((* endOfParagraph).tokenType == END_LINE){
+			 return endOfParagraph;
+		 }
+		 endOfParagraph++;
+	 }
+ 	return tokList.end();
+ }
+ 
+
+
+/* Returns a properly formatted string
+ * up til ANY command or end of paragraph is encountered.
+ */
+string getStringTilCommand(TokenList &tokList){
+	 string description;
+	 if (tokList.peek().tokenType == 0) return "";
+	 while(tokList.peek().tokenType == PLAINSTRING || tokList.peek().tokenType == END_LINE ){
+		 Token currentToken = tokList.next();
+		 if(currentToken.tokenType == PLAINSTRING) {
+			 description = description + currentToken.tokenString + " ";
+		 }
+		 else if (tokList.peek().tokenType == END_LINE) break;
+	 }
+	 
+ 	return description;
+ }
+ 
+/* Returns a properly formatted string
+ * up til the command specified is encountered
+ */
+//TODO check that this behaves properly for formulas
+
+string getStringTilEndCommand(string theCommand, TokenList &tokList){
+	 string description;
+	 if (tokList.peek().tokenType == 0) return "";
+	 while(tokList.peek().tokenString.compare(theCommand) != 0 ){
+		 Token currentToken = tokList.next();
+		 description = description + currentToken.tokenString + " ";
+
+	 }
+	 
+ 	return description;
+ }
+ 
+/* Returns the end of a Paragraph as an iterator-
+ * Paragraph is defined in Doxygen to be a paragraph of text
+ * seperate by either a structural command or a blank line
+ */
+
+list<Token>::iterator getEndOfParagraph(TokenList &tokList){
+	 list<Token>::iterator endOfParagraph = tokList.iteratorCopy();
+	 while(endOfParagraph != tokList.end()){
+		if ((* endOfParagraph).tokenType == COMMAND){
+			 if(isSectionIndicator((* endOfParagraph).tokenString)) return endOfParagraph;
+			 else endOfParagraph++;
+		 }
+		else if((* endOfParagraph).tokenType == PLAINSTRING) {
+			 endOfParagraph++;
+		 }
+		 else if ((* endOfParagraph).tokenType == END_LINE){
+			 endOfParagraph++;
+			 if ((* endOfParagraph).tokenType == END_LINE){
+				 endOfParagraph++;
+				 return endOfParagraph;
+			 }
+		 }
+
+	 }
+	 
+ 	return tokList.end();
+
+ }
+
+/* Returns the end of a section, defined as the first blank line OR first encounter of the same 
+ * command. Example of this behaviour is \arg
+ */
+
+list<Token>::iterator getEndOfSection(string theCommand, TokenList &tokList){
+	 list<Token>::iterator endOfParagraph = tokList.iteratorCopy();
+	 while(endOfParagraph != tokList.end()){
+		if ((* endOfParagraph).tokenType == COMMAND){
+			 if(theCommand.compare((*endOfParagraph).tokenString) == 0) return endOfParagraph;
+			 else endOfParagraph++;
+		 }
+		else if((* endOfParagraph).tokenType == PLAINSTRING) {
+			 endOfParagraph++;
+		 }
+		 else if ((* endOfParagraph).tokenType == END_LINE){
+			 endOfParagraph++;
+			 if ((* endOfParagraph).tokenType == END_LINE){
+				 endOfParagraph++;
+				 return endOfParagraph;
+			 }
+		 }
+
+	 }
+}
+ /* This method is for returning the end of a specific form of doxygen command
+  * that begins with a \command and ends in \endcommand
+  * such as \code and \endcode. The proper usage is
+  * progressTilEndCommand("endcode", tokenList);
+  */
+list<Token>::iterator getEndCommand(string theCommand, TokenList &tokList){
+	list<Token>::iterator endOfCommand = tokList.iteratorCopy();
+ 	while (endOfCommand!= tokList.end()){
+ 		if ((*endOfCommand).tokenType == COMMAND){
+ 			if (theCommand.compare((* endOfCommand).tokenString) == 0){
+ 				return endOfCommand;
+ 			}
+ 			endOfCommand++;
  		}
  	}
-
- 	return aNewList;
+ 	//End command not found
+ 	return tokList.end();
  }
+
+ /* A specialty method for commands such as \arg that end at the end of a paragraph OR when another \arg is encountered
+  */
+ 
+list<Token>::iterator getTilAnyCommand(string theCommand, TokenList &tokList){
+	list<Token>::iterator anIterator;
+	return anIterator;
+ }
+
+
+
  
  /*  Method for Adding a Simple Command
   * Format: @command
   * Plain commands, such as newline etc, they contain no other data
   *  \n \\ \@ \& \$ \# \< \> \%
   */
-  int addSimpleCommand(string theCommand, int &startInd, list <DoxygenEntity> &doxyList, string doxygenString){
+  int addSimpleCommand(string theCommand, list <DoxygenEntity> &doxyList){
 	 
 		if (noisy) cout << "Parsing " << theCommand << endl;
 		doxyList.push_back(DoxygenEntity(theCommand));
@@ -824,7 +381,7 @@ string getStringTilCommand(int &startInd, string doxygenString){
    * Format: @command
    * Plain commands, such as newline etc, they contain no other data
    */
-  int ignoreSimpleCommand(string theCommand, int &startInd, list <DoxygenEntity> &doxyList, string doxygenString){
+  int ignoreSimpleCommand(string theCommand, list <DoxygenEntity> &doxyList){
 	 
 		if (noisy) cout << "Not Adding " << theCommand << endl;
 		return 1;
@@ -836,9 +393,9 @@ string getStringTilCommand(int &startInd, string doxygenString){
    * "a", "b", "c", "e", "em", "p", "def", "enum", "example", "package", 
    * "relates", "namespace", "relatesalso","anchor", "dontinclude", "include", "includelineno"
    */
-  int addCommandWord(string theCommand, int &startInd, list <DoxygenEntity> &doxyList, string doxygenString){
+  int addCommandWord(string theCommand, TokenList &tokList, list <DoxygenEntity> &doxyList){
 	if (noisy) cout << "Parsing " << theCommand << endl;
-	string name = getNextWord(startInd, doxygenString);
+	string name = getNextWord(tokList);
 	if (!name.empty()){ 
 		doxyList.push_back(DoxygenEntity(theCommand, name));
 		return 1;
@@ -851,9 +408,9 @@ string getStringTilCommand(int &startInd, string doxygenString){
    * Commands with a single WORD after then such as @b
    * "copydoc", "copybrief", "copydetails", "verbinclude", "htmlinclude"
    */
-  int ignoreCommandWord(string theCommand, int &startInd, list <DoxygenEntity> &doxyList, string doxygenString){
+  int ignoreCommandWord(string theCommand, TokenList &tokList, list <DoxygenEntity> &doxyList){
 	if (noisy) cout << "Not Adding " << theCommand << endl;
-	string name = getNextWord(startInd, doxygenString);
+	string name = getNextWord(tokList);
 	if (!name.empty()){ 
 		return 1;
 	}
@@ -866,18 +423,14 @@ string getStringTilCommand(int &startInd, string doxygenString){
    * Commands with a single LINE after then such as @var
    * "addindex", "fn", "name", "line", "var", "skipline", "typedef", "skip", "until", "property"
    */
-  int addCommandLine(string theCommand, int &startInd, list <DoxygenEntity> &doxyList, string doxygenString){
+  int addCommandLine(string theCommand, TokenList &tokList, list <DoxygenEntity> &doxyList){
 	if (noisy) cout << "Parsing " << theCommand << endl;
-	string line = getOneLine(startInd, doxygenString);
-	if(!line.empty()){
-		int placement = 0;
+	list<Token>::iterator endOfLine = getOneLine(tokList);
 		list <DoxygenEntity> aNewList;
-		aNewList =  parse(placement, line);
+		aNewList =  parse(endOfLine, tokList);
 		doxyList.push_back( DoxygenEntity(theCommand, aNewList));
 		return 1;
-		}
-	else cout << "No line followed " << theCommand <<  " command. Not added" << endl;
-	return 0;
+
  }
   
   /* NOT INCLUDED CommandLine
@@ -885,14 +438,11 @@ string getStringTilCommand(int &startInd, string doxygenString){
    * Commands with a single LINE after then such as @var
    * 
    */
-  int ignoreCommandLine(string theCommand, int &startInd, list <DoxygenEntity> &doxyList, string doxygenString){
+  int ignoreCommandLine(string theCommand, TokenList &tokList, list <DoxygenEntity> &doxyList){
 	if (noisy) cout << "Not Adding " << theCommand << endl;
-	string line = getOneLine(startInd, doxygenString);
-	if(!line.empty()){
-		return 1;
-		}
-	else cout << "WARNING: No line followed " << theCommand <<  " command." << endl;
-	return 0;
+	list<Token>::iterator endOfLine = getOneLine(tokList);
+	tokList.setIterator(endOfLine);
+	return 1;
  }
   
   /* CommandParagraph
@@ -901,32 +451,28 @@ string getStringTilCommand(int &startInd, string doxygenString){
    * "return", "remarks", "since", "test", "sa", "see", "pre", "post", "details", "invariant", 
    * "deprecated", "date", "note", "warning", "version", "todo", "bug", "attention", "brief", "arg", "author"
    */
-  int addCommandParagraph(string theCommand, int &startInd, list <DoxygenEntity> &doxyList, string doxygenString){
+  int addCommandParagraph(string theCommand, TokenList &tokList, list <DoxygenEntity> &doxyList){
 	if (noisy) cout << "Parsing " << theCommand << endl;
-	string restOfParagraph = getStringTilEndOfParagraph(startInd, doxygenString);
-	if(!restOfParagraph.empty()){
-		int placement = 0;
-		list <DoxygenEntity> aNewList;
-		aNewList =  parse(placement, restOfParagraph);
-		doxyList.push_back( DoxygenEntity(theCommand, aNewList));
-		return 1;
-		}
-	else cout << "No line followed " << theCommand <<  " command. Not added" << endl;
-	return 0;
+	list<Token>::iterator endOfParagraph = getEndOfParagraph(tokList);
+	//if(!restOfParagraph.empty()){
+	list <DoxygenEntity> aNewList;
+	aNewList =  parse(endOfParagraph, tokList);
+	doxyList.push_back( DoxygenEntity(theCommand, aNewList));
+	return 1;
+	//	}
+	//else cout << "No line followed " << theCommand <<  " command. Not added" << endl;
  }
   /* CommandParagraph
    * Format: @command {paragraph}
    * Commands with a single LINE after then such as @var
    * 
    */
-  int ignoreCommandParagraph(string theCommand, int &startInd, list <DoxygenEntity> &doxyList, string doxygenString){
+  int ignoreCommandParagraph(string theCommand, TokenList &tokList, list <DoxygenEntity> &doxyList){
 	if (noisy) cout << "Not Adding " << theCommand << endl;
-	string restOfParagraph = getStringTilEndOfParagraph(startInd, doxygenString);
-	if(!restOfParagraph.empty()){
-		return 1;
-		}
-	else cout << "WARNING: No line followed " << theCommand <<  " command." << endl;
-	return 0;
+	list<Token>::iterator endOfParagraph = getEndOfParagraph(tokList);
+	tokList.setIterator(endOfParagraph);
+	//else cout << "WARNING: No line followed " << theCommand <<  " command." << endl;
+	return 1;
  }
   /* Command EndCommand
    * Format: @command and ends at @endcommand
@@ -936,10 +482,11 @@ string getStringTilCommand(int &startInd, string doxygenString){
    * Returns 1 if success, 0 if the endcommand is never encountered.
    */
   
-  int ignoreCommandEndCommand(string theCommand, int &startInd, list <DoxygenEntity> &doxyList, string doxygenString){
+  int addCommandEndCommand(string theCommand, TokenList &tokList, list <DoxygenEntity> &doxyList){
 	  if (noisy) cout << "Not Adding " << theCommand << endl;
-	  return progressTilEndCommand( "end" + theCommand, startInd, doxygenString);
-	  
+	  string description = getStringTilEndCommand( "end" + theCommand, tokList);
+	  doxyList.push_back(DoxygenEntity(theCommand, description));
+	  return 1;
   }
   
   /* CommandWordParagraph
@@ -947,23 +494,19 @@ string getStringTilCommand(int &startInd, string doxygenString){
    * Commands such as param
    * "param", "tparam", "throw", "retval", "exception"
    */
-  int addCommandWordParagraph(string theCommand, int &startInd, list <DoxygenEntity> &doxyList, string doxygenString){
+  int addCommandWordParagraph(string theCommand, TokenList &tokList, list <DoxygenEntity> &doxyList){
 	if (noisy) cout << "Parsing " << theCommand << endl;
-	string name = getNextWord(startInd, doxygenString);
+	string name = getNextWord(tokList);
 	if (name.empty()){ 
 		cout << "No word followed " << theCommand <<  " command. Not added" << endl;
 		return 0;
 		}
-	string restOfParagraph = getStringTilEndOfParagraph(startInd, doxygenString);
-	int placement = 0;
-	if(!restOfParagraph.empty()){
+	  list<Token>::iterator endOfParagraph = getEndOfParagraph(tokList);
+	    //if(!restOfParagraph.empty()){
 		list <DoxygenEntity> aNewList;
-		aNewList =  parse(placement, restOfParagraph);
+		aNewList =  parse(endOfParagraph, tokList);
 		aNewList.push_front(DoxygenEntity("plainstring", name));
 		doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-		return 1;
-		}
-	else cout << "No paragraph followed " << theCommand <<  " command. Not added" << endl;
 	return 0;
   }
   /* CommandWordLine
@@ -971,40 +514,37 @@ string getStringTilCommand(int &startInd, string doxygenString){
    * Commands such as param
    * "page", "subsection", "subsubsection", "section", "paragraph", "defgroup"
    */
-  int addCommandWordLine(string theCommand, int &startInd, list <DoxygenEntity> &doxyList, string doxygenString){
+  int addCommandWordLine(string theCommand, TokenList &tokList, list <DoxygenEntity> &doxyList){
 	if (noisy) cout << "Parsing " << theCommand << endl;
-	string name = getNextWord(startInd, doxygenString);
+	string name = getNextWord(tokList);
 	if (name.empty()){ 
 		cout << "No word followed " << theCommand <<  " command. Not added" << endl;
 		return 0;
 		}
-	string restOfLine = getStringTilEndOfParagraph(startInd, doxygenString);
-	int placement = 0;
-	if(!restOfLine.empty()){
-		list <DoxygenEntity> aNewList;
-		aNewList =  parse(placement, restOfLine);
-		aNewList.push_front(DoxygenEntity("plainstring", name));
-		doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-		return 1;
-		}
-	else cout << "No line followed " << theCommand <<  " command. Not added" << endl;
-	return 0;
+	list<Token>::iterator endOfLine = getOneLine(tokList);
+	list <DoxygenEntity> aNewList;
+	aNewList =  parse(endOfLine, tokList);
+	aNewList.push_front(DoxygenEntity("plainstring", name));
+	doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+	return 1;
+		
+	//else cout << "No line followed " << theCommand <<  " command. Not added" << endl;
   }
-  
+
   /* Command Word Optional Word Optional Word
    * Format: @command <word> [<header-file>] [<header-name>]
    * Commands such as class
    * "category", "class", "protocol", "interface", "struct", "union"
    */
-  int addCommandWordOWordOWord(string theCommand, int &startInd, list <DoxygenEntity> &doxyList, string doxygenString){
+  int addCommandWordOWordOWord(string theCommand, TokenList &tokList, list <DoxygenEntity> &doxyList){
 	if (noisy) cout << "Parsing " << theCommand << endl;
-	string name = getNextWord(startInd, doxygenString);
+	string name = getNextWord(tokList);
 	if (name.empty()){ 
 			cout << "No word followed " << theCommand <<  " command. Not added" << endl;
 			return 0;
 			}
-	string headerfile = getNextWord(startInd, doxygenString);
-	string headername = getNextWord(startInd, doxygenString);
+	string headerfile = getNextWord(tokList);
+	string headername = getNextWord(tokList);
 	list <DoxygenEntity> aNewList;
 	aNewList.push_back(DoxygenEntity("plainstring", name));
 	if (!headerfile.empty()) aNewList.push_back(DoxygenEntity("plainstring", headerfile));
@@ -1018,12 +558,138 @@ string getStringTilCommand(int &startInd, string doxygenString){
    * Commands such as dir
    * "dir", "file", "cond"
    */
-  int addCommandOWord(string theCommand, int &startInd, list <DoxygenEntity> &doxyList, string doxygenString){
+  int addCommandOWord(string theCommand, TokenList &tokList, list <DoxygenEntity> &doxyList){
 	if (noisy) cout << "Parsing " << theCommand << endl;
-	string name = getNextWord(startInd, doxygenString);
+	string name = getNextWord(tokList);
 	doxyList.push_back(DoxygenEntity(theCommand, name));
 	return 1; 
   }
+ 
+  /* Commands that should not be encountered (such as PHP only)
+   */
+  int addCommandErrorThrow(string theCommand, TokenList &tokList, list <DoxygenEntity> &doxyList){
+	  cout << "Encountered :" << theCommand << endl;
+	  cout << "This command should not have been encountered. Behaviour past this may be unpredictable " << endl;
+  }
+ 
+
+  int addCommandUnique(string theCommand, TokenList &tokList, list <DoxygenEntity> &doxyList){
+	  list <DoxygenEntity> aNewList;
+	  if (theCommand.compare("arg") == 0 || theCommand.compare("li") == 0){
+			list<Token>::iterator endOfSection = getEndOfSection(theCommand, tokList);
+			list <DoxygenEntity> aNewList;
+			aNewList =  parse(endOfSection, tokList);
+			doxyList.push_back( DoxygenEntity(theCommand, aNewList));
+	  }
+	  
+	  // \xrefitem <key> "(heading)" "(list title)" {text}
+	  else if (theCommand.compare("xrefitem") == 0){
+		  //TODO Implement xrefitem
+			if (noisy) cout << "Not Adding " << theCommand << endl;
+			list<Token>::iterator endOfParagraph = getEndOfParagraph(tokList);
+			tokList.setIterator(endOfParagraph);
+		  return 1;
+	  }
+	  // \ingroup (<groupname> [<groupname> <groupname>])
+	  else if (theCommand.compare("ingroup") == 0){
+		  string name = getNextWord(tokList);
+		  aNewList.push_back(DoxygenEntity("plainstring", name));
+		  name = getNextWord(tokList);
+		  if(!name.empty()) aNewList.push_back(DoxygenEntity("plainstring", name));
+		  name = getNextWord(tokList);
+		  if(!name.empty()) aNewList.push_back(DoxygenEntity("plainstring", name));
+		  doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+		  return 1;
+	  }
+	  // \par [(paragraph title)] { paragraph }
+	  else if (theCommand.compare("par") == 0){
+		  list<Token>::iterator endOfLine = getOneLine(tokList);
+		  aNewList =  parse(endOfLine, tokList);
+		  list <DoxygenEntity> aNewList2;
+		  aNewList2 = parse(endOfLine, tokList);
+		  aNewList.splice(aNewList.end(), aNewList2);
+		  doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+		  return 1; 
+	  }
+	  // \headerfile <header-file> [<header-name>]
+	  else if (theCommand.compare("headerfile") == 0){
+		  list <DoxygenEntity> aNewList;
+		  string name = getNextWord(tokList);
+		  aNewList.push_back(DoxygenEntity("plainstring", name));
+		  name = getNextWord(tokList);
+		  if(!name.empty()) aNewList.push_back(DoxygenEntity("plainstring", name));
+		  doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+		  return 1;
+	  }
+	  // \overload [(function declaration)]
+	  else if (theCommand.compare("overload") == 0){
+		  list<Token>::iterator endOfLine = getOneLine(tokList);
+		  if (endOfLine != tokList.current()){
+		  list <DoxygenEntity> aNewList;
+		  aNewList =  parse(endOfLine, tokList);
+		  doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+		  }
+		  else doxyList.push_back(DoxygenEntity(theCommand));
+	  }
+	  // \weakgroup <name> [(title)]
+	  else if (theCommand.compare("weakgroup") == 0){
+		    if (noisy) cout << "Parsing " << theCommand << endl;
+			string name = getNextWord(tokList);
+			if (name.empty()){ 
+				cout << "No word followed " << theCommand <<  " command. Not added" << endl;
+				return 0;
+				}
+			list <DoxygenEntity> aNewList;
+			list<Token>::iterator endOfLine = getOneLine(tokList);
+			if (endOfLine != tokList.current()) {
+				aNewList =  parse(endOfLine, tokList);
+			}
+			aNewList.push_front(DoxygenEntity("plainstring", name));
+			doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+	  }
+	  // \ref <name> ["(text)"]
+	  else if (theCommand.compare("ref") == 0){
+		  //TODO Implement ref
+			if (noisy) cout << "Not Adding " << theCommand << endl;
+			list<Token>::iterator endOfParagraph = getEndOfParagraph(tokList);
+			tokList.setIterator(endOfParagraph);
+	  }
+	  // \subpage <name> ["(text)"]
+	  else if (theCommand.compare("subpage") == 0){
+		  //TODO implement subpage
+			if (noisy) cout << "Not Adding " << theCommand << endl;
+			list<Token>::iterator endOfParagraph = getEndOfParagraph(tokList);
+			tokList.setIterator(endOfParagraph);
+	  }
+	  // \dotfile <file> ["caption"]
+	  else if (theCommand.compare("dotfile") == 0){
+		  //TODO implement dotfile
+			if (noisy) cout << "Not Adding " << theCommand << endl;
+			list<Token>::iterator endOfParagraph = getEndOfParagraph(tokList);
+			tokList.setIterator(endOfParagraph);
+	  }
+	  // \image <format> <file> ["caption"] [<sizeindication>=<size>]
+	  else if (theCommand.compare("image") == 0){
+		  //todo implement image
+	  } 
+	  // \addtogroup <name> [(title)]
+	  else if (theCommand.compare("addtogroup") == 0){
+		    if (noisy) cout << "Parsing " << theCommand << endl;
+			string name = getNextWord(tokList);
+			if (name.empty()){ 
+				cout << "No word followed " << theCommand <<  " command. Not added" << endl;
+				return 0;
+				}
+			list <DoxygenEntity> aNewList;
+			list<Token>::iterator endOfLine = getOneLine(tokList);
+			if (endOfLine != tokList.current()) {
+				aNewList =  parse(endOfLine, tokList);
+			}
+			aNewList.push_front(DoxygenEntity("plainstring", name));
+			doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+	  }
+
+  }
   
  /* The actual "meat" of the doxygen parser. This is not yet fully implemented
   * with my current design- however the skeletal outline is contained in
@@ -1031,121 +697,111 @@ string getStringTilCommand(int &startInd, string doxygenString){
   */
 
 
- int addCommand(string commandString, int &startInd, list <DoxygenEntity> &doxyList, string doxygenString){
+ int addCommand(string commandString, TokenList &tokList,list <DoxygenEntity> &doxyList){
 	 string theCommand = StringToLower(commandString);
-	 string voidArray[] = {""};
-	 	/* @command */
-
-	 
+ 
 	 if (theCommand.compare("plainstring") == 0){
-	 		string nextPhrase = getStringTilCommand(startInd, doxygenString);
+	 		string nextPhrase = getStringTilCommand( tokList);
 	 		if (noisy) cout << "Parsing plain string :" << nextPhrase << endl;
 	 		doxyList.push_back(DoxygenEntity("plainstring", nextPhrase ));
 	 		return 1;
 	 }
 	 int commandNumber = commandBelongs(theCommand);
-	 if (commandNumber == 1){
-	 	return addSimpleCommand(theCommand, startInd,doxyList, doxygenString);
+	 if (commandNumber == SIMPLECOMMAND){
+	 	return addSimpleCommand(theCommand, doxyList);
 	 	}
-	 if (commandNumber == 2){
-	 	return ignoreSimpleCommand(theCommand, startInd,doxyList, doxygenString);
+	 if (commandNumber == IGNOREDSIMPLECOMMAND){
+	 	return ignoreSimpleCommand(theCommand, doxyList);
 	 	}
-	 if (commandNumber == 3){
-	 	return addCommandWord(theCommand, startInd,doxyList, doxygenString);
+	 if (commandNumber == COMMANDWORD){
+	 	return addCommandWord(theCommand, tokList, doxyList);
 	 	}
-	 if (commandNumber == 4){
-	 	return ignoreCommandWord(theCommand, startInd,doxyList, doxygenString);
+	 if (commandNumber == IGNOREDCOMMANDWORD){
+	 	return ignoreCommandWord(theCommand, tokList, doxyList);
 	 	}
-	 if (commandNumber == 5){
-	 	return addCommandLine(theCommand, startInd,doxyList, doxygenString);
+	 if (commandNumber == COMMANDLINE ){
+	 	return addCommandLine(theCommand, tokList, doxyList);
 	 	}
-	 if (commandNumber == 6){
-	 	return ignoreCommandLine(theCommand, startInd,doxyList, doxygenString);
+	 if (commandNumber == IGNOREDCOMMANDLINE ){
+	 	return ignoreCommandLine(theCommand, tokList, doxyList);
 	 	}
-	 if (commandNumber == 7){
-	 	return addCommandParagraph(theCommand, startInd,doxyList, doxygenString);
+	 if (commandNumber == COMMANDPARAGRAPH){
+	 	return addCommandParagraph(theCommand, tokList, doxyList);
 	 	}
-	 if (commandNumber == 8){
-	 	return ignoreCommandParagraph(theCommand, startInd,doxyList, doxygenString);
+	 if (commandNumber == IGNORECOMMANDPARAGRAPH){
+	 	return ignoreCommandParagraph(theCommand, tokList, doxyList);
 	 	}
-	 if (commandNumber == 9){
-	 	return ignoreCommandEndCommand(theCommand, startInd,doxyList, doxygenString);
+	 if (commandNumber == COMMANDENDCOMMAND){
+	 	return addCommandEndCommand(theCommand, tokList, doxyList);
 	 	}
-	 if (commandNumber == 10){
-	 	return addCommandWordParagraph(theCommand, startInd,doxyList, doxygenString);
+	 if (commandNumber == COMMANDWORDPARAGRAPH){
+	 	return addCommandWordParagraph(theCommand, tokList, doxyList);
 	 	}
-	 if (commandNumber == 11){
-	 	return addCommandWordLine(theCommand, startInd,doxyList, doxygenString);
+	 if (commandNumber == COMMANDWORDLINE){
+	 	return addCommandWordLine(theCommand, tokList, doxyList);
 	 	}
-	 if (commandNumber == 12){
-	 	return addCommandWordOWordOWord(theCommand, startInd,doxyList, doxygenString);
+	 if (commandNumber == COMMANDWORDOWORDWORD){
+	 	return addCommandWordOWordOWord(theCommand, tokList, doxyList);
 	 	}
-	 if (commandNumber == 13){
-	 	return addCommandOWord(theCommand, startInd,doxyList, doxygenString);
+	 if (commandNumber == COMMANDOWORD){
+	 	return addCommandOWord(theCommand, tokList, doxyList);
 	 	}
-	 if (commandNumber == 14){
-	 	return 0;
+	 if (commandNumber == COMMANDERRORTHROW){
+	 	return addCommandErrorThrow(theCommand, tokList, doxyList);
 	 	}
-	 if (commandNumber == 15){
-	 	return 0;
+	 if (commandNumber == COMMANDUNIQUE){
+		return addCommandUnique(theCommand, tokList, doxyList);
 	 	}
 	 	
 	 	return 0;
  }
  
- int weirdTest(){
-	 string doxygenString = "this is a test.";
-	 string restOfParagraph;
-	 int startIndex = 0;
-	 restOfParagraph = getStringTilEndOfParagraph(startIndex , doxygenString);
-	 cout << restOfParagraph<< " " << startIndex << endl;
-	 
-	 startIndex = 0;
-	 restOfParagraph = getStringTilCommand(startIndex, doxygenString);
-	 cout << restOfParagraph<< " " << startIndex << endl;
- }
-
+ list<DoxygenEntity> parse(list<Token>::iterator endParsingIndex, TokenList &tokList){
+ 	list <DoxygenEntity> aNewList;
+ 	int currCommand;
+ 	while (tokList.current() != endParsingIndex){ 
+ 		Token currToken = tokList.peek();
+ 		if(noisy) cout << "Parsing for phrase starting in:" << currToken.toString() << endl;
+ 		if(currToken.tokenType == END_LINE ){
+ 			tokList.next();
+ 		}
+ 		else if(currToken.tokenType == COMMAND){
+ 			currCommand = findCommand(currToken.tokenString);
+ 			tokList.next();
+ 			if (currCommand < 0 ){ if(noisy) cout << "BAD COMMAND: " << currToken.tokenString << endl;}
+ 				//cout << "Command: " << currWord << " " << currCommand << endl;
  
+ 			else addCommand(currToken.tokenString, tokList,  aNewList);
+ 		}
+ 		else if (currToken.tokenType == PLAINSTRING){
+ 			addCommand(string("plainstring"), tokList, aNewList);
+ 		}
 
- int doRunExamples(){
-	 string line;
-	 string filename;
-	 string exampleNames[] = {"Examples/Example1","Examples/Example2", "Examples/Example3", "Examples/Example4", "Examples/Example5"};
-	 int placement;
-	 string doxygenString;
-	 ifstream doxCommentFile;
-	 for (int i = 0; i < 5; i++){
-	   doxCommentFile.open(exampleNames[i].c_str());
-	   doxCommentFile >> doxygenString;
-	   while(getline(doxCommentFile, line)){
-	   doxygenString += line + "\n";}
-	   doxCommentFile.close();
-	   placement = 0;
-	   cout << "---RAW CODE---" << endl << doxygenString << endl<<endl;
-	   clearFluff(placement, doxygenString);
-	   rootList = parse(placement, doxygenString);
-
-	   cout << "---THE TREE---" << endl;
-	   printTree();
-	 }
-	return 1; 
- }
- 
- 
- /* Returns a parse tree for a string */
- int main(int argc, char *argv[]){
-	//weirdTest();
- 	if(testCodeCrawlingFunctions) testCCF();
- 	if(runExamples) doRunExamples();
- 	if (demonstrateParsing){
- 		string doxygenString = "//! A normal member taking two arguments and returning an integer value.\n/*!\n \\param a an integer argument. \\param s a constant character pointer\n \\return The test results\n  \\sa Test(), ~Test(), testMeToo() and publicVar()\n */";
- 		//string doxygenString = " /** This is a small sentence.\n *\n@param x this is a parameter. \n \n This is a line with a @b bold letter \n * \n  @brief small @b description. \n\n * **/";
- 		//string doxygenString = "This is a description.";
- 		int placement = 0;
- 		clearFluff(placement, doxygenString);
- 		rootList = parse(placement, doxygenString);
- 		cout << "---THE TREE---" << endl;
- 		printTree();
+ 		
  	}
- 	return 1;
+
+ 	return aNewList;
  }
+
+list<DoxygenEntity> convert(string doxygenBlob){
+ 	TokenList tokList = TokenList(doxygenBlob);
+ 	if(noisy) {
+ 		cout << "---TOKEN LIST---" << endl;
+ 		tokList.printList();
+ 	}
+ 	list <DoxygenEntity> rootList;
+ 	rootList = parse( tokList.end(), tokList);
+ 	cout << "PARSED LIST" << endl;
+ 	printTree(rootList);
+ 	return rootList;
+ }
+
+int main(int argc, char *argv[]){
+	string doxygenString1 = "//! A normal member taking two arguments and returning an integer value.\n/*!\n \\param a an \\b integer argument. \\param s a constant character pointer\n\n\n\n \\return The test results\n  \\sa Test(), ~Test(), testMeToo() and publicVar()\n */";
+	list <DoxygenEntity> rootList = convert(doxygenString1);
+    JavaDocConverter jDC = JavaDocConverter();
+    jDC.convertToJavaDoc(rootList);
+	return 1;
+}
+
+
diff --git a/Source/DoxygenTranslator/JavaDocConverter.cpp b/Source/DoxygenTranslator/JavaDocConverter.cpp
new file mode 100644
index 000000000..4e6fd93e6
--- /dev/null
+++ b/Source/DoxygenTranslator/JavaDocConverter.cpp
@@ -0,0 +1,104 @@
+#include "JavaDocConverter.h"
+#include <cstdlib>
+#include <iostream>
+#include <string>
+#include <list>
+
+int printTree = 1;
+JavaDocConverter::JavaDocConverter()
+{
+}
+
+JavaDocConverter::~JavaDocConverter()
+{
+}
+
+/* Sorts entities by javaDoc standard order for commands
+ * NOTE: will not behave entirely properly until "First level" comments
+ * such as brief descriptions are TAGGED as such
+ */
+bool compare_DoxygenEntities(DoxygenEntity first, DoxygenEntity second){
+	if(first.typeOfEntity.compare("plainstring") == 0) return true;
+	if(second.typeOfEntity.compare("plainstring") == 0) return false;
+	if(first.typeOfEntity.compare("param") == 0){
+		if(second.typeOfEntity.compare("param")== 0) return true;
+		if(second.typeOfEntity.compare("return")== 0) return true;
+		if(second.typeOfEntity.compare("exception")== 0) return true;
+		if(second.typeOfEntity.compare("author")== 0) return true;
+		if(second.typeOfEntity.compare("version")== 0)return true;
+		if(second.typeOfEntity.compare("see")== 0)return true;
+		if(second.typeOfEntity.compare("since")== 0)return true;
+		if(second.typeOfEntity.compare("deprecated")== 0)return true;
+		return false;
+	}
+	if(first.typeOfEntity.compare("return")== 0){
+		if(second.typeOfEntity.compare("return")== 0) return true;
+		if(second.typeOfEntity.compare("exception")== 0) return true;
+		if(second.typeOfEntity.compare("author")== 0) return true;
+		if(second.typeOfEntity.compare("version")== 0)return true;
+		if(second.typeOfEntity.compare("see")== 0)return true;
+		if(second.typeOfEntity.compare("since")== 0)return true;
+		if(second.typeOfEntity.compare("deprecated")== 0)return true;
+		return false;
+		
+	}
+	if(first.typeOfEntity.compare("exception")== 0){
+		if(second.typeOfEntity.compare("exception")== 0) return true;
+		if(second.typeOfEntity.compare("author")== 0) return true;
+		if(second.typeOfEntity.compare("version")== 0)return true;
+		if(second.typeOfEntity.compare("see")== 0)return true;
+		if(second.typeOfEntity.compare("since")== 0)return true;
+		if(second.typeOfEntity.compare("deprecated")== 0)return true;
+		return false;
+	}
+	if(first.typeOfEntity.compare("author")== 0){
+		if(first.typeOfEntity.compare("author")== 0) return true;
+		if(first.typeOfEntity.compare("version")== 0)return true;
+		if(first.typeOfEntity.compare("see")== 0)return true;
+		if(first.typeOfEntity.compare("since")== 0)return true;
+		if(first.typeOfEntity.compare("deprecated")== 0)return true;
+		return false;
+	}
+	if(first.typeOfEntity.compare("version")== 0){
+		if(second.typeOfEntity.compare("version")== 0)return true;
+		if(second.typeOfEntity.compare("see")== 0)return true;
+		if(second.typeOfEntity.compare("since")== 0)return true;
+		if(second.typeOfEntity.compare("deprecated")== 0)return true;
+		return false;
+	}
+	if(first.typeOfEntity.compare("see")== 0){
+		if(second.typeOfEntity.compare("see")== 0)return true;
+		if(second.typeOfEntity.compare("since")== 0)return true;
+		if(second.typeOfEntity.compare("deprecated")== 0)return true;
+		return false;
+	}
+	if(first.typeOfEntity.compare("since")== 0){
+		if(second.typeOfEntity.compare("since")== 0) return true;
+		if(second.typeOfEntity.compare("deprecated")== 0)return true;
+		return false;
+	}
+	if(first.typeOfEntity.compare("deprecated")== 0){
+		if(second.typeOfEntity.compare("deprecated")== 0)return true;
+		return false;
+	}
+	return true;
+}
+
+string JavaDocConverter:: convertToJavaDoc(list <DoxygenEntity> entityList){
+	
+	list<DoxygenEntity>::iterator entityIterator = entityList.begin();
+	entityList.sort(compare_DoxygenEntities);
+
+	cout << "---RESORTED LIST---" << endl;
+	if (printTree ){
+		list<DoxygenEntity>::iterator p = entityList.begin();
+		while (p != entityList.end()){
+			(*p).printEntity(0);
+			p++;
+		}
+	}
+	string javaDocString = "/**\n";
+	
+	javaDocString += "*/\n";
+	return javaDocString;
+}
diff --git a/Source/DoxygenTranslator/JavaDocConverter.h b/Source/DoxygenTranslator/JavaDocConverter.h
new file mode 100644
index 000000000..b1c76ef17
--- /dev/null
+++ b/Source/DoxygenTranslator/JavaDocConverter.h
@@ -0,0 +1,17 @@
+ #include <list>
+ #include <string>
+ #include "DoxygenEntity.h"
+
+#ifndef JAVADOCCONVERTER_H_
+#define JAVADOCCONVERTER_H_
+
+class JavaDocConverter
+{
+public:
+
+	JavaDocConverter();
+	string convertToJavaDoc(list <DoxygenEntity> entityList);
+	~JavaDocConverter();
+};
+
+#endif /*JAVADOCCONVERTER_H_*/
diff --git a/Source/DoxygenTranslator/Token.h b/Source/DoxygenTranslator/Token.h
index d569f5f7b..e98686c14 100644
--- a/Source/DoxygenTranslator/Token.h
+++ b/Source/DoxygenTranslator/Token.h
@@ -13,8 +13,8 @@ class Token
 public:
 	Token(int tType, string tString);
 	~Token();
-	int tokenType;
-	string tokenString;
+	int tokenType; /* currently can be END_LINE, PLAINSTRING, or COMMAND */
+	string tokenString; /* the data , such as param for @param*/
 	string toString();
 };
 
diff --git a/Source/DoxygenTranslator/TokenList.cpp b/Source/DoxygenTranslator/TokenList.cpp
index 6122328c4..0ace41c34 100644
--- a/Source/DoxygenTranslator/TokenList.cpp
+++ b/Source/DoxygenTranslator/TokenList.cpp
@@ -67,11 +67,8 @@ TokenList::TokenList(string doxygenString){
 }
 
 Token TokenList::peek(){
-	list<Token>::iterator p = tokenList.begin();
-	if(p != tokenList.end()){
-		p++;
-		Token returnedToken = (*p);
-		p--;
+	if(tokenListIterator!= tokenList.end()){
+		Token returnedToken = (*tokenListIterator);
 		return returnedToken;
 	}
 	else
@@ -79,15 +76,22 @@ Token TokenList::peek(){
 } 
 
 Token TokenList::next(){
-	list<Token>::iterator p = tokenList.begin();
-	if(p != tokenList.end()){
-		p++;
-		return (*p);
+	if(tokenListIterator != tokenList.end()){
+		Token returnedToken = (*tokenListIterator);
+		tokenListIterator++;
+		return (returnedToken);
 	}
 	else
 		return Token(0, "");
 } 	
 
+list<Token>::iterator TokenList::end(){
+	return tokenList.end();
+}
+
+list<Token>::iterator TokenList::current(){
+	return tokenListIterator;
+}
 void TokenList::printList(){
 	list<Token>::iterator p = tokenList.begin();
 			int i = 1;
@@ -100,4 +104,11 @@ void TokenList::printList(){
 			}
 }
 
-TokenList::	~TokenList(){}
\ No newline at end of file
+list<Token>::iterator  TokenList::iteratorCopy(){
+	list<Token>::iterator p = tokenListIterator;
+	return p;
+}
+void TokenList::setIterator(list<Token>::iterator newPosition){
+	tokenListIterator = newPosition;
+}
+TokenList::	~TokenList(){}
diff --git a/Source/DoxygenTranslator/TokenList.h b/Source/DoxygenTranslator/TokenList.h
index 153c69163..cc61f56e4 100644
--- a/Source/DoxygenTranslator/TokenList.h
+++ b/Source/DoxygenTranslator/TokenList.h
@@ -13,12 +13,15 @@ using namespace std;
 
 class TokenList{
 public:
-	/* constructor takes a blob of Doxygen comment */
-	TokenList(string doxygenString);
+	TokenList(string doxygenString); /* constructor takes a blob of Doxygen comment */
 	~TokenList();
 	Token peek(); 	/* returns next token without advancing */
 	Token next(); 	/* returns next token and advances */
+	list<Token>::iterator end(); /* returns an end iterator */
+	list<Token>::iterator current(); /* returns the current iterator */
 	void printList(); /* prints out the sequence of tokens */
+	list<Token>::iterator  iteratorCopy(); /* returns a copy of the current iterator */
+	void setIterator(list<Token>::iterator  newPosition); /*moves up the iterator*/
 };
 
 #endif /*TOKENLIST_H_*/

From 86b62e146bba6606fe39240faae3b7b15cd45d81 Mon Sep 17 00:00:00 2001
From: Cheryl Foil <cheryl.foil@gmail.com>
Date: Sun, 20 Jul 2008 05:20:17 +0000
Subject: [PATCH 007/314] javDocConvertor now functional for some simple
 commands such as author, param, returns, and b. Commands with a specific
 javaDoc order are sorted appropriately.

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2008-cherylfoil@10686 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 .../DoxygenTranslator/DoxygenTranslator.cpp   |  13 +-
 Source/DoxygenTranslator/JavaDocConverter.cpp | 140 +++++++++++++++---
 Source/DoxygenTranslator/JavaDocConverter.h   |   1 +
 3 files changed, 132 insertions(+), 22 deletions(-)

diff --git a/Source/DoxygenTranslator/DoxygenTranslator.cpp b/Source/DoxygenTranslator/DoxygenTranslator.cpp
index d6129cda0..96fe6b2c5 100644
--- a/Source/DoxygenTranslator/DoxygenTranslator.cpp
+++ b/Source/DoxygenTranslator/DoxygenTranslator.cpp
@@ -69,7 +69,7 @@
  		"sa", "section", "see", "showinitializer", "since", "skip", "skipline", "struct", "subpage",
  		"subsection", "subsubsection", "test", "throw", "todo", "tparam", "typedef", "union", "until",
  		"var", "verbatim", "verbinclude", "version", "warning", "weakgroup", "xmlonly", "xrefitem",
- 		"$", "@", "//","&", "~", "<", ">", "#", "%"};
+ 		"$", "@", "\\","&", "~", "<", ">", "#", "%"};
 
 
  string sectionIndicators[] = { "attention", "author", "brief", "bug", "cond", "date", "deprecated", "details",
@@ -78,7 +78,7 @@
  		"version", "warning", "xrefitem" };
 
  /* All of the doxygen commands divided up by how they are parsed */
- string simpleCommands[] = {"n", "$", "@", "//", "&", "~", "<", ">", "#", "%"};
+ string simpleCommands[] = {"n", "$", "@", "\\", "&", "~", "<", ">", "#", "%"};
  string ignoredSimpleCommands[] = {"nothing at the moment"};
  string commandWords[] = {"a", "b", "c", "e", "em", "p", "def", "enum", "example", "package", 
  		"relates", "namespace", "relatesalso","anchor", "dontinclude", "include", "includelineno"};
@@ -791,13 +791,16 @@ list<DoxygenEntity> convert(string doxygenBlob){
  	}
  	list <DoxygenEntity> rootList;
  	rootList = parse( tokList.end(), tokList);
- 	cout << "PARSED LIST" << endl;
- 	printTree(rootList);
+ 	if(noisy) {
+ 		cout << "PARSED LIST" << endl;
+ 		printTree(rootList);
+ 	}
  	return rootList;
  }
 
 int main(int argc, char *argv[]){
-	string doxygenString1 = "//! A normal member taking two arguments and returning an integer value.\n/*!\n \\param a an \\b integer argument. \\param s a constant character pointer\n\n\n\n \\return The test results\n  \\sa Test(), ~Test(), testMeToo() and publicVar()\n */";
+	string doxygenString1 = "//! A normal member taking two arguments and returning an integer value. This is a very long description for the simple purpose of showing off formatting. Let's make it a bit longer just to be sure. \n/*!\n \\param a an \\b integer argument.\n \\return The test results\n \\param s a constant character pointer. Let's also make this a very long description! \n \\bug this command should, for now, be totally ignored\n \\author cheryl foil\n \\sa Test(), ~Test(), testMeToo() and publicVar()\n */";
+	cout << "---ORIGINAL DOXYGEN--- " << endl << doxygenString1 << endl;
 	list <DoxygenEntity> rootList = convert(doxygenString1);
     JavaDocConverter jDC = JavaDocConverter();
     jDC.convertToJavaDoc(rootList);
diff --git a/Source/DoxygenTranslator/JavaDocConverter.cpp b/Source/DoxygenTranslator/JavaDocConverter.cpp
index 4e6fd93e6..91f52662f 100644
--- a/Source/DoxygenTranslator/JavaDocConverter.cpp
+++ b/Source/DoxygenTranslator/JavaDocConverter.cpp
@@ -3,8 +3,10 @@
 #include <iostream>
 #include <string>
 #include <list>
-
-int printTree = 1;
+#define APPROX_LINE_LENGTH 64//characters per line allowed
+#define TAB_SIZE 8//characters per line allowed
+int printSortedTree2 = 0;
+//TODO {@link} {@linkplain} {@docRoot}, and other useful doxy commands that are not a javadoc tag
 JavaDocConverter::JavaDocConverter()
 {
 }
@@ -40,7 +42,7 @@ bool compare_DoxygenEntities(DoxygenEntity first, DoxygenEntity second){
 		if(second.typeOfEntity.compare("since")== 0)return true;
 		if(second.typeOfEntity.compare("deprecated")== 0)return true;
 		return false;
-		
+
 	}
 	if(first.typeOfEntity.compare("exception")== 0){
 		if(second.typeOfEntity.compare("exception")== 0) return true;
@@ -66,8 +68,9 @@ bool compare_DoxygenEntities(DoxygenEntity first, DoxygenEntity second){
 		if(second.typeOfEntity.compare("deprecated")== 0)return true;
 		return false;
 	}
-	if(first.typeOfEntity.compare("see")== 0){
+	if(first.typeOfEntity.compare("see")== 0 || first.typeOfEntity.compare("sa")== 0){
 		if(second.typeOfEntity.compare("see")== 0)return true;
+		if(second.typeOfEntity.compare("sa")== 0)return true;
 		if(second.typeOfEntity.compare("since")== 0)return true;
 		if(second.typeOfEntity.compare("deprecated")== 0)return true;
 		return false;
@@ -84,21 +87,124 @@ bool compare_DoxygenEntities(DoxygenEntity first, DoxygenEntity second){
 	return true;
 }
 
-string JavaDocConverter:: convertToJavaDoc(list <DoxygenEntity> entityList){
-	
-	list<DoxygenEntity>::iterator entityIterator = entityList.begin();
-	entityList.sort(compare_DoxygenEntities);
+void JavaDocConverter::printSortedTree(list <DoxygenEntity> &entityList){
+	list<DoxygenEntity>::iterator p = entityList.begin();
+	while (p != entityList.end()){
+		(*p).printEntity(0);
+		p++;
+	}
+}
+string formatCommand(string unformattedLine, int indent){
+	string formattedLines = "\n * ";
+	int lastPosition = 0;
+	int i = 0;
+	int isFirstLine  = 1;
+	while (i != -1 && i < unformattedLine.length()){
+		lastPosition = i;
+		if (isFirstLine){
+			i+=APPROX_LINE_LENGTH;
+		}
+		else i+=APPROX_LINE_LENGTH - indent*TAB_SIZE;
+		i = unformattedLine.find(" ", i);
 
-	cout << "---RESORTED LIST---" << endl;
-	if (printTree ){
-		list<DoxygenEntity>::iterator p = entityList.begin();
-		while (p != entityList.end()){
-			(*p).printEntity(0);
+		if (i > 0 && i + 1 < unformattedLine.length()){
+			if (!isFirstLine) for (int j = 0; j < indent; j++) {
+				formattedLines.append("\t");
+				}
+			else {
+				isFirstLine = 0;
+			}
+			formattedLines.append(unformattedLine.substr(lastPosition, i - lastPosition + 1));
+			formattedLines.append("\n *");
+
+		}
+	}
+	if (lastPosition < unformattedLine.length()){
+		if (!isFirstLine) {for (int j = 0; j < indent; j++) {formattedLines.append("\t");}}
+		formattedLines.append(unformattedLine.substr(lastPosition, unformattedLine.length() - lastPosition));
+	}
+
+	return formattedLines;
+}
+
+/* Contains the conversions for tags
+ * could probably be much more efficient...
+ */
+string javaDocFormat(DoxygenEntity &doxygenEntity){
+	if (doxygenEntity.typeOfEntity.compare("plainstring") == 0){
+			return doxygenEntity.data;
+	}
+	else if (doxygenEntity.typeOfEntity.compare("brief") == 0){
+			return doxygenEntity.data;
+	}
+	if (doxygenEntity.typeOfEntity.compare("detailed") == 0){
+			return doxygenEntity.data;
+	}
+	else if (doxygenEntity.typeOfEntity.compare("b") == 0){
+		return "<b>" + doxygenEntity.data + "</b>";
+	}
+	else if (doxygenEntity.typeOfEntity.compare("c") == 0){
+		return "<tt>" + doxygenEntity.data + "</tt>";
+	}
+	return "";
+}
+
+
+string translateSubtree( DoxygenEntity &doxygenEntity){
+	string returnedString;
+	if (doxygenEntity.isLeaf){ return javaDocFormat(doxygenEntity) + " ";}
+	else {
+		returnedString += javaDocFormat(doxygenEntity);
+		list<DoxygenEntity>::iterator p = doxygenEntity.entityList.begin();
+		while (p != doxygenEntity.entityList.end()){
+			returnedString+= translateSubtree(*p);
 			p++;
 		}
 	}
-	string javaDocString = "/**\n";
-	
-	javaDocString += "*/\n";
-	return javaDocString;
+	return returnedString;
 }
+
+string translateEntity(DoxygenEntity &doxyEntity){
+	if(doxyEntity.typeOfEntity.compare("plainstring")== 0 || doxyEntity.typeOfEntity.compare("deprecated")== 0 || doxyEntity.typeOfEntity.compare("brief")== 0)
+		return formatCommand(doxyEntity.data, 0) + "\n * ";
+	else if(doxyEntity.typeOfEntity.compare("see") == 0){
+		return formatCommand(string("@" + doxyEntity.typeOfEntity + "\t\t" + translateSubtree(doxyEntity)), 2);
+	}
+	else if(doxyEntity.typeOfEntity.compare("return")== 0
+			|| doxyEntity.typeOfEntity.compare("author")== 0
+			|| doxyEntity.typeOfEntity.compare("param")== 0
+			|| doxyEntity.typeOfEntity.compare("since")== 0
+			|| doxyEntity.typeOfEntity.compare("version")== 0
+			|| doxyEntity.typeOfEntity.compare("exception") == 0
+			|| doxyEntity.typeOfEntity.compare("deprecated") == 0){
+		return formatCommand(string("@" + doxyEntity.typeOfEntity + "\t" + translateSubtree(doxyEntity)), 2);
+	}
+	else if(doxyEntity.typeOfEntity.compare("sa")== 0){
+		return formatCommand(string("@see\t\t" + translateSubtree(doxyEntity)), 2);
+	}
+
+	return "";
+}
+
+string JavaDocConverter:: convertToJavaDoc(list <DoxygenEntity> entityList){
+
+
+	entityList.sort(compare_DoxygenEntities);
+    if(printSortedTree2){
+	cout << "---RESORTED LIST---" << endl;
+    printSortedTree(entityList);
+    }
+
+	string javaDocString = "/**";
+
+	list<DoxygenEntity>::iterator entityIterator = entityList.begin();
+	while (entityIterator != entityList.end()){
+		javaDocString += translateEntity(*entityIterator);
+		entityIterator++;
+	}
+
+	javaDocString += "\n */\n";
+	cout << "\n---RESULT IN JAVADOC---" << endl;
+	cout << javaDocString;
+	return javaDocString;
+}
\ No newline at end of file
diff --git a/Source/DoxygenTranslator/JavaDocConverter.h b/Source/DoxygenTranslator/JavaDocConverter.h
index b1c76ef17..81122bc5f 100644
--- a/Source/DoxygenTranslator/JavaDocConverter.h
+++ b/Source/DoxygenTranslator/JavaDocConverter.h
@@ -12,6 +12,7 @@ public:
 	JavaDocConverter();
 	string convertToJavaDoc(list <DoxygenEntity> entityList);
 	~JavaDocConverter();
+	void printSortedTree(list <DoxygenEntity> &entityList);
 };
 
 #endif /*JAVADOCCONVERTER_H_*/

From 32beba3cab2943988aad8642d4569a45a761e5ef Mon Sep 17 00:00:00 2001
From: Cheryl Foil <cheryl.foil@gmail.com>
Date: Fri, 25 Jul 2008 06:15:32 +0000
Subject: [PATCH 008/314] Modifications to pick up Doxygen Comments and "post
 doxygen comments" and place them with appropriate attachments in the parse
 tree. Also  a prototype for how to deal with comments describing structures
 marked with tags such as \class

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2008-cherylfoil@10710 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Source/CParse/cscanner.c | 38 +++++++++-------
 Source/CParse/parser.y   | 94 ++++++++++++++++++++++++++++++++++------
 2 files changed, 104 insertions(+), 28 deletions(-)

diff --git a/Source/CParse/cscanner.c b/Source/CParse/cscanner.c
index 140b7fedd..ff7d5343c 100644
--- a/Source/CParse/cscanner.c
+++ b/Source/CParse/cscanner.c
@@ -420,21 +420,29 @@ int yylook(void) {
       return HBLOCK;
       
     case SWIG_TOKEN_COMMENT:
-      {
-	String *cmt = Scanner_text(scan);
-	char *loc = Char(cmt);
-	if ((strncmp(loc,"/*@SWIG@",6) == 0) && (loc[Len(cmt)-3] == '@')) {
-	  scanner_locator(cmt);
-	}
-	
-	if (strncmp(loc, "/**", 3) == 0 || strncmp(loc, "///", 3) == 0||strncmp(loc, "/*!", 3) == 0||strncmp(loc, "//!", 3) == 0) {
-	  printf("Doxygen Comment: %s lines %d-%d [%s]\n", Char(Scanner_file(scan)), Scanner_start_line(scan), Scanner_line(scan), loc);
-	  yylval.str =  NewString(loc);
-	  return DOXYGENSTRING;
-	}
-
-
-      }
+    {
+      String *cmt = Scanner_text(scan);
+	  char *loc = Char(cmt);
+	  if ((strncmp(loc,"/*@SWIG@",6) == 0) && (loc[Len(cmt)-3] == '@')) {
+	    scanner_locator(cmt);
+	  }
+	  if (strncmp(loc, "/**<", 4) == 0 || strncmp(loc, "///<", 3) == 0||strncmp(loc, "/*!<", 3) == 0||strncmp(loc, "//!<", 3) == 0) {
+	    printf("Doxygen Post Comment: %s lines %d-%d [%s]\n", Char(Scanner_file(scan)), Scanner_start_line(scan), Scanner_line(scan), loc);
+	    yylval.str =  NewString(loc);
+	    return DOXYGENPOSTSTRING;
+	  }
+	  if (strncmp(loc, "/**", 3) == 0 || strncmp(loc, "///", 3) == 0||strncmp(loc, "/*!", 3) == 0||strncmp(loc, "//!", 3) == 0) {
+	    printf("Doxygen Comment: %s lines %d-%d [%s]\n", Char(Scanner_file(scan)), Scanner_start_line(scan), Scanner_line(scan), loc);
+	    yylval.str =  NewString(loc);
+	    return DOXYGENSTRING;
+	  }
+	  /*DOES NOT WORK PROPERLY AT THE MINUTE
+	  if (strncmp(loc, "//", 2)== 0) {
+	    printf("C style Comment: %s lines %d-%d [%s]\n", Char(Scanner_file(scan)), Scanner_start_line(scan), Scanner_line(scan), loc);
+	    yylval.str =  NewString(loc);
+	    return C_COMMENT_STRING;
+	  }*/
+    }
       break;
     case SWIG_TOKEN_ENDLINE:
       break;
diff --git a/Source/CParse/parser.y b/Source/CParse/parser.y
index 6a835c7f3..954b4a327 100644
--- a/Source/CParse/parser.y
+++ b/Source/CParse/parser.y
@@ -56,12 +56,36 @@ static int      class_level = 0;
 static Node   **class_decl = NULL;
 
 /* -----------------------------------------------------------------------------
- *                            Doxygen Comment Globals
+ *                            Doxygen Comment Globals and Assist Functions
  * ----------------------------------------------------------------------------- */
+int parseComments = 1; /* set this to activate Doxygen uptake into the parse tree */
+String *currentComment; /* Location of the stored Doxygen Comment */
+String *currentPostComment; /* Location of the stored Doxygen Post-Comment */
+String *currentCComment; /* Location of the stored C Comment */
+static Node *previousNode = NULL; /* Pointer to the previous node (for post comments) */
 
-int isComment = 0; /* boolean for parsing Doxygen Comments */
-String *currentComment = 0; /* Location of the stored Doxygen Comment */
-static String *sideDoxComments = 0;
+/* NOT a safe method at the moment */
+int isStructuralDoxygen(String *s){
+	char *k = Char(s);
+    while (k[0] != '\0' && k[0] != '\\' && k[0] != '@'){
+	  k++;
+	  }
+	if (k[0] == '\0') return 0;
+    k++;
+	if (strncmp(k, "addtogroup", 10) == 0 || strncmp(k, "callgraph", 9) == 0 || strncmp(k, "callergraph", 11) == 0 
+	      || strncmp(k, "category", 8) == 0 || strncmp(k, "class", 5) == 0 || strncmp(k, "def", 3) == 0
+	      || strncmp(k, "defgroup", 8) == 0 || strncmp(k, "dir", 3) == 0 || strncmp(k, "enum", 4) == 0
+	      || strncmp(k, "example", 7) == 0 || strncmp(k, "file", 4) == 0 || strncmp(k, "fn", 2) == 0
+	      || strncmp(k, "headerfile", 9) == 0 || strncmp(k, "hideinitializer", 12) == 0 || strncmp(k, "ingroup", 7) == 0
+	      || strncmp(k, "interface", 9) == 0 || strncmp(k, "internal", 8) == 0 || strncmp(k, "mainpage", 8) == 0
+	      || strncmp(k, "name", 4) == 0 || strncmp(k, "namespace", 9) == 0 || strncmp(k, "nosubgrouping", 13) == 0
+	      || strncmp(k, "overload", 8) == 0 || strncmp(k, "package", 7) == 0 || strncmp(k, "page", 4) == 0
+	      || strncmp(k, "property", 8) == 0 || strncmp(k, "protocol", 8) == 0 || strncmp(k, "relates", 7) == 0
+	      || strncmp(k, "relatesalso", 5) == 0 || strncmp(k, "showinitializer", 5) == 0 || strncmp(k, "struct", 5) == 0
+	      || strncmp(k, "typedef", 7) == 0 || strncmp(k, "union", 5) == 0 || strncmp(k, "var", 3) == 0
+	      || strncmp(k, "weakgroup", 9) == 0){ return 1;}
+	return 0;
+}
 
 /* -----------------------------------------------------------------------------
  *                            Assist Functions
@@ -79,12 +103,21 @@ static Node *new_node(const String_or_char *tag) {
   set_nodeType(n,tag);
   Setfile(n,cparse_file);
   Setline(n,cparse_line);
-  /* Sets Comment if a Comment is Availible */
-  if(isComment){
-    String *copyComment = Copy(currentComment);
-    Setattr(n,"comment",copyComment);
-    isComment = 0;
-  }	 
+  if(parseComments){
+    /* Sets any post comments to the previous node */
+    if(previousNode != NULL && currentPostComment != 0){
+      String *copyPostComment = Copy(currentComment);
+      Setattr(previousNode,"DoxygenPostComment",copyPostComment);
+      currentPostComment = 0;
+    }	 
+    /* Sets Doxygen Comment if a Comment is Availible */
+    if(currentComment != 0){
+      String *copyComment = Copy(currentComment);
+      Setattr(n,"DoxygenComment",copyComment);
+      currentComment = 0;
+    }	
+    previousNode = n;
+  }
   return n;
 }
 
@@ -1455,6 +1488,8 @@ static void tag_nodes(Node *n, const String_or_char *attrname, DOH *value) {
 %token <str> COPERATOR
 %token PARSETYPE PARSEPARM PARSEPARMS
 %token <str> DOXYGENSTRING 
+%token <str> DOXYGENPOSTSTRING 
+%token <str> C_COMMENT_STRING 
 
 %left  CAST
 %left  QUESTIONMARK
@@ -1527,7 +1562,8 @@ static void tag_nodes(Node *n, const String_or_char *attrname, DOH *value) {
 %type <node>     fname stringtype;
 %type <node>     featattr;
 %type <str>	 doxygen_comment;
-
+%type <str>	 c_style_comment;
+%type <str>	 doxygen_post_comment;
 %%
 
 /* ======================================================================
@@ -1585,6 +1621,8 @@ declaration    : swig_directive { $$ = $1; }
                | c_declaration { $$ = $1; } 
                | cpp_declaration { $$ = $1; }
                | doxygen_comment { $$ = $1; }
+               | c_style_comment { $$ = $1; }
+               | doxygen_post_comment { $$ = $1; }
                | SEMI { $$ = 0; }
                | error {
                   $$ = 0;
@@ -3156,12 +3194,40 @@ c_constructor_decl : storage_class type LPAREN parms RPAREN ctor_end {
 
 doxygen_comment : DOXYGENSTRING 
 	{
-		currentComment = NewString($1);
-		isComment = 1;
+	  if(isStructuralDoxygen($1)){
+	    $$ = new_node("doxycomm");
+		Setattr($$,"DoxygenComment",$1);
+	    }
+	  else {  
+	    if(currentComment != 0){
+		    Append(currentComment, $1);
+		    }
+		else currentComment = $1;
+		$$ = 0;
+	    }
+	}
+	;
+
+
+doxygen_post_comment : DOXYGENPOSTSTRING 
+	{
+		if(currentPostComment != 0){
+	      Append(currentPostComment, $1);
+	      }
+	    else currentPostComment = $1;
 		$$ = 0;
 	}
 	;
 
+c_style_comment : C_COMMENT_STRING 
+	{
+		if(currentCComment != 0){
+		  Append(currentCComment, $1);
+		  }
+		else currentCComment = $1;
+		$$ = 0;
+	}
+	;
 
 
 /* ======================================================================
@@ -6009,3 +6075,5 @@ ParmList *Swig_cparse_parms(String *s) {
    /*   Printf(stdout,"typeparse: '%s' ---> '%s'\n", s, top); */
    return top;
 }
+
+

From 4f2a579d6d7cf5f8208c0cb2f3af7de99795ba6d Mon Sep 17 00:00:00 2001
From: Cheryl Foil <cheryl.foil@gmail.com>
Date: Fri, 15 Aug 2008 23:36:18 +0000
Subject: [PATCH 009/314] Now works end to end :) DoxygenTranslator
 restructured and placed into SWIG, Changes to java.cxx and lang.cxx to
 accomodate this

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2008-cherylfoil@10761 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Source/CParse/cscanner.c                      |   8 +-
 Source/CParse/parser.y                        |  44 +-
 Source/DoxygenTranslator/src/.deps/.dirstamp  |   0
 .../src/.deps/DoxygenEntity.Po                | 380 +++++++
 .../src/.deps/DoxygenParser.Po                | 398 ++++++++
 .../src/.deps/DoxygenTranslator.Po            | 401 ++++++++
 .../src/.deps/JavaDocConverter.Po             | 385 ++++++++
 Source/DoxygenTranslator/src/.deps/Token.Po   | 379 +++++++
 .../DoxygenTranslator/src/.deps/TokenList.Po  | 382 ++++++++
 Source/DoxygenTranslator/src/.dirstamp        |   0
 .../DoxygenTranslator/src/DoxygenEntity.cpp   |  89 ++
 Source/DoxygenTranslator/src/DoxygenEntity.h  |  26 +
 .../DoxygenTranslator/src/DoxygenParser.cpp   | 797 +++++++++++++++
 Source/DoxygenTranslator/src/DoxygenParser.h  |  19 +
 .../src/DoxygenTranslator.cpp                 |  41 +
 .../DoxygenTranslator/src/DoxygenTranslator.h |  10 +
 .../src/Examples/DoxygenTransWTokenizer.cpp   | 924 ++++++++++++++++++
 .../src/Examples/DoxygenTransWTokenizer.h     |  11 +
 .../{ => src}/Examples/Example1               |   0
 .../{ => src}/Examples/Example2               |   0
 .../{ => src}/Examples/Example3               |   0
 .../{ => src}/Examples/Example4               |   0
 .../DoxygenTranslator/src/Examples/Example5   |   0
 .../DoxygenTranslator/src/Examples/Example6   |   0
 .../src/Examples/translator.h                 | 144 +++
 .../src/JavaDocConverter.cpp                  | 210 ++++
 .../DoxygenTranslator/src/JavaDocConverter.h  |  18 +
 Source/DoxygenTranslator/src/Token.cpp        |  32 +
 Source/DoxygenTranslator/src/Token.h          |  21 +
 Source/DoxygenTranslator/src/TokenList.cpp    | 116 +++
 Source/DoxygenTranslator/src/TokenList.h      |  27 +
 .../DoxygenTranslator/src/TranslatorTest.cpp  |  68 ++
 Source/DoxygenTranslator/src/TranslatorTest.h |  11 +
 Source/Makefile.am                            |  14 +-
 Source/Modules/java.cxx                       | 119 ++-
 Source/Modules/lang.cxx                       |  21 +-
 Source/Modules/swigmod.h                      |   6 +
 Tools/config/config.guess                     |  34 +-
 Tools/config/config.sub                       |  24 +-
 39 files changed, 5101 insertions(+), 58 deletions(-)
 create mode 100644 Source/DoxygenTranslator/src/.deps/.dirstamp
 create mode 100644 Source/DoxygenTranslator/src/.deps/DoxygenEntity.Po
 create mode 100644 Source/DoxygenTranslator/src/.deps/DoxygenParser.Po
 create mode 100644 Source/DoxygenTranslator/src/.deps/DoxygenTranslator.Po
 create mode 100644 Source/DoxygenTranslator/src/.deps/JavaDocConverter.Po
 create mode 100644 Source/DoxygenTranslator/src/.deps/Token.Po
 create mode 100644 Source/DoxygenTranslator/src/.deps/TokenList.Po
 create mode 100644 Source/DoxygenTranslator/src/.dirstamp
 create mode 100644 Source/DoxygenTranslator/src/DoxygenEntity.cpp
 create mode 100644 Source/DoxygenTranslator/src/DoxygenEntity.h
 create mode 100644 Source/DoxygenTranslator/src/DoxygenParser.cpp
 create mode 100644 Source/DoxygenTranslator/src/DoxygenParser.h
 create mode 100644 Source/DoxygenTranslator/src/DoxygenTranslator.cpp
 create mode 100644 Source/DoxygenTranslator/src/DoxygenTranslator.h
 create mode 100644 Source/DoxygenTranslator/src/Examples/DoxygenTransWTokenizer.cpp
 create mode 100644 Source/DoxygenTranslator/src/Examples/DoxygenTransWTokenizer.h
 rename Source/DoxygenTranslator/{ => src}/Examples/Example1 (100%)
 rename Source/DoxygenTranslator/{ => src}/Examples/Example2 (100%)
 rename Source/DoxygenTranslator/{ => src}/Examples/Example3 (100%)
 rename Source/DoxygenTranslator/{ => src}/Examples/Example4 (100%)
 create mode 100644 Source/DoxygenTranslator/src/Examples/Example5
 create mode 100644 Source/DoxygenTranslator/src/Examples/Example6
 create mode 100644 Source/DoxygenTranslator/src/Examples/translator.h
 create mode 100644 Source/DoxygenTranslator/src/JavaDocConverter.cpp
 create mode 100644 Source/DoxygenTranslator/src/JavaDocConverter.h
 create mode 100644 Source/DoxygenTranslator/src/Token.cpp
 create mode 100644 Source/DoxygenTranslator/src/Token.h
 create mode 100644 Source/DoxygenTranslator/src/TokenList.cpp
 create mode 100644 Source/DoxygenTranslator/src/TokenList.h
 create mode 100644 Source/DoxygenTranslator/src/TranslatorTest.cpp
 create mode 100644 Source/DoxygenTranslator/src/TranslatorTest.h

diff --git a/Source/CParse/cscanner.c b/Source/CParse/cscanner.c
index ff7d5343c..13e976b95 100644
--- a/Source/CParse/cscanner.c
+++ b/Source/CParse/cscanner.c
@@ -426,7 +426,7 @@ int yylook(void) {
 	  if ((strncmp(loc,"/*@SWIG@",6) == 0) && (loc[Len(cmt)-3] == '@')) {
 	    scanner_locator(cmt);
 	  }
-	  if (strncmp(loc, "/**<", 4) == 0 || strncmp(loc, "///<", 3) == 0||strncmp(loc, "/*!<", 3) == 0||strncmp(loc, "//!<", 3) == 0) {
+	  if (strncmp(loc, "/**<", 4) == 0 || strncmp(loc, "///<", 4) == 0||strncmp(loc, "/*!<", 4) == 0||strncmp(loc, "//!<", 4) == 0) {
 	    printf("Doxygen Post Comment: %s lines %d-%d [%s]\n", Char(Scanner_file(scan)), Scanner_start_line(scan), Scanner_line(scan), loc);
 	    yylval.str =  NewString(loc);
 	    return DOXYGENPOSTSTRING;
@@ -436,12 +436,6 @@ int yylook(void) {
 	    yylval.str =  NewString(loc);
 	    return DOXYGENSTRING;
 	  }
-	  /*DOES NOT WORK PROPERLY AT THE MINUTE
-	  if (strncmp(loc, "//", 2)== 0) {
-	    printf("C style Comment: %s lines %d-%d [%s]\n", Char(Scanner_file(scan)), Scanner_start_line(scan), Scanner_line(scan), loc);
-	    yylval.str =  NewString(loc);
-	    return C_COMMENT_STRING;
-	  }*/
     }
       break;
     case SWIG_TOKEN_ENDLINE:
diff --git a/Source/CParse/parser.y b/Source/CParse/parser.y
index 954b4a327..eaf53449b 100644
--- a/Source/CParse/parser.y
+++ b/Source/CParse/parser.y
@@ -64,26 +64,25 @@ String *currentPostComment; /* Location of the stored Doxygen Post-Comment */
 String *currentCComment; /* Location of the stored C Comment */
 static Node *previousNode = NULL; /* Pointer to the previous node (for post comments) */
 
-/* NOT a safe method at the moment */
 int isStructuralDoxygen(String *s){
-	char *k = Char(s);
-    while (k[0] != '\0' && k[0] != '\\' && k[0] != '@'){
-	  k++;
-	  }
-	if (k[0] == '\0') return 0;
-    k++;
-	if (strncmp(k, "addtogroup", 10) == 0 || strncmp(k, "callgraph", 9) == 0 || strncmp(k, "callergraph", 11) == 0 
-	      || strncmp(k, "category", 8) == 0 || strncmp(k, "class", 5) == 0 || strncmp(k, "def", 3) == 0
-	      || strncmp(k, "defgroup", 8) == 0 || strncmp(k, "dir", 3) == 0 || strncmp(k, "enum", 4) == 0
-	      || strncmp(k, "example", 7) == 0 || strncmp(k, "file", 4) == 0 || strncmp(k, "fn", 2) == 0
-	      || strncmp(k, "headerfile", 9) == 0 || strncmp(k, "hideinitializer", 12) == 0 || strncmp(k, "ingroup", 7) == 0
-	      || strncmp(k, "interface", 9) == 0 || strncmp(k, "internal", 8) == 0 || strncmp(k, "mainpage", 8) == 0
-	      || strncmp(k, "name", 4) == 0 || strncmp(k, "namespace", 9) == 0 || strncmp(k, "nosubgrouping", 13) == 0
-	      || strncmp(k, "overload", 8) == 0 || strncmp(k, "package", 7) == 0 || strncmp(k, "page", 4) == 0
-	      || strncmp(k, "property", 8) == 0 || strncmp(k, "protocol", 8) == 0 || strncmp(k, "relates", 7) == 0
-	      || strncmp(k, "relatesalso", 5) == 0 || strncmp(k, "showinitializer", 5) == 0 || strncmp(k, "struct", 5) == 0
-	      || strncmp(k, "typedef", 7) == 0 || strncmp(k, "union", 5) == 0 || strncmp(k, "var", 3) == 0
-	      || strncmp(k, "weakgroup", 9) == 0){ return 1;}
+	char *slashPointer = Strchr(s, '\\');
+	char *atPointer = Strchr(s,'@');
+	if (slashPointer == NULL && atPointer == NULL) return 0;
+	else if( slashPointer == NULL) slashPointer = atPointer;
+	/* Perhaps a better solution exists... */
+	slashPointer++;
+	if (strncmp(slashPointer, "addtogroup", 10) == 0 || strncmp(slashPointer, "callgraph", 9) == 0 || strncmp(slashPointer, "callergraph", 11) == 0 
+	      || strncmp(slashPointer, "category", 8) == 0 || strncmp(slashPointer, "class", 5) == 0 || strncmp(slashPointer, "def", 3) == 0
+	      || strncmp(slashPointer, "defgroup", 8) == 0 || strncmp(slashPointer, "dir", 3) == 0 || strncmp(slashPointer, "enum", 4) == 0
+	      || strncmp(slashPointer, "example", 7) == 0 || strncmp(slashPointer, "file", 4) == 0 || strncmp(slashPointer, "fn", 2) == 0
+	      || strncmp(slashPointer, "headerfile", 9) == 0 || strncmp(slashPointer, "hideinitializer", 12) == 0 || strncmp(slashPointer, "ingroup", 7) == 0
+	      || strncmp(slashPointer, "interface", 9) == 0 || strncmp(slashPointer, "internal", 8) == 0 || strncmp(slashPointer, "mainpage", 8) == 0
+	      || strncmp(slashPointer, "name", 4) == 0 || strncmp(slashPointer, "namespace", 9) == 0 || strncmp(slashPointer, "nosubgrouping", 13) == 0
+	      || strncmp(slashPointer, "overload", 8) == 0 || strncmp(slashPointer, "package", 7) == 0 || strncmp(slashPointer, "page", 4) == 0
+	      || strncmp(slashPointer, "property", 8) == 0 || strncmp(slashPointer, "protocol", 8) == 0 || strncmp(slashPointer, "relates", 7) == 0
+	      || strncmp(slashPointer, "relatesalso", 5) == 0 || strncmp(slashPointer, "showinitializer", 5) == 0 || strncmp(slashPointer, "struct", 5) == 0
+	      || strncmp(slashPointer, "typedef", 7) == 0 || strncmp(slashPointer, "union", 5) == 0 || strncmp(slashPointer, "var", 3) == 0
+	      || strncmp(slashPointer, "weakgroup", 9) == 0){ return 1;}
 	return 0;
 }
 
@@ -4091,8 +4090,8 @@ cpp_members  : cpp_member cpp_members {
 	       appendChild($$,$4);
 	       set_nextSibling($$,$6);
 	     }
-             | include_directive { $$ = $1; }
-             | empty { $$ = 0;}
+         | include_directive { $$ = $1; }
+         | empty { $$ = 0;}
 	     | error {
 	       int start_line = cparse_line;
 	       skip_decl();
@@ -4136,6 +4135,9 @@ cpp_member   : c_declaration { $$ = $1; }
              | storage_class idcolon SEMI { $$ = 0; }
              | cpp_using_decl { $$ = $1; }
              | cpp_template_decl { $$ = $1; }
+             | doxygen_comment{ $$ = $1; }
+             | c_style_comment{ $$ = $1; }
+             | doxygen_post_comment{ $$ = $1; }
              | cpp_catch_decl { $$ = 0; }
              | template_directive { $$ = $1; }
              | warn_directive { $$ = $1; }
diff --git a/Source/DoxygenTranslator/src/.deps/.dirstamp b/Source/DoxygenTranslator/src/.deps/.dirstamp
new file mode 100644
index 000000000..e69de29bb
diff --git a/Source/DoxygenTranslator/src/.deps/DoxygenEntity.Po b/Source/DoxygenTranslator/src/.deps/DoxygenEntity.Po
new file mode 100644
index 000000000..7d2d2e0db
--- /dev/null
+++ b/Source/DoxygenTranslator/src/.deps/DoxygenEntity.Po
@@ -0,0 +1,380 @@
+DoxygenTranslator/src/DoxygenEntity.o \
+  DoxygenTranslator/src/DoxygenEntity.o:  \
+ DoxygenTranslator/src/DoxygenEntity.cpp \
+  DoxygenTranslator/src/DoxygenEntity.h /usr/include/c++/4.2/cstdlib \
+  /usr/include/c++/4.2/i486-linux-gnu/bits/c++config.h \
+  /usr/include/c++/4.2/i486-linux-gnu/bits/os_defines.h \
+  /usr/include/features.h /usr/include/sys/cdefs.h \
+  /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
+  /usr/include/gnu/stubs-32.h \
+  /usr/include/c++/4.2/i486-linux-gnu/bits/cpu_defines.h \
+  /usr/include/c++/4.2/cstddef \
+  /usr/lib/gcc/i486-linux-gnu/4.2.3/include/stddef.h \
+  /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+  /usr/include/bits/waitstatus.h /usr/include/endian.h \
+  /usr/include/bits/endian.h /usr/include/xlocale.h \
+  /usr/include/sys/types.h /usr/include/bits/types.h \
+  /usr/include/bits/typesizes.h /usr/include/time.h \
+  /usr/include/sys/select.h /usr/include/bits/select.h \
+  /usr/include/bits/sigset.h /usr/include/bits/time.h \
+  /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \
+  /usr/include/alloca.h /usr/include/c++/4.2/iostream \
+  /usr/include/c++/4.2/ostream /usr/include/c++/4.2/ios \
+  /usr/include/c++/4.2/iosfwd \
+  /usr/include/c++/4.2/i486-linux-gnu/bits/c++locale.h \
+  /usr/include/c++/4.2/cstring /usr/include/string.h \
+  /usr/include/c++/4.2/cstdio /usr/include/stdio.h /usr/include/libio.h \
+  /usr/include/_G_config.h /usr/include/wchar.h \
+  /usr/lib/gcc/i486-linux-gnu/4.2.3/include/stdarg.h \
+  /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+  /usr/include/c++/4.2/clocale /usr/include/locale.h \
+  /usr/include/bits/locale.h /usr/include/langinfo.h \
+  /usr/include/nl_types.h /usr/include/iconv.h /usr/include/libintl.h \
+  /usr/include/c++/4.2/cstdarg \
+  /usr/include/c++/4.2/i486-linux-gnu/bits/c++io.h \
+  /usr/include/c++/4.2/i486-linux-gnu/bits/gthr.h \
+  /usr/include/c++/4.2/i486-linux-gnu/bits/gthr-default.h \
+  /usr/include/pthread.h /usr/include/sched.h /usr/include/bits/sched.h \
+  /usr/include/signal.h /usr/include/bits/setjmp.h /usr/include/unistd.h \
+  /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \
+  /usr/include/bits/confname.h /usr/include/getopt.h \
+  /usr/include/c++/4.2/cctype /usr/include/ctype.h \
+  /usr/include/c++/4.2/bits/stringfwd.h \
+  /usr/include/c++/4.2/bits/postypes.h /usr/include/c++/4.2/cwchar \
+  /usr/include/c++/4.2/ctime /usr/include/bits/wchar.h \
+  /usr/include/stdint.h /usr/include/c++/4.2/bits/functexcept.h \
+  /usr/include/c++/4.2/exception_defines.h /usr/include/c++/4.2/exception \
+  /usr/include/c++/4.2/bits/char_traits.h \
+  /usr/include/c++/4.2/bits/stl_algobase.h /usr/include/c++/4.2/climits \
+  /usr/lib/gcc/i486-linux-gnu/4.2.3/include/limits.h \
+  /usr/lib/gcc/i486-linux-gnu/4.2.3/include/syslimits.h \
+  /usr/include/limits.h /usr/include/bits/posix1_lim.h \
+  /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
+  /usr/include/bits/posix2_lim.h /usr/include/bits/xopen_lim.h \
+  /usr/include/c++/4.2/bits/stl_pair.h \
+  /usr/include/c++/4.2/bits/cpp_type_traits.h \
+  /usr/include/c++/4.2/ext/type_traits.h /usr/include/c++/4.2/utility \
+  /usr/include/c++/4.2/bits/stl_relops.h \
+  /usr/include/c++/4.2/bits/stl_iterator_base_types.h \
+  /usr/include/c++/4.2/bits/stl_iterator_base_funcs.h \
+  /usr/include/c++/4.2/bits/concept_check.h \
+  /usr/include/c++/4.2/bits/stl_iterator.h \
+  /usr/include/c++/4.2/debug/debug.h \
+  /usr/include/c++/4.2/bits/localefwd.h \
+  /usr/include/c++/4.2/bits/ios_base.h \
+  /usr/include/c++/4.2/ext/atomicity.h \
+  /usr/include/c++/4.2/i486-linux-gnu/bits/atomic_word.h \
+  /usr/include/c++/4.2/bits/locale_classes.h /usr/include/c++/4.2/string \
+  /usr/include/c++/4.2/memory /usr/include/c++/4.2/bits/allocator.h \
+  /usr/include/c++/4.2/i486-linux-gnu/bits/c++allocator.h \
+  /usr/include/c++/4.2/ext/new_allocator.h /usr/include/c++/4.2/new \
+  /usr/include/c++/4.2/bits/stl_construct.h \
+  /usr/include/c++/4.2/bits/stl_uninitialized.h \
+  /usr/include/c++/4.2/bits/stl_raw_storage_iter.h \
+  /usr/include/c++/4.2/limits /usr/include/c++/4.2/bits/ostream_insert.h \
+  /usr/include/c++/4.2/bits/stl_function.h \
+  /usr/include/c++/4.2/bits/basic_string.h /usr/include/c++/4.2/algorithm \
+  /usr/include/c++/4.2/bits/stl_algo.h \
+  /usr/include/c++/4.2/bits/stl_heap.h \
+  /usr/include/c++/4.2/bits/stl_tempbuf.h \
+  /usr/include/c++/4.2/bits/basic_string.tcc \
+  /usr/include/c++/4.2/streambuf /usr/include/c++/4.2/bits/streambuf.tcc \
+  /usr/include/c++/4.2/bits/basic_ios.h \
+  /usr/include/c++/4.2/bits/streambuf_iterator.h \
+  /usr/include/c++/4.2/bits/locale_facets.h /usr/include/c++/4.2/cwctype \
+  /usr/include/wctype.h \
+  /usr/include/c++/4.2/i486-linux-gnu/bits/ctype_base.h \
+  /usr/include/c++/4.2/i486-linux-gnu/bits/ctype_inline.h \
+  /usr/include/c++/4.2/bits/codecvt.h \
+  /usr/include/c++/4.2/i486-linux-gnu/bits/time_members.h \
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new file mode 100644
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new file mode 100644
index 000000000..79a3133a3
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diff --git a/Source/DoxygenTranslator/src/.deps/Token.Po b/Source/DoxygenTranslator/src/.deps/Token.Po
new file mode 100644
index 000000000..9a4bb90f5
--- /dev/null
+++ b/Source/DoxygenTranslator/src/.deps/Token.Po
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diff --git a/Source/DoxygenTranslator/src/.deps/TokenList.Po b/Source/DoxygenTranslator/src/.deps/TokenList.Po
new file mode 100644
index 000000000..74d0e1c79
--- /dev/null
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+/usr/include/c++/4.2/bits/concept_check.h:
+
+/usr/include/c++/4.2/bits/stl_iterator.h:
+
+/usr/include/c++/4.2/debug/debug.h:
+
+/usr/include/c++/4.2/bits/localefwd.h:
+
+/usr/include/c++/4.2/bits/ios_base.h:
+
+/usr/include/c++/4.2/ext/atomicity.h:
+
+/usr/include/c++/4.2/i486-linux-gnu/bits/atomic_word.h:
+
+/usr/include/c++/4.2/bits/locale_classes.h:
+
+/usr/include/c++/4.2/string:
+
+/usr/include/c++/4.2/memory:
+
+/usr/include/c++/4.2/bits/allocator.h:
+
+/usr/include/c++/4.2/i486-linux-gnu/bits/c++allocator.h:
+
+/usr/include/c++/4.2/ext/new_allocator.h:
+
+/usr/include/c++/4.2/new:
+
+/usr/include/c++/4.2/bits/stl_construct.h:
+
+/usr/include/c++/4.2/bits/stl_uninitialized.h:
+
+/usr/include/c++/4.2/bits/stl_raw_storage_iter.h:
+
+/usr/include/c++/4.2/limits:
+
+/usr/include/c++/4.2/bits/ostream_insert.h:
+
+/usr/include/c++/4.2/bits/stl_function.h:
+
+/usr/include/c++/4.2/bits/basic_string.h:
+
+/usr/include/c++/4.2/algorithm:
+
+/usr/include/c++/4.2/bits/stl_algo.h:
+
+/usr/include/c++/4.2/bits/stl_heap.h:
+
+/usr/include/c++/4.2/bits/stl_tempbuf.h:
+
+/usr/include/c++/4.2/bits/basic_string.tcc:
+
+/usr/include/c++/4.2/streambuf:
+
+/usr/include/c++/4.2/bits/streambuf.tcc:
+
+/usr/include/c++/4.2/bits/basic_ios.h:
+
+/usr/include/c++/4.2/bits/streambuf_iterator.h:
+
+/usr/include/c++/4.2/bits/locale_facets.h:
+
+/usr/include/c++/4.2/cwctype:
+
+/usr/include/wctype.h:
+
+/usr/include/c++/4.2/i486-linux-gnu/bits/ctype_base.h:
+
+/usr/include/c++/4.2/i486-linux-gnu/bits/ctype_inline.h:
+
+/usr/include/c++/4.2/bits/codecvt.h:
+
+/usr/include/c++/4.2/i486-linux-gnu/bits/time_members.h:
+
+/usr/include/c++/4.2/i486-linux-gnu/bits/messages_members.h:
+
+/usr/include/c++/4.2/bits/basic_ios.tcc:
+
+/usr/include/c++/4.2/bits/ostream.tcc:
+
+/usr/include/c++/4.2/locale:
+
+/usr/include/c++/4.2/bits/locale_facets.tcc:
+
+/usr/include/c++/4.2/typeinfo:
+
+/usr/include/c++/4.2/istream:
+
+/usr/include/c++/4.2/bits/istream.tcc:
+
+/usr/include/c++/4.2/list:
+
+/usr/include/c++/4.2/bits/stl_list.h:
+
+/usr/include/c++/4.2/bits/list.tcc:
+
+DoxygenTranslator/src/Token.h:
diff --git a/Source/DoxygenTranslator/src/.dirstamp b/Source/DoxygenTranslator/src/.dirstamp
new file mode 100644
index 000000000..e69de29bb
diff --git a/Source/DoxygenTranslator/src/DoxygenEntity.cpp b/Source/DoxygenTranslator/src/DoxygenEntity.cpp
new file mode 100644
index 000000000..6b8755592
--- /dev/null
+++ b/Source/DoxygenTranslator/src/DoxygenEntity.cpp
@@ -0,0 +1,89 @@
+#include "DoxygenEntity.h"
+#include <string>
+
+/* Little data class for Doxygen Commands */
+
+
+/* Basic node for commands that have
+ * nothing after them
+ * example: \n
+ */
+string commandArray2[] = {"a", "addindex", "addtogroup", "anchor", "arg", "attention",
+		"author", "b", "brief", "bug", "c", "callgraph", "callergraph", "category",
+		"class", "code", "cond", "copybrief", "copydetails", "copydoc", "date", "def",
+		"defgroup", "deprecated", "details", "dir", "dontinclude", "dot", "dotfile", "e",
+		"else", "elseif", "em", "endcode", "endcond", "enddot", "endhtmlonly", "endif",
+		"endlatexonly", "endlink", "endmanonly", "endmsc", "endverbatim", "endxmlonly",
+		"enum", "example", "exception", "f$", "f[", "f]", "f{", "f}", "file", "fn", "headerfile",
+		"hideinitializer", "htmlinclude", "htmlonly", "if", "ifnot", "image", "include",
+		"includelineno", "ingroup", "internal", "invariant", "interface", "latexonly", "li",
+		"line", "link", "mainpage", "manonly", "msc", "n", "name", "namespace", "nosubgrouping",
+		"note", "overload", "p", "package", "page", "par", "paragraph", "param", "post", "pre",
+		"private", "privatesection", "property", "protected", "protectedsection", "protocol",
+		"public", "publicsection", "ref", "relates", "relatesalso", "remarks", "return", "retval",
+		"sa", "section", "see", "showinitializer", "since", "skip", "skipline", "struct", "subpage",
+		"subsection", "subsubsection", "test", "throw", "todo", "tparam", "typedef", "union", "until",
+		"var", "verbatim", "verbinclude", "version", "warning", "weakgroup", "xmlonly", "xrefitem",
+		"$", "@", string(1, 92), "&", "~", "<", ">", "#", "%"};
+
+string findCommand(int commandNum){
+
+	int arraySize = sizeof(commandArray2)/sizeof(*commandArray2);
+	if (commandNum - 101 >= 0 && commandNum - 101 < arraySize){
+		return commandArray2[commandNum - 101];
+	}
+
+	return "" ;
+}
+
+DoxygenEntity::DoxygenEntity(string typeEnt){
+    typeOfEntity = typeEnt;
+    data = "";
+    isLeaf = 1;
+}
+
+/* Basic node for commands that have
+ * only 1 thing after them
+ * example: \b word
+ * OR holding a string
+ */
+DoxygenEntity::DoxygenEntity(string typeEnt, string param1){
+    typeOfEntity = typeEnt;
+    data = param1;
+    isLeaf = 1;
+}
+
+/* Nonterminal node
+ * contains
+ */
+DoxygenEntity::DoxygenEntity(string typeEnt, list <DoxygenEntity> &entList ){
+    typeOfEntity = typeEnt;
+    data = "";
+    isLeaf = 0;
+    entityList = entList;
+}
+
+
+void DoxygenEntity::printEntity(int level){
+	int thisLevel = level;
+	if (isLeaf) {
+		for (int i = 0; i < thisLevel; i++) {cout << "\t";}
+		cout << "Node Command: " << typeOfEntity << " ";
+		if (data.compare("") != 0) cout << "Node Data: " << data;
+		cout << endl;
+	}
+	else{
+		for (int i = 0; i < thisLevel; i++) {cout << "\t";}
+		cout << "Node Command : " << typeOfEntity << endl;
+		list<DoxygenEntity>::iterator p = entityList.begin();
+		thisLevel++;
+		while (p != entityList.end()){
+			(*p).printEntity(thisLevel);
+			p++;
+		}
+	}
+}
+
+DoxygenEntity::~DoxygenEntity()
+{
+}
diff --git a/Source/DoxygenTranslator/src/DoxygenEntity.h b/Source/DoxygenTranslator/src/DoxygenEntity.h
new file mode 100644
index 000000000..0605b1cc9
--- /dev/null
+++ b/Source/DoxygenTranslator/src/DoxygenEntity.h
@@ -0,0 +1,26 @@
+#ifndef DOXYGENENTITY_H_
+#define DOXYGENENTITY_H_
+
+#include <cstdlib>
+#include <iostream>
+#include <string>
+#include <list>
+
+using namespace std;
+
+class DoxygenEntity{
+
+public:
+	DoxygenEntity(string typeEnt);
+	DoxygenEntity(string typeEnt, string param1);
+	DoxygenEntity(string typeEnt, list <DoxygenEntity> &entList );
+   ~DoxygenEntity();
+	void printEntity(int level);
+    string typeOfEntity;
+    list <DoxygenEntity> entityList;
+    string data;
+    int isLeaf;
+};
+
+
+#endif /*TOKENLIST_H_*/
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.cpp b/Source/DoxygenTranslator/src/DoxygenParser.cpp
new file mode 100644
index 000000000..226c60720
--- /dev/null
+++ b/Source/DoxygenTranslator/src/DoxygenParser.cpp
@@ -0,0 +1,797 @@
+#include "DoxygenParser.h"
+
+#include <cstdlib>
+#include <iostream>
+#include <fstream>
+#include <string>
+#include <list>
+#include "DoxygenEntity.h"
+#include "TokenList.h"
+#include "JavaDocConverter.h"
+#define SIMPLECOMMAND 1
+#define IGNOREDSIMPLECOMMAND 2
+#define COMMANDWORD 3
+#define IGNOREDCOMMANDWORD 4
+#define COMMANDLINE 5
+#define IGNOREDCOMMANDLINE 6
+#define COMMANDPARAGRAPH 7
+#define IGNORECOMMANDPARAGRAPH 8
+#define COMMANDENDCOMMAND 9
+#define COMMANDWORDPARAGRAPH 10
+#define COMMANDWORDLINE 11
+#define COMMANDWORDOWORDWORD 12
+#define COMMANDOWORD 13
+#define COMMANDERRORTHROW 14
+#define COMMANDUNIQUE 15
+#define  END_LINE 101
+#define PARAGRAPH_END 102
+#define  PLAINSTRING 103
+#define  COMMAND  104
+using namespace std;
+
+//////////////////////////////////////////
+/*Set these to pick what internal functions
+to test. */
+
+//int testCommandParsingFunctions = 1;// not implemented
+
+
+DoxygenParser::DoxygenParser()
+{
+}
+
+DoxygenParser::~DoxygenParser()
+{
+}
+
+int noisy = 0; // set this to 1 for extra chatter from the parsing stage.
+int addCommand(string currCommand, TokenList &tokList,  list <DoxygenEntity> &aNewList);
+list <DoxygenEntity> parse(list<Token>::iterator endParsingIndex, TokenList &tokList);
+
+//////////////////////////////////////////
+
+
+string commandArray[] = {"a", "addindex", "addtogroup", "anchor", "arg", "attention",
+		"author", "b", "brief", "bug", "c", "callgraph", "callergraph", "category",
+		"class", "code", "cond", "copybrief", "copydetails", "copydoc", "date", "def",
+		"defgroup", "deprecated", "details", "dir", "dontinclude", "dot", "dotfile", "e",
+		"else", "elseif", "em", "endcode", "endcond", "enddot", "endhtmlonly", "endif",
+		"endlatexonly", "endlink", "endmanonly", "endmsc", "endverbatim", "endxmlonly",
+		"enum", "example", "exception", "f$", "f[", "f]", "f{", "f}", "file", "fn", "headerfile",
+		"hideinitializer", "htmlinclude", "htmlonly", "if", "ifnot", "image", "include",
+		"includelineno", "ingroup", "internal", "invariant", "interface", "latexonly", "li",
+		"line", "link", "mainpage", "manonly", "msc", "n", "name", "namespace", "nosubgrouping",
+		"note", "overload", "p", "package", "page", "par", "paragraph", "param", "post", "pre",
+		"private", "privatesection", "property", "protected", "protectedsection", "protocol",
+		"public", "publicsection", "ref", "relates", "relatesalso", "remarks", "return", "retval",
+		"sa", "section", "see", "showinitializer", "since", "skip", "skipline", "struct", "subpage",
+		"subsection", "subsubsection", "test", "throw", "todo", "tparam", "typedef", "union", "until",
+		"var", "verbatim", "verbinclude", "version", "warning", "weakgroup", "xmlonly", "xrefitem",
+		"$", "@", "\\","&", "~", "<", ">", "#", "%"};
+
+
+string sectionIndicators[] = { "attention", "author", "brief", "bug", "cond", "date", "deprecated", "details",
+		"else", "elseif", "endcond", "endif", "exception", "if", "ifnot", "invariant", "note", "par", "param",
+		"tparam", "post" , "pre", "remarks", "return", "retval", "sa", "see", "since", "test", "throw", "todo",
+		"version", "warning", "xrefitem" };
+
+/* All of the doxygen commands divided up by how they are parsed */
+string simpleCommands[] = {"n", "$", "@", "\\", "&", "~", "<", ">", "#", "%"};
+string ignoredSimpleCommands[] = {"nothing at the moment"};
+string commandWords[] = {"a", "b", "c", "e", "em", "p", "def", "enum", "example", "package", 
+		"relates", "namespace", "relatesalso","anchor", "dontinclude", "include", "includelineno"};
+string ignoredCommandWords[] = {"copydoc", "copybrief", "copydetails", "verbinclude", "htmlinclude"};
+string commandLines[] = {"addindex", "fn", "name", "line", "var", "skipline", "typedef", "skip", "until", "property"};
+string ignoreCommandLines[] = {"nothing at the moment"};
+string commandParagraph[] = {"return", "remarks", "since", "test", "sa", "see", "pre", "post", "details", "invariant", 
+		    "deprecated", "date", "note", "warning", "version", "todo", "bug", "attention", "brief", "author"};
+string ignoreCommandParagraphs[] = {"nothing at the moment"};
+string commandEndCommands[] = {"code", "dot", "msc", "f$", "f[", "f{environment}{", "htmlonly", "latexonly", "manonly", 
+		   "verbatim", "xmlonly", "cond", "if", "ifnot", "link"};
+string commandWordParagraphs[] = {"param", "tparam", "throw", "retval", "exception"};
+string commandWordLines[] = {"page", "subsection", "subsubsection", "section", "paragraph", "defgroup"};
+string commandWordOWordOWords [] = {"category", "class", "protocol", "interface", "struct", "union"};
+string commandOWords[] = {"dir", "file", "cond"};
+string commandErrorThrowings[] = {"annotatedclasslist", "classhierarchy", "define", "functionindex", "header",
+		"headerfilelist", "inherit", "l", "postheader", "private", "privatesection", "protected", 
+		"protectedsection", "public", "publicsection", "endcode", "enddot", "endmsc", "endhtmlonly", 
+		"endlatexonly", "endmanonly", "endlink", "endverbatim", "endxmlonly", "f]", "f}", "endcond", 
+		"endif"};
+string commandUniques[] = {"xrefitem", "arg", "ingroup", "par", "headerfile", "overload", "weakgroup", "ref",
+		"subpage", "dotfile", "image", "addtogroup", "li"};
+
+
+/* Changes a string to all lower case*/
+string StringToLower(string stringToConvert)
+
+{
+
+   for(unsigned int i=0;i<stringToConvert.length();i++)
+   {
+   stringToConvert[i] = tolower(stringToConvert[i]);
+   }
+   return stringToConvert;//return the converted string
+}
+
+/* finds out if a command exists (is a possible command)
+ * from the string array commandArray
+ * returns -1 if no match is found */
+int findCommand(string smallString){
+
+	smallString = StringToLower(smallString);
+	int a;
+	for (int i = 0; i < sizeof(commandArray)/sizeof(*commandArray); i++){
+		if( (a = smallString.compare(commandArray[i])) == 0){
+			return 101 + i;
+		}
+
+
+	}
+	return -1;
+}
+
+/* isSectionIndicator returns a boolean if the command is a section indicator
+ * This is a helper method for finding the end of a paragraph
+ * by Doxygen's terms
+ */
+int isSectionIndicator(string smallString){
+	smallString = StringToLower(smallString);
+
+	for (int i = 0; i < sizeof( sectionIndicators)/sizeof(* sectionIndicators); i++){
+		if( smallString.compare( sectionIndicators[i]) == 0){
+			return 1;
+		}
+	}
+	return 0;
+}
+
+/* prints the parse tree
+ *
+ */
+void printTree( list <DoxygenEntity> &rootList){
+
+		list<DoxygenEntity>::iterator p = rootList.begin();
+		while (p != rootList.end()){
+			(*p).printEntity(0);
+			p++;
+		}
+
+}
+
+/* Determines how a command should be handled (what group it belongs to
+ * for parsing rules
+ */
+
+int commandBelongs(string theCommand){
+	 string smallString = StringToLower(theCommand );
+	 //cout << " Looking for command " << theCommand << endl;
+	 int i = 0;
+	 for ( i = 0; i < sizeof(simpleCommands)/sizeof(*simpleCommands); i++){
+	 	if(smallString.compare(simpleCommands[i]) == 0){return SIMPLECOMMAND ;}
+	 	}
+	 for ( i = 0; i < sizeof(ignoredSimpleCommands)/sizeof(*ignoredSimpleCommands); i++){
+	 	if(smallString.compare(ignoredSimpleCommands[i]) == 0){return IGNOREDSIMPLECOMMAND;}
+	 	} 
+	 for ( i = 0; i < sizeof(commandWords)/sizeof(*commandWords); i++){
+	 	if(smallString.compare( commandWords[i]) == 0){return COMMANDWORD;}
+	 	} 
+	 for ( i = 0; i < sizeof(ignoredCommandWords)/sizeof(*ignoredCommandWords); i++){
+	 	if(smallString.compare( ignoredCommandWords[i]) == 0){return IGNOREDCOMMANDWORD;}
+	 	} 
+	 for ( i = 0; i < sizeof(commandLines)/sizeof(*commandLines); i++){
+	 	if(smallString.compare( commandLines[i]) == 0){return COMMANDLINE;}
+	 	} 
+	 for ( i = 0; i < sizeof(ignoreCommandLines)/sizeof(*ignoreCommandLines); i++){
+	 	if(smallString.compare( ignoreCommandLines[i]) == 0){return IGNOREDCOMMANDLINE;}
+	 	} 
+	 for ( i = 0; i <  sizeof(commandParagraph)/sizeof(*commandParagraph); i++){
+	 	if(smallString.compare( commandParagraph[i]) == 0){return COMMANDPARAGRAPH;}
+	 	} 
+	 /* IgnoreCommandParagraph */
+	 for ( i = 0; i < sizeof(ignoreCommandParagraphs)/sizeof(*ignoreCommandParagraphs); i++){
+	 	if(smallString.compare( ignoreCommandParagraphs[i]) == 0){return IGNORECOMMANDPARAGRAPH;}
+	 	} 
+	 for ( i = 0; i < sizeof(commandEndCommands)/sizeof(*commandEndCommands); i++){
+	 	if(smallString.compare( commandEndCommands[i]) == 0){return COMMANDENDCOMMAND ;}
+	 	} 
+	 for ( i = 0; i < sizeof(commandWordParagraphs)/sizeof(*commandWordParagraphs); i++){
+	 	if(smallString.compare( commandWordParagraphs[i]) == 0){return COMMANDWORDPARAGRAPH;}
+	 	} 
+	 for ( i = 0; i < sizeof(commandWordLines)/sizeof(*commandWordLines); i++){
+	 	if(smallString.compare( commandWordLines[i]) == 0){return COMMANDWORDLINE ;}
+	 	} 
+	 for ( i = 0; i < sizeof(commandWordOWordOWords)/sizeof(*commandWordOWordOWords); i++){
+	 	if(smallString.compare( commandWordOWordOWords[i]) == 0){return COMMANDWORDOWORDWORD;}
+	 	} 
+	 for ( i = 0; i < sizeof(commandOWords)/sizeof(*commandOWords); i++){
+	 	if(smallString.compare( commandOWords[i]) == 0){return COMMANDOWORD;}
+	 	} 
+	 for ( i = 0; i < sizeof(commandErrorThrowings)/sizeof(*commandErrorThrowings); i++){
+	 	if(smallString.compare( commandErrorThrowings[i]) == 0){return COMMANDERRORTHROW;}
+	 	} 
+	 for ( i = 0; i < sizeof(commandUniques)/sizeof(*commandUniques); i++){
+	 	if(smallString.compare( commandUniques[i]) == 0){return COMMANDUNIQUE;}
+	 	} 
+
+	 	return 0;
+	 
+}
+/* Returns the next word ON THE CURRENT LINE ONLY
+ * if a new line is encountered, returns a blank string.
+ * Updates the index it is given if success.
+ */
+
+string getNextWord(TokenList &tokList){
+	 Token nextToken = tokList.peek();
+	 if (nextToken.tokenType == PLAINSTRING ){
+		 nextToken = tokList.next();
+		 return nextToken.tokenString;
+	 }
+	return "";
+}
+
+/* Returns the location of the end of the line as
+ * an iterator.
+ */
+list<Token>::iterator getOneLine(TokenList &tokList){
+	 list<Token>::iterator endOfParagraph = tokList.iteratorCopy();
+	 while(endOfParagraph != tokList.end()){
+		 if ((* endOfParagraph).tokenType == END_LINE){
+			 return endOfParagraph;
+		 }
+		 endOfParagraph++;
+	 }
+	return tokList.end();
+}
+
+
+
+/* Returns a properly formatted string
+* up til ANY command or end of paragraph is encountered.
+*/
+string getStringTilCommand(TokenList &tokList){
+	 string description;
+	 if (tokList.peek().tokenType == 0) return "";
+	 while(tokList.peek().tokenType == PLAINSTRING || tokList.peek().tokenType == END_LINE ){
+		 Token currentToken = tokList.next();
+		 if(currentToken.tokenType == PLAINSTRING) {
+			 description = description + currentToken.tokenString + " ";
+		 }
+		 else if (tokList.peek().tokenType == END_LINE) break;
+	 }
+	 
+	return description;
+}
+
+/* Returns a properly formatted string
+* up til the command specified is encountered
+*/
+//TODO check that this behaves properly for formulas
+
+string getStringTilEndCommand(string theCommand, TokenList &tokList){
+	 string description;
+	 if (tokList.peek().tokenType == 0) return "";
+	 while(tokList.peek().tokenString.compare(theCommand) != 0 ){
+		 Token currentToken = tokList.next();
+		 description = description + currentToken.tokenString + " ";
+
+	 }
+	 
+	return description;
+}
+
+/* Returns the end of a Paragraph as an iterator-
+* Paragraph is defined in Doxygen to be a paragraph of text
+* seperate by either a structural command or a blank line
+*/
+
+list<Token>::iterator getEndOfParagraph(TokenList &tokList){
+	 list<Token>::iterator endOfParagraph = tokList.iteratorCopy();
+	 while(endOfParagraph != tokList.end()){
+		if ((* endOfParagraph).tokenType == COMMAND){
+			 if(isSectionIndicator((* endOfParagraph).tokenString)) return endOfParagraph;
+			 else endOfParagraph++;
+		 }
+		else if((* endOfParagraph).tokenType == PLAINSTRING) {
+			 endOfParagraph++;
+		 }
+		 else if ((* endOfParagraph).tokenType == END_LINE){
+			 endOfParagraph++;
+			 if ((* endOfParagraph).tokenType == END_LINE){
+				 endOfParagraph++;
+				 return endOfParagraph;
+			 }
+		 }
+
+	 }
+	 
+	return tokList.end();
+
+}
+
+/* Returns the end of a section, defined as the first blank line OR first encounter of the same 
+* command. Example of this behaviour is \arg
+*/
+
+list<Token>::iterator getEndOfSection(string theCommand, TokenList &tokList){
+	 list<Token>::iterator endOfParagraph = tokList.iteratorCopy();
+	 while(endOfParagraph != tokList.end()){
+		if ((* endOfParagraph).tokenType == COMMAND){
+			 if(theCommand.compare((*endOfParagraph).tokenString) == 0) return endOfParagraph;
+			 else endOfParagraph++;
+		 }
+		else if((* endOfParagraph).tokenType == PLAINSTRING) {
+			 endOfParagraph++;
+		 }
+		 else if ((* endOfParagraph).tokenType == END_LINE){
+			 endOfParagraph++;
+			 if ((* endOfParagraph).tokenType == END_LINE){
+				 endOfParagraph++;
+				 return endOfParagraph;
+			 }
+		 }
+
+	 }
+}
+/* This method is for returning the end of a specific form of doxygen command
+ * that begins with a \command and ends in \endcommand
+ * such as \code and \endcode. The proper usage is
+ * progressTilEndCommand("endcode", tokenList);
+ */
+list<Token>::iterator getEndCommand(string theCommand, TokenList &tokList){
+	list<Token>::iterator endOfCommand = tokList.iteratorCopy();
+	while (endOfCommand!= tokList.end()){
+		if ((*endOfCommand).tokenType == COMMAND){
+			if (theCommand.compare((* endOfCommand).tokenString) == 0){
+				return endOfCommand;
+			}
+			endOfCommand++;
+		}
+	}
+	//End command not found
+	return tokList.end();
+}
+
+/* A specialty method for commands such as \arg that end at the end of a paragraph OR when another \arg is encountered
+ */
+
+list<Token>::iterator getTilAnyCommand(string theCommand, TokenList &tokList){
+	list<Token>::iterator anIterator;
+	return anIterator;
+}
+
+
+
+
+/*  Method for Adding a Simple Command
+ * Format: @command
+ * Plain commands, such as newline etc, they contain no other data
+ *  \n \\ \@ \& \$ \# \< \> \%
+ */
+ int addSimpleCommand(string theCommand, list <DoxygenEntity> &doxyList){
+	 
+		if (noisy) cout << "Parsing " << theCommand << endl;
+		doxyList.push_back(DoxygenEntity(theCommand));
+		return 1;
+}
+ 
+ /* NOT INCLUDED Simple Commands
+  * Format: @command
+  * Plain commands, such as newline etc, they contain no other data
+  */
+ int ignoreSimpleCommand(string theCommand, list <DoxygenEntity> &doxyList){
+	 
+		if (noisy) cout << "Not Adding " << theCommand << endl;
+		return 1;
+}
+ 
+ /* CommandWord
+  * Format: @command <word>
+  * Commands with a single WORD after then such as @b
+  * "a", "b", "c", "e", "em", "p", "def", "enum", "example", "package", 
+  * "relates", "namespace", "relatesalso","anchor", "dontinclude", "include", "includelineno"
+  */
+ int addCommandWord(string theCommand, TokenList &tokList, list <DoxygenEntity> &doxyList){
+	if (noisy) cout << "Parsing " << theCommand << endl;
+	string name = getNextWord(tokList);
+	if (!name.empty()){ 
+		doxyList.push_back(DoxygenEntity(theCommand, name));
+		return 1;
+	}
+	else cout << "No word followed " << theCommand <<  " command. Not added" << endl;
+	return 0;
+}
+ /* NOT INCLUDED CommandWord
+  * Format: @command <word>
+  * Commands with a single WORD after then such as @b
+  * "copydoc", "copybrief", "copydetails", "verbinclude", "htmlinclude"
+  */
+ int ignoreCommandWord(string theCommand, TokenList &tokList, list <DoxygenEntity> &doxyList){
+	if (noisy) cout << "Not Adding " << theCommand << endl;
+	string name = getNextWord(tokList);
+	if (!name.empty()){ 
+		return 1;
+	}
+	else cout << "WARNING: No word followed " << theCommand <<  " command." << endl;
+	return 0;
+}
+ 
+ /* CommandLine
+  * Format: @command (line)
+  * Commands with a single LINE after then such as @var
+  * "addindex", "fn", "name", "line", "var", "skipline", "typedef", "skip", "until", "property"
+  */
+ int addCommandLine(string theCommand, TokenList &tokList, list <DoxygenEntity> &doxyList){
+	if (noisy) cout << "Parsing " << theCommand << endl;
+	list<Token>::iterator endOfLine = getOneLine(tokList);
+		list <DoxygenEntity> aNewList;
+		aNewList =  parse(endOfLine, tokList);
+		doxyList.push_back( DoxygenEntity(theCommand, aNewList));
+		return 1;
+
+}
+ 
+ /* NOT INCLUDED CommandLine
+  * Format: @command (line)
+  * Commands with a single LINE after then such as @var
+  * 
+  */
+ int ignoreCommandLine(string theCommand, TokenList &tokList, list <DoxygenEntity> &doxyList){
+	if (noisy) cout << "Not Adding " << theCommand << endl;
+	list<Token>::iterator endOfLine = getOneLine(tokList);
+	tokList.setIterator(endOfLine);
+	return 1;
+}
+ 
+ /* CommandParagraph
+  * Format: @command {paragraph}
+  * Commands with a single paragraph after then such as @return
+  * "return", "remarks", "since", "test", "sa", "see", "pre", "post", "details", "invariant", 
+  * "deprecated", "date", "note", "warning", "version", "todo", "bug", "attention", "brief", "arg", "author"
+  */
+ int addCommandParagraph(string theCommand, TokenList &tokList, list <DoxygenEntity> &doxyList){
+	if (noisy) cout << "Parsing " << theCommand << endl;
+	list<Token>::iterator endOfParagraph = getEndOfParagraph(tokList);
+	//if(!restOfParagraph.empty()){
+	list <DoxygenEntity> aNewList;
+	aNewList =  parse(endOfParagraph, tokList);
+	doxyList.push_back( DoxygenEntity(theCommand, aNewList));
+	return 1;
+	//	}
+	//else cout << "No line followed " << theCommand <<  " command. Not added" << endl;
+}
+ /* CommandParagraph
+  * Format: @command {paragraph}
+  * Commands with a single LINE after then such as @var
+  * 
+  */
+ int ignoreCommandParagraph(string theCommand, TokenList &tokList, list <DoxygenEntity> &doxyList){
+	if (noisy) cout << "Not Adding " << theCommand << endl;
+	list<Token>::iterator endOfParagraph = getEndOfParagraph(tokList);
+	tokList.setIterator(endOfParagraph);
+	//else cout << "WARNING: No line followed " << theCommand <<  " command." << endl;
+	return 1;
+}
+ /* Command EndCommand
+  * Format: @command and ends at @endcommand
+  * Commands that take in a block of text such as @code
+  * "code", "dot", "msc", "f$", "f[", "f{environment}{", "htmlonly", "latexonly", "manonly", 
+  * "verbatim", "xmlonly", "cond", "if", "ifnot", "link"
+  * Returns 1 if success, 0 if the endcommand is never encountered.
+  */
+ 
+ int addCommandEndCommand(string theCommand, TokenList &tokList, list <DoxygenEntity> &doxyList){
+	  if (noisy) cout << "Not Adding " << theCommand << endl;
+	  string description = getStringTilEndCommand( "end" + theCommand, tokList);
+	  doxyList.push_back(DoxygenEntity(theCommand, description));
+	  return 1;
+ }
+ 
+ /* CommandWordParagraph
+  * Format: @command <word> {paragraph}
+  * Commands such as param
+  * "param", "tparam", "throw", "retval", "exception"
+  */
+ int addCommandWordParagraph(string theCommand, TokenList &tokList, list <DoxygenEntity> &doxyList){
+	if (noisy) cout << "Parsing " << theCommand << endl;
+	string name = getNextWord(tokList);
+	if (name.empty()){ 
+		cout << "No word followed " << theCommand <<  " command. Not added" << endl;
+		return 0;
+		}
+	  list<Token>::iterator endOfParagraph = getEndOfParagraph(tokList);
+	    //if(!restOfParagraph.empty()){
+		list <DoxygenEntity> aNewList;
+		aNewList =  parse(endOfParagraph, tokList);
+		aNewList.push_front(DoxygenEntity("plainstring", name));
+		doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+	return 0;
+ }
+ /* CommandWordLine
+  * Format: @command <word> (line)
+  * Commands such as param
+  * "page", "subsection", "subsubsection", "section", "paragraph", "defgroup"
+  */
+ int addCommandWordLine(string theCommand, TokenList &tokList, list <DoxygenEntity> &doxyList){
+	if (noisy) cout << "Parsing " << theCommand << endl;
+	string name = getNextWord(tokList);
+	if (name.empty()){ 
+		cout << "No word followed " << theCommand <<  " command. Not added" << endl;
+		return 0;
+		}
+	list<Token>::iterator endOfLine = getOneLine(tokList);
+	list <DoxygenEntity> aNewList;
+	aNewList =  parse(endOfLine, tokList);
+	aNewList.push_front(DoxygenEntity("plainstring", name));
+	doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+	return 1;
+		
+	//else cout << "No line followed " << theCommand <<  " command. Not added" << endl;
+ }
+
+ /* Command Word Optional Word Optional Word
+  * Format: @command <word> [<header-file>] [<header-name>]
+  * Commands such as class
+  * "category", "class", "protocol", "interface", "struct", "union"
+  */
+ int addCommandWordOWordOWord(string theCommand, TokenList &tokList, list <DoxygenEntity> &doxyList){
+	if (noisy) cout << "Parsing " << theCommand << endl;
+	string name = getNextWord(tokList);
+	if (name.empty()){ 
+			cout << "No word followed " << theCommand <<  " command. Not added" << endl;
+			return 0;
+			}
+	string headerfile = getNextWord(tokList);
+	string headername = getNextWord(tokList);
+	list <DoxygenEntity> aNewList;
+	aNewList.push_back(DoxygenEntity("plainstring", name));
+	if (!headerfile.empty()) aNewList.push_back(DoxygenEntity("plainstring", headerfile));
+	if (!headername.empty()) aNewList.push_back(DoxygenEntity("plainstring", headername));
+	doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+	return 1;
+ }
+ 
+ /* Command Optional Word
+  * Format: @command [<word>]
+  * Commands such as dir
+  * "dir", "file", "cond"
+  */
+ int addCommandOWord(string theCommand, TokenList &tokList, list <DoxygenEntity> &doxyList){
+	if (noisy) cout << "Parsing " << theCommand << endl;
+	string name = getNextWord(tokList);
+	doxyList.push_back(DoxygenEntity(theCommand, name));
+	return 1; 
+ }
+
+ /* Commands that should not be encountered (such as PHP only)
+  */
+ int addCommandErrorThrow(string theCommand, TokenList &tokList, list <DoxygenEntity> &doxyList){
+	  cout << "Encountered :" << theCommand << endl;
+	  cout << "This command should not have been encountered. Behaviour past this may be unpredictable " << endl;
+ }
+
+
+ int addCommandUnique(string theCommand, TokenList &tokList, list <DoxygenEntity> &doxyList){
+	  list <DoxygenEntity> aNewList;
+	  if (theCommand.compare("arg") == 0 || theCommand.compare("li") == 0){
+			list<Token>::iterator endOfSection = getEndOfSection(theCommand, tokList);
+			list <DoxygenEntity> aNewList;
+			aNewList =  parse(endOfSection, tokList);
+			doxyList.push_back( DoxygenEntity(theCommand, aNewList));
+	  }
+	  
+	  // \xrefitem <key> "(heading)" "(list title)" {text}
+	  else if (theCommand.compare("xrefitem") == 0){
+		  //TODO Implement xrefitem
+			if (noisy) cout << "Not Adding " << theCommand << endl;
+			list<Token>::iterator endOfParagraph = getEndOfParagraph(tokList);
+			tokList.setIterator(endOfParagraph);
+		  return 1;
+	  }
+	  // \ingroup (<groupname> [<groupname> <groupname>])
+	  else if (theCommand.compare("ingroup") == 0){
+		  string name = getNextWord(tokList);
+		  aNewList.push_back(DoxygenEntity("plainstring", name));
+		  name = getNextWord(tokList);
+		  if(!name.empty()) aNewList.push_back(DoxygenEntity("plainstring", name));
+		  name = getNextWord(tokList);
+		  if(!name.empty()) aNewList.push_back(DoxygenEntity("plainstring", name));
+		  doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+		  return 1;
+	  }
+	  // \par [(paragraph title)] { paragraph }
+	  else if (theCommand.compare("par") == 0){
+		  list<Token>::iterator endOfLine = getOneLine(tokList);
+		  aNewList =  parse(endOfLine, tokList);
+		  list <DoxygenEntity> aNewList2;
+		  aNewList2 = parse(endOfLine, tokList);
+		  aNewList.splice(aNewList.end(), aNewList2);
+		  doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+		  return 1; 
+	  }
+	  // \headerfile <header-file> [<header-name>]
+	  else if (theCommand.compare("headerfile") == 0){
+		  list <DoxygenEntity> aNewList;
+		  string name = getNextWord(tokList);
+		  aNewList.push_back(DoxygenEntity("plainstring", name));
+		  name = getNextWord(tokList);
+		  if(!name.empty()) aNewList.push_back(DoxygenEntity("plainstring", name));
+		  doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+		  return 1;
+	  }
+	  // \overload [(function declaration)]
+	  else if (theCommand.compare("overload") == 0){
+		  list<Token>::iterator endOfLine = getOneLine(tokList);
+		  if (endOfLine != tokList.current()){
+		  list <DoxygenEntity> aNewList;
+		  aNewList =  parse(endOfLine, tokList);
+		  doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+		  }
+		  else doxyList.push_back(DoxygenEntity(theCommand));
+	  }
+	  // \weakgroup <name> [(title)]
+	  else if (theCommand.compare("weakgroup") == 0){
+		    if (noisy) cout << "Parsing " << theCommand << endl;
+			string name = getNextWord(tokList);
+			if (name.empty()){ 
+				cout << "No word followed " << theCommand <<  " command. Not added" << endl;
+				return 0;
+				}
+			list <DoxygenEntity> aNewList;
+			list<Token>::iterator endOfLine = getOneLine(tokList);
+			if (endOfLine != tokList.current()) {
+				aNewList =  parse(endOfLine, tokList);
+			}
+			aNewList.push_front(DoxygenEntity("plainstring", name));
+			doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+	  }
+	  // \ref <name> ["(text)"]
+	  else if (theCommand.compare("ref") == 0){
+		  //TODO Implement ref
+			if (noisy) cout << "Not Adding " << theCommand << endl;
+			list<Token>::iterator endOfParagraph = getEndOfParagraph(tokList);
+			tokList.setIterator(endOfParagraph);
+	  }
+	  // \subpage <name> ["(text)"]
+	  else if (theCommand.compare("subpage") == 0){
+		  //TODO implement subpage
+			if (noisy) cout << "Not Adding " << theCommand << endl;
+			list<Token>::iterator endOfParagraph = getEndOfParagraph(tokList);
+			tokList.setIterator(endOfParagraph);
+	  }
+	  // \dotfile <file> ["caption"]
+	  else if (theCommand.compare("dotfile") == 0){
+		  //TODO implement dotfile
+			if (noisy) cout << "Not Adding " << theCommand << endl;
+			list<Token>::iterator endOfParagraph = getEndOfParagraph(tokList);
+			tokList.setIterator(endOfParagraph);
+	  }
+	  // \image <format> <file> ["caption"] [<sizeindication>=<size>]
+	  else if (theCommand.compare("image") == 0){
+		  //todo implement image
+	  } 
+	  // \addtogroup <name> [(title)]
+	  else if (theCommand.compare("addtogroup") == 0){
+		    if (noisy) cout << "Parsing " << theCommand << endl;
+			string name = getNextWord(tokList);
+			if (name.empty()){ 
+				cout << "No word followed " << theCommand <<  " command. Not added" << endl;
+				return 0;
+				}
+			list <DoxygenEntity> aNewList;
+			list<Token>::iterator endOfLine = getOneLine(tokList);
+			if (endOfLine != tokList.current()) {
+				aNewList =  parse(endOfLine, tokList);
+			}
+			aNewList.push_front(DoxygenEntity("plainstring", name));
+			doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+	  }
+
+ }
+ 
+/* The actual "meat" of the doxygen parser. This is not yet fully implemented
+ * with my current design- however the skeletal outline is contained in
+ * the file Skeleton
+ */
+
+
+int addCommand(string commandString, TokenList &tokList,list <DoxygenEntity> &doxyList){
+	 string theCommand = StringToLower(commandString);
+
+	 if (theCommand.compare("plainstring") == 0){
+	 		string nextPhrase = getStringTilCommand( tokList);
+	 		if (noisy) cout << "Parsing plain string :" << nextPhrase << endl;
+	 		doxyList.push_back(DoxygenEntity("plainstring", nextPhrase ));
+	 		return 1;
+	 }
+	 int commandNumber = commandBelongs(theCommand);
+	 if (commandNumber == SIMPLECOMMAND){
+	 	return addSimpleCommand(theCommand, doxyList);
+	 	}
+	 if (commandNumber == IGNOREDSIMPLECOMMAND){
+	 	return ignoreSimpleCommand(theCommand, doxyList);
+	 	}
+	 if (commandNumber == COMMANDWORD){
+	 	return addCommandWord(theCommand, tokList, doxyList);
+	 	}
+	 if (commandNumber == IGNOREDCOMMANDWORD){
+	 	return ignoreCommandWord(theCommand, tokList, doxyList);
+	 	}
+	 if (commandNumber == COMMANDLINE ){
+	 	return addCommandLine(theCommand, tokList, doxyList);
+	 	}
+	 if (commandNumber == IGNOREDCOMMANDLINE ){
+	 	return ignoreCommandLine(theCommand, tokList, doxyList);
+	 	}
+	 if (commandNumber == COMMANDPARAGRAPH){
+	 	return addCommandParagraph(theCommand, tokList, doxyList);
+	 	}
+	 if (commandNumber == IGNORECOMMANDPARAGRAPH){
+	 	return ignoreCommandParagraph(theCommand, tokList, doxyList);
+	 	}
+	 if (commandNumber == COMMANDENDCOMMAND){
+	 	return addCommandEndCommand(theCommand, tokList, doxyList);
+	 	}
+	 if (commandNumber == COMMANDWORDPARAGRAPH){
+	 	return addCommandWordParagraph(theCommand, tokList, doxyList);
+	 	}
+	 if (commandNumber == COMMANDWORDLINE){
+	 	return addCommandWordLine(theCommand, tokList, doxyList);
+	 	}
+	 if (commandNumber == COMMANDWORDOWORDWORD){
+	 	return addCommandWordOWordOWord(theCommand, tokList, doxyList);
+	 	}
+	 if (commandNumber == COMMANDOWORD){
+	 	return addCommandOWord(theCommand, tokList, doxyList);
+	 	}
+	 if (commandNumber == COMMANDERRORTHROW){
+	 	return addCommandErrorThrow(theCommand, tokList, doxyList);
+	 	}
+	 if (commandNumber == COMMANDUNIQUE){
+		return addCommandUnique(theCommand, tokList, doxyList);
+	 	}
+	 	
+	 	return 0;
+}
+
+list<DoxygenEntity> parse(list<Token>::iterator endParsingIndex, TokenList &tokList){
+	list <DoxygenEntity> aNewList;
+	int currCommand;
+	while (tokList.current() != endParsingIndex){ 
+		Token currToken = tokList.peek();
+		if(noisy) cout << "Parsing for phrase starting in:" << currToken.toString() << endl;
+		if(currToken.tokenType == END_LINE ){
+			tokList.next();
+		}
+		else if(currToken.tokenType == COMMAND){
+			currCommand = findCommand(currToken.tokenString);
+			tokList.next();
+			if (currCommand < 0 ){ if(noisy) cout << "BAD COMMAND: " << currToken.tokenString << endl;}
+				//cout << "Command: " << currWord << " " << currCommand << endl;
+
+			else addCommand(currToken.tokenString, tokList,  aNewList);
+		}
+		else if (currToken.tokenType == PLAINSTRING){
+			addCommand(string("plainstring"), tokList, aNewList);
+		}
+
+		
+	}
+
+	return aNewList;
+}
+
+list<DoxygenEntity> DoxygenParser::createTree(string doxygenBlob){
+	TokenList tokList = TokenList(doxygenBlob);
+	if(noisy) {
+		cout << "---TOKEN LIST---" << endl;
+		tokList.printList();
+	}
+	list <DoxygenEntity> rootList;
+	rootList = parse( tokList.end(), tokList);
+	if(noisy) {
+		cout << "PARSED LIST" << endl;
+		printTree(rootList);
+	}
+	return rootList;
+}
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.h b/Source/DoxygenTranslator/src/DoxygenParser.h
new file mode 100644
index 000000000..776fcf123
--- /dev/null
+++ b/Source/DoxygenTranslator/src/DoxygenParser.h
@@ -0,0 +1,19 @@
+#ifndef DOXYGENPARSER_H_
+#define DOXYGENPARSER_H_
+#include <cstdlib>
+#include <iostream>
+#include <fstream>
+#include <string>
+#include <list>
+#include "DoxygenEntity.h"
+#include "TokenList.h"
+#include "JavaDocConverter.h"
+class DoxygenParser
+{
+public:
+	DoxygenParser();
+	virtual ~DoxygenParser();
+	list <DoxygenEntity> createTree(string doxygen);
+};
+
+#endif /*DOXYGENPARSER_H_*/
diff --git a/Source/DoxygenTranslator/src/DoxygenTranslator.cpp b/Source/DoxygenTranslator/src/DoxygenTranslator.cpp
new file mode 100644
index 000000000..191057ae7
--- /dev/null
+++ b/Source/DoxygenTranslator/src/DoxygenTranslator.cpp
@@ -0,0 +1,41 @@
+
+
+#include "DoxygenParser.h"
+#include "DoxygenTranslator.h"
+#include <cstdlib>
+#include <iostream>
+#include <fstream>
+#include <string>
+#include <list>
+#include "DoxygenEntity.h"
+#include "TokenList.h"
+#include "JavaDocConverter.h"
+
+DoxygenParser doxyParse;
+JavaDocConverter jDC;
+
+DoxygenTranslator::DoxygenTranslator(){
+	doxyParse = DoxygenParser();
+    JavaDocConverter jDC = JavaDocConverter();
+}
+
+DoxygenTranslator::~DoxygenTranslator(){
+	
+}
+
+
+char *DoxygenTranslator::convert(char* doxygenBlob, char* option){
+	
+	list <DoxygenEntity> rootList = doxyParse.createTree(string(doxygenBlob));
+	rootList = doxyParse.createTree(string(doxygenBlob));
+	string returnedString;
+	if(strcmp(option, "JAVADOC") == 0){
+	    returnedString = jDC.convertToJavaDoc(rootList);
+	}
+	else cout << "Option not current supported.\n";
+	char *nonConstString;
+	nonConstString = (char *)malloc(returnedString.length() + 1);
+	strcpy(nonConstString, returnedString.c_str());
+	return nonConstString;
+}
+
diff --git a/Source/DoxygenTranslator/src/DoxygenTranslator.h b/Source/DoxygenTranslator/src/DoxygenTranslator.h
new file mode 100644
index 000000000..e5fe7bcbb
--- /dev/null
+++ b/Source/DoxygenTranslator/src/DoxygenTranslator.h
@@ -0,0 +1,10 @@
+#ifndef DOXYGENTRANSLATOR_H_
+#define DOXYGENTRANSLATOR_H_
+class DoxygenTranslator
+{
+public:
+	DoxygenTranslator();
+	virtual ~DoxygenTranslator();
+	char* convert(char* doxygenBlob, char* option);
+};
+#endif /*DOXYGENTRANSLATOR_H_*/
diff --git a/Source/DoxygenTranslator/src/Examples/DoxygenTransWTokenizer.cpp b/Source/DoxygenTranslator/src/Examples/DoxygenTransWTokenizer.cpp
new file mode 100644
index 000000000..299f59216
--- /dev/null
+++ b/Source/DoxygenTranslator/src/Examples/DoxygenTransWTokenizer.cpp
@@ -0,0 +1,924 @@
+/* The main class for translating blobs of Doxygen for SWIG
+ * by Cheryl Foil, mentor Olly Betts, for Google's Summer of Code Program
+ * Currently the spacing/format on this is a bit goofy in places, due to shuffling code
+ * between 2 editors! Apologies for anyone combing through it :)
+ */
+//TODO DOH instead of STL?
+//TODO Most commands are not fully implemented
+
+#include <cstdlib>
+#include <iostream>
+#include <fstream>
+#include <string>
+#include <list>
+#include "DoxygenEntity.h"
+#include "TokenList.h"
+#define SIMPLECOMMAND 1
+#define IGNOREDSIMPLECOMMAND 2
+#define COMMANDWORD 3
+#define IGNOREDCOMMANDWORD 4
+#define COMMANDLINE 5
+#define IGNOREDCOMMANDLINE 6
+#define COMMANDPARAGRAPH 7
+#define IGNORECOMMANDPARAGRAPH 8
+#define COMMANDENDCOMMAND 9
+#define COMMANDWORDPARAGRAPH 10
+#define COMMANDWORDLINE 11
+#define COMMANDWORDOWORDWORD 12
+#define COMMANDOWORD 13
+#define COMMANDERRORTHROW 14
+#define COMMANDUNIQUE 15
+using namespace std;
+
+
+//////////////////////////////////////////
+/*Set these to pick what internal functions
+to test. */
+
+//int testCommandParsingFunctions = 1;// not implemented
+
+int testCodeCrawlingFunctions = 0;
+int demonstrateParsing = 0;
+int runExamples = 0;
+int noisy = 0; // set this to 1 for extra chatter from the parsing stage.
+int addCommand(string commandName, int &startInd, list <DoxygenEntity> &doxyList, string doxygenString);
+//////////////////////////////////////////
+
+
+
+/* Globals*/
+
+
+// An array of all the commands and my generic description tag, plaindescription
+
+string commandArray[] = {"a", "addindex", "addtogroup", "anchor", "arg", "attention",
+		"author", "b", "brief", "bug", "c", "callgraph", "callergraph", "category",
+		"class", "code", "cond", "copybrief", "copydetails", "copydoc", "date", "def",
+		"defgroup", "deprecated", "details", "dir", "dontinclude", "dot", "dotfile", "e",
+		"else", "elseif", "em", "endcode", "endcond", "enddot", "endhtmlonly", "endif",
+		"endlatexonly", "endlink", "endmanonly", "endmsc", "endverbatim", "endxmlonly",
+		"enum", "example", "exception", "f$", "f[", "f]", "f{", "f}", "file", "fn", "headerfile",
+		"hideinitializer", "htmlinclude", "htmlonly", "if", "ifnot", "image", "include",
+		"includelineno", "ingroup", "internal", "invariant", "interface", "latexonly", "li",
+		"line", "link", "mainpage", "manonly", "msc", "n", "name", "namespace", "nosubgrouping",
+		"note", "overload", "p", "package", "page", "par", "paragraph", "param", "post", "pre",
+		"private", "privatesection", "property", "protected", "protectedsection", "protocol",
+		"public", "publicsection", "ref", "relates", "relatesalso", "remarks", "return", "retval",
+		"sa", "section", "see", "showinitializer", "since", "skip", "skipline", "struct", "subpage",
+		"subsection", "subsubsection", "test", "throw", "todo", "tparam", "typedef", "union", "until",
+		"var", "verbatim", "verbinclude", "version", "warning", "weakgroup", "xmlonly", "xrefitem",
+		"$", "@", "//","&", "~", "<", ">", "#", "%"};
+
+
+string sectionIndicators[] = { "attention", "author", "brief", "bug", "cond", "date", "deprecated", "details",
+		"else", "elseif", "endcond", "endif", "exception", "if", "ifnot", "invariant", "note", "par", "param",
+		"tparam", "post" , "pre", "remarks", "return", "retval", "sa", "see", "since", "test", "throw", "todo",
+		"version", "warning", "xrefitem" };
+
+/* All of the doxygen commands divided up by how they are parsed */
+string simpleCommands[] = {"n", "$", "@", "//", "&", "~", "<", ">", "#", "%"};
+string ignoredSimpleCommands[] = {"nothing at the moment"};
+string commandWords[] = {"a", "b", "c", "e", "em", "p", "def", "enum", "example", "package", 
+		"relates", "namespace", "relatesalso","anchor", "dontinclude", "include", "includelineno"};
+string ignoredCommandWords[] = {"copydoc", "copybrief", "copydetails", "verbinclude", "htmlinclude"};
+string commandLines[] = {"addindex", "fn", "name", "line", "var", "skipline", "typedef", "skip", "until", "property"};
+string ignoreCommandLines[] = {"nothing at the moment"};
+string commandParagraph[] = {"return", "remarks", "since", "test", "sa", "see", "pre", "post", "details", "invariant", 
+		    "deprecated", "date", "note", "warning", "version", "todo", "bug", "attention", "brief", "arg", "author"};
+string ignoreCommandParagraphs[] = {"nothing at the moment"};
+string commandEndCommands[] = {"code", "dot", "msc", "f$", "f[", "f{environment}{", "htmlonly", "latexonly", "manonly", 
+		   "verbatim", "xmlonly", "cond", "if", "ifnot", "link"};
+string commandWordParagraphs[] = {"param", "tparam", "throw", "retval", "exception"};
+string commandWordLines[] = {"page", "subsection", "subsubsection", "section", "paragraph", "defgroup"};
+string commandWordOWordOWords [] = {"category", "class", "protocol", "interface", "struct", "union"};
+string commandOWords[] = {"dir", "file", "cond"};
+string commandErrorThrowings[] = {"annotatedclasslist", "classhierarchy", "define", "functionindex", "header",
+		"headerfilelist", "inherit", "l", "postheader", "private", "privatesection", "protected", 
+		"protectedsection", "public", "publicsection", "endcode", "enddot", "endmsc", "endhtmlonly", 
+		"endlatexonly", "endmanonly", "endlink", "endverbatim", "endxmlonly", "f]", "f}", "endcond", 
+		"endif"};
+string commandUniques[] = {"xrefitem", "ingroup", "par", "headerfile", "overload", "weakgroup", "ref",
+		"subpage", "dotfile", "image", "addtogroup", "li"};
+
+ //int startIndex = 0;
+ int isNewLine = 0;
+ int briefDescExists = 0;
+
+ /* Entity list is the root list.
+  * it is arranged this way to help documentation modules,
+  * such as the javaDoc one, "sort" entities where they need to.
+  */
+
+ list <DoxygenEntity> rootList;
+
+/* General (untested) assist methods */
+
+ string StringToLower(string stringToConvert)
+
+ {//change each element of the string to lower case
+
+    for(unsigned int i=0;i<stringToConvert.length();i++)
+    {
+    stringToConvert[i] = tolower(stringToConvert[i]);
+    }
+    return stringToConvert;//return the converted string
+ }
+
+ int findCommand(string smallString){
+
+ 	smallString = StringToLower(smallString);
+ 	int a;
+ 	for (int i = 0; i < sizeof(commandArray)/sizeof(*commandArray); i++){
+ 		if( (a = smallString.compare(commandArray[i])) == 0){
+ 			return 101 + i;
+ 		}
+
+
+ 	}
+ 	return -1;
+ }
+ 
+ int commandBelongs(string theCommand){
+	 string smallString = StringToLower(theCommand );
+	 //cout << " Looking for command " << theCommand << endl;
+	 int i = 0;
+	 for ( i = 0; i < sizeof(simpleCommands)/sizeof(*simpleCommands); i++){
+	 	if(smallString.compare(simpleCommands[i]) == 0){return SIMPLECOMMAND ;}
+	 	}
+	 for ( i = 0; i < sizeof(ignoredSimpleCommands)/sizeof(*ignoredSimpleCommands); i++){
+	 	if(smallString.compare(ignoredSimpleCommands[i]) == 0){return IGNOREDSIMPLECOMMAND;}
+	 	} 
+	 for ( i = 0; i < sizeof(commandWords)/sizeof(*commandWords); i++){
+	 	if(smallString.compare( commandWords[i]) == 0){return COMMANDWORD;}
+	 	} 
+	 for ( i = 0; i < sizeof(ignoredCommandWords)/sizeof(*ignoredCommandWords); i++){
+	 	if(smallString.compare( ignoredCommandWords[i]) == 0){return IGNOREDCOMMANDWORD;}
+	 	} 
+	 for ( i = 0; i < sizeof(commandLines)/sizeof(*commandLines); i++){
+	 	if(smallString.compare( commandLines[i]) == 0){return COMMANDLINE;}
+	 	} 
+	 for ( i = 0; i < sizeof(ignoreCommandLines)/sizeof(*ignoreCommandLines); i++){
+	 	if(smallString.compare( ignoreCommandLines[i]) == 0){return IGNOREDCOMMANDLINE;}
+	 	} 
+	 for ( i = 0; i <  sizeof(commandParagraph)/sizeof(*commandParagraph); i++){
+	 	if(smallString.compare( commandParagraph[i]) == 0){return COMMANDPARAGRAPH;}
+	 	} 
+	 /* IgnoreCommandParagraph */
+	 for ( i = 0; i < sizeof(ignoreCommandParagraphs)/sizeof(*ignoreCommandParagraphs); i++){
+	 	if(smallString.compare( ignoreCommandParagraphs[i]) == 0){return IGNORECOMMANDPARAGRAPH;}
+	 	} 
+	 for ( i = 0; i < sizeof(commandEndCommands)/sizeof(*commandEndCommands); i++){
+	 	if(smallString.compare( commandEndCommands[i]) == 0){return COMMANDENDCOMMAND ;}
+	 	} 
+	 for ( i = 0; i < sizeof(commandWordParagraphs)/sizeof(*commandWordParagraphs); i++){
+	 	if(smallString.compare( commandWordParagraphs[i]) == 0){return COMMANDWORDPARAGRAPH;}
+	 	} 
+	 for ( i = 0; i < sizeof(commandWordLines)/sizeof(*commandWordLines); i++){
+	 	if(smallString.compare( commandWordLines[i]) == 0){return COMMANDWORDLINE ;}
+	 	} 
+	 for ( i = 0; i < sizeof(commandWordOWordOWords)/sizeof(*commandWordOWordOWords); i++){
+	 	if(smallString.compare( commandWordOWordOWords[i]) == 0){return COMMANDWORDOWORDWORD;}
+	 	} 
+	 for ( i = 0; i < sizeof(commandOWords)/sizeof(*commandOWords); i++){
+	 	if(smallString.compare( commandOWords[i]) == 0){return COMMANDOWORD;}
+	 	} 
+	 for ( i = 0; i < sizeof(commandErrorThrowings)/sizeof(*commandErrorThrowings); i++){
+	 	if(smallString.compare( commandErrorThrowings[i]) == 0){return COMMANDERRORTHROW;}
+	 	} 
+	 for ( i = 0; i < sizeof(commandUniques)/sizeof(*commandUniques); i++){
+	 	if(smallString.compare( commandUniques[i]) == 0){return COMMANDUNIQUE;}
+	 	} 
+
+	 	return 0;
+	 
+ }
+
+ /* isSectionIndicator returns a boolean if the command is a section indicator
+  * This is a helper method for finding the end of a paragraph
+  * by Doxygen's terms
+  */
+ int isSectionIndicator(string smallString){
+ 	smallString = StringToLower(smallString);
+
+ 	for (int i = 0; i < sizeof( sectionIndicators)/sizeof(* sectionIndicators); i++){
+ 		if( smallString.compare( sectionIndicators[i]) == 0){
+ 			return 1;
+ 		}
+ 	}
+ 	return 0;
+ }
+
+
+ /* HELPER METHODS
+  * To test these, change the flags at the top of this class
+  */
+
+ /* Tiny method to compartmentalise the removal of all optional comment fluff such as ///
+  * or **** that often occurs before commment blobs.
+  */
+ int clearFluff(int &startInd, string doxygenString){
+	int startIndex = startInd;
+ 	int amountRemoved = 0;
+
+ 	while(doxygenString[startIndex] == '/'|| doxygenString[startIndex] == '!' || doxygenString[startIndex] == '*'
+ 			|| doxygenString[startIndex] == '\n' || doxygenString[startIndex] == ' '|| doxygenString[startIndex] == '\t'){
+ 		startIndex++;
+ 		amountRemoved++;
+ 		}
+ 	startInd = startIndex;
+ 	return startIndex;
+ }
+
+ /* Returns the next word ON THE CURRENT LINE ONLY
+  * if a new line is encountered, returns a blank string.
+  * Updates the index it is given after completion.
+  */
+
+ string getNextWord(int &startInd, string doxygenString){
+	int startIndex = startInd;
+ 	string nextWord;
+ 	while (startIndex < doxygenString.length() && (doxygenString[startIndex] == '/'|| doxygenString[startIndex] == ' '
+ 		|| doxygenString[startIndex] == '*' || doxygenString[startIndex]== '\n' || doxygenString[startIndex] == '\t'
+		|| doxygenString[startIndex] == '!')){
+ 		if(doxygenString[startIndex]== '\n'){ startInd = startIndex; return nextWord;}
+ 		startIndex++;
+ 		//cout << "Start Index" << startIndex << endl;
+ 		}
+ 	//cout << doxygenString[startIndex] << endl;
+ 	int endIndex = startIndex;
+
+ 	while (endIndex < doxygenString.length() && (doxygenString[endIndex]!= '\n' && doxygenString[endIndex]!= ' ')){
+ 		endIndex++;
+ 		//cout << "End Index " << endIndex << endl;
+ 		}
+ 	nextWord = doxygenString.substr(startIndex, endIndex - startIndex);
+ 	startInd = endIndex;
+ 	//cout << "Next Word :" << nextWord << ":" << endl;
+ 	return nextWord;
+ }
+
+ /* Returns the string remaining on a line
+  * and moved the index to the NEXT line
+  * returns "" if nothing on the current line.
+  */
+ string getOneLine(int &startInd, string doxygenString){
+	int startIndex = startInd;
+ 	while (doxygenString[startIndex] == '/'|| doxygenString[startIndex] == ' '
+ 		|| doxygenString[startIndex] == '*' || doxygenString[startIndex]== '\n'
+		|| doxygenString[startIndex] == '!' || doxygenString[startIndex] == '\t'){
+ 		if(doxygenString[startIndex]== '\n') return "";
+ 		startIndex++;
+ 		}
+
+	int endIndex = startIndex;
+ 	while ((endIndex != doxygenString.length())&& (doxygenString[endIndex] != '\n')){
+ 		endIndex++;
+ 		//cout << doxygenString[endIndex] << "End Index: " << endIndex << endl;
+ 		}
+ 	string returnedLine = doxygenString.substr(startIndex, endIndex - startIndex);
+ 	if (doxygenString[endIndex] == '\n' && (endIndex < doxygenString.length())) endIndex++;
+ 	startInd = endIndex;
+ 	return returnedLine;
+ }
+/* Returns a properly formatted (all doxygen *, //! etc removed)
+ * up til ANY command or end of paragraph is encountered. Has all the same issues as
+ * getStringTilEndOfParagraph formatting wise.
+ */
+string getStringTilCommand(int &startInd, string doxygenString){
+	 if (startInd >= doxygenString.length()) return "";
+	int startIndex = startInd;
+	int endIndex = startInd;
+ 	string description;
+ 	/* Find the End of the description */
+ 	int keepLooping = 1;
+ 	int spareIndex = 0;
+ 	int counter;
+ 	int finalIndex;
+ 	while(keepLooping){
+ 	 	if(endIndex >= doxygenString.length()){
+ 	 			finalIndex = endIndex;
+ 	 			keepLooping = 0;
+ 	 		}
+ 	 	else if (doxygenString[endIndex] == '\n'){
+			//cout << "1 ";
+			counter = endIndex;
+			if ( keepLooping && endIndex < doxygenString.length()-1) {
+				counter++;
+				//cout << "Counter :" << counter << endl;
+				while(keepLooping && endIndex < doxygenString.length() && (doxygenString[counter] == ' ' ||
+				               doxygenString[counter] == '*'|| doxygenString[counter] == '\n'|| doxygenString[counter] == '/'
+				            	   || doxygenString[counter] == '!' || doxygenString[startIndex] == '\t') ){
+									if(doxygenString[counter] == '\n') {
+										//cout << "Blank line found" << endl;
+										keepLooping = 0;
+										finalIndex = counter;}
+									else{ counter++;}
+									}
+
+			}
+			//endIndex = counter;
+		}
+ 		else if (doxygenString[endIndex] == '\\' || doxygenString[endIndex] == '@'){
+ 			finalIndex = endIndex;
+ 			keepLooping = 0;
+ 			}
+		else if(endIndex < doxygenString.length() -2
+				&& string("**/").compare(doxygenString.substr(endIndex , endIndex  + 2)) == 0){
+			finalIndex = endIndex;
+			//cout << "3 ";
+			keepLooping = 0;
+		}
+ 		if(keepLooping){
+ 			//cout << "4 ";
+ 			endIndex++;
+ 		}
+ 	}
+ 	//cout << "Done with EndIndex" << endl;
+ 	while(doxygenString[startIndex] == '!' || doxygenString[startIndex] == ' '
+ 		|| doxygenString[startIndex] == '/' || doxygenString[startIndex] == '*' || doxygenString[startIndex] == '\t') startIndex++;
+
+ 	for (int i = startIndex; i < endIndex; i++){
+
+ 		if (doxygenString[i] == '\n') {
+
+ 			while ((doxygenString[i] == '\n' || doxygenString[startIndex] == '\t'|| doxygenString[i] == ' '
+ 				|| doxygenString[i] == '*' || doxygenString[i] == '/')&& endIndex < doxygenString.length() - 1){
+ 				i++;
+ 				}
+ 			description.append(" ");
+ 		}
+ 		description.push_back(doxygenString[i]);
+ 		//cout << doxygenString[i];
+ 	}
+ 	//if(noisy) cout << "Final Index is: " << finalIndex << endl;
+ 	startInd = finalIndex;
+ 	return description;
+ }
+ 
+ 
+/* Returns a Paragraph- defined in Doxygen to be a paragraph of text
+ * seperate by either a structural command or a blank line
+ * This method is VERY messy currently
+ */
+ //TODO fix getStringTilEndOfParagraph to be more forgiving, work on ' ' characters
+ string getStringTilEndOfParagraph(int &startInd, string doxygenString){
+	 if (startInd >= doxygenString.length()) return "";
+	int startIndex = startInd;
+	int endIndex = startInd;
+ 	string description;
+ 	/* Find the End of the description */
+ 	int keepLooping = 1;
+ 	int spareIndex = 0;
+ 	int counter;
+ 	int finalIndex;
+ 	while(keepLooping){
+ 		if(endIndex >= doxygenString.length()){
+ 			finalIndex = endIndex;
+ 			keepLooping = 0;
+ 		}
+ 		else if (doxygenString[endIndex] == '\n'){
+			//cout << "1 ";
+			counter = endIndex;
+			if ( keepLooping && endIndex < doxygenString.length()-1) {
+				counter++;
+				//cout << "Counter :" << counter << endl;
+				while(keepLooping && endIndex < doxygenString.length() && (doxygenString[counter] == ' ' ||
+				               doxygenString[counter] == '*'|| doxygenString[startIndex] == '\t' || doxygenString[counter] == '\n'|| doxygenString[counter] == '/'
+				            	   || doxygenString[counter] == '!') ){
+									if(doxygenString[counter] == '\n') {
+										//cout << "Blank line found" << endl;
+										keepLooping = 0;
+										finalIndex = counter;}
+									else{ counter++;}
+									}
+
+			}
+			//endIndex = counter;
+		}
+ 		//todo this fix for not immediately exciting while parsing a paragraph seems somewhat cheap
+ 		else if (endIndex != startInd && doxygenString[endIndex] == '\\' || doxygenString[endIndex] == '@'){
+			spareIndex = endIndex +1;
+			
+ 			if (isSectionIndicator(getNextWord(spareIndex, doxygenString))) {
+ 				keepLooping = 0;
+ 				finalIndex = endIndex;}
+ 			}
+		else if(endIndex < doxygenString.length() - 1
+				&& string("*/").compare(doxygenString.substr(endIndex , endIndex  + 1)) == 0){
+			keepLooping = 0;
+			finalIndex = endIndex;
+		}
+ 		if(keepLooping){
+ 			endIndex++;
+ 		}
+ 	}
+ 	//cout << "Done with EndIndex" << endl;
+ 	while(doxygenString[startIndex] == '!' || doxygenString[startIndex] == ' ' || doxygenString[startIndex] == '\t'
+ 		|| doxygenString[startIndex] == '/' || doxygenString[startIndex] == '*') startIndex++;
+
+ 	for (int i = startIndex; i < endIndex; i++){
+
+ 		if (doxygenString[i] == '\n') {
+
+ 			while ((doxygenString[i] == '\n' || doxygenString[startIndex] == '\t' || doxygenString[i] == ' ' ||doxygenString[startIndex] == '!'
+ 				|| doxygenString[i] == '*' || doxygenString[i] == '/')&& endIndex < doxygenString.length() - 1){
+ 				i++;
+ 				}
+ 			description.append(" ");
+ 		}
+ 		description.push_back(doxygenString[i]);
+ 		//cout << doxygenString[i];
+ 	}
+ 	startInd = finalIndex;
+ 	return description;
+ }
+
+ /* This method is for a specific form of doxygen command
+  * that begins with a \command and ends in \endcommand
+  * such as \code and \endcode. The proper usage is
+  * progressTilEndCommand("endcode", index)
+  * currently this method does NOT process what is in between the two commands
+  */
+ //TODO Make progressTilCommand return a formatted string
+ int progressTilEndCommand(string theCommand, int &startInd, string doxygenString){
+ 	int endIndex = startInd;
+ 	while (endIndex < doxygenString.length()){
+ 		if (doxygenString[endIndex] == '\\' || doxygenString[endIndex] == '@'){
+ 			//cout << doxygenString.substr(endIndex + 1 , theCommand.length())<< endl;
+ 			if (theCommand.compare(doxygenString.substr(endIndex + 1 , theCommand.length())) == 0){
+ 				startInd = endIndex + theCommand.length() + 1;
+ 				return 1;
+ 			}
+ 		}
+ 		endIndex++;
+ 	}
+ 	//End command not found
+ 	return 0;
+ }
+
+ /* A specialty method for commands such as \arg that end at the end of a paragraph OR when another \arg is encountered
+  */
+ 
+ string getStringTilAnyCommand(string theCommand, int &startInd, string doxygenString){
+	 if (startInd >= doxygenString.length()) return "";
+		int startIndex = startInd;
+		int endIndex = startInd;
+	 	string description;
+	 	/* Find the End of the description */
+	 	int keepLooping = 1;
+	 	int spareIndex = 0;
+	 	int counter;
+	 	int finalIndex;
+	 	while(keepLooping){
+	 		if(endIndex >= theCommand.length()){
+	 			finalIndex = endIndex;
+	 			keepLooping = 0;
+	 		}
+	 		else if (doxygenString[endIndex] == '\n'){
+				//cout << "1 ";
+				counter = endIndex;
+				if ( keepLooping && endIndex < doxygenString.length()-1) {
+					counter++;
+					//cout << "Counter :" << counter << endl;
+					while(keepLooping && endIndex < doxygenString.length() && (doxygenString[counter] == ' ' ||
+					               doxygenString[counter] == '*'|| doxygenString[counter] == '\n'|| doxygenString[counter] == '/'
+					            	   || doxygenString[counter] == '!' || doxygenString[startIndex] == '\t') ){
+										if(doxygenString[counter] == '\n') {
+											//cout << "Blank line found" << endl;
+											keepLooping = 0;
+											finalIndex = counter;}
+										else{ counter++;}
+										}
+
+				}
+				//endIndex = counter;
+			}
+	 		else if (doxygenString[endIndex] == '\\' || doxygenString[endIndex] == '@'){
+	 			//cout << "2 ";
+				spareIndex = endIndex;
+	 			if (endIndex + theCommand.length() < theCommand.length() 
+	 					&& theCommand.compare(doxygenString.substr(endIndex, theCommand.length())) == 0) keepLooping = 0;
+	 			}
+			else if(endIndex < doxygenString.length() - 1
+					&& string("*/").compare(doxygenString.substr(endIndex , endIndex  + 1)) == 0){
+				//cout << "3 ";
+				keepLooping = 0;
+			}
+	 		if(keepLooping){
+	 			//cout << "4 ";
+	 			endIndex++;
+	 		}
+	 	}
+	 	//cout << "Done with EndIndex" << endl;
+	 	while(doxygenString[startIndex] == '!' || doxygenString[startIndex] == ' '
+	 		|| doxygenString[startIndex] == '/' || doxygenString[startIndex] == '*' || doxygenString[startIndex] == '\t') startIndex++;
+
+	 	for (int i = startIndex; i < endIndex; i++){
+
+	 		if (doxygenString[i] == '\n') {
+
+	 			while ((doxygenString[i] == '\n' || doxygenString[i] == ' ' || doxygenString[startIndex] == '\t'
+	 				|| doxygenString[i] == '*' || doxygenString[i] == '/')&& endIndex < doxygenString.length() - 1){
+	 				i++;
+	 				}
+	 			description.append(" ");
+	 		}
+	 		description.push_back(doxygenString[i]);
+	 		//cout << doxygenString[i];
+	 	}
+	 	startInd = finalIndex;
+	 	return description;
+ }
+
+
+ /* prints the parse tree
+  *
+  */
+ void printTree(){
+
+		list<DoxygenEntity>::iterator p = rootList.begin();
+		while (p != rootList.end()){
+			(*p).printEntity(0);
+			p++;
+		}
+
+ }
+ 
+ 
+ 
+ list<DoxygenEntity> parse(int startInd, string doxygenString){
+ 	string currWord;
+ 	int startIndex = startInd;
+ 	int savedIndex;
+ 	list <DoxygenEntity> aNewList;
+ 	int endIndex = doxygenString.length();
+ 	int currCommand;
+ 	while (startIndex < endIndex){
+ 		savedIndex = startIndex;
+ 		currWord = getNextWord(startIndex, doxygenString);
+ 		if(noisy) cout << "Parsing for phrase starting in:" << currWord << endl;
+ 		if(currWord == ""){
+ 			if (startIndex < endIndex) startIndex++;
+ 		}
+ 		else if(currWord[0] == '\\' || currWord[0] == '@'){
+ 			currWord = currWord.substr(1, currWord.length() - 1);
+ 			currCommand = findCommand(currWord);
+ 			if (currCommand < 0 ){ if(noisy) cout << "BAD COMMAND: " << currWord << endl;}
+ 				//cout << "Command: " << currWord << " " << currCommand << endl;
+ 			else addCommand(currWord, startIndex, aNewList, doxygenString);
+ 		}
+ 		else{
+ 			startIndex = savedIndex;
+			addCommand(string("plainstring"), startIndex, aNewList, doxygenString);
+
+ 		}
+ 	}
+
+ 	return aNewList;
+ }
+ 
+ /*  Method for Adding a Simple Command
+  * Format: @command
+  * Plain commands, such as newline etc, they contain no other data
+  *  \n \\ \@ \& \$ \# \< \> \%
+  */
+  int addSimpleCommand(string theCommand, int &startInd, list <DoxygenEntity> &doxyList, string doxygenString){
+	 
+		if (noisy) cout << "Parsing " << theCommand << endl;
+		doxyList.push_back(DoxygenEntity(theCommand));
+		return 1;
+ }
+  
+  /* NOT INCLUDED Simple Commands
+   * Format: @command
+   * Plain commands, such as newline etc, they contain no other data
+   */
+  int ignoreSimpleCommand(string theCommand, int &startInd, list <DoxygenEntity> &doxyList, string doxygenString){
+	 
+		if (noisy) cout << "Not Adding " << theCommand << endl;
+		return 1;
+ }
+  
+  /* CommandWord
+   * Format: @command <word>
+   * Commands with a single WORD after then such as @b
+   * "a", "b", "c", "e", "em", "p", "def", "enum", "example", "package", 
+   * "relates", "namespace", "relatesalso","anchor", "dontinclude", "include", "includelineno"
+   */
+  int addCommandWord(string theCommand, int &startInd, list <DoxygenEntity> &doxyList, string doxygenString){
+	if (noisy) cout << "Parsing " << theCommand << endl;
+	string name = getNextWord(startInd, doxygenString);
+	if (!name.empty()){ 
+		doxyList.push_back(DoxygenEntity(theCommand, name));
+		return 1;
+	}
+	else cout << "No word followed " << theCommand <<  " command. Not added" << endl;
+	return 0;
+ }
+  /* NOT INCLUDED CommandWord
+   * Format: @command <word>
+   * Commands with a single WORD after then such as @b
+   * "copydoc", "copybrief", "copydetails", "verbinclude", "htmlinclude"
+   */
+  int ignoreCommandWord(string theCommand, int &startInd, list <DoxygenEntity> &doxyList, string doxygenString){
+	if (noisy) cout << "Not Adding " << theCommand << endl;
+	string name = getNextWord(startInd, doxygenString);
+	if (!name.empty()){ 
+		return 1;
+	}
+	else cout << "WARNING: No word followed " << theCommand <<  " command." << endl;
+	return 0;
+ }
+  
+  /* CommandLine
+   * Format: @command (line)
+   * Commands with a single LINE after then such as @var
+   * "addindex", "fn", "name", "line", "var", "skipline", "typedef", "skip", "until", "property"
+   */
+  int addCommandLine(string theCommand, int &startInd, list <DoxygenEntity> &doxyList, string doxygenString){
+	if (noisy) cout << "Parsing " << theCommand << endl;
+	string line = getOneLine(startInd, doxygenString);
+	if(!line.empty()){
+		int placement = 0;
+		list <DoxygenEntity> aNewList;
+		aNewList =  parse(placement, line);
+		doxyList.push_back( DoxygenEntity(theCommand, aNewList));
+		return 1;
+		}
+	else cout << "No line followed " << theCommand <<  " command. Not added" << endl;
+	return 0;
+ }
+  
+  /* NOT INCLUDED CommandLine
+   * Format: @command (line)
+   * Commands with a single LINE after then such as @var
+   * 
+   */
+  int ignoreCommandLine(string theCommand, int &startInd, list <DoxygenEntity> &doxyList, string doxygenString){
+	if (noisy) cout << "Not Adding " << theCommand << endl;
+	string line = getOneLine(startInd, doxygenString);
+	if(!line.empty()){
+		return 1;
+		}
+	else cout << "WARNING: No line followed " << theCommand <<  " command." << endl;
+	return 0;
+ }
+  
+  /* CommandParagraph
+   * Format: @command {paragraph}
+   * Commands with a single paragraph after then such as @return
+   * "return", "remarks", "since", "test", "sa", "see", "pre", "post", "details", "invariant", 
+   * "deprecated", "date", "note", "warning", "version", "todo", "bug", "attention", "brief", "arg", "author"
+   */
+  int addCommandParagraph(string theCommand, int &startInd, list <DoxygenEntity> &doxyList, string doxygenString){
+	if (noisy) cout << "Parsing " << theCommand << endl;
+	string restOfParagraph = getStringTilEndOfParagraph(startInd, doxygenString);
+	if(!restOfParagraph.empty()){
+		int placement = 0;
+		list <DoxygenEntity> aNewList;
+		aNewList =  parse(placement, restOfParagraph);
+		doxyList.push_back( DoxygenEntity(theCommand, aNewList));
+		return 1;
+		}
+	else cout << "No line followed " << theCommand <<  " command. Not added" << endl;
+	return 0;
+ }
+  /* CommandParagraph
+   * Format: @command {paragraph}
+   * Commands with a single LINE after then such as @var
+   * 
+   */
+  int ignoreCommandParagraph(string theCommand, int &startInd, list <DoxygenEntity> &doxyList, string doxygenString){
+	if (noisy) cout << "Not Adding " << theCommand << endl;
+	string restOfParagraph = getStringTilEndOfParagraph(startInd, doxygenString);
+	if(!restOfParagraph.empty()){
+		return 1;
+		}
+	else cout << "WARNING: No line followed " << theCommand <<  " command." << endl;
+	return 0;
+ }
+  /* Command EndCommand
+   * Format: @command and ends at @endcommand
+   * Commands that take in a block of text such as @code
+   * "code", "dot", "msc", "f$", "f[", "f{environment}{", "htmlonly", "latexonly", "manonly", 
+   * "verbatim", "xmlonly", "cond", "if", "ifnot", "link"
+   * Returns 1 if success, 0 if the endcommand is never encountered.
+   */
+  
+  int ignoreCommandEndCommand(string theCommand, int &startInd, list <DoxygenEntity> &doxyList, string doxygenString){
+	  if (noisy) cout << "Not Adding " << theCommand << endl;
+	  return progressTilEndCommand( "end" + theCommand, startInd, doxygenString);
+	  
+  }
+  
+  /* CommandWordParagraph
+   * Format: @command <word> {paragraph}
+   * Commands such as param
+   * "param", "tparam", "throw", "retval", "exception"
+   */
+  int addCommandWordParagraph(string theCommand, int &startInd, list <DoxygenEntity> &doxyList, string doxygenString){
+	if (noisy) cout << "Parsing " << theCommand << endl;
+	string name = getNextWord(startInd, doxygenString);
+	if (name.empty()){ 
+		cout << "No word followed " << theCommand <<  " command. Not added" << endl;
+		return 0;
+		}
+	string restOfParagraph = getStringTilEndOfParagraph(startInd, doxygenString);
+	int placement = 0;
+	if(!restOfParagraph.empty()){
+		list <DoxygenEntity> aNewList;
+		aNewList =  parse(placement, restOfParagraph);
+		aNewList.push_front(DoxygenEntity("plainstring", name));
+		doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+		return 1;
+		}
+	else cout << "No paragraph followed " << theCommand <<  " command. Not added" << endl;
+	return 0;
+  }
+  /* CommandWordLine
+   * Format: @command <word> (line)
+   * Commands such as param
+   * "page", "subsection", "subsubsection", "section", "paragraph", "defgroup"
+   */
+  int addCommandWordLine(string theCommand, int &startInd, list <DoxygenEntity> &doxyList, string doxygenString){
+	if (noisy) cout << "Parsing " << theCommand << endl;
+	string name = getNextWord(startInd, doxygenString);
+	if (name.empty()){ 
+		cout << "No word followed " << theCommand <<  " command. Not added" << endl;
+		return 0;
+		}
+	string restOfLine = getStringTilEndOfParagraph(startInd, doxygenString);
+	int placement = 0;
+	if(!restOfLine.empty()){
+		list <DoxygenEntity> aNewList;
+		aNewList =  parse(placement, restOfLine);
+		aNewList.push_front(DoxygenEntity("plainstring", name));
+		doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+		return 1;
+		}
+	else cout << "No line followed " << theCommand <<  " command. Not added" << endl;
+	return 0;
+  }
+  
+  /* Command Word Optional Word Optional Word
+   * Format: @command <word> [<header-file>] [<header-name>]
+   * Commands such as class
+   * "category", "class", "protocol", "interface", "struct", "union"
+   */
+  int addCommandWordOWordOWord(string theCommand, int &startInd, list <DoxygenEntity> &doxyList, string doxygenString){
+	if (noisy) cout << "Parsing " << theCommand << endl;
+	string name = getNextWord(startInd, doxygenString);
+	if (name.empty()){ 
+			cout << "No word followed " << theCommand <<  " command. Not added" << endl;
+			return 0;
+			}
+	string headerfile = getNextWord(startInd, doxygenString);
+	string headername = getNextWord(startInd, doxygenString);
+	list <DoxygenEntity> aNewList;
+	aNewList.push_back(DoxygenEntity("plainstring", name));
+	if (!headerfile.empty()) aNewList.push_back(DoxygenEntity("plainstring", headerfile));
+	if (!headername.empty()) aNewList.push_back(DoxygenEntity("plainstring", headername));
+	doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+	return 1;
+  }
+  
+  /* Command Optional Word
+   * Format: @command [<word>]
+   * Commands such as dir
+   * "dir", "file", "cond"
+   */
+  int addCommandOWord(string theCommand, int &startInd, list <DoxygenEntity> &doxyList, string doxygenString){
+	if (noisy) cout << "Parsing " << theCommand << endl;
+	string name = getNextWord(startInd, doxygenString);
+	doxyList.push_back(DoxygenEntity(theCommand, name));
+	return 1; 
+  }
+  
+ /* The actual "meat" of the doxygen parser. This is not yet fully implemented
+  * with my current design- however the skeletal outline is contained in
+  * the file Skeleton
+  */
+
+
+ int addCommand(string commandString, int &startInd, list <DoxygenEntity> &doxyList, string doxygenString){
+	 string theCommand = StringToLower(commandString);
+	 string voidArray[] = {""};
+	 	/* @command */
+
+	 
+	 if (theCommand.compare("plainstring") == 0){
+	 		string nextPhrase = getStringTilCommand(startInd, doxygenString);
+	 		if (noisy) cout << "Parsing plain string :" << nextPhrase << endl;
+	 		doxyList.push_back(DoxygenEntity("plainstring", nextPhrase ));
+	 		return 1;
+	 }
+	 int commandNumber = commandBelongs(theCommand);
+	 if (commandNumber == SIMPLECOMMAND){
+	 	return addSimpleCommand(theCommand, startInd,doxyList, doxygenString);
+	 	}
+	 if (commandNumber == IGNOREDSIMPLECOMMAND){
+	 	return ignoreSimpleCommand(theCommand, startInd,doxyList, doxygenString);
+	 	}
+	 if (commandNumber == COMMANDWORD){
+	 	return addCommandWord(theCommand, startInd,doxyList, doxygenString);
+	 	}
+	 if (commandNumber == IGNOREDCOMMANDWORD){
+	 	return ignoreCommandWord(theCommand, startInd,doxyList, doxygenString);
+	 	}
+	 if (commandNumber == COMMANDLINE ){
+	 	return addCommandLine(theCommand, startInd,doxyList, doxygenString);
+	 	}
+	 if (commandNumber == IGNOREDCOMMANDLINE ){
+	 	return ignoreCommandLine(theCommand, startInd,doxyList, doxygenString);
+	 	}
+	 if (commandNumber == COMMANDPARAGRAPH){
+	 	return addCommandParagraph(theCommand, startInd,doxyList, doxygenString);
+	 	}
+	 if (commandNumber == IGNORECOMMANDPARAGRAPH){
+	 	return ignoreCommandParagraph(theCommand, startInd,doxyList, doxygenString);
+	 	}
+	 if (commandNumber == COMMANDENDCOMMAND){
+	 	return ignoreCommandEndCommand(theCommand, startInd,doxyList, doxygenString);
+	 	}
+	 if (commandNumber == COMMANDWORDPARAGRAPH){
+	 	return addCommandWordParagraph(theCommand, startInd,doxyList, doxygenString);
+	 	}
+	 if (commandNumber == COMMANDWORDLINE){
+	 	return addCommandWordLine(theCommand, startInd,doxyList, doxygenString);
+	 	}
+	 if (commandNumber == COMMANDWORDOWORDWORD){
+	 	return addCommandWordOWordOWord(theCommand, startInd,doxyList, doxygenString);
+	 	}
+	 if (commandNumber == COMMANDOWORD){
+	 	return addCommandOWord(theCommand, startInd,doxyList, doxygenString);
+	 	}
+	 if (commandNumber == COMMANDERRORTHROW){
+	 	return 0;
+	 	}
+	 if (commandNumber == COMMANDUNIQUE){
+	 	return 0;
+	 	}
+	 	
+	 	return 0;
+ }
+ 
+ int weirdTest(){
+	 string doxygenString = "this is a test.";
+	 string restOfParagraph;
+	 int startIndex = 0;
+	 restOfParagraph = getStringTilEndOfParagraph(startIndex , doxygenString);
+	 cout << restOfParagraph<< " " << startIndex << endl;
+	 
+	 startIndex = 0;
+	 restOfParagraph = getStringTilCommand(startIndex, doxygenString);
+	 cout << restOfParagraph<< " " << startIndex << endl;
+ }
+
+ 
+
+ int doRunExamples(){
+	 string line;
+	 string filename;
+	 string exampleNames[] = {"Examples/Example1","Examples/Example2", "Examples/Example3", "Examples/Example4", "Examples/Example5"};
+	 int placement;
+	 string doxygenString;
+	 ifstream doxCommentFile;
+	 for (int i = 0; i < 5; i++){
+	   doxCommentFile.open(exampleNames[i].c_str());
+	   doxCommentFile >> doxygenString;
+	   while(getline(doxCommentFile, line)){
+	   doxygenString += line + "\n";}
+	   doxCommentFile.close();
+	   placement = 0;
+	   cout << "---RAW CODE---" << endl << doxygenString << endl<<endl;
+	   //clearFluff(placement, doxygenString);
+	   //rootList = parse(placement, doxygenString);
+	 	TokenList tokList = TokenList(doxygenString);
+	 	tokList.printList();
+	   cout << "---THE TREE---" << endl;
+	   printTree();
+	 }
+	return 1; 
+ }
+ 
+ 
+ /* Returns a parse tree for a string */
+ int main(int argc, char *argv[]){
+	//weirdTest();
+ 	if(testCodeCrawlingFunctions) testCCF();
+ 	if(runExamples) doRunExamples();
+ 	if (demonstrateParsing){
+ 		string doxygenString = "//! A normal member taking two arguments and returning an integer value.\n/*!\n \\param a an integer argument. \\param s a constant character pointer\n \\return The test results\n  \\sa Test(), ~Test(), testMeToo() and publicVar()\n */";
+ 		//string doxygenString = " /** This is a small sentence.\n *\n@param x this is a parameter. \n \n This is a line with a @b bold letter \n * \n  @brief small @b description. \n\n * **/";
+ 		//string doxygenString = "This is a description.";
+ 		int placement = 0;
+ 		clearFluff(placement, doxygenString);
+ 		rootList = parse(placement, doxygenString);
+ 		cout << "---THE TREE---" << endl;
+ 		printTree();
+ 	}
+ 	string doxygenString2 = "//! A normal member taking two arguments and returning an integer value.\n/*!\n \\param a an integer argument. \\param s a constant character pointer\n\n\n\n \\return The test results\n  \\sa Test(), ~Test(), testMeToo() and publicVar()\n */";
+ 	TokenList tokList = TokenList(doxygenString2);
+ 	tokList.printList();
+ 		return 1;
+ }
\ No newline at end of file
diff --git a/Source/DoxygenTranslator/src/Examples/DoxygenTransWTokenizer.h b/Source/DoxygenTranslator/src/Examples/DoxygenTransWTokenizer.h
new file mode 100644
index 000000000..6b8b15e9b
--- /dev/null
+++ b/Source/DoxygenTranslator/src/Examples/DoxygenTransWTokenizer.h
@@ -0,0 +1,11 @@
+#ifndef DOXYGENTRANSWTOKENIZER_H_
+#define DOXYGENTRANSWTOKENIZER_H_
+
+class DoxygenTransWTokenizer
+{
+public:
+	DoxygenTransWTokenizer();
+	virtual ~DoxygenTransWTokenizer();
+};
+
+#endif /*DOXYGENTRANSWTOKENIZER_H_*/
diff --git a/Source/DoxygenTranslator/Examples/Example1 b/Source/DoxygenTranslator/src/Examples/Example1
similarity index 100%
rename from Source/DoxygenTranslator/Examples/Example1
rename to Source/DoxygenTranslator/src/Examples/Example1
diff --git a/Source/DoxygenTranslator/Examples/Example2 b/Source/DoxygenTranslator/src/Examples/Example2
similarity index 100%
rename from Source/DoxygenTranslator/Examples/Example2
rename to Source/DoxygenTranslator/src/Examples/Example2
diff --git a/Source/DoxygenTranslator/Examples/Example3 b/Source/DoxygenTranslator/src/Examples/Example3
similarity index 100%
rename from Source/DoxygenTranslator/Examples/Example3
rename to Source/DoxygenTranslator/src/Examples/Example3
diff --git a/Source/DoxygenTranslator/Examples/Example4 b/Source/DoxygenTranslator/src/Examples/Example4
similarity index 100%
rename from Source/DoxygenTranslator/Examples/Example4
rename to Source/DoxygenTranslator/src/Examples/Example4
diff --git a/Source/DoxygenTranslator/src/Examples/Example5 b/Source/DoxygenTranslator/src/Examples/Example5
new file mode 100644
index 000000000..e69de29bb
diff --git a/Source/DoxygenTranslator/src/Examples/Example6 b/Source/DoxygenTranslator/src/Examples/Example6
new file mode 100644
index 000000000..e69de29bb
diff --git a/Source/DoxygenTranslator/src/Examples/translator.h b/Source/DoxygenTranslator/src/Examples/translator.h
new file mode 100644
index 000000000..64920c5e0
--- /dev/null
+++ b/Source/DoxygenTranslator/src/Examples/translator.h
@@ -0,0 +1,144 @@
+#ifndef TRANSLATOR_H_
+#define TRANSLATOR_H_
+
+#define BRIEFDESCRIPTION     99
+#define LONGDESCRIPTION      100
+#define A_COMMAND       101  /* \a */
+#define ADDINDEX        102  /* \addindex */
+#define ADDTOGROUP      103  /* \addtogroup */
+#define ANCHOR          104  /* \anchor */
+#define ARG_COMMAND     105   /* \arg */
+#define ATTENTION       106   /* \attention */
+#define AUTHOR          107   /* \author */
+#define B_COMMAND       108    /* \b */
+#define BRIEF           109  /* \brief */
+#define BUG             110   /* \bug */
+#define C_COMMAND       111    /* \c */
+#define CALLGRAPH       112   /* \callgraph */
+#define CALLERGRAPH     113   /* \callergraph */
+#define CATEGORY        114    /* \category */
+#define CLASS_COMMAND   115   /* \class */
+#define CODE            116    /* \code */
+#define COND            117  /* \cond */
+#define COPYBRIEF       118  /* \copybrief */
+#define COPYDETAILS     119    /* \copydetails */
+#define COPYDOC         120  /* \copydoc */
+#define DATE            121    /* \date */
+#define DEF             122  /* \def */
+#define DEFGROUP        123    /* \defgroup */
+#define DEPRECATED      124    /* \deprecated */
+#define DETAILS         125   /* \details */
+#define DIR_COMMAND     126    /* \dir */
+#define DONTINCLUDE     127    /* \dontinclude */
+#define DOT             128    /* \dot */
+#define DOTFILE         129    /* \dotfile */
+#define E_COMMAND       130    /* \e */
+#define ELSE_COMMAND    131    /* \else */
+#define ELSEIF_COMMAND  132    /* \elseif */
+#define EM              133   /* \em */
+#define ENDCODE         134    /* \endcode  */
+#define ENDCOND         135    /* \endcond */
+#define ENDDOT          136   /* \enddot */
+#define ENDHTMLONLY     137    /* \endhtmlonly  */
+#define ENDIF           138    /* \endif */
+#define ENDLATEXONLY    139    /* \endlatexonly  */
+#define ENDLINK         140    /* \endlink */
+#define ENDMANONLY      141    /* \endmanonly */
+#define ENDMSC          142    /* \endmsc */
+#define ENDVERBATIM     143    /* \endverbatim */
+#define ENDXMLONLY      144    /* \endxmlonly */
+#define ENUM            145    /* \enum */
+#define EXAMPLE         146   /* \example */
+#define EXCEPTION       147    /* \exception */
+#define FDOLLAR         148    /* \f$ */
+#define FLEFTSQUAREBRACKET     149    /* \f[ */
+#define FRIGHTSQUAREBRACKET    150    /* \f] */
+#define FLEFTBRACKET           151   /* \f{ */
+#define FRIGHTBRACKET          152  /* \f} */
+#define FILE_COMMAND           153   /* \file */
+#define FN_COMMAND             154   /* \fn */
+#define HEADERFILE             155/* \headerfile */
+#define HIDEINITIALIZER        156    /* \hideinitializer */
+#define HTMLINCLUDE            157  /* \htmlinclude */
+#define HTMLONLY               158  /* \htmlonly */
+#define IF_COMMAND             159   /* \if */
+#define IFNOT_COMMAND          160   /* \ifnot */
+#define IMAGE                  161  /* \image */
+#define INCLUDE_COMMAND        162 /* \include */
+#define INCLUDELINENO          163   /* \includelineno */
+#define INGROUP                164   /* \ingroup */
+#define INTERNAL               165   /* \internal */
+#define INVARIANT              166   /* \invariant */
+#define INTERFACE_COMMAND      167    /* \interface */
+#define LATEXONLY              168   /* \latexonly */
+#define LI                     169 /* \li */
+#define LINE                   170   /* \line */
+#define LINK                   171   /* \link */
+#define MAINPAGE               172    /* \mainpage */
+#define MANONLY                173   /* \manonly */
+#define MSC                    174  /* \msc */
+#define N                      175  /* \n */
+#define NAME                   176  /* \name */
+#define NAMESPACE              177   /* \namespace */
+#define NOSUBGROUPING          178   /* \nosubgrouping */
+#define NOTE                   179   /* \note */
+#define OVERLOAD               180  /* \overload */
+#define P                      181  /* \p */
+#define PACKAGE                182   /* \package */
+#define PAGE                   183  /* \page */
+#define PAR                    184 /* \par */
+#define PARAGRAPH              185   /* \paragraph */
+#define PARAM                  186  /* \param */
+#define POST                   187  /* \post */
+#define PRE                    188   /* \pre */
+#define PRIVATE                189   /* \private (PHP only) */
+#define PRIVATESECTION         190   /* \privatesection (PHP only) */
+#define PROPERTY               191  /* \property */
+#define PROTECTED              192    /* \protected (PHP only) */
+#define PROTECTEDSECTION       193  /* \protectedsection (PHP only) */
+#define PROTOCOL               194    /* \protocol */
+#define PUBLIC                 195    /* \public (PHP only) */
+#define PUBLICSECTION          196    /* \publicsection (PHP only) */
+#define REF                          197 /* \ref */
+#define RELATES                      198    /* \relates */
+#define RELATESALSO                  199    /* \relatesalso */
+#define REMARKS                      200   /* \remarks */
+#define RETURN_COMMAND                       201    /* \return */
+#define RETVAL                       202    /* \retval */
+#define SA                           203    /* \sa */
+#define SECTION                      204   /* \section */
+#define SEE                          205   /* \see */
+#define SHOWINITIALIZER              206    /* \showinitializer */
+#define SINCE                        207  /* \since */
+#define SKIP                         208   /* \skip */
+#define SKIPLINE                     209   /* \skipline */
+#define STRUCT                       210  /* \struct */
+#define SUBPAGE                      211   /* \subpage */
+#define SUBSECTION                   212  /* \subsection */
+#define SUBSUBSECTION                213  /* \subsubsection */
+#define TEST                         214  /* \test */
+#define THROW_COMMAND                215 /* \throw */
+#define TODO_COMMAND                 216 /* \todo */
+#define TPARAM_COMMAND               217  /* \tparam */
+#define TYPEDEF_COMMAND              218   /* \typedef */
+#define UNION_COMMAND                219  /* \union */
+#define UNTIL_COMMAND                220  /* \until */
+#define VAR_COMMAND                  221  /* \var */
+#define VERBATIM                     222 /* \verbatim */
+#define VERBININCLUDE                223  /* \verbinclude */
+#define VERSION                      224 /* \version */
+#define WARNING                      225 /* \warning */
+#define WEAKGROUP                    226  /* \weakgroup */
+#define XMLONLY                      227/* \xmlonly */
+#define XREFITEM                     228  /* \xrefitem */
+#define DOLLAR_COMMAND               229   /* \$ */
+#define AT_COMMAND                   230 /* \@ */
+#define SLASH_COMMAND                231 /* \\ */
+#define AND_COMMAND                  232  /* \& */
+#define TILDE_COMMAND                233  /* \~ */
+#define LEFTANGLEBRACKET             234  /* \< */
+#define RIGHTANGLEBRACKET            235  /* \> */
+#define POUND_COMMAND                236 /* \# */
+#define PERCENT_COMMAND              237  /* \%  */
+
+#endif /*TRANSLATOR_H_*/
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.cpp b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
new file mode 100644
index 000000000..91f52662f
--- /dev/null
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
@@ -0,0 +1,210 @@
+#include "JavaDocConverter.h"
+#include <cstdlib>
+#include <iostream>
+#include <string>
+#include <list>
+#define APPROX_LINE_LENGTH 64//characters per line allowed
+#define TAB_SIZE 8//characters per line allowed
+int printSortedTree2 = 0;
+//TODO {@link} {@linkplain} {@docRoot}, and other useful doxy commands that are not a javadoc tag
+JavaDocConverter::JavaDocConverter()
+{
+}
+
+JavaDocConverter::~JavaDocConverter()
+{
+}
+
+/* Sorts entities by javaDoc standard order for commands
+ * NOTE: will not behave entirely properly until "First level" comments
+ * such as brief descriptions are TAGGED as such
+ */
+bool compare_DoxygenEntities(DoxygenEntity first, DoxygenEntity second){
+	if(first.typeOfEntity.compare("plainstring") == 0) return true;
+	if(second.typeOfEntity.compare("plainstring") == 0) return false;
+	if(first.typeOfEntity.compare("param") == 0){
+		if(second.typeOfEntity.compare("param")== 0) return true;
+		if(second.typeOfEntity.compare("return")== 0) return true;
+		if(second.typeOfEntity.compare("exception")== 0) return true;
+		if(second.typeOfEntity.compare("author")== 0) return true;
+		if(second.typeOfEntity.compare("version")== 0)return true;
+		if(second.typeOfEntity.compare("see")== 0)return true;
+		if(second.typeOfEntity.compare("since")== 0)return true;
+		if(second.typeOfEntity.compare("deprecated")== 0)return true;
+		return false;
+	}
+	if(first.typeOfEntity.compare("return")== 0){
+		if(second.typeOfEntity.compare("return")== 0) return true;
+		if(second.typeOfEntity.compare("exception")== 0) return true;
+		if(second.typeOfEntity.compare("author")== 0) return true;
+		if(second.typeOfEntity.compare("version")== 0)return true;
+		if(second.typeOfEntity.compare("see")== 0)return true;
+		if(second.typeOfEntity.compare("since")== 0)return true;
+		if(second.typeOfEntity.compare("deprecated")== 0)return true;
+		return false;
+
+	}
+	if(first.typeOfEntity.compare("exception")== 0){
+		if(second.typeOfEntity.compare("exception")== 0) return true;
+		if(second.typeOfEntity.compare("author")== 0) return true;
+		if(second.typeOfEntity.compare("version")== 0)return true;
+		if(second.typeOfEntity.compare("see")== 0)return true;
+		if(second.typeOfEntity.compare("since")== 0)return true;
+		if(second.typeOfEntity.compare("deprecated")== 0)return true;
+		return false;
+	}
+	if(first.typeOfEntity.compare("author")== 0){
+		if(first.typeOfEntity.compare("author")== 0) return true;
+		if(first.typeOfEntity.compare("version")== 0)return true;
+		if(first.typeOfEntity.compare("see")== 0)return true;
+		if(first.typeOfEntity.compare("since")== 0)return true;
+		if(first.typeOfEntity.compare("deprecated")== 0)return true;
+		return false;
+	}
+	if(first.typeOfEntity.compare("version")== 0){
+		if(second.typeOfEntity.compare("version")== 0)return true;
+		if(second.typeOfEntity.compare("see")== 0)return true;
+		if(second.typeOfEntity.compare("since")== 0)return true;
+		if(second.typeOfEntity.compare("deprecated")== 0)return true;
+		return false;
+	}
+	if(first.typeOfEntity.compare("see")== 0 || first.typeOfEntity.compare("sa")== 0){
+		if(second.typeOfEntity.compare("see")== 0)return true;
+		if(second.typeOfEntity.compare("sa")== 0)return true;
+		if(second.typeOfEntity.compare("since")== 0)return true;
+		if(second.typeOfEntity.compare("deprecated")== 0)return true;
+		return false;
+	}
+	if(first.typeOfEntity.compare("since")== 0){
+		if(second.typeOfEntity.compare("since")== 0) return true;
+		if(second.typeOfEntity.compare("deprecated")== 0)return true;
+		return false;
+	}
+	if(first.typeOfEntity.compare("deprecated")== 0){
+		if(second.typeOfEntity.compare("deprecated")== 0)return true;
+		return false;
+	}
+	return true;
+}
+
+void JavaDocConverter::printSortedTree(list <DoxygenEntity> &entityList){
+	list<DoxygenEntity>::iterator p = entityList.begin();
+	while (p != entityList.end()){
+		(*p).printEntity(0);
+		p++;
+	}
+}
+string formatCommand(string unformattedLine, int indent){
+	string formattedLines = "\n * ";
+	int lastPosition = 0;
+	int i = 0;
+	int isFirstLine  = 1;
+	while (i != -1 && i < unformattedLine.length()){
+		lastPosition = i;
+		if (isFirstLine){
+			i+=APPROX_LINE_LENGTH;
+		}
+		else i+=APPROX_LINE_LENGTH - indent*TAB_SIZE;
+		i = unformattedLine.find(" ", i);
+
+		if (i > 0 && i + 1 < unformattedLine.length()){
+			if (!isFirstLine) for (int j = 0; j < indent; j++) {
+				formattedLines.append("\t");
+				}
+			else {
+				isFirstLine = 0;
+			}
+			formattedLines.append(unformattedLine.substr(lastPosition, i - lastPosition + 1));
+			formattedLines.append("\n *");
+
+		}
+	}
+	if (lastPosition < unformattedLine.length()){
+		if (!isFirstLine) {for (int j = 0; j < indent; j++) {formattedLines.append("\t");}}
+		formattedLines.append(unformattedLine.substr(lastPosition, unformattedLine.length() - lastPosition));
+	}
+
+	return formattedLines;
+}
+
+/* Contains the conversions for tags
+ * could probably be much more efficient...
+ */
+string javaDocFormat(DoxygenEntity &doxygenEntity){
+	if (doxygenEntity.typeOfEntity.compare("plainstring") == 0){
+			return doxygenEntity.data;
+	}
+	else if (doxygenEntity.typeOfEntity.compare("brief") == 0){
+			return doxygenEntity.data;
+	}
+	if (doxygenEntity.typeOfEntity.compare("detailed") == 0){
+			return doxygenEntity.data;
+	}
+	else if (doxygenEntity.typeOfEntity.compare("b") == 0){
+		return "<b>" + doxygenEntity.data + "</b>";
+	}
+	else if (doxygenEntity.typeOfEntity.compare("c") == 0){
+		return "<tt>" + doxygenEntity.data + "</tt>";
+	}
+	return "";
+}
+
+
+string translateSubtree( DoxygenEntity &doxygenEntity){
+	string returnedString;
+	if (doxygenEntity.isLeaf){ return javaDocFormat(doxygenEntity) + " ";}
+	else {
+		returnedString += javaDocFormat(doxygenEntity);
+		list<DoxygenEntity>::iterator p = doxygenEntity.entityList.begin();
+		while (p != doxygenEntity.entityList.end()){
+			returnedString+= translateSubtree(*p);
+			p++;
+		}
+	}
+	return returnedString;
+}
+
+string translateEntity(DoxygenEntity &doxyEntity){
+	if(doxyEntity.typeOfEntity.compare("plainstring")== 0 || doxyEntity.typeOfEntity.compare("deprecated")== 0 || doxyEntity.typeOfEntity.compare("brief")== 0)
+		return formatCommand(doxyEntity.data, 0) + "\n * ";
+	else if(doxyEntity.typeOfEntity.compare("see") == 0){
+		return formatCommand(string("@" + doxyEntity.typeOfEntity + "\t\t" + translateSubtree(doxyEntity)), 2);
+	}
+	else if(doxyEntity.typeOfEntity.compare("return")== 0
+			|| doxyEntity.typeOfEntity.compare("author")== 0
+			|| doxyEntity.typeOfEntity.compare("param")== 0
+			|| doxyEntity.typeOfEntity.compare("since")== 0
+			|| doxyEntity.typeOfEntity.compare("version")== 0
+			|| doxyEntity.typeOfEntity.compare("exception") == 0
+			|| doxyEntity.typeOfEntity.compare("deprecated") == 0){
+		return formatCommand(string("@" + doxyEntity.typeOfEntity + "\t" + translateSubtree(doxyEntity)), 2);
+	}
+	else if(doxyEntity.typeOfEntity.compare("sa")== 0){
+		return formatCommand(string("@see\t\t" + translateSubtree(doxyEntity)), 2);
+	}
+
+	return "";
+}
+
+string JavaDocConverter:: convertToJavaDoc(list <DoxygenEntity> entityList){
+
+
+	entityList.sort(compare_DoxygenEntities);
+    if(printSortedTree2){
+	cout << "---RESORTED LIST---" << endl;
+    printSortedTree(entityList);
+    }
+
+	string javaDocString = "/**";
+
+	list<DoxygenEntity>::iterator entityIterator = entityList.begin();
+	while (entityIterator != entityList.end()){
+		javaDocString += translateEntity(*entityIterator);
+		entityIterator++;
+	}
+
+	javaDocString += "\n */\n";
+	cout << "\n---RESULT IN JAVADOC---" << endl;
+	cout << javaDocString;
+	return javaDocString;
+}
\ No newline at end of file
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.h b/Source/DoxygenTranslator/src/JavaDocConverter.h
new file mode 100644
index 000000000..81122bc5f
--- /dev/null
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.h
@@ -0,0 +1,18 @@
+ #include <list>
+ #include <string>
+ #include "DoxygenEntity.h"
+
+#ifndef JAVADOCCONVERTER_H_
+#define JAVADOCCONVERTER_H_
+
+class JavaDocConverter
+{
+public:
+
+	JavaDocConverter();
+	string convertToJavaDoc(list <DoxygenEntity> entityList);
+	~JavaDocConverter();
+	void printSortedTree(list <DoxygenEntity> &entityList);
+};
+
+#endif /*JAVADOCCONVERTER_H_*/
diff --git a/Source/DoxygenTranslator/src/Token.cpp b/Source/DoxygenTranslator/src/Token.cpp
new file mode 100644
index 000000000..e85799546
--- /dev/null
+++ b/Source/DoxygenTranslator/src/Token.cpp
@@ -0,0 +1,32 @@
+#include "Token.h"
+#include <cstdlib>
+#include <iostream>
+#include <string>
+#include <list>
+using namespace std;
+
+
+Token::Token(int tType, string tString)
+{	
+	tokenType = tType;
+	tokenString = tString;
+}
+
+string Token::toString()
+{
+	if (tokenType == END_LINE){
+		return "{END OF LINE}";
+	}
+	if (tokenType == PARAGRAPH_END){
+		return "{END OF PARAGRAPH}";
+	}
+	if (tokenType == PLAINSTRING){
+		return tokenString;
+	}
+	if (tokenType == COMMAND){
+		return "{COMMAND : " + tokenString+ "}";
+	}
+	return "";
+}
+
+Token::	~Token(){}
diff --git a/Source/DoxygenTranslator/src/Token.h b/Source/DoxygenTranslator/src/Token.h
new file mode 100644
index 000000000..e98686c14
--- /dev/null
+++ b/Source/DoxygenTranslator/src/Token.h
@@ -0,0 +1,21 @@
+#ifndef TOKEN_H_
+#define TOKEN_H_
+#include <string>
+
+#define  END_LINE 101
+#define PARAGRAPH_END 102
+#define  PLAINSTRING 103
+#define  COMMAND  104
+using namespace std;
+
+class Token
+{
+public:
+	Token(int tType, string tString);
+	~Token();
+	int tokenType; /* currently can be END_LINE, PLAINSTRING, or COMMAND */
+	string tokenString; /* the data , such as param for @param*/
+	string toString();
+};
+
+#endif /*TOKEN_H_*/
diff --git a/Source/DoxygenTranslator/src/TokenList.cpp b/Source/DoxygenTranslator/src/TokenList.cpp
new file mode 100644
index 000000000..eeec6da46
--- /dev/null
+++ b/Source/DoxygenTranslator/src/TokenList.cpp
@@ -0,0 +1,116 @@
+#include "TokenList.h"
+#include <cstdlib>
+#include <iostream>
+#include <string>
+#include <list>
+#include "Token.h"
+#define TOKENSPERLINE 8; //change this to change the printing behaviour of the token list
+#define  END_LINE 101
+#define PARAGRAPH_END 102 //not used at the moment 
+#define  PLAINSTRING 103
+#define  COMMAND  104
+using namespace std;
+
+
+list <Token> tokenList;
+list<Token>::iterator tokenListIterator;
+int noisy2 = 0;
+/* The tokenizer*/
+
+TokenList::TokenList(string doxygenString){
+	int currentIndex = 0;
+	//Regex whitespace("[ \t]+");
+	//Regex newLine("[\n]");
+	//Regex command("[@|\\]{1}[^ \t \n]+"); //the cheap solution 
+	//Regex doxygenFluff("[/*!]+");
+	int nextIndex = 0;
+	int isFluff = 0;
+	string currentWord;
+	while (currentIndex < doxygenString.length()){	
+		if(doxygenString[currentIndex] == '\n'){
+			tokenList.push_back(Token(END_LINE, currentWord));
+			currentIndex++;
+		}
+		while(currentIndex < doxygenString.length() && (doxygenString[currentIndex] == ' ' 
+			|| doxygenString[currentIndex]== '\t')) currentIndex ++;
+		if (currentIndex == doxygenString.length()) {} //do nothing since end of string was reached
+		else {nextIndex = currentIndex;
+		while (nextIndex  < doxygenString.length() && (doxygenString[nextIndex] != ' ' 
+			&& doxygenString[nextIndex]!= '\t' && doxygenString[nextIndex]!= '\n')) nextIndex++;
+		currentWord = doxygenString.substr(currentIndex, nextIndex-currentIndex);
+		if(noisy2) cout << "Current Word: " << currentWord << endl;
+		if (currentWord[0] == '@' || currentWord[0] == '\\'){
+			currentWord = currentWord.substr(1, currentWord.length()-1);
+			tokenList.push_back(Token(COMMAND, currentWord));
+		}
+		else if (currentWord[0] == '\n'){
+			//if ((tokenList.back()).tokenType == END_LINE){}
+			tokenList.push_back(Token(END_LINE, currentWord));
+			
+		}
+		else if (currentWord[0] == '*' || currentWord[0] == '/' ||currentWord[0] == '!'){
+			if (currentWord.length() == 1) {isFluff = 1;}	
+			else { isFluff = 1;
+				for(int i = 1; i < currentWord.length(); i++){
+					if (currentWord[0] != '*' && currentWord[0] != '/' && currentWord[0] != '!') isFluff = 0;
+				}
+				
+			}
+			if(!isFluff) tokenList.push_back(Token(PLAINSTRING, currentWord));
+		}
+		
+		else tokenList.push_back(Token(PLAINSTRING, currentWord));
+		currentIndex = nextIndex;
+	}
+	}
+	tokenListIterator = tokenList.begin(); 
+}
+
+Token TokenList::peek(){
+	if(tokenListIterator!= tokenList.end()){
+		Token returnedToken = (*tokenListIterator);
+		return returnedToken;
+	}
+	else
+		return Token(0, "");
+} 
+
+Token TokenList::next(){
+	if(tokenListIterator != tokenList.end()){
+		Token returnedToken = (*tokenListIterator);
+		tokenListIterator++;
+		return (returnedToken);
+	}
+	else
+		return Token(0, "");
+} 	
+
+list<Token>::iterator TokenList::end(){
+	return tokenList.end();
+}
+
+list<Token>::iterator TokenList::current(){
+	return tokenListIterator;
+}
+void TokenList::printList(){
+	list<Token>::iterator p = tokenList.begin();
+			int i = 1;
+			int b = 0;
+			while (p != tokenList.end()){
+				cout << (*p).toString() << " ";
+				b = i%TOKENSPERLINE;
+				if (b == 0) cout << endl;
+				p++; i++;
+			}
+}
+
+list<Token>::iterator  TokenList::iteratorCopy(){
+	list<Token>::iterator p = tokenListIterator;
+	return p;
+}
+void TokenList::setIterator(list<Token>::iterator newPosition){
+	tokenListIterator = newPosition;
+}
+TokenList::	~TokenList(){
+	tokenList.clear();
+}
diff --git a/Source/DoxygenTranslator/src/TokenList.h b/Source/DoxygenTranslator/src/TokenList.h
new file mode 100644
index 000000000..cc61f56e4
--- /dev/null
+++ b/Source/DoxygenTranslator/src/TokenList.h
@@ -0,0 +1,27 @@
+#ifndef TOKENLIST_H_
+#define TOKENLIST_H_
+#include <cstdlib>
+#include <iostream>
+#include <string>
+#include <list>
+#include "Token.h"
+using namespace std;
+
+/* a small class used to represent the sequence of tokens
+ * that can be derived from a formatted doxygen string
+ */
+
+class TokenList{
+public:
+	TokenList(string doxygenString); /* constructor takes a blob of Doxygen comment */
+	~TokenList();
+	Token peek(); 	/* returns next token without advancing */
+	Token next(); 	/* returns next token and advances */
+	list<Token>::iterator end(); /* returns an end iterator */
+	list<Token>::iterator current(); /* returns the current iterator */
+	void printList(); /* prints out the sequence of tokens */
+	list<Token>::iterator  iteratorCopy(); /* returns a copy of the current iterator */
+	void setIterator(list<Token>::iterator  newPosition); /*moves up the iterator*/
+};
+
+#endif /*TOKENLIST_H_*/
diff --git a/Source/DoxygenTranslator/src/TranslatorTest.cpp b/Source/DoxygenTranslator/src/TranslatorTest.cpp
new file mode 100644
index 000000000..f2bb48983
--- /dev/null
+++ b/Source/DoxygenTranslator/src/TranslatorTest.cpp
@@ -0,0 +1,68 @@
+
+#include <cstdlib>
+#include <iostream>
+#include <fstream>
+#include <string>
+#include <list>
+using namespace std;
+
+
+/* This classes primary function is to test the basic text processing abilities of
+ * the Doxygen parsing class
+ * It is currently a little messy */
+
+
+int testCommandParsingFunctions = 1;
+int testCodeCrawlingFunctions = 1;
+
+
+/*  Testing clearFluff(), a method to scan past all excess / * ! from beginning of
+ * a comment blob. Compartmentalised simply because this is a comment habit that
+ * differs wildly */
+
+int testClearFluff(){
+
+ string cases[] = {"/** WORD", "/*! WORD", "/******* WORD", "///// WORD", "//! WORD", "//! WORD", "///WORD",
+		 "/**\nWORD", "/**\n*WORD", "/** \n WORD"};
+ 
+ return 1;
+ 
+ };
+
+int testCCF(){
+	
+
+	
+	cout << "Testing getNextWord" << endl;
+	// Case 1: \command <name>
+	string case1 = "\b word";
+	string case2 = "\b word ";
+	string case3 = "\b word\n";
+	string case4 = "\b word \n";
+	string case5 = "\b word word";
+	//Case 2: \command {paragraph}
+	
+	//Case 3: \command (text til end of line)
+		
+	
+	return 1;
+}
+
+int testCPF(){
+	// Case 1: \command <name>
+	string case1 = "\b word";
+	//Case 2: \command {paragraph}
+		
+	//Case 3: \command (text til end of line)
+		
+	return 1;
+	
+}
+
+int main(int argc, char *argv[]){
+	if(testCodeCrawlingFunctions) testCCF();
+	if(testCommandParsingFunctions) testCPF();
+	
+	
+	return 1;
+}
diff --git a/Source/DoxygenTranslator/src/TranslatorTest.h b/Source/DoxygenTranslator/src/TranslatorTest.h
new file mode 100644
index 000000000..0014de718
--- /dev/null
+++ b/Source/DoxygenTranslator/src/TranslatorTest.h
@@ -0,0 +1,11 @@
+#ifndef TRANSLATORTEST_H_
+#define TRANSLATORTEST_H_
+
+class TranslatorTest
+{
+public:
+	TranslatorTest();
+	virtual ~TranslatorTest();
+};
+
+#endif /*TRANSLATORTEST_H_*/
diff --git a/Source/Makefile.am b/Source/Makefile.am
index a72671305..1abe41cbd 100644
--- a/Source/Makefile.am
+++ b/Source/Makefile.am
@@ -88,7 +88,19 @@ eswig_SOURCES =	CParse/cscanner.c		\
 		Swig/typemap.c			\
 		Swig/typesys.c			\
 		Swig/warn.c			\
-		Swig/wrapfunc.c			
+		Swig/wrapfunc.c			\
+		DoxygenTranslator/src/DoxygenEntity.h\
+		DoxygenTranslator/src/DoxygenEntity.cpp\
+		DoxygenTranslator/src/DoxygenParser.h\
+		DoxygenTranslator/src/DoxygenParser.cpp\
+		DoxygenTranslator/src/DoxygenTranslator.h\
+		DoxygenTranslator/src/DoxygenTranslator.cpp\
+		DoxygenTranslator/src/JavaDocConverter.h\
+		DoxygenTranslator/src/JavaDocConverter.cpp\
+		DoxygenTranslator/src/Token.h\
+		DoxygenTranslator/src/Token.cpp\
+		DoxygenTranslator/src/TokenList.h\
+		DoxygenTranslator/src/TokenList.cpp
 
 bin_PROGRAMS = eswig
 eswig_LDADD   = @SWIGLIBS@
diff --git a/Source/Modules/java.cxx b/Source/Modules/java.cxx
index 5660b4885..23e233071 100644
--- a/Source/Modules/java.cxx
+++ b/Source/Modules/java.cxx
@@ -13,6 +13,7 @@ char cvsroot_java_cxx[] = "$Id$";
 #include <limits.h>		// for INT_MAX
 #include "cparse.h"
 #include <ctype.h>
+#include "../DoxygenTranslator/src/DoxygenTranslator.h"
 
 /* Hash type used for upcalls from C/C++ */
 typedef DOH UpcallData;
@@ -43,7 +44,7 @@ class JAVA:public Language {
   bool global_variable_flag;	// Flag for when wrapping a global variable
   bool old_variable_names;	// Flag for old style variable names in the intermediary class
   bool member_func_flag;	// flag set when wrapping a member function
-
+  
   String *imclass_name;		// intermediary class name
   String *module_class_name;	// module class name
   String *imclass_class_code;	// intermediary class code
@@ -70,7 +71,8 @@ class JAVA:public Language {
   String *imclass_cppcasts_code;	//C++ casts up inheritance hierarchies intermediary class code
   String *imclass_directors;	// Intermediate class director code
   String *destructor_call;	//C++ destructor call if any
-
+  String *structuralComments;
+  
   // Director method stuff:
   List *dmethods_seq;
   Hash *dmethods_table;
@@ -87,6 +89,11 @@ class JAVA:public Language {
     Setline(p, Getline(n));
     return p;
   }
+  /* DOXYGEN TO JAVADOC globals */
+  bool doxygen_javadoc_flag; //flag for converting found doxygen to javadoc
+  //TODO make this bool a command line option
+  DoxygenTranslator doxyTranslator;
+
 
 public:
 
@@ -141,6 +148,7 @@ public:
       imclass_cppcasts_code(NULL),
       imclass_directors(NULL),
       destructor_call(NULL),
+      structuralComments(NULL),
       dmethods_seq(NULL),
       dmethods_table(NULL),
       n_dmethods(0),
@@ -149,6 +157,7 @@ public:
        should be easy to implement though */
     director_multiple_inheritance = 0;
     director_language = 1;
+    doxyTranslator = DoxygenTranslator();
   }
 
   /* -----------------------------------------------------------------------------
@@ -202,6 +211,7 @@ public:
 
   virtual void main(int argc, char *argv[]) {
 
+	  doxygen_javadoc_flag = true;
     SWIG_library_directory("java");
 
     // Look for certain command line options
@@ -355,6 +365,7 @@ public:
     imclass_imports = NewString("");
     imclass_cppcasts_code = NewString("");
     imclass_directors = NewString("");
+    structuralComments = NewString("");
     upcasts_code = NewString("");
     dmethods_seq = NewList();
     dmethods_table = NewHash();
@@ -432,6 +443,8 @@ public:
       // Start writing out the intermediary class file
       emitBanner(f_im);
 
+    	  
+
       if (Len(package) > 0)
 	Printf(f_im, "package %s;\n", package);
 
@@ -482,13 +495,22 @@ public:
 
       // Start writing out the module class file
       emitBanner(f_module);
-
+      //Add any structural comments to the top
+      if(doxygen_javadoc_flag && structuralComments){
+    	  Printf(f_module, "%s", structuralComments);
+      }
       if (Len(package) > 0)
 	Printf(f_module, "package %s;\n", package);
 
       if (module_imports)
 	Printf(f_module, "%s\n", module_imports);
-
+      
+      if (doxygen_javadoc_flag){
+      	if (Getattr(n,"DoxygenComment")){
+      		  Printf(f_module, "/* This was generated from top() */");
+      		  Printf(f_module, doxyTranslator.convert(Char((String *)Getattr(n,"DoxygenComment")),"JAVADOC")); 	
+      	}
+      }
       if (Len(module_class_modifiers) > 0)
 	Printf(f_module, "%s ", module_class_modifiers);
       Printf(f_module, "%s ", module_class_name);
@@ -921,7 +943,7 @@ public:
       Delete(c_param_type);
       Delete(arg);
     }
-
+    
     Printv(f->code, nondir_args, NIL);
     Delete(nondir_args);
 
@@ -1135,6 +1157,7 @@ public:
     return ret;
   }
 
+  
   /* ----------------------------------------------------------------------
    * enumDeclaration()
    *
@@ -1205,7 +1228,15 @@ public:
 	  // Add extra indentation
 	  Replaceall(enum_code, "\n", "\n  ");
 	  Replaceall(enum_code, "  \n", "\n");
+	    //translate and write javadoc comment if flagged
+	    if (doxygen_javadoc_flag){
+	    	if (Getattr(n,"DoxygenComment")){
+	    		  Printv(proxy_class_constants_code, "/* This was generated from enumvalueDeclaration */", NIL );
 
+	    		  Printv(proxy_class_constants_code, doxyTranslator.convert(Char((const String *)Getattr(n,"DoxygenComment")),"JAVADOC"), NIL); 	
+	    	}
+	    }
+	    
 	  Printv(proxy_class_constants_code, "  ", enum_code, "\n\n", NIL);
 	} else {
 	  // Global enums are defined in their own file
@@ -1267,7 +1298,14 @@ public:
       tmpValue = NewString(name);
     // Note that this is used in enumValue() amongst other places
     Setattr(n, "value", tmpValue);
-
+    
+    //translate and write javadoc comment if flagged
+    if (doxygen_javadoc_flag){
+    	if (Getattr(n,"DoxygenComment")){
+    		  Printf(enum_code, "/* This was generated from enumvalueDeclaration() */" );
+    		  Printf(enum_code, doxyTranslator.convert(Char((String *)Getattr(n,"DoxygenComment")),"JAVADOC")); 	
+    	}
+    }
     {
       EnumFeature enum_feature = decodeEnumFeature(parentNode(n));
 
@@ -1326,6 +1364,21 @@ public:
     return SWIG_OK;
   }
 
+  /* -----------------------------------------------------------------------
+   * doxygenComment()
+   * Simply translates the doxygen comment and places it into the appropriate
+   * file
+   * ------------------------------------------------------------------------ */
+  virtual int doxygenComment(Node *n){
+		 if (doxygen_javadoc_flag){
+		   if (Getattr(n,"DoxygenComment")){
+			    	Printv(structuralComments, "/* This was generated from doxygenComment() */\n", NIL);
+			    	Printv(structuralComments, doxyTranslator.convert(Char((String *)Getattr(n,"DoxygenComment")),"JAVADOC"), NIL);
+		    	}
+		    }
+	 return SWIG_OK;
+  }
+  
   /* -----------------------------------------------------------------------
    * constantWrapper()
    * Used for wrapping constants - #define or %constant.
@@ -1344,7 +1397,14 @@ public:
     String *tm;
     String *return_type = NewString("");
     String *constants_code = NewString("");
-
+    //translate and write javadoc comment if flagged
+    if (doxygen_javadoc_flag){
+    	if (Getattr(n,"DoxygenComment")){
+    		Printf(constants_code, "/* This was generated from enumvalueDeclaration */\n");
+    		  Printf(constants_code, doxyTranslator.convert(Char((String *)Getattr(n,"DoxygenComment")),"JAVADOC")); 	
+    	}
+    }
+    
     if (!addSymbol(symname, n))
       return SWIG_ERROR;
 
@@ -1605,7 +1665,15 @@ public:
 
     // Pure Java interfaces
     const String *pure_interfaces = typemapLookup("javainterfaces", typemap_lookup_type, WARN_NONE);
-
+    
+    //translate and write javadoc comment if flagged
+    if (doxygen_javadoc_flag){
+    	if (Getattr(n,"DoxygenComment")){
+  		  Printv(proxy_class_def, "/* This was generated from emitProxyClassDefAndCPPCasts() */\n", NIL );
+    		Printv(proxy_class_def, doxyTranslator.convert(Char((String *)Getattr(n,"DoxygenComment")),"JAVADOC"), NIL); 	
+    	}
+    }
+    
     // Start writing the proxy class
     Printv(proxy_class_def, typemapLookup("javaimports", typemap_lookup_type, WARN_NONE),	// Import statements
 	   "\n", typemapLookup("javaclassmodifiers", typemap_lookup_type, WARN_JAVA_TYPEMAP_CLASSMOD_UNDEF),	// Class modifiers
@@ -1754,9 +1822,10 @@ public:
       // Start writing out the proxy class file
       emitBanner(f_proxy);
 
-      if (Len(package) > 0)
+      if (Len(package) > 0){
+    Printf(f_proxy, "LETS TEST THIS NAO THX \n\n\n");
 	Printf(f_proxy, "package %s;\n", package);
-
+      }
       Clear(proxy_class_def);
       Clear(proxy_class_code);
 
@@ -1936,7 +2005,16 @@ public:
       // For wrapping member variables (Javabean setter)
       setter_flag = (Cmp(Getattr(n, "sym:name"), Swig_name_set(Swig_name_member(proxy_class_name, variable_name))) == 0);
     }
-
+    
+    
+    //translate and write javadoc comment if flagged
+    if (doxygen_javadoc_flag){
+    	if (Getattr(n,"DoxygenComment")){
+    		  Printf(function_code, "/* This was generated from proxyclassfunctionhandler */");
+    		  Printf(function_code, doxyTranslator.convert(Char((String *)Getattr(n,"DoxygenComment")),"JAVADOC")); 	
+    	}
+    }
+    
     /* Start generating the proxy function */
     const String *methodmods = Getattr(n, "feature:java:methodmodifiers");
     methodmods = methodmods ? methodmods : (is_public(n) ? public_string : protected_string);
@@ -2158,7 +2236,15 @@ public:
 
       tm = Getattr(n, "tmap:jtype"); // typemaps were attached earlier to the node
       Printf(im_return_type, "%s", tm);
-
+      
+	    //translate and write javadoc comment if flagged
+	    if (doxygen_javadoc_flag){
+	    	if (Getattr(n,"DoxygenComment")){
+	    		  Printf(function_code, "/* This was generated from constructionhandler */\n" );
+	    		  Printf(function_code, doxyTranslator.convert(Char((String *)Getattr(n,"DoxygenComment")),"JAVADOC")); 	
+	    	}
+	    }
+	    
       Printf(function_code, "  %s %s(", methodmods, proxy_class_name);
       Printf(helper_code, "  static private %s SwigConstruct%s(", im_return_type, proxy_class_name);
 
@@ -2419,6 +2505,14 @@ public:
     bool setter_flag = false;
     String *pre_code = NewString("");
     String *post_code = NewString("");
+    
+    //translate and write javadoc comment if flagged
+    if (doxygen_javadoc_flag){
+    	if (Getattr(n,"DoxygenComment")){
+    		  Printf(function_code, "/* This was generated from moduleClassFunctionHandler() */\n" );
+    		  Printf(function_code, doxyTranslator.convert(Char((String *)Getattr(n,"DoxygenComment")),"JAVADOC")); 	
+    	}
+    }
 
     if (l) {
       if (SwigType_type(Getattr(l, "type")) == T_VOID) {
@@ -2814,6 +2908,7 @@ public:
     const String *pure_baseclass = typemapLookup("javabase", type, WARN_NONE);
     const String *pure_interfaces = typemapLookup("javainterfaces", type, WARN_NONE);
 
+    
     // Emit the class
     Printv(swigtype, typemapLookup("javaimports", type, WARN_NONE),	// Import statements
 	   "\n", typemapLookup("javaclassmodifiers", type, WARN_JAVA_TYPEMAP_CLASSMOD_UNDEF),	// Class modifiers
diff --git a/Source/Modules/lang.cxx b/Source/Modules/lang.cxx
index 4a7bf8813..368dc2c85 100644
--- a/Source/Modules/lang.cxx
+++ b/Source/Modules/lang.cxx
@@ -132,6 +132,12 @@ int Dispatcher::emit_one(Node *n) {
     ret = namespaceDeclaration(n);
   } else if (strcmp(tag, "template") == 0) {
     ret = templateDeclaration(n);
+  } 
+  /* ===============================================================
+   *  Doxygen Comment
+   * =============================================================== */  
+  else if (strcmp(tag, "doxycomm") == 0) {
+	    ret = doxygenComment(n);
   }
 
   /* ===============================================================
@@ -296,7 +302,9 @@ int Dispatcher::usingDeclaration(Node *n) {
 int Dispatcher::namespaceDeclaration(Node *n) {
   return defaultHandler(n);
 }
-
+int Dispatcher::doxygenComment(Node *n){
+  return defaultHandler(n);
+}
 
 /* Allocators */
 Language::Language():
@@ -2817,6 +2825,17 @@ int Language::usingDeclaration(Node *n) {
 
 /* Stubs. Language modules need to implement these */
 
+/* ----------------------------------------------------------------------
+ * Language::doxygenComment()
+ * ---------------------------------------------------------------------- */
+int Language::doxygenComment(Node *n){
+	
+	String *comment = Getattr(n, "comment");
+
+	return SWIG_OK;
+	
+}
+
 /* ----------------------------------------------------------------------
  * Language::constantWrapper()
  * ---------------------------------------------------------------------- */
diff --git a/Source/Modules/swigmod.h b/Source/Modules/swigmod.h
index 5835c6362..03892e4f6 100644
--- a/Source/Modules/swigmod.h
+++ b/Source/Modules/swigmod.h
@@ -82,6 +82,9 @@ public:
   virtual int typemapcopyDirective(Node *n);
   virtual int typesDirective(Node *n);
 
+  /* Doxygen Comment */
+  virtual int doxygenComment(Node *n);
+  
   /* C/C++ parsing */
 
   virtual int cDeclaration(Node *n);
@@ -159,6 +162,9 @@ public:
   virtual int namespaceDeclaration(Node *n);
   virtual int usingDeclaration(Node *n);
 
+  /* C/C++ parsing */
+  virtual int doxygenComment(Node *n);
+  
   /* Function handlers */
 
   virtual int functionHandler(Node *n);
diff --git a/Tools/config/config.guess b/Tools/config/config.guess
index 396482d6c..278f9e9e0 100755
--- a/Tools/config/config.guess
+++ b/Tools/config/config.guess
@@ -4,7 +4,7 @@
 #   2000, 2001, 2002, 2003, 2004, 2005, 2006 Free Software Foundation,
 #   Inc.
 
-timestamp='2006-07-02'
+timestamp='2007-07-22'
 
 # This file is free software; you can redistribute it and/or modify it
 # under the terms of the GNU General Public License as published by
@@ -161,6 +161,7 @@ case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in
 	    arm*) machine=arm-unknown ;;
 	    sh3el) machine=shl-unknown ;;
 	    sh3eb) machine=sh-unknown ;;
+	    sh5el) machine=sh5le-unknown ;;
 	    *) machine=${UNAME_MACHINE_ARCH}-unknown ;;
 	esac
 	# The Operating System including object format, if it has switched
@@ -329,7 +330,7 @@ case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in
     sun4*:SunOS:5.*:* | tadpole*:SunOS:5.*:*)
 	echo sparc-sun-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
 	exit ;;
-    i86pc:SunOS:5.*:*)
+    i86pc:SunOS:5.*:* | i86xen:SunOS:5.*:*)
 	echo i386-pc-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
 	exit ;;
     sun4*:SunOS:6*:*)
@@ -780,7 +781,7 @@ EOF
     i*:CYGWIN*:*)
 	echo ${UNAME_MACHINE}-pc-cygwin
 	exit ;;
-    i*:MINGW*:*)
+    *:MINGW*:*)
 	echo ${UNAME_MACHINE}-pc-mingw32
 	exit ;;
     i*:windows32*:*)
@@ -790,12 +791,15 @@ EOF
     i*:PW*:*)
 	echo ${UNAME_MACHINE}-pc-pw32
 	exit ;;
-    x86:Interix*:[3456]*)
-	echo i586-pc-interix${UNAME_RELEASE}
-	exit ;;
-    EM64T:Interix*:[3456]*)
-	echo x86_64-unknown-interix${UNAME_RELEASE}
-	exit ;;
+    *:Interix*:[3456]*)
+    	case ${UNAME_MACHINE} in
+	    x86)
+		echo i586-pc-interix${UNAME_RELEASE}
+		exit ;;
+	    EM64T | authenticamd)
+		echo x86_64-unknown-interix${UNAME_RELEASE}
+		exit ;;
+	esac ;;
     [345]86:Windows_95:* | [345]86:Windows_98:* | [345]86:Windows_NT:*)
 	echo i${UNAME_MACHINE}-pc-mks
 	exit ;;
@@ -950,6 +954,9 @@ EOF
     x86_64:Linux:*:*)
 	echo x86_64-unknown-linux-gnu
 	exit ;;
+    xtensa:Linux:*:*)
+    	echo xtensa-unknown-linux-gnu
+	exit ;;
     i*86:Linux:*:*)
 	# The BFD linker knows what the default object file format is, so
 	# first see if it will tell us. cd to the root directory to prevent
@@ -1208,6 +1215,15 @@ EOF
     SX-6:SUPER-UX:*:*)
 	echo sx6-nec-superux${UNAME_RELEASE}
 	exit ;;
+    SX-7:SUPER-UX:*:*)
+	echo sx7-nec-superux${UNAME_RELEASE}
+	exit ;;
+    SX-8:SUPER-UX:*:*)
+	echo sx8-nec-superux${UNAME_RELEASE}
+	exit ;;
+    SX-8R:SUPER-UX:*:*)
+	echo sx8r-nec-superux${UNAME_RELEASE}
+	exit ;;
     Power*:Rhapsody:*:*)
 	echo powerpc-apple-rhapsody${UNAME_RELEASE}
 	exit ;;
diff --git a/Tools/config/config.sub b/Tools/config/config.sub
index fab0aa355..1761d8bdf 100755
--- a/Tools/config/config.sub
+++ b/Tools/config/config.sub
@@ -4,7 +4,7 @@
 #   2000, 2001, 2002, 2003, 2004, 2005, 2006 Free Software Foundation,
 #   Inc.
 
-timestamp='2006-09-20'
+timestamp='2007-06-28'
 
 # This file is (in principle) common to ALL GNU software.
 # The presence of a machine in this file suggests that SOME GNU software
@@ -245,12 +245,12 @@ case $basic_machine in
 	| bfin \
 	| c4x | clipper \
 	| d10v | d30v | dlx | dsp16xx \
-	| fr30 | frv \
+	| fido | fr30 | frv \
 	| h8300 | h8500 | hppa | hppa1.[01] | hppa2.0 | hppa2.0[nw] | hppa64 \
 	| i370 | i860 | i960 | ia64 \
 	| ip2k | iq2000 \
 	| m32c | m32r | m32rle | m68000 | m68k | m88k \
-	| maxq | mb | microblaze | mcore \
+	| maxq | mb | microblaze | mcore | mep \
 	| mips | mipsbe | mipseb | mipsel | mipsle \
 	| mips16 \
 	| mips64 | mips64el \
@@ -324,7 +324,7 @@ case $basic_machine in
 	| clipper-* | craynv-* | cydra-* \
 	| d10v-* | d30v-* | dlx-* \
 	| elxsi-* \
-	| f30[01]-* | f700-* | fr30-* | frv-* | fx80-* \
+	| f30[01]-* | f700-* | fido-* | fr30-* | frv-* | fx80-* \
 	| h8300-* | h8500-* \
 	| hppa-* | hppa1.[01]-* | hppa2.0-* | hppa2.0[nw]-* | hppa64-* \
 	| i*86-* | i860-* | i960-* | ia64-* \
@@ -475,8 +475,8 @@ case $basic_machine in
 		basic_machine=craynv-cray
 		os=-unicosmp
 		;;
-	cr16c)
-		basic_machine=cr16c-unknown
+	cr16)
+		basic_machine=cr16-unknown
 		os=-elf
 		;;
 	crds | unos)
@@ -683,6 +683,10 @@ case $basic_machine in
 		basic_machine=i386-pc
 		os=-mingw32
 		;;
+	mingw32ce)
+		basic_machine=arm-unknown
+		os=-mingw32ce
+		;;
 	miniframe)
 		basic_machine=m68000-convergent
 		;;
@@ -925,6 +929,9 @@ case $basic_machine in
 		basic_machine=sh-hitachi
 		os=-hms
 		;;
+	sh5el)
+		basic_machine=sh5le-unknown
+		;;
 	sh64)
 		basic_machine=sh64-unknown
 		;;
@@ -1219,7 +1226,7 @@ case $os in
 	      | -os2* | -vos* | -palmos* | -uclinux* | -nucleus* \
 	      | -morphos* | -superux* | -rtmk* | -rtmk-nova* | -windiss* \
 	      | -powermax* | -dnix* | -nx6 | -nx7 | -sei* | -dragonfly* \
-	      | -skyos* | -haiku* | -rdos* | -toppers*)
+	      | -skyos* | -haiku* | -rdos* | -toppers* | -drops*)
 	# Remember, each alternative MUST END IN *, to match a version number.
 		;;
 	-qnx*)
@@ -1414,6 +1421,9 @@ case $basic_machine in
 	m68*-cisco)
 		os=-aout
 		;;
+        mep-*)
+		os=-elf
+		;;
 	mips*-cisco)
 		os=-elf
 		;;

From 311ddbc2bf57311750ba4b6ea759e94900b90866 Mon Sep 17 00:00:00 2001
From: Cheryl Foil <cheryl.foil@gmail.com>
Date: Fri, 15 Aug 2008 23:54:53 +0000
Subject: [PATCH 010/314] Added a new Examples folder with modified
 Examples/java files

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2008-cherylfoil@10763 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 .../doxygencomments/java/callback/Makefile    |  18 ++
 .../doxygencomments/java/callback/example.cxx |   4 +
 .../doxygencomments/java/callback/example.h   |  24 +++
 .../doxygencomments/java/callback/example.i   |  14 ++
 .../doxygencomments/java/callback/index.html  |  20 ++
 .../doxygencomments/java/callback/main.java   |  56 +++++
 Examples/doxygencomments/java/check.list      |  15 ++
 Examples/doxygencomments/java/class/Makefile  |  18 ++
 .../doxygencomments/java/class/example.cxx    |  28 +++
 .../doxygencomments/java/class/example.dsp    | 162 ++++++++++++++
 Examples/doxygencomments/java/class/example.h |  45 ++++
 Examples/doxygencomments/java/class/example.i |  10 +
 .../doxygencomments/java/class/index.html     | 197 ++++++++++++++++++
 Examples/doxygencomments/java/class/main.java |  70 +++++++
 .../doxygencomments/java/constants/Makefile   |  18 ++
 .../doxygencomments/java/constants/example.i  |  30 +++
 .../doxygencomments/java/constants/index.html |  52 +++++
 .../doxygencomments/java/constants/main.java  |  44 ++++
 Examples/doxygencomments/java/enum/Makefile   |  18 ++
 .../doxygencomments/java/enum/example.cxx     |  37 ++++
 Examples/doxygencomments/java/enum/example.h  |  23 ++
 Examples/doxygencomments/java/enum/example.i  |  14 ++
 Examples/doxygencomments/java/enum/index.html |  29 +++
 Examples/doxygencomments/java/enum/main.java  |  38 ++++
 Examples/doxygencomments/java/extend/Makefile |  18 ++
 .../doxygencomments/java/extend/example.cxx   |   4 +
 .../doxygencomments/java/extend/example.h     |  60 ++++++
 .../doxygencomments/java/extend/example.i     |  15 ++
 .../doxygencomments/java/extend/index.html    |  19 ++
 .../doxygencomments/java/extend/main.java     |  88 ++++++++
 .../doxygencomments/java/funcptr/Makefile     |  18 ++
 .../doxygencomments/java/funcptr/example.c    |  19 ++
 .../doxygencomments/java/funcptr/example.h    |  10 +
 .../doxygencomments/java/funcptr/example.i    |  16 ++
 .../doxygencomments/java/funcptr/index.html   |  91 ++++++++
 .../doxygencomments/java/funcptr/main.java    |  33 +++
 Examples/doxygencomments/java/index.html      |  65 ++++++
 .../doxygencomments/java/multimap/Makefile    |  18 ++
 .../doxygencomments/java/multimap/example.c   |  53 +++++
 .../doxygencomments/java/multimap/example.dsp | 158 ++++++++++++++
 .../doxygencomments/java/multimap/example.i   | 109 ++++++++++
 .../doxygencomments/java/multimap/main.java   |  40 ++++
 Examples/doxygencomments/java/native/Makefile |  18 ++
 .../doxygencomments/java/native/example.i     |  56 +++++
 .../doxygencomments/java/native/index.html    |  33 +++
 .../doxygencomments/java/native/main.java     |  19 ++
 .../doxygencomments/java/pointer/Makefile     |  18 ++
 .../doxygencomments/java/pointer/example.c    |  16 ++
 .../doxygencomments/java/pointer/example.i    |  30 +++
 .../doxygencomments/java/pointer/index.html   | 165 +++++++++++++++
 .../doxygencomments/java/pointer/main.java    |  55 +++++
 .../doxygencomments/java/reference/Makefile   |  18 ++
 .../java/reference/example.cxx                |  46 ++++
 .../doxygencomments/java/reference/example.h  |  26 +++
 .../doxygencomments/java/reference/example.i  |  46 ++++
 .../doxygencomments/java/reference/index.html | 147 +++++++++++++
 .../doxygencomments/java/reference/main.java  |  79 +++++++
 Examples/doxygencomments/java/simple/Makefile |  18 ++
 .../doxygencomments/java/simple/example.c     |  18 ++
 .../doxygencomments/java/simple/example.dsp   | 158 ++++++++++++++
 .../doxygencomments/java/simple/example.i     |   7 +
 .../doxygencomments/java/simple/index.html    | 108 ++++++++++
 .../doxygencomments/java/simple/main.java     |  32 +++
 .../doxygencomments/java/template/Makefile    |  18 ++
 .../doxygencomments/java/template/example.h   |  32 +++
 .../doxygencomments/java/template/example.i   |  17 ++
 .../doxygencomments/java/template/index.html  | 102 +++++++++
 .../doxygencomments/java/template/main.java   |  45 ++++
 .../doxygencomments/java/typemap/Makefile     |  18 ++
 .../doxygencomments/java/typemap/example.i    | 101 +++++++++
 .../doxygencomments/java/typemap/index.html   |  32 +++
 .../doxygencomments/java/typemap/main.java    |  26 +++
 .../doxygencomments/java/variables/Makefile   |  18 ++
 .../doxygencomments/java/variables/example.c  |  91 ++++++++
 .../doxygencomments/java/variables/example.h  |   6 +
 .../doxygencomments/java/variables/example.i  |  49 +++++
 .../doxygencomments/java/variables/index.html |  85 ++++++++
 .../doxygencomments/java/variables/main.java  |  97 +++++++++
 78 files changed, 3668 insertions(+)
 create mode 100644 Examples/doxygencomments/java/callback/Makefile
 create mode 100644 Examples/doxygencomments/java/callback/example.cxx
 create mode 100644 Examples/doxygencomments/java/callback/example.h
 create mode 100644 Examples/doxygencomments/java/callback/example.i
 create mode 100644 Examples/doxygencomments/java/callback/index.html
 create mode 100644 Examples/doxygencomments/java/callback/main.java
 create mode 100644 Examples/doxygencomments/java/check.list
 create mode 100644 Examples/doxygencomments/java/class/Makefile
 create mode 100644 Examples/doxygencomments/java/class/example.cxx
 create mode 100644 Examples/doxygencomments/java/class/example.dsp
 create mode 100644 Examples/doxygencomments/java/class/example.h
 create mode 100644 Examples/doxygencomments/java/class/example.i
 create mode 100644 Examples/doxygencomments/java/class/index.html
 create mode 100644 Examples/doxygencomments/java/class/main.java
 create mode 100644 Examples/doxygencomments/java/constants/Makefile
 create mode 100644 Examples/doxygencomments/java/constants/example.i
 create mode 100644 Examples/doxygencomments/java/constants/index.html
 create mode 100644 Examples/doxygencomments/java/constants/main.java
 create mode 100644 Examples/doxygencomments/java/enum/Makefile
 create mode 100644 Examples/doxygencomments/java/enum/example.cxx
 create mode 100644 Examples/doxygencomments/java/enum/example.h
 create mode 100644 Examples/doxygencomments/java/enum/example.i
 create mode 100644 Examples/doxygencomments/java/enum/index.html
 create mode 100644 Examples/doxygencomments/java/enum/main.java
 create mode 100644 Examples/doxygencomments/java/extend/Makefile
 create mode 100644 Examples/doxygencomments/java/extend/example.cxx
 create mode 100644 Examples/doxygencomments/java/extend/example.h
 create mode 100644 Examples/doxygencomments/java/extend/example.i
 create mode 100644 Examples/doxygencomments/java/extend/index.html
 create mode 100644 Examples/doxygencomments/java/extend/main.java
 create mode 100644 Examples/doxygencomments/java/funcptr/Makefile
 create mode 100644 Examples/doxygencomments/java/funcptr/example.c
 create mode 100644 Examples/doxygencomments/java/funcptr/example.h
 create mode 100644 Examples/doxygencomments/java/funcptr/example.i
 create mode 100644 Examples/doxygencomments/java/funcptr/index.html
 create mode 100644 Examples/doxygencomments/java/funcptr/main.java
 create mode 100644 Examples/doxygencomments/java/index.html
 create mode 100644 Examples/doxygencomments/java/multimap/Makefile
 create mode 100644 Examples/doxygencomments/java/multimap/example.c
 create mode 100644 Examples/doxygencomments/java/multimap/example.dsp
 create mode 100644 Examples/doxygencomments/java/multimap/example.i
 create mode 100644 Examples/doxygencomments/java/multimap/main.java
 create mode 100644 Examples/doxygencomments/java/native/Makefile
 create mode 100644 Examples/doxygencomments/java/native/example.i
 create mode 100644 Examples/doxygencomments/java/native/index.html
 create mode 100644 Examples/doxygencomments/java/native/main.java
 create mode 100644 Examples/doxygencomments/java/pointer/Makefile
 create mode 100644 Examples/doxygencomments/java/pointer/example.c
 create mode 100644 Examples/doxygencomments/java/pointer/example.i
 create mode 100644 Examples/doxygencomments/java/pointer/index.html
 create mode 100644 Examples/doxygencomments/java/pointer/main.java
 create mode 100644 Examples/doxygencomments/java/reference/Makefile
 create mode 100644 Examples/doxygencomments/java/reference/example.cxx
 create mode 100644 Examples/doxygencomments/java/reference/example.h
 create mode 100644 Examples/doxygencomments/java/reference/example.i
 create mode 100644 Examples/doxygencomments/java/reference/index.html
 create mode 100644 Examples/doxygencomments/java/reference/main.java
 create mode 100644 Examples/doxygencomments/java/simple/Makefile
 create mode 100644 Examples/doxygencomments/java/simple/example.c
 create mode 100644 Examples/doxygencomments/java/simple/example.dsp
 create mode 100644 Examples/doxygencomments/java/simple/example.i
 create mode 100644 Examples/doxygencomments/java/simple/index.html
 create mode 100644 Examples/doxygencomments/java/simple/main.java
 create mode 100644 Examples/doxygencomments/java/template/Makefile
 create mode 100644 Examples/doxygencomments/java/template/example.h
 create mode 100644 Examples/doxygencomments/java/template/example.i
 create mode 100644 Examples/doxygencomments/java/template/index.html
 create mode 100644 Examples/doxygencomments/java/template/main.java
 create mode 100644 Examples/doxygencomments/java/typemap/Makefile
 create mode 100644 Examples/doxygencomments/java/typemap/example.i
 create mode 100644 Examples/doxygencomments/java/typemap/index.html
 create mode 100644 Examples/doxygencomments/java/typemap/main.java
 create mode 100644 Examples/doxygencomments/java/variables/Makefile
 create mode 100644 Examples/doxygencomments/java/variables/example.c
 create mode 100644 Examples/doxygencomments/java/variables/example.h
 create mode 100644 Examples/doxygencomments/java/variables/example.i
 create mode 100644 Examples/doxygencomments/java/variables/index.html
 create mode 100644 Examples/doxygencomments/java/variables/main.java

diff --git a/Examples/doxygencomments/java/callback/Makefile b/Examples/doxygencomments/java/callback/Makefile
new file mode 100644
index 000000000..14c301703
--- /dev/null
+++ b/Examples/doxygencomments/java/callback/Makefile
@@ -0,0 +1,18 @@
+TOP        = ../..
+SWIG       = $(TOP)/../preinst-swig
+CXXSRCS    = example.cxx
+TARGET     = example
+INTERFACE  = example.i
+SWIGOPT    =
+
+all::	java
+
+java::
+	$(MAKE) -f $(TOP)/Makefile CXXSRCS='$(CXXSRCS)' SWIG='$(SWIG)' \
+	SWIGOPT='$(SWIGOPT)' TARGET='$(TARGET)' INTERFACE='$(INTERFACE)' java_cpp
+	javac *.java
+
+clean::
+	$(MAKE) -f $(TOP)/Makefile java_clean
+
+check: all
diff --git a/Examples/doxygencomments/java/callback/example.cxx b/Examples/doxygencomments/java/callback/example.cxx
new file mode 100644
index 000000000..450d75608
--- /dev/null
+++ b/Examples/doxygencomments/java/callback/example.cxx
@@ -0,0 +1,4 @@
+/* File : example.cxx */
+
+#include "example.h"
+
diff --git a/Examples/doxygencomments/java/callback/example.h b/Examples/doxygencomments/java/callback/example.h
new file mode 100644
index 000000000..38ada8b84
--- /dev/null
+++ b/Examples/doxygencomments/java/callback/example.h
@@ -0,0 +1,24 @@
+/* File : example.h */
+
+#include <cstdio>
+#include <iostream>
+
+/** Let's document class CALLBACK! */
+class Callback {
+public:
+	virtual ~Callback() { std::cout << "Callback::~Callback()" << std:: endl; }
+	virtual void run() { std::cout << "Callback::run()" << std::endl; }
+};
+
+/** Let's document class Caller! */
+class Caller {
+private:
+	Callback *_callback;
+public:
+	Caller(): _callback(0) {}
+	~Caller() { delCallback(); }
+	void delCallback() { delete _callback; _callback = 0; }
+	void setCallback(Callback *cb) { delCallback(); _callback = cb; }
+	void call() { if (_callback) _callback->run(); }
+};
+
diff --git a/Examples/doxygencomments/java/callback/example.i b/Examples/doxygencomments/java/callback/example.i
new file mode 100644
index 000000000..5dae4e7c1
--- /dev/null
+++ b/Examples/doxygencomments/java/callback/example.i
@@ -0,0 +1,14 @@
+/* File : example.i */
+/** Let's document module Example! */
+%module(directors="1") example
+%{
+#include "example.h"
+%}
+
+%include "std_string.i"
+
+/* turn on director wrapping Callback */
+%feature("director") Callback;
+
+%include "example.h"
+
diff --git a/Examples/doxygencomments/java/callback/index.html b/Examples/doxygencomments/java/callback/index.html
new file mode 100644
index 000000000..c25452018
--- /dev/null
+++ b/Examples/doxygencomments/java/callback/index.html
@@ -0,0 +1,20 @@
+<html>
+<head>
+<title>SWIG:Examples:java:callback</title>
+</head>
+
+<body bgcolor="#ffffff">
+
+
+<tt>SWIG/Examples/python/extend/</tt>
+<hr>
+
+<H2>Implementing C++ callbacks in Java</H2>
+
+<p>
+This example illustrates how to use directors to implement C++ callbacks in Java.
+</p>
+
+<hr>
+</body>
+</html>
diff --git a/Examples/doxygencomments/java/callback/main.java b/Examples/doxygencomments/java/callback/main.java
new file mode 100644
index 000000000..4800f8cc9
--- /dev/null
+++ b/Examples/doxygencomments/java/callback/main.java
@@ -0,0 +1,56 @@
+public class main
+{
+  static {
+    try {
+        System.loadLibrary("example");
+    } catch (UnsatisfiedLinkError e) {
+      System.err.println("Native code library failed to load. See the chapter on Dynamic Linking Problems in the SWIG Java documentation for help.\n" + e);
+      System.exit(1);
+    }
+  }
+
+  public static void main(String[] args)
+  {
+    System.out.println("Adding and calling a normal C++ callback");
+    System.out.println("----------------------------------------");
+
+    Caller              caller = new Caller();
+    Callback            callback = new Callback();
+    
+    caller.setCallback(callback);
+    caller.call();
+    caller.delCallback();
+
+    callback = new JavaCallback();
+
+    System.out.println();
+    System.out.println("Adding and calling a Java callback");
+    System.out.println("------------------------------------");
+
+    caller.setCallback(callback);
+    caller.call();
+    caller.delCallback();
+
+    // Test that a double delete does not occur as the object has already been deleted from the C++ layer.
+    // Note that the garbage collector can also call the delete() method via the finalizer (callback.finalize())
+    // at any point after here.
+    callback.delete();
+
+    System.out.println();
+    System.out.println("java exit");
+  }
+}
+
+class JavaCallback extends Callback
+{
+  public JavaCallback()
+  {
+    super();
+  }
+
+  public void run()
+  {
+    System.out.println("JavaCallback.run()");
+  }
+}
+
diff --git a/Examples/doxygencomments/java/check.list b/Examples/doxygencomments/java/check.list
new file mode 100644
index 000000000..9728342f2
--- /dev/null
+++ b/Examples/doxygencomments/java/check.list
@@ -0,0 +1,15 @@
+# see top-level Makefile.in
+callback
+class
+constants
+enum
+extend
+funcptr
+multimap
+native
+pointer
+reference
+simple
+template
+typemap
+variables
diff --git a/Examples/doxygencomments/java/class/Makefile b/Examples/doxygencomments/java/class/Makefile
new file mode 100644
index 000000000..14c301703
--- /dev/null
+++ b/Examples/doxygencomments/java/class/Makefile
@@ -0,0 +1,18 @@
+TOP        = ../..
+SWIG       = $(TOP)/../preinst-swig
+CXXSRCS    = example.cxx
+TARGET     = example
+INTERFACE  = example.i
+SWIGOPT    =
+
+all::	java
+
+java::
+	$(MAKE) -f $(TOP)/Makefile CXXSRCS='$(CXXSRCS)' SWIG='$(SWIG)' \
+	SWIGOPT='$(SWIGOPT)' TARGET='$(TARGET)' INTERFACE='$(INTERFACE)' java_cpp
+	javac *.java
+
+clean::
+	$(MAKE) -f $(TOP)/Makefile java_clean
+
+check: all
diff --git a/Examples/doxygencomments/java/class/example.cxx b/Examples/doxygencomments/java/class/example.cxx
new file mode 100644
index 000000000..1e8e203dd
--- /dev/null
+++ b/Examples/doxygencomments/java/class/example.cxx
@@ -0,0 +1,28 @@
+/* File : example.c */
+
+#include "example.h"
+#define M_PI 3.14159265358979323846
+
+/* Move the shape to a new location */
+void Shape::move(double dx, double dy) {
+  x += dx;
+  y += dy;
+}
+
+int Shape::nshapes = 0;
+
+double Circle::area(void) {
+  return M_PI*radius*radius;
+}
+
+double Circle::perimeter(void) {
+  return 2*M_PI*radius;
+}
+
+double Square::area(void) {
+  return width*width;
+}
+
+double Square::perimeter(void) {
+  return 4*width;
+}
diff --git a/Examples/doxygencomments/java/class/example.dsp b/Examples/doxygencomments/java/class/example.dsp
new file mode 100644
index 000000000..fbe87e7a4
--- /dev/null
+++ b/Examples/doxygencomments/java/class/example.dsp
@@ -0,0 +1,162 @@
+# Microsoft Developer Studio Project File - Name="example" - Package Owner=<4>
+# Microsoft Developer Studio Generated Build File, Format Version 6.00
+# ** DO NOT EDIT **
+
+# TARGTYPE "Win32 (x86) Dynamic-Link Library" 0x0102
+
+CFG=example - Win32 Release
+!MESSAGE This is not a valid makefile. To build this project using NMAKE,
+!MESSAGE use the Export Makefile command and run
+!MESSAGE 
+!MESSAGE NMAKE /f "example.mak".
+!MESSAGE 
+!MESSAGE You can specify a configuration when running NMAKE
+!MESSAGE by defining the macro CFG on the command line. For example:
+!MESSAGE 
+!MESSAGE NMAKE /f "example.mak" CFG="example - Win32 Release"
+!MESSAGE 
+!MESSAGE Possible choices for configuration are:
+!MESSAGE 
+!MESSAGE "example - Win32 Debug" (based on "Win32 (x86) Dynamic-Link Library")
+!MESSAGE "example - Win32 Release" (based on "Win32 (x86) Dynamic-Link Library")
+!MESSAGE 
+
+# Begin Project
+# PROP AllowPerConfigDependencies 0
+# PROP Scc_ProjName ""
+# PROP Scc_LocalPath ""
+CPP=cl.exe
+MTL=midl.exe
+RSC=rc.exe
+
+!IF  "$(CFG)" == "example - Win32 Debug"
+
+# PROP BASE Use_MFC 0
+# PROP BASE Use_Debug_Libraries 1
+# PROP BASE Output_Dir "Debug"
+# PROP BASE Intermediate_Dir "Debug"
+# PROP BASE Target_Dir ""
+# PROP Use_MFC 0
+# PROP Use_Debug_Libraries 1
+# PROP Output_Dir "Debug"
+# PROP Intermediate_Dir "Debug"
+# PROP Ignore_Export_Lib 0
+# PROP Target_Dir ""
+# ADD BASE CPP /nologo /MTd /W3 /Gm /GX /ZI /Od /D "WIN32" /D "_DEBUG" /D "_WINDOWS" /D "_MBCS" /D "_USRDLL" /D "EXAMPLE_EXPORTS" /YX /FD /GZ /c
+# ADD CPP /nologo /MTd /W3 /Gm /GX /ZI /Od /I "$(JAVA_INCLUDE)" /I "$(JAVA_INCLUDE)\win32" /D "WIN32" /D "_DEBUG" /D "_WINDOWS" /D "_MBCS" /D "_USRDLL" /D "EXAMPLE_EXPORTS" /YX /FD /GZ /c
+# ADD BASE MTL /nologo /D "_DEBUG" /mktyplib203 /win32
+# ADD MTL /nologo /D "_DEBUG" /mktyplib203 /win32
+# ADD BASE RSC /l 0x809 /d "_DEBUG"
+# ADD RSC /l 0x809 /d "_DEBUG"
+BSC32=bscmake.exe
+# ADD BASE BSC32 /nologo
+# ADD BSC32 /nologo
+LINK32=link.exe
+# ADD BASE LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib /nologo /dll /debug /machine:I386 /pdbtype:sept
+# ADD LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib /nologo /dll /debug /machine:I386 /out:"example.dll" /pdbtype:sept
+# Begin Special Build Tool
+SOURCE="$(InputPath)"
+PostBuild_Desc=Java compile post-build step
+PostBuild_Cmds=echo on	"%JAVA_BIN%\javac" *.java
+# End Special Build Tool
+
+!ELSEIF  "$(CFG)" == "example - Win32 Release"
+
+# PROP BASE Use_MFC 0
+# PROP BASE Use_Debug_Libraries 0
+# PROP BASE Output_Dir "Release"
+# PROP BASE Intermediate_Dir "Release"
+# PROP BASE Target_Dir ""
+# PROP Use_MFC 0
+# PROP Use_Debug_Libraries 0
+# PROP Output_Dir "Release"
+# PROP Intermediate_Dir "Release"
+# PROP Ignore_Export_Lib 0
+# PROP Target_Dir ""
+# ADD BASE CPP /nologo /MT /W3 /GX /O2 /D "WIN32" /D "NDEBUG" /D "_WINDOWS" /D "_MBCS" /D "_USRDLL" /D "EXAMPLE_EXPORTS" /YX /FD /c
+# ADD CPP /nologo /MT /W3 /GX /O2 /I "$(JAVA_INCLUDE)" /I "$(JAVA_INCLUDE)\win32" /D "WIN32" /D "NDEBUG" /D "_WINDOWS" /D "_MBCS" /D "_USRDLL" /D "EXAMPLE_EXPORTS" /YX /FD /c
+# ADD BASE MTL /nologo /D "NDEBUG" /mktyplib203 /win32
+# ADD MTL /nologo /D "NDEBUG" /mktyplib203 /win32
+# ADD BASE RSC /l 0x809 /d "NDEBUG"
+# ADD RSC /l 0x809 /d "NDEBUG"
+BSC32=bscmake.exe
+# ADD BASE BSC32 /nologo
+# ADD BSC32 /nologo
+LINK32=link.exe
+# ADD BASE LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib /nologo /dll /machine:I386
+# ADD LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib /nologo /dll /machine:I386 /out:"example.dll"
+# Begin Special Build Tool
+SOURCE="$(InputPath)"
+PostBuild_Desc=Java compile post-build step
+PostBuild_Cmds=echo on	"%JAVA_BIN%\javac" *.java
+# End Special Build Tool
+
+!ENDIF 
+
+# Begin Target
+
+# Name "example - Win32 Debug"
+# Name "example - Win32 Release"
+# Begin Group "Source Files"
+
+# PROP Default_Filter "cpp;c;cxx;rc;def;r;odl;idl;hpj;bat"
+# Begin Source File
+
+SOURCE=.\example.cxx
+# End Source File
+# Begin Source File
+
+SOURCE=.\example_wrap.cxx
+# End Source File
+# End Group
+# Begin Group "Header Files"
+
+# PROP Default_Filter "h;hpp;hxx;hm;inl"
+# Begin Source File
+
+SOURCE=.\example.h
+# End Source File
+# End Group
+# Begin Group "Resource Files"
+
+# PROP Default_Filter "ico;cur;bmp;dlg;rc2;rct;bin;rgs;gif;jpg;jpeg;jpe"
+# End Group
+# Begin Source File
+
+SOURCE=.\example.i
+
+!IF  "$(CFG)" == "example - Win32 Debug"
+
+# Begin Custom Build
+InputPath=.\example.i
+InputName=example
+
+"$(InputName)_wrap.cxx" : $(SOURCE) "$(INTDIR)" "$(OUTDIR)"
+	echo In order to function correctly, please ensure the following environment variables are correctly set: 
+	echo JAVA_INCLUDE: %JAVA_INCLUDE% 
+	echo JAVA_BIN: %JAVA_BIN% 
+	echo on 
+	..\..\..\swig.exe -c++ -java $(InputPath) 
+	
+# End Custom Build
+
+!ELSEIF  "$(CFG)" == "example - Win32 Release"
+
+# Begin Custom Build
+InputPath=.\example.i
+InputName=example
+
+"$(InputName)_wrap.cxx" : $(SOURCE) "$(INTDIR)" "$(OUTDIR)"
+	echo In order to function correctly, please ensure the following environment variables are correctly set: 
+	echo JAVA_INCLUDE: %JAVA_INCLUDE% 
+	echo JAVA_BIN: %JAVA_BIN% 
+	echo on 
+	..\..\..\swig.exe -c++ -java $(InputPath) 
+	
+# End Custom Build
+
+!ENDIF 
+
+# End Source File
+# End Target
+# End Project
diff --git a/Examples/doxygencomments/java/class/example.h b/Examples/doxygencomments/java/class/example.h
new file mode 100644
index 000000000..7e3e7d540
--- /dev/null
+++ b/Examples/doxygencomments/java/class/example.h
@@ -0,0 +1,45 @@
+/** \file example.h 
+comments on example.h */
+
+/*! This is describing class Shape
+ \author Bob
+ */
+
+class Shape {
+public:
+  Shape() {
+    nshapes++;
+  }
+  virtual ~Shape() {
+    nshapes--;
+  };
+  double  x, y; /*!< Important things  */
+  void    move(double dx, double dy);
+  virtual double area(void) = 0; /*!< \return the area */
+  virtual double perimeter(void) = 0; /*!< \return the perimeter */
+  static  int nshapes;
+};
+/*! This is describing class Circle */
+class Circle : public Shape {
+private:
+  double radius;
+public:
+  Circle(double r) : radius(r) { };
+  virtual double area(void);
+  virtual double perimeter(void);
+};
+
+/*! This is describing class square */
+class Square : public Shape {
+private:
+  double width;
+public:
+  Square(double w) : width(w) { };
+  virtual double area(void);
+  virtual double perimeter(void);
+};
+
+
+
+
+  
diff --git a/Examples/doxygencomments/java/class/example.i b/Examples/doxygencomments/java/class/example.i
new file mode 100644
index 000000000..05c0ca2ab
--- /dev/null
+++ b/Examples/doxygencomments/java/class/example.i
@@ -0,0 +1,10 @@
+/** File : example.i */
+%module example
+
+%{
+#include "example.h"
+%}
+
+/* Let's just grab the original header file here */
+%include "example.h"
+
diff --git a/Examples/doxygencomments/java/class/index.html b/Examples/doxygencomments/java/class/index.html
new file mode 100644
index 000000000..e9db7e94a
--- /dev/null
+++ b/Examples/doxygencomments/java/class/index.html
@@ -0,0 +1,197 @@
+<html>
+<head>
+<title>SWIG:Examples:java:class</title>
+</head>
+
+<body bgcolor="#ffffff">
+
+
+<tt>SWIG/Examples/java/class/</tt>
+<hr>
+
+<H2>Wrapping a simple C++ class</H2>
+
+<p>
+This example illustrates the high level form of C++ class wrapping performed
+by SWIG.  In this case, a C++ class has a proxy Java class, which 
+provides access to C++ class members.
+
+<h2>The C++ Code</h2>
+
+Suppose you have some C++ classes described by the following (and admittedly lame) 
+header file:
+
+<blockquote>
+<pre>
+/* File : example.h */
+
+class Shape {
+public:
+  Shape() {
+    nshapes++;
+  }
+  virtual ~Shape() {
+    nshapes--;
+  };
+  double  x, y;   
+  void    move(double dx, double dy);
+  virtual double area() = 0;
+  virtual double perimeter() = 0;
+  static  int nshapes;
+};
+
+class Circle : public Shape {
+private:
+  double radius;
+public:
+  Circle(double r) : radius(r) { };
+  virtual double area();
+  virtual double perimeter();
+};
+
+class Square : public Shape {
+private:
+  double width;
+public:
+  Square(double w) : width(w) { };
+  virtual double area();
+  virtual double perimeter();
+};
+</pre>
+</blockquote>
+
+<h2>The SWIG interface</h2>
+
+A simple SWIG interface for this can be built by simply grabbing the header file
+like this:
+
+<blockquote>
+<pre>
+/* File : example.i */
+%module example
+
+%{
+#include "example.h"
+%}
+
+/* Let's just grab the original header file here */
+%include "example.h"
+</pre>
+</blockquote>
+
+Note: when creating a C++ extension, you must run SWIG with the <tt>-c++</tt> option like this:
+<blockquote>
+<pre>
+% swig -c++ -java example.i
+</pre>
+</blockquote>
+
+<h2>A sample Java program</h2>
+
+Click <a href="main.java">here</a> to see a Java program that calls the C++ functions from Java.
+
+<h2>Key points</h2>
+
+<ul>
+<li>To create a new object, you call a constructor like this:
+
+<blockquote>
+<pre>
+Circle c = new Circle(10);
+</pre>
+</blockquote>
+
+<p>
+<li>To access member data, a pair of accessor functions are used.
+For example:
+
+<blockquote>
+<pre>
+c.setX(15);        // Set member data
+x = c.getX();      // Get member data
+</pre>
+</blockquote>
+
+<p>
+<li>To invoke a member function, you simply do this
+
+<blockquote>
+<pre>
+System.out.println( "The area is " + c.area() );
+</pre>
+</blockquote>
+
+<p>
+<li>To invoke a destructor, simply do this
+
+<blockquote>
+<pre>
+c.delete();     // Deletes a shape
+</pre>
+</blockquote>
+
+<p>
+<li>Static member variables are wrapped with java static get and set access functions.  For example:
+
+<blockquote>
+<pre>
+n = Shape.getNshapes();     // Get a static data member
+Shape.setNshapes(13);       // Set a static data member
+</pre>
+</blockquote>
+
+</ul>
+
+<h2>General Comments</h2>
+
+<ul>
+<li>This high-level interface using proxy classes is not the only way to handle C++ code. 
+A low level interface using c functions to access member variables and member functions is the alternative SWIG
+approach. This entails passing around the c pointer or c++ 'this' pointer and as such it is not difficult to crash the JVM. 
+The abstraction of the underlying pointer by the java proxy classes far better fits the java programming paradigm.
+
+<p>
+<li>SWIG *does* know how to properly perform upcasting of objects in an inheritance
+hierarchy (including multiple inheritance).  However Java classes can only derive from one base class so multiple inheritance
+is not implemented. Java classes can implement more than one interface so there is scope for improvement in the future. 
+
+<p>
+<li>A wide variety of C++ features are not currently supported by SWIG.  Here is the
+short and incomplete list:
+
+<p>
+<ul>
+<li>Overloaded methods and functions.  SWIG wrappers don't know how to resolve name
+conflicts so you must give an alternative name to any overloaded method name using the
+%name directive like this:
+
+<blockquote>
+<pre>
+void foo(int a);  
+%name(foo2) void foo(double a, double b);
+</pre>
+</blockquote>
+
+<p>
+<li>Overloaded operators.  Not supported at all. The only workaround for this is
+to write a helper function. For example:
+
+<blockquote>
+<pre>
+%inline %{
+    Vector *vector_add(Vector *a, Vector *b) {
+          ... whatever ...
+    }
+%}
+</pre>
+</blockquote>
+
+<p>
+<li>Namespaces.  Not supported at all. Won't be supported until SWIG2.0 (if at all).
+
+</ul>
+</ul>
+
+<hr>
+</body>
+</html>
diff --git a/Examples/doxygencomments/java/class/main.java b/Examples/doxygencomments/java/class/main.java
new file mode 100644
index 000000000..8ef35db6d
--- /dev/null
+++ b/Examples/doxygencomments/java/class/main.java
@@ -0,0 +1,70 @@
+// This example illustrates how C++ classes can be used from Java using SWIG.
+// The Java class gets mapped onto the C++ class and behaves as if it is a Java class.
+
+public class main {
+  static {
+    try {
+        System.loadLibrary("example");
+    } catch (UnsatisfiedLinkError e) {
+      System.err.println("Native code library failed to load. See the chapter on Dynamic Linking Problems in the SWIG Java documentation for help.\n" + e);
+      System.exit(1);
+    }
+  }
+
+  public static void main(String argv[]) 
+  {
+    // ----- Object creation -----
+    
+    System.out.println( "Creating some objects:" );
+    Circle c = new Circle(10);
+    System.out.println( "    Created circle " + c );
+    Square s = new Square(10);
+    System.out.println( "    Created square " + s );
+    
+    // ----- Access a static member -----
+    
+    System.out.println( "\nA total of " + Shape.getNshapes() + " shapes were created" );
+    
+    // ----- Member data access -----
+    
+    // Notice how we can do this using functions specific to
+    // the 'Circle' class.
+    c.setX(20);
+    c.setY(30);
+    
+    // Now use the same functions in the base class
+    Shape shape = s;
+    shape.setX(-10);
+    shape.setY(5);
+    
+    System.out.println( "\nHere is their current position:" );
+    System.out.println( "    Circle = (" + c.getX() + " " + c.getY() + ")" );
+    System.out.println( "    Square = (" + s.getX() + " " + s.getY() + ")" );
+    
+    // ----- Call some methods -----
+    
+    System.out.println( "\nHere are some properties of the shapes:" );
+    Shape[] shapes = {c,s};
+    for (int i=0; i<shapes.length; i++)
+    {
+          System.out.println( "   " + shapes[i].toString() );
+          System.out.println( "        area      = " + shapes[i].area() );
+          System.out.println( "        perimeter = " + shapes[i].perimeter() );
+    }
+    
+    // Notice how the area() and perimeter() functions really
+    // invoke the appropriate virtual method on each object.
+    
+    // ----- Delete everything -----
+    
+    System.out.println( "\nGuess I'll clean up now" );
+    
+    // Note: this invokes the virtual destructor
+    // You could leave this to the garbage collector
+    c.delete();
+    s.delete();
+    
+    System.out.println( Shape.getNshapes() + " shapes remain" );
+    System.out.println( "Goodbye" );
+  }
+}
diff --git a/Examples/doxygencomments/java/constants/Makefile b/Examples/doxygencomments/java/constants/Makefile
new file mode 100644
index 000000000..2b3d35c6a
--- /dev/null
+++ b/Examples/doxygencomments/java/constants/Makefile
@@ -0,0 +1,18 @@
+TOP        = ../..
+SWIG       = $(TOP)/../preinst-swig
+CXXSRCS    = 
+TARGET     = example
+INTERFACE  = example.i
+SWIGOPT    =
+
+all::	java
+
+java::
+	$(MAKE) -f $(TOP)/Makefile CXXSRCS='$(CXXSRCS)' SWIG='$(SWIG)' \
+	SWIGOPT='$(SWIGOPT)' TARGET='$(TARGET)' INTERFACE='$(INTERFACE)' java_cpp
+	javac *.java
+
+clean::
+	$(MAKE) -f $(TOP)/Makefile java_clean
+
+check: all
diff --git a/Examples/doxygencomments/java/constants/example.i b/Examples/doxygencomments/java/constants/example.i
new file mode 100644
index 000000000..5cbcf2463
--- /dev/null
+++ b/Examples/doxygencomments/java/constants/example.i
@@ -0,0 +1,30 @@
+/*! File : example.i */
+%module example
+
+/* Force the generated Java code to use the C constant values rather than making a JNI call */
+%javaconst(1);
+
+/*! A few preprocessor macros */
+
+#define    ICONST      42
+#define    FCONST      2.1828
+#define    CCONST      'x'
+#define    CCONST2     '\n'
+#define    SCONST      "Hello World"
+#define    SCONST2     "\"Hello World\""
+
+/*! This should work just fine */
+#define    EXPR        ICONST + 3*(FCONST)
+
+/*! This shouldn't do anything */
+#define    EXTERN      extern
+
+/*! Neither should this (BAR isn't defined) */
+#define    FOO         (ICONST + BAR)
+
+/*! The following directives also produce constants */
+
+%constant int iconst = 37;
+%constant double fconst = 3.14;
+
+
diff --git a/Examples/doxygencomments/java/constants/index.html b/Examples/doxygencomments/java/constants/index.html
new file mode 100644
index 000000000..8367d0571
--- /dev/null
+++ b/Examples/doxygencomments/java/constants/index.html
@@ -0,0 +1,52 @@
+<html>
+<head>
+<title>SWIG:Examples:java:constants</title>
+</head>
+
+<body bgcolor="#ffffff">
+
+<tt>SWIG/Examples/java/constants/</tt>
+<hr>
+
+<H2>Wrapping C Constants</H2>
+
+<p>
+When SWIG encounters C preprocessor macros and C declarations that look like constants,
+it creates Java constant with an identical value.  Click <a href="example.i">here</a>
+to see a SWIG interface with some constant declarations in it.
+
+
+<h2>Accessing Constants from Java</h2>
+Click <a href="../../../Doc/Manual/Java.html#constants">here</a> for the section on constants in the SWIG and Java documentation.
+<p>
+
+Click <a href="main.java">here</a> to see a Java program that prints out the values
+of the constants contained in the above file.</p>
+<h2>Key points</h2>
+<ul>
+<li>The values of preprocessor macros are converted into Java constants.
+<li>Types are inferred by syntax (e.g., "3" is an integer and "3.5" is a float).
+<li>Character constants such as 'x' are converted into Java strings.
+<li>C string literals such as "Hello World" are converted into Java strings.
+<li>Macros that are not fully defined are simply ignored.  For example:
+<blockquote>
+<pre>
+#define EXTERN extern
+</pre>
+</blockquote>
+is ignored because SWIG has no idea what type of variable this would be.
+
+<p>
+<li>Expressions are allowed provided that all of their components are defined. Otherwise, the constant is ignored.
+
+<li>Certain C declarations involving 'const' are also turned into Java constants. 
+<li>The constants that appear in a SWIG interface file do not have to appear in any sort
+of matching C source file since the creation of a constant does not require linkage
+to a stored value (i.e., a value held in a C global variable or memory location).
+</ul>
+
+<hr>
+
+
+</body>
+</html>
diff --git a/Examples/doxygencomments/java/constants/main.java b/Examples/doxygencomments/java/constants/main.java
new file mode 100644
index 000000000..7130c3d70
--- /dev/null
+++ b/Examples/doxygencomments/java/constants/main.java
@@ -0,0 +1,44 @@
+import java.lang.reflect.*;
+
+public class main {
+  static {
+    try {
+        System.loadLibrary("example");
+    } catch (UnsatisfiedLinkError e) {
+      System.err.println("Native code library failed to load. See the chapter on Dynamic Linking Problems in the SWIG Java documentation for help.\n" + e);
+      System.exit(1);
+    }
+  }
+
+  public static void main(String argv[]) 
+  {
+    System.out.println("ICONST  = " + example.ICONST + " (should be 42)");
+    System.out.println("FCONST  = " + example.FCONST + " (should be 2.1828)");
+    System.out.println("CCONST  = " + example.CCONST + " (should be 'x')");
+    System.out.println("CCONST2 = " + example.CCONST2 + " (this should be on a new line)");
+    System.out.println("SCONST  = " + example.SCONST + " (should be 'Hello World')");
+    System.out.println("SCONST2 = " + example.SCONST2 + " (should be '\"Hello World\"')");
+    System.out.println("EXPR    = " + example.EXPR +   " (should be 48.5484)");
+    System.out.println("iconst  = " + example.iconst + " (should be 37)");
+    System.out.println("fconst  = " + example.fconst + " (should be 3.14)");
+
+// Use reflection to check if these variables are defined:
+    try
+    {
+        System.out.println("EXTERN = " + example.class.getField("EXTERN") + " (Arg! This shouldn't print anything)");
+    }
+    catch (NoSuchFieldException e)
+    {
+        System.out.println("EXTERN isn't defined (good)");
+    }
+
+    try
+    {
+        System.out.println("FOO    = " + example.class.getField("FOO") + " (Arg! This shouldn't print anything)");
+    }
+    catch (NoSuchFieldException e)
+    {
+        System.out.println("FOO isn't defined (good)");
+    }
+  }
+}
diff --git a/Examples/doxygencomments/java/enum/Makefile b/Examples/doxygencomments/java/enum/Makefile
new file mode 100644
index 000000000..14c301703
--- /dev/null
+++ b/Examples/doxygencomments/java/enum/Makefile
@@ -0,0 +1,18 @@
+TOP        = ../..
+SWIG       = $(TOP)/../preinst-swig
+CXXSRCS    = example.cxx
+TARGET     = example
+INTERFACE  = example.i
+SWIGOPT    =
+
+all::	java
+
+java::
+	$(MAKE) -f $(TOP)/Makefile CXXSRCS='$(CXXSRCS)' SWIG='$(SWIG)' \
+	SWIGOPT='$(SWIGOPT)' TARGET='$(TARGET)' INTERFACE='$(INTERFACE)' java_cpp
+	javac *.java
+
+clean::
+	$(MAKE) -f $(TOP)/Makefile java_clean
+
+check: all
diff --git a/Examples/doxygencomments/java/enum/example.cxx b/Examples/doxygencomments/java/enum/example.cxx
new file mode 100644
index 000000000..df7bb6328
--- /dev/null
+++ b/Examples/doxygencomments/java/enum/example.cxx
@@ -0,0 +1,37 @@
+/* File : example.cxx */
+
+#include "example.h"
+#include <stdio.h>
+
+void Foo::enum_test(speed s) {
+  if (s == IMPULSE) {
+    printf("IMPULSE speed\n");
+  } else if (s == WARP) {
+    printf("WARP speed\n");
+  } else if (s == LUDICROUS) {
+    printf("LUDICROUS speed\n");
+  } else {
+    printf("Unknown speed\n");
+  }
+}
+
+void enum_test(color c, Foo::speed s) {
+  if (c == RED) {
+    printf("color = RED, ");
+  } else if (c == BLUE) {
+    printf("color = BLUE, ");
+  } else if (c == GREEN) {
+    printf("color = GREEN, ");
+  } else {
+    printf("color = Unknown color!, ");
+  }
+  if (s == Foo::IMPULSE) {
+    printf("speed = IMPULSE speed\n");
+  } else if (s == Foo::WARP) {
+    printf("speed = WARP speed\n");
+  } else if (s == Foo::LUDICROUS) {
+    printf("speed = LUDICROUS speed\n");
+  } else {
+    printf("speed = Unknown speed!\n");
+  }
+}
diff --git a/Examples/doxygencomments/java/enum/example.h b/Examples/doxygencomments/java/enum/example.h
new file mode 100644
index 000000000..2142d8240
--- /dev/null
+++ b/Examples/doxygencomments/java/enum/example.h
@@ -0,0 +1,23 @@
+
+
+/** This is a block describing enum
+ */
+
+enum color { RED, BLUE, GREEN };
+
+/*! This is describing class foo
+ */
+
+class Foo {
+ public:
+  Foo() { }
+  enum speed { IMPULSE=10, WARP=20, LUDICROUS=30 };
+  void enum_test(speed s);
+};
+
+/*! This is describing enum test
+//! \param c the color c
+//! \param s the speed
+ */
+
+void enum_test(color c, Foo::speed s);
diff --git a/Examples/doxygencomments/java/enum/example.i b/Examples/doxygencomments/java/enum/example.i
new file mode 100644
index 000000000..1f1f9d526
--- /dev/null
+++ b/Examples/doxygencomments/java/enum/example.i
@@ -0,0 +1,14 @@
+/** File : example.i */
+%module example
+
+%{
+#include "example.h"
+%}
+
+/** Force the generated Java code to use the C enum values rather than making a JNI call */
+%javaconst(1);
+
+/** Let's just grab the original header file here */
+
+%include "example.h"
+
diff --git a/Examples/doxygencomments/java/enum/index.html b/Examples/doxygencomments/java/enum/index.html
new file mode 100644
index 000000000..52c06c5d1
--- /dev/null
+++ b/Examples/doxygencomments/java/enum/index.html
@@ -0,0 +1,29 @@
+<html>
+<head>
+<title>SWIG:Examples:java:enum</title>
+</head>
+
+<body bgcolor="#ffffff">
+
+
+<tt>SWIG/Examples/java/enum/</tt>
+<hr>
+
+<H2>Wrapping enumerations</H2>
+
+<p>
+This example tests SWIG's ability to wrap enumerations. 
+SWIG wraps enums in numerous different ways. The default approach is to wrap
+each enum with the typesafe enum pattern. Enums are handled as integers in the JNI layer.
+See the documentation for the other approaches for wrapping enums.
+
+
+<ul>
+<li><a href="example.h">example.h</a>.  Header file containing some enums.
+<li><a href="example.i">example.i</a>.  Interface file.
+<li><a href="main.java">main.java</a>. Sample Java program.
+</ul>
+
+<hr>
+</body>
+</html>
diff --git a/Examples/doxygencomments/java/enum/main.java b/Examples/doxygencomments/java/enum/main.java
new file mode 100644
index 000000000..8646e0087
--- /dev/null
+++ b/Examples/doxygencomments/java/enum/main.java
@@ -0,0 +1,38 @@
+
+public class main {
+  static {
+    try {
+        System.loadLibrary("example");
+    } catch (UnsatisfiedLinkError e) {
+      System.err.println("Native code library failed to load. See the chapter on Dynamic Linking Problems in the SWIG Java documentation for help.\n" + e);
+      System.exit(1);
+    }
+  }
+
+  public static void main(String argv[]) 
+  {
+    // Print out the value of some enums
+    System.out.println("*** color ***");
+    System.out.println("    " + color.RED + " = " + color.RED.swigValue());
+    System.out.println("    " + color.BLUE + " = " + color.BLUE.swigValue());
+    System.out.println("    " + color.GREEN + " = " + color.GREEN.swigValue());
+
+    System.out.println("\n*** Foo::speed ***");
+    System.out.println("    Foo::" + Foo.speed.IMPULSE + " = " + Foo.speed.IMPULSE.swigValue());
+    System.out.println("    Foo::" + Foo.speed.WARP + " = " + Foo.speed.WARP.swigValue());
+    System.out.println("    Foo::" + Foo.speed.LUDICROUS + " = " + Foo.speed.LUDICROUS.swigValue());
+
+    System.out.println("\nTesting use of enums with functions\n");
+
+    example.enum_test(color.RED, Foo.speed.IMPULSE);
+    example.enum_test(color.BLUE, Foo.speed.WARP);
+    example.enum_test(color.GREEN, Foo.speed.LUDICROUS);
+
+    System.out.println( "\nTesting use of enum with class method" );
+    Foo f = new Foo();
+
+    f.enum_test(Foo.speed.IMPULSE);
+    f.enum_test(Foo.speed.WARP);
+    f.enum_test(Foo.speed.LUDICROUS);
+  }
+}
diff --git a/Examples/doxygencomments/java/extend/Makefile b/Examples/doxygencomments/java/extend/Makefile
new file mode 100644
index 000000000..14c301703
--- /dev/null
+++ b/Examples/doxygencomments/java/extend/Makefile
@@ -0,0 +1,18 @@
+TOP        = ../..
+SWIG       = $(TOP)/../preinst-swig
+CXXSRCS    = example.cxx
+TARGET     = example
+INTERFACE  = example.i
+SWIGOPT    =
+
+all::	java
+
+java::
+	$(MAKE) -f $(TOP)/Makefile CXXSRCS='$(CXXSRCS)' SWIG='$(SWIG)' \
+	SWIGOPT='$(SWIGOPT)' TARGET='$(TARGET)' INTERFACE='$(INTERFACE)' java_cpp
+	javac *.java
+
+clean::
+	$(MAKE) -f $(TOP)/Makefile java_clean
+
+check: all
diff --git a/Examples/doxygencomments/java/extend/example.cxx b/Examples/doxygencomments/java/extend/example.cxx
new file mode 100644
index 000000000..450d75608
--- /dev/null
+++ b/Examples/doxygencomments/java/extend/example.cxx
@@ -0,0 +1,4 @@
+/* File : example.cxx */
+
+#include "example.h"
+
diff --git a/Examples/doxygencomments/java/extend/example.h b/Examples/doxygencomments/java/extend/example.h
new file mode 100644
index 000000000..db49ae747
--- /dev/null
+++ b/Examples/doxygencomments/java/extend/example.h
@@ -0,0 +1,60 @@
+/* File : example.h */
+
+#include <cstdio>
+#include <iostream>
+#include <vector>
+#include <string>
+#include <cmath>
+
+/**This is describiing class Employee */
+class Employee {
+private:
+	std::string name;
+public:
+	/** TEST */
+	Employee(const char* n): name(n) {}
+/**This is describing method getTitle */
+	virtual std::string getTitle() { return getPosition() + " " + getName(); }
+	virtual std::string getName() { return name; }
+	virtual std::string getPosition() const { return "Employee"; }
+	virtual ~Employee() { printf("~Employee() @ %p\n", this); }
+};
+
+/**This is describing class Manager */
+class Manager: public Employee {
+public:
+	Manager(const char* n): Employee(n) {}
+	virtual std::string getPosition() const { return "Manager"; }
+};
+
+
+class EmployeeList {
+	std::vector<Employee*> list;
+public:
+	EmployeeList() {
+		list.push_back(new Employee("Bob"));
+		list.push_back(new Employee("Jane"));
+		list.push_back(new Manager("Ted"));
+	}
+	void addEmployee(Employee *p) {
+		list.push_back(p);
+		std::cout << "New employee added.   Current employees are:" << std::endl;
+		std::vector<Employee*>::iterator i;
+		for (i=list.begin(); i!=list.end(); i++) {
+			std::cout << "  " << (*i)->getTitle() << std::endl;
+		}
+	}
+/**This is describing class get item */
+	const Employee *get_item(int i) {
+		return list[i];
+	}
+	~EmployeeList() { 
+		std::vector<Employee*>::iterator i;
+		std::cout << "~EmployeeList, deleting " << list.size() << " employees." << std::endl;
+		for (i=list.begin(); i!=list.end(); i++) {
+			delete *i;
+		}
+		std::cout << "~EmployeeList empty." << std::endl;
+	}
+};
+
diff --git a/Examples/doxygencomments/java/extend/example.i b/Examples/doxygencomments/java/extend/example.i
new file mode 100644
index 000000000..c8ec32e09
--- /dev/null
+++ b/Examples/doxygencomments/java/extend/example.i
@@ -0,0 +1,15 @@
+/* File : example.i */
+%module(directors="1") example
+%{
+#include "example.h"
+%}
+
+%include "std_vector.i"
+%include "std_string.i"
+
+/* turn on director wrapping for Manager */
+%feature("director") Employee;
+%feature("director") Manager;
+
+%include "example.h"
+
diff --git a/Examples/doxygencomments/java/extend/index.html b/Examples/doxygencomments/java/extend/index.html
new file mode 100644
index 000000000..c7c2c127d
--- /dev/null
+++ b/Examples/doxygencomments/java/extend/index.html
@@ -0,0 +1,19 @@
+<html>
+<head>
+<title>SWIG:Examples:java:extend</title>
+</head>
+
+<body bgcolor="#ffffff">
+
+
+<tt>SWIG/Examples/java/extend/</tt>
+<hr>
+
+<H2>Extending a simple C++ class in Java</H2>
+
+<p>
+This example illustrates the extending of a C++ class with cross language polymorphism.
+
+<hr>
+</body>
+</html>
diff --git a/Examples/doxygencomments/java/extend/main.java b/Examples/doxygencomments/java/extend/main.java
new file mode 100644
index 000000000..ee3a94ed0
--- /dev/null
+++ b/Examples/doxygencomments/java/extend/main.java
@@ -0,0 +1,88 @@
+// This file illustrates the cross language polymorphism using directors.
+
+
+// CEO class, which overrides Employee::getPosition().
+
+class CEO extends Manager {
+  public CEO(String name) {
+    super(name);
+    }
+  public String getPosition() {
+    return "CEO";
+    }
+  // Public method to stop the SWIG proxy base class from thinking it owns the underlying C++ memory.
+  public void disownMemory() {
+    swigCMemOwn = false; 
+  } 
+}
+
+
+public class main {
+  static {
+    try {
+        System.loadLibrary("example");
+    } catch (UnsatisfiedLinkError e) {
+      System.err.println("Native code library failed to load. See the chapter on Dynamic Linking Problems in the SWIG Java documentation for help.\n" + e);
+      System.exit(1);
+    }
+  }
+
+  public static void main(String argv[]) 
+  {
+
+    // Create an instance of CEO, a class derived from the Java proxy of the 
+    // underlying C++ class. The calls to getName() and getPosition() are standard,
+    // the call to getTitle() uses the director wrappers to call CEO.getPosition().
+
+    CEO e = new CEO("Alice");
+    System.out.println( e.getName() + " is a " + e.getPosition() );
+    System.out.println( "Just call her \"" + e.getTitle() + "\"" );
+    System.out.println( "----------------------" );
+
+
+    // Create a new EmployeeList instance.  This class does not have a C++
+    // director wrapper, but can be used freely with other classes that do.
+
+    EmployeeList list = new EmployeeList();
+
+    // EmployeeList owns its items, so we must surrender ownership of objects we add.
+    e.disownMemory();
+    list.addEmployee(e);
+    System.out.println( "----------------------" );
+
+    // Now we access the first four items in list (three are C++ objects that
+    // EmployeeList's constructor adds, the last is our CEO). The virtual
+    // methods of all these instances are treated the same. For items 0, 1, and
+    // 2, all methods resolve in C++. For item 3, our CEO, getTitle calls
+    // getPosition which resolves in Java. The call to getPosition is
+    // slightly different, however, because of the overidden getPosition() call, since
+    // now the object reference has been "laundered" by passing through
+    // EmployeeList as an Employee*. Previously, Java resolved the call
+    // immediately in CEO, but now Java thinks the object is an instance of
+    // class Employee. So the call passes through the
+    // Employee proxy class and on to the C wrappers and C++ director,
+    // eventually ending up back at the Java CEO implementation of getPosition().
+    // The call to getTitle() for item 3 runs the C++ Employee::getTitle()
+    // method, which in turn calls getPosition(). This virtual method call
+    // passes down through the C++ director class to the Java implementation
+    // in CEO. All this routing takes place transparently.
+
+    System.out.println( "(position, title) for items 0-3:" );
+
+    System.out.println( "  " + list.get_item(0).getPosition() + ", \"" + list.get_item(0).getTitle() + "\"" );
+    System.out.println( "  " + list.get_item(1).getPosition() + ", \"" + list.get_item(1).getTitle() + "\"" );
+    System.out.println( "  " + list.get_item(2).getPosition() + ", \"" + list.get_item(2).getTitle() + "\"" );
+    System.out.println( "  " + list.get_item(3).getPosition() + ", \"" + list.get_item(3).getTitle() + "\"" );
+    System.out.println( "----------------------" );
+
+    // Time to delete the EmployeeList, which will delete all the Employee*
+    // items it contains. The last item is our CEO, which gets destroyed as well.
+    list.delete();
+    System.out.println( "----------------------" );
+
+    // All done.
+
+    System.out.println( "java exit" );
+
+  }
+}
diff --git a/Examples/doxygencomments/java/funcptr/Makefile b/Examples/doxygencomments/java/funcptr/Makefile
new file mode 100644
index 000000000..968c92c6c
--- /dev/null
+++ b/Examples/doxygencomments/java/funcptr/Makefile
@@ -0,0 +1,18 @@
+TOP        = ../..
+SWIG       = $(TOP)/../preinst-swig
+SRCS       = example.c
+TARGET     = example
+INTERFACE  = example.i
+SWIGOPT    =
+
+all::	java
+
+java::
+	$(MAKE) -f $(TOP)/Makefile SRCS='$(SRCS)' SWIG='$(SWIG)' \
+	SWIGOPT='$(SWIGOPT)' TARGET='$(TARGET)' INTERFACE='$(INTERFACE)' java
+	javac *.java
+
+clean::
+	$(MAKE) -f $(TOP)/Makefile java_clean
+
+check: all
diff --git a/Examples/doxygencomments/java/funcptr/example.c b/Examples/doxygencomments/java/funcptr/example.c
new file mode 100644
index 000000000..5c4a3dabf
--- /dev/null
+++ b/Examples/doxygencomments/java/funcptr/example.c
@@ -0,0 +1,19 @@
+/* File : example.c */
+
+int do_op(int a, int b, int (*op)(int,int)) {
+  return (*op)(a,b);
+}
+
+int add(int a, int b) {
+  return a+b;
+}
+
+int sub(int a, int b) {
+  return a-b;
+}
+
+int mul(int a, int b) {
+  return a*b;
+}
+
+int (*funcvar)(int,int) = add;
diff --git a/Examples/doxygencomments/java/funcptr/example.h b/Examples/doxygencomments/java/funcptr/example.h
new file mode 100644
index 000000000..5285737a3
--- /dev/null
+++ b/Examples/doxygencomments/java/funcptr/example.h
@@ -0,0 +1,10 @@
+/* file: example.h */
+
+extern int do_op(int,int, int (*op)(int,int));
+/*! Describing function add */
+extern int add(int,int);
+extern int sub(int,int);
+extern int mul(int,int);
+
+extern int (*funcvar)(int,int);
+
diff --git a/Examples/doxygencomments/java/funcptr/example.i b/Examples/doxygencomments/java/funcptr/example.i
new file mode 100644
index 000000000..82c3c2201
--- /dev/null
+++ b/Examples/doxygencomments/java/funcptr/example.i
@@ -0,0 +1,16 @@
+/* File : example.i */
+%module example
+%{
+#include "example.h"
+%}
+
+/** Wrap a function taking a pointer to a function */
+extern int  do_op(int a, int b, int (*op)(int, int));
+
+/** Now install a bunch of "ops" as constants */
+%constant int (*ADD)(int,int) = add;
+%constant int (*SUB)(int,int) = sub;
+%constant int (*MUL)(int,int) = mul;
+
+extern int (*funcvar)(int,int);
+
diff --git a/Examples/doxygencomments/java/funcptr/index.html b/Examples/doxygencomments/java/funcptr/index.html
new file mode 100644
index 000000000..0ad2be1cf
--- /dev/null
+++ b/Examples/doxygencomments/java/funcptr/index.html
@@ -0,0 +1,91 @@
+<html>
+<head>
+<title>SWIG:Examples:java:funcptr</title>
+</head>
+
+<body bgcolor="#ffffff">
+
+
+<tt>SWIG/Examples/java/funcptr/</tt>
+<hr>
+
+<H2>Pointers to Functions</H2>
+
+<p>
+Okay, just what in the heck does SWIG do with a declaration like this?
+
+<blockquote>
+<pre>
+int do_op(int a, int b, int (*op)(int, int));
+</pre>
+</blockquote>
+
+Well, it creates a wrapper as usual.  Of course, that does raise some
+questions about the third argument (the pointer to a function). 
+
+<p>
+In this case, SWIG will wrap the function pointer as it does for all other
+pointers.  However, in order to actually call this function from a Java program,
+you will need to pass some kind of C function pointer object.  In C,
+this is easy, you just supply a function name as an argument like this:
+
+<blockquote>
+<pre>
+/* Some callback function */
+int add(int a, int b) {
+   return a+b;
+} 
+...
+int r = do_op(x,y,add);
+</pre>
+</blockquote>
+
+To make this work with SWIG, you will need to do a little extra work.  Specifically,
+you need to create some function pointer objects using the %constant directive like this:
+
+<blockquote>
+<pre>
+%constant(int (*)(int,int)) ADD = add;
+</pre>
+</blockquote>
+
+Now, in a Java program, you would do this:
+
+<blockquote>
+<pre>
+int r = do_op(x,y, example.ADD)
+</pre>
+</blockquote>
+where <tt>example</tt> is the module name.
+
+<h2>An Example</h2>
+
+Here are some files that illustrate this with a simple example:
+
+<ul>
+<li><a href="example.c">example.c</a>
+<li><a href="example.h">example.h</a>
+<li><a href="example.i">example.i</a> (SWIG interface)
+<li><a href="main.java">main.java</a> (Sample program)
+</ul>
+
+<h2>Notes</h2>
+
+<ul>
+<li>The value of a function pointer must correspond to a function written in C or C++.
+It is not possible to pass an arbitrary Java function in as a substitute for a C 
+function pointer.
+
+<p>
+<li>A Java function can be used as a C/C++ callback if you write some
+clever typemaps and are very careful about how you create your extension.
+This is an advanced topic not covered here.
+</ul>
+
+<hr>
+</body>
+</html>
+
+
+
+
diff --git a/Examples/doxygencomments/java/funcptr/main.java b/Examples/doxygencomments/java/funcptr/main.java
new file mode 100644
index 000000000..cf81f92b4
--- /dev/null
+++ b/Examples/doxygencomments/java/funcptr/main.java
@@ -0,0 +1,33 @@
+
+public class main {
+
+  static {
+    try {
+	System.loadLibrary("example");
+    } catch (UnsatisfiedLinkError e) {
+      System.err.println("Native code library failed to load. See the chapter on Dynamic Linking Problems in the SWIG Java documentation for help.\n" + e);
+      System.exit(1);
+    }
+  }
+
+  public static void main(String argv[]) {
+
+
+    int a = 37;
+    int b = 42;
+
+    // Now call our C function with a bunch of callbacks
+
+    System.out.println( "Trying some C callback functions" );
+    System.out.println( "    a        = " + a );
+    System.out.println( "    b        = " + b );
+    System.out.println( "    ADD(a,b) = " + example.do_op(a,b,example.ADD) );
+    System.out.println( "    SUB(a,b) = " + example.do_op(a,b,example.SUB) );
+    System.out.println( "    MUL(a,b) = " + example.do_op(a,b,example.MUL) );
+
+    System.out.println( "Here is what the C callback function classes are called in Java" );
+    System.out.println( "    ADD      = " + example.ADD.getClass().getName() );
+    System.out.println( "    SUB      = " + example.SUB.getClass().getName() );
+    System.out.println( "    MUL      = " + example.MUL.getClass().getName() );
+  }
+}
diff --git a/Examples/doxygencomments/java/index.html b/Examples/doxygencomments/java/index.html
new file mode 100644
index 000000000..d98f9a393
--- /dev/null
+++ b/Examples/doxygencomments/java/index.html
@@ -0,0 +1,65 @@
+<html>
+<head>
+<title>SWIG:Examples:java</title>
+</head>
+
+<body bgcolor="#ffffff">
+<H1>SWIG Java Examples</H1>
+
+<p>
+The following examples illustrate the use of SWIG with Java.
+
+<ul>
+<li><a href="simple/index.html">simple</a>.  A minimal example showing how SWIG can
+be used to wrap a C function, a global variable, and a constant.
+<li><a href="native/index.html">native</a>. Comparing the manual and the SWIG approach to calling native code.
+<li><a href="typemap/index.html">typemap</a>. Modifying the Java module's default behaviour by using typemaps.
+<li><a href="constants/index.html">constants</a>.  This shows how preprocessor macros and
+certain C declarations are turned into constants.
+<li><a href="variables/index.html">variables</a>. An example showing how to access C global variables.
+<li><a href="enum/index.html">enum</a>. Wrapping enumerations.
+<li><a href="class/index.html">class</a>. How to wrap a simple C++ class.
+<li><a href="reference/index.html">reference</a>. C++ references.
+<li><a href="pointer/index.html">pointer</a>. Simple pointer handling.
+<li><a href="template/index.html">template</a>. C++ templates.
+<li><a href="funcptr/index.html">funcptr</a>. Pointers to functions.
+<li><a href="callback/index.html">callback</a>. C++ callbacks using directors.
+<li><a href="extend/index.html">extend</a>. Polymorphism using directors.
+</ul>
+
+<h2>Running the examples</h2>
+Please see the <a href="../../Doc/Manual/Windows.html">Windows</a> page in the main manual for information on using the examples on Windows. <p>
+
+On Unix most of the examples work by making the Makefile before executing the program main.java. The Makefile will output the swig generated JNI c code as well as the Java wrapper classes. Additionally the JNI c/c++ code is compiled into the shared object (dynamic link library) which is needed for dynamic linking to the native code. The Makefiles also compile the Java files using javac. 
+<p>
+Ensure that the dynamic link library file is in the appropriate path before executing the Java program. For example in Unix, libexample.so must be in the LD_LIBRARY_PATH. 
+<p>
+A Unix example:
+<blockquote>
+<pre>
+$ make
+$ export LD_LIBRARY_PATH=. #ksh 
+$ java main
+</pre>
+</blockquote>
+<p>
+
+</ul>
+
+<h2>Compatibility</h2>
+
+The examples have been extensively tested on the following platforms:
+
+<ul>
+<li>Solaris
+<li>Linux
+<li>Cygwin
+<li>Windows
+</ul>
+
+Your mileage may vary.  If you experience a problem, please let us know by 
+contacting us on the <a href="http://www.swig.org/mail.html">mailing lists</a>.
+</body>
+</html>
+
+
diff --git a/Examples/doxygencomments/java/multimap/Makefile b/Examples/doxygencomments/java/multimap/Makefile
new file mode 100644
index 000000000..968c92c6c
--- /dev/null
+++ b/Examples/doxygencomments/java/multimap/Makefile
@@ -0,0 +1,18 @@
+TOP        = ../..
+SWIG       = $(TOP)/../preinst-swig
+SRCS       = example.c
+TARGET     = example
+INTERFACE  = example.i
+SWIGOPT    =
+
+all::	java
+
+java::
+	$(MAKE) -f $(TOP)/Makefile SRCS='$(SRCS)' SWIG='$(SWIG)' \
+	SWIGOPT='$(SWIGOPT)' TARGET='$(TARGET)' INTERFACE='$(INTERFACE)' java
+	javac *.java
+
+clean::
+	$(MAKE) -f $(TOP)/Makefile java_clean
+
+check: all
diff --git a/Examples/doxygencomments/java/multimap/example.c b/Examples/doxygencomments/java/multimap/example.c
new file mode 100644
index 000000000..b8360fa8a
--- /dev/null
+++ b/Examples/doxygencomments/java/multimap/example.c
@@ -0,0 +1,53 @@
+/* File : example.c */
+#include <stdio.h>
+#include <stdlib.h>
+#include <ctype.h>
+
+/* Compute the greatest common divisor of positive integers */
+int gcd(int x, int y) {
+  int g;
+  g = y;
+  while (x > 0) {
+    g = x;
+    x = y % x;
+    y = g;
+  }
+  return g;
+}
+
+int gcdmain(int argc, char *argv[]) {
+  int x,y;
+  if (argc != 3) {
+    printf("usage: gcd x y\n");
+    return -1;
+  }
+  x = atoi(argv[1]);
+  y = atoi(argv[2]);
+  printf("gcd(%d,%d) = %d\n", x,y,gcd(x,y));
+  return 0;
+}
+
+int count(char *bytes, int len, char c) {
+  int i;
+  int count = 0;
+  for (i = 0; i < len; i++) {
+    if (bytes[i] == c) count++;
+  }
+  return count;
+}
+
+void capitalize(char *str, int len) {
+  int i;
+  for (i = 0; i < len; i++) {
+    str[i] = (char)toupper(str[i]);
+  }
+}
+
+void circle(double x, double y) {
+  double a = x*x + y*y;
+  if (a > 1.0) {
+    printf("Bad points %g, %g\n", x,y);
+  } else {
+    printf("Good points %g, %g\n", x,y);
+  }
+}
diff --git a/Examples/doxygencomments/java/multimap/example.dsp b/Examples/doxygencomments/java/multimap/example.dsp
new file mode 100644
index 000000000..8e1f8415e
--- /dev/null
+++ b/Examples/doxygencomments/java/multimap/example.dsp
@@ -0,0 +1,158 @@
+# Microsoft Developer Studio Project File - Name="example" - Package Owner=<4>
+# Microsoft Developer Studio Generated Build File, Format Version 6.00
+# ** DO NOT EDIT **
+
+# TARGTYPE "Win32 (x86) Dynamic-Link Library" 0x0102
+
+CFG=example - Win32 Release
+!MESSAGE This is not a valid makefile. To build this project using NMAKE,
+!MESSAGE use the Export Makefile command and run
+!MESSAGE 
+!MESSAGE NMAKE /f "example.mak".
+!MESSAGE 
+!MESSAGE You can specify a configuration when running NMAKE
+!MESSAGE by defining the macro CFG on the command line. For example:
+!MESSAGE 
+!MESSAGE NMAKE /f "example.mak" CFG="example - Win32 Release"
+!MESSAGE 
+!MESSAGE Possible choices for configuration are:
+!MESSAGE 
+!MESSAGE "example - Win32 Debug" (based on "Win32 (x86) Dynamic-Link Library")
+!MESSAGE "example - Win32 Release" (based on "Win32 (x86) Dynamic-Link Library")
+!MESSAGE 
+
+# Begin Project
+# PROP AllowPerConfigDependencies 0
+# PROP Scc_ProjName ""
+# PROP Scc_LocalPath ""
+CPP=cl.exe
+MTL=midl.exe
+RSC=rc.exe
+
+!IF  "$(CFG)" == "example - Win32 Debug"
+
+# PROP BASE Use_MFC 0
+# PROP BASE Use_Debug_Libraries 1
+# PROP BASE Output_Dir "Debug"
+# PROP BASE Intermediate_Dir "Debug"
+# PROP BASE Target_Dir ""
+# PROP Use_MFC 0
+# PROP Use_Debug_Libraries 1
+# PROP Output_Dir "Debug"
+# PROP Intermediate_Dir "Debug"
+# PROP Ignore_Export_Lib 0
+# PROP Target_Dir ""
+# ADD BASE CPP /nologo /MTd /W3 /Gm /GX /ZI /Od /D "WIN32" /D "_DEBUG" /D "_WINDOWS" /D "_MBCS" /D "_USRDLL" /D "EXAMPLE_EXPORTS" /YX /FD /GZ /c
+# ADD CPP /nologo /MTd /W3 /Gm /GX /ZI /Od /I "$(JAVA_INCLUDE)" /I "$(JAVA_INCLUDE)\win32" /D "WIN32" /D "_DEBUG" /D "_WINDOWS" /D "_MBCS" /D "_USRDLL" /D "EXAMPLE_EXPORTS" /YX /FD /GZ /c
+# ADD BASE MTL /nologo /D "_DEBUG" /mktyplib203 /win32
+# ADD MTL /nologo /D "_DEBUG" /mktyplib203 /win32
+# ADD BASE RSC /l 0x809 /d "_DEBUG"
+# ADD RSC /l 0x809 /d "_DEBUG"
+BSC32=bscmake.exe
+# ADD BASE BSC32 /nologo
+# ADD BSC32 /nologo
+LINK32=link.exe
+# ADD BASE LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib /nologo /dll /debug /machine:I386 /pdbtype:sept
+# ADD LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib /nologo /dll /debug /machine:I386 /out:"example.dll" /pdbtype:sept
+# Begin Special Build Tool
+SOURCE="$(InputPath)"
+PostBuild_Desc=Java compile post-build step
+PostBuild_Cmds=echo on	"%JAVA_BIN%\javac" *.java
+# End Special Build Tool
+
+!ELSEIF  "$(CFG)" == "example - Win32 Release"
+
+# PROP BASE Use_MFC 0
+# PROP BASE Use_Debug_Libraries 0
+# PROP BASE Output_Dir "Release"
+# PROP BASE Intermediate_Dir "Release"
+# PROP BASE Target_Dir ""
+# PROP Use_MFC 0
+# PROP Use_Debug_Libraries 0
+# PROP Output_Dir "Release"
+# PROP Intermediate_Dir "Release"
+# PROP Ignore_Export_Lib 0
+# PROP Target_Dir ""
+# ADD BASE CPP /nologo /MT /W3 /GX /O2 /D "WIN32" /D "NDEBUG" /D "_WINDOWS" /D "_MBCS" /D "_USRDLL" /D "EXAMPLE_EXPORTS" /YX /FD /c
+# ADD CPP /nologo /MT /W3 /GX /O2 /I "$(JAVA_INCLUDE)" /I "$(JAVA_INCLUDE)\win32" /D "WIN32" /D "NDEBUG" /D "_WINDOWS" /D "_MBCS" /D "_USRDLL" /D "EXAMPLE_EXPORTS" /YX /FD /c
+# ADD BASE MTL /nologo /D "NDEBUG" /mktyplib203 /win32
+# ADD MTL /nologo /D "NDEBUG" /mktyplib203 /win32
+# ADD BASE RSC /l 0x809 /d "NDEBUG"
+# ADD RSC /l 0x809 /d "NDEBUG"
+BSC32=bscmake.exe
+# ADD BASE BSC32 /nologo
+# ADD BSC32 /nologo
+LINK32=link.exe
+# ADD BASE LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib /nologo /dll /machine:I386
+# ADD LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib /nologo /dll /machine:I386 /out:"example.dll"
+# Begin Special Build Tool
+SOURCE="$(InputPath)"
+PostBuild_Desc=Java compile post-build step
+PostBuild_Cmds=echo on	"%JAVA_BIN%\javac" *.java
+# End Special Build Tool
+
+!ENDIF 
+
+# Begin Target
+
+# Name "example - Win32 Debug"
+# Name "example - Win32 Release"
+# Begin Group "Source Files"
+
+# PROP Default_Filter "cpp;c;cxx;rc;def;r;odl;idl;hpj;bat"
+# Begin Source File
+
+SOURCE=.\example.c
+# End Source File
+# Begin Source File
+
+SOURCE=.\example_wrap.c
+# End Source File
+# End Group
+# Begin Group "Header Files"
+
+# PROP Default_Filter "h;hpp;hxx;hm;inl"
+# End Group
+# Begin Group "Resource Files"
+
+# PROP Default_Filter "ico;cur;bmp;dlg;rc2;rct;bin;rgs;gif;jpg;jpeg;jpe"
+# End Group
+# Begin Source File
+
+SOURCE=.\example.i
+
+!IF  "$(CFG)" == "example - Win32 Debug"
+
+# Begin Custom Build
+InputPath=.\example.i
+InputName=example
+
+"$(InputName)_wrap.c" : $(SOURCE) "$(INTDIR)" "$(OUTDIR)"
+	echo In order to function correctly, please ensure the following environment variables are correctly set: 
+	echo JAVA_INCLUDE: %JAVA_INCLUDE% 
+	echo JAVA_BIN: %JAVA_BIN% 
+	echo on 
+	..\..\..\swig.exe -java $(InputPath) 
+	
+# End Custom Build
+
+!ELSEIF  "$(CFG)" == "example - Win32 Release"
+
+# Begin Custom Build
+InputPath=.\example.i
+InputName=example
+
+"$(InputName)_wrap.c" : $(SOURCE) "$(INTDIR)" "$(OUTDIR)"
+	echo In order to function correctly, please ensure the following environment variables are correctly set: 
+	echo JAVA_INCLUDE: %JAVA_INCLUDE% 
+	echo JAVA_BIN: %JAVA_BIN% 
+	echo on 
+	..\..\..\swig.exe -java $(InputPath) 
+	
+# End Custom Build
+
+!ENDIF 
+
+# End Source File
+# End Target
+# End Project
diff --git a/Examples/doxygencomments/java/multimap/example.i b/Examples/doxygencomments/java/multimap/example.i
new file mode 100644
index 000000000..8d67282a5
--- /dev/null
+++ b/Examples/doxygencomments/java/multimap/example.i
@@ -0,0 +1,109 @@
+/* File : example.i */
+%module example
+
+%{
+extern int gcd(int x, int y);
+extern int gcdmain(int argc, char *argv[]);
+extern int count(char *bytes, int len, char c);
+extern void capitalize (char *str, int len);
+extern void circle (double cx, double cy);
+extern int squareCubed (int n, int *OUTPUT);
+%}
+
+extern int    gcd(int x, int y);
+
+%typemap(jni) (int argc, char *argv[]) "jobjectArray"
+%typemap(jtype) (int argc, char *argv[]) "String[]"
+%typemap(jstype) (int argc, char *argv[]) "String[]"
+
+%typemap(javain) (int argc, char *argv[]) "$javainput"
+
+%typemap(in) (int argc, char *argv[]) (jstring *jsarray) {
+int i;
+
+  $1 = (*jenv)->GetArrayLength(jenv, $input);
+  if ($1 == 0) {
+    SWIG_JavaThrowException(jenv, SWIG_JavaIndexOutOfBoundsException, "Array must contain at least 1 element");
+    return $null;
+  }
+  $2 = (char **) malloc(($1+1)*sizeof(char *));
+  jsarray = (jstring *) malloc($1*sizeof(jstring));
+  for (i = 0; i < $1; i++) {
+    jsarray[i] = (jstring) (*jenv)->GetObjectArrayElement(jenv, $input, i);
+    $2[i] = (char *) (*jenv)->GetStringUTFChars(jenv, jsarray[i], 0);
+  }
+  $2[i] = 0;
+}
+
+%typemap(argout) (int argc, char *argv[]) "" /* override char *[] default */
+
+%typemap(freearg) (int argc, char *argv[]) {
+int i;
+  for (i = 0; i < $1; i++) {
+    (*jenv)->ReleaseStringUTFChars(jenv, jsarray$argnum[i], $2[i]);
+  }
+  free($2);
+}
+
+extern int gcdmain(int argc, char *argv[]);
+
+%typemap(jni) (char *bytes, int len) "jstring"
+%typemap(jtype) (char *bytes, int len) "String"
+%typemap(jstype) (char *bytes, int len) "String"
+
+%typemap(javain) (char *bytes, int len) "$javainput"
+
+%typemap(in) (char *bytes, int len) {
+  $1 = ($1_type)(*jenv)->GetStringUTFChars(jenv, $input, 0);
+  $2 = (*jenv)->GetStringUTFLength(jenv, $input);
+}
+
+%typemap(freearg) (char *bytes, int len) %{
+  (*jenv)->ReleaseStringUTFChars(jenv, $input, $1);
+%}
+
+extern int count(char *bytes, int len, char c);
+
+/* This example shows how to wrap a function that mutates a c string. A one
+ * element Java string array is used so that the string can be returned modified.*/
+
+%typemap(jni) (char *str, int len) "jobjectArray"
+%typemap(jtype) (char *str, int len) "String[]"
+%typemap(jstype) (char *str, int len) "String[]"
+
+%typemap(javain) (char *str, int len) "$javainput"
+
+%typemap(in) (char *str, int len) (jstring js) {
+  int index = 0;
+  js = (jstring) (*jenv)->GetObjectArrayElement(jenv, $input, index);
+  $1 = (char *) (*jenv)->GetStringUTFChars(jenv, js, 0);
+  $2 = (*jenv)->GetStringUTFLength(jenv, js);
+}
+
+/* Return the mutated string as a modified element in the array. */
+%typemap(argout) (char *str, int len) {
+  jstring newstring = (*jenv)->NewStringUTF(jenv, $1);
+  (*jenv)->SetObjectArrayElement(jenv, $input, 0, newstring);
+}
+
+/* Release memory */
+%typemap(freearg) (char *str, int len) {
+  (*jenv)->ReleaseStringUTFChars(jenv, js$argnum, $1);
+}
+
+extern void capitalize(char *str, int len);
+
+/* A multi-valued constraint.  Force two arguments to lie
+   inside the unit circle */
+
+%typemap(check) (double cx, double cy) {
+   double a = $1*$1 + $2*$2;
+   if (a > 1.0) {
+    SWIG_JavaThrowException(jenv, SWIG_JavaIllegalArgumentException, "$1_name and $2_name must be in unit circle");
+    return;
+   }
+}
+
+extern void circle(double cx, double cy);
+
+
diff --git a/Examples/doxygencomments/java/multimap/main.java b/Examples/doxygencomments/java/multimap/main.java
new file mode 100644
index 000000000..331ac6b89
--- /dev/null
+++ b/Examples/doxygencomments/java/multimap/main.java
@@ -0,0 +1,40 @@
+
+public class main {
+
+  static {
+    try {
+      System.loadLibrary("example");
+    } catch (UnsatisfiedLinkError e) {
+      System.err.println("Native code library failed to load. See the chapter on Dynamic Linking Problems in the SWIG Java documentation for help.\n" + e);
+      System.exit(1);
+    }
+  }
+
+  public static void main(String argv[]) {
+
+    // Call our gcd() function
+    int x = 42;
+    int y = 105;
+    int g = example.gcd(x,y);
+    System.out.println("The gcd of " + x + " and " + y + " is " + g);
+    
+    // Call the gcdmain() function
+    String[] args = {"gcdmain","42","105"};
+    example.gcdmain(args);
+    
+    // Call the count function
+    System.out.println(example.count("Hello World", 'l'));
+    
+    // Call the capitalize function
+    String[] capitalizeMe = {"hello world"};
+    example.capitalize(capitalizeMe);
+    System.out.println(capitalizeMe[0]);
+  }
+}
+
+
+
+
+
+
+
diff --git a/Examples/doxygencomments/java/native/Makefile b/Examples/doxygencomments/java/native/Makefile
new file mode 100644
index 000000000..92afbd4d0
--- /dev/null
+++ b/Examples/doxygencomments/java/native/Makefile
@@ -0,0 +1,18 @@
+TOP        = ../..
+SWIG       = $(TOP)/../preinst-swig
+SRCS       = 
+TARGET     = example
+INTERFACE  = example.i
+SWIGOPT    =
+
+all::	java
+
+java::
+	$(MAKE) -f $(TOP)/Makefile SRCS='$(SRCS)' SWIG='$(SWIG)' \
+	SWIGOPT='$(SWIGOPT)' TARGET='$(TARGET)' INTERFACE='$(INTERFACE)' java
+	javac *.java
+
+clean::
+	$(MAKE) -f $(TOP)/Makefile java_clean
+
+check: all
diff --git a/Examples/doxygencomments/java/native/example.i b/Examples/doxygencomments/java/native/example.i
new file mode 100644
index 000000000..851b6fdc2
--- /dev/null
+++ b/Examples/doxygencomments/java/native/example.i
@@ -0,0 +1,56 @@
+/* File : example.i */
+%module example
+
+%{
+#include <string.h>
+
+typedef struct point {
+  int x;
+  int y;
+} Point;
+
+
+Point *point_create(int x, int y) {
+  Point *p = (Point *) malloc(sizeof(Point));
+  p->x = x;
+  p->y = y;
+
+  return p;
+}
+
+static char *point_toString(char *format, Point *p) {
+  static char buf[80];
+
+  sprintf(buf, format, p->x, p->y);
+
+  return buf;
+}
+
+/* this function will be wrapped by SWIG */
+char *point_toString1(Point *p) {
+  return point_toString("(%d,%d)", p);
+}
+
+/* this one we wrapped manually*/
+JNIEXPORT jstring JNICALL Java_exampleJNI_point_1toString2(JNIEnv *jenv, jclass jcls, jlong jpoint) {
+    Point * p;
+    jstring result;
+
+    (void)jcls;
+
+    p = *(Point **)&jpoint;
+
+    result = (*jenv)->NewStringUTF(jenv, point_toString("[%d,%d]", p));
+
+    return result;
+}
+%}
+
+
+Point *point_create(int x, int y);
+char *point_toString1(Point *p);
+
+/* give access to free() for memory cleanup of the malloc'd Point */
+extern void free(void *memblock);
+
+%native(point_toString2) char *point_toString2(Point *p);
diff --git a/Examples/doxygencomments/java/native/index.html b/Examples/doxygencomments/java/native/index.html
new file mode 100644
index 000000000..7ecf129ce
--- /dev/null
+++ b/Examples/doxygencomments/java/native/index.html
@@ -0,0 +1,33 @@
+<html>
+<head>
+<title>SWIG:Examples:java:native</title>
+</head>
+
+<body bgcolor="#ffffff">
+
+
+<tt>SWIG/Examples/java/native/</tt>
+<hr>
+
+<H2>SWIG wrapped and manually wrapped functions in Java</H2>
+
+Click <a href="../../../Doc/Manual/Java.html#using_own_jni_functions">here</a> for the relevant section in the SWIG and Java documentation.
+<p>
+This example compares wrapping a c global function using the manual way and the SWIG way.
+</p>
+
+<ul>
+<li><a href="example.i">example.i</a>. Interface file comparing code wrapped by SWIG and wrapped manually. 
+<li><a href="main.java">main.java</a>. Sample Java program showing calls to both manually wrapped and SWIG wrapped c functions.
+</ul>
+
+<h2>Notes</h2>
+
+<ul>
+<li>SWIG writes all the awkward JNI code for you. You just have to tell SWIG which functions to wrap.
+<li>If memory is allocated in c it needs to be free'd. A function, such as free(), can be provided with access from Java to free the memory.
+</ul>
+
+<hr>
+</body>
+</html>
diff --git a/Examples/doxygencomments/java/native/main.java b/Examples/doxygencomments/java/native/main.java
new file mode 100644
index 000000000..f4760bb3d
--- /dev/null
+++ b/Examples/doxygencomments/java/native/main.java
@@ -0,0 +1,19 @@
+
+public class main {
+
+  static {
+    try {
+	System.loadLibrary("example");
+    } catch (UnsatisfiedLinkError e) {
+      System.err.println("Native code library failed to load. See the chapter on Dynamic Linking Problems in the SWIG Java documentation for help.\n" + e);
+      System.exit(1);
+    }
+  }
+
+  public static void main(String argv[]) {
+    SWIGTYPE_p_Point p = example.point_create(1, 2);
+    System.out.println("auto wrapped  : " + example.point_toString1(p));
+    System.out.println("manual wrapped: " + example.point_toString2(p));
+    example.free(new SWIGTYPE_p_void(SWIGTYPE_p_Point.getCPtr(p), false)); //clean up c allocated memory
+  }
+}
diff --git a/Examples/doxygencomments/java/pointer/Makefile b/Examples/doxygencomments/java/pointer/Makefile
new file mode 100644
index 000000000..968c92c6c
--- /dev/null
+++ b/Examples/doxygencomments/java/pointer/Makefile
@@ -0,0 +1,18 @@
+TOP        = ../..
+SWIG       = $(TOP)/../preinst-swig
+SRCS       = example.c
+TARGET     = example
+INTERFACE  = example.i
+SWIGOPT    =
+
+all::	java
+
+java::
+	$(MAKE) -f $(TOP)/Makefile SRCS='$(SRCS)' SWIG='$(SWIG)' \
+	SWIGOPT='$(SWIGOPT)' TARGET='$(TARGET)' INTERFACE='$(INTERFACE)' java
+	javac *.java
+
+clean::
+	$(MAKE) -f $(TOP)/Makefile java_clean
+
+check: all
diff --git a/Examples/doxygencomments/java/pointer/example.c b/Examples/doxygencomments/java/pointer/example.c
new file mode 100644
index 000000000..b877d9a5b
--- /dev/null
+++ b/Examples/doxygencomments/java/pointer/example.c
@@ -0,0 +1,16 @@
+/* File : example.c */
+
+void add(int *x, int *y, int *result) {
+  *result = *x + *y;
+}
+
+void sub(int *x, int *y, int *result) {
+  *result = *x - *y;
+}
+
+int divide(int n, int d, int *r) {
+   int q;
+   q = n/d;
+   *r = n - q*d;
+   return q;
+}
diff --git a/Examples/doxygencomments/java/pointer/example.i b/Examples/doxygencomments/java/pointer/example.i
new file mode 100644
index 000000000..a8ac79499
--- /dev/null
+++ b/Examples/doxygencomments/java/pointer/example.i
@@ -0,0 +1,30 @@
+/* File : example.i */
+%module example
+
+%{
+extern void add(int *, int *, int *);
+extern void sub(int *, int *, int *);
+extern int divide(int, int, int *);
+%}
+
+/* This example illustrates a couple of different techniques
+   for manipulating C pointers */
+
+/* First we'll use the pointer library */
+extern void add(int *x, int *y, int *result);
+%include cpointer.i
+%pointer_functions(int, intp);
+
+/* Next we'll use some typemaps */
+
+%include typemaps.i
+extern void sub(int *INPUT, int *INPUT, int *OUTPUT);
+
+/* Next we'll use typemaps and the %apply directive */
+
+%apply int *OUTPUT { int *r };
+extern int divide(int n, int d, int *r);
+
+
+
+
diff --git a/Examples/doxygencomments/java/pointer/index.html b/Examples/doxygencomments/java/pointer/index.html
new file mode 100644
index 000000000..c30d549e6
--- /dev/null
+++ b/Examples/doxygencomments/java/pointer/index.html
@@ -0,0 +1,165 @@
+<html>
+<head>
+<title>SWIG:Examples:java:pointer</title>
+</head>
+
+<body bgcolor="#ffffff">
+
+<tt>SWIG/Examples/java/pointer/</tt>
+<hr>
+
+<H2>Simple Pointer Handling</H2>
+
+<p>
+This example illustrates a couple of techniques for handling
+simple pointers in SWIG.  The prototypical example is a C function
+that operates on pointers such as this:
+
+<blockquote>
+<pre>
+void add(int *x, int *y, int *r) { 
+    *r = *x + *y;
+}
+</pre>
+</blockquote>
+
+By default, SWIG wraps this function exactly as specified and creates
+an interface that expects pointer objects for arguments.  
+SWIG wraps a C pointer with a type wrapper class, for example, SWIGTYPE_p_int for an int*.
+The only problem is how does one go about creating these objects from a Java program?
+<p>
+
+
+<h2>Possible Solutions</h2>
+
+<ul>
+<li>Write some helper functions to explicitly create objects.  For
+example:
+
+<blockquote>
+<pre>
+int *new_int(int ivalue) {
+  int *i = (int *) malloc(sizeof(ivalue));
+  *i = ivalue;
+  return i;
+}
+int get_int(int *i) {
+  return *i;
+}
+
+void delete_int(int *i) {
+  free(i);
+}
+</pre>
+</blockquote>
+
+<p>
+<li>The SWIG pointer library provides an easier way. <br> 
+For example, in the interface file 
+you would do this:
+
+<blockquote>
+<pre>
+%include cpointer.i
+%pointer_functions(int, intp);
+</pre>
+</blockquote>
+
+and from Java you would use pointers like this:
+
+<blockquote>
+<pre>
+SWIGTYPE_p_int a = example.new_intp();
+SWIGTYPE_p_int b = example.new_intp();
+SWIGTYPE_p_int c = example.new_intp();
+example.intp_assign(a,37);
+example.intp_assign(b,42);
+
+// Note that getCPtr() has package access by default
+System.out.println("     a =" + Long.toHexString(SWIGTYPE_p_int.getCPtr(a)));
+System.out.println("     b =" + Long.toHexString(SWIGTYPE_p_int.getCPtr(b)));
+System.out.println("     c =" + Long.toHexString(SWIGTYPE_p_int.getCPtr(c)));
+
+// Call the add() function with some pointers
+example.add(a,b,c);
+
+// Now get the result
+int res = example.intp_value(c);
+System.out.println("     37 + 42 =" + res);
+
+// Clean up the pointers
+example.delete_intp(a);
+example.delete_intp(b);
+example.delete_intp(c);
+</pre>
+</blockquote>
+
+<p>
+<li>Use the SWIG typemap library.  This library allows you to completely
+change the way arguments are processed by SWIG.  For example:
+
+<blockquote>
+<pre>
+%include "typemaps.i"
+void add(int *INPUT, int *INPUT, int *OUTPUT);
+</pre>
+</blockquote>
+
+And in a Java program:
+
+<blockquote>
+<pre>
+int[] r = {0};
+example.sub(37,42,r);
+System.out.println("Result =" + r[0]);
+</pre>
+</blockquote>
+Needless to say, this is substantially easier although a bit unusual.
+
+<p>
+<li>A final alternative is to use the typemaps library in combination
+with the %apply directive.  This allows you to change the names of parameters
+that behave as input or output parameters. For example:
+
+<blockquote>
+<pre>
+%include "typemaps.i"
+%apply int *INPUT {int *x, int *y};
+%apply int *OUTPUT {int *r};
+
+void add(int *x, int *y, int *r);
+void sub(int *x, int *y, int *r);
+void mul(int *x, int *y, int *r);
+... etc ...
+</pre>
+</blockquote>
+
+</ul>
+
+<h2>Example</h2>
+
+The following example illustrates the use of these features for pointer
+extraction.
+
+<ul>
+<li> <a href="example.c">example.c</a>  (C Source)
+<li> <a href="example.i">example.i</a>  (Swig interface)
+<li> <a href="main.java">main.java</a>  (Java program)
+</ul>
+
+<h2>Notes</h2>
+
+<ul>
+<li>Since pointers are used for so many different things (arrays, output values,
+etc...) the complexity of pointer handling can be as complicated as you want to
+make it.
+
+<p>
+<li>More documentation on the typemaps.i and cpointer.i library files can be
+found in the SWIG user manual.  The files also contain documentation.
+
+</ul>
+
+<hr>
+</body>
+</html>
diff --git a/Examples/doxygencomments/java/pointer/main.java b/Examples/doxygencomments/java/pointer/main.java
new file mode 100644
index 000000000..e96e02eaa
--- /dev/null
+++ b/Examples/doxygencomments/java/pointer/main.java
@@ -0,0 +1,55 @@
+
+public class main {
+
+  static {
+    try {
+	System.loadLibrary("example");
+    } catch (UnsatisfiedLinkError e) {
+      System.err.println("Native code library failed to load. See the chapter on Dynamic Linking Problems in the SWIG Java documentation for help.\n" + e);
+      System.exit(1);
+    }
+  }
+
+  public static void main(String argv[]) {
+
+    // First create some objects using the pointer library.
+    System.out.println("Testing the pointer library");
+    SWIGTYPE_p_int a = example.new_intp();
+    SWIGTYPE_p_int b = example.new_intp();
+    SWIGTYPE_p_int c = example.new_intp();
+    example.intp_assign(a,37);
+    example.intp_assign(b,42);
+
+    // Note that getCPtr() has package access by default
+    System.out.println("     a =" + Long.toHexString(SWIGTYPE_p_int.getCPtr(a)));
+    System.out.println("     b =" + Long.toHexString(SWIGTYPE_p_int.getCPtr(b)));
+    System.out.println("     c =" + Long.toHexString(SWIGTYPE_p_int.getCPtr(c)));
+
+    // Call the add() function with some pointers
+    example.add(a,b,c);
+
+    // Now get the result
+    int res = example.intp_value(c);
+    System.out.println("     37 + 42 =" + res);
+
+    // Clean up the pointers
+    example.delete_intp(a);
+    example.delete_intp(b);
+    example.delete_intp(c);
+
+    // Now try the typemap library
+    // Now it is no longer necessary to manufacture pointers.
+    // Instead we use a single element array which in Java is modifiable.
+
+    System.out.println("Trying the typemap library");
+    int[] r = {0};
+    example.sub(37,42,r);
+    System.out.println("     37 - 42 = " + r[0]);
+
+    // Now try the version with return value
+
+    System.out.println("Testing return value");
+    int q = example.divide(42,37,r);
+    System.out.println("     42/37 = " + q + " remainder " + r[0]);
+  }
+}
diff --git a/Examples/doxygencomments/java/reference/Makefile b/Examples/doxygencomments/java/reference/Makefile
new file mode 100644
index 000000000..14c301703
--- /dev/null
+++ b/Examples/doxygencomments/java/reference/Makefile
@@ -0,0 +1,18 @@
+TOP        = ../..
+SWIG       = $(TOP)/../preinst-swig
+CXXSRCS    = example.cxx
+TARGET     = example
+INTERFACE  = example.i
+SWIGOPT    =
+
+all::	java
+
+java::
+	$(MAKE) -f $(TOP)/Makefile CXXSRCS='$(CXXSRCS)' SWIG='$(SWIG)' \
+	SWIGOPT='$(SWIGOPT)' TARGET='$(TARGET)' INTERFACE='$(INTERFACE)' java_cpp
+	javac *.java
+
+clean::
+	$(MAKE) -f $(TOP)/Makefile java_clean
+
+check: all
diff --git a/Examples/doxygencomments/java/reference/example.cxx b/Examples/doxygencomments/java/reference/example.cxx
new file mode 100644
index 000000000..8a513bf49
--- /dev/null
+++ b/Examples/doxygencomments/java/reference/example.cxx
@@ -0,0 +1,46 @@
+/* File : example.cxx */
+
+/* Deal with Microsoft's attempt at deprecating C standard runtime functions */
+#if !defined(SWIG_NO_CRT_SECURE_NO_DEPRECATE) && defined(_MSC_VER)
+# define _CRT_SECURE_NO_DEPRECATE
+#endif
+
+#include "example.h"
+#include <stdio.h>
+#include <stdlib.h>
+
+Vector operator+(const Vector &a, const Vector &b) {
+  Vector r;
+  r.x = a.x + b.x;
+  r.y = a.y + b.y;
+  r.z = a.z + b.z;
+  return r;
+}
+
+char *Vector::print() {
+  static char temp[512];
+  sprintf(temp,"Vector %p (%g,%g,%g)", this, x,y,z);
+  return temp;
+}
+
+VectorArray::VectorArray(int size) {
+  items = new Vector[size];
+  maxsize = size;
+}
+
+VectorArray::~VectorArray() {
+  delete [] items;
+}
+
+Vector &VectorArray::operator[](int index) {
+  if ((index < 0) || (index >= maxsize)) {
+    printf("Panic! Array index out of bounds.\n");
+    exit(1);
+  }
+  return items[index];
+}
+
+int VectorArray::size() {
+  return maxsize;
+}
+
diff --git a/Examples/doxygencomments/java/reference/example.h b/Examples/doxygencomments/java/reference/example.h
new file mode 100644
index 000000000..4915adb1b
--- /dev/null
+++ b/Examples/doxygencomments/java/reference/example.h
@@ -0,0 +1,26 @@
+/* File : example.h */
+
+class Vector {
+private:
+  double x,y,z;
+public:
+  Vector() : x(0), y(0), z(0) { };
+  Vector(double x, double y, double z) : x(x), y(y), z(z) { };
+  friend Vector operator+(const Vector &a, const Vector &b);
+  char *print();
+};
+
+class VectorArray {
+private:
+  Vector *items;
+  int     maxsize;
+public:
+  VectorArray(int maxsize);
+  ~VectorArray();
+  Vector &operator[](int);
+  int size();
+};
+
+
+
+  
diff --git a/Examples/doxygencomments/java/reference/example.i b/Examples/doxygencomments/java/reference/example.i
new file mode 100644
index 000000000..6daa3b1f4
--- /dev/null
+++ b/Examples/doxygencomments/java/reference/example.i
@@ -0,0 +1,46 @@
+/* File : example.i */
+
+/* This file has a few "typical" uses of C++ references. */
+
+%module example
+
+%{
+#include "example.h"
+%}
+
+class Vector {
+public:
+    Vector(double x, double y, double z);
+   ~Vector();
+    char *print();
+};
+
+/* This helper function calls an overloaded operator */
+%inline %{
+Vector addv(Vector &a, Vector &b) {
+  return a+b;
+}
+%}
+
+/* Wrapper around an array of vectors class */
+
+class VectorArray {
+public:
+  VectorArray(int maxsize);
+  ~VectorArray();
+  int size();
+  
+  /* This wrapper provides an alternative to the [] operator */
+  %extend {
+    Vector &get(int index) {
+      return (*$self)[index];
+    }
+    void set(int index, Vector &a) {
+      (*$self)[index] = a;
+    }
+  }
+};
+
+
+
+
diff --git a/Examples/doxygencomments/java/reference/index.html b/Examples/doxygencomments/java/reference/index.html
new file mode 100644
index 000000000..64b129cbb
--- /dev/null
+++ b/Examples/doxygencomments/java/reference/index.html
@@ -0,0 +1,147 @@
+<html>
+<head>
+<title>SWIG:Examples:java:reference</title>
+</head>
+
+<body bgcolor="#ffffff">
+
+
+<tt>SWIG/Examples/java/reference/</tt>
+<hr>
+
+<H2>C++ Reference Handling</H2>
+
+<p>
+This example tests SWIG's handling of C++ references.  Since C++
+references are closely related to pointers (as both refer to a
+location in memory), SWIG simply collapses all references into
+pointers when creating wrappers.
+
+<h2>Some examples</h2>
+
+References are most commonly used as function parameter.  For example,
+you might have an operator like this:
+
+<blockquote>
+<pre>
+Vector operator+(const Vector &amp;a, const Vector &amp;b) {
+   Vector result;
+   result.x = a.x + b.x;
+   result.y = a.y + b.y;
+   result.z = a.z + b.z;
+   return result;
+}
+</pre>
+</blockquote>
+
+or a function:
+
+<blockquote>
+<pre>
+Vector addv(const Vector &amp;a, const Vector &amp;b) {
+   Vector result;
+   result.x = a.x + b.x;
+   result.y = a.y + b.y;
+   result.z = a.z + b.z;
+   return result;
+}
+</pre>
+</blockquote>
+
+In these cases, SWIG transforms everything into a pointer and creates a wrapper
+that looks like this:
+
+<blockquote>
+<pre>
+Vector wrap_addv(Vector *a, Vector *b) {
+    return addv(*a,*b);
+}
+</pre>
+</blockquote>
+
+Occasionally, a reference is used as a return value of a function
+when the return result is to be used as an lvalue in an expression.
+The prototypical example is an operator like this:
+
+<blockquote>
+<pre>
+Vector &amp;operator[](int index);
+</pre>
+</blockquote>
+
+or a method:
+
+<blockquote>
+<pre>
+Vector &amp;get(int index);
+</pre>
+</blockquote>
+
+For functions returning references, a wrapper like this is created:
+
+<blockquote>
+<pre>
+Vector *wrap_Object_get(Object *self, int index) {
+    Vector &amp;result = self-&gt;get(index);
+    return &amp;result;
+}
+</pre>
+</blockquote>
+
+The following <a href="example.h">header file</a> contains some class
+definitions with some operators and use of references.
+
+<h2>SWIG Interface</h2>
+
+SWIG does NOT support overloaded operators so it can not directly build
+an interface to the classes in the above file.   However, a number of workarounds
+can be made.  For example, an overloaded operator can be stuck behind a function
+call such as the <tt>addv()</tt> function above.  Array access can be handled
+with a pair of set/get functions like this:
+
+<blockquote>
+<pre>
+class VectorArray {
+public:
+ ...
+   %addmethods {
+    Vector &amp;get(int index) {
+      return (*self)[index];
+    }
+    void set(int index, Vector &amp;a) {
+      (*self)[index] = a;
+    }
+   }
+   ...
+}
+</pre>
+</blockquote>
+
+Click <a href="example.i">here</a> to see a SWIG interface file with these additions.
+
+<h2>Sample Java program</h2>
+
+Click <a href="main.java">here</a> to see a Java program that manipulates some C++ references.
+
+<h2>Notes:</h2>
+
+<ul>
+<li>C++ references primarily provide notational convenience for C++
+source code.  However, Java only supports the 'x.a' 
+notation so it doesn't much matter.
+
+<p>
+<li>When a program returns a reference, a pointer is returned.
+Unlike return by value, memory is not allocated to hold the
+return result.
+
+<p>
+<li>SWIG has particular trouble handling various combinations of references
+and pointers.  This is side effect of an old parsing scheme and
+type representation that will be replaced in future versions.
+
+</ul>
+
+<hr>
+</body>
+</html>
diff --git a/Examples/doxygencomments/java/reference/main.java b/Examples/doxygencomments/java/reference/main.java
new file mode 100644
index 000000000..4fd354761
--- /dev/null
+++ b/Examples/doxygencomments/java/reference/main.java
@@ -0,0 +1,79 @@
+// This example illustrates the manipulation of C++ references in Java.
+
+public class main {
+  static {
+    try {
+        System.loadLibrary("example");
+    } catch (UnsatisfiedLinkError e) {
+      System.err.println("Native code library failed to load. See the chapter on Dynamic Linking Problems in the SWIG Java documentation for help.\n" + e);
+      System.exit(1);
+    }
+  }
+
+  public static void main(String argv[]) 
+  {
+    System.out.println( "Creating some objects:" );
+    Vector a = new Vector(3,4,5);
+    Vector b = new Vector(10,11,12);
+    
+    System.out.println( "    Created " + a.print() );
+    System.out.println( "    Created " + b.print() );
+    
+    // ----- Call an overloaded operator -----
+    
+    // This calls the wrapper we placed around
+    //
+    //      operator+(const Vector &a, const Vector &) 
+    //
+    // It returns a new allocated object.
+    
+    System.out.println( "Adding a+b" );
+    Vector c = example.addv(a,b);
+    System.out.println( "    a+b = " + c.print() );
+    
+    // Note: Unless we free the result, a memory leak will occur if the -noproxy commandline
+    // is used as the proxy classes define finalizers which call the delete() method. When
+    // -noproxy is not specified the memory management is controlled by the garbage collector.
+    // You can still call delete(). It will free the c++ memory immediately, but not the 
+    // Java memory! You then must be careful not to call any member functions as it will 
+    // use a NULL c pointer on the underlying c++ object. We set the Java object to null
+    // which will then throw a Java exception should we attempt to use it again.
+    c.delete();
+    c = null;
+    
+    // ----- Create a vector array -----
+    
+    System.out.println( "Creating an array of vectors" );
+    VectorArray va = new VectorArray(10);
+    System.out.println( "    va = " + va.toString() );
+    
+    // ----- Set some values in the array -----
+    
+    // These operators copy the value of Vector a and Vector b to the vector array
+    va.set(0,a);
+    va.set(1,b);
+    
+    // This works, but it would cause a memory leak if -noproxy was used!
+    
+    va.set(2,example.addv(a,b));
+    
+
+    // Get some values from the array
+    
+    System.out.println( "Getting some array values" );
+    for (int i=0; i<5; i++)
+        System.out.println( "    va(" + i + ") = " + va.get(i).print() );
+    
+    // Watch under resource meter to check on this
+    System.out.println( "Making sure we don't leak memory." );
+    for (int i=0; i<1000000; i++)
+        c = va.get(i%10);
+    
+    // ----- Clean up -----
+    // This could be omitted. The garbage collector would then clean up for us.
+    System.out.println( "Cleaning up" );
+    va.delete();
+    a.delete();
+    b.delete();
+  }
+}
diff --git a/Examples/doxygencomments/java/simple/Makefile b/Examples/doxygencomments/java/simple/Makefile
new file mode 100644
index 000000000..968c92c6c
--- /dev/null
+++ b/Examples/doxygencomments/java/simple/Makefile
@@ -0,0 +1,18 @@
+TOP        = ../..
+SWIG       = $(TOP)/../preinst-swig
+SRCS       = example.c
+TARGET     = example
+INTERFACE  = example.i
+SWIGOPT    =
+
+all::	java
+
+java::
+	$(MAKE) -f $(TOP)/Makefile SRCS='$(SRCS)' SWIG='$(SWIG)' \
+	SWIGOPT='$(SWIGOPT)' TARGET='$(TARGET)' INTERFACE='$(INTERFACE)' java
+	javac *.java
+
+clean::
+	$(MAKE) -f $(TOP)/Makefile java_clean
+
+check: all
diff --git a/Examples/doxygencomments/java/simple/example.c b/Examples/doxygencomments/java/simple/example.c
new file mode 100644
index 000000000..1c2af789c
--- /dev/null
+++ b/Examples/doxygencomments/java/simple/example.c
@@ -0,0 +1,18 @@
+/* File : example.c */
+
+/* A global variable */
+double Foo = 3.0;
+
+/* Compute the greatest common divisor of positive integers */
+int gcd(int x, int y) {
+  int g;
+  g = y;
+  while (x > 0) {
+    g = x;
+    x = y % x;
+    y = g;
+  }
+  return g;
+}
+
+
diff --git a/Examples/doxygencomments/java/simple/example.dsp b/Examples/doxygencomments/java/simple/example.dsp
new file mode 100644
index 000000000..8e1f8415e
--- /dev/null
+++ b/Examples/doxygencomments/java/simple/example.dsp
@@ -0,0 +1,158 @@
+# Microsoft Developer Studio Project File - Name="example" - Package Owner=<4>
+# Microsoft Developer Studio Generated Build File, Format Version 6.00
+# ** DO NOT EDIT **
+
+# TARGTYPE "Win32 (x86) Dynamic-Link Library" 0x0102
+
+CFG=example - Win32 Release
+!MESSAGE This is not a valid makefile. To build this project using NMAKE,
+!MESSAGE use the Export Makefile command and run
+!MESSAGE 
+!MESSAGE NMAKE /f "example.mak".
+!MESSAGE 
+!MESSAGE You can specify a configuration when running NMAKE
+!MESSAGE by defining the macro CFG on the command line. For example:
+!MESSAGE 
+!MESSAGE NMAKE /f "example.mak" CFG="example - Win32 Release"
+!MESSAGE 
+!MESSAGE Possible choices for configuration are:
+!MESSAGE 
+!MESSAGE "example - Win32 Debug" (based on "Win32 (x86) Dynamic-Link Library")
+!MESSAGE "example - Win32 Release" (based on "Win32 (x86) Dynamic-Link Library")
+!MESSAGE 
+
+# Begin Project
+# PROP AllowPerConfigDependencies 0
+# PROP Scc_ProjName ""
+# PROP Scc_LocalPath ""
+CPP=cl.exe
+MTL=midl.exe
+RSC=rc.exe
+
+!IF  "$(CFG)" == "example - Win32 Debug"
+
+# PROP BASE Use_MFC 0
+# PROP BASE Use_Debug_Libraries 1
+# PROP BASE Output_Dir "Debug"
+# PROP BASE Intermediate_Dir "Debug"
+# PROP BASE Target_Dir ""
+# PROP Use_MFC 0
+# PROP Use_Debug_Libraries 1
+# PROP Output_Dir "Debug"
+# PROP Intermediate_Dir "Debug"
+# PROP Ignore_Export_Lib 0
+# PROP Target_Dir ""
+# ADD BASE CPP /nologo /MTd /W3 /Gm /GX /ZI /Od /D "WIN32" /D "_DEBUG" /D "_WINDOWS" /D "_MBCS" /D "_USRDLL" /D "EXAMPLE_EXPORTS" /YX /FD /GZ /c
+# ADD CPP /nologo /MTd /W3 /Gm /GX /ZI /Od /I "$(JAVA_INCLUDE)" /I "$(JAVA_INCLUDE)\win32" /D "WIN32" /D "_DEBUG" /D "_WINDOWS" /D "_MBCS" /D "_USRDLL" /D "EXAMPLE_EXPORTS" /YX /FD /GZ /c
+# ADD BASE MTL /nologo /D "_DEBUG" /mktyplib203 /win32
+# ADD MTL /nologo /D "_DEBUG" /mktyplib203 /win32
+# ADD BASE RSC /l 0x809 /d "_DEBUG"
+# ADD RSC /l 0x809 /d "_DEBUG"
+BSC32=bscmake.exe
+# ADD BASE BSC32 /nologo
+# ADD BSC32 /nologo
+LINK32=link.exe
+# ADD BASE LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib /nologo /dll /debug /machine:I386 /pdbtype:sept
+# ADD LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib /nologo /dll /debug /machine:I386 /out:"example.dll" /pdbtype:sept
+# Begin Special Build Tool
+SOURCE="$(InputPath)"
+PostBuild_Desc=Java compile post-build step
+PostBuild_Cmds=echo on	"%JAVA_BIN%\javac" *.java
+# End Special Build Tool
+
+!ELSEIF  "$(CFG)" == "example - Win32 Release"
+
+# PROP BASE Use_MFC 0
+# PROP BASE Use_Debug_Libraries 0
+# PROP BASE Output_Dir "Release"
+# PROP BASE Intermediate_Dir "Release"
+# PROP BASE Target_Dir ""
+# PROP Use_MFC 0
+# PROP Use_Debug_Libraries 0
+# PROP Output_Dir "Release"
+# PROP Intermediate_Dir "Release"
+# PROP Ignore_Export_Lib 0
+# PROP Target_Dir ""
+# ADD BASE CPP /nologo /MT /W3 /GX /O2 /D "WIN32" /D "NDEBUG" /D "_WINDOWS" /D "_MBCS" /D "_USRDLL" /D "EXAMPLE_EXPORTS" /YX /FD /c
+# ADD CPP /nologo /MT /W3 /GX /O2 /I "$(JAVA_INCLUDE)" /I "$(JAVA_INCLUDE)\win32" /D "WIN32" /D "NDEBUG" /D "_WINDOWS" /D "_MBCS" /D "_USRDLL" /D "EXAMPLE_EXPORTS" /YX /FD /c
+# ADD BASE MTL /nologo /D "NDEBUG" /mktyplib203 /win32
+# ADD MTL /nologo /D "NDEBUG" /mktyplib203 /win32
+# ADD BASE RSC /l 0x809 /d "NDEBUG"
+# ADD RSC /l 0x809 /d "NDEBUG"
+BSC32=bscmake.exe
+# ADD BASE BSC32 /nologo
+# ADD BSC32 /nologo
+LINK32=link.exe
+# ADD BASE LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib /nologo /dll /machine:I386
+# ADD LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib /nologo /dll /machine:I386 /out:"example.dll"
+# Begin Special Build Tool
+SOURCE="$(InputPath)"
+PostBuild_Desc=Java compile post-build step
+PostBuild_Cmds=echo on	"%JAVA_BIN%\javac" *.java
+# End Special Build Tool
+
+!ENDIF 
+
+# Begin Target
+
+# Name "example - Win32 Debug"
+# Name "example - Win32 Release"
+# Begin Group "Source Files"
+
+# PROP Default_Filter "cpp;c;cxx;rc;def;r;odl;idl;hpj;bat"
+# Begin Source File
+
+SOURCE=.\example.c
+# End Source File
+# Begin Source File
+
+SOURCE=.\example_wrap.c
+# End Source File
+# End Group
+# Begin Group "Header Files"
+
+# PROP Default_Filter "h;hpp;hxx;hm;inl"
+# End Group
+# Begin Group "Resource Files"
+
+# PROP Default_Filter "ico;cur;bmp;dlg;rc2;rct;bin;rgs;gif;jpg;jpeg;jpe"
+# End Group
+# Begin Source File
+
+SOURCE=.\example.i
+
+!IF  "$(CFG)" == "example - Win32 Debug"
+
+# Begin Custom Build
+InputPath=.\example.i
+InputName=example
+
+"$(InputName)_wrap.c" : $(SOURCE) "$(INTDIR)" "$(OUTDIR)"
+	echo In order to function correctly, please ensure the following environment variables are correctly set: 
+	echo JAVA_INCLUDE: %JAVA_INCLUDE% 
+	echo JAVA_BIN: %JAVA_BIN% 
+	echo on 
+	..\..\..\swig.exe -java $(InputPath) 
+	
+# End Custom Build
+
+!ELSEIF  "$(CFG)" == "example - Win32 Release"
+
+# Begin Custom Build
+InputPath=.\example.i
+InputName=example
+
+"$(InputName)_wrap.c" : $(SOURCE) "$(INTDIR)" "$(OUTDIR)"
+	echo In order to function correctly, please ensure the following environment variables are correctly set: 
+	echo JAVA_INCLUDE: %JAVA_INCLUDE% 
+	echo JAVA_BIN: %JAVA_BIN% 
+	echo on 
+	..\..\..\swig.exe -java $(InputPath) 
+	
+# End Custom Build
+
+!ENDIF 
+
+# End Source File
+# End Target
+# End Project
diff --git a/Examples/doxygencomments/java/simple/example.i b/Examples/doxygencomments/java/simple/example.i
new file mode 100644
index 000000000..24093b9bf
--- /dev/null
+++ b/Examples/doxygencomments/java/simple/example.i
@@ -0,0 +1,7 @@
+/* File : example.i */
+%module example
+
+%inline %{
+extern int    gcd(int x, int y);
+extern double Foo;
+%}
diff --git a/Examples/doxygencomments/java/simple/index.html b/Examples/doxygencomments/java/simple/index.html
new file mode 100644
index 000000000..a363327fe
--- /dev/null
+++ b/Examples/doxygencomments/java/simple/index.html
@@ -0,0 +1,108 @@
+<html>
+<head>
+<title>SWIG:Examples:java:simple</title>
+</head>
+
+<body bgcolor="#ffffff">
+
+
+<tt>SWIG/Examples/java/simple/</tt>
+<hr>
+
+<H2>Simple Java Example</H2>
+
+<p>
+This example illustrates how you can hook Java to a very simple C program containing
+a function and a global variable.
+
+<h2>The C Code</h2>
+
+Suppose you have the following C code:
+
+<blockquote>
+<pre>
+/* File : example.c */
+
+/* A global variable */
+double Foo = 3.0;
+
+/* Compute the greatest common divisor of positive integers */
+int gcd(int x, int y) {
+  int g;
+  g = y;
+  while (x &gt; 0) {
+    g = x;
+    x = y % x;
+    y = g;
+  }
+  return g;
+}
+</pre>
+</blockquote>
+
+<h2>The SWIG interface</h2>
+
+Here is a simple SWIG interface file:
+
+<blockquote>
+<pre>
+/* File: example.i */
+%module example
+
+extern int gcd(int x, int y);
+extern double Foo;
+</pre>
+</blockquote>
+
+<h2>Compilation</h2>
+
+<ol>
+<li><tt>swig -java <a href="example.i">example.i</a></tt>
+<p>
+<li>Compile <tt><a href="example_wrap.c">example_wrap.c</a></tt> and <tt><a href="example.c">example.c</a></tt>
+to create the extension <tt>libexample.so (unix)</tt>. 
+</ol>
+
+<h2>Using the extension</h2>
+
+Click <a href="main.java">here</a> to see a program that calls our C functions from Java.
+<p>
+Compile the java files <tt><a href="example.java">example.java</a></tt> and <tt><a href="main.java">main.java</a></tt>
+to create the class files example.class and main.class before running main in the JVM.  Ensure that the libexample.so file is in your LD_LIBRARY_PATH before running. For example:
+<blockquote>
+<pre>
+export LD_LIBRARY_PATH=. #ksh 
+javac *.java
+java main
+</pre>
+</blockquote>
+
+<h2>Key points</h2>
+
+<ul>
+<li>Use the <tt>loadLibrary</tt> statement from java to load and access the generated java classes. For example:
+<blockquote>
+<pre>
+System.loadLibrary("example");
+</pre>
+</blockquote>
+
+<li>C functions work just like Java functions. For example:
+<blockquote>
+<pre>
+int g = example.gcd(42,105);
+</pre>
+</blockquote>
+
+<li>C global variables are accessed through get and set functions in the module class. For example:
+<blockquote>
+<pre>
+double a = example.get_Foo();
+example.set_Foo(20.0);
+</pre>
+</blockquote>
+</ul>
+
+<hr>
+</body>
+</html>
diff --git a/Examples/doxygencomments/java/simple/main.java b/Examples/doxygencomments/java/simple/main.java
new file mode 100644
index 000000000..6d224a4dc
--- /dev/null
+++ b/Examples/doxygencomments/java/simple/main.java
@@ -0,0 +1,32 @@
+
+public class main {
+
+  static {
+    try {
+	System.loadLibrary("example");
+    } catch (UnsatisfiedLinkError e) {
+      System.err.println("Native code library failed to load. See the chapter on Dynamic Linking Problems in the SWIG Java documentation for help.\n" + e);
+      System.exit(1);
+    }
+  }
+
+  public static void main(String argv[]) {
+    // Call our gcd() function
+    
+    int x = 42;
+    int y = 105;
+    int g = example.gcd(x,y);
+    System.out.println("The gcd of " + x + " and " + y + " is " + g);
+    
+    // Manipulate the Foo global variable
+    
+    // Output its current value
+    System.out.println("Foo = " + example.getFoo());
+    
+    // Change its value
+    example.setFoo(3.1415926);
+    
+    // See if the change took effect
+    System.out.println("Foo = " + example.getFoo());
+  }
+}
diff --git a/Examples/doxygencomments/java/template/Makefile b/Examples/doxygencomments/java/template/Makefile
new file mode 100644
index 000000000..2b3d35c6a
--- /dev/null
+++ b/Examples/doxygencomments/java/template/Makefile
@@ -0,0 +1,18 @@
+TOP        = ../..
+SWIG       = $(TOP)/../preinst-swig
+CXXSRCS    = 
+TARGET     = example
+INTERFACE  = example.i
+SWIGOPT    =
+
+all::	java
+
+java::
+	$(MAKE) -f $(TOP)/Makefile CXXSRCS='$(CXXSRCS)' SWIG='$(SWIG)' \
+	SWIGOPT='$(SWIGOPT)' TARGET='$(TARGET)' INTERFACE='$(INTERFACE)' java_cpp
+	javac *.java
+
+clean::
+	$(MAKE) -f $(TOP)/Makefile java_clean
+
+check: all
diff --git a/Examples/doxygencomments/java/template/example.h b/Examples/doxygencomments/java/template/example.h
new file mode 100644
index 000000000..7401df650
--- /dev/null
+++ b/Examples/doxygencomments/java/template/example.h
@@ -0,0 +1,32 @@
+/* File : example.h */
+
+// Some template definitions
+
+template<class T> T max(T a, T b) { return  a>b ? a : b; }
+
+template<class T> class vector {
+  T *v;
+  int sz;
+ public:
+  vector(int _sz) {
+    v = new T[_sz];
+    sz = _sz;
+  }
+  T &get(int index) {
+    return v[index];
+  }
+  void set(int index, T &val) {
+    v[index] = val;
+  }
+#ifdef SWIG
+  %extend {
+    T getitem(int index) {
+      return $self->get(index);
+    }
+    void setitem(int index, T val) {
+      $self->set(index,val);
+    }
+  }
+#endif
+};
+
diff --git a/Examples/doxygencomments/java/template/example.i b/Examples/doxygencomments/java/template/example.i
new file mode 100644
index 000000000..8f94c4da1
--- /dev/null
+++ b/Examples/doxygencomments/java/template/example.i
@@ -0,0 +1,17 @@
+/* File : example.i */
+%module example
+
+%{
+#include "example.h"
+%}
+
+/* Let's just grab the original header file here */
+%include "example.h"
+
+/* Now instantiate some specific template declarations */
+
+%template(maxint) max<int>;
+%template(maxdouble) max<double>;
+%template(vecint) vector<int>;
+%template(vecdouble) vector<double>;
+
diff --git a/Examples/doxygencomments/java/template/index.html b/Examples/doxygencomments/java/template/index.html
new file mode 100644
index 000000000..1aebd4c2a
--- /dev/null
+++ b/Examples/doxygencomments/java/template/index.html
@@ -0,0 +1,102 @@
+<html>
+<head>
+<title>SWIG:Examples:java:template</title>
+</head>
+
+<body bgcolor="#ffffff">
+
+
+<tt>SWIG/Examples/java/template/</tt>
+<hr>
+
+<H2>C++ template support</H2>
+
+<p>
+This example illustrates how C++ templates can be used from Java using SWIG.
+
+<h2>The C++ Code</h2>
+
+Lets take a templated function and a templated class as follows:
+
+<blockquote>
+<pre>
+/* File : example.h */
+
+// Some template definitions
+
+template<class T> T max(T a, T b) { return  a&gt;b ? a : b; }
+
+template<class T> class vector {
+  T *v;
+  int sz;
+ public:
+  vector(int _sz) {
+    v = new T[_sz];
+    sz = _sz;
+  }
+  T &amp;get(int index) {
+    return v[index];
+  }
+  void set(int index, T &amp;val) {
+    v[index] = val;
+  }
+#ifdef SWIG
+  %addmethods {
+    T getitem(int index) {
+      return self-&gt;get(index);
+    }
+    void setitem(int index, T val) {
+      self-&gt;set(index,val);
+    }
+  }
+#endif
+};
+</pre>
+</blockquote>
+The %addmethods is used for a neater interface from Java as the functions <tt>get</tt> and <tt>set</tt> use C++ references to primitive types. These are tricky to use from Java as they end up as a pointer in Java (Java long).
+
+<h2>The SWIG interface</h2>
+
+A simple SWIG interface for this can be built by simply grabbing the header file
+like this:
+
+<blockquote>
+<pre>
+/* File : example.i */
+%module example
+
+%{
+#include "example.h"
+%}
+
+/* Let's just grab the original header file here */
+%include "example.h"
+
+/* Now instantiate some specific template declarations */
+
+%template(maxint) max<int>;
+%template(maxdouble) max<double>;
+%template(vecint) vector<int>;
+%template(vecdouble) vector<double>;
+</pre>
+</blockquote>
+
+Note that SWIG parses the templated function <tt>max</tt> and templated class <tt>vector</tt> and so knows about them. However to generate code for use from Java, SWIG has to be told which class/type to use as the template parameter. The SWIG directive %template is used for this.
+
+<h2>A sample Java program</h2>
+
+Click <a href="main.java">here</a> to see a Java program that calls the C++ functions from Java.
+
+<h2>Notes</h2>
+Use templated classes just like you would any other SWIG generated Java class. Use the classnames specified by the %template directive.
+
+<blockquote>
+<pre>
+vecdouble dv = new vecdouble(1000);
+dv.setitem(i, 12.34));
+</pre>
+</blockquote>
+
+<hr>
+</body>
+</html>
diff --git a/Examples/doxygencomments/java/template/main.java b/Examples/doxygencomments/java/template/main.java
new file mode 100644
index 000000000..9129fcf2a
--- /dev/null
+++ b/Examples/doxygencomments/java/template/main.java
@@ -0,0 +1,45 @@
+// This example illustrates how C++ templates can be used from Java.
+
+public class main {
+  static {
+    try {
+        System.loadLibrary("example");
+    } catch (UnsatisfiedLinkError e) {
+      System.err.println("Native code library failed to load. See the chapter on Dynamic Linking Problems in the SWIG Java documentation for help.\n" + e);
+      System.exit(1);
+    }
+  }
+
+  public static void main(String argv[]) 
+  {
+    // Call some templated functions
+    System.out.println(example.maxint(3,7));
+    System.out.println(example.maxdouble(3.14,2.18));
+    
+    // Create some class
+    
+    vecint iv = new vecint(100);
+    vecdouble dv = new vecdouble(1000);
+    
+    for (int i=0; i<100; i++)
+        iv.setitem(i,2*i);
+    
+    for (int i=0; i<1000; i++)
+          dv.setitem(i, 1.0/(i+1));
+    
+    {
+    int sum = 0;
+    for (int i=0; i<100; i++)
+          sum = sum + iv.getitem(i);
+    
+    System.out.println(sum);
+    }
+    
+    {
+    double sum = 0.0;
+    for (int i=0; i<1000; i++)
+          sum = sum + dv.getitem(i);
+    System.out.println(sum);
+    }
+  }
+}
diff --git a/Examples/doxygencomments/java/typemap/Makefile b/Examples/doxygencomments/java/typemap/Makefile
new file mode 100644
index 000000000..92afbd4d0
--- /dev/null
+++ b/Examples/doxygencomments/java/typemap/Makefile
@@ -0,0 +1,18 @@
+TOP        = ../..
+SWIG       = $(TOP)/../preinst-swig
+SRCS       = 
+TARGET     = example
+INTERFACE  = example.i
+SWIGOPT    =
+
+all::	java
+
+java::
+	$(MAKE) -f $(TOP)/Makefile SRCS='$(SRCS)' SWIG='$(SWIG)' \
+	SWIGOPT='$(SWIGOPT)' TARGET='$(TARGET)' INTERFACE='$(INTERFACE)' java
+	javac *.java
+
+clean::
+	$(MAKE) -f $(TOP)/Makefile java_clean
+
+check: all
diff --git a/Examples/doxygencomments/java/typemap/example.i b/Examples/doxygencomments/java/typemap/example.i
new file mode 100644
index 000000000..7c97e6673
--- /dev/null
+++ b/Examples/doxygencomments/java/typemap/example.i
@@ -0,0 +1,101 @@
+/* File : example.i */
+%module example
+%{
+/*
+   example of a function that returns a value in the char * argument
+   normally used like:
+
+   char buf[bigenough];
+   f1(buf);
+*/
+
+void f1(char *s) {
+  if(s != NULL) {
+    sprintf(s, "hello world");
+  }
+}
+
+void f2(char *s) {
+  f1(s);
+}
+
+void f3(char *s) {
+  f1(s);
+}
+
+%}
+
+/* default behaviour is that of input arg, Java cannot return a value in a 
+ * string argument, so any changes made by f1(char*) will not be seen in the Java
+ * string passed to the f1 function.
+*/
+void f1(char *s);
+
+%include various.i
+
+/* use the BYTE argout typemap to get around this. Changes in the string by 
+ * f2 can be seen in Java. */
+void f2(char *BYTE);
+
+
+
+/* Alternative approach uses a StringBuffer typemap for argout */
+
+/* Define the types to use in the generated JNI C code and Java code */
+%typemap(jni) char *SBUF "jobject"
+%typemap(jtype) char *SBUF "StringBuffer"
+%typemap(jstype) char *SBUF "StringBuffer"
+
+/* How to convert Java(JNI) type to requested C type */
+%typemap(in) char *SBUF {
+
+  $1 = NULL;
+  if($input != NULL) {
+    /* Get the String from the StringBuffer */
+    jmethodID setLengthID;
+    jclass sbufClass = (*jenv)->GetObjectClass(jenv, $input);
+    jmethodID toStringID = (*jenv)->GetMethodID(jenv, sbufClass, "toString", "()Ljava/lang/String;");
+    jstring js = (jstring) (*jenv)->CallObjectMethod(jenv, $input, toStringID);
+
+    /* Convert the String to a C string */
+    const char *pCharStr = (*jenv)->GetStringUTFChars(jenv, js, 0);
+
+    /* Take a copy of the C string as the typemap is for a non const C string */
+    jmethodID capacityID = (*jenv)->GetMethodID(jenv, sbufClass, "capacity", "()I");
+    jint capacity = (*jenv)->CallIntMethod(jenv, $input, capacityID);
+    $1 = (char *) malloc(capacity+1);
+    strcpy($1, pCharStr);
+
+    /* Release the UTF string we obtained with GetStringUTFChars */
+    (*jenv)->ReleaseStringUTFChars(jenv,  js, pCharStr);
+
+    /* Zero the original StringBuffer, so we can replace it with the result */
+    setLengthID = (*jenv)->GetMethodID(jenv, sbufClass, "setLength", "(I)V");
+    (*jenv)->CallVoidMethod(jenv, $input, setLengthID, (jint) 0);
+  }
+}
+
+/* How to convert the C type to the Java(JNI) type */
+%typemap(argout) char *SBUF {
+
+  if($1 != NULL) {
+    /* Append the result to the empty StringBuffer */
+    jstring newString = (*jenv)->NewStringUTF(jenv, $1);
+    jclass sbufClass = (*jenv)->GetObjectClass(jenv, $input);
+    jmethodID appendStringID = (*jenv)->GetMethodID(jenv, sbufClass, "append", "(Ljava/lang/String;)Ljava/lang/StringBuffer;");
+    (*jenv)->CallObjectMethod(jenv, $input, appendStringID, newString);
+
+    /* Clean up the string object, no longer needed */
+    free($1);
+    $1 = NULL;
+  }  
+}
+/* Prevent the default freearg typemap from being used */
+%typemap(freearg) char *SBUF ""
+
+/* Convert the jstype to jtype typemap type */
+%typemap(javain) char *SBUF "$javainput"
+
+/* apply the new typemap to our function */
+void f3(char *SBUF);
+
diff --git a/Examples/doxygencomments/java/typemap/index.html b/Examples/doxygencomments/java/typemap/index.html
new file mode 100644
index 000000000..486aa8e79
--- /dev/null
+++ b/Examples/doxygencomments/java/typemap/index.html
@@ -0,0 +1,32 @@
+<html>
+<head>
+<title>SWIG:Examples:java:typemap</title>
+</head>
+
+<body bgcolor="#ffffff">
+
+
+<tt>SWIG/Examples/java/typemap/</tt>
+<hr>
+
+<H2>Typemaps in Java</H2>
+
+<p>
+This example shows how typemaps can be used to modify the default behaviour of the Java SWIG module.
+
+<ul>
+<li><a href="example.i">example.i</a>. Interface file. 
+<li><a href="main.java">main.java</a>. Sample Java program.
+</ul>
+
+<h2>Notes</h2>
+
+<ul>
+<li>Shows how to pass strings to Java from c and visa versa.
+<li>Typemaps can modify the default behaviour of the Java SWIG module.
+<li>The default c to java mapping can be modified using typemaps.
+</ul>
+
+<hr>
+</body>
+</html>
diff --git a/Examples/doxygencomments/java/typemap/main.java b/Examples/doxygencomments/java/typemap/main.java
new file mode 100644
index 000000000..bd9a4e1b6
--- /dev/null
+++ b/Examples/doxygencomments/java/typemap/main.java
@@ -0,0 +1,26 @@
+
+public class main {
+
+  static {
+    try {
+	System.loadLibrary("example");
+    } catch (UnsatisfiedLinkError e) {
+      System.err.println("Native code library failed to load. See the chapter on Dynamic Linking Problems in the SWIG Java documentation for help.\n" + e);
+      System.exit(1);
+    }
+  }
+
+  public static void main(String argv[]) {
+    String s = "brave new world";
+    example.f1(s);
+    System.out.println("f1(String): " + s);
+
+    byte b[] = new byte[25];
+    example.f2(b);
+    System.out.println("f2(byte[]): " + new String(b));
+
+    StringBuffer sb = new StringBuffer(20);
+    example.f3(sb);
+    System.out.println("f3(StringBuffer): " + sb);
+  }
+}
diff --git a/Examples/doxygencomments/java/variables/Makefile b/Examples/doxygencomments/java/variables/Makefile
new file mode 100644
index 000000000..968c92c6c
--- /dev/null
+++ b/Examples/doxygencomments/java/variables/Makefile
@@ -0,0 +1,18 @@
+TOP        = ../..
+SWIG       = $(TOP)/../preinst-swig
+SRCS       = example.c
+TARGET     = example
+INTERFACE  = example.i
+SWIGOPT    =
+
+all::	java
+
+java::
+	$(MAKE) -f $(TOP)/Makefile SRCS='$(SRCS)' SWIG='$(SWIG)' \
+	SWIGOPT='$(SWIGOPT)' TARGET='$(TARGET)' INTERFACE='$(INTERFACE)' java
+	javac *.java
+
+clean::
+	$(MAKE) -f $(TOP)/Makefile java_clean
+
+check: all
diff --git a/Examples/doxygencomments/java/variables/example.c b/Examples/doxygencomments/java/variables/example.c
new file mode 100644
index 000000000..aa4ffe9b3
--- /dev/null
+++ b/Examples/doxygencomments/java/variables/example.c
@@ -0,0 +1,91 @@
+/* File : example.c */
+
+/* I'm a file containing some C global variables */
+
+/* Deal with Microsoft's attempt at deprecating C standard runtime functions */
+#if !defined(SWIG_NO_CRT_SECURE_NO_DEPRECATE) && defined(_MSC_VER)
+# define _CRT_SECURE_NO_DEPRECATE
+#endif
+
+#include <stdio.h>
+#include <stdlib.h>
+#include "example.h"
+
+int              ivar = 0;                    
+short            svar = 0;
+long             lvar = 0;
+unsigned int     uivar = 0;
+unsigned short   usvar = 0;
+unsigned long    ulvar = 0;
+signed char      scvar = 0;
+unsigned char    ucvar = 0;
+char             cvar = 0;
+float            fvar = 0;
+double           dvar = 0;
+char            *strvar = 0;
+const char       cstrvar[] = "Goodbye";
+int             *iptrvar = 0;
+char             name[256] = "Dave";
+char             path[256] = "/home/beazley";
+
+
+/* Global variables involving a structure */
+Point           *ptptr = 0;
+Point            pt = { 10, 20 };
+
+/* A variable that we will make read-only in the interface */
+int              status = 1;
+
+/* A debugging function to print out their values */
+
+void print_vars() {
+  printf("ivar      = %d\n", ivar);
+  printf("svar      = %d\n", svar);
+  printf("lvar      = %ld\n", lvar);
+  printf("uivar     = %u\n", uivar);
+  printf("usvar     = %u\n", usvar);
+  printf("ulvar     = %lu\n", ulvar);
+  printf("scvar     = %d\n", scvar);
+  printf("ucvar     = %u\n", ucvar);
+  printf("fvar      = %g\n", fvar);
+  printf("dvar      = %g\n", dvar);
+  printf("cvar      = %c\n", cvar);
+  printf("strvar    = %s\n", strvar ? strvar : "(null)");
+  printf("cstrvar   = %s\n", cstrvar ? cstrvar : "(null)");
+  printf("iptrvar   = %p\n", iptrvar);
+  printf("name      = %s\n", name);
+  printf("ptptr     = %p (%d, %d)\n", ptptr, ptptr ? ptptr->x : 0, ptptr ? ptptr->y : 0);
+  printf("pt        = (%d, %d)\n", pt.x, pt.y);
+  printf("status    = %d\n", status);
+}
+
+/* A function to create an integer (to test iptrvar) */
+
+int *new_int(int value) {
+  int *ip = (int *) malloc(sizeof(int));
+  *ip = value;
+  return ip;
+}
+
+/* A function to create a point */
+
+Point *new_Point(int x, int y) {
+  Point *p = (Point *) malloc(sizeof(Point));
+  p->x = x;
+  p->y = y;
+  return p;
+}
+
+char * Point_print(Point *p) {
+  static char buffer[256];
+  if (p) {
+    sprintf(buffer,"(%d,%d)", p->x,p->y);
+  } else {
+    sprintf(buffer,"null");
+  }
+  return buffer;
+}
+
+void pt_print() {
+  printf("(%d, %d)\n", pt.x, pt.y);
+}
diff --git a/Examples/doxygencomments/java/variables/example.h b/Examples/doxygencomments/java/variables/example.h
new file mode 100644
index 000000000..0f7e89594
--- /dev/null
+++ b/Examples/doxygencomments/java/variables/example.h
@@ -0,0 +1,6 @@
+/* File: example.h */
+
+typedef struct {
+  int x,y;
+} Point;
+
diff --git a/Examples/doxygencomments/java/variables/example.i b/Examples/doxygencomments/java/variables/example.i
new file mode 100644
index 000000000..591b871ed
--- /dev/null
+++ b/Examples/doxygencomments/java/variables/example.i
@@ -0,0 +1,49 @@
+/* File : example.i */
+%module example
+%{
+#include "example.h"
+%}
+
+/* Some global variable declarations */
+%inline %{
+extern int              ivar;
+extern short            svar;
+extern long             lvar;
+extern unsigned int     uivar;
+extern unsigned short   usvar;
+extern unsigned long    ulvar;
+extern signed char      scvar;
+extern unsigned char    ucvar;
+extern char             cvar;
+extern float            fvar;
+extern double           dvar;
+extern char            *strvar;
+extern const char       cstrvar[];
+extern int             *iptrvar;
+extern char             name[256];
+
+extern Point           *ptptr;
+extern Point            pt;
+%}
+
+
+/* Some read-only variables */
+
+%immutable;
+
+%inline %{
+extern int  status;
+extern char path[256];
+%}
+
+%mutable;
+
+/* Some helper functions to make it easier to test */
+%inline %{
+extern void  print_vars();
+extern int  *new_int(int value);
+extern Point *new_Point(int x, int y);
+extern char  *Point_print(Point *p);
+extern void  pt_print();
+%}
+
diff --git a/Examples/doxygencomments/java/variables/index.html b/Examples/doxygencomments/java/variables/index.html
new file mode 100644
index 000000000..05aaa2d6e
--- /dev/null
+++ b/Examples/doxygencomments/java/variables/index.html
@@ -0,0 +1,85 @@
+<html>
+<head>
+<title>SWIG:Examples:java:variables</title>
+</head>
+
+<body bgcolor="#ffffff">
+
+<tt>SWIG/Examples/java/variables/</tt>
+<hr>
+
+<H2>Wrapping C Global Variables</H2>
+
+<p>
+When a C global variable appears in an interface file, SWIG tries to
+wrap it using a technique known as "variable linking."  The idea is
+pretty simple---we try to create a Java variable that magically
+retrieves or updates the value of the underlying C variable when it is
+accessed.  Click <a href="example.i">here</a> to see a SWIG interface with some variable
+declarations in it.
+
+
+<p>Click <a href="../../../Doc/Manual/Java.html#global_variables">here</a> for the section on global variables in the SWIG and Java documentation.</p>
+<h2>Manipulating Variables from Java</h2>
+
+C variables are accessed through getters and setters from Java. Unfortunately this is the only way to get current values from variables because it is not possible to overload the dot operator in Java. All global variables are accessible from the module class. For example if the module class is called 'example', the global variable
+
+<blockquote>
+<pre>
+double foo;
+</pre>
+</blockquote>
+
+will be accessed in the Java module as
+<blockquote>
+<pre>
+example.get_foo();
+example.set_foo(12.3);
+</pre>
+</blockquote>
+
+Click <a href="main.java">here</a> to see the example program that updates and prints
+out the values of the variables using this technique.
+
+<h2>Key points</h2>
+
+<ul>
+<li>When a global variable has the type "<tt>char *</tt>", SWIG manages it as a character
+string.   However, whenever the value of such a variable is set from Java, the old
+value is destroyed using <tt>free()</tt> or <tt>delete</tt> (the choice of which depends
+on whether or not SWIG was run with the -c++ option).
+<li><tt>signed char</tt> and <tt>unsigned char</tt> are handled as small 8-bit integers.
+<li>String array variables such as '<tt>char name[256]</tt>' are managed as Java strings, but
+when setting the value, the result is truncated to the maximum length of the array.  Furthermore, the string is assumed to be null-terminated.
+<li>When structures and classes are used as global variables, they are mapped into pointers.
+Getting the "value" returns a pointer to the global variable.  Setting the value of a structure results in a memory copy from a pointer to the global.
+</ul>
+
+<h2>Creating read-only variables</h2>
+
+The <tt>%immutable</tt> and <tt>%mutable</tt> directives can be used to
+specify a collection of read-only variables.  For example:
+
+<blockquote>
+<pre>
+%immutable;
+int    status;
+double blah;
+...
+%mutable;
+</pre>
+</blockquote>
+
+The <tt>%immutable</tt> directive remains in effect until it is explicitly disabled
+using the <tt>%mutable</tt> directive.
+
+<h2>Comments</h2>
+<ul>
+<li>Management of global variables is one of the most problematic aspects 
+of C/C++ wrapping because the Java interface and resulting memory management
+is much trickier than simply creating a wrapper function.
+</ul>
+
+</body>
+</html>
+<hr>
diff --git a/Examples/doxygencomments/java/variables/main.java b/Examples/doxygencomments/java/variables/main.java
new file mode 100644
index 000000000..92745db99
--- /dev/null
+++ b/Examples/doxygencomments/java/variables/main.java
@@ -0,0 +1,97 @@
+// This example illustrates global variable access from Java.
+
+import java.lang.reflect.*;
+
+public class main {
+  static {
+    try {
+        System.loadLibrary("example");
+    } catch (UnsatisfiedLinkError e) {
+      System.err.println("Native code library failed to load. See the chapter on Dynamic Linking Problems in the SWIG Java documentation for help.\n" + e);
+      System.exit(1);
+    }
+  }
+
+  public static void main(String argv[]) {
+
+// Try to set the values of some global variables
+
+    example.setIvar(42);
+    example.setSvar((short)-31000);
+    example.setLvar(65537);
+    example.setUivar(123456);
+    example.setUsvar(61000);
+    example.setUlvar(654321);
+    example.setScvar((byte)-13);
+    example.setUcvar((short)251);
+    example.setCvar('S');
+    example.setFvar((float)3.14159);
+    example.setDvar(2.1828);
+    example.setStrvar("Hello World");
+    example.setIptrvar(example.new_int(37));
+    example.setPtptr(example.new_Point(37,42));
+    example.setName("Bill");
+
+    // Now print out the values of the variables
+
+    System.out.println( "Variables (values printed from Java)" );
+
+    System.out.println( "ivar      =" + example.getIvar() );
+    System.out.println( "svar      =" + example.getSvar() );
+    System.out.println( "lvar      =" + example.getLvar() );
+    System.out.println( "uivar     =" + example.getUivar() );
+    System.out.println( "usvar     =" + example.getUsvar() );
+    System.out.println( "ulvar     =" + example.getUlvar() );
+    System.out.println( "scvar     =" + example.getScvar() );
+    System.out.println( "ucvar     =" + example.getUcvar() );
+    System.out.println( "fvar      =" + example.getFvar() );
+    System.out.println( "dvar      =" + example.getDvar() );
+    System.out.println( "cvar      =" + (char)example.getCvar() );
+    System.out.println( "strvar    =" + example.getStrvar() );
+    System.out.println( "cstrvar   =" + example.getCstrvar() );
+    System.out.println( "iptrvar   =" + Long.toHexString(SWIGTYPE_p_int.getCPtr(example.getIptrvar())) );
+    System.out.println( "name      =" + example.getName() );
+    System.out.println( "ptptr     =" + Long.toHexString(SWIGTYPE_p_Point.getCPtr(example.getPtptr())) + example.Point_print(example.getPtptr()) );
+    System.out.println( "pt        =" + Long.toHexString(SWIGTYPE_p_Point.getCPtr(example.getPt())) + example.Point_print(example.getPt()) );
+
+    System.out.println( "\nVariables (values printed from C)" );
+
+    example.print_vars();
+
+    System.out.println( "\nNow I'm going to try and modify some read only variables" );
+
+    System.out.println( "     Trying to set 'path'" );
+    try {
+        Method m = example.class.getDeclaredMethod("setPath", new Class[] {String.class});
+        m.invoke(example.class, new Object[] {"Whoa!"} );
+        System.out.println( "Hey, what's going on?!?! This shouldn't work" );
+    }
+    catch (NoSuchMethodException e) {
+        System.out.println( "Good." );
+    }
+    catch (Throwable t) {
+        System.out.println( "You shouldn't see this!" );
+    }
+
+    System.out.println( "     Trying to set 'status'" );
+    try {
+        Method m = example.class.getDeclaredMethod("setStatus", new Class[] {Integer.class});
+        m.invoke(example.class, new Object[] {new Integer(0)} );
+        System.out.println( "Hey, what's going on?!?! This shouldn't work" );
+    }
+    catch (NoSuchMethodException e) {
+        System.out.println( "Good." );
+    }
+    catch (Throwable t) {
+        System.out.println( "You shouldn't see this!" );
+    }
+
+    System.out.println( "\nI'm going to try and update a structure variable.\n" );
+
+    example.setPt(example.getPtptr());
+
+    System.out.println( "The new value is" );
+    example.pt_print();
+    System.out.println( "You should see the value" + example.Point_print(example.getPtptr()) );
+  }
+}

From e1a6b2ca3ba4467863b479419537d080435be186 Mon Sep 17 00:00:00 2001
From: Cheryl Foil <cheryl.foil@gmail.com>
Date: Sat, 16 Aug 2008 00:42:37 +0000
Subject: [PATCH 011/314] Cleaning up directories a bit

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2008-cherylfoil@10764 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Source/DoxygenTranslator/DoxygenEntity.cpp    |  89 --
 Source/DoxygenTranslator/DoxygenEntity.h      |  26 -
 .../DoxygenTranslator/DoxygenTranslator.cpp   | 810 ------------------
 Source/DoxygenTranslator/JavaDocConverter.cpp | 210 -----
 Source/DoxygenTranslator/JavaDocConverter.h   |  18 -
 Source/DoxygenTranslator/Token.cpp            |  32 -
 Source/DoxygenTranslator/Token.h              |  21 -
 Source/DoxygenTranslator/TokenList.cpp        | 114 ---
 Source/DoxygenTranslator/TokenList.h          |  27 -
 9 files changed, 1347 deletions(-)
 delete mode 100644 Source/DoxygenTranslator/DoxygenEntity.cpp
 delete mode 100644 Source/DoxygenTranslator/DoxygenEntity.h
 delete mode 100644 Source/DoxygenTranslator/DoxygenTranslator.cpp
 delete mode 100644 Source/DoxygenTranslator/JavaDocConverter.cpp
 delete mode 100644 Source/DoxygenTranslator/JavaDocConverter.h
 delete mode 100644 Source/DoxygenTranslator/Token.cpp
 delete mode 100644 Source/DoxygenTranslator/Token.h
 delete mode 100644 Source/DoxygenTranslator/TokenList.cpp
 delete mode 100644 Source/DoxygenTranslator/TokenList.h

diff --git a/Source/DoxygenTranslator/DoxygenEntity.cpp b/Source/DoxygenTranslator/DoxygenEntity.cpp
deleted file mode 100644
index 6b8755592..000000000
--- a/Source/DoxygenTranslator/DoxygenEntity.cpp
+++ /dev/null
@@ -1,89 +0,0 @@
-#include "DoxygenEntity.h"
-#include <string>
-
-/* Little data class for Doxygen Commands */
-
-
-/* Basic node for commands that have
- * nothing after them
- * example: \n
- */
-string commandArray2[] = {"a", "addindex", "addtogroup", "anchor", "arg", "attention",
-		"author", "b", "brief", "bug", "c", "callgraph", "callergraph", "category",
-		"class", "code", "cond", "copybrief", "copydetails", "copydoc", "date", "def",
-		"defgroup", "deprecated", "details", "dir", "dontinclude", "dot", "dotfile", "e",
-		"else", "elseif", "em", "endcode", "endcond", "enddot", "endhtmlonly", "endif",
-		"endlatexonly", "endlink", "endmanonly", "endmsc", "endverbatim", "endxmlonly",
-		"enum", "example", "exception", "f$", "f[", "f]", "f{", "f}", "file", "fn", "headerfile",
-		"hideinitializer", "htmlinclude", "htmlonly", "if", "ifnot", "image", "include",
-		"includelineno", "ingroup", "internal", "invariant", "interface", "latexonly", "li",
-		"line", "link", "mainpage", "manonly", "msc", "n", "name", "namespace", "nosubgrouping",
-		"note", "overload", "p", "package", "page", "par", "paragraph", "param", "post", "pre",
-		"private", "privatesection", "property", "protected", "protectedsection", "protocol",
-		"public", "publicsection", "ref", "relates", "relatesalso", "remarks", "return", "retval",
-		"sa", "section", "see", "showinitializer", "since", "skip", "skipline", "struct", "subpage",
-		"subsection", "subsubsection", "test", "throw", "todo", "tparam", "typedef", "union", "until",
-		"var", "verbatim", "verbinclude", "version", "warning", "weakgroup", "xmlonly", "xrefitem",
-		"$", "@", string(1, 92), "&", "~", "<", ">", "#", "%"};
-
-string findCommand(int commandNum){
-
-	int arraySize = sizeof(commandArray2)/sizeof(*commandArray2);
-	if (commandNum - 101 >= 0 && commandNum - 101 < arraySize){
-		return commandArray2[commandNum - 101];
-	}
-
-	return "" ;
-}
-
-DoxygenEntity::DoxygenEntity(string typeEnt){
-    typeOfEntity = typeEnt;
-    data = "";
-    isLeaf = 1;
-}
-
-/* Basic node for commands that have
- * only 1 thing after them
- * example: \b word
- * OR holding a string
- */
-DoxygenEntity::DoxygenEntity(string typeEnt, string param1){
-    typeOfEntity = typeEnt;
-    data = param1;
-    isLeaf = 1;
-}
-
-/* Nonterminal node
- * contains
- */
-DoxygenEntity::DoxygenEntity(string typeEnt, list <DoxygenEntity> &entList ){
-    typeOfEntity = typeEnt;
-    data = "";
-    isLeaf = 0;
-    entityList = entList;
-}
-
-
-void DoxygenEntity::printEntity(int level){
-	int thisLevel = level;
-	if (isLeaf) {
-		for (int i = 0; i < thisLevel; i++) {cout << "\t";}
-		cout << "Node Command: " << typeOfEntity << " ";
-		if (data.compare("") != 0) cout << "Node Data: " << data;
-		cout << endl;
-	}
-	else{
-		for (int i = 0; i < thisLevel; i++) {cout << "\t";}
-		cout << "Node Command : " << typeOfEntity << endl;
-		list<DoxygenEntity>::iterator p = entityList.begin();
-		thisLevel++;
-		while (p != entityList.end()){
-			(*p).printEntity(thisLevel);
-			p++;
-		}
-	}
-}
-
-DoxygenEntity::~DoxygenEntity()
-{
-}
diff --git a/Source/DoxygenTranslator/DoxygenEntity.h b/Source/DoxygenTranslator/DoxygenEntity.h
deleted file mode 100644
index 0605b1cc9..000000000
--- a/Source/DoxygenTranslator/DoxygenEntity.h
+++ /dev/null
@@ -1,26 +0,0 @@
-#ifndef DOXYGENENTITY_H_
-#define DOXYGENENTITY_H_
-
-#include <cstdlib>
-#include <iostream>
-#include <string>
-#include <list>
-
-using namespace std;
-
-class DoxygenEntity{
-
-public:
-	DoxygenEntity(string typeEnt);
-	DoxygenEntity(string typeEnt, string param1);
-	DoxygenEntity(string typeEnt, list <DoxygenEntity> &entList );
-   ~DoxygenEntity();
-	void printEntity(int level);
-    string typeOfEntity;
-    list <DoxygenEntity> entityList;
-    string data;
-    int isLeaf;
-};
-
-
-#endif /*TOKENLIST_H_*/
diff --git a/Source/DoxygenTranslator/DoxygenTranslator.cpp b/Source/DoxygenTranslator/DoxygenTranslator.cpp
deleted file mode 100644
index 96fe6b2c5..000000000
--- a/Source/DoxygenTranslator/DoxygenTranslator.cpp
+++ /dev/null
@@ -1,810 +0,0 @@
-
- 
- //THE TOKENIZER REWORK
-
- /* The main class for translating blobs of Doxygen for SWIG
-  * by Cheryl Foil, mentor Olly Betts, for Google's Summer of Code Program
-  * Currently the spacing/format on this is a bit goofy in places, due to shuffling code
-  * between 2 editors! Apologies for anyone combing through it :)
-  */
- //TODO DOH instead of STL?
-//TODO work in Brief descriptions, detailed descriptions for autobrief
-
- #include <cstdlib>
- #include <iostream>
- #include <fstream>
- #include <string>
- #include <list>
- #include "DoxygenEntity.h"
- #include "TokenList.h"
- #include "JavaDocConverter.h"
- #define SIMPLECOMMAND 1
- #define IGNOREDSIMPLECOMMAND 2
- #define COMMANDWORD 3
- #define IGNOREDCOMMANDWORD 4
- #define COMMANDLINE 5
- #define IGNOREDCOMMANDLINE 6
- #define COMMANDPARAGRAPH 7
- #define IGNORECOMMANDPARAGRAPH 8
- #define COMMANDENDCOMMAND 9
- #define COMMANDWORDPARAGRAPH 10
- #define COMMANDWORDLINE 11
- #define COMMANDWORDOWORDWORD 12
- #define COMMANDOWORD 13
- #define COMMANDERRORTHROW 14
- #define COMMANDUNIQUE 15
-#define  END_LINE 101
-#define PARAGRAPH_END 102
-#define  PLAINSTRING 103
-#define  COMMAND  104
- using namespace std;
-
- //////////////////////////////////////////
- /*Set these to pick what internal functions
- to test. */
-
- //int testCommandParsingFunctions = 1;// not implemented
-
-
- int noisy = 0; // set this to 1 for extra chatter from the parsing stage.
- int addCommand(string currCommand, TokenList &tokList,  list <DoxygenEntity> &aNewList);
- list <DoxygenEntity> parse(list<Token>::iterator endParsingIndex, TokenList &tokList);
-
- //////////////////////////////////////////
-
-
- string commandArray[] = {"a", "addindex", "addtogroup", "anchor", "arg", "attention",
- 		"author", "b", "brief", "bug", "c", "callgraph", "callergraph", "category",
- 		"class", "code", "cond", "copybrief", "copydetails", "copydoc", "date", "def",
- 		"defgroup", "deprecated", "details", "dir", "dontinclude", "dot", "dotfile", "e",
- 		"else", "elseif", "em", "endcode", "endcond", "enddot", "endhtmlonly", "endif",
- 		"endlatexonly", "endlink", "endmanonly", "endmsc", "endverbatim", "endxmlonly",
- 		"enum", "example", "exception", "f$", "f[", "f]", "f{", "f}", "file", "fn", "headerfile",
- 		"hideinitializer", "htmlinclude", "htmlonly", "if", "ifnot", "image", "include",
- 		"includelineno", "ingroup", "internal", "invariant", "interface", "latexonly", "li",
- 		"line", "link", "mainpage", "manonly", "msc", "n", "name", "namespace", "nosubgrouping",
- 		"note", "overload", "p", "package", "page", "par", "paragraph", "param", "post", "pre",
- 		"private", "privatesection", "property", "protected", "protectedsection", "protocol",
- 		"public", "publicsection", "ref", "relates", "relatesalso", "remarks", "return", "retval",
- 		"sa", "section", "see", "showinitializer", "since", "skip", "skipline", "struct", "subpage",
- 		"subsection", "subsubsection", "test", "throw", "todo", "tparam", "typedef", "union", "until",
- 		"var", "verbatim", "verbinclude", "version", "warning", "weakgroup", "xmlonly", "xrefitem",
- 		"$", "@", "\\","&", "~", "<", ">", "#", "%"};
-
-
- string sectionIndicators[] = { "attention", "author", "brief", "bug", "cond", "date", "deprecated", "details",
- 		"else", "elseif", "endcond", "endif", "exception", "if", "ifnot", "invariant", "note", "par", "param",
- 		"tparam", "post" , "pre", "remarks", "return", "retval", "sa", "see", "since", "test", "throw", "todo",
- 		"version", "warning", "xrefitem" };
-
- /* All of the doxygen commands divided up by how they are parsed */
- string simpleCommands[] = {"n", "$", "@", "\\", "&", "~", "<", ">", "#", "%"};
- string ignoredSimpleCommands[] = {"nothing at the moment"};
- string commandWords[] = {"a", "b", "c", "e", "em", "p", "def", "enum", "example", "package", 
- 		"relates", "namespace", "relatesalso","anchor", "dontinclude", "include", "includelineno"};
- string ignoredCommandWords[] = {"copydoc", "copybrief", "copydetails", "verbinclude", "htmlinclude"};
- string commandLines[] = {"addindex", "fn", "name", "line", "var", "skipline", "typedef", "skip", "until", "property"};
- string ignoreCommandLines[] = {"nothing at the moment"};
- string commandParagraph[] = {"return", "remarks", "since", "test", "sa", "see", "pre", "post", "details", "invariant", 
- 		    "deprecated", "date", "note", "warning", "version", "todo", "bug", "attention", "brief", "author"};
- string ignoreCommandParagraphs[] = {"nothing at the moment"};
- string commandEndCommands[] = {"code", "dot", "msc", "f$", "f[", "f{environment}{", "htmlonly", "latexonly", "manonly", 
- 		   "verbatim", "xmlonly", "cond", "if", "ifnot", "link"};
- string commandWordParagraphs[] = {"param", "tparam", "throw", "retval", "exception"};
- string commandWordLines[] = {"page", "subsection", "subsubsection", "section", "paragraph", "defgroup"};
- string commandWordOWordOWords [] = {"category", "class", "protocol", "interface", "struct", "union"};
- string commandOWords[] = {"dir", "file", "cond"};
- string commandErrorThrowings[] = {"annotatedclasslist", "classhierarchy", "define", "functionindex", "header",
- 		"headerfilelist", "inherit", "l", "postheader", "private", "privatesection", "protected", 
- 		"protectedsection", "public", "publicsection", "endcode", "enddot", "endmsc", "endhtmlonly", 
- 		"endlatexonly", "endmanonly", "endlink", "endverbatim", "endxmlonly", "f]", "f}", "endcond", 
- 		"endif"};
- string commandUniques[] = {"xrefitem", "arg", "ingroup", "par", "headerfile", "overload", "weakgroup", "ref",
- 		"subpage", "dotfile", "image", "addtogroup", "li"};
-
-
- /* Changes a string to all lower case*/
- string StringToLower(string stringToConvert)
-
- {
-
-    for(unsigned int i=0;i<stringToConvert.length();i++)
-    {
-    stringToConvert[i] = tolower(stringToConvert[i]);
-    }
-    return stringToConvert;//return the converted string
- }
-
- /* finds out if a command exists (is a possible command)
-  * from the string array commandArray
-  * returns -1 if no match is found */
- int findCommand(string smallString){
-
- 	smallString = StringToLower(smallString);
- 	int a;
- 	for (int i = 0; i < sizeof(commandArray)/sizeof(*commandArray); i++){
- 		if( (a = smallString.compare(commandArray[i])) == 0){
- 			return 101 + i;
- 		}
-
-
- 	}
- 	return -1;
- }
-
- /* isSectionIndicator returns a boolean if the command is a section indicator
-  * This is a helper method for finding the end of a paragraph
-  * by Doxygen's terms
-  */
- int isSectionIndicator(string smallString){
- 	smallString = StringToLower(smallString);
-
- 	for (int i = 0; i < sizeof( sectionIndicators)/sizeof(* sectionIndicators); i++){
- 		if( smallString.compare( sectionIndicators[i]) == 0){
- 			return 1;
- 		}
- 	}
- 	return 0;
- }
- 
- /* prints the parse tree
-  *
-  */
- void printTree( list <DoxygenEntity> &rootList){
-
-		list<DoxygenEntity>::iterator p = rootList.begin();
-		while (p != rootList.end()){
-			(*p).printEntity(0);
-			p++;
-		}
-
- }
- 
- /* Determines how a command should be handled (what group it belongs to
-  * for parsing rules
-  */
-
- int commandBelongs(string theCommand){
-	 string smallString = StringToLower(theCommand );
-	 //cout << " Looking for command " << theCommand << endl;
-	 int i = 0;
-	 for ( i = 0; i < sizeof(simpleCommands)/sizeof(*simpleCommands); i++){
-	 	if(smallString.compare(simpleCommands[i]) == 0){return SIMPLECOMMAND ;}
-	 	}
-	 for ( i = 0; i < sizeof(ignoredSimpleCommands)/sizeof(*ignoredSimpleCommands); i++){
-	 	if(smallString.compare(ignoredSimpleCommands[i]) == 0){return IGNOREDSIMPLECOMMAND;}
-	 	} 
-	 for ( i = 0; i < sizeof(commandWords)/sizeof(*commandWords); i++){
-	 	if(smallString.compare( commandWords[i]) == 0){return COMMANDWORD;}
-	 	} 
-	 for ( i = 0; i < sizeof(ignoredCommandWords)/sizeof(*ignoredCommandWords); i++){
-	 	if(smallString.compare( ignoredCommandWords[i]) == 0){return IGNOREDCOMMANDWORD;}
-	 	} 
-	 for ( i = 0; i < sizeof(commandLines)/sizeof(*commandLines); i++){
-	 	if(smallString.compare( commandLines[i]) == 0){return COMMANDLINE;}
-	 	} 
-	 for ( i = 0; i < sizeof(ignoreCommandLines)/sizeof(*ignoreCommandLines); i++){
-	 	if(smallString.compare( ignoreCommandLines[i]) == 0){return IGNOREDCOMMANDLINE;}
-	 	} 
-	 for ( i = 0; i <  sizeof(commandParagraph)/sizeof(*commandParagraph); i++){
-	 	if(smallString.compare( commandParagraph[i]) == 0){return COMMANDPARAGRAPH;}
-	 	} 
-	 /* IgnoreCommandParagraph */
-	 for ( i = 0; i < sizeof(ignoreCommandParagraphs)/sizeof(*ignoreCommandParagraphs); i++){
-	 	if(smallString.compare( ignoreCommandParagraphs[i]) == 0){return IGNORECOMMANDPARAGRAPH;}
-	 	} 
-	 for ( i = 0; i < sizeof(commandEndCommands)/sizeof(*commandEndCommands); i++){
-	 	if(smallString.compare( commandEndCommands[i]) == 0){return COMMANDENDCOMMAND ;}
-	 	} 
-	 for ( i = 0; i < sizeof(commandWordParagraphs)/sizeof(*commandWordParagraphs); i++){
-	 	if(smallString.compare( commandWordParagraphs[i]) == 0){return COMMANDWORDPARAGRAPH;}
-	 	} 
-	 for ( i = 0; i < sizeof(commandWordLines)/sizeof(*commandWordLines); i++){
-	 	if(smallString.compare( commandWordLines[i]) == 0){return COMMANDWORDLINE ;}
-	 	} 
-	 for ( i = 0; i < sizeof(commandWordOWordOWords)/sizeof(*commandWordOWordOWords); i++){
-	 	if(smallString.compare( commandWordOWordOWords[i]) == 0){return COMMANDWORDOWORDWORD;}
-	 	} 
-	 for ( i = 0; i < sizeof(commandOWords)/sizeof(*commandOWords); i++){
-	 	if(smallString.compare( commandOWords[i]) == 0){return COMMANDOWORD;}
-	 	} 
-	 for ( i = 0; i < sizeof(commandErrorThrowings)/sizeof(*commandErrorThrowings); i++){
-	 	if(smallString.compare( commandErrorThrowings[i]) == 0){return COMMANDERRORTHROW;}
-	 	} 
-	 for ( i = 0; i < sizeof(commandUniques)/sizeof(*commandUniques); i++){
-	 	if(smallString.compare( commandUniques[i]) == 0){return COMMANDUNIQUE;}
-	 	} 
-
-	 	return 0;
-	 
- }
- /* Returns the next word ON THE CURRENT LINE ONLY
-  * if a new line is encountered, returns a blank string.
-  * Updates the index it is given if success.
-  */
-
- string getNextWord(TokenList &tokList){
-	 Token nextToken = tokList.peek();
-	 if (nextToken.tokenType == PLAINSTRING ){
-		 nextToken = tokList.next();
-		 return nextToken.tokenString;
-	 }
- 	return "";
- }
-
- /* Returns the location of the end of the line as
-  * an iterator.
-  */
- list<Token>::iterator getOneLine(TokenList &tokList){
-	 list<Token>::iterator endOfParagraph = tokList.iteratorCopy();
-	 while(endOfParagraph != tokList.end()){
-		 if ((* endOfParagraph).tokenType == END_LINE){
-			 return endOfParagraph;
-		 }
-		 endOfParagraph++;
-	 }
- 	return tokList.end();
- }
- 
-
-
-/* Returns a properly formatted string
- * up til ANY command or end of paragraph is encountered.
- */
-string getStringTilCommand(TokenList &tokList){
-	 string description;
-	 if (tokList.peek().tokenType == 0) return "";
-	 while(tokList.peek().tokenType == PLAINSTRING || tokList.peek().tokenType == END_LINE ){
-		 Token currentToken = tokList.next();
-		 if(currentToken.tokenType == PLAINSTRING) {
-			 description = description + currentToken.tokenString + " ";
-		 }
-		 else if (tokList.peek().tokenType == END_LINE) break;
-	 }
-	 
- 	return description;
- }
- 
-/* Returns a properly formatted string
- * up til the command specified is encountered
- */
-//TODO check that this behaves properly for formulas
-
-string getStringTilEndCommand(string theCommand, TokenList &tokList){
-	 string description;
-	 if (tokList.peek().tokenType == 0) return "";
-	 while(tokList.peek().tokenString.compare(theCommand) != 0 ){
-		 Token currentToken = tokList.next();
-		 description = description + currentToken.tokenString + " ";
-
-	 }
-	 
- 	return description;
- }
- 
-/* Returns the end of a Paragraph as an iterator-
- * Paragraph is defined in Doxygen to be a paragraph of text
- * seperate by either a structural command or a blank line
- */
-
-list<Token>::iterator getEndOfParagraph(TokenList &tokList){
-	 list<Token>::iterator endOfParagraph = tokList.iteratorCopy();
-	 while(endOfParagraph != tokList.end()){
-		if ((* endOfParagraph).tokenType == COMMAND){
-			 if(isSectionIndicator((* endOfParagraph).tokenString)) return endOfParagraph;
-			 else endOfParagraph++;
-		 }
-		else if((* endOfParagraph).tokenType == PLAINSTRING) {
-			 endOfParagraph++;
-		 }
-		 else if ((* endOfParagraph).tokenType == END_LINE){
-			 endOfParagraph++;
-			 if ((* endOfParagraph).tokenType == END_LINE){
-				 endOfParagraph++;
-				 return endOfParagraph;
-			 }
-		 }
-
-	 }
-	 
- 	return tokList.end();
-
- }
-
-/* Returns the end of a section, defined as the first blank line OR first encounter of the same 
- * command. Example of this behaviour is \arg
- */
-
-list<Token>::iterator getEndOfSection(string theCommand, TokenList &tokList){
-	 list<Token>::iterator endOfParagraph = tokList.iteratorCopy();
-	 while(endOfParagraph != tokList.end()){
-		if ((* endOfParagraph).tokenType == COMMAND){
-			 if(theCommand.compare((*endOfParagraph).tokenString) == 0) return endOfParagraph;
-			 else endOfParagraph++;
-		 }
-		else if((* endOfParagraph).tokenType == PLAINSTRING) {
-			 endOfParagraph++;
-		 }
-		 else if ((* endOfParagraph).tokenType == END_LINE){
-			 endOfParagraph++;
-			 if ((* endOfParagraph).tokenType == END_LINE){
-				 endOfParagraph++;
-				 return endOfParagraph;
-			 }
-		 }
-
-	 }
-}
- /* This method is for returning the end of a specific form of doxygen command
-  * that begins with a \command and ends in \endcommand
-  * such as \code and \endcode. The proper usage is
-  * progressTilEndCommand("endcode", tokenList);
-  */
-list<Token>::iterator getEndCommand(string theCommand, TokenList &tokList){
-	list<Token>::iterator endOfCommand = tokList.iteratorCopy();
- 	while (endOfCommand!= tokList.end()){
- 		if ((*endOfCommand).tokenType == COMMAND){
- 			if (theCommand.compare((* endOfCommand).tokenString) == 0){
- 				return endOfCommand;
- 			}
- 			endOfCommand++;
- 		}
- 	}
- 	//End command not found
- 	return tokList.end();
- }
-
- /* A specialty method for commands such as \arg that end at the end of a paragraph OR when another \arg is encountered
-  */
- 
-list<Token>::iterator getTilAnyCommand(string theCommand, TokenList &tokList){
-	list<Token>::iterator anIterator;
-	return anIterator;
- }
-
-
-
- 
- /*  Method for Adding a Simple Command
-  * Format: @command
-  * Plain commands, such as newline etc, they contain no other data
-  *  \n \\ \@ \& \$ \# \< \> \%
-  */
-  int addSimpleCommand(string theCommand, list <DoxygenEntity> &doxyList){
-	 
-		if (noisy) cout << "Parsing " << theCommand << endl;
-		doxyList.push_back(DoxygenEntity(theCommand));
-		return 1;
- }
-  
-  /* NOT INCLUDED Simple Commands
-   * Format: @command
-   * Plain commands, such as newline etc, they contain no other data
-   */
-  int ignoreSimpleCommand(string theCommand, list <DoxygenEntity> &doxyList){
-	 
-		if (noisy) cout << "Not Adding " << theCommand << endl;
-		return 1;
- }
-  
-  /* CommandWord
-   * Format: @command <word>
-   * Commands with a single WORD after then such as @b
-   * "a", "b", "c", "e", "em", "p", "def", "enum", "example", "package", 
-   * "relates", "namespace", "relatesalso","anchor", "dontinclude", "include", "includelineno"
-   */
-  int addCommandWord(string theCommand, TokenList &tokList, list <DoxygenEntity> &doxyList){
-	if (noisy) cout << "Parsing " << theCommand << endl;
-	string name = getNextWord(tokList);
-	if (!name.empty()){ 
-		doxyList.push_back(DoxygenEntity(theCommand, name));
-		return 1;
-	}
-	else cout << "No word followed " << theCommand <<  " command. Not added" << endl;
-	return 0;
- }
-  /* NOT INCLUDED CommandWord
-   * Format: @command <word>
-   * Commands with a single WORD after then such as @b
-   * "copydoc", "copybrief", "copydetails", "verbinclude", "htmlinclude"
-   */
-  int ignoreCommandWord(string theCommand, TokenList &tokList, list <DoxygenEntity> &doxyList){
-	if (noisy) cout << "Not Adding " << theCommand << endl;
-	string name = getNextWord(tokList);
-	if (!name.empty()){ 
-		return 1;
-	}
-	else cout << "WARNING: No word followed " << theCommand <<  " command." << endl;
-	return 0;
- }
-  
-  /* CommandLine
-   * Format: @command (line)
-   * Commands with a single LINE after then such as @var
-   * "addindex", "fn", "name", "line", "var", "skipline", "typedef", "skip", "until", "property"
-   */
-  int addCommandLine(string theCommand, TokenList &tokList, list <DoxygenEntity> &doxyList){
-	if (noisy) cout << "Parsing " << theCommand << endl;
-	list<Token>::iterator endOfLine = getOneLine(tokList);
-		list <DoxygenEntity> aNewList;
-		aNewList =  parse(endOfLine, tokList);
-		doxyList.push_back( DoxygenEntity(theCommand, aNewList));
-		return 1;
-
- }
-  
-  /* NOT INCLUDED CommandLine
-   * Format: @command (line)
-   * Commands with a single LINE after then such as @var
-   * 
-   */
-  int ignoreCommandLine(string theCommand, TokenList &tokList, list <DoxygenEntity> &doxyList){
-	if (noisy) cout << "Not Adding " << theCommand << endl;
-	list<Token>::iterator endOfLine = getOneLine(tokList);
-	tokList.setIterator(endOfLine);
-	return 1;
- }
-  
-  /* CommandParagraph
-   * Format: @command {paragraph}
-   * Commands with a single paragraph after then such as @return
-   * "return", "remarks", "since", "test", "sa", "see", "pre", "post", "details", "invariant", 
-   * "deprecated", "date", "note", "warning", "version", "todo", "bug", "attention", "brief", "arg", "author"
-   */
-  int addCommandParagraph(string theCommand, TokenList &tokList, list <DoxygenEntity> &doxyList){
-	if (noisy) cout << "Parsing " << theCommand << endl;
-	list<Token>::iterator endOfParagraph = getEndOfParagraph(tokList);
-	//if(!restOfParagraph.empty()){
-	list <DoxygenEntity> aNewList;
-	aNewList =  parse(endOfParagraph, tokList);
-	doxyList.push_back( DoxygenEntity(theCommand, aNewList));
-	return 1;
-	//	}
-	//else cout << "No line followed " << theCommand <<  " command. Not added" << endl;
- }
-  /* CommandParagraph
-   * Format: @command {paragraph}
-   * Commands with a single LINE after then such as @var
-   * 
-   */
-  int ignoreCommandParagraph(string theCommand, TokenList &tokList, list <DoxygenEntity> &doxyList){
-	if (noisy) cout << "Not Adding " << theCommand << endl;
-	list<Token>::iterator endOfParagraph = getEndOfParagraph(tokList);
-	tokList.setIterator(endOfParagraph);
-	//else cout << "WARNING: No line followed " << theCommand <<  " command." << endl;
-	return 1;
- }
-  /* Command EndCommand
-   * Format: @command and ends at @endcommand
-   * Commands that take in a block of text such as @code
-   * "code", "dot", "msc", "f$", "f[", "f{environment}{", "htmlonly", "latexonly", "manonly", 
-   * "verbatim", "xmlonly", "cond", "if", "ifnot", "link"
-   * Returns 1 if success, 0 if the endcommand is never encountered.
-   */
-  
-  int addCommandEndCommand(string theCommand, TokenList &tokList, list <DoxygenEntity> &doxyList){
-	  if (noisy) cout << "Not Adding " << theCommand << endl;
-	  string description = getStringTilEndCommand( "end" + theCommand, tokList);
-	  doxyList.push_back(DoxygenEntity(theCommand, description));
-	  return 1;
-  }
-  
-  /* CommandWordParagraph
-   * Format: @command <word> {paragraph}
-   * Commands such as param
-   * "param", "tparam", "throw", "retval", "exception"
-   */
-  int addCommandWordParagraph(string theCommand, TokenList &tokList, list <DoxygenEntity> &doxyList){
-	if (noisy) cout << "Parsing " << theCommand << endl;
-	string name = getNextWord(tokList);
-	if (name.empty()){ 
-		cout << "No word followed " << theCommand <<  " command. Not added" << endl;
-		return 0;
-		}
-	  list<Token>::iterator endOfParagraph = getEndOfParagraph(tokList);
-	    //if(!restOfParagraph.empty()){
-		list <DoxygenEntity> aNewList;
-		aNewList =  parse(endOfParagraph, tokList);
-		aNewList.push_front(DoxygenEntity("plainstring", name));
-		doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-	return 0;
-  }
-  /* CommandWordLine
-   * Format: @command <word> (line)
-   * Commands such as param
-   * "page", "subsection", "subsubsection", "section", "paragraph", "defgroup"
-   */
-  int addCommandWordLine(string theCommand, TokenList &tokList, list <DoxygenEntity> &doxyList){
-	if (noisy) cout << "Parsing " << theCommand << endl;
-	string name = getNextWord(tokList);
-	if (name.empty()){ 
-		cout << "No word followed " << theCommand <<  " command. Not added" << endl;
-		return 0;
-		}
-	list<Token>::iterator endOfLine = getOneLine(tokList);
-	list <DoxygenEntity> aNewList;
-	aNewList =  parse(endOfLine, tokList);
-	aNewList.push_front(DoxygenEntity("plainstring", name));
-	doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-	return 1;
-		
-	//else cout << "No line followed " << theCommand <<  " command. Not added" << endl;
-  }
-
-  /* Command Word Optional Word Optional Word
-   * Format: @command <word> [<header-file>] [<header-name>]
-   * Commands such as class
-   * "category", "class", "protocol", "interface", "struct", "union"
-   */
-  int addCommandWordOWordOWord(string theCommand, TokenList &tokList, list <DoxygenEntity> &doxyList){
-	if (noisy) cout << "Parsing " << theCommand << endl;
-	string name = getNextWord(tokList);
-	if (name.empty()){ 
-			cout << "No word followed " << theCommand <<  " command. Not added" << endl;
-			return 0;
-			}
-	string headerfile = getNextWord(tokList);
-	string headername = getNextWord(tokList);
-	list <DoxygenEntity> aNewList;
-	aNewList.push_back(DoxygenEntity("plainstring", name));
-	if (!headerfile.empty()) aNewList.push_back(DoxygenEntity("plainstring", headerfile));
-	if (!headername.empty()) aNewList.push_back(DoxygenEntity("plainstring", headername));
-	doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-	return 1;
-  }
-  
-  /* Command Optional Word
-   * Format: @command [<word>]
-   * Commands such as dir
-   * "dir", "file", "cond"
-   */
-  int addCommandOWord(string theCommand, TokenList &tokList, list <DoxygenEntity> &doxyList){
-	if (noisy) cout << "Parsing " << theCommand << endl;
-	string name = getNextWord(tokList);
-	doxyList.push_back(DoxygenEntity(theCommand, name));
-	return 1; 
-  }
- 
-  /* Commands that should not be encountered (such as PHP only)
-   */
-  int addCommandErrorThrow(string theCommand, TokenList &tokList, list <DoxygenEntity> &doxyList){
-	  cout << "Encountered :" << theCommand << endl;
-	  cout << "This command should not have been encountered. Behaviour past this may be unpredictable " << endl;
-  }
- 
-
-  int addCommandUnique(string theCommand, TokenList &tokList, list <DoxygenEntity> &doxyList){
-	  list <DoxygenEntity> aNewList;
-	  if (theCommand.compare("arg") == 0 || theCommand.compare("li") == 0){
-			list<Token>::iterator endOfSection = getEndOfSection(theCommand, tokList);
-			list <DoxygenEntity> aNewList;
-			aNewList =  parse(endOfSection, tokList);
-			doxyList.push_back( DoxygenEntity(theCommand, aNewList));
-	  }
-	  
-	  // \xrefitem <key> "(heading)" "(list title)" {text}
-	  else if (theCommand.compare("xrefitem") == 0){
-		  //TODO Implement xrefitem
-			if (noisy) cout << "Not Adding " << theCommand << endl;
-			list<Token>::iterator endOfParagraph = getEndOfParagraph(tokList);
-			tokList.setIterator(endOfParagraph);
-		  return 1;
-	  }
-	  // \ingroup (<groupname> [<groupname> <groupname>])
-	  else if (theCommand.compare("ingroup") == 0){
-		  string name = getNextWord(tokList);
-		  aNewList.push_back(DoxygenEntity("plainstring", name));
-		  name = getNextWord(tokList);
-		  if(!name.empty()) aNewList.push_back(DoxygenEntity("plainstring", name));
-		  name = getNextWord(tokList);
-		  if(!name.empty()) aNewList.push_back(DoxygenEntity("plainstring", name));
-		  doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-		  return 1;
-	  }
-	  // \par [(paragraph title)] { paragraph }
-	  else if (theCommand.compare("par") == 0){
-		  list<Token>::iterator endOfLine = getOneLine(tokList);
-		  aNewList =  parse(endOfLine, tokList);
-		  list <DoxygenEntity> aNewList2;
-		  aNewList2 = parse(endOfLine, tokList);
-		  aNewList.splice(aNewList.end(), aNewList2);
-		  doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-		  return 1; 
-	  }
-	  // \headerfile <header-file> [<header-name>]
-	  else if (theCommand.compare("headerfile") == 0){
-		  list <DoxygenEntity> aNewList;
-		  string name = getNextWord(tokList);
-		  aNewList.push_back(DoxygenEntity("plainstring", name));
-		  name = getNextWord(tokList);
-		  if(!name.empty()) aNewList.push_back(DoxygenEntity("plainstring", name));
-		  doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-		  return 1;
-	  }
-	  // \overload [(function declaration)]
-	  else if (theCommand.compare("overload") == 0){
-		  list<Token>::iterator endOfLine = getOneLine(tokList);
-		  if (endOfLine != tokList.current()){
-		  list <DoxygenEntity> aNewList;
-		  aNewList =  parse(endOfLine, tokList);
-		  doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-		  }
-		  else doxyList.push_back(DoxygenEntity(theCommand));
-	  }
-	  // \weakgroup <name> [(title)]
-	  else if (theCommand.compare("weakgroup") == 0){
-		    if (noisy) cout << "Parsing " << theCommand << endl;
-			string name = getNextWord(tokList);
-			if (name.empty()){ 
-				cout << "No word followed " << theCommand <<  " command. Not added" << endl;
-				return 0;
-				}
-			list <DoxygenEntity> aNewList;
-			list<Token>::iterator endOfLine = getOneLine(tokList);
-			if (endOfLine != tokList.current()) {
-				aNewList =  parse(endOfLine, tokList);
-			}
-			aNewList.push_front(DoxygenEntity("plainstring", name));
-			doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-	  }
-	  // \ref <name> ["(text)"]
-	  else if (theCommand.compare("ref") == 0){
-		  //TODO Implement ref
-			if (noisy) cout << "Not Adding " << theCommand << endl;
-			list<Token>::iterator endOfParagraph = getEndOfParagraph(tokList);
-			tokList.setIterator(endOfParagraph);
-	  }
-	  // \subpage <name> ["(text)"]
-	  else if (theCommand.compare("subpage") == 0){
-		  //TODO implement subpage
-			if (noisy) cout << "Not Adding " << theCommand << endl;
-			list<Token>::iterator endOfParagraph = getEndOfParagraph(tokList);
-			tokList.setIterator(endOfParagraph);
-	  }
-	  // \dotfile <file> ["caption"]
-	  else if (theCommand.compare("dotfile") == 0){
-		  //TODO implement dotfile
-			if (noisy) cout << "Not Adding " << theCommand << endl;
-			list<Token>::iterator endOfParagraph = getEndOfParagraph(tokList);
-			tokList.setIterator(endOfParagraph);
-	  }
-	  // \image <format> <file> ["caption"] [<sizeindication>=<size>]
-	  else if (theCommand.compare("image") == 0){
-		  //todo implement image
-	  } 
-	  // \addtogroup <name> [(title)]
-	  else if (theCommand.compare("addtogroup") == 0){
-		    if (noisy) cout << "Parsing " << theCommand << endl;
-			string name = getNextWord(tokList);
-			if (name.empty()){ 
-				cout << "No word followed " << theCommand <<  " command. Not added" << endl;
-				return 0;
-				}
-			list <DoxygenEntity> aNewList;
-			list<Token>::iterator endOfLine = getOneLine(tokList);
-			if (endOfLine != tokList.current()) {
-				aNewList =  parse(endOfLine, tokList);
-			}
-			aNewList.push_front(DoxygenEntity("plainstring", name));
-			doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-	  }
-
-  }
-  
- /* The actual "meat" of the doxygen parser. This is not yet fully implemented
-  * with my current design- however the skeletal outline is contained in
-  * the file Skeleton
-  */
-
-
- int addCommand(string commandString, TokenList &tokList,list <DoxygenEntity> &doxyList){
-	 string theCommand = StringToLower(commandString);
- 
-	 if (theCommand.compare("plainstring") == 0){
-	 		string nextPhrase = getStringTilCommand( tokList);
-	 		if (noisy) cout << "Parsing plain string :" << nextPhrase << endl;
-	 		doxyList.push_back(DoxygenEntity("plainstring", nextPhrase ));
-	 		return 1;
-	 }
-	 int commandNumber = commandBelongs(theCommand);
-	 if (commandNumber == SIMPLECOMMAND){
-	 	return addSimpleCommand(theCommand, doxyList);
-	 	}
-	 if (commandNumber == IGNOREDSIMPLECOMMAND){
-	 	return ignoreSimpleCommand(theCommand, doxyList);
-	 	}
-	 if (commandNumber == COMMANDWORD){
-	 	return addCommandWord(theCommand, tokList, doxyList);
-	 	}
-	 if (commandNumber == IGNOREDCOMMANDWORD){
-	 	return ignoreCommandWord(theCommand, tokList, doxyList);
-	 	}
-	 if (commandNumber == COMMANDLINE ){
-	 	return addCommandLine(theCommand, tokList, doxyList);
-	 	}
-	 if (commandNumber == IGNOREDCOMMANDLINE ){
-	 	return ignoreCommandLine(theCommand, tokList, doxyList);
-	 	}
-	 if (commandNumber == COMMANDPARAGRAPH){
-	 	return addCommandParagraph(theCommand, tokList, doxyList);
-	 	}
-	 if (commandNumber == IGNORECOMMANDPARAGRAPH){
-	 	return ignoreCommandParagraph(theCommand, tokList, doxyList);
-	 	}
-	 if (commandNumber == COMMANDENDCOMMAND){
-	 	return addCommandEndCommand(theCommand, tokList, doxyList);
-	 	}
-	 if (commandNumber == COMMANDWORDPARAGRAPH){
-	 	return addCommandWordParagraph(theCommand, tokList, doxyList);
-	 	}
-	 if (commandNumber == COMMANDWORDLINE){
-	 	return addCommandWordLine(theCommand, tokList, doxyList);
-	 	}
-	 if (commandNumber == COMMANDWORDOWORDWORD){
-	 	return addCommandWordOWordOWord(theCommand, tokList, doxyList);
-	 	}
-	 if (commandNumber == COMMANDOWORD){
-	 	return addCommandOWord(theCommand, tokList, doxyList);
-	 	}
-	 if (commandNumber == COMMANDERRORTHROW){
-	 	return addCommandErrorThrow(theCommand, tokList, doxyList);
-	 	}
-	 if (commandNumber == COMMANDUNIQUE){
-		return addCommandUnique(theCommand, tokList, doxyList);
-	 	}
-	 	
-	 	return 0;
- }
- 
- list<DoxygenEntity> parse(list<Token>::iterator endParsingIndex, TokenList &tokList){
- 	list <DoxygenEntity> aNewList;
- 	int currCommand;
- 	while (tokList.current() != endParsingIndex){ 
- 		Token currToken = tokList.peek();
- 		if(noisy) cout << "Parsing for phrase starting in:" << currToken.toString() << endl;
- 		if(currToken.tokenType == END_LINE ){
- 			tokList.next();
- 		}
- 		else if(currToken.tokenType == COMMAND){
- 			currCommand = findCommand(currToken.tokenString);
- 			tokList.next();
- 			if (currCommand < 0 ){ if(noisy) cout << "BAD COMMAND: " << currToken.tokenString << endl;}
- 				//cout << "Command: " << currWord << " " << currCommand << endl;
- 
- 			else addCommand(currToken.tokenString, tokList,  aNewList);
- 		}
- 		else if (currToken.tokenType == PLAINSTRING){
- 			addCommand(string("plainstring"), tokList, aNewList);
- 		}
-
- 		
- 	}
-
- 	return aNewList;
- }
-
-list<DoxygenEntity> convert(string doxygenBlob){
- 	TokenList tokList = TokenList(doxygenBlob);
- 	if(noisy) {
- 		cout << "---TOKEN LIST---" << endl;
- 		tokList.printList();
- 	}
- 	list <DoxygenEntity> rootList;
- 	rootList = parse( tokList.end(), tokList);
- 	if(noisy) {
- 		cout << "PARSED LIST" << endl;
- 		printTree(rootList);
- 	}
- 	return rootList;
- }
-
-int main(int argc, char *argv[]){
-	string doxygenString1 = "//! A normal member taking two arguments and returning an integer value. This is a very long description for the simple purpose of showing off formatting. Let's make it a bit longer just to be sure. \n/*!\n \\param a an \\b integer argument.\n \\return The test results\n \\param s a constant character pointer. Let's also make this a very long description! \n \\bug this command should, for now, be totally ignored\n \\author cheryl foil\n \\sa Test(), ~Test(), testMeToo() and publicVar()\n */";
-	cout << "---ORIGINAL DOXYGEN--- " << endl << doxygenString1 << endl;
-	list <DoxygenEntity> rootList = convert(doxygenString1);
-    JavaDocConverter jDC = JavaDocConverter();
-    jDC.convertToJavaDoc(rootList);
-	return 1;
-}
-
-
diff --git a/Source/DoxygenTranslator/JavaDocConverter.cpp b/Source/DoxygenTranslator/JavaDocConverter.cpp
deleted file mode 100644
index 91f52662f..000000000
--- a/Source/DoxygenTranslator/JavaDocConverter.cpp
+++ /dev/null
@@ -1,210 +0,0 @@
-#include "JavaDocConverter.h"
-#include <cstdlib>
-#include <iostream>
-#include <string>
-#include <list>
-#define APPROX_LINE_LENGTH 64//characters per line allowed
-#define TAB_SIZE 8//characters per line allowed
-int printSortedTree2 = 0;
-//TODO {@link} {@linkplain} {@docRoot}, and other useful doxy commands that are not a javadoc tag
-JavaDocConverter::JavaDocConverter()
-{
-}
-
-JavaDocConverter::~JavaDocConverter()
-{
-}
-
-/* Sorts entities by javaDoc standard order for commands
- * NOTE: will not behave entirely properly until "First level" comments
- * such as brief descriptions are TAGGED as such
- */
-bool compare_DoxygenEntities(DoxygenEntity first, DoxygenEntity second){
-	if(first.typeOfEntity.compare("plainstring") == 0) return true;
-	if(second.typeOfEntity.compare("plainstring") == 0) return false;
-	if(first.typeOfEntity.compare("param") == 0){
-		if(second.typeOfEntity.compare("param")== 0) return true;
-		if(second.typeOfEntity.compare("return")== 0) return true;
-		if(second.typeOfEntity.compare("exception")== 0) return true;
-		if(second.typeOfEntity.compare("author")== 0) return true;
-		if(second.typeOfEntity.compare("version")== 0)return true;
-		if(second.typeOfEntity.compare("see")== 0)return true;
-		if(second.typeOfEntity.compare("since")== 0)return true;
-		if(second.typeOfEntity.compare("deprecated")== 0)return true;
-		return false;
-	}
-	if(first.typeOfEntity.compare("return")== 0){
-		if(second.typeOfEntity.compare("return")== 0) return true;
-		if(second.typeOfEntity.compare("exception")== 0) return true;
-		if(second.typeOfEntity.compare("author")== 0) return true;
-		if(second.typeOfEntity.compare("version")== 0)return true;
-		if(second.typeOfEntity.compare("see")== 0)return true;
-		if(second.typeOfEntity.compare("since")== 0)return true;
-		if(second.typeOfEntity.compare("deprecated")== 0)return true;
-		return false;
-
-	}
-	if(first.typeOfEntity.compare("exception")== 0){
-		if(second.typeOfEntity.compare("exception")== 0) return true;
-		if(second.typeOfEntity.compare("author")== 0) return true;
-		if(second.typeOfEntity.compare("version")== 0)return true;
-		if(second.typeOfEntity.compare("see")== 0)return true;
-		if(second.typeOfEntity.compare("since")== 0)return true;
-		if(second.typeOfEntity.compare("deprecated")== 0)return true;
-		return false;
-	}
-	if(first.typeOfEntity.compare("author")== 0){
-		if(first.typeOfEntity.compare("author")== 0) return true;
-		if(first.typeOfEntity.compare("version")== 0)return true;
-		if(first.typeOfEntity.compare("see")== 0)return true;
-		if(first.typeOfEntity.compare("since")== 0)return true;
-		if(first.typeOfEntity.compare("deprecated")== 0)return true;
-		return false;
-	}
-	if(first.typeOfEntity.compare("version")== 0){
-		if(second.typeOfEntity.compare("version")== 0)return true;
-		if(second.typeOfEntity.compare("see")== 0)return true;
-		if(second.typeOfEntity.compare("since")== 0)return true;
-		if(second.typeOfEntity.compare("deprecated")== 0)return true;
-		return false;
-	}
-	if(first.typeOfEntity.compare("see")== 0 || first.typeOfEntity.compare("sa")== 0){
-		if(second.typeOfEntity.compare("see")== 0)return true;
-		if(second.typeOfEntity.compare("sa")== 0)return true;
-		if(second.typeOfEntity.compare("since")== 0)return true;
-		if(second.typeOfEntity.compare("deprecated")== 0)return true;
-		return false;
-	}
-	if(first.typeOfEntity.compare("since")== 0){
-		if(second.typeOfEntity.compare("since")== 0) return true;
-		if(second.typeOfEntity.compare("deprecated")== 0)return true;
-		return false;
-	}
-	if(first.typeOfEntity.compare("deprecated")== 0){
-		if(second.typeOfEntity.compare("deprecated")== 0)return true;
-		return false;
-	}
-	return true;
-}
-
-void JavaDocConverter::printSortedTree(list <DoxygenEntity> &entityList){
-	list<DoxygenEntity>::iterator p = entityList.begin();
-	while (p != entityList.end()){
-		(*p).printEntity(0);
-		p++;
-	}
-}
-string formatCommand(string unformattedLine, int indent){
-	string formattedLines = "\n * ";
-	int lastPosition = 0;
-	int i = 0;
-	int isFirstLine  = 1;
-	while (i != -1 && i < unformattedLine.length()){
-		lastPosition = i;
-		if (isFirstLine){
-			i+=APPROX_LINE_LENGTH;
-		}
-		else i+=APPROX_LINE_LENGTH - indent*TAB_SIZE;
-		i = unformattedLine.find(" ", i);
-
-		if (i > 0 && i + 1 < unformattedLine.length()){
-			if (!isFirstLine) for (int j = 0; j < indent; j++) {
-				formattedLines.append("\t");
-				}
-			else {
-				isFirstLine = 0;
-			}
-			formattedLines.append(unformattedLine.substr(lastPosition, i - lastPosition + 1));
-			formattedLines.append("\n *");
-
-		}
-	}
-	if (lastPosition < unformattedLine.length()){
-		if (!isFirstLine) {for (int j = 0; j < indent; j++) {formattedLines.append("\t");}}
-		formattedLines.append(unformattedLine.substr(lastPosition, unformattedLine.length() - lastPosition));
-	}
-
-	return formattedLines;
-}
-
-/* Contains the conversions for tags
- * could probably be much more efficient...
- */
-string javaDocFormat(DoxygenEntity &doxygenEntity){
-	if (doxygenEntity.typeOfEntity.compare("plainstring") == 0){
-			return doxygenEntity.data;
-	}
-	else if (doxygenEntity.typeOfEntity.compare("brief") == 0){
-			return doxygenEntity.data;
-	}
-	if (doxygenEntity.typeOfEntity.compare("detailed") == 0){
-			return doxygenEntity.data;
-	}
-	else if (doxygenEntity.typeOfEntity.compare("b") == 0){
-		return "<b>" + doxygenEntity.data + "</b>";
-	}
-	else if (doxygenEntity.typeOfEntity.compare("c") == 0){
-		return "<tt>" + doxygenEntity.data + "</tt>";
-	}
-	return "";
-}
-
-
-string translateSubtree( DoxygenEntity &doxygenEntity){
-	string returnedString;
-	if (doxygenEntity.isLeaf){ return javaDocFormat(doxygenEntity) + " ";}
-	else {
-		returnedString += javaDocFormat(doxygenEntity);
-		list<DoxygenEntity>::iterator p = doxygenEntity.entityList.begin();
-		while (p != doxygenEntity.entityList.end()){
-			returnedString+= translateSubtree(*p);
-			p++;
-		}
-	}
-	return returnedString;
-}
-
-string translateEntity(DoxygenEntity &doxyEntity){
-	if(doxyEntity.typeOfEntity.compare("plainstring")== 0 || doxyEntity.typeOfEntity.compare("deprecated")== 0 || doxyEntity.typeOfEntity.compare("brief")== 0)
-		return formatCommand(doxyEntity.data, 0) + "\n * ";
-	else if(doxyEntity.typeOfEntity.compare("see") == 0){
-		return formatCommand(string("@" + doxyEntity.typeOfEntity + "\t\t" + translateSubtree(doxyEntity)), 2);
-	}
-	else if(doxyEntity.typeOfEntity.compare("return")== 0
-			|| doxyEntity.typeOfEntity.compare("author")== 0
-			|| doxyEntity.typeOfEntity.compare("param")== 0
-			|| doxyEntity.typeOfEntity.compare("since")== 0
-			|| doxyEntity.typeOfEntity.compare("version")== 0
-			|| doxyEntity.typeOfEntity.compare("exception") == 0
-			|| doxyEntity.typeOfEntity.compare("deprecated") == 0){
-		return formatCommand(string("@" + doxyEntity.typeOfEntity + "\t" + translateSubtree(doxyEntity)), 2);
-	}
-	else if(doxyEntity.typeOfEntity.compare("sa")== 0){
-		return formatCommand(string("@see\t\t" + translateSubtree(doxyEntity)), 2);
-	}
-
-	return "";
-}
-
-string JavaDocConverter:: convertToJavaDoc(list <DoxygenEntity> entityList){
-
-
-	entityList.sort(compare_DoxygenEntities);
-    if(printSortedTree2){
-	cout << "---RESORTED LIST---" << endl;
-    printSortedTree(entityList);
-    }
-
-	string javaDocString = "/**";
-
-	list<DoxygenEntity>::iterator entityIterator = entityList.begin();
-	while (entityIterator != entityList.end()){
-		javaDocString += translateEntity(*entityIterator);
-		entityIterator++;
-	}
-
-	javaDocString += "\n */\n";
-	cout << "\n---RESULT IN JAVADOC---" << endl;
-	cout << javaDocString;
-	return javaDocString;
-}
\ No newline at end of file
diff --git a/Source/DoxygenTranslator/JavaDocConverter.h b/Source/DoxygenTranslator/JavaDocConverter.h
deleted file mode 100644
index 81122bc5f..000000000
--- a/Source/DoxygenTranslator/JavaDocConverter.h
+++ /dev/null
@@ -1,18 +0,0 @@
- #include <list>
- #include <string>
- #include "DoxygenEntity.h"
-
-#ifndef JAVADOCCONVERTER_H_
-#define JAVADOCCONVERTER_H_
-
-class JavaDocConverter
-{
-public:
-
-	JavaDocConverter();
-	string convertToJavaDoc(list <DoxygenEntity> entityList);
-	~JavaDocConverter();
-	void printSortedTree(list <DoxygenEntity> &entityList);
-};
-
-#endif /*JAVADOCCONVERTER_H_*/
diff --git a/Source/DoxygenTranslator/Token.cpp b/Source/DoxygenTranslator/Token.cpp
deleted file mode 100644
index e85799546..000000000
--- a/Source/DoxygenTranslator/Token.cpp
+++ /dev/null
@@ -1,32 +0,0 @@
-#include "Token.h"
-#include <cstdlib>
-#include <iostream>
-#include <string>
-#include <list>
-using namespace std;
-
-
-Token::Token(int tType, string tString)
-{	
-	tokenType = tType;
-	tokenString = tString;
-}
-
-string Token::toString()
-{
-	if (tokenType == END_LINE){
-		return "{END OF LINE}";
-	}
-	if (tokenType == PARAGRAPH_END){
-		return "{END OF PARAGRAPH}";
-	}
-	if (tokenType == PLAINSTRING){
-		return tokenString;
-	}
-	if (tokenType == COMMAND){
-		return "{COMMAND : " + tokenString+ "}";
-	}
-	return "";
-}
-
-Token::	~Token(){}
diff --git a/Source/DoxygenTranslator/Token.h b/Source/DoxygenTranslator/Token.h
deleted file mode 100644
index e98686c14..000000000
--- a/Source/DoxygenTranslator/Token.h
+++ /dev/null
@@ -1,21 +0,0 @@
-#ifndef TOKEN_H_
-#define TOKEN_H_
-#include <string>
-
-#define  END_LINE 101
-#define PARAGRAPH_END 102
-#define  PLAINSTRING 103
-#define  COMMAND  104
-using namespace std;
-
-class Token
-{
-public:
-	Token(int tType, string tString);
-	~Token();
-	int tokenType; /* currently can be END_LINE, PLAINSTRING, or COMMAND */
-	string tokenString; /* the data , such as param for @param*/
-	string toString();
-};
-
-#endif /*TOKEN_H_*/
diff --git a/Source/DoxygenTranslator/TokenList.cpp b/Source/DoxygenTranslator/TokenList.cpp
deleted file mode 100644
index 0ace41c34..000000000
--- a/Source/DoxygenTranslator/TokenList.cpp
+++ /dev/null
@@ -1,114 +0,0 @@
-#include "TokenList.h"
-#include <cstdlib>
-#include <iostream>
-#include <string>
-#include <list>
-#include "Token.h"
-#define TOKENSPERLINE 8; //change this to change the printing behaviour of the token list
-#define  END_LINE 101
-#define PARAGRAPH_END 102 //not used at the moment 
-#define  PLAINSTRING 103
-#define  COMMAND  104
-using namespace std;
-
-
-list <Token> tokenList;
-list<Token>::iterator tokenListIterator;
-int noisy2 = 0;
-/* The tokenizer*/
-
-TokenList::TokenList(string doxygenString){
-	int currentIndex = 0;
-	//Regex whitespace("[ \t]+");
-	//Regex newLine("[\n]");
-	//Regex command("[@|\\]{1}[^ \t \n]+"); //the cheap solution 
-	//Regex doxygenFluff("[/*!]+");
-	int nextIndex = 0;
-	int isFluff = 0;
-	string currentWord;
-	while (currentIndex < doxygenString.length()){	
-		if(doxygenString[currentIndex] == '\n'){
-			tokenList.push_back(Token(END_LINE, currentWord));
-			currentIndex++;
-		}
-		while(currentIndex < doxygenString.length() && (doxygenString[currentIndex] == ' ' 
-			|| doxygenString[currentIndex]== '\t')) currentIndex ++;
-		if (currentIndex == doxygenString.length()) {} //do nothing since end of string was reached
-		else {nextIndex = currentIndex;
-		while (nextIndex  < doxygenString.length() && (doxygenString[nextIndex] != ' ' 
-			&& doxygenString[nextIndex]!= '\t' && doxygenString[nextIndex]!= '\n')) nextIndex++;
-		currentWord = doxygenString.substr(currentIndex, nextIndex-currentIndex);
-		if(noisy2) cout << "Current Word: " << currentWord << endl;
-		if (currentWord[0] == '@' || currentWord[0] == '\\'){
-			currentWord = currentWord.substr(1, currentWord.length()-1);
-			tokenList.push_back(Token(COMMAND, currentWord));
-		}
-		else if (currentWord[0] == '\n'){
-			//if ((tokenList.back()).tokenType == END_LINE){}
-			tokenList.push_back(Token(END_LINE, currentWord));
-			
-		}
-		else if (currentWord[0] == '*' || currentWord[0] == '/' ||currentWord[0] == '!'){
-			if (currentWord.length() == 1) {isFluff = 1;}	
-			else { isFluff = 1;
-				for(int i = 1; i < currentWord.length(); i++){
-					if (currentWord[0] != '*' && currentWord[0] != '/' && currentWord[0] != '!') isFluff = 0;
-				}
-				
-			}
-			if(!isFluff) tokenList.push_back(Token(PLAINSTRING, currentWord));
-		}
-		
-		else tokenList.push_back(Token(PLAINSTRING, currentWord));
-		currentIndex = nextIndex;
-	}
-	}
-	tokenListIterator = tokenList.begin(); 
-}
-
-Token TokenList::peek(){
-	if(tokenListIterator!= tokenList.end()){
-		Token returnedToken = (*tokenListIterator);
-		return returnedToken;
-	}
-	else
-		return Token(0, "");
-} 
-
-Token TokenList::next(){
-	if(tokenListIterator != tokenList.end()){
-		Token returnedToken = (*tokenListIterator);
-		tokenListIterator++;
-		return (returnedToken);
-	}
-	else
-		return Token(0, "");
-} 	
-
-list<Token>::iterator TokenList::end(){
-	return tokenList.end();
-}
-
-list<Token>::iterator TokenList::current(){
-	return tokenListIterator;
-}
-void TokenList::printList(){
-	list<Token>::iterator p = tokenList.begin();
-			int i = 1;
-			int b = 0;
-			while (p != tokenList.end()){
-				cout << (*p).toString() << " ";
-				b = i%TOKENSPERLINE;
-				if (b == 0) cout << endl;
-				p++; i++;
-			}
-}
-
-list<Token>::iterator  TokenList::iteratorCopy(){
-	list<Token>::iterator p = tokenListIterator;
-	return p;
-}
-void TokenList::setIterator(list<Token>::iterator newPosition){
-	tokenListIterator = newPosition;
-}
-TokenList::	~TokenList(){}
diff --git a/Source/DoxygenTranslator/TokenList.h b/Source/DoxygenTranslator/TokenList.h
deleted file mode 100644
index cc61f56e4..000000000
--- a/Source/DoxygenTranslator/TokenList.h
+++ /dev/null
@@ -1,27 +0,0 @@
-#ifndef TOKENLIST_H_
-#define TOKENLIST_H_
-#include <cstdlib>
-#include <iostream>
-#include <string>
-#include <list>
-#include "Token.h"
-using namespace std;
-
-/* a small class used to represent the sequence of tokens
- * that can be derived from a formatted doxygen string
- */
-
-class TokenList{
-public:
-	TokenList(string doxygenString); /* constructor takes a blob of Doxygen comment */
-	~TokenList();
-	Token peek(); 	/* returns next token without advancing */
-	Token next(); 	/* returns next token and advances */
-	list<Token>::iterator end(); /* returns an end iterator */
-	list<Token>::iterator current(); /* returns the current iterator */
-	void printList(); /* prints out the sequence of tokens */
-	list<Token>::iterator  iteratorCopy(); /* returns a copy of the current iterator */
-	void setIterator(list<Token>::iterator  newPosition); /*moves up the iterator*/
-};
-
-#endif /*TOKENLIST_H_*/

From f7e758e59fc01c6fe7add7d208f6706d8f6e7398 Mon Sep 17 00:00:00 2001
From: Cheryl Foil <cheryl.foil@gmail.com>
Date: Sat, 16 Aug 2008 07:08:45 +0000
Subject: [PATCH 012/314] just removing 2 more useless things :)

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2008-cherylfoil@10765 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Source/DoxygenTranslator/Skeleton  | 1070 ----------------------------
 Source/DoxygenTranslator/example.i |   19 -
 2 files changed, 1089 deletions(-)
 delete mode 100755 Source/DoxygenTranslator/Skeleton
 delete mode 100644 Source/DoxygenTranslator/example.i

diff --git a/Source/DoxygenTranslator/Skeleton b/Source/DoxygenTranslator/Skeleton
deleted file mode 100755
index 099b94393..000000000
--- a/Source/DoxygenTranslator/Skeleton
+++ /dev/null
@@ -1,1070 +0,0 @@
-/** NOT A WORKING FILE- NOTES/SCRAPS
- * A result of the initial implementation,
- * stopped early because I changed my design. This is currently
- * being reworked in the actual DoxygenTranslator class
- */
-
-
-
-
-/* The Very Large and Unelegant Solution for dealing with Doxygen commands such as
- * " \param".
- * This is implemented this way because a LARGE number of potential Doxygen commands
- * are not needed (such as PHP only or calling call graphs) and thus are simply
- * thrown out. The more useful functions
- * maybe be compartmentalised into their own method later on.
- */
-
-int addComment(int commentNum){
-	
-	startIndex = endIndex;
-	string name;
-	string nextWordInLine = "";
-	string restOfLine = "";
-	string restOfParagraph = "";
-	string headerfile ="";
-	string headername = "";
-	switch(commentNum){
-	
-
-	/* \a */
-	case 101:
-		nextWordInLine = getNextWord();
-		if((nextWordInLine).empty()){
-			cout << "Error: No word after tag a "<< endl;
-		}
-		else entityList.push_back( DoxygenEntity(101, "", nextWordInLine));
-		startIndex = endIndex;
-		break;
-		
-		/* \addindex */
-	case 102:
-		cout << "Add Index May not be Supported."<< endl;
-		restOfLine = getOneLineSentence();
-		if((restOfLine).empty()){
-			cout << "Error: No word after tag a "<< endl;
-		}
-		else entityList.push_back( DoxygenEntity(102, "", restOfLine));
-		startIndex = endIndex;
-		break;
-	
-	/* \addtogroup */
-	case 103:
-
-	
-		name = getNextWord();
-		if (anythingLeftOnLine()){
-			restOfLine = getOneLineSentence();
-			entityList.push_back( DoxygenEntity(103, "", restOfLine));
-		}
-		else 	cout << "AddtoGroup only supported for <name> [(title)]. Command not added" << endl;
-		break;
-		
-	/* \anchor */
-	case 104 :
-		getNextWord();
-		cout << "Anchor is not supported. Command not added." << endl;
-		break;
-		
-	/* \arg */	
-	case 105:
-
-		break;
-		
-	/* \attention */	
-	case 106:
-		restOfParagraph = stringTilEndOfParagraph(endIndex);
-		if(!restOfParagraph.empty()) entityList.push_back( DoxygenEntity(106, "", restOfLine));
-		else cout << "Nothing followed attention command. Not added" <<endl;
-		break;
-		
-	/* \author */
-	case 107:
-		restOfParagraph = stringTilEndOfParagraph(endIndex);
-		entityList.push_back( DoxygenEntity(107, "", restOfLine));
-		break;
-	
-	/* \b */
-	case 108:
-		name = getNextWord();
-		if (!name.empty()) entityList.push_back( DoxygenEntity(108, "", restOfLine)); 
-		else cout << "No word followed b command. Not added" <<endl;
-		break;
-		
-	/* \brief */
-	case 109:
-		restOfParagraph = stringTilEndOfParagraph(endIndex);
-		if(!restOfParagraph.empty()) entityList.push_back( DoxygenEntity(109, "", restOfLine));
-		else cout << "Nothing followed brief command. Not added" <<endl;
-		break;
-		
-	/* \bug */
-	case 110:
-		restOfParagraph = stringTilEndOfParagraph(endIndex);
-		if(!restOfParagraph.empty()) entityList.push_back( DoxygenEntity(110, "", restOfLine));
-		else cout << "Nothing followed bug command. Not added" <<endl;
-		break;
-	
-	/* \c */
-	case 111:
-		name = getNextWord();
-		if (!name.empty()) entityList.push_back( DoxygenEntity(111, "", restOfLine)); 
-		else cout << "No word followed c command. Not added" <<endl;
-		break;
-
-	/* \callgraph */
-	case 112:
-		cout << "Callgraph is not supported. Command not added." << endl;
-		break;
-	
-	/* \callergraph */
-	case 113:
-		cout << "Callergraph is not supported. Command not added." << endl;
-		break;
-	
-		/* \category */
-	case 114:
-		cout << "Category is a command for Objective C only. Command not added." << endl;
-		break;
-		
-	/* \class <name> [<header-file>] [<header-name>] */
-	case 115:
-		name = getNextWord();
-		if (name.empty()) cout << "No word followed class command. Not added" <<endl;
-		headerfile = getNextWord();
-		headername = getNextWord();
-		entityList.push_back( DoxygenEntity(115, headerfile, headername));
-		break;
-	
-	/* \code */
-	case 116:
-		cout << "Code is not supported. Command not added." << endl;
-		if (progressTilEndCommand("endcode") < 1) cout << "No endcode for command code found" << endl;	
-		break;
-		
-	/* \cond [<section-label>] */
-	case 117:
-		cout << "cond is not supported. Command not added." << endl;
-		if (progressTilEndCommand("endcond") < 1) cout << "No endcode for command code found" << endl;	
-		break;
-		
-	/* \copybrief <link-object> */
-	case 118:
-		getNextWord();
-		cout << "copybrief is not yet implemented. Command not added." << endl;
-		break;
-		
-	/* \copydetails  <link-object> */
-	case 119:
-		getNextWord();
-		cout << "copydetails is not yet implemented. Command not added." << endl;
-		break;
-		
-	/* \copydoc <link-object> */
-	case 120:
-		getNextWord();
-		cout << "copydoc is not yet implemented. Command not added." << endl;
-		break;
-	
-		/* \date { date description } */
-	case 121:
-		restOfParagraph = stringTilEndOfParagraph(endIndex);
-		if(!restOfParagraph.empty()) entityList.push_back( DoxygenEntity(121, "", restOfLine));
-		else cout << "Nothing followed date command. Not added" << endl;
-		break;
-	
-	/* \def <name> */
-	case 122:
-		name = getNextWord();
-		if (!name.empty()) entityList.push_back( DoxygenEntity(122, name, "")); 
-		else cout << "No word followed def command. Not added" << endl;
-		break;
-	
-	/* \defgroup <name> (group title) */
-	case 123:
-		name = getNextWord();
-		if (name.empty())cout << "No word followed def command. Not added" << endl; 
-		else {
-			restOfLine = getOneLineSentence();
-			if((restOfLine).empty()){
-			cout << "Error: No word after tag a "<< endl;
-			}
-			else entityList.push_back( DoxygenEntity(123, name, restOfLine));
-		}
-		break;
-		
-	/* \deprecated { description } */
-	case 124:
-		restOfParagraph = stringTilEndOfParagraph(endIndex);
-		if(!restOfParagraph.empty()) entityList.push_back( DoxygenEntity(124, "", restOfLine));
-		else cout << "Nothing followed deprecated command. Not added" << endl;
-		break;
-		
-	/* \details {detailed decription} */
-	case 125:
-		restOfParagraph = stringTilEndOfParagraph(endIndex);
-		if(!restOfParagraph.empty()) entityList.push_back( DoxygenEntity(125, "", restOfLine));
-		else cout << "Nothing followed details command. Not added" << endl;
-		break;
-	
-	/* \dir [<path fragment>] */
-	case 126:
-		restOfLine = getOneLineSentence();
-		entityList.push_back( DoxygenEntity(126, restOfLine , ""));
-		break;
-		
-	/* \dontinclude <file-name> */
-	case 127:
-		getNextWord();
-		cout << "dontinclude is not implemented. Command not added." << endl;
-		break;
-	
-	/* \dot */
-	case 128:
-		cout << "dot is not implemented. Command not added." << endl;
-		break;
-		
-	/* \dotfile <file> ["caption"] */
-	case 129:
-		getOneLineSentence();
-		cout << "dotfile is not implemented. Command not added." << endl;
-		break;
-		
-	/* \e <word> */
-	case 130:
-		name = getNextWord();
-		if (!name.empty()) entityList.push_back( DoxygenEntity(130, name, "")); 
-		else cout << "No word followed e command. Not added" <<endl;
-	break;
-		   
-	/* \else */
-	case 131:
-		cout << "else not yet implemented." << endl;
-	break;
-		   
-	/* \elseif <section-label> */
-	case 132:
-		getNextWord();
-		cout << "elseif is not implemented. Command not added." << endl;
-	break;
-		   
-	/* \em <word> */
-	/* Identical to e, so calls e */
-	case 133:
-		addComment(130);
-	break;
-		   
-	/* \endcode */
-	case 134:
-		cout << "endcode is not implemented. Command not added." << endl;
-	break;
-		   
-	/* \endcond */
-	case 135:
-		cout << "endcond is not implemented. Command not added." << endl;
-	break;
-		   
-	/* \enddot */
-	case 136:
-		cout << "enddot is not implemented. Command not added." << endl;
-	break;
-		   
-	/* \endhtmlonly */
-	case 137:
-		cout << "endhtmlonly is not implemented. Command not added." << endl;
-	break;
-		   
-	/* \endif */
-	case 138:
-		cout << "endif is not implemented. Command not added." << endl;
-	break;
-		   
-	/* \endlatexonly */
-	case 139:
-		cout << "endlatexonly is not implemented. Command not added." << endl;
-	break;
-		   
-	/* \endlink */
-	case 140:
-		cout << "endlink is not implemented. Command not added." << endl;
-	break;
-		   
-	/* \endmanonly */
-	case 141:
-		cout << "endmanonly is not implemented. Command not added." << endl;
-	break;
-		   
-	/* \endmsc */
-	case 142:
-		cout << "endmsc is not implemented. Command not added." << endl;
-	 break;
-		   
-	/* \endverbatim */
-	case 143:
-		cout << "endmsc is not implemented. Command not added." << endl;
-	break;
-		   
-	/* \endxmlonly */
-	case 144:
-		cout << "endxmlonly is not implemented. Command not added." << endl;
-	break;
-		   
-	/* \enum <name> */
-	case 145:
-		name = getNextWord();
-		if (!name.empty()) entityList.push_back( DoxygenEntity(145, name, "")); 
-		else cout << "No word followed enum command. Not added" <<endl;
-	break;
-		   
-	/* \example <file-name> */
-	case 146:
-		name = getNextWord();
-		if (!name.empty()) entityList.push_back( DoxygenEntity(146, name, "")); 
-		else cout << "No word followed example command. Not added" <<endl;
-	break;
-		   
-	/* \exception <exception-object> { exception description } */
-	case 147:
-		name = getNextWord();
-		if (name.empty()) cout << "No word followed exception command. Not added" <<endl;
-		else {
-			restOfParagraph = stringTilEndOfParagraph(endIndex);
-			if(!restOfParagraph.empty()) entityList.push_back( DoxygenEntity(147, name, restOfParagraph));
-			else cout << "Nothing followed exception <word> command. Not added" << endl;
-		}
-	break;
-		   
-	/* \f$ */
-	case 148:
-		cout << "f$ is not supported. Command not added." << endl;
-		if (progressTilEndCommand("f$") < 1) cout << "No endcode for command f$ found" << endl;	
-	break;
-		   
-	/* \f[ */
-	case 149:
-		cout << "f$ is not supported. Command not added." << endl;
-		if (progressTilEndCommand("f]") < 1) cout << "No endcode for command f] found" << endl;	
-	break;
-		   
-	/* \f] */
-	case 150:
-		cout << "f] is not implemented. Command not added." << endl;
-	break;
-		   
-	/* \f{environment}{ */
-	case 151:
-		cout << "f{environment}{ is not implemented. This may cause abnormal behaviour." << endl;
-	break;
-		   
-	/* \f} */
-	case 152:
-		cout << "f} is not implemented. This may cause abnormal behaviour." << endl;
-	break;
-		   
-	/* \file [<name>] */
-	case 153:
-		name = getNextWord();
-				if (!name.empty()) entityList.push_back( DoxygenEntity(153, name, "")); 
-				else entityList.push_back( DoxygenEntity(153, "", "")); 
-	break;
-		   
-	/* \fn (function declaration) */
-	 case 154:
-			restOfLine = getOneLineSentence();
-			if((restOfLine).empty()){
-			cout << "Error: No word after tag fn "<< endl;
-			}
-			else entityList.push_back( DoxygenEntity(154, restOfLine, ""));
-		 break;
-		   
-	/* \headerfile <header-file> [<header-name>] */
-	case 155:
-		name = getNextWord();
-		if (name.empty())cout << "No word followed headerfile command. Not added" << endl; 
-		else {
-			restOfLine = getNextWord();
-			entityList.push_back( DoxygenEntity(155, name, restOfLine));
-		}
-	break;
-		   
-	/* \hideinitializer */
-	case 156:
-	cout << "hideinitializer is not implemented." << endl;	
-	break;
-		   
-	/* \htmlinclude <file-name>*/
-	case 157:
-		name = getNextWord();
-			if (name.empty())cout << "No word followed htmlinclude command. Not added" << endl; 
-			else {
-				entityList.push_back( DoxygenEntity(157, name,""));
-			}
-	break;
-		   
-	/* \htmlonly */
-	case 158:
-		cout << "htmlonly will be implemented later. For now the html is ignored." << endl;
-		if (progressTilEndCommand("endhtmlonly") < 1) cout << "No endcode for command code found" << endl;
-	break;
-		   
-	/* \if <section-label> */
-	case 159:
-		cout << "if command is not implemented." << endl;
-	break;
-		   
-	/* \ifnot <section-label> */
-	case 160:
-		cout << "ifnot command is not implemented." << endl;
-		break;
-		   
-	/* \image <format> <file> ["caption"] [<sizeindication>=<size>] */
-	case 161:
-		cout << "Image unsupported. Program may behave strangely if command is over one line." << endl;
-		getOneLineSentence();
-		 break;
-		   
-	/* \include <file-name> */
-	case 162:
-		name = getNextWord();
-			if (name.empty())cout << "No word followed include command. Not added" << endl; 
-			else {
-				entityList.push_back( DoxygenEntity(162, name,""));
-			}
-		break;
-		   
-	/* \includelineno <file-name> */
-	case 163:
-		name = getNextWord();
-					if (name.empty())cout << "No word followed includelineno command. Not added" << endl; 
-					else {
-						entityList.push_back( DoxygenEntity(163, name,""));
-					}
-	 break;
-		   
-	/* \ingroup (<groupname> [<groupname> <groupname>]) */
-	case 164:
-		name = getNextWord();
-					if (name.empty())cout << "No word followed ingroup command. Not added" << endl; 
-					else {
-						string groupnames = getOneLineSentence();
-						entityList.push_back( DoxygenEntity(164, name,groupnames));
-					}
-	break;
-		   
-	/* \internal */
-	case 165:
-		entityList.push_back( DoxygenEntity(165, "",""));
-		break;
-		   
-	/* \invariant { description of invariant } */
-	case 166:
-		restOfParagraph = stringTilEndOfParagraph(endIndex);
-		if(!restOfParagraph.empty()) entityList.push_back( DoxygenEntity(166, restOfLine,"" ));
-		else cout << "Nothing followed invariant command. Not added" << endl;
-		 break;
-		   
-	/* \interface <name> [<header-file>] [<header-name>] */
-	case 167:
-		name = getNextWord();
-					if (name.empty())cout << "No word followed ingroup command. Not added" << endl; 
-					else {
-						string groupnames = getOneLineSentence();
-						entityList.push_back( DoxygenEntity(167, name, groupnames));
-					}
-	break;
-		   
-	/* \latexonly */
-	case 168:
-		cout << "latex only is not implemented" << endl;
-		if (progressTilEndCommand("endlatexonly") < 1) cout << "No endcode for command latexonly found" << endl;
-		break;
-		   
-	/* \li { item-description } */
-		//REDO
-	case 169:
-		addComment(105);
-		break;
-		   
-	/* \line ( pattern ) */
-	case 170:
-		restOfLine = getOneLineSentence();
-		if((restOfLine).empty()){
-		cout << "Error: No word after tag line "<< endl;
-		}
-		else entityList.push_back( DoxygenEntity(170, restOfLine, ""));
-	 break;
-		   
-	/* \link <link-object> */
-	case 171:
-		name = getNextWord();
-			if (name.empty())cout << "No word followed link command. Not added" << endl; 
-			else {
-				entityList.push_back( DoxygenEntity(171, name,""));
-			}
-		break;
-		   
-	/* \mainpage [(title)] */
-	case 172:
-		restOfLine = getOneLineSentence();
-		entityList.push_back( DoxygenEntity(172, restOfLine, ""));
-		break;
-		   
-	/* \manonly */
-	case 173:
-		cout << "manonly is not implemented" << endl;
-		if (progressTilEndCommand("endmanonly") < 1) cout << "No endcode for command manonly found" << endl;
-		break;
-		   
-	/* \msc */
-	case 174:
-		cout << "msc is not implemented" << endl;
-		if (progressTilEndCommand("endmanonly") < 1) cout << "No endcode for command mscfound" << endl;
-		break;
-		   
-	/* \n */
-	case 175:
-		entityList.push_back( DoxygenEntity(175, "",""));
-	break;
-		   
-	/* \name (header) */
-	case 176:
-		restOfLine = getOneLineSentence();
-		if((restOfLine).empty()){
-		cout << "Error: No word after header line "<< endl;
-		}
-		else entityList.push_back( DoxygenEntity(176, restOfLine, ""));
-		break;
-		   
-	/* \namespace <name> */
-	case 177:
-		name = getNextWord();
-					if (name.empty())cout << "No word followed namespace command. Not added" << endl; 
-					else {
-						entityList.push_back( DoxygenEntity(177, name,""));
-					}
-		break;
-		   
-	/* \nosubgrouping */
-		case 178:
-			cout << "Nosubgrouping not implemented "<< endl;
-		   break;
-		   
-	 /* \note { text } */
-	case 179:
-		restOfParagraph = stringTilEndOfParagraph(endIndex);
-		if(!restOfParagraph.empty()) entityList.push_back( DoxygenEntity(179, restOfLine,"" ));
-		else cout << "Nothing followed note command. Not added" << endl;
-		break;
-		   
-	/* \overload [(function declaration)] */
-	case 180:
-		restOfLine = getOneLineSentence();
-		entityList.push_back( DoxygenEntity(172, restOfLine, ""));
-		break;
-		   
-	/* \p <word> */
-	case 181:
-		name = getNextWord();
-					if (name.empty())cout << "No word followed p command. Not added" << endl; 
-					else {
-						entityList.push_back( DoxygenEntity(181, name,""));
-					}
-		break;
-		   
-	/* \package <name> */
-	case 182:
-		name = getNextWord();
-					if (name.empty())cout << "No word followed package command. Not added" << endl; 
-					else {
-						entityList.push_back( DoxygenEntity(182, name,""));
-					}
-		 break;
-		   
-	/* \page <name> (title) */
-	case 183:
-		name = getNextWord();
-		if (name.empty())cout << "No word followed page command. Not added" << endl; 
-		else {
-			restOfLine = getOneLineSentence();
-			if((restOfLine).empty()){
-			cout << "Error: No word after tag page "<< endl;
-			}
-			else entityList.push_back( DoxygenEntity(183, name, restOfLine));
-		}
-		break;
-		   
-	/* \par [(paragraph title)] { paragraph } */
-	case 184:
-		name = getOneLineSentence();
-		restOfParagraph = stringTilEndOfParagraph(endIndex);
-		if(!restOfParagraph.empty()) entityList.push_back( DoxygenEntity(184, name, restOfParagraph ));
-				else cout << "Nothing followed par command. Not added" << endl;
-		break;
-		   
-	/* \paragraph <paragraph-name> (paragraph title) */
-	case 185:
-		name = getNextWord();
-		if (name.empty())cout << "No word followed paragraph command. Not added" << endl; 
-		else {
-			restOfLine = getOneLineSentence();
-			if((restOfLine).empty()){
-			cout << "Error: No word after tag paragraph "<< endl;
-			}
-			else entityList.push_back( DoxygenEntity(185, name, restOfLine));
-		}
-		break;
-		   
-	/* \param <parameter-name> { parameter description } */
-	case 186:
-		name = getNextWord();
-		if (name.empty())cout << "No word followed parameter command. Not added" << endl; 
-		else {
-			restOfParagraph = stringTilEndOfParagraph(endIndex);
-			if(!restOfParagraph.empty()) entityList.push_back( DoxygenEntity(186, name, restOfParagraph ));
-				else cout << "Nothing followed parameter command. Not added" << endl;
-		}
-		break;
-		   
-	/* \post { description of the postcondition } */
-	case 187:
-		restOfParagraph = stringTilEndOfParagraph(endIndex);
-		if(!restOfParagraph.empty()) entityList.push_back( DoxygenEntity(187, name, restOfParagraph ));
-			else cout << "Nothing followed post command. Not added" << endl;
-		break;
-		   
-	/* \pre { description of the precondition } */
-	case 188:
-		restOfParagraph = stringTilEndOfParagraph(endIndex);
-		if(!restOfParagraph.empty()) entityList.push_back( DoxygenEntity(187, name, restOfParagraph ));
-			else cout << "Nothing followed post command. Not added" << endl;
-		 break;
-		   
-		    /* \private (PHP only) */
-		    case 189:
-		    	cout << "Private is a PHP Only Command." << endl;
-		        break;
-		   
-		     /* \privatesection (PHP only) */
-		    case 190:
-		    	cout << "Privatesection is a PHP Only Command." << endl;
-		        break;
-		   
-		    /* \property (qualified property name) */
-		    case 191:
-				restOfLine = getOneLineSentence();
-				if(!restOfLine.empty()) entityList.push_back( DoxygenEntity(191, restOfLine, ""));
-				else cout << "Nothing followed property command. Not added" << endl;
-		        break;
-		   
-		    /* \protected (PHP only) */
-		    case 192:
-		    	cout << "Protected is a PHP Only Command." << endl;
-		        break;
-		   
-		    /* \protectedsection (PHP only) */
-		    case 193:
-		    	cout << "Protectedsection is a PHP Only Command." << endl;
-		        break;
-		   
-		    /* \protocol <name> [<header-file>] [<header-name>] */
-		    case 194:
-		        break;
-		   
-		    /* \public (PHP only) */
-		    case 195:
-		    	cout << "Public is a PHP Only Command." << endl;
-		        break;
-		   
-		    /* \publicsection (PHP only) */
-		    case 196:
-		    	cout << "Public Section is a PHP Only Command." << endl;
-		        break;
-		   
-	/* \ref <name> ["(text)"] */
-	 case 197:
-			name = getNextWord();
-			getOneLineSentence();
-			cout << "Ref is currently not supported." << endl;
-		break;
-		   
-	/* \relates <name> */
-	case 198:
-		name = getNextWord();
-					if (name.empty())cout << "No word followed relates command. Not added" << endl; 
-					else {
-						entityList.push_back( DoxygenEntity(198, name,""));
-					}
-		break;
-		   
-	/* \relatesalso <name> */
-	case 199:
-		name = getNextWord();
-					if (name.empty())cout << "No word followed relatesalso command. Not added" << endl; 
-					else {
-						entityList.push_back( DoxygenEntity(199, name,""));
-					}
-		break;
-		   
-	 /* \remarks { remark text } */
-	case 200:
-		restOfParagraph = stringTilEndOfParagraph(endIndex);
-		if(!restOfParagraph.empty()) entityList.push_back( DoxygenEntity(200, restOfParagraph, "" ));
-			else cout << "Nothing followed remarks command. Not added" << endl;
-		break;
-		   
-	/* \return { description of the return value } */
-	case 201:
-		restOfParagraph = stringTilEndOfParagraph(endIndex);
-		if(!restOfParagraph.empty()) entityList.push_back( DoxygenEntity(200, restOfParagraph, "" ));
-			else cout << "Nothing followed return command. Not added" << endl;
-		 break;
-		   
-	/* \retval <return value> { description } */
-	case 202:
-		name = getNextWord();
-		if (name.empty())cout << "No word followed retval command. Not added" << endl; 
-		else {
-			restOfParagraph = stringTilEndOfParagraph(endIndex);
-			if(!restOfParagraph.empty()) entityList.push_back( DoxygenEntity(202, name, restOfParagraph ));
-				else cout << "Nothing followed retval command. Not added" << endl;
-		}
-		break;
-		   
-	/* \sa { references } */
-	case 203:
-		restOfParagraph = stringTilEndOfParagraph(endIndex);
-		if(!restOfParagraph.empty()) entityList.push_back( DoxygenEntity(203, restOfParagraph, "" ));
-			else cout << "Nothing followed sa command. Not added" << endl;
-		break;
-		   
-	/* \section <section-name> (section title) */
-	case 204:
-		name = getNextWord();
-		if (name.empty())cout << "No word followed section command. Not added" << endl; 
-		else {
-			restOfLine = getOneLineSentence();
-			if((restOfLine).empty()){
-			cout << "Error: No word after section paragraph "<< endl;
-			}
-			else entityList.push_back( DoxygenEntity(204, name, restOfLine));
-		}
-		 break;
-		   
-	/* \see { references } */
-	case 205:
-		restOfParagraph = stringTilEndOfParagraph(endIndex);
-		if(!restOfParagraph.empty()) entityList.push_back( DoxygenEntity(205, restOfParagraph, "" ));
-		else cout << "Nothing followed see command. Not added" << endl;
-		break;
-		   
-	/* \showinitializer */
-	case 206:
-		cout << "Showerinitializer command unsupported"<< endl;
-		break;
-		   
-	/* \since { text } */
-	case 207:
-		restOfParagraph = stringTilEndOfParagraph(endIndex);
-		if(!restOfParagraph.empty()) entityList.push_back( DoxygenEntity(207, restOfParagraph, "" ));
-		else cout << "Nothing followed since command. Not added" << endl;
-		 break;
-		   
-	/* \skip ( pattern ) */
-	case 208:
-		getOneLineSentence();
-		cout << "Skip command unsupported"<< endl;
-		break;
-		   
-	/* \skipline ( pattern ) */
-	case 209:
-		getOneLineSentence();
-		cout << "Skipline command unsupported"<< endl;
-		break;
-		   
-	/* \struct <name> [<header-file>] [<header-name>] */
-	case 210:
-		name = getNextWord();
-					if (name.empty())cout << "No word followed struct command. Not added" << endl; 
-					else {
-						string groupnames = getOneLineSentence();
-						entityList.push_back( DoxygenEntity(210, name, groupnames));
-					}
-		break;
-		   
-	/* \subpage <name> ["(text)"] */
-	case 211:
-		getOneLineSentence();
-		cout << "subpag command unsupported"<< endl;
-		break;
-		   
-	/* \subsection <subsection-name> (subsection title) */
-	 case 212:
-			getOneLineSentence();
-		 cout << "subsection command unsupported"<< endl;
-		 break;
-		   
-	/* \subsubsection <subsubsection-name> (subsubsection title) */
-	case 213:
-		getOneLineSentence();
-		cout << "subsubsection  command unsupported"<< endl;
-		break;
-		   
-	/* \test { paragraph describing a test case } */
-	case 214:
-		restOfParagraph = stringTilEndOfParagraph(endIndex);
-		if(!restOfParagraph.empty()) entityList.push_back( DoxygenEntity(214, restOfParagraph, "" ));
-		else cout << "Nothing followed test command. Not added" << endl;
-		break;
-		   
-	/* \throw <exception-object> { exception description } */
-	case 215:
-		name = getNextWord();
-		if (name.empty())cout << "No word followed throw command. Not added" << endl; 
-		else {
-			restOfParagraph = stringTilEndOfParagraph(endIndex);
-			if(!restOfParagraph.empty()) entityList.push_back( DoxygenEntity(215, name, restOfParagraph ));
-				else cout << "Nothing followed throw command. Not added" << endl;  
-			}
-		 break;
-		   
-	/* \todo { paragraph describing what is to be done } */
-	case 216:
-		restOfParagraph = stringTilEndOfParagraph(endIndex);
-		if(!restOfParagraph.empty()) entityList.push_back( DoxygenEntity(216, restOfParagraph, "" ));
-		else cout << "Nothing followed todo command. Not added" << endl;
-		break;
-		   
-	/* \tparam <template-parameter-name> { description } */
-	case 217:
-		name = getNextWord();
-		if (name.empty())cout << "No word followed tparam command. Not added" << endl; 
-		else {
-			restOfParagraph = stringTilEndOfParagraph(endIndex);
-			if(!restOfParagraph.empty()) entityList.push_back( DoxygenEntity(217, name, restOfParagraph ));
-				else cout << "Nothing followed tparam command. Not added" << endl;
-		}
-		   break;
-		   
-	/* \typedef (typedef declaration) */
-	case 218:
-		restOfLine = getOneLineSentence();
-		if(!restOfLine.empty()) entityList.push_back( DoxygenEntity(218, restOfLine, ""));
-		else cout << "Nothing followed typedef command. Not added" << endl;
-		break;
-		   
-	/* \union <name> [<header-file>] [<header-name>] */
-	case 219:
-		name = getNextWord();
-					if (name.empty())cout << "No word followed union command. Not added" << endl; 
-					else {
-						string groupnames = getOneLineSentence();
-						entityList.push_back( DoxygenEntity(219, name, groupnames));
-					}
-		break;
-		   
-	/* \until ( pattern ) */
-	 case 220:
-		restOfLine = getOneLineSentence();
-		if(!restOfLine.empty()) entityList.push_back( DoxygenEntity(220, restOfLine, ""));
-		else cout << "Nothing followed until command. Not added" << endl;
-		break;  
-		   
-		    /* \var (variable declaration) */
-	case 221:
-		restOfLine = getOneLineSentence();
-		if(!restOfLine.empty()) entityList.push_back( DoxygenEntity(221, restOfLine, ""));
-		else cout << "Nothing followed var command. Not added" << endl;
-		break;
-		   
-	/* \verbatim */
-	case 222:
-		cout << "Verbatim is not supported. Command not added." << endl;
-		if (progressTilEndCommand("endverbatim") < 1) cout << "No endcode for command verbatim found" << endl;	
-		break;
-		   
-	/* \verbinclude <file-name> */
-	case 223:
-		name = getNextWord();
-					if (name.empty())cout << "No word followed verbinclude command. Not added" << endl; 
-					else {
-						entityList.push_back( DoxygenEntity(223, name,""));
-					}
-		break;
-		   
-	/* \version { version number } */
-	case 224:
-		restOfParagraph = stringTilEndOfParagraph(endIndex);
-		if(!restOfParagraph.empty()) entityList.push_back( DoxygenEntity(224, restOfParagraph, "" ));
-		else cout << "Nothing followed version command. Not added" << endl;
-		break;
-		   
-	/* \warning { warning message } */
-	case 225:
-		restOfParagraph = stringTilEndOfParagraph(endIndex);
-		if(!restOfParagraph.empty()) entityList.push_back( DoxygenEntity(225, restOfParagraph, "" ));
-		else cout << "Nothing followed warning command. Not added" << endl;
-		break;
-		   
-	/* \weakgroup <name> [(title)] */
-	case 226:
-		name = getNextWord();
-		if (name.empty())cout << "No word followed weakgroup command. Not added" << endl; 
-		else {
-			string groupnames = getOneLineSentence();
-			entityList.push_back( DoxygenEntity(226, name,groupnames));
-			}
-		break;
-		   
-	/* \xmlonly */
-	case 227:
-		cout << "XML is not supported. Command not added." << endl;
-		if (progressTilEndCommand("endxmlonly") < 1) cout << "No endcode for command xmlonly found" << endl;	
-		break;
-		   
-	/* \xrefitem <key> "(heading)" "(list title)" {text} */
-	case 228:
-		//NEED TO IMPLEMENT
-		cout << "xrefitem is not supported yet. Command not added." << endl;
-		break;
-		   
-	/* \$ */
-	case 229:
-		entityList.push_back(229);
-		break;
-		   
-	/* \@ */
-	case 230:
-		entityList.push_back(230);
-		break;
-		   
-	/* \\ */
-	case 231:
-		entityList.push_back(231);
-		break;
-		   
-	/* \& */
-	case 232:
-		entityList.push_back(232);
-		break;
-		   
-	 /* \~[LanguageId] */
-	case 233:
-		break;
-		   
-	/* \< */
-	case 234:
-		entityList.push_back(234);
-		break;
-		   
-	/* \> */
-	case 235:
-		entityList.push_back(235);
-		break;
-		   
-	/* \# */
-	case 236:
-		entityList.push_back(236);
-		break;
-		   
-	/* \%  */
-	case 237:
-		entityList.push_back(237);
-		break;		
-
-		
-}
-		
-		}
-		
-int parse(string commentBlob){
- //NO error checking since this is only for my personal testing
- // usage for now is "program -DocStyle filename
- 
-	/*
- string java = "-java";
-
- 
- if ((argc < 3)||(java.compare(StringToLower(argv[1])))!= 0 ) {cout << "Incorrect Usage. -Docstyle filename only." << endl; exit(1);}
- string line;
- ifstream doxCommentFile(argv[2], ios::in);
- doxCommentFile >> doxygenString;
- while(getline(doxCommentFile, line)){
- doxygenString += line + "\n";}
- doxCommentFile.close();
- */
-	doxygenString = commentBlob;
- cout << doxygenString;
-
-
-if(doxygenString.compare(0, 3, "/**")!= 0 && doxygenString.compare(0, 3, "/*!")!= 0 
-		&& doxygenString.compare(0, 3, "///")!= 0 && doxygenString.compare(0, 3, "//!")!= 0 ){
-	
-	cout << "String Is not in proper Doxygen format." << endl;
-	exit(1);
-	}
-
- 
-if(doxygenString[3] == '<'){
-	cout << "Support for side comments not yet implemented"<<endl;
-	exit(1);
-}
-
-// Plows through the initial fluff
-
-string currWord = "";
-string nextWord = "";
-string currComment = "";
-int currCommand = 0;
-int scanIndex = 0;
-
-
-
-while( clearFluff() > 0){}
-
-while(endIndex < doxygenString.length() && startIndex < doxygenString.length()){
-currWord = getNextWord();
-
-//while((currWord = nextWord()).compare("") == 0 ){ nextLine();}
-
-if(currWord[0] == 92 || currWord[0] == '@'){
-	currWord = doxygenString.substr(startIndex+1, endIndex - startIndex - 1);
-	currCommand = findCommand(currWord);
-	if (currCommand < 0 ){ cout << "BAD COMMAND: " << currWord << endl; exit(1);}
-	cout << "Command: " << currWord << " " << currCommand << endl;
-	startIndex = endIndex;
-}
-
-else if (briefDescriptions && !briefDescExists ){
-	currComment = getOneLineSentence();
-	if (!currComment.empty()){
-	briefDescExists = 1;
-	cout << "Brief Description Found : " << currComment << endl << "-----" << endl;
-	entityList.push_back( DoxygenEntity(99, "", currComment));
-	startIndex = endIndex;
-	}
-	else cout << "Error: Brief comment extends more than 1 line." << endl;
-}
-
-else{ 
-	currComment = getDescription();
-	cout << "Long Description Found : " << currComment << endl << "-----" << endl;
-	entityList.push_back( DoxygenEntity(100, "", currComment));
-	startIndex = endIndex;
-}
-
-}
-
-cout << "Entity List : "<< endl;
-list<DoxygenEntity>::iterator p = entityList.begin();
-while (p != entityList.end()){
-	(*p).printEntity();
-	p++;
-}
-
-		
- return 0;
-}
-
-
-}
-
diff --git a/Source/DoxygenTranslator/example.i b/Source/DoxygenTranslator/example.i
deleted file mode 100644
index 20f2488cb..000000000
--- a/Source/DoxygenTranslator/example.i
+++ /dev/null
@@ -1,19 +0,0 @@
-/** File example. This is the Simple Test File!
- */
-
-%module example
-
-%inline %{
-
-/**   Function for Greater Common Divisor
- * Compute the greatest common divisor of positive integers 
- * @param x an integer argument.
- * @param y another integer argument.
- * @return the GCD
- */
-extern int    gcd(int x, int y);
-
-/** Global Variable Foo. Foo is the value of Foo. 
- */
-extern double Foo;
-%}

From 03fd3d6581dbe5411425a23d455476f4d0d22ef4 Mon Sep 17 00:00:00 2001
From: Cheryl Foil <cheryl.foil@gmail.com>
Date: Sat, 16 Aug 2008 07:11:00 +0000
Subject: [PATCH 013/314] more cleaning up

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2008-cherylfoil@10766 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 .../DoxygenTranslator/src/TranslatorTest.cpp  | 68 -------------------
 Source/DoxygenTranslator/src/TranslatorTest.h | 11 ---
 2 files changed, 79 deletions(-)
 delete mode 100644 Source/DoxygenTranslator/src/TranslatorTest.cpp
 delete mode 100644 Source/DoxygenTranslator/src/TranslatorTest.h

diff --git a/Source/DoxygenTranslator/src/TranslatorTest.cpp b/Source/DoxygenTranslator/src/TranslatorTest.cpp
deleted file mode 100644
index f2bb48983..000000000
--- a/Source/DoxygenTranslator/src/TranslatorTest.cpp
+++ /dev/null
@@ -1,68 +0,0 @@
-
-#include <cstdlib>
-#include <iostream>
-#include <fstream>
-#include <string>
-#include <list>
-using namespace std;
-
-
-/* This classes primary function is to test the basic text processing abilities of
- * the Doxygen parsing class
- * It is currently a little messy */
-
-
-int testCommandParsingFunctions = 1;
-int testCodeCrawlingFunctions = 1;
-
-
-/*  Testing clearFluff(), a method to scan past all excess / * ! from beginning of
- * a comment blob. Compartmentalised simply because this is a comment habit that
- * differs wildly */
-
-int testClearFluff(){
-
- string cases[] = {"/** WORD", "/*! WORD", "/******* WORD", "///// WORD", "//! WORD", "//! WORD", "///WORD",
-		 "/**\nWORD", "/**\n*WORD", "/** \n WORD"};
- 
- return 1;
- 
- };
-
-int testCCF(){
-	
-
-	
-	cout << "Testing getNextWord" << endl;
-	// Case 1: \command <name>
-	string case1 = "\b word";
-	string case2 = "\b word ";
-	string case3 = "\b word\n";
-	string case4 = "\b word \n";
-	string case5 = "\b word word";
-	//Case 2: \command {paragraph}
-	
-	//Case 3: \command (text til end of line)
-		
-	
-	return 1;
-}
-
-int testCPF(){
-	// Case 1: \command <name>
-	string case1 = "\b word";
-	//Case 2: \command {paragraph}
-		
-	//Case 3: \command (text til end of line)
-		
-	return 1;
-	
-}
-
-int main(int argc, char *argv[]){
-	if(testCodeCrawlingFunctions) testCCF();
-	if(testCommandParsingFunctions) testCPF();
-	
-	
-	return 1;
-}
diff --git a/Source/DoxygenTranslator/src/TranslatorTest.h b/Source/DoxygenTranslator/src/TranslatorTest.h
deleted file mode 100644
index 0014de718..000000000
--- a/Source/DoxygenTranslator/src/TranslatorTest.h
+++ /dev/null
@@ -1,11 +0,0 @@
-#ifndef TRANSLATORTEST_H_
-#define TRANSLATORTEST_H_
-
-class TranslatorTest
-{
-public:
-	TranslatorTest();
-	virtual ~TranslatorTest();
-};
-
-#endif /*TRANSLATORTEST_H_*/

From 180171ddffc5f7c2e7d0a20816373c41e0fa6931 Mon Sep 17 00:00:00 2001
From: Cheryl Foil <cheryl.foil@gmail.com>
Date: Sat, 16 Aug 2008 07:31:05 +0000
Subject: [PATCH 014/314] Fixed post comment behaviour

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2008-cherylfoil@10767 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Source/CParse/parser.y | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/Source/CParse/parser.y b/Source/CParse/parser.y
index eaf53449b..09aeb7381 100644
--- a/Source/CParse/parser.y
+++ b/Source/CParse/parser.y
@@ -105,8 +105,14 @@ static Node *new_node(const String_or_char *tag) {
   if(parseComments){
     /* Sets any post comments to the previous node */
     if(previousNode != NULL && currentPostComment != 0){
-      String *copyPostComment = Copy(currentComment);
-      Setattr(previousNode,"DoxygenPostComment",copyPostComment);
+      String *copyPostComment = Copy(currentPostComment);
+      if (!Getattr(previousNode, "DoxygenComment")){
+     	Setattr(previousNode,"DoxygenComment",copyPostComment);}
+      else {
+        Append(copyPostComment, Getattr(previousNode, "DoxygenComment"));
+      	Setattr(previousNode,"DoxygenComment",copyPostComment);
+        }
+      
       currentPostComment = 0;
     }	 
     /* Sets Doxygen Comment if a Comment is Availible */

From 88bd4e6331272a01e3fed7ec66f2b75b42b1424a Mon Sep 17 00:00:00 2001
From: Cheryl Foil <cheryl.foil@gmail.com>
Date: Mon, 18 Aug 2008 04:54:35 +0000
Subject: [PATCH 015/314] Removal of unneeded importants; debugging parser

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2008-cherylfoil@10777 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 .../src/.deps/DoxygenEntity.Po                | 190 +++++------
 .../src/.deps/DoxygenParser.Po                | 211 ++++++------
 .../src/.deps/DoxygenTranslator.Po            | 204 ++++++------
 Source/DoxygenTranslator/src/.deps/Token.Po   |  78 +----
 .../DoxygenTranslator/src/DoxygenEntity.cpp   |   2 +-
 Source/DoxygenTranslator/src/DoxygenEntity.h  |   3 +-
 .../DoxygenTranslator/src/DoxygenParser.cpp   | 306 +++++++++---------
 Source/DoxygenTranslator/src/DoxygenParser.h  |   5 -
 .../src/DoxygenTranslator.cpp                 |  32 +-
 .../src/JavaDocConverter.cpp                  |  33 +-
 Source/DoxygenTranslator/src/Token.cpp        |   6 +-
 Source/DoxygenTranslator/src/TokenList.cpp    |   2 +-
 12 files changed, 498 insertions(+), 574 deletions(-)

diff --git a/Source/DoxygenTranslator/src/.deps/DoxygenEntity.Po b/Source/DoxygenTranslator/src/.deps/DoxygenEntity.Po
index 7d2d2e0db..7a6dbd296 100644
--- a/Source/DoxygenTranslator/src/.deps/DoxygenEntity.Po
+++ b/Source/DoxygenTranslator/src/.deps/DoxygenEntity.Po
@@ -1,36 +1,42 @@
 DoxygenTranslator/src/DoxygenEntity.o \
   DoxygenTranslator/src/DoxygenEntity.o:  \
  DoxygenTranslator/src/DoxygenEntity.cpp \
-  DoxygenTranslator/src/DoxygenEntity.h /usr/include/c++/4.2/cstdlib \
+  DoxygenTranslator/src/DoxygenEntity.h /usr/include/c++/4.2/string \
   /usr/include/c++/4.2/i486-linux-gnu/bits/c++config.h \
   /usr/include/c++/4.2/i486-linux-gnu/bits/os_defines.h \
   /usr/include/features.h /usr/include/sys/cdefs.h \
   /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
   /usr/include/gnu/stubs-32.h \
   /usr/include/c++/4.2/i486-linux-gnu/bits/cpu_defines.h \
+  /usr/include/c++/4.2/bits/stringfwd.h \
+  /usr/include/c++/4.2/bits/char_traits.h /usr/include/c++/4.2/cstring \
   /usr/include/c++/4.2/cstddef \
   /usr/lib/gcc/i486-linux-gnu/4.2.3/include/stddef.h \
+  /usr/include/string.h /usr/include/xlocale.h \
+  /usr/include/c++/4.2/bits/stl_algobase.h /usr/include/c++/4.2/climits \
+  /usr/lib/gcc/i486-linux-gnu/4.2.3/include/limits.h \
+  /usr/lib/gcc/i486-linux-gnu/4.2.3/include/syslimits.h \
+  /usr/include/limits.h /usr/include/bits/posix1_lim.h \
+  /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
+  /usr/include/bits/posix2_lim.h /usr/include/bits/xopen_lim.h \
+  /usr/include/bits/stdio_lim.h /usr/include/c++/4.2/cstdlib \
   /usr/include/stdlib.h /usr/include/bits/waitflags.h \
   /usr/include/bits/waitstatus.h /usr/include/endian.h \
-  /usr/include/bits/endian.h /usr/include/xlocale.h \
-  /usr/include/sys/types.h /usr/include/bits/types.h \
-  /usr/include/bits/typesizes.h /usr/include/time.h \
-  /usr/include/sys/select.h /usr/include/bits/select.h \
-  /usr/include/bits/sigset.h /usr/include/bits/time.h \
-  /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \
-  /usr/include/alloca.h /usr/include/c++/4.2/iostream \
-  /usr/include/c++/4.2/ostream /usr/include/c++/4.2/ios \
+  /usr/include/bits/endian.h /usr/include/sys/types.h \
+  /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+  /usr/include/time.h /usr/include/sys/select.h \
+  /usr/include/bits/select.h /usr/include/bits/sigset.h \
+  /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
+  /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
   /usr/include/c++/4.2/iosfwd \
   /usr/include/c++/4.2/i486-linux-gnu/bits/c++locale.h \
-  /usr/include/c++/4.2/cstring /usr/include/string.h \
   /usr/include/c++/4.2/cstdio /usr/include/stdio.h /usr/include/libio.h \
   /usr/include/_G_config.h /usr/include/wchar.h \
   /usr/lib/gcc/i486-linux-gnu/4.2.3/include/stdarg.h \
-  /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
-  /usr/include/c++/4.2/clocale /usr/include/locale.h \
-  /usr/include/bits/locale.h /usr/include/langinfo.h \
-  /usr/include/nl_types.h /usr/include/iconv.h /usr/include/libintl.h \
-  /usr/include/c++/4.2/cstdarg \
+  /usr/include/bits/sys_errlist.h /usr/include/c++/4.2/clocale \
+  /usr/include/locale.h /usr/include/bits/locale.h \
+  /usr/include/langinfo.h /usr/include/nl_types.h /usr/include/iconv.h \
+  /usr/include/libintl.h /usr/include/c++/4.2/cstdarg \
   /usr/include/c++/4.2/i486-linux-gnu/bits/c++io.h \
   /usr/include/c++/4.2/i486-linux-gnu/bits/gthr.h \
   /usr/include/c++/4.2/i486-linux-gnu/bits/gthr-default.h \
@@ -39,18 +45,10 @@ DoxygenTranslator/src/DoxygenEntity.o \
   /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \
   /usr/include/bits/confname.h /usr/include/getopt.h \
   /usr/include/c++/4.2/cctype /usr/include/ctype.h \
-  /usr/include/c++/4.2/bits/stringfwd.h \
   /usr/include/c++/4.2/bits/postypes.h /usr/include/c++/4.2/cwchar \
   /usr/include/c++/4.2/ctime /usr/include/bits/wchar.h \
   /usr/include/stdint.h /usr/include/c++/4.2/bits/functexcept.h \
-  /usr/include/c++/4.2/exception_defines.h /usr/include/c++/4.2/exception \
-  /usr/include/c++/4.2/bits/char_traits.h \
-  /usr/include/c++/4.2/bits/stl_algobase.h /usr/include/c++/4.2/climits \
-  /usr/lib/gcc/i486-linux-gnu/4.2.3/include/limits.h \
-  /usr/lib/gcc/i486-linux-gnu/4.2.3/include/syslimits.h \
-  /usr/include/limits.h /usr/include/bits/posix1_lim.h \
-  /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
-  /usr/include/bits/posix2_lim.h /usr/include/bits/xopen_lim.h \
+  /usr/include/c++/4.2/exception_defines.h \
   /usr/include/c++/4.2/bits/stl_pair.h \
   /usr/include/c++/4.2/bits/cpp_type_traits.h \
   /usr/include/c++/4.2/ext/type_traits.h /usr/include/c++/4.2/utility \
@@ -59,25 +57,28 @@ DoxygenTranslator/src/DoxygenEntity.o \
   /usr/include/c++/4.2/bits/stl_iterator_base_funcs.h \
   /usr/include/c++/4.2/bits/concept_check.h \
   /usr/include/c++/4.2/bits/stl_iterator.h \
-  /usr/include/c++/4.2/debug/debug.h \
-  /usr/include/c++/4.2/bits/localefwd.h \
-  /usr/include/c++/4.2/bits/ios_base.h \
-  /usr/include/c++/4.2/ext/atomicity.h \
-  /usr/include/c++/4.2/i486-linux-gnu/bits/atomic_word.h \
-  /usr/include/c++/4.2/bits/locale_classes.h /usr/include/c++/4.2/string \
-  /usr/include/c++/4.2/memory /usr/include/c++/4.2/bits/allocator.h \
+  /usr/include/c++/4.2/debug/debug.h /usr/include/c++/4.2/memory \
+  /usr/include/c++/4.2/bits/allocator.h \
   /usr/include/c++/4.2/i486-linux-gnu/bits/c++allocator.h \
   /usr/include/c++/4.2/ext/new_allocator.h /usr/include/c++/4.2/new \
+  /usr/include/c++/4.2/exception \
   /usr/include/c++/4.2/bits/stl_construct.h \
   /usr/include/c++/4.2/bits/stl_uninitialized.h \
   /usr/include/c++/4.2/bits/stl_raw_storage_iter.h \
   /usr/include/c++/4.2/limits /usr/include/c++/4.2/bits/ostream_insert.h \
   /usr/include/c++/4.2/bits/stl_function.h \
-  /usr/include/c++/4.2/bits/basic_string.h /usr/include/c++/4.2/algorithm \
-  /usr/include/c++/4.2/bits/stl_algo.h \
+  /usr/include/c++/4.2/bits/basic_string.h \
+  /usr/include/c++/4.2/ext/atomicity.h \
+  /usr/include/c++/4.2/i486-linux-gnu/bits/atomic_word.h \
+  /usr/include/c++/4.2/algorithm /usr/include/c++/4.2/bits/stl_algo.h \
   /usr/include/c++/4.2/bits/stl_heap.h \
   /usr/include/c++/4.2/bits/stl_tempbuf.h \
-  /usr/include/c++/4.2/bits/basic_string.tcc \
+  /usr/include/c++/4.2/bits/basic_string.tcc /usr/include/c++/4.2/list \
+  /usr/include/c++/4.2/bits/stl_list.h /usr/include/c++/4.2/bits/list.tcc \
+  /usr/include/c++/4.2/iostream /usr/include/c++/4.2/ostream \
+  /usr/include/c++/4.2/ios /usr/include/c++/4.2/bits/localefwd.h \
+  /usr/include/c++/4.2/bits/ios_base.h \
+  /usr/include/c++/4.2/bits/locale_classes.h \
   /usr/include/c++/4.2/streambuf /usr/include/c++/4.2/bits/streambuf.tcc \
   /usr/include/c++/4.2/bits/basic_ios.h \
   /usr/include/c++/4.2/bits/streambuf_iterator.h \
@@ -92,12 +93,11 @@ DoxygenTranslator/src/DoxygenEntity.o \
   /usr/include/c++/4.2/bits/ostream.tcc /usr/include/c++/4.2/locale \
   /usr/include/c++/4.2/bits/locale_facets.tcc \
   /usr/include/c++/4.2/typeinfo /usr/include/c++/4.2/istream \
-  /usr/include/c++/4.2/bits/istream.tcc /usr/include/c++/4.2/list \
-  /usr/include/c++/4.2/bits/stl_list.h /usr/include/c++/4.2/bits/list.tcc
+  /usr/include/c++/4.2/bits/istream.tcc
 
 DoxygenTranslator/src/DoxygenEntity.h:
 
-/usr/include/c++/4.2/cstdlib:
+/usr/include/c++/4.2/string:
 
 /usr/include/c++/4.2/i486-linux-gnu/bits/c++config.h:
 
@@ -115,10 +115,44 @@ DoxygenTranslator/src/DoxygenEntity.h:
 
 /usr/include/c++/4.2/i486-linux-gnu/bits/cpu_defines.h:
 
+/usr/include/c++/4.2/bits/stringfwd.h:
+
+/usr/include/c++/4.2/bits/char_traits.h:
+
+/usr/include/c++/4.2/cstring:
+
 /usr/include/c++/4.2/cstddef:
 
 /usr/lib/gcc/i486-linux-gnu/4.2.3/include/stddef.h:
 
+/usr/include/string.h:
+
+/usr/include/xlocale.h:
+
+/usr/include/c++/4.2/bits/stl_algobase.h:
+
+/usr/include/c++/4.2/climits:
+
+/usr/lib/gcc/i486-linux-gnu/4.2.3/include/limits.h:
+
+/usr/lib/gcc/i486-linux-gnu/4.2.3/include/syslimits.h:
+
+/usr/include/limits.h:
+
+/usr/include/bits/posix1_lim.h:
+
+/usr/include/bits/local_lim.h:
+
+/usr/include/linux/limits.h:
+
+/usr/include/bits/posix2_lim.h:
+
+/usr/include/bits/xopen_lim.h:
+
+/usr/include/bits/stdio_lim.h:
+
+/usr/include/c++/4.2/cstdlib:
+
 /usr/include/stdlib.h:
 
 /usr/include/bits/waitflags.h:
@@ -129,8 +163,6 @@ DoxygenTranslator/src/DoxygenEntity.h:
 
 /usr/include/bits/endian.h:
 
-/usr/include/xlocale.h:
-
 /usr/include/sys/types.h:
 
 /usr/include/bits/types.h:
@@ -153,20 +185,10 @@ DoxygenTranslator/src/DoxygenEntity.h:
 
 /usr/include/alloca.h:
 
-/usr/include/c++/4.2/iostream:
-
-/usr/include/c++/4.2/ostream:
-
-/usr/include/c++/4.2/ios:
-
 /usr/include/c++/4.2/iosfwd:
 
 /usr/include/c++/4.2/i486-linux-gnu/bits/c++locale.h:
 
-/usr/include/c++/4.2/cstring:
-
-/usr/include/string.h:
-
 /usr/include/c++/4.2/cstdio:
 
 /usr/include/stdio.h:
@@ -179,8 +201,6 @@ DoxygenTranslator/src/DoxygenEntity.h:
 
 /usr/lib/gcc/i486-linux-gnu/4.2.3/include/stdarg.h:
 
-/usr/include/bits/stdio_lim.h:
-
 /usr/include/bits/sys_errlist.h:
 
 /usr/include/c++/4.2/clocale:
@@ -229,8 +249,6 @@ DoxygenTranslator/src/DoxygenEntity.h:
 
 /usr/include/ctype.h:
 
-/usr/include/c++/4.2/bits/stringfwd.h:
-
 /usr/include/c++/4.2/bits/postypes.h:
 
 /usr/include/c++/4.2/cwchar:
@@ -245,30 +263,6 @@ DoxygenTranslator/src/DoxygenEntity.h:
 
 /usr/include/c++/4.2/exception_defines.h:
 
-/usr/include/c++/4.2/exception:
-
-/usr/include/c++/4.2/bits/char_traits.h:
-
-/usr/include/c++/4.2/bits/stl_algobase.h:
-
-/usr/include/c++/4.2/climits:
-
-/usr/lib/gcc/i486-linux-gnu/4.2.3/include/limits.h:
-
-/usr/lib/gcc/i486-linux-gnu/4.2.3/include/syslimits.h:
-
-/usr/include/limits.h:
-
-/usr/include/bits/posix1_lim.h:
-
-/usr/include/bits/local_lim.h:
-
-/usr/include/linux/limits.h:
-
-/usr/include/bits/posix2_lim.h:
-
-/usr/include/bits/xopen_lim.h:
-
 /usr/include/c++/4.2/bits/stl_pair.h:
 
 /usr/include/c++/4.2/bits/cpp_type_traits.h:
@@ -289,18 +283,6 @@ DoxygenTranslator/src/DoxygenEntity.h:
 
 /usr/include/c++/4.2/debug/debug.h:
 
-/usr/include/c++/4.2/bits/localefwd.h:
-
-/usr/include/c++/4.2/bits/ios_base.h:
-
-/usr/include/c++/4.2/ext/atomicity.h:
-
-/usr/include/c++/4.2/i486-linux-gnu/bits/atomic_word.h:
-
-/usr/include/c++/4.2/bits/locale_classes.h:
-
-/usr/include/c++/4.2/string:
-
 /usr/include/c++/4.2/memory:
 
 /usr/include/c++/4.2/bits/allocator.h:
@@ -311,6 +293,8 @@ DoxygenTranslator/src/DoxygenEntity.h:
 
 /usr/include/c++/4.2/new:
 
+/usr/include/c++/4.2/exception:
+
 /usr/include/c++/4.2/bits/stl_construct.h:
 
 /usr/include/c++/4.2/bits/stl_uninitialized.h:
@@ -325,6 +309,10 @@ DoxygenTranslator/src/DoxygenEntity.h:
 
 /usr/include/c++/4.2/bits/basic_string.h:
 
+/usr/include/c++/4.2/ext/atomicity.h:
+
+/usr/include/c++/4.2/i486-linux-gnu/bits/atomic_word.h:
+
 /usr/include/c++/4.2/algorithm:
 
 /usr/include/c++/4.2/bits/stl_algo.h:
@@ -335,6 +323,24 @@ DoxygenTranslator/src/DoxygenEntity.h:
 
 /usr/include/c++/4.2/bits/basic_string.tcc:
 
+/usr/include/c++/4.2/list:
+
+/usr/include/c++/4.2/bits/stl_list.h:
+
+/usr/include/c++/4.2/bits/list.tcc:
+
+/usr/include/c++/4.2/iostream:
+
+/usr/include/c++/4.2/ostream:
+
+/usr/include/c++/4.2/ios:
+
+/usr/include/c++/4.2/bits/localefwd.h:
+
+/usr/include/c++/4.2/bits/ios_base.h:
+
+/usr/include/c++/4.2/bits/locale_classes.h:
+
 /usr/include/c++/4.2/streambuf:
 
 /usr/include/c++/4.2/bits/streambuf.tcc:
@@ -372,9 +378,3 @@ DoxygenTranslator/src/DoxygenEntity.h:
 /usr/include/c++/4.2/istream:
 
 /usr/include/c++/4.2/bits/istream.tcc:
-
-/usr/include/c++/4.2/list:
-
-/usr/include/c++/4.2/bits/stl_list.h:
-
-/usr/include/c++/4.2/bits/list.tcc:
diff --git a/Source/DoxygenTranslator/src/.deps/DoxygenParser.Po b/Source/DoxygenTranslator/src/.deps/DoxygenParser.Po
index 3a023d6b9..8ec874c8c 100644
--- a/Source/DoxygenTranslator/src/.deps/DoxygenParser.Po
+++ b/Source/DoxygenTranslator/src/.deps/DoxygenParser.Po
@@ -1,36 +1,42 @@
 DoxygenTranslator/src/DoxygenParser.o \
   DoxygenTranslator/src/DoxygenParser.o:  \
  DoxygenTranslator/src/DoxygenParser.cpp \
-  DoxygenTranslator/src/DoxygenParser.h /usr/include/c++/4.2/cstdlib \
+  DoxygenTranslator/src/DoxygenParser.h /usr/include/c++/4.2/string \
   /usr/include/c++/4.2/i486-linux-gnu/bits/c++config.h \
   /usr/include/c++/4.2/i486-linux-gnu/bits/os_defines.h \
   /usr/include/features.h /usr/include/sys/cdefs.h \
   /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
   /usr/include/gnu/stubs-32.h \
   /usr/include/c++/4.2/i486-linux-gnu/bits/cpu_defines.h \
+  /usr/include/c++/4.2/bits/stringfwd.h \
+  /usr/include/c++/4.2/bits/char_traits.h /usr/include/c++/4.2/cstring \
   /usr/include/c++/4.2/cstddef \
   /usr/lib/gcc/i486-linux-gnu/4.2.3/include/stddef.h \
+  /usr/include/string.h /usr/include/xlocale.h \
+  /usr/include/c++/4.2/bits/stl_algobase.h /usr/include/c++/4.2/climits \
+  /usr/lib/gcc/i486-linux-gnu/4.2.3/include/limits.h \
+  /usr/lib/gcc/i486-linux-gnu/4.2.3/include/syslimits.h \
+  /usr/include/limits.h /usr/include/bits/posix1_lim.h \
+  /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
+  /usr/include/bits/posix2_lim.h /usr/include/bits/xopen_lim.h \
+  /usr/include/bits/stdio_lim.h /usr/include/c++/4.2/cstdlib \
   /usr/include/stdlib.h /usr/include/bits/waitflags.h \
   /usr/include/bits/waitstatus.h /usr/include/endian.h \
-  /usr/include/bits/endian.h /usr/include/xlocale.h \
-  /usr/include/sys/types.h /usr/include/bits/types.h \
-  /usr/include/bits/typesizes.h /usr/include/time.h \
-  /usr/include/sys/select.h /usr/include/bits/select.h \
-  /usr/include/bits/sigset.h /usr/include/bits/time.h \
-  /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \
-  /usr/include/alloca.h /usr/include/c++/4.2/iostream \
-  /usr/include/c++/4.2/ostream /usr/include/c++/4.2/ios \
+  /usr/include/bits/endian.h /usr/include/sys/types.h \
+  /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+  /usr/include/time.h /usr/include/sys/select.h \
+  /usr/include/bits/select.h /usr/include/bits/sigset.h \
+  /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
+  /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
   /usr/include/c++/4.2/iosfwd \
   /usr/include/c++/4.2/i486-linux-gnu/bits/c++locale.h \
-  /usr/include/c++/4.2/cstring /usr/include/string.h \
   /usr/include/c++/4.2/cstdio /usr/include/stdio.h /usr/include/libio.h \
   /usr/include/_G_config.h /usr/include/wchar.h \
   /usr/lib/gcc/i486-linux-gnu/4.2.3/include/stdarg.h \
-  /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
-  /usr/include/c++/4.2/clocale /usr/include/locale.h \
-  /usr/include/bits/locale.h /usr/include/langinfo.h \
-  /usr/include/nl_types.h /usr/include/iconv.h /usr/include/libintl.h \
-  /usr/include/c++/4.2/cstdarg \
+  /usr/include/bits/sys_errlist.h /usr/include/c++/4.2/clocale \
+  /usr/include/locale.h /usr/include/bits/locale.h \
+  /usr/include/langinfo.h /usr/include/nl_types.h /usr/include/iconv.h \
+  /usr/include/libintl.h /usr/include/c++/4.2/cstdarg \
   /usr/include/c++/4.2/i486-linux-gnu/bits/c++io.h \
   /usr/include/c++/4.2/i486-linux-gnu/bits/gthr.h \
   /usr/include/c++/4.2/i486-linux-gnu/bits/gthr-default.h \
@@ -39,18 +45,10 @@ DoxygenTranslator/src/DoxygenParser.o \
   /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \
   /usr/include/bits/confname.h /usr/include/getopt.h \
   /usr/include/c++/4.2/cctype /usr/include/ctype.h \
-  /usr/include/c++/4.2/bits/stringfwd.h \
   /usr/include/c++/4.2/bits/postypes.h /usr/include/c++/4.2/cwchar \
   /usr/include/c++/4.2/ctime /usr/include/bits/wchar.h \
   /usr/include/stdint.h /usr/include/c++/4.2/bits/functexcept.h \
-  /usr/include/c++/4.2/exception_defines.h /usr/include/c++/4.2/exception \
-  /usr/include/c++/4.2/bits/char_traits.h \
-  /usr/include/c++/4.2/bits/stl_algobase.h /usr/include/c++/4.2/climits \
-  /usr/lib/gcc/i486-linux-gnu/4.2.3/include/limits.h \
-  /usr/lib/gcc/i486-linux-gnu/4.2.3/include/syslimits.h \
-  /usr/include/limits.h /usr/include/bits/posix1_lim.h \
-  /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
-  /usr/include/bits/posix2_lim.h /usr/include/bits/xopen_lim.h \
+  /usr/include/c++/4.2/exception_defines.h \
   /usr/include/c++/4.2/bits/stl_pair.h \
   /usr/include/c++/4.2/bits/cpp_type_traits.h \
   /usr/include/c++/4.2/ext/type_traits.h /usr/include/c++/4.2/utility \
@@ -59,25 +57,29 @@ DoxygenTranslator/src/DoxygenParser.o \
   /usr/include/c++/4.2/bits/stl_iterator_base_funcs.h \
   /usr/include/c++/4.2/bits/concept_check.h \
   /usr/include/c++/4.2/bits/stl_iterator.h \
-  /usr/include/c++/4.2/debug/debug.h \
-  /usr/include/c++/4.2/bits/localefwd.h \
-  /usr/include/c++/4.2/bits/ios_base.h \
-  /usr/include/c++/4.2/ext/atomicity.h \
-  /usr/include/c++/4.2/i486-linux-gnu/bits/atomic_word.h \
-  /usr/include/c++/4.2/bits/locale_classes.h /usr/include/c++/4.2/string \
-  /usr/include/c++/4.2/memory /usr/include/c++/4.2/bits/allocator.h \
+  /usr/include/c++/4.2/debug/debug.h /usr/include/c++/4.2/memory \
+  /usr/include/c++/4.2/bits/allocator.h \
   /usr/include/c++/4.2/i486-linux-gnu/bits/c++allocator.h \
   /usr/include/c++/4.2/ext/new_allocator.h /usr/include/c++/4.2/new \
+  /usr/include/c++/4.2/exception \
   /usr/include/c++/4.2/bits/stl_construct.h \
   /usr/include/c++/4.2/bits/stl_uninitialized.h \
   /usr/include/c++/4.2/bits/stl_raw_storage_iter.h \
   /usr/include/c++/4.2/limits /usr/include/c++/4.2/bits/ostream_insert.h \
   /usr/include/c++/4.2/bits/stl_function.h \
-  /usr/include/c++/4.2/bits/basic_string.h /usr/include/c++/4.2/algorithm \
-  /usr/include/c++/4.2/bits/stl_algo.h \
+  /usr/include/c++/4.2/bits/basic_string.h \
+  /usr/include/c++/4.2/ext/atomicity.h \
+  /usr/include/c++/4.2/i486-linux-gnu/bits/atomic_word.h \
+  /usr/include/c++/4.2/algorithm /usr/include/c++/4.2/bits/stl_algo.h \
   /usr/include/c++/4.2/bits/stl_heap.h \
   /usr/include/c++/4.2/bits/stl_tempbuf.h \
-  /usr/include/c++/4.2/bits/basic_string.tcc \
+  /usr/include/c++/4.2/bits/basic_string.tcc /usr/include/c++/4.2/list \
+  /usr/include/c++/4.2/bits/stl_list.h /usr/include/c++/4.2/bits/list.tcc \
+  DoxygenTranslator/src/DoxygenEntity.h DoxygenTranslator/src/TokenList.h \
+  /usr/include/c++/4.2/iostream /usr/include/c++/4.2/ostream \
+  /usr/include/c++/4.2/ios /usr/include/c++/4.2/bits/localefwd.h \
+  /usr/include/c++/4.2/bits/ios_base.h \
+  /usr/include/c++/4.2/bits/locale_classes.h \
   /usr/include/c++/4.2/streambuf /usr/include/c++/4.2/bits/streambuf.tcc \
   /usr/include/c++/4.2/bits/basic_ios.h \
   /usr/include/c++/4.2/bits/streambuf_iterator.h \
@@ -92,16 +94,11 @@ DoxygenTranslator/src/DoxygenParser.o \
   /usr/include/c++/4.2/bits/ostream.tcc /usr/include/c++/4.2/locale \
   /usr/include/c++/4.2/bits/locale_facets.tcc \
   /usr/include/c++/4.2/typeinfo /usr/include/c++/4.2/istream \
-  /usr/include/c++/4.2/bits/istream.tcc /usr/include/c++/4.2/fstream \
-  /usr/include/c++/4.2/i486-linux-gnu/bits/basic_file.h \
-  /usr/include/c++/4.2/bits/fstream.tcc /usr/include/c++/4.2/list \
-  /usr/include/c++/4.2/bits/stl_list.h /usr/include/c++/4.2/bits/list.tcc \
-  DoxygenTranslator/src/DoxygenEntity.h DoxygenTranslator/src/TokenList.h \
-  DoxygenTranslator/src/Token.h DoxygenTranslator/src/JavaDocConverter.h
+  /usr/include/c++/4.2/bits/istream.tcc DoxygenTranslator/src/Token.h
 
 DoxygenTranslator/src/DoxygenParser.h:
 
-/usr/include/c++/4.2/cstdlib:
+/usr/include/c++/4.2/string:
 
 /usr/include/c++/4.2/i486-linux-gnu/bits/c++config.h:
 
@@ -119,10 +116,44 @@ DoxygenTranslator/src/DoxygenParser.h:
 
 /usr/include/c++/4.2/i486-linux-gnu/bits/cpu_defines.h:
 
+/usr/include/c++/4.2/bits/stringfwd.h:
+
+/usr/include/c++/4.2/bits/char_traits.h:
+
+/usr/include/c++/4.2/cstring:
+
 /usr/include/c++/4.2/cstddef:
 
 /usr/lib/gcc/i486-linux-gnu/4.2.3/include/stddef.h:
 
+/usr/include/string.h:
+
+/usr/include/xlocale.h:
+
+/usr/include/c++/4.2/bits/stl_algobase.h:
+
+/usr/include/c++/4.2/climits:
+
+/usr/lib/gcc/i486-linux-gnu/4.2.3/include/limits.h:
+
+/usr/lib/gcc/i486-linux-gnu/4.2.3/include/syslimits.h:
+
+/usr/include/limits.h:
+
+/usr/include/bits/posix1_lim.h:
+
+/usr/include/bits/local_lim.h:
+
+/usr/include/linux/limits.h:
+
+/usr/include/bits/posix2_lim.h:
+
+/usr/include/bits/xopen_lim.h:
+
+/usr/include/bits/stdio_lim.h:
+
+/usr/include/c++/4.2/cstdlib:
+
 /usr/include/stdlib.h:
 
 /usr/include/bits/waitflags.h:
@@ -133,8 +164,6 @@ DoxygenTranslator/src/DoxygenParser.h:
 
 /usr/include/bits/endian.h:
 
-/usr/include/xlocale.h:
-
 /usr/include/sys/types.h:
 
 /usr/include/bits/types.h:
@@ -157,20 +186,10 @@ DoxygenTranslator/src/DoxygenParser.h:
 
 /usr/include/alloca.h:
 
-/usr/include/c++/4.2/iostream:
-
-/usr/include/c++/4.2/ostream:
-
-/usr/include/c++/4.2/ios:
-
 /usr/include/c++/4.2/iosfwd:
 
 /usr/include/c++/4.2/i486-linux-gnu/bits/c++locale.h:
 
-/usr/include/c++/4.2/cstring:
-
-/usr/include/string.h:
-
 /usr/include/c++/4.2/cstdio:
 
 /usr/include/stdio.h:
@@ -183,8 +202,6 @@ DoxygenTranslator/src/DoxygenParser.h:
 
 /usr/lib/gcc/i486-linux-gnu/4.2.3/include/stdarg.h:
 
-/usr/include/bits/stdio_lim.h:
-
 /usr/include/bits/sys_errlist.h:
 
 /usr/include/c++/4.2/clocale:
@@ -233,8 +250,6 @@ DoxygenTranslator/src/DoxygenParser.h:
 
 /usr/include/ctype.h:
 
-/usr/include/c++/4.2/bits/stringfwd.h:
-
 /usr/include/c++/4.2/bits/postypes.h:
 
 /usr/include/c++/4.2/cwchar:
@@ -249,30 +264,6 @@ DoxygenTranslator/src/DoxygenParser.h:
 
 /usr/include/c++/4.2/exception_defines.h:
 
-/usr/include/c++/4.2/exception:
-
-/usr/include/c++/4.2/bits/char_traits.h:
-
-/usr/include/c++/4.2/bits/stl_algobase.h:
-
-/usr/include/c++/4.2/climits:
-
-/usr/lib/gcc/i486-linux-gnu/4.2.3/include/limits.h:
-
-/usr/lib/gcc/i486-linux-gnu/4.2.3/include/syslimits.h:
-
-/usr/include/limits.h:
-
-/usr/include/bits/posix1_lim.h:
-
-/usr/include/bits/local_lim.h:
-
-/usr/include/linux/limits.h:
-
-/usr/include/bits/posix2_lim.h:
-
-/usr/include/bits/xopen_lim.h:
-
 /usr/include/c++/4.2/bits/stl_pair.h:
 
 /usr/include/c++/4.2/bits/cpp_type_traits.h:
@@ -293,18 +284,6 @@ DoxygenTranslator/src/DoxygenParser.h:
 
 /usr/include/c++/4.2/debug/debug.h:
 
-/usr/include/c++/4.2/bits/localefwd.h:
-
-/usr/include/c++/4.2/bits/ios_base.h:
-
-/usr/include/c++/4.2/ext/atomicity.h:
-
-/usr/include/c++/4.2/i486-linux-gnu/bits/atomic_word.h:
-
-/usr/include/c++/4.2/bits/locale_classes.h:
-
-/usr/include/c++/4.2/string:
-
 /usr/include/c++/4.2/memory:
 
 /usr/include/c++/4.2/bits/allocator.h:
@@ -315,6 +294,8 @@ DoxygenTranslator/src/DoxygenParser.h:
 
 /usr/include/c++/4.2/new:
 
+/usr/include/c++/4.2/exception:
+
 /usr/include/c++/4.2/bits/stl_construct.h:
 
 /usr/include/c++/4.2/bits/stl_uninitialized.h:
@@ -329,6 +310,10 @@ DoxygenTranslator/src/DoxygenParser.h:
 
 /usr/include/c++/4.2/bits/basic_string.h:
 
+/usr/include/c++/4.2/ext/atomicity.h:
+
+/usr/include/c++/4.2/i486-linux-gnu/bits/atomic_word.h:
+
 /usr/include/c++/4.2/algorithm:
 
 /usr/include/c++/4.2/bits/stl_algo.h:
@@ -339,6 +324,28 @@ DoxygenTranslator/src/DoxygenParser.h:
 
 /usr/include/c++/4.2/bits/basic_string.tcc:
 
+/usr/include/c++/4.2/list:
+
+/usr/include/c++/4.2/bits/stl_list.h:
+
+/usr/include/c++/4.2/bits/list.tcc:
+
+DoxygenTranslator/src/DoxygenEntity.h:
+
+DoxygenTranslator/src/TokenList.h:
+
+/usr/include/c++/4.2/iostream:
+
+/usr/include/c++/4.2/ostream:
+
+/usr/include/c++/4.2/ios:
+
+/usr/include/c++/4.2/bits/localefwd.h:
+
+/usr/include/c++/4.2/bits/ios_base.h:
+
+/usr/include/c++/4.2/bits/locale_classes.h:
+
 /usr/include/c++/4.2/streambuf:
 
 /usr/include/c++/4.2/bits/streambuf.tcc:
@@ -377,22 +384,4 @@ DoxygenTranslator/src/DoxygenParser.h:
 
 /usr/include/c++/4.2/bits/istream.tcc:
 
-/usr/include/c++/4.2/fstream:
-
-/usr/include/c++/4.2/i486-linux-gnu/bits/basic_file.h:
-
-/usr/include/c++/4.2/bits/fstream.tcc:
-
-/usr/include/c++/4.2/list:
-
-/usr/include/c++/4.2/bits/stl_list.h:
-
-/usr/include/c++/4.2/bits/list.tcc:
-
-DoxygenTranslator/src/DoxygenEntity.h:
-
-DoxygenTranslator/src/TokenList.h:
-
 DoxygenTranslator/src/Token.h:
-
-DoxygenTranslator/src/JavaDocConverter.h:
diff --git a/Source/DoxygenTranslator/src/.deps/DoxygenTranslator.Po b/Source/DoxygenTranslator/src/.deps/DoxygenTranslator.Po
index d71e23830..4cec6c648 100644
--- a/Source/DoxygenTranslator/src/.deps/DoxygenTranslator.Po
+++ b/Source/DoxygenTranslator/src/.deps/DoxygenTranslator.Po
@@ -1,36 +1,42 @@
 DoxygenTranslator/src/DoxygenTranslator.o \
   DoxygenTranslator/src/DoxygenTranslator.o:  \
  DoxygenTranslator/src/DoxygenTranslator.cpp \
-  DoxygenTranslator/src/DoxygenParser.h /usr/include/c++/4.2/cstdlib \
+  DoxygenTranslator/src/DoxygenParser.h /usr/include/c++/4.2/string \
   /usr/include/c++/4.2/i486-linux-gnu/bits/c++config.h \
   /usr/include/c++/4.2/i486-linux-gnu/bits/os_defines.h \
   /usr/include/features.h /usr/include/sys/cdefs.h \
   /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
   /usr/include/gnu/stubs-32.h \
   /usr/include/c++/4.2/i486-linux-gnu/bits/cpu_defines.h \
+  /usr/include/c++/4.2/bits/stringfwd.h \
+  /usr/include/c++/4.2/bits/char_traits.h /usr/include/c++/4.2/cstring \
   /usr/include/c++/4.2/cstddef \
   /usr/lib/gcc/i486-linux-gnu/4.2.3/include/stddef.h \
+  /usr/include/string.h /usr/include/xlocale.h \
+  /usr/include/c++/4.2/bits/stl_algobase.h /usr/include/c++/4.2/climits \
+  /usr/lib/gcc/i486-linux-gnu/4.2.3/include/limits.h \
+  /usr/lib/gcc/i486-linux-gnu/4.2.3/include/syslimits.h \
+  /usr/include/limits.h /usr/include/bits/posix1_lim.h \
+  /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
+  /usr/include/bits/posix2_lim.h /usr/include/bits/xopen_lim.h \
+  /usr/include/bits/stdio_lim.h /usr/include/c++/4.2/cstdlib \
   /usr/include/stdlib.h /usr/include/bits/waitflags.h \
   /usr/include/bits/waitstatus.h /usr/include/endian.h \
-  /usr/include/bits/endian.h /usr/include/xlocale.h \
-  /usr/include/sys/types.h /usr/include/bits/types.h \
-  /usr/include/bits/typesizes.h /usr/include/time.h \
-  /usr/include/sys/select.h /usr/include/bits/select.h \
-  /usr/include/bits/sigset.h /usr/include/bits/time.h \
-  /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \
-  /usr/include/alloca.h /usr/include/c++/4.2/iostream \
-  /usr/include/c++/4.2/ostream /usr/include/c++/4.2/ios \
+  /usr/include/bits/endian.h /usr/include/sys/types.h \
+  /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+  /usr/include/time.h /usr/include/sys/select.h \
+  /usr/include/bits/select.h /usr/include/bits/sigset.h \
+  /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
+  /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
   /usr/include/c++/4.2/iosfwd \
   /usr/include/c++/4.2/i486-linux-gnu/bits/c++locale.h \
-  /usr/include/c++/4.2/cstring /usr/include/string.h \
   /usr/include/c++/4.2/cstdio /usr/include/stdio.h /usr/include/libio.h \
   /usr/include/_G_config.h /usr/include/wchar.h \
   /usr/lib/gcc/i486-linux-gnu/4.2.3/include/stdarg.h \
-  /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
-  /usr/include/c++/4.2/clocale /usr/include/locale.h \
-  /usr/include/bits/locale.h /usr/include/langinfo.h \
-  /usr/include/nl_types.h /usr/include/iconv.h /usr/include/libintl.h \
-  /usr/include/c++/4.2/cstdarg \
+  /usr/include/bits/sys_errlist.h /usr/include/c++/4.2/clocale \
+  /usr/include/locale.h /usr/include/bits/locale.h \
+  /usr/include/langinfo.h /usr/include/nl_types.h /usr/include/iconv.h \
+  /usr/include/libintl.h /usr/include/c++/4.2/cstdarg \
   /usr/include/c++/4.2/i486-linux-gnu/bits/c++io.h \
   /usr/include/c++/4.2/i486-linux-gnu/bits/gthr.h \
   /usr/include/c++/4.2/i486-linux-gnu/bits/gthr-default.h \
@@ -39,18 +45,10 @@ DoxygenTranslator/src/DoxygenTranslator.o \
   /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \
   /usr/include/bits/confname.h /usr/include/getopt.h \
   /usr/include/c++/4.2/cctype /usr/include/ctype.h \
-  /usr/include/c++/4.2/bits/stringfwd.h \
   /usr/include/c++/4.2/bits/postypes.h /usr/include/c++/4.2/cwchar \
   /usr/include/c++/4.2/ctime /usr/include/bits/wchar.h \
   /usr/include/stdint.h /usr/include/c++/4.2/bits/functexcept.h \
-  /usr/include/c++/4.2/exception_defines.h /usr/include/c++/4.2/exception \
-  /usr/include/c++/4.2/bits/char_traits.h \
-  /usr/include/c++/4.2/bits/stl_algobase.h /usr/include/c++/4.2/climits \
-  /usr/lib/gcc/i486-linux-gnu/4.2.3/include/limits.h \
-  /usr/lib/gcc/i486-linux-gnu/4.2.3/include/syslimits.h \
-  /usr/include/limits.h /usr/include/bits/posix1_lim.h \
-  /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
-  /usr/include/bits/posix2_lim.h /usr/include/bits/xopen_lim.h \
+  /usr/include/c++/4.2/exception_defines.h \
   /usr/include/c++/4.2/bits/stl_pair.h \
   /usr/include/c++/4.2/bits/cpp_type_traits.h \
   /usr/include/c++/4.2/ext/type_traits.h /usr/include/c++/4.2/utility \
@@ -59,25 +57,30 @@ DoxygenTranslator/src/DoxygenTranslator.o \
   /usr/include/c++/4.2/bits/stl_iterator_base_funcs.h \
   /usr/include/c++/4.2/bits/concept_check.h \
   /usr/include/c++/4.2/bits/stl_iterator.h \
-  /usr/include/c++/4.2/debug/debug.h \
-  /usr/include/c++/4.2/bits/localefwd.h \
-  /usr/include/c++/4.2/bits/ios_base.h \
-  /usr/include/c++/4.2/ext/atomicity.h \
-  /usr/include/c++/4.2/i486-linux-gnu/bits/atomic_word.h \
-  /usr/include/c++/4.2/bits/locale_classes.h /usr/include/c++/4.2/string \
-  /usr/include/c++/4.2/memory /usr/include/c++/4.2/bits/allocator.h \
+  /usr/include/c++/4.2/debug/debug.h /usr/include/c++/4.2/memory \
+  /usr/include/c++/4.2/bits/allocator.h \
   /usr/include/c++/4.2/i486-linux-gnu/bits/c++allocator.h \
   /usr/include/c++/4.2/ext/new_allocator.h /usr/include/c++/4.2/new \
+  /usr/include/c++/4.2/exception \
   /usr/include/c++/4.2/bits/stl_construct.h \
   /usr/include/c++/4.2/bits/stl_uninitialized.h \
   /usr/include/c++/4.2/bits/stl_raw_storage_iter.h \
   /usr/include/c++/4.2/limits /usr/include/c++/4.2/bits/ostream_insert.h \
   /usr/include/c++/4.2/bits/stl_function.h \
-  /usr/include/c++/4.2/bits/basic_string.h /usr/include/c++/4.2/algorithm \
-  /usr/include/c++/4.2/bits/stl_algo.h \
+  /usr/include/c++/4.2/bits/basic_string.h \
+  /usr/include/c++/4.2/ext/atomicity.h \
+  /usr/include/c++/4.2/i486-linux-gnu/bits/atomic_word.h \
+  /usr/include/c++/4.2/algorithm /usr/include/c++/4.2/bits/stl_algo.h \
   /usr/include/c++/4.2/bits/stl_heap.h \
   /usr/include/c++/4.2/bits/stl_tempbuf.h \
-  /usr/include/c++/4.2/bits/basic_string.tcc \
+  /usr/include/c++/4.2/bits/basic_string.tcc /usr/include/c++/4.2/list \
+  /usr/include/c++/4.2/bits/stl_list.h /usr/include/c++/4.2/bits/list.tcc \
+  DoxygenTranslator/src/DoxygenEntity.h \
+  DoxygenTranslator/src/DoxygenTranslator.h /usr/include/c++/4.2/iostream \
+  /usr/include/c++/4.2/ostream /usr/include/c++/4.2/ios \
+  /usr/include/c++/4.2/bits/localefwd.h \
+  /usr/include/c++/4.2/bits/ios_base.h \
+  /usr/include/c++/4.2/bits/locale_classes.h \
   /usr/include/c++/4.2/streambuf /usr/include/c++/4.2/bits/streambuf.tcc \
   /usr/include/c++/4.2/bits/basic_ios.h \
   /usr/include/c++/4.2/bits/streambuf_iterator.h \
@@ -94,15 +97,12 @@ DoxygenTranslator/src/DoxygenTranslator.o \
   /usr/include/c++/4.2/typeinfo /usr/include/c++/4.2/istream \
   /usr/include/c++/4.2/bits/istream.tcc /usr/include/c++/4.2/fstream \
   /usr/include/c++/4.2/i486-linux-gnu/bits/basic_file.h \
-  /usr/include/c++/4.2/bits/fstream.tcc /usr/include/c++/4.2/list \
-  /usr/include/c++/4.2/bits/stl_list.h /usr/include/c++/4.2/bits/list.tcc \
-  DoxygenTranslator/src/DoxygenEntity.h DoxygenTranslator/src/TokenList.h \
-  DoxygenTranslator/src/Token.h DoxygenTranslator/src/JavaDocConverter.h \
-  DoxygenTranslator/src/DoxygenTranslator.h
+  /usr/include/c++/4.2/bits/fstream.tcc DoxygenTranslator/src/TokenList.h \
+  DoxygenTranslator/src/Token.h DoxygenTranslator/src/JavaDocConverter.h
 
 DoxygenTranslator/src/DoxygenParser.h:
 
-/usr/include/c++/4.2/cstdlib:
+/usr/include/c++/4.2/string:
 
 /usr/include/c++/4.2/i486-linux-gnu/bits/c++config.h:
 
@@ -120,10 +120,44 @@ DoxygenTranslator/src/DoxygenParser.h:
 
 /usr/include/c++/4.2/i486-linux-gnu/bits/cpu_defines.h:
 
+/usr/include/c++/4.2/bits/stringfwd.h:
+
+/usr/include/c++/4.2/bits/char_traits.h:
+
+/usr/include/c++/4.2/cstring:
+
 /usr/include/c++/4.2/cstddef:
 
 /usr/lib/gcc/i486-linux-gnu/4.2.3/include/stddef.h:
 
+/usr/include/string.h:
+
+/usr/include/xlocale.h:
+
+/usr/include/c++/4.2/bits/stl_algobase.h:
+
+/usr/include/c++/4.2/climits:
+
+/usr/lib/gcc/i486-linux-gnu/4.2.3/include/limits.h:
+
+/usr/lib/gcc/i486-linux-gnu/4.2.3/include/syslimits.h:
+
+/usr/include/limits.h:
+
+/usr/include/bits/posix1_lim.h:
+
+/usr/include/bits/local_lim.h:
+
+/usr/include/linux/limits.h:
+
+/usr/include/bits/posix2_lim.h:
+
+/usr/include/bits/xopen_lim.h:
+
+/usr/include/bits/stdio_lim.h:
+
+/usr/include/c++/4.2/cstdlib:
+
 /usr/include/stdlib.h:
 
 /usr/include/bits/waitflags.h:
@@ -134,8 +168,6 @@ DoxygenTranslator/src/DoxygenParser.h:
 
 /usr/include/bits/endian.h:
 
-/usr/include/xlocale.h:
-
 /usr/include/sys/types.h:
 
 /usr/include/bits/types.h:
@@ -158,20 +190,10 @@ DoxygenTranslator/src/DoxygenParser.h:
 
 /usr/include/alloca.h:
 
-/usr/include/c++/4.2/iostream:
-
-/usr/include/c++/4.2/ostream:
-
-/usr/include/c++/4.2/ios:
-
 /usr/include/c++/4.2/iosfwd:
 
 /usr/include/c++/4.2/i486-linux-gnu/bits/c++locale.h:
 
-/usr/include/c++/4.2/cstring:
-
-/usr/include/string.h:
-
 /usr/include/c++/4.2/cstdio:
 
 /usr/include/stdio.h:
@@ -184,8 +206,6 @@ DoxygenTranslator/src/DoxygenParser.h:
 
 /usr/lib/gcc/i486-linux-gnu/4.2.3/include/stdarg.h:
 
-/usr/include/bits/stdio_lim.h:
-
 /usr/include/bits/sys_errlist.h:
 
 /usr/include/c++/4.2/clocale:
@@ -234,8 +254,6 @@ DoxygenTranslator/src/DoxygenParser.h:
 
 /usr/include/ctype.h:
 
-/usr/include/c++/4.2/bits/stringfwd.h:
-
 /usr/include/c++/4.2/bits/postypes.h:
 
 /usr/include/c++/4.2/cwchar:
@@ -250,30 +268,6 @@ DoxygenTranslator/src/DoxygenParser.h:
 
 /usr/include/c++/4.2/exception_defines.h:
 
-/usr/include/c++/4.2/exception:
-
-/usr/include/c++/4.2/bits/char_traits.h:
-
-/usr/include/c++/4.2/bits/stl_algobase.h:
-
-/usr/include/c++/4.2/climits:
-
-/usr/lib/gcc/i486-linux-gnu/4.2.3/include/limits.h:
-
-/usr/lib/gcc/i486-linux-gnu/4.2.3/include/syslimits.h:
-
-/usr/include/limits.h:
-
-/usr/include/bits/posix1_lim.h:
-
-/usr/include/bits/local_lim.h:
-
-/usr/include/linux/limits.h:
-
-/usr/include/bits/posix2_lim.h:
-
-/usr/include/bits/xopen_lim.h:
-
 /usr/include/c++/4.2/bits/stl_pair.h:
 
 /usr/include/c++/4.2/bits/cpp_type_traits.h:
@@ -294,18 +288,6 @@ DoxygenTranslator/src/DoxygenParser.h:
 
 /usr/include/c++/4.2/debug/debug.h:
 
-/usr/include/c++/4.2/bits/localefwd.h:
-
-/usr/include/c++/4.2/bits/ios_base.h:
-
-/usr/include/c++/4.2/ext/atomicity.h:
-
-/usr/include/c++/4.2/i486-linux-gnu/bits/atomic_word.h:
-
-/usr/include/c++/4.2/bits/locale_classes.h:
-
-/usr/include/c++/4.2/string:
-
 /usr/include/c++/4.2/memory:
 
 /usr/include/c++/4.2/bits/allocator.h:
@@ -316,6 +298,8 @@ DoxygenTranslator/src/DoxygenParser.h:
 
 /usr/include/c++/4.2/new:
 
+/usr/include/c++/4.2/exception:
+
 /usr/include/c++/4.2/bits/stl_construct.h:
 
 /usr/include/c++/4.2/bits/stl_uninitialized.h:
@@ -330,6 +314,10 @@ DoxygenTranslator/src/DoxygenParser.h:
 
 /usr/include/c++/4.2/bits/basic_string.h:
 
+/usr/include/c++/4.2/ext/atomicity.h:
+
+/usr/include/c++/4.2/i486-linux-gnu/bits/atomic_word.h:
+
 /usr/include/c++/4.2/algorithm:
 
 /usr/include/c++/4.2/bits/stl_algo.h:
@@ -340,6 +328,28 @@ DoxygenTranslator/src/DoxygenParser.h:
 
 /usr/include/c++/4.2/bits/basic_string.tcc:
 
+/usr/include/c++/4.2/list:
+
+/usr/include/c++/4.2/bits/stl_list.h:
+
+/usr/include/c++/4.2/bits/list.tcc:
+
+DoxygenTranslator/src/DoxygenEntity.h:
+
+DoxygenTranslator/src/DoxygenTranslator.h:
+
+/usr/include/c++/4.2/iostream:
+
+/usr/include/c++/4.2/ostream:
+
+/usr/include/c++/4.2/ios:
+
+/usr/include/c++/4.2/bits/localefwd.h:
+
+/usr/include/c++/4.2/bits/ios_base.h:
+
+/usr/include/c++/4.2/bits/locale_classes.h:
+
 /usr/include/c++/4.2/streambuf:
 
 /usr/include/c++/4.2/bits/streambuf.tcc:
@@ -384,18 +394,8 @@ DoxygenTranslator/src/DoxygenParser.h:
 
 /usr/include/c++/4.2/bits/fstream.tcc:
 
-/usr/include/c++/4.2/list:
-
-/usr/include/c++/4.2/bits/stl_list.h:
-
-/usr/include/c++/4.2/bits/list.tcc:
-
-DoxygenTranslator/src/DoxygenEntity.h:
-
 DoxygenTranslator/src/TokenList.h:
 
 DoxygenTranslator/src/Token.h:
 
 DoxygenTranslator/src/JavaDocConverter.h:
-
-DoxygenTranslator/src/DoxygenTranslator.h:
diff --git a/Source/DoxygenTranslator/src/.deps/Token.Po b/Source/DoxygenTranslator/src/.deps/Token.Po
index 9a4bb90f5..dbfe541b1 100644
--- a/Source/DoxygenTranslator/src/.deps/Token.Po
+++ b/Source/DoxygenTranslator/src/.deps/Token.Po
@@ -72,27 +72,7 @@ DoxygenTranslator/src/Token.o DoxygenTranslator/src/Token.o:  \
   /usr/include/c++/4.2/algorithm /usr/include/c++/4.2/bits/stl_algo.h \
   /usr/include/c++/4.2/bits/stl_heap.h \
   /usr/include/c++/4.2/bits/stl_tempbuf.h \
-  /usr/include/c++/4.2/bits/basic_string.tcc \
-  /usr/include/c++/4.2/iostream /usr/include/c++/4.2/ostream \
-  /usr/include/c++/4.2/ios /usr/include/c++/4.2/bits/localefwd.h \
-  /usr/include/c++/4.2/bits/ios_base.h \
-  /usr/include/c++/4.2/bits/locale_classes.h \
-  /usr/include/c++/4.2/streambuf /usr/include/c++/4.2/bits/streambuf.tcc \
-  /usr/include/c++/4.2/bits/basic_ios.h \
-  /usr/include/c++/4.2/bits/streambuf_iterator.h \
-  /usr/include/c++/4.2/bits/locale_facets.h /usr/include/c++/4.2/cwctype \
-  /usr/include/wctype.h \
-  /usr/include/c++/4.2/i486-linux-gnu/bits/ctype_base.h \
-  /usr/include/c++/4.2/i486-linux-gnu/bits/ctype_inline.h \
-  /usr/include/c++/4.2/bits/codecvt.h \
-  /usr/include/c++/4.2/i486-linux-gnu/bits/time_members.h \
-  /usr/include/c++/4.2/i486-linux-gnu/bits/messages_members.h \
-  /usr/include/c++/4.2/bits/basic_ios.tcc \
-  /usr/include/c++/4.2/bits/ostream.tcc /usr/include/c++/4.2/locale \
-  /usr/include/c++/4.2/bits/locale_facets.tcc \
-  /usr/include/c++/4.2/typeinfo /usr/include/c++/4.2/istream \
-  /usr/include/c++/4.2/bits/istream.tcc /usr/include/c++/4.2/list \
-  /usr/include/c++/4.2/bits/stl_list.h /usr/include/c++/4.2/bits/list.tcc
+  /usr/include/c++/4.2/bits/basic_string.tcc
 
 DoxygenTranslator/src/Token.h:
 
@@ -321,59 +301,3 @@ DoxygenTranslator/src/Token.h:
 /usr/include/c++/4.2/bits/stl_tempbuf.h:
 
 /usr/include/c++/4.2/bits/basic_string.tcc:
-
-/usr/include/c++/4.2/iostream:
-
-/usr/include/c++/4.2/ostream:
-
-/usr/include/c++/4.2/ios:
-
-/usr/include/c++/4.2/bits/localefwd.h:
-
-/usr/include/c++/4.2/bits/ios_base.h:
-
-/usr/include/c++/4.2/bits/locale_classes.h:
-
-/usr/include/c++/4.2/streambuf:
-
-/usr/include/c++/4.2/bits/streambuf.tcc:
-
-/usr/include/c++/4.2/bits/basic_ios.h:
-
-/usr/include/c++/4.2/bits/streambuf_iterator.h:
-
-/usr/include/c++/4.2/bits/locale_facets.h:
-
-/usr/include/c++/4.2/cwctype:
-
-/usr/include/wctype.h:
-
-/usr/include/c++/4.2/i486-linux-gnu/bits/ctype_base.h:
-
-/usr/include/c++/4.2/i486-linux-gnu/bits/ctype_inline.h:
-
-/usr/include/c++/4.2/bits/codecvt.h:
-
-/usr/include/c++/4.2/i486-linux-gnu/bits/time_members.h:
-
-/usr/include/c++/4.2/i486-linux-gnu/bits/messages_members.h:
-
-/usr/include/c++/4.2/bits/basic_ios.tcc:
-
-/usr/include/c++/4.2/bits/ostream.tcc:
-
-/usr/include/c++/4.2/locale:
-
-/usr/include/c++/4.2/bits/locale_facets.tcc:
-
-/usr/include/c++/4.2/typeinfo:
-
-/usr/include/c++/4.2/istream:
-
-/usr/include/c++/4.2/bits/istream.tcc:
-
-/usr/include/c++/4.2/list:
-
-/usr/include/c++/4.2/bits/stl_list.h:
-
-/usr/include/c++/4.2/bits/list.tcc:
diff --git a/Source/DoxygenTranslator/src/DoxygenEntity.cpp b/Source/DoxygenTranslator/src/DoxygenEntity.cpp
index 6b8755592..a2faf67db 100644
--- a/Source/DoxygenTranslator/src/DoxygenEntity.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenEntity.cpp
@@ -1,6 +1,6 @@
 #include "DoxygenEntity.h"
 #include <string>
-
+#include <iostream>
 /* Little data class for Doxygen Commands */
 
 
diff --git a/Source/DoxygenTranslator/src/DoxygenEntity.h b/Source/DoxygenTranslator/src/DoxygenEntity.h
index 0605b1cc9..4313bfb2a 100644
--- a/Source/DoxygenTranslator/src/DoxygenEntity.h
+++ b/Source/DoxygenTranslator/src/DoxygenEntity.h
@@ -1,8 +1,7 @@
 #ifndef DOXYGENENTITY_H_
 #define DOXYGENENTITY_H_
 
-#include <cstdlib>
-#include <iostream>
+
 #include <string>
 #include <list>
 
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.cpp b/Source/DoxygenTranslator/src/DoxygenParser.cpp
index 226c60720..920b7c794 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenParser.cpp
@@ -1,13 +1,5 @@
 #include "DoxygenParser.h"
-
-#include <cstdlib>
-#include <iostream>
-#include <fstream>
-#include <string>
-#include <list>
-#include "DoxygenEntity.h"
 #include "TokenList.h"
-#include "JavaDocConverter.h"
 #define SIMPLECOMMAND 1
 #define IGNOREDSIMPLECOMMAND 2
 #define COMMANDWORD 3
@@ -29,12 +21,6 @@
 #define  COMMAND  104
 using namespace std;
 
-//////////////////////////////////////////
-/*Set these to pick what internal functions
-to test. */
-
-//int testCommandParsingFunctions = 1;// not implemented
-
 
 DoxygenParser::DoxygenParser()
 {
@@ -44,7 +30,8 @@ DoxygenParser::~DoxygenParser()
 {
 }
 
-int noisy = 0; // set this to 1 for extra chatter from the parsing stage.
+//////////////////////////////////////////
+int noisy = 1; // set this to 1 for extra chatter from the parsing stage.
 int addCommand(string currCommand, TokenList &tokList,  list <DoxygenEntity> &aNewList);
 list <DoxygenEntity> parse(list<Token>::iterator endParsingIndex, TokenList &tokList);
 
@@ -101,32 +88,25 @@ string commandUniques[] = {"xrefitem", "arg", "ingroup", "par", "headerfile", "o
 		"subpage", "dotfile", "image", "addtogroup", "li"};
 
 
-/* Changes a string to all lower case*/
-string StringToLower(string stringToConvert)
-
-{
-
-   for(unsigned int i=0;i<stringToConvert.length();i++)
-   {
-   stringToConvert[i] = tolower(stringToConvert[i]);
-   }
-   return stringToConvert;//return the converted string
+/* Changes a string to all lower case */
+string StringToLower(string stringToConvert){
+   for(unsigned int i=0;i<stringToConvert.length();i++){
+	   stringToConvert[i] = tolower(stringToConvert[i]);
+	   }
+   return stringToConvert; //return the converted string
 }
 
 /* finds out if a command exists (is a possible command)
  * from the string array commandArray
  * returns -1 if no match is found */
 int findCommand(string smallString){
-
 	smallString = StringToLower(smallString);
 	int a;
 	for (int i = 0; i < sizeof(commandArray)/sizeof(*commandArray); i++){
 		if( (a = smallString.compare(commandArray[i])) == 0){
 			return 101 + i;
+			}
 		}
-
-
-	}
 	return -1;
 }
 
@@ -136,7 +116,6 @@ int findCommand(string smallString){
  */
 int isSectionIndicator(string smallString){
 	smallString = StringToLower(smallString);
-
 	for (int i = 0; i < sizeof( sectionIndicators)/sizeof(* sectionIndicators); i++){
 		if( smallString.compare( sectionIndicators[i]) == 0){
 			return 1;
@@ -145,29 +124,24 @@ int isSectionIndicator(string smallString){
 	return 0;
 }
 
-/* prints the parse tree
- *
- */
+/* prints the parse tree */
 void printTree( list <DoxygenEntity> &rootList){
-
-		list<DoxygenEntity>::iterator p = rootList.begin();
-		while (p != rootList.end()){
-			(*p).printEntity(0);
-			p++;
+	list<DoxygenEntity>::iterator p = rootList.begin();
+	while (p != rootList.end()){
+		(*p).printEntity(0);
+		p++;
 		}
-
-}
+	}
 
 /* Determines how a command should be handled (what group it belongs to
  * for parsing rules
  */
-
 int commandBelongs(string theCommand){
-	 string smallString = StringToLower(theCommand );
+	 string smallString = StringToLower(theCommand);
 	 //cout << " Looking for command " << theCommand << endl;
 	 int i = 0;
 	 for ( i = 0; i < sizeof(simpleCommands)/sizeof(*simpleCommands); i++){
-	 	if(smallString.compare(simpleCommands[i]) == 0){return SIMPLECOMMAND ;}
+	 	if(smallString.compare(simpleCommands[i]) == 0){return SIMPLECOMMAND;}
 	 	}
 	 for ( i = 0; i < sizeof(ignoredSimpleCommands)/sizeof(*ignoredSimpleCommands); i++){
 	 	if(smallString.compare(ignoredSimpleCommands[i]) == 0){return IGNOREDSIMPLECOMMAND;}
@@ -187,7 +161,6 @@ int commandBelongs(string theCommand){
 	 for ( i = 0; i <  sizeof(commandParagraph)/sizeof(*commandParagraph); i++){
 	 	if(smallString.compare( commandParagraph[i]) == 0){return COMMANDPARAGRAPH;}
 	 	} 
-	 /* IgnoreCommandParagraph */
 	 for ( i = 0; i < sizeof(ignoreCommandParagraphs)/sizeof(*ignoreCommandParagraphs); i++){
 	 	if(smallString.compare( ignoreCommandParagraphs[i]) == 0){return IGNORECOMMANDPARAGRAPH;}
 	 	} 
@@ -211,16 +184,14 @@ int commandBelongs(string theCommand){
 	 	} 
 	 for ( i = 0; i < sizeof(commandUniques)/sizeof(*commandUniques); i++){
 	 	if(smallString.compare( commandUniques[i]) == 0){return COMMANDUNIQUE;}
-	 	} 
-
-	 	return 0;
-	 
+	 	}
+	 	return 0; 
 }
+
 /* Returns the next word ON THE CURRENT LINE ONLY
  * if a new line is encountered, returns a blank string.
  * Updates the index it is given if success.
  */
-
 string getNextWord(TokenList &tokList){
 	 Token nextToken = tokList.peek();
 	 if (nextToken.tokenType == PLAINSTRING ){
@@ -234,17 +205,17 @@ string getNextWord(TokenList &tokList){
  * an iterator.
  */
 list<Token>::iterator getOneLine(TokenList &tokList){
-	 list<Token>::iterator endOfParagraph = tokList.iteratorCopy();
-	 while(endOfParagraph != tokList.end()){
-		 if ((* endOfParagraph).tokenType == END_LINE){
-			 return endOfParagraph;
+	 list<Token>::iterator endOfLine = tokList.iteratorCopy();
+	 while(endOfLine!= tokList.end()){
+		 if ((* endOfLine).tokenType == END_LINE){
+			 endOfLine++;
+			 return endOfLine;
+			 }
+		 endOfLine++;
 		 }
-		 endOfParagraph++;
-	 }
+	 cout << "REACHED END" << endl;
 	return tokList.end();
-}
-
-
+	}
 
 /* Returns a properly formatted string
 * up til ANY command or end of paragraph is encountered.
@@ -256,12 +227,11 @@ string getStringTilCommand(TokenList &tokList){
 		 Token currentToken = tokList.next();
 		 if(currentToken.tokenType == PLAINSTRING) {
 			 description = description + currentToken.tokenString + " ";
-		 }
+			 }
 		 else if (tokList.peek().tokenType == END_LINE) break;
-	 }
-	 
+		 }
 	return description;
-}
+	}
 
 /* Returns a properly formatted string
 * up til the command specified is encountered
@@ -274,69 +244,67 @@ string getStringTilEndCommand(string theCommand, TokenList &tokList){
 	 while(tokList.peek().tokenString.compare(theCommand) != 0 ){
 		 Token currentToken = tokList.next();
 		 description = description + currentToken.tokenString + " ";
-
-	 }
-	 
+		 }
 	return description;
-}
+	}
 
 /* Returns the end of a Paragraph as an iterator-
 * Paragraph is defined in Doxygen to be a paragraph of text
 * seperate by either a structural command or a blank line
 */
-
 list<Token>::iterator getEndOfParagraph(TokenList &tokList){
 	 list<Token>::iterator endOfParagraph = tokList.iteratorCopy();
 	 while(endOfParagraph != tokList.end()){
-		if ((* endOfParagraph).tokenType == COMMAND){
-			 if(isSectionIndicator((* endOfParagraph).tokenString)) return endOfParagraph;
-			 else endOfParagraph++;
-		 }
-		else if((* endOfParagraph).tokenType == PLAINSTRING) {
-			 endOfParagraph++;
-		 }
-		 else if ((* endOfParagraph).tokenType == END_LINE){
+		if ((* endOfParagraph).tokenType == END_LINE){
 			 endOfParagraph++;
 			 if ((* endOfParagraph).tokenType == END_LINE){
 				 endOfParagraph++;
+				 cout << "ENCOUNTERED END OF PARA" << endl;
 				 return endOfParagraph;
+				 }
 			 }
-		 }
-
+		else if ((* endOfParagraph).tokenType == COMMAND){
+			 if(isSectionIndicator((* endOfParagraph).tokenString)) return endOfParagraph;
+			 else endOfParagraph++;
+			 }
+		else if((* endOfParagraph).tokenType == PLAINSTRING) {
+			 endOfParagraph++;
+			 }
+		else return tokList.end();
+		}
+	 return tokList.end();
 	 }
-	 
-	return tokList.end();
-
-}
 
 /* Returns the end of a section, defined as the first blank line OR first encounter of the same 
 * command. Example of this behaviour is \arg
+* if no end is encountered, returns the last token of the list.
 */
-
 list<Token>::iterator getEndOfSection(string theCommand, TokenList &tokList){
 	 list<Token>::iterator endOfParagraph = tokList.iteratorCopy();
 	 while(endOfParagraph != tokList.end()){
 		if ((* endOfParagraph).tokenType == COMMAND){
 			 if(theCommand.compare((*endOfParagraph).tokenString) == 0) return endOfParagraph;
 			 else endOfParagraph++;
-		 }
+			 }
 		else if((* endOfParagraph).tokenType == PLAINSTRING) {
 			 endOfParagraph++;
-		 }
+			 }
 		 else if ((* endOfParagraph).tokenType == END_LINE){
 			 endOfParagraph++;
 			 if ((* endOfParagraph).tokenType == END_LINE){
 				 endOfParagraph++;
 				 return endOfParagraph;
+				 }
 			 }
-		 }
-
+		}
+	 return tokList.end();
 	 }
-}
+
 /* This method is for returning the end of a specific form of doxygen command
  * that begins with a \command and ends in \endcommand
  * such as \code and \endcode. The proper usage is
  * progressTilEndCommand("endcode", tokenList);
+ * If the end is never encountered, it returns the end of the list.
  */
 list<Token>::iterator getEndCommand(string theCommand, TokenList &tokList){
 	list<Token>::iterator endOfCommand = tokList.iteratorCopy();
@@ -354,11 +322,11 @@ list<Token>::iterator getEndCommand(string theCommand, TokenList &tokList){
 
 /* A specialty method for commands such as \arg that end at the end of a paragraph OR when another \arg is encountered
  */
-
+//TODO getTilAnyCommand
 list<Token>::iterator getTilAnyCommand(string theCommand, TokenList &tokList){
 	list<Token>::iterator anIterator;
 	return anIterator;
-}
+	}
 
 
 
@@ -369,21 +337,19 @@ list<Token>::iterator getTilAnyCommand(string theCommand, TokenList &tokList){
  *  \n \\ \@ \& \$ \# \< \> \%
  */
  int addSimpleCommand(string theCommand, list <DoxygenEntity> &doxyList){
-	 
 		if (noisy) cout << "Parsing " << theCommand << endl;
 		doxyList.push_back(DoxygenEntity(theCommand));
 		return 1;
-}
+		}
  
  /* NOT INCLUDED Simple Commands
   * Format: @command
   * Plain commands, such as newline etc, they contain no other data
   */
  int ignoreSimpleCommand(string theCommand, list <DoxygenEntity> &doxyList){
-	 
 		if (noisy) cout << "Not Adding " << theCommand << endl;
 		return 1;
-}
+		}
  
  /* CommandWord
   * Format: @command <word>
@@ -397,10 +363,11 @@ list<Token>::iterator getTilAnyCommand(string theCommand, TokenList &tokList){
 	if (!name.empty()){ 
 		doxyList.push_back(DoxygenEntity(theCommand, name));
 		return 1;
-	}
+		}
 	else cout << "No word followed " << theCommand <<  " command. Not added" << endl;
 	return 0;
-}
+	}
+ 
  /* NOT INCLUDED CommandWord
   * Format: @command <word>
   * Commands with a single WORD after then such as @b
@@ -411,10 +378,10 @@ list<Token>::iterator getTilAnyCommand(string theCommand, TokenList &tokList){
 	string name = getNextWord(tokList);
 	if (!name.empty()){ 
 		return 1;
-	}
+		}
 	else cout << "WARNING: No word followed " << theCommand <<  " command." << endl;
 	return 0;
-}
+	}
  
  /* CommandLine
   * Format: @command (line)
@@ -424,12 +391,11 @@ list<Token>::iterator getTilAnyCommand(string theCommand, TokenList &tokList){
  int addCommandLine(string theCommand, TokenList &tokList, list <DoxygenEntity> &doxyList){
 	if (noisy) cout << "Parsing " << theCommand << endl;
 	list<Token>::iterator endOfLine = getOneLine(tokList);
-		list <DoxygenEntity> aNewList;
-		aNewList =  parse(endOfLine, tokList);
-		doxyList.push_back( DoxygenEntity(theCommand, aNewList));
-		return 1;
-
-}
+	list <DoxygenEntity> aNewList;
+	aNewList =  parse(endOfLine, tokList);
+	doxyList.push_back( DoxygenEntity(theCommand, aNewList));
+	return 1;
+	}
  
  /* NOT INCLUDED CommandLine
   * Format: @command (line)
@@ -452,14 +418,12 @@ list<Token>::iterator getTilAnyCommand(string theCommand, TokenList &tokList){
  int addCommandParagraph(string theCommand, TokenList &tokList, list <DoxygenEntity> &doxyList){
 	if (noisy) cout << "Parsing " << theCommand << endl;
 	list<Token>::iterator endOfParagraph = getEndOfParagraph(tokList);
-	//if(!restOfParagraph.empty()){
 	list <DoxygenEntity> aNewList;
 	aNewList =  parse(endOfParagraph, tokList);
 	doxyList.push_back( DoxygenEntity(theCommand, aNewList));
 	return 1;
-	//	}
-	//else cout << "No line followed " << theCommand <<  " command. Not added" << endl;
-}
+	}
+ 
  /* CommandParagraph
   * Format: @command {paragraph}
   * Commands with a single LINE after then such as @var
@@ -469,9 +433,9 @@ list<Token>::iterator getTilAnyCommand(string theCommand, TokenList &tokList){
 	if (noisy) cout << "Not Adding " << theCommand << endl;
 	list<Token>::iterator endOfParagraph = getEndOfParagraph(tokList);
 	tokList.setIterator(endOfParagraph);
-	//else cout << "WARNING: No line followed " << theCommand <<  " command." << endl;
 	return 1;
 }
+ 
  /* Command EndCommand
   * Format: @command and ends at @endcommand
   * Commands that take in a block of text such as @code
@@ -479,13 +443,12 @@ list<Token>::iterator getTilAnyCommand(string theCommand, TokenList &tokList){
   * "verbatim", "xmlonly", "cond", "if", "ifnot", "link"
   * Returns 1 if success, 0 if the endcommand is never encountered.
   */
- 
  int addCommandEndCommand(string theCommand, TokenList &tokList, list <DoxygenEntity> &doxyList){
 	  if (noisy) cout << "Not Adding " << theCommand << endl;
 	  string description = getStringTilEndCommand( "end" + theCommand, tokList);
 	  doxyList.push_back(DoxygenEntity(theCommand, description));
 	  return 1;
- }
+	  }
  
  /* CommandWordParagraph
   * Format: @command <word> {paragraph}
@@ -499,14 +462,14 @@ list<Token>::iterator getTilAnyCommand(string theCommand, TokenList &tokList){
 		cout << "No word followed " << theCommand <<  " command. Not added" << endl;
 		return 0;
 		}
-	  list<Token>::iterator endOfParagraph = getEndOfParagraph(tokList);
-	    //if(!restOfParagraph.empty()){
-		list <DoxygenEntity> aNewList;
-		aNewList =  parse(endOfParagraph, tokList);
-		aNewList.push_front(DoxygenEntity("plainstring", name));
-		doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-	return 0;
- }
+	list<Token>::iterator endOfParagraph = getEndOfParagraph(tokList);
+	list <DoxygenEntity> aNewList;
+	aNewList =  parse(endOfParagraph, tokList);
+	aNewList.push_front(DoxygenEntity("plainstring", name));
+	doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+	return 1;
+	}
+ 
  /* CommandWordLine
   * Format: @command <word> (line)
   * Commands such as param
@@ -549,7 +512,7 @@ list<Token>::iterator getTilAnyCommand(string theCommand, TokenList &tokList){
 	if (!headername.empty()) aNewList.push_back(DoxygenEntity("plainstring", headername));
 	doxyList.push_back(DoxygenEntity(theCommand, aNewList));
 	return 1;
- }
+	}
  
  /* Command Optional Word
   * Format: @command [<word>]
@@ -564,13 +527,17 @@ list<Token>::iterator getTilAnyCommand(string theCommand, TokenList &tokList){
  }
 
  /* Commands that should not be encountered (such as PHP only)
+  * goes til the end of line then returns
   */
  int addCommandErrorThrow(string theCommand, TokenList &tokList, list <DoxygenEntity> &doxyList){
 	  cout << "Encountered :" << theCommand << endl;
 	  cout << "This command should not have been encountered. Behaviour past this may be unpredictable " << endl;
+	  list<Token>::iterator endOfLine = getOneLine(tokList);
+	  tokList.setIterator(endOfLine);
+	  return 0;
  }
 
-
+/* Adds the unique commands- different process for each unique command */
  int addCommandUnique(string theCommand, TokenList &tokList, list <DoxygenEntity> &doxyList){
 	  list <DoxygenEntity> aNewList;
 	  if (theCommand.compare("arg") == 0 || theCommand.compare("li") == 0){
@@ -578,8 +545,7 @@ list<Token>::iterator getTilAnyCommand(string theCommand, TokenList &tokList){
 			list <DoxygenEntity> aNewList;
 			aNewList =  parse(endOfSection, tokList);
 			doxyList.push_back( DoxygenEntity(theCommand, aNewList));
-	  }
-	  
+			}
 	  // \xrefitem <key> "(heading)" "(list title)" {text}
 	  else if (theCommand.compare("xrefitem") == 0){
 		  //TODO Implement xrefitem
@@ -587,7 +553,7 @@ list<Token>::iterator getTilAnyCommand(string theCommand, TokenList &tokList){
 			list<Token>::iterator endOfParagraph = getEndOfParagraph(tokList);
 			tokList.setIterator(endOfParagraph);
 		  return 1;
-	  }
+		  }
 	  // \ingroup (<groupname> [<groupname> <groupname>])
 	  else if (theCommand.compare("ingroup") == 0){
 		  string name = getNextWord(tokList);
@@ -598,7 +564,7 @@ list<Token>::iterator getTilAnyCommand(string theCommand, TokenList &tokList){
 		  if(!name.empty()) aNewList.push_back(DoxygenEntity("plainstring", name));
 		  doxyList.push_back(DoxygenEntity(theCommand, aNewList));
 		  return 1;
-	  }
+		  }
 	  // \par [(paragraph title)] { paragraph }
 	  else if (theCommand.compare("par") == 0){
 		  list<Token>::iterator endOfLine = getOneLine(tokList);
@@ -608,7 +574,7 @@ list<Token>::iterator getTilAnyCommand(string theCommand, TokenList &tokList){
 		  aNewList.splice(aNewList.end(), aNewList2);
 		  doxyList.push_back(DoxygenEntity(theCommand, aNewList));
 		  return 1; 
-	  }
+		  }
 	  // \headerfile <header-file> [<header-name>]
 	  else if (theCommand.compare("headerfile") == 0){
 		  list <DoxygenEntity> aNewList;
@@ -618,17 +584,18 @@ list<Token>::iterator getTilAnyCommand(string theCommand, TokenList &tokList){
 		  if(!name.empty()) aNewList.push_back(DoxygenEntity("plainstring", name));
 		  doxyList.push_back(DoxygenEntity(theCommand, aNewList));
 		  return 1;
-	  }
+		  }
 	  // \overload [(function declaration)]
 	  else if (theCommand.compare("overload") == 0){
 		  list<Token>::iterator endOfLine = getOneLine(tokList);
 		  if (endOfLine != tokList.current()){
-		  list <DoxygenEntity> aNewList;
-		  aNewList =  parse(endOfLine, tokList);
-		  doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-		  }
+		    list <DoxygenEntity> aNewList;
+		    aNewList =  parse(endOfLine, tokList);
+		    doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+		    }
 		  else doxyList.push_back(DoxygenEntity(theCommand));
-	  }
+		  return 1;
+		  }
 	  // \weakgroup <name> [(title)]
 	  else if (theCommand.compare("weakgroup") == 0){
 		    if (noisy) cout << "Parsing " << theCommand << endl;
@@ -641,35 +608,35 @@ list<Token>::iterator getTilAnyCommand(string theCommand, TokenList &tokList){
 			list<Token>::iterator endOfLine = getOneLine(tokList);
 			if (endOfLine != tokList.current()) {
 				aNewList =  parse(endOfLine, tokList);
-			}
+				}
 			aNewList.push_front(DoxygenEntity("plainstring", name));
 			doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-	  }
+			}
 	  // \ref <name> ["(text)"]
 	  else if (theCommand.compare("ref") == 0){
 		  //TODO Implement ref
 			if (noisy) cout << "Not Adding " << theCommand << endl;
 			list<Token>::iterator endOfParagraph = getEndOfParagraph(tokList);
 			tokList.setIterator(endOfParagraph);
-	  }
+			}
 	  // \subpage <name> ["(text)"]
 	  else if (theCommand.compare("subpage") == 0){
 		  //TODO implement subpage
 			if (noisy) cout << "Not Adding " << theCommand << endl;
 			list<Token>::iterator endOfParagraph = getEndOfParagraph(tokList);
 			tokList.setIterator(endOfParagraph);
-	  }
+			}
 	  // \dotfile <file> ["caption"]
 	  else if (theCommand.compare("dotfile") == 0){
 		  //TODO implement dotfile
 			if (noisy) cout << "Not Adding " << theCommand << endl;
 			list<Token>::iterator endOfParagraph = getEndOfParagraph(tokList);
 			tokList.setIterator(endOfParagraph);
-	  }
+			}
 	  // \image <format> <file> ["caption"] [<sizeindication>=<size>]
 	  else if (theCommand.compare("image") == 0){
 		  //todo implement image
-	  } 
+		  } 
 	  // \addtogroup <name> [(title)]
 	  else if (theCommand.compare("addtogroup") == 0){
 		    if (noisy) cout << "Parsing " << theCommand << endl;
@@ -682,12 +649,12 @@ list<Token>::iterator getTilAnyCommand(string theCommand, TokenList &tokList){
 			list<Token>::iterator endOfLine = getOneLine(tokList);
 			if (endOfLine != tokList.current()) {
 				aNewList =  parse(endOfLine, tokList);
-			}
+				}
 			aNewList.push_front(DoxygenEntity("plainstring", name));
 			doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+			}
+	  return 0;
 	  }
-
- }
  
 /* The actual "meat" of the doxygen parser. This is not yet fully implemented
  * with my current design- however the skeletal outline is contained in
@@ -697,13 +664,12 @@ list<Token>::iterator getTilAnyCommand(string theCommand, TokenList &tokList){
 
 int addCommand(string commandString, TokenList &tokList,list <DoxygenEntity> &doxyList){
 	 string theCommand = StringToLower(commandString);
-
 	 if (theCommand.compare("plainstring") == 0){
 	 		string nextPhrase = getStringTilCommand( tokList);
 	 		if (noisy) cout << "Parsing plain string :" << nextPhrase << endl;
 	 		doxyList.push_back(DoxygenEntity("plainstring", nextPhrase ));
 	 		return 1;
-	 }
+	 		}
 	 int commandNumber = commandBelongs(theCommand);
 	 if (commandNumber == SIMPLECOMMAND){
 	 	return addSimpleCommand(theCommand, doxyList);
@@ -751,8 +717,8 @@ int addCommand(string commandString, TokenList &tokList,list <DoxygenEntity> &do
 		return addCommandUnique(theCommand, tokList, doxyList);
 	 	}
 	 	
-	 	return 0;
-}
+	 return 0;
+	 }
 
 list<DoxygenEntity> parse(list<Token>::iterator endParsingIndex, TokenList &tokList){
 	list <DoxygenEntity> aNewList;
@@ -762,36 +728,64 @@ list<DoxygenEntity> parse(list<Token>::iterator endParsingIndex, TokenList &tokL
 		if(noisy) cout << "Parsing for phrase starting in:" << currToken.toString() << endl;
 		if(currToken.tokenType == END_LINE ){
 			tokList.next();
-		}
+			}
 		else if(currToken.tokenType == COMMAND){
 			currCommand = findCommand(currToken.tokenString);
-			tokList.next();
-			if (currCommand < 0 ){ if(noisy) cout << "BAD COMMAND: " << currToken.tokenString << endl;}
+			if (currCommand < 0 ){
+				if(noisy) cout << "Unidentified Command " << currToken.tokenString << endl;
+				tokList.next();
+				addCommand(string("plainstring"), tokList, aNewList);}
 				//cout << "Command: " << currWord << " " << currCommand << endl;
-
-			else addCommand(currToken.tokenString, tokList,  aNewList);
-		}
+			else { tokList.next();
+			  addCommand(currToken.tokenString, tokList,  aNewList);
+			  }
+			}
 		else if (currToken.tokenType == PLAINSTRING){
 			addCommand(string("plainstring"), tokList, aNewList);
+			}
+		else break;
 		}
-
-		
+	return aNewList;
 	}
 
+list<DoxygenEntity> parseRoot(list<Token>::iterator endParsingIndex, TokenList &tokList){
+	list <DoxygenEntity> aNewList;
+	int currCommand;
+	while (tokList.current() != endParsingIndex){ 
+		Token currToken = tokList.peek();
+		if(noisy) cout << "Parsing for phrase starting in:" << currToken.toString() << endl;
+		if(currToken.tokenType == END_LINE ){
+			tokList.next();
+			}
+		else if(currToken.tokenType == COMMAND){
+			currCommand = findCommand(currToken.tokenString);
+			if (currCommand < 0 ){ 
+				if(noisy) cout << "Unidentified Command " << currToken.tokenString << endl;
+				tokList.next();
+				addCommand(string("details"), tokList, aNewList);}
+				//cout << "Command: " << currWord << " " << currCommand << endl;
+			else { tokList.next();
+			  addCommand(currToken.tokenString, tokList,  aNewList);
+			  }
+			}
+		else if (currToken.tokenType == PLAINSTRING){
+			addCommand(string("details"), tokList, aNewList);
+			}
+		}
 	return aNewList;
-}
+	}
 
 list<DoxygenEntity> DoxygenParser::createTree(string doxygenBlob){
 	TokenList tokList = TokenList(doxygenBlob);
 	if(noisy) {
 		cout << "---TOKEN LIST---" << endl;
 		tokList.printList();
-	}
+		}
 	list <DoxygenEntity> rootList;
-	rootList = parse( tokList.end(), tokList);
+	rootList = parseRoot( tokList.end(), tokList);
 	if(noisy) {
 		cout << "PARSED LIST" << endl;
 		printTree(rootList);
-	}
+		}
 	return rootList;
 }
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.h b/Source/DoxygenTranslator/src/DoxygenParser.h
index 776fcf123..638fdab72 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.h
+++ b/Source/DoxygenTranslator/src/DoxygenParser.h
@@ -1,13 +1,8 @@
 #ifndef DOXYGENPARSER_H_
 #define DOXYGENPARSER_H_
-#include <cstdlib>
-#include <iostream>
-#include <fstream>
 #include <string>
 #include <list>
 #include "DoxygenEntity.h"
-#include "TokenList.h"
-#include "JavaDocConverter.h"
 class DoxygenParser
 {
 public:
diff --git a/Source/DoxygenTranslator/src/DoxygenTranslator.cpp b/Source/DoxygenTranslator/src/DoxygenTranslator.cpp
index 191057ae7..a1789eb74 100644
--- a/Source/DoxygenTranslator/src/DoxygenTranslator.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenTranslator.cpp
@@ -11,6 +11,7 @@
 #include "TokenList.h"
 #include "JavaDocConverter.h"
 
+
 DoxygenParser doxyParse;
 JavaDocConverter jDC;
 
@@ -27,7 +28,7 @@ DoxygenTranslator::~DoxygenTranslator(){
 char *DoxygenTranslator::convert(char* doxygenBlob, char* option){
 	
 	list <DoxygenEntity> rootList = doxyParse.createTree(string(doxygenBlob));
-	rootList = doxyParse.createTree(string(doxygenBlob));
+	
 	string returnedString;
 	if(strcmp(option, "JAVADOC") == 0){
 	    returnedString = jDC.convertToJavaDoc(rootList);
@@ -39,3 +40,32 @@ char *DoxygenTranslator::convert(char* doxygenBlob, char* option){
 	return nonConstString;
 }
 
+int testCommands(){
+	string exampleArray[] = {
+	"/**\n * \n * Random Line \n * \\@ \n * Random Line After */",
+	"/**\n * \n * Random Line Before \n * \\b bold \n * Random Line After */",
+	"/**\n * \n * Random Line \n * \\copydoc bold \n * Random Line After */",
+	"/**\n * \n * Random Line \n * \n * \\addindex An Entire Line\n * \\addindex An Entire Line\n * Random Line After */",
+	"/**\n * \n * Random Line \n * \n * \\return An Entire Paragraph \n * Including This Line \n * \n * Random Line After */",
+	"/**\n * \n * Random Line \n * \\return An Entire Paragraph \n * Including This Line \n * \\author Shouldn't be part of return */",
+	"/**\n * \n * Random Line \n * \\code this should continue \n * until here \\endcode \n * Random Line After */",
+	"/**\n * \n * Random Line \n * \\param singleword then the rest of \n *  the description \n * \n * Random Line After */",
+	"/**\n * \n * Random Line \n * \\page  singleword this should go til here \n * but not this */",
+	"/**\n * \n * Random Line \n * \\page  singleword this should go til here \n * but not this */",
+	"/**\n * \n * Random Line \n * \\category  singleword \n * but not this */",
+	"/**\n * \n * Random Line \n * \\category  singleword oneword \n * but not this */",
+	"/**\n * \n * Random Line \n * \\category  singleword oneword twoword \n * but not this */",
+	"/**\n * \n * Random Line \n * \\dir singleword \n * but not this */",
+	"/**\n * \n * Random Line \n * \\dir \n * but not this */",
+	"/**\n * \n * Random Line \n * \\fakecommand details \n * but not this */"
+	};
+	//string exampleArrayUniques = {};
+	DoxygenTranslator dT = DoxygenTranslator();
+	for (int i = 0; i < 16; i ++ ){
+		cout << "---ORIGINAL DOXYGEN--- " << endl << exampleArray[i] << endl;
+		char *nonConstString = (char *)malloc(exampleArray[i].length()+1);
+		strcpy(nonConstString, exampleArray[i].c_str());
+		dT.convert(nonConstString, "JAVADOC");
+	}
+	return 1;
+}
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.cpp b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
index 91f52662f..c1606cc77 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
@@ -1,8 +1,5 @@
 #include "JavaDocConverter.h"
-#include <cstdlib>
 #include <iostream>
-#include <string>
-#include <list>
 #define APPROX_LINE_LENGTH 64//characters per line allowed
 #define TAB_SIZE 8//characters per line allowed
 int printSortedTree2 = 0;
@@ -20,6 +17,10 @@ JavaDocConverter::~JavaDocConverter()
  * such as brief descriptions are TAGGED as such
  */
 bool compare_DoxygenEntities(DoxygenEntity first, DoxygenEntity second){
+	if(first.typeOfEntity.compare("brief") == 0) return true;
+	if(second.typeOfEntity.compare("brief") == 0) return false;
+	if(first.typeOfEntity.compare("details") == 0) return true;
+	if(second.typeOfEntity.compare("details") == 0) return false;
 	if(first.typeOfEntity.compare("plainstring") == 0) return true;
 	if(second.typeOfEntity.compare("plainstring") == 0) return false;
 	if(first.typeOfEntity.compare("param") == 0){
@@ -54,11 +55,11 @@ bool compare_DoxygenEntities(DoxygenEntity first, DoxygenEntity second){
 		return false;
 	}
 	if(first.typeOfEntity.compare("author")== 0){
-		if(first.typeOfEntity.compare("author")== 0) return true;
-		if(first.typeOfEntity.compare("version")== 0)return true;
-		if(first.typeOfEntity.compare("see")== 0)return true;
-		if(first.typeOfEntity.compare("since")== 0)return true;
-		if(first.typeOfEntity.compare("deprecated")== 0)return true;
+		if(second.typeOfEntity.compare("author")== 0) return true;
+		if(second.typeOfEntity.compare("version")== 0)return true;
+		if(second.typeOfEntity.compare("see")== 0)return true;
+		if(second.typeOfEntity.compare("since")== 0)return true;
+		if(second.typeOfEntity.compare("deprecated")== 0)return true;
 		return false;
 	}
 	if(first.typeOfEntity.compare("version")== 0){
@@ -134,17 +135,11 @@ string javaDocFormat(DoxygenEntity &doxygenEntity){
 	if (doxygenEntity.typeOfEntity.compare("plainstring") == 0){
 			return doxygenEntity.data;
 	}
-	else if (doxygenEntity.typeOfEntity.compare("brief") == 0){
-			return doxygenEntity.data;
-	}
-	if (doxygenEntity.typeOfEntity.compare("detailed") == 0){
-			return doxygenEntity.data;
-	}
 	else if (doxygenEntity.typeOfEntity.compare("b") == 0){
-		return "<b>" + doxygenEntity.data + "</b>";
+		return "\b<b>" + doxygenEntity.data + "</b>";
 	}
 	else if (doxygenEntity.typeOfEntity.compare("c") == 0){
-		return "<tt>" + doxygenEntity.data + "</tt>";
+		return "\b<tt>" + doxygenEntity.data + "</tt>";
 	}
 	return "";
 }
@@ -165,7 +160,9 @@ string translateSubtree( DoxygenEntity &doxygenEntity){
 }
 
 string translateEntity(DoxygenEntity &doxyEntity){
-	if(doxyEntity.typeOfEntity.compare("plainstring")== 0 || doxyEntity.typeOfEntity.compare("deprecated")== 0 || doxyEntity.typeOfEntity.compare("brief")== 0)
+	if ((doxyEntity.typeOfEntity.compare("brief") == 0)||(doxyEntity.typeOfEntity.compare("details") == 0)){
+		return formatCommand(string(translateSubtree(doxyEntity)), 0) + "\n * ";}
+	else if(doxyEntity.typeOfEntity.compare("plainstring")== 0 || doxyEntity.typeOfEntity.compare("deprecated")== 0 || doxyEntity.typeOfEntity.compare("brief")== 0)
 		return formatCommand(doxyEntity.data, 0) + "\n * ";
 	else if(doxyEntity.typeOfEntity.compare("see") == 0){
 		return formatCommand(string("@" + doxyEntity.typeOfEntity + "\t\t" + translateSubtree(doxyEntity)), 2);
@@ -207,4 +204,4 @@ string JavaDocConverter:: convertToJavaDoc(list <DoxygenEntity> entityList){
 	cout << "\n---RESULT IN JAVADOC---" << endl;
 	cout << javaDocString;
 	return javaDocString;
-}
\ No newline at end of file
+}
diff --git a/Source/DoxygenTranslator/src/Token.cpp b/Source/DoxygenTranslator/src/Token.cpp
index e85799546..198b3e442 100644
--- a/Source/DoxygenTranslator/src/Token.cpp
+++ b/Source/DoxygenTranslator/src/Token.cpp
@@ -1,8 +1,4 @@
 #include "Token.h"
-#include <cstdlib>
-#include <iostream>
-#include <string>
-#include <list>
 using namespace std;
 
 
@@ -21,7 +17,7 @@ string Token::toString()
 		return "{END OF PARAGRAPH}";
 	}
 	if (tokenType == PLAINSTRING){
-		return tokenString;
+		return "{PLAINSTRING :" + tokenString + "}";
 	}
 	if (tokenType == COMMAND){
 		return "{COMMAND : " + tokenString+ "}";
diff --git a/Source/DoxygenTranslator/src/TokenList.cpp b/Source/DoxygenTranslator/src/TokenList.cpp
index eeec6da46..a05d2ceef 100644
--- a/Source/DoxygenTranslator/src/TokenList.cpp
+++ b/Source/DoxygenTranslator/src/TokenList.cpp
@@ -59,7 +59,7 @@ TokenList::TokenList(string doxygenString){
 			if(!isFluff) tokenList.push_back(Token(PLAINSTRING, currentWord));
 		}
 		
-		else tokenList.push_back(Token(PLAINSTRING, currentWord));
+		else if (!currentWord.empty())tokenList.push_back(Token(PLAINSTRING, currentWord));
 		currentIndex = nextIndex;
 	}
 	}

From ac7887a940c40f39b45529b9535a6a4de54a4ac3 Mon Sep 17 00:00:00 2001
From: Cheryl Foil <cheryl.foil@gmail.com>
Date: Mon, 18 Aug 2008 04:57:05 +0000
Subject: [PATCH 016/314] Cleaning up unneeded files

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2008-cherylfoil@10778 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Source/DoxygenTranslator/src/.deps/.dirstamp  |   0
 .../src/.deps/DoxygenEntity.Po                | 380 -----------------
 .../src/.deps/DoxygenParser.Po                | 387 -----------------
 .../src/.deps/DoxygenTranslator.Po            | 401 ------------------
 .../src/.deps/JavaDocConverter.Po             | 385 -----------------
 Source/DoxygenTranslator/src/.deps/Token.Po   | 303 -------------
 .../DoxygenTranslator/src/.deps/TokenList.Po  | 382 -----------------
 7 files changed, 2238 deletions(-)
 delete mode 100644 Source/DoxygenTranslator/src/.deps/.dirstamp
 delete mode 100644 Source/DoxygenTranslator/src/.deps/DoxygenEntity.Po
 delete mode 100644 Source/DoxygenTranslator/src/.deps/DoxygenParser.Po
 delete mode 100644 Source/DoxygenTranslator/src/.deps/DoxygenTranslator.Po
 delete mode 100644 Source/DoxygenTranslator/src/.deps/JavaDocConverter.Po
 delete mode 100644 Source/DoxygenTranslator/src/.deps/Token.Po
 delete mode 100644 Source/DoxygenTranslator/src/.deps/TokenList.Po

diff --git a/Source/DoxygenTranslator/src/.deps/.dirstamp b/Source/DoxygenTranslator/src/.deps/.dirstamp
deleted file mode 100644
index e69de29bb..000000000
diff --git a/Source/DoxygenTranslator/src/.deps/DoxygenEntity.Po b/Source/DoxygenTranslator/src/.deps/DoxygenEntity.Po
deleted file mode 100644
index 7a6dbd296..000000000
--- a/Source/DoxygenTranslator/src/.deps/DoxygenEntity.Po
+++ /dev/null
@@ -1,380 +0,0 @@
-DoxygenTranslator/src/DoxygenEntity.o \
-  DoxygenTranslator/src/DoxygenEntity.o:  \
- DoxygenTranslator/src/DoxygenEntity.cpp \
-  DoxygenTranslator/src/DoxygenEntity.h /usr/include/c++/4.2/string \
-  /usr/include/c++/4.2/i486-linux-gnu/bits/c++config.h \
-  /usr/include/c++/4.2/i486-linux-gnu/bits/os_defines.h \
-  /usr/include/features.h /usr/include/sys/cdefs.h \
-  /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
-  /usr/include/gnu/stubs-32.h \
-  /usr/include/c++/4.2/i486-linux-gnu/bits/cpu_defines.h \
-  /usr/include/c++/4.2/bits/stringfwd.h \
-  /usr/include/c++/4.2/bits/char_traits.h /usr/include/c++/4.2/cstring \
-  /usr/include/c++/4.2/cstddef \
-  /usr/lib/gcc/i486-linux-gnu/4.2.3/include/stddef.h \
-  /usr/include/string.h /usr/include/xlocale.h \
-  /usr/include/c++/4.2/bits/stl_algobase.h /usr/include/c++/4.2/climits \
-  /usr/lib/gcc/i486-linux-gnu/4.2.3/include/limits.h \
-  /usr/lib/gcc/i486-linux-gnu/4.2.3/include/syslimits.h \
-  /usr/include/limits.h /usr/include/bits/posix1_lim.h \
-  /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
-  /usr/include/bits/posix2_lim.h /usr/include/bits/xopen_lim.h \
-  /usr/include/bits/stdio_lim.h /usr/include/c++/4.2/cstdlib \
-  /usr/include/stdlib.h /usr/include/bits/waitflags.h \
-  /usr/include/bits/waitstatus.h /usr/include/endian.h \
-  /usr/include/bits/endian.h /usr/include/sys/types.h \
-  /usr/include/bits/types.h /usr/include/bits/typesizes.h \
-  /usr/include/time.h /usr/include/sys/select.h \
-  /usr/include/bits/select.h /usr/include/bits/sigset.h \
-  /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
-  /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
-  /usr/include/c++/4.2/iosfwd \
-  /usr/include/c++/4.2/i486-linux-gnu/bits/c++locale.h \
-  /usr/include/c++/4.2/cstdio /usr/include/stdio.h /usr/include/libio.h \
-  /usr/include/_G_config.h /usr/include/wchar.h \
-  /usr/lib/gcc/i486-linux-gnu/4.2.3/include/stdarg.h \
-  /usr/include/bits/sys_errlist.h /usr/include/c++/4.2/clocale \
-  /usr/include/locale.h /usr/include/bits/locale.h \
-  /usr/include/langinfo.h /usr/include/nl_types.h /usr/include/iconv.h \
-  /usr/include/libintl.h /usr/include/c++/4.2/cstdarg \
-  /usr/include/c++/4.2/i486-linux-gnu/bits/c++io.h \
-  /usr/include/c++/4.2/i486-linux-gnu/bits/gthr.h \
-  /usr/include/c++/4.2/i486-linux-gnu/bits/gthr-default.h \
-  /usr/include/pthread.h /usr/include/sched.h /usr/include/bits/sched.h \
-  /usr/include/signal.h /usr/include/bits/setjmp.h /usr/include/unistd.h \
-  /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \
-  /usr/include/bits/confname.h /usr/include/getopt.h \
-  /usr/include/c++/4.2/cctype /usr/include/ctype.h \
-  /usr/include/c++/4.2/bits/postypes.h /usr/include/c++/4.2/cwchar \
-  /usr/include/c++/4.2/ctime /usr/include/bits/wchar.h \
-  /usr/include/stdint.h /usr/include/c++/4.2/bits/functexcept.h \
-  /usr/include/c++/4.2/exception_defines.h \
-  /usr/include/c++/4.2/bits/stl_pair.h \
-  /usr/include/c++/4.2/bits/cpp_type_traits.h \
-  /usr/include/c++/4.2/ext/type_traits.h /usr/include/c++/4.2/utility \
-  /usr/include/c++/4.2/bits/stl_relops.h \
-  /usr/include/c++/4.2/bits/stl_iterator_base_types.h \
-  /usr/include/c++/4.2/bits/stl_iterator_base_funcs.h \
-  /usr/include/c++/4.2/bits/concept_check.h \
-  /usr/include/c++/4.2/bits/stl_iterator.h \
-  /usr/include/c++/4.2/debug/debug.h /usr/include/c++/4.2/memory \
-  /usr/include/c++/4.2/bits/allocator.h \
-  /usr/include/c++/4.2/i486-linux-gnu/bits/c++allocator.h \
-  /usr/include/c++/4.2/ext/new_allocator.h /usr/include/c++/4.2/new \
-  /usr/include/c++/4.2/exception \
-  /usr/include/c++/4.2/bits/stl_construct.h \
-  /usr/include/c++/4.2/bits/stl_uninitialized.h \
-  /usr/include/c++/4.2/bits/stl_raw_storage_iter.h \
-  /usr/include/c++/4.2/limits /usr/include/c++/4.2/bits/ostream_insert.h \
-  /usr/include/c++/4.2/bits/stl_function.h \
-  /usr/include/c++/4.2/bits/basic_string.h \
-  /usr/include/c++/4.2/ext/atomicity.h \
-  /usr/include/c++/4.2/i486-linux-gnu/bits/atomic_word.h \
-  /usr/include/c++/4.2/algorithm /usr/include/c++/4.2/bits/stl_algo.h \
-  /usr/include/c++/4.2/bits/stl_heap.h \
-  /usr/include/c++/4.2/bits/stl_tempbuf.h \
-  /usr/include/c++/4.2/bits/basic_string.tcc /usr/include/c++/4.2/list \
-  /usr/include/c++/4.2/bits/stl_list.h /usr/include/c++/4.2/bits/list.tcc \
-  /usr/include/c++/4.2/iostream /usr/include/c++/4.2/ostream \
-  /usr/include/c++/4.2/ios /usr/include/c++/4.2/bits/localefwd.h \
-  /usr/include/c++/4.2/bits/ios_base.h \
-  /usr/include/c++/4.2/bits/locale_classes.h \
-  /usr/include/c++/4.2/streambuf /usr/include/c++/4.2/bits/streambuf.tcc \
-  /usr/include/c++/4.2/bits/basic_ios.h \
-  /usr/include/c++/4.2/bits/streambuf_iterator.h \
-  /usr/include/c++/4.2/bits/locale_facets.h /usr/include/c++/4.2/cwctype \
-  /usr/include/wctype.h \
-  /usr/include/c++/4.2/i486-linux-gnu/bits/ctype_base.h \
-  /usr/include/c++/4.2/i486-linux-gnu/bits/ctype_inline.h \
-  /usr/include/c++/4.2/bits/codecvt.h \
-  /usr/include/c++/4.2/i486-linux-gnu/bits/time_members.h \
-  /usr/include/c++/4.2/i486-linux-gnu/bits/messages_members.h \
-  /usr/include/c++/4.2/bits/basic_ios.tcc \
-  /usr/include/c++/4.2/bits/ostream.tcc /usr/include/c++/4.2/locale \
-  /usr/include/c++/4.2/bits/locale_facets.tcc \
-  /usr/include/c++/4.2/typeinfo /usr/include/c++/4.2/istream \
-  /usr/include/c++/4.2/bits/istream.tcc
-
-DoxygenTranslator/src/DoxygenEntity.h:
-
-/usr/include/c++/4.2/string:
-
-/usr/include/c++/4.2/i486-linux-gnu/bits/c++config.h:
-
-/usr/include/c++/4.2/i486-linux-gnu/bits/os_defines.h:
-
-/usr/include/features.h:
-
-/usr/include/sys/cdefs.h:
-
-/usr/include/bits/wordsize.h:
-
-/usr/include/gnu/stubs.h:
-
-/usr/include/gnu/stubs-32.h:
-
-/usr/include/c++/4.2/i486-linux-gnu/bits/cpu_defines.h:
-
-/usr/include/c++/4.2/bits/stringfwd.h:
-
-/usr/include/c++/4.2/bits/char_traits.h:
-
-/usr/include/c++/4.2/cstring:
-
-/usr/include/c++/4.2/cstddef:
-
-/usr/lib/gcc/i486-linux-gnu/4.2.3/include/stddef.h:
-
-/usr/include/string.h:
-
-/usr/include/xlocale.h:
-
-/usr/include/c++/4.2/bits/stl_algobase.h:
-
-/usr/include/c++/4.2/climits:
-
-/usr/lib/gcc/i486-linux-gnu/4.2.3/include/limits.h:
-
-/usr/lib/gcc/i486-linux-gnu/4.2.3/include/syslimits.h:
-
-/usr/include/limits.h:
-
-/usr/include/bits/posix1_lim.h:
-
-/usr/include/bits/local_lim.h:
-
-/usr/include/linux/limits.h:
-
-/usr/include/bits/posix2_lim.h:
-
-/usr/include/bits/xopen_lim.h:
-
-/usr/include/bits/stdio_lim.h:
-
-/usr/include/c++/4.2/cstdlib:
-
-/usr/include/stdlib.h:
-
-/usr/include/bits/waitflags.h:
-
-/usr/include/bits/waitstatus.h:
-
-/usr/include/endian.h:
-
-/usr/include/bits/endian.h:
-
-/usr/include/sys/types.h:
-
-/usr/include/bits/types.h:
-
-/usr/include/bits/typesizes.h:
-
-/usr/include/time.h:
-
-/usr/include/sys/select.h:
-
-/usr/include/bits/select.h:
-
-/usr/include/bits/sigset.h:
-
-/usr/include/bits/time.h:
-
-/usr/include/sys/sysmacros.h:
-
-/usr/include/bits/pthreadtypes.h:
-
-/usr/include/alloca.h:
-
-/usr/include/c++/4.2/iosfwd:
-
-/usr/include/c++/4.2/i486-linux-gnu/bits/c++locale.h:
-
-/usr/include/c++/4.2/cstdio:
-
-/usr/include/stdio.h:
-
-/usr/include/libio.h:
-
-/usr/include/_G_config.h:
-
-/usr/include/wchar.h:
-
-/usr/lib/gcc/i486-linux-gnu/4.2.3/include/stdarg.h:
-
-/usr/include/bits/sys_errlist.h:
-
-/usr/include/c++/4.2/clocale:
-
-/usr/include/locale.h:
-
-/usr/include/bits/locale.h:
-
-/usr/include/langinfo.h:
-
-/usr/include/nl_types.h:
-
-/usr/include/iconv.h:
-
-/usr/include/libintl.h:
-
-/usr/include/c++/4.2/cstdarg:
-
-/usr/include/c++/4.2/i486-linux-gnu/bits/c++io.h:
-
-/usr/include/c++/4.2/i486-linux-gnu/bits/gthr.h:
-
-/usr/include/c++/4.2/i486-linux-gnu/bits/gthr-default.h:
-
-/usr/include/pthread.h:
-
-/usr/include/sched.h:
-
-/usr/include/bits/sched.h:
-
-/usr/include/signal.h:
-
-/usr/include/bits/setjmp.h:
-
-/usr/include/unistd.h:
-
-/usr/include/bits/posix_opt.h:
-
-/usr/include/bits/environments.h:
-
-/usr/include/bits/confname.h:
-
-/usr/include/getopt.h:
-
-/usr/include/c++/4.2/cctype:
-
-/usr/include/ctype.h:
-
-/usr/include/c++/4.2/bits/postypes.h:
-
-/usr/include/c++/4.2/cwchar:
-
-/usr/include/c++/4.2/ctime:
-
-/usr/include/bits/wchar.h:
-
-/usr/include/stdint.h:
-
-/usr/include/c++/4.2/bits/functexcept.h:
-
-/usr/include/c++/4.2/exception_defines.h:
-
-/usr/include/c++/4.2/bits/stl_pair.h:
-
-/usr/include/c++/4.2/bits/cpp_type_traits.h:
-
-/usr/include/c++/4.2/ext/type_traits.h:
-
-/usr/include/c++/4.2/utility:
-
-/usr/include/c++/4.2/bits/stl_relops.h:
-
-/usr/include/c++/4.2/bits/stl_iterator_base_types.h:
-
-/usr/include/c++/4.2/bits/stl_iterator_base_funcs.h:
-
-/usr/include/c++/4.2/bits/concept_check.h:
-
-/usr/include/c++/4.2/bits/stl_iterator.h:
-
-/usr/include/c++/4.2/debug/debug.h:
-
-/usr/include/c++/4.2/memory:
-
-/usr/include/c++/4.2/bits/allocator.h:
-
-/usr/include/c++/4.2/i486-linux-gnu/bits/c++allocator.h:
-
-/usr/include/c++/4.2/ext/new_allocator.h:
-
-/usr/include/c++/4.2/new:
-
-/usr/include/c++/4.2/exception:
-
-/usr/include/c++/4.2/bits/stl_construct.h:
-
-/usr/include/c++/4.2/bits/stl_uninitialized.h:
-
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-/usr/include/c++/4.2/algorithm:
-
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-
-/usr/include/c++/4.2/bits/stl_list.h:
-
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-
-/usr/include/c++/4.2/iostream:
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-/usr/include/c++/4.2/ostream:
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-/usr/include/c++/4.2/ios:
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-
-/usr/include/c++/4.2/streambuf:
-
-/usr/include/c++/4.2/bits/streambuf.tcc:
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-/usr/include/c++/4.2/bits/streambuf_iterator.h:
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-
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-
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-/usr/include/c++/4.2/bits/codecvt.h:
-
-/usr/include/c++/4.2/i486-linux-gnu/bits/time_members.h:
-
-/usr/include/c++/4.2/i486-linux-gnu/bits/messages_members.h:
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-/usr/include/c++/4.2/bits/basic_ios.tcc:
-
-/usr/include/c++/4.2/bits/ostream.tcc:
-
-/usr/include/c++/4.2/locale:
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-/usr/include/c++/4.2/bits/locale_facets.tcc:
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-/usr/include/c++/4.2/typeinfo:
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-/usr/include/c++/4.2/istream:
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-/usr/include/c++/4.2/bits/istream.tcc:
diff --git a/Source/DoxygenTranslator/src/.deps/DoxygenParser.Po b/Source/DoxygenTranslator/src/.deps/DoxygenParser.Po
deleted file mode 100644
index 8ec874c8c..000000000
--- a/Source/DoxygenTranslator/src/.deps/DoxygenParser.Po
+++ /dev/null
@@ -1,387 +0,0 @@
-DoxygenTranslator/src/DoxygenParser.o \
-  DoxygenTranslator/src/DoxygenParser.o:  \
- DoxygenTranslator/src/DoxygenParser.cpp \
-  DoxygenTranslator/src/DoxygenParser.h /usr/include/c++/4.2/string \
-  /usr/include/c++/4.2/i486-linux-gnu/bits/c++config.h \
-  /usr/include/c++/4.2/i486-linux-gnu/bits/os_defines.h \
-  /usr/include/features.h /usr/include/sys/cdefs.h \
-  /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
-  /usr/include/gnu/stubs-32.h \
-  /usr/include/c++/4.2/i486-linux-gnu/bits/cpu_defines.h \
-  /usr/include/c++/4.2/bits/stringfwd.h \
-  /usr/include/c++/4.2/bits/char_traits.h /usr/include/c++/4.2/cstring \
-  /usr/include/c++/4.2/cstddef \
-  /usr/lib/gcc/i486-linux-gnu/4.2.3/include/stddef.h \
-  /usr/include/string.h /usr/include/xlocale.h \
-  /usr/include/c++/4.2/bits/stl_algobase.h /usr/include/c++/4.2/climits \
-  /usr/lib/gcc/i486-linux-gnu/4.2.3/include/limits.h \
-  /usr/lib/gcc/i486-linux-gnu/4.2.3/include/syslimits.h \
-  /usr/include/limits.h /usr/include/bits/posix1_lim.h \
-  /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
-  /usr/include/bits/posix2_lim.h /usr/include/bits/xopen_lim.h \
-  /usr/include/bits/stdio_lim.h /usr/include/c++/4.2/cstdlib \
-  /usr/include/stdlib.h /usr/include/bits/waitflags.h \
-  /usr/include/bits/waitstatus.h /usr/include/endian.h \
-  /usr/include/bits/endian.h /usr/include/sys/types.h \
-  /usr/include/bits/types.h /usr/include/bits/typesizes.h \
-  /usr/include/time.h /usr/include/sys/select.h \
-  /usr/include/bits/select.h /usr/include/bits/sigset.h \
-  /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
-  /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
-  /usr/include/c++/4.2/iosfwd \
-  /usr/include/c++/4.2/i486-linux-gnu/bits/c++locale.h \
-  /usr/include/c++/4.2/cstdio /usr/include/stdio.h /usr/include/libio.h \
-  /usr/include/_G_config.h /usr/include/wchar.h \
-  /usr/lib/gcc/i486-linux-gnu/4.2.3/include/stdarg.h \
-  /usr/include/bits/sys_errlist.h /usr/include/c++/4.2/clocale \
-  /usr/include/locale.h /usr/include/bits/locale.h \
-  /usr/include/langinfo.h /usr/include/nl_types.h /usr/include/iconv.h \
-  /usr/include/libintl.h /usr/include/c++/4.2/cstdarg \
-  /usr/include/c++/4.2/i486-linux-gnu/bits/c++io.h \
-  /usr/include/c++/4.2/i486-linux-gnu/bits/gthr.h \
-  /usr/include/c++/4.2/i486-linux-gnu/bits/gthr-default.h \
-  /usr/include/pthread.h /usr/include/sched.h /usr/include/bits/sched.h \
-  /usr/include/signal.h /usr/include/bits/setjmp.h /usr/include/unistd.h \
-  /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \
-  /usr/include/bits/confname.h /usr/include/getopt.h \
-  /usr/include/c++/4.2/cctype /usr/include/ctype.h \
-  /usr/include/c++/4.2/bits/postypes.h /usr/include/c++/4.2/cwchar \
-  /usr/include/c++/4.2/ctime /usr/include/bits/wchar.h \
-  /usr/include/stdint.h /usr/include/c++/4.2/bits/functexcept.h \
-  /usr/include/c++/4.2/exception_defines.h \
-  /usr/include/c++/4.2/bits/stl_pair.h \
-  /usr/include/c++/4.2/bits/cpp_type_traits.h \
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-  /usr/include/c++/4.2/bits/stl_relops.h \
-  /usr/include/c++/4.2/bits/stl_iterator_base_types.h \
-  /usr/include/c++/4.2/bits/stl_iterator_base_funcs.h \
-  /usr/include/c++/4.2/bits/concept_check.h \
-  /usr/include/c++/4.2/bits/stl_iterator.h \
-  /usr/include/c++/4.2/debug/debug.h /usr/include/c++/4.2/memory \
-  /usr/include/c++/4.2/bits/allocator.h \
-  /usr/include/c++/4.2/i486-linux-gnu/bits/c++allocator.h \
-  /usr/include/c++/4.2/ext/new_allocator.h /usr/include/c++/4.2/new \
-  /usr/include/c++/4.2/exception \
-  /usr/include/c++/4.2/bits/stl_construct.h \
-  /usr/include/c++/4.2/bits/stl_uninitialized.h \
-  /usr/include/c++/4.2/bits/stl_raw_storage_iter.h \
-  /usr/include/c++/4.2/limits /usr/include/c++/4.2/bits/ostream_insert.h \
-  /usr/include/c++/4.2/bits/stl_function.h \
-  /usr/include/c++/4.2/bits/basic_string.h \
-  /usr/include/c++/4.2/ext/atomicity.h \
-  /usr/include/c++/4.2/i486-linux-gnu/bits/atomic_word.h \
-  /usr/include/c++/4.2/algorithm /usr/include/c++/4.2/bits/stl_algo.h \
-  /usr/include/c++/4.2/bits/stl_heap.h \
-  /usr/include/c++/4.2/bits/stl_tempbuf.h \
-  /usr/include/c++/4.2/bits/basic_string.tcc /usr/include/c++/4.2/list \
-  /usr/include/c++/4.2/bits/stl_list.h /usr/include/c++/4.2/bits/list.tcc \
-  DoxygenTranslator/src/DoxygenEntity.h DoxygenTranslator/src/TokenList.h \
-  /usr/include/c++/4.2/iostream /usr/include/c++/4.2/ostream \
-  /usr/include/c++/4.2/ios /usr/include/c++/4.2/bits/localefwd.h \
-  /usr/include/c++/4.2/bits/ios_base.h \
-  /usr/include/c++/4.2/bits/locale_classes.h \
-  /usr/include/c++/4.2/streambuf /usr/include/c++/4.2/bits/streambuf.tcc \
-  /usr/include/c++/4.2/bits/basic_ios.h \
-  /usr/include/c++/4.2/bits/streambuf_iterator.h \
-  /usr/include/c++/4.2/bits/locale_facets.h /usr/include/c++/4.2/cwctype \
-  /usr/include/wctype.h \
-  /usr/include/c++/4.2/i486-linux-gnu/bits/ctype_base.h \
-  /usr/include/c++/4.2/i486-linux-gnu/bits/ctype_inline.h \
-  /usr/include/c++/4.2/bits/codecvt.h \
-  /usr/include/c++/4.2/i486-linux-gnu/bits/time_members.h \
-  /usr/include/c++/4.2/i486-linux-gnu/bits/messages_members.h \
-  /usr/include/c++/4.2/bits/basic_ios.tcc \
-  /usr/include/c++/4.2/bits/ostream.tcc /usr/include/c++/4.2/locale \
-  /usr/include/c++/4.2/bits/locale_facets.tcc \
-  /usr/include/c++/4.2/typeinfo /usr/include/c++/4.2/istream \
-  /usr/include/c++/4.2/bits/istream.tcc DoxygenTranslator/src/Token.h
-
-DoxygenTranslator/src/DoxygenParser.h:
-
-/usr/include/c++/4.2/string:
-
-/usr/include/c++/4.2/i486-linux-gnu/bits/c++config.h:
-
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-
-/usr/include/gnu/stubs.h:
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-/usr/include/gnu/stubs-32.h:
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-/usr/include/c++/4.2/bits/stringfwd.h:
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-
-/usr/include/c++/4.2/climits:
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-/usr/lib/gcc/i486-linux-gnu/4.2.3/include/syslimits.h:
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-
-/usr/include/bits/posix1_lim.h:
-
-/usr/include/bits/local_lim.h:
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-/usr/include/linux/limits.h:
-
-/usr/include/bits/posix2_lim.h:
-
-/usr/include/bits/xopen_lim.h:
-
-/usr/include/bits/stdio_lim.h:
-
-/usr/include/c++/4.2/cstdlib:
-
-/usr/include/stdlib.h:
-
-/usr/include/bits/waitflags.h:
-
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-
-/usr/include/endian.h:
-
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-
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-
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-
-/usr/include/sched.h:
-
-/usr/include/bits/sched.h:
-
-/usr/include/signal.h:
-
-/usr/include/bits/setjmp.h:
-
-/usr/include/unistd.h:
-
-/usr/include/bits/posix_opt.h:
-
-/usr/include/bits/environments.h:
-
-/usr/include/bits/confname.h:
-
-/usr/include/getopt.h:
-
-/usr/include/c++/4.2/cctype:
-
-/usr/include/ctype.h:
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-/usr/include/c++/4.2/bits/postypes.h:
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-/usr/include/c++/4.2/cwchar:
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-
-/usr/include/bits/wchar.h:
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-/usr/include/c++/4.2/memory:
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-
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-
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-/usr/include/c++/4.2/bits/stl_construct.h:
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-
-/usr/include/c++/4.2/limits:
-
-/usr/include/c++/4.2/bits/ostream_insert.h:
-
-/usr/include/c++/4.2/bits/stl_function.h:
-
-/usr/include/c++/4.2/bits/basic_string.h:
-
-/usr/include/c++/4.2/ext/atomicity.h:
-
-/usr/include/c++/4.2/i486-linux-gnu/bits/atomic_word.h:
-
-/usr/include/c++/4.2/algorithm:
-
-/usr/include/c++/4.2/bits/stl_algo.h:
-
-/usr/include/c++/4.2/bits/stl_heap.h:
-
-/usr/include/c++/4.2/bits/stl_tempbuf.h:
-
-/usr/include/c++/4.2/bits/basic_string.tcc:
-
-/usr/include/c++/4.2/list:
-
-/usr/include/c++/4.2/bits/stl_list.h:
-
-/usr/include/c++/4.2/bits/list.tcc:
-
-DoxygenTranslator/src/DoxygenEntity.h:
-
-DoxygenTranslator/src/TokenList.h:
-
-/usr/include/c++/4.2/iostream:
-
-/usr/include/c++/4.2/ostream:
-
-/usr/include/c++/4.2/ios:
-
-/usr/include/c++/4.2/bits/localefwd.h:
-
-/usr/include/c++/4.2/bits/ios_base.h:
-
-/usr/include/c++/4.2/bits/locale_classes.h:
-
-/usr/include/c++/4.2/streambuf:
-
-/usr/include/c++/4.2/bits/streambuf.tcc:
-
-/usr/include/c++/4.2/bits/basic_ios.h:
-
-/usr/include/c++/4.2/bits/streambuf_iterator.h:
-
-/usr/include/c++/4.2/bits/locale_facets.h:
-
-/usr/include/c++/4.2/cwctype:
-
-/usr/include/wctype.h:
-
-/usr/include/c++/4.2/i486-linux-gnu/bits/ctype_base.h:
-
-/usr/include/c++/4.2/i486-linux-gnu/bits/ctype_inline.h:
-
-/usr/include/c++/4.2/bits/codecvt.h:
-
-/usr/include/c++/4.2/i486-linux-gnu/bits/time_members.h:
-
-/usr/include/c++/4.2/i486-linux-gnu/bits/messages_members.h:
-
-/usr/include/c++/4.2/bits/basic_ios.tcc:
-
-/usr/include/c++/4.2/bits/ostream.tcc:
-
-/usr/include/c++/4.2/locale:
-
-/usr/include/c++/4.2/bits/locale_facets.tcc:
-
-/usr/include/c++/4.2/typeinfo:
-
-/usr/include/c++/4.2/istream:
-
-/usr/include/c++/4.2/bits/istream.tcc:
-
-DoxygenTranslator/src/Token.h:
diff --git a/Source/DoxygenTranslator/src/.deps/DoxygenTranslator.Po b/Source/DoxygenTranslator/src/.deps/DoxygenTranslator.Po
deleted file mode 100644
index 4cec6c648..000000000
--- a/Source/DoxygenTranslator/src/.deps/DoxygenTranslator.Po
+++ /dev/null
@@ -1,401 +0,0 @@
-DoxygenTranslator/src/DoxygenTranslator.o \
-  DoxygenTranslator/src/DoxygenTranslator.o:  \
- DoxygenTranslator/src/DoxygenTranslator.cpp \
-  DoxygenTranslator/src/DoxygenParser.h /usr/include/c++/4.2/string \
-  /usr/include/c++/4.2/i486-linux-gnu/bits/c++config.h \
-  /usr/include/c++/4.2/i486-linux-gnu/bits/os_defines.h \
-  /usr/include/features.h /usr/include/sys/cdefs.h \
-  /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
-  /usr/include/gnu/stubs-32.h \
-  /usr/include/c++/4.2/i486-linux-gnu/bits/cpu_defines.h \
-  /usr/include/c++/4.2/bits/stringfwd.h \
-  /usr/include/c++/4.2/bits/char_traits.h /usr/include/c++/4.2/cstring \
-  /usr/include/c++/4.2/cstddef \
-  /usr/lib/gcc/i486-linux-gnu/4.2.3/include/stddef.h \
-  /usr/include/string.h /usr/include/xlocale.h \
-  /usr/include/c++/4.2/bits/stl_algobase.h /usr/include/c++/4.2/climits \
-  /usr/lib/gcc/i486-linux-gnu/4.2.3/include/limits.h \
-  /usr/lib/gcc/i486-linux-gnu/4.2.3/include/syslimits.h \
-  /usr/include/limits.h /usr/include/bits/posix1_lim.h \
-  /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
-  /usr/include/bits/posix2_lim.h /usr/include/bits/xopen_lim.h \
-  /usr/include/bits/stdio_lim.h /usr/include/c++/4.2/cstdlib \
-  /usr/include/stdlib.h /usr/include/bits/waitflags.h \
-  /usr/include/bits/waitstatus.h /usr/include/endian.h \
-  /usr/include/bits/endian.h /usr/include/sys/types.h \
-  /usr/include/bits/types.h /usr/include/bits/typesizes.h \
-  /usr/include/time.h /usr/include/sys/select.h \
-  /usr/include/bits/select.h /usr/include/bits/sigset.h \
-  /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
-  /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
-  /usr/include/c++/4.2/iosfwd \
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-DoxygenTranslator/src/TokenList.h:
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-DoxygenTranslator/src/Token.h:
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-DoxygenTranslator/src/JavaDocConverter.h:
diff --git a/Source/DoxygenTranslator/src/.deps/JavaDocConverter.Po b/Source/DoxygenTranslator/src/.deps/JavaDocConverter.Po
deleted file mode 100644
index 79a3133a3..000000000
--- a/Source/DoxygenTranslator/src/.deps/JavaDocConverter.Po
+++ /dev/null
@@ -1,385 +0,0 @@
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diff --git a/Source/DoxygenTranslator/src/.deps/Token.Po b/Source/DoxygenTranslator/src/.deps/Token.Po
deleted file mode 100644
index dbfe541b1..000000000
--- a/Source/DoxygenTranslator/src/.deps/Token.Po
+++ /dev/null
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-/usr/include/c++/4.2/algorithm:
-
-/usr/include/c++/4.2/bits/stl_algo.h:
-
-/usr/include/c++/4.2/bits/stl_heap.h:
-
-/usr/include/c++/4.2/bits/stl_tempbuf.h:
-
-/usr/include/c++/4.2/bits/basic_string.tcc:
diff --git a/Source/DoxygenTranslator/src/.deps/TokenList.Po b/Source/DoxygenTranslator/src/.deps/TokenList.Po
deleted file mode 100644
index 74d0e1c79..000000000
--- a/Source/DoxygenTranslator/src/.deps/TokenList.Po
+++ /dev/null
@@ -1,382 +0,0 @@
-DoxygenTranslator/src/TokenList.o DoxygenTranslator/src/TokenList.o:  \
- DoxygenTranslator/src/TokenList.cpp DoxygenTranslator/src/TokenList.h \
-  /usr/include/c++/4.2/cstdlib \
-  /usr/include/c++/4.2/i486-linux-gnu/bits/c++config.h \
-  /usr/include/c++/4.2/i486-linux-gnu/bits/os_defines.h \
-  /usr/include/features.h /usr/include/sys/cdefs.h \
-  /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
-  /usr/include/gnu/stubs-32.h \
-  /usr/include/c++/4.2/i486-linux-gnu/bits/cpu_defines.h \
-  /usr/include/c++/4.2/cstddef \
-  /usr/lib/gcc/i486-linux-gnu/4.2.3/include/stddef.h \
-  /usr/include/stdlib.h /usr/include/bits/waitflags.h \
-  /usr/include/bits/waitstatus.h /usr/include/endian.h \
-  /usr/include/bits/endian.h /usr/include/xlocale.h \
-  /usr/include/sys/types.h /usr/include/bits/types.h \
-  /usr/include/bits/typesizes.h /usr/include/time.h \
-  /usr/include/sys/select.h /usr/include/bits/select.h \
-  /usr/include/bits/sigset.h /usr/include/bits/time.h \
-  /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \
-  /usr/include/alloca.h /usr/include/c++/4.2/iostream \
-  /usr/include/c++/4.2/ostream /usr/include/c++/4.2/ios \
-  /usr/include/c++/4.2/iosfwd \
-  /usr/include/c++/4.2/i486-linux-gnu/bits/c++locale.h \
-  /usr/include/c++/4.2/cstring /usr/include/string.h \
-  /usr/include/c++/4.2/cstdio /usr/include/stdio.h /usr/include/libio.h \
-  /usr/include/_G_config.h /usr/include/wchar.h \
-  /usr/lib/gcc/i486-linux-gnu/4.2.3/include/stdarg.h \
-  /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
-  /usr/include/c++/4.2/clocale /usr/include/locale.h \
-  /usr/include/bits/locale.h /usr/include/langinfo.h \
-  /usr/include/nl_types.h /usr/include/iconv.h /usr/include/libintl.h \
-  /usr/include/c++/4.2/cstdarg \
-  /usr/include/c++/4.2/i486-linux-gnu/bits/c++io.h \
-  /usr/include/c++/4.2/i486-linux-gnu/bits/gthr.h \
-  /usr/include/c++/4.2/i486-linux-gnu/bits/gthr-default.h \
-  /usr/include/pthread.h /usr/include/sched.h /usr/include/bits/sched.h \
-  /usr/include/signal.h /usr/include/bits/setjmp.h /usr/include/unistd.h \
-  /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \
-  /usr/include/bits/confname.h /usr/include/getopt.h \
-  /usr/include/c++/4.2/cctype /usr/include/ctype.h \
-  /usr/include/c++/4.2/bits/stringfwd.h \
-  /usr/include/c++/4.2/bits/postypes.h /usr/include/c++/4.2/cwchar \
-  /usr/include/c++/4.2/ctime /usr/include/bits/wchar.h \
-  /usr/include/stdint.h /usr/include/c++/4.2/bits/functexcept.h \
-  /usr/include/c++/4.2/exception_defines.h /usr/include/c++/4.2/exception \
-  /usr/include/c++/4.2/bits/char_traits.h \
-  /usr/include/c++/4.2/bits/stl_algobase.h /usr/include/c++/4.2/climits \
-  /usr/lib/gcc/i486-linux-gnu/4.2.3/include/limits.h \
-  /usr/lib/gcc/i486-linux-gnu/4.2.3/include/syslimits.h \
-  /usr/include/limits.h /usr/include/bits/posix1_lim.h \
-  /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
-  /usr/include/bits/posix2_lim.h /usr/include/bits/xopen_lim.h \
-  /usr/include/c++/4.2/bits/stl_pair.h \
-  /usr/include/c++/4.2/bits/cpp_type_traits.h \
-  /usr/include/c++/4.2/ext/type_traits.h /usr/include/c++/4.2/utility \
-  /usr/include/c++/4.2/bits/stl_relops.h \
-  /usr/include/c++/4.2/bits/stl_iterator_base_types.h \
-  /usr/include/c++/4.2/bits/stl_iterator_base_funcs.h \
-  /usr/include/c++/4.2/bits/concept_check.h \
-  /usr/include/c++/4.2/bits/stl_iterator.h \
-  /usr/include/c++/4.2/debug/debug.h \
-  /usr/include/c++/4.2/bits/localefwd.h \
-  /usr/include/c++/4.2/bits/ios_base.h \
-  /usr/include/c++/4.2/ext/atomicity.h \
-  /usr/include/c++/4.2/i486-linux-gnu/bits/atomic_word.h \
-  /usr/include/c++/4.2/bits/locale_classes.h /usr/include/c++/4.2/string \
-  /usr/include/c++/4.2/memory /usr/include/c++/4.2/bits/allocator.h \
-  /usr/include/c++/4.2/i486-linux-gnu/bits/c++allocator.h \
-  /usr/include/c++/4.2/ext/new_allocator.h /usr/include/c++/4.2/new \
-  /usr/include/c++/4.2/bits/stl_construct.h \
-  /usr/include/c++/4.2/bits/stl_uninitialized.h \
-  /usr/include/c++/4.2/bits/stl_raw_storage_iter.h \
-  /usr/include/c++/4.2/limits /usr/include/c++/4.2/bits/ostream_insert.h \
-  /usr/include/c++/4.2/bits/stl_function.h \
-  /usr/include/c++/4.2/bits/basic_string.h /usr/include/c++/4.2/algorithm \
-  /usr/include/c++/4.2/bits/stl_algo.h \
-  /usr/include/c++/4.2/bits/stl_heap.h \
-  /usr/include/c++/4.2/bits/stl_tempbuf.h \
-  /usr/include/c++/4.2/bits/basic_string.tcc \
-  /usr/include/c++/4.2/streambuf /usr/include/c++/4.2/bits/streambuf.tcc \
-  /usr/include/c++/4.2/bits/basic_ios.h \
-  /usr/include/c++/4.2/bits/streambuf_iterator.h \
-  /usr/include/c++/4.2/bits/locale_facets.h /usr/include/c++/4.2/cwctype \
-  /usr/include/wctype.h \
-  /usr/include/c++/4.2/i486-linux-gnu/bits/ctype_base.h \
-  /usr/include/c++/4.2/i486-linux-gnu/bits/ctype_inline.h \
-  /usr/include/c++/4.2/bits/codecvt.h \
-  /usr/include/c++/4.2/i486-linux-gnu/bits/time_members.h \
-  /usr/include/c++/4.2/i486-linux-gnu/bits/messages_members.h \
-  /usr/include/c++/4.2/bits/basic_ios.tcc \
-  /usr/include/c++/4.2/bits/ostream.tcc /usr/include/c++/4.2/locale \
-  /usr/include/c++/4.2/bits/locale_facets.tcc \
-  /usr/include/c++/4.2/typeinfo /usr/include/c++/4.2/istream \
-  /usr/include/c++/4.2/bits/istream.tcc /usr/include/c++/4.2/list \
-  /usr/include/c++/4.2/bits/stl_list.h /usr/include/c++/4.2/bits/list.tcc \
-  DoxygenTranslator/src/Token.h
-
-DoxygenTranslator/src/TokenList.h:
-
-/usr/include/c++/4.2/cstdlib:
-
-/usr/include/c++/4.2/i486-linux-gnu/bits/c++config.h:
-
-/usr/include/c++/4.2/i486-linux-gnu/bits/os_defines.h:
-
-/usr/include/features.h:
-
-/usr/include/sys/cdefs.h:
-
-/usr/include/bits/wordsize.h:
-
-/usr/include/gnu/stubs.h:
-
-/usr/include/gnu/stubs-32.h:
-
-/usr/include/c++/4.2/i486-linux-gnu/bits/cpu_defines.h:
-
-/usr/include/c++/4.2/cstddef:
-
-/usr/lib/gcc/i486-linux-gnu/4.2.3/include/stddef.h:
-
-/usr/include/stdlib.h:
-
-/usr/include/bits/waitflags.h:
-
-/usr/include/bits/waitstatus.h:
-
-/usr/include/endian.h:
-
-/usr/include/bits/endian.h:
-
-/usr/include/xlocale.h:
-
-/usr/include/sys/types.h:
-
-/usr/include/bits/types.h:
-
-/usr/include/bits/typesizes.h:
-
-/usr/include/time.h:
-
-/usr/include/sys/select.h:
-
-/usr/include/bits/select.h:
-
-/usr/include/bits/sigset.h:
-
-/usr/include/bits/time.h:
-
-/usr/include/sys/sysmacros.h:
-
-/usr/include/bits/pthreadtypes.h:
-
-/usr/include/alloca.h:
-
-/usr/include/c++/4.2/iostream:
-
-/usr/include/c++/4.2/ostream:
-
-/usr/include/c++/4.2/ios:
-
-/usr/include/c++/4.2/iosfwd:
-
-/usr/include/c++/4.2/i486-linux-gnu/bits/c++locale.h:
-
-/usr/include/c++/4.2/cstring:
-
-/usr/include/string.h:
-
-/usr/include/c++/4.2/cstdio:
-
-/usr/include/stdio.h:
-
-/usr/include/libio.h:
-
-/usr/include/_G_config.h:
-
-/usr/include/wchar.h:
-
-/usr/lib/gcc/i486-linux-gnu/4.2.3/include/stdarg.h:
-
-/usr/include/bits/stdio_lim.h:
-
-/usr/include/bits/sys_errlist.h:
-
-/usr/include/c++/4.2/clocale:
-
-/usr/include/locale.h:
-
-/usr/include/bits/locale.h:
-
-/usr/include/langinfo.h:
-
-/usr/include/nl_types.h:
-
-/usr/include/iconv.h:
-
-/usr/include/libintl.h:
-
-/usr/include/c++/4.2/cstdarg:
-
-/usr/include/c++/4.2/i486-linux-gnu/bits/c++io.h:
-
-/usr/include/c++/4.2/i486-linux-gnu/bits/gthr.h:
-
-/usr/include/c++/4.2/i486-linux-gnu/bits/gthr-default.h:
-
-/usr/include/pthread.h:
-
-/usr/include/sched.h:
-
-/usr/include/bits/sched.h:
-
-/usr/include/signal.h:
-
-/usr/include/bits/setjmp.h:
-
-/usr/include/unistd.h:
-
-/usr/include/bits/posix_opt.h:
-
-/usr/include/bits/environments.h:
-
-/usr/include/bits/confname.h:
-
-/usr/include/getopt.h:
-
-/usr/include/c++/4.2/cctype:
-
-/usr/include/ctype.h:
-
-/usr/include/c++/4.2/bits/stringfwd.h:
-
-/usr/include/c++/4.2/bits/postypes.h:
-
-/usr/include/c++/4.2/cwchar:
-
-/usr/include/c++/4.2/ctime:
-
-/usr/include/bits/wchar.h:
-
-/usr/include/stdint.h:
-
-/usr/include/c++/4.2/bits/functexcept.h:
-
-/usr/include/c++/4.2/exception_defines.h:
-
-/usr/include/c++/4.2/exception:
-
-/usr/include/c++/4.2/bits/char_traits.h:
-
-/usr/include/c++/4.2/bits/stl_algobase.h:
-
-/usr/include/c++/4.2/climits:
-
-/usr/lib/gcc/i486-linux-gnu/4.2.3/include/limits.h:
-
-/usr/lib/gcc/i486-linux-gnu/4.2.3/include/syslimits.h:
-
-/usr/include/limits.h:
-
-/usr/include/bits/posix1_lim.h:
-
-/usr/include/bits/local_lim.h:
-
-/usr/include/linux/limits.h:
-
-/usr/include/bits/posix2_lim.h:
-
-/usr/include/bits/xopen_lim.h:
-
-/usr/include/c++/4.2/bits/stl_pair.h:
-
-/usr/include/c++/4.2/bits/cpp_type_traits.h:
-
-/usr/include/c++/4.2/ext/type_traits.h:
-
-/usr/include/c++/4.2/utility:
-
-/usr/include/c++/4.2/bits/stl_relops.h:
-
-/usr/include/c++/4.2/bits/stl_iterator_base_types.h:
-
-/usr/include/c++/4.2/bits/stl_iterator_base_funcs.h:
-
-/usr/include/c++/4.2/bits/concept_check.h:
-
-/usr/include/c++/4.2/bits/stl_iterator.h:
-
-/usr/include/c++/4.2/debug/debug.h:
-
-/usr/include/c++/4.2/bits/localefwd.h:
-
-/usr/include/c++/4.2/bits/ios_base.h:
-
-/usr/include/c++/4.2/ext/atomicity.h:
-
-/usr/include/c++/4.2/i486-linux-gnu/bits/atomic_word.h:
-
-/usr/include/c++/4.2/bits/locale_classes.h:
-
-/usr/include/c++/4.2/string:
-
-/usr/include/c++/4.2/memory:
-
-/usr/include/c++/4.2/bits/allocator.h:
-
-/usr/include/c++/4.2/i486-linux-gnu/bits/c++allocator.h:
-
-/usr/include/c++/4.2/ext/new_allocator.h:
-
-/usr/include/c++/4.2/new:
-
-/usr/include/c++/4.2/bits/stl_construct.h:
-
-/usr/include/c++/4.2/bits/stl_uninitialized.h:
-
-/usr/include/c++/4.2/bits/stl_raw_storage_iter.h:
-
-/usr/include/c++/4.2/limits:
-
-/usr/include/c++/4.2/bits/ostream_insert.h:
-
-/usr/include/c++/4.2/bits/stl_function.h:
-
-/usr/include/c++/4.2/bits/basic_string.h:
-
-/usr/include/c++/4.2/algorithm:
-
-/usr/include/c++/4.2/bits/stl_algo.h:
-
-/usr/include/c++/4.2/bits/stl_heap.h:
-
-/usr/include/c++/4.2/bits/stl_tempbuf.h:
-
-/usr/include/c++/4.2/bits/basic_string.tcc:
-
-/usr/include/c++/4.2/streambuf:
-
-/usr/include/c++/4.2/bits/streambuf.tcc:
-
-/usr/include/c++/4.2/bits/basic_ios.h:
-
-/usr/include/c++/4.2/bits/streambuf_iterator.h:
-
-/usr/include/c++/4.2/bits/locale_facets.h:
-
-/usr/include/c++/4.2/cwctype:
-
-/usr/include/wctype.h:
-
-/usr/include/c++/4.2/i486-linux-gnu/bits/ctype_base.h:
-
-/usr/include/c++/4.2/i486-linux-gnu/bits/ctype_inline.h:
-
-/usr/include/c++/4.2/bits/codecvt.h:
-
-/usr/include/c++/4.2/i486-linux-gnu/bits/time_members.h:
-
-/usr/include/c++/4.2/i486-linux-gnu/bits/messages_members.h:
-
-/usr/include/c++/4.2/bits/basic_ios.tcc:
-
-/usr/include/c++/4.2/bits/ostream.tcc:
-
-/usr/include/c++/4.2/locale:
-
-/usr/include/c++/4.2/bits/locale_facets.tcc:
-
-/usr/include/c++/4.2/typeinfo:
-
-/usr/include/c++/4.2/istream:
-
-/usr/include/c++/4.2/bits/istream.tcc:
-
-/usr/include/c++/4.2/list:
-
-/usr/include/c++/4.2/bits/stl_list.h:
-
-/usr/include/c++/4.2/bits/list.tcc:
-
-DoxygenTranslator/src/Token.h:

From 293747e8c529c635b324e38a94765ef4d611767a Mon Sep 17 00:00:00 2001
From: Cheryl Foil <cheryl.foil@gmail.com>
Date: Mon, 18 Aug 2008 05:08:01 +0000
Subject: [PATCH 017/314] Silencing of some diagnostic print statements for
 what method generated what javadoc

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2008-cherylfoil@10779 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Source/Modules/java.cxx | 40 +++++++++++++++++++++-------------------
 1 file changed, 21 insertions(+), 19 deletions(-)

diff --git a/Source/Modules/java.cxx b/Source/Modules/java.cxx
index 23e233071..ac8bfe13d 100644
--- a/Source/Modules/java.cxx
+++ b/Source/Modules/java.cxx
@@ -91,6 +91,7 @@ class JAVA:public Language {
   }
   /* DOXYGEN TO JAVADOC globals */
   bool doxygen_javadoc_flag; //flag for converting found doxygen to javadoc
+  bool comment_creation_chatter; //flag for getting information about where comments were created in java.cxx
   //TODO make this bool a command line option
   DoxygenTranslator doxyTranslator;
 
@@ -123,6 +124,7 @@ public:
       global_variable_flag(false),
       old_variable_names(false),
       member_func_flag(false),
+      comment_creation_chatter(true),
       imclass_name(NULL),
       module_class_name(NULL),
       imclass_class_code(NULL),
@@ -507,8 +509,8 @@ public:
       
       if (doxygen_javadoc_flag){
       	if (Getattr(n,"DoxygenComment")){
-      		  Printf(f_module, "/* This was generated from top() */");
-      		  Printf(f_module, doxyTranslator.convert(Char((String *)Getattr(n,"DoxygenComment")),"JAVADOC")); 	
+      		  if(comment_creation_chatter) Printf(f_module, "/* This was generated from top() */");
+      		  Printf(f_module, doxyTranslator.convert(Char(Getattr(n,"DoxygenComment")),"JAVADOC")); 	
       	}
       }
       if (Len(module_class_modifiers) > 0)
@@ -1231,9 +1233,9 @@ public:
 	    //translate and write javadoc comment if flagged
 	    if (doxygen_javadoc_flag){
 	    	if (Getattr(n,"DoxygenComment")){
-	    		  Printv(proxy_class_constants_code, "/* This was generated from enumvalueDeclaration */", NIL );
-
-	    		  Printv(proxy_class_constants_code, doxyTranslator.convert(Char((const String *)Getattr(n,"DoxygenComment")),"JAVADOC"), NIL); 	
+	    		if(comment_creation_chatter) Printv(proxy_class_constants_code, "/* This was generated from enumvalueDeclaration */", NIL );
+	    		  Printv(proxy_class_constants_code, 
+	    				  doxyTranslator.convert(Char(Getattr(n,"DoxygenComment")),"JAVADOC"), NIL); 	
 	    	}
 	    }
 	    
@@ -1302,8 +1304,8 @@ public:
     //translate and write javadoc comment if flagged
     if (doxygen_javadoc_flag){
     	if (Getattr(n,"DoxygenComment")){
-    		  Printf(enum_code, "/* This was generated from enumvalueDeclaration() */" );
-    		  Printf(enum_code, doxyTranslator.convert(Char((String *)Getattr(n,"DoxygenComment")),"JAVADOC")); 	
+    		  if(comment_creation_chatter) Printf(enum_code, "/* This was generated from enumvalueDeclaration() */" );
+    		  Printf(enum_code, doxyTranslator.convert(Char(Getattr(n,"DoxygenComment")),"JAVADOC")); 	
     	}
     }
     {
@@ -1372,8 +1374,8 @@ public:
   virtual int doxygenComment(Node *n){
 		 if (doxygen_javadoc_flag){
 		   if (Getattr(n,"DoxygenComment")){
-			    	Printv(structuralComments, "/* This was generated from doxygenComment() */\n", NIL);
-			    	Printv(structuralComments, doxyTranslator.convert(Char((String *)Getattr(n,"DoxygenComment")),"JAVADOC"), NIL);
+			      if(comment_creation_chatter) Printv(structuralComments, "/* This was generated from doxygenComment() */\n", NIL);
+			      Printv(structuralComments, doxyTranslator.convert(Char(Getattr(n,"DoxygenComment")),"JAVADOC"), NIL);
 		    	}
 		    }
 	 return SWIG_OK;
@@ -1400,8 +1402,8 @@ public:
     //translate and write javadoc comment if flagged
     if (doxygen_javadoc_flag){
     	if (Getattr(n,"DoxygenComment")){
-    		Printf(constants_code, "/* This was generated from enumvalueDeclaration */\n");
-    		  Printf(constants_code, doxyTranslator.convert(Char((String *)Getattr(n,"DoxygenComment")),"JAVADOC")); 	
+    		if(comment_creation_chatter) Printf(constants_code, "/* This was generated from enumvalueDeclaration */\n");
+    		Printf(constants_code, doxyTranslator.convert(Char(Getattr(n,"DoxygenComment")),"JAVADOC")); 	
     	}
     }
     
@@ -1669,8 +1671,8 @@ public:
     //translate and write javadoc comment if flagged
     if (doxygen_javadoc_flag){
     	if (Getattr(n,"DoxygenComment")){
-  		  Printv(proxy_class_def, "/* This was generated from emitProxyClassDefAndCPPCasts() */\n", NIL );
-    		Printv(proxy_class_def, doxyTranslator.convert(Char((String *)Getattr(n,"DoxygenComment")),"JAVADOC"), NIL); 	
+    		if(comment_creation_chatter) Printv(proxy_class_def, "/* This was generated from emitProxyClassDefAndCPPCasts() */\n", NIL );
+    		Printv(proxy_class_def, doxyTranslator.convert(Char(Getattr(n,"DoxygenComment")),"JAVADOC"), NIL); 	
     	}
     }
     
@@ -2010,8 +2012,8 @@ public:
     //translate and write javadoc comment if flagged
     if (doxygen_javadoc_flag){
     	if (Getattr(n,"DoxygenComment")){
-    		  Printf(function_code, "/* This was generated from proxyclassfunctionhandler */");
-    		  Printf(function_code, doxyTranslator.convert(Char((String *)Getattr(n,"DoxygenComment")),"JAVADOC")); 	
+    		if(comment_creation_chatter) Printf(function_code, "/* This was generated from proxyclassfunctionhandler */");
+    		  Printf(function_code, doxyTranslator.convert(Char(Getattr(n,"DoxygenComment")),"JAVADOC")); 	
     	}
     }
     
@@ -2240,8 +2242,8 @@ public:
 	    //translate and write javadoc comment if flagged
 	    if (doxygen_javadoc_flag){
 	    	if (Getattr(n,"DoxygenComment")){
-	    		  Printf(function_code, "/* This was generated from constructionhandler */\n" );
-	    		  Printf(function_code, doxyTranslator.convert(Char((String *)Getattr(n,"DoxygenComment")),"JAVADOC")); 	
+	    		if(comment_creation_chatter) Printf(function_code, "/* This was generated from constructionhandler */\n" );
+	    		  Printf(function_code, doxyTranslator.convert(Char(Getattr(n,"DoxygenComment")),"JAVADOC")); 	
 	    	}
 	    }
 	    
@@ -2509,8 +2511,8 @@ public:
     //translate and write javadoc comment if flagged
     if (doxygen_javadoc_flag){
     	if (Getattr(n,"DoxygenComment")){
-    		  Printf(function_code, "/* This was generated from moduleClassFunctionHandler() */\n" );
-    		  Printf(function_code, doxyTranslator.convert(Char((String *)Getattr(n,"DoxygenComment")),"JAVADOC")); 	
+    		if(comment_creation_chatter) Printf(function_code, "/* This was generated from moduleClassFunctionHandler() */\n" );
+    		Printf(function_code, doxyTranslator.convert(Char(Getattr(n,"DoxygenComment")),"JAVADOC")); 	
     	}
     }
 

From d08245c7f997646795cf1e1f85072140230ae79d Mon Sep 17 00:00:00 2001
From: Cheryl Foil <cheryl.foil@gmail.com>
Date: Mon, 18 Aug 2008 07:23:41 +0000
Subject: [PATCH 018/314] memory leak fix for a test method

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2008-cherylfoil@10781 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Source/DoxygenTranslator/src/DoxygenTranslator.cpp | 11 ++++-------
 1 file changed, 4 insertions(+), 7 deletions(-)

diff --git a/Source/DoxygenTranslator/src/DoxygenTranslator.cpp b/Source/DoxygenTranslator/src/DoxygenTranslator.cpp
index a1789eb74..77090573a 100644
--- a/Source/DoxygenTranslator/src/DoxygenTranslator.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenTranslator.cpp
@@ -1,17 +1,11 @@
-
-
 #include "DoxygenParser.h"
 #include "DoxygenTranslator.h"
 #include <cstdlib>
 #include <iostream>
-#include <fstream>
 #include <string>
-#include <list>
 #include "DoxygenEntity.h"
-#include "TokenList.h"
 #include "JavaDocConverter.h"
 
-
 DoxygenParser doxyParse;
 JavaDocConverter jDC;
 
@@ -65,7 +59,10 @@ int testCommands(){
 		cout << "---ORIGINAL DOXYGEN--- " << endl << exampleArray[i] << endl;
 		char *nonConstString = (char *)malloc(exampleArray[i].length()+1);
 		strcpy(nonConstString, exampleArray[i].c_str());
-		dT.convert(nonConstString, "JAVADOC");
+		char * result = dT.convert(nonConstString, "JAVADOC");
+		free(nonConstString);
+		free(result);
 	}
 	return 1;
 }
+

From 4af0c994992b29e264eb3f2cddd486872112fc92 Mon Sep 17 00:00:00 2001
From: Cheryl Foil <cheryl.foil@gmail.com>
Date: Mon, 18 Aug 2008 07:34:27 +0000
Subject: [PATCH 019/314] Memory usage fix in java.cxx

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2008-cherylfoil@10782 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Source/Modules/java.cxx | 41 ++++++++++++++++++++++++++++++-----------
 1 file changed, 30 insertions(+), 11 deletions(-)

diff --git a/Source/Modules/java.cxx b/Source/Modules/java.cxx
index ac8bfe13d..025cfc1c8 100644
--- a/Source/Modules/java.cxx
+++ b/Source/Modules/java.cxx
@@ -124,7 +124,7 @@ public:
       global_variable_flag(false),
       old_variable_names(false),
       member_func_flag(false),
-      comment_creation_chatter(true),
+      comment_creation_chatter(false),
       imclass_name(NULL),
       module_class_name(NULL),
       imclass_class_code(NULL),
@@ -510,7 +510,9 @@ public:
       if (doxygen_javadoc_flag){
       	if (Getattr(n,"DoxygenComment")){
       		  if(comment_creation_chatter) Printf(f_module, "/* This was generated from top() */");
-      		  Printf(f_module, doxyTranslator.convert(Char(Getattr(n,"DoxygenComment")),"JAVADOC")); 	
+      		  char *convertedString = doxyTranslator.convert(Char(Getattr(n,"DoxygenComment")),"JAVADOC");
+      		  Printf(f_module, convertedString); 	
+      		  free(convertedString);
       	}
       }
       if (Len(module_class_modifiers) > 0)
@@ -640,6 +642,8 @@ public:
     module_imports = NULL;
     Delete(module_class_modifiers);
     module_class_modifiers = NULL;
+    Delete(structuralComments);
+    structuralComments = NULL;
     Delete(imclass_imports);
     imclass_imports = NULL;
     Delete(imclass_cppcasts_code);
@@ -1234,8 +1238,9 @@ public:
 	    if (doxygen_javadoc_flag){
 	    	if (Getattr(n,"DoxygenComment")){
 	    		if(comment_creation_chatter) Printv(proxy_class_constants_code, "/* This was generated from enumvalueDeclaration */", NIL );
-	    		  Printv(proxy_class_constants_code, 
-	    				  doxyTranslator.convert(Char(Getattr(n,"DoxygenComment")),"JAVADOC"), NIL); 	
+	    		char *convertedString = doxyTranslator.convert(Char(Getattr(n,"DoxygenComment")),"JAVADOC");
+	    		Printv(proxy_class_constants_code, convertedString, NIL); 	
+	    		free(convertedString); 
 	    	}
 	    }
 	    
@@ -1305,7 +1310,9 @@ public:
     if (doxygen_javadoc_flag){
     	if (Getattr(n,"DoxygenComment")){
     		  if(comment_creation_chatter) Printf(enum_code, "/* This was generated from enumvalueDeclaration() */" );
-    		  Printf(enum_code, doxyTranslator.convert(Char(Getattr(n,"DoxygenComment")),"JAVADOC")); 	
+	    	  char *convertedString = doxyTranslator.convert(Char(Getattr(n,"DoxygenComment")),"JAVADOC");		
+    		  Printf(enum_code, convertedString); 	
+    		  free(convertedString); 
     	}
     }
     {
@@ -1375,7 +1382,9 @@ public:
 		 if (doxygen_javadoc_flag){
 		   if (Getattr(n,"DoxygenComment")){
 			      if(comment_creation_chatter) Printv(structuralComments, "/* This was generated from doxygenComment() */\n", NIL);
-			      Printv(structuralComments, doxyTranslator.convert(Char(Getattr(n,"DoxygenComment")),"JAVADOC"), NIL);
+		    	  char *convertedString = doxyTranslator.convert(Char(Getattr(n,"DoxygenComment")),"JAVADOC");			
+			      Printv(structuralComments, convertedString, NIL);
+			      free(convertedString);
 		    	}
 		    }
 	 return SWIG_OK;
@@ -1403,7 +1412,9 @@ public:
     if (doxygen_javadoc_flag){
     	if (Getattr(n,"DoxygenComment")){
     		if(comment_creation_chatter) Printf(constants_code, "/* This was generated from enumvalueDeclaration */\n");
-    		Printf(constants_code, doxyTranslator.convert(Char(Getattr(n,"DoxygenComment")),"JAVADOC")); 	
+	    	char *convertedString = doxyTranslator.convert(Char(Getattr(n,"DoxygenComment")),"JAVADOC");			
+            Printf(constants_code, convertedString); 	
+		    free(convertedString);
     	}
     }
     
@@ -1672,7 +1683,9 @@ public:
     if (doxygen_javadoc_flag){
     	if (Getattr(n,"DoxygenComment")){
     		if(comment_creation_chatter) Printv(proxy_class_def, "/* This was generated from emitProxyClassDefAndCPPCasts() */\n", NIL );
-    		Printv(proxy_class_def, doxyTranslator.convert(Char(Getattr(n,"DoxygenComment")),"JAVADOC"), NIL); 	
+	    	char *convertedString = doxyTranslator.convert(Char(Getattr(n,"DoxygenComment")),"JAVADOC");			
+	    	Printv(proxy_class_def, convertedString, NIL); 		
+		    free(convertedString);
     	}
     }
     
@@ -2013,7 +2026,9 @@ public:
     if (doxygen_javadoc_flag){
     	if (Getattr(n,"DoxygenComment")){
     		if(comment_creation_chatter) Printf(function_code, "/* This was generated from proxyclassfunctionhandler */");
-    		  Printf(function_code, doxyTranslator.convert(Char(Getattr(n,"DoxygenComment")),"JAVADOC")); 	
+  	    	char *convertedString = doxyTranslator.convert(Char(Getattr(n,"DoxygenComment")),"JAVADOC");			
+  	    	 Printf(function_code, convertedString); 		
+  		    free(convertedString);
     	}
     }
     
@@ -2243,7 +2258,9 @@ public:
 	    if (doxygen_javadoc_flag){
 	    	if (Getattr(n,"DoxygenComment")){
 	    		if(comment_creation_chatter) Printf(function_code, "/* This was generated from constructionhandler */\n" );
-	    		  Printf(function_code, doxyTranslator.convert(Char(Getattr(n,"DoxygenComment")),"JAVADOC")); 	
+	  	    	char *convertedString = doxyTranslator.convert(Char(Getattr(n,"DoxygenComment")),"JAVADOC");			
+	  	    	Printf(function_code, convertedString); 			
+		  		free(convertedString);
 	    	}
 	    }
 	    
@@ -2512,7 +2529,9 @@ public:
     if (doxygen_javadoc_flag){
     	if (Getattr(n,"DoxygenComment")){
     		if(comment_creation_chatter) Printf(function_code, "/* This was generated from moduleClassFunctionHandler() */\n" );
-    		Printf(function_code, doxyTranslator.convert(Char(Getattr(n,"DoxygenComment")),"JAVADOC")); 	
+  	    	char *convertedString = doxyTranslator.convert(Char(Getattr(n,"DoxygenComment")),"JAVADOC");			
+  	    	Printf(function_code, convertedString); 			
+	  		free(convertedString);	
     	}
     }
 

From d621d21617759e346653a57db28c83c1d9c1da71 Mon Sep 17 00:00:00 2001
From: Cheryl Foil <cheryl.foil@gmail.com>
Date: Mon, 18 Aug 2008 12:18:01 +0000
Subject: [PATCH 020/314] Documentation Page (draft) written. Not yet added to
 table of contents.

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2008-cherylfoil@10783 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Doc/Manual/DoxygenTranslation.html | 257 +++++++++++++++++++++++++++++
 Doc/Manual/chapters                |   2 +-
 2 files changed, 258 insertions(+), 1 deletion(-)
 create mode 100644 Doc/Manual/DoxygenTranslation.html

diff --git a/Doc/Manual/DoxygenTranslation.html b/Doc/Manual/DoxygenTranslation.html
new file mode 100644
index 000000000..e3797b56f
--- /dev/null
+++ b/Doc/Manual/DoxygenTranslation.html
@@ -0,0 +1,257 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html>
+<head>
+<title>SWIG and Doxygen Translation</title>
+<link rel="stylesheet" type="text/css" href="style.css">
+</head>
+<body bgcolor="#FFFFFF">
+<H1><a name="Java"></a>SWIG and Doxgeyn Translation</H1>
+<!-- INDEX -->
+<div class="sectiontoc">
+<ul>
+<li><a href="#doxygen_translation_overview">Overview</a>
+<li><a href="#file_preparation">File Preparation</a>
+<ul>
+<li><a href="#running_swig">Running SWIG with Doxygen translation</a>
+<li><a href="#additional_options">Additional Options</a>
+</ul>
+<li><a href="#doxygen_to_javadoc">Doxygen->JavaDoc</a>
+<ul>
+<li><a href="#basic_example">Basic Example</a>
+<li><a href="#javadoc_tags">JavaDoc Tags</a>
+<li><a href="#other_tags">Other Tags</a>
+<li><a href="#bad_behaviour">Bad Behaviour</a>
+</ul>
+<li><a href="#further_details">Further details on Doxygen</a>
+<li><a href="#developer_details">Developer Information</a>
+<ul>
+<li><a href="#module_design">Module Design</a>
+<li><a href="#language_extension">Extending to Other Languages</a>
+</ul>
+</ul>
+
+</div>
+<!-- INDEX -->
+
+<p>
+This chapter describes SWIG's support for translating Doxygen comments found in interface and header files into a target language's normal documentation language. Currently only JavaDoc is supported.
+</p>
+
+<H2><a name="doxygen_translation_overview"></a>Doxygen Translation Overview</H2>
+
+<p>
+The Doxygen Translation Module of SWIG is an ongoing effort from a <A HREF ="http://code.google.com/soc/2008/">Google Summer of Code</A> proposal from Summer 2008. It adds an extra layer of functionality to SWIG, allowing automated translation of <A HREF= "http://www.stack.nl/~dimitri/doxygen/">Doxygen</A> formatted comments from interface files into a documentation language more suited for the target language. Currently this module only translates into JavaDoc for the SWIG Java Module, but other extensions are to be added in time.
+</p>
+
+<p>
+Questions about running SWIG are best answered in the <a href="SWIG.html#SWIG">SWIG Basics</a> chapter as well as the target language modules. (For now, only <A href = "Java.html">Java</A>). The behaviour of this functionality is wildly unpredictable if the interface file is not proper to begin with!
+</p>
+
+<H2><a name="file_preparation"></a>Preparations</H2>
+
+
+<p>
+To make use of the comment translation system, your documentation comments must be in properly formatted <A HREF= "http://www.stack.nl/~dimitri/doxygen/">Doxygen.</A> They can be present in your main interface file or any header file that it imports. It is advised that you are certain your comments compile properly with Doxygen before you try to translate them. Doxygen itself is a deeper tool and can provide you better feedback for correct any syntax errors that may be present. Please look at Doxygen's <A HREF = "http://www.stack.nl/~dimitri/doxygen/docblocks.html"> Documenting the code</A> for proper specificatons for comment format.
+</p>
+
+<div class="code"><pre>
+/*! This is describing class Shape
+ \author Bob
+ */
+
+class Shape {
+</pre></div>
+
+<p>
+Because this functionality is currently only extended to java, you must be able to run SWIG's <A href = "Java.html">Java Module</A> in order to make use of this tool.</p>
+<H3><a name="running_swig"></a> Enabling Doxygen Translation</H3>
+
+
+<p>
+NOT YET ADDED (current development branch has this feature automatically enabled).
+</p>
+
+<H3><a name="additional_options"></a>Additional Commandline Options</H3>
+
+<p>
+ALSO TO BE ADDED (JavaDoc Autobrief?)
+</p>
+
+<H2><a name="doxygen_to_javadoc"></a>Doxygen To JavaDoc</H2>
+
+
+<p>
+If translation is enabled, JavaDoc formatted comments should be automatically placed in the correct locations in the resulting module and proxy files.</p>
+
+<H3><a name="basic_example"></a>Basic Example</H3>
+
+<p> Here is an example segment from an included header file</p>
+<div class="code"><pre>
+/*! This is describing class Shape
+ \author Bob
+ */
+
+class Shape {
+public:
+  Shape() {
+    nshapes++;
+  }
+  virtual ~Shape() {
+    nshapes--;
+  };
+  double  x, y; /*!< Important Variables */
+  void    move(double dx, double dy); /*!< Moves the Shape */
+  virtual double area(void) = 0; /*!< \return the area */
+  virtual double perimeter(void) = 0; /*!< \return the perimeter */
+  static  int nshapes;
+};
+</pre></div>
+
+<p>Simply running SWIG should result in the following code being present in Shapes.java</p>
+
+<div class="targetlang"><pre>
+
+/**
+ * This is describing class Shape  
+ * 
+ * @author	Bob  
+ */
+
+public class Shape {
+
+...
+
+/**
+ * Important things  
+ * 
+ */
+  public void setX(double value) {
+    exampleJNI.Shape_x_set(swigCPtr, this, value);
+  }
+
+...
+
+/**
+ * @return	the area  
+ */
+  public double area() {
+    return exampleJNI.Shape_area(swigCPtr, this);
+  }
+
+/**
+ * @return	the perimeter  
+ */
+  public double perimeter() {
+    return exampleJNI.Shape_perimeter(swigCPtr, this);
+  }
+
+</pre></div>
+
+
+
+<p>
+The code Java-wise should be identical to what would have been generated without this feature enabled. When the Doxygen Translator Module encounters a comment it finds nothing useful in or cannot parse, it should not effect the functionality of the SWIG generated code.</p>
+
+
+<H3><a name="javadoc_tags"></a>JavaDoc Tags</H3>
+
+
+<p>
+Doxygen has a wealth of tags such as @latexonly that have no equivalent in JavaDoc. As a result several tags that have no translation (or particular use, such as some linking and section tags) are supressed. If you are interested in more if the specifics of JavaDoc, please visit <A HREF="http://java.sun.com/j2se/javadoc/writingdoccomments/">How to Write Doc Comments for the Javadoc Tool.</A></p>
+<b>Doxygen and JavaDoc Equivalent Tags</b>
+<div class="diagram"><pre>
+* @param      
+* @return      
+* @exception   
+* @author      
+* @version     
+* @see         
+* @since       
+* @serial      
+* @deprecated  
+</pre></div>
+
+<H3><a name="other_tags"></a>Other Tags</H3>
+
+
+<p>
+Because there are no specific JavaDoc tag for some important information, some tags are given plain-english descriptions of their presence, such as @bug. This is a feature currently still being developed and it is likely that more information from the original Doxygen Comments will be reproduced as this module matures.
+</p>
+<H3><a name="bad_behaviour"></a>Bad Behaviour</H3>
+
+
+<p>
+There are some tags that the Doxygen Translator Module currently does not expect to encounter. This includes the PHP-only Doxygen commands such as @publicsection:
+</p>
+<b> Completely Unsupported Tags</b>
+<div class="diagram"><pre>
+"annotatedclasslist", "classhierarchy", "define", "functionindex", 
+"header", "headerfilelist", "inherit", "l", "postheader", "private",
+ "privatesection", "protected", "protectedsection", "public", "publicsection"
+</pre></div>
+
+<p>
+The parsing behaviour will be unpredictable if any of these are encountered for now. This should eventually be changed so that they are simply ignored.
+</p>
+<p>
+In general parsing errors should not interfere with the operation of SWIG itself. Blank comments or lack of comments could be indication of either a parsing error or a lack of meaningful tags in a specific blob of doxygen. 
+</p>
+
+
+<H3><a name="further_details"></a>Further Details</H3>
+
+
+<p>
+TO BE ADDED.
+</p>
+
+
+<H2><a name="developer_details"></a>Developer Information</H2>
+
+
+<p>
+Currently a good deal of this Module still needs some reworking, particularly on the side of the parser and JavaDoc producer. </p>
+
+<H3><a name="module_design"></a>Module Design</H3>
+
+
+<p>
+If this functionality is turned on, SWIG places all comments found into the SWIG parse tree. Nodes contain an additional attribute called DoxygenComment when a comment is present. Individual nodes containing Doxygen with Structural Indicators, such as @file, as their first command, are also present in the parse tree. These indivudal "blobs" of Doxygen such as :</p>
+<div class="code"><pre>
+/*! This is describing function Foo
+ \param x some random variable
+ \author Bob
+ \return Foo
+ */
+</pre></div>
+
+<p>
+are passed on individually to the DoxygenTranslator Module. This module builds it's own private parse tree and hands it, similar to SWIG itself, to a seperate class to translate into the target documentation language. For example, JavaDocConverter is the JavaDoc module class.
+</p>
+
+<H2><a name="language_extension"></a>Extending to Other Languages</H2>
+
+
+<p>
+In general, extension to another language requires a fairly deep understanding of the target language module- such as Modules/python.cxx for python. Searching for "doxygen" in the java.cxx module can give you a good idea of the process for placing in documentation comments into the correct areas. The basic gist is that anywhere a comment may reside on a node, there needs to be a catch for it in front of where that function, class, or other object is written out to a target language file. The other half of extension is building a target documentation language comment generator that handles 1 blob at a time. However, this is relatively simple- nowhere near as complex as the wrapper generating modules in SWIG. See DoxygenTranslator/JavaDocConverter.cpp for a good example. The target language module hands DoxygenTranslator the blob to translate, and receives back a translated text.
+</p>
+<b> What is given to Doxygen Translator</b>
+<div class="code"><pre>
+/*! This is describing function Foo
+ \param x some random variable
+ \author Bob
+ \return Foo
+ */
+</pre></div>
+<b> What is received back by java.cxx </b>
+<div class="targetlang"><pre>
+/** This is describing function Foo
+ *
+ * @param x some random variable
+ * @author Bob
+ * @return Foo
+ */
+</pre></div>
+<p> Development of the comment translator itself is simplified by the fact that the DoxygenTranslator module can easily include a main in DoxygenTranslator and thus be developed, compiled, and tested independantly of SWIG.</p>
+</body>
+</html>
diff --git a/Doc/Manual/chapters b/Doc/Manual/chapters
index 55a0aec13..2e5a16364 100644
--- a/Doc/Manual/chapters
+++ b/Doc/Manual/chapters
@@ -32,4 +32,4 @@ Ruby.html
 Tcl.html
 R.html
 Extending.html
-
+DoxygenTranslation.html

From 719abc61cc26d208e5831043500b3d70014d282e Mon Sep 17 00:00:00 2001
From: Cheryl Foil <cheryl.foil@gmail.com>
Date: Mon, 18 Aug 2008 16:08:51 +0000
Subject: [PATCH 021/314] parsing fixes, helped behaviour of normal text
 descriptions in comments

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2008-cherylfoil@10788 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Examples/doxygencomments/java/class/example.h | 22 +++++---
 .../DoxygenTranslator/src/DoxygenParser.cpp   | 21 ++++----
 .../src/DoxygenTranslator.cpp                 | 52 +++++++++++++------
 .../src/JavaDocConverter.cpp                  | 43 ++++++++++++---
 .../DoxygenTranslator/src/JavaDocConverter.h  |  1 -
 Source/Modules/java.cxx                       |  6 +--
 6 files changed, 100 insertions(+), 45 deletions(-)

diff --git a/Examples/doxygencomments/java/class/example.h b/Examples/doxygencomments/java/class/example.h
index 7e3e7d540..ce9af23d3 100644
--- a/Examples/doxygencomments/java/class/example.h
+++ b/Examples/doxygencomments/java/class/example.h
@@ -1,8 +1,10 @@
-/** \file example.h 
+/*! \file example.h 
 comments on example.h */
 
 /*! This is describing class Shape
  \author Bob
+ \exception some sort of exception
+ \see OtherShapes()
  */
 
 class Shape {
@@ -13,11 +15,12 @@ public:
   virtual ~Shape() {
     nshapes--;
   };
-  double  x, y; /*!< Important things  */
+  double  x, y; /*!< Important variables  */
   void    move(double dx, double dy);
-  virtual double area(void) = 0; /*!< \return the area */
-  virtual double perimeter(void) = 0; /*!< \return the perimeter */
-  static  int nshapes;
+  virtual double area(void) = 0; /*!< \return the area \exception exception description */
+  virtual double perimeter(void) = 0; /*!< \exception exception description 
+					\return the perimeter */
+  static  int nshapes; /*!< Details about nshapes. */
 };
 /*! This is describing class Circle */
 class Circle : public Shape {
@@ -25,8 +28,9 @@ private:
   double radius;
 public:
   Circle(double r) : radius(r) { };
-  virtual double area(void);
-  virtual double perimeter(void);
+  virtual double area(void); /*!< \return the area \exception exception description */
+  virtual double perimeter(void); /*!< \exception exception description 
+					\return the perimeter */
 };
 
 /*! This is describing class square */
@@ -34,7 +38,9 @@ class Square : public Shape {
 private:
   double width;
 public:
-  Square(double w) : width(w) { };
+  Square(double w) : width(w) { }; /*!< Create square
+					/param w the width
+					/exception some description */
   virtual double area(void);
   virtual double perimeter(void);
 };
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.cpp b/Source/DoxygenTranslator/src/DoxygenParser.cpp
index 920b7c794..d953bc6d4 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenParser.cpp
@@ -31,7 +31,7 @@ DoxygenParser::~DoxygenParser()
 }
 
 //////////////////////////////////////////
-int noisy = 1; // set this to 1 for extra chatter from the parsing stage.
+int noisy = 0; // set this to 1 for extra chatter from the parsing stage.
 int addCommand(string currCommand, TokenList &tokList,  list <DoxygenEntity> &aNewList);
 list <DoxygenEntity> parse(list<Token>::iterator endParsingIndex, TokenList &tokList);
 
@@ -70,7 +70,7 @@ string commandWords[] = {"a", "b", "c", "e", "em", "p", "def", "enum", "example"
 string ignoredCommandWords[] = {"copydoc", "copybrief", "copydetails", "verbinclude", "htmlinclude"};
 string commandLines[] = {"addindex", "fn", "name", "line", "var", "skipline", "typedef", "skip", "until", "property"};
 string ignoreCommandLines[] = {"nothing at the moment"};
-string commandParagraph[] = {"return", "remarks", "since", "test", "sa", "see", "pre", "post", "details", "invariant", 
+string commandParagraph[] = {"partofdescription", "return", "remarks", "since", "test", "sa", "see", "pre", "post", "details", "invariant", 
 		    "deprecated", "date", "note", "warning", "version", "todo", "bug", "attention", "brief", "author"};
 string ignoreCommandParagraphs[] = {"nothing at the moment"};
 string commandEndCommands[] = {"code", "dot", "msc", "f$", "f[", "f{environment}{", "htmlonly", "latexonly", "manonly", 
@@ -208,27 +208,28 @@ list<Token>::iterator getOneLine(TokenList &tokList){
 	 list<Token>::iterator endOfLine = tokList.iteratorCopy();
 	 while(endOfLine!= tokList.end()){
 		 if ((* endOfLine).tokenType == END_LINE){
-			 endOfLine++;
+			 //cout << "REACHED END" << endl;
+			 //endOfLine++;
 			 return endOfLine;
 			 }
+		 //cout << (* endOfLine).toString();
 		 endOfLine++;
 		 }
-	 cout << "REACHED END" << endl;
+	 
 	return tokList.end();
 	}
 
 /* Returns a properly formatted string
-* up til ANY command or end of paragraph is encountered.
+* up til ANY command or end of line is encountered.
 */
 string getStringTilCommand(TokenList &tokList){
 	 string description;
 	 if (tokList.peek().tokenType == 0) return "";
-	 while(tokList.peek().tokenType == PLAINSTRING || tokList.peek().tokenType == END_LINE ){
+	 while(tokList.peek().tokenType == PLAINSTRING){
 		 Token currentToken = tokList.next();
 		 if(currentToken.tokenType == PLAINSTRING) {
 			 description = description + currentToken.tokenString + " ";
 			 }
-		 else if (tokList.peek().tokenType == END_LINE) break;
 		 }
 	return description;
 	}
@@ -259,7 +260,7 @@ list<Token>::iterator getEndOfParagraph(TokenList &tokList){
 			 endOfParagraph++;
 			 if ((* endOfParagraph).tokenType == END_LINE){
 				 endOfParagraph++;
-				 cout << "ENCOUNTERED END OF PARA" << endl;
+				 //cout << "ENCOUNTERED END OF PARA" << endl;
 				 return endOfParagraph;
 				 }
 			 }
@@ -762,14 +763,14 @@ list<DoxygenEntity> parseRoot(list<Token>::iterator endParsingIndex, TokenList &
 			if (currCommand < 0 ){ 
 				if(noisy) cout << "Unidentified Command " << currToken.tokenString << endl;
 				tokList.next();
-				addCommand(string("details"), tokList, aNewList);}
+				addCommand(string("partofdescription"), tokList, aNewList);}
 				//cout << "Command: " << currWord << " " << currCommand << endl;
 			else { tokList.next();
 			  addCommand(currToken.tokenString, tokList,  aNewList);
 			  }
 			}
 		else if (currToken.tokenType == PLAINSTRING){
-			addCommand(string("details"), tokList, aNewList);
+			addCommand(string("partofdescription"), tokList, aNewList);
 			}
 		}
 	return aNewList;
diff --git a/Source/DoxygenTranslator/src/DoxygenTranslator.cpp b/Source/DoxygenTranslator/src/DoxygenTranslator.cpp
index 77090573a..d6f0ae152 100644
--- a/Source/DoxygenTranslator/src/DoxygenTranslator.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenTranslator.cpp
@@ -36,27 +36,27 @@ char *DoxygenTranslator::convert(char* doxygenBlob, char* option){
 
 int testCommands(){
 	string exampleArray[] = {
-	"/**\n * \n * Random Line \n * \\@ \n * Random Line After */",
-	"/**\n * \n * Random Line Before \n * \\b bold \n * Random Line After */",
-	"/**\n * \n * Random Line \n * \\copydoc bold \n * Random Line After */",
-	"/**\n * \n * Random Line \n * \n * \\addindex An Entire Line\n * \\addindex An Entire Line\n * Random Line After */",
-	"/**\n * \n * Random Line \n * \n * \\return An Entire Paragraph \n * Including This Line \n * \n * Random Line After */",
-	"/**\n * \n * Random Line \n * \\return An Entire Paragraph \n * Including This Line \n * \\author Shouldn't be part of return */",
-	"/**\n * \n * Random Line \n * \\code this should continue \n * until here \\endcode \n * Random Line After */",
-	"/**\n * \n * Random Line \n * \\param singleword then the rest of \n *  the description \n * \n * Random Line After */",
-	"/**\n * \n * Random Line \n * \\page  singleword this should go til here \n * but not this */",
-	"/**\n * \n * Random Line \n * \\page  singleword this should go til here \n * but not this */",
-	"/**\n * \n * Random Line \n * \\category  singleword \n * but not this */",
-	"/**\n * \n * Random Line \n * \\category  singleword oneword \n * but not this */",
-	"/**\n * \n * Random Line \n * \\category  singleword oneword twoword \n * but not this */",
-	"/**\n * \n * Random Line \n * \\dir singleword \n * but not this */",
-	"/**\n * \n * Random Line \n * \\dir \n * but not this */",
-	"/**\n * \n * Random Line \n * \\fakecommand details \n * but not this */"
+	"/**\n * Random Line \n * \\@ \n * Random Line After */",
+	"/**\n *  Random Line Before \n * \n * \\b bold \n * Random Line After */",
+	"/**\n *  Random Line \n * \n *\\copydoc bold \n * Random Line After */",
+	"/**\n *  Random Line \n * \n * \\addindex An Entire Line\n * \\addindex An Entire Line\n * Random Line After */",
+	"/**\n *  Random Line \n * \n * \\return An Entire Paragraph \n * Including This Line \n * \n * Random Line After */",
+	"/**\n *  Random Line \n * \n * \\return An Entire Paragraph \n * Including This Line \n * \\author Shouldn't be part of return */",
+	"/**\n *  Random Line \n * \n * \\code this should continue \n * until here \\endcode \n * Random Line After */",
+	"/**\n *  Random Line \n * \n * \\param singleword then the rest of \n *  the description \n * \n * Random Line After */",
+	"/**\n *  Random Line \n * \n * \\page  singleword this should go til here \n * but not this */",
+	"/**\n *  Random Line \n * \n * \\page  singleword this should go til here \n * but not this */",
+	"/**\n *  Random Line \n * \n * \\category  singleword \n * but not this */",
+	"/**\n *  Random Line \n * \n * \\category  singleword oneword \n * but not this */",
+	"/**\n *  Random Line \n * \n * \\category  singleword oneword twoword \n * but not this */",
+	"/**\n *  Random Line \n * \n * \\dir singleword \n * but not this */",
+	"/**\n *  Random Line \n * \n * \\dir \n * but not this */",
+	"/**\n *  Random Line \n * \n * \\fakecommand details \n * but not this */"
 	};
 	//string exampleArrayUniques = {};
 	DoxygenTranslator dT = DoxygenTranslator();
 	for (int i = 0; i < 16; i ++ ){
-		cout << "---ORIGINAL DOXYGEN--- " << endl << exampleArray[i] << endl;
+		//cout << "---ORIGINAL DOXYGEN--- " << endl << exampleArray[i] << endl;
 		char *nonConstString = (char *)malloc(exampleArray[i].length()+1);
 		strcpy(nonConstString, exampleArray[i].c_str());
 		char * result = dT.convert(nonConstString, "JAVADOC");
@@ -66,3 +66,21 @@ int testCommands(){
 	return 1;
 }
 
+//int main(int argc, char *argv[]){
+	//string doxygenString1 = "//! \\brief a brief description \n\n A normal member taking two arguments and returning an \\b integer value. This is a very long description for the simple purpose of showing off formatting. Let's make it a bit longer just to be sure. \n/*!\n \\param a an \\b integer argument.\n \\return The test results\n \\param s a constant character pointer. Let's also make this a very long description! \n \\bug this command should, for now, be totally ignored\n \\author cheryl foil\n \\sa Test(), ~Test(), testMeToo() and publicVar()\n */";
+	//cout << "---ORIGINAL DOXYGEN--- " << endl << doxygenString1 << endl;
+	//char *nonConstString = (char *)malloc(doxygenString1.length()+1);
+	//strcpy(nonConstString, doxygenString1.c_str());
+	//DoxygenTranslator dT = DoxygenTranslator();
+	//char *result = dT.convert("/**\n * \n * Random Line \n * \n * \\name An Entire Line \n * NOT This Line \n * \n * Random Line After */", "JAVADOC");
+	//result = dT.convert(nonConstString, "JAVADOC");
+	//cout << "End";
+	//list <DoxygenEntity> rootList = doxyParse.createTree(doxygenString1);
+    //JavaDocConverter jDC = JavaDocConverter();
+    //jDC.convertToJavaDoc(rootList);
+	//testCommands();
+	//return 1;
+//}
+
+
+
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.cpp b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
index c1606cc77..70c3bb731 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
@@ -21,6 +21,8 @@ bool compare_DoxygenEntities(DoxygenEntity first, DoxygenEntity second){
 	if(second.typeOfEntity.compare("brief") == 0) return false;
 	if(first.typeOfEntity.compare("details") == 0) return true;
 	if(second.typeOfEntity.compare("details") == 0) return false;
+	if(first.typeOfEntity.compare("partofdescription") == 0) return true;
+	if(first.typeOfEntity.compare("partofdescription") == 0) return false;
 	if(first.typeOfEntity.compare("plainstring") == 0) return true;
 	if(second.typeOfEntity.compare("plainstring") == 0) return false;
 	if(first.typeOfEntity.compare("param") == 0){
@@ -132,14 +134,41 @@ string formatCommand(string unformattedLine, int indent){
  * could probably be much more efficient...
  */
 string javaDocFormat(DoxygenEntity &doxygenEntity){
+	if(doxygenEntity.typeOfEntity.compare("partofdescription") == 0){
+				return doxygenEntity.data;
+		}
 	if (doxygenEntity.typeOfEntity.compare("plainstring") == 0){
-			return doxygenEntity.data;
+			return  doxygenEntity.data;
 	}
 	else if (doxygenEntity.typeOfEntity.compare("b") == 0){
-		return "\b<b>" + doxygenEntity.data + "</b>";
+		return "<b>" + doxygenEntity.data + "</b>";
 	}
 	else if (doxygenEntity.typeOfEntity.compare("c") == 0){
-		return "\b<tt>" + doxygenEntity.data + "</tt>";
+		return "<tt>" + doxygenEntity.data + "</tt>";
+	}
+	else if (doxygenEntity.typeOfEntity.compare("@") == 0){
+		return "@";
+	}
+	else if (doxygenEntity.typeOfEntity.compare("\\") == 0){
+		return "\\";
+	}
+	else if (doxygenEntity.typeOfEntity.compare("<") == 0){
+		return "&lt;";
+	}
+	else if (doxygenEntity.typeOfEntity.compare(">") == 0){
+		return "&gt;";
+	}
+	else if (doxygenEntity.typeOfEntity.compare("&") == 0){
+		return "&amp;";
+	}
+	else if (doxygenEntity.typeOfEntity.compare("#") == 0){
+		return "#";
+	}
+	else if (doxygenEntity.typeOfEntity.compare("%") == 0){
+		return "%";
+	}
+	else if (doxygenEntity.typeOfEntity.compare("~") == 0){
+		return "~";
 	}
 	return "";
 }
@@ -160,6 +189,7 @@ string translateSubtree( DoxygenEntity &doxygenEntity){
 }
 
 string translateEntity(DoxygenEntity &doxyEntity){
+	if(doxyEntity.typeOfEntity.compare("partofdescription")== 0) return formatCommand(string(translateSubtree(doxyEntity)), 0);
 	if ((doxyEntity.typeOfEntity.compare("brief") == 0)||(doxyEntity.typeOfEntity.compare("details") == 0)){
 		return formatCommand(string(translateSubtree(doxyEntity)), 0) + "\n * ";}
 	else if(doxyEntity.typeOfEntity.compare("plainstring")== 0 || doxyEntity.typeOfEntity.compare("deprecated")== 0 || doxyEntity.typeOfEntity.compare("brief")== 0)
@@ -179,7 +209,7 @@ string translateEntity(DoxygenEntity &doxyEntity){
 	else if(doxyEntity.typeOfEntity.compare("sa")== 0){
 		return formatCommand(string("@see\t\t" + translateSubtree(doxyEntity)), 2);
 	}
-
+	else return formatCommand(javaDocFormat(doxyEntity), 0 );
 	return "";
 }
 
@@ -201,7 +231,8 @@ string JavaDocConverter:: convertToJavaDoc(list <DoxygenEntity> entityList){
 	}
 
 	javaDocString += "\n */\n";
+	if(printSortedTree2){
 	cout << "\n---RESULT IN JAVADOC---" << endl;
-	cout << javaDocString;
+	cout << javaDocString; }
 	return javaDocString;
-}
+}
\ No newline at end of file
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.h b/Source/DoxygenTranslator/src/JavaDocConverter.h
index 81122bc5f..53a270ce4 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.h
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.h
@@ -1,7 +1,6 @@
  #include <list>
  #include <string>
  #include "DoxygenEntity.h"
-
 #ifndef JAVADOCCONVERTER_H_
 #define JAVADOCCONVERTER_H_
 
diff --git a/Source/Modules/java.cxx b/Source/Modules/java.cxx
index 025cfc1c8..a21e37bf4 100644
--- a/Source/Modules/java.cxx
+++ b/Source/Modules/java.cxx
@@ -44,6 +44,8 @@ class JAVA:public Language {
   bool global_variable_flag;	// Flag for when wrapping a global variable
   bool old_variable_names;	// Flag for old style variable names in the intermediary class
   bool member_func_flag;	// flag set when wrapping a member function
+  bool doxygen_javadoc_flag; //flag for converting found doxygen to javadoc
+  bool comment_creation_chatter; //flag for getting information about where comments were created in java.cxx
   
   String *imclass_name;		// intermediary class name
   String *module_class_name;	// module class name
@@ -90,8 +92,6 @@ class JAVA:public Language {
     return p;
   }
   /* DOXYGEN TO JAVADOC globals */
-  bool doxygen_javadoc_flag; //flag for converting found doxygen to javadoc
-  bool comment_creation_chatter; //flag for getting information about where comments were created in java.cxx
   //TODO make this bool a command line option
   DoxygenTranslator doxyTranslator;
 
@@ -124,6 +124,7 @@ public:
       global_variable_flag(false),
       old_variable_names(false),
       member_func_flag(false),
+	  doxygen_javadoc_flag(true),
       comment_creation_chatter(false),
       imclass_name(NULL),
       module_class_name(NULL),
@@ -213,7 +214,6 @@ public:
 
   virtual void main(int argc, char *argv[]) {
 
-	  doxygen_javadoc_flag = true;
     SWIG_library_directory("java");
 
     // Look for certain command line options

From ad0a3d9179a8650d145c3db0e9b1c1bdc8de79ee Mon Sep 17 00:00:00 2001
From: Cheryl Foil <cheryl.foil@gmail.com>
Date: Mon, 18 Aug 2008 18:30:21 +0000
Subject: [PATCH 022/314] Extra Examples

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2008-cherylfoil@10790 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 .../doxygencomments/java/callback/example.h    |  7 +++++--
 Examples/doxygencomments/java/extend/example.h | 11 +++++++++--
 Examples/doxygencomments/java/native/example.i | 11 +++++++++++
 .../doxygencomments/java/pointer/example.i     | 10 +++++++++-
 .../doxygencomments/java/reference/example.i   | 18 +++++++++++++++---
 Examples/doxygencomments/java/simple/example.i |  6 +++++-
 .../doxygencomments/java/template/example.h    | 11 +++++++++--
 Examples/java/pointer/example.i                |  2 --
 Examples/java/reference/example.i              |  3 ---
 9 files changed, 63 insertions(+), 16 deletions(-)

diff --git a/Examples/doxygencomments/java/callback/example.h b/Examples/doxygencomments/java/callback/example.h
index 38ada8b84..a0c5fc4d2 100644
--- a/Examples/doxygencomments/java/callback/example.h
+++ b/Examples/doxygencomments/java/callback/example.h
@@ -3,9 +3,12 @@
 #include <cstdio>
 #include <iostream>
 
-/** Let's document class CALLBACK! */
+/*! Let's document class CALLBACK! 
+ /author Alfred
+ */
 class Callback {
 public:
+	/** Information about Callback */
 	virtual ~Callback() { std::cout << "Callback::~Callback()" << std:: endl; }
 	virtual void run() { std::cout << "Callback::run()" << std::endl; }
 };
@@ -16,7 +19,7 @@ private:
 	Callback *_callback;
 public:
 	Caller(): _callback(0) {}
-	~Caller() { delCallback(); }
+	~Caller() { delCallback(); }/**< Deletes Callback */
 	void delCallback() { delete _callback; _callback = 0; }
 	void setCallback(Callback *cb) { delCallback(); _callback = cb; }
 	void call() { if (_callback) _callback->run(); }
diff --git a/Examples/doxygencomments/java/extend/example.h b/Examples/doxygencomments/java/extend/example.h
index db49ae747..9b882fd59 100644
--- a/Examples/doxygencomments/java/extend/example.h
+++ b/Examples/doxygencomments/java/extend/example.h
@@ -6,12 +6,15 @@
 #include <string>
 #include <cmath>
 
-/**This is describiing class Employee */
+/**This is describiing class Employee 
+ /author Bob */
 class Employee {
 private:
 	std::string name;
 public:
-	/** TEST */
+	/** Employee
+	 \param n name of Employee
+	 \throws some exception */
 	Employee(const char* n): name(n) {}
 /**This is describing method getTitle */
 	virtual std::string getTitle() { return getPosition() + " " + getName(); }
@@ -31,11 +34,15 @@ public:
 class EmployeeList {
 	std::vector<Employee*> list;
 public:
+	/** Initialises Employee List */
 	EmployeeList() {
 		list.push_back(new Employee("Bob"));
 		list.push_back(new Employee("Jane"));
 		list.push_back(new Manager("Ted"));
 	}
+	/** Add employee
+	 * \param p employee p
+	 * \return void */
 	void addEmployee(Employee *p) {
 		list.push_back(p);
 		std::cout << "New employee added.   Current employees are:" << std::endl;
diff --git a/Examples/doxygencomments/java/native/example.i b/Examples/doxygencomments/java/native/example.i
index 851b6fdc2..21bcf528c 100644
--- a/Examples/doxygencomments/java/native/example.i
+++ b/Examples/doxygencomments/java/native/example.i
@@ -4,11 +4,16 @@
 %{
 #include <string.h>
 
+/*! Structure Point */
 typedef struct point {
   int x;
   int y;
 } Point;
 
+/*! Point_create Description
+ /param x integer x
+ /param y some integer y
+ /return a point */
 
 Point *point_create(int x, int y) {
   Point *p = (Point *) malloc(sizeof(Point));
@@ -18,6 +23,11 @@ Point *point_create(int x, int y) {
   return p;
 }
 
+/*! Point_create Description
+ /param format the format 
+ /param p some p
+ /return a character string of the point p */
+
 static char *point_toString(char *format, Point *p) {
   static char buf[80];
 
@@ -54,3 +64,4 @@ char *point_toString1(Point *p);
 extern void free(void *memblock);
 
 %native(point_toString2) char *point_toString2(Point *p);
+
diff --git a/Examples/doxygencomments/java/pointer/example.i b/Examples/doxygencomments/java/pointer/example.i
index a8ac79499..7ac3b8cf8 100644
--- a/Examples/doxygencomments/java/pointer/example.i
+++ b/Examples/doxygencomments/java/pointer/example.i
@@ -7,10 +7,16 @@ extern void sub(int *, int *, int *);
 extern int divide(int, int, int *);
 %}
 
-/* This example illustrates a couple of different techniques
+/** This example illustrates a couple of different techniques
    for manipulating C pointers */
 
 /* First we'll use the pointer library */
+
+/*! function add
+ \param x some int x
+ \param y some int y
+ \param result some result
+ */
 extern void add(int *x, int *y, int *result);
 %include cpointer.i
 %pointer_functions(int, intp);
@@ -28,3 +34,5 @@ extern int divide(int n, int d, int *r);
 
 
 
+
+
diff --git a/Examples/doxygencomments/java/reference/example.i b/Examples/doxygencomments/java/reference/example.i
index 6daa3b1f4..8e4d05239 100644
--- a/Examples/doxygencomments/java/reference/example.i
+++ b/Examples/doxygencomments/java/reference/example.i
@@ -8,6 +8,12 @@
 #include "example.h"
 %}
 
+/*! Class vector description
+ \author Fred
+ \exception something random 
+ \since 1.0
+ \name ignoreme
+ \see something */
 class Vector {
 public:
     Vector(double x, double y, double z);
@@ -15,15 +21,18 @@ public:
     char *print();
 };
 
-/* This helper function calls an overloaded operator */
+/** This helper function calls an overloaded operator */
 %inline %{
 Vector addv(Vector &a, Vector &b) {
   return a+b;
 }
 %}
 
-/* Wrapper around an array of vectors class */
-
+/*! Class Vector Array
+ \exception something random 
+ \since 1.3
+ \see something
+ \author Fred */
 class VectorArray {
 public:
   VectorArray(int maxsize);
@@ -44,3 +53,6 @@ public:
 
 
 
+
+
+
diff --git a/Examples/doxygencomments/java/simple/example.i b/Examples/doxygencomments/java/simple/example.i
index 24093b9bf..c823bc8b6 100644
--- a/Examples/doxygencomments/java/simple/example.i
+++ b/Examples/doxygencomments/java/simple/example.i
@@ -2,6 +2,10 @@
 %module example
 
 %inline %{
+/*! Function foo
+ \param x int x
+ \param y int y
+ \return the gcd */
 extern int    gcd(int x, int y);
-extern double Foo;
+extern double Foo; /*!< description of double foo
 %}
diff --git a/Examples/doxygencomments/java/template/example.h b/Examples/doxygencomments/java/template/example.h
index 7401df650..9ec711391 100644
--- a/Examples/doxygencomments/java/template/example.h
+++ b/Examples/doxygencomments/java/template/example.h
@@ -2,8 +2,15 @@
 
 // Some template definitions
 
+/*! Template class T 
+ \author cmfoil 
+ \sa something something */
+
 template<class T> T max(T a, T b) { return  a>b ? a : b; }
 
+/*! Template class Vector 
+ \author cmfoil 
+ \sa something something */
 template<class T> class vector {
   T *v;
   int sz;
@@ -17,12 +24,12 @@ template<class T> class vector {
   }
   void set(int index, T &val) {
     v[index] = val;
-  }
+  } /*!< Something about set */
 #ifdef SWIG
   %extend {
     T getitem(int index) {
       return $self->get(index);
-    }
+    }/*!< Something about get item */
     void setitem(int index, T val) {
       $self->set(index,val);
     }
diff --git a/Examples/java/pointer/example.i b/Examples/java/pointer/example.i
index a8ac79499..5b725cee6 100644
--- a/Examples/java/pointer/example.i
+++ b/Examples/java/pointer/example.i
@@ -26,5 +26,3 @@ extern void sub(int *INPUT, int *INPUT, int *OUTPUT);
 extern int divide(int n, int d, int *r);
 
 
-
-
diff --git a/Examples/java/reference/example.i b/Examples/java/reference/example.i
index 6daa3b1f4..fd80f9a94 100644
--- a/Examples/java/reference/example.i
+++ b/Examples/java/reference/example.i
@@ -41,6 +41,3 @@ public:
   }
 };
 
-
-
-

From 6c646831c3400c74ff87affceb7be96604864566 Mon Sep 17 00:00:00 2001
From: Cheryl Foil <cheryl.foil@gmail.com>
Date: Mon, 18 Aug 2008 18:37:41 +0000
Subject: [PATCH 023/314] syntax error

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2008-cherylfoil@10791 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Examples/doxygencomments/java/simple/example.i | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Examples/doxygencomments/java/simple/example.i b/Examples/doxygencomments/java/simple/example.i
index c823bc8b6..d10fe5e19 100644
--- a/Examples/doxygencomments/java/simple/example.i
+++ b/Examples/doxygencomments/java/simple/example.i
@@ -7,5 +7,5 @@
  \param y int y
  \return the gcd */
 extern int    gcd(int x, int y);
-extern double Foo; /*!< description of double foo
+extern double Foo; /*!< description of double foo */
 %}

From 52dd40260d3925d50b9cd672da3d23de38b3792b Mon Sep 17 00:00:00 2001
From: Cheryl Foil <cheryl.foil@gmail.com>
Date: Mon, 18 Aug 2008 18:49:13 +0000
Subject: [PATCH 024/314] One more example, for variables

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2008-cherylfoil@10792 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 .../doxygencomments/java/variables/example.h  |  2 +-
 .../doxygencomments/java/variables/example.i  | 44 +++++++++++--------
 2 files changed, 27 insertions(+), 19 deletions(-)

diff --git a/Examples/doxygencomments/java/variables/example.h b/Examples/doxygencomments/java/variables/example.h
index 0f7e89594..2265a45f3 100644
--- a/Examples/doxygencomments/java/variables/example.h
+++ b/Examples/doxygencomments/java/variables/example.h
@@ -2,5 +2,5 @@
 
 typedef struct {
   int x,y;
-} Point;
+} Point; /*!< Description of struct Point */
 
diff --git a/Examples/doxygencomments/java/variables/example.i b/Examples/doxygencomments/java/variables/example.i
index 591b871ed..b9794f0cf 100644
--- a/Examples/doxygencomments/java/variables/example.i
+++ b/Examples/doxygencomments/java/variables/example.i
@@ -6,24 +6,24 @@
 
 /* Some global variable declarations */
 %inline %{
-extern int              ivar;
-extern short            svar;
-extern long             lvar;
-extern unsigned int     uivar;
-extern unsigned short   usvar;
-extern unsigned long    ulvar;
-extern signed char      scvar;
-extern unsigned char    ucvar;
-extern char             cvar;
-extern float            fvar;
-extern double           dvar;
-extern char            *strvar;
-extern const char       cstrvar[];
-extern int             *iptrvar;
-extern char             name[256];
+extern int              ivar; /*!< Description of ivar */
+extern short            svar; /*!< Description of svar */
+extern long             lvar; /*!< Description of lvar */
+extern unsigned int     uivar; /*!< Description of uivar */
+extern unsigned short   usvar; /*!< Description of usvar */
+extern unsigned long    ulvar; /*!< Description of ulvar */
+extern signed char      scvar; /*!< Description of scvar */
+extern unsigned char    ucvar; /*!< Description of ucvar */
+extern char             cvar; /*!< Description of cvar */
+extern float            fvar; /*!< Description of fvar */
+extern double           dvar; /*!< Description of dvar */
+extern char            *strvar; /*!< Description of strvar */
+extern const char       cstrvar[]; /*!< Description of cstrvar */
+extern int             *iptrvar;  /*!< Description of iptrvar */
+extern char             name[256];  /*!< Description of name */
 
-extern Point           *ptptr;
-extern Point            pt;
+extern Point           *ptptr;  /*!< Description of ptrptr */
+extern Point            pt;  /*!< Description of pt */
 %}
 
 
@@ -40,8 +40,16 @@ extern char path[256];
 
 /* Some helper functions to make it easier to test */
 %inline %{
+/*! this function prints variables
+ \author someone */
 extern void  print_vars();
-extern int  *new_int(int value);
+extern int  *new_int(int value);  /*!< Description of new_int
+				   \param value the value
+				   \return a new int */
+/*! Description of new_point
+  \param x the value x
+  \param y the value y
+ \return a new point */
 extern Point *new_Point(int x, int y);
 extern char  *Point_print(Point *p);
 extern void  pt_print();

From 9f4726743120be21e1675c09d32c963d8b683f2f Mon Sep 17 00:00:00 2001
From: William S Fulton <wsf@fultondesigns.co.uk>
Date: Mon, 8 Sep 2008 19:38:06 +0000
Subject: [PATCH 025/314] Few formatting changes and a couple of minor edits
 after review

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2008-cherylfoil@10817 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Doc/Manual/DoxygenTranslation.html | 164 +++++++++++++++++++----------
 1 file changed, 111 insertions(+), 53 deletions(-)

diff --git a/Doc/Manual/DoxygenTranslation.html b/Doc/Manual/DoxygenTranslation.html
index e3797b56f..f53917e3a 100644
--- a/Doc/Manual/DoxygenTranslation.html
+++ b/Doc/Manual/DoxygenTranslation.html
@@ -5,53 +5,62 @@
 <link rel="stylesheet" type="text/css" href="style.css">
 </head>
 <body bgcolor="#FFFFFF">
-<H1><a name="Java"></a>SWIG and Doxgeyn Translation</H1>
+<H1><a name="Java"></a>35 SWIG and Doxgeyn Translation</H1>
 <!-- INDEX -->
 <div class="sectiontoc">
 <ul>
-<li><a href="#doxygen_translation_overview">Overview</a>
-<li><a href="#file_preparation">File Preparation</a>
+<li><a href="#Doxygen_translation_overview">Doxygen Translation Overview</a>
+<li><a href="#Doxygen_file_preparation">Preparations</a>
 <ul>
-<li><a href="#running_swig">Running SWIG with Doxygen translation</a>
-<li><a href="#additional_options">Additional Options</a>
+<li><a href="#Doxygen_running_swig">Enabling Doxygen Translation</a>
+<li><a href="#Doxygen_additional_options">Additional Commandline Options</a>
 </ul>
-<li><a href="#doxygen_to_javadoc">Doxygen->JavaDoc</a>
+<li><a href="#Doxygen_to_javadoc">Doxygen To JavaDoc</a>
 <ul>
-<li><a href="#basic_example">Basic Example</a>
-<li><a href="#javadoc_tags">JavaDoc Tags</a>
-<li><a href="#other_tags">Other Tags</a>
-<li><a href="#bad_behaviour">Bad Behaviour</a>
+<li><a href="#Doxygen_basic_example">Basic Example</a>
+<li><a href="#Doxygen_javadoc_tags">JavaDoc Tags</a>
+<li><a href="#Doxygen_other_tags">Other Tags</a>
+<li><a href="#Doxygen_bad_behaviour">Bad Behaviour</a>
+<li><a href="#Doxygen_further_details">Further Details</a>
 </ul>
-<li><a href="#further_details">Further details on Doxygen</a>
-<li><a href="#developer_details">Developer Information</a>
+<li><a href="#Doxygen_developer_details">Developer Information</a>
 <ul>
-<li><a href="#module_design">Module Design</a>
-<li><a href="#language_extension">Extending to Other Languages</a>
+<li><a href="#Doxygen_module_design">Module Design</a>
 </ul>
+<li><a href="#Doxygen_language_extension">Extending to Other Languages</a>
 </ul>
-
 </div>
 <!-- INDEX -->
 
+
+
 <p>
-This chapter describes SWIG's support for translating Doxygen comments found in interface and header files into a target language's normal documentation language. Currently only JavaDoc is supported.
+This chapter describes SWIG's support for translating Doxygen comments found in interface and header files into a target language's normal documentation language.
+Currently only JavaDoc is supported.
 </p>
 
-<H2><a name="doxygen_translation_overview"></a>Doxygen Translation Overview</H2>
+<H2><a name="Doxygen_translation_overview"></a>35.1 Doxygen Translation Overview</H2>
+
 
 <p>
-The Doxygen Translation Module of SWIG is an ongoing effort from a <A HREF ="http://code.google.com/soc/2008/">Google Summer of Code</A> proposal from Summer 2008. It adds an extra layer of functionality to SWIG, allowing automated translation of <A HREF= "http://www.stack.nl/~dimitri/doxygen/">Doxygen</A> formatted comments from interface files into a documentation language more suited for the target language. Currently this module only translates into JavaDoc for the SWIG Java Module, but other extensions are to be added in time.
+The Doxygen Translation Module of SWIG is an ongoing effort from a <A HREF ="http://code.google.com/soc/2008/">Google Summer of Code</A> proposal from Summer 2008.
+It adds an extra layer of functionality to SWIG, allowing automated translation of <A HREF= "http://www.stack.nl/~dimitri/doxygen/">Doxygen</A> formatted comments from input files into a documentation language more suited for the target language.
+Currently this module only translates into JavaDoc for the SWIG Java Module, but other extensions are to be added in time.
 </p>
 
 <p>
-Questions about running SWIG are best answered in the <a href="SWIG.html#SWIG">SWIG Basics</a> chapter as well as the target language modules. (For now, only <A href = "Java.html">Java</A>). The behaviour of this functionality is wildly unpredictable if the interface file is not proper to begin with!
+Questions about running SWIG are best answered in the <a href="SWIG.html#SWIG">SWIG Basics</a> chapter as well as the target language modules. (For now, only <A href = "Java.html">Java</A>).
+The behaviour of this functionality is wildly unpredictable if the interface file is not proper to begin with!
 </p>
 
-<H2><a name="file_preparation"></a>Preparations</H2>
+<H2><a name="Doxygen_file_preparation"></a>35.2 Preparations</H2>
 
 
 <p>
-To make use of the comment translation system, your documentation comments must be in properly formatted <A HREF= "http://www.stack.nl/~dimitri/doxygen/">Doxygen.</A> They can be present in your main interface file or any header file that it imports. It is advised that you are certain your comments compile properly with Doxygen before you try to translate them. Doxygen itself is a deeper tool and can provide you better feedback for correct any syntax errors that may be present. Please look at Doxygen's <A HREF = "http://www.stack.nl/~dimitri/doxygen/docblocks.html"> Documenting the code</A> for proper specificatons for comment format.
+To make use of the comment translation system, your documentation comments must be in properly formatted <A HREF= "http://www.stack.nl/~dimitri/doxygen/">Doxygen.</A> They can be present in your main interface file or any header file that it imports.
+It is advised that you are certain your comments compile properly with Doxygen before you try to translate them.
+Doxygen itself is a deeper tool and can provide you better feedback for correct any syntax errors that may be present.
+Please look at Doxygen's <A HREF = "http://www.stack.nl/~dimitri/doxygen/docblocks.html"> Documenting the code</A> for proper specificatons for comment format.
 </p>
 
 <div class="code"><pre>
@@ -63,29 +72,35 @@ class Shape {
 </pre></div>
 
 <p>
-Because this functionality is currently only extended to java, you must be able to run SWIG's <A href = "Java.html">Java Module</A> in order to make use of this tool.</p>
-<H3><a name="running_swig"></a> Enabling Doxygen Translation</H3>
+Because this functionality is currently only extended to Java, you must be able to run SWIG's <A href = "Java.html">Java Module</A> in order to make use of this tool.
+</p>
+<H3><a name="Doxygen_running_swig"></a>35.2.1 Enabling Doxygen Translation</H3>
 
 
 <p>
 NOT YET ADDED (current development branch has this feature automatically enabled).
 </p>
 
-<H3><a name="additional_options"></a>Additional Commandline Options</H3>
+<H3><a name="Doxygen_additional_options"></a>35.2.2 Additional Commandline Options</H3>
+
 
 <p>
 ALSO TO BE ADDED (JavaDoc Autobrief?)
 </p>
 
-<H2><a name="doxygen_to_javadoc"></a>Doxygen To JavaDoc</H2>
+<H2><a name="Doxygen_to_javadoc"></a>35.3 Doxygen To JavaDoc</H2>
 
 
 <p>
-If translation is enabled, JavaDoc formatted comments should be automatically placed in the correct locations in the resulting module and proxy files.</p>
+If translation is enabled, JavaDoc formatted comments should be automatically placed in the correct locations in the resulting module and proxy files.
+</p>
 
-<H3><a name="basic_example"></a>Basic Example</H3>
+<H3><a name="Doxygen_basic_example"></a>35.3.1 Basic Example</H3>
 
-<p> Here is an example segment from an included header file</p>
+
+<p>
+Here is an example segment from an included header file
+</p>
 <div class="code"><pre>
 /*! This is describing class Shape
  \author Bob
@@ -99,15 +114,17 @@ public:
   virtual ~Shape() {
     nshapes--;
   };
-  double  x, y; /*!< Important Variables */
-  void    move(double dx, double dy); /*!< Moves the Shape */
-  virtual double area(void) = 0; /*!< \return the area */
-  virtual double perimeter(void) = 0; /*!< \return the perimeter */
+  double  x, y; /*!&lt; Important Variables */
+  void    move(double dx, double dy); /*!&lt; Moves the Shape */
+  virtual double area(void) = 0; /*!&lt; \return the area */
+  virtual double perimeter(void) = 0; /*!&lt; \return the perimeter */
   static  int nshapes;
 };
 </pre></div>
 
-<p>Simply running SWIG should result in the following code being present in Shapes.java</p>
+<p>
+Simply running SWIG should result in the following code being present in Shapes.java
+</p>
 
 <div class="targetlang"><pre>
 
@@ -122,13 +139,20 @@ public class Shape {
 ...
 
 /**
- * Important things  
+ * Important Variables  
  * 
  */
   public void setX(double value) {
     exampleJNI.Shape_x_set(swigCPtr, this, value);
   }
 
+/**
+ * Important variables  
+ */
+  public double getX() {
+    return exampleJNI.Shape_x_get(swigCPtr, this);
+  }
+
 ...
 
 /**
@@ -150,15 +174,23 @@ public class Shape {
 
 
 <p>
-The code Java-wise should be identical to what would have been generated without this feature enabled. When the Doxygen Translator Module encounters a comment it finds nothing useful in or cannot parse, it should not effect the functionality of the SWIG generated code.</p>
+The code Java-wise should be identical to what would have been generated without this feature enabled.
+When the Doxygen Translator Module encounters a comment it finds nothing useful in or cannot parse, it should not effect the functionality of the SWIG generated code.
+</p>
 
 
-<H3><a name="javadoc_tags"></a>JavaDoc Tags</H3>
+<H3><a name="Doxygen_javadoc_tags"></a>35.3.2 JavaDoc Tags</H3>
 
 
 <p>
-Doxygen has a wealth of tags such as @latexonly that have no equivalent in JavaDoc. As a result several tags that have no translation (or particular use, such as some linking and section tags) are supressed. If you are interested in more if the specifics of JavaDoc, please visit <A HREF="http://java.sun.com/j2se/javadoc/writingdoccomments/">How to Write Doc Comments for the Javadoc Tool.</A></p>
+Doxygen has a wealth of tags such as @latexonly that have no equivalent in JavaDoc.
+As a result several tags that have no translation (or particular use, such as some linking and section tags) are supressed.
+If you are interested in more of the specifics of JavaDoc, please visit <A HREF="http://java.sun.com/j2se/javadoc/writingdoccomments/">How to Write Doc Comments for the Javadoc Tool.</A>
+</p>
+
+<p>
 <b>Doxygen and JavaDoc Equivalent Tags</b>
+</p>
 <div class="diagram"><pre>
 * @param      
 * @return      
@@ -171,19 +203,24 @@ Doxygen has a wealth of tags such as @latexonly that have no equivalent in JavaD
 * @deprecated  
 </pre></div>
 
-<H3><a name="other_tags"></a>Other Tags</H3>
+<H3><a name="Doxygen_other_tags"></a>35.3.3 Other Tags</H3>
 
 
 <p>
-Because there are no specific JavaDoc tag for some important information, some tags are given plain-english descriptions of their presence, such as @bug. This is a feature currently still being developed and it is likely that more information from the original Doxygen Comments will be reproduced as this module matures.
+Because there are no specific JavaDoc tags for some important information, some tags are given plain English descriptions of their presence, such as @bug.
+This is a feature currently still being developed and it is likely that more information from the original Doxygen Comments will be reproduced as this module matures.
 </p>
-<H3><a name="bad_behaviour"></a>Bad Behaviour</H3>
+<H3><a name="Doxygen_bad_behaviour"></a>35.3.4 Bad Behaviour</H3>
 
 
 <p>
-There are some tags that the Doxygen Translator Module currently does not expect to encounter. This includes the PHP-only Doxygen commands such as @publicsection:
+There are some tags that the Doxygen Translator Module currently does not expect to encounter.
+This includes the PHP-only Doxygen commands such as @publicsection:
 </p>
+
+<p>
 <b> Completely Unsupported Tags</b>
+</p>
 <div class="diagram"><pre>
 "annotatedclasslist", "classhierarchy", "define", "functionindex", 
 "header", "headerfilelist", "inherit", "l", "postheader", "private",
@@ -191,14 +228,16 @@ There are some tags that the Doxygen Translator Module currently does not expect
 </pre></div>
 
 <p>
-The parsing behaviour will be unpredictable if any of these are encountered for now. This should eventually be changed so that they are simply ignored.
+The parsing behaviour will be unpredictable if any of these are encountered for now.
+This should eventually be changed so that they are simply ignored.
 </p>
 <p>
-In general parsing errors should not interfere with the operation of SWIG itself. Blank comments or lack of comments could be indication of either a parsing error or a lack of meaningful tags in a specific blob of doxygen. 
+In general parsing errors should not interfere with the operation of SWIG itself.
+Blank comments or lack of comments could be an indication of either a parsing error or a lack of meaningful tags in a specific blob of doxygen. 
 </p>
 
 
-<H3><a name="further_details"></a>Further Details</H3>
+<H3><a name="Doxygen_further_details"></a>35.3.5 Further Details</H3>
 
 
 <p>
@@ -206,17 +245,22 @@ TO BE ADDED.
 </p>
 
 
-<H2><a name="developer_details"></a>Developer Information</H2>
+<H2><a name="Doxygen_developer_details"></a>35.4 Developer Information</H2>
 
 
 <p>
-Currently a good deal of this Module still needs some reworking, particularly on the side of the parser and JavaDoc producer. </p>
+Currently a good deal of this Module still needs some reworking, particularly on the side of the parser and JavaDoc producer.
+</p>
 
-<H3><a name="module_design"></a>Module Design</H3>
+<H3><a name="Doxygen_module_design"></a>35.4.1 Module Design</H3>
 
 
 <p>
-If this functionality is turned on, SWIG places all comments found into the SWIG parse tree. Nodes contain an additional attribute called DoxygenComment when a comment is present. Individual nodes containing Doxygen with Structural Indicators, such as @file, as their first command, are also present in the parse tree. These indivudal "blobs" of Doxygen such as :</p>
+If this functionality is turned on, SWIG places all comments found into the SWIG parse tree.
+Nodes contain an additional attribute called DoxygenComment when a comment is present.
+Individual nodes containing Doxygen with Structural Indicators, such as @file, as their first command, are also present in the parse tree.
+These individual "blobs" of Doxygen such as :
+</p>
 <div class="code"><pre>
 /*! This is describing function Foo
  \param x some random variable
@@ -226,16 +270,26 @@ If this functionality is turned on, SWIG places all comments found into the SWIG
 </pre></div>
 
 <p>
-are passed on individually to the DoxygenTranslator Module. This module builds it's own private parse tree and hands it, similar to SWIG itself, to a seperate class to translate into the target documentation language. For example, JavaDocConverter is the JavaDoc module class.
+are passed on individually to the DoxygenTranslator Module.
+This module builds its own private parse tree and hands it to a separate class for translation into the target documentation language.
+For example, <tt>JavaDocConverter</tt> is the JavaDoc module class.
 </p>
 
-<H2><a name="language_extension"></a>Extending to Other Languages</H2>
+<H2><a name="Doxygen_language_extension"></a>35.5 Extending to Other Languages</H2>
 
 
 <p>
-In general, extension to another language requires a fairly deep understanding of the target language module- such as Modules/python.cxx for python. Searching for "doxygen" in the java.cxx module can give you a good idea of the process for placing in documentation comments into the correct areas. The basic gist is that anywhere a comment may reside on a node, there needs to be a catch for it in front of where that function, class, or other object is written out to a target language file. The other half of extension is building a target documentation language comment generator that handles 1 blob at a time. However, this is relatively simple- nowhere near as complex as the wrapper generating modules in SWIG. See DoxygenTranslator/JavaDocConverter.cpp for a good example. The target language module hands DoxygenTranslator the blob to translate, and receives back a translated text.
+In general, an extension to another language requires a fairly deep understanding of the target language module, such as Modules/python.cxx for Python.
+Searching for "doxygen" in the java.cxx module can give you a good idea of the process for placing documentation comments into the correct areas.
+The basic gist is that anywhere a comment may reside on a node, there needs to be a catch for it in front of where that function, class, or other object is written out to a target language file.
+The other half of extension is building a target documentation language comment generator that handles one blob at a time.
+However, this is relatively simple and nowhere near as complex as the wrapper generating modules in SWIG.
+See DoxygenTranslator/JavaDocConverter.cpp for a good example.
+The target language module hands the DoxygenTranslator the blob to translate, and receives back a translated text.
+</p>
+<p>
+<b> What is given to the Doxygen Translator</b>
 </p>
-<b> What is given to Doxygen Translator</b>
 <div class="code"><pre>
 /*! This is describing function Foo
  \param x some random variable
@@ -243,7 +297,9 @@ In general, extension to another language requires a fairly deep understanding o
  \return Foo
  */
 </pre></div>
+<p>
 <b> What is received back by java.cxx </b>
+</p>
 <div class="targetlang"><pre>
 /** This is describing function Foo
  *
@@ -252,6 +308,8 @@ In general, extension to another language requires a fairly deep understanding o
  * @return Foo
  */
 </pre></div>
-<p> Development of the comment translator itself is simplified by the fact that the DoxygenTranslator module can easily include a main in DoxygenTranslator and thus be developed, compiled, and tested independantly of SWIG.</p>
+<p> Development of the comment translator itself is simplified by the fact that the DoxygenTranslator module can easily include a <tt>main</tt> function and thus be developed, compiled, and tested independently of SWIG.
+</p>
+
 </body>
 </html>

From 8486cc9f4308688e590ba045f222eceafa720502 Mon Sep 17 00:00:00 2001
From: William S Fulton <wsf@fultondesigns.co.uk>
Date: Mon, 8 Sep 2008 19:40:04 +0000
Subject: [PATCH 026/314] rename DoxygenTranslation.html to Doxygen.html

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2008-cherylfoil@10818 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Doc/Manual/Contents.html                      | 28 +++++++++++++++++++
 .../{DoxygenTranslation.html => Doxygen.html} |  0
 Doc/Manual/chapters                           |  2 +-
 3 files changed, 29 insertions(+), 1 deletion(-)
 rename Doc/Manual/{DoxygenTranslation.html => Doxygen.html} (100%)

diff --git a/Doc/Manual/Contents.html b/Doc/Manual/Contents.html
index 5c7a18eaf..9d6e4e66f 100644
--- a/Doc/Manual/Contents.html
+++ b/Doc/Manual/Contents.html
@@ -1533,6 +1533,34 @@
 </div>
 <!-- INDEX -->
 
+<h3><a href="Doxygen.html#Doxygen">35 SWIG and Doxgeyn Translation</a></h3>
+
+<!-- INDEX -->
+<div class="sectiontoc">
+<ul>
+<li><a href="Doxygen.html#Doxygen_translation_overview">Doxygen Translation Overview</a>
+<li><a href="Doxygen.html#Doxygen_file_preparation">Preparations</a>
+<ul>
+<li><a href="Doxygen.html#Doxygen_running_swig">Enabling Doxygen Translation</a>
+<li><a href="Doxygen.html#Doxygen_additional_options">Additional Commandline Options</a>
+</ul>
+<li><a href="Doxygen.html#Doxygen_to_javadoc">Doxygen To JavaDoc</a>
+<ul>
+<li><a href="Doxygen.html#Doxygen_basic_example">Basic Example</a>
+<li><a href="Doxygen.html#Doxygen_javadoc_tags">JavaDoc Tags</a>
+<li><a href="Doxygen.html#Doxygen_other_tags">Other Tags</a>
+<li><a href="Doxygen.html#Doxygen_bad_behaviour">Bad Behaviour</a>
+<li><a href="Doxygen.html#Doxygen_further_details">Further Details</a>
+</ul>
+<li><a href="Doxygen.html#Doxygen_developer_details">Developer Information</a>
+<ul>
+<li><a href="Doxygen.html#Doxygen_module_design">Module Design</a>
+</ul>
+<li><a href="Doxygen.html#Doxygen_language_extension">Extending to Other Languages</a>
+</ul>
+</div>
+<!-- INDEX -->
+
 
 </BODY>
 </HTML>
diff --git a/Doc/Manual/DoxygenTranslation.html b/Doc/Manual/Doxygen.html
similarity index 100%
rename from Doc/Manual/DoxygenTranslation.html
rename to Doc/Manual/Doxygen.html
diff --git a/Doc/Manual/chapters b/Doc/Manual/chapters
index 2e5a16364..c9df298f0 100644
--- a/Doc/Manual/chapters
+++ b/Doc/Manual/chapters
@@ -32,4 +32,4 @@ Ruby.html
 Tcl.html
 R.html
 Extending.html
-DoxygenTranslation.html
+Doxygen.html

From 721327573bb00785ff5d96ae0872e18534fa9aa1 Mon Sep 17 00:00:00 2001
From: William S Fulton <wsf@fultondesigns.co.uk>
Date: Mon, 8 Sep 2008 20:04:34 +0000
Subject: [PATCH 027/314] fix typo and main ref

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2008-cherylfoil@10823 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Doc/Manual/Doxygen.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Doc/Manual/Doxygen.html b/Doc/Manual/Doxygen.html
index f53917e3a..27fc013eb 100644
--- a/Doc/Manual/Doxygen.html
+++ b/Doc/Manual/Doxygen.html
@@ -5,7 +5,7 @@
 <link rel="stylesheet" type="text/css" href="style.css">
 </head>
 <body bgcolor="#FFFFFF">
-<H1><a name="Java"></a>35 SWIG and Doxgeyn Translation</H1>
+<H1><a name="Doxygen"></a>35 SWIG and Doxygen Translation</H1>
 <!-- INDEX -->
 <div class="sectiontoc">
 <ul>

From 825e67b2b0e7a356c678833ae3535b17708701ee Mon Sep 17 00:00:00 2001
From: Jamie Kirkpatrick <gringostarr@users.sourceforge.net>
Date: Fri, 12 Sep 2008 10:51:51 +0000
Subject: [PATCH 028/314] Merged revisions
 10487,10498-10499,10503-10504,10506,10508,10511,10515-10516,10518-10519,10527,10530-10531,10536-10537,10539-10552,10558-10568,10574-10580,10582,10584,10588-10589,10594,10607-10610,10616,10621,10624-10629,10633-10641,10643,10647,10649-10650,10662,10672,10676-10677,10682-10683,10714,10726-10727,10738,10743,10747,10749,10794,10801-10809,10827-10831,10834
 via svnmerge from https://swig.svn.sourceforge.net/svnroot/swig/trunk

................
  r10487 | wsfulton | 2008-05-21 23:15:52 +0100 (Wed, 21 May 2008) | 1 line

  Apply patch from Petr Viktorin to fix some recent regressions in CFFI/CLOS
................
  r10498 | talby | 2008-05-26 21:09:56 +0100 (Mon, 26 May 2008) | 2 lines

  run test cases in the Perl set by the --with-perl5 configure option.
................
  r10499 | talby | 2008-05-26 22:04:06 +0100 (Mon, 26 May 2008) | 3 lines

  The perl5 minherit runtime test will work better if the classes are
  actually built under SWIGPERL.
................
  r10503 | wsfulton | 2008-05-28 10:44:37 +0100 (Wed, 28 May 2008) | 1 line

  Fix variable wrappers when using -proxy. Patch from Jan Jezabek
................
  r10504 | bhy | 2008-05-28 18:27:48 +0100 (Wed, 28 May 2008) | 2 lines

  Fixed SF #1971977:  typo in pycontainer.swg (related to -extranative option)
................
  r10506 | wsfulton | 2008-05-29 01:45:28 +0100 (Thu, 29 May 2008) | 1 line

  Fix variable wrappers when using -noproxy
................
  r10508 | bhy | 2008-05-30 14:53:33 +0100 (Fri, 30 May 2008) | 1 line

  Fixed SF #1976978, apply the macros for primitive types to std::wstring
................
  r10511 | olly | 2008-05-30 17:11:27 +0100 (Fri, 30 May 2008) | 4 lines

  Fix typo in handling of /*@SWIG[...]*/ comments in the scanner.  This just
  meant we were only actually looking for /*@SWI at the start of the comment, so
  was pretty harmless in practice.
................
  r10515 | wsfulton | 2008-06-02 21:10:40 +0100 (Mon, 02 Jun 2008) | 1 line

  Fix samename testcase for c# and java
................
  r10516 | wsfulton | 2008-06-02 21:15:39 +0100 (Mon, 02 Jun 2008) | 1 line

  Fix enums when using -noproxy
................
  r10518 | bhy | 2008-06-07 12:20:07 +0100 (Sat, 07 Jun 2008) | 4 lines

  Added a test case for keyword renaming.
  Now it works for Python in SWIG's -c++ mode,
  but in C mode it doesn't work! (you can try with make keyword_rename.ctest)
................
  r10519 | bhy | 2008-06-07 14:40:51 +0100 (Sat, 07 Jun 2008) | 1 line

  fixed keyword_rename.ctest tese case, caused by a mistake in Swig/naming.c
................
  r10527 | mgossage | 2008-06-17 03:57:15 +0100 (Tue, 17 Jun 2008) | 1 line

  [lua] bugfix 1938142 (bool& and bool* support)
................
  r10530 | wsfulton | 2008-06-19 21:02:13 +0100 (Thu, 19 Jun 2008) | 1 line

  Add R keyword support. Rename keywords for successful compilation of Java and C# code. More consistent keyword warnings across the different languages.
................
  r10531 | wsfulton | 2008-06-19 22:15:48 +0100 (Thu, 19 Jun 2008) | 1 line

  add complete list of R reserved words
................
  r10536 | wsfulton | 2008-06-21 12:35:33 +0100 (Sat, 21 Jun 2008) | 1 line

  better terminology for static types
................
  r10537 | wsfulton | 2008-06-21 12:42:48 +0100 (Sat, 21 Jun 2008) | 1 line

  remove raise as keyword test- it conflicts with _raise in LIBCMT on windows
................
  r10539 | wsfulton | 2008-06-21 16:21:29 +0100 (Sat, 21 Jun 2008) | 1 line

  Lua example warning removal fixes for vc++
................
  r10540 | wsfulton | 2008-06-21 16:23:02 +0100 (Sat, 21 Jun 2008) | 1 line

  Remove some vc++ /W4 warnings
................
  r10541 | wsfulton | 2008-06-21 17:04:55 +0100 (Sat, 21 Jun 2008) | 1 line

  minor vc++ /W4 warning fixes
................
  r10542 | wsfulton | 2008-06-21 20:07:51 +0100 (Sat, 21 Jun 2008) | 1 line

  'byte' is already used in Ruby on windows, so use another keyword
................
  r10543 | wsfulton | 2008-06-21 21:45:32 +0100 (Sat, 21 Jun 2008) | 1 line

  Fix crashing in the Ruby reject method in the STL wrappers
................
  r10544 | wsfulton | 2008-06-21 21:48:28 +0100 (Sat, 21 Jun 2008) | 1 line

  Fix crashing in the Ruby reject method in the STL wrappers
................
  r10545 | wsfulton | 2008-06-21 21:49:10 +0100 (Sat, 21 Jun 2008) | 1 line

  remove unnecessary variable int the char **STRING_ARRAY out typemap
................
  r10546 | wsfulton | 2008-06-21 22:07:49 +0100 (Sat, 21 Jun 2008) | 1 line

  Fix Ruby C++ example dependencies in dsp files
................
  r10547 | wsfulton | 2008-06-21 23:25:36 +0100 (Sat, 21 Jun 2008) | 1 line

  Fix unused parameter warnings in python when using gcc's -W -Wall options
................
  r10548 | wsfulton | 2008-06-21 23:26:35 +0100 (Sat, 21 Jun 2008) | 1 line

  Fix virtual destructor
................
  r10549 | wsfulton | 2008-06-22 00:25:20 +0100 (Sun, 22 Jun 2008) | 1 line

  various warning fixes
................
  r10550 | wsfulton | 2008-06-22 01:09:11 +0100 (Sun, 22 Jun 2008) | 1 line

  Another fix for the JVM hanging on exit problem when using directors
................
  r10551 | wsfulton | 2008-06-22 01:09:51 +0100 (Sun, 22 Jun 2008) | 1 line

  documentation sections update
................
  r10552 | wsfulton | 2008-06-22 01:18:10 +0100 (Sun, 22 Jun 2008) | 1 line

  more docs on defining macros for the thread hanging problem
................
  r10558 | wsfulton | 2008-06-22 22:30:20 +0100 (Sun, 22 Jun 2008) | 1 line

  fix unused parms in last commit for C code
................
  r10559 | wsfulton | 2008-06-22 23:12:43 +0100 (Sun, 22 Jun 2008) | 1 line

  Suppress unused methods warning for VC++
................
  r10560 | wsfulton | 2008-06-23 21:26:07 +0100 (Mon, 23 Jun 2008) | 1 line

  fix partialcheck-test-suite and parallel make for r, chicken, tcl and php
................
  r10561 | wsfulton | 2008-06-23 21:39:41 +0100 (Mon, 23 Jun 2008) | 1 line

  correct message display when running the partialcheck-test-suite make target
................
  r10562 | wsfulton | 2008-06-23 22:14:53 +0100 (Mon, 23 Jun 2008) | 1 line

  fix typo
................
  r10563 | olly | 2008-06-23 22:23:54 +0100 (Mon, 23 Jun 2008) | 3 lines

  Fix bad use of Python API (untested, since I can't even compile this code on
  x86-64!)
................
  r10564 | olly | 2008-06-23 23:58:03 +0100 (Mon, 23 Jun 2008) | 3 lines

  [PHP] Fix segfault when wrapping a non-class function marked with
  %newobject (testcase char_strings).
................
  r10565 | olly | 2008-06-24 01:27:34 +0100 (Tue, 24 Jun 2008) | 3 lines

  [PHP] Fix assertion failure when handling %typemap(in,numinputs=0)
  (testcase ignore_parameter).
................
  r10566 | olly | 2008-06-24 01:33:08 +0100 (Tue, 24 Jun 2008) | 2 lines

  [PHP] Fix typemap_namespace.i to not try to copy a non-existent typemap.
................
  r10567 | olly | 2008-06-24 01:41:07 +0100 (Tue, 24 Jun 2008) | 3 lines

  Clean up dead and unused code in SwigToPhpType(), and rename to
  GetShadowReturnType().
................
  r10568 | olly | 2008-06-24 01:42:29 +0100 (Tue, 24 Jun 2008) | 2 lines

  Fix cosmetic typo in string constant.
................
  r10574 | wsfulton | 2008-06-24 21:10:28 +0100 (Tue, 24 Jun 2008) | 1 line

  zap last entry
................
  r10575 | wsfulton | 2008-06-24 21:11:46 +0100 (Tue, 24 Jun 2008) | 1 line

  variable name changes to remove php keywords
................
  r10576 | wsfulton | 2008-06-24 21:12:08 +0100 (Tue, 24 Jun 2008) | 1 line

  variable name hiding fix
................
  r10577 | wsfulton | 2008-06-24 21:12:43 +0100 (Tue, 24 Jun 2008) | 1 line

  More info about numobjects added
................
  r10578 | wsfulton | 2008-06-24 21:13:41 +0100 (Tue, 24 Jun 2008) | 1 line

  update for 1.3.36 release
................
  r10579 | wsfulton | 2008-06-24 22:48:46 +0100 (Tue, 24 Jun 2008) | 1 line

  remove deprecated -c commandline option (runtime library generation)
................
  r10580 | wsfulton | 2008-06-24 22:53:12 +0100 (Tue, 24 Jun 2008) | 1 line

  correct comment about deprecated option
................
  r10582 | wsfulton | 2008-06-25 00:00:27 +0100 (Wed, 25 Jun 2008) | 1 line

  use rsync and ssh to upload releases to SourceForge as ftp no longer works
................
  r10584 | wsfulton | 2008-06-25 00:24:48 +0100 (Wed, 25 Jun 2008) | 1 line

  correction for 1.3.36
................
  r10588 | wsfulton | 2008-06-25 01:16:04 +0100 (Wed, 25 Jun 2008) | 1 line

  section update
................
  r10589 | wsfulton | 2008-06-25 01:16:40 +0100 (Wed, 25 Jun 2008) | 1 line

  bump version to 1.3.37
................
  r10594 | wsfulton | 2008-06-26 19:33:06 +0100 (Thu, 26 Jun 2008) | 1 line

  correct typo in first entry about %fragment
................
  r10607 | wsfulton | 2008-06-29 01:19:05 +0100 (Sun, 29 Jun 2008) | 1 line

  fix some potential null pointer usage as reported by CoveriCoverity Prevent
................
  r10608 | wsfulton | 2008-06-29 01:50:27 +0100 (Sun, 29 Jun 2008) | 1 line

  fix potential null pointer usage as reported by Coverity Prevent
................
  r10609 | wsfulton | 2008-06-29 10:57:41 +0100 (Sun, 29 Jun 2008) | 1 line

  make life easier for svn status updates as everyone has different autotool versions installed - use svn:ignore on config.sub and config.guess
................
  r10610 | wsfulton | 2008-06-29 11:08:14 +0100 (Sun, 29 Jun 2008) | 1 line

  make life easier for svn status updates as everyone has different autotool versions installed - use svn:ignore on config.sub and config.guess
................
  r10616 | talby | 2008-07-01 00:41:27 +0100 (Tue, 01 Jul 2008) | 2 lines

  Hopefully this provides more portable values for Infinity and NaN in Perl.
................
  r10621 | wsfulton | 2008-07-01 23:02:14 +0100 (Tue, 01 Jul 2008) | 1 line

  update old commandline option
................
  r10624 | olly | 2008-07-02 04:17:46 +0100 (Wed, 02 Jul 2008) | 5 lines

  [Python] Import the C extension differently for Python 2.6 and
  later so that an implicit relative import doesn't produce a
  deprecation warning for 2.6 and a failure for 2.7 and later.
  Patch from Richard Boulton in SF#2008229.
................
  r10625 | bhy | 2008-07-02 05:56:11 +0100 (Wed, 02 Jul 2008) | 1 line

  fix the relative import patch by try both relative and absolute import
................
  r10626 | olly | 2008-07-02 06:55:18 +0100 (Wed, 02 Jul 2008) | 4 lines

  [PHP4] Support for PHP4 has been removed.  The PHP developers are
  no longer making new PHP4 releases, and won't even be patching
  critical security issues after 2008-08-08.
................
  r10627 | bhy | 2008-07-02 07:06:56 +0100 (Wed, 02 Jul 2008) | 1 line

  fix the previous commit -- new approach using imp module
................
  r10628 | bhy | 2008-07-02 07:29:15 +0100 (Wed, 02 Jul 2008) | 1 line

  minor fix on relative import: close fp if exception occured during imp.find_module
................
  r10629 | bhy | 2008-07-02 08:08:00 +0100 (Wed, 02 Jul 2008) | 1 line

  reconstruct the relative import, now the generated code looks better
................
  r10633 | olly | 2008-07-03 01:09:56 +0100 (Thu, 03 Jul 2008) | 9 lines

  WARN_* constants are user visible, so keep existing WARN_PHP4_* for
  backward compatibility, but add preferred forms WARN_PHP_* and use
  these ourselves.

  Rename Lib/php4 to Lib/php, Source/Modules/php4.cxx to Source/Modules/php.cxx.

  Add typemaps for const reference so Examples/test-suite/apply_signed_char.i
  works.
................
  r10634 | olly | 2008-07-03 01:12:58 +0100 (Thu, 03 Jul 2008) | 2 lines

  Remove file added in error.
................
  r10635 | olly | 2008-07-03 01:37:38 +0100 (Thu, 03 Jul 2008) | 2 lines

  Rename php4*.swg to php*.swg.
................
  r10636 | olly | 2008-07-03 02:13:51 +0100 (Thu, 03 Jul 2008) | 2 lines

  Update wrt PHP4.
................
  r10637 | olly | 2008-07-03 03:32:11 +0100 (Thu, 03 Jul 2008) | 4 lines

  [PHP] The deprecated command line option "-phpfull" has been
  removed.  We recommend building your extension as a dynamically
  loadable module.
................
  r10638 | olly | 2008-07-03 03:32:41 +0100 (Thu, 03 Jul 2008) | 2 lines

  Fix version number
................
  r10639 | olly | 2008-07-03 07:04:24 +0100 (Thu, 03 Jul 2008) | 2 lines

  Make t_output_helper() static.
................
  r10640 | olly | 2008-07-03 07:05:34 +0100 (Thu, 03 Jul 2008) | 2 lines

  Make testcase li_typemaps work for PHP.
................
  r10641 | olly | 2008-07-03 10:12:16 +0100 (Thu, 03 Jul 2008) | 2 lines

  Fix check::classname() to compare case-insensitively and not try to interpolate objects into strings.
................
  r10643 | olly | 2008-07-03 23:00:01 +0100 (Thu, 03 Jul 2008) | 4 lines

  The operator& trick in allowexcept.i doesn't work for SWIG/PHP because the
  generated code takes the address of the variable in the code in the "vinit"
  section.  So comment out the private operator& for PHP.
................
  r10647 | olly | 2008-07-04 00:55:33 +0100 (Fri, 04 Jul 2008) | 2 lines

  [PHP] The SWIG cdata.i library module is now supported.
................
  r10649 | olly | 2008-07-04 02:02:22 +0100 (Fri, 04 Jul 2008) | 4 lines

  [PHP] The deprecated command line option "-make" has been removed.
  Searches on Google codesearch suggest that nobody is using it now
  anyway.
................
  r10650 | olly | 2008-07-04 02:22:11 +0100 (Fri, 04 Jul 2008) | 4 lines

  [PHP] For std_vector.i and std_map.i, rename empty() to is_empty()
  since "empty" is a PHP reserved word.  Based of patch from Mark Klein
  in SF#1943417.
................
  r10662 | wsfulton | 2008-07-14 22:09:23 +0100 (Mon, 14 Jul 2008) | 1 line

  Fix director typemaps for pointers so that NULL pointers are correctly marshalled to C#/Java null in director methods
................
  r10672 | olly | 2008-07-17 02:17:08 +0100 (Thu, 17 Jul 2008) | 2 lines

  Fix a typo; improve wording.
................
  r10676 | wsfulton | 2008-07-17 22:05:49 +0100 (Thu, 17 Jul 2008) | 1 line

  SF #2019156 Configuring with --without-octave or --without-alllang did not disable octave.
................
  r10677 | wsfulton | 2008-07-17 22:08:22 +0100 (Thu, 17 Jul 2008) | 1 line

  tidy output after detecting X11 headers
................
  r10682 | wsfulton | 2008-07-19 19:08:06 +0100 (Sat, 19 Jul 2008) | 1 line

  a bit more on pgcpp
................
  r10683 | wsfulton | 2008-07-19 23:45:54 +0100 (Sat, 19 Jul 2008) | 1 line

  Fix building of Tcl examples/test-suite on Mac OSX
................
  r10714 | olly | 2008-07-27 13:51:16 +0100 (Sun, 27 Jul 2008) | 2 lines

  Fix "can can" typo in docs (SF#2026756)
................
  r10726 | wuzzeb | 2008-08-02 09:28:02 +0100 (Sat, 02 Aug 2008) | 1 line

  Commit patch 2019314
................
  r10727 | wuzzeb | 2008-08-02 09:49:43 +0100 (Sat, 02 Aug 2008) | 1 line

  add assert.h to fix chicken build of external runtime (ext_test testsuite)
................
  r10738 | talby | 2008-08-07 07:28:13 +0100 (Thu, 07 Aug 2008) | 2 lines

  hoist globals to local scope where trival.
................
  r10743 | talby | 2008-08-08 04:10:55 +0100 (Fri, 08 Aug 2008) | 2 lines

  initial steps to clean up perl5 class methods (primarily constructors).
................
  r10747 | talby | 2008-08-09 05:08:26 +0100 (Sat, 09 Aug 2008) | 2 lines

  moves perl space constructor fixups into wrapper code.
................
  r10749 | talby | 2008-08-10 00:57:55 +0100 (Sun, 10 Aug 2008) | 2 lines

  usage_func() fix + CHANGES.current entry to explain my past few commits.
................
  r10794 | talby | 2008-08-19 08:09:29 +0100 (Tue, 19 Aug 2008) | 3 lines

  rollback 10737:10749, this work is better left on a branch until it is
  in support a significant feature enhancement.
................
  r10801 | drjoe | 2008-08-31 17:07:43 +0100 (Sun, 31 Aug 2008) | 2 lines

  change Rf_warning to warning.  Looks like a typo
................
  r10802 | wsfulton | 2008-09-01 20:59:23 +0100 (Mon, 01 Sep 2008) | 1 line

  Fix ruby detection problem breaking configure
................
  r10803 | wsfulton | 2008-09-01 21:00:28 +0100 (Mon, 01 Sep 2008) | 1 line

  Fix another perl global namespace pollution
................
  r10804 | wsfulton | 2008-09-01 21:32:53 +0100 (Mon, 01 Sep 2008) | 1 line

  Fix array bounds checking in C# std::vector wrappers
................
  r10805 | wsfulton | 2008-09-01 21:34:49 +0100 (Mon, 01 Sep 2008) | 1 line

  fix runtime problem in Ruby std_vector example
................
  r10806 | wsfulton | 2008-09-01 21:42:40 +0100 (Mon, 01 Sep 2008) | 1 line

  Fix portability problem using /dev/null
................
  r10807 | wsfulton | 2008-09-01 22:46:41 +0100 (Mon, 01 Sep 2008) | 1 line

  patch #2079381 submitted by Boris Smilga - constant exprs put into no-eval context in DEFCENUM
................
  r10808 | wsfulton | 2008-09-02 21:56:52 +0100 (Tue, 02 Sep 2008) | 1 line

  Add new terminator attribute for the csin typemap for C#
................
  r10809 | wsfulton | 2008-09-03 00:01:37 +0100 (Wed, 03 Sep 2008) | 1 line

  Fix #1988296 - Multiple module director linking issue
................
  r10827 | richardb | 2008-09-10 11:08:21 +0100 (Wed, 10 Sep 2008) | 6 lines

  [Python] Commit patch #2089149: Director exception handling mangles
  returned exception.  Exceptions raised by Python code in directors
  are now passed through to the caller without change.  Also, remove
  the ": " prefix which used to be added to other director exceptions
  (eg, those due to incorrect return types).
................
  r10828 | bhy | 2008-09-10 11:45:33 +0100 (Wed, 10 Sep 2008) | 3 lines

  Initialized merge tracking via "svnmerge" with revisions "1-10827" from
  https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2008-bhy
................
  r10829 | bhy | 2008-09-10 12:04:09 +0100 (Wed, 10 Sep 2008) | 4 lines

  Removed merge tracking for "svnmerge" for
  https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2008-bhy
  (Undo the init due to user error)
................
  r10830 | bhy | 2008-09-10 12:08:16 +0100 (Wed, 10 Sep 2008) | 3 lines

  Initialized merge tracking via "svnmerge" with revisions "1-10403" from
  https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2008-bhy
................
  r10831 | bhy | 2008-09-10 12:51:12 +0100 (Wed, 10 Sep 2008) | 11 lines

  (Still trying to set right properity to get svnmerge work...)
  Recorded merge of revisions 10404 via svnmerge from
  https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2008-bhy

  ........
    r10404 | bhy | 2008-05-01 08:35:49 +0800 (Thu, 01 May 2008) | 5 lines

    Start of gsoc2008-bhy branch. This is a branch for Haoyu Bai's Python 3.0 backend project.
    Some file already modified since a little of work already done when starting the branch.
  ........
................
  r10834 | bhy | 2008-09-11 18:18:07 +0100 (Thu, 11 Sep 2008) | 8 lines

  Merged the Python 3.0 support branch. The merging progress is not so smooth, so hope this commit won't make anything broken.

  This is the (incomplemete) log produced by svnmerge.py:

  Merged revisions 10405-10409,10420-10422,10426,10438,10445,10451,10454-10465,10467,10473-10475,10485,10488-10489,10493-10495,10497,10509-10510,10513-10514,10517,10520,10525,10528-10529,10533-10535,10554-10557,10570,10573,10593,10614,10666-10669,10673,10678,10687,10690,10704-10706,10731,10744,10750-10752,10755,10759,10770,10775-10776,10813,10819 via svnmerge from
  https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2008-bhy
................


git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2008-cherylfoil@10837 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 ANNOUNCE                                      |   10 +-
 CHANGES                                       |  159 +-
 CHANGES.current                               |  148 +-
 Doc/Manual/CSharp.html                        |   58 +-
 Doc/Manual/Contents.html                      |    3 +-
 Doc/Manual/Extending.html                     |    3 +-
 Doc/Manual/Java.html                          |   27 +-
 Doc/Manual/Php.html                           |  184 +-
 Doc/Manual/Python.html                        |  253 ++-
 Doc/Manual/SWIG.html                          |   16 +-
 Doc/Manual/SWIGPlus.html                      |    5 +-
 Doc/Manual/Sections.html                      |    2 +-
 Doc/Manual/Typemaps.html                      |   15 +-
 Doc/Manual/Warnings.html                      |    2 +-
 Examples/GIFPlot/Python/full/Makefile         |    3 +-
 Examples/GIFPlot/Python/shadow/Makefile       |    3 +-
 Examples/GIFPlot/Python/simple/Makefile       |    3 +-
 Examples/Makefile.in                          |   77 +-
 Examples/guile/multimap/example.i             |    4 +-
 Examples/guile/multivalue/example.i           |    6 +
 Examples/lua/arrays/example.c                 |    2 +-
 Examples/lua/embed2/embed2.c                  |   13 +-
 Examples/lua/embed3/embed3.cpp                |   14 +-
 Examples/lua/owner/example.cxx                |    4 +-
 Examples/perl5/import/base.h                  |    2 +-
 Examples/perl5/multiple_inheritance/example.h |   23 +-
 Examples/php4/reference/BUILD-proxy.sh        |    5 -
 Examples/python/callback/Makefile             |    1 +
 Examples/python/class/Makefile                |    1 +
 Examples/python/constants/Makefile            |    1 +
 Examples/python/contract/Makefile             |    1 +
 Examples/python/docstrings/Makefile           |    1 +
 Examples/python/enum/Makefile                 |    1 +
 Examples/python/exception/Makefile            |    1 +
 Examples/python/exceptproxy/Makefile          |    1 +
 Examples/python/extend/Makefile               |    1 +
 Examples/python/funcptr/Makefile              |    1 +
 Examples/python/funcptr2/Makefile             |    1 +
 Examples/python/functor/Makefile              |    1 +
 Examples/python/import/Makefile               |    1 +
 Examples/python/import_template/Makefile      |    1 +
 Examples/python/libffi/Makefile               |    1 +
 Examples/python/multimap/Makefile             |    1 +
 Examples/python/multimap/example.i            |   32 +-
 Examples/python/operator/Makefile             |    1 +
 Examples/python/pointer/Makefile              |    1 +
 Examples/python/reference/Makefile            |    1 +
 Examples/python/simple/Makefile               |    1 +
 Examples/python/smartptr/Makefile             |    1 +
 Examples/python/std_map/Makefile              |    1 +
 Examples/python/std_vector/Makefile           |    1 +
 Examples/python/swigrun/Makefile              |    1 +
 Examples/python/template/Makefile             |    1 +
 Examples/python/varargs/Makefile              |    1 +
 Examples/python/variables/Makefile            |    1 +
 Examples/python/weave/Makefile                |    1 +
 Examples/ruby/class/example.dsp               |    4 +-
 Examples/ruby/free_function/example.cxx       |    2 +-
 Examples/ruby/free_function/example.dsp       |    4 +-
 Examples/ruby/import/bar.dsp                  |    4 +-
 Examples/ruby/import/base.dsp                 |    4 +-
 Examples/ruby/import/foo.dsp                  |    4 +-
 Examples/ruby/import/spam.dsp                 |    4 +-
 Examples/ruby/mark_function/example.dsp       |    4 +-
 Examples/ruby/std_vector/runme.rb             |    8 +-
 Examples/tcl/import/base.h                    |    2 +-
 Examples/test-suite/abstract_virtual.i        |    4 +-
 Examples/test-suite/allowexcept.i             |   14 +-
 Examples/test-suite/apply_signed_char.i       |    2 +
 Examples/test-suite/bools.i                   |    2 +
 Examples/test-suite/char_strings.i            |    2 +-
 Examples/test-suite/chicken/Makefile.in       |   12 +-
 Examples/test-suite/common.mk                 |    3 +
 Examples/test-suite/constant_pointers.i       |    6 +
 Examples/test-suite/contract.i                |    2 +-
 Examples/test-suite/cpp_basic.i               |    2 +
 Examples/test-suite/csharp/Makefile.in        |    4 +-
 .../test-suite/csharp/char_strings_runme.cs   |    2 +-
 .../test-suite/csharp/director_basic_runme.cs |   74 +
 Examples/test-suite/csharp_prepost.i          |  101 +-
 Examples/test-suite/default_constructor.i     |    4 +-
 Examples/test-suite/director_basic.i          |    6 +-
 Examples/test-suite/enum_thorough.i           |    2 +
 Examples/test-suite/evil_diamond.i            |    2 +-
 Examples/test-suite/evil_diamond_ns.i         |    2 +-
 Examples/test-suite/evil_diamond_prop.i       |    2 +-
 Examples/test-suite/fvirtual.i                |    4 +-
 Examples/test-suite/guilescm/Makefile.in      |    8 +-
 Examples/test-suite/java/Makefile.in          |    4 +-
 .../test-suite/java/char_strings_runme.java   |    2 +-
 .../test-suite/java/director_basic_runme.java |   57 +-
 Examples/test-suite/java_typemaps_proxy.i     |    2 +
 Examples/test-suite/keyword_rename.i          |   32 +
 Examples/test-suite/li_cstring.i              |    8 +-
 Examples/test-suite/li_cwstring.i             |    8 +-
 Examples/test-suite/li_std_string.i           |    2 +-
 Examples/test-suite/lua/li_typemaps_runme.lua |   40 +
 Examples/test-suite/minherit.i                |    2 +-
 Examples/test-suite/minherit2.i               |    2 +-
 Examples/test-suite/multiple_inheritance.i    |    4 +-
 Examples/test-suite/name_warnings.i           |    3 +-
 Examples/test-suite/namespace_typemap.i       |    2 +-
 Examples/test-suite/octave/fvirtual_runme.m   |    2 +-
 .../test-suite/octave/li_std_string_runme.m   |    2 +-
 Examples/test-suite/operbool.i                |   10 +
 .../test-suite/perl5/li_std_string_runme.pl   |    4 +-
 .../test-suite/perl5/li_typemaps_runme.pl     |   39 +-
 Examples/test-suite/perl5/run-perl-test.pl    |    2 +-
 Examples/test-suite/php4/Makefile.in          |    6 +-
 Examples/test-suite/php4/tests.php4           |    2 +-
 Examples/test-suite/pure_virtual.i            |    2 +-
 Examples/test-suite/python/Makefile.in        |   67 +-
 Examples/test-suite/python/README             |    6 +-
 Examples/test-suite/python/abstractbase.i     |   18 +
 .../test-suite/python/abstractbase_runme3.py  |    8 +
 .../test-suite/python/cpp_namespace_runme.py  |   20 +-
 .../python/director_classic_runme.py          |   68 +-
 .../python/director_exception_runme.py        |   50 +-
 Examples/test-suite/python/file_test_runme.py |    3 +-
 Examples/test-suite/python/fvirtual_runme.py  |    2 +-
 Examples/test-suite/python/hugemod.pl         |    8 +-
 .../test-suite/python/keyword_rename_runme.py |    4 +
 .../test-suite/python/li_std_string_runme.py  |    2 +-
 Examples/test-suite/python/operbool_runme.py  |    4 +
 Examples/test-suite/python/pybuf.i            |   34 +
 Examples/test-suite/python/pybuf_benchmark.i  |   31 +
 .../python/pybuf_benchmark_runme.py           |   16 +
 .../python/pybuf_benchmark_runme3.py          |   16 +
 Examples/test-suite/python/pybuf_runme3.py    |   15 +
 .../python/template_typedef_cplx2_runme.py    |   13 +-
 .../python/template_typedef_cplx_runme.py     |   13 +-
 Examples/test-suite/r/Makefile.in             |    4 +-
 .../test-suite/ruby/li_std_string_runme.rb    |    2 +-
 Examples/test-suite/samename.i                |   13 +-
 .../test-suite/template_inherit_abstract.i    |    2 +-
 Examples/test-suite/template_int_const.i      |    8 +-
 Examples/test-suite/template_typedef_rec.i    |    6 +-
 Examples/test-suite/typemap_namespace.i       |    2 +-
 Examples/test-suite/using_composition.i       |    6 +-
 Examples/test-suite/using_extend.i            |    2 +-
 Examples/test-suite/using_namespace.i         |    2 +-
 Lib/allegrocl/allegrocl.swg                   |   80 +-
 Lib/cdata.i                                   |    9 +-
 Lib/cffi/cffi.swg                             |    7 +-
 Lib/chicken/chicken.swg                       |    1 +
 Lib/chicken/chickenkw.swg                     |    2 +-
 Lib/chicken/chickenrun.swg                    |    1 +
 Lib/csharp/csharp.swg                         |    3 +-
 Lib/csharp/csharphead.swg                     |    4 +-
 Lib/csharp/csharpkw.swg                       |    2 +-
 Lib/csharp/std_vector.i                       |    4 +-
 Lib/java/director.swg                         |   10 +-
 Lib/java/java.swg                             |    3 +-
 Lib/java/javakw.swg                           |    2 +-
 Lib/java/various.i                            |    2 +-
 Lib/lua/luatypemaps.swg                       |    4 +-
 Lib/lua/typemaps.i                            |   21 +
 Lib/ocaml/ocamlkw.swg                         |    2 +-
 Lib/perl5/noembed.h                           |    4 +
 Lib/perl5/perlkw.swg                          |    4 +-
 Lib/{php4 => php}/const.i                     |    0
 Lib/{php4 => php}/globalvar.i                 |    0
 Lib/{php4/php4.swg => php/php.swg}            |   17 +-
 Lib/{php4/php4init.swg => php/phpinit.swg}    |    0
 Lib/{php4/php4kw.swg => php/phpkw.swg}        |   14 +-
 Lib/{php4 => php}/phppointers.i               |    0
 Lib/{php4/php4run.swg => php/phprun.swg}      |    4 +-
 Lib/{php4 => php}/std_common.i                |    0
 Lib/{php4 => php}/std_deque.i                 |    0
 Lib/{php4 => php}/std_map.i                   |    4 +
 Lib/{php4 => php}/std_pair.i                  |    0
 Lib/{php4 => php}/std_string.i                |    0
 Lib/{php4 => php}/std_vector.i                |    2 +
 Lib/{php4 => php}/stl.i                       |    0
 Lib/{php4 => php}/typemaps.i                  |   21 +
 Lib/{php4 => php}/utils.i                     |    4 +-
 Lib/pike/pikekw.swg                           |    2 +-
 Lib/python/director.swg                       |    9 +-
 Lib/python/file.i                             |    4 +-
 Lib/python/pyabc.i                            |   10 +
 Lib/python/pyapi.swg                          |   14 +
 Lib/python/pybuffer.i                         |  107 ++
 Lib/python/pycontainer.swg                    |   65 +-
 Lib/python/pyerrors.swg                       |    6 +-
 Lib/python/pyhead.swg                         |   44 +
 Lib/python/pyinit.swg                         |   68 +-
 Lib/python/pyiterators.swg                    |   14 +-
 Lib/python/pyopers.swg                        |    6 +
 Lib/python/pyrun.swg                          |  113 +-
 Lib/python/pystrings.swg                      |   20 +-
 Lib/python/pythonkw.swg                       |    4 +-
 Lib/python/pywstrings.swg                     |    2 +
 Lib/python/std_map.i                          |    4 +
 Lib/r/r.swg                                   |    4 +-
 Lib/r/rkw.swg                                 |   32 +
 Lib/ruby/rubycontainer.swg                    |    6 +-
 Lib/ruby/rubykw.swg                           |    2 +-
 Lib/swiglabels.swg                            |    6 +
 Lib/typemaps/primtypes.swg                    |    1 +
 README                                        |    9 +-
 Source/CParse/cscanner.c                      |   52 +-
 Source/CParse/parser.y                        |   37 +-
 Source/CParse/templ.c                         |   27 +-
 Source/DOH/hash.c                             |   31 +-
 Source/Include/swigwarn.h                     |   13 +-
 Source/Makefile.am                            |    2 +-
 Source/Modules/allegrocl.cxx                  |   61 +-
 Source/Modules/cffi.cxx                       |    6 +-
 Source/Modules/chicken.cxx                    |   13 +-
 Source/Modules/csharp.cxx                     |   92 +-
 Source/Modules/guile.cxx                      |    2 +-
 Source/Modules/java.cxx                       |   35 +-
 Source/Modules/lang.cxx                       |   61 +-
 Source/Modules/lua.cxx                        |    4 -
 Source/Modules/main.cxx                       |   10 +-
 Source/Modules/modula3.cxx                    |    4 +-
 Source/Modules/ocaml.cxx                      |   82 +-
 Source/Modules/{php4.cxx => php.cxx}          |  944 ++--------
 Source/Modules/python.cxx                     |  527 ++++--
 Source/Modules/r.cxx                          |   17 +-
 Source/Modules/ruby.cxx                       |   10 +-
 Source/Modules/swigmain.cxx                   |    4 +-
 Source/Modules/uffi.cxx                       |   11 +-
 Source/Preprocessor/cpp.c                     |    5 +-
 Source/Swig/cwrap.c                           |    3 +-
 Source/Swig/include.c                         |    3 +-
 Source/Swig/misc.c                            |   23 +-
 Source/Swig/naming.c                          |    6 +-
 Source/Swig/scanner.c                         |    4 +-
 Source/Swig/typeobj.c                         |    3 +-
 Source/Swig/typesys.c                         |   17 +-
 TODO                                          |    2 +-
 Tools/WAD/Python/type.c                       |    2 +-
 Tools/config/config.guess                     | 1516 ---------------
 Tools/config/config.sub                       | 1626 -----------------
 Tools/mkrelease.py                            |    8 +-
 configure.in                                  |  145 +-
 237 files changed, 3218 insertions(+), 5059 deletions(-)
 delete mode 100755 Examples/php4/reference/BUILD-proxy.sh
 create mode 100644 Examples/test-suite/csharp/director_basic_runme.cs
 create mode 100644 Examples/test-suite/keyword_rename.i
 create mode 100644 Examples/test-suite/lua/li_typemaps_runme.lua
 create mode 100644 Examples/test-suite/operbool.i
 create mode 100644 Examples/test-suite/python/abstractbase.i
 create mode 100644 Examples/test-suite/python/abstractbase_runme3.py
 create mode 100644 Examples/test-suite/python/keyword_rename_runme.py
 create mode 100644 Examples/test-suite/python/operbool_runme.py
 create mode 100644 Examples/test-suite/python/pybuf.i
 create mode 100644 Examples/test-suite/python/pybuf_benchmark.i
 create mode 100644 Examples/test-suite/python/pybuf_benchmark_runme.py
 create mode 100644 Examples/test-suite/python/pybuf_benchmark_runme3.py
 create mode 100644 Examples/test-suite/python/pybuf_runme3.py
 rename Lib/{php4 => php}/const.i (100%)
 rename Lib/{php4 => php}/globalvar.i (100%)
 rename Lib/{php4/php4.swg => php/php.swg} (96%)
 rename Lib/{php4/php4init.swg => php/phpinit.swg} (100%)
 rename Lib/{php4/php4kw.swg => php/phpkw.swg} (93%)
 rename Lib/{php4 => php}/phppointers.i (100%)
 rename Lib/{php4/php4run.swg => php/phprun.swg} (99%)
 rename Lib/{php4 => php}/std_common.i (100%)
 rename Lib/{php4 => php}/std_deque.i (100%)
 rename Lib/{php4 => php}/std_map.i (97%)
 rename Lib/{php4 => php}/std_pair.i (100%)
 rename Lib/{php4 => php}/std_string.i (100%)
 rename Lib/{php4 => php}/std_vector.i (98%)
 rename Lib/{php4 => php}/stl.i (100%)
 rename Lib/{php4 => php}/typemaps.i (85%)
 rename Lib/{php4 => php}/utils.i (96%)
 create mode 100644 Lib/python/pyabc.i
 create mode 100644 Lib/python/pybuffer.i
 create mode 100644 Lib/r/rkw.swg
 rename Source/Modules/{php4.cxx => php.cxx} (64%)
 delete mode 100755 Tools/config/config.guess
 delete mode 100755 Tools/config/config.sub

diff --git a/ANNOUNCE b/ANNOUNCE
index 0fb688344..7c0e95e3f 100644
--- a/ANNOUNCE
+++ b/ANNOUNCE
@@ -1,10 +1,10 @@
-*** ANNOUNCE: SWIG 1.3.35 (7 April 2008) ***
+*** ANNOUNCE: SWIG 1.3.36 (24 June 2008) ***
 
 http://www.swig.org
 
 
-We're pleased to announce SWIG-1.3.35, the latest installment in the
-SWIG development effort.  SWIG-1.3.35 includes a number of bug fixes
+We're pleased to announce SWIG-1.3.36, the latest installment in the
+SWIG development effort.  SWIG-1.3.36 includes a number of bug fixes
 and large number of enhancements throughout.
 
 What is SWIG?
@@ -24,11 +24,11 @@ Availability:
 -------------
 The release is available for download on Sourceforge at
 
-     http://prdownloads.sourceforge.net/swig/swig-1.3.35.tar.gz
+     http://prdownloads.sourceforge.net/swig/swig-1.3.36.tar.gz
 
 A Windows version is also available at
 
-     http://prdownloads.sourceforge.net/swig/swigwin-1.3.35.zip
+     http://prdownloads.sourceforge.net/swig/swigwin-1.3.36.zip
 
 Release numbers
 ---------------
diff --git a/CHANGES b/CHANGES
index fc3018a1d..782849c6f 100644
--- a/CHANGES
+++ b/CHANGES
@@ -2,6 +2,162 @@ SWIG (Simplified Wrapper and Interface Generator)
 
 See CHANGES.current for current version.
 
+Version 1.3.36 (24 June 2008)
+=============================
+
+06/24/2008: wsfulton
+            Remove deprecated -c commandline option (runtime library generation).
+
+06/24/2008: olly
+	    [PHP] Fix assertion failure when handling %typemap(in,numinputs=0)
+	    (testcase ignore_parameter).
+
+06/24/2008: olly
+	    [PHP] Fix segfault when wrapping a non-class function marked with
+	    %newobject (testcase char_strings).
+
+06/22/2008: wsfulton
+            [Java] Add a way to use AttachCurrentThreadAsDaemon instead of AttachCurrentThread
+            in director code. Define the SWIG_JAVA_ATTACH_CURRENT_THREAD_AS_DAEMON macro, see
+            Lib/java/director.swg.
+
+06/21/2008: wsfulton
+            [Ruby] Fix crashing in the STL wrappers (reject! and delete_if methods)
+
+06/19/2008: wsfulton
+            [Java, C#] C# and Java keywords will be renamed instead of just issuing a warning
+            and then generating uncompileable code. Warning 314 gives the new name when a 
+            keyword is found.
+
+06/19/2008: wsfulton
+            [R] Keyword handling added. R Keywords will be renamed as necessary.
+            Warning 314 gives the new name when a keyword is found.
+
+06/17/2008: mgossage
+            [Lua] Added missing support for bool& and bool*. Added runtest for li_typemaps testcase.
+            (Bug #1938142)
+
+06/07/2008: bhy
+            Added test case keyword_rename, then made the keyword renaming works properly
+            by fixing Swig_name_make() for a incomplete condition checking.
+
+06/02/2008: wsfulton
+            [Java, C#] Fix enum wrappers when using -noproxy.
+
+05/30/2008: bhy
+            Added std::wstring into Lib/typemaps/primtypes.swg, since it is also a primitive 
+            type in SWIG - fixed SF #1976978.
+
+05/29/2008: wsfulton
+            [Java, C#] Fix variable wrappers when using -noproxy.
+
+05/29/2008: bhy
+            [Python] Fixed a typo of %#ifdef in Lib/python/pycontainer.swg, which is related 
+            to -extranative SWIG option - SF #1971977.
+
+05/20/2008: wsfulton
+            New partialcheck makefile targets for partial testing of the test-suite. These
+            just invoke SWIG, ie no compilation and no runtime testing. It can be faster
+            when developing by just doing a directory diff of the files SWIG generates
+            against those from a previous run. Example usage from the top level directory:
+
+              make partialcheck-test-suite
+              make partialcheck-java-test-suite
+
+            This change also encompasses more flexibility in running the test-suite, eg
+            it is possible to prefix the command line which runs any target language test
+            with a tool. See the RUNTOOL, COMPILETOOL and SWIGTOOL targets in the common.mk
+            file and makefiles in the test-suite directory. For example it is possible to 
+            run the runtime tests through valgrind using:
+
+              make check RUNTOOL="valgrind --leak-check=full"
+
+            or invoke SWIG under valgrind using:
+
+              make check SWIGTOOL="valgrind --tool=memcheck"
+
+05/19/2008: drjoe
+            [R] Fixed define that was breaking pre-2.7.  Checked in
+            patch from Soren Sonnenburg that creates strings in  
+	    version independent way
+
+05/15/2008: wsfulton
+            [Java] Fix variable name clash in directors - SF #1963316 reported by Tristan.
+
+05/14/2008: wsfulton
+            Add an optimisation for functions that return objects by value, reducing
+            the number of copies of the object that are made. Implemented using an
+            optional attribute in the "out" typemap called "optimal". Details in 
+            Typemaps.html.
+
+05/11/2008: olly
+	    [PHP] Check for %feature("notabstract") when generating PHP5 class
+	    wrapper.
+
+05/11/2008: wsfulton
+            Fix SF #1943608 - $self substitution in %contract, patch submitted by
+            Toon Verstraelen.
+
+05/09/2008: olly
+	    [PHP] Fix char * typemaps to work when applied to signed char * and
+	    unsigned char * (uncovered by testcase apply_strings).
+
+05/09/2008: wsfulton
+            Fix wrapping of char * member variables when using allprotected mode.
+            Bug reported by Warren Wang.
+
+05/09/2008: olly
+	    [PHP] Fix bad PHP code generated when wrapping an enum in a
+	    namespace (uncovered by testcase arrays_scope).
+
+05/09/2008: olly
+	    [PHP] SWIG now runs the PHP testsuite using PHP5, not PHP4.  PHP4
+	    is essentially obsolete now, so we care much more about solid PHP5
+	    support.
+
+05/07/2008: wsfulton
+            STL fixes when using %import rather than %include and the Solaris Workshop
+            compiler and the Roguewave STL.
+
+05/07/2008: wsfulton
+            Fix wrapping of overloaded protected methods when using allprotected mode.
+            Bug reported by Warren Wang.
+
+05/03/2008: wsfulton
+            Commit patch #1956607 to add -MT support from Richard Boulton.
+            This patch mirrors the gcc -MT option which allows one to change the default
+            Makefile target being generated when generating makefiles with the -M family
+            of options. For example:
+
+              $ swig -java -MM -MT overiddenname -c++  example.i
+              overiddenname: \
+               example.i \
+               example.h 
+
+04/30/2008: mgossage
+	    [Lua] Removed generation of _wrap_delete_XXXXX (wrappered destructor)
+	    which was unused and causing warning with g++ -Wall.
+	    Removed other unused warning in typemaps.i and other places.
+	    Added Examples/lua/embed3, and run tests a few test cases.
+
+04/24/2008: olly
+	    [Python] Fix generated code for IBM's C++ compiler on AIX (patch
+	    from Goeran Uddeborg in SF#1928048).
+
+04/24/2008: olly
+	    Rename BSIZE in Examples/test-suite/arrays_scope.i to BBSIZE to
+	    avoid a clash with BSIZE defined by headers on AIX with Perl
+	    (reported in SF#1928048).
+
+04/20/2008: wsfulton
+            Add the ability to wrap all protected members when using directors.
+            Previously only the virtual methods were available to the target language.
+            Now all protected members, (static and non-static variables, non-virtual methods
+            and static methods) are wrapped when using the allprotected mode. The allprotected
+            mode is turned on in the module declaration:
+
+              %module(directors="1", allprotected="1") modulename
+
 Version 1.3.35 (7 April 2008)
 =============================
 
@@ -12123,7 +12279,8 @@ Version 1.3.14 (August 12, 2002)
             with helper functions even if they aren't used.    To fix this,
             a new fragment directive is available.  For example:
 
-               %fragment("type_helper","header") %{
+               (corrected typo in line below - 06/26/2008)
+               %fragment("type_header","header") %{
                   void some_helper_function() {
                       ...
                   }
diff --git a/CHANGES.current b/CHANGES.current
index 27e9925d2..6b552c994 100644
--- a/CHANGES.current
+++ b/CHANGES.current
@@ -1,106 +1,80 @@
-Version 1.3.36 (in progress)
+Version 1.3.37 (in progress)
 =============================
 
-05/20/2008: wsfulton
-            New partialcheck makefile targets for partial testing of the test-suite. These
-            just invoke SWIG, ie no compilation and no runtime testing. It can be faster
-            when developing by just doing a directory diff of the files SWIG generates
-            against those from a previous run. Example usage from the top level directory:
+2008-09-02: wsfulton
+	    [Python] Commit patch #2089149: Director exception handling mangles
+	    returned exception.  Exceptions raised by Python code in directors
+	    are now passed through to the caller without change.  Also, remove
+	    the ": " prefix which used to be added to other director exceptions
+	    (eg, those due to incorrect return types).
 
-              make partialcheck-test-suite
-              make partialcheck-java-test-suite
+2008-09-02: wsfulton
+            [Python] Commit patch #1988296 GCItem multiple module linking issue when using 
+            directors.
 
-            This change also encompasses more flexibility in running the test-suite, eg
-            it is possible to prefix the command line which runs any target language test
-            with a tool. See the RUNTOOL, COMPILETOOL and SWIGTOOL targets in the common.mk
-            file and makefiles in the test-suite directory. For example it is possible to 
-            run the runtime tests through valgrind using:
+2008-09-02: wsfulton
+            [C#] Support for 'using' and 'fixed' blocks in the 'csin' typemap is now
+            possible through the use of the pre attribute and the new terminator attribute, eg
 
-              make check RUNTOOL="valgrind --leak-check=full"
+              %typemap(csin, 
+                       pre="    using (CDate temp$csinput = new CDate($csinput)) {",
+                       terminator="    } // terminate temp$csinput using block",
+                      ) const CDate &
+                       "$csclassname.getCPtr(temp$csinput)"
 
-            or invoke SWIG under valgrind using:
+            See CSharp.html for more info.
 
-              make check SWIGTOOL="valgrind --tool=memcheck"
+2008-09-01: wsfulton
+            [CFFI] Commit patch #2079381 submitted by Boris Smilga - constant exprs put into 
+            no-eval context in DEFCENUM
 
-05/19/2008: drjoe
-            [R] Fixed define that was breaking pre-2.7.  Checked in
-            patch from Soren Sonnenburg that creates strings in  
-	    version independent way
+2008-09-01: wsfulton
+            [C#] Correct array bounds checking in std::vector typemaps - Insert and InsertRange
+            methods.
 
-05/15/2008: wsfulton
-            [Java] Fix variable name clash in directors - SF #1963316 reported by Tristan.
+2008-08-02: wuzzeb
+            [Chicken,Allegro] Commit Patch 2019314
+            Fixes a build error in chicken, and several build errors and other errors
+            in Allegro CL
 
-05/14/2008: wsfulton
-            Add an optimisation for functions that return objects by value, reducing
-            the number of copies of the object that are made. Implemented using an
-            optional attribute in the "out" typemap called "optimal". Details in 
-            Typemaps.html.
+2008-07-19: wsfulton
+            Fix building of Tcl examples/test-suite on Mac OSX reported by Gideon Simpson.
 
-05/11/2008: olly
-	    [PHP] Check for %feature("notabstract") when generating PHP5 class
-	    wrapper.
+2008-07-17: wsfulton
+            Fix SF #2019156 Configuring with --without-octave or --without-alllang
+            did not disable octave.
 
-05/11/2008: wsfulton
-            Fix SF #1943608 - $self substitution in %contract, patch submitted by
-            Toon Verstraelen.
+2008-07-14: wsfultonn
+            [Java, C#] Fix director typemaps for pointers so that NULL pointers are correctly 
+            marshalled to C#/Java null in director methods.
 
-05/09/2008: olly
-	    [PHP] Fix char * typemaps to work when applied to signed char * and
-	    unsigned char * (uncovered by testcase apply_strings).
+2008-07-04: olly
+	    [PHP] For std_vector.i and std_map.i, rename empty() to is_empty()
+	    since "empty" is a PHP reserved word.  Based on patch from Mark Klein
+	    in SF#1943417.
 
-05/09/2008: wsfulton
-            Fix wrapping of char * member variables when using allprotected mode.
-            Bug reported by Warren Wang.
+2008-07-04: olly
+	    [PHP] The deprecated command line option "-make" has been removed.  
+	    Searches on Google codesearch suggest that nobody is using it now
+	    anyway.
 
-05/09/2008: olly
-	    [PHP] Fix bad PHP code generated when wrapping an enum in a
-	    namespace (uncovered by testcase arrays_scope).
+2008-07-04: olly
+	    [PHP] The SWIG cdata.i library module is now supported.
 
-05/09/2008: olly
-	    [PHP] SWIG now runs the PHP testsuite using PHP5, not PHP4.  PHP4
-	    is essentially obsolete now, so we care much more about solid PHP5
-	    support.
+2008-07-03: olly
+	    [PHP] The deprecated command line option "-phpfull" has been
+	    removed.  We recommend building your extension as a dynamically
+	    loadable module.
 
-05/07/2008: wsfulton
-            STL fixes when using %import rather than %include and the Solaris Workshop
-            compiler and the Roguewave STL.
+2008-07-02: olly
+	    [PHP4] Support for PHP4 has been removed.  The PHP developers are
+	    no longer making new PHP4 releases, and won't even be providing
+	    patches for critical security issues after 2008-08-08.
 
-05/07/2008: wsfulton
-            Fix wrapping of overloaded protected methods when using allprotected mode.
-            Bug reported by Warren Wang.
-
-05/03/2008: wsfulton
-            Commit patch #1956607 to add -MT support from Richard Boulton.
-            This patch mirrors the gcc -MT option which allows one to change the default
-            Makefile target being generated when generating makefiles with the -M family
-            of options. For example:
-
-              $ swig -java -MM -MT overiddenname -c++  example.i
-              overiddenname: \
-               example.i \
-               example.h 
-
-04/30/2008: mgossage
-	    [Lua] Removed generation of _wrap_delete_XXXXX (wrappered destructor)
-	    which was unused and causing warning with g++ -Wall.
-	    Removed other unused warning in typemaps.i and other places.
-	    Added Examples/lua/embed3, and run tests a few test cases.
-
-04/24/2008: olly
-	    [Python] Fix generated code for IBM's C++ compiler on AIX (patch
-	    from Goeran Uddeborg in SF#1928048).
-
-04/24/2008: olly
-	    Rename BSIZE in Examples/test-suite/arrays_scope.i to BBSIZE to
-	    avoid a clash with BSIZE defined by headers on AIX with Perl
-	    (reported in SF#1928048).
-
-04/20/2008: wsfulton
-            Add the ability to wrap all protected members when using directors.
-            Previously only the virtual methods were available to the target language.
-            Now all protected members, (static and non-static variables, non-virtual methods
-            and static methods) are wrapped when using the allprotected mode. The allprotected
-            mode is turned on in the module declaration:
-
-              %module(directors="1", allprotected="1") modulename
+2008-07-02: olly
+	    [Python] Import the C extension differently for Python 2.6 and
+	    later so that an implicit relative import doesn't produce a
+	    deprecation warning for 2.6 and a failure for 2.7 and later.
+	    Patch from Richard Boulton in SF#2008229, plus follow-up patches
+	    from Richard and Haoyu Bai.
 
diff --git a/Doc/Manual/CSharp.html b/Doc/Manual/CSharp.html
index 97cb75409..a712f82f2 100644
--- a/Doc/Manual/CSharp.html
+++ b/Doc/Manual/CSharp.html
@@ -1567,6 +1567,7 @@ Let's assume the code being wrapped is as follows:
 <pre>
 class CDate {
 public:
+  CDate();
   CDate(int year, int month, int day);
   int getYear();
   int getMonth();
@@ -1649,8 +1650,8 @@ The typemaps to achieve this are shown below.
 <pre>
 %typemap(cstype) const CDate&amp; "System.DateTime"
 %typemap(csin, 
-         pre="    CDate temp$csinput = new CDate($csinput.Year, $csinput.Month, $csinput.Day);")
-         const CDate &amp;
+         pre="    CDate temp$csinput = new CDate($csinput.Year, $csinput.Month, $csinput.Day);"
+        ) const CDate &amp;
          "$csclassname.getCPtr(temp$csinput)"
 
 %typemap(cstype) CDate&amp; "out System.DateTime"
@@ -1658,7 +1659,8 @@ The typemaps to achieve this are shown below.
          pre="    CDate temp$csinput = new CDate();", 
          post="      $csinput = new System.DateTime(temp$csinput.getYear(),"
               " temp$csinput.getMonth(), temp$csinput.getDay(), 0, 0, 0);", 
-         cshin="out $csinput") CDate &amp;
+         cshin="out $csinput"
+        ) CDate &amp;
          "$csclassname.getCPtr(temp$csinput)"
 
 </pre>
@@ -1763,7 +1765,8 @@ will be possible with the following <tt>CDate *</tt> typemaps
          pre="    CDate temp$csinput = new CDate($csinput.Year, $csinput.Month, $csinput.Day);",
          post="      $csinput = new System.DateTime(temp$csinput.getYear(),"
               " temp$csinput.getMonth(), temp$csinput.getDay(), 0, 0, 0);", 
-         cshin="ref $csinput") CDate *
+         cshin="ref $csinput"
+        ) CDate *
          "$csclassname.getCPtr(temp$csinput)"
 </pre>
 </div>
@@ -1788,6 +1791,50 @@ public class example {
 </pre>
 </div>
 
+<p>
+The following typemap is the same as the previous but demonstrates how a using block can be used for the temporary variable.
+The only change to the previous typemap is the introduction of the 'terminator' attribute to terminate the <tt>using</tt> block.
+The <tt>subtractYears</tt> method is nearly identical to the above <tt>addYears</tt> method.
+</p>
+
+<div class="code">
+<pre>
+%typemap(csin,
+         pre="    using (CDate temp$csinput = new CDate($csinput.Year, $csinput.Month, $csinput.Day)) {",
+         post="      $csinput = new System.DateTime(temp$csinput.getYear(),"
+              " temp$csinput.getMonth(), temp$csinput.getDay(), 0, 0, 0);", 
+         terminator="    } // terminate temp$csinput using block",
+         cshin="ref $csinput"
+        ) CDate *
+         "$csclassname.getCPtr(temp$csinput)"
+
+void subtractYears(CDate *pDate, int years) {
+  *pDate = CDate(pDate-&gt;getYear() - years, pDate-&gt;getMonth(), pDate-&gt;getDay());
+}
+</pre>
+</div>
+
+<p>
+The resulting generated code shows the termination of the <tt>using</tt> block:
+</p>
+
+<div class="code">
+<pre>
+public class example {
+  public static void subtractYears(ref System.DateTime pDate, int years) {
+    using (CDate temppDate = new CDate(pDate.Year, pDate.Month, pDate.Day)) {
+    try {
+      examplePINVOKE.subtractYears(CDate.getCPtr(temppDate), years);
+    } finally {
+      pDate = new System.DateTime(temppDate.getYear(), temppDate.getMonth(), temppDate.getDay(), 0, 0, 0);
+    }
+    } // terminate temppDate using block
+  }
+  ...
+}
+</pre>
+</div>
+
 <H3><a name="csharp_date_properties"></a>17.5.4 A date example demonstrating marshalling of C# properties</H3>
 
 
@@ -1827,7 +1874,8 @@ The typemap type required is thus <tt>CDate *</tt>. Given that the previous sect
          pre="    CDate temp$csinput = new CDate($csinput.Year, $csinput.Month, $csinput.Day);",
          post="      $csinput = new System.DateTime(temp$csinput.getYear(),"
               " temp$csinput.getMonth(), temp$csinput.getDay(), 0, 0, 0);", 
-         cshin="ref $csinput") CDate *
+         cshin="ref $csinput"
+        ) CDate *
          "$csclassname.getCPtr(temp$csinput)"
 
 %typemap(csvarin, excode=SWIGEXCODE2) CDate * %{
diff --git a/Doc/Manual/Contents.html b/Doc/Manual/Contents.html
index 9d6e4e66f..d385fec9f 100644
--- a/Doc/Manual/Contents.html
+++ b/Doc/Manual/Contents.html
@@ -380,7 +380,7 @@
 </ul>
 <li><a href="Typemaps.html#Typemaps_nn43">Typemaps for multiple languages</a>
 <li><a href="Typemaps.html#Typemaps_optimal">Optimal code generation when returning by value</a>
-<li><a href="Typemaps.html#Typemaps_nn42">Multi-argument typemaps</a>
+<li><a href="Typemaps.html#Typemaps_multi_argument_typemaps">Multi-argument typemaps</a>
 <li><a href="Typemaps.html#runtime_type_checker">The run-time type checker</a>
 <ul>
 <li><a href="Typemaps.html#Typemaps_nn45">Implementation</a>
@@ -768,6 +768,7 @@
 <li><a href="Java.html#java_directors_classes">Director classes</a>
 <li><a href="Java.html#java_directors_overhead">Overhead and code bloat</a>
 <li><a href="Java.html#java_directors_example">Simple directors example</a>
+<li><a href="Java.html#java_directors_threading">Director threading issues</a>
 </ul>
 <li><a href="Java.html#java_allprotected">Accessing protected members</a>
 <li><a href="Java.html#common_customization">Common customization features</a>
diff --git a/Doc/Manual/Extending.html b/Doc/Manual/Extending.html
index 588912b68..5639663a1 100644
--- a/Doc/Manual/Extending.html
+++ b/Doc/Manual/Extending.html
@@ -448,7 +448,8 @@ of the output.
 <p>
 The contents of each parse tree node consist of a collection of attribute/value
 pairs.  Internally, the nodes are simply represented by hash tables.  A display of
-the entire parse-tree structure can be obtained using <tt>swig -dump_tree</tt>. 
+the entire parse-tree structure can be obtained using <tt>swig -debug-top &lt;n&gt;</tt>, where <tt>n</tt> is
+the stage being processed. 
 There are a number of other parse tree display options, for example, <tt>swig -debug-module &lt;n&gt;</tt> will
 avoid displaying system parse information and only display the parse tree pertaining to the user's module at
 stage <tt>n</tt> of processing.
diff --git a/Doc/Manual/Java.html b/Doc/Manual/Java.html
index 88963caf5..518426f5a 100644
--- a/Doc/Manual/Java.html
+++ b/Doc/Manual/Java.html
@@ -85,6 +85,7 @@
 <li><a href="#java_directors_classes">Director classes</a>
 <li><a href="#java_directors_overhead">Overhead and code bloat</a>
 <li><a href="#java_directors_example">Simple directors example</a>
+<li><a href="#java_directors_threading">Director threading issues</a>
 </ul>
 <li><a href="#java_allprotected">Accessing protected members</a>
 <li><a href="#common_customization">Common customization features</a>
@@ -2856,7 +2857,11 @@ and therefore there is no possibility of premature garbage collection. In practi
 
 <p>
 The premature garbage collection prevention parameter for proxy classes is generated by default whenever proxy classes are passed by value, reference or with a pointer.
-The additional parameters do impose a slight performance overhead and the parameter generation can be suppressed globally with the <tt>-nopgcpp</tt> commandline option.
+The implementation for this extra parameter generation requires the "jtype" typemap to contain <tt>long</tt> and the "jstype" typemap to contain the name of a proxy class.
+<p>
+
+<p>
+The additional parameter does impose a slight performance overhead and the parameter generation can be suppressed globally with the <tt>-nopgcpp</tt> commandline option.
 More selective suppression is possible with the 'nopgcpp' attribute in the "jtype" <a href="#java_typemaps">Java typemap</a>.
 The attribute is a flag and so should be set to "1" to enable the suppression, or it can be omitted or set to "0" to disable.
 For example:
@@ -3450,6 +3455,26 @@ DirectorDerived::upcall_method() invoked.
 </pre>
 </div>
 
+<H3><a name="java_directors_threading"></a>20.5.5 Director threading issues</H3>
+
+
+<p>
+Depending on your operating system and version of Java and how you are using threads, you might find the JVM hangs on exit.
+There are a couple of solutions to try out. The preferred solution requires jdk-1.4 and later and uses <tt>AttachCurrentThreadAsDaemon</tt> instead of <tt>AttachCurrentThread</tt> whenever a call into the JVM is required. This can be enabled by defining the SWIG_JAVA_ATTACH_CURRENT_THREAD_AS_DAEMON macro when compiling the C++ wrapper code. For older JVMs define SWIG_JAVA_NO_DETACH_CURRENT_THREAD instead, to avoid the <tt>DetachCurrentThread</tt> call but this will result in a memory leak instead. For further details inspect the source code in the java/director.swg library file.
+</p>
+
+<p>
+Macros can be defined on the commandline when compiling your C++ code, or alternatively added to the C++ wrapper file as shown below:
+</p>
+
+<div class="code">
+<pre>
+%insert("runtime") %{
+#define SWIG_JAVA_NO_DETACH_CURRENT_THREAD
+%}
+</pre>
+</div>
+
 <H2><a name="java_allprotected"></a>20.6 Accessing protected members</H2>
 
 
diff --git a/Doc/Manual/Php.html b/Doc/Manual/Php.html
index 6b654fde5..8adbc36b1 100644
--- a/Doc/Manual/Php.html
+++ b/Doc/Manual/Php.html
@@ -43,21 +43,24 @@
 <b>Caution: This chapter (and module!) is still under construction</b>
 </p>
 
+<p>
+SWIG supports generating wrappers for PHP5.  Support for PHP4 has been removed
+as of SWIG 1.3.37.  The PHP developers are no longer making new PHP4 releases,
+and won't even be patching critical security issues after 2008-08-08, so it
+doesn't make much sense for SWIG to continue to support PHP4 at this point.
+If you need to continue to use PHP4, stick with SWIG 1.3.36.
+</p>
+
 <p>
 In this chapter, we discuss SWIG's support of PHP.  The PHP module
-was extensively rewritten in release 1.3.26, and although it is
-significantly more functional, it still does not implement all the
+was extensively rewritten in release 1.3.26, and support for generating
+OO wrappers for PHP5 was added in 1.3.30.  The PHP module works fairly
+well, but currently does not implement all the
 features available in some of the other languages.
 </p>
 
 <p>
-The examples and test cases have been developed with PHP4.  Release
-1.3.30 added support for generating PHP5 class wrappers for C++
-libraries.
-</p>
-
-<p>
-In order to use this module, you will need to have a copy of the PHP4 or PHP5
+In order to use this module, you will need to have a copy of the PHP5
 include files to compile the SWIG generated files.  If you installed
 PHP from a binary package, you may need to install a "php-dev" or "php-devel"
 package for these to be installed.  You can find out where these files are
@@ -88,7 +91,7 @@ you wish to statically link the extension into the php interpreter.
 The third file,
 <tt>example.php</tt> can be included by PHP scripts.  It attempts to
 dynamically load the extension and contains extra php code specified
-in the interface file.  If wrapping C++ code for PHP5, it will
+in the interface file.  If wrapping C++ code with PHP classes, it will
 also contain PHP5 class wrappers.
 </p>
 
@@ -100,7 +103,8 @@ more detail in <a href="#Php_nn2_6">section 27.2.6</a>.
 
 <p>
 The usual (and recommended) way is to build the extension as a separate
-dynamically loaded module. You can then specify that this be loaded
+dynamically loaded module (which is supported by all modern operating
+systems).  You can then specify that this be loaded
 automatically in <tt>php.ini</tt> or load it explicitly for any script which
 needs it.
 </p>
@@ -110,17 +114,15 @@ It is also possible to rebuild PHP from source so that your module is
 statically linked into the php executable/library.  This is a lot more
 work, and also requires a full rebuild of PHP to update your module,
 and it doesn't play nicely with package system.  We don't recommend
-this approach, but if you really want to do this, the <tt>-phpfull</tt>
-command line argument to swig may be of use - see below for details.
+this approach, or provide explicit support for it.
 </p>
 
 <H3><a name="Php_nn1_1"></a>28.1.1 Building a loadable extension</H3>
 
-
 <p>
 To build your module as a dynamically loadable extension, use compilation
 commands like these (if you aren't using GCC, the commands will be different,
-and there may be so variation between platforms - these commands should at
+and there may be some variation between platforms - these commands should at
 least work for Linux though):
 </p>
 
@@ -129,137 +131,8 @@ least work for Linux though):
 	gcc -shared example_wrap.o -o example.so
 </pre></div>
 
-<p>
-There is a deprecated <tt>-make</tt> command line argument to swig which will
-generate an additional file <tt>makefile</tt> which can usually build the
-extension (at least on some UNIX platforms), but the Makefile generated isn't
-very flexible, and the commands required are trivial so it is simpler to just
-add them to your Makefile or other build system directly.  We recommend that
-you don't use <tt>-make</tt> and it's likely to be removed at some point.
-</p>
-
-<H3><a name="Php_nn1_2"></a>28.1.2 Building extensions into PHP</H3>
-
-
-<p>
-Note that we don't recommend this approach - it's cleaner and simpler to
-use dynamically loadable modules, which are supported by all modern OSes.
-Support for this may be discontinued entirely in the future.
-</p>
-
-<p>
-It is possible to rebuild PHP itself with your module statically linked
-in.  To do this, you can use the <tt>-phpfull</tt> command line option to
-swig.  Using this option will generate three additional files.  The first
-extra file, <tt>config.m4</tt> contains the m4 and shell code needed to
-enable the extension as part of the PHP build process. The second
-extra file, <tt>Makefile.in</tt> contains the information needed to
-build the final Makefile after substitutions. The third and final
-extra file, <tt>CREDITS</tt> should contain the credits for the
-extension.
-</p>
-
-<p>
-To build with phpize, after you have run swig you will need to run the
-'phpize' command (installed as part of php) in the same
-directory. This re-creates the php build environment in that
-directory. It also creates a configure file which includes the shell
-code from the config.m4 that was generated by SWIG, this configure
-script will accept a command line argument to enable the extension to
-be run (by default the command line argument is --enable-modulename,
-however you can edit the config.m4 file before running phpize to
-accept --with-modulename. You can also add extra tests in config.m4 to
-check that a correct library version is installed or correct header
-files are included, etc, but you must edit this file before running
-phpize.) You can also get SWIG to generate simple extra tests for
-libraries and header files for you.
-</p>
-
-<div class="code"><pre>
-	swig -php -phpfull
-</pre></div>
-
-<p>
-If you depend on source files not generated by SWIG, before generating
-the configure file, you may need to edit the <tt>Makefile.in</tt>
-file. This contains the names of the source files to compile (just the
-wrapper file by default) and any additional libraries needed to be
-linked in. If there are extra C files to compile, you will need to add
-them to the <tt>Makefile.in</tt>, or add the names of libraries if they are
-needed.  In simple cases SWIG is pretty good at generating a complete
-<tt>Makefile.in</tt> and <tt>config.m4</tt> which need no further editing.
-</p>
-
-<p>
-You then run the configure script with the command line argument needed
-to enable the extension. Then run make, which builds the extension.
-The extension object file will be left in the modules sub directory, you can
-move it to wherever it is convenient to call from your php script. 
-</p>
-
-<p>
-When using <tt>-phpfull</tt>, swig also accepts the following
-additional optional arguments:
-</p>
-<ul>
-<li><tt>-withincs "&lt;incs&gt;"</tt> Adds include files to the config.m4 file.
-<li><tt>-withlibs "&lt;libs&gt;"</tt> Links with the specified libraries.
-<li><tt>-withc "&lt;files&gt;"</tt> Compiles and links the additional specified C files.
-<li><tt>-withcxx "&lt;files&gt;"</tt> Compiles and links the additional specified C++ files.
-</ul>
-
-<p>
-After running swig with the <tt>-phpfull</tt> switch, you will be left with a shockingly
-similar set of files to the previous build process. However you will then need
-to move these files to a subdirectory within the php source tree, this subdirectory you will need to create under the ext directory, with the name of the extension (e.g. <tt>mkdir php-4.0.6/ext/modulename</tt>).
-</p>
-
-<p>
-After moving the files into this directory, you will need to run the 'buildall'
-script in the php source directory. This rebuilds the configure script 
-and includes the extra command line arguments from the module you have added. 
-</p>
-
-<p>
-Before running the generated configure file, you may need to edit the <tt>
-Makefile.in</tt>. This contains the names of the source files to compile (
-just the wrapper file by default) and any additional libraries needed to
-link in. If there are extra C files to compile you will need to add them
-to the Makefile, or add the names of libraries if they are needed.
-In most cases <tt>Makefile.in</tt> will be complete, especially if you 
-make use of <tt>-withlibs</tt> and <tt>-withincs</tt>
-</p>
-
-<div class="code"><pre>
-	swig -php -phpfull -withlibs "xapian omquery" --withincs "om.h"
-</pre></div>
-
-<p>
-Will include in the <tt>config.m4</tt> and <tt>Makefile.in</tt> search for
-<tt>libxapian.a</tt> or <tt>libxapian.so</tt> and search for
-<tt>libomquery.a</tt> or <tt>libomquery.so</tt> as well as a 
-search for <tt>om.h</tt>.
-</p>
-
-<p>
-You then need to run the configure command and pass the necessary command
-line arguments to enable your module (by default this is --enable-modulename,
-but this can be changed by editing the config.m4 file in the modules directory
-before running the buildall script. In addition, extra tests can be added to
-the config.m4 file to ensure the correct libraries and header files are 
-installed.)
-</p>
-
-<p>
-Once configure has completed, you can run make to build php. If this all
-compiles correctly, you should end up with a php executable/library
-which contains your new module. You can test it with a php script which
-does not have the 'dl' command as used above.
-</p>
-
 <H3><a name="Php_nn1_3"></a>28.1.3 Using PHP Extensions</H3>
 
-
 <p>
 To test the extension from a PHP script, you need to load it first. You
 can load it for every script by adding this line the <tt>[PHP]</tt> section of
@@ -717,20 +590,9 @@ variable, or assigning <tt>NULL</tt> to a variable.
 
 
 <p>
-SWIG defaults to wrapping C++ structs and classes with PHP classes.  This
-requires SWIG to generate different code for PHP4 and PHP5, so you must
-specify which you want using <tt>-php4</tt> or <tt>-php5</tt> (currently
-<tt>-php</tt> generates PHP4 class wrappers for compatibility with
-SWIG 1.3.29 and earlier, but this may change in the future).
-</p>
-
-<p>
-PHP4 classes are implemented entirely using the Zend C API so
-no additional php code is generated.  For PHP5, a PHP wrapper
+SWIG defaults to wrapping C++ structs and classes with PHP classes
+unless "-noproxy" is specified.  For PHP5, a PHP wrapper
 class is generated which calls a set of flat functions wrapping the C++ class.
-In many cases the PHP4 and PHP5 wrappers will behave the same way,
-but the PHP5 ones make use of better PHP5's better OO functionality
-where appropriate.
 </p>
 
 <p>
@@ -754,7 +616,7 @@ struct Complex {
 </pre></div>
 
 <p>
-Would be used in the following way from either PHP4 or PHP5:
+Would be used in the following way from PHP5:
 </p>
 
 <div class="code"><pre>
@@ -854,9 +716,9 @@ the programmer can either reassign the variable or call
 
 
 <p>
-Static member variables are not supported in PHP4, and it does not
-appear to be possible to intercept accesses to static member variables
-in PHP5. Therefore, static member variables are
+Static member variables in C++ are not wrapped as such in PHP
+as it does not appear to be possible to intercept accesses to such variables.
+Therefore, static member variables are
 wrapped using a class function with the same name, which
 returns the current value of the class variable. For example
 </p>
diff --git a/Doc/Manual/Python.html b/Doc/Manual/Python.html
index 62b72fabf..c0b71b52d 100644
--- a/Doc/Manual/Python.html
+++ b/Doc/Manual/Python.html
@@ -46,7 +46,7 @@
 <li><a href="#Python_nn30">Memory management</a>
 <li><a href="#Python_nn31">Python 2.2 and classic classes</a>
 </ul>
-<li><a href="#directors">Cross language polymorphism</a>
+<li><a href="#Python_directors">Cross language polymorphism</a>
 <ul>
 <li><a href="#Python_nn33">Enabling directors</a>
 <li><a href="#Python_nn34">Director classes</a>
@@ -101,6 +101,12 @@
 <li><a href="#Python_nn71">%feature("docstring")</a>
 </ul>
 <li><a href="#Python_nn72">Python Packages</a>
+<li><a href="#Python_python3support">Python 3 Support</a>
+<ul>
+<li><a href="#Python_nn74">Function annotation</a>
+<li><a href="#Python_nn75">Buffer interface</a>
+<li><a href="#Python_nn76">Abstract base classes</a>
+</ul>
 </ul>
 </div>
 <!-- INDEX -->
@@ -113,9 +119,9 @@
 
 <p>
 This chapter describes SWIG's support of Python.  SWIG is compatible
-with most recent Python versions including Python 2.2 as well as older
-versions dating back to Python 1.5.2.  For the best results, consider using Python
-2.0 or newer.
+with most recent Python versions including Python 3.0 and Python 2.6,
+as well as older versions dating back to Python 2.0.  For the best results,
+consider using Python 2.3 or newer.
 </p>
 
 <p>
@@ -2544,7 +2550,7 @@ class itself.  In Python-2.1 and earlier, they have to be accessed as a global
 function or through an instance (see the earlier section).
 </p>
 
-<H2><a name="directors"></a>30.5 Cross language polymorphism</H2>
+<H2><a name="Python_directors"></a>30.5 Cross language polymorphism</H2>
 
 
 <p>
@@ -4929,7 +4935,7 @@ with more than one line.
 <p>
 Using the <tt>package</tt> option of the <tt>%module</tt> directive
 allows you to specify what Python package that the module will be
-living in when installed. 
+living in when installed.
 </p>
 
 <div class="code">
@@ -4950,6 +4956,241 @@ and also in base class declarations, etc. if the package name is
 different than its own.
 </p>
 
+<H2><a name="Python_python3support"></a>30.12 Python 3 Support</H2>
+
+
+<p>
+SWIG is able to support Python 3.0. The wrapper code generated by
+SWIG can be compiled with both Python 2.x or 3.0. Further more, by
+passing the <tt>-py3</tt> command line option to SWIG, wrapper code
+with some Python 3 specific features can be generated (see below
+subsections for details of these features). The <tt>-py3</tt> option also
+disables some incompatible features for Python 3, such as
+<tt>-classic</tt>.
+
+<p>
+There is a list of known-to-be-broken features in Python 3:
+</p>
+<ul>
+  <li>No more support for FILE* typemaps, because PyFile_AsFile has been dropped
+  in Python 3.</li>
+  <li>The <tt>-apply</tt> command line option is removed and generating
+  code using apply() is no longer supported.</li>
+</ul>
+
+<p>
+The following are Python 3.0 new features that are currently supported by
+SWIG.
+</p>
+
+<H3><a name="Python_nn74"></a>30.12.1 Function annotation</H3>
+
+
+<p>
+The <tt>-py3</tt> option will enable function annotation support. When used
+SWIG is able to generate proxy method definitions like
+this:
+</p>
+
+<div class="code"><pre>
+  def foo(self, bar : "int" = 0) -&gt; "void" : ...
+</pre></div>
+
+<p>
+For details of usage of function annotation, see PEP 3107.
+</p>
+
+<H3><a name="Python_nn75"></a>30.12.2 Buffer interface</H3>
+
+
+<p>
+Buffer protocols were revised in Python 3. SWIG also gains a series of
+new typemaps to support buffer interfaces. These typemap macros are
+defined in <tt>pybuffer.i</tt>, which must be included in order to use them.
+By using these typemaps, your wrapped function will be able to
+accept any Python object that exposes a suitable buffer interface.
+</p>
+
+<p>
+For example, the <tt>get_path()</tt> function puts the path string
+into the memory pointed to by its argument:
+</p>
+
+<div class="code"><pre>
+void get_path(char *s);
+</pre></div>
+
+<p>
+Then you can write a typemap like this: (the following example is
+applied to both Python 3.0 and 2.6, since the <tt>bytearray</tt> type
+is backported to 2.6.
+</p>
+
+
+<div class="code"><pre>
+%include &lt;pybuffer.i&gt;
+%pybuffer_mutable_string(char *str);
+void get_path(char *s);
+</pre></div>
+
+<p>
+And then on the Python side the wrapped <tt>get_path</tt> could be used in this
+way:
+</p>
+
+<div class="targetlang"><pre>
+&gt;&gt;&gt; p = bytearray(10)
+&gt;&gt;&gt; get_path(p)
+&gt;&gt;&gt; print(p)
+bytearray(b'/Foo/Bar/\x00')
+</pre></div>
+
+<p>
+The macros defined in <tt>pybuffer.i</tt> are similar to those in
+<tt>cstring.i</tt>:
+</p>
+
+<p>
+<b>%pybuffer_mutable_binary(parm, size_parm)</b>
+</p>
+
+<div class="indent">
+
+<p>
+The macro can be used to generate a typemap which maps a buffer of an
+object to a pointer provided by <tt>parm</tt> and a size argument
+provided by <tt>size_parm</tt>. For example:
+</p>
+
+<div class="code"><pre>
+%pybuffer_mutable_binary(char *str, size_t size);
+...
+int snprintf(char *str, size_t size, const char *format, ...);
+</pre></div>
+
+<p>
+In Python:
+</p>
+
+<div class="targetlang"><pre>
+&gt;&gt;&gt; buf = bytearray(6)
+&gt;&gt;&gt; snprintf(buf, "Hello world!")
+&gt;&gt;&gt; print(buf)
+bytearray(b'Hello\x00')
+&gt;&gt;&gt; 
+</pre></div>
+
+</div>
+
+<p>
+<b>%pybuffer_mutable_string(parm)</b>
+</p>
+
+<div class="indent">
+
+<p>
+This typemap macro requires the buffer to be a zero terminated string,
+and maps the pointer of the buffer to <tt>parm</tt>. For example:
+</p>
+
+<div class="code"><pre>
+%pybuffer_mutable_string(char *str);
+...
+size_t make_upper(char *str);
+</pre></div>
+
+<p>
+In Python:
+</p>
+
+<div class="targetlang"><pre>
+&gt;&gt;&gt; buf = bytearray(b'foo\x00')
+&gt;&gt;&gt; make_upper(buf)
+&gt;&gt;&gt; print(buf)
+bytearray(b'FOO\x00')
+&gt;&gt;&gt;
+</pre></div>
+
+<p>
+Both <tt>%pybuffer_mutable_binary</tt> and <tt>%pybuffer_mutable_string</tt>
+require the provided buffer to be mutable, eg. they can accept a 
+<tt>bytearray</tt> type but can't accept an immutable <tt>byte</tt>
+type.
+</p>
+
+</div>
+
+<p>
+<b>%pybuffer_binary(parm, size_parm)</b>
+</p>
+
+<div class="indent">
+
+<p>
+This macro maps an object's buffer to a pointer <tt>parm</tt> and a
+size <tt>size_parm</tt>. It is similar to
+<tt>%pybuffer_mutable_binary</tt>, except the
+<tt>%pybuffer_binary</tt> an accept both mutable and immutable
+buffers. As a result, the wrapped function should not modify the buffer.
+</p>
+
+</div>
+
+<p>
+<b>%pybuffer_string(parm)</b>
+</p>
+
+<div class="indent">
+
+<p>
+This macro maps an object's buffer as a string pointer <tt>parm</tt>.
+It is similar to <tt>%pybuffer_mutable_string</tt> but the buffer
+could be both mutable and immutable. And your function should not
+modify the buffer.
+</p>
+
+</div>
+
+
+<H3><a name="Python_nn76"></a>30.12.3 Abstract base classes</H3>
+
+
+<p>
+By including <tt>pyabc.i</tt> and using the <tt>-py3</tt> command
+line option when calling SWIG, the proxy classes of the STL containers
+will automatically gain an appropriate abstract base class. For
+example, the following SWIG interface:
+</p>
+
+<div class="code"><pre>
+%include &lt;pyabc.i&gt;
+%include &lt;std_map.i&gt;
+%include &lt;std_list.i&gt;
+
+namespace std {
+  %template(Mapii) map&lt;int, int&gt;;
+  %template(IntList) list&lt;int&gt;;
+}
+</pre></div>
+
+<p>
+will generate a Python proxy class <tt>Mapii</tt> inheriting from
+<tt>collections.MutableMap</tt> and a proxy class <tt>IntList</tt>
+inheriting from <tt>collections.MutableSequence</tt>.
+</p>
+
+<p>
+<tt>pyabc.i</tt> also provides a macro <tt>%pythonabc</tt> that could be
+used to define an abstract base class for your own C++ class:
+</p>
+
+<div class="code"><pre>
+%pythonabc(MySet, collections.MutableSet);
+</pre></div>
+
+<p>
+For details of abstract base class, please see PEP 3119.
+</p>
 
 </body>
 </html>
diff --git a/Doc/Manual/SWIG.html b/Doc/Manual/SWIG.html
index c22d81c07..c1ffcff60 100644
--- a/Doc/Manual/SWIG.html
+++ b/Doc/Manual/SWIG.html
@@ -53,7 +53,7 @@
 <li><a href="#SWIG_nn33">Character strings and structures</a>
 <li><a href="#SWIG_nn34">Array members</a>
 <li><a href="#SWIG_structure_data_members">Structure data members</a>
-<li><a href="#SWIG_nn36">C constructors and destructors </a>
+<li><a href="#SWIG_nn36">C constructors and destructors</a>
 <li><a href="#SWIG_adding_member_functions">Adding member functions to C structures</a>
 <li><a href="#SWIG_nested_structs">Nested structures</a>
 <li><a href="#SWIG_nn39">Other things to note about structure wrapping</a>
@@ -224,7 +224,7 @@ The C/C++ output file created by SWIG often
 contains everything that is needed to construct a extension module
 for the target scripting language. SWIG is not a stub compiler nor is it
 usually necessary to edit the output file (and if you look at the output,
-you probably won't want to).      To build the final extension module, the
+you probably won't want to). To build the final extension module, the
 SWIG output file is compiled and linked with the rest of your C/C++
 program to create a shared library. 
 </p>
@@ -232,7 +232,7 @@ program to create a shared library.
 <p>
 Many target languages will also generate proxy class files in the
 target language. The default output directory for these language 
-specific files is the same directory as the generated C/C++ file. This can
+specific files is the same directory as the generated C/C++ file. This
 can be modified using the <tt>-outdir</tt> option. For example:
 </p>
 
@@ -2219,13 +2219,13 @@ void Foo_w_set(FOO *f, WORD value) {
 
 
 <p>
-<b>Compatibility Note: </b>  SWIG-1.3.11 and earlier releases transformed all non-primitive member datatypes
-to pointers.  Starting in SWIG-1.3.12,  this transformation <em>only</em> occurs if a datatype is known to be a structure,
-class, or union.    This is unlikely to break existing code.  However, if you need to tell SWIG that an undeclared
+<b>Compatibility Note:</b>  SWIG-1.3.11 and earlier releases transformed all non-primitive member datatypes
+to pointers.  Starting in SWIG-1.3.12, this transformation <em>only</em> occurs if a datatype is known to be a structure,
+class, or union.  This is unlikely to break existing code.  However, if you need to tell SWIG that an undeclared
 datatype is really a struct, simply use a forward struct declaration such as <tt>"struct Foo;"</tt>.
 </p>
 
-<H3><a name="SWIG_nn36"></a>5.5.5 C constructors and destructors </H3>
+<H3><a name="SWIG_nn36"></a>5.5.5 C constructors and destructors</H3>
 
 
 <p>
@@ -2282,7 +2282,7 @@ struct Bar {             // Default constructor generated.
 Since ignoring the implicit or default destructors most of the times
 produce memory leaks, SWIG will always try to generate them. If
 needed, however, you can selectively disable the generation of the
-default/implicit destructor by using <tt>%nodefaultdtor </tt>
+default/implicit destructor by using <tt>%nodefaultdtor</tt>
 </p>
 
 <div class="code">
diff --git a/Doc/Manual/SWIGPlus.html b/Doc/Manual/SWIGPlus.html
index faf0b254c..ef7487ff8 100644
--- a/Doc/Manual/SWIGPlus.html
+++ b/Doc/Manual/SWIGPlus.html
@@ -1153,8 +1153,9 @@ public:
 
 
 <p>
-This is great for reducing the size of the wrappers, but the caveat is it does not work for the strongly typed languages
-which don't have optional arguments in the language, such as C# and Java.
+This is great for reducing the size of the wrappers, but the caveat is it does not work for the statically typed languages,
+such as C# and Java,
+which don't have optional arguments in the language, 
 Another restriction of this feature is that it cannot handle default arguments that are not public.
 The following example illustrates this:
 </p>
diff --git a/Doc/Manual/Sections.html b/Doc/Manual/Sections.html
index b7b4798e7..5406f44ea 100644
--- a/Doc/Manual/Sections.html
+++ b/Doc/Manual/Sections.html
@@ -6,7 +6,7 @@
 <body bgcolor="#ffffff">
 <H1><a name="Sections"></a>SWIG-1.3 Development Documentation</H1>
 
-Last update : SWIG-1.3.36 (in progress)
+Last update : SWIG-1.3.37 (in progress)
 
 <H2>Sections</H2>
 
diff --git a/Doc/Manual/Typemaps.html b/Doc/Manual/Typemaps.html
index e07f9f87e..8f3035dc8 100644
--- a/Doc/Manual/Typemaps.html
+++ b/Doc/Manual/Typemaps.html
@@ -65,7 +65,7 @@
 </ul>
 <li><a href="#Typemaps_nn43">Typemaps for multiple languages</a>
 <li><a href="#Typemaps_optimal">Optimal code generation when returning by value</a>
-<li><a href="#Typemaps_nn42">Multi-argument typemaps</a>
+<li><a href="#Typemaps_multi_argument_typemaps">Multi-argument typemaps</a>
 <li><a href="#runtime_type_checker">The run-time type checker</a>
 <ul>
 <li><a href="#Typemaps_nn45">Implementation</a>
@@ -702,7 +702,7 @@ variables (parms).   The purpose of these variables will be explained shortly.
 </p>
 
 <p><em>code</em> specifies the code used in the typemap.
-Usually this is C/C++ code, but in the strongly typed target languages, such as Java and C#, this can contain target language code for certain typemaps.
+Usually this is C/C++ code, but in the statically typed target languages, such as Java and C#, this can contain target language code for certain typemaps.
 It can take any one of the following forms:
 </p>
 
@@ -1933,7 +1933,7 @@ to implement customized conversions.
 
 <p>
 In addition, the "in" typemap allows the number of converted arguments to be
-specified.  For example:
+specified.  The <tt>numinputs</tt> attributes facilitates this. For example:
 </p>
 
 <div class="code">
@@ -1946,7 +1946,12 @@ specified.  For example:
 </div>
 
 <p>
-At this time, only zero or one arguments may be converted.
+At this time, only zero or one arguments may be converted. 
+When <tt>numinputs</tt> is set to 0, the argument is effectively ignored and cannot be supplied from the target language. 
+The argument is still required when making the C/C++ call and the above typemap
+shows the value used is instead obtained from a locally declared variable called <tt>temp</tt>.
+Usually <tt>numinputs</tt> is not specified, whereupon the default value is 1, that is, there is a one to one mapping of the number of arguments when used from the target language to the C/C++ call. 
+<a href="#Typemaps_multi_argument_typemaps">Multi-argument typemaps</a> provide a similar concept where the number of arguments mapped from the target language to C/C++ can be changed for more tha multiple adjacent C/C++ arguments.
 </p>
 
 <p>
@@ -2811,7 +2816,7 @@ optimal attribute usage in the out typemap at example.i:7.
 However, it doesn't always get it right, for example when <tt>$1</tt> is within some commented out code.
 </p>
 
-<H2><a name="Typemaps_nn42"></a>10.9 Multi-argument typemaps</H2>
+<H2><a name="Typemaps_multi_argument_typemaps"></a>10.9 Multi-argument typemaps</H2>
 
 
 <p>
diff --git a/Doc/Manual/Warnings.html b/Doc/Manual/Warnings.html
index 39d5d3f01..0b3cb37e9 100644
--- a/Doc/Manual/Warnings.html
+++ b/Doc/Manual/Warnings.html
@@ -373,7 +373,7 @@ example.i(4): Syntax error in input.
 <li>117. Deprecated <tt>%new</tt> directive.
 <li>118. Deprecated <tt>%typemap(except)</tt>.
 <li>119. Deprecated <tt>%typemap(ignore)</tt>.
-<li>120. Deprecated command line option (-c).
+<li>120. Deprecated command line option (-runtime, -noruntime).
 <li>121. Deprecated <tt>%name</tt> directive.
 </ul>
 
diff --git a/Examples/GIFPlot/Python/full/Makefile b/Examples/GIFPlot/Python/full/Makefile
index ae927b72b..83a7c864b 100644
--- a/Examples/GIFPlot/Python/full/Makefile
+++ b/Examples/GIFPlot/Python/full/Makefile
@@ -1,5 +1,5 @@
 TOP        = ../../..
-SWIG       = $(TOP)/../swig
+SWIG       = $(TOP)/../preinst-swig
 SWIGOPT    = -I../../Include 
 SRCS       =
 TARGET     = gifplot
@@ -23,3 +23,4 @@ clean::
 	rm -f *.gif
 
 check: all
+	$(MAKE) -f $(TOP)/Makefile python_run
diff --git a/Examples/GIFPlot/Python/shadow/Makefile b/Examples/GIFPlot/Python/shadow/Makefile
index 1f5014895..73fca9673 100644
--- a/Examples/GIFPlot/Python/shadow/Makefile
+++ b/Examples/GIFPlot/Python/shadow/Makefile
@@ -1,5 +1,5 @@
 TOP        = ../../..
-SWIG       = $(TOP)/../swig
+SWIG       = $(TOP)/../preinst-swig
 SWIGOPT    = -I../../Interface
 SRCS       =
 TARGET     = gifplot
@@ -23,3 +23,4 @@ clean::
 	rm -f *.gif
 
 check: all
+	$(MAKE) -f $(TOP)/Makefile python_run
diff --git a/Examples/GIFPlot/Python/simple/Makefile b/Examples/GIFPlot/Python/simple/Makefile
index 5eb0344e8..9fc9a6c72 100644
--- a/Examples/GIFPlot/Python/simple/Makefile
+++ b/Examples/GIFPlot/Python/simple/Makefile
@@ -1,5 +1,5 @@
 TOP        = ../../..
-SWIG       = $(TOP)/../swig
+SWIG       = $(TOP)/../preinst-swig
 SWIGOPT    =
 SRCS       =
 TARGET     = simple
@@ -23,3 +23,4 @@ clean::
 	rm -f *.gif
 
 check: all
+	$(MAKE) -f $(TOP)/Makefile python_run
diff --git a/Examples/Makefile.in b/Examples/Makefile.in
index 0bf9f6767..f85075906 100644
--- a/Examples/Makefile.in
+++ b/Examples/Makefile.in
@@ -40,8 +40,9 @@ LIBCRYPT   = @LIBCRYPT@
 SYSLIBS    = $(LIBM) $(LIBC) $(LIBCRYPT)
 LIBPREFIX  =
 
-# RUNTOOL is for use as with runtime tools, eg set it to valgrind
+# RUNTOOL is for use with runtime tools, eg set it to valgrind
 RUNTOOL    =
+# COMPILETOOL is a way to run the compiler under another tool, or more commonly just to stop the compiler executing
 COMPILETOOL=
 
 # X11 options
@@ -94,9 +95,9 @@ TK_OPTS     = -ltk -ltcl @LIBS@
 
 # Extra Tcl specific dynamic linking options
 TCL_DLNK   = @TCLDYNAMICLINKING@
-TCL_LDSHARED = @TCL_LDSHARED@
-TCL_CXXSHARED = @TCL_CXXSHARED@
 TCL_SO     = @TCL_SO@
+TCLLDSHARED = @TCLLDSHARED@
+TCLCXXSHARED = @TCLCXXSHARED@
 
 # -----------------------------------------------------------
 # Build a new version of the tclsh shell
@@ -135,7 +136,7 @@ wish_cpp: $(SRCS)
 tcl:  $(SRCS)
 	$(SWIG) -tcl8 $(SWIGOPT) $(TCL_SWIGOPTS) $(INTERFACE)
 	$(CC) -c $(CCSHARED) $(CFLAGS) $(SRCS) $(ISRCS) $(INCLUDES) $(TCL_INCLUDE)
-	$(TCL_LDSHARED) $(CFLAGS) $(OBJS) $(IOBJS) $(TCL_DLNK) $(LIBS) -o $(LIBPREFIX)$(TARGET)$(TCL_SO)
+	$(TCLLDSHARED) $(CFLAGS) $(OBJS) $(IOBJS) $(TCL_DLNK) $(LIBS) -o $(LIBPREFIX)$(TARGET)$(TCL_SO)
 
 # -----------------------------------------------------------
 # Build a Tcl7.5 dynamic loadable module for C++
@@ -144,7 +145,7 @@ tcl:  $(SRCS)
 tcl_cpp: $(SRCS)
 	$(SWIG) -tcl8 -c++ $(SWIGOPT) $(TCL_SWIGOPTS) $(INTERFACE)
 	$(CXX) -c $(CCSHARED) $(CFLAGS) $(SRCS) $(CXXSRCS) $(ICXXSRCS) $(INCLUDES) $(TCL_INCLUDE)
-	$(TCL_CXXSHARED) $(CFLAGS) $(OBJS) $(IOBJS) $(TCL_DLNK) $(LIBS) $(CPP_DLLIBS) -o $(LIBPREFIX)$(TARGET)$(TCL_SO)
+	$(TCLCXXSHARED) $(CFLAGS) $(OBJS) $(IOBJS) $(TCL_DLNK) $(LIBS) $(CPP_DLLIBS) -o $(LIBPREFIX)$(TARGET)$(TCL_SO)
 
 # -----------------------------------------------------------------
 # Cleaning the Tcl examples
@@ -222,19 +223,39 @@ perl5_clean:
 ##################################################################
 
 # Make sure these locate your Python installation
-PYTHON_INCLUDE= $(DEFS) @PYINCLUDE@
-PYTHON_LIB    = @PYLIB@
+ifeq (,$(PY3))
+  PYTHON_INCLUDE= $(DEFS) @PYINCLUDE@
+  PYTHON_LIB    = @PYLIB@
+  PYTHON        = @PYTHON@
+else
+  PYTHON_INCLUDE= $(DEFS) @PY3INCLUDE@
+  PYTHON_LIB    = @PY3LIB@
+  PYTHON        = @PYTHON3@
+endif
 
-# Extra Python specific dynamic linking options
-PYTHON_DLNK   = @PYTHONDYNAMICLINKING@
+# Extra Python specific linking options
+ifeq (,$(PY3))
+  PYTHON_DLNK   = @PYTHONDYNAMICLINKING@
+  PYTHON_LINK   = @PYLINK@
+else
+  PYTHON_DLNK   = @PYTHON3DYNAMICLINKING@
+  PYTHON_LINK   = @PY3LINK@
+endif
 PYTHON_SO     = @PYTHON_SO@
 
+# SWIG option for Python
+ifeq (,$(PY3))
+  SWIGPYTHON = $(SWIG) -python
+else
+  SWIGPYTHON = $(SWIG) -python -py3
+endif
+
 # ----------------------------------------------------------------
 # Build a C dynamically loadable module
 # ----------------------------------------------------------------
 
 python: $(SRCS)
-	$(SWIG) -python $(SWIGOPT) $(INTERFACE)
+	$(SWIGPYTHON) $(SWIGOPT) $(INTERFACE)
 	$(CC) -c $(CCSHARED) $(CFLAGS) $(ISRCS) $(SRCS) $(INCLUDES) $(PYTHON_INCLUDE)
 	$(LDSHARED) $(CFLAGS) $(OBJS) $(IOBJS) $(PYTHON_DLNK) $(LIBS) -o $(LIBPREFIX)_$(TARGET)$(PYTHON_SO)
 
@@ -243,7 +264,7 @@ python: $(SRCS)
 # -----------------------------------------------------------------
 
 python_cpp: $(SRCS)
-	$(SWIG) -c++ -python $(SWIGOPT) $(INTERFACE)
+	$(SWIGPYTHON) -c++ $(SWIGOPT) $(INTERFACE)
 	$(CXX) -c $(CCSHARED) $(CFLAGS) $(ICXXSRCS) $(SRCS) $(CXXSRCS) $(INCLUDES) $(PYTHON_INCLUDE)
 	$(CXXSHARED) $(CFLAGS) $(OBJS) $(IOBJS) $(PYTHON_DLNK) $(LIBS) $(CPP_DLLIBS) -o $(LIBPREFIX)_$(TARGET)$(PYTHON_SO)
 
@@ -256,18 +277,37 @@ python_cpp: $(SRCS)
 
 #TKINTER = -L/usr/X11R6.3/lib -L/usr/local/compat/lib -ltk4.0 -ltcl7.4 -lX11
 TKINTER =
-PYTHON_LIBOPTS = @PYLINK@ @LIBS@ $(TKINTER) $(SYSLIBS)
+PYTHON_LIBOPTS = $(PYTHON_LINK) @LIBS@ $(TKINTER) $(SYSLIBS)
 
 python_static: $(SRCS)
-	$(SWIG) -python -lembed.i $(SWIGOPT) $(INTERFACE)
+	$(SWIGPYTHON) -lembed.i $(SWIGOPT) $(INTERFACE)
 	$(CC) $(CFLAGS) @LINKFORSHARED@ $(ISRCS) $(SRCS) $(INCLUDES) \
 	$(PYTHON_INCLUDE) $(LIBS) -L$(PYTHON_LIB) $(PYTHON_LIBOPTS) -o $(TARGET)
 
 python_static_cpp: $(SRCS)
-	$(SWIG) -c++ -python -lembed.i $(SWIGOPT) $(INTERFACE)
+	$(SWIGPYTHON) -c++ -lembed.i $(SWIGOPT) $(INTERFACE)
 	$(CXX) $(CFLAGS) $(ICXXSRCS) $(SRCS) $(CXXSRCS) $(INCLUDES) \
 	$(PYTHON_INCLUDE) $(LIBS)  -L$(PYTHON_LIB) $(PYTHON_LIBOPTS) -o $(TARGET)
 
+# ----------------------------------------------------------------- 
+# Running a Python example
+# ----------------------------------------------------------------- 
+
+ifeq (,$(PY3))
+  SCRIPT = runme.py
+else
+  SCRIPT = runme3.py
+endif
+
+PY2TO3 = 2to3 `2to3 -l | grep -v -E "Available|import$$" | awk '{print "-f "$$0}'`
+
+python_run: $(SCRIPT)
+	env LD_LIBRARY_PATH=.:$$LD_LIBRARY_PATH PYTHONPATH=$(srcdir):$$PYTHONPATH $(PYTHON) $(SCRIPT) >/dev/null
+
+runme3.py: runme.py
+	cp $< $@
+	$(PY2TO3) -w $@ >/dev/null 2>&1 
+
 # -----------------------------------------------------------------
 # Cleaning the python examples
 # -----------------------------------------------------------------
@@ -277,6 +317,7 @@ python_clean:
 	rm -f core @EXTRA_CLEAN@
 	rm -f *.@OBJEXT@ *@SO@ *@PYTHON_SO@
 
+
 ##################################################################
 #####                       OCTAVE                          ######
 ##################################################################
@@ -880,11 +921,11 @@ chicken_static_cpp: $(CXXSRCS) $(CHICKSRCS)
 
 chicken:
 	$(SWIG) -chicken $(SWIGOPT) $(INCLUDE) $(INTERFACE)
-	$(CHICKEN_CSC) -s `echo $(INCLUDES) | sed 's/-I/-C -I/g'` $(CHICKEN_GENERATED_SCHEME) $(SRCS) $(ISRCS) -o $(TARGET)$(SO)
+	$(COMPILETOOL) $(CHICKEN_CSC) -s `echo $(INCLUDES) | sed 's/-I/-C -I/g'` $(CHICKEN_GENERATED_SCHEME) $(SRCS) $(ISRCS) -o $(TARGET)$(SO)
 
 chicken_cpp:
 	$(SWIG) -c++ -chicken $(SWIGOPT) $(INCLUDE) $(INTERFACE)
-	$(CHICKEN_CSC) -s `echo $(INCLUDES) | sed 's/-I/-C -I/g'` $(CHICKEN_GENERATED_SCHEME) $(SRCS) $(ICXXSRCS) $(CXXSRCS) -o $(TARGET)$(SO)
+	$(COMPILETOOL) $(CHICKEN_CSC) -s `echo $(INCLUDES) | sed 's/-I/-C -I/g'` $(CHICKEN_GENERATED_SCHEME) $(SRCS) $(ICXXSRCS) $(CXXSRCS) -o $(TARGET)$(SO)
 
 chicken_externalhdr:
 	$(SWIG) -chicken -external-runtime $(TARGET)
@@ -1078,11 +1119,11 @@ RRSRC = $(INTERFACE:.i=.R)
 
 r: $(SRCS)
 	$(SWIG) -r $(SWIGOPT) $(INTERFACE)
-	+( PKG_LIBS="$(SRCS)" PKG_CPPFLAGS="$(INCLUDES)" $(R) CMD SHLIB -o $(LIBPREFIX)$(TARGET)$(SO) $(ISRCS) )
+	+( PKG_LIBS="$(SRCS)" PKG_CPPFLAGS="$(INCLUDES)" $(COMPILETOOL) $(R) CMD SHLIB -o $(LIBPREFIX)$(TARGET)$(SO) $(ISRCS) )
 
 r_cpp: $(CXXSRCS)
 	$(SWIG) -c++ -r $(SWIGOPT) -o $(RCXXSRCS) $(INTERFACE)
-	+( PKG_LIBS="$(CXXSRCS)" PKG_CPPFLAGS="$(INCLUDES)" $(R) CMD SHLIB -o $(LIBPREFIX)$(TARGET)$(SO) $(RCXXSRCS) )
+	+( PKG_LIBS="$(CXXSRCS)" PKG_CPPFLAGS="$(INCLUDES)" $(COMPILETOOL) $(R) CMD SHLIB -o $(LIBPREFIX)$(TARGET)$(SO) $(RCXXSRCS) )
 
 r_clean:
 	rm -f *_wrap* *~ .~*
diff --git a/Examples/guile/multimap/example.i b/Examples/guile/multimap/example.i
index a1cc0bb67..7337d1e9e 100644
--- a/Examples/guile/multimap/example.i
+++ b/Examples/guile/multimap/example.i
@@ -20,7 +20,7 @@ extern int    gcd(int x, int y);
   SCM *v;
   if (!(SCM_NIMP($input) && SCM_VECTORP($input))) {
     SWIG_exception(SWIG_ValueError, "Expecting a vector");
-    return;
+    return 0;
   }
   $1 = SCM_LENGTH($input);
   if ($1 == 0) {
@@ -32,7 +32,7 @@ extern int    gcd(int x, int y);
     if (!(SCM_NIMP(v[i]) && SCM_STRINGP(v[i]))) {
       free($2);	
       SWIG_exception(SWIG_ValueError, "Vector items must be strings");
-      return;
+      return 0;
     }
     $2[i] = SCM_CHARS(v[i]);
   }
diff --git a/Examples/guile/multivalue/example.i b/Examples/guile/multivalue/example.i
index abc2a6fbc..135389487 100644
--- a/Examples/guile/multivalue/example.i
+++ b/Examples/guile/multivalue/example.i
@@ -2,6 +2,12 @@
 
 %module example;
 
+%{
+void divide_l(int a, int b, int *quotient_p, int *remainder_p);
+void divide_v(int a, int b, int *quotient_p, int *remainder_p);
+void divide_mv(int a, int b, int *quotient_p, int *remainder_p);
+%}
+
 /* Multiple values as lists. By default, if more than one value is to
 be returned, a list of the values is created and returned; to switch
 back to this behavior, use: */
diff --git a/Examples/lua/arrays/example.c b/Examples/lua/arrays/example.c
index 40ed12c79..56c7b19d9 100644
--- a/Examples/lua/arrays/example.c
+++ b/Examples/lua/arrays/example.c
@@ -16,7 +16,7 @@ void sort_int(int* arr, int len)
 // ditto doubles
 int compare_double(const void * a, const void * b)
 {
-  return ( *(double*)a - *(double*)b );
+  return (int)( *(double*)a - *(double*)b );
 }
 
 void sort_double(double* arr, int len)
diff --git a/Examples/lua/embed2/embed2.c b/Examples/lua/embed2/embed2.c
index 07b7a44d2..dac527eb4 100644
--- a/Examples/lua/embed2/embed2.c
+++ b/Examples/lua/embed2/embed2.c
@@ -11,6 +11,17 @@ We will be using the luaL_dostring()/lua_dostring() function to call into lua
  
 */
 
+/* Deal with Microsoft's attempt at deprecating C standard runtime functions */
+#if !defined(SWIG_NO_CRT_SECURE_NO_DEPRECATE) && defined(_MSC_VER) && !defined(_CRT_SECURE_NO_DEPRECATE)
+# define _CRT_SECURE_NO_DEPRECATE
+#endif
+
+/* Deal with Microsoft's attempt at deprecating methods in the standard C++ library */
+#if !defined(SWIG_NO_SCL_SECURE_NO_DEPRECATE) && defined(_MSC_VER) && !defined(_SCL_SECURE_NO_DEPRECATE)
+# define _SCL_SECURE_NO_DEPRECATE
+#endif
+
+
 #include <stdlib.h>
 #include <stdio.h>
 
@@ -108,7 +119,7 @@ int call_va (lua_State *L,const char *func, const char *sig, ...) {
 endwhile:
 
   /* do the call */
-  nres = strlen(sig);  /* number of expected results */
+  nres = (int)strlen(sig);  /* number of expected results */
   if (lua_pcall(L, narg, nres, 0) != 0)  /* do the call */
   {
     printf("error running function `%s': %s\n",func, lua_tostring(L, -1));
diff --git a/Examples/lua/embed3/embed3.cpp b/Examples/lua/embed3/embed3.cpp
index e42401cda..c2424f9af 100644
--- a/Examples/lua/embed3/embed3.cpp
+++ b/Examples/lua/embed3/embed3.cpp
@@ -5,6 +5,17 @@ passing C++ objects to this function.
  
 */
 
+/* Deal with Microsoft's attempt at deprecating C standard runtime functions */
+#if !defined(SWIG_NO_CRT_SECURE_NO_DEPRECATE) && defined(_MSC_VER) && !defined(_CRT_SECURE_NO_DEPRECATE)
+# define _CRT_SECURE_NO_DEPRECATE
+#endif
+
+/* Deal with Microsoft's attempt at deprecating methods in the standard C++ library */
+#if !defined(SWIG_NO_SCL_SECURE_NO_DEPRECATE) && defined(_MSC_VER) && !defined(_SCL_SECURE_NO_DEPRECATE)
+# define _SCL_SECURE_NO_DEPRECATE
+#endif
+
+
 #include <stdlib.h>
 #include <stdio.h>
 #include <string.h>
@@ -70,9 +81,6 @@ int call_onEvent(lua_State *L, Event e) {
 
 
 int main(int argc, char* argv[]) {
-  int ok;
-  int res;
-  char str[80];
   printf("[C++] Welcome to the simple embedded Lua example v3\n");
   printf("[C++] We are in C++\n");
   printf("[C++] opening a Lua state & loading the libraries\n");
diff --git a/Examples/lua/owner/example.cxx b/Examples/lua/owner/example.cxx
index 6e4091327..d6caeef15 100644
--- a/Examples/lua/owner/example.cxx
+++ b/Examples/lua/owner/example.cxx
@@ -54,14 +54,14 @@ void ShapeOwner::add(Shape* ptr) // this method takes ownership of the object
 
 Shape* ShapeOwner::get(int idx) // this pointer is still owned by the class (assessor)
 {
-    if (idx<0 || idx>=shapes.size())
+    if (idx < 0 || idx >= static_cast<int>(shapes.size()))
         return NULL;
     return shapes[idx];
 }
 
 Shape* ShapeOwner::remove(int idx) // this method returns memory which must be deleted
 {
-    if (idx<0 || idx>=shapes.size())
+    if (idx < 0 || idx >= static_cast<int>(shapes.size()))
         return NULL;
     Shape* ptr=shapes[idx];
     shapes.erase(shapes.begin()+idx);
diff --git a/Examples/perl5/import/base.h b/Examples/perl5/import/base.h
index be3cdef7d..5a266f68c 100644
--- a/Examples/perl5/import/base.h
+++ b/Examples/perl5/import/base.h
@@ -3,7 +3,7 @@
 class Base {
  public:
      Base() { };
-    ~Base() { };
+     virtual ~Base() { };
      virtual void A() {
          printf("I'm Base::A\n");
      }
diff --git a/Examples/perl5/multiple_inheritance/example.h b/Examples/perl5/multiple_inheritance/example.h
index ce7dfe6a7..a8f544898 100644
--- a/Examples/perl5/multiple_inheritance/example.h
+++ b/Examples/perl5/multiple_inheritance/example.h
@@ -7,26 +7,25 @@ using namespace std;
 class Bar
 {
  public:
-  virtual void bar ()
-    {
-      cout << "bar" << endl;
-    }
+   virtual void bar () {
+     cout << "bar" << endl;
+   }
+   virtual ~Bar() {}
 };
 
 class Foo
 {
  public:
-  virtual void foo ()
-    {
-      cout << "foo" << endl;
-    }
+   virtual void foo () {
+     cout << "foo" << endl;
+   }
+   virtual ~Foo() {}
 };
 
 class Foo_Bar : public Foo, public Bar
 {
  public:
-  virtual void fooBar ()
-    {
-      cout << "foobar" << endl;
-    }
+   virtual void fooBar () {
+     cout << "foobar" << endl;
+   }
 };
diff --git a/Examples/php4/reference/BUILD-proxy.sh b/Examples/php4/reference/BUILD-proxy.sh
deleted file mode 100755
index b1c8c71a4..000000000
--- a/Examples/php4/reference/BUILD-proxy.sh
+++ /dev/null
@@ -1,5 +0,0 @@
-#! /bin/sh -e
-
-${SWIG:=swig}  -php4 -make -c++ -withcxx example.cxx example.i
-make
-php -d extension_dir=. runme-proxy.php4
diff --git a/Examples/python/callback/Makefile b/Examples/python/callback/Makefile
index ad36d7d7e..a29276e58 100644
--- a/Examples/python/callback/Makefile
+++ b/Examples/python/callback/Makefile
@@ -19,3 +19,4 @@ clean::
 	rm -f $(TARGET).py
 
 check: all
+	$(MAKE) -f $(TOP)/Makefile python_run
diff --git a/Examples/python/class/Makefile b/Examples/python/class/Makefile
index f331b8203..74625b992 100644
--- a/Examples/python/class/Makefile
+++ b/Examples/python/class/Makefile
@@ -18,3 +18,4 @@ clean::
 	rm -f $(TARGET).py
 
 check: all
+	$(MAKE) -f $(TOP)/Makefile python_run
diff --git a/Examples/python/constants/Makefile b/Examples/python/constants/Makefile
index 01d0f943a..1420b4e0b 100644
--- a/Examples/python/constants/Makefile
+++ b/Examples/python/constants/Makefile
@@ -17,3 +17,4 @@ clean::
 	rm -f $(TARGET).py
 
 check: all
+	$(MAKE) -f $(TOP)/Makefile python_run
diff --git a/Examples/python/contract/Makefile b/Examples/python/contract/Makefile
index c7b476995..77fe94b1a 100644
--- a/Examples/python/contract/Makefile
+++ b/Examples/python/contract/Makefile
@@ -17,3 +17,4 @@ clean::
 	rm -f $(TARGET).py
 
 check: all
+	$(MAKE) -f $(TOP)/Makefile python_run
diff --git a/Examples/python/docstrings/Makefile b/Examples/python/docstrings/Makefile
index 74ab112a1..f25450cac 100644
--- a/Examples/python/docstrings/Makefile
+++ b/Examples/python/docstrings/Makefile
@@ -21,3 +21,4 @@ clean::
 	rm -f $(TARGET).py
 
 check: all
+	$(MAKE) -f $(TOP)/Makefile python_run
diff --git a/Examples/python/enum/Makefile b/Examples/python/enum/Makefile
index f331b8203..74625b992 100644
--- a/Examples/python/enum/Makefile
+++ b/Examples/python/enum/Makefile
@@ -18,3 +18,4 @@ clean::
 	rm -f $(TARGET).py
 
 check: all
+	$(MAKE) -f $(TOP)/Makefile python_run
diff --git a/Examples/python/exception/Makefile b/Examples/python/exception/Makefile
index 17c4f30b7..7dbdde944 100644
--- a/Examples/python/exception/Makefile
+++ b/Examples/python/exception/Makefile
@@ -18,3 +18,4 @@ clean::
 	rm -f $(TARGET).py
 
 check: all
+	$(MAKE) -f $(TOP)/Makefile python_run
diff --git a/Examples/python/exceptproxy/Makefile b/Examples/python/exceptproxy/Makefile
index a4f334311..ba5c79827 100644
--- a/Examples/python/exceptproxy/Makefile
+++ b/Examples/python/exceptproxy/Makefile
@@ -19,3 +19,4 @@ clean::
 	rm -f $(TARGET).py
 
 check: all
+	$(MAKE) -f $(TOP)/Makefile python_run
diff --git a/Examples/python/extend/Makefile b/Examples/python/extend/Makefile
index ad36d7d7e..a29276e58 100644
--- a/Examples/python/extend/Makefile
+++ b/Examples/python/extend/Makefile
@@ -19,3 +19,4 @@ clean::
 	rm -f $(TARGET).py
 
 check: all
+	$(MAKE) -f $(TOP)/Makefile python_run
diff --git a/Examples/python/funcptr/Makefile b/Examples/python/funcptr/Makefile
index 4a1e1bb71..0f4a1e077 100644
--- a/Examples/python/funcptr/Makefile
+++ b/Examples/python/funcptr/Makefile
@@ -17,3 +17,4 @@ clean::
 	rm -f $(TARGET).py
 
 check: all
+	$(MAKE) -f $(TOP)/Makefile python_run
diff --git a/Examples/python/funcptr2/Makefile b/Examples/python/funcptr2/Makefile
index 4a1e1bb71..0f4a1e077 100644
--- a/Examples/python/funcptr2/Makefile
+++ b/Examples/python/funcptr2/Makefile
@@ -17,3 +17,4 @@ clean::
 	rm -f $(TARGET).py
 
 check: all
+	$(MAKE) -f $(TOP)/Makefile python_run
diff --git a/Examples/python/functor/Makefile b/Examples/python/functor/Makefile
index c45536529..fe389757a 100644
--- a/Examples/python/functor/Makefile
+++ b/Examples/python/functor/Makefile
@@ -19,3 +19,4 @@ clean::
 	rm -f $(TARGET).py
 
 check: all
+	$(MAKE) -f $(TOP)/Makefile python_run
diff --git a/Examples/python/import/Makefile b/Examples/python/import/Makefile
index e00e81864..74d4f88cf 100644
--- a/Examples/python/import/Makefile
+++ b/Examples/python/import/Makefile
@@ -19,3 +19,4 @@ clean::
 	@rm -f foo.py bar.py spam.py base.py
 
 check: all
+	$(MAKE) -f $(TOP)/Makefile python_run
diff --git a/Examples/python/import_template/Makefile b/Examples/python/import_template/Makefile
index fa49f3145..ee47e994d 100644
--- a/Examples/python/import_template/Makefile
+++ b/Examples/python/import_template/Makefile
@@ -19,3 +19,4 @@ clean::
 	@rm -f foo.py bar.py spam.py base.py
 
 check: all
+	$(MAKE) -f $(TOP)/Makefile python_run
diff --git a/Examples/python/libffi/Makefile b/Examples/python/libffi/Makefile
index 8c7edfa65..fafb7de09 100644
--- a/Examples/python/libffi/Makefile
+++ b/Examples/python/libffi/Makefile
@@ -17,3 +17,4 @@ clean::
 	rm -f $(TARGET).py
 
 check: all
+	$(MAKE) -f $(TOP)/Makefile python_run
diff --git a/Examples/python/multimap/Makefile b/Examples/python/multimap/Makefile
index 4a1e1bb71..0f4a1e077 100644
--- a/Examples/python/multimap/Makefile
+++ b/Examples/python/multimap/Makefile
@@ -17,3 +17,4 @@ clean::
 	rm -f $(TARGET).py
 
 check: all
+	$(MAKE) -f $(TOP)/Makefile python_run
diff --git a/Examples/python/multimap/example.i b/Examples/python/multimap/example.i
index 163d7cc8e..3d5a09771 100644
--- a/Examples/python/multimap/example.i
+++ b/Examples/python/multimap/example.i
@@ -17,6 +17,7 @@ extern int    gcd(int x, int y);
 
 %typemap(in,fragment="t_output_helper") (int argc, char *argv[]) {
   int i;
+  int l;
   if (!PyList_Check($input)) {
     SWIG_exception(SWIG_ValueError, "Expecting a list");
   }
@@ -27,11 +28,21 @@ extern int    gcd(int x, int y);
   $2 = (char **) malloc(($1+1)*sizeof(char *));
   for (i = 0; i < $1; i++) {
     PyObject *s = PyList_GetItem($input,i);
-    if (!PyString_Check(s)) {
+%#if PY_VERSION_HEX >= 0x03000000
+    if (!PyUnicode_Check(s)) 
+%#else
+    if (!PyString_Check(s)) 
+%#endif
+    {
       free($2);
       SWIG_exception(SWIG_ValueError, "List items must be strings");
     }
+%#if PY_VERSION_HEX >= 0x03000000
+    $2[i] = PyUnicode_AsStringAndSize(s, &l);
+%#else
     $2[i] = PyString_AsString(s);
+%#endif
+
   }
   $2[i] = 0;
 }
@@ -39,12 +50,21 @@ extern int    gcd(int x, int y);
 extern int gcdmain(int argc, char *argv[]);
 
 %typemap(in) (char *bytes, int len) {
+
+%#if PY_VERSION_HEX >= 0x03000000
+  if (!PyUnicode_Check($input)) {
+    PyErr_SetString(PyExc_ValueError,"Expected a string");
+    return NULL;
+  }
+  $1 = PyUnicode_AsStringAndSize($input, &$2);
+%#else
   if (!PyString_Check($input)) {
     PyErr_SetString(PyExc_ValueError,"Expected a string");
     return NULL;
   }
   $1 = PyString_AsString($input);
   $2 = PyString_Size($input);
+%#endif
 }
 
 extern int count(char *bytes, int len, char c);
@@ -56,9 +76,15 @@ extern int count(char *bytes, int len, char c);
    so that we don't violate it's mutability */
 
 %typemap(in) (char *str, int len) {
+%#if PY_VERSION_HEX >= 0x03000000
+   $2 = PyUnicode_GetSize($input);
+   $1 = (char *) malloc($2+1);
+   memmove($1,PyUnicode_AsString($input),$2);
+%#else
    $2 = PyString_Size($input);
    $1 = (char *) malloc($2+1);
    memmove($1,PyString_AsString($input),$2);
+%#endif
 }
 
 /* Return the mutated string as a new object.  The t_output_helper
@@ -67,7 +93,11 @@ extern int count(char *bytes, int len, char c);
 
 %typemap(argout) (char *str, int len) {
    PyObject *o;
+%#if PY_VERSION_HEX >= 0x03000000
+   o = PyUnicode_FromStringAndSize($1,$2);
+%#else
    o = PyString_FromStringAndSize($1,$2);
+%#endif
    $result = t_output_helper($result,o);
    free($1);
 }   
diff --git a/Examples/python/operator/Makefile b/Examples/python/operator/Makefile
index c45536529..fe389757a 100644
--- a/Examples/python/operator/Makefile
+++ b/Examples/python/operator/Makefile
@@ -19,3 +19,4 @@ clean::
 	rm -f $(TARGET).py
 
 check: all
+	$(MAKE) -f $(TOP)/Makefile python_run
diff --git a/Examples/python/pointer/Makefile b/Examples/python/pointer/Makefile
index 4a1e1bb71..0f4a1e077 100644
--- a/Examples/python/pointer/Makefile
+++ b/Examples/python/pointer/Makefile
@@ -17,3 +17,4 @@ clean::
 	rm -f $(TARGET).py
 
 check: all
+	$(MAKE) -f $(TOP)/Makefile python_run
diff --git a/Examples/python/reference/Makefile b/Examples/python/reference/Makefile
index f331b8203..74625b992 100644
--- a/Examples/python/reference/Makefile
+++ b/Examples/python/reference/Makefile
@@ -18,3 +18,4 @@ clean::
 	rm -f $(TARGET).py
 
 check: all
+	$(MAKE) -f $(TOP)/Makefile python_run
diff --git a/Examples/python/simple/Makefile b/Examples/python/simple/Makefile
index 4a1e1bb71..0f4a1e077 100644
--- a/Examples/python/simple/Makefile
+++ b/Examples/python/simple/Makefile
@@ -17,3 +17,4 @@ clean::
 	rm -f $(TARGET).py
 
 check: all
+	$(MAKE) -f $(TOP)/Makefile python_run
diff --git a/Examples/python/smartptr/Makefile b/Examples/python/smartptr/Makefile
index 58d139643..f73802a6b 100644
--- a/Examples/python/smartptr/Makefile
+++ b/Examples/python/smartptr/Makefile
@@ -19,3 +19,4 @@ clean::
 	rm -f $(TARGET).py
 
 check: all
+	$(MAKE) -f $(TOP)/Makefile python_run
diff --git a/Examples/python/std_map/Makefile b/Examples/python/std_map/Makefile
index 2d4c1b4a3..5d13da764 100644
--- a/Examples/python/std_map/Makefile
+++ b/Examples/python/std_map/Makefile
@@ -22,3 +22,4 @@ run:
 	python runme.py
 
 check: all
+	$(MAKE) -f $(TOP)/Makefile python_run
diff --git a/Examples/python/std_vector/Makefile b/Examples/python/std_vector/Makefile
index a4f334311..ba5c79827 100644
--- a/Examples/python/std_vector/Makefile
+++ b/Examples/python/std_vector/Makefile
@@ -19,3 +19,4 @@ clean::
 	rm -f $(TARGET).py
 
 check: all
+	$(MAKE) -f $(TOP)/Makefile python_run
diff --git a/Examples/python/swigrun/Makefile b/Examples/python/swigrun/Makefile
index 53bf701c9..2142be5bb 100644
--- a/Examples/python/swigrun/Makefile
+++ b/Examples/python/swigrun/Makefile
@@ -22,3 +22,4 @@ clean::
 
 check: all
 
+	$(MAKE) -f $(TOP)/Makefile python_run
diff --git a/Examples/python/template/Makefile b/Examples/python/template/Makefile
index a4f334311..ba5c79827 100644
--- a/Examples/python/template/Makefile
+++ b/Examples/python/template/Makefile
@@ -19,3 +19,4 @@ clean::
 	rm -f $(TARGET).py
 
 check: all
+	$(MAKE) -f $(TOP)/Makefile python_run
diff --git a/Examples/python/varargs/Makefile b/Examples/python/varargs/Makefile
index 01d0f943a..1420b4e0b 100644
--- a/Examples/python/varargs/Makefile
+++ b/Examples/python/varargs/Makefile
@@ -17,3 +17,4 @@ clean::
 	rm -f $(TARGET).py
 
 check: all
+	$(MAKE) -f $(TOP)/Makefile python_run
diff --git a/Examples/python/variables/Makefile b/Examples/python/variables/Makefile
index 4a1e1bb71..0f4a1e077 100644
--- a/Examples/python/variables/Makefile
+++ b/Examples/python/variables/Makefile
@@ -17,3 +17,4 @@ clean::
 	rm -f $(TARGET).py
 
 check: all
+	$(MAKE) -f $(TOP)/Makefile python_run
diff --git a/Examples/python/weave/Makefile b/Examples/python/weave/Makefile
index 822779bd1..88f95c095 100644
--- a/Examples/python/weave/Makefile
+++ b/Examples/python/weave/Makefile
@@ -19,3 +19,4 @@ clean::
 	rm -f $(TARGET).py
 
 check: all
+	$(MAKE) -f $(TOP)/Makefile python_run
diff --git a/Examples/ruby/class/example.dsp b/Examples/ruby/class/example.dsp
index 49c480575..9a26322ec 100644
--- a/Examples/ruby/class/example.dsp
+++ b/Examples/ruby/class/example.dsp
@@ -123,7 +123,7 @@ SOURCE=.\example.i
 InputPath=.\example.i
 InputName=example
 
-"$(InputName)_wrap.c" : $(SOURCE) "$(INTDIR)" "$(OUTDIR)"
+"$(InputName)_wrap.cxx" : $(SOURCE) "$(INTDIR)" "$(OUTDIR)"
 	echo In order to function correctly, please ensure the following environment variables are correctly set: 
 	echo RUBY_INCLUDE: %RUBY_INCLUDE% 
 	echo RUBY_LIB: %RUBY_LIB% 
@@ -138,7 +138,7 @@ InputName=example
 InputPath=.\example.i
 InputName=example
 
-"$(InputName)_wrap.c" : $(SOURCE) "$(INTDIR)" "$(OUTDIR)"
+"$(InputName)_wrap.cxx" : $(SOURCE) "$(INTDIR)" "$(OUTDIR)"
 	echo In order to function correctly, please ensure the following environment variables are correctly set: 
 	echo RUBY_INCLUDE: %RUBY_INCLUDE% 
 	echo RUBY_LIB: %RUBY_LIB% 
diff --git a/Examples/ruby/free_function/example.cxx b/Examples/ruby/free_function/example.cxx
index 9e0d24b1a..402a947e9 100644
--- a/Examples/ruby/free_function/example.cxx
+++ b/Examples/ruby/free_function/example.cxx
@@ -23,7 +23,7 @@ Zoo::~Zoo()
 	IterType iter = this->animals.begin();
 	IterType end = this->animals.end();
 
-	for(iter; iter != end; ++iter)
+	for(; iter != end; ++iter)
 	{
 		Animal* animal = *iter;
 		delete animal;
diff --git a/Examples/ruby/free_function/example.dsp b/Examples/ruby/free_function/example.dsp
index 49c480575..9a26322ec 100644
--- a/Examples/ruby/free_function/example.dsp
+++ b/Examples/ruby/free_function/example.dsp
@@ -123,7 +123,7 @@ SOURCE=.\example.i
 InputPath=.\example.i
 InputName=example
 
-"$(InputName)_wrap.c" : $(SOURCE) "$(INTDIR)" "$(OUTDIR)"
+"$(InputName)_wrap.cxx" : $(SOURCE) "$(INTDIR)" "$(OUTDIR)"
 	echo In order to function correctly, please ensure the following environment variables are correctly set: 
 	echo RUBY_INCLUDE: %RUBY_INCLUDE% 
 	echo RUBY_LIB: %RUBY_LIB% 
@@ -138,7 +138,7 @@ InputName=example
 InputPath=.\example.i
 InputName=example
 
-"$(InputName)_wrap.c" : $(SOURCE) "$(INTDIR)" "$(OUTDIR)"
+"$(InputName)_wrap.cxx" : $(SOURCE) "$(INTDIR)" "$(OUTDIR)"
 	echo In order to function correctly, please ensure the following environment variables are correctly set: 
 	echo RUBY_INCLUDE: %RUBY_INCLUDE% 
 	echo RUBY_LIB: %RUBY_LIB% 
diff --git a/Examples/ruby/import/bar.dsp b/Examples/ruby/import/bar.dsp
index e897f8d5c..dd09ca021 100644
--- a/Examples/ruby/import/bar.dsp
+++ b/Examples/ruby/import/bar.dsp
@@ -115,7 +115,7 @@ SOURCE=.\bar.i
 InputPath=.\bar.i
 InputName=bar
 
-"$(InputName)_wrap.c" : $(SOURCE) "$(INTDIR)" "$(OUTDIR)"
+"$(InputName)_wrap.cxx" : $(SOURCE) "$(INTDIR)" "$(OUTDIR)"
 	echo In order to function correctly, please ensure the following environment variables are correctly set: 
 	echo RUBY_INCLUDE: %RUBY_INCLUDE% 
 	echo RUBY_LIB: %RUBY_LIB% 
@@ -130,7 +130,7 @@ InputName=bar
 InputPath=.\bar.i
 InputName=bar
 
-"$(InputName)_wrap.c" : $(SOURCE) "$(INTDIR)" "$(OUTDIR)"
+"$(InputName)_wrap.cxx" : $(SOURCE) "$(INTDIR)" "$(OUTDIR)"
 	echo In order to function correctly, please ensure the following environment variables are correctly set: 
 	echo RUBY_INCLUDE: %RUBY_INCLUDE% 
 	echo RUBY_LIB: %RUBY_LIB% 
diff --git a/Examples/ruby/import/base.dsp b/Examples/ruby/import/base.dsp
index 45d2fe2ea..2bd4fa243 100644
--- a/Examples/ruby/import/base.dsp
+++ b/Examples/ruby/import/base.dsp
@@ -115,7 +115,7 @@ SOURCE=.\base.i
 InputPath=.\base.i
 InputName=base
 
-"$(InputName)_wrap.c" : $(SOURCE) "$(INTDIR)" "$(OUTDIR)"
+"$(InputName)_wrap.cxx" : $(SOURCE) "$(INTDIR)" "$(OUTDIR)"
 	echo In order to function correctly, please ensure the following environment variables are correctly set: 
 	echo RUBY_INCLUDE: %RUBY_INCLUDE% 
 	echo RUBY_LIB: %RUBY_LIB% 
@@ -130,7 +130,7 @@ InputName=base
 InputPath=.\base.i
 InputName=base
 
-"$(InputName)_wrap.c" : $(SOURCE) "$(INTDIR)" "$(OUTDIR)"
+"$(InputName)_wrap.cxx" : $(SOURCE) "$(INTDIR)" "$(OUTDIR)"
 	echo In order to function correctly, please ensure the following environment variables are correctly set: 
 	echo RUBY_INCLUDE: %RUBY_INCLUDE% 
 	echo RUBY_LIB: %RUBY_LIB% 
diff --git a/Examples/ruby/import/foo.dsp b/Examples/ruby/import/foo.dsp
index 2dfba9d60..2a764bbd7 100644
--- a/Examples/ruby/import/foo.dsp
+++ b/Examples/ruby/import/foo.dsp
@@ -115,7 +115,7 @@ SOURCE=.\foo.i
 InputPath=.\foo.i
 InputName=foo
 
-"$(InputName)_wrap.c" : $(SOURCE) "$(INTDIR)" "$(OUTDIR)"
+"$(InputName)_wrap.cxx" : $(SOURCE) "$(INTDIR)" "$(OUTDIR)"
 	echo In order to function correctly, please ensure the following environment variables are correctly set: 
 	echo RUBY_INCLUDE: %RUBY_INCLUDE% 
 	echo RUBY_LIB: %RUBY_LIB% 
@@ -130,7 +130,7 @@ InputName=foo
 InputPath=.\foo.i
 InputName=foo
 
-"$(InputName)_wrap.c" : $(SOURCE) "$(INTDIR)" "$(OUTDIR)"
+"$(InputName)_wrap.cxx" : $(SOURCE) "$(INTDIR)" "$(OUTDIR)"
 	echo In order to function correctly, please ensure the following environment variables are correctly set: 
 	echo RUBY_INCLUDE: %RUBY_INCLUDE% 
 	echo RUBY_LIB: %RUBY_LIB% 
diff --git a/Examples/ruby/import/spam.dsp b/Examples/ruby/import/spam.dsp
index 0530b7303..d2d7158bb 100644
--- a/Examples/ruby/import/spam.dsp
+++ b/Examples/ruby/import/spam.dsp
@@ -115,7 +115,7 @@ SOURCE=.\spam.i
 InputPath=.\spam.i
 InputName=spam
 
-"$(InputName)_wrap.c" : $(SOURCE) "$(INTDIR)" "$(OUTDIR)"
+"$(InputName)_wrap.cxx" : $(SOURCE) "$(INTDIR)" "$(OUTDIR)"
 	echo In order to function correctly, please ensure the following environment variables are correctly set: 
 	echo RUBY_INCLUDE: %RUBY_INCLUDE% 
 	echo RUBY_LIB: %RUBY_LIB% 
@@ -130,7 +130,7 @@ InputName=spam
 InputPath=.\spam.i
 InputName=spam
 
-"$(InputName)_wrap.c" : $(SOURCE) "$(INTDIR)" "$(OUTDIR)"
+"$(InputName)_wrap.cxx" : $(SOURCE) "$(INTDIR)" "$(OUTDIR)"
 	echo In order to function correctly, please ensure the following environment variables are correctly set: 
 	echo RUBY_INCLUDE: %RUBY_INCLUDE% 
 	echo RUBY_LIB: %RUBY_LIB% 
diff --git a/Examples/ruby/mark_function/example.dsp b/Examples/ruby/mark_function/example.dsp
index 49c480575..9a26322ec 100644
--- a/Examples/ruby/mark_function/example.dsp
+++ b/Examples/ruby/mark_function/example.dsp
@@ -123,7 +123,7 @@ SOURCE=.\example.i
 InputPath=.\example.i
 InputName=example
 
-"$(InputName)_wrap.c" : $(SOURCE) "$(INTDIR)" "$(OUTDIR)"
+"$(InputName)_wrap.cxx" : $(SOURCE) "$(INTDIR)" "$(OUTDIR)"
 	echo In order to function correctly, please ensure the following environment variables are correctly set: 
 	echo RUBY_INCLUDE: %RUBY_INCLUDE% 
 	echo RUBY_LIB: %RUBY_LIB% 
@@ -138,7 +138,7 @@ InputName=example
 InputPath=.\example.i
 InputName=example
 
-"$(InputName)_wrap.c" : $(SOURCE) "$(INTDIR)" "$(OUTDIR)"
+"$(InputName)_wrap.cxx" : $(SOURCE) "$(INTDIR)" "$(OUTDIR)"
 	echo In order to function correctly, please ensure the following environment variables are correctly set: 
 	echo RUBY_INCLUDE: %RUBY_INCLUDE% 
 	echo RUBY_LIB: %RUBY_LIB% 
diff --git a/Examples/ruby/std_vector/runme.rb b/Examples/ruby/std_vector/runme.rb
index 1529d38c6..851190536 100644
--- a/Examples/ruby/std_vector/runme.rb
+++ b/Examples/ruby/std_vector/runme.rb
@@ -9,7 +9,7 @@ puts Example::average([1,2,3,4])
 # ... or a wrapped std::vector<int>
 
 v = Example::IntVector.new(4)
-0.upto(v.length-1) { |i| v[i] = i+1 }
+0.upto(v.size-1) { |i| v[i] = i+1 }
 puts Example::average(v)
 
 
@@ -17,7 +17,7 @@ puts Example::average(v)
 # Call it with a Ruby array...
 
 w = Example::half([1.0, 1.5, 2.0, 2.5, 3.0])
-0.upto(w.length-1) { |i| print w[i],"; " }
+0.upto(w.size-1) { |i| print w[i],"; " }
 puts
 
 # ... or a wrapped std::vector<double>
@@ -25,12 +25,12 @@ puts
 v = Example::DoubleVector.new
 [1,2,3,4].each { |i| v.push(i) }
 w = Example::half(v)
-0.upto(w.length-1) { |i| print w[i],"; " }
+0.upto(w.size-1) { |i| print w[i],"; " }
 puts
 
 # now halve a wrapped std::vector<double> in place
 
 Example::halve_in_place(v)
-0.upto(v.length-1) { |i| print v[i],"; " }
+0.upto(v.size-1) { |i| print v[i],"; " }
 puts
 
diff --git a/Examples/tcl/import/base.h b/Examples/tcl/import/base.h
index be3cdef7d..5a266f68c 100644
--- a/Examples/tcl/import/base.h
+++ b/Examples/tcl/import/base.h
@@ -3,7 +3,7 @@
 class Base {
  public:
      Base() { };
-    ~Base() { };
+     virtual ~Base() { };
      virtual void A() {
          printf("I'm Base::A\n");
      }
diff --git a/Examples/test-suite/abstract_virtual.i b/Examples/test-suite/abstract_virtual.i
index e2d8054bb..2e4d105b1 100644
--- a/Examples/test-suite/abstract_virtual.i
+++ b/Examples/test-suite/abstract_virtual.i
@@ -2,10 +2,10 @@
 
 %warnfilter(SWIGWARN_JAVA_MULTIPLE_INHERITANCE,
 	    SWIGWARN_CSHARP_MULTIPLE_INHERITANCE,
-	    SWIGWARN_PHP4_MULTIPLE_INHERITANCE) D; /* C#, Java, Php4 multiple inheritance */
+	    SWIGWARN_PHP_MULTIPLE_INHERITANCE) D; /* C#, Java, PHP multiple inheritance */
 %warnfilter(SWIGWARN_JAVA_MULTIPLE_INHERITANCE,
 	    SWIGWARN_CSHARP_MULTIPLE_INHERITANCE,
-	    SWIGWARN_PHP4_MULTIPLE_INHERITANCE) E; /* C#, Java, Php4 multiple inheritance */
+	    SWIGWARN_PHP_MULTIPLE_INHERITANCE) E; /* C#, Java, PHP multiple inheritance */
 
 %inline %{
 #if defined(_MSC_VER)
diff --git a/Examples/test-suite/allowexcept.i b/Examples/test-suite/allowexcept.i
index 14b19b33d..37b01cd75 100644
--- a/Examples/test-suite/allowexcept.i
+++ b/Examples/test-suite/allowexcept.i
@@ -26,14 +26,26 @@ UVW Bar::static_member_variable;
 struct XYZ {
 };
 
+// The operator& trick doesn't work for SWIG/PHP because the generated code
+// takes the address of the variable in the code in the "vinit" section.
+#ifdef SWIGPHP
 %{
 struct XYZ {
   void foo() {}
 private:
   XYZ& operator=(const XYZ& other); // prevent assignment used in normally generated set method
-  XYZ* operator&(); // prevent dereferencing used in normally generated  get method
 };
 %}
+#else
+%{
+struct XYZ {
+  void foo() {}
+private:
+  XYZ& operator=(const XYZ& other); // prevent assignment used in normally generated set method
+  XYZ* operator&(); // prevent dereferencing used in normally generated get method
+};
+%}
+#endif
 #if defined(SWIGUTL)
 %exception {
   /* 
diff --git a/Examples/test-suite/apply_signed_char.i b/Examples/test-suite/apply_signed_char.i
index ff1f1d83f..c0fa00cfe 100644
--- a/Examples/test-suite/apply_signed_char.i
+++ b/Examples/test-suite/apply_signed_char.i
@@ -31,5 +31,7 @@
     const char memberconstchar;
 
     virtual ~DirectorTest() {}
+  private:
+    DirectorTest& operator=(const DirectorTest &);
   };
 %}
diff --git a/Examples/test-suite/bools.i b/Examples/test-suite/bools.i
index 40e8989bd..7b94fcf88 100644
--- a/Examples/test-suite/bools.i
+++ b/Examples/test-suite/bools.i
@@ -57,6 +57,8 @@ struct BoolStructure {
     m_rbool(m_bool2),
     m_const_pbool(m_pbool),
     m_const_rbool(m_rbool) {}
+private:
+  BoolStructure& operator=(const BoolStructure &);
 };
 %}
 
diff --git a/Examples/test-suite/char_strings.i b/Examples/test-suite/char_strings.i
index a91afaded..b06eba773 100644
--- a/Examples/test-suite/char_strings.i
+++ b/Examples/test-suite/char_strings.i
@@ -10,7 +10,7 @@ below.
 %warnfilter(SWIGWARN_TYPEMAP_CHARLEAK_MSG) global_const_char;  // Setting a const char * variable may leak memory.
 
 %{
-#define OTHERLAND_MSG "Little message from the the safe world."
+#define OTHERLAND_MSG "Little message from the safe world."
 #define CPLUSPLUS_MSG "A message from the deep dark world of C++, where anything is possible."
 static char *global_str = NULL;
 const int UINT_DIGITS = 10; // max unsigned int is 4294967295
diff --git a/Examples/test-suite/chicken/Makefile.in b/Examples/test-suite/chicken/Makefile.in
index 0ac37d16a..ef6d7056c 100644
--- a/Examples/test-suite/chicken/Makefile.in
+++ b/Examples/test-suite/chicken/Makefile.in
@@ -40,7 +40,7 @@ SWIGOPT += -nounit
 	$(setup)
 	+$(swig_and_compile_c)
 	$(run_testcase)
-	+if [ -f $(srcdir)/$(SCRIPTPREFIX)$*$(PROXYSUFFIX) ]; then ( \
+	if [ -f $(srcdir)/$(SCRIPTPREFIX)$*$(PROXYSUFFIX) ]; then ( \
 	  $(MAKE) $*.cproxy; ) \
 	fi;
 
@@ -54,7 +54,7 @@ SWIGOPT += -nounit
 
 %.externaltest:
 	$(setup)
-	$(swig_and_compile_external)
+	+$(swig_and_compile_external)
 	$(run_testcase)
 
 # Runs the testcase. A testcase is only run if
@@ -69,21 +69,21 @@ run_testcase = \
 %.cppproxy: SWIGOPT += -proxy
 %.cppproxy: SCRIPTSUFFIX = $(PROXYSUFFIX)
 %.cppproxy:
-	echo "Checking testcase $* (with run test) under chicken with -proxy"
-	$(swig_and_compile_cpp)
+	echo "$(ACTION)ing testcase $* (with run test) under chicken with -proxy"
+	+$(swig_and_compile_cpp)
 	$(run_testcase)
 
 %.cproxy: SWIGOPT += -proxy
 %.cproxy: SCRIPTSUFFIX = $(PROXYSUFFIX)
 %.cproxy:
-	echo "Checking testcase $* (with run test) under chicken with -proxy"
+	echo "$(ACTION)ing testcase $* (with run test) under chicken with -proxy"
 	+$(swig_and_compile_c)
 	$(run_testcase)
 
 %.multiproxy: SWIGOPT += -proxy -noclosuses
 %.multiproxy: SCRIPTSUFFIX = $(PROXYSUFFIX)
 %.multiproxy:
-	echo "Checking testcase $* (with run test) under chicken with -proxy"
+	echo "$(ACTION)ing testcase $* (with run test) under chicken with -proxy"
 	+$(swig_and_compile_multi_cpp)
 	$(run_testcase)
 
diff --git a/Examples/test-suite/common.mk b/Examples/test-suite/common.mk
index 3607a4253..57b57c271 100644
--- a/Examples/test-suite/common.mk
+++ b/Examples/test-suite/common.mk
@@ -202,6 +202,7 @@ CPP_TEST_CASES += \
 	inherit_target_language \
 	inherit_void_arg \
 	inline_initializer \
+        keyword_rename \
 	kind \
 	langobj \
 	li_attribute \
@@ -236,6 +237,7 @@ CPP_TEST_CASES += \
 	null_pointer \
 	operator_overload \
 	operator_overload_break \
+        operbool \
 	ordering \
 	overload_copy \
 	overload_extend \
@@ -422,6 +424,7 @@ C_TEST_CASES += \
 	immutable \
 	inctest \
 	integers \
+        keyword_rename \
 	lextype \
 	li_carrays \
 	li_cdata \
diff --git a/Examples/test-suite/constant_pointers.i b/Examples/test-suite/constant_pointers.i
index 367baf49c..5bd2fd533 100644
--- a/Examples/test-suite/constant_pointers.i
+++ b/Examples/test-suite/constant_pointers.i
@@ -46,6 +46,8 @@ public:
     int* array_member1[ARRAY_SIZE];
     ParametersTest* array_member2[ARRAY_SIZE];
     MemberVariablesTest() : member3(NULL), member4(NULL) {}
+private:
+  MemberVariablesTest& operator=(const MemberVariablesTest&);
 };
 void foo(const int *const i) {}
 
@@ -69,6 +71,8 @@ public:
     void ret6(int*& a) {}
     int*& ret7() {return GlobalIntPtr;}
     ReturnValuesTest() : int3(NULL) {}
+private:
+  ReturnValuesTest& operator=(const ReturnValuesTest&);
 };
 
 const int* globalRet1() {return &GlobalInt;}
@@ -100,6 +104,8 @@ int* const globalRet2() {return &GlobalInt;}
     A* ap;
     const A* cap;
     Acptr acptr;  
+  private:
+    B& operator=(const B&);
   };
 
   const B* bar(const B* b) {
diff --git a/Examples/test-suite/contract.i b/Examples/test-suite/contract.i
index 6ee0a353c..a5732105b 100644
--- a/Examples/test-suite/contract.i
+++ b/Examples/test-suite/contract.i
@@ -3,7 +3,7 @@
 %warnfilter(SWIGWARN_RUBY_MULTIPLE_INHERITANCE,
 	    SWIGWARN_JAVA_MULTIPLE_INHERITANCE,
 	    SWIGWARN_CSHARP_MULTIPLE_INHERITANCE,
-	    SWIGWARN_PHP4_MULTIPLE_INHERITANCE) C; /* Ruby, C#, Java, Php4 multiple inheritance */
+	    SWIGWARN_PHP_MULTIPLE_INHERITANCE) C; /* Ruby, C#, Java, PHP multiple inheritance */
 
 #ifdef SWIGCSHARP
 %ignore B::bar; // otherwise get a warning: `C.bar' no suitable methods found to override
diff --git a/Examples/test-suite/cpp_basic.i b/Examples/test-suite/cpp_basic.i
index becf84708..a247dd268 100644
--- a/Examples/test-suite/cpp_basic.i
+++ b/Examples/test-suite/cpp_basic.i
@@ -55,6 +55,8 @@ class Bar {
     Foo *testFoo(int a, Foo *f) {
       return new Foo(2 * a + (f ? f->num : 0) + fval.num);
     }
+private:
+    Bar& operator=(const Bar&);
 };
 
 %}
diff --git a/Examples/test-suite/csharp/Makefile.in b/Examples/test-suite/csharp/Makefile.in
index 44a1b3675..5fd576ed8 100644
--- a/Examples/test-suite/csharp/Makefile.in
+++ b/Examples/test-suite/csharp/Makefile.in
@@ -51,9 +51,9 @@ intermediary_classname.customtest:
 # Makes a directory for the testcase if it does not exist
 setup = \
 	if [ -f $(srcdir)/$(SCRIPTPREFIX)$*$(SCRIPTSUFFIX) ]; then	  \
-	  echo "Checking testcase $* (with run test) under $(LANGUAGE)" ; \
+	  echo "$(ACTION)ing testcase $* (with run test) under $(LANGUAGE)" ; \
 	else								  \
-	  echo "Checking testcase $* under $(LANGUAGE)" ;		  \
+	  echo "$(ACTION)ing testcase $* under $(LANGUAGE)" ;		  \
 	fi;								  \
 	if [ ! -d $* ]; then						  \
 		mkdir $*;						  \
diff --git a/Examples/test-suite/csharp/char_strings_runme.cs b/Examples/test-suite/csharp/char_strings_runme.cs
index a1e878016..a8907fb16 100644
--- a/Examples/test-suite/csharp/char_strings_runme.cs
+++ b/Examples/test-suite/csharp/char_strings_runme.cs
@@ -5,7 +5,7 @@ using char_stringsNamespace;
 public class char_strings_runme {
 
   private static string CPLUSPLUS_MSG = "A message from the deep dark world of C++, where anything is possible.";
-  private static string OTHERLAND_MSG = "Little message from the the safe world.";
+  private static string OTHERLAND_MSG = "Little message from the safe world.";
 
   public static void Main() {
 
diff --git a/Examples/test-suite/csharp/director_basic_runme.cs b/Examples/test-suite/csharp/director_basic_runme.cs
new file mode 100644
index 000000000..b9916108c
--- /dev/null
+++ b/Examples/test-suite/csharp/director_basic_runme.cs
@@ -0,0 +1,74 @@
+using System;
+
+namespace director_basicNamespace {
+
+public class runme
+{
+  static void Main() 
+  {
+    runme r = new runme();
+    r.run();
+  }
+
+  void run()
+  {
+    director_basic_MyFoo a = new director_basic_MyFoo();
+
+    if (a.ping() != "director_basic_MyFoo::ping()") {
+      throw new Exception ( "a.ping()" );
+    }
+
+    if (a.pong() != "Foo::pong();director_basic_MyFoo::ping()") {
+      throw new Exception ( "a.pong()" );
+    }
+
+    Foo b = new Foo();
+
+    if (b.ping() != "Foo::ping()") {
+      throw new Exception ( "b.ping()" );
+    }
+
+    if (b.pong() != "Foo::pong();Foo::ping()") {
+      throw new Exception ( "b.pong()" );
+    }
+
+    A1 a1 = new A1(1, false);
+    a1.Dispose();
+
+    {
+      MyOverriddenClass my = new MyOverriddenClass();
+
+      my.expectNull = true;
+      if (MyClass.call_pmethod(my, null) != null)
+        throw new Exception("null pointer marshalling problem");
+
+      Bar myBar = new Bar();
+      my.expectNull = false;
+      Bar myNewBar = MyClass.call_pmethod(my, myBar);
+      if (myNewBar == null)
+        throw new Exception("non-null pointer marshalling problem");
+      myNewBar.x = 10;
+    }
+  }
+}
+
+class director_basic_MyFoo : Foo {
+  public director_basic_MyFoo() : base() {
+  }
+
+  public override string ping() {
+    return "director_basic_MyFoo::ping()";
+  }
+}
+
+class MyOverriddenClass : MyClass {
+  public bool expectNull = false;
+  public bool nonNullReceived = false;
+  public override Bar pmethod(Bar b) {
+    if ( expectNull && (b != null) )
+      throw new Exception("null not received as expected");
+    return b;
+  }
+}
+
+}
diff --git a/Examples/test-suite/csharp_prepost.i b/Examples/test-suite/csharp_prepost.i
index 9c2cedc83..0c35c1833 100644
--- a/Examples/test-suite/csharp_prepost.i
+++ b/Examples/test-suite/csharp_prepost.i
@@ -1,6 +1,6 @@
 %module csharp_prepost
 
-// Test the pre, post and cshin attributes for csin typemaps
+// Test the pre, post, terminate and cshin attributes for csin typemaps
 
 %include "std_vector.i"
 
@@ -88,3 +88,102 @@ public:
 };
 %}
 
+
+
+// test Date marshalling with pre post and terminate typemap attributes (Documented in CSharp.html)
+%typemap(cstype) const CDate& "System.DateTime"
+%typemap(csin, 
+         pre="    CDate temp$csinput = new CDate($csinput.Year, $csinput.Month, $csinput.Day);"
+        ) const CDate &
+         "$csclassname.getCPtr(temp$csinput)"
+
+%typemap(cstype) CDate& "out System.DateTime"
+%typemap(csin, 
+         pre="    CDate temp$csinput = new CDate();", 
+         post="      $csinput = new System.DateTime(temp$csinput.getYear(),"
+              " temp$csinput.getMonth(), temp$csinput.getDay(), 0, 0, 0);", 
+         cshin="out $csinput"
+        ) CDate &
+         "$csclassname.getCPtr(temp$csinput)"
+
+
+%inline %{
+class CDate {
+public:
+  CDate();
+  CDate(int year, int month, int day);
+  int getYear();
+  int getMonth();
+  int getDay();
+private:
+  int m_year;
+  int m_month;
+  int m_day;
+};
+struct Action {
+  int doSomething(const CDate &dateIn, CDate &dateOut);
+  Action(const CDate &dateIn, CDate& dateOut);
+};
+%}
+
+%{
+Action::Action(const CDate &dateIn, CDate& dateOut) {dateOut = dateIn;}
+int Action::doSomething(const CDate &dateIn, CDate &dateOut) { dateOut = dateIn; return 0; }
+CDate::CDate() : m_year(0), m_month(0), m_day(0) {}
+CDate::CDate(int year, int month, int day) : m_year(year), m_month(month), m_day(day) {}
+int CDate::getYear() { return m_year; }
+int CDate::getMonth() { return m_month; }
+int CDate::getDay() { return m_day; }
+%}
+
+%typemap(cstype, out="System.DateTime") CDate * "ref System.DateTime"
+
+%typemap(csin,
+         pre="    CDate temp$csinput = new CDate($csinput.Year, $csinput.Month, $csinput.Day);",
+         post="      $csinput = new System.DateTime(temp$csinput.getYear(),"
+              " temp$csinput.getMonth(), temp$csinput.getDay(), 0, 0, 0);", 
+         cshin="ref $csinput"
+        ) CDate *
+         "$csclassname.getCPtr(temp$csinput)"
+
+%inline %{
+void addYears(CDate *pDate, int years) {
+  *pDate = CDate(pDate->getYear() + years, pDate->getMonth(), pDate->getDay());
+}
+%}
+
+%typemap(csin,
+         pre="    using (CDate temp$csinput = new CDate($csinput.Year, $csinput.Month, $csinput.Day)) {",
+         post="      $csinput = new System.DateTime(temp$csinput.getYear(),"
+              " temp$csinput.getMonth(), temp$csinput.getDay(), 0, 0, 0);", 
+         terminator="    } // terminate temp$csinput using block",
+         cshin="ref $csinput"
+        ) CDate *
+         "$csclassname.getCPtr(temp$csinput)"
+
+%inline %{
+void subtractYears(CDate *pDate, int years) {
+  *pDate = CDate(pDate->getYear() - years, pDate->getMonth(), pDate->getDay());
+}
+%}
+
+%typemap(csvarin, excode=SWIGEXCODE2) CDate * %{
+    /* csvarin typemap code */
+    set {
+      CDate temp$csinput = new CDate($csinput.Year, $csinput.Month, $csinput.Day);
+      $imcall;$excode
+    } %}
+
+%typemap(csvarout, excode=SWIGEXCODE2) CDate * %{
+    /* csvarout typemap code */
+    get {
+      IntPtr cPtr = $imcall;
+      CDate tempDate = (cPtr == IntPtr.Zero) ? null : new CDate(cPtr, $owner);$excode
+      return new System.DateTime(tempDate.getYear(), tempDate.getMonth(), tempDate.getDay(),
+                                 0, 0, 0);
+    } %}
+
+%inline %{
+CDate ImportantDate = CDate(1999, 12, 31);
+%}
+
diff --git a/Examples/test-suite/default_constructor.i b/Examples/test-suite/default_constructor.i
index 71600e55a..ff22c7834 100644
--- a/Examples/test-suite/default_constructor.i
+++ b/Examples/test-suite/default_constructor.i
@@ -5,11 +5,11 @@
 
 %warnfilter(SWIGWARN_JAVA_MULTIPLE_INHERITANCE,
 	    SWIGWARN_CSHARP_MULTIPLE_INHERITANCE,
-	    SWIGWARN_PHP4_MULTIPLE_INHERITANCE) EB; /* C#, Java, Php4 multiple inheritance */
+	    SWIGWARN_PHP_MULTIPLE_INHERITANCE) EB; /* C#, Java, PHP multiple inheritance */
 
 %warnfilter(SWIGWARN_JAVA_MULTIPLE_INHERITANCE,
 	    SWIGWARN_CSHARP_MULTIPLE_INHERITANCE,
-	    SWIGWARN_PHP4_MULTIPLE_INHERITANCE) AD; /* C#, Java, Php4 multiple inheritance */
+	    SWIGWARN_PHP_MULTIPLE_INHERITANCE) AD; /* C#, Java, PHP multiple inheritance */
 
 %warnfilter(SWIGWARN_LANG_FRIEND_IGNORE) F; /* friend function */
 
diff --git a/Examples/test-suite/director_basic.i b/Examples/test-suite/director_basic.i
index 986a1706f..12cb0db65 100644
--- a/Examples/test-suite/director_basic.i
+++ b/Examples/test-suite/director_basic.i
@@ -112,12 +112,14 @@ public:
     return vmethod(b);
   }  
 
-
   static MyClass *get_self(MyClass *c) 
   {
     return c;
   }
-  
+
+  static Bar * call_pmethod(MyClass *myclass, Bar *b) {
+    return myclass->pmethod(b);
+  }
 };
 
 template<class T>
diff --git a/Examples/test-suite/enum_thorough.i b/Examples/test-suite/enum_thorough.i
index 4aa0613f2..31e3e2105 100644
--- a/Examples/test-suite/enum_thorough.i
+++ b/Examples/test-suite/enum_thorough.i
@@ -81,6 +81,8 @@ struct SpeedClass {
   const colour myColour2;
   speedtd1 mySpeedtd1;
   SpeedClass() : myColour2(red), mySpeedtd1(slow) { }
+private:
+  SpeedClass& operator=(const SpeedClass&);
 };
 
 int                            speedTest0(int s) { return s; }
diff --git a/Examples/test-suite/evil_diamond.i b/Examples/test-suite/evil_diamond.i
index 33353e32e..7b2e9152f 100644
--- a/Examples/test-suite/evil_diamond.i
+++ b/Examples/test-suite/evil_diamond.i
@@ -6,7 +6,7 @@
 %warnfilter(SWIGWARN_RUBY_WRONG_NAME,
 	    SWIGWARN_JAVA_MULTIPLE_INHERITANCE,
 	    SWIGWARN_CSHARP_MULTIPLE_INHERITANCE,
-	    SWIGWARN_PHP4_MULTIPLE_INHERITANCE) spam;	// Ruby, wrong class name - C# & Java, Php4 multiple inheritance
+	    SWIGWARN_PHP_MULTIPLE_INHERITANCE) spam;	// Ruby, wrong class name - C# & Java, PHP multiple inheritance
 
 %inline %{
 
diff --git a/Examples/test-suite/evil_diamond_ns.i b/Examples/test-suite/evil_diamond_ns.i
index 78a764ccc..515044007 100644
--- a/Examples/test-suite/evil_diamond_ns.i
+++ b/Examples/test-suite/evil_diamond_ns.i
@@ -6,7 +6,7 @@
 %warnfilter(SWIGWARN_RUBY_WRONG_NAME,
 	    SWIGWARN_JAVA_MULTIPLE_INHERITANCE,
 	    SWIGWARN_CSHARP_MULTIPLE_INHERITANCE,
-	    SWIGWARN_PHP4_MULTIPLE_INHERITANCE) Blah::spam;	// Ruby, wrong class name - C# & Java, Php4 multiple inheritance
+	    SWIGWARN_PHP_MULTIPLE_INHERITANCE) Blah::spam;	// Ruby, wrong class name - C# & Java, PHP multiple inheritance
 
 %inline %{
 namespace Blah {
diff --git a/Examples/test-suite/evil_diamond_prop.i b/Examples/test-suite/evil_diamond_prop.i
index e9fc24f4d..804ea66b4 100644
--- a/Examples/test-suite/evil_diamond_prop.i
+++ b/Examples/test-suite/evil_diamond_prop.i
@@ -6,7 +6,7 @@
 %warnfilter(SWIGWARN_RUBY_WRONG_NAME,
 	    SWIGWARN_JAVA_MULTIPLE_INHERITANCE,
 	    SWIGWARN_CSHARP_MULTIPLE_INHERITANCE,
-	    SWIGWARN_PHP4_MULTIPLE_INHERITANCE) spam;	// Ruby, wrong class name - C# & Java, Php4 multiple inheritance
+	    SWIGWARN_PHP_MULTIPLE_INHERITANCE) spam;	// Ruby, wrong class name - C# & Java, PHP multiple inheritance
 
 %inline %{
 
diff --git a/Examples/test-suite/fvirtual.i b/Examples/test-suite/fvirtual.i
index 074202bee..af189ed1f 100644
--- a/Examples/test-suite/fvirtual.i
+++ b/Examples/test-suite/fvirtual.i
@@ -10,11 +10,11 @@
       virtual ~Node() {}
   };
 
-  class Switch : public Node {
+  class NodeSwitch : public Node {
     public :
       virtual int addChild( Node *child ) { return 2; } // This was hidden with -fvirtual
       virtual int addChild( Node *child, bool value ) { return 3; }
-      virtual ~Switch() {}
+      virtual ~NodeSwitch() {}
   };
 %}
 
diff --git a/Examples/test-suite/guilescm/Makefile.in b/Examples/test-suite/guilescm/Makefile.in
index 285426ee8..04de236db 100644
--- a/Examples/test-suite/guilescm/Makefile.in
+++ b/Examples/test-suite/guilescm/Makefile.in
@@ -21,9 +21,9 @@ run_testcase = \
 
 setup = \
 	if [ -f $(srcdir)/$(SCRIPTPREFIX)$*$(SCRIPTSUFFIX) ]; then	  \
-	  echo "Checking testcase $* (with run test) under $(LANGUAGE) (with SCM API)" ; \
+	  echo "$(ACTION)ing testcase $* (with run test) under $(LANGUAGE) (with SCM API)" ; \
 	else								  \
-	  echo "Checking testcase $* under $(LANGUAGE) (with SCM API)" ;		  \
+	  echo "$(ACTION)ing testcase $* under $(LANGUAGE) (with SCM API)" ;		  \
 	fi;
 
 swig_and_compile_multi_cpp = \
@@ -43,9 +43,9 @@ swig_and_compile_multi_cpp = \
 # Same as setup and run_testcase, but without the SCRIPTPREFIX (so the runme comes from the guilescm directory)
 local_setup = \
 	if [ -f $(srcdir)/$*$(SCRIPTSUFFIX) ]; then	  \
-	  echo "Checking testcase $* (with run test) under $(LANGUAGE) (with SCM API)" ; \
+	  echo "$(ACTION)ing testcase $* (with run test) under $(LANGUAGE) (with SCM API)" ; \
 	else								  \
-	  echo "Checking testcase $* under $(LANGUAGE) (with SCM API)" ;		  \
+	  echo "$(ACTION)ing testcase $* under $(LANGUAGE) (with SCM API)" ;		  \
 	fi;
 
 local_run_testcase = \
diff --git a/Examples/test-suite/java/Makefile.in b/Examples/test-suite/java/Makefile.in
index 53816f6d0..ace8dee86 100644
--- a/Examples/test-suite/java/Makefile.in
+++ b/Examples/test-suite/java/Makefile.in
@@ -57,9 +57,9 @@ SWIGOPT += -package $*
 # Makes a directory for the testcase if it does not exist
 setup = \
 	if [ -f $(srcdir)/$(SCRIPTPREFIX)$*$(SCRIPTSUFFIX) ]; then	  \
-	  echo "Checking testcase $* (with run test) under $(LANGUAGE)" ; \
+	  echo "$(ACTION)ing testcase $* (with run test) under $(LANGUAGE)" ; \
 	else								  \
-	  echo "Checking testcase $* under $(LANGUAGE)" ;		  \
+	  echo "$(ACTION)ing testcase $* under $(LANGUAGE)" ;		  \
 	fi;								  \
 	if [ ! -d $* ]; then						  \
 		mkdir $*;						  \
diff --git a/Examples/test-suite/java/char_strings_runme.java b/Examples/test-suite/java/char_strings_runme.java
index 2e62080f5..2c71d3ea7 100644
--- a/Examples/test-suite/java/char_strings_runme.java
+++ b/Examples/test-suite/java/char_strings_runme.java
@@ -12,7 +12,7 @@ public class char_strings_runme {
   }
 
   private static String CPLUSPLUS_MSG = "A message from the deep dark world of C++, where anything is possible.";
-  private static String OTHERLAND_MSG = "Little message from the the safe world.";
+  private static String OTHERLAND_MSG = "Little message from the safe world.";
 
   public static void main(String argv[]) {
 
diff --git a/Examples/test-suite/java/director_basic_runme.java b/Examples/test-suite/java/director_basic_runme.java
index eafe20bec..16a46aa35 100644
--- a/Examples/test-suite/java/director_basic_runme.java
+++ b/Examples/test-suite/java/director_basic_runme.java
@@ -14,28 +14,43 @@ public class director_basic_runme {
 
   public static void main(String argv[]) {
 
-      director_basic_MyFoo a = new director_basic_MyFoo();
+    director_basic_MyFoo a = new director_basic_MyFoo();
 
-      if (!a.ping().equals("director_basic_MyFoo::ping()")) {
-          throw new RuntimeException ( "a.ping()" );
-      }
+    if (!a.ping().equals("director_basic_MyFoo::ping()")) {
+      throw new RuntimeException ( "a.ping()" );
+    }
 
-      if (!a.pong().equals("Foo::pong();director_basic_MyFoo::ping()")) {
-          throw new RuntimeException ( "a.pong()" );
-      }
+    if (!a.pong().equals("Foo::pong();director_basic_MyFoo::ping()")) {
+      throw new RuntimeException ( "a.pong()" );
+    }
 
-      Foo b = new Foo();
+    Foo b = new Foo();
 
-      if (!b.ping().equals("Foo::ping()")) {
-          throw new RuntimeException ( "b.ping()" );
-      }
+    if (!b.ping().equals("Foo::ping()")) {
+      throw new RuntimeException ( "b.ping()" );
+    }
 
-      if (!b.pong().equals("Foo::pong();Foo::ping()")) {
-          throw new RuntimeException ( "b.pong()" );
-      }
+    if (!b.pong().equals("Foo::pong();Foo::ping()")) {
+      throw new RuntimeException ( "b.pong()" );
+    }
 
-      A1 a1 = new A1(1, false);
-      a1.delete();
+    A1 a1 = new A1(1, false);
+    a1.delete();
+
+    {
+      MyOverriddenClass my = new MyOverriddenClass();
+
+      my.expectNull = true;
+      if (MyClass.call_pmethod(my, null) != null)
+        throw new RuntimeException("null pointer marshalling problem");
+
+      Bar myBar = new Bar();
+      my.expectNull = false;
+      Bar myNewBar = MyClass.call_pmethod(my, myBar);
+      if (myNewBar == null)
+        throw new RuntimeException("non-null pointer marshalling problem");
+      myNewBar.setX(10);
+    }
   }
 }
 
@@ -45,3 +60,13 @@ class director_basic_MyFoo extends Foo {
     }
 }
 
+class MyOverriddenClass extends MyClass {
+  public boolean expectNull = false;
+  public boolean nonNullReceived = false;
+  public Bar pmethod(Bar b) {
+    if ( expectNull && (b != null) )
+      throw new RuntimeException("null not received as expected");
+    return b;
+  }
+}
+
diff --git a/Examples/test-suite/java_typemaps_proxy.i b/Examples/test-suite/java_typemaps_proxy.i
index 5a1e61bb2..e315a36b5 100644
--- a/Examples/test-suite/java_typemaps_proxy.i
+++ b/Examples/test-suite/java_typemaps_proxy.i
@@ -119,6 +119,8 @@ public:
   void const_member_method(const ConstWithout *p) const {}
   const ConstWithout * const_var;
   const ConstWithout * const var_const;
+private:
+  ConstWithout& operator=(const ConstWithout &);
 };
 const ConstWithout * global_constwithout = 0;
 void global_method_constwithout(const ConstWithout *p) {}
diff --git a/Examples/test-suite/keyword_rename.i b/Examples/test-suite/keyword_rename.i
new file mode 100644
index 000000000..da9328868
--- /dev/null
+++ b/Examples/test-suite/keyword_rename.i
@@ -0,0 +1,32 @@
+/*
+ * Test reserved keyword renaming
+ */
+
+%module keyword_rename
+
+#pragma SWIG nowarn=SWIGWARN_PARSE_KEYWORD
+
+%inline %{
+
+#define KW(x, y) int x (int y) { return y; }
+
+/* Python keywords */
+KW(in, except)
+KW(except, in)
+KW(pass, in)
+
+/* Perl keywords */
+KW(tie, die)
+KW(use, next)
+
+/* Java keywords */
+KW(implements, native)
+KW(synchronized, final)
+
+/* C# Keywords */
+KW(string, out)
+struct sealed {int i;};
+
+%}
+
+
diff --git a/Examples/test-suite/li_cstring.i b/Examples/test-suite/li_cstring.i
index fd92ac7d3..28e8049e8 100644
--- a/Examples/test-suite/li_cstring.i
+++ b/Examples/test-suite/li_cstring.i
@@ -4,7 +4,7 @@
 
 #ifndef SWIG_CSTRING_UNIMPL
 
-%cstring_input_binary(char *in, int n);
+%cstring_input_binary(char *str_in, int n);
 %cstring_bounded_output(char *out1, 512);
 %cstring_chunk_output(char *out2, 64);
 %cstring_bounded_mutable(char *out3, 512);
@@ -22,13 +22,13 @@
 
 %inline %{
 
-int count(char *in, int n, char c) {
+int count(char *str_in, int n, char c) {
    int r = 0;
    while (n > 0) {
-     if (*in == c) {
+     if (*str_in == c) {
 	r++;
      }
-     in++;
+     str_in++;
      --n;
    }
    return r;
diff --git a/Examples/test-suite/li_cwstring.i b/Examples/test-suite/li_cwstring.i
index dc9a1c4b9..769dcce12 100644
--- a/Examples/test-suite/li_cwstring.i
+++ b/Examples/test-suite/li_cwstring.i
@@ -4,7 +4,7 @@
 
 #ifndef SWIG_CWSTRING_UNIMPL
 
-%cwstring_input_binary(wchar_t *in, int n);
+%cwstring_input_binary(wchar_t *str_in, int n);
 %cwstring_bounded_output(wchar_t *out1, 512);
 %cwstring_chunk_output(wchar_t *out2, 64);
 %cwstring_bounded_mutable(wchar_t *out3, 512);
@@ -22,13 +22,13 @@
 
 %inline %{
 
-int count(wchar_t *in, int n, wchar_t c) {
+int count(wchar_t *str_in, int n, wchar_t c) {
    int r = 0;
    while (n > 0) {
-     if (*in == c) {
+     if (*str_in == c) {
 	r++;
      }
-     in++;
+     str_in++;
      --n;
    }
    return r;
diff --git a/Examples/test-suite/li_std_string.i b/Examples/test-suite/li_std_string.i
index 8c2f1b857..2d0b7503d 100644
--- a/Examples/test-suite/li_std_string.i
+++ b/Examples/test-suite/li_std_string.i
@@ -129,7 +129,7 @@ public:
 %}
 
 %inline %{
-  std::string empty() {
+  std::string stdstring_empty() {
     return std::string();
   }
 
diff --git a/Examples/test-suite/lua/li_typemaps_runme.lua b/Examples/test-suite/lua/li_typemaps_runme.lua
new file mode 100644
index 000000000..77aeb54e4
--- /dev/null
+++ b/Examples/test-suite/lua/li_typemaps_runme.lua
@@ -0,0 +1,40 @@
+require("import")	-- the import fn
+import("li_typemaps")	-- import code
+
+-- catch "undefined" global variables
+setmetatable(getfenv(),{__index=function (t,i) error("undefined global variable `"..i.."'",2) end})
+
+-- Check double INPUT typemaps
+assert(li_typemaps.in_double(22.22) == 22.22)
+assert(li_typemaps.inr_double(22.22) == 22.22)
+
+-- Check double OUTPUT typemaps
+assert(li_typemaps.out_double(22.22) == 22.22)
+assert(li_typemaps.outr_double(22.22) == 22.22)
+
+-- Check double INOUT typemaps
+assert(li_typemaps.inout_double(22.22) == 22.22)
+assert(li_typemaps.inoutr_double(22.22) == 22.22)
+
+-- check long long
+assert(li_typemaps.in_ulonglong(20)==20)
+assert(li_typemaps.inr_ulonglong(20)==20)
+assert(li_typemaps.out_ulonglong(20)==20)
+assert(li_typemaps.outr_ulonglong(20)==20)
+assert(li_typemaps.inout_ulonglong(20)==20)
+assert(li_typemaps.inoutr_ulonglong(20)==20)
+
+-- check bools
+assert(li_typemaps.in_bool(true)==true)
+assert(li_typemaps.inr_bool(false)==false)
+assert(li_typemaps.out_bool(true)==true)
+assert(li_typemaps.outr_bool(false)==false)
+assert(li_typemaps.inout_bool(true)==true)
+assert(li_typemaps.inoutr_bool(false)==false)
+
+-- the others
+a,b=li_typemaps.inoutr_int2(1,2)
+assert(a==1 and b==2)
+
+f,i=li_typemaps.out_foo(10)
+assert(f.a==10 and i==20)
diff --git a/Examples/test-suite/minherit.i b/Examples/test-suite/minherit.i
index aba299387..24092b6c6 100644
--- a/Examples/test-suite/minherit.i
+++ b/Examples/test-suite/minherit.i
@@ -6,7 +6,7 @@
 
 %module(ruby_minherit="1") minherit
 
-#if defined(SWIGPYTHON) || defined(SWIGRUBY) || defined(SWIGOCAML) || defined(SWIGOCTAVE)
+#if defined(SWIGPYTHON) || defined(SWIGRUBY) || defined(SWIGOCAML) || defined(SWIGOCTAVE) || defined(SWIGPERL)
 
 %inline %{
 
diff --git a/Examples/test-suite/minherit2.i b/Examples/test-suite/minherit2.i
index f55131ff5..1bca4fc48 100644
--- a/Examples/test-suite/minherit2.i
+++ b/Examples/test-suite/minherit2.i
@@ -7,7 +7,7 @@
 %warnfilter(SWIGWARN_JAVA_MULTIPLE_INHERITANCE,
 	    SWIGWARN_CSHARP_MULTIPLE_INHERITANCE,
 	    SWIGWARN_RUBY_MULTIPLE_INHERITANCE,
-	    SWIGWARN_PHP4_MULTIPLE_INHERITANCE) RemoteMpe;
+	    SWIGWARN_PHP_MULTIPLE_INHERITANCE) RemoteMpe;
 
 
 #if defined(SWIGJAVA) || defined(SWIGCSHARP)
diff --git a/Examples/test-suite/multiple_inheritance.i b/Examples/test-suite/multiple_inheritance.i
index 1c4458114..1fc68eef9 100644
--- a/Examples/test-suite/multiple_inheritance.i
+++ b/Examples/test-suite/multiple_inheritance.i
@@ -5,11 +5,11 @@ It tests basic multiple inheritance */
 
 %warnfilter(SWIGWARN_JAVA_MULTIPLE_INHERITANCE,
 	    SWIGWARN_CSHARP_MULTIPLE_INHERITANCE,
-	    SWIGWARN_PHP4_MULTIPLE_INHERITANCE) FooBar;	/* C#, Java, Php4 multiple inheritance */
+	    SWIGWARN_PHP_MULTIPLE_INHERITANCE) FooBar;	/* C#, Java, PHP multiple inheritance */
 
 %warnfilter(SWIGWARN_JAVA_MULTIPLE_INHERITANCE,
 	    SWIGWARN_CSHARP_MULTIPLE_INHERITANCE,
-	    SWIGWARN_PHP4_MULTIPLE_INHERITANCE) FooBarSpam;	/* C#, Java, Php4 multiple inheritance */
+	    SWIGWARN_PHP_MULTIPLE_INHERITANCE) FooBarSpam;	/* C#, Java, PHP multiple inheritance */
 
 
 %inline %{
diff --git a/Examples/test-suite/name_warnings.i b/Examples/test-suite/name_warnings.i
index a9cb35686..527dbcfaa 100644
--- a/Examples/test-suite/name_warnings.i
+++ b/Examples/test-suite/name_warnings.i
@@ -58,13 +58,12 @@ namespace std
 
 %template(max_i) max<int>;
 
-
 %inline {
   /* silently rename the parameter names in csharp/java */
 #ifdef SWIGR
   double foo(double inparam, double out) { return 1.0; }
 #else
-  double foo(double in, double out) { return 1.0; }
+  double foo(double abstract, double out) { return 1.0; }
 #endif
   double bar(double native, bool boolean) { return 1.0; }
 }
diff --git a/Examples/test-suite/namespace_typemap.i b/Examples/test-suite/namespace_typemap.i
index e4e0af905..984b93a6f 100644
--- a/Examples/test-suite/namespace_typemap.i
+++ b/Examples/test-suite/namespace_typemap.i
@@ -75,7 +75,7 @@ namespace test {
     class string_class;
 #ifdef SWIGPYTHON
 	%typemap(in) string_class * {
-	    $1 = new string_class(PyString_AsString($input));
+	    $1 = new string_class(SWIG_Python_str_AsChar($input));
 	}
 	%typemap(freearg) string_class * {
 	    delete $1;
diff --git a/Examples/test-suite/octave/fvirtual_runme.m b/Examples/test-suite/octave/fvirtual_runme.m
index 06c6e7ccb..e755a559a 100644
--- a/Examples/test-suite/octave/fvirtual_runme.m
+++ b/Examples/test-suite/octave/fvirtual_runme.m
@@ -1,6 +1,6 @@
 fvirtual
 
-sw = Switch();
+sw = NodeSwitch();
 n = Node();
 i = sw.addChild(n);
 
diff --git a/Examples/test-suite/octave/li_std_string_runme.m b/Examples/test-suite/octave/li_std_string_runme.m
index 1c24ac344..fa0e260e0 100644
--- a/Examples/test-suite/octave/li_std_string_runme.m
+++ b/Examples/test-suite/octave/li_std_string_runme.m
@@ -148,7 +148,7 @@ if (s != "hellohello")
 endif
 
 
-if (li_std_string.empty() != "")
+if (li_std_string.stdstring_empty() != "")
   error
 endif
 
diff --git a/Examples/test-suite/operbool.i b/Examples/test-suite/operbool.i
new file mode 100644
index 000000000..d6d7fc706
--- /dev/null
+++ b/Examples/test-suite/operbool.i
@@ -0,0 +1,10 @@
+%module operbool
+
+%inline %{
+  class Test {
+  public:
+    operator bool() {
+      return false;
+    }
+  };
+%}
diff --git a/Examples/test-suite/perl5/li_std_string_runme.pl b/Examples/test-suite/perl5/li_std_string_runme.pl
index 0ee11bdc7..9ec7dd08c 100644
--- a/Examples/test-suite/perl5/li_std_string_runme.pl
+++ b/Examples/test-suite/perl5/li_std_string_runme.pl
@@ -98,7 +98,7 @@ SKIP: {
 is($gen1->testl("9234567890121111113"), "9234567890121111114", "ulonglong big number");
 
 
-is(li_std_string::empty(), "", "empty");
+is(li_std_string::stdstring_empty(), "", "stdstring_empty");
 
 is(li_std_string::c_empty(),  "", "c_empty");
 
@@ -110,4 +110,4 @@ is(li_std_string::get_null(li_std_string::c_null()), undef, "c_empty");
 
 is(li_std_string::get_null(li_std_string::c_empty()), "non-null", "c_empty");
 
-is(li_std_string::get_null(li_std_string::empty()), "non-null", "c_empty");
+is(li_std_string::get_null(li_std_string::stdstring_empty()), "non-null", "stdstring_empty");
diff --git a/Examples/test-suite/perl5/li_typemaps_runme.pl b/Examples/test-suite/perl5/li_typemaps_runme.pl
index c149284ae..c182cdbb1 100644
--- a/Examples/test-suite/perl5/li_typemaps_runme.pl
+++ b/Examples/test-suite/perl5/li_typemaps_runme.pl
@@ -37,24 +37,29 @@ batch('ulong', 0, 1, 12, 0xffffffff);
 batch('uchar', 0, 1, 12, 0xff);
 batch('schar', -0x80, 0, 1, 12, 0x7f);
 
-# IEEE 754 machine, please!
-batch('float',
-  -(2 - 2 ** -23) * 2 ** 127,
-  -1, -2 ** -149, 0, 2 ** -149, 1,
-  (2 - 2 ** -23) * 2 ** 127,
-  'nan');
-{ local $TODO = "shouldn't some Inf <=> float work?";
-  # I'm going to guess that it could work reasonably as
-  # NV Inf => float Inf
-  # float Inf => NV NaN
-  # but this needs some thought.
-  batch('float', 'inf');
+{
+	use Math::BigInt qw();
+	# the pack dance is to get plain old NVs out of the
+	# Math::BigInt objects.
+	my $inf = unpack 'd', pack 'd', Math::BigInt->binf();
+	my $nan = unpack 'd', pack 'd', Math::BigInt->bnan();
+	batch('float',
+	  -(2 - 2 ** -23) * 2 ** 127,
+	  -1, -2 ** -149, 0, 2 ** -149, 1,
+	  (2 - 2 ** -23) * 2 ** 127,
+	  $nan);
+	{ local $TODO = "float typemaps don't pass infinity";
+	  # it seems as though SWIG is unwilling to pass infinity around
+	  # because that value always fails bounds checking.  I think that
+	  # is a bug.
+	  batch('float', $inf);
+	}
+	batch('double',
+	  -(2 - 2 ** -53) ** 1023,
+	  -1, -2 ** -1074, 0, 2 ** 1074,
+	  (2 - 2 ** -53) ** 1023,
+	  $nan, $inf);
 }
-batch('double',
-  -(2 - 2 ** -53) ** 1023,
-  -1, -2 ** -1074, 0, 2 ** 1074,
-  (2 - 2 ** -53) ** 1023,
-  'nan', 'inf');
 batch('longlong', -1, 0, 1, 12);
 batch('ulonglong', 0, 1, 12);
 SKIP: {
diff --git a/Examples/test-suite/perl5/run-perl-test.pl b/Examples/test-suite/perl5/run-perl-test.pl
index f0e1b0288..106bf002b 100755
--- a/Examples/test-suite/perl5/run-perl-test.pl
+++ b/Examples/test-suite/perl5/run-perl-test.pl
@@ -7,7 +7,7 @@ use strict;
 
 my $command = shift @ARGV;
 
-my $output = `perl $command 2>&1`;
+my $output = `$^X $command 2>&1`;
 
 die "SWIG Perl test failed: \n\n$output\n"
   if $?;
diff --git a/Examples/test-suite/php4/Makefile.in b/Examples/test-suite/php4/Makefile.in
index dbd239964..2e14ef9a2 100644
--- a/Examples/test-suite/php4/Makefile.in
+++ b/Examples/test-suite/php4/Makefile.in
@@ -42,17 +42,17 @@ missingtests: missingcpptests missingctests
 %.cpptest: 
 	$(setup)
 	+$(swig_and_compile_cpp)
-	$(run_testcase)
+	+$(run_testcase)
 
 %.ctest:
 	$(setup)
 	+$(swig_and_compile_c)
-	$(run_testcase)
+	+$(run_testcase)
 
 %.multicpptest: 
 	$(setup)
 	+$(swig_and_compile_multi_cpp)
-	$(run_testcase)
+	+$(run_testcase)
 
 # Runs the testcase. A testcase is only run if
 # a file is found which has _runme.php4 appended after the testcase name.
diff --git a/Examples/test-suite/php4/tests.php4 b/Examples/test-suite/php4/tests.php4
index ae43398df..36e9f4163 100644
--- a/Examples/test-suite/php4/tests.php4
+++ b/Examples/test-suite/php4/tests.php4
@@ -67,7 +67,7 @@ class check {
   }
 
   function classname($string,$object) {
-    if ($string!=($classname=get_class($object))) return check::fail("Object: $object is of class %s not class %s",$classname,$string);
+    if (strtolower($string)!=strtolower($classname=get_class($object))) return check::fail("Object: \$object is of class %s not class %s",$classname,$string);
     return TRUE;
   }
 
diff --git a/Examples/test-suite/pure_virtual.i b/Examples/test-suite/pure_virtual.i
index b41e48a89..aab9741a9 100644
--- a/Examples/test-suite/pure_virtual.i
+++ b/Examples/test-suite/pure_virtual.i
@@ -9,7 +9,7 @@
 
 %warnfilter(SWIGWARN_JAVA_MULTIPLE_INHERITANCE,
 	    SWIGWARN_CSHARP_MULTIPLE_INHERITANCE,
-	    SWIGWARN_PHP4_MULTIPLE_INHERITANCE) E; /* C#, Java, Php4 multiple inheritance */
+	    SWIGWARN_PHP_MULTIPLE_INHERITANCE) E; /* C#, Java, PHP multiple inheritance */
 
 %nodefaultctor C;
 %nodefaultdtor C;
diff --git a/Examples/test-suite/python/Makefile.in b/Examples/test-suite/python/Makefile.in
index 7f11cd495..a3a027453 100644
--- a/Examples/test-suite/python/Makefile.in
+++ b/Examples/test-suite/python/Makefile.in
@@ -2,14 +2,41 @@
 # Makefile for python test-suite
 #######################################################################
 
+ifeq (,$(PY3))
+  PYBIN = @PYTHON@
+else
+  PYBIN = @PYTHON3@
+endif
+
 LANGUAGE     = python
-PYTHON       = @PYTHON@
-SCRIPTSUFFIX = _runme.py
+ifneq (,$(USE_VALGRIND))
+  PYTHON       = valgrind --leak-check=full --suppressions=pyswig.supp $(PYBIN)
+else
+  PYTHON       = $(PYBIN)
+endif
+
+#*_runme.py for Python 2.x, *_runme3.py for Python 3.x
+PY2SCRIPTSUFFIX = _runme.py
+PY3SCRIPTSUFFIX = _runme3.py
+
+ifeq (,$(PY3))
+  SCRIPTSUFFIX = $(PY2SCRIPTSUFFIX)
+else
+  SCRIPTSUFFIX = $(PY3SCRIPTSUFFIX)
+endif
+
 srcdir       = @srcdir@
 top_srcdir   = @top_srcdir@
 top_builddir = @top_builddir@
 
+
+#Use the tricky command because we want to disable the "import" fixer,
+#but currently 2to3 has no option to let us do it
+PY2TO3 = 2to3 `2to3 -l | grep -v -E "Available|import$$" | awk '{print "-f "$$0}'`
+
+
 CPP_TEST_CASES += \
+        abstractbase \
 	argcargvtest \
 	autodoc \
 	callback \
@@ -77,12 +104,35 @@ VALGRIND_OPT += --suppressions=pythonswig.supp
 	+$(swig_and_compile_multi_cpp)
 	$(run_testcase)
 
+
+# Call 2to3 to generate Python 3.x test from the Python 2.x's *_runme.py file
+%$(PY3SCRIPTSUFFIX): %$(PY2SCRIPTSUFFIX)
+	cp $< $@
+	$(PY2TO3) -w $@ >/dev/null 2>&1 
+
+
 # Runs the testcase. A testcase is only run if
-# a file is found which has _runme.py appended after the testcase name.
+# a file is found which has _runme.py (or _runme3.py for Python 3) appended after the testcase name.
+
+run_python = env LD_LIBRARY_PATH=.:$$LD_LIBRARY_PATH PYTHONPATH=$(srcdir):$$PYTHONPATH $(RUNTOOL) $(PYTHON) $(srcdir)/$(SCRIPTPREFIX)$*$(SCRIPTSUFFIX)
+
+ifeq (,$(PY3))
 run_testcase = \
 	if [ -f $(srcdir)/$(SCRIPTPREFIX)$*$(SCRIPTSUFFIX) ]; then (	  \
-	  env LD_LIBRARY_PATH=.:$$LD_LIBRARY_PATH PYTHONPATH=$(srcdir):$$PYTHONPATH $(RUNTOOL) $(PYTHON) $(srcdir)/$(SCRIPTPREFIX)$*$(SCRIPTSUFFIX);) \
+	  $(run_python);)\
 	fi;
+else
+py2_runme = $(srcdir)/$(SCRIPTPREFIX)$*$(PY2SCRIPTSUFFIX)
+py3_runme = $(srcdir)/$(SCRIPTPREFIX)$*$(PY3SCRIPTSUFFIX) 
+
+run_testcase = \
+	if [ -f $(py2_runme) ]; then (	  \
+	  $(MAKE) -f $(srcdir)/Makefile $(py3_runme) && \
+	   $(run_python);) \
+        elif [ -f $(py3_runme)]; then (   \
+          $(run_python);)  \
+	fi;
+endif
 
 # Clean: remove the generated .py file
 %.clean:
@@ -101,14 +151,15 @@ cvsignore:
 	@echo clientdata_prop_b.py 
 	@echo imports_a.py 
 	@echo imports_b.py 
-	@echo mod_a.py mod_b.py 
+	@echo mod_a.py mod_b.py
 	@echo hugemod.h hugemod_a.i hugemod_b.i hugemod_a.py hugemod_b.py hugemod_runme.py
 	@echo template_typedef_import.py
 
+hugemod_runme = hugemod$(SCRIPTPREFIX)
 
 hugemod:
-	perl hugemod.pl
+	perl hugemod.pl $(hugemod_runme) 
 	$(MAKE) hugemod_a.cpptest
 	$(MAKE) hugemod_b.cpptest
-	time $(PYTHON) hugemod_runme.py
-	time $(PYTHON) hugemod_runme.py
+	sh -c "time $(PYTHON) $(hugemod_runme)"
+	sh -c "time $(PYTHON) $(hugemod_runme)"
diff --git a/Examples/test-suite/python/README b/Examples/test-suite/python/README
index b86ec5289..71db759b5 100644
--- a/Examples/test-suite/python/README
+++ b/Examples/test-suite/python/README
@@ -1,4 +1,8 @@
 See ../README for common README file.
 
-Any testcases which have _runme.py appended after the testcase name will be detected and run.
+Any testcases which have _runme.py (or _runme3.py for Python 3) appended after the testcase name will be detected and run.
 
+If you intend to write a testcase for both Python 2.x and 3.x, do *not* directly put the _runme3.py in this directory. Just write Python 2.x's _runme.py testcase and it will be automatically converted to Python 3 code during test.
+
+You can run make with PY3=y to run test case with Python 3.x, eg.
+  $ make voidtest.cpptest PY3=y
diff --git a/Examples/test-suite/python/abstractbase.i b/Examples/test-suite/python/abstractbase.i
new file mode 100644
index 000000000..530f21921
--- /dev/null
+++ b/Examples/test-suite/python/abstractbase.i
@@ -0,0 +1,18 @@
+%module abstractbase
+%include <pyabc.i>
+%include <std_map.i>
+%include <std_multimap.i>
+%include <std_set.i>
+%include <std_multiset.i>
+%include <std_list.i>
+%include <std_vector.i>
+
+namespace std
+{
+  %template(Mapii) map<int, int>;
+  %template(Multimapii) multimap<int, int>;
+  %template(IntSet) set<int>;
+  %template(IntMultiset) multiset<int>;
+  %template(IntVector) vector<int>;
+  %template(IntList) list<int>;
+}
diff --git a/Examples/test-suite/python/abstractbase_runme3.py b/Examples/test-suite/python/abstractbase_runme3.py
new file mode 100644
index 000000000..13a87ee5e
--- /dev/null
+++ b/Examples/test-suite/python/abstractbase_runme3.py
@@ -0,0 +1,8 @@
+from abstractbase import *
+from collections import *
+assert issubclass(Mapii, MutableMapping)
+assert issubclass(Multimapii, MutableMapping)
+assert issubclass(IntSet, MutableSet)
+assert issubclass(IntMultiset, MutableSet)
+assert issubclass(IntVector, MutableSequence)
+assert issubclass(IntList, MutableSequence)
diff --git a/Examples/test-suite/python/cpp_namespace_runme.py b/Examples/test-suite/python/cpp_namespace_runme.py
index 3108b4f47..a454774f5 100644
--- a/Examples/test-suite/python/cpp_namespace_runme.py
+++ b/Examples/test-suite/python/cpp_namespace_runme.py
@@ -3,20 +3,20 @@ import cpp_namespace
 
 n = cpp_namespace.fact(4)
 if n != 24:
-    raise "Bad return value!"
+    raise RuntimeError("Bad return value!")
 
 if cpp_namespace.cvar.Foo != 42:
-    raise "Bad variable value!"
+    raise RuntimeError("Bad variable value!")
 
 t = cpp_namespace.Test()
 if t.method() != "Test::method":
-    raise "Bad method return value!"
+    raise RuntimeError("Bad method return value!")
 
 if cpp_namespace.do_method(t) != "Test::method":
-    raise "Bad return value!"
+    raise RuntimeError("Bad return value!")
 
 if cpp_namespace.do_method2(t) != "Test::method":
-    raise "Bad return value!"
+    raise RuntimeError("Bad return value!")
     
 cpp_namespace.weird("hello", 4)
 
@@ -28,18 +28,18 @@ t4 = cpp_namespace.Test4()
 t5 = cpp_namespace.Test5()
 
 if cpp_namespace.foo3(42) != 42:
-    raise "Bad return value!"
+    raise RuntimeError("Bad return value!")
 
 if cpp_namespace.do_method3(t2,40) != "Test2::method":
-    raise "Bad return value!"
+    raise RuntimeError("Bad return value!")
 
 if cpp_namespace.do_method3(t3,40) != "Test3::method":
-    raise "Bad return value!"
+    raise RuntimeError("Bad return value!")
 
 if cpp_namespace.do_method3(t4,40) != "Test4::method":
-    raise "Bad return value!"
+    raise RuntimeError("Bad return value!")
 
 if cpp_namespace.do_method3(t5,40) != "Test5::method":
-    raise "Bad return value!"
+    raise RuntimeError("Bad return value!")
 
     
diff --git a/Examples/test-suite/python/director_classic_runme.py b/Examples/test-suite/python/director_classic_runme.py
index 878905679..7e18a9a61 100644
--- a/Examples/test-suite/python/director_classic_runme.py
+++ b/Examples/test-suite/python/director_classic_runme.py
@@ -1,56 +1,56 @@
 from director_classic import *
 
 class TargetLangPerson(Person):
-	def __init__(self):
-		Person.__init__(self)
-	def id(self):
-		identifier = "TargetLangPerson"
-                return identifier
+    def __init__(self):
+        Person.__init__(self)
+    def id(self):
+        identifier = "TargetLangPerson"
+        return identifier
 
 class TargetLangChild(Child):
-	def __init__(self):
-		Child.__init__(self)
-	def id(self):
-		identifier = "TargetLangChild"
-                return identifier
+    def __init__(self):
+        Child.__init__(self)
+    def id(self):
+        identifier = "TargetLangChild"
+        return identifier
 
 class TargetLangGrandChild(GrandChild):
-	def __init__(self):
-		GrandChild.__init__(self)
-	def id(self):
-		identifier = "TargetLangGrandChild"
-                return identifier
+    def __init__(self):
+        GrandChild.__init__(self)
+    def id(self):
+        identifier = "TargetLangGrandChild"
+        return identifier
 
 # Semis - don't override id() in target language
 class TargetLangSemiPerson(Person):
-	def __init__(self):
-		Person.__init__(self)
+    def __init__(self):
+        Person.__init__(self)
         # No id() override
 
 class TargetLangSemiChild(Child):
-	def __init__(self):
-		Child.__init__(self)
+    def __init__(self):
+        Child.__init__(self)
         # No id() override
 
 class TargetLangSemiGrandChild(GrandChild):
-	def __init__(self):
-		GrandChild.__init__(self)
+    def __init__(self):
+        GrandChild.__init__(self)
         # No id() override
 
 # Orphans - don't override id() in C++
 class TargetLangOrphanPerson(OrphanPerson):
-	def __init__(self):
-		OrphanPerson.__init__(self)
-	def id(self):
-		identifier = "TargetLangOrphanPerson"
-                return identifier
+    def __init__(self):
+        OrphanPerson.__init__(self)
+    def id(self):
+        identifier = "TargetLangOrphanPerson"
+        return identifier
 
 class TargetLangOrphanChild(OrphanChild):
-	def __init__(self):
-		Child.__init__(self)
-	def id(self):
-		identifier = "TargetLangOrphanChild"
-                return identifier
+    def __init__(self):
+        Child.__init__(self)
+    def id(self):
+        identifier = "TargetLangOrphanChild"
+        return identifier
 
 
 def check(person, expected):
@@ -61,7 +61,7 @@ def check(person, expected):
   if (debug):
     print(ret)
   if (ret != expected):
-    raise ("Failed. Received: " + ret + " Expected: " + expected)
+    raise RuntimeError("Failed. Received: " + str(ret) + " Expected: " + expected)
 
   # Polymorphic call from C++
   caller = Caller()
@@ -70,7 +70,7 @@ def check(person, expected):
   if (debug):
     print(ret)
   if (ret != expected):
-    raise ("Failed. Received: " + ret + " Expected: " + expected)
+    raise RuntimeError("Failed. Received: " + str(ret) + " Expected: " + expected)
 
   # Polymorphic call of object created in target language and passed to C++ and back again
   baseclass = caller.baseClass()
@@ -78,7 +78,7 @@ def check(person, expected):
   if (debug):
     print(ret)
   if (ret != expected):
-    raise ("Failed. Received: " + ret + " Expected: " + expected)
+    raise RuntimeError("Failed. Received: " + str(ret)+ " Expected: " + expected)
 
   caller.resetCallback()
   if (debug):
diff --git a/Examples/test-suite/python/director_exception_runme.py b/Examples/test-suite/python/director_exception_runme.py
index 7c9e69250..ef7a044f1 100644
--- a/Examples/test-suite/python/director_exception_runme.py
+++ b/Examples/test-suite/python/director_exception_runme.py
@@ -1,5 +1,8 @@
 from director_exception import *
-from exceptions import *
+
+class MyException(Exception):
+	def __init__(self, a, b):
+		self.msg = a + b
 
 class MyFoo(Foo):
 	def ping(self):
@@ -7,39 +10,62 @@ class MyFoo(Foo):
 
 class MyFoo2(Foo):
 	def ping(self):
-		return true
+		return True
 		pass # error: should return a string
 
-ok = 0
+class MyFoo3(Foo):
+	def ping(self):
+		raise MyException("foo", "bar")
 
+# Check that the NotImplementedError raised by MyFoo.ping() is returned by
+# MyFoo.pong().
+ok = 0
 a = MyFoo()
 b = launder(a)
-
 try:
 	b.pong()
 except NotImplementedError, e:
-	ok = 1
+	if str(e) == "MyFoo::ping() EXCEPTION":
+		ok = 1
+	else:
+		print "Unexpected error message: %s" % str(e)
 except:
 	pass
-
 if not ok:
 	raise RuntimeError
 
-ok = 0
 
+# Check that the director returns the appropriate TypeError if the return type
+# is wrong.
+ok = 0
 a = MyFoo2()
 b = launder(a)
-
 try:
 	b.pong()
-except:
-	ok = 1
-
-
+except TypeError, e:
+	if str(e) == "Swig director type mismatch in output value of type 'std::string'":
+		ok = 1
+	else:
+		print "Unexpected error message: %s" % str(e)
 if not ok:
 	raise RuntimeError
 
 
+# Check that the director can return an exception which requires two arguments
+# to the constructor, without mangling it.
+ok = 0
+a = MyFoo3()
+b = launder(a)
+try:
+	b.pong()
+except MyException, e:
+	if e.msg == 'foobar':
+		ok = 1
+	else:
+		print "Unexpected error message: %s" % str(e)
+if not ok:
+	raise RuntimeError
+
 try:
 	raise Exception2()
 except Exception2:
diff --git a/Examples/test-suite/python/file_test_runme.py b/Examples/test-suite/python/file_test_runme.py
index 64154c619..de4e2669e 100644
--- a/Examples/test-suite/python/file_test_runme.py
+++ b/Examples/test-suite/python/file_test_runme.py
@@ -1,7 +1,8 @@
 import sys
 import file_test
 
-file_test.nfile(sys.stdout)
+if sys.version_info < (3,0):
+  file_test.nfile(sys.stdout)
 
 cstdout = file_test.GetStdOut()
 
diff --git a/Examples/test-suite/python/fvirtual_runme.py b/Examples/test-suite/python/fvirtual_runme.py
index e06ab5b4f..ada3313de 100644
--- a/Examples/test-suite/python/fvirtual_runme.py
+++ b/Examples/test-suite/python/fvirtual_runme.py
@@ -1,6 +1,6 @@
 from fvirtual import *
 
-sw = Switch()
+sw = NodeSwitch()
 n = Node()
 i = sw.addChild(n);
 
diff --git a/Examples/test-suite/python/hugemod.pl b/Examples/test-suite/python/hugemod.pl
index 15c4ce41b..5420926e4 100644
--- a/Examples/test-suite/python/hugemod.pl
+++ b/Examples/test-suite/python/hugemod.pl
@@ -2,8 +2,12 @@
 
 use strict;
 
+my $modsize = 399; #adjust it so you can have a smaller or bigger hugemod 
+
+my $runme = shift @ARGV;
+
 open HEADER, ">hugemod.h" or die "error";
-open TEST, ">hugemod_runme.py" or die "error";
+open TEST, ">$runme" or die "error";
 open I1, ">hugemod_a.i" or die "error";
 open I2, ">hugemod_b.i" or die "error";
 
@@ -21,7 +25,7 @@ print I2 "\%inline \%{\n";
 
 my $i;
 
-for ($i = 0; $i < 6000; $i++) {
+for ($i = 0; $i < $modsize; $i++) {
   my $t = $i * 4;
   print HEADER "class type$i { public: int a; };\n";
   print I2 "class dtype$i : public type$i { public: int b; };\n";
diff --git a/Examples/test-suite/python/keyword_rename_runme.py b/Examples/test-suite/python/keyword_rename_runme.py
new file mode 100644
index 000000000..5646ce7d6
--- /dev/null
+++ b/Examples/test-suite/python/keyword_rename_runme.py
@@ -0,0 +1,4 @@
+#!/usr/bin/env python
+import keyword_rename
+keyword_rename._in(1)
+keyword_rename._except(1)
diff --git a/Examples/test-suite/python/li_std_string_runme.py b/Examples/test-suite/python/li_std_string_runme.py
index ed79718d2..c0dae1e25 100644
--- a/Examples/test-suite/python/li_std_string_runme.py
+++ b/Examples/test-suite/python/li_std_string_runme.py
@@ -121,7 +121,7 @@ if s != "hellohello":
   raise RuntimeError
 
 
-if li_std_string.empty() != "":
+if li_std_string.stdstring_empty() != "":
   raise RuntimeError
   
 
diff --git a/Examples/test-suite/python/operbool_runme.py b/Examples/test-suite/python/operbool_runme.py
new file mode 100644
index 000000000..4218b5dd4
--- /dev/null
+++ b/Examples/test-suite/python/operbool_runme.py
@@ -0,0 +1,4 @@
+#!/usr/bin/env python
+import operbool
+assert not operbool.Test()
+
diff --git a/Examples/test-suite/python/pybuf.i b/Examples/test-suite/python/pybuf.i
new file mode 100644
index 000000000..207b5b7e9
--- /dev/null
+++ b/Examples/test-suite/python/pybuf.i
@@ -0,0 +1,34 @@
+%module pybuf
+%include<pybuffer.i>
+
+%pybuffer_mutable_binary(char *buf1, int len);
+%pybuffer_mutable_string(char *buf2);
+%pybuffer_binary(const char *buf3, int len);
+%pybuffer_string(const char *buf4);
+
+%inline %{
+  void func1(char *buf1, int len)
+  {
+    int i;
+    for (i=0; i<len; ++i)
+      buf1[i] = 'a';
+    return;
+  }
+  void func2(char *buf2)
+  {
+    strcpy(buf2, "Hello world!");
+  }
+  int func3(const char *buf3, int len)
+  {
+    int count = 0;
+    int i;
+    for(i=0; i<len; ++i)
+      if (isalnum(buf3[i]))
+        ++count;
+    return count;
+  }
+  int func4(const char *buf4)
+  {
+    return strlen(buf4);
+  }  
+%}
diff --git a/Examples/test-suite/python/pybuf_benchmark.i b/Examples/test-suite/python/pybuf_benchmark.i
new file mode 100644
index 000000000..8a793f906
--- /dev/null
+++ b/Examples/test-suite/python/pybuf_benchmark.i
@@ -0,0 +1,31 @@
+%module pybuf_benchmark
+
+%include<pybuffer.i>
+%include<cstring.i>
+%pybuffer_mutable_string(char *str1);
+%cstring_mutable(char *str2);
+
+%inline %{
+void title(char *str) {
+    int outword = 0;
+    while(*str) {
+        if (isalnum(*str)) {
+            if (outword) {
+                outword = 1;
+                *str = toupper(*str);
+            }            
+        }
+        else {
+            outword = 0;
+        }
+        str++;
+    }
+}
+
+void title1(char *str1) {
+    title(str1);
+}
+void title2(char *str2) {
+    title(str2);
+}
+%}
diff --git a/Examples/test-suite/python/pybuf_benchmark_runme.py b/Examples/test-suite/python/pybuf_benchmark_runme.py
new file mode 100644
index 000000000..6676a910b
--- /dev/null
+++ b/Examples/test-suite/python/pybuf_benchmark_runme.py
@@ -0,0 +1,16 @@
+import pybuf
+import time
+k=1000000
+n=7
+
+t=time.time()
+a = bytearray(b'hello world')
+for i in range(k):
+  pybuf.title1(a)
+print "Time used by bytearray:",time.time()-t
+
+t=time.time()
+b = 'hello world'
+for i in range(k):
+  pybuf.title2(b)
+print "Time used by string:",time.time()-t
diff --git a/Examples/test-suite/python/pybuf_benchmark_runme3.py b/Examples/test-suite/python/pybuf_benchmark_runme3.py
new file mode 100644
index 000000000..e412d5993
--- /dev/null
+++ b/Examples/test-suite/python/pybuf_benchmark_runme3.py
@@ -0,0 +1,16 @@
+import pybuf
+import time
+k=1000000
+n=7
+
+t=time.time()
+a = bytearray(b'hello world')
+for i in range(k):
+  pybuf.title1(a)
+print("Time used by bytearray:",time.time()-t)
+
+t=time.time()
+b = 'hello world'
+for i in range(k):
+  pybuf.title2(b)
+print("Time used by string:",time.time()-t)
diff --git a/Examples/test-suite/python/pybuf_runme3.py b/Examples/test-suite/python/pybuf_runme3.py
new file mode 100644
index 000000000..462736bf0
--- /dev/null
+++ b/Examples/test-suite/python/pybuf_runme3.py
@@ -0,0 +1,15 @@
+import pybuf
+buf1 = bytearray(10)
+buf2 = bytearray(50)
+
+pybuf.func1(buf1)
+assert buf1 == b'a'*10
+
+pybuf.func2(buf2)
+assert buf2.startswith(b"Hello world!\x00")
+
+count = pybuf.func3(buf2)
+assert count==10 #number of alpha and number in 'Hello world!'
+
+length = pybuf.func4(buf2)
+assert length==12
diff --git a/Examples/test-suite/python/template_typedef_cplx2_runme.py b/Examples/test-suite/python/template_typedef_cplx2_runme.py
index 030fe02d8..04c599329 100644
--- a/Examples/test-suite/python/template_typedef_cplx2_runme.py
+++ b/Examples/test-suite/python/template_typedef_cplx2_runme.py
@@ -1,4 +1,3 @@
-import string
 from template_typedef_cplx2 import *
 
 #
@@ -13,7 +12,7 @@ except:
   raise RuntimeError
 
 s = '%s' % d
-if string.find(s, 'ArithUnaryFunction') == -1:
+if str.find(s, 'ArithUnaryFunction') == -1:
   print d, "is not an ArithUnaryFunction"
   raise RuntimeError
 
@@ -25,7 +24,7 @@ except:
   raise RuntimeError
 
 s = '%s' % e
-if string.find(s, 'ArithUnaryFunction') == -1:
+if str.find(s, 'ArithUnaryFunction') == -1:
   print e, "is not an ArithUnaryFunction"
   raise RuntimeError
 
@@ -42,7 +41,7 @@ except:
   raise RuntimeError
 
 s = '%s' % c
-if string.find(s, 'ArithUnaryFunction') == -1:
+if str.find(s, 'ArithUnaryFunction') == -1:
   print c, "is not an ArithUnaryFunction"
   raise RuntimeError
 
@@ -54,7 +53,7 @@ except:
   raise RuntimeError
 
 s = '%s' % f
-if string.find(s, 'ArithUnaryFunction') == -1:
+if str.find(s, 'ArithUnaryFunction') == -1:
   print f, "is not an ArithUnaryFunction"
   raise RuntimeError
 
@@ -70,7 +69,7 @@ except:
   raise RuntimeError
 
 s = '%s' % g
-if string.find(s, 'ArithUnaryFunction') == -1:
+if str.find(s, 'ArithUnaryFunction') == -1:
   print g, "is not an ArithUnaryFunction"
   raise RuntimeError
 
@@ -83,7 +82,7 @@ except:
   raise RuntimeError
 
 s = '%s' % h
-if string.find(s, 'ArithUnaryFunction') == -1:
+if str.find(s, 'ArithUnaryFunction') == -1:
   print h, "is not an ArithUnaryFunction"
   raise RuntimeError
 
diff --git a/Examples/test-suite/python/template_typedef_cplx_runme.py b/Examples/test-suite/python/template_typedef_cplx_runme.py
index 99ffcb9aa..2cd9c8348 100644
--- a/Examples/test-suite/python/template_typedef_cplx_runme.py
+++ b/Examples/test-suite/python/template_typedef_cplx_runme.py
@@ -1,4 +1,3 @@
-import string
 from template_typedef_cplx import *
 
 #
@@ -13,7 +12,7 @@ except:
   raise RuntimeError
 
 s = '%s' % d
-if string.find(s, 'ArithUnaryFunction') == -1:
+if str.find(s, 'ArithUnaryFunction') == -1:
   print d, "is not an ArithUnaryFunction"
   raise RuntimeError
 
@@ -25,7 +24,7 @@ except:
   raise RuntimeError
 
 s = '%s' % e
-if string.find(s, 'ArithUnaryFunction') == -1:
+if str.find(s, 'ArithUnaryFunction') == -1:
   print e, "is not an ArithUnaryFunction"
   raise RuntimeError
 
@@ -42,7 +41,7 @@ except:
   raise RuntimeError
 
 s = '%s' % c
-if string.find(s, 'ArithUnaryFunction') == -1:
+if str.find(s, 'ArithUnaryFunction') == -1:
   print c, "is not an ArithUnaryFunction"
   raise RuntimeError
 
@@ -54,7 +53,7 @@ except:
   raise RuntimeError
 
 s = '%s' % f
-if string.find(s, 'ArithUnaryFunction') == -1:
+if str.find(s, 'ArithUnaryFunction') == -1:
   print f, "is not an ArithUnaryFunction"
   raise RuntimeError
 
@@ -70,7 +69,7 @@ except:
   raise RuntimeError
 
 s = '%s' % g
-if string.find(s, 'ArithUnaryFunction') == -1:
+if str.find(s, 'ArithUnaryFunction') == -1:
   print g, "is not an ArithUnaryFunction"
   raise RuntimeError
 
@@ -83,6 +82,6 @@ except:
   raise RuntimeError
 
 s = '%s' % h
-if string.find(s, 'ArithUnaryFunction') == -1:
+if str.find(s, 'ArithUnaryFunction') == -1:
   print h, "is not an ArithUnaryFunction"
   raise RuntimeError
diff --git a/Examples/test-suite/r/Makefile.in b/Examples/test-suite/r/Makefile.in
index 0a1b3567e..70dd62ec5 100644
--- a/Examples/test-suite/r/Makefile.in
+++ b/Examples/test-suite/r/Makefile.in
@@ -42,7 +42,7 @@ run_testcase = \
 	  env LD_LIBRARY_PATH=.:$$LD_LIBRARY_PATH PATH=.:"$$PATH" \
                $(RUNTOOL) $(RUNR) $(srcdir)/$(SCRIPTPREFIX)$*$(SCRIPTSUFFIX) ;) \
 	else \
-	  ($(RUNR) $(srcdir)/$(SCRIPTPREFIX)$*$(WRAPSUFFIX);) \
+	  ($(RUNTOOL) $(RUNR) $(srcdir)/$(SCRIPTPREFIX)$*$(WRAPSUFFIX);) \
 	fi;
 
 run_multitestcase = \
@@ -51,7 +51,7 @@ run_multitestcase = \
 	  env LD_LIBRARY_PATH=.:$$LD_LIBRARY_PATH PATH=.:"$$PATH" \
                $(RUNTOOL) $(RUNR) $(srcdir)/$(SCRIPTPREFIX)$${f}$(SCRIPTSUFFIX) ;) \
 	else \
-	  ($(RUNR) $(srcdir)/$(SCRIPTPREFIX)$${f}$(WRAPSUFFIX);) \
+	  ($(RUNTOOL) $(RUNR) $(srcdir)/$(SCRIPTPREFIX)$${f}$(WRAPSUFFIX);) \
 	fi; \
 	done
 # Clean
diff --git a/Examples/test-suite/ruby/li_std_string_runme.rb b/Examples/test-suite/ruby/li_std_string_runme.rb
index f572573bc..dc85b5dab 100644
--- a/Examples/test-suite/ruby/li_std_string_runme.rb
+++ b/Examples/test-suite/ruby/li_std_string_runme.rb
@@ -124,7 +124,7 @@ if (s != "hellohello")
 end
 
 
-if (empty() != "")
+if (stdstring_empty() != "")
   raise RuntimeError
 end
 
diff --git a/Examples/test-suite/samename.i b/Examples/test-suite/samename.i
index 1e9645e70..819cb4abd 100644
--- a/Examples/test-suite/samename.i
+++ b/Examples/test-suite/samename.i
@@ -1,6 +1,15 @@
 %module samename
 
-%inline {
+#if !(defined(SWIGCSHARP) || defined(SWIGJAVA))
+class samename {
+ public:
+  void do_something() {
+    // ...
+  }
+};
+#endif
+
+%{
 
 class samename {
  public:
@@ -9,5 +18,5 @@ class samename {
   }
 };
 
-}
+%}
 
diff --git a/Examples/test-suite/template_inherit_abstract.i b/Examples/test-suite/template_inherit_abstract.i
index f676b3b3e..89d983de0 100644
--- a/Examples/test-suite/template_inherit_abstract.i
+++ b/Examples/test-suite/template_inherit_abstract.i
@@ -4,7 +4,7 @@
 
 %warnfilter(SWIGWARN_JAVA_MULTIPLE_INHERITANCE,
 	    SWIGWARN_CSHARP_MULTIPLE_INHERITANCE,
-	    SWIGWARN_PHP4_MULTIPLE_INHERITANCE) oss::Module;	/* C#, Java, Php4 multiple inheritance */
+	    SWIGWARN_PHP_MULTIPLE_INHERITANCE) oss::Module;	/* C#, Java, PHP multiple inheritance */
 
 %inline %{ 
  
diff --git a/Examples/test-suite/template_int_const.i b/Examples/test-suite/template_int_const.i
index 37b1cf998..e69a53c4f 100644
--- a/Examples/test-suite/template_int_const.i
+++ b/Examples/test-suite/template_int_const.i
@@ -10,7 +10,7 @@
     static const Polarization polarization = UnaryPolarization; 
   }; 
   template <Polarization P> 
-    struct Interface 
+    struct Interface_
     { 
     }; 
  
@@ -26,16 +26,16 @@
     }; 
 %} 
  
-%template(Interface_UP) Interface<UnaryPolarization>; 
+%template(Interface_UP) Interface_<UnaryPolarization>; 
 %template(Module_1) Module<1>; 
  
 %inline %{ 
   struct ExtInterface1 :  
-    Interface<UnaryPolarization> // works 
+    Interface_<UnaryPolarization> // works 
   { 
   }; 
   struct ExtInterface2 : 
-    Interface<interface_traits::polarization>  // doesn't work 
+    Interface_<interface_traits::polarization>  // doesn't work 
   { 
   }; 
   struct ExtModule1 : 
diff --git a/Examples/test-suite/template_typedef_rec.i b/Examples/test-suite/template_typedef_rec.i
index 83fe2104a..abdf11382 100644
--- a/Examples/test-suite/template_typedef_rec.i
+++ b/Examples/test-suite/template_typedef_rec.i
@@ -16,7 +16,7 @@ public:
 
 
 template <typename T>
-class ArrayIterator
+class ArrayIterator_
 {
  public:
   typedef test_Array::intT    intT;
@@ -38,8 +38,8 @@ class ArrayPrimitiveT
 public:
   typedef T  ValueT;
   typedef T  valueT;
-  typedef ArrayIterator<T>       Iterator;
-  typedef ArrayIterator<const T> ConstIterator;  
+  typedef ArrayIterator_<T>       Iterator;
+  typedef ArrayIterator_<const T> ConstIterator;  
   typedef ArrayReverseIterator<T>       ReverseIterator;
   typedef ArrayReverseIterator<const T> ConstReverseIterator;
 };
diff --git a/Examples/test-suite/typemap_namespace.i b/Examples/test-suite/typemap_namespace.i
index d30a4ddb1..5375c43b6 100644
--- a/Examples/test-suite/typemap_namespace.i
+++ b/Examples/test-suite/typemap_namespace.i
@@ -27,7 +27,7 @@ namespace Foo {
     %typemap(javaout) Str1 * = char *;
 #endif
     %typemap(in) Str1 * = char *;
-#if !(defined(SWIGCSHARP) || defined(SWIGLUA))
+#if !(defined(SWIGCSHARP) || defined(SWIGLUA) || defined(SWIGPHP))
     %typemap(freearg) Str1 * = char *;
 #endif
     %typemap(typecheck) Str1 * = char *;
diff --git a/Examples/test-suite/using_composition.i b/Examples/test-suite/using_composition.i
index 7bb6add2a..bd0f712b5 100644
--- a/Examples/test-suite/using_composition.i
+++ b/Examples/test-suite/using_composition.i
@@ -2,13 +2,13 @@
 
 %warnfilter(SWIGWARN_JAVA_MULTIPLE_INHERITANCE,
 	    SWIGWARN_CSHARP_MULTIPLE_INHERITANCE,
-	    SWIGWARN_PHP4_MULTIPLE_INHERITANCE) FooBar;   // C#, Java, Php4 multiple inheritance
+	    SWIGWARN_PHP_MULTIPLE_INHERITANCE) FooBar;   // C#, Java, PHP multiple inheritance
 %warnfilter(SWIGWARN_JAVA_MULTIPLE_INHERITANCE,
 	    SWIGWARN_CSHARP_MULTIPLE_INHERITANCE,
-	    SWIGWARN_PHP4_MULTIPLE_INHERITANCE) FooBar2;   // C#, Java, Php4 multiple inheritance
+	    SWIGWARN_PHP_MULTIPLE_INHERITANCE) FooBar2;   // C#, Java, PHP multiple inheritance
 %warnfilter(SWIGWARN_JAVA_MULTIPLE_INHERITANCE,
 	    SWIGWARN_CSHARP_MULTIPLE_INHERITANCE,
-	    SWIGWARN_PHP4_MULTIPLE_INHERITANCE) FooBar3;   // C#, Java, Php4 multiple inheritance
+	    SWIGWARN_PHP_MULTIPLE_INHERITANCE) FooBar3;   // C#, Java, PHP multiple inheritance
 #ifdef SWIGLUA	// lua only has one numeric type, so some overloads shadow each other creating warnings
 %warnfilter(SWIGWARN_LANG_OVERLOAD_SHADOW) blah;
 #endif
diff --git a/Examples/test-suite/using_extend.i b/Examples/test-suite/using_extend.i
index 414ceedb4..e14cc28e8 100644
--- a/Examples/test-suite/using_extend.i
+++ b/Examples/test-suite/using_extend.i
@@ -2,7 +2,7 @@
 
 %warnfilter(SWIGWARN_JAVA_MULTIPLE_INHERITANCE,
 	    SWIGWARN_CSHARP_MULTIPLE_INHERITANCE,
-	    SWIGWARN_PHP4_MULTIPLE_INHERITANCE) FooBar;   // C#, Java, Php4 multiple inheritance
+	    SWIGWARN_PHP_MULTIPLE_INHERITANCE) FooBar;   // C#, Java, PHP multiple inheritance
 #ifdef SWIGLUA	// lua only has one numeric type, so some overloads shadow each other creating warnings
 %warnfilter(SWIGWARN_LANG_OVERLOAD_SHADOW) blah;
 #endif
diff --git a/Examples/test-suite/using_namespace.i b/Examples/test-suite/using_namespace.i
index 1989b6a0d..799c7cfb5 100644
--- a/Examples/test-suite/using_namespace.i
+++ b/Examples/test-suite/using_namespace.i
@@ -5,7 +5,7 @@
 
 %warnfilter(SWIGWARN_JAVA_MULTIPLE_INHERITANCE,
 	    SWIGWARN_CSHARP_MULTIPLE_INHERITANCE,
-	    SWIGWARN_PHP4_MULTIPLE_INHERITANCE) Hi<hello::Hello, hi::hi0>; // C#, Java, Php4 multiple inheritance
+	    SWIGWARN_PHP_MULTIPLE_INHERITANCE) Hi<hello::Hello, hi::hi0>; // C#, Java, PHP multiple inheritance
 
 %inline %{
   namespace hello
diff --git a/Lib/allegrocl/allegrocl.swg b/Lib/allegrocl/allegrocl.swg
index 0ae8ed76c..8132e4628 100644
--- a/Lib/allegrocl/allegrocl.swg
+++ b/Lib/allegrocl/allegrocl.swg
@@ -296,15 +296,30 @@ $body)"
 	  sym))))
 
 (cl::defun full-name (id type arity class)
-  (cl::case type
-    (:getter (cl::format nil "~@[~A_~]~A" class id))
-    (:constructor (cl::format nil "new_~A~@[~A~]" id arity))
-    (:destructor (cl::format nil "delete_~A" id))
-    (:type (cl::format nil "ff_~A" id))
-    (:slot id)
-    (:ff-operator (cl::format nil "ffi_~A" id))
-    (otherwise (cl::format nil "~@[~A_~]~A~@[~A~]"
-                       class id arity))))
+  ; We need some kind of a hack here to handle template classes
+  ; and other synonym types right. We need the original name.
+  (let*( (sym (read-symbol-from-string 
+                (if (eq *swig-identifier-converter* 'identifier-convert-lispify)
+                  (string-lispify id)
+                  id)))
+         (sym-class (find-class sym nil))
+         (id (cond ( (not sym-class)
+                     id )
+                   ( (and sym-class
+                          (not (eq (class-name sym-class)
+                                sym)))
+                     (class-name sym-class) )
+                   ( t
+                     id ))) )
+    (cl::case type
+      (:getter (cl::format nil "~@[~A_~]~A" class id))
+      (:constructor (cl::format nil "new_~A~@[~A~]" id arity))
+      (:destructor (cl::format nil "delete_~A" id))
+      (:type (cl::format nil "ff_~A" id))
+      (:slot id)
+      (:ff-operator (cl::format nil "ffi_~A" id))
+      (otherwise (cl::format nil "~@[~A_~]~A~@[~A~]"
+                         class id arity)))))
   
 (cl::defun identifier-convert-null (id &key type class arity)
   (cl::if (cl::eq type :setter)
@@ -312,6 +327,27 @@ $body)"
                id :type :getter :class class :arity arity))
       (read-symbol-from-string (full-name id type arity class))))
 
+(cl::defun string-lispify (str)
+  (cl::let ( (cname (excl::replace-regexp str "_" "-"))
+             (lastcase :other)
+             newcase char res ) 
+    (cl::dotimes (n (cl::length cname))
+      (cl::setf char (cl::schar cname n))
+      (excl::if* (cl::alpha-char-p char)
+         then
+              (cl::setf newcase (cl::if (cl::upper-case-p char) :upper :lower))
+              (cl::when (cl::and (cl::eq lastcase :lower)
+                                 (cl::eq newcase :upper))
+                ;; case change... add a dash
+                (cl::push #\- res)
+                (cl::setf newcase :other))
+              (cl::push (cl::char-downcase char) res)
+              (cl::setf lastcase newcase)
+         else
+              (cl::push char res)
+              (cl::setf lastcase :other)))
+    (cl::coerce (cl::nreverse res) 'string)))
+  
 (cl::defun identifier-convert-lispify (cname &key type class arity)
   (cl::assert (cl::stringp cname))
   (cl::when (cl::eq type :setter)
@@ -321,31 +357,7 @@ $body)"
   (cl::setq cname (full-name cname type arity class))
   (cl::if (cl::eq type :constant)
       (cl::setf cname (cl::format nil "*~A*" cname)))
-  (cl::setf cname (excl::replace-regexp cname "_" "-"))
-  (cl::let ((lastcase :other)
-       	    newcase char res)
-    (cl::dotimes (n (cl::length cname))
-      (cl::setf char (cl::schar cname n))
-      (excl::if* (cl::alpha-char-p char)
-         then
-              (cl::setf newcase (cl::if (cl::upper-case-p char) :upper :lower))
-
-              (cl::when (cl::or (cl::and (cl::eq lastcase :upper)
-	      				 (cl::eq newcase :lower))
-                                (cl::and (cl::eq lastcase :lower)
-					 (cl::eq newcase :upper)))
-                ;; case change... add a dash
-                (cl::push #\- res)
-                (cl::setf newcase :other))
-
-              (cl::push (cl::char-downcase char) res)
-
-              (cl::setf lastcase newcase)
-
-         else
-              (cl::push char res)
-              (cl::setf lastcase :other)))
-    (read-symbol-from-string (cl::coerce (cl::nreverse res) 'string))))
+  (read-symbol-from-string (string-lispify cname)))
 
 (cl::defun id-convert-and-export (name &rest kwargs)
   (cl::multiple-value-bind (symbol package)
diff --git a/Lib/cdata.i b/Lib/cdata.i
index a9e74ed8a..67601f737 100644
--- a/Lib/cdata.i
+++ b/Lib/cdata.i
@@ -29,6 +29,11 @@ typedef struct SWIGCDATA {
   $result = C_string(&string_space, $1.len, $1.data);
 }
 %typemap(in) (const void *indata, int inlen) = (char *STRING, int LENGTH);
+#elif SWIGPHP
+%typemap(out) SWIGCDATA {
+  ZVAL_STRINGL($result, $1.data, $1.len, 1);
+}
+%typemap(in) (const void *indata, int inlen) = (char *STRING, int LENGTH);
 #else
 %echo "cdata.i module not supported."
 #endif
@@ -76,7 +81,3 @@ SWIGCDATA cdata_##NAME(TYPE *ptr, int nelements);
 
 /* Memory move function */
 void memmove(void *data, const void *indata, int inlen);
-
-
-
-
diff --git a/Lib/cffi/cffi.swg b/Lib/cffi/cffi.swg
index 63bd0b040..c832e00d2 100644
--- a/Lib/cffi/cffi.swg
+++ b/Lib/cffi/cffi.swg
@@ -86,7 +86,7 @@
               short, signed short, unsigned short,
               int, signed int, unsigned int,
               long, signed long, unsigned long,
-              float, double, long double, char *, void *
+              float, double, long double, char *, void *,
               enum SWIGTYPE, SWIGTYPE *,
               SWIGTYPE[ANY], SWIGTYPE &    "$result = $1;";
 #ifdef __cplusplus
@@ -125,8 +125,9 @@
                     int, signed int, unsigned int,
                     long, signed long, unsigned long,
                     enum SWIGTYPE       "cl:integer";
-%typemap(lispclass) float "cl:single-float";
-%typemap(lispclass) double "cl:double-float";
+/* CLOS methods can't be specialized on single-float or double-float */
+%typemap(lispclass) float "cl:number";
+%typemap(lispclass) double "cl:number";
 %typemap(lispclass) char * "cl:string";
 
 
diff --git a/Lib/chicken/chicken.swg b/Lib/chicken/chicken.swg
index d8b71874e..a8d1b5a57 100644
--- a/Lib/chicken/chicken.swg
+++ b/Lib/chicken/chicken.swg
@@ -10,6 +10,7 @@
 /* chicken.h has to appear first. */
 
 %insert(runtime) %{
+#include <assert.h>
 #include <chicken.h>
 %}
 
diff --git a/Lib/chicken/chickenkw.swg b/Lib/chicken/chickenkw.swg
index f01faf14f..d2c26c74c 100644
--- a/Lib/chicken/chickenkw.swg
+++ b/Lib/chicken/chickenkw.swg
@@ -3,7 +3,7 @@
 
 /* Warnings for certain CHICKEN keywords. From Section 7.1.1 of
    Revised^5 Report on the Algorithmic Language Scheme */
-#define CHICKENKW(x) %namewarn("314:" #x " is a R^5RS syntatic keyword")  #x
+#define CHICKENKW(x) %namewarn("314: '" #x "' is a R^5RS syntatic keyword")  #x
 
 CHICKENKW(else);
 CHICKENKW(=>);
diff --git a/Lib/chicken/chickenrun.swg b/Lib/chicken/chickenrun.swg
index bd7242407..8703ea65a 100644
--- a/Lib/chicken/chickenrun.swg
+++ b/Lib/chicken/chickenrun.swg
@@ -7,6 +7,7 @@
  * ----------------------------------------------------------------------------- */
 
 #include <chicken.h>
+#include <assert.h>
 #include <stdio.h>
 #include <string.h>
 #include <stdlib.h>
diff --git a/Lib/csharp/csharp.swg b/Lib/csharp/csharp.swg
index 35e5c26d7..e381ff9ae 100644
--- a/Lib/csharp/csharp.swg
+++ b/Lib/csharp/csharp.swg
@@ -428,7 +428,8 @@ SWIGINTERN const char * SWIG_UnpackData(const char *c, void *ptr, size_t sz) {
 %typemap(directorin) SWIGTYPE &
 %{ $input = ($1_ltype) &$1; %}
 
-%typemap(csdirectorin) SWIGTYPE *, SWIGTYPE (CLASS::*), SWIGTYPE & "new $csclassname($iminput, false)"
+%typemap(csdirectorin) SWIGTYPE *, SWIGTYPE (CLASS::*) "($iminput == IntPtr.Zero) ? null : new $csclassname($iminput, false)"
+%typemap(csdirectorin) SWIGTYPE & "new $csclassname($iminput, false)"
 %typemap(csdirectorout) SWIGTYPE *, SWIGTYPE (CLASS::*), SWIGTYPE & "$csclassname.getCPtr($cscall).Handle"
 
 /* Default array handling */
diff --git a/Lib/csharp/csharphead.swg b/Lib/csharp/csharphead.swg
index 7938dee04..ffff70372 100644
--- a/Lib/csharp/csharphead.swg
+++ b/Lib/csharp/csharphead.swg
@@ -73,7 +73,7 @@ static SWIG_CSharpExceptionArgument_t SWIG_csharp_exceptions_argument[] = {
 
 static void SWIGUNUSED SWIG_CSharpSetPendingException(SWIG_CSharpExceptionCodes code, const char *msg) {
   SWIG_CSharpExceptionCallback_t callback = SWIG_csharp_exceptions[SWIG_CSharpApplicationException].callback;
-  if (code >=0 && (size_t)code < sizeof(SWIG_csharp_exceptions)/sizeof(SWIG_CSharpException_t)) {
+  if ((size_t)code < sizeof(SWIG_csharp_exceptions)/sizeof(SWIG_CSharpException_t)) {
     callback = SWIG_csharp_exceptions[code].callback;
   }
   callback(msg);
@@ -81,7 +81,7 @@ static void SWIGUNUSED SWIG_CSharpSetPendingException(SWIG_CSharpExceptionCodes
 
 static void SWIGUNUSED SWIG_CSharpSetPendingExceptionArgument(SWIG_CSharpExceptionArgumentCodes code, const char *msg, const char *param_name) {
   SWIG_CSharpExceptionArgumentCallback_t callback = SWIG_csharp_exceptions_argument[SWIG_CSharpArgumentException].callback;
-  if (code >=0 && (size_t)code < sizeof(SWIG_csharp_exceptions_argument)/sizeof(SWIG_CSharpExceptionArgument_t)) {
+  if ((size_t)code < sizeof(SWIG_csharp_exceptions_argument)/sizeof(SWIG_CSharpExceptionArgument_t)) {
     callback = SWIG_csharp_exceptions_argument[code].callback;
   }
   callback(msg, param_name);
diff --git a/Lib/csharp/csharpkw.swg b/Lib/csharp/csharpkw.swg
index c96042d2d..9a6d979f1 100644
--- a/Lib/csharp/csharpkw.swg
+++ b/Lib/csharp/csharpkw.swg
@@ -2,7 +2,7 @@
 #define CSHARP_CSHARPKW_SWG_
 
 /* Warnings for C# keywords */
-#define CSHARPKW(x) %namewarn("314:" #x " is a csharp keyword")  #x
+#define CSHARPKW(x) %keywordwarn("'" `x` "' is a C# keyword, renaming to '_" `x` "'",rename="_%s")  `x`
 
 /*
    from
diff --git a/Lib/csharp/std_vector.i b/Lib/csharp/std_vector.i
index a04831f75..2e4d47c00 100755
--- a/Lib/csharp/std_vector.i
+++ b/Lib/csharp/std_vector.i
@@ -231,14 +231,14 @@
         return new std::vector<CTYPE >(self->begin()+index, self->begin()+index+count);
       }
       void Insert(int index, const value_type& x) throw (std::out_of_range) {
-        if (index>=0 && index<(int)self->size()+1)
+        if (index>=0 && index<(int)self->size())
           self->insert(self->begin()+index, x);
         else
           throw std::out_of_range("index");
       }
       // Takes a deep copy of the elements unlike ArrayList.InsertRange
       void InsertRange(int index, const std::vector<CTYPE >& values) throw (std::out_of_range) {
-        if (index>=0 && index<(int)self->size()+1)
+        if (index>=0 && index<(int)self->size())
           self->insert(self->begin()+index, values.begin(), values.end());
         else
           throw std::out_of_range("index");
diff --git a/Lib/java/director.swg b/Lib/java/director.swg
index bade80c9d..fa588671d 100644
--- a/Lib/java/director.swg
+++ b/Lib/java/director.swg
@@ -117,12 +117,18 @@ namespace Swig {
       JNIEnv *jenv_;
     public:
       JNIEnvWrapper(const Director *director) : director_(director), jenv_(0) {
+#if defined(SWIG_JAVA_ATTACH_CURRENT_THREAD_AS_DAEMON)
+        // Attach a daemon thread to the JVM. Useful when the JVM should not wait for 
+        // the thread to exit upon shutdown. Only for jdk-1.4 and later.
+        director_->swig_jvm_->AttachCurrentThreadAsDaemon((void **) &jenv_, NULL);
+#else
         director_->swig_jvm_->AttachCurrentThread((void **) &jenv_, NULL);
+#endif
       }
       ~JNIEnvWrapper() {
-// Some JVMs, eg JDK 1.4.2 and lower on Solaris have a bug and crash with the DetachCurrentThread call.
-// However, without this call, the JVM hangs on exit when the thread was not created by the JVM and creates a memory leak.
 #if !defined(SWIG_JAVA_NO_DETACH_CURRENT_THREAD)
+        // Some JVMs, eg jdk-1.4.2 and lower on Solaris have a bug and crash with the DetachCurrentThread call.
+        // However, without this call, the JVM hangs on exit when the thread was not created by the JVM and creates a memory leak.
         director_->swig_jvm_->DetachCurrentThread();
 #endif
       }
diff --git a/Lib/java/java.swg b/Lib/java/java.swg
index b7c5607c3..7d1808632 100644
--- a/Lib/java/java.swg
+++ b/Lib/java/java.swg
@@ -620,7 +620,8 @@
 %typemap(directorin,descriptor="L$packagepath/$javaclassname;") SWIGTYPE &
 %{ *($&1_ltype)&$input = ($1_ltype) &$1; %}
 
-%typemap(javadirectorin) SWIGTYPE *, SWIGTYPE (CLASS::*), SWIGTYPE & "new $javaclassname($jniinput, false)"
+%typemap(javadirectorin) SWIGTYPE *, SWIGTYPE (CLASS::*) "($jniinput == 0) ? null : new $javaclassname($jniinput, false)"
+%typemap(javadirectorin) SWIGTYPE & "new $javaclassname($jniinput, false)"
 %typemap(javadirectorout) SWIGTYPE *, SWIGTYPE (CLASS::*), SWIGTYPE & "$javaclassname.getCPtr($javacall)"
 
 /* Default array handling */
diff --git a/Lib/java/javakw.swg b/Lib/java/javakw.swg
index 9dcd97062..99cd54770 100644
--- a/Lib/java/javakw.swg
+++ b/Lib/java/javakw.swg
@@ -2,7 +2,7 @@
 #define JAVA_JAVAKW_SWG_
 
 /* Warnings for Java keywords */
-#define JAVAKW(x) %namewarn("314:" #x " is a java keyword")  #x
+#define JAVAKW(x) %keywordwarn("'" `x` "' is a java keyword, renaming to '_"`x`"'",rename="_%s")  `x`
 
 /*
    from
diff --git a/Lib/java/various.i b/Lib/java/various.i
index c53f08aa2..733b8fa79 100644
--- a/Lib/java/various.i
+++ b/Lib/java/various.i
@@ -60,7 +60,7 @@
 #endif
 }
 
-%typemap(out) char **STRING_ARRAY (char *s) {
+%typemap(out) char **STRING_ARRAY {
     int i;
     int len=0;
     jstring temp_string;
diff --git a/Lib/lua/luatypemaps.swg b/Lib/lua/luatypemaps.swg
index 462d6a055..0941c9da1 100644
--- a/Lib/lua/luatypemaps.swg
+++ b/Lib/lua/luatypemaps.swg
@@ -73,7 +73,7 @@
 %{$1 = (lua_toboolean(L, $input)!=0);%}
 
 %typemap(out) bool
-%{  lua_pushboolean(L,(int)($1==true)); SWIG_arg++;%}
+%{  lua_pushboolean(L,(int)($1!=0)); SWIG_arg++;%}
 
 // for const bool&, SWIG treats this as a const bool* so we must dereference it
 %typemap(in,checkfn="lua_isboolean") const bool& (bool temp)
@@ -81,7 +81,7 @@
   $1=&temp;%}
 
 %typemap(out) const bool&
-%{  lua_pushboolean(L,(int)(*$1==true)); SWIG_arg++;%}
+%{  lua_pushboolean(L,(int)((*$1)!=0)); SWIG_arg++;%}
 
 // strings (char* and char[])
 %typemap(in,checkfn="lua_isstring") const char*, char*
diff --git a/Lib/lua/typemaps.i b/Lib/lua/typemaps.i
index e0adcf192..fa0c0d0e5 100644
--- a/Lib/lua/typemaps.i
+++ b/Lib/lua/typemaps.i
@@ -80,6 +80,22 @@ SWIG_NUMBER_TYPEMAP(long long); SWIG_NUMBER_TYPEMAP(unsigned long long); SWIG_NU
 
 // note we dont do char, as a char* is probably a string not a ptr to a single char
 
+// similar for booleans
+%typemap(in,checkfn="lua_isboolean") bool *INPUT(bool temp), bool &INPUT(bool temp)
+%{ temp = (lua_toboolean(L,$input)!=0);
+   $1 = &temp; %}
+
+%typemap(in, numinputs=0) bool *OUTPUT (bool temp),bool &OUTPUT (bool temp)
+%{ $1 = &temp; %}
+
+%typemap(argout) bool *OUTPUT,bool &OUTPUT
+%{  lua_pushboolean(L, (int)((*$1)!=0)); SWIG_arg++;%}
+
+%typemap(in) bool *INOUT = bool *INPUT;
+%typemap(argout) bool *INOUT = bool *OUTPUT;
+%typemap(in) bool &INOUT = bool &INPUT;
+%typemap(argout) bool &INOUT = bool &OUTPUT;
+
 /* -----------------------------------------------------------------------------
  *                          Basic Array typemaps
  * ----------------------------------------------------------------------------- */
@@ -320,6 +336,11 @@ for array handling
 %typemap(freearg) (TYPE *INOUT,int)=(TYPE *INPUT,int);
 
 // TODO out variable arrays (is there a standard form for such things?)
+
+// referencing so that (int *INPUT,int) and (int INPUT[],int) are the same
+%typemap(in) (TYPE INPUT[],int)=(TYPE *INPUT,int);
+%typemap(freearg) (TYPE INPUT[],int)=(TYPE *INPUT,int);
+
 %enddef
 
 // the following line of code
diff --git a/Lib/ocaml/ocamlkw.swg b/Lib/ocaml/ocamlkw.swg
index ba06f238e..9b9096e2b 100644
--- a/Lib/ocaml/ocamlkw.swg
+++ b/Lib/ocaml/ocamlkw.swg
@@ -2,7 +2,7 @@
 #define OCAML_OCAMLKW_SWG_
 
 /* Warnings for Ocaml keywords */
-#define OCAMLKW(x) %namewarn("314:" #x " is a ocaml keyword and it will properly renamed")  #x
+#define OCAMLKW(x) %namewarn("314: '" #x "' is a ocaml keyword and it will properly renamed")  #x
 
 /*
   from
diff --git a/Lib/perl5/noembed.h b/Lib/perl5/noembed.h
index a29de61f5..8d3dc7338 100644
--- a/Lib/perl5/noembed.h
+++ b/Lib/perl5/noembed.h
@@ -91,3 +91,7 @@
 #ifdef open
   #undef open
 #endif
+#ifdef readdir
+  #undef readdir
+#endif
+
diff --git a/Lib/perl5/perlkw.swg b/Lib/perl5/perlkw.swg
index 71a229c66..00648e0bf 100644
--- a/Lib/perl5/perlkw.swg
+++ b/Lib/perl5/perlkw.swg
@@ -1,6 +1,6 @@
 /* Warnings for Perl keywords */
-#define PERLKW(x) %keywordwarn(`x` " is a perl keyword")  `x`
-#define PERLBN(x) %builtinwarn(`x` " conflicts with a built-in name in perl")  "::" `x`
+#define PERLKW(x) %keywordwarn("'" `x` "' is a perl keyword")  `x`
+#define PERLBN(x) %builtinwarn("'" `x` "' conflicts with a built-in name in perl")  "::" `x`
 
 
 /*
diff --git a/Lib/php4/const.i b/Lib/php/const.i
similarity index 100%
rename from Lib/php4/const.i
rename to Lib/php/const.i
diff --git a/Lib/php4/globalvar.i b/Lib/php/globalvar.i
similarity index 100%
rename from Lib/php4/globalvar.i
rename to Lib/php/globalvar.i
diff --git a/Lib/php4/php4.swg b/Lib/php/php.swg
similarity index 96%
rename from Lib/php4/php4.swg
rename to Lib/php/php.swg
index feaee68f6..d30e0b2a9 100644
--- a/Lib/php4/php4.swg
+++ b/Lib/php/php.swg
@@ -2,15 +2,15 @@
  * See the LICENSE file for information on copyright, usage and redistribution
  * of SWIG, and the README file for authors - http://www.swig.org/release.html.
  *
- * php4.swg
+ * php.swg
  *
- * PHP4 configuration file
+ * PHP configuration file
  * ----------------------------------------------------------------------------- */
 
 %runtime "swigrun.swg"  // Common C API type-checking code
-%runtime "php4run.swg"	// Php4 runtime functions
+%runtime "phprun.swg"	// PHP runtime functions
 
-%include <php4init.swg> // Php4 initialization routine.
+%include <phpinit.swg> // PHP initialization routine.
 
 %include <globalvar.i>	// Global variables.
 %include <const.i>
@@ -73,6 +73,13 @@
    $1 = ($1_ltype) Z_STRVAL_PP($input);
 }
 
+%typemap(in) (char *STRING, int LENGTH)
+{
+   convert_to_string_ex($input);
+   $1 = ($1_ltype) Z_STRVAL_PP($input);
+   $2 = ($2_ltype) Z_STRLEN_PP($input);
+}
+
 /* Object passed by value. Convert to a pointer */
 %typemap(in) SWIGTYPE ($&1_ltype tmp)
 {
@@ -295,4 +302,4 @@
 
 
 /* php keywords */
-%include <php4kw.swg>
+%include <phpkw.swg>
diff --git a/Lib/php4/php4init.swg b/Lib/php/phpinit.swg
similarity index 100%
rename from Lib/php4/php4init.swg
rename to Lib/php/phpinit.swg
diff --git a/Lib/php4/php4kw.swg b/Lib/php/phpkw.swg
similarity index 93%
rename from Lib/php4/php4kw.swg
rename to Lib/php/phpkw.swg
index 0d28994c5..3d1a62511 100644
--- a/Lib/php4/php4kw.swg
+++ b/Lib/php/phpkw.swg
@@ -2,21 +2,21 @@
  * See the LICENSE file for information on copyright, usage and redistribution
  * of SWIG, and the README file for authors - http://www.swig.org/release.html.
  *
- * php4kw.swg
+ * phpkw.swg
  *
  * The 'keywords' in PHP are global, ie, the following names are fine
  * when used as class methods.
  * ----------------------------------------------------------------------------- */
 
-#define PHPKW(x) %keywordwarn(`x` " is a php keyword, renamed as c_"`x`,sourcefmt="%(lower)s", rename="c_%s",fullname=1)  `x`
+#define PHPKW(x) %keywordwarn("'" `x` "' is a php keyword, renamed as 'c_" `x` "'",sourcefmt="%(lower)s", rename="c_%s",fullname=1)  `x`
 
 %define PHPCN(x) 
-%keywordwarn(`x` " is a php reserved class name, class renamed as c_"`x`,%$isclass,rename="c_%s") `x`;
-%keywordwarn(`x` " is a php reserved class name, constructor renamed as c_"`x`,%$isconstructor,rename="c_%s") `x`;
+%keywordwarn("'" `x` "' is a php reserved class name, class renamed as 'c_" `x` "'",%$isclass,rename="c_%s") `x`;
+%keywordwarn("'" `x` "' is a php reserved class name, constructor renamed as 'c_" `x` "'",%$isconstructor,rename="c_%s") `x`;
 %enddef
 
-#define PHPBN1(x) %builtinwarn(`x` " conflicts with a built-in name in php",sourcefmt="%(lower)s",fullname=1)  `x`
-#define PHPBN2(x) %builtinwarn(`x` " conflicts with a built-in name in php")  "::" `x`
+#define PHPBN1(x) %builtinwarn("'" `x` "' conflicts with a built-in name in php",sourcefmt="%(lower)s",fullname=1)  `x`
+#define PHPBN2(x) %builtinwarn("'" `x` "' conflicts with a built-in name in php")  "::" `x`
 
 
 /*
@@ -67,7 +67,7 @@ PHPKW(include_once);
 PHPKW(isset);
 PHPKW(list);
 PHPKW(new);
-PHPKW(old_function); /* No longer reserved in PHP5 */
+// PHPKW(old_function); /* No longer reserved in PHP5 */
 PHPKW(or);
 PHPKW(print);
 PHPKW(require);
diff --git a/Lib/php4/phppointers.i b/Lib/php/phppointers.i
similarity index 100%
rename from Lib/php4/phppointers.i
rename to Lib/php/phppointers.i
diff --git a/Lib/php4/php4run.swg b/Lib/php/phprun.swg
similarity index 99%
rename from Lib/php4/php4run.swg
rename to Lib/php/phprun.swg
index d38452764..b4e4276f5 100644
--- a/Lib/php4/php4run.swg
+++ b/Lib/php/phprun.swg
@@ -2,9 +2,9 @@
  * See the LICENSE file for information on copyright, usage and redistribution
  * of SWIG, and the README file for authors - http://www.swig.org/release.html.
  *
- * php4run.swg
+ * phprun.swg
  *
- * PHP4 runtime library
+ * PHP runtime library
  * ----------------------------------------------------------------------------- */
 
 #ifdef __cplusplus
diff --git a/Lib/php4/std_common.i b/Lib/php/std_common.i
similarity index 100%
rename from Lib/php4/std_common.i
rename to Lib/php/std_common.i
diff --git a/Lib/php4/std_deque.i b/Lib/php/std_deque.i
similarity index 100%
rename from Lib/php4/std_deque.i
rename to Lib/php/std_deque.i
diff --git a/Lib/php4/std_map.i b/Lib/php/std_map.i
similarity index 97%
rename from Lib/php4/std_map.i
rename to Lib/php/std_map.i
index c35f21dc7..c6721806b 100644
--- a/Lib/php4/std_map.i
+++ b/Lib/php/std_map.i
@@ -30,6 +30,7 @@ namespace std {
         map(const map<K,T> &);
         
         unsigned int size() const;
+        %rename(is_empty) empty;
         bool empty() const;
         void clear();
         %extend {
@@ -69,6 +70,7 @@ namespace std {
         map(const map<K,T> &);
         
         unsigned int size() const;
+        %rename(is_empty) empty;
         bool empty() const;
         void clear();
         %extend {
@@ -105,6 +107,7 @@ namespace std {
         map(const map<K,T> &);
         
         unsigned int size() const;
+        %rename(is_empty) empty;
         bool empty() const;
         void clear();
         %extend {
@@ -142,6 +145,7 @@ namespace std {
         map(const map<K,T> &);
         
         unsigned int size() const;
+        %rename(is_empty) empty;
         bool empty() const;
         void clear();
         %extend {
diff --git a/Lib/php4/std_pair.i b/Lib/php/std_pair.i
similarity index 100%
rename from Lib/php4/std_pair.i
rename to Lib/php/std_pair.i
diff --git a/Lib/php4/std_string.i b/Lib/php/std_string.i
similarity index 100%
rename from Lib/php4/std_string.i
rename to Lib/php/std_string.i
diff --git a/Lib/php4/std_vector.i b/Lib/php/std_vector.i
similarity index 98%
rename from Lib/php4/std_vector.i
rename to Lib/php/std_vector.i
index fe084aca4..b54181618 100644
--- a/Lib/php4/std_vector.i
+++ b/Lib/php/std_vector.i
@@ -48,6 +48,7 @@ namespace std {
       public:
         vector(unsigned int size = 0);
         unsigned int size() const;
+        %rename(is_empty) empty;
         bool empty() const;
         void clear();
         %rename(push) push_back;
@@ -86,6 +87,7 @@ namespace std {
       public:
         vector(unsigned int size = 0);
         unsigned int size() const;
+        %rename(is_empty) empty;
         bool empty() const;
         void clear();
         %rename(push) push_back;
diff --git a/Lib/php4/stl.i b/Lib/php/stl.i
similarity index 100%
rename from Lib/php4/stl.i
rename to Lib/php/stl.i
diff --git a/Lib/php4/typemaps.i b/Lib/php/typemaps.i
similarity index 85%
rename from Lib/php4/typemaps.i
rename to Lib/php/typemaps.i
index c388fdf96..c5b749578 100644
--- a/Lib/php4/typemaps.i
+++ b/Lib/php/typemaps.i
@@ -107,6 +107,17 @@ int_typemap(unsigned char);
 %typemap(in) unsigned long *INOUT = unsigned long *INPUT;
 %typemap(in) unsigned char *INOUT = unsigned char *INPUT;
 
+%typemap(in) float &INOUT = float *INPUT;
+%typemap(in) double &INOUT = double *INPUT;
+
+%typemap(in) int &INOUT = int *INPUT;
+%typemap(in) short &INOUT = short *INPUT;
+%typemap(in) long &INOUT = long *INPUT;
+%typemap(in) unsigned &INOUT = unsigned *INPUT;
+%typemap(in) unsigned short &INOUT = unsigned short *INPUT;
+%typemap(in) unsigned long &INOUT = unsigned long *INPUT;
+%typemap(in) unsigned char &INOUT = unsigned char *INPUT;
+
 %typemap(argout) float *INOUT = float *OUTPUT;
 %typemap(argout) double *INOUT= double *OUTPUT;
 
@@ -117,6 +128,16 @@ int_typemap(unsigned char);
 %typemap(argout) unsigned long *INOUT = unsigned long *OUTPUT;
 %typemap(argout) unsigned char *INOUT = unsigned char *OUTPUT;
 
+%typemap(argout) float &INOUT = float *OUTPUT;
+%typemap(argout) double &INOUT= double *OUTPUT;
+
+%typemap(argout) int &INOUT = int *OUTPUT;
+%typemap(argout) short &INOUT = short *OUTPUT;
+%typemap(argout) long &INOUT= long *OUTPUT;
+%typemap(argout) unsigned short &INOUT= unsigned short *OUTPUT;
+%typemap(argout) unsigned long &INOUT = unsigned long *OUTPUT;
+%typemap(argout) unsigned char &INOUT = unsigned char *OUTPUT;
+
 %typemap(in) char INPUT[ANY] ( char temp[$1_dim0] )
 %{
   convert_to_string_ex($input);
diff --git a/Lib/php4/utils.i b/Lib/php/utils.i
similarity index 96%
rename from Lib/php4/utils.i
rename to Lib/php/utils.i
index f7241187c..661a48777 100644
--- a/Lib/php4/utils.i
+++ b/Lib/php/utils.i
@@ -29,14 +29,14 @@
 %enddef
 
 %define %pass_by_val( TYPE, CONVERT_IN )
-%typemap(in) TYPE
+%typemap(in) TYPE, const TYPE &
 %{
   CONVERT_IN($1,$1_ltype,$input);
 %}
 %enddef
 
 %fragment("t_output_helper","header") %{
-void
+static void
 t_output_helper( zval **target, zval *o) {
   if ( (*target)->type == IS_ARRAY ) {
     /* it's already an array, just append */
diff --git a/Lib/pike/pikekw.swg b/Lib/pike/pikekw.swg
index 85fd091a8..844b1f189 100644
--- a/Lib/pike/pikekw.swg
+++ b/Lib/pike/pikekw.swg
@@ -2,7 +2,7 @@
 #define PIKE_PIKEKW_SWG_
 
 /* Warnings for Pike keywords */
-#define PIKEKW(x) %namewarn("314:" #x " is a pike keyword")  #x
+#define PIKEKW(x) %namewarn("314: '" #x "' is a pike keyword")  #x
 
 /*
    from
diff --git a/Lib/python/director.swg b/Lib/python/director.swg
index 176ee3336..836d107ce 100644
--- a/Lib/python/director.swg
+++ b/Lib/python/director.swg
@@ -107,7 +107,7 @@ namespace Swig {
   /* memory handler */
   struct GCItem 
   {
-    virtual ~GCItem() = 0;
+    virtual ~GCItem() {}
 
     virtual int get_own() const
     {
@@ -115,10 +115,6 @@ namespace Swig {
     }
   };
 
-  GCItem::~GCItem()
-  {
-  }
-
   struct GCItem_var
   {
     GCItem_var(GCItem *item = 0) : _item(item)
@@ -212,10 +208,7 @@ namespace Swig {
         swig_msg += msg;
       }
       if (!PyErr_Occurred()) {
-        swig_msg.insert(0, ": ");
         PyErr_SetString(error, getMessage());
-      } else {
-        SWIG_Python_AddErrorMsg(getMessage());
       }
       SWIG_PYTHON_THREAD_END_BLOCK; 
     }
diff --git a/Lib/python/file.i b/Lib/python/file.i
index c0e7d5ea9..294ab9178 100644
--- a/Lib/python/file.i
+++ b/Lib/python/file.i
@@ -20,11 +20,13 @@ SWIG_AsValFilePtr(PyObject *obj, FILE **val) {
   if ((SWIG_ConvertPtr(obj, &vptr, desc, 0)) == SWIG_OK) {
     if (val) *val = (FILE *)vptr;
     return SWIG_OK;
-  } 
+  }
+%#if PY_VERSION_HEX < 0x03000000
   if (PyFile_Check(obj)) {
     if (val) *val =  PyFile_AsFile(obj);
     return SWIG_OK;
   }
+%#endif
   return SWIG_TypeError;
 }
 }
diff --git a/Lib/python/pyabc.i b/Lib/python/pyabc.i
new file mode 100644
index 000000000..3da06b5a9
--- /dev/null
+++ b/Lib/python/pyabc.i
@@ -0,0 +1,10 @@
+%define %pythonabc(Type, Abc)
+  %feature("python:abc", #Abc) Type;
+%enddef
+%pythoncode {import collections};
+%pythonabc(std::vector, collections.MutableSequence);
+%pythonabc(std::list, collections.MutableSequence);
+%pythonabc(std::map, collections.MutableMapping);
+%pythonabc(std::multimap, collections.MutableMapping);
+%pythonabc(std::set, collections.MutableSet);
+%pythonabc(std::multiset, collections.MutableSet);
diff --git a/Lib/python/pyapi.swg b/Lib/python/pyapi.swg
index 1d5148dbf..d980f9263 100644
--- a/Lib/python/pyapi.swg
+++ b/Lib/python/pyapi.swg
@@ -27,6 +27,20 @@ typedef struct swig_const_info {
   swig_type_info **ptype;
 } swig_const_info;
 
+
+/* -----------------------------------------------------------------------------
+ * Wrapper of PyInstanceMethod_New() used in Python 3
+ * It is exported to the generated module, used for -fastproxy
+ * ----------------------------------------------------------------------------- */
+SWIGRUNTIME PyObject* SWIG_PyInstanceMethod_New(PyObject *self, PyObject *func)
+{
+#if PY_VERSION_HEX >= 0x03000000
+  return PyInstanceMethod_New(func);
+#else
+  return NULL;
+#endif
+}
+
 #ifdef __cplusplus
 #if 0
 { /* cc-mode */
diff --git a/Lib/python/pybuffer.i b/Lib/python/pybuffer.i
new file mode 100644
index 000000000..3dc4c2121
--- /dev/null
+++ b/Lib/python/pybuffer.i
@@ -0,0 +1,107 @@
+/* Impelementing buffer protocol typemaps */
+
+/* %pybuffer_mutable_binary(TYPEMAP, SIZE)
+ *
+ * Macro for functions accept mutable buffer pointer with a size.
+ * This can be used for both input and output. For example:
+ * 
+ *      %pybuffer_mutable_binary(char *buff, int size);
+ *      void foo(char *buff, int size) {
+ *        for(int i=0; i<size; ++i)
+ *          buff[i]++;  
+ *      }
+ */
+
+%define %pybuffer_mutable_binary(TYPEMAP, SIZE)
+%typemap(in) (TYPEMAP, SIZE)
+  (int res, Py_ssize_t size = 0, void *buf = 0) {
+  res = PyObject_AsWriteBuffer($input, &buf, &size);
+  if (res<0) {
+    PyErr_Clear();
+    %argument_fail(res, "(TYPEMAP, SIZE)", $symname, $argnum);
+  }
+  $1 = ($1_ltype) buf;
+  $2 = ($2_ltype) size;
+}
+%enddef
+
+/* %pybuffer_mutable_string(TYPEMAP, SIZE)
+ *
+ * Macro for functions accept mutable zero terminated string pointer.
+ * This can be used for both input and output. For example:
+ * 
+ *      %pybuffer_mutable_string(char *str);
+ *      void foo(char *str) {
+ *        while(*str) {
+ *          *str = toupper(*str);
+ *          str++;
+ *      }
+ */
+
+%define %pybuffer_mutable_string(TYPEMAP)
+%typemap(in) (TYPEMAP)
+  (int res, Py_ssize_t size = 0, void *buf = 0) {
+  res = PyObject_AsWriteBuffer($input, &buf, &size);
+  if (res<0) {
+    PyErr_Clear();
+    %argument_fail(res, "(TYPEMAP, SIZE)", $symname, $argnum);
+  }
+  $1 = ($1_ltype) buf;
+}
+%enddef
+
+/* pybuffer_binary(TYPEMAP, SIZE)
+ *
+ * Macro for functions accept read only buffer pointer with a size.
+ * This must be used for input. For example:
+ * 
+ *      %pybuffer_binary(char *buff, int size);
+ *      int foo(char *buff, int size) {
+ *        int count = 0;
+ *        for(int i=0; i<size; ++i)
+ *          if (0==buff[i]) count++;
+ *        return count;
+ *      }
+ */
+
+%define %pybuffer_binary(TYPEMAP, SIZE)
+%typemap(in) (TYPEMAP, SIZE)
+  (int res, Py_ssize_t size = 0, const void *buf = 0) {
+  res = PyObject_AsReadBuffer($input, &buf, &size);
+  if (res<0) {
+    PyErr_Clear();
+    %argument_fail(res, "(TYPEMAP, SIZE)", $symname, $argnum);
+  }
+  $1 = ($1_ltype) buf;
+  $2 = ($2_ltype) size;
+}
+%enddef
+
+/* %pybuffer_string(TYPEMAP, SIZE)
+ *
+ * Macro for functions accept read only zero terminated string pointer.
+ * This can be used for input. For example:
+ * 
+ *      %pybuffer_string(char *str);
+ *      int foo(char *str) {
+ *        int count = 0;
+ *        while(*str) {
+ *          if (isalnum(*str))
+ *            count++;
+ *          str++;
+ *      }
+ */
+
+%define %pybuffer_string(TYPEMAP)
+%typemap(in) (TYPEMAP)
+  (int res, Py_ssize_t size = 0, const void *buf = 0) {
+  res = PyObject_AsReadBuffer($input, &buf, &size);
+  if (res<0) {
+    %argument_fail(res, "(TYPEMAP, SIZE)", $symname, $argnum);
+  }
+  $1 = ($1_ltype) buf;
+}
+%enddef
+
+
+
diff --git a/Lib/python/pycontainer.swg b/Lib/python/pycontainer.swg
index 8f1db7ce1..58442ef76 100644
--- a/Lib/python/pycontainer.swg
+++ b/Lib/python/pycontainer.swg
@@ -116,6 +116,17 @@ namespace std {
       bool res;
       SWIG_PYTHON_THREAD_BEGIN_BLOCK;
       res = PyObject_Compare(v, w) < 0;
+      /* This may fall into a case of inconsistent
+               eg. ObjA > ObjX > ObjB
+               but ObjA < ObjB
+      */
+      if( PyErr_Occurred() && PyErr_ExceptionMatches(PyExc_TypeError) )
+      {
+        /* Objects can't be compared, this mostly occured in Python 3.0 */
+        /* Compare their ptr directly for a workaround */
+        res = (v < w);
+        PyErr_Clear();
+      }
       SWIG_PYTHON_THREAD_END_BLOCK;
       return res;
     }
@@ -597,6 +608,11 @@ namespace swig
       return !(self->empty());
     }
 
+    /* Alias for Python 3 compatibility */
+    bool __bool__() const {
+      return !(self->empty());
+    }
+
     size_type __len__() const {
       return self->size();
     }
@@ -618,6 +634,14 @@ namespace swig
       return x;
     }
 
+    /* typemap for slice object support */
+    %typemap(in) PySliceObject* {
+      $1 = (PySliceObject *) $input;
+    }
+    %typemap(typecheck,precedence=SWIG_TYPECHECK_POINTER) PySliceObject* {
+      $1 = PySlice_Check($input);
+    }
+
     Sequence* __getslice__(difference_type i, difference_type j) throw (std::out_of_range) {
       return swig::getslice(self, i, j);
     }
@@ -634,6 +658,43 @@ namespace swig
     void __delitem__(difference_type i) throw (std::out_of_range) {
       self->erase(swig::getpos(self,i));
     }
+
+
+    /* Overloaded methods for Python 3 compatibility 
+     * (Also useful in Python 2.x)
+     */
+    Sequence* __getitem__(PySliceObject *slice) throw (std::out_of_range) {
+      Py_ssize_t i, j, step;
+      if( !PySlice_Check(slice) ) {
+        SWIG_Error(SWIG_TypeError, "Slice object expected.");
+        return NULL;
+      }
+      PySlice_GetIndices(slice, self->size(), &i, &j, &step);
+      return swig::getslice(self, i, j);
+    }
+
+    void __setitem__(PySliceObject *slice, const Sequence& v)
+      throw (std::out_of_range, std::invalid_argument) {
+      Py_ssize_t i, j, step;
+      if( !PySlice_Check(slice) ) {
+        SWIG_Error(SWIG_TypeError, "Slice object expected.");
+        return;
+      }
+      PySlice_GetIndices(slice, self->size(), &i, &j, &step);
+      swig::setslice(self, i, j, v);
+    }
+
+    void __delitem__(PySliceObject *slice)
+      throw (std::out_of_range) {
+      Py_ssize_t i, j, step;
+      if( !PySlice_Check(slice) ) {
+        SWIG_Error(SWIG_TypeError, "Slice object expected.");
+        return;
+      }
+      PySlice_GetIndices(slice, self->size(), &i, &j, &step);
+      swig::delslice(self, i,j);
+    }
+     
   }
 %enddef
 
@@ -738,12 +799,12 @@ namespace swig {
     typedef typename sequence::const_iterator const_iterator;
 
     static PyObject *from(const sequence& seq) {
-#ifdef SWIG_PYTHON_EXTRA_NATIVE_CONTAINERS
+%#ifdef SWIG_PYTHON_EXTRA_NATIVE_CONTAINERS
       swig_type_info *desc = swig::type_info<sequence>();
       if (desc && desc->clientdata) {
 	return SWIG_NewPointerObj(new sequence(seq), desc, SWIG_POINTER_OWN);
       }
-#endif
+%#endif
       size_type size = seq.size();
       if (size <= (size_type)INT_MAX) {
 	PyObject *obj = PyTuple_New((int)size);
diff --git a/Lib/python/pyerrors.swg b/Lib/python/pyerrors.swg
index e287e2fc8..01cf53e9b 100644
--- a/Lib/python/pyerrors.swg
+++ b/Lib/python/pyerrors.swg
@@ -58,12 +58,12 @@ SWIG_Python_AddErrorMsg(const char* mesg)
     PyObject *old_str = PyObject_Str(value);
     PyErr_Clear();
     Py_XINCREF(type);
-    PyErr_Format(type, "%s %s", PyString_AsString(old_str), mesg);
+
+    PyErr_Format(type, "%s %s", 
+        SWIG_Python_str_AsChar(old_str), mesg);
     Py_DECREF(old_str);
     Py_DECREF(value);
   } else {
     PyErr_SetString(PyExc_RuntimeError, mesg);
   }
 }
-
-
diff --git a/Lib/python/pyhead.swg b/Lib/python/pyhead.swg
index 7839511bc..d73d3d112 100644
--- a/Lib/python/pyhead.swg
+++ b/Lib/python/pyhead.swg
@@ -1,3 +1,47 @@
+/* Compatibility marcos for Python 3 */
+#if PY_VERSION_HEX >= 0x03000000
+
+#define PyClass_Check(obj) PyObject_IsInstance(obj, (PyObject *)&PyType_Type)
+
+#define PyInt_Check(x) PyLong_Check(x)
+#define PyInt_AsLong(x) PyLong_AsLong(x)
+#define PyInt_FromLong(x) PyLong_FromLong(x)
+
+#define PyString_Format(fmt, args)  PyUnicode_Format(fmt, args)
+#endif
+
+#ifndef Py_TYPE
+#  define Py_TYPE(op) ((op)->ob_type)
+#endif
+
+/* SWIG APIs for compatibility of boht Python 2 & 3 */
+
+#if PY_VERSION_HEX >= 0x03000000
+#  define SWIG_Python_str_FromFormat PyUnicode_FromFormat
+#else
+#  define SWIG_Python_str_FromFormat PyString_FromFormat
+#endif
+
+SWIGINTERN char*
+SWIG_Python_str_AsChar(PyObject *str)
+{
+#if PY_VERSION_HEX >= 0x03000000
+  str = PyUnicode_AsUTF8String(str);
+  return PyBytes_AsString(str);
+#else
+  return PyString_AsString(str);
+#endif
+}
+
+SWIGINTERN PyObject*
+SWIG_Python_str_FromChar(const char *c)
+{
+#if PY_VERSION_HEX >= 0x03000000
+  return PyUnicode_FromString(c); 
+#else
+  return PyString_FromString(c);
+#endif
+}
 
 /* Add PyOS_snprintf for old Pythons */
 #if PY_VERSION_HEX < 0x02020000
diff --git a/Lib/python/pyinit.swg b/Lib/python/pyinit.swg
index e6109b7bd..ab55765ad 100644
--- a/Lib/python/pyinit.swg
+++ b/Lib/python/pyinit.swg
@@ -33,18 +33,48 @@ typedef struct swig_varlinkobject {
 
 SWIGINTERN PyObject *
 swig_varlink_repr(swig_varlinkobject *SWIGUNUSEDPARM(v)) {
+#if PY_VERSION_HEX >= 0x03000000
+  return PyUnicode_InternFromString("<Swig global variables>");
+#else
   return PyString_FromString("<Swig global variables>");
+#endif
 }
 
 SWIGINTERN PyObject *
 swig_varlink_str(swig_varlinkobject *v) {
+#if PY_VERSION_HEX >= 0x03000000
+  PyObject *str = PyUnicode_InternFromString("(");
+  PyObject *tail;
+  PyObject *joined;
+  swig_globalvar *var;
+  for (var = v->vars; var; var=var->next) {
+    tail = PyUnicode_FromString(var->name);
+    joined = PyUnicode_Concat(str, tail);
+    Py_DecRef(str);
+    Py_DecRef(tail);
+    str = joined;
+    if (var->next) {
+        tail = PyUnicode_InternFromString(", ");
+        joined = PyUnicode_Concat(str, tail);
+        Py_DecRef(str);
+        Py_DecRef(tail);
+        str = joined;
+    }
+  }
+  tail = PyUnicode_InternFromString(")");
+  joined = PyUnicode_Concat(str, tail);
+  Py_DecRef(str);
+  Py_DecRef(tail);
+  str = joined;
+#else
   PyObject *str = PyString_FromString("(");
-  swig_globalvar  *var;
+  swig_globalvar *var;
   for (var = v->vars; var; var=var->next) {
     PyString_ConcatAndDel(&str,PyString_FromString(var->name));
     if (var->next) PyString_ConcatAndDel(&str,PyString_FromString(", "));
   }
   PyString_ConcatAndDel(&str,PyString_FromString(")"));
+#endif
   return str;
 }
 
@@ -52,7 +82,7 @@ SWIGINTERN int
 swig_varlink_print(swig_varlinkobject *v, FILE *fp, int SWIGUNUSEDPARM(flags)) {
   PyObject *str = swig_varlink_str(v);
   fprintf(fp,"Swig global variables ");
-  fprintf(fp,"%s\n", PyString_AsString(str));
+  fprintf(fp,"%s\n", SWIG_Python_str_AsChar(str));
   Py_DECREF(str);
   return 0;
 }
@@ -110,8 +140,13 @@ swig_varlink_type(void) {
   if (!type_init) {
     const PyTypeObject tmp
       = {
+      /* PyObject header changed in Python 3 */
+#if PY_VERSION_HEX >= 0x03000000
+      PyVarObject_HEAD_INIT(&PyType_Type, 0)
+#else
       PyObject_HEAD_INIT(NULL)
       0,                                  /* Number of items in variable part (ob_size) */
+#endif
       (char *)"swigvarlink",              /* Type name (tp_name) */
       sizeof(swig_varlinkobject),         /* Basic size (tp_basicsize) */
       0,                                  /* Itemsize (tp_itemsize) */
@@ -147,7 +182,10 @@ swig_varlink_type(void) {
 #endif
     };
     varlink_type = tmp;
+    /* for Python 3 we already assigned the ob_type in PyVarObject_HEAD_INIT() */
+#if PY_VERSION_HEX < 0x03000000
     varlink_type.ob_type = &PyType_Type;
+#endif
     type_init = 1;
   }
   return &varlink_type;
@@ -272,13 +310,35 @@ SWIG_Python_FixMethods(PyMethodDef *methods,
 #ifdef __cplusplus
 extern "C"
 #endif
-SWIGEXPORT void SWIG_init(void) {
+
+SWIGEXPORT 
+#if PY_VERSION_HEX >= 0x03000000
+  PyObject*
+#else
+  void
+#endif
+SWIG_init(void) {
   PyObject *m, *d;
   
   /* Fix SwigMethods to carry the callback ptrs when needed */
   SWIG_Python_FixMethods(SwigMethods, swig_const_table, swig_types, swig_type_initial);
-  
+#if PY_VERSION_HEX >= 0x03000000
+  static struct PyModuleDef SWIG_module = {
+    PyModuleDef_HEAD_INIT,
+    (char *) SWIG_name,
+    NULL,
+    -1,
+    SwigMethods,
+    NULL,
+    NULL,
+    NULL,
+    NULL
+  };
+
+  m = PyModule_Create(&SWIG_module);
+#else
   m = Py_InitModule((char *) SWIG_name, SwigMethods);
+#endif
   d = PyModule_GetDict(m);
   
   SWIG_InitializeModule(0);
diff --git a/Lib/python/pyiterators.swg b/Lib/python/pyiterators.swg
index e2dfbc3f5..62a7eaf70 100644
--- a/Lib/python/pyiterators.swg
+++ b/Lib/python/pyiterators.swg
@@ -38,18 +38,18 @@ namespace swig {
     virtual PySwigIterator *incr(size_t n = 1) = 0;
     
     // Backward iterator method, very common in C++, but not required in Python
-    virtual PySwigIterator *decr(size_t n = 1)
+    virtual PySwigIterator *decr(size_t /*n*/ = 1)
     {
       throw stop_iteration();
     }
 
     // Random access iterator methods, but not required in Python
-    virtual ptrdiff_t distance(const PySwigIterator &x) const
+    virtual ptrdiff_t distance(const PySwigIterator &/*x*/) const
     {
       throw std::invalid_argument("operation not supported");
     }
 
-    virtual bool equal (const PySwigIterator &x) const
+    virtual bool equal (const PySwigIterator &/*x*/) const
     {
       throw std::invalid_argument("operation not supported");
     }
@@ -66,6 +66,12 @@ namespace swig {
       return obj;     
     }
 
+    /* Make an alias for Python 3.x */
+    PyObject *__next__()
+    {
+      return next();
+    }
+
     PyObject *previous()
     {
       SWIG_PYTHON_THREAD_BEGIN_BLOCK; // disable threads       
@@ -335,6 +341,7 @@ namespace swig
   %catches(swig::stop_iteration) PySwigIterator::decr(size_t n = 1);
   %catches(std::invalid_argument) PySwigIterator::distance(const PySwigIterator &x) const;
   %catches(std::invalid_argument) PySwigIterator::equal (const PySwigIterator &x) const;
+  %catches(swig::stop_iteration) PySwigIterator::__next__();
   %catches(swig::stop_iteration) PySwigIterator::next();
   %catches(swig::stop_iteration) PySwigIterator::previous();
   %catches(swig::stop_iteration) PySwigIterator::advance(ptrdiff_t n);
@@ -370,6 +377,7 @@ namespace swig
     virtual PySwigIterator *copy() const = 0;
 
     PyObject *next();
+    PyObject *__next__();
     PyObject *previous();
     PySwigIterator *advance(ptrdiff_t n);
 
diff --git a/Lib/python/pyopers.swg b/Lib/python/pyopers.swg
index 76f1e6789..bd5c954f0 100644
--- a/Lib/python/pyopers.swg
+++ b/Lib/python/pyopers.swg
@@ -33,6 +33,12 @@
 /* Special cases */
 %rename(__invert__)     *::operator~;
 %rename(__call__)       *::operator();
+
+%feature("shadow")      *::operator bool %{
+def __nonzero__(self):
+    return $action(self)
+__bool__ = __nonzero__
+%};
 %rename(__nonzero__)    *::operator bool;
 
 /* Ignored operators */
diff --git a/Lib/python/pyrun.swg b/Lib/python/pyrun.swg
index 844a66bec..4f51d3a95 100644
--- a/Lib/python/pyrun.swg
+++ b/Lib/python/pyrun.swg
@@ -348,9 +348,13 @@ PySwigObject_format(const char* fmt, PySwigObject *v)
   PyObject *args = PyTuple_New(1);
   if (args) {
     if (PyTuple_SetItem(args, 0, PySwigObject_long(v)) == 0) {
-      PyObject *ofmt = PyString_FromString(fmt);
+      PyObject *ofmt = SWIG_Python_str_FromChar(fmt);
       if (ofmt) {
+#if PY_VERSION_HEX >= 0x03000000
+	res = PyUnicode_Format(ofmt,args);
+#else
 	res = PyString_Format(ofmt,args);
+#endif
 	Py_DECREF(ofmt);
       }
       Py_DECREF(args);
@@ -380,7 +384,7 @@ PySwigObject_repr(PySwigObject *v, PyObject *args)
 {
   const char *name = SWIG_TypePrettyName(v->ty);
   PyObject *hex = PySwigObject_hex(v);    
-  PyObject *repr = PyString_FromFormat("<Swig Object of type '%s' at 0x%s>", name, PyString_AsString(hex));
+  PyObject *repr = SWIG_Python_str_FromFormat("<Swig Object of type '%s' at 0x%U>", name, hex);
   Py_DECREF(hex);
   if (v->next) {
 #ifdef METH_NOARGS
@@ -388,7 +392,14 @@ PySwigObject_repr(PySwigObject *v, PyObject *args)
 #else
     PyObject *nrep = PySwigObject_repr((PySwigObject *)v->next, args);
 #endif
+#if PY_VERSION_HEX >= 0x03000000
+    PyObject *joined = PyUnicode_Concat(repr, nrep);
+    Py_DecRef(repr);
+    Py_DecRef(nrep);
+    repr = joined;
+#else
     PyString_ConcatAndDel(&repr,nrep);
+#endif
   }
   return repr;  
 }
@@ -402,7 +413,7 @@ PySwigObject_print(PySwigObject *v, FILE *fp, int SWIGUNUSEDPARM(flags))
   PyObject *repr = PySwigObject_repr(v, NULL);
 #endif
   if (repr) {
-    fputs(PyString_AsString(repr), fp);
+    fputs(SWIG_Python_str_AsChar(repr), fp);
     Py_DECREF(repr);
     return 0; 
   } else {
@@ -415,7 +426,7 @@ PySwigObject_str(PySwigObject *v)
 {
   char result[SWIG_BUFFER_SIZE];
   return SWIG_PackVoidPtr(result, v->ptr, v->ty->name, sizeof(result)) ?
-    PyString_FromString(result) : 0;
+    SWIG_Python_str_FromChar(result) : 0;
 }
 
 SWIGRUNTIME int
@@ -426,6 +437,24 @@ PySwigObject_compare(PySwigObject *v, PySwigObject *w)
   return (i < j) ? -1 : ((i > j) ? 1 : 0);
 }
 
+/* Added for Python 3.x, whould it also useful for Python 2.x? */
+SWIGRUNTIME PyObject*
+PySwigObject_richcompare(PySwigObject *v, PySwigObject *w, int op)
+{
+  PyObject* res;
+  if( op != Py_EQ && op != Py_NE ) {
+    Py_INCREF(Py_NotImplemented);
+    return Py_NotImplemented;
+  }
+  if( (PySwigObject_compare(v, w)==0) == (op == Py_EQ) )
+    res = Py_True;
+  else
+    res = Py_False;
+  Py_INCREF(res);
+  return res;  
+}
+
+
 SWIGRUNTIME PyTypeObject* _PySwigObject_type(void);
 
 SWIGRUNTIME PyTypeObject*
@@ -436,8 +465,8 @@ PySwigObject_type(void) {
 
 SWIGRUNTIMEINLINE int
 PySwigObject_Check(PyObject *op) {
-  return ((op)->ob_type == PySwigObject_type())
-    || (strcmp((op)->ob_type->tp_name,"PySwigObject") == 0);
+  return (Py_TYPE(op) == PySwigObject_type())
+    || (strcmp(Py_TYPE(op)->tp_name,"PySwigObject") == 0);
 }
 
 SWIGRUNTIME PyObject *
@@ -610,7 +639,10 @@ _PySwigObject_type(void) {
     (binaryfunc)0, /*nb_add*/
     (binaryfunc)0, /*nb_subtract*/
     (binaryfunc)0, /*nb_multiply*/
+    /* nb_divide removed in Python 3 */
+#if PY_VERSION_HEX < 0x03000000
     (binaryfunc)0, /*nb_divide*/
+#endif
     (binaryfunc)0, /*nb_remainder*/
     (binaryfunc)0, /*nb_divmod*/
     (ternaryfunc)0,/*nb_power*/
@@ -624,13 +656,19 @@ _PySwigObject_type(void) {
     0,		   /*nb_and*/
     0,		   /*nb_xor*/
     0,		   /*nb_or*/
-    (coercion)0,   /*nb_coerce*/
+#if PY_VERSION_HEX < 0x03000000
+    0,   /*nb_coerce*/
+#endif
     (unaryfunc)PySwigObject_long, /*nb_int*/
     (unaryfunc)PySwigObject_long, /*nb_long*/
     (unaryfunc)0,                 /*nb_float*/
+#if PY_VERSION_HEX < 0x03000000
     (unaryfunc)PySwigObject_oct,  /*nb_oct*/
     (unaryfunc)PySwigObject_hex,  /*nb_hex*/
-#if PY_VERSION_HEX >= 0x02050000 /* 2.5.0 */
+#endif
+#if PY_VERSION_HEX >= 0x03000000 /* 3.0 */
+    0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 /* nb_inplace_add -> nb_index, nb_inplace_divide removed */
+#elif PY_VERSION_HEX >= 0x02050000 /* 2.5.0 */
     0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 /* nb_inplace_add -> nb_index */
 #elif PY_VERSION_HEX >= 0x02020000 /* 2.2.0 */
     0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 /* nb_inplace_add -> nb_inplace_true_divide */
@@ -644,8 +682,13 @@ _PySwigObject_type(void) {
   if (!type_init) {
     const PyTypeObject tmp
       = {
-	PyObject_HEAD_INIT(NULL)
-	0,				    /* ob_size */
+    /* PyOjbect header changed in Python 3 */
+#if PY_VERSION_HEX >= 0x03000000
+    PyVarObject_HEAD_INIT(&PyType_Type, 0)
+#else    
+    PyObject_HEAD_INIT(NULL)
+    0,				    /* ob_size */
+#endif
 	(char *)"PySwigObject",		    /* tp_name */
 	sizeof(PySwigObject),		    /* tp_basicsize */
 	0,			            /* tp_itemsize */
@@ -672,7 +715,7 @@ _PySwigObject_type(void) {
 	swigobject_doc, 	            /* tp_doc */        
 	0,                                  /* tp_traverse */
 	0,                                  /* tp_clear */
-	0,                                  /* tp_richcompare */
+	(richcmpfunc)PySwigObject_richcompare,           /* tp_richcompare */
 	0,                                  /* tp_weaklistoffset */
 #if PY_VERSION_HEX >= 0x02020000
 	0,                                  /* tp_iter */
@@ -704,7 +747,10 @@ _PySwigObject_type(void) {
 #endif
       };
     pyswigobject_type = tmp;
+    /* for Python 3 we already assigned the ob_type in PyVarObject_HEAD_INIT() */
+#if PY_VERSION_HEX < 0x03000000
     pyswigobject_type.ob_type = &PyType_Type;
+#endif
     type_init = 1;
   }
   return &pyswigobject_type;
@@ -753,9 +799,9 @@ PySwigPacked_repr(PySwigPacked *v)
 {
   char result[SWIG_BUFFER_SIZE];
   if (SWIG_PackDataName(result, v->pack, v->size, 0, sizeof(result))) {
-    return PyString_FromFormat("<Swig Packed at %s%s>", result, v->ty->name);
+    return SWIG_Python_str_FromFormat("<Swig Packed at %s%s>", result, v->ty->name);
   } else {
-    return PyString_FromFormat("<Swig Packed %s>", v->ty->name);
+    return SWIG_Python_str_FromFormat("<Swig Packed %s>", v->ty->name);
   }  
 }
 
@@ -764,9 +810,9 @@ PySwigPacked_str(PySwigPacked *v)
 {
   char result[SWIG_BUFFER_SIZE];
   if (SWIG_PackDataName(result, v->pack, v->size, 0, sizeof(result))){
-    return PyString_FromFormat("%s%s", result, v->ty->name);
+    return SWIG_Python_str_FromFormat("%s%s", result, v->ty->name);
   } else {
-    return PyString_FromString(v->ty->name);
+    return SWIG_Python_str_FromChar(v->ty->name);
   }  
 }
 
@@ -811,8 +857,13 @@ _PySwigPacked_type(void) {
   if (!type_init) {
     const PyTypeObject tmp
       = {
+    /* PyObject header changed in Python 3 */
+#if PY_VERSION_HEX>=0x03000000
+    PyVarObject_HEAD_INIT(&PyType_Type, 0)
+#else
 	PyObject_HEAD_INIT(NULL)
-	0,				    /* ob_size */	
+    0,				    /* ob_size */	
+#endif
 	(char *)"PySwigPacked",		    /* tp_name */	
 	sizeof(PySwigPacked),		    /* tp_basicsize */	
 	0,				    /* tp_itemsize */	
@@ -867,7 +918,10 @@ _PySwigPacked_type(void) {
 #endif
       };
     pyswigpacked_type = tmp;
+    /* for Python 3 the ob_type already assigned in PyVarObject_HEAD_INIT() */
+#if PY_VERSION_HEX < 0x03000000
     pyswigpacked_type.ob_type = &PyType_Type;
+#endif
     type_init = 1;
   }
   return &pyswigpacked_type;
@@ -912,7 +966,7 @@ PySwigPacked_UnpackData(PyObject *obj, void *ptr, size_t size)
 SWIGRUNTIMEINLINE PyObject *
 _SWIG_This(void)
 {
-  return PyString_FromString("this");
+    return SWIG_Python_str_FromChar("this");
 }
 
 SWIGRUNTIME PyObject *
@@ -924,6 +978,11 @@ SWIG_This(void)
 
 /* #define SWIG_PYTHON_SLOW_GETSET_THIS */
 
+/* TODO: I don't know how to implement the fast getset in Python 3 right now */
+#if PY_VERSION_HEX>=0x03000000
+#define SWIG_PYTHON_SLOW_GETSET_THIS 
+#endif
+
 SWIGRUNTIME PySwigObject *
 SWIG_Python_GetSwigThis(PyObject *pyobj) 
 {
@@ -1161,10 +1220,17 @@ SWIG_Python_NewShadowInstance(PySwigClientData *data, PyObject *swig_this)
 #endif
     }
   } else {
+#if PY_VERSION_HEX >= 0x03000000
+    inst = PyBaseObject_Type.tp_new((PyTypeObject*) data->newargs, Py_None, Py_None);
+    Py_INCREF(data->newargs);
+    PyObject_SetAttr(inst, SWIG_This(), swig_this);
+    Py_TYPE(inst)->tp_flags &= ~Py_TPFLAGS_VALID_VERSION_TAG;
+#else
     PyObject *dict = PyDict_New();
     PyDict_SetItem(dict, SWIG_This(), swig_this);
     inst = PyInstance_NewRaw(data->newargs, dict);
     Py_DECREF(dict);
+#endif
   }
   return inst;
 #else
@@ -1344,8 +1410,13 @@ SWIGRUNTIME void
 SWIG_Python_SetModule(swig_module_info *swig_module) {
   static PyMethodDef swig_empty_runtime_method_table[] = { {NULL, NULL, 0, NULL} };/* Sentinel */
 
+#if PY_VERSION_HEX >= 0x03000000
+ /* Add a dummy module object into sys.modules */
+  PyObject *module = PyImport_AddModule((char*)"swig_runtime_data" SWIG_RUNTIME_VERSION);
+#else
   PyObject *module = Py_InitModule((char*)"swig_runtime_data" SWIG_RUNTIME_VERSION,
 				   swig_empty_runtime_method_table);
+#endif
   PyObject *pointer = PyCObject_FromVoidPtr((void *) swig_module, SWIG_Python_DestroyModule);
   if (pointer && module) {
     PyModule_AddObject(module, (char*)"type_pointer" SWIG_TYPE_TABLE_NAME, pointer);
@@ -1365,7 +1436,7 @@ SWIGRUNTIME swig_type_info *
 SWIG_Python_TypeQuery(const char *type)
 {
   PyObject *cache = SWIG_Python_TypeCache();
-  PyObject *key = PyString_FromString(type); 
+  PyObject *key = SWIG_Python_str_FromChar(type); 
   PyObject *obj = PyDict_GetItem(cache, key);
   swig_type_info *descriptor;
   if (obj) {
@@ -1403,9 +1474,9 @@ SWIG_Python_AddErrMesg(const char* mesg, int infront)
       Py_XINCREF(type);
       PyErr_Clear();
       if (infront) {
-	PyErr_Format(type, "%s %s", mesg, PyString_AsString(old_str));
+	PyErr_Format(type, "%s %s", mesg, SWIG_Python_str_AsChar(old_str));
       } else {
-	PyErr_Format(type, "%s %s", PyString_AsString(old_str), mesg);
+	PyErr_Format(type, "%s %s", SWIG_Python_str_AsChar(old_str), mesg);
       }
       Py_DECREF(old_str);
     }
@@ -1454,7 +1525,7 @@ SWIG_Python_TypeError(const char *type, PyObject *obj)
       const char *otype = (obj ? obj->ob_type->tp_name : 0); 
       if (otype) {
 	PyObject *str = PyObject_Str(obj);
-	const char *cstr = str ? PyString_AsString(str) : 0;
+	const char *cstr = str ? SWIG_Python_str_AsChar(str) : 0;
 	if (cstr) {
 	  PyErr_Format(PyExc_TypeError, "a '%s' is expected, '%s(%s)' is received",
 		       type, otype, cstr);
diff --git a/Lib/python/pystrings.swg b/Lib/python/pystrings.swg
index d4d60c42b..5a06792d7 100644
--- a/Lib/python/pystrings.swg
+++ b/Lib/python/pystrings.swg
@@ -5,10 +5,20 @@
 SWIGINTERN int
 SWIG_AsCharPtrAndSize(PyObject *obj, char** cptr, size_t* psize, int *alloc)
 {
-  if (PyString_Check(obj)) {
+%#if PY_VERSION_HEX>=0x03000000
+  if (PyUnicode_Check(obj)) 
+%#else  
+  if (PyString_Check(obj)) 
+%#endif
+  {
     char *cstr; Py_ssize_t len;
+%#if PY_VERSION_HEX>=0x03000000
+    obj = PyUnicode_AsUTF8String(obj);
+    PyBytes_AsStringAndSize(obj, &cstr, &len);
+%#else
     PyString_AsStringAndSize(obj, &cstr, &len);
-    if (cptr)  {
+%#endif
+    if (cptr) { 
       if (alloc) {
 	/* 
 	   In python the user should not be able to modify the inner
@@ -33,7 +43,7 @@ SWIG_AsCharPtrAndSize(PyObject *obj, char** cptr, size_t* psize, int *alloc)
 	  *alloc = SWIG_OLDOBJ;
 	}
       } else {
-	*cptr = PyString_AsString(obj);
+	*cptr = SWIG_Python_str_AsChar(obj);
       }
     }
     if (psize) *psize = len + 1;
@@ -64,7 +74,11 @@ SWIG_FromCharPtrAndSize(const char* carray, size_t size)
       return pchar_descriptor ? 
 	SWIG_NewPointerObj(%const_cast(carray,char *), pchar_descriptor, 0) : SWIG_Py_Void();
     } else {
+%#if PY_VERSION_HEX >= 0x03000000
+      return PyUnicode_FromStringAndSize(carray, %numeric_cast(size,int));
+%#else
       return PyString_FromStringAndSize(carray, %numeric_cast(size,int));
+%#endif
     }
   } else {
     return SWIG_Py_Void();
diff --git a/Lib/python/pythonkw.swg b/Lib/python/pythonkw.swg
index f57d34ce4..2ee233516 100644
--- a/Lib/python/pythonkw.swg
+++ b/Lib/python/pythonkw.swg
@@ -2,8 +2,8 @@
   Warnings for Python keywords, built-in names and bad names.
 */
 
-#define PYTHONKW(x) %keywordwarn(`x` " is a python keyword, symbol will be renamed as '_" `x`"'", rename="_%s")  `x`
-#define PYTHONBN(x) %builtinwarn(`x` " conflicts with a built-in name in python")  "::"`x`
+#define PYTHONKW(x) %keywordwarn("'" `x` "' is a python keyword, renaming to '_" `x` "'", rename="_%s")  `x`
+#define PYTHONBN(x) %builtinwarn("'" `x` "' conflicts with a built-in name in python")  "::"`x`
 
 
 /*
diff --git a/Lib/python/pywstrings.swg b/Lib/python/pywstrings.swg
index 8254bf8f7..4161dcb0f 100644
--- a/Lib/python/pywstrings.swg
+++ b/Lib/python/pywstrings.swg
@@ -8,12 +8,14 @@ SWIG_AsWCharPtrAndSize(PyObject *obj, wchar_t **cptr, size_t *psize, int *alloc)
 {
   PyObject *tmp = 0;
   int isunicode = PyUnicode_Check(obj);
+%#if PY_VERSION_HEX < 0x03000000
   if (!isunicode && PyString_Check(obj)) {
     if (cptr) {
       obj = tmp = PyUnicode_FromObject(obj);
     }
     isunicode = 1;
   }
+%#endif
   if (isunicode) {
     int len = PyUnicode_GetSize(obj);
     if (cptr) {
diff --git a/Lib/python/std_map.i b/Lib/python/std_map.i
index 12dc23ccf..b080731f0 100644
--- a/Lib/python/std_map.i
+++ b/Lib/python/std_map.i
@@ -22,6 +22,10 @@
 	int res = SWIG_ERROR;
 	if (PyDict_Check(obj)) {
 	  PyObject_var items = PyObject_CallMethod(obj,(char *)"items",NULL);
+%#if PY_VERSION_HEX >= 0x03000000
+          /* In Python 3.x the ".items()" method return a dict_items object */
+          items = PySequence_Fast(items, ".items() havn't returned a sequence!");
+%#endif
 	  res = traits_asptr_stdseq<std::map<K,T>, std::pair<K, T> >::asptr(items, val);
 	} else {
 	  map_type *p;
diff --git a/Lib/r/r.swg b/Lib/r/r.swg
index 3095529a0..0a4d0c36e 100644
--- a/Lib/r/r.swg
+++ b/Lib/r/r.swg
@@ -12,6 +12,8 @@
 SWIGEXPORT void SWIG_init(void) {
 %}
 
+%include <rkw.swg>
+
 #define %Rruntime %insert("s")
 
 #define SWIG_Object SEXP
@@ -77,7 +79,7 @@ SWIG_InitializeModule(0);
 
 %typemap(scheck) int %{
   if(length($input) > 1) {
-     Rf_warning("using only the first element of $input")
+     warning("using only the first element of $input")
   }
 %}
 
diff --git a/Lib/r/rkw.swg b/Lib/r/rkw.swg
new file mode 100644
index 000000000..2c181faa0
--- /dev/null
+++ b/Lib/r/rkw.swg
@@ -0,0 +1,32 @@
+/*
+  Warnings for R keywords, built-in names and bad names.
+*/
+
+#define RKW(x) %keywordwarn("'" `x` "' is a R keyword, renaming to '_" `x`"'", rename="_%s")  `x`
+
+/*
+  Warnings for R reserved words taken from
+  http://cran.r-project.org/doc/manuals/R-lang.html#Reserved-words
+*/
+
+RKW(if);
+RKW(else);
+RKW(repeat);
+RKW(while);
+RKW(function);
+RKW(for);
+RKW(in);
+RKW(next);
+RKW(break);
+RKW(TRUE);
+RKW(FALSE);
+RKW(NULL);
+RKW(Inf);
+RKW(NaN);
+RKW(NA);
+RKW(NA_integer_);
+RKW(NA_real_);
+RKW(NA_complex_);
+RKW(NA_character_);
+
+#undef RKW
diff --git a/Lib/ruby/rubycontainer.swg b/Lib/ruby/rubycontainer.swg
index e3cae5778..919695ec2 100644
--- a/Lib/ruby/rubycontainer.swg
+++ b/Lib/ruby/rubycontainer.swg
@@ -691,10 +691,12 @@ namespace swig
       for ( ; i != e; )
 	{
 	  VALUE r = swig::from< Sequence::value_type >(*i);
-	  if ( RTEST( rb_yield(r) ) )
+	  if ( RTEST( rb_yield(r) ) ) {
 	    $self->erase(i++);
-	  else
+            e = self->end();
+	  } else {
 	    ++i;
+          }
 	}
 	
       return self;
diff --git a/Lib/ruby/rubykw.swg b/Lib/ruby/rubykw.swg
index fec47baff..194687b95 100644
--- a/Lib/ruby/rubykw.swg
+++ b/Lib/ruby/rubykw.swg
@@ -2,7 +2,7 @@
 #define RUBY_RUBYKW_SWG_
 
 /* Warnings for Ruby keywords */
-#define RUBYKW(x) %keywordwarn("'" `x` "' is a ruby keyword, and it will renamed as 'C_"`x`"'",rename="C_%s",fullname=1)  `x`
+#define RUBYKW(x) %keywordwarn("'" `x` "' is a ruby keyword, renaming to 'C_" `x` "'",rename="C_%s",fullname=1)  `x`
 
 /*
 
diff --git a/Lib/swiglabels.swg b/Lib/swiglabels.swg
index 09de6c969..b943afb47 100644
--- a/Lib/swiglabels.swg
+++ b/Lib/swiglabels.swg
@@ -40,6 +40,12 @@
 # endif
 #endif
 
+#ifndef SWIG_MSC_UNSUPPRESS_4505
+# if defined(_MSC_VER)
+#   pragma warning(disable : 4505) /* unreferenced local function has been removed */
+# endif 
+#endif
+
 #ifndef SWIGUNUSEDPARM
 # ifdef __cplusplus
 #   define SWIGUNUSEDPARM(p)
diff --git a/Lib/typemaps/primtypes.swg b/Lib/typemaps/primtypes.swg
index c59aa1d1e..42728e5fe 100644
--- a/Lib/typemaps/primtypes.swg
+++ b/Lib/typemaps/primtypes.swg
@@ -283,6 +283,7 @@ _apply_macro(Macro, ptrdiff_t          , Arg2);
 _apply_macro(Macro, std::size_t, Arg2);
 _apply_macro(Macro, std::ptrdiff_t, Arg2);
 _apply_macro(Macro, std::string, Arg2);
+_apply_macro(Macro, std::wstring, Arg2);
 _apply_macro(Macro, std::complex<float>, Arg2);
 _apply_macro(Macro, std::complex<double>, Arg2);
 %enddef
diff --git a/README b/README
index 61550e558..2898130b0 100644
--- a/README
+++ b/README
@@ -1,6 +1,6 @@
 SWIG (Simplified Wrapper and Interface Generator)
 
-Version: 1.3.35 (7 April 2008)
+Version: 1.3.36 (24 June 2008)
 
 Tagline: SWIG is a compiler that integrates C and C++ with languages
          including Perl, Python, Tcl, Ruby, PHP, Java, Ocaml, Lua,
@@ -91,6 +91,13 @@ A SWIG FAQ and other hints can be found on the SWIG Wiki:
 What's New?
 ===========
 
+SWIG-1.3.36 summary:
+- Enhancement to directors to wrap all protected members
+- Optimisation feature for objects returned by value
+- A few bugs fixes in the PHP, Java, Ruby, R, C#, Python, Lua and 
+  Perl modules
+- Other minor generic bug fixes
+
 SWIG-1.3.35 summary:
 - Octave language module added
 - Bug fixes in Python, Lua, Java, C#, Perl modules
diff --git a/Source/CParse/cscanner.c b/Source/CParse/cscanner.c
index 13e976b95..12556dcf6 100644
--- a/Source/CParse/cscanner.c
+++ b/Source/CParse/cscanner.c
@@ -420,23 +420,23 @@ int yylook(void) {
       return HBLOCK;
       
     case SWIG_TOKEN_COMMENT:
-    {
-      String *cmt = Scanner_text(scan);
-	  char *loc = Char(cmt);
-	  if ((strncmp(loc,"/*@SWIG@",6) == 0) && (loc[Len(cmt)-3] == '@')) {
-	    scanner_locator(cmt);
-	  }
-	  if (strncmp(loc, "/**<", 4) == 0 || strncmp(loc, "///<", 4) == 0||strncmp(loc, "/*!<", 4) == 0||strncmp(loc, "//!<", 4) == 0) {
-	    printf("Doxygen Post Comment: %s lines %d-%d [%s]\n", Char(Scanner_file(scan)), Scanner_start_line(scan), Scanner_line(scan), loc);
-	    yylval.str =  NewString(loc);
-	    return DOXYGENPOSTSTRING;
-	  }
-	  if (strncmp(loc, "/**", 3) == 0 || strncmp(loc, "///", 3) == 0||strncmp(loc, "/*!", 3) == 0||strncmp(loc, "//!", 3) == 0) {
-	    printf("Doxygen Comment: %s lines %d-%d [%s]\n", Char(Scanner_file(scan)), Scanner_start_line(scan), Scanner_line(scan), loc);
-	    yylval.str =  NewString(loc);
-	    return DOXYGENSTRING;
-	  }
-    }
+      {
+	String *cmt = Scanner_text(scan);
+	char *loc = Char(cmt);
+	if ((strncmp(loc,"/*@SWIG",7) == 0) && (loc[Len(cmt)-3] == '@')) {
+	  scanner_locator(cmt);
+	}
+	if (strncmp(loc, "/**<", 4) == 0 || strncmp(loc, "///<", 4) == 0||strncmp(loc, "/*!<", 4) == 0||strncmp(loc, "//!<", 4) == 0) {
+	  printf("Doxygen Post Comment: %s lines %d-%d [%s]\n", Char(Scanner_file(scan)), Scanner_start_line(scan), Scanner_line(scan), loc);
+	  yylval.str =  NewString(loc);
+	  return DOXYGENPOSTSTRING;
+	}
+	if (strncmp(loc, "/**", 3) == 0 || strncmp(loc, "///", 3) == 0||strncmp(loc, "/*!", 3) == 0||strncmp(loc, "//!", 3) == 0) {
+	  printf("Doxygen Comment: %s lines %d-%d [%s]\n", Char(Scanner_file(scan)), Scanner_start_line(scan), Scanner_line(scan), loc);
+	  yylval.str =  NewString(loc);
+	  return DOXYGENSTRING;
+	}
+      }
       break;
     case SWIG_TOKEN_ENDLINE:
       break;
@@ -700,7 +700,15 @@ int yylex(void) {
 		termtoken = SWIG_TOKEN_LPAREN;
 		termvalue = "(";
 		break;
-	      } else if (nexttok == SWIG_TOKEN_SEMI) {
+              } else if (nexttok == SWIG_TOKEN_CODEBLOCK) {
+                termtoken = SWIG_TOKEN_CODEBLOCK;
+                termvalue = Scanner_text(scan);
+                break;
+              } else if (nexttok == SWIG_TOKEN_LBRACE) {
+                termtoken = SWIG_TOKEN_LBRACE;
+                termvalue = "{";
+                break;
+              } else if (nexttok == SWIG_TOKEN_SEMI) {
 		termtoken = SWIG_TOKEN_SEMI;
 		termvalue = ";";
 		break;
@@ -869,8 +877,14 @@ int yylex(void) {
 	return (INLINE);
       if (strcmp(yytext, "%typemap") == 0)
 	return (TYPEMAP);
-      if (strcmp(yytext, "%feature") == 0)
+      if (strcmp(yytext, "%feature") == 0) {
+        /* The rename_active indicates we don't need the information of the 
+         * following function's return type. This applied for %rename, so do
+         * %feature. 
+         */
+        rename_active = 1;
 	return (FEATURE);
+      }
       if (strcmp(yytext, "%except") == 0)
 	return (EXCEPT);
       if (strcmp(yytext, "%importfile") == 0)
diff --git a/Source/CParse/parser.y b/Source/CParse/parser.y
index 09aeb7381..d16a743e4 100644
--- a/Source/CParse/parser.y
+++ b/Source/CParse/parser.y
@@ -383,7 +383,9 @@ static void add_symbols(Node *n) {
 	  Delete(prefix);
 	}
 
-	if (0 && !Getattr(n,"parentNode") && class_level) set_parentNode(n,class_decl[class_level - 1]);
+        /*
+	if (!Getattr(n,"parentNode") && class_level) set_parentNode(n,class_decl[class_level - 1]);
+        */
 	Setattr(n,"ismember","1");
       }
     }
@@ -2348,21 +2350,25 @@ feature_directive : FEATURE LPAREN idstring RPAREN declarator cpp_const stringbr
                     String *val = $7 ? NewString($7) : NewString("1");
                     new_feature($3, val, 0, $5.id, $5.type, $5.parms, $6.qualifier);
                     $$ = 0;
+                    scanner_clear_rename();
                   }
                   | FEATURE LPAREN idstring COMMA stringnum RPAREN declarator cpp_const SEMI {
                     String *val = Len($5) ? NewString($5) : 0;
                     new_feature($3, val, 0, $7.id, $7.type, $7.parms, $8.qualifier);
                     $$ = 0;
+                    scanner_clear_rename();
                   }
                   | FEATURE LPAREN idstring featattr RPAREN declarator cpp_const stringbracesemi {
                     String *val = $8 ? NewString($8) : NewString("1");
                     new_feature($3, val, $4, $6.id, $6.type, $6.parms, $7.qualifier);
                     $$ = 0;
+                    scanner_clear_rename();
                   }
                   | FEATURE LPAREN idstring COMMA stringnum featattr RPAREN declarator cpp_const SEMI {
                     String *val = Len($5) ? NewString($5) : 0;
                     new_feature($3, val, $6, $8.id, $8.type, $8.parms, $9.qualifier);
                     $$ = 0;
+                    scanner_clear_rename();
                   }
 
                   /* Global feature */
@@ -2370,21 +2376,25 @@ feature_directive : FEATURE LPAREN idstring RPAREN declarator cpp_const stringbr
                     String *val = $5 ? NewString($5) : NewString("1");
                     new_feature($3, val, 0, 0, 0, 0, 0);
                     $$ = 0;
+                    scanner_clear_rename();
                   }
                   | FEATURE LPAREN idstring COMMA stringnum RPAREN SEMI {
                     String *val = Len($5) ? NewString($5) : 0;
                     new_feature($3, val, 0, 0, 0, 0, 0);
                     $$ = 0;
+                    scanner_clear_rename();
                   }
                   | FEATURE LPAREN idstring featattr RPAREN stringbracesemi {
                     String *val = $6 ? NewString($6) : NewString("1");
                     new_feature($3, val, $4, 0, 0, 0, 0);
                     $$ = 0;
+                    scanner_clear_rename();
                   }
                   | FEATURE LPAREN idstring COMMA stringnum featattr RPAREN SEMI {
                     String *val = Len($5) ? NewString($5) : 0;
                     new_feature($3, val, $6, 0, 0, 0, 0);
                     $$ = 0;
+                    scanner_clear_rename();
                   }
                   ;
 
@@ -4215,10 +4225,11 @@ cpp_destructor_decl : NOT idtemplate LPAREN parms RPAREN cpp_end {
 	       /* Check for template names.  If the class is a template
 		  and the constructor is missing the template part, we
 		  add it */
-	        if (Classprefix && (c = strchr(Char(Classprefix),'<'))) {
-		  if (!Strchr($3,'<')) {
-		    $3 = NewStringf("%s%s",$3,c);
-		  }
+	        if (Classprefix) {
+                  c = strchr(Char(Classprefix),'<');
+                  if (c && !Strchr($3,'<')) {
+                    $3 = NewStringf("%s%s",$3,c);
+                  }
 		}
 		Setattr($$,"storage","virtual");
 	        name = NewStringf("%s",$3);
@@ -4534,12 +4545,8 @@ parms          : rawparms {
     	       ;
 
 rawparms          : parm ptail {
-		  if (1) { 
-		    set_nextSibling($1,$2);
-		    $$ = $1;
-		  } else {
-		    $$ = $2;
-		  }
+                  set_nextSibling($1,$2);
+                  $$ = $1;
 		}
                | empty { $$ = 0; }
                ;
@@ -4592,12 +4599,8 @@ valparms        : rawvalparms {
     	       ;
 
 rawvalparms     : valparm valptail {
-		  if (1) { 
-		    set_nextSibling($1,$2);
-		    $$ = $1;
-		  } else {
-		    $$ = $2;
-		  }
+                  set_nextSibling($1,$2);
+                  $$ = $1;
 		}
                | empty { $$ = 0; }
                ;
diff --git a/Source/CParse/templ.c b/Source/CParse/templ.c
index a1f0c8e08..a3e992f83 100644
--- a/Source/CParse/templ.c
+++ b/Source/CParse/templ.c
@@ -167,18 +167,21 @@ static int cparse_template_expand(Node *n, String *tname, String *rname, String
     add_parms(Getattr(n, "throws"), cpatchlist, typelist);
   } else if (Equal(nodeType, "destructor")) {
     String *name = Getattr(n, "name");
-    if (name && strchr(Char(name), '<')) {
-      Append(patchlist, Getattr(n, "name"));
-    } else {
-      Append(name, templateargs);
+    if (name) {
+      if (strchr(Char(name), '<'))
+        Append(patchlist, Getattr(n, "name"));
+      else
+        Append(name, templateargs);
     }
     name = Getattr(n, "sym:name");
-    if (name && strchr(Char(name), '<')) {
-      String *sn = Copy(tname);
-      Setattr(n, "sym:name", sn);
-      Delete(sn);
-    } else {
-      Replace(name, tname, rname, DOH_REPLACE_ANY);
+    if (name) {
+      if (strchr(Char(name), '<')) {
+        String *sn = Copy(tname);
+        Setattr(n, "sym:name", sn);
+        Delete(sn);
+      } else {
+        Replace(name, tname, rname, DOH_REPLACE_ANY);
+      }
     }
     /* Setattr(n,"sym:name",name); */
     Append(cpatchlist, Getattr(n, "code"));
@@ -281,13 +284,13 @@ int Swig_cparse_template_expand(Node *n, String *rname, ParmList *tparms, Symtab
     Delete(ptargs);
   }
 
-  if (0) {
+  /*
     Parm *p = tparms;
     while (p) {
       Printf(stdout, "tparm: '%s' '%s' '%s'\n", Getattr(p, "name"), Getattr(p, "type"), Getattr(p, "value"));
       p = nextSibling(p);
     }
-  }
+  */
 
   /*  Printf(stdout,"targs = '%s'\n", templateargs);
      Printf(stdout,"rname = '%s'\n", rname);
diff --git a/Source/DOH/hash.c b/Source/DOH/hash.c
index ccb94314a..62aef10f2 100644
--- a/Source/DOH/hash.c
+++ b/Source/DOH/hash.c
@@ -112,12 +112,11 @@ static void DelHash(DOH *ho) {
   int i;
 
   for (i = 0; i < h->hashsize; i++) {
-    if ((n = h->hashtable[i])) {
-      while (n) {
-	next = n->next;
-	DelNode(n);
-	n = next;
-      }
+    n = h->hashtable[i];
+    while (n) {
+      next = n->next;
+      DelNode(n);
+      n = next;
     }
   }
   DohFree(h->hashtable);
@@ -138,12 +137,11 @@ static void Hash_clear(DOH *ho) {
   int i;
 
   for (i = 0; i < h->hashsize; i++) {
-    if ((n = h->hashtable[i])) {
-      while (n) {
-	next = n->next;
-	DelNode(n);
-	n = next;
-      }
+    n = h->hashtable[i];
+    while (n) {
+      next = n->next;
+      DelNode(n);
+      n = next;
     }
     h->hashtable[i] = 0;
   }
@@ -454,11 +452,10 @@ static DOH *CopyHash(DOH *ho) {
 
   nho = DohObjMalloc(&DohHashType, nh);
   for (i = 0; i < h->hashsize; i++) {
-    if ((n = h->hashtable[i])) {
-      while (n) {
-	Hash_setattr(nho, n->key, n->object);
-	n = n->next;
-      }
+    n = h->hashtable[i];
+    while (n) {
+      Hash_setattr(nho, n->key, n->object);
+      n = n->next;
     }
   }
   return nho;
diff --git a/Source/Include/swigwarn.h b/Source/Include/swigwarn.h
index 174e8b001..8c4678847 100644
--- a/Source/Include/swigwarn.h
+++ b/Source/Include/swigwarn.h
@@ -247,10 +247,17 @@
 
 /* please leave 850-869 free for Modula 3 */
 
-#define WARN_PHP4_MULTIPLE_INHERITANCE         870
-#define WARN_PHP4_UNKNOWN_PRAGMA               871
+/* These are needed for backward compatibility, but you don't need to add
+ * PHP4 versions of new warnings since existing user interface files can't
+ * be using them.
+ */
+#define WARN_PHP4_MULTIPLE_INHERITANCE        870
+#define WARN_PHP4_UNKNOWN_PRAGMA              871
 
-/* please leave 870-889 free for Php */
+#define WARN_PHP_MULTIPLE_INHERITANCE         870
+#define WARN_PHP_UNKNOWN_PRAGMA               871
+
+/* please leave 870-889 free for PHP */
 
 
 /* Feel free to claim any number in this space that's not currently being used. Just make sure you
diff --git a/Source/Makefile.am b/Source/Makefile.am
index 1abe41cbd..65b5c6f6f 100644
--- a/Source/Makefile.am
+++ b/Source/Makefile.am
@@ -57,7 +57,7 @@ eswig_SOURCES =	CParse/cscanner.c		\
 		Modules/octave.cxx		\
 		Modules/overload.cxx		\
 		Modules/perl5.cxx		\
-		Modules/php4.cxx		\
+		Modules/php.cxx			\
 		Modules/pike.cxx		\
 		Modules/python.cxx		\
 		Modules/r.cxx			\
diff --git a/Source/Modules/allegrocl.cxx b/Source/Modules/allegrocl.cxx
index 561997276..217c89b1f 100644
--- a/Source/Modules/allegrocl.cxx
+++ b/Source/Modules/allegrocl.cxx
@@ -1084,7 +1084,8 @@ void emit_synonym(Node *synonym) {
   of_ltype = lookup_defined_foreign_ltype(of_name);
 
   // Printf(f_clhead,";; from emit-synonym\n");
-  Printf(f_clhead, "(swig-def-synonym-type %s\n   %s\n   %s)\n", syn_ltype, of_ltype, syn_type);
+  if( of_ltype )
+      Printf(f_clhead, "(swig-def-synonym-type %s\n   %s\n   %s)\n", syn_ltype, of_ltype, syn_type);
 
   Delete(synonym_ns);
   Delete(of_ns_list);
@@ -1521,6 +1522,8 @@ void ALLEGROCL::main(int argc, char *argv[]) {
 
   }
 
+  Preprocessor_define("SWIGALLEGROCL 1", 0);
+
   allow_overloading();
 }
 
@@ -1531,7 +1534,7 @@ int ALLEGROCL::top(Node *n) {
 
   swig_package = unique_swig_package ? NewStringf("swig.%s", module_name) : NewString("swig");
 
-  Printf(cl_filename, "%s%s.cl", SWIG_output_directory(), Swig_file_basename(Getattr(n,"infile")));
+  Printf(cl_filename, "%s%s.cl", SWIG_output_directory(), module_name);
 
   f_cl = NewFile(cl_filename, "w");
   if (!f_cl) {
@@ -2271,7 +2274,7 @@ int ALLEGROCL::emit_dispatch_defun(Node *n) {
   return SWIG_OK;
 }
 
-int ALLEGROCL::emit_defun(Node *n, File *f_cl) {
+int ALLEGROCL::emit_defun(Node *n, File *fcl) {
 #ifdef ALLEGROCL_WRAP_DEBUG
   Printf(stderr, "emit_defun: ENTER... ");
 #endif
@@ -2307,27 +2310,27 @@ int ALLEGROCL::emit_defun(Node *n, File *f_cl) {
   if (Generate_Wrapper) {
     String *extra_parms = id_converter_arguments(n)->noname_str();
     if (Getattr(n, "sym:overloaded"))
-      Printf(f_cl, "(swig-defmethod (\"%s\" \"%s\"%s)\n", funcname, mangled_name, extra_parms);
+      Printf(fcl, "(swig-defmethod (\"%s\" \"%s\"%s)\n", funcname, mangled_name, extra_parms);
     else
-      Printf(f_cl, "(swig-defun (\"%s\" \"%s\"%s)\n", funcname, mangled_name, extra_parms);
+      Printf(fcl, "(swig-defun (\"%s\" \"%s\"%s)\n", funcname, mangled_name, extra_parms);
     Delete(extra_parms);
   }
   // Just C
   else {
-    Printf(f_cl, "(swig-defun (\"%s\" \"%s\")\n", funcname, Generate_Wrapper ? mangled_name : funcname);
+    Printf(fcl, "(swig-defun (\"%s\" \"%s\")\n", funcname, Generate_Wrapper ? mangled_name : funcname);
   }
 
   //////////////////////////////////////
   // Lisp foreign call parameter list //
   //////////////////////////////////////
-  Printf(f_cl, "  (");
+  Printf(fcl, "  (");
 
   /* Special cases */
 
   if (ParmList_len(pl) == 0) {
-    Printf(f_cl, ":void");
+    Printf(fcl, ":void");
 /*  } else if (any_varargs(pl)) {
-    Printf(f_cl, "#| varargs |#");
+    Printf(fcl, "#| varargs |#");
     varargs=1; */
   } else {
     String *largs = NewString("");
@@ -2337,7 +2340,7 @@ int ALLEGROCL::emit_defun(Node *n, File *f_cl) {
       SwigType *argtype = Swig_cparse_type(Getattr(p, "tmap:ctype"));
 
       if (!first) {
-	Printf(f_cl, "\n   ");
+	Printf(fcl, "\n   ");
       }
 
       if (SwigType_isvarargs(argtype)) {
@@ -2393,7 +2396,7 @@ int ALLEGROCL::emit_defun(Node *n, File *f_cl) {
 	// if this parameter has been removed from the C/++ wrapper
 	// it shouldn't be in the lisp wrapper either.
 	if (!checkAttribute(p, "tmap:in:numinputs", "0")) {
-	  Printf(f_cl, "(%s %s %s %s %s)",
+	  Printf(fcl, "(%s %s %s %s %s)",
 		 // parms in the ff wrapper, but not in the lisp wrapper.
 		 (checkAttribute(p, "tmap:lin:numinputs", "0") ? ":p-" : ":p+"), argname, dispatchtype, ffitype, lisptype);
 
@@ -2479,12 +2482,12 @@ int ALLEGROCL::emit_defun(Node *n, File *f_cl) {
   Replaceall(wrap->code, "$ldestructor", ldestructor);
   Delete(ldestructor);
 
-  Printf(f_cl, ")\n");		/* finish arg list */
+  Printf(fcl, ")\n");		/* finish arg list */
 
   /////////////////////////////////////////////////////
   // Lisp foreign call return type and optimizations //
   /////////////////////////////////////////////////////
-  Printf(f_cl, "  (:returning (%s %s)", compose_foreign_type(result_type), get_lisp_type(Getattr(n, "type"), "result"));
+  Printf(fcl, "  (:returning (%s %s)", compose_foreign_type(result_type), get_lisp_type(Getattr(n, "type"), "result"));
 
   for (Iterator option = First(n); option.item; option = Next(option)) {
     if (Strncmp("feature:ffargs:", option.key, 15))
@@ -2494,12 +2497,12 @@ int ALLEGROCL::emit_defun(Node *n, File *f_cl) {
     Replaceall(option_name, "_", "-");
 
     // TODO: varargs vs call-direct ?
-    Printf(f_cl, "\n   %s %s", option_name, option_val);
+    Printf(fcl, "\n   %s %s", option_name, option_val);
 
     Delete(option_name);
   }
 
-  Printf(f_cl, ")\n  %s)\n\n", wrap->code);
+  Printf(fcl, ")\n  %s)\n\n", wrap->code);
   // Wrapper_print(wrap, stderr);
 
   Delete(result_type);
@@ -2518,6 +2521,8 @@ int ALLEGROCL::functionWrapper(Node *n) {
 
   ParmList *parms = CopyParmList(Getattr(n, "parms"));
   Wrapper *f = NewWrapper();
+  SwigType *t = Getattr(n, "type");
+  String *name = Getattr(n, "name");
 
   String *raw_return_type = Swig_typemap_lookup("ctype", n, "", 0);
   SwigType *return_type = Swig_cparse_type(raw_return_type);
@@ -2556,7 +2561,7 @@ int ALLEGROCL::functionWrapper(Node *n) {
     if (Getattr(n, "overload:ignore")) {
       // if we're the last overload, make sure to force the emit
       // of the rest of the overloads before we leave.
-      Printf(stderr, "ignored overload %s(%x)\n", Getattr(n, "name"), Getattr(n, "sym:nextSibling"));
+      Printf(stderr, "ignored overload %s(%x)\n", name, Getattr(n, "sym:nextSibling"));
       if (!Getattr(n, "sym:nextSibling")) {
 	update_package_if_needed(n);
 	emit_buffered_defuns(n);
@@ -2571,7 +2576,7 @@ int ALLEGROCL::functionWrapper(Node *n) {
   int gencomma = 0;
 
 #ifdef ALLEGROCL_DEBUG
-  Printf(stderr, "Walking parameters for %s '%s'\n", Getattr(n, "allegrocl:kind"), Getattr(n, "name"));
+  Printf(stderr, "Walking parameters for %s '%s'\n", Getattr(n, "allegrocl:kind"), name);
 #endif
   // Now walk the function parameter list and generate code to get arguments
   String *name_and_parms = NewStringf("%s (", mangled);
@@ -2625,12 +2630,16 @@ int ALLEGROCL::functionWrapper(Node *n) {
 
   String *actioncode = emit_action(n);
 
-  String *result_convert = Swig_typemap_lookup_out("out", n, "result", f, actioncode);
-  Replaceall(result_convert, "$result", "lresult");
-  Printf(f->code, "%s\n", result_convert);
-  Printf(f->code, "    return lresult;\n");
-  Delete(result_convert);
-  emit_return_variable(n, Getattr(n, "type"), f);
+  String *tm = Swig_typemap_lookup_out("out", n, "result", f, actioncode);
+  if (!is_void_return && tm) {
+    Replaceall(tm, "$result", "lresult");
+    Printf(f->code, "%s\n", tm);
+    Printf(f->code, "    return lresult;\n");
+    Delete(tm);
+  } else {
+    Swig_warning(WARN_TYPEMAP_OUT_UNDEF, input_file, line_number, "Unable to use return type %s in function %s.\n", SwigType_str(t, 0), name);
+  }
+  emit_return_variable(n, t, f);
 
   if (CPlusPlus) {
     Printf(f->code, "  } catch (...) {\n");
@@ -2935,11 +2944,9 @@ int ALLEGROCL::classHandler(Node *n) {
 #endif
 
   if (Generate_Wrapper)
-	  return cppClassHandler(n);
+    return cppClassHandler(n);
   else
-	  return cClassHandler(n);
-
-  return SWIG_OK;
+    return cClassHandler(n);
 }
 
 int ALLEGROCL::cClassHandler(Node *n) {
diff --git a/Source/Modules/cffi.cxx b/Source/Modules/cffi.cxx
index fb37392e8..4b3ddac70 100644
--- a/Source/Modules/cffi.cxx
+++ b/Source/Modules/cffi.cxx
@@ -444,7 +444,7 @@ int CFFI::functionWrapper(Node *n) {
   String *result_convert = Swig_typemap_lookup_out("out", n, "result", f, actioncode);
   Replaceall(result_convert, "$result", "lresult");
   Printf(f->code, "%s\n", result_convert);
-  Printf(f->code, "    return lresult;\n");
+  if(!is_void_return) Printf(f->code, "    return lresult;\n");
   Delete(result_convert);
   emit_return_variable(n, Getattr(n, "type"), f);
 
@@ -630,7 +630,7 @@ int CFFI::enumDeclaration(Node *n) {
     else {
       String *type = Getattr(c, "type");
       String *converted_value = convert_literal(value, type);
-      Printf(f_cl, "\n\t(%s %s)", slot_name, converted_value);
+      Printf(f_cl, "\n\t(%s #.%s)", slot_name, converted_value);
       Delete(converted_value);
     }
     Delete(value);
@@ -673,7 +673,7 @@ void CFFI::emit_class(Node *n) {
 
   Printf(supers, ")");
   Printf(f_clos, "\n(cl:defclass %s%s", lisp_name, supers);
-  Printf(f_clos, "\n  ((ff :reader ff-pointer)))\n\n");
+  Printf(f_clos, "\n  ((ff-pointer :reader ff-pointer)))\n\n");
 
   Parm *pattern = NewParm(Getattr(n, "name"), NULL);
 
diff --git a/Source/Modules/chicken.cxx b/Source/Modules/chicken.cxx
index a76e09945..2298d2939 100644
--- a/Source/Modules/chicken.cxx
+++ b/Source/Modules/chicken.cxx
@@ -329,7 +329,6 @@ int CHICKEN::functionWrapper(Node *n) {
   Parm *p;
   int i;
   String *wname;
-  String *source;
   Wrapper *f;
   String *mangle = NewString("");
   String *get_pointers;
@@ -398,8 +397,6 @@ int CHICKEN::functionWrapper(Node *n) {
     SwigType *pt = Getattr(p, "type");
     String *ln = Getattr(p, "lname");
 
-    source = NewStringf("scm%d", i + 1);
-
     Printf(f->def, ", C_word scm%d", i + 1);
     Printf(declfunc, ",C_word");
 
@@ -407,6 +404,7 @@ int CHICKEN::functionWrapper(Node *n) {
     if ((tm = Getattr(p, "tmap:in"))) {
       String *parse = Getattr(p, "tmap:in:parse");
       if (!parse) {
+        String *source = NewStringf("scm%d", i + 1);
 	Replaceall(tm, "$source", source);
 	Replaceall(tm, "$target", ln);
 	Replaceall(tm, "$input", source);
@@ -445,20 +443,15 @@ int CHICKEN::functionWrapper(Node *n) {
 	    }
 	  }
 	}
-
-      } else {
+        Delete(source);
       }
 
-
       p = Getattr(p, "tmap:in:next");
       continue;
     } else {
       Swig_warning(WARN_TYPEMAP_IN_UNDEF, input_file, line_number, "Unable to use type %s as a function argument.\n", SwigType_str(pt, 0));
       break;
     }
-
-    Delete(source);
-    p = nextSibling(p);
   }
 
   /* finish argument marshalling */
@@ -1510,7 +1503,7 @@ int CHICKEN::validIdentifier(String *s) {
   /* ------------------------------------------------------------
    * closNameMapping()
    * Maps the identifier from C++ to the CLOS based on command 
-   * line paramaters and such.
+   * line parameters and such.
    * If class_name = "" that means the mapping is for a function or
    * variable not attached to any class.
    * ------------------------------------------------------------ */
diff --git a/Source/Modules/csharp.cxx b/Source/Modules/csharp.cxx
index df4677e26..431181355 100644
--- a/Source/Modules/csharp.cxx
+++ b/Source/Modules/csharp.cxx
@@ -1073,7 +1073,9 @@ public:
     global_variable_flag = false;
     generate_property_declaration_flag = false;
 
-    Printf(module_class_code, "\n  }\n\n");
+    if (proxy_flag) {
+      Printf(module_class_code, "\n  }\n\n");
+    }
 
     return ret;
   }
@@ -1885,6 +1887,7 @@ public:
     bool setter_flag = false;
     String *pre_code = NewString("");
     String *post_code = NewString("");
+    String *terminator_code = NewString("");
 
     if (!proxy_flag)
       return;
@@ -1924,7 +1927,7 @@ public:
       Swig_warning(WARN_CSHARP_TYPEMAP_CSWTYPE_UNDEF, input_file, line_number, "No cstype typemap defined for %s\n", SwigType_str(t, 0));
     }
 
-    if (proxy_flag && wrapping_member_flag && !enum_constant_flag) {
+    if (wrapping_member_flag && !enum_constant_flag) {
       // Properties
       setter_flag = (Cmp(Getattr(n, "sym:name"), Swig_name_set(Swig_name_member(proxy_class_name, variable_name))) == 0);
       if (setter_flag)
@@ -1996,7 +1999,8 @@ public:
       if (!(variable_wrapper_flag && i == 0)) {
 	SwigType *pt = Getattr(p, "type");
 	String *param_type = NewString("");
-	last_parm = p;
+        if (setter_flag)
+          last_parm = p;
 
 	/* Get the C# parameter type */
 	if ((tm = Getattr(p, "tmap:cstype"))) {
@@ -2032,6 +2036,14 @@ public:
               Printf(post_code, "\n");
             Printv(post_code, post, NIL);
           }
+          String *terminator = Getattr(p, "tmap:csin:terminator");
+          if (terminator) {
+            substituteClassname(pt, terminator);
+            Replaceall(terminator, "$csinput", arg);
+            if (Len(terminator_code) > 0)
+              Insert(terminator_code, 0, "\n");
+            Insert(terminator_code, 0, terminator);
+          }
 	  Printv(imcall, tm, NIL);
 	} else {
 	  Swig_warning(WARN_CSHARP_TYPEMAP_CSIN_UNDEF, input_file, line_number, "No csin typemap defined for %s\n", SwigType_str(pt, 0));
@@ -2057,7 +2069,8 @@ public:
       excodeSubstitute(n, tm, "csout", n);
       bool is_pre_code = Len(pre_code) > 0;
       bool is_post_code = Len(post_code) > 0;
-      if (is_pre_code || is_post_code) {
+      bool is_terminator_code = Len(terminator_code) > 0;
+      if (is_pre_code || is_post_code || is_terminator_code) {
         Replaceall(tm, "\n ", "\n   "); // add extra indentation to code in typemap
         if (is_post_code) {
           Insert(tm, 0, "\n    try ");
@@ -2069,6 +2082,9 @@ public:
           Insert(tm, 0, pre_code);
           Insert(tm, 0, "\n");
         }
+        if (is_terminator_code) {
+          Printv(tm, "\n", terminator_code, NIL);
+        }
 	Insert(tm, 0, "{");
 	Printf(tm, "\n  }");
       }
@@ -2107,7 +2123,7 @@ public:
       Swig_warning(WARN_CSHARP_TYPEMAP_CSOUT_UNDEF, input_file, line_number, "No csout typemap defined for %s\n", SwigType_str(t, 0));
     }
 
-    if (proxy_flag && wrapping_member_flag && !enum_constant_flag) {
+    if (wrapping_member_flag && !enum_constant_flag) {
       // Properties
       if (generate_property_declaration_flag) {	// Ensure the declaration is generated just once should the property contain both a set and get
 	// Get the C# variable type - obtained differently depending on whether a setter is required.
@@ -2168,6 +2184,7 @@ public:
 
     Delete(pre_code);
     Delete(post_code);
+    Delete(terminator_code);
     Delete(function_code);
     Delete(return_type);
     Delete(imcall);
@@ -2188,6 +2205,7 @@ public:
     String *helper_args = NewString("");
     String *pre_code = NewString("");
     String *post_code = NewString("");
+    String *terminator_code = NewString("");
     String *im_return_type = NewString("");
     bool feature_director = (parentNode(n) && Swig_directorclass(n));
 
@@ -2283,6 +2301,14 @@ public:
               Printf(post_code, "\n");
             Printv(post_code, post, NIL);
           }
+          String *terminator = Getattr(p, "tmap:csin:terminator");
+          if (terminator) {
+            substituteClassname(pt, terminator);
+            Replaceall(terminator, "$csinput", arg);
+            if (Len(terminator_code) > 0)
+              Insert(terminator_code, 0, "\n");
+            Insert(terminator_code, 0, terminator);
+          }
           cshin = Getattr(p, "tmap:csin:cshin");
           if (cshin)
             Replaceall(cshin, "$csinput", arg);
@@ -2339,7 +2365,8 @@ public:
 
       bool is_pre_code = Len(pre_code) > 0;
       bool is_post_code = Len(post_code) > 0;
-      if (is_pre_code || is_post_code) {
+      bool is_terminator_code = Len(terminator_code) > 0;
+      if (is_pre_code || is_post_code || is_terminator_code) {
         Printf(helper_code, " {\n");
         if (is_pre_code) {
           Printv(helper_code, pre_code, "\n", NIL);
@@ -2351,6 +2378,9 @@ public:
         } else {
           Printv(helper_code, "    return ", imcall, ";", NIL);
         }
+        if (is_terminator_code) {
+          Printv(helper_code, "\n", terminator_code, NIL);
+        }
         Printf(helper_code, "\n  }\n");
         String *helper_name = NewStringf("%s.SwigConstruct%s(%s)", proxy_class_name, proxy_class_name, helper_args);
         String *im_outattributes = Getattr(n, "tmap:imtype:outattributes");
@@ -2369,6 +2399,7 @@ public:
       Delete(im_return_type);
       Delete(pre_code);
       Delete(post_code);
+      Delete(terminator_code);
       Delete(construct_tm);
       Delete(attributes);
       Delete(overloaded_name);
@@ -2486,6 +2517,7 @@ public:
     bool setter_flag = false;
     String *pre_code = NewString("");
     String *post_code = NewString("");
+    String *terminator_code = NewString("");
 
     if (l) {
       if (SwigType_type(Getattr(l, "type")) == T_VOID) {
@@ -2541,6 +2573,7 @@ public:
     num_arguments = emit_num_arguments(l);
     num_required = emit_num_required(l);
 
+    bool global_or_member_variable = global_variable_flag || (wrapping_member_flag && !enum_constant_flag);
     int gencomma = 0;
 
     /* Output each parameter */
@@ -2567,7 +2600,7 @@ public:
       if (gencomma)
 	Printf(imcall, ", ");
 
-      String *arg = makeParameterName(n, p, i, setter_flag);
+      String *arg = makeParameterName(n, p, i, global_or_member_variable);
 
       // Use typemaps to transform type used in C# wrapper function (in proxy class) to type used in PInvoke function (in intermediary class)
       if ((tm = Getattr(p, "tmap:csin"))) {
@@ -2589,6 +2622,14 @@ public:
             Printf(post_code, "\n");
 	  Printv(post_code, post, NIL);
 	}
+        String *terminator = Getattr(p, "tmap:csin:terminator");
+        if (terminator) {
+          substituteClassname(pt, terminator);
+          Replaceall(terminator, "$csinput", arg);
+          if (Len(terminator_code) > 0)
+            Insert(terminator_code, 0, "\n");
+          Insert(terminator_code, 0, terminator);
+        }
 	Printv(imcall, tm, NIL);
       } else {
 	Swig_warning(WARN_CSHARP_TYPEMAP_CSIN_UNDEF, input_file, line_number, "No csin typemap defined for %s\n", SwigType_str(pt, 0));
@@ -2613,7 +2654,8 @@ public:
       excodeSubstitute(n, tm, "csout", n);
       bool is_pre_code = Len(pre_code) > 0;
       bool is_post_code = Len(post_code) > 0;
-      if (is_pre_code || is_post_code) {
+      bool is_terminator_code = Len(terminator_code) > 0;
+      if (is_pre_code || is_post_code || is_terminator_code) {
         Replaceall(tm, "\n ", "\n   "); // add extra indentation to code in typemap
         if (is_post_code) {
           Insert(tm, 0, "\n    try ");
@@ -2625,6 +2667,9 @@ public:
           Insert(tm, 0, pre_code);
           Insert(tm, 0, "\n");
         }
+        if (is_terminator_code) {
+          Printv(tm, "\n", terminator_code, NIL);
+        }
 	Insert(tm, 0, "{");
 	Printf(tm, "\n  }");
       }
@@ -2700,6 +2745,7 @@ public:
 
     Delete(pre_code);
     Delete(post_code);
+    Delete(terminator_code);
     Delete(function_code);
     Delete(return_type);
     Delete(imcall);
@@ -2755,7 +2801,7 @@ public:
 	value = Getattr(n, "enumvalue") ? Copy(Getattr(n, "enumvalue")) : Copy(Getattr(n, "enumvalueex"));
       } else {
 	// Get the enumvalue from a PINVOKE call
-	if (!getCurrentClass() || !cparse_cplusplus) {
+	if (!getCurrentClass() || !cparse_cplusplus || !proxy_flag) {
 	  // Strange hack to change the name
 	  Setattr(n, "name", Getattr(n, "value"));	/* for wrapping of enums in a namespace when emit_action is used */
 	  constantWrapper(n);
@@ -2877,7 +2923,7 @@ public:
    *   n - Node
    *   p - parameter node
    *   arg_num - parameter argument number
-   *   setter  - set this flag when wrapping member variables
+   *   setter  - set this flag when wrapping variables
    * Return:
    *   arg - a unique parameter name
    * ----------------------------------------------------------------------------- */
@@ -2886,20 +2932,22 @@ public:
 
     String *arg = 0;
     String *pn = Getattr(p, "name");
-    if (setter) {
+
+    // Use C parameter name unless it is a duplicate or an empty parameter name
+    int count = 0;
+    ParmList *plist = Getattr(n, "parms");
+    while (plist) {
+      if ((Cmp(pn, Getattr(plist, "name")) == 0))
+        count++;
+      plist = nextSibling(plist);
+    }
+    String *wrn = pn ? Swig_name_warning(p, 0, pn, 0) : 0;
+    arg = (!pn || (count > 1) || wrn) ? NewStringf("arg%d", arg_num) : Copy(pn);
+
+    if (setter && Cmp(arg, "self") != 0) {
       // Note that in C# properties, the input variable name is always called 'value'
+      Delete(arg);      
       arg = NewString("value");
-    } else {
-      // Use C parameter name unless it is a duplicate or an empty parameter name
-      int count = 0;
-      ParmList *plist = Getattr(n, "parms");
-      while (plist) {
-	if ((Cmp(pn, Getattr(plist, "name")) == 0))
-	  count++;
-	plist = nextSibling(plist);
-      }
-      String *wrn = pn ? Swig_name_warning(p, 0, pn, 0) : 0;
-      arg = (!pn || (count > 1) || wrn) ? NewStringf("arg%d", arg_num) : Copy(pn);
     }
 
     return arg;
diff --git a/Source/Modules/guile.cxx b/Source/Modules/guile.cxx
index 2390e8ad6..f5f080034 100644
--- a/Source/Modules/guile.cxx
+++ b/Source/Modules/guile.cxx
@@ -1649,7 +1649,7 @@ public:
   /* ------------------------------------------------------------
    * goopsNameMapping()
    * Maps the identifier from C++ to the GOOPS based * on command 
-   * line paramaters and such.
+   * line parameters and such.
    * If class_name = "" that means the mapping is for a function or
    * variable not attached to any class.
    * ------------------------------------------------------------ */
diff --git a/Source/Modules/java.cxx b/Source/Modules/java.cxx
index a21e37bf4..961f9098c 100644
--- a/Source/Modules/java.cxx
+++ b/Source/Modules/java.cxx
@@ -2016,7 +2016,7 @@ public:
       Swig_warning(WARN_JAVA_TYPEMAP_JSTYPE_UNDEF, input_file, line_number, "No jstype typemap defined for %s\n", SwigType_str(t, 0));
     }
 
-    if (proxy_flag && wrapping_member_flag && !enum_constant_flag) {
+    if (wrapping_member_flag && !enum_constant_flag) {
       // For wrapping member variables (Javabean setter)
       setter_flag = (Cmp(Getattr(n, "sym:name"), Swig_name_set(Swig_name_member(proxy_class_name, variable_name))) == 0);
     }
@@ -2578,6 +2578,7 @@ public:
     num_arguments = emit_num_arguments(l);
     num_required = emit_num_required(l);
 
+    bool global_or_member_variable = global_variable_flag || (wrapping_member_flag && !enum_constant_flag);
     int gencomma = 0;
 
     /* Output each parameter */
@@ -2602,7 +2603,7 @@ public:
       if (gencomma)
 	Printf(imcall, ", ");
 
-      String *arg = makeParameterName(n, p, i, setter_flag);
+      String *arg = makeParameterName(n, p, i, global_or_member_variable);
 
       // Use typemaps to transform type used in Java wrapper function (in proxy class) to type used in JNI function (in intermediary class)
       if ((tm = Getattr(p, "tmap:javain"))) {
@@ -2747,7 +2748,7 @@ public:
 	value = Getattr(n, "enumvalue") ? Copy(Getattr(n, "enumvalue")) : Copy(Getattr(n, "enumvalueex"));
       } else {
 	// Get the enumvalue from a JNI call
-	if (!getCurrentClass() || !cparse_cplusplus) {
+	if (!getCurrentClass() || !cparse_cplusplus || !proxy_flag) {
 	  // Strange hack to change the name
 	  Setattr(n, "name", Getattr(n, "value"));	/* for wrapping of enums in a namespace when emit_action is used */
 	  constantWrapper(n);
@@ -2874,7 +2875,7 @@ public:
    *   n - Node
    *   p - parameter node
    *   arg_num - parameter argument number
-   *   setter  - set this flag when wrapping member variables
+   *   setter  - set this flag when wrapping variables
    * Return:
    *   arg - a unique parameter name
    * ----------------------------------------------------------------------------- */
@@ -2883,21 +2884,23 @@ public:
 
     String *arg = 0;
     String *pn = Getattr(p, "name");
-    if (setter) {
+
+    // Use C parameter name unless it is a duplicate or an empty parameter name
+    int count = 0;
+    ParmList *plist = Getattr(n, "parms");
+    while (plist) {
+      if ((Cmp(pn, Getattr(plist, "name")) == 0))
+        count++;
+      plist = nextSibling(plist);
+    }
+    String *wrn = pn ? Swig_name_warning(p, 0, pn, 0) : 0;
+    arg = (!pn || (count > 1) || wrn) ? NewStringf("arg%d", arg_num) : Copy(pn);
+
+    if (setter && Cmp(arg, "self") != 0) {
       // Note that for setters the parameter name is always set but sometimes includes C++ 
       // scope resolution, so we need to strip off the scope resolution to make a valid name.
+      Delete(arg);
       arg = NewString("value");	//Swig_scopename_last(pn);
-    } else {
-      // Use C parameter name unless it is a duplicate or an empty parameter name
-      int count = 0;
-      ParmList *plist = Getattr(n, "parms");
-      while (plist) {
-	if ((Cmp(pn, Getattr(plist, "name")) == 0))
-	  count++;
-	plist = nextSibling(plist);
-      }
-      String *wrn = pn ? Swig_name_warning(p, 0, pn, 0) : 0;
-      arg = (!pn || (count > 1) || wrn) ? NewStringf("arg%d", arg_num) : Copy(pn);
     }
 
     return arg;
diff --git a/Source/Modules/lang.cxx b/Source/Modules/lang.cxx
index 368dc2c85..e2fd93f7b 100644
--- a/Source/Modules/lang.cxx
+++ b/Source/Modules/lang.cxx
@@ -1105,38 +1105,33 @@ int Language::globalfunctionHandler(Node *n) {
   String *name = Getattr(n, "name");
   String *symname = Getattr(n, "sym:name");
   SwigType *type = Getattr(n, "type");
-  String *storage = Getattr(n, "storage");
   ParmList *parms = Getattr(n, "parms");
 
-  if (0 && (Cmp(storage, "static") == 0)) {
-    Swig_restore(n);
-    return SWIG_NOWRAP;		/* Can't wrap static functions */
-  } else {
-    /* Check for callback mode */
-    String *cb = GetFlagAttr(n, "feature:callback");
-    if (cb) {
-      String *cbname = Getattr(n, "feature:callback:name");
-      if (!cbname) {
-	cbname = NewStringf(cb, symname);
-	Setattr(n, "feature:callback:name", cbname);
-      }
-
-      callbackfunctionHandler(n);
-      if (Cmp(cbname, symname) == 0) {
-	Delete(cbname);
-	Swig_restore(n);
-	return SWIG_NOWRAP;
-      }
-      Delete(cbname);
+  /* Check for callback mode */
+  String *cb = GetFlagAttr(n, "feature:callback");
+  if (cb) {
+    String *cbname = Getattr(n, "feature:callback:name");
+    if (!cbname) {
+      cbname = NewStringf(cb, symname);
+      Setattr(n, "feature:callback:name", cbname);
     }
-    Setattr(n, "parms", nonvoid_parms(parms));
-    String *call = Swig_cfunction_call(name, parms);
-    String *cres = Swig_cresult(type, "result", call);
-    Setattr(n, "wrap:action", cres);
-    Delete(cres);
-    Delete(call);
-    functionWrapper(n);
+
+    callbackfunctionHandler(n);
+    if (Cmp(cbname, symname) == 0) {
+      Delete(cbname);
+      Swig_restore(n);
+      return SWIG_NOWRAP;
+    }
+    Delete(cbname);
   }
+  Setattr(n, "parms", nonvoid_parms(parms));
+  String *call = Swig_cfunction_call(name, parms);
+  String *cres = Swig_cresult(type, "result", call);
+  Setattr(n, "wrap:action", cres);
+  Delete(cres);
+  Delete(call);
+  functionWrapper(n);
+
   Swig_restore(n);
   return SWIG_OK;
 }
@@ -1384,9 +1379,6 @@ int Language::variableHandler(Node *n) {
  * ---------------------------------------------------------------------- */
 
 int Language::globalvariableHandler(Node *n) {
-  String *storage = Getattr(n, "storage");
-  if (0 && (Cmp(storage, "static") == 0))
-    return SWIG_NOWRAP;
   variableWrapper(n);
   return SWIG_OK;
 }
@@ -2116,8 +2108,8 @@ int Language::classDirector(Node *n) {
   String *using_protected_members_code = NewString("");
   for (ni = Getattr(n, "firstChild"); ni; ni = nextSibling(ni)) {
     Node *nodeType = Getattr(ni, "nodeType");
-    bool cdecl = (Cmp(nodeType, "cdecl") == 0);
-    if (cdecl && !GetFlag(ni, "feature:ignore")) {
+    bool cdeclaration = (Cmp(nodeType, "cdecl") == 0);
+    if (cdeclaration && !GetFlag(ni, "feature:ignore")) {
       if (is_non_virtual_protected_access(ni)) {
         Node *overloaded = Getattr(ni, "sym:overloaded");
         // emit the using base::member statement (but only once if the method is overloaded)
@@ -3410,7 +3402,8 @@ int Language::is_assignable(Node *n) {
   SwigType *ftd = SwigType_typedef_resolve_all(type);
   SwigType *td = SwigType_strip_qualifiers(ftd);
   if (SwigType_type(td) == T_USER) {
-    if ((cn = Swig_symbol_clookup(td, 0))) {
+    cn = Swig_symbol_clookup(td, 0);
+    if (cn) {
       if ((Strcmp(nodeType(cn), "class") == 0)) {
 	if (Getattr(cn, "allocate:noassign")) {
 	  SetFlag(n, "feature:immutable");
diff --git a/Source/Modules/lua.cxx b/Source/Modules/lua.cxx
index f46c9e809..6113da960 100644
--- a/Source/Modules/lua.cxx
+++ b/Source/Modules/lua.cxx
@@ -490,8 +490,6 @@ public:
         Swig_warning(WARN_TYPEMAP_IN_UNDEF, input_file, line_number, "Unable to use type %s as a function argument.\n", SwigType_str(pt, 0));
         break;
       }
-
-      p = nextSibling(p);
     }
 
     // add all argcheck code
@@ -1101,7 +1099,6 @@ public:
   virtual int staticmemberfunctionHandler(Node *n) {
     current = STATIC_FUNC;
     return Language::staticmemberfunctionHandler(n);
-    current = NO_CPP;
   }
 
   /* ------------------------------------------------------------
@@ -1123,7 +1120,6 @@ public:
     //    REPORT("staticmembervariableHandler",n);
     current = STATIC_VAR;
     return Language::staticmembervariableHandler(n);
-    current = NO_CPP;
   }
 
   /* ---------------------------------------------------------------------
diff --git a/Source/Modules/main.cxx b/Source/Modules/main.cxx
index 3453f5de2..901ee812e 100644
--- a/Source/Modules/main.cxx
+++ b/Source/Modules/main.cxx
@@ -33,7 +33,7 @@ int GenerateDefault = 1;	// Generate default constructors
 int Verbose = 0;
 int AddExtern = 0;
 int NoExcept = 0;
-int SwigRuntime = 0;		// 0 = no option, 1 = -c or -runtime, 2 = -noruntime
+int SwigRuntime = 0;		// 0 = no option, 1 = -runtime, 2 = -noruntime
 
 /* Suppress warning messages for private inheritance, preprocessor evaluation etc...
    WARN_PP_EVALUATION            202
@@ -491,13 +491,13 @@ void SWIG_getoptions(int argc, char *argv[]) {
 	Wrapper_compact_print_mode_set(1);
 	Wrapper_virtual_elimination_mode_set(1);
 	Swig_mark_arg(i);
-      } else if (strcmp(argv[i], "-runtime") == 0) {
+      } else if (strcmp(argv[i], "-runtime") == 0) { // Used to also accept -c. removed in swig-1.3.36
 	Swig_mark_arg(i);
-	Swig_warning(WARN_DEPRECATED_OPTC, "SWIG", 1, "-c, -runtime, -noruntime command line options are deprecated.\n");
+	Swig_warning(WARN_DEPRECATED_OPTC, "SWIG", 1, "-runtime, -noruntime command line options are deprecated.\n");
 	SwigRuntime = 1;
-      } else if ((strcmp(argv[i], "-c") == 0) || (strcmp(argv[i], "-noruntime") == 0)) {
+      } else if (strcmp(argv[i], "-noruntime") == 0) {
 	Swig_mark_arg(i);
-	Swig_warning(WARN_DEPRECATED_OPTC, "SWIG", 1, "-c, -runtime, -noruntime command line options are deprecated.\n");
+	Swig_warning(WARN_DEPRECATED_OPTC, "SWIG", 1, "-runtime, -noruntime command line options are deprecated.\n");
 	SwigRuntime = 2;
       } else if (strcmp(argv[i], "-external-runtime") == 0) {
 	external_runtime = 1;
diff --git a/Source/Modules/modula3.cxx b/Source/Modules/modula3.cxx
index 99d28e167..6cb24d39a 100644
--- a/Source/Modules/modula3.cxx
+++ b/Source/Modules/modula3.cxx
@@ -472,9 +472,9 @@ MODULA3():
 	  cap = true;
 	} else {
 	  if (cap) {
-	    m3sym[i] = toupper(c);
+	    m3sym[i] = (char)toupper(c);
 	  } else {
-	    m3sym[i] = tolower(c);
+	    m3sym[i] = (char)tolower(c);
 	  }
 	  cap = false;
 	}
diff --git a/Source/Modules/ocaml.cxx b/Source/Modules/ocaml.cxx
index 9f5677ba5..0d0f4c7f2 100755
--- a/Source/Modules/ocaml.cxx
+++ b/Source/Modules/ocaml.cxx
@@ -1292,56 +1292,50 @@ public:
    * which means looking up and registering by typedef and enum name. */
   int enumDeclaration(Node *n) {
     String *name = Getattr(n, "name");
-    String *oname = name ? NewString(name) : NULL;
-    /* name is now fully qualified */
-    String *fully_qualified_name = NewString(name);
-    bool seen_enum = false;
-    if (name_qualifier)
-      Delete(name_qualifier);
-    char *strip_position;
-    name_qualifier = fully_qualify_enum_name(n, NewString(""));
+    if (name) {
+      String *oname = NewString(name);
+      /* name is now fully qualified */
+      String *fully_qualified_name = NewString(name);
+      bool seen_enum = false;
+      if (name_qualifier)
+        Delete(name_qualifier);
+      char *strip_position;
+      name_qualifier = fully_qualify_enum_name(n, NewString(""));
 
-    /* Recent changes have distrubed enum and template naming again.
-     * Will try to keep it consistent by can't guarantee much given
-     * that these things move around a lot.
-     *
-     * I need to figure out a way to isolate this module better.
-     */
-    if (oname) {
       strip_position = strstr(Char(oname), "::");
 
       while (strip_position) {
-	strip_position += 2;
-	oname = NewString(strip_position);
-	strip_position = strstr(Char(oname), "::");
-      }
-    }
-
-    seen_enum = oname ? (Getattr(seen_enums, fully_qualified_name) ? true : false) : false;
-
-    if (oname && !seen_enum) {
-      const_enum = true;
-      Printf(f_enum_to_int, "| `%s -> (match y with\n", oname);
-      Printf(f_int_to_enum, "| `%s -> C_enum (\n", oname);
-      /* * * * A note about enum name resolution * * * *
-       * This code should now work, but I think we can do a bit better.
-       * The problem I'm having is that swig isn't very precise about
-       * typedef name resolution.  My opinion is that SwigType_typedef
-       * resolve_all should *always* return the enum tag if one exists,
-       * rather than the admittedly friendlier enclosing typedef.
-       * 
-       * This would make one of the cases below unnecessary. 
-       * * * */
-      Printf(f_mlbody, "let _ = Callback.register \"%s_marker\" (`%s)\n", fully_qualified_name, oname);
-      if (!strncmp(Char(fully_qualified_name), "enum ", 5)) {
-	String *fq_noenum = NewString(Char(fully_qualified_name) + 5);
-	Printf(f_mlbody,
-	       "let _ = Callback.register \"%s_marker\" (`%s)\n" "let _ = Callback.register \"%s_marker\" (`%s)\n", fq_noenum, oname, fq_noenum, name);
+        strip_position += 2;
+        oname = NewString(strip_position);
+        strip_position = strstr(Char(oname), "::");
       }
 
-      Printf(f_enumtypes_type, "| `%s\n", oname);
-      Insert(fully_qualified_name, 0, "enum ");
-      Setattr(seen_enums, fully_qualified_name, n);
+      seen_enum = (Getattr(seen_enums, fully_qualified_name) ? true : false);
+
+      if (!seen_enum) {
+        const_enum = true;
+        Printf(f_enum_to_int, "| `%s -> (match y with\n", oname);
+        Printf(f_int_to_enum, "| `%s -> C_enum (\n", oname);
+        /* * * * A note about enum name resolution * * * *
+         * This code should now work, but I think we can do a bit better.
+         * The problem I'm having is that swig isn't very precise about
+         * typedef name resolution.  My opinion is that SwigType_typedef
+         * resolve_all should *always* return the enum tag if one exists,
+         * rather than the admittedly friendlier enclosing typedef.
+         * 
+         * This would make one of the cases below unnecessary. 
+         * * * */
+        Printf(f_mlbody, "let _ = Callback.register \"%s_marker\" (`%s)\n", fully_qualified_name, oname);
+        if (!strncmp(Char(fully_qualified_name), "enum ", 5)) {
+          String *fq_noenum = NewString(Char(fully_qualified_name) + 5);
+          Printf(f_mlbody,
+                 "let _ = Callback.register \"%s_marker\" (`%s)\n" "let _ = Callback.register \"%s_marker\" (`%s)\n", fq_noenum, oname, fq_noenum, name);
+        }
+
+        Printf(f_enumtypes_type, "| `%s\n", oname);
+        Insert(fully_qualified_name, 0, "enum ");
+        Setattr(seen_enums, fully_qualified_name, n);
+      }
     }
 
     int ret = Language::enumDeclaration(n);
diff --git a/Source/Modules/php4.cxx b/Source/Modules/php.cxx
similarity index 64%
rename from Source/Modules/php4.cxx
rename to Source/Modules/php.cxx
index cfe948e3f..9369c2489 100644
--- a/Source/Modules/php4.cxx
+++ b/Source/Modules/php.cxx
@@ -13,11 +13,9 @@
  * Short term:
  *
  * Sort out auto-renaming of method and class names which are reserved
- *   words (e.g. empty, clone, exception, etc.) vs -php4/-php5 in some
- *   sane way.
+ *   words (e.g. empty, clone, exception, etc.)
  *
- * Sort out wrapping of static member variables in OO PHP5 (which first may
- *   mean we need to sort them out for PHP4!)
+ * Sort out wrapping of static member variables in OO PHP5.
  *
  * Medium term:
  *
@@ -39,7 +37,7 @@
 
 /*
  * TODO: Replace remaining stderr messages with Swig_error or Swig_warning
- * (may need to add more WARN_PHP4_xxx codes...)
+ * (may need to add more WARN_PHP_xxx codes...)
  */
 
 char cvsroot_php4_cxx[] = "$Id$";
@@ -50,16 +48,10 @@ char cvsroot_php4_cxx[] = "$Id$";
 #include <errno.h>
 
 static const char *usage = (char *) "\
-PHP Options (available with -php4 or -php5)\n\
+PHP Options (available with -php5)\n\
      -cppext          - cpp file extension (default to .cpp)\n\
      -noproxy         - Don't generate proxy classes.\n\
      -prefix <prefix> - Prepend <prefix> to all class names in PHP5 wrappers\n\
-     -make            - Create simple makefile\n\
-     -phpfull         - Create full make files\n\
-     -withincs <incs> - With -phpfull writes needed incs in config.m4\n\
-     -withlibs <libs> - With -phpfull writes needed libs in config.m4\n\
-     -withc <files>   - With -phpfull makes extra C files in Makefile.in\n\
-     -withcxx <files> - With -phpfull makes extra C++ files in Makefile.in\n\
 \n";
 
 /* The original class wrappers for PHP4 store the pointer to the C++ class in
@@ -76,16 +68,9 @@ static Node *classnode = 0;
 static String *module = 0;
 static String *cap_module = 0;
 static String *prefix = 0;
-static String *withlibs = 0;
-static String *withincs = 0;
-static String *withc = 0;
-static String *withcxx = 0;
 
 static String *shadow_classname = 0;
 
-static int gen_extra = 0;
-static int gen_make = 0;
-
 static File *f_runtime = 0;
 static File *f_h = 0;
 static File *f_phpcode = 0;
@@ -116,9 +101,6 @@ static Node *current_class = 0;
 
 static Hash *shadow_get_vars;
 static Hash *shadow_set_vars;
-#define NATIVE_CONSTRUCTOR 1
-#define ALTERNATIVE_CONSTRUCTOR 2
-static int native_constructor = 0;
 static Hash *zend_types = 0;
 
 static int shadow = 1;
@@ -150,45 +132,44 @@ void SwigPHP_emit_resource_registrations() {
   ki = First(zend_types);
   if (ki.key)
     Printf(s_oinit, "\n/* Register resource destructors for pointer types */\n");
-  while (ki.key)
-    if (1 /* is pointer type */ ) {
-      DOH *key = ki.key;
-      Node *class_node = ki.item;
-      String *human_name = key;
+  while (ki.key) {
+    DOH *key = ki.key;
+    Node *class_node = ki.item;
+    String *human_name = key;
 
-      // Write out destructor function header
-      Printf(s_wrappers, "/* NEW Destructor style */\nstatic ZEND_RSRC_DTOR_FUNC(_wrap_destroy%s) {\n", key);
+    // Write out destructor function header
+    Printf(s_wrappers, "/* NEW Destructor style */\nstatic ZEND_RSRC_DTOR_FUNC(_wrap_destroy%s) {\n", key);
 
-      // write out body
-      if ((class_node != NOTCLASS)) {
-	String *destructor = Getattr(class_node, "destructor");
-	human_name = Getattr(class_node, "sym:name");
-	if (!human_name)
-	  human_name = Getattr(class_node, "name");
-	// Do we have a known destructor for this type?
-	if (destructor) {
-	  Printf(s_wrappers, "  %s(rsrc, SWIGTYPE%s->name TSRMLS_CC);\n", destructor, key);
-	} else {
-	  Printf(s_wrappers, "  /* No destructor for class %s */\n", human_name);
-	}
+    // write out body
+    if ((class_node != NOTCLASS)) {
+      String *destructor = Getattr(class_node, "destructor");
+      human_name = Getattr(class_node, "sym:name");
+      if (!human_name)
+        human_name = Getattr(class_node, "name");
+      // Do we have a known destructor for this type?
+      if (destructor) {
+        Printf(s_wrappers, "  %s(rsrc, SWIGTYPE%s->name TSRMLS_CC);\n", destructor, key);
       } else {
-	Printf(s_wrappers, "  /* No destructor for simple type %s */\n", key);
+        Printf(s_wrappers, "  /* No destructor for class %s */\n", human_name);
       }
-
-      // close function
-      Printf(s_wrappers, "}\n");
-
-      // declare le_swig_<mangled> to store php registration
-      Printf(s_vdecl, "static int le_swig_%s=0; /* handle for %s */\n", key, human_name);
-
-      // register with php
-      Printf(s_oinit, "le_swig_%s=zend_register_list_destructors_ex" "(_wrap_destroy%s,NULL,(char *)(SWIGTYPE%s->name),module_number);\n", key, key, key);
-
-      // store php type in class struct
-      Printf(s_oinit, "SWIG_TypeClientData(SWIGTYPE%s,&le_swig_%s);\n", key, key);
-
-      ki = Next(ki);
+    } else {
+      Printf(s_wrappers, "  /* No destructor for simple type %s */\n", key);
     }
+
+    // close function
+    Printf(s_wrappers, "}\n");
+
+    // declare le_swig_<mangled> to store php registration
+    Printf(s_vdecl, "static int le_swig_%s=0; /* handle for %s */\n", key, human_name);
+
+    // register with php
+    Printf(s_oinit, "le_swig_%s=zend_register_list_destructors_ex" "(_wrap_destroy%s,NULL,(char *)(SWIGTYPE%s->name),module_number);\n", key, key, key);
+
+    // store php type in class struct
+    Printf(s_oinit, "SWIG_TypeClientData(SWIGTYPE%s,&le_swig_%s);\n", key, key);
+
+    ki = Next(ki);
+  }
 }
 
 class PHP:public Language {
@@ -217,327 +198,56 @@ public:
    * ------------------------------------------------------------ */
 
   virtual void main(int argc, char *argv[]) {
-    int i;
-    SWIG_library_directory("php4");
+    SWIG_library_directory("php");
     SWIG_config_cppext("cpp");
 
-    for (i = 1; i < argc; i++) {
-      if (argv[i]) {
-	if (strcmp(argv[i], "-phpfull") == 0) {
-	  gen_extra = 1;
+    for (int i = 1; i < argc; i++) {
+      if (strcmp(argv[i], "-prefix") == 0) {
+	if (argv[i + 1]) {
+	  prefix = NewString(argv[i + 1]);
 	  Swig_mark_arg(i);
-	} else if (strcmp(argv[i], "-dlname") == 0) {
-	  Printf(stderr, "*** -dlname is no longer supported\n*** if you want to change the module name, use -module instead.\n");
-	  SWIG_exit(EXIT_FAILURE);
-	} else if (strcmp(argv[i], "-prefix") == 0) {
-	  if (argv[i + 1]) {
-	    prefix = NewString(argv[i + 1]);
-	    Swig_mark_arg(i);
-	    Swig_mark_arg(i + 1);
-	    i++;
-	  } else {
-	    Swig_arg_error();
-	  }
-	} else if (strcmp(argv[i], "-withlibs") == 0) {
-	  if (argv[i + 1]) {
-	    withlibs = NewString(argv[i + 1]);
-	    Swig_mark_arg(i);
-	    Swig_mark_arg(i + 1);
-	    i++;
-	  } else {
-	    Swig_arg_error();
-	  }
-	} else if (strcmp(argv[i], "-withincs") == 0) {
-	  if (argv[i + 1]) {
-	    withincs = NewString(argv[i + 1]);
-	    Swig_mark_arg(i);
-	    Swig_mark_arg(i + 1);
-	    i++;
-	  } else {
-	    Swig_arg_error();
-	  }
-	} else if (strcmp(argv[i], "-withc") == 0) {
-	  if (argv[i + 1]) {
-	    withc = NewString(argv[i + 1]);
-	    Swig_mark_arg(i);
-	    Swig_mark_arg(i + 1);
-	    i++;
-	  } else {
-	    Swig_arg_error();
-	  }
-	} else if (strcmp(argv[i], "-withcxx") == 0) {
-	  if (argv[i + 1]) {
-	    withcxx = NewString(argv[i + 1]);
-	    Swig_mark_arg(i);
-	    Swig_mark_arg(i + 1);
-	    i++;
-	  } else {
-	    Swig_arg_error();
-	  }
-	} else if (strcmp(argv[i], "-cppext") == 0) {
-	  if (argv[i + 1]) {
-	    SWIG_config_cppext(argv[i + 1]);
-	    Swig_mark_arg(i);
-	    Swig_mark_arg(i + 1);
-	    i++;
-	  } else {
-	    Swig_arg_error();
-	  }
-	} else if ((strcmp(argv[i], "-noshadow") == 0) || (strcmp(argv[i], "-noproxy") == 0)) {
-	  shadow = 0;
-	  Swig_mark_arg(i);
-	} else if (strcmp(argv[i], "-make") == 0) {
-	  gen_make = 1;
-	  Swig_mark_arg(i);
-	} else if (strcmp(argv[i], "-help") == 0) {
-	  fputs(usage, stdout);
+	  Swig_mark_arg(i + 1);
+	  i++;
+	} else {
+	  Swig_arg_error();
 	}
+      } else if (strcmp(argv[i], "-cppext") == 0) {
+	if (argv[i + 1]) {
+	  SWIG_config_cppext(argv[i + 1]);
+	  Swig_mark_arg(i);
+	  Swig_mark_arg(i + 1);
+	  i++;
+	} else {
+	  Swig_arg_error();
+	}
+      } else if ((strcmp(argv[i], "-noshadow") == 0) || (strcmp(argv[i], "-noproxy") == 0)) {
+	shadow = 0;
+	Swig_mark_arg(i);
+      } else if (strcmp(argv[i], "-help") == 0) {
+	fputs(usage, stdout);
+      } else if (strcmp(argv[i], "-make") == 0 ||
+		 strcmp(argv[i], "-withc") == 0 ||
+		 strcmp(argv[i], "-withcxx") == 0) {
+	Printf(stderr, "*** %s is no longer supported.\n", argv[i]);
+	SWIG_exit(EXIT_FAILURE);
+      } else if (strcmp(argv[i], "-phpfull") == 0 ||
+		 strcmp(argv[i], "-withlibs") == 0 ||
+		 strcmp(argv[i], "-withincs") == 0) {
+	Printf(stderr, "*** %s is no longer supported.\n*** We recommend building as a dynamically loadable module.\n", argv[i]);
+	SWIG_exit(EXIT_FAILURE);
+      } else if (strcmp(argv[i], "-dlname") == 0) {
+	Printf(stderr, "*** -dlname is no longer supported.\n*** If you want to change the module name, use -module instead.\n");
+	SWIG_exit(EXIT_FAILURE);
       }
     }
 
-    Preprocessor_define((void *) "SWIGPHP 1", 0);
-    if (php_version == 4) {
-      Preprocessor_define((void *) "SWIGPHP4 1", 0);
-    } else if (php_version == 5) {
-      Preprocessor_define((void *) "SWIGPHP5 1", 0);
-    }
+    Preprocessor_define("SWIGPHP 1", 0);
+    Preprocessor_define("SWIGPHP5 1", 0);
     SWIG_typemap_lang("php4");
-    /* DB: Suggest using a language configuration file */
-    SWIG_config_file("php4.swg");
+    SWIG_config_file("php.swg");
     allow_overloading();
   }
 
-  void create_simple_make(void) {
-    File *f_make;
-
-    f_make = NewFile((void *) "makefile", "w");
-    Printf(f_make, "CC=gcc\n");
-    Printf(f_make, "CXX=g++\n");
-    Printf(f_make, "CXX_SOURCES=%s\n", withcxx);
-    Printf(f_make, "C_SOURCES=%s\n", withc);
-    Printf(f_make, "OBJS=%s_wrap.o $(C_SOURCES:.c=.o) $(CXX_SOURCES:.cxx=.o)\n", module);
-    Printf(f_make, "MODULE=%s.so\n", module);
-    Printf(f_make, "CFLAGS=-fpic\n");
-    Printf(f_make, "LDFLAGS=-shared\n");
-    Printf(f_make, "PHP_INC=`php-config --includes`\n");
-    Printf(f_make, "EXTRA_INC=\n");
-    Printf(f_make, "EXTRA_LIB=\n\n");
-    Printf(f_make, "$(MODULE): $(OBJS)\n");
-    if (CPlusPlus || (withcxx != NULL)) {
-      Printf(f_make, "\t$(CXX) $(LDFLAGS) $(OBJS) -o $@ $(EXTRA_LIB)\n\n");
-    } else {
-      Printf(f_make, "\t$(CC) $(LDFLAGS) $(OBJS) -o $@ $(EXTRA_LIB)\n\n");
-    }
-    Printf(f_make, "%%.o: %%.cpp\n");
-    Printf(f_make, "\t$(CXX) $(EXTRA_INC) $(PHP_INC) $(CFLAGS) -c $<\n");
-    Printf(f_make, "%%.o: %%.cxx\n");
-    Printf(f_make, "\t$(CXX) $(EXTRA_INC) $(PHP_INC) $(CFLAGS) -c $<\n");
-    Printf(f_make, "%%.o: %%.c\n");
-    Printf(f_make, "\t$(CC) $(EXTRA_INC) $(PHP_INC) $(CFLAGS) -c $<\n");
-
-    Close(f_make);
-  }
-
-  void create_extra_files(String *outfile) {
-    File *f_extra;
-
-    static String *configm4 = 0;
-    static String *makefilein = 0;
-    static String *credits = 0;
-
-    configm4 = NewStringEmpty();
-    Printv(configm4, SWIG_output_directory(), "config.m4", NIL);
-
-    makefilein = NewStringEmpty();
-    Printv(makefilein, SWIG_output_directory(), "Makefile.in", NIL);
-
-    credits = NewStringEmpty();
-    Printv(credits, SWIG_output_directory(), "CREDITS", NIL);
-
-    // are we a --with- or --enable-
-    int with = (withincs || withlibs) ? 1 : 0;
-
-    // Note Makefile.in only copes with one source file
-    // also withincs and withlibs only take one name each now
-    // the code they generate should be adapted to take multiple lines
-
-    /* Write out Makefile.in */
-    f_extra = NewFile(makefilein, "w");
-    if (!f_extra) {
-      FileErrorDisplay(makefilein);
-      SWIG_exit(EXIT_FAILURE);
-    }
-
-    Printf(f_extra, "# $Id$\n\n" "LTLIBRARY_NAME          = %s.la\n", module);
-
-    // C++ has more and different entries to C in Makefile.in
-    if (!CPlusPlus) {
-      Printf(f_extra, "LTLIBRARY_SOURCES       = %s %s\n", Swig_file_filename(outfile), withc);
-      Printf(f_extra, "LTLIBRARY_SOURCES_CPP   = %s\n", withcxx);
-    } else {
-      Printf(f_extra, "LTLIBRARY_SOURCES       = %s\n", withc);
-      Printf(f_extra, "LTLIBRARY_SOURCES_CPP   = %s %s\n", Swig_file_filename(outfile), withcxx);
-      Printf(f_extra, "LTLIBRARY_OBJECTS_X = $(LTLIBRARY_SOURCES_CPP:.cpp=.lo) $(LTLIBRARY_SOURCES_CPP:.cxx=.lo)\n");
-    }
-    Printf(f_extra, "LTLIBRARY_SHARED_NAME   = %s.la\n", module);
-    Printf(f_extra, "LTLIBRARY_SHARED_LIBADD = $(%s_SHARED_LIBADD)\n\n", cap_module);
-    Printf(f_extra, "include $(top_srcdir)/build/dynlib.mk\n");
-
-    Printf(f_extra, "\n# patch in .cxx support to php build system to work like .cpp\n");
-    Printf(f_extra, ".SUFFIXES: .cxx\n\n");
-
-    Printf(f_extra, ".cxx.o:\n");
-    Printf(f_extra, "\t$(CXX_COMPILE) -c $<\n\n");
-
-    Printf(f_extra, ".cxx.lo:\n");
-    Printf(f_extra, "\t$(CXX_PHP_COMPILE)\n\n");
-    Printf(f_extra, ".cxx.slo:\n");
-
-    Printf(f_extra, "\t$(CXX_SHARED_COMPILE)\n\n");
-
-    Printf(f_extra, "\n# make it easy to test module\n");
-    Printf(f_extra, "testmodule:\n");
-    Printf(f_extra, "\tphp -q -d extension_dir=modules %s\n\n", Swig_file_filename(phpfilename));
-
-    Close(f_extra);
-
-    /* Now config.m4 */
-    // Note: # comments are OK in config.m4 if you don't mind them
-    // appearing in the final ./configure file
-    // (which can help with ./configure debugging)
-
-    // NOTE2: phpize really ought to be able to write out a sample
-    // config.m4 based on some simple data, I'll take this up with
-    // the php folk!
-    f_extra = NewFile(configm4, "w");
-    if (!f_extra) {
-      FileErrorDisplay(configm4);
-      SWIG_exit(EXIT_FAILURE);
-    }
-
-    Printf(f_extra, "dnl $Id$\n");
-    Printf(f_extra, "dnl ***********************************************************************\n");
-    Printf(f_extra, "dnl ** THIS config.m4 is provided for PHPIZE and PHP's consumption NOT\n");
-    Printf(f_extra, "dnl ** for any part of the rest of the %s build system\n", module);
-    Printf(f_extra, "dnl ***********************************************************************\n\n");
-
-
-    if (!with) {		// must be enable then
-      Printf(f_extra, "PHP_ARG_ENABLE(%s, whether to enable %s support,\n", module, module);
-      Printf(f_extra, "[  --enable-%s             Enable %s support])\n\n", module, module);
-    } else {
-      Printf(f_extra, "PHP_ARG_WITH(%s, for %s support,\n", module, module);
-      Printf(f_extra, "[  --with-%s[=DIR]             Include %s support.])\n\n", module, module);
-      // These tests try and file the library we need
-      Printf(f_extra, "dnl THESE TESTS try and find the library and header files\n");
-      Printf(f_extra, "dnl your new php module needs. YOU MAY NEED TO EDIT THEM\n");
-      Printf(f_extra, "dnl as written they assume your header files are all in the same place\n\n");
-
-      Printf(f_extra, "dnl ** are we looking for %s_lib.h or something else?\n", module);
-      if (withincs)
-	Printf(f_extra, "HNAMES=\"%s\"\n\n", withincs);
-      else
-	Printf(f_extra, "HNAMES=\"\"; # %s_lib.h ?\n\n", module);
-
-      Printf(f_extra, "dnl ** Are we looking for lib%s.a or lib%s.so or something else?\n", module, module);
-
-      if (withlibs)
-	Printf(f_extra, "LIBNAMES=\"%s\"\n\n", withlibs);
-      else
-	Printf(f_extra, "LIBNAMES=\"\"; # lib%s.so ?\n\n", module);
-
-      Printf(f_extra, "dnl IF YOU KNOW one of the symbols in the library and you\n");
-      Printf(f_extra, "dnl specify it below then we can have a link test to see if it works\n");
-      Printf(f_extra, "LIBSYMBOL=\"\"\n\n");
-    }
-
-    // Now write out tests to find thing.. they may need to extend tests
-    Printf(f_extra, "if test \"$PHP_%s\" != \"no\"; then\n\n", cap_module);
-
-    // Ready for when we add libraries as we find them
-    Printf(f_extra, "  PHP_SUBST(%s_SHARED_LIBADD)\n\n", cap_module);
-
-    if (withlibs) {		// find more than one library
-      Printf(f_extra, "  for LIBNAME in $LIBNAMES ; do\n");
-      Printf(f_extra, "    LIBDIR=\"\"\n");
-      // For each path element to try...
-      Printf(f_extra, "    for i in $PHP_%s $PHP_%s/lib /usr/lib /usr/local/lib ; do\n", cap_module, cap_module);
-      Printf(f_extra, "      if test -r $i/lib$LIBNAME.a -o -r $i/lib$LIBNAME.so ; then\n");
-      Printf(f_extra, "        LIBDIR=\"$i\"\n");
-      Printf(f_extra, "        break\n");
-      Printf(f_extra, "      fi\n");
-      Printf(f_extra, "    done\n\n");
-      Printf(f_extra, "    dnl ** and $LIBDIR should be the library path\n");
-      Printf(f_extra, "    if test \"$LIBNAME\" != \"\" -a -z \"$LIBDIR\" ; then\n");
-      Printf(f_extra, "      AC_MSG_RESULT(Library files $LIBNAME not found)\n");
-      Printf(f_extra, "      AC_MSG_ERROR(Is the %s distribution installed properly?)\n", module);
-      Printf(f_extra, "    else\n");
-      Printf(f_extra, "      AC_MSG_RESULT(Library files $LIBNAME found in $LIBDIR)\n");
-      Printf(f_extra, "      PHP_ADD_LIBRARY_WITH_PATH($LIBNAME, $LIBDIR, %s_SHARED_LIBADD)\n", cap_module);
-      Printf(f_extra, "    fi\n");
-      Printf(f_extra, "  done\n\n");
-    }
-
-    if (withincs) {		// Find more than once include
-      Printf(f_extra, "  for HNAME in $HNAMES ; do\n");
-      Printf(f_extra, "    INCDIR=\"\"\n");
-      // For each path element to try...
-      Printf(f_extra, "    for i in $PHP_%s $PHP_%s/include $PHP_%s/includes $PHP_%s/inc $PHP_%s/incs /usr/local/include /usr/include; do\n", cap_module,
-	     cap_module, cap_module, cap_module, cap_module);
-      // Try and find header files
-      Printf(f_extra, "      if test \"$HNAME\" != \"\" -a -r $i/$HNAME ; then\n");
-      Printf(f_extra, "        INCDIR=\"$i\"\n");
-      Printf(f_extra, "        break\n");
-      Printf(f_extra, "      fi\n");
-      Printf(f_extra, "    done\n\n");
-
-      Printf(f_extra, "    dnl ** Now $INCDIR should be the include file path\n");
-      Printf(f_extra, "    if test \"$HNAME\" != \"\" -a -z \"$INCDIR\" ; then\n");
-      Printf(f_extra, "      AC_MSG_RESULT(Include files $HNAME not found)\n");
-      Printf(f_extra, "      AC_MSG_ERROR(Is the %s distribution installed properly?)\n", module);
-      Printf(f_extra, "    else\n");
-      Printf(f_extra, "      AC_MSG_RESULT(Include files $HNAME found in $INCDIR)\n");
-      Printf(f_extra, "      PHP_ADD_INCLUDE($INCDIR)\n");
-      Printf(f_extra, "    fi\n\n");
-      Printf(f_extra, "  done\n\n");
-    }
-
-    if (CPlusPlus) {
-      Printf(f_extra, "  # As this is a C++ module..\n");
-    }
-
-    Printf(f_extra, "  PHP_REQUIRE_CXX\n");
-    Printf(f_extra, "  AC_CHECK_LIB(stdc++, cin)\n");
-
-    if (with) {
-      Printf(f_extra, "  if test \"$LIBSYMBOL\" != \"\" ; then\n");
-      Printf(f_extra, "    old_LIBS=\"$LIBS\"\n");
-      Printf(f_extra, "    LIBS=\"$LIBS -L$TEST_DIR/lib -lm -ldl\"\n");
-      Printf(f_extra, "    AC_CHECK_LIB($LIBNAME, $LIBSYMBOL, [AC_DEFINE(HAVE_TESTLIB,1,  [ ])],\n");
-      Printf(f_extra, "    [AC_MSG_ERROR(wrong test lib version or lib not found)])\n");
-      Printf(f_extra, "    LIBS=\"$old_LIBS\"\n");
-      Printf(f_extra, "  fi\n\n");
-    }
-
-    Printf(f_extra, "  AC_DEFINE(HAVE_%s, 1, [ ])\n", cap_module);
-    Printf(f_extra, "dnl  AC_DEFINE_UNQUOTED(PHP_%s_DIR, \"$%s_DIR\", [ ])\n", cap_module, cap_module);
-    Printf(f_extra, "  PHP_EXTENSION(%s, $ext_shared)\n", module);
-
-    // and thats all!
-    Printf(f_extra, "fi\n");
-
-    Close(f_extra);
-
-    /*  CREDITS */
-    f_extra = NewFile(credits, "w");
-    if (!f_extra) {
-      FileErrorDisplay(credits);
-      SWIG_exit(EXIT_FAILURE);
-    }
-    Printf(f_extra, "%s\n", module);
-    Close(f_extra);
-  }
-
   /* ------------------------------------------------------------
    * top()
    * ------------------------------------------------------------ */
@@ -610,9 +320,8 @@ public:
     Printf(f_phpcode, "  if (strtolower(substr(PHP_OS, 0, 3)) === 'win') {\n");
     Printf(f_phpcode, "    if (!dl('php_%s.dll')) return;\n", module);
     Printf(f_phpcode, "  } else {\n");
-    Printf(f_phpcode, "    // PHP_SHLIB_SUFFIX is available as of PHP 4.3.0, for older PHP assume 'so'.\n");
-    Printf(f_phpcode, "    // It gives 'dylib' on MacOS X which is for libraries, modules are 'so'.\n");
-    Printf(f_phpcode, "    if (PHP_SHLIB_SUFFIX === 'PHP_SHLIB_SUFFIX' || PHP_SHLIB_SUFFIX === 'dylib') {\n");
+    Printf(f_phpcode, "    // PHP_SHLIB_SUFFIX gives 'dylib' on MacOS X but modules are 'so'.\n");
+    Printf(f_phpcode, "    if (PHP_SHLIB_SUFFIX === 'dylib') {\n");
     Printf(f_phpcode, "      if (!dl('%s.so')) return;\n", module);
     Printf(f_phpcode, "    } else {\n");
     Printf(f_phpcode, "      if (!dl('%s.'.PHP_SHLIB_SUFFIX)) return;\n", module);
@@ -728,9 +437,6 @@ public:
     Printf(s_init, "};\n");
     Printf(s_init, "zend_module_entry* SWIG_module_entry = &%s_module_entry;\n\n", module);
 
-    if (gen_extra) {
-      Printf(s_init, "#ifdef COMPILE_DL_%s\n", cap_module);
-    }
     Printf(s_init, "#ifdef __cplusplus\n");
     Printf(s_init, "extern \"C\" {\n");
     Printf(s_init, "#endif\n");
@@ -741,10 +447,6 @@ public:
     Printf(s_init, "}\n");
     Printf(s_init, "#endif\n\n");
 
-    if (gen_extra) {
-      Printf(s_init, "#endif\n\n");
-    }
-
     /* We have to register the constants before they are (possibly) used
      * by the pointer typemaps. This all needs re-arranging really as
      * things are being called in the wrong order
@@ -841,22 +543,12 @@ public:
     Printf(f_phpcode, "%s\n?>\n", s_phpclasses);
     Close(f_phpcode);
 
-    if (gen_extra) {
-      create_extra_files(outfile);
-    } else if (gen_make) {
-      create_simple_make();
-    }
-
     return SWIG_OK;
   }
 
   /* Just need to append function names to function table to register with PHP. */
   void create_command(String *cname, String *iname) {
     // This is for the single main zend_function_entry record
-    if (shadow && php_version == 4) {
-      if (wrapperType != standard)
-	return;
-    }
     Printf(f_h, "ZEND_NAMED_FUNCTION(%s);\n", iname);
     String * s = cs_entry;
     if (!s) s = s_entry;
@@ -873,8 +565,6 @@ public:
     String *tmp = NewStringEmpty();
     String *dispatch = Swig_overload_dispatch(n, "return %s(INTERNAL_FUNCTION_PARAM_PASSTHRU);", &maxargs);
 
-    int has_this_ptr = (wrapperType == memberfn && shadow && php_version == 4);
-
     /* Generate a dispatch wrapper for all overloaded functions */
 
     Wrapper *f = NewWrapper();
@@ -891,13 +581,7 @@ public:
 
     Printf(f->code, "argc = ZEND_NUM_ARGS();\n");
 
-    if (has_this_ptr) {
-      Printf(f->code, "argv[0] = &this_ptr;\n");
-      Printf(f->code, "zend_get_parameters_array_ex(argc,argv+1);\n");
-      Printf(f->code, "argc++;\n");
-    } else {
-      Printf(f->code, "zend_get_parameters_array_ex(argc,argv);\n");
-    }
+    Printf(f->code, "zend_get_parameters_array_ex(argc,argv);\n");
 
     Replaceall(dispatch, "$args", "self,args");
 
@@ -946,8 +630,6 @@ public:
     int numopt;
     String *tm;
     Wrapper *f;
-    bool mvr = (shadow && php_version == 4 && wrapperType == membervar);
-    bool mvrset = (mvr && (Strcmp(iname, Swig_name_set(Swig_name_member(shadow_classname, name))) == 0));
 
     String *wname;
     int overloaded = 0;
@@ -972,19 +654,6 @@ public:
     if (overname) {
       Printf(wname, "%s", overname);
     }
-    // if PHP4, shadow and variable wrapper we want to snag the main contents
-    // of this function to stick in to the property handler...
-    if (mvr) {
-      String *php_function_name = NewString(iname);
-      if (Strcmp(iname, Swig_name_set(Swig_name_member(shadow_classname, name))) == 0) {
-	Setattr(shadow_set_vars, php_function_name, name);
-      }
-      if (Strcmp(iname, Swig_name_get(Swig_name_member(shadow_classname, name))) == 0) {
-	Setattr(shadow_get_vars, php_function_name, name);
-      }
-
-      Delete(php_function_name);
-    }
 
     f = NewWrapper();
     numopt = 0;
@@ -992,20 +661,11 @@ public:
     String *outarg = NewStringEmpty();
     String *cleanup = NewStringEmpty();
 
-    if (mvr) {			// do prop[gs]et header
-      if (mvrset) {
-	Printf(f->def, "static int _wrap_%s(zend_property_reference *property_reference, pval *value) {\n", iname);
-      } else {
-	Printf(f->def, "static pval _wrap_%s(zend_property_reference *property_reference) {\n", iname);
-      }
-    } else {
-      // regular header
-      // Not issued for overloaded functions or static member variables.
-      if (!overloaded && wrapperType != staticmembervar) {
-	create_command(iname, wname);
-      }
-      Printv(f->def, "ZEND_NAMED_FUNCTION(", wname, ") {\n", NIL);
+    // Not issued for overloaded functions or static member variables.
+    if (!overloaded && wrapperType != staticmembervar) {
+      create_command(iname, wname);
     }
+    Printv(f->def, "ZEND_NAMED_FUNCTION(", wname, ") {\n", NIL);
 
     emit_parameter_variables(l, f);
     /* Attach standard typemaps */
@@ -1019,10 +679,8 @@ public:
     int num_required = emit_num_required(l);
     numopt = num_arguments - num_required;
 
-    int has_this_ptr = (wrapperType == memberfn && shadow && php_version == 4);
-
-    if (num_arguments - has_this_ptr > 0) {
-      String *args = NewStringf("zval **args[%d]", num_arguments - has_this_ptr);
+    if (num_arguments > 0) {
+      String *args = NewStringf("zval **args[%d]", num_arguments);
       Wrapper_add_local(f, "args", args);
       Delete(args);
       args = NULL;
@@ -1037,34 +695,17 @@ public:
 
     Printf(f->code, "SWIG_ResetError();\n");
 
-    if (has_this_ptr)
-      Printf(f->code, "/* This function uses a this_ptr*/\n");
-
-    if (native_constructor) {
-      if (native_constructor == NATIVE_CONSTRUCTOR) {
-	Printf(f->code, "/* NATIVE Constructor */\n");
-      } else {
-	Printf(f->code, "/* ALTERNATIVE Constructor */\n");
-      }
-    }
-
-    if (mvr && !mvrset) {
-      Wrapper_add_local(f, "_return_value", "zval _return_value");
-      Wrapper_add_local(f, "return_value", "zval *return_value=&_return_value");
-    }
-
     if (numopt > 0) {		// membervariable wrappers do not have optional args
       Wrapper_add_local(f, "arg_count", "int arg_count");
       Printf(f->code, "arg_count = ZEND_NUM_ARGS();\n");
       Printf(f->code, "if(arg_count<%d || arg_count>%d ||\n", num_required, num_arguments);
       Printf(f->code, "   zend_get_parameters_array_ex(arg_count,args)!=SUCCESS)\n");
       Printf(f->code, "\tWRONG_PARAM_COUNT;\n\n");
-    } else if (!mvr) {
-      int num = num_arguments - has_this_ptr;
-      if (num == 0) {
+    } else {
+      if (num_arguments == 0) {
 	Printf(f->code, "if(ZEND_NUM_ARGS() != 0) {\n");
       } else {
-	Printf(f->code, "if(ZEND_NUM_ARGS() != %d || zend_get_parameters_array_ex(%d, args) != SUCCESS) {\n", num, num);
+	Printf(f->code, "if(ZEND_NUM_ARGS() != %d || zend_get_parameters_array_ex(%d, args) != SUCCESS) {\n", num_arguments, num_arguments);
       }
       Printf(f->code, "WRONG_PARAM_COUNT;\n}\n\n");
     }
@@ -1090,19 +731,7 @@ public:
 
       SwigType *pt = Getattr(p, "type");
 
-      if (mvr) {		// do we assert that numargs=2, that i<2
-	if (i == 0) {
-	  source = NewString("&(property_reference->object)");
-	} else {
-	  source = NewString("&value");
-	}
-      } else {
-	if (i == 0 && has_this_ptr) {
-	  source = NewString("&this_ptr");
-	} else {
-	  source = NewStringf("args[%d]", i - has_this_ptr);
-	}
-      }
+      source = NewStringf("args[%d]", i);
 
       String *ln = Getattr(p, "lname");
 
@@ -1184,24 +813,6 @@ public:
       Replaceall(tm, "$result", "return_value");
       Replaceall(tm, "$owner", newobject ? "1" : "0");
       Printf(f->code, "%s\n", tm);
-      // Are we returning a wrapable object?
-      if (shadow && php_version == 4 && is_shadow(d) && (SwigType_type(d) != T_ARRAY)) {
-	// Make object.
-	Printf(f->code, "{\n/* Wrap this return value */\n");
-	Printf(f->code, "zval *_cPtr;\n");
-	Printf(f->code, "ALLOC_ZVAL(_cPtr);\n");
-	Printf(f->code, "*_cPtr = *return_value;\n");
-	Printf(f->code, "INIT_ZVAL(*return_value);\n");
-	if (native_constructor == NATIVE_CONSTRUCTOR) {
-	  Printf(f->code, "add_property_zval(this_ptr,\"" SWIG_PTR "\",_cPtr);\n");
-	} else {
-	  String *shadowrettype = SwigToPhpType(n, true);
-	  Printf(f->code, "object_init_ex(return_value,ptr_ce_swig_%s);\n", shadowrettype);
-	  Delete(shadowrettype);
-	  Printf(f->code, "add_property_zval(return_value,\"" SWIG_PTR "\",_cPtr);\n");
-	}
-	Printf(f->code, "}\n");
-      }
     } else {
       Swig_warning(WARN_TYPEMAP_OUT_UNDEF, input_file, line_number, "Unable to use return type %s in function %s.\n", SwigType_str(d, 0), name);
     }
@@ -1229,16 +840,7 @@ public:
       Delete(tm);
     }
 
-
-    if (mvr) {
-      if (!mvrset) {
-	Printf(f->code, "return _return_value;\n");
-      } else {
-	Printf(f->code, "return SUCCESS;\n");
-      }
-    } else {
-      Printf(f->code, "return;\n");
-    }
+    Printf(f->code, "return;\n");
 
     /* Error handling code */
     Printf(f->code, "fail:\n");
@@ -1440,6 +1042,10 @@ public:
 	if (wrapperType == memberfn)
 	  p = nextSibling(p);
 	while (p) {
+	  if (GetInt(p, "tmap:in:numinputs") == 0) {
+	    p = nextSibling(p);
+	    continue;
+	  }
 	  assert(0 <= argno && argno < max_num_of_arguments);
 	  String *&pname = arg_names[argno];
 	  const char *pname_cstr = GetChar(p, "name");
@@ -1635,8 +1241,8 @@ public:
       Setattr(seen, "this", seen);
       /* We use $r to store the return value, so disallow that as a parameter
        * name in case the user uses the "call-time pass-by-reference" feature
-       * (it's deprecated and off by default in PHP5 and even later PHP4
-       * versions apparently, but we want to be maximally portable).
+       * (it's deprecated and off by default in PHP5, but we want to be
+       * maximally portable).
        */
       Setattr(seen, "r", seen);
 
@@ -1750,7 +1356,8 @@ public:
       }
 
       Printf(output, "\n");
-      if (wrapperType == memberfn || newobject) {
+      // If it's a member function or a class constructor...
+      if (wrapperType == memberfn || (newobject && current_class)) {
 	Printf(output, "\tfunction %s(%s) {\n", methodname, args);
 	// We don't need this code if the wrapped class has a copy ctor
 	// since the flat function new_CLASSNAME will handle it for us.
@@ -1984,7 +1591,7 @@ public:
 	    Printf(pragma_phpinfo, "%s\n", value);
 	  }
 	} else {
-	  Swig_warning(WARN_PHP4_UNKNOWN_PRAGMA, input_file, line_number, "Unrecognized pragma <%s>.\n", type);
+	  Swig_warning(WARN_PHP_UNKNOWN_PRAGMA, input_file, line_number, "Unrecognized pragma <%s>.\n", type);
 	}
       }
     }
@@ -2014,52 +1621,7 @@ public:
     current_class = n;
     // String *use_class_name=SwigType_manglestr(SwigType_ltype(t));
 
-    if (shadow && php_version == 4) {
-      char *rename = GetChar(n, "sym:name");
-
-      if (!addSymbol(rename, n))
-	return SWIG_ERROR;
-      shadow_classname = NewString(rename);
-      cs_entry = NewStringEmpty();
-      Printf(cs_entry, "/* Function entries for %s */\n", shadow_classname);
-      Printf(cs_entry, "static zend_function_entry %s_functions[] = {\n", shadow_classname);
-
-      if (Strcmp(shadow_classname, module) == 0) {
-	Printf(stderr, "class name cannot be equal to module name: %s\n", module);
-	SWIG_exit(1);
-      }
-
-      shadow_get_vars = NewHash();
-      shadow_set_vars = NewHash();
-
-      /* Deal with inheritance */
-      List *baselist = Getattr(n, "bases");
-      if (baselist) {
-	Iterator base = First(baselist);
-	while (base.item && GetFlag(base.item, "feature:ignore")) {
-	  base = Next(base);
-	}
-	base = Next(base);
-	if (base.item) {
-	  /* Warn about multiple inheritance for additional base class(es) */
-	  while (base.item) {
-	    if (GetFlag(base.item, "feature:ignore")) {
-	      base = Next(base);
-	      continue;
-	    }
-	    String *proxyclassname = SwigType_str(Getattr(n, "classtypeobj"), 0);
-	    String *baseclassname = SwigType_str(Getattr(base.item, "name"), 0);
-	    Swig_warning(WARN_PHP4_MULTIPLE_INHERITANCE, input_file, line_number,
-			 "Warning for %s proxy: Base %s ignored. Multiple inheritance is not supported in Php4.\n", proxyclassname, baseclassname);
-	    base = Next(base);
-	  }
-	}
-      }
-
-      /* Write out class init code */
-      Printf(s_vdecl, "static zend_class_entry ce_swig_%s;\n", shadow_classname);
-      Printf(s_vdecl, "static zend_class_entry* ptr_ce_swig_%s=NULL;\n", shadow_classname);
-    } else if (shadow && php_version == 5) {
+    if (shadow) {
       char *rename = GetChar(n, "sym:name");
 
       if (!addSymbol(rename, n))
@@ -2086,7 +1648,7 @@ public:
 	    }
 	    String *proxyclassname = SwigType_str(Getattr(n, "classtypeobj"), 0);
 	    String *baseclassname = SwigType_str(Getattr(base.item, "name"), 0);
-	    Swig_warning(WARN_PHP4_MULTIPLE_INHERITANCE, input_file, line_number,
+	    Swig_warning(WARN_PHP_MULTIPLE_INHERITANCE, input_file, line_number,
 			 "Warning for %s proxy: Base %s ignored. Multiple inheritance is not supported in PHP.\n", proxyclassname, baseclassname);
 	    base = Next(base);
 	  }
@@ -2098,217 +1660,7 @@ public:
     Language::classHandler(n);
     classnode = 0;
 
-    if (shadow && php_version == 4) {
-      DOH *key;
-      String *s_propget = NewStringEmpty();
-      String *s_propset = NewStringEmpty();
-      List *baselist = Getattr(n, "bases");
-      Iterator ki, base;
-
-      // If no constructor was generated (abstract class) we had better
-      // generate a constructor that raises an error about instantiating
-      // abstract classes
-      if (Getattr(n, "abstract") && constructors == 0) {
-	// have to write out fake constructor which raises an error when called
-	abstractConstructorHandler(n);
-      }
-
-      Printf(s_oinit, "/* Define class %s */\n", shadow_classname);
-      Printf(s_oinit, "INIT_OVERLOADED_CLASS_ENTRY(ce_swig_%s,\"%(lower)s\",%s_functions,", shadow_classname, shadow_classname, shadow_classname);
-      Printf(s_oinit, "NULL,_wrap_propget_%s,_wrap_propset_%s);\n", shadow_classname, shadow_classname);
-
-      // ******** Write property SET handlers
-      Printf(s_header, "static int _wrap_propset_%s(zend_property_reference *property_reference, pval *value);\n", shadow_classname);
-      Printf(s_header, "static int _propset_%s(zend_property_reference *property_reference, pval *value);\n", shadow_classname);
-
-      Printf(s_propset, "static int _wrap_propset_%s(zend_property_reference *property_reference, pval *value) { \n", shadow_classname);
-      Printf(s_propset, "  zval * _value;\n");
-      Printf(s_propset, "  zend_llist_element *element = property_reference->elements_list->head;\n");
-      Printf(s_propset, "  zend_overloaded_element *property=(zend_overloaded_element *)element->data;\n");
-      Printf(s_propset, "  if (_propset_%s(property_reference, value)==SUCCESS) return SUCCESS;\n", shadow_classname);
-      Printf(s_propset, "  /* set it ourselves as it is %s */\n", shadow_classname);
-      Printf(s_propset, "  MAKE_STD_ZVAL(_value);\n");
-      Printf(s_propset, "  *_value=*value;\n");
-      Printf(s_propset, "  INIT_PZVAL(_value);\n");
-      Printf(s_propset, "  zval_copy_ctor(_value);\n");
-      Printf(s_propset,
-	     "  return add_property_zval_ex(property_reference->object,Z_STRVAL_P(&(property->element)),1+Z_STRLEN_P(&(property->element)),_value);\n");
-      Printf(s_propset, "}\n");
-      Printf(s_propset, "static int _propset_%s(zend_property_reference *property_reference, pval *value) {\n", shadow_classname);
-
-
-      if (baselist) {
-	base = First(baselist);
-      } else {
-	base.item = NULL;
-      }
-
-      while (base.item && GetFlag(base.item, "feature:ignore")) {
-	base = Next(base);
-      }
-
-      ki = First(shadow_set_vars);
-      key = ki.key;
-
-      // Print function header; we only need to find property name if there
-      // are properties for this class to look up...
-      if (key || !base.item) {	// or if we are base class and set it ourselves
-	Printf(s_propset, "  /* get the property name */\n");
-	Printf(s_propset, "  zend_llist_element *element = property_reference->elements_list->head;\n");
-	Printf(s_propset, "  zend_overloaded_element *property=(zend_overloaded_element *)element->data;\n");
-	Printf(s_propset, "  char *propname=Z_STRVAL_P(&(property->element));\n");
-      } else {
-	if (base.item) {
-	  Printf(s_propset, "  /* No extra properties for subclass %s */\n", shadow_classname);
-	} else {
-	  Printf(s_propset, "  /* No properties for base class %s */\n", shadow_classname);
-	}
-      }
-
-      while (ki.key) {
-	key = ki.key;
-	Printf(s_propset, "  if (strcmp(propname,\"%s\")==0) return _wrap_%s(property_reference, value);\n", ki.item, key);
-
-	ki = Next(ki);
-      }
-
-      // If the property wasn't in this class, try the handlers of each base
-      // class (if any) in turn until we succeed in setting the property or
-      // have tried all base classes.
-      if (base.item) {
-	Printf(s_propset, "  /* Try base class(es) */\n");
-	while (base.item) {
-	  Printf(s_propset, "  if (_propset_%s(property_reference, value)==SUCCESS) return SUCCESS;\n", GetChar(base.item, "sym:name"));
-
-	  base = Next(base);
-	  while (base.item && GetFlag(base.item, "feature:ignore")) {
-	    base = Next(base);
-	  }
-	}
-      }
-      Printf(s_propset, "  return FAILURE;\n}\n\n");
-
-      // ******** Write property GET handlers
-      Printf(s_header, "static pval _wrap_propget_%s(zend_property_reference *property_reference);\n", shadow_classname);
-      Printf(s_header, "static int _propget_%s(zend_property_reference *property_reference, pval *value);\n", shadow_classname);
-
-      Printf(s_propget, "static pval _wrap_propget_%s(zend_property_reference *property_reference) {\n", shadow_classname);
-      Printf(s_propget, "  pval result;\n");
-      Printf(s_propget, "  pval **_result;\n");
-      Printf(s_propget, "  zend_llist_element *element = property_reference->elements_list->head;\n");
-      Printf(s_propget, "  zend_overloaded_element *property=(zend_overloaded_element *)element->data;\n");
-      Printf(s_propget, "  result.type = IS_NULL;\n");
-      Printf(s_propget, "  if (_propget_%s(property_reference, &result)==SUCCESS) return result;\n", shadow_classname);
-      Printf(s_propget, "  /* return it ourselves */\n");
-      Printf(s_propget,
-	     "  if (zend_hash_find(Z_OBJPROP_P(property_reference->object),Z_STRVAL_P(&(property->element)),1+Z_STRLEN_P(&(property->element)),(void**)&_result)==SUCCESS) {\n");
-      Printf(s_propget, "  zval *_value;\n");
-      Printf(s_propget, "  MAKE_STD_ZVAL(_value);");
-      Printf(s_propget, "  *_value=**_result;\n");
-      Printf(s_propget, "  INIT_PZVAL(_value);\n");
-      Printf(s_propget, "  zval_copy_ctor(_value);\n");
-      Printf(s_propget, "  return *_value;\n");
-      Printf(s_propget, "  }\n");
-      Printf(s_propget, "  result.type = IS_NULL;\n");
-      Printf(s_propget, "  return result;\n");
-      Printf(s_propget, "}\n");
-      Printf(s_propget, "static int _propget_%s(zend_property_reference *property_reference, pval *value) {\n", shadow_classname);
-
-      if (baselist) {
-	base = First(baselist);
-      } else {
-	base.item = NULL;
-      }
-      while (base.item && GetFlag(base.item, "feature:ignore")) {
-	base = Next(base);
-      }
-      ki = First(shadow_get_vars);
-
-      key = ki.key;
-
-      // Print function header; we only need to find property name if there
-      // are properties for this class to look up...
-      if (key || !base.item) {	// or if we are base class...
-	Printf(s_propget, "  /* get the property name */\n");
-	Printf(s_propget, "  zend_llist_element *element = property_reference->elements_list->head;\n");
-	Printf(s_propget, "  zend_overloaded_element *property=(zend_overloaded_element *)element->data;\n");
-	Printf(s_propget, "  char *propname=Z_STRVAL_P(&(property->element));\n");
-      } else {
-	if (base.item) {
-	  Printf(s_propget, "  /* No extra properties for subclass %s */\n", shadow_classname);
-	} else {
-	  Printf(s_propget, "  /* No properties for base class %s */\n", shadow_classname);
-	}
-      }
-
-      while (ki.key) {
-	key = ki.key;
-	Printf(s_propget, "  if (strcmp(propname,\"%s\")==0) {\n", ki.item);
-	Printf(s_propget, "    *value=_wrap_%s(property_reference);\n", key);
-	Printf(s_propget, "    return SUCCESS;\n");
-	Printf(s_propget, "  }\n");
-
-	ki = Next(ki);
-      }
-
-      // If the property wasn't in this class, try the handlers of each base
-      // class (if any) in turn until we succeed in setting the property or
-      // have tried all base classes.
-      if (base.item) {
-	Printf(s_propget, "  /* Try base class(es). */\n");
-	while (base.item) {
-	  Printf(s_propget, "  if (_propget_%s(property_reference, value)==SUCCESS) return SUCCESS;\n", GetChar(base.item, "sym:name"));
-
-	  base = Next(base);
-	  while (base.item && GetFlag(base.item, "feature:ignore")) {
-	    base = Next(base);
-	  }
-	}
-      }
-      Printf(s_propget, "  return FAILURE;\n}\n\n");
-
-      // wrappers generated now...
-
-      // add wrappers to output code
-      Printf(s_wrappers, "/* property handler for class %s */\n", shadow_classname);
-      Printv(s_wrappers, s_propget, s_propset, NIL);
-
-      // Save class in class table
-      if (baselist) {
-	base = First(baselist);
-      } else {
-	base.item = NULL;
-      }
-      while (base.item && GetFlag(base.item, "feature:ignore")) {
-	base = Next(base);
-      }
-
-      if (base.item) {
-	Printf(s_oinit,
-	       "if (! (ptr_ce_swig_%s=zend_register_internal_class_ex(&ce_swig_%s,&ce_swig_%s,NULL TSRMLS_CC))) zend_error(E_ERROR,\"Error registering wrapper for class %s\");\n",
-	       shadow_classname, shadow_classname, GetChar(base.item, "sym:name"), shadow_classname);
-      } else {
-	Printf(s_oinit,
-	       "if (! (ptr_ce_swig_%s=zend_register_internal_class_ex(&ce_swig_%s,NULL,NULL TSRMLS_CC))) zend_error(E_ERROR,\"Error registering wrapper for class %s\");\n",
-	       shadow_classname, shadow_classname, shadow_classname);
-      }
-      Printf(s_oinit, "\n");
-
-      // Write the enum initialisation code in a static block
-      // These are all the enums defined within the C++ class.
-
-      Delete(shadow_classname);
-      shadow_classname = NULL;
-
-      Delete(shadow_set_vars);
-      shadow_set_vars = NULL;
-      Delete(shadow_get_vars);
-      shadow_get_vars = NULL;
-
-      Printv(all_cs_entry, cs_entry, " { NULL, NULL, NULL}\n};\n", NIL);
-      Delete(cs_entry);
-      cs_entry = NULL;
-    } else if (shadow && php_version == 5) {
+    if (shadow) {
       DOH *key;
       List *baselist = Getattr(n, "bases");
       Iterator ki, base;
@@ -2430,21 +1782,10 @@ public:
    * ------------------------------------------------------------ */
 
   virtual int memberfunctionHandler(Node *n) {
-    char *name = GetChar(n, "name");
-    char *iname = GetChar(n, "sym:name");
-
     wrapperType = memberfn;
     this->Language::memberfunctionHandler(n);
     wrapperType = standard;
 
-    // Only declare the member function if
-    // we are doing shadow classes, and the function
-    // is not overloaded, or if it is overloaded, it is the dispatch function.
-    if (shadow && php_version == 4 && (!Getattr(n, "sym:overloaded") || !Getattr(n, "sym:nextSibling"))) {
-      char *realname = iname ? iname : name;
-      String *php_function_name = Swig_name_member(shadow_classname, realname);
-      create_command(realname, Swig_name_wrapper(php_function_name));
-    }
     return SWIG_OK;
   }
 
@@ -2453,7 +1794,6 @@ public:
    * ------------------------------------------------------------ */
 
   virtual int membervariableHandler(Node *n) {
-
     wrapperType = membervar;
     Language::membervariableHandler(n);
     wrapperType = standard;
@@ -2466,7 +1806,6 @@ public:
    * ------------------------------------------------------------ */
 
   virtual int staticmembervariableHandler(Node *n) {
-
     wrapperType = staticmembervar;
     Language::staticmembervariableHandler(n);
     wrapperType = standard;
@@ -2488,12 +1827,13 @@ public:
      * would be available in php as Example::ncount() 
      */
 
-    // If the variable is const, then it's wrapped as a constant with set/get functions.
+    // If the variable is const, then it's wrapped as a constant with set/get
+    // functions.
     if (SwigType_isconst(type))
       return SWIG_OK;
 
-    // This duplicates the logic from Language::variableWrapper() to test if the set wrapper
-    // is made.
+    // This duplicates the logic from Language::variableWrapper() to test if
+    // the set wrapper is made.
     int assignable = is_assignable(n);
     if (assignable) {
       String *tm = Swig_typemap_lookup("globalin", n, name, 0);
@@ -2538,37 +1878,16 @@ public:
    * ------------------------------------------------------------ */
 
   virtual int staticmemberfunctionHandler(Node *n) {
-    char *name = GetChar(n, "name");
-    char *iname = GetChar(n, "sym:name");
-
     wrapperType = staticmemberfn;
     Language::staticmemberfunctionHandler(n);
     wrapperType = standard;
 
-    if (shadow && php_version == 4) {
-      String *symname = Getattr(n, "sym:name");
-      char *realname = iname ? iname : name;
-      String *php_function_name = Swig_name_member(shadow_classname, realname);
-      create_command(symname, Swig_name_wrapper(php_function_name));
-    }
-
     return SWIG_OK;
   }
 
-
-  String * SwigToPhpType(Node *n, int shadow_flag) {
-    String *ptype = 0;
+  String * GetShadowReturnType(Node *n) {
     SwigType *t = Getattr(n, "type");
 
-    if (shadow_flag) {
-      ptype = PhpTypeFromTypemap((char *) "pstype", n, (char *) "");
-    }
-    if (!ptype) {
-      ptype = PhpTypeFromTypemap((char *) "ptype", n, (char *) "");
-    }
-
-    if (ptype) return ptype;
-
     /* Map type here */
     switch (SwigType_type(t)) {
       case T_CHAR:
@@ -2589,7 +1908,7 @@ public:
       case T_POINTER:
       case T_REFERENCE:
       case T_USER:
-	if (shadow_flag && is_shadow(t)) {
+	if (is_shadow(t)) {
 	  return NewString(Char(is_shadow(t)));
 	}
 	break;
@@ -2597,7 +1916,7 @@ public:
 	/* TODO */
 	break;
       default:
-	Printf(stderr, "SwigToPhpType: unhandled data type: %s\n", SwigType_str(t, 0));
+	Printf(stderr, "GetShadowReturnType: unhandled data type: %s\n", SwigType_str(t, 0));
 	break;
     }
 
@@ -2612,54 +1931,20 @@ public:
       return NewStringf("%s", tms);
   }
 
-  int abstractConstructorHandler(Node *n) {
-    String *iname = GetChar(n, "sym:name");
-    if (shadow && php_version == 4) {
-      Wrapper *f = NewWrapper();
-
-      String *wname = NewStringf("_wrap_new_%s", iname);
-      create_command(iname, wname);
-
-      Printf(f->def, "ZEND_NAMED_FUNCTION(_wrap_new_%s) {\n", iname);
-      Printf(f->def, "  zend_error(E_ERROR,\"Cannot create swig object type: %s as the underlying class is abstract\");\n", iname);
-      Printf(f->def, "}\n\n");
-      Wrapper_print(f, s_wrappers);
-      DelWrapper(f);
-      Delete(wname);
-    }
+  int abstractConstructorHandler(Node *) {
     return SWIG_OK;
   }
+
   /* ------------------------------------------------------------
    * constructorHandler()
    * ------------------------------------------------------------ */
 
   virtual int constructorHandler(Node *n) {
-    char *name = GetChar(n, "name");
-    char *iname = GetChar(n, "sym:name");
-
-    if (shadow && php_version == 4) {
-      if (iname && strcmp(iname, Char(shadow_classname)) == 0) {
-	native_constructor = NATIVE_CONSTRUCTOR;
-      } else {
-	native_constructor = ALTERNATIVE_CONSTRUCTOR;
-      }
-    } else {
-      native_constructor = 0;
-    }
     constructors++;
     wrapperType = constructor;
     Language::constructorHandler(n);
     wrapperType = standard;
 
-    if (shadow && php_version == 4) {
-      if (!Getattr(n, "sym:overloaded") || !Getattr(n, "sym:nextSibling")) {
-	char *realname = iname ? iname : name;
-	String *php_function_name = Swig_name_construct(realname);
-	create_command(realname, Swig_name_wrapper(php_function_name));
-      }
-    }
-
-    native_constructor = 0;
     return SWIG_OK;
   }
 
@@ -2770,9 +2055,14 @@ static Language *new_swig_php(int php_version) {
   }
   return maininstance;
 }
+
 extern "C" Language *swig_php4(void) {
-  return new_swig_php(4);
+  Printf(stderr, "*** -php4 is no longer supported.\n"
+		 "*** Either upgrade to PHP5 or use SWIG 1.3.36 or earlier.\n");
+  SWIG_exit(EXIT_FAILURE);
+  return NULL; // To avoid compiler warnings.
 }
+
 extern "C" Language *swig_php5(void) {
   return new_swig_php(5);
 }
diff --git a/Source/Modules/python.cxx b/Source/Modules/python.cxx
index bfdec0d76..7a878b4f8 100644
--- a/Source/Modules/python.cxx
+++ b/Source/Modules/python.cxx
@@ -49,10 +49,11 @@ static String *shadow_indent = 0;
 static int in_class = 0;
 static int classic = 0;
 static int modern = 0;
-static int apply = 0;
 static int new_repr = 1;
 static int no_header_file = 0;
 
+static int py3 = 0;
+
 /* C++ Support + Shadow Classes */
 
 static int have_constructor;
@@ -96,7 +97,6 @@ enum autodoc_t {
 static const char *usage1 = (char *) "\
 Python Options (available with -python)\n\
      -aliasobj0      - Alias obj0 when using fastunpack, needed for some old typemaps \n\
-     -apply          - Use apply() in proxy classes\n\
      -buildnone      - Use Py_BuildValue(" ") to obtain Py_None (default in Windows)\n\
      -castmode       - Enable the casting mode, which allows implicit cast between types in python\n\
      -classic        - Use classic classes only\n\
@@ -148,6 +148,8 @@ static const char *usage3 = (char *) "\
      -O              - Enable all the optimization options: \n\
                          -modern -fastdispatch -dirvtable -nosafecstrings -fvirtual -noproxydel \n\
                          -fastproxy -fastinit -fastunpack -fastquery -modernargs -nobuildnone \n\
+     -py3            - Generate code with Python 3 specific features:\n\
+                         Function annotation \n\
 \n";
 
 class PYTHON:public Language {
@@ -259,9 +261,6 @@ public:
 	} else if ((strcmp(argv[i], "-shadow") == 0) || ((strcmp(argv[i], "-proxy") == 0))) {
 	  shadow = 1;
 	  Swig_mark_arg(i);
-	} else if (strcmp(argv[i], "-apply") == 0) {
-	  apply = 1;
-	  Swig_mark_arg(i);
 	} else if ((strcmp(argv[i], "-new_repr") == 0) || (strcmp(argv[i], "-newrepr") == 0)) {
 	  new_repr = 1;
 	  Swig_mark_arg(i);
@@ -284,7 +283,6 @@ public:
 	} else if (strcmp(argv[i], "-classic") == 0) {
 	  classic = 1;
 	  modernargs = 0;
-	  apply = 1;
 	  modern = 0;
 	  Swig_mark_arg(i);
 	} else if (strcmp(argv[i], "-cppcast") == 0) {
@@ -390,7 +388,6 @@ public:
 	  proxydel = 0;
 	  Swig_mark_arg(i);
 	} else if (strcmp(argv[i], "-modern") == 0) {
-	  apply = 0;
 	  classic = 0;
 	  modern = 1;
 	  modernargs = 1;
@@ -408,7 +405,6 @@ public:
 	  no_header_file = 1;
 	  Swig_mark_arg(i);
 	} else if (strcmp(argv[i], "-O") == 0) {
-	  apply = 0;
 	  classic = 0;
 	  modern = 1;
 	  dirvtable = 1;
@@ -429,8 +425,17 @@ public:
 	  fputs(usage1, stdout);
 	  fputs(usage2, stdout);
 	  fputs(usage3, stdout);
-	}
+	} else if (strcmp(argv[i], "-py3") == 0) {
+      py3 = 1;
+      Swig_mark_arg(i);
+    }
+      
       }
+    } /* for */
+
+    if (py3) {
+        /* force disable features that not compatible with Python 3.x */
+        classic = 0;
     }
 
     if (cppcast) {
@@ -689,13 +694,46 @@ public:
 	mod_docstring = NULL;
       }
 
-      Printf(f_shadow, "\nimport %s\n", module);
+      Printv(f_shadow, "\nfrom sys import version_info\n", NULL);
+
+      if(fastproxy)
+      {
+        Printv(f_shadow, "if version_info >= (3,0,0):\n", NULL);
+        Printf(f_shadow, tab4 "new_instancemethod = lambda func, inst, cls: %s.SWIG_PyInstanceMethod_New(func)\n", module);
+        Printv(f_shadow, "else:\n", NULL);
+        Printv(f_shadow, tab4, "from new import instancemethod as new_instancemethod\n", NULL);
+      }
+      /* Import the C-extension module.  This should be a relative import,
+       * since the shadow module may also have been imported by a relative
+       * import, and there is thus no guarantee that the C-extension is on
+       * sys.path.  Relative imports must be explicitly specified from 2.6.0
+       * onwards (implicit relative imports will raise a DeprecationWarning
+       * in 2.6, and fail in 2.7 onwards), but the relative import syntax
+       * isn't available in python 2.4 or earlier, so we have to write some
+       * code conditional on the python version.
+       */
+      Printv(f_shadow, "if version_info >= (2,6,0):\n", NULL);
+      Printv(f_shadow, tab4, "def swig_import_helper():\n", NULL);
+      Printv(f_shadow, tab8, "from os.path import dirname\n", NULL);
+      Printv(f_shadow, tab8, "import imp\n", NULL);
+      Printv(f_shadow, tab8, "try:\n", NULL);
+      Printf(f_shadow, tab4 tab8 "fp, pathname, description = imp.find_module('%s', [dirname(__file__)])\n", module);
+      Printf(f_shadow, tab4 tab8 "_mod = imp.load_module('%s', fp, pathname, description)\n", module);
+      Printv(f_shadow, tab8, "finally:\n", NULL);
+      Printv(f_shadow, tab4 tab8, "if fp is not None: fp.close()\n", NULL);
+      Printv(f_shadow, tab8, "return _mod\n", NULL);
+      Printf(f_shadow, tab4 "%s = swig_import_helper()\n", module);
+      Printv(f_shadow, tab4, "del swig_import_helper\n", NULL);
+      Printv(f_shadow, "else:\n", NULL);
+      Printf(f_shadow, tab4 "import %s\n", module);
+
+      /* Delete the version_info symbol since we don't use it elsewhere in the
+       * module. */
+      Printv(f_shadow, "del version_info\n", NULL);
 
-      Printv(f_shadow, "import new\n", NULL);
-      Printv(f_shadow, "new_instancemethod = new.instancemethod\n", NULL);
       if (modern || !classic) {
 	Printv(f_shadow, "try:\n", tab4, "_swig_property = property\n", "except NameError:\n", tab4, "pass # Python < 2.2 doesn't have 'property'.\n", NULL);
-      }
+      } 
       /* if (!modern) */
       /* always needed, a class can be forced to be no-modern, such as an exception */
       {
@@ -722,7 +760,7 @@ public:
 	       "def _swig_getattr(self,class_type,name):\n",
 	       tab4, "if (name == \"thisown\"): return self.this.own()\n",
 	       tab4, "method = class_type.__swig_getmethods__.get(name,None)\n",
-	       tab4, "if method: return method(self)\n", tab4, "raise AttributeError,name\n\n", NIL);
+	       tab4, "if method: return method(self)\n", tab4, "raise AttributeError(name)\n\n", NIL);
 
 	Printv(f_shadow,
 	       "def _swig_repr(self):\n",
@@ -730,11 +768,17 @@ public:
 	       tab4, "except: strthis = \"\"\n", tab4, "return \"<%s.%s; %s >\" % (self.__class__.__module__, self.__class__.__name__, strthis,)\n\n", NIL);
 
 	if (!classic) {
+          /* Usage of types.ObjectType is deprecated.
+           * But don't sure wether this would broken old Python?
+           */
 	  Printv(f_shadow,
-		 "import types\n",
+//		 "import types\n",
 		 "try:\n",
-		 "    _object = types.ObjectType\n",
-		 "    _newclass = 1\n", "except AttributeError:\n", "    class _object : pass\n", "    _newclass = 0\n", "del types\n", "\n\n", NIL);
+//		 "    _object = types.ObjectType\n",
+		 "    _object = object\n",
+		 "    _newclass = 1\n", "except AttributeError:\n", "    class _object : pass\n", "    _newclass = 0\n", 
+//                 "del types\n", 
+                 "\n\n", NIL);
 	}
       }
       if (modern) {
@@ -760,7 +804,11 @@ public:
 
     }
 
-    Printf(f_header, "#define SWIG_init    init%s\n\n", module);
+    Printf(f_header, "#if PY_VERSION_HEX >= 0x03000000\n");
+    Printf(f_header, "#  define SWIG_init    PyInit_%s\n\n", module);
+    Printf(f_header, "#else\n");
+    Printf(f_header, "#  define SWIG_init    init%s\n\n", module);
+    Printf(f_header, "#endif\n");
     Printf(f_header, "#define SWIG_name    \"%s\"\n", module);
 
     Printf(f_wrappers, "#ifdef __cplusplus\n");
@@ -769,6 +817,9 @@ public:
     Append(const_code, "static swig_const_info swig_const_table[] = {\n");
     Append(methods, "static PyMethodDef SwigMethods[] = {\n");
 
+    /* the method exported for replacement of new.instancemethod in Python 3 */
+    add_pyinstancemethod_new();
+
     /* emit code */
     Language::top(n);
 
@@ -787,6 +838,12 @@ public:
     Append(const_code, "{0, 0, 0, 0.0, 0, 0}};\n");
     Printf(f_wrappers, "%s\n", const_code);
     initialize_threads(f_init);
+
+    Printf(f_init, "#if PY_VERSION_HEX >= 0x03000000\n");
+    Printf(f_init, "  return m;\n");
+    Printf(f_init, "#else\n");
+    Printf(f_init, "  return;\n");
+    Printf(f_init, "#endif\n");
     Printf(f_init, "}\n");
 
     Printf(f_wrappers, "#ifdef __cplusplus\n");
@@ -794,10 +851,6 @@ public:
     Printf(f_wrappers, "#endif\n");
 
     if (shadow) {
-      /*
-         Printf(f_shadow_imports,"\nimport %s\n", module);
-         Printv(f_shadow_py, f_shadow_imports, "\n",NIL);
-       */
       Printv(f_shadow_py, f_shadow, "\n", NIL);
       Printv(f_shadow_py, f_shadow_stubs, "\n", NIL);
 
@@ -831,6 +884,19 @@ public:
 
     return SWIG_OK;
   }
+  
+  /* ------------------------------------------------------------
+   * Emit the wrapper for PyInstanceMethod_New to MethodDef array.
+   * This wrapper is used to implement -fastproxy,
+   * as a replacement of new.instancemethod in Python 3.
+   * ------------------------------------------------------------ */
+  int add_pyinstancemethod_new()
+  {
+    String* name = NewString("SWIG_PyInstanceMethod_New");
+    Printf(methods, "\t { (char *)\"%s\", (PyCFunction)%s, METH_O, NULL},", name, name);
+    Delete(name);
+    return 0;
+  }
 
   /* ------------------------------------------------------------
    * importDirective()
@@ -874,25 +940,19 @@ public:
     return Language::importDirective(n);
   }
 
-
   /* ------------------------------------------------------------
-   * emitFuncCallHelper()
-   *    Write the shadow code to call a function in the extension
-   *    module.  Takes into account the -apply flag and whether
-   *    to use keyword args or not.
+   * funcCall()
+   *    Emit shadow code to call a function in the extension
+   *    module. Using proper argument and calling style for
+   *    given node n.
    * ------------------------------------------------------------ */
+   String *funcCall(String *name, String *parms) {
+    String *str = NewString("");
 
-  String *funcCallHelper(String *name, int kw) {
-    String *str;
-
-    str = NewString("");
-    if (apply) {
-      Printv(str, "apply(", module, ".", name, ", args", (kw ? ", kwargs" : ""), ")", NIL);
-    } else {
-      Printv(str, module, ".", name, "(*args", (kw ? ", **kwargs" : ""), ")", NIL);
-    }
+    Printv(str, module, ".", name, "(", parms, ")", NIL);
     return str;
-  }
+   }
+
 
   /* ------------------------------------------------------------
    * pythoncode()     - Output python code into the shadow file
@@ -1060,29 +1120,84 @@ public:
     return doc;
   }
 
+   /* -----------------------------------------------------------------------------
+   * makeParameterName()
+   *    Note: the generated name should consist with that in kwnames[]
+   *
+   * Inputs: 
+   *   n - Node
+   *   p - parameter node
+   *   arg_num - parameter argument number
+   * Return:
+   *   arg - a unique parameter name
+   * ----------------------------------------------------------------------------- */
+
+  String *makeParameterName(ParmList *plist, Parm *p, int arg_num) {
+    String *arg = 0;
+    String *pn = Swig_name_make(p, 0, Getattr(p, "name"), 0, 0);
+    // Use C parameter name unless it is a duplicate or an empty parameter name
+    int count = 0;
+    if ( SwigType_isvarargs(Getattr(p, "type")) ) {
+      return NewString("*args");
+    }
+    while (plist) {
+      if ((Cmp(pn, Getattr(plist, "name")) == 0))
+        count++;
+      plist = nextSibling(plist);
+    }
+    arg = (!pn || !Len(pn) || (count > 1)) ? NewStringf("arg%d", arg_num) : Copy(pn);
+    return arg;
+  }
+
+
   /* ------------------------------------------------------------
    * make_autodocParmList()
    *   Generate the documentation for the function parameters
+   *   Parameters:
+   *    func_annotation: Function annotation support
    * ------------------------------------------------------------ */
 
-  String *make_autodocParmList(Node *n, bool showTypes) {
+  String *make_autodocParmList(Node *n, bool showTypes, bool calling=false, bool func_annotation=false) {
+
+ 
     String *doc = NewString("");
     String *pdocs = Copy(Getattr(n, "feature:pdocs"));
     ParmList *plist = CopyParmList(Getattr(n, "parms"));
     Parm *p;
     Parm *pnext;
-    Node *lookup;
+    Node *lookup; 
+
+
     int lines = 0;
+    int arg_num = 0;
     const int maxwidth = 50;
 
+    if(calling)
+      func_annotation = false;
+    
     if (pdocs)
       Append(pdocs, "\n");
 
-
     Swig_typemap_attach_parms("in", plist, 0);
     Swig_typemap_attach_parms("doc", plist, 0);
-
+    
+    if (Strcmp(ParmList_protostr(plist), "void")==0) {
+      //No parameters actually
+      return doc;
+    }
+    
     for (p = plist; p; p = pnext) {
+
+      String *tm = Getattr(p, "tmap:in");
+      if (tm) {
+	pnext = Getattr(p, "tmap:in:next");
+        if (checkAttribute(p, "tmap:in:numinputs", "0")) {
+          continue;
+        }
+      } else {
+	pnext = nextSibling(p);
+      }
+
       String *name = 0;
       String *type = 0;
       String *value = 0;
@@ -1099,12 +1214,14 @@ public:
       type = type ? type : Getattr(p, "type");
       value = value ? value : Getattr(p, "value");
 
-      String *tm = Getattr(p, "tmap:in");
-      if (tm) {
-	pnext = Getattr(p, "tmap:in:next");
-      } else {
-	pnext = nextSibling(p);
-      }
+      name = makeParameterName(plist, p, arg_num);
+      // Reset it for convinient in further use. (mainly for makeParameterName())
+      // Since the plist is created by CopyParmList,
+      // we can hope that the set would have no side effect
+      Setattr(p, "name", name);
+
+      arg_num++;
+
 
       if (Len(doc)) {
 	// add a comma to the previous one if any
@@ -1116,39 +1233,40 @@ public:
 	  lines += 1;
 	}
       }
+      
+      type = SwigType_base(type);
+      lookup = Swig_symbol_clookup(type, 0);
+      if (lookup)
+        type = Getattr(lookup, "sym:name");
+      
       // Do the param type too?
-      if (showTypes) {
-	type = SwigType_base(type);
-	lookup = Swig_symbol_clookup(type, 0);
-	if (lookup)
-	  type = Getattr(lookup, "sym:name");
-	Printf(doc, "%s ", type);
+      if (showTypes)
+        Printf(doc, "%s ", type);
+
+      
+      Append(doc, name);
+      if (pdoc) {
+        if (!pdocs)
+          pdocs = NewString("Parameters:\n");
+        Printf(pdocs, "   %s\n", pdoc);
       }
 
-      if (name) {
-	Append(doc, name);
-	if (pdoc) {
-	  if (!pdocs)
-	    pdocs = NewString("Parameters:\n");
-	  Printf(pdocs, "   %s\n", pdoc);
-	}
-      } else {
-	Append(doc, "?");
-      }
+      // Write the function annoation
+      if (func_annotation)
+        Printf(doc, " : '%s'", type);
 
-      if (value) {
-	if (Strcmp(value, "NULL") == 0)
-	  value = NewString("None");
-	else if (Strcmp(value, "true") == 0 || Strcmp(value, "TRUE") == 0)
-	  value = NewString("True");
-	else if (Strcmp(value, "false") == 0 || Strcmp(value, "FALSE") == 0)
-	  value = NewString("False");
+      // Write default value
+      if (value && !calling) {
+        String* pv = pyvalue(value, Getattr(p, "type"));
+        if (pv)
+          value = pv;
 	else {
 	  lookup = Swig_symbol_clookup(value, 0);
-	  if (lookup)
+	  if (lookup) {
 	    value = Getattr(lookup, "sym:name");
+          }
 	}
-	Printf(doc, "=%s", value);
+	Printf(doc, " = %s", value);        
       }
     }
     if (pdocs)
@@ -1286,6 +1404,132 @@ public:
 
     return doc;
   }
+  
+  /* ------------------------------------------------------------
+   * pyvalue()
+   *    Check if string v can be a Python value literal,
+   *    (eg. number or string), or translate it to a Python literal.
+   * ------------------------------------------------------------ */
+  String* pyvalue(String *v, SwigType *t)
+  {
+    if (v && Len(v)>0) {
+      char fc = (Char(v))[0];
+      if (('0'<=fc && fc<='9') || '\''==fc || '"'==fc) {
+        /* number or string (or maybe NULL pointer)*/
+        if (SwigType_ispointer(t) && Strcmp(v, "0")==0)
+          return NewString("None");
+        else
+          return v;
+      }
+      if (Strcmp(v, "true")==0 || Strcmp(v, "FALSE")==0)
+        return NewString("True");
+      if (Strcmp(v, "false")==0 || Strcmp(v, "FALSE")==0)
+        return NewString("False");
+      if (Strcmp(v, "NULL")==0)
+        return NewString("None");
+    }
+    return 0;
+  }
+  /* ------------------------------------------------------------
+   * is_primitive_defaultargs()
+   *    Check if all the default args have primitive type.
+   *    (So we can generate proper parameter list with default 
+   *    values..)
+   * ------------------------------------------------------------ */
+  bool is_primitive_defaultargs(Node *n)
+  {
+    ParmList *plist = CopyParmList(Getattr(n, "parms"));
+    Parm *p;
+    Parm *pnext;
+
+    Swig_typemap_attach_parms("in", plist, 0);
+    for (p = plist; p; p = pnext) {
+      String *tm = Getattr(p, "tmap:in");
+      if (tm) {
+        pnext = Getattr(p, "tmap:in:next");
+        if (checkAttribute(p, "tmap:in:numinputs", "0")) {
+          continue;
+        }
+      } else {
+        pnext = nextSibling(p);
+      }
+      String *type = Getattr(p, "type");
+      String *value = Getattr(p, "value");
+      if (!pyvalue(value, type))
+        return false;
+    }
+    return true;
+  }
+
+
+  /* ------------------------------------------------------------
+   * is_real_overloaded()
+   *   Check if the function is overloaded, but not just have some
+   *   siblings generated due to the original function have 
+   *   default arguments.
+   * ------------------------------------------------------------ */
+  bool is_real_overloaded(Node *n)
+  {
+    Node *h = Getattr(n, "sym:overloaded");
+    Node *i;
+    if (!h)
+      return false;
+    
+    i = Getattr(h, "sym:nextSibling");
+    while (i) {
+      Node *nn = Getattr(i, "defaultargs");
+      if (nn != h) {
+        /* Check if overloaded function has defaultargs and 
+         * pointed to the first overloaded. */
+        return true;
+      }
+      i = Getattr(i, "sym:nextSibling");
+    }
+
+    return false;
+  }
+
+  /* ------------------------------------------------------------
+   * make_pyParmList()
+   *    Generate parameter list for Python functions or methods,
+   *    reuse make_autodocParmList() to do so.
+   * ------------------------------------------------------------ */
+  String* make_pyParmList(Node *n, bool in_class, bool is_calling, int kw)
+  {
+    /* Get the original function for a defaultargs copy, 
+     * see default_arguments() in parser.y. */
+    Node *nn = Getattr(n, "defaultargs");
+    if (nn) n = nn;
+
+    /* For overloaded function, just use *args */
+    if (is_real_overloaded(n) ||
+        GetFlag(n, "feature:compactdefaultargs") ||
+        !is_primitive_defaultargs(n))
+    {
+      String *parms = NewString("");
+      if(in_class)
+        Printf(parms, "self, ");
+      Printf(parms, "*args");
+      if (kw)
+        Printf(parms, ", **kwargs");
+      return parms;
+    }
+
+    bool funcanno = py3 ? true : false;
+    String *params = NewString("");
+    String *_params = make_autodocParmList(n, false, is_calling, funcanno);
+
+    if (in_class)
+    {      
+      Printf(params, "self");
+      if(Len(_params) > 0)
+        Printf(params, ", ");
+    }
+
+    Printv(params, _params, NULL);
+
+    return params;
+  }
 
   /* ------------------------------------------------------------
    * have_pythonprepend()
@@ -1351,6 +1595,40 @@ public:
     return have_pythonappend(n) || have_pythonprepend(n) || have_docstring(n);
   }
 
+  
+  /* ------------------------------------------------------------
+   * returnTypeAnnotation()
+   *    Helper function for constructing the function annotation
+   *    of the returning type, return a empty string for Python 2.x
+   * ------------------------------------------------------------ */
+  String* returnTypeAnnotation(Node *n)
+  {
+    String *ret=0; 
+    Parm *p = Getattr(n, "parms");
+    String *tm;
+    /* Try to guess the returning type by argout typemap,
+     * however the result may not accurate. */
+    while (p) {
+      if ((tm=Getattr(p, "tmap:argout:match_type"))) {
+        tm = SwigType_str(tm, 0);
+	if (ret)
+          Printv(ret, ", ", tm, NULL);
+        else
+          ret = tm;
+        p = Getattr(p, "tmap:argout:next");
+      } else {
+	p = nextSibling(p);
+      }
+    }
+    /* If no argout typemap, then get the returning type from
+     * the function prototype. */
+    if (!ret) {
+      ret = Getattr(n, "type");
+      if (ret) ret = SwigType_str(ret, 0);
+    }
+    return (ret && py3) ? NewStringf(" -> \"%s\" ", ret)
+                        : NewString("");
+  }
 
   /* ------------------------------------------------------------
    * emitFunctionShadowHelper()
@@ -1360,24 +1638,26 @@ public:
    * ------------------------------------------------------------ */
 
   void emitFunctionShadowHelper(Node *n, File *f_dest, String *name, int kw) {
-    if (Getattr(n, "feature:python:callback") || !have_addtofunc(n)) {
-      /* If there is no addtofunc directive then just assign from the extension module */
-      Printv(f_dest, name, " = ", module, ".", name, "\n", NIL);
+    String *parms = make_pyParmList(n, false, false, kw);
+    String *callParms = make_pyParmList(n, false, true, kw);
+    /* Make a wrapper function to insert the code into */
+    Printv(f_dest, "\ndef ", name, "(", parms, ")", returnTypeAnnotation(n), ":\n", NIL);
+    if (have_docstring(n))
+      Printv(f_dest, ctab4, docstring(n, AUTODOC_FUNC, tab4), "\n", NIL);
+    if (have_pythonprepend(n))
+      Printv(f_dest, ctab4, pythonprepend(n), "\n", NIL);
+    if (have_pythonappend(n)) {
+      Printv(f_dest, ctab4, "val = ", funcCall(name, callParms), "\n", NIL);
+      Printv(f_dest, ctab4, pythonappend(n), "\n", NIL);
+      Printv(f_dest, ctab4, "return val\n", NIL);
     } else {
-      /* Otherwise make a wrapper function to insert the code into */
-      Printv(f_dest, "\ndef ", name, "(*args", (kw ? ", **kwargs" : ""), "):\n", NIL);
-      if (have_docstring(n))
-	Printv(f_dest, ctab4, docstring(n, AUTODOC_FUNC, tab4), "\n", NIL);
-      if (have_pythonprepend(n))
-	Printv(f_dest, ctab4, pythonprepend(n), "\n", NIL);
-      if (have_pythonappend(n)) {
-	Printv(f_dest, ctab4, "val = ", funcCallHelper(name, kw), "\n", NIL);
-	Printv(f_dest, ctab4, pythonappend(n), "\n", NIL);
-	Printv(f_dest, ctab4, "return val\n", NIL);
-      } else {
-	Printv(f_dest, ctab4, "return ", funcCallHelper(name, kw), "\n", NIL);
-      }
+	Printv(f_dest, ctab4, "return ", funcCall(name, callParms), "\n", NIL);
     }
+
+    if (Getattr(n, "feature:python:callback") || !have_addtofunc(n)) {
+      /* If there is no addtofunc directive then just assign from the extension module (for speed up) */
+      Printv(f_dest, name, " = ", module, ".", name, "\n", NIL);
+    } 
   }
 
 
@@ -1773,7 +2053,6 @@ public:
 	Swig_warning(WARN_TYPEMAP_IN_UNDEF, input_file, line_number, "Unable to use type %s as a function argument.\n", SwigType_str(pt, 0));
 	break;
       }
-      p = nextSibling(p);
     }
 
     /* finish argument marshalling */
@@ -2461,7 +2740,7 @@ public:
       Printf(f_directors_h, "    PyObject *swig_get_method(size_t method_index, const char *method_name) const {\n");
       Printf(f_directors_h, "      PyObject *method = vtable[method_index];\n");
       Printf(f_directors_h, "      if (!method) {\n");
-      Printf(f_directors_h, "        swig::PyObject_var name = PyString_FromString(method_name);\n");
+      Printf(f_directors_h, "        swig::PyObject_var name = SWIG_Python_str_FromChar(method_name);\n");
       Printf(f_directors_h, "        method = PyObject_GetAttr(swig_get_self(), name);\n");
       Printf(f_directors_h, "        if (method == NULL) {\n");
       Printf(f_directors_h, "          std::string msg = \"Method in class %s doesn't exist, undefined \";\n", classname);
@@ -2596,6 +2875,16 @@ public:
 	  }
 	}
       }
+
+      /* dealing with abstract base class */
+      String *abcs = Getattr(n, "feature:python:abc");
+      if (py3 && abcs) {
+        if (Len(base_class)) {
+          Putc(',', base_class);
+        }
+        Printv(base_class, abcs, NIL);
+      }
+      
       Printv(f_shadow, "class ", class_name, NIL);
 
       if (Len(base_class)) {
@@ -2604,6 +2893,9 @@ public:
 	if (!classic) {
 	  Printf(f_shadow, modern ? "(object)" : "(_object)");
 	}
+        if (GetFlag(n, "feature:exceptionclass") ) {
+          Printf(f_shadow, "(Exception)");
+        }
       }
       Printf(f_shadow, ":\n");
       if (have_docstring(n)) {
@@ -2694,7 +2986,7 @@ public:
 	Delete(realct);
       }
       if (!have_constructor) {
-	Printv(f_shadow_file, tab4, "def __init__(self, *args, **kwargs): raise AttributeError, \"No constructor defined\"\n", NIL);
+	Printv(f_shadow_file, tab4, "def __init__(self, *args, **kwargs): raise AttributeError(\"No constructor defined\")\n", NIL);
       } else if (fastinit) {
 
 	Printv(f_wrappers, "SWIGINTERN PyObject *", class_name, "_swiginit(PyObject *SWIGUNUSEDPARM(self), PyObject *args) {\n", NIL);
@@ -2807,13 +3099,15 @@ public:
 	  Delete(pycode);
 	  fproxy = 0;
 	} else {
+          String *parms = make_pyParmList(n, true, false, allow_kwargs);
+          String *callParms = make_pyParmList(n, true, true, allow_kwargs);
 	  if (!have_addtofunc(n)) {
 	    if (!fastproxy || olddefs) {
-	      Printv(f_shadow, tab4, "def ", symname, "(*args", (allow_kwargs ? ", **kwargs" : ""), "):", NIL);
-	      Printv(f_shadow, " return ", funcCallHelper(Swig_name_member(class_name, symname), allow_kwargs), "\n", NIL);
+	      Printv(f_shadow, tab4, "def ", symname, "(", parms, ")", returnTypeAnnotation(n), ":", NIL);
+	      Printv(f_shadow, " return ", funcCall(Swig_name_member(class_name, symname), callParms), "\n", NIL);
 	    }
 	  } else {
-	    Printv(f_shadow, tab4, "def ", symname, "(*args", (allow_kwargs ? ", **kwargs" : ""), "):", NIL);
+	    Printv(f_shadow, tab4, "def ", symname, "(",parms , ")", returnTypeAnnotation(n), ":", NIL);
 	    Printv(f_shadow, "\n", NIL);
 	    if (have_docstring(n))
 	      Printv(f_shadow, tab8, docstring(n, AUTODOC_METHOD, tab8), "\n", NIL);
@@ -2823,11 +3117,11 @@ public:
 	    }
 	    if (have_pythonappend(n)) {
 	      fproxy = 0;
-	      Printv(f_shadow, tab8, "val = ", funcCallHelper(Swig_name_member(class_name, symname), allow_kwargs), "\n", NIL);
+	      Printv(f_shadow, tab8, "val = ", funcCall(Swig_name_member(class_name, symname), callParms), "\n", NIL);
 	      Printv(f_shadow, tab8, pythonappend(n), "\n", NIL);
 	      Printv(f_shadow, tab8, "return val\n\n", NIL);
 	    } else {
-	      Printv(f_shadow, tab8, "return ", funcCallHelper(Swig_name_member(class_name, symname), allow_kwargs), "\n\n", NIL);
+	      Printv(f_shadow, tab8, "return ", funcCall(Swig_name_member(class_name, symname), callParms), "\n\n", NIL);
 	    }
 	  }
 	}
@@ -2860,17 +3154,19 @@ public:
     if (shadow) {
       if (!classic && !Getattr(n, "feature:python:callback") && have_addtofunc(n)) {
 	int kw = (check_kwargs(n) && !Getattr(n, "sym:overloaded")) ? 1 : 0;
-	Printv(f_shadow, tab4, "def ", symname, "(*args", (kw ? ", **kwargs" : ""), "):\n", NIL);
+        String *parms = make_pyParmList(n, true, false, kw);
+        String *callParms = make_pyParmList(n, true, true, kw);
+	Printv(f_shadow, tab4, "def ", symname, "(", parms, ")", returnTypeAnnotation(n), ":\n", NIL);
 	if (have_docstring(n))
 	  Printv(f_shadow, tab8, docstring(n, AUTODOC_STATICFUNC, tab8), "\n", NIL);
 	if (have_pythonprepend(n))
 	  Printv(f_shadow, tab8, pythonprepend(n), "\n", NIL);
 	if (have_pythonappend(n)) {
-	  Printv(f_shadow, tab8, "val = ", funcCallHelper(Swig_name_member(class_name, symname), kw), "\n", NIL);
+	  Printv(f_shadow, tab8, "val = ", funcCall(Swig_name_member(class_name, symname), callParms), "\n", NIL);
 	  Printv(f_shadow, tab8, pythonappend(n), "\n", NIL);
 	  Printv(f_shadow, tab8, "return val\n\n", NIL);
 	} else {
-	  Printv(f_shadow, tab8, "return ", funcCallHelper(Swig_name_member(class_name, symname), kw), "\n\n", NIL);
+	  Printv(f_shadow, tab8, "return ", funcCall(Swig_name_member(class_name, symname), callParms), "\n\n", NIL);
 	}
 	Printv(f_shadow, tab4, modern ? "" : "if _newclass:", symname, " = staticmethod(", symname, ")\n", NIL);
 
@@ -2942,8 +3238,8 @@ public:
 	  handled_as_init = (Strcmp(nname, sname) == 0) || (Strcmp(nname, cname) == 0);
 	  Delete(cname);
 	}
-
-	if (!have_constructor && handled_as_init) {
+        
+          if (!have_constructor && handled_as_init) {
 	  if (Getattr(n, "feature:shadow")) {
 	    String *pycode = pythoncode(Getattr(n, "feature:shadow"), tab4);
 	    String *pyaction = NewStringf("%s.%s", module, Swig_name_construct(symname));
@@ -2957,23 +3253,30 @@ public:
 	    String *classname = Swig_class_name(parent);
 	    String *rclassname = Swig_class_name(getCurrentClass());
 	    assert(rclassname);
-	    if (use_director) {
+
+            String *parms = make_pyParmList(n, true, false, allow_kwargs);
+            /* Pass 'self' only if using director */
+            String *callParms = make_pyParmList(n, false, true, allow_kwargs);
+
+            if (use_director) {
+              Insert(callParms, 0, "_self, ");
 	      Printv(pass_self, tab8, NIL);
 	      Printf(pass_self, "if self.__class__ == %s:\n", classname);
-	      Printv(pass_self, tab8, tab4, "args = (None,) + args\n", tab8, "else:\n", tab8, tab4, "args = (self,) + args\n", NIL);
+              //Printv(pass_self, tab8, tab4, "args = (None,) + args\n", tab8, "else:\n", tab8, tab4, "args = (self,) + args\n", NIL);
+              Printv(pass_self, tab8, tab4, "_self = None\n", tab8, "else:\n", tab8, tab4, "_self = self\n", NIL);
 	    }
 
-	    Printv(f_shadow, tab4, "def __init__(self, *args", (allow_kwargs ? ", **kwargs" : ""), "): \n", NIL);
+	    Printv(f_shadow, tab4, "def __init__(", parms, ")", returnTypeAnnotation(n), ": \n", NIL);
 	    if (have_docstring(n))
 	      Printv(f_shadow, tab8, docstring(n, AUTODOC_CTOR, tab8), "\n", NIL);
 	    if (have_pythonprepend(n))
 	      Printv(f_shadow, tab8, pythonprepend(n), "\n", NIL);
 	    Printv(f_shadow, pass_self, NIL);
 	    if (fastinit) {
-	      Printv(f_shadow, tab8, module, ".", class_name, "_swiginit(self,", funcCallHelper(Swig_name_construct(symname), allow_kwargs), ")\n", NIL);
+	      Printv(f_shadow, tab8, module, ".", class_name, "_swiginit(self,", funcCall(Swig_name_construct(symname), callParms), ")\n", NIL);
 	    } else {
 	      Printv(f_shadow,
-		     tab8, "this = ", funcCallHelper(Swig_name_construct(symname), allow_kwargs), "\n",
+		     tab8, "this = ", funcCall(Swig_name_construct(symname), callParms), "\n",
 		     tab8, "try: self.this.append(this)\n", tab8, "except: self.this = this\n", NIL);
 	    }
 	    if (have_pythonappend(n))
@@ -2993,13 +3296,15 @@ public:
 	    Printv(f_shadow_stubs, pycode, "\n", NIL);
 	    Delete(pycode);
 	  } else {
+            String *parms = make_pyParmList(n, true, false, allow_kwargs);
+            String *callParms = make_pyParmList(n, true, true, allow_kwargs);
 
-	    Printv(f_shadow_stubs, "\ndef ", symname, "(*args", (allow_kwargs ? ", **kwargs" : ""), "):\n", NIL);
+	    Printv(f_shadow_stubs, "\ndef ", symname, "(", parms, ")", returnTypeAnnotation(n), ":\n", NIL);
 	    if (have_docstring(n))
 	      Printv(f_shadow_stubs, tab4, docstring(n, AUTODOC_CTOR, tab4), "\n", NIL);
 	    if (have_pythonprepend(n))
 	      Printv(f_shadow_stubs, tab4, pythonprepend(n), "\n", NIL);
-	    Printv(f_shadow_stubs, tab4, "val = ", funcCallHelper(Swig_name_construct(symname), allow_kwargs), "\n", NIL);
+	    Printv(f_shadow_stubs, tab4, "val = ", funcCall(Swig_name_construct(symname), callParms), "\n", NIL);
 #ifdef USE_THISOWN
 	    Printv(f_shadow_stubs, tab4, "val.thisown = 1\n", NIL);
 #endif
@@ -3578,15 +3883,15 @@ int PYTHON::classDirectorMethod(Node *n, Node *parent, String *super) {
       if (use_parse || !modernargs) {
 	Printf(w->code, "swig::PyObject_var result = PyObject_CallMethod(swig_get_self(), (char *)\"%s\", (char *)\"(%s)\" %s);\n",
 	       pyname, parse_args, arglist);
-      } else {
-	Printf(w->code, "swig::PyObject_var swig_method_name = PyString_FromString((char *)\"%s\");\n", pyname);
+      } else {        
+	Printf(w->code, "swig::PyObject_var swig_method_name = SWIG_Python_str_FromChar((char *)\"%s\");\n", pyname);
 	Printf(w->code, "swig::PyObject_var result = PyObject_CallMethodObjArgs(swig_get_self(), (PyObject *) swig_method_name %s, NULL);\n", arglist);
       }
     } else {
       if (!modernargs) {
 	Printf(w->code, "swig::PyObject_var result = PyObject_CallMethod(swig_get_self(), (char *) \"%s\", NULL);\n", pyname);
       } else {
-	Printf(w->code, "swig::PyObject_var swig_method_name = PyString_FromString((char *)\"%s\");\n", pyname);
+	Printf(w->code, "swig::PyObject_var swig_method_name = SWIG_Python_str_FromChar((char *)\"%s\");\n", pyname);
 	Append(w->code, "swig::PyObject_var result = PyObject_CallMethodObjArgs(swig_get_self(), (PyObject *) swig_method_name, NULL);\n");
       }
     }
diff --git a/Source/Modules/r.cxx b/Source/Modules/r.cxx
index 989136a9d..49d3ecc89 100644
--- a/Source/Modules/r.cxx
+++ b/Source/Modules/r.cxx
@@ -57,11 +57,13 @@ static String * getRTypeName(SwigType *t, int *outCount = NULL) {
   Insert(tmp, 0, retName);
   return tmp;
   
+  /*
   if(count)
     return(b);
   
   Delete(b);
   return(NewString(""));
+  */
 }
 
 #if 0
@@ -104,7 +106,7 @@ static String * getRType(Node *n) {
   Now handles arrays, i.e. struct A[2]
 ****************/
 
-static String *getRClassName(String *retType, int addRef = 1, int upRef=0) {
+static String *getRClassName(String *retType, int /*addRef*/ = 1, int upRef=0) {
   String *tmp = NewString("");
   SwigType *resolved = SwigType_typedef_resolve_all(retType);
   char *retName = Char(SwigType_manglestr(resolved));
@@ -115,6 +117,7 @@ static String *getRClassName(String *retType, int addRef = 1, int upRef=0) {
   }
   
   return tmp;
+/*
 #if 1
   List *l = SwigType_split(retType);
   int n = Len(l);
@@ -160,6 +163,7 @@ static String *getRClassName(String *retType, int addRef = 1, int upRef=0) {
 #endif
   
   return tmp;
+*/
 }
 
 /*********************
@@ -1841,6 +1845,9 @@ int R::functionWrapper(Node *n) {
     String   *name  = Getattr(p,"name");
     String   *lname  = Getattr(p,"lname");
 
+    // R keyword renaming
+    if (name && Swig_name_warning(p, 0, name, 0))
+      name = 0;
 
     /* If we have a :: in the parameter name because we are accessing a static member of a class, say, then
        we need to remove that prefix. */
@@ -2027,14 +2034,18 @@ int R::functionWrapper(Node *n) {
       Replaceall(tm,"$owner", "R_SWIG_EXTERNAL");
     }
 
-    if(0 && addCopyParam) {
+#if 0
+    if(addCopyParam) {
       Printf(f->code, "if(LOGICAL(s_swig_copy)[0]) {\n");
       Printf(f->code, "/* Deal with returning a reference. */\nr_ans = R_NilValue;\n");
       Printf(f->code, "}\n else {\n");
     } 
+#endif
     Printf(f->code, "%s\n", tm);
-    if(0 && addCopyParam) 
+#if 0
+    if(addCopyParam) 
       Printf(f->code, "}\n"); /* end of if(s_swig_copy) ... else { ... } */
+#endif
 
   } else {
     Swig_warning(WARN_TYPEMAP_OUT_UNDEF, input_file, line_number,
diff --git a/Source/Modules/ruby.cxx b/Source/Modules/ruby.cxx
index a57571bb8..ad448d34e 100644
--- a/Source/Modules/ruby.cxx
+++ b/Source/Modules/ruby.cxx
@@ -448,7 +448,7 @@ private:
 		    parent_name = Copy( Getattr(mod, "name") );
 		  if ( parent_name )
 		    {
-		      (Char(parent_name))[0] = toupper((Char(parent_name))[0]);
+		      (Char(parent_name))[0] = (char)toupper((Char(parent_name))[0]);
 		    }
 		}
 		if ( parent_name )
@@ -1194,7 +1194,7 @@ public:
 	while (m.item) {
 	  if (Len(m.item) > 0) {
 	    String *cap = NewString(m.item);
-	    (Char(cap))[0] = toupper((Char(cap))[0]);
+	    (Char(cap))[0] = (char)toupper((Char(cap))[0]);
 	    if (last != 0) {
 	      Append(module, "::");
 	    }
@@ -1206,7 +1206,7 @@ public:
 	if (feature == 0) {
 	  feature = Copy(last);
 	}
-	(Char(last))[0] = toupper((Char(last))[0]);
+	(Char(last))[0] = (char)toupper((Char(last))[0]);
 	modvar = NewStringf("m%s", last);
 	Delete(modules);
       }
@@ -2219,7 +2219,7 @@ public:
       return name;
 
     if (islower(name[0])) {
-      name[0] = toupper(name[0]);
+      name[0] = (char)toupper(name[0]);
       Swig_warning(WARN_RUBY_WRONG_NAME, input_file, line_number, "Wrong %s name (corrected to `%s')\n", reason, name);
       return name;
     }
@@ -2545,7 +2545,7 @@ public:
     String *name = Copy(symname);
     char *cname = Char(name);
     if (cname)
-      cname[0] = toupper(cname[0]);
+      cname[0] = (char)toupper(cname[0]);
     Printv(director_prot_ctor_code,
 	   "if ( $comparison ) { /* subclassed */\n",
 	   "  $director_new \n",
diff --git a/Source/Modules/swigmain.cxx b/Source/Modules/swigmain.cxx
index 3b60f2259..5b103e71e 100644
--- a/Source/Modules/swigmain.cxx
+++ b/Source/Modules/swigmain.cxx
@@ -74,8 +74,8 @@ static swig_module modules[] = {
   {"-octave", swig_octave, "Octave"},
   {"-perl", swig_perl5, "Perl"},
   {"-perl5", swig_perl5, 0},
-  {"-php", swig_php4, 0},
-  {"-php4", swig_php4, "PHP4"},
+  {"-php", swig_php5, 0},
+  {"-php4", swig_php4, 0},
   {"-php5", swig_php5, "PHP5"},
   {"-pike", swig_pike, "Pike"},
   {"-python", swig_python, "Python"},
diff --git a/Source/Modules/uffi.cxx b/Source/Modules/uffi.cxx
index 7a94b77bb..5d4affb8c 100644
--- a/Source/Modules/uffi.cxx
+++ b/Source/Modules/uffi.cxx
@@ -26,7 +26,6 @@ public:
 };
 
 static File *f_cl = 0;
-static File *f_null = 0;
 
 static struct {
   int count;
@@ -225,15 +224,7 @@ void UFFI::main(int argc, char *argv[]) {
 int UFFI::top(Node *n) {
   String *module = Getattr(n, "name");
   String *output_filename = NewString("");
-  String *devnull = NewString("/dev/null");
-
-  f_null = NewFile(devnull, "w+");
-  if (!f_null) {
-    FileErrorDisplay(devnull);
-    SWIG_exit(EXIT_FAILURE);
-  }
-  Delete(devnull);
-
+  File *f_null = NewString("");
 
   Printf(output_filename, "%s%s.cl", SWIG_output_directory(), module);
 
diff --git a/Source/Preprocessor/cpp.c b/Source/Preprocessor/cpp.c
index 560d12998..c04f95f00 100644
--- a/Source/Preprocessor/cpp.c
+++ b/Source/Preprocessor/cpp.c
@@ -36,6 +36,7 @@ static int error_as_warning = 0;	/* Understand the cpp #error directive as a spe
 /* Test a character to see if it valid in an identifier (after the first letter) */
 #define isidchar(c) ((isalnum(c)) || (c == '_') || (c == '$'))
 
+DOH *Preprocessor_replace(DOH *);
 
 /* Skip whitespace */
 static void skip_whitespace(String *s, String *out) {
@@ -698,7 +699,6 @@ static String *get_options(String *str) {
 static String *expand_macro(String *name, List *args) {
   String *ns;
   DOH *symbols, *macro, *margs, *mvalue, *temp, *tempa, *e;
-  DOH *Preprocessor_replace(DOH *);
   int i, l;
   int isvarargs = 0;
 
@@ -935,7 +935,6 @@ static String *expand_macro(String *name, List *args) {
 
 List *evaluate_args(List *x) {
   Iterator i;
-  String *Preprocessor_replace(String *);
   List *nl = NewList();
 
   for (i = First(x); i.item; i = Next(i)) {
@@ -1795,7 +1794,7 @@ String *Preprocessor_parse(String *s) {
 	for (i = 0; i < 6;) {
 	  c = Getc(s);
 	  Putc(c, value);
-	  statement[i++] = c;
+	  statement[i++] = (char)c;
 	  if (strncmp(statement, ed, i) && strncmp(statement, df, i))
 	    break;
 	}
diff --git a/Source/Swig/cwrap.c b/Source/Swig/cwrap.c
index 2fc444290..18920ecc2 100644
--- a/Source/Swig/cwrap.c
+++ b/Source/Swig/cwrap.c
@@ -513,7 +513,8 @@ String *Swig_cppconstructor_base_call(String_or_char *name, ParmList *parms, int
 	pname = Swig_cparm_name(p, i);
 	i++;
       } else {
-	if ((pname = Getattr(p, "value")))
+        pname = Getattr(p, "value");
+	if (pname)
 	  pname = Copy(pname);
 	else
 	  pname = Copy(Getattr(p, "name"));
diff --git a/Source/Swig/include.c b/Source/Swig/include.c
index 25ea0683f..3f47be15b 100644
--- a/Source/Swig/include.c
+++ b/Source/Swig/include.c
@@ -352,7 +352,8 @@ char *Swig_file_filename(const String_or_char *filename) {
   char *c;
 
   strcpy(tmp, Char(filename));
-  if ((c = strrchr(tmp, *delim)))
+  c = strrchr(tmp, *delim);
+  if (c)
     return c + 1;
   else
     return tmp;
diff --git a/Source/Swig/misc.c b/Source/Swig/misc.c
index 04691b595..d29250517 100644
--- a/Source/Swig/misc.c
+++ b/Source/Swig/misc.c
@@ -614,7 +614,8 @@ void Swig_scopename_split(String *s, String **rprefix, String **rlast) {
     *rlast = Copy(s);
   }
 
-  if ((co = strstr(cc, "operator "))) {
+  co = strstr(cc, "operator ");
+  if (co) {
     if (co == cc) {
       *rprefix = 0;
       *rlast = Copy(s);
@@ -664,7 +665,9 @@ String *Swig_scopename_prefix(String *s) {
   char *co = 0;
   if (!strstr(c, "::"))
     return 0;
-  if ((co = strstr(cc, "operator "))) {
+  co = strstr(cc, "operator ");
+
+  if (co) {
     if (co == cc) {
       return 0;
     } else {
@@ -715,7 +718,8 @@ String *Swig_scopename_last(String *s) {
   if (!strstr(c, "::"))
     return NewString(s);
 
-  if ((co = strstr(cc, "operator "))) {
+  co = strstr(cc, "operator ");
+  if (co) {
     return NewString(co);
   }
 
@@ -756,7 +760,9 @@ String *Swig_scopename_first(String *s) {
   char *co = 0;
   if (!strstr(c, "::"))
     return 0;
-  if ((co = strstr(c, "operator "))) {
+
+  co = strstr(c, "operator ");
+  if (co) {
     if (co == c) {
       return 0;
     }
@@ -804,7 +810,9 @@ String *Swig_scopename_suffix(String *s) {
   char *co = 0;
   if (!strstr(c, "::"))
     return 0;
-  if ((co = strstr(c, "operator "))) {
+
+  co = strstr(c, "operator ");
+  if (co) {
     if (co == c)
       return 0;
   }
@@ -842,8 +850,9 @@ String *Swig_scopename_suffix(String *s) {
 
 int Swig_scopename_check(String *s) {
   char *c = Char(s);
-  char *co = 0;
-  if ((co = strstr(c, "operator "))) {
+  char *co = strstr(c, "operator ");
+
+  if (co) {
     if (co == c)
       return 0;
   }
diff --git a/Source/Swig/naming.c b/Source/Swig/naming.c
index 519e5b59e..f34a24612 100644
--- a/Source/Swig/naming.c
+++ b/Source/Swig/naming.c
@@ -482,7 +482,8 @@ DOH *Swig_name_object_get(Hash *namehash, String *prefix, String *name, SwigType
 	Delete(t_name);
       }
       /* A template-based class lookup */
-      if (0 && !rn && SwigType_istemplate(prefix)) {
+      /*
+      if (!rn && SwigType_istemplate(prefix)) {
 	String *t_prefix = SwigType_templateprefix(prefix);
 	if (Strcmp(t_prefix, prefix) != 0) {
 	  String *t_name = SwigType_templateprefix(name);
@@ -491,6 +492,7 @@ DOH *Swig_name_object_get(Hash *namehash, String *prefix, String *name, SwigType
 	}
 	Delete(t_prefix);
       }
+      */
     }
     /* A wildcard-based class lookup */
     if (!rn) {
@@ -1477,7 +1479,7 @@ String *Swig_name_make(Node *n, String *prefix, String_or_char *cname, SwigType
   }
 
 
-  if (rename_hash || rename_list) {
+  if (rename_hash || rename_list || namewarn_hash || namewarn_list) {
     Hash *rn = Swig_name_object_get(Swig_name_rename_hash(), prefix, name, decl);
     if (!rn || !Swig_name_match_nameobj(rn, n)) {
       rn = Swig_name_nameobj_lget(Swig_name_rename_list(), n, prefix, name, decl);
diff --git a/Source/Swig/scanner.c b/Source/Swig/scanner.c
index e8b1b5f46..06e78db37 100644
--- a/Source/Swig/scanner.c
+++ b/Source/Swig/scanner.c
@@ -200,7 +200,7 @@ static char nextchar(Scanner * s) {
   if ((nc == '\n') && (!s->freeze_line)) 
     s->line++;
   Putc(nc,s->text);
-  return nc;
+  return (char)nc;
 }
 
 /* -----------------------------------------------------------------------------
@@ -349,7 +349,7 @@ static void get_escape(Scanner *s) {
       } else {
 	char tmp[3];
 	tmp[0] = '\\';
-	tmp[1] = c;
+	tmp[1] = (char)c;
 	tmp[2] = 0;
 	Delitem(s->text, DOH_END);
 	Append(s->text, tmp);
diff --git a/Source/Swig/typeobj.c b/Source/Swig/typeobj.c
index f234839fe..18d1b2304 100644
--- a/Source/Swig/typeobj.c
+++ b/Source/Swig/typeobj.c
@@ -937,7 +937,8 @@ String *SwigType_templateargs(const SwigType *t) {
 
 int SwigType_istemplate(const SwigType *t) {
   char *ct = Char(t);
-  if ((ct = strstr(ct, "<(")) && (strstr(ct + 2, ")>")))
+  ct = strstr(ct, "<(");
+  if (ct && (strstr(ct + 2, ")>")))
     return 1;
   return 0;
 }
diff --git a/Source/Swig/typesys.c b/Source/Swig/typesys.c
index fdf37ece1..a9e2898bd 100644
--- a/Source/Swig/typesys.c
+++ b/Source/Swig/typesys.c
@@ -108,6 +108,8 @@ static Hash *typedef_resolve_cache = 0;
 static Hash *typedef_all_cache = 0;
 static Hash *typedef_qualified_cache = 0;
 
+static Typetab *SwigType_find_scope(Typetab *s, String *nameprefix);
+
 /* common attribute keys, to avoid calling find_key all the times */
 
 /* 
@@ -162,7 +164,6 @@ void SwigType_typesystem_init() {
  * ----------------------------------------------------------------------------- */
 
 int SwigType_typedef(SwigType *type, String_or_char *name) {
-  Typetab *SwigType_find_scope(Typetab *, String *s);
   if (Getattr(current_typetab, name))
     return -1;			/* Already defined */
   if (Strcmp(type, name) == 0) {	/* Can't typedef a name to itself */
@@ -409,7 +410,7 @@ void SwigType_print_scope(Typetab *t) {
   }
 }
 
-Typetab *SwigType_find_scope(Typetab *s, String *nameprefix) {
+static Typetab *SwigType_find_scope(Typetab *s, String *nameprefix) {
   Typetab *ss;
   String *nnameprefix = 0;
   static int check_parent = 1;
@@ -846,7 +847,7 @@ SwigType *SwigType_typedef_qualified(SwigType *t) {
   String *result;
   int i, len;
 
-  if (t && strncmp(Char(t), "::", 2) == 0) {
+  if (strncmp(Char(t), "::", 2) == 0) {
     return Copy(t);
   }
 
@@ -1311,7 +1312,8 @@ SwigType *SwigType_alttype(SwigType *t, int local_tmap) {
       SwigType *ftd = SwigType_typedef_resolve_all(t);
       td = SwigType_strip_qualifiers(ftd);
       Delete(ftd);
-      if ((n = Swig_symbol_clookup(td, 0))) {
+      n = Swig_symbol_clookup(td, 0);
+      if (n) {
 	if (GetFlag(n, "feature:valuewrapper")) {
 	  use_wrapper = 1;
 	} else {
@@ -1334,7 +1336,8 @@ SwigType *SwigType_alttype(SwigType *t, int local_tmap) {
     Delete(ftd);
     if (SwigType_type(td) == T_USER) {
       use_wrapper = 1;
-      if ((n = Swig_symbol_clookup(td, 0))) {
+      n = Swig_symbol_clookup(td, 0);
+      if (n) {
 	if ((Checkattr(n, "nodeType", "class")
 	     && !Getattr(n, "allocate:noassign")
 	     && (Getattr(n, "allocate:default_constructor")))
@@ -1795,13 +1798,15 @@ void SwigType_inherit_equiv(File *out) {
 	String *lprefix = SwigType_lstr(prefix, 0);
         Hash *subhash = Getattr(sub, bk.key);
         String *convcode = Getattr(subhash, "convcode");
-	Printf(out, "static void *%s(void *x, int *newmemory) {", convname);
         if (convcode) {
+          char *newmemoryused = Strstr(convcode, "newmemory"); /* see if newmemory parameter is used in order to avoid unused parameter warnings */
           String *fn = Copy(convcode);
           Replaceall(fn, "$from", "x");
+          Printf(out, "static void *%s(void *x, int *%s) {", convname, newmemoryused ? "newmemory" : "SWIGUNUSEDPARM(newmemory)");
           Printf(out, "%s", fn);
         } else {
           String *cast = Getattr(subhash, "cast");
+          Printf(out, "static void *%s(void *x, int *SWIGUNUSEDPARM(newmemory)) {", convname);
           Printf(out, "\n    return (void *)((%s) ", lkey);
           if (cast)
             Printf(out, "%s", cast);
diff --git a/TODO b/TODO
index d764d1d20..103185d23 100644
--- a/TODO
+++ b/TODO
@@ -1,6 +1,6 @@
 SWIG TO-DO
 
-Release: SWIG-1.3.35
+Release: SWIG-1.3.36
 
 -----------------------------------------------------------------------------
 
diff --git a/Tools/WAD/Python/type.c b/Tools/WAD/Python/type.c
index 5236c1c64..7d8248e0b 100644
--- a/Tools/WAD/Python/type.c
+++ b/Tools/WAD/Python/type.c
@@ -62,7 +62,7 @@ new_wadobject(WadFrame *f, int count) {
 /* release a wad object */
 static void
 wadobject_dealloc(wadobject *self) {
-  PyMem_DEL(self);
+  PyObject_Del(self);
 }
 
 static char message[65536];
diff --git a/Tools/config/config.guess b/Tools/config/config.guess
deleted file mode 100755
index 278f9e9e0..000000000
--- a/Tools/config/config.guess
+++ /dev/null
@@ -1,1516 +0,0 @@
-#! /bin/sh
-# Attempt to guess a canonical system name.
-#   Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999,
-#   2000, 2001, 2002, 2003, 2004, 2005, 2006 Free Software Foundation,
-#   Inc.
-
-timestamp='2007-07-22'
-
-# This file is free software; you can redistribute it and/or modify it
-# under the terms of the GNU General Public License as published by
-# the Free Software Foundation; either version 2 of the License, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-# General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program; if not, write to the Free Software
-# Foundation, Inc., 51 Franklin Street - Fifth Floor, Boston, MA
-# 02110-1301, USA.
-#
-# As a special exception to the GNU General Public License, if you
-# distribute this file as part of a program that contains a
-# configuration script generated by Autoconf, you may include it under
-# the same distribution terms that you use for the rest of that program.
-
-
-# Originally written by Per Bothner <per@bothner.com>.
-# Please send patches to <config-patches@gnu.org>.  Submit a context
-# diff and a properly formatted ChangeLog entry.
-#
-# This script attempts to guess a canonical system name similar to
-# config.sub.  If it succeeds, it prints the system name on stdout, and
-# exits with 0.  Otherwise, it exits with 1.
-#
-# The plan is that this can be called by configure scripts if you
-# don't specify an explicit build system type.
-
-me=`echo "$0" | sed -e 's,.*/,,'`
-
-usage="\
-Usage: $0 [OPTION]
-
-Output the configuration name of the system \`$me' is run on.
-
-Operation modes:
-  -h, --help         print this help, then exit
-  -t, --time-stamp   print date of last modification, then exit
-  -v, --version      print version number, then exit
-
-Report bugs and patches to <config-patches@gnu.org>."
-
-version="\
-GNU config.guess ($timestamp)
-
-Originally written by Per Bothner.
-Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004, 2005
-Free Software Foundation, Inc.
-
-This is free software; see the source for copying conditions.  There is NO
-warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE."
-
-help="
-Try \`$me --help' for more information."
-
-# Parse command line
-while test $# -gt 0 ; do
-  case $1 in
-    --time-stamp | --time* | -t )
-       echo "$timestamp" ; exit ;;
-    --version | -v )
-       echo "$version" ; exit ;;
-    --help | --h* | -h )
-       echo "$usage"; exit ;;
-    -- )     # Stop option processing
-       shift; break ;;
-    - )	# Use stdin as input.
-       break ;;
-    -* )
-       echo "$me: invalid option $1$help" >&2
-       exit 1 ;;
-    * )
-       break ;;
-  esac
-done
-
-if test $# != 0; then
-  echo "$me: too many arguments$help" >&2
-  exit 1
-fi
-
-trap 'exit 1' 1 2 15
-
-# CC_FOR_BUILD -- compiler used by this script. Note that the use of a
-# compiler to aid in system detection is discouraged as it requires
-# temporary files to be created and, as you can see below, it is a
-# headache to deal with in a portable fashion.
-
-# Historically, `CC_FOR_BUILD' used to be named `HOST_CC'. We still
-# use `HOST_CC' if defined, but it is deprecated.
-
-# Portable tmp directory creation inspired by the Autoconf team.
-
-set_cc_for_build='
-trap "exitcode=\$?; (rm -f \$tmpfiles 2>/dev/null; rmdir \$tmp 2>/dev/null) && exit \$exitcode" 0 ;
-trap "rm -f \$tmpfiles 2>/dev/null; rmdir \$tmp 2>/dev/null; exit 1" 1 2 13 15 ;
-: ${TMPDIR=/tmp} ;
- { tmp=`(umask 077 && mktemp -d "$TMPDIR/cgXXXXXX") 2>/dev/null` && test -n "$tmp" && test -d "$tmp" ; } ||
- { test -n "$RANDOM" && tmp=$TMPDIR/cg$$-$RANDOM && (umask 077 && mkdir $tmp) ; } ||
- { tmp=$TMPDIR/cg-$$ && (umask 077 && mkdir $tmp) && echo "Warning: creating insecure temp directory" >&2 ; } ||
- { echo "$me: cannot create a temporary directory in $TMPDIR" >&2 ; exit 1 ; } ;
-dummy=$tmp/dummy ;
-tmpfiles="$dummy.c $dummy.o $dummy.rel $dummy" ;
-case $CC_FOR_BUILD,$HOST_CC,$CC in
- ,,)    echo "int x;" > $dummy.c ;
-	for c in cc gcc c89 c99 ; do
-	  if ($c -c -o $dummy.o $dummy.c) >/dev/null 2>&1 ; then
-	     CC_FOR_BUILD="$c"; break ;
-	  fi ;
-	done ;
-	if test x"$CC_FOR_BUILD" = x ; then
-	  CC_FOR_BUILD=no_compiler_found ;
-	fi
-	;;
- ,,*)   CC_FOR_BUILD=$CC ;;
- ,*,*)  CC_FOR_BUILD=$HOST_CC ;;
-esac ; set_cc_for_build= ;'
-
-# This is needed to find uname on a Pyramid OSx when run in the BSD universe.
-# (ghazi@noc.rutgers.edu 1994-08-24)
-if (test -f /.attbin/uname) >/dev/null 2>&1 ; then
-	PATH=$PATH:/.attbin ; export PATH
-fi
-
-UNAME_MACHINE=`(uname -m) 2>/dev/null` || UNAME_MACHINE=unknown
-UNAME_RELEASE=`(uname -r) 2>/dev/null` || UNAME_RELEASE=unknown
-UNAME_SYSTEM=`(uname -s) 2>/dev/null`  || UNAME_SYSTEM=unknown
-UNAME_VERSION=`(uname -v) 2>/dev/null` || UNAME_VERSION=unknown
-
-# Note: order is significant - the case branches are not exclusive.
-
-case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in
-    *:NetBSD:*:*)
-	# NetBSD (nbsd) targets should (where applicable) match one or
-	# more of the tupples: *-*-netbsdelf*, *-*-netbsdaout*,
-	# *-*-netbsdecoff* and *-*-netbsd*.  For targets that recently
-	# switched to ELF, *-*-netbsd* would select the old
-	# object file format.  This provides both forward
-	# compatibility and a consistent mechanism for selecting the
-	# object file format.
-	#
-	# Note: NetBSD doesn't particularly care about the vendor
-	# portion of the name.  We always set it to "unknown".
-	sysctl="sysctl -n hw.machine_arch"
-	UNAME_MACHINE_ARCH=`(/sbin/$sysctl 2>/dev/null || \
-	    /usr/sbin/$sysctl 2>/dev/null || echo unknown)`
-	case "${UNAME_MACHINE_ARCH}" in
-	    armeb) machine=armeb-unknown ;;
-	    arm*) machine=arm-unknown ;;
-	    sh3el) machine=shl-unknown ;;
-	    sh3eb) machine=sh-unknown ;;
-	    sh5el) machine=sh5le-unknown ;;
-	    *) machine=${UNAME_MACHINE_ARCH}-unknown ;;
-	esac
-	# The Operating System including object format, if it has switched
-	# to ELF recently, or will in the future.
-	case "${UNAME_MACHINE_ARCH}" in
-	    arm*|i386|m68k|ns32k|sh3*|sparc|vax)
-		eval $set_cc_for_build
-		if echo __ELF__ | $CC_FOR_BUILD -E - 2>/dev/null \
-			| grep __ELF__ >/dev/null
-		then
-		    # Once all utilities can be ECOFF (netbsdecoff) or a.out (netbsdaout).
-		    # Return netbsd for either.  FIX?
-		    os=netbsd
-		else
-		    os=netbsdelf
-		fi
-		;;
-	    *)
-	        os=netbsd
-		;;
-	esac
-	# The OS release
-	# Debian GNU/NetBSD machines have a different userland, and
-	# thus, need a distinct triplet. However, they do not need
-	# kernel version information, so it can be replaced with a
-	# suitable tag, in the style of linux-gnu.
-	case "${UNAME_VERSION}" in
-	    Debian*)
-		release='-gnu'
-		;;
-	    *)
-		release=`echo ${UNAME_RELEASE}|sed -e 's/[-_].*/\./'`
-		;;
-	esac
-	# Since CPU_TYPE-MANUFACTURER-KERNEL-OPERATING_SYSTEM:
-	# contains redundant information, the shorter form:
-	# CPU_TYPE-MANUFACTURER-OPERATING_SYSTEM is used.
-	echo "${machine}-${os}${release}"
-	exit ;;
-    *:OpenBSD:*:*)
-	UNAME_MACHINE_ARCH=`arch | sed 's/OpenBSD.//'`
-	echo ${UNAME_MACHINE_ARCH}-unknown-openbsd${UNAME_RELEASE}
-	exit ;;
-    *:ekkoBSD:*:*)
-	echo ${UNAME_MACHINE}-unknown-ekkobsd${UNAME_RELEASE}
-	exit ;;
-    *:SolidBSD:*:*)
-	echo ${UNAME_MACHINE}-unknown-solidbsd${UNAME_RELEASE}
-	exit ;;
-    macppc:MirBSD:*:*)
-	echo powerpc-unknown-mirbsd${UNAME_RELEASE}
-	exit ;;
-    *:MirBSD:*:*)
-	echo ${UNAME_MACHINE}-unknown-mirbsd${UNAME_RELEASE}
-	exit ;;
-    alpha:OSF1:*:*)
-	case $UNAME_RELEASE in
-	*4.0)
-		UNAME_RELEASE=`/usr/sbin/sizer -v | awk '{print $3}'`
-		;;
-	*5.*)
-	        UNAME_RELEASE=`/usr/sbin/sizer -v | awk '{print $4}'`
-		;;
-	esac
-	# According to Compaq, /usr/sbin/psrinfo has been available on
-	# OSF/1 and Tru64 systems produced since 1995.  I hope that
-	# covers most systems running today.  This code pipes the CPU
-	# types through head -n 1, so we only detect the type of CPU 0.
-	ALPHA_CPU_TYPE=`/usr/sbin/psrinfo -v | sed -n -e 's/^  The alpha \(.*\) processor.*$/\1/p' | head -n 1`
-	case "$ALPHA_CPU_TYPE" in
-	    "EV4 (21064)")
-		UNAME_MACHINE="alpha" ;;
-	    "EV4.5 (21064)")
-		UNAME_MACHINE="alpha" ;;
-	    "LCA4 (21066/21068)")
-		UNAME_MACHINE="alpha" ;;
-	    "EV5 (21164)")
-		UNAME_MACHINE="alphaev5" ;;
-	    "EV5.6 (21164A)")
-		UNAME_MACHINE="alphaev56" ;;
-	    "EV5.6 (21164PC)")
-		UNAME_MACHINE="alphapca56" ;;
-	    "EV5.7 (21164PC)")
-		UNAME_MACHINE="alphapca57" ;;
-	    "EV6 (21264)")
-		UNAME_MACHINE="alphaev6" ;;
-	    "EV6.7 (21264A)")
-		UNAME_MACHINE="alphaev67" ;;
-	    "EV6.8CB (21264C)")
-		UNAME_MACHINE="alphaev68" ;;
-	    "EV6.8AL (21264B)")
-		UNAME_MACHINE="alphaev68" ;;
-	    "EV6.8CX (21264D)")
-		UNAME_MACHINE="alphaev68" ;;
-	    "EV6.9A (21264/EV69A)")
-		UNAME_MACHINE="alphaev69" ;;
-	    "EV7 (21364)")
-		UNAME_MACHINE="alphaev7" ;;
-	    "EV7.9 (21364A)")
-		UNAME_MACHINE="alphaev79" ;;
-	esac
-	# A Pn.n version is a patched version.
-	# A Vn.n version is a released version.
-	# A Tn.n version is a released field test version.
-	# A Xn.n version is an unreleased experimental baselevel.
-	# 1.2 uses "1.2" for uname -r.
-	echo ${UNAME_MACHINE}-dec-osf`echo ${UNAME_RELEASE} | sed -e 's/^[PVTX]//' | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz'`
-	exit ;;
-    Alpha\ *:Windows_NT*:*)
-	# How do we know it's Interix rather than the generic POSIX subsystem?
-	# Should we change UNAME_MACHINE based on the output of uname instead
-	# of the specific Alpha model?
-	echo alpha-pc-interix
-	exit ;;
-    21064:Windows_NT:50:3)
-	echo alpha-dec-winnt3.5
-	exit ;;
-    Amiga*:UNIX_System_V:4.0:*)
-	echo m68k-unknown-sysv4
-	exit ;;
-    *:[Aa]miga[Oo][Ss]:*:*)
-	echo ${UNAME_MACHINE}-unknown-amigaos
-	exit ;;
-    *:[Mm]orph[Oo][Ss]:*:*)
-	echo ${UNAME_MACHINE}-unknown-morphos
-	exit ;;
-    *:OS/390:*:*)
-	echo i370-ibm-openedition
-	exit ;;
-    *:z/VM:*:*)
-	echo s390-ibm-zvmoe
-	exit ;;
-    *:OS400:*:*)
-        echo powerpc-ibm-os400
-	exit ;;
-    arm:RISC*:1.[012]*:*|arm:riscix:1.[012]*:*)
-	echo arm-acorn-riscix${UNAME_RELEASE}
-	exit ;;
-    arm:riscos:*:*|arm:RISCOS:*:*)
-	echo arm-unknown-riscos
-	exit ;;
-    SR2?01:HI-UX/MPP:*:* | SR8000:HI-UX/MPP:*:*)
-	echo hppa1.1-hitachi-hiuxmpp
-	exit ;;
-    Pyramid*:OSx*:*:* | MIS*:OSx*:*:* | MIS*:SMP_DC-OSx*:*:*)
-	# akee@wpdis03.wpafb.af.mil (Earle F. Ake) contributed MIS and NILE.
-	if test "`(/bin/universe) 2>/dev/null`" = att ; then
-		echo pyramid-pyramid-sysv3
-	else
-		echo pyramid-pyramid-bsd
-	fi
-	exit ;;
-    NILE*:*:*:dcosx)
-	echo pyramid-pyramid-svr4
-	exit ;;
-    DRS?6000:unix:4.0:6*)
-	echo sparc-icl-nx6
-	exit ;;
-    DRS?6000:UNIX_SV:4.2*:7* | DRS?6000:isis:4.2*:7*)
-	case `/usr/bin/uname -p` in
-	    sparc) echo sparc-icl-nx7; exit ;;
-	esac ;;
-    sun4H:SunOS:5.*:*)
-	echo sparc-hal-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
-	exit ;;
-    sun4*:SunOS:5.*:* | tadpole*:SunOS:5.*:*)
-	echo sparc-sun-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
-	exit ;;
-    i86pc:SunOS:5.*:* | i86xen:SunOS:5.*:*)
-	echo i386-pc-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
-	exit ;;
-    sun4*:SunOS:6*:*)
-	# According to config.sub, this is the proper way to canonicalize
-	# SunOS6.  Hard to guess exactly what SunOS6 will be like, but
-	# it's likely to be more like Solaris than SunOS4.
-	echo sparc-sun-solaris3`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
-	exit ;;
-    sun4*:SunOS:*:*)
-	case "`/usr/bin/arch -k`" in
-	    Series*|S4*)
-		UNAME_RELEASE=`uname -v`
-		;;
-	esac
-	# Japanese Language versions have a version number like `4.1.3-JL'.
-	echo sparc-sun-sunos`echo ${UNAME_RELEASE}|sed -e 's/-/_/'`
-	exit ;;
-    sun3*:SunOS:*:*)
-	echo m68k-sun-sunos${UNAME_RELEASE}
-	exit ;;
-    sun*:*:4.2BSD:*)
-	UNAME_RELEASE=`(sed 1q /etc/motd | awk '{print substr($5,1,3)}') 2>/dev/null`
-	test "x${UNAME_RELEASE}" = "x" && UNAME_RELEASE=3
-	case "`/bin/arch`" in
-	    sun3)
-		echo m68k-sun-sunos${UNAME_RELEASE}
-		;;
-	    sun4)
-		echo sparc-sun-sunos${UNAME_RELEASE}
-		;;
-	esac
-	exit ;;
-    aushp:SunOS:*:*)
-	echo sparc-auspex-sunos${UNAME_RELEASE}
-	exit ;;
-    # The situation for MiNT is a little confusing.  The machine name
-    # can be virtually everything (everything which is not
-    # "atarist" or "atariste" at least should have a processor
-    # > m68000).  The system name ranges from "MiNT" over "FreeMiNT"
-    # to the lowercase version "mint" (or "freemint").  Finally
-    # the system name "TOS" denotes a system which is actually not
-    # MiNT.  But MiNT is downward compatible to TOS, so this should
-    # be no problem.
-    atarist[e]:*MiNT:*:* | atarist[e]:*mint:*:* | atarist[e]:*TOS:*:*)
-        echo m68k-atari-mint${UNAME_RELEASE}
-	exit ;;
-    atari*:*MiNT:*:* | atari*:*mint:*:* | atarist[e]:*TOS:*:*)
-	echo m68k-atari-mint${UNAME_RELEASE}
-        exit ;;
-    *falcon*:*MiNT:*:* | *falcon*:*mint:*:* | *falcon*:*TOS:*:*)
-        echo m68k-atari-mint${UNAME_RELEASE}
-	exit ;;
-    milan*:*MiNT:*:* | milan*:*mint:*:* | *milan*:*TOS:*:*)
-        echo m68k-milan-mint${UNAME_RELEASE}
-        exit ;;
-    hades*:*MiNT:*:* | hades*:*mint:*:* | *hades*:*TOS:*:*)
-        echo m68k-hades-mint${UNAME_RELEASE}
-        exit ;;
-    *:*MiNT:*:* | *:*mint:*:* | *:*TOS:*:*)
-        echo m68k-unknown-mint${UNAME_RELEASE}
-        exit ;;
-    m68k:machten:*:*)
-	echo m68k-apple-machten${UNAME_RELEASE}
-	exit ;;
-    powerpc:machten:*:*)
-	echo powerpc-apple-machten${UNAME_RELEASE}
-	exit ;;
-    RISC*:Mach:*:*)
-	echo mips-dec-mach_bsd4.3
-	exit ;;
-    RISC*:ULTRIX:*:*)
-	echo mips-dec-ultrix${UNAME_RELEASE}
-	exit ;;
-    VAX*:ULTRIX*:*:*)
-	echo vax-dec-ultrix${UNAME_RELEASE}
-	exit ;;
-    2020:CLIX:*:* | 2430:CLIX:*:*)
-	echo clipper-intergraph-clix${UNAME_RELEASE}
-	exit ;;
-    mips:*:*:UMIPS | mips:*:*:RISCos)
-	eval $set_cc_for_build
-	sed 's/^	//' << EOF >$dummy.c
-#ifdef __cplusplus
-#include <stdio.h>  /* for printf() prototype */
-	int main (int argc, char *argv[]) {
-#else
-	int main (argc, argv) int argc; char *argv[]; {
-#endif
-	#if defined (host_mips) && defined (MIPSEB)
-	#if defined (SYSTYPE_SYSV)
-	  printf ("mips-mips-riscos%ssysv\n", argv[1]); exit (0);
-	#endif
-	#if defined (SYSTYPE_SVR4)
-	  printf ("mips-mips-riscos%ssvr4\n", argv[1]); exit (0);
-	#endif
-	#if defined (SYSTYPE_BSD43) || defined(SYSTYPE_BSD)
-	  printf ("mips-mips-riscos%sbsd\n", argv[1]); exit (0);
-	#endif
-	#endif
-	  exit (-1);
-	}
-EOF
-	$CC_FOR_BUILD -o $dummy $dummy.c &&
-	  dummyarg=`echo "${UNAME_RELEASE}" | sed -n 's/\([0-9]*\).*/\1/p'` &&
-	  SYSTEM_NAME=`$dummy $dummyarg` &&
-	    { echo "$SYSTEM_NAME"; exit; }
-	echo mips-mips-riscos${UNAME_RELEASE}
-	exit ;;
-    Motorola:PowerMAX_OS:*:*)
-	echo powerpc-motorola-powermax
-	exit ;;
-    Motorola:*:4.3:PL8-*)
-	echo powerpc-harris-powermax
-	exit ;;
-    Night_Hawk:*:*:PowerMAX_OS | Synergy:PowerMAX_OS:*:*)
-	echo powerpc-harris-powermax
-	exit ;;
-    Night_Hawk:Power_UNIX:*:*)
-	echo powerpc-harris-powerunix
-	exit ;;
-    m88k:CX/UX:7*:*)
-	echo m88k-harris-cxux7
-	exit ;;
-    m88k:*:4*:R4*)
-	echo m88k-motorola-sysv4
-	exit ;;
-    m88k:*:3*:R3*)
-	echo m88k-motorola-sysv3
-	exit ;;
-    AViiON:dgux:*:*)
-        # DG/UX returns AViiON for all architectures
-        UNAME_PROCESSOR=`/usr/bin/uname -p`
-	if [ $UNAME_PROCESSOR = mc88100 ] || [ $UNAME_PROCESSOR = mc88110 ]
-	then
-	    if [ ${TARGET_BINARY_INTERFACE}x = m88kdguxelfx ] || \
-	       [ ${TARGET_BINARY_INTERFACE}x = x ]
-	    then
-		echo m88k-dg-dgux${UNAME_RELEASE}
-	    else
-		echo m88k-dg-dguxbcs${UNAME_RELEASE}
-	    fi
-	else
-	    echo i586-dg-dgux${UNAME_RELEASE}
-	fi
- 	exit ;;
-    M88*:DolphinOS:*:*)	# DolphinOS (SVR3)
-	echo m88k-dolphin-sysv3
-	exit ;;
-    M88*:*:R3*:*)
-	# Delta 88k system running SVR3
-	echo m88k-motorola-sysv3
-	exit ;;
-    XD88*:*:*:*) # Tektronix XD88 system running UTekV (SVR3)
-	echo m88k-tektronix-sysv3
-	exit ;;
-    Tek43[0-9][0-9]:UTek:*:*) # Tektronix 4300 system running UTek (BSD)
-	echo m68k-tektronix-bsd
-	exit ;;
-    *:IRIX*:*:*)
-	echo mips-sgi-irix`echo ${UNAME_RELEASE}|sed -e 's/-/_/g'`
-	exit ;;
-    ????????:AIX?:[12].1:2)   # AIX 2.2.1 or AIX 2.1.1 is RT/PC AIX.
-	echo romp-ibm-aix     # uname -m gives an 8 hex-code CPU id
-	exit ;;               # Note that: echo "'`uname -s`'" gives 'AIX '
-    i*86:AIX:*:*)
-	echo i386-ibm-aix
-	exit ;;
-    ia64:AIX:*:*)
-	if [ -x /usr/bin/oslevel ] ; then
-		IBM_REV=`/usr/bin/oslevel`
-	else
-		IBM_REV=${UNAME_VERSION}.${UNAME_RELEASE}
-	fi
-	echo ${UNAME_MACHINE}-ibm-aix${IBM_REV}
-	exit ;;
-    *:AIX:2:3)
-	if grep bos325 /usr/include/stdio.h >/dev/null 2>&1; then
-		eval $set_cc_for_build
-		sed 's/^		//' << EOF >$dummy.c
-		#include <sys/systemcfg.h>
-
-		main()
-			{
-			if (!__power_pc())
-				exit(1);
-			puts("powerpc-ibm-aix3.2.5");
-			exit(0);
-			}
-EOF
-		if $CC_FOR_BUILD -o $dummy $dummy.c && SYSTEM_NAME=`$dummy`
-		then
-			echo "$SYSTEM_NAME"
-		else
-			echo rs6000-ibm-aix3.2.5
-		fi
-	elif grep bos324 /usr/include/stdio.h >/dev/null 2>&1; then
-		echo rs6000-ibm-aix3.2.4
-	else
-		echo rs6000-ibm-aix3.2
-	fi
-	exit ;;
-    *:AIX:*:[45])
-	IBM_CPU_ID=`/usr/sbin/lsdev -C -c processor -S available | sed 1q | awk '{ print $1 }'`
-	if /usr/sbin/lsattr -El ${IBM_CPU_ID} | grep ' POWER' >/dev/null 2>&1; then
-		IBM_ARCH=rs6000
-	else
-		IBM_ARCH=powerpc
-	fi
-	if [ -x /usr/bin/oslevel ] ; then
-		IBM_REV=`/usr/bin/oslevel`
-	else
-		IBM_REV=${UNAME_VERSION}.${UNAME_RELEASE}
-	fi
-	echo ${IBM_ARCH}-ibm-aix${IBM_REV}
-	exit ;;
-    *:AIX:*:*)
-	echo rs6000-ibm-aix
-	exit ;;
-    ibmrt:4.4BSD:*|romp-ibm:BSD:*)
-	echo romp-ibm-bsd4.4
-	exit ;;
-    ibmrt:*BSD:*|romp-ibm:BSD:*)            # covers RT/PC BSD and
-	echo romp-ibm-bsd${UNAME_RELEASE}   # 4.3 with uname added to
-	exit ;;                             # report: romp-ibm BSD 4.3
-    *:BOSX:*:*)
-	echo rs6000-bull-bosx
-	exit ;;
-    DPX/2?00:B.O.S.:*:*)
-	echo m68k-bull-sysv3
-	exit ;;
-    9000/[34]??:4.3bsd:1.*:*)
-	echo m68k-hp-bsd
-	exit ;;
-    hp300:4.4BSD:*:* | 9000/[34]??:4.3bsd:2.*:*)
-	echo m68k-hp-bsd4.4
-	exit ;;
-    9000/[34678]??:HP-UX:*:*)
-	HPUX_REV=`echo ${UNAME_RELEASE}|sed -e 's/[^.]*.[0B]*//'`
-	case "${UNAME_MACHINE}" in
-	    9000/31? )            HP_ARCH=m68000 ;;
-	    9000/[34]?? )         HP_ARCH=m68k ;;
-	    9000/[678][0-9][0-9])
-		if [ -x /usr/bin/getconf ]; then
-		    sc_cpu_version=`/usr/bin/getconf SC_CPU_VERSION 2>/dev/null`
-                    sc_kernel_bits=`/usr/bin/getconf SC_KERNEL_BITS 2>/dev/null`
-                    case "${sc_cpu_version}" in
-                      523) HP_ARCH="hppa1.0" ;; # CPU_PA_RISC1_0
-                      528) HP_ARCH="hppa1.1" ;; # CPU_PA_RISC1_1
-                      532)                      # CPU_PA_RISC2_0
-                        case "${sc_kernel_bits}" in
-                          32) HP_ARCH="hppa2.0n" ;;
-                          64) HP_ARCH="hppa2.0w" ;;
-			  '') HP_ARCH="hppa2.0" ;;   # HP-UX 10.20
-                        esac ;;
-                    esac
-		fi
-		if [ "${HP_ARCH}" = "" ]; then
-		    eval $set_cc_for_build
-		    sed 's/^              //' << EOF >$dummy.c
-
-              #define _HPUX_SOURCE
-              #include <stdlib.h>
-              #include <unistd.h>
-
-              int main ()
-              {
-              #if defined(_SC_KERNEL_BITS)
-                  long bits = sysconf(_SC_KERNEL_BITS);
-              #endif
-                  long cpu  = sysconf (_SC_CPU_VERSION);
-
-                  switch (cpu)
-              	{
-              	case CPU_PA_RISC1_0: puts ("hppa1.0"); break;
-              	case CPU_PA_RISC1_1: puts ("hppa1.1"); break;
-              	case CPU_PA_RISC2_0:
-              #if defined(_SC_KERNEL_BITS)
-              	    switch (bits)
-              		{
-              		case 64: puts ("hppa2.0w"); break;
-              		case 32: puts ("hppa2.0n"); break;
-              		default: puts ("hppa2.0"); break;
-              		} break;
-              #else  /* !defined(_SC_KERNEL_BITS) */
-              	    puts ("hppa2.0"); break;
-              #endif
-              	default: puts ("hppa1.0"); break;
-              	}
-                  exit (0);
-              }
-EOF
-		    (CCOPTS= $CC_FOR_BUILD -o $dummy $dummy.c 2>/dev/null) && HP_ARCH=`$dummy`
-		    test -z "$HP_ARCH" && HP_ARCH=hppa
-		fi ;;
-	esac
-	if [ ${HP_ARCH} = "hppa2.0w" ]
-	then
-	    eval $set_cc_for_build
-
-	    # hppa2.0w-hp-hpux* has a 64-bit kernel and a compiler generating
-	    # 32-bit code.  hppa64-hp-hpux* has the same kernel and a compiler
-	    # generating 64-bit code.  GNU and HP use different nomenclature:
-	    #
-	    # $ CC_FOR_BUILD=cc ./config.guess
-	    # => hppa2.0w-hp-hpux11.23
-	    # $ CC_FOR_BUILD="cc +DA2.0w" ./config.guess
-	    # => hppa64-hp-hpux11.23
-
-	    if echo __LP64__ | (CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) |
-		grep __LP64__ >/dev/null
-	    then
-		HP_ARCH="hppa2.0w"
-	    else
-		HP_ARCH="hppa64"
-	    fi
-	fi
-	echo ${HP_ARCH}-hp-hpux${HPUX_REV}
-	exit ;;
-    ia64:HP-UX:*:*)
-	HPUX_REV=`echo ${UNAME_RELEASE}|sed -e 's/[^.]*.[0B]*//'`
-	echo ia64-hp-hpux${HPUX_REV}
-	exit ;;
-    3050*:HI-UX:*:*)
-	eval $set_cc_for_build
-	sed 's/^	//' << EOF >$dummy.c
-	#include <unistd.h>
-	int
-	main ()
-	{
-	  long cpu = sysconf (_SC_CPU_VERSION);
-	  /* The order matters, because CPU_IS_HP_MC68K erroneously returns
-	     true for CPU_PA_RISC1_0.  CPU_IS_PA_RISC returns correct
-	     results, however.  */
-	  if (CPU_IS_PA_RISC (cpu))
-	    {
-	      switch (cpu)
-		{
-		  case CPU_PA_RISC1_0: puts ("hppa1.0-hitachi-hiuxwe2"); break;
-		  case CPU_PA_RISC1_1: puts ("hppa1.1-hitachi-hiuxwe2"); break;
-		  case CPU_PA_RISC2_0: puts ("hppa2.0-hitachi-hiuxwe2"); break;
-		  default: puts ("hppa-hitachi-hiuxwe2"); break;
-		}
-	    }
-	  else if (CPU_IS_HP_MC68K (cpu))
-	    puts ("m68k-hitachi-hiuxwe2");
-	  else puts ("unknown-hitachi-hiuxwe2");
-	  exit (0);
-	}
-EOF
-	$CC_FOR_BUILD -o $dummy $dummy.c && SYSTEM_NAME=`$dummy` &&
-		{ echo "$SYSTEM_NAME"; exit; }
-	echo unknown-hitachi-hiuxwe2
-	exit ;;
-    9000/7??:4.3bsd:*:* | 9000/8?[79]:4.3bsd:*:* )
-	echo hppa1.1-hp-bsd
-	exit ;;
-    9000/8??:4.3bsd:*:*)
-	echo hppa1.0-hp-bsd
-	exit ;;
-    *9??*:MPE/iX:*:* | *3000*:MPE/iX:*:*)
-	echo hppa1.0-hp-mpeix
-	exit ;;
-    hp7??:OSF1:*:* | hp8?[79]:OSF1:*:* )
-	echo hppa1.1-hp-osf
-	exit ;;
-    hp8??:OSF1:*:*)
-	echo hppa1.0-hp-osf
-	exit ;;
-    i*86:OSF1:*:*)
-	if [ -x /usr/sbin/sysversion ] ; then
-	    echo ${UNAME_MACHINE}-unknown-osf1mk
-	else
-	    echo ${UNAME_MACHINE}-unknown-osf1
-	fi
-	exit ;;
-    parisc*:Lites*:*:*)
-	echo hppa1.1-hp-lites
-	exit ;;
-    C1*:ConvexOS:*:* | convex:ConvexOS:C1*:*)
-	echo c1-convex-bsd
-        exit ;;
-    C2*:ConvexOS:*:* | convex:ConvexOS:C2*:*)
-	if getsysinfo -f scalar_acc
-	then echo c32-convex-bsd
-	else echo c2-convex-bsd
-	fi
-        exit ;;
-    C34*:ConvexOS:*:* | convex:ConvexOS:C34*:*)
-	echo c34-convex-bsd
-        exit ;;
-    C38*:ConvexOS:*:* | convex:ConvexOS:C38*:*)
-	echo c38-convex-bsd
-        exit ;;
-    C4*:ConvexOS:*:* | convex:ConvexOS:C4*:*)
-	echo c4-convex-bsd
-        exit ;;
-    CRAY*Y-MP:*:*:*)
-	echo ymp-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/'
-	exit ;;
-    CRAY*[A-Z]90:*:*:*)
-	echo ${UNAME_MACHINE}-cray-unicos${UNAME_RELEASE} \
-	| sed -e 's/CRAY.*\([A-Z]90\)/\1/' \
-	      -e y/ABCDEFGHIJKLMNOPQRSTUVWXYZ/abcdefghijklmnopqrstuvwxyz/ \
-	      -e 's/\.[^.]*$/.X/'
-	exit ;;
-    CRAY*TS:*:*:*)
-	echo t90-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/'
-	exit ;;
-    CRAY*T3E:*:*:*)
-	echo alphaev5-cray-unicosmk${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/'
-	exit ;;
-    CRAY*SV1:*:*:*)
-	echo sv1-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/'
-	exit ;;
-    *:UNICOS/mp:*:*)
-	echo craynv-cray-unicosmp${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/'
-	exit ;;
-    F30[01]:UNIX_System_V:*:* | F700:UNIX_System_V:*:*)
-	FUJITSU_PROC=`uname -m | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz'`
-        FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'`
-        FUJITSU_REL=`echo ${UNAME_RELEASE} | sed -e 's/ /_/'`
-        echo "${FUJITSU_PROC}-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}"
-        exit ;;
-    5000:UNIX_System_V:4.*:*)
-        FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'`
-        FUJITSU_REL=`echo ${UNAME_RELEASE} | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/ /_/'`
-        echo "sparc-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}"
-	exit ;;
-    i*86:BSD/386:*:* | i*86:BSD/OS:*:* | *:Ascend\ Embedded/OS:*:*)
-	echo ${UNAME_MACHINE}-pc-bsdi${UNAME_RELEASE}
-	exit ;;
-    sparc*:BSD/OS:*:*)
-	echo sparc-unknown-bsdi${UNAME_RELEASE}
-	exit ;;
-    *:BSD/OS:*:*)
-	echo ${UNAME_MACHINE}-unknown-bsdi${UNAME_RELEASE}
-	exit ;;
-    *:FreeBSD:*:*)
-	case ${UNAME_MACHINE} in
-	    pc98)
-		echo i386-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` ;;
-	    amd64)
-		echo x86_64-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` ;;
-	    *)
-		echo ${UNAME_MACHINE}-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` ;;
-	esac
-	exit ;;
-    i*:CYGWIN*:*)
-	echo ${UNAME_MACHINE}-pc-cygwin
-	exit ;;
-    *:MINGW*:*)
-	echo ${UNAME_MACHINE}-pc-mingw32
-	exit ;;
-    i*:windows32*:*)
-    	# uname -m includes "-pc" on this system.
-    	echo ${UNAME_MACHINE}-mingw32
-	exit ;;
-    i*:PW*:*)
-	echo ${UNAME_MACHINE}-pc-pw32
-	exit ;;
-    *:Interix*:[3456]*)
-    	case ${UNAME_MACHINE} in
-	    x86)
-		echo i586-pc-interix${UNAME_RELEASE}
-		exit ;;
-	    EM64T | authenticamd)
-		echo x86_64-unknown-interix${UNAME_RELEASE}
-		exit ;;
-	esac ;;
-    [345]86:Windows_95:* | [345]86:Windows_98:* | [345]86:Windows_NT:*)
-	echo i${UNAME_MACHINE}-pc-mks
-	exit ;;
-    i*:Windows_NT*:* | Pentium*:Windows_NT*:*)
-	# How do we know it's Interix rather than the generic POSIX subsystem?
-	# It also conflicts with pre-2.0 versions of AT&T UWIN. Should we
-	# UNAME_MACHINE based on the output of uname instead of i386?
-	echo i586-pc-interix
-	exit ;;
-    i*:UWIN*:*)
-	echo ${UNAME_MACHINE}-pc-uwin
-	exit ;;
-    amd64:CYGWIN*:*:* | x86_64:CYGWIN*:*:*)
-	echo x86_64-unknown-cygwin
-	exit ;;
-    p*:CYGWIN*:*)
-	echo powerpcle-unknown-cygwin
-	exit ;;
-    prep*:SunOS:5.*:*)
-	echo powerpcle-unknown-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
-	exit ;;
-    *:GNU:*:*)
-	# the GNU system
-	echo `echo ${UNAME_MACHINE}|sed -e 's,[-/].*$,,'`-unknown-gnu`echo ${UNAME_RELEASE}|sed -e 's,/.*$,,'`
-	exit ;;
-    *:GNU/*:*:*)
-	# other systems with GNU libc and userland
-	echo ${UNAME_MACHINE}-unknown-`echo ${UNAME_SYSTEM} | sed 's,^[^/]*/,,' | tr '[A-Z]' '[a-z]'``echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'`-gnu
-	exit ;;
-    i*86:Minix:*:*)
-	echo ${UNAME_MACHINE}-pc-minix
-	exit ;;
-    arm*:Linux:*:*)
-	echo ${UNAME_MACHINE}-unknown-linux-gnu
-	exit ;;
-    avr32*:Linux:*:*)
-	echo ${UNAME_MACHINE}-unknown-linux-gnu
-	exit ;;
-    cris:Linux:*:*)
-	echo cris-axis-linux-gnu
-	exit ;;
-    crisv32:Linux:*:*)
-	echo crisv32-axis-linux-gnu
-	exit ;;
-    frv:Linux:*:*)
-    	echo frv-unknown-linux-gnu
-	exit ;;
-    ia64:Linux:*:*)
-	echo ${UNAME_MACHINE}-unknown-linux-gnu
-	exit ;;
-    m32r*:Linux:*:*)
-	echo ${UNAME_MACHINE}-unknown-linux-gnu
-	exit ;;
-    m68*:Linux:*:*)
-	echo ${UNAME_MACHINE}-unknown-linux-gnu
-	exit ;;
-    mips:Linux:*:*)
-	eval $set_cc_for_build
-	sed 's/^	//' << EOF >$dummy.c
-	#undef CPU
-	#undef mips
-	#undef mipsel
-	#if defined(__MIPSEL__) || defined(__MIPSEL) || defined(_MIPSEL) || defined(MIPSEL)
-	CPU=mipsel
-	#else
-	#if defined(__MIPSEB__) || defined(__MIPSEB) || defined(_MIPSEB) || defined(MIPSEB)
-	CPU=mips
-	#else
-	CPU=
-	#endif
-	#endif
-EOF
-	eval "`$CC_FOR_BUILD -E $dummy.c 2>/dev/null | sed -n '
-	    /^CPU/{
-		s: ::g
-		p
-	    }'`"
-	test x"${CPU}" != x && { echo "${CPU}-unknown-linux-gnu"; exit; }
-	;;
-    mips64:Linux:*:*)
-	eval $set_cc_for_build
-	sed 's/^	//' << EOF >$dummy.c
-	#undef CPU
-	#undef mips64
-	#undef mips64el
-	#if defined(__MIPSEL__) || defined(__MIPSEL) || defined(_MIPSEL) || defined(MIPSEL)
-	CPU=mips64el
-	#else
-	#if defined(__MIPSEB__) || defined(__MIPSEB) || defined(_MIPSEB) || defined(MIPSEB)
-	CPU=mips64
-	#else
-	CPU=
-	#endif
-	#endif
-EOF
-	eval "`$CC_FOR_BUILD -E $dummy.c 2>/dev/null | sed -n '
-	    /^CPU/{
-		s: ::g
-		p
-	    }'`"
-	test x"${CPU}" != x && { echo "${CPU}-unknown-linux-gnu"; exit; }
-	;;
-    or32:Linux:*:*)
-	echo or32-unknown-linux-gnu
-	exit ;;
-    ppc:Linux:*:*)
-	echo powerpc-unknown-linux-gnu
-	exit ;;
-    ppc64:Linux:*:*)
-	echo powerpc64-unknown-linux-gnu
-	exit ;;
-    alpha:Linux:*:*)
-	case `sed -n '/^cpu model/s/^.*: \(.*\)/\1/p' < /proc/cpuinfo` in
-	  EV5)   UNAME_MACHINE=alphaev5 ;;
-	  EV56)  UNAME_MACHINE=alphaev56 ;;
-	  PCA56) UNAME_MACHINE=alphapca56 ;;
-	  PCA57) UNAME_MACHINE=alphapca56 ;;
-	  EV6)   UNAME_MACHINE=alphaev6 ;;
-	  EV67)  UNAME_MACHINE=alphaev67 ;;
-	  EV68*) UNAME_MACHINE=alphaev68 ;;
-        esac
-	objdump --private-headers /bin/sh | grep ld.so.1 >/dev/null
-	if test "$?" = 0 ; then LIBC="libc1" ; else LIBC="" ; fi
-	echo ${UNAME_MACHINE}-unknown-linux-gnu${LIBC}
-	exit ;;
-    parisc:Linux:*:* | hppa:Linux:*:*)
-	# Look for CPU level
-	case `grep '^cpu[^a-z]*:' /proc/cpuinfo 2>/dev/null | cut -d' ' -f2` in
-	  PA7*) echo hppa1.1-unknown-linux-gnu ;;
-	  PA8*) echo hppa2.0-unknown-linux-gnu ;;
-	  *)    echo hppa-unknown-linux-gnu ;;
-	esac
-	exit ;;
-    parisc64:Linux:*:* | hppa64:Linux:*:*)
-	echo hppa64-unknown-linux-gnu
-	exit ;;
-    s390:Linux:*:* | s390x:Linux:*:*)
-	echo ${UNAME_MACHINE}-ibm-linux
-	exit ;;
-    sh64*:Linux:*:*)
-    	echo ${UNAME_MACHINE}-unknown-linux-gnu
-	exit ;;
-    sh*:Linux:*:*)
-	echo ${UNAME_MACHINE}-unknown-linux-gnu
-	exit ;;
-    sparc:Linux:*:* | sparc64:Linux:*:*)
-	echo ${UNAME_MACHINE}-unknown-linux-gnu
-	exit ;;
-    vax:Linux:*:*)
-	echo ${UNAME_MACHINE}-dec-linux-gnu
-	exit ;;
-    x86_64:Linux:*:*)
-	echo x86_64-unknown-linux-gnu
-	exit ;;
-    xtensa:Linux:*:*)
-    	echo xtensa-unknown-linux-gnu
-	exit ;;
-    i*86:Linux:*:*)
-	# The BFD linker knows what the default object file format is, so
-	# first see if it will tell us. cd to the root directory to prevent
-	# problems with other programs or directories called `ld' in the path.
-	# Set LC_ALL=C to ensure ld outputs messages in English.
-	ld_supported_targets=`cd /; LC_ALL=C ld --help 2>&1 \
-			 | sed -ne '/supported targets:/!d
-				    s/[ 	][ 	]*/ /g
-				    s/.*supported targets: *//
-				    s/ .*//
-				    p'`
-        case "$ld_supported_targets" in
-	  elf32-i386)
-		TENTATIVE="${UNAME_MACHINE}-pc-linux-gnu"
-		;;
-	  a.out-i386-linux)
-		echo "${UNAME_MACHINE}-pc-linux-gnuaout"
-		exit ;;
-	  coff-i386)
-		echo "${UNAME_MACHINE}-pc-linux-gnucoff"
-		exit ;;
-	  "")
-		# Either a pre-BFD a.out linker (linux-gnuoldld) or
-		# one that does not give us useful --help.
-		echo "${UNAME_MACHINE}-pc-linux-gnuoldld"
-		exit ;;
-	esac
-	# Determine whether the default compiler is a.out or elf
-	eval $set_cc_for_build
-	sed 's/^	//' << EOF >$dummy.c
-	#include <features.h>
-	#ifdef __ELF__
-	# ifdef __GLIBC__
-	#  if __GLIBC__ >= 2
-	LIBC=gnu
-	#  else
-	LIBC=gnulibc1
-	#  endif
-	# else
-	LIBC=gnulibc1
-	# endif
-	#else
-	#if defined(__INTEL_COMPILER) || defined(__PGI) || defined(__SUNPRO_C) || defined(__SUNPRO_CC)
-	LIBC=gnu
-	#else
-	LIBC=gnuaout
-	#endif
-	#endif
-	#ifdef __dietlibc__
-	LIBC=dietlibc
-	#endif
-EOF
-	eval "`$CC_FOR_BUILD -E $dummy.c 2>/dev/null | sed -n '
-	    /^LIBC/{
-		s: ::g
-		p
-	    }'`"
-	test x"${LIBC}" != x && {
-		echo "${UNAME_MACHINE}-pc-linux-${LIBC}"
-		exit
-	}
-	test x"${TENTATIVE}" != x && { echo "${TENTATIVE}"; exit; }
-	;;
-    i*86:DYNIX/ptx:4*:*)
-	# ptx 4.0 does uname -s correctly, with DYNIX/ptx in there.
-	# earlier versions are messed up and put the nodename in both
-	# sysname and nodename.
-	echo i386-sequent-sysv4
-	exit ;;
-    i*86:UNIX_SV:4.2MP:2.*)
-        # Unixware is an offshoot of SVR4, but it has its own version
-        # number series starting with 2...
-        # I am not positive that other SVR4 systems won't match this,
-	# I just have to hope.  -- rms.
-        # Use sysv4.2uw... so that sysv4* matches it.
-	echo ${UNAME_MACHINE}-pc-sysv4.2uw${UNAME_VERSION}
-	exit ;;
-    i*86:OS/2:*:*)
-	# If we were able to find `uname', then EMX Unix compatibility
-	# is probably installed.
-	echo ${UNAME_MACHINE}-pc-os2-emx
-	exit ;;
-    i*86:XTS-300:*:STOP)
-	echo ${UNAME_MACHINE}-unknown-stop
-	exit ;;
-    i*86:atheos:*:*)
-	echo ${UNAME_MACHINE}-unknown-atheos
-	exit ;;
-    i*86:syllable:*:*)
-	echo ${UNAME_MACHINE}-pc-syllable
-	exit ;;
-    i*86:LynxOS:2.*:* | i*86:LynxOS:3.[01]*:* | i*86:LynxOS:4.0*:*)
-	echo i386-unknown-lynxos${UNAME_RELEASE}
-	exit ;;
-    i*86:*DOS:*:*)
-	echo ${UNAME_MACHINE}-pc-msdosdjgpp
-	exit ;;
-    i*86:*:4.*:* | i*86:SYSTEM_V:4.*:*)
-	UNAME_REL=`echo ${UNAME_RELEASE} | sed 's/\/MP$//'`
-	if grep Novell /usr/include/link.h >/dev/null 2>/dev/null; then
-		echo ${UNAME_MACHINE}-univel-sysv${UNAME_REL}
-	else
-		echo ${UNAME_MACHINE}-pc-sysv${UNAME_REL}
-	fi
-	exit ;;
-    i*86:*:5:[678]*)
-    	# UnixWare 7.x, OpenUNIX and OpenServer 6.
-	case `/bin/uname -X | grep "^Machine"` in
-	    *486*)	     UNAME_MACHINE=i486 ;;
-	    *Pentium)	     UNAME_MACHINE=i586 ;;
-	    *Pent*|*Celeron) UNAME_MACHINE=i686 ;;
-	esac
-	echo ${UNAME_MACHINE}-unknown-sysv${UNAME_RELEASE}${UNAME_SYSTEM}${UNAME_VERSION}
-	exit ;;
-    i*86:*:3.2:*)
-	if test -f /usr/options/cb.name; then
-		UNAME_REL=`sed -n 's/.*Version //p' </usr/options/cb.name`
-		echo ${UNAME_MACHINE}-pc-isc$UNAME_REL
-	elif /bin/uname -X 2>/dev/null >/dev/null ; then
-		UNAME_REL=`(/bin/uname -X|grep Release|sed -e 's/.*= //')`
-		(/bin/uname -X|grep i80486 >/dev/null) && UNAME_MACHINE=i486
-		(/bin/uname -X|grep '^Machine.*Pentium' >/dev/null) \
-			&& UNAME_MACHINE=i586
-		(/bin/uname -X|grep '^Machine.*Pent *II' >/dev/null) \
-			&& UNAME_MACHINE=i686
-		(/bin/uname -X|grep '^Machine.*Pentium Pro' >/dev/null) \
-			&& UNAME_MACHINE=i686
-		echo ${UNAME_MACHINE}-pc-sco$UNAME_REL
-	else
-		echo ${UNAME_MACHINE}-pc-sysv32
-	fi
-	exit ;;
-    pc:*:*:*)
-	# Left here for compatibility:
-        # uname -m prints for DJGPP always 'pc', but it prints nothing about
-        # the processor, so we play safe by assuming i386.
-	echo i386-pc-msdosdjgpp
-        exit ;;
-    Intel:Mach:3*:*)
-	echo i386-pc-mach3
-	exit ;;
-    paragon:*:*:*)
-	echo i860-intel-osf1
-	exit ;;
-    i860:*:4.*:*) # i860-SVR4
-	if grep Stardent /usr/include/sys/uadmin.h >/dev/null 2>&1 ; then
-	  echo i860-stardent-sysv${UNAME_RELEASE} # Stardent Vistra i860-SVR4
-	else # Add other i860-SVR4 vendors below as they are discovered.
-	  echo i860-unknown-sysv${UNAME_RELEASE}  # Unknown i860-SVR4
-	fi
-	exit ;;
-    mini*:CTIX:SYS*5:*)
-	# "miniframe"
-	echo m68010-convergent-sysv
-	exit ;;
-    mc68k:UNIX:SYSTEM5:3.51m)
-	echo m68k-convergent-sysv
-	exit ;;
-    M680?0:D-NIX:5.3:*)
-	echo m68k-diab-dnix
-	exit ;;
-    M68*:*:R3V[5678]*:*)
-	test -r /sysV68 && { echo 'm68k-motorola-sysv'; exit; } ;;
-    3[345]??:*:4.0:3.0 | 3[34]??A:*:4.0:3.0 | 3[34]??,*:*:4.0:3.0 | 3[34]??/*:*:4.0:3.0 | 4400:*:4.0:3.0 | 4850:*:4.0:3.0 | SKA40:*:4.0:3.0 | SDS2:*:4.0:3.0 | SHG2:*:4.0:3.0 | S7501*:*:4.0:3.0)
-	OS_REL=''
-	test -r /etc/.relid \
-	&& OS_REL=.`sed -n 's/[^ ]* [^ ]* \([0-9][0-9]\).*/\1/p' < /etc/.relid`
-	/bin/uname -p 2>/dev/null | grep 86 >/dev/null \
-	  && { echo i486-ncr-sysv4.3${OS_REL}; exit; }
-	/bin/uname -p 2>/dev/null | /bin/grep entium >/dev/null \
-	  && { echo i586-ncr-sysv4.3${OS_REL}; exit; } ;;
-    3[34]??:*:4.0:* | 3[34]??,*:*:4.0:*)
-        /bin/uname -p 2>/dev/null | grep 86 >/dev/null \
-          && { echo i486-ncr-sysv4; exit; } ;;
-    m68*:LynxOS:2.*:* | m68*:LynxOS:3.0*:*)
-	echo m68k-unknown-lynxos${UNAME_RELEASE}
-	exit ;;
-    mc68030:UNIX_System_V:4.*:*)
-	echo m68k-atari-sysv4
-	exit ;;
-    TSUNAMI:LynxOS:2.*:*)
-	echo sparc-unknown-lynxos${UNAME_RELEASE}
-	exit ;;
-    rs6000:LynxOS:2.*:*)
-	echo rs6000-unknown-lynxos${UNAME_RELEASE}
-	exit ;;
-    PowerPC:LynxOS:2.*:* | PowerPC:LynxOS:3.[01]*:* | PowerPC:LynxOS:4.0*:*)
-	echo powerpc-unknown-lynxos${UNAME_RELEASE}
-	exit ;;
-    SM[BE]S:UNIX_SV:*:*)
-	echo mips-dde-sysv${UNAME_RELEASE}
-	exit ;;
-    RM*:ReliantUNIX-*:*:*)
-	echo mips-sni-sysv4
-	exit ;;
-    RM*:SINIX-*:*:*)
-	echo mips-sni-sysv4
-	exit ;;
-    *:SINIX-*:*:*)
-	if uname -p 2>/dev/null >/dev/null ; then
-		UNAME_MACHINE=`(uname -p) 2>/dev/null`
-		echo ${UNAME_MACHINE}-sni-sysv4
-	else
-		echo ns32k-sni-sysv
-	fi
-	exit ;;
-    PENTIUM:*:4.0*:*) # Unisys `ClearPath HMP IX 4000' SVR4/MP effort
-                      # says <Richard.M.Bartel@ccMail.Census.GOV>
-        echo i586-unisys-sysv4
-        exit ;;
-    *:UNIX_System_V:4*:FTX*)
-	# From Gerald Hewes <hewes@openmarket.com>.
-	# How about differentiating between stratus architectures? -djm
-	echo hppa1.1-stratus-sysv4
-	exit ;;
-    *:*:*:FTX*)
-	# From seanf@swdc.stratus.com.
-	echo i860-stratus-sysv4
-	exit ;;
-    i*86:VOS:*:*)
-	# From Paul.Green@stratus.com.
-	echo ${UNAME_MACHINE}-stratus-vos
-	exit ;;
-    *:VOS:*:*)
-	# From Paul.Green@stratus.com.
-	echo hppa1.1-stratus-vos
-	exit ;;
-    mc68*:A/UX:*:*)
-	echo m68k-apple-aux${UNAME_RELEASE}
-	exit ;;
-    news*:NEWS-OS:6*:*)
-	echo mips-sony-newsos6
-	exit ;;
-    R[34]000:*System_V*:*:* | R4000:UNIX_SYSV:*:* | R*000:UNIX_SV:*:*)
-	if [ -d /usr/nec ]; then
-	        echo mips-nec-sysv${UNAME_RELEASE}
-	else
-	        echo mips-unknown-sysv${UNAME_RELEASE}
-	fi
-        exit ;;
-    BeBox:BeOS:*:*)	# BeOS running on hardware made by Be, PPC only.
-	echo powerpc-be-beos
-	exit ;;
-    BeMac:BeOS:*:*)	# BeOS running on Mac or Mac clone, PPC only.
-	echo powerpc-apple-beos
-	exit ;;
-    BePC:BeOS:*:*)	# BeOS running on Intel PC compatible.
-	echo i586-pc-beos
-	exit ;;
-    SX-4:SUPER-UX:*:*)
-	echo sx4-nec-superux${UNAME_RELEASE}
-	exit ;;
-    SX-5:SUPER-UX:*:*)
-	echo sx5-nec-superux${UNAME_RELEASE}
-	exit ;;
-    SX-6:SUPER-UX:*:*)
-	echo sx6-nec-superux${UNAME_RELEASE}
-	exit ;;
-    SX-7:SUPER-UX:*:*)
-	echo sx7-nec-superux${UNAME_RELEASE}
-	exit ;;
-    SX-8:SUPER-UX:*:*)
-	echo sx8-nec-superux${UNAME_RELEASE}
-	exit ;;
-    SX-8R:SUPER-UX:*:*)
-	echo sx8r-nec-superux${UNAME_RELEASE}
-	exit ;;
-    Power*:Rhapsody:*:*)
-	echo powerpc-apple-rhapsody${UNAME_RELEASE}
-	exit ;;
-    *:Rhapsody:*:*)
-	echo ${UNAME_MACHINE}-apple-rhapsody${UNAME_RELEASE}
-	exit ;;
-    *:Darwin:*:*)
-	UNAME_PROCESSOR=`uname -p` || UNAME_PROCESSOR=unknown
-	case $UNAME_PROCESSOR in
-	    unknown) UNAME_PROCESSOR=powerpc ;;
-	esac
-	echo ${UNAME_PROCESSOR}-apple-darwin${UNAME_RELEASE}
-	exit ;;
-    *:procnto*:*:* | *:QNX:[0123456789]*:*)
-	UNAME_PROCESSOR=`uname -p`
-	if test "$UNAME_PROCESSOR" = "x86"; then
-		UNAME_PROCESSOR=i386
-		UNAME_MACHINE=pc
-	fi
-	echo ${UNAME_PROCESSOR}-${UNAME_MACHINE}-nto-qnx${UNAME_RELEASE}
-	exit ;;
-    *:QNX:*:4*)
-	echo i386-pc-qnx
-	exit ;;
-    NSE-?:NONSTOP_KERNEL:*:*)
-	echo nse-tandem-nsk${UNAME_RELEASE}
-	exit ;;
-    NSR-?:NONSTOP_KERNEL:*:*)
-	echo nsr-tandem-nsk${UNAME_RELEASE}
-	exit ;;
-    *:NonStop-UX:*:*)
-	echo mips-compaq-nonstopux
-	exit ;;
-    BS2000:POSIX*:*:*)
-	echo bs2000-siemens-sysv
-	exit ;;
-    DS/*:UNIX_System_V:*:*)
-	echo ${UNAME_MACHINE}-${UNAME_SYSTEM}-${UNAME_RELEASE}
-	exit ;;
-    *:Plan9:*:*)
-	# "uname -m" is not consistent, so use $cputype instead. 386
-	# is converted to i386 for consistency with other x86
-	# operating systems.
-	if test "$cputype" = "386"; then
-	    UNAME_MACHINE=i386
-	else
-	    UNAME_MACHINE="$cputype"
-	fi
-	echo ${UNAME_MACHINE}-unknown-plan9
-	exit ;;
-    *:TOPS-10:*:*)
-	echo pdp10-unknown-tops10
-	exit ;;
-    *:TENEX:*:*)
-	echo pdp10-unknown-tenex
-	exit ;;
-    KS10:TOPS-20:*:* | KL10:TOPS-20:*:* | TYPE4:TOPS-20:*:*)
-	echo pdp10-dec-tops20
-	exit ;;
-    XKL-1:TOPS-20:*:* | TYPE5:TOPS-20:*:*)
-	echo pdp10-xkl-tops20
-	exit ;;
-    *:TOPS-20:*:*)
-	echo pdp10-unknown-tops20
-	exit ;;
-    *:ITS:*:*)
-	echo pdp10-unknown-its
-	exit ;;
-    SEI:*:*:SEIUX)
-        echo mips-sei-seiux${UNAME_RELEASE}
-	exit ;;
-    *:DragonFly:*:*)
-	echo ${UNAME_MACHINE}-unknown-dragonfly`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'`
-	exit ;;
-    *:*VMS:*:*)
-    	UNAME_MACHINE=`(uname -p) 2>/dev/null`
-	case "${UNAME_MACHINE}" in
-	    A*) echo alpha-dec-vms ; exit ;;
-	    I*) echo ia64-dec-vms ; exit ;;
-	    V*) echo vax-dec-vms ; exit ;;
-	esac ;;
-    *:XENIX:*:SysV)
-	echo i386-pc-xenix
-	exit ;;
-    i*86:skyos:*:*)
-	echo ${UNAME_MACHINE}-pc-skyos`echo ${UNAME_RELEASE}` | sed -e 's/ .*$//'
-	exit ;;
-    i*86:rdos:*:*)
-	echo ${UNAME_MACHINE}-pc-rdos
-	exit ;;
-esac
-
-#echo '(No uname command or uname output not recognized.)' 1>&2
-#echo "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" 1>&2
-
-eval $set_cc_for_build
-cat >$dummy.c <<EOF
-#ifdef _SEQUENT_
-# include <sys/types.h>
-# include <sys/utsname.h>
-#endif
-main ()
-{
-#if defined (sony)
-#if defined (MIPSEB)
-  /* BFD wants "bsd" instead of "newsos".  Perhaps BFD should be changed,
-     I don't know....  */
-  printf ("mips-sony-bsd\n"); exit (0);
-#else
-#include <sys/param.h>
-  printf ("m68k-sony-newsos%s\n",
-#ifdef NEWSOS4
-          "4"
-#else
-	  ""
-#endif
-         ); exit (0);
-#endif
-#endif
-
-#if defined (__arm) && defined (__acorn) && defined (__unix)
-  printf ("arm-acorn-riscix\n"); exit (0);
-#endif
-
-#if defined (hp300) && !defined (hpux)
-  printf ("m68k-hp-bsd\n"); exit (0);
-#endif
-
-#if defined (NeXT)
-#if !defined (__ARCHITECTURE__)
-#define __ARCHITECTURE__ "m68k"
-#endif
-  int version;
-  version=`(hostinfo | sed -n 's/.*NeXT Mach \([0-9]*\).*/\1/p') 2>/dev/null`;
-  if (version < 4)
-    printf ("%s-next-nextstep%d\n", __ARCHITECTURE__, version);
-  else
-    printf ("%s-next-openstep%d\n", __ARCHITECTURE__, version);
-  exit (0);
-#endif
-
-#if defined (MULTIMAX) || defined (n16)
-#if defined (UMAXV)
-  printf ("ns32k-encore-sysv\n"); exit (0);
-#else
-#if defined (CMU)
-  printf ("ns32k-encore-mach\n"); exit (0);
-#else
-  printf ("ns32k-encore-bsd\n"); exit (0);
-#endif
-#endif
-#endif
-
-#if defined (__386BSD__)
-  printf ("i386-pc-bsd\n"); exit (0);
-#endif
-
-#if defined (sequent)
-#if defined (i386)
-  printf ("i386-sequent-dynix\n"); exit (0);
-#endif
-#if defined (ns32000)
-  printf ("ns32k-sequent-dynix\n"); exit (0);
-#endif
-#endif
-
-#if defined (_SEQUENT_)
-    struct utsname un;
-
-    uname(&un);
-
-    if (strncmp(un.version, "V2", 2) == 0) {
-	printf ("i386-sequent-ptx2\n"); exit (0);
-    }
-    if (strncmp(un.version, "V1", 2) == 0) { /* XXX is V1 correct? */
-	printf ("i386-sequent-ptx1\n"); exit (0);
-    }
-    printf ("i386-sequent-ptx\n"); exit (0);
-
-#endif
-
-#if defined (vax)
-# if !defined (ultrix)
-#  include <sys/param.h>
-#  if defined (BSD)
-#   if BSD == 43
-      printf ("vax-dec-bsd4.3\n"); exit (0);
-#   else
-#    if BSD == 199006
-      printf ("vax-dec-bsd4.3reno\n"); exit (0);
-#    else
-      printf ("vax-dec-bsd\n"); exit (0);
-#    endif
-#   endif
-#  else
-    printf ("vax-dec-bsd\n"); exit (0);
-#  endif
-# else
-    printf ("vax-dec-ultrix\n"); exit (0);
-# endif
-#endif
-
-#if defined (alliant) && defined (i860)
-  printf ("i860-alliant-bsd\n"); exit (0);
-#endif
-
-  exit (1);
-}
-EOF
-
-$CC_FOR_BUILD -o $dummy $dummy.c 2>/dev/null && SYSTEM_NAME=`$dummy` &&
-	{ echo "$SYSTEM_NAME"; exit; }
-
-# Apollos put the system type in the environment.
-
-test -d /usr/apollo && { echo ${ISP}-apollo-${SYSTYPE}; exit; }
-
-# Convex versions that predate uname can use getsysinfo(1)
-
-if [ -x /usr/convex/getsysinfo ]
-then
-    case `getsysinfo -f cpu_type` in
-    c1*)
-	echo c1-convex-bsd
-	exit ;;
-    c2*)
-	if getsysinfo -f scalar_acc
-	then echo c32-convex-bsd
-	else echo c2-convex-bsd
-	fi
-	exit ;;
-    c34*)
-	echo c34-convex-bsd
-	exit ;;
-    c38*)
-	echo c38-convex-bsd
-	exit ;;
-    c4*)
-	echo c4-convex-bsd
-	exit ;;
-    esac
-fi
-
-cat >&2 <<EOF
-$0: unable to guess system type
-
-This script, last modified $timestamp, has failed to recognize
-the operating system you are using. It is advised that you
-download the most up to date version of the config scripts from
-
-  http://savannah.gnu.org/cgi-bin/viewcvs/*checkout*/config/config/config.guess
-and
-  http://savannah.gnu.org/cgi-bin/viewcvs/*checkout*/config/config/config.sub
-
-If the version you run ($0) is already up to date, please
-send the following data and any information you think might be
-pertinent to <config-patches@gnu.org> in order to provide the needed
-information to handle your system.
-
-config.guess timestamp = $timestamp
-
-uname -m = `(uname -m) 2>/dev/null || echo unknown`
-uname -r = `(uname -r) 2>/dev/null || echo unknown`
-uname -s = `(uname -s) 2>/dev/null || echo unknown`
-uname -v = `(uname -v) 2>/dev/null || echo unknown`
-
-/usr/bin/uname -p = `(/usr/bin/uname -p) 2>/dev/null`
-/bin/uname -X     = `(/bin/uname -X) 2>/dev/null`
-
-hostinfo               = `(hostinfo) 2>/dev/null`
-/bin/universe          = `(/bin/universe) 2>/dev/null`
-/usr/bin/arch -k       = `(/usr/bin/arch -k) 2>/dev/null`
-/bin/arch              = `(/bin/arch) 2>/dev/null`
-/usr/bin/oslevel       = `(/usr/bin/oslevel) 2>/dev/null`
-/usr/convex/getsysinfo = `(/usr/convex/getsysinfo) 2>/dev/null`
-
-UNAME_MACHINE = ${UNAME_MACHINE}
-UNAME_RELEASE = ${UNAME_RELEASE}
-UNAME_SYSTEM  = ${UNAME_SYSTEM}
-UNAME_VERSION = ${UNAME_VERSION}
-EOF
-
-exit 1
-
-# Local variables:
-# eval: (add-hook 'write-file-hooks 'time-stamp)
-# time-stamp-start: "timestamp='"
-# time-stamp-format: "%:y-%02m-%02d"
-# time-stamp-end: "'"
-# End:
diff --git a/Tools/config/config.sub b/Tools/config/config.sub
deleted file mode 100755
index 1761d8bdf..000000000
--- a/Tools/config/config.sub
+++ /dev/null
@@ -1,1626 +0,0 @@
-#! /bin/sh
-# Configuration validation subroutine script.
-#   Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999,
-#   2000, 2001, 2002, 2003, 2004, 2005, 2006 Free Software Foundation,
-#   Inc.
-
-timestamp='2007-06-28'
-
-# This file is (in principle) common to ALL GNU software.
-# The presence of a machine in this file suggests that SOME GNU software
-# can handle that machine.  It does not imply ALL GNU software can.
-#
-# This file is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation; either version 2 of the License, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program; if not, write to the Free Software
-# Foundation, Inc., 51 Franklin Street - Fifth Floor, Boston, MA
-# 02110-1301, USA.
-#
-# As a special exception to the GNU General Public License, if you
-# distribute this file as part of a program that contains a
-# configuration script generated by Autoconf, you may include it under
-# the same distribution terms that you use for the rest of that program.
-
-
-# Please send patches to <config-patches@gnu.org>.  Submit a context
-# diff and a properly formatted ChangeLog entry.
-#
-# Configuration subroutine to validate and canonicalize a configuration type.
-# Supply the specified configuration type as an argument.
-# If it is invalid, we print an error message on stderr and exit with code 1.
-# Otherwise, we print the canonical config type on stdout and succeed.
-
-# This file is supposed to be the same for all GNU packages
-# and recognize all the CPU types, system types and aliases
-# that are meaningful with *any* GNU software.
-# Each package is responsible for reporting which valid configurations
-# it does not support.  The user should be able to distinguish
-# a failure to support a valid configuration from a meaningless
-# configuration.
-
-# The goal of this file is to map all the various variations of a given
-# machine specification into a single specification in the form:
-#	CPU_TYPE-MANUFACTURER-OPERATING_SYSTEM
-# or in some cases, the newer four-part form:
-#	CPU_TYPE-MANUFACTURER-KERNEL-OPERATING_SYSTEM
-# It is wrong to echo any other type of specification.
-
-me=`echo "$0" | sed -e 's,.*/,,'`
-
-usage="\
-Usage: $0 [OPTION] CPU-MFR-OPSYS
-       $0 [OPTION] ALIAS
-
-Canonicalize a configuration name.
-
-Operation modes:
-  -h, --help         print this help, then exit
-  -t, --time-stamp   print date of last modification, then exit
-  -v, --version      print version number, then exit
-
-Report bugs and patches to <config-patches@gnu.org>."
-
-version="\
-GNU config.sub ($timestamp)
-
-Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004, 2005
-Free Software Foundation, Inc.
-
-This is free software; see the source for copying conditions.  There is NO
-warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE."
-
-help="
-Try \`$me --help' for more information."
-
-# Parse command line
-while test $# -gt 0 ; do
-  case $1 in
-    --time-stamp | --time* | -t )
-       echo "$timestamp" ; exit ;;
-    --version | -v )
-       echo "$version" ; exit ;;
-    --help | --h* | -h )
-       echo "$usage"; exit ;;
-    -- )     # Stop option processing
-       shift; break ;;
-    - )	# Use stdin as input.
-       break ;;
-    -* )
-       echo "$me: invalid option $1$help"
-       exit 1 ;;
-
-    *local*)
-       # First pass through any local machine types.
-       echo $1
-       exit ;;
-
-    * )
-       break ;;
-  esac
-done
-
-case $# in
- 0) echo "$me: missing argument$help" >&2
-    exit 1;;
- 1) ;;
- *) echo "$me: too many arguments$help" >&2
-    exit 1;;
-esac
-
-# Separate what the user gave into CPU-COMPANY and OS or KERNEL-OS (if any).
-# Here we must recognize all the valid KERNEL-OS combinations.
-maybe_os=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\2/'`
-case $maybe_os in
-  nto-qnx* | linux-gnu* | linux-dietlibc | linux-newlib* | linux-uclibc* | \
-  uclinux-uclibc* | uclinux-gnu* | kfreebsd*-gnu* | knetbsd*-gnu* | netbsd*-gnu* | \
-  storm-chaos* | os2-emx* | rtmk-nova*)
-    os=-$maybe_os
-    basic_machine=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\1/'`
-    ;;
-  *)
-    basic_machine=`echo $1 | sed 's/-[^-]*$//'`
-    if [ $basic_machine != $1 ]
-    then os=`echo $1 | sed 's/.*-/-/'`
-    else os=; fi
-    ;;
-esac
-
-### Let's recognize common machines as not being operating systems so
-### that things like config.sub decstation-3100 work.  We also
-### recognize some manufacturers as not being operating systems, so we
-### can provide default operating systems below.
-case $os in
-	-sun*os*)
-		# Prevent following clause from handling this invalid input.
-		;;
-	-dec* | -mips* | -sequent* | -encore* | -pc532* | -sgi* | -sony* | \
-	-att* | -7300* | -3300* | -delta* | -motorola* | -sun[234]* | \
-	-unicom* | -ibm* | -next | -hp | -isi* | -apollo | -altos* | \
-	-convergent* | -ncr* | -news | -32* | -3600* | -3100* | -hitachi* |\
-	-c[123]* | -convex* | -sun | -crds | -omron* | -dg | -ultra | -tti* | \
-	-harris | -dolphin | -highlevel | -gould | -cbm | -ns | -masscomp | \
-	-apple | -axis | -knuth | -cray)
-		os=
-		basic_machine=$1
-		;;
-	-sim | -cisco | -oki | -wec | -winbond)
-		os=
-		basic_machine=$1
-		;;
-	-scout)
-		;;
-	-wrs)
-		os=-vxworks
-		basic_machine=$1
-		;;
-	-chorusos*)
-		os=-chorusos
-		basic_machine=$1
-		;;
- 	-chorusrdb)
- 		os=-chorusrdb
-		basic_machine=$1
- 		;;
-	-hiux*)
-		os=-hiuxwe2
-		;;
-	-sco6)
-		os=-sco5v6
-		basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
-		;;
-	-sco5)
-		os=-sco3.2v5
-		basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
-		;;
-	-sco4)
-		os=-sco3.2v4
-		basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
-		;;
-	-sco3.2.[4-9]*)
-		os=`echo $os | sed -e 's/sco3.2./sco3.2v/'`
-		basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
-		;;
-	-sco3.2v[4-9]*)
-		# Don't forget version if it is 3.2v4 or newer.
-		basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
-		;;
-	-sco5v6*)
-		# Don't forget version if it is 3.2v4 or newer.
-		basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
-		;;
-	-sco*)
-		os=-sco3.2v2
-		basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
-		;;
-	-udk*)
-		basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
-		;;
-	-isc)
-		os=-isc2.2
-		basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
-		;;
-	-clix*)
-		basic_machine=clipper-intergraph
-		;;
-	-isc*)
-		basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
-		;;
-	-lynx*)
-		os=-lynxos
-		;;
-	-ptx*)
-		basic_machine=`echo $1 | sed -e 's/86-.*/86-sequent/'`
-		;;
-	-windowsnt*)
-		os=`echo $os | sed -e 's/windowsnt/winnt/'`
-		;;
-	-psos*)
-		os=-psos
-		;;
-	-mint | -mint[0-9]*)
-		basic_machine=m68k-atari
-		os=-mint
-		;;
-esac
-
-# Decode aliases for certain CPU-COMPANY combinations.
-case $basic_machine in
-	# Recognize the basic CPU types without company name.
-	# Some are omitted here because they have special meanings below.
-	1750a | 580 \
-	| a29k \
-	| alpha | alphaev[4-8] | alphaev56 | alphaev6[78] | alphapca5[67] \
-	| alpha64 | alpha64ev[4-8] | alpha64ev56 | alpha64ev6[78] | alpha64pca5[67] \
-	| am33_2.0 \
-	| arc | arm | arm[bl]e | arme[lb] | armv[2345] | armv[345][lb] | avr | avr32 \
-	| bfin \
-	| c4x | clipper \
-	| d10v | d30v | dlx | dsp16xx \
-	| fido | fr30 | frv \
-	| h8300 | h8500 | hppa | hppa1.[01] | hppa2.0 | hppa2.0[nw] | hppa64 \
-	| i370 | i860 | i960 | ia64 \
-	| ip2k | iq2000 \
-	| m32c | m32r | m32rle | m68000 | m68k | m88k \
-	| maxq | mb | microblaze | mcore | mep \
-	| mips | mipsbe | mipseb | mipsel | mipsle \
-	| mips16 \
-	| mips64 | mips64el \
-	| mips64vr | mips64vrel \
-	| mips64orion | mips64orionel \
-	| mips64vr4100 | mips64vr4100el \
-	| mips64vr4300 | mips64vr4300el \
-	| mips64vr5000 | mips64vr5000el \
-	| mips64vr5900 | mips64vr5900el \
-	| mipsisa32 | mipsisa32el \
-	| mipsisa32r2 | mipsisa32r2el \
-	| mipsisa64 | mipsisa64el \
-	| mipsisa64r2 | mipsisa64r2el \
-	| mipsisa64sb1 | mipsisa64sb1el \
-	| mipsisa64sr71k | mipsisa64sr71kel \
-	| mipstx39 | mipstx39el \
-	| mn10200 | mn10300 \
-	| mt \
-	| msp430 \
-	| nios | nios2 \
-	| ns16k | ns32k \
-	| or32 \
-	| pdp10 | pdp11 | pj | pjl \
-	| powerpc | powerpc64 | powerpc64le | powerpcle | ppcbe \
-	| pyramid \
-	| score \
-	| sh | sh[1234] | sh[24]a | sh[23]e | sh[34]eb | sheb | shbe | shle | sh[1234]le | sh3ele \
-	| sh64 | sh64le \
-	| sparc | sparc64 | sparc64b | sparc64v | sparc86x | sparclet | sparclite \
-	| sparcv8 | sparcv9 | sparcv9b | sparcv9v \
-	| spu | strongarm \
-	| tahoe | thumb | tic4x | tic80 | tron \
-	| v850 | v850e \
-	| we32k \
-	| x86 | xc16x | xscale | xscalee[bl] | xstormy16 | xtensa \
-	| z8k)
-		basic_machine=$basic_machine-unknown
-		;;
-	m6811 | m68hc11 | m6812 | m68hc12)
-		# Motorola 68HC11/12.
-		basic_machine=$basic_machine-unknown
-		os=-none
-		;;
-	m88110 | m680[12346]0 | m683?2 | m68360 | m5200 | v70 | w65 | z8k)
-		;;
-	ms1)
-		basic_machine=mt-unknown
-		;;
-
-	# We use `pc' rather than `unknown'
-	# because (1) that's what they normally are, and
-	# (2) the word "unknown" tends to confuse beginning users.
-	i*86 | x86_64)
-	  basic_machine=$basic_machine-pc
-	  ;;
-	# Object if more than one company name word.
-	*-*-*)
-		echo Invalid configuration \`$1\': machine \`$basic_machine\' not recognized 1>&2
-		exit 1
-		;;
-	# Recognize the basic CPU types with company name.
-	580-* \
-	| a29k-* \
-	| alpha-* | alphaev[4-8]-* | alphaev56-* | alphaev6[78]-* \
-	| alpha64-* | alpha64ev[4-8]-* | alpha64ev56-* | alpha64ev6[78]-* \
-	| alphapca5[67]-* | alpha64pca5[67]-* | arc-* \
-	| arm-*  | armbe-* | armle-* | armeb-* | armv*-* \
-	| avr-* | avr32-* \
-	| bfin-* | bs2000-* \
-	| c[123]* | c30-* | [cjt]90-* | c4x-* | c54x-* | c55x-* | c6x-* \
-	| clipper-* | craynv-* | cydra-* \
-	| d10v-* | d30v-* | dlx-* \
-	| elxsi-* \
-	| f30[01]-* | f700-* | fido-* | fr30-* | frv-* | fx80-* \
-	| h8300-* | h8500-* \
-	| hppa-* | hppa1.[01]-* | hppa2.0-* | hppa2.0[nw]-* | hppa64-* \
-	| i*86-* | i860-* | i960-* | ia64-* \
-	| ip2k-* | iq2000-* \
-	| m32c-* | m32r-* | m32rle-* \
-	| m68000-* | m680[012346]0-* | m68360-* | m683?2-* | m68k-* \
-	| m88110-* | m88k-* | maxq-* | mcore-* \
-	| mips-* | mipsbe-* | mipseb-* | mipsel-* | mipsle-* \
-	| mips16-* \
-	| mips64-* | mips64el-* \
-	| mips64vr-* | mips64vrel-* \
-	| mips64orion-* | mips64orionel-* \
-	| mips64vr4100-* | mips64vr4100el-* \
-	| mips64vr4300-* | mips64vr4300el-* \
-	| mips64vr5000-* | mips64vr5000el-* \
-	| mips64vr5900-* | mips64vr5900el-* \
-	| mipsisa32-* | mipsisa32el-* \
-	| mipsisa32r2-* | mipsisa32r2el-* \
-	| mipsisa64-* | mipsisa64el-* \
-	| mipsisa64r2-* | mipsisa64r2el-* \
-	| mipsisa64sb1-* | mipsisa64sb1el-* \
-	| mipsisa64sr71k-* | mipsisa64sr71kel-* \
-	| mipstx39-* | mipstx39el-* \
-	| mmix-* \
-	| mt-* \
-	| msp430-* \
-	| nios-* | nios2-* \
-	| none-* | np1-* | ns16k-* | ns32k-* \
-	| orion-* \
-	| pdp10-* | pdp11-* | pj-* | pjl-* | pn-* | power-* \
-	| powerpc-* | powerpc64-* | powerpc64le-* | powerpcle-* | ppcbe-* \
-	| pyramid-* \
-	| romp-* | rs6000-* \
-	| sh-* | sh[1234]-* | sh[24]a-* | sh[23]e-* | sh[34]eb-* | sheb-* | shbe-* \
-	| shle-* | sh[1234]le-* | sh3ele-* | sh64-* | sh64le-* \
-	| sparc-* | sparc64-* | sparc64b-* | sparc64v-* | sparc86x-* | sparclet-* \
-	| sparclite-* \
-	| sparcv8-* | sparcv9-* | sparcv9b-* | sparcv9v-* | strongarm-* | sv1-* | sx?-* \
-	| tahoe-* | thumb-* \
-	| tic30-* | tic4x-* | tic54x-* | tic55x-* | tic6x-* | tic80-* \
-	| tron-* \
-	| v850-* | v850e-* | vax-* \
-	| we32k-* \
-	| x86-* | x86_64-* | xc16x-* | xps100-* | xscale-* | xscalee[bl]-* \
-	| xstormy16-* | xtensa-* \
-	| ymp-* \
-	| z8k-*)
-		;;
-	# Recognize the various machine names and aliases which stand
-	# for a CPU type and a company and sometimes even an OS.
-	386bsd)
-		basic_machine=i386-unknown
-		os=-bsd
-		;;
-	3b1 | 7300 | 7300-att | att-7300 | pc7300 | safari | unixpc)
-		basic_machine=m68000-att
-		;;
-	3b*)
-		basic_machine=we32k-att
-		;;
-	a29khif)
-		basic_machine=a29k-amd
-		os=-udi
-		;;
-    	abacus)
-		basic_machine=abacus-unknown
-		;;
-	adobe68k)
-		basic_machine=m68010-adobe
-		os=-scout
-		;;
-	alliant | fx80)
-		basic_machine=fx80-alliant
-		;;
-	altos | altos3068)
-		basic_machine=m68k-altos
-		;;
-	am29k)
-		basic_machine=a29k-none
-		os=-bsd
-		;;
-	amd64)
-		basic_machine=x86_64-pc
-		;;
-	amd64-*)
-		basic_machine=x86_64-`echo $basic_machine | sed 's/^[^-]*-//'`
-		;;
-	amdahl)
-		basic_machine=580-amdahl
-		os=-sysv
-		;;
-	amiga | amiga-*)
-		basic_machine=m68k-unknown
-		;;
-	amigaos | amigados)
-		basic_machine=m68k-unknown
-		os=-amigaos
-		;;
-	amigaunix | amix)
-		basic_machine=m68k-unknown
-		os=-sysv4
-		;;
-	apollo68)
-		basic_machine=m68k-apollo
-		os=-sysv
-		;;
-	apollo68bsd)
-		basic_machine=m68k-apollo
-		os=-bsd
-		;;
-	aux)
-		basic_machine=m68k-apple
-		os=-aux
-		;;
-	balance)
-		basic_machine=ns32k-sequent
-		os=-dynix
-		;;
-	c90)
-		basic_machine=c90-cray
-		os=-unicos
-		;;
-	convex-c1)
-		basic_machine=c1-convex
-		os=-bsd
-		;;
-	convex-c2)
-		basic_machine=c2-convex
-		os=-bsd
-		;;
-	convex-c32)
-		basic_machine=c32-convex
-		os=-bsd
-		;;
-	convex-c34)
-		basic_machine=c34-convex
-		os=-bsd
-		;;
-	convex-c38)
-		basic_machine=c38-convex
-		os=-bsd
-		;;
-	cray | j90)
-		basic_machine=j90-cray
-		os=-unicos
-		;;
-	craynv)
-		basic_machine=craynv-cray
-		os=-unicosmp
-		;;
-	cr16)
-		basic_machine=cr16-unknown
-		os=-elf
-		;;
-	crds | unos)
-		basic_machine=m68k-crds
-		;;
-	crisv32 | crisv32-* | etraxfs*)
-		basic_machine=crisv32-axis
-		;;
-	cris | cris-* | etrax*)
-		basic_machine=cris-axis
-		;;
-	crx)
-		basic_machine=crx-unknown
-		os=-elf
-		;;
-	da30 | da30-*)
-		basic_machine=m68k-da30
-		;;
-	decstation | decstation-3100 | pmax | pmax-* | pmin | dec3100 | decstatn)
-		basic_machine=mips-dec
-		;;
-	decsystem10* | dec10*)
-		basic_machine=pdp10-dec
-		os=-tops10
-		;;
-	decsystem20* | dec20*)
-		basic_machine=pdp10-dec
-		os=-tops20
-		;;
-	delta | 3300 | motorola-3300 | motorola-delta \
-	      | 3300-motorola | delta-motorola)
-		basic_machine=m68k-motorola
-		;;
-	delta88)
-		basic_machine=m88k-motorola
-		os=-sysv3
-		;;
-	djgpp)
-		basic_machine=i586-pc
-		os=-msdosdjgpp
-		;;
-	dpx20 | dpx20-*)
-		basic_machine=rs6000-bull
-		os=-bosx
-		;;
-	dpx2* | dpx2*-bull)
-		basic_machine=m68k-bull
-		os=-sysv3
-		;;
-	ebmon29k)
-		basic_machine=a29k-amd
-		os=-ebmon
-		;;
-	elxsi)
-		basic_machine=elxsi-elxsi
-		os=-bsd
-		;;
-	encore | umax | mmax)
-		basic_machine=ns32k-encore
-		;;
-	es1800 | OSE68k | ose68k | ose | OSE)
-		basic_machine=m68k-ericsson
-		os=-ose
-		;;
-	fx2800)
-		basic_machine=i860-alliant
-		;;
-	genix)
-		basic_machine=ns32k-ns
-		;;
-	gmicro)
-		basic_machine=tron-gmicro
-		os=-sysv
-		;;
-	go32)
-		basic_machine=i386-pc
-		os=-go32
-		;;
-	h3050r* | hiux*)
-		basic_machine=hppa1.1-hitachi
-		os=-hiuxwe2
-		;;
-	h8300hms)
-		basic_machine=h8300-hitachi
-		os=-hms
-		;;
-	h8300xray)
-		basic_machine=h8300-hitachi
-		os=-xray
-		;;
-	h8500hms)
-		basic_machine=h8500-hitachi
-		os=-hms
-		;;
-	harris)
-		basic_machine=m88k-harris
-		os=-sysv3
-		;;
-	hp300-*)
-		basic_machine=m68k-hp
-		;;
-	hp300bsd)
-		basic_machine=m68k-hp
-		os=-bsd
-		;;
-	hp300hpux)
-		basic_machine=m68k-hp
-		os=-hpux
-		;;
-	hp3k9[0-9][0-9] | hp9[0-9][0-9])
-		basic_machine=hppa1.0-hp
-		;;
-	hp9k2[0-9][0-9] | hp9k31[0-9])
-		basic_machine=m68000-hp
-		;;
-	hp9k3[2-9][0-9])
-		basic_machine=m68k-hp
-		;;
-	hp9k6[0-9][0-9] | hp6[0-9][0-9])
-		basic_machine=hppa1.0-hp
-		;;
-	hp9k7[0-79][0-9] | hp7[0-79][0-9])
-		basic_machine=hppa1.1-hp
-		;;
-	hp9k78[0-9] | hp78[0-9])
-		# FIXME: really hppa2.0-hp
-		basic_machine=hppa1.1-hp
-		;;
-	hp9k8[67]1 | hp8[67]1 | hp9k80[24] | hp80[24] | hp9k8[78]9 | hp8[78]9 | hp9k893 | hp893)
-		# FIXME: really hppa2.0-hp
-		basic_machine=hppa1.1-hp
-		;;
-	hp9k8[0-9][13679] | hp8[0-9][13679])
-		basic_machine=hppa1.1-hp
-		;;
-	hp9k8[0-9][0-9] | hp8[0-9][0-9])
-		basic_machine=hppa1.0-hp
-		;;
-	hppa-next)
-		os=-nextstep3
-		;;
-	hppaosf)
-		basic_machine=hppa1.1-hp
-		os=-osf
-		;;
-	hppro)
-		basic_machine=hppa1.1-hp
-		os=-proelf
-		;;
-	i370-ibm* | ibm*)
-		basic_machine=i370-ibm
-		;;
-# I'm not sure what "Sysv32" means.  Should this be sysv3.2?
-	i*86v32)
-		basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'`
-		os=-sysv32
-		;;
-	i*86v4*)
-		basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'`
-		os=-sysv4
-		;;
-	i*86v)
-		basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'`
-		os=-sysv
-		;;
-	i*86sol2)
-		basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'`
-		os=-solaris2
-		;;
-	i386mach)
-		basic_machine=i386-mach
-		os=-mach
-		;;
-	i386-vsta | vsta)
-		basic_machine=i386-unknown
-		os=-vsta
-		;;
-	iris | iris4d)
-		basic_machine=mips-sgi
-		case $os in
-		    -irix*)
-			;;
-		    *)
-			os=-irix4
-			;;
-		esac
-		;;
-	isi68 | isi)
-		basic_machine=m68k-isi
-		os=-sysv
-		;;
-	m88k-omron*)
-		basic_machine=m88k-omron
-		;;
-	magnum | m3230)
-		basic_machine=mips-mips
-		os=-sysv
-		;;
-	merlin)
-		basic_machine=ns32k-utek
-		os=-sysv
-		;;
-	mingw32)
-		basic_machine=i386-pc
-		os=-mingw32
-		;;
-	mingw32ce)
-		basic_machine=arm-unknown
-		os=-mingw32ce
-		;;
-	miniframe)
-		basic_machine=m68000-convergent
-		;;
-	*mint | -mint[0-9]* | *MiNT | *MiNT[0-9]*)
-		basic_machine=m68k-atari
-		os=-mint
-		;;
-	mips3*-*)
-		basic_machine=`echo $basic_machine | sed -e 's/mips3/mips64/'`
-		;;
-	mips3*)
-		basic_machine=`echo $basic_machine | sed -e 's/mips3/mips64/'`-unknown
-		;;
-	monitor)
-		basic_machine=m68k-rom68k
-		os=-coff
-		;;
-	morphos)
-		basic_machine=powerpc-unknown
-		os=-morphos
-		;;
-	msdos)
-		basic_machine=i386-pc
-		os=-msdos
-		;;
-	ms1-*)
-		basic_machine=`echo $basic_machine | sed -e 's/ms1-/mt-/'`
-		;;
-	mvs)
-		basic_machine=i370-ibm
-		os=-mvs
-		;;
-	ncr3000)
-		basic_machine=i486-ncr
-		os=-sysv4
-		;;
-	netbsd386)
-		basic_machine=i386-unknown
-		os=-netbsd
-		;;
-	netwinder)
-		basic_machine=armv4l-rebel
-		os=-linux
-		;;
-	news | news700 | news800 | news900)
-		basic_machine=m68k-sony
-		os=-newsos
-		;;
-	news1000)
-		basic_machine=m68030-sony
-		os=-newsos
-		;;
-	news-3600 | risc-news)
-		basic_machine=mips-sony
-		os=-newsos
-		;;
-	necv70)
-		basic_machine=v70-nec
-		os=-sysv
-		;;
-	next | m*-next )
-		basic_machine=m68k-next
-		case $os in
-		    -nextstep* )
-			;;
-		    -ns2*)
-		      os=-nextstep2
-			;;
-		    *)
-		      os=-nextstep3
-			;;
-		esac
-		;;
-	nh3000)
-		basic_machine=m68k-harris
-		os=-cxux
-		;;
-	nh[45]000)
-		basic_machine=m88k-harris
-		os=-cxux
-		;;
-	nindy960)
-		basic_machine=i960-intel
-		os=-nindy
-		;;
-	mon960)
-		basic_machine=i960-intel
-		os=-mon960
-		;;
-	nonstopux)
-		basic_machine=mips-compaq
-		os=-nonstopux
-		;;
-	np1)
-		basic_machine=np1-gould
-		;;
-	nsr-tandem)
-		basic_machine=nsr-tandem
-		;;
-	op50n-* | op60c-*)
-		basic_machine=hppa1.1-oki
-		os=-proelf
-		;;
-	openrisc | openrisc-*)
-		basic_machine=or32-unknown
-		;;
-	os400)
-		basic_machine=powerpc-ibm
-		os=-os400
-		;;
-	OSE68000 | ose68000)
-		basic_machine=m68000-ericsson
-		os=-ose
-		;;
-	os68k)
-		basic_machine=m68k-none
-		os=-os68k
-		;;
-	pa-hitachi)
-		basic_machine=hppa1.1-hitachi
-		os=-hiuxwe2
-		;;
-	paragon)
-		basic_machine=i860-intel
-		os=-osf
-		;;
-	pbd)
-		basic_machine=sparc-tti
-		;;
-	pbb)
-		basic_machine=m68k-tti
-		;;
-	pc532 | pc532-*)
-		basic_machine=ns32k-pc532
-		;;
-	pc98)
-		basic_machine=i386-pc
-		;;
-	pc98-*)
-		basic_machine=i386-`echo $basic_machine | sed 's/^[^-]*-//'`
-		;;
-	pentium | p5 | k5 | k6 | nexgen | viac3)
-		basic_machine=i586-pc
-		;;
-	pentiumpro | p6 | 6x86 | athlon | athlon_*)
-		basic_machine=i686-pc
-		;;
-	pentiumii | pentium2 | pentiumiii | pentium3)
-		basic_machine=i686-pc
-		;;
-	pentium4)
-		basic_machine=i786-pc
-		;;
-	pentium-* | p5-* | k5-* | k6-* | nexgen-* | viac3-*)
-		basic_machine=i586-`echo $basic_machine | sed 's/^[^-]*-//'`
-		;;
-	pentiumpro-* | p6-* | 6x86-* | athlon-*)
-		basic_machine=i686-`echo $basic_machine | sed 's/^[^-]*-//'`
-		;;
-	pentiumii-* | pentium2-* | pentiumiii-* | pentium3-*)
-		basic_machine=i686-`echo $basic_machine | sed 's/^[^-]*-//'`
-		;;
-	pentium4-*)
-		basic_machine=i786-`echo $basic_machine | sed 's/^[^-]*-//'`
-		;;
-	pn)
-		basic_machine=pn-gould
-		;;
-	power)	basic_machine=power-ibm
-		;;
-	ppc)	basic_machine=powerpc-unknown
-		;;
-	ppc-*)	basic_machine=powerpc-`echo $basic_machine | sed 's/^[^-]*-//'`
-		;;
-	ppcle | powerpclittle | ppc-le | powerpc-little)
-		basic_machine=powerpcle-unknown
-		;;
-	ppcle-* | powerpclittle-*)
-		basic_machine=powerpcle-`echo $basic_machine | sed 's/^[^-]*-//'`
-		;;
-	ppc64)	basic_machine=powerpc64-unknown
-		;;
-	ppc64-*) basic_machine=powerpc64-`echo $basic_machine | sed 's/^[^-]*-//'`
-		;;
-	ppc64le | powerpc64little | ppc64-le | powerpc64-little)
-		basic_machine=powerpc64le-unknown
-		;;
-	ppc64le-* | powerpc64little-*)
-		basic_machine=powerpc64le-`echo $basic_machine | sed 's/^[^-]*-//'`
-		;;
-	ps2)
-		basic_machine=i386-ibm
-		;;
-	pw32)
-		basic_machine=i586-unknown
-		os=-pw32
-		;;
-	rdos)
-		basic_machine=i386-pc
-		os=-rdos
-		;;
-	rom68k)
-		basic_machine=m68k-rom68k
-		os=-coff
-		;;
-	rm[46]00)
-		basic_machine=mips-siemens
-		;;
-	rtpc | rtpc-*)
-		basic_machine=romp-ibm
-		;;
-	s390 | s390-*)
-		basic_machine=s390-ibm
-		;;
-	s390x | s390x-*)
-		basic_machine=s390x-ibm
-		;;
-	sa29200)
-		basic_machine=a29k-amd
-		os=-udi
-		;;
-	sb1)
-		basic_machine=mipsisa64sb1-unknown
-		;;
-	sb1el)
-		basic_machine=mipsisa64sb1el-unknown
-		;;
-	sde)
-		basic_machine=mipsisa32-sde
-		os=-elf
-		;;
-	sei)
-		basic_machine=mips-sei
-		os=-seiux
-		;;
-	sequent)
-		basic_machine=i386-sequent
-		;;
-	sh)
-		basic_machine=sh-hitachi
-		os=-hms
-		;;
-	sh5el)
-		basic_machine=sh5le-unknown
-		;;
-	sh64)
-		basic_machine=sh64-unknown
-		;;
-	sparclite-wrs | simso-wrs)
-		basic_machine=sparclite-wrs
-		os=-vxworks
-		;;
-	sps7)
-		basic_machine=m68k-bull
-		os=-sysv2
-		;;
-	spur)
-		basic_machine=spur-unknown
-		;;
-	st2000)
-		basic_machine=m68k-tandem
-		;;
-	stratus)
-		basic_machine=i860-stratus
-		os=-sysv4
-		;;
-	sun2)
-		basic_machine=m68000-sun
-		;;
-	sun2os3)
-		basic_machine=m68000-sun
-		os=-sunos3
-		;;
-	sun2os4)
-		basic_machine=m68000-sun
-		os=-sunos4
-		;;
-	sun3os3)
-		basic_machine=m68k-sun
-		os=-sunos3
-		;;
-	sun3os4)
-		basic_machine=m68k-sun
-		os=-sunos4
-		;;
-	sun4os3)
-		basic_machine=sparc-sun
-		os=-sunos3
-		;;
-	sun4os4)
-		basic_machine=sparc-sun
-		os=-sunos4
-		;;
-	sun4sol2)
-		basic_machine=sparc-sun
-		os=-solaris2
-		;;
-	sun3 | sun3-*)
-		basic_machine=m68k-sun
-		;;
-	sun4)
-		basic_machine=sparc-sun
-		;;
-	sun386 | sun386i | roadrunner)
-		basic_machine=i386-sun
-		;;
-	sv1)
-		basic_machine=sv1-cray
-		os=-unicos
-		;;
-	symmetry)
-		basic_machine=i386-sequent
-		os=-dynix
-		;;
-	t3e)
-		basic_machine=alphaev5-cray
-		os=-unicos
-		;;
-	t90)
-		basic_machine=t90-cray
-		os=-unicos
-		;;
-	tic54x | c54x*)
-		basic_machine=tic54x-unknown
-		os=-coff
-		;;
-	tic55x | c55x*)
-		basic_machine=tic55x-unknown
-		os=-coff
-		;;
-	tic6x | c6x*)
-		basic_machine=tic6x-unknown
-		os=-coff
-		;;
-	tx39)
-		basic_machine=mipstx39-unknown
-		;;
-	tx39el)
-		basic_machine=mipstx39el-unknown
-		;;
-	toad1)
-		basic_machine=pdp10-xkl
-		os=-tops20
-		;;
-	tower | tower-32)
-		basic_machine=m68k-ncr
-		;;
-	tpf)
-		basic_machine=s390x-ibm
-		os=-tpf
-		;;
-	udi29k)
-		basic_machine=a29k-amd
-		os=-udi
-		;;
-	ultra3)
-		basic_machine=a29k-nyu
-		os=-sym1
-		;;
-	v810 | necv810)
-		basic_machine=v810-nec
-		os=-none
-		;;
-	vaxv)
-		basic_machine=vax-dec
-		os=-sysv
-		;;
-	vms)
-		basic_machine=vax-dec
-		os=-vms
-		;;
-	vpp*|vx|vx-*)
-		basic_machine=f301-fujitsu
-		;;
-	vxworks960)
-		basic_machine=i960-wrs
-		os=-vxworks
-		;;
-	vxworks68)
-		basic_machine=m68k-wrs
-		os=-vxworks
-		;;
-	vxworks29k)
-		basic_machine=a29k-wrs
-		os=-vxworks
-		;;
-	w65*)
-		basic_machine=w65-wdc
-		os=-none
-		;;
-	w89k-*)
-		basic_machine=hppa1.1-winbond
-		os=-proelf
-		;;
-	xbox)
-		basic_machine=i686-pc
-		os=-mingw32
-		;;
-	xps | xps100)
-		basic_machine=xps100-honeywell
-		;;
-	ymp)
-		basic_machine=ymp-cray
-		os=-unicos
-		;;
-	z8k-*-coff)
-		basic_machine=z8k-unknown
-		os=-sim
-		;;
-	none)
-		basic_machine=none-none
-		os=-none
-		;;
-
-# Here we handle the default manufacturer of certain CPU types.  It is in
-# some cases the only manufacturer, in others, it is the most popular.
-	w89k)
-		basic_machine=hppa1.1-winbond
-		;;
-	op50n)
-		basic_machine=hppa1.1-oki
-		;;
-	op60c)
-		basic_machine=hppa1.1-oki
-		;;
-	romp)
-		basic_machine=romp-ibm
-		;;
-	mmix)
-		basic_machine=mmix-knuth
-		;;
-	rs6000)
-		basic_machine=rs6000-ibm
-		;;
-	vax)
-		basic_machine=vax-dec
-		;;
-	pdp10)
-		# there are many clones, so DEC is not a safe bet
-		basic_machine=pdp10-unknown
-		;;
-	pdp11)
-		basic_machine=pdp11-dec
-		;;
-	we32k)
-		basic_machine=we32k-att
-		;;
-	sh[1234] | sh[24]a | sh[34]eb | sh[1234]le | sh[23]ele)
-		basic_machine=sh-unknown
-		;;
-	sparc | sparcv8 | sparcv9 | sparcv9b | sparcv9v)
-		basic_machine=sparc-sun
-		;;
-	cydra)
-		basic_machine=cydra-cydrome
-		;;
-	orion)
-		basic_machine=orion-highlevel
-		;;
-	orion105)
-		basic_machine=clipper-highlevel
-		;;
-	mac | mpw | mac-mpw)
-		basic_machine=m68k-apple
-		;;
-	pmac | pmac-mpw)
-		basic_machine=powerpc-apple
-		;;
-	*-unknown)
-		# Make sure to match an already-canonicalized machine name.
-		;;
-	*)
-		echo Invalid configuration \`$1\': machine \`$basic_machine\' not recognized 1>&2
-		exit 1
-		;;
-esac
-
-# Here we canonicalize certain aliases for manufacturers.
-case $basic_machine in
-	*-digital*)
-		basic_machine=`echo $basic_machine | sed 's/digital.*/dec/'`
-		;;
-	*-commodore*)
-		basic_machine=`echo $basic_machine | sed 's/commodore.*/cbm/'`
-		;;
-	*)
-		;;
-esac
-
-# Decode manufacturer-specific aliases for certain operating systems.
-
-if [ x"$os" != x"" ]
-then
-case $os in
-        # First match some system type aliases
-        # that might get confused with valid system types.
-	# -solaris* is a basic system type, with this one exception.
-	-solaris1 | -solaris1.*)
-		os=`echo $os | sed -e 's|solaris1|sunos4|'`
-		;;
-	-solaris)
-		os=-solaris2
-		;;
-	-svr4*)
-		os=-sysv4
-		;;
-	-unixware*)
-		os=-sysv4.2uw
-		;;
-	-gnu/linux*)
-		os=`echo $os | sed -e 's|gnu/linux|linux-gnu|'`
-		;;
-	# First accept the basic system types.
-	# The portable systems comes first.
-	# Each alternative MUST END IN A *, to match a version number.
-	# -sysv* is not here because it comes later, after sysvr4.
-	-gnu* | -bsd* | -mach* | -minix* | -genix* | -ultrix* | -irix* \
-	      | -*vms* | -sco* | -esix* | -isc* | -aix* | -sunos | -sunos[34]*\
-	      | -hpux* | -unos* | -osf* | -luna* | -dgux* | -solaris* | -sym* \
-	      | -amigaos* | -amigados* | -msdos* | -newsos* | -unicos* | -aof* \
-	      | -aos* \
-	      | -nindy* | -vxsim* | -vxworks* | -ebmon* | -hms* | -mvs* \
-	      | -clix* | -riscos* | -uniplus* | -iris* | -rtu* | -xenix* \
-	      | -hiux* | -386bsd* | -knetbsd* | -mirbsd* | -netbsd* \
-	      | -openbsd* | -solidbsd* \
-	      | -ekkobsd* | -kfreebsd* | -freebsd* | -riscix* | -lynxos* \
-	      | -bosx* | -nextstep* | -cxux* | -aout* | -elf* | -oabi* \
-	      | -ptx* | -coff* | -ecoff* | -winnt* | -domain* | -vsta* \
-	      | -udi* | -eabi* | -lites* | -ieee* | -go32* | -aux* \
-	      | -chorusos* | -chorusrdb* \
-	      | -cygwin* | -pe* | -psos* | -moss* | -proelf* | -rtems* \
-	      | -mingw32* | -linux-gnu* | -linux-newlib* | -linux-uclibc* \
-	      | -uxpv* | -beos* | -mpeix* | -udk* \
-	      | -interix* | -uwin* | -mks* | -rhapsody* | -darwin* | -opened* \
-	      | -openstep* | -oskit* | -conix* | -pw32* | -nonstopux* \
-	      | -storm-chaos* | -tops10* | -tenex* | -tops20* | -its* \
-	      | -os2* | -vos* | -palmos* | -uclinux* | -nucleus* \
-	      | -morphos* | -superux* | -rtmk* | -rtmk-nova* | -windiss* \
-	      | -powermax* | -dnix* | -nx6 | -nx7 | -sei* | -dragonfly* \
-	      | -skyos* | -haiku* | -rdos* | -toppers* | -drops*)
-	# Remember, each alternative MUST END IN *, to match a version number.
-		;;
-	-qnx*)
-		case $basic_machine in
-		    x86-* | i*86-*)
-			;;
-		    *)
-			os=-nto$os
-			;;
-		esac
-		;;
-	-nto-qnx*)
-		;;
-	-nto*)
-		os=`echo $os | sed -e 's|nto|nto-qnx|'`
-		;;
-	-sim | -es1800* | -hms* | -xray | -os68k* | -none* | -v88r* \
-	      | -windows* | -osx | -abug | -netware* | -os9* | -beos* | -haiku* \
-	      | -macos* | -mpw* | -magic* | -mmixware* | -mon960* | -lnews*)
-		;;
-	-mac*)
-		os=`echo $os | sed -e 's|mac|macos|'`
-		;;
-	-linux-dietlibc)
-		os=-linux-dietlibc
-		;;
-	-linux*)
-		os=`echo $os | sed -e 's|linux|linux-gnu|'`
-		;;
-	-sunos5*)
-		os=`echo $os | sed -e 's|sunos5|solaris2|'`
-		;;
-	-sunos6*)
-		os=`echo $os | sed -e 's|sunos6|solaris3|'`
-		;;
-	-opened*)
-		os=-openedition
-		;;
-        -os400*)
-		os=-os400
-		;;
-	-wince*)
-		os=-wince
-		;;
-	-osfrose*)
-		os=-osfrose
-		;;
-	-osf*)
-		os=-osf
-		;;
-	-utek*)
-		os=-bsd
-		;;
-	-dynix*)
-		os=-bsd
-		;;
-	-acis*)
-		os=-aos
-		;;
-	-atheos*)
-		os=-atheos
-		;;
-	-syllable*)
-		os=-syllable
-		;;
-	-386bsd)
-		os=-bsd
-		;;
-	-ctix* | -uts*)
-		os=-sysv
-		;;
-	-nova*)
-		os=-rtmk-nova
-		;;
-	-ns2 )
-		os=-nextstep2
-		;;
-	-nsk*)
-		os=-nsk
-		;;
-	# Preserve the version number of sinix5.
-	-sinix5.*)
-		os=`echo $os | sed -e 's|sinix|sysv|'`
-		;;
-	-sinix*)
-		os=-sysv4
-		;;
-        -tpf*)
-		os=-tpf
-		;;
-	-triton*)
-		os=-sysv3
-		;;
-	-oss*)
-		os=-sysv3
-		;;
-	-svr4)
-		os=-sysv4
-		;;
-	-svr3)
-		os=-sysv3
-		;;
-	-sysvr4)
-		os=-sysv4
-		;;
-	# This must come after -sysvr4.
-	-sysv*)
-		;;
-	-ose*)
-		os=-ose
-		;;
-	-es1800*)
-		os=-ose
-		;;
-	-xenix)
-		os=-xenix
-		;;
-	-*mint | -mint[0-9]* | -*MiNT | -MiNT[0-9]*)
-		os=-mint
-		;;
-	-aros*)
-		os=-aros
-		;;
-	-kaos*)
-		os=-kaos
-		;;
-	-zvmoe)
-		os=-zvmoe
-		;;
-	-none)
-		;;
-	*)
-		# Get rid of the `-' at the beginning of $os.
-		os=`echo $os | sed 's/[^-]*-//'`
-		echo Invalid configuration \`$1\': system \`$os\' not recognized 1>&2
-		exit 1
-		;;
-esac
-else
-
-# Here we handle the default operating systems that come with various machines.
-# The value should be what the vendor currently ships out the door with their
-# machine or put another way, the most popular os provided with the machine.
-
-# Note that if you're going to try to match "-MANUFACTURER" here (say,
-# "-sun"), then you have to tell the case statement up towards the top
-# that MANUFACTURER isn't an operating system.  Otherwise, code above
-# will signal an error saying that MANUFACTURER isn't an operating
-# system, and we'll never get to this point.
-
-case $basic_machine in
-        score-*)
-		os=-elf
-		;;
-        spu-*)
-		os=-elf
-		;;
-	*-acorn)
-		os=-riscix1.2
-		;;
-	arm*-rebel)
-		os=-linux
-		;;
-	arm*-semi)
-		os=-aout
-		;;
-        c4x-* | tic4x-*)
-        	os=-coff
-		;;
-	# This must come before the *-dec entry.
-	pdp10-*)
-		os=-tops20
-		;;
-	pdp11-*)
-		os=-none
-		;;
-	*-dec | vax-*)
-		os=-ultrix4.2
-		;;
-	m68*-apollo)
-		os=-domain
-		;;
-	i386-sun)
-		os=-sunos4.0.2
-		;;
-	m68000-sun)
-		os=-sunos3
-		# This also exists in the configure program, but was not the
-		# default.
-		# os=-sunos4
-		;;
-	m68*-cisco)
-		os=-aout
-		;;
-        mep-*)
-		os=-elf
-		;;
-	mips*-cisco)
-		os=-elf
-		;;
-	mips*-*)
-		os=-elf
-		;;
-	or32-*)
-		os=-coff
-		;;
-	*-tti)	# must be before sparc entry or we get the wrong os.
-		os=-sysv3
-		;;
-	sparc-* | *-sun)
-		os=-sunos4.1.1
-		;;
-	*-be)
-		os=-beos
-		;;
-	*-haiku)
-		os=-haiku
-		;;
-	*-ibm)
-		os=-aix
-		;;
-    	*-knuth)
-		os=-mmixware
-		;;
-	*-wec)
-		os=-proelf
-		;;
-	*-winbond)
-		os=-proelf
-		;;
-	*-oki)
-		os=-proelf
-		;;
-	*-hp)
-		os=-hpux
-		;;
-	*-hitachi)
-		os=-hiux
-		;;
-	i860-* | *-att | *-ncr | *-altos | *-motorola | *-convergent)
-		os=-sysv
-		;;
-	*-cbm)
-		os=-amigaos
-		;;
-	*-dg)
-		os=-dgux
-		;;
-	*-dolphin)
-		os=-sysv3
-		;;
-	m68k-ccur)
-		os=-rtu
-		;;
-	m88k-omron*)
-		os=-luna
-		;;
-	*-next )
-		os=-nextstep
-		;;
-	*-sequent)
-		os=-ptx
-		;;
-	*-crds)
-		os=-unos
-		;;
-	*-ns)
-		os=-genix
-		;;
-	i370-*)
-		os=-mvs
-		;;
-	*-next)
-		os=-nextstep3
-		;;
-	*-gould)
-		os=-sysv
-		;;
-	*-highlevel)
-		os=-bsd
-		;;
-	*-encore)
-		os=-bsd
-		;;
-	*-sgi)
-		os=-irix
-		;;
-	*-siemens)
-		os=-sysv4
-		;;
-	*-masscomp)
-		os=-rtu
-		;;
-	f30[01]-fujitsu | f700-fujitsu)
-		os=-uxpv
-		;;
-	*-rom68k)
-		os=-coff
-		;;
-	*-*bug)
-		os=-coff
-		;;
-	*-apple)
-		os=-macos
-		;;
-	*-atari*)
-		os=-mint
-		;;
-	*)
-		os=-none
-		;;
-esac
-fi
-
-# Here we handle the case where we know the os, and the CPU type, but not the
-# manufacturer.  We pick the logical manufacturer.
-vendor=unknown
-case $basic_machine in
-	*-unknown)
-		case $os in
-			-riscix*)
-				vendor=acorn
-				;;
-			-sunos*)
-				vendor=sun
-				;;
-			-aix*)
-				vendor=ibm
-				;;
-			-beos*)
-				vendor=be
-				;;
-			-hpux*)
-				vendor=hp
-				;;
-			-mpeix*)
-				vendor=hp
-				;;
-			-hiux*)
-				vendor=hitachi
-				;;
-			-unos*)
-				vendor=crds
-				;;
-			-dgux*)
-				vendor=dg
-				;;
-			-luna*)
-				vendor=omron
-				;;
-			-genix*)
-				vendor=ns
-				;;
-			-mvs* | -opened*)
-				vendor=ibm
-				;;
-			-os400*)
-				vendor=ibm
-				;;
-			-ptx*)
-				vendor=sequent
-				;;
-			-tpf*)
-				vendor=ibm
-				;;
-			-vxsim* | -vxworks* | -windiss*)
-				vendor=wrs
-				;;
-			-aux*)
-				vendor=apple
-				;;
-			-hms*)
-				vendor=hitachi
-				;;
-			-mpw* | -macos*)
-				vendor=apple
-				;;
-			-*mint | -mint[0-9]* | -*MiNT | -MiNT[0-9]*)
-				vendor=atari
-				;;
-			-vos*)
-				vendor=stratus
-				;;
-		esac
-		basic_machine=`echo $basic_machine | sed "s/unknown/$vendor/"`
-		;;
-esac
-
-echo $basic_machine$os
-exit
-
-# Local variables:
-# eval: (add-hook 'write-file-hooks 'time-stamp)
-# time-stamp-start: "timestamp='"
-# time-stamp-format: "%:y-%02m-%02d"
-# time-stamp-end: "'"
-# End:
diff --git a/Tools/mkrelease.py b/Tools/mkrelease.py
index 574720dab..d7927f8e6 100755
--- a/Tools/mkrelease.py
+++ b/Tools/mkrelease.py
@@ -21,8 +21,8 @@ except:
    print "where version should be 1.3.x and username is your SF username"
    sys.exit(1)
 
-print "Looking for wput"
-os.system("which wput") and failed("wput not installed/found. Please install.")
+print "Looking for rsync"
+os.system("which rsync") and failed("rsync not installed/found. Please install.")
 
 print "Making source tarball"
 os.system("python ./mkdist.py " + version) and failed("")
@@ -31,8 +31,8 @@ print "Build Windows package"
 os.system("./mkwindows.sh " + version) and failed("")
 
 print "Uploading to Sourceforge"
-os.system("wput --verbose --binary swig-" + version + ".tar.gz ftp://anonymous:" + username + "@users.sourceforge.net@upload.sourceforge.net/incoming/") and failed("")
-os.system("wput --verbose --binary swigwin-" + version + ".zip ftp://anonymous:" + username + "@users.sourceforge.net@upload.sourceforge.net/incoming/") and failed("")
+os.system("rsync --archive --verbose -P --times -e ssh swig-" + version + ".tar.gz " + username + "@frs.sourceforge.net:uploads/") and failed("")
+os.system("rsync --archive --verbose -P --times -e ssh swigwin-" + version + ".zip " + username + "@frs.sourceforge.net:uploads/") and failed("")
 
 os.system("svn copy -m \"rel-" + version + "\" https://swig.svn.sourceforge.net/svnroot/swig/trunk https://swig.svn.sourceforge.net/svnroot/swig/tags/rel-" + version + "/")
 
diff --git a/configure.in b/configure.in
index 82d83a4f0..8a09cd6f7 100644
--- a/configure.in
+++ b/configure.in
@@ -2,7 +2,7 @@ dnl Process this file with autoconf to produce a configure script.
 dnl The macros which aren't shipped with the autotools are stored in the
 dnl Tools/config directory in .m4 files.
 
-AC_INIT([swig],[1.3.36],[http://www.swig.org])
+AC_INIT([swig],[1.3.37],[http://www.swig.org])
 AC_PREREQ(2.58)
 AC_CONFIG_SRCDIR([Source/Swig/swig.h])
 AC_CONFIG_AUX_DIR([Tools/config])
@@ -254,18 +254,6 @@ case $host in
    *) MZSCHEME_SO=.so;;
 esac
 
-AC_SUBST(TCL_LDSHARED)
-case $host in
-   *-*-darwin*) TCL_LDSHARED="gcc -dynamiclib -flat_namespace -undefined suppress";;
-   *) TCL_LDSHARED=$LDSHARED;;
-esac
-
-AC_SUBST(TCL_CXXSHARED)
-case $host in
-   *-*-darwin*) TCL_CXXSHARED="g++ -dynamiclib -flat_namespace -undefined suppress";;
-   *) TCL_CXXSHARED=$TRYLINKINGWITHCXX;;
-esac
-
 AC_SUBST(LUA_SO)
 case $host in
    *-*-darwin*) LUA_SO=.so;;
@@ -388,12 +376,12 @@ if test "$no_x" = "yes" -o "$not_really_there" = "yes"; then
         dirs="/usr/unsupported/include /usr/local/include /usr/X386/include /usr/include/X11R4 /usr/X11R5/include /usr/include/X11R5 /usr/openwin/include /usr/X11/include /usr/sww/include /usr/X11R6/include /usr/include/X11R6"
         for i in $dirs ; do
 	    if test -r $i/X11/Intrinsic.h; then
-		AC_MSG_RESULT($i)
 	        XINCLUDES=" -I$i"
 		break
 	    fi
         done
     fi
+    AC_MSG_RESULT($XINCLUDES)
 else
     if test "$x_includes" != ""; then
 	XINCLUDES=-I$x_includes
@@ -547,11 +535,25 @@ case $host in
 *-*-cygwin* | *-*-mingw*) TCLDYNAMICLINKING="$TCLLIB";;
 *)TCLDYNAMICLINKING="";;
 esac
+
+case $host in
+*-*-darwin*) 
+    TCLLDSHARED='$(CC) -dynamiclib -undefined suppress -flat_namespace'
+    TCLCXXSHARED='$(CXX) -dynamiclib -undefined suppress -flat_namespace'
+    ;;
+*)
+    TCLLDSHARED='$(LDSHARED)'
+    TCLCXXSHARED='$(CXXSHARED)'
+    ;;
+esac
+
 fi
 
 AC_SUBST(TCLINCLUDE)
 AC_SUBST(TCLLIB)
 AC_SUBST(TCLDYNAMICLINKING)
+AC_SUBST(TCLLDSHARED)
+AC_SUBST(TCLCXXSHARED)
 
 #----------------------------------------------------------------
 # Look for Python
@@ -571,7 +573,7 @@ else
 # First figure out the name of the Python executable
 
 if test "x$PYBIN" = xyes; then
-AC_CHECK_PROGS(PYTHON, python python2.8 python2.7 python2.6 python2.5 python2.4 python2.3 python2.2 python2.1 python2.0 python1.6 python1.5 python1.4 python)
+AC_CHECK_PROGS(PYTHON, [python python2.8 python2.7 python2.6 python2.5 python2.4 python2.3 python2.2 python2.1 python2.0 python1.6 python1.5 python1.4 python])
 else
 PYTHON="$PYBIN"
 fi
@@ -655,6 +657,103 @@ AC_SUBST(PYLIB)
 AC_SUBST(PYLINK)
 AC_SUBST(PYTHONDYNAMICLINKING)
 
+
+#----------------------------------------------------------------
+# Look for Python 3.x
+#----------------------------------------------------------------
+
+# mostly copy & pasted from "Look for Python" section,
+# did some trim, fix and rename
+
+PY3INCLUDE=
+PY3LIB=
+PY3PACKAGE=
+
+AC_ARG_WITH(python3, AS_HELP_STRING([--without-python3], [Disable Python 3.x support])
+AS_HELP_STRING([--with-python3=path], [Set location of Python 3.x executable]),[ PY3BIN="$withval"], [PY3BIN=yes])
+
+# First, check for "--without-python3" or "--with-python3=no".
+if test x"${PY3BIN}" = xno -o x"${with_alllang}" = xno ; then 
+AC_MSG_NOTICE([Disabling Python 3.x support])
+else
+# First figure out the name of the Python3 executable 
+
+if test "x$PY3BIN" = xyes; then
+AC_CHECK_PROGS(PYTHON3, [python3 python3.0])
+else
+PYTHON3="$PY3BIN"
+fi
+
+# Check for Python 3.x development tools (header files, static library and python3-config)
+AC_CHECK_PROGS(PY3CONFIG, [$PYTHON3-config python3-config python3.0-config])
+
+if test -n "$PYTHON3" -a -n "$PY3CONFIG"; then
+    AC_MSG_CHECKING([for Python 3.x prefix])
+    PY3PREFIX=`($PY3CONFIG --prefix) 2>/dev/null`
+    AC_MSG_RESULT($PY3PREFIX)
+    AC_MSG_CHECKING(for Python 3.x exec-prefix)
+    PY3EPREFIX=`($PY3CONFIG --exec-prefix) 2>/dev/null`
+    AC_MSG_RESULT($PY3EPREFIX)
+
+    # Note: I could not think of a standard way to get the version string from different versions.
+    # This trick pulls it out of the file location for a standard library file.
+    
+    AC_MSG_CHECKING([for Python 3.x version])
+
+    # Need to do this hack since autoconf replaces __file__ with the name of the configure file
+    filehack="file__"
+    PY3VERSION=`($PYTHON3 -c "import string,operator,os.path; print(operator.getitem(os.path.split(operator.getitem(os.path.split(string.__$filehack),0)),1))")`
+    AC_MSG_RESULT($PY3VERSION)
+
+    # Find the directory for libraries this is necessary to deal with
+    # platforms that can have apps built for multiple archs: e.g. x86_64
+    AC_MSG_CHECKING([for Python 3.x lib dir])
+    PY3LIBDIR=`($PYTHON3 -c "import sys; print(sys.lib)") 2>/dev/null`
+    if test -z "$PY3LIBDIR"; then
+      # some dists don't have sys.lib  so the best we can do is assume lib
+      PY3LIBDIR="lib" 
+    fi
+    AC_MSG_RESULT($PY3LIBDIR)
+    
+    # Set the include directory
+
+    AC_MSG_CHECKING([for Python 3.x header files])
+    PY3INCLUDE=`($PY3CONFIG --includes) 2>/dev/null`
+    AC_MSG_RESULT($PY3INCLUDE)
+
+    # Set the library directory blindly.   This probably won't work with older versions
+    AC_MSG_CHECKING([for Python 3.x library])
+    dirs="$PY3VERSION/config $PY3VERSION/$PY3LIBDIR python/$PY3LIBDIR"
+    for i in $dirs; do
+        if test -d $PY3EPREFIX/$PY3LIBDIR/$i; then
+           PY3LIB="$PY3EPREFIX/$PY3LIBDIR/$i"
+           break
+        fi
+    done
+    if test -z "$PY3LIB"; then
+        AC_MSG_RESULT([Not found])
+    else
+        AC_MSG_RESULT($PY3LIB)
+    fi
+
+    PY3LINK="-l$PY3VERSION"
+fi
+
+# Cygwin (Windows) needs the library for dynamic linking
+case $host in
+*-*-cygwin* | *-*-mingw*) PYTHON3DYNAMICLINKING="-L$PYLIB $PY3LINK"
+         DEFS="-DUSE_DL_IMPORT $DEFS" PY3INCLUDE="$PY3INCLUDE"
+         ;;
+*)PYTHON3DYNAMICLINKING="";;
+esac
+fi
+
+AC_SUBST(PY3INCLUDE)
+AC_SUBST(PY3LIB)
+AC_SUBST(PY3LINK)
+AC_SUBST(PYTHON3DYNAMICLINKING)
+
+
 #----------------------------------------------------------------
 # Look for Perl5
 #----------------------------------------------------------------
@@ -743,13 +842,13 @@ OCTAVEDYNAMICLINKING=
 OCTAVE_SO=.oct
 
 AC_ARG_WITH(octave, AS_HELP_STRING([--without-octave], [Disable Octave])
-AS_HELP_STRING([--with-octave=path], [Set location of Octave executable]),[ OCTAVEBIN="$withval"], [OCTAVEBIN=yes])
+AS_HELP_STRING([--with-octave=path], [Set location of Octave executable]),[OCTAVEBIN="$withval"], [OCTAVEBIN=yes])
 
 # First, check for "--without-octave" or "--with-octave=no".
 if test x"${OCTAVEBIN}" = xno -o x"${with_alllang}" = xno ; then 
 AC_MSG_NOTICE([Disabling Octave])
 OCTAVE=
-fi
+else
 
 # First figure out what the name of Octave is
 
@@ -790,6 +889,8 @@ else
        	AC_MSG_RESULT(could not figure out how to run octave)
 fi
 
+fi
+
 AC_SUBST(OCTAVE)
 AC_SUBST(OCTAVEEXT)
 AC_SUBST(OCTAVE_SO)
@@ -1125,7 +1226,7 @@ fi
 AC_MSG_CHECKING(for Ruby header files)
 if test -n "$RUBY"; then
 	RUBYDIR=`($RUBY -rmkmf -e 'print Config::CONFIG[["archdir"]] || $archdir') 2>/dev/null`
-	if test "$RUBYDIR" != ""; then
+	if test x"$RUBYDIR" != x""; then
 		dirs="$RUBYDIR"
 		RUBYINCLUDE=none
 		for i in $dirs; do
@@ -1852,11 +1953,17 @@ AC_SUBST(SKIP_OCTAVE)
 
 
 SKIP_PYTHON=
-if test -z "$PYINCLUDE" || test -z "$PYLIB" ; then
+if (test -z "$PYINCLUDE" || test -z "$PYLIB") &&
+   (test -z "$PY3INCLUDE" || test -z "PY3LIB") ; then
     SKIP_PYTHON="1"
 fi
 AC_SUBST(SKIP_PYTHON)
 
+SKIP_PYTHON3=
+if test -z "$PY3INCLUDE" || test -z "$PY3LIB" ; then
+    SKIP_PYTHON3="1"
+fi
+AC_SUBST(SKIP_PYTHON3)
 
 SKIP_JAVA=
 if test -z "$JAVA" || test -z "$JAVAC" || test -z "$JAVAINC" ; then

From 0db7edfa6341841c9802bce8deb2b2f21af60688 Mon Sep 17 00:00:00 2001
From: Jamie Kirkpatrick <gringostarr@users.sourceforge.net>
Date: Fri, 12 Sep 2008 11:17:39 +0000
Subject: [PATCH 029/314] Progress towards a working pydoc implementation.

- Nodes are now passed to the documentation translator so that type information can be looked up and used in parameter comments.
- Class comments are now inserted as well as some method information,


git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2008-cherylfoil@10838 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Source/CParse/parser.y                        |   9 +-
 Source/DoxygenTranslator/src/DoxygenEntity.h  |  12 +
 .../src/DoxygenTranslator.cpp                 |  12 +-
 .../DoxygenTranslator/src/DoxygenTranslator.h |   5 +-
 .../src/JavaDocConverter.cpp                  |   2 +-
 .../DoxygenTranslator/src/JavaDocConverter.h  |  10 +-
 .../DoxygenTranslator/src/PyDocConverter.cpp  | 205 ++++++++++++++++++
 Source/DoxygenTranslator/src/PyDocConverter.h |  29 +++
 Source/Makefile.am                            |   2 +
 Source/Modules/java.cxx                       |  18 +-
 Source/Modules/python.cxx                     |  33 ++-
 11 files changed, 314 insertions(+), 23 deletions(-)
 create mode 100644 Source/DoxygenTranslator/src/PyDocConverter.cpp
 create mode 100644 Source/DoxygenTranslator/src/PyDocConverter.h

diff --git a/Source/CParse/parser.y b/Source/CParse/parser.y
index d16a743e4..95bd8701d 100644
--- a/Source/CParse/parser.y
+++ b/Source/CParse/parser.y
@@ -13,7 +13,7 @@
 
 #define yylex yylex
 
-char cvsroot_parser_y[] = "$Id$";
+char cvsroot_parser_y[] = "$Id: parser.y 10767 2008-08-16 07:31:05Z cherylfoil $";
 
 #include "swig.h"
 #include "cparse.h"
@@ -3209,15 +3209,18 @@ c_constructor_decl : storage_class type LPAREN parms RPAREN ctor_end {
 
 doxygen_comment : DOXYGENSTRING 
 	{
+		while(Strchr($1,'/') == Char($1))
+			Replace($1,"/","",DOH_REPLACE_FIRST);
 	  if(isStructuralDoxygen($1)){
 	    $$ = new_node("doxycomm");
 		Setattr($$,"DoxygenComment",$1);
 	    }
 	  else {  
 	    if(currentComment != 0){
-		    Append(currentComment, $1);
+				Append(currentComment,$1);
 		    }
-		else currentComment = $1;
+			else 
+				currentComment = $1;
 		$$ = 0;
 	    }
 	}
diff --git a/Source/DoxygenTranslator/src/DoxygenEntity.h b/Source/DoxygenTranslator/src/DoxygenEntity.h
index 4313bfb2a..779065bdf 100644
--- a/Source/DoxygenTranslator/src/DoxygenEntity.h
+++ b/Source/DoxygenTranslator/src/DoxygenEntity.h
@@ -21,5 +21,17 @@ public:
     int isLeaf;
 };
 
+struct find_entity {
+	find_entity(string typeString) {
+		typeOfEntity = typeString;
+	}
+	
+	bool operator()(DoxygenEntity& entity) {
+		return entity.typeOfEntity == typeOfEntity;
+	}
+	
+	string typeOfEntity;
+};
+
 
 #endif /*TOKENLIST_H_*/
diff --git a/Source/DoxygenTranslator/src/DoxygenTranslator.cpp b/Source/DoxygenTranslator/src/DoxygenTranslator.cpp
index d6f0ae152..7fe2897c5 100644
--- a/Source/DoxygenTranslator/src/DoxygenTranslator.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenTranslator.cpp
@@ -5,13 +5,16 @@
 #include <string>
 #include "DoxygenEntity.h"
 #include "JavaDocConverter.h"
+#include "PyDocConverter.h"
 
 DoxygenParser doxyParse;
 JavaDocConverter jDC;
+PyDocConverter pyDC;
 
 DoxygenTranslator::DoxygenTranslator(){
 	doxyParse = DoxygenParser();
     JavaDocConverter jDC = JavaDocConverter();
+    PyDocConverter pyDC = PyDocConverter();
 }
 
 DoxygenTranslator::~DoxygenTranslator(){
@@ -19,13 +22,16 @@ DoxygenTranslator::~DoxygenTranslator(){
 }
 
 
-char *DoxygenTranslator::convert(char* doxygenBlob, char* option){
+char *DoxygenTranslator::convert(Node *n, char* doxygenBlob, char* option){
 	
 	list <DoxygenEntity> rootList = doxyParse.createTree(string(doxygenBlob));
 	
 	string returnedString;
 	if(strcmp(option, "JAVADOC") == 0){
-	    returnedString = jDC.convertToJavaDoc(rootList);
+	    returnedString = jDC.convertToJavaDoc(n, rootList);
+	}
+	else if(strcmp(option, "PYDOC") == 0){
+	    returnedString = pyDC.convertToPyDoc(n, rootList);
 	}
 	else cout << "Option not current supported.\n";
 	char *nonConstString;
@@ -59,7 +65,7 @@ int testCommands(){
 		//cout << "---ORIGINAL DOXYGEN--- " << endl << exampleArray[i] << endl;
 		char *nonConstString = (char *)malloc(exampleArray[i].length()+1);
 		strcpy(nonConstString, exampleArray[i].c_str());
-		char * result = dT.convert(nonConstString, "JAVADOC");
+		char * result = dT.convert(NULL, nonConstString, "JAVADOC");
 		free(nonConstString);
 		free(result);
 	}
diff --git a/Source/DoxygenTranslator/src/DoxygenTranslator.h b/Source/DoxygenTranslator/src/DoxygenTranslator.h
index e5fe7bcbb..3c26e3a25 100644
--- a/Source/DoxygenTranslator/src/DoxygenTranslator.h
+++ b/Source/DoxygenTranslator/src/DoxygenTranslator.h
@@ -1,10 +1,13 @@
 #ifndef DOXYGENTRANSLATOR_H_
 #define DOXYGENTRANSLATOR_H_
+
+#include "swig.h"
+
 class DoxygenTranslator
 {
 public:
 	DoxygenTranslator();
 	virtual ~DoxygenTranslator();
-	char* convert(char* doxygenBlob, char* option);
+	char* convert(Node *n, char* doxygenBlob, char* option);
 };
 #endif /*DOXYGENTRANSLATOR_H_*/
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.cpp b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
index 70c3bb731..b611cddf9 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
@@ -213,7 +213,7 @@ string translateEntity(DoxygenEntity &doxyEntity){
 	return "";
 }
 
-string JavaDocConverter:: convertToJavaDoc(list <DoxygenEntity> entityList){
+string JavaDocConverter:: convertToJavaDoc(Node *n, list <DoxygenEntity> entityList){
 
 
 	entityList.sort(compare_DoxygenEntities);
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.h b/Source/DoxygenTranslator/src/JavaDocConverter.h
index 53a270ce4..39de3dd15 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.h
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.h
@@ -1,15 +1,17 @@
- #include <list>
- #include <string>
- #include "DoxygenEntity.h"
 #ifndef JAVADOCCONVERTER_H_
 #define JAVADOCCONVERTER_H_
 
+#include <list>
+#include <string>
+#include "swig.h"
+#include "DoxygenEntity.h"
+
 class JavaDocConverter
 {
 public:
 
 	JavaDocConverter();
-	string convertToJavaDoc(list <DoxygenEntity> entityList);
+	string convertToJavaDoc(Node *n, list <DoxygenEntity> entityList);
 	~JavaDocConverter();
 	void printSortedTree(list <DoxygenEntity> &entityList);
 };
diff --git a/Source/DoxygenTranslator/src/PyDocConverter.cpp b/Source/DoxygenTranslator/src/PyDocConverter.cpp
new file mode 100644
index 000000000..ad675e273
--- /dev/null
+++ b/Source/DoxygenTranslator/src/PyDocConverter.cpp
@@ -0,0 +1,205 @@
+#include "PyDocConverter.h"
+#include <iostream>
+#include <sstream>
+
+#define APPROX_LINE_LENGTH 64//characters per line allowed
+#define TAB_SIZE 8//characters per line allowed
+
+//TODO {@link} {@linkplain} {@docRoot}, and other useful doxy commands that are not a pydoc tag
+PyDocConverter::PyDocConverter()
+{
+    debug = 1;
+}
+
+PyDocConverter::~PyDocConverter()
+{
+}
+
+/* Sorts entities by pyDoc standard order for commands
+ * NOTE: will not behave entirely properly until "First level" comments
+ * such as brief descriptions are TAGGED as such
+ */
+bool compare_DoxygenEntities(DoxygenEntity first, DoxygenEntity second);
+ 
+void PyDocConverter::printSortedTree(list <DoxygenEntity> &entityList){
+	list<DoxygenEntity>::iterator p = entityList.begin();
+	while (p != entityList.end()){
+		(*p).printEntity(0);
+		p++;
+	}
+}
+
+string PyDocConverter::formatParam(Node *n, DoxygenEntity &doxygenEntity) {
+	string result;
+	ParmList *plist = CopyParmList(Getattr(n, "parms"));
+	Parm *p = NULL;
+	
+	DoxygenEntity& paramNameEntity = *doxygenEntity.entityList.begin();
+	DoxygenEntity& paramDescriptionEntity = *(++doxygenEntity.entityList.begin());
+	
+	for (p = plist; p;) {
+		if(Char(Getattr(p, "name")) == paramNameEntity.data) {
+			std::string name = Char(Swig_name_make(n, 0, Getattr(p, "name"), 0, 0));
+			std::string type = Char(Swig_name_make(n, 0, Getattr(p, "type"), 0, 0));
+			
+			std::ostringstream parameterDocString;
+			
+			parameterDocString << std::endl << name << " (" << type << "): ";
+			parameterDocString << paramDescriptionEntity.data;
+			
+			result = parameterDocString.str();
+			break;
+		}
+		p = Getattr(p, "tmap:in") ? Getattr(p, "tmap:in:next") : nextSibling(p);
+	}
+
+	Delete(plist);
+	return result;
+}
+
+string PyDocConverter::formatCommand(string unformattedLine, int indent){
+	string formattedLines = "\n";
+	int lastPosition = 0;
+	int i = 0;
+	int isFirstLine  = 1;
+	while (i != -1 && i < unformattedLine.length()){
+		lastPosition = i;
+		if (isFirstLine){
+			i+=APPROX_LINE_LENGTH;
+		}
+		else i+=APPROX_LINE_LENGTH - indent*TAB_SIZE;
+		i = unformattedLine.find(" ", i);
+
+		if (i > 0 && i + 1 < unformattedLine.length()){
+			if (!isFirstLine) for (int j = 0; j < indent; j++) {
+				formattedLines.append("\t");
+				}
+			else {
+				isFirstLine = 0;
+			}
+			formattedLines.append(unformattedLine.substr(lastPosition, i - lastPosition + 1));
+			formattedLines.append("\n");
+
+		}
+	}
+	if (lastPosition < unformattedLine.length()){
+		if (!isFirstLine) {for (int j = 0; j < indent; j++) {formattedLines.append("\t");}}
+		formattedLines.append(unformattedLine.substr(lastPosition, unformattedLine.length() - lastPosition));
+	}
+
+	return formattedLines;
+}
+
+/* Contains the conversions for tags
+ * could probably be much more efficient...
+ */
+string PyDocConverter::pyDocFormat(DoxygenEntity &doxygenEntity){
+	if(doxygenEntity.typeOfEntity.compare("partofdescription") == 0){
+				return doxygenEntity.data;
+		}
+	if (doxygenEntity.typeOfEntity.compare("plainstring") == 0){
+			return  doxygenEntity.data;
+	}
+	else if (doxygenEntity.typeOfEntity.compare("b") == 0){
+		return "<b>" + doxygenEntity.data + "</b>";
+	}
+	else if (doxygenEntity.typeOfEntity.compare("c") == 0){
+		return "<tt>" + doxygenEntity.data + "</tt>";
+	}
+	else if (doxygenEntity.typeOfEntity.compare("@") == 0){
+		return "@";
+	}
+	else if (doxygenEntity.typeOfEntity.compare("\\") == 0){
+		return "\\";
+	}
+	else if (doxygenEntity.typeOfEntity.compare("<") == 0){
+		return "&lt;";
+	}
+	else if (doxygenEntity.typeOfEntity.compare(">") == 0){
+		return "&gt;";
+	}
+	else if (doxygenEntity.typeOfEntity.compare("&") == 0){
+		return "&amp;";
+	}
+	else if (doxygenEntity.typeOfEntity.compare("#") == 0){
+		return "#";
+	}
+	else if (doxygenEntity.typeOfEntity.compare("%") == 0){
+		return "%";
+	}
+	else if (doxygenEntity.typeOfEntity.compare("~") == 0){
+		return "~";
+	}
+	return "";
+}
+
+
+string PyDocConverter::translateSubtree( DoxygenEntity &doxygenEntity){
+	string returnedString;
+	if (doxygenEntity.isLeaf){ return pyDocFormat(doxygenEntity) + " ";}
+	else {
+		returnedString += pyDocFormat(doxygenEntity);
+		list<DoxygenEntity>::iterator p = doxygenEntity.entityList.begin();
+		while (p != doxygenEntity.entityList.end()){
+			returnedString+= translateSubtree(*p);
+			p++;
+		}
+	}
+	return returnedString;
+}
+
+string PyDocConverter::translateEntity(Node *n, DoxygenEntity &doxyEntity){
+	if(doxyEntity.typeOfEntity.compare("partofdescription")== 0) return formatCommand(string(translateSubtree(doxyEntity)), 0);
+	if ((doxyEntity.typeOfEntity.compare("brief") == 0)||(doxyEntity.typeOfEntity.compare("details") == 0)){
+		return formatCommand(string(translateSubtree(doxyEntity)), 0) + "\n * ";}
+	else if(doxyEntity.typeOfEntity.compare("plainstring")== 0 
+			|| doxyEntity.typeOfEntity.compare("deprecated")== 0 
+			|| doxyEntity.typeOfEntity.compare("brief")== 0)
+		return formatCommand(doxyEntity.data, 0) + "\n * ";
+	else if(doxyEntity.typeOfEntity.compare("see") == 0){
+		return formatCommand(string("@" + doxyEntity.typeOfEntity + "\t\t" + translateSubtree(doxyEntity)), 2);
+	}
+	else if(doxyEntity.typeOfEntity.compare("param") == 0) {
+		return formatParam(n, doxyEntity);
+	}
+	else if(doxyEntity.typeOfEntity.compare("return")== 0
+			|| doxyEntity.typeOfEntity.compare("author")== 0
+			|| doxyEntity.typeOfEntity.compare("param")== 0
+			|| doxyEntity.typeOfEntity.compare("since")== 0
+			|| doxyEntity.typeOfEntity.compare("version")== 0
+			|| doxyEntity.typeOfEntity.compare("exception") == 0
+			|| doxyEntity.typeOfEntity.compare("deprecated") == 0){
+		return formatCommand(string("@" + doxyEntity.typeOfEntity + "\t" + translateSubtree(doxyEntity)), 2);
+	}
+	else if(doxyEntity.typeOfEntity.compare("sa")== 0){
+		return formatCommand(string("@see\t\t" + translateSubtree(doxyEntity)), 2);
+	}
+	else return formatCommand(pyDocFormat(doxyEntity), 0 );
+	return "";
+}
+
+string PyDocConverter::convertToPyDoc(Node *n, list <DoxygenEntity> entityList){
+	entityList.sort(compare_DoxygenEntities);
+	
+    if(debug){
+	    cout << "---RESORTED LIST---" << endl;
+        printSortedTree(entityList);
+    }
+
+	string pyDocString = "\"\"\"";
+
+	list<DoxygenEntity>::iterator entityIterator = entityList.begin();
+	while (entityIterator != entityList.end()){
+		pyDocString += translateEntity(n, *entityIterator);
+		entityIterator++;
+	}
+
+	pyDocString += "\n\"\"\"\n";
+	
+	if(debug){
+	    cout << "\n---RESULT IN PYDOC---" << endl;
+	    cout << pyDocString; 
+	}
+	
+	return pyDocString;
+}
\ No newline at end of file
diff --git a/Source/DoxygenTranslator/src/PyDocConverter.h b/Source/DoxygenTranslator/src/PyDocConverter.h
new file mode 100644
index 000000000..b9d813476
--- /dev/null
+++ b/Source/DoxygenTranslator/src/PyDocConverter.h
@@ -0,0 +1,29 @@
+#ifndef PYDOCCONVERTER_H_
+#define PYDOCCONVERTER_H_
+
+#include <list>
+#include <string>
+#include "swig.h"
+#include "DoxygenEntity.h"
+
+class PyDocConverter
+{
+public:
+
+    PyDocConverter();
+    string convertToPyDoc(Node *n, list <DoxygenEntity> entityList);
+    ~PyDocConverter();
+    void printSortedTree(list <DoxygenEntity> &entityList);
+
+protected:
+	std::string formatParam(Node *n, DoxygenEntity &doxygenEntity);
+    std::string formatCommand(string unformattedLine, int indent);
+    std::string pyDocFormat(DoxygenEntity &doxygenEntity);
+    std::string translateSubtree( DoxygenEntity &doxygenEntity);
+    std::string translateEntity(Node *n, DoxygenEntity &doxyEntity);
+    
+private:
+    bool debug;
+};
+
+#endif /*PYDOCCONVERTER_H_*/
diff --git a/Source/Makefile.am b/Source/Makefile.am
index 65b5c6f6f..bfa6b3413 100644
--- a/Source/Makefile.am
+++ b/Source/Makefile.am
@@ -97,6 +97,8 @@ eswig_SOURCES =	CParse/cscanner.c		\
 		DoxygenTranslator/src/DoxygenTranslator.cpp\
 		DoxygenTranslator/src/JavaDocConverter.h\
 		DoxygenTranslator/src/JavaDocConverter.cpp\
+		DoxygenTranslator/src/PyDocConverter.h\
+		DoxygenTranslator/src/PyDocConverter.cpp\
 		DoxygenTranslator/src/Token.h\
 		DoxygenTranslator/src/Token.cpp\
 		DoxygenTranslator/src/TokenList.h\
diff --git a/Source/Modules/java.cxx b/Source/Modules/java.cxx
index 961f9098c..edb88ebbb 100644
--- a/Source/Modules/java.cxx
+++ b/Source/Modules/java.cxx
@@ -510,7 +510,7 @@ public:
       if (doxygen_javadoc_flag){
       	if (Getattr(n,"DoxygenComment")){
       		  if(comment_creation_chatter) Printf(f_module, "/* This was generated from top() */");
-      		  char *convertedString = doxyTranslator.convert(Char(Getattr(n,"DoxygenComment")),"JAVADOC");
+      		  char *convertedString = doxyTranslator.convert(n, Char(Getattr(n,"DoxygenComment")),"JAVADOC");
       		  Printf(f_module, convertedString); 	
       		  free(convertedString);
       	}
@@ -1238,7 +1238,7 @@ public:
 	    if (doxygen_javadoc_flag){
 	    	if (Getattr(n,"DoxygenComment")){
 	    		if(comment_creation_chatter) Printv(proxy_class_constants_code, "/* This was generated from enumvalueDeclaration */", NIL );
-	    		char *convertedString = doxyTranslator.convert(Char(Getattr(n,"DoxygenComment")),"JAVADOC");
+	    		char *convertedString = doxyTranslator.convert(n, Char(Getattr(n,"DoxygenComment")),"JAVADOC");
 	    		Printv(proxy_class_constants_code, convertedString, NIL); 	
 	    		free(convertedString); 
 	    	}
@@ -1310,7 +1310,7 @@ public:
     if (doxygen_javadoc_flag){
     	if (Getattr(n,"DoxygenComment")){
     		  if(comment_creation_chatter) Printf(enum_code, "/* This was generated from enumvalueDeclaration() */" );
-	    	  char *convertedString = doxyTranslator.convert(Char(Getattr(n,"DoxygenComment")),"JAVADOC");		
+	    	  char *convertedString = doxyTranslator.convert(n, Char(Getattr(n,"DoxygenComment")),"JAVADOC");		
     		  Printf(enum_code, convertedString); 	
     		  free(convertedString); 
     	}
@@ -1382,7 +1382,7 @@ public:
 		 if (doxygen_javadoc_flag){
 		   if (Getattr(n,"DoxygenComment")){
 			      if(comment_creation_chatter) Printv(structuralComments, "/* This was generated from doxygenComment() */\n", NIL);
-		    	  char *convertedString = doxyTranslator.convert(Char(Getattr(n,"DoxygenComment")),"JAVADOC");			
+		    	  char *convertedString = doxyTranslator.convert(n, Char(Getattr(n,"DoxygenComment")),"JAVADOC");			
 			      Printv(structuralComments, convertedString, NIL);
 			      free(convertedString);
 		    	}
@@ -1412,7 +1412,7 @@ public:
     if (doxygen_javadoc_flag){
     	if (Getattr(n,"DoxygenComment")){
     		if(comment_creation_chatter) Printf(constants_code, "/* This was generated from enumvalueDeclaration */\n");
-	    	char *convertedString = doxyTranslator.convert(Char(Getattr(n,"DoxygenComment")),"JAVADOC");			
+	    	char *convertedString = doxyTranslator.convert(n, Char(Getattr(n,"DoxygenComment")),"JAVADOC");			
             Printf(constants_code, convertedString); 	
 		    free(convertedString);
     	}
@@ -1683,7 +1683,7 @@ public:
     if (doxygen_javadoc_flag){
     	if (Getattr(n,"DoxygenComment")){
     		if(comment_creation_chatter) Printv(proxy_class_def, "/* This was generated from emitProxyClassDefAndCPPCasts() */\n", NIL );
-	    	char *convertedString = doxyTranslator.convert(Char(Getattr(n,"DoxygenComment")),"JAVADOC");			
+	    	char *convertedString = doxyTranslator.convert(n, Char(Getattr(n,"DoxygenComment")),"JAVADOC");			
 	    	Printv(proxy_class_def, convertedString, NIL); 		
 		    free(convertedString);
     	}
@@ -2026,7 +2026,7 @@ public:
     if (doxygen_javadoc_flag){
     	if (Getattr(n,"DoxygenComment")){
     		if(comment_creation_chatter) Printf(function_code, "/* This was generated from proxyclassfunctionhandler */");
-  	    	char *convertedString = doxyTranslator.convert(Char(Getattr(n,"DoxygenComment")),"JAVADOC");			
+  	    	char *convertedString = doxyTranslator.convert(n, Char(Getattr(n,"DoxygenComment")),"JAVADOC");			
   	    	 Printf(function_code, convertedString); 		
   		    free(convertedString);
     	}
@@ -2258,7 +2258,7 @@ public:
 	    if (doxygen_javadoc_flag){
 	    	if (Getattr(n,"DoxygenComment")){
 	    		if(comment_creation_chatter) Printf(function_code, "/* This was generated from constructionhandler */\n" );
-	  	    	char *convertedString = doxyTranslator.convert(Char(Getattr(n,"DoxygenComment")),"JAVADOC");			
+	  	    	char *convertedString = doxyTranslator.convert(n, Char(Getattr(n,"DoxygenComment")),"JAVADOC");			
 	  	    	Printf(function_code, convertedString); 			
 		  		free(convertedString);
 	    	}
@@ -2529,7 +2529,7 @@ public:
     if (doxygen_javadoc_flag){
     	if (Getattr(n,"DoxygenComment")){
     		if(comment_creation_chatter) Printf(function_code, "/* This was generated from moduleClassFunctionHandler() */\n" );
-  	    	char *convertedString = doxyTranslator.convert(Char(Getattr(n,"DoxygenComment")),"JAVADOC");			
+  	    	char *convertedString = doxyTranslator.convert(n, Char(Getattr(n,"DoxygenComment")),"JAVADOC");			
   	    	Printf(function_code, convertedString); 			
 	  		free(convertedString);	
     	}
diff --git a/Source/Modules/python.cxx b/Source/Modules/python.cxx
index 7a878b4f8..ba02eae2e 100644
--- a/Source/Modules/python.cxx
+++ b/Source/Modules/python.cxx
@@ -7,7 +7,7 @@
  * Python language module for SWIG.
  * ----------------------------------------------------------------------------- */
 
-char cvsroot_python_cxx[] = "$Id$";
+char cvsroot_python_cxx[] = "$Id: python.cxx 10453 2008-05-15 21:18:44Z wsfulton $";
 
 #include "swigmod.h"
 #define ctab2  " "
@@ -18,6 +18,7 @@ char cvsroot_python_cxx[] = "$Id$";
 static int treduce = SWIG_cparse_template_reduce(0);
 
 #include <ctype.h>
+#include "../DoxygenTranslator/src/DoxygenTranslator.h"
 
 #define PYSHADOW_MEMBER  0x2
 
@@ -70,6 +71,7 @@ static int buildnone = 0;
 static int nobuildnone = 0;
 static int safecstrings = 0;
 static int dirvtable = 0;
+static int doxygen = 1;
 static int proxydel = 1;
 static int fastunpack = 0;
 static int fastproxy = 0;
@@ -83,6 +85,8 @@ static int extranative = 0;
 static int outputtuple = 0;
 static int nortti = 0;
 
+static DoxygenTranslator doxyTranslator;
+
 /* flags for the make_autodoc function */
 enum autodoc_t {
   AUTODOC_CLASS,
@@ -103,6 +107,7 @@ Python Options (available with -python)\n\
      -classptr       - Generate shadow 'ClassPtr' as in older swig versions\n\
      -cppcast        - Enable C++ casting operators (default) \n\
      -dirvtable      - Generate a pseudo virtual table for directors for faster dispatch \n\
+	 -doxygen		 - Convert C++ doxygen comments to pydoc comments in proxy classes \n\
      -extranative    - Return extra native C++ wraps for std containers when possible \n\
      -fastinit       - Use fast init mechanism for classes (default)\n\
      -fastunpack     - Use fast unpack mechanism to parse the argument functions \n\
@@ -324,6 +329,9 @@ public:
 	} else if (strcmp(argv[i], "-dirvtable") == 0) {
 	  dirvtable = 1;
 	  Swig_mark_arg(i);
+	} else if (strcmp(argv[i], "-doxygen") == 0) {
+	  doxygen = 1;
+	  Swig_mark_arg(i);
 	} else if (strcmp(argv[i], "-nodirvtable") == 0) {
 	  dirvtable = 0;
 	  Swig_mark_arg(i);
@@ -2898,11 +2906,24 @@ public:
         }
       }
       Printf(f_shadow, ":\n");
-      if (have_docstring(n)) {
+		
+	//translate and write pydoc comment if flagged
+	if (doxygen){
+		if (Getattr(n,"DoxygenComment")){
+			//if(comment_creation_chatter) Printf(function_code, "/* This was generated from classHandler */");
+			char *convertedString = doxyTranslator.convert(n, Char(Getattr(n,"DoxygenComment")), "PYDOC");			
+			Printf(f_shadow, Char(pythoncode(convertedString, shadow_indent))); 		
+			free(convertedString);
+		}
+	}
+	
+	// otherwise use default docstrings if requested
+	else if (have_docstring(n)) {
 	String *str = docstring(n, AUTODOC_CLASS, tab4);
 	if (str != NULL && Len(str))
 	  Printv(f_shadow, tab4, str, "\n", NIL);
       }
+		
       if (!modern) {
 	Printv(f_shadow, tab4, "__swig_setmethods__ = {}\n", NIL);
 	if (Len(base_class)) {
@@ -3109,6 +3130,14 @@ public:
 	  } else {
 	    Printv(f_shadow, tab4, "def ", symname, "(",parms , ")", returnTypeAnnotation(n), ":", NIL);
 	    Printv(f_shadow, "\n", NIL);
+		if (doxygen) {
+			if (Getattr(n,"DoxygenComment")){
+				//if(comment_creation_chatter) Printf(function_code, "/* This was generated from classHandler */");
+				char *convertedString = doxyTranslator.convert(n, Char(Getattr(n,"DoxygenComment")), "PYDOC");			
+				Printf(f_shadow, Char(pythoncode(convertedString, tab8))); 		
+				free(convertedString);
+			}
+		}
 	    if (have_docstring(n))
 	      Printv(f_shadow, tab8, docstring(n, AUTODOC_METHOD, tab8), "\n", NIL);
 	    if (have_pythonprepend(n)) {

From d12b8bc06ecf87f07a1961b976b077747501b423 Mon Sep 17 00:00:00 2001
From: Jamie Kirkpatrick <gringostarr@users.sourceforge.net>
Date: Fri, 12 Sep 2008 11:18:35 +0000
Subject: [PATCH 030/314] Remove "using std" clause and use namespaces
 properly.  Minor refactoring as well.

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2008-cherylfoil@10839 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 .../DoxygenTranslator/src/DoxygenEntity.cpp   | 176 +++++++--
 Source/DoxygenTranslator/src/DoxygenEntity.h  |  55 +--
 .../DoxygenTranslator/src/DoxygenParser.cpp   | 272 +++++++-------
 Source/DoxygenTranslator/src/DoxygenParser.h  |   6 +-
 .../src/DoxygenTranslator.cpp                 |  77 +---
 .../src/JavaDocConverter.cpp                  | 343 +++++++-----------
 .../DoxygenTranslator/src/JavaDocConverter.h  |   9 +-
 .../DoxygenTranslator/src/PyDocConverter.cpp  | 336 +++++++++--------
 Source/DoxygenTranslator/src/PyDocConverter.h |  21 +-
 9 files changed, 638 insertions(+), 657 deletions(-)

diff --git a/Source/DoxygenTranslator/src/DoxygenEntity.cpp b/Source/DoxygenTranslator/src/DoxygenEntity.cpp
index a2faf67db..dcca1d032 100644
--- a/Source/DoxygenTranslator/src/DoxygenEntity.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenEntity.cpp
@@ -1,19 +1,24 @@
+/* -----------------------------------------------------------------------------
+ * See the LICENSE file for information on copyright, usage and redistribution
+ * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ *
+ * python.cxx
+ *
+ * Part of the Doxygen comment translation module of SWIG.
+ * ----------------------------------------------------------------------------- */
+
 #include "DoxygenEntity.h"
-#include <string>
 #include <iostream>
-/* Little data class for Doxygen Commands */
 
-
-/* Basic node for commands that have
- * nothing after them
- * example: \n
+/* 
+ * Basic node for commands that have nothing after them (eg: \n)
  */
-string commandArray2[] = {"a", "addindex", "addtogroup", "anchor", "arg", "attention",
+std::string DoxygenEntity::commandArray[] = {"a", "addindex", "addtogroup", "anchor", "arg", "attention",
 		"author", "b", "brief", "bug", "c", "callgraph", "callergraph", "category",
 		"class", "code", "cond", "copybrief", "copydetails", "copydoc", "date", "def",
 		"defgroup", "deprecated", "details", "dir", "dontinclude", "dot", "dotfile", "e",
 		"else", "elseif", "em", "endcode", "endcond", "enddot", "endhtmlonly", "endif",
-		"endlatexonly", "endlink", "endmanonly", "endmsc", "endverbatim", "endxmlonly",
+		"std::endlatexonly", "std::endlink", "endmanonly", "endmsc", "endverbatim", "endxmlonly",
 		"enum", "example", "exception", "f$", "f[", "f]", "f{", "f}", "file", "fn", "headerfile",
 		"hideinitializer", "htmlinclude", "htmlonly", "if", "ifnot", "image", "include",
 		"includelineno", "ingroup", "internal", "invariant", "interface", "latexonly", "li",
@@ -24,19 +29,9 @@ string commandArray2[] = {"a", "addindex", "addtogroup", "anchor", "arg", "atten
 		"sa", "section", "see", "showinitializer", "since", "skip", "skipline", "struct", "subpage",
 		"subsection", "subsubsection", "test", "throw", "todo", "tparam", "typedef", "union", "until",
 		"var", "verbatim", "verbinclude", "version", "warning", "weakgroup", "xmlonly", "xrefitem",
-		"$", "@", string(1, 92), "&", "~", "<", ">", "#", "%"};
+		"$", "@", std::string(1, 92), "&", "~", "<", ">", "#", "%"};
 
-string findCommand(int commandNum){
-
-	int arraySize = sizeof(commandArray2)/sizeof(*commandArray2);
-	if (commandNum - 101 >= 0 && commandNum - 101 < arraySize){
-		return commandArray2[commandNum - 101];
-	}
-
-	return "" ;
-}
-
-DoxygenEntity::DoxygenEntity(string typeEnt){
+DoxygenEntity::DoxygenEntity(std::string typeEnt){
     typeOfEntity = typeEnt;
     data = "";
     isLeaf = 1;
@@ -45,9 +40,9 @@ DoxygenEntity::DoxygenEntity(string typeEnt){
 /* Basic node for commands that have
  * only 1 thing after them
  * example: \b word
- * OR holding a string
+ * OR holding a std::string
  */
-DoxygenEntity::DoxygenEntity(string typeEnt, string param1){
+DoxygenEntity::DoxygenEntity(std::string typeEnt, std::string param1){
     typeOfEntity = typeEnt;
     data = param1;
     isLeaf = 1;
@@ -56,26 +51,25 @@ DoxygenEntity::DoxygenEntity(string typeEnt, string param1){
 /* Nonterminal node
  * contains
  */
-DoxygenEntity::DoxygenEntity(string typeEnt, list <DoxygenEntity> &entList ){
+DoxygenEntity::DoxygenEntity(std::string typeEnt, std::list <DoxygenEntity> &entList ){
     typeOfEntity = typeEnt;
     data = "";
     isLeaf = 0;
     entityList = entList;
 }
 
-
 void DoxygenEntity::printEntity(int level){
 	int thisLevel = level;
 	if (isLeaf) {
-		for (int i = 0; i < thisLevel; i++) {cout << "\t";}
-		cout << "Node Command: " << typeOfEntity << " ";
-		if (data.compare("") != 0) cout << "Node Data: " << data;
-		cout << endl;
+		for (int i = 0; i < thisLevel; i++) {std::cout << "\t";}
+		std::cout << "Node Command: " << typeOfEntity << " ";
+		if (data.compare("") != 0) std::cout << "Node Data: " << data;
+		std::cout << std::endl;
 	}
 	else{
-		for (int i = 0; i < thisLevel; i++) {cout << "\t";}
-		cout << "Node Command : " << typeOfEntity << endl;
-		list<DoxygenEntity>::iterator p = entityList.begin();
+		for (int i = 0; i < thisLevel; i++) {std::cout << "\t";}
+		std::cout << "Node Command : " << typeOfEntity << std::endl;
+		std::list<DoxygenEntity>::iterator p = entityList.begin();
 		thisLevel++;
 		while (p != entityList.end()){
 			(*p).printEntity(thisLevel);
@@ -84,6 +78,122 @@ void DoxygenEntity::printEntity(int level){
 	}
 }
 
-DoxygenEntity::~DoxygenEntity()
-{
+bool CompareDoxygenEntities::operator()(DoxygenEntity& first, DoxygenEntity& second){
+  if(first.typeOfEntity.compare("brief") == 0) 
+    return true;
+  if(second.typeOfEntity.compare("brief") == 0) 
+    return false;
+  if(first.typeOfEntity.compare("details") == 0) 
+    return true;
+  if(second.typeOfEntity.compare("details") == 0) 
+    return false;
+  if(first.typeOfEntity.compare("partofdescription") == 0) 
+    return true;
+  if(first.typeOfEntity.compare("partofdescription") == 0) 
+    return false;
+  if(first.typeOfEntity.compare("plainstd::string") == 0) 
+    return true;
+  if(second.typeOfEntity.compare("plainstd::string") == 0) 
+    return false;
+  if(first.typeOfEntity.compare("param") == 0){
+    if(second.typeOfEntity.compare("param")== 0) 
+      return true;
+    if(second.typeOfEntity.compare("return")== 0) 
+      return true;
+    if(second.typeOfEntity.compare("exception")== 0) 
+      return true;
+    if(second.typeOfEntity.compare("author")== 0) 
+      return true;
+    if(second.typeOfEntity.compare("version")== 0)
+      return true;
+    if(second.typeOfEntity.compare("see")== 0)
+      return true;
+    if(second.typeOfEntity.compare("since")== 0)
+      return true;
+    if(second.typeOfEntity.compare("deprecated")== 0)
+      return true;
+    return false;
+  }
+  if(first.typeOfEntity.compare("return")== 0){
+    if(second.typeOfEntity.compare("return")== 0) 
+      return true;
+    if(second.typeOfEntity.compare("exception")== 0) 
+      return true;
+    if(second.typeOfEntity.compare("author")== 0) 
+      return true;
+    if(second.typeOfEntity.compare("version")== 0)
+      return true;
+    if(second.typeOfEntity.compare("see")== 0)
+      return true;
+    if(second.typeOfEntity.compare("since")== 0)
+      return true;
+    if(second.typeOfEntity.compare("deprecated")== 0
+      )return true;
+    return false;
+  }
+  if(first.typeOfEntity.compare("exception")== 0){
+    if(second.typeOfEntity.compare("exception")== 0) 
+      return true;
+    if(second.typeOfEntity.compare("author")== 0) 
+      return true;
+    if(second.typeOfEntity.compare("version")== 0)
+      return true;
+    if(second.typeOfEntity.compare("see")== 0)
+      return true;
+    if(second.typeOfEntity.compare("since")== 0)
+      return true;
+    if(second.typeOfEntity.compare("deprecated")== 0)
+      return true;
+    return false;
+  }
+  if(first.typeOfEntity.compare("author")== 0){
+    if(second.typeOfEntity.compare("author")== 0) 
+      return true;
+    if(second.typeOfEntity.compare("version")== 0)
+      return true;
+    if(second.typeOfEntity.compare("see")== 0)
+      return true;
+    if(second.typeOfEntity.compare("since")== 0)
+      return true;
+    if(second.typeOfEntity.compare("deprecated")== 0)
+      return true;
+    return false;
+  }
+  if(first.typeOfEntity.compare("version")== 0){
+    if(second.typeOfEntity.compare("version")== 0)
+      return true;
+    if(second.typeOfEntity.compare("see")== 0)
+      return true;
+    if(second.typeOfEntity.compare("since")== 0)
+      return true;
+    if(second.typeOfEntity.compare("deprecated")== 0)
+      return true;
+    return false;
+  }
+  if(first.typeOfEntity.compare("see")== 0 || first.typeOfEntity.compare("sa")== 0){
+    if(second.typeOfEntity.compare("see")== 0)
+      return true;
+    if(second.typeOfEntity.compare("sa")== 0)
+      return true;
+    if(second.typeOfEntity.compare("since")== 0)
+      return true;
+    if(second.typeOfEntity.compare("deprecated")== 0)
+      return true;
+    return false;
+  }
+  if(first.typeOfEntity.compare("since")== 0){
+    if(second.typeOfEntity.compare("since")== 0) 
+      return true;
+    if(second.typeOfEntity.compare("deprecated")== 0)
+      return true;
+    return false;
+  }
+  if(first.typeOfEntity.compare("deprecated")== 0){
+    if(second.typeOfEntity.compare("deprecated")== 0)
+      return true;
+    return false;
+  }
+  return true;
 }
+
+
diff --git a/Source/DoxygenTranslator/src/DoxygenEntity.h b/Source/DoxygenTranslator/src/DoxygenEntity.h
index 779065bdf..3bec0bb0c 100644
--- a/Source/DoxygenTranslator/src/DoxygenEntity.h
+++ b/Source/DoxygenTranslator/src/DoxygenEntity.h
@@ -1,37 +1,40 @@
+/* -----------------------------------------------------------------------------
+ * See the LICENSE file for information on copyright, usage and redistribution
+ * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ *
+ * python.cxx
+ *
+ * Part of the Doxygen comment translation module of SWIG.
+ * ----------------------------------------------------------------------------- */
+
 #ifndef DOXYGENENTITY_H_
 #define DOXYGENENTITY_H_
 
-
 #include <string>
 #include <list>
 
-using namespace std;
-
-class DoxygenEntity{
-
-public:
-	DoxygenEntity(string typeEnt);
-	DoxygenEntity(string typeEnt, string param1);
-	DoxygenEntity(string typeEnt, list <DoxygenEntity> &entList );
-   ~DoxygenEntity();
-	void printEntity(int level);
-    string typeOfEntity;
-    list <DoxygenEntity> entityList;
-    string data;
-    int isLeaf;
+/*
+ * Structure to represent a doxygen comment entry
+ */
+struct DoxygenEntity{
+  DoxygenEntity(std::string typeEnt);
+  DoxygenEntity(std::string typeEnt, std::string param1);
+  DoxygenEntity(std::string typeEnt, std::list <DoxygenEntity> &entList );
+  void printEntity(int level);
+  std::string typeOfEntity;
+  std::list <DoxygenEntity> entityList;
+  std::string data;
+  int isLeaf;
+  static std::string commandArray[];
 };
 
-struct find_entity {
-	find_entity(string typeString) {
-		typeOfEntity = typeString;
-	}
-	
-	bool operator()(DoxygenEntity& entity) {
-		return entity.typeOfEntity == typeOfEntity;
-	}
-	
-	string typeOfEntity;
+/* 
+ * Functor that sorts entities by javaDoc standard order for commands.
+ * NOTE: will not behave entirely properly until "First level" comments
+ * such as brief descriptions are TAGGED as such
+ */
+struct CompareDoxygenEntities {
+  bool operator()(DoxygenEntity& first, DoxygenEntity& second);
 };
 
-
 #endif /*TOKENLIST_H_*/
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.cpp b/Source/DoxygenTranslator/src/DoxygenParser.cpp
index d953bc6d4..ba624239a 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenParser.cpp
@@ -19,8 +19,6 @@
 #define PARAGRAPH_END 102
 #define  PLAINSTRING 103
 #define  COMMAND  104
-using namespace std;
-
 
 DoxygenParser::DoxygenParser()
 {
@@ -32,13 +30,13 @@ DoxygenParser::~DoxygenParser()
 
 //////////////////////////////////////////
 int noisy = 0; // set this to 1 for extra chatter from the parsing stage.
-int addCommand(string currCommand, TokenList &tokList,  list <DoxygenEntity> &aNewList);
-list <DoxygenEntity> parse(list<Token>::iterator endParsingIndex, TokenList &tokList);
+int addCommand(std::string currCommand, TokenList &tokList,  std::list <DoxygenEntity> &aNewList);
+std::list <DoxygenEntity> parse(std::list<Token>::iterator endParsingIndex, TokenList &tokList);
 
 //////////////////////////////////////////
 
 
-string commandArray[] = {"a", "addindex", "addtogroup", "anchor", "arg", "attention",
+std::string commandArray[] = {"a", "addindex", "addtogroup", "anchor", "arg", "attention",
 		"author", "b", "brief", "bug", "c", "callgraph", "callergraph", "category",
 		"class", "code", "cond", "copybrief", "copydetails", "copydoc", "date", "def",
 		"defgroup", "deprecated", "details", "dir", "dontinclude", "dot", "dotfile", "e",
@@ -57,49 +55,49 @@ string commandArray[] = {"a", "addindex", "addtogroup", "anchor", "arg", "attent
 		"$", "@", "\\","&", "~", "<", ">", "#", "%"};
 
 
-string sectionIndicators[] = { "attention", "author", "brief", "bug", "cond", "date", "deprecated", "details",
+std::string sectionIndicators[] = { "attention", "author", "brief", "bug", "cond", "date", "deprecated", "details",
 		"else", "elseif", "endcond", "endif", "exception", "if", "ifnot", "invariant", "note", "par", "param",
 		"tparam", "post" , "pre", "remarks", "return", "retval", "sa", "see", "since", "test", "throw", "todo",
 		"version", "warning", "xrefitem" };
 
 /* All of the doxygen commands divided up by how they are parsed */
-string simpleCommands[] = {"n", "$", "@", "\\", "&", "~", "<", ">", "#", "%"};
-string ignoredSimpleCommands[] = {"nothing at the moment"};
-string commandWords[] = {"a", "b", "c", "e", "em", "p", "def", "enum", "example", "package", 
+std::string simpleCommands[] = {"n", "$", "@", "\\", "&", "~", "<", ">", "#", "%"};
+std::string ignoredSimpleCommands[] = {"nothing at the moment"};
+std::string commandWords[] = {"a", "b", "c", "e", "em", "p", "def", "enum", "example", "package", 
 		"relates", "namespace", "relatesalso","anchor", "dontinclude", "include", "includelineno"};
-string ignoredCommandWords[] = {"copydoc", "copybrief", "copydetails", "verbinclude", "htmlinclude"};
-string commandLines[] = {"addindex", "fn", "name", "line", "var", "skipline", "typedef", "skip", "until", "property"};
-string ignoreCommandLines[] = {"nothing at the moment"};
-string commandParagraph[] = {"partofdescription", "return", "remarks", "since", "test", "sa", "see", "pre", "post", "details", "invariant", 
+std::string ignoredCommandWords[] = {"copydoc", "copybrief", "copydetails", "verbinclude", "htmlinclude"};
+std::string commandLines[] = {"addindex", "fn", "name", "line", "var", "skipline", "typedef", "skip", "until", "property"};
+std::string ignoreCommandLines[] = {"nothing at the moment"};
+std::string commandParagraph[] = {"partofdescription", "return", "remarks", "since", "test", "sa", "see", "pre", "post", "details", "invariant", 
 		    "deprecated", "date", "note", "warning", "version", "todo", "bug", "attention", "brief", "author"};
-string ignoreCommandParagraphs[] = {"nothing at the moment"};
-string commandEndCommands[] = {"code", "dot", "msc", "f$", "f[", "f{environment}{", "htmlonly", "latexonly", "manonly", 
+std::string ignoreCommandParagraphs[] = {"nothing at the moment"};
+std::string commandEndCommands[] = {"code", "dot", "msc", "f$", "f[", "f{environment}{", "htmlonly", "latexonly", "manonly", 
 		   "verbatim", "xmlonly", "cond", "if", "ifnot", "link"};
-string commandWordParagraphs[] = {"param", "tparam", "throw", "retval", "exception"};
-string commandWordLines[] = {"page", "subsection", "subsubsection", "section", "paragraph", "defgroup"};
-string commandWordOWordOWords [] = {"category", "class", "protocol", "interface", "struct", "union"};
-string commandOWords[] = {"dir", "file", "cond"};
-string commandErrorThrowings[] = {"annotatedclasslist", "classhierarchy", "define", "functionindex", "header",
-		"headerfilelist", "inherit", "l", "postheader", "private", "privatesection", "protected", 
+std::string commandWordParagraphs[] = {"param", "tparam", "throw", "retval", "exception"};
+std::string commandWordLines[] = {"page", "subsection", "subsubsection", "section", "paragraph", "defgroup"};
+std::string commandWordOWordOWords [] = {"category", "class", "protocol", "interface", "struct", "union"};
+std::string commandOWords[] = {"dir", "file", "cond"};
+std::string commandErrorThrowings[] = {"annotatedclassstd::list", "classhierarchy", "define", "functionindex", "header",
+		"headerfilestd::list", "inherit", "l", "postheader", "private", "privatesection", "protected", 
 		"protectedsection", "public", "publicsection", "endcode", "enddot", "endmsc", "endhtmlonly", 
 		"endlatexonly", "endmanonly", "endlink", "endverbatim", "endxmlonly", "f]", "f}", "endcond", 
 		"endif"};
-string commandUniques[] = {"xrefitem", "arg", "ingroup", "par", "headerfile", "overload", "weakgroup", "ref",
+std::string commandUniques[] = {"xrefitem", "arg", "ingroup", "par", "headerfile", "overload", "weakgroup", "ref",
 		"subpage", "dotfile", "image", "addtogroup", "li"};
 
 
-/* Changes a string to all lower case */
-string StringToLower(string stringToConvert){
+/* Changes a std::string to all lower case */
+std::string StringToLower(std::string stringToConvert){
    for(unsigned int i=0;i<stringToConvert.length();i++){
 	   stringToConvert[i] = tolower(stringToConvert[i]);
 	   }
-   return stringToConvert; //return the converted string
+   return stringToConvert; //return the converted std::string
 }
 
 /* finds out if a command exists (is a possible command)
- * from the string array commandArray
+ * from the std::string array commandArray
  * returns -1 if no match is found */
-int findCommand(string smallString){
+int findCommand(std::string smallString){
 	smallString = StringToLower(smallString);
 	int a;
 	for (int i = 0; i < sizeof(commandArray)/sizeof(*commandArray); i++){
@@ -114,7 +112,7 @@ int findCommand(string smallString){
  * This is a helper method for finding the end of a paragraph
  * by Doxygen's terms
  */
-int isSectionIndicator(string smallString){
+int isSectionIndicator(std::string smallString){
 	smallString = StringToLower(smallString);
 	for (int i = 0; i < sizeof( sectionIndicators)/sizeof(* sectionIndicators); i++){
 		if( smallString.compare( sectionIndicators[i]) == 0){
@@ -125,8 +123,8 @@ int isSectionIndicator(string smallString){
 }
 
 /* prints the parse tree */
-void printTree( list <DoxygenEntity> &rootList){
-	list<DoxygenEntity>::iterator p = rootList.begin();
+void printTree( std::list <DoxygenEntity> &rootList){
+	std::list<DoxygenEntity>::iterator p = rootList.begin();
 	while (p != rootList.end()){
 		(*p).printEntity(0);
 		p++;
@@ -136,8 +134,8 @@ void printTree( list <DoxygenEntity> &rootList){
 /* Determines how a command should be handled (what group it belongs to
  * for parsing rules
  */
-int commandBelongs(string theCommand){
-	 string smallString = StringToLower(theCommand);
+int commandBelongs(std::string theCommand){
+	 std::string smallString = StringToLower(theCommand);
 	 //cout << " Looking for command " << theCommand << endl;
 	 int i = 0;
 	 for ( i = 0; i < sizeof(simpleCommands)/sizeof(*simpleCommands); i++){
@@ -189,10 +187,10 @@ int commandBelongs(string theCommand){
 }
 
 /* Returns the next word ON THE CURRENT LINE ONLY
- * if a new line is encountered, returns a blank string.
+ * if a new line is encountered, returns a blank std::string.
  * Updates the index it is given if success.
  */
-string getNextWord(TokenList &tokList){
+std::string getNextWord(TokenList &tokList){
 	 Token nextToken = tokList.peek();
 	 if (nextToken.tokenType == PLAINSTRING ){
 		 nextToken = tokList.next();
@@ -204,8 +202,8 @@ string getNextWord(TokenList &tokList){
 /* Returns the location of the end of the line as
  * an iterator.
  */
-list<Token>::iterator getOneLine(TokenList &tokList){
-	 list<Token>::iterator endOfLine = tokList.iteratorCopy();
+std::list<Token>::iterator getOneLine(TokenList &tokList){
+	 std::list<Token>::iterator endOfLine = tokList.iteratorCopy();
 	 while(endOfLine!= tokList.end()){
 		 if ((* endOfLine).tokenType == END_LINE){
 			 //cout << "REACHED END" << endl;
@@ -219,11 +217,11 @@ list<Token>::iterator getOneLine(TokenList &tokList){
 	return tokList.end();
 	}
 
-/* Returns a properly formatted string
+/* Returns a properly formatted std::string
 * up til ANY command or end of line is encountered.
 */
-string getStringTilCommand(TokenList &tokList){
-	 string description;
+std::string getStringTilCommand(TokenList &tokList){
+	 std::string description;
 	 if (tokList.peek().tokenType == 0) return "";
 	 while(tokList.peek().tokenType == PLAINSTRING){
 		 Token currentToken = tokList.next();
@@ -234,13 +232,13 @@ string getStringTilCommand(TokenList &tokList){
 	return description;
 	}
 
-/* Returns a properly formatted string
+/* Returns a properly formatted std::string
 * up til the command specified is encountered
 */
 //TODO check that this behaves properly for formulas
 
-string getStringTilEndCommand(string theCommand, TokenList &tokList){
-	 string description;
+std::string getStringTilEndCommand(std::string theCommand, TokenList &tokList){
+	 std::string description;
 	 if (tokList.peek().tokenType == 0) return "";
 	 while(tokList.peek().tokenString.compare(theCommand) != 0 ){
 		 Token currentToken = tokList.next();
@@ -253,8 +251,8 @@ string getStringTilEndCommand(string theCommand, TokenList &tokList){
 * Paragraph is defined in Doxygen to be a paragraph of text
 * seperate by either a structural command or a blank line
 */
-list<Token>::iterator getEndOfParagraph(TokenList &tokList){
-	 list<Token>::iterator endOfParagraph = tokList.iteratorCopy();
+std::list<Token>::iterator getEndOfParagraph(TokenList &tokList){
+	 std::list<Token>::iterator endOfParagraph = tokList.iteratorCopy();
 	 while(endOfParagraph != tokList.end()){
 		if ((* endOfParagraph).tokenType == END_LINE){
 			 endOfParagraph++;
@@ -278,10 +276,10 @@ list<Token>::iterator getEndOfParagraph(TokenList &tokList){
 
 /* Returns the end of a section, defined as the first blank line OR first encounter of the same 
 * command. Example of this behaviour is \arg
-* if no end is encountered, returns the last token of the list.
+* if no end is encountered, returns the last token of the std::list.
 */
-list<Token>::iterator getEndOfSection(string theCommand, TokenList &tokList){
-	 list<Token>::iterator endOfParagraph = tokList.iteratorCopy();
+std::list<Token>::iterator getEndOfSection(std::string theCommand, TokenList &tokList){
+	 std::list<Token>::iterator endOfParagraph = tokList.iteratorCopy();
 	 while(endOfParagraph != tokList.end()){
 		if ((* endOfParagraph).tokenType == COMMAND){
 			 if(theCommand.compare((*endOfParagraph).tokenString) == 0) return endOfParagraph;
@@ -305,10 +303,10 @@ list<Token>::iterator getEndOfSection(string theCommand, TokenList &tokList){
  * that begins with a \command and ends in \endcommand
  * such as \code and \endcode. The proper usage is
  * progressTilEndCommand("endcode", tokenList);
- * If the end is never encountered, it returns the end of the list.
+ * If the end is never encountered, it returns the end of the std::list.
  */
-list<Token>::iterator getEndCommand(string theCommand, TokenList &tokList){
-	list<Token>::iterator endOfCommand = tokList.iteratorCopy();
+std::list<Token>::iterator getEndCommand(std::string theCommand, TokenList &tokList){
+	std::list<Token>::iterator endOfCommand = tokList.iteratorCopy();
 	while (endOfCommand!= tokList.end()){
 		if ((*endOfCommand).tokenType == COMMAND){
 			if (theCommand.compare((* endOfCommand).tokenString) == 0){
@@ -324,8 +322,8 @@ list<Token>::iterator getEndCommand(string theCommand, TokenList &tokList){
 /* A specialty method for commands such as \arg that end at the end of a paragraph OR when another \arg is encountered
  */
 //TODO getTilAnyCommand
-list<Token>::iterator getTilAnyCommand(string theCommand, TokenList &tokList){
-	list<Token>::iterator anIterator;
+std::list<Token>::iterator getTilAnyCommand(std::string theCommand, TokenList &tokList){
+	std::list<Token>::iterator anIterator;
 	return anIterator;
 	}
 
@@ -337,7 +335,7 @@ list<Token>::iterator getTilAnyCommand(string theCommand, TokenList &tokList){
  * Plain commands, such as newline etc, they contain no other data
  *  \n \\ \@ \& \$ \# \< \> \%
  */
- int addSimpleCommand(string theCommand, list <DoxygenEntity> &doxyList){
+ int addSimpleCommand(std::string theCommand, std::list <DoxygenEntity> &doxyList){
 		if (noisy) cout << "Parsing " << theCommand << endl;
 		doxyList.push_back(DoxygenEntity(theCommand));
 		return 1;
@@ -347,7 +345,7 @@ list<Token>::iterator getTilAnyCommand(string theCommand, TokenList &tokList){
   * Format: @command
   * Plain commands, such as newline etc, they contain no other data
   */
- int ignoreSimpleCommand(string theCommand, list <DoxygenEntity> &doxyList){
+ int ignoreSimpleCommand(std::string theCommand, std::list <DoxygenEntity> &doxyList){
 		if (noisy) cout << "Not Adding " << theCommand << endl;
 		return 1;
 		}
@@ -358,9 +356,9 @@ list<Token>::iterator getTilAnyCommand(string theCommand, TokenList &tokList){
   * "a", "b", "c", "e", "em", "p", "def", "enum", "example", "package", 
   * "relates", "namespace", "relatesalso","anchor", "dontinclude", "include", "includelineno"
   */
- int addCommandWord(string theCommand, TokenList &tokList, list <DoxygenEntity> &doxyList){
+ int addCommandWord(std::string theCommand, TokenList &tokList, std::list <DoxygenEntity> &doxyList){
 	if (noisy) cout << "Parsing " << theCommand << endl;
-	string name = getNextWord(tokList);
+	std::string name = getNextWord(tokList);
 	if (!name.empty()){ 
 		doxyList.push_back(DoxygenEntity(theCommand, name));
 		return 1;
@@ -374,9 +372,9 @@ list<Token>::iterator getTilAnyCommand(string theCommand, TokenList &tokList){
   * Commands with a single WORD after then such as @b
   * "copydoc", "copybrief", "copydetails", "verbinclude", "htmlinclude"
   */
- int ignoreCommandWord(string theCommand, TokenList &tokList, list <DoxygenEntity> &doxyList){
+ int ignoreCommandWord(std::string theCommand, TokenList &tokList, std::list <DoxygenEntity> &doxyList){
 	if (noisy) cout << "Not Adding " << theCommand << endl;
-	string name = getNextWord(tokList);
+	std::string name = getNextWord(tokList);
 	if (!name.empty()){ 
 		return 1;
 		}
@@ -389,10 +387,10 @@ list<Token>::iterator getTilAnyCommand(string theCommand, TokenList &tokList){
   * Commands with a single LINE after then such as @var
   * "addindex", "fn", "name", "line", "var", "skipline", "typedef", "skip", "until", "property"
   */
- int addCommandLine(string theCommand, TokenList &tokList, list <DoxygenEntity> &doxyList){
+ int addCommandLine(std::string theCommand, TokenList &tokList, std::list <DoxygenEntity> &doxyList){
 	if (noisy) cout << "Parsing " << theCommand << endl;
-	list<Token>::iterator endOfLine = getOneLine(tokList);
-	list <DoxygenEntity> aNewList;
+	std::list<Token>::iterator endOfLine = getOneLine(tokList);
+	std::list <DoxygenEntity> aNewList;
 	aNewList =  parse(endOfLine, tokList);
 	doxyList.push_back( DoxygenEntity(theCommand, aNewList));
 	return 1;
@@ -403,9 +401,9 @@ list<Token>::iterator getTilAnyCommand(string theCommand, TokenList &tokList){
   * Commands with a single LINE after then such as @var
   * 
   */
- int ignoreCommandLine(string theCommand, TokenList &tokList, list <DoxygenEntity> &doxyList){
+ int ignoreCommandLine(std::string theCommand, TokenList &tokList, std::list <DoxygenEntity> &doxyList){
 	if (noisy) cout << "Not Adding " << theCommand << endl;
-	list<Token>::iterator endOfLine = getOneLine(tokList);
+	std::list<Token>::iterator endOfLine = getOneLine(tokList);
 	tokList.setIterator(endOfLine);
 	return 1;
 }
@@ -416,10 +414,10 @@ list<Token>::iterator getTilAnyCommand(string theCommand, TokenList &tokList){
   * "return", "remarks", "since", "test", "sa", "see", "pre", "post", "details", "invariant", 
   * "deprecated", "date", "note", "warning", "version", "todo", "bug", "attention", "brief", "arg", "author"
   */
- int addCommandParagraph(string theCommand, TokenList &tokList, list <DoxygenEntity> &doxyList){
+ int addCommandParagraph(std::string theCommand, TokenList &tokList, std::list <DoxygenEntity> &doxyList){
 	if (noisy) cout << "Parsing " << theCommand << endl;
-	list<Token>::iterator endOfParagraph = getEndOfParagraph(tokList);
-	list <DoxygenEntity> aNewList;
+	std::list<Token>::iterator endOfParagraph = getEndOfParagraph(tokList);
+	std::list <DoxygenEntity> aNewList;
 	aNewList =  parse(endOfParagraph, tokList);
 	doxyList.push_back( DoxygenEntity(theCommand, aNewList));
 	return 1;
@@ -430,9 +428,9 @@ list<Token>::iterator getTilAnyCommand(string theCommand, TokenList &tokList){
   * Commands with a single LINE after then such as @var
   * 
   */
- int ignoreCommandParagraph(string theCommand, TokenList &tokList, list <DoxygenEntity> &doxyList){
+ int ignoreCommandParagraph(std::string theCommand, TokenList &tokList, std::list <DoxygenEntity> &doxyList){
 	if (noisy) cout << "Not Adding " << theCommand << endl;
-	list<Token>::iterator endOfParagraph = getEndOfParagraph(tokList);
+	std::list<Token>::iterator endOfParagraph = getEndOfParagraph(tokList);
 	tokList.setIterator(endOfParagraph);
 	return 1;
 }
@@ -444,9 +442,9 @@ list<Token>::iterator getTilAnyCommand(string theCommand, TokenList &tokList){
   * "verbatim", "xmlonly", "cond", "if", "ifnot", "link"
   * Returns 1 if success, 0 if the endcommand is never encountered.
   */
- int addCommandEndCommand(string theCommand, TokenList &tokList, list <DoxygenEntity> &doxyList){
+ int addCommandEndCommand(std::string theCommand, TokenList &tokList, std::list <DoxygenEntity> &doxyList){
 	  if (noisy) cout << "Not Adding " << theCommand << endl;
-	  string description = getStringTilEndCommand( "end" + theCommand, tokList);
+	  std::string description = getStringTilEndCommand( "end" + theCommand, tokList);
 	  doxyList.push_back(DoxygenEntity(theCommand, description));
 	  return 1;
 	  }
@@ -456,17 +454,17 @@ list<Token>::iterator getTilAnyCommand(string theCommand, TokenList &tokList){
   * Commands such as param
   * "param", "tparam", "throw", "retval", "exception"
   */
- int addCommandWordParagraph(string theCommand, TokenList &tokList, list <DoxygenEntity> &doxyList){
+ int addCommandWordParagraph(std::string theCommand, TokenList &tokList, std::list <DoxygenEntity> &doxyList){
 	if (noisy) cout << "Parsing " << theCommand << endl;
-	string name = getNextWord(tokList);
+	std::string name = getNextWord(tokList);
 	if (name.empty()){ 
 		cout << "No word followed " << theCommand <<  " command. Not added" << endl;
 		return 0;
 		}
-	list<Token>::iterator endOfParagraph = getEndOfParagraph(tokList);
-	list <DoxygenEntity> aNewList;
+	std::list<Token>::iterator endOfParagraph = getEndOfParagraph(tokList);
+	std::list <DoxygenEntity> aNewList;
 	aNewList =  parse(endOfParagraph, tokList);
-	aNewList.push_front(DoxygenEntity("plainstring", name));
+	aNewList.push_front(DoxygenEntity("plainstd::string", name));
 	doxyList.push_back(DoxygenEntity(theCommand, aNewList));
 	return 1;
 	}
@@ -476,17 +474,17 @@ list<Token>::iterator getTilAnyCommand(string theCommand, TokenList &tokList){
   * Commands such as param
   * "page", "subsection", "subsubsection", "section", "paragraph", "defgroup"
   */
- int addCommandWordLine(string theCommand, TokenList &tokList, list <DoxygenEntity> &doxyList){
+ int addCommandWordLine(std::string theCommand, TokenList &tokList, std::list <DoxygenEntity> &doxyList){
 	if (noisy) cout << "Parsing " << theCommand << endl;
-	string name = getNextWord(tokList);
+	std::string name = getNextWord(tokList);
 	if (name.empty()){ 
 		cout << "No word followed " << theCommand <<  " command. Not added" << endl;
 		return 0;
 		}
-	list<Token>::iterator endOfLine = getOneLine(tokList);
-	list <DoxygenEntity> aNewList;
+	std::list<Token>::iterator endOfLine = getOneLine(tokList);
+	std::list <DoxygenEntity> aNewList;
 	aNewList =  parse(endOfLine, tokList);
-	aNewList.push_front(DoxygenEntity("plainstring", name));
+	aNewList.push_front(DoxygenEntity("plainstd::string", name));
 	doxyList.push_back(DoxygenEntity(theCommand, aNewList));
 	return 1;
 		
@@ -498,19 +496,19 @@ list<Token>::iterator getTilAnyCommand(string theCommand, TokenList &tokList){
   * Commands such as class
   * "category", "class", "protocol", "interface", "struct", "union"
   */
- int addCommandWordOWordOWord(string theCommand, TokenList &tokList, list <DoxygenEntity> &doxyList){
+ int addCommandWordOWordOWord(std::string theCommand, TokenList &tokList, std::list <DoxygenEntity> &doxyList){
 	if (noisy) cout << "Parsing " << theCommand << endl;
-	string name = getNextWord(tokList);
+	std::string name = getNextWord(tokList);
 	if (name.empty()){ 
 			cout << "No word followed " << theCommand <<  " command. Not added" << endl;
 			return 0;
 			}
-	string headerfile = getNextWord(tokList);
-	string headername = getNextWord(tokList);
-	list <DoxygenEntity> aNewList;
-	aNewList.push_back(DoxygenEntity("plainstring", name));
-	if (!headerfile.empty()) aNewList.push_back(DoxygenEntity("plainstring", headerfile));
-	if (!headername.empty()) aNewList.push_back(DoxygenEntity("plainstring", headername));
+	std::string headerfile = getNextWord(tokList);
+	std::string headername = getNextWord(tokList);
+	std::list <DoxygenEntity> aNewList;
+	aNewList.push_back(DoxygenEntity("plainstd::string", name));
+	if (!headerfile.empty()) aNewList.push_back(DoxygenEntity("plainstd::string", headerfile));
+	if (!headername.empty()) aNewList.push_back(DoxygenEntity("plainstd::string", headername));
 	doxyList.push_back(DoxygenEntity(theCommand, aNewList));
 	return 1;
 	}
@@ -520,9 +518,9 @@ list<Token>::iterator getTilAnyCommand(string theCommand, TokenList &tokList){
   * Commands such as dir
   * "dir", "file", "cond"
   */
- int addCommandOWord(string theCommand, TokenList &tokList, list <DoxygenEntity> &doxyList){
+ int addCommandOWord(std::string theCommand, TokenList &tokList, std::list <DoxygenEntity> &doxyList){
 	if (noisy) cout << "Parsing " << theCommand << endl;
-	string name = getNextWord(tokList);
+	std::string name = getNextWord(tokList);
 	doxyList.push_back(DoxygenEntity(theCommand, name));
 	return 1; 
  }
@@ -530,47 +528,47 @@ list<Token>::iterator getTilAnyCommand(string theCommand, TokenList &tokList){
  /* Commands that should not be encountered (such as PHP only)
   * goes til the end of line then returns
   */
- int addCommandErrorThrow(string theCommand, TokenList &tokList, list <DoxygenEntity> &doxyList){
+ int addCommandErrorThrow(std::string theCommand, TokenList &tokList, std::list <DoxygenEntity> &doxyList){
 	  cout << "Encountered :" << theCommand << endl;
 	  cout << "This command should not have been encountered. Behaviour past this may be unpredictable " << endl;
-	  list<Token>::iterator endOfLine = getOneLine(tokList);
+	  std::list<Token>::iterator endOfLine = getOneLine(tokList);
 	  tokList.setIterator(endOfLine);
 	  return 0;
  }
 
 /* Adds the unique commands- different process for each unique command */
- int addCommandUnique(string theCommand, TokenList &tokList, list <DoxygenEntity> &doxyList){
-	  list <DoxygenEntity> aNewList;
+ int addCommandUnique(std::string theCommand, TokenList &tokList, std::list <DoxygenEntity> &doxyList){
+	  std::list <DoxygenEntity> aNewList;
 	  if (theCommand.compare("arg") == 0 || theCommand.compare("li") == 0){
-			list<Token>::iterator endOfSection = getEndOfSection(theCommand, tokList);
-			list <DoxygenEntity> aNewList;
+			std::list<Token>::iterator endOfSection = getEndOfSection(theCommand, tokList);
+			std::list <DoxygenEntity> aNewList;
 			aNewList =  parse(endOfSection, tokList);
 			doxyList.push_back( DoxygenEntity(theCommand, aNewList));
 			}
-	  // \xrefitem <key> "(heading)" "(list title)" {text}
+	  // \xrefitem <key> "(heading)" "(std::list title)" {text}
 	  else if (theCommand.compare("xrefitem") == 0){
 		  //TODO Implement xrefitem
 			if (noisy) cout << "Not Adding " << theCommand << endl;
-			list<Token>::iterator endOfParagraph = getEndOfParagraph(tokList);
+			std::list<Token>::iterator endOfParagraph = getEndOfParagraph(tokList);
 			tokList.setIterator(endOfParagraph);
 		  return 1;
 		  }
 	  // \ingroup (<groupname> [<groupname> <groupname>])
 	  else if (theCommand.compare("ingroup") == 0){
-		  string name = getNextWord(tokList);
-		  aNewList.push_back(DoxygenEntity("plainstring", name));
+		  std::string name = getNextWord(tokList);
+		  aNewList.push_back(DoxygenEntity("plainstd::string", name));
 		  name = getNextWord(tokList);
-		  if(!name.empty()) aNewList.push_back(DoxygenEntity("plainstring", name));
+		  if(!name.empty()) aNewList.push_back(DoxygenEntity("plainstd::string", name));
 		  name = getNextWord(tokList);
-		  if(!name.empty()) aNewList.push_back(DoxygenEntity("plainstring", name));
+		  if(!name.empty()) aNewList.push_back(DoxygenEntity("plainstd::string", name));
 		  doxyList.push_back(DoxygenEntity(theCommand, aNewList));
 		  return 1;
 		  }
 	  // \par [(paragraph title)] { paragraph }
 	  else if (theCommand.compare("par") == 0){
-		  list<Token>::iterator endOfLine = getOneLine(tokList);
+		  std::list<Token>::iterator endOfLine = getOneLine(tokList);
 		  aNewList =  parse(endOfLine, tokList);
-		  list <DoxygenEntity> aNewList2;
+		  std::list <DoxygenEntity> aNewList2;
 		  aNewList2 = parse(endOfLine, tokList);
 		  aNewList.splice(aNewList.end(), aNewList2);
 		  doxyList.push_back(DoxygenEntity(theCommand, aNewList));
@@ -578,19 +576,19 @@ list<Token>::iterator getTilAnyCommand(string theCommand, TokenList &tokList){
 		  }
 	  // \headerfile <header-file> [<header-name>]
 	  else if (theCommand.compare("headerfile") == 0){
-		  list <DoxygenEntity> aNewList;
-		  string name = getNextWord(tokList);
-		  aNewList.push_back(DoxygenEntity("plainstring", name));
+		  std::list <DoxygenEntity> aNewList;
+		  std::string name = getNextWord(tokList);
+		  aNewList.push_back(DoxygenEntity("plainstd::string", name));
 		  name = getNextWord(tokList);
-		  if(!name.empty()) aNewList.push_back(DoxygenEntity("plainstring", name));
+		  if(!name.empty()) aNewList.push_back(DoxygenEntity("plainstd::string", name));
 		  doxyList.push_back(DoxygenEntity(theCommand, aNewList));
 		  return 1;
 		  }
 	  // \overload [(function declaration)]
 	  else if (theCommand.compare("overload") == 0){
-		  list<Token>::iterator endOfLine = getOneLine(tokList);
+		  std::list<Token>::iterator endOfLine = getOneLine(tokList);
 		  if (endOfLine != tokList.current()){
-		    list <DoxygenEntity> aNewList;
+		    std::list <DoxygenEntity> aNewList;
 		    aNewList =  parse(endOfLine, tokList);
 		    doxyList.push_back(DoxygenEntity(theCommand, aNewList));
 		    }
@@ -600,38 +598,38 @@ list<Token>::iterator getTilAnyCommand(string theCommand, TokenList &tokList){
 	  // \weakgroup <name> [(title)]
 	  else if (theCommand.compare("weakgroup") == 0){
 		    if (noisy) cout << "Parsing " << theCommand << endl;
-			string name = getNextWord(tokList);
+			std::string name = getNextWord(tokList);
 			if (name.empty()){ 
 				cout << "No word followed " << theCommand <<  " command. Not added" << endl;
 				return 0;
 				}
-			list <DoxygenEntity> aNewList;
-			list<Token>::iterator endOfLine = getOneLine(tokList);
+			std::list <DoxygenEntity> aNewList;
+			std::list<Token>::iterator endOfLine = getOneLine(tokList);
 			if (endOfLine != tokList.current()) {
 				aNewList =  parse(endOfLine, tokList);
 				}
-			aNewList.push_front(DoxygenEntity("plainstring", name));
+			aNewList.push_front(DoxygenEntity("plainstd::string", name));
 			doxyList.push_back(DoxygenEntity(theCommand, aNewList));
 			}
 	  // \ref <name> ["(text)"]
 	  else if (theCommand.compare("ref") == 0){
 		  //TODO Implement ref
 			if (noisy) cout << "Not Adding " << theCommand << endl;
-			list<Token>::iterator endOfParagraph = getEndOfParagraph(tokList);
+			std::list<Token>::iterator endOfParagraph = getEndOfParagraph(tokList);
 			tokList.setIterator(endOfParagraph);
 			}
 	  // \subpage <name> ["(text)"]
 	  else if (theCommand.compare("subpage") == 0){
 		  //TODO implement subpage
 			if (noisy) cout << "Not Adding " << theCommand << endl;
-			list<Token>::iterator endOfParagraph = getEndOfParagraph(tokList);
+			std::list<Token>::iterator endOfParagraph = getEndOfParagraph(tokList);
 			tokList.setIterator(endOfParagraph);
 			}
 	  // \dotfile <file> ["caption"]
 	  else if (theCommand.compare("dotfile") == 0){
 		  //TODO implement dotfile
 			if (noisy) cout << "Not Adding " << theCommand << endl;
-			list<Token>::iterator endOfParagraph = getEndOfParagraph(tokList);
+			std::list<Token>::iterator endOfParagraph = getEndOfParagraph(tokList);
 			tokList.setIterator(endOfParagraph);
 			}
 	  // \image <format> <file> ["caption"] [<sizeindication>=<size>]
@@ -641,17 +639,17 @@ list<Token>::iterator getTilAnyCommand(string theCommand, TokenList &tokList){
 	  // \addtogroup <name> [(title)]
 	  else if (theCommand.compare("addtogroup") == 0){
 		    if (noisy) cout << "Parsing " << theCommand << endl;
-			string name = getNextWord(tokList);
+			std::string name = getNextWord(tokList);
 			if (name.empty()){ 
 				cout << "No word followed " << theCommand <<  " command. Not added" << endl;
 				return 0;
 				}
-			list <DoxygenEntity> aNewList;
-			list<Token>::iterator endOfLine = getOneLine(tokList);
+			std::list <DoxygenEntity> aNewList;
+			std::list<Token>::iterator endOfLine = getOneLine(tokList);
 			if (endOfLine != tokList.current()) {
 				aNewList =  parse(endOfLine, tokList);
 				}
-			aNewList.push_front(DoxygenEntity("plainstring", name));
+			aNewList.push_front(DoxygenEntity("plainstd::string", name));
 			doxyList.push_back(DoxygenEntity(theCommand, aNewList));
 			}
 	  return 0;
@@ -663,12 +661,12 @@ list<Token>::iterator getTilAnyCommand(string theCommand, TokenList &tokList){
  */
 
 
-int addCommand(string commandString, TokenList &tokList,list <DoxygenEntity> &doxyList){
-	 string theCommand = StringToLower(commandString);
-	 if (theCommand.compare("plainstring") == 0){
-	 		string nextPhrase = getStringTilCommand( tokList);
-	 		if (noisy) cout << "Parsing plain string :" << nextPhrase << endl;
-	 		doxyList.push_back(DoxygenEntity("plainstring", nextPhrase ));
+int addCommand(std::string commandString, TokenList &tokList,std::list <DoxygenEntity> &doxyList){
+	 std::string theCommand = StringToLower(commandString);
+	 if (theCommand.compare("plainstd::string") == 0){
+	 		std::string nextPhrase = getStringTilCommand( tokList);
+	 		if (noisy) cout << "Parsing plain std::string :" << nextPhrase << endl;
+	 		doxyList.push_back(DoxygenEntity("plainstd::string", nextPhrase ));
 	 		return 1;
 	 		}
 	 int commandNumber = commandBelongs(theCommand);
@@ -721,8 +719,8 @@ int addCommand(string commandString, TokenList &tokList,list <DoxygenEntity> &do
 	 return 0;
 	 }
 
-list<DoxygenEntity> parse(list<Token>::iterator endParsingIndex, TokenList &tokList){
-	list <DoxygenEntity> aNewList;
+std::list<DoxygenEntity> parse(std::list<Token>::iterator endParsingIndex, TokenList &tokList){
+	std::list <DoxygenEntity> aNewList;
 	int currCommand;
 	while (tokList.current() != endParsingIndex){ 
 		Token currToken = tokList.peek();
@@ -735,22 +733,22 @@ list<DoxygenEntity> parse(list<Token>::iterator endParsingIndex, TokenList &tokL
 			if (currCommand < 0 ){
 				if(noisy) cout << "Unidentified Command " << currToken.tokenString << endl;
 				tokList.next();
-				addCommand(string("plainstring"), tokList, aNewList);}
+				addCommand(std::string("plainstd::string"), tokList, aNewList);}
 				//cout << "Command: " << currWord << " " << currCommand << endl;
 			else { tokList.next();
 			  addCommand(currToken.tokenString, tokList,  aNewList);
 			  }
 			}
 		else if (currToken.tokenType == PLAINSTRING){
-			addCommand(string("plainstring"), tokList, aNewList);
+			addCommand(std::string("plainstd::string"), tokList, aNewList);
 			}
 		else break;
 		}
 	return aNewList;
 	}
 
-list<DoxygenEntity> parseRoot(list<Token>::iterator endParsingIndex, TokenList &tokList){
-	list <DoxygenEntity> aNewList;
+std::list<DoxygenEntity> parseRoot(std::list<Token>::iterator endParsingIndex, TokenList &tokList){
+	std::list <DoxygenEntity> aNewList;
 	int currCommand;
 	while (tokList.current() != endParsingIndex){ 
 		Token currToken = tokList.peek();
@@ -763,26 +761,26 @@ list<DoxygenEntity> parseRoot(list<Token>::iterator endParsingIndex, TokenList &
 			if (currCommand < 0 ){ 
 				if(noisy) cout << "Unidentified Command " << currToken.tokenString << endl;
 				tokList.next();
-				addCommand(string("partofdescription"), tokList, aNewList);}
+				addCommand(std::string("partofdescription"), tokList, aNewList);}
 				//cout << "Command: " << currWord << " " << currCommand << endl;
 			else { tokList.next();
 			  addCommand(currToken.tokenString, tokList,  aNewList);
 			  }
 			}
 		else if (currToken.tokenType == PLAINSTRING){
-			addCommand(string("partofdescription"), tokList, aNewList);
+			addCommand(std::string("partofdescription"), tokList, aNewList);
 			}
 		}
 	return aNewList;
 	}
 
-list<DoxygenEntity> DoxygenParser::createTree(string doxygenBlob){
+std::list<DoxygenEntity> DoxygenParser::createTree(std::string doxygenBlob){
 	TokenList tokList = TokenList(doxygenBlob);
 	if(noisy) {
 		cout << "---TOKEN LIST---" << endl;
 		tokList.printList();
 		}
-	list <DoxygenEntity> rootList;
+	std::list <DoxygenEntity> rootList;
 	rootList = parseRoot( tokList.end(), tokList);
 	if(noisy) {
 		cout << "PARSED LIST" << endl;
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.h b/Source/DoxygenTranslator/src/DoxygenParser.h
index 638fdab72..2269e6788 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.h
+++ b/Source/DoxygenTranslator/src/DoxygenParser.h
@@ -6,9 +6,9 @@
 class DoxygenParser
 {
 public:
-	DoxygenParser();
-	virtual ~DoxygenParser();
-	list <DoxygenEntity> createTree(string doxygen);
+  DoxygenParser();
+  virtual ~DoxygenParser();
+  std::list <DoxygenEntity> createTree(std::string doxygen);
 };
 
 #endif /*DOXYGENPARSER_H_*/
diff --git a/Source/DoxygenTranslator/src/DoxygenTranslator.cpp b/Source/DoxygenTranslator/src/DoxygenTranslator.cpp
index 7fe2897c5..fc74c5c20 100644
--- a/Source/DoxygenTranslator/src/DoxygenTranslator.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenTranslator.cpp
@@ -24,69 +24,20 @@ DoxygenTranslator::~DoxygenTranslator(){
 
 char *DoxygenTranslator::convert(Node *n, char* doxygenBlob, char* option){
 	
-	list <DoxygenEntity> rootList = doxyParse.createTree(string(doxygenBlob));
+  std::list <DoxygenEntity> rootList = doxyParse.createTree(std::string(doxygenBlob));
+  std::string returnedString;
+  
+  if(strcmp(option, "JAVADOC") == 0)
+    returnedString = jDC.convertToJavaDoc(n, rootList);
+  else if(strcmp(option, "PYDOC") == 0)
+    returnedString = pyDC.convertToPyDoc(n, rootList);
+  else 
+    std::cout << "Option not current supported." << std::endl;
 	
-	string returnedString;
-	if(strcmp(option, "JAVADOC") == 0){
-	    returnedString = jDC.convertToJavaDoc(n, rootList);
-	}
-	else if(strcmp(option, "PYDOC") == 0){
-	    returnedString = pyDC.convertToPyDoc(n, rootList);
-	}
-	else cout << "Option not current supported.\n";
-	char *nonConstString;
-	nonConstString = (char *)malloc(returnedString.length() + 1);
-	strcpy(nonConstString, returnedString.c_str());
-	return nonConstString;
+  char *nonConstString;
+  nonConstString = (char *)malloc(returnedString.length() + 1);
+  strcpy(nonConstString, returnedString.c_str());
+  
+  return nonConstString;
 }
 
-int testCommands(){
-	string exampleArray[] = {
-	"/**\n * Random Line \n * \\@ \n * Random Line After */",
-	"/**\n *  Random Line Before \n * \n * \\b bold \n * Random Line After */",
-	"/**\n *  Random Line \n * \n *\\copydoc bold \n * Random Line After */",
-	"/**\n *  Random Line \n * \n * \\addindex An Entire Line\n * \\addindex An Entire Line\n * Random Line After */",
-	"/**\n *  Random Line \n * \n * \\return An Entire Paragraph \n * Including This Line \n * \n * Random Line After */",
-	"/**\n *  Random Line \n * \n * \\return An Entire Paragraph \n * Including This Line \n * \\author Shouldn't be part of return */",
-	"/**\n *  Random Line \n * \n * \\code this should continue \n * until here \\endcode \n * Random Line After */",
-	"/**\n *  Random Line \n * \n * \\param singleword then the rest of \n *  the description \n * \n * Random Line After */",
-	"/**\n *  Random Line \n * \n * \\page  singleword this should go til here \n * but not this */",
-	"/**\n *  Random Line \n * \n * \\page  singleword this should go til here \n * but not this */",
-	"/**\n *  Random Line \n * \n * \\category  singleword \n * but not this */",
-	"/**\n *  Random Line \n * \n * \\category  singleword oneword \n * but not this */",
-	"/**\n *  Random Line \n * \n * \\category  singleword oneword twoword \n * but not this */",
-	"/**\n *  Random Line \n * \n * \\dir singleword \n * but not this */",
-	"/**\n *  Random Line \n * \n * \\dir \n * but not this */",
-	"/**\n *  Random Line \n * \n * \\fakecommand details \n * but not this */"
-	};
-	//string exampleArrayUniques = {};
-	DoxygenTranslator dT = DoxygenTranslator();
-	for (int i = 0; i < 16; i ++ ){
-		//cout << "---ORIGINAL DOXYGEN--- " << endl << exampleArray[i] << endl;
-		char *nonConstString = (char *)malloc(exampleArray[i].length()+1);
-		strcpy(nonConstString, exampleArray[i].c_str());
-		char * result = dT.convert(NULL, nonConstString, "JAVADOC");
-		free(nonConstString);
-		free(result);
-	}
-	return 1;
-}
-
-//int main(int argc, char *argv[]){
-	//string doxygenString1 = "//! \\brief a brief description \n\n A normal member taking two arguments and returning an \\b integer value. This is a very long description for the simple purpose of showing off formatting. Let's make it a bit longer just to be sure. \n/*!\n \\param a an \\b integer argument.\n \\return The test results\n \\param s a constant character pointer. Let's also make this a very long description! \n \\bug this command should, for now, be totally ignored\n \\author cheryl foil\n \\sa Test(), ~Test(), testMeToo() and publicVar()\n */";
-	//cout << "---ORIGINAL DOXYGEN--- " << endl << doxygenString1 << endl;
-	//char *nonConstString = (char *)malloc(doxygenString1.length()+1);
-	//strcpy(nonConstString, doxygenString1.c_str());
-	//DoxygenTranslator dT = DoxygenTranslator();
-	//char *result = dT.convert("/**\n * \n * Random Line \n * \n * \\name An Entire Line \n * NOT This Line \n * \n * Random Line After */", "JAVADOC");
-	//result = dT.convert(nonConstString, "JAVADOC");
-	//cout << "End";
-	//list <DoxygenEntity> rootList = doxyParse.createTree(doxygenString1);
-    //JavaDocConverter jDC = JavaDocConverter();
-    //jDC.convertToJavaDoc(rootList);
-	//testCommands();
-	//return 1;
-//}
-
-
-
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.cpp b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
index b611cddf9..dbf606bfd 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
@@ -12,227 +12,152 @@ JavaDocConverter::~JavaDocConverter()
 {
 }
 
-/* Sorts entities by javaDoc standard order for commands
- * NOTE: will not behave entirely properly until "First level" comments
- * such as brief descriptions are TAGGED as such
- */
-bool compare_DoxygenEntities(DoxygenEntity first, DoxygenEntity second){
-	if(first.typeOfEntity.compare("brief") == 0) return true;
-	if(second.typeOfEntity.compare("brief") == 0) return false;
-	if(first.typeOfEntity.compare("details") == 0) return true;
-	if(second.typeOfEntity.compare("details") == 0) return false;
-	if(first.typeOfEntity.compare("partofdescription") == 0) return true;
-	if(first.typeOfEntity.compare("partofdescription") == 0) return false;
-	if(first.typeOfEntity.compare("plainstring") == 0) return true;
-	if(second.typeOfEntity.compare("plainstring") == 0) return false;
-	if(first.typeOfEntity.compare("param") == 0){
-		if(second.typeOfEntity.compare("param")== 0) return true;
-		if(second.typeOfEntity.compare("return")== 0) return true;
-		if(second.typeOfEntity.compare("exception")== 0) return true;
-		if(second.typeOfEntity.compare("author")== 0) return true;
-		if(second.typeOfEntity.compare("version")== 0)return true;
-		if(second.typeOfEntity.compare("see")== 0)return true;
-		if(second.typeOfEntity.compare("since")== 0)return true;
-		if(second.typeOfEntity.compare("deprecated")== 0)return true;
-		return false;
-	}
-	if(first.typeOfEntity.compare("return")== 0){
-		if(second.typeOfEntity.compare("return")== 0) return true;
-		if(second.typeOfEntity.compare("exception")== 0) return true;
-		if(second.typeOfEntity.compare("author")== 0) return true;
-		if(second.typeOfEntity.compare("version")== 0)return true;
-		if(second.typeOfEntity.compare("see")== 0)return true;
-		if(second.typeOfEntity.compare("since")== 0)return true;
-		if(second.typeOfEntity.compare("deprecated")== 0)return true;
-		return false;
-
-	}
-	if(first.typeOfEntity.compare("exception")== 0){
-		if(second.typeOfEntity.compare("exception")== 0) return true;
-		if(second.typeOfEntity.compare("author")== 0) return true;
-		if(second.typeOfEntity.compare("version")== 0)return true;
-		if(second.typeOfEntity.compare("see")== 0)return true;
-		if(second.typeOfEntity.compare("since")== 0)return true;
-		if(second.typeOfEntity.compare("deprecated")== 0)return true;
-		return false;
-	}
-	if(first.typeOfEntity.compare("author")== 0){
-		if(second.typeOfEntity.compare("author")== 0) return true;
-		if(second.typeOfEntity.compare("version")== 0)return true;
-		if(second.typeOfEntity.compare("see")== 0)return true;
-		if(second.typeOfEntity.compare("since")== 0)return true;
-		if(second.typeOfEntity.compare("deprecated")== 0)return true;
-		return false;
-	}
-	if(first.typeOfEntity.compare("version")== 0){
-		if(second.typeOfEntity.compare("version")== 0)return true;
-		if(second.typeOfEntity.compare("see")== 0)return true;
-		if(second.typeOfEntity.compare("since")== 0)return true;
-		if(second.typeOfEntity.compare("deprecated")== 0)return true;
-		return false;
-	}
-	if(first.typeOfEntity.compare("see")== 0 || first.typeOfEntity.compare("sa")== 0){
-		if(second.typeOfEntity.compare("see")== 0)return true;
-		if(second.typeOfEntity.compare("sa")== 0)return true;
-		if(second.typeOfEntity.compare("since")== 0)return true;
-		if(second.typeOfEntity.compare("deprecated")== 0)return true;
-		return false;
-	}
-	if(first.typeOfEntity.compare("since")== 0){
-		if(second.typeOfEntity.compare("since")== 0) return true;
-		if(second.typeOfEntity.compare("deprecated")== 0)return true;
-		return false;
-	}
-	if(first.typeOfEntity.compare("deprecated")== 0){
-		if(second.typeOfEntity.compare("deprecated")== 0)return true;
-		return false;
-	}
-	return true;
+void JavaDocConverter::printSortedTree(std::list<DoxygenEntity> &entityList){
+  std::list<DoxygenEntity>::iterator p = entityList.begin();
+  while (p != entityList.end()){
+    (*p).printEntity(0);
+    p++;
+  }
 }
 
-void JavaDocConverter::printSortedTree(list <DoxygenEntity> &entityList){
-	list<DoxygenEntity>::iterator p = entityList.begin();
-	while (p != entityList.end()){
-		(*p).printEntity(0);
-		p++;
-	}
-}
-string formatCommand(string unformattedLine, int indent){
-	string formattedLines = "\n * ";
-	int lastPosition = 0;
-	int i = 0;
-	int isFirstLine  = 1;
-	while (i != -1 && i < unformattedLine.length()){
-		lastPosition = i;
-		if (isFirstLine){
-			i+=APPROX_LINE_LENGTH;
-		}
-		else i+=APPROX_LINE_LENGTH - indent*TAB_SIZE;
-		i = unformattedLine.find(" ", i);
+std::string formatCommand(std::string unformattedLine, int indent){
+  std::string formattedLines = "\n * ";
+  int lastPosition = 0;
+  int i = 0;
+  int isFirstLine  = 1;
+  while (i != -1 && i < unformattedLine.length()){
+    lastPosition = i;
+    if (isFirstLine){
+      i+=APPROX_LINE_LENGTH;
+    }
+    else i+=APPROX_LINE_LENGTH - indent*TAB_SIZE;
+    i = unformattedLine.find(" ", i);
 
-		if (i > 0 && i + 1 < unformattedLine.length()){
-			if (!isFirstLine) for (int j = 0; j < indent; j++) {
-				formattedLines.append("\t");
-				}
-			else {
-				isFirstLine = 0;
-			}
-			formattedLines.append(unformattedLine.substr(lastPosition, i - lastPosition + 1));
-			formattedLines.append("\n *");
+    if (i > 0 && i + 1 < unformattedLine.length()){
+      if (!isFirstLine) for (int j = 0; j < indent; j++) {
+        formattedLines.append("\t");
+        }
+      else {
+        isFirstLine = 0;
+      }
+      formattedLines.append(unformattedLine.substr(lastPosition, i - lastPosition + 1));
+      formattedLines.append("\n *");
 
-		}
-	}
-	if (lastPosition < unformattedLine.length()){
-		if (!isFirstLine) {for (int j = 0; j < indent; j++) {formattedLines.append("\t");}}
-		formattedLines.append(unformattedLine.substr(lastPosition, unformattedLine.length() - lastPosition));
-	}
+    }
+  }
+  if (lastPosition < unformattedLine.length()){
+    if (!isFirstLine) {for (int j = 0; j < indent; j++) {formattedLines.append("\t");}}
+    formattedLines.append(unformattedLine.substr(lastPosition, unformattedLine.length() - lastPosition));
+  }
 
-	return formattedLines;
+  return formattedLines;
 }
 
 /* Contains the conversions for tags
  * could probably be much more efficient...
  */
-string javaDocFormat(DoxygenEntity &doxygenEntity){
-	if(doxygenEntity.typeOfEntity.compare("partofdescription") == 0){
-				return doxygenEntity.data;
-		}
-	if (doxygenEntity.typeOfEntity.compare("plainstring") == 0){
-			return  doxygenEntity.data;
-	}
-	else if (doxygenEntity.typeOfEntity.compare("b") == 0){
-		return "<b>" + doxygenEntity.data + "</b>";
-	}
-	else if (doxygenEntity.typeOfEntity.compare("c") == 0){
-		return "<tt>" + doxygenEntity.data + "</tt>";
-	}
-	else if (doxygenEntity.typeOfEntity.compare("@") == 0){
-		return "@";
-	}
-	else if (doxygenEntity.typeOfEntity.compare("\\") == 0){
-		return "\\";
-	}
-	else if (doxygenEntity.typeOfEntity.compare("<") == 0){
-		return "&lt;";
-	}
-	else if (doxygenEntity.typeOfEntity.compare(">") == 0){
-		return "&gt;";
-	}
-	else if (doxygenEntity.typeOfEntity.compare("&") == 0){
-		return "&amp;";
-	}
-	else if (doxygenEntity.typeOfEntity.compare("#") == 0){
-		return "#";
-	}
-	else if (doxygenEntity.typeOfEntity.compare("%") == 0){
-		return "%";
-	}
-	else if (doxygenEntity.typeOfEntity.compare("~") == 0){
-		return "~";
-	}
-	return "";
-}
-
-
-string translateSubtree( DoxygenEntity &doxygenEntity){
-	string returnedString;
-	if (doxygenEntity.isLeaf){ return javaDocFormat(doxygenEntity) + " ";}
-	else {
-		returnedString += javaDocFormat(doxygenEntity);
-		list<DoxygenEntity>::iterator p = doxygenEntity.entityList.begin();
-		while (p != doxygenEntity.entityList.end()){
-			returnedString+= translateSubtree(*p);
-			p++;
-		}
-	}
-	return returnedString;
-}
-
-string translateEntity(DoxygenEntity &doxyEntity){
-	if(doxyEntity.typeOfEntity.compare("partofdescription")== 0) return formatCommand(string(translateSubtree(doxyEntity)), 0);
-	if ((doxyEntity.typeOfEntity.compare("brief") == 0)||(doxyEntity.typeOfEntity.compare("details") == 0)){
-		return formatCommand(string(translateSubtree(doxyEntity)), 0) + "\n * ";}
-	else if(doxyEntity.typeOfEntity.compare("plainstring")== 0 || doxyEntity.typeOfEntity.compare("deprecated")== 0 || doxyEntity.typeOfEntity.compare("brief")== 0)
-		return formatCommand(doxyEntity.data, 0) + "\n * ";
-	else if(doxyEntity.typeOfEntity.compare("see") == 0){
-		return formatCommand(string("@" + doxyEntity.typeOfEntity + "\t\t" + translateSubtree(doxyEntity)), 2);
-	}
-	else if(doxyEntity.typeOfEntity.compare("return")== 0
-			|| doxyEntity.typeOfEntity.compare("author")== 0
-			|| doxyEntity.typeOfEntity.compare("param")== 0
-			|| doxyEntity.typeOfEntity.compare("since")== 0
-			|| doxyEntity.typeOfEntity.compare("version")== 0
-			|| doxyEntity.typeOfEntity.compare("exception") == 0
-			|| doxyEntity.typeOfEntity.compare("deprecated") == 0){
-		return formatCommand(string("@" + doxyEntity.typeOfEntity + "\t" + translateSubtree(doxyEntity)), 2);
-	}
-	else if(doxyEntity.typeOfEntity.compare("sa")== 0){
-		return formatCommand(string("@see\t\t" + translateSubtree(doxyEntity)), 2);
-	}
-	else return formatCommand(javaDocFormat(doxyEntity), 0 );
-	return "";
-}
-
-string JavaDocConverter:: convertToJavaDoc(Node *n, list <DoxygenEntity> entityList){
-
-
-	entityList.sort(compare_DoxygenEntities);
-    if(printSortedTree2){
-	cout << "---RESORTED LIST---" << endl;
-    printSortedTree(entityList);
+std::string javaDocFormat(DoxygenEntity &doxygenEntity){
+  if(doxygenEntity.typeOfEntity.compare("partofdescription") == 0){
+        return doxygenEntity.data;
     }
+  if (doxygenEntity.typeOfEntity.compare("plainstring") == 0){
+      return  doxygenEntity.data;
+  }
+  else if (doxygenEntity.typeOfEntity.compare("b") == 0){
+    return "<b>" + doxygenEntity.data + "</b>";
+  }
+  else if (doxygenEntity.typeOfEntity.compare("c") == 0){
+    return "<tt>" + doxygenEntity.data + "</tt>";
+  }
+  else if (doxygenEntity.typeOfEntity.compare("@") == 0){
+    return "@";
+  }
+  else if (doxygenEntity.typeOfEntity.compare("\\") == 0){
+    return "\\";
+  }
+  else if (doxygenEntity.typeOfEntity.compare("<") == 0){
+    return "&lt;";
+  }
+  else if (doxygenEntity.typeOfEntity.compare(">") == 0){
+    return "&gt;";
+  }
+  else if (doxygenEntity.typeOfEntity.compare("&") == 0){
+    return "&amp;";
+  }
+  else if (doxygenEntity.typeOfEntity.compare("#") == 0){
+    return "#";
+  }
+  else if (doxygenEntity.typeOfEntity.compare("%") == 0){
+    return "%";
+  }
+  else if (doxygenEntity.typeOfEntity.compare("~") == 0){
+    return "~";
+  }
+  return "";
+}
 
-	string javaDocString = "/**";
 
-	list<DoxygenEntity>::iterator entityIterator = entityList.begin();
-	while (entityIterator != entityList.end()){
-		javaDocString += translateEntity(*entityIterator);
-		entityIterator++;
-	}
+std::string translateSubtree( DoxygenEntity &doxygenEntity){
+  std::string returnedString;
+  if (doxygenEntity.isLeaf){ return javaDocFormat(doxygenEntity) + " ";}
+  else {
+    returnedString += javaDocFormat(doxygenEntity);
+    std::list<DoxygenEntity>::iterator p = doxygenEntity.entityList.begin();
+    while (p != doxygenEntity.entityList.end()){
+      returnedString+= translateSubtree(*p);
+      p++;
+    }
+  }
+  return returnedString;
+}
 
-	javaDocString += "\n */\n";
-	if(printSortedTree2){
-	cout << "\n---RESULT IN JAVADOC---" << endl;
-	cout << javaDocString; }
-	return javaDocString;
+std::string translateEntity(DoxygenEntity &doxyEntity){
+  if(doxyEntity.typeOfEntity.compare("partofdescription")== 0) return formatCommand(std::string(translateSubtree(doxyEntity)), 0);
+  if ((doxyEntity.typeOfEntity.compare("brief") == 0)||(doxyEntity.typeOfEntity.compare("details") == 0)){
+  return formatCommand(std::string(translateSubtree(doxyEntity)), 0) + "\n * ";}
+  else if(doxyEntity.typeOfEntity.compare("plainstring")== 0 || doxyEntity.typeOfEntity.compare("deprecated")== 0 || doxyEntity.typeOfEntity.compare("brief")== 0)
+    return formatCommand(doxyEntity.data, 0) + "\n * ";
+  else if(doxyEntity.typeOfEntity.compare("see") == 0){
+    return formatCommand(std::string("@" + doxyEntity.typeOfEntity + "\t\t" + translateSubtree(doxyEntity)), 2);
+  }
+  else if(doxyEntity.typeOfEntity.compare("return")== 0
+      || doxyEntity.typeOfEntity.compare("author")== 0
+      || doxyEntity.typeOfEntity.compare("param")== 0
+      || doxyEntity.typeOfEntity.compare("since")== 0
+      || doxyEntity.typeOfEntity.compare("version")== 0
+      || doxyEntity.typeOfEntity.compare("exception") == 0
+      || doxyEntity.typeOfEntity.compare("deprecated") == 0){
+    return formatCommand(std::string("@" + doxyEntity.typeOfEntity + "\t" + translateSubtree(doxyEntity)), 2);
+  }
+  else if(doxyEntity.typeOfEntity.compare("sa")== 0){
+    return formatCommand(std::string("@see\t\t" + translateSubtree(doxyEntity)), 2);
+  }
+  else return formatCommand(javaDocFormat(doxyEntity), 0 );
+  return "";
+}
+
+std::string JavaDocConverter:: convertToJavaDoc(Node *n, std::list <DoxygenEntity> entityList){
+  #pragma unused(n)
+  entityList.sort(CompareDoxygenEntities());
+  
+  if(printSortedTree2){
+    std::cout << "---RESORTED LIST---" << std::endl;
+    printSortedTree(entityList);
+  }
+
+  std::string javaDocString = "/**";
+  
+  for(std::list<DoxygenEntity>::iterator entityIterator = entityList.begin(); entityIterator != entityList.end();){
+    javaDocString += translateEntity(*entityIterator);
+    entityIterator++;
+  }
+
+  javaDocString += "\n */\n";
+  
+  if(printSortedTree2){
+    std::cout << "\n---RESULT IN JAVADOC---" << std::endl;
+    std::cout << javaDocString; 
+  }
+  
+  return javaDocString;
 }
\ No newline at end of file
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.h b/Source/DoxygenTranslator/src/JavaDocConverter.h
index 39de3dd15..0a329c27a 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.h
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.h
@@ -9,11 +9,10 @@
 class JavaDocConverter
 {
 public:
-
-	JavaDocConverter();
-	string convertToJavaDoc(Node *n, list <DoxygenEntity> entityList);
-	~JavaDocConverter();
-	void printSortedTree(list <DoxygenEntity> &entityList);
+  JavaDocConverter();
+  std::string convertToJavaDoc(Node *n, std::list <DoxygenEntity> entityList);
+  ~JavaDocConverter();
+  void printSortedTree(std::list <DoxygenEntity> &entityList);
 };
 
 #endif /*JAVADOCCONVERTER_H_*/
diff --git a/Source/DoxygenTranslator/src/PyDocConverter.cpp b/Source/DoxygenTranslator/src/PyDocConverter.cpp
index ad675e273..1e4d6a73e 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/PyDocConverter.cpp
@@ -14,192 +14,188 @@ PyDocConverter::PyDocConverter()
 PyDocConverter::~PyDocConverter()
 {
 }
-
-/* Sorts entities by pyDoc standard order for commands
- * NOTE: will not behave entirely properly until "First level" comments
- * such as brief descriptions are TAGGED as such
- */
-bool compare_DoxygenEntities(DoxygenEntity first, DoxygenEntity second);
  
-void PyDocConverter::printSortedTree(list <DoxygenEntity> &entityList){
-	list<DoxygenEntity>::iterator p = entityList.begin();
-	while (p != entityList.end()){
-		(*p).printEntity(0);
-		p++;
-	}
+void PyDocConverter::printSortedTree(std::list <DoxygenEntity> &entityList){
+  std::list<DoxygenEntity>::iterator p = entityList.begin();
+  while (p != entityList.end()){
+    (*p).printEntity(0);
+    p++;
+  }
 }
 
-string PyDocConverter::formatParam(Node *n, DoxygenEntity &doxygenEntity) {
-	string result;
-	ParmList *plist = CopyParmList(Getattr(n, "parms"));
-	Parm *p = NULL;
-	
-	DoxygenEntity& paramNameEntity = *doxygenEntity.entityList.begin();
-	DoxygenEntity& paramDescriptionEntity = *(++doxygenEntity.entityList.begin());
-	
-	for (p = plist; p;) {
-		if(Char(Getattr(p, "name")) == paramNameEntity.data) {
-			std::string name = Char(Swig_name_make(n, 0, Getattr(p, "name"), 0, 0));
-			std::string type = Char(Swig_name_make(n, 0, Getattr(p, "type"), 0, 0));
-			
-			std::ostringstream parameterDocString;
-			
-			parameterDocString << std::endl << name << " (" << type << "): ";
-			parameterDocString << paramDescriptionEntity.data;
-			
-			result = parameterDocString.str();
-			break;
-		}
-		p = Getattr(p, "tmap:in") ? Getattr(p, "tmap:in:next") : nextSibling(p);
-	}
+std::string PyDocConverter::formatParam(Node *n, DoxygenEntity &doxygenEntity) {
+  std::string result;
+  ParmList *plist = CopyParmList(Getattr(n, "parms"));
+  Parm *p = NULL;
+  
+  DoxygenEntity& paramNameEntity = *doxygenEntity.entityList.begin();
+  DoxygenEntity& paramDescriptionEntity = *(++doxygenEntity.entityList.begin());
+  
+  for (p = plist; p;) {
+    if(Char(Getattr(p, "name")) == paramNameEntity.data) {
+      std::string name = Char(Swig_name_make(n, 0, Getattr(p, "name"), 0, 0));
+      std::string type = Char(Swig_name_make(n, 0, Getattr(p, "type"), 0, 0));
+      
+      std::ostringstream parameterDocString;
+      
+      parameterDocString << std::endl << name << " (" << type << ") -- ";
+      parameterDocString << paramDescriptionEntity.data;
+      
+      result = parameterDocString.str();
+      break;
+    }
+    p = Getattr(p, "tmap:in") ? Getattr(p, "tmap:in:next") : nextSibling(p);
+  }
 
-	Delete(plist);
-	return result;
+  Delete(plist);
+  return result;
 }
 
-string PyDocConverter::formatCommand(string unformattedLine, int indent){
-	string formattedLines = "\n";
-	int lastPosition = 0;
-	int i = 0;
-	int isFirstLine  = 1;
-	while (i != -1 && i < unformattedLine.length()){
-		lastPosition = i;
-		if (isFirstLine){
-			i+=APPROX_LINE_LENGTH;
-		}
-		else i+=APPROX_LINE_LENGTH - indent*TAB_SIZE;
-		i = unformattedLine.find(" ", i);
+std::string PyDocConverter::formatCommand(std::string unformattedLine, int indent){
+  std::string formattedLines = "\n";
+  int lastPosition = 0;
+  signed int i = 0;
+  bool isFirstLine  = true;
+  while (i != -1 && i < (int)unformattedLine.length()){
+    lastPosition = i;
+    if (isFirstLine){
+      i+=APPROX_LINE_LENGTH;
+    }
+    else i+=APPROX_LINE_LENGTH - indent*TAB_SIZE;
+    i = unformattedLine.find(" ", i);
 
-		if (i > 0 && i + 1 < unformattedLine.length()){
-			if (!isFirstLine) for (int j = 0; j < indent; j++) {
-				formattedLines.append("\t");
-				}
-			else {
-				isFirstLine = 0;
-			}
-			formattedLines.append(unformattedLine.substr(lastPosition, i - lastPosition + 1));
-			formattedLines.append("\n");
+    if (i > 0 && i + 1 < (int)unformattedLine.length()){
+      if (!isFirstLine) for (int j = 0; j < indent; j++) {
+        formattedLines.append("\t");
+        }
+      else {
+        isFirstLine = false;
+      }
+      formattedLines.append(unformattedLine.substr(lastPosition, i - lastPosition + 1));
+      formattedLines.append("\n");
 
-		}
-	}
-	if (lastPosition < unformattedLine.length()){
-		if (!isFirstLine) {for (int j = 0; j < indent; j++) {formattedLines.append("\t");}}
-		formattedLines.append(unformattedLine.substr(lastPosition, unformattedLine.length() - lastPosition));
-	}
+    }
+  }
+  if (lastPosition < (int)unformattedLine.length()){
+    if (!isFirstLine) {for (int j = 0; j < indent; j++) {formattedLines.append("\t");}}
+    formattedLines.append(unformattedLine.substr(lastPosition, unformattedLine.length() - lastPosition));
+  }
 
-	return formattedLines;
+  return formattedLines;
 }
 
 /* Contains the conversions for tags
  * could probably be much more efficient...
  */
-string PyDocConverter::pyDocFormat(DoxygenEntity &doxygenEntity){
-	if(doxygenEntity.typeOfEntity.compare("partofdescription") == 0){
-				return doxygenEntity.data;
-		}
-	if (doxygenEntity.typeOfEntity.compare("plainstring") == 0){
-			return  doxygenEntity.data;
-	}
-	else if (doxygenEntity.typeOfEntity.compare("b") == 0){
-		return "<b>" + doxygenEntity.data + "</b>";
-	}
-	else if (doxygenEntity.typeOfEntity.compare("c") == 0){
-		return "<tt>" + doxygenEntity.data + "</tt>";
-	}
-	else if (doxygenEntity.typeOfEntity.compare("@") == 0){
-		return "@";
-	}
-	else if (doxygenEntity.typeOfEntity.compare("\\") == 0){
-		return "\\";
-	}
-	else if (doxygenEntity.typeOfEntity.compare("<") == 0){
-		return "&lt;";
-	}
-	else if (doxygenEntity.typeOfEntity.compare(">") == 0){
-		return "&gt;";
-	}
-	else if (doxygenEntity.typeOfEntity.compare("&") == 0){
-		return "&amp;";
-	}
-	else if (doxygenEntity.typeOfEntity.compare("#") == 0){
-		return "#";
-	}
-	else if (doxygenEntity.typeOfEntity.compare("%") == 0){
-		return "%";
-	}
-	else if (doxygenEntity.typeOfEntity.compare("~") == 0){
-		return "~";
-	}
-	return "";
-}
-
-
-string PyDocConverter::translateSubtree( DoxygenEntity &doxygenEntity){
-	string returnedString;
-	if (doxygenEntity.isLeaf){ return pyDocFormat(doxygenEntity) + " ";}
-	else {
-		returnedString += pyDocFormat(doxygenEntity);
-		list<DoxygenEntity>::iterator p = doxygenEntity.entityList.begin();
-		while (p != doxygenEntity.entityList.end()){
-			returnedString+= translateSubtree(*p);
-			p++;
-		}
-	}
-	return returnedString;
-}
-
-string PyDocConverter::translateEntity(Node *n, DoxygenEntity &doxyEntity){
-	if(doxyEntity.typeOfEntity.compare("partofdescription")== 0) return formatCommand(string(translateSubtree(doxyEntity)), 0);
-	if ((doxyEntity.typeOfEntity.compare("brief") == 0)||(doxyEntity.typeOfEntity.compare("details") == 0)){
-		return formatCommand(string(translateSubtree(doxyEntity)), 0) + "\n * ";}
-	else if(doxyEntity.typeOfEntity.compare("plainstring")== 0 
-			|| doxyEntity.typeOfEntity.compare("deprecated")== 0 
-			|| doxyEntity.typeOfEntity.compare("brief")== 0)
-		return formatCommand(doxyEntity.data, 0) + "\n * ";
-	else if(doxyEntity.typeOfEntity.compare("see") == 0){
-		return formatCommand(string("@" + doxyEntity.typeOfEntity + "\t\t" + translateSubtree(doxyEntity)), 2);
-	}
-	else if(doxyEntity.typeOfEntity.compare("param") == 0) {
-		return formatParam(n, doxyEntity);
-	}
-	else if(doxyEntity.typeOfEntity.compare("return")== 0
-			|| doxyEntity.typeOfEntity.compare("author")== 0
-			|| doxyEntity.typeOfEntity.compare("param")== 0
-			|| doxyEntity.typeOfEntity.compare("since")== 0
-			|| doxyEntity.typeOfEntity.compare("version")== 0
-			|| doxyEntity.typeOfEntity.compare("exception") == 0
-			|| doxyEntity.typeOfEntity.compare("deprecated") == 0){
-		return formatCommand(string("@" + doxyEntity.typeOfEntity + "\t" + translateSubtree(doxyEntity)), 2);
-	}
-	else if(doxyEntity.typeOfEntity.compare("sa")== 0){
-		return formatCommand(string("@see\t\t" + translateSubtree(doxyEntity)), 2);
-	}
-	else return formatCommand(pyDocFormat(doxyEntity), 0 );
-	return "";
-}
-
-string PyDocConverter::convertToPyDoc(Node *n, list <DoxygenEntity> entityList){
-	entityList.sort(compare_DoxygenEntities);
-	
-    if(debug){
-	    cout << "---RESORTED LIST---" << endl;
-        printSortedTree(entityList);
+std::string PyDocConverter::pyDocFormat(DoxygenEntity &doxygenEntity){
+  if(doxygenEntity.typeOfEntity.compare("partofdescription") == 0){
+        return doxygenEntity.data;
     }
+  if (doxygenEntity.typeOfEntity.compare("plainstd::string") == 0){
+      return  doxygenEntity.data;
+  }
+  else if (doxygenEntity.typeOfEntity.compare("b") == 0){
+    return "<b>" + doxygenEntity.data + "</b>";
+  }
+  else if (doxygenEntity.typeOfEntity.compare("c") == 0){
+    return "<tt>" + doxygenEntity.data + "</tt>";
+  }
+  else if (doxygenEntity.typeOfEntity.compare("@") == 0){
+    return "@";
+  }
+  else if (doxygenEntity.typeOfEntity.compare("\\") == 0){
+    return "\\";
+  }
+  else if (doxygenEntity.typeOfEntity.compare("<") == 0){
+    return "&lt;";
+  }
+  else if (doxygenEntity.typeOfEntity.compare(">") == 0){
+    return "&gt;";
+  }
+  else if (doxygenEntity.typeOfEntity.compare("&") == 0){
+    return "&amp;";
+  }
+  else if (doxygenEntity.typeOfEntity.compare("#") == 0){
+    return "#";
+  }
+  else if (doxygenEntity.typeOfEntity.compare("%") == 0){
+    return "%";
+  }
+  else if (doxygenEntity.typeOfEntity.compare("~") == 0){
+    return "~";
+  }
+  return "";
+}
 
-	string pyDocString = "\"\"\"";
 
-	list<DoxygenEntity>::iterator entityIterator = entityList.begin();
-	while (entityIterator != entityList.end()){
-		pyDocString += translateEntity(n, *entityIterator);
-		entityIterator++;
-	}
+std::string PyDocConverter::translateSubtree( DoxygenEntity &doxygenEntity){
+  std::string returnedString;
+  if (doxygenEntity.isLeaf){ return pyDocFormat(doxygenEntity) + " ";}
+  else {
+    returnedString += pyDocFormat(doxygenEntity);
+    std::list<DoxygenEntity>::iterator p = doxygenEntity.entityList.begin();
+    while (p != doxygenEntity.entityList.end()){
+      returnedString+= translateSubtree(*p);
+      p++;
+    }
+  }
+  return returnedString;
+}
 
-	pyDocString += "\n\"\"\"\n";
-	
-	if(debug){
-	    cout << "\n---RESULT IN PYDOC---" << endl;
-	    cout << pyDocString; 
-	}
-	
-	return pyDocString;
+std::string PyDocConverter::translateEntity(Node *n, DoxygenEntity &doxyEntity){
+  if(doxyEntity.typeOfEntity.compare("partofdescription")== 0) 
+    return formatCommand(std::string(translateSubtree(doxyEntity)), 0);
+  
+  if ((doxyEntity.typeOfEntity.compare("brief") == 0)||(doxyEntity.typeOfEntity.compare("details") == 0)){
+    return formatCommand(std::string(translateSubtree(doxyEntity)), 0) + "\n * ";}
+  
+  if(doxyEntity.typeOfEntity.compare("plainstd::string")== 0 
+      || doxyEntity.typeOfEntity.compare("deprecated")== 0 
+      || doxyEntity.typeOfEntity.compare("brief")== 0)
+    return formatCommand(doxyEntity.data, 0) + "\n * ";
+  
+  if(doxyEntity.typeOfEntity.compare("see") == 0)
+    return formatCommand(std::string("@" + doxyEntity.typeOfEntity + "\t\t" + translateSubtree(doxyEntity)), 2);
+  
+  if(doxyEntity.typeOfEntity.compare("param") == 0)
+    return formatParam(n, doxyEntity);
+
+  if(doxyEntity.typeOfEntity.compare("return")== 0
+      || doxyEntity.typeOfEntity.compare("author")== 0
+      || doxyEntity.typeOfEntity.compare("param")== 0
+      || doxyEntity.typeOfEntity.compare("since")== 0
+      || doxyEntity.typeOfEntity.compare("version")== 0
+      || doxyEntity.typeOfEntity.compare("exception") == 0
+      || doxyEntity.typeOfEntity.compare("deprecated") == 0)
+    return formatCommand(std::string("@" + doxyEntity.typeOfEntity + "\t" + translateSubtree(doxyEntity)), 2);
+  
+  if(doxyEntity.typeOfEntity.compare("sa")== 0)
+    return formatCommand(std::string("@see\t\t" + translateSubtree(doxyEntity)), 2);
+
+  return formatCommand(pyDocFormat(doxyEntity), 0);
+}
+
+std::string PyDocConverter::convertToPyDoc(Node *n, std::list<DoxygenEntity> entityList){
+  entityList.sort(CompareDoxygenEntities());
+  
+  if(debug){
+    std::cout << "---RESORTED LIST---" << std::endl;
+    printSortedTree(entityList);
+  }
+
+  std::string pyDocString = "\"\"\"";
+  
+  for(std::list<DoxygenEntity>::iterator entityIterator = entityList.begin(); entityIterator != entityList.end();){
+    pyDocString += translateEntity(n, *entityIterator);
+    entityIterator++;
+  }
+
+  pyDocString += "\n\"\"\"\n";
+  
+  if(debug){
+    std::cout << "\n---RESULT IN PYDOC---" << std::endl;
+    std::cout << pyDocString; 
+  }
+  
+  return pyDocString;
 }
\ No newline at end of file
diff --git a/Source/DoxygenTranslator/src/PyDocConverter.h b/Source/DoxygenTranslator/src/PyDocConverter.h
index b9d813476..27faaf6c3 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.h
+++ b/Source/DoxygenTranslator/src/PyDocConverter.h
@@ -9,21 +9,20 @@
 class PyDocConverter
 {
 public:
-
-    PyDocConverter();
-    string convertToPyDoc(Node *n, list <DoxygenEntity> entityList);
-    ~PyDocConverter();
-    void printSortedTree(list <DoxygenEntity> &entityList);
+  PyDocConverter();
+  std::string convertToPyDoc(Node *n, std::list <DoxygenEntity> entityList);
+  ~PyDocConverter();
+  void printSortedTree(std::list <DoxygenEntity> &entityList);
 
 protected:
-	std::string formatParam(Node *n, DoxygenEntity &doxygenEntity);
-    std::string formatCommand(string unformattedLine, int indent);
-    std::string pyDocFormat(DoxygenEntity &doxygenEntity);
-    std::string translateSubtree( DoxygenEntity &doxygenEntity);
-    std::string translateEntity(Node *n, DoxygenEntity &doxyEntity);
+  std::string formatParam(Node *n, DoxygenEntity &doxygenEntity);
+  std::string formatCommand(std::string unformattedLine, int indent);
+  std::string pyDocFormat(DoxygenEntity &doxygenEntity);
+  std::string translateSubtree( DoxygenEntity &doxygenEntity);
+  std::string translateEntity(Node *n, DoxygenEntity &doxyEntity);
     
 private:
-    bool debug;
+  bool debug;
 };
 
 #endif /*PYDOCCONVERTER_H_*/

From eb38ea3a4330001f59b814491de3b2c34b9bef2d Mon Sep 17 00:00:00 2001
From: Jamie Kirkpatrick <gringostarr@users.sourceforge.net>
Date: Fri, 12 Sep 2008 11:19:07 +0000
Subject: [PATCH 031/314] Whitespace corrects.

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2008-cherylfoil@10840 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 .../DoxygenTranslator/src/DoxygenEntity.cpp   |   21 -
 Source/DoxygenTranslator/src/DoxygenEntity.h  |    1 -
 .../DoxygenTranslator/src/DoxygenParser.cpp   | 1275 +++++++++--------
 3 files changed, 659 insertions(+), 638 deletions(-)

diff --git a/Source/DoxygenTranslator/src/DoxygenEntity.cpp b/Source/DoxygenTranslator/src/DoxygenEntity.cpp
index dcca1d032..52fb60d90 100644
--- a/Source/DoxygenTranslator/src/DoxygenEntity.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenEntity.cpp
@@ -10,27 +10,6 @@
 #include "DoxygenEntity.h"
 #include <iostream>
 
-/* 
- * Basic node for commands that have nothing after them (eg: \n)
- */
-std::string DoxygenEntity::commandArray[] = {"a", "addindex", "addtogroup", "anchor", "arg", "attention",
-		"author", "b", "brief", "bug", "c", "callgraph", "callergraph", "category",
-		"class", "code", "cond", "copybrief", "copydetails", "copydoc", "date", "def",
-		"defgroup", "deprecated", "details", "dir", "dontinclude", "dot", "dotfile", "e",
-		"else", "elseif", "em", "endcode", "endcond", "enddot", "endhtmlonly", "endif",
-		"std::endlatexonly", "std::endlink", "endmanonly", "endmsc", "endverbatim", "endxmlonly",
-		"enum", "example", "exception", "f$", "f[", "f]", "f{", "f}", "file", "fn", "headerfile",
-		"hideinitializer", "htmlinclude", "htmlonly", "if", "ifnot", "image", "include",
-		"includelineno", "ingroup", "internal", "invariant", "interface", "latexonly", "li",
-		"line", "link", "mainpage", "manonly", "msc", "n", "name", "namespace", "nosubgrouping",
-		"note", "overload", "p", "package", "page", "par", "paragraph", "param", "post", "pre",
-		"private", "privatesection", "property", "protected", "protectedsection", "protocol",
-		"public", "publicsection", "ref", "relates", "relatesalso", "remarks", "return", "retval",
-		"sa", "section", "see", "showinitializer", "since", "skip", "skipline", "struct", "subpage",
-		"subsection", "subsubsection", "test", "throw", "todo", "tparam", "typedef", "union", "until",
-		"var", "verbatim", "verbinclude", "version", "warning", "weakgroup", "xmlonly", "xrefitem",
-		"$", "@", std::string(1, 92), "&", "~", "<", ">", "#", "%"};
-
 DoxygenEntity::DoxygenEntity(std::string typeEnt){
     typeOfEntity = typeEnt;
     data = "";
diff --git a/Source/DoxygenTranslator/src/DoxygenEntity.h b/Source/DoxygenTranslator/src/DoxygenEntity.h
index 3bec0bb0c..6a0b2e48c 100644
--- a/Source/DoxygenTranslator/src/DoxygenEntity.h
+++ b/Source/DoxygenTranslator/src/DoxygenEntity.h
@@ -25,7 +25,6 @@ struct DoxygenEntity{
   std::list <DoxygenEntity> entityList;
   std::string data;
   int isLeaf;
-  static std::string commandArray[];
 };
 
 /* 
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.cpp b/Source/DoxygenTranslator/src/DoxygenParser.cpp
index ba624239a..cdc2d709f 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenParser.cpp
@@ -37,75 +37,75 @@ std::list <DoxygenEntity> parse(std::list<Token>::iterator endParsingIndex, Toke
 
 
 std::string commandArray[] = {"a", "addindex", "addtogroup", "anchor", "arg", "attention",
-		"author", "b", "brief", "bug", "c", "callgraph", "callergraph", "category",
-		"class", "code", "cond", "copybrief", "copydetails", "copydoc", "date", "def",
-		"defgroup", "deprecated", "details", "dir", "dontinclude", "dot", "dotfile", "e",
-		"else", "elseif", "em", "endcode", "endcond", "enddot", "endhtmlonly", "endif",
-		"endlatexonly", "endlink", "endmanonly", "endmsc", "endverbatim", "endxmlonly",
-		"enum", "example", "exception", "f$", "f[", "f]", "f{", "f}", "file", "fn", "headerfile",
-		"hideinitializer", "htmlinclude", "htmlonly", "if", "ifnot", "image", "include",
-		"includelineno", "ingroup", "internal", "invariant", "interface", "latexonly", "li",
-		"line", "link", "mainpage", "manonly", "msc", "n", "name", "namespace", "nosubgrouping",
-		"note", "overload", "p", "package", "page", "par", "paragraph", "param", "post", "pre",
-		"private", "privatesection", "property", "protected", "protectedsection", "protocol",
-		"public", "publicsection", "ref", "relates", "relatesalso", "remarks", "return", "retval",
-		"sa", "section", "see", "showinitializer", "since", "skip", "skipline", "struct", "subpage",
-		"subsection", "subsubsection", "test", "throw", "todo", "tparam", "typedef", "union", "until",
-		"var", "verbatim", "verbinclude", "version", "warning", "weakgroup", "xmlonly", "xrefitem",
-		"$", "@", "\\","&", "~", "<", ">", "#", "%"};
+    "author", "b", "brief", "bug", "c", "callgraph", "callergraph", "category",
+    "class", "code", "cond", "copybrief", "copydetails", "copydoc", "date", "def",
+    "defgroup", "deprecated", "details", "dir", "dontinclude", "dot", "dotfile", "e",
+    "else", "elseif", "em", "endcode", "endcond", "enddot", "endhtmlonly", "endif",
+    "endlatexonly", "endlink", "endmanonly", "endmsc", "endverbatim", "endxmlonly",
+    "enum", "example", "exception", "f$", "f[", "f]", "f{", "f}", "file", "fn", "headerfile",
+    "hideinitializer", "htmlinclude", "htmlonly", "if", "ifnot", "image", "include",
+    "includelineno", "ingroup", "internal", "invariant", "interface", "latexonly", "li",
+    "line", "link", "mainpage", "manonly", "msc", "n", "name", "namespace", "nosubgrouping",
+    "note", "overload", "p", "package", "page", "par", "paragraph", "param", "post", "pre",
+    "private", "privatesection", "property", "protected", "protectedsection", "protocol",
+    "public", "publicsection", "ref", "relates", "relatesalso", "remarks", "return", "retval",
+    "sa", "section", "see", "showinitializer", "since", "skip", "skipline", "struct", "subpage",
+    "subsection", "subsubsection", "test", "throw", "todo", "tparam", "typedef", "union", "until",
+    "var", "verbatim", "verbinclude", "version", "warning", "weakgroup", "xmlonly", "xrefitem",
+    "$", "@", "\\","&", "~", "<", ">", "#", "%"};
 
 
 std::string sectionIndicators[] = { "attention", "author", "brief", "bug", "cond", "date", "deprecated", "details",
-		"else", "elseif", "endcond", "endif", "exception", "if", "ifnot", "invariant", "note", "par", "param",
-		"tparam", "post" , "pre", "remarks", "return", "retval", "sa", "see", "since", "test", "throw", "todo",
-		"version", "warning", "xrefitem" };
+    "else", "elseif", "endcond", "endif", "exception", "if", "ifnot", "invariant", "note", "par", "param",
+    "tparam", "post" , "pre", "remarks", "return", "retval", "sa", "see", "since", "test", "throw", "todo",
+    "version", "warning", "xrefitem" };
 
 /* All of the doxygen commands divided up by how they are parsed */
 std::string simpleCommands[] = {"n", "$", "@", "\\", "&", "~", "<", ">", "#", "%"};
 std::string ignoredSimpleCommands[] = {"nothing at the moment"};
 std::string commandWords[] = {"a", "b", "c", "e", "em", "p", "def", "enum", "example", "package", 
-		"relates", "namespace", "relatesalso","anchor", "dontinclude", "include", "includelineno"};
+    "relates", "namespace", "relatesalso","anchor", "dontinclude", "include", "includelineno"};
 std::string ignoredCommandWords[] = {"copydoc", "copybrief", "copydetails", "verbinclude", "htmlinclude"};
 std::string commandLines[] = {"addindex", "fn", "name", "line", "var", "skipline", "typedef", "skip", "until", "property"};
 std::string ignoreCommandLines[] = {"nothing at the moment"};
 std::string commandParagraph[] = {"partofdescription", "return", "remarks", "since", "test", "sa", "see", "pre", "post", "details", "invariant", 
-		    "deprecated", "date", "note", "warning", "version", "todo", "bug", "attention", "brief", "author"};
+        "deprecated", "date", "note", "warning", "version", "todo", "bug", "attention", "brief", "author"};
 std::string ignoreCommandParagraphs[] = {"nothing at the moment"};
 std::string commandEndCommands[] = {"code", "dot", "msc", "f$", "f[", "f{environment}{", "htmlonly", "latexonly", "manonly", 
-		   "verbatim", "xmlonly", "cond", "if", "ifnot", "link"};
+       "verbatim", "xmlonly", "cond", "if", "ifnot", "link"};
 std::string commandWordParagraphs[] = {"param", "tparam", "throw", "retval", "exception"};
 std::string commandWordLines[] = {"page", "subsection", "subsubsection", "section", "paragraph", "defgroup"};
 std::string commandWordOWordOWords [] = {"category", "class", "protocol", "interface", "struct", "union"};
 std::string commandOWords[] = {"dir", "file", "cond"};
 std::string commandErrorThrowings[] = {"annotatedclassstd::list", "classhierarchy", "define", "functionindex", "header",
-		"headerfilestd::list", "inherit", "l", "postheader", "private", "privatesection", "protected", 
-		"protectedsection", "public", "publicsection", "endcode", "enddot", "endmsc", "endhtmlonly", 
-		"endlatexonly", "endmanonly", "endlink", "endverbatim", "endxmlonly", "f]", "f}", "endcond", 
-		"endif"};
+    "headerfilestd::list", "inherit", "l", "postheader", "private", "privatesection", "protected", 
+    "protectedsection", "public", "publicsection", "endcode", "enddot", "endmsc", "endhtmlonly", 
+    "endlatexonly", "endmanonly", "endlink", "endverbatim", "endxmlonly", "f]", "f}", "endcond", 
+    "endif"};
 std::string commandUniques[] = {"xrefitem", "arg", "ingroup", "par", "headerfile", "overload", "weakgroup", "ref",
-		"subpage", "dotfile", "image", "addtogroup", "li"};
+"subpage", "dotfile", "image", "addtogroup", "li"};
 
 
 /* Changes a std::string to all lower case */
 std::string StringToLower(std::string stringToConvert){
-   for(unsigned int i=0;i<stringToConvert.length();i++){
-	   stringToConvert[i] = tolower(stringToConvert[i]);
-	   }
-   return stringToConvert; //return the converted std::string
+  for(unsigned int i=0;i<stringToConvert.length();i++){
+    stringToConvert[i] = tolower(stringToConvert[i]);
+  }
+  return stringToConvert; //return the converted std::string
 }
 
 /* finds out if a command exists (is a possible command)
  * from the std::string array commandArray
  * returns -1 if no match is found */
 int findCommand(std::string smallString){
-	smallString = StringToLower(smallString);
-	int a;
-	for (int i = 0; i < sizeof(commandArray)/sizeof(*commandArray); i++){
-		if( (a = smallString.compare(commandArray[i])) == 0){
-			return 101 + i;
-			}
-		}
-	return -1;
+  smallString = StringToLower(smallString);
+  int a;
+  for (unsigned i = 0; i < sizeof(commandArray)/sizeof(*commandArray); i++){
+    if( (a = smallString.compare(commandArray[i])) == 0){
+      return 101 + i;
+    }
+  }
+  return -1;
 }
 
 /* isSectionIndicator returns a boolean if the command is a section indicator
@@ -113,77 +113,92 @@ int findCommand(std::string smallString){
  * by Doxygen's terms
  */
 int isSectionIndicator(std::string smallString){
-	smallString = StringToLower(smallString);
-	for (int i = 0; i < sizeof( sectionIndicators)/sizeof(* sectionIndicators); i++){
-		if( smallString.compare( sectionIndicators[i]) == 0){
-			return 1;
-		}
-	}
-	return 0;
+  smallString = StringToLower(smallString);
+  for (unsigned i = 0; i < sizeof( sectionIndicators)/sizeof(* sectionIndicators); i++){
+    if( smallString.compare( sectionIndicators[i]) == 0){
+      return 1;
+    }
+  }
+  return 0;
 }
 
 /* prints the parse tree */
 void printTree( std::list <DoxygenEntity> &rootList){
-	std::list<DoxygenEntity>::iterator p = rootList.begin();
-	while (p != rootList.end()){
-		(*p).printEntity(0);
-		p++;
-		}
-	}
+  std::list<DoxygenEntity>::iterator p = rootList.begin();
+  while (p != rootList.end()){
+    (*p).printEntity(0);
+    p++;
+  }
+}
 
 /* Determines how a command should be handled (what group it belongs to
  * for parsing rules
  */
 int commandBelongs(std::string theCommand){
-	 std::string smallString = StringToLower(theCommand);
-	 //cout << " Looking for command " << theCommand << endl;
-	 int i = 0;
-	 for ( i = 0; i < sizeof(simpleCommands)/sizeof(*simpleCommands); i++){
-	 	if(smallString.compare(simpleCommands[i]) == 0){return SIMPLECOMMAND;}
-	 	}
-	 for ( i = 0; i < sizeof(ignoredSimpleCommands)/sizeof(*ignoredSimpleCommands); i++){
-	 	if(smallString.compare(ignoredSimpleCommands[i]) == 0){return IGNOREDSIMPLECOMMAND;}
-	 	} 
-	 for ( i = 0; i < sizeof(commandWords)/sizeof(*commandWords); i++){
-	 	if(smallString.compare( commandWords[i]) == 0){return COMMANDWORD;}
-	 	} 
-	 for ( i = 0; i < sizeof(ignoredCommandWords)/sizeof(*ignoredCommandWords); i++){
-	 	if(smallString.compare( ignoredCommandWords[i]) == 0){return IGNOREDCOMMANDWORD;}
-	 	} 
-	 for ( i = 0; i < sizeof(commandLines)/sizeof(*commandLines); i++){
-	 	if(smallString.compare( commandLines[i]) == 0){return COMMANDLINE;}
-	 	} 
-	 for ( i = 0; i < sizeof(ignoreCommandLines)/sizeof(*ignoreCommandLines); i++){
-	 	if(smallString.compare( ignoreCommandLines[i]) == 0){return IGNOREDCOMMANDLINE;}
-	 	} 
-	 for ( i = 0; i <  sizeof(commandParagraph)/sizeof(*commandParagraph); i++){
-	 	if(smallString.compare( commandParagraph[i]) == 0){return COMMANDPARAGRAPH;}
-	 	} 
-	 for ( i = 0; i < sizeof(ignoreCommandParagraphs)/sizeof(*ignoreCommandParagraphs); i++){
-	 	if(smallString.compare( ignoreCommandParagraphs[i]) == 0){return IGNORECOMMANDPARAGRAPH;}
-	 	} 
-	 for ( i = 0; i < sizeof(commandEndCommands)/sizeof(*commandEndCommands); i++){
-	 	if(smallString.compare( commandEndCommands[i]) == 0){return COMMANDENDCOMMAND ;}
-	 	} 
-	 for ( i = 0; i < sizeof(commandWordParagraphs)/sizeof(*commandWordParagraphs); i++){
-	 	if(smallString.compare( commandWordParagraphs[i]) == 0){return COMMANDWORDPARAGRAPH;}
-	 	} 
-	 for ( i = 0; i < sizeof(commandWordLines)/sizeof(*commandWordLines); i++){
-	 	if(smallString.compare( commandWordLines[i]) == 0){return COMMANDWORDLINE ;}
-	 	} 
-	 for ( i = 0; i < sizeof(commandWordOWordOWords)/sizeof(*commandWordOWordOWords); i++){
-	 	if(smallString.compare( commandWordOWordOWords[i]) == 0){return COMMANDWORDOWORDWORD;}
-	 	} 
-	 for ( i = 0; i < sizeof(commandOWords)/sizeof(*commandOWords); i++){
-	 	if(smallString.compare( commandOWords[i]) == 0){return COMMANDOWORD;}
-	 	} 
-	 for ( i = 0; i < sizeof(commandErrorThrowings)/sizeof(*commandErrorThrowings); i++){
-	 	if(smallString.compare( commandErrorThrowings[i]) == 0){return COMMANDERRORTHROW;}
-	 	} 
-	 for ( i = 0; i < sizeof(commandUniques)/sizeof(*commandUniques); i++){
-	 	if(smallString.compare( commandUniques[i]) == 0){return COMMANDUNIQUE;}
-	 	}
-	 	return 0; 
+   std::string smallString = StringToLower(theCommand);
+   //cout << " Looking for command " << theCommand << endl;
+  unsigned i = 0;
+  for (i = 0; i < sizeof(simpleCommands)/sizeof(*simpleCommands); i++){
+    if(smallString.compare(simpleCommands[i]) == 0)
+      return SIMPLECOMMAND;
+  }
+  for (i = 0; i < sizeof(ignoredSimpleCommands)/sizeof(*ignoredSimpleCommands); i++){
+    if(smallString.compare(ignoredSimpleCommands[i]) == 0)
+      return IGNOREDSIMPLECOMMAND;
+  } 
+  for (i = 0; i < sizeof(commandWords)/sizeof(*commandWords); i++){
+    if(smallString.compare( commandWords[i]) == 0)
+      return COMMANDWORD;
+  } 
+  for (i = 0; i < sizeof(ignoredCommandWords)/sizeof(*ignoredCommandWords); i++){
+    if(smallString.compare( ignoredCommandWords[i]) == 0)
+      return IGNOREDCOMMANDWORD;
+  } 
+  for (i = 0; i < sizeof(commandLines)/sizeof(*commandLines); i++){
+    if(smallString.compare( commandLines[i]) == 0)
+      return COMMANDLINE;
+  } 
+  for (i = 0; i < sizeof(ignoreCommandLines)/sizeof(*ignoreCommandLines); i++){
+    if(smallString.compare( ignoreCommandLines[i]) == 0)
+      return IGNOREDCOMMANDLINE;
+  } 
+  for (i = 0; i <  sizeof(commandParagraph)/sizeof(*commandParagraph); i++){
+    if(smallString.compare( commandParagraph[i]) == 0)
+      return COMMANDPARAGRAPH;
+  } 
+  for (i = 0; i < sizeof(ignoreCommandParagraphs)/sizeof(*ignoreCommandParagraphs); i++){
+    if(smallString.compare( ignoreCommandParagraphs[i]) == 0)
+      return IGNORECOMMANDPARAGRAPH;
+  } 
+  for (i = 0; i < sizeof(commandEndCommands)/sizeof(*commandEndCommands); i++){
+    if(smallString.compare( commandEndCommands[i]) == 0)
+      return COMMANDENDCOMMAND;
+  } 
+  for (i = 0; i < sizeof(commandWordParagraphs)/sizeof(*commandWordParagraphs); i++){
+    if(smallString.compare( commandWordParagraphs[i]) == 0)
+      return COMMANDWORDPARAGRAPH;
+  } 
+  for (i = 0; i < sizeof(commandWordLines)/sizeof(*commandWordLines); i++){
+    if(smallString.compare( commandWordLines[i]) == 0)
+      return COMMANDWORDLINE;
+  } 
+  for (i = 0; i < sizeof(commandWordOWordOWords)/sizeof(*commandWordOWordOWords); i++){
+    if(smallString.compare( commandWordOWordOWords[i]) == 0)
+      return COMMANDWORDOWORDWORD;
+  } 
+  for (i = 0; i < sizeof(commandOWords)/sizeof(*commandOWords); i++){
+    if(smallString.compare( commandOWords[i]) == 0)
+      return COMMANDOWORD;
+  } 
+  for (i = 0; i < sizeof(commandErrorThrowings)/sizeof(*commandErrorThrowings); i++){
+    if(smallString.compare( commandErrorThrowings[i]) == 0)
+      return COMMANDERRORTHROW;
+  } 
+  for (i = 0; i < sizeof(commandUniques)/sizeof(*commandUniques); i++){
+    if(smallString.compare( commandUniques[i]) == 0)
+      return COMMANDUNIQUE;
+  }
+  return 0; 
 }
 
 /* Returns the next word ON THE CURRENT LINE ONLY
@@ -191,46 +206,46 @@ int commandBelongs(std::string theCommand){
  * Updates the index it is given if success.
  */
 std::string getNextWord(TokenList &tokList){
-	 Token nextToken = tokList.peek();
-	 if (nextToken.tokenType == PLAINSTRING ){
-		 nextToken = tokList.next();
-		 return nextToken.tokenString;
-	 }
-	return "";
+   Token nextToken = tokList.peek();
+   if (nextToken.tokenType == PLAINSTRING ){
+     nextToken = tokList.next();
+     return nextToken.tokenString;
+   }
+  return "";
 }
 
 /* Returns the location of the end of the line as
  * an iterator.
  */
 std::list<Token>::iterator getOneLine(TokenList &tokList){
-	 std::list<Token>::iterator endOfLine = tokList.iteratorCopy();
-	 while(endOfLine!= tokList.end()){
-		 if ((* endOfLine).tokenType == END_LINE){
-			 //cout << "REACHED END" << endl;
-			 //endOfLine++;
-			 return endOfLine;
-			 }
-		 //cout << (* endOfLine).toString();
-		 endOfLine++;
-		 }
-	 
-	return tokList.end();
-	}
+   std::list<Token>::iterator endOfLine = tokList.iteratorCopy();
+   while(endOfLine!= tokList.end()){
+     if ((* endOfLine).tokenType == END_LINE){
+       //cout << "REACHED END" << endl;
+       //endOfLine++;
+       return endOfLine;
+       }
+     //cout << (* endOfLine).toString();
+     endOfLine++;
+     }
+   
+  return tokList.end();
+  }
 
 /* Returns a properly formatted std::string
 * up til ANY command or end of line is encountered.
 */
 std::string getStringTilCommand(TokenList &tokList){
-	 std::string description;
-	 if (tokList.peek().tokenType == 0) return "";
-	 while(tokList.peek().tokenType == PLAINSTRING){
-		 Token currentToken = tokList.next();
-		 if(currentToken.tokenType == PLAINSTRING) {
-			 description = description + currentToken.tokenString + " ";
-			 }
-		 }
-	return description;
-	}
+   std::string description;
+   if (tokList.peek().tokenType == 0) return "";
+   while(tokList.peek().tokenType == PLAINSTRING){
+     Token currentToken = tokList.next();
+     if(currentToken.tokenType == PLAINSTRING) {
+       description = description + currentToken.tokenString + " ";
+       }
+     }
+  return description;
+  }
 
 /* Returns a properly formatted std::string
 * up til the command specified is encountered
@@ -238,66 +253,66 @@ std::string getStringTilCommand(TokenList &tokList){
 //TODO check that this behaves properly for formulas
 
 std::string getStringTilEndCommand(std::string theCommand, TokenList &tokList){
-	 std::string description;
-	 if (tokList.peek().tokenType == 0) return "";
-	 while(tokList.peek().tokenString.compare(theCommand) != 0 ){
-		 Token currentToken = tokList.next();
-		 description = description + currentToken.tokenString + " ";
-		 }
-	return description;
-	}
+   std::string description;
+   if (tokList.peek().tokenType == 0) return "";
+   while(tokList.peek().tokenString.compare(theCommand) != 0 ){
+     Token currentToken = tokList.next();
+     description = description + currentToken.tokenString + " ";
+     }
+  return description;
+  }
 
 /* Returns the end of a Paragraph as an iterator-
 * Paragraph is defined in Doxygen to be a paragraph of text
 * seperate by either a structural command or a blank line
 */
 std::list<Token>::iterator getEndOfParagraph(TokenList &tokList){
-	 std::list<Token>::iterator endOfParagraph = tokList.iteratorCopy();
-	 while(endOfParagraph != tokList.end()){
-		if ((* endOfParagraph).tokenType == END_LINE){
-			 endOfParagraph++;
-			 if ((* endOfParagraph).tokenType == END_LINE){
-				 endOfParagraph++;
-				 //cout << "ENCOUNTERED END OF PARA" << endl;
-				 return endOfParagraph;
-				 }
-			 }
-		else if ((* endOfParagraph).tokenType == COMMAND){
-			 if(isSectionIndicator((* endOfParagraph).tokenString)) return endOfParagraph;
-			 else endOfParagraph++;
-			 }
-		else if((* endOfParagraph).tokenType == PLAINSTRING) {
-			 endOfParagraph++;
-			 }
-		else return tokList.end();
-		}
-	 return tokList.end();
-	 }
+   std::list<Token>::iterator endOfParagraph = tokList.iteratorCopy();
+   while(endOfParagraph != tokList.end()){
+    if ((* endOfParagraph).tokenType == END_LINE){
+       endOfParagraph++;
+       if ((* endOfParagraph).tokenType == END_LINE){
+         endOfParagraph++;
+         //cout << "ENCOUNTERED END OF PARA" << endl;
+         return endOfParagraph;
+         }
+       }
+    else if ((* endOfParagraph).tokenType == COMMAND){
+       if(isSectionIndicator((* endOfParagraph).tokenString)) return endOfParagraph;
+       else endOfParagraph++;
+       }
+    else if((* endOfParagraph).tokenType == PLAINSTRING) {
+       endOfParagraph++;
+       }
+    else return tokList.end();
+    }
+   return tokList.end();
+   }
 
 /* Returns the end of a section, defined as the first blank line OR first encounter of the same 
 * command. Example of this behaviour is \arg
 * if no end is encountered, returns the last token of the std::list.
 */
 std::list<Token>::iterator getEndOfSection(std::string theCommand, TokenList &tokList){
-	 std::list<Token>::iterator endOfParagraph = tokList.iteratorCopy();
-	 while(endOfParagraph != tokList.end()){
-		if ((* endOfParagraph).tokenType == COMMAND){
-			 if(theCommand.compare((*endOfParagraph).tokenString) == 0) return endOfParagraph;
-			 else endOfParagraph++;
-			 }
-		else if((* endOfParagraph).tokenType == PLAINSTRING) {
-			 endOfParagraph++;
-			 }
-		 else if ((* endOfParagraph).tokenType == END_LINE){
-			 endOfParagraph++;
-			 if ((* endOfParagraph).tokenType == END_LINE){
-				 endOfParagraph++;
-				 return endOfParagraph;
-				 }
-			 }
-		}
-	 return tokList.end();
-	 }
+   std::list<Token>::iterator endOfParagraph = tokList.iteratorCopy();
+   while(endOfParagraph != tokList.end()){
+    if ((* endOfParagraph).tokenType == COMMAND){
+       if(theCommand.compare((*endOfParagraph).tokenString) == 0) return endOfParagraph;
+       else endOfParagraph++;
+       }
+    else if((* endOfParagraph).tokenType == PLAINSTRING) {
+       endOfParagraph++;
+       }
+     else if ((* endOfParagraph).tokenType == END_LINE){
+       endOfParagraph++;
+       if ((* endOfParagraph).tokenType == END_LINE){
+         endOfParagraph++;
+         return endOfParagraph;
+         }
+       }
+    }
+   return tokList.end();
+   }
 
 /* This method is for returning the end of a specific form of doxygen command
  * that begins with a \command and ends in \endcommand
@@ -306,26 +321,27 @@ std::list<Token>::iterator getEndOfSection(std::string theCommand, TokenList &to
  * If the end is never encountered, it returns the end of the std::list.
  */
 std::list<Token>::iterator getEndCommand(std::string theCommand, TokenList &tokList){
-	std::list<Token>::iterator endOfCommand = tokList.iteratorCopy();
-	while (endOfCommand!= tokList.end()){
-		if ((*endOfCommand).tokenType == COMMAND){
-			if (theCommand.compare((* endOfCommand).tokenString) == 0){
-				return endOfCommand;
-			}
-			endOfCommand++;
-		}
-	}
-	//End command not found
-	return tokList.end();
+  std::list<Token>::iterator endOfCommand = tokList.iteratorCopy();
+  while (endOfCommand!= tokList.end()){
+    if ((*endOfCommand).tokenType == COMMAND){
+      if (theCommand.compare((* endOfCommand).tokenString) == 0){
+        return endOfCommand;
+      }
+      endOfCommand++;
+    }
+  }
+  //End command not found
+  return tokList.end();
 }
 
 /* A specialty method for commands such as \arg that end at the end of a paragraph OR when another \arg is encountered
  */
 //TODO getTilAnyCommand
 std::list<Token>::iterator getTilAnyCommand(std::string theCommand, TokenList &tokList){
-	std::list<Token>::iterator anIterator;
-	return anIterator;
-	}
+#pragma unused(theCommand,tokList)
+  std::list<Token>::iterator anIterator;
+  return anIterator;
+}
 
 
 
@@ -335,325 +351,349 @@ std::list<Token>::iterator getTilAnyCommand(std::string theCommand, TokenList &t
  * Plain commands, such as newline etc, they contain no other data
  *  \n \\ \@ \& \$ \# \< \> \%
  */
- int addSimpleCommand(std::string theCommand, std::list <DoxygenEntity> &doxyList){
-		if (noisy) cout << "Parsing " << theCommand << endl;
-		doxyList.push_back(DoxygenEntity(theCommand));
-		return 1;
-		}
- 
- /* NOT INCLUDED Simple Commands
-  * Format: @command
-  * Plain commands, such as newline etc, they contain no other data
-  */
- int ignoreSimpleCommand(std::string theCommand, std::list <DoxygenEntity> &doxyList){
-		if (noisy) cout << "Not Adding " << theCommand << endl;
-		return 1;
-		}
- 
- /* CommandWord
-  * Format: @command <word>
-  * Commands with a single WORD after then such as @b
-  * "a", "b", "c", "e", "em", "p", "def", "enum", "example", "package", 
-  * "relates", "namespace", "relatesalso","anchor", "dontinclude", "include", "includelineno"
-  */
- int addCommandWord(std::string theCommand, TokenList &tokList, std::list <DoxygenEntity> &doxyList){
-	if (noisy) cout << "Parsing " << theCommand << endl;
-	std::string name = getNextWord(tokList);
-	if (!name.empty()){ 
-		doxyList.push_back(DoxygenEntity(theCommand, name));
-		return 1;
-		}
-	else cout << "No word followed " << theCommand <<  " command. Not added" << endl;
-	return 0;
-	}
- 
- /* NOT INCLUDED CommandWord
-  * Format: @command <word>
-  * Commands with a single WORD after then such as @b
-  * "copydoc", "copybrief", "copydetails", "verbinclude", "htmlinclude"
-  */
- int ignoreCommandWord(std::string theCommand, TokenList &tokList, std::list <DoxygenEntity> &doxyList){
-	if (noisy) cout << "Not Adding " << theCommand << endl;
-	std::string name = getNextWord(tokList);
-	if (!name.empty()){ 
-		return 1;
-		}
-	else cout << "WARNING: No word followed " << theCommand <<  " command." << endl;
-	return 0;
-	}
- 
- /* CommandLine
-  * Format: @command (line)
-  * Commands with a single LINE after then such as @var
-  * "addindex", "fn", "name", "line", "var", "skipline", "typedef", "skip", "until", "property"
-  */
- int addCommandLine(std::string theCommand, TokenList &tokList, std::list <DoxygenEntity> &doxyList){
-	if (noisy) cout << "Parsing " << theCommand << endl;
-	std::list<Token>::iterator endOfLine = getOneLine(tokList);
-	std::list <DoxygenEntity> aNewList;
-	aNewList =  parse(endOfLine, tokList);
-	doxyList.push_back( DoxygenEntity(theCommand, aNewList));
-	return 1;
-	}
- 
- /* NOT INCLUDED CommandLine
-  * Format: @command (line)
-  * Commands with a single LINE after then such as @var
-  * 
-  */
- int ignoreCommandLine(std::string theCommand, TokenList &tokList, std::list <DoxygenEntity> &doxyList){
-	if (noisy) cout << "Not Adding " << theCommand << endl;
-	std::list<Token>::iterator endOfLine = getOneLine(tokList);
-	tokList.setIterator(endOfLine);
-	return 1;
+int addSimpleCommand(std::string theCommand, std::list <DoxygenEntity> &doxyList){
+  if (noisy) cout << "Parsing " << theCommand << endl;
+  doxyList.push_back(DoxygenEntity(theCommand));
+  return 1;
 }
  
- /* CommandParagraph
-  * Format: @command {paragraph}
-  * Commands with a single paragraph after then such as @return
-  * "return", "remarks", "since", "test", "sa", "see", "pre", "post", "details", "invariant", 
-  * "deprecated", "date", "note", "warning", "version", "todo", "bug", "attention", "brief", "arg", "author"
-  */
- int addCommandParagraph(std::string theCommand, TokenList &tokList, std::list <DoxygenEntity> &doxyList){
-	if (noisy) cout << "Parsing " << theCommand << endl;
-	std::list<Token>::iterator endOfParagraph = getEndOfParagraph(tokList);
-	std::list <DoxygenEntity> aNewList;
-	aNewList =  parse(endOfParagraph, tokList);
-	doxyList.push_back( DoxygenEntity(theCommand, aNewList));
-	return 1;
-	}
- 
- /* CommandParagraph
-  * Format: @command {paragraph}
-  * Commands with a single LINE after then such as @var
-  * 
-  */
- int ignoreCommandParagraph(std::string theCommand, TokenList &tokList, std::list <DoxygenEntity> &doxyList){
-	if (noisy) cout << "Not Adding " << theCommand << endl;
-	std::list<Token>::iterator endOfParagraph = getEndOfParagraph(tokList);
-	tokList.setIterator(endOfParagraph);
-	return 1;
+/* NOT INCLUDED Simple Commands
+* Format: @command
+* Plain commands, such as newline etc, they contain no other data
+*/
+int ignoreSimpleCommand(std::string theCommand, std::list <DoxygenEntity> &doxyList){
+#pragma unused(doxyList)
+  if (noisy) cout << "Not Adding " << theCommand << endl;
+  return 1;
 }
  
- /* Command EndCommand
-  * Format: @command and ends at @endcommand
-  * Commands that take in a block of text such as @code
-  * "code", "dot", "msc", "f$", "f[", "f{environment}{", "htmlonly", "latexonly", "manonly", 
-  * "verbatim", "xmlonly", "cond", "if", "ifnot", "link"
-  * Returns 1 if success, 0 if the endcommand is never encountered.
-  */
- int addCommandEndCommand(std::string theCommand, TokenList &tokList, std::list <DoxygenEntity> &doxyList){
-	  if (noisy) cout << "Not Adding " << theCommand << endl;
-	  std::string description = getStringTilEndCommand( "end" + theCommand, tokList);
-	  doxyList.push_back(DoxygenEntity(theCommand, description));
-	  return 1;
-	  }
+/* CommandWord
+* Format: @command <word>
+* Commands with a single WORD after then such as @b
+* "a", "b", "c", "e", "em", "p", "def", "enum", "example", "package", 
+* "relates", "namespace", "relatesalso","anchor", "dontinclude", "include", "includelineno"
+*/
+int addCommandWord(std::string theCommand, TokenList &tokList, std::list <DoxygenEntity> &doxyList){
+  if (noisy) cout << "Parsing " << theCommand << endl;
+  std::string name = getNextWord(tokList);
+  if (!name.empty()){ 
+    doxyList.push_back(DoxygenEntity(theCommand, name));
+    return 1;
+  }
+  else 
+    cout << "No word followed " << theCommand <<  " command. Not added" << endl;
+  return 0;
+}
  
- /* CommandWordParagraph
-  * Format: @command <word> {paragraph}
-  * Commands such as param
-  * "param", "tparam", "throw", "retval", "exception"
-  */
- int addCommandWordParagraph(std::string theCommand, TokenList &tokList, std::list <DoxygenEntity> &doxyList){
-	if (noisy) cout << "Parsing " << theCommand << endl;
-	std::string name = getNextWord(tokList);
-	if (name.empty()){ 
-		cout << "No word followed " << theCommand <<  " command. Not added" << endl;
-		return 0;
-		}
-	std::list<Token>::iterator endOfParagraph = getEndOfParagraph(tokList);
-	std::list <DoxygenEntity> aNewList;
-	aNewList =  parse(endOfParagraph, tokList);
-	aNewList.push_front(DoxygenEntity("plainstd::string", name));
-	doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-	return 1;
-	}
- 
- /* CommandWordLine
-  * Format: @command <word> (line)
-  * Commands such as param
-  * "page", "subsection", "subsubsection", "section", "paragraph", "defgroup"
-  */
- int addCommandWordLine(std::string theCommand, TokenList &tokList, std::list <DoxygenEntity> &doxyList){
-	if (noisy) cout << "Parsing " << theCommand << endl;
-	std::string name = getNextWord(tokList);
-	if (name.empty()){ 
-		cout << "No word followed " << theCommand <<  " command. Not added" << endl;
-		return 0;
-		}
-	std::list<Token>::iterator endOfLine = getOneLine(tokList);
-	std::list <DoxygenEntity> aNewList;
-	aNewList =  parse(endOfLine, tokList);
-	aNewList.push_front(DoxygenEntity("plainstd::string", name));
-	doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-	return 1;
-		
-	//else cout << "No line followed " << theCommand <<  " command. Not added" << endl;
- }
+/* NOT INCLUDED CommandWord
+* Format: @command <word>
+* Commands with a single WORD after then such as @b
+* "copydoc", "copybrief", "copydetails", "verbinclude", "htmlinclude"
+*/
+int ignoreCommandWord(std::string theCommand, TokenList &tokList, std::list <DoxygenEntity> &doxyList){
+#pragma unused(doxyList)
+  if (noisy) 
+    cout << "Not Adding " << theCommand << endl;
+  std::string name = getNextWord(tokList);
+  if (!name.empty())
+    return 1;
+  else 
+    cout << "WARNING: No word followed " << theCommand <<  " command." << endl;
+  return 0;
+}
 
- /* Command Word Optional Word Optional Word
-  * Format: @command <word> [<header-file>] [<header-name>]
-  * Commands such as class
-  * "category", "class", "protocol", "interface", "struct", "union"
-  */
- int addCommandWordOWordOWord(std::string theCommand, TokenList &tokList, std::list <DoxygenEntity> &doxyList){
-	if (noisy) cout << "Parsing " << theCommand << endl;
-	std::string name = getNextWord(tokList);
-	if (name.empty()){ 
-			cout << "No word followed " << theCommand <<  " command. Not added" << endl;
-			return 0;
-			}
-	std::string headerfile = getNextWord(tokList);
-	std::string headername = getNextWord(tokList);
-	std::list <DoxygenEntity> aNewList;
-	aNewList.push_back(DoxygenEntity("plainstd::string", name));
-	if (!headerfile.empty()) aNewList.push_back(DoxygenEntity("plainstd::string", headerfile));
-	if (!headername.empty()) aNewList.push_back(DoxygenEntity("plainstd::string", headername));
-	doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-	return 1;
-	}
+/* CommandLine
+* Format: @command (line)
+* Commands with a single LINE after then such as @var
+* "addindex", "fn", "name", "line", "var", "skipline", "typedef", "skip", "until", "property"
+*/
+int addCommandLine(std::string theCommand, TokenList &tokList, std::list <DoxygenEntity> &doxyList){
+  if (noisy) 
+    cout << "Parsing " << theCommand << endl;
+  std::list<Token>::iterator endOfLine = getOneLine(tokList);
+  std::list <DoxygenEntity> aNewList = parse(endOfLine, tokList);
+  doxyList.push_back( DoxygenEntity(theCommand, aNewList));
+  return 1;
+}
+
+/* NOT INCLUDED CommandLine
+* Format: @command (line)
+* Commands with a single LINE after then such as @var
+* 
+*/
+int ignoreCommandLine(std::string theCommand, TokenList &tokList, std::list <DoxygenEntity> &doxyList){
+#pragma unused(doxyList)
+  if (noisy) 
+    cout << "Not Adding " << theCommand << endl;
+  std::list<Token>::iterator endOfLine = getOneLine(tokList);
+  tokList.setIterator(endOfLine);
+  return 1;
+}
+
+/* CommandParagraph
+* Format: @command {paragraph}
+* Commands with a single paragraph after then such as @return
+* "return", "remarks", "since", "test", "sa", "see", "pre", "post", "details", "invariant", 
+* "deprecated", "date", "note", "warning", "version", "todo", "bug", "attention", "brief", "arg", "author"
+*/
+int addCommandParagraph(std::string theCommand, TokenList &tokList, std::list <DoxygenEntity> &doxyList){
+  if (noisy) 
+    cout << "Parsing " << theCommand << endl;
+  std::list<Token>::iterator endOfParagraph = getEndOfParagraph(tokList);
+  std::list <DoxygenEntity> aNewList;
+  aNewList =  parse(endOfParagraph, tokList);
+  doxyList.push_back( DoxygenEntity(theCommand, aNewList));
+  return 1;
+}
  
- /* Command Optional Word
-  * Format: @command [<word>]
-  * Commands such as dir
-  * "dir", "file", "cond"
-  */
- int addCommandOWord(std::string theCommand, TokenList &tokList, std::list <DoxygenEntity> &doxyList){
-	if (noisy) cout << "Parsing " << theCommand << endl;
-	std::string name = getNextWord(tokList);
-	doxyList.push_back(DoxygenEntity(theCommand, name));
-	return 1; 
- }
+/* CommandParagraph
+* Format: @command {paragraph}
+* Commands with a single LINE after then such as @var
+* 
+*/
+int ignoreCommandParagraph(std::string theCommand, TokenList &tokList, std::list <DoxygenEntity> &doxyList){
+#pragma unused(doxyList)
+  if (noisy) 
+    cout << "Not Adding " << theCommand << endl;
+  std::list<Token>::iterator endOfParagraph = getEndOfParagraph(tokList);
+  tokList.setIterator(endOfParagraph);
+  return 1;
+}
+ 
+/* Command EndCommand
+* Format: @command and ends at @endcommand
+* Commands that take in a block of text such as @code
+* "code", "dot", "msc", "f$", "f[", "f{environment}{", "htmlonly", "latexonly", "manonly", 
+* "verbatim", "xmlonly", "cond", "if", "ifnot", "link"
+* Returns 1 if success, 0 if the endcommand is never encountered.
+*/
+int addCommandEndCommand(std::string theCommand, TokenList &tokList, std::list <DoxygenEntity> &doxyList){
+  if (noisy) 
+    cout << "Not Adding " << theCommand << endl;
+  std::string description = getStringTilEndCommand( "end" + theCommand, tokList);
+  doxyList.push_back(DoxygenEntity(theCommand, description));
+  return 1;
+}
+ 
+/* CommandWordParagraph
+* Format: @command <word> {paragraph}
+* Commands such as param
+* "param", "tparam", "throw", "retval", "exception"
+*/
+int addCommandWordParagraph(std::string theCommand, TokenList &tokList, std::list <DoxygenEntity> &doxyList){
+  if (noisy) 
+    cout << "Parsing " << theCommand << endl;
+  std::string name = getNextWord(tokList);
+  if (name.empty()){ 
+    cout << "No word followed " << theCommand <<  " command. Not added" << endl;
+    return 0;
+    }
+  std::list<Token>::iterator endOfParagraph = getEndOfParagraph(tokList);
+  std::list <DoxygenEntity> aNewList;
+  aNewList =  parse(endOfParagraph, tokList);
+  aNewList.push_front(DoxygenEntity("plainstd::string", name));
+  doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+  return 1;
+}
+
+/* CommandWordLine
+* Format: @command <word> (line)
+* Commands such as param
+* "page", "subsection", "subsubsection", "section", "paragraph", "defgroup"
+*/
+int addCommandWordLine(std::string theCommand, TokenList &tokList, std::list <DoxygenEntity> &doxyList){
+  if (noisy) cout << "Parsing " << theCommand << endl;
+    std::string name = getNextWord(tokList);
+  if (name.empty()){ 
+    cout << "No word followed " << theCommand <<  " command. Not added" << endl;
+    return 0;
+    }
+  std::list<Token>::iterator endOfLine = getOneLine(tokList);
+  std::list <DoxygenEntity> aNewList;
+  aNewList =  parse(endOfLine, tokList);
+  aNewList.push_front(DoxygenEntity("plainstd::string", name));
+  doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+  return 1;
+  //else cout << "No line followed " << theCommand <<  " command. Not added" << endl;
+}
+
+/* Command Word Optional Word Optional Word
+* Format: @command <word> [<header-file>] [<header-name>]
+* Commands such as class
+* "category", "class", "protocol", "interface", "struct", "union"
+*/
+int addCommandWordOWordOWord(std::string theCommand, TokenList &tokList, std::list <DoxygenEntity> &doxyList){
+  if (noisy) 
+    cout << "Parsing " << theCommand << endl;
+  std::string name = getNextWord(tokList);
+  if (name.empty()){ 
+      cout << "No word followed " << theCommand <<  " command. Not added" << endl;
+      return 0;
+      }
+  std::string headerfile = getNextWord(tokList);
+  std::string headername = getNextWord(tokList);
+  std::list <DoxygenEntity> aNewList;
+  aNewList.push_back(DoxygenEntity("plainstd::string", name));
+  if (!headerfile.empty()) 
+    aNewList.push_back(DoxygenEntity("plainstd::string", headerfile));
+  if (!headername.empty()) 
+    aNewList.push_back(DoxygenEntity("plainstd::string", headername));
+  doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+  return 1;
+}
+
+/* Command Optional Word
+* Format: @command [<word>]
+* Commands such as dir
+* "dir", "file", "cond"
+*/
+int addCommandOWord(std::string theCommand, TokenList &tokList, std::list <DoxygenEntity> &doxyList){
+  if (noisy) 
+    cout << "Parsing " << theCommand << endl;
+  std::string name = getNextWord(tokList);
+  doxyList.push_back(DoxygenEntity(theCommand, name));
+  return 1; 
+}
 
  /* Commands that should not be encountered (such as PHP only)
   * goes til the end of line then returns
   */
- int addCommandErrorThrow(std::string theCommand, TokenList &tokList, std::list <DoxygenEntity> &doxyList){
-	  cout << "Encountered :" << theCommand << endl;
-	  cout << "This command should not have been encountered. Behaviour past this may be unpredictable " << endl;
-	  std::list<Token>::iterator endOfLine = getOneLine(tokList);
-	  tokList.setIterator(endOfLine);
-	  return 0;
+int addCommandErrorThrow(std::string theCommand, TokenList &tokList, std::list <DoxygenEntity> &doxyList){
+#pragma unused(doxyList)
+    cout << "Encountered :" << theCommand << endl;
+    cout << "This command should not have been encountered. Behaviour past this may be unpredictable " << endl;
+    std::list<Token>::iterator endOfLine = getOneLine(tokList);
+    tokList.setIterator(endOfLine);
+    return 0;
  }
 
 /* Adds the unique commands- different process for each unique command */
- int addCommandUnique(std::string theCommand, TokenList &tokList, std::list <DoxygenEntity> &doxyList){
-	  std::list <DoxygenEntity> aNewList;
-	  if (theCommand.compare("arg") == 0 || theCommand.compare("li") == 0){
-			std::list<Token>::iterator endOfSection = getEndOfSection(theCommand, tokList);
-			std::list <DoxygenEntity> aNewList;
-			aNewList =  parse(endOfSection, tokList);
-			doxyList.push_back( DoxygenEntity(theCommand, aNewList));
-			}
-	  // \xrefitem <key> "(heading)" "(std::list title)" {text}
-	  else if (theCommand.compare("xrefitem") == 0){
-		  //TODO Implement xrefitem
-			if (noisy) cout << "Not Adding " << theCommand << endl;
-			std::list<Token>::iterator endOfParagraph = getEndOfParagraph(tokList);
-			tokList.setIterator(endOfParagraph);
-		  return 1;
-		  }
-	  // \ingroup (<groupname> [<groupname> <groupname>])
-	  else if (theCommand.compare("ingroup") == 0){
-		  std::string name = getNextWord(tokList);
-		  aNewList.push_back(DoxygenEntity("plainstd::string", name));
-		  name = getNextWord(tokList);
-		  if(!name.empty()) aNewList.push_back(DoxygenEntity("plainstd::string", name));
-		  name = getNextWord(tokList);
-		  if(!name.empty()) aNewList.push_back(DoxygenEntity("plainstd::string", name));
-		  doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-		  return 1;
-		  }
-	  // \par [(paragraph title)] { paragraph }
-	  else if (theCommand.compare("par") == 0){
-		  std::list<Token>::iterator endOfLine = getOneLine(tokList);
-		  aNewList =  parse(endOfLine, tokList);
-		  std::list <DoxygenEntity> aNewList2;
-		  aNewList2 = parse(endOfLine, tokList);
-		  aNewList.splice(aNewList.end(), aNewList2);
-		  doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-		  return 1; 
-		  }
-	  // \headerfile <header-file> [<header-name>]
-	  else if (theCommand.compare("headerfile") == 0){
-		  std::list <DoxygenEntity> aNewList;
-		  std::string name = getNextWord(tokList);
-		  aNewList.push_back(DoxygenEntity("plainstd::string", name));
-		  name = getNextWord(tokList);
-		  if(!name.empty()) aNewList.push_back(DoxygenEntity("plainstd::string", name));
-		  doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-		  return 1;
-		  }
-	  // \overload [(function declaration)]
-	  else if (theCommand.compare("overload") == 0){
-		  std::list<Token>::iterator endOfLine = getOneLine(tokList);
-		  if (endOfLine != tokList.current()){
-		    std::list <DoxygenEntity> aNewList;
-		    aNewList =  parse(endOfLine, tokList);
-		    doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-		    }
-		  else doxyList.push_back(DoxygenEntity(theCommand));
-		  return 1;
-		  }
-	  // \weakgroup <name> [(title)]
-	  else if (theCommand.compare("weakgroup") == 0){
-		    if (noisy) cout << "Parsing " << theCommand << endl;
-			std::string name = getNextWord(tokList);
-			if (name.empty()){ 
-				cout << "No word followed " << theCommand <<  " command. Not added" << endl;
-				return 0;
-				}
-			std::list <DoxygenEntity> aNewList;
-			std::list<Token>::iterator endOfLine = getOneLine(tokList);
-			if (endOfLine != tokList.current()) {
-				aNewList =  parse(endOfLine, tokList);
-				}
-			aNewList.push_front(DoxygenEntity("plainstd::string", name));
-			doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-			}
-	  // \ref <name> ["(text)"]
-	  else if (theCommand.compare("ref") == 0){
-		  //TODO Implement ref
-			if (noisy) cout << "Not Adding " << theCommand << endl;
-			std::list<Token>::iterator endOfParagraph = getEndOfParagraph(tokList);
-			tokList.setIterator(endOfParagraph);
-			}
-	  // \subpage <name> ["(text)"]
-	  else if (theCommand.compare("subpage") == 0){
-		  //TODO implement subpage
-			if (noisy) cout << "Not Adding " << theCommand << endl;
-			std::list<Token>::iterator endOfParagraph = getEndOfParagraph(tokList);
-			tokList.setIterator(endOfParagraph);
-			}
-	  // \dotfile <file> ["caption"]
-	  else if (theCommand.compare("dotfile") == 0){
-		  //TODO implement dotfile
-			if (noisy) cout << "Not Adding " << theCommand << endl;
-			std::list<Token>::iterator endOfParagraph = getEndOfParagraph(tokList);
-			tokList.setIterator(endOfParagraph);
-			}
-	  // \image <format> <file> ["caption"] [<sizeindication>=<size>]
-	  else if (theCommand.compare("image") == 0){
-		  //todo implement image
-		  } 
-	  // \addtogroup <name> [(title)]
-	  else if (theCommand.compare("addtogroup") == 0){
-		    if (noisy) cout << "Parsing " << theCommand << endl;
-			std::string name = getNextWord(tokList);
-			if (name.empty()){ 
-				cout << "No word followed " << theCommand <<  " command. Not added" << endl;
-				return 0;
-				}
-			std::list <DoxygenEntity> aNewList;
-			std::list<Token>::iterator endOfLine = getOneLine(tokList);
-			if (endOfLine != tokList.current()) {
-				aNewList =  parse(endOfLine, tokList);
-				}
-			aNewList.push_front(DoxygenEntity("plainstd::string", name));
-			doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-			}
-	  return 0;
-	  }
+int addCommandUnique(std::string theCommand, TokenList &tokList, std::list <DoxygenEntity> &doxyList){
+  std::list <DoxygenEntity> aNewList;
+  if (theCommand.compare("arg") == 0 || theCommand.compare("li") == 0){
+    std::list<Token>::iterator endOfSection = getEndOfSection(theCommand, tokList);
+    std::list <DoxygenEntity> aNewList;
+    aNewList =  parse(endOfSection, tokList);
+    doxyList.push_back( DoxygenEntity(theCommand, aNewList));
+  }
+  // \xrefitem <key> "(heading)" "(std::list title)" {text}
+  else if (theCommand.compare("xrefitem") == 0){
+    //TODO Implement xrefitem
+    if (noisy) 
+      cout << "Not Adding " << theCommand << endl;
+    std::list<Token>::iterator endOfParagraph = getEndOfParagraph(tokList);
+    tokList.setIterator(endOfParagraph);
+    return 1;
+  }
+  // \ingroup (<groupname> [<groupname> <groupname>])
+  else if (theCommand.compare("ingroup") == 0){
+    std::string name = getNextWord(tokList);
+    aNewList.push_back(DoxygenEntity("plainstd::string", name));
+    name = getNextWord(tokList);
+    if(!name.empty()) 
+      aNewList.push_back(DoxygenEntity("plainstd::string", name));
+    name = getNextWord(tokList);
+    if(!name.empty()) 
+      aNewList.push_back(DoxygenEntity("plainstd::string", name));
+    doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+    return 1;
+  }
+  // \par [(paragraph title)] { paragraph }
+  else if (theCommand.compare("par") == 0){
+    std::list<Token>::iterator endOfLine = getOneLine(tokList);
+    aNewList =  parse(endOfLine, tokList);
+    std::list <DoxygenEntity> aNewList2;
+    aNewList2 = parse(endOfLine, tokList);
+    aNewList.splice(aNewList.end(), aNewList2);
+    doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+    return 1; 
+  }
+  // \headerfile <header-file> [<header-name>]
+  else if (theCommand.compare("headerfile") == 0){
+    std::list <DoxygenEntity> aNewList;
+    std::string name = getNextWord(tokList);
+    aNewList.push_back(DoxygenEntity("plainstd::string", name));
+    name = getNextWord(tokList);
+    if(!name.empty()) 
+      aNewList.push_back(DoxygenEntity("plainstd::string", name));
+    doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+    return 1;
+  }
+  // \overload [(function declaration)]
+  else if (theCommand.compare("overload") == 0){
+    std::list<Token>::iterator endOfLine = getOneLine(tokList);
+    if (endOfLine != tokList.current()){
+      std::list <DoxygenEntity> aNewList;
+      aNewList =  parse(endOfLine, tokList);
+      doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+    }
+    else 
+      doxyList.push_back(DoxygenEntity(theCommand));
+    return 1;
+  }
+  // \weakgroup <name> [(title)]
+  else if (theCommand.compare("weakgroup") == 0){
+    if (noisy) cout << "Parsing " << theCommand << endl;
+      std::string name = getNextWord(tokList);
+      if (name.empty()){ 
+	cout << "No word followed " << theCommand <<  " command. Not added" << endl;
+      return 0;
+    }
+    std::list <DoxygenEntity> aNewList;
+    std::list<Token>::iterator endOfLine = getOneLine(tokList);
+    if (endOfLine != tokList.current()) {
+      aNewList =  parse(endOfLine, tokList);
+    }
+    aNewList.push_front(DoxygenEntity("plainstd::string", name));
+    doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+  }
+  // \ref <name> ["(text)"]
+  else if (theCommand.compare("ref") == 0){
+    //TODO Implement ref
+    if (noisy) 
+      cout << "Not Adding " << theCommand << endl;
+    std::list<Token>::iterator endOfParagraph = getEndOfParagraph(tokList);
+    tokList.setIterator(endOfParagraph);
+  }
+  // \subpage <name> ["(text)"]
+  else if (theCommand.compare("subpage") == 0){
+    //TODO implement subpage
+    if (noisy) 
+      cout << "Not Adding " << theCommand << endl;
+    std::list<Token>::iterator endOfParagraph = getEndOfParagraph(tokList);
+    tokList.setIterator(endOfParagraph);
+  }
+  // \dotfile <file> ["caption"]
+  else if (theCommand.compare("dotfile") == 0){
+    //TODO implement dotfile
+    if (noisy) 
+      cout << "Not Adding " << theCommand << endl;
+    std::list<Token>::iterator endOfParagraph = getEndOfParagraph(tokList);
+    tokList.setIterator(endOfParagraph);
+  }
+  // \image <format> <file> ["caption"] [<sizeindication>=<size>]
+  else if (theCommand.compare("image") == 0){
+  //todo implement image
+  } 
+  // \addtogroup <name> [(title)]
+  else if (theCommand.compare("addtogroup") == 0){
+    if (noisy) 
+      cout << "Parsing " << theCommand << endl;
+    std::string name = getNextWord(tokList);
+    if (name.empty()){ 
+      cout << "No word followed " << theCommand <<  " command. Not added" << endl;
+      return 0;
+    }
+    std::list <DoxygenEntity> aNewList;
+    std::list<Token>::iterator endOfLine = getOneLine(tokList);
+    if (endOfLine != tokList.current()) {
+      aNewList =  parse(endOfLine, tokList);
+    }
+    aNewList.push_front(DoxygenEntity("plainstd::string", name));
+    doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+  }
+  return 0;
+}
  
 /* The actual "meat" of the doxygen parser. This is not yet fully implemented
  * with my current design- however the skeletal outline is contained in
@@ -662,129 +702,132 @@ std::list<Token>::iterator getTilAnyCommand(std::string theCommand, TokenList &t
 
 
 int addCommand(std::string commandString, TokenList &tokList,std::list <DoxygenEntity> &doxyList){
-	 std::string theCommand = StringToLower(commandString);
-	 if (theCommand.compare("plainstd::string") == 0){
-	 		std::string nextPhrase = getStringTilCommand( tokList);
-	 		if (noisy) cout << "Parsing plain std::string :" << nextPhrase << endl;
-	 		doxyList.push_back(DoxygenEntity("plainstd::string", nextPhrase ));
-	 		return 1;
-	 		}
-	 int commandNumber = commandBelongs(theCommand);
-	 if (commandNumber == SIMPLECOMMAND){
-	 	return addSimpleCommand(theCommand, doxyList);
-	 	}
-	 if (commandNumber == IGNOREDSIMPLECOMMAND){
-	 	return ignoreSimpleCommand(theCommand, doxyList);
-	 	}
-	 if (commandNumber == COMMANDWORD){
-	 	return addCommandWord(theCommand, tokList, doxyList);
-	 	}
-	 if (commandNumber == IGNOREDCOMMANDWORD){
-	 	return ignoreCommandWord(theCommand, tokList, doxyList);
-	 	}
-	 if (commandNumber == COMMANDLINE ){
-	 	return addCommandLine(theCommand, tokList, doxyList);
-	 	}
-	 if (commandNumber == IGNOREDCOMMANDLINE ){
-	 	return ignoreCommandLine(theCommand, tokList, doxyList);
-	 	}
-	 if (commandNumber == COMMANDPARAGRAPH){
-	 	return addCommandParagraph(theCommand, tokList, doxyList);
-	 	}
-	 if (commandNumber == IGNORECOMMANDPARAGRAPH){
-	 	return ignoreCommandParagraph(theCommand, tokList, doxyList);
-	 	}
-	 if (commandNumber == COMMANDENDCOMMAND){
-	 	return addCommandEndCommand(theCommand, tokList, doxyList);
-	 	}
-	 if (commandNumber == COMMANDWORDPARAGRAPH){
-	 	return addCommandWordParagraph(theCommand, tokList, doxyList);
-	 	}
-	 if (commandNumber == COMMANDWORDLINE){
-	 	return addCommandWordLine(theCommand, tokList, doxyList);
-	 	}
-	 if (commandNumber == COMMANDWORDOWORDWORD){
-	 	return addCommandWordOWordOWord(theCommand, tokList, doxyList);
-	 	}
-	 if (commandNumber == COMMANDOWORD){
-	 	return addCommandOWord(theCommand, tokList, doxyList);
-	 	}
-	 if (commandNumber == COMMANDERRORTHROW){
-	 	return addCommandErrorThrow(theCommand, tokList, doxyList);
-	 	}
-	 if (commandNumber == COMMANDUNIQUE){
-		return addCommandUnique(theCommand, tokList, doxyList);
-	 	}
-	 	
-	 return 0;
-	 }
+   std::string theCommand = StringToLower(commandString);
+   if (theCommand.compare("plainstd::string") == 0){
+       std::string nextPhrase = getStringTilCommand( tokList);
+       if (noisy) cout << "Parsing plain std::string :" << nextPhrase << endl;
+       doxyList.push_back(DoxygenEntity("plainstd::string", nextPhrase ));
+       return 1;
+       }
+   int commandNumber = commandBelongs(theCommand);
+   if (commandNumber == SIMPLECOMMAND){
+     return addSimpleCommand(theCommand, doxyList);
+     }
+   if (commandNumber == IGNOREDSIMPLECOMMAND){
+     return ignoreSimpleCommand(theCommand, doxyList);
+     }
+   if (commandNumber == COMMANDWORD){
+     return addCommandWord(theCommand, tokList, doxyList);
+     }
+   if (commandNumber == IGNOREDCOMMANDWORD){
+     return ignoreCommandWord(theCommand, tokList, doxyList);
+     }
+   if (commandNumber == COMMANDLINE ){
+     return addCommandLine(theCommand, tokList, doxyList);
+     }
+   if (commandNumber == IGNOREDCOMMANDLINE ){
+     return ignoreCommandLine(theCommand, tokList, doxyList);
+     }
+   if (commandNumber == COMMANDPARAGRAPH){
+     return addCommandParagraph(theCommand, tokList, doxyList);
+     }
+   if (commandNumber == IGNORECOMMANDPARAGRAPH){
+     return ignoreCommandParagraph(theCommand, tokList, doxyList);
+     }
+   if (commandNumber == COMMANDENDCOMMAND){
+     return addCommandEndCommand(theCommand, tokList, doxyList);
+     }
+   if (commandNumber == COMMANDWORDPARAGRAPH){
+     return addCommandWordParagraph(theCommand, tokList, doxyList);
+     }
+   if (commandNumber == COMMANDWORDLINE){
+     return addCommandWordLine(theCommand, tokList, doxyList);
+     }
+   if (commandNumber == COMMANDWORDOWORDWORD){
+     return addCommandWordOWordOWord(theCommand, tokList, doxyList);
+     }
+   if (commandNumber == COMMANDOWORD){
+     return addCommandOWord(theCommand, tokList, doxyList);
+     }
+   if (commandNumber == COMMANDERRORTHROW){
+     return addCommandErrorThrow(theCommand, tokList, doxyList);
+     }
+   if (commandNumber == COMMANDUNIQUE){
+    return addCommandUnique(theCommand, tokList, doxyList);
+     }
+     
+   return 0;
+   }
 
 std::list<DoxygenEntity> parse(std::list<Token>::iterator endParsingIndex, TokenList &tokList){
-	std::list <DoxygenEntity> aNewList;
-	int currCommand;
-	while (tokList.current() != endParsingIndex){ 
-		Token currToken = tokList.peek();
-		if(noisy) cout << "Parsing for phrase starting in:" << currToken.toString() << endl;
-		if(currToken.tokenType == END_LINE ){
-			tokList.next();
-			}
-		else if(currToken.tokenType == COMMAND){
-			currCommand = findCommand(currToken.tokenString);
-			if (currCommand < 0 ){
-				if(noisy) cout << "Unidentified Command " << currToken.tokenString << endl;
-				tokList.next();
-				addCommand(std::string("plainstd::string"), tokList, aNewList);}
-				//cout << "Command: " << currWord << " " << currCommand << endl;
-			else { tokList.next();
-			  addCommand(currToken.tokenString, tokList,  aNewList);
-			  }
-			}
-		else if (currToken.tokenType == PLAINSTRING){
-			addCommand(std::string("plainstd::string"), tokList, aNewList);
-			}
-		else break;
-		}
-	return aNewList;
-	}
+  std::list <DoxygenEntity> aNewList;
+  int currCommand;
+  while (tokList.current() != endParsingIndex){ 
+    Token currToken = tokList.peek();
+    if(noisy) 
+      cout << "Parsing for phrase starting in:" << currToken.toString() << endl;
+    if(currToken.tokenType == END_LINE ){
+      tokList.next();
+    }
+    else if(currToken.tokenType == COMMAND){
+      currCommand = findCommand(currToken.tokenString);
+      if (currCommand < 0 ){
+	if(noisy) 
+	  cout << "Unidentified Command " << currToken.tokenString << endl;
+	tokList.next();
+	addCommand(std::string("plainstd::string"), tokList, aNewList);
+      }
+      else { tokList.next();
+	addCommand(currToken.tokenString, tokList,  aNewList);
+      }
+    }
+    else if (currToken.tokenType == PLAINSTRING){
+      addCommand(std::string("plainstd::string"), tokList, aNewList);
+    }
+    break;
+  }
+  return aNewList;
+}
 
 std::list<DoxygenEntity> parseRoot(std::list<Token>::iterator endParsingIndex, TokenList &tokList){
-	std::list <DoxygenEntity> aNewList;
-	int currCommand;
-	while (tokList.current() != endParsingIndex){ 
-		Token currToken = tokList.peek();
-		if(noisy) cout << "Parsing for phrase starting in:" << currToken.toString() << endl;
-		if(currToken.tokenType == END_LINE ){
-			tokList.next();
-			}
-		else if(currToken.tokenType == COMMAND){
-			currCommand = findCommand(currToken.tokenString);
-			if (currCommand < 0 ){ 
-				if(noisy) cout << "Unidentified Command " << currToken.tokenString << endl;
-				tokList.next();
-				addCommand(std::string("partofdescription"), tokList, aNewList);}
-				//cout << "Command: " << currWord << " " << currCommand << endl;
-			else { tokList.next();
-			  addCommand(currToken.tokenString, tokList,  aNewList);
-			  }
-			}
-		else if (currToken.tokenType == PLAINSTRING){
-			addCommand(std::string("partofdescription"), tokList, aNewList);
-			}
-		}
-	return aNewList;
-	}
+  std::list <DoxygenEntity> aNewList;
+  int currCommand;
+  while (tokList.current() != endParsingIndex){ 
+    Token currToken = tokList.peek();
+    if(noisy) cout << "Parsing for phrase starting in:" << currToken.toString() << endl;
+    if(currToken.tokenType == END_LINE ){
+      tokList.next();
+    }
+    else if(currToken.tokenType == COMMAND){
+      currCommand = findCommand(currToken.tokenString);
+      if (currCommand < 0 ){ 
+        if(noisy) 
+	  cout << "Unidentified Command " << currToken.tokenString << endl;
+        tokList.next();
+      addCommand(std::string("partofdescription"), tokList, aNewList);}
+      //cout << "Command: " << currWord << " " << currCommand << endl;
+      else { tokList.next();
+        addCommand(currToken.tokenString, tokList,  aNewList);
+      }
+    }
+    else if (currToken.tokenType == PLAINSTRING){
+      addCommand(std::string("partofdescription"), tokList, aNewList);
+    }
+  }
+  return aNewList;
+}
 
 std::list<DoxygenEntity> DoxygenParser::createTree(std::string doxygenBlob){
-	TokenList tokList = TokenList(doxygenBlob);
-	if(noisy) {
-		cout << "---TOKEN LIST---" << endl;
-		tokList.printList();
-		}
-	std::list <DoxygenEntity> rootList;
-	rootList = parseRoot( tokList.end(), tokList);
-	if(noisy) {
-		cout << "PARSED LIST" << endl;
-		printTree(rootList);
-		}
-	return rootList;
+  TokenList tokList = TokenList(doxygenBlob);
+  if(noisy) {
+    cout << "---TOKEN LIST---" << endl;
+    tokList.printList();
+  }
+  std::list <DoxygenEntity> rootList;
+  rootList = parseRoot( tokList.end(), tokList);
+  if(noisy) {
+    cout << "PARSED LIST" << endl;
+    printTree(rootList);
+  }
+  return rootList;
 }

From d7f2ceedd4246b9ad8f4ac6c7ee2a6bf593676d0 Mon Sep 17 00:00:00 2001
From: Jamie Kirkpatrick <gringostarr@users.sourceforge.net>
Date: Fri, 12 Sep 2008 11:19:32 +0000
Subject: [PATCH 032/314] Improve output so that the width of the docstrings
 can be controlled.

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2008-cherylfoil@10841 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 .../DoxygenTranslator/src/PyDocConverter.cpp  | 155 ++++++------------
 Source/DoxygenTranslator/src/PyDocConverter.h |   8 +-
 2 files changed, 56 insertions(+), 107 deletions(-)

diff --git a/Source/DoxygenTranslator/src/PyDocConverter.cpp b/Source/DoxygenTranslator/src/PyDocConverter.cpp
index 1e4d6a73e..5bbda8dc2 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/PyDocConverter.cpp
@@ -2,9 +2,6 @@
 #include <iostream>
 #include <sstream>
 
-#define APPROX_LINE_LENGTH 64//characters per line allowed
-#define TAB_SIZE 8//characters per line allowed
-
 //TODO {@link} {@linkplain} {@docRoot}, and other useful doxy commands that are not a pydoc tag
 PyDocConverter::PyDocConverter()
 {
@@ -15,7 +12,7 @@ PyDocConverter::~PyDocConverter()
 {
 }
  
-void PyDocConverter::printSortedTree(std::list <DoxygenEntity> &entityList){
+void PyDocConverter::printTree(std::list <DoxygenEntity> &entityList){
   std::list<DoxygenEntity>::iterator p = entityList.begin();
   while (p != entityList.end()){
     (*p).printEntity(0);
@@ -24,24 +21,23 @@ void PyDocConverter::printSortedTree(std::list <DoxygenEntity> &entityList){
 }
 
 std::string PyDocConverter::formatParam(Node *n, DoxygenEntity &doxygenEntity) {
-  std::string result;
   ParmList *plist = CopyParmList(Getattr(n, "parms"));
   Parm *p = NULL;
   
   DoxygenEntity& paramNameEntity = *doxygenEntity.entityList.begin();
   DoxygenEntity& paramDescriptionEntity = *(++doxygenEntity.entityList.begin());
   
+  std::string result;
+  std::string paramDescription = formatCommand(paramDescriptionEntity.data, DOC_PARAM_STRING_LENGTH);
+  
   for (p = plist; p;) {
     if(Char(Getattr(p, "name")) == paramNameEntity.data) {
       std::string name = Char(Swig_name_make(n, 0, Getattr(p, "name"), 0, 0));
       std::string type = Char(Swig_name_make(n, 0, Getattr(p, "type"), 0, 0));
       
-      std::ostringstream parameterDocString;
-      
-      parameterDocString << std::endl << name << " (" << type << ") -- ";
-      parameterDocString << paramDescriptionEntity.data;
-      
-      result = parameterDocString.str();
+      result = name + " (" + type + ") ";
+      result.resize(DOC_PARAM_STRING_LENGTH - 3, ' ');
+      result += "-- " + paramDescription.substr(DOC_PARAM_STRING_LENGTH);
       break;
     }
     p = Getattr(p, "tmap:in") ? Getattr(p, "tmap:in:next") : nextSibling(p);
@@ -51,88 +47,33 @@ std::string PyDocConverter::formatParam(Node *n, DoxygenEntity &doxygenEntity) {
   return result;
 }
 
-std::string PyDocConverter::formatCommand(std::string unformattedLine, int indent){
-  std::string formattedLines = "\n";
-  int lastPosition = 0;
-  signed int i = 0;
-  bool isFirstLine  = true;
-  while (i != -1 && i < (int)unformattedLine.length()){
-    lastPosition = i;
-    if (isFirstLine){
-      i+=APPROX_LINE_LENGTH;
-    }
-    else i+=APPROX_LINE_LENGTH - indent*TAB_SIZE;
-    i = unformattedLine.find(" ", i);
-
-    if (i > 0 && i + 1 < (int)unformattedLine.length()){
-      if (!isFirstLine) for (int j = 0; j < indent; j++) {
-        formattedLines.append("\t");
-        }
-      else {
-        isFirstLine = false;
-      }
-      formattedLines.append(unformattedLine.substr(lastPosition, i - lastPosition + 1));
-      formattedLines.append("\n");
-
+std::string PyDocConverter::formatCommand(std::string documentString, int indent, int maxWidth){
+  std::ostringstream formattedString;
+  std::string currentLine;
+  
+  for(std::string::iterator stringPosition = documentString.begin(); stringPosition != documentString.end(); ++stringPosition)
+  {
+    if(currentLine.length() == 0)
+      currentLine.resize(indent, ' ');
+    
+    currentLine += *stringPosition;
+      
+    if(*stringPosition == ' ' && (int)currentLine.size() >= maxWidth || (stringPosition + 1) == documentString.end())
+    {
+      formattedString << currentLine << std::endl;
+      currentLine = "";
     }
   }
-  if (lastPosition < (int)unformattedLine.length()){
-    if (!isFirstLine) {for (int j = 0; j < indent; j++) {formattedLines.append("\t");}}
-    formattedLines.append(unformattedLine.substr(lastPosition, unformattedLine.length() - lastPosition));
-  }
-
-  return formattedLines;
+  
+  return formattedString.str();
 }
 
-/* Contains the conversions for tags
- * could probably be much more efficient...
- */
-std::string PyDocConverter::pyDocFormat(DoxygenEntity &doxygenEntity){
-  if(doxygenEntity.typeOfEntity.compare("partofdescription") == 0){
-        return doxygenEntity.data;
-    }
-  if (doxygenEntity.typeOfEntity.compare("plainstd::string") == 0){
-      return  doxygenEntity.data;
-  }
-  else if (doxygenEntity.typeOfEntity.compare("b") == 0){
-    return "<b>" + doxygenEntity.data + "</b>";
-  }
-  else if (doxygenEntity.typeOfEntity.compare("c") == 0){
-    return "<tt>" + doxygenEntity.data + "</tt>";
-  }
-  else if (doxygenEntity.typeOfEntity.compare("@") == 0){
-    return "@";
-  }
-  else if (doxygenEntity.typeOfEntity.compare("\\") == 0){
-    return "\\";
-  }
-  else if (doxygenEntity.typeOfEntity.compare("<") == 0){
-    return "&lt;";
-  }
-  else if (doxygenEntity.typeOfEntity.compare(">") == 0){
-    return "&gt;";
-  }
-  else if (doxygenEntity.typeOfEntity.compare("&") == 0){
-    return "&amp;";
-  }
-  else if (doxygenEntity.typeOfEntity.compare("#") == 0){
-    return "#";
-  }
-  else if (doxygenEntity.typeOfEntity.compare("%") == 0){
-    return "%";
-  }
-  else if (doxygenEntity.typeOfEntity.compare("~") == 0){
-    return "~";
-  }
-  return "";
-}
-
-
 std::string PyDocConverter::translateSubtree( DoxygenEntity &doxygenEntity){
   std::string returnedString;
-  if (doxygenEntity.isLeaf){ return pyDocFormat(doxygenEntity) + " ";}
+  if (doxygenEntity.isLeaf)
+    return doxygenEntity.data + " ";
   else {
-    returnedString += pyDocFormat(doxygenEntity);
+    returnedString += doxygenEntity.data;
     std::list<DoxygenEntity>::iterator p = doxygenEntity.entityList.begin();
     while (p != doxygenEntity.entityList.end()){
       returnedString+= translateSubtree(*p);
@@ -150,8 +91,8 @@ std::string PyDocConverter::translateEntity(Node *n, DoxygenEntity &doxyEntity){
     return formatCommand(std::string(translateSubtree(doxyEntity)), 0) + "\n * ";}
   
   if(doxyEntity.typeOfEntity.compare("plainstd::string")== 0 
-      || doxyEntity.typeOfEntity.compare("deprecated")== 0 
-      || doxyEntity.typeOfEntity.compare("brief")== 0)
+    || doxyEntity.typeOfEntity.compare("deprecated")== 0 
+    || doxyEntity.typeOfEntity.compare("brief")== 0)
     return formatCommand(doxyEntity.data, 0) + "\n * ";
   
   if(doxyEntity.typeOfEntity.compare("see") == 0)
@@ -159,33 +100,38 @@ std::string PyDocConverter::translateEntity(Node *n, DoxygenEntity &doxyEntity){
   
   if(doxyEntity.typeOfEntity.compare("param") == 0)
     return formatParam(n, doxyEntity);
+  
+  if(doxyEntity.typeOfEntity.compare("return")== 0)
+    
 
-  if(doxyEntity.typeOfEntity.compare("return")== 0
-      || doxyEntity.typeOfEntity.compare("author")== 0
-      || doxyEntity.typeOfEntity.compare("param")== 0
-      || doxyEntity.typeOfEntity.compare("since")== 0
-      || doxyEntity.typeOfEntity.compare("version")== 0
-      || doxyEntity.typeOfEntity.compare("exception") == 0
-      || doxyEntity.typeOfEntity.compare("deprecated") == 0)
+  if(doxyEntity.typeOfEntity.compare("author")== 0
+    || doxyEntity.typeOfEntity.compare("param")== 0
+    || doxyEntity.typeOfEntity.compare("since")== 0
+    || doxyEntity.typeOfEntity.compare("version")== 0
+    || doxyEntity.typeOfEntity.compare("exception") == 0
+    || doxyEntity.typeOfEntity.compare("deprecated") == 0)
     return formatCommand(std::string("@" + doxyEntity.typeOfEntity + "\t" + translateSubtree(doxyEntity)), 2);
   
   if(doxyEntity.typeOfEntity.compare("sa")== 0)
     return formatCommand(std::string("@see\t\t" + translateSubtree(doxyEntity)), 2);
 
-  return formatCommand(pyDocFormat(doxyEntity), 0);
+  return formatCommand(doxyEntity.data, 0);
 }
 
 std::string PyDocConverter::convertToPyDoc(Node *n, std::list<DoxygenEntity> entityList){
-  entityList.sort(CompareDoxygenEntities());
+  std::string pyDocString = "\"\"\"\n";
   
-  if(debug){
-    std::cout << "---RESORTED LIST---" << std::endl;
-    printSortedTree(entityList);
-  }
-
-  std::string pyDocString = "\"\"\"";
+  bool inParamsSection = false;
   
   for(std::list<DoxygenEntity>::iterator entityIterator = entityList.begin(); entityIterator != entityList.end();){
+    if(entityIterator->typeOfEntity.compare("param") == 0 && !inParamsSection)
+    {
+      inParamsSection = true;
+      pyDocString += "\nArguments:\n";
+    }
+    else if(entityIterator->typeOfEntity.compare("param") != 0 && inParamsSection)
+      inParamsSection = false;
+    
     pyDocString += translateEntity(n, *entityIterator);
     entityIterator++;
   }
@@ -194,7 +140,8 @@ std::string PyDocConverter::convertToPyDoc(Node *n, std::list<DoxygenEntity> ent
   
   if(debug){
     std::cout << "\n---RESULT IN PYDOC---" << std::endl;
-    std::cout << pyDocString; 
+    std::cout << pyDocString;
+    std::cout << std::endl;
   }
   
   return pyDocString;
diff --git a/Source/DoxygenTranslator/src/PyDocConverter.h b/Source/DoxygenTranslator/src/PyDocConverter.h
index 27faaf6c3..4c7fdd4db 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.h
+++ b/Source/DoxygenTranslator/src/PyDocConverter.h
@@ -6,18 +6,20 @@
 #include "swig.h"
 #include "DoxygenEntity.h"
 
+#define DOC_STRING_LENGTH	  64  // characters per line allowed
+#define DOC_PARAM_STRING_LENGTH	  30  // characters reserved for param name / type
+
 class PyDocConverter
 {
 public:
   PyDocConverter();
   std::string convertToPyDoc(Node *n, std::list <DoxygenEntity> entityList);
   ~PyDocConverter();
-  void printSortedTree(std::list <DoxygenEntity> &entityList);
+  void printTree(std::list <DoxygenEntity> &entityList);
 
 protected:
   std::string formatParam(Node *n, DoxygenEntity &doxygenEntity);
-  std::string formatCommand(std::string unformattedLine, int indent);
-  std::string pyDocFormat(DoxygenEntity &doxygenEntity);
+  std::string formatCommand(std::string unformattedLine, int indent, int maxWidth = DOC_STRING_LENGTH);
   std::string translateSubtree( DoxygenEntity &doxygenEntity);
   std::string translateEntity(Node *n, DoxygenEntity &doxyEntity);
     

From 0f41d25c0938566f4037fd117526f848009d3887 Mon Sep 17 00:00:00 2001
From: Jamie Kirkpatrick <gringostarr@users.sourceforge.net>
Date: Fri, 12 Sep 2008 11:19:53 +0000
Subject: [PATCH 033/314] Ensure doxygen comments are copied to overloaded
 function nodes.

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2008-cherylfoil@10842 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Source/CParse/parser.y | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/Source/CParse/parser.y b/Source/CParse/parser.y
index 95bd8701d..06b0685c6 100644
--- a/Source/CParse/parser.y
+++ b/Source/CParse/parser.y
@@ -1363,6 +1363,10 @@ static void default_arguments(Node *n) {
           if (throws) Setattr(new_function,"throws",pl);
 	  Delete(pl);
         }
+	
+	/* copy doxygen comments if found */
+	if(Getattr(function,"DoxygenComment"))
+	  Setattr(new_function,"DoxygenComment",Getattr(function,"DoxygenComment"));
 
         /* copy specific attributes for global (or in a namespace) template functions - these are not templated class methods */
         if (strcmp(cntype,"template") == 0) {

From 01695a31285dc7101b07b09deae7465caeaad0f3 Mon Sep 17 00:00:00 2001
From: Jamie Kirkpatrick <gringostarr@users.sourceforge.net>
Date: Fri, 12 Sep 2008 11:20:58 +0000
Subject: [PATCH 034/314] Major refactoring: translation now takes a node and
 returns a translated comment if there is one.

This is to allow for situations where you need to use several nodes to create a comment, for example where there are multiple overloads for the same function but the target language doesnt support overloading: in this case we want to combine comments to explain the possible overloads.


git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2008-cherylfoil@10843 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 .../src/DoxygenTranslator.cpp                 |  63 ++++----
 .../DoxygenTranslator/src/DoxygenTranslator.h |  58 ++++++-
 .../src/JavaDocConverter.cpp                  |  51 +++---
 .../DoxygenTranslator/src/JavaDocConverter.h  |  34 ++--
 .../DoxygenTranslator/src/PyDocConverter.cpp  |  59 ++++---
 Source/DoxygenTranslator/src/PyDocConverter.h |  43 +++++-
 Source/Modules/java.cxx                       | 145 +++++++++---------
 Source/Modules/python.cxx                     |  58 ++++---
 Source/Swig/misc.c                            |  11 ++
 Source/Swig/swig.h                            |   3 +-
 10 files changed, 324 insertions(+), 201 deletions(-)

diff --git a/Source/DoxygenTranslator/src/DoxygenTranslator.cpp b/Source/DoxygenTranslator/src/DoxygenTranslator.cpp
index fc74c5c20..025670796 100644
--- a/Source/DoxygenTranslator/src/DoxygenTranslator.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenTranslator.cpp
@@ -1,43 +1,32 @@
-#include "DoxygenParser.h"
+/* -----------------------------------------------------------------------------
+ * See the LICENSE file for information on copyright, usage and redistribution
+ * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ *
+ * DoxygenTranslator.cpp
+ *
+ * Module to return documentation for nodes formatted for various documentation
+ * systems.
+ * ----------------------------------------------------------------------------- */
+
 #include "DoxygenTranslator.h"
-#include <cstdlib>
-#include <iostream>
-#include <string>
-#include "DoxygenEntity.h"
 #include "JavaDocConverter.h"
 #include "PyDocConverter.h"
 
-DoxygenParser doxyParse;
-JavaDocConverter jDC;
-PyDocConverter pyDC;
-
-DoxygenTranslator::DoxygenTranslator(){
-	doxyParse = DoxygenParser();
-    JavaDocConverter jDC = JavaDocConverter();
-    PyDocConverter pyDC = PyDocConverter();
-}
-
-DoxygenTranslator::~DoxygenTranslator(){
-	
-}
-
-
-char *DoxygenTranslator::convert(Node *n, char* doxygenBlob, char* option){
-	
-  std::list <DoxygenEntity> rootList = doxyParse.createTree(std::string(doxygenBlob));
-  std::string returnedString;
-  
-  if(strcmp(option, "JAVADOC") == 0)
-    returnedString = jDC.convertToJavaDoc(n, rootList);
-  else if(strcmp(option, "PYDOC") == 0)
-    returnedString = pyDC.convertToPyDoc(n, rootList);
-  else 
-    std::cout << "Option not current supported." << std::endl;
-	
-  char *nonConstString;
-  nonConstString = (char *)malloc(returnedString.length() + 1);
-  strcpy(nonConstString, returnedString.c_str());
-  
-  return nonConstString;
+bool DoxygenTranslator::getDocumentation(Node *node, DocumentationFormat format, String *&documentation){
+  switch(format){
+    case JavaDoc:   
+      return JavaDocConverter().getDocumentation(node, documentation);
+    case PyDoc:   
+      return PyDocConverter().getDocumentation(node, documentation);
+    default:
+      return false;
+  }
 }
 
+void DoxygenTranslator::printTree(std::list<DoxygenEntity> &entityList){  
+  std::list<DoxygenEntity>::iterator p = entityList.begin();
+  while (p != entityList.end()){
+    (*p).printEntity(0);
+    p++;
+  }
+}
\ No newline at end of file
diff --git a/Source/DoxygenTranslator/src/DoxygenTranslator.h b/Source/DoxygenTranslator/src/DoxygenTranslator.h
index 3c26e3a25..4be1e97e3 100644
--- a/Source/DoxygenTranslator/src/DoxygenTranslator.h
+++ b/Source/DoxygenTranslator/src/DoxygenTranslator.h
@@ -1,13 +1,65 @@
+/* -----------------------------------------------------------------------------
+ * See the LICENSE file for information on copyright, usage and redistribution
+ * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ *
+ * DoxygenTranslator.h
+ *
+ * Module to return documentation for nodes formatted for various documentation
+ * systems.
+ * ----------------------------------------------------------------------------- */
+
 #ifndef DOXYGENTRANSLATOR_H_
 #define DOXYGENTRANSLATOR_H_
 
 #include "swig.h"
+#include "DoxygenEntity.h"
+#include <list>
 
+/*
+ * Describes the availible documentation systems
+ * that can be translated to.
+ */
+enum DocumentationFormat {
+  JavaDoc = 1,
+  PyDoc = 2
+};
+
+/*
+ * A class to translate doxygen comments attacted to parser nodes
+ * into alternative formats for use in code generated for target languages.
+ */
 class DoxygenTranslator
 {
 public:
-	DoxygenTranslator();
-	virtual ~DoxygenTranslator();
-	char* convert(Node *n, char* doxygenBlob, char* option);
+  /*
+   * Virtual destructor.
+   */
+  virtual ~DoxygenTranslator(){}
+  
+  /*
+   * Return the documentation for a given node formated for the correct 
+   * documentation system.
+   * @param node The node to extract and translate documentation for.
+   * @param format The documentation format to output.
+   * @param documentation The returned documentation string.
+   * @return A bool to indicate if there was documentation to return for the node.
+   */
+  static bool getDocumentation(Node *node, DocumentationFormat format, String *&documentation);
+  
+protected:
+  /*
+   * Overridden in subclasses to return the documentation formatted for a given
+   * documentation system.
+   * @param node The node to extract and translate documentation for.
+   * @param documentation The returned documentation string.
+   * @return A bool to indicate if there was documentation to return for the node.
+   */
+  virtual bool getDocumentation(Node *node, String *&documentation) = 0;
+  
+  /*
+   * Prints the details of a parsed entity list to stdout (for debugging).
+   */
+  void printTree(std::list<DoxygenEntity> &entityList);
 };
+
 #endif /*DOXYGENTRANSLATOR_H_*/
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.cpp b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
index dbf606bfd..5081156bd 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
@@ -1,31 +1,17 @@
 #include "JavaDocConverter.h"
+#include "DoxygenParser.h"
 #include <iostream>
 #define APPROX_LINE_LENGTH 64//characters per line allowed
 #define TAB_SIZE 8//characters per line allowed
 int printSortedTree2 = 0;
 //TODO {@link} {@linkplain} {@docRoot}, and other useful doxy commands that are not a javadoc tag
-JavaDocConverter::JavaDocConverter()
-{
-}
 
-JavaDocConverter::~JavaDocConverter()
-{
-}
-
-void JavaDocConverter::printSortedTree(std::list<DoxygenEntity> &entityList){
-  std::list<DoxygenEntity>::iterator p = entityList.begin();
-  while (p != entityList.end()){
-    (*p).printEntity(0);
-    p++;
-  }
-}
-
-std::string formatCommand(std::string unformattedLine, int indent){
+std::string JavaDocConverter::formatCommand(std::string unformattedLine, int indent){
   std::string formattedLines = "\n * ";
   int lastPosition = 0;
   int i = 0;
   int isFirstLine  = 1;
-  while (i != -1 && i < unformattedLine.length()){
+  while (i != -1 && i < (int)unformattedLine.length()){
     lastPosition = i;
     if (isFirstLine){
       i+=APPROX_LINE_LENGTH;
@@ -33,7 +19,7 @@ std::string formatCommand(std::string unformattedLine, int indent){
     else i+=APPROX_LINE_LENGTH - indent*TAB_SIZE;
     i = unformattedLine.find(" ", i);
 
-    if (i > 0 && i + 1 < unformattedLine.length()){
+    if (i > 0 && i + 1 < (int)unformattedLine.length()){
       if (!isFirstLine) for (int j = 0; j < indent; j++) {
         formattedLines.append("\t");
         }
@@ -45,7 +31,7 @@ std::string formatCommand(std::string unformattedLine, int indent){
 
     }
   }
-  if (lastPosition < unformattedLine.length()){
+  if (lastPosition < (int)unformattedLine.length()){
     if (!isFirstLine) {for (int j = 0; j < indent; j++) {formattedLines.append("\t");}}
     formattedLines.append(unformattedLine.substr(lastPosition, unformattedLine.length() - lastPosition));
   }
@@ -56,7 +42,7 @@ std::string formatCommand(std::string unformattedLine, int indent){
 /* Contains the conversions for tags
  * could probably be much more efficient...
  */
-std::string javaDocFormat(DoxygenEntity &doxygenEntity){
+std::string JavaDocConverter::javaDocFormat(DoxygenEntity &doxygenEntity){
   if(doxygenEntity.typeOfEntity.compare("partofdescription") == 0){
         return doxygenEntity.data;
     }
@@ -97,7 +83,7 @@ std::string javaDocFormat(DoxygenEntity &doxygenEntity){
 }
 
 
-std::string translateSubtree( DoxygenEntity &doxygenEntity){
+std::string JavaDocConverter::translateSubtree( DoxygenEntity &doxygenEntity){
   std::string returnedString;
   if (doxygenEntity.isLeaf){ return javaDocFormat(doxygenEntity) + " ";}
   else {
@@ -111,7 +97,7 @@ std::string translateSubtree( DoxygenEntity &doxygenEntity){
   return returnedString;
 }
 
-std::string translateEntity(DoxygenEntity &doxyEntity){
+std::string JavaDocConverter::translateEntity(DoxygenEntity &doxyEntity){
   if(doxyEntity.typeOfEntity.compare("partofdescription")== 0) return formatCommand(std::string(translateSubtree(doxyEntity)), 0);
   if ((doxyEntity.typeOfEntity.compare("brief") == 0)||(doxyEntity.typeOfEntity.compare("details") == 0)){
   return formatCommand(std::string(translateSubtree(doxyEntity)), 0) + "\n * ";}
@@ -136,13 +122,19 @@ std::string translateEntity(DoxygenEntity &doxyEntity){
   return "";
 }
 
-std::string JavaDocConverter:: convertToJavaDoc(Node *n, std::list <DoxygenEntity> entityList){
-  #pragma unused(n)
+bool JavaDocConverter::getDocumentation(Node *n, String *&documentation){
+  documentation = Getattr(n,"DoxygenComment");
+  if(documentation == NULL)
+    return false;
+  
+  std::list <DoxygenEntity> entityList = DoxygenParser().createTree(Char(documentation));
+  Delete(documentation);
+  
   entityList.sort(CompareDoxygenEntities());
   
-  if(printSortedTree2){
+  if(debug){
     std::cout << "---RESORTED LIST---" << std::endl;
-    printSortedTree(entityList);
+    printTree(entityList);
   }
 
   std::string javaDocString = "/**";
@@ -154,10 +146,11 @@ std::string JavaDocConverter:: convertToJavaDoc(Node *n, std::list <DoxygenEntit
 
   javaDocString += "\n */\n";
   
-  if(printSortedTree2){
+  if(debug){
     std::cout << "\n---RESULT IN JAVADOC---" << std::endl;
     std::cout << javaDocString; 
   }
   
-  return javaDocString;
-}
\ No newline at end of file
+  documentation = NewString(javaDocString.c_str());
+  return true;
+}
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.h b/Source/DoxygenTranslator/src/JavaDocConverter.h
index 0a329c27a..e2a25d4ff 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.h
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.h
@@ -1,18 +1,34 @@
+/* -----------------------------------------------------------------------------
+ * See the LICENSE file for information on copyright, usage and redistribution
+ * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ *
+ * JavaDocConverter.h
+ *
+ * Module to return documentation for nodes formatted for JavaDoc
+ * ----------------------------------------------------------------------------- */
+
 #ifndef JAVADOCCONVERTER_H_
 #define JAVADOCCONVERTER_H_
 
-#include <list>
-#include <string>
-#include "swig.h"
-#include "DoxygenEntity.h"
+#include "DoxygenTranslator.h"
 
-class JavaDocConverter
+/*
+ * A class to translate doxygen comments into JavaDoc style comments.
+ */
+class JavaDocConverter : public DoxygenTranslator
 {
 public:
-  JavaDocConverter();
-  std::string convertToJavaDoc(Node *n, std::list <DoxygenEntity> entityList);
-  ~JavaDocConverter();
-  void printSortedTree(std::list <DoxygenEntity> &entityList);
+  JavaDocConverter() : debug( true ){}
+  virtual bool getDocumentation(Node *node, String *&documentation);
+  
+protected:
+  std::string formatCommand(std::string unformattedLine, int indent);
+  std::string translateEntity(DoxygenEntity &doxyEntity);
+  std::string javaDocFormat(DoxygenEntity &doxygenEntity);
+  std::string translateSubtree( DoxygenEntity &doxygenEntity);
+  
+private:
+  bool debug;
 };
 
 #endif /*JAVADOCCONVERTER_H_*/
diff --git a/Source/DoxygenTranslator/src/PyDocConverter.cpp b/Source/DoxygenTranslator/src/PyDocConverter.cpp
index 5bbda8dc2..2065b090e 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/PyDocConverter.cpp
@@ -1,4 +1,14 @@
+/* -----------------------------------------------------------------------------
+ * See the LICENSE file for information on copyright, usage and redistribution
+ * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ *
+ * PyDocConverter.cpp
+ *
+ * Module to return documentation for nodes formatted for PyDoc
+ * ----------------------------------------------------------------------------- */
+
 #include "PyDocConverter.h"
+#include "DoxygenParser.h"
 #include <iostream>
 #include <sstream>
 
@@ -8,18 +18,6 @@ PyDocConverter::PyDocConverter()
     debug = 1;
 }
 
-PyDocConverter::~PyDocConverter()
-{
-}
- 
-void PyDocConverter::printTree(std::list <DoxygenEntity> &entityList){
-  std::list<DoxygenEntity>::iterator p = entityList.begin();
-  while (p != entityList.end()){
-    (*p).printEntity(0);
-    p++;
-  }
-}
-
 std::string PyDocConverter::formatParam(Node *n, DoxygenEntity &doxygenEntity) {
   ParmList *plist = CopyParmList(Getattr(n, "parms"));
   Parm *p = NULL;
@@ -28,7 +26,7 @@ std::string PyDocConverter::formatParam(Node *n, DoxygenEntity &doxygenEntity) {
   DoxygenEntity& paramDescriptionEntity = *(++doxygenEntity.entityList.begin());
   
   std::string result;
-  std::string paramDescription = formatCommand(paramDescriptionEntity.data, DOC_PARAM_STRING_LENGTH);
+  std::string paramDescription = justifyString(paramDescriptionEntity.data, DOC_PARAM_STRING_LENGTH);
   
   for (p = plist; p;) {
     if(Char(Getattr(p, "name")) == paramNameEntity.data) {
@@ -47,7 +45,12 @@ std::string PyDocConverter::formatParam(Node *n, DoxygenEntity &doxygenEntity) {
   return result;
 }
 
-std::string PyDocConverter::formatCommand(std::string documentString, int indent, int maxWidth){
+std::string PyDocConverter::formatReturnDescription(Node *node, DoxygenEntity &doxygenEntity){
+#pragma unused(node)
+  return "\nResult:\n" + justifyString(translateSubtree(doxygenEntity));
+}
+
+std::string PyDocConverter::justifyString(std::string documentString, int indent, int maxWidth){
   std::ostringstream formattedString;
   std::string currentLine;
   
@@ -85,24 +88,24 @@ std::string PyDocConverter::translateSubtree( DoxygenEntity &doxygenEntity){
 
 std::string PyDocConverter::translateEntity(Node *n, DoxygenEntity &doxyEntity){
   if(doxyEntity.typeOfEntity.compare("partofdescription")== 0) 
-    return formatCommand(std::string(translateSubtree(doxyEntity)), 0);
+    return justifyString(std::string(translateSubtree(doxyEntity)), 0);
   
   if ((doxyEntity.typeOfEntity.compare("brief") == 0)||(doxyEntity.typeOfEntity.compare("details") == 0)){
-    return formatCommand(std::string(translateSubtree(doxyEntity)), 0) + "\n * ";}
+    return justifyString(std::string(translateSubtree(doxyEntity)), 0) + "\n * ";}
   
   if(doxyEntity.typeOfEntity.compare("plainstd::string")== 0 
     || doxyEntity.typeOfEntity.compare("deprecated")== 0 
     || doxyEntity.typeOfEntity.compare("brief")== 0)
-    return formatCommand(doxyEntity.data, 0) + "\n * ";
+    return justifyString(doxyEntity.data, 0) + "\n * ";
   
   if(doxyEntity.typeOfEntity.compare("see") == 0)
-    return formatCommand(std::string("@" + doxyEntity.typeOfEntity + "\t\t" + translateSubtree(doxyEntity)), 2);
+    return justifyString(std::string("@" + doxyEntity.typeOfEntity + "\t\t" + translateSubtree(doxyEntity)), 2);
   
   if(doxyEntity.typeOfEntity.compare("param") == 0)
     return formatParam(n, doxyEntity);
   
   if(doxyEntity.typeOfEntity.compare("return")== 0)
-    
+    return formatReturnDescription(n, doxyEntity);
 
   if(doxyEntity.typeOfEntity.compare("author")== 0
     || doxyEntity.typeOfEntity.compare("param")== 0
@@ -110,15 +113,22 @@ std::string PyDocConverter::translateEntity(Node *n, DoxygenEntity &doxyEntity){
     || doxyEntity.typeOfEntity.compare("version")== 0
     || doxyEntity.typeOfEntity.compare("exception") == 0
     || doxyEntity.typeOfEntity.compare("deprecated") == 0)
-    return formatCommand(std::string("@" + doxyEntity.typeOfEntity + "\t" + translateSubtree(doxyEntity)), 2);
+    return justifyString(std::string("@" + doxyEntity.typeOfEntity + "\t" + translateSubtree(doxyEntity)), 2);
   
   if(doxyEntity.typeOfEntity.compare("sa")== 0)
-    return formatCommand(std::string("@see\t\t" + translateSubtree(doxyEntity)), 2);
+    return justifyString(std::string("@see\t\t" + translateSubtree(doxyEntity)), 2);
 
-  return formatCommand(doxyEntity.data, 0);
+  return justifyString(doxyEntity.data);
 }
 
-std::string PyDocConverter::convertToPyDoc(Node *n, std::list<DoxygenEntity> entityList){
+bool PyDocConverter::getDocumentation(Node *n, String *&documentation){
+  documentation = Getattr(n,"DoxygenComment");
+  if(documentation == NULL)
+    return false;
+  
+  std::list <DoxygenEntity> entityList = DoxygenParser().createTree(Char(documentation));
+  Delete(documentation);
+  
   std::string pyDocString = "\"\"\"\n";
   
   bool inParamsSection = false;
@@ -144,5 +154,6 @@ std::string PyDocConverter::convertToPyDoc(Node *n, std::list<DoxygenEntity> ent
     std::cout << std::endl;
   }
   
-  return pyDocString;
+  documentation = NewString(pyDocString.c_str());
+  return true;
 }
\ No newline at end of file
diff --git a/Source/DoxygenTranslator/src/PyDocConverter.h b/Source/DoxygenTranslator/src/PyDocConverter.h
index 4c7fdd4db..5da58e4ec 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.h
+++ b/Source/DoxygenTranslator/src/PyDocConverter.h
@@ -1,3 +1,12 @@
+/* -----------------------------------------------------------------------------
+ * See the LICENSE file for information on copyright, usage and redistribution
+ * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ *
+ * PyDocConverter.h
+ *
+ * Module to return documentation for nodes formatted for PyDoc
+ * ----------------------------------------------------------------------------- */
+
 #ifndef PYDOCCONVERTER_H_
 #define PYDOCCONVERTER_H_
 
@@ -5,21 +14,41 @@
 #include <string>
 #include "swig.h"
 #include "DoxygenEntity.h"
+#include "DoxygenTranslator.h"
 
 #define DOC_STRING_LENGTH	  64  // characters per line allowed
 #define DOC_PARAM_STRING_LENGTH	  30  // characters reserved for param name / type
 
-class PyDocConverter
+class PyDocConverter : public DoxygenTranslator
 {
 public:
   PyDocConverter();
-  std::string convertToPyDoc(Node *n, std::list <DoxygenEntity> entityList);
-  ~PyDocConverter();
-  void printTree(std::list <DoxygenEntity> &entityList);
-
+  bool getDocumentation(Node *node, String *&documentation);
+  
 protected:
-  std::string formatParam(Node *n, DoxygenEntity &doxygenEntity);
-  std::string formatCommand(std::string unformattedLine, int indent, int maxWidth = DOC_STRING_LENGTH);
+  /*
+   * Format the doxygen comment relating to a function or method parameter
+   * @param node The parse tree node that the parameter relates to.
+   * @param doxygenEntity The doxygen entity relating to the parameter docstring.
+   */
+  std::string formatParam(Node *node, DoxygenEntity &doxygenEntity);
+  
+  /*
+   * Format the doxygen comment relating to the return value for a method or function.
+   * @param node The parse tree node that the parameter relates to.
+   * @param doxygenEntity The doxygen entity relating to the parameter docstring.
+   */
+  std::string formatReturnDescription(Node *node, DoxygenEntity &doxygenEntity);
+  
+  /*
+   * Format a string so it is justified and split over several lines 
+   * not exeeding a given length.
+   * @param unformattedLine The string to justify and split.
+   * @param indent An optional number of spaces to indent each line by.
+   * @param maxWidth The approximate maximum line width.
+   */
+  std::string justifyString(std::string unformattedLine, int indent = 0, int maxWidth = DOC_STRING_LENGTH);
+  
   std::string translateSubtree( DoxygenEntity &doxygenEntity);
   std::string translateEntity(Node *n, DoxygenEntity &doxyEntity);
     
diff --git a/Source/Modules/java.cxx b/Source/Modules/java.cxx
index edb88ebbb..42ba5b396 100644
--- a/Source/Modules/java.cxx
+++ b/Source/Modules/java.cxx
@@ -91,10 +91,6 @@ class JAVA:public Language {
     Setline(p, Getline(n));
     return p;
   }
-  /* DOXYGEN TO JAVADOC globals */
-  //TODO make this bool a command line option
-  DoxygenTranslator doxyTranslator;
-
 
 public:
 
@@ -124,7 +120,7 @@ public:
       global_variable_flag(false),
       old_variable_names(false),
       member_func_flag(false),
-	  doxygen_javadoc_flag(true),
+      doxygen_javadoc_flag(true),
       comment_creation_chatter(false),
       imclass_name(NULL),
       module_class_name(NULL),
@@ -160,7 +156,6 @@ public:
        should be easy to implement though */
     director_multiple_inheritance = 0;
     director_language = 1;
-    doxyTranslator = DoxygenTranslator();
   }
 
   /* -----------------------------------------------------------------------------
@@ -508,12 +503,13 @@ public:
 	Printf(f_module, "%s\n", module_imports);
       
       if (doxygen_javadoc_flag){
-      	if (Getattr(n,"DoxygenComment")){
-      		  if(comment_creation_chatter) Printf(f_module, "/* This was generated from top() */");
-      		  char *convertedString = doxyTranslator.convert(n, Char(Getattr(n,"DoxygenComment")),"JAVADOC");
-      		  Printf(f_module, convertedString); 	
-      		  free(convertedString);
-      	}
+	String *doxygen_comments;
+	if(DoxygenTranslator::getDocumentation(n, JavaDoc,doxygen_comments)){
+	  if(comment_creation_chatter)
+	    Printf(f_module, "/* This was generated from top() */");
+	  Printf(f_module, Char(doxygen_comments)); 
+	  Delete(doxygen_comments);
+	}
       }
       if (Len(module_class_modifiers) > 0)
 	Printf(f_module, "%s ", module_class_modifiers);
@@ -1234,15 +1230,17 @@ public:
 	  // Add extra indentation
 	  Replaceall(enum_code, "\n", "\n  ");
 	  Replaceall(enum_code, "  \n", "\n");
-	    //translate and write javadoc comment if flagged
-	    if (doxygen_javadoc_flag){
-	    	if (Getattr(n,"DoxygenComment")){
-	    		if(comment_creation_chatter) Printv(proxy_class_constants_code, "/* This was generated from enumvalueDeclaration */", NIL );
-	    		char *convertedString = doxyTranslator.convert(n, Char(Getattr(n,"DoxygenComment")),"JAVADOC");
-	    		Printv(proxy_class_constants_code, convertedString, NIL); 	
-	    		free(convertedString); 
-	    	}
+	  
+	  //translate and write javadoc comment if flagged
+	  if (doxygen_javadoc_flag){
+	    String *doxygen_comments;
+	    if(DoxygenTranslator::getDocumentation(n, JavaDoc,doxygen_comments)){
+	      if(comment_creation_chatter)
+		Printf(proxy_class_constants_code, "/* This was generated from enumvalueDeclaration() */");
+	      Printf(proxy_class_constants_code, Char(doxygen_comments)); 
+	      Delete(doxygen_comments);
 	    }
+	  }
 	    
 	  Printv(proxy_class_constants_code, "  ", enum_code, "\n\n", NIL);
 	} else {
@@ -1308,12 +1306,13 @@ public:
     
     //translate and write javadoc comment if flagged
     if (doxygen_javadoc_flag){
-    	if (Getattr(n,"DoxygenComment")){
-    		  if(comment_creation_chatter) Printf(enum_code, "/* This was generated from enumvalueDeclaration() */" );
-	    	  char *convertedString = doxyTranslator.convert(n, Char(Getattr(n,"DoxygenComment")),"JAVADOC");		
-    		  Printf(enum_code, convertedString); 	
-    		  free(convertedString); 
-    	}
+      String *doxygen_comments;
+      if(DoxygenTranslator::getDocumentation(n, JavaDoc,doxygen_comments)){
+	if(comment_creation_chatter)
+	  Printf(enum_code, "/* This was generated from enumvalueDeclaration() */");
+	Printf(enum_code, Char(doxygen_comments)); 
+	Delete(doxygen_comments);
+      }
     }
     {
       EnumFeature enum_feature = decodeEnumFeature(parentNode(n));
@@ -1379,15 +1378,16 @@ public:
    * file
    * ------------------------------------------------------------------------ */
   virtual int doxygenComment(Node *n){
-		 if (doxygen_javadoc_flag){
-		   if (Getattr(n,"DoxygenComment")){
-			      if(comment_creation_chatter) Printv(structuralComments, "/* This was generated from doxygenComment() */\n", NIL);
-		    	  char *convertedString = doxyTranslator.convert(n, Char(Getattr(n,"DoxygenComment")),"JAVADOC");			
-			      Printv(structuralComments, convertedString, NIL);
-			      free(convertedString);
-		    	}
-		    }
-	 return SWIG_OK;
+    if (doxygen_javadoc_flag){
+      String *doxygen_comments;
+      if(DoxygenTranslator::getDocumentation(n, JavaDoc, doxygen_comments)){
+	if(comment_creation_chatter)
+	  Printf(structuralComments, "/* This was generated from doxygenComment() */");
+	Printf(structuralComments, Char(doxygen_comments)); 
+	Delete(doxygen_comments);
+      }
+    }
+    return SWIG_OK;
   }
   
   /* -----------------------------------------------------------------------
@@ -1408,14 +1408,16 @@ public:
     String *tm;
     String *return_type = NewString("");
     String *constants_code = NewString("");
+    
     //translate and write javadoc comment if flagged
     if (doxygen_javadoc_flag){
-    	if (Getattr(n,"DoxygenComment")){
-    		if(comment_creation_chatter) Printf(constants_code, "/* This was generated from enumvalueDeclaration */\n");
-	    	char *convertedString = doxyTranslator.convert(n, Char(Getattr(n,"DoxygenComment")),"JAVADOC");			
-            Printf(constants_code, convertedString); 	
-		    free(convertedString);
-    	}
+      String *doxygen_comments;
+      if(DoxygenTranslator::getDocumentation(n, JavaDoc, doxygen_comments)){
+	if(comment_creation_chatter)
+	  Printf(constants_code, "/* This was generated from constantWrapper() */");
+	Printf(constants_code, Char(doxygen_comments)); 
+	Delete(doxygen_comments);
+      }
     }
     
     if (!addSymbol(symname, n))
@@ -1681,12 +1683,13 @@ public:
     
     //translate and write javadoc comment if flagged
     if (doxygen_javadoc_flag){
-    	if (Getattr(n,"DoxygenComment")){
-    		if(comment_creation_chatter) Printv(proxy_class_def, "/* This was generated from emitProxyClassDefAndCPPCasts() */\n", NIL );
-	    	char *convertedString = doxyTranslator.convert(n, Char(Getattr(n,"DoxygenComment")),"JAVADOC");			
-	    	Printv(proxy_class_def, convertedString, NIL); 		
-		    free(convertedString);
-    	}
+      String *doxygen_comments;
+      if(DoxygenTranslator::getDocumentation(n, JavaDoc, doxygen_comments)){
+	if(comment_creation_chatter)
+	  Printf(proxy_class_def, "/* This was generated from emitProxyClassDefAndCPPCasts() */");
+	Printf(proxy_class_def, Char(doxygen_comments)); 
+	Delete(doxygen_comments);
+      }
     }
     
     // Start writing the proxy class
@@ -2021,15 +2024,15 @@ public:
       setter_flag = (Cmp(Getattr(n, "sym:name"), Swig_name_set(Swig_name_member(proxy_class_name, variable_name))) == 0);
     }
     
-    
     //translate and write javadoc comment if flagged
     if (doxygen_javadoc_flag){
-    	if (Getattr(n,"DoxygenComment")){
-    		if(comment_creation_chatter) Printf(function_code, "/* This was generated from proxyclassfunctionhandler */");
-  	    	char *convertedString = doxyTranslator.convert(n, Char(Getattr(n,"DoxygenComment")),"JAVADOC");			
-  	    	 Printf(function_code, convertedString); 		
-  		    free(convertedString);
-    	}
+      String *doxygen_comments;
+      if(DoxygenTranslator::getDocumentation(n, JavaDoc, doxygen_comments)){
+	if(comment_creation_chatter)
+	  Printf(function_code, "/* This was generated from proxyclassfunctionhandler() */");
+	Printf(function_code, Char(doxygen_comments)); 
+	Delete(doxygen_comments);
+      }
     }
     
     /* Start generating the proxy function */
@@ -2254,15 +2257,16 @@ public:
       tm = Getattr(n, "tmap:jtype"); // typemaps were attached earlier to the node
       Printf(im_return_type, "%s", tm);
       
-	    //translate and write javadoc comment if flagged
-	    if (doxygen_javadoc_flag){
-	    	if (Getattr(n,"DoxygenComment")){
-	    		if(comment_creation_chatter) Printf(function_code, "/* This was generated from constructionhandler */\n" );
-	  	    	char *convertedString = doxyTranslator.convert(n, Char(Getattr(n,"DoxygenComment")),"JAVADOC");			
-	  	    	Printf(function_code, convertedString); 			
-		  		free(convertedString);
-	    	}
-	    }
+      //translate and write javadoc comment if flagged
+      if (doxygen_javadoc_flag){
+	String *doxygen_comments;
+	if(DoxygenTranslator::getDocumentation(n, JavaDoc, doxygen_comments)){
+	  if(comment_creation_chatter)
+	    Printf(function_code, "/* This was generated from constructionhandler() */");
+	  Printf(function_code, Char(doxygen_comments)); 
+	  Delete(doxygen_comments);
+	}
+      }
 	    
       Printf(function_code, "  %s %s(", methodmods, proxy_class_name);
       Printf(helper_code, "  static private %s SwigConstruct%s(", im_return_type, proxy_class_name);
@@ -2525,14 +2529,15 @@ public:
     String *pre_code = NewString("");
     String *post_code = NewString("");
     
-    //translate and write javadoc comment if flagged
+    // translate and write javadoc comment if flagged
     if (doxygen_javadoc_flag){
-    	if (Getattr(n,"DoxygenComment")){
-    		if(comment_creation_chatter) Printf(function_code, "/* This was generated from moduleClassFunctionHandler() */\n" );
-  	    	char *convertedString = doxyTranslator.convert(n, Char(Getattr(n,"DoxygenComment")),"JAVADOC");			
-  	    	Printf(function_code, convertedString); 			
-	  		free(convertedString);	
-    	}
+      String *doxygen_comments;
+      if(DoxygenTranslator::getDocumentation(n, JavaDoc, doxygen_comments)){
+	if(comment_creation_chatter)
+	  Printf(function_code, "/* This was generated from moduleClassFunctionHandler() */");
+	Printf(function_code, Char(doxygen_comments)); 
+	Delete(doxygen_comments);
+      }
     }
 
     if (l) {
diff --git a/Source/Modules/python.cxx b/Source/Modules/python.cxx
index ba02eae2e..94b3c1377 100644
--- a/Source/Modules/python.cxx
+++ b/Source/Modules/python.cxx
@@ -18,6 +18,7 @@ char cvsroot_python_cxx[] = "$Id: python.cxx 10453 2008-05-15 21:18:44Z wsfulton
 static int treduce = SWIG_cparse_template_reduce(0);
 
 #include <ctype.h>
+#include <sstream>
 #include "../DoxygenTranslator/src/DoxygenTranslator.h"
 
 #define PYSHADOW_MEMBER  0x2
@@ -85,8 +86,6 @@ static int extranative = 0;
 static int outputtuple = 0;
 static int nortti = 0;
 
-static DoxygenTranslator doxyTranslator;
-
 /* flags for the make_autodoc function */
 enum autodoc_t {
   AUTODOC_CLASS,
@@ -2906,19 +2905,18 @@ public:
         }
       }
       Printf(f_shadow, ":\n");
-		
-	//translate and write pydoc comment if flagged
-	if (doxygen){
-		if (Getattr(n,"DoxygenComment")){
-			//if(comment_creation_chatter) Printf(function_code, "/* This was generated from classHandler */");
-			char *convertedString = doxyTranslator.convert(n, Char(Getattr(n,"DoxygenComment")), "PYDOC");			
-			Printf(f_shadow, Char(pythoncode(convertedString, shadow_indent))); 		
-			free(convertedString);
-		}
+      
+      // translate and write pydoc comment if flagged
+      if (doxygen){
+	String *doxygen_comments;
+	if(DoxygenTranslator::getDocumentation(n, PyDoc, doxygen_comments)){
+	  Printf(f_shadow, Char(pythoncode(doxygen_comments, shadow_indent))); 
+	  Delete(doxygen_comments);
 	}
+      }
 	
-	// otherwise use default docstrings if requested
-	else if (have_docstring(n)) {
+      // otherwise use default docstrings if requested
+      else if (have_docstring(n)) {
 	String *str = docstring(n, AUTODOC_CLASS, tab4);
 	if (str != NULL && Len(str))
 	  Printv(f_shadow, tab4, str, "\n", NIL);
@@ -3130,15 +3128,33 @@ public:
 	  } else {
 	    Printv(f_shadow, tab4, "def ", symname, "(",parms , ")", returnTypeAnnotation(n), ":", NIL);
 	    Printv(f_shadow, "\n", NIL);
-		if (doxygen) {
-			if (Getattr(n,"DoxygenComment")){
-				//if(comment_creation_chatter) Printf(function_code, "/* This was generated from classHandler */");
-				char *convertedString = doxyTranslator.convert(n, Char(Getattr(n,"DoxygenComment")), "PYDOC");			
-				Printf(f_shadow, Char(pythoncode(convertedString, tab8))); 		
-				free(convertedString);
-			}
+	    if (doxygen) {
+	      /*Node *documented_node = n;
+	      if(Getattr(n, "sym:overloaded")){
+		// If the function is overloaded then this funciton is called
+		// for the last one.  Rewind to the first so the docstrings are
+		// in order.
+		while (Getattr(documented_node, "sym:previousSibling"))
+		  documented_node = Getattr(documented_node, "sym:previousSibling");
+		
+		int real_overload_count = 0;
+		std::ostringstream all_documentation;
+		
+		// for each real method (not a generated overload) append the documentation
+		while(documented_node){
+		  if(!is_generated_overload(documented_node) && Getattr(documented_node,"DoxygenComment")){
+		    all_documentation << "Overload " << ++real_overload_count << ":" << std::endl;
+		    all_documentation << Char(Getattr(documented_node,"DoxygenComment")) << std::endl;
+		  }
+		  documented_node = Getattr(documented_node, "sym:nextSibling");
 		}
-	    if (have_docstring(n))
+		
+		char *convertedString = doxyTranslator.convert(n,const_cast< char *>(all_documentation.str().c_str()), "PYDOC");	
+		Printf(f_shadow, Char(pythoncode(convertedString, tab8))); 		
+		free(convertedString);
+	      }*/
+	    }
+	    else if (have_docstring(n))
 	      Printv(f_shadow, tab8, docstring(n, AUTODOC_METHOD, tab8), "\n", NIL);
 	    if (have_pythonprepend(n)) {
 	      fproxy = 0;
diff --git a/Source/Swig/misc.c b/Source/Swig/misc.c
index d29250517..a9c64011e 100644
--- a/Source/Swig/misc.c
+++ b/Source/Swig/misc.c
@@ -1032,6 +1032,17 @@ String *Swig_string_rxspencer(String *s) {
 }
 #endif
 
+/* ------------------------------------------------------------
+ * is_generated_overload()
+ * Check if the function is an automatically generated
+ * overload created because a method has default parameters. 
+ * ------------------------------------------------------------ */
+int Swig_is_generated_overload(Node *n)
+{
+  Node *base_method = Getattr(n, "sym:overloaded");
+  Node *default_args = Getattr(n, "defaultargs");
+  return ((base_method != NULL) && (default_args != NULL) && (base_method == default_args));
+}
 
 /* -----------------------------------------------------------------------------
  * Swig_init()
diff --git a/Source/Swig/swig.h b/Source/Swig/swig.h
index 451de86c4..3f736bbd5 100644
--- a/Source/Swig/swig.h
+++ b/Source/Swig/swig.h
@@ -300,8 +300,9 @@ extern int        ParmList_is_compactdefargs(ParmList *p);
 
   extern void Swig_init(void);
   extern void Swig_warn(const char *filename, int line, const char *msg);
-
+  
   extern int Swig_value_wrapper_mode(int mode);
+  extern int Swig_is_generated_overload(Node *n);
 
 
 #define WARNING(msg) Swig_warn(__FILE__,__LINE__,msg)

From 83cef07b9025935338499a0b2b9fd70bb7d4706a Mon Sep 17 00:00:00 2001
From: Jamie Kirkpatrick <gringostarr@users.sourceforge.net>
Date: Fri, 12 Sep 2008 11:21:40 +0000
Subject: [PATCH 035/314] Multiple documentation sections are now concatted
 into one where there are various overloads for methods with the same name.

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2008-cherylfoil@10844 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 .../src/JavaDocConverter.cpp                  |   2 -
 .../DoxygenTranslator/src/PyDocConverter.cpp  | 101 +++++++++++++-----
 Source/DoxygenTranslator/src/PyDocConverter.h |  13 +++
 Source/Modules/python.cxx                     |  29 +----
 4 files changed, 95 insertions(+), 50 deletions(-)

diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.cpp b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
index 5081156bd..0ba97fc60 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
@@ -128,8 +128,6 @@ bool JavaDocConverter::getDocumentation(Node *n, String *&documentation){
     return false;
   
   std::list <DoxygenEntity> entityList = DoxygenParser().createTree(Char(documentation));
-  Delete(documentation);
-  
   entityList.sort(CompareDoxygenEntities());
   
   if(debug){
diff --git a/Source/DoxygenTranslator/src/PyDocConverter.cpp b/Source/DoxygenTranslator/src/PyDocConverter.cpp
index 2065b090e..dbee97233 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/PyDocConverter.cpp
@@ -9,8 +9,9 @@
 
 #include "PyDocConverter.h"
 #include "DoxygenParser.h"
-#include <iostream>
 #include <sstream>
+#include <vector>
+#include <iostream>
 
 //TODO {@link} {@linkplain} {@docRoot}, and other useful doxy commands that are not a pydoc tag
 PyDocConverter::PyDocConverter()
@@ -121,39 +122,91 @@ std::string PyDocConverter::translateEntity(Node *n, DoxygenEntity &doxyEntity){
   return justifyString(doxyEntity.data);
 }
 
-bool PyDocConverter::getDocumentation(Node *n, String *&documentation){
-  documentation = Getattr(n,"DoxygenComment");
-  if(documentation == NULL)
-    return false;
-  
-  std::list <DoxygenEntity> entityList = DoxygenParser().createTree(Char(documentation));
-  Delete(documentation);
-  
-  std::string pyDocString = "\"\"\"\n";
-  
+std::string PyDocConverter::processEntityList(Node *n, std::list<DoxygenEntity>& entityList){
+  std::string result;
   bool inParamsSection = false;
   
   for(std::list<DoxygenEntity>::iterator entityIterator = entityList.begin(); entityIterator != entityList.end();){
-    if(entityIterator->typeOfEntity.compare("param") == 0 && !inParamsSection)
-    {
+    if(entityIterator->typeOfEntity.compare("param") == 0 && !inParamsSection){
       inParamsSection = true;
-      pyDocString += "\nArguments:\n";
+      result += "\nArguments:\n";
     }
     else if(entityIterator->typeOfEntity.compare("param") != 0 && inParamsSection)
       inParamsSection = false;
     
-    pyDocString += translateEntity(n, *entityIterator);
+    result += translateEntity(n, *entityIterator);
     entityIterator++;
-  }
+  }  
+  
+  return result;
+}
 
-  pyDocString += "\n\"\"\"\n";
+bool PyDocConverter::getDocumentation(Node *n, String *&documentation){
+  std::string pyDocString, result;
   
-  if(debug){
-    std::cout << "\n---RESULT IN PYDOC---" << std::endl;
-    std::cout << pyDocString;
-    std::cout << std::endl;
+  // for overloaded functions we must concat documentation for underlying overloads
+  if(Checkattr(n, "kind", "function") && Getattr(n, "sym:overloaded")){
+    // rewind to the first overload
+    while (Getattr(n, "sym:previousSibling"))
+      n = Getattr(n, "sym:previousSibling");
+    
+    std::vector<std::string> allDocumentation;
+    
+    // for each real method (not a generated overload) append the documentation
+    while(n){
+      documentation = Getattr(n,"DoxygenComment");
+      if(!Swig_is_generated_overload(n) && documentation){
+	std::list<DoxygenEntity> entityList = DoxygenParser().createTree(Char(documentation));
+	allDocumentation.push_back(processEntityList(n, entityList));
+      }
+      n = Getattr(n, "sym:nextSibling");
+    }
+    
+    // construct final documentation string
+    if(allDocumentation.size() > 1){
+      std::ostringstream concatDocString;
+      for(int realOverloadCount = 0; realOverloadCount < (int)allDocumentation.size(); realOverloadCount++){
+	concatDocString << generateDivider();
+	concatDocString << "Overload " << (realOverloadCount + 1) << ":" << std::endl;
+	concatDocString << generateDivider();
+	concatDocString << allDocumentation[realOverloadCount] << std::endl;
+      }
+      pyDocString = concatDocString.str();
+    } 
+    else if (allDocumentation.size() == 1) {
+      pyDocString = *(allDocumentation.begin());
+    }
+  } 
+  // for other nodes just process as normal
+  else {
+    documentation = Getattr(n,"DoxygenComment");
+    if(documentation != NULL){
+      std::list<DoxygenEntity> entityList = DoxygenParser().createTree(Char(documentation));
+      pyDocString = processEntityList(n, entityList);
+    }
   }
   
-  documentation = NewString(pyDocString.c_str());
-  return true;
-}
\ No newline at end of file
+  // if we got something log the result and construct DOH string to return
+  if(pyDocString.length()) {
+    result = "\"\"\"\n" + pyDocString + "\"\"\"\n";
+    
+    if(debug){
+      std::cout << "\n---RESULT IN PYDOC---" << std::endl;
+      std::cout << result;
+      std::cout << std::endl;
+    }
+    
+    documentation = NewString(result.c_str());
+    return true;
+  }
+  
+  return false;
+}
+
+std::string PyDocConverter::generateDivider(){
+  std::ostringstream dividerString;
+  for(int i = 0; i < DOC_STRING_LENGTH; i++)
+    dividerString << '-';
+  dividerString << std::endl;
+  return dividerString.str();
+}
diff --git a/Source/DoxygenTranslator/src/PyDocConverter.h b/Source/DoxygenTranslator/src/PyDocConverter.h
index 5da58e4ec..500e39fe8 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.h
+++ b/Source/DoxygenTranslator/src/PyDocConverter.h
@@ -26,6 +26,14 @@ public:
   bool getDocumentation(Node *node, String *&documentation);
   
 protected:
+  
+  /*
+   * Process the contents of the entity list producing a documentation string.
+   * @param node The parse tree node that the entity list relates to.
+   * @param entityList The entity list to process
+   */
+  std::string processEntityList(Node *node, std::list<DoxygenEntity>& entityList);
+  
   /*
    * Format the doxygen comment relating to a function or method parameter
    * @param node The parse tree node that the parameter relates to.
@@ -51,6 +59,11 @@ protected:
   
   std::string translateSubtree( DoxygenEntity &doxygenEntity);
   std::string translateEntity(Node *n, DoxygenEntity &doxyEntity);
+  
+  /*
+   * Utility method to generate a diving line for a documentation string.
+   */
+  std::string generateDivider();
     
 private:
   bool debug;
diff --git a/Source/Modules/python.cxx b/Source/Modules/python.cxx
index 94b3c1377..8a3160ef3 100644
--- a/Source/Modules/python.cxx
+++ b/Source/Modules/python.cxx
@@ -3129,30 +3129,11 @@ public:
 	    Printv(f_shadow, tab4, "def ", symname, "(",parms , ")", returnTypeAnnotation(n), ":", NIL);
 	    Printv(f_shadow, "\n", NIL);
 	    if (doxygen) {
-	      /*Node *documented_node = n;
-	      if(Getattr(n, "sym:overloaded")){
-		// If the function is overloaded then this funciton is called
-		// for the last one.  Rewind to the first so the docstrings are
-		// in order.
-		while (Getattr(documented_node, "sym:previousSibling"))
-		  documented_node = Getattr(documented_node, "sym:previousSibling");
-		
-		int real_overload_count = 0;
-		std::ostringstream all_documentation;
-		
-		// for each real method (not a generated overload) append the documentation
-		while(documented_node){
-		  if(!is_generated_overload(documented_node) && Getattr(documented_node,"DoxygenComment")){
-		    all_documentation << "Overload " << ++real_overload_count << ":" << std::endl;
-		    all_documentation << Char(Getattr(documented_node,"DoxygenComment")) << std::endl;
-		  }
-		  documented_node = Getattr(documented_node, "sym:nextSibling");
-		}
-		
-		char *convertedString = doxyTranslator.convert(n,const_cast< char *>(all_documentation.str().c_str()), "PYDOC");	
-		Printf(f_shadow, Char(pythoncode(convertedString, tab8))); 		
-		free(convertedString);
-	      }*/
+	      String *doxygen_comments;
+	      if(DoxygenTranslator::getDocumentation(n, PyDoc, doxygen_comments)){
+		Printf(f_shadow, Char(pythoncode(doxygen_comments, tab8))); 
+		Delete(doxygen_comments);
+	      }
 	    }
 	    else if (have_docstring(n))
 	      Printv(f_shadow, tab8, docstring(n, AUTODOC_METHOD, tab8), "\n", NIL);

From 8d28e0faadbfb6ce9a1d6695d11cc1f15fc8ccbb Mon Sep 17 00:00:00 2001
From: Jamie Kirkpatrick <gringostarr@users.sourceforge.net>
Date: Fri, 12 Sep 2008 11:22:04 +0000
Subject: [PATCH 036/314] Reformatting.

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2008-cherylfoil@10845 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 .../DoxygenTranslator/src/PyDocConverter.cpp  | 39 ++++++++-----------
 1 file changed, 17 insertions(+), 22 deletions(-)

diff --git a/Source/DoxygenTranslator/src/PyDocConverter.cpp b/Source/DoxygenTranslator/src/PyDocConverter.cpp
index dbee97233..bb36aa382 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/PyDocConverter.cpp
@@ -14,8 +14,7 @@
 #include <iostream>
 
 //TODO {@link} {@linkplain} {@docRoot}, and other useful doxy commands that are not a pydoc tag
-PyDocConverter::PyDocConverter()
-{
+PyDocConverter::PyDocConverter(){
     debug = 1;
 }
 
@@ -88,36 +87,32 @@ std::string PyDocConverter::translateSubtree( DoxygenEntity &doxygenEntity){
 }
 
 std::string PyDocConverter::translateEntity(Node *n, DoxygenEntity &doxyEntity){
-  if(doxyEntity.typeOfEntity.compare("partofdescription")== 0) 
+  if(doxyEntity.typeOfEntity.compare("partofdescription") == 0) 
     return justifyString(std::string(translateSubtree(doxyEntity)), 0);
   
-  if ((doxyEntity.typeOfEntity.compare("brief") == 0)||(doxyEntity.typeOfEntity.compare("details") == 0)){
-    return justifyString(std::string(translateSubtree(doxyEntity)), 0) + "\n * ";}
+  if ((doxyEntity.typeOfEntity.compare("brief") == 0)
+      ||(doxyEntity.typeOfEntity.compare("details") == 0))
+    return justifyString(std::string(translateSubtree(doxyEntity)), 0) + "\n";
   
-  if(doxyEntity.typeOfEntity.compare("plainstd::string")== 0 
-    || doxyEntity.typeOfEntity.compare("deprecated")== 0 
-    || doxyEntity.typeOfEntity.compare("brief")== 0)
-    return justifyString(doxyEntity.data, 0) + "\n * ";
-  
-  if(doxyEntity.typeOfEntity.compare("see") == 0)
-    return justifyString(std::string("@" + doxyEntity.typeOfEntity + "\t\t" + translateSubtree(doxyEntity)), 2);
+  if(doxyEntity.typeOfEntity.compare("plainstring") == 0 
+    || doxyEntity.typeOfEntity.compare("deprecated") == 0 
+    || doxyEntity.typeOfEntity.compare("brief") == 0)
+    return justifyString(doxyEntity.data, 0) + "\n";
   
   if(doxyEntity.typeOfEntity.compare("param") == 0)
     return formatParam(n, doxyEntity);
   
-  if(doxyEntity.typeOfEntity.compare("return")== 0)
+  if(doxyEntity.typeOfEntity.compare("return") == 0)
     return formatReturnDescription(n, doxyEntity);
 
-  if(doxyEntity.typeOfEntity.compare("author")== 0
-    || doxyEntity.typeOfEntity.compare("param")== 0
-    || doxyEntity.typeOfEntity.compare("since")== 0
-    || doxyEntity.typeOfEntity.compare("version")== 0
+  if(doxyEntity.typeOfEntity.compare("author") == 0
+    || doxyEntity.typeOfEntity.compare("param") == 0
+    || doxyEntity.typeOfEntity.compare("since") == 0
+    || doxyEntity.typeOfEntity.compare("version") == 0
     || doxyEntity.typeOfEntity.compare("exception") == 0
-    || doxyEntity.typeOfEntity.compare("deprecated") == 0)
-    return justifyString(std::string("@" + doxyEntity.typeOfEntity + "\t" + translateSubtree(doxyEntity)), 2);
-  
-  if(doxyEntity.typeOfEntity.compare("sa")== 0)
-    return justifyString(std::string("@see\t\t" + translateSubtree(doxyEntity)), 2);
+    || doxyEntity.typeOfEntity.compare("deprecated") == 0
+    || doxyEntity.typeOfEntity.compare("sa") == 0)
+    return "";
 
   return justifyString(doxyEntity.data);
 }

From 2cd2dac7e6dd91f17b634f373a28cc009e067d85 Mon Sep 17 00:00:00 2001
From: William S Fulton <wsf@fultondesigns.co.uk>
Date: Sat, 1 Nov 2008 21:48:20 +0000
Subject: [PATCH 037/314] type fix

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2008-cherylfoil@10895 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Doc/Manual/Doxygen.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Doc/Manual/Doxygen.html b/Doc/Manual/Doxygen.html
index 27fc013eb..54161eeb3 100644
--- a/Doc/Manual/Doxygen.html
+++ b/Doc/Manual/Doxygen.html
@@ -59,7 +59,7 @@ The behaviour of this functionality is wildly unpredictable if the interface fil
 <p>
 To make use of the comment translation system, your documentation comments must be in properly formatted <A HREF= "http://www.stack.nl/~dimitri/doxygen/">Doxygen.</A> They can be present in your main interface file or any header file that it imports.
 It is advised that you are certain your comments compile properly with Doxygen before you try to translate them.
-Doxygen itself is a deeper tool and can provide you better feedback for correct any syntax errors that may be present.
+Doxygen itself is a deeper tool and can provide you better feedback for correcting any syntax errors that may be present.
 Please look at Doxygen's <A HREF = "http://www.stack.nl/~dimitri/doxygen/docblocks.html"> Documenting the code</A> for proper specificatons for comment format.
 </p>
 

From 45518cd0d1c413da083d85c140c3bd640f139303 Mon Sep 17 00:00:00 2001
From: William S Fulton <wsf@fultondesigns.co.uk>
Date: Tue, 13 Oct 2009 21:27:09 +0000
Subject: [PATCH 038/314] apply doxygen-svndiff.patch from #2763155

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2008-cherylfoil@11697 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Source/CParse/cscanner.c                      |   4 +-
 Source/CParse/parser.y                        | 192 ++++++++++++++++--
 .../DoxygenTranslator/src/DoxygenEntity.cpp   |  31 ++-
 Source/DoxygenTranslator/src/DoxygenEntity.h  |  35 +++-
 .../DoxygenTranslator/src/DoxygenParser.cpp   |  72 +++----
 .../src/Examples/DoxygenTransWTokenizer.cpp   |  16 +-
 .../src/JavaDocConverter.cpp                  |  77 +++++--
 .../DoxygenTranslator/src/JavaDocConverter.h  |   2 +-
 .../DoxygenTranslator/src/PyDocConverter.cpp  |   2 +-
 Source/DoxygenTranslator/src/Token.cpp        |   1 +
 Source/DoxygenTranslator/src/Token.h          |   5 +-
 Source/DoxygenTranslator/src/TokenList.cpp    | 155 +++++++++-----
 Source/DoxygenTranslator/src/TokenList.h      |  19 +-
 Source/Modules/java.cxx                       |  17 +-
 Source/Modules/python.cxx                     |   9 +-
 15 files changed, 467 insertions(+), 170 deletions(-)

diff --git a/Source/CParse/cscanner.c b/Source/CParse/cscanner.c
index 12556dcf6..68d50cd2d 100644
--- a/Source/CParse/cscanner.c
+++ b/Source/CParse/cscanner.c
@@ -427,12 +427,12 @@ int yylook(void) {
 	  scanner_locator(cmt);
 	}
 	if (strncmp(loc, "/**<", 4) == 0 || strncmp(loc, "///<", 4) == 0||strncmp(loc, "/*!<", 4) == 0||strncmp(loc, "//!<", 4) == 0) {
-	  printf("Doxygen Post Comment: %s lines %d-%d [%s]\n", Char(Scanner_file(scan)), Scanner_start_line(scan), Scanner_line(scan), loc);
+	  /* printf("Doxygen Post Comment: %s lines %d-%d [%s]\n", Char(Scanner_file(scan)), Scanner_start_line(scan), Scanner_line(scan), loc); */
 	  yylval.str =  NewString(loc);
 	  return DOXYGENPOSTSTRING;
 	}
 	if (strncmp(loc, "/**", 3) == 0 || strncmp(loc, "///", 3) == 0||strncmp(loc, "/*!", 3) == 0||strncmp(loc, "//!", 3) == 0) {
-	  printf("Doxygen Comment: %s lines %d-%d [%s]\n", Char(Scanner_file(scan)), Scanner_start_line(scan), Scanner_line(scan), loc);
+	  /* printf("Doxygen Comment: %s lines %d-%d [%s]\n", Char(Scanner_file(scan)), Scanner_start_line(scan), Scanner_line(scan), loc);  */
 	  yylval.str =  NewString(loc);
 	  return DOXYGENSTRING;
 	}
diff --git a/Source/CParse/parser.y b/Source/CParse/parser.y
index 06b0685c6..d28516206 100644
--- a/Source/CParse/parser.y
+++ b/Source/CParse/parser.y
@@ -13,7 +13,7 @@
 
 #define yylex yylex
 
-char cvsroot_parser_y[] = "$Id: parser.y 10767 2008-08-16 07:31:05Z cherylfoil $";
+char cvsroot_parser_y[] = "$Id$";
 
 #include "swig.h"
 #include "cparse.h"
@@ -1575,6 +1575,7 @@ static void tag_nodes(Node *n, const String_or_char *attrname, DOH *value) {
 %type <str>	 doxygen_comment;
 %type <str>	 c_style_comment;
 %type <str>	 doxygen_post_comment;
+%type <str>	 doxygen_post_comment_item;
 %%
 
 /* ======================================================================
@@ -3213,9 +3214,17 @@ c_constructor_decl : storage_class type LPAREN parms RPAREN ctor_end {
 
 doxygen_comment : DOXYGENSTRING 
 	{
-		while(Strchr($1,'/') == Char($1))
-			Replace($1,"/","",DOH_REPLACE_FIRST);
-	  if(isStructuralDoxygen($1)){
+            /* while(Strchr($1,'/') == Char($1))
+               Replace($1,"/","",DOH_REPLACE_FIRST); */
+          DohReplace($1, "/**", "", 0);
+          DohReplace($1, "/*!", "", 0);
+          DohReplace($1, "///", "", 0);
+          DohReplace($1, "*/", "", 0);
+
+          /* isStructuralDoxygen() is disabled, since no comment
+             appears in such case. Need to fix. (most commands are
+             not translatable to javadoc anyway) */
+	  if(0  &&  isStructuralDoxygen($1)){
 	    $$ = new_node("doxycomm");
 		Setattr($$,"DoxygenComment",$1);
 	    }
@@ -3231,13 +3240,26 @@ doxygen_comment : DOXYGENSTRING
 	;
 
 
-doxygen_post_comment : DOXYGENPOSTSTRING 
+doxygen_post_comment_item : DOXYGENPOSTSTRING 
 	{
-		if(currentPostComment != 0){
-	      Append(currentPostComment, $1);
-	      }
-	    else currentPostComment = $1;
-		$$ = 0;
+	  DohReplace($1, "///<", "", 0);
+	  DohReplace($1, "/**<", "", 0);
+	  DohReplace($1, "/*!<", "", 0);
+	  DohReplace($1, "//!<", "", 0);
+	  DohReplace($1, "*/", "", 0);
+	  
+	  $$ = $1;
+	}
+	;
+
+doxygen_post_comment : doxygen_post_comment doxygen_post_comment_item
+                       { 
+			 Append($1, $2);
+			 $$ = $1;
+                       }
+                     | doxygen_post_comment_item
+                       {
+                         $$ = $1;
 	}
 	;
 
@@ -4541,13 +4563,38 @@ storage_class  : EXTERN { $$ = "extern"; }
    ------------------------------------------------------------------------------ */
 
 parms          : rawparms {
-                 Parm *p;
+                 Parm *p, *nextSibling;
 		 $$ = $1;
 		 p = $1;
-                 while (p) {
+		 while (p) {
+		   String *postComment = NULL;
+		   nextSibling = nextSibling(p);
+		   if (nextSibling != NULL) {
+		     postComment = Getattr(nextSibling, "postComment");
+		   } else {
+		     /* the last functino parameter has two attributes -
+			post comment of the previous params and its own post
+			comment.
+		      */
+		     postComment = Getattr(p, "lastParamPostComment");
+		   }
+		   if (postComment != NULL) {
+		     String *param = NewString("\n@param ");
+		     if (currentComment != 0) {
+		       Append(currentComment, param);
+		       Append(currentComment, Getattr(p, "name"));
+		       Append(currentComment, postComment);
+		     }
+		     else {
+		       currentComment = param;
+		       Append(currentComment, Getattr(p, "name"));
+		       Append(currentComment, postComment);
+		     }
+		   }
+
 		   Replace(Getattr(p,"type"),"typename ", "", DOH_REPLACE_ANY);
-		   p = nextSibling(p);
-                 }
+		   p = nextSibling;
+		 }
                }
     	       ;
 
@@ -4562,6 +4609,34 @@ ptail          : COMMA parm ptail {
                  set_nextSibling($2,$3);
 		 $$ = $2;
                 }
+               | COMMA doxygen_post_comment parm ptail {
+		 set_nextSibling($3,$4);
+		 $$ = $3;
+		 
+		 /** because function parameters are not nodes,
+		    it must be the current function node, which
+		    gets doxy comment set.
+		 */
+		
+		 Setattr($3, "postComment", $2);
+		 /*
+		 currentPostComment = $2;
+		 if (previousParmName != 0) {
+		     String *param = NewString("\n@param ");
+		     if (currentComment != 0) {
+			 Append(currentComment, param);
+			 Append(currentComment, previousParmName );
+			 Append(currentComment, currentPostComment);
+		     }
+		     else {
+			 currentComment = param;
+			 Append(currentComment, Getattr($3, "name") );
+			 Append(currentComment, currentPostComment);
+		     }
+		 }  
+		 currentPostComment = 0;
+		 */
+                }
                | empty { $$ = 0; }
                ;
 
@@ -4575,6 +4650,36 @@ parm           : rawtype parameter_declarator {
 		     Setattr($$,"value",$2.defarg);
 		   }
 		}
+                | rawtype parameter_declarator doxygen_post_comment {
+		  /** handles the last function parameter, which is not followed by comma */
+		  /* 
+		  String *param = NewString("@param ");
+		  String *name = NewString($2.id);
+
+		  if (currentComment != 0) {
+		    Append(currentComment, param);
+		  }
+		  else {
+		     currentComment = param;
+		  }
+
+		  Append(currentComment, name);
+		  Append(currentComment, $3);
+
+		  if (currentPostComment != 0) {
+		  } 
+		  currentPostComment = 0;
+		  */
+
+		  SwigType_push($1,$2.type);
+		  $$ = NewParm($1,$2.id);
+		  Setattr($$, "lastParamPostComment", $3);
+		  Setfile($$,cparse_file);
+		  Setline($$,cparse_line);
+		  if ($2.defarg) {
+		    Setattr($$,"value",$2.defarg);
+		  }
+		}
 
                 | TEMPLATE LESSTHAN cpptype GREATERTHAN cpptype idcolon def_args {
                   $$ = NewParm(NewStringf("template<class> %s %s", $5,$6), 0);
@@ -5462,6 +5567,65 @@ edecl          :  ID {
 		   }
 		   SetFlag($$,"feature:immutable");
                  }
+
+                 | doxygen_comment ID EQUAL etype {
+		   $$ = new_node("enumitem");
+		   Setattr($$,"name",$2);
+		   Setattr($$,"enumvalue", $4.val);
+	           if ($4.type == T_CHAR) {
+		     SwigType *type = NewSwigType(T_CHAR);
+		     Setattr($$,"value",NewStringf("\'%(escape)s\'", $4.val));
+		     Setattr($$,"type",type);
+		     Delete(type);
+		   } else {
+		     SwigType *type = NewSwigType(T_INT);
+		     Setattr($$,"value",$2);
+		     Setattr($$,"type",type);
+		     Delete(type);
+		   }
+		   SetFlag($$,"feature:immutable");
+                 }
+
+                 | doxygen_post_comment ID EQUAL etype {
+                   currentPostComment = $1;
+		   $$ = new_node("enumitem");
+		   Setattr($$,"name",$2);
+		   Setattr($$,"enumvalue", $4.val);
+	           if ($4.type == T_CHAR) {
+		     SwigType *type = NewSwigType(T_CHAR);
+		     Setattr($$,"value",NewStringf("\'%(escape)s\'", $4.val));
+		     Setattr($$,"type",type);
+		     Delete(type);
+		   } else {
+		     SwigType *type = NewSwigType(T_INT);
+		     Setattr($$,"value",$2);
+		     Setattr($$,"type",type);
+		     Delete(type);
+		   }
+		   SetFlag($$,"feature:immutable");
+                 }
+
+                 | doxygen_comment ID {
+		   SwigType *type = NewSwigType(T_INT);
+		   $$ = new_node("enumitem");
+		   Setattr($$,"name",$2);
+		   Setattr($$,"type",type);
+		   SetFlag($$,"feature:immutable");
+		   Delete(type);
+		 }
+                 | doxygen_post_comment ID {
+		   SwigType *type = NewSwigType(T_INT);
+                   currentPostComment = $1;
+		   $$ = new_node("enumitem");
+		   Setattr($$,"name",$2);
+		   Setattr($$,"type",type);
+		   SetFlag($$,"feature:immutable");
+		   Delete(type);
+		 }
+                 | doxygen_post_comment {
+                     currentPostComment = $1;
+                     $$ = $1;
+                   }
                  | empty { $$ = 0; }
                  ;
 
diff --git a/Source/DoxygenTranslator/src/DoxygenEntity.cpp b/Source/DoxygenTranslator/src/DoxygenEntity.cpp
index 52fb60d90..b2b156b5d 100644
--- a/Source/DoxygenTranslator/src/DoxygenEntity.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenEntity.cpp
@@ -13,7 +13,7 @@
 DoxygenEntity::DoxygenEntity(std::string typeEnt){
     typeOfEntity = typeEnt;
     data = "";
-    isLeaf = 1;
+    isLeaf = true;
 }
 
 /* Basic node for commands that have
@@ -24,7 +24,7 @@ DoxygenEntity::DoxygenEntity(std::string typeEnt){
 DoxygenEntity::DoxygenEntity(std::string typeEnt, std::string param1){
     typeOfEntity = typeEnt;
     data = param1;
-    isLeaf = 1;
+    isLeaf = true;
 }
 
 /* Nonterminal node
@@ -33,23 +33,35 @@ DoxygenEntity::DoxygenEntity(std::string typeEnt, std::string param1){
 DoxygenEntity::DoxygenEntity(std::string typeEnt, std::list <DoxygenEntity> &entList ){
     typeOfEntity = typeEnt;
     data = "";
-    isLeaf = 0;
+    isLeaf = false;
     entityList = entList;
 }
 
 void DoxygenEntity::printEntity(int level){
 	int thisLevel = level;
 	if (isLeaf) {
-		for (int i = 0; i < thisLevel; i++) {std::cout << "\t";}
+		for (int i = 0; i < thisLevel; i++) {
+            std::cout << "\t";
+        }
+		
 		std::cout << "Node Command: " << typeOfEntity << " ";
-		if (data.compare("") != 0) std::cout << "Node Data: " << data;
+        
+        if (data.compare("") != 0) {
+            std::cout << "Node Data: " << data;
+        }
 		std::cout << std::endl;
+
+	} else {
+
+		for (int i = 0; i < thisLevel; i++) {
+            std::cout << "\t";
 	}
-	else{
-		for (int i = 0; i < thisLevel; i++) {std::cout << "\t";}
+
 		std::cout << "Node Command : " << typeOfEntity << std::endl;
+
 		std::list<DoxygenEntity>::iterator p = entityList.begin();
 		thisLevel++;
+
 		while (p != entityList.end()){
 			(*p).printEntity(thisLevel);
 			p++;
@@ -57,7 +69,10 @@ void DoxygenEntity::printEntity(int level){
 	}
 }
 
+// not used, completely wrong - currently std lib reports 'invalid operator <'
 bool CompareDoxygenEntities::operator()(DoxygenEntity& first, DoxygenEntity& second){
+
+   // return first.typeOfEntity < second.typeOfEntity;
   if(first.typeOfEntity.compare("brief") == 0) 
     return true;
   if(second.typeOfEntity.compare("brief") == 0) 
@@ -68,7 +83,7 @@ bool CompareDoxygenEntities::operator()(DoxygenEntity& first, DoxygenEntity& sec
     return false;
   if(first.typeOfEntity.compare("partofdescription") == 0) 
     return true;
-  if(first.typeOfEntity.compare("partofdescription") == 0) 
+  if(second.typeOfEntity.compare("partofdescription") == 0) 
     return false;
   if(first.typeOfEntity.compare("plainstd::string") == 0) 
     return true;
diff --git a/Source/DoxygenTranslator/src/DoxygenEntity.h b/Source/DoxygenTranslator/src/DoxygenEntity.h
index 6a0b2e48c..4c1ab7ff9 100644
--- a/Source/DoxygenTranslator/src/DoxygenEntity.h
+++ b/Source/DoxygenTranslator/src/DoxygenEntity.h
@@ -13,18 +13,43 @@
 #include <string>
 #include <list>
 
+
+typedef enum {
+  SIMPLECOMMAND, 
+  IGNOREDSIMPLECOMMAND,
+  COMMANDWORD,
+  IGNOREDCOMMANDWORD,
+  COMMANDLINE,
+  IGNOREDCOMMANDLINE,
+  COMMANDPARAGRAPH,
+  IGNORECOMMANDPARAGRAPH,
+  COMMANDENDCOMMAND,
+  COMMANDWORDPARAGRAPH,
+  COMMANDWORDLINE,
+  COMMANDWORDOWORDWORD,
+  COMMANDOWORD,
+  COMMANDERRORTHROW,
+  COMMANDUNIQUE,
+  END_LINE,
+  PARAGRAPH_END,
+  PLAINSTRING,
+  COMMAND
+} DoxyCommandEnum;
+
 /*
  * Structure to represent a doxygen comment entry
  */
 struct DoxygenEntity{
-  DoxygenEntity(std::string typeEnt);
-  DoxygenEntity(std::string typeEnt, std::string param1);
-  DoxygenEntity(std::string typeEnt, std::list <DoxygenEntity> &entList );
-  void printEntity(int level);
   std::string typeOfEntity;
   std::list <DoxygenEntity> entityList;
   std::string data;
-  int isLeaf;
+  bool isLeaf;
+
+  DoxygenEntity(std::string typeEnt);
+  DoxygenEntity(std::string typeEnt, std::string param1);
+  DoxygenEntity(std::string typeEnt, std::list <DoxygenEntity> &entList );
+
+  void printEntity(int level);
 };
 
 /* 
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.cpp b/Source/DoxygenTranslator/src/DoxygenParser.cpp
index cdc2d709f..78072852d 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenParser.cpp
@@ -1,24 +1,6 @@
 #include "DoxygenParser.h"
 #include "TokenList.h"
-#define SIMPLECOMMAND 1
-#define IGNOREDSIMPLECOMMAND 2
-#define COMMANDWORD 3
-#define IGNOREDCOMMANDWORD 4
-#define COMMANDLINE 5
-#define IGNOREDCOMMANDLINE 6
-#define COMMANDPARAGRAPH 7
-#define IGNORECOMMANDPARAGRAPH 8
-#define COMMANDENDCOMMAND 9
-#define COMMANDWORDPARAGRAPH 10
-#define COMMANDWORDLINE 11
-#define COMMANDWORDOWORDWORD 12
-#define COMMANDOWORD 13
-#define COMMANDERRORTHROW 14
-#define COMMANDUNIQUE 15
-#define  END_LINE 101
-#define PARAGRAPH_END 102
-#define  PLAINSTRING 103
-#define  COMMAND  104
+
 
 DoxygenParser::DoxygenParser()
 {
@@ -50,14 +32,14 @@ std::string commandArray[] = {"a", "addindex", "addtogroup", "anchor", "arg", "a
     "private", "privatesection", "property", "protected", "protectedsection", "protocol",
     "public", "publicsection", "ref", "relates", "relatesalso", "remarks", "return", "retval",
     "sa", "section", "see", "showinitializer", "since", "skip", "skipline", "struct", "subpage",
-    "subsection", "subsubsection", "test", "throw", "todo", "tparam", "typedef", "union", "until",
+    "subsection", "subsubsection", "test", "throw", "throws", "todo", "tparam", "typedef", "union", "until",
     "var", "verbatim", "verbinclude", "version", "warning", "weakgroup", "xmlonly", "xrefitem",
     "$", "@", "\\","&", "~", "<", ">", "#", "%"};
 
 
 std::string sectionIndicators[] = { "attention", "author", "brief", "bug", "cond", "date", "deprecated", "details",
     "else", "elseif", "endcond", "endif", "exception", "if", "ifnot", "invariant", "note", "par", "param",
-    "tparam", "post" , "pre", "remarks", "return", "retval", "sa", "see", "since", "test", "throw", "todo",
+    "tparam", "post" , "pre", "remarks", "return", "retval", "sa", "see", "since", "test", "throw", "throws", "todo",
     "version", "warning", "xrefitem" };
 
 /* All of the doxygen commands divided up by how they are parsed */
@@ -73,7 +55,7 @@ std::string commandParagraph[] = {"partofdescription", "return", "remarks", "sin
 std::string ignoreCommandParagraphs[] = {"nothing at the moment"};
 std::string commandEndCommands[] = {"code", "dot", "msc", "f$", "f[", "f{environment}{", "htmlonly", "latexonly", "manonly", 
        "verbatim", "xmlonly", "cond", "if", "ifnot", "link"};
-std::string commandWordParagraphs[] = {"param", "tparam", "throw", "retval", "exception"};
+std::string commandWordParagraphs[] = {"param", "tparam", "throw", "throws", "retval", "exception"};
 std::string commandWordLines[] = {"page", "subsection", "subsubsection", "section", "paragraph", "defgroup"};
 std::string commandWordOWordOWords [] = {"category", "class", "protocol", "interface", "struct", "union"};
 std::string commandOWords[] = {"dir", "file", "cond"};
@@ -264,28 +246,33 @@ std::string getStringTilEndCommand(std::string theCommand, TokenList &tokList){
 
 /* Returns the end of a Paragraph as an iterator-
 * Paragraph is defined in Doxygen to be a paragraph of text
-* seperate by either a structural command or a blank line
+ * separated by either a structural command or a blank line
 */
 std::list<Token>::iterator getEndOfParagraph(TokenList &tokList){
    std::list<Token>::iterator endOfParagraph = tokList.iteratorCopy();
    while(endOfParagraph != tokList.end()){
     if ((* endOfParagraph).tokenType == END_LINE){
        endOfParagraph++;
-       if ((* endOfParagraph).tokenType == END_LINE){
+       if (endOfParagraph != tokList.end()  &&  (* endOfParagraph).tokenType == END_LINE) {
          endOfParagraph++;
          //cout << "ENCOUNTERED END OF PARA" << endl;
          return endOfParagraph;
          }
+
+        } else if ((*endOfParagraph).tokenType == COMMAND) {
+
+            if (isSectionIndicator((* endOfParagraph).tokenString)) {
+                return endOfParagraph;
        }
-    else if ((* endOfParagraph).tokenType == COMMAND){
-       if(isSectionIndicator((* endOfParagraph).tokenString)) return endOfParagraph;
        else endOfParagraph++;
-       }
-    else if((* endOfParagraph).tokenType == PLAINSTRING) {
+
+        } else if ((*endOfParagraph).tokenType == PLAINSTRING) {
        endOfParagraph++;
+        } else {
+            return tokList.end();
        }
-    else return tokList.end();
     }
+
    return tokList.end();
    }
 
@@ -478,7 +465,7 @@ int addCommandEndCommand(std::string theCommand, TokenList &tokList, std::list <
 /* CommandWordParagraph
 * Format: @command <word> {paragraph}
 * Commands such as param
-* "param", "tparam", "throw", "retval", "exception"
+ * "param", "tparam", "throw", "throws", "retval", "exception"
 */
 int addCommandWordParagraph(std::string theCommand, TokenList &tokList, std::list <DoxygenEntity> &doxyList){
   if (noisy) 
@@ -560,8 +547,10 @@ int addCommandOWord(std::string theCommand, TokenList &tokList, std::list <Doxyg
   */
 int addCommandErrorThrow(std::string theCommand, TokenList &tokList, std::list <DoxygenEntity> &doxyList){
 #pragma unused(doxyList)
-    cout << "Encountered :" << theCommand << endl;
-    cout << "This command should not have been encountered. Behaviour past this may be unpredictable " << endl;
+    if (noisy) {
+      cout << "Encountered :" << theCommand << endl;
+      cout << "This command should not have been encountered. Behaviour past this may be unpredictable " << endl;
+    }
     std::list<Token>::iterator endOfLine = getOneLine(tokList);
     tokList.setIterator(endOfLine);
     return 0;
@@ -699,8 +688,6 @@ int addCommandUnique(std::string theCommand, TokenList &tokList, std::list <Doxy
  * with my current design- however the skeletal outline is contained in
  * the file Skeleton
  */
-
-
 int addCommand(std::string commandString, TokenList &tokList,std::list <DoxygenEntity> &doxyList){
    std::string theCommand = StringToLower(commandString);
    if (theCommand.compare("plainstd::string") == 0){
@@ -790,23 +777,30 @@ std::list<DoxygenEntity> parse(std::list<Token>::iterator endParsingIndex, Token
 }
 
 std::list<DoxygenEntity> parseRoot(std::list<Token>::iterator endParsingIndex, TokenList &tokList){
+
   std::list <DoxygenEntity> aNewList;
   int currCommand;
+
   while (tokList.current() != endParsingIndex){ 
+
     Token currToken = tokList.peek();
-    if(noisy) cout << "Parsing for phrase starting in:" << currToken.toString() << endl;
+    if(noisy) {
+      cout << "Parsing for phrase starting in:" << currToken.toString() << endl;
+    }
+
     if(currToken.tokenType == END_LINE ){
       tokList.next();
     }
     else if(currToken.tokenType == COMMAND){
       currCommand = findCommand(currToken.tokenString);
       if (currCommand < 0 ){ 
-        if(noisy) 
+	if(noisy) {
 	  cout << "Unidentified Command " << currToken.tokenString << endl;
+	}
+	tokList.next();
+	addCommand(std::string("partofdescription"), tokList, aNewList);
+      } else { 
         tokList.next();
-      addCommand(std::string("partofdescription"), tokList, aNewList);}
-      //cout << "Command: " << currWord << " " << currCommand << endl;
-      else { tokList.next();
         addCommand(currToken.tokenString, tokList,  aNewList);
       }
     }
diff --git a/Source/DoxygenTranslator/src/Examples/DoxygenTransWTokenizer.cpp b/Source/DoxygenTranslator/src/Examples/DoxygenTransWTokenizer.cpp
index 299f59216..dacb31f77 100644
--- a/Source/DoxygenTranslator/src/Examples/DoxygenTransWTokenizer.cpp
+++ b/Source/DoxygenTranslator/src/Examples/DoxygenTransWTokenizer.cpp
@@ -569,7 +569,7 @@ string getStringTilCommand(int &startInd, string doxygenString){
  		}
  		else{
  			startIndex = savedIndex;
-			addCommand(string("plainstring"), startIndex, aNewList, doxygenString);
+			addCommand(string("plainstd::string"), startIndex, aNewList, doxygenString);
 
  		}
  	}
@@ -728,7 +728,7 @@ string getStringTilCommand(int &startInd, string doxygenString){
 	if(!restOfParagraph.empty()){
 		list <DoxygenEntity> aNewList;
 		aNewList =  parse(placement, restOfParagraph);
-		aNewList.push_front(DoxygenEntity("plainstring", name));
+		aNewList.push_front(DoxygenEntity("plainstd::string", name));
 		doxyList.push_back(DoxygenEntity(theCommand, aNewList));
 		return 1;
 		}
@@ -752,7 +752,7 @@ string getStringTilCommand(int &startInd, string doxygenString){
 	if(!restOfLine.empty()){
 		list <DoxygenEntity> aNewList;
 		aNewList =  parse(placement, restOfLine);
-		aNewList.push_front(DoxygenEntity("plainstring", name));
+		aNewList.push_front(DoxygenEntity("plainstd::string", name));
 		doxyList.push_back(DoxygenEntity(theCommand, aNewList));
 		return 1;
 		}
@@ -775,9 +775,9 @@ string getStringTilCommand(int &startInd, string doxygenString){
 	string headerfile = getNextWord(startInd, doxygenString);
 	string headername = getNextWord(startInd, doxygenString);
 	list <DoxygenEntity> aNewList;
-	aNewList.push_back(DoxygenEntity("plainstring", name));
-	if (!headerfile.empty()) aNewList.push_back(DoxygenEntity("plainstring", headerfile));
-	if (!headername.empty()) aNewList.push_back(DoxygenEntity("plainstring", headername));
+	aNewList.push_back(DoxygenEntity("plainstd::string", name));
+	if (!headerfile.empty()) aNewList.push_back(DoxygenEntity("plainstd::string", headerfile));
+	if (!headername.empty()) aNewList.push_back(DoxygenEntity("plainstd::string", headername));
 	doxyList.push_back(DoxygenEntity(theCommand, aNewList));
 	return 1;
   }
@@ -806,10 +806,10 @@ string getStringTilCommand(int &startInd, string doxygenString){
 	 	/* @command */
 
 	 
-	 if (theCommand.compare("plainstring") == 0){
+	 if (theCommand.compare("plainstd::string") == 0){
 	 		string nextPhrase = getStringTilCommand(startInd, doxygenString);
 	 		if (noisy) cout << "Parsing plain string :" << nextPhrase << endl;
-	 		doxyList.push_back(DoxygenEntity("plainstring", nextPhrase ));
+	 		doxyList.push_back(DoxygenEntity("plainstd::string", nextPhrase ));
 	 		return 1;
 	 }
 	 int commandNumber = commandBelongs(theCommand);
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.cpp b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
index 0ba97fc60..33a62ff77 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
@@ -15,15 +15,16 @@ std::string JavaDocConverter::formatCommand(std::string unformattedLine, int ind
     lastPosition = i;
     if (isFirstLine){
       i+=APPROX_LINE_LENGTH;
+    } else {
+        i+=APPROX_LINE_LENGTH - indent*TAB_SIZE;
     }
-    else i+=APPROX_LINE_LENGTH - indent*TAB_SIZE;
+
     i = unformattedLine.find(" ", i);
 
     if (i > 0 && i + 1 < (int)unformattedLine.length()){
       if (!isFirstLine) for (int j = 0; j < indent; j++) {
         formattedLines.append("\t");
-        }
-      else {
+      } else {
         isFirstLine = 0;
       }
       formattedLines.append(unformattedLine.substr(lastPosition, i - lastPosition + 1));
@@ -32,7 +33,11 @@ std::string JavaDocConverter::formatCommand(std::string unformattedLine, int ind
     }
   }
   if (lastPosition < (int)unformattedLine.length()){
-    if (!isFirstLine) {for (int j = 0; j < indent; j++) {formattedLines.append("\t");}}
+    if (!isFirstLine) {
+        for (int j = 0; j < indent; j++) { 
+            formattedLines.append("\t");
+        }
+    }
     formattedLines.append(unformattedLine.substr(lastPosition, unformattedLine.length() - lastPosition));
   }
 
@@ -46,7 +51,7 @@ std::string JavaDocConverter::javaDocFormat(DoxygenEntity &doxygenEntity){
   if(doxygenEntity.typeOfEntity.compare("partofdescription") == 0){
         return doxygenEntity.data;
     }
-  if (doxygenEntity.typeOfEntity.compare("plainstring") == 0){
+  if (doxygenEntity.typeOfEntity.compare("plainstd::string") == 0){
       return  doxygenEntity.data;
   }
   else if (doxygenEntity.typeOfEntity.compare("b") == 0){
@@ -85,10 +90,12 @@ std::string JavaDocConverter::javaDocFormat(DoxygenEntity &doxygenEntity){
 
 std::string JavaDocConverter::translateSubtree( DoxygenEntity &doxygenEntity){
   std::string returnedString;
-  if (doxygenEntity.isLeaf){ return javaDocFormat(doxygenEntity) + " ";}
-  else {
+  if (doxygenEntity.isLeaf) { 
+    return javaDocFormat(doxygenEntity) + " ";
+  } else {
     returnedString += javaDocFormat(doxygenEntity);
     std::list<DoxygenEntity>::iterator p = doxygenEntity.entityList.begin();
+
     while (p != doxygenEntity.entityList.end()){
       returnedString+= translateSubtree(*p);
       p++;
@@ -97,38 +104,64 @@ std::string JavaDocConverter::translateSubtree( DoxygenEntity &doxygenEntity){
   return returnedString;
 }
 
+
 std::string JavaDocConverter::translateEntity(DoxygenEntity &doxyEntity){
-  if(doxyEntity.typeOfEntity.compare("partofdescription")== 0) return formatCommand(std::string(translateSubtree(doxyEntity)), 0);
-  if ((doxyEntity.typeOfEntity.compare("brief") == 0)||(doxyEntity.typeOfEntity.compare("details") == 0)){
-  return formatCommand(std::string(translateSubtree(doxyEntity)), 0) + "\n * ";}
-  else if(doxyEntity.typeOfEntity.compare("plainstring")== 0 || doxyEntity.typeOfEntity.compare("deprecated")== 0 || doxyEntity.typeOfEntity.compare("brief")== 0)
-    return formatCommand(doxyEntity.data, 0) + "\n * ";
-  else if(doxyEntity.typeOfEntity.compare("see") == 0){
-    return formatCommand(std::string("@" + doxyEntity.typeOfEntity + "\t\t" + translateSubtree(doxyEntity)), 2);
+  if (doxyEntity.typeOfEntity.compare("partofdescription") == 0) {
+    return formatCommand(std::string(translateSubtree(doxyEntity)), 0);
   }
-  else if(doxyEntity.typeOfEntity.compare("return")== 0
+
+  if ((doxyEntity.typeOfEntity.compare("brief") == 0)  ||  
+      (doxyEntity.typeOfEntity.compare("details") == 0)) {
+    return formatCommand(std::string(translateSubtree(doxyEntity)), 0) + "\n * ";
+
+  } else if(doxyEntity.typeOfEntity.compare("plainstd::string")== 0 || 
+      doxyEntity.typeOfEntity.compare("deprecated")== 0 || 
+      doxyEntity.typeOfEntity.compare("brief")== 0) {
+    return formatCommand(doxyEntity.data, 0) + "\n * ";
+
+  } else if(doxyEntity.typeOfEntity.compare("see") == 0) {
+    return formatCommand(std::string("@" + doxyEntity.typeOfEntity + "\t\t" + 
+	  translateSubtree(doxyEntity)), 2);
+
+  } else if(doxyEntity.typeOfEntity.compare("return")== 0
       || doxyEntity.typeOfEntity.compare("author")== 0
       || doxyEntity.typeOfEntity.compare("param")== 0
+      || doxyEntity.typeOfEntity.compare("throw")== 0
+      || doxyEntity.typeOfEntity.compare("throws")== 0
       || doxyEntity.typeOfEntity.compare("since")== 0
       || doxyEntity.typeOfEntity.compare("version")== 0
       || doxyEntity.typeOfEntity.compare("exception") == 0
       || doxyEntity.typeOfEntity.compare("deprecated") == 0){
+
+    // this 'if' is a hack - convert doxyEntity.typeOfEntity at the time of parsing
+    if (doxyEntity.typeOfEntity.compare("throw")== 0) {
+      doxyEntity.typeOfEntity = "throws";
+    }
     return formatCommand(std::string("@" + doxyEntity.typeOfEntity + "\t" + translateSubtree(doxyEntity)), 2);
-  }
-  else if(doxyEntity.typeOfEntity.compare("sa")== 0){
+
+  } else if(doxyEntity.typeOfEntity.compare("sa")== 0) {
     return formatCommand(std::string("@see\t\t" + translateSubtree(doxyEntity)), 2);
+
+  } else {
+    return formatCommand(javaDocFormat(doxyEntity), 0 );
   }
-  else return formatCommand(javaDocFormat(doxyEntity), 0 );
+
   return "";
 }
 
-bool JavaDocConverter::getDocumentation(Node *n, String *&documentation){
-  documentation = Getattr(n,"DoxygenComment");
-  if(documentation == NULL)
+
+bool JavaDocConverter::getDocumentation(Node *node, String *&documentation) {
+
+  documentation = Getattr(node, "DoxygenComment");
+
+  if (documentation == NULL) {
     return false;
+  }
   
   std::list <DoxygenEntity> entityList = DoxygenParser().createTree(Char(documentation));
-  entityList.sort(CompareDoxygenEntities());
+
+    // entityList.sort(CompareDoxygenEntities()); sorting currently not used,
+    // see CompareDoxygenEntities::operator() in DoxygenEntity.cpp
   
   if(debug){
     std::cout << "---RESORTED LIST---" << std::endl;
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.h b/Source/DoxygenTranslator/src/JavaDocConverter.h
index e2a25d4ff..8651bb1cf 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.h
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.h
@@ -18,7 +18,7 @@
 class JavaDocConverter : public DoxygenTranslator
 {
 public:
-  JavaDocConverter() : debug( true ){}
+  JavaDocConverter() : debug( false ){}
   virtual bool getDocumentation(Node *node, String *&documentation);
   
 protected:
diff --git a/Source/DoxygenTranslator/src/PyDocConverter.cpp b/Source/DoxygenTranslator/src/PyDocConverter.cpp
index bb36aa382..6418ee73c 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/PyDocConverter.cpp
@@ -94,7 +94,7 @@ std::string PyDocConverter::translateEntity(Node *n, DoxygenEntity &doxyEntity){
       ||(doxyEntity.typeOfEntity.compare("details") == 0))
     return justifyString(std::string(translateSubtree(doxyEntity)), 0) + "\n";
   
-  if(doxyEntity.typeOfEntity.compare("plainstring") == 0 
+  if(doxyEntity.typeOfEntity.compare("plainstd::string") == 0 
     || doxyEntity.typeOfEntity.compare("deprecated") == 0 
     || doxyEntity.typeOfEntity.compare("brief") == 0)
     return justifyString(doxyEntity.data, 0) + "\n";
diff --git a/Source/DoxygenTranslator/src/Token.cpp b/Source/DoxygenTranslator/src/Token.cpp
index 198b3e442..2ac03afe5 100644
--- a/Source/DoxygenTranslator/src/Token.cpp
+++ b/Source/DoxygenTranslator/src/Token.cpp
@@ -1,4 +1,5 @@
 #include "Token.h"
+#include "DoxygenEntity.h"
 using namespace std;
 
 
diff --git a/Source/DoxygenTranslator/src/Token.h b/Source/DoxygenTranslator/src/Token.h
index e98686c14..cf28c90b7 100644
--- a/Source/DoxygenTranslator/src/Token.h
+++ b/Source/DoxygenTranslator/src/Token.h
@@ -2,10 +2,6 @@
 #define TOKEN_H_
 #include <string>
 
-#define  END_LINE 101
-#define PARAGRAPH_END 102
-#define  PLAINSTRING 103
-#define  COMMAND  104
 using namespace std;
 
 class Token
@@ -13,6 +9,7 @@ class Token
 public:
 	Token(int tType, string tString);
 	~Token();
+
 	int tokenType; /* currently can be END_LINE, PLAINSTRING, or COMMAND */
 	string tokenString; /* the data , such as param for @param*/
 	string toString();
diff --git a/Source/DoxygenTranslator/src/TokenList.cpp b/Source/DoxygenTranslator/src/TokenList.cpp
index a05d2ceef..1a9ff0a7a 100644
--- a/Source/DoxygenTranslator/src/TokenList.cpp
+++ b/Source/DoxygenTranslator/src/TokenList.cpp
@@ -4,99 +4,162 @@
 #include <string>
 #include <list>
 #include "Token.h"
+#include "DoxygenEntity.h"
 #define TOKENSPERLINE 8; //change this to change the printing behaviour of the token list
-#define  END_LINE 101
-#define PARAGRAPH_END 102 //not used at the moment 
-#define  PLAINSTRING 103
-#define  COMMAND  104
+
 using namespace std;
 
-
-list <Token> tokenList;
-list<Token>::iterator tokenListIterator;
 int noisy2 = 0;
 /* The tokenizer*/
+TokenList::TokenList(const std::string &doxygenStringConst){
+    size_t commentPos;
+    string doxygenString = doxygenStringConst;
+
+    /* Comment start tokens are replaced in parser.y, see doxygen_comment and
+       doxygen_post_comment_item
+       do {
+        commentPos = doxygenString.find("///<");
+        if (commentPos != string::npos) {
+            doxygenString.replace(commentPos, 4, " ");
+            continue;
+        }
+        commentPos = doxygenString.find("/**<");
+        if (commentPos != string::npos) {
+            doxygenString.replace(commentPos, 4, " ");
+            continue;
+        }
+        commentPos = doxygenString.find("/*!<");
+        if (commentPos != string::npos) {
+            doxygenString.replace(commentPos, 4, " ");
+            continue;
+        }
+        commentPos = doxygenString.find("//!<");
+        if (commentPos != string::npos) {
+            doxygenString.replace(commentPos, 4, " ");
+            continue;
+        }
+        break;
+    } while (true); */
+
+    size_t currentIndex = 0;
+    size_t nextIndex = 0;
 
-TokenList::TokenList(string doxygenString){
-	int currentIndex = 0;
-	//Regex whitespace("[ \t]+");
-	//Regex newLine("[\n]");
-	//Regex command("[@|\\]{1}[^ \t \n]+"); //the cheap solution 
-	//Regex doxygenFluff("[/*!]+");
-	int nextIndex = 0;
-	int isFluff = 0;
 	string currentWord;
+
 	while (currentIndex < doxygenString.length()){	
+
 		if(doxygenString[currentIndex] == '\n'){
-			tokenList.push_back(Token(END_LINE, currentWord));
+            m_tokenList.push_back(Token(END_LINE, currentWord));
 			currentIndex++;
 		}
+
+        // skip WS, except \n
 		while(currentIndex < doxygenString.length() && (doxygenString[currentIndex] == ' ' 
 			|| doxygenString[currentIndex]== '\t')) currentIndex ++;
-		if (currentIndex == doxygenString.length()) {} //do nothing since end of string was reached
-		else {nextIndex = currentIndex;
+
+        if (currentIndex < doxygenString.length()) {
+
+            nextIndex = currentIndex;
+
+            // skip non WS
 		while (nextIndex  < doxygenString.length() && (doxygenString[nextIndex] != ' ' 
-			&& doxygenString[nextIndex]!= '\t' && doxygenString[nextIndex]!= '\n')) nextIndex++;
+                   && doxygenString[nextIndex] != '\t' && doxygenString[nextIndex]!= '\n')) 
+                nextIndex++;
+
+            // now we have a token
 		currentWord = doxygenString.substr(currentIndex, nextIndex-currentIndex);
-		if(noisy2) cout << "Current Word: " << currentWord << endl;
+
+            if(noisy2) 
+                cout << "Current Word: " << currentWord << endl;
+
 		if (currentWord[0] == '@' || currentWord[0] == '\\'){
+                // it is doxygen command
 			currentWord = currentWord.substr(1, currentWord.length()-1);
-			tokenList.push_back(Token(COMMAND, currentWord));
-		}
-		else if (currentWord[0] == '\n'){
-			//if ((tokenList.back()).tokenType == END_LINE){}
-			tokenList.push_back(Token(END_LINE, currentWord));
+                m_tokenList.push_back(Token(COMMAND, currentWord));
+
+            } else if (currentWord[0] == '\n'){
+
+                m_tokenList.push_back(Token(END_LINE, currentWord));
 			
 		}
 		else if (currentWord[0] == '*' || currentWord[0] == '/' ||currentWord[0] == '!'){
-			if (currentWord.length() == 1) {isFluff = 1;}	
-			else { isFluff = 1;
-				for(int i = 1; i < currentWord.length(); i++){
-					if (currentWord[0] != '*' && currentWord[0] != '/' && currentWord[0] != '!') isFluff = 0;
-				}
 				
+                bool isPlainString = false;
+
+                if (currentWord.length() > 1) {
+
+                    for(size_t i = 1; i < currentWord.length(); i++){
+                        if (currentWord[i] != '*' && currentWord[i] != '/' && 
+                            currentWord[i] != '!') {
+                                isPlainString = true;
+                                break;
+                        }
 			}
-			if(!isFluff) tokenList.push_back(Token(PLAINSTRING, currentWord));
 		}
 		
-		else if (!currentWord.empty())tokenList.push_back(Token(PLAINSTRING, currentWord));
+                if(isPlainString) 
+                    m_tokenList.push_back(Token(PLAINSTRING, currentWord));
+
+            } else if (!currentWord.empty()) {
+                m_tokenList.push_back(Token(PLAINSTRING, currentWord));
+            }
 		currentIndex = nextIndex;
 	}
 	}
-	tokenListIterator = tokenList.begin(); 
+
+    m_tokenListIter = m_tokenList.begin(); 
+}
+
+
+TokenList::	~TokenList(){
 }
 
 Token TokenList::peek(){
-	if(tokenListIterator!= tokenList.end()){
-		Token returnedToken = (*tokenListIterator);
+    if(m_tokenListIter!= m_tokenList.end()){
+        Token returnedToken = (*m_tokenListIter);
 		return returnedToken;
 	}
 	else
 		return Token(0, "");
 } 
 
+
 Token TokenList::next(){
-	if(tokenListIterator != tokenList.end()){
-		Token returnedToken = (*tokenListIterator);
-		tokenListIterator++;
+    if(m_tokenListIter != m_tokenList.end()){
+        Token returnedToken = (*m_tokenListIter);
+        m_tokenListIter++;
 		return (returnedToken);
 	}
 	else
 		return Token(0, "");
 } 	
 
+
 list<Token>::iterator TokenList::end(){
 	return tokenList.end();
 }
 
+
 list<Token>::iterator TokenList::current(){
-	return tokenListIterator;
+  return m_tokenListIter;
 }
+
+
+list<Token>::iterator TokenList::iteratorCopy(){
+  return m_tokenListIter;
+}
+
+
+void TokenList::setIterator(list<Token>::iterator newPosition){
+  m_tokenListIter = newPosition;
+}
+
+
 void TokenList::printList(){
-	list<Token>::iterator p = tokenList.begin();
+    list<Token>::iterator p = m_tokenList.begin();
 			int i = 1;
 			int b = 0;
-			while (p != tokenList.end()){
+    while (p != m_tokenList.end()){
 				cout << (*p).toString() << " ";
 				b = i%TOKENSPERLINE;
 				if (b == 0) cout << endl;
@@ -104,13 +167,3 @@ void TokenList::printList(){
 			}
 }
 
-list<Token>::iterator  TokenList::iteratorCopy(){
-	list<Token>::iterator p = tokenListIterator;
-	return p;
-}
-void TokenList::setIterator(list<Token>::iterator newPosition){
-	tokenListIterator = newPosition;
-}
-TokenList::	~TokenList(){
-	tokenList.clear();
-}
diff --git a/Source/DoxygenTranslator/src/TokenList.h b/Source/DoxygenTranslator/src/TokenList.h
index cc61f56e4..0f5710e0f 100644
--- a/Source/DoxygenTranslator/src/TokenList.h
+++ b/Source/DoxygenTranslator/src/TokenList.h
@@ -5,23 +5,30 @@
 #include <string>
 #include <list>
 #include "Token.h"
-using namespace std;
 
 /* a small class used to represent the sequence of tokens
  * that can be derived from a formatted doxygen string
  */
 
 class TokenList{
+private:
+  std::list<Token> m_tokenList;
+  std::list<Token>::iterator m_tokenListIter;
+
 public:
-	TokenList(string doxygenString); /* constructor takes a blob of Doxygen comment */
+	TokenList(const std::string &doxygenString); /* constructor takes a blob of Doxygen comment */
 	~TokenList();
+
 	Token peek(); 	/* returns next token without advancing */
 	Token next(); 	/* returns next token and advances */
-	list<Token>::iterator end(); /* returns an end iterator */
-	list<Token>::iterator current(); /* returns the current iterator */
-	void printList(); /* prints out the sequence of tokens */
-	list<Token>::iterator  iteratorCopy(); /* returns a copy of the current iterator */
+
+	std::list<Token>::iterator end(); /* returns an end iterator */
+	std::list<Token>::iterator current(); /* returns the current iterator */
+
+	std::list<Token>::iterator iteratorCopy(); /* returns a copy of the current iterator */
 	void setIterator(list<Token>::iterator  newPosition); /*moves up the iterator*/
+
+	void printList(); /* prints out the sequence of tokens */
 };
 
 #endif /*TOKENLIST_H_*/
diff --git a/Source/Modules/java.cxx b/Source/Modules/java.cxx
index 42ba5b396..532dfd305 100644
--- a/Source/Modules/java.cxx
+++ b/Source/Modules/java.cxx
@@ -1304,6 +1304,15 @@ public:
     // Note that this is used in enumValue() amongst other places
     Setattr(n, "value", tmpValue);
     
+    {
+      EnumFeature enum_feature = decodeEnumFeature(parentNode(n));
+
+      if ((enum_feature == ProperEnum) && Getattr(parentNode(n), "sym:name") && !Getattr(parentNode(n), "unnamedinstance")) {
+	// Wrap (non-anonymous) C/C++ enum with a proper Java enum
+	// Emit the enum item.
+	if (!Getattr(n, "_last"))	// Only the first enum item has this attribute set
+	  Printf(enum_code, ",\n");
+
     //translate and write javadoc comment if flagged
     if (doxygen_javadoc_flag){
       String *doxygen_comments;
@@ -1314,14 +1323,7 @@ public:
 	Delete(doxygen_comments);
       }
     }
-    {
-      EnumFeature enum_feature = decodeEnumFeature(parentNode(n));
 
-      if ((enum_feature == ProperEnum) && Getattr(parentNode(n), "sym:name") && !Getattr(parentNode(n), "unnamedinstance")) {
-	// Wrap (non-anonymous) C/C++ enum with a proper Java enum
-	// Emit the enum item.
-	if (!Getattr(n, "_last"))	// Only the first enum item has this attribute set
-	  Printf(enum_code, ",\n");
 	Printf(enum_code, "  %s", symname);
 	if (Getattr(n, "enumvalue")) {
 	  String *value = enumValue(n);
@@ -1841,7 +1843,6 @@ public:
       emitBanner(f_proxy);
 
       if (Len(package) > 0){
-    Printf(f_proxy, "LETS TEST THIS NAO THX \n\n\n");
 	Printf(f_proxy, "package %s;\n", package);
       }
       Clear(proxy_class_def);
diff --git a/Source/Modules/python.cxx b/Source/Modules/python.cxx
index 8a3160ef3..bfbada1da 100644
--- a/Source/Modules/python.cxx
+++ b/Source/Modules/python.cxx
@@ -7,7 +7,7 @@
  * Python language module for SWIG.
  * ----------------------------------------------------------------------------- */
 
-char cvsroot_python_cxx[] = "$Id: python.cxx 10453 2008-05-15 21:18:44Z wsfulton $";
+char cvsroot_python_cxx[] = "$Id$";
 
 #include "swigmod.h"
 #define ctab2  " "
@@ -3124,6 +3124,13 @@ public:
 	    if (!fastproxy || olddefs) {
 	      Printv(f_shadow, tab4, "def ", symname, "(", parms, ")", returnTypeAnnotation(n), ":", NIL);
 	      Printv(f_shadow, " return ", funcCall(Swig_name_member(class_name, symname), callParms), "\n", NIL);
+	      if (doxygen) {
+		String *doxygen_comments;
+		if (DoxygenTranslator::getDocumentation(n, PyDoc, doxygen_comments)) {
+		  Printf(f_shadow, Char(pythoncode(doxygen_comments, tab8))); 
+		  Delete(doxygen_comments);
+		}
+	      }
 	    }
 	  } else {
 	    Printv(f_shadow, tab4, "def ", symname, "(",parms , ")", returnTypeAnnotation(n), ":", NIL);

From ad9eb0e0bb066100fc1c4ca84982c3c9dd96347d Mon Sep 17 00:00:00 2001
From: William S Fulton <wsf@fultondesigns.co.uk>
Date: Tue, 13 Oct 2009 23:22:52 +0000
Subject: [PATCH 039/314] fix compile error introduced in last patch

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2008-cherylfoil@11698 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Source/DoxygenTranslator/src/TokenList.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Source/DoxygenTranslator/src/TokenList.cpp b/Source/DoxygenTranslator/src/TokenList.cpp
index 1a9ff0a7a..9efd7e9ef 100644
--- a/Source/DoxygenTranslator/src/TokenList.cpp
+++ b/Source/DoxygenTranslator/src/TokenList.cpp
@@ -136,7 +136,7 @@ Token TokenList::next(){
 
 
 list<Token>::iterator TokenList::end(){
-	return tokenList.end();
+	return m_tokenList.end();
 }
 
 

From 19d90026ef5c0c7f595b08495f8105063bced1ba Mon Sep 17 00:00:00 2001
From: William S Fulton <wsf@fultondesigns.co.uk>
Date: Tue, 13 Oct 2009 23:26:01 +0000
Subject: [PATCH 040/314] formatting fixes after running make beautify plus a
 few manual formatting fixes

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2008-cherylfoil@11699 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 .../DoxygenTranslator/src/DoxygenEntity.cpp   |  204 ++-
 Source/DoxygenTranslator/src/DoxygenEntity.h  |   12 +-
 .../DoxygenTranslator/src/DoxygenParser.cpp   |  862 +++++-----
 Source/DoxygenTranslator/src/DoxygenParser.h  |    7 +-
 .../src/DoxygenTranslator.cpp                 |   24 +-
 .../DoxygenTranslator/src/DoxygenTranslator.h |   15 +-
 .../src/Examples/DoxygenTransWTokenizer.cpp   | 1483 +++++++++--------
 .../src/Examples/DoxygenTransWTokenizer.h     |    9 +-
 .../src/Examples/translator.h                 |  252 +--
 .../src/JavaDocConverter.cpp                  |  147 +-
 .../DoxygenTranslator/src/JavaDocConverter.h  |   18 +-
 .../DoxygenTranslator/src/PyDocConverter.cpp  |  156 +-
 Source/DoxygenTranslator/src/PyDocConverter.h |   35 +-
 Source/DoxygenTranslator/src/Token.cpp        |   39 +-
 Source/DoxygenTranslator/src/Token.h          |   15 +-
 Source/DoxygenTranslator/src/TokenList.cpp    |  230 ++-
 Source/DoxygenTranslator/src/TokenList.h      |   26 +-
 17 files changed, 1805 insertions(+), 1729 deletions(-)

diff --git a/Source/DoxygenTranslator/src/DoxygenEntity.cpp b/Source/DoxygenTranslator/src/DoxygenEntity.cpp
index b2b156b5d..f770dc514 100644
--- a/Source/DoxygenTranslator/src/DoxygenEntity.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenEntity.cpp
@@ -10,10 +10,10 @@
 #include "DoxygenEntity.h"
 #include <iostream>
 
-DoxygenEntity::DoxygenEntity(std::string typeEnt){
-    typeOfEntity = typeEnt;
-    data = "";
-    isLeaf = true;
+DoxygenEntity::DoxygenEntity(std::string typeEnt) {
+  typeOfEntity = typeEnt;
+  data = "";
+  isLeaf = true;
 }
 
 /* Basic node for commands that have
@@ -21,173 +21,171 @@ DoxygenEntity::DoxygenEntity(std::string typeEnt){
  * example: \b word
  * OR holding a std::string
  */
-DoxygenEntity::DoxygenEntity(std::string typeEnt, std::string param1){
-    typeOfEntity = typeEnt;
-    data = param1;
-    isLeaf = true;
+DoxygenEntity::DoxygenEntity(std::string typeEnt, std::string param1) {
+  typeOfEntity = typeEnt;
+  data = param1;
+  isLeaf = true;
 }
 
 /* Nonterminal node
  * contains
  */
-DoxygenEntity::DoxygenEntity(std::string typeEnt, std::list <DoxygenEntity> &entList ){
-    typeOfEntity = typeEnt;
-    data = "";
-    isLeaf = false;
-    entityList = entList;
+DoxygenEntity::DoxygenEntity(std::string typeEnt, std::list < DoxygenEntity > &entList) {
+  typeOfEntity = typeEnt;
+  data = "";
+  isLeaf = false;
+  entityList = entList;
 }
 
-void DoxygenEntity::printEntity(int level){
-	int thisLevel = level;
-	if (isLeaf) {
-		for (int i = 0; i < thisLevel; i++) {
-            std::cout << "\t";
-        }
-		
-		std::cout << "Node Command: " << typeOfEntity << " ";
-        
-        if (data.compare("") != 0) {
-            std::cout << "Node Data: " << data;
-        }
-		std::cout << std::endl;
+void DoxygenEntity::printEntity(int level) {
+  int thisLevel = level;
+  if (isLeaf) {
+    for (int i = 0; i < thisLevel; i++) {
+      std::cout << "\t";
+    }
 
-	} else {
+    std::cout << "Node Command: " << typeOfEntity << " ";
 
-		for (int i = 0; i < thisLevel; i++) {
-            std::cout << "\t";
-	}
+    if (data.compare("") != 0) {
+      std::cout << "Node Data: " << data;
+    }
+    std::cout << std::endl;
 
-		std::cout << "Node Command : " << typeOfEntity << std::endl;
+  } else {
 
-		std::list<DoxygenEntity>::iterator p = entityList.begin();
-		thisLevel++;
+    for (int i = 0; i < thisLevel; i++) {
+      std::cout << "\t";
+    }
 
-		while (p != entityList.end()){
-			(*p).printEntity(thisLevel);
-			p++;
-		}
-	}
+    std::cout << "Node Command : " << typeOfEntity << std::endl;
+
+    std::list < DoxygenEntity >::iterator p = entityList.begin();
+    thisLevel++;
+
+    while (p != entityList.end()) {
+      (*p).printEntity(thisLevel);
+      p++;
+    }
+  }
 }
 
 // not used, completely wrong - currently std lib reports 'invalid operator <'
-bool CompareDoxygenEntities::operator()(DoxygenEntity& first, DoxygenEntity& second){
+bool CompareDoxygenEntities::operator() (DoxygenEntity & first, DoxygenEntity & second) {
 
-   // return first.typeOfEntity < second.typeOfEntity;
-  if(first.typeOfEntity.compare("brief") == 0) 
+  // return first.typeOfEntity < second.typeOfEntity;
+  if (first.typeOfEntity.compare("brief") == 0)
     return true;
-  if(second.typeOfEntity.compare("brief") == 0) 
+  if (second.typeOfEntity.compare("brief") == 0)
     return false;
-  if(first.typeOfEntity.compare("details") == 0) 
+  if (first.typeOfEntity.compare("details") == 0)
     return true;
-  if(second.typeOfEntity.compare("details") == 0) 
+  if (second.typeOfEntity.compare("details") == 0)
     return false;
-  if(first.typeOfEntity.compare("partofdescription") == 0) 
+  if (first.typeOfEntity.compare("partofdescription") == 0)
     return true;
-  if(second.typeOfEntity.compare("partofdescription") == 0) 
+  if (second.typeOfEntity.compare("partofdescription") == 0)
     return false;
-  if(first.typeOfEntity.compare("plainstd::string") == 0) 
+  if (first.typeOfEntity.compare("plainstd::string") == 0)
     return true;
-  if(second.typeOfEntity.compare("plainstd::string") == 0) 
+  if (second.typeOfEntity.compare("plainstd::string") == 0)
     return false;
-  if(first.typeOfEntity.compare("param") == 0){
-    if(second.typeOfEntity.compare("param")== 0) 
+  if (first.typeOfEntity.compare("param") == 0) {
+    if (second.typeOfEntity.compare("param") == 0)
       return true;
-    if(second.typeOfEntity.compare("return")== 0) 
+    if (second.typeOfEntity.compare("return") == 0)
       return true;
-    if(second.typeOfEntity.compare("exception")== 0) 
+    if (second.typeOfEntity.compare("exception") == 0)
       return true;
-    if(second.typeOfEntity.compare("author")== 0) 
+    if (second.typeOfEntity.compare("author") == 0)
       return true;
-    if(second.typeOfEntity.compare("version")== 0)
+    if (second.typeOfEntity.compare("version") == 0)
       return true;
-    if(second.typeOfEntity.compare("see")== 0)
+    if (second.typeOfEntity.compare("see") == 0)
       return true;
-    if(second.typeOfEntity.compare("since")== 0)
+    if (second.typeOfEntity.compare("since") == 0)
       return true;
-    if(second.typeOfEntity.compare("deprecated")== 0)
+    if (second.typeOfEntity.compare("deprecated") == 0)
       return true;
     return false;
   }
-  if(first.typeOfEntity.compare("return")== 0){
-    if(second.typeOfEntity.compare("return")== 0) 
+  if (first.typeOfEntity.compare("return") == 0) {
+    if (second.typeOfEntity.compare("return") == 0)
       return true;
-    if(second.typeOfEntity.compare("exception")== 0) 
+    if (second.typeOfEntity.compare("exception") == 0)
       return true;
-    if(second.typeOfEntity.compare("author")== 0) 
+    if (second.typeOfEntity.compare("author") == 0)
       return true;
-    if(second.typeOfEntity.compare("version")== 0)
+    if (second.typeOfEntity.compare("version") == 0)
       return true;
-    if(second.typeOfEntity.compare("see")== 0)
+    if (second.typeOfEntity.compare("see") == 0)
       return true;
-    if(second.typeOfEntity.compare("since")== 0)
+    if (second.typeOfEntity.compare("since") == 0)
       return true;
-    if(second.typeOfEntity.compare("deprecated")== 0
-      )return true;
-    return false;
-  }
-  if(first.typeOfEntity.compare("exception")== 0){
-    if(second.typeOfEntity.compare("exception")== 0) 
-      return true;
-    if(second.typeOfEntity.compare("author")== 0) 
-      return true;
-    if(second.typeOfEntity.compare("version")== 0)
-      return true;
-    if(second.typeOfEntity.compare("see")== 0)
-      return true;
-    if(second.typeOfEntity.compare("since")== 0)
-      return true;
-    if(second.typeOfEntity.compare("deprecated")== 0)
+    if (second.typeOfEntity.compare("deprecated") == 0)
       return true;
     return false;
   }
-  if(first.typeOfEntity.compare("author")== 0){
-    if(second.typeOfEntity.compare("author")== 0) 
+  if (first.typeOfEntity.compare("exception") == 0) {
+    if (second.typeOfEntity.compare("exception") == 0)
       return true;
-    if(second.typeOfEntity.compare("version")== 0)
+    if (second.typeOfEntity.compare("author") == 0)
       return true;
-    if(second.typeOfEntity.compare("see")== 0)
+    if (second.typeOfEntity.compare("version") == 0)
       return true;
-    if(second.typeOfEntity.compare("since")== 0)
+    if (second.typeOfEntity.compare("see") == 0)
       return true;
-    if(second.typeOfEntity.compare("deprecated")== 0)
+    if (second.typeOfEntity.compare("since") == 0)
+      return true;
+    if (second.typeOfEntity.compare("deprecated") == 0)
       return true;
     return false;
   }
-  if(first.typeOfEntity.compare("version")== 0){
-    if(second.typeOfEntity.compare("version")== 0)
+  if (first.typeOfEntity.compare("author") == 0) {
+    if (second.typeOfEntity.compare("author") == 0)
       return true;
-    if(second.typeOfEntity.compare("see")== 0)
+    if (second.typeOfEntity.compare("version") == 0)
       return true;
-    if(second.typeOfEntity.compare("since")== 0)
+    if (second.typeOfEntity.compare("see") == 0)
       return true;
-    if(second.typeOfEntity.compare("deprecated")== 0)
+    if (second.typeOfEntity.compare("since") == 0)
+      return true;
+    if (second.typeOfEntity.compare("deprecated") == 0)
       return true;
     return false;
   }
-  if(first.typeOfEntity.compare("see")== 0 || first.typeOfEntity.compare("sa")== 0){
-    if(second.typeOfEntity.compare("see")== 0)
+  if (first.typeOfEntity.compare("version") == 0) {
+    if (second.typeOfEntity.compare("version") == 0)
       return true;
-    if(second.typeOfEntity.compare("sa")== 0)
+    if (second.typeOfEntity.compare("see") == 0)
       return true;
-    if(second.typeOfEntity.compare("since")== 0)
+    if (second.typeOfEntity.compare("since") == 0)
       return true;
-    if(second.typeOfEntity.compare("deprecated")== 0)
+    if (second.typeOfEntity.compare("deprecated") == 0)
       return true;
     return false;
   }
-  if(first.typeOfEntity.compare("since")== 0){
-    if(second.typeOfEntity.compare("since")== 0) 
+  if (first.typeOfEntity.compare("see") == 0 || first.typeOfEntity.compare("sa") == 0) {
+    if (second.typeOfEntity.compare("see") == 0)
       return true;
-    if(second.typeOfEntity.compare("deprecated")== 0)
+    if (second.typeOfEntity.compare("sa") == 0)
+      return true;
+    if (second.typeOfEntity.compare("since") == 0)
+      return true;
+    if (second.typeOfEntity.compare("deprecated") == 0)
       return true;
     return false;
   }
-  if(first.typeOfEntity.compare("deprecated")== 0){
-    if(second.typeOfEntity.compare("deprecated")== 0)
+  if (first.typeOfEntity.compare("since") == 0) {
+    if (second.typeOfEntity.compare("since") == 0)
+      return true;
+    if (second.typeOfEntity.compare("deprecated") == 0)
+      return true;
+    return false;
+  }
+  if (first.typeOfEntity.compare("deprecated") == 0) {
+    if (second.typeOfEntity.compare("deprecated") == 0)
       return true;
     return false;
   }
   return true;
 }
-
-
diff --git a/Source/DoxygenTranslator/src/DoxygenEntity.h b/Source/DoxygenTranslator/src/DoxygenEntity.h
index 4c1ab7ff9..ca42393db 100644
--- a/Source/DoxygenTranslator/src/DoxygenEntity.h
+++ b/Source/DoxygenTranslator/src/DoxygenEntity.h
@@ -15,7 +15,7 @@
 
 
 typedef enum {
-  SIMPLECOMMAND, 
+  SIMPLECOMMAND,
   IGNOREDSIMPLECOMMAND,
   COMMANDWORD,
   IGNOREDCOMMANDWORD,
@@ -39,15 +39,15 @@ typedef enum {
 /*
  * Structure to represent a doxygen comment entry
  */
-struct DoxygenEntity{
+struct DoxygenEntity {
   std::string typeOfEntity;
-  std::list <DoxygenEntity> entityList;
+  std::list < DoxygenEntity > entityList;
   std::string data;
   bool isLeaf;
 
   DoxygenEntity(std::string typeEnt);
   DoxygenEntity(std::string typeEnt, std::string param1);
-  DoxygenEntity(std::string typeEnt, std::list <DoxygenEntity> &entList );
+  DoxygenEntity(std::string typeEnt, std::list < DoxygenEntity > &entList);
 
   void printEntity(int level);
 };
@@ -58,7 +58,7 @@ struct DoxygenEntity{
  * such as brief descriptions are TAGGED as such
  */
 struct CompareDoxygenEntities {
-  bool operator()(DoxygenEntity& first, DoxygenEntity& second);
+  bool operator() (DoxygenEntity & first, DoxygenEntity & second);
 };
 
-#endif /*TOKENLIST_H_*/
+#endif
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.cpp b/Source/DoxygenTranslator/src/DoxygenParser.cpp
index 78072852d..f4bce5445 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenParser.cpp
@@ -2,88 +2,110 @@
 #include "TokenList.h"
 
 
-DoxygenParser::DoxygenParser()
-{
+DoxygenParser::DoxygenParser() {
 }
 
-DoxygenParser::~DoxygenParser()
-{
+DoxygenParser::~DoxygenParser() {
 }
 
 //////////////////////////////////////////
-int noisy = 0; // set this to 1 for extra chatter from the parsing stage.
-int addCommand(std::string currCommand, TokenList &tokList,  std::list <DoxygenEntity> &aNewList);
-std::list <DoxygenEntity> parse(std::list<Token>::iterator endParsingIndex, TokenList &tokList);
+int noisy = 0;			// set this to 1 for extra chatter from the parsing stage.
+int addCommand(std::string currCommand, TokenList & tokList, std::list < DoxygenEntity > &aNewList);
+std::list < DoxygenEntity > parse(std::list < Token >::iterator endParsingIndex, TokenList & tokList);
 
 //////////////////////////////////////////
 
 
-std::string commandArray[] = {"a", "addindex", "addtogroup", "anchor", "arg", "attention",
-    "author", "b", "brief", "bug", "c", "callgraph", "callergraph", "category",
-    "class", "code", "cond", "copybrief", "copydetails", "copydoc", "date", "def",
-    "defgroup", "deprecated", "details", "dir", "dontinclude", "dot", "dotfile", "e",
-    "else", "elseif", "em", "endcode", "endcond", "enddot", "endhtmlonly", "endif",
-    "endlatexonly", "endlink", "endmanonly", "endmsc", "endverbatim", "endxmlonly",
-    "enum", "example", "exception", "f$", "f[", "f]", "f{", "f}", "file", "fn", "headerfile",
-    "hideinitializer", "htmlinclude", "htmlonly", "if", "ifnot", "image", "include",
-    "includelineno", "ingroup", "internal", "invariant", "interface", "latexonly", "li",
-    "line", "link", "mainpage", "manonly", "msc", "n", "name", "namespace", "nosubgrouping",
-    "note", "overload", "p", "package", "page", "par", "paragraph", "param", "post", "pre",
-    "private", "privatesection", "property", "protected", "protectedsection", "protocol",
-    "public", "publicsection", "ref", "relates", "relatesalso", "remarks", "return", "retval",
-    "sa", "section", "see", "showinitializer", "since", "skip", "skipline", "struct", "subpage",
-    "subsection", "subsubsection", "test", "throw", "throws", "todo", "tparam", "typedef", "union", "until",
-    "var", "verbatim", "verbinclude", "version", "warning", "weakgroup", "xmlonly", "xrefitem",
-    "$", "@", "\\","&", "~", "<", ">", "#", "%"};
+std::string commandArray[] = {
+  "a", "addindex", "addtogroup", "anchor", "arg", "attention",
+  "author", "b", "brief", "bug", "c", "callgraph", "callergraph", "category",
+  "class", "code", "cond", "copybrief", "copydetails", "copydoc", "date", "def",
+  "defgroup", "deprecated", "details", "dir", "dontinclude", "dot", "dotfile", "e",
+  "else", "elseif", "em", "endcode", "endcond", "enddot", "endhtmlonly", "endif",
+  "endlatexonly", "endlink", "endmanonly", "endmsc", "endverbatim", "endxmlonly",
+  "enum", "example", "exception", "f$", "f[", "f]", "f{", "f}", "file", "fn", "headerfile",
+  "hideinitializer", "htmlinclude", "htmlonly", "if", "ifnot", "image", "include",
+  "includelineno", "ingroup", "internal", "invariant", "interface", "latexonly", "li",
+  "line", "link", "mainpage", "manonly", "msc", "n", "name", "namespace", "nosubgrouping",
+  "note", "overload", "p", "package", "page", "par", "paragraph", "param", "post", "pre",
+  "private", "privatesection", "property", "protected", "protectedsection", "protocol",
+  "public", "publicsection", "ref", "relates", "relatesalso", "remarks", "return", "retval",
+  "sa", "section", "see", "showinitializer", "since", "skip", "skipline", "struct", "subpage",
+  "subsection", "subsubsection", "test", "throw", "throws", "todo", "tparam", "typedef", "union", "until",
+  "var", "verbatim", "verbinclude", "version", "warning", "weakgroup", "xmlonly", "xrefitem", "$", "@", "\\", "&", "~", "<", ">", "#", "%"};
 
 
-std::string sectionIndicators[] = { "attention", "author", "brief", "bug", "cond", "date", "deprecated", "details",
-    "else", "elseif", "endcond", "endif", "exception", "if", "ifnot", "invariant", "note", "par", "param",
-    "tparam", "post" , "pre", "remarks", "return", "retval", "sa", "see", "since", "test", "throw", "throws", "todo",
-    "version", "warning", "xrefitem" };
+std::string sectionIndicators[] = {
+  "attention", "author", "brief", "bug", "cond", "date", "deprecated", "details",
+  "else", "elseif", "endcond", "endif", "exception", "if", "ifnot", "invariant", "note", "par", "param",
+  "tparam", "post", "pre", "remarks", "return", "retval", "sa", "see", "since", "test", "throw", "throws", "todo", "version", "warning", "xrefitem"};
 
 /* All of the doxygen commands divided up by how they are parsed */
-std::string simpleCommands[] = {"n", "$", "@", "\\", "&", "~", "<", ">", "#", "%"};
-std::string ignoredSimpleCommands[] = {"nothing at the moment"};
-std::string commandWords[] = {"a", "b", "c", "e", "em", "p", "def", "enum", "example", "package", 
-    "relates", "namespace", "relatesalso","anchor", "dontinclude", "include", "includelineno"};
-std::string ignoredCommandWords[] = {"copydoc", "copybrief", "copydetails", "verbinclude", "htmlinclude"};
-std::string commandLines[] = {"addindex", "fn", "name", "line", "var", "skipline", "typedef", "skip", "until", "property"};
-std::string ignoreCommandLines[] = {"nothing at the moment"};
-std::string commandParagraph[] = {"partofdescription", "return", "remarks", "since", "test", "sa", "see", "pre", "post", "details", "invariant", 
-        "deprecated", "date", "note", "warning", "version", "todo", "bug", "attention", "brief", "author"};
-std::string ignoreCommandParagraphs[] = {"nothing at the moment"};
-std::string commandEndCommands[] = {"code", "dot", "msc", "f$", "f[", "f{environment}{", "htmlonly", "latexonly", "manonly", 
-       "verbatim", "xmlonly", "cond", "if", "ifnot", "link"};
-std::string commandWordParagraphs[] = {"param", "tparam", "throw", "throws", "retval", "exception"};
-std::string commandWordLines[] = {"page", "subsection", "subsubsection", "section", "paragraph", "defgroup"};
-std::string commandWordOWordOWords [] = {"category", "class", "protocol", "interface", "struct", "union"};
-std::string commandOWords[] = {"dir", "file", "cond"};
-std::string commandErrorThrowings[] = {"annotatedclassstd::list", "classhierarchy", "define", "functionindex", "header",
-    "headerfilestd::list", "inherit", "l", "postheader", "private", "privatesection", "protected", 
-    "protectedsection", "public", "publicsection", "endcode", "enddot", "endmsc", "endhtmlonly", 
-    "endlatexonly", "endmanonly", "endlink", "endverbatim", "endxmlonly", "f]", "f}", "endcond", 
-    "endif"};
-std::string commandUniques[] = {"xrefitem", "arg", "ingroup", "par", "headerfile", "overload", "weakgroup", "ref",
-"subpage", "dotfile", "image", "addtogroup", "li"};
+std::string simpleCommands[] = {
+  "n", "$", "@", "\\", "&", "~", "<", ">", "#", "%"};
+
+std::string ignoredSimpleCommands[] = {
+  "nothing at the moment"};
+
+std::string commandWords[] = {
+  "a", "b", "c", "e", "em", "p", "def", "enum", "example", "package", "relates", "namespace", "relatesalso", "anchor", "dontinclude", "include", "includelineno"};
+
+std::string ignoredCommandWords[] = {
+  "copydoc", "copybrief", "copydetails", "verbinclude", "htmlinclude"};
+
+std::string commandLines[] = {
+  "addindex", "fn", "name", "line", "var", "skipline", "typedef", "skip", "until", "property"};
+
+std::string ignoreCommandLines[] = {
+  "nothing at the moment"};
+
+std::string commandParagraph[] = {
+  "partofdescription", "return", "remarks", "since", "test", "sa", "see", "pre", "post", "details", "invariant",
+  "deprecated", "date", "note", "warning", "version", "todo", "bug", "attention", "brief", "author"};
+
+std::string ignoreCommandParagraphs[] = {
+  "nothing at the moment"};
+
+std::string commandEndCommands[] = {
+  "code", "dot", "msc", "f$", "f[", "f{environment}{", "htmlonly", "latexonly", "manonly", "verbatim", "xmlonly", "cond", "if", "ifnot", "link"};
+
+std::string commandWordParagraphs[] = {
+  "param", "tparam", "throw", "throws", "retval", "exception"};
+
+std::string commandWordLines[] = {
+  "page", "subsection", "subsubsection", "section", "paragraph", "defgroup"};
+
+std::string commandWordOWordOWords[] = {
+  "category", "class", "protocol", "interface", "struct", "union"};
+
+std::string commandOWords[] = {
+  "dir", "file", "cond"};
+
+std::string commandErrorThrowings[] = {
+  "annotatedclassstd::list", "classhierarchy", "define", "functionindex", "header",
+  "headerfilestd::list", "inherit", "l", "postheader", "private", "privatesection", "protected",
+  "protectedsection", "public", "publicsection", "endcode", "enddot", "endmsc", "endhtmlonly",
+  "endlatexonly", "endmanonly", "endlink", "endverbatim", "endxmlonly", "f]", "f}", "endcond", "endif"};
+std::string commandUniques[] = {
+  "xrefitem", "arg", "ingroup", "par", "headerfile", "overload", "weakgroup", "ref", "subpage", "dotfile", "image", "addtogroup", "li"};
 
 
 /* Changes a std::string to all lower case */
-std::string StringToLower(std::string stringToConvert){
-  for(unsigned int i=0;i<stringToConvert.length();i++){
+std::string StringToLower(std::string stringToConvert) {
+  for (unsigned int i = 0; i < stringToConvert.length(); i++) {
     stringToConvert[i] = tolower(stringToConvert[i]);
   }
-  return stringToConvert; //return the converted std::string
+  return stringToConvert;	//return the converted std::string
 }
 
 /* finds out if a command exists (is a possible command)
  * from the std::string array commandArray
  * returns -1 if no match is found */
-int findCommand(std::string smallString){
+int findCommand(std::string smallString) {
   smallString = StringToLower(smallString);
   int a;
-  for (unsigned i = 0; i < sizeof(commandArray)/sizeof(*commandArray); i++){
-    if( (a = smallString.compare(commandArray[i])) == 0){
+  for (unsigned i = 0; i < sizeof(commandArray) / sizeof(*commandArray); i++) {
+    if ((a = smallString.compare(commandArray[i])) == 0) {
       return 101 + i;
     }
   }
@@ -94,10 +116,10 @@ int findCommand(std::string smallString){
  * This is a helper method for finding the end of a paragraph
  * by Doxygen's terms
  */
-int isSectionIndicator(std::string smallString){
+int isSectionIndicator(std::string smallString) {
   smallString = StringToLower(smallString);
-  for (unsigned i = 0; i < sizeof( sectionIndicators)/sizeof(* sectionIndicators); i++){
-    if( smallString.compare( sectionIndicators[i]) == 0){
+  for (unsigned i = 0; i < sizeof(sectionIndicators) / sizeof(*sectionIndicators); i++) {
+    if (smallString.compare(sectionIndicators[i]) == 0) {
       return 1;
     }
   }
@@ -105,9 +127,9 @@ int isSectionIndicator(std::string smallString){
 }
 
 /* prints the parse tree */
-void printTree( std::list <DoxygenEntity> &rootList){
-  std::list<DoxygenEntity>::iterator p = rootList.begin();
-  while (p != rootList.end()){
+void printTree(std::list < DoxygenEntity > &rootList) {
+  std::list < DoxygenEntity >::iterator p = rootList.begin();
+  while (p != rootList.end()) {
     (*p).printEntity(0);
     p++;
   }
@@ -116,190 +138,192 @@ void printTree( std::list <DoxygenEntity> &rootList){
 /* Determines how a command should be handled (what group it belongs to
  * for parsing rules
  */
-int commandBelongs(std::string theCommand){
-   std::string smallString = StringToLower(theCommand);
-   //cout << " Looking for command " << theCommand << endl;
+int commandBelongs(std::string theCommand) {
+  std::string smallString = StringToLower(theCommand);
+  //cout << " Looking for command " << theCommand << endl;
   unsigned i = 0;
-  for (i = 0; i < sizeof(simpleCommands)/sizeof(*simpleCommands); i++){
-    if(smallString.compare(simpleCommands[i]) == 0)
+  for (i = 0; i < sizeof(simpleCommands) / sizeof(*simpleCommands); i++) {
+    if (smallString.compare(simpleCommands[i]) == 0)
       return SIMPLECOMMAND;
   }
-  for (i = 0; i < sizeof(ignoredSimpleCommands)/sizeof(*ignoredSimpleCommands); i++){
-    if(smallString.compare(ignoredSimpleCommands[i]) == 0)
+  for (i = 0; i < sizeof(ignoredSimpleCommands) / sizeof(*ignoredSimpleCommands); i++) {
+    if (smallString.compare(ignoredSimpleCommands[i]) == 0)
       return IGNOREDSIMPLECOMMAND;
-  } 
-  for (i = 0; i < sizeof(commandWords)/sizeof(*commandWords); i++){
-    if(smallString.compare( commandWords[i]) == 0)
+  }
+  for (i = 0; i < sizeof(commandWords) / sizeof(*commandWords); i++) {
+    if (smallString.compare(commandWords[i]) == 0)
       return COMMANDWORD;
-  } 
-  for (i = 0; i < sizeof(ignoredCommandWords)/sizeof(*ignoredCommandWords); i++){
-    if(smallString.compare( ignoredCommandWords[i]) == 0)
+  }
+  for (i = 0; i < sizeof(ignoredCommandWords) / sizeof(*ignoredCommandWords); i++) {
+    if (smallString.compare(ignoredCommandWords[i]) == 0)
       return IGNOREDCOMMANDWORD;
-  } 
-  for (i = 0; i < sizeof(commandLines)/sizeof(*commandLines); i++){
-    if(smallString.compare( commandLines[i]) == 0)
+  }
+  for (i = 0; i < sizeof(commandLines) / sizeof(*commandLines); i++) {
+    if (smallString.compare(commandLines[i]) == 0)
       return COMMANDLINE;
-  } 
-  for (i = 0; i < sizeof(ignoreCommandLines)/sizeof(*ignoreCommandLines); i++){
-    if(smallString.compare( ignoreCommandLines[i]) == 0)
+  }
+  for (i = 0; i < sizeof(ignoreCommandLines) / sizeof(*ignoreCommandLines); i++) {
+    if (smallString.compare(ignoreCommandLines[i]) == 0)
       return IGNOREDCOMMANDLINE;
-  } 
-  for (i = 0; i <  sizeof(commandParagraph)/sizeof(*commandParagraph); i++){
-    if(smallString.compare( commandParagraph[i]) == 0)
+  }
+  for (i = 0; i < sizeof(commandParagraph) / sizeof(*commandParagraph); i++) {
+    if (smallString.compare(commandParagraph[i]) == 0)
       return COMMANDPARAGRAPH;
-  } 
-  for (i = 0; i < sizeof(ignoreCommandParagraphs)/sizeof(*ignoreCommandParagraphs); i++){
-    if(smallString.compare( ignoreCommandParagraphs[i]) == 0)
+  }
+  for (i = 0; i < sizeof(ignoreCommandParagraphs) / sizeof(*ignoreCommandParagraphs); i++) {
+    if (smallString.compare(ignoreCommandParagraphs[i]) == 0)
       return IGNORECOMMANDPARAGRAPH;
-  } 
-  for (i = 0; i < sizeof(commandEndCommands)/sizeof(*commandEndCommands); i++){
-    if(smallString.compare( commandEndCommands[i]) == 0)
+  }
+  for (i = 0; i < sizeof(commandEndCommands) / sizeof(*commandEndCommands); i++) {
+    if (smallString.compare(commandEndCommands[i]) == 0)
       return COMMANDENDCOMMAND;
-  } 
-  for (i = 0; i < sizeof(commandWordParagraphs)/sizeof(*commandWordParagraphs); i++){
-    if(smallString.compare( commandWordParagraphs[i]) == 0)
+  }
+  for (i = 0; i < sizeof(commandWordParagraphs) / sizeof(*commandWordParagraphs); i++) {
+    if (smallString.compare(commandWordParagraphs[i]) == 0)
       return COMMANDWORDPARAGRAPH;
-  } 
-  for (i = 0; i < sizeof(commandWordLines)/sizeof(*commandWordLines); i++){
-    if(smallString.compare( commandWordLines[i]) == 0)
+  }
+  for (i = 0; i < sizeof(commandWordLines) / sizeof(*commandWordLines); i++) {
+    if (smallString.compare(commandWordLines[i]) == 0)
       return COMMANDWORDLINE;
-  } 
-  for (i = 0; i < sizeof(commandWordOWordOWords)/sizeof(*commandWordOWordOWords); i++){
-    if(smallString.compare( commandWordOWordOWords[i]) == 0)
+  }
+  for (i = 0; i < sizeof(commandWordOWordOWords) / sizeof(*commandWordOWordOWords); i++) {
+    if (smallString.compare(commandWordOWordOWords[i]) == 0)
       return COMMANDWORDOWORDWORD;
-  } 
-  for (i = 0; i < sizeof(commandOWords)/sizeof(*commandOWords); i++){
-    if(smallString.compare( commandOWords[i]) == 0)
+  }
+  for (i = 0; i < sizeof(commandOWords) / sizeof(*commandOWords); i++) {
+    if (smallString.compare(commandOWords[i]) == 0)
       return COMMANDOWORD;
-  } 
-  for (i = 0; i < sizeof(commandErrorThrowings)/sizeof(*commandErrorThrowings); i++){
-    if(smallString.compare( commandErrorThrowings[i]) == 0)
+  }
+  for (i = 0; i < sizeof(commandErrorThrowings) / sizeof(*commandErrorThrowings); i++) {
+    if (smallString.compare(commandErrorThrowings[i]) == 0)
       return COMMANDERRORTHROW;
-  } 
-  for (i = 0; i < sizeof(commandUniques)/sizeof(*commandUniques); i++){
-    if(smallString.compare( commandUniques[i]) == 0)
+  }
+  for (i = 0; i < sizeof(commandUniques) / sizeof(*commandUniques); i++) {
+    if (smallString.compare(commandUniques[i]) == 0)
       return COMMANDUNIQUE;
   }
-  return 0; 
+  return 0;
 }
 
 /* Returns the next word ON THE CURRENT LINE ONLY
  * if a new line is encountered, returns a blank std::string.
  * Updates the index it is given if success.
  */
-std::string getNextWord(TokenList &tokList){
-   Token nextToken = tokList.peek();
-   if (nextToken.tokenType == PLAINSTRING ){
-     nextToken = tokList.next();
-     return nextToken.tokenString;
-   }
+std::string getNextWord(TokenList & tokList) {
+  Token nextToken = tokList.peek();
+  if (nextToken.tokenType == PLAINSTRING) {
+    nextToken = tokList.next();
+    return nextToken.tokenString;
+  }
   return "";
 }
 
 /* Returns the location of the end of the line as
  * an iterator.
  */
-std::list<Token>::iterator getOneLine(TokenList &tokList){
-   std::list<Token>::iterator endOfLine = tokList.iteratorCopy();
-   while(endOfLine!= tokList.end()){
-     if ((* endOfLine).tokenType == END_LINE){
-       //cout << "REACHED END" << endl;
-       //endOfLine++;
-       return endOfLine;
-       }
-     //cout << (* endOfLine).toString();
-     endOfLine++;
-     }
-   
-  return tokList.end();
+std::list < Token >::iterator getOneLine(TokenList & tokList) {
+  std::list < Token >::iterator endOfLine = tokList.iteratorCopy();
+  while (endOfLine != tokList.end()) {
+    if ((*endOfLine).tokenType == END_LINE) {
+      //cout << "REACHED END" << endl;
+      //endOfLine++;
+      return endOfLine;
+    }
+    //cout << (* endOfLine).toString();
+    endOfLine++;
   }
 
+  return tokList.end();
+}
+
 /* Returns a properly formatted std::string
 * up til ANY command or end of line is encountered.
 */
-std::string getStringTilCommand(TokenList &tokList){
-   std::string description;
-   if (tokList.peek().tokenType == 0) return "";
-   while(tokList.peek().tokenType == PLAINSTRING){
-     Token currentToken = tokList.next();
-     if(currentToken.tokenType == PLAINSTRING) {
-       description = description + currentToken.tokenString + " ";
-       }
-     }
-  return description;
+std::string getStringTilCommand(TokenList & tokList) {
+  std::string description;
+  if (tokList.peek().tokenType == 0)
+    return "";
+  while (tokList.peek().tokenType == PLAINSTRING) {
+    Token currentToken = tokList.next();
+    if (currentToken.tokenType == PLAINSTRING) {
+      description = description + currentToken.tokenString + " ";
+    }
   }
+  return description;
+}
 
 /* Returns a properly formatted std::string
 * up til the command specified is encountered
 */
 //TODO check that this behaves properly for formulas
 
-std::string getStringTilEndCommand(std::string theCommand, TokenList &tokList){
-   std::string description;
-   if (tokList.peek().tokenType == 0) return "";
-   while(tokList.peek().tokenString.compare(theCommand) != 0 ){
-     Token currentToken = tokList.next();
-     description = description + currentToken.tokenString + " ";
-     }
-  return description;
+std::string getStringTilEndCommand(std::string theCommand, TokenList & tokList) {
+  std::string description;
+  if (tokList.peek().tokenType == 0)
+    return "";
+  while (tokList.peek().tokenString.compare(theCommand) != 0) {
+    Token currentToken = tokList.next();
+    description = description + currentToken.tokenString + " ";
   }
+  return description;
+}
 
 /* Returns the end of a Paragraph as an iterator-
 * Paragraph is defined in Doxygen to be a paragraph of text
  * separated by either a structural command or a blank line
 */
-std::list<Token>::iterator getEndOfParagraph(TokenList &tokList){
-   std::list<Token>::iterator endOfParagraph = tokList.iteratorCopy();
-   while(endOfParagraph != tokList.end()){
-    if ((* endOfParagraph).tokenType == END_LINE){
-       endOfParagraph++;
-       if (endOfParagraph != tokList.end()  &&  (* endOfParagraph).tokenType == END_LINE) {
-         endOfParagraph++;
-         //cout << "ENCOUNTERED END OF PARA" << endl;
-         return endOfParagraph;
-         }
+std::list < Token >::iterator getEndOfParagraph(TokenList & tokList) {
+  std::list < Token >::iterator endOfParagraph = tokList.iteratorCopy();
+  while (endOfParagraph != tokList.end()) {
+    if ((*endOfParagraph).tokenType == END_LINE) {
+      endOfParagraph++;
+      if (endOfParagraph != tokList.end() && (*endOfParagraph).tokenType == END_LINE) {
+	endOfParagraph++;
+	//cout << "ENCOUNTERED END OF PARA" << endl;
+	return endOfParagraph;
+      }
 
-        } else if ((*endOfParagraph).tokenType == COMMAND) {
+    } else if ((*endOfParagraph).tokenType == COMMAND) {
 
-            if (isSectionIndicator((* endOfParagraph).tokenString)) {
-                return endOfParagraph;
-       }
-       else endOfParagraph++;
+      if (isSectionIndicator((*endOfParagraph).tokenString)) {
+	return endOfParagraph;
+      } else
+	endOfParagraph++;
 
-        } else if ((*endOfParagraph).tokenType == PLAINSTRING) {
-       endOfParagraph++;
-        } else {
-            return tokList.end();
-       }
+    } else if ((*endOfParagraph).tokenType == PLAINSTRING) {
+      endOfParagraph++;
+    } else {
+      return tokList.end();
     }
+  }
 
-   return tokList.end();
-   }
+  return tokList.end();
+}
 
 /* Returns the end of a section, defined as the first blank line OR first encounter of the same 
 * command. Example of this behaviour is \arg
 * if no end is encountered, returns the last token of the std::list.
 */
-std::list<Token>::iterator getEndOfSection(std::string theCommand, TokenList &tokList){
-   std::list<Token>::iterator endOfParagraph = tokList.iteratorCopy();
-   while(endOfParagraph != tokList.end()){
-    if ((* endOfParagraph).tokenType == COMMAND){
-       if(theCommand.compare((*endOfParagraph).tokenString) == 0) return endOfParagraph;
-       else endOfParagraph++;
-       }
-    else if((* endOfParagraph).tokenType == PLAINSTRING) {
-       endOfParagraph++;
-       }
-     else if ((* endOfParagraph).tokenType == END_LINE){
-       endOfParagraph++;
-       if ((* endOfParagraph).tokenType == END_LINE){
-         endOfParagraph++;
-         return endOfParagraph;
-         }
-       }
+std::list < Token >::iterator getEndOfSection(std::string theCommand, TokenList & tokList) {
+  std::list < Token >::iterator endOfParagraph = tokList.iteratorCopy();
+  while (endOfParagraph != tokList.end()) {
+    if ((*endOfParagraph).tokenType == COMMAND) {
+      if (theCommand.compare((*endOfParagraph).tokenString) == 0)
+	return endOfParagraph;
+      else
+	endOfParagraph++;
+    } else if ((*endOfParagraph).tokenType == PLAINSTRING) {
+      endOfParagraph++;
+    } else if ((*endOfParagraph).tokenType == END_LINE) {
+      endOfParagraph++;
+      if ((*endOfParagraph).tokenType == END_LINE) {
+	endOfParagraph++;
+	return endOfParagraph;
+      }
     }
-   return tokList.end();
-   }
+  }
+  return tokList.end();
+}
 
 /* This method is for returning the end of a specific form of doxygen command
  * that begins with a \command and ends in \endcommand
@@ -307,12 +331,12 @@ std::list<Token>::iterator getEndOfSection(std::string theCommand, TokenList &to
  * progressTilEndCommand("endcode", tokenList);
  * If the end is never encountered, it returns the end of the std::list.
  */
-std::list<Token>::iterator getEndCommand(std::string theCommand, TokenList &tokList){
-  std::list<Token>::iterator endOfCommand = tokList.iteratorCopy();
-  while (endOfCommand!= tokList.end()){
-    if ((*endOfCommand).tokenType == COMMAND){
-      if (theCommand.compare((* endOfCommand).tokenString) == 0){
-        return endOfCommand;
+std::list < Token >::iterator getEndCommand(std::string theCommand, TokenList & tokList) {
+  std::list < Token >::iterator endOfCommand = tokList.iteratorCopy();
+  while (endOfCommand != tokList.end()) {
+    if ((*endOfCommand).tokenType == COMMAND) {
+      if (theCommand.compare((*endOfCommand).tokenString) == 0) {
+	return endOfCommand;
       }
       endOfCommand++;
     }
@@ -324,9 +348,9 @@ std::list<Token>::iterator getEndCommand(std::string theCommand, TokenList &tokL
 /* A specialty method for commands such as \arg that end at the end of a paragraph OR when another \arg is encountered
  */
 //TODO getTilAnyCommand
-std::list<Token>::iterator getTilAnyCommand(std::string theCommand, TokenList &tokList){
+std::list < Token >::iterator getTilAnyCommand(std::string theCommand, TokenList & tokList) {
 #pragma unused(theCommand,tokList)
-  std::list<Token>::iterator anIterator;
+  std::list < Token >::iterator anIterator;
   return anIterator;
 }
 
@@ -338,54 +362,56 @@ std::list<Token>::iterator getTilAnyCommand(std::string theCommand, TokenList &t
  * Plain commands, such as newline etc, they contain no other data
  *  \n \\ \@ \& \$ \# \< \> \%
  */
-int addSimpleCommand(std::string theCommand, std::list <DoxygenEntity> &doxyList){
-  if (noisy) cout << "Parsing " << theCommand << endl;
+int addSimpleCommand(std::string theCommand, std::list < DoxygenEntity > &doxyList) {
+  if (noisy)
+    cout << "Parsing " << theCommand << endl;
   doxyList.push_back(DoxygenEntity(theCommand));
   return 1;
 }
- 
+
 /* NOT INCLUDED Simple Commands
 * Format: @command
 * Plain commands, such as newline etc, they contain no other data
 */
-int ignoreSimpleCommand(std::string theCommand, std::list <DoxygenEntity> &doxyList){
+int ignoreSimpleCommand(std::string theCommand, std::list < DoxygenEntity > &doxyList) {
 #pragma unused(doxyList)
-  if (noisy) cout << "Not Adding " << theCommand << endl;
+  if (noisy)
+    cout << "Not Adding " << theCommand << endl;
   return 1;
 }
- 
+
 /* CommandWord
 * Format: @command <word>
 * Commands with a single WORD after then such as @b
 * "a", "b", "c", "e", "em", "p", "def", "enum", "example", "package", 
 * "relates", "namespace", "relatesalso","anchor", "dontinclude", "include", "includelineno"
 */
-int addCommandWord(std::string theCommand, TokenList &tokList, std::list <DoxygenEntity> &doxyList){
-  if (noisy) cout << "Parsing " << theCommand << endl;
+int addCommandWord(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
+  if (noisy)
+    cout << "Parsing " << theCommand << endl;
   std::string name = getNextWord(tokList);
-  if (!name.empty()){ 
+  if (!name.empty()) {
     doxyList.push_back(DoxygenEntity(theCommand, name));
     return 1;
-  }
-  else 
-    cout << "No word followed " << theCommand <<  " command. Not added" << endl;
+  } else
+    cout << "No word followed " << theCommand << " command. Not added" << endl;
   return 0;
 }
- 
+
 /* NOT INCLUDED CommandWord
 * Format: @command <word>
 * Commands with a single WORD after then such as @b
 * "copydoc", "copybrief", "copydetails", "verbinclude", "htmlinclude"
 */
-int ignoreCommandWord(std::string theCommand, TokenList &tokList, std::list <DoxygenEntity> &doxyList){
+int ignoreCommandWord(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
 #pragma unused(doxyList)
-  if (noisy) 
+  if (noisy)
     cout << "Not Adding " << theCommand << endl;
   std::string name = getNextWord(tokList);
   if (!name.empty())
     return 1;
-  else 
-    cout << "WARNING: No word followed " << theCommand <<  " command." << endl;
+  else
+    cout << "WARNING: No word followed " << theCommand << " command." << endl;
   return 0;
 }
 
@@ -394,12 +420,12 @@ int ignoreCommandWord(std::string theCommand, TokenList &tokList, std::list <Dox
 * Commands with a single LINE after then such as @var
 * "addindex", "fn", "name", "line", "var", "skipline", "typedef", "skip", "until", "property"
 */
-int addCommandLine(std::string theCommand, TokenList &tokList, std::list <DoxygenEntity> &doxyList){
-  if (noisy) 
+int addCommandLine(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
+  if (noisy)
     cout << "Parsing " << theCommand << endl;
-  std::list<Token>::iterator endOfLine = getOneLine(tokList);
-  std::list <DoxygenEntity> aNewList = parse(endOfLine, tokList);
-  doxyList.push_back( DoxygenEntity(theCommand, aNewList));
+  std::list < Token >::iterator endOfLine = getOneLine(tokList);
+  std::list < DoxygenEntity > aNewList = parse(endOfLine, tokList);
+  doxyList.push_back(DoxygenEntity(theCommand, aNewList));
   return 1;
 }
 
@@ -408,11 +434,11 @@ int addCommandLine(std::string theCommand, TokenList &tokList, std::list <Doxyge
 * Commands with a single LINE after then such as @var
 * 
 */
-int ignoreCommandLine(std::string theCommand, TokenList &tokList, std::list <DoxygenEntity> &doxyList){
+int ignoreCommandLine(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
 #pragma unused(doxyList)
-  if (noisy) 
+  if (noisy)
     cout << "Not Adding " << theCommand << endl;
-  std::list<Token>::iterator endOfLine = getOneLine(tokList);
+  std::list < Token >::iterator endOfLine = getOneLine(tokList);
   tokList.setIterator(endOfLine);
   return 1;
 }
@@ -423,30 +449,30 @@ int ignoreCommandLine(std::string theCommand, TokenList &tokList, std::list <Dox
 * "return", "remarks", "since", "test", "sa", "see", "pre", "post", "details", "invariant", 
 * "deprecated", "date", "note", "warning", "version", "todo", "bug", "attention", "brief", "arg", "author"
 */
-int addCommandParagraph(std::string theCommand, TokenList &tokList, std::list <DoxygenEntity> &doxyList){
-  if (noisy) 
+int addCommandParagraph(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
+  if (noisy)
     cout << "Parsing " << theCommand << endl;
-  std::list<Token>::iterator endOfParagraph = getEndOfParagraph(tokList);
-  std::list <DoxygenEntity> aNewList;
-  aNewList =  parse(endOfParagraph, tokList);
-  doxyList.push_back( DoxygenEntity(theCommand, aNewList));
+  std::list < Token >::iterator endOfParagraph = getEndOfParagraph(tokList);
+  std::list < DoxygenEntity > aNewList;
+  aNewList = parse(endOfParagraph, tokList);
+  doxyList.push_back(DoxygenEntity(theCommand, aNewList));
   return 1;
 }
- 
+
 /* CommandParagraph
 * Format: @command {paragraph}
 * Commands with a single LINE after then such as @var
 * 
 */
-int ignoreCommandParagraph(std::string theCommand, TokenList &tokList, std::list <DoxygenEntity> &doxyList){
+int ignoreCommandParagraph(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
 #pragma unused(doxyList)
-  if (noisy) 
+  if (noisy)
     cout << "Not Adding " << theCommand << endl;
-  std::list<Token>::iterator endOfParagraph = getEndOfParagraph(tokList);
+  std::list < Token >::iterator endOfParagraph = getEndOfParagraph(tokList);
   tokList.setIterator(endOfParagraph);
   return 1;
 }
- 
+
 /* Command EndCommand
 * Format: @command and ends at @endcommand
 * Commands that take in a block of text such as @code
@@ -454,30 +480,30 @@ int ignoreCommandParagraph(std::string theCommand, TokenList &tokList, std::list
 * "verbatim", "xmlonly", "cond", "if", "ifnot", "link"
 * Returns 1 if success, 0 if the endcommand is never encountered.
 */
-int addCommandEndCommand(std::string theCommand, TokenList &tokList, std::list <DoxygenEntity> &doxyList){
-  if (noisy) 
+int addCommandEndCommand(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
+  if (noisy)
     cout << "Not Adding " << theCommand << endl;
-  std::string description = getStringTilEndCommand( "end" + theCommand, tokList);
+  std::string description = getStringTilEndCommand("end" + theCommand, tokList);
   doxyList.push_back(DoxygenEntity(theCommand, description));
   return 1;
 }
- 
+
 /* CommandWordParagraph
 * Format: @command <word> {paragraph}
 * Commands such as param
  * "param", "tparam", "throw", "throws", "retval", "exception"
 */
-int addCommandWordParagraph(std::string theCommand, TokenList &tokList, std::list <DoxygenEntity> &doxyList){
-  if (noisy) 
+int addCommandWordParagraph(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
+  if (noisy)
     cout << "Parsing " << theCommand << endl;
   std::string name = getNextWord(tokList);
-  if (name.empty()){ 
-    cout << "No word followed " << theCommand <<  " command. Not added" << endl;
+  if (name.empty()) {
+    cout << "No word followed " << theCommand << " command. Not added" << endl;
     return 0;
-    }
-  std::list<Token>::iterator endOfParagraph = getEndOfParagraph(tokList);
-  std::list <DoxygenEntity> aNewList;
-  aNewList =  parse(endOfParagraph, tokList);
+  }
+  std::list < Token >::iterator endOfParagraph = getEndOfParagraph(tokList);
+  std::list < DoxygenEntity > aNewList;
+  aNewList = parse(endOfParagraph, tokList);
   aNewList.push_front(DoxygenEntity("plainstd::string", name));
   doxyList.push_back(DoxygenEntity(theCommand, aNewList));
   return 1;
@@ -488,16 +514,17 @@ int addCommandWordParagraph(std::string theCommand, TokenList &tokList, std::lis
 * Commands such as param
 * "page", "subsection", "subsubsection", "section", "paragraph", "defgroup"
 */
-int addCommandWordLine(std::string theCommand, TokenList &tokList, std::list <DoxygenEntity> &doxyList){
-  if (noisy) cout << "Parsing " << theCommand << endl;
-    std::string name = getNextWord(tokList);
-  if (name.empty()){ 
-    cout << "No word followed " << theCommand <<  " command. Not added" << endl;
+int addCommandWordLine(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
+  if (noisy)
+    cout << "Parsing " << theCommand << endl;
+  std::string name = getNextWord(tokList);
+  if (name.empty()) {
+    cout << "No word followed " << theCommand << " command. Not added" << endl;
     return 0;
-    }
-  std::list<Token>::iterator endOfLine = getOneLine(tokList);
-  std::list <DoxygenEntity> aNewList;
-  aNewList =  parse(endOfLine, tokList);
+  }
+  std::list < Token >::iterator endOfLine = getOneLine(tokList);
+  std::list < DoxygenEntity > aNewList;
+  aNewList = parse(endOfLine, tokList);
   aNewList.push_front(DoxygenEntity("plainstd::string", name));
   doxyList.push_back(DoxygenEntity(theCommand, aNewList));
   return 1;
@@ -509,21 +536,21 @@ int addCommandWordLine(std::string theCommand, TokenList &tokList, std::list <Do
 * Commands such as class
 * "category", "class", "protocol", "interface", "struct", "union"
 */
-int addCommandWordOWordOWord(std::string theCommand, TokenList &tokList, std::list <DoxygenEntity> &doxyList){
-  if (noisy) 
+int addCommandWordOWordOWord(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
+  if (noisy)
     cout << "Parsing " << theCommand << endl;
   std::string name = getNextWord(tokList);
-  if (name.empty()){ 
-      cout << "No word followed " << theCommand <<  " command. Not added" << endl;
-      return 0;
-      }
+  if (name.empty()) {
+    cout << "No word followed " << theCommand << " command. Not added" << endl;
+    return 0;
+  }
   std::string headerfile = getNextWord(tokList);
   std::string headername = getNextWord(tokList);
-  std::list <DoxygenEntity> aNewList;
+  std::list < DoxygenEntity > aNewList;
   aNewList.push_back(DoxygenEntity("plainstd::string", name));
-  if (!headerfile.empty()) 
+  if (!headerfile.empty())
     aNewList.push_back(DoxygenEntity("plainstd::string", headerfile));
-  if (!headername.empty()) 
+  if (!headername.empty())
     aNewList.push_back(DoxygenEntity("plainstd::string", headername));
   doxyList.push_back(DoxygenEntity(theCommand, aNewList));
   return 1;
@@ -534,241 +561,240 @@ int addCommandWordOWordOWord(std::string theCommand, TokenList &tokList, std::li
 * Commands such as dir
 * "dir", "file", "cond"
 */
-int addCommandOWord(std::string theCommand, TokenList &tokList, std::list <DoxygenEntity> &doxyList){
-  if (noisy) 
+int addCommandOWord(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
+  if (noisy)
     cout << "Parsing " << theCommand << endl;
   std::string name = getNextWord(tokList);
   doxyList.push_back(DoxygenEntity(theCommand, name));
-  return 1; 
+  return 1;
 }
 
  /* Commands that should not be encountered (such as PHP only)
   * goes til the end of line then returns
   */
-int addCommandErrorThrow(std::string theCommand, TokenList &tokList, std::list <DoxygenEntity> &doxyList){
+int addCommandErrorThrow(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
 #pragma unused(doxyList)
-    if (noisy) {
-      cout << "Encountered :" << theCommand << endl;
-      cout << "This command should not have been encountered. Behaviour past this may be unpredictable " << endl;
-    }
-    std::list<Token>::iterator endOfLine = getOneLine(tokList);
-    tokList.setIterator(endOfLine);
-    return 0;
- }
+  if (noisy) {
+    cout << "Encountered :" << theCommand << endl;
+    cout << "This command should not have been encountered. Behaviour past this may be unpredictable " << endl;
+  }
+  std::list < Token >::iterator endOfLine = getOneLine(tokList);
+  tokList.setIterator(endOfLine);
+  return 0;
+}
 
 /* Adds the unique commands- different process for each unique command */
-int addCommandUnique(std::string theCommand, TokenList &tokList, std::list <DoxygenEntity> &doxyList){
-  std::list <DoxygenEntity> aNewList;
-  if (theCommand.compare("arg") == 0 || theCommand.compare("li") == 0){
-    std::list<Token>::iterator endOfSection = getEndOfSection(theCommand, tokList);
-    std::list <DoxygenEntity> aNewList;
-    aNewList =  parse(endOfSection, tokList);
-    doxyList.push_back( DoxygenEntity(theCommand, aNewList));
+int addCommandUnique(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
+  std::list < DoxygenEntity > aNewList;
+  if (theCommand.compare("arg") == 0 || theCommand.compare("li") == 0) {
+    std::list < Token >::iterator endOfSection = getEndOfSection(theCommand, tokList);
+    std::list < DoxygenEntity > aNewList;
+    aNewList = parse(endOfSection, tokList);
+    doxyList.push_back(DoxygenEntity(theCommand, aNewList));
   }
   // \xrefitem <key> "(heading)" "(std::list title)" {text}
-  else if (theCommand.compare("xrefitem") == 0){
+  else if (theCommand.compare("xrefitem") == 0) {
     //TODO Implement xrefitem
-    if (noisy) 
+    if (noisy)
       cout << "Not Adding " << theCommand << endl;
-    std::list<Token>::iterator endOfParagraph = getEndOfParagraph(tokList);
+    std::list < Token >::iterator endOfParagraph = getEndOfParagraph(tokList);
     tokList.setIterator(endOfParagraph);
     return 1;
   }
   // \ingroup (<groupname> [<groupname> <groupname>])
-  else if (theCommand.compare("ingroup") == 0){
+  else if (theCommand.compare("ingroup") == 0) {
     std::string name = getNextWord(tokList);
     aNewList.push_back(DoxygenEntity("plainstd::string", name));
     name = getNextWord(tokList);
-    if(!name.empty()) 
+    if (!name.empty())
       aNewList.push_back(DoxygenEntity("plainstd::string", name));
     name = getNextWord(tokList);
-    if(!name.empty()) 
+    if (!name.empty())
       aNewList.push_back(DoxygenEntity("plainstd::string", name));
     doxyList.push_back(DoxygenEntity(theCommand, aNewList));
     return 1;
   }
   // \par [(paragraph title)] { paragraph }
-  else if (theCommand.compare("par") == 0){
-    std::list<Token>::iterator endOfLine = getOneLine(tokList);
-    aNewList =  parse(endOfLine, tokList);
-    std::list <DoxygenEntity> aNewList2;
+  else if (theCommand.compare("par") == 0) {
+    std::list < Token >::iterator endOfLine = getOneLine(tokList);
+    aNewList = parse(endOfLine, tokList);
+    std::list < DoxygenEntity > aNewList2;
     aNewList2 = parse(endOfLine, tokList);
     aNewList.splice(aNewList.end(), aNewList2);
     doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-    return 1; 
+    return 1;
   }
   // \headerfile <header-file> [<header-name>]
-  else if (theCommand.compare("headerfile") == 0){
-    std::list <DoxygenEntity> aNewList;
+  else if (theCommand.compare("headerfile") == 0) {
+    std::list < DoxygenEntity > aNewList;
     std::string name = getNextWord(tokList);
     aNewList.push_back(DoxygenEntity("plainstd::string", name));
     name = getNextWord(tokList);
-    if(!name.empty()) 
+    if (!name.empty())
       aNewList.push_back(DoxygenEntity("plainstd::string", name));
     doxyList.push_back(DoxygenEntity(theCommand, aNewList));
     return 1;
   }
   // \overload [(function declaration)]
-  else if (theCommand.compare("overload") == 0){
-    std::list<Token>::iterator endOfLine = getOneLine(tokList);
-    if (endOfLine != tokList.current()){
-      std::list <DoxygenEntity> aNewList;
-      aNewList =  parse(endOfLine, tokList);
+  else if (theCommand.compare("overload") == 0) {
+    std::list < Token >::iterator endOfLine = getOneLine(tokList);
+    if (endOfLine != tokList.current()) {
+      std::list < DoxygenEntity > aNewList;
+      aNewList = parse(endOfLine, tokList);
       doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-    }
-    else 
+    } else
       doxyList.push_back(DoxygenEntity(theCommand));
     return 1;
   }
   // \weakgroup <name> [(title)]
-  else if (theCommand.compare("weakgroup") == 0){
-    if (noisy) cout << "Parsing " << theCommand << endl;
-      std::string name = getNextWord(tokList);
-      if (name.empty()){ 
-	cout << "No word followed " << theCommand <<  " command. Not added" << endl;
+  else if (theCommand.compare("weakgroup") == 0) {
+    if (noisy)
+      cout << "Parsing " << theCommand << endl;
+    std::string name = getNextWord(tokList);
+    if (name.empty()) {
+      cout << "No word followed " << theCommand << " command. Not added" << endl;
       return 0;
     }
-    std::list <DoxygenEntity> aNewList;
-    std::list<Token>::iterator endOfLine = getOneLine(tokList);
+    std::list < DoxygenEntity > aNewList;
+    std::list < Token >::iterator endOfLine = getOneLine(tokList);
     if (endOfLine != tokList.current()) {
-      aNewList =  parse(endOfLine, tokList);
+      aNewList = parse(endOfLine, tokList);
     }
     aNewList.push_front(DoxygenEntity("plainstd::string", name));
     doxyList.push_back(DoxygenEntity(theCommand, aNewList));
   }
   // \ref <name> ["(text)"]
-  else if (theCommand.compare("ref") == 0){
+  else if (theCommand.compare("ref") == 0) {
     //TODO Implement ref
-    if (noisy) 
+    if (noisy)
       cout << "Not Adding " << theCommand << endl;
-    std::list<Token>::iterator endOfParagraph = getEndOfParagraph(tokList);
+    std::list < Token >::iterator endOfParagraph = getEndOfParagraph(tokList);
     tokList.setIterator(endOfParagraph);
   }
   // \subpage <name> ["(text)"]
-  else if (theCommand.compare("subpage") == 0){
+  else if (theCommand.compare("subpage") == 0) {
     //TODO implement subpage
-    if (noisy) 
+    if (noisy)
       cout << "Not Adding " << theCommand << endl;
-    std::list<Token>::iterator endOfParagraph = getEndOfParagraph(tokList);
+    std::list < Token >::iterator endOfParagraph = getEndOfParagraph(tokList);
     tokList.setIterator(endOfParagraph);
   }
   // \dotfile <file> ["caption"]
-  else if (theCommand.compare("dotfile") == 0){
+  else if (theCommand.compare("dotfile") == 0) {
     //TODO implement dotfile
-    if (noisy) 
+    if (noisy)
       cout << "Not Adding " << theCommand << endl;
-    std::list<Token>::iterator endOfParagraph = getEndOfParagraph(tokList);
+    std::list < Token >::iterator endOfParagraph = getEndOfParagraph(tokList);
     tokList.setIterator(endOfParagraph);
   }
   // \image <format> <file> ["caption"] [<sizeindication>=<size>]
-  else if (theCommand.compare("image") == 0){
-  //todo implement image
-  } 
+  else if (theCommand.compare("image") == 0) {
+    //todo implement image
+  }
   // \addtogroup <name> [(title)]
-  else if (theCommand.compare("addtogroup") == 0){
-    if (noisy) 
+  else if (theCommand.compare("addtogroup") == 0) {
+    if (noisy)
       cout << "Parsing " << theCommand << endl;
     std::string name = getNextWord(tokList);
-    if (name.empty()){ 
-      cout << "No word followed " << theCommand <<  " command. Not added" << endl;
+    if (name.empty()) {
+      cout << "No word followed " << theCommand << " command. Not added" << endl;
       return 0;
     }
-    std::list <DoxygenEntity> aNewList;
-    std::list<Token>::iterator endOfLine = getOneLine(tokList);
+    std::list < DoxygenEntity > aNewList;
+    std::list < Token >::iterator endOfLine = getOneLine(tokList);
     if (endOfLine != tokList.current()) {
-      aNewList =  parse(endOfLine, tokList);
+      aNewList = parse(endOfLine, tokList);
     }
     aNewList.push_front(DoxygenEntity("plainstd::string", name));
     doxyList.push_back(DoxygenEntity(theCommand, aNewList));
   }
   return 0;
 }
- 
+
 /* The actual "meat" of the doxygen parser. This is not yet fully implemented
  * with my current design- however the skeletal outline is contained in
  * the file Skeleton
  */
-int addCommand(std::string commandString, TokenList &tokList,std::list <DoxygenEntity> &doxyList){
-   std::string theCommand = StringToLower(commandString);
-   if (theCommand.compare("plainstd::string") == 0){
-       std::string nextPhrase = getStringTilCommand( tokList);
-       if (noisy) cout << "Parsing plain std::string :" << nextPhrase << endl;
-       doxyList.push_back(DoxygenEntity("plainstd::string", nextPhrase ));
-       return 1;
-       }
-   int commandNumber = commandBelongs(theCommand);
-   if (commandNumber == SIMPLECOMMAND){
-     return addSimpleCommand(theCommand, doxyList);
-     }
-   if (commandNumber == IGNOREDSIMPLECOMMAND){
-     return ignoreSimpleCommand(theCommand, doxyList);
-     }
-   if (commandNumber == COMMANDWORD){
-     return addCommandWord(theCommand, tokList, doxyList);
-     }
-   if (commandNumber == IGNOREDCOMMANDWORD){
-     return ignoreCommandWord(theCommand, tokList, doxyList);
-     }
-   if (commandNumber == COMMANDLINE ){
-     return addCommandLine(theCommand, tokList, doxyList);
-     }
-   if (commandNumber == IGNOREDCOMMANDLINE ){
-     return ignoreCommandLine(theCommand, tokList, doxyList);
-     }
-   if (commandNumber == COMMANDPARAGRAPH){
-     return addCommandParagraph(theCommand, tokList, doxyList);
-     }
-   if (commandNumber == IGNORECOMMANDPARAGRAPH){
-     return ignoreCommandParagraph(theCommand, tokList, doxyList);
-     }
-   if (commandNumber == COMMANDENDCOMMAND){
-     return addCommandEndCommand(theCommand, tokList, doxyList);
-     }
-   if (commandNumber == COMMANDWORDPARAGRAPH){
-     return addCommandWordParagraph(theCommand, tokList, doxyList);
-     }
-   if (commandNumber == COMMANDWORDLINE){
-     return addCommandWordLine(theCommand, tokList, doxyList);
-     }
-   if (commandNumber == COMMANDWORDOWORDWORD){
-     return addCommandWordOWordOWord(theCommand, tokList, doxyList);
-     }
-   if (commandNumber == COMMANDOWORD){
-     return addCommandOWord(theCommand, tokList, doxyList);
-     }
-   if (commandNumber == COMMANDERRORTHROW){
-     return addCommandErrorThrow(theCommand, tokList, doxyList);
-     }
-   if (commandNumber == COMMANDUNIQUE){
+int addCommand(std::string commandString, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
+  std::string theCommand = StringToLower(commandString);
+  if (theCommand.compare("plainstd::string") == 0) {
+    std::string nextPhrase = getStringTilCommand(tokList);
+    if (noisy)
+      cout << "Parsing plain std::string :" << nextPhrase << endl;
+    doxyList.push_back(DoxygenEntity("plainstd::string", nextPhrase));
+    return 1;
+  }
+  int commandNumber = commandBelongs(theCommand);
+  if (commandNumber == SIMPLECOMMAND) {
+    return addSimpleCommand(theCommand, doxyList);
+  }
+  if (commandNumber == IGNOREDSIMPLECOMMAND) {
+    return ignoreSimpleCommand(theCommand, doxyList);
+  }
+  if (commandNumber == COMMANDWORD) {
+    return addCommandWord(theCommand, tokList, doxyList);
+  }
+  if (commandNumber == IGNOREDCOMMANDWORD) {
+    return ignoreCommandWord(theCommand, tokList, doxyList);
+  }
+  if (commandNumber == COMMANDLINE) {
+    return addCommandLine(theCommand, tokList, doxyList);
+  }
+  if (commandNumber == IGNOREDCOMMANDLINE) {
+    return ignoreCommandLine(theCommand, tokList, doxyList);
+  }
+  if (commandNumber == COMMANDPARAGRAPH) {
+    return addCommandParagraph(theCommand, tokList, doxyList);
+  }
+  if (commandNumber == IGNORECOMMANDPARAGRAPH) {
+    return ignoreCommandParagraph(theCommand, tokList, doxyList);
+  }
+  if (commandNumber == COMMANDENDCOMMAND) {
+    return addCommandEndCommand(theCommand, tokList, doxyList);
+  }
+  if (commandNumber == COMMANDWORDPARAGRAPH) {
+    return addCommandWordParagraph(theCommand, tokList, doxyList);
+  }
+  if (commandNumber == COMMANDWORDLINE) {
+    return addCommandWordLine(theCommand, tokList, doxyList);
+  }
+  if (commandNumber == COMMANDWORDOWORDWORD) {
+    return addCommandWordOWordOWord(theCommand, tokList, doxyList);
+  }
+  if (commandNumber == COMMANDOWORD) {
+    return addCommandOWord(theCommand, tokList, doxyList);
+  }
+  if (commandNumber == COMMANDERRORTHROW) {
+    return addCommandErrorThrow(theCommand, tokList, doxyList);
+  }
+  if (commandNumber == COMMANDUNIQUE) {
     return addCommandUnique(theCommand, tokList, doxyList);
-     }
-     
-   return 0;
-   }
+  }
 
-std::list<DoxygenEntity> parse(std::list<Token>::iterator endParsingIndex, TokenList &tokList){
-  std::list <DoxygenEntity> aNewList;
+  return 0;
+}
+
+std::list < DoxygenEntity > parse(std::list < Token >::iterator endParsingIndex, TokenList & tokList) {
+  std::list < DoxygenEntity > aNewList;
   int currCommand;
-  while (tokList.current() != endParsingIndex){ 
+  while (tokList.current() != endParsingIndex) {
     Token currToken = tokList.peek();
-    if(noisy) 
+    if (noisy)
       cout << "Parsing for phrase starting in:" << currToken.toString() << endl;
-    if(currToken.tokenType == END_LINE ){
+    if (currToken.tokenType == END_LINE) {
       tokList.next();
-    }
-    else if(currToken.tokenType == COMMAND){
+    } else if (currToken.tokenType == COMMAND) {
       currCommand = findCommand(currToken.tokenString);
-      if (currCommand < 0 ){
-	if(noisy) 
+      if (currCommand < 0) {
+	if (noisy)
 	  cout << "Unidentified Command " << currToken.tokenString << endl;
 	tokList.next();
 	addCommand(std::string("plainstd::string"), tokList, aNewList);
+      } else {
+	tokList.next();
+	addCommand(currToken.tokenString, tokList, aNewList);
       }
-      else { tokList.next();
-	addCommand(currToken.tokenString, tokList,  aNewList);
-      }
-    }
-    else if (currToken.tokenType == PLAINSTRING){
+    } else if (currToken.tokenType == PLAINSTRING) {
       addCommand(std::string("plainstd::string"), tokList, aNewList);
     }
     break;
@@ -776,50 +802,48 @@ std::list<DoxygenEntity> parse(std::list<Token>::iterator endParsingIndex, Token
   return aNewList;
 }
 
-std::list<DoxygenEntity> parseRoot(std::list<Token>::iterator endParsingIndex, TokenList &tokList){
+std::list < DoxygenEntity > parseRoot(std::list < Token >::iterator endParsingIndex, TokenList & tokList) {
 
-  std::list <DoxygenEntity> aNewList;
+  std::list < DoxygenEntity > aNewList;
   int currCommand;
 
-  while (tokList.current() != endParsingIndex){ 
+  while (tokList.current() != endParsingIndex) {
 
     Token currToken = tokList.peek();
-    if(noisy) {
+    if (noisy) {
       cout << "Parsing for phrase starting in:" << currToken.toString() << endl;
     }
 
-    if(currToken.tokenType == END_LINE ){
+    if (currToken.tokenType == END_LINE) {
       tokList.next();
-    }
-    else if(currToken.tokenType == COMMAND){
+    } else if (currToken.tokenType == COMMAND) {
       currCommand = findCommand(currToken.tokenString);
-      if (currCommand < 0 ){ 
-	if(noisy) {
+      if (currCommand < 0) {
+	if (noisy) {
 	  cout << "Unidentified Command " << currToken.tokenString << endl;
 	}
 	tokList.next();
 	addCommand(std::string("partofdescription"), tokList, aNewList);
-      } else { 
-        tokList.next();
-        addCommand(currToken.tokenString, tokList,  aNewList);
+      } else {
+	tokList.next();
+	addCommand(currToken.tokenString, tokList, aNewList);
       }
-    }
-    else if (currToken.tokenType == PLAINSTRING){
+    } else if (currToken.tokenType == PLAINSTRING) {
       addCommand(std::string("partofdescription"), tokList, aNewList);
     }
   }
   return aNewList;
 }
 
-std::list<DoxygenEntity> DoxygenParser::createTree(std::string doxygenBlob){
+std::list < DoxygenEntity > DoxygenParser::createTree(std::string doxygenBlob) {
   TokenList tokList = TokenList(doxygenBlob);
-  if(noisy) {
+  if (noisy) {
     cout << "---TOKEN LIST---" << endl;
     tokList.printList();
   }
-  std::list <DoxygenEntity> rootList;
-  rootList = parseRoot( tokList.end(), tokList);
-  if(noisy) {
+  std::list < DoxygenEntity > rootList;
+  rootList = parseRoot(tokList.end(), tokList);
+  if (noisy) {
     cout << "PARSED LIST" << endl;
     printTree(rootList);
   }
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.h b/Source/DoxygenTranslator/src/DoxygenParser.h
index 2269e6788..c298a92f3 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.h
+++ b/Source/DoxygenTranslator/src/DoxygenParser.h
@@ -3,12 +3,11 @@
 #include <string>
 #include <list>
 #include "DoxygenEntity.h"
-class DoxygenParser
-{
+class DoxygenParser {
 public:
   DoxygenParser();
   virtual ~DoxygenParser();
-  std::list <DoxygenEntity> createTree(std::string doxygen);
+  std::list < DoxygenEntity > createTree(std::string doxygen);
 };
 
-#endif /*DOXYGENPARSER_H_*/
+#endif
diff --git a/Source/DoxygenTranslator/src/DoxygenTranslator.cpp b/Source/DoxygenTranslator/src/DoxygenTranslator.cpp
index 025670796..6fe97d298 100644
--- a/Source/DoxygenTranslator/src/DoxygenTranslator.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenTranslator.cpp
@@ -12,21 +12,21 @@
 #include "JavaDocConverter.h"
 #include "PyDocConverter.h"
 
-bool DoxygenTranslator::getDocumentation(Node *node, DocumentationFormat format, String *&documentation){
-  switch(format){
-    case JavaDoc:   
-      return JavaDocConverter().getDocumentation(node, documentation);
-    case PyDoc:   
-      return PyDocConverter().getDocumentation(node, documentation);
-    default:
-      return false;
+bool DoxygenTranslator::getDocumentation(Node *node, DocumentationFormat format, String *&documentation) {
+  switch (format) {
+  case JavaDoc:
+    return JavaDocConverter().getDocumentation(node, documentation);
+  case PyDoc:
+    return PyDocConverter().getDocumentation(node, documentation);
+  default:
+    return false;
   }
 }
 
-void DoxygenTranslator::printTree(std::list<DoxygenEntity> &entityList){  
-  std::list<DoxygenEntity>::iterator p = entityList.begin();
-  while (p != entityList.end()){
+void DoxygenTranslator::printTree(std::list < DoxygenEntity > &entityList) {
+  std::list < DoxygenEntity >::iterator p = entityList.begin();
+  while (p != entityList.end()) {
     (*p).printEntity(0);
     p++;
   }
-}
\ No newline at end of file
+}
diff --git a/Source/DoxygenTranslator/src/DoxygenTranslator.h b/Source/DoxygenTranslator/src/DoxygenTranslator.h
index 4be1e97e3..566b1551d 100644
--- a/Source/DoxygenTranslator/src/DoxygenTranslator.h
+++ b/Source/DoxygenTranslator/src/DoxygenTranslator.h
@@ -28,14 +28,13 @@ enum DocumentationFormat {
  * A class to translate doxygen comments attacted to parser nodes
  * into alternative formats for use in code generated for target languages.
  */
-class DoxygenTranslator
-{
+class DoxygenTranslator {
 public:
   /*
    * Virtual destructor.
    */
-  virtual ~DoxygenTranslator(){}
-  
+  virtual ~ DoxygenTranslator() {
+  }
   /*
    * Return the documentation for a given node formated for the correct 
    * documentation system.
@@ -45,7 +44,7 @@ public:
    * @return A bool to indicate if there was documentation to return for the node.
    */
   static bool getDocumentation(Node *node, DocumentationFormat format, String *&documentation);
-  
+
 protected:
   /*
    * Overridden in subclasses to return the documentation formatted for a given
@@ -55,11 +54,11 @@ protected:
    * @return A bool to indicate if there was documentation to return for the node.
    */
   virtual bool getDocumentation(Node *node, String *&documentation) = 0;
-  
+
   /*
    * Prints the details of a parsed entity list to stdout (for debugging).
    */
-  void printTree(std::list<DoxygenEntity> &entityList);
+  void printTree(std::list < DoxygenEntity > &entityList);
 };
 
-#endif /*DOXYGENTRANSLATOR_H_*/
+#endif
diff --git a/Source/DoxygenTranslator/src/Examples/DoxygenTransWTokenizer.cpp b/Source/DoxygenTranslator/src/Examples/DoxygenTransWTokenizer.cpp
index dacb31f77..930141c97 100644
--- a/Source/DoxygenTranslator/src/Examples/DoxygenTransWTokenizer.cpp
+++ b/Source/DoxygenTranslator/src/Examples/DoxygenTransWTokenizer.cpp
@@ -1,7 +1,5 @@
 /* The main class for translating blobs of Doxygen for SWIG
  * by Cheryl Foil, mentor Olly Betts, for Google's Summer of Code Program
- * Currently the spacing/format on this is a bit goofy in places, due to shuffling code
- * between 2 editors! Apologies for anyone combing through it :)
  */
 //TODO DOH instead of STL?
 //TODO Most commands are not fully implemented
@@ -40,8 +38,8 @@ to test. */
 int testCodeCrawlingFunctions = 0;
 int demonstrateParsing = 0;
 int runExamples = 0;
-int noisy = 0; // set this to 1 for extra chatter from the parsing stage.
-int addCommand(string commandName, int &startInd, list <DoxygenEntity> &doxyList, string doxygenString);
+int noisy = 0;			// set this to 1 for extra chatter from the parsing stage.
+int addCommand(string commandName, int &startInd, list < DoxygenEntity > &doxyList, string doxygenString);
 //////////////////////////////////////////
 
 
@@ -51,162 +49,203 @@ int addCommand(string commandName, int &startInd, list <DoxygenEntity> &doxyList
 
 // An array of all the commands and my generic description tag, plaindescription
 
-string commandArray[] = {"a", "addindex", "addtogroup", "anchor", "arg", "attention",
-		"author", "b", "brief", "bug", "c", "callgraph", "callergraph", "category",
-		"class", "code", "cond", "copybrief", "copydetails", "copydoc", "date", "def",
-		"defgroup", "deprecated", "details", "dir", "dontinclude", "dot", "dotfile", "e",
-		"else", "elseif", "em", "endcode", "endcond", "enddot", "endhtmlonly", "endif",
-		"endlatexonly", "endlink", "endmanonly", "endmsc", "endverbatim", "endxmlonly",
-		"enum", "example", "exception", "f$", "f[", "f]", "f{", "f}", "file", "fn", "headerfile",
-		"hideinitializer", "htmlinclude", "htmlonly", "if", "ifnot", "image", "include",
-		"includelineno", "ingroup", "internal", "invariant", "interface", "latexonly", "li",
-		"line", "link", "mainpage", "manonly", "msc", "n", "name", "namespace", "nosubgrouping",
-		"note", "overload", "p", "package", "page", "par", "paragraph", "param", "post", "pre",
-		"private", "privatesection", "property", "protected", "protectedsection", "protocol",
-		"public", "publicsection", "ref", "relates", "relatesalso", "remarks", "return", "retval",
-		"sa", "section", "see", "showinitializer", "since", "skip", "skipline", "struct", "subpage",
-		"subsection", "subsubsection", "test", "throw", "todo", "tparam", "typedef", "union", "until",
-		"var", "verbatim", "verbinclude", "version", "warning", "weakgroup", "xmlonly", "xrefitem",
-		"$", "@", "//","&", "~", "<", ">", "#", "%"};
+string commandArray[] = { "a", "addindex", "addtogroup", "anchor", "arg", "attention",
+  "author", "b", "brief", "bug", "c", "callgraph", "callergraph", "category",
+  "class", "code", "cond", "copybrief", "copydetails", "copydoc", "date", "def",
+  "defgroup", "deprecated", "details", "dir", "dontinclude", "dot", "dotfile", "e",
+  "else", "elseif", "em", "endcode", "endcond", "enddot", "endhtmlonly", "endif",
+  "endlatexonly", "endlink", "endmanonly", "endmsc", "endverbatim", "endxmlonly",
+  "enum", "example", "exception", "f$", "f[", "f]", "f{", "f}", "file", "fn", "headerfile",
+  "hideinitializer", "htmlinclude", "htmlonly", "if", "ifnot", "image", "include",
+  "includelineno", "ingroup", "internal", "invariant", "interface", "latexonly", "li",
+  "line", "link", "mainpage", "manonly", "msc", "n", "name", "namespace", "nosubgrouping",
+  "note", "overload", "p", "package", "page", "par", "paragraph", "param", "post", "pre",
+  "private", "privatesection", "property", "protected", "protectedsection", "protocol",
+  "public", "publicsection", "ref", "relates", "relatesalso", "remarks", "return", "retval",
+  "sa", "section", "see", "showinitializer", "since", "skip", "skipline", "struct", "subpage",
+  "subsection", "subsubsection", "test", "throw", "todo", "tparam", "typedef", "union", "until",
+  "var", "verbatim", "verbinclude", "version", "warning", "weakgroup", "xmlonly", "xrefitem",
+  "$", "@", "//", "&", "~", "<", ">", "#", "%"
+};
 
 
 string sectionIndicators[] = { "attention", "author", "brief", "bug", "cond", "date", "deprecated", "details",
-		"else", "elseif", "endcond", "endif", "exception", "if", "ifnot", "invariant", "note", "par", "param",
-		"tparam", "post" , "pre", "remarks", "return", "retval", "sa", "see", "since", "test", "throw", "todo",
-		"version", "warning", "xrefitem" };
+  "else", "elseif", "endcond", "endif", "exception", "if", "ifnot", "invariant", "note", "par", "param",
+  "tparam", "post", "pre", "remarks", "return", "retval", "sa", "see", "since", "test", "throw", "todo",
+  "version", "warning", "xrefitem"
+};
 
 /* All of the doxygen commands divided up by how they are parsed */
-string simpleCommands[] = {"n", "$", "@", "//", "&", "~", "<", ">", "#", "%"};
-string ignoredSimpleCommands[] = {"nothing at the moment"};
-string commandWords[] = {"a", "b", "c", "e", "em", "p", "def", "enum", "example", "package", 
-		"relates", "namespace", "relatesalso","anchor", "dontinclude", "include", "includelineno"};
-string ignoredCommandWords[] = {"copydoc", "copybrief", "copydetails", "verbinclude", "htmlinclude"};
-string commandLines[] = {"addindex", "fn", "name", "line", "var", "skipline", "typedef", "skip", "until", "property"};
-string ignoreCommandLines[] = {"nothing at the moment"};
-string commandParagraph[] = {"return", "remarks", "since", "test", "sa", "see", "pre", "post", "details", "invariant", 
-		    "deprecated", "date", "note", "warning", "version", "todo", "bug", "attention", "brief", "arg", "author"};
-string ignoreCommandParagraphs[] = {"nothing at the moment"};
-string commandEndCommands[] = {"code", "dot", "msc", "f$", "f[", "f{environment}{", "htmlonly", "latexonly", "manonly", 
-		   "verbatim", "xmlonly", "cond", "if", "ifnot", "link"};
-string commandWordParagraphs[] = {"param", "tparam", "throw", "retval", "exception"};
-string commandWordLines[] = {"page", "subsection", "subsubsection", "section", "paragraph", "defgroup"};
-string commandWordOWordOWords [] = {"category", "class", "protocol", "interface", "struct", "union"};
-string commandOWords[] = {"dir", "file", "cond"};
-string commandErrorThrowings[] = {"annotatedclasslist", "classhierarchy", "define", "functionindex", "header",
-		"headerfilelist", "inherit", "l", "postheader", "private", "privatesection", "protected", 
-		"protectedsection", "public", "publicsection", "endcode", "enddot", "endmsc", "endhtmlonly", 
-		"endlatexonly", "endmanonly", "endlink", "endverbatim", "endxmlonly", "f]", "f}", "endcond", 
-		"endif"};
-string commandUniques[] = {"xrefitem", "ingroup", "par", "headerfile", "overload", "weakgroup", "ref",
-		"subpage", "dotfile", "image", "addtogroup", "li"};
+string simpleCommands[] = { "n", "$", "@", "//", "&", "~", "<", ">", "#", "%" };
+string ignoredSimpleCommands[] = { "nothing at the moment" };
+
+string commandWords[] = { "a", "b", "c", "e", "em", "p", "def", "enum", "example", "package",
+  "relates", "namespace", "relatesalso", "anchor", "dontinclude", "include", "includelineno"
+};
+string ignoredCommandWords[] = { "copydoc", "copybrief", "copydetails", "verbinclude", "htmlinclude" };
+string commandLines[] = { "addindex", "fn", "name", "line", "var", "skipline", "typedef", "skip", "until", "property" };
+string ignoreCommandLines[] = { "nothing at the moment" };
+
+string commandParagraph[] = { "return", "remarks", "since", "test", "sa", "see", "pre", "post", "details", "invariant",
+  "deprecated", "date", "note", "warning", "version", "todo", "bug", "attention", "brief", "arg", "author"
+};
+string ignoreCommandParagraphs[] = { "nothing at the moment" };
+
+string commandEndCommands[] = { "code", "dot", "msc", "f$", "f[", "f{environment}{", "htmlonly", "latexonly", "manonly",
+  "verbatim", "xmlonly", "cond", "if", "ifnot", "link"
+};
+string commandWordParagraphs[] = { "param", "tparam", "throw", "retval", "exception" };
+string commandWordLines[] = { "page", "subsection", "subsubsection", "section", "paragraph", "defgroup" };
+string commandWordOWordOWords[] = { "category", "class", "protocol", "interface", "struct", "union" };
+string commandOWords[] = { "dir", "file", "cond" };
+
+string commandErrorThrowings[] = { "annotatedclasslist", "classhierarchy", "define", "functionindex", "header",
+  "headerfilelist", "inherit", "l", "postheader", "private", "privatesection", "protected",
+  "protectedsection", "public", "publicsection", "endcode", "enddot", "endmsc", "endhtmlonly",
+  "endlatexonly", "endmanonly", "endlink", "endverbatim", "endxmlonly", "f]", "f}", "endcond",
+  "endif"
+};
+
+string commandUniques[] = { "xrefitem", "ingroup", "par", "headerfile", "overload", "weakgroup", "ref",
+  "subpage", "dotfile", "image", "addtogroup", "li"
+};
 
  //int startIndex = 0;
- int isNewLine = 0;
- int briefDescExists = 0;
+int isNewLine = 0;
+int briefDescExists = 0;
 
  /* Entity list is the root list.
   * it is arranged this way to help documentation modules,
   * such as the javaDoc one, "sort" entities where they need to.
   */
 
- list <DoxygenEntity> rootList;
+list < DoxygenEntity > rootList;
 
 /* General (untested) assist methods */
 
- string StringToLower(string stringToConvert)
+string StringToLower(string stringToConvert)
+{
+  //change each element of the string to lower case
 
- {//change each element of the string to lower case
-
-    for(unsigned int i=0;i<stringToConvert.length();i++)
-    {
+  for (unsigned int i = 0; i < stringToConvert.length(); i++) {
     stringToConvert[i] = tolower(stringToConvert[i]);
+  }
+  return stringToConvert;	//return the converted string
+}
+
+int findCommand(string smallString) {
+
+  smallString = StringToLower(smallString);
+  int a;
+  for (int i = 0; i < sizeof(commandArray) / sizeof(*commandArray); i++) {
+    if ((a = smallString.compare(commandArray[i])) == 0) {
+      return 101 + i;
     }
-    return stringToConvert;//return the converted string
- }
-
- int findCommand(string smallString){
-
- 	smallString = StringToLower(smallString);
- 	int a;
- 	for (int i = 0; i < sizeof(commandArray)/sizeof(*commandArray); i++){
- 		if( (a = smallString.compare(commandArray[i])) == 0){
- 			return 101 + i;
- 		}
 
 
- 	}
- 	return -1;
- }
- 
- int commandBelongs(string theCommand){
-	 string smallString = StringToLower(theCommand );
-	 //cout << " Looking for command " << theCommand << endl;
-	 int i = 0;
-	 for ( i = 0; i < sizeof(simpleCommands)/sizeof(*simpleCommands); i++){
-	 	if(smallString.compare(simpleCommands[i]) == 0){return SIMPLECOMMAND ;}
-	 	}
-	 for ( i = 0; i < sizeof(ignoredSimpleCommands)/sizeof(*ignoredSimpleCommands); i++){
-	 	if(smallString.compare(ignoredSimpleCommands[i]) == 0){return IGNOREDSIMPLECOMMAND;}
-	 	} 
-	 for ( i = 0; i < sizeof(commandWords)/sizeof(*commandWords); i++){
-	 	if(smallString.compare( commandWords[i]) == 0){return COMMANDWORD;}
-	 	} 
-	 for ( i = 0; i < sizeof(ignoredCommandWords)/sizeof(*ignoredCommandWords); i++){
-	 	if(smallString.compare( ignoredCommandWords[i]) == 0){return IGNOREDCOMMANDWORD;}
-	 	} 
-	 for ( i = 0; i < sizeof(commandLines)/sizeof(*commandLines); i++){
-	 	if(smallString.compare( commandLines[i]) == 0){return COMMANDLINE;}
-	 	} 
-	 for ( i = 0; i < sizeof(ignoreCommandLines)/sizeof(*ignoreCommandLines); i++){
-	 	if(smallString.compare( ignoreCommandLines[i]) == 0){return IGNOREDCOMMANDLINE;}
-	 	} 
-	 for ( i = 0; i <  sizeof(commandParagraph)/sizeof(*commandParagraph); i++){
-	 	if(smallString.compare( commandParagraph[i]) == 0){return COMMANDPARAGRAPH;}
-	 	} 
-	 /* IgnoreCommandParagraph */
-	 for ( i = 0; i < sizeof(ignoreCommandParagraphs)/sizeof(*ignoreCommandParagraphs); i++){
-	 	if(smallString.compare( ignoreCommandParagraphs[i]) == 0){return IGNORECOMMANDPARAGRAPH;}
-	 	} 
-	 for ( i = 0; i < sizeof(commandEndCommands)/sizeof(*commandEndCommands); i++){
-	 	if(smallString.compare( commandEndCommands[i]) == 0){return COMMANDENDCOMMAND ;}
-	 	} 
-	 for ( i = 0; i < sizeof(commandWordParagraphs)/sizeof(*commandWordParagraphs); i++){
-	 	if(smallString.compare( commandWordParagraphs[i]) == 0){return COMMANDWORDPARAGRAPH;}
-	 	} 
-	 for ( i = 0; i < sizeof(commandWordLines)/sizeof(*commandWordLines); i++){
-	 	if(smallString.compare( commandWordLines[i]) == 0){return COMMANDWORDLINE ;}
-	 	} 
-	 for ( i = 0; i < sizeof(commandWordOWordOWords)/sizeof(*commandWordOWordOWords); i++){
-	 	if(smallString.compare( commandWordOWordOWords[i]) == 0){return COMMANDWORDOWORDWORD;}
-	 	} 
-	 for ( i = 0; i < sizeof(commandOWords)/sizeof(*commandOWords); i++){
-	 	if(smallString.compare( commandOWords[i]) == 0){return COMMANDOWORD;}
-	 	} 
-	 for ( i = 0; i < sizeof(commandErrorThrowings)/sizeof(*commandErrorThrowings); i++){
-	 	if(smallString.compare( commandErrorThrowings[i]) == 0){return COMMANDERRORTHROW;}
-	 	} 
-	 for ( i = 0; i < sizeof(commandUniques)/sizeof(*commandUniques); i++){
-	 	if(smallString.compare( commandUniques[i]) == 0){return COMMANDUNIQUE;}
-	 	} 
+  }
+  return -1;
+}
 
-	 	return 0;
-	 
- }
+int commandBelongs(string theCommand) {
+  string smallString = StringToLower(theCommand);
+  //cout << " Looking for command " << theCommand << endl;
+  int i = 0;
+  for (i = 0; i < sizeof(simpleCommands) / sizeof(*simpleCommands); i++) {
+    if (smallString.compare(simpleCommands[i]) == 0) {
+      return SIMPLECOMMAND;
+    }
+  }
+  for (i = 0; i < sizeof(ignoredSimpleCommands) / sizeof(*ignoredSimpleCommands); i++) {
+    if (smallString.compare(ignoredSimpleCommands[i]) == 0) {
+      return IGNOREDSIMPLECOMMAND;
+    }
+  }
+  for (i = 0; i < sizeof(commandWords) / sizeof(*commandWords); i++) {
+    if (smallString.compare(commandWords[i]) == 0) {
+      return COMMANDWORD;
+    }
+  }
+  for (i = 0; i < sizeof(ignoredCommandWords) / sizeof(*ignoredCommandWords); i++) {
+    if (smallString.compare(ignoredCommandWords[i]) == 0) {
+      return IGNOREDCOMMANDWORD;
+    }
+  }
+  for (i = 0; i < sizeof(commandLines) / sizeof(*commandLines); i++) {
+    if (smallString.compare(commandLines[i]) == 0) {
+      return COMMANDLINE;
+    }
+  }
+  for (i = 0; i < sizeof(ignoreCommandLines) / sizeof(*ignoreCommandLines); i++) {
+    if (smallString.compare(ignoreCommandLines[i]) == 0) {
+      return IGNOREDCOMMANDLINE;
+    }
+  }
+  for (i = 0; i < sizeof(commandParagraph) / sizeof(*commandParagraph); i++) {
+    if (smallString.compare(commandParagraph[i]) == 0) {
+      return COMMANDPARAGRAPH;
+    }
+  }
+  /* IgnoreCommandParagraph */
+  for (i = 0; i < sizeof(ignoreCommandParagraphs) / sizeof(*ignoreCommandParagraphs); i++) {
+    if (smallString.compare(ignoreCommandParagraphs[i]) == 0) {
+      return IGNORECOMMANDPARAGRAPH;
+    }
+  }
+  for (i = 0; i < sizeof(commandEndCommands) / sizeof(*commandEndCommands); i++) {
+    if (smallString.compare(commandEndCommands[i]) == 0) {
+      return COMMANDENDCOMMAND;
+    }
+  }
+  for (i = 0; i < sizeof(commandWordParagraphs) / sizeof(*commandWordParagraphs); i++) {
+    if (smallString.compare(commandWordParagraphs[i]) == 0) {
+      return COMMANDWORDPARAGRAPH;
+    }
+  }
+  for (i = 0; i < sizeof(commandWordLines) / sizeof(*commandWordLines); i++) {
+    if (smallString.compare(commandWordLines[i]) == 0) {
+      return COMMANDWORDLINE;
+    }
+  }
+  for (i = 0; i < sizeof(commandWordOWordOWords) / sizeof(*commandWordOWordOWords); i++) {
+    if (smallString.compare(commandWordOWordOWords[i]) == 0) {
+      return COMMANDWORDOWORDWORD;
+    }
+  }
+  for (i = 0; i < sizeof(commandOWords) / sizeof(*commandOWords); i++) {
+    if (smallString.compare(commandOWords[i]) == 0) {
+      return COMMANDOWORD;
+    }
+  }
+  for (i = 0; i < sizeof(commandErrorThrowings) / sizeof(*commandErrorThrowings); i++) {
+    if (smallString.compare(commandErrorThrowings[i]) == 0) {
+      return COMMANDERRORTHROW;
+    }
+  }
+  for (i = 0; i < sizeof(commandUniques) / sizeof(*commandUniques); i++) {
+    if (smallString.compare(commandUniques[i]) == 0) {
+      return COMMANDUNIQUE;
+    }
+  }
+
+  return 0;
+
+}
 
  /* isSectionIndicator returns a boolean if the command is a section indicator
   * This is a helper method for finding the end of a paragraph
   * by Doxygen's terms
   */
- int isSectionIndicator(string smallString){
- 	smallString = StringToLower(smallString);
+int isSectionIndicator(string smallString) {
+  smallString = StringToLower(smallString);
 
- 	for (int i = 0; i < sizeof( sectionIndicators)/sizeof(* sectionIndicators); i++){
- 		if( smallString.compare( sectionIndicators[i]) == 0){
- 			return 1;
- 		}
- 	}
- 	return 0;
- }
+  for (int i = 0; i < sizeof(sectionIndicators) / sizeof(*sectionIndicators); i++) {
+    if (smallString.compare(sectionIndicators[i]) == 0) {
+      return 1;
+    }
+  }
+  return 0;
+}
 
 
  /* HELPER METHODS
@@ -216,222 +255,231 @@ string commandUniques[] = {"xrefitem", "ingroup", "par", "headerfile", "overload
  /* Tiny method to compartmentalise the removal of all optional comment fluff such as ///
   * or **** that often occurs before commment blobs.
   */
- int clearFluff(int &startInd, string doxygenString){
-	int startIndex = startInd;
- 	int amountRemoved = 0;
+int clearFluff(int &startInd, string doxygenString) {
+  int startIndex = startInd;
+  int amountRemoved = 0;
 
- 	while(doxygenString[startIndex] == '/'|| doxygenString[startIndex] == '!' || doxygenString[startIndex] == '*'
- 			|| doxygenString[startIndex] == '\n' || doxygenString[startIndex] == ' '|| doxygenString[startIndex] == '\t'){
- 		startIndex++;
- 		amountRemoved++;
- 		}
- 	startInd = startIndex;
- 	return startIndex;
- }
+  while (doxygenString[startIndex] == '/' || doxygenString[startIndex] == '!' || doxygenString[startIndex] == '*'
+	 || doxygenString[startIndex] == '\n' || doxygenString[startIndex] == ' ' || doxygenString[startIndex] == '\t') {
+    startIndex++;
+    amountRemoved++;
+  }
+  startInd = startIndex;
+  return startIndex;
+}
 
  /* Returns the next word ON THE CURRENT LINE ONLY
   * if a new line is encountered, returns a blank string.
   * Updates the index it is given after completion.
   */
 
- string getNextWord(int &startInd, string doxygenString){
-	int startIndex = startInd;
- 	string nextWord;
- 	while (startIndex < doxygenString.length() && (doxygenString[startIndex] == '/'|| doxygenString[startIndex] == ' '
- 		|| doxygenString[startIndex] == '*' || doxygenString[startIndex]== '\n' || doxygenString[startIndex] == '\t'
-		|| doxygenString[startIndex] == '!')){
- 		if(doxygenString[startIndex]== '\n'){ startInd = startIndex; return nextWord;}
- 		startIndex++;
- 		//cout << "Start Index" << startIndex << endl;
- 		}
- 	//cout << doxygenString[startIndex] << endl;
- 	int endIndex = startIndex;
+string getNextWord(int &startInd, string doxygenString) {
+  int startIndex = startInd;
+  string nextWord;
+  while (startIndex < doxygenString.length() && (doxygenString[startIndex] == '/' || doxygenString[startIndex] == ' '
+						 || doxygenString[startIndex] == '*' || doxygenString[startIndex] == '\n' || doxygenString[startIndex] == '\t'
+						 || doxygenString[startIndex] == '!')) {
+    if (doxygenString[startIndex] == '\n') {
+      startInd = startIndex;
+      return nextWord;
+    }
+    startIndex++;
+    //cout << "Start Index" << startIndex << endl;
+  }
+  //cout << doxygenString[startIndex] << endl;
+  int endIndex = startIndex;
 
- 	while (endIndex < doxygenString.length() && (doxygenString[endIndex]!= '\n' && doxygenString[endIndex]!= ' ')){
- 		endIndex++;
- 		//cout << "End Index " << endIndex << endl;
- 		}
- 	nextWord = doxygenString.substr(startIndex, endIndex - startIndex);
- 	startInd = endIndex;
- 	//cout << "Next Word :" << nextWord << ":" << endl;
- 	return nextWord;
- }
+  while (endIndex < doxygenString.length() && (doxygenString[endIndex] != '\n' && doxygenString[endIndex] != ' ')) {
+    endIndex++;
+    //cout << "End Index " << endIndex << endl;
+  }
+  nextWord = doxygenString.substr(startIndex, endIndex - startIndex);
+  startInd = endIndex;
+  //cout << "Next Word :" << nextWord << ":" << endl;
+  return nextWord;
+}
 
  /* Returns the string remaining on a line
   * and moved the index to the NEXT line
   * returns "" if nothing on the current line.
   */
- string getOneLine(int &startInd, string doxygenString){
-	int startIndex = startInd;
- 	while (doxygenString[startIndex] == '/'|| doxygenString[startIndex] == ' '
- 		|| doxygenString[startIndex] == '*' || doxygenString[startIndex]== '\n'
-		|| doxygenString[startIndex] == '!' || doxygenString[startIndex] == '\t'){
- 		if(doxygenString[startIndex]== '\n') return "";
- 		startIndex++;
- 		}
+string getOneLine(int &startInd, string doxygenString) {
+  int startIndex = startInd;
+  while (doxygenString[startIndex] == '/' || doxygenString[startIndex] == ' '
+	 || doxygenString[startIndex] == '*' || doxygenString[startIndex] == '\n' || doxygenString[startIndex] == '!' || doxygenString[startIndex] == '\t') {
+    if (doxygenString[startIndex] == '\n')
+      return "";
+    startIndex++;
+  }
+
+  int endIndex = startIndex;
+  while ((endIndex != doxygenString.length()) && (doxygenString[endIndex] != '\n')) {
+    endIndex++;
+    //cout << doxygenString[endIndex] << "End Index: " << endIndex << endl;
+  }
+  string returnedLine = doxygenString.substr(startIndex, endIndex - startIndex);
+  if (doxygenString[endIndex] == '\n' && (endIndex < doxygenString.length()))
+    endIndex++;
+  startInd = endIndex;
+  return returnedLine;
+}
 
-	int endIndex = startIndex;
- 	while ((endIndex != doxygenString.length())&& (doxygenString[endIndex] != '\n')){
- 		endIndex++;
- 		//cout << doxygenString[endIndex] << "End Index: " << endIndex << endl;
- 		}
- 	string returnedLine = doxygenString.substr(startIndex, endIndex - startIndex);
- 	if (doxygenString[endIndex] == '\n' && (endIndex < doxygenString.length())) endIndex++;
- 	startInd = endIndex;
- 	return returnedLine;
- }
 /* Returns a properly formatted (all doxygen *, //! etc removed)
  * up til ANY command or end of paragraph is encountered. Has all the same issues as
  * getStringTilEndOfParagraph formatting wise.
  */
-string getStringTilCommand(int &startInd, string doxygenString){
-	 if (startInd >= doxygenString.length()) return "";
-	int startIndex = startInd;
-	int endIndex = startInd;
- 	string description;
- 	/* Find the End of the description */
- 	int keepLooping = 1;
- 	int spareIndex = 0;
- 	int counter;
- 	int finalIndex;
- 	while(keepLooping){
- 	 	if(endIndex >= doxygenString.length()){
- 	 			finalIndex = endIndex;
- 	 			keepLooping = 0;
- 	 		}
- 	 	else if (doxygenString[endIndex] == '\n'){
-			//cout << "1 ";
-			counter = endIndex;
-			if ( keepLooping && endIndex < doxygenString.length()-1) {
-				counter++;
-				//cout << "Counter :" << counter << endl;
-				while(keepLooping && endIndex < doxygenString.length() && (doxygenString[counter] == ' ' ||
-				               doxygenString[counter] == '*'|| doxygenString[counter] == '\n'|| doxygenString[counter] == '/'
-				            	   || doxygenString[counter] == '!' || doxygenString[startIndex] == '\t') ){
-									if(doxygenString[counter] == '\n') {
-										//cout << "Blank line found" << endl;
-										keepLooping = 0;
-										finalIndex = counter;}
-									else{ counter++;}
-									}
+string getStringTilCommand(int &startInd, string doxygenString) {
+  if (startInd >= doxygenString.length())
+    return "";
+  int startIndex = startInd;
+  int endIndex = startInd;
+  string description;
+  /* Find the End of the description */
+  int keepLooping = 1;
+  int spareIndex = 0;
+  int counter;
+  int finalIndex;
+  while (keepLooping) {
+    if (endIndex >= doxygenString.length()) {
+      finalIndex = endIndex;
+      keepLooping = 0;
+    } else if (doxygenString[endIndex] == '\n') {
+      //cout << "1 ";
+      counter = endIndex;
+      if (keepLooping && endIndex < doxygenString.length() - 1) {
+	counter++;
+	//cout << "Counter :" << counter << endl;
+	while (keepLooping && endIndex < doxygenString.length() && (doxygenString[counter] == ' ' ||
+								    doxygenString[counter] == '*' || doxygenString[counter] == '\n'
+								    || doxygenString[counter] == '/' || doxygenString[counter] == '!'
+								    || doxygenString[startIndex] == '\t')) {
+	  if (doxygenString[counter] == '\n') {
+	    //cout << "Blank line found" << endl;
+	    keepLooping = 0;
+	    finalIndex = counter;
+	  } else {
+	    counter++;
+	  }
+	}
 
-			}
-			//endIndex = counter;
-		}
- 		else if (doxygenString[endIndex] == '\\' || doxygenString[endIndex] == '@'){
- 			finalIndex = endIndex;
- 			keepLooping = 0;
- 			}
-		else if(endIndex < doxygenString.length() -2
-				&& string("**/").compare(doxygenString.substr(endIndex , endIndex  + 2)) == 0){
-			finalIndex = endIndex;
-			//cout << "3 ";
-			keepLooping = 0;
-		}
- 		if(keepLooping){
- 			//cout << "4 ";
- 			endIndex++;
- 		}
- 	}
- 	//cout << "Done with EndIndex" << endl;
- 	while(doxygenString[startIndex] == '!' || doxygenString[startIndex] == ' '
- 		|| doxygenString[startIndex] == '/' || doxygenString[startIndex] == '*' || doxygenString[startIndex] == '\t') startIndex++;
+      }
+      //endIndex = counter;
+    } else if (doxygenString[endIndex] == '\\' || doxygenString[endIndex] == '@') {
+      finalIndex = endIndex;
+      keepLooping = 0;
+    } else if (endIndex < doxygenString.length() - 2 && string("**/").compare(doxygenString.substr(endIndex, endIndex + 2)) == 0) {
+      finalIndex = endIndex;
+      //cout << "3 ";
+      keepLooping = 0;
+    }
+    if (keepLooping) {
+      //cout << "4 ";
+      endIndex++;
+    }
+  }
+  //cout << "Done with EndIndex" << endl;
+  while (doxygenString[startIndex] == '!' || doxygenString[startIndex] == ' '
+	 || doxygenString[startIndex] == '/' || doxygenString[startIndex] == '*' || doxygenString[startIndex] == '\t')
+    startIndex++;
 
- 	for (int i = startIndex; i < endIndex; i++){
+  for (int i = startIndex; i < endIndex; i++) {
+
+    if (doxygenString[i] == '\n') {
+
+      while ((doxygenString[i] == '\n' || doxygenString[startIndex] == '\t' || doxygenString[i] == ' '
+	      || doxygenString[i] == '*' || doxygenString[i] == '/') && endIndex < doxygenString.length() - 1) {
+	i++;
+      }
+      description.append(" ");
+    }
+    description.push_back(doxygenString[i]);
+    //cout << doxygenString[i];
+  }
+  //if(noisy) cout << "Final Index is: " << finalIndex << endl;
+  startInd = finalIndex;
+  return description;
+}
 
- 		if (doxygenString[i] == '\n') {
 
- 			while ((doxygenString[i] == '\n' || doxygenString[startIndex] == '\t'|| doxygenString[i] == ' '
- 				|| doxygenString[i] == '*' || doxygenString[i] == '/')&& endIndex < doxygenString.length() - 1){
- 				i++;
- 				}
- 			description.append(" ");
- 		}
- 		description.push_back(doxygenString[i]);
- 		//cout << doxygenString[i];
- 	}
- 	//if(noisy) cout << "Final Index is: " << finalIndex << endl;
- 	startInd = finalIndex;
- 	return description;
- }
- 
- 
 /* Returns a Paragraph- defined in Doxygen to be a paragraph of text
  * seperate by either a structural command or a blank line
  * This method is VERY messy currently
  */
  //TODO fix getStringTilEndOfParagraph to be more forgiving, work on ' ' characters
- string getStringTilEndOfParagraph(int &startInd, string doxygenString){
-	 if (startInd >= doxygenString.length()) return "";
-	int startIndex = startInd;
-	int endIndex = startInd;
- 	string description;
- 	/* Find the End of the description */
- 	int keepLooping = 1;
- 	int spareIndex = 0;
- 	int counter;
- 	int finalIndex;
- 	while(keepLooping){
- 		if(endIndex >= doxygenString.length()){
- 			finalIndex = endIndex;
- 			keepLooping = 0;
- 		}
- 		else if (doxygenString[endIndex] == '\n'){
-			//cout << "1 ";
-			counter = endIndex;
-			if ( keepLooping && endIndex < doxygenString.length()-1) {
-				counter++;
-				//cout << "Counter :" << counter << endl;
-				while(keepLooping && endIndex < doxygenString.length() && (doxygenString[counter] == ' ' ||
-				               doxygenString[counter] == '*'|| doxygenString[startIndex] == '\t' || doxygenString[counter] == '\n'|| doxygenString[counter] == '/'
-				            	   || doxygenString[counter] == '!') ){
-									if(doxygenString[counter] == '\n') {
-										//cout << "Blank line found" << endl;
-										keepLooping = 0;
-										finalIndex = counter;}
-									else{ counter++;}
-									}
+string getStringTilEndOfParagraph(int &startInd, string doxygenString) {
+  if (startInd >= doxygenString.length())
+    return "";
+  int startIndex = startInd;
+  int endIndex = startInd;
+  string description;
+  /* Find the End of the description */
+  int keepLooping = 1;
+  int spareIndex = 0;
+  int counter;
+  int finalIndex;
+  while (keepLooping) {
+    if (endIndex >= doxygenString.length()) {
+      finalIndex = endIndex;
+      keepLooping = 0;
+    } else if (doxygenString[endIndex] == '\n') {
+      //cout << "1 ";
+      counter = endIndex;
+      if (keepLooping && endIndex < doxygenString.length() - 1) {
+	counter++;
+	//cout << "Counter :" << counter << endl;
+	while (keepLooping && endIndex < doxygenString.length() && (doxygenString[counter] == ' ' ||
+								    doxygenString[counter] == '*' || doxygenString[startIndex] == '\t'
+								    || doxygenString[counter] == '\n' || doxygenString[counter] == '/'
+								    || doxygenString[counter] == '!')) {
+	  if (doxygenString[counter] == '\n') {
+	    //cout << "Blank line found" << endl;
+	    keepLooping = 0;
+	    finalIndex = counter;
+	  } else {
+	    counter++;
+	  }
+	}
 
-			}
-			//endIndex = counter;
-		}
- 		//todo this fix for not immediately exciting while parsing a paragraph seems somewhat cheap
- 		else if (endIndex != startInd && doxygenString[endIndex] == '\\' || doxygenString[endIndex] == '@'){
-			spareIndex = endIndex +1;
-			
- 			if (isSectionIndicator(getNextWord(spareIndex, doxygenString))) {
- 				keepLooping = 0;
- 				finalIndex = endIndex;}
- 			}
-		else if(endIndex < doxygenString.length() - 1
-				&& string("*/").compare(doxygenString.substr(endIndex , endIndex  + 1)) == 0){
-			keepLooping = 0;
-			finalIndex = endIndex;
-		}
- 		if(keepLooping){
- 			endIndex++;
- 		}
- 	}
- 	//cout << "Done with EndIndex" << endl;
- 	while(doxygenString[startIndex] == '!' || doxygenString[startIndex] == ' ' || doxygenString[startIndex] == '\t'
- 		|| doxygenString[startIndex] == '/' || doxygenString[startIndex] == '*') startIndex++;
+      }
+      //endIndex = counter;
+    }
+    //todo this fix for not immediately exciting while parsing a paragraph seems somewhat cheap
+    else if (endIndex != startInd && doxygenString[endIndex] == '\\' || doxygenString[endIndex] == '@') {
+      spareIndex = endIndex + 1;
 
- 	for (int i = startIndex; i < endIndex; i++){
+      if (isSectionIndicator(getNextWord(spareIndex, doxygenString))) {
+	keepLooping = 0;
+	finalIndex = endIndex;
+      }
+    } else if (endIndex < doxygenString.length() - 1 && string("*/").compare(doxygenString.substr(endIndex, endIndex + 1)) == 0) {
+      keepLooping = 0;
+      finalIndex = endIndex;
+    }
+    if (keepLooping) {
+      endIndex++;
+    }
+  }
+  //cout << "Done with EndIndex" << endl;
+  while (doxygenString[startIndex] == '!' || doxygenString[startIndex] == ' ' || doxygenString[startIndex] == '\t'
+	 || doxygenString[startIndex] == '/' || doxygenString[startIndex] == '*')
+    startIndex++;
 
- 		if (doxygenString[i] == '\n') {
+  for (int i = startIndex; i < endIndex; i++) {
 
- 			while ((doxygenString[i] == '\n' || doxygenString[startIndex] == '\t' || doxygenString[i] == ' ' ||doxygenString[startIndex] == '!'
- 				|| doxygenString[i] == '*' || doxygenString[i] == '/')&& endIndex < doxygenString.length() - 1){
- 				i++;
- 				}
- 			description.append(" ");
- 		}
- 		description.push_back(doxygenString[i]);
- 		//cout << doxygenString[i];
- 	}
- 	startInd = finalIndex;
- 	return description;
- }
+    if (doxygenString[i] == '\n') {
+
+      while ((doxygenString[i] == '\n' || doxygenString[startIndex] == '\t' || doxygenString[i] == ' ' || doxygenString[startIndex] == '!'
+	      || doxygenString[i] == '*' || doxygenString[i] == '/') && endIndex < doxygenString.length() - 1) {
+	i++;
+      }
+      description.append(" ");
+    }
+    description.push_back(doxygenString[i]);
+    //cout << doxygenString[i];
+  }
+  startInd = finalIndex;
+  return description;
+}
 
  /* This method is for a specific form of doxygen command
   * that begins with a \command and ends in \endcommand
@@ -440,263 +488,280 @@ string getStringTilCommand(int &startInd, string doxygenString){
   * currently this method does NOT process what is in between the two commands
   */
  //TODO Make progressTilCommand return a formatted string
- int progressTilEndCommand(string theCommand, int &startInd, string doxygenString){
- 	int endIndex = startInd;
- 	while (endIndex < doxygenString.length()){
- 		if (doxygenString[endIndex] == '\\' || doxygenString[endIndex] == '@'){
- 			//cout << doxygenString.substr(endIndex + 1 , theCommand.length())<< endl;
- 			if (theCommand.compare(doxygenString.substr(endIndex + 1 , theCommand.length())) == 0){
- 				startInd = endIndex + theCommand.length() + 1;
- 				return 1;
- 			}
- 		}
- 		endIndex++;
- 	}
- 	//End command not found
- 	return 0;
- }
+int progressTilEndCommand(string theCommand, int &startInd, string doxygenString) {
+  int endIndex = startInd;
+  while (endIndex < doxygenString.length()) {
+    if (doxygenString[endIndex] == '\\' || doxygenString[endIndex] == '@') {
+      //cout << doxygenString.substr(endIndex + 1 , theCommand.length())<< endl;
+      if (theCommand.compare(doxygenString.substr(endIndex + 1, theCommand.length())) == 0) {
+	startInd = endIndex + theCommand.length() + 1;
+	return 1;
+      }
+    }
+    endIndex++;
+  }
+  //End command not found
+  return 0;
+}
 
  /* A specialty method for commands such as \arg that end at the end of a paragraph OR when another \arg is encountered
   */
- 
- string getStringTilAnyCommand(string theCommand, int &startInd, string doxygenString){
-	 if (startInd >= doxygenString.length()) return "";
-		int startIndex = startInd;
-		int endIndex = startInd;
-	 	string description;
-	 	/* Find the End of the description */
-	 	int keepLooping = 1;
-	 	int spareIndex = 0;
-	 	int counter;
-	 	int finalIndex;
-	 	while(keepLooping){
-	 		if(endIndex >= theCommand.length()){
-	 			finalIndex = endIndex;
-	 			keepLooping = 0;
-	 		}
-	 		else if (doxygenString[endIndex] == '\n'){
-				//cout << "1 ";
-				counter = endIndex;
-				if ( keepLooping && endIndex < doxygenString.length()-1) {
-					counter++;
-					//cout << "Counter :" << counter << endl;
-					while(keepLooping && endIndex < doxygenString.length() && (doxygenString[counter] == ' ' ||
-					               doxygenString[counter] == '*'|| doxygenString[counter] == '\n'|| doxygenString[counter] == '/'
-					            	   || doxygenString[counter] == '!' || doxygenString[startIndex] == '\t') ){
-										if(doxygenString[counter] == '\n') {
-											//cout << "Blank line found" << endl;
-											keepLooping = 0;
-											finalIndex = counter;}
-										else{ counter++;}
-										}
 
-				}
-				//endIndex = counter;
-			}
-	 		else if (doxygenString[endIndex] == '\\' || doxygenString[endIndex] == '@'){
-	 			//cout << "2 ";
-				spareIndex = endIndex;
-	 			if (endIndex + theCommand.length() < theCommand.length() 
-	 					&& theCommand.compare(doxygenString.substr(endIndex, theCommand.length())) == 0) keepLooping = 0;
-	 			}
-			else if(endIndex < doxygenString.length() - 1
-					&& string("*/").compare(doxygenString.substr(endIndex , endIndex  + 1)) == 0){
-				//cout << "3 ";
-				keepLooping = 0;
-			}
-	 		if(keepLooping){
-	 			//cout << "4 ";
-	 			endIndex++;
-	 		}
-	 	}
-	 	//cout << "Done with EndIndex" << endl;
-	 	while(doxygenString[startIndex] == '!' || doxygenString[startIndex] == ' '
-	 		|| doxygenString[startIndex] == '/' || doxygenString[startIndex] == '*' || doxygenString[startIndex] == '\t') startIndex++;
+string getStringTilAnyCommand(string theCommand, int &startInd, string doxygenString) {
+  if (startInd >= doxygenString.length())
+    return "";
+  int startIndex = startInd;
+  int endIndex = startInd;
+  string description;
+  /* Find the End of the description */
+  int keepLooping = 1;
+  int spareIndex = 0;
+  int counter;
+  int finalIndex;
+  while (keepLooping) {
+    if (endIndex >= theCommand.length()) {
+      finalIndex = endIndex;
+      keepLooping = 0;
+    } else if (doxygenString[endIndex] == '\n') {
+      //cout << "1 ";
+      counter = endIndex;
+      if (keepLooping && endIndex < doxygenString.length() - 1) {
+	counter++;
+	//cout << "Counter :" << counter << endl;
+	while (keepLooping && endIndex < doxygenString.length() && (doxygenString[counter] == ' ' ||
+								    doxygenString[counter] == '*' || doxygenString[counter] == '\n'
+								    || doxygenString[counter] == '/' || doxygenString[counter] == '!'
+								    || doxygenString[startIndex] == '\t')) {
+	  if (doxygenString[counter] == '\n') {
+	    //cout << "Blank line found" << endl;
+	    keepLooping = 0;
+	    finalIndex = counter;
+	  } else {
+	    counter++;
+	  }
+	}
 
-	 	for (int i = startIndex; i < endIndex; i++){
+      }
+      //endIndex = counter;
+    } else if (doxygenString[endIndex] == '\\' || doxygenString[endIndex] == '@') {
+      //cout << "2 ";
+      spareIndex = endIndex;
+      if (endIndex + theCommand.length() < theCommand.length()
+	  && theCommand.compare(doxygenString.substr(endIndex, theCommand.length())) == 0)
+	keepLooping = 0;
+    } else if (endIndex < doxygenString.length() - 1 && string("*/").compare(doxygenString.substr(endIndex, endIndex + 1)) == 0) {
+      //cout << "3 ";
+      keepLooping = 0;
+    }
+    if (keepLooping) {
+      //cout << "4 ";
+      endIndex++;
+    }
+  }
+  //cout << "Done with EndIndex" << endl;
+  while (doxygenString[startIndex] == '!' || doxygenString[startIndex] == ' '
+	 || doxygenString[startIndex] == '/' || doxygenString[startIndex] == '*' || doxygenString[startIndex] == '\t')
+    startIndex++;
 
-	 		if (doxygenString[i] == '\n') {
+  for (int i = startIndex; i < endIndex; i++) {
 
-	 			while ((doxygenString[i] == '\n' || doxygenString[i] == ' ' || doxygenString[startIndex] == '\t'
-	 				|| doxygenString[i] == '*' || doxygenString[i] == '/')&& endIndex < doxygenString.length() - 1){
-	 				i++;
-	 				}
-	 			description.append(" ");
-	 		}
-	 		description.push_back(doxygenString[i]);
-	 		//cout << doxygenString[i];
-	 	}
-	 	startInd = finalIndex;
-	 	return description;
- }
+    if (doxygenString[i] == '\n') {
+
+      while ((doxygenString[i] == '\n' || doxygenString[i] == ' ' || doxygenString[startIndex] == '\t'
+	      || doxygenString[i] == '*' || doxygenString[i] == '/') && endIndex < doxygenString.length() - 1) {
+	i++;
+      }
+      description.append(" ");
+    }
+    description.push_back(doxygenString[i]);
+    //cout << doxygenString[i];
+  }
+  startInd = finalIndex;
+  return description;
+}
 
 
  /* prints the parse tree
   *
   */
- void printTree(){
+void printTree() {
 
-		list<DoxygenEntity>::iterator p = rootList.begin();
-		while (p != rootList.end()){
-			(*p).printEntity(0);
-			p++;
-		}
+  list < DoxygenEntity >::iterator p = rootList.begin();
+  while (p != rootList.end()) {
+    (*p).printEntity(0);
+    p++;
+  }
 
- }
- 
- 
- 
- list<DoxygenEntity> parse(int startInd, string doxygenString){
- 	string currWord;
- 	int startIndex = startInd;
- 	int savedIndex;
- 	list <DoxygenEntity> aNewList;
- 	int endIndex = doxygenString.length();
- 	int currCommand;
- 	while (startIndex < endIndex){
- 		savedIndex = startIndex;
- 		currWord = getNextWord(startIndex, doxygenString);
- 		if(noisy) cout << "Parsing for phrase starting in:" << currWord << endl;
- 		if(currWord == ""){
- 			if (startIndex < endIndex) startIndex++;
- 		}
- 		else if(currWord[0] == '\\' || currWord[0] == '@'){
- 			currWord = currWord.substr(1, currWord.length() - 1);
- 			currCommand = findCommand(currWord);
- 			if (currCommand < 0 ){ if(noisy) cout << "BAD COMMAND: " << currWord << endl;}
- 				//cout << "Command: " << currWord << " " << currCommand << endl;
- 			else addCommand(currWord, startIndex, aNewList, doxygenString);
- 		}
- 		else{
- 			startIndex = savedIndex;
-			addCommand(string("plainstd::string"), startIndex, aNewList, doxygenString);
+}
 
- 		}
- 	}
 
- 	return aNewList;
- }
- 
+
+list < DoxygenEntity > parse(int startInd, string doxygenString) {
+  string currWord;
+  int startIndex = startInd;
+  int savedIndex;
+  list < DoxygenEntity > aNewList;
+  int endIndex = doxygenString.length();
+  int currCommand;
+  while (startIndex < endIndex) {
+    savedIndex = startIndex;
+    currWord = getNextWord(startIndex, doxygenString);
+    if (noisy)
+      cout << "Parsing for phrase starting in:" << currWord << endl;
+    if (currWord == "") {
+      if (startIndex < endIndex)
+	startIndex++;
+    } else if (currWord[0] == '\\' || currWord[0] == '@') {
+      currWord = currWord.substr(1, currWord.length() - 1);
+      currCommand = findCommand(currWord);
+      if (currCommand < 0) {
+	if (noisy)
+	  cout << "BAD COMMAND: " << currWord << endl;
+      }
+      //cout << "Command: " << currWord << " " << currCommand << endl;
+      else
+	addCommand(currWord, startIndex, aNewList, doxygenString);
+    } else {
+      startIndex = savedIndex;
+      addCommand(string("plainstd::string"), startIndex, aNewList, doxygenString);
+
+    }
+  }
+
+  return aNewList;
+}
+
  /*  Method for Adding a Simple Command
   * Format: @command
   * Plain commands, such as newline etc, they contain no other data
   *  \n \\ \@ \& \$ \# \< \> \%
   */
-  int addSimpleCommand(string theCommand, int &startInd, list <DoxygenEntity> &doxyList, string doxygenString){
-	 
-		if (noisy) cout << "Parsing " << theCommand << endl;
-		doxyList.push_back(DoxygenEntity(theCommand));
-		return 1;
- }
-  
+int addSimpleCommand(string theCommand, int &startInd, list < DoxygenEntity > &doxyList, string doxygenString) {
+
+  if (noisy)
+    cout << "Parsing " << theCommand << endl;
+  doxyList.push_back(DoxygenEntity(theCommand));
+  return 1;
+}
+
   /* NOT INCLUDED Simple Commands
    * Format: @command
    * Plain commands, such as newline etc, they contain no other data
    */
-  int ignoreSimpleCommand(string theCommand, int &startInd, list <DoxygenEntity> &doxyList, string doxygenString){
-	 
-		if (noisy) cout << "Not Adding " << theCommand << endl;
-		return 1;
- }
-  
+int ignoreSimpleCommand(string theCommand, int &startInd, list < DoxygenEntity > &doxyList, string doxygenString) {
+
+  if (noisy)
+    cout << "Not Adding " << theCommand << endl;
+  return 1;
+}
+
   /* CommandWord
    * Format: @command <word>
    * Commands with a single WORD after then such as @b
    * "a", "b", "c", "e", "em", "p", "def", "enum", "example", "package", 
    * "relates", "namespace", "relatesalso","anchor", "dontinclude", "include", "includelineno"
    */
-  int addCommandWord(string theCommand, int &startInd, list <DoxygenEntity> &doxyList, string doxygenString){
-	if (noisy) cout << "Parsing " << theCommand << endl;
-	string name = getNextWord(startInd, doxygenString);
-	if (!name.empty()){ 
-		doxyList.push_back(DoxygenEntity(theCommand, name));
-		return 1;
-	}
-	else cout << "No word followed " << theCommand <<  " command. Not added" << endl;
-	return 0;
- }
+int addCommandWord(string theCommand, int &startInd, list < DoxygenEntity > &doxyList, string doxygenString) {
+  if (noisy)
+    cout << "Parsing " << theCommand << endl;
+  string name = getNextWord(startInd, doxygenString);
+  if (!name.empty()) {
+    doxyList.push_back(DoxygenEntity(theCommand, name));
+    return 1;
+  } else
+    cout << "No word followed " << theCommand << " command. Not added" << endl;
+  return 0;
+}
+
   /* NOT INCLUDED CommandWord
    * Format: @command <word>
    * Commands with a single WORD after then such as @b
    * "copydoc", "copybrief", "copydetails", "verbinclude", "htmlinclude"
    */
-  int ignoreCommandWord(string theCommand, int &startInd, list <DoxygenEntity> &doxyList, string doxygenString){
-	if (noisy) cout << "Not Adding " << theCommand << endl;
-	string name = getNextWord(startInd, doxygenString);
-	if (!name.empty()){ 
-		return 1;
-	}
-	else cout << "WARNING: No word followed " << theCommand <<  " command." << endl;
-	return 0;
- }
-  
+int ignoreCommandWord(string theCommand, int &startInd, list < DoxygenEntity > &doxyList, string doxygenString) {
+  if (noisy)
+    cout << "Not Adding " << theCommand << endl;
+  string name = getNextWord(startInd, doxygenString);
+  if (!name.empty()) {
+    return 1;
+  } else
+    cout << "WARNING: No word followed " << theCommand << " command." << endl;
+  return 0;
+}
+
   /* CommandLine
    * Format: @command (line)
    * Commands with a single LINE after then such as @var
    * "addindex", "fn", "name", "line", "var", "skipline", "typedef", "skip", "until", "property"
    */
-  int addCommandLine(string theCommand, int &startInd, list <DoxygenEntity> &doxyList, string doxygenString){
-	if (noisy) cout << "Parsing " << theCommand << endl;
-	string line = getOneLine(startInd, doxygenString);
-	if(!line.empty()){
-		int placement = 0;
-		list <DoxygenEntity> aNewList;
-		aNewList =  parse(placement, line);
-		doxyList.push_back( DoxygenEntity(theCommand, aNewList));
-		return 1;
-		}
-	else cout << "No line followed " << theCommand <<  " command. Not added" << endl;
-	return 0;
- }
-  
+int addCommandLine(string theCommand, int &startInd, list < DoxygenEntity > &doxyList, string doxygenString) {
+  if (noisy)
+    cout << "Parsing " << theCommand << endl;
+  string line = getOneLine(startInd, doxygenString);
+  if (!line.empty()) {
+    int placement = 0;
+    list < DoxygenEntity > aNewList;
+    aNewList = parse(placement, line);
+    doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+    return 1;
+  } else
+    cout << "No line followed " << theCommand << " command. Not added" << endl;
+  return 0;
+}
+
   /* NOT INCLUDED CommandLine
    * Format: @command (line)
    * Commands with a single LINE after then such as @var
    * 
    */
-  int ignoreCommandLine(string theCommand, int &startInd, list <DoxygenEntity> &doxyList, string doxygenString){
-	if (noisy) cout << "Not Adding " << theCommand << endl;
-	string line = getOneLine(startInd, doxygenString);
-	if(!line.empty()){
-		return 1;
-		}
-	else cout << "WARNING: No line followed " << theCommand <<  " command." << endl;
-	return 0;
- }
-  
+int ignoreCommandLine(string theCommand, int &startInd, list < DoxygenEntity > &doxyList, string doxygenString) {
+  if (noisy)
+    cout << "Not Adding " << theCommand << endl;
+  string line = getOneLine(startInd, doxygenString);
+  if (!line.empty()) {
+    return 1;
+  } else
+    cout << "WARNING: No line followed " << theCommand << " command." << endl;
+  return 0;
+}
+
   /* CommandParagraph
    * Format: @command {paragraph}
    * Commands with a single paragraph after then such as @return
    * "return", "remarks", "since", "test", "sa", "see", "pre", "post", "details", "invariant", 
    * "deprecated", "date", "note", "warning", "version", "todo", "bug", "attention", "brief", "arg", "author"
    */
-  int addCommandParagraph(string theCommand, int &startInd, list <DoxygenEntity> &doxyList, string doxygenString){
-	if (noisy) cout << "Parsing " << theCommand << endl;
-	string restOfParagraph = getStringTilEndOfParagraph(startInd, doxygenString);
-	if(!restOfParagraph.empty()){
-		int placement = 0;
-		list <DoxygenEntity> aNewList;
-		aNewList =  parse(placement, restOfParagraph);
-		doxyList.push_back( DoxygenEntity(theCommand, aNewList));
-		return 1;
-		}
-	else cout << "No line followed " << theCommand <<  " command. Not added" << endl;
-	return 0;
- }
+int addCommandParagraph(string theCommand, int &startInd, list < DoxygenEntity > &doxyList, string doxygenString) {
+  if (noisy)
+    cout << "Parsing " << theCommand << endl;
+  string restOfParagraph = getStringTilEndOfParagraph(startInd, doxygenString);
+  if (!restOfParagraph.empty()) {
+    int placement = 0;
+    list < DoxygenEntity > aNewList;
+    aNewList = parse(placement, restOfParagraph);
+    doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+    return 1;
+  } else
+    cout << "No line followed " << theCommand << " command. Not added" << endl;
+  return 0;
+}
+
   /* CommandParagraph
    * Format: @command {paragraph}
    * Commands with a single LINE after then such as @var
    * 
    */
-  int ignoreCommandParagraph(string theCommand, int &startInd, list <DoxygenEntity> &doxyList, string doxygenString){
-	if (noisy) cout << "Not Adding " << theCommand << endl;
-	string restOfParagraph = getStringTilEndOfParagraph(startInd, doxygenString);
-	if(!restOfParagraph.empty()){
-		return 1;
-		}
-	else cout << "WARNING: No line followed " << theCommand <<  " command." << endl;
-	return 0;
- }
+int ignoreCommandParagraph(string theCommand, int &startInd, list < DoxygenEntity > &doxyList, string doxygenString) {
+  if (noisy)
+    cout << "Not Adding " << theCommand << endl;
+  string restOfParagraph = getStringTilEndOfParagraph(startInd, doxygenString);
+  if (!restOfParagraph.empty()) {
+    return 1;
+  } else
+    cout << "WARNING: No line followed " << theCommand << " command." << endl;
+  return 0;
+}
+
   /* Command EndCommand
    * Format: @command and ends at @endcommand
    * Commands that take in a block of text such as @code
@@ -704,221 +769,235 @@ string getStringTilCommand(int &startInd, string doxygenString){
    * "verbatim", "xmlonly", "cond", "if", "ifnot", "link"
    * Returns 1 if success, 0 if the endcommand is never encountered.
    */
-  
-  int ignoreCommandEndCommand(string theCommand, int &startInd, list <DoxygenEntity> &doxyList, string doxygenString){
-	  if (noisy) cout << "Not Adding " << theCommand << endl;
-	  return progressTilEndCommand( "end" + theCommand, startInd, doxygenString);
-	  
-  }
-  
+
+int ignoreCommandEndCommand(string theCommand, int &startInd, list < DoxygenEntity > &doxyList, string doxygenString) {
+  if (noisy)
+    cout << "Not Adding " << theCommand << endl;
+  return progressTilEndCommand("end" + theCommand, startInd, doxygenString);
+
+}
+
   /* CommandWordParagraph
    * Format: @command <word> {paragraph}
    * Commands such as param
    * "param", "tparam", "throw", "retval", "exception"
    */
-  int addCommandWordParagraph(string theCommand, int &startInd, list <DoxygenEntity> &doxyList, string doxygenString){
-	if (noisy) cout << "Parsing " << theCommand << endl;
-	string name = getNextWord(startInd, doxygenString);
-	if (name.empty()){ 
-		cout << "No word followed " << theCommand <<  " command. Not added" << endl;
-		return 0;
-		}
-	string restOfParagraph = getStringTilEndOfParagraph(startInd, doxygenString);
-	int placement = 0;
-	if(!restOfParagraph.empty()){
-		list <DoxygenEntity> aNewList;
-		aNewList =  parse(placement, restOfParagraph);
-		aNewList.push_front(DoxygenEntity("plainstd::string", name));
-		doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-		return 1;
-		}
-	else cout << "No paragraph followed " << theCommand <<  " command. Not added" << endl;
-	return 0;
+int addCommandWordParagraph(string theCommand, int &startInd, list < DoxygenEntity > &doxyList, string doxygenString) {
+  if (noisy)
+    cout << "Parsing " << theCommand << endl;
+  string name = getNextWord(startInd, doxygenString);
+  if (name.empty()) {
+    cout << "No word followed " << theCommand << " command. Not added" << endl;
+    return 0;
   }
+  string restOfParagraph = getStringTilEndOfParagraph(startInd, doxygenString);
+  int placement = 0;
+  if (!restOfParagraph.empty()) {
+    list < DoxygenEntity > aNewList;
+    aNewList = parse(placement, restOfParagraph);
+    aNewList.push_front(DoxygenEntity("plainstd::string", name));
+    doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+    return 1;
+  } else
+    cout << "No paragraph followed " << theCommand << " command. Not added" << endl;
+  return 0;
+}
+
   /* CommandWordLine
    * Format: @command <word> (line)
    * Commands such as param
    * "page", "subsection", "subsubsection", "section", "paragraph", "defgroup"
    */
-  int addCommandWordLine(string theCommand, int &startInd, list <DoxygenEntity> &doxyList, string doxygenString){
-	if (noisy) cout << "Parsing " << theCommand << endl;
-	string name = getNextWord(startInd, doxygenString);
-	if (name.empty()){ 
-		cout << "No word followed " << theCommand <<  " command. Not added" << endl;
-		return 0;
-		}
-	string restOfLine = getStringTilEndOfParagraph(startInd, doxygenString);
-	int placement = 0;
-	if(!restOfLine.empty()){
-		list <DoxygenEntity> aNewList;
-		aNewList =  parse(placement, restOfLine);
-		aNewList.push_front(DoxygenEntity("plainstd::string", name));
-		doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-		return 1;
-		}
-	else cout << "No line followed " << theCommand <<  " command. Not added" << endl;
-	return 0;
+int addCommandWordLine(string theCommand, int &startInd, list < DoxygenEntity > &doxyList, string doxygenString) {
+  if (noisy)
+    cout << "Parsing " << theCommand << endl;
+  string name = getNextWord(startInd, doxygenString);
+  if (name.empty()) {
+    cout << "No word followed " << theCommand << " command. Not added" << endl;
+    return 0;
   }
-  
+  string restOfLine = getStringTilEndOfParagraph(startInd, doxygenString);
+  int placement = 0;
+  if (!restOfLine.empty()) {
+    list < DoxygenEntity > aNewList;
+    aNewList = parse(placement, restOfLine);
+    aNewList.push_front(DoxygenEntity("plainstd::string", name));
+    doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+    return 1;
+  } else
+    cout << "No line followed " << theCommand << " command. Not added" << endl;
+  return 0;
+}
+
   /* Command Word Optional Word Optional Word
    * Format: @command <word> [<header-file>] [<header-name>]
    * Commands such as class
    * "category", "class", "protocol", "interface", "struct", "union"
    */
-  int addCommandWordOWordOWord(string theCommand, int &startInd, list <DoxygenEntity> &doxyList, string doxygenString){
-	if (noisy) cout << "Parsing " << theCommand << endl;
-	string name = getNextWord(startInd, doxygenString);
-	if (name.empty()){ 
-			cout << "No word followed " << theCommand <<  " command. Not added" << endl;
-			return 0;
-			}
-	string headerfile = getNextWord(startInd, doxygenString);
-	string headername = getNextWord(startInd, doxygenString);
-	list <DoxygenEntity> aNewList;
-	aNewList.push_back(DoxygenEntity("plainstd::string", name));
-	if (!headerfile.empty()) aNewList.push_back(DoxygenEntity("plainstd::string", headerfile));
-	if (!headername.empty()) aNewList.push_back(DoxygenEntity("plainstd::string", headername));
-	doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-	return 1;
+int addCommandWordOWordOWord(string theCommand, int &startInd, list < DoxygenEntity > &doxyList, string doxygenString) {
+  if (noisy)
+    cout << "Parsing " << theCommand << endl;
+  string name = getNextWord(startInd, doxygenString);
+  if (name.empty()) {
+    cout << "No word followed " << theCommand << " command. Not added" << endl;
+    return 0;
   }
-  
+  string headerfile = getNextWord(startInd, doxygenString);
+  string headername = getNextWord(startInd, doxygenString);
+  list < DoxygenEntity > aNewList;
+  aNewList.push_back(DoxygenEntity("plainstd::string", name));
+  if (!headerfile.empty())
+    aNewList.push_back(DoxygenEntity("plainstd::string", headerfile));
+  if (!headername.empty())
+    aNewList.push_back(DoxygenEntity("plainstd::string", headername));
+  doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+  return 1;
+}
+
   /* Command Optional Word
    * Format: @command [<word>]
    * Commands such as dir
    * "dir", "file", "cond"
    */
-  int addCommandOWord(string theCommand, int &startInd, list <DoxygenEntity> &doxyList, string doxygenString){
-	if (noisy) cout << "Parsing " << theCommand << endl;
-	string name = getNextWord(startInd, doxygenString);
-	doxyList.push_back(DoxygenEntity(theCommand, name));
-	return 1; 
-  }
-  
+int addCommandOWord(string theCommand, int &startInd, list < DoxygenEntity > &doxyList, string doxygenString) {
+  if (noisy)
+    cout << "Parsing " << theCommand << endl;
+  string name = getNextWord(startInd, doxygenString);
+  doxyList.push_back(DoxygenEntity(theCommand, name));
+  return 1;
+}
+
  /* The actual "meat" of the doxygen parser. This is not yet fully implemented
   * with my current design- however the skeletal outline is contained in
   * the file Skeleton
   */
 
 
- int addCommand(string commandString, int &startInd, list <DoxygenEntity> &doxyList, string doxygenString){
-	 string theCommand = StringToLower(commandString);
-	 string voidArray[] = {""};
-	 	/* @command */
+int addCommand(string commandString, int &startInd, list < DoxygenEntity > &doxyList, string doxygenString) {
+  string theCommand = StringToLower(commandString);
+  string voidArray[] = { "" };
+  /* @command */
 
-	 
-	 if (theCommand.compare("plainstd::string") == 0){
-	 		string nextPhrase = getStringTilCommand(startInd, doxygenString);
-	 		if (noisy) cout << "Parsing plain string :" << nextPhrase << endl;
-	 		doxyList.push_back(DoxygenEntity("plainstd::string", nextPhrase ));
-	 		return 1;
-	 }
-	 int commandNumber = commandBelongs(theCommand);
-	 if (commandNumber == SIMPLECOMMAND){
-	 	return addSimpleCommand(theCommand, startInd,doxyList, doxygenString);
-	 	}
-	 if (commandNumber == IGNOREDSIMPLECOMMAND){
-	 	return ignoreSimpleCommand(theCommand, startInd,doxyList, doxygenString);
-	 	}
-	 if (commandNumber == COMMANDWORD){
-	 	return addCommandWord(theCommand, startInd,doxyList, doxygenString);
-	 	}
-	 if (commandNumber == IGNOREDCOMMANDWORD){
-	 	return ignoreCommandWord(theCommand, startInd,doxyList, doxygenString);
-	 	}
-	 if (commandNumber == COMMANDLINE ){
-	 	return addCommandLine(theCommand, startInd,doxyList, doxygenString);
-	 	}
-	 if (commandNumber == IGNOREDCOMMANDLINE ){
-	 	return ignoreCommandLine(theCommand, startInd,doxyList, doxygenString);
-	 	}
-	 if (commandNumber == COMMANDPARAGRAPH){
-	 	return addCommandParagraph(theCommand, startInd,doxyList, doxygenString);
-	 	}
-	 if (commandNumber == IGNORECOMMANDPARAGRAPH){
-	 	return ignoreCommandParagraph(theCommand, startInd,doxyList, doxygenString);
-	 	}
-	 if (commandNumber == COMMANDENDCOMMAND){
-	 	return ignoreCommandEndCommand(theCommand, startInd,doxyList, doxygenString);
-	 	}
-	 if (commandNumber == COMMANDWORDPARAGRAPH){
-	 	return addCommandWordParagraph(theCommand, startInd,doxyList, doxygenString);
-	 	}
-	 if (commandNumber == COMMANDWORDLINE){
-	 	return addCommandWordLine(theCommand, startInd,doxyList, doxygenString);
-	 	}
-	 if (commandNumber == COMMANDWORDOWORDWORD){
-	 	return addCommandWordOWordOWord(theCommand, startInd,doxyList, doxygenString);
-	 	}
-	 if (commandNumber == COMMANDOWORD){
-	 	return addCommandOWord(theCommand, startInd,doxyList, doxygenString);
-	 	}
-	 if (commandNumber == COMMANDERRORTHROW){
-	 	return 0;
-	 	}
-	 if (commandNumber == COMMANDUNIQUE){
-	 	return 0;
-	 	}
-	 	
-	 	return 0;
- }
- 
- int weirdTest(){
-	 string doxygenString = "this is a test.";
-	 string restOfParagraph;
-	 int startIndex = 0;
-	 restOfParagraph = getStringTilEndOfParagraph(startIndex , doxygenString);
-	 cout << restOfParagraph<< " " << startIndex << endl;
-	 
-	 startIndex = 0;
-	 restOfParagraph = getStringTilCommand(startIndex, doxygenString);
-	 cout << restOfParagraph<< " " << startIndex << endl;
- }
 
- 
+  if (theCommand.compare("plainstd::string") == 0) {
+    string nextPhrase = getStringTilCommand(startInd, doxygenString);
+    if (noisy)
+      cout << "Parsing plain string :" << nextPhrase << endl;
+    doxyList.push_back(DoxygenEntity("plainstd::string", nextPhrase));
+    return 1;
+  }
+  int commandNumber = commandBelongs(theCommand);
+  if (commandNumber == SIMPLECOMMAND) {
+    return addSimpleCommand(theCommand, startInd, doxyList, doxygenString);
+  }
+  if (commandNumber == IGNOREDSIMPLECOMMAND) {
+    return ignoreSimpleCommand(theCommand, startInd, doxyList, doxygenString);
+  }
+  if (commandNumber == COMMANDWORD) {
+    return addCommandWord(theCommand, startInd, doxyList, doxygenString);
+  }
+  if (commandNumber == IGNOREDCOMMANDWORD) {
+    return ignoreCommandWord(theCommand, startInd, doxyList, doxygenString);
+  }
+  if (commandNumber == COMMANDLINE) {
+    return addCommandLine(theCommand, startInd, doxyList, doxygenString);
+  }
+  if (commandNumber == IGNOREDCOMMANDLINE) {
+    return ignoreCommandLine(theCommand, startInd, doxyList, doxygenString);
+  }
+  if (commandNumber == COMMANDPARAGRAPH) {
+    return addCommandParagraph(theCommand, startInd, doxyList, doxygenString);
+  }
+  if (commandNumber == IGNORECOMMANDPARAGRAPH) {
+    return ignoreCommandParagraph(theCommand, startInd, doxyList, doxygenString);
+  }
+  if (commandNumber == COMMANDENDCOMMAND) {
+    return ignoreCommandEndCommand(theCommand, startInd, doxyList, doxygenString);
+  }
+  if (commandNumber == COMMANDWORDPARAGRAPH) {
+    return addCommandWordParagraph(theCommand, startInd, doxyList, doxygenString);
+  }
+  if (commandNumber == COMMANDWORDLINE) {
+    return addCommandWordLine(theCommand, startInd, doxyList, doxygenString);
+  }
+  if (commandNumber == COMMANDWORDOWORDWORD) {
+    return addCommandWordOWordOWord(theCommand, startInd, doxyList, doxygenString);
+  }
+  if (commandNumber == COMMANDOWORD) {
+    return addCommandOWord(theCommand, startInd, doxyList, doxygenString);
+  }
+  if (commandNumber == COMMANDERRORTHROW) {
+    return 0;
+  }
+  if (commandNumber == COMMANDUNIQUE) {
+    return 0;
+  }
+
+  return 0;
+}
+
+int weirdTest() {
+  string doxygenString = "this is a test.";
+  string restOfParagraph;
+  int startIndex = 0;
+  restOfParagraph = getStringTilEndOfParagraph(startIndex, doxygenString);
+  cout << restOfParagraph << " " << startIndex << endl;
+
+  startIndex = 0;
+  restOfParagraph = getStringTilCommand(startIndex, doxygenString);
+  cout << restOfParagraph << " " << startIndex << endl;
+}
+
+
+
+int doRunExamples() {
+  string line;
+  string filename;
+  string exampleNames[] = { "Examples/Example1", "Examples/Example2", "Examples/Example3", "Examples/Example4", "Examples/Example5" };
+  int placement;
+  string doxygenString;
+  ifstream doxCommentFile;
+  for (int i = 0; i < 5; i++) {
+    doxCommentFile.open(exampleNames[i].c_str());
+    doxCommentFile >> doxygenString;
+    while (getline(doxCommentFile, line)) {
+      doxygenString += line + "\n";
+    }
+    doxCommentFile.close();
+    placement = 0;
+    cout << "---RAW CODE---" << endl << doxygenString << endl << endl;
+    //clearFluff(placement, doxygenString);
+    //rootList = parse(placement, doxygenString);
+    TokenList tokList = TokenList(doxygenString);
+    tokList.printList();
+    cout << "---THE TREE---" << endl;
+    printTree();
+  }
+  return 1;
+}
+
 
- int doRunExamples(){
-	 string line;
-	 string filename;
-	 string exampleNames[] = {"Examples/Example1","Examples/Example2", "Examples/Example3", "Examples/Example4", "Examples/Example5"};
-	 int placement;
-	 string doxygenString;
-	 ifstream doxCommentFile;
-	 for (int i = 0; i < 5; i++){
-	   doxCommentFile.open(exampleNames[i].c_str());
-	   doxCommentFile >> doxygenString;
-	   while(getline(doxCommentFile, line)){
-	   doxygenString += line + "\n";}
-	   doxCommentFile.close();
-	   placement = 0;
-	   cout << "---RAW CODE---" << endl << doxygenString << endl<<endl;
-	   //clearFluff(placement, doxygenString);
-	   //rootList = parse(placement, doxygenString);
-	 	TokenList tokList = TokenList(doxygenString);
-	 	tokList.printList();
-	   cout << "---THE TREE---" << endl;
-	   printTree();
-	 }
-	return 1; 
- }
- 
- 
  /* Returns a parse tree for a string */
- int main(int argc, char *argv[]){
-	//weirdTest();
- 	if(testCodeCrawlingFunctions) testCCF();
- 	if(runExamples) doRunExamples();
- 	if (demonstrateParsing){
- 		string doxygenString = "//! A normal member taking two arguments and returning an integer value.\n/*!\n \\param a an integer argument. \\param s a constant character pointer\n \\return The test results\n  \\sa Test(), ~Test(), testMeToo() and publicVar()\n */";
- 		//string doxygenString = " /** This is a small sentence.\n *\n@param x this is a parameter. \n \n This is a line with a @b bold letter \n * \n  @brief small @b description. \n\n * **/";
- 		//string doxygenString = "This is a description.";
- 		int placement = 0;
- 		clearFluff(placement, doxygenString);
- 		rootList = parse(placement, doxygenString);
- 		cout << "---THE TREE---" << endl;
- 		printTree();
- 	}
- 	string doxygenString2 = "//! A normal member taking two arguments and returning an integer value.\n/*!\n \\param a an integer argument. \\param s a constant character pointer\n\n\n\n \\return The test results\n  \\sa Test(), ~Test(), testMeToo() and publicVar()\n */";
- 	TokenList tokList = TokenList(doxygenString2);
- 	tokList.printList();
- 		return 1;
- }
\ No newline at end of file
+int main(int argc, char *argv[]) {
+  //weirdTest();
+  if (testCodeCrawlingFunctions)
+    testCCF();
+  if (runExamples)
+    doRunExamples();
+  if (demonstrateParsing) {
+    string doxygenString =
+	"//! A normal member taking two arguments and returning an integer value.\n/*!\n \\param a an integer argument. \\param s a constant character pointer\n \\return The test results\n  \\sa Test(), ~Test(), testMeToo() and publicVar()\n */";
+    //string doxygenString = " /** This is a small sentence.\n *\n@param x this is a parameter. \n \n This is a line with a @b bold letter \n * \n  @brief small @b description. \n\n * **/";
+    //string doxygenString = "This is a description.";
+    int placement = 0;
+    clearFluff(placement, doxygenString);
+    rootList = parse(placement, doxygenString);
+    cout << "---THE TREE---" << endl;
+    printTree();
+  }
+  string doxygenString2 =
+      "//! A normal member taking two arguments and returning an integer value.\n/*!\n \\param a an integer argument. \\param s a constant character pointer\n\n\n\n \\return The test results\n  \\sa Test(), ~Test(), testMeToo() and publicVar()\n */";
+  TokenList tokList = TokenList(doxygenString2);
+  tokList.printList();
+  return 1;
+}
diff --git a/Source/DoxygenTranslator/src/Examples/DoxygenTransWTokenizer.h b/Source/DoxygenTranslator/src/Examples/DoxygenTransWTokenizer.h
index 6b8b15e9b..fb3181d25 100644
--- a/Source/DoxygenTranslator/src/Examples/DoxygenTransWTokenizer.h
+++ b/Source/DoxygenTranslator/src/Examples/DoxygenTransWTokenizer.h
@@ -1,11 +1,10 @@
 #ifndef DOXYGENTRANSWTOKENIZER_H_
 #define DOXYGENTRANSWTOKENIZER_H_
 
-class DoxygenTransWTokenizer
-{
+class DoxygenTransWTokenizer {
 public:
-	DoxygenTransWTokenizer();
-	virtual ~DoxygenTransWTokenizer();
+  DoxygenTransWTokenizer();
+  virtual ~DoxygenTransWTokenizer();
 };
 
-#endif /*DOXYGENTRANSWTOKENIZER_H_*/
+#endif
diff --git a/Source/DoxygenTranslator/src/Examples/translator.h b/Source/DoxygenTranslator/src/Examples/translator.h
index 64920c5e0..0ae58f714 100644
--- a/Source/DoxygenTranslator/src/Examples/translator.h
+++ b/Source/DoxygenTranslator/src/Examples/translator.h
@@ -1,144 +1,144 @@
 #ifndef TRANSLATOR_H_
 #define TRANSLATOR_H_
 
-#define BRIEFDESCRIPTION     99
-#define LONGDESCRIPTION      100
-#define A_COMMAND       101  /* \a */
-#define ADDINDEX        102  /* \addindex */
-#define ADDTOGROUP      103  /* \addtogroup */
-#define ANCHOR          104  /* \anchor */
-#define ARG_COMMAND     105   /* \arg */
-#define ATTENTION       106   /* \attention */
-#define AUTHOR          107   /* \author */
-#define B_COMMAND       108    /* \b */
-#define BRIEF           109  /* \brief */
-#define BUG             110   /* \bug */
-#define C_COMMAND       111    /* \c */
-#define CALLGRAPH       112   /* \callgraph */
-#define CALLERGRAPH     113   /* \callergraph */
-#define CATEGORY        114    /* \category */
-#define CLASS_COMMAND   115   /* \class */
-#define CODE            116    /* \code */
-#define COND            117  /* \cond */
-#define COPYBRIEF       118  /* \copybrief */
-#define COPYDETAILS     119    /* \copydetails */
-#define COPYDOC         120  /* \copydoc */
-#define DATE            121    /* \date */
-#define DEF             122  /* \def */
-#define DEFGROUP        123    /* \defgroup */
-#define DEPRECATED      124    /* \deprecated */
-#define DETAILS         125   /* \details */
-#define DIR_COMMAND     126    /* \dir */
-#define DONTINCLUDE     127    /* \dontinclude */
-#define DOT             128    /* \dot */
-#define DOTFILE         129    /* \dotfile */
-#define E_COMMAND       130    /* \e */
-#define ELSE_COMMAND    131    /* \else */
-#define ELSEIF_COMMAND  132    /* \elseif */
-#define EM              133   /* \em */
-#define ENDCODE         134    /* \endcode  */
-#define ENDCOND         135    /* \endcond */
-#define ENDDOT          136   /* \enddot */
-#define ENDHTMLONLY     137    /* \endhtmlonly  */
-#define ENDIF           138    /* \endif */
-#define ENDLATEXONLY    139    /* \endlatexonly  */
-#define ENDLINK         140    /* \endlink */
-#define ENDMANONLY      141    /* \endmanonly */
-#define ENDMSC          142    /* \endmsc */
-#define ENDVERBATIM     143    /* \endverbatim */
-#define ENDXMLONLY      144    /* \endxmlonly */
-#define ENUM            145    /* \enum */
-#define EXAMPLE         146   /* \example */
-#define EXCEPTION       147    /* \exception */
-#define FDOLLAR         148    /* \f$ */
-#define FLEFTSQUAREBRACKET     149    /* \f[ */
-#define FRIGHTSQUAREBRACKET    150    /* \f] */
-#define FLEFTBRACKET           151   /* \f{ */
+#define BRIEFDESCRIPTION       99
+#define LONGDESCRIPTION        100
+#define A_COMMAND              101  /* \a */
+#define ADDINDEX               102  /* \addindex */
+#define ADDTOGROUP             103  /* \addtogroup */
+#define ANCHOR                 104  /* \anchor */
+#define ARG_COMMAND            105  /* \arg */
+#define ATTENTION              106  /* \attention */
+#define AUTHOR                 107  /* \author */
+#define B_COMMAND              108  /* \b */
+#define BRIEF                  109  /* \brief */
+#define BUG                    110  /* \bug */
+#define C_COMMAND              111  /* \c */
+#define CALLGRAPH              112  /* \callgraph */
+#define CALLERGRAPH            113  /* \callergraph */
+#define CATEGORY               114  /* \category */
+#define CLASS_COMMAND          115  /* \class */
+#define CODE                   116  /* \code */
+#define COND                   117  /* \cond */
+#define COPYBRIEF              118  /* \copybrief */
+#define COPYDETAILS            119  /* \copydetails */
+#define COPYDOC                120  /* \copydoc */
+#define DATE                   121  /* \date */
+#define DEF                    122  /* \def */
+#define DEFGROUP               123  /* \defgroup */
+#define DEPRECATED             124  /* \deprecated */
+#define DETAILS                125  /* \details */
+#define DIR_COMMAND            126  /* \dir */
+#define DONTINCLUDE            127  /* \dontinclude */
+#define DOT                    128  /* \dot */
+#define DOTFILE                129  /* \dotfile */
+#define E_COMMAND              130  /* \e */
+#define ELSE_COMMAND           131  /* \else */
+#define ELSEIF_COMMAND         132  /* \elseif */
+#define EM                     133  /* \em */
+#define ENDCODE                134  /* \endcode  */
+#define ENDCOND                135  /* \endcond */
+#define ENDDOT                 136  /* \enddot */
+#define ENDHTMLONLY            137  /* \endhtmlonly  */
+#define ENDIF                  138  /* \endif */
+#define ENDLATEXONLY           139  /* \endlatexonly  */
+#define ENDLINK                140  /* \endlink */
+#define ENDMANONLY             141  /* \endmanonly */
+#define ENDMSC                 142  /* \endmsc */
+#define ENDVERBATIM            143  /* \endverbatim */
+#define ENDXMLONLY             144  /* \endxmlonly */
+#define ENUM                   145  /* \enum */
+#define EXAMPLE                146  /* \example */
+#define EXCEPTION              147  /* \exception */
+#define FDOLLAR                148  /* \f$ */
+#define FLEFTSQUAREBRACKET     149  /* \f[ */
+#define FRIGHTSQUAREBRACKET    150  /* \f] */
+#define FLEFTBRACKET           151  /* \f{ */
 #define FRIGHTBRACKET          152  /* \f} */
-#define FILE_COMMAND           153   /* \file */
-#define FN_COMMAND             154   /* \fn */
-#define HEADERFILE             155/* \headerfile */
-#define HIDEINITIALIZER        156    /* \hideinitializer */
+#define FILE_COMMAND           153  /* \file */
+#define FN_COMMAND             154  /* \fn */
+#define HEADERFILE             155  /* \headerfile */
+#define HIDEINITIALIZER        156  /* \hideinitializer */
 #define HTMLINCLUDE            157  /* \htmlinclude */
 #define HTMLONLY               158  /* \htmlonly */
-#define IF_COMMAND             159   /* \if */
-#define IFNOT_COMMAND          160   /* \ifnot */
+#define IF_COMMAND             159  /* \if */
+#define IFNOT_COMMAND          160  /* \ifnot */
 #define IMAGE                  161  /* \image */
-#define INCLUDE_COMMAND        162 /* \include */
-#define INCLUDELINENO          163   /* \includelineno */
-#define INGROUP                164   /* \ingroup */
-#define INTERNAL               165   /* \internal */
-#define INVARIANT              166   /* \invariant */
-#define INTERFACE_COMMAND      167    /* \interface */
-#define LATEXONLY              168   /* \latexonly */
-#define LI                     169 /* \li */
-#define LINE                   170   /* \line */
-#define LINK                   171   /* \link */
-#define MAINPAGE               172    /* \mainpage */
-#define MANONLY                173   /* \manonly */
+#define INCLUDE_COMMAND        162  /* \include */
+#define INCLUDELINENO          163  /* \includelineno */
+#define INGROUP                164  /* \ingroup */
+#define INTERNAL               165  /* \internal */
+#define INVARIANT              166  /* \invariant */
+#define INTERFACE_COMMAND      167  /* \interface */
+#define LATEXONLY              168  /* \latexonly */
+#define LI                     169  /* \li */
+#define LINE                   170  /* \line */
+#define LINK                   171  /* \link */
+#define MAINPAGE               172  /* \mainpage */
+#define MANONLY                173  /* \manonly */
 #define MSC                    174  /* \msc */
 #define N                      175  /* \n */
 #define NAME                   176  /* \name */
-#define NAMESPACE              177   /* \namespace */
-#define NOSUBGROUPING          178   /* \nosubgrouping */
-#define NOTE                   179   /* \note */
+#define NAMESPACE              177  /* \namespace */
+#define NOSUBGROUPING          178  /* \nosubgrouping */
+#define NOTE                   179  /* \note */
 #define OVERLOAD               180  /* \overload */
 #define P                      181  /* \p */
-#define PACKAGE                182   /* \package */
+#define PACKAGE                182  /* \package */
 #define PAGE                   183  /* \page */
-#define PAR                    184 /* \par */
-#define PARAGRAPH              185   /* \paragraph */
+#define PAR                    184  /* \par */
+#define PARAGRAPH              185  /* \paragraph */
 #define PARAM                  186  /* \param */
 #define POST                   187  /* \post */
-#define PRE                    188   /* \pre */
-#define PRIVATE                189   /* \private (PHP only) */
-#define PRIVATESECTION         190   /* \privatesection (PHP only) */
+#define PRE                    188  /* \pre */
+#define PRIVATE                189  /* \private (PHP only) */
+#define PRIVATESECTION         190  /* \privatesection (PHP only) */
 #define PROPERTY               191  /* \property */
-#define PROTECTED              192    /* \protected (PHP only) */
+#define PROTECTED              192  /* \protected (PHP only) */
 #define PROTECTEDSECTION       193  /* \protectedsection (PHP only) */
-#define PROTOCOL               194    /* \protocol */
-#define PUBLIC                 195    /* \public (PHP only) */
-#define PUBLICSECTION          196    /* \publicsection (PHP only) */
-#define REF                          197 /* \ref */
-#define RELATES                      198    /* \relates */
-#define RELATESALSO                  199    /* \relatesalso */
-#define REMARKS                      200   /* \remarks */
-#define RETURN_COMMAND                       201    /* \return */
-#define RETVAL                       202    /* \retval */
-#define SA                           203    /* \sa */
-#define SECTION                      204   /* \section */
-#define SEE                          205   /* \see */
-#define SHOWINITIALIZER              206    /* \showinitializer */
-#define SINCE                        207  /* \since */
-#define SKIP                         208   /* \skip */
-#define SKIPLINE                     209   /* \skipline */
-#define STRUCT                       210  /* \struct */
-#define SUBPAGE                      211   /* \subpage */
-#define SUBSECTION                   212  /* \subsection */
-#define SUBSUBSECTION                213  /* \subsubsection */
-#define TEST                         214  /* \test */
-#define THROW_COMMAND                215 /* \throw */
-#define TODO_COMMAND                 216 /* \todo */
-#define TPARAM_COMMAND               217  /* \tparam */
-#define TYPEDEF_COMMAND              218   /* \typedef */
-#define UNION_COMMAND                219  /* \union */
-#define UNTIL_COMMAND                220  /* \until */
-#define VAR_COMMAND                  221  /* \var */
-#define VERBATIM                     222 /* \verbatim */
-#define VERBININCLUDE                223  /* \verbinclude */
-#define VERSION                      224 /* \version */
-#define WARNING                      225 /* \warning */
-#define WEAKGROUP                    226  /* \weakgroup */
-#define XMLONLY                      227/* \xmlonly */
-#define XREFITEM                     228  /* \xrefitem */
-#define DOLLAR_COMMAND               229   /* \$ */
-#define AT_COMMAND                   230 /* \@ */
-#define SLASH_COMMAND                231 /* \\ */
-#define AND_COMMAND                  232  /* \& */
-#define TILDE_COMMAND                233  /* \~ */
-#define LEFTANGLEBRACKET             234  /* \< */
-#define RIGHTANGLEBRACKET            235  /* \> */
-#define POUND_COMMAND                236 /* \# */
-#define PERCENT_COMMAND              237  /* \%  */
+#define PROTOCOL               194  /* \protocol */
+#define PUBLIC                 195  /* \public (PHP only) */
+#define PUBLICSECTION          196  /* \publicsection (PHP only) */
+#define REF                    197  /* \ref */
+#define RELATES                198  /* \relates */
+#define RELATESALSO            199  /* \relatesalso */
+#define REMARKS                200  /* \remarks */
+#define RETURN_COMMAND         201  /* \return */
+#define RETVAL                 202  /* \retval */
+#define SA                     203  /* \sa */
+#define SECTION                204  /* \section */
+#define SEE                    205  /* \see */
+#define SHOWINITIALIZER        206  /* \showinitializer */
+#define SINCE                  207  /* \since */
+#define SKIP                   208  /* \skip */
+#define SKIPLINE               209  /* \skipline */
+#define STRUCT                 210  /* \struct */
+#define SUBPAGE                211  /* \subpage */
+#define SUBSECTION             212  /* \subsection */
+#define SUBSUBSECTION          213  /* \subsubsection */
+#define TEST                   214  /* \test */
+#define THROW_COMMAND          215  /* \throw */
+#define TODO_COMMAND           216  /* \todo */
+#define TPARAM_COMMAND         217  /* \tparam */
+#define TYPEDEF_COMMAND        218  /* \typedef */
+#define UNION_COMMAND          219  /* \union */
+#define UNTIL_COMMAND          220  /* \until */
+#define VAR_COMMAND            221  /* \var */
+#define VERBATIM               222  /* \verbatim */
+#define VERBININCLUDE          223  /* \verbinclude */
+#define VERSION                224  /* \version */
+#define WARNING                225  /* \warning */
+#define WEAKGROUP              226  /* \weakgroup */
+#define XMLONLY                227  /* \xmlonly */
+#define XREFITEM               228  /* \xrefitem */
+#define DOLLAR_COMMAND         229  /* \$ */
+#define AT_COMMAND             230  /* \@ */
+#define SLASH_COMMAND          231  /* \\ */
+#define AND_COMMAND            232  /* \& */
+#define TILDE_COMMAND          233  /* \~ */
+#define LEFTANGLEBRACKET       234  /* \< */
+#define RIGHTANGLEBRACKET      235  /* \> */
+#define POUND_COMMAND          236  /* \# */
+#define PERCENT_COMMAND        237  /* \%  */
 
-#endif /*TRANSLATOR_H_*/
+#endif
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.cpp b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
index 33a62ff77..9de2f99f3 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
@@ -1,42 +1,43 @@
 #include "JavaDocConverter.h"
 #include "DoxygenParser.h"
 #include <iostream>
-#define APPROX_LINE_LENGTH 64//characters per line allowed
-#define TAB_SIZE 8//characters per line allowed
+#define APPROX_LINE_LENGTH 64	//characters per line allowed
+#define TAB_SIZE 8		//characters per line allowed
 int printSortedTree2 = 0;
 //TODO {@link} {@linkplain} {@docRoot}, and other useful doxy commands that are not a javadoc tag
 
-std::string JavaDocConverter::formatCommand(std::string unformattedLine, int indent){
+std::string JavaDocConverter::formatCommand(std::string unformattedLine, int indent) {
   std::string formattedLines = "\n * ";
   int lastPosition = 0;
   int i = 0;
-  int isFirstLine  = 1;
-  while (i != -1 && i < (int)unformattedLine.length()){
+  int isFirstLine = 1;
+  while (i != -1 && i < (int) unformattedLine.length()) {
     lastPosition = i;
-    if (isFirstLine){
-      i+=APPROX_LINE_LENGTH;
+    if (isFirstLine) {
+      i += APPROX_LINE_LENGTH;
     } else {
-        i+=APPROX_LINE_LENGTH - indent*TAB_SIZE;
+      i += APPROX_LINE_LENGTH - indent * TAB_SIZE;
     }
 
     i = unformattedLine.find(" ", i);
 
-    if (i > 0 && i + 1 < (int)unformattedLine.length()){
-      if (!isFirstLine) for (int j = 0; j < indent; j++) {
-        formattedLines.append("\t");
+    if (i > 0 && i + 1 < (int) unformattedLine.length()) {
+      if (!isFirstLine)
+	for (int j = 0; j < indent; j++) {
+	  formattedLines.append("\t");
       } else {
-        isFirstLine = 0;
+	isFirstLine = 0;
       }
       formattedLines.append(unformattedLine.substr(lastPosition, i - lastPosition + 1));
       formattedLines.append("\n *");
 
     }
   }
-  if (lastPosition < (int)unformattedLine.length()){
+  if (lastPosition < (int) unformattedLine.length()) {
     if (!isFirstLine) {
-        for (int j = 0; j < indent; j++) { 
-            formattedLines.append("\t");
-        }
+      for (int j = 0; j < indent; j++) {
+	formattedLines.append("\t");
+      }
     }
     formattedLines.append(unformattedLine.substr(lastPosition, unformattedLine.length() - lastPosition));
   }
@@ -47,57 +48,47 @@ std::string JavaDocConverter::formatCommand(std::string unformattedLine, int ind
 /* Contains the conversions for tags
  * could probably be much more efficient...
  */
-std::string JavaDocConverter::javaDocFormat(DoxygenEntity &doxygenEntity){
-  if(doxygenEntity.typeOfEntity.compare("partofdescription") == 0){
-        return doxygenEntity.data;
-    }
-  if (doxygenEntity.typeOfEntity.compare("plainstd::string") == 0){
-      return  doxygenEntity.data;
+std::string JavaDocConverter::javaDocFormat(DoxygenEntity & doxygenEntity) {
+  if (doxygenEntity.typeOfEntity.compare("partofdescription") == 0) {
+    return doxygenEntity.data;
   }
-  else if (doxygenEntity.typeOfEntity.compare("b") == 0){
+  if (doxygenEntity.typeOfEntity.compare("plainstd::string") == 0) {
+    return doxygenEntity.data;
+  } else if (doxygenEntity.typeOfEntity.compare("b") == 0) {
     return "<b>" + doxygenEntity.data + "</b>";
-  }
-  else if (doxygenEntity.typeOfEntity.compare("c") == 0){
+  } else if (doxygenEntity.typeOfEntity.compare("c") == 0) {
     return "<tt>" + doxygenEntity.data + "</tt>";
-  }
-  else if (doxygenEntity.typeOfEntity.compare("@") == 0){
+  } else if (doxygenEntity.typeOfEntity.compare("@") == 0) {
     return "@";
-  }
-  else if (doxygenEntity.typeOfEntity.compare("\\") == 0){
+  } else if (doxygenEntity.typeOfEntity.compare("\\") == 0) {
     return "\\";
-  }
-  else if (doxygenEntity.typeOfEntity.compare("<") == 0){
+  } else if (doxygenEntity.typeOfEntity.compare("<") == 0) {
     return "&lt;";
-  }
-  else if (doxygenEntity.typeOfEntity.compare(">") == 0){
+  } else if (doxygenEntity.typeOfEntity.compare(">") == 0) {
     return "&gt;";
-  }
-  else if (doxygenEntity.typeOfEntity.compare("&") == 0){
+  } else if (doxygenEntity.typeOfEntity.compare("&") == 0) {
     return "&amp;";
-  }
-  else if (doxygenEntity.typeOfEntity.compare("#") == 0){
+  } else if (doxygenEntity.typeOfEntity.compare("#") == 0) {
     return "#";
-  }
-  else if (doxygenEntity.typeOfEntity.compare("%") == 0){
+  } else if (doxygenEntity.typeOfEntity.compare("%") == 0) {
     return "%";
-  }
-  else if (doxygenEntity.typeOfEntity.compare("~") == 0){
+  } else if (doxygenEntity.typeOfEntity.compare("~") == 0) {
     return "~";
   }
   return "";
 }
 
 
-std::string JavaDocConverter::translateSubtree( DoxygenEntity &doxygenEntity){
+std::string JavaDocConverter::translateSubtree(DoxygenEntity & doxygenEntity) {
   std::string returnedString;
-  if (doxygenEntity.isLeaf) { 
+  if (doxygenEntity.isLeaf) {
     return javaDocFormat(doxygenEntity) + " ";
   } else {
     returnedString += javaDocFormat(doxygenEntity);
-    std::list<DoxygenEntity>::iterator p = doxygenEntity.entityList.begin();
+    std::list < DoxygenEntity >::iterator p = doxygenEntity.entityList.begin();
 
-    while (p != doxygenEntity.entityList.end()){
-      returnedString+= translateSubtree(*p);
+    while (p != doxygenEntity.entityList.end()) {
+      returnedString += translateSubtree(*p);
       p++;
     }
   }
@@ -105,45 +96,43 @@ std::string JavaDocConverter::translateSubtree( DoxygenEntity &doxygenEntity){
 }
 
 
-std::string JavaDocConverter::translateEntity(DoxygenEntity &doxyEntity){
+std::string JavaDocConverter::translateEntity(DoxygenEntity & doxyEntity) {
   if (doxyEntity.typeOfEntity.compare("partofdescription") == 0) {
     return formatCommand(std::string(translateSubtree(doxyEntity)), 0);
   }
 
-  if ((doxyEntity.typeOfEntity.compare("brief") == 0)  ||  
-      (doxyEntity.typeOfEntity.compare("details") == 0)) {
+  if ((doxyEntity.typeOfEntity.compare("brief") == 0) || (doxyEntity.typeOfEntity.compare("details") == 0)) {
     return formatCommand(std::string(translateSubtree(doxyEntity)), 0) + "\n * ";
 
-  } else if(doxyEntity.typeOfEntity.compare("plainstd::string")== 0 || 
-      doxyEntity.typeOfEntity.compare("deprecated")== 0 || 
-      doxyEntity.typeOfEntity.compare("brief")== 0) {
+  } else if (doxyEntity.typeOfEntity.compare("plainstd::string") == 0 ||
+	     doxyEntity.typeOfEntity.compare("deprecated") == 0 || 
+	     doxyEntity.typeOfEntity.compare("brief") == 0) {
     return formatCommand(doxyEntity.data, 0) + "\n * ";
 
-  } else if(doxyEntity.typeOfEntity.compare("see") == 0) {
-    return formatCommand(std::string("@" + doxyEntity.typeOfEntity + "\t\t" + 
-	  translateSubtree(doxyEntity)), 2);
+  } else if (doxyEntity.typeOfEntity.compare("see") == 0) {
+    return formatCommand(std::string("@" + doxyEntity.typeOfEntity + "\t\t" + translateSubtree(doxyEntity)), 2);
 
-  } else if(doxyEntity.typeOfEntity.compare("return")== 0
-      || doxyEntity.typeOfEntity.compare("author")== 0
-      || doxyEntity.typeOfEntity.compare("param")== 0
-      || doxyEntity.typeOfEntity.compare("throw")== 0
-      || doxyEntity.typeOfEntity.compare("throws")== 0
-      || doxyEntity.typeOfEntity.compare("since")== 0
-      || doxyEntity.typeOfEntity.compare("version")== 0
-      || doxyEntity.typeOfEntity.compare("exception") == 0
-      || doxyEntity.typeOfEntity.compare("deprecated") == 0){
+  } else if (doxyEntity.typeOfEntity.compare("return") == 0
+	     || doxyEntity.typeOfEntity.compare("author") == 0
+	     || doxyEntity.typeOfEntity.compare("param") == 0
+	     || doxyEntity.typeOfEntity.compare("throw") == 0
+	     || doxyEntity.typeOfEntity.compare("throws") == 0
+	     || doxyEntity.typeOfEntity.compare("since") == 0
+	     || doxyEntity.typeOfEntity.compare("version") == 0
+	     || doxyEntity.typeOfEntity.compare("exception") == 0
+	     || doxyEntity.typeOfEntity.compare("deprecated") == 0) {
 
     // this 'if' is a hack - convert doxyEntity.typeOfEntity at the time of parsing
-    if (doxyEntity.typeOfEntity.compare("throw")== 0) {
+    if (doxyEntity.typeOfEntity.compare("throw") == 0) {
       doxyEntity.typeOfEntity = "throws";
     }
     return formatCommand(std::string("@" + doxyEntity.typeOfEntity + "\t" + translateSubtree(doxyEntity)), 2);
 
-  } else if(doxyEntity.typeOfEntity.compare("sa")== 0) {
+  } else if (doxyEntity.typeOfEntity.compare("sa") == 0) {
     return formatCommand(std::string("@see\t\t" + translateSubtree(doxyEntity)), 2);
 
   } else {
-    return formatCommand(javaDocFormat(doxyEntity), 0 );
+    return formatCommand(javaDocFormat(doxyEntity), 0);
   }
 
   return "";
@@ -157,31 +146,31 @@ bool JavaDocConverter::getDocumentation(Node *node, String *&documentation) {
   if (documentation == NULL) {
     return false;
   }
-  
-  std::list <DoxygenEntity> entityList = DoxygenParser().createTree(Char(documentation));
 
-    // entityList.sort(CompareDoxygenEntities()); sorting currently not used,
-    // see CompareDoxygenEntities::operator() in DoxygenEntity.cpp
-  
-  if(debug){
+  std::list < DoxygenEntity > entityList = DoxygenParser().createTree(Char(documentation));
+
+  // entityList.sort(CompareDoxygenEntities()); sorting currently not used,
+  // see CompareDoxygenEntities::operator() in DoxygenEntity.cpp
+
+  if (debug) {
     std::cout << "---RESORTED LIST---" << std::endl;
     printTree(entityList);
   }
 
   std::string javaDocString = "/**";
-  
-  for(std::list<DoxygenEntity>::iterator entityIterator = entityList.begin(); entityIterator != entityList.end();){
+
+  for (std::list < DoxygenEntity >::iterator entityIterator = entityList.begin(); entityIterator != entityList.end();) {
     javaDocString += translateEntity(*entityIterator);
     entityIterator++;
   }
 
   javaDocString += "\n */\n";
-  
-  if(debug){
+
+  if (debug) {
     std::cout << "\n---RESULT IN JAVADOC---" << std::endl;
-    std::cout << javaDocString; 
+    std::cout << javaDocString;
   }
-  
+
   documentation = NewString(javaDocString.c_str());
   return true;
 }
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.h b/Source/DoxygenTranslator/src/JavaDocConverter.h
index 8651bb1cf..d898265ba 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.h
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.h
@@ -15,20 +15,20 @@
 /*
  * A class to translate doxygen comments into JavaDoc style comments.
  */
-class JavaDocConverter : public DoxygenTranslator
-{
+class JavaDocConverter : public DoxygenTranslator {
 public:
-  JavaDocConverter() : debug( false ){}
+  JavaDocConverter() : debug(false) {
+  }
   virtual bool getDocumentation(Node *node, String *&documentation);
-  
+
 protected:
   std::string formatCommand(std::string unformattedLine, int indent);
-  std::string translateEntity(DoxygenEntity &doxyEntity);
-  std::string javaDocFormat(DoxygenEntity &doxygenEntity);
-  std::string translateSubtree( DoxygenEntity &doxygenEntity);
-  
+  std::string translateEntity(DoxygenEntity & doxyEntity);
+  std::string javaDocFormat(DoxygenEntity & doxygenEntity);
+  std::string translateSubtree(DoxygenEntity & doxygenEntity);
+
 private:
   bool debug;
 };
 
-#endif /*JAVADOCCONVERTER_H_*/
+#endif
diff --git a/Source/DoxygenTranslator/src/PyDocConverter.cpp b/Source/DoxygenTranslator/src/PyDocConverter.cpp
index 6418ee73c..44dec4cbf 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/PyDocConverter.cpp
@@ -14,25 +14,25 @@
 #include <iostream>
 
 //TODO {@link} {@linkplain} {@docRoot}, and other useful doxy commands that are not a pydoc tag
-PyDocConverter::PyDocConverter(){
-    debug = 1;
+PyDocConverter::PyDocConverter() {
+  debug = 1;
 }
 
-std::string PyDocConverter::formatParam(Node *n, DoxygenEntity &doxygenEntity) {
+std::string PyDocConverter::formatParam(Node *n, DoxygenEntity & doxygenEntity) {
   ParmList *plist = CopyParmList(Getattr(n, "parms"));
   Parm *p = NULL;
-  
-  DoxygenEntity& paramNameEntity = *doxygenEntity.entityList.begin();
-  DoxygenEntity& paramDescriptionEntity = *(++doxygenEntity.entityList.begin());
-  
+
+  DoxygenEntity & paramNameEntity = *doxygenEntity.entityList.begin();
+  DoxygenEntity & paramDescriptionEntity = *(++doxygenEntity.entityList.begin());
+
   std::string result;
   std::string paramDescription = justifyString(paramDescriptionEntity.data, DOC_PARAM_STRING_LENGTH);
-  
+
   for (p = plist; p;) {
-    if(Char(Getattr(p, "name")) == paramNameEntity.data) {
+    if (Char(Getattr(p, "name")) == paramNameEntity.data) {
       std::string name = Char(Swig_name_make(n, 0, Getattr(p, "name"), 0, 0));
       std::string type = Char(Swig_name_make(n, 0, Getattr(p, "type"), 0, 0));
-      
+
       result = name + " (" + type + ") ";
       result.resize(DOC_PARAM_STRING_LENGTH - 3, ' ');
       result += "-- " + paramDescription.substr(DOC_PARAM_STRING_LENGTH);
@@ -45,162 +45,158 @@ std::string PyDocConverter::formatParam(Node *n, DoxygenEntity &doxygenEntity) {
   return result;
 }
 
-std::string PyDocConverter::formatReturnDescription(Node *node, DoxygenEntity &doxygenEntity){
+std::string PyDocConverter::formatReturnDescription(Node *node, DoxygenEntity & doxygenEntity) {
 #pragma unused(node)
   return "\nResult:\n" + justifyString(translateSubtree(doxygenEntity));
 }
 
-std::string PyDocConverter::justifyString(std::string documentString, int indent, int maxWidth){
+std::string PyDocConverter::justifyString(std::string documentString, int indent, int maxWidth) {
   std::ostringstream formattedString;
   std::string currentLine;
-  
-  for(std::string::iterator stringPosition = documentString.begin(); stringPosition != documentString.end(); ++stringPosition)
-  {
-    if(currentLine.length() == 0)
+
+  for (std::string::iterator stringPosition = documentString.begin(); stringPosition != documentString.end(); ++stringPosition) {
+    if (currentLine.length() == 0)
       currentLine.resize(indent, ' ');
-    
+
     currentLine += *stringPosition;
-      
-    if(*stringPosition == ' ' && (int)currentLine.size() >= maxWidth || (stringPosition + 1) == documentString.end())
-    {
+
+    if (*stringPosition == ' ' && (int) currentLine.size() >= maxWidth || (stringPosition + 1) == documentString.end()) {
       formattedString << currentLine << std::endl;
       currentLine = "";
     }
   }
-  
+
   return formattedString.str();
 }
 
-std::string PyDocConverter::translateSubtree( DoxygenEntity &doxygenEntity){
+std::string PyDocConverter::translateSubtree(DoxygenEntity & doxygenEntity) {
   std::string returnedString;
   if (doxygenEntity.isLeaf)
     return doxygenEntity.data + " ";
   else {
     returnedString += doxygenEntity.data;
-    std::list<DoxygenEntity>::iterator p = doxygenEntity.entityList.begin();
-    while (p != doxygenEntity.entityList.end()){
-      returnedString+= translateSubtree(*p);
+    std::list < DoxygenEntity >::iterator p = doxygenEntity.entityList.begin();
+    while (p != doxygenEntity.entityList.end()) {
+      returnedString += translateSubtree(*p);
       p++;
     }
   }
   return returnedString;
 }
 
-std::string PyDocConverter::translateEntity(Node *n, DoxygenEntity &doxyEntity){
-  if(doxyEntity.typeOfEntity.compare("partofdescription") == 0) 
+std::string PyDocConverter::translateEntity(Node *n, DoxygenEntity & doxyEntity) {
+  if (doxyEntity.typeOfEntity.compare("partofdescription") == 0)
     return justifyString(std::string(translateSubtree(doxyEntity)), 0);
-  
+
   if ((doxyEntity.typeOfEntity.compare("brief") == 0)
-      ||(doxyEntity.typeOfEntity.compare("details") == 0))
+      || (doxyEntity.typeOfEntity.compare("details") == 0))
     return justifyString(std::string(translateSubtree(doxyEntity)), 0) + "\n";
-  
-  if(doxyEntity.typeOfEntity.compare("plainstd::string") == 0 
-    || doxyEntity.typeOfEntity.compare("deprecated") == 0 
-    || doxyEntity.typeOfEntity.compare("brief") == 0)
+
+  if (doxyEntity.typeOfEntity.compare("plainstd::string") == 0
+      || doxyEntity.typeOfEntity.compare("deprecated") == 0
+      || doxyEntity.typeOfEntity.compare("brief") == 0)
     return justifyString(doxyEntity.data, 0) + "\n";
-  
-  if(doxyEntity.typeOfEntity.compare("param") == 0)
+
+  if (doxyEntity.typeOfEntity.compare("param") == 0)
     return formatParam(n, doxyEntity);
-  
-  if(doxyEntity.typeOfEntity.compare("return") == 0)
+
+  if (doxyEntity.typeOfEntity.compare("return") == 0)
     return formatReturnDescription(n, doxyEntity);
 
-  if(doxyEntity.typeOfEntity.compare("author") == 0
-    || doxyEntity.typeOfEntity.compare("param") == 0
-    || doxyEntity.typeOfEntity.compare("since") == 0
-    || doxyEntity.typeOfEntity.compare("version") == 0
-    || doxyEntity.typeOfEntity.compare("exception") == 0
-    || doxyEntity.typeOfEntity.compare("deprecated") == 0
-    || doxyEntity.typeOfEntity.compare("sa") == 0)
+  if (doxyEntity.typeOfEntity.compare("author") == 0
+      || doxyEntity.typeOfEntity.compare("param") == 0
+      || doxyEntity.typeOfEntity.compare("since") == 0
+      || doxyEntity.typeOfEntity.compare("version") == 0
+      || doxyEntity.typeOfEntity.compare("exception") == 0
+      || doxyEntity.typeOfEntity.compare("deprecated") == 0
+      || doxyEntity.typeOfEntity.compare("sa") == 0)
     return "";
 
   return justifyString(doxyEntity.data);
 }
 
-std::string PyDocConverter::processEntityList(Node *n, std::list<DoxygenEntity>& entityList){
+std::string PyDocConverter::processEntityList(Node *n, std::list < DoxygenEntity > &entityList) {
   std::string result;
   bool inParamsSection = false;
-  
-  for(std::list<DoxygenEntity>::iterator entityIterator = entityList.begin(); entityIterator != entityList.end();){
-    if(entityIterator->typeOfEntity.compare("param") == 0 && !inParamsSection){
+
+  for (std::list < DoxygenEntity >::iterator entityIterator = entityList.begin(); entityIterator != entityList.end();) {
+    if (entityIterator->typeOfEntity.compare("param") == 0 && !inParamsSection) {
       inParamsSection = true;
       result += "\nArguments:\n";
-    }
-    else if(entityIterator->typeOfEntity.compare("param") != 0 && inParamsSection)
+    } else if (entityIterator->typeOfEntity.compare("param") != 0 && inParamsSection)
       inParamsSection = false;
-    
+
     result += translateEntity(n, *entityIterator);
     entityIterator++;
-  }  
-  
+  }
+
   return result;
 }
 
-bool PyDocConverter::getDocumentation(Node *n, String *&documentation){
+bool PyDocConverter::getDocumentation(Node *n, String *&documentation) {
   std::string pyDocString, result;
-  
+
   // for overloaded functions we must concat documentation for underlying overloads
-  if(Checkattr(n, "kind", "function") && Getattr(n, "sym:overloaded")){
+  if (Checkattr(n, "kind", "function") && Getattr(n, "sym:overloaded")) {
     // rewind to the first overload
     while (Getattr(n, "sym:previousSibling"))
       n = Getattr(n, "sym:previousSibling");
-    
-    std::vector<std::string> allDocumentation;
-    
+
+    std::vector < std::string > allDocumentation;
+
     // for each real method (not a generated overload) append the documentation
-    while(n){
-      documentation = Getattr(n,"DoxygenComment");
-      if(!Swig_is_generated_overload(n) && documentation){
-	std::list<DoxygenEntity> entityList = DoxygenParser().createTree(Char(documentation));
+    while (n) {
+      documentation = Getattr(n, "DoxygenComment");
+      if (!Swig_is_generated_overload(n) && documentation) {
+	std::list < DoxygenEntity > entityList = DoxygenParser().createTree(Char(documentation));
 	allDocumentation.push_back(processEntityList(n, entityList));
       }
       n = Getattr(n, "sym:nextSibling");
     }
-    
+
     // construct final documentation string
-    if(allDocumentation.size() > 1){
+    if (allDocumentation.size() > 1) {
       std::ostringstream concatDocString;
-      for(int realOverloadCount = 0; realOverloadCount < (int)allDocumentation.size(); realOverloadCount++){
+      for (int realOverloadCount = 0; realOverloadCount < (int) allDocumentation.size(); realOverloadCount++) {
 	concatDocString << generateDivider();
 	concatDocString << "Overload " << (realOverloadCount + 1) << ":" << std::endl;
 	concatDocString << generateDivider();
 	concatDocString << allDocumentation[realOverloadCount] << std::endl;
       }
       pyDocString = concatDocString.str();
-    } 
-    else if (allDocumentation.size() == 1) {
+    } else if (allDocumentation.size() == 1) {
       pyDocString = *(allDocumentation.begin());
     }
-  } 
+  }
   // for other nodes just process as normal
   else {
-    documentation = Getattr(n,"DoxygenComment");
-    if(documentation != NULL){
-      std::list<DoxygenEntity> entityList = DoxygenParser().createTree(Char(documentation));
+    documentation = Getattr(n, "DoxygenComment");
+    if (documentation != NULL) {
+      std::list < DoxygenEntity > entityList = DoxygenParser().createTree(Char(documentation));
       pyDocString = processEntityList(n, entityList);
     }
   }
-  
+
   // if we got something log the result and construct DOH string to return
-  if(pyDocString.length()) {
+  if (pyDocString.length()) {
     result = "\"\"\"\n" + pyDocString + "\"\"\"\n";
-    
-    if(debug){
+
+    if (debug) {
       std::cout << "\n---RESULT IN PYDOC---" << std::endl;
       std::cout << result;
       std::cout << std::endl;
     }
-    
+
     documentation = NewString(result.c_str());
     return true;
   }
-  
+
   return false;
 }
 
-std::string PyDocConverter::generateDivider(){
+std::string PyDocConverter::generateDivider() {
   std::ostringstream dividerString;
-  for(int i = 0; i < DOC_STRING_LENGTH; i++)
+  for (int i = 0; i < DOC_STRING_LENGTH; i++)
     dividerString << '-';
   dividerString << std::endl;
   return dividerString.str();
diff --git a/Source/DoxygenTranslator/src/PyDocConverter.h b/Source/DoxygenTranslator/src/PyDocConverter.h
index 500e39fe8..5680480fc 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.h
+++ b/Source/DoxygenTranslator/src/PyDocConverter.h
@@ -16,38 +16,37 @@
 #include "DoxygenEntity.h"
 #include "DoxygenTranslator.h"
 
-#define DOC_STRING_LENGTH	  64  // characters per line allowed
-#define DOC_PARAM_STRING_LENGTH	  30  // characters reserved for param name / type
+#define DOC_STRING_LENGTH	  64	// characters per line allowed
+#define DOC_PARAM_STRING_LENGTH	  30	// characters reserved for param name / type
 
-class PyDocConverter : public DoxygenTranslator
-{
+class PyDocConverter : public DoxygenTranslator {
 public:
   PyDocConverter();
   bool getDocumentation(Node *node, String *&documentation);
-  
+
 protected:
-  
+
   /*
    * Process the contents of the entity list producing a documentation string.
    * @param node The parse tree node that the entity list relates to.
    * @param entityList The entity list to process
    */
-  std::string processEntityList(Node *node, std::list<DoxygenEntity>& entityList);
-  
+  std::string processEntityList(Node *node, std::list < DoxygenEntity > &entityList);
+
   /*
    * Format the doxygen comment relating to a function or method parameter
    * @param node The parse tree node that the parameter relates to.
    * @param doxygenEntity The doxygen entity relating to the parameter docstring.
    */
-  std::string formatParam(Node *node, DoxygenEntity &doxygenEntity);
-  
+  std::string formatParam(Node *node, DoxygenEntity & doxygenEntity);
+
   /*
    * Format the doxygen comment relating to the return value for a method or function.
    * @param node The parse tree node that the parameter relates to.
    * @param doxygenEntity The doxygen entity relating to the parameter docstring.
    */
-  std::string formatReturnDescription(Node *node, DoxygenEntity &doxygenEntity);
-  
+  std::string formatReturnDescription(Node *node, DoxygenEntity & doxygenEntity);
+
   /*
    * Format a string so it is justified and split over several lines 
    * not exeeding a given length.
@@ -56,17 +55,17 @@ protected:
    * @param maxWidth The approximate maximum line width.
    */
   std::string justifyString(std::string unformattedLine, int indent = 0, int maxWidth = DOC_STRING_LENGTH);
-  
-  std::string translateSubtree( DoxygenEntity &doxygenEntity);
-  std::string translateEntity(Node *n, DoxygenEntity &doxyEntity);
-  
+
+  std::string translateSubtree(DoxygenEntity & doxygenEntity);
+  std::string translateEntity(Node *n, DoxygenEntity & doxyEntity);
+
   /*
    * Utility method to generate a diving line for a documentation string.
    */
   std::string generateDivider();
-    
+
 private:
   bool debug;
 };
 
-#endif /*PYDOCCONVERTER_H_*/
+#endif
diff --git a/Source/DoxygenTranslator/src/Token.cpp b/Source/DoxygenTranslator/src/Token.cpp
index 2ac03afe5..f7c02b021 100644
--- a/Source/DoxygenTranslator/src/Token.cpp
+++ b/Source/DoxygenTranslator/src/Token.cpp
@@ -3,27 +3,26 @@
 using namespace std;
 
 
-Token::Token(int tType, string tString)
-{	
-	tokenType = tType;
-	tokenString = tString;
+Token::Token(int tType, string tString) {
+  tokenType = tType;
+  tokenString = tString;
 }
 
-string Token::toString()
-{
-	if (tokenType == END_LINE){
-		return "{END OF LINE}";
-	}
-	if (tokenType == PARAGRAPH_END){
-		return "{END OF PARAGRAPH}";
-	}
-	if (tokenType == PLAINSTRING){
-		return "{PLAINSTRING :" + tokenString + "}";
-	}
-	if (tokenType == COMMAND){
-		return "{COMMAND : " + tokenString+ "}";
-	}
-	return "";
+string Token::toString() {
+  if (tokenType == END_LINE) {
+    return "{END OF LINE}";
+  }
+  if (tokenType == PARAGRAPH_END) {
+    return "{END OF PARAGRAPH}";
+  }
+  if (tokenType == PLAINSTRING) {
+    return "{PLAINSTRING :" + tokenString + "}";
+  }
+  if (tokenType == COMMAND) {
+    return "{COMMAND : " + tokenString + "}";
+  }
+  return "";
 }
 
-Token::	~Token(){}
+Token::~Token() {
+}
diff --git a/Source/DoxygenTranslator/src/Token.h b/Source/DoxygenTranslator/src/Token.h
index cf28c90b7..4ae44b65f 100644
--- a/Source/DoxygenTranslator/src/Token.h
+++ b/Source/DoxygenTranslator/src/Token.h
@@ -4,15 +4,14 @@
 
 using namespace std;
 
-class Token
-{
+class Token {
 public:
-	Token(int tType, string tString);
-	~Token();
+  Token(int tType, string tString);
+  ~Token();
 
-	int tokenType; /* currently can be END_LINE, PLAINSTRING, or COMMAND */
-	string tokenString; /* the data , such as param for @param*/
-	string toString();
+  int tokenType;		/* currently can be END_LINE, PLAINSTRING, or COMMAND */
+  string tokenString;		/* the data , such as param for @param */
+  string toString();
 };
 
-#endif /*TOKEN_H_*/
+#endif
diff --git a/Source/DoxygenTranslator/src/TokenList.cpp b/Source/DoxygenTranslator/src/TokenList.cpp
index 9efd7e9ef..8eeef97b2 100644
--- a/Source/DoxygenTranslator/src/TokenList.cpp
+++ b/Source/DoxygenTranslator/src/TokenList.cpp
@@ -5,165 +5,161 @@
 #include <list>
 #include "Token.h"
 #include "DoxygenEntity.h"
-#define TOKENSPERLINE 8; //change this to change the printing behaviour of the token list
+#define TOKENSPERLINE 8;	//change this to change the printing behaviour of the token list
 
 using namespace std;
 
 int noisy2 = 0;
 /* The tokenizer*/
-TokenList::TokenList(const std::string &doxygenStringConst){
-    size_t commentPos;
-    string doxygenString = doxygenStringConst;
+TokenList::TokenList(const std::string & doxygenStringConst) {
+  size_t commentPos;
+  string doxygenString = doxygenStringConst;
 
-    /* Comment start tokens are replaced in parser.y, see doxygen_comment and
-       doxygen_post_comment_item
-       do {
-        commentPos = doxygenString.find("///<");
-        if (commentPos != string::npos) {
-            doxygenString.replace(commentPos, 4, " ");
-            continue;
-        }
-        commentPos = doxygenString.find("/**<");
-        if (commentPos != string::npos) {
-            doxygenString.replace(commentPos, 4, " ");
-            continue;
-        }
-        commentPos = doxygenString.find("/*!<");
-        if (commentPos != string::npos) {
-            doxygenString.replace(commentPos, 4, " ");
-            continue;
-        }
-        commentPos = doxygenString.find("//!<");
-        if (commentPos != string::npos) {
-            doxygenString.replace(commentPos, 4, " ");
-            continue;
-        }
-        break;
-    } while (true); */
+   /* Comment start tokens are replaced in parser.y, see doxygen_comment and
+      doxygen_post_comment_item
+   do {
+    commentPos = doxygenString.find("///<");
+    if (commentPos != string::npos) {
+      doxygenString.replace(commentPos, 4, " ");
+      continue;
+    }
+    commentPos = doxygenString.find("/**<");
+    if (commentPos != string::npos) {
+      doxygenString.replace(commentPos, 4, " ");
+      continue;
+    }
+    commentPos = doxygenString.find("/*!<");
+    if (commentPos != string::npos) {
+      doxygenString.replace(commentPos, 4, " ");
+      continue;
+    }
+    commentPos = doxygenString.find("//!<");
+    if (commentPos != string::npos) {
+      doxygenString.replace(commentPos, 4, " ");
+      continue;
+    }
+    break;
+  } while (true);
+  */
 
-    size_t currentIndex = 0;
-    size_t nextIndex = 0;
+  size_t currentIndex = 0;
+  size_t nextIndex = 0;
 
-	string currentWord;
+  string currentWord;
 
-	while (currentIndex < doxygenString.length()){	
+  while (currentIndex < doxygenString.length()) {
 
-		if(doxygenString[currentIndex] == '\n'){
-            m_tokenList.push_back(Token(END_LINE, currentWord));
-			currentIndex++;
-		}
+    if (doxygenString[currentIndex] == '\n') {
+      m_tokenList.push_back(Token(END_LINE, currentWord));
+      currentIndex++;
+    }
+    // skip WS, except \n
+    while (currentIndex < doxygenString.length() && (doxygenString[currentIndex] == ' ' || doxygenString[currentIndex] == '\t'))
+      currentIndex++;
 
-        // skip WS, except \n
-		while(currentIndex < doxygenString.length() && (doxygenString[currentIndex] == ' ' 
-			|| doxygenString[currentIndex]== '\t')) currentIndex ++;
+    if (currentIndex < doxygenString.length()) {
 
-        if (currentIndex < doxygenString.length()) {
+      nextIndex = currentIndex;
 
-            nextIndex = currentIndex;
+      // skip non WS
+      while (nextIndex < doxygenString.length() && (doxygenString[nextIndex] != ' ' && doxygenString[nextIndex] != '\t' && doxygenString[nextIndex] != '\n'))
+	nextIndex++;
 
-            // skip non WS
-		while (nextIndex  < doxygenString.length() && (doxygenString[nextIndex] != ' ' 
-                   && doxygenString[nextIndex] != '\t' && doxygenString[nextIndex]!= '\n')) 
-                nextIndex++;
+      // now we have a token
+      currentWord = doxygenString.substr(currentIndex, nextIndex - currentIndex);
 
-            // now we have a token
-		currentWord = doxygenString.substr(currentIndex, nextIndex-currentIndex);
+      if (noisy2)
+	cout << "Current Word: " << currentWord << endl;
 
-            if(noisy2) 
-                cout << "Current Word: " << currentWord << endl;
+      if (currentWord[0] == '@' || currentWord[0] == '\\') {
+	// it is doxygen command
+	currentWord = currentWord.substr(1, currentWord.length() - 1);
+	m_tokenList.push_back(Token(COMMAND, currentWord));
 
-		if (currentWord[0] == '@' || currentWord[0] == '\\'){
-                // it is doxygen command
-			currentWord = currentWord.substr(1, currentWord.length()-1);
-                m_tokenList.push_back(Token(COMMAND, currentWord));
+      } else if (currentWord[0] == '\n') {
 
-            } else if (currentWord[0] == '\n'){
+	m_tokenList.push_back(Token(END_LINE, currentWord));
 
-                m_tokenList.push_back(Token(END_LINE, currentWord));
-			
-		}
-		else if (currentWord[0] == '*' || currentWord[0] == '/' ||currentWord[0] == '!'){
-				
-                bool isPlainString = false;
+      } else if (currentWord[0] == '*' || currentWord[0] == '/' || currentWord[0] == '!') {
 
-                if (currentWord.length() > 1) {
+	bool isPlainString = false;
 
-                    for(size_t i = 1; i < currentWord.length(); i++){
-                        if (currentWord[i] != '*' && currentWord[i] != '/' && 
-                            currentWord[i] != '!') {
-                                isPlainString = true;
-                                break;
-                        }
-			}
-		}
-		
-                if(isPlainString) 
-                    m_tokenList.push_back(Token(PLAINSTRING, currentWord));
+	if (currentWord.length() > 1) {
 
-            } else if (!currentWord.empty()) {
-                m_tokenList.push_back(Token(PLAINSTRING, currentWord));
-            }
-		currentIndex = nextIndex;
-	}
+	  for (size_t i = 1; i < currentWord.length(); i++) {
+	    if (currentWord[i] != '*' && currentWord[i] != '/' && currentWord[i] != '!') {
+	      isPlainString = true;
+	      break;
+	    }
+	  }
 	}
 
-    m_tokenListIter = m_tokenList.begin(); 
+	if (isPlainString)
+	  m_tokenList.push_back(Token(PLAINSTRING, currentWord));
+
+      } else if (!currentWord.empty()) {
+	m_tokenList.push_back(Token(PLAINSTRING, currentWord));
+      }
+      currentIndex = nextIndex;
+    }
+  }
+
+  m_tokenListIter = m_tokenList.begin();
 }
 
 
-TokenList::	~TokenList(){
+TokenList::~TokenList() {
 }
 
-Token TokenList::peek(){
-    if(m_tokenListIter!= m_tokenList.end()){
-        Token returnedToken = (*m_tokenListIter);
-		return returnedToken;
-	}
-	else
-		return Token(0, "");
-} 
-
-
-Token TokenList::next(){
-    if(m_tokenListIter != m_tokenList.end()){
-        Token returnedToken = (*m_tokenListIter);
-        m_tokenListIter++;
-		return (returnedToken);
-	}
-	else
-		return Token(0, "");
-} 	
-
-
-list<Token>::iterator TokenList::end(){
-	return m_tokenList.end();
+Token TokenList::peek() {
+  if (m_tokenListIter != m_tokenList.end()) {
+    Token returnedToken = (*m_tokenListIter);
+    return returnedToken;
+  } else
+    return Token(0, "");
 }
 
 
-list<Token>::iterator TokenList::current(){
+Token TokenList::next() {
+  if (m_tokenListIter != m_tokenList.end()) {
+    Token returnedToken = (*m_tokenListIter);
+    m_tokenListIter++;
+    return (returnedToken);
+  } else
+    return Token(0, "");
+}
+
+
+list < Token >::iterator TokenList::end() {
+  return m_tokenList.end();
+}
+
+
+list < Token >::iterator TokenList::current() {
   return m_tokenListIter;
 }
 
 
-list<Token>::iterator TokenList::iteratorCopy(){
+list < Token >::iterator TokenList::iteratorCopy() {
   return m_tokenListIter;
 }
 
 
-void TokenList::setIterator(list<Token>::iterator newPosition){
+void TokenList::setIterator(list < Token >::iterator newPosition) {
   m_tokenListIter = newPosition;
 }
 
 
-void TokenList::printList(){
-    list<Token>::iterator p = m_tokenList.begin();
-			int i = 1;
-			int b = 0;
-    while (p != m_tokenList.end()){
-				cout << (*p).toString() << " ";
-				b = i%TOKENSPERLINE;
-				if (b == 0) cout << endl;
-				p++; i++;
-			}
+void TokenList::printList() {
+  list < Token >::iterator p = m_tokenList.begin();
+  int i = 1;
+  int b = 0;
+  while (p != m_tokenList.end()) {
+    cout << (*p).toString() << " ";
+    b = i % TOKENSPERLINE;
+    if (b == 0)
+      cout << endl;
+    p++;
+    i++;
+  }
 }
-
diff --git a/Source/DoxygenTranslator/src/TokenList.h b/Source/DoxygenTranslator/src/TokenList.h
index 0f5710e0f..841d66e1a 100644
--- a/Source/DoxygenTranslator/src/TokenList.h
+++ b/Source/DoxygenTranslator/src/TokenList.h
@@ -10,25 +10,25 @@
  * that can be derived from a formatted doxygen string
  */
 
-class TokenList{
+class TokenList {
 private:
-  std::list<Token> m_tokenList;
-  std::list<Token>::iterator m_tokenListIter;
+  std::list < Token > m_tokenList;
+  std::list < Token >::iterator m_tokenListIter;
 
 public:
-	TokenList(const std::string &doxygenString); /* constructor takes a blob of Doxygen comment */
-	~TokenList();
+  TokenList(const std::string & doxygenString);	/* constructor takes a blob of Doxygen comment */
+  ~TokenList();
 
-	Token peek(); 	/* returns next token without advancing */
-	Token next(); 	/* returns next token and advances */
+  Token peek();			/* returns next token without advancing */
+  Token next();			/* returns next token and advances */
 
-	std::list<Token>::iterator end(); /* returns an end iterator */
-	std::list<Token>::iterator current(); /* returns the current iterator */
+  std::list < Token >::iterator end();	/* returns an end iterator */
+  std::list < Token >::iterator current();	/* returns the current iterator */
 
-	std::list<Token>::iterator iteratorCopy(); /* returns a copy of the current iterator */
-	void setIterator(list<Token>::iterator  newPosition); /*moves up the iterator*/
+  std::list < Token >::iterator iteratorCopy();	/* returns a copy of the current iterator */
+  void setIterator(list < Token >::iterator newPosition);	/*moves up the iterator */
 
-	void printList(); /* prints out the sequence of tokens */
+  void printList();		/* prints out the sequence of tokens */
 };
 
-#endif /*TOKENLIST_H_*/
+#endif

From 06269a50a5a1af69f856c41d0eecdb9e167f0bbe Mon Sep 17 00:00:00 2001
From: William S Fulton <wsf@fultondesigns.co.uk>
Date: Sun, 1 Nov 2009 22:05:01 +0000
Subject: [PATCH 041/314] Apply modified patch 2879724 from Marko Klopcic

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2008-cherylfoil@11716 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Source/DoxygenTranslator/src/PyDocConverter.cpp | 12 +++++++++++-
 Source/Modules/java.cxx                         |  4 ++--
 2 files changed, 13 insertions(+), 3 deletions(-)

diff --git a/Source/DoxygenTranslator/src/PyDocConverter.cpp b/Source/DoxygenTranslator/src/PyDocConverter.cpp
index 44dec4cbf..cbe81571b 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/PyDocConverter.cpp
@@ -19,6 +19,13 @@ PyDocConverter::PyDocConverter() {
 }
 
 std::string PyDocConverter::formatParam(Node *n, DoxygenEntity & doxygenEntity) {
+
+  if (doxygenEntity.entityList.size() < 2) {
+    /* if 'paramDescriptionEntity' is not there, ignore param. Better than crash!
+       TODO: log error! */
+    return "";
+  }
+
   ParmList *plist = CopyParmList(Getattr(n, "parms"));
   Parm *p = NULL;
 
@@ -34,7 +41,10 @@ std::string PyDocConverter::formatParam(Node *n, DoxygenEntity & doxygenEntity)
       std::string type = Char(Swig_name_make(n, 0, Getattr(p, "type"), 0, 0));
 
       result = name + " (" + type + ") ";
-      result.resize(DOC_PARAM_STRING_LENGTH - 3, ' ');
+      if (result.size() < (DOC_PARAM_STRING_LENGTH - 3)) {
+	/* do not cut info away - it is better to have not so nice output than type information missing. */
+	result.resize(DOC_PARAM_STRING_LENGTH - 3, ' ');
+      }
       result += "-- " + paramDescription.substr(DOC_PARAM_STRING_LENGTH);
       break;
     }
diff --git a/Source/Modules/java.cxx b/Source/Modules/java.cxx
index 532dfd305..0c5ad5401 100644
--- a/Source/Modules/java.cxx
+++ b/Source/Modules/java.cxx
@@ -2533,10 +2533,10 @@ public:
     // translate and write javadoc comment if flagged
     if (doxygen_javadoc_flag){
       String *doxygen_comments;
-      if(DoxygenTranslator::getDocumentation(n, JavaDoc, doxygen_comments)){
+      if(DoxygenTranslator::getDocumentation(n, JavaDoc, doxygen_comments)) {
 	if(comment_creation_chatter)
 	  Printf(function_code, "/* This was generated from moduleClassFunctionHandler() */");
-	Printf(function_code, Char(doxygen_comments)); 
+	Printv(function_code, doxygen_comments, NIL);
 	Delete(doxygen_comments);
       }
     }

From 2b1f0a14bcc9649be42f34cd7812ab09c6963f0b Mon Sep 17 00:00:00 2001
From: William S Fulton <wsf@fultondesigns.co.uk>
Date: Fri, 5 Mar 2010 23:43:39 +0000
Subject: [PATCH 042/314] merge revisions 11872:11876 from trunk to
 gsoc2008-cherylfoil branch - license changes

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2008-cherylfoil@11900 626c5289-ae23-0410-ae9c-e8d60b6d4f22
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 Source/Swig/swigopt.h                         |    8 +-
 Source/Swig/swigparm.h                        |    8 +-
 Source/Swig/swigscan.h                        |    8 +-
 Source/Swig/swigtree.h                        |    8 +-
 Source/Swig/swigwrap.h                        |    8 +-
 Source/Swig/symbol.c                          |    8 +-
 Source/Swig/tree.c                            |    8 +-
 Source/Swig/typemap.c                         |    8 +-
 Source/Swig/typeobj.c                         |    8 +-
 Source/Swig/typesys.c                         |    8 +-
 Source/Swig/wrapfunc.c                        |    8 +-
 configure.in                                  |    4 +-
 426 files changed, 1379 insertions(+), 12512 deletions(-)
 create mode 100644 COPYRIGHT
 delete mode 100644 Examples/GIFPlot/Chicken/check.list
 delete mode 100644 Examples/GIFPlot/Chicken/full/Makefile
 delete mode 100644 Examples/GIFPlot/Chicken/full/README
 delete mode 100644 Examples/GIFPlot/Chicken/full/cmap
 delete mode 100644 Examples/GIFPlot/Chicken/full/gifplot.i
 delete mode 100644 Examples/GIFPlot/Chicken/full/test-gifplot.scm
 delete mode 100644 Examples/GIFPlot/Chicken/simple/Makefile
 delete mode 100644 Examples/GIFPlot/Chicken/simple/README
 delete mode 100644 Examples/GIFPlot/Chicken/simple/simple.i
 delete mode 100644 Examples/GIFPlot/Chicken/simple/test-simple.scm
 delete mode 100644 Examples/GIFPlot/Common-Lisp/full/cmap
 delete mode 100644 Examples/GIFPlot/Common-Lisp/full/gifplot.i
 delete mode 100644 Examples/GIFPlot/Common-Lisp/full/runme.lisp
 delete mode 100644 Examples/GIFPlot/Guile/check.list
 delete mode 100644 Examples/GIFPlot/Guile/full/Makefile
 delete mode 100644 Examples/GIFPlot/Guile/full/README
 delete mode 100644 Examples/GIFPlot/Guile/full/cmap
 delete mode 100644 Examples/GIFPlot/Guile/full/gifplot.i
 delete mode 100644 Examples/GIFPlot/Guile/full/runme.scm
 delete mode 100644 Examples/GIFPlot/Guile/simple/Makefile
 delete mode 100644 Examples/GIFPlot/Guile/simple/README
 delete mode 100644 Examples/GIFPlot/Guile/simple/runme.scm
 delete mode 100644 Examples/GIFPlot/Guile/simple/simple.i
 delete mode 100644 Examples/GIFPlot/Include/gifplot.h
 delete mode 100644 Examples/GIFPlot/Interface/gifplot.i
 delete mode 100644 Examples/GIFPlot/Java/check.list
 delete mode 100644 Examples/GIFPlot/Java/full/Makefile
 delete mode 100644 Examples/GIFPlot/Java/full/README
 delete mode 100644 Examples/GIFPlot/Java/full/cmap
 delete mode 100644 Examples/GIFPlot/Java/full/gifplot.i
 delete mode 100644 Examples/GIFPlot/Java/full/main.java
 delete mode 100644 Examples/GIFPlot/Java/shadow/Makefile
 delete mode 100644 Examples/GIFPlot/Java/shadow/README
 delete mode 100644 Examples/GIFPlot/Java/shadow/cmap
 delete mode 100644 Examples/GIFPlot/Java/shadow/main.java
 delete mode 100644 Examples/GIFPlot/Java/simple/Makefile
 delete mode 100644 Examples/GIFPlot/Java/simple/README
 delete mode 100644 Examples/GIFPlot/Java/simple/main.java
 delete mode 100644 Examples/GIFPlot/Java/simple/simple.i
 delete mode 100644 Examples/GIFPlot/Lib/Makefile.in
 delete mode 100644 Examples/GIFPlot/Lib/color.c
 delete mode 100644 Examples/GIFPlot/Lib/font.c
 delete mode 100644 Examples/GIFPlot/Lib/frame.c
 delete mode 100644 Examples/GIFPlot/Lib/gif.c
 delete mode 100644 Examples/GIFPlot/Lib/matrix.c
 delete mode 100644 Examples/GIFPlot/Lib/pixmap.c
 delete mode 100644 Examples/GIFPlot/Lib/plot2d.c
 delete mode 100644 Examples/GIFPlot/Lib/plot3d.c
 delete mode 100644 Examples/GIFPlot/Makefile.in
 delete mode 100644 Examples/GIFPlot/Ocaml/check.list
 delete mode 100644 Examples/GIFPlot/Ocaml/full/Makefile
 delete mode 100644 Examples/GIFPlot/Ocaml/full/README
 delete mode 100644 Examples/GIFPlot/Ocaml/full/cmap
 delete mode 100644 Examples/GIFPlot/Ocaml/full/gifplot.i
 delete mode 100644 Examples/GIFPlot/Ocaml/full/runme.ml
 delete mode 100644 Examples/GIFPlot/Ocaml/simple/Makefile
 delete mode 100644 Examples/GIFPlot/Ocaml/simple/cmap
 delete mode 100644 Examples/GIFPlot/Ocaml/simple/runme.ml
 delete mode 100644 Examples/GIFPlot/Ocaml/simple/simple.i
 delete mode 100644 Examples/GIFPlot/Perl5/check.list
 delete mode 100644 Examples/GIFPlot/Perl5/full/Makefile
 delete mode 100644 Examples/GIFPlot/Perl5/full/README
 delete mode 100644 Examples/GIFPlot/Perl5/full/cmap
 delete mode 100644 Examples/GIFPlot/Perl5/full/gifplot.i
 delete mode 100644 Examples/GIFPlot/Perl5/full/runme.pl
 delete mode 100644 Examples/GIFPlot/Perl5/shadow/Makefile
 delete mode 100644 Examples/GIFPlot/Perl5/shadow/README
 delete mode 100644 Examples/GIFPlot/Perl5/shadow/cmap
 delete mode 100644 Examples/GIFPlot/Perl5/shadow/runme.pl
 delete mode 100644 Examples/GIFPlot/Perl5/simple/Makefile
 delete mode 100644 Examples/GIFPlot/Perl5/simple/README
 delete mode 100644 Examples/GIFPlot/Perl5/simple/runme.pl
 delete mode 100644 Examples/GIFPlot/Perl5/simple/simple.i
 delete mode 100644 Examples/GIFPlot/Php4/check.list
 delete mode 100644 Examples/GIFPlot/Php4/full/Makefile
 delete mode 100644 Examples/GIFPlot/Php4/full/README
 delete mode 100644 Examples/GIFPlot/Php4/full/cmap
 delete mode 100644 Examples/GIFPlot/Php4/full/gifplot.i
 delete mode 100644 Examples/GIFPlot/Php4/full/runme.php4
 delete mode 100644 Examples/GIFPlot/Php4/shadow/Makefile
 delete mode 100644 Examples/GIFPlot/Php4/shadow/README
 delete mode 100644 Examples/GIFPlot/Php4/shadow/cmap
 delete mode 100644 Examples/GIFPlot/Php4/shadow/runme.php4
 delete mode 100644 Examples/GIFPlot/Php4/simple/Makefile
 delete mode 100644 Examples/GIFPlot/Php4/simple/README
 delete mode 100644 Examples/GIFPlot/Php4/simple/runme.php4
 delete mode 100644 Examples/GIFPlot/Php4/simple/simple.i
 delete mode 100644 Examples/GIFPlot/Pike/check.list
 delete mode 100644 Examples/GIFPlot/Pike/simple/Makefile
 delete mode 100644 Examples/GIFPlot/Pike/simple/README
 delete mode 100644 Examples/GIFPlot/Pike/simple/runme.pike
 delete mode 100644 Examples/GIFPlot/Pike/simple/simple.i
 delete mode 100644 Examples/GIFPlot/Python/check.list
 delete mode 100644 Examples/GIFPlot/Python/full/Makefile
 delete mode 100644 Examples/GIFPlot/Python/full/README
 delete mode 100644 Examples/GIFPlot/Python/full/cmap
 delete mode 100644 Examples/GIFPlot/Python/full/gifplot.i
 delete mode 100644 Examples/GIFPlot/Python/full/runme.py
 delete mode 100644 Examples/GIFPlot/Python/shadow/Makefile
 delete mode 100644 Examples/GIFPlot/Python/shadow/README
 delete mode 100644 Examples/GIFPlot/Python/shadow/cmap
 delete mode 100644 Examples/GIFPlot/Python/shadow/runme.py
 delete mode 100644 Examples/GIFPlot/Python/simple/Makefile
 delete mode 100644 Examples/GIFPlot/Python/simple/README
 delete mode 100644 Examples/GIFPlot/Python/simple/runme.py
 delete mode 100644 Examples/GIFPlot/Python/simple/simple.i
 delete mode 100644 Examples/GIFPlot/README
 delete mode 100644 Examples/GIFPlot/Ruby/check.list
 delete mode 100644 Examples/GIFPlot/Ruby/full/Makefile
 delete mode 100644 Examples/GIFPlot/Ruby/full/README
 delete mode 100644 Examples/GIFPlot/Ruby/full/cmap
 delete mode 100644 Examples/GIFPlot/Ruby/full/gifplot.i
 delete mode 100644 Examples/GIFPlot/Ruby/full/runme.rb
 delete mode 100644 Examples/GIFPlot/Ruby/shadow/Makefile
 delete mode 100644 Examples/GIFPlot/Ruby/shadow/README
 delete mode 100644 Examples/GIFPlot/Ruby/shadow/cmap
 delete mode 100644 Examples/GIFPlot/Ruby/shadow/runme.rb
 delete mode 100644 Examples/GIFPlot/Ruby/simple/Makefile
 delete mode 100644 Examples/GIFPlot/Ruby/simple/README
 delete mode 100644 Examples/GIFPlot/Ruby/simple/runme.rb
 delete mode 100644 Examples/GIFPlot/Ruby/simple/simple.i
 delete mode 100644 Examples/GIFPlot/Tcl/check.list
 delete mode 100644 Examples/GIFPlot/Tcl/full/Makefile
 delete mode 100644 Examples/GIFPlot/Tcl/full/README
 delete mode 100644 Examples/GIFPlot/Tcl/full/cmap
 delete mode 100644 Examples/GIFPlot/Tcl/full/gifplot.i
 delete mode 100644 Examples/GIFPlot/Tcl/full/runme.tcl
 delete mode 100644 Examples/GIFPlot/Tcl/mandel/Makefile
 delete mode 100644 Examples/GIFPlot/Tcl/mandel/README
 delete mode 100644 Examples/GIFPlot/Tcl/mandel/cmap
 delete mode 100644 Examples/GIFPlot/Tcl/mandel/display.tcl
 delete mode 100644 Examples/GIFPlot/Tcl/mandel/mandel.i
 delete mode 100644 Examples/GIFPlot/Tcl/mandel/mandel.tcl
 delete mode 100644 Examples/GIFPlot/Tcl/simple/Makefile
 delete mode 100644 Examples/GIFPlot/Tcl/simple/README
 delete mode 100644 Examples/GIFPlot/Tcl/simple/runme.tcl
 delete mode 100644 Examples/GIFPlot/Tcl/simple/simple.i
 delete mode 100644 Examples/chicken/zlib/Makefile
 delete mode 100644 Examples/chicken/zlib/README.html
 delete mode 100644 Examples/chicken/zlib/example.i
 delete mode 100644 Examples/chicken/zlib/test-zlib.scm
 delete mode 100644 Examples/xml/example_gif.i
 create mode 100644 LICENSE-GPL
 create mode 100644 LICENSE-UNIVERSITIES
 delete mode 100644 Lib/tcl/mactclinit.c

diff --git a/ANNOUNCE b/ANNOUNCE
index 7c0e95e3f..5f19da9c0 100644
--- a/ANNOUNCE
+++ b/ANNOUNCE
@@ -1,11 +1,11 @@
-*** ANNOUNCE: SWIG 1.3.36 (24 June 2008) ***
+*** ANNOUNCE: SWIG 2.0.0 (in progress) ***
 
 http://www.swig.org
 
 
-We're pleased to announce SWIG-1.3.36, the latest installment in the
-SWIG development effort.  SWIG-1.3.36 includes a number of bug fixes
-and large number of enhancements throughout.
+We're pleased to announce SWIG-2.0.0, the latest installment in the
+SWIG development effort.  SWIG-2.0.0 includes a number of bug fixes
+and enhancements.
 
 What is SWIG?
 -------------
@@ -24,11 +24,11 @@ Availability:
 -------------
 The release is available for download on Sourceforge at
 
-     http://prdownloads.sourceforge.net/swig/swig-1.3.36.tar.gz
+     http://prdownloads.sourceforge.net/swig/swig-2.0.0.tar.gz
 
 A Windows version is also available at
 
-     http://prdownloads.sourceforge.net/swig/swigwin-1.3.36.zip
+     http://prdownloads.sourceforge.net/swig/swigwin-2.0.0.zip
 
 Release numbers
 ---------------
diff --git a/COPYRIGHT b/COPYRIGHT
new file mode 100644
index 000000000..45f9d6b45
--- /dev/null
+++ b/COPYRIGHT
@@ -0,0 +1,63 @@
+SWIG Copyright and Authors
+--------------------------
+
+Copyright (c) 1995-2010 The SWIG Developers
+Copyright (c) 2005-2006 Arizona Board of Regents (University of Arizona).
+Copyright (c) 1998-2005 University of Chicago.
+Copyright (c) 1995-1998 The University of Utah and the Regents of the University of California
+
+Portions also copyrighted by:
+ Network Applied Communication Laboratory, Inc
+ Information-technology Promotion Agency, Japan
+
+Active SWIG Developers:
+ William Fulton (wsf@fultondesigns.co.uk)               (SWIG core, Java, C#, Windows, Cygwin)
+ Olly Betts (olly@survex.com)                           (PHP)
+ Joseph Wang (joequant@gmail.com)                       (R)
+ Xavier Delacour (xavier.delacour@gmail.com)            (Octave)
+
+Past SWIG developers and major contributors include:
+ Dave Beazley (dave-swig@dabeaz.com)                    (SWIG core, Python, Tcl, Perl)
+ Henning Thielemann (swig@henning-thielemann.de)        (Modula3)
+ Matthias Köppe (mkoeppe@mail.math.uni-magdeburg.de)    (Guile, MzScheme)
+ Luigi Ballabio (luigi.ballabio@fastwebnet.it)          (STL wrapping)
+ Mikel Bancroft (mikel@franz.com)                       (Allegro CL)
+ Surendra Singhi (efuzzyone@netscape.net)               (CLISP, CFFI)
+ Marcelo Matus (mmatus@acms.arizona.edu)                (SWIG core, Python, UTL[python,perl,tcl,ruby])
+ Art Yerkes (ayerkes@speakeasy.net)                     (Ocaml)
+ Lyle Johnson (lyle@users.sourceforge.net)              (Ruby)
+ Charlie Savage (cfis@interserv.com)                    (Ruby)
+ Thien-Thi Nguyen (ttn@glug.org)                        (build/test/misc)
+ Richard Palmer (richard@magicality.org)                (PHP)
+ Sam Liddicott - Anonova Ltd (saml@liddicott.com)       (PHP)
+ Tim Hockin - Sun Microsystems (thockin@sun.com)        (PHP)
+ Kevin Ruland                                           (PHP)
+ Shibukawa Yoshiki                                      (Japanese Translation)
+ Jason Stewart (jason@openinformatics.com)              (Perl5)
+ Loic Dachary                                           (Perl5)
+ David Fletcher                                         (Perl5)
+ Gary Holt                                              (Perl5)
+ Masaki Fukushima                                       (Ruby)
+ Scott Michel (scottm@cs.ucla.edu)                      (Java directors)
+ Tiger Feng (songyanf@cs.uchicago.edu)                  (SWIG core)
+ Mark Rose (mrose@stm.lbl.gov)                          (Directors)
+ Jonah Beckford (beckford@usermail.com)                 (CHICKEN)
+ Ahmon Dancy (dancy@franz.com)				(Allegro CL)
+ Dirk Gerrits                                           (Allegro CL)
+ Neil Cawse                                             (C#)
+ Harco de Hilster                                       (Java)
+ Alexey Dyachenko (dyachenko@fromru.com)                (Tcl)
+ Bob Techentin                                          (Tcl)
+ Martin Froehlich <MartinFroehlich@ACM.org>             (Guile)
+ Marcio Luis Teixeira <marciot@holly.colostate.edu>     (Guile)
+ Duncan Temple Lang                                     (R)
+ Miklos Vajna <vmiklos@frugalware.org>                  (PHP directors)
+ Mark Gossage (mark@gossage.cjb.net)                    (Lua)
+ Gonzalo Garramuno (ggarra@advancedsl.com.ar)           (Ruby, Ruby's UTL)
+ John Lenz                                              (Guile, MzScheme updates, Chicken module, runtime system)
+
+Past contributors include:
+ James Michael DuPont, Clark McGrew, Dustin Mitchell, Ian Cooke, Catalin Dumitrescu, Baran
+ Kovuk, Oleg Tolmatcev, Tal Shalif, Lluis Padro, Chris Seatory, Igor Bely, Robin Dunn
+ (See CHANGES and CHANGES.current for a more complete list).
+
diff --git a/Doc/Manual/Sections.html b/Doc/Manual/Sections.html
index 5406f44ea..98f90bc1b 100644
--- a/Doc/Manual/Sections.html
+++ b/Doc/Manual/Sections.html
@@ -6,7 +6,7 @@
 <body bgcolor="#ffffff">
 <H1><a name="Sections"></a>SWIG-1.3 Development Documentation</H1>
 
-Last update : SWIG-1.3.37 (in progress)
+Last update : SWIG-2.0.0 (in progress)
 
 <H2>Sections</H2>
 
diff --git a/Examples/GIFPlot/Chicken/check.list b/Examples/GIFPlot/Chicken/check.list
deleted file mode 100644
index e75ee586a..000000000
--- a/Examples/GIFPlot/Chicken/check.list
+++ /dev/null
@@ -1,3 +0,0 @@
-# see top-level Makefile.in
-full
-simple
diff --git a/Examples/GIFPlot/Chicken/full/Makefile b/Examples/GIFPlot/Chicken/full/Makefile
deleted file mode 100644
index 2ae4fd7ea..000000000
--- a/Examples/GIFPlot/Chicken/full/Makefile
+++ /dev/null
@@ -1,28 +0,0 @@
-TOP         = ../../..
-SWIG        = $(TOP)/../preinst-swig
-INTERFACE   = gifplot.i
-SRCS        = 
-CXXSRCS     = 
-TARGET      = gifplot
-INCLUDE     = -I. -I../../Include
-SWIGOPT     = -I../../Include
-CFLAGS      = 
-VARIANT     = 
-LIBS        = -L../.. -lgifplot -lm
-
-# comment the following two lines to build a dynamic so file
-CHICKEN_MAIN = test-gifplot.scm
-VARIANT      = _static
-
-all:: $(TARGET)
-
-$(TARGET): $(INTERFACE) $(SRCS)
-	$(MAKE) -f $(TOP)/Makefile \
-		SRCS='$(SRCS)' CXXSRCS='$(CXXSRCS)' CHICKEN_MAIN='$(CHICKEN_MAIN)' \
-		INCLUDE='$(INCLUDE)' SWIGOPT='$(SWIGOPT)' LIBS='$(LIBS)' TARGET='$(TARGET)' \
-		SWIG='$(SWIG)' INTERFACE='$(INTERFACE)' CHICKENOPTS='$(CHICKENOPTS)' chicken$(VARIANT)
-
-clean::
-	$(MAKE) -f $(TOP)/Makefile chicken_clean
-	rm -f gifplot.scm image.gif
-	rm -f $(TARGET)
diff --git a/Examples/GIFPlot/Chicken/full/README b/Examples/GIFPlot/Chicken/full/README
deleted file mode 100644
index e5ddd7af1..000000000
--- a/Examples/GIFPlot/Chicken/full/README
+++ /dev/null
@@ -1,6 +0,0 @@
-This example runs the entire gifplot.h header file through SWIG without
-any changes.  The Scheme program 'test-gifplot.scm' does something a 
-little more interesting.  You'll have to go look at the header file to
-get a complete listing of the functions.
-
-`make' will build a static binary.  Run ./gifplot to test it.
diff --git a/Examples/GIFPlot/Chicken/full/cmap b/Examples/GIFPlot/Chicken/full/cmap
deleted file mode 100644
index a20c331a9573dd8443380680bfe2cc428780d8a9..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

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znmh34m-nxpKDd4D;+bOy_iW#^cE#d(Gbi_Tw$xXZ7G$R-M27|XxI5We80l&#%Snpx
zbFrd(h8Vt}lCeu@T6xFJRlCpJeMef510DGC$^DyG&YwK8f9IC<tCq~4HKo4`=)RKt
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Xo3`&c2#k+ww;w!x^&XgFNDnap(k+Jt

diff --git a/Examples/GIFPlot/Chicken/full/gifplot.i b/Examples/GIFPlot/Chicken/full/gifplot.i
deleted file mode 100644
index f6741864a..000000000
--- a/Examples/GIFPlot/Chicken/full/gifplot.i
+++ /dev/null
@@ -1,26 +0,0 @@
-/* Oh what the heck, let's just grab the whole darn header file
-   and see what happens. */
-
-%module gifplot
-%{
-
-/* Note: You still need this part because the %include directive
-   merely causes SWIG to interpret the contents of a file.  It doesn't
-   include the right include headers for the resulting C code */
-
-#include "gifplot.h"
-
-%}
-
-/* Pixel is typedef'd to unsigned char, and SWIG will translate this
-   type into Scheme characters. We would like to translate Pixels to
-   Scheme integers instead, so: */
-
-SIMPLE_TYPEMAP(Pixel, C_unfix, C_fix, C_swig_is_fixnum, (int), 0);
-
-%{
-static Pixel int_to_Pixel (int v) { return (Pixel) v; }
-%}
-extern Pixel int_to_Pixel (int v);
-
-%include gifplot.h
diff --git a/Examples/GIFPlot/Chicken/full/test-gifplot.scm b/Examples/GIFPlot/Chicken/full/test-gifplot.scm
deleted file mode 100644
index c290af54d..000000000
--- a/Examples/GIFPlot/Chicken/full/test-gifplot.scm
+++ /dev/null
@@ -1,66 +0,0 @@
-;;; Plot a 3D function
-
-(declare (uses gifplot))
-
-;; Here is the function to plot
-(define (func x y)
-  (* 5
-     (cos (* 2 (sqrt (+ (* x x) (* y y)))))
-     (exp (* -0.3 (sqrt (+ (* x x) (* y y)))))))
-
-;; Here are some plotting parameters
-(define xmin -5.0)
-(define xmax  5.0)
-(define ymin -5.0)
-(define ymax  5.0)
-(define zmin -5.0)
-(define zmax  5.0)
-
-;; Grid resolution
-(define nxpoints  60)
-(define nypoints  60)
-
-(define cmap (gifplot:new-ColorMap "cmap"))
-(define frame (gifplot:new-FrameBuffer 500 500))
-(gifplot:FrameBuffer-clear frame (gifplot:BLACK))
-
-(define p3 (gifplot:new-Plot3D frame xmin ymin zmin xmax ymax zmax))
-(gifplot:Plot3D-lookat p3 (* 2 (- zmax zmin)))
-(gifplot:Plot3D-autoperspective p3 40.0)
-(gifplot:Plot3D-rotu p3 60.0)
-(gifplot:Plot3D-rotr p3 30.0)
-(gifplot:Plot3D-rotd p3 10.0)
-
-(define (drawsolid)
-  (gifplot:Plot3D-clear p3 (gifplot:BLACK))
-  (gifplot:Plot3D-start p3)
-  (let ((dx (/ (- xmax xmin) nxpoints))
-	(dy (/ (- ymax ymin) nypoints))
-	(cscale (/ 240 (- zmax zmin))))
-    (let x-loop ((x xmin) (i 0))
-      (cond
-       ((< i nxpoints)
-	(let y-loop ((y ymin) (j 0))
-	  (cond
-	   ((< j nypoints)
-	    (let* ((z1 (func x y))
-		   (z2 (func (+ x dx) y))
-		   (z3 (func (+ x dx) (+ y dy)))
-		   (z4 (func x (+ y dy)))
-		   (c1 (* cscale (- z1 zmin)))
-		   (c2 (* cscale (- z2 zmin)))
-		   (c3 (* cscale (- z3 zmin)))
-		   (c4 (* cscale (- z4 zmin)))
-		   (cc (/ (+ c1 c2 c3 c4) 4))
-		   (c  (inexact->exact (round (max (min cc 239) 0)))))
-	      (gifplot:Plot3D-solidquad p3 x y z1 (+ x dx) y z2 (+ x dx) (+ y dy)
-				z3 x (+ y dy) z4 
-                                (gifplot:int->Pixel (+ c 16))))
-	    (y-loop (+ y dy) (+ j 1)))))
-	(x-loop (+ x dx) (+ i 1)))))))
-
-(display "Making a nice 3D plot...\n")
-(drawsolid)
-
-(gifplot:FrameBuffer-writeGIF frame cmap "image.gif")
-(display "Wrote image.gif\n")
diff --git a/Examples/GIFPlot/Chicken/simple/Makefile b/Examples/GIFPlot/Chicken/simple/Makefile
deleted file mode 100644
index 484e58390..000000000
--- a/Examples/GIFPlot/Chicken/simple/Makefile
+++ /dev/null
@@ -1,28 +0,0 @@
-TOP         = ../../..
-SWIG        = $(TOP)/../preinst-swig
-INTERFACE   = simple.i
-SRCS        = 
-CXXSRCS     = 
-TARGET      = simple
-INCLUDE     = -I. -I../../Include
-SWIGOPT     = -I../../Include
-CFLAGS      = 
-VARIANT     = 
-LIBS        = -L../.. -lgifplot -lm
-
-# comment the following two lines to build a dynamic so file
-CHICKEN_MAIN = test-simple.scm
-VARIANT      = _static
-
-all:: $(TARGET)
-
-$(TARGET): $(INTERFACE) $(SRCS)
-	$(MAKE) -f $(TOP)/Makefile \
-		SRCS='$(SRCS)' CXXSRCS='$(CXXSRCS)' CHICKEN_MAIN='$(CHICKEN_MAIN)' \
-		INCLUDE='$(INCLUDE)' SWIGOPT='$(SWIGOPT)' LIBS='$(LIBS)' TARGET='$(TARGET)' \
-		SWIG='$(SWIG)' INTERFACE='$(INTERFACE)' CHICKENOPTS='$(CHICKENOPTS)' chicken$(VARIANT)
-
-clean::
-	$(MAKE) -f $(TOP)/Makefile chicken_clean
-	rm -f simple.scm image.gif
-	rm -f $(TARGET)
diff --git a/Examples/GIFPlot/Chicken/simple/README b/Examples/GIFPlot/Chicken/simple/README
deleted file mode 100644
index 3b138f381..000000000
--- a/Examples/GIFPlot/Chicken/simple/README
+++ /dev/null
@@ -1,5 +0,0 @@
-This is a very minimalistic example in which just a few functions
-and constants from library are wrapped and used to draw some simple
-shapes.  
-
-`make' will build an exe.  Run ./simple to test it.
diff --git a/Examples/GIFPlot/Chicken/simple/simple.i b/Examples/GIFPlot/Chicken/simple/simple.i
deleted file mode 100644
index 23ac8a856..000000000
--- a/Examples/GIFPlot/Chicken/simple/simple.i
+++ /dev/null
@@ -1,34 +0,0 @@
-/* This example shows a very simple interface wrapping a few 
-   primitive declarations */
-
-%module simple
-%{
-#include "gifplot.h"
-%}
-
-typedef unsigned int Pixel;
-
-/* Here are a few useful functions */
-
-ColorMap    *new_ColorMap(char *filename = 0);
-void         delete_ColorMap(ColorMap *cmap);
-
-FrameBuffer *new_FrameBuffer(unsigned int width, unsigned int height);
-void         delete_FrameBuffer(FrameBuffer *frame);
-void         FrameBuffer_clear(FrameBuffer *frame, Pixel color);
-void         FrameBuffer_line(FrameBuffer *frame, int x1, int y1, int x2, int y2, Pixel color);
-void         FrameBuffer_box(FrameBuffer *frame, int x1, int y1, int x2, int y2, Pixel color);
-void         FrameBuffer_circle(FrameBuffer *frame, int x1, int y1, int radius, Pixel color);
-int          FrameBuffer_writeGIF(FrameBuffer *f, ColorMap *c, char *filename);
-
-/* And some useful constants, which we redefine (from gifplot.h) so
-   that SWIG sees them */
-#define BLACK   0
-#define WHITE   1
-#define RED     2
-#define GREEN   3
-#define BLUE    4
-#define YELLOW  5
-#define CYAN    6
-#define MAGENTA 7
-
diff --git a/Examples/GIFPlot/Chicken/simple/test-simple.scm b/Examples/GIFPlot/Chicken/simple/test-simple.scm
deleted file mode 100644
index 43250d8e9..000000000
--- a/Examples/GIFPlot/Chicken/simple/test-simple.scm
+++ /dev/null
@@ -1,29 +0,0 @@
-;;; Draw some simple shapes
-
-(declare (uses simple))
-
-(display "Drawing some basic shapes\n")
-
-(define cmap (simple:new-ColorMap #f))
-(define f (simple:new-FrameBuffer 400 400))
-
-;; Clear the picture
-(simple:FrameBuffer-clear f (simple:BLACK))
-
-;; Make a red box
-(simple:FrameBuffer-box f 40 40 200 200 (simple:RED))
-
-;; Make a blue circle
-(simple:FrameBuffer-circle f 200 200 40 (simple:BLUE))
-
-;; Make green line
-(simple:FrameBuffer-line f 10 390 390 200 (simple:GREEN))
-
-;; Write an image out to disk
-
-(simple:FrameBuffer-writeGIF f cmap "image.gif")
-(display "Wrote image.gif\n")
-
-(simple:delete-FrameBuffer f)
-(simple:delete-ColorMap cmap)
-
diff --git a/Examples/GIFPlot/Common-Lisp/full/cmap b/Examples/GIFPlot/Common-Lisp/full/cmap
deleted file mode 100644
index a20c331a9573dd8443380680bfe2cc428780d8a9..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

literal 768
zcmZQzpd(=A5)hSEP}Mdtvvzdz4h)M)OwTDSuW4%Uoiu&!q7`d5@7R0z#JS5i?>&C`
z?#s{r^Z@9-XXO?YlTlLFHMX#G@$?UkN=VBFxv-;m^2~WlR;}N<`@pd?7q8!a^y1xT
znmh34m-nxpKDd4D;+bOy_iW#^cE#d(Gbi_Tw$xXZ7G$R-M27|XxI5We80l&#%Snpx
zbFrd(h8Vt}lCeu@T6xFJRlCpJeMef510DGC$^DyG&YwK8f9IC<tCq~4HKo4`=)RKt
ztd#huP=7C1dn;3YEme6bQ8Jvz%Ed1tDW|Lfj0{^Rcb~wpXkcs<lvdTZboK$GWATc$
Xo3`&c2#k+ww;w!x^&XgFNDnap(k+Jt

diff --git a/Examples/GIFPlot/Common-Lisp/full/gifplot.i b/Examples/GIFPlot/Common-Lisp/full/gifplot.i
deleted file mode 100644
index e5c15aa2b..000000000
--- a/Examples/GIFPlot/Common-Lisp/full/gifplot.i
+++ /dev/null
@@ -1,21 +0,0 @@
-/* Oh what the heck, let's just grab the whole darn header file
-   and see what happens. */
-
-%module gifplot
-%{
-
-/* Note: You still need this part because the %include directive
-   merely causes SWIG to interpret the contents of a file.  It doesn't
-   include the right include headers for the resulting C code */
-
-#include "gifplot.h"
-
-%}
-
-/* Pixel is typedef'd to unsigned char, and SWIG will translate this
-   type into Scheme characters. We would like to translate Pixels to
-   Scheme integers instead, so: */
-
-SIMPLE_MAP(Pixel, gh_scm2int, gh_int2scm, integer);
-
-%include gifplot.h
diff --git a/Examples/GIFPlot/Common-Lisp/full/runme.lisp b/Examples/GIFPlot/Common-Lisp/full/runme.lisp
deleted file mode 100644
index 48f804201..000000000
--- a/Examples/GIFPlot/Common-Lisp/full/runme.lisp
+++ /dev/null
@@ -1,59 +0,0 @@
-;;; Plot a 3D function
-
-;; Here is the function to plot
-(defun func (x y)
-  (* 5
-     (cos (* 2 (sqrt (+ (* x x) (* y y)))))
-     (exp (* -0.3 (sqrt (+ (* x x) (* y y)))))))
-
-;; Here are some plotting parameters
-(defvar xmin -5D0)
-(defvar xmax  5D0)
-(defvar ymin -5D0)
-(defvar ymax  5D0)
-(defvar zmin -5D0)
-(defvar zmax  5D0)
-
-;; Grid resolution
-(defvar nxpoints  60)
-(defvar nypoints  60)
-
-(defun drawsolid (p3)
-  (Plot3D-clear p3 0)
-  (Plot3D-start p3)
-  (let ((dx (/ (- xmax xmin) nxpoints))
-	(dy (/ (- ymax ymin) nypoints))
-	(cscale (/ 240 (- zmax zmin))))
-    (loop for x from xmin by dx
-	  repeat nxpoints
-	  do (loop for y from ymin by dy
-		   repeat nypoints
-		   do (let* ((z1 (func x y))
-			     (z2 (func (+ x dx) y))
-			     (z3 (func (+ x dx) (+ y dy)))
-			     (z4 (func x (+ y dy)))
-			     (c1 (* cscale (- z1 zmin)))
-			     (c2 (* cscale (- z2 zmin)))
-			     (c3 (* cscale (- z3 zmin)))
-			     (c4 (* cscale (- z4 zmin)))
-			     (cc (/ (+ c1 c2 c3 c4) 4))
-			     (c  (round (max (min cc 239) 0))))
-			(Plot3D-solidquad p3 x y z1 (+ x dx) y z2 (+ x dx) (+ y dy)
-					  z3 x (+ y dy) z4 (+ c 16)))))))
-
-(defun action (cmap-filename)
-  (let ((cmap (new-ColorMap cmap-filename))
-	(frame (new-FrameBuffer 500 500)))
-    (format t "Making a nice 3D plot...~%")
-    (FrameBuffer-clear frame 0)
-    (let ((p3 (new-Plot3D frame xmin ymin zmin xmax ymax zmax)))
-      (Plot3D-lookat p3 (* 2 (- zmax zmin)))
-      (Plot3D-autoperspective p3 40D0)
-      (Plot3D-rotu p3 60D0)
-      (Plot3D-rotr p3 30D0)
-      (Plot3D-rotd p3 10D0)
-      (drawsolid p3))
-    (FrameBuffer-writeGIF frame cmap "/tmp/image.gif")
-    (format t "Wrote image.gif~%")))
-
-
diff --git a/Examples/GIFPlot/Guile/check.list b/Examples/GIFPlot/Guile/check.list
deleted file mode 100644
index e75ee586a..000000000
--- a/Examples/GIFPlot/Guile/check.list
+++ /dev/null
@@ -1,3 +0,0 @@
-# see top-level Makefile.in
-full
-simple
diff --git a/Examples/GIFPlot/Guile/full/Makefile b/Examples/GIFPlot/Guile/full/Makefile
deleted file mode 100644
index 1fcdf58d2..000000000
--- a/Examples/GIFPlot/Guile/full/Makefile
+++ /dev/null
@@ -1,28 +0,0 @@
-TOP        = ../../..
-SWIG       = $(TOP)/../swig
-SWIGOPT    = -I../../Include
-SRCS       =
-TARGET     = gifplot
-INTERFACE  = gifplot.i
-LIBS       = -L../.. -lgifplot -lm
-INCLUDES   = -I../../Include
-
-all:: static
-
-dynamic:: 
-	$(MAKE) -f $(TOP)/Makefile TOP='$(TOP)' \
-	SRCS='$(SRCS)' SWIG='$(SWIG)' \
-	INCLUDES='$(INCLUDES)' LIBS='$(LIBS)' SWIGOPT='$(SWIGOPT)' \
-	TARGET='$(TARGET)' INTERFACE='$(INTERFACE)' guile
-
-static::
-	$(MAKE) -f $(TOP)/Makefile TOP='$(TOP)' \
-	SRCS='$(SRCS)' SWIG='$(SWIG)' \
-	INCLUDES='$(INCLUDES)' LIBS='$(LIBS)' SWIGOPT='$(SWIGOPT)' \
-	TARGET='$(TARGET)' INTERFACE='$(INTERFACE)' guile_static
-
-clean::
-	$(MAKE) -f $(TOP)/Makefile TARGET='$(TARGET)' guile_clean
-	rm -f *.gif
-
-check: all
diff --git a/Examples/GIFPlot/Guile/full/README b/Examples/GIFPlot/Guile/full/README
deleted file mode 100644
index 9780988d2..000000000
--- a/Examples/GIFPlot/Guile/full/README
+++ /dev/null
@@ -1,8 +0,0 @@
-This example runs the entire gifplot.h header file through SWIG without
-any changes.  The Scheme program 'runme.scm' does something a little more 
-interesting.   You'll have to go look at the header file to get a complete
-listing of the functions.
-
-
-
-
diff --git a/Examples/GIFPlot/Guile/full/cmap b/Examples/GIFPlot/Guile/full/cmap
deleted file mode 100644
index a20c331a9573dd8443380680bfe2cc428780d8a9..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

literal 768
zcmZQzpd(=A5)hSEP}Mdtvvzdz4h)M)OwTDSuW4%Uoiu&!q7`d5@7R0z#JS5i?>&C`
z?#s{r^Z@9-XXO?YlTlLFHMX#G@$?UkN=VBFxv-;m^2~WlR;}N<`@pd?7q8!a^y1xT
znmh34m-nxpKDd4D;+bOy_iW#^cE#d(Gbi_Tw$xXZ7G$R-M27|XxI5We80l&#%Snpx
zbFrd(h8Vt}lCeu@T6xFJRlCpJeMef510DGC$^DyG&YwK8f9IC<tCq~4HKo4`=)RKt
ztd#huP=7C1dn;3YEme6bQ8Jvz%Ed1tDW|Lfj0{^Rcb~wpXkcs<lvdTZboK$GWATc$
Xo3`&c2#k+ww;w!x^&XgFNDnap(k+Jt

diff --git a/Examples/GIFPlot/Guile/full/gifplot.i b/Examples/GIFPlot/Guile/full/gifplot.i
deleted file mode 100644
index e5c15aa2b..000000000
--- a/Examples/GIFPlot/Guile/full/gifplot.i
+++ /dev/null
@@ -1,21 +0,0 @@
-/* Oh what the heck, let's just grab the whole darn header file
-   and see what happens. */
-
-%module gifplot
-%{
-
-/* Note: You still need this part because the %include directive
-   merely causes SWIG to interpret the contents of a file.  It doesn't
-   include the right include headers for the resulting C code */
-
-#include "gifplot.h"
-
-%}
-
-/* Pixel is typedef'd to unsigned char, and SWIG will translate this
-   type into Scheme characters. We would like to translate Pixels to
-   Scheme integers instead, so: */
-
-SIMPLE_MAP(Pixel, gh_scm2int, gh_int2scm, integer);
-
-%include gifplot.h
diff --git a/Examples/GIFPlot/Guile/full/runme.scm b/Examples/GIFPlot/Guile/full/runme.scm
deleted file mode 100644
index 0ffe92167..000000000
--- a/Examples/GIFPlot/Guile/full/runme.scm
+++ /dev/null
@@ -1,66 +0,0 @@
-;;; Plot a 3D function
-
-;; Use the wrapped GIFPlot library
-(use-modules (gifplot))
-
-;; Here is the function to plot
-(define (func x y)
-  (* 5
-     (cos (* 2 (sqrt (+ (* x x) (* y y)))))
-     (exp (* -0.3 (sqrt (+ (* x x) (* y y)))))))
-
-;; Here are some plotting parameters
-(define xmin -5.0)
-(define xmax  5.0)
-(define ymin -5.0)
-(define ymax  5.0)
-(define zmin -5.0)
-(define zmax  5.0)
-
-;; Grid resolution
-(define nxpoints  60)
-(define nypoints  60)
-
-(define cmap (new-ColorMap "cmap"))
-(define frame (new-FrameBuffer 500 500))
-(FrameBuffer-clear frame (BLACK))
-
-(define p3 (new-Plot3D frame xmin ymin zmin xmax ymax zmax))
-(Plot3D-lookat p3 (* 2 (- zmax zmin)))
-(Plot3D-autoperspective p3 40)
-(Plot3D-rotu p3 60)
-(Plot3D-rotr p3 30)
-(Plot3D-rotd p3 10)
-
-(define (drawsolid)
-  (Plot3D-clear p3 (BLACK))
-  (Plot3D-start p3)
-  (let ((dx (/ (- xmax xmin) nxpoints))
-	(dy (/ (- ymax ymin) nypoints))
-	(cscale (/ 240 (- zmax zmin))))
-    (let x-loop ((x xmin) (i 0))
-      (cond
-       ((< i nxpoints)
-	(let y-loop ((y ymin) (j 0))
-	  (cond
-	   ((< j nypoints)
-	    (let* ((z1 (func x y))
-		   (z2 (func (+ x dx) y))
-		   (z3 (func (+ x dx) (+ y dy)))
-		   (z4 (func x (+ y dy)))
-		   (c1 (* cscale (- z1 zmin)))
-		   (c2 (* cscale (- z2 zmin)))
-		   (c3 (* cscale (- z3 zmin)))
-		   (c4 (* cscale (- z4 zmin)))
-		   (cc (/ (+ c1 c2 c3 c4) 4))
-		   (c  (round (max (min cc 239) 0))))
-	      (Plot3D-solidquad p3 x y z1 (+ x dx) y z2 (+ x dx) (+ y dy)
-				z3 x (+ y dy) z4 (+ c 16)))
-	    (y-loop (+ y dy) (+ j 1)))))
-	(x-loop (+ x dx) (+ i 1)))))))
-
-(display "Making a nice 3D plot...\n")
-(drawsolid)
-
-(FrameBuffer-writeGIF frame cmap "image.gif")
-(display "Wrote image.gif\n")
diff --git a/Examples/GIFPlot/Guile/simple/Makefile b/Examples/GIFPlot/Guile/simple/Makefile
deleted file mode 100644
index 7986214a0..000000000
--- a/Examples/GIFPlot/Guile/simple/Makefile
+++ /dev/null
@@ -1,28 +0,0 @@
-TOP        = ../../..
-SWIG       = $(TOP)/../swig
-SWIGOPT    =
-SRCS       =
-TARGET     = simple
-INTERFACE  = simple.i
-LIBS       = -L../.. -lgifplot
-INCLUDES   = -I../../Include
-
-all:: static
-
-dynamic::
-	$(MAKE) -f $(TOP)/Makefile TOP='$(TOP)' \
-	SRCS='$(SRCS)' SWIG='$(SWIG)' \
-	INCLUDES='$(INCLUDES)' LIBS='$(LIBS)' SWIGOPT='$(SWIGOPT)' \
-	TARGET='$(TARGET)' INTERFACE='$(INTERFACE)' guile
-
-static::
-	$(MAKE) -f $(TOP)/Makefile TOP='$(TOP)' \
-	SRCS='$(SRCS)' SWIG='$(SWIG)' \
-	INCLUDES='$(INCLUDES)' LIBS='$(LIBS)' SWIGOPT='$(SWIGOPT)' \
-	TARGET='$(TARGET)' INTERFACE='$(INTERFACE)' guile_static
-
-clean::
-	$(MAKE) -f $(TOP)/Makefile TARGET='$(TARGET)' guile_clean
-	rm -f *.gif
-
-check: all
diff --git a/Examples/GIFPlot/Guile/simple/README b/Examples/GIFPlot/Guile/simple/README
deleted file mode 100644
index 1925efa93..000000000
--- a/Examples/GIFPlot/Guile/simple/README
+++ /dev/null
@@ -1,11 +0,0 @@
-This is a very minimalistic example in which just a few functions
-and constants from library are wrapped and used to draw some simple
-shapes.  
-
-`make' will build a version of Guile which defines an additional
-module (simple).  Run `./simple-guile -s runme.scm' to test it.
-
-`make dynamic' will build a dynamically loadable module, which can be
-loaded from any Guile interpreter.  Run `guile -s runme.scm' to test
-it.  The `use-modules' call in `runme.scm' dynamically loads the
-module. 
diff --git a/Examples/GIFPlot/Guile/simple/runme.scm b/Examples/GIFPlot/Guile/simple/runme.scm
deleted file mode 100644
index 40ec18101..000000000
--- a/Examples/GIFPlot/Guile/simple/runme.scm
+++ /dev/null
@@ -1,30 +0,0 @@
-;;; Draw some simple shapes
-
-;; Use the wrapped GIFPlot library
-(use-modules (simple))
-
-(display "Drawing some basic shapes\n")
-
-(define cmap (new-ColorMap))
-(define f (new-FrameBuffer 400 400))
-
-;; Clear the picture
-(FrameBuffer-clear f (BLACK))
-
-;; Make a red box
-(FrameBuffer-box f 40 40 200 200 (RED))
-
-;; Make a blue circle
-(FrameBuffer-circle f 200 200 40 (BLUE))
-
-;; Make green line
-(FrameBuffer-line f 10 390 390 200 (GREEN))
-
-;; Write an image out to disk
-
-(FrameBuffer-writeGIF f cmap "image.gif")
-(display "Wrote image.gif\n")
-
-(delete-FrameBuffer f)
-(delete-ColorMap cmap)
-
diff --git a/Examples/GIFPlot/Guile/simple/simple.i b/Examples/GIFPlot/Guile/simple/simple.i
deleted file mode 100644
index 86eaabdc0..000000000
--- a/Examples/GIFPlot/Guile/simple/simple.i
+++ /dev/null
@@ -1,34 +0,0 @@
-/* This example shows a very simple interface wrapping a few 
-   primitive declarations */
-
-%module simple
-%{
-#include "gifplot.h"
-%}
-
-typedef unsigned int Pixel;
-
-/* Here are a few useful functions */
-
-ColorMap    *new_ColorMap(char *filename = 0);
-void         delete_ColorMap(ColorMap *cmap);
-
-FrameBuffer *new_FrameBuffer(unsigned int width, unsigned int height);
-void         delete_FrameBuffer(FrameBuffer *frame);
-void         FrameBuffer_clear(FrameBuffer *frame, Pixel color);
-void         FrameBuffer_line(FrameBuffer *frame, int x1, int y1, int x2, int y2, Pixel color);
-void         FrameBuffer_box(FrameBuffer *frame, int x1, int y1, int x2, int y2, Pixel color);
-void         FrameBuffer_circle(FrameBuffer *frame, int x1, int y1, int radius, Pixel color);
-int          FrameBuffer_writeGIF(FrameBuffer *f, ColorMap *c, char *filename);
-
-/* And some useful constants */
-
-#define BLACK   0
-#define WHITE   1
-#define RED     2
-#define GREEN   3
-#define BLUE    4
-#define YELLOW  5
-#define CYAN    6
-#define MAGENTA 7
-
diff --git a/Examples/GIFPlot/Include/gifplot.h b/Examples/GIFPlot/Include/gifplot.h
deleted file mode 100644
index 85e4c10b3..000000000
--- a/Examples/GIFPlot/Include/gifplot.h
+++ /dev/null
@@ -1,333 +0,0 @@
-/* ----------------------------------------------------------------------------- 
- * gifplot.h
- *
- *     Main header file for the GIFPlot library.
- * 
- * Author(s) : David Beazley (beazley@cs.uchicago.edu)
- * Copyright (C) 1995-1996
- *
- * See the file LICENSE for information on usage and redistribution.	
- * ----------------------------------------------------------------------------- */
-
-#include <stdio.h>
-#include <fcntl.h>
-#include <float.h>
-#include <stdlib.h>
-#include <string.h>
-#include <limits.h>
-
-#ifndef GIFPLOT_H
-
-#ifdef SWIG
-%nodefault;
-#endif
-
-/* Pixel is 8-bits */
-
-typedef unsigned char Pixel;
-typedef float Zvalue;
-
-/* ------------------------------------------------------------------------
-   ColorMap
-
-   Definition and methods for colormaps
-   ------------------------------------------------------------------------ */
-
-typedef struct ColorMap {
-  unsigned char          *cmap;
-  char                   *name;
-} ColorMap;
-
-extern ColorMap *new_ColorMap(char *filename);
-extern void      delete_ColorMap(ColorMap *c);
-extern void      ColorMap_default(ColorMap *c);
-extern void      ColorMap_assign(ColorMap *c, int index, int r, int g, int b);
-extern int       ColorMap_getitem(ColorMap *c, int index);
-extern void      ColorMap_setitem(ColorMap *c, int index, int value);
-extern int       ColorMap_write(ColorMap *c, char *filename);
-
-/* Some default colors */
-
-#define BLACK   0
-#define WHITE   1
-#define RED     2
-#define GREEN   3
-#define BLUE    4
-#define YELLOW  5
-#define CYAN    6
-#define MAGENTA 7
-
-/*-------------------------------------------------------------------------
-  FrameBuffer
-
-  This structure defines a simple 8 bit framebuffer.  
-  ------------------------------------------------------------------------- */
-
-typedef struct FrameBuffer {
-  Pixel         **pixels;
-  Zvalue        **zbuffer;
-  unsigned int    height;
-  unsigned int    width;
-  int             xmin;      /* These are used for clipping */
-  int             ymin;
-  int             xmax;
-  int             ymax;
-} FrameBuffer;
-
-#define ZMIN  1e+36
-
-/* FrameBuffer Methods */
-
-extern FrameBuffer *new_FrameBuffer(unsigned int width, unsigned int height);
-extern void         delete_FrameBuffer(FrameBuffer *frame);
-extern int          FrameBuffer_resize(FrameBuffer *frame, int width, int height);
-extern void         FrameBuffer_clear(FrameBuffer *frame, Pixel color);
-extern void         FrameBuffer_plot(FrameBuffer *frame, int x, int y, Pixel color);
-extern void         FrameBuffer_horizontal(FrameBuffer *frame, int xmin, int xmax, int y, Pixel color);
-extern void         FrameBuffer_horizontalinterp(FrameBuffer *f, int xmin, int xmax, int y,  Pixel c1, Pixel c2);
-extern void         FrameBuffer_vertical(FrameBuffer *frame, int ymin, int ymax, int x, Pixel color);
-extern void         FrameBuffer_box(FrameBuffer *frame, int x1, int y1, int x2, int y2, Pixel color);
-extern void         FrameBuffer_solidbox(FrameBuffer *frame, int x1, int y1, int x2, int y2, Pixel color);
-extern void         FrameBuffer_interpbox(FrameBuffer *f, int x1, int y1, int x2, int y2, Pixel c1, Pixel c2, Pixel c3, Pixel c4);
-extern void         FrameBuffer_circle(FrameBuffer *frame, int x1, int y1, int radius, Pixel color);
-extern void         FrameBuffer_solidcircle(FrameBuffer *frame, int x1, int y1, int radius, Pixel color);
-extern void         FrameBuffer_line(FrameBuffer *frame, int x1, int y1, int x2, int y2, Pixel color);
-extern void         FrameBuffer_setclip(FrameBuffer *frame, int xmin, int ymin, int xmax, int ymax);
-extern void         FrameBuffer_noclip(FrameBuffer *frame);
-extern int          FrameBuffer_makeGIF(FrameBuffer *frame, ColorMap *cmap, void *buffer, unsigned int maxsize);
-extern int          FrameBuffer_writeGIF(FrameBuffer *f, ColorMap *c, char *filename);
-extern void         FrameBuffer_zresize(FrameBuffer *f, int width, int height);
-extern void         FrameBuffer_zclear(FrameBuffer *f);
-extern void         FrameBuffer_solidtriangle(FrameBuffer *f, int x1, int y1, int x2, int y2, int x3, int y3, Pixel c);
-extern void         FrameBuffer_interptriangle(FrameBuffer *f, int tx1, int ty1, Pixel c1,
-                                               int tx2, int ty2, Pixel c2, int tx3, int ty3, Pixel c3);
-
-#define  HORIZONTAL  1
-#define  VERTICAL    2
-
-extern void         FrameBuffer_drawchar(FrameBuffer *frame, int x, int y, int fgcolor, int bgcolor, char chr, int orientation);
-extern void         FrameBuffer_drawstring(FrameBuffer *f, int x, int y, int fgcolor, int bgcolor, char *text, int orientation);
-
-/* ------------------------------------------------------------------------
-   PixMap
-
-   The equivalent of "bit-maps".
-   ------------------------------------------------------------------------ */
-
-typedef struct PixMap {
-  int    width;
-  int    height;
-  int    centerx;
-  int    centery;
-  int   *map;
-} PixMap;
-
-/* PIXMAP methods */
-
-extern PixMap   *new_PixMap(int width, int height, int centerx, int centery);
-extern void      delete_PixMap(PixMap *pm);
-extern void      PixMap_set(PixMap *pm, int x, int y, int pix);
-extern void      FrameBuffer_drawpixmap(FrameBuffer *f, PixMap *pm, int x, int y, int fgcolor, int bgcolor);
-
-#define   GIFPLOT_TRANSPARENT  0
-#define   GIFPLOT_FOREGROUND   1
-#define   GIFPLOT_BACKGROUND   2
-
-/* ------------------------------------------------------------------------
-   Plot2D
-
-   Definition and methods for 2D plots.
-   ------------------------------------------------------------------------ */
-
-typedef struct Plot2D {
-  FrameBuffer    *frame;        /* what frame buffer are we using     */
-  int             view_xmin;    /* Minimum coordinates of view region */
-  int             view_ymin;    
-  int             view_xmax;    /* Maximum coordinates of view region */
-  int             view_ymax;    
-  double          xmin;         /* Minimum coordinates of plot region */
-  double          ymin;
-  double          xmax;         /* Maximum coordinates of plot region */
-  double          ymax;
-  int             xscale;       /* Type of scaling (LINEAR, LOG, etc..) */
-  int             yscale;       
-  double          dx;           /* Private scaling parameters         */
-  double          dy;
-} Plot2D;
-
-/* 2D Plot methods */
-
-extern Plot2D  *new_Plot2D(FrameBuffer *frame,double xmin,double ymin, double xmax, double ymax);
-extern void     delete_Plot2D(Plot2D *p2);
-extern Plot2D  *Plot2D_copy(Plot2D *p2);
-extern void     Plot2D_clear(Plot2D *p2, Pixel c);
-extern void     Plot2D_setview(Plot2D *p2, int vxmin, int vymin, int vxmax, int vymax);
-extern void     Plot2D_setrange(Plot2D *p2, double xmin, double ymin, double xmax, double ymax);
-extern void     Plot2D_setscale(Plot2D *p2, int xscale, int yscale);
-extern void     Plot2D_plot(Plot2D *p2, double x, double y, Pixel color);
-extern void     Plot2D_box(Plot2D *p2, double x1, double y1,  double x2, double y2, Pixel color);
-extern void     Plot2D_solidbox(Plot2D *p2, double x1, double y1,double x2, double y2, Pixel color);
-extern void     Plot2D_interpbox(Plot2D *p2, double x1, double y1, double x2, double y2, Pixel c1, Pixel c2, Pixel c3, Pixel c4);
-extern void     Plot2D_circle(Plot2D *p2, double x, double y, double radius, Pixel color);
-extern void     Plot2D_solidcircle(Plot2D *p2, double x, double y, double radius, Pixel color);
-extern void     Plot2D_line(Plot2D *p2, double x1, double y1, double x2, double y2, Pixel color);
-extern void     Plot2D_start(Plot2D *p2);
-extern void     Plot2D_drawpixmap(Plot2D *p2, PixMap *pm, double x, double y, Pixel color, Pixel bgcolor);
-extern void     Plot2D_xaxis(Plot2D *p2, double x, double y, double xtick, int ticklength, Pixel c);
-extern void     Plot2D_yaxis(Plot2D *p2, double x, double y, double ytick, int ticklength, Pixel c);
-extern void     Plot2D_triangle(Plot2D *p2, double x1, double y1, double x2, double y2, double x3, double y3, Pixel c);
-extern void     Plot2D_solidtriangle(Plot2D *p2, double x1, double y1, double x2, double y2, double x3, double y3, Pixel c);
-extern void     Plot2D_interptriangle(Plot2D *p2, double x1, double y1, Pixel c1,
-                                                  double x2, double y2, Pixel c2,
-                                                  double x3, double y3, Pixel c3);
-
-#define LINEAR     10
-#define LOG        11
-
-/* -----------------------------------------------------------------------
-   Matrix
-   
-   Operations on 4x4 transformation matrices and vectors.
-   Matrices are represented as a double array of 16 elements
-   ----------------------------------------------------------------------- */
-
-typedef  double *Matrix;
-typedef struct GL_Vector {
-  double x;
-  double y;
-  double z;
-  double w;
-} GL_Vector;
-
-extern Matrix new_Matrix();
-extern void   delete_Matrix(Matrix a);
-extern Matrix Matrix_copy(Matrix a);
-extern void   Matrix_multiply(Matrix a, Matrix b, Matrix c);
-extern void   Matrix_identity(Matrix a);
-extern void   Matrix_zero(Matrix a);
-extern void   Matrix_transpose(Matrix a, Matrix result);
-extern void   Matrix_invert(Matrix a, Matrix inva);
-extern void   Matrix_transform(Matrix a, GL_Vector *r, GL_Vector *t);
-extern void   Matrix_transform4(Matrix a, double rx, double ry, double rz,
-				double rw, GL_Vector *t);
-
-extern void   Matrix_print(Matrix a);
-extern void   Matrix_translate(Matrix a, double tx, double ty, double tz);
-extern void   Matrix_rotatex(Matrix a, double deg);
-extern void   Matrix_rotatey(Matrix a, double deg);
-extern void   Matrix_rotatez(Matrix a, double deg);
-
-/* -----------------------------------------------------------------------
-   Plot3D
-
-   Data Structure for 3-D plots
-   ------------------------------------------------------------------------ */
-
-typedef struct Plot3D {
-  FrameBuffer   *frame;      /* Frame buffer being used */
-  int            view_xmin;  /* Viewing region */
-  int            view_ymin;
-  int            view_xmax;
-  int            view_ymax;
-  double         xmin;       /* Bounding box */
-  double         ymin;
-  double         zmin;
-  double         xmax;
-  double         ymax;
-  double         zmax;
-  double         xcenter;    /* Center point */
-  double         ycenter;
-  double         zcenter;
-  double         fovy;       /* Field of view */
-  double         aspect;     /* Aspect ratio  */
-  double         znear;      /* near "clipping" plane */
-  double         zfar;       /* far "clipping" plane */
-  Matrix         center_mat; /* Matrix used for centering the model */
-  Matrix         model_mat;  /* Model rotation matrix */
-  Matrix         view_mat;   /* Viewing matrix */
-  Matrix         fullmodel_mat;  /* Full model matrix.  Used by sphere plot */
-  Matrix         trans_mat;  /* Total transformation matrix */
-  double         lookatz;    /* Where is the z-lookat point */
-  double         xshift;     /* Used for translation and stuff */
-  double         yshift;
-  double         zoom;
-  int            width;
-  int            height;
-  int            pers_mode;  /* Perspective mode (private) */
-  double         ortho_left,ortho_right,ortho_bottom,ortho_top;
-} Plot3D;
-
-extern Plot3D *new_Plot3D(FrameBuffer *frame, double xmin, double ymin, double zmin,
-			  double xmax, double ymax, double zmax);
-extern void   delete_Plot3D(Plot3D *p3);
-extern Plot3D *Plot3D_copy(Plot3D *p3);
-extern void   Plot3D_clear(Plot3D *p3, Pixel Color);
-extern void   Plot3D_perspective(Plot3D *p3, double fovy, double znear, double zfar);
-extern void   Plot3D_ortho(Plot3D *p3, double left, double right, double top, double bottom);
-extern void   Plot3D_lookat(Plot3D *p3, double z);
-extern void   Plot3D_autoperspective(Plot3D *p3, double fovy);
-extern void   Plot3D_autoortho(Plot3D *p3);
-extern void   Plot3D_rotx(Plot3D *p3, double deg);
-extern void   Plot3D_roty(Plot3D *p3, double deg);
-extern void   Plot3D_rotz(Plot3D *p3, double deg);
-extern void   Plot3D_rotl(Plot3D *p3, double deg);
-extern void   Plot3D_rotr(Plot3D *p3, double deg);
-extern void   Plot3D_rotd(Plot3D *p3, double deg);
-extern void   Plot3D_rotu(Plot3D *p3, double deg);
-extern void   Plot3D_rotc(Plot3D *p3, double deg);
-extern void   Plot3D_zoom(Plot3D *p3, double percent);
-extern void   Plot3D_left(Plot3D *p3, double percent);
-extern void   Plot3D_right(Plot3D *p3, double percent);
-extern void   Plot3D_down(Plot3D *p3, double percent);
-extern void   Plot3D_up(Plot3D *p3, double percent);
-extern void   Plot3D_center(Plot3D *p3, double cx, double cy);
-
-extern void   Plot3D_plot(Plot3D *p3, double x, double y, double z, Pixel Color);
-
-extern void   Plot3D_setview(Plot3D *p3, int vxmin, int vymin, int vxmax, int vymax);
-extern void   Plot3D_start(Plot3D *p3);
-extern void   Plot3D_line(Plot3D *p3, double x1, double y1, double z1,
-			 double x2, double y2, double z2, Pixel color);
-extern void   Plot3D_triangle(Plot3D *p3, double x1, double y1, double z1,
-		     double x2, double y2, double z2,
-		     double x3, double y3, double z3, Pixel color);
-extern void   Plot3D_solidtriangle(Plot3D *p3, double x1, double y1, double z1,
-		     double x2, double y2, double z2,
-		     double x3, double y3, double z3, Pixel color);
-
-extern void Plot3D_interptriangle(Plot3D *p3,
-			   double x1, double y1, double z1, Pixel c1,
-			   double x2, double y2, double z2, Pixel c2,
-			   double x3, double y3, double z3, Pixel c3);
-
-extern void   Plot3D_quad(Plot3D *p3, double x1, double y1, double z1,
-		 double x2, double y2, double z2,
-		 double x3, double y3, double z3,
-		 double x4, double y4, double z4,
-		 Pixel color);
-
-extern void   Plot3D_solidquad(Plot3D *p3, double x1, double y1, double z1,
-		 double x2, double y2, double z2,
-		 double x3, double y3, double z3,
-		 double x4, double y4, double z4,
-		 Pixel color);
-
-extern void   Plot3D_interpquad(Plot3D *p3, double x1, double y1, double z1, Pixel c1,
-		       double x2, double y2, double z2, Pixel c2,
-		       double x3, double y3, double z3, Pixel c3,
-		       double x4, double y4, double z4, Pixel c4);
-
-
-extern void   Plot3D_solidsphere(Plot3D *p3, double x, double y, double z, double radius,Pixel c);
-
-extern void   Plot3D_outlinesphere(Plot3D *p3, double x, double y, double z, double radius,Pixel c, Pixel bc);
-
-extern PixMap  PixMap_SQUARE;
-extern PixMap  PixMap_TRIANGLE;
-extern PixMap  PixMap_CROSS;
-
-#endif
-#define GIFPLOT_H
-
-
-
diff --git a/Examples/GIFPlot/Interface/gifplot.i b/Examples/GIFPlot/Interface/gifplot.i
deleted file mode 100644
index fdf661c5e..000000000
--- a/Examples/GIFPlot/Interface/gifplot.i
+++ /dev/null
@@ -1,264 +0,0 @@
-//
-// Graphics module
-//
-%module gifplot
-%{
-#include "gifplot.h"
-%}
-
-#if defined(SWIGJAVA ) || defined(SWIGPHP)
-  %rename(make_default) ColorMap::default();
-#endif
-
-%rename(__getitem__)  ColorMap::getitem(int index);
-%rename(__setitem__)  ColorMap::setitem(int index, int value);
-
-/* Pixel is 8-bits */
-
-typedef unsigned char Pixel;
-typedef float Zvalue;
-
-/* ------------------------------------------------------------------------
-   ColorMap
-
-   Definition and methods for colormaps
-   ------------------------------------------------------------------------ */
-
-typedef struct ColorMap {
-  char          *name;
-
-//
-// %extend adds some C methods to this structure to make it
-// look like a C++ class in Python.
-// These are really named things like ColorMap_default, ColorMap_assign, etc...
-
-  %extend {
-    ColorMap(char *filename);
-    ~ColorMap();
-    void        default();
-    void        assign(int index,int r, int g, int b);
-    int getitem(int index);
-    void setitem(int index, int value);
-    int         write(char *filename);
-  }
-} ColorMap;
-
-/* Some default colors */
-
-#define BLACK   0
-#define WHITE   1
-#define RED     2
-#define GREEN   3
-#define BLUE    4
-#define YELLOW  5
-#define CYAN    6
-#define MAGENTA 7
-
-/*-------------------------------------------------------------------------
-  FrameBuffer
-
-  This structure defines a simple 8 bit framebuffer.  
-  ------------------------------------------------------------------------- */
-
-typedef struct FrameBuffer {
-  unsigned int    height;
-  unsigned int    width;
-  int             xmin;      /* These are used for clipping */
-  int             ymin;
-  int             xmax;
-  int             ymax;
-  %extend {
-    FrameBuffer(unsigned int width, unsigned int height);
-    ~FrameBuffer();
-    void resize(int width, int height);
-    void clear(Pixel color);
-    void plot(int x, int y, Pixel color);
-    void horizontal(int xmin, int xmax, int y, Pixel color);
-    void horizontalinterp(int xmin, int xmax, int y,  Pixel c1, Pixel c2);
-    void vertical(int ymin, int ymax, int x, Pixel color);
-    void box(int x1, int y1,  int x2, int y2, Pixel color);
-    void solidbox(int x1, int y1, int x2, int y2, Pixel color);
-    void interpbox(int x1, int y1, int x2, int y2, Pixel c1, Pixel c2, Pixel c3, Pixel c4);
-    void circle(int x1, int y1, int radius, Pixel color);
-    void solidcircle(int x1, int y1, int radius, Pixel color);
-    void line(int x1, int y1, int x2, int y2, Pixel color);
-    void setclip(int xmin, int ymin, int xmax, int ymax);
-    void noclip();
-    int  makeGIF(ColorMap *cmap, void *buffer, unsigned int maxsize);
-    void zresize(int width, int height);
-    void zclear();
-    void drawchar(int x, int y, int fgcolor, int bgcolor, char chr, int orientation);
-    void drawstring(int x, int y, int fgcolor, int bgcolor, char *text, int orientation);
-    void drawpixmap(PixMap *pm, int x, int y, int fgcolor, int bgcolor);
-    int  writeGIF(ColorMap *cmap, char *filename);	
-  }
-} FrameBuffer;
-
-#define  HORIZONTAL  1
-#define  VERTICAL    2
-
-/* --------------------------------------------------------------------------
-   PixMap
-
-   The equivalent of "bit-maps".
-   -------------------------------------------------------------------------- */
-
-/* PIXMAP methods */
-
-extern PixMap   *new_PixMap(int width, int height, int centerx, int centery);
-extern void      delete_PixMap(PixMap *pm);
-extern void      PixMap_set(PixMap *pm, int x, int y, int pix);
-
-#define   GIFPLOT_TRANSPARENT  0
-#define   GIFPLOT_FOREGROUND   1
-#define   GIFPLOT_BACKGROUND   2
-
-/* --------------------------------------------------------------------------
-   Plot2D
-
-   Definition and methods for 2D plots.
-   --------------------------------------------------------------------------- */
-
-typedef struct Plot2D {
-  FrameBuffer     *frame;
-  int             view_xmin;    /* Minimum coordinates of view region */
-  int             view_ymin;    
-  int             view_xmax;    /* Maximum coordinates of view region */
-  int             view_ymax;    
-  double          xmin;         /* Minimum coordinates of plot region */
-  double          ymin;
-  double          xmax;         /* Maximum coordinates of plot region */
-  double          ymax;
-  int             xscale;       /* Type of scaling (LINEAR, LOG, etc..) */
-  int             yscale;       
-  %extend {
-       Plot2D(FrameBuffer *frame,double xmin,double ymin,  double xmax, double ymax);
-       ~Plot2D();
-       Plot2D  *copy();
-       void     clear(Pixel c);
-       void     setview(int vxmin, int vymin, int vxmax, int vymax);
-       void     setrange(double xmin, double ymin, double xmax, double ymax);
-       void     setscale(int xscale, int yscale);
-       void     plot(double x, double y, Pixel color);
-       void     box(double x1, double y1, double x2, double y2, Pixel color);
-       void     solidbox(double x1, double y1,	double x2, double y2, Pixel color);
-       void     interpbox(double x1, double y1, double x2, double y2, Pixel c1, Pixel c2, Pixel c3, Pixel c4);
-
-       void     circle(double x, double y, double radius, Pixel color);
-       void     solidcircle(double x, double y,  double radius, Pixel color);
-       void     line(double x1, double y1,  double x2, double y2, Pixel color);
-       void     start();
-       void     drawpixmap(PixMap *pm, double x, double y, Pixel color, Pixel bgcolor);
-       void     xaxis(double x, double y, double xtick, int ticklength, Pixel color);
-       void     yaxis(double x, double y, double ytick, int ticklength, Pixel color);
-       void     triangle(double x1, double y1, double x2, double y2, double x3, double y3, Pixel c);
-
-       void     solidtriangle(double x1, double y1, double x2, double y2, double x3, double y3, Pixel c);
-
-       void     interptriangle(double x1, double y1, Pixel c1,
-			   double x2, double y2, Pixel c2,
-			   double x3, double y3, Pixel c3);
-
-  }
-} Plot2D;
-
-#define LINEAR     10
-#define LOG        11
-
-/* ------------------------------------------------------------------------------
-   Plot3D
-
-   Data Structure for 3-D plots
-   ------------------------------------------------------------------------------ */
-
-typedef struct Plot3D {
-  FrameBuffer    *frame;
-  int            view_xmin;  /* Viewing region */
-  int            view_ymin;
-  int            view_xmax;
-  int            view_ymax;
-  double         xmin;       /* Bounding box */
-  double         ymin;
-  double         zmin;
-  double         xmax;
-  double         ymax;
-  double         zmax;
-  double         xcenter;    /* Center point */
-  double         ycenter;
-  double         zcenter;
-  double         fovy;       /* Field of view */
-  double         aspect;     /* Aspect ratio  */
-  double         znear;      /* near "clipping" plane */
-  double         zfar;       /* far "clipping" plane */
-  double         lookatz;    /* Where is the z-lookat point */
-  double         xshift;     /* Used for translation and stuff */
-  double         yshift;
-  %extend {
-    Plot3D(FrameBuffer *frame, double xmin, double ymin, double zmin, double xmax, double ymax, double zmax);
-    ~Plot3D();
-    Plot3D *copy();
-    void   clear(Pixel bgcolor);
-    void   perspective( double fovy, double znear, double zfar);
-    void   lookat( double z);
-    void   autoperspective( double fovy);
-    void   ortho(double left, double right, double bottom, double top);
-    void   autoortho();
-    void   rotx( double deg);
-    void   roty( double deg);
-    void   rotz( double deg);
-    void   rotl( double deg);
-    void   rotr( double deg);
-    void   rotd( double deg);
-    void   rotu( double deg);
-    void   rotc( double deg);
-    void   zoom( double percent);
-    void   left( double percent);
-    void   right( double percent);
-    void   down( double percent);
-    void   up( double percent);
-    void   center( double cx, double cy);
-    void   plot( double x, double y, double z, Pixel Color);
-    void   setview( int vxmin, int vymin, int vxmax, int vymax);
-    void   start();
-    void   line( double x1, double y1, double z1,
-		 double x2, double y2, double z2, Pixel color);
-    void   triangle( double x1, double y1, double z1,
-		     double x2, double y2, double z2,
-		     double x3, double y3, double z3, Pixel color);
-    void   solidtriangle( double x1, double y1, double z1,
-			  double x2, double y2, double z2,
-			  double x3, double y3, double z3, Pixel color);
-    void interptriangle(double x1, double y1, double z1, Pixel c1,
-			double x2, double y2, double z2, Pixel c2,
-			double x3, double y3, double z3, Pixel c3);
-    void   quad( double x1, double y1, double z1,
-		 double x2, double y2, double z2,
-		 double x3, double y3, double z3,
-		 double x4, double y4, double z4,
-		 Pixel color);
-    void   solidquad( double x1, double y1, double z1,
-		      double x2, double y2, double z2,
-		      double x3, double y3, double z3,
-		      double x4, double y4, double z4,
-		      Pixel color);
-    void   interpquad( double x1, double y1, double z1, Pixel c1,
-		       double x2, double y2, double z2, Pixel c2,
-		       double x3, double y3, double z3, Pixel c3,
-		       double x4, double y4, double z4, Pixel c4);
-    void   solidsphere( double x, double y, double z, double radius,Pixel c);
-    void   outlinesphere( double x, double y, double z, double radius,Pixel c, Pixel bc);
-  }
-} Plot3D;
-
-#ifndef SWIGJAVA
-/* These directives create constants of a specific type.  They
-   do not correspond to any C variable or declared constant in the
-   header file */
-%constant PixMap * SQUARE = &PixMap_SQUARE;
-%constant PixMap * TRIANGLE = &PixMap_TRIANGLE;
-%constant PixMap * CROSS = &PixMap_CROSS;
-#endif
-
-
-
-
diff --git a/Examples/GIFPlot/Java/check.list b/Examples/GIFPlot/Java/check.list
deleted file mode 100644
index 13de977af..000000000
--- a/Examples/GIFPlot/Java/check.list
+++ /dev/null
@@ -1,4 +0,0 @@
-# see top-level Makefile.in
-full
-shadow
-simple
diff --git a/Examples/GIFPlot/Java/full/Makefile b/Examples/GIFPlot/Java/full/Makefile
deleted file mode 100644
index 8f167237d..000000000
--- a/Examples/GIFPlot/Java/full/Makefile
+++ /dev/null
@@ -1,20 +0,0 @@
-TOP        = ../../..
-SWIG       = $(TOP)/../swig
-SWIGOPT    = -I../../Include -noproxy
-SRCS       =
-TARGET     = gifplot
-INTERFACE  = gifplot.i
-LIBS       = -L../.. -lgifplot
-INCLUDES   = -I../../Include
-
-all::
-	$(MAKE) -f $(TOP)/Makefile SRCS='$(SRCS)' SWIG='$(SWIG)' \
-	INCLUDES='$(INCLUDES)' LIBS='$(LIBS)' SWIGOPT='$(SWIGOPT)' \
-	TARGET='$(TARGET)' INTERFACE='$(INTERFACE)' java
-	javac *.java
-
-clean::
-	$(MAKE) -f $(TOP)/Makefile java_clean
-	rm -f *.gif
-
-check: all
diff --git a/Examples/GIFPlot/Java/full/README b/Examples/GIFPlot/Java/full/README
deleted file mode 100644
index f536864de..000000000
--- a/Examples/GIFPlot/Java/full/README
+++ /dev/null
@@ -1,8 +0,0 @@
-This example runs the entire gifplot.h header file through SWIG without
-any changes.  The program 'main.java' does something a little more 
-interesting. After doing a make, run it using 'java main'. You'll have to go 
-look at the header file to get a complete listing of the functions.
-
-Note the differences in the main.java files between this example and the  
-'full' example. This example does not use shadow classes.
-
diff --git a/Examples/GIFPlot/Java/full/cmap b/Examples/GIFPlot/Java/full/cmap
deleted file mode 100644
index a20c331a9573dd8443380680bfe2cc428780d8a9..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

literal 768
zcmZQzpd(=A5)hSEP}Mdtvvzdz4h)M)OwTDSuW4%Uoiu&!q7`d5@7R0z#JS5i?>&C`
z?#s{r^Z@9-XXO?YlTlLFHMX#G@$?UkN=VBFxv-;m^2~WlR;}N<`@pd?7q8!a^y1xT
znmh34m-nxpKDd4D;+bOy_iW#^cE#d(Gbi_Tw$xXZ7G$R-M27|XxI5We80l&#%Snpx
zbFrd(h8Vt}lCeu@T6xFJRlCpJeMef510DGC$^DyG&YwK8f9IC<tCq~4HKo4`=)RKt
ztd#huP=7C1dn;3YEme6bQ8Jvz%Ed1tDW|Lfj0{^Rcb~wpXkcs<lvdTZboK$GWATc$
Xo3`&c2#k+ww;w!x^&XgFNDnap(k+Jt

diff --git a/Examples/GIFPlot/Java/full/gifplot.i b/Examples/GIFPlot/Java/full/gifplot.i
deleted file mode 100644
index 5a7f5008f..000000000
--- a/Examples/GIFPlot/Java/full/gifplot.i
+++ /dev/null
@@ -1,15 +0,0 @@
-/* Oh what the heck, let's just grab the whole darn header file
-   and see what happens. */
-
-%module gifplot
-%{
-
-/* Note: You still need this part because the %include directive
-   merely causes SWIG to interpret the contents of a file.  It doesn't
-   include the right include headers for the resulting C code */
-
-#include "gifplot.h"
-
-%}
-
-%include gifplot.h
diff --git a/Examples/GIFPlot/Java/full/main.java b/Examples/GIFPlot/Java/full/main.java
deleted file mode 100644
index 8fb65c86d..000000000
--- a/Examples/GIFPlot/Java/full/main.java
+++ /dev/null
@@ -1,75 +0,0 @@
-// Plot a 3D function
-import java.lang.Math;
-
-public class main {
-
-  static {
-    try {
-        System.loadLibrary("gifplot");
-    } catch (UnsatisfiedLinkError e) {
-      System.err.println("Native code library failed to load. See the chapter on Dynamic Linking Problems in the SWIG Java documentation for help.\n" + e);
-      System.exit(1);
-    }
-  }
-
-  public static void main(String argv[]) {
-    
-    // Here are some plotting parameters
-    double xmin = -5.0;
-    double xmax =  5.0;
-    double ymin = -5.0;
-    double ymax =  5.0;
-    double zmin = -5.0;
-    double zmax =  5.0;
-    
-    // Grid resolution
-    int nxpoints =  60;
-    int nypoints =  60;
-    
-    SWIGTYPE_p_ColorMap cmap  = gifplot.new_ColorMap("cmap");
-    SWIGTYPE_p_FrameBuffer frame = gifplot.new_FrameBuffer(500,500);
-    gifplot.FrameBuffer_clear(frame,(short)gifplot.BLACK);
-    
-    SWIGTYPE_p_Plot3D p3    = gifplot.new_Plot3D(frame,xmin,ymin,zmin,xmax,ymax,zmax);
-    gifplot.Plot3D_lookat(p3,2*(zmax-zmin));
-    gifplot.Plot3D_autoperspective(p3,40);
-    gifplot.Plot3D_rotu(p3,60);
-    gifplot.Plot3D_rotr(p3,30);
-    gifplot.Plot3D_rotd(p3,10);
-    
-    System.out.println( "Making a nice 3D plot..." );
-    gifplot.Plot3D_clear(p3,(short)gifplot.BLACK);
-    gifplot.Plot3D_start(p3);
-    double dx = 1.0*(xmax-xmin)/nxpoints;
-    double dy = 1.0*(ymax-ymin)/nypoints;
-    double cscale = 240.0/(zmax-zmin);
-    double x = xmin;
-    for (int i = 0; i < nxpoints; i++) {
-      double y = ymin;
-      for (int j = 0; j < nypoints; j++) {
-        double z1 = func(x,y);
-        double z2 = func(x+dx,y);
-        double z3 = func(x+dx,y+dy);
-        double z4 = func(x,y+dy);
-        double c1 = cscale*(z1-zmin);
-        double c2 = cscale*(z2-zmin);
-        double c3 = cscale*(z3-zmin);
-        double c4 = cscale*(z4-zmin);
-        double c = (c1+c2+c3+c4)/4;
-        if (c < 0) c = 0;
-        if (c > 239) c = 239;
-        gifplot.Plot3D_solidquad(p3,x,y,z1,x+dx,y,z2,x+dx,y+dy,z3,x,y+dy,z4,(short)(c+16));
-        y = y + dy;
-      }
-      x = x + dx;
-    }
-
-    gifplot.FrameBuffer_writeGIF(frame,cmap,"image.gif");
-    System.out.println( "Wrote image.gif" );
-  } 
-
-  // Here is the function to plot
-  public static double func(double x, double y) {
-    return 5*java.lang.Math.cos(2*java.lang.Math.sqrt(x*x+y*y))*java.lang.Math.exp(-0.3*java.lang.Math.sqrt(x*x+y*y));
-  }
-}
diff --git a/Examples/GIFPlot/Java/shadow/Makefile b/Examples/GIFPlot/Java/shadow/Makefile
deleted file mode 100644
index e513b9b5a..000000000
--- a/Examples/GIFPlot/Java/shadow/Makefile
+++ /dev/null
@@ -1,20 +0,0 @@
-TOP        = ../../..
-SWIG       = $(TOP)/../swig
-SWIGOPT    = -I../../Interface
-SRCS       =
-TARGET     = gifplot
-INTERFACE  = gifplot.i
-LIBS       = -L../.. -lgifplot
-INCLUDES   = -I../../Include
-
-all::
-	$(MAKE) -f $(TOP)/Makefile SRCS='$(SRCS)' SWIG='$(SWIG)' \
-	INCLUDES='$(INCLUDES)' LIBS='$(LIBS)' SWIGOPT='$(SWIGOPT)' \
-	TARGET='$(TARGET)' INTERFACE='$(INTERFACE)' java
-	javac *.java
-
-clean::
-	$(MAKE) -f $(TOP)/Makefile java_clean
-	rm -f *.gif
-
-check: all
diff --git a/Examples/GIFPlot/Java/shadow/README b/Examples/GIFPlot/Java/shadow/README
deleted file mode 100644
index 4adbde306..000000000
--- a/Examples/GIFPlot/Java/shadow/README
+++ /dev/null
@@ -1,5 +0,0 @@
-This example uses the file in ../../Interface/gifplot.i to build
-an interface with shadow classes.  After doing a make, run the program main, ie: 'java main'.
-
-Note the differences in the main.java files between this example and the  
-'full' example. This example uses the shadow classes.
diff --git a/Examples/GIFPlot/Java/shadow/cmap b/Examples/GIFPlot/Java/shadow/cmap
deleted file mode 100644
index a20c331a9573dd8443380680bfe2cc428780d8a9..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

literal 768
zcmZQzpd(=A5)hSEP}Mdtvvzdz4h)M)OwTDSuW4%Uoiu&!q7`d5@7R0z#JS5i?>&C`
z?#s{r^Z@9-XXO?YlTlLFHMX#G@$?UkN=VBFxv-;m^2~WlR;}N<`@pd?7q8!a^y1xT
znmh34m-nxpKDd4D;+bOy_iW#^cE#d(Gbi_Tw$xXZ7G$R-M27|XxI5We80l&#%Snpx
zbFrd(h8Vt}lCeu@T6xFJRlCpJeMef510DGC$^DyG&YwK8f9IC<tCq~4HKo4`=)RKt
ztd#huP=7C1dn;3YEme6bQ8Jvz%Ed1tDW|Lfj0{^Rcb~wpXkcs<lvdTZboK$GWATc$
Xo3`&c2#k+ww;w!x^&XgFNDnap(k+Jt

diff --git a/Examples/GIFPlot/Java/shadow/main.java b/Examples/GIFPlot/Java/shadow/main.java
deleted file mode 100644
index fbcf6e792..000000000
--- a/Examples/GIFPlot/Java/shadow/main.java
+++ /dev/null
@@ -1,76 +0,0 @@
-// Plot a 3D function
-
-import java.lang.Math;
-
-public class main {
-
-  static {
-    try {
-        System.loadLibrary("gifplot");
-    } catch (UnsatisfiedLinkError e) {
-      System.err.println("Native code library failed to load. See the chapter on Dynamic Linking Problems in the SWIG Java documentation for help.\n" + e);
-      System.exit(1);
-    }
-  }
-
-  public static void main(String argv[]) {
-    
-    // Here are some plotting parameters
-    double xmin = -5.0;
-    double xmax =  5.0;
-    double ymin = -5.0;
-    double ymax =  5.0;
-    double zmin = -5.0;
-    double zmax =  5.0;
-    
-    // Grid resolution
-    int nxpoints =  60;
-    int nypoints =  60;
-    
-    ColorMap cmap = new ColorMap("cmap");
-    FrameBuffer frame = new FrameBuffer(500,500);
-    frame.clear((short)gifplot.BLACK);
-    
-    Plot3D p3 = new Plot3D(frame,xmin,ymin,zmin,xmax,ymax,zmax);
-    p3.lookat(2*(zmax-zmin));
-    p3.autoperspective(40);
-    p3.rotu(60);
-    p3.rotr(30);
-    p3.rotd(10);
-    
-    System.out.println( "Making a nice 3D plot..." );
-    p3.clear((short)gifplot.BLACK);
-    p3.start();
-    double dx = 1.0*(xmax-xmin)/nxpoints;
-    double dy = 1.0*(ymax-ymin)/nypoints;
-    double cscale = 240.0/(zmax-zmin);
-    double x = xmin;
-    for (int i = 0; i < nxpoints; i++) {
-      double y = ymin;
-      for (int j = 0; j < nypoints; j++) {
-        double z1 = func(x,y);
-        double z2 = func(x+dx,y);
-        double z3 = func(x+dx,y+dy);
-        double z4 = func(x,y+dy);
-        double c1 = cscale*(z1-zmin);
-        double c2 = cscale*(z2-zmin);
-        double c3 = cscale*(z3-zmin);
-        double c4 = cscale*(z4-zmin);
-        double c = (c1+c2+c3+c4)/4;
-        if (c < 0) c = 0;
-        if (c > 239) c = 239;
-        p3.solidquad(x,y,z1,x+dx,y,z2,x+dx,y+dy,z3,x,y+dy,z4,(short)(c+16));
-        y = y + dy;
-      }
-      x = x + dx;
-    }
-
-    frame.writeGIF(cmap,"image.gif");
-    System.out.println( "Wrote image.gif" );
-  } 
-
-  // Here is the function to plot
-  public static double func(double x, double y) {
-    return 5*java.lang.Math.cos(2*java.lang.Math.sqrt(x*x+y*y))*java.lang.Math.exp(-0.3*java.lang.Math.sqrt(x*x+y*y));
-  }
-}
diff --git a/Examples/GIFPlot/Java/simple/Makefile b/Examples/GIFPlot/Java/simple/Makefile
deleted file mode 100644
index d707fd458..000000000
--- a/Examples/GIFPlot/Java/simple/Makefile
+++ /dev/null
@@ -1,21 +0,0 @@
-TOP        = ../../..
-SWIG       = $(TOP)/../swig
-SWIGOPT    = -noproxy
-SRCS       =
-TARGET     = simple
-INTERFACE  = simple.i
-LIBS       = -L../.. -lgifplot
-INCLUDES   = -I../../Include
-
-all::
-	$(MAKE) -f $(TOP)/Makefile SRCS='$(SRCS)' SWIG='$(SWIG)' \
-	INCLUDES='$(INCLUDES)' LIBS='$(LIBS)' SWIGOPT='$(SWIGOPT)' \
-	TARGET='$(TARGET)' INTERFACE='$(INTERFACE)' java
-	javac *.java
-
-
-clean::
-	$(MAKE) -f $(TOP)/Makefile java_clean
-	rm -f *.gif
-
-check: all
diff --git a/Examples/GIFPlot/Java/simple/README b/Examples/GIFPlot/Java/simple/README
deleted file mode 100644
index 1fb8453f0..000000000
--- a/Examples/GIFPlot/Java/simple/README
+++ /dev/null
@@ -1,5 +0,0 @@
-This is a very minimalistic example in which just a few functions
-and constants from library are wrapped and used to draw some simple
-shapes.  After doing a make, run the java program, ie 'java main'.
-
-
diff --git a/Examples/GIFPlot/Java/simple/main.java b/Examples/GIFPlot/Java/simple/main.java
deleted file mode 100644
index b165a4baa..000000000
--- a/Examples/GIFPlot/Java/simple/main.java
+++ /dev/null
@@ -1,41 +0,0 @@
-
-public class main {
-
-  static {
-    try {
-        System.loadLibrary("simple");
-    } catch (UnsatisfiedLinkError e) {
-      System.err.println("Native code library failed to load. See the chapter on Dynamic Linking Problems in the SWIG Java documentation for help.\n" + e);
-      System.exit(1);
-    }
-  }
-
-  public static void main(String argv[]) {
-
-    // Draw some simple shapes
-    System.out.println( "Drawing some basic shapes" );
-    
-    SWIGTYPE_p_ColorMap cmap = simple.new_ColorMap(null);
-    SWIGTYPE_p_FrameBuffer f    = simple.new_FrameBuffer(400,400);
-    
-    // Clear the picture
-    simple.FrameBuffer_clear(f,(short)simple.BLACK);
-    
-    // Make a red box
-    simple.FrameBuffer_box(f,40,40,200,200,(short)simple.RED);
-    
-    // Make a blue circle
-    simple.FrameBuffer_circle(f,200,200,40,(short)simple.BLUE);
-    
-    // Make green line
-    simple.FrameBuffer_line(f,10,390,390,200, (short)simple.GREEN);
-    
-    // Write an image out to disk
-    
-    simple.FrameBuffer_writeGIF(f,cmap,"image.gif");
-    System.out.println( "Wrote image.gif" );
-    
-    simple.delete_FrameBuffer(f);
-    simple.delete_ColorMap(cmap);
-    }
-}
diff --git a/Examples/GIFPlot/Java/simple/simple.i b/Examples/GIFPlot/Java/simple/simple.i
deleted file mode 100644
index 457bc4c09..000000000
--- a/Examples/GIFPlot/Java/simple/simple.i
+++ /dev/null
@@ -1,38 +0,0 @@
-/* This example shows a very simple interface wrapping a few 
-   primitive declarations */
-
-%module simple
-%{
-#include "gifplot.h"
-%}
-
-typedef unsigned char Pixel;
-
-/* Here are a few useful functions */
-
-ColorMap    *new_ColorMap(char *filename = 0);
-void         delete_ColorMap(ColorMap *cmap);
-
-FrameBuffer *new_FrameBuffer(unsigned int width, unsigned int height);
-void         delete_FrameBuffer(FrameBuffer *frame);
-void         FrameBuffer_clear(FrameBuffer *frame, Pixel color);
-void         FrameBuffer_line(FrameBuffer *frame, int x1, int y1, int x2, int y2, Pixel color);
-void         FrameBuffer_box(FrameBuffer *frame, int x1, int y1, int x2, int y2, Pixel color);
-void         FrameBuffer_circle(FrameBuffer *frame, int x1, int y1, int radius, Pixel color);
-int          FrameBuffer_writeGIF(FrameBuffer *f, ColorMap *c, char *filename);
-
-/* And some useful constants */
-
-#define BLACK   0
-#define WHITE   1
-#define RED     2
-#define GREEN   3
-#define BLUE    4
-#define YELLOW  5
-#define CYAN    6
-#define MAGENTA 7
-
-
-
-
-
diff --git a/Examples/GIFPlot/Lib/Makefile.in b/Examples/GIFPlot/Lib/Makefile.in
deleted file mode 100644
index 9db828eb2..000000000
--- a/Examples/GIFPlot/Lib/Makefile.in
+++ /dev/null
@@ -1,22 +0,0 @@
-CC      = @CC@
-CCSHARED= @CCSHARED@ 
-INCLUDES= -I../Include
-CFLAGS  = -O
-SRCS    = frame.c color.c plot2d.c plot3d.c font.c pixmap.c matrix.c gif.c
-OBJS    = $(SRCS:.c=.@OBJEXT@)
-AR      = @AR@
-RANLIB  = @RANLIB@
-TARGET  = ../libgifplot.a
-
-.c.@OBJEXT@: 
-	$(CC) $(CCSHARED) $(INCLUDES) $(CFLAGS) -c -o $*.@OBJEXT@ $<
-
-all:  $(OBJS)
-	@rm -f ../libgifplot.a
-	$(AR) cr $(TARGET) $(OBJS)
-	$(RANLIB) $(TARGET)
-
-clean:
-	rm -f *.@OBJEXT@ *~ $(TARGET)
-
-check: all
diff --git a/Examples/GIFPlot/Lib/color.c b/Examples/GIFPlot/Lib/color.c
deleted file mode 100644
index a4eaf285e..000000000
--- a/Examples/GIFPlot/Lib/color.c
+++ /dev/null
@@ -1,140 +0,0 @@
-/* ----------------------------------------------------------------------------- 
- * color.c
- *
- *     Colormaps
- * 
- * Author(s) : David Beazley (beazley@cs.uchicago.edu)
- * Copyright (C) 1995-1996
- *
- * See the file LICENSE for information on usage and redistribution.	
- * ----------------------------------------------------------------------------- */
-
-#define COLORMAP
-#include "gifplot.h"
-#include <string.h>
-
-/* ------------------------------------------------------------------------
-   ColorMap *new_ColorMap(char *filename)
-
-   Read a colormap from a file.
-   ------------------------------------------------------------------------ */
-
-ColorMap *new_ColorMap(char *filename) {
-  ColorMap *c;
-  FILE *cm;
-  void ColorMap_default(ColorMap *);
-  
-  if (!filename) {
-    c = (ColorMap *) malloc(sizeof(ColorMap));
-    c->cmap = (unsigned char *) malloc(768*sizeof(char));
-    c->name = 0;
-    ColorMap_default(c);
-    return c;
-  }
-  if (strlen(filename) == 0) {
-    c = (ColorMap *) malloc(sizeof(ColorMap));
-    c->cmap = (unsigned char *) malloc(768*sizeof(char));
-    ColorMap_default(c);
-    return c;
-  }
-  if ((cm = fopen(filename,"rb")) == NULL) {
-    return (ColorMap *) 0;
-  }
-  c = (ColorMap *) malloc(sizeof(ColorMap));
-  c->cmap = (unsigned char *) malloc(768*sizeof(char));
-  if (fread(c->cmap, 768, 1, cm) != 1) {
-    free((char *)c->cmap);
-    free((char *)c);
-    fclose(cm);
-    return (ColorMap *) 0;
-  }
-  fclose(cm);
-  c->name = (char *) malloc(strlen(filename)+1);
-  strcpy(c->name, filename);
-  ColorMap_default(c);
-  return c;
-}
-
-/* --------------------------------------------------------------------------
-   delete_ColorMap(ColorMap *cm)
-
-   Destroy a ColorMap
-   -------------------------------------------------------------------------- */
-
-void delete_ColorMap(ColorMap *cm) {
-  if (cm) {
-    free((char *)cm->cmap);
-    if (cm->name)
-      free((char *)cm->name);
-    free((char *)cm);
-  }
-}
-
-/* --------------------------------------------------------------------------
-   ColorMap_default(ColorMap *cm)
-
-   This function fills in default values for the first 8 entries of the
-   colormap.  These are *fixed* values---used internally.
-   -------------------------------------------------------------------------- */
-
-void ColorMap_default(ColorMap *cm) {
-  unsigned char *r,*g,*b;
-  if (cm) {
-    r = cm->cmap;
-    g = cm->cmap+256;
-    b = cm->cmap+512;
-
-    r[0] = 0;   g[0] = 0;   b[0] = 0;      /* BLACK */
-    r[1] = 255; g[1] = 255; b[1] = 255;    /* WHITE */
-    r[2] = 255; g[2] = 0;   b[2] = 0;      /* RED   */
-    r[3] = 0;   g[3] = 255; b[3] = 0;      /* GREEN */
-    r[4] = 0;   g[4] = 0;   b[4] = 255;    /* BLUE  */
-    r[5] = 255; g[5] = 255; b[5] = 0;      /* YELLOW */
-    r[6] = 0;   g[6] = 255; b[6] = 255;    /* CYAN   */
-    r[7] = 255; g[7] = 0;   b[7] = 255;    /* MAGENTA */
-  }
-}
-
-void ColorMap_assign(ColorMap *cm, int index, int r, int g, int b) {
-  unsigned char *rb,*gb,*bb;
-
-  rb = cm->cmap;
-  gb = cm->cmap+256;
-  bb = cm->cmap+512;
-
-  rb[index] = r;
-  gb[index] = g;
-  bb[index] = b;
-}
-
-int ColorMap_getitem(ColorMap *cm, int index) {
-  if ((index < 0) && (index >= 768)) return -1;
-  return cm->cmap[index];
-}
-
-void ColorMap_setitem(ColorMap *cm, int index, int value) {
-  if ((index < 0) && (index >= 768)) return;
-  cm->cmap[index]=value;
-}  
-
-/* --------------------------------------------------------------------
-   ColorMap_write(ColorMap *cm, char *filename)
-
-   Write out a colormap to disk.
-   -------------------------------------------------------------------- */
-
-int ColorMap_write(ColorMap *cm, char *filename) {
-
-  FILE *f;
-  if (!cm) return -1;
-  if (!filename) return -1;
-  if (strlen(filename) == 0) return -1;
-
-  f = fopen(filename,"w");
-  
-  fwrite(cm->cmap,768,1,f);
-  fclose(f);
-  return 0;
-}
-
-#undef COLORMAP
diff --git a/Examples/GIFPlot/Lib/font.c b/Examples/GIFPlot/Lib/font.c
deleted file mode 100644
index b30ee9b14..000000000
--- a/Examples/GIFPlot/Lib/font.c
+++ /dev/null
@@ -1,705 +0,0 @@
-/* ----------------------------------------------------------------------------- 
- * font.c
- *
- *     Some basic fonts.
- * 
- * Author(s) : David Beazley (beazley@cs.uchicago.edu)
- * Copyright (C) 1995-1996
- *
- * See the file LICENSE for information on usage and redistribution.	
- * ----------------------------------------------------------------------------- */
-
-#define FONT
-#include "gifplot.h"
-
-static char Char_A[80] = "\
-...x....\
-...x....\
-..x.x...\
-..x.x...\
-.x...x..\
-.xxxxx..\
-x.....x.\
-x.....x.\
-x.....x.\
-........";
-
-static char Char_B[80] = "\
-xxxxxx..\
-x.....x.\
-x.....x.\
-x.....x.\
-xxxxxx..\
-x.....x.\
-x.....x.\
-x.....x.\
-xxxxxx..\
-........";
-
-static char Char_C[80] = "\
-..xxxx..\
-.x....x.\
-x.......\
-x.......\
-x.......\
-x.......\
-x.......\
-.x....x.\
-..xxxx..\
-........";
-
-static char Char_D[80] = "\
-xxxxx...\
-x....x..\
-x.....x.\
-x.....x.\
-x.....x.\
-x.....x.\
-x.....x.\
-x....x..\
-xxxxx...\
-........";
-static char Char_E[80] = "\
-xxxxxxx.\
-x.......\
-x.......\
-x.......\
-xxxxx...\
-x.......\
-x.......\
-x.......\
-xxxxxxx.\
-........";
-static char Char_F[80] = "\
-xxxxxxx.\
-x.......\
-x.......\
-x.......\
-xxxxx...\
-x.......\
-x.......\
-x.......\
-x.......\
-........";
-static char Char_G[80] = "\
-.xxxxx..\
-x.....x.\
-x.......\
-x.......\
-x...xxx.\
-x.....x.\
-x.....x.\
-x.....x.\
-.xxxxx..\
-........";
-static char Char_H[80] = "\
-x.....x.\
-x.....x.\
-x.....x.\
-x.....x.\
-xxxxxxx.\
-x.....x.\
-x.....x.\
-x.....x.\
-x.....x.\
-........";
-static char Char_I[80] = "\
-xxxxxxx.\
-...x....\
-...x....\
-...x....\
-...x....\
-...x....\
-...x....\
-...x....\
-xxxxxxx.\
-........";
-static char Char_J[80] = "\
-......x.\
-......x.\
-......x.\
-......x.\
-......x.\
-......x.\
-x.....x.\
-.x...x..\
-..xxx...\
-........";
-static char Char_K[80] = "\
-x.....x.\
-x....x..\
-x...x...\
-x..x....\
-xxx.....\
-x..x....\
-x...x...\
-x....x..\
-x.....x.\
-........";
-static char Char_L[80] = "\
-x.......\
-x.......\
-x.......\
-x.......\
-x.......\
-x.......\
-x.......\
-x.......\
-xxxxxxx.\
-........";
-static char Char_M[80] = "\
-x.....x.\
-xx...xx.\
-xx...xx.\
-x.x.x.x.\
-x.x.x.x.\
-x..x..x.\
-x..x..x.\
-x.....x.\
-x.....x.\
-........";
-static char Char_N[80] = "\
-x.....x.\
-xx....x.\
-x.x...x.\
-x.x...x.\
-x..x..x.\
-x...x.x.\
-x...x.x.\
-x....xx.\
-x.....x.\
-........";
-static char Char_O[80] = "\
-.xxxxx..\
-x.....x.\
-x.....x.\
-x.....x.\
-x.....x.\
-x.....x.\
-x.....x.\
-x.....x.\
-.xxxxx..\
-........";
-static char Char_P[80] = "\
-xxxxxx..\
-x.....x.\
-x.....x.\
-x.....x.\
-xxxxxx..\
-x.......\
-x.......\
-x.......\
-x.......\
-........";
-static char Char_Q[80] = "\
-.xxxxx..\
-x.....x.\
-x.....x.\
-x.....x.\
-x.....x.\
-x.....x.\
-x...x.x.\
-x....x..\
-.xxxx.x.\
-........";
-static char Char_R[80] = "\
-xxxxxx..\
-x.....x.\
-x.....x.\
-x.....x.\
-xxxxxx..\
-x..x....\
-x...x...\
-x....x..\
-x.....x.\
-........";
-static char Char_S[80] = "\
-.xxxxx..\
-x.....x.\
-x.......\
-x.......\
-.xxxxx..\
-......x.\
-......x.\
-x.....x.\
-.xxxxx..\
-........";
-static char Char_T[80] = "\
-xxxxxxx.\
-...x....\
-...x....\
-...x....\
-...x....\
-...x....\
-...x....\
-...x....\
-...x....\
-........";
-static char Char_U[80] = "\
-x.....x.\
-x.....x.\
-x.....x.\
-x.....x.\
-x.....x.\
-x.....x.\
-x.....x.\
-x.....x.\
-.xxxxx..\
-........";
-static char Char_V[80] = "\
-x.....x.\
-x.....x.\
-.x...x..\
-.x...x..\
-..x.x...\
-..x.x...\
-...x....\
-...x....\
-...x....\
-........";
-static char Char_W[80] = "\
-x.....x.\
-x.....x.\
-x.....x.\
-x.....x.\
-x.....x.\
-x..x..x.\
-x..x..x.\
-x.x.x.x.\
-.x...x..\
-........";
-static char Char_X[80] = "\
-x.....x.\
-x.....x.\
-.x...x..\
-..x.x...\
-...x....\
-..x.x...\
-.x...x..\
-x.....x.\
-x.....x.\
-........";
-static char Char_Y[80] = "\
-x.....x.\
-x.....x.\
-.x...x..\
-..x.x...\
-...x....\
-...x....\
-...x....\
-...x....\
-...x....\
-........";
-static char Char_Z[80] = "\
-xxxxxxx.\
-......x.\
-.....x..\
-....x...\
-...x....\
-..x.....\
-.x......\
-x.......\
-xxxxxxx.\
-........";
-static char Char_0[80] = "\
-.xxxxx..\
-x....xx.\
-x...x.x.\
-x..x..x.\
-x..x..x.\
-x.x...x.\
-x.x...x.\
-xx....x.\
-.xxxxx..\
-........";
-static char Char_1[80] = "\
-...x....\
-..xx....\
-...x....\
-...x....\
-...x....\
-...x....\
-...x....\
-...x....\
-..xxx...\
-........";
-static char Char_2[80] = "\
-..xxxx..\
-.x....x.\
-x.....x.\
-.....x..\
-....x...\
-...x....\
-..x.....\
-.x......\
-xxxxxxx.\
-........";
-static char Char_3[80] = "\
-.xxxxx..\
-x.....x.\
-......x.\
-......x.\
-...xxx..\
-......x.\
-......x.\
-x.....x.\
-.xxxxx..\
-........";
-static char Char_4[80] = "\
-....xx..\
-...x.x..\
-..x..x..\
-.x...x..\
-xxxxxxx.\
-.....x..\
-.....x..\
-.....x..\
-.....x..\
-........";
-static char Char_5[80] = "\
-xxxxxxx.\
-x.......\
-x.......\
-x.......\
-xxxxxx..\
-......x.\
-......x.\
-x.....x.\
-.xxxxx..\
-........";
-static char Char_6[80] = "\
-....xxx.\
-..xx....\
-.x......\
-x.......\
-x.xxx...\
-xx...x..\
-x.....x.\
-.x...x..\
-..xxx...\
-........";
-static char Char_7[80] = "\
-xxxxxxx.\
-x.....x.\
-.....x..\
-....x...\
-...x....\
-..x.....\
-.x......\
-x.......\
-x.......\
-........";
-static char Char_8[80] = "\
-.xxxxx..\
-x.....x.\
-x.....x.\
-x.....x.\
-.xxxxx..\
-x.....x.\
-x.....x.\
-x.....x.\
-.xxxxx..\
-........";
-static char Char_9[80] = "\
-..xxxx..\
-.x....x.\
-x.....x.\
-x....xx.\
-.xxxx.x.\
-......x.\
-......x.\
-....xx..\
-.xxx....\
-........";
-static char Char_MINUS[80] = "\
-........\
-........\
-........\
-........\
-.xxxxxx.\
-........\
-........\
-........\
-........\
-........";
-static char Char_PLUS[80] = "\
-........\
-........\
-...x....\
-...x....\
-.xxxxx..\
-...x....\
-...x....\
-........\
-........\
-........";
-static char Char_EQUAL[80] = "\
-........\
-........\
-........\
-.xxxxx..\
-........\
-.xxxxx..\
-........\
-........\
-........\
-........";
-static char Char_LPAREN[80] = "\
-....x...\
-...x....\
-..x.....\
-.x......\
-.x......\
-.x......\
-..x.....\
-...x....\
-....x...\
-........";
-static char Char_RPAREN[80] = "\
-...x....\
-....x...\
-.....x..\
-......x.\
-......x.\
-......x.\
-.....x..\
-....x...\
-...x....\
-........";
-static char Char_QUOTE[80] = "\
-..x.x...\
-..x.x...\
-........\
-........\
-........\
-........\
-........\
-........\
-........\
-........";
-static char Char_COLON[80] = "\
-........\
-........\
-...xx...\
-...xx...\
-........\
-...xx...\
-...xx...\
-........\
-........\
-........";
-static char Char_PERIOD[80] = "\
-........\
-........\
-........\
-........\
-........\
-........\
-........\
-...xx...\
-...xx...\
-........";
-static char Char_COMMA[80] = "\
-........\
-........\
-........\
-........\
-........\
-........\
-...xx...\
-...xx...\
-....x...\
-...x....";
-
-static char Char_SLASH[80] = "\
-........\
-......x.\
-.....x..\
-....x...\
-...x....\
-..x.....\
-.x......\
-x.......\
-........\
-........";
-
-static char Char_SPACE[80] = "\
-........\
-........\
-........\
-........\
-........\
-........\
-........\
-........\
-........\
-........";
-
-static char  *GP_Font[128];
-static int    InitGP_Font = 0;
-
-static void initGP_Fonts(void) {
-
-  int i;
-  for (i = 0; i < 128; i++)
-    GP_Font[i] = (char *) 0;
-  
-  GP_Font['A'] = GP_Font['a'] = Char_A;
-  GP_Font['B'] = GP_Font['b'] = Char_B;
-  GP_Font['C'] = GP_Font['c'] = Char_C;
-  GP_Font['D'] = GP_Font['d'] = Char_D;
-  GP_Font['E'] = GP_Font['e'] = Char_E;
-  GP_Font['F'] = GP_Font['f'] = Char_F;
-  GP_Font['G'] = GP_Font['g'] = Char_G;
-  GP_Font['H'] = GP_Font['h'] = Char_H;
-  GP_Font['I'] = GP_Font['i'] = Char_I;
-  GP_Font['J'] = GP_Font['j'] = Char_J;
-  GP_Font['K'] = GP_Font['k'] = Char_K;
-  GP_Font['L'] = GP_Font['l'] = Char_L;
-  GP_Font['M'] = GP_Font['m'] = Char_M;
-  GP_Font['N'] = GP_Font['n'] = Char_N;
-  GP_Font['O'] = GP_Font['o'] = Char_O;
-  GP_Font['P'] = GP_Font['p'] = Char_P;
-  GP_Font['Q'] = GP_Font['q'] = Char_Q;
-  GP_Font['R'] = GP_Font['r'] = Char_R;
-  GP_Font['S'] = GP_Font['s'] = Char_S;
-  GP_Font['T'] = GP_Font['t'] = Char_T;
-  GP_Font['U'] = GP_Font['u'] = Char_U;
-  GP_Font['V'] = GP_Font['v'] = Char_V;
-  GP_Font['W'] = GP_Font['w'] = Char_W;
-  GP_Font['X'] = GP_Font['x'] = Char_X;
-  GP_Font['Y'] = GP_Font['y'] = Char_Y;
-  GP_Font['Z'] = GP_Font['z'] = Char_Z;
-  GP_Font['0'] = Char_0;
-  GP_Font['1'] = Char_1;
-  GP_Font['2'] = Char_2;
-  GP_Font['3'] = Char_3;
-  GP_Font['4'] = Char_4;
-  GP_Font['5'] = Char_5;
-  GP_Font['6'] = Char_6;
-  GP_Font['7'] = Char_7;
-  GP_Font['8'] = Char_8;
-  GP_Font['9'] = Char_9;
-  GP_Font['.'] = Char_PERIOD;
-  GP_Font[','] = Char_COMMA;
-  GP_Font['='] = Char_EQUAL;
-  GP_Font['-'] = Char_MINUS;
-  GP_Font['+'] = Char_PLUS;
-  GP_Font['\"'] = Char_QUOTE;
-  GP_Font['('] = Char_LPAREN;
-  GP_Font[')'] = Char_RPAREN;
-  GP_Font[':'] = Char_COLON;
-  GP_Font['/'] = Char_SLASH;
-  GP_Font[' '] = Char_SPACE;
-  InitGP_Font = 1;
-}
-
-/* -----------------------------------------------------------------------
-   void FrameBuffer_drawchar(FrameBuffer *f, int x, int y, Pixel fgcolor, Pixel bgcolor, char chr, int orientation)
-
-   Draws a character at location x, y with given color and orientation parameters.
-   Orientation can either be HORIZONTAL or VERTICAL
-   ----------------------------------------------------------------------- */
-void FrameBuffer_drawchar(FrameBuffer *f, int x, int y, int fgcolor,
-			  int bgcolor, char chr, int orientation) {
-
-  Pixel c, bc,*p,*p1;
-  char *ch;
-  int i,j;
-  int xpixels,ypixels;
-
-  if (!InitGP_Font) initGP_Fonts();
-  
-  c =  (Pixel) fgcolor;
-  bc = (Pixel) bgcolor;
-  xpixels = f->width;
-  ypixels = f->height;
-
-  if (orientation == HORIZONTAL) {
-    if ((x < f->xmin) || (x > f->xmax-8) ||
-	(y < f->ymin) || (y > f->ymax-10)) return;
-  
-    ch = GP_Font[(int) chr];
-    if (!ch) return;
-    p = &f->pixels[y+9][x];
-    for (i = 0; i < 10; i++) {
-      p1 = p;
-      for (j = 0; j< 8; j++) {
-	if (*(ch++) == 'x') *p= c;
-	else if (bgcolor >= 0)
-	  *p = bc;
-	p++;
-      }
-      p = (p1 - xpixels);
-    }
-  } else {
-    if ((x < f->xmin+10) || (x >= f->xmax) ||
-	(y < f->ymin) || (y > f->ymax-8)) return;
-  
-    ch = GP_Font[(int) chr];
-    if (!ch) return;
-    p = &f->pixels[y][x-9];
-    for (i = 0; i < 10; i++) {
-      p1 = p;
-      for (j = 0; j< 8; j++) {
-	if (*(ch++) == 'x') *p= c;
-	else if (bgcolor >= 0)
-	  *p = bc;
-	p+=xpixels;
-      }
-      p = p1 + 1;
-    }
-  }    
-}
-
-/* ----------------------------------------------------------------------
-   void FrameBuffer_drawstring(FrameBuffer *f, int x, int y, int fgcolor,
-                               int bgcolor, char *text, int orientation)
-
-   Draws an ASCII string on the framebuffer.   Can be oriented either horizontally
-   or vertically.  
-   ---------------------------------------------------------------------- */
-
-void FrameBuffer_drawstring(FrameBuffer *f, int x, int y, int fgcolor, int bgcolor, char *text, int orientation) {
-
-  char *c;
-  int  x1, y1;
-  int xpixels, ypixels;
-  
-  x1 = x;
-  y1 = y;
-  xpixels = f->width;
-  ypixels = f->height;
-  c = text;
-  while (*c) {
-    if (*c == '\n') {
-      if (orientation == HORIZONTAL) {
-	x1 = x; y1= y1- 10*xpixels;
-      } else {
-	y1 = y; x1= x1 + 10*ypixels;
-      }
-    } else {
-      FrameBuffer_drawchar(f, x1,y1,fgcolor, bgcolor,*c, orientation);
-      if (orientation == HORIZONTAL) {
-	x1+=8;
-	if (x1 >= (xpixels-8)) {
-	  x1 = x; y1= y1- 10;}
-	if (y1 < 0) return;
-      } else {
-	y1 += 8;
-	if (y1 >= (ypixels-8)) {
-	  y1 = y; x1 = x1 + 10;}
-	if (x1 > (xpixels-10)) return;
-      }
-    }
-    c++;
-  }
-}
-
-
-  
-  
-  
-  
-  
-
diff --git a/Examples/GIFPlot/Lib/frame.c b/Examples/GIFPlot/Lib/frame.c
deleted file mode 100644
index e006f0daf..000000000
--- a/Examples/GIFPlot/Lib/frame.c
+++ /dev/null
@@ -1,924 +0,0 @@
-/* ----------------------------------------------------------------------------- 
- * frame.c
- *
- *     Frame buffer management
- * 
- * Author(s) : David Beazley (beazley@cs.uchicago.edu)
- * Copyright (C) 1995-1996
- *
- * See the file LICENSE for information on usage and redistribution.	
- * ----------------------------------------------------------------------------- */
-
-#define FRAME
-#include "gifplot.h"
-#include <float.h>
-
-/* ------------------------------------------------------------------------
-   FrameBuffer *new_FrameBuffer(int width, int height)
-
-   Creates a new framebuffer for storing data.
-   ------------------------------------------------------------------------ */
-
-FrameBuffer *new_FrameBuffer(unsigned int width, unsigned int height) {
-
-  FrameBuffer *f;
-  int  FrameBuffer_resize(FrameBuffer *f, int width, int height);
-
-  /* Create a new frame buffer */
-  
-  f = (FrameBuffer *) malloc(sizeof(FrameBuffer));
-  f->pixels = (Pixel **) 0;
-  f->zbuffer = (Zvalue **) 0;
-  /* Set its size */
-  
-  if (FrameBuffer_resize(f, width, height) == -1) {
-    free((char *) f);
-    return (FrameBuffer *) 0;
-  }
-
-  f->xmin = 0;
-  f->ymin = 0;
-  f->xmax = width;
-  f->ymax = height;
-  return f;
-}
-
-/* ------------------------------------------------------------------------
-   void delete_FrameBuffer(FrameBuffer *f)
-
-   Destroys the given framebuffer
-   ------------------------------------------------------------------------ */
-
-void delete_FrameBuffer(FrameBuffer *f) {
-
-  if (f) {
-    if (f->pixels) {
-      free((char *) f->pixels[0]);
-      free((char *) f->pixels);
-    }
-    if (f->zbuffer) {
-      free((char *) f->zbuffer[0]);
-      free((char *) f->zbuffer);
-    }
-    free((char *)f);
-  }
-}
-
-/* ------------------------------------------------------------------------
-   int *FrameBuffer_resize(FrameBuffer *f, int width, int height)
-
-   Resize the given framebuffer. Returns 0 on success, -1 on failure.
-   ------------------------------------------------------------------------ */
-
-int FrameBuffer_resize(FrameBuffer *f, int width, int height) {
-  int i;
-  if ((f) && (width > 0) && (height > 0)) {
-    if (f->pixels) {
-      free((char *)f->pixels[0]);
-      free((char *)f->pixels);
-    }
-    f->pixels = (Pixel **) malloc (height*sizeof(Pixel *));
-    if (!f->pixels) return -1;
-    f->pixels[0] = (Pixel *) malloc(height*width*sizeof(Pixel));
-    if (!f->pixels[0]) {
-      free((char *)f->pixels);
-      return -1;
-    }
-    for (i = 0; i < height; i++) 
-      f->pixels[i] = f->pixels[0] + i*width;
-    f->width = width;
-    f->height = height;
-    if (f->zbuffer) {
-      FrameBuffer_zresize(f,width,height);
-    }
-    return 0;
-  } else {
-    return -1;
-  }
-}
-
-/* ------------------------------------------------------------------------
-   void FrameBuffer_clear(FrameBuffer *f, Pixel color)
-
-   Clears the current FrameBuffer
-   ------------------------------------------------------------------------ */
-
-void FrameBuffer_clear(FrameBuffer *f, Pixel color) {
-  Pixel *p;
-  unsigned int i;
-  p = &f->pixels[0][0];
-
-  for (i = 0; i < f->width*f->height; i++, p++)
-    *p = color;
-}
-
-/* ------------------------------------------------------------------------
-   void FrameBuffer_plot(FrameBuffer *f, int x1, int y1, Pixel color)
-
-   Plots a point and does a bounds check.
-   ------------------------------------------------------------------------ */
-
-void FrameBuffer_plot(FrameBuffer *f, int x1, int y1, Pixel color) {
-
-  if ((x1 < f->xmin) || (x1 >= f->xmax) || (y1 < f->ymin) || (y1 >= f->ymax))
-    return;
-  f->pixels[y1][x1] = color;
-
-}
-
-/* ------------------------------------------------------------------------
-   FrameBuffer_horizontal(Framebuffer *f, int xmin, int xmax, int y, Pixel color)
-
-   Draw a horizontal line (clipped)
-   ------------------------------------------------------------------------ */
-
-void FrameBuffer_horizontal(FrameBuffer *f, int xmin, int xmax, int y, Pixel color) {
-  
-  Pixel *p;
-  int    i;
-  
-  if ((y < f->ymin) || (y >= f->ymax)) return;
-  if (xmin < f->xmin) xmin = f->xmin;
-  if (xmax >= f->xmax) xmax = f->xmax - 1;
-
-  p = &f->pixels[y][xmin];
-  for (i = xmin; i <= xmax; i++, p++)
-    *p = color;
-
-}
-
-/* ------------------------------------------------------------------------
-   FrameBuffer_horizontalinterp(Framebuffer *f, int xmin, int xmax, int y,
-                                Pixel c1, Pixel c2)
-
-   Draw a horizontal line (clipped) with color interpolation.
-   ------------------------------------------------------------------------ */
-
-void FrameBuffer_horizontalinterp(FrameBuffer *f, int xmin, int xmax, int y,
-				  Pixel c1, Pixel c2) {
-  
-  Pixel *p;
-  int    i;
-  double mc;
-  int    x1;
-  if ((y < f->ymin) || (y >= f->ymax)) return;
-
-  x1 = xmin;
-  if (xmin < f->xmin) xmin = f->xmin;
-  if (xmax >= f->xmax) xmax = f->xmax - 1;
-  if (xmax < f->xmin) return;
-  if (xmin >= f->xmax) return;
-
-  if (xmin != xmax)
-    mc = (double)(c2 - c1)/(double) (xmax - xmin);
-  else
-    mc = 0.0;
-
-  p = &f->pixels[y][xmin];
-  for (i = xmin; i <= xmax; i++, p++) 
-    *p = (Pixel) (mc*(i-x1) + c1);
-  
-}
-
-
-/* ------------------------------------------------------------------------
-   FrameBuffer_vertical(Framebuffer *f, int xmin, int xmax, int y, Pixel color)
-
-   Draw a Vertical line (clipped)
-   ------------------------------------------------------------------------ */
-
-void FrameBuffer_vertical(FrameBuffer *f, int ymin, int ymax, int x, Pixel color) {
-  
-  Pixel *p;
-  int    i;
-  
-  if ((x < f->xmin) || (x >= f->xmax)) return;
-  if (ymax < f->ymin) return;
-  if (ymin > f->ymax) return;
-  if (ymin < f->ymin) ymin = f->ymin;
-  if (ymax >= f->ymax) ymax = f->ymax - 1;
-
-  p = &f->pixels[ymin][x];
-  for (i = 0; i <= (ymax - ymin); i++, p+=f->width)
-    *p = color;
-
-}
-  
-/* ------------------------------------------------------------------------
-   void FrameBuffer_box(FrameBuffer *f, int x1, int y1, int x2, int y2, Pixel color)
-
-   Makes an outline box.
-   ------------------------------------------------------------------------ */
-
-void FrameBuffer_box(FrameBuffer *f, int x1, int y1, int x2, int y2, Pixel color) {
-
-  int  xt, yt;
-
-  /* Make sure points are in correct order */
-
-  if (x2 < x1) {
-    xt = x2;
-    x2 = x1;
-    x1 = xt;
-  }
-  if (y2 < y1) {
-    yt = y2;
-    y2 = y1;
-    y1 = yt;
-  }
-
-  /* Draw lower edge */
-
-  FrameBuffer_horizontal(f,x1,x2,y1,color);
-
-  /* Draw upper edge */
-
-  FrameBuffer_horizontal(f,x1,x2,y2,color);
-
-  /* Draw left side */
-
-  FrameBuffer_vertical(f,y1,y2,x1,color);
-
-  /* Draw right side */
-
-  FrameBuffer_vertical(f,y1,y2,x2,color);
-  
-}
-
-/* ------------------------------------------------------------------------
-   void FrameBuffer_solidbox(FrameBuffer *f, int x1, int y1, int x2, int y2, Pixel color)
-
-   Makes an solid box.
-   ------------------------------------------------------------------------ */
-
-void FrameBuffer_solidbox(FrameBuffer *f, int x1, int y1, int x2, int y2, Pixel color) {
-
-  int  xt, yt;
-
-  /* Make sure points are in correct order */
-
-  if (x2 < x1) {
-    xt = x2;
-    x2 = x1;
-    x1 = xt;
-  }
-  if (y2 < y1) {
-    yt = y2;
-    y2 = y1;
-    y1 = yt;
-  }
-
-  /* Now perform some clipping */
-
-  if (y1 < f->ymin) y1 = f->ymin;
-  if (y2 >= f->ymax) y2 = f->ymax - 1;
-
-  /* Fill it in using horizontal lines */
-  
-  for (yt = y1; yt <= y2; yt++)
-    FrameBuffer_horizontal(f,x1,x2,yt,color);
-
-}
-
-/* ------------------------------------------------------------------------
-   void FrameBuffer_interpbox(FrameBuffer *f, int x1, int y1, int x2, int y2
-                              Pixel c1, Pixel c2, Pixel c3, Pixel c4)
-
-   Makes a box with interpolated color.   Colors are assigned as follows :
-   (x1,y1) = c1
-   (x1,y2) = c2
-   (x2,y1) = c3
-   (x2,y2) = c4
-   ------------------------------------------------------------------------ */
-
-void FrameBuffer_interpbox(FrameBuffer *f, int x1, int y1, int x2, int y2,
-			   Pixel c1, Pixel c2, Pixel c3, Pixel c4) {
-
-  int  xt, yt;
-  Pixel ct;
-  double  mc1,mc2;
-  int  ystart;
-  /* Make sure points are in correct order */
-
-  if (x2 < x1) {
-    xt = x2;
-    x2 = x1;
-    x1 = xt;
-    ct = c1;
-    c1 = c3;
-    c3 = ct;
-    ct = c2;
-    c2 = c4;
-    c4 = ct;
-  }
-  if (y2 < y1) {
-    yt = y2;
-    y2 = y1;
-    y1 = yt;
-    ct = c1;
-    c1 = c2;
-    c2 = ct;
-    ct = c3;
-    c3 = c4;
-    c4 = ct;
-  }
-
-  /* Now perform some clipping */
-
-  ystart = y1;
-  mc1 = (double) (c2 - c1)/(double) (y2 - y1);
-  mc2 = (double) (c4 - c3)/(double) (y2 - y1);
-  if (y1 < f->ymin) y1 = f->ymin;
-  if (y2 >= f->ymax) y2 = f->ymax - 1;
-
-  /* Fill it in using horizontal lines */
-  
-  for (yt = y1; yt <= y2; yt++)
-    FrameBuffer_horizontalinterp(f,x1,x2,yt,(Pixel) ((mc1*(yt - ystart)) + c1),
-				  (Pixel) ((mc2*(yt-ystart))+c3));
-
-}
-
-/* ---------------------------------------------------------------------------
-   FrameBuffer_line(FrameBuffer *f, int x1, int y1, int x2, int y2, color)
-
-   Draws a line on the framebuffer using the Bresenham line algorithm.  The
-   line is clipped to fit within the current view window.
-   ---------------------------------------------------------------------------- */
-
-void FrameBuffer_line(FrameBuffer *f, int x1, int y1, int x2, int y2, Pixel c) {
-
-  int  dx,dy,dxneg,dyneg, inc1,inc2,di;
-  int  x, y, xpixels, ypixels, xt, yt;
-  Pixel *p;
-  double m;
-  int  end1 = 0, end2 = 0;
-  
-  /* Need to figure out where in the heck this line is */
-
-  dx = x2 - x1;
-  dy = y2 - y1;
-
-  if (dx == 0) {
-    /* Draw a Vertical Line */
-    if (y1 < y2)
-      FrameBuffer_vertical(f,y1,y2,x1,c);
-    else
-      FrameBuffer_vertical(f,y2,y1,x1,c);
-    return;
-  }
-  if (dy == 0) {
-    /* Draw a Horizontal Line */
-    if (x1 < x2)
-      FrameBuffer_horizontal(f,x1,x2,y1,c);
-    else
-      FrameBuffer_horizontal(f,x2,x1,y1,c);
-    return;
-  }
-
-  /* Figure out where in the heck these lines are using the
-     Cohen-Sutherland Line Clipping Scheme. */
-
-  end1 = ((x1 - f->xmin) < 0) |
-    (((f->xmax- 1 - x1) < 0) << 1) |
-    (((y1 - f->ymin) < 0) << 2) |
-    (((f->ymax-1 - y1) < 0) << 3);
-
-  end2 = ((x2 - f->xmin) < 0) |
-    (((f->xmax-1 - x2) < 0) << 1) |
-    (((y2 - f->ymin) < 0) << 2) |
-    (((f->ymax-1 - y2) < 0) << 3);
-
-  if (end1 & end2) return;      /* Nope : Not visible */
-
-  /* Make sure points have a favorable orientation */
-  
-  if (x1 > x2) {
-    xt = x1;
-    x1 = x2;
-    x2 = xt;
-    yt = y1;
-    y1 = y2;
-    y2 = yt;
-  }
-  
-  /* Clip against the boundaries */
-  m = (y2 - y1)/(double) (x2-x1);
-  if (x1 < f->xmin) {
-    y1 = (int) ((f->xmin - x1)*m + y1);
-    x1 = (int) f->xmin;
-  }
-  if (x2 >= f->xmax) {
-    y2 = (int) ((f->xmax -1 -x1)*m + y1);
-    x2 = (int) (f->xmax - 1);
-  }
-
-  if (y1 > y2) {
-    xt = x1;
-    x1 = x2;
-    x2 = xt;
-    yt = y1;
-    y1 = y2;
-    y2 = yt;
-  }
-
-  m = 1/m;
-  if (y1 < f->ymin) {
-    x1 = (int) ((f->ymin - y1)*m + x1);
-    y1 = (int) f->ymin;
-  }
-  if (y2 >= f->ymax) {
-    x2 = (int) ((f->ymax-1-y1)*m + x1);
-    y2 = (int) (f->ymax-1);
-  }
-
-  if ((x1 < f->xmin) || (x1 >= f->xmax) || (y1 < f->ymin) || (y1 >= f->ymax) ||
-      (x2 < f->xmin) || (x2 >= f->xmax) || (y2 < f->ymin) || (y2 >= f->ymax)) return;
-
-  dx = x2 - x1;
-  dy = y2 - y1;
-  xpixels = f->width;
-  ypixels = f->height;
-  
-  dxneg = (dx < 0) ? 1 : 0;
-  dyneg = (dy < 0) ? 1 : 0;
-  
-  dx = abs(dx);
-  dy = abs(dy);
-  if (dx >= dy) {
-    /* Slope between -1 and 1. */
-    if (dxneg) {
-      x = x1;
-      y = y1;
-      x1 = x2;
-      y1 = y2;
-      x2 = x;
-      y2 = y;
-      dyneg = !dyneg;
-    }
-    inc1 = 2*dy;
-    inc2 = 2*(dy-dx);
-    di = 2*dy-dx;
-
-    /* Draw a line using x as independent variable */
-    
-    p = &f->pixels[y1][x1];
-    x = x1;
-    while (x <= x2) {
-      *(p++) = c;
-      if (di < 0) {
-	di = di + inc1;
-      } else {
-	if (dyneg) {
-	  p = p - xpixels;
-	  di = di + inc2;
-	} else {
-	  p = p + xpixels;
-	  di = di + inc2;
-	}
-      }
-      x++;
-    }
-  } else {
-    /* Slope < -1 or > 1 */
-    if (dyneg) {
-      x = x1;
-      y = y1;
-      x1 = x2;
-      y1 = y2;
-      x2 = x;
-      y2 = y;
-      dxneg = !dxneg;
-    }
-    inc1 = 2*dx;
-    inc2 = 2*(dx-dy);
-    di = 2*dx-dy;
-
-    /* Draw a line using y as independent variable */
-    
-    p = &f->pixels[y1][x1];
-    y = y1;
-    while (y <= y2) {
-      *p = c;
-      p = p + xpixels;
-      if (di < 0) {
-	di = di + inc1;
-      } else {
-	if (dxneg) {
-	  p = p - 1;
-	  di = di + inc2;
-	} else {
-	  p = p + 1;
-	  di = di + inc2;
-	}
-      }
-      y++;
-    }
-  }    
-}
-
-
-/* -------------------------------------------------------------------------
-   FrameBuffer_circle(FrameBuffer f, int xc, int yc, int radius, Pixel c)
-
-   Create an outline circle
-   ------------------------------------------------------------------------- */
-
-#define plot_circle(x,y,c) \
-   if ((x >= xmin) && (x < xmax) && \
-       (y >= ymin) && (y < ymax)) \
-        pixels[y][x] = c;
-	
-void FrameBuffer_circle(FrameBuffer *f, int xc, int yc, int radius, Pixel c) {
-
-  int xpixels, ypixels, x, y, p;
-  int xmin, ymin, xmax, ymax;
-  Pixel **pixels;
-
-  if (radius <= 0) return;
-  xpixels = f->width;
-  ypixels = f->height;
-  pixels = f->pixels;
-  xmin = f->xmin;
-  ymin = f->ymin;
-  xmax = f->xmax;
-  ymax = f->ymax;
-  x = 0;
-  y = radius;
-  p = 3-2*radius;
-  while (x <= y) {
-    plot_circle(xc+x,yc+y,c);
-    plot_circle(xc-x,yc+y,c);
-    plot_circle(xc+x,yc-y,c);
-    plot_circle(xc-x,yc-y,c);
-    plot_circle(xc+y,yc+x,c);
-    plot_circle(xc-y,yc+x,c);
-    plot_circle(xc+y,yc-x,c);
-    plot_circle(xc-y,yc-x,c);
-    if (p < 0) p = p + 4*x + 6;
-    else {
-      p = p + 4*(x-y) + 10;
-      y = y -1;
-    }
-    x++;
-  }
-}
-
-
-/* -------------------------------------------------------------------------
-   FrameBuffer_solidcircle(FrameBuffer f, int xc, int yc, int radius, Pixel c)
-
-   Create an filled circle
-   ------------------------------------------------------------------------- */
-
-       
-#define fill_circle(x,y,c) \
-       x1 = xc - x; \
-       x2 = xc + x; \
-       FrameBuffer_horizontal(f,x1,x2,y,c);
-	
-void FrameBuffer_solidcircle(FrameBuffer *f, int xc, int yc, int radius, Pixel c) {
-
-  int xpixels, ypixels, x, y, p;
-  int x1,x2;
-  int xmin, ymin, xmax, ymax;
-  Pixel **pixels;
-
-  if (radius <= 0) return;
-  xpixels = f->width;
-  ypixels = f->height;
-  pixels = f->pixels;
-  xmin = f->xmin;
-  ymin = f->ymin;
-  xmax = f->xmax;
-  ymax = f->ymax;
-  x = 0;
-  y = radius;
-  p = 3-2*radius;
-  while (x <= y) {
-    fill_circle(x,yc+y,c);
-    fill_circle(x,yc-y,c);
-    fill_circle(y,yc+x,c);
-    fill_circle(y,yc-x,c);
-    if (p < 0) p = p + 4*x + 6;
-    else {
-      p = p + 4*(x-y) + 10;
-      y = y -1;
-    }
-    x++;
-  }
-}
-
-/* ------------------------------------------------------------------------
-   void FrameBuffer_setclip(f,xmin,ymin,xmax,ymax)
-
-   Set clipping region for plotting
-   ------------------------------------------------------------------------ */
-
-void FrameBuffer_setclip(FrameBuffer *f, int xmin, int ymin, int xmax, int ymax) {
-
-  if (xmin >= xmax) return;
-  if (ymin >= ymax) return;
-
-  if (xmin < 0) xmin = 0;
-  if (ymin < 0) ymin = 0;
-  if (xmax > (int) f->width) xmax = f->width;
-  if (ymax > (int) f->height) ymax = f->height;
-
-  f->xmin = xmin;
-  f->ymin = ymin;
-  f->xmax = xmax;
-  f->ymax = ymax;
-}
-
-/* ------------------------------------------------------------------------
-   void FrameBuffer_noclip(f)
-
-   Disable clipping region
-   ------------------------------------------------------------------------ */
-
-void FrameBuffer_noclip(FrameBuffer *f) {
-  f->xmin = 0;
-  f->ymin = 0;
-  f->xmax = f->width;
-  f->ymax = f->height;
-}
-
-
-/* ------------------------------------------------------------------------
-   FrameBuffer_zresize(FrameBuffer *f, int width, int height)
-
-   This function resizes the framebuffer's zbuffer.  If none exist, it
-   creates a new one.
-   ------------------------------------------------------------------------ */
-
-void FrameBuffer_zresize(FrameBuffer *f, int width, int height) {
-  int i;
-
-  if (f->zbuffer) {
-    free((char *)f->zbuffer[0]);
-    free((char *)f->zbuffer);
-  }
-  f->zbuffer = (Zvalue **) malloc(height*sizeof(Zvalue *));
-  f->zbuffer[0] = (Zvalue *) malloc(height*width*sizeof(Zvalue));
-  for (i = 0; i < height; i++)
-    f->zbuffer[i] = f->zbuffer[0]+i*width;
-}
-
-/* ------------------------------------------------------------------------
-   FrameBuffer_zclear(FrameBuffer *f)
-
-   Clears the z-buffer for a particular frame.   Sets all of the z-values to
-   ZMIN.
-   ------------------------------------------------------------------------- */
-
-void FrameBuffer_zclear(FrameBuffer *f) {
-  unsigned int i,j;
-  if (f) {
-    if (f->zbuffer) {
-      for (i = 0; i < f->width; i++)
-	for (j = 0; j < f->height; j++)
-	  f->zbuffer[j][i] = ZMIN;
-    }
-  }
-}
-   
-
-
-/* -------------------------------------------------------------------------
-   FrameBuffer_solidtriangle(FrameBuffer *f, int tx1, int ty2, 
-                                 int tx2, int ty2, 
-				 int tx3, int ty3, Pixel color) 
-
-   This function draws a 2D filled triangle.   
-
-   General idea :
-         1.   Transform the three points into screen coordinates
-	 2.   Order three points vertically on screen.
-	 3.   Check for degenerate cases (where 3 points are colinear).
-	 4.   Fill in the resulting triangle using horizontal lines.
-   -------------------------------------------------------------------------- */
-
-void FrameBuffer_solidtriangle(FrameBuffer *f, int tx1, int ty1, 
-			       int tx2, int ty2,
-			       int tx3, int ty3, Pixel color) {
-  int        tempx, tempy;
-  double     m1,m2,m3;
-  int        y;
-  int        ix1, ix2;
-
-  /* Figure out which point has the greatest "y" value */
-
-  if (ty2 > ty1) {   /* Swap points 1 and 2 if 2 is higher */
-    tempx = tx1;
-    tempy = ty1;
-    tx1 = tx2;
-    ty1 = ty2;
-    tx2 = tempx;
-    ty2 = tempy;
-  }
-  if (ty3 > ty1) {  /* Swap points 1 and 3 if 3 is higher */
-    tempx = tx1;
-    tempy = ty1;
-    tx1 = tx3;
-    ty1 = ty3;
-    tx3 = tempx;
-    ty3 = tempy;
-  }
-  if (ty3 > ty2) { /* Swap points 2 and 3 if 3 is higher */ 
-    tempx = tx2;
-    tempy = ty2;
-    tx2 = tx3;
-    ty2 = ty3;
-    tx3 = tempx;
-    ty3 = tempy;
-  }
-
-  /* Points are now order so that t_1 is the highest point, t_2 is the
-     middle point, and t_3 is the lowest point */
-
-  /* Check for degenerate cases here */
-
-  if ((ty1 == ty2) && (ty2 == ty3)) {
-
-    /* Points are aligned horizontally.   Handle as a special case */
-    /* Just draw three lines using the outline color */
-
-    FrameBuffer_line(f,tx1,ty1,tx2,ty2,color);
-    FrameBuffer_line(f,tx1,ty1,tx3,ty3,color);
-    FrameBuffer_line(f,tx2,ty2,tx3,ty3,color);
-
-  } else {
-
-    if (ty2 < ty1) {
-      /* First process line segments between (x1,y1)-(x2,y2)
-	 And between (x1,y1),(x3,y3) */
-
-      m1 = (double) (tx2 - tx1)/(double) (ty2 - ty1);
-      m2 = (double) (tx3 - tx1)/(double) (ty3 - ty1);
-
-      y = ty1;
-      while (y >= ty2) {
-	/* Calculate x values from slope */
-	ix1 = (int) (m1*(y-ty1)+0.5) + tx1;
-	ix2 = (int) (m2*(y-ty1)+0.5) + tx1;
-	if (ix1 > ix2) 
-	  FrameBuffer_horizontal(f,ix2,ix1,y,color);
-	else
-	  FrameBuffer_horizontal(f,ix1,ix2,y,color);
-	y--;
-      }
-    }
-    if (ty3 < ty2) {
-      /* Draw lower half of the triangle */
-      m2 = (double) (tx3 - tx1)/(double) (ty3 - ty1);
-      m3 = (double) (tx3 - tx2)/(double)(ty3 - ty2);
-      y = ty2;
-      while (y >= ty3) {
-	ix1 = (int) (m3*(y-ty2)+0.5)+tx2;
-	ix2 = (int) (m2*(y-ty1)+0.5)+tx1;
-	if (ix1 > ix2)
-	  FrameBuffer_horizontal(f,ix2,ix1,y,color);
-	else
-	  FrameBuffer_horizontal(f,ix1,ix2,y,color);
-	y--;
-      }
-    }
-  }
-}
-
-/* -------------------------------------------------------------------------
-   FrameBuffer_interptriangle(FrameBuffer *f,
-   int tx1, int ty2, Pixel c1,
-   int tx2, int ty2, Pixel c2,
-   int tx3, int ty3, Pixel c3)
-
-   This function draws a filled triangle with color
-   interpolation.  
-
-   General idea :
-         1.   Transform the three points into screen coordinates
-	 2.   Order three points vertically on screen.
-	 3.   Check for degenerate cases (where 3 points are colinear).
-	 4.   Fill in the resulting triangle using horizontal lines.
-	 5.   Colors are interpolated between end points
-   -------------------------------------------------------------------------- */
-
-void FrameBuffer_interptriangle(FrameBuffer *f,
-				int tx1, int ty1, Pixel c1,
-				int tx2, int ty2, Pixel c2,
-				int tx3, int ty3, Pixel c3) {
-  int        tempx, tempy;
-  double     m1,m2,m3;
-  double     mc1,mc2,mc3;
-  Pixel      ic1,ic2,tempc;
-  int        y;
-  int        ix1, ix2;
-
-  /* Figure out which point has the greatest "y" value */
-
-  if (ty2 > ty1) {   /* Swap points 1 and 2 if 2 is higher */
-    tempx = tx1;
-    tempy = ty1;
-    tempc = c1;
-    tx1 = tx2;
-    ty1 = ty2;
-    c1 = c2;
-    tx2 = tempx;
-    ty2 = tempy;
-    c2 = tempc;
-  }
-  if (ty3 > ty1) {  /* Swap points 1 and 3 if 3 is higher */
-    tempx = tx1;
-    tempy = ty1;
-    tempc = c1;
-    tx1 = tx3;
-    ty1 = ty3;
-    c1 = c3;
-    tx3 = tempx;
-    ty3 = tempy;
-    c3 = tempc;
-  }
-  if (ty3 > ty2) { /* Swap points 2 and 3 if 3 is higher */ 
-    tempx = tx2;
-    tempy = ty2;
-    tempc = c2;
-    tx2 = tx3;
-    ty2 = ty3;
-    c2 = c3;
-    tx3 = tempx;
-    ty3 = tempy;
-    c3 = tempc;
-  }
-
-  /* Points are now order so that t_1 is the highest point, t_2 is the
-     middle point, and t_3 is the lowest point */
-
-  /* Check for degenerate cases here */
-
-  if ((ty1 == ty2) && (ty2 == ty3)) {
-
-    /* Points are aligned horizontally.   Handle as a special case */
-    /* Just draw three lines using the outline color */
-
-    if (tx2 > tx1)
-      FrameBuffer_horizontalinterp(f,tx1,tx2,ty1,c1,c2);
-    else
-      FrameBuffer_horizontalinterp(f,tx2,tx1,ty1,c2,c1);
-    if (tx3 > tx1)
-      FrameBuffer_horizontalinterp(f,tx1,tx3,ty1,c1,c3);
-    else
-      FrameBuffer_horizontalinterp(f,tx3,tx1,ty1,c3,c1);
-    if (tx3 > tx2)
-      FrameBuffer_horizontalinterp(f,tx2,tx3,ty2,c2,c3);
-    else
-      FrameBuffer_horizontalinterp(f,tx3,tx2,ty2,c3,c2);
-    
-  } else {
-
-    /* First process line segments between (x1,y1)-(x2,y2)
-       And between (x1,y1),(x3,y3) */
-
-    if (ty2 < ty1) {
-      m1 = (double) (tx2 - tx1)/(double) (ty2 - ty1);
-      m2 = (double) (tx3 - tx1)/(double) (ty3 - ty1);
-      mc1 = (c2 - c1)/(double) (ty2 - ty1);
-      mc2 = (c3 - c1)/(double) (ty3 - ty1);
-
-      y = ty1;
-      while (y >= ty2) {
-	/* Calculate x values from slope */
-	ix1 = (int) (m1*(y-ty1)+0.5) + tx1;
-	ix2 = (int) (m2*(y-ty1)+0.5) + tx1;
-	ic1 = (int) (mc1*(y-ty1) + c1);
-	ic2 = (int) (mc2*(y-ty1) + c1);
-	if (ix1 > ix2) 
-	  FrameBuffer_horizontalinterp(f,ix2,ix1,y,ic2,ic1);
-	else
-	  FrameBuffer_horizontalinterp(f,ix1,ix2,y,ic1,ic2);
-	y--;
-      }
-    }
-    if (ty3 < ty2) {
-      /* Draw lower half of the triangle */
-      m2 = (double) (tx3 - tx1)/(double) (ty3 - ty1);
-      mc2 = (c3 - c1)/(double) (ty3 - ty1);
-      m3 = (double) (tx3 - tx2)/(double)(ty3 - ty2);
-      mc3 = (c3 - c2)/(double) (ty3 - ty2);
-      y = ty2;
-      while (y >= ty3) {
-	ix1 = (int) (m3*(y-ty2)+0.5)+tx2;
-	ix2 = (int) (m2*(y-ty1)+0.5)+tx1;
-	ic1 = (int) (mc3*(y-ty2)+c2);
-	ic2 = (int) (mc2*(y-ty1)+c1);
-	if (ix1 > ix2)
-	  FrameBuffer_horizontalinterp(f,ix2,ix1,y,ic2,ic1);
-	else
-	  FrameBuffer_horizontalinterp(f,ix1,ix2,y,ic1,ic2);
-	y--;
-      }
-    }
-  }
-}
-
-
diff --git a/Examples/GIFPlot/Lib/gif.c b/Examples/GIFPlot/Lib/gif.c
deleted file mode 100644
index a0cfca1d5..000000000
--- a/Examples/GIFPlot/Lib/gif.c
+++ /dev/null
@@ -1,668 +0,0 @@
-
-/**********************************************************************
- * GIFPlot 0.0
- * 
- * Dave Beazley
- * 
- * Department of Computer Science        Theoretical Division (T-11)        
- * University of Utah                    Los Alamos National Laboratory     
- * Salt Lake City, Utah 84112            Los Alamos, New Mexico  87545      
- * beazley@cs.utah.edu                   beazley@lanl.gov                   
- *
- * Copyright (c) 1996
- * The Regents of the University of California and the University of Utah
- * All Rights Reserved
- *
- * Permission is hereby granted, without written agreement and without
- * license or royalty fees, to use, copy, modify, and distribute this
- * software and its documentation for any purpose, provided that 
- * (1) The above copyright notice and the following two paragraphs
- * appear in all copies of the source code and (2) redistributions
- * including binaries reproduces these notices in the supporting
- * documentation.   Substantial modifications to this software may be
- * copyrighted by their authors and need not follow the licensing terms
- * described here, provided that the new terms are clearly indicated in
- * all files where they apply.
- * 
- * IN NO EVENT SHALL THE AUTHOR, THE UNIVERSITY OF CALIFORNIA, THE 
- * UNIVERSITY OF UTAH OR DISTRIBUTORS OF THIS SOFTWARE BE LIABLE TO ANY
- * PARTY FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL
- * DAMAGES ARISING OUT OF THE USE OF THIS SOFTWARE AND ITS DOCUMENTATION,
- * EVEN IF THE AUTHORS OR ANY OF THE ABOVE PARTIES HAVE BEEN ADVISED OF
- * THE POSSIBILITY OF SUCH DAMAGE.
- *
- * THE AUTHOR, THE UNIVERSITY OF CALIFORNIA, AND THE UNIVERSITY OF UTAH
- * SPECIFICALLY DISCLAIM ANY WARRANTIES,INCLUDING, BUT NOT LIMITED TO, 
- * THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
- * PURPOSE. THE SOFTWARE PROVIDED HEREUNDER IS ON AN "AS IS" BASIS, AND 
- * THE AUTHORS AND DISTRIBUTORS HAVE NO OBLIGATION TO PROVIDE MAINTENANCE,
- * SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS.
- *
- **************************************************************************/
-
-/*******************************************************************
- * Creates a GIF format file.  
- *
- * Dave Beazley (T-11)
- * August 11, 1995
- *
- * Rather than writing directly to files, this module fills out
- * output buffer.
- * 
- * Note : To save memory, this routine uses approximately 50K of the
- * output buffer as temporary storage (for hash tables and compression codes).
- * The remainder of the output buffer is used to store the final image.
- * This feature allows GIF images to be created with no additional
- * memory overhead.
- *
- * -- Revision History 
- * $Log$
- * Revision 1.2  2003/09/01 16:23:31  beazley
- * Restored the 'mojo'.
- *
- * Revision 1.2  1996/09/25 22:39:30  dmb
- * Fixed prototypes and use of void pointers for compatibility with the Cray T3D
- *
- * Revision 1.1  1996/09/10 17:44:00  dmb
- * Initial revision
- *
- * Revision 1.2  1995/08/31 14:46:07  beazley
- * Minor changes to support comments and a few bug fixes.
- *
- *
- ******************************************************************/
-
-
-/*
- * xvgifwr.c  -  handles writing of GIF files.  based on flgife.c and
- *               flgifc.c from the FBM Library, by Michael Maudlin
- *
- * Contains: 
- *   WriteGIF(fp, pic, ptype, w, h, rmap, gmap, bmap, numcols, colorstyle,
- *            comment)
- *
- * Note: slightly brain-damaged, in that it'll only write non-interlaced 
- *       GIF files (in the interests of speed, or something)
- *
- */
-
-
-
-/*****************************************************************
- * Portions of this code Copyright (C) 1989 by Michael Mauldin.
- * Permission is granted to use this file in whole or in
- * part for any purpose, educational, recreational or commercial,
- * provided that this copyright notice is retained unchanged.
- * This software is available to all free of charge by anonymous
- * FTP and in the UUNET archives.
- *
- *
- * Authors:  Michael Mauldin (mlm@cs.cmu.edu)
- *           David Rowley (mgardi@watdcsu.waterloo.edu)
- *
- * Based on: compress.c - File compression ala IEEE Computer, June 1984.
- *
- *	Spencer W. Thomas       (decvax!harpo!utah-cs!utah-gr!thomas)
- *	Jim McKie               (decvax!mcvax!jim)
- *	Steve Davies            (decvax!vax135!petsd!peora!srd)
- *	Ken Turkowski           (decvax!decwrl!turtlevax!ken)
- *	James A. Woods          (decvax!ihnp4!ames!jaw)
- *	Joe Orost               (decvax!vax135!petsd!joe)
- *****************************************************************/
-
-#include "gifplot.h"
-#include <string.h> 
-typedef long int        count_int;
-typedef unsigned char   byte;
-
-static int  gif_error;
-static unsigned char *op;
-static int  Width, Height;
-static int  curx, cury;
-static int  Interlace;
-
-static void putgifword(int);
-static void compress(int, byte **, int);
-static void output_GIF(int);
-static void cl_block(void);
-static void cl_hash(count_int);
-static void char_init(void);
-static void char_out(int);
-static void flush_char(void);
-static void *OutBuffer;
-static int   OutBufSize;
-static FrameBuffer *GIF_frame;
-
-static unsigned char pc2nc[256],r1[256],g1[256],b1[256];
-
-/*************************************************************/
-int FrameBuffer_makeGIF(FrameBuffer *f, ColorMap *c, void *outbuffer, unsigned int outbufsize)
-{
-  int   RWidth, RHeight;
-  int   LeftOfs, TopOfs;
-  int   ColorMapSize, InitCodeSize, Background, BitsPerPixel;
-  int   i,j,nc;
-  char *rmap, *gmap, *bmap;
-  char *cmap;
-  int   count;
-
-  Interlace = 0;
-  Background = 0;
-  OutBuffer = outbuffer;
-  OutBufSize = outbufsize;
-  GIF_frame = f;
-  cmap = (char *) c->cmap;
-  
-  op = (unsigned char *) outbuffer;
-  gif_error = 0;
-  for (i=0; i<256; i++) { pc2nc[i] = r1[i] = g1[i] = b1[i] = 0; }
-
-  /* compute number of unique colors */
-  nc = 0;
-  rmap = &cmap[0];
-  gmap = &cmap[256];
-  bmap = &cmap[512];
-
-  for (i=0; i<256; i++) {
-    /* see if color #i is already used */
-    for (j=0; j<i; j++) {
-      if (rmap[i] == rmap[j] && gmap[i] == gmap[j] && 
-	  bmap[i] == bmap[j]) break;
-    }
-
-    if (j==i) {  /* wasn't found */
-      pc2nc[i] = nc;
-      r1[nc] = rmap[i];
-      g1[nc] = gmap[i];
-      b1[nc] = bmap[i];
-      nc++;
-    }
-    else pc2nc[i] = pc2nc[j];
-  }
-
-  /* figure out 'BitsPerPixel' */
-  for (i=1; i<8; i++)
-    if ( (1<<i) >= nc) break;
-  
-  BitsPerPixel = i;
-
-  ColorMapSize = 1 << BitsPerPixel;
-	
-  RWidth  = Width  = f->width;
-  RHeight = Height = f->height;
-  LeftOfs = TopOfs = 0;
-
-  if (BitsPerPixel <= 1) InitCodeSize = 2;
-                    else InitCodeSize = BitsPerPixel;
-
-  curx = 0;
-  cury = f->height - 1;
-
-  strcpy((char *) op,"GIF89a");        /* Put in GIF magic number */
-  op+=6;
-  putgifword(RWidth);           /* screen descriptor */
-  putgifword(RHeight);
-
-  i = 0x80;	                 /* Yes, there is a color map */
-  i |= (8-1)<<4;                 /* OR in the color resolution (hardwired 8) */
-  i |= (BitsPerPixel - 1);       /* OR in the # of bits per pixel */
-  *(op++) = i;
-  *(op++) = Background;          /* background color */
-  *(op++) = 0;
-  for (i=0; i<ColorMapSize; i++) {       /* write out Global colormap */
-    *(op++) = r1[i];
-    *(op++) = g1[i];
-    *(op++) = b1[i];
-  }
-
-  *(op++) = ',';                /* image separator */
-
-  /* Write the Image header */
-  putgifword(LeftOfs);
-  putgifword(TopOfs);
-  putgifword(Width);
-  putgifword(Height);
-  *(op++) = 0;
-  *(op++) = InitCodeSize;
-
-  compress(InitCodeSize+1, f->pixels, f->width*f->height);
-
-  *(op++) = 0;
-  *(op++) = ';';
-  
-  count = (op - (unsigned char *) OutBuffer);
-  if (gif_error) return -1;
-  else return count;
-}
-
-/******************************/
-static void putgifword(w)
-int w;
-{
-  /* writes a 16-bit integer in GIF order (LSB first) */
-  *(op++) = w & 0xff;
-  *(op++) = (w>>8)&0xff;
-}
-
-/***********************************************************************/
-
-
-static unsigned long cur_accum = 0;
-static int           cur_bits = 0;
-
-
-
-
-#define GP_BITS	12    /* BITS was already defined on some systems */
-
-#define HSIZE  5003            /* 80% occupancy */
-
-typedef unsigned char   char_type;
-
-static int n_bits;                    /* number of bits/code */
-static int maxbits = GP_BITS;         /* user settable max # bits/code */
-static int maxcode;                   /* maximum code, given n_bits */
-static int maxmaxcode = 1 << GP_BITS; /* NEVER generate this */
-
-#define MAXCODE(n_bits)     ( (1 << (n_bits)) - 1)
-
-static  count_int      *htab;
-static  unsigned short *codetab;
-static  GIFOutBufSize;
-
-/* static  count_int      htab [HSIZE];
-static  unsigned short codetab [HSIZE]; */
-
-#define HashTabOf(i)   htab[i]
-#define CodeTabOf(i)   codetab[i]
-
-static int hsize = HSIZE;            /* for dynamic table sizing */
-
-/*
- * To save much memory, we overlay the table used by compress() with those
- * used by decompress().  The tab_prefix table is the same size and type
- * as the codetab.  The tab_suffix table needs 2**BITS characters.  We
- * get this from the beginning of htab.  The output stack uses the rest
- * of htab, and contains characters.  There is plenty of room for any
- * possible stack (stack used to be 8000 characters).
- */
-
-#define tab_prefixof(i) CodeTabOf(i)
-#define tab_suffixof(i)        ((char_type *)(htab))[i]
-#define de_stack               ((char_type *)&tab_suffixof(1<<GP_BITS))
-
-static int free_ent = 0;                  /* first unused entry */
-
-/*
- * block compression parameters -- after all codes are used up,
- * and compression rate changes, start over.
- */
-static int clear_flg = 0;
-
-static long int out_count = 0;           /* # of codes output (for debugging) */
-
-/*
- * compress stdin to stdout
- *
- * Algorithm:  use open addressing double hashing (no chaining) on the 
- * prefix code / next character combination.  We do a variant of Knuth's
- * algorithm D (vol. 3, sec. 6.4) along with G. Knott's relatively-prime
- * secondary probe.  Here, the modular division first probe is gives way
- * to a faster exclusive-or manipulation.  Also do block compression with
- * an adaptive reset, whereby the code table is cleared when the compression
- * ratio decreases, but after the table fills.  The variable-length output
- * codes are re-sized at this point, and a special CLEAR code is generated
- * for the decompressor.  Late addition:  construct the table according to
- * file size for noticeable speed improvement on small files.  Please direct
- * questions about this implementation to ames!jaw.
- */
-
-static int g_init_bits;
-
-static int ClearCode;
-static int EOFCode;
-
-
-/********************************************************/
-static void compress(init_bits, data, len)
-         int   init_bits;
-         unsigned char **data;
-         int   len;
-{
-  register long fcode;
-  register int i = 0;
-  register int c;
-  register int ent;
-  register int disp;
-  register int hsize_reg;
-  register int hshift;
-  int      code_count = 0;
-
-  /* Use the output buffer as temporary storage for GIF data */
-
-  if (OutBufSize < HSIZE*(sizeof(count_int) + sizeof(unsigned short))) {
-    gif_error =1;
-    return;
-  }
-
-  /* Put htab and codetab arrays into the output buffer */
-
-  GIFOutBufSize = OutBufSize - HSIZE*(sizeof(count_int) + sizeof(unsigned short)) - 16;
-  GIFOutBufSize = GIFOutBufSize & (~0x3);       /* Make sure it's double word alligned */
-
-  htab = (count_int *) ((char *) OutBuffer + GIFOutBufSize);
-  codetab = (unsigned short *) ((char *) OutBuffer + GIFOutBufSize + HSIZE*sizeof(count_int));
-
-  /*
-   * Set up the globals:  g_init_bits - initial number of bits
-   *                      g_outfile   - pointer to output file
-   */
-  g_init_bits = init_bits;
-
-
-  /* initialize 'compress' globals */
-  maxbits = GP_BITS;
-  maxmaxcode = 1<<GP_BITS;
-  memset(htab,0,sizeof(htab));
-  memset(codetab,0,sizeof(codetab));
-  hsize = HSIZE;
-  free_ent = 0;
-  clear_flg = 0;
-  out_count = 0;
-  cur_accum = 0;
-  cur_bits = 0;
-
-  /*
-   * Set up the necessary values
-   */
-  out_count = 0;
-  clear_flg = 0;
-  maxcode = MAXCODE(n_bits = g_init_bits);
-
-  ClearCode = (1 << (init_bits - 1));
-  EOFCode = ClearCode + 1;
-  free_ent = ClearCode + 2;
-
-  char_init();
-  ent = pc2nc[data[cury][curx]];
-  curx++;
-  if (curx >= GIF_frame->width) {
-    curx = 0;
-    cury--;
-  }
-  len--;
-
-  hshift = 0;
-  for ( fcode = (long) hsize;  fcode < 65536L; fcode *= 2L )
-    hshift++;
-  hshift = 8 - hshift;                /* set hash code range bound */
-
-  hsize_reg = hsize;
-  cl_hash( (count_int) hsize_reg);            /* clear hash table */
-
-  output_GIF(ClearCode);
-  while (len) {
-    c = pc2nc[data[cury][curx]];
-    curx++;
-    if (curx >= GIF_frame->width) {
-      curx = 0;
-      cury--;
-    }
-    len--;
-
-    fcode = (long) ( ( (long) c << maxbits) + ent);
-       i = (((int) c << hshift) ^ ent);    /* xor hashing */
-
-    if ( HashTabOf (i) == fcode ) {
-      ent = CodeTabOf (i);
-      continue;
-    }
-
-    if ( (long)HashTabOf (i) < 0 )      /* empty slot */
-      goto nomatch;
-
-    disp = hsize_reg - i;           /* secondary hash (after G. Knott) */
-    if ( i == 0 )
-      disp = 1;
-
-probe:
-    if ( (i -= disp) < 0 )
-      i += hsize_reg;
-
-    if ( HashTabOf (i) == fcode ) {
-      ent = CodeTabOf (i);
-      continue;
-    }
-
-    if ( (long)HashTabOf (i) >= 0 ) 
-      goto probe;
-
-nomatch:
-    output_GIF(ent);
-    out_count++;
-    ent = c;
-
-    if ( free_ent < maxmaxcode ) {
-      CodeTabOf (i) = free_ent++; /* code -> hashtable */
-      HashTabOf (i) = fcode;
-    }
-    else
-      cl_block();
-
-  }
-  /* Put out the final code */
-  output_GIF(ent);
-  output_GIF(EOFCode);
-}
-
-
-/*****************************************************************
- * TAG( output_GIF )
- *
- * Output the given code.
- * Inputs:
- *      code:   A n_bits-bit integer.  If == -1, then EOF.  This assumes
- *              that n_bits =< (long)wordsize - 1.
- * Outputs:
- *      Outputs code to the file.
- * Assumptions:
- *      Chars are 8 bits long.
- * Algorithm:
- *      Maintain a BITS character long buffer (so that 8 codes will
- * fit in it exactly).  Use the VAX insv instruction to insert each
- * code in turn.  When the buffer fills up empty it and start over.
- */
-
-static
-unsigned long masks[] = { 0x0000, 0x0001, 0x0003, 0x0007, 0x000F,
-                                  0x001F, 0x003F, 0x007F, 0x00FF,
-                                  0x01FF, 0x03FF, 0x07FF, 0x0FFF,
-                                  0x1FFF, 0x3FFF, 0x7FFF, 0xFFFF };
-
-static void output_GIF(code)
-int code;
-{
-  cur_accum &= masks[cur_bits];
-
-  if (cur_bits > 0)
-    cur_accum |= ((long)code << cur_bits);
-  else
-    cur_accum = code;
-	
-  cur_bits += n_bits;
-
-  while( cur_bits >= 8 ) {
-    char_out( (int) (cur_accum & 0xff) );
-    cur_accum >>= 8;
-    cur_bits -= 8;
-  }
-
-  /*
-   * If the next entry is going to be too big for the code size,
-   * then increase it, if possible.
-   */
-
-  if (free_ent > maxcode || clear_flg) {
-
-    if( clear_flg ) {
-      maxcode = MAXCODE (n_bits = g_init_bits);
-      clear_flg = 0;
-    }
-    else {
-      n_bits++;
-      if ( n_bits == maxbits )
-	maxcode = maxmaxcode;
-      else
-	maxcode = MAXCODE(n_bits);
-    }
-  }
-	
-  if( code == EOFCode ) {
-    /* At EOF, write the rest of the buffer */
-    while( cur_bits > 0 ) {
-      char_out( (int)(cur_accum & 0xff) );
-      cur_accum >>= 8;
-      cur_bits -= 8;
-    }
-
-    flush_char();
-  }
-}
-
-
-/********************************/
-static void cl_block ()             /* table clear for block compress */
-{
-  /* Clear out the hash table */
-
-  cl_hash ( (count_int) hsize );
-  free_ent = ClearCode + 2;
-  clear_flg = 1;
-
-  output_GIF(ClearCode);
-}
-
-
-/********************************/
-static void cl_hash(hsize)          /* reset code table */
-register count_int hsize;
-{
-  register count_int *htab_p = htab+hsize;
-  register long i;
-  register long m1 = -1;
-
-  i = hsize - 16;
-  do {                            /* might use Sys V memset(3) here */
-    *(htab_p-16) = m1;
-    *(htab_p-15) = m1;
-    *(htab_p-14) = m1;
-    *(htab_p-13) = m1;
-    *(htab_p-12) = m1;
-    *(htab_p-11) = m1;
-    *(htab_p-10) = m1;
-    *(htab_p-9) = m1;
-    *(htab_p-8) = m1;
-    *(htab_p-7) = m1;
-    *(htab_p-6) = m1;
-    *(htab_p-5) = m1;
-    *(htab_p-4) = m1;
-    *(htab_p-3) = m1;
-    *(htab_p-2) = m1;
-    *(htab_p-1) = m1;
-    htab_p -= 16;
-  } while ((i -= 16) >= 0);
-
-  for ( i += 16; i > 0; i-- )
-    *--htab_p = m1;
-}
-
-
-/******************************************************************************
- *
- * GIF Specific routines
- *
- ******************************************************************************/
-
-/*
- * Number of characters so far in this 'packet'
- */
-static int a_count;
-
-/*
- * Set up the 'byte output' routine
- */
-static void char_init()
-{
-	a_count = 0;
-}
-
-/*
- * Define the storage for the packet accumulator
- */
-static char accum[ 256 ];
-
-/*
- * Add a character to the end of the current packet, and if it is 254
- * characters, flush the packet to disk.
- */
-static void char_out(c)
-int c;
-{
-  accum[ a_count++ ] = c;
-  if( a_count >= 254 ) 
-    flush_char();
-}
-
-/*
- * Flush the packet to disk, and reset the accumulator
- */
-static void flush_char()
-{
-  if (gif_error) return;
-  if( a_count > 0 ) {
-    *(op++) = a_count;
-    memcpy(op,accum,a_count);
-    op+=a_count;
-    a_count = 0;
-    
-    if (op > (unsigned char *) ((char *) OutBuffer + (GIFOutBufSize - 2048))) {
-      gif_error = 1;
-    }
-  } 
-}	
-
-
-/* ----------------------------------------------------------------------
-   int FrameBuffer_writeGIF(char *filename)
-   
-   Write a GIF file to filename
-   ----------------------------------------------------------------------- */
-
-int FrameBuffer_writeGIF(FrameBuffer *f, ColorMap *c, char *filename) {
-
-  FILE *file;
-  void *buffer;
-  int nbytes;
-  int bufsize;
-
-  file = fopen(filename,"wb");
-  if (file == NULL) return -1;
-
-  bufsize = (f->width*f->height*3)/2;
-  buffer = (void *) malloc(bufsize);
-  nbytes = FrameBuffer_makeGIF(f,c,buffer,bufsize);
-  if (nbytes == -1) { 
-    free(buffer);
-    fclose(file);
-    return -1;
-  }
-  fwrite(buffer,nbytes,1,file);
-  fclose(file);
-  free(buffer);
-  return 0;
-}
-
-    
-  
-  
-  
diff --git a/Examples/GIFPlot/Lib/matrix.c b/Examples/GIFPlot/Lib/matrix.c
deleted file mode 100644
index ef0cf3aab..000000000
--- a/Examples/GIFPlot/Lib/matrix.c
+++ /dev/null
@@ -1,343 +0,0 @@
-/* ----------------------------------------------------------------------------- 
- * matrix.c
- *
- *     Some 4x4 matrix operations
- * 
- * Author(s) : David Beazley (beazley@cs.uchicago.edu)
- * Copyright (C) 1995-1996
- *
- * See the file LICENSE for information on usage and redistribution.	
- * ----------------------------------------------------------------------------- */
-
-#define MATRIX
-#include "gifplot.h"
-#include <math.h>
-
-/* ------------------------------------------------------------------------
-   Matrix new_Matrix()
-
-   Create a new 4x4 matrix.
-   ------------------------------------------------------------------------ */
-Matrix
-new_Matrix() {
-  Matrix m;
-  m = (Matrix) malloc(16*sizeof(double));
-  return m;
-}
-
-/* ------------------------------------------------------------------------
-   delete_Matrix(Matrix *m);
-
-   Destroy a matrix
-   ------------------------------------------------------------------------ */
-
-void
-delete_Matrix(Matrix m) {
-  if (m)
-    free((char *) m);
-}
-
-/* ------------------------------------------------------------------------
-   Matrix Matrix_copy(Matrix a)
-
-   Makes a copy of matrix a and returns it.
-   ------------------------------------------------------------------------ */
-
-Matrix Matrix_copy(Matrix a) {
-  int i;
-  Matrix r = 0;
-  if (a) {
-    r = new_Matrix();
-    if (r) {
-      for (i = 0; i < 16; i++)
-	r[i] = a[i];
-    }
-  }
-  return r;
-}
-    
-/* ------------------------------------------------------------------------
-   Matrix_multiply(Matrix a, Matrix b, Matrix c)
-
-   Multiplies a*b = c
-   c may be one of the source matrices
-   ------------------------------------------------------------------------ */
-void
-Matrix_multiply(Matrix a, Matrix b, Matrix c) {
-  double temp[16];
-  int    i,j,k;
-
-  for (i =0; i < 4; i++)
-    for (j = 0; j < 4; j++) {
-      temp[i*4+j] = 0.0;
-      for (k = 0; k < 4; k++) 
-	temp[i*4+j] += a[i*4+k]*b[k*4+j];
-    }
-  for (i = 0; i < 16; i++)
-    c[i] = temp[i];
-}
-  
-/* ------------------------------------------------------------------------
-   Matrix_identity(Matrix a)
-
-   Puts an identity matrix in matrix a
-   ------------------------------------------------------------------------ */
-
-void
-Matrix_identity(Matrix a) {
-  int i;
-  for (i = 0; i < 16; i++) a[i] = 0;
-  a[0] = 1;
-  a[5] = 1;
-  a[10] = 1;
-  a[15] = 1;
-}
-
-/* ------------------------------------------------------------------------
-   Matrix_zero(Matrix a)
-   
-   Puts a zero matrix in matrix a
-   ------------------------------------------------------------------------ */
-void
-Matrix_zero(Matrix a) {
-  int i;
-  for (i = 0; i < 16; i++) a[i] = 0;
-}
-
-/* ------------------------------------------------------------------------
-   Matrix_transpose(Matrix a, Matrix result)
-
-   Transposes matrix a and puts it in result.
-   ------------------------------------------------------------------------ */
-void
-Matrix_transpose(Matrix a, Matrix result) {
-  double temp[16];
-  int i,j;
-
-  for (i = 0; i < 4; i++)
-    for (j = 0; j < 4; j++) 
-      temp[4*i+j] = a[4*j+i];
-
-  for (i = 0; i < 16; i++)
-    result[i] = temp[i];
-}
-
-
-/* ------------------------------------------------------------------------
-   Matrix_gauss(Matrix a, Matrix b)
-
-   Solves ax=b for x, using Gaussian elimination. Destroys a.
-   Really only used for calculating inverses of 4x4 transformation
-   matrices.
-   ------------------------------------------------------------------------ */
-
-void Matrix_gauss(Matrix a, Matrix b) {
-  int ipiv[4], indxr[4], indxc[4];
-  int i,j,k,l,ll;
-  int irow=0, icol=0;
-  double big, pivinv;
-  double dum;
-  for (j = 0; j < 4; j++)
-    ipiv[j] = 0;
-  for (i = 0; i < 4; i++) {
-    big = 0;
-    for (j = 0; j < 4; j++) {
-      if (ipiv[j] != 1) {
-	for (k = 0; k < 4; k++) {
-	  if (ipiv[k] == 0) {
-	    if (fabs(a[4*j+k]) >= big) {
-	      big = fabs(a[4*j+k]);
-	      irow = j;
-	      icol = k;
-	    }
-	  } else if (ipiv[k] > 1)
-	    return;  /* Singular matrix */
-	}
-      }
-    }
-    ipiv[icol] = ipiv[icol]+1;
-    if (irow != icol) {
-      for (l = 0; l < 4; l++) {
-	dum = a[4*irow+l];
-	a[4*irow+l] = a[4*icol+l];
-	a[4*icol+l] = dum;
-      }
-      for (l = 0; l < 4; l++) {
-	dum = b[4*irow+l];
-	b[4*irow+l] = b[4*icol+l];
-	b[4*icol+l] = dum;
-      }
-    }
-    indxr[i] = irow;
-    indxc[i] = icol;
-    if (a[4*icol+icol] == 0) return;
-    pivinv = 1.0/a[4*icol+icol];
-    a[4*icol+icol] = 1.0;
-    for (l = 0; l < 4; l++)
-      a[4*icol+l] = a[4*icol+l]*pivinv;
-    for (l = 0; l < 4; l++)
-      b[4*icol+l] = b[4*icol+l]*pivinv;
-    for (ll = 0; ll < 4; ll++) {
-      if (ll != icol) {
-	dum = a[4*ll+icol];
-	a[4*ll+icol] = 0;
-	for (l = 0; l < 4; l++)
-	  a[4*ll+l] = a[4*ll+l] - a[4*icol+l]*dum;
-	for (l = 0; l < 4; l++)
-	  b[4*ll+l] = b[4*ll+l] - b[4*icol+l]*dum;
-      }
-    }
-  }
-  for (l = 3; l >= 0; l--) {
-    if (indxr[l] != indxc[l]) {
-      for (k = 0; k < 4; k++) {
-	dum = a[4*k+indxr[l]];
-	a[4*k+indxr[l]] = a[4*k+indxc[l]];
-	a[4*k+indxc[l]] = dum;
-      }
-    }
-  }
-}
-
-/* ------------------------------------------------------------------------
-   Matrix_invert(Matrix a, Matrix inva)
-
-   Inverts Matrix a and places the result in inva.
-   Relies on the Gaussian Elimination code above. (See Numerical recipes).
-   ------------------------------------------------------------------------ */
-void
-Matrix_invert(Matrix a, Matrix inva) {
-
-  double  temp[16];
-  int     i;
-
-  for (i = 0; i < 16; i++)
-    temp[i] = a[i];
-  Matrix_identity(inva);
-  Matrix_gauss(temp,inva);
-}
-    
-/* ------------------------------------------------------------------------
-   Matrix_transform(Matrix a, GL_Vector *r, GL_Vector *t)
-
-   Transform a vector.    a*r ----> t
-   ------------------------------------------------------------------------ */
-
-void   Matrix_transform(Matrix a, GL_Vector *r, GL_Vector *t) {
-
-  double  rx, ry, rz, rw;
-
-  rx = r->x;
-  ry = r->y;
-  rz = r->z;
-  rw = r->w;
-  t->x = a[0]*rx + a[1]*ry + a[2]*rz + a[3]*rw;
-  t->y = a[4]*rx + a[5]*ry + a[6]*rz + a[7]*rw;
-  t->z = a[8]*rx + a[9]*ry + a[10]*rz + a[11]*rw;
-  t->w = a[12]*rx + a[13]*ry + a[14]*rz + a[15]*rw;
-}
-
-/* ------------------------------------------------------------------------
-   Matrix_transform4(Matrix a, double x, double y, double z, double w, GL_Vector *t)
-
-   Transform a vector from a point specified as 4 doubles
-   ------------------------------------------------------------------------ */
-
-void   Matrix_transform4(Matrix a, double rx, double ry, double rz, double rw,
-			 GL_Vector *t) {
-
-  t->x = a[0]*rx + a[1]*ry + a[2]*rz + a[3]*rw;
-  t->y = a[4]*rx + a[5]*ry + a[6]*rz + a[7]*rw;
-  t->z = a[8]*rx + a[9]*ry + a[10]*rz + a[11]*rw;
-  t->w = a[12]*rx + a[13]*ry + a[14]*rz + a[15]*rw;
-}
-
-/* ---------------------------------------------------------------------
-   Matrix_translate(Matrix a, double tx, double ty, double tz)
-
-   Put a translation matrix in Matrix a
-   ---------------------------------------------------------------------- */
-
-void Matrix_translate(Matrix a, double tx, double ty, double tz) {
-  Matrix_identity(a);
-  a[3] = tx;
-  a[7] = ty;
-  a[11] = tz;
-  a[15] = 1;
-}
-
-/* -----------------------------------------------------------------------
-   Matrix_rotatex(Matrix a, double deg)
-
-   Produce an x-rotation matrix for given angle in degrees.
-   ----------------------------------------------------------------------- */
-void
-Matrix_rotatex(Matrix a, double deg) {
-  double r;
-
-  r = 3.1415926*deg/180.0;
-  Matrix_zero(a);
-  a[0] = 1.0;
-  a[5] = cos(r);
-  a[6] = -sin(r);
-  a[9] = sin(r);
-  a[10] = cos(r);
-  a[15] = 1.0;
-}
-
-/* -----------------------------------------------------------------------
-   Matrix_rotatey(Matrix a, double deg)
-
-   Produce an y-rotation matrix for given angle in degrees.
-   ----------------------------------------------------------------------- */
-void
-Matrix_rotatey(Matrix a, double deg) {
-  double r;
-
-  r = 3.1415926*deg/180.0;
-  Matrix_zero(a);
-  a[0] = cos(r);
-  a[2] = sin(r);
-  a[5] = 1.0;
-  a[8] = -sin(r);
-  a[10] = cos(r);
-  a[15] = 1;
-  
-}
-/* -----------------------------------------------------------------------
-   Matrix_RotateZ(Matrix a, double deg)
-
-   Produce an z-rotation matrix for given angle in degrees.
-   ----------------------------------------------------------------------- */
-void
-Matrix_rotatez(Matrix a, double deg) {
-  double r;
-
-  r = 3.1415926*deg/180.0;
-  Matrix_zero(a);
-  a[0] = cos(r);
-  a[1] = -sin(r);
-  a[4] = sin(r);
-  a[5] = cos(r);
-  a[10] = 1.0;
-  a[15] = 1.0;
-}
-
-
-/* A debugging routine */
-
-void Matrix_set(Matrix a, int i, int j, double val) {
-  a[4*j+i] = val;
-}
-
-void Matrix_print(Matrix a) {
-  int i,j;
-  for (i = 0; i < 4; i++) {
-    for (j = 0; j < 4; j++) {
-      fprintf(stdout,"%10f ",a[4*i+j]);
-    }
-    fprintf(stdout,"\n");
-  }
-  fprintf(stdout,"\n");
-}
-
diff --git a/Examples/GIFPlot/Lib/pixmap.c b/Examples/GIFPlot/Lib/pixmap.c
deleted file mode 100644
index a55cf041f..000000000
--- a/Examples/GIFPlot/Lib/pixmap.c
+++ /dev/null
@@ -1,159 +0,0 @@
-/* ----------------------------------------------------------------------------- 
- * pixmap.c
- *
- *     Pixel maps (i.e., bitmaps)
- * 
- * Author(s) : David Beazley (beazley@cs.uchicago.edu)
- * Copyright (C) 1995-1996
- *
- * See the file LICENSE for information on usage and redistribution.	
- * ----------------------------------------------------------------------------- */
-
-#define PIXMAP
-#include "gifplot.h"
-
-/* -----------------------------------------------------------------------
-   PixMap *new_PixMap(int width, int height, int centerx, int centery)
-
-   Create a new pixmap of given size
-   ----------------------------------------------------------------------- */
-PixMap *new_PixMap(int width, int height, int centerx, int centery) {
-  PixMap *pm;
-  if ((width > 0) && (height > 0)) {
-    pm = (PixMap *) malloc(sizeof(PixMap));
-    pm->width = width;
-    pm->height = height;
-    pm->centerx = centerx;
-    pm->centery = centery;
-    pm->map = (int *) malloc(height*width*sizeof(int));
-    return pm;
-  }
-  return (PixMap *) 0;
-}
-
-/* --------------------------------------------------------------------------
-   void delete_PixMap(PixMap *pm)
-
-   Destroy a pixmap
-   -------------------------------------------------------------------------- */
-
-void delete_PixMap(PixMap *pm) {
-  if (pm) {
-    free((char *) pm->map);
-    free((char *) pm);
-  }
-}
-
-/* ---------------------------------------------------------------------------
-   void PixMap_set(PixMap *pm, int x, int y, int pix)
-
-   Set a pixel in the bitmap
-   --------------------------------------------------------------------------- */
-void
-PixMap_set(PixMap *pm, int x, int y, int pix) {
-  if ((x < 0) || (x>=pm->width)) return;
-  if ((y < 0) || (y>=pm->height)) return;
-
-  pm->map[pm->width*y + x] = pix;
-}
-
-/* -----------------------------------------------------------------------------
-   void FrameBuffer_drawpixmap(FrameBuffer *f, PixMap *pm, int x, int y, int fgcolor, int bgcolor) 
-
-   Draw a pixmap onto the framebuffer.   This is somewhat optimized for speed.
-   ------------------------------------------------------------------------------ */
-
-void
-FrameBuffer_drawpixmap(FrameBuffer *f, PixMap *pm, int x, int y, int fgcolor, int bgcolor) {
-
-  int startx, starty;         /* Starting location on framebuffer */
-  int startpixx = 0, startpixy = 0;   /* Starting location in pixmap      */
-  int endx, endy;             /* Ending location on framebuffer   */
-  int i,j, px, py;
-  int c;
-  
-  startx = x - pm->centerx;
-  starty = y + pm->centery;
-  endx = startx + pm->width;
-  endy = starty - pm->height;
-
-  /* Figure out if we need to clip */
-
-  if (startx < f->xmin) {
-    startpixx = f->xmin - startx;
-    startx = f->xmin;
-  }
-  if (starty >= f->ymax) {
-    startpixy = starty - f->ymax;
-    starty = f->ymax-1;
-  }
-  if (endx >= f->xmax) {
-    endx = f->xmax-1;
-  }
-  if (endy < f->ymin) {
-    endy = f->ymin;
-  }
-  py = startpixy;
-  for (j = starty; j >= endy; j--) {
-    px = startpixx;
-    for (i = startx; i < endx; i++) {
-      c = pm->map[py*pm->width + px];
-      switch (c) {
-      case GIFPLOT_FOREGROUND:
-	f->pixels[j][i] = fgcolor;
-	break;
-      case GIFPLOT_BACKGROUND:
-	f->pixels[j][i] = bgcolor;
-	break;
-      default:
-	break;
-      }
-      px++;
-    }
-    py++;
-  }
-}
-
-/**************************************************************************
- * Some common PixMaps  (for plotting)
- *
- **************************************************************************/
-
-int _SQUARE_MAP[] = {
-  0,1,1,1,1,1,1,1,
-  0,1,1,1,1,1,1,1,
-  0,1,1,1,1,1,1,1,
-  0,1,1,1,1,1,1,1,
-  0,1,1,1,1,1,1,1,
-  0,1,1,1,1,1,1,1,
-  0,1,1,1,1,1,1,1,
-  0,0,0,0,0,0,0,0 };
-
-PixMap  PixMap_SQUARE = { 8,8,4,4, _SQUARE_MAP};
-
-int _TRIANGLE_MAP[] = {
-  0,0,0,1,0,0,0,0,
-  0,0,0,1,0,0,0,0,
-  0,0,1,1,1,0,0,0,
-  0,0,1,1,1,0,0,0,
-  0,1,1,1,1,1,0,0,
-  0,1,1,1,1,1,0,0,
-  1,1,1,1,1,1,1,0,
-  0,0,0,0,0,0,0,0 };
-
-PixMap  PixMap_TRIANGLE = { 8,8,4,4,_TRIANGLE_MAP};
-
-int _CROSS_MAP[] = {
-  0,0,0,1,0,0,0,0,
-  0,0,0,1,0,0,0,0,
-  0,0,0,1,0,0,0,0,
-  1,1,1,1,1,1,1,0,
-  0,0,0,1,0,0,0,0,
-  0,0,0,1,0,0,0,0,
-  0,0,0,1,0,0,0,0,
-  0,0,0,0,0,0,0,0 };
-
-PixMap  PixMap_CROSS = { 8,8,4,4,_CROSS_MAP};
-
-  
-      
diff --git a/Examples/GIFPlot/Lib/plot2d.c b/Examples/GIFPlot/Lib/plot2d.c
deleted file mode 100644
index e78107bf1..000000000
--- a/Examples/GIFPlot/Lib/plot2d.c
+++ /dev/null
@@ -1,445 +0,0 @@
-/* ----------------------------------------------------------------------------- 
- * plot2d.c
- *
- *     2-Dimensional plotting
- * 
- * Author(s) : David Beazley (beazley@cs.uchicago.edu)
- * Copyright (C) 1995-1996
- *
- * See the file LICENSE for information on usage and redistribution.	
- * ----------------------------------------------------------------------------- */
-
-#define PLOT2D
-
-#include "gifplot.h"
-
-/* ------------------------------------------------------------------------
-   Plot2D *new_Plot2D(FrameBuffer *frame, xmin, ymin, xmax, ymax)
-
-   Create a new 2D plot with given minimum and maximum coordinates.
-   ------------------------------------------------------------------------ */
-Plot2D  *new_Plot2D(FrameBuffer *frame,double xmin,double ymin,double xmax,double ymax) {
-  Plot2D  *p2;
-  if (frame) {
-    if (xmax <= xmin) return (Plot2D *) 0;
-    if (ymax <= ymin) return (Plot2D *) 0;
-    p2 = (Plot2D *) malloc(sizeof(Plot2D));
-    p2->frame = frame;
-    p2->xmin = xmin;
-    p2->ymin = ymin;
-    p2->xmax = xmax;
-    p2->ymax = ymax;
-    p2->view_xmin = 0;
-    p2->view_xmax = frame->width;
-    p2->view_ymin = 0;
-    p2->view_ymax = frame->height;
-    p2->xscale = LINEAR;
-    p2->yscale = LINEAR;
-    p2->dx = (p2->view_xmax - p2->view_xmin)/(p2->xmax - p2->xmin);
-    p2->dy = (p2->view_ymax - p2->view_ymin)/(p2->ymax - p2->ymin);
-    return p2;
-  }
-  return (Plot2D *) 0;
-}
-
-/* ----------------------------------------------------------------------------
-   delete_Plot2D(Plot2D *p2)
-
-   Delete a 2D plot
-   ---------------------------------------------------------------------------- */
-void
-delete_Plot2D(Plot2D *p2) {
-  if (p2)
-    free((char *) p2);
-}
-
-/* -----------------------------------------------------------------------------
-   Plot2D *Plot2D_copy(Plot2D *p2)
-
-   Makes a copy of the Plot2D data structure.
-   ----------------------------------------------------------------------------- */
-
-Plot2D *Plot2D_copy(Plot2D *p2) {
-  Plot2D *c2;
-  if (p2) {
-    c2 = (Plot2D *) malloc(sizeof(Plot2D));
-    if (c2) {
-      c2->frame = p2->frame;
-      c2->view_xmin = p2->view_xmin;
-      c2->view_ymin = p2->view_ymin;
-      c2->view_xmax = p2->view_xmax;
-      c2->view_ymax = p2->view_ymax;
-      c2->xmin = p2->xmin;
-      c2->ymin = p2->ymin;
-      c2->xmax = p2->xmax;
-      c2->ymax = p2->ymax;
-      c2->xscale = p2->xscale;
-      c2->yscale = p2->yscale;
-      c2->dx = p2->dx;
-      c2->dy = p2->dy;
-    }
-    return c2;
-  } else {
-    return (Plot2D *) 0;
-  }
-}
-
-/* -----------------------------------------------------------------------------
-   Plot2D_clear(Plot2D *p2, Pixel c)
-
-   Clear the region assigned to this plot to the given color.
-   -------------------------------------------------------------------------- */
-
-void Plot2D_clear(Plot2D *p2, Pixel c) {
-  int i,j;
-  for (i = p2->view_xmin; i < p2->view_xmax; i++)
-    for (j = p2->view_ymin; j < p2->view_ymax; j++) {
-      p2->frame->pixels[j][i] = c;
-    }
-}
-
-/* ------------------------------------------------------------------------------
-   Plot2D_setview
-
-   Sets the plot region on the framebuffer
-   ------------------------------------------------------------------------------ */
-
-void
-Plot2D_setview(Plot2D *p2, int vxmin, int vymin, int vxmax, int vymax) {
-  if (p2) {
-    p2->view_xmin = vxmin;
-    p2->view_ymin = vymin;
-    p2->view_xmax = vxmax;
-    p2->view_ymax = vymax;
-    p2->dx = (p2->view_xmax - p2->view_xmin)/(p2->xmax - p2->xmin);
-    p2->dy = (p2->view_ymax - p2->view_ymin)/(p2->ymax - p2->ymin);
-    FrameBuffer_setclip(p2->frame,vxmin,vymin,vxmax,vymax);
-  }
-}
-
-/* -------------------------------------------------------------------------------
-   Plot2D_setrange(Plot2D *p2, double xmin, double ymin, double xmax, double ymax)
-
-   Sets the plotting range.
-   ------------------------------------------------------------------------------- */
-
-void
-Plot2D_setrange(Plot2D *p2, double xmin, double ymin, double xmax, double ymax) {
-  if (p2) {
-    p2->xmin = xmin;
-    p2->ymin = ymin;
-    p2->xmax = xmax;
-    p2->ymax = ymax;
-    p2->dx = (p2->view_xmax - p2->view_xmin)/(p2->xmax - p2->xmin);
-    p2->dy = (p2->view_ymax - p2->view_ymin)/(p2->ymax - p2->ymin);
-  }
-}
-
-/* -------------------------------------------------------------------------------
-   Plot2D_setscale(Plot2D *p2, int xscale, int yscale)
-
-   Sets the plotting scaling method
-   ------------------------------------------------------------------------------- */
-
-void
-Plot2D_setscale(Plot2D *p2, int xscale, int yscale) {
-  if (p2) {
-    p2->xscale = xscale;
-    p2->yscale = yscale;
-  }
-}
-
-/* ----------------------------------------------------------------------------
-   Plot2D_transform(Plot2D *p2, double x, double y, int *px, int *py)
-   
-   Transforms x,y into screen coordinates px and py.  Result is returned
-   in px and py.  Rounds to the nearest pixel instead of truncating.
-   ----------------------------------------------------------------------------- */
-
-void
-Plot2D_transform(Plot2D *p2, double x, double y, int *px, int *py) {
-  if (p2) {
-    *px = p2->view_xmin + (int) (p2->dx*(x-p2->xmin) + 0.5);
-    *py = p2->view_ymin + (int) (p2->dy*(y-p2->ymin) + 0.5);
-  }
-}
-
-/* -------------------------------------------------------------------------------
-   Plot2D_plot(Plot2D *p2, double x, double y, Pixel color)
-
-   Plot a 2D Point of a given color
-   ------------------------------------------------------------------------------- */
-void
-Plot2D_plot(Plot2D *p2, double x, double y, Pixel color) {
-  int px, py;
-
-  Plot2D_transform(p2,x,y,&px,&py);
-  FrameBuffer_plot(p2->frame, px, py, color);
-}
-
-/* -------------------------------------------------------------------------------
-   Plot2D_box(Plot2D *p2, double x1, double y1, double x2, double y2, Pixel Color)
-
-   Plot an outline box on the 2D plot
-   ------------------------------------------------------------------------------- */
-void
-Plot2D_box(Plot2D *p2, double x1, double y1,double x2, double y2, Pixel color) {
-  int ix1, ix2,iy1, iy2;
-
-  Plot2D_transform(p2,x1,y1,&ix1,&iy1);
-  Plot2D_transform(p2,x2,y2,&ix2,&iy2);
-  FrameBuffer_box(p2->frame,ix1,iy1,ix2,iy2,color);
-}
-
-/* -------------------------------------------------------------------------------
-   Plot2D_solidbox(Plot2D *p2, double x1, double y1, double x2, double y2, Pixel Color)
-
-   Plot a solid box box on the 2D plot
-   ------------------------------------------------------------------------------- */
-void
-Plot2D_solidbox(Plot2D *p2, double x1, double y1,double x2, double y2, Pixel color) {
-  int ix1, ix2,iy1, iy2;
-
-  Plot2D_transform(p2,x1,y1,&ix1,&iy1);
-  Plot2D_transform(p2,x2,y2,&ix2,&iy2);
-  FrameBuffer_solidbox(p2->frame,ix1,iy1,ix2,iy2,color);
-}
-
-/* -------------------------------------------------------------------------------
-   Plot2D_interpbox(Plot2D *p2, double x1, double y1, double x2, double y2,
-                    Pixel c1, Pixel c2, Pixel c3, Pixel c4)
-
-   Plot a color-interpolated box on the 2D plot
-   ------------------------------------------------------------------------------- */
-void
-Plot2D_interpbox(Plot2D *p2, double x1, double y1,double x2, double y2,
-		 Pixel c1, Pixel c2, Pixel c3, Pixel c4) {
-  int ix1, ix2,iy1, iy2;
-
-  Plot2D_transform(p2,x1,y1,&ix1,&iy1);
-  Plot2D_transform(p2,x2,y2,&ix2,&iy2);
-  FrameBuffer_interpbox(p2->frame,ix1,iy1,ix2,iy2,c1,c2,c3,c4);
-}
-
-/* -------------------------------------------------------------------------------
-   Plot2D_circle(Plot2D *p2, double x, double y, double radius, Pixel color)
-
-   Make an outline circle on the 2D plot.
-   ------------------------------------------------------------------------------- */
-void
-Plot2D_circle(Plot2D *p2, double x, double y, double radius, Pixel color) {
-  int ix, iy, ir;
-
-  Plot2D_transform(p2,x,y,&ix,&iy);
-  ir = p2->dx * radius;        /* This is really incorrect. Will need ellipse */
-  if (ir > 1) 
-    FrameBuffer_circle(p2->frame,ix,iy,ir,color);
-  else
-    FrameBuffer_plot(p2->frame,ix,iy,color);
-  
-}
-  
-/* -------------------------------------------------------------------------------
-   Plot2D_solidcircle(Plot2D *p2, double x, double y, double radius, Pixel color)
-
-   Make an solid circle on the 2D plot.
-   ------------------------------------------------------------------------------- */
-void
-Plot2D_solidcircle(Plot2D *p2, double x, double y, double radius, Pixel color) {
-  int ix, iy, ir;
-
-  Plot2D_transform(p2,x,y,&ix,&iy);
-  ir = p2->dx * radius;        /* This is really incorrect. Will need ellipse */
-  if (ir > 1) 
-    FrameBuffer_solidcircle(p2->frame,ix,iy,ir,color);
-  else
-    FrameBuffer_plot(p2->frame,ix,iy,color);
-}
-
-/* -------------------------------------------------------------------------------
-   Plot2D_line(Plot2D *p2, double x1, double y1, double x2, double y2, Pixel color)
-
-   Draw a line
-   ------------------------------------------------------------------------------- */
-
-void
-Plot2D_line(Plot2D *p2, double x1, double y1, double x2, double y2, Pixel color) {
-  int ix1, ix2, iy1, iy2;
-
-  Plot2D_transform(p2,x1,y1,&ix1,&iy1);
-  Plot2D_transform(p2,x2,y2,&ix2,&iy2);
-  FrameBuffer_line(p2->frame,ix1,iy1,ix2,iy2,color);
-}
-
-
-
-/* -------------------------------------------------------------------------------
-   Plot2D_start(Plot2D *p2)
-
-   This should be called before starting to make a 2D plot. It will change
-   the viewport coordinates for the framebuffer and do other stuff.
-   ------------------------------------------------------------------------------- */
-
-void Plot2D_start(Plot2D *p2) {
-  if (p2) {
-    FrameBuffer_setclip(p2->frame, p2->view_xmin,p2->view_ymin,p2->view_xmax, p2->view_ymax);
-    p2->dx = (p2->view_xmax - p2->view_xmin)/(p2->xmax - p2->xmin);
-    p2->dy = (p2->view_ymax - p2->view_ymin)/(p2->ymax - p2->ymin);
-  }
-}
-
-/* --------------------------------------------------------------------------
-   void Plot2D_drawpixmap(Plot2D *p2, PixMap *pm, double x, double y, Pixel color, Pixel bgcolor)
-
-   Draw a pixel map at the given coordinates.  (Used for putting symbols on 2D
-   plots).
-   -------------------------------------------------------------------------- */
-void
-Plot2D_drawpixmap(Plot2D *p2, PixMap *pm, double x, double y, Pixel color, Pixel bgcolor) {
-  int ix, iy;
-
-  Plot2D_transform(p2,x,y,&ix,&iy);
-  FrameBuffer_drawpixmap(p2->frame,pm,ix,iy,color,bgcolor);
-}
-
-/* ----------------------------------------------------------------------------
-   void Plot2D_xaxis(Plot2D *p2, double x, double y, double xtick, int ticklength, Pixel color)
-
-   Draw an X axis bar at location x,y with ticks spaced every xtick units.
-   Ticks are spaced starting at "x"
-   ----------------------------------------------------------------------------- */
-
-void Plot2D_xaxis(Plot2D *p2, double x, double y, double xtick, int ticklength, Pixel color) {
-  int ix, iy,iy2;
-  double xt;
-
-  /* Draw a line fox the axis */
-  
-  Plot2D_line(p2,p2->xmin,y,p2->xmax,y,color);
-  xt = x;
-  while (xt >= p2->xmin) {
-    Plot2D_transform(p2,xt,y,&ix,&iy);
-    iy2 = iy+ticklength;
-    iy = iy-ticklength;
-    FrameBuffer_line(p2->frame,ix,iy,ix,iy2,color);
-    xt = xt - xtick;
-  }
-  xt = x + xtick;
-  while (xt < p2->xmax) {
-    Plot2D_transform(p2,xt,y,&ix,&iy);
-    iy2 = iy+ticklength;
-    iy = iy-ticklength;
-    FrameBuffer_line(p2->frame,ix,iy,ix,iy2,color);
-    xt = xt + xtick;
-  }
-}
-
-
-/* ----------------------------------------------------------------------------
-   void Plot2D_yaxis(Plot2D *p2, double x, double y, double ytick, int ticklength, Pixel c)
-
-   Draw an Y axis bar at location x,y with ticks spaced every xtick units.
-   Ticks are spaced starting at "y"
-   ----------------------------------------------------------------------------- */
-
-void Plot2D_yaxis(Plot2D *p2, double x, double y, double ytick, int ticklength, Pixel color) {
-  int ix, iy, ix2;
-  double yt;
-
-  /* Draw a line fox the axis */
-  
-  Plot2D_line(p2,x,p2->ymin,x,p2->ymax,color);
-  yt = y;
-  while (yt >= p2->ymin) {
-    Plot2D_transform(p2,x,yt,&ix,&iy);
-    ix2 = ix+ticklength;
-    ix = ix-ticklength;
-    FrameBuffer_line(p2->frame,ix,iy,ix2,iy,color);
-    yt = yt - ytick;
-  }
-  yt = y + ytick;
-  while (yt < p2->ymax) {
-    Plot2D_transform(p2,x,yt,&ix,&iy);
-    ix2 = ix+ticklength;
-    ix = ix-ticklength;
-    FrameBuffer_line(p2->frame,ix,iy,ix2,iy,color);
-    yt = yt + ytick;
-  }
-}
-
-
-/* -------------------------------------------------------------------------
-   Plot2D_triangle(Plot2D *p2, double x1, double y1, 
-                               double x2, double y2, 
-			       double x3, double y3, 
-			       Pixel fillcolor)
-
-   This function draws a 2D outline triangle.
-   -------------------------------------------------------------------------- */
-
-void Plot2D_triangle(Plot2D *p2, double x1, double y1,
-		     double x2, double y2, 
-		     double x3, double y3, Pixel color) {
-
-  Plot2D_line(p2,x1,y1,x2,y2,color);
-  Plot2D_line(p2,x2,y2,x3,y3,color);
-  Plot2D_line(p2,x3,y3,x1,y1,color);
-
-}
-
-
-/* -------------------------------------------------------------------------
-   Plot2D_solidtriangle(Plot2D *p2, double x1, double y1, 
-                               double x2, double y2, 
-			       double x3, double y3, 
-			       Pixel color)
-
-   This function draws a 2D filled triangle.    Can be used to
-   draw other primitives such as quadralaterals, etc...
-
-   -------------------------------------------------------------------------- */
-
-void Plot2D_solidtriangle(Plot2D *p2, double x1, double y1, 
-
-			  double x2, double y2, 
-			  double x3, double y3, Pixel color) {
-
-  int        tx1, tx2, tx3, ty1, ty2, ty3;
-  
-  /* Transform the three points into screen coordinates */
-
-  Plot2D_transform(p2,x1,y1,&tx1,&ty1);
-  Plot2D_transform(p2,x2,y2,&tx2,&ty2);
-  Plot2D_transform(p2,x3,y3,&tx3,&ty3);
-
-  FrameBuffer_solidtriangle(p2->frame,tx1,ty1,tx2,ty2,tx3,ty3,color);
-  
-}    
-
-/* -------------------------------------------------------------------------
-   Plot2D_interptriangle(Plot2D *p2, double x1, double y1, Pixel c1,
-                               double x2, double y2, Pixel c2,
-			       double x3, double y3, Pixel c3);
-
-   This function draws a 2D filled triangle with color interpolation.
-   Can be used to draw other primitives such as quadralaterals, etc...
-   -------------------------------------------------------------------------- */
-
-void Plot2D_interptriangle(Plot2D *p2, double x1, double y1, Pixel c1,
-			   double x2, double y2, Pixel c2,
-			   double x3, double y3, Pixel c3) {
-
-  int        tx1, tx2, tx3, ty1, ty2, ty3;
-  
-  /* Transform the three points into screen coordinates */
-
-  Plot2D_transform(p2,x1,y1,&tx1,&ty1);
-  Plot2D_transform(p2,x2,y2,&tx2,&ty2);
-  Plot2D_transform(p2,x3,y3,&tx3,&ty3);
-
-  FrameBuffer_interptriangle(p2->frame,tx1,ty1,c1,tx2,ty2,c2,tx3,ty3,c3);
-  
-}    
-  
-  
-
diff --git a/Examples/GIFPlot/Lib/plot3d.c b/Examples/GIFPlot/Lib/plot3d.c
deleted file mode 100644
index 387e420e2..000000000
--- a/Examples/GIFPlot/Lib/plot3d.c
+++ /dev/null
@@ -1,2181 +0,0 @@
-/* ----------------------------------------------------------------------------- 
- * plot3d.c
- *
- *     Three-dimensional plotting.
- * 
- * Author(s) : David Beazley (beazley@cs.uchicago.edu)
- * Copyright (C) 1995-1996
- *
- * See the file LICENSE for information on usage and redistribution.	
- * ----------------------------------------------------------------------------- */
-
-#define PLOT3D
-#include "gifplot.h"
-#include <math.h>
-#include <float.h>
-
-#define ORTHO        1
-#define PERSPECTIVE  2
-/* ------------------------------------------------------------------------
-   Plot3D *new_Plot3D(FrameBuffer *f, double xmin, double ymin, double zmin,
-   double xmax, double ymax, double zmax)
-
-   Creates a new 3D plot.  Min and max coordinates are primarily used to
-   pick some default parameters.  Returns NULL on failure
-   ------------------------------------------------------------------------- */
-
-Plot3D *new_Plot3D(FrameBuffer *f, double xmin, double ymin, double zmin,
-		   double xmax, double ymax, double zmax) {
-
-  Plot3D  *p3;
-  void Plot3D_maketransform(Plot3D *p3);
-  
-  /* Check to make sure the framebuffer and min/max parameters are valid */
-
-  if (!f) return (Plot3D *) 0;
-  if ((xmin > xmax) || (ymin > ymax) || (zmin > zmax)) return (Plot3D *) 0;
-
-  p3 = (Plot3D *) malloc(sizeof(Plot3D));
-  p3->frame = f;
-  p3->xmin = xmin;
-  p3->ymin = ymin;
-  p3->zmin = zmin;
-  p3->xmax = xmax;
-  p3->ymax = ymax;
-  p3->zmax = zmax;
-
-  /* Set view region to the entire size of the framebuffer */
-
-  p3->view_xmin = 0;
-  p3->view_ymin = 0;
-  p3->view_xmax = f->width;
-  p3->view_ymax = f->height;
-  p3->width = f->width;
-  p3->height = f->height;
-  
-  /* Calculate a center point based off the min and max coordinates given */
-
-  p3->xcenter = (xmax - xmin)/2.0 + xmin;
-  p3->ycenter = (ymax - ymin)/2.0 + ymin;
-  p3->zcenter = (zmax - zmin)/2.0 + zmin;
-
-  /* Calculate the aspect ratio of the viewing region */
-
-  p3->aspect = (double) f->width/(double) f->height;
-
-  /* Set default view parameters */
-  p3->xshift = 1.0;
-  p3->yshift = 1.0;
-  p3->zoom   = 0.5;
-  p3->fovy   = 40.0;         /* 40 degree field of view */
-
-  /* Create matrices */
-
-  p3->model_mat = new_Matrix();
-  p3->view_mat = new_Matrix();
-  p3->center_mat = new_Matrix();
-  p3->fullmodel_mat = new_Matrix();
-  p3->trans_mat = new_Matrix();
-  p3->pers_mode = ORTHO;
-
-  FrameBuffer_zresize(p3->frame,p3->width, p3->height);
-  Matrix_identity(p3->view_mat);
-  Matrix_identity(p3->model_mat);
-  Matrix_translate(p3->center_mat, -p3->xcenter,-p3->ycenter,-p3->zcenter);
-  Plot3D_maketransform(p3);
-  return p3;
-}
-
-/* ---------------------------------------------------------------------
-   delete_Plot3D(Plot3D *p3)
-
-   Deletes a 3D plot
-   --------------------------------------------------------------------- */
-
-void delete_Plot3D(Plot3D *p3) {
-  if (p3) {
-    delete_Matrix(p3->view_mat);
-    delete_Matrix(p3->model_mat);
-    delete_Matrix(p3->trans_mat);
-    free((char *) p3);
-  }
-}
-
-/* ---------------------------------------------------------------------
-   Plot3D *Plot3D_copy(Plot3D *p3)
-
-   This makes a copy of the 3D plot structure and returns a pointer to it.
-   --------------------------------------------------------------------- */
-
-Plot3D *Plot3D_copy(Plot3D *p3) {
-  Plot3D *c3;
-  if (p3) {
-    c3 = (Plot3D *) malloc(sizeof(Plot3D));
-    if (c3) {
-      c3->frame = p3->frame;
-      c3->view_xmin = p3->view_xmin;
-      c3->view_ymin = p3->view_ymin;
-      c3->view_xmax = p3->view_xmax;
-      c3->view_ymax = p3->view_ymax;
-      c3->xmin = p3->xmin;
-      c3->ymin = p3->ymin;
-      c3->zmin = p3->zmin;
-      c3->xmax = p3->xmax;
-      c3->ymax = p3->ymax;
-      c3->zmax = p3->zmax;
-      c3->xcenter = p3->xcenter;
-      c3->ycenter = p3->ycenter;
-      c3->zcenter = p3->zcenter;
-      c3->fovy = p3->fovy;
-      c3->aspect = p3->aspect;
-      c3->znear = p3->znear;
-      c3->zfar = p3->zfar;
-      c3->center_mat = Matrix_copy(p3->center_mat);
-      c3->model_mat = Matrix_copy(p3->model_mat);
-      c3->view_mat = Matrix_copy(p3->view_mat);
-      c3->fullmodel_mat = Matrix_copy(p3->fullmodel_mat);
-      c3->trans_mat = Matrix_copy(p3->trans_mat);
-      c3->lookatz = p3->lookatz;
-      c3->xshift = p3->xshift;
-      c3->yshift = p3->yshift;
-      c3->zoom = p3->zoom;
-      c3->width = p3->width;
-      c3->height = p3->height;
-      c3->pers_mode = p3->pers_mode;
-    }
-    return c3;
-  } else {
-    return (Plot3D *) 0;
-  }
-}
-
-/* ----------------------------------------------------------------------
-   Plot3D_clear(Plot3D *p3, Pixel bgcolor)
-
-   Clear the pixel and zbuffer only for the view region of this image.
-   ---------------------------------------------------------------------- */
-void
-Plot3D_clear(Plot3D *p3, Pixel bgcolor) {
-  int i,j;
-
-  for (i = p3->view_xmin; i < p3->view_xmax; i++)
-    for (j = p3->view_ymin; j < p3->view_ymax; j++) {
-      p3->frame->pixels[j][i] = bgcolor;
-      p3->frame->zbuffer[j][i] = ZMIN;
-    }
-}
-
-/* ---------------------------------------------------------------------
-   Plot3D_maketransform(Plot3D *p3)
-
-   This function builds the total 3D transformation matrix from a
-   collection of components.
-
-   Trans = View * Rotation * Center
-
-   Where View is the viewing transformation matrix, Rotation is the
-   model rotation matrix, Center is the translation matrix used to
-   center the Model at the origin.
-   --------------------------------------------------------------------- */
-
-void
-Plot3D_maketransform(Plot3D *p3) {
-
-  Matrix_multiply(p3->model_mat,p3->center_mat, p3->fullmodel_mat);
-  Matrix_multiply(p3->view_mat,p3->fullmodel_mat, p3->trans_mat);
-}
-   
-/* ---------------------------------------------------------------------
-   Plot3D_perspective(Plot3D *p3, double fovy, double znear, double zfar)
-
-   Sets up the perspective viewing transformation.   Assumes "lookat"
-   has already been called.
-   --------------------------------------------------------------------- */
-
-void
-Plot3D_perspective(Plot3D *p3, double fovy, double znear, double zfar) {
-  double theta;
-  double mat[16];
-
-  p3->fovy = fovy;
-  p3->znear = znear;
-  p3->zfar = zfar;
-
-  theta = 3.1415926*fovy/180.0;
-
-  Matrix_identity(mat);
-  mat[0] = cos(theta/2.0)/(sin(theta/2.0)*p3->aspect);
-  mat[5] = cos(theta/2.0)/(sin(theta/2.0));
-  mat[10] = -(zfar + znear)/(zfar-znear);
-  mat[14] = -1.0;
-  mat[11] = -(2*zfar*znear)/(zfar - znear);
-  mat[15] = 0.0;
-
-  /* Update the view transformation matrix */
-  
-  Matrix_multiply(mat,p3->view_mat,p3->view_mat);
-
-  /* Update the global transformation matrix */
-  
-  Plot3D_maketransform(p3);
-  p3->pers_mode = PERSPECTIVE;
-
-}
-
-/* ---------------------------------------------------------------------
-   Plot3D_lookat(Plot3D *p3, double z)
-
-   A greatly simplified version of (lookat).  Specifies the position
-   of the viewpoint. (can be used for moving image in or out).
-
-   Destroys the current viewing transformation matrix, so it will have
-   to be recalculated.
-   --------------------------------------------------------------------- */
-  
-void
-Plot3D_lookat(Plot3D *p3, double z) {
-  if (p3) {
-    Matrix_translate(p3->view_mat, 0,0,-z);
-    p3->lookatz = z;
-    Plot3D_maketransform(p3);
-  }
-}
-
-/* -------------------------------------------------------------------------
-   Plot3D_autoperspective(Plot3D *p3, double fovy)
-
-   Automatically figures out a semi-decent viewpoint given the
-   min,max parameters currently set for this image
-   ------------------------------------------------------------------------- */
-
-void
-Plot3D_autoperspective(Plot3D *p3, double fovy) {
-
-  /* Make a perspective transformation matrix for this system */
-
-  double  zfar;
-  double  znear;
-  double  d, dmax;
-  double  cx,cy,cz;
-  double  xmin,xmax,ymin,ymax,zmin,zmax;
-
-  xmin = p3->xmin;
-  ymin = p3->ymin;
-  zmin = p3->zmin;
-  xmax = p3->xmax;
-  ymax = p3->ymax;
-  zmax = p3->zmax;
-  cx = p3->xcenter;
-  cy = p3->ycenter;
-  cz = p3->zcenter;
-  
-  /* Calculate longest point from center point */
-
-  dmax = (xmin-cx)*(xmin-cx) + (ymin-cy)*(ymin-cy) + (zmin-cz)*(zmin-cz);
-  d = (xmax-cx)*(xmax-cx) + (ymin-cy)*(ymin-cy) + (zmin-cz)*(zmin-cz);
-  if (d > dmax) dmax = d;
-  d = (xmin-cx)*(xmin-cx) + (ymax-cy)*(ymax-cy) + (zmin-cz)*(zmin-cz);
-  if (d > dmax) dmax = d;
-  d = (xmax-cx)*(xmax-cx) + (ymax-cy)*(ymax-cy) + (zmin-cz)*(zmin-cz);
-  if (d > dmax) dmax = d;
-  d = (xmin-cx)*(xmin-cx) + (ymin-cy)*(ymin-cy) + (zmax-cz)*(zmax-cz);
-  if (d > dmax) dmax = d;
-  d = (xmax-cx)*(xmax-cx) + (ymin-cy)*(ymin-cy) + (zmax-cz)*(zmax-cz);
-  if (d > dmax) dmax = d;
-  d = (xmin-cx)*(xmin-cx) + (ymax-cy)*(ymax-cy) + (zmax-cz)*(zmax-cz);
-  if (d > dmax) dmax = d;
-  d = (xmax-cx)*(xmax-cx) + (ymax-cy)*(ymax-cy) + (zmax-cz)*(zmax-cz);
-  if (d > dmax) dmax = d;
-
-  dmax = sqrt(dmax);
-  d = p3->lookatz;
-  
-  znear = d - dmax;
-  zfar = znear+1.5*dmax;
-  Plot3D_perspective(p3, fovy,znear,zfar);
-  
-}
-
-   
-/* ---------------------------------------------------------------------
-   Plot3D_ortho(Plot3D *p3, double left, double right, double bottom, double top)
-
-   Sets up an orthographic viewing transformation.   
-   --------------------------------------------------------------------- */
-
-void
-Plot3D_ortho(Plot3D *p3, double left, double right, double bottom, double top) {
-
-
-  Matrix_identity(p3->view_mat);
-  p3->view_mat[0] = (2.0/(right - left))/p3->aspect;
-  p3->view_mat[5] = 2.0/(top - bottom);
-  p3->view_mat[10] = -1;
-  p3->view_mat[15] = 1.0;
-  p3->view_mat[3] = -(right+left)/(right-left);
-  p3->view_mat[7] = -(top+bottom)/(top-bottom);
-
-  /* Update the global transformation matrix */
-  
-  Plot3D_maketransform(p3);
-  p3->pers_mode = ORTHO;
-  p3->ortho_left = left;
-  p3->ortho_right = right;
-  p3->ortho_bottom = bottom;
-  p3->ortho_top = top;
-
-}
-
-/* ---------------------------------------------------------------------
-   Plot3D_autoortho(Plot3D *p3)
-
-   Automatically pick an orthographic projection that's probably
-   pretty good.
-   --------------------------------------------------------------------- */
-
-void
-Plot3D_autoortho(Plot3D *p3) {
-
-  /* Make a perspective transformation matrix for this system */
-
-  double  d, dmax;
-  double  cx,cy,cz;
-  double  xmin,xmax,ymin,ymax,zmin,zmax;
-
-  xmin = p3->xmin;
-  ymin = p3->ymin;
-  zmin = p3->zmin;
-  xmax = p3->xmax;
-  ymax = p3->ymax;
-  zmax = p3->zmax;
-  cx = p3->xcenter;
-  cy = p3->ycenter;
-  cz = p3->zcenter;
-  
-  /* Calculate longest point from center point */
-
-  dmax = (xmin-cx)*(xmin-cx) + (ymin-cy)*(ymin-cy) + (zmin-cz)*(zmin-cz);
-  d = (xmax-cx)*(xmax-cx) + (ymin-cy)*(ymin-cy) + (zmin-cz)*(zmin-cz);
-  if (d > dmax) dmax = d;
-  d = (xmin-cx)*(xmin-cx) + (ymax-cy)*(ymax-cy) + (zmin-cz)*(zmin-cz);
-  if (d > dmax) dmax = d;
-  d = (xmax-cx)*(xmax-cx) + (ymax-cy)*(ymax-cy) + (zmin-cz)*(zmin-cz);
-  if (d > dmax) dmax = d;
-  d = (xmin-cx)*(xmin-cx) + (ymin-cy)*(ymin-cy) + (zmax-cz)*(zmax-cz);
-  if (d > dmax) dmax = d;
-  d = (xmax-cx)*(xmax-cx) + (ymin-cy)*(ymin-cy) + (zmax-cz)*(zmax-cz);
-  if (d > dmax) dmax = d;
-  d = (xmin-cx)*(xmin-cx) + (ymax-cy)*(ymax-cy) + (zmax-cz)*(zmax-cz);
-  if (d > dmax) dmax = d;
-  d = (xmax-cx)*(xmax-cx) + (ymax-cy)*(ymax-cy) + (zmax-cz)*(zmax-cz);
-  if (d > dmax) dmax = d;
-
-  dmax = sqrt(dmax);
-
-  Plot3D_ortho(p3,-dmax,dmax,-dmax,dmax);
-  
-}
-
-
-
-/* -------------------------------------------------------------------------
-   Plot3D_setview(Plot3D *p3, int vxmin, int vymin, int vxmax, int vymax)
-
-   Sets the viewport for this 3D graph.  Will recalculate all of the
-   local viewing transformation matrices accordingly.
-   ------------------------------------------------------------------------- */
-void
-Plot3D_setview(Plot3D *p3, int vxmin, int vymin, int vxmax, int vymax) {
-  if (p3) {
-    if ((vxmin > vxmax) || (vymin >vymax)) return;
-    p3->view_xmin = vxmin;
-    p3->view_ymin = vymin;
-    p3->view_xmax = vxmax;
-    p3->view_ymax = vymax;
-    p3->width = (vxmax - vxmin);
-    p3->height = (vymax - vymin);
-    p3->aspect = (double) p3->width/(double) p3->height;
-
-    /* Fix up the viewing transformation matrix */
-
-    if (p3->pers_mode == PERSPECTIVE) {
-      Plot3D_lookat(p3,p3->lookatz);
-      Plot3D_perspective(p3,p3->fovy,p3->znear,p3->zfar);
-    } else {
-      Plot3D_ortho(p3,p3->ortho_left,p3->ortho_right,p3->ortho_bottom, p3->ortho_top);
-    }
-    FrameBuffer_setclip(p3->frame,vxmin,vymin,vxmax,vymax);
-  }
-}
-
-/* ---------------------------------------------------------------------------
-   Plot2D_start(Plot2D *p3)
-
-   Set up viewing region and other parameters for this image.
-   --------------------------------------------------------------------------- */
-
-void
-Plot3D_start(Plot3D *p3) {
-  if (p3)
-    FrameBuffer_setclip(p3->frame, p3->view_xmin,p3->view_ymin,p3->view_xmax, p3->view_ymax);
-
-}
-
-/* -------------------------------------------------------------------------
-   Plot3D_plot(Plot3D *p3, double x, double y, double z, Pixel Color)
-
-   Plot a 3D point
-   ------------------------------------------------------------------------- */
-   
-void
-Plot3D_plot(Plot3D *p3, double x, double y, double z, Pixel color) { 
-
-  GL_Vector t;
-  int      ix, iy;
-  double   invw;
-  FrameBuffer *f;
-  
-  /* Perform a transformation */
-
-  Matrix_transform4(p3->trans_mat,x,y,z,1,&t);
-
-  /* Scale the coordinates into unit cube */
-  
-  invw = 1.0/t.w;
-  t.x = t.x *invw;
-  t.y = t.y *invw;
-  t.z = t.z *invw;
-#ifdef GL_DEBUG
-  fprintf(stdout,"t.x = %g,   t.y = %g,    t.z = %g\n", t.x,t.y,t.z);
-#endif
-  /* Calculate the x and y coordinates */
-
-  ix = (int) ((t.x +p3->xshift)*p3->zoom*p3->width + 0.5); 
-  iy = (int) ((t.y +p3->yshift)*p3->zoom*p3->height + 0.5); 
-
-  if ((ix >= 0) && (ix < p3->width) &&
-      (iy >= 0) && (ix < p3->height)) {
-    ix += p3->view_xmin;
-    iy += p3->view_ymin;
-    f = p3->frame;
-    if (t.z <= f->zbuffer[iy][ix]) {
-      f->pixels[iy][ix] = color;
-      f->zbuffer[iy][ix] = t.z;
-    }
-  }
-}
-
-/* ----------------------------------------------------------------------
-   Plot3D_rotx(Plot3D *p3, double deg)
-
-   Rotate the model around its x axis.
-   ---------------------------------------------------------------------- */
-
-void
-Plot3D_rotx(Plot3D *p3, double deg) {
-  double temp[16];
-
-  Matrix_rotatex(temp,deg);         /* Construct a x rotation matrix */
-  Matrix_multiply(p3->model_mat,temp,p3->model_mat);
-  Plot3D_maketransform(p3);
-
-}
-
-/* ----------------------------------------------------------------------
-   Plot3D_roty(Plot3D *p3, double deg)
-
-   Rotate the model around its y axis.
-   ---------------------------------------------------------------------- */
-
-void
-Plot3D_roty(Plot3D *p3, double deg) {
-  double temp[16];
-
-  Matrix_rotatey(temp,deg);         /* Construct a y rotation matrix */
-  Matrix_multiply(p3->model_mat,temp,p3->model_mat);
-  Plot3D_maketransform(p3);
-
-}
-
-/* ----------------------------------------------------------------------
-   Plot3D_rotz(Plot3D *p3, double deg)
-
-   Rotate the model around its z axis.
-   ---------------------------------------------------------------------- */
-
-void
-Plot3D_rotz(Plot3D *p3, double deg) {
-  double temp[16];
-
-  Matrix_rotatez(temp,deg);         /* Construct a z rotation matrix */
-  Matrix_multiply(p3->model_mat,temp,p3->model_mat);
-  Plot3D_maketransform(p3);
-
-}
-
-
-/* ----------------------------------------------------------------------
-   Plot3D_rotd(Plot3D *p3, double deg)
-
-   Rotate the model down
-   ---------------------------------------------------------------------- */
-
-void
-Plot3D_rotd(Plot3D *p3, double deg) {
-  double temp[16];
-
-  Matrix_rotatex(temp,deg);         /* Construct a x rotation matrix */
-  Matrix_multiply(temp, p3->model_mat,p3->model_mat);
-  Plot3D_maketransform(p3);
-
-}
-    
-
-/* ----------------------------------------------------------------------
-   Plot3D_rotu(Plot3D *p3, double deg)
-
-   Rotate the model up
-   ---------------------------------------------------------------------- */
-
-void
-Plot3D_rotu(Plot3D *p3, double deg) {
-  double temp[16];
-
-  Matrix_rotatex(temp,-deg);         /* Construct a x rotation matrix */
-  Matrix_multiply(temp,p3->model_mat,p3->model_mat);
-  Plot3D_maketransform(p3);
-
-}
-
-
-/* ----------------------------------------------------------------------
-   Plot3D_rotr(Plot3D *p3, double deg)
-
-   Rotate the model down
-   ---------------------------------------------------------------------- */
-
-void
-Plot3D_rotr(Plot3D *p3, double deg) {
-  double temp[16];
-
-  Matrix_rotatey(temp,deg);         /* Construct a y rotation matrix */
-  Matrix_multiply(temp, p3->model_mat,p3->model_mat);
-  Plot3D_maketransform(p3);
-
-}
-    
-
-/* ----------------------------------------------------------------------
-   Plot3D_rotl(Plot3D *p3, double deg)
-
-   Rotate the model left
-   ---------------------------------------------------------------------- */
-
-void
-Plot3D_rotl(Plot3D *p3, double deg) {
-  double temp[16];
-
-  Matrix_rotatey(temp,-deg);         /* Construct a y rotation matrix */
-  Matrix_multiply(temp,p3->model_mat,p3->model_mat);
-  Plot3D_maketransform(p3);
-
-}
-
-
-/* ----------------------------------------------------------------------
-   Plot3D_rotc(Plot3D *p3, double deg)
-
-   Rotate the model around center point
-   ---------------------------------------------------------------------- */
-
-void
-Plot3D_rotc(Plot3D *p3, double deg) {
-  double temp[16];
-
-  Matrix_rotatez(temp,-deg);         /* Construct a z rotation matrix */
-  Matrix_multiply(temp,p3->model_mat,p3->model_mat);
-  Plot3D_maketransform(p3);
-}
-
-/* -------------------------------------------------------------------------
-   Plot3D_zoom(Plot3D *p3, double percent)
-
-   Zooms in or out the current image.   percent defines a percentage of
-   zoom.
-
-   Zooming is actually done by adjusting the perspective field of view
-   instead of scaling the model or moving in the viewpoint.    This
-   seems to work the best.
-   ------------------------------------------------------------------------- */
-
-void
-Plot3D_zoom(Plot3D *p3, double percent) {
-
-  double scale;
-  double dx;
-  if (percent <= 0) return;
-  scale = percent/100.0;
-
-  dx = (1.0/scale - 1.0)/(2*p3->zoom); /* Don't even ask where this came from */
-  p3->xshift += dx;
-  p3->yshift += dx;
-  p3->zoom = p3->zoom*scale;
-
-#ifdef OLD
-  p3->fovy = p3->fovy*scale;
-  if (p3->fovy > 170.0) p3->fovy = 170.0;
-  if (p3->fovy == 0) p3->fovy = 0.0001;
-  Plot3D_lookat(p3,p3->lookatz);
-  Plot3D_perspective(p3,p3->fovy,p3->znear,p3->zfar);
-#endif
-}
-
-/* --------------------------------------------------------------------------
-   Plot3D_left(Plot3D *p3, double s)
-
-   Shifts the image to the left by s units.   This is a little funky.
-
-   s is scaled so that s = 100 equals one full screen.
-   -------------------------------------------------------------------------- */
-void
-Plot3D_left(Plot3D *p3, double s) {
-  p3->xshift -= (s/100.0)/p3->zoom;
-}
-
-/* --------------------------------------------------------------------------
-   Plot3D_right(Plot3D *p3, double s)
-
-   Shifts the image to the right by s units. 
-
-   s is scaled so that s = 100 equals one full screen.
-   -------------------------------------------------------------------------- */
-void
-Plot3D_right(Plot3D *p3, double s) {
-  p3->xshift += (s/100.0)/p3->zoom;
-}
-
-/* --------------------------------------------------------------------------
-   Plot3D_up(Plot3D *p3, double s)
-
-   Shifts the image up left by s units.
-
-   s is scaled so that s = 100 equals one full screen.
-   -------------------------------------------------------------------------- */
-void
-Plot3D_up(Plot3D *p3, double s) {
-  p3->yshift += (s/100.0)/p3->zoom;
-}
-
-/* --------------------------------------------------------------------------
-   Plot3D_down(Plot3D *p3, double s)
-
-   Shifts the image down by s units.  
-
-   s is scaled so that s = 100 equals one full screen.
-   -------------------------------------------------------------------------- */
-void
-Plot3D_down(Plot3D *p3, double s) {
-  p3->yshift -= (s/100.0)/p3->zoom;
-}
-
-/* -------------------------------------------------------------------------
-   Plot3D_center(Plot3D *p3, double cx, double cy)
-
-   Centers the image on a point in the range (0,0) - (100,100)
-   ------------------------------------------------------------------------- */
-void
-Plot3D_center(Plot3D *p3, double cx, double cy) {
-  Plot3D_left(p3,cx-50);
-  Plot3D_down(p3,cy-50);
-}
-
-
-
-/***************************************************************************
- *                       3d Primitives                                     *
- ***************************************************************************/
-
-/* -------------------------------------------------------------------------
-   Plot3D_horizontal(Plot3D *p3, int xmin, int xmax, int y, double z1, double z2, Pixel color)
-
-   Draws a "Horizontal" line on the framebuffer between two screen coordinates,
-   but also supplies z-values and zbuffering.   This function probably isn't
-   too useful by itself, but will be used by a number of other primitives.
-   -------------------------------------------------------------------------- */
-
-void Plot3D_horizontal(Plot3D *p3, int xmin, int xmax, int y, Zvalue z1, Zvalue z2, Pixel color) {
-  Pixel  *p;
-  FrameBuffer *f;
-  int     i;
-  Zvalue  *zbuf,z,mz;
-  int     startx, endx;
-
-  f = p3->frame;
-  if ((y < f->ymin) || (y >= f->ymax)) return;
-  if (xmin > f->xmax) return;
-  if (xmin < f->xmin) startx = f->xmin;
-  else startx = xmin;
-  if (xmax < f->xmin) return;
-  if (xmax >= f->xmax) endx = f->xmax - 1;
-  else endx = xmax;
-
-  /* Calculate z slope */
-
-  if (xmax != xmin) {
-    mz = (Zvalue) ((double) (z2 - z1)/(double) (xmax - xmin));
-  } else {
-    mz = 0;
-  }
-
-  /* Draw it */
-  
-  p = &f->pixels[y][startx];
-  zbuf = &f->zbuffer[y][startx];
-  z = (Zvalue) (mz*(startx-xmin) + z1);
-  for (i = startx; i <= endx; i++, p++, zbuf++,z+=mz) {
-    if (z <= *zbuf) {
-      *p = color;
-      *zbuf = z;
-    }
-  }
-}
-
-
-/* -------------------------------------------------------------------------
-   Plot3D_vertical(Plot3D *p3, int ymin, int ymax, int x, double z1, double z2, Pixel color)
-
-   Draws a "Vertical" line on the framebuffer between two screen coordinates,
-   but also supplies z-values and zbuffering.   This function probably isn't
-   too useful by itself, but will be used by a number of other primitives.
-   -------------------------------------------------------------------------- */
-
-void Plot3D_vertical(Plot3D *p3, int ymin, int ymax, int x, Zvalue z1, Zvalue z2, Pixel color) {
-  Pixel  *p;
-  FrameBuffer *f;
-  int     i;
-  Zvalue  *zbuf,z,mz;
-  int     starty, endy;
-
-  f = p3->frame;
-  if ((x < f->xmin) || (x >= f->xmax)) return;
-  if (ymin >= f->ymax) return;
-  if (ymin < f->ymin) starty = f->ymin;
-  else starty = ymin;
-  if (ymax < f->ymin) return;
-  if (ymax >= f->ymax) endy = f->ymax - 1;
-  else endy = ymax;
-
-  /* Calculate z slope */
-
-  mz = (double) (z2 - z1)/(double) (ymax - ymin);
-
-  /* Draw it */
-  
-  p = &f->pixels[starty][x];
-  zbuf = &f->zbuffer[starty][x];
-  for (i = starty; i <= endy; i++, p+=f->width, zbuf+=f->width) {
-    z = (Zvalue) (mz*(i-ymin) + z1);
-    if (z <= *zbuf) {
-      *p = color;
-      *zbuf = z;
-    }
-  }
-}
-
-/* -------------------------------------------------------------------------------
-   Plot3D_linetransform(Plot3D *p3, int x1, int y1, Zvalue z1,
-                                    int x2, int y2, Zvalue z2, Pixel c)
-
-   Draw a 3D line between points that have already been transformed into
-   3D space.
-
-   Uses a Bresenham line algorithm, but with linear interpolation between
-   Zvalues.
-   ------------------------------------------------------------------------------- */
-   
-void
-Plot3D_linetransform(Plot3D *p3, int x1, int y1, Zvalue z1, int x2, int y2, Zvalue z2, Pixel c) {
-
-  int       orig_x1, orig_y1, orig_x2,orig_y2;
-  Zvalue    zt;
-  
-  /* Bresenham line drawing parameters */
-  FrameBuffer *f;
-  int  dx,dy,dxneg,dyneg, inc1,inc2,di;
-  int  x, y, xpixels, ypixels, xt, yt;
-  Pixel *p;
-  double m;
-  int  end1 = 0, end2 = 0;
-  Zvalue  *zbuf,mz,z;
-
-  f = p3->frame;
-    
-  /* Need to figure out where in the heck this line is */
-
-  dx = x2 - x1;
-  dy = y2 - y1;
-
-  if ((dx == 0) && (dy == 0)) {
-    if ((x1 < f->xmin) || (x1 >= f->xmax) ||
-	(y1 < f->ymin) || (y1 >= f->ymax)) return;
-    if (z1 <= f->zbuffer[y1][x1]) {
-      f->pixels[y1][x1] = c;
-    }
-    return;
-  }
-  if (dx == 0) {
-    /* Draw a Vertical Line */
-    if (y1 < y2)
-      Plot3D_vertical(p3,y1,y2,x1,z1,z2,c);
-    else
-      Plot3D_vertical(p3,y2,y1,x1,z2,z1,c);
-    return;
-  }
-  if (dy == 0) {
-    /* Draw a Horizontal Line */
-    if (x1 < x2)
-      Plot3D_horizontal(p3,x1,x2,y1,z1,z2,c);
-    else
-      Plot3D_horizontal(p3,x2,x1,y1,z2,z1,c);
-    return;
-  }
-
-  /* Figure out where in the heck these lines are using the
-     Cohen-Sutherland Line Clipping Scheme. */
-
-  end1 = ((x1 - f->xmin) < 0) |
-    (((f->xmax- 1 - x1) < 0) << 1) |
-    (((y1 - f->ymin) < 0) << 2) |
-    (((f->ymax-1 - y1) < 0) << 3);
-
-  end2 = ((x2 - f->xmin) < 0) |
-    (((f->xmax-1 - x2) < 0) << 1) |
-    (((y2 - f->ymin) < 0) << 2) |
-    (((f->ymax-1 - y2) < 0) << 3);
-
-  if (end1 & end2) return;      /* Nope : Not visible */
-  
-  /* Make sure points have a favorable orientation */
-  
-  if (x1 > x2) {
-    xt = x1;
-    x1 = x2;
-    x2 = xt;
-    yt = y1;
-    y1 = y2;
-    y2 = yt;
-    zt = z1;
-    z1 = z2;
-    z2 = zt;
-  }
-
-  /* Save original points before we clip them off */
-  orig_x1 = x1;
-  orig_y1 = y1;
-  orig_x2 = x2;
-  orig_y2 = y2;
-  
-  /* Clip against the boundaries */
-  m = (y2 - y1)/(double) (x2-x1);
-  if (x1 < f->xmin) {
-    y1 = (f->xmin - x1)*m + y1;
-    x1 = f->xmin;
-  }
-  if (x2 >= f->xmax) {
-    y2 = (f->xmax -1 -x1)*m + y1;
-    x2 = f->xmax - 1;
-  }
-
-  if (y1 > y2) {
-    xt = x1;
-    x1 = x2;
-    x2 = xt;
-    yt = y1;
-    y1 = y2;
-    y2 = yt;
-    zt = z1;
-    z1 = z2;
-    z2 = zt;
-
-    /* Swap original points */
-
-    xt = orig_x1;
-    orig_x1 = orig_x2;
-    orig_x2 = xt;
-    yt = orig_y1;
-    orig_y1 = orig_y2;
-    orig_y2 = yt;
-  }
-
-  m = 1/m;
-  if (y1 < f->ymin) {
-    x1 = (f->ymin - y1)*m + x1;
-    y1 = f->ymin;
-  }
-  if (y2 >= f->ymax) {
-    x2 = (f->ymax-1-y1)*m + x1;
-    y2 = f->ymax-1;
-  }
-
-  if ((x1 < f->xmin) || (x1 >= f->xmax) || (y1 < f->ymin) || (y1 >= f->ymax) ||
-      (x2 < f->xmin) || (x2 >= f->xmax) || (y2 < f->ymin) || (y2 >= f->ymax)) return;
-
-  dx = x2 - x1;
-  dy = y2 - y1;
-  xpixels = f->width;
-  ypixels = f->height;
-  
-  dxneg = (dx < 0) ? 1 : 0;
-  dyneg = (dy < 0) ? 1 : 0;
-  
-  dx = abs(dx);
-  dy = abs(dy);
-  if (dx >= dy) {
-    /* Slope between -1 and 1. */
-    mz = (z2 - z1)/(orig_x2 - orig_x1);    /* Z interpolation slope */
-    if (dxneg) {
-      x = x1;
-      y = y1;
-      x1 = x2;
-      y1 = y2;
-      x2 = x;
-      y2 = y;
-      dyneg = !dyneg;
-    }
-    inc1 = 2*dy;
-    inc2 = 2*(dy-dx);
-    di = 2*dy-dx;
-
-    /* Draw a line using x as independent variable */
-    
-    p = &f->pixels[y1][x1];
-    zbuf = &f->zbuffer[y1][x1];
-    x = x1;
-    while (x <= x2) {
-      /* Do a z-buffer check */
-      z = mz*(x-orig_x1)+z1;
-      if (z <= *zbuf){
-	*p = c;
-	*zbuf = z;
-      }
-      p++;
-      zbuf++;
-      if (di < 0) {
-	di = di + inc1;
-      } else {
-	if (dyneg) {
-	  p = p - xpixels;
-	  zbuf = zbuf - xpixels;
-	  di = di + inc2;
-	} else {
-	  p = p + xpixels;
-	  zbuf = zbuf + xpixels;
-	  di = di + inc2;
-	}
-      }
-      x++;
-    }
-  } else {
-    /* Slope < -1 or > 1 */
-    mz = (z2 - z1)/(double) (orig_y2 - orig_y1);
-    if (dyneg) {
-      x = x1;
-      y = y1;
-      x1 = x2;
-      y1 = y2;
-      x2 = x;
-      y2 = y;
-      dxneg = !dxneg;
-    }
-    inc1 = 2*dx;
-    inc2 = 2*(dx-dy);
-    di = 2*dx-dy;
-
-    /* Draw a line using y as independent variable */
-    
-    p = &f->pixels[y1][x1];
-    zbuf = &f->zbuffer[y1][x1];
-    y = y1;
-    while (y <= y2) {
-      /* Do a z-buffer check */
-      z = mz*(y-orig_y1)+z1;
-      if (z <= *zbuf) {
-	*p = c;
-	*zbuf = z;
-      }
-      p = p + xpixels;
-      zbuf = zbuf + xpixels;
-      if (di < 0) {
-	di = di + inc1;
-      } else {
-	if (dxneg) {
-	  p = p - 1;
-	  zbuf = zbuf - 1;
-	  di = di + inc2;
-	} else {
-	  p = p + 1;
-	  zbuf = zbuf + 1;
-	  di = di + inc2;
-	}
-      }
-      y++;
-    }
-  }    
-}
-
-/* ---------------------------------------------------------------------------
-   Plot3D_line(Plot3D *p3, double x1, double y1, double z1, double x2, double y2, double z2,int color)
-
-   Draws a line in 3D space.   This is done as follows (for lack of a better
-   method).
-
-   1.  The points (x1,y1,z1) and (x2,y2,z2) are transformed into screen coordinates
-   2.  We draw the line using a modified Bresenham line algorithm.
-   3.  Zbuffer values are linearly interpolated between the two points.
-   ---------------------------------------------------------------------------- */
-
-void
-Plot3D_line(Plot3D *p3, double fx1, double fy1, double fz1, double fx2, double fy2,
-	    double fz2, Pixel c) {
-
-  /* 3D Transformation parameters */
-  GL_Vector t;
-  double    invw;
-  int       x1,y1,x2,y2;
-  Zvalue    z1,z2;
-  
-  /* Transform the two points into screen coordinates */
-  
-  Matrix_transform4(p3->trans_mat,fx1,fy1,fz1,1,&t);  /* Point 1 */
-  invw = 1.0/t.w;
-  t.x = t.x *invw;
-  t.y = t.y *invw;
-  t.z = t.z *invw;
-  x1 = (int) ((t.x +p3->xshift)*p3->zoom*p3->width + 0.5) + p3->view_xmin; 
-  y1 = (int) ((t.y +p3->yshift)*p3->zoom*p3->height + 0.5) + p3->view_ymin;
-  z1 = t.z;
-  
-  Matrix_transform4(p3->trans_mat,fx2,fy2,fz2,1,&t);  /* Point 2 */
-  invw = 1.0/t.w;
-  t.x = t.x *invw;
-  t.y = t.y *invw;
-  t.z = t.z *invw;
-  x2 = (int) ((t.x +p3->xshift)*p3->zoom*p3->width + 0.5) + p3->view_xmin; 
-  y2 = (int) ((t.y +p3->yshift)*p3->zoom*p3->height + 0.5) + p3->view_ymin;
-  z2 = t.z;
-  Plot3D_linetransform(p3,x1,y1,z1,x2,y2,z2,c);
-}
-
-
-/* -------------------------------------------------------------------------
-   Plot3D_triangle(Plot3D *p3, double x1, double y1, double z1,
-                               double x2, double y2, double z2,
-			       double x3, double y3, double z3,
-			       Pixel fillcolor)
-
-   This function draws a 3D z-buffered outline triangle.
-   -------------------------------------------------------------------------- */
-
-void Plot3D_triangle(Plot3D *p3, double x1, double y1, double z1,
-		     double x2, double y2, double z2,
-		     double x3, double y3, double z3, Pixel color) {
-
-  int        tx1, tx2, tx3, ty1, ty2, ty3;
-  Zvalue     tz1, tz2, tz3;
-  GL_Vector  t;
-  double     invw;
-  
-  /* Transform the three points into screen coordinates */
-
-  Matrix_transform4(p3->trans_mat,x1,y1,z1,1,&t);  /* Point 1 */
-  invw = 1.0/t.w;
-  t.x = t.x *invw;
-  t.y = t.y *invw;
-  t.z = t.z *invw;
-  tx1 = (int) ((t.x +p3->xshift)*p3->zoom*p3->width + 0.5) + p3->view_xmin; 
-  ty1 = (int) ((t.y +p3->yshift)*p3->zoom*p3->height + 0.5) + p3->view_ymin;
-  tz1 = (Zvalue) t.z;
-  
-  Matrix_transform4(p3->trans_mat,x2,y2,z2,1,&t);  /* Point 2 */
-  invw = 1.0/t.w;
-  t.x = t.x *invw;
-  t.y = t.y *invw;
-  t.z = t.z *invw;
-  tx2 = (int) ((t.x +p3->xshift)*p3->zoom*p3->width + 0.5) + p3->view_xmin; 
-  ty2 = (int) ((t.y +p3->yshift)*p3->zoom*p3->height + 0.5) + p3->view_ymin;
-  tz2 = (Zvalue) t.z;
-
-  Matrix_transform4(p3->trans_mat,x3,y3,z3,1,&t);  /* Point 3 */
-  invw = 1.0/t.w;
-  t.x = t.x *invw;
-  t.y = t.y *invw;
-  t.z = t.z *invw;
-  tx3 = (int) ((t.x +p3->xshift)*p3->zoom*p3->width + 0.5) + p3->view_xmin; 
-  ty3 = (int) ((t.y +p3->yshift)*p3->zoom*p3->height + 0.5) + p3->view_ymin;
-  tz3 = (Zvalue) t.z;
-
-
-  Plot3D_linetransform(p3,tx1,ty1,tz1,tx2,ty2,tz2,color);
-  Plot3D_linetransform(p3,tx1,ty1,tz1,tx3,ty3,tz3,color);
-  Plot3D_linetransform(p3,tx2,ty2,tz2,tx3,ty3,tz3,color);
-}
-
-
-/* -------------------------------------------------------------------------
-   Plot3D_solidtriangletransform(Plot3D *p3, int tx1, int ty2, Zvalue tz1,
-                                 int tx2, int ty2, Zvalue tz2,
-				 int tx3, int ty3, Zvalue tz3, Pixel color) 
-
-   This function draws a 3D z-buffered filled triangle.   Assumes three
-   points have already been transformed into screen coordinates.
-
-   General idea :
-         1.   Transform the three points into screen coordinates
-	 2.   Order three points vertically on screen.
-	 3.   Check for degenerate cases (where 3 points are colinear).
-	 4.   Fill in the resulting triangle using horizontal lines.
-   -------------------------------------------------------------------------- */
-
-void Plot3D_solidtriangletransform(Plot3D *p3, int tx1, int ty1, Zvalue tz1,
-				   int tx2, int ty2, Zvalue tz2,
-				   int tx3, int ty3, Zvalue tz3, Pixel color) {
-  int        tempx, tempy;
-  Zvalue     tempz;
-  double     m1,m2,m3, mz1, mz2, mz3;
-  int        y;
-  int        ix1, ix2;
-  Zvalue     zz1, zz2;
-  FrameBuffer *f;
-  register   double fy1,fy2;
-  register   Zvalue fz1,fz2;
-
-  f = p3->frame;
-
-  /* Check for degenerate cases here */
-
-  if ((ty1 == ty2) && (ty2 == ty3)) {
-    if (tx2 < tx1) {   /* Swap points 1 and 2 if 2 is higher */
-      tempx = tx1;
-      tempz = tz1;
-      tx1 = tx2;
-      tz1 = tz2;
-      tx2 = tempx;
-      tz2 = tempz;
-    }
-    if (tx3 < tx1) {  /* Swap points 1 and 3 if 3 is higher */
-      tempx = tx1;
-      tempz = tz1;
-      tx1 = tx3;
-      tz1 = tz3;
-      tx3 = tempx;
-      tz3 = tempz;
-    }
-    if (tx3 < tx2) { /* Swap points 2 and 3 if 3 is higher */ 
-      tempx = tx2;
-      tempz = tz2;
-      tx2 = tx3;
-      tz2 = tz3;
-      tx3 = tempx;
-      tz3 = tempz;
-    }
-
-    /* Points are aligned horizontally.   Handle as a special case */
-    /* Just draw three lines using the outline color */
-
-    Plot3D_horizontal(p3,tx1,tx2,ty1,tz1,tz3,color);
-
-    /*    Plot3D_linetransform(p3,tx1,ty1,tz1,tx2,ty2,tz2,color);
-    Plot3D_linetransform(p3,tx1,ty1,tz1,tx3,ty3,tz3,color);
-    Plot3D_linetransform(p3,tx2,ty2,tz2,tx3,ty3,tz3,color);
-    */
-
-    return;
-  }
-
-  /* Figure out which point has the greatest "y" value */
-
-  if (ty2 > ty1) {   /* Swap points 1 and 2 if 2 is higher */
-    tempx = tx1;
-    tempy = ty1;
-    tempz = tz1;
-    tx1 = tx2;
-    ty1 = ty2;
-    tz1 = tz2;
-    tx2 = tempx;
-    ty2 = tempy;
-    tz2 = tempz;
-  }
-  if (ty3 > ty1) {  /* Swap points 1 and 3 if 3 is higher */
-    tempx = tx1;
-    tempy = ty1;
-    tempz = tz1;
-    tx1 = tx3;
-    ty1 = ty3;
-    tz1 = tz3;
-    tx3 = tempx;
-    ty3 = tempy;
-    tz3 = tempz;
-  }
-  if (ty3 > ty2) { /* Swap points 2 and 3 if 3 is higher */ 
-    tempx = tx2;
-    tempy = ty2;
-    tempz = tz2;
-    tx2 = tx3;
-    ty2 = ty3;
-    tz2 = tz3;
-    tx3 = tempx;
-    ty3 = tempy;
-    tz3 = tempz;
-  }
-
-  /* Points are now order so that t_1 is the highest point, t_2 is the
-     middle point, and t_3 is the lowest point */
-
-    if (ty2 < ty1) {
-      /* First process line segments between (x1,y1)-(x2,y2)
-	 And between (x1,y1),(x3,y3) */
-
-      m1 = (double) (tx2 - tx1)/(double) (ty2 - ty1);
-      m2 = (double) (tx3 - tx1)/(double) (ty3 - ty1);
-      mz1 = (tz2 - tz1)/(double) (ty2 - ty1);
-      mz2 = (tz3 - tz1)/(double) (ty3 - ty1);
-
-      y = ty1;
-      fy1 = m1*(y-ty1)+0.5 + tx1;
-      fy2 = m2*(y-ty1)+0.5 + tx1;
-      fz1 = mz1*(y-ty1) + tz1;
-      fz2 = mz2*(y-ty1) + tz1;
-      while (y >= ty2) {
-	/* Replace with bresenham scheme */
-	/* Calculate x values from slope */
-	ix1 = (int) fy1;
-	ix2 = (int) fy2;
-	zz1 = fz1;
-	zz2 = fz2;
-	fy1-= m1;
-	fy2-= m2;
-	fz1-= mz1;
-	fz2-= mz2;
-	if (ix1 > ix2) 
-	  Plot3D_horizontal(p3,ix2,ix1,y,zz2,zz1,color);
-	else
-	  Plot3D_horizontal(p3,ix1,ix2,y,zz1,zz2,color);
-	y--;
-      }
-    }
-    if (ty3 < ty2) {
-      /* Draw lower half of the triangle */
-      m2 = (double) (tx3 - tx1)/(double) (ty3 - ty1);
-      m3 = (double) (tx3 - tx2)/(double)(ty3 - ty2);
-      mz2 = (tz3 - tz1)/(double) (ty3 - ty1);
-      mz3 = (tz3 - tz2)/(double) (ty3 - ty2);
-      y = ty2;
-      while (y >= ty3) {
-	ix1 = (int) (m3*(y-ty2)+0.5)+tx2;
-	ix2 = (int) (m2*(y-ty1)+0.5)+tx1;
-	zz1 = mz3*(y-ty2)+tz2;
-	zz2 = mz2*(y-ty1)+tz1;
-	if (ix1 > ix2)
-	  Plot3D_horizontal(p3,ix2,ix1,y,zz2,zz1,color);
-	else
-	  Plot3D_horizontal(p3,ix1,ix2,y,zz1,zz2,color);
-	y--;
-      }
-    }
-}
-
-/* -------------------------------------------------------------------------
-   Plot3D_solidtriangle(Plot3D *p3, double x1, double y1, double z1,
-                               double x2, double y2, double z2,
-			       double x3, double y3, double z3,
-			       Pixel color)
-
-   This function draws a 3D z-buffered filled triangle.    Can be used to
-   draw other primitives such as quadralaterals, etc...
-
-   This function simply transforms the given points and calls
-   Plot3D_SolidTriangleTransform().
-   -------------------------------------------------------------------------- */
-
-void Plot3D_solidtriangle(Plot3D *p3, double x1, double y1, double z1,
-			  double x2, double y2, double z2,
-			  double x3, double y3, double z3, Pixel color) {
-
-  int        tx1, tx2, tx3, ty1, ty2, ty3;
-  Zvalue     tz1, tz2, tz3;
-  GL_Vector  t;
-  double     invw;
-  Matrix     a;
-  register double     xshift, yshift, zoom, width, height, view_xmin, view_ymin;
-
-  a = p3->trans_mat;
-  xshift = p3->xshift;
-  yshift = p3->yshift;
-  zoom = p3->zoom;
-  height = p3->height;
-  width = p3->width;
-  view_xmin = p3->view_xmin;
-  view_ymin = p3->view_ymin;
-
-  /* Transform the three points into screen coordinates */
-
-  t.w = a[12]*x1 + a[13]*y1 + a[14]*z1 + a[15];
-  invw = 1.0/t.w;
-  t.x = (a[0]*x1 + a[1]*y1 + a[2]*z1 + a[3])*invw;
-  t.y = (a[4]*x1 + a[5]*y1 + a[6]*z1 + a[7])*invw;
-  t.z = (a[8]*x1 + a[9]*y1 + a[10]*z1 + a[11])*invw;
-
-  tx1 = (int) ((t.x +xshift)*zoom*width + 0.5) + view_xmin; 
-  ty1 = (int) ((t.y +yshift)*zoom*height + 0.5) + view_ymin;
-  tz1 = (Zvalue) t.z;
-
-
-  t.w = a[12]*x2 + a[13]*y2 + a[14]*z2 + a[15];
-  invw = 1.0/t.w;
-  t.x = (a[0]*x2 + a[1]*y2 + a[2]*z2 + a[3])*invw;
-  t.y = (a[4]*x2 + a[5]*y2 + a[6]*z2 + a[7])*invw;
-  t.z = (a[8]*x2 + a[9]*y2 + a[10]*z2 + a[11])*invw;
-  tx2 = (int) ((t.x +xshift)*zoom*width + 0.5) + view_xmin; 
-  ty2 = (int) ((t.y +yshift)*zoom*height + 0.5) + view_ymin;
-  tz2 = (Zvalue) t.z;
-
-  t.w = a[12]*x3 + a[13]*y3 + a[14]*z3 + a[15];
-  invw = 1.0/t.w;
-  t.x = (a[0]*x3 + a[1]*y3 + a[2]*z3 + a[3])*invw;
-  t.y = (a[4]*x3 + a[5]*y3 + a[6]*z3 + a[7])*invw;
-  t.z = (a[8]*x3 + a[9]*y3 + a[10]*z3 + a[11])*invw;
-  tx3 = (int) ((t.x +xshift)*zoom*width + 0.5) + view_xmin; 
-  ty3 = (int) ((t.y +yshift)*zoom*height + 0.5) + view_ymin;
-  tz3 = (Zvalue) t.z;
-
-  Plot3D_solidtriangletransform(p3,tx1,ty1,tz1,tx2,ty2,tz2,tx3,ty3,tz3,color); 
-  
-}    
-
-
-/* -------------------------------------------------------------------------
-   Plot3D_horizontalinterp(Plot3D *p3, int xmin, int xmax, int y,
-                           double z1, double z2, Pixel c1, Pixel c2)
-
-   Draws a "Horizontal" line on the framebuffer between two screen coordinates,
-   but also supplies z-values and zbuffering.  Performs a color interpolation
-   between c1 and c2.  This is primarily used by the SolidTriangleInterp()
-   function to give the illusion of smooth surfaces.
-   -------------------------------------------------------------------------- */
-
-void Plot3D_horizontalinterp(Plot3D *p3, int xmin, int xmax, int y,
-			     Zvalue z1, Zvalue z2, Pixel c1, Pixel c2) {
-  Pixel  *p;
-  FrameBuffer *f;
-  int     i;
-  Zvalue  *zbuf,z,mz;
-  double   mc;
-  int     startx, endx;
-  double   invdx;
-  
-  f = p3->frame;
-  if ((y < f->ymin) || (y >= f->ymax)) return;
-  if (xmin >= f->xmax) return;
-  if (xmin < f->xmin) startx = f->xmin;
-  else startx = xmin;
-  if (xmax < f->xmin) return;
-  if (xmax >= f->xmax) endx = f->xmax - 1;
-  else endx = xmax;
-
-  /* Calculate z slope */
-  if (xmax != xmin) {
-    invdx = 1.0/(double) (xmax-xmin);
-  } else {
-    invdx = 0;
-  }
-
-  mz = (Zvalue) (z2 - z1)*invdx;
-
-  /* Calculate c slope */
-
-  mc = (double) (c2 - c1)*invdx;
-    
-  /* Draw it */
-  
-  p = &f->pixels[y][startx];
-  zbuf = &f->zbuffer[y][startx];
-  for (i = startx; i <= endx; i++, p++, zbuf++) {
-    z = (Zvalue) (mz*(i-xmin) + z1);
-    if (z <= *zbuf) {
-      *p = (Pixel) (mc*(i-xmin)+c1);
-      *zbuf = z;
-    }
-  }
-}
-
-/* -------------------------------------------------------------------------
-   Plot3D_interptriangletransform(Plot3D *p3,
-                                  int tx1, int ty2, Zvalue tz1, Pixel c1,
-                                  int tx2, int ty2, Zvalue tz2, Pixel c2,
-				  int tx3, int ty3, Zvalue tz3, Pixel c3)
-
-   This function draws a 3D z-buffered filled triangle with color
-   interpolation.   Assumes three points have already been transformed
-   into screen coordinates.
-
-   General idea :
-         1.   Transform the three points into screen coordinates
-	 2.   Order three points vertically on screen.
-	 3.   Check for degenerate cases (where 3 points are colinear).
-	 4.   Fill in the resulting triangle using horizontal lines.
-	 5.   Colors are interpolated between end points
-   -------------------------------------------------------------------------- */
-
-void Plot3D_interptriangletransform(Plot3D *p3,
-				    int tx1, int ty1, Zvalue tz1, Pixel c1,
-				    int tx2, int ty2, Zvalue tz2, Pixel c2,
-				    int tx3, int ty3, Zvalue tz3, Pixel c3) {
-  int        tempx, tempy;
-  Zvalue     tempz;
-  double     m1,m2,m3, mz1, mz2, mz3;
-  double     mc1,mc2,mc3;
-  Pixel      ic1,ic2,tempc;
-  int        y;
-  int        ix1, ix2;
-  Zvalue     zz1, zz2;
-  FrameBuffer *f;
-  
-  f = p3->frame;
-
-  /* Figure out which point has the greatest "y" value */
-
-  if (ty2 > ty1) {   /* Swap points 1 and 2 if 2 is higher */
-    tempx = tx1;
-    tempy = ty1;
-    tempz = tz1;
-    tempc = c1;
-    tx1 = tx2;
-    ty1 = ty2;
-    tz1 = tz2;
-    c1 = c2;
-    tx2 = tempx;
-    ty2 = tempy;
-    tz2 = tempz;
-    c2 = tempc;
-  }
-  if (ty3 > ty1) {  /* Swap points 1 and 3 if 3 is higher */
-    tempx = tx1;
-    tempy = ty1;
-    tempz = tz1;
-    tempc = c1;
-    tx1 = tx3;
-    ty1 = ty3;
-    tz1 = tz3;
-    c1 = c3;
-    tx3 = tempx;
-    ty3 = tempy;
-    tz3 = tempz;
-    c3 = tempc;
-  }
-  if (ty3 > ty2) { /* Swap points 2 and 3 if 3 is higher */ 
-    tempx = tx2;
-    tempy = ty2;
-    tempz = tz2;
-    tempc = c2;
-    tx2 = tx3;
-    ty2 = ty3;
-    tz2 = tz3;
-    c2 = c3;
-    tx3 = tempx;
-    ty3 = tempy;
-    tz3 = tempz;
-    c3 = tempc;
-  }
-
-  /* Points are now order so that t_1 is the highest point, t_2 is the
-     middle point, and t_3 is the lowest point */
-
-  /* Check for degenerate cases here */
-
-  if ((ty1 == ty2) && (ty2 == ty3)) {
-
-    /* Points are aligned horizontally.   Handle as a special case */
-    /* Just draw three lines using the outline color */
-
-    if (tx2 > tx1)
-      Plot3D_horizontalinterp(p3,tx1,tx2,ty1,tz1,tz2,c1,c2);
-    else
-      Plot3D_horizontalinterp(p3,tx2,tx1,ty1,tz2,tz1,c2,c1);
-    if (tx3 > tx1)
-      Plot3D_horizontalinterp(p3,tx1,tx3,ty1,tz1,tz3,c1,c3);
-    else
-      Plot3D_horizontalinterp(p3,tx3,tx1,ty1,tz3,tz1,c3,c1);
-    if (tx3 > tx2)
-      Plot3D_horizontalinterp(p3,tx2,tx3,ty2,tz2,tz3,c2,c3);
-    else
-      Plot3D_horizontalinterp(p3,tx3,tx2,ty2,tz3,tz2,c3,c2);
-    
-  } else {
-
-    /* First process line segments between (x1,y1)-(x2,y2)
-       And between (x1,y1),(x3,y3) */
-
-    if (ty2 < ty1) {
-      m1 = (double) (tx2 - tx1)/(double) (ty2 - ty1);
-      m2 = (double) (tx3 - tx1)/(double) (ty3 - ty1);
-      mz1 = (tz2 - tz1)/(double) (ty2 - ty1);
-      mz2 = (tz3 - tz1)/(double) (ty3 - ty1);
-      mc1 = (c2 - c1)/(double) (ty2 - ty1);
-      mc2 = (c3 - c1)/(double) (ty3 - ty1);
-
-      y = ty1;
-      while (y >= ty2) {
-	/* Calculate x values from slope */
-	ix1 = (int) (m1*(y-ty1)+0.5) + tx1;
-	ix2 = (int) (m2*(y-ty1)+0.5) + tx1;
-	zz1 = mz1*(y-ty1) + tz1;
-	zz2 = mz2*(y-ty1) + tz1;
-	ic1 = mc1*(y-ty1) + c1;
-	ic2 = mc2*(y-ty1) + c1;
-	if (ix1 > ix2) 
-	  Plot3D_horizontalinterp(p3,ix2,ix1,y,zz2,zz1,ic2,ic1);
-	else
-	  Plot3D_horizontalinterp(p3,ix1,ix2,y,zz1,zz2,ic1,ic2);
-	y--;
-      }
-    }
-    if (ty3 < ty2) {
-      /* Draw lower half of the triangle */
-      m2 = (double) (tx3 - tx1)/(double) (ty3 - ty1);
-      mz2 = (tz3 - tz1)/(double) (ty3 - ty1);
-      mc2 = (c3 - c1)/(double) (ty3 - ty1);
-      m3 = (double) (tx3 - tx2)/(double)(ty3 - ty2);
-      mz3 = (tz3 - tz2)/(double) (ty3 - ty2);
-      mc3 = (c3 - c2)/(double) (ty3 - ty2);
-      y = ty2;
-      while (y >= ty3) {
-	ix1 = (int) (m3*(y-ty2)+0.5)+tx2;
-	ix2 = (int) (m2*(y-ty1)+0.5)+tx1;
-	zz1 = mz3*(y-ty2)+tz2;
-	zz2 = mz2*(y-ty1)+tz1;
-	ic1 = mc3*(y-ty2)+c2;
-	ic2 = mc2*(y-ty1)+c1;
-	if (ix1 > ix2)
-	  Plot3D_horizontalinterp(p3,ix2,ix1,y,zz2,zz1,ic2,ic1);
-	else
-	  Plot3D_horizontalinterp(p3,ix1,ix2,y,zz1,zz2,ic1,ic2);
-	y--;
-      }
-    }
-  }
-}
-
-/* -------------------------------------------------------------------------
-   Plot3D_interptriangle(Plot3D *p3,
-                         double x1, double y1, double z1, Pixel c1,
-			 double x2, double y2, double z2, Pixel c2,
-			 double x3, double y3, double z3, Pixel c3)
-
-   This function draws a 3D z-buffered filled triangle with color
-   interpolation.
-
-   This function simply transforms the given points and calls
-   Plot3D_InterpTriangleTransform().
-   -------------------------------------------------------------------------- */
-
-void Plot3D_interptriangle(Plot3D *p3,
-			   double x1, double y1, double z1, Pixel c1,
-			   double x2, double y2, double z2, Pixel c2,
-			   double x3, double y3, double z3, Pixel c3) {
-
-  int        tx1, tx2, tx3, ty1, ty2, ty3;
-  Zvalue     tz1, tz2, tz3;
-  GL_Vector  t;
-  double     invw;
-  
-  /* Transform the three points into screen coordinates */
-
-  Matrix_transform4(p3->trans_mat,x1,y1,z1,1,&t);  /* Point 1 */
-  invw = 1.0/t.w;
-  t.x = t.x *invw;
-  t.y = t.y *invw;
-  t.z = t.z *invw;
-  tx1 = (int) ((t.x +p3->xshift)*p3->zoom*p3->width + 0.5) + p3->view_xmin; 
-  ty1 = (int) ((t.y +p3->yshift)*p3->zoom*p3->height + 0.5) + p3->view_ymin;
-  tz1 = (Zvalue) t.z;
-  
-  Matrix_transform4(p3->trans_mat,x2,y2,z2,1,&t);  /* Point 2 */
-  invw = 1.0/t.w;
-  t.x = t.x *invw;
-  t.y = t.y *invw;
-  t.z = t.z *invw;
-  tx2 = (int) ((t.x +p3->xshift)*p3->zoom*p3->width + 0.5) + p3->view_xmin; 
-  ty2 = (int) ((t.y +p3->yshift)*p3->zoom*p3->height + 0.5) + p3->view_ymin;
-  tz2 = (Zvalue) t.z;
-
-  Matrix_transform4(p3->trans_mat,x3,y3,z3,1,&t);  /* Point 3 */
-  invw = 1.0/t.w;
-  t.x = t.x *invw;
-  t.y = t.y *invw;
-  t.z = t.z *invw;
-  tx3 = (int) ((t.x +p3->xshift)*p3->zoom*p3->width + 0.5) + p3->view_xmin; 
-  ty3 = (int) ((t.y +p3->yshift)*p3->zoom*p3->height + 0.5) + p3->view_ymin;
-  tz3 = (Zvalue) t.z;
-
-  Plot3D_interptriangletransform(p3,tx1,ty1,tz1,c1,tx2,ty2,tz2,c2,tx3,ty3,tz3,c3);
-}    
-
-/* -------------------------------------------------------------------------
-   Plot3D_quad(Plot3D *p3, double x1, double y1, double z1,
-                           double x2, double y2, double z2,
-    		           double x3, double y3, double z3,
-			   double x4, double y4, double z4,
- 		           Pixel fillcolor)
-
-   This function draws a 3D outlined Quadralateral.  Used primarily for
-   drawing meshes and other things.
-
-   Plotting is done in the following order :
-       (x1,y1,z1)  --> (x2,y2,z2)
-       (x2,y2,z2)  --> (x3,y3,z3)
-       (x3,y3,z3)  --> (x4,y4,z4)
-       (x4,y4,z4)  --> (x1,y1,z1)
-   -------------------------------------------------------------------------- */
-
-void Plot3D_quad(Plot3D *p3, double x1, double y1, double z1,
-		 double x2, double y2, double z2,
-		 double x3, double y3, double z3,
-		 double x4, double y4, double z4,
-		 Pixel color) {
-
-  int        tx1, tx2, tx3, tx4, ty1, ty2, ty3, ty4;
-  Zvalue     tz1, tz2, tz3, tz4;
-  GL_Vector  t;
-  double     invw;
-  
-  /* Transform the three points into screen coordinates */
-
-  Matrix_transform4(p3->trans_mat,x1,y1,z1,1,&t);  /* Point 1 */
-  invw = 1.0/t.w;
-  t.x = t.x *invw;
-  t.y = t.y *invw;
-  t.z = t.z *invw;
-  tx1 = (int) ((t.x +p3->xshift)*p3->zoom*p3->width + 0.5) + p3->view_xmin; 
-  ty1 = (int) ((t.y +p3->yshift)*p3->zoom*p3->height + 0.5) + p3->view_ymin;
-  tz1 = (Zvalue) t.z;
-  
-  Matrix_transform4(p3->trans_mat,x2,y2,z2,1,&t);  /* Point 2 */
-  invw = 1.0/t.w;
-  t.x = t.x *invw;
-  t.y = t.y *invw;
-  t.z = t.z *invw;
-  tx2 = (int) ((t.x +p3->xshift)*p3->zoom*p3->width + 0.5) + p3->view_xmin; 
-  ty2 = (int) ((t.y +p3->yshift)*p3->zoom*p3->height + 0.5) + p3->view_ymin;
-  tz2 = (Zvalue) t.z;
-
-  Matrix_transform4(p3->trans_mat,x3,y3,z3,1,&t);  /* Point 3 */
-  invw = 1.0/t.w;
-  t.x = t.x *invw;
-  t.y = t.y *invw;
-  t.z = t.z *invw;
-  tx3 = (int) ((t.x +p3->xshift)*p3->zoom*p3->width + 0.5) + p3->view_xmin; 
-  ty3 = (int) ((t.y +p3->yshift)*p3->zoom*p3->height + 0.5) + p3->view_ymin;
-  tz3 = (Zvalue) t.z;
-
-  Matrix_transform4(p3->trans_mat,x4,y4,z4,1,&t);  /* Point 3 */
-  invw = 1.0/t.w;
-  t.x = t.x *invw;
-  t.y = t.y *invw;
-  t.z = t.z *invw;
-  tx4 = (int) ((t.x +p3->xshift)*p3->zoom*p3->width + 0.5) + p3->view_xmin; 
-  ty4 = (int) ((t.y +p3->yshift)*p3->zoom*p3->height + 0.5) + p3->view_ymin;
-  tz4 = (Zvalue) t.z;
-
-  Plot3D_linetransform(p3,tx1,ty1,tz1,tx2,ty2,tz2,color);
-  Plot3D_linetransform(p3,tx2,ty2,tz2,tx3,ty3,tz3,color);
-  Plot3D_linetransform(p3,tx3,ty3,tz3,tx4,ty4,tz4,color);
-  Plot3D_linetransform(p3,tx4,ty4,tz4,tx1,ty1,tz1,color);
-  
-}
-
-
-/* -------------------------------------------------------------------------
-   Plot3D_solidquad(Plot3D *p3, double x1, double y1, double z1,
-                           double x2, double y2, double z2,
-    		           double x3, double y3, double z3,
-			   double x4, double y4, double z4,
- 		           Pixel fillcolor)
-
-   This function draws a 3D solid Quadralateral. Uses the function
-   Plot3D_SolidTriangleTransform() to fill in the region.
-
-   Plotting is done in the following order :
-       (x1,y1,z1)  --> (x2,y2,z2)
-       (x2,y2,z2)  --> (x3,y3,z3)
-       (x3,y3,z3)  --> (x4,y4,z4)
-       (x4,y4,z4)  --> (x1,y1,z1)
-   -------------------------------------------------------------------------- */
-
-void Plot3D_solidquad(Plot3D *p3, double x1, double y1, double z1,
-		 double x2, double y2, double z2,
-		 double x3, double y3, double z3,
-		 double x4, double y4, double z4,
-		 Pixel color) {
-
-  int        tx1, tx2, tx3, tx4, ty1, ty2, ty3, ty4;
-  Zvalue     tz1, tz2, tz3, tz4;
-  GL_Vector  t;
-  double     invw;
-  
-  /* Transform the three points into screen coordinates */
-
-  Matrix_transform4(p3->trans_mat,x1,y1,z1,1,&t);  /* Point 1 */
-  invw = 1.0/t.w;
-  t.x = t.x *invw;
-  t.y = t.y *invw;
-  t.z = t.z *invw;
-  tx1 = (int) ((t.x +p3->xshift)*p3->zoom*p3->width + 0.5) + p3->view_xmin; 
-  ty1 = (int) ((t.y +p3->yshift)*p3->zoom*p3->height + 0.5) + p3->view_ymin;
-  tz1 = (Zvalue) t.z;
-  
-  Matrix_transform4(p3->trans_mat,x2,y2,z2,1,&t);  /* Point 2 */
-  invw = 1.0/t.w;
-  t.x = t.x *invw;
-  t.y = t.y *invw;
-  t.z = t.z *invw;
-  tx2 = (int) ((t.x +p3->xshift)*p3->zoom*p3->width + 0.5) + p3->view_xmin; 
-  ty2 = (int) ((t.y +p3->yshift)*p3->zoom*p3->height + 0.5) + p3->view_ymin;
-  tz2 = (Zvalue) t.z;
-
-  Matrix_transform4(p3->trans_mat,x3,y3,z3,1,&t);  /* Point 3 */
-  invw = 1.0/t.w;
-  t.x = t.x *invw;
-  t.y = t.y *invw;
-  t.z = t.z *invw;
-  tx3 = (int) ((t.x +p3->xshift)*p3->zoom*p3->width + 0.5) + p3->view_xmin; 
-  ty3 = (int) ((t.y +p3->yshift)*p3->zoom*p3->height + 0.5) + p3->view_ymin;
-  tz3 = (Zvalue) t.z;
-
-  Matrix_transform4(p3->trans_mat,x4,y4,z4,1,&t);  /* Point 3 */
-  invw = 1.0/t.w;
-  t.x = t.x *invw;
-  t.y = t.y *invw;
-  t.z = t.z *invw;
-  tx4 = (int) ((t.x +p3->xshift)*p3->zoom*p3->width + 0.5) + p3->view_xmin; 
-  ty4 = (int) ((t.y +p3->yshift)*p3->zoom*p3->height + 0.5) + p3->view_ymin;
-  tz4 = (Zvalue) t.z;
-
-  Plot3D_solidtriangletransform(p3,tx1,ty1,tz1,tx2,ty2,tz2,tx3,ty3,tz3,color);
-  Plot3D_solidtriangletransform(p3,tx1,ty1,tz1,tx4,ty4,tz4,tx3,ty3,tz3,color);
-}
-
-/* -------------------------------------------------------------------------
-   Plot3D_interpquad(Plot3D *p3, double x1, double y1, double z1, Pixel c1,
-                           double x2, double y2, double z2, Pixel c2,
-    		           double x3, double y3, double z3, Pixel c3,
-			   double x4, double y4, double z4, Pixel c4)
-
-   This function draws a 3D color-interpolated Quadralateral. Uses the function
-   Plot3D_InterpTriangleTransform() to fill in the region.
-
-   Plotting is done in the following order :
-       (x1,y1,z1)  --> (x2,y2,z2)
-       (x2,y2,z2)  --> (x3,y3,z3)
-       (x3,y3,z3)  --> (x4,y4,z4)
-       (x4,y4,z4)  --> (x1,y1,z1)
-   -------------------------------------------------------------------------- */
-
-void Plot3D_interpquad(Plot3D *p3, double x1, double y1, double z1, Pixel c1,
-		       double x2, double y2, double z2, Pixel c2,
-		       double x3, double y3, double z3, Pixel c3,
-		       double x4, double y4, double z4, Pixel c4) {
-
-
-  int        tx1, tx2, tx3, tx4, ty1, ty2, ty3, ty4;
-  Zvalue     tz1, tz2, tz3, tz4;
-  GL_Vector  t;
-  double     invw;
-  
-  /* Transform the three points into screen coordinates */
-
-  Matrix_transform4(p3->trans_mat,x1,y1,z1,1,&t);  /* Point 1 */
-  invw = 1.0/t.w;
-  t.x = t.x *invw;
-  t.y = t.y *invw;
-  t.z = t.z *invw;
-  tx1 = (int) ((t.x +p3->xshift)*p3->zoom*p3->width + 0.5) + p3->view_xmin; 
-  ty1 = (int) ((t.y +p3->yshift)*p3->zoom*p3->height + 0.5) + p3->view_ymin;
-  tz1 = (Zvalue) t.z;
-  
-  Matrix_transform4(p3->trans_mat,x2,y2,z2,1,&t);  /* Point 2 */
-  invw = 1.0/t.w;
-  t.x = t.x *invw;
-  t.y = t.y *invw;
-  t.z = t.z *invw;
-  tx2 = (int) ((t.x +p3->xshift)*p3->zoom*p3->width + 0.5) + p3->view_xmin; 
-  ty2 = (int) ((t.y +p3->yshift)*p3->zoom*p3->height + 0.5) + p3->view_ymin;
-  tz2 = (Zvalue) t.z;
-
-  Matrix_transform4(p3->trans_mat,x3,y3,z3,1,&t);  /* Point 3 */
-  invw = 1.0/t.w;
-  t.x = t.x *invw;
-  t.y = t.y *invw;
-  t.z = t.z *invw;
-  tx3 = (int) ((t.x +p3->xshift)*p3->zoom*p3->width + 0.5) + p3->view_xmin; 
-  ty3 = (int) ((t.y +p3->yshift)*p3->zoom*p3->height + 0.5) + p3->view_ymin;
-  tz3 = (Zvalue) t.z;
-
-  Matrix_transform4(p3->trans_mat,x4,y4,z4,1,&t);  /* Point 3 */
-  invw = 1.0/t.w;
-  t.x = t.x *invw;
-  t.y = t.y *invw;
-  t.z = t.z *invw;
-  tx4 = (int) ((t.x +p3->xshift)*p3->zoom*p3->width + 0.5) + p3->view_xmin; 
-  ty4 = (int) ((t.y +p3->yshift)*p3->zoom*p3->height + 0.5) + p3->view_ymin;
-  tz4 = (Zvalue) t.z;
-
-  Plot3D_interptriangletransform(p3,tx1,ty1,tz1,c1,tx2,ty2,tz2,c2,tx3,ty3,tz3,c3);
-  Plot3D_interptriangletransform(p3,tx1,ty1,tz1,c1,tx4,ty4,tz4,c4,tx3,ty3,tz3,c3);
-  
-}
-
-/* --------------------------------------------------------------------------
-   Plot3D_solidsphere(Plot3 *p3, double x, double y, double z, double radius,
-                      Pixel c)
-
-   Makes a 3D sphere at x,y,z with given radius and color. 
-
-   Basic strategy :
-      1.  Transform point to screen coordinates
-      2.  Figure out what the radius is in screen coordinates
-      3.  Use bresenham algorithm for large spheres
-      4.  Use bitmaps for small spheres
-   -------------------------------------------------------------------------- */
-
-/* This is used to fill in spheres */
-static int s_xmin;
-static int s_ymin;
-static int s_xmax;
-static int s_ymax;
-static Pixel **s_pixels;
-static Zvalue **s_zbuffer;
-
-void Plot3D_spherehorizontal(int xmin, int xmax, int y, Zvalue z, Pixel color) {
-  int     i;
-  int     startx, endx;
-  Pixel   *p;
-  Zvalue  *zbuf;
-  
-  if ((y < s_ymin) || (y >= s_ymax)) return;
-  if (xmin < s_xmin) startx = s_xmin;
-  else startx = xmin;
-  if (xmax >= s_xmax) endx = s_xmax - 1;
-  else endx = xmax;
-
-  /* Draw it */
-  
-  p = &s_pixels[y][xmin];
-  zbuf = &s_zbuffer[y][xmin];
-  for (i = startx; i <= endx; i++, p++, zbuf++) {
-    if (z <= *zbuf) {
-      *p = color;
-      *zbuf = z;
-    }
-  }
-}
-
-void Plot3D_solidsphere(Plot3D *p3, double x, double y, double z, double radius,
-			Pixel c) {
-
-  GL_Vector  t,r;
-  double     rad;
-  int        tx,ty, irad;
-  Zvalue     tz;
-  double     invw;
-  int        ix, iy, ix1,ix2,p;
-  FrameBuffer *f;
-
-  /* First transform the point into model coordinates */
-
-  Matrix_transform4(p3->fullmodel_mat,x,y,z,1,&t);  
-
-  /* Now transform two points in order to find proper sphere radius */
-
-  Matrix_transform4(p3->view_mat,t.x+radius,t.y,t.z,t.w,&r);  /* transform radius */
-  Matrix_transform4(p3->view_mat,t.x,t.y,t.z,t.w,&t);
-
-  invw = 1.0/t.w;
-  t.x = t.x*invw;
-  t.y = t.y*invw;
-  t.z = t.z*invw;
-  invw = 1.0/r.w;
-  r.x = r.x*invw;
-  r.y = r.y*invw;
-  r.z = r.z*invw;
-  invw = 1.0/r.w;
-  
-  rad = fabs(t.x - r.x);
-  
-  /* Transform everything into screen coordinates */
-  
-  tx = (int) ((t.x +p3->xshift)*p3->zoom*p3->width + 0.5) + p3->view_xmin; 
-  ty = (int) ((t.y +p3->yshift)*p3->zoom*p3->height + 0.5) + p3->view_ymin;
-  tz = (Zvalue) t.z;
-  irad = (int) (p3->zoom*(rad*p3->width + 0.5));
-
-  /* This is only a temporary solution (maybe). */
-         
-#define fill_zcircle(x,y,c) \
-  ix1 = tx - x; \
-  ix2 = tx + x; \
-  if (ix1 < s_xmin) ix1 = s_xmin; \
-  if (ix2 >= s_xmax) ix2 = s_xmax; \
-  Plot3D_spherehorizontal(ix1,ix2,y,tz,c);
-  
-  f = p3->frame;
-  s_xmin = f->xmin;
-  s_ymin = f->ymin;
-  s_xmax = f->xmax;
-  s_ymax = f->ymax;
-  s_pixels = f->pixels;
-  s_zbuffer = f->zbuffer;
-  if (irad <= 1) {
-    /* Plot a single pixel */
-    if ((tx >= f->xmin) && (tx < f->xmax)) {
-      if ((ty >= f->ymin) && (ty <f->ymax)) {
-        if (tz <= f->zbuffer[ty][tx]) {
-	  f->pixels[ty][tx] = c;
-	  f->zbuffer[ty][tx] = tz;
-	}
-      }
-    }
-    return;
-  }
-  ix = 0;
-  iy = irad;
-  p = 3-2*irad;
-  while (ix <= iy) {
-    fill_zcircle(ix,ty+iy,c);
-    fill_zcircle(ix,ty-iy,c);
-    fill_zcircle(iy,ty+ix,c);
-    fill_zcircle(iy,ty-ix,c);
-    if (p < 0) p = p + 4*ix + 6;
-    else {
-      p = p + 4*(ix-iy) + 10;
-      iy = iy -1;
-    }
-    ix++;
-  }
-}
-
-
-/* --------------------------------------------------------------------
-   Plot3D_outlinesphere(Plot3D *p3, double x, double y, double z,
-                        double radius, Pixel color, Pixel bc)
-
-   Draws an outlined sphere.
-   -------------------------------------------------------------------- */
-
-void Plot3D_outlinesphere(Plot3D *p3, double x, double y, double z,
-			  double radius, Pixel c, Pixel bc)
-{
-  GL_Vector  t,r;
-  double     rad;
-  int        tx,ty, irad;
-  Zvalue     tz;
-  double     invw;
-  int        ix, iy, ix1,ix2,p;
-  
-  FrameBuffer *f;
-
-  /* First transform the point into model coordinates */
-
-  Matrix_transform4(p3->fullmodel_mat,x,y,z,1,&t);  
-
-  /* Now transform two points in order to find proper sphere radius */
-
-  Matrix_transform4(p3->view_mat,t.x+radius,t.y,t.z,t.w,&r);  /* transform radius */
-  Matrix_transform4(p3->view_mat,t.x,t.y,t.z,t.w,&t);
-
-  invw = 1.0/t.w;
-  t.x = t.x*invw;
-  t.y = t.y*invw;
-  t.z = t.z*invw;
-  invw = 1.0/r.w;
-  r.x = r.x*invw;
-  r.y = r.y*invw;
-  r.z = r.z*invw;
-  invw = 1.0/r.w;
-  
-  rad = fabs(t.x - r.x);
-  
-  /* Transform everything into screen coordinates */
-  
-  tx = (int) ((t.x +p3->xshift)*p3->zoom*p3->width + 0.5) + p3->view_xmin; 
-  ty = (int) ((t.y +p3->yshift)*p3->zoom*p3->height + 0.5) + p3->view_ymin;
-  tz = (Zvalue) t.z;
-  irad = (int) (p3->zoom*(rad*p3->width + 0.5));
-
-  /* This is only a temporary solution (maybe). */
-#define plot_zcircle(x,y,c) \
-   if ((x >= s_xmin) && (x < s_xmax) && \
-       (y >= s_ymin) && (y < s_ymax)) {\
-         if (tz <= s_zbuffer[y][x]) { \
-             s_pixels[y][x] = c; \
-	     s_zbuffer[y][x] = tz; } \
-   }
-     
-  f = p3->frame;
-  s_xmin = f->xmin;
-  s_ymin = f->ymin;
-  s_xmax = f->xmax;
-  s_ymax = f->ymax;
-  s_pixels = f->pixels;
-  s_zbuffer = f->zbuffer;
-  
-  if (irad <= 1) {
-    /* Plot a single pixel */
-    if ((tx >= f->xmin) && (tx < f->xmax)) {
-      if ((ty >= f->ymin) && (ty <f->ymax)) {
-        if (tz <= f->zbuffer[ty][tx]) {
-	  f->pixels[ty][tx] = c;
-	  f->zbuffer[ty][tx] = tz;
-	}
-      }
-    }
-    return;
-  }
-  ix = 0;
-  iy = irad;
-  p = 3-2*irad;
-  while (ix <= iy) {
-    fill_zcircle(ix,ty+iy,c);
-    fill_zcircle(ix,ty-iy,c);
-    fill_zcircle(iy,ty+ix,c);
-    fill_zcircle(iy,ty-ix,c);
-    
-    plot_zcircle(tx+ix,ty+iy,bc);
-    plot_zcircle(tx-ix,ty+iy,bc);
-    plot_zcircle(tx+ix,ty-iy,bc);
-    plot_zcircle(tx-ix,ty-iy,bc);
-    plot_zcircle(tx+iy,ty+ix,bc);
-    plot_zcircle(tx-iy,ty+ix,bc);
-    plot_zcircle(tx+iy,ty-ix,bc);
-    plot_zcircle(tx-iy,ty-ix,bc);
-    if (p < 0) p = p + 4*ix + 6;
-    else {
-      p = p + 4*(ix-iy) + 10;
-      iy = iy -1;
-    }
-    ix++;
-  }
-}
-
-/* QUAD Test
-   Test out quad functions for graphing */
-
-double zf(double x, double y) {
-  return cos(sqrt(x*x + y*y)*10.0)/(sqrt(x*x+y*y)+1);
-}
-
-void Quad_Test(Plot3D *p3, int npoints) {
-  int i,j;
-  double dx;
-  double x1,y1,z1,x2,y2,z2,x3,y3,z3,x4,y4,z4,za;
-  int c;
-  dx = 2.0/npoints;
-
-  
-  for (i = 0; i < npoints; i++)
-    for (j = 0; j < npoints; j++) {
-      x1 = i*dx + -1.0;
-      y1 = j*dx + -1.0;
-      x2 = x1 + dx;
-      x3 = x1 + dx;
-      x4 = x1;
-      y2 = y1;
-      y3 = y1 + dx;
-      y4 = y1 + dx;
-      z1 = zf(x1,y1);
-      z2 = zf(x2,y2);
-      z3 = zf(x3,y3);
-      z4 = zf(x4,y4);
-      za = 0.25*(z1+z2+z3+z4);
-      c = 16+((za + 1)*120);
-      if (c > 254) c = 254;
-      Plot3D_quad(p3,x1,y1,z1,x2,y2,z2,x3,y3,z3,x4,y4,z4,(Pixel) c);
-    }
-}
-
-
-void Quad_SolidTest(Plot3D *p3, int npoints) {
-  int i,j;
-  double dx;
-  double x1,y1,z1,x2,y2,z2,x3,y3,z3,x4,y4,z4,za;
-  int c;
-  dx = 2.0/npoints;
-
-  
-  for (i = 0; i < npoints; i++)
-    for (j = 0; j < npoints; j++) {
-      x1 = i*dx + -1.0;
-      y1 = j*dx + -1.0;
-      x2 = x1 + dx;
-      x3 = x1 + dx;
-      x4 = x1;
-      y2 = y1;
-      y3 = y1 + dx;
-      y4 = y1 + dx;
-      z1 = zf(x1,y1);
-      z2 = zf(x2,y2);
-      z3 = zf(x3,y3);
-      z4 = zf(x4,y4);
-      za = 0.25*(z1+z2+z3+z4);
-      c = 16+((za + 1)*120);
-      if (c > 254) c = 254;
-      Plot3D_solidquad(p3,x1,y1,z1,x2,y2,z2,x3,y3,z3,x4,y4,z4,(Pixel) c);
-    }
-}
-
-
-
-void Quad_InterpTest(Plot3D *p3, int npoints) {
-  int i,j;
-  double dx;
-  double x1,y1,z1,x2,y2,z2,x3,y3,z3,x4,y4,z4;
-  int c1,c2,c3,c4;
-  dx = 2.0/npoints;
-
-  
-  for (i = 0; i < npoints; i++)
-    for (j = 0; j < npoints; j++) {
-      x1 = i*dx + -1.0;
-      y1 = j*dx + -1.0;
-      x2 = x1 + dx;
-      x3 = x1 + dx;
-      x4 = x1;
-      y2 = y1;
-      y3 = y1 + dx;
-      y4 = y1 + dx;
-      z1 = zf(x1,y1);
-      z2 = zf(x2,y2);
-      z3 = zf(x3,y3);
-      z4 = zf(x4,y4);
-      c1 = 16+((z1 + 1)*120);
-      c2 = 16+((z2 + 1)*120);
-      c3 = 16+((z3 + 1)*120);
-      c4 = 16+((z4 + 1)*120);
-      if (c1 > 254) c1 = 254;
-      if (c2 > 254) c2 = 254;
-      if (c3 > 254) c3 = 254;
-      if (c4 > 254) c4 = 254;
-      Plot3D_interpquad(p3,x1,y1,z1,(Pixel) c1,x2,y2,z2,(Pixel) c2,x3,y3,z3,(Pixel) c3,x4,y4,z4,(Pixel) c4);
-    }
-}
-
-
-
-  
-  
-  
-   
-
-
-  
-  
-  
diff --git a/Examples/GIFPlot/Makefile.in b/Examples/GIFPlot/Makefile.in
deleted file mode 100644
index 4e51360c8..000000000
--- a/Examples/GIFPlot/Makefile.in
+++ /dev/null
@@ -1,23 +0,0 @@
-prefix      = @prefix@
-exec_prefix = @exec_prefix@
-RANLIB      = @RANLIB@
-OPT         =
-
-INSTALL        = ../install-sh -c
-INSTALL_DATA   = ${INSTALL} -m 644
-SHELL          = /bin/sh
-
-all:	
-	cd Lib && $(MAKE) OPT="$(OPT)"
-
-install: 
-	$(INSTALL_DATA) Include/gifplot.h $(prefix)/include/gifplot.h
-	$(INSTALL_DATA) libgifplot.a $(exec_prefix)/lib/libgifplot.a
-	$(RANLIB) $(exec_prefix)/lib/libgifplot.a
-
-clean::
-	rm -f *.@OBJEXT@ *~ libgifplot.a *_wrap* *_man*
-	cd Lib && $(MAKE) clean
-	rm -f config.log config.status config.cache
-
-check: all
diff --git a/Examples/GIFPlot/Ocaml/check.list b/Examples/GIFPlot/Ocaml/check.list
deleted file mode 100644
index e75ee586a..000000000
--- a/Examples/GIFPlot/Ocaml/check.list
+++ /dev/null
@@ -1,3 +0,0 @@
-# see top-level Makefile.in
-full
-simple
diff --git a/Examples/GIFPlot/Ocaml/full/Makefile b/Examples/GIFPlot/Ocaml/full/Makefile
deleted file mode 100644
index 4f35c43f9..000000000
--- a/Examples/GIFPlot/Ocaml/full/Makefile
+++ /dev/null
@@ -1,33 +0,0 @@
-TOP        = ../../..
-SWIG       = $(TOP)/../swig
-SWIGOPT    = -I../../Include
-SRCS       = 
-TARGET     = gifcaml
-INTERFACE  = gifplot.i
-LIBS       = -L../.. -lgifplot -lm
-INCLUDES   = -I../../Include
-MLFILE     = gifplot.ml
-IOBJS      = runme.cmo
-PROGFILE   = runme.ml
-
-all:: static
-
-static::
-	$(MAKE) -f $(TOP)/Makefile TOP='$(TOP)' \
-	IOBJS='$(IOBJS)' PROGFILE='$(PROGFILE)' \
-	SRCS='$(SRCS)' SWIG='$(SWIG)' MLFILE='$(MLFILE)' \
-	INCLUDES='$(INCLUDES)' LIBS='$(LIBS)' SWIGOPT='$(SWIGOPT)' \
-	TARGET='$(TARGET)' INTERFACE='$(INTERFACE)' ocaml_static
-
-dynamic::
-	$(MAKE) -f $(TOP)/Makefile TOP='$(TOP)' \
-	IOBJS='$(IOBJS)' PROGFILE='$(PROGFILE)' \
-	SRCS='$(SRCS)' SWIG='$(SWIG)' MLFILE='$(MLFILE)' \
-	INCLUDES='$(INCLUDES)' LIBS='$(LIBS)' SWIGOPT='$(SWIGOPT)' \
-	TARGET='$(TARGET)' INTERFACE='$(INTERFACE)' ocaml_dynamic
-
-clean::
-	$(MAKE) -f $(TOP)/Makefile MLFILE='$(MLFILE)' ocaml_clean
-	rm -f *.gif
-
-check: all
diff --git a/Examples/GIFPlot/Ocaml/full/README b/Examples/GIFPlot/Ocaml/full/README
deleted file mode 100644
index 4a2b400b5..000000000
--- a/Examples/GIFPlot/Ocaml/full/README
+++ /dev/null
@@ -1,8 +0,0 @@
-This example runs the entire gifplot.h header file through SWIG without
-any changes.  The ocaml program 'runme.ml' does something a little more 
-interesting.   You'll have to go look at the header file to get a complete
-listing of the functions.
-
-
-
-
diff --git a/Examples/GIFPlot/Ocaml/full/cmap b/Examples/GIFPlot/Ocaml/full/cmap
deleted file mode 100644
index a20c331a9573dd8443380680bfe2cc428780d8a9..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

literal 768
zcmZQzpd(=A5)hSEP}Mdtvvzdz4h)M)OwTDSuW4%Uoiu&!q7`d5@7R0z#JS5i?>&C`
z?#s{r^Z@9-XXO?YlTlLFHMX#G@$?UkN=VBFxv-;m^2~WlR;}N<`@pd?7q8!a^y1xT
znmh34m-nxpKDd4D;+bOy_iW#^cE#d(Gbi_Tw$xXZ7G$R-M27|XxI5We80l&#%Snpx
zbFrd(h8Vt}lCeu@T6xFJRlCpJeMef510DGC$^DyG&YwK8f9IC<tCq~4HKo4`=)RKt
ztd#huP=7C1dn;3YEme6bQ8Jvz%Ed1tDW|Lfj0{^Rcb~wpXkcs<lvdTZboK$GWATc$
Xo3`&c2#k+ww;w!x^&XgFNDnap(k+Jt

diff --git a/Examples/GIFPlot/Ocaml/full/gifplot.i b/Examples/GIFPlot/Ocaml/full/gifplot.i
deleted file mode 100644
index 22f4df672..000000000
--- a/Examples/GIFPlot/Ocaml/full/gifplot.i
+++ /dev/null
@@ -1,15 +0,0 @@
-/* Oh what the heck, let's just grab the whole darn header file
-   and see what happens. */
-
-%module gifplot
-%{
-
-/* Note: You still need this part because the %include directive
-   merely causes SWIG to interpret the contents of a file.  It doesn't
-   include the right include headers for the resulting C code */
-
-#include "gifplot.h"
-%}
-
-typedef int Pixel;
-%include gifplot.h
diff --git a/Examples/GIFPlot/Ocaml/full/runme.ml b/Examples/GIFPlot/Ocaml/full/runme.ml
deleted file mode 100644
index 0dfa98569..000000000
--- a/Examples/GIFPlot/Ocaml/full/runme.ml
+++ /dev/null
@@ -1,87 +0,0 @@
-(* Plot a 3D Function *)
-
-(* Use the wrapped GIFPlot library *)
-open Swig
-open Gifplot
-open Int32
-
-(* Here is the function to plot *)
-let func x y = 
-  5.0 *. 
-    (cos (2.0 *. (sqrt (x *. x) +. (y *. y)))) *.
-    (exp (-0.3 *. (sqrt (x *. x) +. (y *. y)))) 
-
-(* Here are some plotting parameters *)
-
-let xmin = -5.0
-let xmax =  5.0
-let ymin = -5.0
-let ymax =  5.0
-let zmin = -5.0
-let zmax =  5.0
-
-(* Grid resolution *)
-let nxpoints = 60
-let nypoints = 60
-
-let cmap = _new_ColorMap (C_string "cmap")
-let frame = _new_FrameBuffer (C_list [ C_int 500 ;
-				      C_int 500 ]) 
-let _ = _FrameBuffer_clear (C_list [ frame ; _BLACK C_void ])
-
-let p2 = _new_Plot3D (C_list [ frame ; 
-			       C_float xmin ; C_float ymin ; C_float zmin ; 
-			       C_float xmax ; C_float ymax ; C_float zmax ])
-let _ = _Plot3D_lookat (C_list [ p2 ; C_float (2.0 *. (zmax -. zmin)) ])
-let _ = _Plot3D_autoperspective (C_list [ p2 ; C_float 40.0 ])
-let _ = _Plot3D_rotu (C_list [ p2 ; C_float 60.0 ])
-let _ = _Plot3D_rotr (C_list [ p2 ; C_float 30.0 ])
-let _ = _Plot3D_rotd (C_list [ p2 ; C_float 10.0 ])
-
-let drawsolid () =
-  begin
-    _Plot3D_clear (C_list [ p2 ; _BLACK C_void ]) ;
-    _Plot3D_start p2 ;
-    let dx = ((xmax -. xmin) /. (float_of_int nxpoints))
-    and dy = ((ymax -. ymin) /. (float_of_int nypoints)) 
-    and cscale = (240.0 /. (zmax -. zmin)) in
-    let rec x_loop x i =
-      if i < nxpoints then
-	begin
-	  let rec y_loop y j =
-	    begin
-	      if j < nypoints then
-		let z1 = func x y
-		and z2 = func (x +. dx) y
-		and z3 = func (x +. dx) (y +. dy)
-		and z4 = func x (y +. dy) in
-		let c1 = cscale *. (z1 -. zmin)
-		and c2 = cscale *. (z2 -. zmin)
-		and c3 = cscale *. (z3 -. zmin)
-		and c4 = cscale *. (z4 -. zmin) in
-		let cc = (c1 +. c2 +. c3 +. c4) /. 4.0 in
-		let c =  (max (min (int_of_float cc) 239) 0) in
-		  _Plot3D_solidquad 
-		    (C_list (p2 ::
-			       (List.map 
-				  (fun x -> C_float x)
-				  [ x ; y ; z1 ;
-				    (x +. dx) ; y ; z2 ;
-				    (x +. dx) ; (y +. dy) ; z3 ;
-				    x ; (y +. dx) ; z4 ;
-				    (float_of_int (c + 16)) ]))) ;
-		  y_loop (y +. dy) (j + 1) 
-	    end in
-	  begin
-	    y_loop ymin 0 ;
-	    x_loop (x +. dx) (i + 1)
-	  end 
-	end in
-    x_loop xmin 0
-  end
-
-let _ = print_endline "Making a nice 3D plot..."
-let _ = drawsolid ()
-
-let _ = _FrameBuffer_writeGIF (C_list [ frame ; cmap ; C_string "image.gif" ])
-let _ = print_endline "Write image.gif"
diff --git a/Examples/GIFPlot/Ocaml/simple/Makefile b/Examples/GIFPlot/Ocaml/simple/Makefile
deleted file mode 100644
index 50492efc7..000000000
--- a/Examples/GIFPlot/Ocaml/simple/Makefile
+++ /dev/null
@@ -1,33 +0,0 @@
-TOP        = ../../..
-SWIG       = $(TOP)/../swig
-SWIGOPT    = -I../../Include
-SRCS       = 
-TARGET     = gifsimple
-INTERFACE  = simple.i
-LIBS       = -L../.. -lgifplot -lm
-INCLUDES   = -I../../Include
-MLFILE     = simple.ml
-IOBJS      = simple_wrap.o simple.cmo runme.cmo
-PROGFILE   = runme.ml
-
-all:: static
-
-static::
-	$(MAKE) -f $(TOP)/Makefile TOP='$(TOP)' \
-	IOBJS='$(IOBJS)' PROGFILE='$(PROGFILE)' \
-	SRCS='$(SRCS)' SWIG='$(SWIG)' MLFILE='$(MLFILE)' \
-	INCLUDES='$(INCLUDES)' LIBS='$(LIBS)' SWIGOPT='$(SWIGOPT)' \
-	TARGET='$(TARGET)' INTERFACE='$(INTERFACE)' ocaml_static
-
-dynamic::
-	$(MAKE) -f $(TOP)/Makefile TOP='$(TOP)' \
-	IOBJS='$(IOBJS)' PROGFILE='$(PROGFILE)' \
-	SRCS='$(SRCS)' SWIG='$(SWIG)' MLFILE='$(MLFILE)' \
-	INCLUDES='$(INCLUDES)' LIBS='$(LIBS)' SWIGOPT='$(SWIGOPT)' \
-	TARGET='$(TARGET)' INTERFACE='$(INTERFACE)' ocaml_static
-
-clean::
-	$(MAKE) -f $(TOP)/Makefile MLFILE='$(MLFILE)' ocaml_clean
-	rm -f *.gif
-
-check: all
diff --git a/Examples/GIFPlot/Ocaml/simple/cmap b/Examples/GIFPlot/Ocaml/simple/cmap
deleted file mode 100644
index a20c331a9573dd8443380680bfe2cc428780d8a9..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

literal 768
zcmZQzpd(=A5)hSEP}Mdtvvzdz4h)M)OwTDSuW4%Uoiu&!q7`d5@7R0z#JS5i?>&C`
z?#s{r^Z@9-XXO?YlTlLFHMX#G@$?UkN=VBFxv-;m^2~WlR;}N<`@pd?7q8!a^y1xT
znmh34m-nxpKDd4D;+bOy_iW#^cE#d(Gbi_Tw$xXZ7G$R-M27|XxI5We80l&#%Snpx
zbFrd(h8Vt}lCeu@T6xFJRlCpJeMef510DGC$^DyG&YwK8f9IC<tCq~4HKo4`=)RKt
ztd#huP=7C1dn;3YEme6bQ8Jvz%Ed1tDW|Lfj0{^Rcb~wpXkcs<lvdTZboK$GWATc$
Xo3`&c2#k+ww;w!x^&XgFNDnap(k+Jt

diff --git a/Examples/GIFPlot/Ocaml/simple/runme.ml b/Examples/GIFPlot/Ocaml/simple/runme.ml
deleted file mode 100644
index 3b6602cbc..000000000
--- a/Examples/GIFPlot/Ocaml/simple/runme.ml
+++ /dev/null
@@ -1,35 +0,0 @@
-(* Draw some simple shapes *)
-
-(* Use the wrapped GIFPlot library *)
-open Swig
-open Simple
-open Int32
-
-let _ = print_endline "Drawing some basic shapes"
-
-let cmap = _new_ColorMap (C_string "cmap")
-let f = _new_FrameBuffer (C_list [ C_int 400 ; C_int 400 ])
-
-(* Clear the picture *)
-let _ = _FrameBuffer_clear (C_list [ f ; _BLACK C_void ])
-
-(* Make a red box *)
-let _ = _FrameBuffer_box 
-	  (C_list [ f ; C_int 40 ; C_int 40 ; C_int 200 ; C_int 200 ; _RED C_void ])
-
-(* Make a blue circle *)
-let _ = _FrameBuffer_circle 
-	  (C_list [ f ; C_int 200 ; C_int 200 ; C_int 40 ; _BLUE C_void ])
-
-(* Make green line *)
-let _ = _FrameBuffer_line 
-	  (C_list [ f ; C_int 10 ; C_int 390 ; C_int 390 ; C_int 200 ; _GREEN C_void ])
-
-(* Write an image out to disk *)
-
-let _ = _FrameBuffer_writeGIF (C_list [ f ; cmap ; C_string "image.gif" ])
-let _ = print_endline "Wrote image.gif"
-
-let _ = _delete_FrameBuffer f
-let _ = _delete_ColorMap cmap
-
diff --git a/Examples/GIFPlot/Ocaml/simple/simple.i b/Examples/GIFPlot/Ocaml/simple/simple.i
deleted file mode 100644
index 33297f491..000000000
--- a/Examples/GIFPlot/Ocaml/simple/simple.i
+++ /dev/null
@@ -1,33 +0,0 @@
-/* This example shows a very simple interface wrapping a few 
-   primitive declarations */
-
-%module simple
-%{
-#include "gifplot.h"
-%}
-
-typedef int Pixel;
-
-/* Here are a few useful functions */
-
-ColorMap    *new_ColorMap(char *filename = 0);
-void         delete_ColorMap(ColorMap *cmap);
-
-FrameBuffer *new_FrameBuffer(unsigned int width, unsigned int height);
-void         delete_FrameBuffer(FrameBuffer *frame);
-void         FrameBuffer_clear(FrameBuffer *frame, Pixel color);
-void         FrameBuffer_line(FrameBuffer *frame, int x1, int y1, int x2, int y2, Pixel color);
-void         FrameBuffer_box(FrameBuffer *frame, int x1, int y1, int x2, int y2, Pixel color);
-void         FrameBuffer_circle(FrameBuffer *frame, int x1, int y1, int radius, Pixel color);
-int          FrameBuffer_writeGIF(FrameBuffer *f, ColorMap *c, char *filename);
-
-/* And some useful constants */
-
-#define BLACK   0
-#define WHITE   1
-#define RED     2
-#define GREEN   3
-#define BLUE    4
-#define YELLOW  5
-#define CYAN    6
-#define MAGENTA 7
diff --git a/Examples/GIFPlot/Perl5/check.list b/Examples/GIFPlot/Perl5/check.list
deleted file mode 100644
index 13de977af..000000000
--- a/Examples/GIFPlot/Perl5/check.list
+++ /dev/null
@@ -1,4 +0,0 @@
-# see top-level Makefile.in
-full
-shadow
-simple
diff --git a/Examples/GIFPlot/Perl5/full/Makefile b/Examples/GIFPlot/Perl5/full/Makefile
deleted file mode 100644
index 0e0878d03..000000000
--- a/Examples/GIFPlot/Perl5/full/Makefile
+++ /dev/null
@@ -1,24 +0,0 @@
-TOP        = ../../..
-SWIG       = $(TOP)/../swig
-SWIGOPT    = -I../../Include -noproxy
-SRCS       =
-TARGET     = gifplot
-INTERFACE  = gifplot.i
-LIBS       = -L../.. -lgifplot -lm
-INCLUDES   = -I../../Include
-
-all::
-	$(MAKE) -f $(TOP)/Makefile SRCS='$(SRCS)' SWIG='$(SWIG)' \
-	INCLUDES='$(INCLUDES)' LIBS='$(LIBS)' SWIGOPT='$(SWIGOPT)' \
-	TARGET='$(TARGET)' INTERFACE='$(INTERFACE)' perl5
-
-static::
-	$(MAKE) -f $(TOP)/Makefile SRCS='$(SRCS)' SWIG='$(SWIG)' \
-	INCLUDES='$(INCLUDES)' LIBS='$(LIBS)' SWIGOPT='$(SWIGOPT)' \
-	TARGET='myperl' INTERFACE='$(INTERFACE)' perl5_static
-
-clean::
-	$(MAKE) -f $(TOP)/Makefile perl5_clean
-	rm -f *.gif
-
-check: all
diff --git a/Examples/GIFPlot/Perl5/full/README b/Examples/GIFPlot/Perl5/full/README
deleted file mode 100644
index 05c685a80..000000000
--- a/Examples/GIFPlot/Perl5/full/README
+++ /dev/null
@@ -1,8 +0,0 @@
-This example runs the entire gifplot.h header file through SWIG without
-any changes.  The script 'runme.pl' does something a little more 
-interesting.   You'll have to go look at the header file to get a complete
-listing of the functions.
-
-
-
-
diff --git a/Examples/GIFPlot/Perl5/full/cmap b/Examples/GIFPlot/Perl5/full/cmap
deleted file mode 100644
index a20c331a9573dd8443380680bfe2cc428780d8a9..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

literal 768
zcmZQzpd(=A5)hSEP}Mdtvvzdz4h)M)OwTDSuW4%Uoiu&!q7`d5@7R0z#JS5i?>&C`
z?#s{r^Z@9-XXO?YlTlLFHMX#G@$?UkN=VBFxv-;m^2~WlR;}N<`@pd?7q8!a^y1xT
znmh34m-nxpKDd4D;+bOy_iW#^cE#d(Gbi_Tw$xXZ7G$R-M27|XxI5We80l&#%Snpx
zbFrd(h8Vt}lCeu@T6xFJRlCpJeMef510DGC$^DyG&YwK8f9IC<tCq~4HKo4`=)RKt
ztd#huP=7C1dn;3YEme6bQ8Jvz%Ed1tDW|Lfj0{^Rcb~wpXkcs<lvdTZboK$GWATc$
Xo3`&c2#k+ww;w!x^&XgFNDnap(k+Jt

diff --git a/Examples/GIFPlot/Perl5/full/gifplot.i b/Examples/GIFPlot/Perl5/full/gifplot.i
deleted file mode 100644
index 5a7f5008f..000000000
--- a/Examples/GIFPlot/Perl5/full/gifplot.i
+++ /dev/null
@@ -1,15 +0,0 @@
-/* Oh what the heck, let's just grab the whole darn header file
-   and see what happens. */
-
-%module gifplot
-%{
-
-/* Note: You still need this part because the %include directive
-   merely causes SWIG to interpret the contents of a file.  It doesn't
-   include the right include headers for the resulting C code */
-
-#include "gifplot.h"
-
-%}
-
-%include gifplot.h
diff --git a/Examples/GIFPlot/Perl5/full/runme.pl b/Examples/GIFPlot/Perl5/full/runme.pl
deleted file mode 100644
index 77fd321c9..000000000
--- a/Examples/GIFPlot/Perl5/full/runme.pl
+++ /dev/null
@@ -1,68 +0,0 @@
-# Plot a 3D function
-use gifplot;
-package gifplot;
-
-# Here is the function to plot
-sub func {
-    my $x = shift;
-    my $y = shift;
-    return 5*cos(2*sqrt($x*$x+$y*$y))*exp(-0.3*sqrt($x*$x+$y*$y));
-}
-
-# Here are some plotting parameters
-$xmin = -5.0;
-$xmax =  5.0;
-$ymin = -5.0;
-$ymax =  5.0;
-$zmin = -5.0;
-$zmax =  5.0;
-
-# Grid resolution
-$nxpoints =  60;
-$nypoints =  60;
-
-$cmap  = new_ColorMap("cmap");
-$frame = new_FrameBuffer(500,500);
-FrameBuffer_clear($frame,$BLACK);
-
-$p3    = new_Plot3D($frame,$xmin,$ymin,$zmin,$xmax,$ymax,$zmax);
-Plot3D_lookat($p3,2*($zmax-$zmin));
-Plot3D_autoperspective($p3,40);
-Plot3D_rotu($p3,60);
-Plot3D_rotr($p3,30);
-Plot3D_rotd($p3,10);
-
-sub drawsolid {
-    Plot3D_clear($p3,$BLACK);
-    Plot3D_start($p3);
-    my $dx = 1.0*($xmax-$xmin)/$nxpoints;
-    my $dy = 1.0*($ymax-$ymin)/$nypoints;
-    my $cscale = 240.0/($zmax-$zmin);
-    my $x = $xmin;
-    for ($i = 0; $i < $nxpoints; $i++) {
-	my $y = $ymin;
-	for ($j = 0; $j < $nypoints; $j++) {
-	    my $z1 = func($x,$y);
-	    my $z2 = func($x+$dx,$y);
-	    my $z3 = func($x+$dx,$y+$dy);
-	    my $z4 = func($x,$y+$dy);
-	    my $c1 = $cscale*($z1-$zmin);
-	    my $c2 = $cscale*($z2-$zmin);
-	    my $c3 = $cscale*($z3-$zmin);
-	    my $c4 = $cscale*($z4-$zmin);
-	    my $c = ($c1+$c2+$c3+$c4)/4;
-	    if ($c < 0) { $c = 0; }
-	    if ($c > 239) { $c = 239; }
-	    Plot3D_solidquad($p3,$x,$y,$z1,$x+$dx,$y,$z2,$x+$dx,$y+$dy,$z3,$x,$y+$dy,$z4,$c+16);
-	    $y = $y + $dy;
-	}
-	$x = $x + $dx;
-    }
-}
-
-print "Making a nice 3D plot...\n";
-drawsolid();
-
-FrameBuffer_writeGIF($frame,$cmap,"image.gif");
-print "Wrote image.gif\n";
-
diff --git a/Examples/GIFPlot/Perl5/shadow/Makefile b/Examples/GIFPlot/Perl5/shadow/Makefile
deleted file mode 100644
index c5cb7aec4..000000000
--- a/Examples/GIFPlot/Perl5/shadow/Makefile
+++ /dev/null
@@ -1,24 +0,0 @@
-TOP        = ../../..
-SWIG       = $(TOP)/../swig
-SWIGOPT    = -I../../Interface
-SRCS       =
-TARGET     = gifplot
-INTERFACE  = gifplot.i
-LIBS       = -L../.. -lgifplot -lm
-INCLUDES   = -I../../Include
-
-all::
-	$(MAKE) -f $(TOP)/Makefile SRCS='$(SRCS)' SWIG='$(SWIG)' \
-	INCLUDES='$(INCLUDES)' LIBS='$(LIBS)' SWIGOPT='$(SWIGOPT)' \
-	TARGET='$(TARGET)' INTERFACE='$(INTERFACE)' perl5
-
-static::
-	$(MAKE) -f $(TOP)/Makefile SRCS='$(SRCS)' SWIG='$(SWIG)' \
-	INCLUDES='$(INCLUDES)' LIBS='$(LIBS)' SWIGOPT='$(SWIGOPT)' \
-	TARGET='myperl' INTERFACE='$(INTERFACE)' perl5_static
-
-clean::
-	$(MAKE) -f $(TOP)/Makefile perl5_clean
-	rm -f *.gif
-
-check: all
diff --git a/Examples/GIFPlot/Perl5/shadow/README b/Examples/GIFPlot/Perl5/shadow/README
deleted file mode 100644
index ab12e344e..000000000
--- a/Examples/GIFPlot/Perl5/shadow/README
+++ /dev/null
@@ -1,2 +0,0 @@
-This example use the file in ../../Interface/gifplot.i to build
-an interface with shadow classes.  Run the script 'runme.pl'.
diff --git a/Examples/GIFPlot/Perl5/shadow/cmap b/Examples/GIFPlot/Perl5/shadow/cmap
deleted file mode 100644
index a20c331a9573dd8443380680bfe2cc428780d8a9..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

literal 768
zcmZQzpd(=A5)hSEP}Mdtvvzdz4h)M)OwTDSuW4%Uoiu&!q7`d5@7R0z#JS5i?>&C`
z?#s{r^Z@9-XXO?YlTlLFHMX#G@$?UkN=VBFxv-;m^2~WlR;}N<`@pd?7q8!a^y1xT
znmh34m-nxpKDd4D;+bOy_iW#^cE#d(Gbi_Tw$xXZ7G$R-M27|XxI5We80l&#%Snpx
zbFrd(h8Vt}lCeu@T6xFJRlCpJeMef510DGC$^DyG&YwK8f9IC<tCq~4HKo4`=)RKt
ztd#huP=7C1dn;3YEme6bQ8Jvz%Ed1tDW|Lfj0{^Rcb~wpXkcs<lvdTZboK$GWATc$
Xo3`&c2#k+ww;w!x^&XgFNDnap(k+Jt

diff --git a/Examples/GIFPlot/Perl5/shadow/runme.pl b/Examples/GIFPlot/Perl5/shadow/runme.pl
deleted file mode 100644
index c396251af..000000000
--- a/Examples/GIFPlot/Perl5/shadow/runme.pl
+++ /dev/null
@@ -1,68 +0,0 @@
-# Plot a 3D function
-use gifplot;
-package gifplot;
-
-# Here is the function to plot
-sub func {
-    my $x = shift;
-    my $y = shift;
-    return 5*cos(2*sqrt($x*$x+$y*$y))*exp(-0.3*sqrt($x*$x+$y*$y));
-}
-
-# Here are some plotting parameters
-$xmin = -5.0;
-$xmax =  5.0;
-$ymin = -5.0;
-$ymax =  5.0;
-$zmin = -5.0;
-$zmax =  5.0;
-
-# Grid resolution
-$nxpoints =  60;
-$nypoints =  60;
-
-$cmap  = new gifplot::ColorMap("cmap");
-$frame = new gifplot::FrameBuffer(500,500);
-$frame->clear($BLACK);
-
-$p3    = new gifplot::Plot3D($frame,$xmin,$ymin,$zmin,$xmax,$ymax,$zmax);
-$p3->lookat(2*($zmax-$zmin));
-$p3->autoperspective(40);
-$p3->rotu(60);
-$p3->rotr(30);
-$p3->rotd(10);
-
-sub drawsolid {
-    $p3->clear($BLACK);
-    $p3->start();
-    my $dx = 1.0*($xmax-$xmin)/$nxpoints;
-    my $dy = 1.0*($ymax-$ymin)/$nypoints;
-    my $cscale = 240.0/($zmax-$zmin);
-    my $x = $xmin;
-    for ($i = 0; $i < $nxpoints; $i++) {
-	my $y = $ymin;
-	for ($j = 0; $j < $nypoints; $j++) {
-	    my $z1 = func($x,$y);
-	    my $z2 = func($x+$dx,$y);
-	    my $z3 = func($x+$dx,$y+$dy);
-	    my $z4 = func($x,$y+$dy);
-	    my $c1 = $cscale*($z1-$zmin);
-	    my $c2 = $cscale*($z2-$zmin);
-	    my $c3 = $cscale*($z3-$zmin);
-	    my $c4 = $cscale*($z4-$zmin);
-	    my $c = ($c1+$c2+$c3+$c4)/4;
-	    if ($c < 0) { $c = 0; }
-	    if ($c > 239) { $c = 239; }
-	    $p3->solidquad($x,$y,$z1,$x+$dx,$y,$z2,$x+$dx,$y+$dy,$z3,$x,$y+$dy,$z4,$c+16);
-	    $y = $y + $dy;
-	}
-	$x = $x + $dx;
-    }
-}
-
-print "Making a nice 3D plot...\n";
-drawsolid();
-
-$frame->writeGIF($cmap,"image.gif");
-print "Wrote image.gif\n";
-
diff --git a/Examples/GIFPlot/Perl5/simple/Makefile b/Examples/GIFPlot/Perl5/simple/Makefile
deleted file mode 100644
index 36a8fa938..000000000
--- a/Examples/GIFPlot/Perl5/simple/Makefile
+++ /dev/null
@@ -1,24 +0,0 @@
-TOP        = ../../..
-SWIG       = $(TOP)/../swig
-SWIGOPT    =
-SRCS       =
-TARGET     = simple
-INTERFACE  = simple.i
-LIBS       = -L../.. -lgifplot
-INCLUDES   = -I../../Include
-
-all::
-	$(MAKE) -f $(TOP)/Makefile SRCS='$(SRCS)' SWIG='$(SWIG)' \
-	INCLUDES='$(INCLUDES)' LIBS='$(LIBS)' SWIGOPT='$(SWIGOPT)' \
-	TARGET='$(TARGET)' INTERFACE='$(INTERFACE)' perl5
-
-static::
-	$(MAKE) -f $(TOP)/Makefile SRCS='$(SRCS)' SWIG='$(SWIG)' \
-	INCLUDES='$(INCLUDES)' LIBS='$(LIBS)' SWIGOPT='$(SWIGOPT)' \
-	TARGET='myperl' INTERFACE='$(INTERFACE)' perl5_static
-
-clean::
-	$(MAKE) -f $(TOP)/Makefile perl5_clean
-	rm -f *.gif
-
-check: all
diff --git a/Examples/GIFPlot/Perl5/simple/README b/Examples/GIFPlot/Perl5/simple/README
deleted file mode 100644
index c2c799a70..000000000
--- a/Examples/GIFPlot/Perl5/simple/README
+++ /dev/null
@@ -1,5 +0,0 @@
-This is a very minimalistic example in which just a few functions
-and constants from library are wrapped and used to draw some simple
-shapes.  The script 'runme.pl' runs the example.
-
-
diff --git a/Examples/GIFPlot/Perl5/simple/runme.pl b/Examples/GIFPlot/Perl5/simple/runme.pl
deleted file mode 100644
index f28255e7c..000000000
--- a/Examples/GIFPlot/Perl5/simple/runme.pl
+++ /dev/null
@@ -1,28 +0,0 @@
-# Draw some simple shapes
-print "Drawing some basic shapes\n";
-
-use simple;
-
-$cmap = simple::new_ColorMap();
-$f    = simple::new_FrameBuffer(400,400);
-
-# Clear the picture
-simple::FrameBuffer_clear($f,$simple::BLACK);
-
-# Make a red box
-simple::FrameBuffer_box($f,40,40,200,200,$simple::RED);
-
-# Make a blue circle
-simple::FrameBuffer_circle($f,200,200,40,$simple::BLUE);
-
-# Make green line
-simple::FrameBuffer_line($f,10,390,390,200, $simple::GREEN);
-
-# Write an image out to disk
-
-simple::FrameBuffer_writeGIF($f,$cmap,"image.gif");
-print "Wrote image.gif\n";
-
-simple::delete_FrameBuffer($f);
-simple::delete_ColorMap($cmap);
-
diff --git a/Examples/GIFPlot/Perl5/simple/simple.i b/Examples/GIFPlot/Perl5/simple/simple.i
deleted file mode 100644
index 457bc4c09..000000000
--- a/Examples/GIFPlot/Perl5/simple/simple.i
+++ /dev/null
@@ -1,38 +0,0 @@
-/* This example shows a very simple interface wrapping a few 
-   primitive declarations */
-
-%module simple
-%{
-#include "gifplot.h"
-%}
-
-typedef unsigned char Pixel;
-
-/* Here are a few useful functions */
-
-ColorMap    *new_ColorMap(char *filename = 0);
-void         delete_ColorMap(ColorMap *cmap);
-
-FrameBuffer *new_FrameBuffer(unsigned int width, unsigned int height);
-void         delete_FrameBuffer(FrameBuffer *frame);
-void         FrameBuffer_clear(FrameBuffer *frame, Pixel color);
-void         FrameBuffer_line(FrameBuffer *frame, int x1, int y1, int x2, int y2, Pixel color);
-void         FrameBuffer_box(FrameBuffer *frame, int x1, int y1, int x2, int y2, Pixel color);
-void         FrameBuffer_circle(FrameBuffer *frame, int x1, int y1, int radius, Pixel color);
-int          FrameBuffer_writeGIF(FrameBuffer *f, ColorMap *c, char *filename);
-
-/* And some useful constants */
-
-#define BLACK   0
-#define WHITE   1
-#define RED     2
-#define GREEN   3
-#define BLUE    4
-#define YELLOW  5
-#define CYAN    6
-#define MAGENTA 7
-
-
-
-
-
diff --git a/Examples/GIFPlot/Php4/check.list b/Examples/GIFPlot/Php4/check.list
deleted file mode 100644
index e75ee586a..000000000
--- a/Examples/GIFPlot/Php4/check.list
+++ /dev/null
@@ -1,3 +0,0 @@
-# see top-level Makefile.in
-full
-simple
diff --git a/Examples/GIFPlot/Php4/full/Makefile b/Examples/GIFPlot/Php4/full/Makefile
deleted file mode 100644
index 3aa632b99..000000000
--- a/Examples/GIFPlot/Php4/full/Makefile
+++ /dev/null
@@ -1,20 +0,0 @@
-TOP        = ../../..
-SWIG       = $(TOP)/../swig
-SWIGOPT    = -I../../Include -noproxy
-SRCS       =
-TARGET     = php_gifplot
-INTERFACE  = gifplot.i
-LIBS       = -L../.. -lgifplot -lm
-INCLUDES   = -I../../Include
-
-all::
-	$(MAKE) -f $(TOP)/Makefile SRCS='$(SRCS)' SWIG='$(SWIG)' \
-	INCLUDES='$(INCLUDES)' LIBS='$(LIBS)' SWIGOPT='$(SWIGOPT)' \
-	TARGET='$(TARGET)' INTERFACE='$(INTERFACE)' php4
-
-clean::
-	$(MAKE) -f $(TOP)/Makefile php4_clean
-	rm -f *.gif
-	rm -f php_gifplot.h
-
-check: all
diff --git a/Examples/GIFPlot/Php4/full/README b/Examples/GIFPlot/Php4/full/README
deleted file mode 100644
index f8d38d9af..000000000
--- a/Examples/GIFPlot/Php4/full/README
+++ /dev/null
@@ -1,4 +0,0 @@
-This example runs the entire gifplot.h header file through SWIG without
-any changes.  The script 'runme.php3' does something a little more 
-interesting.   You'll have to go look at the header file to get a complete
-listing of the functions.
diff --git a/Examples/GIFPlot/Php4/full/cmap b/Examples/GIFPlot/Php4/full/cmap
deleted file mode 100644
index a20c331a9573dd8443380680bfe2cc428780d8a9..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

literal 768
zcmZQzpd(=A5)hSEP}Mdtvvzdz4h)M)OwTDSuW4%Uoiu&!q7`d5@7R0z#JS5i?>&C`
z?#s{r^Z@9-XXO?YlTlLFHMX#G@$?UkN=VBFxv-;m^2~WlR;}N<`@pd?7q8!a^y1xT
znmh34m-nxpKDd4D;+bOy_iW#^cE#d(Gbi_Tw$xXZ7G$R-M27|XxI5We80l&#%Snpx
zbFrd(h8Vt}lCeu@T6xFJRlCpJeMef510DGC$^DyG&YwK8f9IC<tCq~4HKo4`=)RKt
ztd#huP=7C1dn;3YEme6bQ8Jvz%Ed1tDW|Lfj0{^Rcb~wpXkcs<lvdTZboK$GWATc$
Xo3`&c2#k+ww;w!x^&XgFNDnap(k+Jt

diff --git a/Examples/GIFPlot/Php4/full/gifplot.i b/Examples/GIFPlot/Php4/full/gifplot.i
deleted file mode 100644
index 5a7f5008f..000000000
--- a/Examples/GIFPlot/Php4/full/gifplot.i
+++ /dev/null
@@ -1,15 +0,0 @@
-/* Oh what the heck, let's just grab the whole darn header file
-   and see what happens. */
-
-%module gifplot
-%{
-
-/* Note: You still need this part because the %include directive
-   merely causes SWIG to interpret the contents of a file.  It doesn't
-   include the right include headers for the resulting C code */
-
-#include "gifplot.h"
-
-%}
-
-%include gifplot.h
diff --git a/Examples/GIFPlot/Php4/full/runme.php4 b/Examples/GIFPlot/Php4/full/runme.php4
deleted file mode 100644
index de5371ee8..000000000
--- a/Examples/GIFPlot/Php4/full/runme.php4
+++ /dev/null
@@ -1,78 +0,0 @@
-<?
-
-# Plot a 3D function
-require "gifplot.php";
-
-# Here is the function to plot
-function func($x, $y) {
-    return 5*cos(2*sqrt($x*$x+$y*$y))*exp(-0.3*sqrt($x*$x+$y*$y));
-}
-
-# Here are some plotting parameters
-$xmin = -5.0;
-$xmax =  5.0;
-$ymin = -5.0;
-$ymax =  5.0;
-$zmin = -5.0;
-$zmax =  5.0;
-
-# Grid resolution
-$nxpoints =  60;
-$nypoints =  60;
-
-$cmap  = new_ColorMap("cmap");
-$frame = new_FrameBuffer(500,500);
-FrameBuffer_clear($frame, BLACK);
-
-$p3    = new_Plot3D($frame,$xmin,$ymin,$zmin,$xmax,$ymax,$zmax);
-Plot3D_lookat($p3, 2*($zmax-$zmin));
-Plot3D_autoperspective($p3, 40);
-Plot3D_rotu($p3, 60);
-Plot3D_rotr($p3, 30);
-Plot3D_rotd($p3, 10);
-
-function drawsolid() {
-	global $p3;
-	global $xmax;
-	global $xmin;
-	global $ymax;
-	global $ymin;
-	global $zmin;
-	global $zmax;
-	global $nxpoints;
-	global $nypoints;
-
-    Plot3D_clear($p3, BLACK);
-    Plot3D_start($p3);
-    $dx = 1.0*($xmax-$xmin)/$nxpoints;
-    $dy = 1.0*($ymax-$ymin)/$nypoints;
-    $cscale = 240.0/($zmax-$zmin);
-    $x = $xmin;
-    for ($i = 0; $i < $nxpoints; $i++) {
-	$y = $ymin;
-	for ($j = 0; $j < $nypoints; $j++) {
-	    $z1 = func($x,$y);
-	    $z2 = func($x+$dx,$y);
-	    $z3 = func($x+$dx,$y+$dy);
-	    $z4 = func($x,$y+$dy);
-	    $c1 = $cscale*($z1-$zmin);
-	    $c2 = $cscale*($z2-$zmin);
-	    $c3 = $cscale*($z3-$zmin);
-	    $c4 = $cscale*($z4-$zmin);
-	    $c = ($c1+$c2+$c3+$c4)/4;
-	    if ($c < 0) { $c = 0; }
-	    if ($c > 239) { $c = 239; }
-	    Plot3D_solidquad($p3, $x,$y,$z1,$x+$dx,$y,$z2,$x+$dx,$y+$dy,$z3,$x,$y+$dy,$z4,$c+16);
-	    $y = $y + $dy;
-	}
-	$x = $x + $dx;
-    }
-}
-
-print "Making a nice 3D plot...\n";
-drawsolid();
-
-FrameBuffer_writeGIF($frame, $cmap,"image.gif");
-print "Wrote image.gif\n";
-
-?>
diff --git a/Examples/GIFPlot/Php4/shadow/Makefile b/Examples/GIFPlot/Php4/shadow/Makefile
deleted file mode 100644
index 5627e53a0..000000000
--- a/Examples/GIFPlot/Php4/shadow/Makefile
+++ /dev/null
@@ -1,19 +0,0 @@
-TOP        = ../../..
-SWIG       = $(TOP)/../swig
-SWIGOPT    = -I../../Interface
-SRCS       =
-TARGET     = php_gifplot
-INTERFACE  = gifplot.i
-LIBS       = -L../.. -lgifplot -lm
-INCLUDES   = -I../../Include
-
-all::
-	$(MAKE) -f $(TOP)/Makefile SRCS='$(SRCS)' SWIG='$(SWIG)' \
-	INCLUDES='$(INCLUDES)' LIBS='$(LIBS)' SWIGOPT='$(SWIGOPT)' \
-	TARGET='$(TARGET)' INTERFACE='$(INTERFACE)' php4
-
-clean::
-	$(MAKE) -f $(TOP)/Makefile php4_clean
-	rm -f *.gif
-
-check: all
diff --git a/Examples/GIFPlot/Php4/shadow/README b/Examples/GIFPlot/Php4/shadow/README
deleted file mode 100644
index 3e91f7d59..000000000
--- a/Examples/GIFPlot/Php4/shadow/README
+++ /dev/null
@@ -1,2 +0,0 @@
-This example use the file in ../../Interface/gifplot.i to build
-an interface with shadow classes.  Run the script 'runme.php3'.
diff --git a/Examples/GIFPlot/Php4/shadow/cmap b/Examples/GIFPlot/Php4/shadow/cmap
deleted file mode 100644
index a20c331a9573dd8443380680bfe2cc428780d8a9..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

literal 768
zcmZQzpd(=A5)hSEP}Mdtvvzdz4h)M)OwTDSuW4%Uoiu&!q7`d5@7R0z#JS5i?>&C`
z?#s{r^Z@9-XXO?YlTlLFHMX#G@$?UkN=VBFxv-;m^2~WlR;}N<`@pd?7q8!a^y1xT
znmh34m-nxpKDd4D;+bOy_iW#^cE#d(Gbi_Tw$xXZ7G$R-M27|XxI5We80l&#%Snpx
zbFrd(h8Vt}lCeu@T6xFJRlCpJeMef510DGC$^DyG&YwK8f9IC<tCq~4HKo4`=)RKt
ztd#huP=7C1dn;3YEme6bQ8Jvz%Ed1tDW|Lfj0{^Rcb~wpXkcs<lvdTZboK$GWATc$
Xo3`&c2#k+ww;w!x^&XgFNDnap(k+Jt

diff --git a/Examples/GIFPlot/Php4/shadow/runme.php4 b/Examples/GIFPlot/Php4/shadow/runme.php4
deleted file mode 100644
index 3dffba050..000000000
--- a/Examples/GIFPlot/Php4/shadow/runme.php4
+++ /dev/null
@@ -1,79 +0,0 @@
-<?
-
-# Plot a 3D function
-include("gifplot.php");
-
-# Here is the function to plot
-function func($x, $y) {
-    return 5*cos(2*sqrt($x*$x+$y*$y))*exp(-0.3*sqrt($x*$x+$y*$y));
-}
-
-# Here are some plotting parameters
-$xmin = -5.0;
-$xmax =  5.0;
-$ymin = -5.0;
-$ymax =  5.0;
-$zmin = -5.0;
-$zmax =  5.0;
-
-# Grid resolution
-$nxpoints =  60;
-$nypoints =  60;
-
-$cmap  = new ColorMap("cmap");
-$frame = new FrameBuffer(500,500);
-$frame->clear(BLACK);
-
-
-$p3    = new Plot3D($frame,$xmin,$ymin,$zmin,$xmax,$ymax,$zmax);
-$p3->lookat(2*($zmax-$zmin));
-$p3->autoperspective(40);
-$p3->rotu(60);
-$p3->rotr(30);
-$p3->rotd(10);
-
-function drawsolid() {
-	global $xmax;
-	global $xmin;
-	global $ymax;
-	global $ymin;
-	global $zmin;
-	global $zmax;
-	global $nxpoints;
-	global $nypoints;
-	global $p3;
-
-    $p3->clear(BLACK);
-    $p3->start();
-    $dx = 1.0*($xmax-$xmin)/$nxpoints;
-    $dy = 1.0*($ymax-$ymin)/$nypoints;
-    $cscale = 240.0/($zmax-$zmin);
-    $x = $xmin;
-    for ($i = 0; $i < $nxpoints; $i++) {
-	$y = $ymin;
-	for ($j = 0; $j < $nypoints; $j++) {
-	    $z1 = func($x,$y);
-	    $z2 = func($x+$dx,$y);
-	    $z3 = func($x+$dx,$y+$dy);
-	    $z4 = func($x,$y+$dy);
-	    $c1 = $cscale*($z1-$zmin);
-	    $c2 = $cscale*($z2-$zmin);
-	    $c3 = $cscale*($z3-$zmin);
-	    $c4 = $cscale*($z4-$zmin);
-	    $c = ($c1+$c2+$c3+$c4)/4;
-	    if ($c < 0) { $c = 0; }
-	    if ($c > 239) { $c = 239; }
-	    $p3->solidquad($x,$y,$z1,$x+$dx,$y,$z2,$x+$dx,$y+$dy,$z3,$x,$y+$dy,$z4,$c+16);
-	    $y = $y + $dy;
-	}
-	$x = $x + $dx;
-    }
-}
-
-print "Making a nice 3D plot...\n";
-drawsolid();
-
-$frame->writeGIF($cmap,"image.gif");
-print "Wrote image.gif\n";
-
-?>
diff --git a/Examples/GIFPlot/Php4/simple/Makefile b/Examples/GIFPlot/Php4/simple/Makefile
deleted file mode 100644
index 6903bec0b..000000000
--- a/Examples/GIFPlot/Php4/simple/Makefile
+++ /dev/null
@@ -1,20 +0,0 @@
-TOP        = ../../..
-SWIG       = $(TOP)/../swig
-SWIGOPT    = -noproxy
-SRCS       =
-TARGET     = php_simple
-INTERFACE  = simple.i
-LIBS       = -L../.. -lgifplot
-INCLUDES   = -I../../Include
-
-all::
-	$(MAKE) -f $(TOP)/Makefile SRCS='$(SRCS)' SWIG='$(SWIG)' \
-	INCLUDES='$(INCLUDES)' LIBS='$(LIBS)' SWIGOPT='$(SWIGOPT)' \
-	TARGET='$(TARGET)' INTERFACE='$(INTERFACE)' php4
-
-clean::
-	$(MAKE) -f $(TOP)/Makefile php4_clean
-	rm -f *.gif
-	rm -f php_simple.h
-
-check: all
diff --git a/Examples/GIFPlot/Php4/simple/README b/Examples/GIFPlot/Php4/simple/README
deleted file mode 100644
index c2c799a70..000000000
--- a/Examples/GIFPlot/Php4/simple/README
+++ /dev/null
@@ -1,5 +0,0 @@
-This is a very minimalistic example in which just a few functions
-and constants from library are wrapped and used to draw some simple
-shapes.  The script 'runme.pl' runs the example.
-
-
diff --git a/Examples/GIFPlot/Php4/simple/runme.php4 b/Examples/GIFPlot/Php4/simple/runme.php4
deleted file mode 100644
index cf21a0927..000000000
--- a/Examples/GIFPlot/Php4/simple/runme.php4
+++ /dev/null
@@ -1,32 +0,0 @@
-<?
-
-# Draw some simple shapes
-print "Drawing some basic shapes\n";
-
-require "simple.php";
-
-$cmap = new_ColorMap();
-$f    = new_FrameBuffer(400,400);
-
-# Clear the picture
-FrameBuffer_clear($f,BLACK);
-
-# Make a red box
-FrameBuffer_box($f,40,40,200,200,RED);
-
-# Make a blue circle
-FrameBuffer_circle($f,200,200,40,BLUE);
-
-# Make green line
-FrameBuffer_line($f,10,390,390,200, GREEN);
-
-# Write an image out to disk
-
-FrameBuffer_writeGIF($f,$cmap,"image.gif");
-print "Wrote image.gif\n";
-
-delete_FrameBuffer($f);
-delete_ColorMap($cmap);
-
-?>
-
diff --git a/Examples/GIFPlot/Php4/simple/simple.i b/Examples/GIFPlot/Php4/simple/simple.i
deleted file mode 100644
index 457bc4c09..000000000
--- a/Examples/GIFPlot/Php4/simple/simple.i
+++ /dev/null
@@ -1,38 +0,0 @@
-/* This example shows a very simple interface wrapping a few 
-   primitive declarations */
-
-%module simple
-%{
-#include "gifplot.h"
-%}
-
-typedef unsigned char Pixel;
-
-/* Here are a few useful functions */
-
-ColorMap    *new_ColorMap(char *filename = 0);
-void         delete_ColorMap(ColorMap *cmap);
-
-FrameBuffer *new_FrameBuffer(unsigned int width, unsigned int height);
-void         delete_FrameBuffer(FrameBuffer *frame);
-void         FrameBuffer_clear(FrameBuffer *frame, Pixel color);
-void         FrameBuffer_line(FrameBuffer *frame, int x1, int y1, int x2, int y2, Pixel color);
-void         FrameBuffer_box(FrameBuffer *frame, int x1, int y1, int x2, int y2, Pixel color);
-void         FrameBuffer_circle(FrameBuffer *frame, int x1, int y1, int radius, Pixel color);
-int          FrameBuffer_writeGIF(FrameBuffer *f, ColorMap *c, char *filename);
-
-/* And some useful constants */
-
-#define BLACK   0
-#define WHITE   1
-#define RED     2
-#define GREEN   3
-#define BLUE    4
-#define YELLOW  5
-#define CYAN    6
-#define MAGENTA 7
-
-
-
-
-
diff --git a/Examples/GIFPlot/Pike/check.list b/Examples/GIFPlot/Pike/check.list
deleted file mode 100644
index d38998cab..000000000
--- a/Examples/GIFPlot/Pike/check.list
+++ /dev/null
@@ -1,2 +0,0 @@
-# see top-level Makefile.in
-simple
diff --git a/Examples/GIFPlot/Pike/simple/Makefile b/Examples/GIFPlot/Pike/simple/Makefile
deleted file mode 100644
index d339e0333..000000000
--- a/Examples/GIFPlot/Pike/simple/Makefile
+++ /dev/null
@@ -1,24 +0,0 @@
-TOP        = ../../..
-SWIG       = $(TOP)/../swig
-SWIGOPT    =
-SRCS       =
-TARGET     = simple
-INTERFACE  = simple.i
-LIBS       = -L../.. -lgifplot
-INCLUDES   = -I../../Include
-
-all::
-	$(MAKE) -f $(TOP)/Makefile SRCS='$(SRCS)' SWIG='$(SWIG)' \
-	INCLUDES='$(INCLUDES)' LIBS='$(LIBS)' SWIGOPT='$(SWIGOPT)' \
-	TARGET='$(TARGET)' INTERFACE='$(INTERFACE)' pike
-
-static::
-	$(MAKE) -f $(TOP)/Makefile SRCS='$(SRCS)' SWIG='$(SWIG)' \
-	INCLUDES='$(INCLUDES)' LIBS='$(LIBS)' SWIGOPT='$(SWIGOPT)' \
-	TARGET='mypike' INTERFACE='$(INTERFACE)' pike_static
-
-clean::
-	$(MAKE) -f $(TOP)/Makefile pike_clean
-	rm -f *.gif
-
-check: all
diff --git a/Examples/GIFPlot/Pike/simple/README b/Examples/GIFPlot/Pike/simple/README
deleted file mode 100644
index 177b3633b..000000000
--- a/Examples/GIFPlot/Pike/simple/README
+++ /dev/null
@@ -1,5 +0,0 @@
-This is a very minimalistic example in which just a few functions
-and constants from library are wrapped and used to draw some simple
-shapes.  The script 'runme.pike' runs the example.
-
-
diff --git a/Examples/GIFPlot/Pike/simple/runme.pike b/Examples/GIFPlot/Pike/simple/runme.pike
deleted file mode 100644
index 0e70235f1..000000000
--- a/Examples/GIFPlot/Pike/simple/runme.pike
+++ /dev/null
@@ -1,30 +0,0 @@
-int main()
-{
-  // Draw some simple shapes
-  write("Drawing some basic shapes\n");
-
-   .simple.ColorMap cmap = .simple.new_ColorMap();
-   .simple.FrameBuffer f = .simple.new_FrameBuffer(400, 400);
-
-  // Clear the picture
-  .simple.FrameBuffer_clear(f, .simple.BLACK);
-
-  // Make a red box
-  .simple.FrameBuffer_box(f, 40, 40, 200, 200, .simple.RED);
-
-  // Make a blue circle
-  .simple.FrameBuffer_circle(f, 200, 200, 40, .simple.BLUE);
-
-  // Make green line
-  .simple.FrameBuffer_line(f, 10, 390, 390, 200, .simple.GREEN);
-
-  // Write an image out to disk
-  .simple.FrameBuffer_writeGIF(f, cmap, "image.gif");
-  write("Wrote image.gif\n");
-
-  .simple.delete_FrameBuffer(f);
-  .simple.delete_ColorMap(cmap);
-  
-  return 0;
-}
-
diff --git a/Examples/GIFPlot/Pike/simple/simple.i b/Examples/GIFPlot/Pike/simple/simple.i
deleted file mode 100644
index 457bc4c09..000000000
--- a/Examples/GIFPlot/Pike/simple/simple.i
+++ /dev/null
@@ -1,38 +0,0 @@
-/* This example shows a very simple interface wrapping a few 
-   primitive declarations */
-
-%module simple
-%{
-#include "gifplot.h"
-%}
-
-typedef unsigned char Pixel;
-
-/* Here are a few useful functions */
-
-ColorMap    *new_ColorMap(char *filename = 0);
-void         delete_ColorMap(ColorMap *cmap);
-
-FrameBuffer *new_FrameBuffer(unsigned int width, unsigned int height);
-void         delete_FrameBuffer(FrameBuffer *frame);
-void         FrameBuffer_clear(FrameBuffer *frame, Pixel color);
-void         FrameBuffer_line(FrameBuffer *frame, int x1, int y1, int x2, int y2, Pixel color);
-void         FrameBuffer_box(FrameBuffer *frame, int x1, int y1, int x2, int y2, Pixel color);
-void         FrameBuffer_circle(FrameBuffer *frame, int x1, int y1, int radius, Pixel color);
-int          FrameBuffer_writeGIF(FrameBuffer *f, ColorMap *c, char *filename);
-
-/* And some useful constants */
-
-#define BLACK   0
-#define WHITE   1
-#define RED     2
-#define GREEN   3
-#define BLUE    4
-#define YELLOW  5
-#define CYAN    6
-#define MAGENTA 7
-
-
-
-
-
diff --git a/Examples/GIFPlot/Python/check.list b/Examples/GIFPlot/Python/check.list
deleted file mode 100644
index 13de977af..000000000
--- a/Examples/GIFPlot/Python/check.list
+++ /dev/null
@@ -1,4 +0,0 @@
-# see top-level Makefile.in
-full
-shadow
-simple
diff --git a/Examples/GIFPlot/Python/full/Makefile b/Examples/GIFPlot/Python/full/Makefile
deleted file mode 100644
index 83a7c864b..000000000
--- a/Examples/GIFPlot/Python/full/Makefile
+++ /dev/null
@@ -1,26 +0,0 @@
-TOP        = ../../..
-SWIG       = $(TOP)/../preinst-swig
-SWIGOPT    = -I../../Include 
-SRCS       =
-TARGET     = gifplot
-INTERFACE  = gifplot.i
-LIBS       = -L../.. -lgifplot
-INCLUDES   = -I../../Include
-
-all::
-	$(MAKE) -f $(TOP)/Makefile SRCS='$(SRCS)' SWIG='$(SWIG)' \
-	INCLUDES='$(INCLUDES)' LIBS='$(LIBS)' SWIGOPT='$(SWIGOPT)' \
-	TARGET='$(TARGET)' INTERFACE='$(INTERFACE)' python
-
-static::
-	$(MAKE) -f $(TOP)/Makefile SRCS='$(SRCS)' SWIG='$(SWIG)' \
-	INCLUDES='$(INCLUDES)' LIBS='$(LIBS)' SWIGOPT='$(SWIGOPT)' \
-	TARGET='mypython' INTERFACE='$(INTERFACE)' python_static
-
-clean::
-	$(MAKE) -f $(TOP)/Makefile python_clean
-	rm -f $(TARGET).py
-	rm -f *.gif
-
-check: all
-	$(MAKE) -f $(TOP)/Makefile python_run
diff --git a/Examples/GIFPlot/Python/full/README b/Examples/GIFPlot/Python/full/README
deleted file mode 100644
index 52971e40a..000000000
--- a/Examples/GIFPlot/Python/full/README
+++ /dev/null
@@ -1,8 +0,0 @@
-This example runs the entire gifplot.h header file through SWIG without
-any changes.  The script 'runme.py' does something a little more 
-interesting.   You'll have to go look at the header file to get a complete
-listing of the functions.
-
-
-
-
diff --git a/Examples/GIFPlot/Python/full/cmap b/Examples/GIFPlot/Python/full/cmap
deleted file mode 100644
index a20c331a9573dd8443380680bfe2cc428780d8a9..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

literal 768
zcmZQzpd(=A5)hSEP}Mdtvvzdz4h)M)OwTDSuW4%Uoiu&!q7`d5@7R0z#JS5i?>&C`
z?#s{r^Z@9-XXO?YlTlLFHMX#G@$?UkN=VBFxv-;m^2~WlR;}N<`@pd?7q8!a^y1xT
znmh34m-nxpKDd4D;+bOy_iW#^cE#d(Gbi_Tw$xXZ7G$R-M27|XxI5We80l&#%Snpx
zbFrd(h8Vt}lCeu@T6xFJRlCpJeMef510DGC$^DyG&YwK8f9IC<tCq~4HKo4`=)RKt
ztd#huP=7C1dn;3YEme6bQ8Jvz%Ed1tDW|Lfj0{^Rcb~wpXkcs<lvdTZboK$GWATc$
Xo3`&c2#k+ww;w!x^&XgFNDnap(k+Jt

diff --git a/Examples/GIFPlot/Python/full/gifplot.i b/Examples/GIFPlot/Python/full/gifplot.i
deleted file mode 100644
index 5a7f5008f..000000000
--- a/Examples/GIFPlot/Python/full/gifplot.i
+++ /dev/null
@@ -1,15 +0,0 @@
-/* Oh what the heck, let's just grab the whole darn header file
-   and see what happens. */
-
-%module gifplot
-%{
-
-/* Note: You still need this part because the %include directive
-   merely causes SWIG to interpret the contents of a file.  It doesn't
-   include the right include headers for the resulting C code */
-
-#include "gifplot.h"
-
-%}
-
-%include gifplot.h
diff --git a/Examples/GIFPlot/Python/full/runme.py b/Examples/GIFPlot/Python/full/runme.py
deleted file mode 100644
index cb324c814..000000000
--- a/Examples/GIFPlot/Python/full/runme.py
+++ /dev/null
@@ -1,64 +0,0 @@
-# Plot a 3D function
-# This example uses the low-level C interface.
-
-from _gifplot import *
-from math import *
-
-# Here is the function to plot
-def func(x,y):
-	return 5*cos(2*sqrt(x*x+y*y))*exp(-0.3*sqrt(x*x+y*y))
-
-# Here are some plotting parameters
-xmin = -5.0
-xmax =  5.0
-ymin = -5.0
-ymax =  5.0
-zmin = -5.0
-zmax =  5.0
-
-# Grid resolution
-nxpoints =  60
-nypoints =  60
-
-cmap  = new_ColorMap("cmap")
-frame = new_FrameBuffer(500,500)
-FrameBuffer_clear(frame,BLACK)
-
-p3    = new_Plot3D(frame,xmin,ymin,zmin,xmax,ymax,zmax)
-Plot3D_lookat(p3,2*max([xmax-xmin,ymax-ymin,zmax-zmin]))
-Plot3D_autoperspective(p3,40)
-Plot3D_rotu(p3,60)
-Plot3D_rotr(p3,30)
-Plot3D_rotd(p3,10)
-
-def drawsolid():
-	Plot3D_clear(p3,BLACK)
-	Plot3D_start(p3)
-	dx = 1.0*(xmax-xmin)/nxpoints
-	dy = 1.0*(ymax-ymin)/nypoints
-	cscale = 240.0/(zmax-zmin)
-	x = xmin
-	for i in xrange(0,nxpoints):
-		y = ymin
-		for j in xrange(0,nypoints):
-			z1 = func(x,y)
-			z2 = func(x+dx,y)
-			z3 = func(x+dx,y+dy)
-			z4 = func(x,y+dy)
-			c1 = cscale*(z1-zmin)
-			c2 = cscale*(z2-zmin)
-			c3 = cscale*(z3-zmin)
-			c4 = cscale*(z4-zmin)
-			c = int((c1+c2+c3+c4)/4)
-			if (c < 0) : c = 0
-			if c > 239 : c = 239
-			Plot3D_solidquad(p3,x,y,z1,x+dx,y,z2,x+dx,y+dy,z3,x,y+dy,z4,c+16)
-			y = y + dy		
-		x = x + dx
-
-print "Making a nice 3D plot..."
-drawsolid()
-
-FrameBuffer_writeGIF(frame,cmap,"image.gif")
-print "Wrote image.gif"
-
diff --git a/Examples/GIFPlot/Python/shadow/Makefile b/Examples/GIFPlot/Python/shadow/Makefile
deleted file mode 100644
index 73fca9673..000000000
--- a/Examples/GIFPlot/Python/shadow/Makefile
+++ /dev/null
@@ -1,26 +0,0 @@
-TOP        = ../../..
-SWIG       = $(TOP)/../preinst-swig
-SWIGOPT    = -I../../Interface
-SRCS       =
-TARGET     = gifplot
-INTERFACE  = gifplot.i
-LIBS       = -L../.. -lgifplot
-INCLUDES   = -I../../Include
-
-all::
-	$(MAKE) -f $(TOP)/Makefile SRCS='$(SRCS)' SWIG='$(SWIG)' \
-	INCLUDES='$(INCLUDES)' LIBS='$(LIBS)' SWIGOPT='$(SWIGOPT)' \
-	TARGET='$(TARGET)' INTERFACE='$(INTERFACE)' python
-
-static::
-	$(MAKE) -f $(TOP)/Makefile SRCS='$(SRCS)' SWIG='$(SWIG)' \
-	INCLUDES='$(INCLUDES)' LIBS='$(LIBS)' SWIGOPT='$(SWIGOPT)' \
-	TARGET='mypython' INTERFACE='$(INTERFACE)' python_static
-
-clean::
-	$(MAKE) -f $(TOP)/Makefile python_clean
-	rm -f $(TARGET).py
-	rm -f *.gif
-
-check: all
-	$(MAKE) -f $(TOP)/Makefile python_run
diff --git a/Examples/GIFPlot/Python/shadow/README b/Examples/GIFPlot/Python/shadow/README
deleted file mode 100644
index aa761e240..000000000
--- a/Examples/GIFPlot/Python/shadow/README
+++ /dev/null
@@ -1,8 +0,0 @@
-This example illustrates Python shadow classes. Take a look at
-the file GIFPlot/Interface/gifplot.i
-
-
-
-
-
-
diff --git a/Examples/GIFPlot/Python/shadow/cmap b/Examples/GIFPlot/Python/shadow/cmap
deleted file mode 100644
index a20c331a9573dd8443380680bfe2cc428780d8a9..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

literal 768
zcmZQzpd(=A5)hSEP}Mdtvvzdz4h)M)OwTDSuW4%Uoiu&!q7`d5@7R0z#JS5i?>&C`
z?#s{r^Z@9-XXO?YlTlLFHMX#G@$?UkN=VBFxv-;m^2~WlR;}N<`@pd?7q8!a^y1xT
znmh34m-nxpKDd4D;+bOy_iW#^cE#d(Gbi_Tw$xXZ7G$R-M27|XxI5We80l&#%Snpx
zbFrd(h8Vt}lCeu@T6xFJRlCpJeMef510DGC$^DyG&YwK8f9IC<tCq~4HKo4`=)RKt
ztd#huP=7C1dn;3YEme6bQ8Jvz%Ed1tDW|Lfj0{^Rcb~wpXkcs<lvdTZboK$GWATc$
Xo3`&c2#k+ww;w!x^&XgFNDnap(k+Jt

diff --git a/Examples/GIFPlot/Python/shadow/runme.py b/Examples/GIFPlot/Python/shadow/runme.py
deleted file mode 100644
index d91460121..000000000
--- a/Examples/GIFPlot/Python/shadow/runme.py
+++ /dev/null
@@ -1,62 +0,0 @@
-# Plot a 3D function
-import gifplot
-from math import *
-
-# Here is the function to plot
-def func(x,y):
-	return 5*cos(2*sqrt(x*x+y*y))*exp(-0.3*sqrt(x*x+y*y))
-
-# Here are some plotting parameters
-xmin = -5.0
-xmax =  5.0
-ymin = -5.0
-ymax =  5.0
-zmin = -5.0
-zmax =  5.0
-
-# Grid resolution
-nxpoints =  60
-nypoints =  60
-
-cmap  = gifplot.ColorMap("cmap")
-frame = gifplot.FrameBuffer(500,500)
-frame.clear(gifplot.BLACK)
-
-p3    = gifplot.Plot3D(frame,xmin,ymin,zmin,xmax,ymax,zmax)
-p3.lookat(2*max([xmax-xmin,ymax-ymin,zmax-zmin]))
-p3.autoperspective(40)
-p3.rotu(60)
-p3.rotr(30)
-p3.rotd(10)
-
-def drawsolid():
-	p3.clear(gifplot.BLACK)
-	p3.start()
-	dx = 1.0*(xmax-xmin)/nxpoints
-	dy = 1.0*(ymax-ymin)/nypoints
-	cscale = 240.0/(zmax-zmin)
-	x = xmin
-	for i in xrange(0,nxpoints):
-		y = ymin
-		for j in xrange(0,nypoints):
-			z1 = func(x,y)
-			z2 = func(x+dx,y)
-			z3 = func(x+dx,y+dy)
-			z4 = func(x,y+dy)
-			c1 = cscale*(z1-zmin)
-			c2 = cscale*(z2-zmin)
-			c3 = cscale*(z3-zmin)
-			c4 = cscale*(z4-zmin)
-			c = int((c1+c2+c3+c4)/4)
-			if (c < 0) : c = 0
-			if c > 239 : c = 239
-			p3.solidquad(x,y,z1,x+dx,y,z2,x+dx,y+dy,z3,x,y+dy,z4,c+16)
-			y = y + dy		
-		x = x + dx
-
-print "Making a nice 3D plot..."
-drawsolid()
-
-frame.writeGIF(cmap,"image.gif")
-print "Wrote image.gif"
-
diff --git a/Examples/GIFPlot/Python/simple/Makefile b/Examples/GIFPlot/Python/simple/Makefile
deleted file mode 100644
index 9fc9a6c72..000000000
--- a/Examples/GIFPlot/Python/simple/Makefile
+++ /dev/null
@@ -1,26 +0,0 @@
-TOP        = ../../..
-SWIG       = $(TOP)/../preinst-swig
-SWIGOPT    =
-SRCS       =
-TARGET     = simple
-INTERFACE  = simple.i
-LIBS       = -L../.. -lgifplot
-INCLUDES   = -I../../Include
-
-all::
-	$(MAKE) -f $(TOP)/Makefile SRCS='$(SRCS)' SWIG='$(SWIG)' \
-	INCLUDES='$(INCLUDES)' LIBS='$(LIBS)' SWIGOPT='$(SWIGOPT)' \
-	TARGET='$(TARGET)' INTERFACE='$(INTERFACE)' python
-
-static::
-	$(MAKE) -f $(TOP)/Makefile SRCS='$(SRCS)' SWIG='$(SWIG)' \
-	INCLUDES='$(INCLUDES)' LIBS='$(LIBS)' SWIGOPT='$(SWIGOPT)' \
-	TARGET='mypython' INTERFACE='$(INTERFACE)' python_static
-
-clean::
-	$(MAKE) -f $(TOP)/Makefile python_clean
-	rm -f $(TARGET).py
-	rm -f *.gif
-
-check: all
-	$(MAKE) -f $(TOP)/Makefile python_run
diff --git a/Examples/GIFPlot/Python/simple/README b/Examples/GIFPlot/Python/simple/README
deleted file mode 100644
index 22152c665..000000000
--- a/Examples/GIFPlot/Python/simple/README
+++ /dev/null
@@ -1,5 +0,0 @@
-This is a very minimalistic example in which just a few functions
-and constants from library are wrapped and used to draw some simple
-shapes.  The script 'runme.py' runs the example.
-
-
diff --git a/Examples/GIFPlot/Python/simple/runme.py b/Examples/GIFPlot/Python/simple/runme.py
deleted file mode 100644
index dade67767..000000000
--- a/Examples/GIFPlot/Python/simple/runme.py
+++ /dev/null
@@ -1,27 +0,0 @@
-# Draw some simple shapes
-print "Drawing some basic shapes"
-import simple
-
-cmap = simple.new_ColorMap()
-f    = simple.new_FrameBuffer(400,400)
-
-# Clear the picture
-simple.FrameBuffer_clear(f,simple.BLACK)
-
-# Make a red box
-simple.FrameBuffer_box(f,40,40,200,200,simple.RED)
-
-# Make a blue circle
-simple.FrameBuffer_circle(f,200,200,40,simple.BLUE)
-
-# Make green line
-simple.FrameBuffer_line(f,10,390,390,200, simple.GREEN)
-
-# Write an image out to disk
-
-simple.FrameBuffer_writeGIF(f,cmap,"image.gif")
-print "Wrote image.gif"
-
-simple.delete_FrameBuffer(f)
-simple.delete_ColorMap(cmap)
-
diff --git a/Examples/GIFPlot/Python/simple/simple.i b/Examples/GIFPlot/Python/simple/simple.i
deleted file mode 100644
index 457bc4c09..000000000
--- a/Examples/GIFPlot/Python/simple/simple.i
+++ /dev/null
@@ -1,38 +0,0 @@
-/* This example shows a very simple interface wrapping a few 
-   primitive declarations */
-
-%module simple
-%{
-#include "gifplot.h"
-%}
-
-typedef unsigned char Pixel;
-
-/* Here are a few useful functions */
-
-ColorMap    *new_ColorMap(char *filename = 0);
-void         delete_ColorMap(ColorMap *cmap);
-
-FrameBuffer *new_FrameBuffer(unsigned int width, unsigned int height);
-void         delete_FrameBuffer(FrameBuffer *frame);
-void         FrameBuffer_clear(FrameBuffer *frame, Pixel color);
-void         FrameBuffer_line(FrameBuffer *frame, int x1, int y1, int x2, int y2, Pixel color);
-void         FrameBuffer_box(FrameBuffer *frame, int x1, int y1, int x2, int y2, Pixel color);
-void         FrameBuffer_circle(FrameBuffer *frame, int x1, int y1, int radius, Pixel color);
-int          FrameBuffer_writeGIF(FrameBuffer *f, ColorMap *c, char *filename);
-
-/* And some useful constants */
-
-#define BLACK   0
-#define WHITE   1
-#define RED     2
-#define GREEN   3
-#define BLUE    4
-#define YELLOW  5
-#define CYAN    6
-#define MAGENTA 7
-
-
-
-
-
diff --git a/Examples/GIFPlot/README b/Examples/GIFPlot/README
deleted file mode 100644
index ac1025a42..000000000
--- a/Examples/GIFPlot/README
+++ /dev/null
@@ -1,59 +0,0 @@
-GIFPlot
-=======
-
-To illustrate various SWIG features, the following examples involve
-building an interface to a small, but somewhat useful graphics library
-for creating 2D and 3D images in the form of GIF files.  The Perl,
-Python, Tcl, Java, Ruby etc. directories contain various examples specific to
-those languages.
-
-This library was originally developed as part of the SPaSM molecular
-dynamics project at Los Alamos National Laboratory.  However, due to
-patent enforcement issues related to LZW encoding and a general lack
-of time on the part of the author, the library was never officially
-released.  On the plus side, a number of people have found it to be a
-useful easter egg within the SWIG distribution :-).
-
-<LEGAL>
-DUE TO PATENT RESTRICTIONS ON THE LZW COMPRESSION ALGORITHM, THIS
-LIBRARY ONLY PRODUCES UNCOMPRESSED GIF FILES.  SO THERE.
-</LEGAL>
-
-Building the Library
-====================
-
-In order to run the examples, it is first necessary to build the GIFPlot
-C library.  To do this, simply run make:
-
-	make
-
-Running the Examples
-====================
-
-Once the library has been built, go to your chosen language directory,
-that is, Perl, Python, Tcl, Java, Ruby etc. Each example should have a
-README file with a description.
-
-Each example can be compiled using the makefile in each example directory. This
-makefile uses the top level makefile in the "Examples" directory of the distribution.
-If the example doesn't compile, you will need to adjust the settings in this file.
-
-Documentation
-=============
-
-Read the source Luke.   The examples should be pretty much self-explanatory.
-The header file Include/gifplot.h contains the full API.
-
-The original documentation for the library can be found online at:
-
-          http://www.dabeaz.com/gifplot/index.html
-
-
-Let me know what you think!
-===========================
-If you found this example to be useful, confusing, or otherwise, I would like to know
-about it.   Suggestions for improvement are welcome.
-
--- Dave (dave@dabeaz.com)
-
-
diff --git a/Examples/GIFPlot/Ruby/check.list b/Examples/GIFPlot/Ruby/check.list
deleted file mode 100644
index 13de977af..000000000
--- a/Examples/GIFPlot/Ruby/check.list
+++ /dev/null
@@ -1,4 +0,0 @@
-# see top-level Makefile.in
-full
-shadow
-simple
diff --git a/Examples/GIFPlot/Ruby/full/Makefile b/Examples/GIFPlot/Ruby/full/Makefile
deleted file mode 100644
index 5af8bc832..000000000
--- a/Examples/GIFPlot/Ruby/full/Makefile
+++ /dev/null
@@ -1,24 +0,0 @@
-TOP        = ../../..
-SWIG       = $(TOP)/../swig
-SWIGOPT    = -I../../Include
-SRCS       =
-TARGET     = gifplot
-INTERFACE  = gifplot.i
-LIBS       = -L../.. -lgifplot
-INCLUDES   = -I../../Include
-
-all::
-	$(MAKE) -f $(TOP)/Makefile SRCS='$(SRCS)' SWIG='$(SWIG)' \
-	INCLUDES='$(INCLUDES)' LIBS='$(LIBS)' SWIGOPT='$(SWIGOPT)' \
-	TARGET='$(TARGET)' INTERFACE='$(INTERFACE)' ruby
-
-static::
-	$(MAKE) -f $(TOP)/Makefile SRCS='$(SRCS)' SWIG='$(SWIG)' \
-	INCLUDES='$(INCLUDES)' LIBS='$(LIBS)' SWIGOPT='$(SWIGOPT)' \
-	TARGET='myruby' INTERFACE='$(INTERFACE)' ruby_static
-
-clean::
-	$(MAKE) -f $(TOP)/Makefile ruby_clean
-	rm -f *.gif
-
-check: all
diff --git a/Examples/GIFPlot/Ruby/full/README b/Examples/GIFPlot/Ruby/full/README
deleted file mode 100644
index 22af6cb06..000000000
--- a/Examples/GIFPlot/Ruby/full/README
+++ /dev/null
@@ -1,8 +0,0 @@
-This example runs the entire gifplot.h header file through SWIG without
-any changes.  The script 'runme.rb' does something a little more 
-interesting.   You'll have to go look at the header file to get a complete
-listing of the functions.
-
-
-
-
diff --git a/Examples/GIFPlot/Ruby/full/cmap b/Examples/GIFPlot/Ruby/full/cmap
deleted file mode 100644
index a20c331a9573dd8443380680bfe2cc428780d8a9..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

literal 768
zcmZQzpd(=A5)hSEP}Mdtvvzdz4h)M)OwTDSuW4%Uoiu&!q7`d5@7R0z#JS5i?>&C`
z?#s{r^Z@9-XXO?YlTlLFHMX#G@$?UkN=VBFxv-;m^2~WlR;}N<`@pd?7q8!a^y1xT
znmh34m-nxpKDd4D;+bOy_iW#^cE#d(Gbi_Tw$xXZ7G$R-M27|XxI5We80l&#%Snpx
zbFrd(h8Vt}lCeu@T6xFJRlCpJeMef510DGC$^DyG&YwK8f9IC<tCq~4HKo4`=)RKt
ztd#huP=7C1dn;3YEme6bQ8Jvz%Ed1tDW|Lfj0{^Rcb~wpXkcs<lvdTZboK$GWATc$
Xo3`&c2#k+ww;w!x^&XgFNDnap(k+Jt

diff --git a/Examples/GIFPlot/Ruby/full/gifplot.i b/Examples/GIFPlot/Ruby/full/gifplot.i
deleted file mode 100644
index 5a7f5008f..000000000
--- a/Examples/GIFPlot/Ruby/full/gifplot.i
+++ /dev/null
@@ -1,15 +0,0 @@
-/* Oh what the heck, let's just grab the whole darn header file
-   and see what happens. */
-
-%module gifplot
-%{
-
-/* Note: You still need this part because the %include directive
-   merely causes SWIG to interpret the contents of a file.  It doesn't
-   include the right include headers for the resulting C code */
-
-#include "gifplot.h"
-
-%}
-
-%include gifplot.h
diff --git a/Examples/GIFPlot/Ruby/full/runme.rb b/Examples/GIFPlot/Ruby/full/runme.rb
deleted file mode 100644
index 5c118b2fa..000000000
--- a/Examples/GIFPlot/Ruby/full/runme.rb
+++ /dev/null
@@ -1,66 +0,0 @@
-# Plot a 3D function
-require 'gifplot'
-include Gifplot
-include Math
-
-# Here is the function to plot
-def func(x,y)
-  return 5*cos(2*sqrt(x*x+y*y))*exp(-0.3*sqrt(x*x+y*y))
-end
-
-# Here are some plotting parameters
-XMIN = -5.0
-XMAX =  5.0
-YMIN = -5.0
-YMAX =  5.0
-ZMIN = -5.0
-ZMAX =  5.0
-
-# Grid resolution
-NXPOINTS =  60
-NYPOINTS =  60
-
-cmap  = new_ColorMap("cmap")
-frame = new_FrameBuffer(500,500)
-FrameBuffer_clear(frame,BLACK)
-
-P3    = new_Plot3D(frame,XMIN,YMIN,ZMIN,XMAX,YMAX,ZMAX)
-Plot3D_lookat(P3,2*[XMAX-XMIN,YMAX-YMIN,ZMAX-ZMIN].max)
-Plot3D_autoperspective(P3,40)
-Plot3D_rotu(P3,60)
-Plot3D_rotr(P3,30)
-Plot3D_rotd(P3,10)
-
-def drawsolid()
-  Plot3D_clear(P3,BLACK)
-  Plot3D_start(P3)
-  dx = 1.0*(XMAX-XMIN)/NXPOINTS
-  dy = 1.0*(YMAX-YMIN)/NYPOINTS
-  cscale = 240.0/(ZMAX-ZMIN)
-  x = XMIN
-  for i in 0...NXPOINTS
-    y = YMIN
-    for j in 0...NYPOINTS
-      z1 = func(x,y)
-      z2 = func(x+dx,y)
-      z3 = func(x+dx,y+dy)
-      z4 = func(x,y+dy)
-      c1 = cscale*(z1-ZMIN)
-      c2 = cscale*(z2-ZMIN)
-      c3 = cscale*(z3-ZMIN)
-      c4 = cscale*(z4-ZMIN)
-      c = (c1+c2+c3+c4)/4
-      c = 0 if (c < 0)
-      c = 239 if c > 239
-      Plot3D_solidquad(P3,x,y,z1,x+dx,y,z2,x+dx,y+dy,z3,x,y+dy,z4,c+16)
-      y = y + dy
-    end
-    x = x + dx
-  end
-end
-
-puts "Making a nice 3D plot..."
-drawsolid()
-
-FrameBuffer_writeGIF(frame,cmap,"image.gif")
-puts "Wrote image.gif"
diff --git a/Examples/GIFPlot/Ruby/shadow/Makefile b/Examples/GIFPlot/Ruby/shadow/Makefile
deleted file mode 100644
index ea382ea88..000000000
--- a/Examples/GIFPlot/Ruby/shadow/Makefile
+++ /dev/null
@@ -1,24 +0,0 @@
-TOP        = ../../..
-SWIG       = $(TOP)/../swig
-SWIGOPT    = -I../../Interface
-SRCS       =
-TARGET     = gifplot
-INTERFACE  = gifplot.i
-LIBS       = -L../.. -lgifplot
-INCLUDES   = -I../../Include
-
-all::
-	$(MAKE) -f $(TOP)/Makefile SRCS='$(SRCS)' SWIG='$(SWIG)' \
-	INCLUDES='$(INCLUDES)' LIBS='$(LIBS)' SWIGOPT='$(SWIGOPT)' \
-	TARGET='$(TARGET)' INTERFACE='$(INTERFACE)' ruby
-
-static::
-	$(MAKE) -f $(TOP)/Makefile SRCS='$(SRCS)' SWIG='$(SWIG)' \
-	INCLUDES='$(INCLUDES)' LIBS='$(LIBS)' SWIGOPT='$(SWIGOPT)' \
-	TARGET='myruby' INTERFACE='$(INTERFACE)' ruby_static
-
-clean::
-	$(MAKE) -f $(TOP)/Makefile ruby_clean
-	rm -f *.gif
-
-check: all
diff --git a/Examples/GIFPlot/Ruby/shadow/README b/Examples/GIFPlot/Ruby/shadow/README
deleted file mode 100644
index 7a33e137f..000000000
--- a/Examples/GIFPlot/Ruby/shadow/README
+++ /dev/null
@@ -1,5 +0,0 @@
-This example illustrates Ruby shadow classes. Take a look at
-the file GIFPlot/Interface/gifplot.i
-
-Actually Ruby module of SWIG needs no shadow class.  But this example
-is named "shadow" in order to be consistent with other languages.
diff --git a/Examples/GIFPlot/Ruby/shadow/cmap b/Examples/GIFPlot/Ruby/shadow/cmap
deleted file mode 100644
index a20c331a9573dd8443380680bfe2cc428780d8a9..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

literal 768
zcmZQzpd(=A5)hSEP}Mdtvvzdz4h)M)OwTDSuW4%Uoiu&!q7`d5@7R0z#JS5i?>&C`
z?#s{r^Z@9-XXO?YlTlLFHMX#G@$?UkN=VBFxv-;m^2~WlR;}N<`@pd?7q8!a^y1xT
znmh34m-nxpKDd4D;+bOy_iW#^cE#d(Gbi_Tw$xXZ7G$R-M27|XxI5We80l&#%Snpx
zbFrd(h8Vt}lCeu@T6xFJRlCpJeMef510DGC$^DyG&YwK8f9IC<tCq~4HKo4`=)RKt
ztd#huP=7C1dn;3YEme6bQ8Jvz%Ed1tDW|Lfj0{^Rcb~wpXkcs<lvdTZboK$GWATc$
Xo3`&c2#k+ww;w!x^&XgFNDnap(k+Jt

diff --git a/Examples/GIFPlot/Ruby/shadow/runme.rb b/Examples/GIFPlot/Ruby/shadow/runme.rb
deleted file mode 100644
index 0afcceef9..000000000
--- a/Examples/GIFPlot/Ruby/shadow/runme.rb
+++ /dev/null
@@ -1,66 +0,0 @@
-# Plot a 3D function
-require 'gifplot'
-include Math
-
-# Here is the function to plot
-def func(x,y)
-  return 5*cos(2*sqrt(x*x+y*y))*exp(-0.3*sqrt(x*x+y*y))
-end
-
-# Here are some plotting parameters
-XMIN = -5.0
-XMAX =  5.0
-YMIN = -5.0
-YMAX =  5.0
-ZMIN = -5.0
-ZMAX =  5.0
-
-# Grid resolution
-NXPOINTS =  60
-NYPOINTS =  60
-
-cmap  = Gifplot::ColorMap.new("cmap")
-frame = Gifplot::FrameBuffer.new(500,500)
-frame.clear(Gifplot::BLACK)
-
-P3    = Gifplot::Plot3D.new(frame,XMIN,YMIN,ZMIN,XMAX,YMAX,ZMAX)
-P3.lookat(2*[XMAX-XMIN,YMAX-YMIN,ZMAX-ZMIN].max)
-P3.autoperspective(40)
-P3.rotu(60)
-P3.rotr(30)
-P3.rotd(10)
-
-def drawsolid()
-  P3.clear(Gifplot::BLACK)
-  P3.start()
-  dx = 1.0*(XMAX-XMIN)/NXPOINTS
-  dy = 1.0*(YMAX-YMIN)/NYPOINTS
-  cscale = 240.0/(ZMAX-ZMIN)
-  x = XMIN
-  for i in 0...NXPOINTS
-    y = YMIN
-    for j in 0...NYPOINTS
-      z1 = func(x,y)
-      z2 = func(x+dx,y)
-      z3 = func(x+dx,y+dy)
-      z4 = func(x,y+dy)
-      c1 = cscale*(z1-ZMIN)
-      c2 = cscale*(z2-ZMIN)
-      c3 = cscale*(z3-ZMIN)
-      c4 = cscale*(z4-ZMIN)
-      c = (c1+c2+c3+c4)/4
-      c = 0 if (c < 0)
-      c = 239 if c > 239
-      P3.solidquad(x,y,z1,x+dx,y,z2,x+dx,y+dy,z3,x,y+dy,z4,c+16)
-      y = y + dy
-    end
-    x = x + dx
-  end
-end
-
-puts "Making a nice 3D plot..."
-drawsolid()
-
-frame.writeGIF(cmap,"image.gif")
-puts "Wrote image.gif"
-
diff --git a/Examples/GIFPlot/Ruby/simple/Makefile b/Examples/GIFPlot/Ruby/simple/Makefile
deleted file mode 100644
index f7ca1a7d8..000000000
--- a/Examples/GIFPlot/Ruby/simple/Makefile
+++ /dev/null
@@ -1,24 +0,0 @@
-TOP        = ../../..
-SWIG       = $(TOP)/../swig
-SWIGOPT    =
-SRCS       =
-TARGET     = simple
-INTERFACE  = simple.i
-LIBS       = -L../.. -lgifplot
-INCLUDES   = -I../../Include
-
-all::
-	$(MAKE) -f $(TOP)/Makefile SRCS='$(SRCS)' SWIG='$(SWIG)' \
-	INCLUDES='$(INCLUDES)' LIBS='$(LIBS)' SWIGOPT='$(SWIGOPT)' \
-	TARGET='$(TARGET)' INTERFACE='$(INTERFACE)' ruby
-
-static::
-	$(MAKE) -f $(TOP)/Makefile SRCS='$(SRCS)' SWIG='$(SWIG)' \
-	INCLUDES='$(INCLUDES)' LIBS='$(LIBS)' SWIGOPT='$(SWIGOPT)' \
-	TARGET='myruby' INTERFACE='$(INTERFACE)' ruby_static
-
-clean::
-	$(MAKE) -f $(TOP)/Makefile ruby_clean
-	rm -f *.gif
-
-check: all
diff --git a/Examples/GIFPlot/Ruby/simple/README b/Examples/GIFPlot/Ruby/simple/README
deleted file mode 100644
index 9b51038bf..000000000
--- a/Examples/GIFPlot/Ruby/simple/README
+++ /dev/null
@@ -1,5 +0,0 @@
-This is a very minimalistic example in which just a few functions
-and constants from library are wrapped and used to draw some simple
-shapes.  The script 'runme.rb' runs the example.
-
-
diff --git a/Examples/GIFPlot/Ruby/simple/runme.rb b/Examples/GIFPlot/Ruby/simple/runme.rb
deleted file mode 100644
index e8bf5a40f..000000000
--- a/Examples/GIFPlot/Ruby/simple/runme.rb
+++ /dev/null
@@ -1,27 +0,0 @@
-# Draw some simple shapes
-puts "Drawing some basic shapes"
-require 'simple'
-
-cmap = Simple.new_ColorMap()
-f    = Simple.new_FrameBuffer(400,400)
-
-# Clear the picture
-Simple.FrameBuffer_clear(f,Simple::BLACK)
-
-# Make a red box
-Simple.FrameBuffer_box(f,40,40,200,200,Simple::RED)
-
-# Make a blue circle
-Simple.FrameBuffer_circle(f,200,200,40,Simple::BLUE)
-
-# Make green line
-Simple.FrameBuffer_line(f,10,390,390,200, Simple::GREEN)
-
-# Write an image out to disk
-
-Simple.FrameBuffer_writeGIF(f,cmap,"image.gif")
-puts "Wrote image.gif"
-
-Simple.delete_FrameBuffer(f)
-Simple.delete_ColorMap(cmap)
-
diff --git a/Examples/GIFPlot/Ruby/simple/simple.i b/Examples/GIFPlot/Ruby/simple/simple.i
deleted file mode 100644
index 457bc4c09..000000000
--- a/Examples/GIFPlot/Ruby/simple/simple.i
+++ /dev/null
@@ -1,38 +0,0 @@
-/* This example shows a very simple interface wrapping a few 
-   primitive declarations */
-
-%module simple
-%{
-#include "gifplot.h"
-%}
-
-typedef unsigned char Pixel;
-
-/* Here are a few useful functions */
-
-ColorMap    *new_ColorMap(char *filename = 0);
-void         delete_ColorMap(ColorMap *cmap);
-
-FrameBuffer *new_FrameBuffer(unsigned int width, unsigned int height);
-void         delete_FrameBuffer(FrameBuffer *frame);
-void         FrameBuffer_clear(FrameBuffer *frame, Pixel color);
-void         FrameBuffer_line(FrameBuffer *frame, int x1, int y1, int x2, int y2, Pixel color);
-void         FrameBuffer_box(FrameBuffer *frame, int x1, int y1, int x2, int y2, Pixel color);
-void         FrameBuffer_circle(FrameBuffer *frame, int x1, int y1, int radius, Pixel color);
-int          FrameBuffer_writeGIF(FrameBuffer *f, ColorMap *c, char *filename);
-
-/* And some useful constants */
-
-#define BLACK   0
-#define WHITE   1
-#define RED     2
-#define GREEN   3
-#define BLUE    4
-#define YELLOW  5
-#define CYAN    6
-#define MAGENTA 7
-
-
-
-
-
diff --git a/Examples/GIFPlot/Tcl/check.list b/Examples/GIFPlot/Tcl/check.list
deleted file mode 100644
index 2b6e3d28a..000000000
--- a/Examples/GIFPlot/Tcl/check.list
+++ /dev/null
@@ -1,4 +0,0 @@
-# see top-level Makefile.in
-full
-mandel
-simple
diff --git a/Examples/GIFPlot/Tcl/full/Makefile b/Examples/GIFPlot/Tcl/full/Makefile
deleted file mode 100644
index 0c016e364..000000000
--- a/Examples/GIFPlot/Tcl/full/Makefile
+++ /dev/null
@@ -1,24 +0,0 @@
-TOP        = ../../..
-SWIG       = $(TOP)/../swig
-SWIGOPT    = -I../../Include
-SRCS       =
-TARGET     = gifplot
-INTERFACE  = gifplot.i
-LIBS       = -L../.. -lgifplot
-INCLUDES   = -I../../Include
-
-all::
-	$(MAKE) -f $(TOP)/Makefile SRCS='$(SRCS)' SWIG='$(SWIG)' \
-	INCLUDES='$(INCLUDES)' LIBS='$(LIBS)' SWIGOPT='$(SWIGOPT)' \
-	TARGET='$(TARGET)' INTERFACE='$(INTERFACE)' tcl
-
-static::
-	$(MAKE) -f $(TOP)/Makefile SRCS='$(SRCS)' SWIG='$(SWIG)' \
-	INCLUDES='$(INCLUDES)' LIBS='$(LIBS)' SWIGOPT='$(SWIGOPT)' \
-	TARGET='mytclsh' INTERFACE='$(INTERFACE)' tclsh
-
-clean::
-	$(MAKE) -f $(TOP)/Makefile tcl_clean
-	rm -f *.gif
-
-check: all
diff --git a/Examples/GIFPlot/Tcl/full/README b/Examples/GIFPlot/Tcl/full/README
deleted file mode 100644
index bdba4e8b0..000000000
--- a/Examples/GIFPlot/Tcl/full/README
+++ /dev/null
@@ -1,8 +0,0 @@
-This example runs the entire gifplot.h header file through SWIG without
-any changes.  The script 'runme.tcl' does something a little more 
-interesting.   You'll have to go look at the header file to get a complete
-listing of the functions.
-
-
-
-
diff --git a/Examples/GIFPlot/Tcl/full/cmap b/Examples/GIFPlot/Tcl/full/cmap
deleted file mode 100644
index a20c331a9573dd8443380680bfe2cc428780d8a9..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

literal 768
zcmZQzpd(=A5)hSEP}Mdtvvzdz4h)M)OwTDSuW4%Uoiu&!q7`d5@7R0z#JS5i?>&C`
z?#s{r^Z@9-XXO?YlTlLFHMX#G@$?UkN=VBFxv-;m^2~WlR;}N<`@pd?7q8!a^y1xT
znmh34m-nxpKDd4D;+bOy_iW#^cE#d(Gbi_Tw$xXZ7G$R-M27|XxI5We80l&#%Snpx
zbFrd(h8Vt}lCeu@T6xFJRlCpJeMef510DGC$^DyG&YwK8f9IC<tCq~4HKo4`=)RKt
ztd#huP=7C1dn;3YEme6bQ8Jvz%Ed1tDW|Lfj0{^Rcb~wpXkcs<lvdTZboK$GWATc$
Xo3`&c2#k+ww;w!x^&XgFNDnap(k+Jt

diff --git a/Examples/GIFPlot/Tcl/full/gifplot.i b/Examples/GIFPlot/Tcl/full/gifplot.i
deleted file mode 100644
index 5a7f5008f..000000000
--- a/Examples/GIFPlot/Tcl/full/gifplot.i
+++ /dev/null
@@ -1,15 +0,0 @@
-/* Oh what the heck, let's just grab the whole darn header file
-   and see what happens. */
-
-%module gifplot
-%{
-
-/* Note: You still need this part because the %include directive
-   merely causes SWIG to interpret the contents of a file.  It doesn't
-   include the right include headers for the resulting C code */
-
-#include "gifplot.h"
-
-%}
-
-%include gifplot.h
diff --git a/Examples/GIFPlot/Tcl/full/runme.tcl b/Examples/GIFPlot/Tcl/full/runme.tcl
deleted file mode 100644
index f469e71dd..000000000
--- a/Examples/GIFPlot/Tcl/full/runme.tcl
+++ /dev/null
@@ -1,67 +0,0 @@
-# Plot a 3D function
-
-catch { load ./gifplot[info sharedlibextension] gifplot}
-
-# Here is the function to plot
-proc func { x y } {
-    return [expr { 5*cos(2*sqrt($x*$x+$y*$y))*exp(-0.3*sqrt($x*$x+$y*$y)) }]
-}
-
-# Here are some plotting parameters
-set xmin  -5.0
-set xmax   5.0
-set ymin  -5.0
-set ymax   5.0
-set zmin  -5.0
-set zmax   5.0
-
-# Grid resolution
-set nxpoints  60
-set nypoints  60
-
-set cmap [new_ColorMap cmap]
-set frame [new_FrameBuffer 500 500]
-FrameBuffer_clear $frame $BLACK
-
-set p3 [new_Plot3D $frame $xmin $ymin $zmin $xmax $ymax $zmax ]
-Plot3D_lookat $p3 [expr {2*($zmax-$zmin)}]
-Plot3D_autoperspective $p3 40
-Plot3D_rotu $p3 60
-Plot3D_rotr $p3 30
-Plot3D_rotd $p3 10
-
-proc drawsolid { } {
-    global xmin ymin zmin xmax ymax zmax nxpoints nypoints p3 BLACK
-    Plot3D_clear $p3 $BLACK
-    Plot3D_start $p3
-    set dx [expr {1.0*($xmax-$xmin)/$nxpoints}]
-    set dy [expr {1.0*($ymax-$ymin)/$nypoints}]
-    set cscale [expr {240.0/($zmax-$zmin)}]
-    set x $xmin
-    for {set i 0} {$i < $nxpoints} {incr i 1} {
-	set y $ymin
-	for {set j 0} {$j < $nypoints} {incr j 1} {
-	    set z1  [func $x $y]
-	    set z2  [func [expr {$x+$dx}] $y]
-	    set z3  [func [expr {$x+$dx}] [expr {$y+$dy}]]
-	    set z4  [func $x [expr {$y+$dy}]]
-	    set c1  [expr {$cscale*($z1-$zmin)}]
-	    set c2  [expr {$cscale*($z2-$zmin)}]
-	    set c3  [expr {$cscale*($z3-$zmin)}]
-	    set c4  [expr {$cscale*($z4-$zmin)}]
-	    set c [expr {int(($c1+$c2+$c3+$c4)/4)}]
-	    if {$c < 0} { set c 0 }
-	    if {$c > 239} { set c 239 }
-	    Plot3D_solidquad $p3 $x $y $z1 [expr {$x+$dx}] $y $z2 [expr {$x+$dx}] [expr {$y+$dy}] $z3 $x [expr {$y+$dy}] $z4 [expr {$c+16}]
-	    set y [expr {$y + $dy}]
-	}
-	set x [expr {$x + $dx}]
-    }
-}
-
-puts "Making a nice 3D plot..."
-drawsolid
-
-FrameBuffer_writeGIF $frame $cmap "image.gif"
-puts "Wrote image.gif"
-
diff --git a/Examples/GIFPlot/Tcl/mandel/Makefile b/Examples/GIFPlot/Tcl/mandel/Makefile
deleted file mode 100644
index 9280d7bb2..000000000
--- a/Examples/GIFPlot/Tcl/mandel/Makefile
+++ /dev/null
@@ -1,24 +0,0 @@
-TOP        = ../../..
-SWIG       = $(TOP)/../swig
-SWIGOPT    = -I../../Interface
-SRCS       =
-TARGET     = gifplot
-INTERFACE  = mandel.i
-LIBS       = -L../.. -lgifplot
-INCLUDES   = -I../../Include
-
-all::
-	$(MAKE) -f $(TOP)/Makefile SRCS='$(SRCS)' SWIG='$(SWIG)' \
-	INCLUDES='$(INCLUDES)' LIBS='$(LIBS)' SWIGOPT='$(SWIGOPT)' \
-	TARGET='$(TARGET)' INTERFACE='$(INTERFACE)' tcl
-
-static::
-	$(MAKE) -f $(TOP)/Makefile SRCS='$(SRCS)' SWIG='$(SWIG)' \
-	INCLUDES='$(INCLUDES)' LIBS='$(LIBS)' SWIGOPT='$(SWIGOPT)' \
-	TARGET='mywish' INTERFACE='$(INTERFACE)' wish
-
-clean::
-	$(MAKE) -f $(TOP)/Makefile tcl_clean
-	rm -f *.gif
-
-check: all
diff --git a/Examples/GIFPlot/Tcl/mandel/README b/Examples/GIFPlot/Tcl/mandel/README
deleted file mode 100644
index a533d09b8..000000000
--- a/Examples/GIFPlot/Tcl/mandel/README
+++ /dev/null
@@ -1,6 +0,0 @@
-Kill lots of time exploring the Mandelbrot set.  This example uses
-the full SWIG interface file located in ../../Interface.  To run
-the program, type 'wish mandel.tcl'.
-
-
-
diff --git a/Examples/GIFPlot/Tcl/mandel/cmap b/Examples/GIFPlot/Tcl/mandel/cmap
deleted file mode 100644
index a20c331a9573dd8443380680bfe2cc428780d8a9..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

literal 768
zcmZQzpd(=A5)hSEP}Mdtvvzdz4h)M)OwTDSuW4%Uoiu&!q7`d5@7R0z#JS5i?>&C`
z?#s{r^Z@9-XXO?YlTlLFHMX#G@$?UkN=VBFxv-;m^2~WlR;}N<`@pd?7q8!a^y1xT
znmh34m-nxpKDd4D;+bOy_iW#^cE#d(Gbi_Tw$xXZ7G$R-M27|XxI5We80l&#%Snpx
zbFrd(h8Vt}lCeu@T6xFJRlCpJeMef510DGC$^DyG&YwK8f9IC<tCq~4HKo4`=)RKt
ztd#huP=7C1dn;3YEme6bQ8Jvz%Ed1tDW|Lfj0{^Rcb~wpXkcs<lvdTZboK$GWATc$
Xo3`&c2#k+ww;w!x^&XgFNDnap(k+Jt

diff --git a/Examples/GIFPlot/Tcl/mandel/display.tcl b/Examples/GIFPlot/Tcl/mandel/display.tcl
deleted file mode 100644
index 89eedf044..000000000
--- a/Examples/GIFPlot/Tcl/mandel/display.tcl
+++ /dev/null
@@ -1,68 +0,0 @@
-# Tcl code to display a image in a widget
-
-set __imageno 0
-
-proc dismiss {t i} {
-    destroy $t
-    image delete $i
-}
-
-proc BoxInit { c p2 mxmin mymin mxmax mymax func } {
-    bind $c <Button-1> {BoxBegin %W %x %y}
-    bind $c <B1-Motion> {BoxDrag %W %x %y}
-    bind $c <ButtonRelease-1> "BoxFinish %W %x %y $p2 $mxmin $mymin $mxmax $mymax $func"
-}
-
-proc BoxBegin {w x y} {
-    global box
-    set box(anchor) [list $x $y]
-    catch {unset box(last)}
-}
-
-proc BoxDrag { w x y} {
-    global  box
-    catch {$w delete $box(last)}
-    set box(last) [eval {$w create rect} $box(anchor) {$x $y -tag box -outline white}]
-}
-
-proc BoxFinish {w x y p2 mxmin mymin mxmax mymax func } {
-    global box
-    set start $box(anchor)
-    set x1 [lrange $start 0 0]
-    set y1 [lrange $start 1 1]
-    catch {$w delete $box(last)}
-# Call the handler function
-    $func $p2 $mxmin $mymin $mxmax $mymax $x1 $y1 $x $y
-}
-
-proc display_image {filename p2 handler} {
-    global __imageno __images
-    set i [image create photo -file $filename]
-    set tl .image$__imageno
-    toplevel $tl 
-    frame $tl.img
-    frame $tl.button
-
-    set width [image width $i]
-    set height [image height $i]
-    canvas $tl.img.c -width [expr {$width+0}] -height [expr {$height+0}]
-    pack $tl.img.c
-    $tl.img.c create image 0 0 -image $i -anchor nw 
-    label $tl.button.label -text $filename 
-    pack $tl.button.label -side left
-    button $tl.button.dismiss -text "Dismiss" -command "dismiss $tl $i" -width 10 
-    pack $tl.button.dismiss -side right
-    pack $tl.img $tl.button -side top -fill x   
-    BoxInit $tl.img.c $p2 [$p2 cget -xmin] [$p2 cget -ymin] [$p2 cget -xmax] [$p2 cget -ymax] $handler
-    bind $tl <Key-q> "dismiss $tl $i"
-    bind $tl <Key-Escape> "dismiss $tl $i"
-
-    # Bind some actions to the canvas
-
-    incr __imageno 1
-}
-
-proc test {} {
-    puts "hello"
-}
-
diff --git a/Examples/GIFPlot/Tcl/mandel/mandel.i b/Examples/GIFPlot/Tcl/mandel/mandel.i
deleted file mode 100644
index 0b19f4727..000000000
--- a/Examples/GIFPlot/Tcl/mandel/mandel.i
+++ /dev/null
@@ -1,47 +0,0 @@
-// Special module to run the mandlebrot set
-%module gifplot
-%include gifplot.i
-
-%inline %{
-
-void mandel(Plot2D *p2, int tol) {
-	double scalingx;
-	double scalingy;
-	double zr,zi,ztr,zti,cr,ci;
-	double cscale;
-	int    i,j,n;
-	FrameBuffer *f;
-
-	f = p2->frame;
-	scalingx = (p2->xmax-p2->xmin)/f->width;
-	scalingy = (p2->ymax-p2->ymin)/f->height;
-	
-	cscale = 239.0/tol;
-	printf("working...\n");
-	for (i = 0; i < f->width; i++) {
-	  for (j = 0; j < f->height; j++) {
-	    zr = scalingx*i + p2->xmin;
-	    zi = scalingy*j + p2->ymin;
-	    cr = zr;
-	    ci = zi;
-	    n = 0;
-	    while (n < tol) {
-	      ztr = zr*zr-zi*zi + cr;
-	      zti = 2*zr*zi + ci;
-	      zr = ztr;
-	      zi = zti;
-	      if (ztr*ztr + zti*zti > 20) break;
-	      n = n + 1;
-	    }
-	    
-	    if (n >= tol) FrameBuffer_plot(f,i,j,BLACK);
-	    else FrameBuffer_plot(f,i,j,16+(int) (n*cscale));
-	  }
-	  if ((i % 10) == 0) printf("%d\n",i);
-	}
-
-}
-		
-%}
-	
-
diff --git a/Examples/GIFPlot/Tcl/mandel/mandel.tcl b/Examples/GIFPlot/Tcl/mandel/mandel.tcl
deleted file mode 100644
index 3e1600bc1..000000000
--- a/Examples/GIFPlot/Tcl/mandel/mandel.tcl
+++ /dev/null
@@ -1,170 +0,0 @@
-catch { load ./gifplot[info sharedlibextension] }
-source display.tcl
-set tcl_precision 17
-set f [FrameBuffer -args 400 400]
-set cmap [ColorMap -args cmap]
-set p2 [Plot2D -args $f -3 -2 1 2]
-
-set xmin -3
-set xmax 1
-set ymin -2.0
-set ymax 2.0
-set tolerance 240
-set filename mandel.gif
-
-# Make a plot from the above parms
-
-proc make_plot {} {
-    global p2 cmap tolerance
-    global xmin ymin xmax ymax filename
-    $p2 setrange $xmin $ymin $xmax $ymax
-    $p2 start
-    . config -cursor watch
-    update
-    mandel $p2 $tolerance
-    . config -cursor arrow
-    [$p2 cget -frame] writeGIF $cmap $filename
-    display_image $filename $p2 set_zoom
-}
-
-
-# Take some screen coordinates and set global min and max values 
-
-proc set_zoom {p2 mxmin mymin mxmax mymax x1 y1 x2 y2} {
-    global xmin ymin xmax ymax
-
-    set frame [$p2 cget -frame]
-    set width [$frame cget -width]
-    set height [$frame cget -height]
-
-    if {$x1 < 0} {set x1 0}
-    if {$x1 > ($width)} {set x1 $width}
-    if {$x2 < 0} {set x2 0}
-    if {$x2 > ($width)} {set x2 $width}
-    if {$x1 < $x2} {set ixmin $x1; set ixmax $x2} {set ixmin $x2; set ixmax $x1}
-
-    if {$y1 < 0} {set y1 0}
-    if {$y1 > ($height)} {set y1 $height}
-    if {$y2 < 0} {set y2 0}
-    if {$y2 > ($height)} {set y2 $height}
-    if {$y1 < $y2} {set iymin $y1; set iymax $y2} {set iymin $y2; set iymax $y1}
-
-    # Now determine new min and max values based on screen location
-
-    set xmin [expr {$mxmin + ($mxmax-$mxmin)*($ixmin)/($width)}]
-    set xmax [expr {$mxmin + ($mxmax-$mxmin)*($ixmax)/($width)}]
-    set ymin [expr {$mymin + ($mymax-$mymin)*(($height)-($iymax))/($height)}]
-    set ymax [expr {$mymin + ($mymax-$mymin)*(($height)-($iymin))/($height)}]
-
-    catch {make_plot}
-}
-
-# Box drag constrained to a square
-proc BoxDrag { w x y} {
-    global box
-    catch {$w delete $box(last)}
-    set x1 [lrange $box(anchor) 0 0]
-    set y1 [lrange $box(anchor) 1 1]
-    set dx [expr {$x - $x1}]
-    set dy [expr {$y - $y1}]
-    if {abs($dy) > abs($dx)} {set dx $dy}
-    set newx [expr {$x1 + $dx}]
-    set newy [expr {$y1 + $dx}]
-    set box(last) [eval {$w create rect} $box(anchor) {$newx $newy -tag box -outline white}]
-}
-
-
-proc BoxFinish {w x y p2 mxmin mymin mxmax mymax func } {
-    global box
-    set start $box(anchor)
-    set x1 [lrange $box(anchor) 0 0]
-    set y1 [lrange $box(anchor) 1 1]
-    set dx [expr {$x - $x1}]
-    set dy [expr {$y - $y1}]
-    if {($dx == 0) || ($dy == 0)} {
-	catch {$w delete $box(last)}
-	return
-    }
-    if {abs($dy) > abs($dx)} {set dx $dy}
-    set newx [expr {$x1 + $dx}]
-    set newy [expr {$y1 + $dx}]
-    $w config -cursor watch
-    update
-# Call the handler function
-    $func $p2 $mxmin $mymin $mxmax $mymax $x1 $y1 $newx $newy
-    catch {$w delete $box(last)}
-    $w config -cursor arrow
-}
-
-
-# Create a few frames
-
-wm title . Mandelbrot
-frame .title -relief groove -borderwidth 1
-label .title.name -text "Mandelbrot Set" 
-button .title.quit -text "Quit" -command "exit"
-button .title.about -text "About" -command "about"
-pack .title.name -side left
-pack .title.quit .title.about -side right
-
-frame .func -relief groove -borderwidth 1
-
-frame .func.xrange
-label .func.xrange.xrlabel -text "X range" -width 12
-entry .func.xrange.xmin -textvar xmin -width 8
-label .func.xrange.xtolabel -text "to"
-entry .func.xrange.xmax -textvar xmax -width 8
-pack  .func.xrange.xrlabel .func.xrange.xmin .func.xrange.xtolabel .func.xrange.xmax -side left
-
-frame .func.yrange
-label .func.yrange.yrlabel -text "Y range" -width 12
-entry .func.yrange.ymin -textvar ymin -width 8
-label .func.yrange.ytolabel -text "to"
-entry .func.yrange.ymax -textvar ymax -width 8
-pack  .func.yrange.yrlabel .func.yrange.ymin .func.yrange.ytolabel .func.yrange.ymax -side left
-
-frame .func.npoints 
-label .func.npoints.label -text "Tolerance " -width 12
-entry .func.npoints.npoints -textvar tolerance -width 8
-scale .func.npoints.scale -from 0 -to 2500 -variable tolerance -orient horizontal -showvalue false \
-                          -sliderlength 13 -bigincrement 10 -resolution 10
-pack .func.npoints.label .func.npoints.npoints .func.npoints.scale -side left
-
-pack .func.xrange .func.yrange .func.npoints -side top -fill x
-
-# Filename dialog
-
-frame .save -relief groove -borderwidth 1
-
-frame .save.file
-label .save.file.label -text "Save as" -width 12
-entry .save.file.filename -textvar filename -width 20
-pack .save.file.label .save.file.filename -side left
-pack .save.file -side left -fill x
-button .save.go -text "Plot" -command "make_plot"
-pack .save.go -side right
-
-bind .save.file.filename <Return> {make_plot}
-
-pack .title .func .save -side top -fill both
-
-proc about { } {
-    toplevel .about -width 350
-
-    message .about.m -text "\
-Mandelbrot Set\n\n\
-Copyright (c) 1997\n\
-Dave Beazley\n\
-University of Utah\n\n\
-Creates a plot of the Mandelbrot set.  Any displayed image can be zoomed by clicking and \
-dragging.  Although the main calculation is written in C, it may take awhile for each \
-image to be calculated (be patient).   Image quality can be improved at the expense of speed \
-by increasing the tolerance value.\n"
-
-button .about.okay -text "Ok" -command {destroy .about}
-
-pack .about.m .about.okay -side top
-focus .about.okay
-}
-
-make_plot
diff --git a/Examples/GIFPlot/Tcl/simple/Makefile b/Examples/GIFPlot/Tcl/simple/Makefile
deleted file mode 100644
index 752d79c10..000000000
--- a/Examples/GIFPlot/Tcl/simple/Makefile
+++ /dev/null
@@ -1,24 +0,0 @@
-TOP        = ../../..
-SWIG       = $(TOP)/../swig
-SWIGOPT    =
-SRCS       =
-TARGET     = simple
-INTERFACE  = simple.i
-LIBS       = -L../.. -lgifplot
-INCLUDES   = -I../../Include
-
-all::
-	$(MAKE) -f $(TOP)/Makefile SRCS='$(SRCS)' SWIG='$(SWIG)' \
-	INCLUDES='$(INCLUDES)' LIBS='$(LIBS)' SWIGOPT='$(SWIGOPT)' \
-	TARGET='$(TARGET)' INTERFACE='$(INTERFACE)' tcl
-
-static::
-	$(MAKE) -f $(TOP)/Makefile SRCS='$(SRCS)' SWIG='$(SWIG)' \
-	INCLUDES='$(INCLUDES)' LIBS='$(LIBS)' SWIGOPT='$(SWIGOPT)' \
-	TARGET='mytclsh' INTERFACE='$(INTERFACE)' tclsh
-
-clean::
-	$(MAKE) -f $(TOP)/Makefile tcl_clean
-	rm -f *.gif
-
-check: all
diff --git a/Examples/GIFPlot/Tcl/simple/README b/Examples/GIFPlot/Tcl/simple/README
deleted file mode 100644
index d6b291c92..000000000
--- a/Examples/GIFPlot/Tcl/simple/README
+++ /dev/null
@@ -1,5 +0,0 @@
-This is a very minimalistic example in which just a few functions
-and constants from library are wrapped and used to draw some simple
-shapes.  The script 'runme.tcl' runs the example.
-
-
diff --git a/Examples/GIFPlot/Tcl/simple/runme.tcl b/Examples/GIFPlot/Tcl/simple/runme.tcl
deleted file mode 100644
index e3f41266c..000000000
--- a/Examples/GIFPlot/Tcl/simple/runme.tcl
+++ /dev/null
@@ -1,27 +0,0 @@
-# Draw some simple shapes
-puts "Drawing some basic shapes"
-
-catch { load ./simple[info sharedlibextension] simple}
-
-set cmap [new_ColorMap]
-set f    [new_FrameBuffer 400 400]
-
-# Clear the picture
-FrameBuffer_clear $f $BLACK
-
-# Make a red box
-FrameBuffer_box $f 40 40 200 200 $RED
-
-# Make a blue circle
-FrameBuffer_circle $f 200 200 40 $BLUE
-
-# Make green line
-FrameBuffer_line $f 10 390 390 200 $GREEN
-
-# Write an image out to disk
-FrameBuffer_writeGIF $f $cmap image.gif
-puts "Wrote image.gif"
-
-delete_FrameBuffer $f
-delete_ColorMap $cmap
-
diff --git a/Examples/GIFPlot/Tcl/simple/simple.i b/Examples/GIFPlot/Tcl/simple/simple.i
deleted file mode 100644
index 457bc4c09..000000000
--- a/Examples/GIFPlot/Tcl/simple/simple.i
+++ /dev/null
@@ -1,38 +0,0 @@
-/* This example shows a very simple interface wrapping a few 
-   primitive declarations */
-
-%module simple
-%{
-#include "gifplot.h"
-%}
-
-typedef unsigned char Pixel;
-
-/* Here are a few useful functions */
-
-ColorMap    *new_ColorMap(char *filename = 0);
-void         delete_ColorMap(ColorMap *cmap);
-
-FrameBuffer *new_FrameBuffer(unsigned int width, unsigned int height);
-void         delete_FrameBuffer(FrameBuffer *frame);
-void         FrameBuffer_clear(FrameBuffer *frame, Pixel color);
-void         FrameBuffer_line(FrameBuffer *frame, int x1, int y1, int x2, int y2, Pixel color);
-void         FrameBuffer_box(FrameBuffer *frame, int x1, int y1, int x2, int y2, Pixel color);
-void         FrameBuffer_circle(FrameBuffer *frame, int x1, int y1, int radius, Pixel color);
-int          FrameBuffer_writeGIF(FrameBuffer *f, ColorMap *c, char *filename);
-
-/* And some useful constants */
-
-#define BLACK   0
-#define WHITE   1
-#define RED     2
-#define GREEN   3
-#define BLUE    4
-#define YELLOW  5
-#define CYAN    6
-#define MAGENTA 7
-
-
-
-
-
diff --git a/Examples/chicken/zlib/Makefile b/Examples/chicken/zlib/Makefile
deleted file mode 100644
index 720701444..000000000
--- a/Examples/chicken/zlib/Makefile
+++ /dev/null
@@ -1,28 +0,0 @@
-TOP         = ../..
-SWIG        = $(TOP)/../preinst-swig
-INTERFACE   = example.i
-SRCS        =
-CXXSRCS     = 
-TARGET      = zlib
-INCLUDE     =
-SWIGOPT     = -I/usr/include
-CFLAGS      = 
-VARIANT     = 
-LIBS        = -lz
-VARIANT     = _direct
-
-all:: $(TARGET)
-
-$(TARGET): $(INTERFACE) $(SRCS)
-	$(MAKE) -f $(TOP)/Makefile \
-		SRCS='$(SRCS)' CXXSRCS='$(CXXSRCS)' \
-		INCLUDE='$(INCLUDE)' SWIGOPT='$(SWIGOPT)' LIBS='$(LIBS)' TARGET='$(TARGET)' \
-		SWIG='$(SWIG)' INTERFACE='$(INTERFACE)' CHICKENOPTS='$(CHICKENOPTS)' chicken$(VARIANT)
-
-clean::
-	$(MAKE) -f $(TOP)/Makefile chicken_clean
-	rm -f example.scm
-	rm -f $(TARGET)
-
-check::
-	csi test-zlib.scm
diff --git a/Examples/chicken/zlib/README.html b/Examples/chicken/zlib/README.html
deleted file mode 100644
index b082a310c..000000000
--- a/Examples/chicken/zlib/README.html
+++ /dev/null
@@ -1,1666 +0,0 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
-"http://www.w3.org/TR/html4/loose.dtd">
-<html>
-  <head>
-    <title>zlib - Chicken - SWIG example</title>
-  </head>
-  <body>
-    <center><h1>zlib - Chicken - SWIG</h1></center>
-
-    <h2>Table of Contents</h2>
-    <a href="#build">Building the example</a><br>
-    <a href="#zlibh">zlib.h</a><br>
-    <a href="#devel">How the zlib wrapper was developed</a><br>
-
-    <center><h2><a name="build">Building the example</a></h2></center>
-
-    zlib must be installed for this example to work.<br>
-
-    Just type <code>make</code> to build this example.<br>
-
-    If zlib is not installed in /usr/lib and /usr/include, then do
-    something similar to the following:
-
-    <blockquote>
-      <pre>make SWIGOPT="-I/usr/local/include" LIBS="-L/usr/local/lib -lz"</pre>
-    </blockquote>
-
-    <center><h2><a name="zlibh">zlib.h</a></h2></center>
-    <blockquote>
-      <pre>
-<font color="blue">001:</font> /* zlib.h -- interface of the 'zlib' general purpose compression library
-<font color="blue">002:</font>   version 1.1.4, March 11th, 2002
-<font color="blue">003:</font> 
-<font color="blue">004:</font>   Copyright (C) 1995-2002 Jean-loup Gailly and Mark Adler
-<font color="blue">005:</font> 
-<font color="blue">006:</font>   This software is provided 'as-is', without any express or implied
-<font color="blue">007:</font>   warranty.  In no event will the authors be held liable for any damages
-<font color="blue">008:</font>   arising from the use of this software.
-<font color="blue">009:</font> 
-<font color="blue">010:</font>   Permission is granted to anyone to use this software for any purpose,
-<font color="blue">011:</font>   including commercial applications, and to alter it and redistribute it
-<font color="blue">012:</font>   freely, subject to the following restrictions:
-<font color="blue">013:</font> 
-<font color="blue">014:</font>   1. The origin of this software must not be misrepresented; you must not
-<font color="blue">015:</font>      claim that you wrote the original software. If you use this software
-<font color="blue">016:</font>      in a product, an acknowledgment in the product documentation would be
-<font color="blue">017:</font>      appreciated but is not required.
-<font color="blue">018:</font>   2. Altered source versions must be plainly marked as such, and must not be
-<font color="blue">019:</font>      misrepresented as being the original software.
-<font color="blue">020:</font>   3. This notice may not be removed or altered from any source distribution.
-<font color="blue">021:</font> 
-<font color="blue">022:</font>   Jean-loup Gailly        Mark Adler
-<font color="blue">023:</font>   jloup@gzip.org          madler@alumni.caltech.edu
-<font color="blue">024:</font> 
-<font color="blue">025:</font> 
-<font color="blue">026:</font>   The data format used by the zlib library is described by RFCs (Request for
-<font color="blue">027:</font>   Comments) 1950 to 1952 in the files ftp://ds.internic.net/rfc/rfc1950.txt
-<font color="blue">028:</font>   (zlib format), rfc1951.txt (deflate format) and rfc1952.txt (gzip format).
-<font color="blue">029:</font> */
-<font color="blue">030:</font> 
-<font color="blue">031:</font> #ifndef _ZLIB_H
-<font color="blue">032:</font> #define _ZLIB_H
-<font color="blue">033:</font> 
-<font color="blue">034:</font> #include "zconf.h"
-<font color="blue">035:</font> 
-<font color="blue">036:</font> #ifdef __cplusplus
-<font color="blue">037:</font> extern "C" {
-<font color="blue">038:</font> #endif
-<font color="blue">039:</font> 
-<font color="blue">040:</font> #define ZLIB_VERSION "1.1.4"
-<font color="blue">041:</font> 
-<font color="blue">042:</font> /* 
-<font color="blue">043:</font>      The 'zlib' compression library provides in-memory compression and
-<font color="blue">044:</font>   decompression functions, including integrity checks of the uncompressed
-<font color="blue">045:</font>   data.  This version of the library supports only one compression method
-<font color="blue">046:</font>   (deflation) but other algorithms will be added later and will have the same
-<font color="blue">047:</font>   stream interface.
-<font color="blue">048:</font> 
-<font color="blue">049:</font>      Compression can be done in a single step if the buffers are large
-<font color="blue">050:</font>   enough (for example if an input file is mmap'ed), or can be done by
-<font color="blue">051:</font>   repeated calls of the compression function.  In the latter case, the
-<font color="blue">052:</font>   application must provide more input and/or consume the output
-<font color="blue">053:</font>   (providing more output space) before each call.
-<font color="blue">054:</font> 
-<font color="blue">055:</font>      The library also supports reading and writing files in gzip (.gz) format
-<font color="blue">056:</font>   with an interface similar to that of stdio.
-<font color="blue">057:</font> 
-<font color="blue">058:</font>      The library does not install any signal handler. The decoder checks
-<font color="blue">059:</font>   the consistency of the compressed data, so the library should never
-<font color="blue">060:</font>   crash even in case of corrupted input.
-<font color="blue">061:</font> */
-<font color="blue">062:</font> 
-<font color="blue"><a name="l63">063:</a></font> typedef voidpf (*alloc_func) OF((voidpf opaque, uInt items, uInt size));
-<font color="blue">064:</font> typedef void   (*free_func)  OF((voidpf opaque, voidpf address));
-<font color="blue">065:</font> 
-<font color="blue">066:</font> struct internal_state;
-<font color="blue">067:</font> 
-<font color="blue">068:</font> typedef struct z_stream_s {
-<font color="blue">069:</font>     Bytef    *next_in;  /* next input byte */
-<font color="blue">070:</font>     uInt     avail_in;  /* number of bytes available at next_in */
-<font color="blue">071:</font>     uLong    total_in;  /* total nb of input bytes read so far */
-<font color="blue">072:</font> 
-<font color="blue">073:</font>     Bytef    *next_out; /* next output byte should be put there */
-<font color="blue">074:</font>     uInt     avail_out; /* remaining free space at next_out */
-<font color="blue">075:</font>     uLong    total_out; /* total nb of bytes output so far */
-<font color="blue">076:</font> 
-<font color="blue">077:</font>     char     *msg;      /* last error message, NULL if no error */
-<font color="blue"><a name="l78">078:</a></font>     struct internal_state FAR *state; /* not visible by applications */
-<font color="blue">079:</font> 
-<font color="blue"><a name="l80">080:</a></font>     alloc_func zalloc;  /* used to allocate the internal state */
-<font color="blue">081:</font>     free_func  zfree;   /* used to free the internal state */
-<font color="blue">082:</font>     voidpf     opaque;  /* private data object passed to zalloc and zfree */
-<font color="blue">083:</font> 
-<font color="blue">084:</font>     int     data_type;  /* best guess about the data type: ascii or binary */
-<font color="blue">085:</font>     uLong   adler;      /* adler32 value of the uncompressed data */
-<font color="blue">086:</font>     uLong   reserved;   /* reserved for future use */
-<font color="blue">087:</font> } z_stream;
-<font color="blue">088:</font> 
-<font color="blue">089:</font> typedef z_stream FAR *z_streamp;
-<font color="blue">090:</font> 
-<font color="blue">091:</font> /*
-<font color="blue">092:</font>    The application must update next_in and avail_in when avail_in has
-<font color="blue">093:</font>    dropped to zero. It must update next_out and avail_out when avail_out
-<font color="blue">094:</font>    has dropped to zero. The application must initialize zalloc, zfree and
-<font color="blue">095:</font>    opaque before calling the init function. All other fields are set by the
-<font color="blue">096:</font>    compression library and must not be updated by the application.
-<font color="blue">097:</font> 
-<font color="blue">098:</font>    The opaque value provided by the application will be passed as the first
-<font color="blue">099:</font>    parameter for calls of zalloc and zfree. This can be useful for custom
-<font color="blue">100:</font>    memory management. The compression library attaches no meaning to the
-<font color="blue">101:</font>    opaque value.
-<font color="blue">102:</font> 
-<font color="blue">103:</font>    zalloc must return Z_NULL if there is not enough memory for the object.
-<font color="blue">104:</font>    If zlib is used in a multi-threaded application, zalloc and zfree must be
-<font color="blue">105:</font>    thread safe.
-<font color="blue">106:</font> 
-<font color="blue">107:</font>    On 16-bit systems, the functions zalloc and zfree must be able to allocate
-<font color="blue">108:</font>    exactly 65536 bytes, but will not be required to allocate more than this
-<font color="blue">109:</font>    if the symbol MAXSEG_64K is defined (see zconf.h). WARNING: On MSDOS,
-<font color="blue">110:</font>    pointers returned by zalloc for objects of exactly 65536 bytes *must*
-<font color="blue">111:</font>    have their offset normalized to zero. The default allocation function
-<font color="blue">112:</font>    provided by this library ensures this (see zutil.c). To reduce memory
-<font color="blue">113:</font>    requirements and avoid any allocation of 64K objects, at the expense of
-<font color="blue">114:</font>    compression ratio, compile the library with -DMAX_WBITS=14 (see zconf.h).
-<font color="blue">115:</font> 
-<font color="blue">116:</font>    The fields total_in and total_out can be used for statistics or
-<font color="blue">117:</font>    progress reports. After compression, total_in holds the total size of
-<font color="blue">118:</font>    the uncompressed data and may be saved for use in the decompressor
-<font color="blue">119:</font>    (particularly if the decompressor wants to decompress everything in
-<font color="blue">120:</font>    a single step).
-<font color="blue">121:</font> */
-<font color="blue">122:</font> 
-<font color="blue">123:</font>                         /* constants */
-<font color="blue">124:</font> 
-<font color="blue">125:</font> #define Z_NO_FLUSH      0
-<font color="blue">126:</font> #define Z_PARTIAL_FLUSH 1 /* will be removed, use Z_SYNC_FLUSH instead */
-<font color="blue">127:</font> #define Z_SYNC_FLUSH    2
-<font color="blue">128:</font> #define Z_FULL_FLUSH    3
-<font color="blue">129:</font> #define Z_FINISH        4
-<font color="blue">130:</font> /* Allowed flush values; see deflate() below for details */
-<font color="blue">131:</font> 
-<font color="blue">132:</font> #define Z_OK            0
-<font color="blue">133:</font> #define Z_STREAM_END    1
-<font color="blue">134:</font> #define Z_NEED_DICT     2
-<font color="blue">135:</font> #define Z_ERRNO        (-1)
-<font color="blue">136:</font> #define Z_STREAM_ERROR (-2)
-<font color="blue">137:</font> #define Z_DATA_ERROR   (-3)
-<font color="blue">138:</font> #define Z_MEM_ERROR    (-4)
-<font color="blue">139:</font> #define Z_BUF_ERROR    (-5)
-<font color="blue">140:</font> #define Z_VERSION_ERROR (-6)
-<font color="blue">141:</font> /* Return codes for the compression/decompression functions. Negative
-<font color="blue">142:</font>  * values are errors, positive values are used for special but normal events.
-<font color="blue">143:</font>  */
-<font color="blue">144:</font> 
-<font color="blue">145:</font> #define Z_NO_COMPRESSION         0
-<font color="blue">146:</font> #define Z_BEST_SPEED             1
-<font color="blue">147:</font> #define Z_BEST_COMPRESSION       9
-<font color="blue">148:</font> #define Z_DEFAULT_COMPRESSION  (-1)
-<font color="blue">149:</font> /* compression levels */
-<font color="blue">150:</font> 
-<font color="blue">151:</font> #define Z_FILTERED            1
-<font color="blue">152:</font> #define Z_HUFFMAN_ONLY        2
-<font color="blue">153:</font> #define Z_DEFAULT_STRATEGY    0
-<font color="blue">154:</font> /* compression strategy; see deflateInit2() below for details */
-<font color="blue">155:</font> 
-<font color="blue">156:</font> #define Z_BINARY   0
-<font color="blue">157:</font> #define Z_ASCII    1
-<font color="blue">158:</font> #define Z_UNKNOWN  2
-<font color="blue">159:</font> /* Possible values of the data_type field */
-<font color="blue">160:</font> 
-<font color="blue">161:</font> #define Z_DEFLATED   8
-<font color="blue">162:</font> /* The deflate compression method (the only one supported in this version) */
-<font color="blue">163:</font> 
-<font color="blue">164:</font> #define Z_NULL  0  /* for initializing zalloc, zfree, opaque */
-<font color="blue">165:</font> 
-<font color="blue">166:</font> #define zlib_version zlibVersion()
-<font color="blue">167:</font> /* for compatibility with versions &lt; 1.0.2 */
-<font color="blue">168:</font> 
-<font color="blue">169:</font>                         /* basic functions */
-<font color="blue">170:</font> 
-<font color="blue">171:</font> ZEXTERN const char * ZEXPORT zlibVersion OF((void));
-<font color="blue">172:</font> /* The application can compare zlibVersion and ZLIB_VERSION for consistency.
-<font color="blue">173:</font>    If the first character differs, the library code actually used is
-<font color="blue">174:</font>    not compatible with the zlib.h header file used by the application.
-<font color="blue">175:</font>    This check is automatically made by deflateInit and inflateInit.
-<font color="blue">176:</font>  */
-<font color="blue">177:</font> 
-<font color="blue">178:</font> /* 
-<font color="blue">179:</font> ZEXTERN int ZEXPORT deflateInit OF((z_streamp strm, int level));
-<font color="blue">180:</font> 
-<font color="blue">181:</font>      Initializes the internal stream state for compression. The fields
-<font color="blue">182:</font>    zalloc, zfree and opaque must be initialized before by the caller.
-<font color="blue">183:</font>    If zalloc and zfree are set to Z_NULL, deflateInit updates them to
-<font color="blue">184:</font>    use default allocation functions.
-<font color="blue">185:</font> 
-<font color="blue">186:</font>      The compression level must be Z_DEFAULT_COMPRESSION, or between 0 and 9:
-<font color="blue">187:</font>    1 gives best speed, 9 gives best compression, 0 gives no compression at
-<font color="blue">188:</font>    all (the input data is simply copied a block at a time).
-<font color="blue">189:</font>    Z_DEFAULT_COMPRESSION requests a default compromise between speed and
-<font color="blue">190:</font>    compression (currently equivalent to level 6).
-<font color="blue">191:</font> 
-<font color="blue">192:</font>      deflateInit returns Z_OK if success, Z_MEM_ERROR if there was not
-<font color="blue">193:</font>    enough memory, Z_STREAM_ERROR if level is not a valid compression level,
-<font color="blue">194:</font>    Z_VERSION_ERROR if the zlib library version (zlib_version) is incompatible
-<font color="blue">195:</font>    with the version assumed by the caller (ZLIB_VERSION).
-<font color="blue">196:</font>    msg is set to null if there is no error message.  deflateInit does not
-<font color="blue">197:</font>    perform any compression: this will be done by deflate().
-<font color="blue">198:</font> */
-<font color="blue">199:</font> 
-<font color="blue">200:</font> 
-<font color="blue">201:</font> ZEXTERN int ZEXPORT deflate OF((z_streamp strm, int flush));
-<font color="blue">202:</font> /*
-<font color="blue">203:</font>     deflate compresses as much data as possible, and stops when the input
-<font color="blue">204:</font>   buffer becomes empty or the output buffer becomes full. It may introduce some
-<font color="blue">205:</font>   output latency (reading input without producing any output) except when
-<font color="blue">206:</font>   forced to flush.
-<font color="blue">207:</font> 
-<font color="blue">208:</font>     The detailed semantics are as follows. deflate performs one or both of the
-<font color="blue">209:</font>   following actions:
-<font color="blue">210:</font> 
-<font color="blue">211:</font>   - Compress more input starting at next_in and update next_in and avail_in
-<font color="blue">212:</font>     accordingly. If not all input can be processed (because there is not
-<font color="blue">213:</font>     enough room in the output buffer), next_in and avail_in are updated and
-<font color="blue">214:</font>     processing will resume at this point for the next call of deflate().
-<font color="blue">215:</font> 
-<font color="blue">216:</font>   - Provide more output starting at next_out and update next_out and avail_out
-<font color="blue">217:</font>     accordingly. This action is forced if the parameter flush is non zero.
-<font color="blue">218:</font>     Forcing flush frequently degrades the compression ratio, so this parameter
-<font color="blue">219:</font>     should be set only when necessary (in interactive applications).
-<font color="blue">220:</font>     Some output may be provided even if flush is not set.
-<font color="blue">221:</font> 
-<font color="blue">222:</font>   Before the call of deflate(), the application should ensure that at least
-<font color="blue">223:</font>   one of the actions is possible, by providing more input and/or consuming
-<font color="blue">224:</font>   more output, and updating avail_in or avail_out accordingly; avail_out
-<font color="blue">225:</font>   should never be zero before the call. The application can consume the
-<font color="blue">226:</font>   compressed output when it wants, for example when the output buffer is full
-<font color="blue">227:</font>   (avail_out == 0), or after each call of deflate(). If deflate returns Z_OK
-<font color="blue">228:</font>   and with zero avail_out, it must be called again after making room in the
-<font color="blue">229:</font>   output buffer because there might be more output pending.
-<font color="blue">230:</font> 
-<font color="blue">231:</font>     If the parameter flush is set to Z_SYNC_FLUSH, all pending output is
-<font color="blue">232:</font>   flushed to the output buffer and the output is aligned on a byte boundary, so
-<font color="blue">233:</font>   that the decompressor can get all input data available so far. (In particular
-<font color="blue">234:</font>   avail_in is zero after the call if enough output space has been provided
-<font color="blue">235:</font>   before the call.)  Flushing may degrade compression for some compression
-<font color="blue">236:</font>   algorithms and so it should be used only when necessary.
-<font color="blue">237:</font> 
-<font color="blue">238:</font>     If flush is set to Z_FULL_FLUSH, all output is flushed as with
-<font color="blue">239:</font>   Z_SYNC_FLUSH, and the compression state is reset so that decompression can
-<font color="blue">240:</font>   restart from this point if previous compressed data has been damaged or if
-<font color="blue">241:</font>   random access is desired. Using Z_FULL_FLUSH too often can seriously degrade
-<font color="blue">242:</font>   the compression.
-<font color="blue">243:</font> 
-<font color="blue">244:</font>     If deflate returns with avail_out == 0, this function must be called again
-<font color="blue">245:</font>   with the same value of the flush parameter and more output space (updated
-<font color="blue">246:</font>   avail_out), until the flush is complete (deflate returns with non-zero
-<font color="blue">247:</font>   avail_out).
-<font color="blue">248:</font> 
-<font color="blue">249:</font>     If the parameter flush is set to Z_FINISH, pending input is processed,
-<font color="blue">250:</font>   pending output is flushed and deflate returns with Z_STREAM_END if there
-<font color="blue">251:</font>   was enough output space; if deflate returns with Z_OK, this function must be
-<font color="blue">252:</font>   called again with Z_FINISH and more output space (updated avail_out) but no
-<font color="blue">253:</font>   more input data, until it returns with Z_STREAM_END or an error. After
-<font color="blue">254:</font>   deflate has returned Z_STREAM_END, the only possible operations on the
-<font color="blue">255:</font>   stream are deflateReset or deflateEnd.
-<font color="blue">256:</font>   
-<font color="blue">257:</font>     Z_FINISH can be used immediately after deflateInit if all the compression
-<font color="blue">258:</font>   is to be done in a single step. In this case, avail_out must be at least
-<font color="blue">259:</font>   0.1% larger than avail_in plus 12 bytes.  If deflate does not return
-<font color="blue">260:</font>   Z_STREAM_END, then it must be called again as described above.
-<font color="blue">261:</font> 
-<font color="blue">262:</font>     deflate() sets strm-&gt;adler to the adler32 checksum of all input read
-<font color="blue">263:</font>   so far (that is, total_in bytes).
-<font color="blue">264:</font> 
-<font color="blue">265:</font>     deflate() may update data_type if it can make a good guess about
-<font color="blue">266:</font>   the input data type (Z_ASCII or Z_BINARY). In doubt, the data is considered
-<font color="blue">267:</font>   binary. This field is only for information purposes and does not affect
-<font color="blue">268:</font>   the compression algorithm in any manner.
-<font color="blue">269:</font> 
-<font color="blue">270:</font>     deflate() returns Z_OK if some progress has been made (more input
-<font color="blue">271:</font>   processed or more output produced), Z_STREAM_END if all input has been
-<font color="blue">272:</font>   consumed and all output has been produced (only when flush is set to
-<font color="blue">273:</font>   Z_FINISH), Z_STREAM_ERROR if the stream state was inconsistent (for example
-<font color="blue">274:</font>   if next_in or next_out was NULL), Z_BUF_ERROR if no progress is possible
-<font color="blue">275:</font>   (for example avail_in or avail_out was zero).
-<font color="blue">276:</font> */
-<font color="blue">277:</font> 
-<font color="blue">278:</font> 
-<font color="blue">279:</font> ZEXTERN int ZEXPORT deflateEnd OF((z_streamp strm));
-<font color="blue">280:</font> /*
-<font color="blue">281:</font>      All dynamically allocated data structures for this stream are freed.
-<font color="blue">282:</font>    This function discards any unprocessed input and does not flush any
-<font color="blue">283:</font>    pending output.
-<font color="blue">284:</font> 
-<font color="blue">285:</font>      deflateEnd returns Z_OK if success, Z_STREAM_ERROR if the
-<font color="blue">286:</font>    stream state was inconsistent, Z_DATA_ERROR if the stream was freed
-<font color="blue">287:</font>    prematurely (some input or output was discarded). In the error case,
-<font color="blue">288:</font>    msg may be set but then points to a static string (which must not be
-<font color="blue">289:</font>    deallocated).
-<font color="blue">290:</font> */
-<font color="blue">291:</font> 
-<font color="blue">292:</font> 
-<font color="blue">293:</font> /* 
-<font color="blue">294:</font> ZEXTERN int ZEXPORT inflateInit OF((z_streamp strm));
-<font color="blue">295:</font> 
-<font color="blue">296:</font>      Initializes the internal stream state for decompression. The fields
-<font color="blue">297:</font>    next_in, avail_in, zalloc, zfree and opaque must be initialized before by
-<font color="blue">298:</font>    the caller. If next_in is not Z_NULL and avail_in is large enough (the exact
-<font color="blue">299:</font>    value depends on the compression method), inflateInit determines the
-<font color="blue">300:</font>    compression method from the zlib header and allocates all data structures
-<font color="blue">301:</font>    accordingly; otherwise the allocation will be deferred to the first call of
-<font color="blue">302:</font>    inflate.  If zalloc and zfree are set to Z_NULL, inflateInit updates them to
-<font color="blue">303:</font>    use default allocation functions.
-<font color="blue">304:</font> 
-<font color="blue">305:</font>      inflateInit returns Z_OK if success, Z_MEM_ERROR if there was not enough
-<font color="blue">306:</font>    memory, Z_VERSION_ERROR if the zlib library version is incompatible with the
-<font color="blue">307:</font>    version assumed by the caller.  msg is set to null if there is no error
-<font color="blue">308:</font>    message. inflateInit does not perform any decompression apart from reading
-<font color="blue">309:</font>    the zlib header if present: this will be done by inflate().  (So next_in and
-<font color="blue">310:</font>    avail_in may be modified, but next_out and avail_out are unchanged.)
-<font color="blue">311:</font> */
-<font color="blue">312:</font> 
-<font color="blue">313:</font> 
-<font color="blue">314:</font> ZEXTERN int ZEXPORT inflate OF((z_streamp strm, int flush));
-<font color="blue">315:</font> /*
-<font color="blue">316:</font>     inflate decompresses as much data as possible, and stops when the input
-<font color="blue">317:</font>   buffer becomes empty or the output buffer becomes full. It may some
-<font color="blue">318:</font>   introduce some output latency (reading input without producing any output)
-<font color="blue">319:</font>   except when forced to flush.
-<font color="blue">320:</font> 
-<font color="blue">321:</font>   The detailed semantics are as follows. inflate performs one or both of the
-<font color="blue">322:</font>   following actions:
-<font color="blue">323:</font> 
-<font color="blue">324:</font>   - Decompress more input starting at next_in and update next_in and avail_in
-<font color="blue">325:</font>     accordingly. If not all input can be processed (because there is not
-<font color="blue">326:</font>     enough room in the output buffer), next_in is updated and processing
-<font color="blue">327:</font>     will resume at this point for the next call of inflate().
-<font color="blue">328:</font> 
-<font color="blue">329:</font>   - Provide more output starting at next_out and update next_out and avail_out
-<font color="blue">330:</font>     accordingly.  inflate() provides as much output as possible, until there
-<font color="blue">331:</font>     is no more input data or no more space in the output buffer (see below
-<font color="blue">332:</font>     about the flush parameter).
-<font color="blue">333:</font> 
-<font color="blue">334:</font>   Before the call of inflate(), the application should ensure that at least
-<font color="blue">335:</font>   one of the actions is possible, by providing more input and/or consuming
-<font color="blue">336:</font>   more output, and updating the next_* and avail_* values accordingly.
-<font color="blue">337:</font>   The application can consume the uncompressed output when it wants, for
-<font color="blue">338:</font>   example when the output buffer is full (avail_out == 0), or after each
-<font color="blue">339:</font>   call of inflate(). If inflate returns Z_OK and with zero avail_out, it
-<font color="blue">340:</font>   must be called again after making room in the output buffer because there
-<font color="blue">341:</font>   might be more output pending.
-<font color="blue">342:</font> 
-<font color="blue">343:</font>     If the parameter flush is set to Z_SYNC_FLUSH, inflate flushes as much
-<font color="blue">344:</font>   output as possible to the output buffer. The flushing behavior of inflate is
-<font color="blue">345:</font>   not specified for values of the flush parameter other than Z_SYNC_FLUSH
-<font color="blue">346:</font>   and Z_FINISH, but the current implementation actually flushes as much output
-<font color="blue">347:</font>   as possible anyway.
-<font color="blue">348:</font> 
-<font color="blue">349:</font>     inflate() should normally be called until it returns Z_STREAM_END or an
-<font color="blue">350:</font>   error. However if all decompression is to be performed in a single step
-<font color="blue">351:</font>   (a single call of inflate), the parameter flush should be set to
-<font color="blue">352:</font>   Z_FINISH. In this case all pending input is processed and all pending
-<font color="blue">353:</font>   output is flushed; avail_out must be large enough to hold all the
-<font color="blue">354:</font>   uncompressed data. (The size of the uncompressed data may have been saved
-<font color="blue">355:</font>   by the compressor for this purpose.) The next operation on this stream must
-<font color="blue">356:</font>   be inflateEnd to deallocate the decompression state. The use of Z_FINISH
-<font color="blue">357:</font>   is never required, but can be used to inform inflate that a faster routine
-<font color="blue">358:</font>   may be used for the single inflate() call.
-<font color="blue">359:</font> 
-<font color="blue">360:</font>      If a preset dictionary is needed at this point (see inflateSetDictionary
-<font color="blue">361:</font>   below), inflate sets strm-adler to the adler32 checksum of the
-<font color="blue">362:</font>   dictionary chosen by the compressor and returns Z_NEED_DICT; otherwise 
-<font color="blue">363:</font>   it sets strm-&gt;adler to the adler32 checksum of all output produced
-<font color="blue">364:</font>   so far (that is, total_out bytes) and returns Z_OK, Z_STREAM_END or
-<font color="blue">365:</font>   an error code as described below. At the end of the stream, inflate()
-<font color="blue">366:</font>   checks that its computed adler32 checksum is equal to that saved by the
-<font color="blue">367:</font>   compressor and returns Z_STREAM_END only if the checksum is correct.
-<font color="blue">368:</font> 
-<font color="blue">369:</font>     inflate() returns Z_OK if some progress has been made (more input processed
-<font color="blue">370:</font>   or more output produced), Z_STREAM_END if the end of the compressed data has
-<font color="blue">371:</font>   been reached and all uncompressed output has been produced, Z_NEED_DICT if a
-<font color="blue">372:</font>   preset dictionary is needed at this point, Z_DATA_ERROR if the input data was
-<font color="blue">373:</font>   corrupted (input stream not conforming to the zlib format or incorrect
-<font color="blue">374:</font>   adler32 checksum), Z_STREAM_ERROR if the stream structure was inconsistent
-<font color="blue">375:</font>   (for example if next_in or next_out was NULL), Z_MEM_ERROR if there was not
-<font color="blue">376:</font>   enough memory, Z_BUF_ERROR if no progress is possible or if there was not
-<font color="blue">377:</font>   enough room in the output buffer when Z_FINISH is used. In the Z_DATA_ERROR
-<font color="blue">378:</font>   case, the application may then call inflateSync to look for a good
-<font color="blue">379:</font>   compression block.
-<font color="blue">380:</font> */
-<font color="blue">381:</font> 
-<font color="blue">382:</font> 
-<font color="blue">383:</font> ZEXTERN int ZEXPORT inflateEnd OF((z_streamp strm));
-<font color="blue">384:</font> /*
-<font color="blue">385:</font>      All dynamically allocated data structures for this stream are freed.
-<font color="blue">386:</font>    This function discards any unprocessed input and does not flush any
-<font color="blue">387:</font>    pending output.
-<font color="blue">388:</font> 
-<font color="blue">389:</font>      inflateEnd returns Z_OK if success, Z_STREAM_ERROR if the stream state
-<font color="blue">390:</font>    was inconsistent. In the error case, msg may be set but then points to a
-<font color="blue">391:</font>    static string (which must not be deallocated).
-<font color="blue">392:</font> */
-<font color="blue">393:</font> 
-<font color="blue">394:</font>                         /* Advanced functions */
-<font color="blue">395:</font> 
-<font color="blue">396:</font> /*
-<font color="blue">397:</font>     The following functions are needed only in some special applications.
-<font color="blue">398:</font> */
-<font color="blue">399:</font> 
-<font color="blue">400:</font> /*   
-<font color="blue">401:</font> ZEXTERN int ZEXPORT deflateInit2 OF((z_streamp strm,
-<font color="blue">402:</font>                                      int  level,
-<font color="blue">403:</font>                                      int  method,
-<font color="blue">404:</font>                                      int  windowBits,
-<font color="blue">405:</font>                                      int  memLevel,
-<font color="blue">406:</font>                                      int  strategy));
-<font color="blue">407:</font> 
-<font color="blue">408:</font>      This is another version of deflateInit with more compression options. The
-<font color="blue">409:</font>    fields next_in, zalloc, zfree and opaque must be initialized before by
-<font color="blue">410:</font>    the caller.
-<font color="blue">411:</font> 
-<font color="blue">412:</font>      The method parameter is the compression method. It must be Z_DEFLATED in
-<font color="blue">413:</font>    this version of the library.
-<font color="blue">414:</font> 
-<font color="blue">415:</font>      The windowBits parameter is the base two logarithm of the window size
-<font color="blue">416:</font>    (the size of the history buffer).  It should be in the range 8..15 for this
-<font color="blue">417:</font>    version of the library. Larger values of this parameter result in better
-<font color="blue">418:</font>    compression at the expense of memory usage. The default value is 15 if
-<font color="blue">419:</font>    deflateInit is used instead.
-<font color="blue">420:</font> 
-<font color="blue">421:</font>      The memLevel parameter specifies how much memory should be allocated
-<font color="blue">422:</font>    for the internal compression state. memLevel=1 uses minimum memory but
-<font color="blue">423:</font>    is slow and reduces compression ratio; memLevel=9 uses maximum memory
-<font color="blue">424:</font>    for optimal speed. The default value is 8. See zconf.h for total memory
-<font color="blue">425:</font>    usage as a function of windowBits and memLevel.
-<font color="blue">426:</font> 
-<font color="blue">427:</font>      The strategy parameter is used to tune the compression algorithm. Use the
-<font color="blue">428:</font>    value Z_DEFAULT_STRATEGY for normal data, Z_FILTERED for data produced by a
-<font color="blue">429:</font>    filter (or predictor), or Z_HUFFMAN_ONLY to force Huffman encoding only (no
-<font color="blue">430:</font>    string match).  Filtered data consists mostly of small values with a
-<font color="blue">431:</font>    somewhat random distribution. In this case, the compression algorithm is
-<font color="blue">432:</font>    tuned to compress them better. The effect of Z_FILTERED is to force more
-<font color="blue">433:</font>    Huffman coding and less string matching; it is somewhat intermediate
-<font color="blue">434:</font>    between Z_DEFAULT and Z_HUFFMAN_ONLY. The strategy parameter only affects
-<font color="blue">435:</font>    the compression ratio but not the correctness of the compressed output even
-<font color="blue">436:</font>    if it is not set appropriately.
-<font color="blue">437:</font> 
-<font color="blue">438:</font>       deflateInit2 returns Z_OK if success, Z_MEM_ERROR if there was not enough
-<font color="blue">439:</font>    memory, Z_STREAM_ERROR if a parameter is invalid (such as an invalid
-<font color="blue">440:</font>    method). msg is set to null if there is no error message.  deflateInit2 does
-<font color="blue">441:</font>    not perform any compression: this will be done by deflate().
-<font color="blue">442:</font> */
-<font color="blue">443:</font>                             
-<font color="blue">444:</font> ZEXTERN int ZEXPORT deflateSetDictionary OF((z_streamp strm,
-<font color="blue">445:</font>                                              const Bytef *dictionary,
-<font color="blue">446:</font>                                              uInt  dictLength));
-<font color="blue">447:</font> /*
-<font color="blue">448:</font>      Initializes the compression dictionary from the given byte sequence
-<font color="blue">449:</font>    without producing any compressed output. This function must be called
-<font color="blue">450:</font>    immediately after deflateInit, deflateInit2 or deflateReset, before any
-<font color="blue">451:</font>    call of deflate. The compressor and decompressor must use exactly the same
-<font color="blue">452:</font>    dictionary (see inflateSetDictionary).
-<font color="blue">453:</font> 
-<font color="blue">454:</font>      The dictionary should consist of strings (byte sequences) that are likely
-<font color="blue">455:</font>    to be encountered later in the data to be compressed, with the most commonly
-<font color="blue">456:</font>    used strings preferably put towards the end of the dictionary. Using a
-<font color="blue">457:</font>    dictionary is most useful when the data to be compressed is short and can be
-<font color="blue">458:</font>    predicted with good accuracy; the data can then be compressed better than
-<font color="blue">459:</font>    with the default empty dictionary.
-<font color="blue">460:</font> 
-<font color="blue">461:</font>      Depending on the size of the compression data structures selected by
-<font color="blue">462:</font>    deflateInit or deflateInit2, a part of the dictionary may in effect be
-<font color="blue">463:</font>    discarded, for example if the dictionary is larger than the window size in
-<font color="blue">464:</font>    deflate or deflate2. Thus the strings most likely to be useful should be
-<font color="blue">465:</font>    put at the end of the dictionary, not at the front.
-<font color="blue">466:</font> 
-<font color="blue">467:</font>      Upon return of this function, strm-&gt;adler is set to the Adler32 value
-<font color="blue">468:</font>    of the dictionary; the decompressor may later use this value to determine
-<font color="blue">469:</font>    which dictionary has been used by the compressor. (The Adler32 value
-<font color="blue">470:</font>    applies to the whole dictionary even if only a subset of the dictionary is
-<font color="blue">471:</font>    actually used by the compressor.)
-<font color="blue">472:</font> 
-<font color="blue">473:</font>      deflateSetDictionary returns Z_OK if success, or Z_STREAM_ERROR if a
-<font color="blue">474:</font>    parameter is invalid (such as NULL dictionary) or the stream state is
-<font color="blue">475:</font>    inconsistent (for example if deflate has already been called for this stream
-<font color="blue">476:</font>    or if the compression method is bsort). deflateSetDictionary does not
-<font color="blue">477:</font>    perform any compression: this will be done by deflate().
-<font color="blue">478:</font> */
-<font color="blue">479:</font> 
-<font color="blue">480:</font> ZEXTERN int ZEXPORT deflateCopy OF((z_streamp dest,
-<font color="blue">481:</font>                                     z_streamp source));
-<font color="blue">482:</font> /*
-<font color="blue">483:</font>      Sets the destination stream as a complete copy of the source stream.
-<font color="blue">484:</font> 
-<font color="blue">485:</font>      This function can be useful when several compression strategies will be
-<font color="blue">486:</font>    tried, for example when there are several ways of pre-processing the input
-<font color="blue">487:</font>    data with a filter. The streams that will be discarded should then be freed
-<font color="blue">488:</font>    by calling deflateEnd.  Note that deflateCopy duplicates the internal
-<font color="blue">489:</font>    compression state which can be quite large, so this strategy is slow and
-<font color="blue">490:</font>    can consume lots of memory.
-<font color="blue">491:</font> 
-<font color="blue">492:</font>      deflateCopy returns Z_OK if success, Z_MEM_ERROR if there was not
-<font color="blue">493:</font>    enough memory, Z_STREAM_ERROR if the source stream state was inconsistent
-<font color="blue">494:</font>    (such as zalloc being NULL). msg is left unchanged in both source and
-<font color="blue">495:</font>    destination.
-<font color="blue">496:</font> */
-<font color="blue">497:</font> 
-<font color="blue">498:</font> ZEXTERN int ZEXPORT deflateReset OF((z_streamp strm));
-<font color="blue">499:</font> /*
-<font color="blue">500:</font>      This function is equivalent to deflateEnd followed by deflateInit,
-<font color="blue">501:</font>    but does not free and reallocate all the internal compression state.
-<font color="blue">502:</font>    The stream will keep the same compression level and any other attributes
-<font color="blue">503:</font>    that may have been set by deflateInit2.
-<font color="blue">504:</font> 
-<font color="blue">505:</font>       deflateReset returns Z_OK if success, or Z_STREAM_ERROR if the source
-<font color="blue">506:</font>    stream state was inconsistent (such as zalloc or state being NULL).
-<font color="blue">507:</font> */
-<font color="blue">508:</font> 
-<font color="blue">509:</font> ZEXTERN int ZEXPORT deflateParams OF((z_streamp strm,
-<font color="blue">510:</font> 				      int level,
-<font color="blue">511:</font> 				      int strategy));
-<font color="blue">512:</font> /*
-<font color="blue">513:</font>      Dynamically update the compression level and compression strategy.  The
-<font color="blue">514:</font>    interpretation of level and strategy is as in deflateInit2.  This can be
-<font color="blue">515:</font>    used to switch between compression and straight copy of the input data, or
-<font color="blue">516:</font>    to switch to a different kind of input data requiring a different
-<font color="blue">517:</font>    strategy. If the compression level is changed, the input available so far
-<font color="blue">518:</font>    is compressed with the old level (and may be flushed); the new level will
-<font color="blue">519:</font>    take effect only at the next call of deflate().
-<font color="blue">520:</font> 
-<font color="blue">521:</font>      Before the call of deflateParams, the stream state must be set as for
-<font color="blue">522:</font>    a call of deflate(), since the currently available input may have to
-<font color="blue">523:</font>    be compressed and flushed. In particular, strm-&gt;avail_out must be non-zero.
-<font color="blue">524:</font> 
-<font color="blue">525:</font>      deflateParams returns Z_OK if success, Z_STREAM_ERROR if the source
-<font color="blue">526:</font>    stream state was inconsistent or if a parameter was invalid, Z_BUF_ERROR
-<font color="blue">527:</font>    if strm-&gt;avail_out was zero.
-<font color="blue">528:</font> */
-<font color="blue">529:</font> 
-<font color="blue">530:</font> /*   
-<font color="blue">531:</font> ZEXTERN int ZEXPORT inflateInit2 OF((z_streamp strm,
-<font color="blue">532:</font>                                      int  windowBits));
-<font color="blue">533:</font> 
-<font color="blue">534:</font>      This is another version of inflateInit with an extra parameter. The
-<font color="blue">535:</font>    fields next_in, avail_in, zalloc, zfree and opaque must be initialized
-<font color="blue">536:</font>    before by the caller.
-<font color="blue">537:</font> 
-<font color="blue">538:</font>      The windowBits parameter is the base two logarithm of the maximum window
-<font color="blue">539:</font>    size (the size of the history buffer).  It should be in the range 8..15 for
-<font color="blue">540:</font>    this version of the library. The default value is 15 if inflateInit is used
-<font color="blue">541:</font>    instead. If a compressed stream with a larger window size is given as
-<font color="blue">542:</font>    input, inflate() will return with the error code Z_DATA_ERROR instead of
-<font color="blue">543:</font>    trying to allocate a larger window.
-<font color="blue">544:</font> 
-<font color="blue">545:</font>       inflateInit2 returns Z_OK if success, Z_MEM_ERROR if there was not enough
-<font color="blue">546:</font>    memory, Z_STREAM_ERROR if a parameter is invalid (such as a negative
-<font color="blue">547:</font>    memLevel). msg is set to null if there is no error message.  inflateInit2
-<font color="blue">548:</font>    does not perform any decompression apart from reading the zlib header if
-<font color="blue">549:</font>    present: this will be done by inflate(). (So next_in and avail_in may be
-<font color="blue">550:</font>    modified, but next_out and avail_out are unchanged.)
-<font color="blue">551:</font> */
-<font color="blue">552:</font> 
-<font color="blue">553:</font> ZEXTERN int ZEXPORT inflateSetDictionary OF((z_streamp strm,
-<font color="blue">554:</font>                                              const Bytef *dictionary,
-<font color="blue">555:</font>                                              uInt  dictLength));
-<font color="blue">556:</font> /*
-<font color="blue">557:</font>      Initializes the decompression dictionary from the given uncompressed byte
-<font color="blue">558:</font>    sequence. This function must be called immediately after a call of inflate
-<font color="blue">559:</font>    if this call returned Z_NEED_DICT. The dictionary chosen by the compressor
-<font color="blue">560:</font>    can be determined from the Adler32 value returned by this call of
-<font color="blue">561:</font>    inflate. The compressor and decompressor must use exactly the same
-<font color="blue">562:</font>    dictionary (see deflateSetDictionary).
-<font color="blue">563:</font> 
-<font color="blue">564:</font>      inflateSetDictionary returns Z_OK if success, Z_STREAM_ERROR if a
-<font color="blue">565:</font>    parameter is invalid (such as NULL dictionary) or the stream state is
-<font color="blue">566:</font>    inconsistent, Z_DATA_ERROR if the given dictionary doesn't match the
-<font color="blue">567:</font>    expected one (incorrect Adler32 value). inflateSetDictionary does not
-<font color="blue">568:</font>    perform any decompression: this will be done by subsequent calls of
-<font color="blue">569:</font>    inflate().
-<font color="blue">570:</font> */
-<font color="blue">571:</font> 
-<font color="blue">572:</font> ZEXTERN int ZEXPORT inflateSync OF((z_streamp strm));
-<font color="blue">573:</font> /* 
-<font color="blue">574:</font>     Skips invalid compressed data until a full flush point (see above the
-<font color="blue">575:</font>   description of deflate with Z_FULL_FLUSH) can be found, or until all
-<font color="blue">576:</font>   available input is skipped. No output is provided.
-<font color="blue">577:</font> 
-<font color="blue">578:</font>     inflateSync returns Z_OK if a full flush point has been found, Z_BUF_ERROR
-<font color="blue">579:</font>   if no more input was provided, Z_DATA_ERROR if no flush point has been found,
-<font color="blue">580:</font>   or Z_STREAM_ERROR if the stream structure was inconsistent. In the success
-<font color="blue">581:</font>   case, the application may save the current current value of total_in which
-<font color="blue">582:</font>   indicates where valid compressed data was found. In the error case, the
-<font color="blue">583:</font>   application may repeatedly call inflateSync, providing more input each time,
-<font color="blue">584:</font>   until success or end of the input data.
-<font color="blue">585:</font> */
-<font color="blue">586:</font> 
-<font color="blue">587:</font> ZEXTERN int ZEXPORT inflateReset OF((z_streamp strm));
-<font color="blue">588:</font> /*
-<font color="blue">589:</font>      This function is equivalent to inflateEnd followed by inflateInit,
-<font color="blue">590:</font>    but does not free and reallocate all the internal decompression state.
-<font color="blue">591:</font>    The stream will keep attributes that may have been set by inflateInit2.
-<font color="blue">592:</font> 
-<font color="blue">593:</font>       inflateReset returns Z_OK if success, or Z_STREAM_ERROR if the source
-<font color="blue">594:</font>    stream state was inconsistent (such as zalloc or state being NULL).
-<font color="blue">595:</font> */
-<font color="blue">596:</font> 
-<font color="blue">597:</font> 
-<font color="blue">598:</font>                         /* utility functions */
-<font color="blue">599:</font> 
-<font color="blue">600:</font> /*
-<font color="blue">601:</font>      The following utility functions are implemented on top of the
-<font color="blue">602:</font>    basic stream-oriented functions. To simplify the interface, some
-<font color="blue">603:</font>    default options are assumed (compression level and memory usage,
-<font color="blue">604:</font>    standard memory allocation functions). The source code of these
-<font color="blue">605:</font>    utility functions can easily be modified if you need special options.
-<font color="blue">606:</font> */
-<font color="blue">607:</font> 
-<font color="blue">608:</font> ZEXTERN int ZEXPORT compress OF((Bytef *dest,   uLongf *destLen,
-<font color="blue">609:</font>                                  const Bytef *source, uLong sourceLen));
-<font color="blue">610:</font> /*
-<font color="blue">611:</font>      Compresses the source buffer into the destination buffer.  sourceLen is
-<font color="blue">612:</font>    the byte length of the source buffer. Upon entry, destLen is the total
-<font color="blue">613:</font>    size of the destination buffer, which must be at least 0.1% larger than
-<font color="blue">614:</font>    sourceLen plus 12 bytes. Upon exit, destLen is the actual size of the
-<font color="blue">615:</font>    compressed buffer.
-<font color="blue">616:</font>      This function can be used to compress a whole file at once if the
-<font color="blue">617:</font>    input file is mmap'ed.
-<font color="blue">618:</font>      compress returns Z_OK if success, Z_MEM_ERROR if there was not
-<font color="blue">619:</font>    enough memory, Z_BUF_ERROR if there was not enough room in the output
-<font color="blue">620:</font>    buffer.
-<font color="blue">621:</font> */
-<font color="blue">622:</font> 
-<font color="blue">623:</font> ZEXTERN int ZEXPORT compress2 OF((Bytef *dest,   uLongf *destLen,
-<font color="blue">624:</font>                                   const Bytef *source, uLong sourceLen,
-<font color="blue">625:</font>                                   int level));
-<font color="blue">626:</font> /*
-<font color="blue">627:</font>      Compresses the source buffer into the destination buffer. The level
-<font color="blue">628:</font>    parameter has the same meaning as in deflateInit.  sourceLen is the byte
-<font color="blue">629:</font>    length of the source buffer. Upon entry, destLen is the total size of the
-<font color="blue">630:</font>    destination buffer, which must be at least 0.1% larger than sourceLen plus
-<font color="blue">631:</font>    12 bytes. Upon exit, destLen is the actual size of the compressed buffer.
-<font color="blue">632:</font> 
-<font color="blue">633:</font>      compress2 returns Z_OK if success, Z_MEM_ERROR if there was not enough
-<font color="blue">634:</font>    memory, Z_BUF_ERROR if there was not enough room in the output buffer,
-<font color="blue">635:</font>    Z_STREAM_ERROR if the level parameter is invalid.
-<font color="blue">636:</font> */
-<font color="blue">637:</font> 
-<font color="blue">638:</font> ZEXTERN int ZEXPORT uncompress OF((Bytef *dest,   uLongf *destLen,
-<font color="blue">639:</font>                                    const Bytef *source, uLong sourceLen));
-<font color="blue">640:</font> /*
-<font color="blue">641:</font>      Decompresses the source buffer into the destination buffer.  sourceLen is
-<font color="blue">642:</font>    the byte length of the source buffer. Upon entry, destLen is the total
-<font color="blue">643:</font>    size of the destination buffer, which must be large enough to hold the
-<font color="blue">644:</font>    entire uncompressed data. (The size of the uncompressed data must have
-<font color="blue">645:</font>    been saved previously by the compressor and transmitted to the decompressor
-<font color="blue">646:</font>    by some mechanism outside the scope of this compression library.)
-<font color="blue">647:</font>    Upon exit, destLen is the actual size of the compressed buffer.
-<font color="blue">648:</font>      This function can be used to decompress a whole file at once if the
-<font color="blue">649:</font>    input file is mmap'ed.
-<font color="blue">650:</font> 
-<font color="blue">651:</font>      uncompress returns Z_OK if success, Z_MEM_ERROR if there was not
-<font color="blue">652:</font>    enough memory, Z_BUF_ERROR if there was not enough room in the output
-<font color="blue">653:</font>    buffer, or Z_DATA_ERROR if the input data was corrupted.
-<font color="blue">654:</font> */
-<font color="blue">655:</font> 
-<font color="blue">656:</font> 
-<font color="blue">657:</font> typedef voidp gzFile;
-<font color="blue">658:</font> 
-<font color="blue">659:</font> ZEXTERN gzFile ZEXPORT gzopen  OF((const char *path, const char *mode));
-<font color="blue">660:</font> /*
-<font color="blue">661:</font>      Opens a gzip (.gz) file for reading or writing. The mode parameter
-<font color="blue">662:</font>    is as in fopen ("rb" or "wb") but can also include a compression level
-<font color="blue">663:</font>    ("wb9") or a strategy: 'f' for filtered data as in "wb6f", 'h' for
-<font color="blue">664:</font>    Huffman only compression as in "wb1h". (See the description
-<font color="blue">665:</font>    of deflateInit2 for more information about the strategy parameter.)
-<font color="blue">666:</font> 
-<font color="blue">667:</font>      gzopen can be used to read a file which is not in gzip format; in this
-<font color="blue">668:</font>    case gzread will directly read from the file without decompression.
-<font color="blue">669:</font> 
-<font color="blue">670:</font>      gzopen returns NULL if the file could not be opened or if there was
-<font color="blue">671:</font>    insufficient memory to allocate the (de)compression state; errno
-<font color="blue">672:</font>    can be checked to distinguish the two cases (if errno is zero, the
-<font color="blue">673:</font>    zlib error is Z_MEM_ERROR).  */
-<font color="blue">674:</font> 
-<font color="blue">675:</font> ZEXTERN gzFile ZEXPORT gzdopen  OF((int fd, const char *mode));
-<font color="blue">676:</font> /*
-<font color="blue">677:</font>      gzdopen() associates a gzFile with the file descriptor fd.  File
-<font color="blue">678:</font>    descriptors are obtained from calls like open, dup, creat, pipe or
-<font color="blue">679:</font>    fileno (in the file has been previously opened with fopen).
-<font color="blue">680:</font>    The mode parameter is as in gzopen.
-<font color="blue">681:</font>      The next call of gzclose on the returned gzFile will also close the
-<font color="blue">682:</font>    file descriptor fd, just like fclose(fdopen(fd), mode) closes the file
-<font color="blue">683:</font>    descriptor fd. If you want to keep fd open, use gzdopen(dup(fd), mode).
-<font color="blue">684:</font>      gzdopen returns NULL if there was insufficient memory to allocate
-<font color="blue">685:</font>    the (de)compression state.
-<font color="blue">686:</font> */
-<font color="blue">687:</font> 
-<font color="blue">688:</font> ZEXTERN int ZEXPORT gzsetparams OF((gzFile file, int level, int strategy));
-<font color="blue">689:</font> /*
-<font color="blue">690:</font>      Dynamically update the compression level or strategy. See the description
-<font color="blue">691:</font>    of deflateInit2 for the meaning of these parameters.
-<font color="blue">692:</font>      gzsetparams returns Z_OK if success, or Z_STREAM_ERROR if the file was not
-<font color="blue">693:</font>    opened for writing.
-<font color="blue">694:</font> */
-<font color="blue">695:</font> 
-<font color="blue">696:</font> ZEXTERN int ZEXPORT    gzread  OF((gzFile file, voidp buf, unsigned len));
-<font color="blue">697:</font> /*
-<font color="blue">698:</font>      Reads the given number of uncompressed bytes from the compressed file.
-<font color="blue">699:</font>    If the input file was not in gzip format, gzread copies the given number
-<font color="blue">700:</font>    of bytes into the buffer.
-<font color="blue">701:</font>      gzread returns the number of uncompressed bytes actually read (0 for
-<font color="blue">702:</font>    end of file, -1 for error). */
-<font color="blue">703:</font> 
-<font color="blue">704:</font> ZEXTERN int ZEXPORT    gzwrite OF((gzFile file, 
-<font color="blue">705:</font> 				   const voidp buf, unsigned len));
-<font color="blue">706:</font> /*
-<font color="blue">707:</font>      Writes the given number of uncompressed bytes into the compressed file.
-<font color="blue">708:</font>    gzwrite returns the number of uncompressed bytes actually written
-<font color="blue">709:</font>    (0 in case of error).
-<font color="blue">710:</font> */
-<font color="blue">711:</font> 
-<font color="blue">712:</font> ZEXTERN int ZEXPORTVA   gzprintf OF((gzFile file, const char *format, ...));
-<font color="blue">713:</font> /*
-<font color="blue">714:</font>      Converts, formats, and writes the args to the compressed file under
-<font color="blue">715:</font>    control of the format string, as in fprintf. gzprintf returns the number of
-<font color="blue">716:</font>    uncompressed bytes actually written (0 in case of error).
-<font color="blue">717:</font> */
-<font color="blue">718:</font> 
-<font color="blue">719:</font> ZEXTERN int ZEXPORT gzputs OF((gzFile file, const char *s));
-<font color="blue">720:</font> /*
-<font color="blue">721:</font>       Writes the given null-terminated string to the compressed file, excluding
-<font color="blue">722:</font>    the terminating null character.
-<font color="blue">723:</font>       gzputs returns the number of characters written, or -1 in case of error.
-<font color="blue">724:</font> */
-<font color="blue">725:</font> 
-<font color="blue">726:</font> ZEXTERN char * ZEXPORT gzgets OF((gzFile file, char *buf, int len));
-<font color="blue">727:</font> /*
-<font color="blue">728:</font>       Reads bytes from the compressed file until len-1 characters are read, or
-<font color="blue">729:</font>    a newline character is read and transferred to buf, or an end-of-file
-<font color="blue">730:</font>    condition is encountered.  The string is then terminated with a null
-<font color="blue">731:</font>    character.
-<font color="blue">732:</font>       gzgets returns buf, or Z_NULL in case of error.
-<font color="blue">733:</font> */
-<font color="blue">734:</font> 
-<font color="blue">735:</font> ZEXTERN int ZEXPORT    gzputc OF((gzFile file, int c));
-<font color="blue">736:</font> /*
-<font color="blue">737:</font>       Writes c, converted to an unsigned char, into the compressed file.
-<font color="blue">738:</font>    gzputc returns the value that was written, or -1 in case of error.
-<font color="blue">739:</font> */
-<font color="blue">740:</font> 
-<font color="blue">741:</font> ZEXTERN int ZEXPORT    gzgetc OF((gzFile file));
-<font color="blue">742:</font> /*
-<font color="blue">743:</font>       Reads one byte from the compressed file. gzgetc returns this byte
-<font color="blue">744:</font>    or -1 in case of end of file or error.
-<font color="blue">745:</font> */
-<font color="blue">746:</font> 
-<font color="blue">747:</font> ZEXTERN int ZEXPORT    gzflush OF((gzFile file, int flush));
-<font color="blue">748:</font> /*
-<font color="blue">749:</font>      Flushes all pending output into the compressed file. The parameter
-<font color="blue">750:</font>    flush is as in the deflate() function. The return value is the zlib
-<font color="blue">751:</font>    error number (see function gzerror below). gzflush returns Z_OK if
-<font color="blue">752:</font>    the flush parameter is Z_FINISH and all output could be flushed.
-<font color="blue">753:</font>      gzflush should be called only when strictly necessary because it can
-<font color="blue">754:</font>    degrade compression.
-<font color="blue">755:</font> */
-<font color="blue">756:</font> 
-<font color="blue">757:</font> ZEXTERN z_off_t ZEXPORT    gzseek OF((gzFile file,
-<font color="blue">758:</font> 				      z_off_t offset, int whence));
-<font color="blue">759:</font> /* 
-<font color="blue">760:</font>       Sets the starting position for the next gzread or gzwrite on the
-<font color="blue">761:</font>    given compressed file. The offset represents a number of bytes in the
-<font color="blue">762:</font>    uncompressed data stream. The whence parameter is defined as in lseek(2);
-<font color="blue">763:</font>    the value SEEK_END is not supported.
-<font color="blue">764:</font>      If the file is opened for reading, this function is emulated but can be
-<font color="blue">765:</font>    extremely slow. If the file is opened for writing, only forward seeks are
-<font color="blue">766:</font>    supported; gzseek then compresses a sequence of zeroes up to the new
-<font color="blue">767:</font>    starting position.
-<font color="blue">768:</font> 
-<font color="blue">769:</font>       gzseek returns the resulting offset location as measured in bytes from
-<font color="blue">770:</font>    the beginning of the uncompressed stream, or -1 in case of error, in
-<font color="blue">771:</font>    particular if the file is opened for writing and the new starting position
-<font color="blue">772:</font>    would be before the current position.
-<font color="blue">773:</font> */
-<font color="blue">774:</font> 
-<font color="blue">775:</font> ZEXTERN int ZEXPORT    gzrewind OF((gzFile file));
-<font color="blue">776:</font> /*
-<font color="blue">777:</font>      Rewinds the given file. This function is supported only for reading.
-<font color="blue">778:</font> 
-<font color="blue">779:</font>    gzrewind(file) is equivalent to (int)gzseek(file, 0L, SEEK_SET)
-<font color="blue">780:</font> */
-<font color="blue">781:</font> 
-<font color="blue">782:</font> ZEXTERN z_off_t ZEXPORT    gztell OF((gzFile file));
-<font color="blue">783:</font> /*
-<font color="blue">784:</font>      Returns the starting position for the next gzread or gzwrite on the
-<font color="blue">785:</font>    given compressed file. This position represents a number of bytes in the
-<font color="blue">786:</font>    uncompressed data stream.
-<font color="blue">787:</font> 
-<font color="blue">788:</font>    gztell(file) is equivalent to gzseek(file, 0L, SEEK_CUR)
-<font color="blue">789:</font> */
-<font color="blue">790:</font> 
-<font color="blue">791:</font> ZEXTERN int ZEXPORT gzeof OF((gzFile file));
-<font color="blue">792:</font> /*
-<font color="blue">793:</font>      Returns 1 when EOF has previously been detected reading the given
-<font color="blue">794:</font>    input stream, otherwise zero.
-<font color="blue">795:</font> */
-<font color="blue">796:</font> 
-<font color="blue">797:</font> ZEXTERN int ZEXPORT    gzclose OF((gzFile file));
-<font color="blue">798:</font> /*
-<font color="blue">799:</font>      Flushes all pending output if necessary, closes the compressed file
-<font color="blue">800:</font>    and deallocates all the (de)compression state. The return value is the zlib
-<font color="blue">801:</font>    error number (see function gzerror below).
-<font color="blue">802:</font> */
-<font color="blue">803:</font> 
-<font color="blue">804:</font> ZEXTERN const char * ZEXPORT gzerror OF((gzFile file, int *errnum));
-<font color="blue">805:</font> /*
-<font color="blue">806:</font>      Returns the error message for the last error which occurred on the
-<font color="blue">807:</font>    given compressed file. errnum is set to zlib error number. If an
-<font color="blue">808:</font>    error occurred in the file system and not in the compression library,
-<font color="blue">809:</font>    errnum is set to Z_ERRNO and the application may consult errno
-<font color="blue">810:</font>    to get the exact error code.
-<font color="blue">811:</font> */
-<font color="blue">812:</font> 
-<font color="blue">813:</font>                         /* checksum functions */
-<font color="blue">814:</font> 
-<font color="blue">815:</font> /*
-<font color="blue">816:</font>      These functions are not related to compression but are exported
-<font color="blue">817:</font>    anyway because they might be useful in applications using the
-<font color="blue">818:</font>    compression library.
-<font color="blue">819:</font> */
-<font color="blue">820:</font> 
-<font color="blue">821:</font> ZEXTERN uLong ZEXPORT adler32 OF((uLong adler, const Bytef *buf, uInt len));
-<font color="blue">822:</font> 
-<font color="blue">823:</font> /*
-<font color="blue">824:</font>      Update a running Adler-32 checksum with the bytes buf[0..len-1] and
-<font color="blue">825:</font>    return the updated checksum. If buf is NULL, this function returns
-<font color="blue">826:</font>    the required initial value for the checksum.
-<font color="blue">827:</font>    An Adler-32 checksum is almost as reliable as a CRC32 but can be computed
-<font color="blue">828:</font>    much faster. Usage example:
-<font color="blue">829:</font> 
-<font color="blue">830:</font>      uLong adler = adler32(0L, Z_NULL, 0);
-<font color="blue">831:</font> 
-<font color="blue">832:</font>      while (read_buffer(buffer, length) != EOF) {
-<font color="blue">833:</font>        adler = adler32(adler, buffer, length);
-<font color="blue">834:</font>      }
-<font color="blue">835:</font>      if (adler != original_adler) error();
-<font color="blue">836:</font> */
-<font color="blue">837:</font> 
-<font color="blue">838:</font> ZEXTERN uLong ZEXPORT crc32   OF((uLong crc, const Bytef *buf, uInt len));
-<font color="blue">839:</font> /*
-<font color="blue">840:</font>      Update a running crc with the bytes buf[0..len-1] and return the updated
-<font color="blue">841:</font>    crc. If buf is NULL, this function returns the required initial value
-<font color="blue">842:</font>    for the crc. Pre- and post-conditioning (one's complement) is performed
-<font color="blue">843:</font>    within this function so it shouldn't be done by the application.
-<font color="blue">844:</font>    Usage example:
-<font color="blue">845:</font> 
-<font color="blue">846:</font>      uLong crc = crc32(0L, Z_NULL, 0);
-<font color="blue">847:</font> 
-<font color="blue">848:</font>      while (read_buffer(buffer, length) != EOF) {
-<font color="blue">849:</font>        crc = crc32(crc, buffer, length);
-<font color="blue">850:</font>      }
-<font color="blue">851:</font>      if (crc != original_crc) error();
-<font color="blue">852:</font> */
-<font color="blue">853:</font> 
-<font color="blue">854:</font> 
-<font color="blue">855:</font>                         /* various hacks, don't look :) */
-<font color="blue">856:</font> 
-<font color="blue">857:</font> /* deflateInit and inflateInit are macros to allow checking the zlib version
-<font color="blue">858:</font>  * and the compiler's view of z_stream:
-<font color="blue">859:</font>  */
-<font color="blue">860:</font> ZEXTERN int ZEXPORT deflateInit_ OF((z_streamp strm, int level,
-<font color="blue">861:</font>                                      const char *version, int stream_size));
-<font color="blue">862:</font> ZEXTERN int ZEXPORT inflateInit_ OF((z_streamp strm,
-<font color="blue">863:</font>                                      const char *version, int stream_size));
-<font color="blue">864:</font> ZEXTERN int ZEXPORT deflateInit2_ OF((z_streamp strm, int  level, int  method,
-<font color="blue">865:</font>                                       int windowBits, int memLevel,
-<font color="blue">866:</font>                                       int strategy, const char *version,
-<font color="blue">867:</font>                                       int stream_size));
-<font color="blue">868:</font> ZEXTERN int ZEXPORT inflateInit2_ OF((z_streamp strm, int  windowBits,
-<font color="blue">869:</font>                                       const char *version, int stream_size));
-<font color="blue"><a name="initmacros">870:</a></font> #define deflateInit(strm, level) \
-<font color="blue">871:</font>         deflateInit_((strm), (level),       ZLIB_VERSION, sizeof(z_stream))
-<font color="blue">872:</font> #define inflateInit(strm) \
-<font color="blue">873:</font>         inflateInit_((strm),                ZLIB_VERSION, sizeof(z_stream))
-<font color="blue">874:</font> #define deflateInit2(strm, level, method, windowBits, memLevel, strategy) \
-<font color="blue">875:</font>         deflateInit2_((strm),(level),(method),(windowBits),(memLevel),\
-<font color="blue">876:</font>                       (strategy),           ZLIB_VERSION, sizeof(z_stream))
-<font color="blue">877:</font> #define inflateInit2(strm, windowBits) \
-<font color="blue">878:</font>         inflateInit2_((strm), (windowBits), ZLIB_VERSION, sizeof(z_stream))
-<font color="blue">879:</font> 
-<font color="blue">880:</font> 
-<font color="blue">881:</font> #if !defined(_Z_UTIL_H) &amp;&amp; !defined(NO_DUMMY_DECL)
-<font color="blue">882:</font>     struct internal_state {int dummy;}; /* hack for buggy compilers */
-<font color="blue">883:</font> #endif
-<font color="blue">884:</font> 
-<font color="blue">885:</font> ZEXTERN const char   * ZEXPORT zError           OF((int err));
-<font color="blue">886:</font> ZEXTERN int            ZEXPORT inflateSyncPoint OF((z_streamp z));
-<font color="blue">887:</font> ZEXTERN const uLongf * ZEXPORT get_crc_table    OF((void));
-<font color="blue">888:</font> 
-<font color="blue">889:</font> #ifdef __cplusplus
-<font color="blue">890:</font> }
-<font color="blue">891:</font> #endif
-<font color="blue">892:</font> 
-<font color="blue">893:</font> #endif /* _ZLIB_H */
-      </pre>
-    </blockquote>
-
-    <center><h2><a name="devel">How the zlib wrapper was developed</a></h2></center>
-
-    <h3>Attempt #1</h3>
-    <blockquote>
-      <pre>
-/* File : example.i */
-%module example
-%{
-/* Put headers and other declarations here */
-#include "zlib.h"
-%}
-
-%include typemaps.i
-
-%include "zlib.h"
-      </pre>
-    </blockquote>
-
-    The result is:
-
-    <blockquote>
-      <pre>
-% swig -chicken -I/usr/include example.i
-<a href="#l63">/usr/include/zlib.h:63</a>: Syntax error in input.
-<a href="#l78">/usr/include/zlib.h:78</a>: Syntax error in input.
-<a href="#l80">/usr/include/zlib.h:80</a>: Syntax error in input.
-      </pre>
-    </blockquote>
-
-    The first problem we see is that the macro <code>OF(...)</code> is
-    not defined.
-
-    <h3>Attempt #2</h3>
-
-    We make sure to include <tt>zconf.h</tt> so that SWIG can see the
-    definition of <code>OF(...)</code>.  We try again.
-
-    <blockquote>
-      <pre>
-/* File : example.i */
-%module example
-%{
-/* Put headers and other declarations here */
-#include "zlib.h"
-%}
-
-%include typemaps.i
-
-<font color="red">%include "zconf.h"</font>
-%include "zlib.h"
-      </pre>
-    </blockquote>
-
-    The result is:
-
-    <blockquote>
-      <pre>
-% swig -chicken -I/usr/include example.i
-      </pre>
-    </blockquote>
-
-    This seems to work!  But we should take a peek inside the generated
-    <tt>example_wrap.c</tt> to see what the names of the Scheme
-    procedures will be.
-
-    <blockquote>
-      <pre>
-% grep C_intern example_wrap.c
-  C_word err = C_intern2 (&amp;a, errorhook);
-    sym = C_intern (&amp;a, 21, "example:max-mem-level");
-    sym = C_intern (&amp;a, 17, "example:max-wbits");
-    sym = C_intern (&amp;a, 16, "example:seek-set");
-    sym = C_intern (&amp;a, 16, "example:seek-cur");
-    sym = C_intern (&amp;a, 16, "example:seek-end");
-    sym = C_intern (&amp;a, 20, "example:zlib-version");
-    sym = C_intern (&amp;a, 28, "example:z-stream-next-in-set");
-    sym = C_intern (&amp;a, 28, "example:z-stream-next-in-get");
-    sym = C_intern (&amp;a, 29, "example:z-stream-avail-in-set");
-    sym = C_intern (&amp;a, 29, "example:z-stream-avail-in-get");
-    sym = C_intern (&amp;a, 29, "example:z-stream-total-in-set");
-    sym = C_intern (&amp;a, 29, "example:z-stream-total-in-get");
-    sym = C_intern (&amp;a, 29, "example:z-stream-next-out-set");
-    sym = C_intern (&amp;a, 29, "example:z-stream-next-out-get");
-    sym = C_intern (&amp;a, 30, "example:z-stream-avail-out-set");
-    sym = C_intern (&amp;a, 30, "example:z-stream-avail-out-get");
-    sym = C_intern (&amp;a, 30, "example:z-stream-total-out-set");
-    sym = C_intern (&amp;a, 30, "example:z-stream-total-out-get");
-    sym = C_intern (&amp;a, 24, "example:z-stream-msg-set");
-    sym = C_intern (&amp;a, 24, "example:z-stream-msg-get");
-    sym = C_intern (&amp;a, 26, "example:z-stream-state-set");
-    sym = C_intern (&amp;a, 26, "example:z-stream-state-get");
-    sym = C_intern (&amp;a, 27, "example:z-stream-zalloc-set");
-    sym = C_intern (&amp;a, 27, "example:z-stream-zalloc-get");
-    sym = C_intern (&amp;a, 26, "example:z-stream-zfree-set");
-    sym = C_intern (&amp;a, 26, "example:z-stream-zfree-get");
-    sym = C_intern (&amp;a, 27, "example:z-stream-opaque-set");
-    sym = C_intern (&amp;a, 27, "example:z-stream-opaque-get");
-    sym = C_intern (&amp;a, 30, "example:z-stream-data-type-set");
-    sym = C_intern (&amp;a, 30, "example:z-stream-data-type-get");
-    sym = C_intern (&amp;a, 26, "example:z-stream-adler-set");
-    sym = C_intern (&amp;a, 26, "example:z-stream-adler-get");
-    sym = C_intern (&amp;a, 29, "example:z-stream-reserved-set");
-    sym = C_intern (&amp;a, 29, "example:z-stream-reserved-get");
-    sym = C_intern (&amp;a, 20, "example:new-z-stream");
-    sym = C_intern (&amp;a, 23, "example:delete-z-stream");
-    sym = C_intern (&amp;a, 18, "example:z-no-flush");
-    sym = C_intern (&amp;a, 23, "example:z-partial-flush");
-    sym = C_intern (&amp;a, 20, "example:z-sync-flush");
-    sym = C_intern (&amp;a, 20, "example:z-full-flush");
-    sym = C_intern (&amp;a, 16, "example:z-finish");
-    sym = C_intern (&amp;a, 12, "example:z-ok");
-    sym = C_intern (&amp;a, 20, "example:z-stream-end");
-    sym = C_intern (&amp;a, 19, "example:z-need-dict");
-    sym = C_intern (&amp;a, 15, "example:z-errno");
-    sym = C_intern (&amp;a, 22, "example:z-stream-error");
-    sym = C_intern (&amp;a, 20, "example:z-data-error");
-    sym = C_intern (&amp;a, 19, "example:z-mem-error");
-    sym = C_intern (&amp;a, 19, "example:z-buf-error");
-    sym = C_intern (&amp;a, 23, "example:z-version-error");
-    sym = C_intern (&amp;a, 24, "example:z-no-compression");
-    sym = C_intern (&amp;a, 20, "example:z-best-speed");
-    sym = C_intern (&amp;a, 26, "example:z-best-compression");
-    sym = C_intern (&amp;a, 29, "example:z-default-compression");
-    sym = C_intern (&amp;a, 18, "example:z-filtered");
-    sym = C_intern (&amp;a, 22, "example:z-huffman-only");
-    sym = C_intern (&amp;a, 26, "example:z-default-strategy");
-    sym = C_intern (&amp;a, 16, "example:z-binary");
-    sym = C_intern (&amp;a, 15, "example:z-ascii");
-    sym = C_intern (&amp;a, 17, "example:z-unknown");
-    sym = C_intern (&amp;a, 18, "example:z-deflated");
-    sym = C_intern (&amp;a, 14, "example:z-null");
-    sym = C_intern (&amp;a, 19, "example:zlibversion");
-    sym = C_intern (&amp;a, 15, "example:deflate");
-    sym = C_intern (&amp;a, 18, "example:deflateend");
-    sym = C_intern (&amp;a, 15, "example:inflate");
-    sym = C_intern (&amp;a, 18, "example:inflateend");
-    sym = C_intern (&amp;a, 28, "example:deflatesetdictionary");
-    sym = C_intern (&amp;a, 19, "example:deflatecopy");
-    sym = C_intern (&amp;a, 20, "example:deflatereset");
-    sym = C_intern (&amp;a, 21, "example:deflateparams");
-    sym = C_intern (&amp;a, 28, "example:inflatesetdictionary");
-    sym = C_intern (&amp;a, 19, "example:inflatesync");
-    sym = C_intern (&amp;a, 20, "example:inflatereset");
-    sym = C_intern (&amp;a, 16, "example:compress");
-    sym = C_intern (&amp;a, 17, "example:compress2");
-    sym = C_intern (&amp;a, 18, "example:uncompress");
-    sym = C_intern (&amp;a, 14, "example:gzopen");
-    sym = C_intern (&amp;a, 15, "example:gzdopen");
-    sym = C_intern (&amp;a, 19, "example:gzsetparams");
-    sym = C_intern (&amp;a, 14, "example:gzread");
-    sym = C_intern (&amp;a, 15, "example:gzwrite");
-    sym = C_intern (&amp;a, 16, "example:gzprintf");
-    sym = C_intern (&amp;a, 14, "example:gzputs");
-    sym = C_intern (&amp;a, 14, "example:gzgets");
-    sym = C_intern (&amp;a, 14, "example:gzputc");
-    sym = C_intern (&amp;a, 14, "example:gzgetc");
-    sym = C_intern (&amp;a, 15, "example:gzflush");
-    sym = C_intern (&amp;a, 14, "example:gzseek");
-    sym = C_intern (&amp;a, 16, "example:gzrewind");
-    sym = C_intern (&amp;a, 14, "example:gztell");
-    sym = C_intern (&amp;a, 13, "example:gzeof");
-    sym = C_intern (&amp;a, 15, "example:gzclose");
-    sym = C_intern (&amp;a, 15, "example:gzerror");
-    sym = C_intern (&amp;a, 15, "example:adler32");
-    sym = C_intern (&amp;a, 13, "example:crc32");
-    sym = C_intern (&amp;a, 20, "example:deflateinit-");
-    sym = C_intern (&amp;a, 20, "example:inflateinit-");
-    sym = C_intern (&amp;a, 21, "example:deflateinit2-");
-    sym = C_intern (&amp;a, 21, "example:inflateinit2-");
-    sym = C_intern (&amp;a, 32, "example:internal-state-dummy-set");
-    sym = C_intern (&amp;a, 32, "example:internal-state-dummy-get");
-    sym = C_intern (&amp;a, 26, "example:new-internal-state");
-    sym = C_intern (&amp;a, 29, "example:delete-internal-state");
-    sym = C_intern (&amp;a, 14, "example:zerror");
-    sym = C_intern (&amp;a, 24, "example:inflatesyncpoint");
-    sym = C_intern (&amp;a, 21, "example:get-crc-table");
-      </pre>
-    </blockquote>
-
-    In fact, we want the Scheme procedure names to begin with
-    <code>zlib</code> instead of <code>example</code>.  For
-    <code>example:zlib-version</code>, we want
-    <code>zlib-version</code>.  And we want dashes when the case
-    switches to/from upper/lowercase; ex. the function
-    <code>deflateEnd()</code> should be the Scheme procedure
-    <code>zlib-deflate-end</code>.
-
-    <h3>Attempt #3</h3>
-
-    We make sure to add <tt>-prefix zlib -mixed</tt> to the
-    <tt>swig</tt> command line, and we rename
-    <code>ZLIB_VERSION</code> to <code>VERSION</code>.  We try again.
-
-    <blockquote>
-      <pre>
-/* File : example.i */
-%module example
-%{
-/* Put headers and other declarations here */
-#include "zlib.h"
-%}
-
-%include typemaps.i
-
-<font color="red">%rename(VERSION) ZLIB_VERSION;</font>
-
-%include "zconf.h"
-%include "zlib.h"
-      </pre>
-    </blockquote>
-
-    The result is:
-
-    <blockquote>
-      <pre>
-% swig -chicken <font color="red">-prefix zlib -mixed</font> -I/usr/include example.i
-% grep C_intern example_wrap.c
-  C_word err = C_intern2 (&amp;a, errorhook);
-    sym = C_intern (&amp;a, 18, "zlib:max-mem-level");
-    sym = C_intern (&amp;a, 14, "zlib:max-wbits");
-    sym = C_intern (&amp;a, 13, "zlib:seek-set");
-    sym = C_intern (&amp;a, 13, "zlib:seek-cur");
-    sym = C_intern (&amp;a, 13, "zlib:seek-end");
-    sym = C_intern (&amp;a, 12, "zlib:version");
-    sym = C_intern (&amp;a, 25, "zlib:z-stream-next-in-set");
-    sym = C_intern (&amp;a, 25, "zlib:z-stream-next-in-get");
-    sym = C_intern (&amp;a, 26, "zlib:z-stream-avail-in-set");
-    sym = C_intern (&amp;a, 26, "zlib:z-stream-avail-in-get");
-    sym = C_intern (&amp;a, 26, "zlib:z-stream-total-in-set");
-    sym = C_intern (&amp;a, 26, "zlib:z-stream-total-in-get");
-    sym = C_intern (&amp;a, 26, "zlib:z-stream-next-out-set");
-    sym = C_intern (&amp;a, 26, "zlib:z-stream-next-out-get");
-    sym = C_intern (&amp;a, 27, "zlib:z-stream-avail-out-set");
-    sym = C_intern (&amp;a, 27, "zlib:z-stream-avail-out-get");
-    sym = C_intern (&amp;a, 27, "zlib:z-stream-total-out-set");
-    sym = C_intern (&amp;a, 27, "zlib:z-stream-total-out-get");
-    sym = C_intern (&amp;a, 21, "zlib:z-stream-msg-set");
-    sym = C_intern (&amp;a, 21, "zlib:z-stream-msg-get");
-    sym = C_intern (&amp;a, 23, "zlib:z-stream-state-set");
-    sym = C_intern (&amp;a, 23, "zlib:z-stream-state-get");
-    sym = C_intern (&amp;a, 24, "zlib:z-stream-zalloc-set");
-    sym = C_intern (&amp;a, 24, "zlib:z-stream-zalloc-get");
-    sym = C_intern (&amp;a, 23, "zlib:z-stream-zfree-set");
-    sym = C_intern (&amp;a, 23, "zlib:z-stream-zfree-get");
-    sym = C_intern (&amp;a, 24, "zlib:z-stream-opaque-set");
-    sym = C_intern (&amp;a, 24, "zlib:z-stream-opaque-get");
-    sym = C_intern (&amp;a, 27, "zlib:z-stream-data-type-set");
-    sym = C_intern (&amp;a, 27, "zlib:z-stream-data-type-get");
-    sym = C_intern (&amp;a, 23, "zlib:z-stream-adler-set");
-    sym = C_intern (&amp;a, 23, "zlib:z-stream-adler-get");
-    sym = C_intern (&amp;a, 26, "zlib:z-stream-reserved-set");
-    sym = C_intern (&amp;a, 26, "zlib:z-stream-reserved-get");
-    sym = C_intern (&amp;a, 17, "zlib:new-z-stream");
-    sym = C_intern (&amp;a, 20, "zlib:delete-z-stream");
-    sym = C_intern (&amp;a, 15, "zlib:z-no-flush");
-    sym = C_intern (&amp;a, 20, "zlib:z-partial-flush");
-    sym = C_intern (&amp;a, 17, "zlib:z-sync-flush");
-    sym = C_intern (&amp;a, 17, "zlib:z-full-flush");
-    sym = C_intern (&amp;a, 13, "zlib:z-finish");
-    sym = C_intern (&amp;a, 9, "zlib:z-ok");
-    sym = C_intern (&amp;a, 17, "zlib:z-stream-end");
-    sym = C_intern (&amp;a, 16, "zlib:z-need-dict");
-    sym = C_intern (&amp;a, 12, "zlib:z-errno");
-    sym = C_intern (&amp;a, 19, "zlib:z-stream-error");
-    sym = C_intern (&amp;a, 17, "zlib:z-data-error");
-    sym = C_intern (&amp;a, 16, "zlib:z-mem-error");
-    sym = C_intern (&amp;a, 16, "zlib:z-buf-error");
-    sym = C_intern (&amp;a, 20, "zlib:z-version-error");
-    sym = C_intern (&amp;a, 21, "zlib:z-no-compression");
-    sym = C_intern (&amp;a, 17, "zlib:z-best-speed");
-    sym = C_intern (&amp;a, 23, "zlib:z-best-compression");
-    sym = C_intern (&amp;a, 26, "zlib:z-default-compression");
-    sym = C_intern (&amp;a, 15, "zlib:z-filtered");
-    sym = C_intern (&amp;a, 19, "zlib:z-huffman-only");
-    sym = C_intern (&amp;a, 23, "zlib:z-default-strategy");
-    sym = C_intern (&amp;a, 13, "zlib:z-binary");
-    sym = C_intern (&amp;a, 12, "zlib:z-ascii");
-    sym = C_intern (&amp;a, 14, "zlib:z-unknown");
-    sym = C_intern (&amp;a, 15, "zlib:z-deflated");
-    sym = C_intern (&amp;a, 11, "zlib:z-null");
-    sym = C_intern (&amp;a, 17, "zlib:zlib-version");
-    sym = C_intern (&amp;a, 12, "zlib:deflate");
-    sym = C_intern (&amp;a, 16, "zlib:deflate-end");
-    sym = C_intern (&amp;a, 12, "zlib:inflate");
-    sym = C_intern (&amp;a, 16, "zlib:inflate-end");
-    sym = C_intern (&amp;a, 27, "zlib:deflate-set-dictionary");
-    sym = C_intern (&amp;a, 17, "zlib:deflate-copy");
-    sym = C_intern (&amp;a, 18, "zlib:deflate-reset");
-    sym = C_intern (&amp;a, 19, "zlib:deflate-params");
-    sym = C_intern (&amp;a, 27, "zlib:inflate-set-dictionary");
-    sym = C_intern (&amp;a, 17, "zlib:inflate-sync");
-    sym = C_intern (&amp;a, 18, "zlib:inflate-reset");
-    sym = C_intern (&amp;a, 13, "zlib:compress");
-    sym = C_intern (&amp;a, 14, "zlib:compress2");
-    sym = C_intern (&amp;a, 15, "zlib:uncompress");
-    sym = C_intern (&amp;a, 11, "zlib:gzopen");
-    sym = C_intern (&amp;a, 12, "zlib:gzdopen");
-    sym = C_intern (&amp;a, 16, "zlib:gzsetparams");
-    sym = C_intern (&amp;a, 11, "zlib:gzread");
-    sym = C_intern (&amp;a, 12, "zlib:gzwrite");
-    sym = C_intern (&amp;a, 13, "zlib:gzprintf");
-    sym = C_intern (&amp;a, 11, "zlib:gzputs");
-    sym = C_intern (&amp;a, 11, "zlib:gzgets");
-    sym = C_intern (&amp;a, 11, "zlib:gzputc");
-    sym = C_intern (&amp;a, 11, "zlib:gzgetc");
-    sym = C_intern (&amp;a, 12, "zlib:gzflush");
-    sym = C_intern (&amp;a, 11, "zlib:gzseek");
-    sym = C_intern (&amp;a, 13, "zlib:gzrewind");
-    sym = C_intern (&amp;a, 11, "zlib:gztell");
-    sym = C_intern (&amp;a, 10, "zlib:gzeof");
-    sym = C_intern (&amp;a, 12, "zlib:gzclose");
-    sym = C_intern (&amp;a, 12, "zlib:gzerror");
-    sym = C_intern (&amp;a, 12, "zlib:adler32");
-    sym = C_intern (&amp;a, 10, "zlib:crc32");
-    sym = C_intern (&amp;a, 18, "zlib:deflate-init-");
-    sym = C_intern (&amp;a, 18, "zlib:inflate-init-");
-    sym = C_intern (&amp;a, 19, "zlib:deflate-init2-");
-    sym = C_intern (&amp;a, 19, "zlib:inflate-init2-");
-    sym = C_intern (&amp;a, 29, "zlib:internal-state-dummy-set");
-    sym = C_intern (&amp;a, 29, "zlib:internal-state-dummy-get");
-    sym = C_intern (&amp;a, 23, "zlib:new-internal-state");
-    sym = C_intern (&amp;a, 26, "zlib:delete-internal-state");
-    sym = C_intern (&amp;a, 12, "zlib:ze-rror");
-    sym = C_intern (&amp;a, 23, "zlib:inflate-sync-point");
-    sym = C_intern (&amp;a, 18, "zlib:get-crc-table");
-      </pre>
-    </blockquote>
-
-    Much better.  The only problem is the identifier
-    <code>zlib:ze-rror</code>, and we are missing
-    <code>zlib:deflate-init</code> and <code>zlib:inflate-init</code>
-    because they are defined as macros (see <a
-      href="#initmacros">macro definitions</a>).
-
-    <h3>Attempt #4</h3>
-
-    We make sure to rename <code>zError</code> to
-    <code>z_error</code>, and we inline some helper functions for the
-    <code>zlib:...-init</code> macros.  We try again.
-
-    <blockquote>
-      <pre>
-/* File : example.i */
-%module example
-%{
-/* Put headers and other declarations here */
-#include "zlib.h"
-%}
-
-%include typemaps.i
-
-%rename(VERSION) ZLIB_VERSION;
-<font color="red">%rename(z_error) zError;</font>
-
-%include "zconf.h"
-%include "zlib.h"
-
-<font color="red">%inline %{
-/* %inline blocks are seen by SWIG and are inserted into the header
-   portion of example_wrap.c, so that they are also seen by the C
-   compiler. */
-int deflate_init(z_streamp strm, int level) {
-  return deflateInit(strm,level); /* call macro */
-}
-int inflate_init(z_streamp strm) {
-  return inflateInit(strm); /* call macro */
-}
-%}
-</font>
-
-      </pre>
-    </blockquote>
-
-    The result is:
-
-    <blockquote>
-      <pre>
-% swig -chicken -prefix zlib -mixed -I/usr/include example.i
-% grep C_intern example_wrap.c
-  C_word err = C_intern2 (&amp;a, errorhook);
-    sym = C_intern (&amp;a, 18, "zlib:max-mem-level");
-    sym = C_intern (&amp;a, 14, "zlib:max-wbits");
-    sym = C_intern (&amp;a, 13, "zlib:seek-set");
-    sym = C_intern (&amp;a, 13, "zlib:seek-cur");
-    sym = C_intern (&amp;a, 13, "zlib:seek-end");
-    sym = C_intern (&amp;a, 12, "zlib:version");
-    sym = C_intern (&amp;a, 25, "zlib:z-stream-next-in-set");
-    sym = C_intern (&amp;a, 25, "zlib:z-stream-next-in-get");
-    sym = C_intern (&amp;a, 26, "zlib:z-stream-avail-in-set");
-    sym = C_intern (&amp;a, 26, "zlib:z-stream-avail-in-get");
-    sym = C_intern (&amp;a, 26, "zlib:z-stream-total-in-set");
-    sym = C_intern (&amp;a, 26, "zlib:z-stream-total-in-get");
-    sym = C_intern (&amp;a, 26, "zlib:z-stream-next-out-set");
-    sym = C_intern (&amp;a, 26, "zlib:z-stream-next-out-get");
-    sym = C_intern (&amp;a, 27, "zlib:z-stream-avail-out-set");
-    sym = C_intern (&amp;a, 27, "zlib:z-stream-avail-out-get");
-    sym = C_intern (&amp;a, 27, "zlib:z-stream-total-out-set");
-    sym = C_intern (&amp;a, 27, "zlib:z-stream-total-out-get");
-    sym = C_intern (&amp;a, 21, "zlib:z-stream-msg-set");
-    sym = C_intern (&amp;a, 21, "zlib:z-stream-msg-get");
-    sym = C_intern (&amp;a, 23, "zlib:z-stream-state-set");
-    sym = C_intern (&amp;a, 23, "zlib:z-stream-state-get");
-    sym = C_intern (&amp;a, 24, "zlib:z-stream-zalloc-set");
-    sym = C_intern (&amp;a, 24, "zlib:z-stream-zalloc-get");
-    sym = C_intern (&amp;a, 23, "zlib:z-stream-zfree-set");
-    sym = C_intern (&amp;a, 23, "zlib:z-stream-zfree-get");
-    sym = C_intern (&amp;a, 24, "zlib:z-stream-opaque-set");
-    sym = C_intern (&amp;a, 24, "zlib:z-stream-opaque-get");
-    sym = C_intern (&amp;a, 27, "zlib:z-stream-data-type-set");
-    sym = C_intern (&amp;a, 27, "zlib:z-stream-data-type-get");
-    sym = C_intern (&amp;a, 23, "zlib:z-stream-adler-set");
-    sym = C_intern (&amp;a, 23, "zlib:z-stream-adler-get");
-    sym = C_intern (&amp;a, 26, "zlib:z-stream-reserved-set");
-    sym = C_intern (&amp;a, 26, "zlib:z-stream-reserved-get");
-    sym = C_intern (&amp;a, 17, "zlib:new-z-stream");
-    sym = C_intern (&amp;a, 20, "zlib:delete-z-stream");
-    sym = C_intern (&amp;a, 15, "zlib:z-no-flush");
-    sym = C_intern (&amp;a, 20, "zlib:z-partial-flush");
-    sym = C_intern (&amp;a, 17, "zlib:z-sync-flush");
-    sym = C_intern (&amp;a, 17, "zlib:z-full-flush");
-    sym = C_intern (&amp;a, 13, "zlib:z-finish");
-    sym = C_intern (&amp;a, 9, "zlib:z-ok");
-    sym = C_intern (&amp;a, 17, "zlib:z-stream-end");
-    sym = C_intern (&amp;a, 16, "zlib:z-need-dict");
-    sym = C_intern (&amp;a, 12, "zlib:z-errno");
-    sym = C_intern (&amp;a, 19, "zlib:z-stream-error");
-    sym = C_intern (&amp;a, 17, "zlib:z-data-error");
-    sym = C_intern (&amp;a, 16, "zlib:z-mem-error");
-    sym = C_intern (&amp;a, 16, "zlib:z-buf-error");
-    sym = C_intern (&amp;a, 20, "zlib:z-version-error");
-    sym = C_intern (&amp;a, 21, "zlib:z-no-compression");
-    sym = C_intern (&amp;a, 17, "zlib:z-best-speed");
-    sym = C_intern (&amp;a, 23, "zlib:z-best-compression");
-    sym = C_intern (&amp;a, 26, "zlib:z-default-compression");
-    sym = C_intern (&amp;a, 15, "zlib:z-filtered");
-    sym = C_intern (&amp;a, 19, "zlib:z-huffman-only");
-    sym = C_intern (&amp;a, 23, "zlib:z-default-strategy");
-    sym = C_intern (&amp;a, 13, "zlib:z-binary");
-    sym = C_intern (&amp;a, 12, "zlib:z-ascii");
-    sym = C_intern (&amp;a, 14, "zlib:z-unknown");
-    sym = C_intern (&amp;a, 15, "zlib:z-deflated");
-    sym = C_intern (&amp;a, 11, "zlib:z-null");
-    sym = C_intern (&amp;a, 17, "zlib:zlib-version");
-    sym = C_intern (&amp;a, 12, "zlib:deflate");
-    sym = C_intern (&amp;a, 16, "zlib:deflate-end");
-    sym = C_intern (&amp;a, 12, "zlib:inflate");
-    sym = C_intern (&amp;a, 16, "zlib:inflate-end");
-    sym = C_intern (&amp;a, 27, "zlib:deflate-set-dictionary");
-    sym = C_intern (&amp;a, 17, "zlib:deflate-copy");
-    sym = C_intern (&amp;a, 18, "zlib:deflate-reset");
-    sym = C_intern (&amp;a, 19, "zlib:deflate-params");
-    sym = C_intern (&amp;a, 27, "zlib:inflate-set-dictionary");
-    sym = C_intern (&amp;a, 17, "zlib:inflate-sync");
-    sym = C_intern (&amp;a, 18, "zlib:inflate-reset");
-    sym = C_intern (&amp;a, 13, "zlib:compress");
-    sym = C_intern (&amp;a, 14, "zlib:compress2");
-    sym = C_intern (&amp;a, 15, "zlib:uncompress");
-    sym = C_intern (&amp;a, 11, "zlib:gzopen");
-    sym = C_intern (&amp;a, 12, "zlib:gzdopen");
-    sym = C_intern (&amp;a, 16, "zlib:gzsetparams");
-    sym = C_intern (&amp;a, 11, "zlib:gzread");
-    sym = C_intern (&amp;a, 12, "zlib:gzwrite");
-    sym = C_intern (&amp;a, 13, "zlib:gzprintf");
-    sym = C_intern (&amp;a, 11, "zlib:gzputs");
-    sym = C_intern (&amp;a, 11, "zlib:gzgets");
-    sym = C_intern (&amp;a, 11, "zlib:gzputc");
-    sym = C_intern (&amp;a, 11, "zlib:gzgetc");
-    sym = C_intern (&amp;a, 12, "zlib:gzflush");
-    sym = C_intern (&amp;a, 11, "zlib:gzseek");
-    sym = C_intern (&amp;a, 13, "zlib:gzrewind");
-    sym = C_intern (&amp;a, 11, "zlib:gztell");
-    sym = C_intern (&amp;a, 10, "zlib:gzeof");
-    sym = C_intern (&amp;a, 12, "zlib:gzclose");
-    sym = C_intern (&amp;a, 12, "zlib:gzerror");
-    sym = C_intern (&amp;a, 12, "zlib:adler32");
-    sym = C_intern (&amp;a, 10, "zlib:crc32");
-    sym = C_intern (&amp;a, 18, "zlib:deflate-init-");
-    sym = C_intern (&amp;a, 18, "zlib:inflate-init-");
-    sym = C_intern (&amp;a, 19, "zlib:deflate-init2-");
-    sym = C_intern (&amp;a, 19, "zlib:inflate-init2-");
-    sym = C_intern (&amp;a, 29, "zlib:internal-state-dummy-set");
-    sym = C_intern (&amp;a, 29, "zlib:internal-state-dummy-get");
-    sym = C_intern (&amp;a, 23, "zlib:new-internal-state");
-    sym = C_intern (&amp;a, 26, "zlib:delete-internal-state");
-    sym = C_intern (&amp;a, 12, "zlib:z-error");
-    sym = C_intern (&amp;a, 23, "zlib:inflate-sync-point");
-    sym = C_intern (&amp;a, 18, "zlib:get-crc-table");
-    sym = C_intern (&amp;a, 17, "zlib:deflate-init");
-    sym = C_intern (&amp;a, 17, "zlib:inflate-init");
-      </pre>
-    </blockquote>
-
-    Perfect!  Now let's integrate this zlib extension into a
-    CHICKEN interpreter.  To save some time, in this
-    Examples/chicken/zlib directory:
-    <ol>
-      <li>Backup the original <tt>example.i</tt>.</li>
-      <li>Copy and paste the <tt>example.i</tt> text from above and
-	put it into the file called <tt>example.i</tt></li>
-      <li>Run 'make' as per <a href="#build">Building the
-	  example</a>.</li>
-      <li>Run the resultant executable <tt>zlib</tt>.</li>
-    </ol>
-
-    The interpreter interaction is as follows:
-
-    <blockquote>
-      <pre>
-% ./zlib
-zlib
-
-  A SWIG example for the CHICKEN compiler
-  Author: Jonah Beckford, February 2003
-
-Scheme Procedures:
-
-zlib:max-mem-level
-zlib:max-wbits
-zlib:seek-set
-zlib:seek-cur
-zlib:seek-end
-zlib:version
-zlib:z-stream-next-in-set
-zlib:z-stream-next-in-get
-zlib:z-stream-avail-in-set
-...
-zlib:get-crc-table
-zlib:deflate-init
-zlib:inflate-init
-; This is the CHICKEN interpreter - Version 0, Build 1095 - windows-cygwin-x86
-; (c)2000-2003 Felix L. Winkelmann
-&gt;&gt;&gt; (define s (zlib:new-z-stream))
-&gt;&gt;&gt; s
-#&lt;tagged pointer #&lt;c++ "z_stream *"&gt;(#&lt;pointer 6d9290&gt;)&gt;
-&gt;&gt;&gt; (zlib:z-stream-next-in-get s)
-#f
-&gt;&gt;&gt; (zlib:z-stream-next-in-set s "some dummy stream data")
-Error: Type error. Expected _p_Bytef: "bad argument type"
-&gt;&gt;&gt; (exit)
-      </pre>
-    </blockquote>
-
-    Apparently we cannot use Scheme strings as <code>Bytef *</code>.  The SWIG
-    manual shows many ways how to handle strings and byte arrays, but
-    to be simplistic, let's just make the <code>Bytef *</code> look
-    like a <code>char *</code>, which is automatically handled as a
-    string by SWIG CHICKEN.
-
-    <h3>Attempt #5</h3>
-
-    We make sure to add an %apply construct so that <code>Bytef
-    *</code> is handled the same as <code>char *</code> to SWIG.  We
-    try again.
-
-    <blockquote>
-      <pre>
-/* File : example.i */
-%module example
-%{
-/* Put headers and other declarations here */
-#include "zlib.h"
-%}
-
-%include typemaps.i
-
-%rename(VERSION) ZLIB_VERSION;
-%rename(z_error) zError;
-<font color="red">%apply char * { Bytef * };</font>
-
-%include "zconf.h"
-%include "zlib.h"
-
-%inline %{
-/* %inline blocks are seen by SWIG and are inserted into the header
-   portion of example_wrap.c, so that they are also seen by the C
-   compiler. */
-int deflate_init(z_streamp strm, int level) {
-  return deflateInit(strm,level); /* call macro */
-}
-int inflate_init(z_streamp strm) {
-  return inflateInit(strm); /* call macro */
-}
-%}
-      </pre>
-    </blockquote>
-
-    Build the example once more.<br>
-
-    The interpreter interaction is as follows:
-
-    <blockquote>
-      <pre>
-% ./zlib
-zlib
-
-  A SWIG example for the CHICKEN compiler
-  Author: Jonah Beckford, February 2003
-
-Scheme Procedures:
-
-zlib:max-mem-level
-zlib:max-wbits
-zlib:seek-set
-zlib:seek-cur
-zlib:seek-end
-zlib:version
-zlib:z-stream-next-in-set
-zlib:z-stream-next-in-get
-zlib:z-stream-avail-in-set
-...
-zlib:get-crc-table
-zlib:deflate-init
-zlib:inflate-init
-; This is the CHICKEN interpreter - Version 0, Build 1095 - windows-cygwin-x86
-; (c)2000-2003 Felix L. Winkelmann
-&gt;&gt;&gt; (define s (zlib:new-z-stream))
-<em>Init zstream</em>
-&gt;&gt;&gt; (zlib:z-stream-zalloc-set s #f) 
-&gt;&gt;&gt; (zlib:z-stream-zfree-set s #f)
-&gt;&gt;&gt; (zlib:z-stream-opaque-set s #f)
-&gt;&gt;&gt; (zlib:deflate-init s (zlib:z-default-compression))
-0
-<em>Deflate something small so we don't need to loop/stream data</em>
-&gt;&gt;&gt; (define in "some dummy data")
-&gt;&gt;&gt; (define out (make-string 1000))
-&gt;&gt;&gt; (zlib:z-stream-next-in-set s in)
-&gt;&gt;&gt; (zlib:z-stream-avail-in-set s (string-length in))
-&gt;&gt;&gt; (zlib:z-stream-next-out-set s out)
-&gt;&gt;&gt; (zlib:z-stream-avail-out-set s (string-length out))
-&gt;&gt;&gt; (zlib:deflate s (zlib:z-finish))
-1 <em>;; (zlib:z-stream-end) == 1, which is good</em>
-&gt;&gt;&gt; (zlib:z-stream-total-out-get s)
-23.
-&gt;&gt;&gt; out
-"                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        "
-      </pre>
-    </blockquote>
-
-    We see the problem ... the compression is occurring as it should,
-    but we cannot see any of the compressed output.  This is because
-    when SWIG CHICKEN passes a Scheme string to a C function, it
-    duplicates the string before calling the C function.  We want to
-    save the memory address that
-    <code>zlib:z-stream-next-out-set</code> is using, so we can
-    display this later.  While we are at it, we can foresee that
-    <code>compress</code>, <code>compress2</code> and
-    <code>uncompress</code> will all need some finessing to work with
-    mutating strings.
-
-    <h3>Attempt #6</h3>
-
-    When we have to finesse strings, we must use typemaps.  As well,
-    we define some functions to save and restore the
-    <code>next_out</code> element.  We try again.
-
-    <blockquote>
-      <pre>
-/* File : example.i */
-%module example
-%{
-/* Put headers and other declarations here */
-#include "zlib.h"
-%}
-
-%include typemaps.i
-
-%rename(VERSION) ZLIB_VERSION;
-%rename(z_error) zError;
-%apply char * { Bytef * };
-	<font color="red">
-/* Allow the sourceLen to be automatically filled in from the length
-   of the 'source' string */
-%typemap(in) (const Bytef *source, uLong sourceLen)
-%{  if (!C_swig_is_string ($input)) {
-    swig_barf (SWIG_BARF1_BAD_ARGUMENT_TYPE, "Argument $input is not a string");
-  }
-  $2 = (uLong) C_header_size ($input);
-  $1 = C_c_string ($input);
-%}
-
-/* Allocate space the size of which is determined by the Scheme
-   integer argument, and make a temporary integer so we can set
-   destLen. */
-%typemap(in) (Bytef *dest, uLongf *destLen) (uLong len)
-%{  if (!C_swig_is_fixnum ($input)) {
-    swig_barf (SWIG_BARF1_BAD_ARGUMENT_TYPE, "Argument $input is not a integer");
-  }
-  len = (uLong) C_unfix ($input);
-  $2 = &amp;len;
-  $1 = (char *) malloc (*$2);
-%}
-
-/* Return the mutated string as a new object. */
-%typemap(argout) (Bytef *dest, uLongf *destLen) 
-(C_word *scmstr) 
-%{  scmstr = C_alloc (C_SIZEOF_STRING (*$2));
-  SWIG_APPEND_VALUE(C_string (&amp;scmstr, *$2, $1));
-  free ($1);
-%}
-	</font>
-%include "zconf.h"
-%include "zlib.h"
-	<font color="red">
-/* Ignore destLen as an input argument, and make a temporary integer so
-   we can set destLen. */
-%typemap(in, numinputs=0) uLongf *destLen (uLong len)
-"$1 = &amp;len;";
-
-/* Return a sized string as a new object. */
-%typemap(argout)
-(void *outstr, uLongf *destLen) (C_word *scmstr) 
-%{  scmstr = C_alloc (C_SIZEOF_STRING (*$2));
-  SWIG_APPEND_VALUE(C_string (&amp;scmstr, *$2, $1));
-%}
-	</font>
-%inline %{
-/* %inline blocks are seen by SWIG and are inserted into the header
-   portion of example_wrap.c, so that they are also seen by the C
-   compiler. */
-int deflate_init(z_streamp strm, int level) {
-  return deflateInit(strm,level); /* call macro */
-}
-int inflate_init(z_streamp strm) {
-  return inflateInit(strm); /* call macro */
-}
-<font color="red">void* z_stream_save_next_out(z_streamp strm) {
-  return (void*) strm-&gt;next_out;
-}
-void z_stream_get_next_chunk(z_streamp strm, void *outstr, uLongf *destLen) {
-  *destLen = strm-&gt;next_out - (Bytef*)outstr;
-}</font>
-%}
-      </pre>
-    </blockquote>
-
-    And that's it.  Try building the entire example from the
-    Makefile.  Run <tt>./zlib test-zlib.scm</tt> to test it out.
-
-  </body>
-</html>
diff --git a/Examples/chicken/zlib/example.i b/Examples/chicken/zlib/example.i
deleted file mode 100644
index dd962ad56..000000000
--- a/Examples/chicken/zlib/example.i
+++ /dev/null
@@ -1,76 +0,0 @@
-/* File : example.i */
-%module example
-%{
-/* Put headers and other declarations here */
-#include "zlib.h"
-%}
-
-%include typemaps.i
-
-%rename(VERSION) ZLIB_VERSION;
-%rename(z_error) zError;
-%apply char * { Bytef * };
-
-/* Allow the sourceLen to be automatically filled in from the length
-   of the 'source' string */
-%typemap(in) (const Bytef *source, uLong sourceLen)
-%{  if (!C_swig_is_string ($input)) {
-    swig_barf (SWIG_BARF1_BAD_ARGUMENT_TYPE, "Argument $input is not a string");
-  }
-  $2 = (uLong) C_header_size ($input);
-  $1 = C_c_string ($input);
-%}
-
-/* Allocate space the size of which is determined by the Scheme
-   integer argument, and make a temporary integer so we can set
-   destLen. */
-%typemap(in) (Bytef *dest, uLongf *destLen) (uLong len)
-%{  if (!C_swig_is_fixnum ($input)) {
-    swig_barf (SWIG_BARF1_BAD_ARGUMENT_TYPE, "Argument $input is not a integer");
-  }
-  len = (uLong) C_unfix ($input);
-  $2 = &len;
-  $1 = (char *) malloc (*$2);
-%}
-
-/* Return the mutated string as a new object. */
-%typemap(argout) (Bytef *dest, uLongf *destLen) 
-(C_word *scmstr) 
-%{  scmstr = C_alloc (C_SIZEOF_STRING (*$2));
-  SWIG_APPEND_VALUE(C_string (&scmstr, *$2, $1));
-  free ($1);
-%}
-
-%include "zconf.h"
-%include "zlib.h"
-
-/* Ignore destLen as an input argument, and make a temporary integer so
-   we can set destLen. */
-%typemap(numinputs=0) uLongf *destLen (uLong len)
-"$1 = &len;";
-
-/* Return a sized string as a new object. */
-%typemap(argout)
-(void *outstr, uLongf *destLen) (C_word *scmstr) 
-%{  scmstr = C_alloc (C_SIZEOF_STRING (*$2));
-  SWIG_APPEND_VALUE(C_string (&scmstr, *$2, $1));
-%}
-
-%inline %{
-/* %inline blocks are seen by SWIG and are inserted into the header
-   portion of example_wrap.c, so that they are also seen by the C
-   compiler. */
-int deflate_init(z_streamp strm, int level) {
-  return deflateInit(strm,level); /* call macro */
-}
-int inflate_init(z_streamp strm) {
-  return inflateInit(strm); /* call macro */
-}
-void* z_stream_save_next_out(z_streamp strm) {
-  return (void*) strm->next_out;
-}
-void z_stream_get_next_chunk(z_streamp strm, void *outstr, uLongf *destLen) {
-  *destLen = strm->next_out - (Bytef*)outstr;
-}
-%}
-
diff --git a/Examples/chicken/zlib/test-zlib.scm b/Examples/chicken/zlib/test-zlib.scm
deleted file mode 100644
index a13d801b8..000000000
--- a/Examples/chicken/zlib/test-zlib.scm
+++ /dev/null
@@ -1,41 +0,0 @@
-(load-library 'example "./zlib.so")
-
-;; Init zstream
-(define s (new-z-stream))
-(z-stream-zalloc-set s #f)
-(z-stream-zfree-set s #f)
-(z-stream-opaque-set s #f)
-(deflate-init s (Z-DEFAULT-COMPRESSION))
-
-;; Deflate something small so we don't need to loop/stream data
-(define in "some pony et jumping et jack et flash et had a jack pony")
-(define out (make-string 1000))
-(printf "to be compressed: ~A~%to be compressed bytes: ~A~%~%" in (string-length in))
-(z-stream-next-in-set s in)
-(z-stream-avail-in-set s (string-length in))
-(z-stream-next-out-set s out)
-(z-stream-avail-out-set s (string-length out))
-(let*
-    ((saved-out (z-stream-save-next-out s))
-     (ret (deflate s (Z-FINISH))))
-  (cond
-   ((= ret (Z-STREAM-END))
-    (printf "deflated properly!~%compressed bytes: ~A~%compressed stream: ~A~%" 
-            (z-stream-total-out-get s) (z-stream-get-next-chunk s saved-out)))
-   ((= ret (Z-OK))
-    (display "only partial deflation ... not enough output space\n"))
-   (else
-    (printf "deflate error(~D): ~A ~%" ret (z-stream-msg-get s)))))
-
-;; Use simple compress routine, and set max output size to 100
-(newline)
-(call-with-values (lambda () (compress 100 in))
-  (lambda (ret compressed)
-    (cond
-     ((= ret (Z-OK))
-      (printf "compressed properly!~%compressed bytes: ~A~%compressed stream: ~A~%"
-              (string-length compressed) compressed))
-     (else
-      (printf "compress error(~D): ~A ~%" ret (z-error ret))))))
-
-(exit 0)
diff --git a/Examples/guile/check.list b/Examples/guile/check.list
index d35b2d693..7ccd0730a 100644
--- a/Examples/guile/check.list
+++ b/Examples/guile/check.list
@@ -1,6 +1,5 @@
 # see top-level Makefile.in
 constants
-matrix
 simple
 port
 multimap
diff --git a/Examples/lua/lua.c b/Examples/lua/lua.c
index e06e2c5fc..8cffaa503 100644
--- a/Examples/lua/lua.c
+++ b/Examples/lua/lua.c
@@ -1,5 +1,4 @@
 /*
-** $Id$
 ** Lua stand-alone interpreter
 ** See Copyright Notice in lua.h
 */
diff --git a/Examples/test-suite/li_std_set.i b/Examples/test-suite/li_std_set.i
index c2cdc2ebe..3c06ddc9a 100644
--- a/Examples/test-suite/li_std_set.i
+++ b/Examples/test-suite/li_std_set.i
@@ -1,18 +1,12 @@
-/**
- * @file   li_std_set.i
- * @author gga
- * @date   Tue May  1 02:52:47 2007
- * 
- * @brief  a test of set containers. 
- *         Languages should define swig::LANGUAGE_OBJ to be
- *         an entity of their native pointer type which can be
- *         included in a STL container.
+/*
+ * a test of set containers. 
+ * Languages should define swig::LANGUAGE_OBJ to be
+ * an entity of their native pointer type which can be
+ * included in a STL container.
  *
- *         For example:
- *                swig::LANGUAGE_OBJ  is  GC_VALUE in Ruby
- *                swig::LANGUAGE_OBJ  is  PyObject_ptr in python
- * 
- * 
+ * For example:
+ *   swig::LANGUAGE_OBJ  is  GC_VALUE in Ruby
+ *   swig::LANGUAGE_OBJ  is  SwigPtr_PyObject in python
  */
 
 %module li_std_set
diff --git a/Examples/xml/example_gif.i b/Examples/xml/example_gif.i
deleted file mode 100644
index f0fb3b183..000000000
--- a/Examples/xml/example_gif.i
+++ /dev/null
@@ -1,329 +0,0 @@
-/* ----------------------------------------------------------------------------- 
- * gifplot.h
- *
- *     Main header file for the GIFPlot library.
- * 
- * Author(s) : David Beazley (beazley@cs.uchicago.edu)
- * Copyright (C) 1995-1996
- *
- * See the file LICENSE for information on usage and redistribution.	
- * ----------------------------------------------------------------------------- */
-
-#include <stdio.h>
-#include <fcntl.h>
-#include <float.h>
-#include <stdlib.h>
-#include <string.h>
-#include <limits.h>
-
-#ifndef GIFPLOT_H
-
-/* Pixel is 8-bits */
-
-typedef unsigned char Pixel;
-typedef float Zvalue;
-
-/* ------------------------------------------------------------------------
-   ColorMap
-
-   Definition and methods for colormaps
-   ------------------------------------------------------------------------ */
-
-typedef struct ColorMap {
-  unsigned char          *cmap;
-  char                   *name;
-} ColorMap;
-
-extern ColorMap *new_ColorMap(char *filename);
-extern void      delete_ColorMap(ColorMap *c);
-extern void      ColorMap_default(ColorMap *c);
-extern void      ColorMap_assign(ColorMap *c, int index, int r, int g, int b);
-extern int       ColorMap_getitem(ColorMap *c, int index);
-extern void      ColorMap_setitem(ColorMap *c, int index, int value);
-extern int       ColorMap_write(ColorMap *c, char *filename);
-
-/* Some default colors */
-
-#define BLACK   0
-#define WHITE   1
-#define RED     2
-#define GREEN   3
-#define BLUE    4
-#define YELLOW  5
-#define CYAN    6
-#define MAGENTA 7
-
-/*-------------------------------------------------------------------------
-  FrameBuffer
-
-  This structure defines a simple 8 bit framebuffer.  
-  ------------------------------------------------------------------------- */
-
-typedef struct FrameBuffer {
-  Pixel         **pixels;
-  Zvalue        **zbuffer;
-  unsigned int    height;
-  unsigned int    width;
-  int             xmin;      /* These are used for clipping */
-  int             ymin;
-  int             xmax;
-  int             ymax;
-} FrameBuffer;
-
-#define ZMIN  1e+36
-
-/* FrameBuffer Methods */
-
-extern FrameBuffer *new_FrameBuffer(unsigned int width, unsigned int height);
-extern void         delete_FrameBuffer(FrameBuffer *frame);
-extern int          FrameBuffer_resize(FrameBuffer *frame, int width, int height);
-extern void         FrameBuffer_clear(FrameBuffer *frame, Pixel color);
-extern void         FrameBuffer_plot(FrameBuffer *frame, int x, int y, Pixel color);
-extern void         FrameBuffer_horizontal(FrameBuffer *frame, int xmin, int xmax, int y, Pixel color);
-extern void         FrameBuffer_horizontalinterp(FrameBuffer *f, int xmin, int xmax, int y,  Pixel c1, Pixel c2);
-extern void         FrameBuffer_vertical(FrameBuffer *frame, int ymin, int ymax, int x, Pixel color);
-extern void         FrameBuffer_box(FrameBuffer *frame, int x1, int y1, int x2, int y2, Pixel color);
-extern void         FrameBuffer_solidbox(FrameBuffer *frame, int x1, int y1, int x2, int y2, Pixel color);
-extern void         FrameBuffer_interpbox(FrameBuffer *f, int x1, int y1, int x2, int y2, Pixel c1, Pixel c2, Pixel c3, Pixel c4);
-extern void         FrameBuffer_circle(FrameBuffer *frame, int x1, int y1, int radius, Pixel color);
-extern void         FrameBuffer_solidcircle(FrameBuffer *frame, int x1, int y1, int radius, Pixel color);
-extern void         FrameBuffer_line(FrameBuffer *frame, int x1, int y1, int x2, int y2, Pixel color);
-extern void         FrameBuffer_setclip(FrameBuffer *frame, int xmin, int ymin, int xmax, int ymax);
-extern void         FrameBuffer_noclip(FrameBuffer *frame);
-extern int          FrameBuffer_makeGIF(FrameBuffer *frame, ColorMap *cmap, void *buffer, unsigned int maxsize);
-extern int          FrameBuffer_writeGIF(FrameBuffer *f, ColorMap *c, char *filename);
-extern void         FrameBuffer_zresize(FrameBuffer *f, int width, int height);
-extern void         FrameBuffer_zclear(FrameBuffer *f);
-extern void         FrameBuffer_solidtriangle(FrameBuffer *f, int x1, int y1, int x2, int y2, int x3, int y3, Pixel c);
-extern void         FrameBuffer_interptriangle(FrameBuffer *f, int tx1, int ty1, Pixel c1,
-                                               int tx2, int ty2, Pixel c2, int tx3, int ty3, Pixel c3);
-
-#define  HORIZONTAL  1
-#define  VERTICAL    2
-
-extern void         FrameBuffer_drawchar(FrameBuffer *frame, int x, int y, int fgcolor, int bgcolor, char chr, int orientation);
-extern void         FrameBuffer_drawstring(FrameBuffer *f, int x, int y, int fgcolor, int bgcolor, char *text, int orientation);
-
-/* ------------------------------------------------------------------------
-   PixMap
-
-   The equivalent of "bit-maps".
-   ------------------------------------------------------------------------ */
-
-typedef struct PixMap {
-  int    width;
-  int    height;
-  int    centerx;
-  int    centery;
-  int   *map;
-} PixMap;
-
-/* PIXMAP methods */
-
-extern PixMap   *new_PixMap(int width, int height, int centerx, int centery);
-extern void      delete_PixMap(PixMap *pm);
-extern void      PixMap_set(PixMap *pm, int x, int y, int pix);
-extern void      FrameBuffer_drawpixmap(FrameBuffer *f, PixMap *pm, int x, int y, int fgcolor, int bgcolor);
-
-#define   TRANSPARENT  0
-#define   FOREGROUND   1
-#define   BACKGROUND   2
-
-/* ------------------------------------------------------------------------
-   Plot2D
-
-   Definition and methods for 2D plots.
-   ------------------------------------------------------------------------ */
-
-typedef struct Plot2D {
-  FrameBuffer    *frame;        /* what frame buffer are we using     */
-  int             view_xmin;    /* Minimum coordinates of view region */
-  int             view_ymin;    
-  int             view_xmax;    /* Maximum coordinates of view region */
-  int             view_ymax;    
-  double          xmin;         /* Minimum coordinates of plot region */
-  double          ymin;
-  double          xmax;         /* Maximum coordinates of plot region */
-  double          ymax;
-  int             xscale;       /* Type of scaling (LINEAR, LOG, etc..) */
-  int             yscale;       
-  double          dx;           /* Private scaling parameters         */
-  double          dy;
-} Plot2D;
-
-/* 2D Plot methods */
-
-extern Plot2D  *new_Plot2D(FrameBuffer *frame,double xmin,double ymin, double xmax, double ymax);
-extern void     delete_Plot2D(Plot2D *p2);
-extern Plot2D  *Plot2D_copy(Plot2D *p2);
-extern void     Plot2D_clear(Plot2D *p2, Pixel c);
-extern void     Plot2D_setview(Plot2D *p2, int vxmin, int vymin, int vxmax, int vymax);
-extern void     Plot2D_setrange(Plot2D *p2, double xmin, double ymin, double xmax, double ymax);
-extern void     Plot2D_setscale(Plot2D *p2, int xscale, int yscale);
-extern void     Plot2D_plot(Plot2D *p2, double x, double y, Pixel color);
-extern void     Plot2D_box(Plot2D *p2, double x1, double y1,  double x2, double y2, Pixel color);
-extern void     Plot2D_solidbox(Plot2D *p2, double x1, double y1,double x2, double y2, Pixel color);
-extern void     Plot2D_interpbox(Plot2D *p2, double x1, double y1, double x2, double y2, Pixel c1, Pixel c2, Pixel c3, Pixel c4);
-extern void     Plot2D_circle(Plot2D *p2, double x, double y, double radius, Pixel color);
-extern void     Plot2D_solidcircle(Plot2D *p2, double x, double y, double radius, Pixel color);
-extern void     Plot2D_line(Plot2D *p2, double x1, double y1, double x2, double y2, Pixel color);
-extern void     Plot2D_start(Plot2D *p2);
-extern void     Plot2D_drawpixmap(Plot2D *p2, PixMap *pm, double x, double y, Pixel color, Pixel bgcolor);
-extern void     Plot2D_xaxis(Plot2D *p2, double x, double y, double xtick, int ticklength, Pixel c);
-extern void     Plot2D_yaxis(Plot2D *p2, double x, double y, double ytick, int ticklength, Pixel c);
-extern void     Plot2D_triangle(Plot2D *p2, double x1, double y1, double x2, double y2, double x3, double y3, Pixel c);
-extern void     Plot2D_solidtriangle(Plot2D *p2, double x1, double y1, double x2, double y2, double x3, double y3, Pixel c);
-extern void     Plot2D_interptriangle(Plot2D *p2, double x1, double y1, Pixel c1,
-                                                  double x2, double y2, Pixel c2,
-                                                  double x3, double y3, Pixel c3);
-
-#define LINEAR     10
-#define LOG        11
-
-/* -----------------------------------------------------------------------
-   Matrix
-   
-   Operations on 4x4 transformation matrices and vectors.
-   Matrices are represented as a double array of 16 elements
-   ----------------------------------------------------------------------- */
-
-typedef  double *Matrix;
-typedef struct GL_Vector {
-  double x;
-  double y;
-  double z;
-  double w;
-} GL_Vector;
-
-extern Matrix new_Matrix();
-extern void   delete_Matrix(Matrix a);
-extern Matrix Matrix_copy(Matrix a);
-extern void   Matrix_multiply(Matrix a, Matrix b, Matrix c);
-extern void   Matrix_identity(Matrix a);
-extern void   Matrix_zero(Matrix a);
-extern void   Matrix_transpose(Matrix a, Matrix result);
-extern void   Matrix_invert(Matrix a, Matrix inva);
-extern void   Matrix_transform(Matrix a, GL_Vector *r, GL_Vector *t);
-extern void   Matrix_transform4(Matrix a, double rx, double ry, double rz,
-				double rw, GL_Vector *t);
-
-extern void   Matrix_print(Matrix a);
-extern void   Matrix_translate(Matrix a, double tx, double ty, double tz);
-extern void   Matrix_rotatex(Matrix a, double deg);
-extern void   Matrix_rotatey(Matrix a, double deg);
-extern void   Matrix_rotatez(Matrix a, double deg);
-
-/* -----------------------------------------------------------------------
-   Plot3D
-
-   Data Structure for 3-D plots
-   ------------------------------------------------------------------------ */
-
-typedef struct Plot3D {
-  FrameBuffer   *frame;      /* Frame buffer being used */
-  int            view_xmin;  /* Viewing region */
-  int            view_ymin;
-  int            view_xmax;
-  int            view_ymax;
-  double         xmin;       /* Bounding box */
-  double         ymin;
-  double         zmin;
-  double         xmax;
-  double         ymax;
-  double         zmax;
-  double         xcenter;    /* Center point */
-  double         ycenter;
-  double         zcenter;
-  double         fovy;       /* Field of view */
-  double         aspect;     /* Aspect ratio  */
-  double         znear;      /* near "clipping" plane */
-  double         zfar;       /* far "clipping" plane */
-  Matrix         center_mat; /* Matrix used for centering the model */
-  Matrix         model_mat;  /* Model rotation matrix */
-  Matrix         view_mat;   /* Viewing matrix */
-  Matrix         fullmodel_mat;  /* Full model matrix.  Used by sphere plot */
-  Matrix         trans_mat;  /* Total transformation matrix */
-  double         lookatz;    /* Where is the z-lookat point */
-  double         xshift;     /* Used for translation and stuff */
-  double         yshift;
-  double         zoom;
-  int            width;
-  int            height;
-  int            pers_mode;  /* Perspective mode (private) */
-  double         ortho_left,ortho_right,ortho_bottom,ortho_top;
-} Plot3D;
-
-extern Plot3D *new_Plot3D(FrameBuffer *frame, double xmin, double ymin, double zmin,
-			  double xmax, double ymax, double zmax);
-extern void   delete_Plot3D(Plot3D *p3);
-extern Plot3D *Plot3D_copy(Plot3D *p3);
-extern void   Plot3D_clear(Plot3D *p3, Pixel Color);
-extern void   Plot3D_perspective(Plot3D *p3, double fovy, double znear, double zfar);
-extern void   Plot3D_ortho(Plot3D *p3, double left, double right, double top, double bottom);
-extern void   Plot3D_lookat(Plot3D *p3, double z);
-extern void   Plot3D_autoperspective(Plot3D *p3, double fovy);
-extern void   Plot3D_autoortho(Plot3D *p3);
-extern void   Plot3D_rotx(Plot3D *p3, double deg);
-extern void   Plot3D_roty(Plot3D *p3, double deg);
-extern void   Plot3D_rotz(Plot3D *p3, double deg);
-extern void   Plot3D_rotl(Plot3D *p3, double deg);
-extern void   Plot3D_rotr(Plot3D *p3, double deg);
-extern void   Plot3D_rotd(Plot3D *p3, double deg);
-extern void   Plot3D_rotu(Plot3D *p3, double deg);
-extern void   Plot3D_rotc(Plot3D *p3, double deg);
-extern void   Plot3D_zoom(Plot3D *p3, double percent);
-extern void   Plot3D_left(Plot3D *p3, double percent);
-extern void   Plot3D_right(Plot3D *p3, double percent);
-extern void   Plot3D_down(Plot3D *p3, double percent);
-extern void   Plot3D_up(Plot3D *p3, double percent);
-extern void   Plot3D_center(Plot3D *p3, double cx, double cy);
-
-extern void   Plot3D_plot(Plot3D *p3, double x, double y, double z, Pixel Color);
-
-extern void   Plot3D_setview(Plot3D *p3, int vxmin, int vymin, int vxmax, int vymax);
-extern void   Plot3D_start(Plot3D *p3);
-extern void   Plot3D_line(Plot3D *p3, double x1, double y1, double z1,
-			 double x2, double y2, double z2, Pixel color);
-extern void   Plot3D_triangle(Plot3D *p3, double x1, double y1, double z1,
-		     double x2, double y2, double z2,
-		     double x3, double y3, double z3, Pixel color);
-extern void   Plot3D_solidtriangle(Plot3D *p3, double x1, double y1, double z1,
-		     double x2, double y2, double z2,
-		     double x3, double y3, double z3, Pixel color);
-
-extern void Plot3D_interptriangle(Plot3D *p3,
-			   double x1, double y1, double z1, Pixel c1,
-			   double x2, double y2, double z2, Pixel c2,
-			   double x3, double y3, double z3, Pixel c3);
-
-extern void   Plot3D_quad(Plot3D *p3, double x1, double y1, double z1,
-		 double x2, double y2, double z2,
-		 double x3, double y3, double z3,
-		 double x4, double y4, double z4,
-		 Pixel color);
-
-extern void   Plot3D_solidquad(Plot3D *p3, double x1, double y1, double z1,
-		 double x2, double y2, double z2,
-		 double x3, double y3, double z3,
-		 double x4, double y4, double z4,
-		 Pixel color);
-
-extern void   Plot3D_interpquad(Plot3D *p3, double x1, double y1, double z1, Pixel c1,
-		       double x2, double y2, double z2, Pixel c2,
-		       double x3, double y3, double z3, Pixel c3,
-		       double x4, double y4, double z4, Pixel c4);
-
-
-extern void   Plot3D_solidsphere(Plot3D *p3, double x, double y, double z, double radius,Pixel c);
-
-extern void   Plot3D_outlinesphere(Plot3D *p3, double x, double y, double z, double radius,Pixel c, Pixel bc);
-
-extern PixMap  PixMap_SQUARE;
-extern PixMap  PixMap_TRIANGLE;
-extern PixMap  PixMap_CROSS;
-
-#endif
-#define GIFPLOT_H
-
-
-
diff --git a/LICENSE b/LICENSE
index fdb73d916..d7a422fda 100644
--- a/LICENSE
+++ b/LICENSE
@@ -1,95 +1,22 @@
-SWIG is distributed under the following terms:
+SWIG is free software: you can redistribute it and/or modify it
+under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version. See the LICENSE-GPL file for
+the full terms of the GNU General Public license version 3.
 
-I.  
+Portions of SWIG are also licensed under the terms of the licenses
+in the file LICENSE-UNIVERSITIES. You must observe the terms of
+these licenses, as well as the terms of the GNU General Public License,
+when you distribute SWIG.
 
-Copyright (c) 1995-1998
-The University of Utah and the Regents of the University of California
-All Rights Reserved
+The SWIG library and examples, under the Lib and Examples top level 
+directories, are distributed under the following terms:
 
-Permission is hereby granted, without written agreement and without
-license or royalty fees, to use, copy, modify, and distribute this
-software and its documentation for any purpose, provided that 
-(1) The above copyright notice and the following two paragraphs
-appear in all copies of the source code and (2) redistributions
-including binaries reproduces these notices in the supporting
-documentation.   Substantial modifications to this software may be
-copyrighted by their authors and need not follow the licensing terms
-described here, provided that the new terms are clearly indicated in
-all files where they apply.
-
-IN NO EVENT SHALL THE AUTHOR, THE UNIVERSITY OF CALIFORNIA, THE 
-UNIVERSITY OF UTAH OR DISTRIBUTORS OF THIS SOFTWARE BE LIABLE TO ANY
-PARTY FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL
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-EVEN IF THE AUTHORS OR ANY OF THE ABOVE PARTIES HAVE BEEN ADVISED OF
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-SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS.
-
-
-II. 
-
-This software includes contributions that are Copyright (c) 1998-2005
-University of Chicago.
-All rights reserved.
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-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are
-met:
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-III.  
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-This software includes contributions that are Copyright (c) 2005-2006
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-Permission is hereby granted, without written agreement and without
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+  restriction. If you distribute the software to others, you may do
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+  is, without warranty of any kind.
 
+See the COPYRIGHT file for a list of contributors to SWIG and their
+copyright notices.
diff --git a/LICENSE-GPL b/LICENSE-GPL
new file mode 100644
index 000000000..94a9ed024
--- /dev/null
+++ b/LICENSE-GPL
@@ -0,0 +1,674 @@
+                    GNU GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
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+  A patent license is "discriminatory" if it does not include within
+the scope of its coverage, prohibits the exercise of, or is
+conditioned on the non-exercise of one or more of the rights that are
+specifically granted under this License.  You may not convey a covered
+work if you are a party to an arrangement with a third party that is
+in the business of distributing software, under which you make payment
+to the third party based on the extent of your activity of conveying
+the work, and under which the third party grants, to any of the
+parties who would receive the covered work from you, a discriminatory
+patent license (a) in connection with copies of the covered work
+conveyed by you (or copies made from those copies), or (b) primarily
+for and in connection with specific products or compilations that
+contain the covered work, unless you entered into that arrangement,
+or that patent license was granted, prior to 28 March 2007.
+
+  Nothing in this License shall be construed as excluding or limiting
+any implied license or other defenses to infringement that may
+otherwise be available to you under applicable patent law.
+
+  12. No Surrender of Others' Freedom.
+
+  If conditions are imposed on you (whether by court order, agreement or
+otherwise) that contradict the conditions of this License, they do not
+excuse you from the conditions of this License.  If you cannot convey a
+covered work so as to satisfy simultaneously your obligations under this
+License and any other pertinent obligations, then as a consequence you may
+not convey it at all.  For example, if you agree to terms that obligate you
+to collect a royalty for further conveying from those to whom you convey
+the Program, the only way you could satisfy both those terms and this
+License would be to refrain entirely from conveying the Program.
+
+  13. Use with the GNU Affero General Public License.
+
+  Notwithstanding any other provision of this License, you have
+permission to link or combine any covered work with a work licensed
+under version 3 of the GNU Affero General Public License into a single
+combined work, and to convey the resulting work.  The terms of this
+License will continue to apply to the part which is the covered work,
+but the special requirements of the GNU Affero General Public License,
+section 13, concerning interaction through a network will apply to the
+combination as such.
+
+  14. Revised Versions of this License.
+
+  The Free Software Foundation may publish revised and/or new versions of
+the GNU General Public License from time to time.  Such new versions will
+be similar in spirit to the present version, but may differ in detail to
+address new problems or concerns.
+
+  Each version is given a distinguishing version number.  If the
+Program specifies that a certain numbered version of the GNU General
+Public License "or any later version" applies to it, you have the
+option of following the terms and conditions either of that numbered
+version or of any later version published by the Free Software
+Foundation.  If the Program does not specify a version number of the
+GNU General Public License, you may choose any version ever published
+by the Free Software Foundation.
+
+  If the Program specifies that a proxy can decide which future
+versions of the GNU General Public License can be used, that proxy's
+public statement of acceptance of a version permanently authorizes you
+to choose that version for the Program.
+
+  Later license versions may give you additional or different
+permissions.  However, no additional obligations are imposed on any
+author or copyright holder as a result of your choosing to follow a
+later version.
+
+  15. Disclaimer of Warranty.
+
+  THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
+APPLICABLE LAW.  EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
+HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
+OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+PURPOSE.  THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
+IS WITH YOU.  SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
+ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+  16. Limitation of Liability.
+
+  IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
+THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
+USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
+DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
+PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGES.
+
+  17. Interpretation of Sections 15 and 16.
+
+  If the disclaimer of warranty and limitation of liability provided
+above cannot be given local legal effect according to their terms,
+reviewing courts shall apply local law that most closely approximates
+an absolute waiver of all civil liability in connection with the
+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.
+
+                     END OF TERMS AND CONDITIONS
+
+            How to Apply These Terms to Your New Programs
+
+  If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+  To do so, attach the following notices to the program.  It is safest
+to attach them to the start of each source file to most effectively
+state the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+    <one line to give the program's name and a brief idea of what it does.>
+    Copyright (C) <year>  <name of author>
+
+    This program is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
+  If the program does terminal interaction, make it output a short
+notice like this when it starts in an interactive mode:
+
+    <program>  Copyright (C) <year>  <name of author>
+    This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+    This is free software, and you are welcome to redistribute it
+    under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License.  Of course, your program's commands
+might be different; for a GUI interface, you would use an "about box".
+
+  You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU GPL, see
+<http://www.gnu.org/licenses/>.
+
+  The GNU General Public License does not permit incorporating your program
+into proprietary programs.  If your program is a subroutine library, you
+may consider it more useful to permit linking proprietary applications with
+the library.  If this is what you want to do, use the GNU Lesser General
+Public License instead of this License.  But first, please read
+<http://www.gnu.org/philosophy/why-not-lgpl.html>.
diff --git a/LICENSE-UNIVERSITIES b/LICENSE-UNIVERSITIES
new file mode 100644
index 000000000..fdb73d916
--- /dev/null
+++ b/LICENSE-UNIVERSITIES
@@ -0,0 +1,95 @@
+SWIG is distributed under the following terms:
+
+I.  
+
+Copyright (c) 1995-1998
+The University of Utah and the Regents of the University of California
+All Rights Reserved
+
+Permission is hereby granted, without written agreement and without
+license or royalty fees, to use, copy, modify, and distribute this
+software and its documentation for any purpose, provided that 
+(1) The above copyright notice and the following two paragraphs
+appear in all copies of the source code and (2) redistributions
+including binaries reproduces these notices in the supporting
+documentation.   Substantial modifications to this software may be
+copyrighted by their authors and need not follow the licensing terms
+described here, provided that the new terms are clearly indicated in
+all files where they apply.
+
+IN NO EVENT SHALL THE AUTHOR, THE UNIVERSITY OF CALIFORNIA, THE 
+UNIVERSITY OF UTAH OR DISTRIBUTORS OF THIS SOFTWARE BE LIABLE TO ANY
+PARTY FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL
+DAMAGES ARISING OUT OF THE USE OF THIS SOFTWARE AND ITS DOCUMENTATION,
+EVEN IF THE AUTHORS OR ANY OF THE ABOVE PARTIES HAVE BEEN ADVISED OF
+THE POSSIBILITY OF SUCH DAMAGE.
+
+THE AUTHOR, THE UNIVERSITY OF CALIFORNIA, AND THE UNIVERSITY OF UTAH
+SPECIFICALLY DISCLAIM ANY WARRANTIES,INCLUDING, BUT NOT LIMITED TO, 
+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+PURPOSE. THE SOFTWARE PROVIDED HEREUNDER IS ON AN "AS IS" BASIS, AND 
+THE AUTHORS AND DISTRIBUTORS HAVE NO OBLIGATION TO PROVIDE MAINTENANCE,
+SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS.
+
+
+II. 
+
+This software includes contributions that are Copyright (c) 1998-2005
+University of Chicago.
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+Redistributions of source code must retain the above copyright notice,
+this list of conditions and the following disclaimer.  Redistributions
+in binary form must reproduce the above copyright notice, this list of
+conditions and the following disclaimer in the documentation and/or
+other materials provided with the distribution.  Neither the name of
+the University of Chicago nor the names of its contributors may be
+used to endorse or promote products derived from this software without
+specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE UNIVERSITY OF CHICAGO AND CONTRIBUTORS
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE UNIVERSITY OF
+CHICAGO OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED
+TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+
+III.  
+
+This software includes contributions that are Copyright (c) 2005-2006
+Arizona Board of Regents (University of Arizona).
+All Rights Reserved
+
+Permission is hereby granted, without written agreement and without
+license or royalty fees, to use, copy, modify, and distribute this
+software and its documentation for any purpose, provided that 
+(1) The above copyright notice and the following two paragraphs
+appear in all copies of the source code and (2) redistributions
+including binaries reproduces these notices in the supporting
+documentation.   Substantial modifications to this software may be
+copyrighted by their authors and need not follow the licensing terms
+described here, provided that the new terms are clearly indicated in
+all files where they apply.
+
+THIS SOFTWARE IS PROVIDED BY THE UNIVERSITY OF ARIZONA AND CONTRIBUTORS
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE UNIVERSITY OF
+ARIZONA OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED
+TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
diff --git a/Lib/allegrocl/allegrocl.swg b/Lib/allegrocl/allegrocl.swg
index 8132e4628..eb4e87973 100644
--- a/Lib/allegrocl/allegrocl.swg
+++ b/Lib/allegrocl/allegrocl.swg
@@ -246,8 +246,6 @@ $body)"
 #endif
 
 %insert("lisphead") %{
-;; $Id$
-
 (eval-when (compile load eval)
 
   ;; avoid compiling ef-templates at runtime
diff --git a/Lib/allegrocl/longlongs.i b/Lib/allegrocl/longlongs.i
index b887a8a0a..4aa54660b 100755
--- a/Lib/allegrocl/longlongs.i
+++ b/Lib/allegrocl/longlongs.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * longlongs.i
  *
  * Typemap addition for support of 'long long' type and 'unsigned long long 
diff --git a/Lib/allegrocl/std_list.i b/Lib/allegrocl/std_list.i
index c8ab45649..4e260897f 100755
--- a/Lib/allegrocl/std_list.i
+++ b/Lib/allegrocl/std_list.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * std_list.i
  *
  * SWIG typemaps for std::list types
diff --git a/Lib/allegrocl/std_string.i b/Lib/allegrocl/std_string.i
index 4da0148fe..becc322e9 100755
--- a/Lib/allegrocl/std_string.i
+++ b/Lib/allegrocl/std_string.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * std_string.i
  *
  * SWIG typemaps for std::string
diff --git a/Lib/attribute.i b/Lib/attribute.i
index 45c3c5b64..0cc3ff1a3 100644
--- a/Lib/attribute.i
+++ b/Lib/attribute.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * attribute.i
  *
  * SWIG library file for implementing attributes.
diff --git a/Lib/carrays.i b/Lib/carrays.i
index 738b4577a..5fc78877c 100644
--- a/Lib/carrays.i
+++ b/Lib/carrays.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * carrays.i
  *
  * SWIG library file containing macros that can be used to manipulate simple
diff --git a/Lib/cdata.i b/Lib/cdata.i
index 67601f737..41e8f86ce 100644
--- a/Lib/cdata.i
+++ b/Lib/cdata.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * cdata.i
  *
  * SWIG library file containing macros for manipulating raw C data as strings.
diff --git a/Lib/chicken/chicken.swg b/Lib/chicken/chicken.swg
index a8d1b5a57..68f022570 100644
--- a/Lib/chicken/chicken.swg
+++ b/Lib/chicken/chicken.swg
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * chicken.swg
  *
  * CHICKEN configuration module.
diff --git a/Lib/chicken/chickenrun.swg b/Lib/chicken/chickenrun.swg
index 8703ea65a..f4e94d6f6 100644
--- a/Lib/chicken/chickenrun.swg
+++ b/Lib/chicken/chickenrun.swg
@@ -1,9 +1,5 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * chickenrun.swg
- *
  * ----------------------------------------------------------------------------- */
 
 #include <chicken.h>
diff --git a/Lib/chicken/multi-generic.scm b/Lib/chicken/multi-generic.scm
index ae822f37b..9d2e31d34 100644
--- a/Lib/chicken/multi-generic.scm
+++ b/Lib/chicken/multi-generic.scm
@@ -21,7 +21,7 @@
 ;; which functions are used when.
 
 ;; Comments, bugs, suggestions: send either to chicken-users@nongnu.org or to
-;; Author: John Lenz <lenz@cs.wisc.edu>, most code copied from TinyCLOS
+;; Most code copied from TinyCLOS
 
 (define <multi-generic> (make <entity-class>
 			  'name "multi-generic"
diff --git a/Lib/chicken/std_string.i b/Lib/chicken/std_string.i
index 2955d0e2f..ce24cba32 100644
--- a/Lib/chicken/std_string.i
+++ b/Lib/chicken/std_string.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * std_string.i
  *
  * SWIG typemaps for std::string
diff --git a/Lib/chicken/typemaps.i b/Lib/chicken/typemaps.i
index d79e20184..56cd18a5d 100644
--- a/Lib/chicken/typemaps.i
+++ b/Lib/chicken/typemaps.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * typemaps.i
  *
  * Pointer handling
diff --git a/Lib/clisp/clisp.swg b/Lib/clisp/clisp.swg
index fb6cdbf2a..e1d330cb3 100644
--- a/Lib/clisp/clisp.swg
+++ b/Lib/clisp/clisp.swg
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * clisp.swg
  * ----------------------------------------------------------------------------- */
 
diff --git a/Lib/cmalloc.i b/Lib/cmalloc.i
index 03a61351c..9f58bc03c 100644
--- a/Lib/cmalloc.i
+++ b/Lib/cmalloc.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * cmalloc.i
  *
  * SWIG library file containing macros that can be used to create objects using
diff --git a/Lib/constraints.i b/Lib/constraints.i
index 2deb1168a..8bc7f9159 100644
--- a/Lib/constraints.i
+++ b/Lib/constraints.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * constraints.i
  *
  * SWIG constraints library.
diff --git a/Lib/cpointer.i b/Lib/cpointer.i
index 1a6e51741..6b15a8417 100644
--- a/Lib/cpointer.i
+++ b/Lib/cpointer.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * cpointer.i
  *
  * SWIG library file containing macros that can be used to manipulate simple
diff --git a/Lib/csharp/csharp.swg b/Lib/csharp/csharp.swg
index e381ff9ae..0cdc2ba05 100644
--- a/Lib/csharp/csharp.swg
+++ b/Lib/csharp/csharp.swg
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * csharp.swg
  *
  * C# typemaps
diff --git a/Lib/csharp/csharphead.swg b/Lib/csharp/csharphead.swg
index ffff70372..eec4a2f2c 100644
--- a/Lib/csharp/csharphead.swg
+++ b/Lib/csharp/csharphead.swg
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * csharphead.swg
  *
  * Support code for exceptions if the SWIG_CSHARP_NO_EXCEPTION_HELPER is not defined
diff --git a/Lib/csharp/director.swg b/Lib/csharp/director.swg
index 8957ecf42..7768d8c02 100644
--- a/Lib/csharp/director.swg
+++ b/Lib/csharp/director.swg
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * director.swg
  *
  * This file contains support for director classes so that C# proxy 
diff --git a/Lib/csharp/enums.swg b/Lib/csharp/enums.swg
index be2a6063b..6605da8c8 100644
--- a/Lib/csharp/enums.swg
+++ b/Lib/csharp/enums.swg
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * enums.swg
  *
  * Include this file in order for C/C++ enums to be wrapped by proper C# enums.
diff --git a/Lib/csharp/enumsimple.swg b/Lib/csharp/enumsimple.swg
index f50849892..2b1cb182b 100644
--- a/Lib/csharp/enumsimple.swg
+++ b/Lib/csharp/enumsimple.swg
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * enumsimple.swg
  *
  * This file provides backwards compatible enum wrapping. SWIG versions 1.3.21
diff --git a/Lib/csharp/enumtypesafe.swg b/Lib/csharp/enumtypesafe.swg
index 8ba7838ef..a6bf64b9a 100644
--- a/Lib/csharp/enumtypesafe.swg
+++ b/Lib/csharp/enumtypesafe.swg
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * enumtypesafe.swg
  *
  * Include this file in order for C/C++ enums to be wrapped by the so called
diff --git a/Lib/csharp/std_except.i b/Lib/csharp/std_except.i
index c86e97a54..27eb84bc2 100644
--- a/Lib/csharp/std_except.i
+++ b/Lib/csharp/std_except.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * std_except.i
  *
  * Typemaps used by the STL wrappers that throw exceptions. These typemaps are
diff --git a/Lib/csharp/std_map.i b/Lib/csharp/std_map.i
index c35f21dc7..b19414597 100644
--- a/Lib/csharp/std_map.i
+++ b/Lib/csharp/std_map.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * std_map.i
  *
  * SWIG typemaps for std::map
diff --git a/Lib/csharp/std_pair.i b/Lib/csharp/std_pair.i
index 78142ffa6..0712ad762 100644
--- a/Lib/csharp/std_pair.i
+++ b/Lib/csharp/std_pair.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * std_pair.i
  *
  * SWIG typemaps for std::pair
diff --git a/Lib/csharp/std_string.i b/Lib/csharp/std_string.i
index d29692717..0d804518b 100644
--- a/Lib/csharp/std_string.i
+++ b/Lib/csharp/std_string.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * std_string.i
  *
  * Typemaps for std::string and const std::string&
diff --git a/Lib/csharp/std_vector.i b/Lib/csharp/std_vector.i
index 2e4d47c00..11d57e43d 100755
--- a/Lib/csharp/std_vector.i
+++ b/Lib/csharp/std_vector.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * std_vector.i
  *
  * SWIG typemaps for std::vector
diff --git a/Lib/csharp/std_wstring.i b/Lib/csharp/std_wstring.i
index 938070e4b..9142d36a5 100755
--- a/Lib/csharp/std_wstring.i
+++ b/Lib/csharp/std_wstring.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * std_wstring.i
  *
  * Typemaps for std::wstring and const std::wstring&
diff --git a/Lib/csharp/stl.i b/Lib/csharp/stl.i
index 66b72e073..9d2e91eee 100644
--- a/Lib/csharp/stl.i
+++ b/Lib/csharp/stl.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * stl.i
  *
  * Initial STL definition. extended as needed in each language
diff --git a/Lib/csharp/typemaps.i b/Lib/csharp/typemaps.i
index ddfbd1b0c..ac8398021 100644
--- a/Lib/csharp/typemaps.i
+++ b/Lib/csharp/typemaps.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * typemaps.i
  *
  * Pointer and reference handling typemap library
diff --git a/Lib/csharp/wchar.i b/Lib/csharp/wchar.i
index be87560c3..f02c09a53 100755
--- a/Lib/csharp/wchar.i
+++ b/Lib/csharp/wchar.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * wchar.i
  *
  * Typemaps for the wchar_t type
diff --git a/Lib/cstring.i b/Lib/cstring.i
index 4ebdf6857..6829f7597 100644
--- a/Lib/cstring.i
+++ b/Lib/cstring.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * cstring.i
  * ----------------------------------------------------------------------------- */
 
diff --git a/Lib/cwstring.i b/Lib/cwstring.i
index a6b08ae40..f0631d328 100644
--- a/Lib/cwstring.i
+++ b/Lib/cwstring.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * cwstring.i
  * ----------------------------------------------------------------------------- */
 
diff --git a/Lib/exception.i b/Lib/exception.i
index e30ac1a5d..7297a77f5 100644
--- a/Lib/exception.i
+++ b/Lib/exception.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * exception.i
  *
  * SWIG library file providing language independent exception handling
diff --git a/Lib/gcj/cni.swg b/Lib/gcj/cni.swg
index 247909a4a..4bd07df06 100644
--- a/Lib/gcj/cni.swg
+++ b/Lib/gcj/cni.swg
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * cni.swg
  * ----------------------------------------------------------------------------- */
 
diff --git a/Lib/guile/common.scm b/Lib/guile/common.scm
index a51d3a71d..17c9ab580 100644
--- a/Lib/guile/common.scm
+++ b/Lib/guile/common.scm
@@ -3,12 +3,6 @@
 ;;;*
 ;;;*     This file contains generic SWIG GOOPS classes for generated
 ;;;*     GOOPS file support
-;;;*
-;;;* Copyright (C) 2003 John Lenz (jelenz@wisc.edu)
-;;;* Copyright (C) 2004 Matthias Koeppe (mkoeppe@mail.math.uni-magdeburg.de)
-;;;*
-;;;* This file may be freely redistributed without license or fee provided
-;;;* this copyright message remains intact.
 ;;;************************************************************************
 
 (define-module (Swig swigrun))
diff --git a/Lib/guile/cplusplus.i b/Lib/guile/cplusplus.i
index cb4cf7434..0dfe71754 100644
--- a/Lib/guile/cplusplus.i
+++ b/Lib/guile/cplusplus.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * cplusplus.i
  *
  * SWIG typemaps for C++
diff --git a/Lib/guile/guile.i b/Lib/guile/guile.i
index 1bf28d6f3..ef270d74b 100644
--- a/Lib/guile/guile.i
+++ b/Lib/guile/guile.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * guile.i
  *
  * SWIG Configuration File for Guile.
diff --git a/Lib/guile/guile_gh.swg b/Lib/guile/guile_gh.swg
index 6412a4c61..3b65af897 100644
--- a/Lib/guile/guile_gh.swg
+++ b/Lib/guile/guile_gh.swg
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * guile_gh.swg
  *
  * This SWIG interface file is processed if the Guile module is run
diff --git a/Lib/guile/guile_gh_run.swg b/Lib/guile/guile_gh_run.swg
index 5b1fca0aa..0eba1f97e 100644
--- a/Lib/guile/guile_gh_run.swg
+++ b/Lib/guile/guile_gh_run.swg
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * guile_gh_run.swg
  *
  * Guile GH runtime file
diff --git a/Lib/guile/guile_scm.swg b/Lib/guile/guile_scm.swg
index caded728d..d12401451 100644
--- a/Lib/guile/guile_scm.swg
+++ b/Lib/guile/guile_scm.swg
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * guile_scm.swg
  *
  * This SWIG interface file is processed if the Guile module is run
diff --git a/Lib/guile/guile_scm_run.swg b/Lib/guile/guile_scm_run.swg
index 5da8558fc..91b74095d 100644
--- a/Lib/guile/guile_scm_run.swg
+++ b/Lib/guile/guile_scm_run.swg
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * guile_scm_run.swg
  * ----------------------------------------------------------------------------- */
 
diff --git a/Lib/guile/guilemain.i b/Lib/guile/guilemain.i
index 6f4e4d94d..925b81fee 100644
--- a/Lib/guile/guilemain.i
+++ b/Lib/guile/guilemain.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * guilemain.i
  *
  * The main functions for a user augmented guile
diff --git a/Lib/guile/interpreter.i b/Lib/guile/interpreter.i
index 7e8f0777a..524e0694a 100644
--- a/Lib/guile/interpreter.i
+++ b/Lib/guile/interpreter.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * interpreter.i
  *
  * SWIG file for a simple Guile interpreter
diff --git a/Lib/guile/list-vector.i b/Lib/guile/list-vector.i
index d98cae59a..c2cd1aea2 100644
--- a/Lib/guile/list-vector.i
+++ b/Lib/guile/list-vector.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * list_vector.i
  *
  * Guile typemaps for converting between arrays and Scheme lists or vectors  
diff --git a/Lib/guile/pointer-in-out.i b/Lib/guile/pointer-in-out.i
index bc6438759..d8a631ca9 100644
--- a/Lib/guile/pointer-in-out.i
+++ b/Lib/guile/pointer-in-out.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * pointer-in-out.i
  *
  * Guile typemaps for passing pointers indirectly 
diff --git a/Lib/guile/ports.i b/Lib/guile/ports.i
index 0d0e142e1..5940b4d3b 100644
--- a/Lib/guile/ports.i
+++ b/Lib/guile/ports.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * ports.i
  *
  * Guile typemaps for handling ports
diff --git a/Lib/guile/std_common.i b/Lib/guile/std_common.i
index ace5d65a8..a46c42c69 100644
--- a/Lib/guile/std_common.i
+++ b/Lib/guile/std_common.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * std_common.i
  *
  * SWIG typemaps for STL - common utilities
diff --git a/Lib/guile/std_map.i b/Lib/guile/std_map.i
index cc53e1560..19c863096 100644
--- a/Lib/guile/std_map.i
+++ b/Lib/guile/std_map.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * std_map.i
  *
  * SWIG typemaps for std::map
diff --git a/Lib/guile/std_pair.i b/Lib/guile/std_pair.i
index f8c2ea688..35f0cfad5 100644
--- a/Lib/guile/std_pair.i
+++ b/Lib/guile/std_pair.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * std_pair.i
  *
  * SWIG typemaps for std::pair
diff --git a/Lib/guile/std_string.i b/Lib/guile/std_string.i
index f80a65ca5..c10806e98 100644
--- a/Lib/guile/std_string.i
+++ b/Lib/guile/std_string.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * std_string.i
  *
  * SWIG typemaps for std::string
diff --git a/Lib/guile/std_vector.i b/Lib/guile/std_vector.i
index 145db945b..6801daee8 100644
--- a/Lib/guile/std_vector.i
+++ b/Lib/guile/std_vector.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * std_vector.i
  *
  * SWIG typemaps for std::vector
diff --git a/Lib/guile/stl.i b/Lib/guile/stl.i
index 66b72e073..9d2e91eee 100644
--- a/Lib/guile/stl.i
+++ b/Lib/guile/stl.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * stl.i
  *
  * Initial STL definition. extended as needed in each language
diff --git a/Lib/guile/typemaps.i b/Lib/guile/typemaps.i
index d9f972850..4f306f7f8 100644
--- a/Lib/guile/typemaps.i
+++ b/Lib/guile/typemaps.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * typemaps.i
  *
  * Guile-specific typemaps
diff --git a/Lib/inttypes.i b/Lib/inttypes.i
index 0cc81948e..8450cb840 100644
--- a/Lib/inttypes.i
+++ b/Lib/inttypes.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * inttypes.i
  *
  * SWIG library file  for ISO C99 types: 7.8 Format conversion of integer types <inttypes.h>
diff --git a/Lib/java/arrays_java.i b/Lib/java/arrays_java.i
index 95510c3f9..ddaf7408c 100644
--- a/Lib/java/arrays_java.i
+++ b/Lib/java/arrays_java.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * arrays_java.i
  *
  * These typemaps give more natural support for arrays. The typemaps are not efficient
diff --git a/Lib/java/director.swg b/Lib/java/director.swg
index fa588671d..07e5a1af1 100644
--- a/Lib/java/director.swg
+++ b/Lib/java/director.swg
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * director.swg
  *
  * This file contains support for director classes that proxy
diff --git a/Lib/java/enums.swg b/Lib/java/enums.swg
index 1a8f89b3a..edb67c417 100644
--- a/Lib/java/enums.swg
+++ b/Lib/java/enums.swg
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * enums.swg
  *
  * Include this file in order for C/C++ enums to be wrapped by proper Java enums.
diff --git a/Lib/java/enumsimple.swg b/Lib/java/enumsimple.swg
index f45774d0c..e08401869 100644
--- a/Lib/java/enumsimple.swg
+++ b/Lib/java/enumsimple.swg
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * enumsimple.swg
  *
  * This file provides backwards compatible enum wrapping. SWIG versions 1.3.21
diff --git a/Lib/java/enumtypesafe.swg b/Lib/java/enumtypesafe.swg
index a49a9d134..d6c6e5190 100644
--- a/Lib/java/enumtypesafe.swg
+++ b/Lib/java/enumtypesafe.swg
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * enumtypesafe.swg
  *
  * Include this file in order for C/C++ enums to be wrapped by the so called
diff --git a/Lib/java/enumtypeunsafe.swg b/Lib/java/enumtypeunsafe.swg
index bda055113..d9a7c4d29 100644
--- a/Lib/java/enumtypeunsafe.swg
+++ b/Lib/java/enumtypeunsafe.swg
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * enumtypeunsafe.swg
  *
  * Include this file in order for C/C++ enums to be wrapped by integers values.
diff --git a/Lib/java/java.swg b/Lib/java/java.swg
index 7d1808632..b5b1bc431 100644
--- a/Lib/java/java.swg
+++ b/Lib/java/java.swg
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * java.swg
  *
  * Java typemaps
diff --git a/Lib/java/javahead.swg b/Lib/java/javahead.swg
index 4aa0c84b5..f348b9d54 100644
--- a/Lib/java/javahead.swg
+++ b/Lib/java/javahead.swg
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * javahead.swg
  *
  * Java support code
diff --git a/Lib/java/std_except.i b/Lib/java/std_except.i
index 15be1deb8..9e23d50e6 100644
--- a/Lib/java/std_except.i
+++ b/Lib/java/std_except.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * std_except.i
  *
  * Typemaps used by the STL wrappers that throw exceptions.
diff --git a/Lib/java/std_map.i b/Lib/java/std_map.i
index 00967d3f9..a7020532c 100644
--- a/Lib/java/std_map.i
+++ b/Lib/java/std_map.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * std_map.i
  *
  * SWIG typemaps for std::map
diff --git a/Lib/java/std_pair.i b/Lib/java/std_pair.i
index dc0604dc5..fe45ee676 100644
--- a/Lib/java/std_pair.i
+++ b/Lib/java/std_pair.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * std_pair.i
  *
  * SWIG typemaps for std::pair
diff --git a/Lib/java/std_string.i b/Lib/java/std_string.i
index 789e17a65..f0d837696 100644
--- a/Lib/java/std_string.i
+++ b/Lib/java/std_string.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * std_string.i
  *
  * Typemaps for std::string and const std::string&
diff --git a/Lib/java/std_vector.i b/Lib/java/std_vector.i
index 92fa25ac2..e243eec1b 100644
--- a/Lib/java/std_vector.i
+++ b/Lib/java/std_vector.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * std_vector.i
  * ----------------------------------------------------------------------------- */
 
diff --git a/Lib/java/std_wstring.i b/Lib/java/std_wstring.i
index 989176500..12d8fc14f 100644
--- a/Lib/java/std_wstring.i
+++ b/Lib/java/std_wstring.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * std_wstring.i
  *
  * Typemaps for std::wstring and const std::wstring&
diff --git a/Lib/java/stl.i b/Lib/java/stl.i
index b8d7a654c..04f86014f 100644
--- a/Lib/java/stl.i
+++ b/Lib/java/stl.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * stl.i
  * ----------------------------------------------------------------------------- */
 
diff --git a/Lib/java/typemaps.i b/Lib/java/typemaps.i
index 59f7af99a..74ed99374 100644
--- a/Lib/java/typemaps.i
+++ b/Lib/java/typemaps.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * typemaps.i
  *
  * Pointer and reference handling typemap library
diff --git a/Lib/java/various.i b/Lib/java/various.i
index 733b8fa79..7c396de3e 100644
--- a/Lib/java/various.i
+++ b/Lib/java/various.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * various.i
  *
  * SWIG Typemap library for Java.
diff --git a/Lib/lua/_std_common.i b/Lib/lua/_std_common.i
index 33cc513c3..e552d0c8f 100644
--- a/Lib/lua/_std_common.i
+++ b/Lib/lua/_std_common.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * _std_common.i
  *
  * std::helpers for LUA
diff --git a/Lib/lua/lua.swg b/Lib/lua/lua.swg
index b6d888670..c3f5cecc5 100644
--- a/Lib/lua/lua.swg
+++ b/Lib/lua/lua.swg
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * lua.swg
  *
  * SWIG Configuration File for Lua.
diff --git a/Lib/lua/lua_fnptr.i b/Lib/lua/lua_fnptr.i
index c7df6f5a3..7e9facdf3 100644
--- a/Lib/lua/lua_fnptr.i
+++ b/Lib/lua/lua_fnptr.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * lua_fnptr.i
  *
  * SWIG Library file containing the main typemap code to support Lua modules.
diff --git a/Lib/lua/luarun.swg b/Lib/lua/luarun.swg
index 32e1b1617..4c9aa5144 100644
--- a/Lib/lua/luarun.swg
+++ b/Lib/lua/luarun.swg
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * luarun.swg
  *
  * This file contains the runtime support for Lua modules
diff --git a/Lib/lua/luaruntime.swg b/Lib/lua/luaruntime.swg
index b82cd56d7..5823d4fcf 100644
--- a/Lib/lua/luaruntime.swg
+++ b/Lib/lua/luaruntime.swg
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * luaruntime.swg
  *
  * all the runtime code for .
diff --git a/Lib/lua/luatypemaps.swg b/Lib/lua/luatypemaps.swg
index 0941c9da1..34db14a17 100644
--- a/Lib/lua/luatypemaps.swg
+++ b/Lib/lua/luatypemaps.swg
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * luatypemaps.swg
  *
  * basic typemaps for Lua.
diff --git a/Lib/lua/std_except.i b/Lib/lua/std_except.i
index ce148ef63..9c736b9ef 100644
--- a/Lib/lua/std_except.i
+++ b/Lib/lua/std_except.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * Typemaps used by the STL wrappers that throw exceptions.
  * These typemaps are used when methods are declared with an STL exception
  * specification, such as:
diff --git a/Lib/lua/std_map.i b/Lib/lua/std_map.i
index dd22443d5..84b0c74ff 100644
--- a/Lib/lua/std_map.i
+++ b/Lib/lua/std_map.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * std_map.i
  *
  * SWIG typemaps for std::map
diff --git a/Lib/lua/std_pair.i b/Lib/lua/std_pair.i
index 1b20f74e0..c76361554 100644
--- a/Lib/lua/std_pair.i
+++ b/Lib/lua/std_pair.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * std_pair.i
  *
  * std::pair typemaps for LUA
diff --git a/Lib/lua/std_string.i b/Lib/lua/std_string.i
index fa58f10bb..92f27d738 100644
--- a/Lib/lua/std_string.i
+++ b/Lib/lua/std_string.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * std_string.i
  *
  * std::string typemaps for LUA
diff --git a/Lib/lua/std_vector.i b/Lib/lua/std_vector.i
index c6778087f..f248f0340 100644
--- a/Lib/lua/std_vector.i
+++ b/Lib/lua/std_vector.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * std_vector.i
  *
  * std::vector typemaps for LUA
diff --git a/Lib/lua/stl.i b/Lib/lua/stl.i
index b8d7a654c..04f86014f 100644
--- a/Lib/lua/stl.i
+++ b/Lib/lua/stl.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * stl.i
  * ----------------------------------------------------------------------------- */
 
diff --git a/Lib/lua/typemaps.i b/Lib/lua/typemaps.i
index fa0c0d0e5..084726e58 100644
--- a/Lib/lua/typemaps.i
+++ b/Lib/lua/typemaps.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * typemaps.swg
  *
  * SWIG Library file containing the main typemap code to support Lua modules.
diff --git a/Lib/lua/wchar.i b/Lib/lua/wchar.i
index 5b206eb71..5021c1604 100644
--- a/Lib/lua/wchar.i
+++ b/Lib/lua/wchar.i
@@ -1,12 +1,8 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * wchar.i
  *
  * Typemaps for the wchar_t type
  * These are mapped to a Lua string and are passed around by value.
- *
  * ----------------------------------------------------------------------------- */
 
 // note: only support for pointer right now, not fixed length strings
@@ -43,4 +39,4 @@ if ($1==0) {lua_pushfstring(L,"Error in converting to wchar (arg %d)",$input);go
 free($1);
 %}
 
-%typemap(typecheck) wchar_t * = char *;
\ No newline at end of file
+%typemap(typecheck) wchar_t * = char *;
diff --git a/Lib/math.i b/Lib/math.i
index be931d71b..a37c92d19 100644
--- a/Lib/math.i
+++ b/Lib/math.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * math.i
  *
  * SWIG library file for floating point operations.
diff --git a/Lib/modula3/modula3.swg b/Lib/modula3/modula3.swg
index 6a1b4d94d..599a12e5a 100644
--- a/Lib/modula3/modula3.swg
+++ b/Lib/modula3/modula3.swg
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * modula3.swg
  *
  * Modula3 typemaps
diff --git a/Lib/modula3/modula3head.swg b/Lib/modula3/modula3head.swg
index b2426be5f..af96a78d1 100644
--- a/Lib/modula3/modula3head.swg
+++ b/Lib/modula3/modula3head.swg
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * modula3head.swg
  *
  * Modula3 support code
diff --git a/Lib/modula3/typemaps.i b/Lib/modula3/typemaps.i
index 79ddfda0f..1d76ab5e0 100644
--- a/Lib/modula3/typemaps.i
+++ b/Lib/modula3/typemaps.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * typemaps.i
  *
  * Pointer and reference handling typemap library
diff --git a/Lib/mzscheme/mzrun.swg b/Lib/mzscheme/mzrun.swg
index 3b05d2406..a5128da56 100644
--- a/Lib/mzscheme/mzrun.swg
+++ b/Lib/mzscheme/mzrun.swg
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * mzrun.swg
  * ----------------------------------------------------------------------------- */
 
diff --git a/Lib/mzscheme/mzscheme.swg b/Lib/mzscheme/mzscheme.swg
index ed4b2ec9d..9ae242845 100644
--- a/Lib/mzscheme/mzscheme.swg
+++ b/Lib/mzscheme/mzscheme.swg
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * mzscheme.swg
  *
  * SWIG Configuration File for MzScheme.
diff --git a/Lib/mzscheme/std_common.i b/Lib/mzscheme/std_common.i
index 8732f811c..1f1ae1ab7 100644
--- a/Lib/mzscheme/std_common.i
+++ b/Lib/mzscheme/std_common.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * std_common.i
  *
  * SWIG typemaps for STL - common utilities
diff --git a/Lib/mzscheme/std_map.i b/Lib/mzscheme/std_map.i
index aff720db6..b2c894509 100644
--- a/Lib/mzscheme/std_map.i
+++ b/Lib/mzscheme/std_map.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * std_map.i
  *
  * SWIG typemaps for std::map
diff --git a/Lib/mzscheme/std_pair.i b/Lib/mzscheme/std_pair.i
index 2ac331e71..d5a65470d 100644
--- a/Lib/mzscheme/std_pair.i
+++ b/Lib/mzscheme/std_pair.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * std_pair.i
  *
  * SWIG typemaps for std::pair
diff --git a/Lib/mzscheme/std_string.i b/Lib/mzscheme/std_string.i
index c9a82efe4..b8b99d9ad 100644
--- a/Lib/mzscheme/std_string.i
+++ b/Lib/mzscheme/std_string.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * std_string.i
  *
  * SWIG typemaps for std::string types
diff --git a/Lib/mzscheme/std_vector.i b/Lib/mzscheme/std_vector.i
index 90a52fc0a..22e1fa96b 100644
--- a/Lib/mzscheme/std_vector.i
+++ b/Lib/mzscheme/std_vector.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * std_vector.i
  *
  * SWIG typemaps for std::vector
diff --git a/Lib/mzscheme/stl.i b/Lib/mzscheme/stl.i
index 946e4b7f0..b19eae58b 100644
--- a/Lib/mzscheme/stl.i
+++ b/Lib/mzscheme/stl.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * stl.i
  *
  * Initial STL definition. extended as needed in each language
diff --git a/Lib/mzscheme/typemaps.i b/Lib/mzscheme/typemaps.i
index 334893242..b9f22440c 100644
--- a/Lib/mzscheme/typemaps.i
+++ b/Lib/mzscheme/typemaps.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * typemaps.i
  * ----------------------------------------------------------------------------- */
 
diff --git a/Lib/ocaml/cstring.i b/Lib/ocaml/cstring.i
index e56258264..0d6aa4b69 100644
--- a/Lib/ocaml/cstring.i
+++ b/Lib/ocaml/cstring.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * cstring.i
  *
  * This file provides typemaps and macros for dealing with various forms
diff --git a/Lib/ocaml/director.swg b/Lib/ocaml/director.swg
index 87333168f..a21f62102 100644
--- a/Lib/ocaml/director.swg
+++ b/Lib/ocaml/director.swg
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * director.swg
  *
  * This file contains support for director classes that proxy
diff --git a/Lib/ocaml/ocaml.i b/Lib/ocaml/ocaml.i
index a46e239d1..e099f7c10 100644
--- a/Lib/ocaml/ocaml.i
+++ b/Lib/ocaml/ocaml.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * ocaml.i
  *
  * SWIG Configuration File for Ocaml
diff --git a/Lib/ocaml/ocamldec.swg b/Lib/ocaml/ocamldec.swg
index 3b5290fa1..8e452d3f9 100644
--- a/Lib/ocaml/ocamldec.swg
+++ b/Lib/ocaml/ocamldec.swg
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * ocamldec.swg
  *
  * Ocaml runtime code -- declarations
diff --git a/Lib/ocaml/std_common.i b/Lib/ocaml/std_common.i
index b2dff61d2..1c397050c 100644
--- a/Lib/ocaml/std_common.i
+++ b/Lib/ocaml/std_common.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * std_common.i
  *
  * SWIG typemaps for STL - common utilities
diff --git a/Lib/ocaml/std_deque.i b/Lib/ocaml/std_deque.i
index 44815ebda..a6c489597 100644
--- a/Lib/ocaml/std_deque.i
+++ b/Lib/ocaml/std_deque.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * std_deque.i
  *
  * Default std_deque wrapper
diff --git a/Lib/ocaml/std_list.i b/Lib/ocaml/std_list.i
index 0aea90767..06181cca8 100644
--- a/Lib/ocaml/std_list.i
+++ b/Lib/ocaml/std_list.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * std_list.i
  *
  * SWIG typemaps for std::list types
diff --git a/Lib/ocaml/std_map.i b/Lib/ocaml/std_map.i
index f174f2872..f202e74ed 100644
--- a/Lib/ocaml/std_map.i
+++ b/Lib/ocaml/std_map.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * std_map.i
  *
  * SWIG typemaps for std::map
diff --git a/Lib/ocaml/std_pair.i b/Lib/ocaml/std_pair.i
index dc0604dc5..fe45ee676 100644
--- a/Lib/ocaml/std_pair.i
+++ b/Lib/ocaml/std_pair.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * std_pair.i
  *
  * SWIG typemaps for std::pair
diff --git a/Lib/ocaml/std_string.i b/Lib/ocaml/std_string.i
index 7add3a070..e75e95304 100644
--- a/Lib/ocaml/std_string.i
+++ b/Lib/ocaml/std_string.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * std_string.i
  *
  * SWIG typemaps for std::string
diff --git a/Lib/ocaml/std_vector.i b/Lib/ocaml/std_vector.i
index 91c335562..53d107447 100644
--- a/Lib/ocaml/std_vector.i
+++ b/Lib/ocaml/std_vector.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * std_vector.i
  *
  * SWIG typemaps for std::vector types
diff --git a/Lib/ocaml/stl.i b/Lib/ocaml/stl.i
index 66b72e073..9d2e91eee 100644
--- a/Lib/ocaml/stl.i
+++ b/Lib/ocaml/stl.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * stl.i
  *
  * Initial STL definition. extended as needed in each language
diff --git a/Lib/ocaml/typecheck.i b/Lib/ocaml/typecheck.i
index 51e66061b..4c3500690 100644
--- a/Lib/ocaml/typecheck.i
+++ b/Lib/ocaml/typecheck.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * typecheck.i
  *
  * Typechecking rules
diff --git a/Lib/ocaml/typemaps.i b/Lib/ocaml/typemaps.i
index 7f978bf7f..39544de94 100644
--- a/Lib/ocaml/typemaps.i
+++ b/Lib/ocaml/typemaps.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * typemaps.i
  *
  * The Ocaml module handles all types uniformly via typemaps. Here
diff --git a/Lib/octave/octcontainer.swg b/Lib/octave/octcontainer.swg
index bb1122a7b..d0e37112e 100644
--- a/Lib/octave/octcontainer.swg
+++ b/Lib/octave/octcontainer.swg
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * octcontainer.swg
  *
  * Octave cell <-> C++ container wrapper
diff --git a/Lib/octave/octiterators.swg b/Lib/octave/octiterators.swg
index 926361e10..0e3fe7033 100644
--- a/Lib/octave/octiterators.swg
+++ b/Lib/octave/octiterators.swg
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * octiterators.swg
  *
  * Users can derive form the OctSwigIterator to implemet their
diff --git a/Lib/perl5/perlmain.i b/Lib/perl5/perlmain.i
index f224b9c75..18ecb7eb5 100644
--- a/Lib/perl5/perlmain.i
+++ b/Lib/perl5/perlmain.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * perlmain.i
  *
  * Code to statically rebuild perl5.
diff --git a/Lib/perl5/reference.i b/Lib/perl5/reference.i
index d3d745cfc..06712bbd5 100644
--- a/Lib/perl5/reference.i
+++ b/Lib/perl5/reference.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * reference.i
  *
  * Accept Perl references as pointers
diff --git a/Lib/perl5/std_common.i b/Lib/perl5/std_common.i
index bc25b353f..c36513912 100644
--- a/Lib/perl5/std_common.i
+++ b/Lib/perl5/std_common.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * std_common.i
  *
  * SWIG typemaps for STL - common utilities
diff --git a/Lib/perl5/std_list.i b/Lib/perl5/std_list.i
index 633e40d9a..c6bca18f6 100644
--- a/Lib/perl5/std_list.i
+++ b/Lib/perl5/std_list.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * std_list.i
  *
  * SWIG typemaps for std::list types
diff --git a/Lib/perl5/std_map.i b/Lib/perl5/std_map.i
index c35f21dc7..b19414597 100644
--- a/Lib/perl5/std_map.i
+++ b/Lib/perl5/std_map.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * std_map.i
  *
  * SWIG typemaps for std::map
diff --git a/Lib/perl5/std_pair.i b/Lib/perl5/std_pair.i
index 78142ffa6..0712ad762 100644
--- a/Lib/perl5/std_pair.i
+++ b/Lib/perl5/std_pair.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * std_pair.i
  *
  * SWIG typemaps for std::pair
diff --git a/Lib/perl5/std_vector.i b/Lib/perl5/std_vector.i
index b1f722d4b..c6cacfe7e 100644
--- a/Lib/perl5/std_vector.i
+++ b/Lib/perl5/std_vector.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * std_vector.i
  *
  * SWIG typemaps for std::vector types
diff --git a/Lib/perl5/stl.i b/Lib/perl5/stl.i
index 946e4b7f0..b19eae58b 100644
--- a/Lib/perl5/stl.i
+++ b/Lib/perl5/stl.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * stl.i
  *
  * Initial STL definition. extended as needed in each language
diff --git a/Lib/perl5/typemaps.i b/Lib/perl5/typemaps.i
index fc6d8f874..7d96f2ace 100644
--- a/Lib/perl5/typemaps.i
+++ b/Lib/perl5/typemaps.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * typemaps.i
  *
  * The SWIG typemap library provides a language independent mechanism for
diff --git a/Lib/php/const.i b/Lib/php/const.i
index 6ddd403d0..08096c98b 100644
--- a/Lib/php/const.i
+++ b/Lib/php/const.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * const.i
  *
  * Typemaps for constants
diff --git a/Lib/php/globalvar.i b/Lib/php/globalvar.i
index a75b1a41e..3027ca84e 100644
--- a/Lib/php/globalvar.i
+++ b/Lib/php/globalvar.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * globalvar.i
  *
  * Global variables - add the variable to PHP
diff --git a/Lib/php/php.swg b/Lib/php/php.swg
index d30e0b2a9..903af5612 100644
--- a/Lib/php/php.swg
+++ b/Lib/php/php.swg
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * php.swg
  *
  * PHP configuration file
diff --git a/Lib/php/phpkw.swg b/Lib/php/phpkw.swg
index 3d1a62511..e7d4f2fda 100644
--- a/Lib/php/phpkw.swg
+++ b/Lib/php/phpkw.swg
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * phpkw.swg
  *
  * The 'keywords' in PHP are global, ie, the following names are fine
diff --git a/Lib/php/phprun.swg b/Lib/php/phprun.swg
index b4e4276f5..c7976a3dc 100644
--- a/Lib/php/phprun.swg
+++ b/Lib/php/phprun.swg
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * phprun.swg
  *
  * PHP runtime library
diff --git a/Lib/php/std_common.i b/Lib/php/std_common.i
index a779649dd..092bf012b 100644
--- a/Lib/php/std_common.i
+++ b/Lib/php/std_common.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * std_common.i
  *
  * SWIG typemaps for STL - common utilities
diff --git a/Lib/php/std_map.i b/Lib/php/std_map.i
index c6721806b..ede5fbe30 100644
--- a/Lib/php/std_map.i
+++ b/Lib/php/std_map.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * std_map.i
  *
  * SWIG typemaps for std::map
diff --git a/Lib/php/std_pair.i b/Lib/php/std_pair.i
index dc0604dc5..fe45ee676 100644
--- a/Lib/php/std_pair.i
+++ b/Lib/php/std_pair.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * std_pair.i
  *
  * SWIG typemaps for std::pair
diff --git a/Lib/php/std_string.i b/Lib/php/std_string.i
index 08a7cdac9..22c953bf5 100644
--- a/Lib/php/std_string.i
+++ b/Lib/php/std_string.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * std_string.i
  *
  * SWIG typemaps for std::string types
diff --git a/Lib/php/std_vector.i b/Lib/php/std_vector.i
index b54181618..4cfc94f74 100644
--- a/Lib/php/std_vector.i
+++ b/Lib/php/std_vector.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * std_vector.i
  *
  * SWIG typemaps for std::vector types
diff --git a/Lib/php/stl.i b/Lib/php/stl.i
index 66b72e073..9d2e91eee 100644
--- a/Lib/php/stl.i
+++ b/Lib/php/stl.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * stl.i
  *
  * Initial STL definition. extended as needed in each language
diff --git a/Lib/php/typemaps.i b/Lib/php/typemaps.i
index c5b749578..30235f278 100644
--- a/Lib/php/typemaps.i
+++ b/Lib/php/typemaps.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * typemaps.i.
  *
  * SWIG Typemap library for PHP4.
diff --git a/Lib/pike/pike.swg b/Lib/pike/pike.swg
index e72da8fba..2ba27671e 100644
--- a/Lib/pike/pike.swg
+++ b/Lib/pike/pike.swg
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * pike.swg
  *
  * Pike configuration module.
diff --git a/Lib/pike/pikerun.swg b/Lib/pike/pikerun.swg
index 875fcf4e2..451a4e092 100644
--- a/Lib/pike/pikerun.swg
+++ b/Lib/pike/pikerun.swg
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * pikerun.swg
  *
  * This file contains the runtime support for Pike modules
diff --git a/Lib/pike/std_string.i b/Lib/pike/std_string.i
index ca1fad822..0694035bf 100644
--- a/Lib/pike/std_string.i
+++ b/Lib/pike/std_string.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * std_string.i
  *
  * SWIG typemaps for std::string
diff --git a/Lib/pointer.i b/Lib/pointer.i
index 16e11b7d1..8015317d7 100644
--- a/Lib/pointer.i
+++ b/Lib/pointer.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * pointer.i
  * ----------------------------------------------------------------------------- */
 
diff --git a/Lib/python/ccomplex.i b/Lib/python/ccomplex.i
index 30f797d74..28872b985 100644
--- a/Lib/python/ccomplex.i
+++ b/Lib/python/ccomplex.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * ccomplex.i
  *
  * C complex typemaps
diff --git a/Lib/python/director.swg b/Lib/python/director.swg
index 836d107ce..090da0205 100644
--- a/Lib/python/director.swg
+++ b/Lib/python/director.swg
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * director.swg
  *
  * This file contains support for director classes that proxy
diff --git a/Lib/python/embed15.i b/Lib/python/embed15.i
index f677d166e..4abfbba75 100644
--- a/Lib/python/embed15.i
+++ b/Lib/python/embed15.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * embed15.i
  *
  * SWIG file embedding the Python interpreter in something else.
diff --git a/Lib/python/file.i b/Lib/python/file.i
index 294ab9178..359c34d2c 100644
--- a/Lib/python/file.i
+++ b/Lib/python/file.i
@@ -1,11 +1,7 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * file.i
  *
  * Typemaps for FILE*
- * From the ideas of Luigi Ballabio
  * ----------------------------------------------------------------------------- */
 
 %types(FILE *);
diff --git a/Lib/python/pycontainer.swg b/Lib/python/pycontainer.swg
index 58442ef76..006ab016f 100644
--- a/Lib/python/pycontainer.swg
+++ b/Lib/python/pycontainer.swg
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * pycontainer.swg
  *
  * Python sequence <-> C++ container wrapper
diff --git a/Lib/python/pyiterators.swg b/Lib/python/pyiterators.swg
index 62a7eaf70..9f85ffc4a 100644
--- a/Lib/python/pyiterators.swg
+++ b/Lib/python/pyiterators.swg
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * pyiterators.swg
  *
  * Implement a python 'output' iterator for Python 2.2 or higher.
diff --git a/Lib/python/pyrun.swg b/Lib/python/pyrun.swg
index 4f51d3a95..1aae2d7aa 100644
--- a/Lib/python/pyrun.swg
+++ b/Lib/python/pyrun.swg
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * pyrun.swg
  *
  * This file contains the runtime support for Python modules
diff --git a/Lib/python/typemaps.i b/Lib/python/typemaps.i
index 1c87de61d..5d438ecab 100644
--- a/Lib/python/typemaps.i
+++ b/Lib/python/typemaps.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * typemaps.i
  *
  * Pointer handling
diff --git a/Lib/ruby/director.swg b/Lib/ruby/director.swg
index 9a6371ad9..60c086f5b 100644
--- a/Lib/ruby/director.swg
+++ b/Lib/ruby/director.swg
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * director.swg
  *
  * This file contains support for director classes that proxy
diff --git a/Lib/ruby/rubyautodoc.swg b/Lib/ruby/rubyautodoc.swg
index ade4bde1d..1e6b0d9dc 100644
--- a/Lib/ruby/rubyautodoc.swg
+++ b/Lib/ruby/rubyautodoc.swg
@@ -1,13 +1,8 @@
-/**
- * @file   rubyautodoc.swg
- * @author gga
- * @date   Wed May  2 16:41:59 2007
- * 
- * @brief  This file implements autodoc typemaps for some common
- *         ruby methods.
- * 
- * 
- */
+/* -----------------------------------------------------------------------------
+ * rubyautodoc.swg
+ *
+ * This file implements autodoc typemaps for some common ruby methods.
+ * ----------------------------------------------------------------------------- */
 
 %define AUTODOC(func, str)
   %feature("autodoc", str) func;
diff --git a/Lib/ruby/rubycontainer.swg b/Lib/ruby/rubycontainer.swg
index 919695ec2..c93094aeb 100644
--- a/Lib/ruby/rubycontainer.swg
+++ b/Lib/ruby/rubycontainer.swg
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * rubycontainer.swg
  *
  * Ruby sequence <-> C++ container wrapper
diff --git a/Lib/ruby/rubycontainer_extended.swg b/Lib/ruby/rubycontainer_extended.swg
index 360e399ce..09be64aee 100644
--- a/Lib/ruby/rubycontainer_extended.swg
+++ b/Lib/ruby/rubycontainer_extended.swg
@@ -1,17 +1,13 @@
-/**
- * @file   rubycontainer_extended.swg
- * @author gga
- * @date   Sat May  5 05:36:01 2007
- * 
- * @brief  This file contains additional functions that make containers
- *         behave closer to ruby primitive types.
- *         However, some of these functions place some restrictions on
- *         the underlying object inside of the container and the iterator
- *        (that it has to have an == comparison function, that it has to have 
- *         an = assignment operator, etc).
- * 
- */
-
+/* -----------------------------------------------------------------------------
+ * rubycontainer_extended.swg
+ *
+ * This file contains additional functions that make containers
+ * behave closer to ruby primitive types.
+ * However, some of these functions place some restrictions on
+ * the underlying object inside of the container and the iterator
+ * (that it has to have an == comparison function, that it has to have 
+ * an = assignment operator, etc).
+ * ----------------------------------------------------------------------------- */
 
 /** 
  * Macro used to add extend functions that require operator== in object.
diff --git a/Lib/ruby/rubyiterators.swg b/Lib/ruby/rubyiterators.swg
index 466ae221b..aba156a2b 100644
--- a/Lib/ruby/rubyiterators.swg
+++ b/Lib/ruby/rubyiterators.swg
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * rubyiterators.swg
  *
  * Implement a C++ 'output' iterator for Ruby.
diff --git a/Lib/ruby/rubyprimtypes.swg b/Lib/ruby/rubyprimtypes.swg
index c2d577995..aff35dcf1 100644
--- a/Lib/ruby/rubyprimtypes.swg
+++ b/Lib/ruby/rubyprimtypes.swg
@@ -1,9 +1,5 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * rubyprimtypes.swg
- *
  * ----------------------------------------------------------------------------- */
 /* ------------------------------------------------------------
  * Primitive Types
diff --git a/Lib/ruby/rubyrun.swg b/Lib/ruby/rubyrun.swg
index 24d861d5a..ccc997a71 100644
--- a/Lib/ruby/rubyrun.swg
+++ b/Lib/ruby/rubyrun.swg
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * rubyrun.swg
  *
  * This file contains the runtime support for Ruby modules
diff --git a/Lib/ruby/rubystdautodoc.swg b/Lib/ruby/rubystdautodoc.swg
index ad70f7f8b..e14f65902 100644
--- a/Lib/ruby/rubystdautodoc.swg
+++ b/Lib/ruby/rubystdautodoc.swg
@@ -1,12 +1,8 @@
-/**
- * @file   rubystdautodoc.swg
- * @author gga
- * @date   Wed May  2 17:20:39 2007
+/* -----------------------------------------------------------------------------
+ * rubystdautodoc.swg
  * 
- * @brief  This file contains autodocs for standard STL functions.
- * 
- * 
- */
+ * This file contains autodocs for standard STL functions.
+ * ----------------------------------------------------------------------------- */
 
 //
 // For STL autodocumentation
diff --git a/Lib/ruby/rubytracking.swg b/Lib/ruby/rubytracking.swg
index 959d2087e..0a36f4a05 100644
--- a/Lib/ruby/rubytracking.swg
+++ b/Lib/ruby/rubytracking.swg
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * rubytracking.swg
  *
  * This file contains support for tracking mappings from 
diff --git a/Lib/ruby/rubywstrings.swg b/Lib/ruby/rubywstrings.swg
index 0cf9d7ed9..d1fe918ad 100644
--- a/Lib/ruby/rubywstrings.swg
+++ b/Lib/ruby/rubywstrings.swg
@@ -1,15 +1,11 @@
-/**
- * @file   rubywstrings.swg
- * @author 
- * @date   Fri May  4 17:49:40 2007
- * 
- * @brief  Currently, Ruby does not support Unicode or WChar properly, so these
- *         are still treated as char arrays for now.
- *         There are other libraries available that add support to this in
- *         ruby including WString, FXString, etc.
- * 
- * 
- */
+/* -----------------------------------------------------------------------------
+ * rubywstrings.swg
+ *
+ * Currently, Ruby does not support Unicode or WChar properly, so these
+ * are still treated as char arrays for now.
+ * There are other libraries available that add support to this in
+ * ruby including WString, FXString, etc.
+ * ----------------------------------------------------------------------------- */
 
 /* ------------------------------------------------------------
  *  utility methods for wchar_t strings 
diff --git a/Lib/ruby/stl.i b/Lib/ruby/stl.i
index 66b72e073..9d2e91eee 100644
--- a/Lib/ruby/stl.i
+++ b/Lib/ruby/stl.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * stl.i
  *
  * Initial STL definition. extended as needed in each language
diff --git a/Lib/ruby/typemaps.i b/Lib/ruby/typemaps.i
index 2492e2e03..c4db82161 100644
--- a/Lib/ruby/typemaps.i
+++ b/Lib/ruby/typemaps.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * typemaps.i
  *
  * Pointer handling
diff --git a/Lib/std/_std_deque.i b/Lib/std/_std_deque.i
index 026f373d6..c30523c0d 100644
--- a/Lib/std/_std_deque.i
+++ b/Lib/std/_std_deque.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * _std_deque.i
  *
  * This file contains a generic definition of std::deque along with
diff --git a/Lib/std_except.i b/Lib/std_except.i
index af9803a62..769a68995 100644
--- a/Lib/std_except.i
+++ b/Lib/std_except.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * std_except.i
  *
  * SWIG library file with typemaps to handle and throw STD exceptions in a
diff --git a/Lib/stdint.i b/Lib/stdint.i
index 7b48ca388..14fe6195e 100644
--- a/Lib/stdint.i
+++ b/Lib/stdint.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * stdint.i
  *
  * SWIG library file for ISO C99 types: 7.18 Integer types <stdint.h>
diff --git a/Lib/stl.i b/Lib/stl.i
index c3ade01ea..0b236afda 100644
--- a/Lib/stl.i
+++ b/Lib/stl.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * stl.i
  * ----------------------------------------------------------------------------- */
 
diff --git a/Lib/swigarch.i b/Lib/swigarch.i
index 260b60880..f5aea4678 100644
--- a/Lib/swigarch.i
+++ b/Lib/swigarch.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * swigarch.i
  *
  * SWIG library file for 32bit/64bit code specialization and checking.
diff --git a/Lib/swigrun.i b/Lib/swigrun.i
index 17a140968..6026a9151 100644
--- a/Lib/swigrun.i
+++ b/Lib/swigrun.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * swigrun.i
  *
  * Empty module (for now).  Placeholder for runtime libs
diff --git a/Lib/tcl/mactclinit.c b/Lib/tcl/mactclinit.c
deleted file mode 100644
index 5dcf8e7f3..000000000
--- a/Lib/tcl/mactclinit.c
+++ /dev/null
@@ -1,93 +0,0 @@
-/* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
- * mactclinit.c
- * ----------------------------------------------------------------------------- */
-
-/* 
- * tclMacAppInit.c --
- *
- *	Provides a version of the Tcl_AppInit procedure for the example shell.
- *
- * Copyright (c) 1993-1994 Lockheed Missle & Space Company, AI Center
- * Copyright (c) 1995-1997 Sun Microsystems, Inc.
- *
- * See the file "license.terms" for information on usage and redistribution
- * of this file, and for a DISCLAIMER OF ALL WARRANTIES.
- *
- * SCCS: @(#) tclMacAppInit.c 1.17 97/01/21 18:13:34
- */
-
-#include "tcl.h"
-#include "tclInt.h"
-#include "tclMacInt.h"
-
-#if defined(THINK_C)
-#   include <console.h>
-#elif defined(__MWERKS__)
-#   include <SIOUX.h>
-short InstallConsole _ANSI_ARGS_((short fd));
-#endif
-
-
-
-/*
- *----------------------------------------------------------------------
- *
- * MacintoshInit --
- *
- *	This procedure calls initalization routines to set up a simple
- *	console on a Macintosh.  This is necessary as the Mac doesn't
- *	have a stdout & stderr by default.
- *
- * Results:
- *	Returns TCL_OK if everything went fine.  If it didn't the 
- *	application should probably fail.
- *
- * Side effects:
- *	Inits the appropiate console package.
- *
- *----------------------------------------------------------------------
- */
-
-#ifdef __cplusplus
-extern "C"
-#endif
-extern int
-MacintoshInit()
-{
-#if defined(THINK_C)
-
-    /* Set options for Think C console package */
-    /* The console package calls the Mac init calls */
-    console_options.pause_atexit = 0;
-    console_options.title = "\pTcl Interpreter";
-		
-#elif defined(__MWERKS__)
-
-    /* Set options for CodeWarrior SIOUX package */
-    SIOUXSettings.autocloseonquit = true;
-    SIOUXSettings.showstatusline = true;
-    SIOUXSettings.asktosaveonclose = false;
-    InstallConsole(0);
-    SIOUXSetTitle("\pTcl Interpreter");
-		
-#elif defined(applec)
-
-    /* Init packages used by MPW SIOW package */
-    InitGraf((Ptr)&qd.thePort);
-    InitFonts();
-    InitWindows();
-    InitMenus();
-    TEInit();
-    InitDialogs(nil);
-    InitCursor();
-		
-#endif
-
-    TclMacSetEventProc((TclMacConvertEventPtr) SIOUXHandleOneEvent);
-    
-    /* No problems with initialization */
-    return TCL_OK;
-}
diff --git a/Lib/tcl/mactkinit.c b/Lib/tcl/mactkinit.c
index bfe74029c..78391d445 100644
--- a/Lib/tcl/mactkinit.c
+++ b/Lib/tcl/mactkinit.c
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * mactkinit.c
  *
  * This is a support file needed to build a new version of Wish.
diff --git a/Lib/tcl/std_common.i b/Lib/tcl/std_common.i
index 3a6f47042..0718facb8 100644
--- a/Lib/tcl/std_common.i
+++ b/Lib/tcl/std_common.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * std_common.i
  *
  * SWIG typemaps for STL - common utilities
diff --git a/Lib/tcl/std_pair.i b/Lib/tcl/std_pair.i
index 52e96674f..1448d6524 100644
--- a/Lib/tcl/std_pair.i
+++ b/Lib/tcl/std_pair.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * std_pair.i
  *
  * Typemaps for std::pair
diff --git a/Lib/tcl/std_vector.i b/Lib/tcl/std_vector.i
index d913f00cc..3c8dd24b7 100644
--- a/Lib/tcl/std_vector.i
+++ b/Lib/tcl/std_vector.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * std_vector.i
  * ----------------------------------------------------------------------------- */
 
diff --git a/Lib/tcl/stl.i b/Lib/tcl/stl.i
index afd121341..40c7584ec 100644
--- a/Lib/tcl/stl.i
+++ b/Lib/tcl/stl.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * stl.i
  * ----------------------------------------------------------------------------- */
 
diff --git a/Lib/tcl/tcl8.swg b/Lib/tcl/tcl8.swg
index c33cc7681..5da1bc07c 100644
--- a/Lib/tcl/tcl8.swg
+++ b/Lib/tcl/tcl8.swg
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * tcl8.swg
  *
  * Tcl configuration module.
diff --git a/Lib/tcl/tclinterp.i b/Lib/tcl/tclinterp.i
index 48cdb6066..3b45b6d4b 100644
--- a/Lib/tcl/tclinterp.i
+++ b/Lib/tcl/tclinterp.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * tclinterp.i
  *
  * Tcl_Interp *interp
diff --git a/Lib/tcl/tclopers.swg b/Lib/tcl/tclopers.swg
index 26b74203d..f113ccd19 100644
--- a/Lib/tcl/tclopers.swg
+++ b/Lib/tcl/tclopers.swg
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * tclopers.swg
  *
  * C++ overloaded operators.
diff --git a/Lib/tcl/tclresult.i b/Lib/tcl/tclresult.i
index ca0106432..c63b3ee19 100644
--- a/Lib/tcl/tclresult.i
+++ b/Lib/tcl/tclresult.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * tclresult.i
  * ----------------------------------------------------------------------------- */
 
diff --git a/Lib/tcl/tclrun.swg b/Lib/tcl/tclrun.swg
index 6387fb008..eb8bd253c 100644
--- a/Lib/tcl/tclrun.swg
+++ b/Lib/tcl/tclrun.swg
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * tclrun.swg
  *
  * This file contains the runtime support for Tcl modules and includes
diff --git a/Lib/tcl/tclsh.i b/Lib/tcl/tclsh.i
index 2e8ed3316..160ba8d8f 100644
--- a/Lib/tcl/tclsh.i
+++ b/Lib/tcl/tclsh.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * tclsh.i
  *
  * SWIG File for building new tclsh program
diff --git a/Lib/tcl/tclwstrings.swg b/Lib/tcl/tclwstrings.swg
index 2d344c20f..b3b682e30 100644
--- a/Lib/tcl/tclwstrings.swg
+++ b/Lib/tcl/tclwstrings.swg
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * tclwstrings.wg
  *
  * Utility methods for wchar strings 
diff --git a/Lib/tcl/typemaps.i b/Lib/tcl/typemaps.i
index 7c9e04a8b..8bee672cc 100644
--- a/Lib/tcl/typemaps.i
+++ b/Lib/tcl/typemaps.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * typemaps.i
  *
  * Swig typemap library for Tcl8.  This file contains various sorts
diff --git a/Lib/tcl/wish.i b/Lib/tcl/wish.i
index 077ded61f..260032a81 100644
--- a/Lib/tcl/wish.i
+++ b/Lib/tcl/wish.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * wish.i
  *
  * SWIG File for making wish
diff --git a/Lib/typemaps/attribute.swg b/Lib/typemaps/attribute.swg
index f6335be82..19b22ed01 100644
--- a/Lib/typemaps/attribute.swg
+++ b/Lib/typemaps/attribute.swg
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * attribute.swg
  *
  * Attribute implementation
diff --git a/Lib/typemaps/carrays.swg b/Lib/typemaps/carrays.swg
index 27ca11779..cdeab36b7 100644
--- a/Lib/typemaps/carrays.swg
+++ b/Lib/typemaps/carrays.swg
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * carrays.swg
  *
  * This library file contains macros that can be used to manipulate simple
diff --git a/Lib/typemaps/cdata.swg b/Lib/typemaps/cdata.swg
index 32b3f5a77..5baf7904c 100644
--- a/Lib/typemaps/cdata.swg
+++ b/Lib/typemaps/cdata.swg
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * cdata.swg
  *
  * This library file contains macros for manipulating raw C data as strings.
diff --git a/Lib/typemaps/cmalloc.swg b/Lib/typemaps/cmalloc.swg
index 15f962930..45a6ab990 100644
--- a/Lib/typemaps/cmalloc.swg
+++ b/Lib/typemaps/cmalloc.swg
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * cmalloc.swg
  *
  * This library file contains macros that can be used to create objects using
diff --git a/Lib/typemaps/cpointer.swg b/Lib/typemaps/cpointer.swg
index ce1af169e..f797a6895 100644
--- a/Lib/typemaps/cpointer.swg
+++ b/Lib/typemaps/cpointer.swg
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * cpointer.swg
  *
  * This library file contains macros that can be used to manipulate simple
diff --git a/Lib/typemaps/cstrings.swg b/Lib/typemaps/cstrings.swg
index 9144da790..c60ef6496 100644
--- a/Lib/typemaps/cstrings.swg
+++ b/Lib/typemaps/cstrings.swg
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * cstrings.swg
  *
  * This file provides typemaps and macros for dealing with various forms
diff --git a/Lib/typemaps/exception.swg b/Lib/typemaps/exception.swg
index 17a819cd7..12c4ea658 100644
--- a/Lib/typemaps/exception.swg
+++ b/Lib/typemaps/exception.swg
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * exceptions.swg
  *
  * This SWIG library file provides language independent exception handling
diff --git a/Lib/typemaps/ptrtypes.swg b/Lib/typemaps/ptrtypes.swg
index 803377afe..e1bc476ed 100644
--- a/Lib/typemaps/ptrtypes.swg
+++ b/Lib/typemaps/ptrtypes.swg
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * ptrtypes.swg
  *
  * Value typemaps (Type, const Type&) for "Ptr" types, such as swig
diff --git a/Lib/typemaps/swigtypemaps.swg b/Lib/typemaps/swigtypemaps.swg
index 08abab028..0e39afe4c 100644
--- a/Lib/typemaps/swigtypemaps.swg
+++ b/Lib/typemaps/swigtypemaps.swg
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * swigtypemaps.swg
  *
  * Unified Typemap Library frontend
diff --git a/Lib/typemaps/typemaps.swg b/Lib/typemaps/typemaps.swg
index 6e7505765..4629e8dfa 100644
--- a/Lib/typemaps/typemaps.swg
+++ b/Lib/typemaps/typemaps.swg
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * typemaps.swg
  *
  * Tcl Pointer handling
diff --git a/Lib/uffi/uffi.swg b/Lib/uffi/uffi.swg
index 78bd23534..41b085998 100644
--- a/Lib/uffi/uffi.swg
+++ b/Lib/uffi/uffi.swg
@@ -27,8 +27,6 @@
 typedef long size_t;
 
 %wrapper %{
-;; $Id$
-
 (eval-when (compile eval)
 
 ;;; You can define your own identifier converter if you want.
diff --git a/Lib/wchar.i b/Lib/wchar.i
index f106a3529..14de34634 100644
--- a/Lib/wchar.i
+++ b/Lib/wchar.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * wchar.i
  * ----------------------------------------------------------------------------- */
 
diff --git a/Lib/windows.i b/Lib/windows.i
index 08ddc2b22..2c093dacc 100644
--- a/Lib/windows.i
+++ b/Lib/windows.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * windows.i
  *
  * SWIG library file to support types found in windows.h as well as Microsoft
diff --git a/Makefile.in b/Makefile.in
index ebfc03656..9760fdd9c 100644
--- a/Makefile.in
+++ b/Makefile.in
@@ -162,50 +162,6 @@ java.actionexample:
 	  (cd Examples/$(LANGUAGE)/java && $(MAKE) -s $(chk-set-env) $(ACTION)) \
 	fi;							\
 
-gifplot-library:
-	@echo $(ACTION)ing Examples/GIFPlot/Lib
-	@cd Examples/GIFPlot/Lib && $(MAKE) -k -s $(ACTION)
-
-check-gifplot:					\
-	check-tcl-gifplot			\
-	check-perl5-gifplot			\
-	check-python-gifplot			\
-	check-java-gifplot			\
-	check-guile-gifplot			\
-	check-mzscheme-gifplot			\
-	check-ruby-gifplot			\
-	check-ocaml-gifplot			\
-	check-octave-gifplot			\
-	check-php4-gifplot			\
-	check-pike-gifplot			\
-	check-chicken-gifplot                   \
-#	check-lua-gifplot                  	\
-#	check-csharp-gifplot                    \
-#	check-modula3-gifplot
-
-check-%-gifplot: gifplot-library
-	@if test -z "$(skip-$*)"; then				\
-	  echo $* unknown;					\
-	  exit 1;						\
-	fi
-	@passed=true;						\
-	up=`$(srcdir)/Tools/capitalize $*`;			\
-	dir="Examples/GIFPlot/$$up";				\
-	if $(skip-$*); then					\
-	  echo skipping $$up $(ACTION);				\
-	elif [ ! -f $$dir/check.list ]; then			\
-	  echo skipping $$up $(ACTION) "(no $$dir/check.list)";	\
-	else							\
-	  all=`sed '/^#/d' $$dir/check.list`;			\
-	  for a in $$all; do					\
-	    echo $(ACTION)ing $$dir/$$a;			\
-	    (cd $$dir/$$a &&					\
-	    $(MAKE) -k -s $(chk-set-env) $(ACTION))		\
-	    || passed=false;					\
-	  done;							\
-	fi;							\
-	test $$passed = true
-
 # Checks testcases in the test-suite excluding those which are known to be broken
 check-test-suite:				\
 	check-tcl-test-suite			\
@@ -255,7 +211,7 @@ partialcheck-test-suite:
 partialcheck-%-test-suite:
 	@$(MAKE) -k -s check-$*-test-suite ACTION=partialcheck
 
-check: check-aliveness check-examples check-gifplot check-test-suite
+check: check-aliveness check-examples check-test-suite
 
 # Run known-to-be-broken as well as not broken testcases in the test-suite
 all-test-suite:					\
@@ -315,7 +271,7 @@ broken-%-test-suite:
 # CLEAN
 #####################################################################
 
-clean: clean-objects clean-libfiles clean-examples clean-gifplot clean-test-suite clean-docs
+clean: clean-objects clean-libfiles clean-examples clean-test-suite clean-docs
 
 clean-objects: clean-source
 
@@ -330,9 +286,6 @@ clean-libfiles:
 clean-examples:
 	@$(MAKE) -k -s check-examples ACTION=clean
 
-clean-gifplot:
-	@$(MAKE) -k -s check-gifplot ACTION=clean
-
 clean-test-suite:
 	@$(MAKE) -k -s check-test-suite ACTION=clean
 
@@ -342,9 +295,6 @@ clean-%-examples:
 clean-%-test-suite:
 	@$(MAKE) -k -s check-$*-test-suite ACTION=clean
 
-clean-%-gifplot:
-	@$(MAKE) -k -s check-$*-gifplot ACTION=clean
-
 clean-docs:
 	@echo cleaning Docs
 	@test -d $(DOCS) || exit 0; cd $(DOCS) && $(MAKE) -s clean
@@ -358,7 +308,7 @@ maintainer-clean: clean-libfiles
 
 DISTCLEAN-DEAD = config.status config.log config.cache swig.spec Makefile mkmf.log libtool
 
-distclean: distclean-objects clean-examples clean-gifplot distclean-test-suite clean-docs distclean-dead
+distclean: distclean-objects clean-examples distclean-test-suite clean-docs distclean-dead
 
 distclean-objects: distclean-source
 
diff --git a/README b/README
index 2898130b0..d6174bda5 100644
--- a/README
+++ b/README
@@ -1,6 +1,6 @@
 SWIG (Simplified Wrapper and Interface Generator)
 
-Version: 1.3.36 (24 June 2008)
+Version: 2.0.0 (in progress)
 
 Tagline: SWIG is a compiler that integrates C and C++ with languages
          including Perl, Python, Tcl, Ruby, PHP, Java, Ocaml, Lua,
@@ -13,61 +13,6 @@ the listed languages, or to extend C/C++ programs with a scripting
 language.
 
 This distribution represents the latest development release of SWIG.
-The guilty parties working on this are:
-
-Active Developers:
- William Fulton (wsf@fultondesigns.co.uk)               (SWIG core, Java, C#, Windows, Cygwin)
- Olly Betts (olly@survex.com)                           (PHP)
- John Lenz                                              (Guile, MzScheme updates, Chicken module, runtime system)
- Mark Gossage (mark@gossage.cjb.net)                    (Lua)
- Joseph Wang (joe@gnacademy.org)                        (R)
- Gonzalo Garramuno (ggarra@advancedsl.com.ar)           (Ruby, Ruby's UTL)
- Xavier Delacour (xavier.delacour@gmail.com)            (Octave)
-
-Major contributors include:
- Dave Beazley (dave-swig@dabeaz.com)                    (SWIG core, Python, Tcl, Perl)
- Henning Thielemann (swig@henning-thielemann.de)        (Modula3)
- Matthias Köppe (mkoeppe@mail.math.uni-magdeburg.de)    (Guile, MzScheme)
- Luigi Ballabio (luigi.ballabio@fastwebnet.it)          (STL wrapping)
- Mikel Bancroft (mikel@franz.com)                       (Allegro CL)
- Surendra Singhi (efuzzyone@netscape.net)               (CLISP, CFFI)
- Marcelo Matus (mmatus@acms.arizona.edu)                (SWIG core, Python, UTL[python,perl,tcl,ruby])
- Art Yerkes (ayerkes@speakeasy.net)                     (Ocaml)
- Lyle Johnson (lyle@users.sourceforge.net)              (Ruby)
- Charlie Savage (cfis@interserv.com)                    (Ruby)
- Thien-Thi Nguyen (ttn@glug.org)                        (build/test/misc)
- Richard Palmer (richard@magicality.org)                (PHP)
- Sam Liddicott - Anonova Ltd (saml@liddicott.com)       (PHP)
- Tim Hockin - Sun Microsystems (thockin@sun.com)        (PHP)
- Kevin Ruland                                           (PHP)
- Shibukawa Yoshiki                                      (Japanese Translation)
- Jason Stewart (jason@openinformatics.com)              (Perl5)
- Loic Dachary                                           (Perl5)
- David Fletcher                                         (Perl5)
- Gary Holt                                              (Perl5)
- Masaki Fukushima                                       (Ruby)
- Scott Michel (scottm@cs.ucla.edu)                      (Java directors)
- Tiger Feng (songyanf@cs.uchicago.edu)                  (SWIG core)
- Mark Rose (mrose@stm.lbl.gov)                          (Directors)
- Jonah Beckford (beckford@usermail.com)                 (CHICKEN)
- Ahmon Dancy (dancy@franz.com)				(Allegro CL)
- Dirk Gerrits                                           (Allegro CL)
- Neil Cawse                                             (C#)
- Harco de Hilster                                       (Java)
- Alexey Dyachenko (dyachenko@fromru.com)                (Tcl)
- Bob Techentin                                          (Tcl)
- Martin Froehlich <MartinFroehlich@ACM.org>             (Guile)
- Marcio Luis Teixeira <marciot@holly.colostate.edu>     (Guile)
- Duncan Temple Lang                                     (R)
-
-Past contributors include:
- James Michael DuPont, Clark McGrew, Dustin Mitchell, Ian Cooke, Catalin Dumitrescu, Baran
- Kovuk, Oleg Tolmatcev, Tal Shalif, Lluis Padro, Chris Seatory, Igor Bely, Robin Dunn
- (See CHANGES for a more complete list).
-
-Portions also copyrighted by companies/corporations;
- Network Applied Communication Laboratory, Inc
- Information-technology Promotion Agency, Japan
 
 Up-to-date SWIG related information can be found at
 
diff --git a/Source/CParse/cparse.h b/Source/CParse/cparse.h
index 06a901c0d..522ca778f 100644
--- a/Source/CParse/cparse.h
+++ b/Source/CParse/cparse.h
@@ -1,6 +1,10 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * cparse.h
  *
diff --git a/Source/CParse/cscanner.c b/Source/CParse/cscanner.c
index 68d50cd2d..ea265bb56 100644
--- a/Source/CParse/cscanner.c
+++ b/Source/CParse/cscanner.c
@@ -1,6 +1,10 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * scanner.c
  *
diff --git a/Source/CParse/parser.y b/Source/CParse/parser.y
index d28516206..1b055edd9 100644
--- a/Source/CParse/parser.y
+++ b/Source/CParse/parser.y
@@ -1,6 +1,10 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * parser.y
  *
diff --git a/Source/CParse/templ.c b/Source/CParse/templ.c
index a3e992f83..120b75670 100644
--- a/Source/CParse/templ.c
+++ b/Source/CParse/templ.c
@@ -1,6 +1,10 @@
 /* ----------------------------------------------------------------------------- 
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * templ.c
  *
diff --git a/Source/CParse/util.c b/Source/CParse/util.c
index efae41051..fa934ffc0 100644
--- a/Source/CParse/util.c
+++ b/Source/CParse/util.c
@@ -1,6 +1,10 @@
 /* ----------------------------------------------------------------------------- 
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * util.c
  *
diff --git a/Source/DOH/base.c b/Source/DOH/base.c
index dcb0140e0..7d19e6c3d 100644
--- a/Source/DOH/base.c
+++ b/Source/DOH/base.c
@@ -1,13 +1,15 @@
 /* -----------------------------------------------------------------------------
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
+ *
  * base.c 
  *
  *     This file contains the function entry points for dispatching methods on
  *     DOH objects.  A number of small utility functions are also included.
- *
- * Author(s) : David Beazley (beazley@cs.uchicago.edu)
- *
- * Copyright (C) 1999-2000.  The University of Chicago
- * See the file LICENSE for information on usage and redistribution.
  * ----------------------------------------------------------------------------- */
 
 char cvsroot_base_c[] = "$Id$";
diff --git a/Source/DOH/doh.h b/Source/DOH/doh.h
index 7ab244fab..396a9cacf 100644
--- a/Source/DOH/doh.h
+++ b/Source/DOH/doh.h
@@ -1,14 +1,14 @@
 /* -----------------------------------------------------------------------------
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
+ *
  * doh.h
  *
  *     This file describes of the externally visible functions in DOH.
- *
- * Author(s) : David Beazley (beazley@cs.uchicago.edu)
- *
- * Copyright (C) 1999-2000.  The University of Chicago
- * See the file LICENSE for information on usage and redistribution.
- *
- * $Id$
  * ----------------------------------------------------------------------------- */
 
 #ifndef _DOH_H
diff --git a/Source/DOH/dohint.h b/Source/DOH/dohint.h
index 1fc5eb7c9..661bed075 100644
--- a/Source/DOH/dohint.h
+++ b/Source/DOH/dohint.h
@@ -1,15 +1,14 @@
-
 /* -----------------------------------------------------------------------------
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
+ *
  * dohint.h
  *
  *     This file describes internally managed objects.
- *
- * Author(s) : David Beazley (beazley@cs.uchicago.edu)
- *
- * Copyright (C) 1999-2000.  The University of Chicago
- * See the file LICENSE for information on usage and redistribution.
- *
- * $Id$
  * ----------------------------------------------------------------------------- */
 
 #ifndef _DOHINT_H
diff --git a/Source/DOH/file.c b/Source/DOH/file.c
index 8c53978ee..3d8d20284 100644
--- a/Source/DOH/file.c
+++ b/Source/DOH/file.c
@@ -1,13 +1,15 @@
 /* ----------------------------------------------------------------------------- 
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
+ *
  * file.c
  *
  *     This file implements a file-like object that can be built around an 
  *     ordinary FILE * or integer file descriptor.
- * 
- * Author(s) : David Beazley (beazley@cs.uchicago.edu)
- *
- * Copyright (C) 1999-2000.  The University of Chicago
- * See the file LICENSE for information on usage and redistribution.	
  * ----------------------------------------------------------------------------- */
 
 char cvsroot_file_c[] = "$Id$";
diff --git a/Source/DOH/fio.c b/Source/DOH/fio.c
index f544cee64..2ef605c32 100644
--- a/Source/DOH/fio.c
+++ b/Source/DOH/fio.c
@@ -1,13 +1,15 @@
 /* ----------------------------------------------------------------------------- 
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
+ *
  * fio.c
  *
  *     This file implements a number of standard I/O operations included
  *     formatted output, readline, and splitting.
- * 
- * Author(s) : David Beazley (beazley@cs.uchicago.edu)
- *
- * Copyright (C) 1999-2000.  The University of Chicago
- * See the file LICENSE for information on usage and redistribution.	
  * ----------------------------------------------------------------------------- */
 
 char cvsroot_fio_c[] = "$Id$";
diff --git a/Source/DOH/hash.c b/Source/DOH/hash.c
index 62aef10f2..ab90e725e 100644
--- a/Source/DOH/hash.c
+++ b/Source/DOH/hash.c
@@ -1,12 +1,14 @@
 /* -----------------------------------------------------------------------------
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
+ *
  * hash.c
  *
  *     Implements a simple hash table object.
- *
- * Author(s) : David Beazley (beazley@cs.uchicago.edu)
- *
- * Copyright (C) 1999-2000.  The University of Chicago
- * See the file LICENSE for information on usage and redistribution.
  * ----------------------------------------------------------------------------- */
 
 char cvsroot_hash_c[] = "$Id$";
diff --git a/Source/DOH/list.c b/Source/DOH/list.c
index a45731de1..f3be4fba1 100644
--- a/Source/DOH/list.c
+++ b/Source/DOH/list.c
@@ -1,12 +1,14 @@
 /* ----------------------------------------------------------------------------- 
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
+ *
  * list.c
  *
  *     Implements a simple list object.
- * 
- * Author(s) : David Beazley (beazley@cs.uchicago.edu)
- *
- * Copyright (C) 1999-2000.  The University of Chicago
- * See the file LICENSE for information on usage and redistribution.	
  * ----------------------------------------------------------------------------- */
 
 char cvsroot_list_c[] = "$Id$";
diff --git a/Source/DOH/memory.c b/Source/DOH/memory.c
index 1c6063ef3..fcacd6170 100644
--- a/Source/DOH/memory.c
+++ b/Source/DOH/memory.c
@@ -1,13 +1,15 @@
 /* ----------------------------------------------------------------------------- 
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
+ *
  * memory.c
  *
  *     This file implements all of DOH's memory management including allocation
  *     of objects and checking of objects.
- * 
- * Author(s) : David Beazley (beazley@cs.uchicago.edu)
- *
- * Copyright (C) 1999-2000.  The University of Chicago
- * See the file LICENSE for information on usage and redistribution.	
  * ----------------------------------------------------------------------------- */
 
 char cvsroot_memory_c[] = "$Id$";
diff --git a/Source/DOH/string.c b/Source/DOH/string.c
index 1498d717a..ea6b46cb2 100644
--- a/Source/DOH/string.c
+++ b/Source/DOH/string.c
@@ -1,13 +1,15 @@
 /* -----------------------------------------------------------------------------
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
+ *
  * string.c
  *
  *     Implements a string object that supports both sequence operations and
  *     file semantics.
- *
- * Author(s) : David Beazley (beazley@cs.uchicago.edu)
- *
- * Copyright (C) 1999-2000.  The University of Chicago
- * See the file LICENSE for information on usage and redistribution.	
  * ----------------------------------------------------------------------------- */
 
 char cvsroot_string_c[] = "$Id$";
diff --git a/Source/DOH/void.c b/Source/DOH/void.c
index 0be01561a..2d684b9cd 100644
--- a/Source/DOH/void.c
+++ b/Source/DOH/void.c
@@ -1,13 +1,15 @@
 /* ----------------------------------------------------------------------------- 
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
+ *
  * void.c
  *
  *     Implements a "void" object that is really just a DOH container around
  *     an arbitrary C object represented as a void *.
- * 
- * Author(s) : David Beazley (beazley@cs.uchicago.edu)
- *
- * Copyright (C) 1999-2000.  The University of Chicago
- * See the file LICENSE for information on usage and redistribution.	
  * ----------------------------------------------------------------------------- */
 
 char cvsroot_void_c[] = "$Id$";
diff --git a/Source/Include/swigwarn.h b/Source/Include/swigwarn.h
index 8c4678847..d7a06c46c 100644
--- a/Source/Include/swigwarn.h
+++ b/Source/Include/swigwarn.h
@@ -1,6 +1,10 @@
 /* ----------------------------------------------------------------------------- 
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * swigwarn.h
  *
@@ -16,8 +20,6 @@
  * numbers in this file.
  * ----------------------------------------------------------------------------- */
 
-/* $Id$ */
-
 #ifndef SWIGWARN_H_
 #define SWIGWARN_H_
 
diff --git a/Source/Modules/allegrocl.cxx b/Source/Modules/allegrocl.cxx
index 217c89b1f..34ca51f8d 100644
--- a/Source/Modules/allegrocl.cxx
+++ b/Source/Modules/allegrocl.cxx
@@ -1,6 +1,10 @@
 /* ----------------------------------------------------------------------------- 
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * allegrocl.cxx
  *
diff --git a/Source/Modules/allocate.cxx b/Source/Modules/allocate.cxx
index e8397e6a6..31f27e1eb 100644
--- a/Source/Modules/allocate.cxx
+++ b/Source/Modules/allocate.cxx
@@ -1,6 +1,10 @@
 /* ----------------------------------------------------------------------------- 
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * allocate.cxx
  *
diff --git a/Source/Modules/browser.cxx b/Source/Modules/browser.cxx
index b1bc7349c..592e12783 100644
--- a/Source/Modules/browser.cxx
+++ b/Source/Modules/browser.cxx
@@ -1,6 +1,10 @@
 /* ----------------------------------------------------------------------------- 
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * browser.cxx
  *
diff --git a/Source/Modules/cffi.cxx b/Source/Modules/cffi.cxx
index 4b3ddac70..97859f090 100644
--- a/Source/Modules/cffi.cxx
+++ b/Source/Modules/cffi.cxx
@@ -1,6 +1,10 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * cffi.cxx
  *
diff --git a/Source/Modules/chicken.cxx b/Source/Modules/chicken.cxx
index 2298d2939..ec77f1870 100644
--- a/Source/Modules/chicken.cxx
+++ b/Source/Modules/chicken.cxx
@@ -1,6 +1,10 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * chicken.cxx
  *
diff --git a/Source/Modules/clisp.cxx b/Source/Modules/clisp.cxx
index 823f22e2c..f0e57f3f0 100644
--- a/Source/Modules/clisp.cxx
+++ b/Source/Modules/clisp.cxx
@@ -1,6 +1,10 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * clisp.cxx
  *
diff --git a/Source/Modules/contract.cxx b/Source/Modules/contract.cxx
index 9bf8decf6..e8687c90b 100644
--- a/Source/Modules/contract.cxx
+++ b/Source/Modules/contract.cxx
@@ -1,6 +1,10 @@
 /* ----------------------------------------------------------------------------- 
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * contract.cxx
  *
diff --git a/Source/Modules/csharp.cxx b/Source/Modules/csharp.cxx
index 431181355..7992b260a 100644
--- a/Source/Modules/csharp.cxx
+++ b/Source/Modules/csharp.cxx
@@ -1,6 +1,10 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * csharp.cxx
  *
diff --git a/Source/Modules/directors.cxx b/Source/Modules/directors.cxx
index 4363cd813..2050d953e 100644
--- a/Source/Modules/directors.cxx
+++ b/Source/Modules/directors.cxx
@@ -1,6 +1,10 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * directors.cxx
  *
diff --git a/Source/Modules/emit.cxx b/Source/Modules/emit.cxx
index a4cf8cebc..fde3b2457 100644
--- a/Source/Modules/emit.cxx
+++ b/Source/Modules/emit.cxx
@@ -1,6 +1,10 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * emit.cxx
  *
diff --git a/Source/Modules/guile.cxx b/Source/Modules/guile.cxx
index f5f080034..d64c87b49 100644
--- a/Source/Modules/guile.cxx
+++ b/Source/Modules/guile.cxx
@@ -1,6 +1,10 @@
 /* ----------------------------------------------------------------------------- 
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * guile.cxx
  *
diff --git a/Source/Modules/java.cxx b/Source/Modules/java.cxx
index 0c5ad5401..279eb530e 100644
--- a/Source/Modules/java.cxx
+++ b/Source/Modules/java.cxx
@@ -1,6 +1,10 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * java.cxx
  *
diff --git a/Source/Modules/lang.cxx b/Source/Modules/lang.cxx
index e2fd93f7b..122270a9d 100644
--- a/Source/Modules/lang.cxx
+++ b/Source/Modules/lang.cxx
@@ -1,6 +1,10 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * lang.cxx
  *
diff --git a/Source/Modules/lua.cxx b/Source/Modules/lua.cxx
index 6113da960..e81974c9b 100644
--- a/Source/Modules/lua.cxx
+++ b/Source/Modules/lua.cxx
@@ -1,6 +1,10 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * lua.cxx
  *
diff --git a/Source/Modules/main.cxx b/Source/Modules/main.cxx
index 901ee812e..055af907f 100644
--- a/Source/Modules/main.cxx
+++ b/Source/Modules/main.cxx
@@ -1,6 +1,10 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * main.cxx
  *
diff --git a/Source/Modules/modula3.cxx b/Source/Modules/modula3.cxx
index 6cb24d39a..5ee3c6b5c 100644
--- a/Source/Modules/modula3.cxx
+++ b/Source/Modules/modula3.cxx
@@ -1,6 +1,10 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * modula3.cxx
  *
diff --git a/Source/Modules/module.cxx b/Source/Modules/module.cxx
index 6a0d6bbb9..f4ab560dd 100644
--- a/Source/Modules/module.cxx
+++ b/Source/Modules/module.cxx
@@ -1,6 +1,10 @@
 /* ----------------------------------------------------------------------------- 
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * module.cxx
  *
diff --git a/Source/Modules/mzscheme.cxx b/Source/Modules/mzscheme.cxx
index 78d4a4b65..01e3b9c8c 100644
--- a/Source/Modules/mzscheme.cxx
+++ b/Source/Modules/mzscheme.cxx
@@ -1,6 +1,10 @@
 /* ----------------------------------------------------------------------------- 
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * mzscheme.cxx
  *
diff --git a/Source/Modules/ocaml.cxx b/Source/Modules/ocaml.cxx
index 0d0f4c7f2..b8d932ffb 100755
--- a/Source/Modules/ocaml.cxx
+++ b/Source/Modules/ocaml.cxx
@@ -1,6 +1,10 @@
 /* ----------------------------------------------------------------------------- 
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * ocaml.cxx
  *
diff --git a/Source/Modules/octave.cxx b/Source/Modules/octave.cxx
index d582e8a6c..4aa9c0ab8 100644
--- a/Source/Modules/octave.cxx
+++ b/Source/Modules/octave.cxx
@@ -1,6 +1,10 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * octave.cxx
  *
diff --git a/Source/Modules/overload.cxx b/Source/Modules/overload.cxx
index d16913885..793511c57 100644
--- a/Source/Modules/overload.cxx
+++ b/Source/Modules/overload.cxx
@@ -1,6 +1,10 @@
 /* ----------------------------------------------------------------------------- 
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * overload.cxx
  *
diff --git a/Source/Modules/perl5.cxx b/Source/Modules/perl5.cxx
index 6e706fc8d..8faff7d7f 100644
--- a/Source/Modules/perl5.cxx
+++ b/Source/Modules/perl5.cxx
@@ -1,10 +1,10 @@
-/* -*- mode: c++; c-basic-offset: 2; indent-tabs-mode: nil; -*-
- *  vim:expandtab:shiftwidth=2:tabstop=8:smarttab:
- */
-
 /* ----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * perl5.cxx
  *
diff --git a/Source/Modules/php.cxx b/Source/Modules/php.cxx
index 9369c2489..66ca6eff2 100644
--- a/Source/Modules/php.cxx
+++ b/Source/Modules/php.cxx
@@ -1,6 +1,10 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * php4.cxx
  *
diff --git a/Source/Modules/pike.cxx b/Source/Modules/pike.cxx
index 30f9b3d74..f4a6c13e6 100644
--- a/Source/Modules/pike.cxx
+++ b/Source/Modules/pike.cxx
@@ -1,6 +1,10 @@
 /* ----------------------------------------------------------------------------- 
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * pike.cxx
  *
diff --git a/Source/Modules/python.cxx b/Source/Modules/python.cxx
index bfbada1da..c8d7e06ca 100644
--- a/Source/Modules/python.cxx
+++ b/Source/Modules/python.cxx
@@ -1,6 +1,10 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * python.cxx
  *
diff --git a/Source/Modules/r.cxx b/Source/Modules/r.cxx
index 49d3ecc89..9035f5e9e 100644
--- a/Source/Modules/r.cxx
+++ b/Source/Modules/r.cxx
@@ -1,6 +1,10 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * r.cxx
  *
diff --git a/Source/Modules/ruby.cxx b/Source/Modules/ruby.cxx
index ad448d34e..ec0d3dee9 100644
--- a/Source/Modules/ruby.cxx
+++ b/Source/Modules/ruby.cxx
@@ -1,6 +1,10 @@
 /* ----------------------------------------------------------------------------- 
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * ruby.cxx
  *
diff --git a/Source/Modules/s-exp.cxx b/Source/Modules/s-exp.cxx
index b89b3097f..86213fcab 100644
--- a/Source/Modules/s-exp.cxx
+++ b/Source/Modules/s-exp.cxx
@@ -1,6 +1,10 @@
 /* ----------------------------------------------------------------------------- 
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * s-exp.cxx
  *
diff --git a/Source/Modules/swigmain.cxx b/Source/Modules/swigmain.cxx
index 5b103e71e..7cd913e2a 100644
--- a/Source/Modules/swigmain.cxx
+++ b/Source/Modules/swigmain.cxx
@@ -1,11 +1,15 @@
 /* ----------------------------------------------------------------------------- 
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
- * Simplified Wrapper and Interface Generator  (SWIG)
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * swigmain.cxx
  *
+ * Simplified Wrapper and Interface Generator  (SWIG)
+ *
  * This file is the main entry point to SWIG.  It collects the command
  * line options, registers built-in language modules, and instantiates
  * a module for code generation.   If adding new language modules
diff --git a/Source/Modules/swigmod.h b/Source/Modules/swigmod.h
index 03892e4f6..5dc6fd390 100644
--- a/Source/Modules/swigmod.h
+++ b/Source/Modules/swigmod.h
@@ -1,6 +1,10 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * swigmod.h
  *
diff --git a/Source/Modules/tcl8.cxx b/Source/Modules/tcl8.cxx
index 09bd266c3..7a86108bb 100644
--- a/Source/Modules/tcl8.cxx
+++ b/Source/Modules/tcl8.cxx
@@ -1,6 +1,10 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * tcl8.cxx
  *
diff --git a/Source/Modules/typepass.cxx b/Source/Modules/typepass.cxx
index d663aed6e..e972cea05 100644
--- a/Source/Modules/typepass.cxx
+++ b/Source/Modules/typepass.cxx
@@ -1,6 +1,10 @@
 /* ----------------------------------------------------------------------------- 
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * typepass.cxx
  *
diff --git a/Source/Modules/uffi.cxx b/Source/Modules/uffi.cxx
index 5d4affb8c..c35ca2666 100644
--- a/Source/Modules/uffi.cxx
+++ b/Source/Modules/uffi.cxx
@@ -1,6 +1,10 @@
 /* ----------------------------------------------------------------------------- 
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * uffi.cxx
  *
diff --git a/Source/Modules/utils.cxx b/Source/Modules/utils.cxx
index bf8211903..3fe7a2709 100644
--- a/Source/Modules/utils.cxx
+++ b/Source/Modules/utils.cxx
@@ -1,6 +1,10 @@
 /* ----------------------------------------------------------------------------- 
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * utils.cxx
  *
diff --git a/Source/Modules/xml.cxx b/Source/Modules/xml.cxx
index c74b48d7c..bd595d526 100644
--- a/Source/Modules/xml.cxx
+++ b/Source/Modules/xml.cxx
@@ -1,6 +1,10 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * xml.cxx
  *
diff --git a/Source/Preprocessor/cpp.c b/Source/Preprocessor/cpp.c
index c04f95f00..1e05af6ef 100644
--- a/Source/Preprocessor/cpp.c
+++ b/Source/Preprocessor/cpp.c
@@ -1,6 +1,10 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * cpp.c
  *
diff --git a/Source/Preprocessor/expr.c b/Source/Preprocessor/expr.c
index 4da24a774..3e3f39480 100644
--- a/Source/Preprocessor/expr.c
+++ b/Source/Preprocessor/expr.c
@@ -1,6 +1,10 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * expr.c
  *
diff --git a/Source/Preprocessor/preprocessor.h b/Source/Preprocessor/preprocessor.h
index 4f7ff8804..199e5ae3c 100644
--- a/Source/Preprocessor/preprocessor.h
+++ b/Source/Preprocessor/preprocessor.h
@@ -1,6 +1,10 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * preprocessor.h
  *
diff --git a/Source/Swig/cwrap.c b/Source/Swig/cwrap.c
index 18920ecc2..714613d81 100644
--- a/Source/Swig/cwrap.c
+++ b/Source/Swig/cwrap.c
@@ -1,6 +1,10 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * cwrap.c
  *
diff --git a/Source/Swig/deprecate.c b/Source/Swig/deprecate.c
index 475d2c6cf..f25b9a650 100644
--- a/Source/Swig/deprecate.c
+++ b/Source/Swig/deprecate.c
@@ -1,6 +1,10 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * deprecate.c
  *
diff --git a/Source/Swig/error.c b/Source/Swig/error.c
index 1eaba1f17..0ce53dd5b 100644
--- a/Source/Swig/error.c
+++ b/Source/Swig/error.c
@@ -1,6 +1,10 @@
 /* ----------------------------------------------------------------------------- 
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * error.c
  *
diff --git a/Source/Swig/fragment.c b/Source/Swig/fragment.c
index 510a01875..896461b30 100644
--- a/Source/Swig/fragment.c
+++ b/Source/Swig/fragment.c
@@ -1,6 +1,10 @@
 /* ----------------------------------------------------------------------------- 
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * fragment.c
  *
diff --git a/Source/Swig/getopt.c b/Source/Swig/getopt.c
index 87b0f7c9d..b8389b476 100644
--- a/Source/Swig/getopt.c
+++ b/Source/Swig/getopt.c
@@ -1,6 +1,10 @@
 /* ----------------------------------------------------------------------------- 
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * getopt.c
  *
diff --git a/Source/Swig/include.c b/Source/Swig/include.c
index 3f47be15b..79b97b4d6 100644
--- a/Source/Swig/include.c
+++ b/Source/Swig/include.c
@@ -1,6 +1,10 @@
 /* ----------------------------------------------------------------------------- 
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * include.c
  *
diff --git a/Source/Swig/misc.c b/Source/Swig/misc.c
index a9c64011e..03dc28d2a 100644
--- a/Source/Swig/misc.c
+++ b/Source/Swig/misc.c
@@ -1,6 +1,10 @@
 /* ----------------------------------------------------------------------------- 
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * misc.c
  *
diff --git a/Source/Swig/naming.c b/Source/Swig/naming.c
index f34a24612..31cf116dc 100644
--- a/Source/Swig/naming.c
+++ b/Source/Swig/naming.c
@@ -1,6 +1,10 @@
 /* ----------------------------------------------------------------------------- 
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * naming.c
  *
diff --git a/Source/Swig/parms.c b/Source/Swig/parms.c
index baa1dfbf3..267852cf0 100644
--- a/Source/Swig/parms.c
+++ b/Source/Swig/parms.c
@@ -1,6 +1,10 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * parms.c
  *
diff --git a/Source/Swig/scanner.c b/Source/Swig/scanner.c
index 06e78db37..a082036a5 100644
--- a/Source/Swig/scanner.c
+++ b/Source/Swig/scanner.c
@@ -1,6 +1,10 @@
 /* ----------------------------------------------------------------------------- 
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * scanner.c
  *
diff --git a/Source/Swig/stype.c b/Source/Swig/stype.c
index 5ffd28eec..30a80b4bd 100644
--- a/Source/Swig/stype.c
+++ b/Source/Swig/stype.c
@@ -1,6 +1,10 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * stype.c
  *
diff --git a/Source/Swig/swig.h b/Source/Swig/swig.h
index 3f736bbd5..9501eaa55 100644
--- a/Source/Swig/swig.h
+++ b/Source/Swig/swig.h
@@ -1,6 +1,10 @@
 /* ----------------------------------------------------------------------------- 
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * swig.h
  *
diff --git a/Source/Swig/swigfile.h b/Source/Swig/swigfile.h
index c945fb1ac..4f6869109 100644
--- a/Source/Swig/swigfile.h
+++ b/Source/Swig/swigfile.h
@@ -1,6 +1,10 @@
 /* ----------------------------------------------------------------------------- 
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * swigfile.h
  *
diff --git a/Source/Swig/swigopt.h b/Source/Swig/swigopt.h
index 428d90dce..433ca07e5 100644
--- a/Source/Swig/swigopt.h
+++ b/Source/Swig/swigopt.h
@@ -1,6 +1,10 @@
 /* ----------------------------------------------------------------------------- 
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * swigopt.h
  *
diff --git a/Source/Swig/swigparm.h b/Source/Swig/swigparm.h
index 529438bae..6ea849424 100644
--- a/Source/Swig/swigparm.h
+++ b/Source/Swig/swigparm.h
@@ -1,6 +1,10 @@
 /* ----------------------------------------------------------------------------- 
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * swigparm.h
  *
diff --git a/Source/Swig/swigscan.h b/Source/Swig/swigscan.h
index 2486286a9..31b0c2705 100644
--- a/Source/Swig/swigscan.h
+++ b/Source/Swig/swigscan.h
@@ -1,6 +1,10 @@
 /* ----------------------------------------------------------------------------- 
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * swigscan.h
  *
diff --git a/Source/Swig/swigtree.h b/Source/Swig/swigtree.h
index 2e5c4da36..d4221207c 100644
--- a/Source/Swig/swigtree.h
+++ b/Source/Swig/swigtree.h
@@ -1,6 +1,10 @@
 /* ----------------------------------------------------------------------------- 
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * swigtree.h
  *
diff --git a/Source/Swig/swigwrap.h b/Source/Swig/swigwrap.h
index 25eeb6f7f..bd1009d0e 100644
--- a/Source/Swig/swigwrap.h
+++ b/Source/Swig/swigwrap.h
@@ -1,6 +1,10 @@
 /* ----------------------------------------------------------------------------- 
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * swigwrap.h
  *
diff --git a/Source/Swig/symbol.c b/Source/Swig/symbol.c
index c9691fa54..3d6eb508b 100644
--- a/Source/Swig/symbol.c
+++ b/Source/Swig/symbol.c
@@ -1,6 +1,10 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * symbol.c
  *
diff --git a/Source/Swig/tree.c b/Source/Swig/tree.c
index 61dca8353..b6cbca352 100644
--- a/Source/Swig/tree.c
+++ b/Source/Swig/tree.c
@@ -1,6 +1,10 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * tree.c
  *
diff --git a/Source/Swig/typemap.c b/Source/Swig/typemap.c
index 6cbeb67ea..5ee74b629 100644
--- a/Source/Swig/typemap.c
+++ b/Source/Swig/typemap.c
@@ -1,6 +1,10 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * typemap.c
  *
diff --git a/Source/Swig/typeobj.c b/Source/Swig/typeobj.c
index 18d1b2304..2732e2fd5 100644
--- a/Source/Swig/typeobj.c
+++ b/Source/Swig/typeobj.c
@@ -1,6 +1,10 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * typeobj.c
  *
diff --git a/Source/Swig/typesys.c b/Source/Swig/typesys.c
index a9e2898bd..90df2ebd1 100644
--- a/Source/Swig/typesys.c
+++ b/Source/Swig/typesys.c
@@ -1,6 +1,10 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * typesys.c
  *
diff --git a/Source/Swig/wrapfunc.c b/Source/Swig/wrapfunc.c
index 3778066ce..2e18474aa 100644
--- a/Source/Swig/wrapfunc.c
+++ b/Source/Swig/wrapfunc.c
@@ -1,6 +1,10 @@
 /* ----------------------------------------------------------------------------- 
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * wrapfunc.c
  *
diff --git a/configure.in b/configure.in
index 8a09cd6f7..dada26c7f 100644
--- a/configure.in
+++ b/configure.in
@@ -2,7 +2,7 @@ dnl Process this file with autoconf to produce a configure script.
 dnl The macros which aren't shipped with the autotools are stored in the
 dnl Tools/config directory in .m4 files.
 
-AC_INIT([swig],[1.3.37],[http://www.swig.org])
+AC_INIT([swig],[2.0.0],[http://www.swig.org])
 AC_PREREQ(2.58)
 AC_CONFIG_SRCDIR([Source/Swig/swig.h])
 AC_CONFIG_AUX_DIR([Tools/config])
@@ -2135,8 +2135,6 @@ AC_CONFIG_FILES([			        \
     Examples/Makefile			        \
     Examples/guile/Makefile		        \
     Examples/xml/Makefile		        \
-    Examples/GIFPlot/Makefile		        \
-    Examples/GIFPlot/Lib/Makefile	        \
     Examples/test-suite/chicken/Makefile	\
     Examples/test-suite/csharp/Makefile	        \
     Examples/test-suite/guile/Makefile	        \

From 02fbe37ae6147b64e21c153b45a9a09313668438 Mon Sep 17 00:00:00 2001
From: William S Fulton <wsf@fultondesigns.co.uk>
Date: Sat, 6 Mar 2010 11:47:21 +0000
Subject: [PATCH 043/314] Add new GPL license headers to source files added in
 this branch

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2008-cherylfoil@11911 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Source/DoxygenTranslator/src/DoxygenEntity.cpp   | 12 ++++++++----
 Source/DoxygenTranslator/src/DoxygenEntity.h     | 10 +++++++---
 Source/DoxygenTranslator/src/DoxygenParser.cpp   | 11 +++++++++++
 Source/DoxygenTranslator/src/DoxygenParser.h     | 11 +++++++++++
 .../DoxygenTranslator/src/DoxygenTranslator.cpp  | 10 +++++++---
 Source/DoxygenTranslator/src/DoxygenTranslator.h |  8 ++++++--
 .../src/Examples/DoxygenTransWTokenizer.cpp      | 16 +++++++++++++---
 .../src/Examples/DoxygenTransWTokenizer.h        | 11 +++++++++++
 .../DoxygenTranslator/src/Examples/translator.h  | 11 +++++++++++
 .../DoxygenTranslator/src/JavaDocConverter.cpp   | 11 +++++++++++
 Source/DoxygenTranslator/src/JavaDocConverter.h  |  8 ++++++--
 Source/DoxygenTranslator/src/PyDocConverter.cpp  | 10 +++++++---
 Source/DoxygenTranslator/src/PyDocConverter.h    |  8 ++++++--
 Source/DoxygenTranslator/src/Token.cpp           | 11 +++++++++++
 Source/DoxygenTranslator/src/Token.h             | 11 +++++++++++
 Source/DoxygenTranslator/src/TokenList.cpp       | 11 +++++++++++
 Source/DoxygenTranslator/src/TokenList.h         | 11 +++++++++++
 Source/Swig/warn.c                               |  8 ++++++--
 18 files changed, 165 insertions(+), 24 deletions(-)

diff --git a/Source/DoxygenTranslator/src/DoxygenEntity.cpp b/Source/DoxygenTranslator/src/DoxygenEntity.cpp
index f770dc514..dc49c803e 100644
--- a/Source/DoxygenTranslator/src/DoxygenEntity.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenEntity.cpp
@@ -1,8 +1,12 @@
-/* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+/* ----------------------------------------------------------------------------- 
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
- * python.cxx
+ * DoxygenEntity.cpp
  *
  * Part of the Doxygen comment translation module of SWIG.
  * ----------------------------------------------------------------------------- */
diff --git a/Source/DoxygenTranslator/src/DoxygenEntity.h b/Source/DoxygenTranslator/src/DoxygenEntity.h
index ca42393db..dcdba7644 100644
--- a/Source/DoxygenTranslator/src/DoxygenEntity.h
+++ b/Source/DoxygenTranslator/src/DoxygenEntity.h
@@ -1,8 +1,12 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
- * python.cxx
+ * DoxygenEntity.h
  *
  * Part of the Doxygen comment translation module of SWIG.
  * ----------------------------------------------------------------------------- */
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.cpp b/Source/DoxygenTranslator/src/DoxygenParser.cpp
index f4bce5445..030d8bee9 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenParser.cpp
@@ -1,3 +1,14 @@
+/* ----------------------------------------------------------------------------- 
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
+ *
+ * DoxygenParser.cpp
+ * ----------------------------------------------------------------------------- */
+
 #include "DoxygenParser.h"
 #include "TokenList.h"
 
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.h b/Source/DoxygenTranslator/src/DoxygenParser.h
index c298a92f3..0c1f2d1cb 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.h
+++ b/Source/DoxygenTranslator/src/DoxygenParser.h
@@ -1,3 +1,14 @@
+/* -----------------------------------------------------------------------------
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
+ *
+ * DoxygenParser.h
+ * ----------------------------------------------------------------------------- */
+
 #ifndef DOXYGENPARSER_H_
 #define DOXYGENPARSER_H_
 #include <string>
diff --git a/Source/DoxygenTranslator/src/DoxygenTranslator.cpp b/Source/DoxygenTranslator/src/DoxygenTranslator.cpp
index 6fe97d298..36ca95579 100644
--- a/Source/DoxygenTranslator/src/DoxygenTranslator.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenTranslator.cpp
@@ -1,6 +1,10 @@
-/* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+/* ----------------------------------------------------------------------------- 
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * DoxygenTranslator.cpp
  *
diff --git a/Source/DoxygenTranslator/src/DoxygenTranslator.h b/Source/DoxygenTranslator/src/DoxygenTranslator.h
index 566b1551d..1a14a4db2 100644
--- a/Source/DoxygenTranslator/src/DoxygenTranslator.h
+++ b/Source/DoxygenTranslator/src/DoxygenTranslator.h
@@ -1,6 +1,10 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * DoxygenTranslator.h
  *
diff --git a/Source/DoxygenTranslator/src/Examples/DoxygenTransWTokenizer.cpp b/Source/DoxygenTranslator/src/Examples/DoxygenTransWTokenizer.cpp
index 930141c97..dd803b75f 100644
--- a/Source/DoxygenTranslator/src/Examples/DoxygenTransWTokenizer.cpp
+++ b/Source/DoxygenTranslator/src/Examples/DoxygenTransWTokenizer.cpp
@@ -1,6 +1,16 @@
-/* The main class for translating blobs of Doxygen for SWIG
- * by Cheryl Foil, mentor Olly Betts, for Google's Summer of Code Program
- */
+/* ----------------------------------------------------------------------------- 
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
+ *
+ * DoxygenTransWTokenizer.cpp
+ *
+ * The main class for translating blobs of Doxygen for SWIG
+ * ----------------------------------------------------------------------------- */
+
 //TODO DOH instead of STL?
 //TODO Most commands are not fully implemented
 
diff --git a/Source/DoxygenTranslator/src/Examples/DoxygenTransWTokenizer.h b/Source/DoxygenTranslator/src/Examples/DoxygenTransWTokenizer.h
index fb3181d25..8a51b4d02 100644
--- a/Source/DoxygenTranslator/src/Examples/DoxygenTransWTokenizer.h
+++ b/Source/DoxygenTranslator/src/Examples/DoxygenTransWTokenizer.h
@@ -1,3 +1,14 @@
+/* -----------------------------------------------------------------------------
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
+ *
+ * DoxygenTransWTokenizer.h
+ * ----------------------------------------------------------------------------- */
+
 #ifndef DOXYGENTRANSWTOKENIZER_H_
 #define DOXYGENTRANSWTOKENIZER_H_
 
diff --git a/Source/DoxygenTranslator/src/Examples/translator.h b/Source/DoxygenTranslator/src/Examples/translator.h
index 0ae58f714..f9da98180 100644
--- a/Source/DoxygenTranslator/src/Examples/translator.h
+++ b/Source/DoxygenTranslator/src/Examples/translator.h
@@ -1,3 +1,14 @@
+/* -----------------------------------------------------------------------------
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
+ *
+ * translator.h
+ * ----------------------------------------------------------------------------- */
+
 #ifndef TRANSLATOR_H_
 #define TRANSLATOR_H_
 
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.cpp b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
index 9de2f99f3..8cca8b3a5 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
@@ -1,3 +1,14 @@
+/* ----------------------------------------------------------------------------- 
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
+ *
+ * JavaDocConverter.cpp
+ * ----------------------------------------------------------------------------- */
+
 #include "JavaDocConverter.h"
 #include "DoxygenParser.h"
 #include <iostream>
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.h b/Source/DoxygenTranslator/src/JavaDocConverter.h
index d898265ba..69fc8d75d 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.h
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.h
@@ -1,6 +1,10 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * JavaDocConverter.h
  *
diff --git a/Source/DoxygenTranslator/src/PyDocConverter.cpp b/Source/DoxygenTranslator/src/PyDocConverter.cpp
index cbe81571b..3b305b9fd 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/PyDocConverter.cpp
@@ -1,6 +1,10 @@
-/* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+/* ----------------------------------------------------------------------------- 
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * PyDocConverter.cpp
  *
diff --git a/Source/DoxygenTranslator/src/PyDocConverter.h b/Source/DoxygenTranslator/src/PyDocConverter.h
index 5680480fc..ecd033af5 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.h
+++ b/Source/DoxygenTranslator/src/PyDocConverter.h
@@ -1,6 +1,10 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * PyDocConverter.h
  *
diff --git a/Source/DoxygenTranslator/src/Token.cpp b/Source/DoxygenTranslator/src/Token.cpp
index f7c02b021..6ade97163 100644
--- a/Source/DoxygenTranslator/src/Token.cpp
+++ b/Source/DoxygenTranslator/src/Token.cpp
@@ -1,3 +1,14 @@
+/* ----------------------------------------------------------------------------- 
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
+ *
+ * Token.cpp
+ * ----------------------------------------------------------------------------- */
+
 #include "Token.h"
 #include "DoxygenEntity.h"
 using namespace std;
diff --git a/Source/DoxygenTranslator/src/Token.h b/Source/DoxygenTranslator/src/Token.h
index 4ae44b65f..6e10fd338 100644
--- a/Source/DoxygenTranslator/src/Token.h
+++ b/Source/DoxygenTranslator/src/Token.h
@@ -1,3 +1,14 @@
+/* -----------------------------------------------------------------------------
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
+ *
+ * Token.h
+ * ----------------------------------------------------------------------------- */
+
 #ifndef TOKEN_H_
 #define TOKEN_H_
 #include <string>
diff --git a/Source/DoxygenTranslator/src/TokenList.cpp b/Source/DoxygenTranslator/src/TokenList.cpp
index 8eeef97b2..5e13fe164 100644
--- a/Source/DoxygenTranslator/src/TokenList.cpp
+++ b/Source/DoxygenTranslator/src/TokenList.cpp
@@ -1,3 +1,14 @@
+/* ----------------------------------------------------------------------------- 
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
+ *
+ * TokenList.cpp
+ * ----------------------------------------------------------------------------- */
+
 #include "TokenList.h"
 #include <cstdlib>
 #include <iostream>
diff --git a/Source/DoxygenTranslator/src/TokenList.h b/Source/DoxygenTranslator/src/TokenList.h
index 841d66e1a..057f67ed4 100644
--- a/Source/DoxygenTranslator/src/TokenList.h
+++ b/Source/DoxygenTranslator/src/TokenList.h
@@ -1,3 +1,14 @@
+/* -----------------------------------------------------------------------------
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
+ *
+ * TokenList.h
+ * ----------------------------------------------------------------------------- */
+
 #ifndef TOKENLIST_H_
 #define TOKENLIST_H_
 #include <cstdlib>
diff --git a/Source/Swig/warn.c b/Source/Swig/warn.c
index a8dadc70b..b01815354 100644
--- a/Source/Swig/warn.c
+++ b/Source/Swig/warn.c
@@ -1,6 +1,10 @@
 /* ----------------------------------------------------------------------------- 
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
+ * This file is part of SWIG, which is licensed as a whole under version 3 
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
  *
  * warn.c
  *

From d590621eae215b6be8eb11d22dd59e74b69b3f38 Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Tue, 8 May 2012 19:48:49 +0000
Subject: [PATCH 044/314] Added myself to the COPYRIGHT

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13050 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 COPYRIGHT | 1 +
 1 file changed, 1 insertion(+)

diff --git a/COPYRIGHT b/COPYRIGHT
index 2fe0099b8..dc61d89b4 100644
--- a/COPYRIGHT
+++ b/COPYRIGHT
@@ -19,6 +19,7 @@ Active SWIG Developers:
 
 Past SWIG developers and major contributors include:
  Dave Beazley (dave-swig@dabeaz.com)                    (SWIG core, Python, Tcl, Perl)
+ Dmitry Kabak (userdima@gmail.com)                      (Doxygen)
  Henning Thielemann (swig@henning-thielemann.de)        (Modula3)
  Matthias Köppe (mkoeppe@mail.math.uni-magdeburg.de)    (Guile, MzScheme)
  Luigi Ballabio (luigi.ballabio@fastwebnet.it)          (STL wrapping)

From ce39e74f28286e104ae0caff9d78d2cafb11e369 Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Mon, 28 May 2012 19:47:03 +0000
Subject: [PATCH 045/314] Applied Christopher Mangiardi's patch that fixes
 incorrect comment placement in python single line functions

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13133 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Source/Modules/python.cxx | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/Source/Modules/python.cxx b/Source/Modules/python.cxx
index d3d652eb0..c47f695aa 100644
--- a/Source/Modules/python.cxx
+++ b/Source/Modules/python.cxx
@@ -3979,7 +3979,7 @@ public:
 	  if (!have_addtofunc(n)) {
 	    if (!fastproxy || olddefs) {
 	      Printv(f_shadow, tab4, "def ", symname, "(", parms, ")", returnTypeAnnotation(n), ":", NIL);
-	      Printv(f_shadow, " return ", funcCall(fullname, callParms), "\n", NIL);
+	      Printv(f_shadow, "\n", NIL);
 	      if (doxygen) {
 		String *doxygen_comments;
 		if (DoxygenTranslator::getDocumentation(n, PyDoc, doxygen_comments)) {
@@ -3987,6 +3987,7 @@ public:
 		  Delete(doxygen_comments);
 		}
 	      }
+	      Printv(f_shadow, tab8, "return ", funcCall(fullname, callParms), "\n", NIL);
 	    }
 	  } else {
 	    Printv(f_shadow, tab4, "def ", symname, "(", parms, ")", returnTypeAnnotation(n), ":", NIL);

From 744d59c9d000444606cf043947bf829d100f802f Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Sun, 3 Jun 2012 16:40:31 +0000
Subject: [PATCH 046/314] Small documentation fix in Doxygen.html

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13141 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Doc/Manual/Doxygen.html | 44 +++++++++++++++++++++++++++++++++++++----
 1 file changed, 40 insertions(+), 4 deletions(-)

diff --git a/Doc/Manual/Doxygen.html b/Doc/Manual/Doxygen.html
index 54161eeb3..989fb0dc4 100644
--- a/Doc/Manual/Doxygen.html
+++ b/Doc/Manual/Doxygen.html
@@ -36,7 +36,7 @@
 
 <p>
 This chapter describes SWIG's support for translating Doxygen comments found in interface and header files into a target language's normal documentation language.
-Currently only JavaDoc is supported.
+Currently only JavaDoc and PythonDoc is supported.
 </p>
 
 <H2><a name="Doxygen_translation_overview"></a>35.1 Doxygen Translation Overview</H2>
@@ -45,11 +45,11 @@ Currently only JavaDoc is supported.
 <p>
 The Doxygen Translation Module of SWIG is an ongoing effort from a <A HREF ="http://code.google.com/soc/2008/">Google Summer of Code</A> proposal from Summer 2008.
 It adds an extra layer of functionality to SWIG, allowing automated translation of <A HREF= "http://www.stack.nl/~dimitri/doxygen/">Doxygen</A> formatted comments from input files into a documentation language more suited for the target language.
-Currently this module only translates into JavaDoc for the SWIG Java Module, but other extensions are to be added in time.
+Currently this module only translates into JavaDoc and PythonDoc for the SWIG Java and Python Modules, but other extensions are to be added in time.
 </p>
 
 <p>
-Questions about running SWIG are best answered in the <a href="SWIG.html#SWIG">SWIG Basics</a> chapter as well as the target language modules. (For now, only <A href = "Java.html">Java</A>).
+Questions about running SWIG are best answered in the <a href="SWIG.html#SWIG">SWIG Basics</a> chapter as well as the target language modules. (For now, only <A href = "Java.html">Java</A> and <A href = "Python.html">Python</A>).
 The behaviour of this functionality is wildly unpredictable if the interface file is not proper to begin with!
 </p>
 
@@ -72,7 +72,43 @@ class Shape {
 </pre></div>
 
 <p>
-Because this functionality is currently only extended to Java, you must be able to run SWIG's <A href = "Java.html">Java Module</A> in order to make use of this tool.
+Please note, as SWIG parses input file by itself with strict grammar, there is only a limited support for various cases of comment placement in the file.
+Comments can be placed between two C expressions on separate lines:
+</p>
+
+<div class="code"><pre>
+void someOtherFunction();
+/**
+ * Some comment
+ */
+void someFunction();
+</pre></div>
+
+<p>
+and in some special cases, like function parameter comments:
+</p>
+
+<div class="code"><pre>
+void someFunction(
+         int a ///< Some parameter 
+     );
+</pre></div>
+
+<p>
+or enum element comments:
+</p>
+
+<div class="code"><pre>
+enum E_NUMBERS
+{
+    EN_ZERO, ///< The first enum item, gets zero as it's value
+    EN_ONE, ///< The second, EN_ONE=1
+    EN_THREE
+};
+</pre></div>
+
+<p>
+Just remember, if SWIG shows syntax error parsing the file because of your comment, try to move it in some other, 'safer' place as desribed above.
 </p>
 <H3><a name="Doxygen_running_swig"></a>35.2.1 Enabling Doxygen Translation</H3>
 

From ac6b51f13e02dc137f639c6465d227eee7442e08 Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Mon, 4 Jun 2012 18:02:51 +0000
Subject: [PATCH 047/314] Fix to include comment for non-member functions in
 python

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13149 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Source/Modules/python.cxx | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/Source/Modules/python.cxx b/Source/Modules/python.cxx
index c47f695aa..f0f6d0671 100644
--- a/Source/Modules/python.cxx
+++ b/Source/Modules/python.cxx
@@ -1780,6 +1780,13 @@ public:
     String *callParms = make_pyParmList(n, false, true, kw);
     /* Make a wrapper function to insert the code into */
     Printv(f_dest, "\ndef ", name, "(", parms, ")", returnTypeAnnotation(n), ":\n", NIL);
+    if (doxygen) {
+      String *doxygen_comments;
+      if (DoxygenTranslator::getDocumentation(n, PyDoc, doxygen_comments)) {
+	Printf(f_dest, Char(pythoncode(doxygen_comments, tab2)));
+	Delete(doxygen_comments);
+      }
+    }
     if (have_docstring(n))
       Printv(f_dest, "  ", docstring(n, AUTODOC_FUNC, tab4), "\n", NIL);
     if (have_pythonprepend(n))

From e3f41f32a6096f8f8273fb4ba4ca610050f16961 Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Mon, 4 Jun 2012 18:11:29 +0000
Subject: [PATCH 048/314] Added test case to check Doxygen comments parsing,
 including java and python runtime tests

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13150 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Examples/test-suite/common.mk                 |  1 +
 Examples/test-suite/doxygen_parsing.i         | 84 +++++++++++++++++
 Examples/test-suite/java/Makefile.in          |  4 +-
 .../java/doxygen_parsing_runme.java           | 89 +++++++++++++++++++
 .../python/doxygen_parsing_runme.py           | 19 ++++
 5 files changed, 195 insertions(+), 2 deletions(-)
 create mode 100644 Examples/test-suite/doxygen_parsing.i
 create mode 100644 Examples/test-suite/java/doxygen_parsing_runme.java
 create mode 100644 Examples/test-suite/python/doxygen_parsing_runme.py

diff --git a/Examples/test-suite/common.mk b/Examples/test-suite/common.mk
index 7cc410e7a..ec47ffaa0 100644
--- a/Examples/test-suite/common.mk
+++ b/Examples/test-suite/common.mk
@@ -187,6 +187,7 @@ CPP_TEST_CASES += \
 	director_using \
 	director_wombat \
 	disown \
+	doxygen_parsing \
 	dynamic_cast \
 	empty \
 	enum_rename \
diff --git a/Examples/test-suite/doxygen_parsing.i b/Examples/test-suite/doxygen_parsing.i
new file mode 100644
index 000000000..20781cfa8
--- /dev/null
+++ b/Examples/test-suite/doxygen_parsing.i
@@ -0,0 +1,84 @@
+%module doxygen_parsing
+
+%inline %{
+
+/**
+ * This is simple comment for a var
+ */
+int simpleVar=42;
+/*!
+ * This is another type of comment for a var
+ */
+int simpleVarTwo=42;
+
+/// This is again another type of comment for a var
+int simpleVarThree=42;
+//! This is the last type of comment for a var
+int simpleVarFour=42;
+
+/*
+  We assume that all this comment types are ok,
+  and later we only use the first-type comments.
+*/
+
+
+/**
+ * This is simple comment for a function
+ */
+void simpleFunction(int arg)
+{
+}
+
+/**
+ * This is simple comment for a class
+ */
+class CSimpleClass
+{
+private:
+  /** Some member var */
+  int simpleVar;
+
+public:
+  /** 
+   * Simple method
+   */
+  void simpleMethod(int asd)
+  {
+  }
+  /**
+   * Simple method with parameter
+   */
+  void simpleMethodWithParameter(
+	int param /**< Some test param */
+	)
+  {
+  }
+};
+
+/** Test enumeration */
+enum E_TEST
+{
+  /** the first item */
+  E_TEST_ONE,
+  E_TEST_TWO = 2, /**< the second */
+  E_TEST_THREE = 2+1
+};
+
+/**
+ * Comment for template class
+ */
+template <typename T>
+class CTemplateClass
+{
+public:
+  /**
+   * Template method
+   */
+  void templateMethod(T arg)
+  {
+  }
+};
+
+%}
+
+%template(CTemplateClassInt) CTemplateClass<int>;
\ No newline at end of file
diff --git a/Examples/test-suite/java/Makefile.in b/Examples/test-suite/java/Makefile.in
index ef3c981a4..813232620 100644
--- a/Examples/test-suite/java/Makefile.in
+++ b/Examples/test-suite/java/Makefile.in
@@ -79,8 +79,8 @@ setup = \
 run_testcase = \
 	cd $(JAVA_PACKAGE) && $(COMPILETOOL) $(JAVAC) -classpath . `find . -name "*.java"` && cd .. && \
 	if [ -f $(srcdir)/$(SCRIPTPREFIX)$*$(SCRIPTSUFFIX) ]; then \
-	  $(COMPILETOOL) $(JAVAC) -classpath . -d . $(srcdir)/$(SCRIPTPREFIX)$*$(SCRIPTSUFFIX) && \
-	  env LD_LIBRARY_PATH="$(JAVA_PACKAGE):$$LD_LIBRARY_PATH" PATH="$(JAVA_PACKAGE):$$PATH" SHLIB_PATH="$(JAVA_PACKAGE):$$SHLIB_PATH" DYLD_LIBRARY_PATH="$(JAVA_PACKAGE):$$DYLD_LIBRARY_PATH" $(RUNTOOL) $(JAVA) $(JAVAFLAGS) -classpath . $*_runme; \
+	  $(COMPILETOOL) $(JAVAC) -classpath $(JAVA_HOME)/lib/tools.jar:. -d . $(srcdir)/$(SCRIPTPREFIX)$*$(SCRIPTSUFFIX) && \
+	  env LD_LIBRARY_PATH="$(JAVA_PACKAGE):$$LD_LIBRARY_PATH" PATH="$(JAVA_PACKAGE):$$PATH" SHLIB_PATH="$(JAVA_PACKAGE):$$SHLIB_PATH" DYLD_LIBRARY_PATH="$(JAVA_PACKAGE):$$DYLD_LIBRARY_PATH" $(RUNTOOL) $(JAVA) $(JAVAFLAGS) -classpath $(JAVA_HOME)/lib/tools.jar:. $*_runme; \
 	fi
 
 # Clean: remove testcase directories
diff --git a/Examples/test-suite/java/doxygen_parsing_runme.java b/Examples/test-suite/java/doxygen_parsing_runme.java
new file mode 100644
index 000000000..c4264d003
--- /dev/null
+++ b/Examples/test-suite/java/doxygen_parsing_runme.java
@@ -0,0 +1,89 @@
+
+import doxygen_parsing.*;
+import com.sun.javadoc.*;
+import java.util.HashMap;
+import java.util.Map.Entry;
+import java.util.Iterator;
+
+public class doxygen_parsing_runme {
+  static {
+    try {
+      System.loadLibrary("doxygen_parsing");
+    } catch (UnsatisfiedLinkError e) {
+      System.err.println("Native code library failed to load. See the chapter on Dynamic Linking Problems in the SWIG Java documentation for help.\n" + e);
+      System.exit(1);
+    }
+  }
+
+  static HashMap<String, String> parsedComments = new HashMap<String, String>();
+  static HashMap<String, String> wantedComments = new HashMap<String, String>();
+
+  public static boolean start(RootDoc root) {
+    
+    /*
+      This method is called by 'javadoc' and gets the whole parsed
+      java file, we get comments and store them
+    */
+
+    ClassDoc[] classes = root.classes();
+
+    for (int i = 0; i < classes.length; i++) {
+
+      if (classes[i].getRawCommentText().length() > 0)
+	parsedComments.put(classes[i].name(), classes[i].getRawCommentText());
+
+      MethodDoc[] methods = classes[i].methods();
+      for (int j = 0; j < methods.length; j++) {
+        MethodDoc m = methods[j];
+	if (m.getRawCommentText().length() > 0)
+	  parsedComments.put(m.name(), m.getRawCommentText());
+      }
+    }
+    return true;
+  }
+
+  public static void main(String argv[]) 
+  {
+    /*
+      Here we are using internal javadoc tool, it accepts the name of the class as paramterer,
+      and calls the start() method of that class with parsed information.
+    */
+    com.sun.tools.javadoc.Main.execute("doxygen_parsing runtime test",
+	"doxygen_parsing_runme", new String[]{"-quiet", "doxygen_parsing"});
+
+    wantedComments.put("simpleFunction", " This is simple comment for a function  \n");
+
+    wantedComments.put("CSimpleClass", " This is simple comment for a class  \n");
+    wantedComments.put("simpleMethod", " Simple method  \n");
+    wantedComments.put("simpleMethodWithParameter", " Simple method with parameter  \n @param\tparam Some test param  \n");
+    wantedComments.put("CTemplateClassInt", " Comment for template class  \n");
+    wantedComments.put("templateMethod", " Template method  \n");
+
+    wantedComments.put("setSimpleVar", " This is simple comment for a var  \n");
+    wantedComments.put("getSimpleVar", " This is simple comment for a var  \n");
+    wantedComments.put("setSimpleVarTwo", " This is another type of comment for a var  \n");
+    wantedComments.put("getSimpleVarTwo", " This is another type of comment for a var  \n");
+    wantedComments.put("setSimpleVarThree", " This is again another type of comment for a var  \n");
+    wantedComments.put("getSimpleVarThree", " This is again another type of comment for a var  \n");
+    wantedComments.put("setSimpleVarFour", " This is the last type of comment for a var  \n");
+    wantedComments.put("getSimpleVarFour", " This is the last type of comment for a var  \n");
+
+
+    int errorCount=0;
+    Iterator< Entry<String, String> > it = parsedComments.entrySet().iterator();
+
+    while (it.hasNext())
+    {
+	Entry<String, String> e = (Entry<String, String>) it.next();
+
+	if (!e.getValue().equals(wantedComments.get(e.getKey()))) {
+	    System.out.println("Documentation comments for " + e.getKey() + " does not match: ");
+	    System.out.println("\texpected:"+wantedComments.get(e.getKey()));
+	    System.out.println("\tgot:\t"+e.getValue());
+	    errorCount++;
+	}
+    }
+
+    System.exit(errorCount);
+  }
+}
diff --git a/Examples/test-suite/python/doxygen_parsing_runme.py b/Examples/test-suite/python/doxygen_parsing_runme.py
new file mode 100644
index 000000000..eef840818
--- /dev/null
+++ b/Examples/test-suite/python/doxygen_parsing_runme.py
@@ -0,0 +1,19 @@
+#!/usr/bin/python
+
+import doxygen_parsing
+import sys
+import re
+
+def check(got, expected):
+  if not re.match(str(expected), str(got)):
+    raise RuntimeError("\n" + "Expected: [" + str(expected) + "]\n" + "Got     : [" + str(got) + "]")
+
+check(doxygen_parsing.simpleFunction.__doc__, '\s+This is simple comment for a function\s+')
+check(doxygen_parsing.CSimpleClass.__doc__, '\s+This is simple comment for a class\s+')
+check(doxygen_parsing.CSimpleClass.simpleMethod.__doc__, '\s+Simple method\s+')
+check(doxygen_parsing.CSimpleClass.simpleMethodWithParameter.__doc__, ''
+'\s+Simple method with parameter'
+'\s+Arguments:\s+param \(int\)\s+-- Some test param\s+'
+)
+check(doxygen_parsing.CTemplateClassInt.__doc__, '\s+Comment for template class\s+')
+check(doxygen_parsing.CTemplateClassInt.templateMethod.__doc__, '\s+Template method\s+')
\ No newline at end of file

From b0f8e594c98d56abda1a461212466b72ace351e5 Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Mon, 18 Jun 2012 18:30:18 +0000
Subject: [PATCH 049/314] Implement toggling comment parsing feature on and off

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13182 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Source/CParse/cparse.h   |  1 +
 Source/CParse/cscanner.c | 23 ++++++++++++++---------
 Source/CParse/parser.y   |  3 +--
 3 files changed, 16 insertions(+), 11 deletions(-)

diff --git a/Source/CParse/cparse.h b/Source/CParse/cparse.h
index 922bbfcdc..895118363 100644
--- a/Source/CParse/cparse.h
+++ b/Source/CParse/cparse.h
@@ -26,6 +26,7 @@ extern "C" {
   extern int cparse_line;
   extern int cparse_cplusplus;
   extern int cparse_start_line;
+  extern int scan_doxygen_comments;
 
   extern void Swig_cparse_cplusplus(int);
   extern void scanner_file(File *);
diff --git a/Source/CParse/cscanner.c b/Source/CParse/cscanner.c
index 66a570a95..44af1069b 100644
--- a/Source/CParse/cscanner.c
+++ b/Source/CParse/cscanner.c
@@ -46,6 +46,9 @@ static int last_brace = 0;
 static int last_id = 0;
 static int rename_active = 0;
 
+/* Doxygen comments scanning */
+int scan_doxygen_comments = 1;
+
 /* -----------------------------------------------------------------------------
  * Swig_cparse_cplusplus()
  * ----------------------------------------------------------------------------- */
@@ -337,15 +340,17 @@ static int yylook(void) {
 	if ((strncmp(loc,"/*@SWIG",7) == 0) && (loc[Len(cmt)-3] == '@')) {
 	  Scanner_locator(scan, cmt);
 	}
-	if (strncmp(loc, "/**<", 4) == 0 || strncmp(loc, "///<", 4) == 0||strncmp(loc, "/*!<", 4) == 0||strncmp(loc, "//!<", 4) == 0) {
-	  /* printf("Doxygen Post Comment: %s lines %d-%d [%s]\n", Char(Scanner_file(scan)), Scanner_start_line(scan), Scanner_line(scan), loc); */
-	  yylval.str =  NewString(loc);
-	  return DOXYGENPOSTSTRING;
-	}
-	if (strncmp(loc, "/**", 3) == 0 || strncmp(loc, "///", 3) == 0||strncmp(loc, "/*!", 3) == 0||strncmp(loc, "//!", 3) == 0) {
-	  /* printf("Doxygen Comment: %s lines %d-%d [%s]\n", Char(Scanner_file(scan)), Scanner_start_line(scan), Scanner_line(scan), loc);  */
-	  yylval.str =  NewString(loc);
-	  return DOXYGENSTRING;
+	if (scan_doxygen_comments) { /* else just skip this node, to avoid crashes in parser module*/
+	  if (strncmp(loc, "/**<", 4) == 0 || strncmp(loc, "///<", 4) == 0||strncmp(loc, "/*!<", 4) == 0||strncmp(loc, "//!<", 4) == 0) {
+	    /* printf("Doxygen Post Comment: %s lines %d-%d [%s]\n", Char(Scanner_file(scan)), Scanner_start_line(scan), Scanner_line(scan), loc); */
+	    yylval.str =  NewString(loc);
+	    return DOXYGENPOSTSTRING;
+	  }
+	  if (strncmp(loc, "/**", 3) == 0 || strncmp(loc, "///", 3) == 0||strncmp(loc, "/*!", 3) == 0||strncmp(loc, "//!", 3) == 0) {
+	    /* printf("Doxygen Comment: %s lines %d-%d [%s]\n", Char(Scanner_file(scan)), Scanner_start_line(scan), Scanner_line(scan), loc);  */
+	    yylval.str =  NewString(loc);
+	    return DOXYGENSTRING;
+	  }
 	}
       }
       break;
diff --git a/Source/CParse/parser.y b/Source/CParse/parser.y
index 39028cfe7..ffba04884 100644
--- a/Source/CParse/parser.y
+++ b/Source/CParse/parser.y
@@ -63,7 +63,6 @@ static Node   **class_decl = NULL;
 /* -----------------------------------------------------------------------------
  *                            Doxygen Comment Globals and Assist Functions
  * ----------------------------------------------------------------------------- */
-int parseComments = 1; /* set this to activate Doxygen uptake into the parse tree */
 String *currentComment; /* Location of the stored Doxygen Comment */
 String *currentPostComment; /* Location of the stored Doxygen Post-Comment */
 String *currentCComment; /* Location of the stored C Comment */
@@ -107,7 +106,7 @@ static Node *new_node(const_String_or_char_ptr tag) {
   set_nodeType(n,tag);
   Setfile(n,cparse_file);
   Setline(n,cparse_line);
-  if(parseComments){
+  if(scan_doxygen_comments){
     /* Sets any post comments to the previous node */
     if(previousNode != NULL && currentPostComment != 0){
       String *copyPostComment = Copy(currentPostComment);

From 72b23954fb58b89083045ae562420dcd59472c44 Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Mon, 18 Jun 2012 18:33:30 +0000
Subject: [PATCH 050/314] Fix integration of doxygen with autodoc feature,
 fixed autodoc test and some code refactored

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13183 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Examples/test-suite/python/autodoc_runme.py   |  6 +-
 .../DoxygenTranslator/src/PyDocConverter.cpp  |  2 +-
 Source/Modules/python.cxx                     | 67 ++++++++-----------
 3 files changed, 32 insertions(+), 43 deletions(-)

diff --git a/Examples/test-suite/python/autodoc_runme.py b/Examples/test-suite/python/autodoc_runme.py
index dc843ae96..b0359f2e0 100644
--- a/Examples/test-suite/python/autodoc_runme.py
+++ b/Examples/test-suite/python/autodoc_runme.py
@@ -165,9 +165,9 @@ check(F.__init__.__doc__, "\n"
 check(B.funk.__doc__, "funk(B self, int c, int d) -> int")
 check(funk.__doc__, "funk(A e, short arg2, int c, int d) -> int")
 check(funkdefaults.__doc__, "\n"
-"    funkdefaults(A e, short arg2, int c, int d, double f=2) -> int\n"
-"    funkdefaults(A e, short arg2, int c, int d) -> int\n"
-"    "
+"  funkdefaults(A e, short arg2, int c, int d, double f=2) -> int\n"
+"  funkdefaults(A e, short arg2, int c, int d) -> int\n"
+"  "
 )
 
 check(func_input.__doc__, "func_input(int * INPUT) -> int")
diff --git a/Source/DoxygenTranslator/src/PyDocConverter.cpp b/Source/DoxygenTranslator/src/PyDocConverter.cpp
index 3b305b9fd..55c3ba61b 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/PyDocConverter.cpp
@@ -193,7 +193,7 @@ bool PyDocConverter::getDocumentation(Node *n, String *&documentation) {
 
   // if we got something log the result and construct DOH string to return
   if (pyDocString.length()) {
-    result = "\"\"\"\n" + pyDocString + "\"\"\"\n";
+    result = pyDocString;
 
     if (debug) {
       std::cout << "\n---RESULT IN PYDOC---" << std::endl;
diff --git a/Source/Modules/python.cxx b/Source/Modules/python.cxx
index f0f6d0671..07437715d 100644
--- a/Source/Modules/python.cxx
+++ b/Source/Modules/python.cxx
@@ -21,6 +21,7 @@ static int treduce = SWIG_cparse_template_reduce(0);
 #include <ctype.h>
 #include <sstream>
 #include "../DoxygenTranslator/src/DoxygenTranslator.h"
+#include "../../../swig/bug.h"
 
 #define PYSHADOW_MEMBER  0x2
 #define WARN_PYTHON_MULTIPLE_INH 405
@@ -120,7 +121,7 @@ Python Options (available with -python)\n\
      -classptr       - Generate shadow 'ClassPtr' as in older swig versions\n\
      -cppcast        - Enable C++ casting operators (default) \n\
      -dirvtable      - Generate a pseudo virtual table for directors for faster dispatch \n\
-	 -doxygen		 - Convert C++ doxygen comments to pydoc comments in proxy classes \n\
+     -doxygen        - Convert C++ doxygen comments to pydoc comments in proxy classes (default) \n\
      -extranative    - Return extra native C++ wraps for std containers when possible \n\
      -fastinit       - Use fast init mechanism for classes (default)\n\
      -fastunpack     - Use fast unpack mechanism to parse the argument functions \n\
@@ -139,6 +140,7 @@ static const char *usage2 = (char *) "\
      -nocastmode     - Disable the casting mode (default)\n\
      -nocppcast      - Disable C++ casting operators, useful for generating bugs\n\
      -nodirvtable    - Don't use the virtual table feature, resolve the python method each time (default)\n\
+     -nodoxygen      - Don't convert C++ doxygen comments to pydoc comments in proxy classes \n\
      -noexcept       - No automatic exception handling\n\
      -noextranative  - Don't use extra native C++ wraps for std containers when possible (default) \n\
      -nofastinit     - Use traditional init mechanism for classes \n\
@@ -418,12 +420,17 @@ public:
 	} else if (strcmp(argv[i], "-dirvtable") == 0) {
 	  dirvtable = 1;
 	  Swig_mark_arg(i);
-	} else if (strcmp(argv[i], "-doxygen") == 0) {
-	  doxygen = 1;
-	  Swig_mark_arg(i);
 	} else if (strcmp(argv[i], "-nodirvtable") == 0) {
 	  dirvtable = 0;
 	  Swig_mark_arg(i);
+	} else if (strcmp(argv[i], "-doxygen") == 0) {
+	  doxygen = 1;
+	  scan_doxygen_comments = 1;
+	  Swig_mark_arg(i);
+	} else if (strcmp(argv[i], "-nodoxygen") == 0) {
+	  doxygen = 0;
+	  scan_doxygen_comments = 0;
+	  Swig_mark_arg(i);
 	} else if (strcmp(argv[i], "-fastunpack") == 0) {
 	  fastunpack = 1;
 	  Swig_mark_arg(i);
@@ -1194,7 +1201,10 @@ public:
 
   bool have_docstring(Node *n) {
     String *str = Getattr(n, "feature:docstring");
-    return (str && Len(str) > 0) || (Getattr(n, "feature:autodoc") && !GetFlag(n, "feature:noautodoc"));
+    return ((str && Len(str) > 0)
+	|| (Getattr(n, "feature:autodoc") && !GetFlag(n, "feature:noautodoc"))
+	|| (doxygen && Getattr(n, "DoxygenComment"))
+      );
   }
 
   /* ------------------------------------------------------------
@@ -1206,8 +1216,10 @@ public:
 
   String *docstring(Node *n, autodoc_t ad_type, const String *indent, bool use_triple = true) {
     String *str = Getattr(n, "feature:docstring");
+    String *doxygen_comment = 0;
     bool have_ds = (str && Len(str) > 0);
     bool have_auto = (Getattr(n, "feature:autodoc") && !GetFlag(n, "feature:noautodoc"));
+    bool have_doxygen = doxygen && DoxygenTranslator::getDocumentation(n, PyDoc, doxygen_comment);
     const char *triple_double = use_triple ? "\"\"\"" : "";
     String *autodoc = NULL;
     String *doc = NULL;
@@ -1224,6 +1236,9 @@ public:
       autodoc = make_autodoc(n, ad_type);
       have_auto = (autodoc && Len(autodoc) > 0);
     }
+    if (have_doxygen) {
+      have_doxygen = (doxygen_comment && Len(doxygen_comment) > 0);
+    }
     // If there is more than one line then make docstrings like this:
     //
     //      """
@@ -1250,7 +1265,11 @@ public:
 	doc = NewString("");
 	Printv(doc, triple_double, "\n", pythoncode(autodoc, indent), indent, triple_double, NIL);
       }
-    } else
+    } else if (have_doxygen) { // the lowest priority
+      doc = NewString("");
+      Printv(doc, triple_double, "\n", pythoncode(doxygen_comment, indent), indent, triple_double, NIL);
+    }
+    else
       doc = NewString("");
 
     // Save the generated strings in the parse tree in case they are used later
@@ -1780,15 +1799,8 @@ public:
     String *callParms = make_pyParmList(n, false, true, kw);
     /* Make a wrapper function to insert the code into */
     Printv(f_dest, "\ndef ", name, "(", parms, ")", returnTypeAnnotation(n), ":\n", NIL);
-    if (doxygen) {
-      String *doxygen_comments;
-      if (DoxygenTranslator::getDocumentation(n, PyDoc, doxygen_comments)) {
-	Printf(f_dest, Char(pythoncode(doxygen_comments, tab2)));
-	Delete(doxygen_comments);
-      }
-    }
     if (have_docstring(n))
-      Printv(f_dest, "  ", docstring(n, AUTODOC_FUNC, tab4), "\n", NIL);
+      Printv(f_dest, "  ", docstring(n, AUTODOC_FUNC, tab2), "\n", NIL);
     if (have_pythonprepend(n))
       Printv(f_dest, pythoncode(pythonprepend(n), "  "), "\n", NIL);
     if (have_pythonappend(n)) {
@@ -3700,16 +3712,7 @@ public:
 
 	Printf(f_shadow, ":\n");
 
-	// translate and write pydoc comment if flagged
-	if (doxygen){
-	  String *doxygen_comments;
-	  if(DoxygenTranslator::getDocumentation(n, PyDoc, doxygen_comments)){
-	    Printf(f_shadow, Char(pythoncode(doxygen_comments, shadow_indent))); 
-	    Delete(doxygen_comments);
-	  }
-	}
-
-	// otherwise use default docstrings if requested
+	// write docstrings if requested
 	if (have_docstring(n)) {
 	  String *str = docstring(n, AUTODOC_CLASS, tab4);
 	  if (str && Len(str))
@@ -3987,26 +3990,12 @@ public:
 	    if (!fastproxy || olddefs) {
 	      Printv(f_shadow, tab4, "def ", symname, "(", parms, ")", returnTypeAnnotation(n), ":", NIL);
 	      Printv(f_shadow, "\n", NIL);
-	      if (doxygen) {
-		String *doxygen_comments;
-		if (DoxygenTranslator::getDocumentation(n, PyDoc, doxygen_comments)) {
-		  Printf(f_shadow, Char(pythoncode(doxygen_comments, tab8))); 
-		  Delete(doxygen_comments);
-		}
-	      }
 	      Printv(f_shadow, tab8, "return ", funcCall(fullname, callParms), "\n", NIL);
 	    }
 	  } else {
 	    Printv(f_shadow, tab4, "def ", symname, "(", parms, ")", returnTypeAnnotation(n), ":", NIL);
 	    Printv(f_shadow, "\n", NIL);
-	    if (doxygen) {
-	      String *doxygen_comments;
-	      if(DoxygenTranslator::getDocumentation(n, PyDoc, doxygen_comments)){
-		Printf(f_shadow, Char(pythoncode(doxygen_comments, tab8))); 
-		Delete(doxygen_comments);
-	      }
-	    }
-	    else if (have_docstring(n))
+	    if (have_docstring(n))
 	      Printv(f_shadow, tab8, docstring(n, AUTODOC_METHOD, tab8), "\n", NIL);
 	    if (have_pythonprepend(n)) {
 	      fproxy = 0;

From b88de2aa89f297b0c9bda42843836e3cab39f84b Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Mon, 18 Jun 2012 19:13:23 +0000
Subject: [PATCH 051/314] Fixed enum comments generation, added testcases

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13184 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Examples/test-suite/doxygen_parsing.i         |  9 --
 Examples/test-suite/doxygen_parsing_enums.i   | 15 +++
 .../test-suite/doxygen_parsing_enums_proper.i |  7 ++
 .../test-suite/doxygen_parsing_enums_simple.i |  6 ++
 .../doxygen_parsing_enums_typesafe.i          |  8 ++
 .../doxygen_parsing_enums_typeunsafe.i        |  6 ++
 Examples/test-suite/java/Makefile.in          |  4 +
 .../doxygen_parsing_enums_proper_runme.java   | 93 +++++++++++++++++++
 .../doxygen_parsing_enums_simple_runme.java   | 93 +++++++++++++++++++
 .../doxygen_parsing_enums_typesafe_runme.java | 93 +++++++++++++++++++
 ...oxygen_parsing_enums_typeunsafe_runme.java | 93 +++++++++++++++++++
 .../java/doxygen_parsing_runme.java           | 18 ++++
 .../src/JavaDocConverter.cpp                  |  2 +-
 Source/Modules/java.cxx                       | 68 +++++++-------
 14 files changed, 470 insertions(+), 45 deletions(-)
 create mode 100644 Examples/test-suite/doxygen_parsing_enums.i
 create mode 100644 Examples/test-suite/doxygen_parsing_enums_proper.i
 create mode 100644 Examples/test-suite/doxygen_parsing_enums_simple.i
 create mode 100644 Examples/test-suite/doxygen_parsing_enums_typesafe.i
 create mode 100644 Examples/test-suite/doxygen_parsing_enums_typeunsafe.i
 create mode 100644 Examples/test-suite/java/doxygen_parsing_enums_proper_runme.java
 create mode 100644 Examples/test-suite/java/doxygen_parsing_enums_simple_runme.java
 create mode 100644 Examples/test-suite/java/doxygen_parsing_enums_typesafe_runme.java
 create mode 100644 Examples/test-suite/java/doxygen_parsing_enums_typeunsafe_runme.java

diff --git a/Examples/test-suite/doxygen_parsing.i b/Examples/test-suite/doxygen_parsing.i
index 20781cfa8..b61317bcd 100644
--- a/Examples/test-suite/doxygen_parsing.i
+++ b/Examples/test-suite/doxygen_parsing.i
@@ -55,15 +55,6 @@ public:
   }
 };
 
-/** Test enumeration */
-enum E_TEST
-{
-  /** the first item */
-  E_TEST_ONE,
-  E_TEST_TWO = 2, /**< the second */
-  E_TEST_THREE = 2+1
-};
-
 /**
  * Comment for template class
  */
diff --git a/Examples/test-suite/doxygen_parsing_enums.i b/Examples/test-suite/doxygen_parsing_enums.i
new file mode 100644
index 000000000..317abf384
--- /dev/null
+++ b/Examples/test-suite/doxygen_parsing_enums.i
@@ -0,0 +1,15 @@
+%module doxygen_parsing_enums
+
+%inline %{
+
+
+/** Test enumeration */
+enum E_TEST
+{
+  /** the first item */
+  E_TEST_ONE,
+  E_TEST_TWO = 2, /**< the second */
+  E_TEST_THREE = 2+1
+};
+
+%}
\ No newline at end of file
diff --git a/Examples/test-suite/doxygen_parsing_enums_proper.i b/Examples/test-suite/doxygen_parsing_enums_proper.i
new file mode 100644
index 000000000..1a69a84f1
--- /dev/null
+++ b/Examples/test-suite/doxygen_parsing_enums_proper.i
@@ -0,0 +1,7 @@
+%module "doxygen_parsing_enums_proper"
+
+// Test enum commenting using the proper enums in the target language
+%include "enums.swg"
+
+%include "doxygen_parsing_enums.i"
+
diff --git a/Examples/test-suite/doxygen_parsing_enums_simple.i b/Examples/test-suite/doxygen_parsing_enums_simple.i
new file mode 100644
index 000000000..823a27584
--- /dev/null
+++ b/Examples/test-suite/doxygen_parsing_enums_simple.i
@@ -0,0 +1,6 @@
+%module "doxygen_parsing_enums_simple"
+
+// Test enum commenting using simple constants (SWIG-1.3.21 and earlier default enum wrapping for C# and Java)
+%include "enumsimple.swg"
+
+%include "doxygen_parsing_enums.i"
\ No newline at end of file
diff --git a/Examples/test-suite/doxygen_parsing_enums_typesafe.i b/Examples/test-suite/doxygen_parsing_enums_typesafe.i
new file mode 100644
index 000000000..25e355ee2
--- /dev/null
+++ b/Examples/test-suite/doxygen_parsing_enums_typesafe.i
@@ -0,0 +1,8 @@
+%module "doxygen_parsing_enums_typesafe"
+
+// Test enum commenting using the typesafe enum pattern in the target language
+%include "enumtypesafe.swg"
+
+#define SWIG_TEST_NOCSCONST // For C# typesafe enums
+
+%include "doxygen_parsing_enums.i"
\ No newline at end of file
diff --git a/Examples/test-suite/doxygen_parsing_enums_typeunsafe.i b/Examples/test-suite/doxygen_parsing_enums_typeunsafe.i
new file mode 100644
index 000000000..e001035df
--- /dev/null
+++ b/Examples/test-suite/doxygen_parsing_enums_typeunsafe.i
@@ -0,0 +1,6 @@
+%module "doxygen_parsing_enums_typeunsafe"
+
+// Test enum commenting using a type unsafe enum pattern (constant integers in a class for the enum type)
+%include "enumtypeunsafe.swg"
+
+%include "doxygen_parsing_enums.i"
\ No newline at end of file
diff --git a/Examples/test-suite/java/Makefile.in b/Examples/test-suite/java/Makefile.in
index 813232620..3cb9d0c23 100644
--- a/Examples/test-suite/java/Makefile.in
+++ b/Examples/test-suite/java/Makefile.in
@@ -16,6 +16,10 @@ C_TEST_CASES = \
 	java_lib_various
 
 CPP_TEST_CASES = \
+	doxygen_parsing_enums_simple \
+	doxygen_parsing_enums_proper \
+	doxygen_parsing_enums_typesafe \
+	doxygen_parsing_enums_typeunsafe \
 	enum_thorough_proper \
 	enum_thorough_simple \
 	enum_thorough_typeunsafe \
diff --git a/Examples/test-suite/java/doxygen_parsing_enums_proper_runme.java b/Examples/test-suite/java/doxygen_parsing_enums_proper_runme.java
new file mode 100644
index 000000000..503e2c68e
--- /dev/null
+++ b/Examples/test-suite/java/doxygen_parsing_enums_proper_runme.java
@@ -0,0 +1,93 @@
+
+import doxygen_parsing_enums_proper.*;
+import com.sun.javadoc.*;
+import java.util.HashMap;
+import java.util.Map.Entry;
+import java.util.Iterator;
+
+public class doxygen_parsing_enums_proper_runme {
+  static {
+    try {
+      System.loadLibrary("doxygen_parsing_enums_proper");
+    } catch (UnsatisfiedLinkError e) {
+      System.err.println("Native code library failed to load. See the chapter on Dynamic Linking Problems in the SWIG Java documentation for help.\n" + e);
+      System.exit(1);
+    }
+  }
+
+  static HashMap<String, String> parsedComments = new HashMap<String, String>();
+  static HashMap<String, String> wantedComments = new HashMap<String, String>();
+
+  public static boolean start(RootDoc root) {
+    
+    /*
+      This method is called by 'javadoc' and gets the whole parsed
+      java file, we get comments and store them
+    */
+
+    ClassDoc[] classes = root.classes();
+
+    for (int i = 0; i < classes.length; i++) {
+
+      if (classes[i].getRawCommentText().length() > 0)
+	parsedComments.put(classes[i].name(), classes[i].getRawCommentText());
+
+      MethodDoc[] methods = classes[i].methods();
+      FieldDoc[] fields = classes[i].fields();
+      FieldDoc[] constants = classes[i].enumConstants();
+
+      for (int j = 0; j < constants.length; j++) {
+        FieldDoc f = constants[j];
+	if (f.getRawCommentText().length() > 0)
+	  parsedComments.put(f.name(), f.getRawCommentText());
+      }
+      for (int j = 0; j < fields.length; j++) {
+        FieldDoc f = fields[j];
+	if (f.getRawCommentText().length() > 0)
+	  parsedComments.put(f.name(), f.getRawCommentText());
+      }
+      for (int j = 0; j < methods.length; j++) {
+        MethodDoc m = methods[j];
+	if (m.getRawCommentText().length() > 0)
+	  parsedComments.put(m.name(), m.getRawCommentText());
+      }
+    }
+    return true;
+  }
+
+  public static void main(String argv[]) 
+  {
+    /*
+      Here we are using internal javadoc tool, it accepts the name of the class as paramterer,
+      and calls the start() method of that class with parsed information.
+    */
+    com.sun.tools.javadoc.Main.execute("doxygen_parsing_enums_proper runtime test",
+	"doxygen_parsing_enums_proper_runme", new String[]{"-quiet", "doxygen_parsing_enums_proper"});
+
+    wantedComments.put("E_TEST", " Test enumeration  \n");
+    wantedComments.put("E_TEST_ONE", " the first item  \n");
+    wantedComments.put("E_TEST_TWO", " the second  \n");
+
+    int errorCount=0;
+    Iterator< Entry<String, String> > it = parsedComments.entrySet().iterator();
+
+    while (it.hasNext())
+    {
+	Entry<String, String> e = (Entry<String, String>) it.next();
+
+	if (!e.getValue().equals(wantedComments.get(e.getKey()))) {
+	    System.out.println("Documentation comments for " + e.getKey() + " does not match: ");
+	    System.out.println("\texpected:"+wantedComments.get(e.getKey()));
+	    System.out.println("\tgot:\t"+e.getValue());
+	    errorCount++;
+	}
+    }
+
+    if (parsedComments.size() != wantedComments.size()) {
+	System.out.println("Found " + (wantedComments.size()-parsedComments.size()) + " missed comment(s)!");
+	errorCount++;
+    }
+
+    System.exit(errorCount);
+  }
+}
diff --git a/Examples/test-suite/java/doxygen_parsing_enums_simple_runme.java b/Examples/test-suite/java/doxygen_parsing_enums_simple_runme.java
new file mode 100644
index 000000000..ca640b3f0
--- /dev/null
+++ b/Examples/test-suite/java/doxygen_parsing_enums_simple_runme.java
@@ -0,0 +1,93 @@
+
+import doxygen_parsing_enums_simple.*;
+import com.sun.javadoc.*;
+import java.util.HashMap;
+import java.util.Map.Entry;
+import java.util.Iterator;
+
+public class doxygen_parsing_enums_simple_runme {
+  static {
+    try {
+      System.loadLibrary("doxygen_parsing_enums_simple");
+    } catch (UnsatisfiedLinkError e) {
+      System.err.println("Native code library failed to load. See the chapter on Dynamic Linking Problems in the SWIG Java documentation for help.\n" + e);
+      System.exit(1);
+    }
+  }
+
+  static HashMap<String, String> parsedComments = new HashMap<String, String>();
+  static HashMap<String, String> wantedComments = new HashMap<String, String>();
+
+  public static boolean start(RootDoc root) {
+    
+    /*
+      This method is called by 'javadoc' and gets the whole parsed
+      java file, we get comments and store them
+    */
+
+    ClassDoc[] classes = root.classes();
+
+    for (int i = 0; i < classes.length; i++) {
+
+      if (classes[i].getRawCommentText().length() > 0)
+	parsedComments.put(classes[i].name(), classes[i].getRawCommentText());
+
+      MethodDoc[] methods = classes[i].methods();
+      FieldDoc[] fields = classes[i].fields();
+      FieldDoc[] constants = classes[i].enumConstants();
+
+      for (int j = 0; j < constants.length; j++) {
+        FieldDoc f = constants[j];
+	if (f.getRawCommentText().length() > 0)
+	  parsedComments.put(f.name(), f.getRawCommentText());
+      }
+      for (int j = 0; j < fields.length; j++) {
+        FieldDoc f = fields[j];
+	if (f.getRawCommentText().length() > 0)
+	  parsedComments.put(f.name(), f.getRawCommentText());
+      }
+      for (int j = 0; j < methods.length; j++) {
+        MethodDoc m = methods[j];
+	if (m.getRawCommentText().length() > 0)
+	  parsedComments.put(m.name(), m.getRawCommentText());
+      }
+    }
+    return true;
+  }
+
+  public static void main(String argv[]) 
+  {
+    /*
+      Here we are using internal javadoc tool, it accepts the name of the class as paramterer,
+      and calls the start() method of that class with parsed information.
+    */
+    com.sun.tools.javadoc.Main.execute("doxygen_parsing_enums_simple runtime test",
+	"doxygen_parsing_enums_simple_runme", new String[]{"-quiet", "doxygen_parsing_enums_simple"});
+
+    wantedComments.put("E_TEST", " Test enumeration  \n");
+    wantedComments.put("E_TEST_ONE", " the first item  \n");
+    wantedComments.put("E_TEST_TWO", " the second  \n");
+
+    int errorCount=0;
+    Iterator< Entry<String, String> > it = parsedComments.entrySet().iterator();
+
+    while (it.hasNext())
+    {
+	Entry<String, String> e = (Entry<String, String>) it.next();
+
+	if (!e.getValue().equals(wantedComments.get(e.getKey()))) {
+	    System.out.println("Documentation comments for " + e.getKey() + " does not match: ");
+	    System.out.println("\texpected:"+wantedComments.get(e.getKey()));
+	    System.out.println("\tgot:\t"+e.getValue());
+	    errorCount++;
+	}
+    }
+
+    if (parsedComments.size() != wantedComments.size()) {
+	System.out.println("Found " + (wantedComments.size()-parsedComments.size()) + " missed comment(s)!");
+	errorCount++;
+    }
+
+    System.exit(errorCount);
+  }
+}
diff --git a/Examples/test-suite/java/doxygen_parsing_enums_typesafe_runme.java b/Examples/test-suite/java/doxygen_parsing_enums_typesafe_runme.java
new file mode 100644
index 000000000..8d87c82d0
--- /dev/null
+++ b/Examples/test-suite/java/doxygen_parsing_enums_typesafe_runme.java
@@ -0,0 +1,93 @@
+
+import doxygen_parsing_enums_typesafe.*;
+import com.sun.javadoc.*;
+import java.util.HashMap;
+import java.util.Map.Entry;
+import java.util.Iterator;
+
+public class doxygen_parsing_enums_typesafe_runme {
+  static {
+    try {
+      System.loadLibrary("doxygen_parsing_enums_typesafe");
+    } catch (UnsatisfiedLinkError e) {
+      System.err.println("Native code library failed to load. See the chapter on Dynamic Linking Problems in the SWIG Java documentation for help.\n" + e);
+      System.exit(1);
+    }
+  }
+
+  static HashMap<String, String> parsedComments = new HashMap<String, String>();
+  static HashMap<String, String> wantedComments = new HashMap<String, String>();
+
+  public static boolean start(RootDoc root) {
+    
+    /*
+      This method is called by 'javadoc' and gets the whole parsed
+      java file, we get comments and store them
+    */
+
+    ClassDoc[] classes = root.classes();
+
+    for (int i = 0; i < classes.length; i++) {
+
+      if (classes[i].getRawCommentText().length() > 0)
+	parsedComments.put(classes[i].name(), classes[i].getRawCommentText());
+
+      MethodDoc[] methods = classes[i].methods();
+      FieldDoc[] fields = classes[i].fields();
+      FieldDoc[] constants = classes[i].enumConstants();
+
+      for (int j = 0; j < constants.length; j++) {
+        FieldDoc f = constants[j];
+	if (f.getRawCommentText().length() > 0)
+	  parsedComments.put(f.name(), f.getRawCommentText());
+      }
+      for (int j = 0; j < fields.length; j++) {
+        FieldDoc f = fields[j];
+	if (f.getRawCommentText().length() > 0)
+	  parsedComments.put(f.name(), f.getRawCommentText());
+      }
+      for (int j = 0; j < methods.length; j++) {
+        MethodDoc m = methods[j];
+	if (m.getRawCommentText().length() > 0)
+	  parsedComments.put(m.name(), m.getRawCommentText());
+      }
+    }
+    return true;
+  }
+
+  public static void main(String argv[]) 
+  {
+    /*
+      Here we are using internal javadoc tool, it accepts the name of the class as paramterer,
+      and calls the start() method of that class with parsed information.
+    */
+    com.sun.tools.javadoc.Main.execute("doxygen_parsing_enums_typesafe runtime test",
+	"doxygen_parsing_enums_typesafe_runme", new String[]{"-quiet", "doxygen_parsing_enums_typesafe"});
+
+    wantedComments.put("E_TEST", " Test enumeration  \n");
+    wantedComments.put("E_TEST_ONE", " the first item  \n");
+    wantedComments.put("E_TEST_TWO", " the second  \n");
+
+    int errorCount=0;
+    Iterator< Entry<String, String> > it = parsedComments.entrySet().iterator();
+
+    while (it.hasNext())
+    {
+	Entry<String, String> e = (Entry<String, String>) it.next();
+
+	if (!e.getValue().equals(wantedComments.get(e.getKey()))) {
+	    System.out.println("Documentation comments for " + e.getKey() + " does not match: ");
+	    System.out.println("\texpected:"+wantedComments.get(e.getKey()));
+	    System.out.println("\tgot:\t"+e.getValue());
+	    errorCount++;
+	}
+    }
+
+    if (parsedComments.size() != wantedComments.size()) {
+	System.out.println("Found " + (wantedComments.size()-parsedComments.size()) + " missed comment(s)!");
+	errorCount++;
+    }
+
+    System.exit(errorCount);
+  }
+}
diff --git a/Examples/test-suite/java/doxygen_parsing_enums_typeunsafe_runme.java b/Examples/test-suite/java/doxygen_parsing_enums_typeunsafe_runme.java
new file mode 100644
index 000000000..a01007db1
--- /dev/null
+++ b/Examples/test-suite/java/doxygen_parsing_enums_typeunsafe_runme.java
@@ -0,0 +1,93 @@
+
+import doxygen_parsing_enums_typeunsafe.*;
+import com.sun.javadoc.*;
+import java.util.HashMap;
+import java.util.Map.Entry;
+import java.util.Iterator;
+
+public class doxygen_parsing_enums_typeunsafe_runme {
+  static {
+    try {
+      System.loadLibrary("doxygen_parsing_enums_typeunsafe");
+    } catch (UnsatisfiedLinkError e) {
+      System.err.println("Native code library failed to load. See the chapter on Dynamic Linking Problems in the SWIG Java documentation for help.\n" + e);
+      System.exit(1);
+    }
+  }
+
+  static HashMap<String, String> parsedComments = new HashMap<String, String>();
+  static HashMap<String, String> wantedComments = new HashMap<String, String>();
+
+  public static boolean start(RootDoc root) {
+    
+    /*
+      This method is called by 'javadoc' and gets the whole parsed
+      java file, we get comments and store them
+    */
+
+    ClassDoc[] classes = root.classes();
+
+    for (int i = 0; i < classes.length; i++) {
+
+      if (classes[i].getRawCommentText().length() > 0)
+	parsedComments.put(classes[i].name(), classes[i].getRawCommentText());
+
+      MethodDoc[] methods = classes[i].methods();
+      FieldDoc[] fields = classes[i].fields();
+      FieldDoc[] constants = classes[i].enumConstants();
+
+      for (int j = 0; j < constants.length; j++) {
+        FieldDoc f = constants[j];
+	if (f.getRawCommentText().length() > 0)
+	  parsedComments.put(f.name(), f.getRawCommentText());
+      }
+      for (int j = 0; j < fields.length; j++) {
+        FieldDoc f = fields[j];
+	if (f.getRawCommentText().length() > 0)
+	  parsedComments.put(f.name(), f.getRawCommentText());
+      }
+      for (int j = 0; j < methods.length; j++) {
+        MethodDoc m = methods[j];
+	if (m.getRawCommentText().length() > 0)
+	  parsedComments.put(m.name(), m.getRawCommentText());
+      }
+    }
+    return true;
+  }
+
+  public static void main(String argv[]) 
+  {
+    /*
+      Here we are using internal javadoc tool, it accepts the name of the class as paramterer,
+      and calls the start() method of that class with parsed information.
+    */
+    com.sun.tools.javadoc.Main.execute("doxygen_parsing_enums_typeunsafe runtime test",
+	"doxygen_parsing_enums_typeunsafe_runme", new String[]{"-quiet", "doxygen_parsing_enums_typeunsafe"});
+
+    wantedComments.put("E_TEST", " Test enumeration  \n");
+    wantedComments.put("E_TEST_ONE", " the first item  \n");
+    wantedComments.put("E_TEST_TWO", " the second  \n");
+
+    int errorCount=0;
+    Iterator< Entry<String, String> > it = parsedComments.entrySet().iterator();
+
+    while (it.hasNext())
+    {
+	Entry<String, String> e = (Entry<String, String>) it.next();
+
+	if (!e.getValue().equals(wantedComments.get(e.getKey()))) {
+	    System.out.println("Documentation comments for " + e.getKey() + " does not match: ");
+	    System.out.println("\texpected:"+wantedComments.get(e.getKey()));
+	    System.out.println("\tgot:\t"+e.getValue());
+	    errorCount++;
+	}
+    }
+
+    if (parsedComments.size() != wantedComments.size()) {
+	System.out.println("Found " + (wantedComments.size()-parsedComments.size()) + " missed comment(s)!");
+	errorCount++;
+    }
+
+    System.exit(errorCount);
+  }
+}
diff --git a/Examples/test-suite/java/doxygen_parsing_runme.java b/Examples/test-suite/java/doxygen_parsing_runme.java
index c4264d003..fe4b75fa5 100644
--- a/Examples/test-suite/java/doxygen_parsing_runme.java
+++ b/Examples/test-suite/java/doxygen_parsing_runme.java
@@ -33,6 +33,19 @@ public class doxygen_parsing_runme {
 	parsedComments.put(classes[i].name(), classes[i].getRawCommentText());
 
       MethodDoc[] methods = classes[i].methods();
+      FieldDoc[] fields = classes[i].fields();
+      FieldDoc[] constants = classes[i].enumConstants();
+
+      for (int j = 0; j < constants.length; j++) {
+        FieldDoc f = constants[j];
+	if (f.getRawCommentText().length() > 0)
+	  parsedComments.put(f.name(), f.getRawCommentText());
+      }
+      for (int j = 0; j < fields.length; j++) {
+        FieldDoc f = fields[j];
+	if (f.getRawCommentText().length() > 0)
+	  parsedComments.put(f.name(), f.getRawCommentText());
+      }
       for (int j = 0; j < methods.length; j++) {
         MethodDoc m = methods[j];
 	if (m.getRawCommentText().length() > 0)
@@ -84,6 +97,11 @@ public class doxygen_parsing_runme {
 	}
     }
 
+    if (parsedComments.size() != wantedComments.size()) {
+	System.out.println("Found " + (wantedComments.size()-parsedComments.size()) + " missed comment(s)!");
+	errorCount++;
+    }
+
     System.exit(errorCount);
   }
 }
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.cpp b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
index 8cca8b3a5..23f8c6d3e 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
@@ -13,7 +13,7 @@
 #include "DoxygenParser.h"
 #include <iostream>
 #define APPROX_LINE_LENGTH 64	//characters per line allowed
-#define TAB_SIZE 8		//characters per line allowed
+#define TAB_SIZE 8		//current tab size in spaces
 int printSortedTree2 = 0;
 //TODO {@link} {@linkplain} {@docRoot}, and other useful doxy commands that are not a javadoc tag
 
diff --git a/Source/Modules/java.cxx b/Source/Modules/java.cxx
index bfde4f19a..8455fbbf6 100644
--- a/Source/Modules/java.cxx
+++ b/Source/Modules/java.cxx
@@ -49,7 +49,7 @@ class JAVA:public Language {
   bool global_variable_flag;	// Flag for when wrapping a global variable
   bool old_variable_names;	// Flag for old style variable names in the intermediary class
   bool member_func_flag;	// flag set when wrapping a member function
-  bool doxygen_javadoc_flag; //flag for converting found doxygen to javadoc
+  bool doxygen;			//flag for converting found doxygen to javadoc
   bool comment_creation_chatter; //flag for getting information about where comments were created in java.cxx
   
   String *imclass_name;		// intermediary class name
@@ -123,7 +123,7 @@ public:
       global_variable_flag(false),
       old_variable_names(false),
       member_func_flag(false),
-      doxygen_javadoc_flag(true),
+      doxygen(true),
       comment_creation_chatter(false),
       imclass_name(NULL),
       module_class_name(NULL),
@@ -255,6 +255,14 @@ public:
 	  Printf(stderr, "Deprecated command line option: %s. Proxy classes are now generated by default.\n", argv[i]);
 	  Swig_mark_arg(i);
 	  proxy_flag = true;
+	} else if ((strcmp(argv[i], "-doxygen") == 0)) {
+	  Swig_mark_arg(i);
+	  doxygen = true;
+	  scan_doxygen_comments = true;
+	} else if ((strcmp(argv[i], "-nodoxygen") == 0)) {
+	  Swig_mark_arg(i);
+	  doxygen = false;
+	  scan_doxygen_comments = false;
 	} else if ((strcmp(argv[i], "-noproxy") == 0)) {
 	  Swig_mark_arg(i);
 	  proxy_flag = false;
@@ -528,7 +536,7 @@ public:
       // Start writing out the module class file
       emitBanner(f_module);
       //Add any structural comments to the top
-      if(doxygen_javadoc_flag && structuralComments){
+      if(doxygen && structuralComments){
     	  Printf(f_module, "%s", structuralComments);
       }
       if (package)
@@ -537,7 +545,7 @@ public:
       if (module_imports)
 	Printf(f_module, "%s\n", module_imports);
       
-      if (doxygen_javadoc_flag){
+      if (doxygen){
 	String *doxygen_comments;
 	if(DoxygenTranslator::getDocumentation(n, JavaDoc,doxygen_comments)){
 	  if(comment_creation_chatter)
@@ -1292,17 +1300,6 @@ public:
 	  // Add extra indentation
 	  Replaceall(enum_code, "\n", "\n  ");
 	  Replaceall(enum_code, "  \n", "\n");
-	  
-	  //translate and write javadoc comment if flagged
-	  if (doxygen_javadoc_flag){
-	    String *doxygen_comments;
-	    if(DoxygenTranslator::getDocumentation(n, JavaDoc,doxygen_comments)){
-	      if(comment_creation_chatter)
-		Printf(proxy_class_constants_code, "/* This was generated from enumvalueDeclaration() */");
-	      Printf(proxy_class_constants_code, Char(doxygen_comments)); 
-	      Delete(doxygen_comments);
-	    }
-	  }
 	    
 	  Printv(proxy_class_constants_code, "  ", enum_code, "\n\n", NIL);
 	} else {
@@ -1418,30 +1415,29 @@ public:
       }
       if (!addSymbol(name, n, scope))
 	return SWIG_ERROR;
+      
+      //translate and write javadoc comment if flagged
+      if (doxygen){
+	String *doxygen_comments;
+	if(DoxygenTranslator::getDocumentation(n, JavaDoc, doxygen_comments)){
+	  if(comment_creation_chatter)
+	    Printf(enum_code, "/* This was generated from enumvalueDeclaration() */");
+	  Printf(enum_code, Char(doxygen_comments)); 
+	  Delete(doxygen_comments);
+	}
+      }
 
       if ((enum_feature == ProperEnum) && parent_name && !unnamedinstance) {
 	// Wrap (non-anonymous) C/C++ enum with a proper Java enum
 	// Emit the enum item.
-	if (!GetFlag(n, "firstenumitem"))
-	  Printf(enum_code, ",\n");
-
-    //translate and write javadoc comment if flagged
-    if (doxygen_javadoc_flag){
-      String *doxygen_comments;
-      if(DoxygenTranslator::getDocumentation(n, JavaDoc,doxygen_comments)){
-	if(comment_creation_chatter)
-	  Printf(enum_code, "/* This was generated from enumvalueDeclaration() */");
-	Printf(enum_code, Char(doxygen_comments)); 
-	Delete(doxygen_comments);
-      }
-    }
-
+	
 	Printf(enum_code, "  %s", symname);
 	if (Getattr(n, "enumvalue")) {
 	  String *value = enumValue(n);
 	  Printf(enum_code, "(%s)", value);
 	  Delete(value);
 	}
+	Printf(enum_code, ",\n");
       } else {
 	// Wrap C/C++ enums with constant integers or use the typesafe enum pattern
 	SwigType *typemap_lookup_type = parent_name ? parent_name : NewString("enum ");
@@ -1493,7 +1489,7 @@ public:
    * file
    * ------------------------------------------------------------------------ */
   virtual int doxygenComment(Node *n){
-    if (doxygen_javadoc_flag){
+    if (doxygen){
       String *doxygen_comments;
       if(DoxygenTranslator::getDocumentation(n, JavaDoc, doxygen_comments)){
 	if(comment_creation_chatter)
@@ -1527,7 +1523,7 @@ public:
     Swig_save("constantWrapper", n, "value", NIL);
 
     //translate and write javadoc comment if flagged
-    if (doxygen_javadoc_flag){
+    if (doxygen){
       String *doxygen_comments;
       if(DoxygenTranslator::getDocumentation(n, JavaDoc, doxygen_comments)){
 	if(comment_creation_chatter)
@@ -1825,7 +1821,7 @@ public:
     const String *pure_interfaces = typemapLookup(n, "javainterfaces", typemap_lookup_type, WARN_NONE);
     
     //translate and write javadoc comment if flagged
-    if (doxygen_javadoc_flag){
+    if (doxygen){
       String *doxygen_comments;
       if(DoxygenTranslator::getDocumentation(n, JavaDoc, doxygen_comments)){
 	if(comment_creation_chatter)
@@ -2231,7 +2227,7 @@ public:
     }
     
     //translate and write javadoc comment if flagged
-    if (doxygen_javadoc_flag){
+    if (doxygen){
       String *doxygen_comments;
       if(DoxygenTranslator::getDocumentation(n, JavaDoc, doxygen_comments)){
 	if(comment_creation_chatter)
@@ -2464,7 +2460,7 @@ public:
       Printf(im_return_type, "%s", tm);
       
       //translate and write javadoc comment if flagged
-      if (doxygen_javadoc_flag){
+      if (doxygen){
 	String *doxygen_comments;
 	if(DoxygenTranslator::getDocumentation(n, JavaDoc, doxygen_comments)){
 	  if(comment_creation_chatter)
@@ -2736,7 +2732,7 @@ public:
     String *post_code = NewString("");
     
     // translate and write javadoc comment if flagged
-    if (doxygen_javadoc_flag){
+    if (doxygen){
       String *doxygen_comments;
       if(DoxygenTranslator::getDocumentation(n, JavaDoc, doxygen_comments)) {
 	if(comment_creation_chatter)
@@ -4523,6 +4519,8 @@ extern "C" Language *swig_java(void) {
 
 const char *JAVA::usage = (char *) "\
 Java Options (available with -java)\n\
+     -doxygen        - Convert C++ doxygen comments to JavaDoc comments in proxy classes (default)\n\
+     -nodoxygen      - Don't convert C++ doxygen comments to JavaDoc comments in proxy classes\n\
      -nopgcpp        - Suppress premature garbage collection prevention parameter\n\
      -noproxy        - Generate the low-level functional interface instead\n\
                        of proxy classes\n\

From 4141c9fd8712797401da42be00ad8e7c5bf498c0 Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Mon, 18 Jun 2012 19:31:35 +0000
Subject: [PATCH 052/314] Added doxygen switches doc

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13185 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Doc/Manual/Doxygen.html | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/Doc/Manual/Doxygen.html b/Doc/Manual/Doxygen.html
index 989fb0dc4..d0e837756 100644
--- a/Doc/Manual/Doxygen.html
+++ b/Doc/Manual/Doxygen.html
@@ -114,7 +114,16 @@ Just remember, if SWIG shows syntax error parsing the file because of your comme
 
 
 <p>
-NOT YET ADDED (current development branch has this feature automatically enabled).
+There are switches like '-doxygen' and '-nodoxygen' in every module that supports converting
+documentation comments. The first one is default, so that swig by default produces correct
+proxy files with comments. Some comments in some target languages can be manually overriden by specific
+swig's features, like <i>feature:docstring</i> or <i>feature:autodoc</i>, in this cases doxygen comments
+have lowest priority.
+</p>
+<p>
+Switching off may be needed if swig cannot correctly parse your comments, for example showing <i>Error:
+Syntax error in input(1).</i> message. Then it will just strip out every comment out of the code and
+continue happily.
 </p>
 
 <H3><a name="Doxygen_additional_options"></a>35.2.2 Additional Commandline Options</H3>

From 4289b8e27374bdab773a90b5ab9792f7e659ce45 Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Mon, 25 Jun 2012 15:47:36 +0000
Subject: [PATCH 053/314] Refactored comment translator class, implemented
 result caching

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13191 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 .../src/DoxygenTranslator.cpp                 |  45 ++++--
 .../DoxygenTranslator/src/DoxygenTranslator.h |  42 ++++--
 .../src/JavaDocConverter.cpp                  |  11 +-
 .../DoxygenTranslator/src/JavaDocConverter.h  |   2 +-
 .../DoxygenTranslator/src/PyDocConverter.cpp  |  23 ++--
 Source/DoxygenTranslator/src/PyDocConverter.h |   2 +-
 Source/Modules/java.cxx                       | 128 +++++++++---------
 Source/Modules/lang.cxx                       |   5 +-
 Source/Modules/python.cxx                     |  10 +-
 Source/Modules/swigmod.h                      |   3 +
 10 files changed, 159 insertions(+), 112 deletions(-)

diff --git a/Source/DoxygenTranslator/src/DoxygenTranslator.cpp b/Source/DoxygenTranslator/src/DoxygenTranslator.cpp
index 36ca95579..a733fdbc7 100644
--- a/Source/DoxygenTranslator/src/DoxygenTranslator.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenTranslator.cpp
@@ -13,18 +13,41 @@
  * ----------------------------------------------------------------------------- */
 
 #include "DoxygenTranslator.h"
-#include "JavaDocConverter.h"
-#include "PyDocConverter.h"
 
-bool DoxygenTranslator::getDocumentation(Node *node, DocumentationFormat format, String *&documentation) {
-  switch (format) {
-  case JavaDoc:
-    return JavaDocConverter().getDocumentation(node, documentation);
-  case PyDoc:
-    return PyDocConverter().getDocumentation(node, documentation);
-  default:
-    return false;
-  }
+DoxygenTranslator::DoxygenTranslator() {
+  // Init the cache
+  resultsCache = NewHash();
+}
+DoxygenTranslator::~DoxygenTranslator() {
+  // Clean up the cache
+  Delete(resultsCache);
+}
+
+bool DoxygenTranslator::hasDocumentation(Node *node) {
+  return getDoxygenComment(node);
+}
+
+String *DoxygenTranslator::getDoxygenComment(Node *node) {
+  return Getattr(node, "DoxygenComment");
+}
+
+
+String *DoxygenTranslator::getDocumentation(Node *node) {
+  
+  if (!hasDocumentation(node))
+    return 0;
+  
+  // get from cache
+  String *resultedDocs = Getattr(resultsCache, getDoxygenComment(node));
+  
+  if (resultedDocs)
+    return resultedDocs;
+  
+  // not found in cache, produce it
+  resultedDocs = makeDocumentation(node);
+  Setattr(resultsCache, getDoxygenComment(node), resultedDocs);
+  
+  return resultedDocs;
 }
 
 void DoxygenTranslator::printTree(std::list < DoxygenEntity > &entityList) {
diff --git a/Source/DoxygenTranslator/src/DoxygenTranslator.h b/Source/DoxygenTranslator/src/DoxygenTranslator.h
index 1a14a4db2..023bdac89 100644
--- a/Source/DoxygenTranslator/src/DoxygenTranslator.h
+++ b/Source/DoxygenTranslator/src/DoxygenTranslator.h
@@ -17,16 +17,9 @@
 
 #include "swig.h"
 #include "DoxygenEntity.h"
+#include "DoxygenParser.h"
 #include <list>
 
-/*
- * Describes the availible documentation systems
- * that can be translated to.
- */
-enum DocumentationFormat {
-  JavaDoc = 1,
-  PyDoc = 2
-};
 
 /*
  * A class to translate doxygen comments attacted to parser nodes
@@ -34,20 +27,31 @@ enum DocumentationFormat {
  */
 class DoxygenTranslator {
 public:
+  /*
+   * Constructor
+   */
+  DoxygenTranslator();
   /*
    * Virtual destructor.
    */
-  virtual ~ DoxygenTranslator() {
-  }
+  virtual ~ DoxygenTranslator();
   /*
    * Return the documentation for a given node formated for the correct 
-   * documentation system.
+   * documentation system. The result is cached and translated only once.
    * @param node The node to extract and translate documentation for.
    * @param format The documentation format to output.
    * @param documentation The returned documentation string.
    * @return A bool to indicate if there was documentation to return for the node.
    */
-  static bool getDocumentation(Node *node, DocumentationFormat format, String *&documentation);
+  String *getDocumentation(Node *node);
+  /*
+   * Whether the specified node has comment or not
+   */
+  bool hasDocumentation(Node *node);
+  /*
+   * Get original, Doxygen-format comment string
+   */
+  String *getDoxygenComment(Node *node);
 
 protected:
   /*
@@ -57,12 +61,22 @@ protected:
    * @param documentation The returned documentation string.
    * @return A bool to indicate if there was documentation to return for the node.
    */
-  virtual bool getDocumentation(Node *node, String *&documentation) = 0;
-
+  virtual String *makeDocumentation(Node *node) = 0;
+  
   /*
    * Prints the details of a parsed entity list to stdout (for debugging).
    */
   void printTree(std::list < DoxygenEntity > &entityList);
+  
+  /*
+   * Doxygen parser object
+   */
+  DoxygenParser parser;
+  
+  /*
+   * Cache of translated comments
+   */
+  Hash *resultsCache;
 };
 
 #endif
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.cpp b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
index 23f8c6d3e..812a6c34d 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
@@ -150,12 +150,12 @@ std::string JavaDocConverter::translateEntity(DoxygenEntity & doxyEntity) {
 }
 
 
-bool JavaDocConverter::getDocumentation(Node *node, String *&documentation) {
+String *JavaDocConverter::makeDocumentation(Node *node) {
 
-  documentation = Getattr(node, "DoxygenComment");
+  String *documentation = getDoxygenComment(node);
 
   if (documentation == NULL) {
-    return false;
+    return NULL;
   }
 
   std::list < DoxygenEntity > entityList = DoxygenParser().createTree(Char(documentation));
@@ -181,7 +181,6 @@ bool JavaDocConverter::getDocumentation(Node *node, String *&documentation) {
     std::cout << "\n---RESULT IN JAVADOC---" << std::endl;
     std::cout << javaDocString;
   }
-
-  documentation = NewString(javaDocString.c_str());
-  return true;
+  
+  return NewString(javaDocString.c_str());
 }
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.h b/Source/DoxygenTranslator/src/JavaDocConverter.h
index 69fc8d75d..1d54e2514 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.h
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.h
@@ -23,7 +23,7 @@ class JavaDocConverter : public DoxygenTranslator {
 public:
   JavaDocConverter() : debug(false) {
   }
-  virtual bool getDocumentation(Node *node, String *&documentation);
+  String *makeDocumentation(Node *node);
 
 protected:
   std::string formatCommand(std::string unformattedLine, int indent);
diff --git a/Source/DoxygenTranslator/src/PyDocConverter.cpp b/Source/DoxygenTranslator/src/PyDocConverter.cpp
index 55c3ba61b..b1e94a062 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/PyDocConverter.cpp
@@ -19,7 +19,7 @@
 
 //TODO {@link} {@linkplain} {@docRoot}, and other useful doxy commands that are not a pydoc tag
 PyDocConverter::PyDocConverter() {
-  debug = 1;
+  debug = 0;
 }
 
 std::string PyDocConverter::formatParam(Node *n, DoxygenEntity & doxygenEntity) {
@@ -40,6 +40,8 @@ std::string PyDocConverter::formatParam(Node *n, DoxygenEntity & doxygenEntity)
   std::string paramDescription = justifyString(paramDescriptionEntity.data, DOC_PARAM_STRING_LENGTH);
 
   for (p = plist; p;) {
+    
+    //Swig_print(p, 1);
     if (Char(Getattr(p, "name")) == paramNameEntity.data) {
       std::string name = Char(Swig_name_make(n, 0, Getattr(p, "name"), 0, 0));
       std::string type = Char(Swig_name_make(n, 0, Getattr(p, "type"), 0, 0));
@@ -52,7 +54,12 @@ std::string PyDocConverter::formatParam(Node *n, DoxygenEntity & doxygenEntity)
       result += "-- " + paramDescription.substr(DOC_PARAM_STRING_LENGTH);
       break;
     }
-    p = Getattr(p, "tmap:in") ? Getattr(p, "tmap:in:next") : nextSibling(p);
+    /*
+     * doesn't seem to work always: in some cases (especially for 'self' parameters)
+     * tmap:in is present, but tmap:in:next is not and so this code skips all the parameters
+     */
+    //p = Getattr(p, "tmap:in") ? Getattr(p, "tmap:in:next") : nextSibling(p);
+    p = nextSibling(p);
   }
 
   Delete(plist);
@@ -147,7 +154,8 @@ std::string PyDocConverter::processEntityList(Node *n, std::list < DoxygenEntity
   return result;
 }
 
-bool PyDocConverter::getDocumentation(Node *n, String *&documentation) {
+String *PyDocConverter::makeDocumentation(Node *n) {
+  String *documentation;
   std::string pyDocString, result;
 
   // for overloaded functions we must concat documentation for underlying overloads
@@ -160,7 +168,7 @@ bool PyDocConverter::getDocumentation(Node *n, String *&documentation) {
 
     // for each real method (not a generated overload) append the documentation
     while (n) {
-      documentation = Getattr(n, "DoxygenComment");
+      documentation = getDoxygenComment(n);
       if (!Swig_is_generated_overload(n) && documentation) {
 	std::list < DoxygenEntity > entityList = DoxygenParser().createTree(Char(documentation));
 	allDocumentation.push_back(processEntityList(n, entityList));
@@ -184,7 +192,7 @@ bool PyDocConverter::getDocumentation(Node *n, String *&documentation) {
   }
   // for other nodes just process as normal
   else {
-    documentation = Getattr(n, "DoxygenComment");
+    documentation = getDoxygenComment(n);
     if (documentation != NULL) {
       std::list < DoxygenEntity > entityList = DoxygenParser().createTree(Char(documentation));
       pyDocString = processEntityList(n, entityList);
@@ -201,11 +209,10 @@ bool PyDocConverter::getDocumentation(Node *n, String *&documentation) {
       std::cout << std::endl;
     }
 
-    documentation = NewString(result.c_str());
-    return true;
+    return NewString(result.c_str());
   }
 
-  return false;
+  return 0;
 }
 
 std::string PyDocConverter::generateDivider() {
diff --git a/Source/DoxygenTranslator/src/PyDocConverter.h b/Source/DoxygenTranslator/src/PyDocConverter.h
index ecd033af5..2d910c8f9 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.h
+++ b/Source/DoxygenTranslator/src/PyDocConverter.h
@@ -26,7 +26,7 @@
 class PyDocConverter : public DoxygenTranslator {
 public:
   PyDocConverter();
-  bool getDocumentation(Node *node, String *&documentation);
+  String *makeDocumentation(Node *node);
 
 protected:
 
diff --git a/Source/Modules/java.cxx b/Source/Modules/java.cxx
index 8455fbbf6..2c6e1b08c 100644
--- a/Source/Modules/java.cxx
+++ b/Source/Modules/java.cxx
@@ -17,7 +17,7 @@ char cvsroot_java_cxx[] = "$Id$";
 #include <limits.h>		// for INT_MAX
 #include "cparse.h"
 #include <ctype.h>
-#include "../DoxygenTranslator/src/DoxygenTranslator.h"
+#include "../DoxygenTranslator/src/JavaDocConverter.h"
 
 /* Hash type used for upcalls from C/C++ */
 typedef DOH UpcallData;
@@ -158,11 +158,19 @@ public:
       dmethods_seq(NULL),
       dmethods_table(NULL),
       n_dmethods(0),
-      n_directors(0) {
+      n_directors(0){
     /* for now, multiple inheritance in directors is disabled, this
        should be easy to implement though */
     director_multiple_inheritance = 0;
     director_language = 1;
+    
+    if (doxygen)
+      doxygenTranslator = new JavaDocConverter();
+  }
+  
+  ~JAVA() {
+    if (doxygen)
+      delete doxygenTranslator;
   }
 
   /* -----------------------------------------------------------------------------
@@ -286,6 +294,9 @@ public:
 	}
       }
     }
+    
+    if (doxygen)
+      doxygenTranslator = new JavaDocConverter();
 
     // Add a symbol to the parser for conditional compilation
     Preprocessor_define("SWIGJAVA 1", 0);
@@ -545,14 +556,12 @@ public:
       if (module_imports)
 	Printf(f_module, "%s\n", module_imports);
       
-      if (doxygen){
-	String *doxygen_comments;
-	if(DoxygenTranslator::getDocumentation(n, JavaDoc,doxygen_comments)){
-	  if(comment_creation_chatter)
-	    Printf(f_module, "/* This was generated from top() */");
-	  Printf(f_module, Char(doxygen_comments)); 
-	  Delete(doxygen_comments);
-	}
+      if (doxygen && doxygenTranslator->hasDocumentation(n)){
+	String *doxygen_comments=doxygenTranslator->getDocumentation(n);
+	if(comment_creation_chatter)
+	  Printf(f_module, "/* This was generated from top() */");
+	Printf(f_module, Char(doxygen_comments)); 
+	Delete(doxygen_comments);
       }
       if (Len(module_class_modifiers) > 0)
 	Printf(f_module, "%s ", module_class_modifiers);
@@ -1417,14 +1426,12 @@ public:
 	return SWIG_ERROR;
       
       //translate and write javadoc comment if flagged
-      if (doxygen){
-	String *doxygen_comments;
-	if(DoxygenTranslator::getDocumentation(n, JavaDoc, doxygen_comments)){
-	  if(comment_creation_chatter)
-	    Printf(enum_code, "/* This was generated from enumvalueDeclaration() */");
-	  Printf(enum_code, Char(doxygen_comments)); 
-	  Delete(doxygen_comments);
-	}
+      if (doxygen && doxygenTranslator->hasDocumentation(n)){
+	String *doxygen_comments=doxygenTranslator->getDocumentation(n);
+	if(comment_creation_chatter)
+	  Printf(enum_code, "/* This was generated from enumvalueDeclaration() */");
+	Printf(enum_code, Char(doxygen_comments)); 
+	Delete(doxygen_comments);
       }
 
       if ((enum_feature == ProperEnum) && parent_name && !unnamedinstance) {
@@ -1489,14 +1496,12 @@ public:
    * file
    * ------------------------------------------------------------------------ */
   virtual int doxygenComment(Node *n){
-    if (doxygen){
-      String *doxygen_comments;
-      if(DoxygenTranslator::getDocumentation(n, JavaDoc, doxygen_comments)){
-	if(comment_creation_chatter)
-	  Printf(structuralComments, "/* This was generated from doxygenComment() */");
-	Printf(structuralComments, Char(doxygen_comments)); 
-	Delete(doxygen_comments);
-      }
+    if (doxygen && doxygenTranslator->hasDocumentation(n)){
+      String *doxygen_comments=doxygenTranslator->getDocumentation(n);
+      if(comment_creation_chatter)
+	Printf(structuralComments, "/* This was generated from doxygenComment() */");
+      Printf(structuralComments, Char(doxygen_comments)); 
+      Delete(doxygen_comments);
     }
     return SWIG_OK;
   }
@@ -1523,14 +1528,12 @@ public:
     Swig_save("constantWrapper", n, "value", NIL);
 
     //translate and write javadoc comment if flagged
-    if (doxygen){
-      String *doxygen_comments;
-      if(DoxygenTranslator::getDocumentation(n, JavaDoc, doxygen_comments)){
-	if(comment_creation_chatter)
-	  Printf(constants_code, "/* This was generated from constantWrapper() */");
-	Printf(constants_code, Char(doxygen_comments)); 
-	Delete(doxygen_comments);
-      }
+    if (doxygen && doxygenTranslator->hasDocumentation(n)){
+      String *doxygen_comments=doxygenTranslator->getDocumentation(n);
+      if(comment_creation_chatter)
+	Printf(constants_code, "/* This was generated from constantWrapper() */");
+      Printf(constants_code, Char(doxygen_comments)); 
+      Delete(doxygen_comments);
     }
     
     bool is_enum_item = (Cmp(nodeType(n), "enumitem") == 0);
@@ -1821,14 +1824,12 @@ public:
     const String *pure_interfaces = typemapLookup(n, "javainterfaces", typemap_lookup_type, WARN_NONE);
     
     //translate and write javadoc comment if flagged
-    if (doxygen){
-      String *doxygen_comments;
-      if(DoxygenTranslator::getDocumentation(n, JavaDoc, doxygen_comments)){
-	if(comment_creation_chatter)
-	  Printf(proxy_class_def, "/* This was generated from emitProxyClassDefAndCPPCasts() */");
-	Printf(proxy_class_def, Char(doxygen_comments)); 
-	Delete(doxygen_comments);
-      }
+    if (doxygen && doxygenTranslator->hasDocumentation(n)){
+      String *doxygen_comments=doxygenTranslator->getDocumentation(n);
+      if(comment_creation_chatter)
+	Printf(proxy_class_def, "/* This was generated from emitProxyClassDefAndCPPCasts() */");
+      Printf(proxy_class_def, Char(doxygen_comments)); 
+      Delete(doxygen_comments);
     }
     
     // Start writing the proxy class
@@ -2227,14 +2228,12 @@ public:
     }
     
     //translate and write javadoc comment if flagged
-    if (doxygen){
-      String *doxygen_comments;
-      if(DoxygenTranslator::getDocumentation(n, JavaDoc, doxygen_comments)){
-	if(comment_creation_chatter)
-	  Printf(function_code, "/* This was generated from proxyclassfunctionhandler() */");
-	Printf(function_code, Char(doxygen_comments)); 
-	Delete(doxygen_comments);
-      }
+    if (doxygen && doxygenTranslator->hasDocumentation(n)){
+      String *doxygen_comments=doxygenTranslator->getDocumentation(n);
+      if(comment_creation_chatter)
+	Printf(function_code, "/* This was generated from proxyclassfunctionhandler() */");
+      Printf(function_code, Char(doxygen_comments)); 
+      Delete(doxygen_comments);
     }
     
     /* Start generating the proxy function */
@@ -2460,14 +2459,12 @@ public:
       Printf(im_return_type, "%s", tm);
       
       //translate and write javadoc comment if flagged
-      if (doxygen){
-	String *doxygen_comments;
-	if(DoxygenTranslator::getDocumentation(n, JavaDoc, doxygen_comments)){
-	  if(comment_creation_chatter)
-	    Printf(function_code, "/* This was generated from constructionhandler() */");
-	  Printf(function_code, Char(doxygen_comments)); 
-	  Delete(doxygen_comments);
-	}
+    if (doxygen && doxygenTranslator->hasDocumentation(n)){
+      String *doxygen_comments=doxygenTranslator->getDocumentation(n);
+	if(comment_creation_chatter)
+	  Printf(function_code, "/* This was generated from constructionhandler() */");
+	Printf(function_code, Char(doxygen_comments)); 
+	Delete(doxygen_comments);
       }
 	    
       Printf(function_code, "  %s %s(", methodmods, proxy_class_name);
@@ -2732,14 +2729,12 @@ public:
     String *post_code = NewString("");
     
     // translate and write javadoc comment if flagged
-    if (doxygen){
-      String *doxygen_comments;
-      if(DoxygenTranslator::getDocumentation(n, JavaDoc, doxygen_comments)) {
-	if(comment_creation_chatter)
-	  Printf(function_code, "/* This was generated from moduleClassFunctionHandler() */");
-	Printv(function_code, doxygen_comments, NIL);
-	Delete(doxygen_comments);
-      }
+    if (doxygen && doxygenTranslator->hasDocumentation(n)){
+      String *doxygen_comments=doxygenTranslator->getDocumentation(n);
+      if(comment_creation_chatter)
+	Printf(function_code, "/* This was generated from moduleClassFunctionHandler() */");
+      Printv(function_code, doxygen_comments, NIL);
+      Delete(doxygen_comments);
     }
 
     if (l) {
@@ -4527,3 +4522,4 @@ Java Options (available with -java)\n\
      -oldvarnames    - Old intermediary method names for variable wrappers\n\
      -package <name> - Set name of the Java package to <name>\n\
 \n";
+
diff --git a/Source/Modules/lang.cxx b/Source/Modules/lang.cxx
index d89ef3e40..9e10e0f0b 100644
--- a/Source/Modules/lang.cxx
+++ b/Source/Modules/lang.cxx
@@ -2869,9 +2869,10 @@ int Language::usingDeclaration(Node *n) {
  * ---------------------------------------------------------------------- */
 int Language::doxygenComment(Node *n){
 	
-	String *comment = Getattr(n, "comment");
+  String *comment = Getattr(n, "comment");
+  Printf(stdout, "doxygenComment   : %s\n", comment);
 
-	return SWIG_OK;
+  return SWIG_OK;
 	
 }
 
diff --git a/Source/Modules/python.cxx b/Source/Modules/python.cxx
index 07437715d..40a50d45e 100644
--- a/Source/Modules/python.cxx
+++ b/Source/Modules/python.cxx
@@ -20,7 +20,7 @@ static int treduce = SWIG_cparse_template_reduce(0);
 
 #include <ctype.h>
 #include <sstream>
-#include "../DoxygenTranslator/src/DoxygenTranslator.h"
+#include "../DoxygenTranslator/src/PyDocConverter.h"
 #include "../../../swig/bug.h"
 
 #define PYSHADOW_MEMBER  0x2
@@ -548,6 +548,9 @@ public:
     if (cppcast) {
       Preprocessor_define((DOH *) "SWIG_CPLUSPLUS_CAST", 0);
     }
+    
+    if (doxygen)
+      doxygenTranslator = new PyDocConverter;
 
     if (!global_name)
       global_name = NewString("cvar");
@@ -1203,7 +1206,7 @@ public:
     String *str = Getattr(n, "feature:docstring");
     return ((str && Len(str) > 0)
 	|| (Getattr(n, "feature:autodoc") && !GetFlag(n, "feature:noautodoc"))
-	|| (doxygen && Getattr(n, "DoxygenComment"))
+	|| (doxygen && doxygenTranslator->hasDocumentation(n))
       );
   }
 
@@ -1219,7 +1222,7 @@ public:
     String *doxygen_comment = 0;
     bool have_ds = (str && Len(str) > 0);
     bool have_auto = (Getattr(n, "feature:autodoc") && !GetFlag(n, "feature:noautodoc"));
-    bool have_doxygen = doxygen && DoxygenTranslator::getDocumentation(n, PyDoc, doxygen_comment);
+    bool have_doxygen = doxygen && doxygenTranslator->hasDocumentation(n);
     const char *triple_double = use_triple ? "\"\"\"" : "";
     String *autodoc = NULL;
     String *doc = NULL;
@@ -1237,6 +1240,7 @@ public:
       have_auto = (autodoc && Len(autodoc) > 0);
     }
     if (have_doxygen) {
+      doxygen_comment = doxygenTranslator->getDocumentation(n);
       have_doxygen = (doxygen_comment && Len(doxygen_comment) > 0);
     }
     // If there is more than one line then make docstrings like this:
diff --git a/Source/Modules/swigmod.h b/Source/Modules/swigmod.h
index 897aaa9ef..0acbc1fe7 100644
--- a/Source/Modules/swigmod.h
+++ b/Source/Modules/swigmod.h
@@ -17,6 +17,7 @@
 #include "swig.h"
 #include "preprocessor.h"
 #include "swigwarn.h"
+#include "../DoxygenTranslator/src/DoxygenTranslator.h"
 
 #if !defined(HAVE_BOOL)
 typedef int bool;
@@ -315,6 +316,8 @@ protected:
   /* Director language module */
   int director_language;
 
+  // Class instance to translate comments
+  DoxygenTranslator *doxygenTranslator;
 private:
   Hash *symtabs; /* symbol tables */
   Hash *classtypes;

From 304e232dbcf576c160edefb29abea66e28bc9a10 Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Fri, 29 Jun 2012 19:28:21 +0000
Subject: [PATCH 054/314] Fixed enum comments generation in java

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13209 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 .../doxygen_parsing_enums_simple_runme.java   |  1 -
 Source/Modules/java.cxx                       | 21 ++++++++++++++++---
 2 files changed, 18 insertions(+), 4 deletions(-)

diff --git a/Examples/test-suite/java/doxygen_parsing_enums_simple_runme.java b/Examples/test-suite/java/doxygen_parsing_enums_simple_runme.java
index ca640b3f0..ee422e2c4 100644
--- a/Examples/test-suite/java/doxygen_parsing_enums_simple_runme.java
+++ b/Examples/test-suite/java/doxygen_parsing_enums_simple_runme.java
@@ -64,7 +64,6 @@ public class doxygen_parsing_enums_simple_runme {
     com.sun.tools.javadoc.Main.execute("doxygen_parsing_enums_simple runtime test",
 	"doxygen_parsing_enums_simple_runme", new String[]{"-quiet", "doxygen_parsing_enums_simple"});
 
-    wantedComments.put("E_TEST", " Test enumeration  \n");
     wantedComments.put("E_TEST_ONE", " the first item  \n");
     wantedComments.put("E_TEST_TWO", " the second  \n");
 
diff --git a/Source/Modules/java.cxx b/Source/Modules/java.cxx
index 2c6e1b08c..71de5380c 100644
--- a/Source/Modules/java.cxx
+++ b/Source/Modules/java.cxx
@@ -1279,8 +1279,12 @@ public:
 	  Replaceall(enum_code, "$static ", "");
 	Delete(scope);
       } else {
-	// Wrap C++ enum with integers - just indicate start of enum with a comment, no comment for anonymous enums of any sort
-	if (symname && !Getattr(n, "unnamedinstance"))
+	//translate and write javadoc comment for the enum itself if flagged
+	if (doxygen && doxygenTranslator->hasDocumentation(n)){
+	  Printf(stdout, "Warning: Not emitting comment for %s, not supported in simple enums mode.\n",
+	    Getattr(n, "unnamedinstance") ? "unnamed enum" : symname);
+	}
+	else if (symname && !Getattr(n, "unnamedinstance"))
 	  Printf(constants_code, "  // %s \n", symname);
       }
 
@@ -1337,7 +1341,18 @@ public:
 	  }
 
 	  Printv(f_enum, typemapLookup(n, "javaimports", typemap_lookup_type, WARN_NONE), // Import statements
-		 "\n", enum_code, "\n", NIL);
+		 "\n\n", NIL);
+	  
+	  //translate and write javadoc comment if flagged
+	  if (doxygen && doxygenTranslator->hasDocumentation(n)){
+	    String *doxygen_comments=doxygenTranslator->getDocumentation(n);
+	    if(comment_creation_chatter)
+	      Printf(f_enum, "/* This was generated from enumDeclaration() */");
+	    Printf(f_enum, Char(doxygen_comments)); 
+	    Delete(doxygen_comments);
+	  }
+	  
+	  Printv(f_enum, enum_code, "\n", NIL);
 
 	  Printf(f_enum, "\n");
 	  Close(f_enum);

From 774cbc3ef216d9428620c0076dd569af61107da3 Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Fri, 29 Jun 2012 19:37:42 +0000
Subject: [PATCH 055/314] Fixed comments parsing, but broken
 li_boost_shared_ptr_bits test

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13210 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Examples/test-suite/doxygen_parsing.i         |   6 +-
 .../java/doxygen_parsing_runme.java           |   6 +-
 .../python/doxygen_parsing_runme.py           |   1 +
 Source/CParse/parser.y                        | 328 +++++++-----------
 4 files changed, 138 insertions(+), 203 deletions(-)

diff --git a/Examples/test-suite/doxygen_parsing.i b/Examples/test-suite/doxygen_parsing.i
index b61317bcd..a83cd77ed 100644
--- a/Examples/test-suite/doxygen_parsing.i
+++ b/Examples/test-suite/doxygen_parsing.i
@@ -16,6 +16,9 @@ int simpleVarThree=42;
 //! This is the last type of comment for a var
 int simpleVarFour=42;
 
+int simpleVarFive=42;
+///< This is a post comment
+
 /*
   We assume that all this comment types are ok,
   and later we only use the first-type comments.
@@ -49,7 +52,8 @@ public:
    * Simple method with parameter
    */
   void simpleMethodWithParameter(
-	int param /**< Some test param */
+	int param, /**< Some test param */
+	int argument /**< Some test argument */
 	)
   {
   }
diff --git a/Examples/test-suite/java/doxygen_parsing_runme.java b/Examples/test-suite/java/doxygen_parsing_runme.java
index fe4b75fa5..909de9312 100644
--- a/Examples/test-suite/java/doxygen_parsing_runme.java
+++ b/Examples/test-suite/java/doxygen_parsing_runme.java
@@ -68,7 +68,9 @@ public class doxygen_parsing_runme {
 
     wantedComments.put("CSimpleClass", " This is simple comment for a class  \n");
     wantedComments.put("simpleMethod", " Simple method  \n");
-    wantedComments.put("simpleMethodWithParameter", " Simple method with parameter  \n @param\tparam Some test param  \n");
+    wantedComments.put("simpleMethodWithParameter", " Simple method with parameter  \n" +
+						    " @param\tparam Some test param  \n" +
+						    " @param\targument Some test argument  \n");
     wantedComments.put("CTemplateClassInt", " Comment for template class  \n");
     wantedComments.put("templateMethod", " Template method  \n");
 
@@ -80,6 +82,8 @@ public class doxygen_parsing_runme {
     wantedComments.put("getSimpleVarThree", " This is again another type of comment for a var  \n");
     wantedComments.put("setSimpleVarFour", " This is the last type of comment for a var  \n");
     wantedComments.put("getSimpleVarFour", " This is the last type of comment for a var  \n");
+    wantedComments.put("setSimpleVarFive", " This is a post comment  \n");
+    wantedComments.put("getSimpleVarFive", " This is a post comment  \n");
 
 
     int errorCount=0;
diff --git a/Examples/test-suite/python/doxygen_parsing_runme.py b/Examples/test-suite/python/doxygen_parsing_runme.py
index eef840818..097c18f8c 100644
--- a/Examples/test-suite/python/doxygen_parsing_runme.py
+++ b/Examples/test-suite/python/doxygen_parsing_runme.py
@@ -14,6 +14,7 @@ check(doxygen_parsing.CSimpleClass.simpleMethod.__doc__, '\s+Simple method\s+')
 check(doxygen_parsing.CSimpleClass.simpleMethodWithParameter.__doc__, ''
 '\s+Simple method with parameter'
 '\s+Arguments:\s+param \(int\)\s+-- Some test param\s+'
+'argument \(int\)\s+-- Some test argument\s+'
 )
 check(doxygen_parsing.CTemplateClassInt.__doc__, '\s+Comment for template class\s+')
 check(doxygen_parsing.CTemplateClassInt.templateMethod.__doc__, '\s+Template method\s+')
\ No newline at end of file
diff --git a/Source/CParse/parser.y b/Source/CParse/parser.y
index ffba04884..70f420411 100644
--- a/Source/CParse/parser.y
+++ b/Source/CParse/parser.y
@@ -24,6 +24,7 @@ char cvsroot_parser_y[] = "$Id$";
 #include "preprocessor.h"
 #include <ctype.h>
 
+
 /* We do this for portability */
 #undef alloca
 #define alloca malloc
@@ -67,6 +68,7 @@ String *currentComment; /* Location of the stored Doxygen Comment */
 String *currentPostComment; /* Location of the stored Doxygen Post-Comment */
 String *currentCComment; /* Location of the stored C Comment */
 static Node *previousNode = NULL; /* Pointer to the previous node (for post comments) */
+static Node *currentNode = NULL; /* Pointer to the current node (for post comments) */
 
 int isStructuralDoxygen(String *s){
 	char *slashPointer = Strchr(s, '\\');
@@ -106,27 +108,9 @@ static Node *new_node(const_String_or_char_ptr tag) {
   set_nodeType(n,tag);
   Setfile(n,cparse_file);
   Setline(n,cparse_line);
-  if(scan_doxygen_comments){
-    /* Sets any post comments to the previous node */
-    if(previousNode != NULL && currentPostComment != 0){
-      String *copyPostComment = Copy(currentPostComment);
-      if (!Getattr(previousNode, "DoxygenComment")){
-     	Setattr(previousNode,"DoxygenComment",copyPostComment);}
-      else {
-        Append(copyPostComment, Getattr(previousNode, "DoxygenComment"));
-      	Setattr(previousNode,"DoxygenComment",copyPostComment);
-        }
-      
-      currentPostComment = 0;
-    }	 
-    /* Sets Doxygen Comment if a Comment is Availible */
-    if(currentComment != 0){
-      String *copyComment = Copy(currentComment);
-      Setattr(n,"DoxygenComment",copyComment);
-      currentComment = 0;
-    }	
-    previousNode = n;
-  }
+  /* Remember the previous node in case it will need a post-comment */
+  previousNode = currentNode;
+  currentNode = n;
   return n;
 }
 
@@ -205,6 +189,25 @@ static Node *copy_node(Node *n) {
   return nn;
 }
 
+static void set_comment(Node *n, String *comment) {
+  Parm *p;
+  if (!n || !comment)
+    return;
+
+  if (Getattr(n, "DoxygenComment"))
+    Append(Getattr(n, "DoxygenComment"), comment);
+  else {
+    Setattr(n, "DoxygenComment", comment);
+    /* This is the first comment, populate it with @params, if any */
+    p = Getattr(n, "parms");
+    while (p) {
+      if (Getattr(p, "DoxygenComment"))
+	Printv(comment, "\n@param ", Getattr(p, "name"), Getattr(p, "DoxygenComment"), NIL);
+      p=nextSibling(p);
+    }
+  }
+}
+
 /* -----------------------------------------------------------------------------
  *                              Variables
  * ----------------------------------------------------------------------------- */
@@ -1496,6 +1499,7 @@ static void default_arguments(Node *n) {
   Node *function = n;
 
   if (function) {
+
     ParmList *varargs = Getattr(function,"feature:varargs");
     if (varargs) {
       /* Handles the %varargs directive by looking for "feature:varargs" and 
@@ -1793,6 +1797,7 @@ static void tag_nodes(Node *n, const_String_or_char_ptr attrname, DOH *value) {
 %type <node>     fname stringtype;
 %type <node>     featattr;
 %type <str>	 doxygen_comment;
+%type <str>	 doxygen_comment_item;
 %type <str>	 c_style_comment;
 %type <str>	 doxygen_post_comment;
 %type <str>	 doxygen_post_comment_item;
@@ -1852,9 +1857,7 @@ interface      : interface declaration {
 declaration    : swig_directive { $$ = $1; }
                | c_declaration { $$ = $1; } 
                | cpp_declaration { $$ = $1; }
-               | doxygen_comment { $$ = $1; }
                | c_style_comment { $$ = $1; }
-               | doxygen_post_comment { $$ = $1; }
                | SEMI { $$ = 0; }
                | error {
                   $$ = 0;
@@ -1878,6 +1881,14 @@ declaration    : swig_directive { $$ = $1; }
 
  */
 
+	       | doxygen_comment declaration {
+		  $$ = $2;
+		  set_comment($2, $1);
+	       }
+	       | declaration doxygen_post_comment {
+		  $$ = $1;
+		  set_comment($1, $2);
+	       }
                | error COPERATOR {
                   $$ = 0;
                   skip_decl();
@@ -3442,67 +3453,65 @@ c_constructor_decl : storage_class type LPAREN parms RPAREN ctor_end {
    A Doxygen Comment (a string in Doxygen Format)
    ------------------------------------------------------------ */
 
-doxygen_comment : DOXYGENSTRING 
-	{
-            /* while(Strchr($1,'/') == Char($1))
-               Replace($1,"/","",DOH_REPLACE_FIRST); */
-          DohReplace($1, "/**", "", 0);
-          DohReplace($1, "/*!", "", 0);
-          DohReplace($1, "///", "", 0);
-          DohReplace($1, "*/", "", 0);
+doxygen_comment_item : DOXYGENSTRING {
+		  DohReplace($1, "/**", "", 0);
+		  DohReplace($1, "/*!", "", 0);
+		  DohReplace($1, "///", "", 0);
+		  DohReplace($1, "//!", "", 0);
+		  DohReplace($1, "*/", "", 0);
 
-          /* isStructuralDoxygen() is disabled, since no comment
-             appears in such case. Need to fix. (most commands are
-             not translatable to javadoc anyway) */
-	  if(0  &&  isStructuralDoxygen($1)){
-	    $$ = new_node("doxycomm");
-		Setattr($$,"DoxygenComment",$1);
-	    }
-	  else {  
-	    if(currentComment != 0){
-				Append(currentComment,$1);
-		    }
-			else 
-				currentComment = $1;
-		$$ = 0;
-	    }
-	}
-	;
-
-
-doxygen_post_comment_item : DOXYGENPOSTSTRING 
-	{
-	  DohReplace($1, "///<", "", 0);
-	  DohReplace($1, "/**<", "", 0);
-	  DohReplace($1, "/*!<", "", 0);
-	  DohReplace($1, "//!<", "", 0);
-	  DohReplace($1, "*/", "", 0);
-	  
-	  $$ = $1;
-	}
-	;
-
-doxygen_post_comment : doxygen_post_comment doxygen_post_comment_item
-                       { 
-			 Append($1, $2);
-			 $$ = $1;
-                       }
-                     | doxygen_post_comment_item
-                       {
-                         $$ = $1;
-	}
-	;
-
-c_style_comment : C_COMMENT_STRING 
-	{
-		if(currentCComment != 0){
-		  Append(currentCComment, $1);
+		  /* isStructuralDoxygen() is disabled, since no comment
+		    appears in such case. Need to fix. (most commands are
+		    not translatable to javadoc anyway) */
+		  if(0  &&  isStructuralDoxygen($1)){
+		    $$ = new_node("doxycomm");
+		    Setattr($$,"DoxygenComment",$1);
+		  }
+		  else {
+		    $$ = $1;
 		  }
-		else currentCComment = $1;
-		$$ = 0;
-	}
-	;
 
+		}
+		;
+
+doxygen_comment : doxygen_comment doxygen_comment_item { 
+		  Append($1, $2);
+		  $$ = $1;
+		}
+                | doxygen_comment_item {
+                  $$ = $1;
+		}
+		;
+
+
+doxygen_post_comment_item : DOXYGENPOSTSTRING {
+		  DohReplace($1, "///<", "", 0);
+		  DohReplace($1, "/**<", "", 0);
+		  DohReplace($1, "/*!<", "", 0);
+		  DohReplace($1, "//!<", "", 0);
+		  DohReplace($1, "*/", "", 0);
+		  
+		  $$ = $1;
+		}
+		;
+
+doxygen_post_comment : doxygen_post_comment doxygen_post_comment_item { 
+		  Append($1, $2);
+		  $$ = $1;
+		}
+                | doxygen_post_comment_item {
+                  $$ = $1;
+		}
+		;
+
+c_style_comment : C_COMMENT_STRING {
+		  if(currentCComment != 0){
+		    Append(currentCComment, $1);
+		  }
+		  else currentCComment = $1;
+		  $$ = 0;
+                }
+                ;
 
 /* ======================================================================
  *                       C++ Support
@@ -4480,9 +4489,7 @@ cpp_member   : c_declaration { $$ = $1; }
              | storage_class idcolon SEMI { $$ = 0; }
              | cpp_using_decl { $$ = $1; }
              | cpp_template_decl { $$ = $1; }
-             | doxygen_comment{ $$ = $1; }
              | c_style_comment{ $$ = $1; }
-             | doxygen_post_comment{ $$ = $1; }
              | cpp_catch_decl { $$ = 0; }
              | template_directive { $$ = $1; }
              | warn_directive { $$ = $1; }
@@ -4490,6 +4497,14 @@ cpp_member   : c_declaration { $$ = $1; }
              | fragment_directive {$$ = $1; }
              | types_directive {$$ = $1; }
              | SEMI { $$ = 0; }
+             | doxygen_comment cpp_member {
+	         $$ = $2;
+		 set_comment($2, $1);
+	     }
+             | cpp_member doxygen_post_comment {
+	         $$ = $1;
+		 set_comment($1, $2);
+	     }
              ;
 
 /* Possibly a constructor */
@@ -4890,41 +4905,18 @@ rawparms          : parm ptail {
                   set_nextSibling($1,$2);
                   $$ = $1;
 		}
-               | empty { $$ = 0; }
+               | empty { $$ = 0; previousNode = currentNode; currentNode=0; }
                ;
 
 ptail          : COMMA parm ptail {
                  set_nextSibling($2,$3);
 		 $$ = $2;
-                }
-               | COMMA doxygen_post_comment parm ptail {
-		 set_nextSibling($3,$4);
+               }
+	       | COMMA doxygen_post_comment parm ptail {
+		 set_comment(previousNode, $2);
+                 set_nextSibling($3,$4);
 		 $$ = $3;
-		 
-		 /** because function parameters are not nodes,
-		    it must be the current function node, which
-		    gets doxy comment set.
-		 */
-		
-		 Setattr($3, "postComment", $2);
-		 /*
-		 currentPostComment = $2;
-		 if (previousParmName != 0) {
-		     String *param = NewString("\n@param ");
-		     if (currentComment != 0) {
-			 Append(currentComment, param);
-			 Append(currentComment, previousParmName );
-			 Append(currentComment, currentPostComment);
-		     }
-		     else {
-			 currentComment = param;
-			 Append(currentComment, Getattr($3, "name") );
-			 Append(currentComment, currentPostComment);
-		     }
-		 }  
-		 currentPostComment = 0;
-		 */
-                }
+               }
                | empty { $$ = 0; }
                ;
 
@@ -4932,45 +4924,18 @@ ptail          : COMMA parm ptail {
 parm           : rawtype parameter_declarator {
                    SwigType_push($1,$2.type);
 		   $$ = NewParmWithoutFileLineInfo($1,$2.id);
+		   previousNode = currentNode;
+		   currentNode = $$;
 		   Setfile($$,cparse_file);
 		   Setline($$,cparse_line);
 		   if ($2.defarg) {
 		     Setattr($$,"value",$2.defarg);
 		   }
 		}
-                | rawtype parameter_declarator doxygen_post_comment {
-		  /** handles the last function parameter, which is not followed by comma */
-		  /* 
-		  String *param = NewString("@param ");
-		  String *name = NewString($2.id);
-
-		  if (currentComment != 0) {
-		    Append(currentComment, param);
-		  }
-		  else {
-		     currentComment = param;
-		  }
-
-		  Append(currentComment, name);
-		  Append(currentComment, $3);
-
-		  if (currentPostComment != 0) {
-		  } 
-		  currentPostComment = 0;
-		  */
-
-		  SwigType_push($1,$2.type);
-		  $$ = NewParmWithoutFileLineInfo($1,$2.id);
-		  Setattr($$, "lastParamPostComment", $3);
-		  Setfile($$,cparse_file);
-		  Setline($$,cparse_line);
-		  if ($2.defarg) {
-		    Setattr($$,"value",$2.defarg);
-		  }
-		}
-
                 | TEMPLATE LESSTHAN cpptype GREATERTHAN cpptype idcolon def_args {
                   $$ = NewParmWithoutFileLineInfo(NewStringf("template<class> %s %s", $5,$6), 0);
+		  previousNode = currentNode;
+		  currentNode = $$;
 		  Setfile($$,cparse_file);
 		  Setline($$,cparse_line);
                   if ($7.val) {
@@ -4980,9 +4945,19 @@ parm           : rawtype parameter_declarator {
                 | PERIOD PERIOD PERIOD {
 		  SwigType *t = NewString("v(...)");
 		  $$ = NewParmWithoutFileLineInfo(t, 0);
+		  previousNode = currentNode;
+		  currentNode = $$;
 		  Setfile($$,cparse_file);
 		  Setline($$,cparse_line);
 		}
+		| doxygen_comment parm {
+		  $$ = $2;
+		  set_comment($2, $1);
+		}
+		| parm doxygen_post_comment {
+		  $$ = $1;
+		  set_comment($1, $2);
+		}
 		;
 
 valparms        : rawvalparms {
@@ -5848,66 +5823,15 @@ edecl          :  ID {
 		   Setattr($$,"value",$1);
 		   Delete(type);
                  }
-
-                 | doxygen_comment ID EQUAL etype {
-		   $$ = new_node("enumitem");
-		   Setattr($$,"name",$2);
-		   Setattr($$,"enumvalue", $4.val);
-	           if ($4.type == T_CHAR) {
-		     SwigType *type = NewSwigType(T_CHAR);
-		     Setattr($$,"value",NewStringf("\'%(escape)s\'", $4.val));
-		     Setattr($$,"type",type);
-		     Delete(type);
-		   } else {
-		     SwigType *type = NewSwigType(T_INT);
-		     Setattr($$,"value",$2);
-		     Setattr($$,"type",type);
-		     Delete(type);
-		   }
-		   SetFlag($$,"feature:immutable");
-                 }
-
-                 | doxygen_post_comment ID EQUAL etype {
-                   currentPostComment = $1;
-		   $$ = new_node("enumitem");
-		   Setattr($$,"name",$2);
-		   Setattr($$,"enumvalue", $4.val);
-	           if ($4.type == T_CHAR) {
-		     SwigType *type = NewSwigType(T_CHAR);
-		     Setattr($$,"value",NewStringf("\'%(escape)s\'", $4.val));
-		     Setattr($$,"type",type);
-		     Delete(type);
-		   } else {
-		     SwigType *type = NewSwigType(T_INT);
-		     Setattr($$,"value",$2);
-		     Setattr($$,"type",type);
-		     Delete(type);
-		   }
-		   SetFlag($$,"feature:immutable");
-                 }
-
-                 | doxygen_comment ID {
-		   SwigType *type = NewSwigType(T_INT);
-		   $$ = new_node("enumitem");
-		   Setattr($$,"name",$2);
-		   Setattr($$,"type",type);
-		   SetFlag($$,"feature:immutable");
-		   Delete(type);
+		 | doxygen_comment edecl {
+		   $$ = $2;
+		   set_comment($2, $1);
 		 }
-                 | doxygen_post_comment ID {
-		   SwigType *type = NewSwigType(T_INT);
-                   currentPostComment = $1;
-		   $$ = new_node("enumitem");
-		   Setattr($$,"name",$2);
-		   Setattr($$,"type",type);
-		   SetFlag($$,"feature:immutable");
-		   Delete(type);
+		 | doxygen_post_comment edecl {
+		   $$ = $2;
+		   set_comment(previousNode, $1);
 		 }
-                 | doxygen_post_comment {
-                     currentPostComment = $1;
-                     $$ = $1;
-                   }
-                 | empty { $$ = 0; }
+                 | empty { $$ = 0; previousNode = currentNode; currentNode = 0; }
                  ;
 
 etype            : expr {
@@ -6557,3 +6481,5 @@ ParmList *Swig_cparse_parms(String *s, Node *file_line_node) {
 }
 
 
+
+struct S;

From 46feb36cfb0f523161f02158c6727cce1a9861b3 Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Sun, 1 Jul 2012 18:42:43 +0000
Subject: [PATCH 056/314] Another fix for enums_simple case, now emitting
 comment

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13216 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Source/Modules/java.cxx | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/Source/Modules/java.cxx b/Source/Modules/java.cxx
index 71de5380c..49a5e9901 100644
--- a/Source/Modules/java.cxx
+++ b/Source/Modules/java.cxx
@@ -1281,8 +1281,14 @@ public:
       } else {
 	//translate and write javadoc comment for the enum itself if flagged
 	if (doxygen && doxygenTranslator->hasDocumentation(n)){
-	  Printf(stdout, "Warning: Not emitting comment for %s, not supported in simple enums mode.\n",
-	    Getattr(n, "unnamedinstance") ? "unnamed enum" : symname);
+	  String *doxygen_comments=doxygenTranslator->getDocumentation(n);
+	  if(comment_creation_chatter)
+	    Printf(constants_code, "/* This was generated from enumDeclaration() */");
+	  Printf(constants_code, "/* Comment for enum %s */\n",
+		 Getattr(n, "unnamedinstance") ? "" : symname);
+	  Printf(constants_code, Char(doxygen_comments));
+	  Printf(constants_code, "\n");
+	  Delete(doxygen_comments);
 	}
 	else if (symname && !Getattr(n, "unnamedinstance"))
 	  Printf(constants_code, "  // %s \n", symname);

From 4c215eb33756199f8505bb9d7a6bbd471d70444e Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Mon, 2 Jul 2012 20:29:49 +0000
Subject: [PATCH 057/314] Refactored most of comments translating code for
 java, preliminary version, lots of bugs right now

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13217 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Examples/test-suite/common.mk                 |   1 +
 Examples/test-suite/doxygen_basic_translate.i |  16 ++
 .../java/doxygen_basic_translate_runme.java   |  94 +++++++++
 .../src/JavaDocConverter.cpp                  | 194 ++++++++++--------
 .../DoxygenTranslator/src/JavaDocConverter.h  |  37 +++-
 5 files changed, 249 insertions(+), 93 deletions(-)
 create mode 100644 Examples/test-suite/doxygen_basic_translate.i
 create mode 100644 Examples/test-suite/java/doxygen_basic_translate_runme.java

diff --git a/Examples/test-suite/common.mk b/Examples/test-suite/common.mk
index ec47ffaa0..ed2d74cd9 100644
--- a/Examples/test-suite/common.mk
+++ b/Examples/test-suite/common.mk
@@ -188,6 +188,7 @@ CPP_TEST_CASES += \
 	director_wombat \
 	disown \
 	doxygen_parsing \
+	doxygen_basic_translate \
 	dynamic_cast \
 	empty \
 	enum_rename \
diff --git a/Examples/test-suite/doxygen_basic_translate.i b/Examples/test-suite/doxygen_basic_translate.i
new file mode 100644
index 000000000..c961164d5
--- /dev/null
+++ b/Examples/test-suite/doxygen_basic_translate.i
@@ -0,0 +1,16 @@
+%module doxygen_basic_translate
+
+%inline %{
+
+/**
+ * \brief Brief description.
+ * The comment text
+ * \author Some author
+ * \return Some number
+ * \sa function2
+ */
+int function()
+{
+}
+
+%}
\ No newline at end of file
diff --git a/Examples/test-suite/java/doxygen_basic_translate_runme.java b/Examples/test-suite/java/doxygen_basic_translate_runme.java
new file mode 100644
index 000000000..7aee4221b
--- /dev/null
+++ b/Examples/test-suite/java/doxygen_basic_translate_runme.java
@@ -0,0 +1,94 @@
+
+import doxygen_basic_translate.*;
+import com.sun.javadoc.*;
+import java.util.HashMap;
+import java.util.Map.Entry;
+import java.util.Iterator;
+
+public class doxygen_basic_translate_runme {
+  static {
+    try {
+      System.loadLibrary("doxygen_basic_translate");
+    } catch (UnsatisfiedLinkError e) {
+      System.err.println("Native code library failed to load. See the chapter on Dynamic Linking Problems in the SWIG Java documentation for help.\n" + e);
+      System.exit(1);
+    }
+  }
+
+  static HashMap<String, String> parsedComments = new HashMap<String, String>();
+  static HashMap<String, String> wantedComments = new HashMap<String, String>();
+
+  public static boolean start(RootDoc root) {
+    
+    /*
+      This method is called by 'javadoc' and gets the whole parsed
+      java file, we get comments and store them
+    */
+
+    ClassDoc[] classes = root.classes();
+
+    for (int i = 0; i < classes.length; i++) {
+
+      if (classes[i].getRawCommentText().length() > 0)
+	parsedComments.put(classes[i].name(), classes[i].getRawCommentText());
+
+      MethodDoc[] methods = classes[i].methods();
+      FieldDoc[] fields = classes[i].fields();
+      FieldDoc[] constants = classes[i].enumConstants();
+
+      for (int j = 0; j < constants.length; j++) {
+        FieldDoc f = constants[j];
+	if (f.getRawCommentText().length() > 0)
+	  parsedComments.put(f.name(), f.getRawCommentText());
+      }
+      for (int j = 0; j < fields.length; j++) {
+        FieldDoc f = fields[j];
+	if (f.getRawCommentText().length() > 0)
+	  parsedComments.put(f.name(), f.getRawCommentText());
+      }
+      for (int j = 0; j < methods.length; j++) {
+        MethodDoc m = methods[j];
+	if (m.getRawCommentText().length() > 0)
+	  parsedComments.put(m.name(), m.getRawCommentText());
+      }
+    }
+    return true;
+  }
+
+  public static void main(String argv[]) 
+  {
+    /*
+      Here we are using internal javadoc tool, it accepts the name of the class as paramterer,
+      and calls the start() method of that class with parsed information.
+    */
+    com.sun.tools.javadoc.Main.execute("doxygen_basic_translate runtime test",
+	"doxygen_basic_translate_runme", new String[]{"-quiet", "doxygen_basic_translate"});
+
+    wantedComments.put("function", " Brief description.  \n The comment text  \n" +
+				   " @author\tSome author  \n" +
+				   " @return\tSome number  \n" +
+				   " @see\tfunction2  \n");
+
+    int errorCount=0;
+    Iterator< Entry<String, String> > it = parsedComments.entrySet().iterator();
+
+    while (it.hasNext())
+    {
+	Entry<String, String> e = (Entry<String, String>) it.next();
+
+	if (!e.getValue().equals(wantedComments.get(e.getKey()))) {
+	    System.out.println("Documentation comments for " + e.getKey() + " does not match: ");
+	    System.out.println("\texpected:"+wantedComments.get(e.getKey()));
+	    System.out.println("\tgot:\t"+e.getValue());
+	    errorCount++;
+	}
+    }
+
+    if (parsedComments.size() != wantedComments.size()) {
+	System.out.println("Found " + (wantedComments.size()-parsedComments.size()) + " missed comment(s)!");
+	errorCount++;
+    }
+
+    System.exit(errorCount);
+  }
+}
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.cpp b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
index 812a6c34d..0c332c3b9 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
@@ -14,9 +14,64 @@
 #include <iostream>
 #define APPROX_LINE_LENGTH 64	//characters per line allowed
 #define TAB_SIZE 8		//current tab size in spaces
-int printSortedTree2 = 0;
 //TODO {@link} {@linkplain} {@docRoot}, and other useful doxy commands that are not a javadoc tag
 
+// define static escape table, it is filled in JavaDocConverter's constructor
+std::map<std::string, std::string> JavaDocConverter::escapeTable;
+
+void JavaDocConverter::fillEscapeTable() {
+  if (escapeTable.size()) // fill only once
+    return;
+  
+  escapeTable["&"] = "&amp";
+  escapeTable["\'"] = "&apos";
+  escapeTable["\""] = "&quot";
+  escapeTable["<"] = "&lt";
+  escapeTable[">"] = "&gt";
+}
+
+
+JavaDocConverter::JavaDocConverter() : debug(false) {
+  
+  fillEscapeTable();
+  
+  // these commands insert HTML tags
+  tagHandlers["c"] = &handleTagC;
+  tagHandlers["b"] = &handleTagB;
+  // these commands insert just a single char, all of them need to be escaped
+  tagHandlers["$"] = &handleTagChar;
+  tagHandlers["@"] = &handleTagChar;
+  tagHandlers["\\"] = &handleTagChar;
+  tagHandlers["<"] = &handleTagChar;
+  tagHandlers[">"] = &handleTagChar;
+  tagHandlers["&"] = &handleTagChar;
+  tagHandlers["#"] = &handleTagChar;
+  tagHandlers["%"] = &handleTagChar;
+  tagHandlers["~"] = &handleTagChar;
+  tagHandlers["\""] = &handleTagChar;
+  tagHandlers["."] = &handleTagChar;
+  tagHandlers["::"] = &handleTagChar;
+  // these commands are stripped out
+  tagHandlers["brief"] = &handleTagStrip;
+  tagHandlers["details"] = &handleTagStrip;
+  tagHandlers["partofdescription"] = &handleTagStrip;
+  // these commands are kept as-is, they are supported by JavaDoc
+  tagHandlers["sa"] = &handleTagSeeAll;
+  tagHandlers["see"] = &handleTagSame;
+  tagHandlers["param"] = &handleTagSame;
+  tagHandlers["return"] = &handleTagSame;
+  tagHandlers["throws"] = &handleTagSame;
+  tagHandlers["throw"] = &handleTagThrow;
+  tagHandlers["author"] = &handleTagSame;
+  tagHandlers["since"] = &handleTagSame;
+  tagHandlers["version"] = &handleTagSame;
+  tagHandlers["exception"] = &handleTagSame;
+  tagHandlers["deprecated"] = &handleTagSame;
+  // this command just prints it's contents
+  // (it is internal command of swig's parser, contains plain text)
+  tagHandlers["plainstd::string"] = &handleTagData;
+}
+
 std::string JavaDocConverter::formatCommand(std::string unformattedLine, int indent) {
   std::string formattedLines = "\n * ";
   int lastPosition = 0;
@@ -56,99 +111,58 @@ std::string JavaDocConverter::formatCommand(std::string unformattedLine, int ind
   return formattedLines;
 }
 
-/* Contains the conversions for tags
- * could probably be much more efficient...
- */
-std::string JavaDocConverter::javaDocFormat(DoxygenEntity & doxygenEntity) {
-  if (doxygenEntity.typeOfEntity.compare("partofdescription") == 0) {
-    return doxygenEntity.data;
-  }
-  if (doxygenEntity.typeOfEntity.compare("plainstd::string") == 0) {
-    return doxygenEntity.data;
-  } else if (doxygenEntity.typeOfEntity.compare("b") == 0) {
-    return "<b>" + doxygenEntity.data + "</b>";
-  } else if (doxygenEntity.typeOfEntity.compare("c") == 0) {
-    return "<tt>" + doxygenEntity.data + "</tt>";
-  } else if (doxygenEntity.typeOfEntity.compare("@") == 0) {
-    return "@";
-  } else if (doxygenEntity.typeOfEntity.compare("\\") == 0) {
-    return "\\";
-  } else if (doxygenEntity.typeOfEntity.compare("<") == 0) {
-    return "&lt;";
-  } else if (doxygenEntity.typeOfEntity.compare(">") == 0) {
-    return "&gt;";
-  } else if (doxygenEntity.typeOfEntity.compare("&") == 0) {
-    return "&amp;";
-  } else if (doxygenEntity.typeOfEntity.compare("#") == 0) {
-    return "#";
-  } else if (doxygenEntity.typeOfEntity.compare("%") == 0) {
-    return "%";
-  } else if (doxygenEntity.typeOfEntity.compare("~") == 0) {
-    return "~";
-  }
-  return "";
-}
-
-
 std::string JavaDocConverter::translateSubtree(DoxygenEntity & doxygenEntity) {
-  std::string returnedString;
-  if (doxygenEntity.isLeaf) {
-    return javaDocFormat(doxygenEntity) + " ";
-  } else {
-    returnedString += javaDocFormat(doxygenEntity);
-    std::list < DoxygenEntity >::iterator p = doxygenEntity.entityList.begin();
-
-    while (p != doxygenEntity.entityList.end()) {
-      returnedString += translateSubtree(*p);
-      p++;
-    }
+  std::string translatedComment;
+  
+  if (doxygenEntity.isLeaf)
+    return translatedComment;
+  
+  std::list < DoxygenEntity >::iterator p = doxygenEntity.entityList.begin();
+  while (p != doxygenEntity.entityList.end()) {
+    translateEntity(*p, translatedComment);
+    translateSubtree(*p);
+    p++;
   }
-  return returnedString;
+  
+  return translatedComment;
 }
 
-
-std::string JavaDocConverter::translateEntity(DoxygenEntity & doxyEntity) {
-  if (doxyEntity.typeOfEntity.compare("partofdescription") == 0) {
-    return formatCommand(std::string(translateSubtree(doxyEntity)), 0);
-  }
-
-  if ((doxyEntity.typeOfEntity.compare("brief") == 0) || (doxyEntity.typeOfEntity.compare("details") == 0)) {
-    return formatCommand(std::string(translateSubtree(doxyEntity)), 0) + "\n * ";
-
-  } else if (doxyEntity.typeOfEntity.compare("plainstd::string") == 0 ||
-	     doxyEntity.typeOfEntity.compare("deprecated") == 0 || 
-	     doxyEntity.typeOfEntity.compare("brief") == 0) {
-    return formatCommand(doxyEntity.data, 0) + "\n * ";
-
-  } else if (doxyEntity.typeOfEntity.compare("see") == 0) {
-    return formatCommand(std::string("@" + doxyEntity.typeOfEntity + "\t\t" + translateSubtree(doxyEntity)), 2);
-
-  } else if (doxyEntity.typeOfEntity.compare("return") == 0
-	     || doxyEntity.typeOfEntity.compare("author") == 0
-	     || doxyEntity.typeOfEntity.compare("param") == 0
-	     || doxyEntity.typeOfEntity.compare("throw") == 0
-	     || doxyEntity.typeOfEntity.compare("throws") == 0
-	     || doxyEntity.typeOfEntity.compare("since") == 0
-	     || doxyEntity.typeOfEntity.compare("version") == 0
-	     || doxyEntity.typeOfEntity.compare("exception") == 0
-	     || doxyEntity.typeOfEntity.compare("deprecated") == 0) {
-
-    // this 'if' is a hack - convert doxyEntity.typeOfEntity at the time of parsing
-    if (doxyEntity.typeOfEntity.compare("throw") == 0) {
-      doxyEntity.typeOfEntity = "throws";
-    }
-    return formatCommand(std::string("@" + doxyEntity.typeOfEntity + "\t" + translateSubtree(doxyEntity)), 2);
-
-  } else if (doxyEntity.typeOfEntity.compare("sa") == 0) {
-    return formatCommand(std::string("@see\t\t" + translateSubtree(doxyEntity)), 2);
-
-  } else {
-    return formatCommand(javaDocFormat(doxyEntity), 0);
-  }
-
-  return "";
+void JavaDocConverter::translateEntity(DoxygenEntity& tag, std::string& translatedComment) {
+  // check if we have needed handler and call it
+  if (tagHandlers.find(tag.typeOfEntity)!=tagHandlers.end())
+    tagHandlers[tag.typeOfEntity](this, tag, translatedComment);
 }
 
+void JavaDocConverter::handleTagC(JavaDocConverter* converter, DoxygenEntity& tag, std::string& translatedComment) {
+  translatedComment += "<tt>" + tag.data + "</tt>";
+}
+void JavaDocConverter::handleTagB(JavaDocConverter* converter, DoxygenEntity& tag, std::string& translatedComment) {
+  translatedComment += "<b>" + tag.data + "</b>";
+}
+void JavaDocConverter::handleTagThrow(JavaDocConverter* converter, DoxygenEntity& tag, std::string& translatedComment) {
+  tag.typeOfEntity = "throws";
+  handleTagSame(converter, tag, translatedComment);
+}
+void JavaDocConverter::handleTagSeeAll(JavaDocConverter* converter, DoxygenEntity& tag, std::string& translatedComment) {
+  tag.typeOfEntity = "see";
+  handleTagSame(converter, tag, translatedComment);
+}
+void JavaDocConverter::handleTagChar(JavaDocConverter* converter, DoxygenEntity& tag, std::string& translatedComment) {
+  // escape it if we can, else just print
+  if (escapeTable.find(tag.typeOfEntity)!=escapeTable.end())
+    translatedComment += escapeTable[tag.typeOfEntity];
+  else
+    translatedComment += tag.typeOfEntity;
+}
+void JavaDocConverter::handleTagSame(JavaDocConverter* converter, DoxygenEntity& tag, std::string& translatedComment) {
+  translatedComment += converter->formatCommand(std::string("@" + tag.typeOfEntity + "\t" + converter->translateSubtree(tag)), 2);
+}
+void JavaDocConverter::handleTagStrip(JavaDocConverter* converter, DoxygenEntity& tag, std::string& translatedComment) {
+  translatedComment += converter->formatCommand(converter->translateSubtree(tag), 0);
+}
+void JavaDocConverter::handleTagData(JavaDocConverter* converter, DoxygenEntity& tag, std::string& translatedComment) {
+  translatedComment += tag.data + " ";
+}
 
 String *JavaDocConverter::makeDocumentation(Node *node) {
 
@@ -158,7 +172,7 @@ String *JavaDocConverter::makeDocumentation(Node *node) {
     return NULL;
   }
 
-  std::list < DoxygenEntity > entityList = DoxygenParser().createTree(Char(documentation));
+  std::list < DoxygenEntity > entityList = parser.createTree(Char(documentation));
 
   // entityList.sort(CompareDoxygenEntities()); sorting currently not used,
   // see CompareDoxygenEntities::operator() in DoxygenEntity.cpp
@@ -171,7 +185,7 @@ String *JavaDocConverter::makeDocumentation(Node *node) {
   std::string javaDocString = "/**";
 
   for (std::list < DoxygenEntity >::iterator entityIterator = entityList.begin(); entityIterator != entityList.end();) {
-    javaDocString += translateEntity(*entityIterator);
+    translateEntity(*entityIterator, javaDocString);
     entityIterator++;
   }
 
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.h b/Source/DoxygenTranslator/src/JavaDocConverter.h
index 1d54e2514..408ec4bb2 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.h
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.h
@@ -15,24 +15,55 @@
 #define JAVADOCCONVERTER_H_
 
 #include "DoxygenTranslator.h"
+#include <map>
 
 /*
  * A class to translate doxygen comments into JavaDoc style comments.
  */
 class JavaDocConverter : public DoxygenTranslator {
 public:
-  JavaDocConverter() : debug(false) {
-  }
+  JavaDocConverter();
   String *makeDocumentation(Node *node);
 
 protected:
   std::string formatCommand(std::string unformattedLine, int indent);
-  std::string translateEntity(DoxygenEntity & doxyEntity);
   std::string javaDocFormat(DoxygenEntity & doxygenEntity);
   std::string translateSubtree(DoxygenEntity & doxygenEntity);
+  void translateEntity(DoxygenEntity &tag, std::string &translatedComment);
+  
+  /*
+   * Typedef for the function that handles one tag
+   */
+  typedef void (*tagHandler)(JavaDocConverter *converter, DoxygenEntity &tag, std::string &translatedComment);
+  /*
+   * Here comes various tag handlers
+   */
+  static void handleTagC(JavaDocConverter *converter, DoxygenEntity &tag, std::string &translatedComment);
+  static void handleTagB(JavaDocConverter *converter, DoxygenEntity &tag, std::string &translatedComment);
+  static void handleTagThrow(JavaDocConverter *converter, DoxygenEntity &tag, std::string &translatedComment);
+  static void handleTagSeeAll(JavaDocConverter *converter, DoxygenEntity &tag, std::string &translatedComment);
+  /*
+   * Print the name of tag to the output, used for escape-commands
+   */
+  static void handleTagChar(JavaDocConverter *converter, DoxygenEntity &tag, std::string &translatedComment);
+  /*
+   * Do not translate and print as-is
+   */
+  static void handleTagSame(JavaDocConverter *converter, DoxygenEntity &tag, std::string &translatedComment);
+  /*
+   * Print only the content and strip original tag
+   */
+  static void handleTagStrip(JavaDocConverter *converter, DoxygenEntity &tag, std::string &translatedComment);
+  /*
+   * Print only data part of code
+   */
+  static void handleTagData(JavaDocConverter *converter, DoxygenEntity &tag, std::string &translatedComment);
 
 private:
   bool debug;
+  std::map<std::string, tagHandler> tagHandlers;
+  static std::map<std::string, std::string> escapeTable;
+  void fillEscapeTable();
 };
 
 #endif

From 48e9052e223a41aad5a543b238a1bc2f58980ec0 Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Mon, 2 Jul 2012 21:43:15 +0000
Subject: [PATCH 058/314] Comment fixed

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13247 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Source/DoxygenTranslator/src/DoxygenTranslator.h | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/Source/DoxygenTranslator/src/DoxygenTranslator.h b/Source/DoxygenTranslator/src/DoxygenTranslator.h
index 023bdac89..7ddaba9a8 100644
--- a/Source/DoxygenTranslator/src/DoxygenTranslator.h
+++ b/Source/DoxygenTranslator/src/DoxygenTranslator.h
@@ -39,9 +39,7 @@ public:
    * Return the documentation for a given node formated for the correct 
    * documentation system. The result is cached and translated only once.
    * @param node The node to extract and translate documentation for.
-   * @param format The documentation format to output.
-   * @param documentation The returned documentation string.
-   * @return A bool to indicate if there was documentation to return for the node.
+   * @return The resulted documentation string.
    */
   String *getDocumentation(Node *node);
   /*

From 2004ff23b913d398998a51427113de9af6888b64 Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Wed, 4 Jul 2012 21:47:57 +0000
Subject: [PATCH 059/314] Removed the unwanted header

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13251 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Source/Modules/python.cxx | 1 -
 1 file changed, 1 deletion(-)

diff --git a/Source/Modules/python.cxx b/Source/Modules/python.cxx
index 40a50d45e..5d9a97952 100644
--- a/Source/Modules/python.cxx
+++ b/Source/Modules/python.cxx
@@ -21,7 +21,6 @@ static int treduce = SWIG_cparse_template_reduce(0);
 #include <ctype.h>
 #include <sstream>
 #include "../DoxygenTranslator/src/PyDocConverter.h"
-#include "../../../swig/bug.h"
 
 #define PYSHADOW_MEMBER  0x2
 #define WARN_PYTHON_MULTIPLE_INH 405

From 75961bc7d1965b4edf5a4dcd50ae23ae2d3b59fc Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Wed, 4 Jul 2012 22:04:52 +0000
Subject: [PATCH 060/314] Fixed double-search in map in JavaDocConverter.cpp

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13252 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Source/DoxygenTranslator/src/JavaDocConverter.cpp | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.cpp b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
index 0c332c3b9..a3abf100a 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
@@ -129,8 +129,10 @@ std::string JavaDocConverter::translateSubtree(DoxygenEntity & doxygenEntity) {
 
 void JavaDocConverter::translateEntity(DoxygenEntity& tag, std::string& translatedComment) {
   // check if we have needed handler and call it
-  if (tagHandlers.find(tag.typeOfEntity)!=tagHandlers.end())
-    tagHandlers[tag.typeOfEntity](this, tag, translatedComment);
+  std::map<std::string, tagHandler>::iterator it;
+  it = tagHandlers.find(tag.typeOfEntity); 
+  if (it!=tagHandlers.end())
+    (*it).second(this, tag, translatedComment);
 }
 
 void JavaDocConverter::handleTagC(JavaDocConverter* converter, DoxygenEntity& tag, std::string& translatedComment) {

From 13adf595ecd3c4481a14e68a9edaac4a49a0dc04 Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Wed, 4 Jul 2012 22:23:22 +0000
Subject: [PATCH 061/314] Refactored the code, got rid of global objects, got
 rid of tons of string comparisons

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13253 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 .../DoxygenTranslator/src/DoxygenCommands.h   |  95 ++++
 .../DoxygenTranslator/src/DoxygenParser.cpp   | 410 +++++-------------
 Source/DoxygenTranslator/src/DoxygenParser.h  | 215 +++++++++
 3 files changed, 410 insertions(+), 310 deletions(-)
 create mode 100644 Source/DoxygenTranslator/src/DoxygenCommands.h

diff --git a/Source/DoxygenTranslator/src/DoxygenCommands.h b/Source/DoxygenTranslator/src/DoxygenCommands.h
new file mode 100644
index 000000000..e1eba33f4
--- /dev/null
+++ b/Source/DoxygenTranslator/src/DoxygenCommands.h
@@ -0,0 +1,95 @@
+
+#ifndef DOXYGENCOMMANDS_H
+#define DOXYGENCOMMANDS_H
+
+const char *commandArray[] = {
+  "a", "addindex", "addtogroup", "anchor", "arg", "attention",
+  "author", "b", "brief", "bug", "c", "callgraph", "callergraph", "category",
+  "class", "code", "cond", "copybrief", "copydetails", "copydoc", "date", "def",
+  "defgroup", "deprecated", "details", "dir", "dontinclude", "dot", "dotfile", "e",
+  "else", "elseif", "em", "endcode", "endcond", "enddot", "endhtmlonly", "endif",
+  "endlatexonly", "endlink", "endmanonly", "endmsc", "endverbatim", "endxmlonly",
+  "enum", "example", "exception", "f$", "f[", "f]", "f{", "f}", "file", "fn", "headerfile",
+  "hideinitializer", "htmlinclude", "htmlonly", "if", "ifnot", "image", "include",
+  "includelineno", "ingroup", "internal", "invariant", "interface", "latexonly", "li",
+  "line", "link", "mainpage", "manonly", "msc", "n", "name", "namespace", "nosubgrouping",
+  "note", "overload", "p", "package", "page", "par", "paragraph", "param", "post", "pre",
+  "private", "privatesection", "property", "protected", "protectedsection", "protocol",
+  "public", "publicsection", "ref", "relates", "relatesalso", "remarks", "return", "retval",
+  "sa", "section", "see", "showinitializer", "since", "skip", "skipline", "struct", "subpage",
+  "subsection", "subsubsection", "test", "throw", "throws", "todo", "tparam", "typedef", "union", "until",
+  "var", "verbatim", "verbinclude", "version", "warning", "weakgroup", "xmlonly", "xrefitem", "$", "@", "\\", "&", "~", "<", ">", "#", "%"};
+
+
+const char *sectionIndicators[] = {
+  "attention", "author", "brief", "bug", "cond", "date", "deprecated", "details",
+  "else", "elseif", "endcond", "endif", "exception", "if", "ifnot", "invariant", "note", "par", "param",
+  "tparam", "post", "pre", "remarks", "return", "retval", "sa", "see", "since", "test", "throw", "throws", "todo", "version", "warning", "xrefitem"};
+const int sectionIndicatorsSize = sizeof(sectionIndicators) / sizeof(*sectionIndicators);
+
+/* All of the doxygen commands divided up by how they are parsed */
+const char *simpleCommands[] = {
+  "n", "$", "@", "\\", "&", "~", "<", ">", "#", "%"};
+const int simpleCommandsSize = sizeof(simpleCommands) / sizeof(*simpleCommands);
+
+const char *ignoredSimpleCommands[] = {
+  "nothing at the moment"};
+const int ignoredSimpleCommandsSize = sizeof(ignoredSimpleCommands) / sizeof(*ignoredSimpleCommands);
+
+const char *commandWords[] = {
+  "a", "b", "c", "e", "em", "p", "def", "enum", "example", "package", "relates", "namespace", "relatesalso", "anchor", "dontinclude", "include", "includelineno"};
+const int commandWordsSize = sizeof(commandWords) / sizeof(*commandWords);
+
+const char *ignoredCommandWords[] = {
+  "copydoc", "copybrief", "copydetails", "verbinclude", "htmlinclude"};
+const int ignoredCommandWordsSize = sizeof(ignoredCommandWords) / sizeof(*ignoredCommandWords);
+
+const char *commandLines[] = {
+  "addindex", "fn", "name", "line", "var", "skipline", "typedef", "skip", "until", "property"};
+const int commandLinesSize = sizeof(commandLines) / sizeof(*commandLines);
+
+const char *ignoreCommandLines[] = {
+  "nothing at the moment"};
+const int ignoreCommandLinesSize = sizeof(ignoreCommandLines) / sizeof(*ignoreCommandLines);
+
+const char *commandParagraph[] = {
+  "partofdescription", "return", "remarks", "since", "test", "sa", "see", "pre", "post", "details", "invariant",
+  "deprecated", "date", "note", "warning", "version", "todo", "bug", "attention", "brief", "author"};
+const int commandParagraphSize = sizeof(commandParagraph) / sizeof(*commandParagraph);
+
+const char *ignoreCommandParagraphs[] = {
+  "nothing at the moment"};
+const int ignoreCommandParagraphsSize = sizeof(ignoreCommandParagraphs) / sizeof(*ignoreCommandParagraphs);
+
+const char *commandEndCommands[] = {
+  "code", "dot", "msc", "f$", "f[", "f{environment}{", "htmlonly", "latexonly", "manonly", "verbatim", "xmlonly", "cond", "if", "ifnot", "link"};
+const int commandEndCommandsSize = sizeof(commandEndCommands) / sizeof(*commandEndCommands);
+
+const char *commandWordParagraphs[] = {
+  "param", "tparam", "throw", "throws", "retval", "exception"};
+const int commandWordParagraphsSize = sizeof(commandWordParagraphs) / sizeof(*commandWordParagraphs);
+
+const char *commandWordLines[] = {
+  "page", "subsection", "subsubsection", "section", "paragraph", "defgroup"};
+const int commandWordLinesSize = sizeof(commandWordLines) / sizeof(*commandWordLines);
+
+const char *commandWordOWordOWords[] = {
+  "category", "class", "protocol", "interface", "struct", "union"};
+const int commandWordOWordOWordsSize = sizeof(commandWordOWordOWords) / sizeof(*commandWordOWordOWords);
+
+const char *commandOWords[] = {
+  "dir", "file", "cond"};
+const int commandOWordsSize = sizeof(commandOWords) / sizeof(*commandOWords);
+
+const char *commandErrorThrowings[] = {
+  "annotatedclassstd::list", "classhierarchy", "define", "functionindex", "header",
+  "headerfilestd::list", "inherit", "l", "postheader", "private", "privatesection", "protected",
+  "protectedsection", "public", "publicsection", "endcode", "enddot", "endmsc", "endhtmlonly",
+  "endlatexonly", "endmanonly", "endlink", "endverbatim", "endxmlonly", "f]", "f}", "endcond", "endif"};
+const int commandErrorThrowingsSize = sizeof(commandErrorThrowings) / sizeof(*commandErrorThrowings);
+
+const char *commandUniques[] = {
+  "xrefitem", "arg", "ingroup", "par", "headerfile", "overload", "weakgroup", "ref", "subpage", "dotfile", "image", "addtogroup", "li"};
+const int commandUniquesSize = sizeof(commandUniques) / sizeof(*commandUniques);
+
+#endif
\ No newline at end of file
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.cpp b/Source/DoxygenTranslator/src/DoxygenParser.cpp
index 030d8bee9..fe4dc5ec0 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenParser.cpp
@@ -10,135 +10,96 @@
  * ----------------------------------------------------------------------------- */
 
 #include "DoxygenParser.h"
-#include "TokenList.h"
+#include "DoxygenCommands.h"
+
+#include <stdio.h>
+
+// Define static class members
+std::map<std::string, DoxyCommandEnum> DoxygenParser::doxygenCommands;
+std::set<std::string> DoxygenParser::doxygenSectionIndicators;
 
 
-DoxygenParser::DoxygenParser() {
+DoxygenParser::DoxygenParser() : noisy(true) {
+  fillTables();
 }
 
 DoxygenParser::~DoxygenParser() {
 }
 
-//////////////////////////////////////////
-int noisy = 0;			// set this to 1 for extra chatter from the parsing stage.
-int addCommand(std::string currCommand, TokenList & tokList, std::list < DoxygenEntity > &aNewList);
-std::list < DoxygenEntity > parse(std::list < Token >::iterator endParsingIndex, TokenList & tokList);
+void DoxygenParser::fillTables() {
+  // run it only once
+  if (doxygenCommands.size())
+    return;
+  
+  // fill in tables with data from DxygenCommands.h
+  for (int i = 0; i < simpleCommandsSize; i++)
+    doxygenCommands[simpleCommands[i]] = SIMPLECOMMAND;
+  for (int i = 0; i < ignoredSimpleCommandsSize; i++)
+    doxygenCommands[ignoredSimpleCommands[i]] = IGNOREDSIMPLECOMMAND;
+  
+  for (int i = 0; i < commandWordsSize; i++)
+    doxygenCommands[commandWords[i]] = COMMANDWORD;
+  for (int i = 0; i < ignoredCommandWordsSize; i++)
+    doxygenCommands[ignoredCommandWords[i]] = IGNOREDCOMMANDWORD;
+  
+  for (int i = 0; i < commandLinesSize; i++)
+    doxygenCommands[commandLines[i]] = COMMANDLINE;
+  for (int i = 0; i < ignoreCommandLinesSize; i++)
+    doxygenCommands[ignoreCommandLines[i]] = IGNOREDCOMMANDLINE;
+  
+  for (int i = 0; i < commandParagraphSize; i++)
+    doxygenCommands[commandParagraph[i]] = COMMANDPARAGRAPH;
+  for (int i = 0; i < ignoreCommandParagraphsSize; i++)
+    doxygenCommands[ignoreCommandParagraphs[i]] = IGNORECOMMANDPARAGRAPH;
+  
+  for (int i = 0; i < commandEndCommandsSize; i++)
+    doxygenCommands[commandEndCommands[i]] = COMMANDENDCOMMAND;
+  for (int i = 0; i < commandWordParagraphsSize; i++)
+    doxygenCommands[commandWordParagraphs[i]] = COMMANDWORDPARAGRAPH;
+  for (int i = 0; i < commandWordLinesSize; i++)
+    doxygenCommands[commandWordLines[i]] = COMMANDWORDLINE;
+  for (int i = 0; i < commandWordOWordOWordsSize; i++)
+    doxygenCommands[commandWordOWordOWords[i]] = COMMANDWORDOWORDWORD;
+  for (int i = 0; i < commandOWordsSize; i++)
+    doxygenCommands[commandOWords[i]] = COMMANDOWORD;
+  for (int i = 0; i < commandErrorThrowingsSize; i++)
+    doxygenCommands[commandErrorThrowings[i]] = COMMANDERRORTHROW;
+  for (int i = 0; i < commandUniquesSize; i++)
+    doxygenCommands[commandUniques[i]] = COMMANDUNIQUE;
+  
+  // fill section indicators command set
+  for (int i = 0; i < sectionIndicatorsSize; i++)
+    doxygenSectionIndicators.insert(sectionIndicators[i]);
+}
 
-//////////////////////////////////////////
-
-
-std::string commandArray[] = {
-  "a", "addindex", "addtogroup", "anchor", "arg", "attention",
-  "author", "b", "brief", "bug", "c", "callgraph", "callergraph", "category",
-  "class", "code", "cond", "copybrief", "copydetails", "copydoc", "date", "def",
-  "defgroup", "deprecated", "details", "dir", "dontinclude", "dot", "dotfile", "e",
-  "else", "elseif", "em", "endcode", "endcond", "enddot", "endhtmlonly", "endif",
-  "endlatexonly", "endlink", "endmanonly", "endmsc", "endverbatim", "endxmlonly",
-  "enum", "example", "exception", "f$", "f[", "f]", "f{", "f}", "file", "fn", "headerfile",
-  "hideinitializer", "htmlinclude", "htmlonly", "if", "ifnot", "image", "include",
-  "includelineno", "ingroup", "internal", "invariant", "interface", "latexonly", "li",
-  "line", "link", "mainpage", "manonly", "msc", "n", "name", "namespace", "nosubgrouping",
-  "note", "overload", "p", "package", "page", "par", "paragraph", "param", "post", "pre",
-  "private", "privatesection", "property", "protected", "protectedsection", "protocol",
-  "public", "publicsection", "ref", "relates", "relatesalso", "remarks", "return", "retval",
-  "sa", "section", "see", "showinitializer", "since", "skip", "skipline", "struct", "subpage",
-  "subsection", "subsubsection", "test", "throw", "throws", "todo", "tparam", "typedef", "union", "until",
-  "var", "verbatim", "verbinclude", "version", "warning", "weakgroup", "xmlonly", "xrefitem", "$", "@", "\\", "&", "~", "<", ">", "#", "%"};
-
-
-std::string sectionIndicators[] = {
-  "attention", "author", "brief", "bug", "cond", "date", "deprecated", "details",
-  "else", "elseif", "endcond", "endif", "exception", "if", "ifnot", "invariant", "note", "par", "param",
-  "tparam", "post", "pre", "remarks", "return", "retval", "sa", "see", "since", "test", "throw", "throws", "todo", "version", "warning", "xrefitem"};
-
-/* All of the doxygen commands divided up by how they are parsed */
-std::string simpleCommands[] = {
-  "n", "$", "@", "\\", "&", "~", "<", ">", "#", "%"};
-
-std::string ignoredSimpleCommands[] = {
-  "nothing at the moment"};
-
-std::string commandWords[] = {
-  "a", "b", "c", "e", "em", "p", "def", "enum", "example", "package", "relates", "namespace", "relatesalso", "anchor", "dontinclude", "include", "includelineno"};
-
-std::string ignoredCommandWords[] = {
-  "copydoc", "copybrief", "copydetails", "verbinclude", "htmlinclude"};
-
-std::string commandLines[] = {
-  "addindex", "fn", "name", "line", "var", "skipline", "typedef", "skip", "until", "property"};
-
-std::string ignoreCommandLines[] = {
-  "nothing at the moment"};
-
-std::string commandParagraph[] = {
-  "partofdescription", "return", "remarks", "since", "test", "sa", "see", "pre", "post", "details", "invariant",
-  "deprecated", "date", "note", "warning", "version", "todo", "bug", "attention", "brief", "author"};
-
-std::string ignoreCommandParagraphs[] = {
-  "nothing at the moment"};
-
-std::string commandEndCommands[] = {
-  "code", "dot", "msc", "f$", "f[", "f{environment}{", "htmlonly", "latexonly", "manonly", "verbatim", "xmlonly", "cond", "if", "ifnot", "link"};
-
-std::string commandWordParagraphs[] = {
-  "param", "tparam", "throw", "throws", "retval", "exception"};
-
-std::string commandWordLines[] = {
-  "page", "subsection", "subsubsection", "section", "paragraph", "defgroup"};
-
-std::string commandWordOWordOWords[] = {
-  "category", "class", "protocol", "interface", "struct", "union"};
-
-std::string commandOWords[] = {
-  "dir", "file", "cond"};
-
-std::string commandErrorThrowings[] = {
-  "annotatedclassstd::list", "classhierarchy", "define", "functionindex", "header",
-  "headerfilestd::list", "inherit", "l", "postheader", "private", "privatesection", "protected",
-  "protectedsection", "public", "publicsection", "endcode", "enddot", "endmsc", "endhtmlonly",
-  "endlatexonly", "endmanonly", "endlink", "endverbatim", "endxmlonly", "f]", "f}", "endcond", "endif"};
-std::string commandUniques[] = {
-  "xrefitem", "arg", "ingroup", "par", "headerfile", "overload", "weakgroup", "ref", "subpage", "dotfile", "image", "addtogroup", "li"};
-
-
-/* Changes a std::string to all lower case */
-std::string StringToLower(std::string stringToConvert) {
+std::string DoxygenParser::StringToLower(std::string stringToConvert) {
   for (unsigned int i = 0; i < stringToConvert.length(); i++) {
     stringToConvert[i] = tolower(stringToConvert[i]);
   }
   return stringToConvert;	//return the converted std::string
 }
 
-/* finds out if a command exists (is a possible command)
- * from the std::string array commandArray
- * returns -1 if no match is found */
-int findCommand(std::string smallString) {
+int DoxygenParser::findCommand(std::string smallString) {
+  std::map<std::string, DoxyCommandEnum>::iterator it;
   smallString = StringToLower(smallString);
-  int a;
-  for (unsigned i = 0; i < sizeof(commandArray) / sizeof(*commandArray); i++) {
-    if ((a = smallString.compare(commandArray[i])) == 0) {
-      return 101 + i;
-    }
-  }
+  // I'm not sure if we can really do so, because there are different commands
+  // in doxygenCommands and original commandArray
+  it = doxygenCommands.find(smallString);
+  if (it != doxygenCommands.end())
+    return 1;
   return -1;
 }
 
-/* isSectionIndicator returns a boolean if the command is a section indicator
- * This is a helper method for finding the end of a paragraph
- * by Doxygen's terms
- */
-int isSectionIndicator(std::string smallString) {
+int DoxygenParser::isSectionIndicator(std::string smallString) {
   smallString = StringToLower(smallString);
-  for (unsigned i = 0; i < sizeof(sectionIndicators) / sizeof(*sectionIndicators); i++) {
-    if (smallString.compare(sectionIndicators[i]) == 0) {
-      return 1;
-    }
-  }
+  std::set<std::string>::iterator it;
+  it = doxygenSectionIndicators.find(smallString);
+  if (it != doxygenSectionIndicators.end())
+    return 1;
   return 0;
 }
 
-/* prints the parse tree */
-void printTree(std::list < DoxygenEntity > &rootList) {
+void DoxygenParser::printTree(std::list < DoxygenEntity > &rootList) {
   std::list < DoxygenEntity >::iterator p = rootList.begin();
   while (p != rootList.end()) {
     (*p).printEntity(0);
@@ -146,81 +107,17 @@ void printTree(std::list < DoxygenEntity > &rootList) {
   }
 }
 
-/* Determines how a command should be handled (what group it belongs to
- * for parsing rules
- */
-int commandBelongs(std::string theCommand) {
+int DoxygenParser::commandBelongs(std::string theCommand) {
   std::string smallString = StringToLower(theCommand);
   //cout << " Looking for command " << theCommand << endl;
-  unsigned i = 0;
-  for (i = 0; i < sizeof(simpleCommands) / sizeof(*simpleCommands); i++) {
-    if (smallString.compare(simpleCommands[i]) == 0)
-      return SIMPLECOMMAND;
-  }
-  for (i = 0; i < sizeof(ignoredSimpleCommands) / sizeof(*ignoredSimpleCommands); i++) {
-    if (smallString.compare(ignoredSimpleCommands[i]) == 0)
-      return IGNOREDSIMPLECOMMAND;
-  }
-  for (i = 0; i < sizeof(commandWords) / sizeof(*commandWords); i++) {
-    if (smallString.compare(commandWords[i]) == 0)
-      return COMMANDWORD;
-  }
-  for (i = 0; i < sizeof(ignoredCommandWords) / sizeof(*ignoredCommandWords); i++) {
-    if (smallString.compare(ignoredCommandWords[i]) == 0)
-      return IGNOREDCOMMANDWORD;
-  }
-  for (i = 0; i < sizeof(commandLines) / sizeof(*commandLines); i++) {
-    if (smallString.compare(commandLines[i]) == 0)
-      return COMMANDLINE;
-  }
-  for (i = 0; i < sizeof(ignoreCommandLines) / sizeof(*ignoreCommandLines); i++) {
-    if (smallString.compare(ignoreCommandLines[i]) == 0)
-      return IGNOREDCOMMANDLINE;
-  }
-  for (i = 0; i < sizeof(commandParagraph) / sizeof(*commandParagraph); i++) {
-    if (smallString.compare(commandParagraph[i]) == 0)
-      return COMMANDPARAGRAPH;
-  }
-  for (i = 0; i < sizeof(ignoreCommandParagraphs) / sizeof(*ignoreCommandParagraphs); i++) {
-    if (smallString.compare(ignoreCommandParagraphs[i]) == 0)
-      return IGNORECOMMANDPARAGRAPH;
-  }
-  for (i = 0; i < sizeof(commandEndCommands) / sizeof(*commandEndCommands); i++) {
-    if (smallString.compare(commandEndCommands[i]) == 0)
-      return COMMANDENDCOMMAND;
-  }
-  for (i = 0; i < sizeof(commandWordParagraphs) / sizeof(*commandWordParagraphs); i++) {
-    if (smallString.compare(commandWordParagraphs[i]) == 0)
-      return COMMANDWORDPARAGRAPH;
-  }
-  for (i = 0; i < sizeof(commandWordLines) / sizeof(*commandWordLines); i++) {
-    if (smallString.compare(commandWordLines[i]) == 0)
-      return COMMANDWORDLINE;
-  }
-  for (i = 0; i < sizeof(commandWordOWordOWords) / sizeof(*commandWordOWordOWords); i++) {
-    if (smallString.compare(commandWordOWordOWords[i]) == 0)
-      return COMMANDWORDOWORDWORD;
-  }
-  for (i = 0; i < sizeof(commandOWords) / sizeof(*commandOWords); i++) {
-    if (smallString.compare(commandOWords[i]) == 0)
-      return COMMANDOWORD;
-  }
-  for (i = 0; i < sizeof(commandErrorThrowings) / sizeof(*commandErrorThrowings); i++) {
-    if (smallString.compare(commandErrorThrowings[i]) == 0)
-      return COMMANDERRORTHROW;
-  }
-  for (i = 0; i < sizeof(commandUniques) / sizeof(*commandUniques); i++) {
-    if (smallString.compare(commandUniques[i]) == 0)
-      return COMMANDUNIQUE;
-  }
+  std::map<std::string, DoxyCommandEnum>::iterator it;
+  it = doxygenCommands.find(smallString);
+  if (it!=doxygenCommands.end())
+    return it->second;
   return 0;
 }
 
-/* Returns the next word ON THE CURRENT LINE ONLY
- * if a new line is encountered, returns a blank std::string.
- * Updates the index it is given if success.
- */
-std::string getNextWord(TokenList & tokList) {
+std::string DoxygenParser::getNextWord(TokenList & tokList) {
   Token nextToken = tokList.peek();
   if (nextToken.tokenType == PLAINSTRING) {
     nextToken = tokList.next();
@@ -229,10 +126,7 @@ std::string getNextWord(TokenList & tokList) {
   return "";
 }
 
-/* Returns the location of the end of the line as
- * an iterator.
- */
-std::list < Token >::iterator getOneLine(TokenList & tokList) {
+std::list < Token >::iterator DoxygenParser::getOneLine(TokenList & tokList) {
   std::list < Token >::iterator endOfLine = tokList.iteratorCopy();
   while (endOfLine != tokList.end()) {
     if ((*endOfLine).tokenType == END_LINE) {
@@ -247,10 +141,7 @@ std::list < Token >::iterator getOneLine(TokenList & tokList) {
   return tokList.end();
 }
 
-/* Returns a properly formatted std::string
-* up til ANY command or end of line is encountered.
-*/
-std::string getStringTilCommand(TokenList & tokList) {
+std::string DoxygenParser::getStringTilCommand(TokenList & tokList) {
   std::string description;
   if (tokList.peek().tokenType == 0)
     return "";
@@ -263,12 +154,7 @@ std::string getStringTilCommand(TokenList & tokList) {
   return description;
 }
 
-/* Returns a properly formatted std::string
-* up til the command specified is encountered
-*/
-//TODO check that this behaves properly for formulas
-
-std::string getStringTilEndCommand(std::string theCommand, TokenList & tokList) {
+std::string DoxygenParser::getStringTilEndCommand(std::string theCommand, TokenList & tokList) {
   std::string description;
   if (tokList.peek().tokenType == 0)
     return "";
@@ -279,11 +165,7 @@ std::string getStringTilEndCommand(std::string theCommand, TokenList & tokList)
   return description;
 }
 
-/* Returns the end of a Paragraph as an iterator-
-* Paragraph is defined in Doxygen to be a paragraph of text
- * separated by either a structural command or a blank line
-*/
-std::list < Token >::iterator getEndOfParagraph(TokenList & tokList) {
+std::list < Token >::iterator DoxygenParser::getEndOfParagraph(TokenList & tokList) {
   std::list < Token >::iterator endOfParagraph = tokList.iteratorCopy();
   while (endOfParagraph != tokList.end()) {
     if ((*endOfParagraph).tokenType == END_LINE) {
@@ -311,11 +193,7 @@ std::list < Token >::iterator getEndOfParagraph(TokenList & tokList) {
   return tokList.end();
 }
 
-/* Returns the end of a section, defined as the first blank line OR first encounter of the same 
-* command. Example of this behaviour is \arg
-* if no end is encountered, returns the last token of the std::list.
-*/
-std::list < Token >::iterator getEndOfSection(std::string theCommand, TokenList & tokList) {
+std::list < Token >::iterator DoxygenParser::getEndOfSection(std::string theCommand, TokenList & tokList) {
   std::list < Token >::iterator endOfParagraph = tokList.iteratorCopy();
   while (endOfParagraph != tokList.end()) {
     if ((*endOfParagraph).tokenType == COMMAND) {
@@ -336,13 +214,7 @@ std::list < Token >::iterator getEndOfSection(std::string theCommand, TokenList
   return tokList.end();
 }
 
-/* This method is for returning the end of a specific form of doxygen command
- * that begins with a \command and ends in \endcommand
- * such as \code and \endcode. The proper usage is
- * progressTilEndCommand("endcode", tokenList);
- * If the end is never encountered, it returns the end of the std::list.
- */
-std::list < Token >::iterator getEndCommand(std::string theCommand, TokenList & tokList) {
+std::list < Token >::iterator DoxygenParser::getEndCommand(std::string theCommand, TokenList & tokList) {
   std::list < Token >::iterator endOfCommand = tokList.iteratorCopy();
   while (endOfCommand != tokList.end()) {
     if ((*endOfCommand).tokenType == COMMAND) {
@@ -356,48 +228,27 @@ std::list < Token >::iterator getEndCommand(std::string theCommand, TokenList &
   return tokList.end();
 }
 
-/* A specialty method for commands such as \arg that end at the end of a paragraph OR when another \arg is encountered
- */
-//TODO getTilAnyCommand
-std::list < Token >::iterator getTilAnyCommand(std::string theCommand, TokenList & tokList) {
+std::list < Token >::iterator DoxygenParser::getTilAnyCommand(std::string theCommand, TokenList & tokList) {
 #pragma unused(theCommand,tokList)
   std::list < Token >::iterator anIterator;
   return anIterator;
 }
 
-
-
-
-/*  Method for Adding a Simple Command
- * Format: @command
- * Plain commands, such as newline etc, they contain no other data
- *  \n \\ \@ \& \$ \# \< \> \%
- */
-int addSimpleCommand(std::string theCommand, std::list < DoxygenEntity > &doxyList) {
+int DoxygenParser::addSimpleCommand(std::string theCommand, std::list < DoxygenEntity > &doxyList) {
   if (noisy)
     cout << "Parsing " << theCommand << endl;
   doxyList.push_back(DoxygenEntity(theCommand));
   return 1;
 }
 
-/* NOT INCLUDED Simple Commands
-* Format: @command
-* Plain commands, such as newline etc, they contain no other data
-*/
-int ignoreSimpleCommand(std::string theCommand, std::list < DoxygenEntity > &doxyList) {
+int DoxygenParser::ignoreSimpleCommand(std::string theCommand, std::list < DoxygenEntity > &doxyList) {
 #pragma unused(doxyList)
   if (noisy)
     cout << "Not Adding " << theCommand << endl;
   return 1;
 }
 
-/* CommandWord
-* Format: @command <word>
-* Commands with a single WORD after then such as @b
-* "a", "b", "c", "e", "em", "p", "def", "enum", "example", "package", 
-* "relates", "namespace", "relatesalso","anchor", "dontinclude", "include", "includelineno"
-*/
-int addCommandWord(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
+int DoxygenParser::addCommandWord(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
   if (noisy)
     cout << "Parsing " << theCommand << endl;
   std::string name = getNextWord(tokList);
@@ -409,12 +260,7 @@ int addCommandWord(std::string theCommand, TokenList & tokList, std::list < Doxy
   return 0;
 }
 
-/* NOT INCLUDED CommandWord
-* Format: @command <word>
-* Commands with a single WORD after then such as @b
-* "copydoc", "copybrief", "copydetails", "verbinclude", "htmlinclude"
-*/
-int ignoreCommandWord(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
+int DoxygenParser::ignoreCommandWord(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
 #pragma unused(doxyList)
   if (noisy)
     cout << "Not Adding " << theCommand << endl;
@@ -426,12 +272,7 @@ int ignoreCommandWord(std::string theCommand, TokenList & tokList, std::list < D
   return 0;
 }
 
-/* CommandLine
-* Format: @command (line)
-* Commands with a single LINE after then such as @var
-* "addindex", "fn", "name", "line", "var", "skipline", "typedef", "skip", "until", "property"
-*/
-int addCommandLine(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
+int DoxygenParser::addCommandLine(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
   if (noisy)
     cout << "Parsing " << theCommand << endl;
   std::list < Token >::iterator endOfLine = getOneLine(tokList);
@@ -440,12 +281,7 @@ int addCommandLine(std::string theCommand, TokenList & tokList, std::list < Doxy
   return 1;
 }
 
-/* NOT INCLUDED CommandLine
-* Format: @command (line)
-* Commands with a single LINE after then such as @var
-* 
-*/
-int ignoreCommandLine(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
+int DoxygenParser::ignoreCommandLine(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
 #pragma unused(doxyList)
   if (noisy)
     cout << "Not Adding " << theCommand << endl;
@@ -454,13 +290,7 @@ int ignoreCommandLine(std::string theCommand, TokenList & tokList, std::list < D
   return 1;
 }
 
-/* CommandParagraph
-* Format: @command {paragraph}
-* Commands with a single paragraph after then such as @return
-* "return", "remarks", "since", "test", "sa", "see", "pre", "post", "details", "invariant", 
-* "deprecated", "date", "note", "warning", "version", "todo", "bug", "attention", "brief", "arg", "author"
-*/
-int addCommandParagraph(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
+int DoxygenParser::addCommandParagraph(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
   if (noisy)
     cout << "Parsing " << theCommand << endl;
   std::list < Token >::iterator endOfParagraph = getEndOfParagraph(tokList);
@@ -470,12 +300,7 @@ int addCommandParagraph(std::string theCommand, TokenList & tokList, std::list <
   return 1;
 }
 
-/* CommandParagraph
-* Format: @command {paragraph}
-* Commands with a single LINE after then such as @var
-* 
-*/
-int ignoreCommandParagraph(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
+int DoxygenParser::ignoreCommandParagraph(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
 #pragma unused(doxyList)
   if (noisy)
     cout << "Not Adding " << theCommand << endl;
@@ -484,27 +309,15 @@ int ignoreCommandParagraph(std::string theCommand, TokenList & tokList, std::lis
   return 1;
 }
 
-/* Command EndCommand
-* Format: @command and ends at @endcommand
-* Commands that take in a block of text such as @code
-* "code", "dot", "msc", "f$", "f[", "f{environment}{", "htmlonly", "latexonly", "manonly", 
-* "verbatim", "xmlonly", "cond", "if", "ifnot", "link"
-* Returns 1 if success, 0 if the endcommand is never encountered.
-*/
-int addCommandEndCommand(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
+int DoxygenParser::addCommandEndCommand(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
   if (noisy)
-    cout << "Not Adding " << theCommand << endl;
+    cout << "Parsing " << theCommand << endl;
   std::string description = getStringTilEndCommand("end" + theCommand, tokList);
   doxyList.push_back(DoxygenEntity(theCommand, description));
   return 1;
 }
 
-/* CommandWordParagraph
-* Format: @command <word> {paragraph}
-* Commands such as param
- * "param", "tparam", "throw", "throws", "retval", "exception"
-*/
-int addCommandWordParagraph(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
+int DoxygenParser::addCommandWordParagraph(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
   if (noisy)
     cout << "Parsing " << theCommand << endl;
   std::string name = getNextWord(tokList);
@@ -520,12 +333,7 @@ int addCommandWordParagraph(std::string theCommand, TokenList & tokList, std::li
   return 1;
 }
 
-/* CommandWordLine
-* Format: @command <word> (line)
-* Commands such as param
-* "page", "subsection", "subsubsection", "section", "paragraph", "defgroup"
-*/
-int addCommandWordLine(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
+int DoxygenParser::addCommandWordLine(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
   if (noisy)
     cout << "Parsing " << theCommand << endl;
   std::string name = getNextWord(tokList);
@@ -542,12 +350,7 @@ int addCommandWordLine(std::string theCommand, TokenList & tokList, std::list <
   //else cout << "No line followed " << theCommand <<  " command. Not added" << endl;
 }
 
-/* Command Word Optional Word Optional Word
-* Format: @command <word> [<header-file>] [<header-name>]
-* Commands such as class
-* "category", "class", "protocol", "interface", "struct", "union"
-*/
-int addCommandWordOWordOWord(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
+int DoxygenParser::addCommandWordOWordOWord(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
   if (noisy)
     cout << "Parsing " << theCommand << endl;
   std::string name = getNextWord(tokList);
@@ -567,12 +370,7 @@ int addCommandWordOWordOWord(std::string theCommand, TokenList & tokList, std::l
   return 1;
 }
 
-/* Command Optional Word
-* Format: @command [<word>]
-* Commands such as dir
-* "dir", "file", "cond"
-*/
-int addCommandOWord(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
+int DoxygenParser::addCommandOWord(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
   if (noisy)
     cout << "Parsing " << theCommand << endl;
   std::string name = getNextWord(tokList);
@@ -580,10 +378,7 @@ int addCommandOWord(std::string theCommand, TokenList & tokList, std::list < Dox
   return 1;
 }
 
- /* Commands that should not be encountered (such as PHP only)
-  * goes til the end of line then returns
-  */
-int addCommandErrorThrow(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
+int DoxygenParser::addCommandErrorThrow(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
 #pragma unused(doxyList)
   if (noisy) {
     cout << "Encountered :" << theCommand << endl;
@@ -594,8 +389,7 @@ int addCommandErrorThrow(std::string theCommand, TokenList & tokList, std::list
   return 0;
 }
 
-/* Adds the unique commands- different process for each unique command */
-int addCommandUnique(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
+int DoxygenParser::addCommandUnique(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
   std::list < DoxygenEntity > aNewList;
   if (theCommand.compare("arg") == 0 || theCommand.compare("li") == 0) {
     std::list < Token >::iterator endOfSection = getEndOfSection(theCommand, tokList);
@@ -722,11 +516,7 @@ int addCommandUnique(std::string theCommand, TokenList & tokList, std::list < Do
   return 0;
 }
 
-/* The actual "meat" of the doxygen parser. This is not yet fully implemented
- * with my current design- however the skeletal outline is contained in
- * the file Skeleton
- */
-int addCommand(std::string commandString, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
+int DoxygenParser::addCommand(std::string commandString, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
   std::string theCommand = StringToLower(commandString);
   if (theCommand.compare("plainstd::string") == 0) {
     std::string nextPhrase = getStringTilCommand(tokList);
@@ -785,7 +575,7 @@ int addCommand(std::string commandString, TokenList & tokList, std::list < Doxyg
   return 0;
 }
 
-std::list < DoxygenEntity > parse(std::list < Token >::iterator endParsingIndex, TokenList & tokList) {
+std::list < DoxygenEntity > DoxygenParser::parse(std::list < Token >::iterator endParsingIndex, TokenList & tokList) {
   std::list < DoxygenEntity > aNewList;
   int currCommand;
   while (tokList.current() != endParsingIndex) {
@@ -813,7 +603,7 @@ std::list < DoxygenEntity > parse(std::list < Token >::iterator endParsingIndex,
   return aNewList;
 }
 
-std::list < DoxygenEntity > parseRoot(std::list < Token >::iterator endParsingIndex, TokenList & tokList) {
+std::list < DoxygenEntity > DoxygenParser::parseRoot(std::list < Token >::iterator endParsingIndex, TokenList & tokList) {
 
   std::list < DoxygenEntity > aNewList;
   int currCommand;
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.h b/Source/DoxygenTranslator/src/DoxygenParser.h
index 0c1f2d1cb..e64644725 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.h
+++ b/Source/DoxygenTranslator/src/DoxygenParser.h
@@ -13,12 +13,227 @@
 #define DOXYGENPARSER_H_
 #include <string>
 #include <list>
+#include <map>
+#include <set>
 #include "DoxygenEntity.h"
+#include "TokenList.h"
 class DoxygenParser {
 public:
   DoxygenParser();
   virtual ~DoxygenParser();
   std::list < DoxygenEntity > createTree(std::string doxygen);
+private:
+  
+  /*
+   *Changes a std::string to all lower case
+   */
+  std::string StringToLower(std::string stringToConvert);
+
+  /* 
+   * Finds out if a command exists (is a possible command)
+   * returns -1 if no match is found
+   */
+  int findCommand(std::string smallString);
+  /* 
+   * isSectionIndicator returns a boolean if the command is a section indicator
+   * This is a helper method for finding the end of a paragraph
+   * by Doxygen's terms
+   */
+  int isSectionIndicator(std::string smallString);
+  /*
+   * Determines how a command should be handled (what group it belongs to
+   * for parsing rules
+   */
+  int commandBelongs(std::string theCommand);
+
+  /*
+   *prints the parse tree
+   */
+  void printTree(std::list < DoxygenEntity > &rootList);
+
+  /*
+   * Returns the next word ON THE CURRENT LINE ONLY
+   * if a new line is encountered, returns a blank std::string.
+   * Updates the index it is given if success.
+   */
+  std::string getNextWord(TokenList & tokList);
+
+  /* 
+   * Returns the location of the end of the line as
+   * an iterator.
+   */
+  std::list < Token >::iterator getOneLine(TokenList & tokList);
+
+  /*
+   * Returns a properly formatted std::string
+   * up til ANY command or end of line is encountered.
+   */
+  std::string getStringTilCommand(TokenList & tokList);
+
+  /*
+   * Returns a properly formatted std::string
+   * up til the command specified is encountered
+   */
+  //TODO check that this behaves properly for formulas
+  std::string getStringTilEndCommand(std::string theCommand, TokenList & tokList);
+
+  /*
+   * Returns the end of a Paragraph as an iterator-
+   * Paragraph is defined in Doxygen to be a paragraph of text
+   * separated by either a structural command or a blank line
+   */
+  std::list < Token >::iterator getEndOfParagraph(TokenList & tokList);
+
+  /*
+   * Returns the end of a section, defined as the first blank line OR first encounter of the same 
+   * command. Example of this behaviour is \arg
+   * if no end is encountered, returns the last token of the std::list.
+   */
+  std::list < Token >::iterator getEndOfSection(std::string theCommand, TokenList & tokList);
+
+  /*
+   * This method is for returning the end of a specific form of doxygen command
+   * that begins with a \command and ends in \endcommand
+   * such as \code and \endcode. The proper usage is
+   * progressTilEndCommand("endcode", tokenList);
+   * If the end is never encountered, it returns the end of the std::list.
+   */
+  std::list < Token >::iterator getEndCommand(std::string theCommand, TokenList & tokList);
+  /*
+   * A specialty method for commands such as \arg that end at the end of a paragraph OR when another \arg is encountered
+   */
+  //TODO getTilAnyCommand
+  std::list < Token >::iterator getTilAnyCommand(std::string theCommand, TokenList & tokList);
+
+  /*
+   * Method for Adding a Simple Command
+   * Format: @command
+   * Plain commands, such as newline etc, they contain no other data
+   *  \n \\ \@ \& \$ \# \< \> \%
+   */
+  int addSimpleCommand(std::string theCommand, std::list < DoxygenEntity > &doxyList);
+  /*
+   * NOT INCLUDED Simple Commands
+   * Format: @command
+   * Plain commands, such as newline etc, they contain no other data
+   */
+  int ignoreSimpleCommand(std::string theCommand, std::list < DoxygenEntity > &doxyList);
+  /*
+   * CommandWord
+   * Format: @command <word>
+   * Commands with a single WORD after then such as @b
+   * "a", "b", "c", "e", "em", "p", "def", "enum", "example", "package", 
+   * "relates", "namespace", "relatesalso","anchor", "dontinclude", "include", "includelineno"
+   */
+  int addCommandWord(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList);
+  /*
+   * NOT INCLUDED CommandWord
+   * Format: @command <word>
+   * Commands with a single WORD after then such as @b
+   * "copydoc", "copybrief", "copydetails", "verbinclude", "htmlinclude"
+   */
+  int ignoreCommandWord(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList);
+  /*
+   * CommandLine
+   * Format: @command (line)
+   * Commands with a single LINE after then such as @var
+   * "addindex", "fn", "name", "line", "var", "skipline", "typedef", "skip", "until", "property"
+   */
+  int addCommandLine(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList);
+  /*
+   * NOT INCLUDED CommandLine
+   * Format: @command (line)
+   * Commands with a single LINE after then such as @var
+   */
+  int ignoreCommandLine(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList);
+  /*
+   * CommandParagraph
+   * Format: @command {paragraph}
+   * Commands with a single paragraph after then such as @return
+   * "return", "remarks", "since", "test", "sa", "see", "pre", "post", "details", "invariant", 
+   * "deprecated", "date", "note", "warning", "version", "todo", "bug", "attention", "brief", "arg", "author"
+   */
+  int addCommandParagraph(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList);
+  /*
+   * CommandParagraph
+   * Format: @command {paragraph}
+   * Commands with a single LINE after then such as @var
+   */
+  int ignoreCommandParagraph(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList);
+  /*
+   * Command EndCommand
+   * Format: @command and ends at @endcommand
+   * Commands that take in a block of text such as @code
+   * "code", "dot", "msc", "f$", "f[", "f{environment}{", "htmlonly", "latexonly", "manonly", 
+   * "verbatim", "xmlonly", "cond", "if", "ifnot", "link"
+   * Returns 1 if success, 0 if the endcommand is never encountered.
+   */
+  int addCommandEndCommand(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList);
+  /*
+   * CommandWordParagraph
+   * Format: @command <word> {paragraph}
+   * Commands such as param
+   * "param", "tparam", "throw", "throws", "retval", "exception"
+   */
+  int addCommandWordParagraph(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList);
+  /*
+   * CommandWordLine
+   * Format: @command <word> (line)
+   * Commands such as param
+   * "page", "subsection", "subsubsection", "section", "paragraph", "defgroup"
+   */
+  int addCommandWordLine(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList);
+  /*
+   * Command Word Optional Word Optional Word
+   * Format: @command <word> [<header-file>] [<header-name>]
+   * Commands such as class
+   * "category", "class", "protocol", "interface", "struct", "union"
+   */
+  int addCommandWordOWordOWord(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList);
+  /*
+   * Command Optional Word
+   * Format: @command [<word>]
+   * Commands such as dir
+   * "dir", "file", "cond"
+   */
+  int addCommandOWord(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList);
+  /*
+   * Commands that should not be encountered (such as PHP only)
+   * goes til the end of line then returns
+   */
+  int addCommandErrorThrow(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList);
+  /*
+   *Adds the unique commands- different process for each unique command
+   */
+  int addCommandUnique(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList);
+  /* 
+   * The actual "meat" of the doxygen parser. This is not yet fully implemented
+   * with my current design- however the skeletal outline is contained in
+   * the file Skeleton
+   */
+  int addCommand(std::string commandString, TokenList & tokList, std::list < DoxygenEntity > &doxyList);
+
+  std::list < DoxygenEntity > parse(std::list < Token >::iterator endParsingIndex, TokenList & tokList);
+  std::list < DoxygenEntity > parseRoot(std::list < Token >::iterator endParsingIndex, TokenList & tokList);
+  
+  /*
+   * Fill static doxygenCommands and sectionIndicators containers
+   */
+  void fillTables();
+  
+  /*
+   * Whether to print lots of debug info during parsing
+   */
+  bool noisy;
+  
+  /* 
+   * Map of Doxygen commands to determine if a string is a
+   * command and how it needs to be parsed 
+   */
+  static std::map<std::string, DoxyCommandEnum> doxygenCommands;
+  
+  static std::set<std::string> doxygenSectionIndicators;
 };
 
 #endif
+

From 4398d1aee4a7237f514d3cc54e2befa5dbd65d99 Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Wed, 4 Jul 2012 22:28:41 +0000
Subject: [PATCH 062/314] Fixed a bug in parser with doxygen commands like
 code, dot, verbatim and so on

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13254 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Source/DoxygenTranslator/src/DoxygenParser.cpp | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/Source/DoxygenTranslator/src/DoxygenParser.cpp b/Source/DoxygenTranslator/src/DoxygenParser.cpp
index fe4dc5ec0..b760fcf42 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenParser.cpp
@@ -158,10 +158,14 @@ std::string DoxygenParser::getStringTilEndCommand(std::string theCommand, TokenL
   std::string description;
   if (tokList.peek().tokenType == 0)
     return "";
-  while (tokList.peek().tokenString.compare(theCommand) != 0) {
-    Token currentToken = tokList.next();
-    description = description + currentToken.tokenString + " ";
+  while (tokList.next().tokenString.compare(theCommand) != 0) {
+    //TODO: it won't output doxygen commands, need a way to fix it
+    if (tokList.peek().tokenType == PLAINSTRING)
+      description += tokList.peek().tokenString + " ";
+    if (tokList.peek().tokenType == END_LINE)
+      description += "\n";
   }
+  tokList.next(); // eat the end command itself
   return description;
 }
 

From f57b515ee7a813995b80913471769b8eb3666fee Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Wed, 4 Jul 2012 22:54:37 +0000
Subject: [PATCH 063/314] Got rid of translated comments cache, seems very
 inefficient

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13255 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 .../DoxygenTranslator/src/DoxygenTranslator.cpp  | 16 +---------------
 Source/DoxygenTranslator/src/DoxygenTranslator.h |  9 ++-------
 2 files changed, 3 insertions(+), 22 deletions(-)

diff --git a/Source/DoxygenTranslator/src/DoxygenTranslator.cpp b/Source/DoxygenTranslator/src/DoxygenTranslator.cpp
index a733fdbc7..18cf24c85 100644
--- a/Source/DoxygenTranslator/src/DoxygenTranslator.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenTranslator.cpp
@@ -15,12 +15,8 @@
 #include "DoxygenTranslator.h"
 
 DoxygenTranslator::DoxygenTranslator() {
-  // Init the cache
-  resultsCache = NewHash();
 }
 DoxygenTranslator::~DoxygenTranslator() {
-  // Clean up the cache
-  Delete(resultsCache);
 }
 
 bool DoxygenTranslator::hasDocumentation(Node *node) {
@@ -37,17 +33,7 @@ String *DoxygenTranslator::getDocumentation(Node *node) {
   if (!hasDocumentation(node))
     return 0;
   
-  // get from cache
-  String *resultedDocs = Getattr(resultsCache, getDoxygenComment(node));
-  
-  if (resultedDocs)
-    return resultedDocs;
-  
-  // not found in cache, produce it
-  resultedDocs = makeDocumentation(node);
-  Setattr(resultsCache, getDoxygenComment(node), resultedDocs);
-  
-  return resultedDocs;
+  return makeDocumentation(node);
 }
 
 void DoxygenTranslator::printTree(std::list < DoxygenEntity > &entityList) {
diff --git a/Source/DoxygenTranslator/src/DoxygenTranslator.h b/Source/DoxygenTranslator/src/DoxygenTranslator.h
index 7ddaba9a8..637b30a9e 100644
--- a/Source/DoxygenTranslator/src/DoxygenTranslator.h
+++ b/Source/DoxygenTranslator/src/DoxygenTranslator.h
@@ -22,7 +22,7 @@
 
 
 /*
- * A class to translate doxygen comments attacted to parser nodes
+ * A class to translate doxygen comments attached to parser nodes
  * into alternative formats for use in code generated for target languages.
  */
 class DoxygenTranslator {
@@ -37,7 +37,7 @@ public:
   virtual ~ DoxygenTranslator();
   /*
    * Return the documentation for a given node formated for the correct 
-   * documentation system. The result is cached and translated only once.
+   * documentation system.
    * @param node The node to extract and translate documentation for.
    * @return The resulted documentation string.
    */
@@ -70,11 +70,6 @@ protected:
    * Doxygen parser object
    */
   DoxygenParser parser;
-  
-  /*
-   * Cache of translated comments
-   */
-  Hash *resultsCache;
 };
 
 #endif

From 501bb822e6be59b6407e1317c1e046a388aa22bf Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Wed, 4 Jul 2012 22:56:29 +0000
Subject: [PATCH 064/314] Oops, debug output should be left off by default

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13256 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Source/DoxygenTranslator/src/DoxygenParser.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Source/DoxygenTranslator/src/DoxygenParser.cpp b/Source/DoxygenTranslator/src/DoxygenParser.cpp
index b760fcf42..07e61b590 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenParser.cpp
@@ -19,7 +19,7 @@ std::map<std::string, DoxyCommandEnum> DoxygenParser::doxygenCommands;
 std::set<std::string> DoxygenParser::doxygenSectionIndicators;
 
 
-DoxygenParser::DoxygenParser() : noisy(true) {
+DoxygenParser::DoxygenParser() : noisy(false) {
   fillTables();
 }
 

From 93a02cc728a5e5f2431445ae808c89d686f62aa5 Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Sat, 7 Jul 2012 13:40:41 +0000
Subject: [PATCH 065/314] Refactored doxygen tests

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13261 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Examples/test-suite/doxygen_basic_translate.i |  6 +-
 Examples/test-suite/doxygen_parsing_enums.i   |  4 +-
 Examples/test-suite/java/commentParser.java   | 71 ++++++++++++++++
 .../java/doxygen_basic_translate_runme.java   | 82 +++----------------
 .../doxygen_parsing_enums_proper_runme.java   | 75 ++---------------
 .../doxygen_parsing_enums_simple_runme.java   | 75 ++---------------
 .../doxygen_parsing_enums_typesafe_runme.java | 75 ++---------------
 ...oxygen_parsing_enums_typeunsafe_runme.java | 75 ++---------------
 .../java/doxygen_parsing_runme.java           | 71 ++--------------
 9 files changed, 131 insertions(+), 403 deletions(-)
 create mode 100644 Examples/test-suite/java/commentParser.java

diff --git a/Examples/test-suite/doxygen_basic_translate.i b/Examples/test-suite/doxygen_basic_translate.i
index c961164d5..af449eb49 100644
--- a/Examples/test-suite/doxygen_basic_translate.i
+++ b/Examples/test-suite/doxygen_basic_translate.i
@@ -3,7 +3,9 @@
 %inline %{
 
 /**
- * \brief Brief description.
+ * \brief
+ * Brief description.
+ * 
  * The comment text
  * \author Some author
  * \return Some number
@@ -13,4 +15,4 @@ int function()
 {
 }
 
-%}
\ No newline at end of file
+%}
diff --git a/Examples/test-suite/doxygen_parsing_enums.i b/Examples/test-suite/doxygen_parsing_enums.i
index 317abf384..222356510 100644
--- a/Examples/test-suite/doxygen_parsing_enums.i
+++ b/Examples/test-suite/doxygen_parsing_enums.i
@@ -9,7 +9,7 @@ enum E_TEST
   /** the first item */
   E_TEST_ONE,
   E_TEST_TWO = 2, /**< the second */
-  E_TEST_THREE = 2+1
+  E_TEST_THREE = 2+1 /**< the last item */
 };
 
-%}
\ No newline at end of file
+%}
diff --git a/Examples/test-suite/java/commentParser.java b/Examples/test-suite/java/commentParser.java
new file mode 100644
index 000000000..3877f5f4d
--- /dev/null
+++ b/Examples/test-suite/java/commentParser.java
@@ -0,0 +1,71 @@
+
+import com.sun.javadoc.*;
+import java.util.HashMap;
+import java.util.Map.Entry;
+import java.util.Iterator;
+
+public class commentParser {
+	static HashMap<String, String> parsedComments = new HashMap<String, String>();
+
+	public static boolean start(RootDoc root) {
+
+		/*
+		 * This method is called by 'javadoc' and gets the whole parsed java
+		 * file, we get comments and store them
+		 */
+
+		ClassDoc[] classes = root.classes();
+
+		for (int i = 0; i < classes.length; i++) {
+
+			if (classes[i].getRawCommentText().length() > 0)
+				parsedComments.put(classes[i].name(),
+						classes[i].getRawCommentText());
+
+			MethodDoc[] methods = classes[i].methods();
+			FieldDoc[] fields = classes[i].fields();
+			FieldDoc[] constants = classes[i].enumConstants();
+
+			for (int j = 0; j < constants.length; j++) {
+				FieldDoc f = constants[j];
+				if (f.getRawCommentText().length() > 0)
+					parsedComments.put(f.name(), f.getRawCommentText());
+			}
+			for (int j = 0; j < fields.length; j++) {
+				FieldDoc f = fields[j];
+				if (f.getRawCommentText().length() > 0)
+					parsedComments.put(f.name(), f.getRawCommentText());
+			}
+			for (int j = 0; j < methods.length; j++) {
+				MethodDoc m = methods[j];
+				if (m.getRawCommentText().length() > 0)
+					parsedComments.put(m.name(), m.getRawCommentText());
+			}
+		}
+		return true;
+	}
+
+	public static int check(HashMap<String, String> wantedComments) {
+		int errorCount=0;
+		Iterator< Entry<String, String> > it = parsedComments.entrySet().iterator();
+
+		while (it.hasNext())
+		{
+			Entry<String, String> e = (Entry<String, String>) it.next();
+
+			if (!e.getValue().equals(wantedComments.get(e.getKey()))) {
+				System.out.println("Documentation comments for " + e.getKey() + " does not match: ");
+				System.out.println("\texpected:"+wantedComments.get(e.getKey()));
+				System.out.println("\tgot:\t"+e.getValue());
+				errorCount++;
+			}
+		}
+
+		if (parsedComments.size() < wantedComments.size()) {
+			System.out.println("Found " + (wantedComments.size()-parsedComments.size()) + " missed comment(s)!");
+			errorCount++;
+		}
+		
+		return errorCount;
+	}
+}
\ No newline at end of file
diff --git a/Examples/test-suite/java/doxygen_basic_translate_runme.java b/Examples/test-suite/java/doxygen_basic_translate_runme.java
index 7aee4221b..34270de56 100644
--- a/Examples/test-suite/java/doxygen_basic_translate_runme.java
+++ b/Examples/test-suite/java/doxygen_basic_translate_runme.java
@@ -2,8 +2,6 @@
 import doxygen_basic_translate.*;
 import com.sun.javadoc.*;
 import java.util.HashMap;
-import java.util.Map.Entry;
-import java.util.Iterator;
 
 public class doxygen_basic_translate_runme {
   static {
@@ -14,81 +12,25 @@ public class doxygen_basic_translate_runme {
       System.exit(1);
     }
   }
-
-  static HashMap<String, String> parsedComments = new HashMap<String, String>();
-  static HashMap<String, String> wantedComments = new HashMap<String, String>();
-
-  public static boolean start(RootDoc root) {
-    
-    /*
-      This method is called by 'javadoc' and gets the whole parsed
-      java file, we get comments and store them
-    */
-
-    ClassDoc[] classes = root.classes();
-
-    for (int i = 0; i < classes.length; i++) {
-
-      if (classes[i].getRawCommentText().length() > 0)
-	parsedComments.put(classes[i].name(), classes[i].getRawCommentText());
-
-      MethodDoc[] methods = classes[i].methods();
-      FieldDoc[] fields = classes[i].fields();
-      FieldDoc[] constants = classes[i].enumConstants();
-
-      for (int j = 0; j < constants.length; j++) {
-        FieldDoc f = constants[j];
-	if (f.getRawCommentText().length() > 0)
-	  parsedComments.put(f.name(), f.getRawCommentText());
-      }
-      for (int j = 0; j < fields.length; j++) {
-        FieldDoc f = fields[j];
-	if (f.getRawCommentText().length() > 0)
-	  parsedComments.put(f.name(), f.getRawCommentText());
-      }
-      for (int j = 0; j < methods.length; j++) {
-        MethodDoc m = methods[j];
-	if (m.getRawCommentText().length() > 0)
-	  parsedComments.put(m.name(), m.getRawCommentText());
-      }
-    }
-    return true;
-  }
-
+  
   public static void main(String argv[]) 
   {
     /*
       Here we are using internal javadoc tool, it accepts the name of the class as paramterer,
       and calls the start() method of that class with parsed information.
     */
+	commentParser parser = new commentParser();
     com.sun.tools.javadoc.Main.execute("doxygen_basic_translate runtime test",
-	"doxygen_basic_translate_runme", new String[]{"-quiet", "doxygen_basic_translate"});
+	"commentParser", new String[]{"-quiet", "doxygen_basic_translate"});
 
+    HashMap<String, String> wantedComments = new HashMap<String, String>();
+    
     wantedComments.put("function", " Brief description.  \n The comment text  \n" +
-				   " @author\tSome author  \n" +
-				   " @return\tSome number  \n" +
-				   " @see\tfunction2  \n");
-
-    int errorCount=0;
-    Iterator< Entry<String, String> > it = parsedComments.entrySet().iterator();
-
-    while (it.hasNext())
-    {
-	Entry<String, String> e = (Entry<String, String>) it.next();
-
-	if (!e.getValue().equals(wantedComments.get(e.getKey()))) {
-	    System.out.println("Documentation comments for " + e.getKey() + " does not match: ");
-	    System.out.println("\texpected:"+wantedComments.get(e.getKey()));
-	    System.out.println("\tgot:\t"+e.getValue());
-	    errorCount++;
-	}
-    }
-
-    if (parsedComments.size() != wantedComments.size()) {
-	System.out.println("Found " + (wantedComments.size()-parsedComments.size()) + " missed comment(s)!");
-	errorCount++;
-    }
-
-    System.exit(errorCount);
+			   " @author\tSome author  \n" +
+			   " @return\tSome number  \n" +
+			   " @see\tfunction2  \n");
+    
+    // and ask the parser to check comments for us
+    System.exit(parser.check(wantedComments));
   }
-}
+}
\ No newline at end of file
diff --git a/Examples/test-suite/java/doxygen_parsing_enums_proper_runme.java b/Examples/test-suite/java/doxygen_parsing_enums_proper_runme.java
index 503e2c68e..d3993f201 100644
--- a/Examples/test-suite/java/doxygen_parsing_enums_proper_runme.java
+++ b/Examples/test-suite/java/doxygen_parsing_enums_proper_runme.java
@@ -2,8 +2,6 @@
 import doxygen_parsing_enums_proper.*;
 import com.sun.javadoc.*;
 import java.util.HashMap;
-import java.util.Map.Entry;
-import java.util.Iterator;
 
 public class doxygen_parsing_enums_proper_runme {
   static {
@@ -14,80 +12,25 @@ public class doxygen_parsing_enums_proper_runme {
       System.exit(1);
     }
   }
-
-  static HashMap<String, String> parsedComments = new HashMap<String, String>();
-  static HashMap<String, String> wantedComments = new HashMap<String, String>();
-
-  public static boolean start(RootDoc root) {
-    
-    /*
-      This method is called by 'javadoc' and gets the whole parsed
-      java file, we get comments and store them
-    */
-
-    ClassDoc[] classes = root.classes();
-
-    for (int i = 0; i < classes.length; i++) {
-
-      if (classes[i].getRawCommentText().length() > 0)
-	parsedComments.put(classes[i].name(), classes[i].getRawCommentText());
-
-      MethodDoc[] methods = classes[i].methods();
-      FieldDoc[] fields = classes[i].fields();
-      FieldDoc[] constants = classes[i].enumConstants();
-
-      for (int j = 0; j < constants.length; j++) {
-        FieldDoc f = constants[j];
-	if (f.getRawCommentText().length() > 0)
-	  parsedComments.put(f.name(), f.getRawCommentText());
-      }
-      for (int j = 0; j < fields.length; j++) {
-        FieldDoc f = fields[j];
-	if (f.getRawCommentText().length() > 0)
-	  parsedComments.put(f.name(), f.getRawCommentText());
-      }
-      for (int j = 0; j < methods.length; j++) {
-        MethodDoc m = methods[j];
-	if (m.getRawCommentText().length() > 0)
-	  parsedComments.put(m.name(), m.getRawCommentText());
-      }
-    }
-    return true;
-  }
-
+  
   public static void main(String argv[]) 
   {
     /*
       Here we are using internal javadoc tool, it accepts the name of the class as paramterer,
       and calls the start() method of that class with parsed information.
     */
+	commentParser parser = new commentParser();
     com.sun.tools.javadoc.Main.execute("doxygen_parsing_enums_proper runtime test",
-	"doxygen_parsing_enums_proper_runme", new String[]{"-quiet", "doxygen_parsing_enums_proper"});
+	"commentParser", new String[]{"-quiet", "doxygen_parsing_enums_proper"});
 
+    HashMap<String, String> wantedComments = new HashMap<String, String>();
+    
     wantedComments.put("E_TEST", " Test enumeration  \n");
     wantedComments.put("E_TEST_ONE", " the first item  \n");
     wantedComments.put("E_TEST_TWO", " the second  \n");
-
-    int errorCount=0;
-    Iterator< Entry<String, String> > it = parsedComments.entrySet().iterator();
-
-    while (it.hasNext())
-    {
-	Entry<String, String> e = (Entry<String, String>) it.next();
-
-	if (!e.getValue().equals(wantedComments.get(e.getKey()))) {
-	    System.out.println("Documentation comments for " + e.getKey() + " does not match: ");
-	    System.out.println("\texpected:"+wantedComments.get(e.getKey()));
-	    System.out.println("\tgot:\t"+e.getValue());
-	    errorCount++;
-	}
-    }
-
-    if (parsedComments.size() != wantedComments.size()) {
-	System.out.println("Found " + (wantedComments.size()-parsedComments.size()) + " missed comment(s)!");
-	errorCount++;
-    }
-
-    System.exit(errorCount);
+    wantedComments.put("E_TEST_THREE", " the last item  \n");
+    
+    // and ask the parser to check comments for us
+    System.exit(parser.check(wantedComments));
   }
 }
diff --git a/Examples/test-suite/java/doxygen_parsing_enums_simple_runme.java b/Examples/test-suite/java/doxygen_parsing_enums_simple_runme.java
index ee422e2c4..1dffe4466 100644
--- a/Examples/test-suite/java/doxygen_parsing_enums_simple_runme.java
+++ b/Examples/test-suite/java/doxygen_parsing_enums_simple_runme.java
@@ -2,8 +2,6 @@
 import doxygen_parsing_enums_simple.*;
 import com.sun.javadoc.*;
 import java.util.HashMap;
-import java.util.Map.Entry;
-import java.util.Iterator;
 
 public class doxygen_parsing_enums_simple_runme {
   static {
@@ -14,79 +12,24 @@ public class doxygen_parsing_enums_simple_runme {
       System.exit(1);
     }
   }
-
-  static HashMap<String, String> parsedComments = new HashMap<String, String>();
-  static HashMap<String, String> wantedComments = new HashMap<String, String>();
-
-  public static boolean start(RootDoc root) {
-    
-    /*
-      This method is called by 'javadoc' and gets the whole parsed
-      java file, we get comments and store them
-    */
-
-    ClassDoc[] classes = root.classes();
-
-    for (int i = 0; i < classes.length; i++) {
-
-      if (classes[i].getRawCommentText().length() > 0)
-	parsedComments.put(classes[i].name(), classes[i].getRawCommentText());
-
-      MethodDoc[] methods = classes[i].methods();
-      FieldDoc[] fields = classes[i].fields();
-      FieldDoc[] constants = classes[i].enumConstants();
-
-      for (int j = 0; j < constants.length; j++) {
-        FieldDoc f = constants[j];
-	if (f.getRawCommentText().length() > 0)
-	  parsedComments.put(f.name(), f.getRawCommentText());
-      }
-      for (int j = 0; j < fields.length; j++) {
-        FieldDoc f = fields[j];
-	if (f.getRawCommentText().length() > 0)
-	  parsedComments.put(f.name(), f.getRawCommentText());
-      }
-      for (int j = 0; j < methods.length; j++) {
-        MethodDoc m = methods[j];
-	if (m.getRawCommentText().length() > 0)
-	  parsedComments.put(m.name(), m.getRawCommentText());
-      }
-    }
-    return true;
-  }
-
+  
   public static void main(String argv[]) 
   {
     /*
       Here we are using internal javadoc tool, it accepts the name of the class as paramterer,
       and calls the start() method of that class with parsed information.
     */
+	commentParser parser = new commentParser();
     com.sun.tools.javadoc.Main.execute("doxygen_parsing_enums_simple runtime test",
-	"doxygen_parsing_enums_simple_runme", new String[]{"-quiet", "doxygen_parsing_enums_simple"});
+	"commentParser", new String[]{"-quiet", "doxygen_parsing_enums_simple"});
 
+    HashMap<String, String> wantedComments = new HashMap<String, String>();
+    
     wantedComments.put("E_TEST_ONE", " the first item  \n");
     wantedComments.put("E_TEST_TWO", " the second  \n");
-
-    int errorCount=0;
-    Iterator< Entry<String, String> > it = parsedComments.entrySet().iterator();
-
-    while (it.hasNext())
-    {
-	Entry<String, String> e = (Entry<String, String>) it.next();
-
-	if (!e.getValue().equals(wantedComments.get(e.getKey()))) {
-	    System.out.println("Documentation comments for " + e.getKey() + " does not match: ");
-	    System.out.println("\texpected:"+wantedComments.get(e.getKey()));
-	    System.out.println("\tgot:\t"+e.getValue());
-	    errorCount++;
-	}
-    }
-
-    if (parsedComments.size() != wantedComments.size()) {
-	System.out.println("Found " + (wantedComments.size()-parsedComments.size()) + " missed comment(s)!");
-	errorCount++;
-    }
-
-    System.exit(errorCount);
+    wantedComments.put("E_TEST_THREE", " the last item  \n");
+    
+    // and ask the parser to check comments for us
+    System.exit(parser.check(wantedComments));
   }
 }
diff --git a/Examples/test-suite/java/doxygen_parsing_enums_typesafe_runme.java b/Examples/test-suite/java/doxygen_parsing_enums_typesafe_runme.java
index 8d87c82d0..5aed9327e 100644
--- a/Examples/test-suite/java/doxygen_parsing_enums_typesafe_runme.java
+++ b/Examples/test-suite/java/doxygen_parsing_enums_typesafe_runme.java
@@ -2,8 +2,6 @@
 import doxygen_parsing_enums_typesafe.*;
 import com.sun.javadoc.*;
 import java.util.HashMap;
-import java.util.Map.Entry;
-import java.util.Iterator;
 
 public class doxygen_parsing_enums_typesafe_runme {
   static {
@@ -14,80 +12,25 @@ public class doxygen_parsing_enums_typesafe_runme {
       System.exit(1);
     }
   }
-
-  static HashMap<String, String> parsedComments = new HashMap<String, String>();
-  static HashMap<String, String> wantedComments = new HashMap<String, String>();
-
-  public static boolean start(RootDoc root) {
-    
-    /*
-      This method is called by 'javadoc' and gets the whole parsed
-      java file, we get comments and store them
-    */
-
-    ClassDoc[] classes = root.classes();
-
-    for (int i = 0; i < classes.length; i++) {
-
-      if (classes[i].getRawCommentText().length() > 0)
-	parsedComments.put(classes[i].name(), classes[i].getRawCommentText());
-
-      MethodDoc[] methods = classes[i].methods();
-      FieldDoc[] fields = classes[i].fields();
-      FieldDoc[] constants = classes[i].enumConstants();
-
-      for (int j = 0; j < constants.length; j++) {
-        FieldDoc f = constants[j];
-	if (f.getRawCommentText().length() > 0)
-	  parsedComments.put(f.name(), f.getRawCommentText());
-      }
-      for (int j = 0; j < fields.length; j++) {
-        FieldDoc f = fields[j];
-	if (f.getRawCommentText().length() > 0)
-	  parsedComments.put(f.name(), f.getRawCommentText());
-      }
-      for (int j = 0; j < methods.length; j++) {
-        MethodDoc m = methods[j];
-	if (m.getRawCommentText().length() > 0)
-	  parsedComments.put(m.name(), m.getRawCommentText());
-      }
-    }
-    return true;
-  }
-
+  
   public static void main(String argv[]) 
   {
     /*
       Here we are using internal javadoc tool, it accepts the name of the class as paramterer,
       and calls the start() method of that class with parsed information.
     */
+	commentParser parser = new commentParser();
     com.sun.tools.javadoc.Main.execute("doxygen_parsing_enums_typesafe runtime test",
-	"doxygen_parsing_enums_typesafe_runme", new String[]{"-quiet", "doxygen_parsing_enums_typesafe"});
+	"commentParser", new String[]{"-quiet", "doxygen_parsing_enums_typesafe"});
 
+    HashMap<String, String> wantedComments = new HashMap<String, String>();
+    
     wantedComments.put("E_TEST", " Test enumeration  \n");
     wantedComments.put("E_TEST_ONE", " the first item  \n");
     wantedComments.put("E_TEST_TWO", " the second  \n");
-
-    int errorCount=0;
-    Iterator< Entry<String, String> > it = parsedComments.entrySet().iterator();
-
-    while (it.hasNext())
-    {
-	Entry<String, String> e = (Entry<String, String>) it.next();
-
-	if (!e.getValue().equals(wantedComments.get(e.getKey()))) {
-	    System.out.println("Documentation comments for " + e.getKey() + " does not match: ");
-	    System.out.println("\texpected:"+wantedComments.get(e.getKey()));
-	    System.out.println("\tgot:\t"+e.getValue());
-	    errorCount++;
-	}
-    }
-
-    if (parsedComments.size() != wantedComments.size()) {
-	System.out.println("Found " + (wantedComments.size()-parsedComments.size()) + " missed comment(s)!");
-	errorCount++;
-    }
-
-    System.exit(errorCount);
+    wantedComments.put("E_TEST_THREE", " the last item  \n");
+    
+    // and ask the parser to check comments for us
+    System.exit(parser.check(wantedComments));
   }
 }
diff --git a/Examples/test-suite/java/doxygen_parsing_enums_typeunsafe_runme.java b/Examples/test-suite/java/doxygen_parsing_enums_typeunsafe_runme.java
index a01007db1..44405f837 100644
--- a/Examples/test-suite/java/doxygen_parsing_enums_typeunsafe_runme.java
+++ b/Examples/test-suite/java/doxygen_parsing_enums_typeunsafe_runme.java
@@ -2,8 +2,6 @@
 import doxygen_parsing_enums_typeunsafe.*;
 import com.sun.javadoc.*;
 import java.util.HashMap;
-import java.util.Map.Entry;
-import java.util.Iterator;
 
 public class doxygen_parsing_enums_typeunsafe_runme {
   static {
@@ -14,80 +12,25 @@ public class doxygen_parsing_enums_typeunsafe_runme {
       System.exit(1);
     }
   }
-
-  static HashMap<String, String> parsedComments = new HashMap<String, String>();
-  static HashMap<String, String> wantedComments = new HashMap<String, String>();
-
-  public static boolean start(RootDoc root) {
-    
-    /*
-      This method is called by 'javadoc' and gets the whole parsed
-      java file, we get comments and store them
-    */
-
-    ClassDoc[] classes = root.classes();
-
-    for (int i = 0; i < classes.length; i++) {
-
-      if (classes[i].getRawCommentText().length() > 0)
-	parsedComments.put(classes[i].name(), classes[i].getRawCommentText());
-
-      MethodDoc[] methods = classes[i].methods();
-      FieldDoc[] fields = classes[i].fields();
-      FieldDoc[] constants = classes[i].enumConstants();
-
-      for (int j = 0; j < constants.length; j++) {
-        FieldDoc f = constants[j];
-	if (f.getRawCommentText().length() > 0)
-	  parsedComments.put(f.name(), f.getRawCommentText());
-      }
-      for (int j = 0; j < fields.length; j++) {
-        FieldDoc f = fields[j];
-	if (f.getRawCommentText().length() > 0)
-	  parsedComments.put(f.name(), f.getRawCommentText());
-      }
-      for (int j = 0; j < methods.length; j++) {
-        MethodDoc m = methods[j];
-	if (m.getRawCommentText().length() > 0)
-	  parsedComments.put(m.name(), m.getRawCommentText());
-      }
-    }
-    return true;
-  }
-
+  
   public static void main(String argv[]) 
   {
     /*
       Here we are using internal javadoc tool, it accepts the name of the class as paramterer,
       and calls the start() method of that class with parsed information.
     */
+	commentParser parser = new commentParser();
     com.sun.tools.javadoc.Main.execute("doxygen_parsing_enums_typeunsafe runtime test",
-	"doxygen_parsing_enums_typeunsafe_runme", new String[]{"-quiet", "doxygen_parsing_enums_typeunsafe"});
+	"commentParser", new String[]{"-quiet", "doxygen_parsing_enums_typeunsafe"});
 
+    HashMap<String, String> wantedComments = new HashMap<String, String>();
+    
     wantedComments.put("E_TEST", " Test enumeration  \n");
     wantedComments.put("E_TEST_ONE", " the first item  \n");
     wantedComments.put("E_TEST_TWO", " the second  \n");
-
-    int errorCount=0;
-    Iterator< Entry<String, String> > it = parsedComments.entrySet().iterator();
-
-    while (it.hasNext())
-    {
-	Entry<String, String> e = (Entry<String, String>) it.next();
-
-	if (!e.getValue().equals(wantedComments.get(e.getKey()))) {
-	    System.out.println("Documentation comments for " + e.getKey() + " does not match: ");
-	    System.out.println("\texpected:"+wantedComments.get(e.getKey()));
-	    System.out.println("\tgot:\t"+e.getValue());
-	    errorCount++;
-	}
-    }
-
-    if (parsedComments.size() != wantedComments.size()) {
-	System.out.println("Found " + (wantedComments.size()-parsedComments.size()) + " missed comment(s)!");
-	errorCount++;
-    }
-
-    System.exit(errorCount);
+    wantedComments.put("E_TEST_THREE", " the last item  \n");
+    
+    // and ask the parser to check comments for us
+    System.exit(parser.check(wantedComments));
   }
 }
diff --git a/Examples/test-suite/java/doxygen_parsing_runme.java b/Examples/test-suite/java/doxygen_parsing_runme.java
index 909de9312..ae426da58 100644
--- a/Examples/test-suite/java/doxygen_parsing_runme.java
+++ b/Examples/test-suite/java/doxygen_parsing_runme.java
@@ -2,8 +2,6 @@
 import doxygen_parsing.*;
 import com.sun.javadoc.*;
 import java.util.HashMap;
-import java.util.Map.Entry;
-import java.util.Iterator;
 
 public class doxygen_parsing_runme {
   static {
@@ -15,55 +13,18 @@ public class doxygen_parsing_runme {
     }
   }
 
-  static HashMap<String, String> parsedComments = new HashMap<String, String>();
-  static HashMap<String, String> wantedComments = new HashMap<String, String>();
-
-  public static boolean start(RootDoc root) {
-    
-    /*
-      This method is called by 'javadoc' and gets the whole parsed
-      java file, we get comments and store them
-    */
-
-    ClassDoc[] classes = root.classes();
-
-    for (int i = 0; i < classes.length; i++) {
-
-      if (classes[i].getRawCommentText().length() > 0)
-	parsedComments.put(classes[i].name(), classes[i].getRawCommentText());
-
-      MethodDoc[] methods = classes[i].methods();
-      FieldDoc[] fields = classes[i].fields();
-      FieldDoc[] constants = classes[i].enumConstants();
-
-      for (int j = 0; j < constants.length; j++) {
-        FieldDoc f = constants[j];
-	if (f.getRawCommentText().length() > 0)
-	  parsedComments.put(f.name(), f.getRawCommentText());
-      }
-      for (int j = 0; j < fields.length; j++) {
-        FieldDoc f = fields[j];
-	if (f.getRawCommentText().length() > 0)
-	  parsedComments.put(f.name(), f.getRawCommentText());
-      }
-      for (int j = 0; j < methods.length; j++) {
-        MethodDoc m = methods[j];
-	if (m.getRawCommentText().length() > 0)
-	  parsedComments.put(m.name(), m.getRawCommentText());
-      }
-    }
-    return true;
-  }
-
   public static void main(String argv[]) 
   {
     /*
       Here we are using internal javadoc tool, it accepts the name of the class as paramterer,
       and calls the start() method of that class with parsed information.
     */
+	commentParser parser = new commentParser();
     com.sun.tools.javadoc.Main.execute("doxygen_parsing runtime test",
-	"doxygen_parsing_runme", new String[]{"-quiet", "doxygen_parsing"});
+	"commentParser", new String[]{"-quiet", "doxygen_parsing"});
 
+    HashMap<String, String> wantedComments = new HashMap<String, String>();
+    
     wantedComments.put("simpleFunction", " This is simple comment for a function  \n");
 
     wantedComments.put("CSimpleClass", " This is simple comment for a class  \n");
@@ -85,27 +46,7 @@ public class doxygen_parsing_runme {
     wantedComments.put("setSimpleVarFive", " This is a post comment  \n");
     wantedComments.put("getSimpleVarFive", " This is a post comment  \n");
 
-
-    int errorCount=0;
-    Iterator< Entry<String, String> > it = parsedComments.entrySet().iterator();
-
-    while (it.hasNext())
-    {
-	Entry<String, String> e = (Entry<String, String>) it.next();
-
-	if (!e.getValue().equals(wantedComments.get(e.getKey()))) {
-	    System.out.println("Documentation comments for " + e.getKey() + " does not match: ");
-	    System.out.println("\texpected:"+wantedComments.get(e.getKey()));
-	    System.out.println("\tgot:\t"+e.getValue());
-	    errorCount++;
-	}
-    }
-
-    if (parsedComments.size() != wantedComments.size()) {
-	System.out.println("Found " + (wantedComments.size()-parsedComments.size()) + " missed comment(s)!");
-	errorCount++;
-    }
-
-    System.exit(errorCount);
+    // and ask the parser to check comments for us
+    System.exit(parser.check(wantedComments));
   }
 }

From 293c5cfc1fea4153660fc15776ce0ae71c7cb269 Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Sat, 7 Jul 2012 13:43:19 +0000
Subject: [PATCH 066/314] Added support for commenting the last enum item in
 parser.y

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13262 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Source/CParse/parser.y | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/Source/CParse/parser.y b/Source/CParse/parser.y
index 70f420411..4bf63b40f 100644
--- a/Source/CParse/parser.y
+++ b/Source/CParse/parser.y
@@ -5831,6 +5831,10 @@ edecl          :  ID {
 		   $$ = $2;
 		   set_comment(previousNode, $1);
 		 }
+		 | edecl doxygen_post_comment {
+		   $$ = $1;
+		   set_comment($1, $2);
+		 }
                  | empty { $$ = 0; previousNode = currentNode; currentNode = 0; }
                  ;
 

From 509cbd72b0823381fbcc2ac9c9dab6b3bdbd5ede Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Sat, 7 Jul 2012 13:47:35 +0000
Subject: [PATCH 067/314] Small JavaDoc converter and doxygen parser
 improvements, now basic tags working

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13263 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 .../DoxygenTranslator/src/DoxygenParser.cpp   | 1022 ++++++++---------
 Source/DoxygenTranslator/src/DoxygenParser.h  |    3 +-
 .../src/JavaDocConverter.cpp                  |   88 +-
 .../DoxygenTranslator/src/JavaDocConverter.h  |    8 +-
 4 files changed, 543 insertions(+), 578 deletions(-)

diff --git a/Source/DoxygenTranslator/src/DoxygenParser.cpp b/Source/DoxygenTranslator/src/DoxygenParser.cpp
index 07e61b590..e7104b9e0 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenParser.cpp
@@ -12,645 +12,611 @@
 #include "DoxygenParser.h"
 #include "DoxygenCommands.h"
 
-#include <stdio.h>
-
 // Define static class members
 std::map<std::string, DoxyCommandEnum> DoxygenParser::doxygenCommands;
 std::set<std::string> DoxygenParser::doxygenSectionIndicators;
 
 
-DoxygenParser::DoxygenParser() : noisy(false) {
-  fillTables();
+DoxygenParser::DoxygenParser() : noisy(true) {
+	fillTables();
 }
 
 DoxygenParser::~DoxygenParser() {
 }
 
 void DoxygenParser::fillTables() {
-  // run it only once
-  if (doxygenCommands.size())
-    return;
-  
-  // fill in tables with data from DxygenCommands.h
-  for (int i = 0; i < simpleCommandsSize; i++)
-    doxygenCommands[simpleCommands[i]] = SIMPLECOMMAND;
-  for (int i = 0; i < ignoredSimpleCommandsSize; i++)
-    doxygenCommands[ignoredSimpleCommands[i]] = IGNOREDSIMPLECOMMAND;
-  
-  for (int i = 0; i < commandWordsSize; i++)
-    doxygenCommands[commandWords[i]] = COMMANDWORD;
-  for (int i = 0; i < ignoredCommandWordsSize; i++)
-    doxygenCommands[ignoredCommandWords[i]] = IGNOREDCOMMANDWORD;
-  
-  for (int i = 0; i < commandLinesSize; i++)
-    doxygenCommands[commandLines[i]] = COMMANDLINE;
-  for (int i = 0; i < ignoreCommandLinesSize; i++)
-    doxygenCommands[ignoreCommandLines[i]] = IGNOREDCOMMANDLINE;
-  
-  for (int i = 0; i < commandParagraphSize; i++)
-    doxygenCommands[commandParagraph[i]] = COMMANDPARAGRAPH;
-  for (int i = 0; i < ignoreCommandParagraphsSize; i++)
-    doxygenCommands[ignoreCommandParagraphs[i]] = IGNORECOMMANDPARAGRAPH;
-  
-  for (int i = 0; i < commandEndCommandsSize; i++)
-    doxygenCommands[commandEndCommands[i]] = COMMANDENDCOMMAND;
-  for (int i = 0; i < commandWordParagraphsSize; i++)
-    doxygenCommands[commandWordParagraphs[i]] = COMMANDWORDPARAGRAPH;
-  for (int i = 0; i < commandWordLinesSize; i++)
-    doxygenCommands[commandWordLines[i]] = COMMANDWORDLINE;
-  for (int i = 0; i < commandWordOWordOWordsSize; i++)
-    doxygenCommands[commandWordOWordOWords[i]] = COMMANDWORDOWORDWORD;
-  for (int i = 0; i < commandOWordsSize; i++)
-    doxygenCommands[commandOWords[i]] = COMMANDOWORD;
-  for (int i = 0; i < commandErrorThrowingsSize; i++)
-    doxygenCommands[commandErrorThrowings[i]] = COMMANDERRORTHROW;
-  for (int i = 0; i < commandUniquesSize; i++)
-    doxygenCommands[commandUniques[i]] = COMMANDUNIQUE;
-  
-  // fill section indicators command set
-  for (int i = 0; i < sectionIndicatorsSize; i++)
-    doxygenSectionIndicators.insert(sectionIndicators[i]);
+	// run it only once
+	if (doxygenCommands.size())
+		return;
+
+	// fill in tables with data from DxygenCommands.h
+	for (int i = 0; i < simpleCommandsSize; i++)
+		doxygenCommands[simpleCommands[i]] = SIMPLECOMMAND;
+	for (int i = 0; i < ignoredSimpleCommandsSize; i++)
+		doxygenCommands[ignoredSimpleCommands[i]] = IGNOREDSIMPLECOMMAND;
+
+	for (int i = 0; i < commandWordsSize; i++)
+		doxygenCommands[commandWords[i]] = COMMANDWORD;
+	for (int i = 0; i < ignoredCommandWordsSize; i++)
+		doxygenCommands[ignoredCommandWords[i]] = IGNOREDCOMMANDWORD;
+
+	for (int i = 0; i < commandLinesSize; i++)
+		doxygenCommands[commandLines[i]] = COMMANDLINE;
+	for (int i = 0; i < ignoreCommandLinesSize; i++)
+		doxygenCommands[ignoreCommandLines[i]] = IGNOREDCOMMANDLINE;
+
+	for (int i = 0; i < commandParagraphSize; i++)
+		doxygenCommands[commandParagraph[i]] = COMMANDPARAGRAPH;
+	for (int i = 0; i < ignoreCommandParagraphsSize; i++)
+		doxygenCommands[ignoreCommandParagraphs[i]] = IGNORECOMMANDPARAGRAPH;
+
+	for (int i = 0; i < commandEndCommandsSize; i++)
+		doxygenCommands[commandEndCommands[i]] = COMMANDENDCOMMAND;
+	for (int i = 0; i < commandWordParagraphsSize; i++)
+		doxygenCommands[commandWordParagraphs[i]] = COMMANDWORDPARAGRAPH;
+	for (int i = 0; i < commandWordLinesSize; i++)
+		doxygenCommands[commandWordLines[i]] = COMMANDWORDLINE;
+	for (int i = 0; i < commandWordOWordOWordsSize; i++)
+		doxygenCommands[commandWordOWordOWords[i]] = COMMANDWORDOWORDWORD;
+	for (int i = 0; i < commandOWordsSize; i++)
+		doxygenCommands[commandOWords[i]] = COMMANDOWORD;
+	for (int i = 0; i < commandErrorThrowingsSize; i++)
+		doxygenCommands[commandErrorThrowings[i]] = COMMANDERRORTHROW;
+	for (int i = 0; i < commandUniquesSize; i++)
+		doxygenCommands[commandUniques[i]] = COMMANDUNIQUE;
+
+	// fill section indicators command set
+	for (int i = 0; i < sectionIndicatorsSize; i++)
+		doxygenSectionIndicators.insert(sectionIndicators[i]);
 }
 
 std::string DoxygenParser::StringToLower(std::string stringToConvert) {
-  for (unsigned int i = 0; i < stringToConvert.length(); i++) {
-    stringToConvert[i] = tolower(stringToConvert[i]);
-  }
-  return stringToConvert;	//return the converted std::string
+	for (unsigned int i = 0; i < stringToConvert.length(); i++) {
+		stringToConvert[i] = tolower(stringToConvert[i]);
+	}
+	return stringToConvert;	//return the converted std::string
 }
 
 int DoxygenParser::findCommand(std::string smallString) {
-  std::map<std::string, DoxyCommandEnum>::iterator it;
-  smallString = StringToLower(smallString);
-  // I'm not sure if we can really do so, because there are different commands
-  // in doxygenCommands and original commandArray
-  it = doxygenCommands.find(smallString);
-  if (it != doxygenCommands.end())
-    return 1;
-  return -1;
+	std::map<std::string, DoxyCommandEnum>::iterator it;
+	smallString = StringToLower(smallString);
+	// I'm not sure if we can really do so, because there are different commands
+	// in doxygenCommands and original commandArray
+	it = doxygenCommands.find(smallString);
+	if (it != doxygenCommands.end())
+		return 1;
+	return -1;
 }
 
 int DoxygenParser::isSectionIndicator(std::string smallString) {
-  smallString = StringToLower(smallString);
-  std::set<std::string>::iterator it;
-  it = doxygenSectionIndicators.find(smallString);
-  if (it != doxygenSectionIndicators.end())
-    return 1;
-  return 0;
+	smallString = StringToLower(smallString);
+	std::set<std::string>::iterator it;
+	it = doxygenSectionIndicators.find(smallString);
+	if (it != doxygenSectionIndicators.end())
+		return 1;
+	return 0;
 }
 
 void DoxygenParser::printTree(std::list < DoxygenEntity > &rootList) {
-  std::list < DoxygenEntity >::iterator p = rootList.begin();
-  while (p != rootList.end()) {
-    (*p).printEntity(0);
-    p++;
-  }
+	std::list < DoxygenEntity >::iterator p = rootList.begin();
+	while (p != rootList.end()) {
+		(*p).printEntity(0);
+		p++;
+	}
 }
 
 int DoxygenParser::commandBelongs(std::string theCommand) {
-  std::string smallString = StringToLower(theCommand);
-  //cout << " Looking for command " << theCommand << endl;
-  std::map<std::string, DoxyCommandEnum>::iterator it;
-  it = doxygenCommands.find(smallString);
-  if (it!=doxygenCommands.end())
-    return it->second;
-  return 0;
+	std::string smallString = StringToLower(theCommand);
+	//cout << " Looking for command " << theCommand << endl;
+	std::map<std::string, DoxyCommandEnum>::iterator it;
+	it = doxygenCommands.find(smallString);
+	if (it!=doxygenCommands.end())
+		return it->second;
+	return 0;
 }
 
 std::string DoxygenParser::getNextWord(TokenList & tokList) {
-  Token nextToken = tokList.peek();
-  if (nextToken.tokenType == PLAINSTRING) {
-    nextToken = tokList.next();
-    return nextToken.tokenString;
-  }
-  return "";
+	Token nextToken = tokList.peek();
+	if (nextToken.tokenType == PLAINSTRING) {
+		nextToken = tokList.next();
+		return nextToken.tokenString;
+	}
+	return "";
 }
 
 std::list < Token >::iterator DoxygenParser::getOneLine(TokenList & tokList) {
-  std::list < Token >::iterator endOfLine = tokList.iteratorCopy();
-  while (endOfLine != tokList.end()) {
-    if ((*endOfLine).tokenType == END_LINE) {
-      //cout << "REACHED END" << endl;
-      //endOfLine++;
-      return endOfLine;
-    }
-    //cout << (* endOfLine).toString();
-    endOfLine++;
-  }
+	std::list < Token >::iterator endOfLine = tokList.iteratorCopy();
+	while (endOfLine != tokList.end()) {
+		if ((*endOfLine).tokenType == END_LINE) {
+			//cout << "REACHED END" << endl;
+			//endOfLine++;
+			return endOfLine;
+		}
+		//cout << (* endOfLine).toString();
+		endOfLine++;
+	}
 
-  return tokList.end();
+	return tokList.end();
 }
 
 std::string DoxygenParser::getStringTilCommand(TokenList & tokList) {
-  std::string description;
-  if (tokList.peek().tokenType == 0)
-    return "";
-  while (tokList.peek().tokenType == PLAINSTRING) {
-    Token currentToken = tokList.next();
-    if (currentToken.tokenType == PLAINSTRING) {
-      description = description + currentToken.tokenString + " ";
-    }
-  }
-  return description;
+	std::string description;
+	if (tokList.peek().tokenType == 0)
+		return "";
+	while (tokList.peek().tokenType == PLAINSTRING) {
+		Token currentToken = tokList.next();
+		if (currentToken.tokenType == PLAINSTRING) {
+			description = description + currentToken.tokenString + " ";
+		}
+	}
+	return description;
 }
 
 std::string DoxygenParser::getStringTilEndCommand(std::string theCommand, TokenList & tokList) {
-  std::string description;
-  if (tokList.peek().tokenType == 0)
-    return "";
-  while (tokList.next().tokenString.compare(theCommand) != 0) {
-    //TODO: it won't output doxygen commands, need a way to fix it
-    if (tokList.peek().tokenType == PLAINSTRING)
-      description += tokList.peek().tokenString + " ";
-    if (tokList.peek().tokenType == END_LINE)
-      description += "\n";
-  }
-  tokList.next(); // eat the end command itself
-  return description;
+	std::string description;
+	if (tokList.peek().tokenType == 0)
+		return "";
+	while (tokList.next().tokenString.compare(theCommand) != 0) {
+		//TODO: it won't output doxygen commands, need a way to fix it
+		if (tokList.peek().tokenType == PLAINSTRING)
+			description += tokList.peek().tokenString + " ";
+		if (tokList.peek().tokenType == END_LINE)
+			description += "\n";
+	}
+	tokList.next(); // eat the end command itself
+	return description;
 }
 
 std::list < Token >::iterator DoxygenParser::getEndOfParagraph(TokenList & tokList) {
-  std::list < Token >::iterator endOfParagraph = tokList.iteratorCopy();
-  while (endOfParagraph != tokList.end()) {
-    if ((*endOfParagraph).tokenType == END_LINE) {
-      endOfParagraph++;
-      if (endOfParagraph != tokList.end() && (*endOfParagraph).tokenType == END_LINE) {
-	endOfParagraph++;
-	//cout << "ENCOUNTERED END OF PARA" << endl;
-	return endOfParagraph;
-      }
+	std::list < Token >::iterator endOfParagraph = tokList.iteratorCopy();
+	while (endOfParagraph != tokList.end()) {
+		if ((*endOfParagraph).tokenType == END_LINE) {
+			endOfParagraph++;
+			if (endOfParagraph != tokList.end() && (*endOfParagraph).tokenType == END_LINE) {
+				endOfParagraph++;
+				//cout << "ENCOUNTERED END OF PARA" << endl;
+				return endOfParagraph;
+			}
 
-    } else if ((*endOfParagraph).tokenType == COMMAND) {
+		} else if ((*endOfParagraph).tokenType == COMMAND) {
 
-      if (isSectionIndicator((*endOfParagraph).tokenString)) {
-	return endOfParagraph;
-      } else
-	endOfParagraph++;
+			if (isSectionIndicator((*endOfParagraph).tokenString)) {
+				return endOfParagraph;
+			} else
+				endOfParagraph++;
 
-    } else if ((*endOfParagraph).tokenType == PLAINSTRING) {
-      endOfParagraph++;
-    } else {
-      return tokList.end();
-    }
-  }
+		} else if ((*endOfParagraph).tokenType == PLAINSTRING) {
+			endOfParagraph++;
+		} else {
+			return tokList.end();
+		}
+	}
 
-  return tokList.end();
+	return tokList.end();
 }
 
 std::list < Token >::iterator DoxygenParser::getEndOfSection(std::string theCommand, TokenList & tokList) {
-  std::list < Token >::iterator endOfParagraph = tokList.iteratorCopy();
-  while (endOfParagraph != tokList.end()) {
-    if ((*endOfParagraph).tokenType == COMMAND) {
-      if (theCommand.compare((*endOfParagraph).tokenString) == 0)
-	return endOfParagraph;
-      else
-	endOfParagraph++;
-    } else if ((*endOfParagraph).tokenType == PLAINSTRING) {
-      endOfParagraph++;
-    } else if ((*endOfParagraph).tokenType == END_LINE) {
-      endOfParagraph++;
-      if ((*endOfParagraph).tokenType == END_LINE) {
-	endOfParagraph++;
-	return endOfParagraph;
-      }
-    }
-  }
-  return tokList.end();
+	std::list < Token >::iterator endOfParagraph = tokList.iteratorCopy();
+	while (endOfParagraph != tokList.end()) {
+		if ((*endOfParagraph).tokenType == COMMAND) {
+			if (theCommand.compare((*endOfParagraph).tokenString) == 0)
+				return endOfParagraph;
+			else
+				endOfParagraph++;
+		} else if ((*endOfParagraph).tokenType == PLAINSTRING) {
+			endOfParagraph++;
+		} else if ((*endOfParagraph).tokenType == END_LINE) {
+			endOfParagraph++;
+			if ((*endOfParagraph).tokenType == END_LINE) {
+				endOfParagraph++;
+				return endOfParagraph;
+			}
+		}
+	}
+	return tokList.end();
 }
 
 std::list < Token >::iterator DoxygenParser::getEndCommand(std::string theCommand, TokenList & tokList) {
-  std::list < Token >::iterator endOfCommand = tokList.iteratorCopy();
-  while (endOfCommand != tokList.end()) {
-    if ((*endOfCommand).tokenType == COMMAND) {
-      if (theCommand.compare((*endOfCommand).tokenString) == 0) {
-	return endOfCommand;
-      }
-      endOfCommand++;
-    }
-  }
-  //End command not found
-  return tokList.end();
+	std::list < Token >::iterator endOfCommand = tokList.iteratorCopy();
+	while (endOfCommand != tokList.end()) {
+		if ((*endOfCommand).tokenType == COMMAND) {
+			if (theCommand.compare((*endOfCommand).tokenString) == 0) {
+				return endOfCommand;
+			}
+			endOfCommand++;
+		}
+	}
+	//End command not found
+	return tokList.end();
 }
 
 std::list < Token >::iterator DoxygenParser::getTilAnyCommand(std::string theCommand, TokenList & tokList) {
 #pragma unused(theCommand,tokList)
-  std::list < Token >::iterator anIterator;
-  return anIterator;
+	std::list < Token >::iterator anIterator;
+	return anIterator;
 }
 
 int DoxygenParser::addSimpleCommand(std::string theCommand, std::list < DoxygenEntity > &doxyList) {
-  if (noisy)
-    cout << "Parsing " << theCommand << endl;
-  doxyList.push_back(DoxygenEntity(theCommand));
-  return 1;
+	if (noisy)
+		cout << "Parsing " << theCommand << endl;
+	doxyList.push_back(DoxygenEntity(theCommand));
+	return 1;
 }
 
 int DoxygenParser::ignoreSimpleCommand(std::string theCommand, std::list < DoxygenEntity > &doxyList) {
 #pragma unused(doxyList)
-  if (noisy)
-    cout << "Not Adding " << theCommand << endl;
-  return 1;
+	if (noisy)
+		cout << "Not Adding " << theCommand << endl;
+	return 1;
 }
 
 int DoxygenParser::addCommandWord(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
-  if (noisy)
-    cout << "Parsing " << theCommand << endl;
-  std::string name = getNextWord(tokList);
-  if (!name.empty()) {
-    doxyList.push_back(DoxygenEntity(theCommand, name));
-    return 1;
-  } else
-    cout << "No word followed " << theCommand << " command. Not added" << endl;
-  return 0;
+	if (noisy)
+		cout << "Parsing " << theCommand << endl;
+	std::string name = getNextWord(tokList);
+	if (!name.empty()) {
+		doxyList.push_back(DoxygenEntity(theCommand, name));
+		return 1;
+	} else
+		cout << "No word followed " << theCommand << " command. Not added" << endl;
+	return 0;
 }
 
 int DoxygenParser::ignoreCommandWord(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
 #pragma unused(doxyList)
-  if (noisy)
-    cout << "Not Adding " << theCommand << endl;
-  std::string name = getNextWord(tokList);
-  if (!name.empty())
-    return 1;
-  else
-    cout << "WARNING: No word followed " << theCommand << " command." << endl;
-  return 0;
+	if (noisy)
+		cout << "Not Adding " << theCommand << endl;
+	std::string name = getNextWord(tokList);
+	if (!name.empty())
+		return 1;
+	else
+		cout << "WARNING: No word followed " << theCommand << " command." << endl;
+	return 0;
 }
 
 int DoxygenParser::addCommandLine(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
-  if (noisy)
-    cout << "Parsing " << theCommand << endl;
-  std::list < Token >::iterator endOfLine = getOneLine(tokList);
-  std::list < DoxygenEntity > aNewList = parse(endOfLine, tokList);
-  doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-  return 1;
+	if (noisy)
+		cout << "Parsing " << theCommand << endl;
+	std::list < Token >::iterator endOfLine = getOneLine(tokList);
+	std::list < DoxygenEntity > aNewList = parse(endOfLine, tokList);
+	doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+	return 1;
 }
 
 int DoxygenParser::ignoreCommandLine(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
 #pragma unused(doxyList)
-  if (noisy)
-    cout << "Not Adding " << theCommand << endl;
-  std::list < Token >::iterator endOfLine = getOneLine(tokList);
-  tokList.setIterator(endOfLine);
-  return 1;
+	if (noisy)
+		cout << "Not Adding " << theCommand << endl;
+	std::list < Token >::iterator endOfLine = getOneLine(tokList);
+	tokList.setIterator(endOfLine);
+	return 1;
 }
 
 int DoxygenParser::addCommandParagraph(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
-  if (noisy)
-    cout << "Parsing " << theCommand << endl;
-  std::list < Token >::iterator endOfParagraph = getEndOfParagraph(tokList);
-  std::list < DoxygenEntity > aNewList;
-  aNewList = parse(endOfParagraph, tokList);
-  doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-  return 1;
+	if (noisy)
+		cout << "Parsing " << theCommand << endl;
+	std::list < Token >::iterator endOfParagraph = getEndOfParagraph(tokList);
+	std::list < DoxygenEntity > aNewList;
+	aNewList = parse(endOfParagraph, tokList);
+	doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+	return 1;
 }
 
 int DoxygenParser::ignoreCommandParagraph(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
 #pragma unused(doxyList)
-  if (noisy)
-    cout << "Not Adding " << theCommand << endl;
-  std::list < Token >::iterator endOfParagraph = getEndOfParagraph(tokList);
-  tokList.setIterator(endOfParagraph);
-  return 1;
+	if (noisy)
+		cout << "Not Adding " << theCommand << endl;
+	std::list < Token >::iterator endOfParagraph = getEndOfParagraph(tokList);
+	tokList.setIterator(endOfParagraph);
+	return 1;
 }
 
 int DoxygenParser::addCommandEndCommand(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
-  if (noisy)
-    cout << "Parsing " << theCommand << endl;
-  std::string description = getStringTilEndCommand("end" + theCommand, tokList);
-  doxyList.push_back(DoxygenEntity(theCommand, description));
-  return 1;
+	if (noisy)
+		cout << "Parsing " << theCommand << endl;
+	std::string description = getStringTilEndCommand("end" + theCommand, tokList);
+	doxyList.push_back(DoxygenEntity(theCommand, description));
+	return 1;
 }
 
 int DoxygenParser::addCommandWordParagraph(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
-  if (noisy)
-    cout << "Parsing " << theCommand << endl;
-  std::string name = getNextWord(tokList);
-  if (name.empty()) {
-    cout << "No word followed " << theCommand << " command. Not added" << endl;
-    return 0;
-  }
-  std::list < Token >::iterator endOfParagraph = getEndOfParagraph(tokList);
-  std::list < DoxygenEntity > aNewList;
-  aNewList = parse(endOfParagraph, tokList);
-  aNewList.push_front(DoxygenEntity("plainstd::string", name));
-  doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-  return 1;
+	if (noisy)
+		cout << "Parsing " << theCommand << endl;
+	std::string name = getNextWord(tokList);
+	if (name.empty()) {
+		cout << "No word followed " << theCommand << " command. Not added" << endl;
+		return 0;
+	}
+	std::list < Token >::iterator endOfParagraph = getEndOfParagraph(tokList);
+	std::list < DoxygenEntity > aNewList;
+	aNewList = parse(endOfParagraph, tokList);
+	aNewList.push_front(DoxygenEntity("plainstd::string", name));
+	doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+	return 1;
 }
 
 int DoxygenParser::addCommandWordLine(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
-  if (noisy)
-    cout << "Parsing " << theCommand << endl;
-  std::string name = getNextWord(tokList);
-  if (name.empty()) {
-    cout << "No word followed " << theCommand << " command. Not added" << endl;
-    return 0;
-  }
-  std::list < Token >::iterator endOfLine = getOneLine(tokList);
-  std::list < DoxygenEntity > aNewList;
-  aNewList = parse(endOfLine, tokList);
-  aNewList.push_front(DoxygenEntity("plainstd::string", name));
-  doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-  return 1;
-  //else cout << "No line followed " << theCommand <<  " command. Not added" << endl;
+	if (noisy)
+		cout << "Parsing " << theCommand << endl;
+	std::string name = getNextWord(tokList);
+	if (name.empty()) {
+		cout << "No word followed " << theCommand << " command. Not added" << endl;
+		return 0;
+	}
+	std::list < Token >::iterator endOfLine = getOneLine(tokList);
+	std::list < DoxygenEntity > aNewList;
+	aNewList = parse(endOfLine, tokList);
+	aNewList.push_front(DoxygenEntity("plainstd::string", name));
+	doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+	return 1;
+	//else cout << "No line followed " << theCommand <<  " command. Not added" << endl;
 }
 
 int DoxygenParser::addCommandWordOWordOWord(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
-  if (noisy)
-    cout << "Parsing " << theCommand << endl;
-  std::string name = getNextWord(tokList);
-  if (name.empty()) {
-    cout << "No word followed " << theCommand << " command. Not added" << endl;
-    return 0;
-  }
-  std::string headerfile = getNextWord(tokList);
-  std::string headername = getNextWord(tokList);
-  std::list < DoxygenEntity > aNewList;
-  aNewList.push_back(DoxygenEntity("plainstd::string", name));
-  if (!headerfile.empty())
-    aNewList.push_back(DoxygenEntity("plainstd::string", headerfile));
-  if (!headername.empty())
-    aNewList.push_back(DoxygenEntity("plainstd::string", headername));
-  doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-  return 1;
+	if (noisy)
+		cout << "Parsing " << theCommand << endl;
+	std::string name = getNextWord(tokList);
+	if (name.empty()) {
+		cout << "No word followed " << theCommand << " command. Not added" << endl;
+		return 0;
+	}
+	std::string headerfile = getNextWord(tokList);
+	std::string headername = getNextWord(tokList);
+	std::list < DoxygenEntity > aNewList;
+	aNewList.push_back(DoxygenEntity("plainstd::string", name));
+	if (!headerfile.empty())
+		aNewList.push_back(DoxygenEntity("plainstd::string", headerfile));
+	if (!headername.empty())
+		aNewList.push_back(DoxygenEntity("plainstd::string", headername));
+	doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+	return 1;
 }
 
 int DoxygenParser::addCommandOWord(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
-  if (noisy)
-    cout << "Parsing " << theCommand << endl;
-  std::string name = getNextWord(tokList);
-  doxyList.push_back(DoxygenEntity(theCommand, name));
-  return 1;
+	if (noisy)
+		cout << "Parsing " << theCommand << endl;
+	std::string name = getNextWord(tokList);
+	doxyList.push_back(DoxygenEntity(theCommand, name));
+	return 1;
 }
 
 int DoxygenParser::addCommandErrorThrow(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
 #pragma unused(doxyList)
-  if (noisy) {
-    cout << "Encountered :" << theCommand << endl;
-    cout << "This command should not have been encountered. Behaviour past this may be unpredictable " << endl;
-  }
-  std::list < Token >::iterator endOfLine = getOneLine(tokList);
-  tokList.setIterator(endOfLine);
-  return 0;
+	if (noisy) {
+		cout << "Encountered :" << theCommand << endl;
+		cout << "This command should not have been encountered. Behaviour past this may be unpredictable " << endl;
+	}
+	std::list < Token >::iterator endOfLine = getOneLine(tokList);
+	tokList.setIterator(endOfLine);
+	return 0;
 }
 
 int DoxygenParser::addCommandUnique(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
-  std::list < DoxygenEntity > aNewList;
-  if (theCommand.compare("arg") == 0 || theCommand.compare("li") == 0) {
-    std::list < Token >::iterator endOfSection = getEndOfSection(theCommand, tokList);
-    std::list < DoxygenEntity > aNewList;
-    aNewList = parse(endOfSection, tokList);
-    doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-  }
-  // \xrefitem <key> "(heading)" "(std::list title)" {text}
-  else if (theCommand.compare("xrefitem") == 0) {
-    //TODO Implement xrefitem
-    if (noisy)
-      cout << "Not Adding " << theCommand << endl;
-    std::list < Token >::iterator endOfParagraph = getEndOfParagraph(tokList);
-    tokList.setIterator(endOfParagraph);
-    return 1;
-  }
-  // \ingroup (<groupname> [<groupname> <groupname>])
-  else if (theCommand.compare("ingroup") == 0) {
-    std::string name = getNextWord(tokList);
-    aNewList.push_back(DoxygenEntity("plainstd::string", name));
-    name = getNextWord(tokList);
-    if (!name.empty())
-      aNewList.push_back(DoxygenEntity("plainstd::string", name));
-    name = getNextWord(tokList);
-    if (!name.empty())
-      aNewList.push_back(DoxygenEntity("plainstd::string", name));
-    doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-    return 1;
-  }
-  // \par [(paragraph title)] { paragraph }
-  else if (theCommand.compare("par") == 0) {
-    std::list < Token >::iterator endOfLine = getOneLine(tokList);
-    aNewList = parse(endOfLine, tokList);
-    std::list < DoxygenEntity > aNewList2;
-    aNewList2 = parse(endOfLine, tokList);
-    aNewList.splice(aNewList.end(), aNewList2);
-    doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-    return 1;
-  }
-  // \headerfile <header-file> [<header-name>]
-  else if (theCommand.compare("headerfile") == 0) {
-    std::list < DoxygenEntity > aNewList;
-    std::string name = getNextWord(tokList);
-    aNewList.push_back(DoxygenEntity("plainstd::string", name));
-    name = getNextWord(tokList);
-    if (!name.empty())
-      aNewList.push_back(DoxygenEntity("plainstd::string", name));
-    doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-    return 1;
-  }
-  // \overload [(function declaration)]
-  else if (theCommand.compare("overload") == 0) {
-    std::list < Token >::iterator endOfLine = getOneLine(tokList);
-    if (endOfLine != tokList.current()) {
-      std::list < DoxygenEntity > aNewList;
-      aNewList = parse(endOfLine, tokList);
-      doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-    } else
-      doxyList.push_back(DoxygenEntity(theCommand));
-    return 1;
-  }
-  // \weakgroup <name> [(title)]
-  else if (theCommand.compare("weakgroup") == 0) {
-    if (noisy)
-      cout << "Parsing " << theCommand << endl;
-    std::string name = getNextWord(tokList);
-    if (name.empty()) {
-      cout << "No word followed " << theCommand << " command. Not added" << endl;
-      return 0;
-    }
-    std::list < DoxygenEntity > aNewList;
-    std::list < Token >::iterator endOfLine = getOneLine(tokList);
-    if (endOfLine != tokList.current()) {
-      aNewList = parse(endOfLine, tokList);
-    }
-    aNewList.push_front(DoxygenEntity("plainstd::string", name));
-    doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-  }
-  // \ref <name> ["(text)"]
-  else if (theCommand.compare("ref") == 0) {
-    //TODO Implement ref
-    if (noisy)
-      cout << "Not Adding " << theCommand << endl;
-    std::list < Token >::iterator endOfParagraph = getEndOfParagraph(tokList);
-    tokList.setIterator(endOfParagraph);
-  }
-  // \subpage <name> ["(text)"]
-  else if (theCommand.compare("subpage") == 0) {
-    //TODO implement subpage
-    if (noisy)
-      cout << "Not Adding " << theCommand << endl;
-    std::list < Token >::iterator endOfParagraph = getEndOfParagraph(tokList);
-    tokList.setIterator(endOfParagraph);
-  }
-  // \dotfile <file> ["caption"]
-  else if (theCommand.compare("dotfile") == 0) {
-    //TODO implement dotfile
-    if (noisy)
-      cout << "Not Adding " << theCommand << endl;
-    std::list < Token >::iterator endOfParagraph = getEndOfParagraph(tokList);
-    tokList.setIterator(endOfParagraph);
-  }
-  // \image <format> <file> ["caption"] [<sizeindication>=<size>]
-  else if (theCommand.compare("image") == 0) {
-    //todo implement image
-  }
-  // \addtogroup <name> [(title)]
-  else if (theCommand.compare("addtogroup") == 0) {
-    if (noisy)
-      cout << "Parsing " << theCommand << endl;
-    std::string name = getNextWord(tokList);
-    if (name.empty()) {
-      cout << "No word followed " << theCommand << " command. Not added" << endl;
-      return 0;
-    }
-    std::list < DoxygenEntity > aNewList;
-    std::list < Token >::iterator endOfLine = getOneLine(tokList);
-    if (endOfLine != tokList.current()) {
-      aNewList = parse(endOfLine, tokList);
-    }
-    aNewList.push_front(DoxygenEntity("plainstd::string", name));
-    doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-  }
-  return 0;
+	std::list < DoxygenEntity > aNewList;
+	if (theCommand.compare("arg") == 0 || theCommand.compare("li") == 0) {
+		std::list < Token >::iterator endOfSection = getEndOfSection(theCommand, tokList);
+		std::list < DoxygenEntity > aNewList;
+		aNewList = parse(endOfSection, tokList);
+		doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+	}
+	// \xrefitem <key> "(heading)" "(std::list title)" {text}
+	else if (theCommand.compare("xrefitem") == 0) {
+		//TODO Implement xrefitem
+		if (noisy)
+			cout << "Not Adding " << theCommand << endl;
+		std::list < Token >::iterator endOfParagraph = getEndOfParagraph(tokList);
+		tokList.setIterator(endOfParagraph);
+		return 1;
+	}
+	// \ingroup (<groupname> [<groupname> <groupname>])
+	else if (theCommand.compare("ingroup") == 0) {
+		std::string name = getNextWord(tokList);
+		aNewList.push_back(DoxygenEntity("plainstd::string", name));
+		name = getNextWord(tokList);
+		if (!name.empty())
+			aNewList.push_back(DoxygenEntity("plainstd::string", name));
+		name = getNextWord(tokList);
+		if (!name.empty())
+			aNewList.push_back(DoxygenEntity("plainstd::string", name));
+		doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+		return 1;
+	}
+	// \par [(paragraph title)] { paragraph }
+	else if (theCommand.compare("par") == 0) {
+		std::list < Token >::iterator endOfLine = getOneLine(tokList);
+		aNewList = parse(endOfLine, tokList);
+		std::list < DoxygenEntity > aNewList2;
+		aNewList2 = parse(endOfLine, tokList);
+		aNewList.splice(aNewList.end(), aNewList2);
+		doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+		return 1;
+	}
+	// \headerfile <header-file> [<header-name>]
+	else if (theCommand.compare("headerfile") == 0) {
+		std::list < DoxygenEntity > aNewList;
+		std::string name = getNextWord(tokList);
+		aNewList.push_back(DoxygenEntity("plainstd::string", name));
+		name = getNextWord(tokList);
+		if (!name.empty())
+			aNewList.push_back(DoxygenEntity("plainstd::string", name));
+		doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+		return 1;
+	}
+	// \overload [(function declaration)]
+	else if (theCommand.compare("overload") == 0) {
+		std::list < Token >::iterator endOfLine = getOneLine(tokList);
+		if (endOfLine != tokList.current()) {
+			std::list < DoxygenEntity > aNewList;
+			aNewList = parse(endOfLine, tokList);
+			doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+		} else
+			doxyList.push_back(DoxygenEntity(theCommand));
+		return 1;
+	}
+	// \weakgroup <name> [(title)]
+	else if (theCommand.compare("weakgroup") == 0) {
+		if (noisy)
+			cout << "Parsing " << theCommand << endl;
+		std::string name = getNextWord(tokList);
+		if (name.empty()) {
+			cout << "No word followed " << theCommand << " command. Not added" << endl;
+			return 0;
+		}
+		std::list < DoxygenEntity > aNewList;
+		std::list < Token >::iterator endOfLine = getOneLine(tokList);
+		if (endOfLine != tokList.current()) {
+			aNewList = parse(endOfLine, tokList);
+		}
+		aNewList.push_front(DoxygenEntity("plainstd::string", name));
+		doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+	}
+	// \ref <name> ["(text)"]
+	else if (theCommand.compare("ref") == 0) {
+		//TODO Implement ref
+		if (noisy)
+			cout << "Not Adding " << theCommand << endl;
+		std::list < Token >::iterator endOfParagraph = getEndOfParagraph(tokList);
+		tokList.setIterator(endOfParagraph);
+	}
+	// \subpage <name> ["(text)"]
+	else if (theCommand.compare("subpage") == 0) {
+		//TODO implement subpage
+		if (noisy)
+			cout << "Not Adding " << theCommand << endl;
+		std::list < Token >::iterator endOfParagraph = getEndOfParagraph(tokList);
+		tokList.setIterator(endOfParagraph);
+	}
+	// \dotfile <file> ["caption"]
+	else if (theCommand.compare("dotfile") == 0) {
+		//TODO implement dotfile
+		if (noisy)
+			cout << "Not Adding " << theCommand << endl;
+		std::list < Token >::iterator endOfParagraph = getEndOfParagraph(tokList);
+		tokList.setIterator(endOfParagraph);
+	}
+	// \image <format> <file> ["caption"] [<sizeindication>=<size>]
+	else if (theCommand.compare("image") == 0) {
+		//todo implement image
+	}
+	// \addtogroup <name> [(title)]
+	else if (theCommand.compare("addtogroup") == 0) {
+		if (noisy)
+			cout << "Parsing " << theCommand << endl;
+		std::string name = getNextWord(tokList);
+		if (name.empty()) {
+			cout << "No word followed " << theCommand << " command. Not added" << endl;
+			return 0;
+		}
+		std::list < DoxygenEntity > aNewList;
+		std::list < Token >::iterator endOfLine = getOneLine(tokList);
+		if (endOfLine != tokList.current()) {
+			aNewList = parse(endOfLine, tokList);
+		}
+		aNewList.push_front(DoxygenEntity("plainstd::string", name));
+		doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+	}
+	return 0;
 }
 
 int DoxygenParser::addCommand(std::string commandString, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
-  std::string theCommand = StringToLower(commandString);
-  if (theCommand.compare("plainstd::string") == 0) {
-    std::string nextPhrase = getStringTilCommand(tokList);
-    if (noisy)
-      cout << "Parsing plain std::string :" << nextPhrase << endl;
-    doxyList.push_back(DoxygenEntity("plainstd::string", nextPhrase));
-    return 1;
-  }
-  int commandNumber = commandBelongs(theCommand);
-  if (commandNumber == SIMPLECOMMAND) {
-    return addSimpleCommand(theCommand, doxyList);
-  }
-  if (commandNumber == IGNOREDSIMPLECOMMAND) {
-    return ignoreSimpleCommand(theCommand, doxyList);
-  }
-  if (commandNumber == COMMANDWORD) {
-    return addCommandWord(theCommand, tokList, doxyList);
-  }
-  if (commandNumber == IGNOREDCOMMANDWORD) {
-    return ignoreCommandWord(theCommand, tokList, doxyList);
-  }
-  if (commandNumber == COMMANDLINE) {
-    return addCommandLine(theCommand, tokList, doxyList);
-  }
-  if (commandNumber == IGNOREDCOMMANDLINE) {
-    return ignoreCommandLine(theCommand, tokList, doxyList);
-  }
-  if (commandNumber == COMMANDPARAGRAPH) {
-    return addCommandParagraph(theCommand, tokList, doxyList);
-  }
-  if (commandNumber == IGNORECOMMANDPARAGRAPH) {
-    return ignoreCommandParagraph(theCommand, tokList, doxyList);
-  }
-  if (commandNumber == COMMANDENDCOMMAND) {
-    return addCommandEndCommand(theCommand, tokList, doxyList);
-  }
-  if (commandNumber == COMMANDWORDPARAGRAPH) {
-    return addCommandWordParagraph(theCommand, tokList, doxyList);
-  }
-  if (commandNumber == COMMANDWORDLINE) {
-    return addCommandWordLine(theCommand, tokList, doxyList);
-  }
-  if (commandNumber == COMMANDWORDOWORDWORD) {
-    return addCommandWordOWordOWord(theCommand, tokList, doxyList);
-  }
-  if (commandNumber == COMMANDOWORD) {
-    return addCommandOWord(theCommand, tokList, doxyList);
-  }
-  if (commandNumber == COMMANDERRORTHROW) {
-    return addCommandErrorThrow(theCommand, tokList, doxyList);
-  }
-  if (commandNumber == COMMANDUNIQUE) {
-    return addCommandUnique(theCommand, tokList, doxyList);
-  }
-
-  return 0;
-}
-
-std::list < DoxygenEntity > DoxygenParser::parse(std::list < Token >::iterator endParsingIndex, TokenList & tokList) {
-  std::list < DoxygenEntity > aNewList;
-  int currCommand;
-  while (tokList.current() != endParsingIndex) {
-    Token currToken = tokList.peek();
-    if (noisy)
-      cout << "Parsing for phrase starting in:" << currToken.toString() << endl;
-    if (currToken.tokenType == END_LINE) {
-      tokList.next();
-    } else if (currToken.tokenType == COMMAND) {
-      currCommand = findCommand(currToken.tokenString);
-      if (currCommand < 0) {
-	if (noisy)
-	  cout << "Unidentified Command " << currToken.tokenString << endl;
-	tokList.next();
-	addCommand(std::string("plainstd::string"), tokList, aNewList);
-      } else {
-	tokList.next();
-	addCommand(currToken.tokenString, tokList, aNewList);
-      }
-    } else if (currToken.tokenType == PLAINSTRING) {
-      addCommand(std::string("plainstd::string"), tokList, aNewList);
-    }
-    break;
-  }
-  return aNewList;
-}
-
-std::list < DoxygenEntity > DoxygenParser::parseRoot(std::list < Token >::iterator endParsingIndex, TokenList & tokList) {
-
-  std::list < DoxygenEntity > aNewList;
-  int currCommand;
-
-  while (tokList.current() != endParsingIndex) {
-
-    Token currToken = tokList.peek();
-    if (noisy) {
-      cout << "Parsing for phrase starting in:" << currToken.toString() << endl;
-    }
-
-    if (currToken.tokenType == END_LINE) {
-      tokList.next();
-    } else if (currToken.tokenType == COMMAND) {
-      currCommand = findCommand(currToken.tokenString);
-      if (currCommand < 0) {
-	if (noisy) {
-	  cout << "Unidentified Command " << currToken.tokenString << endl;
+	std::string theCommand = StringToLower(commandString);
+	if (theCommand.compare("plainstd::string") == 0) {
+		std::string nextPhrase = getStringTilCommand(tokList);
+		if (noisy)
+			cout << "Parsing plain std::string :" << nextPhrase << endl;
+		doxyList.push_back(DoxygenEntity("plainstd::string", nextPhrase));
+		return 1;
 	}
-	tokList.next();
-	addCommand(std::string("partofdescription"), tokList, aNewList);
-      } else {
-	tokList.next();
-	addCommand(currToken.tokenString, tokList, aNewList);
-      }
-    } else if (currToken.tokenType == PLAINSTRING) {
-      addCommand(std::string("partofdescription"), tokList, aNewList);
-    }
-  }
-  return aNewList;
+	int commandNumber = commandBelongs(theCommand);
+	if (commandNumber == SIMPLECOMMAND) {
+		return addSimpleCommand(theCommand, doxyList);
+	}
+	if (commandNumber == IGNOREDSIMPLECOMMAND) {
+		return ignoreSimpleCommand(theCommand, doxyList);
+	}
+	if (commandNumber == COMMANDWORD) {
+		return addCommandWord(theCommand, tokList, doxyList);
+	}
+	if (commandNumber == IGNOREDCOMMANDWORD) {
+		return ignoreCommandWord(theCommand, tokList, doxyList);
+	}
+	if (commandNumber == COMMANDLINE) {
+		return addCommandLine(theCommand, tokList, doxyList);
+	}
+	if (commandNumber == IGNOREDCOMMANDLINE) {
+		return ignoreCommandLine(theCommand, tokList, doxyList);
+	}
+	if (commandNumber == COMMANDPARAGRAPH) {
+		return addCommandParagraph(theCommand, tokList, doxyList);
+	}
+	if (commandNumber == IGNORECOMMANDPARAGRAPH) {
+		return ignoreCommandParagraph(theCommand, tokList, doxyList);
+	}
+	if (commandNumber == COMMANDENDCOMMAND) {
+		return addCommandEndCommand(theCommand, tokList, doxyList);
+	}
+	if (commandNumber == COMMANDWORDPARAGRAPH) {
+		return addCommandWordParagraph(theCommand, tokList, doxyList);
+	}
+	if (commandNumber == COMMANDWORDLINE) {
+		return addCommandWordLine(theCommand, tokList, doxyList);
+	}
+	if (commandNumber == COMMANDWORDOWORDWORD) {
+		return addCommandWordOWordOWord(theCommand, tokList, doxyList);
+	}
+	if (commandNumber == COMMANDOWORD) {
+		return addCommandOWord(theCommand, tokList, doxyList);
+	}
+	if (commandNumber == COMMANDERRORTHROW) {
+		return addCommandErrorThrow(theCommand, tokList, doxyList);
+	}
+	if (commandNumber == COMMANDUNIQUE) {
+		return addCommandUnique(theCommand, tokList, doxyList);
+	}
+
+	return 0;
+}
+
+std::list < DoxygenEntity > DoxygenParser::parse(std::list < Token >::iterator endParsingIndex, TokenList & tokList, bool root) {
+	// if we are root, than any strings should be added as 'partofdescription', else as 'plainstd::string'
+	std::string currPlainstringCommandType = root ? "partofdescription" : "plainstd::string";
+	std::list < DoxygenEntity > aNewList;
+	int currCommand;
+	while (tokList.current() != endParsingIndex) {
+		Token currToken = tokList.peek();
+		if (noisy)
+			cout << "Parsing for phrase starting in:" << currToken.toString() << endl;
+		if (currToken.tokenType == END_LINE) {
+			tokList.next();
+		} else if (currToken.tokenType == COMMAND) {
+			currCommand = findCommand(currToken.tokenString);
+			if (currCommand < 0) {
+				if (noisy)
+					cout << "Unidentified Command " << currToken.tokenString << endl;
+				tokList.next();
+				addCommand(currPlainstringCommandType, tokList, aNewList);
+			} else {
+				tokList.next();
+				addCommand(currToken.tokenString, tokList, aNewList);
+			}
+		} else if (currToken.tokenType == PLAINSTRING) {
+			addCommand(currPlainstringCommandType, tokList, aNewList);
+		}
+	}
+	return aNewList;
 }
 
 std::list < DoxygenEntity > DoxygenParser::createTree(std::string doxygenBlob) {
-  TokenList tokList = TokenList(doxygenBlob);
-  if (noisy) {
-    cout << "---TOKEN LIST---" << endl;
-    tokList.printList();
-  }
-  std::list < DoxygenEntity > rootList;
-  rootList = parseRoot(tokList.end(), tokList);
-  if (noisy) {
-    cout << "PARSED LIST" << endl;
-    printTree(rootList);
-  }
-  return rootList;
+	TokenList tokList = TokenList(doxygenBlob);
+	if (noisy) {
+		cout << "---TOKEN LIST---" << endl;
+		tokList.printList();
+	}
+	std::list < DoxygenEntity > rootList;
+	rootList = parse(tokList.end(), tokList, true);
+	if (noisy) {
+		cout << "PARSED LIST" << endl;
+		printTree(rootList);
+	}
+	return rootList;
 }
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.h b/Source/DoxygenTranslator/src/DoxygenParser.h
index e64644725..8becdff02 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.h
+++ b/Source/DoxygenTranslator/src/DoxygenParser.h
@@ -213,8 +213,7 @@ private:
    */
   int addCommand(std::string commandString, TokenList & tokList, std::list < DoxygenEntity > &doxyList);
 
-  std::list < DoxygenEntity > parse(std::list < Token >::iterator endParsingIndex, TokenList & tokList);
-  std::list < DoxygenEntity > parseRoot(std::list < Token >::iterator endParsingIndex, TokenList & tokList);
+  std::list < DoxygenEntity > parse(std::list < Token >::iterator endParsingIndex, TokenList & tokList, bool root=false);
   
   /*
    * Fill static doxygenCommands and sectionIndicators containers
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.cpp b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
index a3abf100a..7bdda082e 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
@@ -16,10 +16,11 @@
 #define TAB_SIZE 8		//current tab size in spaces
 //TODO {@link} {@linkplain} {@docRoot}, and other useful doxy commands that are not a javadoc tag
 
-// define static escape table, it is filled in JavaDocConverter's constructor
+// define static tables, they are filled in JavaDocConverter's constructor
 std::map<std::string, std::string> JavaDocConverter::escapeTable;
+std::map<std::string, JavaDocConverter::tagHandler> JavaDocConverter::tagHandlers;
 
-void JavaDocConverter::fillEscapeTable() {
+void JavaDocConverter::fillStaticTables() {
   if (escapeTable.size()) // fill only once
     return;
   
@@ -28,48 +29,47 @@ void JavaDocConverter::fillEscapeTable() {
   escapeTable["\""] = "&quot";
   escapeTable["<"] = "&lt";
   escapeTable[">"] = "&gt";
+
+  // these commands insert HTML tags
+	tagHandlers["c"] = &handleTagC;
+	tagHandlers["b"] = &handleTagB;
+	// these commands insert just a single char, some of them need to be escaped
+	tagHandlers["$"] = &handleTagChar;
+	tagHandlers["@"] = &handleTagChar;
+	tagHandlers["\\"] = &handleTagChar;
+	tagHandlers["<"] = &handleTagChar;
+	tagHandlers[">"] = &handleTagChar;
+	tagHandlers["&"] = &handleTagChar;
+	tagHandlers["#"] = &handleTagChar;
+	tagHandlers["%"] = &handleTagChar;
+	tagHandlers["~"] = &handleTagChar;
+	tagHandlers["\""] = &handleTagChar;
+	tagHandlers["."] = &handleTagChar;
+	tagHandlers["::"] = &handleTagChar;
+	// these commands are stripped out
+	tagHandlers["brief"] = &handleParagraph;
+	tagHandlers["details"] = &handleParagraph;
+	tagHandlers["partofdescription"] = &handleParagraph;
+	// these commands are kept as-is, they are supported by JavaDoc
+	tagHandlers["sa"] = &handleTagSeeAll;
+	tagHandlers["see"] = &handleTagSame;
+	tagHandlers["param"] = &handleTagSame;
+	tagHandlers["return"] = &handleTagSame;
+	tagHandlers["throws"] = &handleTagSame;
+	tagHandlers["throw"] = &handleTagThrow;
+	tagHandlers["author"] = &handleTagSame;
+	tagHandlers["since"] = &handleTagSame;
+	tagHandlers["version"] = &handleTagSame;
+	tagHandlers["exception"] = &handleTagSame;
+	tagHandlers["deprecated"] = &handleTagSame;
+	// this command just prints it's contents
+	// (it is internal command of swig's parser, contains plain text)
+	tagHandlers["plainstd::string"] = &handlePlainString;
 }
 
 
 JavaDocConverter::JavaDocConverter() : debug(false) {
-  
-  fillEscapeTable();
-  
-  // these commands insert HTML tags
-  tagHandlers["c"] = &handleTagC;
-  tagHandlers["b"] = &handleTagB;
-  // these commands insert just a single char, all of them need to be escaped
-  tagHandlers["$"] = &handleTagChar;
-  tagHandlers["@"] = &handleTagChar;
-  tagHandlers["\\"] = &handleTagChar;
-  tagHandlers["<"] = &handleTagChar;
-  tagHandlers[">"] = &handleTagChar;
-  tagHandlers["&"] = &handleTagChar;
-  tagHandlers["#"] = &handleTagChar;
-  tagHandlers["%"] = &handleTagChar;
-  tagHandlers["~"] = &handleTagChar;
-  tagHandlers["\""] = &handleTagChar;
-  tagHandlers["."] = &handleTagChar;
-  tagHandlers["::"] = &handleTagChar;
-  // these commands are stripped out
-  tagHandlers["brief"] = &handleTagStrip;
-  tagHandlers["details"] = &handleTagStrip;
-  tagHandlers["partofdescription"] = &handleTagStrip;
-  // these commands are kept as-is, they are supported by JavaDoc
-  tagHandlers["sa"] = &handleTagSeeAll;
-  tagHandlers["see"] = &handleTagSame;
-  tagHandlers["param"] = &handleTagSame;
-  tagHandlers["return"] = &handleTagSame;
-  tagHandlers["throws"] = &handleTagSame;
-  tagHandlers["throw"] = &handleTagThrow;
-  tagHandlers["author"] = &handleTagSame;
-  tagHandlers["since"] = &handleTagSame;
-  tagHandlers["version"] = &handleTagSame;
-  tagHandlers["exception"] = &handleTagSame;
-  tagHandlers["deprecated"] = &handleTagSame;
-  // this command just prints it's contents
-  // (it is internal command of swig's parser, contains plain text)
-  tagHandlers["plainstd::string"] = &handleTagData;
+  fillStaticTables();
 }
 
 std::string JavaDocConverter::formatCommand(std::string unformattedLine, int indent) {
@@ -136,10 +136,10 @@ void JavaDocConverter::translateEntity(DoxygenEntity& tag, std::string& translat
 }
 
 void JavaDocConverter::handleTagC(JavaDocConverter* converter, DoxygenEntity& tag, std::string& translatedComment) {
-  translatedComment += "<tt>" + tag.data + "</tt>";
+  translatedComment += "<tt>" + tag.data + "</tt> ";
 }
 void JavaDocConverter::handleTagB(JavaDocConverter* converter, DoxygenEntity& tag, std::string& translatedComment) {
-  translatedComment += "<b>" + tag.data + "</b>";
+  translatedComment += "<b>" + tag.data + "</b> ";
 }
 void JavaDocConverter::handleTagThrow(JavaDocConverter* converter, DoxygenEntity& tag, std::string& translatedComment) {
   tag.typeOfEntity = "throws";
@@ -159,10 +159,10 @@ void JavaDocConverter::handleTagChar(JavaDocConverter* converter, DoxygenEntity&
 void JavaDocConverter::handleTagSame(JavaDocConverter* converter, DoxygenEntity& tag, std::string& translatedComment) {
   translatedComment += converter->formatCommand(std::string("@" + tag.typeOfEntity + "\t" + converter->translateSubtree(tag)), 2);
 }
-void JavaDocConverter::handleTagStrip(JavaDocConverter* converter, DoxygenEntity& tag, std::string& translatedComment) {
+void JavaDocConverter::handleParagraph(JavaDocConverter* converter, DoxygenEntity& tag, std::string& translatedComment) {
   translatedComment += converter->formatCommand(converter->translateSubtree(tag), 0);
 }
-void JavaDocConverter::handleTagData(JavaDocConverter* converter, DoxygenEntity& tag, std::string& translatedComment) {
+void JavaDocConverter::handlePlainString(JavaDocConverter* converter, DoxygenEntity& tag, std::string& translatedComment) {
   translatedComment += tag.data + " ";
 }
 
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.h b/Source/DoxygenTranslator/src/JavaDocConverter.h
index 408ec4bb2..9776a17e0 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.h
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.h
@@ -53,17 +53,17 @@ protected:
   /*
    * Print only the content and strip original tag
    */
-  static void handleTagStrip(JavaDocConverter *converter, DoxygenEntity &tag, std::string &translatedComment);
+  static void handleParagraph(JavaDocConverter *converter, DoxygenEntity &tag, std::string &translatedComment);
   /*
    * Print only data part of code
    */
-  static void handleTagData(JavaDocConverter *converter, DoxygenEntity &tag, std::string &translatedComment);
+  static void handlePlainString(JavaDocConverter *converter, DoxygenEntity &tag, std::string &translatedComment);
 
 private:
   bool debug;
-  std::map<std::string, tagHandler> tagHandlers;
+  static std::map<std::string, tagHandler> tagHandlers;
   static std::map<std::string, std::string> escapeTable;
-  void fillEscapeTable();
+  void fillStaticTables();
 };
 
 #endif

From 92112f69f159ca8ffc2caf21c6815d610a1f27b3 Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Sat, 7 Jul 2012 13:55:25 +0000
Subject: [PATCH 068/314] Refactored java commentParser class

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13264 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Examples/test-suite/java/commentParser.java | 22 ++++++---------------
 1 file changed, 6 insertions(+), 16 deletions(-)

diff --git a/Examples/test-suite/java/commentParser.java b/Examples/test-suite/java/commentParser.java
index 3877f5f4d..1b167cfcd 100644
--- a/Examples/test-suite/java/commentParser.java
+++ b/Examples/test-suite/java/commentParser.java
@@ -14,30 +14,20 @@ public class commentParser {
 		 * file, we get comments and store them
 		 */
 
-		ClassDoc[] classes = root.classes();
+		for (ClassDoc classDoc : root.classes()) {
 
-		for (int i = 0; i < classes.length; i++) {
+			if (classDoc.getRawCommentText().length() > 0)
+				parsedComments.put(classDoc.name(), classDoc.getRawCommentText());
 
-			if (classes[i].getRawCommentText().length() > 0)
-				parsedComments.put(classes[i].name(),
-						classes[i].getRawCommentText());
-
-			MethodDoc[] methods = classes[i].methods();
-			FieldDoc[] fields = classes[i].fields();
-			FieldDoc[] constants = classes[i].enumConstants();
-
-			for (int j = 0; j < constants.length; j++) {
-				FieldDoc f = constants[j];
+			for (FieldDoc f : classDoc.enumConstants()) {
 				if (f.getRawCommentText().length() > 0)
 					parsedComments.put(f.name(), f.getRawCommentText());
 			}
-			for (int j = 0; j < fields.length; j++) {
-				FieldDoc f = fields[j];
+			for (FieldDoc f : classDoc.fields()) {
 				if (f.getRawCommentText().length() > 0)
 					parsedComments.put(f.name(), f.getRawCommentText());
 			}
-			for (int j = 0; j < methods.length; j++) {
-				MethodDoc m = methods[j];
+			for (MethodDoc m : classDoc.methods()) {
 				if (m.getRawCommentText().length() > 0)
 					parsedComments.put(m.name(), m.getRawCommentText());
 			}

From 2d47ffc87d2900273b09e837ff24d48e38587f09 Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Sat, 7 Jul 2012 15:24:35 +0000
Subject: [PATCH 069/314] Fixed small bug in DoxygenParser.cpp, now it won't
 freeze if it doesn't find doxygen ending tag. Also turned debug output off

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13265 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Source/DoxygenTranslator/src/DoxygenParser.cpp | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/Source/DoxygenTranslator/src/DoxygenParser.cpp b/Source/DoxygenTranslator/src/DoxygenParser.cpp
index e7104b9e0..238a6c75b 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenParser.cpp
@@ -17,7 +17,7 @@ std::map<std::string, DoxyCommandEnum> DoxygenParser::doxygenCommands;
 std::set<std::string> DoxygenParser::doxygenSectionIndicators;
 
 
-DoxygenParser::DoxygenParser() : noisy(true) {
+DoxygenParser::DoxygenParser() : noisy(false) {
 	fillTables();
 }
 
@@ -156,7 +156,8 @@ std::string DoxygenParser::getStringTilEndCommand(std::string theCommand, TokenL
 	std::string description;
 	if (tokList.peek().tokenType == 0)
 		return "";
-	while (tokList.next().tokenString.compare(theCommand) != 0) {
+	while (tokList.current() != tokList.end()
+			&& tokList.next().tokenString.compare(theCommand) != 0) {
 		//TODO: it won't output doxygen commands, need a way to fix it
 		if (tokList.peek().tokenType == PLAINSTRING)
 			description += tokList.peek().tokenString + " ";

From b3f53b98a079ee006a2a95c82d2b853fa413627d Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Sat, 7 Jul 2012 18:48:10 +0000
Subject: [PATCH 070/314] Added error reporting in case when there is no
 closing doxygen tag

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13266 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Source/DoxygenTranslator/src/DoxygenParser.cpp | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/Source/DoxygenTranslator/src/DoxygenParser.cpp b/Source/DoxygenTranslator/src/DoxygenParser.cpp
index 238a6c75b..623d37658 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenParser.cpp
@@ -156,13 +156,17 @@ std::string DoxygenParser::getStringTilEndCommand(std::string theCommand, TokenL
 	std::string description;
 	if (tokList.peek().tokenType == 0)
 		return "";
-	while (tokList.current() != tokList.end()
-			&& tokList.next().tokenString.compare(theCommand) != 0) {
+	while (tokList.next().tokenString.compare(theCommand) != 0) {
 		//TODO: it won't output doxygen commands, need a way to fix it
 		if (tokList.peek().tokenType == PLAINSTRING)
 			description += tokList.peek().tokenString + " ";
 		if (tokList.peek().tokenType == END_LINE)
 			description += "\n";
+
+		if (tokList.current() == tokList.end()) {
+			cout << "Error, @" << theCommand << " command expected." << endl;
+			break;
+		}
 	}
 	tokList.next(); // eat the end command itself
 	return description;

From db3b39bc85dd50a2dff276dd368e0e966d12e22f Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Mon, 9 Jul 2012 08:19:17 +0000
Subject: [PATCH 071/314] Added project plan to SVN

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13267 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Doc/Devel/plan-gsoc-2012.txt | 285 +++++++++++++++++++++++++++++++++++
 1 file changed, 285 insertions(+)
 create mode 100644 Doc/Devel/plan-gsoc-2012.txt

diff --git a/Doc/Devel/plan-gsoc-2012.txt b/Doc/Devel/plan-gsoc-2012.txt
new file mode 100644
index 000000000..1796bcf78
--- /dev/null
+++ b/Doc/Devel/plan-gsoc-2012.txt
@@ -0,0 +1,285 @@
+                                                                     
+                                                                     
+                                                                     
+                                             
+This document describes goals for the Google Summer of Code 2012,
+SWIG code documentation project.
+
+Author: Marko Klopcic
+
+
+Introduction
+============
+
+The goal of this project is _not_ to translate _any_ possible doxygen
+formatted comment to JavaDoc or PyDoc, but to make it possible to
+translate a subset of comment types in C/C++ code to
+JavaDoc and PyDoc. Covering all the Doxygen functionality would be to
+complex for the limited time. Hovewer, the code must be extendable so
+that implementing missing features would not require redesign of the
+comment handling code in SWIG.
+
+There will also be a possiblity to add untranslated comments to Java
+and Python code (## comments, see Doxygen manual), if the user will
+prefer to use Doxygen on the generated code.
+
+Abbreviations:
+    JD - JavaDoc
+    PD - PyDoc
+
+
+Functionality
+=============
+
+  Types of comments
+  -----------------
+  
+  Note:
+     See 'http://www.stack.nl/~dimitri/doxygen/docblocks.html' for
+     the detailed description of Doxygen syntax and terms used in this
+     section.
+
+  1. Only JavaDoc (/** */) and Qt (/*! */) styles of comment blocks
+     will be supported by SWIG translator.
+
+  2. The following doc after members will be supported:
+  
+     int var; ///< Detailed description after the member
+              //!< 
+
+     int var; //!< Brief description after the member
+
+     int var; ///< Brief description after the member
+
+  3. Only comments before or after declaration/definition will be
+     supported. Comments with structural commands will be ignored
+     (warning will be written). (What about writing them to
+     'package.info.java' for JD?)
+  
+
+  Tags
+  ----
+
+  This section contains all doxygen tags taken from 
+  http://www.stack.nl/~dimitri/doxygen/commands.html. If a tag is
+  marked as 'ignored', then the tag is ignored, but the text is copied
+  to the destination documentation.
+
+    Supported:     
+
+    \a - translated to <i></i> in JD, surrounded with _ in PD
+    \addindex - ignored
+    \addtogroup - ignored
+    \anchor - ignored, not supported by JD and PD 
+    \arg - translated to @param in JD, special formatting in PD
+    \attention - ignored, content printed out
+    \authors, \author - translated to @author in JD, 'Author:' in PD
+    \b - <b></b> in JD, surrounded with __ in PD
+    \brief - ignored, content printed out
+    \bug - ignored, content printed out
+    \c - translated to <code></code> in JD, ignored in PD
+    \callgraph - ignored, not supported by JD and PD
+    \callergraph - ignored, not supported by JD and PD
+    \category - ignored, used only in Objective C
+    \cite - translated to <i></i> in JD, single quotes in PD
+    \class - ignored (structural command)
+    \code - translated to <code></code> in JD, ignored in PD
+    \cond - translated to 'Conditional comment: <condition>'. Later
+            SWIG may support definitions of conditions in config file.
+    \copybrief - ignored. Later SWIG may support this command by
+                  performing copy
+    \copydetails - ignored. Later SWIG may support this command by
+                   performing copy
+    \copydoc - ignored. Later SWIG may support this command by
+               performing copy
+    \copyright - replaced with text 'Copyright' in PD and PD
+    \date - ignored, content printed out
+    \def
+    \defgroup
+    \deprecated - translated to @deprecated in JD, 'Deprecated:' in PD
+    \details - ignored, content printed out
+    \dir - not supported
+    \dontinclude - not supported
+    \dot - not supported. Later SWIG may call dot and produce the graph image to include in JD and PD
+    \dotfile - see note for \dot
+    \e - translated to <i></i> in JD
+    \else - see note for \cond
+    \elseif - see note for \cond
+    \em - translated to <em></em> in JD
+    \endcode - see note for \code
+    \endcond - translated to 'End of conditional comment: <condition>'. Later
+               SWIG may support definitions of conditions in config file.
+    \enddot - see note for \dot
+    \endhtmlonly - not supported
+    \endif - see note for \cond
+    \endinternal - not supported
+    \endlatexonly - not supported
+    \endlink - see note for \link
+    \endmanonly - not supported
+    \endmsc - see note for \msc
+    \endrtfonly - not supported
+    \endverbatim - see note for \verbatim
+    \endxmlonly - not supported
+    \enum - ignored (structural command)
+    \example - translated to 'Example:' in JD and PD
+    \exception - equivalent to throws 
+    \extends - not supported
+    \f$
+    \f[
+    \f]
+    \f{
+    \f}
+    \file
+    \fn
+    \headerfile
+    \hideinitializer
+    \htmlinclude
+    \htmlonly
+    \if
+    \ifnot
+    \image
+    \implements
+    \include
+    \includelineno
+    \ingroup
+    \internal
+    \invariant
+    \interface
+    \latexonly
+    \li
+    \line
+    \link
+    \mainpage
+    \manonly
+    \memberof
+    \msc
+    \mscfile
+    \n
+    \name
+    \namespace
+    \nosubgrouping
+    \note
+    \overload
+    \p
+    \package
+    \page
+    \par
+    \paragraph
+    \param
+    \post
+    \pre
+    \private
+    \privatesection
+    \property
+    \protected
+    \protectedsection
+    \protocol
+    \public
+    \publicsection
+    \ref - ignored, not supported by JD and PD
+    \related
+    \relates
+    \relatedalso
+    \relatesalso
+    \remark
+    \remarks
+    \result
+    \return
+    \returns
+    \retval
+    \rtfonly
+    \sa
+    \section
+    \see
+    \short
+    \showinitializer
+    \since
+    \skip
+    \skipline
+    \snippet
+    \struct
+    \subpage
+    \subsection
+    \subsubsection
+    \tableofcontents
+    \test
+    \throw
+    \throws
+    \todo
+    \tparam
+    \typedef
+    \union
+    \until
+    \var
+    \verbatim
+    \verbinclude
+    \version
+    \warning
+    \weakgroup
+    \xmlonly
+    \xrefitem
+    \$
+    \@
+    \\
+    \&
+    \~
+    \<
+    \>
+    \#
+    \%
+    \"
+    \.
+    \::
+
+          
+Tests
+=====
+
+The following test cases will be implemented:
+
+- Class comments, JD and Qt style.
+- Class comments, JD and Qt style.
+
+- Struct comments, JD and Qt style.
+- Enum comments, JD and Qt style.
+
+- Class attributes, JD and Qt style, comment before and after declaration.
+- Class methods, JD and Qt style, comment of parameters in function
+  comment.
+- Class methods, JD and Qt style, comment of parameters 
+  after parameter declaration.
+  
+- Struct attributes, JD and Qt style, comment before and after declaration.
+- Struct methods, JD and Qt style, comment of parameters in function
+  comment.
+- Struct methods, JD and Qt style, comment of parameters 
+  after parameter declaration.
+
+- Enum items JD and Qt style, comment before items
+- Enum items JD and Qt style, comment after items
+
+- Class comment, JD and Qt style, with all supported tags.
+- Class comment, JD and Qt style, with all doxygen tags, including
+  ignored ones.
+
+  
+Refactoring
+===========
+
+All the code in directory _DoxygenTranslator_ should be refactored:
+- all methods should be class members
+- most static methods should be normal members
+- replace C arrays of strings and sequential searches with STL data
+  structures and algorithms.
+- use singletons instead of class instantiaion for each comment found.
+
+
+Documentation
+=============
+
+SWIG documentation will contain:
+- command line options
+- list of implemented features (types and placements of comments)
+- list of unimplemented features (types and placements of comments)
+- list of tags and their translations (all Doxygen tags).
+

From 0e2f37bc544dd0fbaad632ef4101dc1d7e44cae0 Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Mon, 9 Jul 2012 10:11:29 +0000
Subject: [PATCH 072/314] Extended project plan, now it is also the description
 of how are the doxygen tags translated

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13269 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Doc/Devel/plan-gsoc-2012.txt | 218 ++++++++++++++++++-----------------
 1 file changed, 114 insertions(+), 104 deletions(-)

diff --git a/Doc/Devel/plan-gsoc-2012.txt b/Doc/Devel/plan-gsoc-2012.txt
index 1796bcf78..faf9359f9 100644
--- a/Doc/Devel/plan-gsoc-2012.txt
+++ b/Doc/Devel/plan-gsoc-2012.txt
@@ -64,19 +64,22 @@ Functionality
   http://www.stack.nl/~dimitri/doxygen/commands.html. If a tag is
   marked as 'ignored', then the tag is ignored, but the text is copied
   to the destination documentation.
+  Not all of the tags are currently implemented. The status of
+  implementation and time estimation for every tag may be seen in
+  plan-gsoc-2012-timings.txt
 
-    Supported:     
+    Doxygen tags:     
 
     \a - translated to <i></i> in JD, surrounded with _ in PD
     \addindex - ignored
     \addtogroup - ignored
     \anchor - ignored, not supported by JD and PD 
     \arg - translated to @param in JD, special formatting in PD
-    \attention - ignored, content printed out
+    \attention - ignored
     \authors, \author - translated to @author in JD, 'Author:' in PD
     \b - <b></b> in JD, surrounded with __ in PD
-    \brief - ignored, content printed out
-    \bug - ignored, content printed out
+    \brief - ignored
+    \bug - ignored
     \c - translated to <code></code> in JD, ignored in PD
     \callgraph - ignored, not supported by JD and PD
     \callergraph - ignored, not supported by JD and PD
@@ -93,132 +96,139 @@ Functionality
     \copydoc - ignored. Later SWIG may support this command by
                performing copy
     \copyright - replaced with text 'Copyright' in PD and PD
-    \date - ignored, content printed out
+    \date - ignored
     \def
     \defgroup
     \deprecated - translated to @deprecated in JD, 'Deprecated:' in PD
-    \details - ignored, content printed out
+    \details - ignored
     \dir - not supported
     \dontinclude - not supported
-    \dot - not supported. Later SWIG may call dot and produce the graph image to include in JD and PD
+    \dot - not supported. Later SWIG may call dot and produce the graph image
+           to include in JD and PD
     \dotfile - see note for \dot
-    \e - translated to <i></i> in JD
+    \e - equivalent \a
     \else - see note for \cond
     \elseif - see note for \cond
-    \em - translated to <em></em> in JD
+    \em - equivalent to \a
     \endcode - see note for \code
     \endcond - translated to 'End of conditional comment: <condition>'. Later
                SWIG may support definitions of conditions in config file.
     \enddot - see note for \dot
-    \endhtmlonly - not supported
+    \endhtmlonly - ignored
     \endif - see note for \cond
-    \endinternal - not supported
-    \endlatexonly - not supported
+    \endinternal - ignored
+    \endlatexonly - ignored
     \endlink - see note for \link
-    \endmanonly - not supported
+    \endmanonly - ignored
     \endmsc - see note for \msc
-    \endrtfonly - not supported
+    \endrtfonly - ignored
     \endverbatim - see note for \verbatim
-    \endxmlonly - not supported
+    \endxmlonly - ignored
     \enum - ignored (structural command)
     \example - translated to 'Example:' in JD and PD
-    \exception - equivalent to throws 
+    \exception - equivalent to throws, but translates to @exception in JD 
     \extends - not supported
     \f$
     \f[
     \f]
     \f{
     \f}
-    \file
+    \file 
     \fn
-    \headerfile
-    \hideinitializer
-    \htmlinclude
-    \htmlonly
-    \if
-    \ifnot
-    \image
-    \implements
-    \include
-    \includelineno
-    \ingroup
-    \internal
-    \invariant
-    \interface
-    \latexonly
-    \li
-    \line
-    \link
-    \mainpage
-    \manonly
-    \memberof
-    \msc
-    \mscfile
-    \n
-    \name
-    \namespace
-    \nosubgrouping
-    \note
-    \overload
-    \p
-    \package
-    \page
-    \par
-    \paragraph
-    \param
-    \post
-    \pre
-    \private
-    \privatesection
-    \property
-    \protected
-    \protectedsection
-    \protocol
-    \public
-    \publicsection
+    \headerfile - not supported
+    \hideinitializer - not supported
+    \htmlinclude - not supported
+    \htmlonly - not supported
+    \if - see note for \cond 
+    \ifnot - see note for \cond
+    \image - translated to <img/> in JD only when target=HTML, ignored in PD
+    \implements - not supported
+    \include - not supported
+    \includelineno - not supported
+    \ingroup - not supported. Later swig may print group names as plain text
+               in comments like 'Code group: something' in both JD and PD
+    \internal - ignored
+    \invariant - ignored
+    \interface - ignored (structural command)
+    \latexonly - ignored
+    \li - trabslated to <li></li> in JD, ignored in PD
+    \line - not supported
+    \link - translated to {@link ...} in JD, ignored in PD
+    \mainpage - ignored
+    \manonly - ignored
+    \memberof - not supported
+    \msc - not supported. Later SWIG may call dot and produce the graph image
+           to include in JD and PD
+    \mscfile - see note for \msc
+    \n - prints the new line
+    \name - ignored
+    \namespace - included in package-info.java if nspace feature is enabled,
+                 otherwise ignored, ignored in PD
+    \nosubgrouping - ignored
+    \note - ignored in JD, translated to 'Note:' in PD
+    \overload - prints 'This is an overloaded member function, provided for
+                convenience. It differs from the above function only in what
+                argument(s) it accepts.' to the output in both JD and PD
+    \p - equivalent to \c
+    \package - is kept same in JD (it is already a JD tag), ignored in PD
+    \page - ignored
+    \par - translated to <p alt='title'></p> in JD, 'Title: ...' in PD 
+    \paragraph - ignored
+    \param - equivalent to \arg
+    \post - ignored
+    \pre - ignored
+    \private - ignored
+    \privatesection - ignored
+    \property - ignored
+    \protected - ignored
+    \protectedsection - ignored
+    \protocol - ignored (Objective-C tag)
+    \public - ignored
+    \publicsection - ignored
     \ref - ignored, not supported by JD and PD
-    \related
-    \relates
-    \relatedalso
-    \relatesalso
-    \remark
-    \remarks
-    \result
-    \return
-    \returns
-    \retval
-    \rtfonly
-    \sa
-    \section
-    \see
-    \short
-    \showinitializer
-    \since
-    \skip
-    \skipline
-    \snippet
-    \struct
-    \subpage
-    \subsection
-    \subsubsection
-    \tableofcontents
-    \test
-    \throw
-    \throws
-    \todo
-    \tparam
-    \typedef
-    \union
-    \until
-    \var
-    \verbatim
-    \verbinclude
-    \version
-    \warning
-    \weakgroup
-    \xmlonly
-    \xrefitem
-    \$
+    \related - ignored 
+    \relates - ignored
+    \relatedalso - ignored
+    \relatesalso - ignored
+    \remark - translated to 'Remarks:' in both JD and PD
+    \remarks - equivalent to remark
+    \result - translated to @return in JD, 'Return:' in PD
+    \return - equivalent to result
+    \returns - equivalent to result
+    \retval - ignored
+    \rtfonly - ignored
+    \sa - translated to @see in JD, 'See also:' in PD
+    \section - not supported
+    \see - equivalent to \sa
+    \short - equivalent to \brief
+    \showinitializer - not supported
+    \since - translated to @since in JD, 'Since:' in PD
+    \skip - not supported
+    \skipline - not supported
+    \snippet - not supported
+    \struct - ignored (structural command)
+    \subpage - not supported
+    \subsection - not supported
+    \subsubsection - not supported
+    \tableofcontents - not supported
+    \test - ignored
+    \throw - translated to @throws in JD, 'Throws:' in PD 
+    \throws - equivalent to \throw
+    \todo - translated to 'TODO:' in both JD and PD
+    \tparam - similar to \arg
+    \typedef - ignored (structural command)
+    \union - ignored (structural command)
+    \until - not supported
+    \var - ignored (structural command)
+    \verbatim - translated to {@literal ...} in JD, ignored in PD
+    \verbinclude - ignored
+    \version - translated to @version in JD, 'Version:' in PD
+    \warning - translated to 'Warning:' in both JD and PD
+    \weakgroup - not supported
+    \xmlonly - ignored
+    \xrefitem - ignored
+    \$ - this and all the others below: these commands insert single char,
+         it is escaped as HTML char in JD, kept as-is in PD
     \@
     \\
     \&

From 32166f96f4b44d18d823a208ebf5b732f8e02041 Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Mon, 9 Jul 2012 11:08:56 +0000
Subject: [PATCH 073/314] New fixes for the project plan

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13273 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Doc/Devel/plan-gsoc-2012.txt | 33 ++++++++++++++++++++-------------
 1 file changed, 20 insertions(+), 13 deletions(-)

diff --git a/Doc/Devel/plan-gsoc-2012.txt b/Doc/Devel/plan-gsoc-2012.txt
index faf9359f9..570457e1a 100644
--- a/Doc/Devel/plan-gsoc-2012.txt
+++ b/Doc/Devel/plan-gsoc-2012.txt
@@ -23,6 +23,10 @@ There will also be a possiblity to add untranslated comments to Java
 and Python code (## comments, see Doxygen manual), if the user will
 prefer to use Doxygen on the generated code.
 
+Note:
+time format below is HH:MM. '--Done' tick means that the item is
+implemented, commited and working.
+
 Abbreviations:
     JD - JavaDoc
     PD - PyDoc
@@ -41,6 +45,7 @@ Functionality
 
   1. Only JavaDoc (/** */) and Qt (/*! */) styles of comment blocks
      will be supported by SWIG translator.
+     --Done
 
   2. The following doc after members will be supported:
   
@@ -50,11 +55,14 @@ Functionality
      int var; //!< Brief description after the member
 
      int var; ///< Brief description after the member
+     
+     --Done
 
   3. Only comments before or after declaration/definition will be
      supported. Comments with structural commands will be ignored
      (warning will be written). (What about writing them to
      'package.info.java' for JD?)
+     --Done
   
 
   Tags
@@ -63,10 +71,8 @@ Functionality
   This section contains all doxygen tags taken from 
   http://www.stack.nl/~dimitri/doxygen/commands.html. If a tag is
   marked as 'ignored', then the tag is ignored, but the text is copied
-  to the destination documentation.
-  Not all of the tags are currently implemented. The status of
-  implementation and time estimation for every tag may be seen in
-  plan-gsoc-2012-timings.txt
+  to the destination documentation. 'Not implemented' means that the
+  tag with it's contents is stripped out of the output.
 
     Doxygen tags:     
 
@@ -97,8 +103,8 @@ Functionality
                performing copy
     \copyright - replaced with text 'Copyright' in PD and PD
     \date - ignored
-    \def
-    \defgroup
+    \def - ignored (structural command)
+    \defgroup - not supported
     \deprecated - translated to @deprecated in JD, 'Deprecated:' in PD
     \details - ignored
     \dir - not supported
@@ -128,13 +134,14 @@ Functionality
     \example - translated to 'Example:' in JD and PD
     \exception - equivalent to throws, but translates to @exception in JD 
     \extends - not supported
-    \f$
-    \f[
-    \f]
-    \f{
-    \f}
-    \file 
-    \fn
+    \f$ - not supported. Later swig may call LATeX to produce bitmaps with formulas
+          to include in JD and PD
+    \f[ - see note for \f$
+    \f] - see note for \f$
+    \f{ - see note for \f$
+    \f} - see note for \f$
+    \file - ignored (structural command)
+    \fn - ignored (structural command)
     \headerfile - not supported
     \hideinitializer - not supported
     \htmlinclude - not supported

From 3a3c2b8063154316a51c4fa3f22bfd1382366ae4 Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Mon, 9 Jul 2012 13:56:45 +0000
Subject: [PATCH 074/314] Extended commentParser.java to the standalone java
 app to print parsed comments

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13274 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Examples/test-suite/java/commentParser.java | 24 +++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/Examples/test-suite/java/commentParser.java b/Examples/test-suite/java/commentParser.java
index 1b167cfcd..93785669e 100644
--- a/Examples/test-suite/java/commentParser.java
+++ b/Examples/test-suite/java/commentParser.java
@@ -58,4 +58,28 @@ public class commentParser {
 		
 		return errorCount;
 	}
+	
+	public static void printCommentListForJavaSource() {
+		Iterator< Entry<String, String> > it = parsedComments.entrySet().iterator();
+		while (it.hasNext())
+		{
+			Entry<String, String> e = (Entry<String, String>) it.next();
+			System.out.format("wantedComments.put(\"%s\", \"%s\");\n", e.getKey(), e.getValue());
+		}
+	}
+	
+	public static void main(String argv[]) {
+		
+		if (argv.length<1) {
+			System.out.format("Usage:\n\tcommentParsing <package to parse>\n");
+			System.exit(1);
+		}
+		
+		com.sun.tools.javadoc.Main.execute("The comment parser program",
+				"commentParser", new String[]{"-quiet", argv[0]});
+		
+		// if we are run as standalone app, print the list of found comments as it would appear in java source
+		
+		printCommentListForJavaSource();
+	}
 }
\ No newline at end of file

From dc432411301cd18f5591cebe70e4f660c496f649 Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Mon, 9 Jul 2012 14:02:23 +0000
Subject: [PATCH 075/314] Rewritten doxygen_parsing.cpptest according to the
 project plan

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13275 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Examples/test-suite/doxygen_parsing.i         | 152 +++++++++++-------
 Examples/test-suite/doxygen_parsing_enums.i   |  36 ++++-
 .../doxygen_parsing_enums_proper_runme.java   |  12 +-
 .../doxygen_parsing_enums_simple_runme.java   |   9 +-
 .../doxygen_parsing_enums_typesafe_runme.java |  12 +-
 ...oxygen_parsing_enums_typeunsafe_runme.java |  12 +-
 .../java/doxygen_parsing_runme.java           |  44 ++---
 .../python/doxygen_parsing_runme.py           |  37 +++--
 8 files changed, 207 insertions(+), 107 deletions(-)

diff --git a/Examples/test-suite/doxygen_parsing.i b/Examples/test-suite/doxygen_parsing.i
index a83cd77ed..b4579c886 100644
--- a/Examples/test-suite/doxygen_parsing.i
+++ b/Examples/test-suite/doxygen_parsing.i
@@ -3,77 +3,119 @@
 %inline %{
 
 /**
- * This is simple comment for a var
+ * The class comment
  */
-int simpleVar=42;
-/*!
- * This is another type of comment for a var
- */
-int simpleVarTwo=42;
-
-/// This is again another type of comment for a var
-int simpleVarThree=42;
-//! This is the last type of comment for a var
-int simpleVarFour=42;
-
-int simpleVarFive=42;
-///< This is a post comment
-
-/*
-  We assume that all this comment types are ok,
-  and later we only use the first-type comments.
-*/
-
+class SomeClass
+{
+};
 
 /**
- * This is simple comment for a function
+ * The function comment
  */
-void simpleFunction(int arg)
+void someFunction()
 {
 }
 
 /**
- * This is simple comment for a class
+ * The enum comment
  */
-class CSimpleClass
+enum SomeEnum
 {
-private:
-  /** Some member var */
-  int simpleVar;
-
-public:
-  /** 
-   * Simple method
-   */
-  void simpleMethod(int asd)
-  {
-  }
-  /**
-   * Simple method with parameter
-   */
-  void simpleMethodWithParameter(
-	int param, /**< Some test param */
-	int argument /**< Some test argument */
-	)
-  {
-  }
+	SOME_ENUM_ITEM
 };
 
 /**
- * Comment for template class
+ * The struct comment
  */
-template <typename T>
-class CTemplateClass
+struct SomeStruct
+{
+};
+
+/**
+ * The var comment
+ */
+int someVar=42;
+
+class SomeAnotherClass
 {
 public:
-  /**
-   * Template method
-   */
-  void templateMethod(T arg)
-  {
-  }
+
+	/**
+	 * The class attribute comment
+	 */
+	int classAttr;
+
+	int classAttr2; ///< The class attribute post-comment
+
+	int classAttr3; ///< The class attribute post-comment
+									//!< with details
+
+	/**
+	 * The class method comment
+	 */
+	void classMethod()
+	{
+	}
+
+	/**
+	 * The class method with parameter
+	 */
+	void classMethodExtended(
+			int a, ///< Parameter a
+			int b  ///< Parameter b
+			)
+	{
+	}
+
+	/**
+	 * The class method with parameter
+	 *
+	 * @param a Parameter a
+	 * @param b Parameter b
+	 */
+	void classMethodExtended2(int a, int b)
+	{
+	}
+};
+
+struct SomeAnotherStruct
+{
+	/**
+	 * The struct attribute comment
+	 */
+	int structAttr;
+
+	int structAttr2; ///< The struct attribute post-comment
+
+	int structAttr3; ///< The struct attribute post-comment
+									 //!< with details
+
+	/**
+	 * The struct method comment
+	 */
+	void structMethod()
+	{
+	}
+
+	/**
+	 * The struct method with parameter
+	 */
+	void structMethodExtended(
+			int a, ///< Parameter a
+			int b  ///< Parameter b
+			)
+	{
+	}
+
+	/**
+	 * The struct method with parameter
+	 *
+	 * @param a Parameter a
+	 * @param b Parameter b
+	 */
+	void structMethodExtended2(int a, int b)
+	{
+	}
 };
 
 %}
-
-%template(CTemplateClassInt) CTemplateClass<int>;
\ No newline at end of file
diff --git a/Examples/test-suite/doxygen_parsing_enums.i b/Examples/test-suite/doxygen_parsing_enums.i
index 222356510..5c48f4801 100644
--- a/Examples/test-suite/doxygen_parsing_enums.i
+++ b/Examples/test-suite/doxygen_parsing_enums.i
@@ -3,13 +3,33 @@
 %inline %{
 
 
-/** Test enumeration */
-enum E_TEST
-{
-  /** the first item */
-  E_TEST_ONE,
-  E_TEST_TWO = 2, /**< the second */
-  E_TEST_THREE = 2+1 /**< the last item */
-};
+	/**
+	 * Testing comments before enum items
+	 */
+	enum SomeAnotherEnum
+	{
+		/**
+		 * The comment for the first item
+		 */
+		SOME_ITEM_1,
+		/**
+		 * The comment for the second item
+		 */
+		SOME_ITEM_2,
+		/**
+		 * The comment for the third item
+		 */
+		SOME_ITEM_3
+	};
+
+	/**
+	 * Testing comments after enum items
+	 */
+	enum SomeAnotherEnum2
+	{
+		SOME_ITEM_10, ///< Post comment for the first item
+		SOME_ITEM_20, ///< Post comment for the second item
+		SOME_ITEM_30  ///< Post comment for the third item
+	};
 
 %}
diff --git a/Examples/test-suite/java/doxygen_parsing_enums_proper_runme.java b/Examples/test-suite/java/doxygen_parsing_enums_proper_runme.java
index d3993f201..4531ada51 100644
--- a/Examples/test-suite/java/doxygen_parsing_enums_proper_runme.java
+++ b/Examples/test-suite/java/doxygen_parsing_enums_proper_runme.java
@@ -25,10 +25,14 @@ public class doxygen_parsing_enums_proper_runme {
 
     HashMap<String, String> wantedComments = new HashMap<String, String>();
     
-    wantedComments.put("E_TEST", " Test enumeration  \n");
-    wantedComments.put("E_TEST_ONE", " the first item  \n");
-    wantedComments.put("E_TEST_TWO", " the second  \n");
-    wantedComments.put("E_TEST_THREE", " the last item  \n");
+    wantedComments.put("SomeAnotherEnum", " Testing comments before enum items \n");
+    wantedComments.put("SOME_ITEM_1", " The comment for the first item \n");
+    wantedComments.put("SOME_ITEM_2", " The comment for the second item \n");
+    wantedComments.put("SOME_ITEM_3", " The comment for the third item \n");
+    wantedComments.put("SomeAnotherEnum2", " Testing comments after enum items \n");
+    wantedComments.put("SOME_ITEM_10", " Post comment for the first item \n");
+    wantedComments.put("SOME_ITEM_20", " Post comment for the second item \n");
+    wantedComments.put("SOME_ITEM_30", " Post comment for the third item \n");
     
     // and ask the parser to check comments for us
     System.exit(parser.check(wantedComments));
diff --git a/Examples/test-suite/java/doxygen_parsing_enums_simple_runme.java b/Examples/test-suite/java/doxygen_parsing_enums_simple_runme.java
index 1dffe4466..7fba76d5c 100644
--- a/Examples/test-suite/java/doxygen_parsing_enums_simple_runme.java
+++ b/Examples/test-suite/java/doxygen_parsing_enums_simple_runme.java
@@ -25,9 +25,12 @@ public class doxygen_parsing_enums_simple_runme {
 
     HashMap<String, String> wantedComments = new HashMap<String, String>();
     
-    wantedComments.put("E_TEST_ONE", " the first item  \n");
-    wantedComments.put("E_TEST_TWO", " the second  \n");
-    wantedComments.put("E_TEST_THREE", " the last item  \n");
+    wantedComments.put("SOME_ITEM_1", " The comment for the first item \n");
+    wantedComments.put("SOME_ITEM_2", " The comment for the second item \n");
+    wantedComments.put("SOME_ITEM_3", " The comment for the third item \n");
+    wantedComments.put("SOME_ITEM_10", " Post comment for the first item \n");
+    wantedComments.put("SOME_ITEM_20", " Post comment for the second item \n");
+    wantedComments.put("SOME_ITEM_30", " Post comment for the third item \n");
     
     // and ask the parser to check comments for us
     System.exit(parser.check(wantedComments));
diff --git a/Examples/test-suite/java/doxygen_parsing_enums_typesafe_runme.java b/Examples/test-suite/java/doxygen_parsing_enums_typesafe_runme.java
index 5aed9327e..f853ffb3b 100644
--- a/Examples/test-suite/java/doxygen_parsing_enums_typesafe_runme.java
+++ b/Examples/test-suite/java/doxygen_parsing_enums_typesafe_runme.java
@@ -25,10 +25,14 @@ public class doxygen_parsing_enums_typesafe_runme {
 
     HashMap<String, String> wantedComments = new HashMap<String, String>();
     
-    wantedComments.put("E_TEST", " Test enumeration  \n");
-    wantedComments.put("E_TEST_ONE", " the first item  \n");
-    wantedComments.put("E_TEST_TWO", " the second  \n");
-    wantedComments.put("E_TEST_THREE", " the last item  \n");
+    wantedComments.put("SomeAnotherEnum", " Testing comments before enum items \n");
+    wantedComments.put("SOME_ITEM_1", " The comment for the first item \n");
+    wantedComments.put("SOME_ITEM_2", " The comment for the second item \n");
+    wantedComments.put("SOME_ITEM_3", " The comment for the third item \n");
+    wantedComments.put("SomeAnotherEnum2", " Testing comments after enum items \n");
+    wantedComments.put("SOME_ITEM_10", " Post comment for the first item \n");
+    wantedComments.put("SOME_ITEM_20", " Post comment for the second item \n");
+    wantedComments.put("SOME_ITEM_30", " Post comment for the third item \n");
     
     // and ask the parser to check comments for us
     System.exit(parser.check(wantedComments));
diff --git a/Examples/test-suite/java/doxygen_parsing_enums_typeunsafe_runme.java b/Examples/test-suite/java/doxygen_parsing_enums_typeunsafe_runme.java
index 44405f837..9788ae1d3 100644
--- a/Examples/test-suite/java/doxygen_parsing_enums_typeunsafe_runme.java
+++ b/Examples/test-suite/java/doxygen_parsing_enums_typeunsafe_runme.java
@@ -25,10 +25,14 @@ public class doxygen_parsing_enums_typeunsafe_runme {
 
     HashMap<String, String> wantedComments = new HashMap<String, String>();
     
-    wantedComments.put("E_TEST", " Test enumeration  \n");
-    wantedComments.put("E_TEST_ONE", " the first item  \n");
-    wantedComments.put("E_TEST_TWO", " the second  \n");
-    wantedComments.put("E_TEST_THREE", " the last item  \n");
+    wantedComments.put("SomeAnotherEnum", " Testing comments before enum items \n");
+    wantedComments.put("SOME_ITEM_1", " The comment for the first item \n");
+    wantedComments.put("SOME_ITEM_2", " The comment for the second item \n");
+    wantedComments.put("SOME_ITEM_3", " The comment for the third item \n");
+    wantedComments.put("SomeAnotherEnum2", " Testing comments after enum items \n");
+    wantedComments.put("SOME_ITEM_10", " Post comment for the first item \n");
+    wantedComments.put("SOME_ITEM_20", " Post comment for the second item \n");
+    wantedComments.put("SOME_ITEM_30", " Post comment for the third item \n");
     
     // and ask the parser to check comments for us
     System.exit(parser.check(wantedComments));
diff --git a/Examples/test-suite/java/doxygen_parsing_runme.java b/Examples/test-suite/java/doxygen_parsing_runme.java
index ae426da58..e0719c586 100644
--- a/Examples/test-suite/java/doxygen_parsing_runme.java
+++ b/Examples/test-suite/java/doxygen_parsing_runme.java
@@ -25,26 +25,30 @@ public class doxygen_parsing_runme {
 
     HashMap<String, String> wantedComments = new HashMap<String, String>();
     
-    wantedComments.put("simpleFunction", " This is simple comment for a function  \n");
-
-    wantedComments.put("CSimpleClass", " This is simple comment for a class  \n");
-    wantedComments.put("simpleMethod", " Simple method  \n");
-    wantedComments.put("simpleMethodWithParameter", " Simple method with parameter  \n" +
-						    " @param\tparam Some test param  \n" +
-						    " @param\targument Some test argument  \n");
-    wantedComments.put("CTemplateClassInt", " Comment for template class  \n");
-    wantedComments.put("templateMethod", " Template method  \n");
-
-    wantedComments.put("setSimpleVar", " This is simple comment for a var  \n");
-    wantedComments.put("getSimpleVar", " This is simple comment for a var  \n");
-    wantedComments.put("setSimpleVarTwo", " This is another type of comment for a var  \n");
-    wantedComments.put("getSimpleVarTwo", " This is another type of comment for a var  \n");
-    wantedComments.put("setSimpleVarThree", " This is again another type of comment for a var  \n");
-    wantedComments.put("getSimpleVarThree", " This is again another type of comment for a var  \n");
-    wantedComments.put("setSimpleVarFour", " This is the last type of comment for a var  \n");
-    wantedComments.put("getSimpleVarFour", " This is the last type of comment for a var  \n");
-    wantedComments.put("setSimpleVarFive", " This is a post comment  \n");
-    wantedComments.put("getSimpleVarFive", " This is a post comment  \n");
+    wantedComments.put("someFunction", " The function comment \n");
+    wantedComments.put("SomeEnum", " The enum comment \n");
+    wantedComments.put("setSomeVar", " The var comment \n");
+    wantedComments.put("getSomeVar", " The var comment \n");
+    wantedComments.put("SomeClass", " The class comment \n");
+    wantedComments.put("setClassAttr", " The class attribute comment \n");
+    wantedComments.put("getClassAttr", " The class attribute comment \n");
+    wantedComments.put("setClassAttr2", " The class attribute post-comment \n");
+    wantedComments.put("getClassAttr2", " The class attribute post-comment \n");
+    wantedComments.put("setClassAttr3", " The class attribute post-comment with details \n");
+    wantedComments.put("getClassAttr3", " The class attribute post-comment with details \n");
+    wantedComments.put("classMethod", " The class method comment \n");
+    wantedComments.put("classMethodExtended", " The class method with parameter \n @param	a Parameter a \n @param	b Parameter b \n");
+    wantedComments.put("classMethodExtended2", " The class method with parameter \n @param	a Parameter a \n @param	b Parameter b \n");
+    wantedComments.put("SomeStruct", " The struct comment \n");
+    wantedComments.put("setStructAttr", " The struct attribute comment \n");
+    wantedComments.put("getStructAttr", " The struct attribute comment \n");
+    wantedComments.put("setStructAttr2", " The struct attribute post-comment \n");
+    wantedComments.put("getStructAttr2", " The struct attribute post-comment \n");
+    wantedComments.put("setStructAttr3", " The struct attribute post-comment with details \n");
+    wantedComments.put("getStructAttr3", " The struct attribute post-comment with details \n");
+    wantedComments.put("structMethod", " The struct method comment \n");
+    wantedComments.put("structMethodExtended", " The struct method with parameter \n @param	a Parameter a \n @param	b Parameter b \n");
+    wantedComments.put("structMethodExtended2", " The struct method with parameter \n @param	a Parameter a \n @param	b Parameter b \n");
 
     // and ask the parser to check comments for us
     System.exit(parser.check(wantedComments));
diff --git a/Examples/test-suite/python/doxygen_parsing_runme.py b/Examples/test-suite/python/doxygen_parsing_runme.py
index 097c18f8c..b814a68ed 100644
--- a/Examples/test-suite/python/doxygen_parsing_runme.py
+++ b/Examples/test-suite/python/doxygen_parsing_runme.py
@@ -8,13 +8,32 @@ def check(got, expected):
   if not re.match(str(expected), str(got)):
     raise RuntimeError("\n" + "Expected: [" + str(expected) + "]\n" + "Got     : [" + str(got) + "]")
 
-check(doxygen_parsing.simpleFunction.__doc__, '\s+This is simple comment for a function\s+')
-check(doxygen_parsing.CSimpleClass.__doc__, '\s+This is simple comment for a class\s+')
-check(doxygen_parsing.CSimpleClass.simpleMethod.__doc__, '\s+Simple method\s+')
-check(doxygen_parsing.CSimpleClass.simpleMethodWithParameter.__doc__, ''
-'\s+Simple method with parameter'
-'\s+Arguments:\s+param \(int\)\s+-- Some test param\s+'
-'argument \(int\)\s+-- Some test argument\s+'
+check(doxygen_parsing.someFunction.__doc__, '\s+The function comment\s+')
+check(doxygen_parsing.SomeClass.__doc__, '\s+The class comment\s+')
+check(doxygen_parsing.SomeStruct.__doc__, '\s+The struct comment\s+')
+check(doxygen_parsing.SomeAnotherClass.classMethod.__doc__, '\s+The class method comment\s+')
+check(doxygen_parsing.SomeAnotherClass.classMethodExtended.__doc__, ''
+'\s+The class method with parameter'
+'\s+Arguments:\s+'
+'a \(int\)\s+-- Parameter a\s+'
+'b \(int\)\s+-- Parameter b\s+'
 )
-check(doxygen_parsing.CTemplateClassInt.__doc__, '\s+Comment for template class\s+')
-check(doxygen_parsing.CTemplateClassInt.templateMethod.__doc__, '\s+Template method\s+')
\ No newline at end of file
+check(doxygen_parsing.SomeAnotherClass.classMethodExtended2.__doc__, ''
+'\s+The class method with parameter'
+'\s+Arguments:\s+'
+'a \(int\)\s+-- Parameter a\s+'
+'b \(int\)\s+-- Parameter b\s+'
+)
+check(doxygen_parsing.SomeAnotherStruct.structMethod.__doc__, '\s+The struct method comment\s+')
+check(doxygen_parsing.SomeAnotherStruct.structMethodExtended.__doc__, ''
+'\s+The struct method with parameter'
+'\s+Arguments:\s+'
+'a \(int\)\s+-- Parameter a\s+'
+'b \(int\)\s+-- Parameter b\s+'
+)
+check(doxygen_parsing.SomeAnotherStruct.structMethodExtended2.__doc__, ''
+'\s+The struct method with parameter'
+'\s+Arguments:\s+'
+'a \(int\)\s+-- Parameter a\s+'
+'b \(int\)\s+-- Parameter b\s+'
+)
\ No newline at end of file

From 9404bb442cf333b11603c6409871c93cdf16a631 Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Mon, 9 Jul 2012 21:30:11 +0000
Subject: [PATCH 076/314] Added optional functionality section to the project
 plan.

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13309 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Doc/Devel/plan-gsoc-2012.txt | 61 +++++++++++++++++++++++-------------
 1 file changed, 40 insertions(+), 21 deletions(-)

diff --git a/Doc/Devel/plan-gsoc-2012.txt b/Doc/Devel/plan-gsoc-2012.txt
index 570457e1a..f9b6849c5 100644
--- a/Doc/Devel/plan-gsoc-2012.txt
+++ b/Doc/Devel/plan-gsoc-2012.txt
@@ -24,8 +24,8 @@ and Python code (## comments, see Doxygen manual), if the user will
 prefer to use Doxygen on the generated code.
 
 Note:
-time format below is HH:MM. '--Done' tick means that the item is
-implemented, commited and working.
+'--Done' tick below means that the item is implemented, commited and
+working.
 
 Abbreviations:
     JD - JavaDoc
@@ -248,35 +248,54 @@ Functionality
     \.
     \::
 
-          
+Optional functionality
+======================
+
+That section describes some complex cases where the current code
+not behaves really well. Like a short to-do list of special cases.
+
+- When translating functions with default parameters in swig to
+java, it creates overloaded functions with all the parameters
+except the default ones. We need to copy the doxygen comment to
+such functions and correct the list of @param tags.
+
+- In doxygen there is a special tags (and even a special option)
+to create links to some code members from the current comment.
+Sometimes it needs a type of parameters specified because of the
+overloaded functions. And the same linking tags are supported in JD,
+but it has a completely different typesystem, so we need to translate
+the types of function parameters in comments also. For example:
+ 
+    
 Tests
 =====
 
 The following test cases will be implemented:
 
-- Class comments, JD and Qt style.
-- Class comments, JD and Qt style.
+- Class comments. --Done
 
-- Struct comments, JD and Qt style.
-- Enum comments, JD and Qt style.
+- Struct comments. --Done
+- Enum comments. --Done
+- Function comments. --Done
+- Var comments. --Done
 
-- Class attributes, JD and Qt style, comment before and after declaration.
-- Class methods, JD and Qt style, comment of parameters in function
-  comment.
-- Class methods, JD and Qt style, comment of parameters 
-  after parameter declaration.
+- Class attributes, comment before and after declaration. --Done
+- Class methods, comment of parameters in function
+  comment. --Done
+- Class methods, comment of parameters
+  after parameter declaration. --Done
   
-- Struct attributes, JD and Qt style, comment before and after declaration.
-- Struct methods, JD and Qt style, comment of parameters in function
-  comment.
-- Struct methods, JD and Qt style, comment of parameters 
-  after parameter declaration.
+- Struct attributes, comment before and after declaration. --Done
+- Struct methods, comment of parameters in function
+  comment. --Done
+- Struct methods, comment of parameters 
+  after parameter declaration. --Done
 
-- Enum items JD and Qt style, comment before items
-- Enum items JD and Qt style, comment after items
+- Enum items JD and Qt style, comment before items --Done
+- Enum items JD and Qt style, comment after items --Done
 
-- Class comment, JD and Qt style, with all supported tags.
-- Class comment, JD and Qt style, with all doxygen tags, including
+- Class comment, with all supported tags.
+- Class comment, with all doxygen tags, including
   ignored ones.
 
   

From ed1bd4fbb98662886ccd493a58891dcb65a4428b Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Tue, 10 Jul 2012 17:17:51 +0000
Subject: [PATCH 077/314] Implemented nice error output, with filename and line
 number information.

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13313 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Source/CParse/cscanner.c                      |  4 ++
 .../DoxygenTranslator/src/DoxygenParser.cpp   | 37 +++++++++---------
 Source/DoxygenTranslator/src/DoxygenParser.h  |  2 +-
 .../src/JavaDocConverter.cpp                  |  6 ++-
 .../DoxygenTranslator/src/PyDocConverter.cpp  |  4 +-
 Source/DoxygenTranslator/src/TokenList.cpp    | 39 ++++++-------------
 Source/DoxygenTranslator/src/TokenList.h      |  6 ++-
 7 files changed, 46 insertions(+), 52 deletions(-)

diff --git a/Source/CParse/cscanner.c b/Source/CParse/cscanner.c
index 44af1069b..e15201b93 100644
--- a/Source/CParse/cscanner.c
+++ b/Source/CParse/cscanner.c
@@ -344,11 +344,15 @@ static int yylook(void) {
 	  if (strncmp(loc, "/**<", 4) == 0 || strncmp(loc, "///<", 4) == 0||strncmp(loc, "/*!<", 4) == 0||strncmp(loc, "//!<", 4) == 0) {
 	    /* printf("Doxygen Post Comment: %s lines %d-%d [%s]\n", Char(Scanner_file(scan)), Scanner_start_line(scan), Scanner_line(scan), loc); */
 	    yylval.str =  NewString(loc);
+	    Setline(yylval.str, Scanner_start_line(scan));
+	    Setfile(yylval.str, Scanner_file(scan));
 	    return DOXYGENPOSTSTRING;
 	  }
 	  if (strncmp(loc, "/**", 3) == 0 || strncmp(loc, "///", 3) == 0||strncmp(loc, "/*!", 3) == 0||strncmp(loc, "//!", 3) == 0) {
 	    /* printf("Doxygen Comment: %s lines %d-%d [%s]\n", Char(Scanner_file(scan)), Scanner_start_line(scan), Scanner_line(scan), loc);  */
 	    yylval.str =  NewString(loc);
+	    Setline(yylval.str, Scanner_start_line(scan));
+	    Setfile(yylval.str, Scanner_file(scan));
 	    return DOXYGENSTRING;
 	  }
 	}
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.cpp b/Source/DoxygenTranslator/src/DoxygenParser.cpp
index 623d37658..4106cad44 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenParser.cpp
@@ -156,19 +156,22 @@ std::string DoxygenParser::getStringTilEndCommand(std::string theCommand, TokenL
 	std::string description;
 	if (tokList.peek().tokenType == 0)
 		return "";
-	while (tokList.next().tokenString.compare(theCommand) != 0) {
+	while (tokList.current() != tokList.end()) {
+
 		//TODO: it won't output doxygen commands, need a way to fix it
 		if (tokList.peek().tokenType == PLAINSTRING)
 			description += tokList.peek().tokenString + " ";
 		if (tokList.peek().tokenType == END_LINE)
 			description += "\n";
 
-		if (tokList.current() == tokList.end()) {
-			cout << "Error, @" << theCommand << " command expected." << endl;
-			break;
+		if (tokList.peek().tokenString.compare(theCommand) == 0) {
+			tokList.next();
+			return description;
 		}
+
+		tokList.next();
 	}
-	tokList.next(); // eat the end command itself
+	tokList.printListError(theCommand + " command expected");
 	return description;
 }
 
@@ -263,7 +266,7 @@ int DoxygenParser::addCommandWord(std::string theCommand, TokenList & tokList, s
 		doxyList.push_back(DoxygenEntity(theCommand, name));
 		return 1;
 	} else
-		cout << "No word followed " << theCommand << " command. Not added" << endl;
+		tokList.printListError("No word followed " + theCommand + " command. Not added");
 	return 0;
 }
 
@@ -275,7 +278,7 @@ int DoxygenParser::ignoreCommandWord(std::string theCommand, TokenList & tokList
 	if (!name.empty())
 		return 1;
 	else
-		cout << "WARNING: No word followed " << theCommand << " command." << endl;
+		tokList.printListError("No word followed " + theCommand + " command.");
 	return 0;
 }
 
@@ -329,7 +332,7 @@ int DoxygenParser::addCommandWordParagraph(std::string theCommand, TokenList & t
 		cout << "Parsing " << theCommand << endl;
 	std::string name = getNextWord(tokList);
 	if (name.empty()) {
-		cout << "No word followed " << theCommand << " command. Not added" << endl;
+		tokList.printListError("No word followed " + theCommand + " command. Not added");
 		return 0;
 	}
 	std::list < Token >::iterator endOfParagraph = getEndOfParagraph(tokList);
@@ -345,7 +348,7 @@ int DoxygenParser::addCommandWordLine(std::string theCommand, TokenList & tokLis
 		cout << "Parsing " << theCommand << endl;
 	std::string name = getNextWord(tokList);
 	if (name.empty()) {
-		cout << "No word followed " << theCommand << " command. Not added" << endl;
+		tokList.printListError("No word followed " + theCommand + " command. Not added");
 		return 0;
 	}
 	std::list < Token >::iterator endOfLine = getOneLine(tokList);
@@ -362,7 +365,7 @@ int DoxygenParser::addCommandWordOWordOWord(std::string theCommand, TokenList &
 		cout << "Parsing " << theCommand << endl;
 	std::string name = getNextWord(tokList);
 	if (name.empty()) {
-		cout << "No word followed " << theCommand << " command. Not added" << endl;
+		tokList.printListError("No word followed " + theCommand + " command. Not added");
 		return 0;
 	}
 	std::string headerfile = getNextWord(tokList);
@@ -387,10 +390,8 @@ int DoxygenParser::addCommandOWord(std::string theCommand, TokenList & tokList,
 
 int DoxygenParser::addCommandErrorThrow(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
 #pragma unused(doxyList)
-	if (noisy) {
-		cout << "Encountered :" << theCommand << endl;
-		cout << "This command should not have been encountered. Behaviour past this may be unpredictable " << endl;
-	}
+	tokList.printListError("Encountered: " + theCommand +
+			"\nThis command should not have been encountered. Behaviour past this may be unpredictable");
 	std::list < Token >::iterator endOfLine = getOneLine(tokList);
 	tokList.setIterator(endOfLine);
 	return 0;
@@ -464,7 +465,7 @@ int DoxygenParser::addCommandUnique(std::string theCommand, TokenList & tokList,
 			cout << "Parsing " << theCommand << endl;
 		std::string name = getNextWord(tokList);
 		if (name.empty()) {
-			cout << "No word followed " << theCommand << " command. Not added" << endl;
+			tokList.printListError("No word followed " + theCommand + " command. Not added");
 			return 0;
 		}
 		std::list < DoxygenEntity > aNewList;
@@ -509,7 +510,7 @@ int DoxygenParser::addCommandUnique(std::string theCommand, TokenList & tokList,
 			cout << "Parsing " << theCommand << endl;
 		std::string name = getNextWord(tokList);
 		if (name.empty()) {
-			cout << "No word followed " << theCommand << " command. Not added" << endl;
+			tokList.printListError("No word followed " + theCommand + " command. Not added");
 			return 0;
 		}
 		std::list < DoxygenEntity > aNewList;
@@ -611,8 +612,8 @@ std::list < DoxygenEntity > DoxygenParser::parse(std::list < Token >::iterator e
 	return aNewList;
 }
 
-std::list < DoxygenEntity > DoxygenParser::createTree(std::string doxygenBlob) {
-	TokenList tokList = TokenList(doxygenBlob);
+std::list < DoxygenEntity > DoxygenParser::createTree(std::string doxygenBlob, std::string fileName, int lineNumber) {
+	TokenList tokList(doxygenBlob, fileName, lineNumber);
 	if (noisy) {
 		cout << "---TOKEN LIST---" << endl;
 		tokList.printList();
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.h b/Source/DoxygenTranslator/src/DoxygenParser.h
index 8becdff02..c72ca6fed 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.h
+++ b/Source/DoxygenTranslator/src/DoxygenParser.h
@@ -21,7 +21,7 @@ class DoxygenParser {
 public:
   DoxygenParser();
   virtual ~DoxygenParser();
-  std::list < DoxygenEntity > createTree(std::string doxygen);
+  std::list < DoxygenEntity > createTree(std::string doxygen, std::string fileName, int lineNumber);
 private:
   
   /*
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.cpp b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
index 7bdda082e..2bc3165f4 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
@@ -163,7 +163,9 @@ void JavaDocConverter::handleParagraph(JavaDocConverter* converter, DoxygenEntit
   translatedComment += converter->formatCommand(converter->translateSubtree(tag), 0);
 }
 void JavaDocConverter::handlePlainString(JavaDocConverter* converter, DoxygenEntity& tag, std::string& translatedComment) {
-  translatedComment += tag.data + " ";
+  translatedComment += tag.data;
+  if (tag.data.size() && tag.data[tag.data.size()-1] != ' ')
+  	translatedComment += " ";
 }
 
 String *JavaDocConverter::makeDocumentation(Node *node) {
@@ -174,7 +176,7 @@ String *JavaDocConverter::makeDocumentation(Node *node) {
     return NULL;
   }
 
-  std::list < DoxygenEntity > entityList = parser.createTree(Char(documentation));
+  std::list < DoxygenEntity > entityList = parser.createTree(Char(documentation), Char(Getfile(documentation)), Getline(documentation));
 
   // entityList.sort(CompareDoxygenEntities()); sorting currently not used,
   // see CompareDoxygenEntities::operator() in DoxygenEntity.cpp
diff --git a/Source/DoxygenTranslator/src/PyDocConverter.cpp b/Source/DoxygenTranslator/src/PyDocConverter.cpp
index b1e94a062..819c6bc6c 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/PyDocConverter.cpp
@@ -170,7 +170,7 @@ String *PyDocConverter::makeDocumentation(Node *n) {
     while (n) {
       documentation = getDoxygenComment(n);
       if (!Swig_is_generated_overload(n) && documentation) {
-	std::list < DoxygenEntity > entityList = DoxygenParser().createTree(Char(documentation));
+	std::list < DoxygenEntity > entityList = parser.createTree(Char(documentation), Char(Getfile(documentation)), Getline(documentation));
 	allDocumentation.push_back(processEntityList(n, entityList));
       }
       n = Getattr(n, "sym:nextSibling");
@@ -194,7 +194,7 @@ String *PyDocConverter::makeDocumentation(Node *n) {
   else {
     documentation = getDoxygenComment(n);
     if (documentation != NULL) {
-      std::list < DoxygenEntity > entityList = DoxygenParser().createTree(Char(documentation));
+      std::list < DoxygenEntity > entityList = parser.createTree(Char(documentation), Char(Getfile(documentation)), Getline(documentation));
       pyDocString = processEntityList(n, entityList);
     }
   }
diff --git a/Source/DoxygenTranslator/src/TokenList.cpp b/Source/DoxygenTranslator/src/TokenList.cpp
index 5e13fe164..8624fb4a2 100644
--- a/Source/DoxygenTranslator/src/TokenList.cpp
+++ b/Source/DoxygenTranslator/src/TokenList.cpp
@@ -14,6 +14,7 @@
 #include <iostream>
 #include <string>
 #include <list>
+#include "swig.h"
 #include "Token.h"
 #include "DoxygenEntity.h"
 #define TOKENSPERLINE 8;	//change this to change the printing behaviour of the token list
@@ -22,37 +23,11 @@ using namespace std;
 
 int noisy2 = 0;
 /* The tokenizer*/
-TokenList::TokenList(const std::string & doxygenStringConst) {
+TokenList::TokenList(const std::string & doxygenStringConst, const std::string fileName, int fileLine)
+	: fileName(fileName), fileLine(fileLine) {
   size_t commentPos;
   string doxygenString = doxygenStringConst;
 
-   /* Comment start tokens are replaced in parser.y, see doxygen_comment and
-      doxygen_post_comment_item
-   do {
-    commentPos = doxygenString.find("///<");
-    if (commentPos != string::npos) {
-      doxygenString.replace(commentPos, 4, " ");
-      continue;
-    }
-    commentPos = doxygenString.find("/**<");
-    if (commentPos != string::npos) {
-      doxygenString.replace(commentPos, 4, " ");
-      continue;
-    }
-    commentPos = doxygenString.find("/*!<");
-    if (commentPos != string::npos) {
-      doxygenString.replace(commentPos, 4, " ");
-      continue;
-    }
-    commentPos = doxygenString.find("//!<");
-    if (commentPos != string::npos) {
-      doxygenString.replace(commentPos, 4, " ");
-      continue;
-    }
-    break;
-  } while (true);
-  */
-
   size_t currentIndex = 0;
   size_t nextIndex = 0;
 
@@ -174,3 +149,11 @@ void TokenList::printList() {
     i++;
   }
 }
+
+void TokenList::printListError(std::string message) {
+	int curLine = fileLine;
+	for (list< Token >::iterator it = m_tokenList.begin(); it != current(); it++)
+		if (it->tokenType == END_LINE)
+			curLine++;
+	Swig_error(fileName.c_str(), curLine, "Doxygen parser error: %s. \n", message.c_str());
+}
diff --git a/Source/DoxygenTranslator/src/TokenList.h b/Source/DoxygenTranslator/src/TokenList.h
index 057f67ed4..d38fec792 100644
--- a/Source/DoxygenTranslator/src/TokenList.h
+++ b/Source/DoxygenTranslator/src/TokenList.h
@@ -25,9 +25,12 @@ class TokenList {
 private:
   std::list < Token > m_tokenList;
   std::list < Token >::iterator m_tokenListIter;
+  // location info for error output
+  std::string fileName;
+  int fileLine;
 
 public:
-  TokenList(const std::string & doxygenString);	/* constructor takes a blob of Doxygen comment */
+  TokenList(const std::string & doxygenString, const std::string fileName, int fileLine);	/* constructor takes a blob of Doxygen comment */
   ~TokenList();
 
   Token peek();			/* returns next token without advancing */
@@ -40,6 +43,7 @@ public:
   void setIterator(list < Token >::iterator newPosition);	/*moves up the iterator */
 
   void printList();		/* prints out the sequence of tokens */
+  void printListError(std::string message); /* prints properly formatted error message */
 };
 
 #endif

From be2116603477e83f708fd9151fac745eec6b41e0 Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Wed, 11 Jul 2012 22:24:36 +0000
Subject: [PATCH 078/314] Added parsing support for some new commands

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13314 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 .../DoxygenTranslator/src/DoxygenCommands.h   | 26 ++++++++++---------
 1 file changed, 14 insertions(+), 12 deletions(-)

diff --git a/Source/DoxygenTranslator/src/DoxygenCommands.h b/Source/DoxygenTranslator/src/DoxygenCommands.h
index e1eba33f4..93898193c 100644
--- a/Source/DoxygenTranslator/src/DoxygenCommands.h
+++ b/Source/DoxygenTranslator/src/DoxygenCommands.h
@@ -4,8 +4,8 @@
 
 const char *commandArray[] = {
   "a", "addindex", "addtogroup", "anchor", "arg", "attention",
-  "author", "b", "brief", "bug", "c", "callgraph", "callergraph", "category",
-  "class", "code", "cond", "copybrief", "copydetails", "copydoc", "date", "def",
+  "author", "authors", "b", "brief", "bug", "c", "callgraph", "callergraph", "category", "cite",
+  "class", "code", "cond", "copybrief", "copydetails", "copydoc", "copyright", "date", "def",
   "defgroup", "deprecated", "details", "dir", "dontinclude", "dot", "dotfile", "e",
   "else", "elseif", "em", "endcode", "endcond", "enddot", "endhtmlonly", "endif",
   "endlatexonly", "endlink", "endmanonly", "endmsc", "endverbatim", "endxmlonly",
@@ -15,21 +15,21 @@ const char *commandArray[] = {
   "line", "link", "mainpage", "manonly", "msc", "n", "name", "namespace", "nosubgrouping",
   "note", "overload", "p", "package", "page", "par", "paragraph", "param", "post", "pre",
   "private", "privatesection", "property", "protected", "protectedsection", "protocol",
-  "public", "publicsection", "ref", "relates", "relatesalso", "remarks", "return", "retval",
+  "public", "publicsection", "ref", "relates", "relatesalso", "remarks", "remark", "result", "return", "returns", "retval",
   "sa", "section", "see", "showinitializer", "since", "skip", "skipline", "struct", "subpage",
   "subsection", "subsubsection", "test", "throw", "throws", "todo", "tparam", "typedef", "union", "until",
   "var", "verbatim", "verbinclude", "version", "warning", "weakgroup", "xmlonly", "xrefitem", "$", "@", "\\", "&", "~", "<", ">", "#", "%"};
 
 
 const char *sectionIndicators[] = {
-  "attention", "author", "brief", "bug", "cond", "date", "deprecated", "details",
+  "attention", "author", "authors", "brief", "bug", "cond", "date", "deprecated", "details",
   "else", "elseif", "endcond", "endif", "exception", "if", "ifnot", "invariant", "note", "par", "param",
-  "tparam", "post", "pre", "remarks", "return", "retval", "sa", "see", "since", "test", "throw", "throws", "todo", "version", "warning", "xrefitem"};
+  "tparam", "post", "pre", "remarks", "remark", "result", "return", "returns", "retval", "sa", "see", "since", "test", "throw", "throws", "todo", "version", "warning", "xrefitem"};
 const int sectionIndicatorsSize = sizeof(sectionIndicators) / sizeof(*sectionIndicators);
 
 /* All of the doxygen commands divided up by how they are parsed */
 const char *simpleCommands[] = {
-  "n", "$", "@", "\\", "&", "~", "<", ">", "#", "%"};
+  "n", "$", "@", "\\", "&", "~", "<", ">", "#", "%", "\"", ".", "::", "endcond"};
 const int simpleCommandsSize = sizeof(simpleCommands) / sizeof(*simpleCommands);
 
 const char *ignoredSimpleCommands[] = {
@@ -37,7 +37,8 @@ const char *ignoredSimpleCommands[] = {
 const int ignoredSimpleCommandsSize = sizeof(ignoredSimpleCommands) / sizeof(*ignoredSimpleCommands);
 
 const char *commandWords[] = {
-  "a", "b", "c", "e", "em", "p", "def", "enum", "example", "package", "relates", "namespace", "relatesalso", "anchor", "dontinclude", "include", "includelineno"};
+  "a", "b", "c", "e", "em", "p", "def", "enum", "example", "package", "relates", "namespace", "relatesalso", "anchor", "dontinclude", "include",
+  "includelineno"};
 const int commandWordsSize = sizeof(commandWords) / sizeof(*commandWords);
 
 const char *ignoredCommandWords[] = {
@@ -53,8 +54,9 @@ const char *ignoreCommandLines[] = {
 const int ignoreCommandLinesSize = sizeof(ignoreCommandLines) / sizeof(*ignoreCommandLines);
 
 const char *commandParagraph[] = {
-  "partofdescription", "return", "remarks", "since", "test", "sa", "see", "pre", "post", "details", "invariant",
-  "deprecated", "date", "note", "warning", "version", "todo", "bug", "attention", "brief", "author"};
+  "partofdescription", "result", "return", "returns", "remarks", "remark", "since", "test", "sa", "see", "pre", "post", "details", "invariant",
+  "deprecated", "date", "note", "warning", "version", "todo", "bug", "attention", "brief", "author", "authors", "cite",
+  "copyright"};
 const int commandParagraphSize = sizeof(commandParagraph) / sizeof(*commandParagraph);
 
 const char *ignoreCommandParagraphs[] = {
@@ -62,7 +64,7 @@ const char *ignoreCommandParagraphs[] = {
 const int ignoreCommandParagraphsSize = sizeof(ignoreCommandParagraphs) / sizeof(*ignoreCommandParagraphs);
 
 const char *commandEndCommands[] = {
-  "code", "dot", "msc", "f$", "f[", "f{environment}{", "htmlonly", "latexonly", "manonly", "verbatim", "xmlonly", "cond", "if", "ifnot", "link"};
+  "code", "dot", "msc", "f$", "f[", "f{environment}{", "htmlonly", "latexonly", "manonly", "verbatim", "xmlonly", "if", "ifnot", "link"};
 const int commandEndCommandsSize = sizeof(commandEndCommands) / sizeof(*commandEndCommands);
 
 const char *commandWordParagraphs[] = {
@@ -85,11 +87,11 @@ const char *commandErrorThrowings[] = {
   "annotatedclassstd::list", "classhierarchy", "define", "functionindex", "header",
   "headerfilestd::list", "inherit", "l", "postheader", "private", "privatesection", "protected",
   "protectedsection", "public", "publicsection", "endcode", "enddot", "endmsc", "endhtmlonly",
-  "endlatexonly", "endmanonly", "endlink", "endverbatim", "endxmlonly", "f]", "f}", "endcond", "endif"};
+  "endlatexonly", "endmanonly", "endlink", "endverbatim", "endxmlonly", "f]", "f}", "endif"};
 const int commandErrorThrowingsSize = sizeof(commandErrorThrowings) / sizeof(*commandErrorThrowings);
 
 const char *commandUniques[] = {
   "xrefitem", "arg", "ingroup", "par", "headerfile", "overload", "weakgroup", "ref", "subpage", "dotfile", "image", "addtogroup", "li"};
 const int commandUniquesSize = sizeof(commandUniques) / sizeof(*commandUniques);
 
-#endif
\ No newline at end of file
+#endif

From c461f1110d9a4351913c37ee84e9d37a0c406118 Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Wed, 11 Jul 2012 22:25:34 +0000
Subject: [PATCH 079/314] Small fixes to the project plan

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13315 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Doc/Devel/plan-gsoc-2012.txt | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/Doc/Devel/plan-gsoc-2012.txt b/Doc/Devel/plan-gsoc-2012.txt
index f9b6849c5..a32878375 100644
--- a/Doc/Devel/plan-gsoc-2012.txt
+++ b/Doc/Devel/plan-gsoc-2012.txt
@@ -80,7 +80,7 @@ Functionality
     \addindex - ignored
     \addtogroup - ignored
     \anchor - ignored, not supported by JD and PD 
-    \arg - translated to @param in JD, special formatting in PD
+    \arg - equivalent to \li
     \attention - ignored
     \authors, \author - translated to @author in JD, 'Author:' in PD
     \b - <b></b> in JD, surrounded with __ in PD
@@ -134,7 +134,7 @@ Functionality
     \example - translated to 'Example:' in JD and PD
     \exception - equivalent to throws, but translates to @exception in JD 
     \extends - not supported
-    \f$ - not supported. Later swig may call LATeX to produce bitmaps with formulas
+    \f$ - ignored. Later swig may call LATeX to produce bitmaps with formulas
           to include in JD and PD
     \f[ - see note for \f$
     \f] - see note for \f$
@@ -145,7 +145,7 @@ Functionality
     \headerfile - not supported
     \hideinitializer - not supported
     \htmlinclude - not supported
-    \htmlonly - not supported
+    \htmlonly - ignored
     \if - see note for \cond 
     \ifnot - see note for \cond
     \image - translated to <img/> in JD only when target=HTML, ignored in PD
@@ -181,7 +181,7 @@ Functionality
     \page - ignored
     \par - translated to <p alt='title'></p> in JD, 'Title: ...' in PD 
     \paragraph - ignored
-    \param - equivalent to \arg
+    \param - translated to @param in JD, special formatting in PD
     \post - ignored
     \pre - ignored
     \private - ignored

From 5500046b09468d7b86e43c7f9f284969b8d754dc Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Wed, 11 Jul 2012 22:27:34 +0000
Subject: [PATCH 080/314] Added testcase with a set of all supported doxygen
 tags

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13316 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Examples/test-suite/doxygen_translate.i | 115 ++++++++++++++++++++++++
 1 file changed, 115 insertions(+)
 create mode 100644 Examples/test-suite/doxygen_translate.i

diff --git a/Examples/test-suite/doxygen_translate.i b/Examples/test-suite/doxygen_translate.i
new file mode 100644
index 000000000..5f3bd1b39
--- /dev/null
+++ b/Examples/test-suite/doxygen_translate.i
@@ -0,0 +1,115 @@
+%module doxygen_translate
+
+%inline %{
+
+/**
+ * \a Hello
+ * 
+ * \arg some list item
+ * 
+ * \authors lots of them
+ * 
+ * \author Zubr
+ * 
+ * \b boldword
+ * 
+ * \c codeword
+ * 
+ * \cite citationword
+ * 
+ * \code some test code \endcode
+ * 
+ * \cond SOMECONDITION
+ * Some conditional comment
+ * \endcond
+ * 
+ * \copyright some copyright
+ * 
+ * \deprecated Now use another function
+ * 
+ * \e italicword
+ * 
+ * \if ANOTHERCONDITION
+ * 	First part of comment
+ * \else
+ * 	Second part of comment
+ * \endif
+ * 
+ * \example someFile.txt
+ * Some details on using the example
+ * 
+ * \exception SuperError
+ * 
+ * \ifnot CONDITION
+ *  Write something if not
+ * \endifnot
+ * 
+ * \image html testImage.bmp
+ * 
+ * <ul>
+ * 
+ * \li Some unordered list
+ * \li With lots of items
+ * \li lots of lots of items
+ * 
+ * </ul>
+ * 
+ * \link someMember Some description follows \endlink
+ * 
+ * \n \n \n
+ * 
+ * \overload
+ * 
+ * \p someword
+ * 
+ * \package superPackage
+ * 
+ * \par The paragraph title
+ * The paragraph text.
+ * Maybe even multiline
+ * 
+ * \param a the first param
+ * 
+ * \remark Some remark text
+ * 
+ * \remarks Another remarks section
+ * 
+ * \result Whatever
+ * 
+ * \return it
+ * 
+ * \returns may return
+ * 
+ * \sa someOtherMethod
+ * 
+ * \see function
+ * 
+ * \since version 0.0.0.1
+ * 
+ * \throw superException
+ * 
+ * \throws RuntimeError
+ * 
+ * \todo Some very important task
+ * 
+ * \tparam b B is mentioned again...
+ * 
+ * \verbatim
+ * very long
+ * text with tags <sometag>
+ * \endverbatim
+ * 
+ * \version 0.0.0.2
+ * 
+ * \warning This is senseless!
+ * 
+ * Here goes test of symbols:
+ * \$ \@ \\ \& \~ \< \> \# \% \" \. \::
+ * 
+ * And here goes simple text
+ */
+int function(int a, float b)
+{
+}
+
+%}
\ No newline at end of file

From 6a54fe93ad625e0c41699837db7efe91ccf40949 Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Thu, 12 Jul 2012 17:02:04 +0000
Subject: [PATCH 081/314] Added support for parsing of nested conditional
 comments and extended the test

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13317 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Examples/test-suite/doxygen_translate.i       | 28 +++++--
 .../DoxygenTranslator/src/DoxygenCommands.h   |  7 +-
 .../DoxygenTranslator/src/DoxygenParser.cpp   | 84 +++++++++++++++----
 3 files changed, 91 insertions(+), 28 deletions(-)

diff --git a/Examples/test-suite/doxygen_translate.i b/Examples/test-suite/doxygen_translate.i
index 5f3bd1b39..04f70f014 100644
--- a/Examples/test-suite/doxygen_translate.i
+++ b/Examples/test-suite/doxygen_translate.i
@@ -29,20 +29,30 @@
  * 
  * \e italicword
  * 
- * \if ANOTHERCONDITION
- * 	First part of comment
- * \else
- * 	Second part of comment
- * \endif
- * 
  * \example someFile.txt
  * Some details on using the example
  * 
  * \exception SuperError
  * 
- * \ifnot CONDITION
- *  Write something if not
- * \endifnot
+ * \if ANOTHERCONDITION
+ *   First part of comment
+ *   \if SECONDCONDITION
+ *     Nested condition text
+ *   \elseif THIRDCONDITION
+ *     The third condition text
+ *   \else
+ *     The last text block
+ *   \endif
+ * \else
+ *   Second part of comment
+ *   \if CONDITION
+ *     Second part extended
+ *   \endif
+ * \endif
+ * 
+ * \ifnot SOMECONDITION
+ *   This is printed if not
+ * \endif
  * 
  * \image html testImage.bmp
  * 
diff --git a/Source/DoxygenTranslator/src/DoxygenCommands.h b/Source/DoxygenTranslator/src/DoxygenCommands.h
index 93898193c..8b933878b 100644
--- a/Source/DoxygenTranslator/src/DoxygenCommands.h
+++ b/Source/DoxygenTranslator/src/DoxygenCommands.h
@@ -64,7 +64,7 @@ const char *ignoreCommandParagraphs[] = {
 const int ignoreCommandParagraphsSize = sizeof(ignoreCommandParagraphs) / sizeof(*ignoreCommandParagraphs);
 
 const char *commandEndCommands[] = {
-  "code", "dot", "msc", "f$", "f[", "f{environment}{", "htmlonly", "latexonly", "manonly", "verbatim", "xmlonly", "if", "ifnot", "link"};
+  "code", "dot", "msc", "f$", "f[", "f{environment}{", "htmlonly", "latexonly", "manonly", "verbatim", "xmlonly", "link"};
 const int commandEndCommandsSize = sizeof(commandEndCommands) / sizeof(*commandEndCommands);
 
 const char *commandWordParagraphs[] = {
@@ -87,11 +87,12 @@ const char *commandErrorThrowings[] = {
   "annotatedclassstd::list", "classhierarchy", "define", "functionindex", "header",
   "headerfilestd::list", "inherit", "l", "postheader", "private", "privatesection", "protected",
   "protectedsection", "public", "publicsection", "endcode", "enddot", "endmsc", "endhtmlonly",
-  "endlatexonly", "endmanonly", "endlink", "endverbatim", "endxmlonly", "f]", "f}", "endif"};
+  "endlatexonly", "endmanonly", "endlink", "endverbatim", "endxmlonly", "f]", "f}", "endif", "else"};
 const int commandErrorThrowingsSize = sizeof(commandErrorThrowings) / sizeof(*commandErrorThrowings);
 
 const char *commandUniques[] = {
-  "xrefitem", "arg", "ingroup", "par", "headerfile", "overload", "weakgroup", "ref", "subpage", "dotfile", "image", "addtogroup", "li"};
+  "xrefitem", "arg", "ingroup", "par", "headerfile", "overload", "weakgroup", "ref", "subpage", "dotfile", "image", "addtogroup", "li",
+  "if", "ifnot", "elseif", "else"};
 const int commandUniquesSize = sizeof(commandUniques) / sizeof(*commandUniques);
 
 #endif
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.cpp b/Source/DoxygenTranslator/src/DoxygenParser.cpp
index 4106cad44..b47320268 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenParser.cpp
@@ -164,7 +164,7 @@ std::string DoxygenParser::getStringTilEndCommand(std::string theCommand, TokenL
 		if (tokList.peek().tokenType == END_LINE)
 			description += "\n";
 
-		if (tokList.peek().tokenString.compare(theCommand) == 0) {
+		if (tokList.peek().tokenString == theCommand) {
 			tokList.next();
 			return description;
 		}
@@ -207,7 +207,7 @@ std::list < Token >::iterator DoxygenParser::getEndOfSection(std::string theComm
 	std::list < Token >::iterator endOfParagraph = tokList.iteratorCopy();
 	while (endOfParagraph != tokList.end()) {
 		if ((*endOfParagraph).tokenType == COMMAND) {
-			if (theCommand.compare((*endOfParagraph).tokenString) == 0)
+			if (theCommand == (*endOfParagraph).tokenString)
 				return endOfParagraph;
 			else
 				endOfParagraph++;
@@ -228,7 +228,7 @@ std::list < Token >::iterator DoxygenParser::getEndCommand(std::string theComman
 	std::list < Token >::iterator endOfCommand = tokList.iteratorCopy();
 	while (endOfCommand != tokList.end()) {
 		if ((*endOfCommand).tokenType == COMMAND) {
-			if (theCommand.compare((*endOfCommand).tokenString) == 0) {
+			if (theCommand == (*endOfCommand).tokenString) {
 				return endOfCommand;
 			}
 			endOfCommand++;
@@ -399,14 +399,14 @@ int DoxygenParser::addCommandErrorThrow(std::string theCommand, TokenList & tokL
 
 int DoxygenParser::addCommandUnique(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
 	std::list < DoxygenEntity > aNewList;
-	if (theCommand.compare("arg") == 0 || theCommand.compare("li") == 0) {
+	if (theCommand == "arg" || theCommand == "li") {
 		std::list < Token >::iterator endOfSection = getEndOfSection(theCommand, tokList);
 		std::list < DoxygenEntity > aNewList;
 		aNewList = parse(endOfSection, tokList);
 		doxyList.push_back(DoxygenEntity(theCommand, aNewList));
 	}
 	// \xrefitem <key> "(heading)" "(std::list title)" {text}
-	else if (theCommand.compare("xrefitem") == 0) {
+	else if (theCommand == "xrefitem") {
 		//TODO Implement xrefitem
 		if (noisy)
 			cout << "Not Adding " << theCommand << endl;
@@ -415,7 +415,7 @@ int DoxygenParser::addCommandUnique(std::string theCommand, TokenList & tokList,
 		return 1;
 	}
 	// \ingroup (<groupname> [<groupname> <groupname>])
-	else if (theCommand.compare("ingroup") == 0) {
+	else if (theCommand == "ingroup") {
 		std::string name = getNextWord(tokList);
 		aNewList.push_back(DoxygenEntity("plainstd::string", name));
 		name = getNextWord(tokList);
@@ -428,7 +428,7 @@ int DoxygenParser::addCommandUnique(std::string theCommand, TokenList & tokList,
 		return 1;
 	}
 	// \par [(paragraph title)] { paragraph }
-	else if (theCommand.compare("par") == 0) {
+	else if (theCommand == "par") {
 		std::list < Token >::iterator endOfLine = getOneLine(tokList);
 		aNewList = parse(endOfLine, tokList);
 		std::list < DoxygenEntity > aNewList2;
@@ -438,7 +438,7 @@ int DoxygenParser::addCommandUnique(std::string theCommand, TokenList & tokList,
 		return 1;
 	}
 	// \headerfile <header-file> [<header-name>]
-	else if (theCommand.compare("headerfile") == 0) {
+	else if (theCommand == "headerfile") {
 		std::list < DoxygenEntity > aNewList;
 		std::string name = getNextWord(tokList);
 		aNewList.push_back(DoxygenEntity("plainstd::string", name));
@@ -449,7 +449,7 @@ int DoxygenParser::addCommandUnique(std::string theCommand, TokenList & tokList,
 		return 1;
 	}
 	// \overload [(function declaration)]
-	else if (theCommand.compare("overload") == 0) {
+	else if (theCommand == "overload") {
 		std::list < Token >::iterator endOfLine = getOneLine(tokList);
 		if (endOfLine != tokList.current()) {
 			std::list < DoxygenEntity > aNewList;
@@ -460,7 +460,7 @@ int DoxygenParser::addCommandUnique(std::string theCommand, TokenList & tokList,
 		return 1;
 	}
 	// \weakgroup <name> [(title)]
-	else if (theCommand.compare("weakgroup") == 0) {
+	else if (theCommand == "weakgroup") {
 		if (noisy)
 			cout << "Parsing " << theCommand << endl;
 		std::string name = getNextWord(tokList);
@@ -477,7 +477,7 @@ int DoxygenParser::addCommandUnique(std::string theCommand, TokenList & tokList,
 		doxyList.push_back(DoxygenEntity(theCommand, aNewList));
 	}
 	// \ref <name> ["(text)"]
-	else if (theCommand.compare("ref") == 0) {
+	else if (theCommand == "ref") {
 		//TODO Implement ref
 		if (noisy)
 			cout << "Not Adding " << theCommand << endl;
@@ -485,7 +485,7 @@ int DoxygenParser::addCommandUnique(std::string theCommand, TokenList & tokList,
 		tokList.setIterator(endOfParagraph);
 	}
 	// \subpage <name> ["(text)"]
-	else if (theCommand.compare("subpage") == 0) {
+	else if (theCommand == "subpage") {
 		//TODO implement subpage
 		if (noisy)
 			cout << "Not Adding " << theCommand << endl;
@@ -493,7 +493,7 @@ int DoxygenParser::addCommandUnique(std::string theCommand, TokenList & tokList,
 		tokList.setIterator(endOfParagraph);
 	}
 	// \dotfile <file> ["caption"]
-	else if (theCommand.compare("dotfile") == 0) {
+	else if (theCommand == "dotfile") {
 		//TODO implement dotfile
 		if (noisy)
 			cout << "Not Adding " << theCommand << endl;
@@ -501,11 +501,11 @@ int DoxygenParser::addCommandUnique(std::string theCommand, TokenList & tokList,
 		tokList.setIterator(endOfParagraph);
 	}
 	// \image <format> <file> ["caption"] [<sizeindication>=<size>]
-	else if (theCommand.compare("image") == 0) {
+	else if (theCommand == "image") {
 		//todo implement image
 	}
 	// \addtogroup <name> [(title)]
-	else if (theCommand.compare("addtogroup") == 0) {
+	else if (theCommand == "addtogroup") {
 		if (noisy)
 			cout << "Parsing " << theCommand << endl;
 		std::string name = getNextWord(tokList);
@@ -521,12 +521,64 @@ int DoxygenParser::addCommandUnique(std::string theCommand, TokenList & tokList,
 		aNewList.push_front(DoxygenEntity("plainstd::string", name));
 		doxyList.push_back(DoxygenEntity(theCommand, aNewList));
 	}
+	// \if <cond> [\else ...] [\elseif <cond> ...] \endif
+	else if (theCommand == "if" || theCommand == "ifnot" ||
+					 theCommand == "else" || theCommand == "elseif") {
+		if (noisy)
+			cout << "Parsing " << theCommand << endl;
+
+		std::string cond;
+		bool skipEndif = false; // if true then we skip endif after parsing block of code
+		bool needsCond = (theCommand == "if" || theCommand == "ifnot" || theCommand == "elseif");
+		if (needsCond) {
+			cond = getNextWord(tokList);
+			if (cond.empty()) {
+				tokList.printListError("No word followed " + theCommand + " command. Not added");
+				return 0;
+			}
+		}
+
+		int nestedCounter = 1;
+		std::list < Token >::iterator endCommand = tokList.end();
+		// go through the commands and find closing endif or else or elseif
+		std::list < Token >::iterator it=tokList.iteratorCopy();
+		for (; it!=tokList.end(); it++) {
+			if (it->tokenType == COMMAND) {
+				if (it->tokenString == "if" || it->tokenString == "ifnot")
+					nestedCounter++;
+				else if (it->tokenString == "endif")
+					nestedCounter--;
+				if (nestedCounter == 1 && (it->tokenString == "else" || it->tokenString == "elseif")) { // else found
+					endCommand = it;
+					break;
+				}
+				if (nestedCounter == 0) { // endif found
+					endCommand = it;
+					skipEndif = true;
+					break;
+				}
+			}
+		}
+
+		if (endCommand == tokList.end()) {
+			tokList.printListError("No corresponding endif found");
+			return 0;
+		}
+
+		std::list < DoxygenEntity > aNewList;
+		aNewList = parse(endCommand, tokList);
+		if (skipEndif)
+			tokList.next();
+		if (needsCond)
+			aNewList.push_front(DoxygenEntity("plainstd::string", cond));
+		doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+	}
 	return 0;
 }
 
 int DoxygenParser::addCommand(std::string commandString, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
 	std::string theCommand = StringToLower(commandString);
-	if (theCommand.compare("plainstd::string") == 0) {
+	if (theCommand == "plainstd::string") {
 		std::string nextPhrase = getStringTilCommand(tokList);
 		if (noisy)
 			cout << "Parsing plain std::string :" << nextPhrase << endl;

From 6a7fe334beee85e9d169d7c3330e1d9756e2d105 Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Fri, 13 Jul 2012 10:46:59 +0000
Subject: [PATCH 082/314] Implemented parsing support for missing commands:
 \xrefitem, \ref, \subpage, \dotfile, \mscfile, \image, fixed \par

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13319 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 .../DoxygenTranslator/src/DoxygenCommands.h   |  8 +-
 .../DoxygenTranslator/src/DoxygenParser.cpp   | 98 +++++++++++++++----
 2 files changed, 84 insertions(+), 22 deletions(-)

diff --git a/Source/DoxygenTranslator/src/DoxygenCommands.h b/Source/DoxygenTranslator/src/DoxygenCommands.h
index 8b933878b..1b24eff33 100644
--- a/Source/DoxygenTranslator/src/DoxygenCommands.h
+++ b/Source/DoxygenTranslator/src/DoxygenCommands.h
@@ -12,7 +12,7 @@ const char *commandArray[] = {
   "enum", "example", "exception", "f$", "f[", "f]", "f{", "f}", "file", "fn", "headerfile",
   "hideinitializer", "htmlinclude", "htmlonly", "if", "ifnot", "image", "include",
   "includelineno", "ingroup", "internal", "invariant", "interface", "latexonly", "li",
-  "line", "link", "mainpage", "manonly", "msc", "n", "name", "namespace", "nosubgrouping",
+  "line", "link", "mainpage", "manonly", "msc", "mscfile", "n", "name", "namespace", "nosubgrouping",
   "note", "overload", "p", "package", "page", "par", "paragraph", "param", "post", "pre",
   "private", "privatesection", "property", "protected", "protectedsection", "protocol",
   "public", "publicsection", "ref", "relates", "relatesalso", "remarks", "remark", "result", "return", "returns", "retval",
@@ -37,7 +37,7 @@ const char *ignoredSimpleCommands[] = {
 const int ignoredSimpleCommandsSize = sizeof(ignoredSimpleCommands) / sizeof(*ignoredSimpleCommands);
 
 const char *commandWords[] = {
-  "a", "b", "c", "e", "em", "p", "def", "enum", "example", "package", "relates", "namespace", "relatesalso", "anchor", "dontinclude", "include",
+  "a", "b", "c", "e", "em", "p", "def", "enum", "package", "relates", "namespace", "relatesalso", "anchor", "dontinclude", "include",
   "includelineno"};
 const int commandWordsSize = sizeof(commandWords) / sizeof(*commandWords);
 
@@ -68,7 +68,7 @@ const char *commandEndCommands[] = {
 const int commandEndCommandsSize = sizeof(commandEndCommands) / sizeof(*commandEndCommands);
 
 const char *commandWordParagraphs[] = {
-  "param", "tparam", "throw", "throws", "retval", "exception"};
+  "param", "tparam", "throw", "throws", "retval", "exception", "example"};
 const int commandWordParagraphsSize = sizeof(commandWordParagraphs) / sizeof(*commandWordParagraphs);
 
 const char *commandWordLines[] = {
@@ -92,7 +92,7 @@ const int commandErrorThrowingsSize = sizeof(commandErrorThrowings) / sizeof(*co
 
 const char *commandUniques[] = {
   "xrefitem", "arg", "ingroup", "par", "headerfile", "overload", "weakgroup", "ref", "subpage", "dotfile", "image", "addtogroup", "li",
-  "if", "ifnot", "elseif", "else"};
+  "if", "ifnot", "elseif", "else", "mscfile"};
 const int commandUniquesSize = sizeof(commandUniques) / sizeof(*commandUniques);
 
 #endif
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.cpp b/Source/DoxygenTranslator/src/DoxygenParser.cpp
index b47320268..4fee595a6 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenParser.cpp
@@ -407,11 +407,28 @@ int DoxygenParser::addCommandUnique(std::string theCommand, TokenList & tokList,
 	}
 	// \xrefitem <key> "(heading)" "(std::list title)" {text}
 	else if (theCommand == "xrefitem") {
-		//TODO Implement xrefitem
 		if (noisy)
-			cout << "Not Adding " << theCommand << endl;
+			cout << "Parsing " << theCommand << endl;
+		std::string key = getNextWord(tokList);
+		if (key.empty()) {
+			tokList.printListError("No key followed " + theCommand + " command. Not added");
+			return 0;
+		}
+		std::string heading = getNextWord(tokList);
+		if (key.empty()) {
+			tokList.printListError("No heading followed " + theCommand + " command. Not added");
+			return 0;
+		}
+		std::string title = getNextWord(tokList);
+		if (title.empty()) {
+			tokList.printListError("No title followed " + theCommand + " command. Not added");
+			return 0;
+		}
 		std::list < Token >::iterator endOfParagraph = getEndOfParagraph(tokList);
-		tokList.setIterator(endOfParagraph);
+		aNewList = parse(endOfParagraph, tokList);
+		aNewList.push_front(DoxygenEntity("plainstd::string", title));
+		aNewList.push_front(DoxygenEntity("plainstd::string", heading));
+		aNewList.push_front(DoxygenEntity("plainstd::string", key));
 		return 1;
 	}
 	// \ingroup (<groupname> [<groupname> <groupname>])
@@ -432,7 +449,8 @@ int DoxygenParser::addCommandUnique(std::string theCommand, TokenList & tokList,
 		std::list < Token >::iterator endOfLine = getOneLine(tokList);
 		aNewList = parse(endOfLine, tokList);
 		std::list < DoxygenEntity > aNewList2;
-		aNewList2 = parse(endOfLine, tokList);
+		std::list < Token >::iterator endOfParagraph = getEndOfParagraph(tokList);
+		aNewList2 = parse(endOfParagraph, tokList);
 		aNewList.splice(aNewList.end(), aNewList2);
 		doxyList.push_back(DoxygenEntity(theCommand, aNewList));
 		return 1;
@@ -478,31 +496,75 @@ int DoxygenParser::addCommandUnique(std::string theCommand, TokenList & tokList,
 	}
 	// \ref <name> ["(text)"]
 	else if (theCommand == "ref") {
-		//TODO Implement ref
 		if (noisy)
-			cout << "Not Adding " << theCommand << endl;
-		std::list < Token >::iterator endOfParagraph = getEndOfParagraph(tokList);
-		tokList.setIterator(endOfParagraph);
+			cout << "Parsing " << theCommand << endl;
+		std::string name = getNextWord(tokList);
+		if (name.empty()) {
+			tokList.printListError("No key followed " + theCommand + " command. Not added");
+			return 0;
+		}
+		std::string text = getNextWord(tokList);
+		aNewList.push_back(DoxygenEntity("plainstd::string", name));
+		if (!text.empty())
+			aNewList.push_back(DoxygenEntity("plainstd::string", text));
+		doxyList.push_back(DoxygenEntity(theCommand, aNewList));
 	}
 	// \subpage <name> ["(text)"]
 	else if (theCommand == "subpage") {
-		//TODO implement subpage
 		if (noisy)
-			cout << "Not Adding " << theCommand << endl;
-		std::list < Token >::iterator endOfParagraph = getEndOfParagraph(tokList);
-		tokList.setIterator(endOfParagraph);
+			cout << "Parsing " << theCommand << endl;
+		std::string name = getNextWord(tokList);
+		if (name.empty()) {
+			tokList.printListError("No name followed " + theCommand + " command. Not added");
+			return 0;
+		}
+		std::string text = getNextWord(tokList);
+		aNewList.push_back(DoxygenEntity("plainstd::string", name));
+		if (!text.empty())
+			aNewList.push_back(DoxygenEntity("plainstd::string", text));
+		doxyList.push_back(DoxygenEntity(theCommand, aNewList));
 	}
 	// \dotfile <file> ["caption"]
-	else if (theCommand == "dotfile") {
-		//TODO implement dotfile
+	// \mscfile <file> ["caption"]
+	else if (theCommand == "dotfile" || theCommand == "mscfile") {
 		if (noisy)
-			cout << "Not Adding " << theCommand << endl;
-		std::list < Token >::iterator endOfParagraph = getEndOfParagraph(tokList);
-		tokList.setIterator(endOfParagraph);
+			cout << "Parsing " << theCommand << endl;
+		std::string file = getNextWord(tokList);
+		if (file.empty()) {
+			tokList.printListError("No file followed " + theCommand + " command. Not added");
+			return 0;
+		}
+		std::string caption = getNextWord(tokList);
+		aNewList.push_back(DoxygenEntity("plainstd::string", file));
+		if (!caption.empty())
+			aNewList.push_back(DoxygenEntity("plainstd::string", caption));
+		doxyList.push_back(DoxygenEntity(theCommand, aNewList));
 	}
 	// \image <format> <file> ["caption"] [<sizeindication>=<size>]
 	else if (theCommand == "image") {
-		//todo implement image
+		if (noisy)
+			cout << "Parsing " << theCommand << endl;
+		std::string format = getNextWord(tokList);
+		if (format.empty()) {
+			tokList.printListError("No format followed " + theCommand + " command. Not added");
+			return 0;
+		}
+		std::string file = getNextWord(tokList);
+		if (file.empty()) {
+			tokList.printListError("No name followed " + theCommand + " command. Not added");
+			return 0;
+		}
+		std::string caption = getNextWord(tokList);
+		std::string size = getNextWord(tokList);
+
+		std::list < DoxygenEntity > aNewList;
+		aNewList.push_back(DoxygenEntity("plainstd::string", format));
+		aNewList.push_back(DoxygenEntity("plainstd::string", file));
+		if (!caption.empty())
+			aNewList.push_back(DoxygenEntity("plainstd::string", caption));
+		if (!size.empty())
+			aNewList.push_back(DoxygenEntity("plainstd::string", size));
+		doxyList.push_back(DoxygenEntity(theCommand, aNewList));
 	}
 	// \addtogroup <name> [(title)]
 	else if (theCommand == "addtogroup") {

From b99221e8af48dc9ece97a619934276bd64913a23 Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Fri, 13 Jul 2012 14:08:37 +0000
Subject: [PATCH 083/314] Refactored TokenList class

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13320 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 .../DoxygenTranslator/src/DoxygenParser.cpp   |   2 +-
 Source/DoxygenTranslator/src/TokenList.cpp    | 116 +++++++-----------
 Source/DoxygenTranslator/src/TokenList.h      |   8 +-
 3 files changed, 55 insertions(+), 71 deletions(-)

diff --git a/Source/DoxygenTranslator/src/DoxygenParser.cpp b/Source/DoxygenTranslator/src/DoxygenParser.cpp
index 4fee595a6..6161d00b9 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenParser.cpp
@@ -727,7 +727,7 @@ std::list < DoxygenEntity > DoxygenParser::parse(std::list < Token >::iterator e
 }
 
 std::list < DoxygenEntity > DoxygenParser::createTree(std::string doxygenBlob, std::string fileName, int lineNumber) {
-	TokenList tokList(doxygenBlob, fileName, lineNumber);
+	TokenList tokList = TokenList::tokenizeDoxygenComment(doxygenBlob, fileName, lineNumber);
 	if (noisy) {
 		cout << "---TOKEN LIST---" << endl;
 		tokList.printList();
diff --git a/Source/DoxygenTranslator/src/TokenList.cpp b/Source/DoxygenTranslator/src/TokenList.cpp
index 8624fb4a2..6bb6c8cd4 100644
--- a/Source/DoxygenTranslator/src/TokenList.cpp
+++ b/Source/DoxygenTranslator/src/TokenList.cpp
@@ -21,75 +21,53 @@
 
 using namespace std;
 
-int noisy2 = 0;
-/* The tokenizer*/
-TokenList::TokenList(const std::string & doxygenStringConst, const std::string fileName, int fileLine)
-	: fileName(fileName), fileLine(fileLine) {
-  size_t commentPos;
-  string doxygenString = doxygenStringConst;
-
-  size_t currentIndex = 0;
-  size_t nextIndex = 0;
+TokenList TokenList::tokenizeDoxygenComment(const std::string &doxygenComment, const std::string &fileName, int fileLine) {
+  TokenList tokList;
+  tokList.fileLine = fileLine;
+  tokList.fileName = fileName;
 
+  string::size_type pos, lastPos = 0;
   string currentWord;
-
-  while (currentIndex < doxygenString.length()) {
-
-    if (doxygenString[currentIndex] == '\n') {
-      m_tokenList.push_back(Token(END_LINE, currentWord));
-      currentIndex++;
-    }
-    // skip WS, except \n
-    while (currentIndex < doxygenString.length() && (doxygenString[currentIndex] == ' ' || doxygenString[currentIndex] == '\t'))
-      currentIndex++;
-
-    if (currentIndex < doxygenString.length()) {
-
-      nextIndex = currentIndex;
-
-      // skip non WS
-      while (nextIndex < doxygenString.length() && (doxygenString[nextIndex] != ' ' && doxygenString[nextIndex] != '\t' && doxygenString[nextIndex] != '\n'))
-	nextIndex++;
-
-      // now we have a token
-      currentWord = doxygenString.substr(currentIndex, nextIndex - currentIndex);
-
-      if (noisy2)
-	cout << "Current Word: " << currentWord << endl;
-
-      if (currentWord[0] == '@' || currentWord[0] == '\\') {
-	// it is doxygen command
-	currentWord = currentWord.substr(1, currentWord.length() - 1);
-	m_tokenList.push_back(Token(COMMAND, currentWord));
-
-      } else if (currentWord[0] == '\n') {
-
-	m_tokenList.push_back(Token(END_LINE, currentWord));
-
-      } else if (currentWord[0] == '*' || currentWord[0] == '/' || currentWord[0] == '!') {
-
-	bool isPlainString = false;
-
-	if (currentWord.length() > 1) {
-
-	  for (size_t i = 1; i < currentWord.length(); i++) {
-	    if (currentWord[i] != '*' && currentWord[i] != '/' && currentWord[i] != '!') {
-	      isPlainString = true;
-	      break;
-	    }
-	  }
-	}
-
-	if (isPlainString)
-	  m_tokenList.push_back(Token(PLAINSTRING, currentWord));
-
-      } else if (!currentWord.empty()) {
-	m_tokenList.push_back(Token(PLAINSTRING, currentWord));
+  while (true) {
+    pos = doxygenComment.find_first_of("\t\n ", lastPos);
+    if (pos == string::npos)
+      pos = doxygenComment.size();
+    if (pos > lastPos) {
+      currentWord = doxygenComment.substr(lastPos, pos-lastPos);
+      if (currentWord[0] == '\\' || currentWord[0] == '@') {
+        // it's a doxygen command
+        currentWord = currentWord.substr(1, currentWord.length() - 1);
+        tokList.m_tokenList.push_back(Token(COMMAND, currentWord));
       }
-      currentIndex = nextIndex;
+      else if (currentWord[0] == '!' || currentWord[0] == '*' || currentWord[0] == '/') {
+        // check if it's one of the '!!!', '***', '///' of any length
+        char c = currentWord[0];
+        bool isPlainString = false;
+        for (int i=0; i<currentWord.size(); i++)
+          if (currentWord[i] != c) {
+            isPlainString = true;
+            break;
+          }
+        if (isPlainString)
+          tokList.m_tokenList.push_back(Token(PLAINSTRING, currentWord));
+      }
+      else // it is a plain string
+        tokList.m_tokenList.push_back(Token(PLAINSTRING, currentWord));
     }
-  }
 
+    lastPos = pos + 1;
+    if (lastPos >= doxygenComment.size())
+      break;
+
+    if (doxygenComment[pos] == '\n')
+      tokList.m_tokenList.push_back(Token(END_LINE, "\n"));
+  }
+  tokList.m_tokenListIter = tokList.m_tokenList.begin();
+  return tokList;
+}
+
+TokenList::TokenList()
+: fileName(""), fileLine(0) {
   m_tokenListIter = m_tokenList.begin();
 }
 
@@ -151,9 +129,9 @@ void TokenList::printList() {
 }
 
 void TokenList::printListError(std::string message) {
-	int curLine = fileLine;
-	for (list< Token >::iterator it = m_tokenList.begin(); it != current(); it++)
-		if (it->tokenType == END_LINE)
-			curLine++;
-	Swig_error(fileName.c_str(), curLine, "Doxygen parser error: %s. \n", message.c_str());
+  int curLine = fileLine;
+  for (list< Token >::iterator it = m_tokenList.begin(); it != current(); it++)
+    if (it->tokenType == END_LINE)
+      curLine++;
+  Swig_error(fileName.c_str(), curLine, "Doxygen parser error: %s. \n", message.c_str());
 }
diff --git a/Source/DoxygenTranslator/src/TokenList.h b/Source/DoxygenTranslator/src/TokenList.h
index d38fec792..ce9d14c45 100644
--- a/Source/DoxygenTranslator/src/TokenList.h
+++ b/Source/DoxygenTranslator/src/TokenList.h
@@ -30,7 +30,7 @@ private:
   int fileLine;
 
 public:
-  TokenList(const std::string & doxygenString, const std::string fileName, int fileLine);	/* constructor takes a blob of Doxygen comment */
+  TokenList(); // construct an empty TokenList
   ~TokenList();
 
   Token peek();			/* returns next token without advancing */
@@ -44,6 +44,12 @@ public:
 
   void printList();		/* prints out the sequence of tokens */
   void printListError(std::string message); /* prints properly formatted error message */
+
+  /*
+   * Create TokenList and populate it with tokens from
+   * a blob of Doxygen comment
+   */
+  static TokenList tokenizeDoxygenComment(const std::string &doxygenComment, const std::string &fileName, int fileLine);
 };
 
 #endif

From 34dc515a4041c079db4d4c5b3bc241efa6d96d34 Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Fri, 13 Jul 2012 15:16:58 +0000
Subject: [PATCH 084/314] Fixed bug with quoted strings in doxygen comments

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13321 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Source/DoxygenTranslator/src/TokenList.cpp | 27 ++++++++++++++++++----
 1 file changed, 23 insertions(+), 4 deletions(-)

diff --git a/Source/DoxygenTranslator/src/TokenList.cpp b/Source/DoxygenTranslator/src/TokenList.cpp
index 6bb6c8cd4..1ade6375e 100644
--- a/Source/DoxygenTranslator/src/TokenList.cpp
+++ b/Source/DoxygenTranslator/src/TokenList.cpp
@@ -26,6 +26,7 @@ TokenList TokenList::tokenizeDoxygenComment(const std::string &doxygenComment, c
   tokList.fileLine = fileLine;
   tokList.fileName = fileName;
 
+  bool isPlainString = false;
   string::size_type pos, lastPos = 0;
   string currentWord;
   while (true) {
@@ -42,17 +43,35 @@ TokenList TokenList::tokenizeDoxygenComment(const std::string &doxygenComment, c
       else if (currentWord[0] == '!' || currentWord[0] == '*' || currentWord[0] == '/') {
         // check if it's one of the '!!!', '***', '///' of any length
         char c = currentWord[0];
-        bool isPlainString = false;
+        isPlainString = false;
         for (int i=0; i<currentWord.size(); i++)
           if (currentWord[i] != c) {
             isPlainString = true;
             break;
           }
-        if (isPlainString)
+      }
+      else
+        isPlainString = true;
+
+      if (isPlainString) {
+        // handle quoted words
+        string::size_type qPos = currentWord.find('"', 0);
+        if (qPos != string::npos) {
+          lastPos += qPos;
+          pos = doxygenComment.find_first_of("\"\n", lastPos + 1);
+          if (pos == string::npos)
+            pos = doxygenComment.size();
+          if (pos == doxygenComment.size() || doxygenComment[pos] != '"') {
+            // hack to print error message before the list is constructed
+            tokList.m_tokenListIter = tokList.m_tokenList.end();
+            tokList.printListError("Unterminated string");
+          }
+          // also strip quotes
+          currentWord = doxygenComment.substr(lastPos + 1, pos-lastPos-1);
+        }
+        if (currentWord.size())
           tokList.m_tokenList.push_back(Token(PLAINSTRING, currentWord));
       }
-      else // it is a plain string
-        tokList.m_tokenList.push_back(Token(PLAINSTRING, currentWord));
     }
 
     lastPos = pos + 1;

From 4ce9f2361ccb92785d20893ff8e7703f5a888c95 Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Sat, 14 Jul 2012 22:41:41 +0000
Subject: [PATCH 085/314] Added support for parsing of missing doxygen
 commands. Now parser produces correct parse tree for every doxygen tag, at
 least for those included in the testcase. Also added the test with all the
 tags, even those that will be ignored later.

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13322 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 .../test-suite/doxygen_translate_all_tags.i   | 338 ++++++++++++++++++
 .../DoxygenTranslator/src/DoxygenCommands.h   |  24 +-
 .../DoxygenTranslator/src/DoxygenParser.cpp   |  51 ++-
 Source/DoxygenTranslator/src/TokenList.cpp    |   5 +-
 4 files changed, 401 insertions(+), 17 deletions(-)
 create mode 100644 Examples/test-suite/doxygen_translate_all_tags.i

diff --git a/Examples/test-suite/doxygen_translate_all_tags.i b/Examples/test-suite/doxygen_translate_all_tags.i
new file mode 100644
index 000000000..ae66cc5de
--- /dev/null
+++ b/Examples/test-suite/doxygen_translate_all_tags.i
@@ -0,0 +1,338 @@
+%module doxygen_translate
+
+%inline %{
+
+/**
+ * \a Hello
+ * 
+ * \addindex SomeLatexIndex
+ *
+ * \addtogroup someGroup "Some title"
+ *
+ * \anchor theAnchor
+ *
+ * \arg some list item
+ * 
+ * \attention This is attention!
+ * You were warned!
+ *
+ * \authors lots of them
+ * 
+ * \author Zubr
+ * 
+ * \b boldword
+ * 
+ * \brief Some brief description,
+ * extended to many lines.
+ *
+ * \bug Not everything works right now...
+ *
+ * \c codeword
+ * 
+ * \callgraph
+ *
+ * \callergraph
+ *
+ * \category someCategory headerFile.h headerName
+ *
+ * \cite citationword
+ * 
+ * \class someClass headerFile.h headerName
+ *
+ * \code some test code \endcode
+ * 
+ * \cond SOMECONDITION
+ * Some conditional comment
+ * \endcond
+ * 
+ * \copybrief someClass::someMethod
+ *
+ * \copydetails someClass::someMethod2
+ *
+ * \copydoc  someClass::someMethod3
+ *
+ * \copyright some copyright
+ * 
+ * \date 1970 - 2012
+ *
+ * \def someDefine
+ *
+ * \defgroup someGroup Some titles
+ *
+ * \deprecated Now use another function
+ * 
+ * \details This is very large
+ * and detailed description of some thing
+ *
+ * \dir /somePath/someFolder
+ *
+ * \dontinclude someFile.h
+ *
+ * \dot
+ * digraph example {
+ * node [shape=record, fontname=Helvetica, fontsize=10];
+ * b [ label="class B" URL="\ref B"];
+ * c [ label="class C" URL="\ref C"];
+ * b -> c [ arrowhead="open", style="dashed" ];
+ * }
+ * \enddot
+ *
+ * \dotfile dotFile.dot "The caption"
+ *
+ * \e italicword
+ * 
+ * \em emphazedWord
+ *
+ * \enum someEnum
+ *
+ * \example someFile.txt
+ * Some details on using the example
+ * 
+ * \exception SuperError
+ * 
+ * \extends someOtherFunction
+ *
+ * \f$ \sqrt{(x_2-x_1)^2+(y_2-y_1)^2} \f$
+ *
+ * \f[
+ *   \sqrt{(x_2-x_1)^2+(y_2-y_1)^2}
+ * \f]
+ *
+ * \f{
+ *   \sqrt{(x_2-x_1)^2+(y_2-y_1)^2}
+ * \f}
+ *
+ * \file file.h
+ *
+ * \fn someFn
+ *
+ * \headerfile someHeader.h "Header name"
+ *
+ * \hideinitializer
+ *
+ * \htmlinclude htmlFile.htm
+ *
+ * \htmlonly
+ * This will only appear in hmtl
+ * \endhtmlonly
+ *
+ * \if ANOTHERCONDITION
+ *   First part of comment
+ *   \if SECONDCONDITION
+ *     Nested condition text
+ *   \elseif THIRDCONDITION
+ *     The third condition text
+ *   \else
+ *     The last text block
+ *   \endif
+ * \else
+ *   Second part of comment
+ *   \if CONDITION
+ *     Second part extended
+ *   \endif
+ * \endif
+ * 
+ * \ifnot SOMECONDITION
+ *   This is printed if not
+ * \endif
+ * 
+ * \image html testImage.bmp "Hello, world!" asd=10qwe
+ * 
+ * \implements someFunction
+ *
+ * \include header.h
+ *
+ * \includelineno header2.h
+ *
+ * \ingroup someGroup anotherGroup
+ *
+ * \internal
+ *
+ * \invariant Some text
+ * describing invariant.
+ *
+ * \interface someInterface someHeader.h "Header name"
+ *
+ * \latexonly
+ * This will only appear in LATeX
+ * \endlatexonly
+ *
+ * <ul>
+ * 
+ * \li Some unordered list
+ * \li With lots of items
+ * \li lots of lots of items
+ * 
+ * </ul>
+ * 
+ * \line example
+ *
+ * \link someMember Some description follows \endlink
+ * 
+ * \mainpage Some title
+ *
+ * \manonly
+ * This will only appear in man
+ * \endmanonly
+ *
+ * \memberof someThing
+ *
+ * \msc
+ * Sender,Receiver;
+ * Sender->Receiver [label="Command()", URL="\ref Receiver::Command()"];
+ * Sender<-Receiver [label="Ack()", URL="\ref Ack()", ID="1"];
+ * \endmsc
+ *
+ * \mscfile mscFile.msc "The caption"
+ *
+ * \n \n \n
+ * 
+ * \name someHeader.h
+ *
+ * \namespace someNamespace
+ *
+ * \nosubgrouping
+ *
+ * \note Here
+ * is the note!
+ *
+ * \overload
+ * 
+ * \p someword
+ * 
+ * \package superPackage
+ * 
+ * \page somePage The title
+ *
+ * \par The paragraph title
+ * The paragraph text.
+ * Maybe even multiline
+ * 
+ * \paragraph someParagraph Paragraph title
+ *
+ * \param a the first param
+ * 
+ * \post Some description
+ *
+ * \pre Some description
+ *
+ * \private
+ *
+ * \privatesection
+ *
+ * \property someVar
+ *
+ * \protected
+ *
+ * \protectedsection
+ *
+ * \protocol someProtocol header.h "Header name"
+ *
+ * \public
+ *
+ * \publicsection
+ *
+ * \ref someAnchor
+ *
+ * \related toSomething
+ *
+ * \relates toSomethingElse
+ *
+ * \relatedalso someName
+ *
+ * \relatesalso someName
+ *
+ * \remark Some remark text
+ * 
+ * \remarks Another remarks section
+ * 
+ * \result Whatever
+ * 
+ * \return it
+ * 
+ * \returns may return
+ * 
+ * \retval someValue Some description
+ *
+ * \rtfonly
+ * This will only appear in RTF
+ * \endrtfonly
+ *
+ * \sa someOtherMethod
+ * 
+ * \section someSection Some title
+ *
+ * \see function
+ * 
+ * \short Same as
+ * brief description
+ *
+ * \showinitializer
+ *
+ * \since version 0.0.0.1
+ * 
+ * \skip somePattern
+ *
+ * \skipline someLine
+ *
+ * \snippet example.h Some snippet
+ *
+ * \struct someStruct
+ *
+ * \subpage someSubpage "Some description"
+ *
+ * \subsection someSubsection Some title
+ *
+ * \subsubsection someSubsection Some title
+ *
+ * \tableofcontents
+ *
+ * \test Some
+ * description of the
+ * test case
+ *
+ * \throw superException
+ * 
+ * \throws RuntimeError
+ * 
+ * \todo Some very important task
+ * 
+ * \tparam b B is mentioned again...
+ * 
+ * \typedef someTypedef
+ *
+ * \union someUnion
+ *
+ * \until somePattern
+ *
+ * \var someVar
+ *
+ * \verbatim
+ * very long
+ * text with tags <sometag>
+ * \endverbatim
+ * 
+ * \verbinclude someFile.h
+ *
+ * \version 0.0.0.2
+ * 
+ * \warning This is senseless!
+ * 
+ * \weakgroup someGroup Some title
+ *
+ * \xmlonly
+ * This will only appear in XML
+ * \endxmlonly
+ *
+ * \xrefitem todo "Todo" "Todo List"
+ *
+ * Here goes test of symbols:
+ * \$ \@ \\ \& \~ \< \> \# \% \" \. \::
+ * 
+ * And here goes simple text
+ */
+int function(int a, float b)
+{
+}
+
+%}
diff --git a/Source/DoxygenTranslator/src/DoxygenCommands.h b/Source/DoxygenTranslator/src/DoxygenCommands.h
index 1b24eff33..27611cdcb 100644
--- a/Source/DoxygenTranslator/src/DoxygenCommands.h
+++ b/Source/DoxygenTranslator/src/DoxygenCommands.h
@@ -29,7 +29,10 @@ const int sectionIndicatorsSize = sizeof(sectionIndicators) / sizeof(*sectionInd
 
 /* All of the doxygen commands divided up by how they are parsed */
 const char *simpleCommands[] = {
-  "n", "$", "@", "\\", "&", "~", "<", ">", "#", "%", "\"", ".", "::", "endcond"};
+  "n", "$", "@", "\\", "&", "~", "<", ">", "#", "%", "\"", ".", "::", "endcond",
+  "callgraph", "callergraph", "showinitializer", "hideinitializer", "internal",
+  "nosubgrouping", "public", "publicsection", "private", "privatesection",
+  "protected", "protectedsection", "tableofcontents"};
 const int simpleCommandsSize = sizeof(simpleCommands) / sizeof(*simpleCommands);
 
 const char *ignoredSimpleCommands[] = {
@@ -38,11 +41,12 @@ const int ignoredSimpleCommandsSize = sizeof(ignoredSimpleCommands) / sizeof(*ig
 
 const char *commandWords[] = {
   "a", "b", "c", "e", "em", "p", "def", "enum", "package", "relates", "namespace", "relatesalso", "anchor", "dontinclude", "include",
-  "includelineno"};
+  "includelineno", "copydoc", "copybrief", "copydetails", "verbinclude", "htmlinclude", "extends", "implements", "memberof", "related",
+  "relatedalso"};
 const int commandWordsSize = sizeof(commandWords) / sizeof(*commandWords);
 
 const char *ignoredCommandWords[] = {
-  "copydoc", "copybrief", "copydetails", "verbinclude", "htmlinclude"};
+  "nothing at the moment"};
 const int ignoredCommandWordsSize = sizeof(ignoredCommandWords) / sizeof(*ignoredCommandWords);
 
 const char *commandLines[] = {
@@ -56,7 +60,7 @@ const int ignoreCommandLinesSize = sizeof(ignoreCommandLines) / sizeof(*ignoreCo
 const char *commandParagraph[] = {
   "partofdescription", "result", "return", "returns", "remarks", "remark", "since", "test", "sa", "see", "pre", "post", "details", "invariant",
   "deprecated", "date", "note", "warning", "version", "todo", "bug", "attention", "brief", "author", "authors", "cite",
-  "copyright"};
+  "copyright", "short"};
 const int commandParagraphSize = sizeof(commandParagraph) / sizeof(*commandParagraph);
 
 const char *ignoreCommandParagraphs[] = {
@@ -64,7 +68,7 @@ const char *ignoreCommandParagraphs[] = {
 const int ignoreCommandParagraphsSize = sizeof(ignoreCommandParagraphs) / sizeof(*ignoreCommandParagraphs);
 
 const char *commandEndCommands[] = {
-  "code", "dot", "msc", "f$", "f[", "f{environment}{", "htmlonly", "latexonly", "manonly", "verbatim", "xmlonly", "link"};
+  "htmlonly", "latexonly", "manonly", "xmlonly", "link", "rtfonly"};
 const int commandEndCommandsSize = sizeof(commandEndCommands) / sizeof(*commandEndCommands);
 
 const char *commandWordParagraphs[] = {
@@ -72,7 +76,7 @@ const char *commandWordParagraphs[] = {
 const int commandWordParagraphsSize = sizeof(commandWordParagraphs) / sizeof(*commandWordParagraphs);
 
 const char *commandWordLines[] = {
-  "page", "subsection", "subsubsection", "section", "paragraph", "defgroup"};
+  "page", "subsection", "subsubsection", "section", "paragraph", "defgroup", "snippet", "mainpage"};
 const int commandWordLinesSize = sizeof(commandWordLines) / sizeof(*commandWordLines);
 
 const char *commandWordOWordOWords[] = {
@@ -85,14 +89,14 @@ const int commandOWordsSize = sizeof(commandOWords) / sizeof(*commandOWords);
 
 const char *commandErrorThrowings[] = {
   "annotatedclassstd::list", "classhierarchy", "define", "functionindex", "header",
-  "headerfilestd::list", "inherit", "l", "postheader", "private", "privatesection", "protected",
-  "protectedsection", "public", "publicsection", "endcode", "enddot", "endmsc", "endhtmlonly",
-  "endlatexonly", "endmanonly", "endlink", "endverbatim", "endxmlonly", "f]", "f}", "endif", "else"};
+  "headerfilestd::list", "inherit", "l", "postheader", "endcode", "enddot", "endmsc", "endhtmlonly",
+  "endlatexonly", "endmanonly", "endlink", "endverbatim", "endxmlonly", "f]", "f}", "endif", "else",
+  "endrtfonly"};
 const int commandErrorThrowingsSize = sizeof(commandErrorThrowings) / sizeof(*commandErrorThrowings);
 
 const char *commandUniques[] = {
   "xrefitem", "arg", "ingroup", "par", "headerfile", "overload", "weakgroup", "ref", "subpage", "dotfile", "image", "addtogroup", "li",
-  "if", "ifnot", "elseif", "else", "mscfile"};
+  "if", "ifnot", "elseif", "else", "mscfile", "code", "verbatim", "f{", "f[", "f$", "dot", "msc"};
 const int commandUniquesSize = sizeof(commandUniques) / sizeof(*commandUniques);
 
 #endif
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.cpp b/Source/DoxygenTranslator/src/DoxygenParser.cpp
index 6161d00b9..3e94bd538 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenParser.cpp
@@ -227,11 +227,11 @@ std::list < Token >::iterator DoxygenParser::getEndOfSection(std::string theComm
 std::list < Token >::iterator DoxygenParser::getEndCommand(std::string theCommand, TokenList & tokList) {
 	std::list < Token >::iterator endOfCommand = tokList.iteratorCopy();
 	while (endOfCommand != tokList.end()) {
+        endOfCommand++;
 		if ((*endOfCommand).tokenType == COMMAND) {
 			if (theCommand == (*endOfCommand).tokenString) {
 				return endOfCommand;
 			}
-			endOfCommand++;
 		}
 	}
 	//End command not found
@@ -263,7 +263,9 @@ int DoxygenParser::addCommandWord(std::string theCommand, TokenList & tokList, s
 		cout << "Parsing " << theCommand << endl;
 	std::string name = getNextWord(tokList);
 	if (!name.empty()) {
-		doxyList.push_back(DoxygenEntity(theCommand, name));
+	    std::list < DoxygenEntity > aNewList;
+	    aNewList.push_back(DoxygenEntity("plainstd::string", name));
+		doxyList.push_back(DoxygenEntity(theCommand, aNewList));
 		return 1;
 	} else
 		tokList.printListError("No word followed " + theCommand + " command. Not added");
@@ -322,8 +324,15 @@ int DoxygenParser::ignoreCommandParagraph(std::string theCommand, TokenList & to
 int DoxygenParser::addCommandEndCommand(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
 	if (noisy)
 		cout << "Parsing " << theCommand << endl;
-	std::string description = getStringTilEndCommand("end" + theCommand, tokList);
-	doxyList.push_back(DoxygenEntity(theCommand, description));
+	std::list < Token >::iterator endCommand = getEndCommand("end" + theCommand, tokList);
+	if (endCommand == tokList.end()) {
+	  tokList.printListError("Expected end" + theCommand);
+	  return 0;
+	}
+	std::list < DoxygenEntity > aNewList;
+	aNewList = parse(endCommand, tokList);
+    tokList.next();
+	doxyList.push_back(DoxygenEntity(theCommand, aNewList));
 	return 1;
 }
 
@@ -398,6 +407,7 @@ int DoxygenParser::addCommandErrorThrow(std::string theCommand, TokenList & tokL
 }
 
 int DoxygenParser::addCommandUnique(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
+    static std::map<std::string, std::string> endCommands;
 	std::list < DoxygenEntity > aNewList;
 	if (theCommand == "arg" || theCommand == "li") {
 		std::list < Token >::iterator endOfSection = getEndOfSection(theCommand, tokList);
@@ -524,6 +534,39 @@ int DoxygenParser::addCommandUnique(std::string theCommand, TokenList & tokList,
 			aNewList.push_back(DoxygenEntity("plainstd::string", text));
 		doxyList.push_back(DoxygenEntity(theCommand, aNewList));
 	}
+    // \code ... \endcode
+    // \verbatim ... \endverbatim
+	// \dot dotcode \enddot
+	// \msc msccode \endmsc
+	// \f[ ... \f]
+	// \f{ ... \f}
+	// \f{env}{ ... \f}
+	// \f$ ... \f$
+    else if (theCommand == "code" || theCommand == "verbatim"
+        || theCommand == "dot" || theCommand == "msc"
+        || theCommand == "f[" || theCommand == "f{"
+        || theCommand == "f$") {
+        if (!endCommands.size()) {
+          // fill in static table of end commands
+          endCommands["f["] = "f]";
+          endCommands["f{"] = "f}";
+          endCommands["f$"] = "f$";
+        }
+        if (noisy)
+            cout << "Parsing " << theCommand << endl;
+
+        std::string endCommand;
+        std::map <std::string, std::string>::iterator it;
+        it = endCommands.find(theCommand);
+        if (it != endCommands.end())
+          endCommand = it->second;
+        else
+          endCommand = "end" + theCommand;
+
+        std::string content = getStringTilEndCommand(endCommand, tokList);
+        aNewList.push_back(DoxygenEntity("plainstd::string", content));
+        doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+    }
 	// \dotfile <file> ["caption"]
 	// \mscfile <file> ["caption"]
 	else if (theCommand == "dotfile" || theCommand == "mscfile") {
diff --git a/Source/DoxygenTranslator/src/TokenList.cpp b/Source/DoxygenTranslator/src/TokenList.cpp
index 1ade6375e..62dbdc997 100644
--- a/Source/DoxygenTranslator/src/TokenList.cpp
+++ b/Source/DoxygenTranslator/src/TokenList.cpp
@@ -30,6 +30,7 @@ TokenList TokenList::tokenizeDoxygenComment(const std::string &doxygenComment, c
   string::size_type pos, lastPos = 0;
   string currentWord;
   while (true) {
+    isPlainString = false;
     pos = doxygenComment.find_first_of("\t\n ", lastPos);
     if (pos == string::npos)
       pos = doxygenComment.size();
@@ -55,9 +56,7 @@ TokenList TokenList::tokenizeDoxygenComment(const std::string &doxygenComment, c
 
       if (isPlainString) {
         // handle quoted words
-        string::size_type qPos = currentWord.find('"', 0);
-        if (qPos != string::npos) {
-          lastPos += qPos;
+        if (currentWord[0] == '"') {
           pos = doxygenComment.find_first_of("\"\n", lastPos + 1);
           if (pos == string::npos)
             pos = doxygenComment.size();

From f0aa6b750179663ffe8dc8b72cb13a0b2fb5a437 Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Mon, 16 Jul 2012 19:36:23 +0000
Subject: [PATCH 086/314] Fixed \cite doxygen command parsing

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13325 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Source/DoxygenTranslator/src/DoxygenCommands.h | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/Source/DoxygenTranslator/src/DoxygenCommands.h b/Source/DoxygenTranslator/src/DoxygenCommands.h
index 27611cdcb..96fde4a7c 100644
--- a/Source/DoxygenTranslator/src/DoxygenCommands.h
+++ b/Source/DoxygenTranslator/src/DoxygenCommands.h
@@ -42,7 +42,7 @@ const int ignoredSimpleCommandsSize = sizeof(ignoredSimpleCommands) / sizeof(*ig
 const char *commandWords[] = {
   "a", "b", "c", "e", "em", "p", "def", "enum", "package", "relates", "namespace", "relatesalso", "anchor", "dontinclude", "include",
   "includelineno", "copydoc", "copybrief", "copydetails", "verbinclude", "htmlinclude", "extends", "implements", "memberof", "related",
-  "relatedalso"};
+  "relatedalso", "cite"};
 const int commandWordsSize = sizeof(commandWords) / sizeof(*commandWords);
 
 const char *ignoredCommandWords[] = {
@@ -59,7 +59,7 @@ const int ignoreCommandLinesSize = sizeof(ignoreCommandLines) / sizeof(*ignoreCo
 
 const char *commandParagraph[] = {
   "partofdescription", "result", "return", "returns", "remarks", "remark", "since", "test", "sa", "see", "pre", "post", "details", "invariant",
-  "deprecated", "date", "note", "warning", "version", "todo", "bug", "attention", "brief", "author", "authors", "cite",
+  "deprecated", "date", "note", "warning", "version", "todo", "bug", "attention", "brief", "author", "authors",
   "copyright", "short"};
 const int commandParagraphSize = sizeof(commandParagraph) / sizeof(*commandParagraph);
 

From 32154a91e4e3e32b80dde69bf112586e96534c21 Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Mon, 16 Jul 2012 19:37:05 +0000
Subject: [PATCH 087/314] Normalized parameters handling, included newlines to
 the parsed tree

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13326 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Source/DoxygenTranslator/src/DoxygenParser.cpp | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/Source/DoxygenTranslator/src/DoxygenParser.cpp b/Source/DoxygenTranslator/src/DoxygenParser.cpp
index 3e94bd538..a44b79abe 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenParser.cpp
@@ -263,8 +263,8 @@ int DoxygenParser::addCommandWord(std::string theCommand, TokenList & tokList, s
 		cout << "Parsing " << theCommand << endl;
 	std::string name = getNextWord(tokList);
 	if (!name.empty()) {
-	    std::list < DoxygenEntity > aNewList;
-	    aNewList.push_back(DoxygenEntity("plainstd::string", name));
+    std::list < DoxygenEntity > aNewList;
+    aNewList.push_back(DoxygenEntity("plainstd::string", name));
 		doxyList.push_back(DoxygenEntity(theCommand, aNewList));
 		return 1;
 	} else
@@ -393,7 +393,9 @@ int DoxygenParser::addCommandOWord(std::string theCommand, TokenList & tokList,
 	if (noisy)
 		cout << "Parsing " << theCommand << endl;
 	std::string name = getNextWord(tokList);
-	doxyList.push_back(DoxygenEntity(theCommand, name));
+	std::list < DoxygenEntity > aNewList;
+  aNewList.push_back(DoxygenEntity("plainstd::string", name));
+	doxyList.push_back(DoxygenEntity(theCommand, aNewList));
 	return 1;
 }
 
@@ -750,6 +752,7 @@ std::list < DoxygenEntity > DoxygenParser::parse(std::list < Token >::iterator e
 		if (noisy)
 			cout << "Parsing for phrase starting in:" << currToken.toString() << endl;
 		if (currToken.tokenType == END_LINE) {
+		  aNewList.push_back(DoxygenEntity("plainstd::endl"));
 			tokList.next();
 		} else if (currToken.tokenType == COMMAND) {
 			currCommand = findCommand(currToken.tokenString);

From db9659c286f57be807f181a72afde6f1b55e6dba Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Mon, 16 Jul 2012 19:42:30 +0000
Subject: [PATCH 088/314] Implemented most of non-ignored doxygen commands
 translating for java, fixed testcase. The output is not really nice right
 now, but almost all the commands mentioned in the project plan work ok

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13327 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Doc/Devel/plan-gsoc-2012.txt                  |   4 +-
 Examples/test-suite/common.mk                 |   2 +-
 Examples/test-suite/doxygen_translate.i       |   7 +-
 .../src/JavaDocConverter.cpp                  | 229 ++++++++++++------
 .../DoxygenTranslator/src/JavaDocConverter.h  |  54 ++++-
 5 files changed, 203 insertions(+), 93 deletions(-)

diff --git a/Doc/Devel/plan-gsoc-2012.txt b/Doc/Devel/plan-gsoc-2012.txt
index a32878375..3750a27ca 100644
--- a/Doc/Devel/plan-gsoc-2012.txt
+++ b/Doc/Devel/plan-gsoc-2012.txt
@@ -92,7 +92,7 @@ Functionality
     \category - ignored, used only in Objective C
     \cite - translated to <i></i> in JD, single quotes in PD
     \class - ignored (structural command)
-    \code - translated to <code></code> in JD, ignored in PD
+    \code - translated to {@code ...} in JD, ignored in PD
     \cond - translated to 'Conditional comment: <condition>'. Later
             SWIG may support definitions of conditions in config file.
     \copybrief - ignored. Later SWIG may support this command by
@@ -172,7 +172,7 @@ Functionality
     \namespace - included in package-info.java if nspace feature is enabled,
                  otherwise ignored, ignored in PD
     \nosubgrouping - ignored
-    \note - ignored in JD, translated to 'Note:' in PD
+    \note - translated to 'Note:' in both JD and PD
     \overload - prints 'This is an overloaded member function, provided for
                 convenience. It differs from the above function only in what
                 argument(s) it accepts.' to the output in both JD and PD
diff --git a/Examples/test-suite/common.mk b/Examples/test-suite/common.mk
index ed2d74cd9..9f91cec8c 100644
--- a/Examples/test-suite/common.mk
+++ b/Examples/test-suite/common.mk
@@ -188,7 +188,7 @@ CPP_TEST_CASES += \
 	director_wombat \
 	disown \
 	doxygen_parsing \
-	doxygen_basic_translate \
+	doxygen_translate \
 	dynamic_cast \
 	empty \
 	enum_rename \
diff --git a/Examples/test-suite/doxygen_translate.i b/Examples/test-suite/doxygen_translate.i
index 04f70f014..8bfd3d250 100644
--- a/Examples/test-suite/doxygen_translate.i
+++ b/Examples/test-suite/doxygen_translate.i
@@ -54,7 +54,7 @@
  *   This is printed if not
  * \endif
  * 
- * \image html testImage.bmp
+ * \image html testImage.bmp "Hello, world!" asd=10qwe
  * 
  * <ul>
  * 
@@ -68,6 +68,9 @@
  * 
  * \n \n \n
  * 
+ * \note Here
+ * is the note!
+ *
  * \overload
  * 
  * \p someword
@@ -122,4 +125,4 @@ int function(int a, float b)
 {
 }
 
-%}
\ No newline at end of file
+%}
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.cpp b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
index 2bc3165f4..42b5fcb80 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
@@ -17,54 +17,82 @@
 //TODO {@link} {@linkplain} {@docRoot}, and other useful doxy commands that are not a javadoc tag
 
 // define static tables, they are filled in JavaDocConverter's constructor
-std::map<std::string, std::string> JavaDocConverter::escapeTable;
-std::map<std::string, JavaDocConverter::tagHandler> JavaDocConverter::tagHandlers;
+std::map<std::string, std::pair<JavaDocConverter::tagHandler, std::string > > JavaDocConverter::tagHandlers;
 
 void JavaDocConverter::fillStaticTables() {
-  if (escapeTable.size()) // fill only once
-    return;
-  
-  escapeTable["&"] = "&amp";
-  escapeTable["\'"] = "&apos";
-  escapeTable["\""] = "&quot";
-  escapeTable["<"] = "&lt";
-  escapeTable[">"] = "&gt";
+  if (tagHandlers.size()) // fill only once
 
   // these commands insert HTML tags
-	tagHandlers["c"] = &handleTagC;
-	tagHandlers["b"] = &handleTagB;
-	// these commands insert just a single char, some of them need to be escaped
-	tagHandlers["$"] = &handleTagChar;
-	tagHandlers["@"] = &handleTagChar;
-	tagHandlers["\\"] = &handleTagChar;
-	tagHandlers["<"] = &handleTagChar;
-	tagHandlers[">"] = &handleTagChar;
-	tagHandlers["&"] = &handleTagChar;
-	tagHandlers["#"] = &handleTagChar;
-	tagHandlers["%"] = &handleTagChar;
-	tagHandlers["~"] = &handleTagChar;
-	tagHandlers["\""] = &handleTagChar;
-	tagHandlers["."] = &handleTagChar;
-	tagHandlers["::"] = &handleTagChar;
-	// these commands are stripped out
-	tagHandlers["brief"] = &handleParagraph;
-	tagHandlers["details"] = &handleParagraph;
-	tagHandlers["partofdescription"] = &handleParagraph;
-	// these commands are kept as-is, they are supported by JavaDoc
-	tagHandlers["sa"] = &handleTagSeeAll;
-	tagHandlers["see"] = &handleTagSame;
-	tagHandlers["param"] = &handleTagSame;
-	tagHandlers["return"] = &handleTagSame;
-	tagHandlers["throws"] = &handleTagSame;
-	tagHandlers["throw"] = &handleTagThrow;
-	tagHandlers["author"] = &handleTagSame;
-	tagHandlers["since"] = &handleTagSame;
-	tagHandlers["version"] = &handleTagSame;
-	tagHandlers["exception"] = &handleTagSame;
-	tagHandlers["deprecated"] = &handleTagSame;
-	// this command just prints it's contents
-	// (it is internal command of swig's parser, contains plain text)
-	tagHandlers["plainstd::string"] = &handlePlainString;
+  tagHandlers["a"] = make_pair(&JavaDocConverter::handleTagHtml, "i");
+  tagHandlers["arg"] = make_pair(&JavaDocConverter::handleTagHtml, "li");
+  tagHandlers["b"] = make_pair(&JavaDocConverter::handleTagHtml, "b");
+  tagHandlers["c"] = make_pair(&JavaDocConverter::handleTagHtml, "code");
+  tagHandlers["cite"] = make_pair(&JavaDocConverter::handleTagHtml, "i");
+  tagHandlers["e"] = make_pair(&JavaDocConverter::handleTagHtml, "i");
+  tagHandlers["li"] = make_pair(&JavaDocConverter::handleTagHtml, "li");
+  tagHandlers["p"] = make_pair(&JavaDocConverter::handleTagHtml, "code");
+  // these commands insert just a single char, some of them need to be escaped
+  tagHandlers["$"] = make_pair(&JavaDocConverter::handleTagChar, "");
+  tagHandlers["@"] = make_pair(&JavaDocConverter::handleTagChar, "");
+  tagHandlers["\\"] = make_pair(&JavaDocConverter::handleTagChar, "");
+  tagHandlers["<"] = make_pair(&JavaDocConverter::handleTagChar, "");
+  tagHandlers[">"] = make_pair(&JavaDocConverter::handleTagChar, "");
+  tagHandlers["&"] = make_pair(&JavaDocConverter::handleTagChar, "");
+  tagHandlers["#"] = make_pair(&JavaDocConverter::handleTagChar, "");
+  tagHandlers["%"] = make_pair(&JavaDocConverter::handleTagChar, "");
+  tagHandlers["~"] = make_pair(&JavaDocConverter::handleTagChar, "");
+  tagHandlers["\""] = make_pair(&JavaDocConverter::handleTagChar, "");
+  tagHandlers["."] = make_pair(&JavaDocConverter::handleTagChar, "");
+  tagHandlers["::"] = make_pair(&JavaDocConverter::handleTagChar, "");
+  // these commands are stripped out
+  tagHandlers["attention"] = make_pair(&JavaDocConverter::handleParagraph, "");
+  tagHandlers["brief"] = make_pair(&JavaDocConverter::handleParagraph, "");
+  tagHandlers["date"] = make_pair(&JavaDocConverter::handleParagraph, "");
+  tagHandlers["details"] = make_pair(&JavaDocConverter::handleParagraph, "");
+  tagHandlers["partofdescription"] = make_pair(&JavaDocConverter::handleParagraph, "");
+  // these commands are kept as-is, they are supported by JavaDoc
+  tagHandlers["author"] = make_pair(&JavaDocConverter::handleTagSame, "");
+  tagHandlers["authors"] = make_pair(&JavaDocConverter::handleTagSame, "author");
+  tagHandlers["deprecated"] = make_pair(&JavaDocConverter::handleTagSame, "");
+  tagHandlers["exception"] = make_pair(&JavaDocConverter::handleTagSame, "");
+  tagHandlers["package"] = make_pair(&JavaDocConverter::handleTagSame, "");
+  tagHandlers["param"] = make_pair(&JavaDocConverter::handleTagSame, "");
+  tagHandlers["tparam"] = make_pair(&JavaDocConverter::handleTagSame, "param");
+  tagHandlers["result"] = make_pair(&JavaDocConverter::handleTagSame, "return");
+  tagHandlers["return"] = make_pair(&JavaDocConverter::handleTagSame, "");
+  tagHandlers["returns"] = make_pair(&JavaDocConverter::handleTagSame, "return");
+  tagHandlers["see"] = make_pair(&JavaDocConverter::handleTagSame, "");
+  tagHandlers["sa"] = make_pair(&JavaDocConverter::handleTagSame, "see");
+  tagHandlers["since"] = make_pair(&JavaDocConverter::handleTagSame, "");
+  tagHandlers["throws"] = make_pair(&JavaDocConverter::handleTagSame, "");
+  tagHandlers["throw"] = make_pair(&JavaDocConverter::handleTagSame, "throws");
+  tagHandlers["version"] = make_pair(&JavaDocConverter::handleTagSame, "");
+  // these commands have special handlers
+  tagHandlers["code"] = make_pair(&JavaDocConverter::handleTagExtended, "code");
+  tagHandlers["cond"] = make_pair(&JavaDocConverter::handleTagMessage, "Conditional comment: ");
+  tagHandlers["copyright"] = make_pair(&JavaDocConverter::handleTagMessage, "Copyright: ");
+  tagHandlers["else"] = make_pair(&JavaDocConverter::handleTagIf, "Else: ");
+  tagHandlers["elseif"] = make_pair(&JavaDocConverter::handleTagIf, "Else if: ");
+  tagHandlers["endcond"] = make_pair(&JavaDocConverter::handleTagMessage, "End of conditional comment.");
+  tagHandlers["if"] = make_pair(&JavaDocConverter::handleTagIf, "If: ");
+  tagHandlers["ifnot"] = make_pair(&JavaDocConverter::handleTagIf, "If not: ");
+  tagHandlers["image"] = make_pair(&JavaDocConverter::handleTagImage, "");
+  tagHandlers["link"] = make_pair(&JavaDocConverter::handleTagExtended, "link");
+  tagHandlers["note"] = make_pair(&JavaDocConverter::handleTagMessage, "Note: ");
+  tagHandlers["overload"] = make_pair(&JavaDocConverter::handleTagMessage, "This is an overloaded member function, provided for"
+      " convenience. It differs from the above function only in what"
+      " argument(s) it accepts.");
+  tagHandlers["par"] = make_pair(&JavaDocConverter::handleTagPar, "");
+  tagHandlers["remark"] = make_pair(&JavaDocConverter::handleTagMessage, "Remarks: ");
+  tagHandlers["remarks"] = make_pair(&JavaDocConverter::handleTagMessage, "Remarks: ");
+  tagHandlers["todo"] = make_pair(&JavaDocConverter::handleTagMessage, "TODO: ");
+  tagHandlers["verbatim"] = make_pair(&JavaDocConverter::handleTagExtended, "literal");
+  tagHandlers["warning"] = make_pair(&JavaDocConverter::handleTagMessage, "Warning: ");
+  // this command just prints it's contents
+  // (it is internal command of swig's parser, contains plain text)
+  tagHandlers["plainstd::string"] = make_pair(&JavaDocConverter::handlePlainString, "");
+  tagHandlers["plainstd::endl"] = make_pair(&JavaDocConverter::handleNewLine, "");
+  tagHandlers["n"] = make_pair(&JavaDocConverter::handleNewLine, "");
 }
 
 
@@ -73,7 +101,7 @@ JavaDocConverter::JavaDocConverter() : debug(false) {
 }
 
 std::string JavaDocConverter::formatCommand(std::string unformattedLine, int indent) {
-  std::string formattedLines = "\n * ";
+  std::string formattedLines;
   int lastPosition = 0;
   int i = 0;
   int isFirstLine = 1;
@@ -89,11 +117,11 @@ std::string JavaDocConverter::formatCommand(std::string unformattedLine, int ind
 
     if (i > 0 && i + 1 < (int) unformattedLine.length()) {
       if (!isFirstLine)
-	for (int j = 0; j < indent; j++) {
-	  formattedLines.append("\t");
-      } else {
-	isFirstLine = 0;
-      }
+        for (int j = 0; j < indent; j++) {
+          formattedLines.append("\t");
+        } else {
+          isFirstLine = 0;
+        }
       formattedLines.append(unformattedLine.substr(lastPosition, i - lastPosition + 1));
       formattedLines.append("\n *");
 
@@ -102,7 +130,7 @@ std::string JavaDocConverter::formatCommand(std::string unformattedLine, int ind
   if (lastPosition < (int) unformattedLine.length()) {
     if (!isFirstLine) {
       for (int j = 0; j < indent; j++) {
-	formattedLines.append("\t");
+        formattedLines.append("\t");
       }
     }
     formattedLines.append(unformattedLine.substr(lastPosition, unformattedLine.length() - lastPosition));
@@ -129,45 +157,96 @@ std::string JavaDocConverter::translateSubtree(DoxygenEntity & doxygenEntity) {
 
 void JavaDocConverter::translateEntity(DoxygenEntity& tag, std::string& translatedComment) {
   // check if we have needed handler and call it
-  std::map<std::string, tagHandler>::iterator it;
-  it = tagHandlers.find(tag.typeOfEntity); 
+  std::map<std::string, std::pair<tagHandler, std::string > >::iterator it;
+  it = tagHandlers.find(tag.typeOfEntity);
   if (it!=tagHandlers.end())
-    (*it).second(this, tag, translatedComment);
+    (this->*(it->second.first))(tag, translatedComment, it->second.second);
 }
 
-void JavaDocConverter::handleTagC(JavaDocConverter* converter, DoxygenEntity& tag, std::string& translatedComment) {
-  translatedComment += "<tt>" + tag.data + "</tt> ";
+void JavaDocConverter::handleTagHtml(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
+  if (tag.entityList.size()) // do not include empty tags
+    translatedComment += "<" + arg + ">" + translateSubtree(tag) + "</" + arg + ">";
 }
-void JavaDocConverter::handleTagB(JavaDocConverter* converter, DoxygenEntity& tag, std::string& translatedComment) {
-  translatedComment += "<b>" + tag.data + "</b> ";
+void JavaDocConverter::handleNewLine(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
+  translatedComment += "\n * ";
 }
-void JavaDocConverter::handleTagThrow(JavaDocConverter* converter, DoxygenEntity& tag, std::string& translatedComment) {
-  tag.typeOfEntity = "throws";
-  handleTagSame(converter, tag, translatedComment);
-}
-void JavaDocConverter::handleTagSeeAll(JavaDocConverter* converter, DoxygenEntity& tag, std::string& translatedComment) {
-  tag.typeOfEntity = "see";
-  handleTagSame(converter, tag, translatedComment);
-}
-void JavaDocConverter::handleTagChar(JavaDocConverter* converter, DoxygenEntity& tag, std::string& translatedComment) {
-  // escape it if we can, else just print
-  if (escapeTable.find(tag.typeOfEntity)!=escapeTable.end())
-    translatedComment += escapeTable[tag.typeOfEntity];
+void JavaDocConverter::handleTagChar(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
+  // escape it if we need to, else just print
+  if (arg.size())
+    translatedComment += arg;
   else
     translatedComment += tag.typeOfEntity;
+  translatedComment += " ";
 }
-void JavaDocConverter::handleTagSame(JavaDocConverter* converter, DoxygenEntity& tag, std::string& translatedComment) {
-  translatedComment += converter->formatCommand(std::string("@" + tag.typeOfEntity + "\t" + converter->translateSubtree(tag)), 2);
+void JavaDocConverter::handleTagSame(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
+  if (arg.size())
+    tag.typeOfEntity = arg;
+  translatedComment += formatCommand(std::string("@" + tag.typeOfEntity + " " + translateSubtree(tag)), 2);
 }
-void JavaDocConverter::handleParagraph(JavaDocConverter* converter, DoxygenEntity& tag, std::string& translatedComment) {
-  translatedComment += converter->formatCommand(converter->translateSubtree(tag), 0);
+void JavaDocConverter::handleParagraph(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
+  translatedComment += formatCommand(translateSubtree(tag), 0);
 }
-void JavaDocConverter::handlePlainString(JavaDocConverter* converter, DoxygenEntity& tag, std::string& translatedComment) {
+void JavaDocConverter::handlePlainString(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
   translatedComment += tag.data;
   if (tag.data.size() && tag.data[tag.data.size()-1] != ' ')
   	translatedComment += " ";
 }
 
+void JavaDocConverter::handleTagExtended(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
+  std::string dummy;
+  translatedComment += "{@" + arg + " ";
+  handleParagraph(tag, translatedComment, dummy);
+  translatedComment += "}";
+}
+void JavaDocConverter::handleTagIf(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
+  std::string dummy;
+  translatedComment += arg;
+  if (tag.entityList.size()) {
+    translatedComment += tag.entityList.begin()->data;
+    //handleNewLine(tag, translatedComment, dummy);
+    tag.entityList.pop_front();
+    translatedComment += " {" + translateSubtree(tag) + "}";
+  }
+}
+void JavaDocConverter::handleTagMessage(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
+  std::string dummy;
+  translatedComment += formatCommand(arg, 0);
+  handleParagraph(tag, translatedComment, dummy);
+}
+void JavaDocConverter::handleTagImage(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
+  if (tag.entityList.size() < 2)
+    return;
+
+  std::string file;
+  std::string title;
+
+  std::list <DoxygenEntity>::iterator it = tag.entityList.begin();
+  if (it->data != "html")
+    return;
+
+  it++;
+  file = it->data;
+
+  it++;
+  if (it != tag.entityList.end())
+    title = it->data;
+
+  translatedComment += "<img src=" + file;
+  if (title.size())
+    translatedComment += " alt=\"" + title +"\"";
+  translatedComment += " />";
+}
+void JavaDocConverter::handleTagPar(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
+  std::string dummy;
+  translatedComment += "<p";
+  if (tag.entityList.size())
+    translatedComment += " alt=\"" + tag.entityList.begin()->data + "\"";
+  translatedComment += ">";
+  tag.entityList.pop_front();
+  handleParagraph(tag, translatedComment, dummy);
+  translatedComment += "</p>";
+}
+
 String *JavaDocConverter::makeDocumentation(Node *node) {
 
   String *documentation = getDoxygenComment(node);
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.h b/Source/DoxygenTranslator/src/JavaDocConverter.h
index 9776a17e0..cb876ed6b 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.h
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.h
@@ -27,42 +27,70 @@ public:
 
 protected:
   std::string formatCommand(std::string unformattedLine, int indent);
-  std::string javaDocFormat(DoxygenEntity & doxygenEntity);
   std::string translateSubtree(DoxygenEntity & doxygenEntity);
   void translateEntity(DoxygenEntity &tag, std::string &translatedComment);
   
   /*
    * Typedef for the function that handles one tag
+   * arg - some string argument to easily pass it through lookup table
    */
-  typedef void (*tagHandler)(JavaDocConverter *converter, DoxygenEntity &tag, std::string &translatedComment);
+  typedef void (JavaDocConverter::*tagHandler)(DoxygenEntity &tag,
+      std::string &translatedComment, std::string &arg);
   /*
-   * Here comes various tag handlers
+   * Wrap the command data with the html tag
+   * arg - html tag, with no braces
    */
-  static void handleTagC(JavaDocConverter *converter, DoxygenEntity &tag, std::string &translatedComment);
-  static void handleTagB(JavaDocConverter *converter, DoxygenEntity &tag, std::string &translatedComment);
-  static void handleTagThrow(JavaDocConverter *converter, DoxygenEntity &tag, std::string &translatedComment);
-  static void handleTagSeeAll(JavaDocConverter *converter, DoxygenEntity &tag, std::string &translatedComment);
+  void handleTagHtml(DoxygenEntity &tag, std::string &translatedComment, std::string &arg);
+  /*
+   * Just prints new line
+   */
+  void handleNewLine(DoxygenEntity &tag, std::string &translatedComment, std::string &arg);
   /*
    * Print the name of tag to the output, used for escape-commands
+   * arg - html-escaped variant, if not provided the command data is used
    */
-  static void handleTagChar(JavaDocConverter *converter, DoxygenEntity &tag, std::string &translatedComment);
+  void handleTagChar(DoxygenEntity &tag, std::string &translatedComment, std::string &arg);
   /*
    * Do not translate and print as-is
+   * arg - the new tag name, if it needs to be renamed
    */
-  static void handleTagSame(JavaDocConverter *converter, DoxygenEntity &tag, std::string &translatedComment);
+  void handleTagSame(DoxygenEntity &tag, std::string &translatedComment, std::string &arg);
   /*
    * Print only the content and strip original tag
    */
-  static void handleParagraph(JavaDocConverter *converter, DoxygenEntity &tag, std::string &translatedComment);
+  void handleParagraph(DoxygenEntity &tag, std::string &translatedComment, std::string &arg);
   /*
    * Print only data part of code
    */
-  static void handlePlainString(JavaDocConverter *converter, DoxygenEntity &tag, std::string &translatedComment);
+  void handlePlainString(DoxygenEntity &tag, std::string &translatedComment, std::string &arg);
+  /*
+   * Print extended Javadoc command, like {@code ...} or {@literal ...}
+   * arg - command name
+   */
+  void handleTagExtended(DoxygenEntity &tag, std::string &translatedComment, std::string &arg);
+  /*
+   * Print the if-elseif-else-endif section
+   */
+  void handleTagIf(DoxygenEntity &tag, std::string &translatedComment, std::string &arg);
+  /*
+   * Prints the specified message, than the contents of the tag
+   * arg - message
+   */
+  void handleTagMessage(DoxygenEntity &tag, std::string &translatedComment, std::string &arg);
+  /*
+   * Insert <img src=... /> tag if the 'format' field is specified as 'html'
+   */
+  void handleTagImage(DoxygenEntity &tag, std::string &translatedComment, std::string &arg);
+  /*
+   * Insert <p alt='title'>...</p>
+   */
+  void handleTagPar(DoxygenEntity &tag, std::string &translatedComment, std::string &arg);
+
 
 private:
   bool debug;
-  static std::map<std::string, tagHandler> tagHandlers;
-  static std::map<std::string, std::string> escapeTable;
+  // this contains the handler pointer and one string argument
+  static std::map<std::string, std::pair<tagHandler, std::string> > tagHandlers;
   void fillStaticTables();
 };
 

From ff0ec620b2d5a73ccbdfea6ed53b7b89e8215570 Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Mon, 16 Jul 2012 19:51:43 +0000
Subject: [PATCH 089/314] Added runtime test

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13328 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 .../java/doxygen_translate_runme.java         | 149 ++++++++++++++++++
 1 file changed, 149 insertions(+)
 create mode 100644 Examples/test-suite/java/doxygen_translate_runme.java

diff --git a/Examples/test-suite/java/doxygen_translate_runme.java b/Examples/test-suite/java/doxygen_translate_runme.java
new file mode 100644
index 000000000..6eec790e2
--- /dev/null
+++ b/Examples/test-suite/java/doxygen_translate_runme.java
@@ -0,0 +1,149 @@
+
+import doxygen_translate.*;
+import com.sun.javadoc.*;
+import java.util.HashMap;
+
+public class doxygen_translate_runme {
+  static {
+    try {
+      System.loadLibrary("doxygen_translate");
+    } catch (UnsatisfiedLinkError e) {
+      System.err.println("Native code library failed to load. See the chapter on Dynamic Linking Problems in the SWIG Java documentation for help.\n" + e);
+      System.exit(1);
+    }
+  }
+  
+  public static void main(String argv[]) 
+  {
+    /*
+      Here we are using internal javadoc tool, it accepts the name of the class as paramterer,
+      and calls the start() method of that class with parsed information.
+    */
+	commentParser parser = new commentParser();
+    com.sun.tools.javadoc.Main.execute("doxygen_translate runtime test",
+	"commentParser", new String[]{"-quiet", "doxygen_translate"});
+
+    HashMap<String, String> wantedComments = new HashMap<String, String>();
+    
+    wantedComments.put("function", " <i>Hello </i>\n" +
+    		" \n" +
+    		" <li>some list item \n" +
+    		" \n" +
+    		" </li>@author lots of them \n" +
+    		" \n" +
+    		" @author Zubr \n" +
+    		" \n" +
+    		" <b>boldword </b>\n" +
+    		" \n" +
+    		" <code>codeword </code>\n" +
+    		" \n" +
+    		" <i>citationword </i>\n" +
+    		" \n" +
+    		" {@code some test code }\n" +
+    		" \n" +
+    		" Conditional comment: SOMECONDITION \n" +
+    		" Some conditional comment \n" +
+    		" End of conditional comment.\n" +
+    		" \n" +
+    		" Copyright: some copyright \n" +
+    		" \n" +
+    		" @deprecated Now use another function \n" +
+    		" \n" +
+    		" <i>italicword </i>\n" +
+    		" \n" +
+    		" @exception SuperError \n" +
+    		" \n" +
+    		" If: ANOTHERCONDITION {\n" +
+    		" First part of comment \n" +
+    		" If: SECONDCONDITION {\n" +
+    		" Nested condition text \n" +
+    		" }Else if: THIRDCONDITION {\n" +
+    		" The third condition text \n" +
+    		" }Else:  {The last text block \n" +
+    		" }\n" +
+    		" }Else:  {Second part of comment \n" +
+    		" If: CONDITION {\n" +
+    		" Second part extended \n" +
+    		" }\n" +
+    		" }\n" +
+    		" \n" +
+    		" If not: SOMECONDITION {\n" +
+    		" This is printed if not \n" +
+    		" }\n" +
+    		" \n" +
+    		" <img src=testImage.bmp alt=\"Hello, world!\" />\n" +
+    		" \n" +
+    		" <ul> \n" +
+    		" \n" +
+    		" <li>Some unordered list \n" +
+    		" </li><li>With lots of items \n" +
+    		" </li><li>lots of lots of items \n" +
+    		" \n" +
+    		" </li></ul> \n" +
+    		" \n" +
+    		" {@link someMember Some description follows }\n" +
+    		" \n" +
+    		" \n" +
+    		" \n" +
+    		" \n" +
+    		" \n" +
+    		" \n" +
+    		" Note: Here \n" +
+    		" is the note! \n" +
+    		" \n" +
+    		" This is an overloaded member function, provided for convenience. \n" +
+    		" It differs from the above function only in what argument(s) it accepts.\n" +
+    		" \n" +
+    		" <code>someword </code>\n" +
+    		" \n" +
+    		" @package superPackage \n" +
+    		" \n" +
+    		" <p alt=\"The paragraph title \">\n" +
+    		" The paragraph text. \n" +
+    		" Maybe even multiline \n" +
+    		" \n" +
+    		" </p>@param a the first param \n" +
+    		" \n" +
+    		" Remarks: Some remark text \n" +
+    		" \n" +
+    		" Remarks: Another remarks section \n" +
+    		" \n" +
+    		" @return Whatever \n" +
+    		" \n" +
+    		" @return it \n" +
+    		" \n" +
+    		" @return may return \n" +
+    		" \n" +
+    		" @see someOtherMethod \n" +
+    		" \n" +
+    		" @see function \n" +
+    		" \n" +
+    		" @since version 0.0.0.1 \n" +
+    		" \n" +
+    		" @throws superException \n" +
+    		" \n" +
+    		" @throws RuntimeError \n" +
+    		" \n" +
+    		" TODO: Some very important task \n" +
+    		" \n" +
+    		" @param b B is mentioned again... \n" +
+    		" \n" +
+    		" {@literal \n" +
+    		"very long \n" +
+    		"text with tags <sometag> \n" +
+    		" }\n" +
+    		" \n" +
+    		" @version 0.0.0.2 \n" +
+    		" \n" +
+    		" Warning: This is senseless! \n" +
+    		" \n" +
+    		" Here goes test of symbols: \n" +
+    		" $ @ \\ & ~ < > # % \" . :: \n" +
+    		" \n" +
+    		" And here goes simple text \n" +
+    		" \n");
+    
+    // and ask the parser to check comments for us
+    System.exit(parser.check(wantedComments));
+  }
+}
\ No newline at end of file

From 9e1e514fbcc161765e0e69336a8d0ab96803b4d8 Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Mon, 16 Jul 2012 19:57:28 +0000
Subject: [PATCH 090/314] Updated project plan

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13329 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Doc/Devel/plan-gsoc-2012.txt | 58 ++++++++++++++++++------------------
 1 file changed, 29 insertions(+), 29 deletions(-)

diff --git a/Doc/Devel/plan-gsoc-2012.txt b/Doc/Devel/plan-gsoc-2012.txt
index 3750a27ca..6566598fe 100644
--- a/Doc/Devel/plan-gsoc-2012.txt
+++ b/Doc/Devel/plan-gsoc-2012.txt
@@ -24,7 +24,7 @@ and Python code (## comments, see Doxygen manual), if the user will
 prefer to use Doxygen on the generated code.
 
 Note:
-'--Done' tick below means that the item is implemented, commited and
+'-OK-' tick below means that the item is implemented, commited and
 working.
 
 Abbreviations:
@@ -43,11 +43,10 @@ Functionality
      the detailed description of Doxygen syntax and terms used in this
      section.
 
-  1. Only JavaDoc (/** */) and Qt (/*! */) styles of comment blocks
+  1. -OK- Only JavaDoc (/** */) and Qt (/*! */) styles of comment blocks
      will be supported by SWIG translator.
-     --Done
 
-  2. The following doc after members will be supported:
+  2. -OK- The following doc after members will be supported:
   
      int var; ///< Detailed description after the member
               //!< 
@@ -56,13 +55,11 @@ Functionality
 
      int var; ///< Brief description after the member
      
-     --Done
 
-  3. Only comments before or after declaration/definition will be
+  3. -OK- Only comments before or after declaration/definition will be
      supported. Comments with structural commands will be ignored
      (warning will be written). (What about writing them to
      'package.info.java' for JD?)
-     --Done
   
 
   Tags
@@ -265,6 +262,9 @@ Sometimes it needs a type of parameters specified because of the
 overloaded functions. And the same linking tags are supported in JD,
 but it has a completely different typesystem, so we need to translate
 the types of function parameters in comments also. For example:
+{@link MyClass#doSomething(const std::string &)}
+does not make sense in Java, so the type should be converted.
+{@link MyClass#doSomething(String)}
  
     
 Tests
@@ -272,30 +272,30 @@ Tests
 
 The following test cases will be implemented:
 
-- Class comments. --Done
+-OK- Class comments.
 
-- Struct comments. --Done
-- Enum comments. --Done
-- Function comments. --Done
-- Var comments. --Done
+-OK- Struct comments.
+-OK- Enum comments.
+-OK- Function comments.
+-OK- Var comments.
 
-- Class attributes, comment before and after declaration. --Done
-- Class methods, comment of parameters in function
-  comment. --Done
-- Class methods, comment of parameters
-  after parameter declaration. --Done
+-OK- Class attributes, comment before and after declaration.
+-OK- Class methods, comment of parameters in function
+  comment.
+-OK- Class methods, comment of parameters
+  after parameter declaration.
   
-- Struct attributes, comment before and after declaration. --Done
-- Struct methods, comment of parameters in function
-  comment. --Done
-- Struct methods, comment of parameters 
-  after parameter declaration. --Done
+-OK- Struct attributes, comment before and after declaration.
+-OK- Struct methods, comment of parameters in function
+  comment.
+-OK- Struct methods, comment of parameters 
+  after parameter declaration.
 
-- Enum items JD and Qt style, comment before items --Done
-- Enum items JD and Qt style, comment after items --Done
+-OK- Enum items JD and Qt style, comment before items
+-OK- Enum items JD and Qt style, comment after items
 
-- Class comment, with all supported tags.
-- Class comment, with all doxygen tags, including
+-OK- Class comment, with all supported tags.
+-OK- Class comment, with all doxygen tags, including
   ignored ones.
 
   
@@ -303,9 +303,9 @@ Refactoring
 ===========
 
 All the code in directory _DoxygenTranslator_ should be refactored:
-- all methods should be class members
-- most static methods should be normal members
-- replace C arrays of strings and sequential searches with STL data
+-OK- all methods should be class members
+-OK- most static methods should be normal members
+-OK- replace C arrays of strings and sequential searches with STL data
   structures and algorithms.
 - use singletons instead of class instantiaion for each comment found.
 

From 3d5d66dbd31963debd9fa94674d89757f9a81b57 Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Tue, 17 Jul 2012 23:17:17 +0000
Subject: [PATCH 091/314] Fixed a bug with freezing on commands like \code,
 \link and others

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13330 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Source/DoxygenTranslator/src/DoxygenParser.cpp | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/Source/DoxygenTranslator/src/DoxygenParser.cpp b/Source/DoxygenTranslator/src/DoxygenParser.cpp
index a44b79abe..80ded041a 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenParser.cpp
@@ -331,7 +331,7 @@ int DoxygenParser::addCommandEndCommand(std::string theCommand, TokenList & tokL
 	}
 	std::list < DoxygenEntity > aNewList;
 	aNewList = parse(endCommand, tokList);
-    tokList.next();
+	tokList.next();
 	doxyList.push_back(DoxygenEntity(theCommand, aNewList));
 	return 1;
 }
@@ -768,6 +768,12 @@ std::list < DoxygenEntity > DoxygenParser::parse(std::list < Token >::iterator e
 		} else if (currToken.tokenType == PLAINSTRING) {
 			addCommand(currPlainstringCommandType, tokList, aNewList);
 		}
+
+		if (endParsingIndex != tokList.end() && tokList.current() == tokList.end()) {
+		  // this could happen if we cant reach the original endParsingIndex
+		  tokList.printListError("Unexpected end of comment encountered");
+		  break;
+		}
 	}
 	return aNewList;
 }

From d9e8d140e76d6eaf498230efd66a9c7bce0955d8 Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Wed, 18 Jul 2012 22:05:19 +0000
Subject: [PATCH 092/314] Refactored PyDocConverter class, implemented some
 commands

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13331 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 .../DoxygenTranslator/src/PyDocConverter.cpp  | 200 +++++++++++-------
 Source/DoxygenTranslator/src/PyDocConverter.h |  63 +++++-
 2 files changed, 183 insertions(+), 80 deletions(-)

diff --git a/Source/DoxygenTranslator/src/PyDocConverter.cpp b/Source/DoxygenTranslator/src/PyDocConverter.cpp
index 819c6bc6c..3dd42677e 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/PyDocConverter.cpp
@@ -17,9 +17,74 @@
 #include <vector>
 #include <iostream>
 
-//TODO {@link} {@linkplain} {@docRoot}, and other useful doxy commands that are not a pydoc tag
-PyDocConverter::PyDocConverter() {
-  debug = 0;
+// define static tables, they are filled in PyDocConverter's constructor
+std::map<std::string, std::pair<PyDocConverter::tagHandler, std::string > > PyDocConverter::tagHandlers;
+std::map<std::string, std::string> PyDocConverter::sectionTitles;
+
+void PyDocConverter::fillStaticTables() {
+  if (tagHandlers.size()) // fill only once
+    return;
+
+  sectionTitles["author"] = "Authors:";
+  sectionTitles["authors"] = "Authors:";
+  sectionTitles["copyright"] = "Copyright:";
+  sectionTitles["deprecated"] = "Deprecated:";
+  sectionTitles["param"] = "Arguments:";
+  sectionTitles["tparam"] = "Arguments:";
+  sectionTitles["note"] = "Notes:";
+  sectionTitles["remark"] = "Remarks:";
+  sectionTitles["remarks"] = "Remarks:";
+  sectionTitles["warning"] = "Warning:";
+  sectionTitles["result"] = "Return:";
+  sectionTitles["return"] = "Return:";
+  sectionTitles["returns"] = "Return:";
+
+  // these commands insert HTML tags
+  tagHandlers["a"] = make_pair(&PyDocConverter::handleTagWrap, "_");
+  tagHandlers["b"] = make_pair(&PyDocConverter::handleTagWrap, "__");
+  tagHandlers["cite"] = make_pair(&PyDocConverter::handleTagWrap, "'");
+  tagHandlers["e"] = make_pair(&PyDocConverter::handleTagWrap, "_");
+  // these commands insert just a single char, some of them need to be escaped
+  tagHandlers["$"] = make_pair(&PyDocConverter::handleTagChar, "");
+  tagHandlers["@"] = make_pair(&PyDocConverter::handleTagChar, "");
+  tagHandlers["\\"] = make_pair(&PyDocConverter::handleTagChar, "");
+  tagHandlers["<"] = make_pair(&PyDocConverter::handleTagChar, "");
+  tagHandlers[">"] = make_pair(&PyDocConverter::handleTagChar, "");
+  tagHandlers["&"] = make_pair(&PyDocConverter::handleTagChar, "");
+  tagHandlers["#"] = make_pair(&PyDocConverter::handleTagChar, "");
+  tagHandlers["%"] = make_pair(&PyDocConverter::handleTagChar, "");
+  tagHandlers["~"] = make_pair(&PyDocConverter::handleTagChar, "");
+  tagHandlers["\""] = make_pair(&PyDocConverter::handleTagChar, "");
+  tagHandlers["."] = make_pair(&PyDocConverter::handleTagChar, "");
+  tagHandlers["::"] = make_pair(&PyDocConverter::handleTagChar, "");
+  // these commands are stripped out
+  tagHandlers["attention"] = make_pair(&PyDocConverter::handleParagraph, "");
+  tagHandlers["author"] = make_pair(&PyDocConverter::handleParagraph, "");
+  tagHandlers["authors"] = make_pair(&PyDocConverter::handleParagraph, "");
+  tagHandlers["brief"] = make_pair(&PyDocConverter::handleParagraph, "");
+  tagHandlers["c"] = make_pair(&PyDocConverter::handleParagraph, "");
+  tagHandlers["code"] = make_pair(&PyDocConverter::handleParagraph, "");
+  tagHandlers["copyright"] = make_pair(&PyDocConverter::handleParagraph, "");
+  tagHandlers["date"] = make_pair(&PyDocConverter::handleParagraph, "");
+  tagHandlers["deprecated"] = make_pair(&PyDocConverter::handleParagraph, "");
+  tagHandlers["details"] = make_pair(&PyDocConverter::handleParagraph, "");
+  tagHandlers["note"] = make_pair(&PyDocConverter::handleParagraph, "");
+  tagHandlers["partofdescription"] = make_pair(&PyDocConverter::handleParagraph, "");
+  tagHandlers["remark"] = make_pair(&PyDocConverter::handleParagraph, "");
+  tagHandlers["remarks"] = make_pair(&PyDocConverter::handleParagraph, "");
+  tagHandlers["warning"] = make_pair(&PyDocConverter::handleParagraph, "");
+  // these commands have special handlers
+  tagHandlers["cond"] = make_pair(&PyDocConverter::handleTagMessage, "Conditional comment: ");
+  tagHandlers["endcond"] = make_pair(&PyDocConverter::handleTagMessage, "End of conditional comment.");
+  // this command just prints it's contents
+  // (it is internal command of swig's parser, contains plain text)
+  tagHandlers["plainstd::string"] = make_pair(&PyDocConverter::handlePlainString, "");
+  tagHandlers["plainstd::endl"] = make_pair(&PyDocConverter::handleNewLine, "");
+  tagHandlers["n"] = make_pair(&PyDocConverter::handleNewLine, "");
+}
+
+PyDocConverter::PyDocConverter() : debug(false) {
+  fillStaticTables();
 }
 
 std::string PyDocConverter::formatParam(Node *n, DoxygenEntity & doxygenEntity) {
@@ -27,6 +92,7 @@ std::string PyDocConverter::formatParam(Node *n, DoxygenEntity & doxygenEntity)
   if (doxygenEntity.entityList.size() < 2) {
     /* if 'paramDescriptionEntity' is not there, ignore param. Better than crash!
        TODO: log error! */
+
     return "";
   }
 
@@ -91,67 +157,60 @@ std::string PyDocConverter::justifyString(std::string documentString, int indent
 }
 
 std::string PyDocConverter::translateSubtree(DoxygenEntity & doxygenEntity) {
-  std::string returnedString;
+  std::string translatedComment;
+
   if (doxygenEntity.isLeaf)
-    return doxygenEntity.data + " ";
-  else {
-    returnedString += doxygenEntity.data;
-    std::list < DoxygenEntity >::iterator p = doxygenEntity.entityList.begin();
-    while (p != doxygenEntity.entityList.end()) {
-      returnedString += translateSubtree(*p);
-      p++;
+    return translatedComment;
+
+  std::string currentSection;
+  std::list < DoxygenEntity >::iterator p = doxygenEntity.entityList.begin();
+  while (p != doxygenEntity.entityList.end()) {
+    std::map<std::string, std::string>::iterator it;
+    it = sectionTitles.find(p->typeOfEntity);
+    if (it != sectionTitles.end()) {
+      if (it->second != currentSection) {
+        currentSection = it->second;
+        translatedComment += currentSection + "\n";
+      }
     }
-  }
-  return returnedString;
-}
-
-std::string PyDocConverter::translateEntity(Node *n, DoxygenEntity & doxyEntity) {
-  if (doxyEntity.typeOfEntity.compare("partofdescription") == 0)
-    return justifyString(std::string(translateSubtree(doxyEntity)), 0);
-
-  if ((doxyEntity.typeOfEntity.compare("brief") == 0)
-      || (doxyEntity.typeOfEntity.compare("details") == 0))
-    return justifyString(std::string(translateSubtree(doxyEntity)), 0) + "\n";
-
-  if (doxyEntity.typeOfEntity.compare("plainstd::string") == 0
-      || doxyEntity.typeOfEntity.compare("deprecated") == 0
-      || doxyEntity.typeOfEntity.compare("brief") == 0)
-    return justifyString(doxyEntity.data, 0) + "\n";
-
-  if (doxyEntity.typeOfEntity.compare("param") == 0)
-    return formatParam(n, doxyEntity);
-
-  if (doxyEntity.typeOfEntity.compare("return") == 0)
-    return formatReturnDescription(n, doxyEntity);
-
-  if (doxyEntity.typeOfEntity.compare("author") == 0
-      || doxyEntity.typeOfEntity.compare("param") == 0
-      || doxyEntity.typeOfEntity.compare("since") == 0
-      || doxyEntity.typeOfEntity.compare("version") == 0
-      || doxyEntity.typeOfEntity.compare("exception") == 0
-      || doxyEntity.typeOfEntity.compare("deprecated") == 0
-      || doxyEntity.typeOfEntity.compare("sa") == 0)
-    return "";
-
-  return justifyString(doxyEntity.data);
-}
-
-std::string PyDocConverter::processEntityList(Node *n, std::list < DoxygenEntity > &entityList) {
-  std::string result;
-  bool inParamsSection = false;
-
-  for (std::list < DoxygenEntity >::iterator entityIterator = entityList.begin(); entityIterator != entityList.end();) {
-    if (entityIterator->typeOfEntity.compare("param") == 0 && !inParamsSection) {
-      inParamsSection = true;
-      result += "\nArguments:\n";
-    } else if (entityIterator->typeOfEntity.compare("param") != 0 && inParamsSection)
-      inParamsSection = false;
-
-    result += translateEntity(n, *entityIterator);
-    entityIterator++;
+    translateEntity(*p, translatedComment);
+    translateSubtree(*p);
+    p++;
   }
 
-  return result;
+  return translatedComment;
+}
+
+void PyDocConverter::translateEntity(DoxygenEntity & doxyEntity, std::string &translatedComment) {
+  // check if we have needed handler and call it
+  std::map<std::string, std::pair<tagHandler, std::string > >::iterator it;
+  it = tagHandlers.find(doxyEntity.typeOfEntity);
+  if (it!=tagHandlers.end())
+    (this->*(it->second.first))(doxyEntity, translatedComment, it->second.second);
+}
+
+void PyDocConverter::handleParagraph(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
+  translatedComment += translateSubtree(tag);
+}
+void PyDocConverter::handlePlainString(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
+  translatedComment += tag.data;
+  if (tag.data.size() && tag.data[tag.data.size()-1] != ' ')
+    translatedComment += "";
+}
+void PyDocConverter::handleTagMessage(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
+  std::string dummy;
+  translatedComment += arg;
+  handleParagraph(tag, translatedComment, dummy);
+}
+void PyDocConverter::handleTagChar(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
+  translatedComment += tag.typeOfEntity;
+}
+void PyDocConverter::handleTagWrap(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
+  if (tag.entityList.size()) // do not include empty tags
+    translatedComment += arg + translateSubtree(tag) + arg;
+}
+void PyDocConverter::handleNewLine(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
+  translatedComment += "\n";
 }
 
 String *PyDocConverter::makeDocumentation(Node *n) {
@@ -171,7 +230,8 @@ String *PyDocConverter::makeDocumentation(Node *n) {
       documentation = getDoxygenComment(n);
       if (!Swig_is_generated_overload(n) && documentation) {
 	std::list < DoxygenEntity > entityList = parser.createTree(Char(documentation), Char(Getfile(documentation)), Getline(documentation));
-	allDocumentation.push_back(processEntityList(n, entityList));
+	DoxygenEntity root("root", entityList);
+	allDocumentation.push_back(translateSubtree(root));
       }
       n = Getattr(n, "sym:nextSibling");
     }
@@ -180,10 +240,10 @@ String *PyDocConverter::makeDocumentation(Node *n) {
     if (allDocumentation.size() > 1) {
       std::ostringstream concatDocString;
       for (int realOverloadCount = 0; realOverloadCount < (int) allDocumentation.size(); realOverloadCount++) {
-	concatDocString << generateDivider();
-	concatDocString << "Overload " << (realOverloadCount + 1) << ":" << std::endl;
-	concatDocString << generateDivider();
-	concatDocString << allDocumentation[realOverloadCount] << std::endl;
+        concatDocString << generateDivider();
+        concatDocString << "Overload " << (realOverloadCount + 1) << ":" << std::endl;
+        concatDocString << generateDivider();
+        concatDocString << allDocumentation[realOverloadCount] << std::endl;
       }
       pyDocString = concatDocString.str();
     } else if (allDocumentation.size() == 1) {
@@ -195,7 +255,8 @@ String *PyDocConverter::makeDocumentation(Node *n) {
     documentation = getDoxygenComment(n);
     if (documentation != NULL) {
       std::list < DoxygenEntity > entityList = parser.createTree(Char(documentation), Char(Getfile(documentation)), Getline(documentation));
-      pyDocString = processEntityList(n, entityList);
+      DoxygenEntity root("root", entityList);
+      pyDocString = translateSubtree(root);
     }
   }
 
@@ -216,9 +277,6 @@ String *PyDocConverter::makeDocumentation(Node *n) {
 }
 
 std::string PyDocConverter::generateDivider() {
-  std::ostringstream dividerString;
-  for (int i = 0; i < DOC_STRING_LENGTH; i++)
-    dividerString << '-';
-  dividerString << std::endl;
-  return dividerString.str();
+  static string dividerString('-', DOC_STRING_LENGTH);
+  return dividerString;
 }
diff --git a/Source/DoxygenTranslator/src/PyDocConverter.h b/Source/DoxygenTranslator/src/PyDocConverter.h
index 2d910c8f9..319f62875 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.h
+++ b/Source/DoxygenTranslator/src/PyDocConverter.h
@@ -29,14 +29,6 @@ public:
   String *makeDocumentation(Node *node);
 
 protected:
-
-  /*
-   * Process the contents of the entity list producing a documentation string.
-   * @param node The parse tree node that the entity list relates to.
-   * @param entityList The entity list to process
-   */
-  std::string processEntityList(Node *node, std::list < DoxygenEntity > &entityList);
-
   /*
    * Format the doxygen comment relating to a function or method parameter
    * @param node The parse tree node that the parameter relates to.
@@ -61,7 +53,53 @@ protected:
   std::string justifyString(std::string unformattedLine, int indent = 0, int maxWidth = DOC_STRING_LENGTH);
 
   std::string translateSubtree(DoxygenEntity & doxygenEntity);
-  std::string translateEntity(Node *n, DoxygenEntity & doxyEntity);
+  void translateEntity(DoxygenEntity & doxyEntity, std::string &translatedComment);
+
+  /*
+   * Typedef for the function that handles one tag
+   * arg - some string argument to easily pass it through lookup table
+   */
+  typedef void (PyDocConverter::*tagHandler)(DoxygenEntity &tag,
+      std::string &translatedComment, std::string &arg);
+
+  /*
+   * Wrap the command data with the some string
+   * arg - string to wrap with, like '_' or '*'
+   */
+  void handleTagWrap(DoxygenEntity &tag, std::string &translatedComment, std::string &arg);
+  /*
+   * Just prints new line
+   */
+  void handleNewLine(DoxygenEntity &tag, std::string &translatedComment, std::string &arg);
+  /*
+   * Print the name of tag to the output, used for escape-commands
+   */
+  void handleTagChar(DoxygenEntity &tag, std::string &translatedComment, std::string &arg);
+  /*
+   * Print only the content and strip original tag
+   */
+  void handleParagraph(DoxygenEntity &tag, std::string &translatedComment, std::string &arg);
+  /*
+   * Print only data part of code
+   */
+  void handlePlainString(DoxygenEntity &tag, std::string &translatedComment, std::string &arg);
+  /*
+   * Print the if-elseif-else-endif section
+   */
+  void handleTagIf(DoxygenEntity &tag, std::string &translatedComment, std::string &arg);
+  /*
+   * Prints the specified message, than the contents of the tag
+   * arg - message
+   */
+  void handleTagMessage(DoxygenEntity &tag, std::string &translatedComment, std::string &arg);
+  /*
+   * Insert 'Image: ...'
+   */
+  void handleTagImage(DoxygenEntity &tag, std::string &translatedComment, std::string &arg);
+  /*
+   * Insert 'Title: ...'
+   */
+  void handleTagPar(DoxygenEntity &tag, std::string &translatedComment, std::string &arg);
 
   /*
    * Utility method to generate a diving line for a documentation string.
@@ -70,6 +108,13 @@ protected:
 
 private:
   bool debug;
+  // temporary thing, should be refactored somehow
+  Node *currentNode;
+  // this contains the handler pointer and one string argument
+  static std::map<std::string, std::pair<tagHandler, std::string> > tagHandlers;
+  // this cointains the sectins titiles, like 'Arguments:' or 'Notes:', that are printed only once
+  static std::map<std::string, std::string> sectionTitles;
+  void fillStaticTables();
 };
 
 #endif

From b23cb40cf94ee6a5c1f2e818c30beb0ca9f3862b Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Thu, 19 Jul 2012 16:05:46 +0000
Subject: [PATCH 093/314] Added some doxygen tests, currently with no runtime
 parts

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13333 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Examples/test-suite/common.mk                 |  2 +
 Examples/test-suite/doxygen_basic_translate.i | 51 +++++++++++++++++++
 .../test-suite/doxygen_translate_all_tags.i   |  2 +-
 3 files changed, 54 insertions(+), 1 deletion(-)

diff --git a/Examples/test-suite/common.mk b/Examples/test-suite/common.mk
index 9f91cec8c..eb8f7b03a 100644
--- a/Examples/test-suite/common.mk
+++ b/Examples/test-suite/common.mk
@@ -188,7 +188,9 @@ CPP_TEST_CASES += \
 	director_wombat \
 	disown \
 	doxygen_parsing \
+	doxygen_basic_translate \
 	doxygen_translate \
+	doxygen_translate_all_tags \
 	dynamic_cast \
 	empty \
 	enum_rename \
diff --git a/Examples/test-suite/doxygen_basic_translate.i b/Examples/test-suite/doxygen_basic_translate.i
index af449eb49..c06cbddc9 100644
--- a/Examples/test-suite/doxygen_basic_translate.i
+++ b/Examples/test-suite/doxygen_basic_translate.i
@@ -15,4 +15,55 @@ int function()
 {
 }
 
+/**
+ * A test of a very very very very very very very very very very very very very very very very
+ * very very very very very long comment string.
+ */
+int function2()
+{
+}
+
+/**
+ * A test for overloaded functions
+ * This is function \b one
+ */
+int function3(int a)
+{
+}
+
+/**
+ * A test for overloaded functions
+ * This is function \b two
+ */
+int function3(int a, int b)
+{
+}
+
+/**
+ * A test of some mixed tag usage
+ * \if CONDITION
+ * This \a code fragment shows us something \.
+ * \par Minuses:
+ * \arg it's senseless
+ * \arg it's stupid
+ * \arg it's null
+ *
+ * \warning This may not work as expected
+ *
+ * \code
+ * int main() { while(true); }
+ * \endcode
+ * \endif
+ */
+int function4()
+{
+}
+
+/**
+ * Test for default args
+ */
+int function5(int a=42)
+{
+}
+
 %}
diff --git a/Examples/test-suite/doxygen_translate_all_tags.i b/Examples/test-suite/doxygen_translate_all_tags.i
index ae66cc5de..cb3332179 100644
--- a/Examples/test-suite/doxygen_translate_all_tags.i
+++ b/Examples/test-suite/doxygen_translate_all_tags.i
@@ -1,4 +1,4 @@
-%module doxygen_translate
+%module doxygen_translate_all_tags
 
 %inline %{
 

From 2ae18d9a0fe1e5a37684a0338580dd6f7f59cc62 Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Thu, 19 Jul 2012 16:06:48 +0000
Subject: [PATCH 094/314] Some test fixes to the java comment translator

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13334 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Source/DoxygenTranslator/src/JavaDocConverter.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.cpp b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
index 42b5fcb80..62b9762f4 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
@@ -102,6 +102,7 @@ JavaDocConverter::JavaDocConverter() : debug(false) {
 
 std::string JavaDocConverter::formatCommand(std::string unformattedLine, int indent) {
   std::string formattedLines;
+  return unformattedLine;
   int lastPosition = 0;
   int i = 0;
   int isFirstLine = 1;
@@ -203,7 +204,6 @@ void JavaDocConverter::handleTagIf(DoxygenEntity& tag, std::string& translatedCo
   translatedComment += arg;
   if (tag.entityList.size()) {
     translatedComment += tag.entityList.begin()->data;
-    //handleNewLine(tag, translatedComment, dummy);
     tag.entityList.pop_front();
     translatedComment += " {" + translateSubtree(tag) + "}";
   }

From c56d5fcf90a1ddbc6e27c0c0c8631b8208578da7 Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Thu, 19 Jul 2012 16:08:11 +0000
Subject: [PATCH 095/314] Some code refactoring and all of the doxy commands
 are working for the python comment translator

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13335 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 .../DoxygenTranslator/src/PyDocConverter.cpp  | 143 ++++++++++--------
 Source/DoxygenTranslator/src/PyDocConverter.h |  39 ++---
 2 files changed, 103 insertions(+), 79 deletions(-)

diff --git a/Source/DoxygenTranslator/src/PyDocConverter.cpp b/Source/DoxygenTranslator/src/PyDocConverter.cpp
index 3dd42677e..5b6f39adf 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/PyDocConverter.cpp
@@ -25,10 +25,14 @@ void PyDocConverter::fillStaticTables() {
   if (tagHandlers.size()) // fill only once
     return;
 
+  // table of section titles, they are printed only once
+  // for each group of specified doxygen commands
   sectionTitles["author"] = "Authors:";
   sectionTitles["authors"] = "Authors:";
   sectionTitles["copyright"] = "Copyright:";
   sectionTitles["deprecated"] = "Deprecated:";
+  sectionTitles["example"] = "Example:";
+  sectionTitles["exception"] = "Throws:";
   sectionTitles["param"] = "Arguments:";
   sectionTitles["tparam"] = "Arguments:";
   sectionTitles["note"] = "Notes:";
@@ -38,6 +42,13 @@ void PyDocConverter::fillStaticTables() {
   sectionTitles["result"] = "Return:";
   sectionTitles["return"] = "Return:";
   sectionTitles["returns"] = "Return:";
+  sectionTitles["sa"] = "See also:";
+  sectionTitles["see"] = "See also:";
+  sectionTitles["since"] = "Since:";
+  sectionTitles["throw"] = "Throws:";
+  sectionTitles["throws"] = "Throws:";
+  sectionTitles["todo"] = "TODO:";
+  sectionTitles["version"] = "Version:";
 
   // these commands insert HTML tags
   tagHandlers["a"] = make_pair(&PyDocConverter::handleTagWrap, "_");
@@ -57,25 +68,22 @@ void PyDocConverter::fillStaticTables() {
   tagHandlers["\""] = make_pair(&PyDocConverter::handleTagChar, "");
   tagHandlers["."] = make_pair(&PyDocConverter::handleTagChar, "");
   tagHandlers["::"] = make_pair(&PyDocConverter::handleTagChar, "");
-  // these commands are stripped out
-  tagHandlers["attention"] = make_pair(&PyDocConverter::handleParagraph, "");
-  tagHandlers["author"] = make_pair(&PyDocConverter::handleParagraph, "");
-  tagHandlers["authors"] = make_pair(&PyDocConverter::handleParagraph, "");
-  tagHandlers["brief"] = make_pair(&PyDocConverter::handleParagraph, "");
-  tagHandlers["c"] = make_pair(&PyDocConverter::handleParagraph, "");
-  tagHandlers["code"] = make_pair(&PyDocConverter::handleParagraph, "");
-  tagHandlers["copyright"] = make_pair(&PyDocConverter::handleParagraph, "");
-  tagHandlers["date"] = make_pair(&PyDocConverter::handleParagraph, "");
-  tagHandlers["deprecated"] = make_pair(&PyDocConverter::handleParagraph, "");
-  tagHandlers["details"] = make_pair(&PyDocConverter::handleParagraph, "");
-  tagHandlers["note"] = make_pair(&PyDocConverter::handleParagraph, "");
-  tagHandlers["partofdescription"] = make_pair(&PyDocConverter::handleParagraph, "");
-  tagHandlers["remark"] = make_pair(&PyDocConverter::handleParagraph, "");
-  tagHandlers["remarks"] = make_pair(&PyDocConverter::handleParagraph, "");
-  tagHandlers["warning"] = make_pair(&PyDocConverter::handleParagraph, "");
   // these commands have special handlers
+  tagHandlers["arg"] = make_pair(&PyDocConverter::handleTagMessage, " -");
   tagHandlers["cond"] = make_pair(&PyDocConverter::handleTagMessage, "Conditional comment: ");
+  tagHandlers["else"] = make_pair(&PyDocConverter::handleTagIf, "Else: ");
+  tagHandlers["elseif"] = make_pair(&PyDocConverter::handleTagIf, "Else if: ");
   tagHandlers["endcond"] = make_pair(&PyDocConverter::handleTagMessage, "End of conditional comment.");
+  tagHandlers["if"] = make_pair(&PyDocConverter::handleTagIf, "If: ");
+  tagHandlers["ifnot"] = make_pair(&PyDocConverter::handleTagIf, "If not: ");
+  tagHandlers["image"] = make_pair(&PyDocConverter::handleTagMessage, "Image: ");
+  tagHandlers["li"] = make_pair(&PyDocConverter::handleTagMessage, " -");
+  tagHandlers["overload"] = make_pair(&PyDocConverter::handleTagMessage, "This is an overloaded member function, provided for"
+      " convenience.\nIt differs from the above function only in what"
+      " argument(s) it accepts.");
+  tagHandlers["par"] = make_pair(&PyDocConverter::handleTagPar, "");
+  tagHandlers["param"] = make_pair(&PyDocConverter::handleTagParam, "");
+  tagHandlers["tparam"] = make_pair(&PyDocConverter::handleTagParam, "");
   // this command just prints it's contents
   // (it is internal command of swig's parser, contains plain text)
   tagHandlers["plainstd::string"] = make_pair(&PyDocConverter::handlePlainString, "");
@@ -87,38 +95,13 @@ PyDocConverter::PyDocConverter() : debug(false) {
   fillStaticTables();
 }
 
-std::string PyDocConverter::formatParam(Node *n, DoxygenEntity & doxygenEntity) {
-
-  if (doxygenEntity.entityList.size() < 2) {
-    /* if 'paramDescriptionEntity' is not there, ignore param. Better than crash!
-       TODO: log error! */
-
-    return "";
-  }
-
-  ParmList *plist = CopyParmList(Getattr(n, "parms"));
+std::string PyDocConverter::getParamType(std::string param) {
+  ParmList *plist = CopyParmList(Getattr(currentNode, "parms"));
   Parm *p = NULL;
-
-  DoxygenEntity & paramNameEntity = *doxygenEntity.entityList.begin();
-  DoxygenEntity & paramDescriptionEntity = *(++doxygenEntity.entityList.begin());
-
-  std::string result;
-  std::string paramDescription = justifyString(paramDescriptionEntity.data, DOC_PARAM_STRING_LENGTH);
-
   for (p = plist; p;) {
-    
-    //Swig_print(p, 1);
-    if (Char(Getattr(p, "name")) == paramNameEntity.data) {
-      std::string name = Char(Swig_name_make(n, 0, Getattr(p, "name"), 0, 0));
-      std::string type = Char(Swig_name_make(n, 0, Getattr(p, "type"), 0, 0));
-
-      result = name + " (" + type + ") ";
-      if (result.size() < (DOC_PARAM_STRING_LENGTH - 3)) {
-	/* do not cut info away - it is better to have not so nice output than type information missing. */
-	result.resize(DOC_PARAM_STRING_LENGTH - 3, ' ');
-      }
-      result += "-- " + paramDescription.substr(DOC_PARAM_STRING_LENGTH);
-      break;
+    if (Char(Getattr(p, "name")) == param) {
+      std::string type = Char(Swig_name_make(currentNode, 0, Getattr(p, "type"), 0, 0));
+      return type;
     }
     /*
      * doesn't seem to work always: in some cases (especially for 'self' parameters)
@@ -127,18 +110,12 @@ std::string PyDocConverter::formatParam(Node *n, DoxygenEntity & doxygenEntity)
     //p = Getattr(p, "tmap:in") ? Getattr(p, "tmap:in:next") : nextSibling(p);
     p = nextSibling(p);
   }
-
   Delete(plist);
-  return result;
-}
-
-std::string PyDocConverter::formatReturnDescription(Node *node, DoxygenEntity & doxygenEntity) {
-#pragma unused(node)
-  return "\nResult:\n" + justifyString(translateSubtree(doxygenEntity));
+  return "";
 }
 
 std::string PyDocConverter::justifyString(std::string documentString, int indent, int maxWidth) {
-  std::ostringstream formattedString;
+  std::string formattedString;
   std::string currentLine;
 
   for (std::string::iterator stringPosition = documentString.begin(); stringPosition != documentString.end(); ++stringPosition) {
@@ -147,13 +124,17 @@ std::string PyDocConverter::justifyString(std::string documentString, int indent
 
     currentLine += *stringPosition;
 
-    if (*stringPosition == ' ' && (int) currentLine.size() >= maxWidth || (stringPosition + 1) == documentString.end()) {
-      formattedString << currentLine << std::endl;
+    if (iswspace(*stringPosition) && (int) currentLine.size() >= maxWidth || (stringPosition + 1) == documentString.end()) {
+      formattedString += currentLine + "\n";
       currentLine = "";
     }
   }
 
-  return formattedString.str();
+  // strip the last endl
+  if (formattedString.size())
+    formattedString = formattedString.substr(0, formattedString.size() - 1);
+
+  return formattedString;
 }
 
 std::string PyDocConverter::translateSubtree(DoxygenEntity & doxygenEntity) {
@@ -183,14 +164,17 @@ std::string PyDocConverter::translateSubtree(DoxygenEntity & doxygenEntity) {
 
 void PyDocConverter::translateEntity(DoxygenEntity & doxyEntity, std::string &translatedComment) {
   // check if we have needed handler and call it
+  std::string dummy;
   std::map<std::string, std::pair<tagHandler, std::string > >::iterator it;
   it = tagHandlers.find(doxyEntity.typeOfEntity);
   if (it!=tagHandlers.end())
     (this->*(it->second.first))(doxyEntity, translatedComment, it->second.second);
+  else
+    handleParagraph(doxyEntity, translatedComment, dummy);
 }
 
 void PyDocConverter::handleParagraph(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
-  translatedComment += translateSubtree(tag);
+  translatedComment += justifyString(translateSubtree(tag), 0);
 }
 void PyDocConverter::handlePlainString(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
   translatedComment += tag.data;
@@ -205,6 +189,42 @@ void PyDocConverter::handleTagMessage(DoxygenEntity& tag, std::string& translate
 void PyDocConverter::handleTagChar(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
   translatedComment += tag.typeOfEntity;
 }
+void PyDocConverter::handleTagIf(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
+  std::string dummy;
+  translatedComment += arg;
+  if (tag.entityList.size()) {
+    translatedComment += tag.entityList.begin()->data;
+    tag.entityList.pop_front();
+    translatedComment += " {" + translateSubtree(tag) + "}";
+  }
+}
+void PyDocConverter::handleTagPar(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
+  std::string dummy;
+  translatedComment += "Title: ";
+  if (tag.entityList.size())
+    translatedComment += tag.entityList.begin()->data;
+  tag.entityList.pop_front();
+  handleParagraph(tag, translatedComment, dummy);
+}
+void PyDocConverter::handleTagParam(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
+  std::string dummy;
+  if (tag.entityList.size() < 2) {
+    // TODO: log error
+    return;
+  }
+  DoxygenEntity paramNameEntity = *tag.entityList.begin();
+  std::string paramDescription = "-- ";
+
+  tag.entityList.pop_front();
+  handleParagraph(tag, paramDescription, dummy);
+  paramDescription = justifyString(paramDescription, DOC_PARAM_STRING_LENGTH);
+
+  std::string paramType = getParamType(paramNameEntity.data);
+  if (!paramType.size())
+    paramType = "none";
+
+  translatedComment += paramNameEntity.data + " (" + paramType + ")" + paramDescription;
+}
 void PyDocConverter::handleTagWrap(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
   if (tag.entityList.size()) // do not include empty tags
     translatedComment += arg + translateSubtree(tag) + arg;
@@ -217,6 +237,9 @@ String *PyDocConverter::makeDocumentation(Node *n) {
   String *documentation;
   std::string pyDocString, result;
 
+  // store the node, we may need it later
+  currentNode = n;
+
   // for overloaded functions we must concat documentation for underlying overloads
   if (Checkattr(n, "kind", "function") && Getattr(n, "sym:overloaded")) {
     // rewind to the first overload
@@ -240,7 +263,7 @@ String *PyDocConverter::makeDocumentation(Node *n) {
     if (allDocumentation.size() > 1) {
       std::ostringstream concatDocString;
       for (int realOverloadCount = 0; realOverloadCount < (int) allDocumentation.size(); realOverloadCount++) {
-        concatDocString << generateDivider();
+        concatDocString << generateDivider() << std::endl;
         concatDocString << "Overload " << (realOverloadCount + 1) << ":" << std::endl;
         concatDocString << generateDivider();
         concatDocString << allDocumentation[realOverloadCount] << std::endl;
@@ -277,6 +300,6 @@ String *PyDocConverter::makeDocumentation(Node *n) {
 }
 
 std::string PyDocConverter::generateDivider() {
-  static string dividerString('-', DOC_STRING_LENGTH);
+  static string dividerString(DOC_STRING_LENGTH, '-');
   return dividerString;
 }
diff --git a/Source/DoxygenTranslator/src/PyDocConverter.h b/Source/DoxygenTranslator/src/PyDocConverter.h
index 319f62875..f14a130ac 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.h
+++ b/Source/DoxygenTranslator/src/PyDocConverter.h
@@ -29,20 +29,6 @@ public:
   String *makeDocumentation(Node *node);
 
 protected:
-  /*
-   * Format the doxygen comment relating to a function or method parameter
-   * @param node The parse tree node that the parameter relates to.
-   * @param doxygenEntity The doxygen entity relating to the parameter docstring.
-   */
-  std::string formatParam(Node *node, DoxygenEntity & doxygenEntity);
-
-  /*
-   * Format the doxygen comment relating to the return value for a method or function.
-   * @param node The parse tree node that the parameter relates to.
-   * @param doxygenEntity The doxygen entity relating to the parameter docstring.
-   */
-  std::string formatReturnDescription(Node *node, DoxygenEntity & doxygenEntity);
-
   /*
    * Format a string so it is justified and split over several lines 
    * not exeeding a given length.
@@ -51,8 +37,16 @@ protected:
    * @param maxWidth The approximate maximum line width.
    */
   std::string justifyString(std::string unformattedLine, int indent = 0, int maxWidth = DOC_STRING_LENGTH);
-
+  /*
+   * Translate every entity in a tree, also manages sections
+   * display. Prints title for every group of tags that have
+   * a section title associated with them
+   */
   std::string translateSubtree(DoxygenEntity & doxygenEntity);
+  /*
+   * Translate one entity with the appropriate handler, acording
+   * to the tagHandlers
+   */
   void translateEntity(DoxygenEntity & doxyEntity, std::string &translatedComment);
 
   /*
@@ -92,20 +86,27 @@ protected:
    * arg - message
    */
   void handleTagMessage(DoxygenEntity &tag, std::string &translatedComment, std::string &arg);
-  /*
-   * Insert 'Image: ...'
-   */
-  void handleTagImage(DoxygenEntity &tag, std::string &translatedComment, std::string &arg);
   /*
    * Insert 'Title: ...'
    */
   void handleTagPar(DoxygenEntity &tag, std::string &translatedComment, std::string &arg);
+  /*
+   * Format nice param description with type information
+   */
+  void handleTagParam(DoxygenEntity &tag, std::string &translatedComment, std::string &arg);
 
   /*
    * Utility method to generate a diving line for a documentation string.
    */
   std::string generateDivider();
 
+  /*
+   * Simple helper function that calculates correct parameter type
+   * of the node stored in 'currentNode'
+   * If param with specified name is not found, empty string is returned
+   */
+  std::string getParamType(std::string name);
+
 private:
   bool debug;
   // temporary thing, should be refactored somehow

From 791ea1ba3a5a6f697fc873de7e9d1a15eb9cdab0 Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Mon, 23 Jul 2012 10:52:59 +0000
Subject: [PATCH 096/314] Enhanced commentParser.java, improved string
 comparison (now ignoring whitespaces), improved comments text output

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13342 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Examples/test-suite/java/commentParser.java | 30 ++++++++++++++++-----
 1 file changed, 23 insertions(+), 7 deletions(-)

diff --git a/Examples/test-suite/java/commentParser.java b/Examples/test-suite/java/commentParser.java
index 93785669e..94beb8c2f 100644
--- a/Examples/test-suite/java/commentParser.java
+++ b/Examples/test-suite/java/commentParser.java
@@ -17,19 +17,19 @@ public class commentParser {
 		for (ClassDoc classDoc : root.classes()) {
 
 			if (classDoc.getRawCommentText().length() > 0)
-				parsedComments.put(classDoc.name(), classDoc.getRawCommentText());
+				parsedComments.put(classDoc.qualifiedName(), classDoc.getRawCommentText());
 
 			for (FieldDoc f : classDoc.enumConstants()) {
 				if (f.getRawCommentText().length() > 0)
-					parsedComments.put(f.name(), f.getRawCommentText());
+					parsedComments.put(f.qualifiedName(), f.getRawCommentText());
 			}
 			for (FieldDoc f : classDoc.fields()) {
 				if (f.getRawCommentText().length() > 0)
-					parsedComments.put(f.name(), f.getRawCommentText());
+					parsedComments.put(f.qualifiedName(), f.getRawCommentText());
 			}
 			for (MethodDoc m : classDoc.methods()) {
 				if (m.getRawCommentText().length() > 0)
-					parsedComments.put(m.name(), m.getRawCommentText());
+					parsedComments.put(m.toString(), m.getRawCommentText());
 			}
 		}
 		return true;
@@ -42,9 +42,21 @@ public class commentParser {
 		while (it.hasNext())
 		{
 			Entry<String, String> e = (Entry<String, String>) it.next();
+			String actualStr = e.getValue();
+			String wantedStr = wantedComments.get(e.getKey());
+			// this may be weird, but I don't know any more effective solution
+			actualStr = actualStr.replace(" ", "");
+			actualStr = actualStr.replace("\n", "");
+			actualStr = actualStr.replace("\t", "");
+			if (wantedStr != null) {
+				wantedStr = wantedStr.replace(" ", "");
+				wantedStr = wantedStr.replace("\n", "");
+				wantedStr = wantedStr.replace("\t", "");
+			}
 
-			if (!e.getValue().equals(wantedComments.get(e.getKey()))) {
+			if (!actualStr.equals(wantedStr)) {
 				System.out.println("Documentation comments for " + e.getKey() + " does not match: ");
+				// here we print original strings, for nicer output
 				System.out.println("\texpected:"+wantedComments.get(e.getKey()));
 				System.out.println("\tgot:\t"+e.getValue());
 				errorCount++;
@@ -64,7 +76,11 @@ public class commentParser {
 		while (it.hasNext())
 		{
 			Entry<String, String> e = (Entry<String, String>) it.next();
-			System.out.format("wantedComments.put(\"%s\", \"%s\");\n", e.getKey(), e.getValue());
+			String commentText = e.getValue();
+			commentText = commentText.replace("\\", "\\\\");
+			commentText = commentText.replace("\"", "\\\"");
+			commentText = commentText.replace("\n", "\\n\" +\n\t\t\"");
+			System.out.format("wantedComments.put(\"%s\",\n\t\t\"%s\");\n", e.getKey(), commentText);
 		}
 	}
 	
@@ -82,4 +98,4 @@ public class commentParser {
 		
 		printCommentListForJavaSource();
 	}
-}
\ No newline at end of file
+}

From 07552d3b094daed26ec520399d94690abf850a20 Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Mon, 23 Jul 2012 11:17:42 +0000
Subject: [PATCH 097/314] Fixed ignored commands in JavaDocConverter

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13343 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Source/DoxygenTranslator/src/JavaDocConverter.cpp | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.cpp b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
index 62b9762f4..8f6725f5c 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
@@ -29,6 +29,7 @@ void JavaDocConverter::fillStaticTables() {
   tagHandlers["c"] = make_pair(&JavaDocConverter::handleTagHtml, "code");
   tagHandlers["cite"] = make_pair(&JavaDocConverter::handleTagHtml, "i");
   tagHandlers["e"] = make_pair(&JavaDocConverter::handleTagHtml, "i");
+  tagHandlers["em"] = make_pair(&JavaDocConverter::handleTagHtml, "i");
   tagHandlers["li"] = make_pair(&JavaDocConverter::handleTagHtml, "li");
   tagHandlers["p"] = make_pair(&JavaDocConverter::handleTagHtml, "code");
   // these commands insert just a single char, some of them need to be escaped
@@ -47,9 +48,17 @@ void JavaDocConverter::fillStaticTables() {
   // these commands are stripped out
   tagHandlers["attention"] = make_pair(&JavaDocConverter::handleParagraph, "");
   tagHandlers["brief"] = make_pair(&JavaDocConverter::handleParagraph, "");
+  tagHandlers["bug"] = make_pair(&JavaDocConverter::handleParagraph, "");
   tagHandlers["date"] = make_pair(&JavaDocConverter::handleParagraph, "");
   tagHandlers["details"] = make_pair(&JavaDocConverter::handleParagraph, "");
+  tagHandlers["htmlonly"] = make_pair(&JavaDocConverter::handleParagraph, "");
+  tagHandlers["invariant"] = make_pair(&JavaDocConverter::handleParagraph, "");
+  tagHandlers["latexonly"] = make_pair(&JavaDocConverter::handleParagraph, "");
+  tagHandlers["manonly"] = make_pair(&JavaDocConverter::handleParagraph, "");
   tagHandlers["partofdescription"] = make_pair(&JavaDocConverter::handleParagraph, "");
+  tagHandlers["rtfonly"] = make_pair(&JavaDocConverter::handleParagraph, "");
+  tagHandlers["short"] = make_pair(&JavaDocConverter::handleParagraph, "");
+  tagHandlers["xmlonly"] = make_pair(&JavaDocConverter::handleParagraph, "");
   // these commands are kept as-is, they are supported by JavaDoc
   tagHandlers["author"] = make_pair(&JavaDocConverter::handleTagSame, "");
   tagHandlers["authors"] = make_pair(&JavaDocConverter::handleTagSame, "author");

From 32ac8c0be4c89606a13c997eb3fdd7d9741ebe3b Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Mon, 23 Jul 2012 11:19:04 +0000
Subject: [PATCH 098/314] Added doxygen_basic_translate runtime test for java

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13344 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 .../java/doxygen_basic_translate_runme.java   | 50 +++++++++++++++++--
 1 file changed, 46 insertions(+), 4 deletions(-)

diff --git a/Examples/test-suite/java/doxygen_basic_translate_runme.java b/Examples/test-suite/java/doxygen_basic_translate_runme.java
index 34270de56..50d6cedda 100644
--- a/Examples/test-suite/java/doxygen_basic_translate_runme.java
+++ b/Examples/test-suite/java/doxygen_basic_translate_runme.java
@@ -25,10 +25,52 @@ public class doxygen_basic_translate_runme {
 
     HashMap<String, String> wantedComments = new HashMap<String, String>();
     
-    wantedComments.put("function", " Brief description.  \n The comment text  \n" +
-			   " @author\tSome author  \n" +
-			   " @return\tSome number  \n" +
-			   " @see\tfunction2  \n");
+    wantedComments.put("doxygen_basic_translate.doxygen_basic_translate.function()",
+    		" \n" +
+    		" Brief description. \n" +
+    		" \n" +
+    		" The comment text \n" +
+    		" @author Some author \n" +
+    		" @return Some number \n" +
+    		" @see function2 \n" +
+    		" \n" +
+    		"");
+    wantedComments.put("doxygen_basic_translate.doxygen_basic_translate.function2()",
+    		" A test of a very very very very very very very very very very very very very very very very \n" +
+    		" very very very very very long comment string. \n" +
+    		" \n" +
+    		"");
+    wantedComments.put("doxygen_basic_translate.doxygen_basic_translate.function4()",
+    		" A test of some mixed tag usage \n" +
+    		" If: CONDITION {\n" +
+    		" This <i>code </i>fragment shows us something . \n" +
+    		" <p alt=\"Minuses: \">\n" +
+    		" <li>it's senseless \n" +
+    		" </li><li>it's stupid \n" +
+    		" </li><li>it's null \n" +
+    		" \n" +
+    		" </li></p>Warning: This may not work as expected \n" +
+    		" \n" +
+    		" {@code \n" +
+    		"int main() { while(true); } \n" +
+    		" }\n" +
+    		" }\n" +
+    		" \n" +
+    		"");
+    wantedComments.put("doxygen_basic_translate.doxygen_basic_translate.function3(int)",
+    		" A test for overloaded functions \n" +
+    		" This is function <b>one </b>\n" +
+    		" \n" +
+    		"");
+    wantedComments.put("doxygen_basic_translate.doxygen_basic_translate.function5(int)",
+    		" Test for default args \n" +
+    		" \n" +
+    		"");
+    wantedComments.put("doxygen_basic_translate.doxygen_basic_translate.function3(int, int)",
+    		" A test for overloaded functions \n" +
+    		" This is function <b>two </b>\n" +
+    		" \n" +
+    		"");
     
     // and ask the parser to check comments for us
     System.exit(parser.check(wantedComments));

From 4c293c828282c6b95639797a17d4455b97cc2915 Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Mon, 23 Jul 2012 11:23:47 +0000
Subject: [PATCH 099/314] Enhanced and unified all java doxygen tests

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13345 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 .../doxygen_parsing_enums_proper_runme.java   |  37 ++++--
 .../doxygen_parsing_enums_simple_runme.java   |  27 +++-
 .../doxygen_parsing_enums_typesafe_runme.java |  38 ++++--
 ...oxygen_parsing_enums_typeunsafe_runme.java |  37 ++++--
 .../java/doxygen_parsing_runme.java           | 124 ++++++++++++++----
 .../doxygen_translate_all_tags_runme.java     | 120 +++++++++++++++++
 .../java/doxygen_translate_runme.java         |  10 +-
 7 files changed, 333 insertions(+), 60 deletions(-)
 create mode 100644 Examples/test-suite/java/doxygen_translate_all_tags_runme.java

diff --git a/Examples/test-suite/java/doxygen_parsing_enums_proper_runme.java b/Examples/test-suite/java/doxygen_parsing_enums_proper_runme.java
index 4531ada51..b96ee66ea 100644
--- a/Examples/test-suite/java/doxygen_parsing_enums_proper_runme.java
+++ b/Examples/test-suite/java/doxygen_parsing_enums_proper_runme.java
@@ -25,14 +25,35 @@ public class doxygen_parsing_enums_proper_runme {
 
     HashMap<String, String> wantedComments = new HashMap<String, String>();
     
-    wantedComments.put("SomeAnotherEnum", " Testing comments before enum items \n");
-    wantedComments.put("SOME_ITEM_1", " The comment for the first item \n");
-    wantedComments.put("SOME_ITEM_2", " The comment for the second item \n");
-    wantedComments.put("SOME_ITEM_3", " The comment for the third item \n");
-    wantedComments.put("SomeAnotherEnum2", " Testing comments after enum items \n");
-    wantedComments.put("SOME_ITEM_10", " Post comment for the first item \n");
-    wantedComments.put("SOME_ITEM_20", " Post comment for the second item \n");
-    wantedComments.put("SOME_ITEM_30", " Post comment for the third item \n");
+    wantedComments.put("doxygen_parsing_enums_proper.SomeAnotherEnum2.SOME_ITEM_10",
+    		"Post comment for the first item \n" +
+    		"");
+    wantedComments.put("doxygen_parsing_enums_proper.SomeAnotherEnum.SOME_ITEM_1",
+    		" The comment for the first item \n" +
+    		" \n" +
+    		"");
+    wantedComments.put("doxygen_parsing_enums_proper.SomeAnotherEnum",
+    		" Testing comments before enum items \n" +
+    		" \n" +
+    		"");
+    wantedComments.put("doxygen_parsing_enums_proper.SomeAnotherEnum2.SOME_ITEM_30",
+    		"Post comment for the third item \n" +
+    		"");
+    wantedComments.put("doxygen_parsing_enums_proper.SomeAnotherEnum2",
+    		" Testing comments after enum items \n" +
+    		" \n" +
+    		"");
+    wantedComments.put("doxygen_parsing_enums_proper.SomeAnotherEnum.SOME_ITEM_3",
+    		" The comment for the third item \n" +
+    		" \n" +
+    		"");
+    wantedComments.put("doxygen_parsing_enums_proper.SomeAnotherEnum.SOME_ITEM_2",
+    		" The comment for the second item \n" +
+    		" \n" +
+    		"");
+    wantedComments.put("doxygen_parsing_enums_proper.SomeAnotherEnum2.SOME_ITEM_20",
+    		"Post comment for the second item \n" +
+    		"");
     
     // and ask the parser to check comments for us
     System.exit(parser.check(wantedComments));
diff --git a/Examples/test-suite/java/doxygen_parsing_enums_simple_runme.java b/Examples/test-suite/java/doxygen_parsing_enums_simple_runme.java
index 7fba76d5c..cd97c9a4f 100644
--- a/Examples/test-suite/java/doxygen_parsing_enums_simple_runme.java
+++ b/Examples/test-suite/java/doxygen_parsing_enums_simple_runme.java
@@ -25,12 +25,27 @@ public class doxygen_parsing_enums_simple_runme {
 
     HashMap<String, String> wantedComments = new HashMap<String, String>();
     
-    wantedComments.put("SOME_ITEM_1", " The comment for the first item \n");
-    wantedComments.put("SOME_ITEM_2", " The comment for the second item \n");
-    wantedComments.put("SOME_ITEM_3", " The comment for the third item \n");
-    wantedComments.put("SOME_ITEM_10", " Post comment for the first item \n");
-    wantedComments.put("SOME_ITEM_20", " Post comment for the second item \n");
-    wantedComments.put("SOME_ITEM_30", " Post comment for the third item \n");
+    wantedComments.put("doxygen_parsing_enums_simple.doxygen_parsing_enums_simpleConstants.SOME_ITEM_30",
+    		"Post comment for the third item \n" +
+    		"");
+    wantedComments.put("doxygen_parsing_enums_simple.doxygen_parsing_enums_simpleConstants.SOME_ITEM_3",
+    		" The comment for the third item \n" +
+    		" \n" +
+    		"");
+    wantedComments.put("doxygen_parsing_enums_simple.doxygen_parsing_enums_simpleConstants.SOME_ITEM_2",
+    		" The comment for the second item \n" +
+    		" \n" +
+    		"");
+    wantedComments.put("doxygen_parsing_enums_simple.doxygen_parsing_enums_simpleConstants.SOME_ITEM_10",
+    		"Post comment for the first item \n" +
+    		"");
+    wantedComments.put("doxygen_parsing_enums_simple.doxygen_parsing_enums_simpleConstants.SOME_ITEM_20",
+    		"Post comment for the second item \n" +
+    		"");
+    wantedComments.put("doxygen_parsing_enums_simple.doxygen_parsing_enums_simpleConstants.SOME_ITEM_1",
+    		" The comment for the first item \n" +
+    		" \n" +
+    		"");
     
     // and ask the parser to check comments for us
     System.exit(parser.check(wantedComments));
diff --git a/Examples/test-suite/java/doxygen_parsing_enums_typesafe_runme.java b/Examples/test-suite/java/doxygen_parsing_enums_typesafe_runme.java
index f853ffb3b..85ac15fe8 100644
--- a/Examples/test-suite/java/doxygen_parsing_enums_typesafe_runme.java
+++ b/Examples/test-suite/java/doxygen_parsing_enums_typesafe_runme.java
@@ -25,14 +25,36 @@ public class doxygen_parsing_enums_typesafe_runme {
 
     HashMap<String, String> wantedComments = new HashMap<String, String>();
     
-    wantedComments.put("SomeAnotherEnum", " Testing comments before enum items \n");
-    wantedComments.put("SOME_ITEM_1", " The comment for the first item \n");
-    wantedComments.put("SOME_ITEM_2", " The comment for the second item \n");
-    wantedComments.put("SOME_ITEM_3", " The comment for the third item \n");
-    wantedComments.put("SomeAnotherEnum2", " Testing comments after enum items \n");
-    wantedComments.put("SOME_ITEM_10", " Post comment for the first item \n");
-    wantedComments.put("SOME_ITEM_20", " Post comment for the second item \n");
-    wantedComments.put("SOME_ITEM_30", " Post comment for the third item \n");
+    wantedComments.put("doxygen_parsing_enums_typesafe.SomeAnotherEnum.SOME_ITEM_1",
+    		" The comment for the first item \n" +
+    		" \n" +
+    		"");
+    wantedComments.put("doxygen_parsing_enums_typesafe.SomeAnotherEnum2",
+    		" Testing comments after enum items \n" +
+    		" \n" +
+    		"");
+    wantedComments.put("doxygen_parsing_enums_typesafe.SomeAnotherEnum.SOME_ITEM_2",
+    		" The comment for the second item \n" +
+    		" \n" +
+    		"");
+    wantedComments.put("doxygen_parsing_enums_typesafe.SomeAnotherEnum2.SOME_ITEM_20",
+    		"Post comment for the second item \n" +
+    		"");
+    wantedComments.put("doxygen_parsing_enums_typesafe.SomeAnotherEnum",
+    		" Testing comments before enum items \n" +
+    		" \n" +
+    		"");
+    wantedComments.put("doxygen_parsing_enums_typesafe.SomeAnotherEnum2.SOME_ITEM_10",
+    		"Post comment for the first item \n" +
+    		"");
+    wantedComments.put("doxygen_parsing_enums_typesafe.SomeAnotherEnum.SOME_ITEM_3",
+    		" The comment for the third item \n" +
+    		" \n" +
+    		"");
+    wantedComments.put("doxygen_parsing_enums_typesafe.SomeAnotherEnum2.SOME_ITEM_30",
+    		"Post comment for the third item \n" +
+    		"");
+
     
     // and ask the parser to check comments for us
     System.exit(parser.check(wantedComments));
diff --git a/Examples/test-suite/java/doxygen_parsing_enums_typeunsafe_runme.java b/Examples/test-suite/java/doxygen_parsing_enums_typeunsafe_runme.java
index 9788ae1d3..6f453060d 100644
--- a/Examples/test-suite/java/doxygen_parsing_enums_typeunsafe_runme.java
+++ b/Examples/test-suite/java/doxygen_parsing_enums_typeunsafe_runme.java
@@ -25,14 +25,35 @@ public class doxygen_parsing_enums_typeunsafe_runme {
 
     HashMap<String, String> wantedComments = new HashMap<String, String>();
     
-    wantedComments.put("SomeAnotherEnum", " Testing comments before enum items \n");
-    wantedComments.put("SOME_ITEM_1", " The comment for the first item \n");
-    wantedComments.put("SOME_ITEM_2", " The comment for the second item \n");
-    wantedComments.put("SOME_ITEM_3", " The comment for the third item \n");
-    wantedComments.put("SomeAnotherEnum2", " Testing comments after enum items \n");
-    wantedComments.put("SOME_ITEM_10", " Post comment for the first item \n");
-    wantedComments.put("SOME_ITEM_20", " Post comment for the second item \n");
-    wantedComments.put("SOME_ITEM_30", " Post comment for the third item \n");
+    wantedComments.put("doxygen_parsing_enums_typeunsafe.SomeAnotherEnum.SOME_ITEM_2",
+    		" The comment for the second item \n" +
+    		" \n" +
+    		"");
+    wantedComments.put("doxygen_parsing_enums_typeunsafe.SomeAnotherEnum.SOME_ITEM_3",
+    		" The comment for the third item \n" +
+    		" \n" +
+    		"");
+    wantedComments.put("doxygen_parsing_enums_typeunsafe.SomeAnotherEnum.SOME_ITEM_1",
+    		" The comment for the first item \n" +
+    		" \n" +
+    		"");
+    wantedComments.put("doxygen_parsing_enums_typeunsafe.SomeAnotherEnum2.SOME_ITEM_20",
+    		"Post comment for the second item \n" +
+    		"");
+    wantedComments.put("doxygen_parsing_enums_typeunsafe.SomeAnotherEnum",
+    		" Testing comments before enum items \n" +
+    		" \n" +
+    		"");
+    wantedComments.put("doxygen_parsing_enums_typeunsafe.SomeAnotherEnum2",
+    		" Testing comments after enum items \n" +
+    		" \n" +
+    		"");
+    wantedComments.put("doxygen_parsing_enums_typeunsafe.SomeAnotherEnum2.SOME_ITEM_30",
+    		"Post comment for the third item \n" +
+    		"");
+    wantedComments.put("doxygen_parsing_enums_typeunsafe.SomeAnotherEnum2.SOME_ITEM_10",
+    		"Post comment for the first item \n" +
+    		"");
     
     // and ask the parser to check comments for us
     System.exit(parser.check(wantedComments));
diff --git a/Examples/test-suite/java/doxygen_parsing_runme.java b/Examples/test-suite/java/doxygen_parsing_runme.java
index e0719c586..322a4e42c 100644
--- a/Examples/test-suite/java/doxygen_parsing_runme.java
+++ b/Examples/test-suite/java/doxygen_parsing_runme.java
@@ -25,31 +25,105 @@ public class doxygen_parsing_runme {
 
     HashMap<String, String> wantedComments = new HashMap<String, String>();
     
-    wantedComments.put("someFunction", " The function comment \n");
-    wantedComments.put("SomeEnum", " The enum comment \n");
-    wantedComments.put("setSomeVar", " The var comment \n");
-    wantedComments.put("getSomeVar", " The var comment \n");
-    wantedComments.put("SomeClass", " The class comment \n");
-    wantedComments.put("setClassAttr", " The class attribute comment \n");
-    wantedComments.put("getClassAttr", " The class attribute comment \n");
-    wantedComments.put("setClassAttr2", " The class attribute post-comment \n");
-    wantedComments.put("getClassAttr2", " The class attribute post-comment \n");
-    wantedComments.put("setClassAttr3", " The class attribute post-comment with details \n");
-    wantedComments.put("getClassAttr3", " The class attribute post-comment with details \n");
-    wantedComments.put("classMethod", " The class method comment \n");
-    wantedComments.put("classMethodExtended", " The class method with parameter \n @param	a Parameter a \n @param	b Parameter b \n");
-    wantedComments.put("classMethodExtended2", " The class method with parameter \n @param	a Parameter a \n @param	b Parameter b \n");
-    wantedComments.put("SomeStruct", " The struct comment \n");
-    wantedComments.put("setStructAttr", " The struct attribute comment \n");
-    wantedComments.put("getStructAttr", " The struct attribute comment \n");
-    wantedComments.put("setStructAttr2", " The struct attribute post-comment \n");
-    wantedComments.put("getStructAttr2", " The struct attribute post-comment \n");
-    wantedComments.put("setStructAttr3", " The struct attribute post-comment with details \n");
-    wantedComments.put("getStructAttr3", " The struct attribute post-comment with details \n");
-    wantedComments.put("structMethod", " The struct method comment \n");
-    wantedComments.put("structMethodExtended", " The struct method with parameter \n @param	a Parameter a \n @param	b Parameter b \n");
-    wantedComments.put("structMethodExtended2", " The struct method with parameter \n @param	a Parameter a \n @param	b Parameter b \n");
-
+    wantedComments.put("doxygen_parsing.SomeAnotherClass.getClassAttr()",
+    		" The class attribute comment \n" +
+    		" \n" +
+    		"");
+    wantedComments.put("doxygen_parsing.SomeAnotherClass.setClassAttr3(int)",
+    		"The class attribute post-comment with details \n" +
+    		"");
+    wantedComments.put("doxygen_parsing.SomeAnotherStruct.setStructAttr3(int)",
+    		"The struct attribute post-comment with details \n" +
+    		"");
+    wantedComments.put("doxygen_parsing.SomeAnotherClass.classMethodExtended2(int, int)",
+    		" The class method with parameter \n" +
+    		" \n" +
+    		" @param a Parameter a \n" +
+    		" @param b Parameter b \n" +
+    		" \n" +
+    		"");
+    wantedComments.put("doxygen_parsing.SomeStruct",
+    		" The struct comment \n" +
+    		" \n" +
+    		"");
+    wantedComments.put("doxygen_parsing.doxygen_parsing.setSomeVar(int)",
+    		" The var comment \n" +
+    		" \n" +
+    		"");
+    wantedComments.put("doxygen_parsing.SomeAnotherStruct.structMethod()",
+    		" The struct method comment \n" +
+    		" \n" +
+    		"");
+    wantedComments.put("doxygen_parsing.doxygen_parsing.someFunction()",
+    		" The function comment \n" +
+    		" \n" +
+    		"");
+    wantedComments.put("doxygen_parsing.SomeAnotherClass.classMethodExtended(int, int)",
+    		" The class method with parameter \n" +
+    		" \n" +
+    		" @param a Parameter a \n" +
+    		" @param b Parameter b \n" +
+    		"");
+    wantedComments.put("doxygen_parsing.SomeAnotherClass.setClassAttr(int)",
+    		" The class attribute comment \n" +
+    		" \n" +
+    		"");
+    wantedComments.put("doxygen_parsing.SomeAnotherStruct.structMethodExtended(int, int)",
+    		" The struct method with parameter \n" +
+    		" \n" +
+    		" @param a Parameter a \n" +
+    		" @param b Parameter b \n" +
+    		"");
+    wantedComments.put("doxygen_parsing.SomeAnotherStruct.getStructAttr()",
+    		" The struct attribute comment \n" +
+    		" \n" +
+    		"");
+    wantedComments.put("doxygen_parsing.SomeClass",
+    		" The class comment \n" +
+    		" \n" +
+    		"");
+    wantedComments.put("doxygen_parsing.SomeAnotherStruct.getStructAttr3()",
+    		"The struct attribute post-comment with details \n" +
+    		"");
+    wantedComments.put("doxygen_parsing.doxygen_parsing.getSomeVar()",
+    		" The var comment \n" +
+    		" \n" +
+    		"");
+    wantedComments.put("doxygen_parsing.SomeAnotherStruct.setStructAttr2(int)",
+    		"The struct attribute post-comment \n" +
+    		"");
+    wantedComments.put("doxygen_parsing.SomeAnotherClass.getClassAttr2()",
+    		"The class attribute post-comment \n" +
+    		"");
+    wantedComments.put("doxygen_parsing.SomeAnotherStruct.getStructAttr2()",
+    		"The struct attribute post-comment \n" +
+    		"");
+    wantedComments.put("doxygen_parsing.SomeAnotherStruct.setStructAttr(int)",
+    		" The struct attribute comment \n" +
+    		" \n" +
+    		"");
+    wantedComments.put("doxygen_parsing.SomeEnum",
+    		" The enum comment \n" +
+    		" \n" +
+    		"");
+    wantedComments.put("doxygen_parsing.SomeAnotherClass.getClassAttr3()",
+    		"The class attribute post-comment with details \n" +
+    		"");
+    wantedComments.put("doxygen_parsing.SomeAnotherClass.classMethod()",
+    		" The class method comment \n" +
+    		" \n" +
+    		"");
+    wantedComments.put("doxygen_parsing.SomeAnotherStruct.structMethodExtended2(int, int)",
+    		" The struct method with parameter \n" +
+    		" \n" +
+    		" @param a Parameter a \n" +
+    		" @param b Parameter b \n" +
+    		" \n" +
+    		"");
+    wantedComments.put("doxygen_parsing.SomeAnotherClass.setClassAttr2(int)",
+    		"The class attribute post-comment \n" +
+    		"");
+    
     // and ask the parser to check comments for us
     System.exit(parser.check(wantedComments));
   }
diff --git a/Examples/test-suite/java/doxygen_translate_all_tags_runme.java b/Examples/test-suite/java/doxygen_translate_all_tags_runme.java
new file mode 100644
index 000000000..065dfa27e
--- /dev/null
+++ b/Examples/test-suite/java/doxygen_translate_all_tags_runme.java
@@ -0,0 +1,120 @@
+
+import doxygen_translate_all_tags.*;
+import com.sun.javadoc.*;
+import java.util.HashMap;
+
+public class doxygen_translate_all_tags_runme {
+  static {
+    try {
+      System.loadLibrary("doxygen_translate_all_tags");
+    } catch (UnsatisfiedLinkError e) {
+      System.err.println("Native code library failed to load. See the chapter on Dynamic Linking Problems in the SWIG Java documentation for help.\n" + e);
+      System.exit(1);
+    }
+  }
+  
+  public static void main(String argv[]) 
+  {
+    /*
+      Here we are using internal javadoc tool, it accepts the name of the class as paramterer,
+      and calls the start() method of that class with parsed information.
+    */
+	commentParser parser = new commentParser();
+    com.sun.tools.javadoc.Main.execute("doxygen_translate_all_tags runtime test",
+	"commentParser", new String[]{"-quiet", "doxygen_translate_all_tags"});
+
+    HashMap<String, String> wantedComments = new HashMap<String, String>();
+    
+    wantedComments.put("doxygen_translate_all_tags.doxygen_translate_all_tags.function(int, float)",
+    		" <i>Hello </i>\n" +
+    		" <li>some list item \n" +
+    		" </li>This is attention! \n" +
+    		" You were warned! \n" +
+    		" @author lots of them \n" +
+    		" @author Zubr \n" +
+    		" <b>boldword </b>\n" +
+    		" Some brief description, \n" +
+    		" extended to many lines. \n" +
+    		" Not everything works right now... \n" +
+    		" <code>codeword </code>\n" +
+    		" <i>citationword </i>\n" +
+    		" {@code some test code }\n" +
+    		" Conditional comment: SOMECONDITION \n" +
+    		" Some conditional comment \n" +
+    		" End of conditional comment.\n" +
+    		" Copyright: some copyright \n" +
+    		" 1970 - 2012 \n" +
+    		" @deprecated Now use another function \n" +
+    		" This is very large \n" +
+    		" and detailed description of some thing \n" +
+    		" <i>italicword </i>\n" +
+    		" <i>emphazedWord </i>\n" +
+    		" @exception SuperError \n" +
+    		" This will only appear in hmtl \n" +
+    		" If: ANOTHERCONDITION {\n" +
+    		" First part of comment \n" +
+    		" If: SECONDCONDITION {\n" +
+    		" Nested condition text \n" +
+    		" }Else if: THIRDCONDITION {\n" +
+    		" The third condition text \n" +
+    		" }Else:  {The last text block \n" +
+    		" }\n" +
+    		" }Else:  {Second part of comment \n" +
+    		" If: CONDITION {\n" +
+    		" Second part extended \n" +
+    		" }\n" +
+    		" }\n" +
+    		" If not: SOMECONDITION {\n" +
+    		" This is printed if not \n" +
+    		" }\n" +
+    		" <img src=testImage.bmp alt=\"Hello, world!\" />\n" +
+    		" Some text \n" +
+    		" describing invariant. \n" +
+    		" This will only appear in LATeX \n" +
+    		" <ul> \n" +
+    		" <li>Some unordered list \n" +
+    		" </li><li>With lots of items \n" +
+    		" </li><li>lots of lots of items \n" +
+    		" </li></ul> \n" +
+    		" {@link someMember Some description follows }\n" +
+    		" This will only appear in man \n" +
+    		" Note: Here \n" +
+    		" is the note! \n" +
+    		" This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.\n" +
+    		" <code>someword </code>\n" +
+    		" @package superPackage \n" +
+    		" <p alt=\"The paragraph title \">\n" +
+    		" The paragraph text. \n" +
+    		" Maybe even multiline \n" +
+    		" </p>\n" +
+    		" @param a the first param \n" +
+    		" Remarks: Some remark text \n" +
+    		" Remarks: Another remarks section \n" +
+    		" @return Whatever \n" +
+    		" @return it \n" +
+    		" @return may return \n" +
+    		" This will only appear in RTF \n" +
+    		" @see someOtherMethod \n" +
+    		" @see function \n" +
+    		" Same as \n" +
+    		" brief description \n" +
+    		" @since version 0.0.0.1 \n" +
+    		" @throws superException \n" +
+    		" @throws RuntimeError \n" +
+    		" TODO: Some very important task \n" +
+    		" @param b B is mentioned again... \n" +
+    		" {@literal \n" +
+    		"very long \n" +
+    		"text with tags <sometag> \n" +
+    		" }\n" +
+    		" @version 0.0.0.2 \n" +
+    		" Warning: This is senseless! \n" +
+    		" This will only appear in XML \n" +
+    		" Here goes test of symbols: \n" +
+    		" $ @ \\ & ~ < > # % \" . :: \n" +
+    		" And here goes simple text \n" +
+    		"");
+    // and ask the parser to check comments for us
+    System.exit(parser.check(wantedComments));
+  }
+}
\ No newline at end of file
diff --git a/Examples/test-suite/java/doxygen_translate_runme.java b/Examples/test-suite/java/doxygen_translate_runme.java
index 6eec790e2..cfd62d79c 100644
--- a/Examples/test-suite/java/doxygen_translate_runme.java
+++ b/Examples/test-suite/java/doxygen_translate_runme.java
@@ -25,7 +25,8 @@ public class doxygen_translate_runme {
 
     HashMap<String, String> wantedComments = new HashMap<String, String>();
     
-    wantedComments.put("function", " <i>Hello </i>\n" +
+    wantedComments.put("doxygen_translate.doxygen_translate.function(int, float)",
+    		" <i>Hello </i>\n" +
     		" \n" +
     		" <li>some list item \n" +
     		" \n" +
@@ -91,8 +92,7 @@ public class doxygen_translate_runme {
     		" Note: Here \n" +
     		" is the note! \n" +
     		" \n" +
-    		" This is an overloaded member function, provided for convenience. \n" +
-    		" It differs from the above function only in what argument(s) it accepts.\n" +
+    		" This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.\n" +
     		" \n" +
     		" <code>someword </code>\n" +
     		" \n" +
@@ -141,8 +141,8 @@ public class doxygen_translate_runme {
     		" $ @ \\ & ~ < > # % \" . :: \n" +
     		" \n" +
     		" And here goes simple text \n" +
-    		" \n");
-    
+    		" \n" +
+    		"");
     // and ask the parser to check comments for us
     System.exit(parser.check(wantedComments));
   }

From 8a683e42d0341388a46b964572d46ecf40a69796 Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Mon, 23 Jul 2012 13:50:27 +0000
Subject: [PATCH 100/314] Fixed and updated all doxygen python tests

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13346 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 .../python/doxygen_basic_translate_runme.py   |  62 ++++
 .../python/doxygen_parsing_runme.py           |  56 +--
 .../doxygen_translate_all_tags_runme.py       | 320 ++++++++++++++++++
 .../python/doxygen_translate_runme.py         | 148 ++++++++
 4 files changed, 562 insertions(+), 24 deletions(-)
 create mode 100644 Examples/test-suite/python/doxygen_basic_translate_runme.py
 create mode 100644 Examples/test-suite/python/doxygen_translate_all_tags_runme.py
 create mode 100644 Examples/test-suite/python/doxygen_translate_runme.py

diff --git a/Examples/test-suite/python/doxygen_basic_translate_runme.py b/Examples/test-suite/python/doxygen_basic_translate_runme.py
new file mode 100644
index 000000000..95596c1f3
--- /dev/null
+++ b/Examples/test-suite/python/doxygen_basic_translate_runme.py
@@ -0,0 +1,62 @@
+#!/usr/bin/python
+
+import doxygen_basic_translate
+import string
+import sys
+
+def check(got, expected):
+  #if got is Null
+  #  raise RuntimeError('Expected comment string\n')
+  gotStr = string.replace(got, ' ', '')
+  gotStr = string.replace(gotStr, '\n', '')
+  gotStr = string.replace(gotStr, '\t', '')
+  expectedStr = string.replace(expected, ' ', '')
+  expectedStr = string.replace(expectedStr, '\n', '')
+  expectedStr = string.replace(expectedStr, '\t', '')
+  if not gotStr == expectedStr:
+    raise RuntimeError("Expected: [" + str(expected) + "]\n" + "Got     : [" + str(got) + "]\n")
+
+check(doxygen_basic_translate.function.__doc__, ''
+'  Brief description.\n'
+'  The comment text\n'
+'  Authors:\n'
+'  Some author\n'
+'  Return:\n'
+'  Some number\n'
+'  See also:\n'
+'  function2\n'
+)
+check(doxygen_basic_translate.function2.__doc__, ''
+'  A test of a very very very very very very very very very very very'
+'  very very very very very'
+'  very very very very very long comment'
+'  string.'
+)
+check(doxygen_basic_translate.function3.__doc__, ''
+'  ----------------------------------------------------------------\n'
+'  Overload 1:\n'
+'  ----------------------------------------------------------------\n'
+'  A test for overloaded functions\n'
+'  This is function __one__\n'
+'  ----------------------------------------------------------------\n'
+'  Overload 2:\n'
+'  ----------------------------------------------------------------\n'
+'  A test for overloaded functions\n'
+'  This is function __two__\n'
+)
+check(doxygen_basic_translate.function4.__doc__, ''
+'  A test of some mixed tag usage\n' 
+'  If: CONDITION {\n'
+'  This _code_fragment shows us something .\n'
+'  Title: Minuses:\n'
+'   -it\'s senseless\n'
+'   -it\'s stupid\n'
+'   -it\'s null\n'
+'  Warning:\n'
+'  This may not work as expected\n'
+'  int main() { while(true); }\n'
+'  }'
+)
+check(doxygen_basic_translate.function5.__doc__, ''
+'  Test for default args'
+)
\ No newline at end of file
diff --git a/Examples/test-suite/python/doxygen_parsing_runme.py b/Examples/test-suite/python/doxygen_parsing_runme.py
index b814a68ed..cb22bb369 100644
--- a/Examples/test-suite/python/doxygen_parsing_runme.py
+++ b/Examples/test-suite/python/doxygen_parsing_runme.py
@@ -1,39 +1,47 @@
 #!/usr/bin/python
 
 import doxygen_parsing
+import string
 import sys
-import re
 
 def check(got, expected):
-  if not re.match(str(expected), str(got)):
-    raise RuntimeError("\n" + "Expected: [" + str(expected) + "]\n" + "Got     : [" + str(got) + "]")
+  #if got is Null
+  #  raise RuntimeError('Expected comment string\n')
+  gotStr = string.replace(got, ' ', '')
+  gotStr = string.replace(gotStr, '\n', '')
+  gotStr = string.replace(gotStr, '\t', '')
+  expectedStr = string.replace(expected, ' ', '')
+  expectedStr = string.replace(expectedStr, '\n', '')
+  expectedStr = string.replace(expectedStr, '\t', '')
+  if not gotStr == expectedStr:
+    raise RuntimeError("Expected: [" + str(expected) + "]\n" + "Got     : [" + str(got) + "]\n")
 
-check(doxygen_parsing.someFunction.__doc__, '\s+The function comment\s+')
-check(doxygen_parsing.SomeClass.__doc__, '\s+The class comment\s+')
-check(doxygen_parsing.SomeStruct.__doc__, '\s+The struct comment\s+')
-check(doxygen_parsing.SomeAnotherClass.classMethod.__doc__, '\s+The class method comment\s+')
+check(doxygen_parsing.someFunction.__doc__, 'The function comment')
+check(doxygen_parsing.SomeClass.__doc__, 'The class comment')
+check(doxygen_parsing.SomeStruct.__doc__, 'The struct comment')
+check(doxygen_parsing.SomeAnotherClass.classMethod.__doc__, 'The class method comment')
 check(doxygen_parsing.SomeAnotherClass.classMethodExtended.__doc__, ''
-'\s+The class method with parameter'
-'\s+Arguments:\s+'
-'a \(int\)\s+-- Parameter a\s+'
-'b \(int\)\s+-- Parameter b\s+'
+'The class method with parameter\n'
+'Arguments:\n'
+'a (int) -- Parameter a\n'
+'b (int) -- Parameter b\n'
 )
 check(doxygen_parsing.SomeAnotherClass.classMethodExtended2.__doc__, ''
-'\s+The class method with parameter'
-'\s+Arguments:\s+'
-'a \(int\)\s+-- Parameter a\s+'
-'b \(int\)\s+-- Parameter b\s+'
+'The class method with parameter\n'
+'Arguments:\n'
+'a (int)-- Parameter a\n'
+'b (int)-- Parameter b\n'
 )
-check(doxygen_parsing.SomeAnotherStruct.structMethod.__doc__, '\s+The struct method comment\s+')
+check(doxygen_parsing.SomeAnotherStruct.structMethod.__doc__, 'The struct method comment')
 check(doxygen_parsing.SomeAnotherStruct.structMethodExtended.__doc__, ''
-'\s+The struct method with parameter'
-'\s+Arguments:\s+'
-'a \(int\)\s+-- Parameter a\s+'
-'b \(int\)\s+-- Parameter b\s+'
+'The struct method with parameter\n'
+'Arguments:\n'
+'a (int)-- Parameter a\n'
+'b (int)-- Parameter b\n'
 )
 check(doxygen_parsing.SomeAnotherStruct.structMethodExtended2.__doc__, ''
-'\s+The struct method with parameter'
-'\s+Arguments:\s+'
-'a \(int\)\s+-- Parameter a\s+'
-'b \(int\)\s+-- Parameter b\s+'
+'The struct method with parameter\n'
+'Arguments:\n'
+'a (int)-- Parameter a\n'
+'b (int)-- Parameter b\n'
 )
\ No newline at end of file
diff --git a/Examples/test-suite/python/doxygen_translate_all_tags_runme.py b/Examples/test-suite/python/doxygen_translate_all_tags_runme.py
new file mode 100644
index 000000000..768ccf1ba
--- /dev/null
+++ b/Examples/test-suite/python/doxygen_translate_all_tags_runme.py
@@ -0,0 +1,320 @@
+#!/usr/bin/python
+
+import doxygen_translate_all_tags
+import string
+import sys
+
+def check(got, expected):
+  #if got is Null
+  #  raise RuntimeError('Expected comment string\n')
+  gotStr = string.replace(got, ' ', '')
+  gotStr = string.replace(gotStr, '\n', '')
+  gotStr = string.replace(gotStr, '\t', '')
+  expectedStr = string.replace(expected, ' ', '')
+  expectedStr = string.replace(expectedStr, '\n', '')
+  expectedStr = string.replace(expectedStr, '\t', '')
+  if not gotStr == expectedStr:
+    raise RuntimeError("Expected: [" + str(expected) + "]\n" + "Got     : [" + str(got) + "]\n")
+
+check(doxygen_translate_all_tags.function.__doc__, ''
+'  _Hello_'
+''
+'  SomeLatexIndex '
+''
+'  someGroupSome title '
+''
+'  theAnchor'
+''
+'   -some list item '
+''
+'  This is attention! '
+'  You were warned! '
+''
+'  Authors:'
+'  lots of them '
+''
+'  Zubr '
+''
+'  __boldword__'
+''
+'  Some brief description, '
+'  extended to many lines. '
+''
+'  Not everything works right now... '
+''
+'  codeword'
+''
+'  someCategoryheaderFile.hheaderName'
+''
+'  \'citationword\''
+''
+'  someClassheaderFile.hheaderName'
+''
+'  some test code '
+''
+'  Conditional comment: SOMECONDITION'
+'  Some conditional comment '
+'  End of conditional comment.'
+''
+'  someClass::someMethod'
+''
+'  someClass::someMethod2'
+''
+'  someClass::someMethod3'
+''
+'  Copyright:'
+'  some copyright '
+''
+'  1970 - 2012 '
+''
+'  someDefine'
+''
+'  someGroupSome titles '
+''
+'  Deprecated:'
+'  Now use another function '
+''
+'  This is very large '
+'  and detailed description of some thing '
+''
+'  /somePath/someFolder'
+''
+'  someFile.h'
+''
+'  digraph example { '
+'  node [shape=record, fontname=Helvetica, fontsize=10]; '
+''
+'  b [ label="class B" URL="\ref B"]; '
+'  c [ label="class C" URL="\ref C"]; '
+'  b -> c [ arrowhead="open", style="dashed" ]; '
+'  } '
+''
+''
+'  dotFile.dotThe caption'
+''
+'  _italicword_'
+''
+'  emphazedWord'
+''
+'  someEnum'
+''
+'  Example:'
+'  someFile.txt'
+'  Some details on using the example '
+''
+'  Throws:'
+'  SuperError'
+''
+'  someOtherFunction'
+''
+'  file.h'
+''
+'  someFn '
+''
+'  someHeader.hHeader name'
+''
+'  htmlFile.htm'
+''
+'  This will only appear in hmtl '
+''
+'  If: ANOTHERCONDITION {'
+'  First part of comment '
+'  If: SECONDCONDITION {'
+'  Nested condition text '
+'  }Else if: THIRDCONDITION {'
+'  The third condition text '
+'  }Else:  {The last text block '
+'  }'
+'  }Else:  {Second part of comment '
+'  If: CONDITION {'
+'  Second part extended '
+'  }'
+'  }'
+''
+'  If not: SOMECONDITION {'
+'  This is printed if not '
+'  }'
+''
+'  Image: htmltestImage.bmpHello, world!asd=10qwe'
+''
+'  someFunction'
+''
+'  header.h'
+''
+'  header2.h'
+''
+'  someGroupanotherGroup'
+''
+'  Some text '
+'  describing invariant. '
+''
+'  someInterfacesomeHeader.hHeader name'
+''
+'  This will only appear in LATeX '
+''
+'  <ul> '
+''
+'   -Some unordered list '
+'   -With lots of items '
+'   -lots of lots of items '
+''
+'  </ul> '
+''
+'  example '
+''
+'  someMember Some description follows '
+''
+'  Sometitle '
+''
+'  This will only appear in man '
+''
+'  someThing'
+''
+'  Sender,Receiver; '
+'  Sender->Receiver [label="Command()", URL="\ref '
+'  Receiver::Command()"]; '
+'  Sender<-Receiver [label="Ack()", URL="\ref '
+'  Ack()", ID="1"]; '
+''
+'  mscFile.mscThe caption'
+''
+'  someHeader.h '
+''
+'  someNamespace'
+''
+'  Notes:'
+'  Here '
+'  is the note! '
+''
+'  This is an overloaded member function, provided for convenience.'
+'  It differs from the above function only in what argument(s) it accepts.'
+''
+'  someword'
+''
+'  superPackage'
+''
+'  somePageThe title '
+''
+'  Title: The paragraph title '
+'  The paragraph text. '
+'  Maybe even multiline '
+''
+'  someParagraphParagraph title '
+''
+'  Arguments:'
+'  a (int)                              -- the first param '
+''
+'  Some description '
+''
+'  Some description '
+''
+'  someVar '
+''
+'  someProtocolheader.hHeader name'
+''
+'  someAnchor'
+''
+'  toSomething'
+''
+'  toSomethingElse'
+''
+'  someName'
+''
+'  someName'
+''
+'  Remarks:'
+'  Some remark text '
+''
+'  Another remarks section '
+''
+'  Return:'
+'  Whatever '
+''
+'  it '
+''
+'  may return '
+''
+'  someValueSome description '
+''
+''
+'  This will only appear in RTF '
+''
+''
+'  See also:'
+'  someOtherMethod '
+''
+'  someSectionSome title '
+''
+'  function '
+''
+'  Same as '
+'  brief description '
+''
+''
+''
+'  Since:'
+'  version 0.0.0.1 '
+''
+'  somePattern '
+''
+'  someLine '
+''
+'  example.hSome snippet '
+''
+'  someStruct'
+''
+'  someSubpageSome description'
+''
+'  someSubsectionSome title '
+''
+'  someSubsectionSome title '
+''
+''
+''
+'  Some '
+'  description of the '
+'  test case '
+''
+'  Throws:'
+'  superException'
+''
+'  RuntimeError'
+''
+'  TODO:'
+'  Some very important task '
+''
+'  Arguments:'
+'  b (float)                              -- B is mentioned again... '
+''
+'  someTypedef '
+''
+'  someUnion'
+''
+'  somePattern '
+''
+'  someVar '
+''
+''
+'  very long '
+'  text with tags <sometag> '
+''
+''
+'  someFile.h'
+''
+'  Version:'
+'  0.0.0.2 '
+''
+'  Warning:'
+'  This is senseless! '
+''
+'  someGroupSome title '
+''
+''
+'  This will only appear in XML '
+''
+''
+'  Here goes test of symbols: '
+'  $@\&~<>#%".::'
+''
+'  And here goes simple text '
+)
\ No newline at end of file
diff --git a/Examples/test-suite/python/doxygen_translate_runme.py b/Examples/test-suite/python/doxygen_translate_runme.py
new file mode 100644
index 000000000..61e5f5398
--- /dev/null
+++ b/Examples/test-suite/python/doxygen_translate_runme.py
@@ -0,0 +1,148 @@
+#!/usr/bin/python
+
+import doxygen_translate
+import string
+import sys
+
+def check(got, expected):
+  #if got is Null
+  #  raise RuntimeError('Expected comment string\n')
+  gotStr = string.replace(got, ' ', '')
+  gotStr = string.replace(gotStr, '\n', '')
+  gotStr = string.replace(gotStr, '\t', '')
+  expectedStr = string.replace(expected, ' ', '')
+  expectedStr = string.replace(expectedStr, '\n', '')
+  expectedStr = string.replace(expectedStr, '\t', '')
+  if not gotStr == expectedStr:
+    raise RuntimeError("Expected: [" + str(expected) + "]\n" + "Got     : [" + str(got) + "]\n")
+
+check(doxygen_translate.function.__doc__, ''
+'  _Hello_'
+''
+'   -some list item '
+''
+'  Authors:'
+'  lots of them '
+''
+'  Zubr '
+''
+'  __boldword__'
+''
+'  codeword'
+''
+'  \'citationword\''
+''
+'  some test code '
+''
+'  Conditional comment: SOMECONDITION'
+'  Some conditional comment '
+'  End of conditional comment.'
+''
+'  Copyright:'
+'  some copyright '
+''
+'  Deprecated:'
+'  Now use another function '
+''
+'  _italicword_'
+''
+'  Example:'
+'  someFile.txt'
+'  Some details on using the example '
+''
+'  Throws:'
+'  SuperError'
+''
+'  If: ANOTHERCONDITION {'
+'  First part of comment '
+'  If: SECONDCONDITION {'
+'  Nested condition text '
+'  }Else if: THIRDCONDITION {'
+'  The third condition text '
+'  }Else:  {The last text block '
+'  }'
+'  }Else:  {Second part of comment '
+'  If: CONDITION {'
+'  Second part extended '
+'  }'
+'  }'
+''
+'  If not: SOMECONDITION {'
+'  This is printed if not '
+'  }'
+''
+'  Image: htmltestImage.bmpHello, world!asd=10qwe'
+''
+'  <ul> '
+''
+'   -Some unordered list '
+'   -With lots of items '
+'   -lots of lots of items '
+''
+'  </ul> '
+''
+'  someMember Some description follows '
+''
+'  Notes:'
+'  Here '
+'  is the note! '
+''
+'  This is an overloaded member function, provided for convenience.'
+'  It differs from the above function only in what argument(s) it accepts.'
+''
+'  someword'
+''
+'  superPackage'
+''
+'  Title: The paragraph title '
+'  The paragraph text. '
+'  Maybe even multiline '
+''
+'  Arguments:'
+'  a (int)                              -- the first param '
+''
+'  Remarks:'
+'  Some remark text '
+''
+'  Another remarks section '
+''
+'  Return:'
+'  Whatever '
+''
+'  it '
+''
+'  may return '
+''
+'  See also:'
+'  someOtherMethod '
+''
+'  function '
+''
+'  Since:'
+'  version 0.0.0.1 '
+''
+'  Throws:'
+'  superException'
+''
+'  RuntimeError'
+''
+'  TODO:'
+'  Some very important task '
+''
+'  Arguments:'
+'  b (float)                              -- B is mentioned again... '
+''
+'  very long '
+'  text with tags <sometag> '
+''
+'  Version:'
+'  0.0.0.2 '
+''
+'  Warning:'
+'  This is senseless! '
+''
+'  Here goes test of symbols: '
+'  $@\&~<>#%".::'
+''
+'  And here goes simple text '
+)
\ No newline at end of file

From a7ae017d55078cf675d130c846ff05f78531d61c Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Wed, 25 Jul 2012 07:52:54 +0000
Subject: [PATCH 101/314] Fixed some spelling in project plan

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13396 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Doc/Devel/plan-gsoc-2012.txt | 18 ++++++++++++------
 1 file changed, 12 insertions(+), 6 deletions(-)

diff --git a/Doc/Devel/plan-gsoc-2012.txt b/Doc/Devel/plan-gsoc-2012.txt
index 6566598fe..6f012cd4b 100644
--- a/Doc/Devel/plan-gsoc-2012.txt
+++ b/Doc/Devel/plan-gsoc-2012.txt
@@ -2,29 +2,35 @@
                                                                      
                                                                      
                                              
+                   Project Plan
+                   ============
+                SWIG Code Comments
+             Google Summer of Code 2012
+
+
 This document describes goals for the Google Summer of Code 2012,
 SWIG code documentation project.
 
-Author: Marko Klopcic
+Author: Marko Klopcic, Dmitry Kabak
 
 
 Introduction
 ============
 
-The goal of this project is _not_ to translate _any_ possible doxygen
+The goal of this project is _not_ to translate _any_ possible Doxygen
 formatted comment to JavaDoc or PyDoc, but to make it possible to
 translate a subset of comment types in C/C++ code to
 JavaDoc and PyDoc. Covering all the Doxygen functionality would be to
-complex for the limited time. Hovewer, the code must be extendable so
+complex for the limited time. However, the code must be flexible so
 that implementing missing features would not require redesign of the
 comment handling code in SWIG.
 
-There will also be a possiblity to add untranslated comments to Java
+There will also be a possibility to add untranslated comments to Java
 and Python code (## comments, see Doxygen manual), if the user will
 prefer to use Doxygen on the generated code.
 
 Note:
-'-OK-' tick below means that the item is implemented, commited and
+'-OK-' tick below means that the item is implemented, committed and
 working.
 
 Abbreviations:
@@ -249,7 +255,7 @@ Optional functionality
 ======================
 
 That section describes some complex cases where the current code
-not behaves really well. Like a short to-do list of special cases.
+does not behave really well. Like a short to-do list of special cases.
 
 - When translating functions with default parameters in swig to
 java, it creates overloaded functions with all the parameters

From 0b7d1ffc454522da7eb7b761cece8217ddf98b2d Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Wed, 25 Jul 2012 12:11:28 +0000
Subject: [PATCH 102/314] Small fix to correctly generate overloaded method
 comments in python

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13400 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Source/DoxygenTranslator/src/PyDocConverter.cpp | 1 +
 1 file changed, 1 insertion(+)

diff --git a/Source/DoxygenTranslator/src/PyDocConverter.cpp b/Source/DoxygenTranslator/src/PyDocConverter.cpp
index 5b6f39adf..3ae018cf9 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/PyDocConverter.cpp
@@ -252,6 +252,7 @@ String *PyDocConverter::makeDocumentation(Node *n) {
     while (n) {
       documentation = getDoxygenComment(n);
       if (!Swig_is_generated_overload(n) && documentation) {
+	currentNode = n;
 	std::list < DoxygenEntity > entityList = parser.createTree(Char(documentation), Char(Getfile(documentation)), Getline(documentation));
 	DoxygenEntity root("root", entityList);
 	allDocumentation.push_back(translateSubtree(root));

From 4951d4a9007a0a64ed67b56e4d0d12a56097fe97 Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Sat, 28 Jul 2012 09:19:23 +0000
Subject: [PATCH 103/314] Got rid of 81 reduce/reduce warnings in parser.y

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13424 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Source/CParse/parser.y | 48 ++++++++++++++++--------------------------
 1 file changed, 18 insertions(+), 30 deletions(-)

diff --git a/Source/CParse/parser.y b/Source/CParse/parser.y
index 4bf63b40f..6aed8c3f9 100644
--- a/Source/CParse/parser.y
+++ b/Source/CParse/parser.y
@@ -1798,7 +1798,6 @@ static void tag_nodes(Node *n, const_String_or_char_ptr attrname, DOH *value) {
 %type <node>     featattr;
 %type <str>	 doxygen_comment;
 %type <str>	 doxygen_comment_item;
-%type <str>	 c_style_comment;
 %type <str>	 doxygen_post_comment;
 %type <str>	 doxygen_post_comment_item;
 %%
@@ -1849,6 +1848,16 @@ interface      : interface declaration {
                    appendChild($1,$2);
                    $$ = $1;
                }
+               | interface doxygen_comment declaration {
+                   set_comment($3, $2);
+                   appendChild($1, $3);
+                   $$ = $1;
+               }
+               | interface declaration doxygen_post_comment {
+                   set_comment($2, $3);
+                   appendChild($1, $2);
+                   $$ = $1;
+               }
                | empty {
                    $$ = new_node("top");
                }
@@ -1857,7 +1866,6 @@ interface      : interface declaration {
 declaration    : swig_directive { $$ = $1; }
                | c_declaration { $$ = $1; } 
                | cpp_declaration { $$ = $1; }
-               | c_style_comment { $$ = $1; }
                | SEMI { $$ = 0; }
                | error {
                   $$ = 0;
@@ -1880,15 +1888,6 @@ declaration    : swig_directive { $$ = $1; }
    COPERATOR token---discarding the rest of the definition. Ugh.
 
  */
-
-	       | doxygen_comment declaration {
-		  $$ = $2;
-		  set_comment($2, $1);
-	       }
-	       | declaration doxygen_post_comment {
-		  $$ = $1;
-		  set_comment($1, $2);
-	       }
                | error COPERATOR {
                   $$ = 0;
                   skip_decl();
@@ -3470,15 +3469,14 @@ doxygen_comment_item : DOXYGENSTRING {
 		  else {
 		    $$ = $1;
 		  }
-
 		}
-		;
-
-doxygen_comment : doxygen_comment doxygen_comment_item { 
+		| doxygen_comment_item doxygen_comment_item {
 		  Append($1, $2);
 		  $$ = $1;
 		}
-                | doxygen_comment_item {
+		;
+
+doxygen_comment : doxygen_comment_item {
                   $$ = $1;
 		}
 		;
@@ -3493,26 +3491,17 @@ doxygen_post_comment_item : DOXYGENPOSTSTRING {
 		  
 		  $$ = $1;
 		}
-		;
-
-doxygen_post_comment : doxygen_post_comment doxygen_post_comment_item { 
+		| doxygen_post_comment_item doxygen_post_comment_item {
 		  Append($1, $2);
 		  $$ = $1;
 		}
-                | doxygen_post_comment_item {
+		;
+
+doxygen_post_comment : doxygen_post_comment_item {
                   $$ = $1;
 		}
 		;
 
-c_style_comment : C_COMMENT_STRING {
-		  if(currentCComment != 0){
-		    Append(currentCComment, $1);
-		  }
-		  else currentCComment = $1;
-		  $$ = 0;
-                }
-                ;
-
 /* ======================================================================
  *                       C++ Support
  * ====================================================================== */
@@ -4489,7 +4478,6 @@ cpp_member   : c_declaration { $$ = $1; }
              | storage_class idcolon SEMI { $$ = 0; }
              | cpp_using_decl { $$ = $1; }
              | cpp_template_decl { $$ = $1; }
-             | c_style_comment{ $$ = $1; }
              | cpp_catch_decl { $$ = 0; }
              | template_directive { $$ = $1; }
              | warn_directive { $$ = $1; }

From 5fe88acdfb47b68e32e2323d004aefc115f998f0 Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Sun, 29 Jul 2012 11:37:38 +0000
Subject: [PATCH 104/314] Forgot to escape special HTML-chars in
 JavaDocConverter

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13425 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 .../test-suite/java/doxygen_translate_all_tags_runme.java | 4 ++--
 Examples/test-suite/java/doxygen_translate_runme.java     | 4 ++--
 Source/DoxygenTranslator/src/JavaDocConverter.cpp         | 8 ++++----
 3 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/Examples/test-suite/java/doxygen_translate_all_tags_runme.java b/Examples/test-suite/java/doxygen_translate_all_tags_runme.java
index 065dfa27e..6db1f6686 100644
--- a/Examples/test-suite/java/doxygen_translate_all_tags_runme.java
+++ b/Examples/test-suite/java/doxygen_translate_all_tags_runme.java
@@ -111,10 +111,10 @@ public class doxygen_translate_all_tags_runme {
     		" Warning: This is senseless! \n" +
     		" This will only appear in XML \n" +
     		" Here goes test of symbols: \n" +
-    		" $ @ \\ & ~ < > # % \" . :: \n" +
+    		" $ @ \\ &amp; ~ &lt; &gt; # % &quot; . :: \n" +
     		" And here goes simple text \n" +
     		"");
     // and ask the parser to check comments for us
     System.exit(parser.check(wantedComments));
   }
-}
\ No newline at end of file
+}
diff --git a/Examples/test-suite/java/doxygen_translate_runme.java b/Examples/test-suite/java/doxygen_translate_runme.java
index cfd62d79c..8aa80a6ed 100644
--- a/Examples/test-suite/java/doxygen_translate_runme.java
+++ b/Examples/test-suite/java/doxygen_translate_runme.java
@@ -138,7 +138,7 @@ public class doxygen_translate_runme {
     		" Warning: This is senseless! \n" +
     		" \n" +
     		" Here goes test of symbols: \n" +
-    		" $ @ \\ & ~ < > # % \" . :: \n" +
+    		" $ @ \\ &amp; ~ &lt; &gt; # % &quot; . :: \n" +
     		" \n" +
     		" And here goes simple text \n" +
     		" \n" +
@@ -146,4 +146,4 @@ public class doxygen_translate_runme {
     // and ask the parser to check comments for us
     System.exit(parser.check(wantedComments));
   }
-}
\ No newline at end of file
+}
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.cpp b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
index 8f6725f5c..636d49ebf 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
@@ -36,13 +36,13 @@ void JavaDocConverter::fillStaticTables() {
   tagHandlers["$"] = make_pair(&JavaDocConverter::handleTagChar, "");
   tagHandlers["@"] = make_pair(&JavaDocConverter::handleTagChar, "");
   tagHandlers["\\"] = make_pair(&JavaDocConverter::handleTagChar, "");
-  tagHandlers["<"] = make_pair(&JavaDocConverter::handleTagChar, "");
-  tagHandlers[">"] = make_pair(&JavaDocConverter::handleTagChar, "");
-  tagHandlers["&"] = make_pair(&JavaDocConverter::handleTagChar, "");
+  tagHandlers["<"] = make_pair(&JavaDocConverter::handleTagChar, "&lt;");
+  tagHandlers[">"] = make_pair(&JavaDocConverter::handleTagChar, "&gt;");
+  tagHandlers["&"] = make_pair(&JavaDocConverter::handleTagChar, "&amp;");
   tagHandlers["#"] = make_pair(&JavaDocConverter::handleTagChar, "");
   tagHandlers["%"] = make_pair(&JavaDocConverter::handleTagChar, "");
   tagHandlers["~"] = make_pair(&JavaDocConverter::handleTagChar, "");
-  tagHandlers["\""] = make_pair(&JavaDocConverter::handleTagChar, "");
+  tagHandlers["\""] = make_pair(&JavaDocConverter::handleTagChar, "&quot;");
   tagHandlers["."] = make_pair(&JavaDocConverter::handleTagChar, "");
   tagHandlers["::"] = make_pair(&JavaDocConverter::handleTagChar, "");
   // these commands are stripped out

From 03da0be1fafce6b67e1d8fef033a1a0dd02a3687 Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Sun, 29 Jul 2012 11:53:01 +0000
Subject: [PATCH 105/314] Fixed numerous 'unused argument' warnings

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13426 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Source/DoxygenTranslator/src/JavaDocConverter.cpp | 10 +++++-----
 Source/DoxygenTranslator/src/PyDocConverter.cpp   | 14 +++++++-------
 2 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.cpp b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
index 636d49ebf..1f0ea9437 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
@@ -177,7 +177,7 @@ void JavaDocConverter::handleTagHtml(DoxygenEntity& tag, std::string& translated
   if (tag.entityList.size()) // do not include empty tags
     translatedComment += "<" + arg + ">" + translateSubtree(tag) + "</" + arg + ">";
 }
-void JavaDocConverter::handleNewLine(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
+void JavaDocConverter::handleNewLine(DoxygenEntity&, std::string& translatedComment, std::string&) {
   translatedComment += "\n * ";
 }
 void JavaDocConverter::handleTagChar(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
@@ -193,10 +193,10 @@ void JavaDocConverter::handleTagSame(DoxygenEntity& tag, std::string& translated
     tag.typeOfEntity = arg;
   translatedComment += formatCommand(std::string("@" + tag.typeOfEntity + " " + translateSubtree(tag)), 2);
 }
-void JavaDocConverter::handleParagraph(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
+void JavaDocConverter::handleParagraph(DoxygenEntity& tag, std::string& translatedComment, std::string&) {
   translatedComment += formatCommand(translateSubtree(tag), 0);
 }
-void JavaDocConverter::handlePlainString(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
+void JavaDocConverter::handlePlainString(DoxygenEntity& tag, std::string& translatedComment, std::string&) {
   translatedComment += tag.data;
   if (tag.data.size() && tag.data[tag.data.size()-1] != ' ')
   	translatedComment += " ";
@@ -222,7 +222,7 @@ void JavaDocConverter::handleTagMessage(DoxygenEntity& tag, std::string& transla
   translatedComment += formatCommand(arg, 0);
   handleParagraph(tag, translatedComment, dummy);
 }
-void JavaDocConverter::handleTagImage(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
+void JavaDocConverter::handleTagImage(DoxygenEntity& tag, std::string& translatedComment, std::string&) {
   if (tag.entityList.size() < 2)
     return;
 
@@ -245,7 +245,7 @@ void JavaDocConverter::handleTagImage(DoxygenEntity& tag, std::string& translate
     translatedComment += " alt=\"" + title +"\"";
   translatedComment += " />";
 }
-void JavaDocConverter::handleTagPar(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
+void JavaDocConverter::handleTagPar(DoxygenEntity& tag, std::string& translatedComment, std::string&) {
   std::string dummy;
   translatedComment += "<p";
   if (tag.entityList.size())
diff --git a/Source/DoxygenTranslator/src/PyDocConverter.cpp b/Source/DoxygenTranslator/src/PyDocConverter.cpp
index 3ae018cf9..5dd622760 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/PyDocConverter.cpp
@@ -124,7 +124,7 @@ std::string PyDocConverter::justifyString(std::string documentString, int indent
 
     currentLine += *stringPosition;
 
-    if (iswspace(*stringPosition) && (int) currentLine.size() >= maxWidth || (stringPosition + 1) == documentString.end()) {
+    if ((iswspace(*stringPosition) && (int) currentLine.size() >= maxWidth) || (stringPosition + 1) == documentString.end()) {
       formattedString += currentLine + "\n";
       currentLine = "";
     }
@@ -173,10 +173,10 @@ void PyDocConverter::translateEntity(DoxygenEntity & doxyEntity, std::string &tr
     handleParagraph(doxyEntity, translatedComment, dummy);
 }
 
-void PyDocConverter::handleParagraph(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
+void PyDocConverter::handleParagraph(DoxygenEntity& tag, std::string& translatedComment, std::string&) {
   translatedComment += justifyString(translateSubtree(tag), 0);
 }
-void PyDocConverter::handlePlainString(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
+void PyDocConverter::handlePlainString(DoxygenEntity& tag, std::string& translatedComment, std::string&) {
   translatedComment += tag.data;
   if (tag.data.size() && tag.data[tag.data.size()-1] != ' ')
     translatedComment += "";
@@ -186,7 +186,7 @@ void PyDocConverter::handleTagMessage(DoxygenEntity& tag, std::string& translate
   translatedComment += arg;
   handleParagraph(tag, translatedComment, dummy);
 }
-void PyDocConverter::handleTagChar(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
+void PyDocConverter::handleTagChar(DoxygenEntity& tag, std::string& translatedComment, std::string&) {
   translatedComment += tag.typeOfEntity;
 }
 void PyDocConverter::handleTagIf(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
@@ -198,7 +198,7 @@ void PyDocConverter::handleTagIf(DoxygenEntity& tag, std::string& translatedComm
     translatedComment += " {" + translateSubtree(tag) + "}";
   }
 }
-void PyDocConverter::handleTagPar(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
+void PyDocConverter::handleTagPar(DoxygenEntity& tag, std::string& translatedComment, std::string&) {
   std::string dummy;
   translatedComment += "Title: ";
   if (tag.entityList.size())
@@ -206,7 +206,7 @@ void PyDocConverter::handleTagPar(DoxygenEntity& tag, std::string& translatedCom
   tag.entityList.pop_front();
   handleParagraph(tag, translatedComment, dummy);
 }
-void PyDocConverter::handleTagParam(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
+void PyDocConverter::handleTagParam(DoxygenEntity& tag, std::string& translatedComment, std::string&) {
   std::string dummy;
   if (tag.entityList.size() < 2) {
     // TODO: log error
@@ -229,7 +229,7 @@ void PyDocConverter::handleTagWrap(DoxygenEntity& tag, std::string& translatedCo
   if (tag.entityList.size()) // do not include empty tags
     translatedComment += arg + translateSubtree(tag) + arg;
 }
-void PyDocConverter::handleNewLine(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
+void PyDocConverter::handleNewLine(DoxygenEntity&, std::string& translatedComment, std::string&) {
   translatedComment += "\n";
 }
 

From 3fbe45f0c619e33f482782af2af8e2955860c2d1 Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Sun, 29 Jul 2012 13:48:03 +0000
Subject: [PATCH 106/314] Added nice doxygen debug switching
 (-debug-doxygen-parser and -debug-doxygen-translator)

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13427 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Source/DoxygenTranslator/src/DoxygenParser.cpp   |  2 +-
 Source/DoxygenTranslator/src/DoxygenParser.h     |  2 +-
 .../DoxygenTranslator/src/DoxygenTranslator.cpp  |  3 ++-
 Source/DoxygenTranslator/src/DoxygenTranslator.h |  3 ++-
 .../DoxygenTranslator/src/JavaDocConverter.cpp   |  4 +++-
 Source/DoxygenTranslator/src/JavaDocConverter.h  |  3 +--
 Source/DoxygenTranslator/src/PyDocConverter.cpp  |  3 ++-
 Source/DoxygenTranslator/src/PyDocConverter.h    |  3 +--
 Source/Modules/java.cxx                          | 16 ++++++++++++----
 Source/Modules/python.cxx                        | 13 ++++++++++++-
 10 files changed, 37 insertions(+), 15 deletions(-)

diff --git a/Source/DoxygenTranslator/src/DoxygenParser.cpp b/Source/DoxygenTranslator/src/DoxygenParser.cpp
index 80ded041a..8ed186727 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenParser.cpp
@@ -17,7 +17,7 @@ std::map<std::string, DoxyCommandEnum> DoxygenParser::doxygenCommands;
 std::set<std::string> DoxygenParser::doxygenSectionIndicators;
 
 
-DoxygenParser::DoxygenParser() : noisy(false) {
+DoxygenParser::DoxygenParser(bool noisy) : noisy(noisy) {
 	fillTables();
 }
 
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.h b/Source/DoxygenTranslator/src/DoxygenParser.h
index c72ca6fed..5f6432d87 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.h
+++ b/Source/DoxygenTranslator/src/DoxygenParser.h
@@ -19,7 +19,7 @@
 #include "TokenList.h"
 class DoxygenParser {
 public:
-  DoxygenParser();
+  DoxygenParser(bool noisy = false);
   virtual ~DoxygenParser();
   std::list < DoxygenEntity > createTree(std::string doxygen, std::string fileName, int lineNumber);
 private:
diff --git a/Source/DoxygenTranslator/src/DoxygenTranslator.cpp b/Source/DoxygenTranslator/src/DoxygenTranslator.cpp
index 18cf24c85..10f6a4585 100644
--- a/Source/DoxygenTranslator/src/DoxygenTranslator.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenTranslator.cpp
@@ -14,7 +14,8 @@
 
 #include "DoxygenTranslator.h"
 
-DoxygenTranslator::DoxygenTranslator() {
+DoxygenTranslator::DoxygenTranslator(bool debugTranslator, bool debugParser)
+: debug(debugTranslator), parser(debugParser) {
 }
 DoxygenTranslator::~DoxygenTranslator() {
 }
diff --git a/Source/DoxygenTranslator/src/DoxygenTranslator.h b/Source/DoxygenTranslator/src/DoxygenTranslator.h
index 637b30a9e..97be4ee35 100644
--- a/Source/DoxygenTranslator/src/DoxygenTranslator.h
+++ b/Source/DoxygenTranslator/src/DoxygenTranslator.h
@@ -30,7 +30,7 @@ public:
   /*
    * Constructor
    */
-  DoxygenTranslator();
+  DoxygenTranslator(bool debugTranslator = false, bool debugParser = false);
   /*
    * Virtual destructor.
    */
@@ -52,6 +52,7 @@ public:
   String *getDoxygenComment(Node *node);
 
 protected:
+  bool debug;
   /*
    * Overridden in subclasses to return the documentation formatted for a given
    * documentation system.
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.cpp b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
index 1f0ea9437..165075708 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
@@ -21,6 +21,7 @@ std::map<std::string, std::pair<JavaDocConverter::tagHandler, std::string > > Ja
 
 void JavaDocConverter::fillStaticTables() {
   if (tagHandlers.size()) // fill only once
+    return;
 
   // these commands insert HTML tags
   tagHandlers["a"] = make_pair(&JavaDocConverter::handleTagHtml, "i");
@@ -105,7 +106,8 @@ void JavaDocConverter::fillStaticTables() {
 }
 
 
-JavaDocConverter::JavaDocConverter() : debug(false) {
+JavaDocConverter::JavaDocConverter(bool debugTranslator, bool debugParser)
+: DoxygenTranslator(debugTranslator, debugParser) {
   fillStaticTables();
 }
 
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.h b/Source/DoxygenTranslator/src/JavaDocConverter.h
index cb876ed6b..1d51a8d7b 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.h
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.h
@@ -22,7 +22,7 @@
  */
 class JavaDocConverter : public DoxygenTranslator {
 public:
-  JavaDocConverter();
+  JavaDocConverter(bool debugTranslator = false, bool debugParser = false);
   String *makeDocumentation(Node *node);
 
 protected:
@@ -88,7 +88,6 @@ protected:
 
 
 private:
-  bool debug;
   // this contains the handler pointer and one string argument
   static std::map<std::string, std::pair<tagHandler, std::string> > tagHandlers;
   void fillStaticTables();
diff --git a/Source/DoxygenTranslator/src/PyDocConverter.cpp b/Source/DoxygenTranslator/src/PyDocConverter.cpp
index 5dd622760..a873cfb16 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/PyDocConverter.cpp
@@ -91,7 +91,8 @@ void PyDocConverter::fillStaticTables() {
   tagHandlers["n"] = make_pair(&PyDocConverter::handleNewLine, "");
 }
 
-PyDocConverter::PyDocConverter() : debug(false) {
+PyDocConverter::PyDocConverter(bool debugTranslator, bool debugParser)
+: DoxygenTranslator(debugTranslator, debugParser) {
   fillStaticTables();
 }
 
diff --git a/Source/DoxygenTranslator/src/PyDocConverter.h b/Source/DoxygenTranslator/src/PyDocConverter.h
index f14a130ac..9787891c8 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.h
+++ b/Source/DoxygenTranslator/src/PyDocConverter.h
@@ -25,7 +25,7 @@
 
 class PyDocConverter : public DoxygenTranslator {
 public:
-  PyDocConverter();
+  PyDocConverter(bool debugTranslator = false, bool debugParser = false);
   String *makeDocumentation(Node *node);
 
 protected:
@@ -108,7 +108,6 @@ protected:
   std::string getParamType(std::string name);
 
 private:
-  bool debug;
   // temporary thing, should be refactored somehow
   Node *currentNode;
   // this contains the handler pointer and one string argument
diff --git a/Source/Modules/java.cxx b/Source/Modules/java.cxx
index 49a5e9901..c7174d0fc 100644
--- a/Source/Modules/java.cxx
+++ b/Source/Modules/java.cxx
@@ -163,9 +163,6 @@ public:
        should be easy to implement though */
     director_multiple_inheritance = 0;
     director_language = 1;
-    
-    if (doxygen)
-      doxygenTranslator = new JavaDocConverter();
   }
   
   ~JAVA() {
@@ -242,6 +239,9 @@ public:
 
     SWIG_library_directory("java");
 
+    bool debug_doxygen_translator = false;
+    bool debug_doxygen_parser = false;
+
     // Look for certain command line options
     for (int i = 1; i < argc; i++) {
       if (argv[i]) {
@@ -271,6 +271,12 @@ public:
 	  Swig_mark_arg(i);
 	  doxygen = false;
 	  scan_doxygen_comments = false;
+  } else if ((strcmp(argv[i], "-debug-doxygen-translator") == 0)) {
+    Swig_mark_arg(i);
+    debug_doxygen_translator = true;
+  } else if ((strcmp(argv[i], "-debug-doxygen-parser") == 0)) {
+    Swig_mark_arg(i);
+    debug_doxygen_parser = true;
 	} else if ((strcmp(argv[i], "-noproxy") == 0)) {
 	  Swig_mark_arg(i);
 	  proxy_flag = false;
@@ -296,7 +302,7 @@ public:
     }
     
     if (doxygen)
-      doxygenTranslator = new JavaDocConverter();
+      doxygenTranslator = new JavaDocConverter(debug_doxygen_translator, debug_doxygen_parser);
 
     // Add a symbol to the parser for conditional compilation
     Preprocessor_define("SWIGJAVA 1", 0);
@@ -4537,6 +4543,8 @@ const char *JAVA::usage = (char *) "\
 Java Options (available with -java)\n\
      -doxygen        - Convert C++ doxygen comments to JavaDoc comments in proxy classes (default)\n\
      -nodoxygen      - Don't convert C++ doxygen comments to JavaDoc comments in proxy classes\n\
+     -debug-doxygen-parser     - Display doxygen parser module debugging information\n\
+     -debug-doxygen-translator - Display doxygen translator module debugging information\n\
      -nopgcpp        - Suppress premature garbage collection prevention parameter\n\
      -noproxy        - Generate the low-level functional interface instead\n\
                        of proxy classes\n\
diff --git a/Source/Modules/python.cxx b/Source/Modules/python.cxx
index 5d9a97952..f7c9c00c1 100644
--- a/Source/Modules/python.cxx
+++ b/Source/Modules/python.cxx
@@ -121,6 +121,8 @@ Python Options (available with -python)\n\
      -cppcast        - Enable C++ casting operators (default) \n\
      -dirvtable      - Generate a pseudo virtual table for directors for faster dispatch \n\
      -doxygen        - Convert C++ doxygen comments to pydoc comments in proxy classes (default) \n\
+     -debug-doxygen-parser     - Display doxygen parser module debugging information\n\
+     -debug-doxygen-translator - Display doxygen translator module debugging information\n\
      -extranative    - Return extra native C++ wraps for std containers when possible \n\
      -fastinit       - Use fast init mechanism for classes (default)\n\
      -fastunpack     - Use fast unpack mechanism to parse the argument functions \n\
@@ -332,6 +334,9 @@ public:
 
     SWIG_library_directory("python");
 
+    bool debug_doxygen_parser = false;
+    bool debug_doxygen_translator = false;
+
     for (int i = 1; i < argc; i++) {
       if (argv[i]) {
 	if (strcmp(argv[i], "-interface") == 0) {
@@ -430,6 +435,12 @@ public:
 	  doxygen = 0;
 	  scan_doxygen_comments = 0;
 	  Swig_mark_arg(i);
+  } else if (strcmp(argv[i], "-debug-doxygen-translator") == 0) {
+    debug_doxygen_translator = true;
+    Swig_mark_arg(i);
+  } else if (strcmp(argv[i], "-debug-doxygen-parser") == 0) {
+    debug_doxygen_parser = true;
+    Swig_mark_arg(i);
 	} else if (strcmp(argv[i], "-fastunpack") == 0) {
 	  fastunpack = 1;
 	  Swig_mark_arg(i);
@@ -549,7 +560,7 @@ public:
     }
     
     if (doxygen)
-      doxygenTranslator = new PyDocConverter;
+      doxygenTranslator = new PyDocConverter(debug_doxygen_translator, debug_doxygen_parser);
 
     if (!global_name)
       global_name = NewString("cvar");

From 8260f4219f39abef61808211206db54b739664d4 Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Sun, 29 Jul 2012 22:26:31 +0000
Subject: [PATCH 107/314] Expanded the Doxygen docs

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13428 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Doc/Devel/plan-gsoc-2012.txt |   4 +-
 Doc/Manual/Contents.html     |  32 +-
 Doc/Manual/Doxygen.html      | 554 ++++++++++++++++++++++++++++++-----
 3 files changed, 489 insertions(+), 101 deletions(-)

diff --git a/Doc/Devel/plan-gsoc-2012.txt b/Doc/Devel/plan-gsoc-2012.txt
index 6f012cd4b..a3bf2ca39 100644
--- a/Doc/Devel/plan-gsoc-2012.txt
+++ b/Doc/Devel/plan-gsoc-2012.txt
@@ -320,8 +320,8 @@ Documentation
 =============
 
 SWIG documentation will contain:
-- command line options
-- list of implemented features (types and placements of comments)
+-OK- command line options
+-OK- list of implemented features (types and placements of comments)
 - list of unimplemented features (types and placements of comments)
 - list of tags and their translations (all Doxygen tags).
 
diff --git a/Doc/Manual/Contents.html b/Doc/Manual/Contents.html
index 7a05527c6..77518c268 100644
--- a/Doc/Manual/Contents.html
+++ b/Doc/Manual/Contents.html
@@ -524,32 +524,6 @@
 </div>
 <!-- INDEX -->
 
-<h3><a href="CCache.html#CCache">16 Using SWIG with ccache - ccache-swig(1) manpage</a></h3>
-
-<!-- INDEX -->
-<div class="sectiontoc">
-<ul>
-<li><a href="CCache.html#CCache_nn2">NAME</a>
-<li><a href="CCache.html#CCache_nn3">SYNOPSIS</a>
-<li><a href="CCache.html#CCache_nn4">DESCRIPTION</a>
-<li><a href="CCache.html#CCache_nn5">OPTIONS SUMMARY</a>
-<li><a href="CCache.html#CCache_nn6">OPTIONS</a>
-<li><a href="CCache.html#CCache_nn7">INSTALLATION</a>
-<li><a href="CCache.html#CCache_nn8">EXTRA OPTIONS</a>
-<li><a href="CCache.html#CCache_nn9">ENVIRONMENT VARIABLES</a>
-<li><a href="CCache.html#CCache_nn10">CACHE SIZE MANAGEMENT</a>
-<li><a href="CCache.html#CCache_nn11">CACHE COMPRESSION</a>
-<li><a href="CCache.html#CCache_nn12">HOW IT WORKS</a>
-<li><a href="CCache.html#CCache_nn13">USING CCACHE WITH DISTCC</a>
-<li><a href="CCache.html#CCache_nn14">SHARING A CACHE</a>
-<li><a href="CCache.html#CCache_nn15">HISTORY</a>
-<li><a href="CCache.html#CCache_nn16">DIFFERENCES FROM COMPILERCACHE</a>
-<li><a href="CCache.html#CCache_nn17">CREDITS</a>
-<li><a href="CCache.html#CCache_nn18">AUTHOR</a>
-</ul>
-</div>
-<!-- INDEX -->
-
 <h3><a href="Allegrocl.html#Allegrocl">17 SWIG and Allegro Common Lisp</a></h3>
 
 <!-- INDEX -->
@@ -1717,7 +1691,7 @@
 </div>
 <!-- INDEX -->
 
-<h3><a href="Doxygen.html#Doxygen">35 SWIG and Doxgeyn Translation</a></h3>
+<h3><a href="Doxygen.html#Doxygen">39 SWIG and Doxygen Translation</a></h3>
 
 <!-- INDEX -->
 <div class="sectiontoc">
@@ -1732,13 +1706,13 @@
 <ul>
 <li><a href="Doxygen.html#Doxygen_basic_example">Basic Example</a>
 <li><a href="Doxygen.html#Doxygen_javadoc_tags">JavaDoc Tags</a>
-<li><a href="Doxygen.html#Doxygen_other_tags">Other Tags</a>
-<li><a href="Doxygen.html#Doxygen_bad_behaviour">Bad Behaviour</a>
+<li><a href="Doxygen.html#Doxygen_unsupported_tags">Unsupported tags</a>
 <li><a href="Doxygen.html#Doxygen_further_details">Further Details</a>
 </ul>
 <li><a href="Doxygen.html#Doxygen_developer_details">Developer Information</a>
 <ul>
 <li><a href="Doxygen.html#Doxygen_module_design">Module Design</a>
+<li><a href="Doxygen.html#Doxygen_debugging_commands">Debugging commands</a>
 </ul>
 <li><a href="Doxygen.html#Doxygen_language_extension">Extending to Other Languages</a>
 </ul>
diff --git a/Doc/Manual/Doxygen.html b/Doc/Manual/Doxygen.html
index d0e837756..54fa1b6bf 100644
--- a/Doc/Manual/Doxygen.html
+++ b/Doc/Manual/Doxygen.html
@@ -5,7 +5,7 @@
 <link rel="stylesheet" type="text/css" href="style.css">
 </head>
 <body bgcolor="#FFFFFF">
-<H1><a name="Doxygen"></a>35 SWIG and Doxygen Translation</H1>
+<H1><a name="Doxygen"></a>39 SWIG and Doxygen Translation</H1>
 <!-- INDEX -->
 <div class="sectiontoc">
 <ul>
@@ -19,13 +19,13 @@
 <ul>
 <li><a href="#Doxygen_basic_example">Basic Example</a>
 <li><a href="#Doxygen_javadoc_tags">JavaDoc Tags</a>
-<li><a href="#Doxygen_other_tags">Other Tags</a>
-<li><a href="#Doxygen_bad_behaviour">Bad Behaviour</a>
+<li><a href="#Doxygen_unsupported_tags">Unsupported tags</a>
 <li><a href="#Doxygen_further_details">Further Details</a>
 </ul>
 <li><a href="#Doxygen_developer_details">Developer Information</a>
 <ul>
 <li><a href="#Doxygen_module_design">Module Design</a>
+<li><a href="#Doxygen_debugging_commands">Debugging commands</a>
 </ul>
 <li><a href="#Doxygen_language_extension">Extending to Other Languages</a>
 </ul>
@@ -39,7 +39,7 @@ This chapter describes SWIG's support for translating Doxygen comments found in
 Currently only JavaDoc and PythonDoc is supported.
 </p>
 
-<H2><a name="Doxygen_translation_overview"></a>35.1 Doxygen Translation Overview</H2>
+<H2><a name="Doxygen_translation_overview"></a>39.1 Doxygen Translation Overview</H2>
 
 
 <p>
@@ -53,7 +53,7 @@ Questions about running SWIG are best answered in the <a href="SWIG.html#SWIG">S
 The behaviour of this functionality is wildly unpredictable if the interface file is not proper to begin with!
 </p>
 
-<H2><a name="Doxygen_file_preparation"></a>35.2 Preparations</H2>
+<H2><a name="Doxygen_file_preparation"></a>39.2 Preparations</H2>
 
 
 <p>
@@ -61,6 +61,7 @@ To make use of the comment translation system, your documentation comments must
 It is advised that you are certain your comments compile properly with Doxygen before you try to translate them.
 Doxygen itself is a deeper tool and can provide you better feedback for correcting any syntax errors that may be present.
 Please look at Doxygen's <A HREF = "http://www.stack.nl/~dimitri/doxygen/docblocks.html"> Documenting the code</A> for proper specificatons for comment format.
+However, SWIG's Doxygen parser will still point you most of errors and warnings found in comments (like unterminated strings or missing ending tags).
 </p>
 
 <div class="code"><pre>
@@ -71,17 +72,63 @@ Please look at Doxygen's <A HREF = "http://www.stack.nl/~dimitri/doxygen/docbloc
 class Shape {
 </pre></div>
 
+<p>
+Currently, the whole subset of Doxygen comment styles is supported (See <A HREF = "http://www.stack.nl/~dimitri/doxygen/docblocks.html"> Documenting the code</A>)
+Here they are:
+<div class="code"><pre>
+/**
+ * JavaDoc style comment, multiline
+ */
+/*!
+ * QT-style comment, multiline
+ */
+/**
+ Any of the above, but without intermediate *'s
+ */
+/// Single-line comment
+//! Another single-line comment
+</pre></div>
+</p>
+
+<p>
+Also any of the above with '<' added after comment-starting symbol, like <i>/**&lt;, /*!&lt;, ///&lt;, </i> or <i> //!&lt;</i>
+will be treated as post-comment and will be assigned to the node before the comment.
+<br>
+Any number of '*' or '/' in doxygen comment is considered to be a separator and is not included in final comment, so you may safely use
+comments like <i>/*********/</i> or <i>//////////</i>.
+</p>
+
 <p>
 Please note, as SWIG parses input file by itself with strict grammar, there is only a limited support for various cases of comment placement in the file.
-Comments can be placed between two C expressions on separate lines:
+<br>
+Comments can be placed before C\C++ expressions on separate lines:
 </p>
 
 <div class="code"><pre>
+/**
+ * Some comment
+ */
 void someOtherFunction();
 /**
  * Some comment
  */
 void someFunction();
+
+class Shape {
+  /*
+   * Calculate the area in cm^2
+   */
+  int getArea();
+}
+</pre></div>
+
+<p>
+After C\C++ expressions at the end of the line:
+</p>
+
+<div class="code"><pre>
+int someVariable = 9; ///< This is a var holding magic number 9
+void doNothing(); ///< This does nothing, nop
 </pre></div>
 
 <p>
@@ -109,38 +156,37 @@ enum E_NUMBERS
 
 <p>
 Just remember, if SWIG shows syntax error parsing the file because of your comment, try to move it in some other, 'safer' place as desribed above.
+<br>
+Also, currently only the comments directly before or after the nodes are supported. Doxygen structural comments are stripped out and not assigned to anything.
 </p>
-<H3><a name="Doxygen_running_swig"></a>35.2.1 Enabling Doxygen Translation</H3>
+<H3><a name="Doxygen_running_swig"></a>39.2.1 Enabling Doxygen Translation</H3>
 
 
 <p>
-There are switches like '-doxygen' and '-nodoxygen' in every module that supports converting
-documentation comments. The first one is default, so that swig by default produces correct
-proxy files with comments. Some comments in some target languages can be manually overriden by specific
+There is a switch '-doxygen' in every module that supports converting
+documentation comments. Some comments in some target languages can be manually overriden by specific
 swig's features, like <i>feature:docstring</i> or <i>feature:autodoc</i>, in this cases doxygen comments
 have lowest priority.
 </p>
 <p>
-Switching off may be needed if swig cannot correctly parse your comments, for example showing <i>Error:
-Syntax error in input(1).</i> message. Then it will just strip out every comment out of the code and
-continue happily.
+If doxygen parsing is switched off, then all the comments are stripped out in parser and all the resources used by comment parser and translator are freed.
 </p>
 
-<H3><a name="Doxygen_additional_options"></a>35.2.2 Additional Commandline Options</H3>
+<H3><a name="Doxygen_additional_options"></a>39.2.2 Additional Commandline Options</H3>
 
 
 <p>
 ALSO TO BE ADDED (JavaDoc Autobrief?)
 </p>
 
-<H2><a name="Doxygen_to_javadoc"></a>35.3 Doxygen To JavaDoc</H2>
+<H2><a name="Doxygen_to_javadoc"></a>39.3 Doxygen To JavaDoc</H2>
 
 
 <p>
 If translation is enabled, JavaDoc formatted comments should be automatically placed in the correct locations in the resulting module and proxy files.
 </p>
 
-<H3><a name="Doxygen_basic_example"></a>35.3.1 Basic Example</H3>
+<H3><a name="Doxygen_basic_example"></a>39.3.1 Basic Example</H3>
 
 
 <p>
@@ -224,80 +270,436 @@ When the Doxygen Translator Module encounters a comment it finds nothing useful
 </p>
 
 
-<H3><a name="Doxygen_javadoc_tags"></a>35.3.2 JavaDoc Tags</H3>
+<H3><a name="Doxygen_javadoc_tags"></a>39.3.2 JavaDoc Tags</H3>
+
+
+<p>
+Here is the list of all doxygen tags and the description of how they are translated to JavaDoc
+<br>
+<b>Doxygen tags:</b>
+</p>
+<div class="diagram"><pre>
+<table border="0">
+<tr>
+<td>\a</td>
+<td>wraped with &lt;i&gt; html tag</td>
+</tr>
+<tr>
+<td>\arg</td>
+<td>wrapped with &lt;li&gt; html tag</td>
+</tr>
+<tr>
+<td>\author</td>
+<td>translated to @author</td>
+</tr>
+<tr>
+<td>\authors</td>
+<td>translated to @author</td>
+</tr>
+<tr>
+<td>\b</td>
+<td>wrapped with &lt;b&gt; html tag</td>
+</tr>
+<tr>
+<td>\c</td>
+<td>wrapped with &lt;code&gt; html tag</td>
+</tr>
+<tr>
+<tr>
+<td>\cite</td>
+<td>wrapped with &lt;i&gt; html tag</td>
+</tr>
+<tr>
+<td>\code</td>
+<td>translated to {@code ...}</td>
+</tr>
+<tr>
+<td>\cond</td>
+<td>translated to 'Conditional comment: &lt;condition&gt;'</td>
+</tr>
+<tr>
+<td>\copyright</td>
+<td>replaced with 'Copyrigth:'</td>
+</tr>
+<tr>
+<td>\deprecated</td>
+<td>translated to @deprecated</td>
+</tr>
+<tr>
+<td>\e</td>
+<td>wraped with &lt;i&gt; html tag</td>
+</tr>
+<tr>
+<td>\else</td>
+<td>replaced with '}Else:{'</td>
+</tr>
+<tr>
+<td>\elseif</td>
+<td>replaced with '}Else if: &lt;condition&gt;{'</td>
+</tr>
+<tr>
+<td>\em</td>
+<td>wraped with &lt;i&gt; html tag</td>
+</tr>
+<tr>
+<td>\endcode</td>
+<td>see note for \code</td>
+</tr>
+<tr>
+<td>\endcond</td>
+<td>replaced with 'End of conditional comment.'</td>
+</tr>
+<tr>
+<td>\endif</td>
+<td>replaced with '}'</td>
+</tr>
+<tr>
+<td>\endlink</td>
+<td>see note for \link</td>
+</tr>
+<tr>
+<td>\endverbatim</td>
+<td>see note for \verbatim</td>
+</tr>
+<tr>
+<td>\exception</td>
+<td>translated to @exception</td>
+</tr>
+<tr>
+<td>\if</td>
+<td>replaced with 'If: &lt;condition&gt; {'</td>
+</tr>
+<tr>
+<td>\ifnot</td>
+<td>replaced with 'If not: &lt;condition&gt; {'</td>
+</tr>
+<tr>
+<td>\image</td>
+<td>translated to &lt;img/&gt; html tag only if target=HTML</td>
+</tr>
+<tr>
+<td>\li</td>
+<td>wraped with &lt;li&gt; html tag</td>
+</tr>
+<tr>
+<td>\link</td>
+<td>translated to {@link ...}</td>
+</tr>
+<tr>
+<td>\n</td>
+<td>replaced with new line char</td>
+</tr>
+<tr>
+<td>\note</td>
+<td>replaced with 'Note:'</td>
+</tr>
+<tr>
+<td>\overload</td>
+<td>prints 'This is an overloaded ...' according to Doxygen docs</td>
+</tr>
+<tr>
+<td>\p</td>
+<td>wraped with &lt;code&gt; html tag</td>
+</tr>
+<tr>
+<td>\par</td>
+<td>replaced with &lt;p alt='title'&gt;...&lt/p&gt;</td>
+</tr>
+<tr>
+<td>\param</td>
+<td>translated to @param</td>
+</tr>
+<tr>
+<td>\remark</td>
+<td>replaced with 'Remarks:'</td>
+</tr>
+<tr>
+<td>\remarks</td>
+<td>replaced with 'Remarks:'</td>
+</tr>
+<tr>
+<td>\result</td>
+<td>translated to @return</td>
+</tr>
+<tr>
+<td>\return</td>
+<td>translated to @return</td>
+</tr>
+<tr>
+<td>\returns</td>
+<td>translated to @return</td>
+</tr>
+<tr>
+<td>\sa</td>
+<td>translated to @see</td>
+</tr>
+<tr>
+<td>\see</td>
+<td>translated to @see</td>
+</tr>
+<tr>
+<td>\since</td>
+<td>translated to @since</td>
+</tr>
+<tr>
+<td>\throw</td>
+<td>translated to @throws</td>
+</tr>
+<tr>
+<td>\throws</td>
+<td>translated to @thtows</td>
+</tr>
+<tr>
+<td>\todo</td>
+<td>replaced with 'TODO:'</td>
+</tr>
+<tr>
+<td>\tparam</td>
+<td>translated to @param</td>
+</tr>
+<tr>
+<td>\verbatim</td>
+<td>translated to {@literal ...}</td>
+</tr>
+<tr>
+<td>\version</td>
+<td>translated to @version</td>
+</tr>
+<tr>
+<td>\warning</td>
+<td>translated to 'Warning:'</td>
+</tr>
+<tr>
+<td>\$</td>
+<td>prints $ char</td>
+</tr>
+<tr>
+<td>\@</td>
+<td>prints @ char</td>
+</tr>
+<tr>
+<td>\\</td>
+<td>prints \ char</td>
+</tr>
+<tr>
+<td>\&amp;</td>
+<td>prints &amp; char</td>
+</tr>
+<tr>
+<td>\~</td>
+<td>prints ~ char</td>
+</tr>
+<tr>
+<td>\&lt;</td>
+<td>prints &lt; char</td>
+</tr>
+<tr>
+<td>\&gt;</td>
+<td>prints &gt; char</td>
+</tr>
+<tr>
+<td>\#</td>
+<td>prints # char</td>
+</tr>
+<tr>
+<td>\%</td>
+<td>prints % char</td>
+</tr>
+<tr>
+<td>\&quot;</td>
+<td>prints &quot; char</td>
+</tr>
+<tr>
+<td>\.</td>
+<td>prints . char</td>
+</tr>
+<tr>
+<td>\::</td>
+<td>prints ::</td>
+</tr>
+</table>
+</pre></div>
+
+<H3><a name="Doxygen_unsupported_tags"></a>39.3.3 Unsupported tags</H3>
 
 
 <p>
 Doxygen has a wealth of tags such as @latexonly that have no equivalent in JavaDoc.
-As a result several tags that have no translation (or particular use, such as some linking and section tags) are supressed.
+As a result several tags that have no translation (or particular use, such as some linking and section tags) are supressed with their content just printed out (if it has any sense, typically text content).
 If you are interested in more of the specifics of JavaDoc, please visit <A HREF="http://java.sun.com/j2se/javadoc/writingdoccomments/">How to Write Doc Comments for the Javadoc Tool.</A>
-</p>
-
-<p>
-<b>Doxygen and JavaDoc Equivalent Tags</b>
+<br>
+Here is the list of these tags:
 </p>
 <div class="diagram"><pre>
-* @param      
-* @return      
-* @exception   
-* @author      
-* @version     
-* @see         
-* @since       
-* @serial      
-* @deprecated  
+<table border="0">
+<tr>
+<td>\addindex</td>
+<td>\addtogroup</td>
+<td>\anchor</td>
+<td>\attention</td>
+</tr>
+<tr>
+<td>\brief</td>
+<td>\bug</td>
+<td>\callgraph</td>
+<td>\callergraph</td>
+</tr>
+<tr>
+<td>\class</td>
+<td>\copybrief</td>
+<td>\copydetails</td>
+<td>\copydoc</td>
+</tr>
+<tr>
+<td>\date</td>
+<td>\def</td>
+<td>\defgroup</td>
+<td>\details</td>
+</tr>
+<tr>
+<td>\dir</td>
+<td>\dontinclude</td>
+<td>\dot</td>
+<td>\dotfile</td>
+</tr>
+<tr>
+<td>\enddot</td>
+<td>\endhtmlonly</td>
+<td>\endinternal</td>
+<td>\endlatexonly</td>
+</tr>
+<tr>
+<td>\endmanonly</td>
+<td>\endmsc</td>
+<td>\endrtfonly</td>
+<td>\endxmlonly</td>
+</tr>
+<tr>
+<td>\enum</td>
+<td>\example</td>
+<td>\extends</td>
+<td>\f$</td>
+</tr>
+<tr>
+<td>\f[</td>
+<td>\f]</td>
+<td>\f{</td>
+<td>\f}</td>
+</tr>
+<tr>
+<td>\file</td>
+<td>\fn</td>
+<td>\headerfile</td>
+<td>\hideinitializer</td>
+</tr>
+<tr>
+<td>\htmlinclude</td>
+<td>\htmlonly</td>
+<td>\implements</td>
+<td>\include</td>
+</tr>
+<tr>
+<td>\includelineno</td>
+<td>\ingroup</td>
+<td>\internal</td>
+<td>\invariant</td>
+</tr>
+<tr>
+<td>\interface</td>
+<td>\latexonly</td>
+<td>\line</td>
+<td>\mainpage</td>
+</tr>
+<tr>
+<td>\manonly</td>
+<td>\memberof</td>
+<td>\msc</td>
+<td>\mscfile</td>
+</tr>
+<tr>
+<td>\name</td>
+<td>\namespace</td>
+<td>\nosubgrouping</td>
+<td>\package</td>
+</tr>
+<tr>
+<td>\page</td>
+<td>\paragraph</td>
+<td>\post</td>
+<td>\pre</td>
+</tr>
+<tr>
+<td>\private</td>
+<td>\privatesection</td>
+<td>\property</td>
+<td>\protected</td>
+</tr>
+<tr>
+<td>\protectedsection</td>
+<td>\protocol</td>
+<td>\public</td>
+<td>\publicsection</td>
+</tr>
+<tr>
+<td>\ref</td>
+<td>\related</td>
+<td>\relates</td>
+<td>\relatedalso</td>
+</tr>
+<tr>
+<td>\relatesalso</td>
+<td>\retval</td>
+<td>\rtfonly</td>
+<td>\section</td>
+</tr>
+<tr>
+<td>\short</td>
+<td>\showinitializer</td>
+<td>\skip</td>
+<td>\skipline</td>
+</tr>
+<tr>
+<td>\snippet</td>
+<td>\struct</td>
+<td>\subpage</td>
+<td>\subsection</td>
+</tr>
+<tr>
+<td>\subsubsection</td>
+<td>\tableofcontents</td>
+<td>\test</td>
+<td>\typedef</td>
+</tr>
+<tr>
+<td>\union</td>
+<td>\until</td>
+<td>\var</td>
+<td>\verbinclude</td>
+</tr>
+<tr>
+<td>\weakgroup</td>
+<td>\xmlonly</td>
+<td>\xrefitem</td>
+<td>\category</td>
+</tr>
+</table>
 </pre></div>
 
-<H3><a name="Doxygen_other_tags"></a>35.3.3 Other Tags</H3>
-
-
-<p>
-Because there are no specific JavaDoc tags for some important information, some tags are given plain English descriptions of their presence, such as @bug.
-This is a feature currently still being developed and it is likely that more information from the original Doxygen Comments will be reproduced as this module matures.
-</p>
-<H3><a name="Doxygen_bad_behaviour"></a>35.3.4 Bad Behaviour</H3>
-
-
-<p>
-There are some tags that the Doxygen Translator Module currently does not expect to encounter.
-This includes the PHP-only Doxygen commands such as @publicsection:
-</p>
-
-<p>
-<b> Completely Unsupported Tags</b>
-</p>
-<div class="diagram"><pre>
-"annotatedclasslist", "classhierarchy", "define", "functionindex", 
-"header", "headerfilelist", "inherit", "l", "postheader", "private",
- "privatesection", "protected", "protectedsection", "public", "publicsection"
-</pre></div>
-
-<p>
-The parsing behaviour will be unpredictable if any of these are encountered for now.
-This should eventually be changed so that they are simply ignored.
-</p>
-<p>
-In general parsing errors should not interfere with the operation of SWIG itself.
-Blank comments or lack of comments could be an indication of either a parsing error or a lack of meaningful tags in a specific blob of doxygen. 
-</p>
-
-
-<H3><a name="Doxygen_further_details"></a>35.3.5 Further Details</H3>
+<H3><a name="Doxygen_further_details"></a>39.3.4 Further Details</H3>
 
 
 <p>
 TO BE ADDED.
 </p>
 
-
-<H2><a name="Doxygen_developer_details"></a>35.4 Developer Information</H2>
+<H2><a name="Doxygen_developer_details"></a>39.4 Developer Information</H2>
 
 
 <p>
 Currently a good deal of this Module still needs some reworking, particularly on the side of the parser and JavaDoc producer.
 </p>
 
-<H3><a name="Doxygen_module_design"></a>35.4.1 Module Design</H3>
+<H3><a name="Doxygen_module_design"></a>39.4.1 Module Design</H3>
 
 
 <p>
@@ -320,7 +722,19 @@ This module builds its own private parse tree and hands it to a separate class f
 For example, <tt>JavaDocConverter</tt> is the JavaDoc module class.
 </p>
 
-<H2><a name="Doxygen_language_extension"></a>35.5 Extending to Other Languages</H2>
+<H3><a name="Doxygen_debugging_commands"></a>39.4.2 Debugging commands</H3>
+
+
+<p>
+There are two handy command line switches, that enable lots of detailed debug information printing.
+</p>
+
+<div class="shell"><pre>
+  -debug-doxygen-parser     - Display doxygen parser module debugging information
+  -debug-doxygen-translator - Display doxygen translator module debugging information
+</pre></div>
+
+<H2><a name="Doxygen_language_extension"></a>39.5 Extending to Other Languages</H2>
 
 
 <p>

From 64b5efc5d7d69b36a3c3b1d448edfa702e43cad1 Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Mon, 30 Jul 2012 08:07:15 +0000
Subject: [PATCH 108/314] Updated documentation, added description of PyDoc
 tags

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13429 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Doc/Devel/plan-gsoc-2012.txt |   4 +-
 Doc/Manual/Contents.html     |   7 +
 Doc/Manual/Doxygen.html      | 532 +++++++++++++++++++++++++++++++++--
 3 files changed, 519 insertions(+), 24 deletions(-)

diff --git a/Doc/Devel/plan-gsoc-2012.txt b/Doc/Devel/plan-gsoc-2012.txt
index a3bf2ca39..43fc1adc3 100644
--- a/Doc/Devel/plan-gsoc-2012.txt
+++ b/Doc/Devel/plan-gsoc-2012.txt
@@ -322,6 +322,6 @@ Documentation
 SWIG documentation will contain:
 -OK- command line options
 -OK- list of implemented features (types and placements of comments)
-- list of unimplemented features (types and placements of comments)
-- list of tags and their translations (all Doxygen tags).
+-OK- list of unimplemented features (types and placements of comments)
+-OK- list of tags and their translations (all Doxygen tags).
 
diff --git a/Doc/Manual/Contents.html b/Doc/Manual/Contents.html
index 77518c268..ca66d87cc 100644
--- a/Doc/Manual/Contents.html
+++ b/Doc/Manual/Contents.html
@@ -1709,6 +1709,13 @@
 <li><a href="Doxygen.html#Doxygen_unsupported_tags">Unsupported tags</a>
 <li><a href="Doxygen.html#Doxygen_further_details">Further Details</a>
 </ul>
+<li><a href="Doxygen.html#Doxygen_to_pydoc">Doxygen To PythonDoc</a>
+<ul>
+<li><a href="Doxygen.html#Doxygen_python_basic_example">Basic Example</a>
+<li><a href="Doxygen.html#Doxygen_pydoc_tags">PyDoc translator</a>
+<li><a href="Doxygen.html#Doxygen_python_unsupported_tags">Unsupported tags</a>
+<li><a href="Doxygen.html#Doxygen_python_further_details">Further Details</a>
+</ul>
 <li><a href="Doxygen.html#Doxygen_developer_details">Developer Information</a>
 <ul>
 <li><a href="Doxygen.html#Doxygen_module_design">Module Design</a>
diff --git a/Doc/Manual/Doxygen.html b/Doc/Manual/Doxygen.html
index 54fa1b6bf..77c00b40e 100644
--- a/Doc/Manual/Doxygen.html
+++ b/Doc/Manual/Doxygen.html
@@ -22,6 +22,13 @@
 <li><a href="#Doxygen_unsupported_tags">Unsupported tags</a>
 <li><a href="#Doxygen_further_details">Further Details</a>
 </ul>
+<li><a href="#Doxygen_to_pydoc">Doxygen To PythonDoc</a>
+<ul>
+<li><a href="#Doxygen_python_basic_example">Basic Example</a>
+<li><a href="#Doxygen_pydoc_tags">PyDoc translator</a>
+<li><a href="#Doxygen_python_unsupported_tags">Unsupported tags</a>
+<li><a href="#Doxygen_python_further_details">Further Details</a>
+</ul>
 <li><a href="#Doxygen_developer_details">Developer Information</a>
 <ul>
 <li><a href="#Doxygen_module_design">Module Design</a>
@@ -220,9 +227,9 @@ Simply running SWIG should result in the following code being present in Shapes.
 <div class="targetlang"><pre>
 
 /**
- * This is describing class Shape  
+ * This is describing class Shape 
+ * @author Bob 
  * 
- * @author	Bob  
  */
 
 public class Shape {
@@ -230,35 +237,40 @@ public class Shape {
 ...
 
 /**
- * Important Variables  
- * 
+ * Important Variables 
  */
   public void setX(double value) {
-    exampleJNI.Shape_x_set(swigCPtr, this, value);
+    ShapesJNI.Shape_x_set(swigCPtr, this, value);
   }
 
 /**
- * Important variables  
+ * Important Variables 
  */
   public double getX() {
-    return exampleJNI.Shape_x_get(swigCPtr, this);
+    return ShapesJNI.Shape_x_get(swigCPtr, this);
   }
 
-...
+/**
+ * Moves the Shape 
+ */
+  public void move(double dx, double dy) {
+    ShapesJNI.Shape_move(swigCPtr, this, dx, dy);
+  }
 
 /**
- * @return	the area  
+ * @return the area 
  */
   public double area() {
-    return exampleJNI.Shape_area(swigCPtr, this);
+    return ShapesJNI.Shape_area(swigCPtr, this);
   }
 
 /**
- * @return	the perimeter  
+ * @return the perimeter 
  */
   public double perimeter() {
-    return exampleJNI.Shape_perimeter(swigCPtr, this);
+    return ShapesJNI.Shape_perimeter(swigCPtr, this);
   }
+}
 
 </pre></div>
 
@@ -282,7 +294,7 @@ Here is the list of all doxygen tags and the description of how they are transla
 <table border="0">
 <tr>
 <td>\a</td>
-<td>wraped with &lt;i&gt; html tag</td>
+<td>wrapped with &lt;i&gt; html tag</td>
 </tr>
 <tr>
 <td>\arg</td>
@@ -327,7 +339,7 @@ Here is the list of all doxygen tags and the description of how they are transla
 </tr>
 <tr>
 <td>\e</td>
-<td>wraped with &lt;i&gt; html tag</td>
+<td>wrapped with &lt;i&gt; html tag</td>
 </tr>
 <tr>
 <td>\else</td>
@@ -339,7 +351,7 @@ Here is the list of all doxygen tags and the description of how they are transla
 </tr>
 <tr>
 <td>\em</td>
-<td>wraped with &lt;i&gt; html tag</td>
+<td>wrapped with &lt;i&gt; html tag</td>
 </tr>
 <tr>
 <td>\endcode</td>
@@ -379,7 +391,7 @@ Here is the list of all doxygen tags and the description of how they are transla
 </tr>
 <tr>
 <td>\li</td>
-<td>wraped with &lt;li&gt; html tag</td>
+<td>wrapped with &lt;li&gt; html tag</td>
 </tr>
 <tr>
 <td>\link</td>
@@ -399,7 +411,7 @@ Here is the list of all doxygen tags and the description of how they are transla
 </tr>
 <tr>
 <td>\p</td>
-<td>wraped with &lt;code&gt; html tag</td>
+<td>wrapped with &lt;code&gt; html tag</td>
 </tr>
 <tr>
 <td>\par</td>
@@ -692,14 +704,490 @@ Here is the list of these tags:
 TO BE ADDED.
 </p>
 
-<H2><a name="Doxygen_developer_details"></a>39.4 Developer Information</H2>
+<H2><a name="Doxygen_to_pydoc"></a>39.4 Doxygen To PythonDoc</H2>
 
 
 <p>
-Currently a good deal of this Module still needs some reworking, particularly on the side of the parser and JavaDoc producer.
+If translation is enabled, PyDoc formatted comments should be automatically placed in the correct locations in the resulting module and proxy files.
+The problem is that PyDoc has no tag mechanism like Doxygen or JavaDoc, so most of Doxygen commands are translated as English plaintext pieces.
 </p>
 
-<H3><a name="Doxygen_module_design"></a>39.4.1 Module Design</H3>
+<H3><a name="Doxygen_python_basic_example"></a>39.4.1 Basic Example</H3>
+
+
+<p>
+Here is an example segment from an included header file
+</p>
+<div class="code"><pre>
+/*! This is describing class Shape
+ \author Bob
+ */
+
+class Shape {
+public:
+  Shape() {
+    nshapes++;
+  }
+  virtual ~Shape() {
+    nshapes--;
+  };
+  double  x, y; /*!&lt; Important Variables */
+  void    move(double dx, double dy); /*!&lt; Moves the Shape */
+  virtual double area(void) = 0; /*!&lt; \return the area */
+  virtual double perimeter(void) = 0; /*!&lt; \return the perimeter */
+  static  int nshapes;
+};
+</pre></div>
+
+<p>
+Simply running SWIG should result in the following code being present in Shapes.py
+</p>
+
+<div class="targetlang"><pre>
+
+...
+
+class Shape(_object):
+    """
+    This is describing class Shape 
+    Authors:
+    Bob 
+
+    """
+    
+    ...
+    
+    def move(self, *args):
+        """
+        Moves the Shape 
+        """
+        return _Shapes.Shape_move(self, *args)
+
+    def area(self):
+        """
+        Return:
+        the area 
+        """
+        return _Shapes.Shape_area(self)
+
+    def perimeter(self):
+        """
+        Return:
+        the perimeter 
+        """
+        return _Shapes.Shape_perimeter(self)
+</pre></div>
+
+<p>
+Currently Doxygen comments assigned to vars are not present in proxy file, so they have no comment translated for them.
+</p>
+
+<H3><a name="Doxygen_pydoc_tags"></a>39.4.2 PyDoc translator</H3>
+
+
+<p>
+Here is the list of all doxygen tags and the description of how they are translated to PyDoc
+<br>
+<b>Doxygen tags:</b>
+</p>
+<div class="diagram"><pre>
+<table border="0">
+<tr>
+<td>\a</td>
+<td>wrapped with '_'</td>
+</tr>
+<tr>
+<td>\arg</td>
+<td>prepended with ' --'</td>
+</tr>
+<tr>
+<td>\author</td>
+<td>prints 'Author:'</td>
+</tr>
+<tr>
+<td>\authors</td>
+<td>prints 'Author:'</td>
+</tr>
+<tr>
+<td>\b</td>
+<td>wrapped with '__'</td>
+</tr>
+<tr>
+<td>\cite</td>
+<td>wrapped with single quotes</td>
+</tr>
+<tr>
+<td>\cond</td>
+<td>translated to 'Conditional comment: &lt;condition&gt;'</td>
+</tr>
+<tr>
+<td>\copyright</td>
+<td>prints'Copyrigth:'</td>
+</tr>
+<tr>
+<td>\deprecated</td>
+<td>prints 'Deprecated:'</td>
+</tr>
+<tr>
+<td>\e</td>
+<td>wrapped with '_'</td>
+</tr>
+<tr>
+<td>\else</td>
+<td>replaced with '}Else:{'</td>
+</tr>
+<tr>
+<td>\elseif</td>
+<td>replaced with '}Else if: &lt;condition&gt;{'</td>
+</tr>
+<tr>
+<td>\em</td>
+<td>wrapped with '_'</td>
+</tr>
+<tr>
+<td>\endcond</td>
+<td>replaced with 'End of conditional comment.'</td>
+</tr>
+<tr>
+<td>\endif</td>
+<td>replaced with '}'</td>
+</tr>
+<tr>
+<td>\exception</td>
+<td>replaced with 'Throws:'</td>
+</tr>
+<tr>
+<td>\if</td>
+<td>replaced with 'If: &lt;condition&gt; {'</td>
+</tr>
+<tr>
+<td>\ifnot</td>
+<td>replaced with 'If not: &lt;condition&gt; {'</td>
+</tr>
+<tr>
+<td>\li</td>
+<td>prepended with ' --'</td>
+</tr>
+<tr>
+<td>\n</td>
+<td>replaced with new line char</td>
+</tr>
+<tr>
+<td>\note</td>
+<td>replaced with 'Note:'</td>
+</tr>
+<tr>
+<td>\overload</td>
+<td>prints 'This is an overloaded ...' according to Doxygen docs</td>
+</tr>
+<tr>
+<td>\par</td>
+<td>replaced with 'Title: ...'</td>
+</tr>
+<tr>
+<td>\param</td>
+<td>translated to 'Arguments:\n param(type) --description'</td>
+</tr>
+<tr>
+<td>\remark</td>
+<td>replaced with 'Remarks:'</td>
+</tr>
+<tr>
+<td>\remarks</td>
+<td>replaced with 'Remarks:'</td>
+</tr>
+<tr>
+<td>\result</td>
+<td>replaced with 'Result:'</td>
+</tr>
+<tr>
+<td>\return</td>
+<td>replaced with 'Result:'</td>
+</tr>
+<tr>
+<td>\returns</td>
+<td>replaced with 'Result:'</td>
+</tr>
+<tr>
+<td>\sa</td>
+<td>replaced with 'See also:'</td>
+</tr>
+<tr>
+<td>\see</td>
+<td>replaced with 'See also:'</td>
+</tr>
+<tr>
+<td>\since</td>
+<td>replaced with 'Since:'</td>
+</tr>
+<tr>
+<td>\throw</td>
+<td>replaced with 'Throws:'</td>
+</tr>
+<tr>
+<td>\throws</td>
+<td>replaced wih 'Throws:'</td>
+</tr>
+<tr>
+<td>\todo</td>
+<td>replaced with 'TODO:'</td>
+</tr>
+<tr>
+<td>\tparam</td>
+<td>translated to 'Arguments:\n param(type) --description'</td>
+</tr>
+<tr>
+<td>\version</td>
+<td>replaced with 'Version:'</td>
+</tr>
+<tr>
+<td>\warning</td>
+<td>translated to 'Warning:'</td>
+</tr>
+<tr>
+<td>\$</td>
+<td>prints $ char</td>
+</tr>
+<tr>
+<td>\@</td>
+<td>prints @ char</td>
+</tr>
+<tr>
+<td>\\</td>
+<td>prints \ char</td>
+</tr>
+<tr>
+<td>\&amp;</td>
+<td>prints &amp; char</td>
+</tr>
+<tr>
+<td>\~</td>
+<td>prints ~ char</td>
+</tr>
+<tr>
+<td>\&lt;</td>
+<td>prints &lt; char</td>
+</tr>
+<tr>
+<td>\&gt;</td>
+<td>prints &gt; char</td>
+</tr>
+<tr>
+<td>\#</td>
+<td>prints # char</td>
+</tr>
+<tr>
+<td>\%</td>
+<td>prints % char</td>
+</tr>
+<tr>
+<td>\&quot;</td>
+<td>prints &quot; char</td>
+</tr>
+<tr>
+<td>\.</td>
+<td>prints . char</td>
+</tr>
+<tr>
+<td>\::</td>
+<td>prints ::</td>
+</tr>
+</table>
+</pre></div>
+
+<H3><a name="Doxygen_python_unsupported_tags"></a>39.4.3 Unsupported tags</H3>
+
+
+<p>
+Doxygen has a wealth of tags such as @latexonly that have no equivalent in PyDoc.
+As a result several tags that have no translation (or particular use, such as some linking and section tags) are supressed with their content just printed out (if it has any sense, typically text content).
+<br>
+Here is the list of these tags:
+</p>
+<div class="diagram"><pre>
+<table border="0">
+<tr>
+<td>\addindex</td>
+<td>\addtogroup</td>
+<td>\anchor</td>
+<td>\attention</td>
+</tr>
+<tr>
+<td>\brief</td>
+<td>\bug</td>
+<td>\callgraph</td>
+<td>\callergraph</td>
+</tr>
+<tr>
+<td>\class</td>
+<td>\copybrief</td>
+<td>\copydetails</td>
+<td>\copydoc</td>
+</tr>
+<tr>
+<td>\date</td>
+<td>\def</td>
+<td>\defgroup</td>
+<td>\details</td>
+</tr>
+<tr>
+<td>\dir</td>
+<td>\dontinclude</td>
+<td>\dot</td>
+<td>\dotfile</td>
+</tr>
+<tr>
+<td>\code</td>
+<td>\endcode</td>
+<td>\endverbatim</td>
+<td>\endlink</td>
+</tr>
+<tr>
+<td>\enddot</td>
+<td>\endhtmlonly</td>
+<td>\endinternal</td>
+<td>\endlatexonly</td>
+</tr>
+<tr>
+<td>\endmanonly</td>
+<td>\endmsc</td>
+<td>\endrtfonly</td>
+<td>\endxmlonly</td>
+</tr>
+<tr>
+<td>\enum</td>
+<td>\example</td>
+<td>\extends</td>
+<td>\f$</td>
+</tr>
+<tr>
+<td>\f[</td>
+<td>\f]</td>
+<td>\f{</td>
+<td>\f}</td>
+</tr>
+<tr>
+<td>\file</td>
+<td>\fn</td>
+<td>\headerfile</td>
+<td>\hideinitializer</td>
+</tr>
+<tr>
+<td>\htmlinclude</td>
+<td>\htmlonly</td>
+<td>\implements</td>
+<td>\include</td>
+</tr>
+<tr>
+<td>\image</td>
+<td>\link</td>
+<td>\verbatim</td>
+<td>\p</td>
+</tr>
+<tr>
+<td>\includelineno</td>
+<td>\ingroup</td>
+<td>\internal</td>
+<td>\invariant</td>
+</tr>
+<tr>
+<td>\interface</td>
+<td>\latexonly</td>
+<td>\line</td>
+<td>\mainpage</td>
+</tr>
+<tr>
+<td>\manonly</td>
+<td>\memberof</td>
+<td>\msc</td>
+<td>\mscfile</td>
+</tr>
+<tr>
+<td>\name</td>
+<td>\namespace</td>
+<td>\nosubgrouping</td>
+<td>\package</td>
+</tr>
+<tr>
+<td>\page</td>
+<td>\paragraph</td>
+<td>\post</td>
+<td>\pre</td>
+</tr>
+<tr>
+<td>\private</td>
+<td>\privatesection</td>
+<td>\property</td>
+<td>\protected</td>
+</tr>
+<tr>
+<td>\protectedsection</td>
+<td>\protocol</td>
+<td>\public</td>
+<td>\publicsection</td>
+</tr>
+<tr>
+<td>\ref</td>
+<td>\related</td>
+<td>\relates</td>
+<td>\relatedalso</td>
+</tr>
+<tr>
+<td>\relatesalso</td>
+<td>\retval</td>
+<td>\rtfonly</td>
+<td>\section</td>
+</tr>
+<tr>
+<td>\short</td>
+<td>\showinitializer</td>
+<td>\skip</td>
+<td>\skipline</td>
+</tr>
+<tr>
+<td>\snippet</td>
+<td>\struct</td>
+<td>\subpage</td>
+<td>\subsection</td>
+</tr>
+<tr>
+<td>\subsubsection</td>
+<td>\tableofcontents</td>
+<td>\test</td>
+<td>\typedef</td>
+</tr>
+<tr>
+<td>\union</td>
+<td>\until</td>
+<td>\var</td>
+<td>\verbinclude</td>
+</tr>
+<tr>
+<td>\weakgroup</td>
+<td>\xmlonly</td>
+<td>\xrefitem</td>
+<td>\category</td>
+</tr>
+<tr>
+<td>\c</td>
+</tr>
+</table>
+</pre></div>
+
+<H3><a name="Doxygen_python_further_details"></a>39.4.4 Further Details</H3>
+
+
+<p>
+TO BE ADDED.
+</p>
+
+<H2><a name="Doxygen_developer_details"></a>39.5 Developer Information</H2>
+
+
+<p>
+</p>
+
+<H3><a name="Doxygen_module_design"></a>39.5.1 Module Design</H3>
 
 
 <p>
@@ -722,7 +1210,7 @@ This module builds its own private parse tree and hands it to a separate class f
 For example, <tt>JavaDocConverter</tt> is the JavaDoc module class.
 </p>
 
-<H3><a name="Doxygen_debugging_commands"></a>39.4.2 Debugging commands</H3>
+<H3><a name="Doxygen_debugging_commands"></a>39.5.2 Debugging commands</H3>
 
 
 <p>
@@ -734,7 +1222,7 @@ There are two handy command line switches, that enable lots of detailed debug in
   -debug-doxygen-translator - Display doxygen translator module debugging information
 </pre></div>
 
-<H2><a name="Doxygen_language_extension"></a>39.5 Extending to Other Languages</H2>
+<H2><a name="Doxygen_language_extension"></a>39.6 Extending to Other Languages</H2>
 
 
 <p>

From e764c9a73e738aabe0a0a8dbd3cdc5b357de636e Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Mon, 30 Jul 2012 08:09:14 +0000
Subject: [PATCH 109/314] Made JavaDoc output nicer

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13430 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Source/DoxygenTranslator/src/JavaDocConverter.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.cpp b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
index 165075708..0856eabf1 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
@@ -276,7 +276,7 @@ String *JavaDocConverter::makeDocumentation(Node *node) {
     printTree(entityList);
   }
 
-  std::string javaDocString = "/**";
+  std::string javaDocString = "/**\n * ";
 
   for (std::list < DoxygenEntity >::iterator entityIterator = entityList.begin(); entityIterator != entityList.end();) {
     translateEntity(*entityIterator, javaDocString);

From fb3ee4fb78dd3be28fdd8308af33ae5818e031b6 Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Thu, 2 Aug 2012 10:31:02 +0000
Subject: [PATCH 110/314] Implemented support for default args - overloaded
 functions, optional feature 1 in my project plan. Extended testcase.

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13483 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Examples/test-suite/doxygen_basic_translate.i |  1 +
 .../java/doxygen_basic_translate_runme.java   |  5 +++
 .../python/doxygen_basic_translate_runme.py   |  4 +-
 Source/CParse/parser.y                        | 15 +++++--
 .../src/JavaDocConverter.cpp                  | 44 ++++++++++++++++---
 .../DoxygenTranslator/src/JavaDocConverter.h  |  7 +++
 6 files changed, 66 insertions(+), 10 deletions(-)

diff --git a/Examples/test-suite/doxygen_basic_translate.i b/Examples/test-suite/doxygen_basic_translate.i
index c06cbddc9..9cef037b1 100644
--- a/Examples/test-suite/doxygen_basic_translate.i
+++ b/Examples/test-suite/doxygen_basic_translate.i
@@ -61,6 +61,7 @@ int function4()
 
 /**
  * Test for default args
+ * @param a Some parameter, default is 42
  */
 int function5(int a=42)
 {
diff --git a/Examples/test-suite/java/doxygen_basic_translate_runme.java b/Examples/test-suite/java/doxygen_basic_translate_runme.java
index 50d6cedda..4e95b73a7 100644
--- a/Examples/test-suite/java/doxygen_basic_translate_runme.java
+++ b/Examples/test-suite/java/doxygen_basic_translate_runme.java
@@ -63,6 +63,11 @@ public class doxygen_basic_translate_runme {
     		" \n" +
     		"");
     wantedComments.put("doxygen_basic_translate.doxygen_basic_translate.function5(int)",
+    		" Test for default args \n" +
+    		" @param a Some parameter, default is 42" +
+    		" \n" +
+    		"");
+    wantedComments.put("doxygen_basic_translate.doxygen_basic_translate.function5()",
     		" Test for default args \n" +
     		" \n" +
     		"");
diff --git a/Examples/test-suite/python/doxygen_basic_translate_runme.py b/Examples/test-suite/python/doxygen_basic_translate_runme.py
index 95596c1f3..a952df8b0 100644
--- a/Examples/test-suite/python/doxygen_basic_translate_runme.py
+++ b/Examples/test-suite/python/doxygen_basic_translate_runme.py
@@ -58,5 +58,7 @@ check(doxygen_basic_translate.function4.__doc__, ''
 '  }'
 )
 check(doxygen_basic_translate.function5.__doc__, ''
-'  Test for default args'
+'  Test for default args \n'
+'  Arguments: \n'
+'  a (int) -- Some parameter, default is 42\n'
 )
\ No newline at end of file
diff --git a/Source/CParse/parser.y b/Source/CParse/parser.y
index 6aed8c3f9..e331752bf 100644
--- a/Source/CParse/parser.y
+++ b/Source/CParse/parser.y
@@ -190,6 +190,7 @@ static Node *copy_node(Node *n) {
 }
 
 static void set_comment(Node *n, String *comment) {
+  String *name;
   Parm *p;
   if (!n || !comment)
     return;
@@ -206,6 +207,16 @@ static void set_comment(Node *n, String *comment) {
       p=nextSibling(p);
     }
   }
+  
+  /* Append same comment to every generated overload */
+  name = Getattr(n, "name");
+  if (!name)
+    return;
+  n = nextSibling(n);
+  while (n && Getattr(n, "name") && Strcmp(Getattr(n, "name"), name) == 0) {
+    Setattr(n, "DoxygenComment", comment);
+    n = nextSibling(n);
+  }
 }
 
 /* -----------------------------------------------------------------------------
@@ -1586,10 +1597,6 @@ static void default_arguments(Node *n) {
           if (throws) Setattr(new_function,"throws",pl);
 	  Delete(pl);
         }
-	
-	/* copy doxygen comments if found */
-	if(Getattr(function,"DoxygenComment"))
-	  Setattr(new_function,"DoxygenComment",Getattr(function,"DoxygenComment"));
 
         /* copy specific attributes for global (or in a namespace) template functions - these are not templated class methods */
         if (strcmp(cntype,"template") == 0) {
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.cpp b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
index 0856eabf1..421134828 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
@@ -66,8 +66,8 @@ void JavaDocConverter::fillStaticTables() {
   tagHandlers["deprecated"] = make_pair(&JavaDocConverter::handleTagSame, "");
   tagHandlers["exception"] = make_pair(&JavaDocConverter::handleTagSame, "");
   tagHandlers["package"] = make_pair(&JavaDocConverter::handleTagSame, "");
-  tagHandlers["param"] = make_pair(&JavaDocConverter::handleTagSame, "");
-  tagHandlers["tparam"] = make_pair(&JavaDocConverter::handleTagSame, "param");
+  tagHandlers["param"] = make_pair(&JavaDocConverter::handleTagParam, "");
+  tagHandlers["tparam"] = make_pair(&JavaDocConverter::handleTagParam, "");
   tagHandlers["result"] = make_pair(&JavaDocConverter::handleTagSame, "return");
   tagHandlers["return"] = make_pair(&JavaDocConverter::handleTagSame, "");
   tagHandlers["returns"] = make_pair(&JavaDocConverter::handleTagSame, "return");
@@ -151,6 +151,23 @@ std::string JavaDocConverter::formatCommand(std::string unformattedLine, int ind
   return formattedLines;
 }
 
+bool JavaDocConverter::paramExists(std::string param) {
+  ParmList *plist = CopyParmList(Getattr(currentNode, "parms"));
+  Parm *p = NULL;
+  for (p = plist; p;) {
+    if (Char(Getattr(p, "name")) == param)
+      return true;
+    /*
+     * doesn't seem to work always: in some cases (especially for 'self' parameters)
+     * tmap:in is present, but tmap:in:next is not and so this code skips all the parameters
+     */
+    //p = Getattr(p, "tmap:in") ? Getattr(p, "tmap:in:next") : nextSibling(p);
+    p = nextSibling(p);
+  }
+  Delete(plist);
+  return false;
+}
+
 std::string JavaDocConverter::translateSubtree(DoxygenEntity & doxygenEntity) {
   std::string translatedComment;
   
@@ -250,12 +267,26 @@ void JavaDocConverter::handleTagImage(DoxygenEntity& tag, std::string& translate
 void JavaDocConverter::handleTagPar(DoxygenEntity& tag, std::string& translatedComment, std::string&) {
   std::string dummy;
   translatedComment += "<p";
-  if (tag.entityList.size())
+  if (tag.entityList.size()) {
     translatedComment += " alt=\"" + tag.entityList.begin()->data + "\"";
-  translatedComment += ">";
+    translatedComment += ">";
+    tag.entityList.pop_front();
+    handleParagraph(tag, translatedComment, dummy);
+  }
+  translatedComment += "</p>";
+}
+
+void JavaDocConverter::handleTagParam(DoxygenEntity& tag, std::string& translatedComment, std::string&) {
+  std::string dummy;
+  if (!tag.entityList.size())
+    return;
+  if (!paramExists(tag.entityList.begin()->data))
+    return;
+
+  translatedComment += "@param ";
+  translatedComment += tag.entityList.begin()->data + " ";
   tag.entityList.pop_front();
   handleParagraph(tag, translatedComment, dummy);
-  translatedComment += "</p>";
 }
 
 String *JavaDocConverter::makeDocumentation(Node *node) {
@@ -278,6 +309,9 @@ String *JavaDocConverter::makeDocumentation(Node *node) {
 
   std::string javaDocString = "/**\n * ";
 
+  // store the current node
+  // (currently just to handle params)
+  currentNode = node;
   for (std::list < DoxygenEntity >::iterator entityIterator = entityList.begin(); entityIterator != entityList.end();) {
     translateEntity(*entityIterator, javaDocString);
     entityIterator++;
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.h b/Source/DoxygenTranslator/src/JavaDocConverter.h
index 1d51a8d7b..f68a712b9 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.h
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.h
@@ -85,12 +85,19 @@ protected:
    * Insert <p alt='title'>...</p>
    */
   void handleTagPar(DoxygenEntity &tag, std::string &translatedComment, std::string &arg);
+  /*
+   * Insert @param command, if it is really a function param
+   */
+  void handleTagParam(DoxygenEntity &tag, std::string &translatedComment, std::string &arg);
 
 
 private:
+  Node *currentNode;
   // this contains the handler pointer and one string argument
   static std::map<std::string, std::pair<tagHandler, std::string> > tagHandlers;
   void fillStaticTables();
+
+  bool paramExists(std::string param);
 };
 
 #endif

From c72a56c6f1d5f1366e09bd99e8bef5b31b0c9598 Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Thu, 2 Aug 2012 12:22:26 +0000
Subject: [PATCH 111/314] Small fix to display params type correctly in
 PyDocConverter

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13484 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Source/DoxygenTranslator/src/PyDocConverter.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Source/DoxygenTranslator/src/PyDocConverter.cpp b/Source/DoxygenTranslator/src/PyDocConverter.cpp
index a873cfb16..df9466067 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/PyDocConverter.cpp
@@ -101,7 +101,7 @@ std::string PyDocConverter::getParamType(std::string param) {
   Parm *p = NULL;
   for (p = plist; p;) {
     if (Char(Getattr(p, "name")) == param) {
-      std::string type = Char(Swig_name_make(currentNode, 0, Getattr(p, "type"), 0, 0));
+      std::string type = Char(SwigType_str(Getattr(p, "type"), ""));
       return type;
     }
     /*

From 174e20318038b2311051938a88fa0233f744e50c Mon Sep 17 00:00:00 2001
From: Marko Klopcic <marko.klopcic@isystem.si>
Date: Thu, 2 Aug 2012 20:48:28 +0000
Subject: [PATCH 112/314] Fixed problem with doxygen comments at the end of a
 file or in a file without declarations.

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13485 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Examples/test-suite/doxygen_basic_translate.h |  5 +++++
 Examples/test-suite/doxygen_basic_translate.i | 13 ++++++++++++-
 Source/CParse/parser.y                        | 19 ++++++++++++-------
 3 files changed, 29 insertions(+), 8 deletions(-)
 create mode 100644 Examples/test-suite/doxygen_basic_translate.h

diff --git a/Examples/test-suite/doxygen_basic_translate.h b/Examples/test-suite/doxygen_basic_translate.h
new file mode 100644
index 000000000..7b2b3f58a
--- /dev/null
+++ b/Examples/test-suite/doxygen_basic_translate.h
@@ -0,0 +1,5 @@
+
+/**
+ * This file contains only doxygen comment without a declaration -
+ * it should be ignored by SWIG and must not trigger syntax error.
+ */
diff --git a/Examples/test-suite/doxygen_basic_translate.i b/Examples/test-suite/doxygen_basic_translate.i
index 9cef037b1..11c6a75ac 100644
--- a/Examples/test-suite/doxygen_basic_translate.i
+++ b/Examples/test-suite/doxygen_basic_translate.i
@@ -1,5 +1,7 @@
 %module doxygen_basic_translate
 
+%include "doxygen_basic_translate.h"
+
 %inline %{
 
 /**
@@ -59,12 +61,21 @@ int function4()
 {
 }
 
+
+int function5(int a)
+{
+}
+/**< This is a post comment. */
+
 /**
  * Test for default args
  * @param a Some parameter, default is 42
  */
-int function5(int a=42)
+int function6(int a=42)
 {
 }
 
+/**
+ * Comment at the end of file should be ignored.
+ */
 %}
diff --git a/Source/CParse/parser.y b/Source/CParse/parser.y
index e331752bf..41c94a5f3 100644
--- a/Source/CParse/parser.y
+++ b/Source/CParse/parser.y
@@ -66,7 +66,7 @@ static Node   **class_decl = NULL;
  * ----------------------------------------------------------------------------- */
 String *currentComment; /* Location of the stored Doxygen Comment */
 String *currentPostComment; /* Location of the stored Doxygen Post-Comment */
-String *currentCComment; /* Location of the stored C Comment */
+static String *currentDeclComment = NULL; /* Comment of C/C++ declaration. */
 static Node *previousNode = NULL; /* Pointer to the previous node (for post comments) */
 static Node *currentNode = NULL; /* Pointer to the current node (for post comments) */
 
@@ -1852,17 +1852,22 @@ program        :  interface {
 
 interface      : interface declaration {  
                    /* add declaration to end of linked list (the declaration isn't always a single declaration, sometimes it is a linked list itself) */
+                   if (currentDeclComment != NULL) {
+                       set_comment($2, currentDeclComment);
+                       currentDeclComment = NULL;
+                   }                                      
                    appendChild($1,$2);
                    $$ = $1;
                }
-               | interface doxygen_comment declaration {
-                   set_comment($3, $2);
-                   appendChild($1, $3);
+               | interface doxygen_comment {
+                   currentDeclComment = $2; 
                    $$ = $1;
                }
-               | interface declaration doxygen_post_comment {
-                   set_comment($2, $3);
-                   appendChild($1, $2);
+               | interface doxygen_post_comment {
+                   Node *node = lastChild($1);
+                   if (node) {
+                       set_comment(node, $2);
+                   }
                    $$ = $1;
                }
                | empty {

From 1881130f10cf70b6a0c398cd8c9ae89aa6e5e3f4 Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Thu, 2 Aug 2012 22:01:54 +0000
Subject: [PATCH 113/314] Fixed doxygen_basic_translate java runtime test

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13486 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 .../test-suite/java/doxygen_basic_translate_runme.java | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/Examples/test-suite/java/doxygen_basic_translate_runme.java b/Examples/test-suite/java/doxygen_basic_translate_runme.java
index 4e95b73a7..946988c57 100644
--- a/Examples/test-suite/java/doxygen_basic_translate_runme.java
+++ b/Examples/test-suite/java/doxygen_basic_translate_runme.java
@@ -63,14 +63,22 @@ public class doxygen_basic_translate_runme {
     		" \n" +
     		"");
     wantedComments.put("doxygen_basic_translate.doxygen_basic_translate.function5(int)",
+    		" This is a post comment. \n" +
+    		"");
+    wantedComments.put("doxygen_basic_translate.doxygen_basic_translate.function6(int)",
     		" Test for default args \n" +
     		" @param a Some parameter, default is 42" +
     		" \n" +
     		"");
-    wantedComments.put("doxygen_basic_translate.doxygen_basic_translate.function5()",
+    wantedComments.put("doxygen_basic_translate.doxygen_basic_translate.function6()",
     		" Test for default args \n" +
     		" \n" +
     		"");
+    wantedComments.put("doxygen_basic_translate.doxygen_basic_translate.function7(doxygen_basic_translate.SWIGTYPE_p_p_p_Shape)",
+    		" Test for a parameter with difficult type \n" +
+    		" (mostly for python) \n" +
+    		" @param a Very strange param \n" +
+    		"");
     wantedComments.put("doxygen_basic_translate.doxygen_basic_translate.function3(int, int)",
     		" A test for overloaded functions \n" +
     		" This is function <b>two </b>\n" +

From 9d3446d8030ec226a7aa1e43daae13d0f1a8143b Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Fri, 3 Aug 2012 18:44:47 +0000
Subject: [PATCH 114/314] Fixed critical bug with doxygen comments, containing
 % symbol

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13487 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Source/Modules/java.cxx | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/Source/Modules/java.cxx b/Source/Modules/java.cxx
index c7174d0fc..3591b7363 100644
--- a/Source/Modules/java.cxx
+++ b/Source/Modules/java.cxx
@@ -566,7 +566,7 @@ public:
 	String *doxygen_comments=doxygenTranslator->getDocumentation(n);
 	if(comment_creation_chatter)
 	  Printf(f_module, "/* This was generated from top() */");
-	Printf(f_module, Char(doxygen_comments)); 
+	Printv(f_module, Char(doxygen_comments), NIL);
 	Delete(doxygen_comments);
       }
       if (Len(module_class_modifiers) > 0)
@@ -1360,7 +1360,7 @@ public:
 	    String *doxygen_comments=doxygenTranslator->getDocumentation(n);
 	    if(comment_creation_chatter)
 	      Printf(f_enum, "/* This was generated from enumDeclaration() */");
-	    Printf(f_enum, Char(doxygen_comments)); 
+	    Printv(f_enum, Char(doxygen_comments), NIL);
 	    Delete(doxygen_comments);
 	  }
 	  
@@ -1457,7 +1457,7 @@ public:
 	String *doxygen_comments=doxygenTranslator->getDocumentation(n);
 	if(comment_creation_chatter)
 	  Printf(enum_code, "/* This was generated from enumvalueDeclaration() */");
-	Printf(enum_code, Char(doxygen_comments)); 
+	Printv(enum_code, Char(doxygen_comments), NIL);
 	Delete(doxygen_comments);
       }
 
@@ -1527,7 +1527,7 @@ public:
       String *doxygen_comments=doxygenTranslator->getDocumentation(n);
       if(comment_creation_chatter)
 	Printf(structuralComments, "/* This was generated from doxygenComment() */");
-      Printf(structuralComments, Char(doxygen_comments)); 
+      Printv(structuralComments, Char(doxygen_comments), NIL);
       Delete(doxygen_comments);
     }
     return SWIG_OK;
@@ -1559,7 +1559,7 @@ public:
       String *doxygen_comments=doxygenTranslator->getDocumentation(n);
       if(comment_creation_chatter)
 	Printf(constants_code, "/* This was generated from constantWrapper() */");
-      Printf(constants_code, Char(doxygen_comments)); 
+      Printv(constants_code, Char(doxygen_comments), NIL);
       Delete(doxygen_comments);
     }
     
@@ -1855,7 +1855,7 @@ public:
       String *doxygen_comments=doxygenTranslator->getDocumentation(n);
       if(comment_creation_chatter)
 	Printf(proxy_class_def, "/* This was generated from emitProxyClassDefAndCPPCasts() */");
-      Printf(proxy_class_def, Char(doxygen_comments)); 
+      Printv(proxy_class_def, Char(doxygen_comments), NIL);
       Delete(doxygen_comments);
     }
     
@@ -2259,7 +2259,7 @@ public:
       String *doxygen_comments=doxygenTranslator->getDocumentation(n);
       if(comment_creation_chatter)
 	Printf(function_code, "/* This was generated from proxyclassfunctionhandler() */");
-      Printf(function_code, Char(doxygen_comments)); 
+      Printv(function_code, Char(doxygen_comments), NIL);
       Delete(doxygen_comments);
     }
     
@@ -2490,7 +2490,7 @@ public:
       String *doxygen_comments=doxygenTranslator->getDocumentation(n);
 	if(comment_creation_chatter)
 	  Printf(function_code, "/* This was generated from constructionhandler() */");
-	Printf(function_code, Char(doxygen_comments)); 
+	Printv(function_code, Char(doxygen_comments), NIL);
 	Delete(doxygen_comments);
       }
 	    

From 3b280b6ffe51fed5bdbfad261b58fa369476bf77 Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Fri, 3 Aug 2012 19:34:56 +0000
Subject: [PATCH 115/314] Fixed doxygen_basic_translate testcase. Why do I
 always have the tests messed up?

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13488 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Examples/test-suite/doxygen_basic_translate.i | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/Examples/test-suite/doxygen_basic_translate.i b/Examples/test-suite/doxygen_basic_translate.i
index 11c6a75ac..e8c21f452 100644
--- a/Examples/test-suite/doxygen_basic_translate.i
+++ b/Examples/test-suite/doxygen_basic_translate.i
@@ -75,6 +75,21 @@ int function6(int a=42)
 {
 }
 
+class Shape
+{
+public:
+  typedef Shape* superType;
+};
+
+/**
+ * Test for a parameter with difficult type
+ * (mostly for python)
+ * @param a Very strange param
+ */
+void function7(Shape::superType *a[10])
+{
+}
+
 /**
  * Comment at the end of file should be ignored.
  */

From d99fe121b8cd3fda73aa2b0822fbcdbf09b4abab Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Fri, 3 Aug 2012 19:43:35 +0000
Subject: [PATCH 116/314] Fixed python doxygen_basic_translate runtime test

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13489 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Examples/test-suite/python/doxygen_basic_translate_runme.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/Examples/test-suite/python/doxygen_basic_translate_runme.py b/Examples/test-suite/python/doxygen_basic_translate_runme.py
index a952df8b0..4698e0f6c 100644
--- a/Examples/test-suite/python/doxygen_basic_translate_runme.py
+++ b/Examples/test-suite/python/doxygen_basic_translate_runme.py
@@ -58,7 +58,10 @@ check(doxygen_basic_translate.function4.__doc__, ''
 '  }'
 )
 check(doxygen_basic_translate.function5.__doc__, ''
+'  This is a post comment. \n'
+)
+check(doxygen_basic_translate.function6.__doc__, ''
 '  Test for default args \n'
 '  Arguments: \n'
 '  a (int) -- Some parameter, default is 42\n'
-)
\ No newline at end of file
+)

From 380b71eb561f7c74848e16607c21d23ce509c5af Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Fri, 3 Aug 2012 21:43:02 +0000
Subject: [PATCH 117/314] Implemented automatic translation of links in doxygen
 comments, for example @see function(std::string) -> @see function(String) in
 java. Also included testcase for that

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13490 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Examples/test-suite/doxygen_translate_links.i |  67 ++++++++++
 .../java/doxygen_translate_links_runme.java   |  68 ++++++++++
 .../src/JavaDocConverter.cpp                  | 123 +++++++++++++++++-
 .../DoxygenTranslator/src/JavaDocConverter.h  |  15 +++
 4 files changed, 269 insertions(+), 4 deletions(-)
 create mode 100644 Examples/test-suite/doxygen_translate_links.i
 create mode 100644 Examples/test-suite/java/doxygen_translate_links_runme.java

diff --git a/Examples/test-suite/doxygen_translate_links.i b/Examples/test-suite/doxygen_translate_links.i
new file mode 100644
index 000000000..5eee1d67f
--- /dev/null
+++ b/Examples/test-suite/doxygen_translate_links.i
@@ -0,0 +1,67 @@
+
+
+%module doxygen_translate_links
+%include "std_string.i"
+
+%inline %{
+
+class Shape
+{
+public:
+  typedef Shape* superType;
+};
+
+/**
+ * Testing typenames converting in \@ link
+ *
+ * \link superFunc(int,std::string)
+ * Test for std_string member
+ * \endlink
+ *
+ * \link superFunc(int,long,void*)
+ * Test for simple types
+ * \endlink
+ *
+ * \link superFunc(Shape::superType*)
+ * Test for custom types
+ * \endlink
+ * 
+ * \link superFunc(int**[13])
+ * Test for complex types
+ * \endlink
+ * 
+ * same works for 'See also:' links:
+ *
+ * \sa superFunc(int,std::string)
+ * \sa superFunc(int,long,void*)
+ * \sa superFunc(Shape::superType*)
+ * \sa superFunc(int**[13])
+ * 
+ * some failing params:
+ *
+ * \sa superFunc()
+ * \sa superFunc()
+ * \sa superFunc()
+ *
+ */
+int function()
+{
+}
+
+void superFunc(int, std::string)
+{
+}
+
+void superFunc(int, long, void *)
+{
+}
+
+void superFunc(Shape::superType *)
+{
+}
+
+void superFunc(int **arr[13])
+{
+}
+
+%}
diff --git a/Examples/test-suite/java/doxygen_translate_links_runme.java b/Examples/test-suite/java/doxygen_translate_links_runme.java
new file mode 100644
index 000000000..080063430
--- /dev/null
+++ b/Examples/test-suite/java/doxygen_translate_links_runme.java
@@ -0,0 +1,68 @@
+
+import doxygen_translate_links.*;
+import com.sun.javadoc.*;
+import java.util.HashMap;
+
+public class doxygen_translate_links_runme {
+  static {
+    try {
+      System.loadLibrary("doxygen_translate_links");
+    } catch (UnsatisfiedLinkError e) {
+      System.err.println("Native code library failed to load. See the chapter on Dynamic Linking Problems in the SWIG Java documentation for help.\n" + e);
+      System.exit(1);
+    }
+  }
+  
+  public static void main(String argv[]) 
+  {
+    /*
+      Here we are using internal javadoc tool, it accepts the name of the class as paramterer,
+      and calls the start() method of that class with parsed information.
+    */
+	commentParser parser = new commentParser();
+    com.sun.tools.javadoc.Main.execute("doxygen_translate_links runtime test",
+	"commentParser", new String[]{"-quiet", "doxygen_translate_links"});
+
+    HashMap<String, String> wantedComments = new HashMap<String, String>();
+    
+    
+    wantedComments.put("doxygen_translate_links.doxygen_translate_links.function()",
+    		" \n" +
+    		" Testing typenames converting in @ link \n" +
+    		" \n" +
+    		" {@link superFunc(int,String) \n" +
+    		" Test for std_string member \n" +
+    		" }\n" +
+    		" \n" +
+    		" {@link superFunc(int,int,SWIGTYPE_p_void) \n" +
+    		" Test for simple types \n" +
+    		" }\n" +
+    		" \n" +
+    		" {@link superFunc(SWIGTYPE_p_p_Shape) \n" +
+    		" Test for custom types \n" +
+    		" }\n" +
+    		" \n" +
+    		" {@link superFunc(SWIGTYPE_p_p_p_int) \n" +
+    		" Test for complex types \n" +
+    		" }\n" +
+    		" \n" +
+    		" same works for 'See also:' links: \n" +
+    		" \n" +
+    		" @see superFunc(int,String)\n" +
+    		" @see superFunc(int,int,SWIGTYPE_p_void)\n" +
+    		" @see superFunc(SWIGTYPE_p_p_Shape)\n" +
+    		" @see superFunc(SWIGTYPE_p_p_p_int)\n" +
+    		" \n" +
+    		" some failing params: \n" +
+    		" \n" +
+    		" @see superFunc() \n" +
+    		" @see superFunc() \n" +
+    		" @see superFunc() \n" +
+    		" \n" +
+    		" \n" +
+    		"");
+    
+    // and ask the parser to check comments for us
+    System.exit(parser.check(wantedComments));
+  }
+}
\ No newline at end of file
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.cpp b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
index 421134828..123eb040b 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
@@ -12,6 +12,8 @@
 #include "JavaDocConverter.h"
 #include "DoxygenParser.h"
 #include <iostream>
+#include <vector>
+#include "../../Modules/swigmod.h"
 #define APPROX_LINE_LENGTH 64	//characters per line allowed
 #define TAB_SIZE 8		//current tab size in spaces
 //TODO {@link} {@linkplain} {@docRoot}, and other useful doxy commands that are not a javadoc tag
@@ -71,8 +73,8 @@ void JavaDocConverter::fillStaticTables() {
   tagHandlers["result"] = make_pair(&JavaDocConverter::handleTagSame, "return");
   tagHandlers["return"] = make_pair(&JavaDocConverter::handleTagSame, "");
   tagHandlers["returns"] = make_pair(&JavaDocConverter::handleTagSame, "return");
-  tagHandlers["see"] = make_pair(&JavaDocConverter::handleTagSame, "");
-  tagHandlers["sa"] = make_pair(&JavaDocConverter::handleTagSame, "see");
+  //tagHandlers["see"] = make_pair(&JavaDocConverter::handleTagSame, "");
+  //tagHandlers["sa"] = make_pair(&JavaDocConverter::handleTagSame, "see");
   tagHandlers["since"] = make_pair(&JavaDocConverter::handleTagSame, "");
   tagHandlers["throws"] = make_pair(&JavaDocConverter::handleTagSame, "");
   tagHandlers["throw"] = make_pair(&JavaDocConverter::handleTagSame, "throws");
@@ -87,7 +89,9 @@ void JavaDocConverter::fillStaticTables() {
   tagHandlers["if"] = make_pair(&JavaDocConverter::handleTagIf, "If: ");
   tagHandlers["ifnot"] = make_pair(&JavaDocConverter::handleTagIf, "If not: ");
   tagHandlers["image"] = make_pair(&JavaDocConverter::handleTagImage, "");
-  tagHandlers["link"] = make_pair(&JavaDocConverter::handleTagExtended, "link");
+  tagHandlers["link"] = make_pair(&JavaDocConverter::handleTagLink, "");
+  tagHandlers["see"] = make_pair(&JavaDocConverter::handleTagSee, "");
+  tagHandlers["sa"] = make_pair(&JavaDocConverter::handleTagSee, "");
   tagHandlers["note"] = make_pair(&JavaDocConverter::handleTagMessage, "Note: ");
   tagHandlers["overload"] = make_pair(&JavaDocConverter::handleTagMessage, "This is an overloaded member function, provided for"
       " convenience. It differs from the above function only in what"
@@ -152,10 +156,12 @@ std::string JavaDocConverter::formatCommand(std::string unformattedLine, int ind
 }
 
 bool JavaDocConverter::paramExists(std::string param) {
+  if (GetFlag(currentNode, "feature:doxygen:nostripparams"))
+    return true;
   ParmList *plist = CopyParmList(Getattr(currentNode, "parms"));
   Parm *p = NULL;
   for (p = plist; p;) {
-    if (Char(Getattr(p, "name")) == param)
+    if (Getattr(p, "name") && Char(Getattr(p, "name")) == param)
       return true;
     /*
      * doesn't seem to work always: in some cases (especially for 'self' parameters)
@@ -289,6 +295,115 @@ void JavaDocConverter::handleTagParam(DoxygenEntity& tag, std::string& translate
   handleParagraph(tag, translatedComment, dummy);
 }
 
+string JavaDocConverter::convertLink(string linkObject) {
+  if (GetFlag(currentNode, "feature:doxygen:nolinktranslate"))
+    return linkObject;
+  // find the params in function in linkObject (if any)
+  size_t lbracePos = linkObject.find('(', 0);
+  size_t rbracePos = linkObject.find(')', 0);
+  if (lbracePos == string::npos && rbracePos == string::npos && lbracePos >= rbracePos)
+    return "";
+
+  string paramsStr = linkObject.substr(lbracePos + 1, rbracePos - lbracePos - 1);
+  // strip the params, to fill them later
+  linkObject = linkObject.substr(0, lbracePos);
+
+  // find all the params
+  vector<string> params;
+  size_t lastPos = 0, commaPos = 0;
+  while (true) {
+    commaPos = paramsStr.find(',', lastPos);
+    if (commaPos == string::npos)
+      commaPos = paramsStr.size();
+    string param = paramsStr.substr(lastPos, commaPos - lastPos);
+    // if any param type is empty, we are failed
+    if (!param.size())
+      return "";
+    params.push_back(param);
+    lastPos = commaPos + 1;
+    if (lastPos >= paramsStr.size())
+      break;
+  }
+
+  linkObject += "(";
+  for (size_t i=0; i<params.size(); i++) {
+    // translate c/c++ type string to swig's type
+    // i e 'int **arr[100][10]' -> 'a(100).a(10).p.p.int'
+    // also converting arrays to pointers
+    string paramStr = params[i];
+    String *swigType = NewString("");
+    for (int j=(int)params[i].size() - 1; j>=0; j--) {
+      // skip all the [...] blocks, write 'p.' for every of it
+      if (paramStr[j] == ']') {
+        while (j>=0 && paramStr[j] != '[')
+          j--;
+        // no closing brace
+        if (!j)
+          return "";
+        Append(swigType, "p.");
+        continue;
+      }
+      else if (paramStr[j] == '*')
+        Append(swigType, "p.");
+      else if (isalnum(paramStr[j])) {
+        Append(swigType, paramStr.substr(0, j + 1).c_str());
+        break;
+      }
+    }
+
+    // make dummy param list, to lookup typemaps for it
+    Parm *dummyParam = NewParm(swigType, "", 0);
+    Swig_typemap_attach_parms("jstype", dummyParam, NULL);
+    Language::instance()->replaceSpecialVariables(0, Getattr(dummyParam, "tmap:jstype"), dummyParam);
+
+    //Swig_print(dummyParam, 1);
+    linkObject += Char(Getattr(dummyParam, "tmap:jstype"));
+    if (i != params.size() - 1)
+      linkObject += ",";
+
+    Delete(dummyParam);
+    Delete(swigType);
+  }
+  linkObject += ")";
+
+  return linkObject;
+}
+
+void JavaDocConverter::handleTagLink(DoxygenEntity& tag, std::string& translatedComment, std::string&) {
+  std::string dummy;
+  if (!tag.entityList.size())
+    return;
+
+  string linkObject = convertLink(tag.entityList.begin()->data);
+  if (!linkObject.size())
+    linkObject = tag.entityList.begin()->data;
+  tag.entityList.pop_front();
+
+  translatedComment += "{@link ";
+  translatedComment += linkObject + " ";
+  handleParagraph(tag, translatedComment, dummy);
+  translatedComment += "}";
+}
+
+void JavaDocConverter::handleTagSee(DoxygenEntity& tag, std::string& translatedComment, std::string&) {
+  std::string dummy;
+  if (!tag.entityList.size())
+    return;
+
+  list<DoxygenEntity>::iterator it;
+  for (it = tag.entityList.begin(); it!=tag.entityList.end(); it++) {
+    if (it->typeOfEntity == "plainstd::endl")
+      handleNewLine(*it, translatedComment, dummy);
+    if (it->typeOfEntity != "plainstd::string")
+      continue;
+    translatedComment += "@see ";
+    string linkObject = convertLink(it->data);
+    if (!linkObject.size())
+      linkObject = it->data;
+    translatedComment += linkObject;
+  }
+}
+
 String *JavaDocConverter::makeDocumentation(Node *node) {
 
   String *documentation = getDoxygenComment(node);
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.h b/Source/DoxygenTranslator/src/JavaDocConverter.h
index f68a712b9..a547a17f8 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.h
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.h
@@ -30,6 +30,11 @@ protected:
   std::string translateSubtree(DoxygenEntity & doxygenEntity);
   void translateEntity(DoxygenEntity &tag, std::string &translatedComment);
   
+  /*
+   * Convert params in link-objects and references
+   */
+  std::string convertLink(std::string linkObject);
+
   /*
    * Typedef for the function that handles one tag
    * arg - some string argument to easily pass it through lookup table
@@ -89,6 +94,16 @@ protected:
    * Insert @param command, if it is really a function param
    */
   void handleTagParam(DoxygenEntity &tag, std::string &translatedComment, std::string &arg);
+  /*
+   * Insert {@link...} command, and handle all the <link-object>s correctly
+   * (like converting types of params, etc)
+   */
+  void handleTagLink(DoxygenEntity &tag, std::string &translatedComment, std::string &arg);
+  /*
+   * Insert @see command, and handle all the <link-object>s correctly
+   * (like converting types of params, etc)
+   */
+  void handleTagSee(DoxygenEntity &tag, std::string &translatedComment, std::string &arg);
 
 
 private:

From e05d88b83cfbd1baef54988346911c3b1df8f5a7 Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Fri, 3 Aug 2012 21:53:48 +0000
Subject: [PATCH 118/314] Removed some old unused code from parser.y

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13491 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Source/CParse/parser.y | 31 ++-----------------------------
 1 file changed, 2 insertions(+), 29 deletions(-)

diff --git a/Source/CParse/parser.y b/Source/CParse/parser.y
index 41c94a5f3..27957d9ab 100644
--- a/Source/CParse/parser.y
+++ b/Source/CParse/parser.y
@@ -64,8 +64,6 @@ static Node   **class_decl = NULL;
 /* -----------------------------------------------------------------------------
  *                            Doxygen Comment Globals and Assist Functions
  * ----------------------------------------------------------------------------- */
-String *currentComment; /* Location of the stored Doxygen Comment */
-String *currentPostComment; /* Location of the stored Doxygen Post-Comment */
 static String *currentDeclComment = NULL; /* Comment of C/C++ declaration. */
 static Node *previousNode = NULL; /* Pointer to the previous node (for post comments) */
 static Node *currentNode = NULL; /* Pointer to the current node (for post comments) */
@@ -4866,37 +4864,12 @@ storage_class  : EXTERN { $$ = "extern"; }
    ------------------------------------------------------------------------------ */
 
 parms          : rawparms {
-                 Parm *p, *nextSibling;
+                 Parm *p;
 		 $$ = $1;
 		 p = $1;
 		 while (p) {
-		   String *postComment = NULL;
-		   nextSibling = nextSibling(p);
-		   if (nextSibling != NULL) {
-		     postComment = Getattr(nextSibling, "postComment");
-		   } else {
-		     /* the last functino parameter has two attributes -
-			post comment of the previous params and its own post
-			comment.
-		      */
-		     postComment = Getattr(p, "lastParamPostComment");
-		   }
-		   if (postComment != NULL) {
-		     String *param = NewString("\n@param ");
-		     if (currentComment != 0) {
-		       Append(currentComment, param);
-		       Append(currentComment, Getattr(p, "name"));
-		       Append(currentComment, postComment);
-		     }
-		     else {
-		       currentComment = param;
-		       Append(currentComment, Getattr(p, "name"));
-		       Append(currentComment, postComment);
-		     }
-		   }
-
 		   Replace(Getattr(p,"type"),"typename ", "", DOH_REPLACE_ANY);
-		   p = nextSibling;
+		   p = nextSibling(p);
 		 }
                }
     	       ;

From 6365770c7fe90d449ccea50823146ff15736afb0 Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Sun, 5 Aug 2012 13:31:19 +0000
Subject: [PATCH 119/314] Added missing test part to python testsuite

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13516 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Examples/test-suite/python/doxygen_basic_translate_runme.py | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/Examples/test-suite/python/doxygen_basic_translate_runme.py b/Examples/test-suite/python/doxygen_basic_translate_runme.py
index 4698e0f6c..4c1376f44 100644
--- a/Examples/test-suite/python/doxygen_basic_translate_runme.py
+++ b/Examples/test-suite/python/doxygen_basic_translate_runme.py
@@ -65,3 +65,9 @@ check(doxygen_basic_translate.function6.__doc__, ''
 '  Arguments: \n'
 '  a (int) -- Some parameter, default is 42\n'
 )
+check(doxygen_basic_translate.function7.__doc__, ''
+' Test for a parameter with difficult type \n'
+'  (mostly for python) \n'
+'  Arguments: \n'
+'  a (Shape::superType *[10])                              -- Very strange param \n'
+)

From 346fdfcab7d8532ec4a702d5edd0bf6575b29605 Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Sun, 5 Aug 2012 14:16:57 +0000
Subject: [PATCH 120/314] Added doxygen:notranslate feature, to prevent running
 of automatic comment translation

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13517 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Examples/test-suite/common.mk                 |   2 +
 .../test-suite/doxygen_basic_notranslate.i    | 103 ++++++++++++++++++
 .../src/JavaDocConverter.cpp                  |  10 ++
 .../DoxygenTranslator/src/PyDocConverter.cpp  |  30 ++++-
 4 files changed, 139 insertions(+), 6 deletions(-)
 create mode 100644 Examples/test-suite/doxygen_basic_notranslate.i

diff --git a/Examples/test-suite/common.mk b/Examples/test-suite/common.mk
index eb8f7b03a..86e33037a 100644
--- a/Examples/test-suite/common.mk
+++ b/Examples/test-suite/common.mk
@@ -189,8 +189,10 @@ CPP_TEST_CASES += \
 	disown \
 	doxygen_parsing \
 	doxygen_basic_translate \
+	doxygen_basic_notranslate \
 	doxygen_translate \
 	doxygen_translate_all_tags \
+	doxygen_translate_links \
 	dynamic_cast \
 	empty \
 	enum_rename \
diff --git a/Examples/test-suite/doxygen_basic_notranslate.i b/Examples/test-suite/doxygen_basic_notranslate.i
new file mode 100644
index 000000000..8699e3289
--- /dev/null
+++ b/Examples/test-suite/doxygen_basic_notranslate.i
@@ -0,0 +1,103 @@
+%module doxygen_basic_notranslate
+
+%include "doxygen_basic_translate.h"
+%feature("doxygen:notranslate") function;
+%feature("doxygen:notranslate") function2;
+%feature("doxygen:notranslate") function3;
+%feature("doxygen:notranslate") function4;
+%feature("doxygen:notranslate") function5;
+%feature("doxygen:notranslate") function6;
+%feature("doxygen:notranslate") function7;
+
+%inline %{
+
+/**
+ * \brief
+ * Brief description.
+ * 
+ * The comment text
+ * \author Some author
+ * \return Some number
+ * \sa function2
+ */
+int function()
+{
+}
+
+/**
+ * A test of a very very very very very very very very very very very very very very very very
+ * very very very very very long comment string.
+ */
+int function2()
+{
+}
+
+/**
+ * A test for overloaded functions
+ * This is function \b one
+ */
+int function3(int a)
+{
+}
+
+/**
+ * A test for overloaded functions
+ * This is function \b two
+ */
+int function3(int a, int b)
+{
+}
+
+/**
+ * A test of some mixed tag usage
+ * \if CONDITION
+ * This \a code fragment shows us something \.
+ * \par Minuses:
+ * \arg it's senseless
+ * \arg it's stupid
+ * \arg it's null
+ *
+ * \warning This may not work as expected
+ *
+ * \code
+ * int main() { while(true); }
+ * \endcode
+ * \endif
+ */
+int function4()
+{
+}
+
+
+int function5(int a)
+{
+}
+/**< This is a post comment. */
+
+/**
+ * Test for default args
+ * @param a Some parameter, default is 42
+ */
+int function6(int a=42)
+{
+}
+
+class Shape
+{
+public:
+  typedef Shape* superType;
+};
+
+/**
+ * Test for a parameter with difficult type
+ * (mostly for python)
+ * @param a Very strange param
+ */
+void function7(Shape::superType *a[10])
+{
+}
+
+/**
+ * Comment at the end of file should be ignored.
+ */
+%}
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.cpp b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
index 123eb040b..b03556b47 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
@@ -412,6 +412,16 @@ String *JavaDocConverter::makeDocumentation(Node *node) {
     return NULL;
   }
 
+  if (GetFlag(node, "feature:doxygen:notranslate")) {
+    String *comment = NewString("/**\n");
+    Append(comment, documentation);
+    // reformat the comment
+    Replaceall(comment, "\n *", "\n");
+    Replaceall(comment, "\n", "\n * ");
+    Append(comment, "\n */\n");
+    return comment;
+  }
+
   std::list < DoxygenEntity > entityList = parser.createTree(Char(documentation), Char(Getfile(documentation)), Getline(documentation));
 
   // entityList.sort(CompareDoxygenEntities()); sorting currently not used,
diff --git a/Source/DoxygenTranslator/src/PyDocConverter.cpp b/Source/DoxygenTranslator/src/PyDocConverter.cpp
index df9466067..777a54201 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/PyDocConverter.cpp
@@ -254,9 +254,18 @@ String *PyDocConverter::makeDocumentation(Node *n) {
       documentation = getDoxygenComment(n);
       if (!Swig_is_generated_overload(n) && documentation) {
 	currentNode = n;
-	std::list < DoxygenEntity > entityList = parser.createTree(Char(documentation), Char(Getfile(documentation)), Getline(documentation));
-	DoxygenEntity root("root", entityList);
-	allDocumentation.push_back(translateSubtree(root));
+	if (GetFlag(n, "feature:doxygen:notranslate")) {
+	  String *comment = NewString("");
+	  Append(comment, documentation);
+	  Replaceall(comment, "\n *", "\n");
+	  allDocumentation.push_back(Char(comment));
+	  Delete(comment);
+	}
+	else {
+	  std::list < DoxygenEntity > entityList = parser.createTree(Char(documentation), Char(Getfile(documentation)), Getline(documentation));
+	  DoxygenEntity root("root", entityList);
+	  allDocumentation.push_back(translateSubtree(root));
+	}
       }
       n = Getattr(n, "sym:nextSibling");
     }
@@ -279,9 +288,18 @@ String *PyDocConverter::makeDocumentation(Node *n) {
   else {
     documentation = getDoxygenComment(n);
     if (documentation != NULL) {
-      std::list < DoxygenEntity > entityList = parser.createTree(Char(documentation), Char(Getfile(documentation)), Getline(documentation));
-      DoxygenEntity root("root", entityList);
-      pyDocString = translateSubtree(root);
+      if (GetFlag(n, "feature:doxygen:notranslate")) {
+        String *comment = NewString("");
+        Append(comment, documentation);
+        Replaceall(comment, "\n *", "\n");
+        pyDocString = Char(comment);
+        Delete(comment);
+      }
+      else {
+        std::list < DoxygenEntity > entityList = parser.createTree(Char(documentation), Char(Getfile(documentation)), Getline(documentation));
+        DoxygenEntity root("root", entityList);
+        pyDocString = translateSubtree(root);
+      }
     }
   }
 

From 0a3db948cca61b0976b68eed5a2bc777da0d38b2 Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Sun, 5 Aug 2012 14:18:46 +0000
Subject: [PATCH 121/314] Fixed possible bug: as the return value of
 makeDocumentation is never checked, don't return null pointers, even in case
 of errors

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13518 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Source/DoxygenTranslator/src/JavaDocConverter.cpp | 2 +-
 Source/DoxygenTranslator/src/PyDocConverter.cpp   | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.cpp b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
index b03556b47..c7485ab4f 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
@@ -409,7 +409,7 @@ String *JavaDocConverter::makeDocumentation(Node *node) {
   String *documentation = getDoxygenComment(node);
 
   if (documentation == NULL) {
-    return NULL;
+    return NewString("");
   }
 
   if (GetFlag(node, "feature:doxygen:notranslate")) {
diff --git a/Source/DoxygenTranslator/src/PyDocConverter.cpp b/Source/DoxygenTranslator/src/PyDocConverter.cpp
index 777a54201..7937b5ba5 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/PyDocConverter.cpp
@@ -316,7 +316,7 @@ String *PyDocConverter::makeDocumentation(Node *n) {
     return NewString(result.c_str());
   }
 
-  return 0;
+  return NewString("");
 }
 
 std::string PyDocConverter::generateDivider() {

From 51e184f134cf1a7897aac7e5c4f1a3229c74c3db Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Sun, 5 Aug 2012 16:22:48 +0000
Subject: [PATCH 122/314] Added special doxygen features description to docs

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13523 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Doc/Manual/Doxygen.html | 90 ++++++++++++++++++++++++++++++++++++-----
 1 file changed, 81 insertions(+), 9 deletions(-)

diff --git a/Doc/Manual/Doxygen.html b/Doc/Manual/Doxygen.html
index 77c00b40e..3178f70c2 100644
--- a/Doc/Manual/Doxygen.html
+++ b/Doc/Manual/Doxygen.html
@@ -101,7 +101,7 @@ Here they are:
 Also any of the above with '<' added after comment-starting symbol, like <i>/**&lt;, /*!&lt;, ///&lt;, </i> or <i> //!&lt;</i>
 will be treated as post-comment and will be assigned to the node before the comment.
 <br>
-Any number of '*' or '/' in doxygen comment is considered to be a separator and is not included in final comment, so you may safely use
+Any number of '*' or '/' in Doxygen comment is considered to be a separator and is not included in final comment, so you may safely use
 comments like <i>/*********/</i> or <i>//////////</i>.
 </p>
 
@@ -172,11 +172,11 @@ Also, currently only the comments directly before or after the nodes are support
 <p>
 There is a switch '-doxygen' in every module that supports converting
 documentation comments. Some comments in some target languages can be manually overriden by specific
-swig's features, like <i>feature:docstring</i> or <i>feature:autodoc</i>, in this cases doxygen comments
+swig's features, like <i>feature:docstring</i> or <i>feature:autodoc</i>, in this cases Doxygen comments
 have lowest priority.
 </p>
 <p>
-If doxygen parsing is switched off, then all the comments are stripped out in parser and all the resources used by comment parser and translator are freed.
+If Doxygen parsing is switched off, then all the comments are stripped out in parser and all the resources used by comment parser and translator are freed.
 </p>
 
 <H3><a name="Doxygen_additional_options"></a>39.2.2 Additional Commandline Options</H3>
@@ -274,19 +274,61 @@ public class Shape {
 
 </pre></div>
 
-
-
 <p>
 The code Java-wise should be identical to what would have been generated without this feature enabled.
 When the Doxygen Translator Module encounters a comment it finds nothing useful in or cannot parse, it should not effect the functionality of the SWIG generated code.
 </p>
 
+<p>
+JavaDoc translator will handle most of the tags conversions (see the table below). It will also automatically translate link-objects
+params, in \see and \link...\endlink commands. For example, 'someFunction(std::string)' will be converted to 'someFunction(String)'.
+If this works not really good for you, or if you don't want such behaviour, you could turn this off by using 'doxygen:nolinktranslate'
+feature. Also all '\param' and '\tparam' commands are stripped out, if specified parameter is not present in function. Use 'doxygen:nostripparams'
+to avoid.
+<br>
+If you intend to use resulting proxy files with Doxygen docs generator, rather than JavaDoc, you may want to turn off translator completely
+(doxygen:notranslate feature).
+Then SWIG will just copy the comments to the proxy file and reformat them if needed, but all the comment content will be left as is.
+</p>
+
+<p>
+JavaDoc translator features summary (see <a href="Customization.html#Customization_features">%feature directives</a>):
+<br>
+
+</p>
+
+<div class="shell"><pre>
+<table>
+<tr>
+<td>doxygen:noranslate</td>
+<td>
+Turn off the whole Doxygen translator.
+The Doxygen comment will be attached to the right node,
+but all the commands and text will be left as-is
+</td>
+</tr>
+
+<tr>
+<td>doxygen:notlinkranslate</td>
+<td>Turn off automatic link-objects translation</td>
+</tr>
+
+<tr>
+<td>doxygen:nostripparams</td>
+<td>
+Turn off stripping of @param and @tparam
+Doxygen commands if such parameter is not found
+</td>
+</tr>
+</table>
+</pre></div>
+
 
 <H3><a name="Doxygen_javadoc_tags"></a>39.3.2 JavaDoc Tags</H3>
 
 
 <p>
-Here is the list of all doxygen tags and the description of how they are translated to JavaDoc
+Here is the list of all Doxygen tags and the description of how they are translated to JavaDoc
 <br>
 <b>Doxygen tags:</b>
 </p>
@@ -782,11 +824,41 @@ class Shape(_object):
 Currently Doxygen comments assigned to vars are not present in proxy file, so they have no comment translated for them.
 </p>
 
+<p>
+Since all the overloaded functions in c++ are wrapped into one Python function, PyDoc translator will combine every comment of every
+overloaded function and put it in the comment for wrapping function.
+<br>
+If you intend to use resulting proxy files with Doxygen docs generator, rather than PyDoc, you may want to turn off translator completely
+(doxygen:notranslate feature).
+Then SWIG will just copy the comments to the proxy file and reformat them if needed, but all the comment content will be left as is. As Doxygen
+don't support special commands in Python comments (see <a href="http://www.stack.nl/~dimitri/doxygen/docblocks.html#pythonblocks">Doxygen docs</a>),
+you may want to use some tool like doxypy (<a href="http://code.foosel.org/doxypy">http://code.foosel.org/doxypy</a>) to do the work.
+</p>
+
+<p>
+PyDoc translator features summary (see <a href="Customization.html#Customization_features">%feature directives</a>):
+<br>
+
+</p>
+
+<div class="shell"><pre>
+<table>
+<tr>
+<td>doxygen:noranslate</td>
+<td>
+Turn off the whole Doxygen translator.
+The Doxygen comment will be attached to the right node,
+but all the commands and text will be left as-is
+</td>
+</tr>
+</table>
+</pre></div>
+
 <H3><a name="Doxygen_pydoc_tags"></a>39.4.2 PyDoc translator</H3>
 
 
 <p>
-Here is the list of all doxygen tags and the description of how they are translated to PyDoc
+Here is the list of all Doxygen tags and the description of how they are translated to PyDoc
 <br>
 <b>Doxygen tags:</b>
 </p>
@@ -1218,8 +1290,8 @@ There are two handy command line switches, that enable lots of detailed debug in
 </p>
 
 <div class="shell"><pre>
-  -debug-doxygen-parser     - Display doxygen parser module debugging information
-  -debug-doxygen-translator - Display doxygen translator module debugging information
+  -debug-doxygen-parser     - Display Doxygen parser module debugging information
+  -debug-doxygen-translator - Display Doxygen translator module debugging information
 </pre></div>
 
 <H2><a name="Doxygen_language_extension"></a>39.6 Extending to Other Languages</H2>

From cecc793782e329b1f811b49960d84d5a89e4fc81 Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Tue, 7 Aug 2012 20:04:23 +0000
Subject: [PATCH 123/314] Various small code fixes. Some unwanted code removed.

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13551 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 .../DoxygenTranslator/src/DoxygenCommands.h   |  35 -----
 Source/DoxygenTranslator/src/DoxygenEntity.h  |   4 -
 .../DoxygenTranslator/src/DoxygenParser.cpp   | 134 ++++--------------
 Source/DoxygenTranslator/src/DoxygenParser.h  |  31 +---
 .../src/DoxygenTranslator.cpp                 |   2 +-
 .../DoxygenTranslator/src/DoxygenTranslator.h |   5 +-
 Source/DoxygenTranslator/src/TokenList.cpp    |   2 +-
 7 files changed, 36 insertions(+), 177 deletions(-)

diff --git a/Source/DoxygenTranslator/src/DoxygenCommands.h b/Source/DoxygenTranslator/src/DoxygenCommands.h
index 96fde4a7c..10ebca862 100644
--- a/Source/DoxygenTranslator/src/DoxygenCommands.h
+++ b/Source/DoxygenTranslator/src/DoxygenCommands.h
@@ -2,25 +2,6 @@
 #ifndef DOXYGENCOMMANDS_H
 #define DOXYGENCOMMANDS_H
 
-const char *commandArray[] = {
-  "a", "addindex", "addtogroup", "anchor", "arg", "attention",
-  "author", "authors", "b", "brief", "bug", "c", "callgraph", "callergraph", "category", "cite",
-  "class", "code", "cond", "copybrief", "copydetails", "copydoc", "copyright", "date", "def",
-  "defgroup", "deprecated", "details", "dir", "dontinclude", "dot", "dotfile", "e",
-  "else", "elseif", "em", "endcode", "endcond", "enddot", "endhtmlonly", "endif",
-  "endlatexonly", "endlink", "endmanonly", "endmsc", "endverbatim", "endxmlonly",
-  "enum", "example", "exception", "f$", "f[", "f]", "f{", "f}", "file", "fn", "headerfile",
-  "hideinitializer", "htmlinclude", "htmlonly", "if", "ifnot", "image", "include",
-  "includelineno", "ingroup", "internal", "invariant", "interface", "latexonly", "li",
-  "line", "link", "mainpage", "manonly", "msc", "mscfile", "n", "name", "namespace", "nosubgrouping",
-  "note", "overload", "p", "package", "page", "par", "paragraph", "param", "post", "pre",
-  "private", "privatesection", "property", "protected", "protectedsection", "protocol",
-  "public", "publicsection", "ref", "relates", "relatesalso", "remarks", "remark", "result", "return", "returns", "retval",
-  "sa", "section", "see", "showinitializer", "since", "skip", "skipline", "struct", "subpage",
-  "subsection", "subsubsection", "test", "throw", "throws", "todo", "tparam", "typedef", "union", "until",
-  "var", "verbatim", "verbinclude", "version", "warning", "weakgroup", "xmlonly", "xrefitem", "$", "@", "\\", "&", "~", "<", ">", "#", "%"};
-
-
 const char *sectionIndicators[] = {
   "attention", "author", "authors", "brief", "bug", "cond", "date", "deprecated", "details",
   "else", "elseif", "endcond", "endif", "exception", "if", "ifnot", "invariant", "note", "par", "param",
@@ -35,38 +16,22 @@ const char *simpleCommands[] = {
   "protected", "protectedsection", "tableofcontents"};
 const int simpleCommandsSize = sizeof(simpleCommands) / sizeof(*simpleCommands);
 
-const char *ignoredSimpleCommands[] = {
-  "nothing at the moment"};
-const int ignoredSimpleCommandsSize = sizeof(ignoredSimpleCommands) / sizeof(*ignoredSimpleCommands);
-
 const char *commandWords[] = {
   "a", "b", "c", "e", "em", "p", "def", "enum", "package", "relates", "namespace", "relatesalso", "anchor", "dontinclude", "include",
   "includelineno", "copydoc", "copybrief", "copydetails", "verbinclude", "htmlinclude", "extends", "implements", "memberof", "related",
   "relatedalso", "cite"};
 const int commandWordsSize = sizeof(commandWords) / sizeof(*commandWords);
 
-const char *ignoredCommandWords[] = {
-  "nothing at the moment"};
-const int ignoredCommandWordsSize = sizeof(ignoredCommandWords) / sizeof(*ignoredCommandWords);
-
 const char *commandLines[] = {
   "addindex", "fn", "name", "line", "var", "skipline", "typedef", "skip", "until", "property"};
 const int commandLinesSize = sizeof(commandLines) / sizeof(*commandLines);
 
-const char *ignoreCommandLines[] = {
-  "nothing at the moment"};
-const int ignoreCommandLinesSize = sizeof(ignoreCommandLines) / sizeof(*ignoreCommandLines);
-
 const char *commandParagraph[] = {
   "partofdescription", "result", "return", "returns", "remarks", "remark", "since", "test", "sa", "see", "pre", "post", "details", "invariant",
   "deprecated", "date", "note", "warning", "version", "todo", "bug", "attention", "brief", "author", "authors",
   "copyright", "short"};
 const int commandParagraphSize = sizeof(commandParagraph) / sizeof(*commandParagraph);
 
-const char *ignoreCommandParagraphs[] = {
-  "nothing at the moment"};
-const int ignoreCommandParagraphsSize = sizeof(ignoreCommandParagraphs) / sizeof(*ignoreCommandParagraphs);
-
 const char *commandEndCommands[] = {
   "htmlonly", "latexonly", "manonly", "xmlonly", "link", "rtfonly"};
 const int commandEndCommandsSize = sizeof(commandEndCommands) / sizeof(*commandEndCommands);
diff --git a/Source/DoxygenTranslator/src/DoxygenEntity.h b/Source/DoxygenTranslator/src/DoxygenEntity.h
index dcdba7644..64b692ba0 100644
--- a/Source/DoxygenTranslator/src/DoxygenEntity.h
+++ b/Source/DoxygenTranslator/src/DoxygenEntity.h
@@ -20,13 +20,9 @@
 
 typedef enum {
   SIMPLECOMMAND,
-  IGNOREDSIMPLECOMMAND,
   COMMANDWORD,
-  IGNOREDCOMMANDWORD,
   COMMANDLINE,
-  IGNOREDCOMMANDLINE,
   COMMANDPARAGRAPH,
-  IGNORECOMMANDPARAGRAPH,
   COMMANDENDCOMMAND,
   COMMANDWORDPARAGRAPH,
   COMMANDWORDLINE,
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.cpp b/Source/DoxygenTranslator/src/DoxygenParser.cpp
index 8ed186727..4df82b2d7 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenParser.cpp
@@ -32,24 +32,12 @@ void DoxygenParser::fillTables() {
 	// fill in tables with data from DxygenCommands.h
 	for (int i = 0; i < simpleCommandsSize; i++)
 		doxygenCommands[simpleCommands[i]] = SIMPLECOMMAND;
-	for (int i = 0; i < ignoredSimpleCommandsSize; i++)
-		doxygenCommands[ignoredSimpleCommands[i]] = IGNOREDSIMPLECOMMAND;
-
 	for (int i = 0; i < commandWordsSize; i++)
 		doxygenCommands[commandWords[i]] = COMMANDWORD;
-	for (int i = 0; i < ignoredCommandWordsSize; i++)
-		doxygenCommands[ignoredCommandWords[i]] = IGNOREDCOMMANDWORD;
-
 	for (int i = 0; i < commandLinesSize; i++)
 		doxygenCommands[commandLines[i]] = COMMANDLINE;
-	for (int i = 0; i < ignoreCommandLinesSize; i++)
-		doxygenCommands[ignoreCommandLines[i]] = IGNOREDCOMMANDLINE;
-
 	for (int i = 0; i < commandParagraphSize; i++)
 		doxygenCommands[commandParagraph[i]] = COMMANDPARAGRAPH;
-	for (int i = 0; i < ignoreCommandParagraphsSize; i++)
-		doxygenCommands[ignoreCommandParagraphs[i]] = IGNORECOMMANDPARAGRAPH;
-
 	for (int i = 0; i < commandEndCommandsSize; i++)
 		doxygenCommands[commandEndCommands[i]] = COMMANDENDCOMMAND;
 	for (int i = 0; i < commandWordParagraphsSize; i++)
@@ -70,7 +58,7 @@ void DoxygenParser::fillTables() {
 		doxygenSectionIndicators.insert(sectionIndicators[i]);
 }
 
-std::string DoxygenParser::StringToLower(std::string stringToConvert) {
+std::string DoxygenParser::stringToLower(std::string &stringToConvert) {
 	for (unsigned int i = 0; i < stringToConvert.length(); i++) {
 		stringToConvert[i] = tolower(stringToConvert[i]);
 	}
@@ -79,7 +67,7 @@ std::string DoxygenParser::StringToLower(std::string stringToConvert) {
 
 int DoxygenParser::findCommand(std::string smallString) {
 	std::map<std::string, DoxyCommandEnum>::iterator it;
-	smallString = StringToLower(smallString);
+	smallString = stringToLower(smallString);
 	// I'm not sure if we can really do so, because there are different commands
 	// in doxygenCommands and original commandArray
 	it = doxygenCommands.find(smallString);
@@ -89,7 +77,7 @@ int DoxygenParser::findCommand(std::string smallString) {
 }
 
 int DoxygenParser::isSectionIndicator(std::string smallString) {
-	smallString = StringToLower(smallString);
+	smallString = stringToLower(smallString);
 	std::set<std::string>::iterator it;
 	it = doxygenSectionIndicators.find(smallString);
 	if (it != doxygenSectionIndicators.end())
@@ -106,7 +94,7 @@ void DoxygenParser::printTree(std::list < DoxygenEntity > &rootList) {
 }
 
 int DoxygenParser::commandBelongs(std::string theCommand) {
-	std::string smallString = StringToLower(theCommand);
+	std::string smallString = stringToLower(theCommand);
 	//cout << " Looking for command " << theCommand << endl;
 	std::map<std::string, DoxyCommandEnum>::iterator it;
 	it = doxygenCommands.find(smallString);
@@ -238,8 +226,7 @@ std::list < Token >::iterator DoxygenParser::getEndCommand(std::string theComman
 	return tokList.end();
 }
 
-std::list < Token >::iterator DoxygenParser::getTilAnyCommand(std::string theCommand, TokenList & tokList) {
-#pragma unused(theCommand,tokList)
+std::list < Token >::iterator DoxygenParser::getTilAnyCommand(std::string, TokenList &) {
 	std::list < Token >::iterator anIterator;
 	return anIterator;
 }
@@ -251,13 +238,6 @@ int DoxygenParser::addSimpleCommand(std::string theCommand, std::list < DoxygenE
 	return 1;
 }
 
-int DoxygenParser::ignoreSimpleCommand(std::string theCommand, std::list < DoxygenEntity > &doxyList) {
-#pragma unused(doxyList)
-	if (noisy)
-		cout << "Not Adding " << theCommand << endl;
-	return 1;
-}
-
 int DoxygenParser::addCommandWord(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
 	if (noisy)
 		cout << "Parsing " << theCommand << endl;
@@ -272,18 +252,6 @@ int DoxygenParser::addCommandWord(std::string theCommand, TokenList & tokList, s
 	return 0;
 }
 
-int DoxygenParser::ignoreCommandWord(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
-#pragma unused(doxyList)
-	if (noisy)
-		cout << "Not Adding " << theCommand << endl;
-	std::string name = getNextWord(tokList);
-	if (!name.empty())
-		return 1;
-	else
-		tokList.printListError("No word followed " + theCommand + " command.");
-	return 0;
-}
-
 int DoxygenParser::addCommandLine(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
 	if (noisy)
 		cout << "Parsing " << theCommand << endl;
@@ -293,15 +261,6 @@ int DoxygenParser::addCommandLine(std::string theCommand, TokenList & tokList, s
 	return 1;
 }
 
-int DoxygenParser::ignoreCommandLine(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
-#pragma unused(doxyList)
-	if (noisy)
-		cout << "Not Adding " << theCommand << endl;
-	std::list < Token >::iterator endOfLine = getOneLine(tokList);
-	tokList.setIterator(endOfLine);
-	return 1;
-}
-
 int DoxygenParser::addCommandParagraph(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
 	if (noisy)
 		cout << "Parsing " << theCommand << endl;
@@ -312,15 +271,6 @@ int DoxygenParser::addCommandParagraph(std::string theCommand, TokenList & tokLi
 	return 1;
 }
 
-int DoxygenParser::ignoreCommandParagraph(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
-#pragma unused(doxyList)
-	if (noisy)
-		cout << "Not Adding " << theCommand << endl;
-	std::list < Token >::iterator endOfParagraph = getEndOfParagraph(tokList);
-	tokList.setIterator(endOfParagraph);
-	return 1;
-}
-
 int DoxygenParser::addCommandEndCommand(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
 	if (noisy)
 		cout << "Parsing " << theCommand << endl;
@@ -399,8 +349,7 @@ int DoxygenParser::addCommandOWord(std::string theCommand, TokenList & tokList,
 	return 1;
 }
 
-int DoxygenParser::addCommandErrorThrow(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
-#pragma unused(doxyList)
+int DoxygenParser::addCommandErrorThrow(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &) {
 	tokList.printListError("Encountered: " + theCommand +
 			"\nThis command should not have been encountered. Behaviour past this may be unpredictable");
 	std::list < Token >::iterator endOfLine = getOneLine(tokList);
@@ -684,7 +633,7 @@ int DoxygenParser::addCommandUnique(std::string theCommand, TokenList & tokList,
 }
 
 int DoxygenParser::addCommand(std::string commandString, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
-	std::string theCommand = StringToLower(commandString);
+	std::string theCommand = stringToLower(commandString);
 	if (theCommand == "plainstd::string") {
 		std::string nextPhrase = getStringTilCommand(tokList);
 		if (noisy)
@@ -692,53 +641,30 @@ int DoxygenParser::addCommand(std::string commandString, TokenList & tokList, st
 		doxyList.push_back(DoxygenEntity("plainstd::string", nextPhrase));
 		return 1;
 	}
-	int commandNumber = commandBelongs(theCommand);
-	if (commandNumber == SIMPLECOMMAND) {
-		return addSimpleCommand(theCommand, doxyList);
+	switch (commandBelongs(theCommand)) {
+		case SIMPLECOMMAND:
+			return addSimpleCommand(theCommand, doxyList);
+		case COMMANDWORD:
+			return addCommandWord(theCommand, tokList, doxyList);
+		case COMMANDLINE:
+			return addCommandLine(theCommand, tokList, doxyList);
+		case COMMANDPARAGRAPH:
+			return addCommandParagraph(theCommand, tokList, doxyList);
+		case COMMANDENDCOMMAND:
+			return addCommandEndCommand(theCommand, tokList, doxyList);
+		case COMMANDWORDPARAGRAPH:
+			return addCommandWordParagraph(theCommand, tokList, doxyList);
+		case COMMANDWORDLINE:
+			return addCommandWordLine(theCommand, tokList, doxyList);
+		case COMMANDWORDOWORDWORD:
+			return addCommandWordOWordOWord(theCommand, tokList, doxyList);
+		case COMMANDOWORD:
+			return addCommandOWord(theCommand, tokList, doxyList);
+		case COMMANDERRORTHROW:
+			return addCommandErrorThrow(theCommand, tokList, doxyList);
+		case COMMANDUNIQUE:
+			return addCommandUnique(theCommand, tokList, doxyList);
 	}
-	if (commandNumber == IGNOREDSIMPLECOMMAND) {
-		return ignoreSimpleCommand(theCommand, doxyList);
-	}
-	if (commandNumber == COMMANDWORD) {
-		return addCommandWord(theCommand, tokList, doxyList);
-	}
-	if (commandNumber == IGNOREDCOMMANDWORD) {
-		return ignoreCommandWord(theCommand, tokList, doxyList);
-	}
-	if (commandNumber == COMMANDLINE) {
-		return addCommandLine(theCommand, tokList, doxyList);
-	}
-	if (commandNumber == IGNOREDCOMMANDLINE) {
-		return ignoreCommandLine(theCommand, tokList, doxyList);
-	}
-	if (commandNumber == COMMANDPARAGRAPH) {
-		return addCommandParagraph(theCommand, tokList, doxyList);
-	}
-	if (commandNumber == IGNORECOMMANDPARAGRAPH) {
-		return ignoreCommandParagraph(theCommand, tokList, doxyList);
-	}
-	if (commandNumber == COMMANDENDCOMMAND) {
-		return addCommandEndCommand(theCommand, tokList, doxyList);
-	}
-	if (commandNumber == COMMANDWORDPARAGRAPH) {
-		return addCommandWordParagraph(theCommand, tokList, doxyList);
-	}
-	if (commandNumber == COMMANDWORDLINE) {
-		return addCommandWordLine(theCommand, tokList, doxyList);
-	}
-	if (commandNumber == COMMANDWORDOWORDWORD) {
-		return addCommandWordOWordOWord(theCommand, tokList, doxyList);
-	}
-	if (commandNumber == COMMANDOWORD) {
-		return addCommandOWord(theCommand, tokList, doxyList);
-	}
-	if (commandNumber == COMMANDERRORTHROW) {
-		return addCommandErrorThrow(theCommand, tokList, doxyList);
-	}
-	if (commandNumber == COMMANDUNIQUE) {
-		return addCommandUnique(theCommand, tokList, doxyList);
-	}
-
 	return 0;
 }
 
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.h b/Source/DoxygenTranslator/src/DoxygenParser.h
index 5f6432d87..376676e08 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.h
+++ b/Source/DoxygenTranslator/src/DoxygenParser.h
@@ -27,7 +27,7 @@ private:
   /*
    *Changes a std::string to all lower case
    */
-  std::string StringToLower(std::string stringToConvert);
+  std::string stringToLower(std::string &stringToConvert);
 
   /* 
    * Finds out if a command exists (is a possible command)
@@ -112,12 +112,6 @@ private:
    *  \n \\ \@ \& \$ \# \< \> \%
    */
   int addSimpleCommand(std::string theCommand, std::list < DoxygenEntity > &doxyList);
-  /*
-   * NOT INCLUDED Simple Commands
-   * Format: @command
-   * Plain commands, such as newline etc, they contain no other data
-   */
-  int ignoreSimpleCommand(std::string theCommand, std::list < DoxygenEntity > &doxyList);
   /*
    * CommandWord
    * Format: @command <word>
@@ -126,13 +120,6 @@ private:
    * "relates", "namespace", "relatesalso","anchor", "dontinclude", "include", "includelineno"
    */
   int addCommandWord(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList);
-  /*
-   * NOT INCLUDED CommandWord
-   * Format: @command <word>
-   * Commands with a single WORD after then such as @b
-   * "copydoc", "copybrief", "copydetails", "verbinclude", "htmlinclude"
-   */
-  int ignoreCommandWord(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList);
   /*
    * CommandLine
    * Format: @command (line)
@@ -140,12 +127,6 @@ private:
    * "addindex", "fn", "name", "line", "var", "skipline", "typedef", "skip", "until", "property"
    */
   int addCommandLine(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList);
-  /*
-   * NOT INCLUDED CommandLine
-   * Format: @command (line)
-   * Commands with a single LINE after then such as @var
-   */
-  int ignoreCommandLine(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList);
   /*
    * CommandParagraph
    * Format: @command {paragraph}
@@ -154,12 +135,6 @@ private:
    * "deprecated", "date", "note", "warning", "version", "todo", "bug", "attention", "brief", "arg", "author"
    */
   int addCommandParagraph(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList);
-  /*
-   * CommandParagraph
-   * Format: @command {paragraph}
-   * Commands with a single LINE after then such as @var
-   */
-  int ignoreCommandParagraph(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList);
   /*
    * Command EndCommand
    * Format: @command and ends at @endcommand
@@ -207,9 +182,7 @@ private:
    */
   int addCommandUnique(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList);
   /* 
-   * The actual "meat" of the doxygen parser. This is not yet fully implemented
-   * with my current design- however the skeletal outline is contained in
-   * the file Skeleton
+   * The actual "meat" of the doxygen parser. Calls the correct addCommand* function
    */
   int addCommand(std::string commandString, TokenList & tokList, std::list < DoxygenEntity > &doxyList);
 
diff --git a/Source/DoxygenTranslator/src/DoxygenTranslator.cpp b/Source/DoxygenTranslator/src/DoxygenTranslator.cpp
index 10f6a4585..51df52f59 100644
--- a/Source/DoxygenTranslator/src/DoxygenTranslator.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenTranslator.cpp
@@ -32,7 +32,7 @@ String *DoxygenTranslator::getDoxygenComment(Node *node) {
 String *DoxygenTranslator::getDocumentation(Node *node) {
   
   if (!hasDocumentation(node))
-    return 0;
+    return NewString("");
   
   return makeDocumentation(node);
 }
diff --git a/Source/DoxygenTranslator/src/DoxygenTranslator.h b/Source/DoxygenTranslator/src/DoxygenTranslator.h
index 97be4ee35..7d2e64542 100644
--- a/Source/DoxygenTranslator/src/DoxygenTranslator.h
+++ b/Source/DoxygenTranslator/src/DoxygenTranslator.h
@@ -39,7 +39,7 @@ public:
    * Return the documentation for a given node formated for the correct 
    * documentation system.
    * @param node The node to extract and translate documentation for.
-   * @return The resulted documentation string.
+   * @return The resulted documentation string, or empty string in case of any errors.
    */
   String *getDocumentation(Node *node);
   /*
@@ -57,8 +57,7 @@ protected:
    * Overridden in subclasses to return the documentation formatted for a given
    * documentation system.
    * @param node The node to extract and translate documentation for.
-   * @param documentation The returned documentation string.
-   * @return A bool to indicate if there was documentation to return for the node.
+   * @return The resulted documentation string
    */
   virtual String *makeDocumentation(Node *node) = 0;
   
diff --git a/Source/DoxygenTranslator/src/TokenList.cpp b/Source/DoxygenTranslator/src/TokenList.cpp
index 62dbdc997..fd5850ffe 100644
--- a/Source/DoxygenTranslator/src/TokenList.cpp
+++ b/Source/DoxygenTranslator/src/TokenList.cpp
@@ -45,7 +45,7 @@ TokenList TokenList::tokenizeDoxygenComment(const std::string &doxygenComment, c
         // check if it's one of the '!!!', '***', '///' of any length
         char c = currentWord[0];
         isPlainString = false;
-        for (int i=0; i<currentWord.size(); i++)
+        for (size_t i=0; i<currentWord.size(); i++)
           if (currentWord[i] != c) {
             isPlainString = true;
             break;

From 342bff6ec94ca42049ac070b018e7d3afa7b6783 Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Wed, 8 Aug 2012 14:16:48 +0000
Subject: [PATCH 124/314] Changed quoted strings handling. Also not missing any
 doxygen commands now.

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13563 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 .../doxygen_translate_all_tags_runme.py       | 13 ++--
 .../DoxygenTranslator/src/DoxygenParser.cpp   | 20 +++++-
 Source/DoxygenTranslator/src/TokenList.cpp    | 67 ++++++++-----------
 3 files changed, 52 insertions(+), 48 deletions(-)

diff --git a/Examples/test-suite/python/doxygen_translate_all_tags_runme.py b/Examples/test-suite/python/doxygen_translate_all_tags_runme.py
index 768ccf1ba..e1d7a33b7 100644
--- a/Examples/test-suite/python/doxygen_translate_all_tags_runme.py
+++ b/Examples/test-suite/python/doxygen_translate_all_tags_runme.py
@@ -21,7 +21,7 @@ check(doxygen_translate_all_tags.function.__doc__, ''
 ''
 '  SomeLatexIndex '
 ''
-'  someGroupSome title '
+'  someGroup"Some title" '
 ''
 '  theAnchor'
 ''
@@ -84,8 +84,8 @@ check(doxygen_translate_all_tags.function.__doc__, ''
 '  digraph example { '
 '  node [shape=record, fontname=Helvetica, fontsize=10]; '
 ''
-'  b [ label="class B" URL="\ref B"]; '
-'  c [ label="class C" URL="\ref C"]; '
+'  b [ label="class B" URL=" B"]; '
+'  c [ label="class C" URL=" C"]; '
 '  b -> c [ arrowhead="open", style="dashed" ]; '
 '  } '
 ''
@@ -171,9 +171,9 @@ check(doxygen_translate_all_tags.function.__doc__, ''
 '  someThing'
 ''
 '  Sender,Receiver; '
-'  Sender->Receiver [label="Command()", URL="\ref '
+'  Sender->Receiver [label="Command()", URL=" '
 '  Receiver::Command()"]; '
-'  Sender<-Receiver [label="Ack()", URL="\ref '
+'  Sender<-Receiver [label="Ack()", URL=" '
 '  Ack()", ID="1"]; '
 ''
 '  mscFile.mscThe caption'
@@ -312,9 +312,10 @@ check(doxygen_translate_all_tags.function.__doc__, ''
 ''
 '  This will only appear in XML '
 ''
+'  todo"Todo"Todo List'
 ''
 '  Here goes test of symbols: '
 '  $@\&~<>#%".::'
 ''
 '  And here goes simple text '
-)
\ No newline at end of file
+)
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.cpp b/Source/DoxygenTranslator/src/DoxygenParser.cpp
index 4df82b2d7..dd2e556eb 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenParser.cpp
@@ -106,7 +106,23 @@ int DoxygenParser::commandBelongs(std::string theCommand) {
 std::string DoxygenParser::getNextWord(TokenList & tokList) {
 	Token nextToken = tokList.peek();
 	if (nextToken.tokenType == PLAINSTRING) {
-		nextToken = tokList.next();
+		// handle quoted strings as words
+		if (nextToken.tokenString[0] == '"'
+				&& nextToken.tokenString[nextToken.tokenString.size() - 1] != '"') {
+			string word = nextToken.tokenString + " ";
+			nextToken = tokList.next();
+			while (true) {
+				string nextWord = getNextWord(tokList);
+				if (!nextWord.size()) // maybe report unterminated string error
+					return word;
+				word += nextWord;
+				if (word[word.size() - 1] == '"') // strip quotes
+					return word.substr(1, word.size() - 2);
+				word += " ";
+			}
+		}
+
+		tokList.next();
 		return nextToken.tokenString;
 	}
 	return "";
@@ -120,7 +136,6 @@ std::list < Token >::iterator DoxygenParser::getOneLine(TokenList & tokList) {
 			//endOfLine++;
 			return endOfLine;
 		}
-		//cout << (* endOfLine).toString();
 		endOfLine++;
 	}
 
@@ -390,6 +405,7 @@ int DoxygenParser::addCommandUnique(std::string theCommand, TokenList & tokList,
 		aNewList.push_front(DoxygenEntity("plainstd::string", title));
 		aNewList.push_front(DoxygenEntity("plainstd::string", heading));
 		aNewList.push_front(DoxygenEntity("plainstd::string", key));
+		doxyList.push_back(DoxygenEntity(theCommand, aNewList));
 		return 1;
 	}
 	// \ingroup (<groupname> [<groupname> <groupname>])
diff --git a/Source/DoxygenTranslator/src/TokenList.cpp b/Source/DoxygenTranslator/src/TokenList.cpp
index fd5850ffe..d69721e9a 100644
--- a/Source/DoxygenTranslator/src/TokenList.cpp
+++ b/Source/DoxygenTranslator/src/TokenList.cpp
@@ -28,57 +28,44 @@ TokenList TokenList::tokenizeDoxygenComment(const std::string &doxygenComment, c
 
   bool isPlainString = false;
   string::size_type pos, lastPos = 0;
+  char prevChar = doxygenComment[lastPos];
   string currentWord;
   while (true) {
     isPlainString = false;
-    pos = doxygenComment.find_first_of("\t\n ", lastPos);
+    pos = doxygenComment.find_first_of("\\@\t\n ", lastPos);
     if (pos == string::npos)
       pos = doxygenComment.size();
-    if (pos > lastPos) {
-      currentWord = doxygenComment.substr(lastPos, pos-lastPos);
-      if (currentWord[0] == '\\' || currentWord[0] == '@') {
-        // it's a doxygen command
-        currentWord = currentWord.substr(1, currentWord.length() - 1);
-        tokList.m_tokenList.push_back(Token(COMMAND, currentWord));
-      }
-      else if (currentWord[0] == '!' || currentWord[0] == '*' || currentWord[0] == '/') {
-        // check if it's one of the '!!!', '***', '///' of any length
-        char c = currentWord[0];
-        isPlainString = false;
-        for (size_t i=0; i<currentWord.size(); i++)
-          if (currentWord[i] != c) {
-            isPlainString = true;
-            break;
-          }
-      }
-      else
-        isPlainString = true;
 
-      if (isPlainString) {
-        // handle quoted words
-        if (currentWord[0] == '"') {
-          pos = doxygenComment.find_first_of("\"\n", lastPos + 1);
-          if (pos == string::npos)
-            pos = doxygenComment.size();
-          if (pos == doxygenComment.size() || doxygenComment[pos] != '"') {
-            // hack to print error message before the list is constructed
-            tokList.m_tokenListIter = tokList.m_tokenList.end();
-            tokList.printListError("Unterminated string");
-          }
-          // also strip quotes
-          currentWord = doxygenComment.substr(lastPos + 1, pos-lastPos-1);
-        }
-        if (currentWord.size())
-          tokList.m_tokenList.push_back(Token(PLAINSTRING, currentWord));
-      }
+    currentWord = doxygenComment.substr(lastPos, pos-lastPos);
+    if (prevChar == '\n')
+      tokList.m_tokenList.push_back(Token(END_LINE, "\n"));
+    else if (prevChar == '\\' || prevChar == '@') {
+      // it's a doxygen command
+      // hack to get commands like \\ or \@ or @\ or @@
+      if (doxygenComment[pos] == '@' || doxygenComment[pos] == '\\')
+        currentWord += doxygenComment[pos];
+      tokList.m_tokenList.push_back(Token(COMMAND, currentWord));
     }
+    else if (currentWord.size() && (currentWord[0] == '!' || currentWord[0] == '*' || currentWord[0] == '/')) {
+      // check if it's one of the '!!!', '***', '///' of any length
+      char c = currentWord[0];
+      isPlainString = false;
+      for (size_t i=0; i<currentWord.size(); i++)
+        if (currentWord[i] != c) {
+          isPlainString = true;
+          break;
+        }
+    }
+    else
+      isPlainString = true;
 
+    if (isPlainString && currentWord.size())
+      tokList.m_tokenList.push_back(Token(PLAINSTRING, currentWord));
+
+    prevChar = doxygenComment[pos];
     lastPos = pos + 1;
     if (lastPos >= doxygenComment.size())
       break;
-
-    if (doxygenComment[pos] == '\n')
-      tokList.m_tokenList.push_back(Token(END_LINE, "\n"));
   }
   tokList.m_tokenListIter = tokList.m_tokenList.begin();
   return tokList;

From 7178385d48763cae99421c948657cd05d1d8e59b Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Thu, 9 Aug 2012 18:58:53 +0000
Subject: [PATCH 125/314] Made comment output nicer, now printing _someword_
 instead of _someword _

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13576 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 .../DoxygenTranslator/src/JavaDocConverter.cpp | 18 ++++++++++++++++--
 .../DoxygenTranslator/src/PyDocConverter.cpp   | 11 +++++++++--
 2 files changed, 25 insertions(+), 4 deletions(-)

diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.cpp b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
index c7485ab4f..fb13728ea 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
@@ -199,8 +199,15 @@ void JavaDocConverter::translateEntity(DoxygenEntity& tag, std::string& translat
 }
 
 void JavaDocConverter::handleTagHtml(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
-  if (tag.entityList.size()) // do not include empty tags
-    translatedComment += "<" + arg + ">" + translateSubtree(tag) + "</" + arg + ">";
+  if (tag.entityList.size()) { // do not include empty tags
+    std::string tagData = translateSubtree(tag);
+    // wrap the thing, ignoring whitespaces
+    size_t wsPos = tagData.find_last_not_of("\n\t ");
+    if (wsPos != std::string::npos)
+      translatedComment += "<" + arg + ">" + tagData.substr(0, wsPos + 1) + "</" + arg + ">" + tagData.substr(wsPos + 1);
+    else
+      translatedComment += "<" + arg + ">" + translateSubtree(tag) + "</" + arg + "> ";
+  }
 }
 void JavaDocConverter::handleNewLine(DoxygenEntity&, std::string& translatedComment, std::string&) {
   translatedComment += "\n * ";
@@ -434,6 +441,13 @@ String *JavaDocConverter::makeDocumentation(Node *node) {
 
   std::string javaDocString = "/**\n * ";
 
+  // strip endlines at the beginning
+  while (entityList.begin()->typeOfEntity == "plainstd::endl")
+    entityList.pop_front();
+  // and at the end
+  while (entityList.rbegin()->typeOfEntity == "plainstd::endl")
+    entityList.pop_back();
+
   // store the current node
   // (currently just to handle params)
   currentNode = node;
diff --git a/Source/DoxygenTranslator/src/PyDocConverter.cpp b/Source/DoxygenTranslator/src/PyDocConverter.cpp
index 7937b5ba5..0f1f32cbb 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/PyDocConverter.cpp
@@ -227,8 +227,15 @@ void PyDocConverter::handleTagParam(DoxygenEntity& tag, std::string& translatedC
   translatedComment += paramNameEntity.data + " (" + paramType + ")" + paramDescription;
 }
 void PyDocConverter::handleTagWrap(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
-  if (tag.entityList.size()) // do not include empty tags
-    translatedComment += arg + translateSubtree(tag) + arg;
+  if (tag.entityList.size()) { // do not include empty tags
+    std::string tagData = translateSubtree(tag);
+    // wrap the thing, ignoring whitespaces
+    int wsPos = tagData.find_last_not_of("\n\t ");
+    if (wsPos != std::string::npos)
+      translatedComment += arg + tagData.substr(0, wsPos + 1) + arg + tagData.substr(wsPos + 1);
+    else
+      translatedComment += arg + tagData + arg + " ";
+  }
 }
 void PyDocConverter::handleNewLine(DoxygenEntity&, std::string& translatedComment, std::string&) {
   translatedComment += "\n";

From 423915eef695b50790d4345441bba161b5a845e9 Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Thu, 9 Aug 2012 19:06:58 +0000
Subject: [PATCH 126/314] Added some docs, updated project-plan

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13577 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Doc/Devel/plan-gsoc-2012.txt | 20 +++++++++++++----
 Doc/Manual/Contents.html     |  3 ++-
 Doc/Manual/Doxygen.html      | 42 ++++++++++++++++++++++++++++++++++--
 3 files changed, 58 insertions(+), 7 deletions(-)

diff --git a/Doc/Devel/plan-gsoc-2012.txt b/Doc/Devel/plan-gsoc-2012.txt
index 43fc1adc3..7e8ecf541 100644
--- a/Doc/Devel/plan-gsoc-2012.txt
+++ b/Doc/Devel/plan-gsoc-2012.txt
@@ -77,7 +77,9 @@ Functionality
   to the destination documentation. 'Not implemented' means that the
   tag with it's contents is stripped out of the output.
 
-    Doxygen tags:     
+    Doxygen tags:
+    
+    All tags: -OK-     
 
     \a - translated to <i></i> in JD, surrounded with _ in PD
     \addindex - ignored
@@ -257,12 +259,12 @@ Optional functionality
 That section describes some complex cases where the current code
 does not behave really well. Like a short to-do list of special cases.
 
-- When translating functions with default parameters in swig to
+-OK- When translating functions with default parameters in swig to
 java, it creates overloaded functions with all the parameters
 except the default ones. We need to copy the doxygen comment to
 such functions and correct the list of @param tags.
 
-- In doxygen there is a special tags (and even a special option)
+-OK- In doxygen there is a special tags (and even a special option)
 to create links to some code members from the current comment.
 Sometimes it needs a type of parameters specified because of the
 overloaded functions. And the same linking tags are supported in JD,
@@ -303,6 +305,15 @@ The following test cases will be implemented:
 -OK- Class comment, with all supported tags.
 -OK- Class comment, with all doxygen tags, including
   ignored ones.
+  
+The list of all tests, in form of shell commands to make it simple
+to test project by copying the text below into terminal program.
+make doxygen_parsing.cpptest -s
+make doxygen_translate.cpptest -s
+make doxygen_translate_all_tags.cpptest -s
+make doxygen_basic_translate.cpptest -s
+make doxygen_basic_notranslate.cpptest -s
+make doxygen_translate_links.cpptest -s
 
   
 Refactoring
@@ -313,7 +324,7 @@ All the code in directory _DoxygenTranslator_ should be refactored:
 -OK- most static methods should be normal members
 -OK- replace C arrays of strings and sequential searches with STL data
   structures and algorithms.
-- use singletons instead of class instantiaion for each comment found.
+-OK- use singletons instead of class instantiaion for each comment found.
 
 
 Documentation
@@ -324,4 +335,5 @@ SWIG documentation will contain:
 -OK- list of implemented features (types and placements of comments)
 -OK- list of unimplemented features (types and placements of comments)
 -OK- list of tags and their translations (all Doxygen tags).
+-OK- some amount of debugging and development information
 
diff --git a/Doc/Manual/Contents.html b/Doc/Manual/Contents.html
index ca66d87cc..137c746ab 100644
--- a/Doc/Manual/Contents.html
+++ b/Doc/Manual/Contents.html
@@ -1719,7 +1719,8 @@
 <li><a href="Doxygen.html#Doxygen_developer_details">Developer Information</a>
 <ul>
 <li><a href="Doxygen.html#Doxygen_module_design">Module Design</a>
-<li><a href="Doxygen.html#Doxygen_debugging_commands">Debugging commands</a>
+<li><a href="Doxygen.html#Doxygen_debugging_commands">Debugging Doxygen parser and translator</a>
+<li><a href="Doxygen.html#Doxygen_debugging_commands">Tests</a>
 </ul>
 <li><a href="Doxygen.html#Doxygen_language_extension">Extending to Other Languages</a>
 </ul>
diff --git a/Doc/Manual/Doxygen.html b/Doc/Manual/Doxygen.html
index 3178f70c2..cb79ef83c 100644
--- a/Doc/Manual/Doxygen.html
+++ b/Doc/Manual/Doxygen.html
@@ -32,7 +32,8 @@
 <li><a href="#Doxygen_developer_details">Developer Information</a>
 <ul>
 <li><a href="#Doxygen_module_design">Module Design</a>
-<li><a href="#Doxygen_debugging_commands">Debugging commands</a>
+<li><a href="#Doxygen_debugging_commands">Debugging Doxygen parser and translator</a>
+<li><a href="#Doxygen_debugging_commands">Tests</a>
 </ul>
 <li><a href="#Doxygen_language_extension">Extending to Other Languages</a>
 </ul>
@@ -1282,7 +1283,7 @@ This module builds its own private parse tree and hands it to a separate class f
 For example, <tt>JavaDocConverter</tt> is the JavaDoc module class.
 </p>
 
-<H3><a name="Doxygen_debugging_commands"></a>39.5.2 Debugging commands</H3>
+<H3><a name="Doxygen_debugging_commands"></a>39.5.2 Debugging Doxygen parser and translator</H3>
 
 
 <p>
@@ -1294,6 +1295,43 @@ There are two handy command line switches, that enable lots of detailed debug in
   -debug-doxygen-translator - Display Doxygen translator module debugging information
 </pre></div>
 
+<H3><a name="Doxygen_tests"></a>39.5.3 Tests</H3>
+
+
+<p>
+This part of SWIG currently has 6 runtime tests in both Java and Python.
+</p>
+
+<div class="shell"><pre>
+  doxygen_parsing
+  doxygen_translate
+  doxygen_translate_all_tags
+  doxygen_basic_translate
+  doxygen_basic_notranslate
+  doxygen_translate_links
+</pre></div>
+
+<p>
+All this tests are included in common.mk and are build with the commands like 'make check-test-suite'
+or 'make check-python-test-suite'. To run them individually, type 'make <testname>.cpptest -s' in the
+language-specific subdir in Examples\test-suite.
+<br>
+Runtime tests in Java are implemented using JavaDoc doclets. To make that work, you
+should have tools.jar from the JDK in your classpath. Or you should have JAVA_HOME
+environmental var defined and pointing to the JDK location.
+<br>
+The Java's comment parsing code (the testing part) is located in commentParser.java.
+You may see it to understand how the checking process works. There is also a possibility
+to run that file as stand-alone program, with 'java commentParser <some java package>',
+and it will print the list of comments found in the specified dir (in the format it's used
+in runtime tests). So, when you want to create the new test of Doxygen comment translator,
+just copy any existing one, and replace the actual comment content (section of entries in
+form 'wantedComments.put(...)' with the output of the above command.
+<br>
+Runtime tests in Python are just plain strings comparison with the use of __doc__
+properties.
+</p>
+
 <H2><a name="Doxygen_language_extension"></a>39.6 Extending to Other Languages</H2>
 
 

From f7f3960d1126069aa2c7414b66dbf437879d3f5d Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Fri, 10 Aug 2012 12:27:40 +0000
Subject: [PATCH 127/314] Eliminate 'signed/unsigned comparison' compiler
 warning

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13582 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Source/DoxygenTranslator/src/PyDocConverter.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Source/DoxygenTranslator/src/PyDocConverter.cpp b/Source/DoxygenTranslator/src/PyDocConverter.cpp
index 0f1f32cbb..1826bcab5 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/PyDocConverter.cpp
@@ -230,7 +230,7 @@ void PyDocConverter::handleTagWrap(DoxygenEntity& tag, std::string& translatedCo
   if (tag.entityList.size()) { // do not include empty tags
     std::string tagData = translateSubtree(tag);
     // wrap the thing, ignoring whitespaces
-    int wsPos = tagData.find_last_not_of("\n\t ");
+    size_t wsPos = tagData.find_last_not_of("\n\t ");
     if (wsPos != std::string::npos)
       translatedComment += arg + tagData.substr(0, wsPos + 1) + arg + tagData.substr(wsPos + 1);
     else

From 9600bb310f675b1462dd35e3cb074dfe388e3253 Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Fri, 10 Aug 2012 21:21:16 +0000
Subject: [PATCH 128/314] Improved unknown Doxygen commands handling

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13591 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Source/DoxygenTranslator/src/DoxygenParser.cpp | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/Source/DoxygenTranslator/src/DoxygenParser.cpp b/Source/DoxygenTranslator/src/DoxygenParser.cpp
index dd2e556eb..cffdd6b0d 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenParser.cpp
@@ -701,7 +701,8 @@ std::list < DoxygenEntity > DoxygenParser::parse(std::list < Token >::iterator e
 			if (currCommand < 0) {
 				if (noisy)
 					cout << "Unidentified Command " << currToken.tokenString << endl;
-				tokList.next();
+				tokList.printListError("Unsupported command: " + currToken.tokenString + ". Ignored");
+				tokList.current()->tokenType = PLAINSTRING; // little hack to add the command as plaintext
 				addCommand(currPlainstringCommandType, tokList, aNewList);
 			} else {
 				tokList.next();

From 771c61f9f18bc1a8feb74d24ccffa7cd296232ae Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Sat, 11 Aug 2012 14:34:48 +0000
Subject: [PATCH 129/314] Renamed DoxygenComment to doxygen to better comply
 swig's attribute namings

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13597 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Source/CParse/parser.y                             | 14 +++++++-------
 Source/DoxygenTranslator/src/DoxygenTranslator.cpp |  2 +-
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/Source/CParse/parser.y b/Source/CParse/parser.y
index 27957d9ab..ddcdc5477 100644
--- a/Source/CParse/parser.y
+++ b/Source/CParse/parser.y
@@ -193,15 +193,15 @@ static void set_comment(Node *n, String *comment) {
   if (!n || !comment)
     return;
 
-  if (Getattr(n, "DoxygenComment"))
-    Append(Getattr(n, "DoxygenComment"), comment);
+  if (Getattr(n, "doxygen"))
+    Append(Getattr(n, "doxygen"), comment);
   else {
-    Setattr(n, "DoxygenComment", comment);
+    Setattr(n, "doxygen", comment);
     /* This is the first comment, populate it with @params, if any */
     p = Getattr(n, "parms");
     while (p) {
-      if (Getattr(p, "DoxygenComment"))
-	Printv(comment, "\n@param ", Getattr(p, "name"), Getattr(p, "DoxygenComment"), NIL);
+      if (Getattr(p, "doxygen"))
+	Printv(comment, "\n@param ", Getattr(p, "name"), Getattr(p, "doxygen"), NIL);
       p=nextSibling(p);
     }
   }
@@ -212,7 +212,7 @@ static void set_comment(Node *n, String *comment) {
     return;
   n = nextSibling(n);
   while (n && Getattr(n, "name") && Strcmp(Getattr(n, "name"), name) == 0) {
-    Setattr(n, "DoxygenComment", comment);
+    Setattr(n, "doxygen", comment);
     n = nextSibling(n);
   }
 }
@@ -3474,7 +3474,7 @@ doxygen_comment_item : DOXYGENSTRING {
 		    not translatable to javadoc anyway) */
 		  if(0  &&  isStructuralDoxygen($1)){
 		    $$ = new_node("doxycomm");
-		    Setattr($$,"DoxygenComment",$1);
+		    set_comment($$, $1);
 		  }
 		  else {
 		    $$ = $1;
diff --git a/Source/DoxygenTranslator/src/DoxygenTranslator.cpp b/Source/DoxygenTranslator/src/DoxygenTranslator.cpp
index 51df52f59..d9bf5f059 100644
--- a/Source/DoxygenTranslator/src/DoxygenTranslator.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenTranslator.cpp
@@ -25,7 +25,7 @@ bool DoxygenTranslator::hasDocumentation(Node *node) {
 }
 
 String *DoxygenTranslator::getDoxygenComment(Node *node) {
-  return Getattr(node, "DoxygenComment");
+  return Getattr(node, "doxygen");
 }
 
 

From 3eed72b659b456613ba3b1c5e942833003a2247b Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Sat, 11 Aug 2012 15:23:18 +0000
Subject: [PATCH 130/314] Updated Doxygen warning system

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13598 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 .../DoxygenTranslator/src/DoxygenParser.cpp   | 42 +++++++++----------
 Source/DoxygenTranslator/src/TokenList.cpp    |  8 ++--
 Source/DoxygenTranslator/src/TokenList.h      |  3 +-
 Source/Include/swigwarn.h                     |  8 ++++
 4 files changed, 36 insertions(+), 25 deletions(-)

diff --git a/Source/DoxygenTranslator/src/DoxygenParser.cpp b/Source/DoxygenTranslator/src/DoxygenParser.cpp
index cffdd6b0d..8be8660d7 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenParser.cpp
@@ -174,7 +174,7 @@ std::string DoxygenParser::getStringTilEndCommand(std::string theCommand, TokenL
 
 		tokList.next();
 	}
-	tokList.printListError(theCommand + " command expected");
+	tokList.printListError(WARN_DOXYGEN_COMMAND_EXPECTED, theCommand + " command expected");
 	return description;
 }
 
@@ -263,7 +263,7 @@ int DoxygenParser::addCommandWord(std::string theCommand, TokenList & tokList, s
 		doxyList.push_back(DoxygenEntity(theCommand, aNewList));
 		return 1;
 	} else
-		tokList.printListError("No word followed " + theCommand + " command. Not added");
+		tokList.printListError(WARN_DOXYGEN_COMMAND_ERROR, "No word followed " + theCommand + " command. Not added");
 	return 0;
 }
 
@@ -291,7 +291,7 @@ int DoxygenParser::addCommandEndCommand(std::string theCommand, TokenList & tokL
 		cout << "Parsing " << theCommand << endl;
 	std::list < Token >::iterator endCommand = getEndCommand("end" + theCommand, tokList);
 	if (endCommand == tokList.end()) {
-	  tokList.printListError("Expected end" + theCommand);
+	  tokList.printListError(WARN_DOXYGEN_COMMAND_EXPECTED, "Expected end" + theCommand);
 	  return 0;
 	}
 	std::list < DoxygenEntity > aNewList;
@@ -306,7 +306,7 @@ int DoxygenParser::addCommandWordParagraph(std::string theCommand, TokenList & t
 		cout << "Parsing " << theCommand << endl;
 	std::string name = getNextWord(tokList);
 	if (name.empty()) {
-		tokList.printListError("No word followed " + theCommand + " command. Not added");
+		tokList.printListError(WARN_DOXYGEN_COMMAND_ERROR, "No word followed " + theCommand + " command. Not added");
 		return 0;
 	}
 	std::list < Token >::iterator endOfParagraph = getEndOfParagraph(tokList);
@@ -322,7 +322,7 @@ int DoxygenParser::addCommandWordLine(std::string theCommand, TokenList & tokLis
 		cout << "Parsing " << theCommand << endl;
 	std::string name = getNextWord(tokList);
 	if (name.empty()) {
-		tokList.printListError("No word followed " + theCommand + " command. Not added");
+		tokList.printListError(WARN_DOXYGEN_COMMAND_ERROR, "No word followed " + theCommand + " command. Not added");
 		return 0;
 	}
 	std::list < Token >::iterator endOfLine = getOneLine(tokList);
@@ -339,7 +339,7 @@ int DoxygenParser::addCommandWordOWordOWord(std::string theCommand, TokenList &
 		cout << "Parsing " << theCommand << endl;
 	std::string name = getNextWord(tokList);
 	if (name.empty()) {
-		tokList.printListError("No word followed " + theCommand + " command. Not added");
+		tokList.printListError(WARN_DOXYGEN_COMMAND_ERROR, "No word followed " + theCommand + " command. Not added");
 		return 0;
 	}
 	std::string headerfile = getNextWord(tokList);
@@ -365,7 +365,7 @@ int DoxygenParser::addCommandOWord(std::string theCommand, TokenList & tokList,
 }
 
 int DoxygenParser::addCommandErrorThrow(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &) {
-	tokList.printListError("Encountered: " + theCommand +
+	tokList.printListError(WARN_DOXYGEN_COMMAND_ERROR, "Encountered: " + theCommand +
 			"\nThis command should not have been encountered. Behaviour past this may be unpredictable");
 	std::list < Token >::iterator endOfLine = getOneLine(tokList);
 	tokList.setIterator(endOfLine);
@@ -387,17 +387,17 @@ int DoxygenParser::addCommandUnique(std::string theCommand, TokenList & tokList,
 			cout << "Parsing " << theCommand << endl;
 		std::string key = getNextWord(tokList);
 		if (key.empty()) {
-			tokList.printListError("No key followed " + theCommand + " command. Not added");
+			tokList.printListError(WARN_DOXYGEN_COMMAND_ERROR, "No key followed " + theCommand + " command. Not added");
 			return 0;
 		}
 		std::string heading = getNextWord(tokList);
 		if (key.empty()) {
-			tokList.printListError("No heading followed " + theCommand + " command. Not added");
+			tokList.printListError(WARN_DOXYGEN_COMMAND_ERROR, "No heading followed " + theCommand + " command. Not added");
 			return 0;
 		}
 		std::string title = getNextWord(tokList);
 		if (title.empty()) {
-			tokList.printListError("No title followed " + theCommand + " command. Not added");
+			tokList.printListError(WARN_DOXYGEN_COMMAND_ERROR, "No title followed " + theCommand + " command. Not added");
 			return 0;
 		}
 		std::list < Token >::iterator endOfParagraph = getEndOfParagraph(tokList);
@@ -460,7 +460,7 @@ int DoxygenParser::addCommandUnique(std::string theCommand, TokenList & tokList,
 			cout << "Parsing " << theCommand << endl;
 		std::string name = getNextWord(tokList);
 		if (name.empty()) {
-			tokList.printListError("No word followed " + theCommand + " command. Not added");
+			tokList.printListError(WARN_DOXYGEN_COMMAND_ERROR, "No word followed " + theCommand + " command. Not added");
 			return 0;
 		}
 		std::list < DoxygenEntity > aNewList;
@@ -477,7 +477,7 @@ int DoxygenParser::addCommandUnique(std::string theCommand, TokenList & tokList,
 			cout << "Parsing " << theCommand << endl;
 		std::string name = getNextWord(tokList);
 		if (name.empty()) {
-			tokList.printListError("No key followed " + theCommand + " command. Not added");
+			tokList.printListError(WARN_DOXYGEN_COMMAND_ERROR, "No key followed " + theCommand + " command. Not added");
 			return 0;
 		}
 		std::string text = getNextWord(tokList);
@@ -492,7 +492,7 @@ int DoxygenParser::addCommandUnique(std::string theCommand, TokenList & tokList,
 			cout << "Parsing " << theCommand << endl;
 		std::string name = getNextWord(tokList);
 		if (name.empty()) {
-			tokList.printListError("No name followed " + theCommand + " command. Not added");
+			tokList.printListError(WARN_DOXYGEN_COMMAND_ERROR, "No name followed " + theCommand + " command. Not added");
 			return 0;
 		}
 		std::string text = getNextWord(tokList);
@@ -541,7 +541,7 @@ int DoxygenParser::addCommandUnique(std::string theCommand, TokenList & tokList,
 			cout << "Parsing " << theCommand << endl;
 		std::string file = getNextWord(tokList);
 		if (file.empty()) {
-			tokList.printListError("No file followed " + theCommand + " command. Not added");
+			tokList.printListError(WARN_DOXYGEN_COMMAND_ERROR, "No file followed " + theCommand + " command. Not added");
 			return 0;
 		}
 		std::string caption = getNextWord(tokList);
@@ -556,12 +556,12 @@ int DoxygenParser::addCommandUnique(std::string theCommand, TokenList & tokList,
 			cout << "Parsing " << theCommand << endl;
 		std::string format = getNextWord(tokList);
 		if (format.empty()) {
-			tokList.printListError("No format followed " + theCommand + " command. Not added");
+			tokList.printListError(WARN_DOXYGEN_COMMAND_ERROR, "No format followed " + theCommand + " command. Not added");
 			return 0;
 		}
 		std::string file = getNextWord(tokList);
 		if (file.empty()) {
-			tokList.printListError("No name followed " + theCommand + " command. Not added");
+			tokList.printListError(WARN_DOXYGEN_COMMAND_ERROR, "No name followed " + theCommand + " command. Not added");
 			return 0;
 		}
 		std::string caption = getNextWord(tokList);
@@ -582,7 +582,7 @@ int DoxygenParser::addCommandUnique(std::string theCommand, TokenList & tokList,
 			cout << "Parsing " << theCommand << endl;
 		std::string name = getNextWord(tokList);
 		if (name.empty()) {
-			tokList.printListError("No word followed " + theCommand + " command. Not added");
+			tokList.printListError(WARN_DOXYGEN_COMMAND_ERROR, "No word followed " + theCommand + " command. Not added");
 			return 0;
 		}
 		std::list < DoxygenEntity > aNewList;
@@ -605,7 +605,7 @@ int DoxygenParser::addCommandUnique(std::string theCommand, TokenList & tokList,
 		if (needsCond) {
 			cond = getNextWord(tokList);
 			if (cond.empty()) {
-				tokList.printListError("No word followed " + theCommand + " command. Not added");
+				tokList.printListError(WARN_DOXYGEN_COMMAND_ERROR, "No word followed " + theCommand + " command. Not added");
 				return 0;
 			}
 		}
@@ -633,7 +633,7 @@ int DoxygenParser::addCommandUnique(std::string theCommand, TokenList & tokList,
 		}
 
 		if (endCommand == tokList.end()) {
-			tokList.printListError("No corresponding endif found");
+			tokList.printListError(WARN_DOXYGEN_COMMAND_EXPECTED, "No corresponding endif found");
 			return 0;
 		}
 
@@ -701,7 +701,7 @@ std::list < DoxygenEntity > DoxygenParser::parse(std::list < Token >::iterator e
 			if (currCommand < 0) {
 				if (noisy)
 					cout << "Unidentified Command " << currToken.tokenString << endl;
-				tokList.printListError("Unsupported command: " + currToken.tokenString + ". Ignored");
+				tokList.printListError(WARN_DOXYGEN_UNKNOWN_COMMAND, "Unsupported command: '" + currToken.tokenString + "'. Ignored");
 				tokList.current()->tokenType = PLAINSTRING; // little hack to add the command as plaintext
 				addCommand(currPlainstringCommandType, tokList, aNewList);
 			} else {
@@ -714,7 +714,7 @@ std::list < DoxygenEntity > DoxygenParser::parse(std::list < Token >::iterator e
 
 		if (endParsingIndex != tokList.end() && tokList.current() == tokList.end()) {
 		  // this could happen if we cant reach the original endParsingIndex
-		  tokList.printListError("Unexpected end of comment encountered");
+		  tokList.printListError(WARN_DOXYGEN_UNEXPECTED_END_OF_COMMENT, "Unexpected end of comment encountered");
 		  break;
 		}
 	}
diff --git a/Source/DoxygenTranslator/src/TokenList.cpp b/Source/DoxygenTranslator/src/TokenList.cpp
index d69721e9a..037518263 100644
--- a/Source/DoxygenTranslator/src/TokenList.cpp
+++ b/Source/DoxygenTranslator/src/TokenList.cpp
@@ -42,8 +42,10 @@ TokenList TokenList::tokenizeDoxygenComment(const std::string &doxygenComment, c
     else if (prevChar == '\\' || prevChar == '@') {
       // it's a doxygen command
       // hack to get commands like \\ or \@ or @\ or @@
-      if (doxygenComment[pos] == '@' || doxygenComment[pos] == '\\')
+      if (doxygenComment[pos] == '@' || doxygenComment[pos] == '\\') {
         currentWord += doxygenComment[pos];
+        pos++;
+      }
       tokList.m_tokenList.push_back(Token(COMMAND, currentWord));
     }
     else if (currentWord.size() && (currentWord[0] == '!' || currentWord[0] == '*' || currentWord[0] == '/')) {
@@ -133,10 +135,10 @@ void TokenList::printList() {
   }
 }
 
-void TokenList::printListError(std::string message) {
+void TokenList::printListError(int warningType, std::string message) {
   int curLine = fileLine;
   for (list< Token >::iterator it = m_tokenList.begin(); it != current(); it++)
     if (it->tokenType == END_LINE)
       curLine++;
-  Swig_error(fileName.c_str(), curLine, "Doxygen parser error: %s. \n", message.c_str());
+  Swig_warning(warningType, fileName.c_str(), curLine, "Doxygen parser warning: %s. \n", message.c_str());
 }
diff --git a/Source/DoxygenTranslator/src/TokenList.h b/Source/DoxygenTranslator/src/TokenList.h
index ce9d14c45..69580f11c 100644
--- a/Source/DoxygenTranslator/src/TokenList.h
+++ b/Source/DoxygenTranslator/src/TokenList.h
@@ -16,6 +16,7 @@
 #include <string>
 #include <list>
 #include "Token.h"
+#include "swigwarn.h"
 
 /* a small class used to represent the sequence of tokens
  * that can be derived from a formatted doxygen string
@@ -43,7 +44,7 @@ public:
   void setIterator(list < Token >::iterator newPosition);	/*moves up the iterator */
 
   void printList();		/* prints out the sequence of tokens */
-  void printListError(std::string message); /* prints properly formatted error message */
+  void printListError(int warningType, std::string message); /* prints properly formatted error message */
 
   /*
    * Create TokenList and populate it with tokens from
diff --git a/Source/Include/swigwarn.h b/Source/Include/swigwarn.h
index 1aae86fdd..68f35e02f 100644
--- a/Source/Include/swigwarn.h
+++ b/Source/Include/swigwarn.h
@@ -221,6 +221,14 @@
 
 /* please leave 700-719 free for D */
 
+#define WARN_DOXYGEN_UNKNOWN_COMMAND          720
+#define WARN_DOXYGEN_UNEXPECTED_END_OF_COMMENT   721
+#define WARN_DOXYGEN_COMMAND_EXPECTED         722
+#define WARN_DOXYGEN_UNTERMINATED_STRING      723
+#define WARN_DOXYGEN_COMMAND_ERROR            724
+
+/* please leave 720-729 free for Doxygen */
+
 #define WARN_RUBY_WRONG_NAME                  801
 #define WARN_RUBY_MULTIPLE_INHERITANCE        802
 

From c592e0db5126796221d83bd9b7e68fa68088cdef Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Mon, 13 Aug 2012 09:09:25 +0000
Subject: [PATCH 131/314] Made doxygen parsing switched off by default

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13602 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Examples/test-suite/common.mk | 2 +-
 Source/CParse/cscanner.c      | 2 +-
 Source/Modules/java.cxx       | 9 ++-------
 Source/Modules/python.cxx     | 9 ++-------
 4 files changed, 6 insertions(+), 16 deletions(-)

diff --git a/Examples/test-suite/common.mk b/Examples/test-suite/common.mk
index 86e33037a..e7f757f0e 100644
--- a/Examples/test-suite/common.mk
+++ b/Examples/test-suite/common.mk
@@ -64,7 +64,7 @@ CXXSRCS    =
 CSRCS      = 
 TARGETPREFIX = 
 TARGETSUFFIX = 
-SWIGOPT    = -outcurrentdir -I$(top_srcdir)/$(EXAMPLES)/$(TEST_SUITE)
+SWIGOPT    = -doxygen -outcurrentdir -I$(top_srcdir)/$(EXAMPLES)/$(TEST_SUITE)
 INCLUDES   = -I$(top_srcdir)/$(EXAMPLES)/$(TEST_SUITE)
 LIBS       = -L.
 LIBPREFIX  = lib
diff --git a/Source/CParse/cscanner.c b/Source/CParse/cscanner.c
index e15201b93..fb5754856 100644
--- a/Source/CParse/cscanner.c
+++ b/Source/CParse/cscanner.c
@@ -47,7 +47,7 @@ static int last_id = 0;
 static int rename_active = 0;
 
 /* Doxygen comments scanning */
-int scan_doxygen_comments = 1;
+int scan_doxygen_comments = 0;
 
 /* -----------------------------------------------------------------------------
  * Swig_cparse_cplusplus()
diff --git a/Source/Modules/java.cxx b/Source/Modules/java.cxx
index 3591b7363..910d481ab 100644
--- a/Source/Modules/java.cxx
+++ b/Source/Modules/java.cxx
@@ -123,7 +123,7 @@ public:
       global_variable_flag(false),
       old_variable_names(false),
       member_func_flag(false),
-      doxygen(true),
+      doxygen(false),
       comment_creation_chatter(false),
       imclass_name(NULL),
       module_class_name(NULL),
@@ -267,10 +267,6 @@ public:
 	  Swig_mark_arg(i);
 	  doxygen = true;
 	  scan_doxygen_comments = true;
-	} else if ((strcmp(argv[i], "-nodoxygen") == 0)) {
-	  Swig_mark_arg(i);
-	  doxygen = false;
-	  scan_doxygen_comments = false;
   } else if ((strcmp(argv[i], "-debug-doxygen-translator") == 0)) {
     Swig_mark_arg(i);
     debug_doxygen_translator = true;
@@ -4541,8 +4537,7 @@ extern "C" Language *swig_java(void) {
 
 const char *JAVA::usage = (char *) "\
 Java Options (available with -java)\n\
-     -doxygen        - Convert C++ doxygen comments to JavaDoc comments in proxy classes (default)\n\
-     -nodoxygen      - Don't convert C++ doxygen comments to JavaDoc comments in proxy classes\n\
+     -doxygen        - Convert C++ doxygen comments to JavaDoc comments in proxy classes\n\
      -debug-doxygen-parser     - Display doxygen parser module debugging information\n\
      -debug-doxygen-translator - Display doxygen translator module debugging information\n\
      -nopgcpp        - Suppress premature garbage collection prevention parameter\n\
diff --git a/Source/Modules/python.cxx b/Source/Modules/python.cxx
index f7c9c00c1..1d2096c81 100644
--- a/Source/Modules/python.cxx
+++ b/Source/Modules/python.cxx
@@ -85,7 +85,7 @@ static int buildnone = 0;
 static int nobuildnone = 0;
 static int safecstrings = 0;
 static int dirvtable = 0;
-static int doxygen = 1;
+static int doxygen = 0;
 static int proxydel = 1;
 static int fastunpack = 0;
 static int fastproxy = 0;
@@ -120,7 +120,7 @@ Python Options (available with -python)\n\
      -classptr       - Generate shadow 'ClassPtr' as in older swig versions\n\
      -cppcast        - Enable C++ casting operators (default) \n\
      -dirvtable      - Generate a pseudo virtual table for directors for faster dispatch \n\
-     -doxygen        - Convert C++ doxygen comments to pydoc comments in proxy classes (default) \n\
+     -doxygen        - Convert C++ doxygen comments to pydoc comments in proxy classes \n\
      -debug-doxygen-parser     - Display doxygen parser module debugging information\n\
      -debug-doxygen-translator - Display doxygen translator module debugging information\n\
      -extranative    - Return extra native C++ wraps for std containers when possible \n\
@@ -141,7 +141,6 @@ static const char *usage2 = (char *) "\
      -nocastmode     - Disable the casting mode (default)\n\
      -nocppcast      - Disable C++ casting operators, useful for generating bugs\n\
      -nodirvtable    - Don't use the virtual table feature, resolve the python method each time (default)\n\
-     -nodoxygen      - Don't convert C++ doxygen comments to pydoc comments in proxy classes \n\
      -noexcept       - No automatic exception handling\n\
      -noextranative  - Don't use extra native C++ wraps for std containers when possible (default) \n\
      -nofastinit     - Use traditional init mechanism for classes \n\
@@ -431,10 +430,6 @@ public:
 	  doxygen = 1;
 	  scan_doxygen_comments = 1;
 	  Swig_mark_arg(i);
-	} else if (strcmp(argv[i], "-nodoxygen") == 0) {
-	  doxygen = 0;
-	  scan_doxygen_comments = 0;
-	  Swig_mark_arg(i);
   } else if (strcmp(argv[i], "-debug-doxygen-translator") == 0) {
     debug_doxygen_translator = true;
     Swig_mark_arg(i);

From a9cdb000bac276c5750fa785a8e230a757dd4d8a Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Thu, 16 Aug 2012 11:35:02 +0000
Subject: [PATCH 132/314] Made swig strip out all structural comments

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13622 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Source/CParse/parser.y | 19 +++++++++----------
 1 file changed, 9 insertions(+), 10 deletions(-)

diff --git a/Source/CParse/parser.y b/Source/CParse/parser.y
index ddcdc5477..24c1842c0 100644
--- a/Source/CParse/parser.y
+++ b/Source/CParse/parser.y
@@ -3469,19 +3469,18 @@ doxygen_comment_item : DOXYGENSTRING {
 		  DohReplace($1, "//!", "", 0);
 		  DohReplace($1, "*/", "", 0);
 
-		  /* isStructuralDoxygen() is disabled, since no comment
-		    appears in such case. Need to fix. (most commands are
-		    not translatable to javadoc anyway) */
-		  if(0  &&  isStructuralDoxygen($1)){
-		    $$ = new_node("doxycomm");
-		    set_comment($$, $1);
-		  }
-		  else {
-		    $$ = $1;
+		  /* Throw out all structural comments */
+		  if (isStructuralDoxygen($1)) {
+		    Delete($1);
+		    $1 = 0;
 		  }
+		  $$ = $1;
 		}
 		| doxygen_comment_item doxygen_comment_item {
-		  Append($1, $2);
+		  if ($1)
+		    Append($1, $2);
+		  else
+		    $1 = $2;
 		  $$ = $1;
 		}
 		;

From 40ce1b412ad7d038e9e114ad94049ffe5faad7aa Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Thu, 16 Aug 2012 14:16:59 +0000
Subject: [PATCH 133/314] Now commands with no whitespace following them are
 also parsed

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13632 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Source/DoxygenTranslator/src/TokenList.cpp | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/Source/DoxygenTranslator/src/TokenList.cpp b/Source/DoxygenTranslator/src/TokenList.cpp
index 037518263..ceea0ba17 100644
--- a/Source/DoxygenTranslator/src/TokenList.cpp
+++ b/Source/DoxygenTranslator/src/TokenList.cpp
@@ -46,6 +46,14 @@ TokenList TokenList::tokenizeDoxygenComment(const std::string &doxygenComment, c
         currentWord += doxygenComment[pos];
         pos++;
       }
+      // also strip the command till the first nonalpha char
+      for (int i=2; i<currentWord.size(); i++)
+        if (!isalpha(currentWord[i])) {
+          currentWord = currentWord.substr(0, i);
+          // set current parsing pos back, to parse the rest of the command
+          pos = lastPos + i - 1;
+          break;
+        }
       tokList.m_tokenList.push_back(Token(COMMAND, currentWord));
     }
     else if (currentWord.size() && (currentWord[0] == '!' || currentWord[0] == '*' || currentWord[0] == '/')) {

From 316be573f8bc8f75a9a7d80b015a72d1d43cffe3 Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Thu, 16 Aug 2012 14:18:47 +0000
Subject: [PATCH 134/314] Fixed lots of PyDoc converter problems, see
 doxygen_tricky_constructs test

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13633 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 .../test-suite/doxygen_tricky_constructs.i    | 106 +++++++++++++
 .../doxygen_translate_all_tags_runme.py       | 145 +-----------------
 .../python/doxygen_translate_runme.py         |   6 +-
 .../DoxygenTranslator/src/PyDocConverter.cpp  |  62 +++++++-
 Source/DoxygenTranslator/src/PyDocConverter.h |   4 +
 5 files changed, 169 insertions(+), 154 deletions(-)
 create mode 100644 Examples/test-suite/doxygen_tricky_constructs.i

diff --git a/Examples/test-suite/doxygen_tricky_constructs.i b/Examples/test-suite/doxygen_tricky_constructs.i
new file mode 100644
index 000000000..96b1dfae3
--- /dev/null
+++ b/Examples/test-suite/doxygen_tricky_constructs.i
@@ -0,0 +1,106 @@
+# This file contains tests for situations, which do not normally
+# appear in the code, but must neverthless be handled correctly.
+
+%module doxygen_tricky_constructs
+
+%inline %{
+
+    # Bug 1: Tag '@endink' is not recognized becuse it is not
+    # followed by whitespace.
+
+    /** 
+     * Tag endlink must be recognized also when followed by nonspace charater.
+     *
+     * @link Connection::getId() @endlink<br>
+     */
+    char g_counter;
+
+
+    /** 
+     * Tag endlink must be recognized also when it is the last token
+     * in the commment.
+     *
+     * @link Connection::getId() @endlink<br>
+     * @link debugIdeTraceProfilerCoverageSample.py Python example. @endlink
+     */
+    int g_zipCode;
+
+
+    # Bug 2: Paramter 'isReportSize' is missing in comment of the overload, which
+    # has it. This bug disappears if @endlink is follwed by a space.
+    #
+    # Bug 3: Empty line before the link is missing,
+    # making the link text part of parameter description. This bug appears also
+    # when there is ordinary text in place of the link in case of overload
+    # with only 2 parameters.
+    /**
+     * Returns address of file line.
+     *
+     * @param fileName name of the file, where the source line is located
+     * @param line line number
+     * @param isGetSize if set, for every object location both address and size are returned
+     *
+     * @link Connection::getId() @endlink <br>
+     */
+    std::vector<DWORD> getAddress(const std::string &fileName, 
+                                  int line, 
+                                  bool isGetSize = false);
+
+    # Bug 4: The first comment is attached to the second in Python (wrong),
+    # but not in Java (correct).
+    /** 
+     * \defgroup icFacade isystem.connect Facade
+     *
+     * This page shows the core classes, which can be used to control
+     * all aspects of winIDEA, for example: debugging, analyzers, IO module, ...
+     */
+
+    /** 
+     * This class contains information for connection to winIDEA. Its methods 
+     * return reference to self, so we can use it like this:
+     * <pre>
+     * CConnectionConfig config = new CConnectionConfig();
+     * config.discoveryPort(5534).dllPath("C:\\myWinIDEA\\connect.dll").id("main");
+     * </pre>
+     *
+     * All parameters are optional. Set only what is required, default values are
+     * used for unspecified parameters.
+     * <p>
+     *
+     * @link advancedWinIDEALaunching.py Python example. @endlink <br>
+     */
+    class CConnectionConfig
+    {
+    };
+
+    # Bug 5: Text after '\c' has no space following in Python.
+    # There are also to many empty lines in multiline comments in Python.
+    # Whitespaces are really a problem in Python (space and newlines),
+    # I like a parameter type added to each parameter description!
+    #    """
+    #    Determines how long the isystem.connectshould wait for running 
+    #
+    #    instances to respond. Only one of lfWaitXXXflags from IConnect::ELaunchFlags 
+    #
+    #    may be specified. 
+    #
+    #    """
+
+    /**
+     * Determines how long the \c isystem.connect should wait for running 
+     * instances to respond. Only one of \c lfWaitXXX flags from IConnect::ELaunchFlags
+     * may be specified.
+     */
+    int waitTime(long waitTime);
+
+
+    # Bug 6: Text after tag \ingroup appears in Python comment (empty line in
+    # Java, which is acceptable):
+    /** \ingroup icFacade
+     *
+     * This class manages connection.
+     */
+    int getConnection();
+    
+    
+%}
diff --git a/Examples/test-suite/python/doxygen_translate_all_tags_runme.py b/Examples/test-suite/python/doxygen_translate_all_tags_runme.py
index e1d7a33b7..f71cb7e11 100644
--- a/Examples/test-suite/python/doxygen_translate_all_tags_runme.py
+++ b/Examples/test-suite/python/doxygen_translate_all_tags_runme.py
@@ -19,12 +19,6 @@ def check(got, expected):
 check(doxygen_translate_all_tags.function.__doc__, ''
 '  _Hello_'
 ''
-'  SomeLatexIndex '
-''
-'  someGroup"Some title" '
-''
-'  theAnchor'
-''
 '   -some list item '
 ''
 '  This is attention! '
@@ -44,60 +38,29 @@ check(doxygen_translate_all_tags.function.__doc__, ''
 ''
 '  codeword'
 ''
-'  someCategoryheaderFile.hheaderName'
-''
 '  \'citationword\''
 ''
-'  someClassheaderFile.hheaderName'
-''
 '  some test code '
 ''
 '  Conditional comment: SOMECONDITION'
 '  Some conditional comment '
 '  End of conditional comment.'
 ''
-'  someClass::someMethod'
-''
-'  someClass::someMethod2'
-''
-'  someClass::someMethod3'
-''
 '  Copyright:'
 '  some copyright '
 ''
 '  1970 - 2012 '
 ''
-'  someDefine'
-''
-'  someGroupSome titles '
-''
 '  Deprecated:'
 '  Now use another function '
 ''
 '  This is very large '
 '  and detailed description of some thing '
 ''
-'  /somePath/someFolder'
-''
-'  someFile.h'
-''
-'  digraph example { '
-'  node [shape=record, fontname=Helvetica, fontsize=10]; '
-''
-'  b [ label="class B" URL=" B"]; '
-'  c [ label="class C" URL=" C"]; '
-'  b -> c [ arrowhead="open", style="dashed" ]; '
-'  } '
-''
-''
-'  dotFile.dotThe caption'
-''
 '  _italicword_'
 ''
 '  emphazedWord'
 ''
-'  someEnum'
-''
 '  Example:'
 '  someFile.txt'
 '  Some details on using the example '
@@ -105,16 +68,6 @@ check(doxygen_translate_all_tags.function.__doc__, ''
 '  Throws:'
 '  SuperError'
 ''
-'  someOtherFunction'
-''
-'  file.h'
-''
-'  someFn '
-''
-'  someHeader.hHeader name'
-''
-'  htmlFile.htm'
-''
 '  This will only appear in hmtl '
 ''
 '  If: ANOTHERCONDITION {'
@@ -135,21 +88,11 @@ check(doxygen_translate_all_tags.function.__doc__, ''
 '  This is printed if not '
 '  }'
 ''
-'  Image: htmltestImage.bmpHello, world!asd=10qwe'
-''
-'  someFunction'
-''
-'  header.h'
-''
-'  header2.h'
-''
-'  someGroupanotherGroup'
+'  Image: testImage.bmp(Hello, world!)'
 ''
 '  Some text '
 '  describing invariant. '
 ''
-'  someInterfacesomeHeader.hHeader name'
-''
 '  This will only appear in LATeX '
 ''
 '  <ul> '
@@ -160,28 +103,10 @@ check(doxygen_translate_all_tags.function.__doc__, ''
 ''
 '  </ul> '
 ''
-'  example '
-''
 '  someMember Some description follows '
 ''
-'  Sometitle '
-''
 '  This will only appear in man '
 ''
-'  someThing'
-''
-'  Sender,Receiver; '
-'  Sender->Receiver [label="Command()", URL=" '
-'  Receiver::Command()"]; '
-'  Sender<-Receiver [label="Ack()", URL=" '
-'  Ack()", ID="1"]; '
-''
-'  mscFile.mscThe caption'
-''
-'  someHeader.h '
-''
-'  someNamespace'
-''
 '  Notes:'
 '  Here '
 '  is the note! '
@@ -191,37 +116,13 @@ check(doxygen_translate_all_tags.function.__doc__, ''
 ''
 '  someword'
 ''
-'  superPackage'
-''
-'  somePageThe title '
-''
 '  Title: The paragraph title '
 '  The paragraph text. '
 '  Maybe even multiline '
 ''
-'  someParagraphParagraph title '
-''
 '  Arguments:'
 '  a (int)                              -- the first param '
 ''
-'  Some description '
-''
-'  Some description '
-''
-'  someVar '
-''
-'  someProtocolheader.hHeader name'
-''
-'  someAnchor'
-''
-'  toSomething'
-''
-'  toSomethingElse'
-''
-'  someName'
-''
-'  someName'
-''
 '  Remarks:'
 '  Some remark text '
 ''
@@ -234,47 +135,20 @@ check(doxygen_translate_all_tags.function.__doc__, ''
 ''
 '  may return '
 ''
-'  someValueSome description '
-''
-''
 '  This will only appear in RTF '
 ''
 ''
 '  See also:'
 '  someOtherMethod '
 ''
-'  someSectionSome title '
-''
 '  function '
 ''
 '  Same as '
 '  brief description '
 ''
-''
-''
 '  Since:'
 '  version 0.0.0.1 '
 ''
-'  somePattern '
-''
-'  someLine '
-''
-'  example.hSome snippet '
-''
-'  someStruct'
-''
-'  someSubpageSome description'
-''
-'  someSubsectionSome title '
-''
-'  someSubsectionSome title '
-''
-''
-''
-'  Some '
-'  description of the '
-'  test case '
-''
 '  Throws:'
 '  superException'
 ''
@@ -286,34 +160,17 @@ check(doxygen_translate_all_tags.function.__doc__, ''
 '  Arguments:'
 '  b (float)                              -- B is mentioned again... '
 ''
-'  someTypedef '
-''
-'  someUnion'
-''
-'  somePattern '
-''
-'  someVar '
-''
-''
 '  very long '
 '  text with tags <sometag> '
 ''
-''
-'  someFile.h'
-''
 '  Version:'
 '  0.0.0.2 '
 ''
 '  Warning:'
 '  This is senseless! '
 ''
-'  someGroupSome title '
-''
-''
 '  This will only appear in XML '
 ''
-'  todo"Todo"Todo List'
-''
 '  Here goes test of symbols: '
 '  $@\&~<>#%".::'
 ''
diff --git a/Examples/test-suite/python/doxygen_translate_runme.py b/Examples/test-suite/python/doxygen_translate_runme.py
index 61e5f5398..e7d819199 100644
--- a/Examples/test-suite/python/doxygen_translate_runme.py
+++ b/Examples/test-suite/python/doxygen_translate_runme.py
@@ -71,7 +71,7 @@ check(doxygen_translate.function.__doc__, ''
 '  This is printed if not '
 '  }'
 ''
-'  Image: htmltestImage.bmpHello, world!asd=10qwe'
+'  Image: testImage.bmp(Hello, world!)'
 ''
 '  <ul> '
 ''
@@ -92,7 +92,7 @@ check(doxygen_translate.function.__doc__, ''
 ''
 '  someword'
 ''
-'  superPackage'
+''
 ''
 '  Title: The paragraph title '
 '  The paragraph text. '
@@ -145,4 +145,4 @@ check(doxygen_translate.function.__doc__, ''
 '  $@\&~<>#%".::'
 ''
 '  And here goes simple text '
-)
\ No newline at end of file
+)
diff --git a/Source/DoxygenTranslator/src/PyDocConverter.cpp b/Source/DoxygenTranslator/src/PyDocConverter.cpp
index 1826bcab5..d7b1f937f 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/PyDocConverter.cpp
@@ -68,6 +68,46 @@ void PyDocConverter::fillStaticTables() {
   tagHandlers["\""] = make_pair(&PyDocConverter::handleTagChar, "");
   tagHandlers["."] = make_pair(&PyDocConverter::handleTagChar, "");
   tagHandlers["::"] = make_pair(&PyDocConverter::handleTagChar, "");
+  // these commands are stripped out, and only their content is printed
+  tagHandlers["attention"] = make_pair(&PyDocConverter::handleParagraph, "");
+  tagHandlers["author"] = make_pair(&PyDocConverter::handleParagraph, "");
+  tagHandlers["authors"] = make_pair(&PyDocConverter::handleParagraph, "");
+  tagHandlers["brief"] = make_pair(&PyDocConverter::handleParagraph, "");
+  tagHandlers["bug"] = make_pair(&PyDocConverter::handleParagraph, "");
+  tagHandlers["c"] = make_pair(&PyDocConverter::handleParagraph, " ");
+  tagHandlers["code"] = make_pair(&PyDocConverter::handleParagraph, "");
+  tagHandlers["copyright"] = make_pair(&PyDocConverter::handleParagraph, "");
+  tagHandlers["date"] = make_pair(&PyDocConverter::handleParagraph, "");
+  tagHandlers["deprecated"] = make_pair(&PyDocConverter::handleParagraph, "");
+  tagHandlers["details"] = make_pair(&PyDocConverter::handleParagraph, "");
+  tagHandlers["em"] = make_pair(&PyDocConverter::handleParagraph, " ");
+  tagHandlers["example"] = make_pair(&PyDocConverter::handleParagraph, "");
+  tagHandlers["exception"] = make_pair(&PyDocConverter::handleParagraph, "");
+  tagHandlers["htmlonly"] = make_pair(&PyDocConverter::handleParagraph, "");
+  tagHandlers["invariant"] = make_pair(&PyDocConverter::handleParagraph, "");
+  tagHandlers["latexonly"] = make_pair(&PyDocConverter::handleParagraph, "");
+  tagHandlers["link"] = make_pair(&PyDocConverter::handleParagraph, "");
+  tagHandlers["manonly"] = make_pair(&PyDocConverter::handleParagraph, "");
+  tagHandlers["note"] = make_pair(&PyDocConverter::handleParagraph, "");
+  tagHandlers["p"] = make_pair(&PyDocConverter::handleParagraph, "");
+  tagHandlers["partofdescription"] = make_pair(&PyDocConverter::handleParagraph, " ");
+  tagHandlers["rtfonly"] = make_pair(&PyDocConverter::handleParagraph, "");
+  tagHandlers["return"] = make_pair(&PyDocConverter::handleParagraph, "");
+  tagHandlers["returns"] = make_pair(&PyDocConverter::handleParagraph, "");
+  tagHandlers["result"] = make_pair(&PyDocConverter::handleParagraph, "");
+  tagHandlers["remark"] = make_pair(&PyDocConverter::handleParagraph, "");
+  tagHandlers["remarks"] = make_pair(&PyDocConverter::handleParagraph, "");
+  tagHandlers["sa"] = make_pair(&PyDocConverter::handleParagraph, "");
+  tagHandlers["see"] = make_pair(&PyDocConverter::handleParagraph, "");
+  tagHandlers["since"] = make_pair(&PyDocConverter::handleParagraph, "");
+  tagHandlers["short"] = make_pair(&PyDocConverter::handleParagraph, "");
+  tagHandlers["throw"] = make_pair(&PyDocConverter::handleParagraph, "");
+  tagHandlers["throws"] = make_pair(&PyDocConverter::handleParagraph, "");
+  tagHandlers["todo"] = make_pair(&PyDocConverter::handleParagraph, "");
+  tagHandlers["version"] = make_pair(&PyDocConverter::handleParagraph, "");
+  tagHandlers["verbatim"] = make_pair(&PyDocConverter::handleParagraph, "");
+  tagHandlers["warning"] = make_pair(&PyDocConverter::handleParagraph, "");
+  tagHandlers["xmlonly"] = make_pair(&PyDocConverter::handleParagraph, "");
   // these commands have special handlers
   tagHandlers["arg"] = make_pair(&PyDocConverter::handleTagMessage, " -");
   tagHandlers["cond"] = make_pair(&PyDocConverter::handleTagMessage, "Conditional comment: ");
@@ -76,7 +116,7 @@ void PyDocConverter::fillStaticTables() {
   tagHandlers["endcond"] = make_pair(&PyDocConverter::handleTagMessage, "End of conditional comment.");
   tagHandlers["if"] = make_pair(&PyDocConverter::handleTagIf, "If: ");
   tagHandlers["ifnot"] = make_pair(&PyDocConverter::handleTagIf, "If not: ");
-  tagHandlers["image"] = make_pair(&PyDocConverter::handleTagMessage, "Image: ");
+  tagHandlers["image"] = make_pair(&PyDocConverter::handleTagImage, "");
   tagHandlers["li"] = make_pair(&PyDocConverter::handleTagMessage, " -");
   tagHandlers["overload"] = make_pair(&PyDocConverter::handleTagMessage, "This is an overloaded member function, provided for"
       " convenience.\nIt differs from the above function only in what"
@@ -165,17 +205,14 @@ std::string PyDocConverter::translateSubtree(DoxygenEntity & doxygenEntity) {
 
 void PyDocConverter::translateEntity(DoxygenEntity & doxyEntity, std::string &translatedComment) {
   // check if we have needed handler and call it
-  std::string dummy;
   std::map<std::string, std::pair<tagHandler, std::string > >::iterator it;
   it = tagHandlers.find(doxyEntity.typeOfEntity);
   if (it!=tagHandlers.end())
     (this->*(it->second.first))(doxyEntity, translatedComment, it->second.second);
-  else
-    handleParagraph(doxyEntity, translatedComment, dummy);
 }
 
-void PyDocConverter::handleParagraph(DoxygenEntity& tag, std::string& translatedComment, std::string&) {
-  translatedComment += justifyString(translateSubtree(tag), 0);
+void PyDocConverter::handleParagraph(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
+  translatedComment += translateSubtree(tag) + arg;
 }
 void PyDocConverter::handlePlainString(DoxygenEntity& tag, std::string& translatedComment, std::string&) {
   translatedComment += tag.data;
@@ -207,6 +244,17 @@ void PyDocConverter::handleTagPar(DoxygenEntity& tag, std::string& translatedCom
   tag.entityList.pop_front();
   handleParagraph(tag, translatedComment, dummy);
 }
+void PyDocConverter::handleTagImage(DoxygenEntity& tag, std::string& translatedComment, std::string&) {
+  std::string dummy = " ";
+  if (tag.entityList.size() < 2)
+    return;
+  tag.entityList.pop_front();
+  translatedComment += "Image: ";
+  translatedComment += tag.entityList.begin()->data;
+  tag.entityList.pop_front();
+  if (tag.entityList.size())
+    translatedComment += "(" + tag.entityList.begin()->data + ")";
+}
 void PyDocConverter::handleTagParam(DoxygenEntity& tag, std::string& translatedComment, std::string&) {
   std::string dummy;
   if (tag.entityList.size() < 2) {
@@ -231,7 +279,7 @@ void PyDocConverter::handleTagWrap(DoxygenEntity& tag, std::string& translatedCo
     std::string tagData = translateSubtree(tag);
     // wrap the thing, ignoring whitespaces
     size_t wsPos = tagData.find_last_not_of("\n\t ");
-    if (wsPos != std::string::npos)
+    if (wsPos != std::string::npos && wsPos != tagData.size() - 1)
       translatedComment += arg + tagData.substr(0, wsPos + 1) + arg + tagData.substr(wsPos + 1);
     else
       translatedComment += arg + tagData + arg + " ";
diff --git a/Source/DoxygenTranslator/src/PyDocConverter.h b/Source/DoxygenTranslator/src/PyDocConverter.h
index 9787891c8..6094b4100 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.h
+++ b/Source/DoxygenTranslator/src/PyDocConverter.h
@@ -90,6 +90,10 @@ protected:
    * Insert 'Title: ...'
    */
   void handleTagPar(DoxygenEntity &tag, std::string &translatedComment, std::string &arg);
+  /*
+   * Insert 'Image: ...'
+   */
+  void handleTagImage(DoxygenEntity &tag, std::string &translatedComment, std::string &arg);
   /*
    * Format nice param description with type information
    */

From 393ffd09da03bf065a511c4d26abebd95ac67203 Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Thu, 16 Aug 2012 14:19:26 +0000
Subject: [PATCH 135/314] Fixed structural command list

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13634 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Source/CParse/parser.y | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Source/CParse/parser.y b/Source/CParse/parser.y
index 24c1842c0..57669cb8a 100644
--- a/Source/CParse/parser.y
+++ b/Source/CParse/parser.y
@@ -79,7 +79,7 @@ int isStructuralDoxygen(String *s){
 	      || strncmp(slashPointer, "category", 8) == 0 || strncmp(slashPointer, "class", 5) == 0 || strncmp(slashPointer, "def", 3) == 0
 	      || strncmp(slashPointer, "defgroup", 8) == 0 || strncmp(slashPointer, "dir", 3) == 0 || strncmp(slashPointer, "enum", 4) == 0
 	      || strncmp(slashPointer, "example", 7) == 0 || strncmp(slashPointer, "file", 4) == 0 || strncmp(slashPointer, "fn", 2) == 0
-	      || strncmp(slashPointer, "headerfile", 9) == 0 || strncmp(slashPointer, "hideinitializer", 12) == 0 || strncmp(slashPointer, "ingroup", 7) == 0
+	      || strncmp(slashPointer, "headerfile", 9) == 0 || strncmp(slashPointer, "hideinitializer", 12) == 0
 	      || strncmp(slashPointer, "interface", 9) == 0 || strncmp(slashPointer, "internal", 8) == 0 || strncmp(slashPointer, "mainpage", 8) == 0
 	      || strncmp(slashPointer, "name", 4) == 0 || strncmp(slashPointer, "namespace", 9) == 0 || strncmp(slashPointer, "nosubgrouping", 13) == 0
 	      || strncmp(slashPointer, "overload", 8) == 0 || strncmp(slashPointer, "package", 7) == 0 || strncmp(slashPointer, "page", 4) == 0

From 3ca3848464e5b34558046d3e4ad9a3f33a3ca5fa Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Thu, 16 Aug 2012 15:10:07 +0000
Subject: [PATCH 136/314] Implemented missing runtime tests

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13635 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Examples/test-suite/common.mk                 |   1 +
 .../test-suite/doxygen_tricky_constructs.i    |  64 ++++++-----
 .../java/doxygen_basic_notranslate_runme.java | 100 +++++++++++++++++
 .../java/doxygen_tricky_constructs_runme.java | 105 ++++++++++++++++++
 .../python/doxygen_tricky_constructs_runme.py |  54 +++++++++
 5 files changed, 295 insertions(+), 29 deletions(-)
 create mode 100644 Examples/test-suite/java/doxygen_basic_notranslate_runme.java
 create mode 100644 Examples/test-suite/java/doxygen_tricky_constructs_runme.java
 create mode 100644 Examples/test-suite/python/doxygen_tricky_constructs_runme.py

diff --git a/Examples/test-suite/common.mk b/Examples/test-suite/common.mk
index e7f757f0e..729d04d66 100644
--- a/Examples/test-suite/common.mk
+++ b/Examples/test-suite/common.mk
@@ -193,6 +193,7 @@ CPP_TEST_CASES += \
 	doxygen_translate \
 	doxygen_translate_all_tags \
 	doxygen_translate_links \
+	doxygen_tricky_constructs \
 	dynamic_cast \
 	empty \
 	enum_rename \
diff --git a/Examples/test-suite/doxygen_tricky_constructs.i b/Examples/test-suite/doxygen_tricky_constructs.i
index 96b1dfae3..44cbb0426 100644
--- a/Examples/test-suite/doxygen_tricky_constructs.i
+++ b/Examples/test-suite/doxygen_tricky_constructs.i
@@ -5,8 +5,8 @@
 
 %inline %{
 
-    # Bug 1: Tag '@endink' is not recognized becuse it is not
-    # followed by whitespace.
+    // Bug 1: Tag '@endink' is not recognized becuse it is not
+    // followed by whitespace.
 
     /** 
      * Tag endlink must be recognized also when followed by nonspace charater.
@@ -26,13 +26,13 @@
     int g_zipCode;
 
 
-    # Bug 2: Paramter 'isReportSize' is missing in comment of the overload, which
-    # has it. This bug disappears if @endlink is follwed by a space.
-    #
-    # Bug 3: Empty line before the link is missing,
-    # making the link text part of parameter description. This bug appears also
-    # when there is ordinary text in place of the link in case of overload
-    # with only 2 parameters.
+    // Bug 2: Paramter 'isReportSize' is missing in comment of the overload, which
+    // has it. This bug disappears if @endlink is follwed by a space.
+    //
+    // Bug 3: Empty line before the link is missing,
+    // making the link text part of parameter description. This bug appears also
+    // when there is ordinary text in place of the link in case of overload
+    // with only 2 parameters.
     /**
      * Returns address of file line.
      *
@@ -42,12 +42,14 @@
      *
      * @link Connection::getId() @endlink <br>
      */
-    std::vector<DWORD> getAddress(const std::string &fileName, 
+    void getAddress(int &fileName, 
                                   int line, 
-                                  bool isGetSize = false);
+                                  bool isGetSize = false)
+    {
+    }
 
-    # Bug 4: The first comment is attached to the second in Python (wrong),
-    # but not in Java (correct).
+    // Bug 4: The first comment is attached to the second in Python (wrong),
+    // but not in Java (correct).
     /** 
      * \defgroup icFacade isystem.connect Facade
      *
@@ -73,34 +75,38 @@
     {
     };
 
-    # Bug 5: Text after '\c' has no space following in Python.
-    # There are also to many empty lines in multiline comments in Python.
-    # Whitespaces are really a problem in Python (space and newlines),
-    # I like a parameter type added to each parameter description!
-    #    """
-    #    Determines how long the isystem.connectshould wait for running 
-    #
-    #    instances to respond. Only one of lfWaitXXXflags from IConnect::ELaunchFlags 
-    #
-    #    may be specified. 
-    #
-    #    """
+    // Bug 5: Text after '\c' has no space following in Python.
+    // There are also to many empty lines in multiline comments in Python.
+    // Whitespaces are really a problem in Python (space and newlines),
+    // I like a parameter type added to each parameter description!
+    //    """
+    //    Determines how long the isystem.connectshould wait for running 
+    //
+    //    instances to respond. Only one of lfWaitXXXflags from IConnect::ELaunchFlags 
+    //
+    //    may be specified. 
+    //
+    //    """
 
     /**
      * Determines how long the \c isystem.connect should wait for running 
      * instances to respond. Only one of \c lfWaitXXX flags from IConnect::ELaunchFlags
      * may be specified.
      */
-    int waitTime(long waitTime);
+    int waitTime(long waitTime)
+    {
+    }
 
 
-    # Bug 6: Text after tag \ingroup appears in Python comment (empty line in
-    # Java, which is acceptable):
+    // Bug 6: Text after tag \ingroup appears in Python comment (empty line in
+    // Java, which is acceptable):
     /** \ingroup icFacade
      *
      * This class manages connection.
      */
-    int getConnection();
+    int getConnection()
+    {
+    }
     
     
 %}
diff --git a/Examples/test-suite/java/doxygen_basic_notranslate_runme.java b/Examples/test-suite/java/doxygen_basic_notranslate_runme.java
new file mode 100644
index 000000000..711cfbb88
--- /dev/null
+++ b/Examples/test-suite/java/doxygen_basic_notranslate_runme.java
@@ -0,0 +1,100 @@
+
+import doxygen_basic_notranslate.*;
+import com.sun.javadoc.*;
+import java.util.HashMap;
+
+public class doxygen_basic_notranslate_runme {
+  static {
+    try {
+      System.loadLibrary("doxygen_basic_notranslate");
+    } catch (UnsatisfiedLinkError e) {
+      System.err.println("Native code library failed to load. See the chapter on Dynamic Linking Problems in the SWIG Java documentation for help.\n" + e);
+      System.exit(1);
+    }
+  }
+  
+  public static void main(String argv[]) 
+  {
+    /*
+      Here we are using internal javadoc tool, it accepts the name of the class as paramterer,
+      and calls the start() method of that class with parsed information.
+    */
+	commentParser parser = new commentParser();
+    com.sun.tools.javadoc.Main.execute("doxygen_basic_notranslate runtime test",
+	"commentParser", new String[]{"-quiet", "doxygen_basic_notranslate"});
+
+    HashMap<String, String> wantedComments = new HashMap<String, String>();
+    wantedComments.put("doxygen_basic_notranslate.doxygen_basic_notranslate.function3(int)",
+    		" \n" +
+    		"  A test for overloaded functions\n" +
+    		"  This is function \\b one\n" +
+    		"  \n" +
+    		"");
+    wantedComments.put("doxygen_basic_notranslate.doxygen_basic_notranslate.function4()",
+    		" \n" +
+    		"  A test of some mixed tag usage\n" +
+    		"  \\if CONDITION\n" +
+    		"  This \\a code fragment shows us something \\.\n" +
+    		"  \\par Minuses:\n" +
+    		"  \\arg it's senseless\n" +
+    		"  \\arg it's stupid\n" +
+    		"  \\arg it's null\n" +
+    		" \n" +
+    		"  \\warning This may not work as expected\n" +
+    		" \n" +
+    		"  \\code\n" +
+    		"  int main() { while(true); }\n" +
+    		"  \\endcode\n" +
+    		"  \\endif\n" +
+    		"  \n" +
+    		"");
+    wantedComments.put("doxygen_basic_notranslate.doxygen_basic_notranslate.function()",
+    		" \n" +
+    		"  \\brief\n" +
+    		"  Brief description.\n" +
+    		"  \n" +
+    		"  The comment text\n" +
+    		"  \\author Some author\n" +
+    		"  \\return Some number\n" +
+    		"  \\sa function2\n" +
+    		"  \n" +
+    		"");
+    wantedComments.put("doxygen_basic_notranslate.doxygen_basic_notranslate.function5(int)",
+    		"  This is a post comment. \n" +
+    		"");
+    wantedComments.put("doxygen_basic_notranslate.doxygen_basic_notranslate.function7(doxygen_basic_notranslate.SWIGTYPE_p_p_p_Shape)",
+    		" \n" +
+    		"  Test for a parameter with difficult type\n" +
+    		"  (mostly for python)\n" +
+    		"  @param a Very strange param\n" +
+    		"  \n" +
+    		"");
+    wantedComments.put("doxygen_basic_notranslate.doxygen_basic_notranslate.function3(int, int)",
+    		" \n" +
+    		"  A test for overloaded functions\n" +
+    		"  This is function \\b two\n" +
+    		"  \n" +
+    		"");
+    wantedComments.put("doxygen_basic_notranslate.doxygen_basic_notranslate.function6(int)",
+    		" \n" +
+    		"  Test for default args\n" +
+    		"  @param a Some parameter, default is 42\n" +
+    		"  \n" +
+    		"");
+    wantedComments.put("doxygen_basic_notranslate.doxygen_basic_notranslate.function6()",
+    		" \n" +
+    		"  Test for default args\n" +
+    		"  @param a Some parameter, default is 42\n" +
+    		"  \n" +
+    		"");
+    wantedComments.put("doxygen_basic_notranslate.doxygen_basic_notranslate.function2()",
+    		" \n" +
+    		"  A test of a very very very very very very very very very very very very very very very very\n" +
+    		"  very very very very very long comment string.\n" +
+    		"  \n" +
+    		"");
+    
+    // and ask the parser to check comments for us
+    System.exit(parser.check(wantedComments));
+  }
+}
\ No newline at end of file
diff --git a/Examples/test-suite/java/doxygen_tricky_constructs_runme.java b/Examples/test-suite/java/doxygen_tricky_constructs_runme.java
new file mode 100644
index 000000000..bb4f69839
--- /dev/null
+++ b/Examples/test-suite/java/doxygen_tricky_constructs_runme.java
@@ -0,0 +1,105 @@
+
+import doxygen_tricky_constructs.*;
+import com.sun.javadoc.*;
+import java.util.HashMap;
+
+public class doxygen_tricky_constructs_runme {
+  static {
+    try {
+      System.loadLibrary("doxygen_tricky_constructs");
+    } catch (UnsatisfiedLinkError e) {
+      System.err.println("Native code library failed to load. See the chapter on Dynamic Linking Problems in the SWIG Java documentation for help.\n" + e);
+      System.exit(1);
+    }
+  }
+  
+  public static void main(String argv[]) 
+  {
+    /*
+      Here we are using internal javadoc tool, it accepts the name of the class as paramterer,
+      and calls the start() method of that class with parsed information.
+    */
+	commentParser parser = new commentParser();
+    com.sun.tools.javadoc.Main.execute("doxygen_tricky_constructs runtime test",
+	"commentParser", new String[]{"-quiet", "doxygen_tricky_constructs"});
+
+    HashMap<String, String> wantedComments = new HashMap<String, String>();
+    
+    wantedComments.put("doxygen_tricky_constructs.doxygen_tricky_constructs.getConnection()",
+    		" \n" +
+    		" \n" +
+    		" This class manages connection. \n" +
+    		" \n" +
+    		"");
+    wantedComments.put("doxygen_tricky_constructs.doxygen_tricky_constructs.getAddress(doxygen_tricky_constructs.SWIGTYPE_p_int, int)",
+    		" Returns address of file line. \n" +
+    		" \n" +
+    		" @param fileName name of the file, where the source line is located \n" +
+    		" @param line line number \n" +
+    		" {@link Connection::getId()  }<br> \n" +
+    		" \n" +
+    		"");
+    wantedComments.put("doxygen_tricky_constructs.doxygen_tricky_constructs.getG_zipCode()",
+    		" Tag endlink must be recognized also when it is the last token \n" +
+    		" in the commment. \n" +
+    		" \n" +
+    		" {@link Connection::getId()  }<br> \n" +
+    		" {@link debugIdeTraceProfilerCoverageSample.py Python example.  }\n" +
+    		" \n" +
+    		"");
+    wantedComments.put("doxygen_tricky_constructs.doxygen_tricky_constructs.setG_zipCode(int)",
+    		" Tag endlink must be recognized also when it is the last token \n" +
+    		" in the commment. \n" +
+    		" \n" +
+    		" {@link Connection::getId()  }<br> \n" +
+    		" {@link debugIdeTraceProfilerCoverageSample.py Python example.  }\n" +
+    		" \n" +
+    		"");
+    wantedComments.put("doxygen_tricky_constructs.doxygen_tricky_constructs.getG_counter()",
+    		" Tag endlink must be recognized also when followed by nonspace charater. \n" +
+    		" \n" +
+    		" {@link Connection::getId()  }<br> \n" +
+    		" \n" +
+    		"");
+    wantedComments.put("doxygen_tricky_constructs.doxygen_tricky_constructs.waitTime(int)",
+    		" Determines how long the <code>isystem.connect</code> should wait for running \n" +
+    		" instances to respond. Only one of <code>lfWaitXXX</code> flags from IConnect::ELaunchFlags \n" +
+    		" may be specified. \n" +
+    		" \n" +
+    		"");
+    wantedComments.put("doxygen_tricky_constructs.CConnectionConfig",
+    		" This class contains information for connection to winIDEA. Its methods \n" +
+    		" return reference to self, so we can use it like this: \n" +
+    		" <pre> \n" +
+    		" CConnectionConfig config = new CConnectionConfig(); \n" +
+    		" config.discoveryPort(5534).dllPath(\"C: \\ yWinIDEA \\ onnect.dll\").id(\"main\"); \n" +
+    		" </pre> \n" +
+    		" \n" +
+    		" All parameters are optional. Set only what is required, default values are \n" +
+    		" used for unspecified parameters. \n" +
+    		" <p> \n" +
+    		" \n" +
+    		" {@link advancedWinIDEALaunching.py Python example.  }<br> \n" +
+    		" \n" +
+    		"");
+    wantedComments.put("doxygen_tricky_constructs.doxygen_tricky_constructs.getAddress(doxygen_tricky_constructs.SWIGTYPE_p_int, int, boolean)",
+    		" Returns address of file line. \n" +
+    		" \n" +
+    		" @param fileName name of the file, where the source line is located \n" +
+    		" @param line line number \n" +
+    		" @param isGetSize if set, for every object location both address and size are returned \n" +
+    		" \n" +
+    		" {@link Connection::getId()  }<br> \n" +
+    		" \n" +
+    		"");
+    wantedComments.put("doxygen_tricky_constructs.doxygen_tricky_constructs.setG_counter(char)",
+    		" Tag endlink must be recognized also when followed by nonspace charater. \n" +
+    		" \n" +
+    		" {@link Connection::getId()  }<br> \n" +
+    		" \n" +
+    		"");
+    
+    // and ask the parser to check comments for us
+    System.exit(parser.check(wantedComments));
+  }
+}
\ No newline at end of file
diff --git a/Examples/test-suite/python/doxygen_tricky_constructs_runme.py b/Examples/test-suite/python/doxygen_tricky_constructs_runme.py
new file mode 100644
index 000000000..156a279b7
--- /dev/null
+++ b/Examples/test-suite/python/doxygen_tricky_constructs_runme.py
@@ -0,0 +1,54 @@
+#!/usr/bin/python
+
+import doxygen_tricky_constructs
+import string
+import sys
+
+def check(got, expected):
+  #if got is Null
+  #  raise RuntimeError('Expected comment string\n')
+  gotStr = string.replace(got, ' ', '')
+  gotStr = string.replace(gotStr, '\n', '')
+  gotStr = string.replace(gotStr, '\t', '')
+  expectedStr = string.replace(expected, ' ', '')
+  expectedStr = string.replace(expectedStr, '\n', '')
+  expectedStr = string.replace(expectedStr, '\t', '')
+  if not gotStr == expectedStr:
+    raise RuntimeError("Expected: [" + str(expected) + "]\n" + "Got     : [" + str(got) + "]\n")
+
+check(doxygen_tricky_constructs.getAddress.__doc__, ''
+'Returns address of file line.'
+''
+'   Arguments:'
+'  fileName (int &)                              -- name of the file, where the source'
+'                                line is located'
+'  line (int)                              -- line number'
+'  isGetSize (bool)                              -- if set, for every object location'
+'                                both address and size are returned'
+''
+''
+'  Connection::getId() <br>'
+)
+check(doxygen_tricky_constructs.CConnectionConfig.__doc__, ''
+'    This class contains information for connection to winIDEA. Its methods'
+'    return reference to self, so we can use it like this:'
+'    <pre>'
+'    CConnectionConfig config = new CConnectionConfig();'
+'    config.discoveryPort(5534).dllPath("C: \yWinIDEA \onnect.dll").id("main");'
+'    </pre>'
+''
+'     All parameters are optional. Set only what is required, default values are'
+'    used for unspecified parameters.'
+'    <p>'
+''
+'     advancedWinIDEALaunching.py Python example. <br>'
+''
+)
+check(doxygen_tricky_constructs.waitTime.__doc__, ''
+'  Determines how long the isystem.connect should wait for running'
+'  instances to respond. Only one of lfWaitXXX flags from IConnect::ELaunchFlags'
+'  may be specified.'
+)
+check(doxygen_tricky_constructs.getConnection.__doc__, ''
+'This class manages connection.'
+)
\ No newline at end of file

From 1eb664cad280579e97e1fef1ca8708482d234200 Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Thu, 16 Aug 2012 15:13:35 +0000
Subject: [PATCH 137/314] Updated docs

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13636 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Doc/Devel/plan-gsoc-2012.txt | 4 +++-
 Doc/Manual/Doxygen.html      | 1 +
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/Doc/Devel/plan-gsoc-2012.txt b/Doc/Devel/plan-gsoc-2012.txt
index 7e8ecf541..51d387d3c 100644
--- a/Doc/Devel/plan-gsoc-2012.txt
+++ b/Doc/Devel/plan-gsoc-2012.txt
@@ -153,7 +153,8 @@ Functionality
     \htmlonly - ignored
     \if - see note for \cond 
     \ifnot - see note for \cond
-    \image - translated to <img/> in JD only when target=HTML, ignored in PD
+    \image - translated to <img/> in JD only when target=HTML, translated to
+             'Image: filename(Title)'
     \implements - not supported
     \include - not supported
     \includelineno - not supported
@@ -314,6 +315,7 @@ make doxygen_translate_all_tags.cpptest -s
 make doxygen_basic_translate.cpptest -s
 make doxygen_basic_notranslate.cpptest -s
 make doxygen_translate_links.cpptest -s
+make doxygen_tricky_constructs.cpptest -s
 
   
 Refactoring
diff --git a/Doc/Manual/Doxygen.html b/Doc/Manual/Doxygen.html
index cb79ef83c..d21c12d7e 100644
--- a/Doc/Manual/Doxygen.html
+++ b/Doc/Manual/Doxygen.html
@@ -1309,6 +1309,7 @@ This part of SWIG currently has 6 runtime tests in both Java and Python.
   doxygen_basic_translate
   doxygen_basic_notranslate
   doxygen_translate_links
+  doxygen_tricky_constructs
 </pre></div>
 
 <p>

From 0d3578572411e6861e0a5b5ab615a2e7224dc9e1 Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Fri, 17 Aug 2012 23:47:56 +0000
Subject: [PATCH 138/314] Small cosmetic changes to generated comments

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13647 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Source/DoxygenTranslator/src/PyDocConverter.cpp | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/Source/DoxygenTranslator/src/PyDocConverter.cpp b/Source/DoxygenTranslator/src/PyDocConverter.cpp
index d7b1f937f..39ae43c69 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/PyDocConverter.cpp
@@ -90,7 +90,7 @@ void PyDocConverter::fillStaticTables() {
   tagHandlers["manonly"] = make_pair(&PyDocConverter::handleParagraph, "");
   tagHandlers["note"] = make_pair(&PyDocConverter::handleParagraph, "");
   tagHandlers["p"] = make_pair(&PyDocConverter::handleParagraph, "");
-  tagHandlers["partofdescription"] = make_pair(&PyDocConverter::handleParagraph, " ");
+  tagHandlers["partofdescription"] = make_pair(&PyDocConverter::handleParagraph, "");
   tagHandlers["rtfonly"] = make_pair(&PyDocConverter::handleParagraph, "");
   tagHandlers["return"] = make_pair(&PyDocConverter::handleParagraph, "");
   tagHandlers["returns"] = make_pair(&PyDocConverter::handleParagraph, "");
@@ -245,7 +245,6 @@ void PyDocConverter::handleTagPar(DoxygenEntity& tag, std::string& translatedCom
   handleParagraph(tag, translatedComment, dummy);
 }
 void PyDocConverter::handleTagImage(DoxygenEntity& tag, std::string& translatedComment, std::string&) {
-  std::string dummy = " ";
   if (tag.entityList.size() < 2)
     return;
   tag.entityList.pop_front();

From faf72f01bf54e58e07ba5ae0c7bcae9228d57f58 Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Sun, 19 Aug 2012 09:43:19 +0000
Subject: [PATCH 139/314] Fixed problems with new lines in JavaDoc translator

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13661 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 .../src/JavaDocConverter.cpp                  | 63 +++++++++++++++----
 .../DoxygenTranslator/src/JavaDocConverter.h  |  4 ++
 2 files changed, 54 insertions(+), 13 deletions(-)

diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.cpp b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
index fb13728ea..465119c48 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
@@ -411,6 +411,42 @@ void JavaDocConverter::handleTagSee(DoxygenEntity& tag, std::string& translatedC
   }
 }
 
+int JavaDocConverter::cleanUpTree(DoxygenEntity &root, int level)
+{
+  // this function should move all endlines out of the child entities
+  // for example:
+  // root
+  // -param
+  // --paramText
+  // --endline
+  // should be turned to
+  // root
+  // -param
+  // --paramText
+  // -endline
+
+  std::list < DoxygenEntity >::iterator it = root.entityList.begin();
+  while (it != root.entityList.end()) {
+    // remove endlines
+    int ret = cleanUpTree(*it, level + 1);
+    // insert them after this element
+    it++;
+    for (int i=0; i<ret; i++)
+      root.entityList.insert(it, DoxygenEntity("plainstd::endl"));
+  }
+
+  // continue only if we are not root
+  if (!level)
+    return 0;
+
+  int removedCount = 0;
+  while (root.entityList.rbegin()->typeOfEntity == "plainstd::endl") {
+    root.entityList.pop_back();
+    removedCount++;
+  }
+  return removedCount;
+}
+
 String *JavaDocConverter::makeDocumentation(Node *node) {
 
   String *documentation = getDoxygenComment(node);
@@ -439,22 +475,23 @@ String *JavaDocConverter::makeDocumentation(Node *node) {
     printTree(entityList);
   }
 
-  std::string javaDocString = "/**\n * ";
-
-  // strip endlines at the beginning
-  while (entityList.begin()->typeOfEntity == "plainstd::endl")
-    entityList.pop_front();
-  // and at the end
-  while (entityList.rbegin()->typeOfEntity == "plainstd::endl")
-    entityList.pop_back();
-
   // store the current node
   // (currently just to handle params)
   currentNode = node;
-  for (std::list < DoxygenEntity >::iterator entityIterator = entityList.begin(); entityIterator != entityList.end();) {
-    translateEntity(*entityIterator, javaDocString);
-    entityIterator++;
-  }
+
+  std::string javaDocString = "/**\n * ";
+
+  DoxygenEntity root("root", entityList);
+
+  cleanUpTree(root);
+  // strip endlines at the beginning
+  while (root.entityList.begin()->typeOfEntity == "plainstd::endl")
+    root.entityList.pop_front();
+  // and at the end
+  while (root.entityList.rbegin()->typeOfEntity == "plainstd::endl")
+    root.entityList.pop_back();
+
+  javaDocString += translateSubtree(root);
 
   javaDocString += "\n */\n";
 
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.h b/Source/DoxygenTranslator/src/JavaDocConverter.h
index a547a17f8..752bb9b5f 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.h
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.h
@@ -29,6 +29,10 @@ protected:
   std::string formatCommand(std::string unformattedLine, int indent);
   std::string translateSubtree(DoxygenEntity & doxygenEntity);
   void translateEntity(DoxygenEntity &tag, std::string &translatedComment);
+  /*
+   * Fix all endlines location, etc
+   */
+  int cleanUpTree(DoxygenEntity &root, int level = 0);
   
   /*
    * Convert params in link-objects and references

From 99bc7e9eb02e94ba730689d7c57106c3bbe5c6cf Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Sun, 19 Aug 2012 13:49:21 +0000
Subject: [PATCH 140/314] Added support for const qualifier and references in
 link-objects in JavaDoc link translator

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13663 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 .../src/JavaDocConverter.cpp                  | 21 +++++++++++++++----
 1 file changed, 17 insertions(+), 4 deletions(-)

diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.cpp b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
index 465119c48..204c07b61 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
@@ -339,21 +339,34 @@ string JavaDocConverter::convertLink(string linkObject) {
     // also converting arrays to pointers
     string paramStr = params[i];
     String *swigType = NewString("");
+
+    // handle const qualifier
+    if (paramStr.find("const") != string::npos)
+      SwigType_add_qualifier(swigType, "const");
+
+    // handle pointers, references and arrays
     for (int j=(int)params[i].size() - 1; j>=0; j--) {
       // skip all the [...] blocks, write 'p.' for every of it
       if (paramStr[j] == ']') {
         while (j>=0 && paramStr[j] != '[')
           j--;
         // no closing brace
-        if (!j)
+        if (j < 0)
           return "";
-        Append(swigType, "p.");
+        SwigType_add_pointer(swigType);
         continue;
       }
       else if (paramStr[j] == '*')
-        Append(swigType, "p.");
+        SwigType_add_pointer(swigType);
+      else if (paramStr[j] == '&')
+        SwigType_add_reference(swigType);
       else if (isalnum(paramStr[j])) {
-        Append(swigType, paramStr.substr(0, j + 1).c_str());
+        size_t typeNameStart = paramStr.find_last_of(' ', j + 1);
+        if (typeNameStart == string::npos)
+          typeNameStart = 0;
+        else
+          typeNameStart++;
+        Append(swigType, paramStr.substr(typeNameStart, j - typeNameStart + 1).c_str());
         break;
       }
     }

From dfad1c8156ceda43e7104688df84944a39b172c3 Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Sun, 19 Aug 2012 13:58:12 +0000
Subject: [PATCH 141/314] Fixed param description alignment in PyDoc translator

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13667 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Source/DoxygenTranslator/src/PyDocConverter.cpp | 12 ++++--------
 1 file changed, 4 insertions(+), 8 deletions(-)

diff --git a/Source/DoxygenTranslator/src/PyDocConverter.cpp b/Source/DoxygenTranslator/src/PyDocConverter.cpp
index 39ae43c69..26b4a3c92 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/PyDocConverter.cpp
@@ -256,22 +256,18 @@ void PyDocConverter::handleTagImage(DoxygenEntity& tag, std::string& translatedC
 }
 void PyDocConverter::handleTagParam(DoxygenEntity& tag, std::string& translatedComment, std::string&) {
   std::string dummy;
-  if (tag.entityList.size() < 2) {
-    // TODO: log error
+  if (tag.entityList.size() < 2)
     return;
-  }
-  DoxygenEntity paramNameEntity = *tag.entityList.begin();
-  std::string paramDescription = "-- ";
 
+  DoxygenEntity paramNameEntity = *tag.entityList.begin();
   tag.entityList.pop_front();
-  handleParagraph(tag, paramDescription, dummy);
-  paramDescription = justifyString(paramDescription, DOC_PARAM_STRING_LENGTH);
 
   std::string paramType = getParamType(paramNameEntity.data);
   if (!paramType.size())
     paramType = "none";
 
-  translatedComment += paramNameEntity.data + " (" + paramType + ")" + paramDescription;
+  translatedComment += paramNameEntity.data + " (" + paramType + ") -- ";
+  handleParagraph(tag, translatedComment, dummy);
 }
 void PyDocConverter::handleTagWrap(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
   if (tag.entityList.size()) { // do not include empty tags

From 549b2046b1d3a7e1d2948fe6700fc6b6fe5c45fe Mon Sep 17 00:00:00 2001
From: Dmitry Kabak <userdima@gmail.com>
Date: Sun, 19 Aug 2012 14:42:26 +0000
Subject: [PATCH 142/314] Fixed comments in the source code

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13668 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Source/DoxygenTranslator/src/DoxygenTranslator.h |  4 ----
 Source/DoxygenTranslator/src/JavaDocConverter.h  | 12 +++++++++++-
 Source/DoxygenTranslator/src/PyDocConverter.h    |  3 ---
 3 files changed, 11 insertions(+), 8 deletions(-)

diff --git a/Source/DoxygenTranslator/src/DoxygenTranslator.h b/Source/DoxygenTranslator/src/DoxygenTranslator.h
index 7d2e64542..1b90dbc43 100644
--- a/Source/DoxygenTranslator/src/DoxygenTranslator.h
+++ b/Source/DoxygenTranslator/src/DoxygenTranslator.h
@@ -38,8 +38,6 @@ public:
   /*
    * Return the documentation for a given node formated for the correct 
    * documentation system.
-   * @param node The node to extract and translate documentation for.
-   * @return The resulted documentation string, or empty string in case of any errors.
    */
   String *getDocumentation(Node *node);
   /*
@@ -56,8 +54,6 @@ protected:
   /*
    * Overridden in subclasses to return the documentation formatted for a given
    * documentation system.
-   * @param node The node to extract and translate documentation for.
-   * @return The resulted documentation string
    */
   virtual String *makeDocumentation(Node *node) = 0;
   
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.h b/Source/DoxygenTranslator/src/JavaDocConverter.h
index 752bb9b5f..cad228038 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.h
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.h
@@ -26,8 +26,18 @@ public:
   String *makeDocumentation(Node *node);
 
 protected:
+  /*
+   * Used to properly format JavaDoc-style command
+   */
   std::string formatCommand(std::string unformattedLine, int indent);
+  /*
+   * Translate every entity in a tree.
+   */
   std::string translateSubtree(DoxygenEntity & doxygenEntity);
+  /*
+   * Translate one entity with the appropriate handler, acording
+   * to the tagHandlers
+   */
   void translateEntity(DoxygenEntity &tag, std::string &translatedComment);
   /*
    * Fix all endlines location, etc
@@ -95,7 +105,7 @@ protected:
    */
   void handleTagPar(DoxygenEntity &tag, std::string &translatedComment, std::string &arg);
   /*
-   * Insert @param command, if it is really a function param
+   * Insert \@param command, if it is really a function param
    */
   void handleTagParam(DoxygenEntity &tag, std::string &translatedComment, std::string &arg);
   /*
diff --git a/Source/DoxygenTranslator/src/PyDocConverter.h b/Source/DoxygenTranslator/src/PyDocConverter.h
index 6094b4100..ee4d436c3 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.h
+++ b/Source/DoxygenTranslator/src/PyDocConverter.h
@@ -32,9 +32,6 @@ protected:
   /*
    * Format a string so it is justified and split over several lines 
    * not exeeding a given length.
-   * @param unformattedLine The string to justify and split.
-   * @param indent An optional number of spaces to indent each line by.
-   * @param maxWidth The approximate maximum line width.
    */
   std::string justifyString(std::string unformattedLine, int indent = 0, int maxWidth = DOC_STRING_LENGTH);
   /*

From ed6df45c0adc636659e45c6ef1bb4137c59de6be Mon Sep 17 00:00:00 2001
From: Marko Klopcic <marko.klopcic@isystem.si>
Date: Sun, 26 Aug 2012 13:00:52 +0000
Subject: [PATCH 143/314] refactored DoxygenParser: class Token is now nested
 in Doxygen parser because it is only used there, class TokenList has been
 removed - it more or less duplicated std::list, other code moved to
 DoxygenParser

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13722 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 .project                                      |  21 +
 .../DoxygenTranslator/src/DoxygenEntity.cpp   |   4 +-
 Source/DoxygenTranslator/src/DoxygenEntity.h  |   2 +-
 .../DoxygenTranslator/src/DoxygenParser.cpp   | 536 ++++++++++++------
 Source/DoxygenTranslator/src/DoxygenParser.h  | 162 ++++--
 .../DoxygenTranslator/src/DoxygenTranslator.h |   1 +
 .../src/JavaDocConverter.cpp                  |   5 +
 .../DoxygenTranslator/src/PyDocConverter.cpp  |   4 +
 8 files changed, 521 insertions(+), 214 deletions(-)

diff --git a/.project b/.project
index 86af75213..a7f89f57a 100644
--- a/.project
+++ b/.project
@@ -5,7 +5,28 @@
 	<projects>
 	</projects>
 	<buildSpec>
+		<buildCommand>
+			<name>org.eclipse.cdt.autotools.core.genmakebuilderV2</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.cdt.managedbuilder.core.genmakebuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.cdt.managedbuilder.core.ScannerConfigBuilder</name>
+			<triggers>full,incremental,</triggers>
+			<arguments>
+			</arguments>
+		</buildCommand>
 	</buildSpec>
 	<natures>
+		<nature>org.eclipse.cdt.core.cnature</nature>
+		<nature>org.eclipse.cdt.core.ccnature</nature>
+		<nature>org.eclipse.cdt.managedbuilder.core.managedBuildNature</nature>
+		<nature>org.eclipse.cdt.managedbuilder.core.ScannerConfigNature</nature>
+		<nature>org.eclipse.cdt.autotools.core.autotoolsNatureV2</nature>
 	</natures>
 </projectDescription>
diff --git a/Source/DoxygenTranslator/src/DoxygenEntity.cpp b/Source/DoxygenTranslator/src/DoxygenEntity.cpp
index dc49c803e..4039ccc99 100644
--- a/Source/DoxygenTranslator/src/DoxygenEntity.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenEntity.cpp
@@ -41,7 +41,7 @@ DoxygenEntity::DoxygenEntity(std::string typeEnt, std::list < DoxygenEntity > &e
   entityList = entList;
 }
 
-void DoxygenEntity::printEntity(int level) {
+void DoxygenEntity::printEntity(int level) const {
   int thisLevel = level;
   if (isLeaf) {
     for (int i = 0; i < thisLevel; i++) {
@@ -63,7 +63,7 @@ void DoxygenEntity::printEntity(int level) {
 
     std::cout << "Node Command : " << typeOfEntity << std::endl;
 
-    std::list < DoxygenEntity >::iterator p = entityList.begin();
+    std::list < DoxygenEntity >::const_iterator p = entityList.begin();
     thisLevel++;
 
     while (p != entityList.end()) {
diff --git a/Source/DoxygenTranslator/src/DoxygenEntity.h b/Source/DoxygenTranslator/src/DoxygenEntity.h
index 64b692ba0..9e6fda4cb 100644
--- a/Source/DoxygenTranslator/src/DoxygenEntity.h
+++ b/Source/DoxygenTranslator/src/DoxygenEntity.h
@@ -49,7 +49,7 @@ struct DoxygenEntity {
   DoxygenEntity(std::string typeEnt, std::string param1);
   DoxygenEntity(std::string typeEnt, std::list < DoxygenEntity > &entList);
 
-  void printEntity(int level);
+  void printEntity(int level) const;
 };
 
 /* 
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.cpp b/Source/DoxygenTranslator/src/DoxygenParser.cpp
index 8be8660d7..10126808d 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenParser.cpp
@@ -11,11 +11,22 @@
 
 #include "DoxygenParser.h"
 #include "DoxygenCommands.h"
+#include "swig.h"
+#include "swigwarn.h"
+
+#include <iostream>
+#include <algorithm>
+
+using std::string;
+using std::cout;
+using std::endl;
 
 // Define static class members
 std::map<std::string, DoxyCommandEnum> DoxygenParser::doxygenCommands;
 std::set<std::string> DoxygenParser::doxygenSectionIndicators;
 
+const int TOKENSPERLINE = 8;    //change this to change the printing behaviour of the token list
+
 
 DoxygenParser::DoxygenParser(bool noisy) : noisy(noisy) {
 	fillTables();
@@ -58,42 +69,48 @@ void DoxygenParser::fillTables() {
 		doxygenSectionIndicators.insert(sectionIndicators[i]);
 }
 
-std::string DoxygenParser::stringToLower(std::string &stringToConvert) {
-	for (unsigned int i = 0; i < stringToConvert.length(); i++) {
-		stringToConvert[i] = tolower(stringToConvert[i]);
+
+std::string DoxygenParser::stringToLower(const std::string &stringToConvert) {
+
+	string result(stringToConvert.size(), ' ');
+
+	for (size_t i = 0; i < result.size(); i++) {
+	    result[i] = tolower(stringToConvert[i]);
 	}
-	return stringToConvert;	//return the converted std::string
+
+	return result;
 }
 
-int DoxygenParser::findCommand(std::string smallString) {
-	std::map<std::string, DoxyCommandEnum>::iterator it;
-	smallString = stringToLower(smallString);
-	// I'm not sure if we can really do so, because there are different commands
-	// in doxygenCommands and original commandArray
-	it = doxygenCommands.find(smallString);
-	if (it != doxygenCommands.end())
-		return 1;
-	return -1;
+
+bool DoxygenParser::findCommand(const std::string &smallString) {
+    // I'm not sure if we can really do so, because there are different commands
+    // in doxygenCommands and original commandArray
+
+    std::map<std::string, DoxyCommandEnum>::iterator it =
+                    doxygenCommands.find(stringToLower(smallString));
+
+	return it != doxygenCommands.end(); // returns true if command was found
 }
 
-int DoxygenParser::isSectionIndicator(std::string smallString) {
-	smallString = stringToLower(smallString);
-	std::set<std::string>::iterator it;
-	it = doxygenSectionIndicators.find(smallString);
-	if (it != doxygenSectionIndicators.end())
-		return 1;
-	return 0;
+
+bool DoxygenParser::isSectionIndicator(const std::string &smallString) {
+
+    std::set<std::string>::iterator it =
+                    doxygenSectionIndicators.find(stringToLower(smallString));
+
+	return it != doxygenSectionIndicators.end();
 }
 
-void DoxygenParser::printTree(std::list < DoxygenEntity > &rootList) {
-	std::list < DoxygenEntity >::iterator p = rootList.begin();
+
+void DoxygenParser::printTree(const std::list <DoxygenEntity> &rootList) {
+	std::list < DoxygenEntity >::const_iterator p = rootList.begin();
 	while (p != rootList.end()) {
 		(*p).printEntity(0);
 		p++;
 	}
 }
 
-int DoxygenParser::commandBelongs(std::string theCommand) {
+int DoxygenParser::commandBelongs(const std::string &theCommand) {
 	std::string smallString = stringToLower(theCommand);
 	//cout << " Looking for command " << theCommand << endl;
 	std::map<std::string, DoxyCommandEnum>::iterator it;
@@ -103,100 +120,123 @@ int DoxygenParser::commandBelongs(std::string theCommand) {
 	return 0;
 }
 
-std::string DoxygenParser::getNextWord(TokenList & tokList) {
-	Token nextToken = tokList.peek();
-	if (nextToken.tokenType == PLAINSTRING) {
+std::string DoxygenParser::getNextWord(const TokenList &tokList) {
+	// MK Token nextToken = tokList.peek();
+    if (m_tokenListIt == m_tokenList.end()) {
+        return "";
+    }
+    Token nextToken = *m_tokenListIt;
+	if (nextToken.m_tokenType == PLAINSTRING) {
 		// handle quoted strings as words
-		if (nextToken.tokenString[0] == '"'
-				&& nextToken.tokenString[nextToken.tokenString.size() - 1] != '"') {
-			string word = nextToken.tokenString + " ";
-			nextToken = tokList.next();
+		if (nextToken.m_tokenString[0] == '"'
+				&& nextToken.m_tokenString[nextToken.m_tokenString.size() - 1] != '"') {
+
+			string word = nextToken.m_tokenString + " ";
+			nextToken = *m_tokenListIt++;
 			while (true) {
 				string nextWord = getNextWord(tokList);
-				if (!nextWord.size()) // maybe report unterminated string error
+				if (!nextWord.size()) {// maybe report unterminated string error
 					return word;
+				}
 				word += nextWord;
-				if (word[word.size() - 1] == '"') // strip quotes
+				if (word[word.size() - 1] == '"') { // strip quotes
 					return word.substr(1, word.size() - 2);
+				}
 				word += " ";
 			}
 		}
 
-		tokList.next();
-		return nextToken.tokenString;
+		m_tokenListIt++;
+		return nextToken.m_tokenString;
 	}
 	return "";
 }
 
-std::list < Token >::iterator DoxygenParser::getOneLine(TokenList & tokList) {
-	std::list < Token >::iterator endOfLine = tokList.iteratorCopy();
-	while (endOfLine != tokList.end()) {
-		if ((*endOfLine).tokenType == END_LINE) {
-			//cout << "REACHED END" << endl;
-			//endOfLine++;
-			return endOfLine;
+
+DoxygenParser::TokenListCIt DoxygenParser::getOneLine(const TokenList &tokList) {
+
+	TokenListCIt endOfLineIt = m_tokenListIt;
+
+	while (endOfLineIt != tokList.end()) {
+		if (endOfLineIt->m_tokenType == END_LINE) {
+			return endOfLineIt;
 		}
-		endOfLine++;
+		endOfLineIt++;
 	}
 
 	return tokList.end();
 }
 
-std::string DoxygenParser::getStringTilCommand(TokenList & tokList) {
-	std::string description;
-	if (tokList.peek().tokenType == 0)
+
+std::string DoxygenParser::getStringTilCommand(const TokenList & tokList) {
+
+	if (m_tokenListIt == tokList.end()) {
 		return "";
-	while (tokList.peek().tokenType == PLAINSTRING) {
-		Token currentToken = tokList.next();
-		if (currentToken.tokenType == PLAINSTRING) {
-			description = description + currentToken.tokenString + " ";
+	}
+
+    string description;
+
+    while (m_tokenListIt->m_tokenType == PLAINSTRING) {
+		const Token &currentToken = *m_tokenListIt++;
+		if (currentToken.m_tokenType == PLAINSTRING) {
+			description = description + currentToken.m_tokenString + " ";
 		}
 	}
 	return description;
 }
 
-std::string DoxygenParser::getStringTilEndCommand(std::string theCommand, TokenList & tokList) {
-	std::string description;
-	if (tokList.peek().tokenType == 0)
-		return "";
-	while (tokList.current() != tokList.end()) {
+
+std::string DoxygenParser::getStringTilEndCommand(const std::string & theCommand, const TokenList & tokList) {
+
+    if (m_tokenListIt == tokList.end()) {
+        return "";
+    }
+
+	string description;
+	while (m_tokenListIt != tokList.end()) {
 
 		//TODO: it won't output doxygen commands, need a way to fix it
-		if (tokList.peek().tokenType == PLAINSTRING)
-			description += tokList.peek().tokenString + " ";
-		if (tokList.peek().tokenType == END_LINE)
+		if (m_tokenListIt->m_tokenType == PLAINSTRING) {
+			description += m_tokenListIt->m_tokenString + " ";
+		} else if (m_tokenListIt->m_tokenType == END_LINE) {
 			description += "\n";
+	    }
 
-		if (tokList.peek().tokenString == theCommand) {
-			tokList.next();
+		if (m_tokenListIt->m_tokenString == theCommand) {
+		    m_tokenListIt++;
 			return description;
 		}
 
-		tokList.next();
+		m_tokenListIt++;
 	}
-	tokList.printListError(WARN_DOXYGEN_COMMAND_EXPECTED, theCommand + " command expected");
+
+	printListError(WARN_DOXYGEN_COMMAND_EXPECTED, theCommand + " command expected");
+
 	return description;
 }
 
-std::list < Token >::iterator DoxygenParser::getEndOfParagraph(TokenList & tokList) {
-	std::list < Token >::iterator endOfParagraph = tokList.iteratorCopy();
+
+DoxygenParser::TokenListCIt DoxygenParser::getEndOfParagraph(const TokenList & tokList) {
+
+	TokenListCIt endOfParagraph = m_tokenListIt;
+
 	while (endOfParagraph != tokList.end()) {
-		if ((*endOfParagraph).tokenType == END_LINE) {
+		if ((*endOfParagraph).m_tokenType == END_LINE) {
 			endOfParagraph++;
-			if (endOfParagraph != tokList.end() && (*endOfParagraph).tokenType == END_LINE) {
+			if (endOfParagraph != tokList.end() && (*endOfParagraph).m_tokenType == END_LINE) {
 				endOfParagraph++;
 				//cout << "ENCOUNTERED END OF PARA" << endl;
 				return endOfParagraph;
 			}
 
-		} else if ((*endOfParagraph).tokenType == COMMAND) {
+		} else if ((*endOfParagraph).m_tokenType == COMMAND) {
 
-			if (isSectionIndicator((*endOfParagraph).tokenString)) {
+			if (isSectionIndicator((*endOfParagraph).m_tokenString)) {
 				return endOfParagraph;
 			} else
 				endOfParagraph++;
 
-		} else if ((*endOfParagraph).tokenType == PLAINSTRING) {
+		} else if ((*endOfParagraph).m_tokenType == PLAINSTRING) {
 			endOfParagraph++;
 		} else {
 			return tokList.end();
@@ -206,19 +246,23 @@ std::list < Token >::iterator DoxygenParser::getEndOfParagraph(TokenList & tokLi
 	return tokList.end();
 }
 
-std::list < Token >::iterator DoxygenParser::getEndOfSection(std::string theCommand, TokenList & tokList) {
-	std::list < Token >::iterator endOfParagraph = tokList.iteratorCopy();
+
+DoxygenParser::TokenListCIt DoxygenParser::getEndOfSection(const std::string & theCommand,
+                                                                 const TokenList & tokList) {
+
+    TokenListCIt endOfParagraph = m_tokenListIt;
+
 	while (endOfParagraph != tokList.end()) {
-		if ((*endOfParagraph).tokenType == COMMAND) {
-			if (theCommand == (*endOfParagraph).tokenString)
+		if ((*endOfParagraph).m_tokenType == COMMAND) {
+			if (theCommand == (*endOfParagraph).m_tokenString)
 				return endOfParagraph;
 			else
 				endOfParagraph++;
-		} else if ((*endOfParagraph).tokenType == PLAINSTRING) {
+		} else if ((*endOfParagraph).m_tokenType == PLAINSTRING) {
 			endOfParagraph++;
-		} else if ((*endOfParagraph).tokenType == END_LINE) {
+		} else if ((*endOfParagraph).m_tokenType == END_LINE) {
 			endOfParagraph++;
-			if ((*endOfParagraph).tokenType == END_LINE) {
+			if ((*endOfParagraph).m_tokenType == END_LINE) {
 				endOfParagraph++;
 				return endOfParagraph;
 			}
@@ -227,12 +271,16 @@ std::list < Token >::iterator DoxygenParser::getEndOfSection(std::string theComm
 	return tokList.end();
 }
 
-std::list < Token >::iterator DoxygenParser::getEndCommand(std::string theCommand, TokenList & tokList) {
-	std::list < Token >::iterator endOfCommand = tokList.iteratorCopy();
+
+DoxygenParser::TokenListCIt DoxygenParser::getEndCommand(const std::string & theCommand,
+                                                              const TokenList & tokList) {
+
+    TokenListCIt endOfCommand = m_tokenListIt;
+
 	while (endOfCommand != tokList.end()) {
         endOfCommand++;
-		if ((*endOfCommand).tokenType == COMMAND) {
-			if (theCommand == (*endOfCommand).tokenString) {
+		if ((*endOfCommand).m_tokenType == COMMAND) {
+			if (theCommand == (*endOfCommand).m_tokenString) {
 				return endOfCommand;
 			}
 		}
@@ -241,75 +289,99 @@ std::list < Token >::iterator DoxygenParser::getEndCommand(std::string theComman
 	return tokList.end();
 }
 
-std::list < Token >::iterator DoxygenParser::getTilAnyCommand(std::string, TokenList &) {
-	std::list < Token >::iterator anIterator;
+/* DoxygenParser::TokenListIt DoxygenParser::getTilAnyCommand(const std::string &,
+                                                                  TokenList &) {
+    TokenListIt anIterator;
 	return anIterator;
-}
+} */
 
-int DoxygenParser::addSimpleCommand(std::string theCommand, std::list < DoxygenEntity > &doxyList) {
+
+int DoxygenParser::addSimpleCommand(const std::string &theCommand,
+                                         std::list < DoxygenEntity > &doxyList) {
 	if (noisy)
 		cout << "Parsing " << theCommand << endl;
+
 	doxyList.push_back(DoxygenEntity(theCommand));
 	return 1;
 }
 
-int DoxygenParser::addCommandWord(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
+
+int DoxygenParser::addCommandWord(const std::string &theCommand,
+                                       const TokenList &tokList,
+                                       std::list < DoxygenEntity > &doxyList) {
 	if (noisy)
 		cout << "Parsing " << theCommand << endl;
+
 	std::string name = getNextWord(tokList);
 	if (!name.empty()) {
     std::list < DoxygenEntity > aNewList;
     aNewList.push_back(DoxygenEntity("plainstd::string", name));
 		doxyList.push_back(DoxygenEntity(theCommand, aNewList));
 		return 1;
-	} else
-		tokList.printListError(WARN_DOXYGEN_COMMAND_ERROR, "No word followed " + theCommand + " command. Not added");
+	} else {
+		printListError(WARN_DOXYGEN_COMMAND_ERROR, "No word followed " + theCommand + " command. Not added");
+	}
 	return 0;
 }
 
-int DoxygenParser::addCommandLine(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
+
+int DoxygenParser::addCommandLine(const std::string &theCommand,
+                                       const TokenList &tokList,
+                                       std::list < DoxygenEntity > &doxyList) {
 	if (noisy)
 		cout << "Parsing " << theCommand << endl;
-	std::list < Token >::iterator endOfLine = getOneLine(tokList);
+	TokenListCIt endOfLine = getOneLine(tokList);
 	std::list < DoxygenEntity > aNewList = parse(endOfLine, tokList);
 	doxyList.push_back(DoxygenEntity(theCommand, aNewList));
 	return 1;
 }
 
-int DoxygenParser::addCommandParagraph(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
+
+int DoxygenParser::addCommandParagraph(const std::string &theCommand,
+                                            const TokenList &tokList,
+                                            std::list < DoxygenEntity > &doxyList) {
 	if (noisy)
 		cout << "Parsing " << theCommand << endl;
-	std::list < Token >::iterator endOfParagraph = getEndOfParagraph(tokList);
+
+	TokenListCIt endOfParagraph = getEndOfParagraph(tokList);
 	std::list < DoxygenEntity > aNewList;
 	aNewList = parse(endOfParagraph, tokList);
 	doxyList.push_back(DoxygenEntity(theCommand, aNewList));
 	return 1;
 }
 
-int DoxygenParser::addCommandEndCommand(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
+
+int DoxygenParser::addCommandEndCommand(const std::string &theCommand,
+                                             const TokenList & tokList,
+                                             std::list < DoxygenEntity > &doxyList) {
 	if (noisy)
 		cout << "Parsing " << theCommand << endl;
-	std::list < Token >::iterator endCommand = getEndCommand("end" + theCommand, tokList);
+	TokenListCIt endCommand = getEndCommand("end" + theCommand, tokList);
 	if (endCommand == tokList.end()) {
-	  tokList.printListError(WARN_DOXYGEN_COMMAND_EXPECTED, "Expected end" + theCommand);
+	  printListError(WARN_DOXYGEN_COMMAND_EXPECTED, "Expected end" + theCommand);
 	  return 0;
 	}
 	std::list < DoxygenEntity > aNewList;
 	aNewList = parse(endCommand, tokList);
-	tokList.next();
+	m_tokenListIt++;
 	doxyList.push_back(DoxygenEntity(theCommand, aNewList));
 	return 1;
 }
 
-int DoxygenParser::addCommandWordParagraph(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
+
+int DoxygenParser::addCommandWordParagraph(const std::string &theCommand,
+                                                 const TokenList &tokList,
+                                                 std::list < DoxygenEntity > &doxyList) {
 	if (noisy)
 		cout << "Parsing " << theCommand << endl;
+
 	std::string name = getNextWord(tokList);
+
 	if (name.empty()) {
-		tokList.printListError(WARN_DOXYGEN_COMMAND_ERROR, "No word followed " + theCommand + " command. Not added");
+		printListError(WARN_DOXYGEN_COMMAND_ERROR, "No word followed " + theCommand + " command. Not added");
 		return 0;
 	}
-	std::list < Token >::iterator endOfParagraph = getEndOfParagraph(tokList);
+	TokenListCIt endOfParagraph = getEndOfParagraph(tokList);
 	std::list < DoxygenEntity > aNewList;
 	aNewList = parse(endOfParagraph, tokList);
 	aNewList.push_front(DoxygenEntity("plainstd::string", name));
@@ -317,15 +389,18 @@ int DoxygenParser::addCommandWordParagraph(std::string theCommand, TokenList & t
 	return 1;
 }
 
-int DoxygenParser::addCommandWordLine(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
+int DoxygenParser::addCommandWordLine(const std::string &theCommand,
+                                           const TokenList & tokList,
+                                           std::list < DoxygenEntity > &doxyList) {
 	if (noisy)
 		cout << "Parsing " << theCommand << endl;
 	std::string name = getNextWord(tokList);
 	if (name.empty()) {
-		tokList.printListError(WARN_DOXYGEN_COMMAND_ERROR, "No word followed " + theCommand + " command. Not added");
+		printListError(WARN_DOXYGEN_COMMAND_ERROR, "No word followed " + theCommand + " command. Not added");
 		return 0;
 	}
-	std::list < Token >::iterator endOfLine = getOneLine(tokList);
+
+	TokenListCIt endOfLine = getOneLine(tokList);
 	std::list < DoxygenEntity > aNewList;
 	aNewList = parse(endOfLine, tokList);
 	aNewList.push_front(DoxygenEntity("plainstd::string", name));
@@ -334,12 +409,15 @@ int DoxygenParser::addCommandWordLine(std::string theCommand, TokenList & tokLis
 	//else cout << "No line followed " << theCommand <<  " command. Not added" << endl;
 }
 
-int DoxygenParser::addCommandWordOWordOWord(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
+int DoxygenParser::addCommandWordOWordOWord(const std::string &theCommand,
+                                                  const TokenList &tokList,
+                                                  std::list < DoxygenEntity > &doxyList) {
 	if (noisy)
 		cout << "Parsing " << theCommand << endl;
+
 	std::string name = getNextWord(tokList);
 	if (name.empty()) {
-		tokList.printListError(WARN_DOXYGEN_COMMAND_ERROR, "No word followed " + theCommand + " command. Not added");
+		printListError(WARN_DOXYGEN_COMMAND_ERROR, "No word followed " + theCommand + " command. Not added");
 		return 0;
 	}
 	std::string headerfile = getNextWord(tokList);
@@ -354,29 +432,40 @@ int DoxygenParser::addCommandWordOWordOWord(std::string theCommand, TokenList &
 	return 1;
 }
 
-int DoxygenParser::addCommandOWord(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
+
+int DoxygenParser::addCommandOWord(const std::string &theCommand,
+                                        const TokenList &tokList,
+                                        std::list < DoxygenEntity > &doxyList) {
 	if (noisy)
 		cout << "Parsing " << theCommand << endl;
+
 	std::string name = getNextWord(tokList);
 	std::list < DoxygenEntity > aNewList;
-  aNewList.push_back(DoxygenEntity("plainstd::string", name));
+	aNewList.push_back(DoxygenEntity("plainstd::string", name));
 	doxyList.push_back(DoxygenEntity(theCommand, aNewList));
 	return 1;
 }
 
-int DoxygenParser::addCommandErrorThrow(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &) {
-	tokList.printListError(WARN_DOXYGEN_COMMAND_ERROR, "Encountered: " + theCommand +
+
+int DoxygenParser::addCommandErrorThrow(const std::string &theCommand,
+                                             const TokenList &tokList,
+                                             std::list < DoxygenEntity > &) {
+
+	printListError(WARN_DOXYGEN_COMMAND_ERROR, "Encountered: " + theCommand +
 			"\nThis command should not have been encountered. Behaviour past this may be unpredictable");
-	std::list < Token >::iterator endOfLine = getOneLine(tokList);
-	tokList.setIterator(endOfLine);
+	m_tokenListIt = getOneLine(tokList);
 	return 0;
 }
 
-int DoxygenParser::addCommandUnique(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
+
+int DoxygenParser::addCommandUnique(const std::string &theCommand,
+                                         const TokenList &tokList,
+                                         std::list < DoxygenEntity > &doxyList) {
+
     static std::map<std::string, std::string> endCommands;
 	std::list < DoxygenEntity > aNewList;
 	if (theCommand == "arg" || theCommand == "li") {
-		std::list < Token >::iterator endOfSection = getEndOfSection(theCommand, tokList);
+		TokenListCIt endOfSection = getEndOfSection(theCommand, tokList);
 		std::list < DoxygenEntity > aNewList;
 		aNewList = parse(endOfSection, tokList);
 		doxyList.push_back(DoxygenEntity(theCommand, aNewList));
@@ -387,20 +476,20 @@ int DoxygenParser::addCommandUnique(std::string theCommand, TokenList & tokList,
 			cout << "Parsing " << theCommand << endl;
 		std::string key = getNextWord(tokList);
 		if (key.empty()) {
-			tokList.printListError(WARN_DOXYGEN_COMMAND_ERROR, "No key followed " + theCommand + " command. Not added");
+			printListError(WARN_DOXYGEN_COMMAND_ERROR, "No key followed " + theCommand + " command. Not added");
 			return 0;
 		}
 		std::string heading = getNextWord(tokList);
 		if (key.empty()) {
-			tokList.printListError(WARN_DOXYGEN_COMMAND_ERROR, "No heading followed " + theCommand + " command. Not added");
+			printListError(WARN_DOXYGEN_COMMAND_ERROR, "No heading followed " + theCommand + " command. Not added");
 			return 0;
 		}
 		std::string title = getNextWord(tokList);
 		if (title.empty()) {
-			tokList.printListError(WARN_DOXYGEN_COMMAND_ERROR, "No title followed " + theCommand + " command. Not added");
+			printListError(WARN_DOXYGEN_COMMAND_ERROR, "No title followed " + theCommand + " command. Not added");
 			return 0;
 		}
-		std::list < Token >::iterator endOfParagraph = getEndOfParagraph(tokList);
+		TokenListCIt endOfParagraph = getEndOfParagraph(tokList);
 		aNewList = parse(endOfParagraph, tokList);
 		aNewList.push_front(DoxygenEntity("plainstd::string", title));
 		aNewList.push_front(DoxygenEntity("plainstd::string", heading));
@@ -423,10 +512,10 @@ int DoxygenParser::addCommandUnique(std::string theCommand, TokenList & tokList,
 	}
 	// \par [(paragraph title)] { paragraph }
 	else if (theCommand == "par") {
-		std::list < Token >::iterator endOfLine = getOneLine(tokList);
+	    TokenListCIt endOfLine = getOneLine(tokList);
 		aNewList = parse(endOfLine, tokList);
 		std::list < DoxygenEntity > aNewList2;
-		std::list < Token >::iterator endOfParagraph = getEndOfParagraph(tokList);
+		TokenListCIt endOfParagraph = getEndOfParagraph(tokList);
 		aNewList2 = parse(endOfParagraph, tokList);
 		aNewList.splice(aNewList.end(), aNewList2);
 		doxyList.push_back(DoxygenEntity(theCommand, aNewList));
@@ -445,8 +534,8 @@ int DoxygenParser::addCommandUnique(std::string theCommand, TokenList & tokList,
 	}
 	// \overload [(function declaration)]
 	else if (theCommand == "overload") {
-		std::list < Token >::iterator endOfLine = getOneLine(tokList);
-		if (endOfLine != tokList.current()) {
+	    TokenListCIt endOfLine = getOneLine(tokList);
+		if (endOfLine != m_tokenListIt) {
 			std::list < DoxygenEntity > aNewList;
 			aNewList = parse(endOfLine, tokList);
 			doxyList.push_back(DoxygenEntity(theCommand, aNewList));
@@ -460,12 +549,12 @@ int DoxygenParser::addCommandUnique(std::string theCommand, TokenList & tokList,
 			cout << "Parsing " << theCommand << endl;
 		std::string name = getNextWord(tokList);
 		if (name.empty()) {
-			tokList.printListError(WARN_DOXYGEN_COMMAND_ERROR, "No word followed " + theCommand + " command. Not added");
+			printListError(WARN_DOXYGEN_COMMAND_ERROR, "No word followed " + theCommand + " command. Not added");
 			return 0;
 		}
 		std::list < DoxygenEntity > aNewList;
-		std::list < Token >::iterator endOfLine = getOneLine(tokList);
-		if (endOfLine != tokList.current()) {
+		TokenListCIt endOfLine = getOneLine(tokList);
+		if (endOfLine != m_tokenListIt) {
 			aNewList = parse(endOfLine, tokList);
 		}
 		aNewList.push_front(DoxygenEntity("plainstd::string", name));
@@ -477,7 +566,7 @@ int DoxygenParser::addCommandUnique(std::string theCommand, TokenList & tokList,
 			cout << "Parsing " << theCommand << endl;
 		std::string name = getNextWord(tokList);
 		if (name.empty()) {
-			tokList.printListError(WARN_DOXYGEN_COMMAND_ERROR, "No key followed " + theCommand + " command. Not added");
+			printListError(WARN_DOXYGEN_COMMAND_ERROR, "No key followed " + theCommand + " command. Not added");
 			return 0;
 		}
 		std::string text = getNextWord(tokList);
@@ -492,7 +581,7 @@ int DoxygenParser::addCommandUnique(std::string theCommand, TokenList & tokList,
 			cout << "Parsing " << theCommand << endl;
 		std::string name = getNextWord(tokList);
 		if (name.empty()) {
-			tokList.printListError(WARN_DOXYGEN_COMMAND_ERROR, "No name followed " + theCommand + " command. Not added");
+			printListError(WARN_DOXYGEN_COMMAND_ERROR, "No name followed " + theCommand + " command. Not added");
 			return 0;
 		}
 		std::string text = getNextWord(tokList);
@@ -541,7 +630,7 @@ int DoxygenParser::addCommandUnique(std::string theCommand, TokenList & tokList,
 			cout << "Parsing " << theCommand << endl;
 		std::string file = getNextWord(tokList);
 		if (file.empty()) {
-			tokList.printListError(WARN_DOXYGEN_COMMAND_ERROR, "No file followed " + theCommand + " command. Not added");
+			printListError(WARN_DOXYGEN_COMMAND_ERROR, "No file followed " + theCommand + " command. Not added");
 			return 0;
 		}
 		std::string caption = getNextWord(tokList);
@@ -556,12 +645,12 @@ int DoxygenParser::addCommandUnique(std::string theCommand, TokenList & tokList,
 			cout << "Parsing " << theCommand << endl;
 		std::string format = getNextWord(tokList);
 		if (format.empty()) {
-			tokList.printListError(WARN_DOXYGEN_COMMAND_ERROR, "No format followed " + theCommand + " command. Not added");
+			printListError(WARN_DOXYGEN_COMMAND_ERROR, "No format followed " + theCommand + " command. Not added");
 			return 0;
 		}
 		std::string file = getNextWord(tokList);
 		if (file.empty()) {
-			tokList.printListError(WARN_DOXYGEN_COMMAND_ERROR, "No name followed " + theCommand + " command. Not added");
+			printListError(WARN_DOXYGEN_COMMAND_ERROR, "No name followed " + theCommand + " command. Not added");
 			return 0;
 		}
 		std::string caption = getNextWord(tokList);
@@ -582,12 +671,12 @@ int DoxygenParser::addCommandUnique(std::string theCommand, TokenList & tokList,
 			cout << "Parsing " << theCommand << endl;
 		std::string name = getNextWord(tokList);
 		if (name.empty()) {
-			tokList.printListError(WARN_DOXYGEN_COMMAND_ERROR, "No word followed " + theCommand + " command. Not added");
+			printListError(WARN_DOXYGEN_COMMAND_ERROR, "No word followed " + theCommand + " command. Not added");
 			return 0;
 		}
 		std::list < DoxygenEntity > aNewList;
-		std::list < Token >::iterator endOfLine = getOneLine(tokList);
-		if (endOfLine != tokList.current()) {
+		TokenListCIt endOfLine = getOneLine(tokList);
+		if (endOfLine != m_tokenListIt) {
 			aNewList = parse(endOfLine, tokList);
 		}
 		aNewList.push_front(DoxygenEntity("plainstd::string", name));
@@ -605,22 +694,22 @@ int DoxygenParser::addCommandUnique(std::string theCommand, TokenList & tokList,
 		if (needsCond) {
 			cond = getNextWord(tokList);
 			if (cond.empty()) {
-				tokList.printListError(WARN_DOXYGEN_COMMAND_ERROR, "No word followed " + theCommand + " command. Not added");
+				printListError(WARN_DOXYGEN_COMMAND_ERROR, "No word followed " + theCommand + " command. Not added");
 				return 0;
 			}
 		}
 
 		int nestedCounter = 1;
-		std::list < Token >::iterator endCommand = tokList.end();
+		TokenListCIt endCommand = tokList.end();
+
 		// go through the commands and find closing endif or else or elseif
-		std::list < Token >::iterator it=tokList.iteratorCopy();
-		for (; it!=tokList.end(); it++) {
-			if (it->tokenType == COMMAND) {
-				if (it->tokenString == "if" || it->tokenString == "ifnot")
+		for (TokenListCIt it = m_tokenListIt; it!=tokList.end(); it++) {
+			if (it->m_tokenType == COMMAND) {
+				if (it->m_tokenString == "if" || it->m_tokenString == "ifnot")
 					nestedCounter++;
-				else if (it->tokenString == "endif")
+				else if (it->m_tokenString == "endif")
 					nestedCounter--;
-				if (nestedCounter == 1 && (it->tokenString == "else" || it->tokenString == "elseif")) { // else found
+				if (nestedCounter == 1 && (it->m_tokenString == "else" || it->m_tokenString == "elseif")) { // else found
 					endCommand = it;
 					break;
 				}
@@ -633,14 +722,14 @@ int DoxygenParser::addCommandUnique(std::string theCommand, TokenList & tokList,
 		}
 
 		if (endCommand == tokList.end()) {
-			tokList.printListError(WARN_DOXYGEN_COMMAND_EXPECTED, "No corresponding endif found");
+			printListError(WARN_DOXYGEN_COMMAND_EXPECTED, "No corresponding endif found");
 			return 0;
 		}
 
 		std::list < DoxygenEntity > aNewList;
 		aNewList = parse(endCommand, tokList);
 		if (skipEndif)
-			tokList.next();
+			m_tokenListIt++;
 		if (needsCond)
 			aNewList.push_front(DoxygenEntity("plainstd::string", cond));
 		doxyList.push_back(DoxygenEntity(theCommand, aNewList));
@@ -648,7 +737,11 @@ int DoxygenParser::addCommandUnique(std::string theCommand, TokenList & tokList,
 	return 0;
 }
 
-int DoxygenParser::addCommand(std::string commandString, TokenList & tokList, std::list < DoxygenEntity > &doxyList) {
+
+int DoxygenParser::addCommand(const std::string &commandString,
+                                  const TokenList &tokList,
+                                  std::list < DoxygenEntity > &doxyList) {
+
 	std::string theCommand = stringToLower(commandString);
 	if (theCommand == "plainstd::string") {
 		std::string nextPhrase = getStringTilCommand(tokList);
@@ -684,48 +777,46 @@ int DoxygenParser::addCommand(std::string commandString, TokenList & tokList, st
 	return 0;
 }
 
-std::list < DoxygenEntity > DoxygenParser::parse(std::list < Token >::iterator endParsingIndex, TokenList & tokList, bool root) {
+
+std::list < DoxygenEntity > DoxygenParser::parse(TokenListCIt endParsingIndex,
+                                                       const TokenList &tokList,
+                                                       bool root) {
 	// if we are root, than any strings should be added as 'partofdescription', else as 'plainstd::string'
 	std::string currPlainstringCommandType = root ? "partofdescription" : "plainstd::string";
 	std::list < DoxygenEntity > aNewList;
-	int currCommand;
-	while (tokList.current() != endParsingIndex) {
-		Token currToken = tokList.peek();
+
+	while (m_tokenListIt != endParsingIndex) {
+
+		Token currToken = *m_tokenListIt;
+
 		if (noisy)
 			cout << "Parsing for phrase starting in:" << currToken.toString() << endl;
-		if (currToken.tokenType == END_LINE) {
-		  aNewList.push_back(DoxygenEntity("plainstd::endl"));
-			tokList.next();
-		} else if (currToken.tokenType == COMMAND) {
-			currCommand = findCommand(currToken.tokenString);
-			if (currCommand < 0) {
-				if (noisy)
-					cout << "Unidentified Command " << currToken.tokenString << endl;
-				tokList.printListError(WARN_DOXYGEN_UNKNOWN_COMMAND, "Unsupported command: '" + currToken.tokenString + "'. Ignored");
-				tokList.current()->tokenType = PLAINSTRING; // little hack to add the command as plaintext
-				addCommand(currPlainstringCommandType, tokList, aNewList);
-			} else {
-				tokList.next();
-				addCommand(currToken.tokenString, tokList, aNewList);
-			}
-		} else if (currToken.tokenType == PLAINSTRING) {
+
+		if (currToken.m_tokenType == END_LINE) {
+		    aNewList.push_back(DoxygenEntity("plainstd::endl"));
+		    m_tokenListIt++;
+		} else if (currToken.m_tokenType == COMMAND) {
+		    m_tokenListIt++;
+		    addCommand(currToken.m_tokenString, tokList, aNewList);
+		} else if (currToken.m_tokenType == PLAINSTRING) {
 			addCommand(currPlainstringCommandType, tokList, aNewList);
 		}
 
-		if (endParsingIndex != tokList.end() && tokList.current() == tokList.end()) {
-		  // this could happen if we cant reach the original endParsingIndex
-		  tokList.printListError(WARN_DOXYGEN_UNEXPECTED_END_OF_COMMENT, "Unexpected end of comment encountered");
+		if (endParsingIndex != tokList.end() && m_tokenListIt == tokList.end()) {
+		  // this could happen if we can't reach the original endParsingIndex
+		  printListError(WARN_DOXYGEN_UNEXPECTED_END_OF_COMMENT, "Unexpected end of comment encountered");
 		  break;
 		}
 	}
 	return aNewList;
 }
 
-std::list < DoxygenEntity > DoxygenParser::createTree(std::string doxygenBlob, std::string fileName, int lineNumber) {
-	TokenList tokList = TokenList::tokenizeDoxygenComment(doxygenBlob, fileName, lineNumber);
+
+std::list < DoxygenEntity > DoxygenParser::createTree(const std::string &doxygenBlob, const std::string &fileName, int lineNumber) {
+	TokenList tokList = tokenizeDoxygenComment(doxygenBlob, fileName, lineNumber);
 	if (noisy) {
 		cout << "---TOKEN LIST---" << endl;
-		tokList.printList();
+		printList();
 	}
 	std::list < DoxygenEntity > rootList;
 	rootList = parse(tokList.end(), tokList, true);
@@ -735,3 +826,116 @@ std::list < DoxygenEntity > DoxygenParser::createTree(std::string doxygenBlob, s
 	}
 	return rootList;
 }
+
+
+DoxygenParser::TokenList DoxygenParser::tokenizeDoxygenComment(const std::string &doxygenComment,
+                                                                      const std::string &fileName,
+                                                                      int fileLine) {
+  TokenList tokList;
+  m_fileLineNo = fileLine;
+  m_fileName = fileName;
+
+  bool isPlainString = false;
+  string::size_type pos, lastPos = 0;
+  char prevChar = doxygenComment[lastPos];
+  string currentWord;
+  while (true) {
+    isPlainString = false;
+    pos = doxygenComment.find_first_of("\\@\t\n ", lastPos);
+    if (pos == string::npos)
+      pos = doxygenComment.size();
+
+    currentWord = doxygenComment.substr(lastPos, pos-lastPos);
+    if (prevChar == '\n')
+      tokList.push_back(Token(END_LINE, "\n"));
+    else if (prevChar == '\\' || prevChar == '@') {
+      // it's a doxygen command
+      // hack to get commands like \\ or \@ or @\ or @@
+      if (doxygenComment[pos] == '@' || doxygenComment[pos] == '\\') {
+        currentWord += doxygenComment[pos];
+        pos++;
+      }
+      // also strip the command till the first nonalpha char
+      for (int i = 2; i < currentWord.size(); i++) {
+        if (!isalpha(currentWord[i])) {
+          currentWord = currentWord.substr(0, i);
+          // set current parsing pos back, to parse the rest of the command
+          pos = lastPos + i - 1;
+          break;
+        }
+      }
+
+      if (findCommand(currentWord)) {
+          tokList.push_back(Token(COMMAND, currentWord));
+      } else {
+          // unknown commands are not translated - treated as literal string
+          tokList.push_back(Token(PLAINSTRING, currentWord));
+      }
+    }
+    else if (currentWord.size() && (currentWord[0] == '!' || currentWord[0] == '*' || currentWord[0] == '/')) {
+      // check if it's one of the '!!!', '***', '///' of any length
+      char c = currentWord[0];
+      isPlainString = false;
+      for (size_t i=0; i<currentWord.size(); i++)
+        if (currentWord[i] != c) {
+          isPlainString = true;
+          break;
+        }
+    }
+    else
+      isPlainString = true;
+
+    if (isPlainString && currentWord.size())
+      tokList.push_back(Token(PLAINSTRING, currentWord));
+
+    prevChar = doxygenComment[pos];
+    lastPos = pos + 1;
+    if (lastPos >= doxygenComment.size())
+      break;
+  }
+
+  m_tokenListIt = tokList.begin();
+
+  return tokList;
+}
+
+
+void DoxygenParser::printList() {
+  TokenListIt p = m_tokenList.begin();
+  int i = 1;
+  int b = 0;
+  while (p != m_tokenList.end()) {
+    cout << (*p).toString() << " ";
+    b = i % TOKENSPERLINE;
+    if (b == 0)
+      cout << endl;
+    p++;
+    i++;
+  }
+
+  TokenListCIt startIt = m_tokenList.begin();
+
+  int tokNo = 0;
+  for (TokenListCIt it = startIt; it != m_tokenList.end(); it++, tokNo++) {
+    cout << it->toString() << " ";
+
+    if ((tokNo % TOKENSPERLINE) == 0) {
+      cout << endl;
+    }
+  }
+}
+
+void DoxygenParser::printListError(int warningType,
+                                        const std::string &message) {
+  int curLine = m_fileLineNo;
+  for (TokenListCIt it = m_tokenList.begin(); it != m_tokenListIt; it++) {
+    if (it->m_tokenType == END_LINE) {
+      curLine++;
+    }
+  }
+
+  Swig_warning(warningType, m_fileName.c_str(),
+                 curLine,
+                 "Doxygen parser warning: %s. \n",
+                 message.c_str());
+}
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.h b/Source/DoxygenTranslator/src/DoxygenParser.h
index 376676e08..2dea05f6e 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.h
+++ b/Source/DoxygenTranslator/src/DoxygenParser.h
@@ -16,80 +16,128 @@
 #include <map>
 #include <set>
 #include "DoxygenEntity.h"
-#include "TokenList.h"
+
 class DoxygenParser {
-public:
-  DoxygenParser(bool noisy = false);
-  virtual ~DoxygenParser();
-  std::list < DoxygenEntity > createTree(std::string doxygen, std::string fileName, int lineNumber);
 private:
-  
+
+    /** This class contains parts of Doxygen comment as a token. */
+    class Token {
+    public:
+        // typedef enum {COMMAND, PLAINSTRING, END_LINE, PARAGRAPH_END} ETokenType;
+        DoxyCommandEnum m_tokenType;
+        std::string m_tokenString;		/* the data , such as param for @param */
+
+        Token(DoxyCommandEnum tType, std::string tString) :
+            m_tokenType(tType),
+            m_tokenString(tString) {}
+
+        std::string toString() const {
+
+            switch (m_tokenType) {
+            case END_LINE:
+                return "{END OF LINE}";
+            case PARAGRAPH_END:
+                return "{END OF PARAGRAPH}";
+            case PLAINSTRING:
+                return "{PLAINSTRING :" + m_tokenString + "}";
+            case COMMAND:
+                return "{COMMAND : " + m_tokenString + "}";
+            default:
+                return "";
+            }
+        }
+    };
+
+
+    typedef std::list<Token> TokenList;
+    typedef TokenList::const_iterator TokenListCIt;
+    typedef TokenList::iterator TokenListIt;
+
+    TokenList m_tokenList;
+    TokenListCIt m_tokenListIt;
+    std::string m_fileName;
+    int m_fileLineNo;
+
+    /*
+     * Whether to print lots of debug info during parsing
+     */
+    bool noisy;
+
+    /*
+     * Map of Doxygen commands to determine if a string is a
+     * command and how it needs to be parsed
+     */
+    static std::map<std::string, DoxyCommandEnum> doxygenCommands;
+    static std::set<std::string> doxygenSectionIndicators;
+
   /*
    *Changes a std::string to all lower case
    */
-  std::string stringToLower(std::string &stringToConvert);
+  std::string stringToLower(const std::string &stringToConvert);
 
   /* 
    * Finds out if a command exists (is a possible command)
    * returns -1 if no match is found
    */
-  int findCommand(std::string smallString);
+  bool findCommand(const std::string &smallString);
   /* 
    * isSectionIndicator returns a boolean if the command is a section indicator
    * This is a helper method for finding the end of a paragraph
    * by Doxygen's terms
    */
-  int isSectionIndicator(std::string smallString);
+  bool isSectionIndicator(const std::string &smallString);
   /*
    * Determines how a command should be handled (what group it belongs to
    * for parsing rules
    */
-  int commandBelongs(std::string theCommand);
+  int commandBelongs(const std::string &theCommand);
 
   /*
    *prints the parse tree
    */
-  void printTree(std::list < DoxygenEntity > &rootList);
+  void printTree(const std::list <DoxygenEntity> &rootList);
 
   /*
    * Returns the next word ON THE CURRENT LINE ONLY
    * if a new line is encountered, returns a blank std::string.
    * Updates the index it is given if success.
    */
-  std::string getNextWord(TokenList & tokList);
+  std::string getNextWord(const TokenList &tokList);
 
   /* 
    * Returns the location of the end of the line as
    * an iterator.
    */
-  std::list < Token >::iterator getOneLine(TokenList & tokList);
+  TokenListCIt getOneLine(const TokenList &tokList);
 
   /*
    * Returns a properly formatted std::string
    * up til ANY command or end of line is encountered.
    */
-  std::string getStringTilCommand(TokenList & tokList);
+  std::string getStringTilCommand(const TokenList &tokList);
 
   /*
    * Returns a properly formatted std::string
    * up til the command specified is encountered
    */
   //TODO check that this behaves properly for formulas
-  std::string getStringTilEndCommand(std::string theCommand, TokenList & tokList);
+  std::string getStringTilEndCommand(const std::string &theCommand,
+		  	  	  	  	  	  	  	  	const TokenList &tokList);
 
   /*
    * Returns the end of a Paragraph as an iterator-
    * Paragraph is defined in Doxygen to be a paragraph of text
    * separated by either a structural command or a blank line
    */
-  std::list < Token >::iterator getEndOfParagraph(TokenList & tokList);
+  TokenListCIt getEndOfParagraph(const TokenList &tokList);
 
   /*
    * Returns the end of a section, defined as the first blank line OR first encounter of the same 
    * command. Example of this behaviour is \arg
    * if no end is encountered, returns the last token of the std::list.
    */
-  std::list < Token >::iterator getEndOfSection(std::string theCommand, TokenList & tokList);
+  TokenListCIt getEndOfSection(const std::string &theCommand,
+		                         const TokenList &tokList);
 
   /*
    * This method is for returning the end of a specific form of doxygen command
@@ -98,12 +146,14 @@ private:
    * progressTilEndCommand("endcode", tokenList);
    * If the end is never encountered, it returns the end of the std::list.
    */
-  std::list < Token >::iterator getEndCommand(std::string theCommand, TokenList & tokList);
+  TokenListCIt getEndCommand(const std::string &theCommand,
+		                       const TokenList &tokList);
   /*
    * A specialty method for commands such as \arg that end at the end of a paragraph OR when another \arg is encountered
-   */
   //TODO getTilAnyCommand
-  std::list < Token >::iterator getTilAnyCommand(std::string theCommand, TokenList & tokList);
+  TokenListCIt getTilAnyCommand(const std::string &theCommand,
+                                  const TokenList &tokList);
+   */
 
   /*
    * Method for Adding a Simple Command
@@ -111,7 +161,8 @@ private:
    * Plain commands, such as newline etc, they contain no other data
    *  \n \\ \@ \& \$ \# \< \> \%
    */
-  int addSimpleCommand(std::string theCommand, std::list < DoxygenEntity > &doxyList);
+  int addSimpleCommand(const std::string &theCommand,
+		                 std::list < DoxygenEntity > &doxyList);
   /*
    * CommandWord
    * Format: @command <word>
@@ -119,14 +170,18 @@ private:
    * "a", "b", "c", "e", "em", "p", "def", "enum", "example", "package", 
    * "relates", "namespace", "relatesalso","anchor", "dontinclude", "include", "includelineno"
    */
-  int addCommandWord(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList);
+  int addCommandWord(const std::string &theCommand,
+		               const TokenList &tokList,
+		               std::list < DoxygenEntity > &doxyList);
   /*
    * CommandLine
    * Format: @command (line)
    * Commands with a single LINE after then such as @var
    * "addindex", "fn", "name", "line", "var", "skipline", "typedef", "skip", "until", "property"
    */
-  int addCommandLine(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList);
+  int addCommandLine(const std::string &theCommand,
+		               const TokenList &tokList,
+		               std::list < DoxygenEntity > &doxyList);
   /*
    * CommandParagraph
    * Format: @command {paragraph}
@@ -134,7 +189,9 @@ private:
    * "return", "remarks", "since", "test", "sa", "see", "pre", "post", "details", "invariant", 
    * "deprecated", "date", "note", "warning", "version", "todo", "bug", "attention", "brief", "arg", "author"
    */
-  int addCommandParagraph(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList);
+  int addCommandParagraph(const std::string &theCommand,
+		  	  	  	  	     const TokenList &tokList,
+		                     std::list < DoxygenEntity > &doxyList);
   /*
    * Command EndCommand
    * Format: @command and ends at @endcommand
@@ -143,68 +200,83 @@ private:
    * "verbatim", "xmlonly", "cond", "if", "ifnot", "link"
    * Returns 1 if success, 0 if the endcommand is never encountered.
    */
-  int addCommandEndCommand(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList);
+  int addCommandEndCommand(const std::string &theCommand,
+		                      const TokenList & tokList,
+		                      std::list < DoxygenEntity > &doxyList);
   /*
    * CommandWordParagraph
    * Format: @command <word> {paragraph}
    * Commands such as param
    * "param", "tparam", "throw", "throws", "retval", "exception"
    */
-  int addCommandWordParagraph(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList);
+  int addCommandWordParagraph(const std::string &theCommand,
+		  	  	  	  	  	      const TokenList & tokList,
+		  	  	  	  	  	      std::list < DoxygenEntity > &doxyList);
   /*
    * CommandWordLine
    * Format: @command <word> (line)
    * Commands such as param
    * "page", "subsection", "subsubsection", "section", "paragraph", "defgroup"
    */
-  int addCommandWordLine(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList);
+  int addCommandWordLine(const std::string &theCommand,
+                            const TokenList &tokList,
+                            std::list < DoxygenEntity > &doxyList);
   /*
    * Command Word Optional Word Optional Word
    * Format: @command <word> [<header-file>] [<header-name>]
    * Commands such as class
    * "category", "class", "protocol", "interface", "struct", "union"
    */
-  int addCommandWordOWordOWord(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList);
+  int addCommandWordOWordOWord(const std::string &theCommand, const TokenList &tokList,
+                                   std::list < DoxygenEntity > &doxyList);
   /*
    * Command Optional Word
    * Format: @command [<word>]
    * Commands such as dir
    * "dir", "file", "cond"
    */
-  int addCommandOWord(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList);
+  int addCommandOWord(const std::string &theCommand,
+                         const TokenList &tokList,
+                         std::list < DoxygenEntity > &doxyList);
   /*
    * Commands that should not be encountered (such as PHP only)
    * goes til the end of line then returns
    */
-  int addCommandErrorThrow(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList);
+  int addCommandErrorThrow(const std::string &theCommand,
+                              const TokenList &tokList,
+                              std::list < DoxygenEntity > &doxyList);
   /*
    *Adds the unique commands- different process for each unique command
    */
-  int addCommandUnique(std::string theCommand, TokenList & tokList, std::list < DoxygenEntity > &doxyList);
+  int addCommandUnique(const std::string &theCommand, const TokenList &tokList, std::list < DoxygenEntity > &doxyList);
   /* 
    * The actual "meat" of the doxygen parser. Calls the correct addCommand* function
    */
-  int addCommand(std::string commandString, TokenList & tokList, std::list < DoxygenEntity > &doxyList);
+  int addCommand(const std::string &commandString,
+                   const TokenList &tokList,
+                   std::list < DoxygenEntity > &doxyList);
 
-  std::list < DoxygenEntity > parse(std::list < Token >::iterator endParsingIndex, TokenList & tokList, bool root=false);
+  std::list < DoxygenEntity > parse(TokenListCIt endParsingIndex,
+		                                const TokenList &tokList,
+		                                bool root = false);
   
   /*
    * Fill static doxygenCommands and sectionIndicators containers
    */
   void fillTables();
   
-  /*
-   * Whether to print lots of debug info during parsing
-   */
-  bool noisy;
-  
-  /* 
-   * Map of Doxygen commands to determine if a string is a
-   * command and how it needs to be parsed 
-   */
-  static std::map<std::string, DoxyCommandEnum> doxygenCommands;
-  
-  static std::set<std::string> doxygenSectionIndicators;
+  TokenList tokenizeDoxygenComment(const std::string &doxygenComment,
+		                              const std::string &fileName,
+		                              int fileLine);
+  void printList();
+  void printListError(int warningType, const std::string &message);
+
+public:
+  DoxygenParser(bool noisy = false);
+  virtual ~DoxygenParser();
+  std::list < DoxygenEntity > createTree(const std::string &doxygen,
+		  	  	  	  	  	  	  	  	     const std::string &fileName,
+		  	  	  	  	  	  	  	  	     int lineNumber);
 };
 
 #endif
diff --git a/Source/DoxygenTranslator/src/DoxygenTranslator.h b/Source/DoxygenTranslator/src/DoxygenTranslator.h
index 1b90dbc43..f24ad6c86 100644
--- a/Source/DoxygenTranslator/src/DoxygenTranslator.h
+++ b/Source/DoxygenTranslator/src/DoxygenTranslator.h
@@ -19,6 +19,7 @@
 #include "DoxygenEntity.h"
 #include "DoxygenParser.h"
 #include <list>
+#include <string>
 
 
 /*
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.cpp b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
index 204c07b61..20fc175da 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
@@ -13,6 +13,7 @@
 #include "DoxygenParser.h"
 #include <iostream>
 #include <vector>
+#include <list>
 #include "../../Modules/swigmod.h"
 #define APPROX_LINE_LENGTH 64	//characters per line allowed
 #define TAB_SIZE 8		//current tab size in spaces
@@ -21,6 +22,10 @@
 // define static tables, they are filled in JavaDocConverter's constructor
 std::map<std::string, std::pair<JavaDocConverter::tagHandler, std::string > > JavaDocConverter::tagHandlers;
 
+using std::string;
+using std::list;
+using std::vector;
+
 void JavaDocConverter::fillStaticTables() {
   if (tagHandlers.size()) // fill only once
     return;
diff --git a/Source/DoxygenTranslator/src/PyDocConverter.cpp b/Source/DoxygenTranslator/src/PyDocConverter.cpp
index 26b4a3c92..4f3566635 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/PyDocConverter.cpp
@@ -14,6 +14,7 @@
 #include "PyDocConverter.h"
 #include "DoxygenParser.h"
 #include <sstream>
+#include <string>
 #include <vector>
 #include <iostream>
 
@@ -21,6 +22,9 @@
 std::map<std::string, std::pair<PyDocConverter::tagHandler, std::string > > PyDocConverter::tagHandlers;
 std::map<std::string, std::string> PyDocConverter::sectionTitles;
 
+using std::string;
+
+
 void PyDocConverter::fillStaticTables() {
   if (tagHandlers.size()) // fill only once
     return;

From a753f3e799170959c2dcfef2f4cd60efe31b20c6 Mon Sep 17 00:00:00 2001
From: Marko Klopcic <marko.klopcic@isystem.si>
Date: Sun, 26 Aug 2012 13:07:09 +0000
Subject: [PATCH 144/314] removed files with classes wich were made obsolete by
 previous commit

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13723 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Source/DoxygenTranslator/src/Token.cpp     |  39 ------
 Source/DoxygenTranslator/src/Token.h       |  28 ----
 Source/DoxygenTranslator/src/TokenList.cpp | 152 ---------------------
 Source/DoxygenTranslator/src/TokenList.h   |  56 --------
 4 files changed, 275 deletions(-)
 delete mode 100644 Source/DoxygenTranslator/src/Token.cpp
 delete mode 100644 Source/DoxygenTranslator/src/Token.h
 delete mode 100644 Source/DoxygenTranslator/src/TokenList.cpp
 delete mode 100644 Source/DoxygenTranslator/src/TokenList.h

diff --git a/Source/DoxygenTranslator/src/Token.cpp b/Source/DoxygenTranslator/src/Token.cpp
deleted file mode 100644
index 6ade97163..000000000
--- a/Source/DoxygenTranslator/src/Token.cpp
+++ /dev/null
@@ -1,39 +0,0 @@
-/* ----------------------------------------------------------------------------- 
- * This file is part of SWIG, which is licensed as a whole under version 3 
- * (or any later version) of the GNU General Public License. Some additional
- * terms also apply to certain portions of SWIG. The full details of the SWIG
- * license and copyrights can be found in the LICENSE and COPYRIGHT files
- * included with the SWIG source code as distributed by the SWIG developers
- * and at http://www.swig.org/legal.html.
- *
- * Token.cpp
- * ----------------------------------------------------------------------------- */
-
-#include "Token.h"
-#include "DoxygenEntity.h"
-using namespace std;
-
-
-Token::Token(int tType, string tString) {
-  tokenType = tType;
-  tokenString = tString;
-}
-
-string Token::toString() {
-  if (tokenType == END_LINE) {
-    return "{END OF LINE}";
-  }
-  if (tokenType == PARAGRAPH_END) {
-    return "{END OF PARAGRAPH}";
-  }
-  if (tokenType == PLAINSTRING) {
-    return "{PLAINSTRING :" + tokenString + "}";
-  }
-  if (tokenType == COMMAND) {
-    return "{COMMAND : " + tokenString + "}";
-  }
-  return "";
-}
-
-Token::~Token() {
-}
diff --git a/Source/DoxygenTranslator/src/Token.h b/Source/DoxygenTranslator/src/Token.h
deleted file mode 100644
index 6e10fd338..000000000
--- a/Source/DoxygenTranslator/src/Token.h
+++ /dev/null
@@ -1,28 +0,0 @@
-/* -----------------------------------------------------------------------------
- * This file is part of SWIG, which is licensed as a whole under version 3 
- * (or any later version) of the GNU General Public License. Some additional
- * terms also apply to certain portions of SWIG. The full details of the SWIG
- * license and copyrights can be found in the LICENSE and COPYRIGHT files
- * included with the SWIG source code as distributed by the SWIG developers
- * and at http://www.swig.org/legal.html.
- *
- * Token.h
- * ----------------------------------------------------------------------------- */
-
-#ifndef TOKEN_H_
-#define TOKEN_H_
-#include <string>
-
-using namespace std;
-
-class Token {
-public:
-  Token(int tType, string tString);
-  ~Token();
-
-  int tokenType;		/* currently can be END_LINE, PLAINSTRING, or COMMAND */
-  string tokenString;		/* the data , such as param for @param */
-  string toString();
-};
-
-#endif
diff --git a/Source/DoxygenTranslator/src/TokenList.cpp b/Source/DoxygenTranslator/src/TokenList.cpp
deleted file mode 100644
index ceea0ba17..000000000
--- a/Source/DoxygenTranslator/src/TokenList.cpp
+++ /dev/null
@@ -1,152 +0,0 @@
-/* ----------------------------------------------------------------------------- 
- * This file is part of SWIG, which is licensed as a whole under version 3 
- * (or any later version) of the GNU General Public License. Some additional
- * terms also apply to certain portions of SWIG. The full details of the SWIG
- * license and copyrights can be found in the LICENSE and COPYRIGHT files
- * included with the SWIG source code as distributed by the SWIG developers
- * and at http://www.swig.org/legal.html.
- *
- * TokenList.cpp
- * ----------------------------------------------------------------------------- */
-
-#include "TokenList.h"
-#include <cstdlib>
-#include <iostream>
-#include <string>
-#include <list>
-#include "swig.h"
-#include "Token.h"
-#include "DoxygenEntity.h"
-#define TOKENSPERLINE 8;	//change this to change the printing behaviour of the token list
-
-using namespace std;
-
-TokenList TokenList::tokenizeDoxygenComment(const std::string &doxygenComment, const std::string &fileName, int fileLine) {
-  TokenList tokList;
-  tokList.fileLine = fileLine;
-  tokList.fileName = fileName;
-
-  bool isPlainString = false;
-  string::size_type pos, lastPos = 0;
-  char prevChar = doxygenComment[lastPos];
-  string currentWord;
-  while (true) {
-    isPlainString = false;
-    pos = doxygenComment.find_first_of("\\@\t\n ", lastPos);
-    if (pos == string::npos)
-      pos = doxygenComment.size();
-
-    currentWord = doxygenComment.substr(lastPos, pos-lastPos);
-    if (prevChar == '\n')
-      tokList.m_tokenList.push_back(Token(END_LINE, "\n"));
-    else if (prevChar == '\\' || prevChar == '@') {
-      // it's a doxygen command
-      // hack to get commands like \\ or \@ or @\ or @@
-      if (doxygenComment[pos] == '@' || doxygenComment[pos] == '\\') {
-        currentWord += doxygenComment[pos];
-        pos++;
-      }
-      // also strip the command till the first nonalpha char
-      for (int i=2; i<currentWord.size(); i++)
-        if (!isalpha(currentWord[i])) {
-          currentWord = currentWord.substr(0, i);
-          // set current parsing pos back, to parse the rest of the command
-          pos = lastPos + i - 1;
-          break;
-        }
-      tokList.m_tokenList.push_back(Token(COMMAND, currentWord));
-    }
-    else if (currentWord.size() && (currentWord[0] == '!' || currentWord[0] == '*' || currentWord[0] == '/')) {
-      // check if it's one of the '!!!', '***', '///' of any length
-      char c = currentWord[0];
-      isPlainString = false;
-      for (size_t i=0; i<currentWord.size(); i++)
-        if (currentWord[i] != c) {
-          isPlainString = true;
-          break;
-        }
-    }
-    else
-      isPlainString = true;
-
-    if (isPlainString && currentWord.size())
-      tokList.m_tokenList.push_back(Token(PLAINSTRING, currentWord));
-
-    prevChar = doxygenComment[pos];
-    lastPos = pos + 1;
-    if (lastPos >= doxygenComment.size())
-      break;
-  }
-  tokList.m_tokenListIter = tokList.m_tokenList.begin();
-  return tokList;
-}
-
-TokenList::TokenList()
-: fileName(""), fileLine(0) {
-  m_tokenListIter = m_tokenList.begin();
-}
-
-
-TokenList::~TokenList() {
-}
-
-Token TokenList::peek() {
-  if (m_tokenListIter != m_tokenList.end()) {
-    Token returnedToken = (*m_tokenListIter);
-    return returnedToken;
-  } else
-    return Token(0, "");
-}
-
-
-Token TokenList::next() {
-  if (m_tokenListIter != m_tokenList.end()) {
-    Token returnedToken = (*m_tokenListIter);
-    m_tokenListIter++;
-    return (returnedToken);
-  } else
-    return Token(0, "");
-}
-
-
-list < Token >::iterator TokenList::end() {
-  return m_tokenList.end();
-}
-
-
-list < Token >::iterator TokenList::current() {
-  return m_tokenListIter;
-}
-
-
-list < Token >::iterator TokenList::iteratorCopy() {
-  return m_tokenListIter;
-}
-
-
-void TokenList::setIterator(list < Token >::iterator newPosition) {
-  m_tokenListIter = newPosition;
-}
-
-
-void TokenList::printList() {
-  list < Token >::iterator p = m_tokenList.begin();
-  int i = 1;
-  int b = 0;
-  while (p != m_tokenList.end()) {
-    cout << (*p).toString() << " ";
-    b = i % TOKENSPERLINE;
-    if (b == 0)
-      cout << endl;
-    p++;
-    i++;
-  }
-}
-
-void TokenList::printListError(int warningType, std::string message) {
-  int curLine = fileLine;
-  for (list< Token >::iterator it = m_tokenList.begin(); it != current(); it++)
-    if (it->tokenType == END_LINE)
-      curLine++;
-  Swig_warning(warningType, fileName.c_str(), curLine, "Doxygen parser warning: %s. \n", message.c_str());
-}
diff --git a/Source/DoxygenTranslator/src/TokenList.h b/Source/DoxygenTranslator/src/TokenList.h
deleted file mode 100644
index 69580f11c..000000000
--- a/Source/DoxygenTranslator/src/TokenList.h
+++ /dev/null
@@ -1,56 +0,0 @@
-/* -----------------------------------------------------------------------------
- * This file is part of SWIG, which is licensed as a whole under version 3 
- * (or any later version) of the GNU General Public License. Some additional
- * terms also apply to certain portions of SWIG. The full details of the SWIG
- * license and copyrights can be found in the LICENSE and COPYRIGHT files
- * included with the SWIG source code as distributed by the SWIG developers
- * and at http://www.swig.org/legal.html.
- *
- * TokenList.h
- * ----------------------------------------------------------------------------- */
-
-#ifndef TOKENLIST_H_
-#define TOKENLIST_H_
-#include <cstdlib>
-#include <iostream>
-#include <string>
-#include <list>
-#include "Token.h"
-#include "swigwarn.h"
-
-/* a small class used to represent the sequence of tokens
- * that can be derived from a formatted doxygen string
- */
-
-class TokenList {
-private:
-  std::list < Token > m_tokenList;
-  std::list < Token >::iterator m_tokenListIter;
-  // location info for error output
-  std::string fileName;
-  int fileLine;
-
-public:
-  TokenList(); // construct an empty TokenList
-  ~TokenList();
-
-  Token peek();			/* returns next token without advancing */
-  Token next();			/* returns next token and advances */
-
-  std::list < Token >::iterator end();	/* returns an end iterator */
-  std::list < Token >::iterator current();	/* returns the current iterator */
-
-  std::list < Token >::iterator iteratorCopy();	/* returns a copy of the current iterator */
-  void setIterator(list < Token >::iterator newPosition);	/*moves up the iterator */
-
-  void printList();		/* prints out the sequence of tokens */
-  void printListError(int warningType, std::string message); /* prints properly formatted error message */
-
-  /*
-   * Create TokenList and populate it with tokens from
-   * a blob of Doxygen comment
-   */
-  static TokenList tokenizeDoxygenComment(const std::string &doxygenComment, const std::string &fileName, int fileLine);
-};
-
-#endif

From c9eda79264ecb1b82c69ec7bf611918aa5feb9bf Mon Sep 17 00:00:00 2001
From: Marko Klopcic <marko.klopcic@isystem.si>
Date: Sun, 26 Aug 2012 15:34:46 +0000
Subject: [PATCH 145/314] refactored DoxygenEntity class

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13724 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 .../DoxygenTranslator/src/DoxygenEntity.cpp   | 182 ++++--------------
 Source/DoxygenTranslator/src/DoxygenEntity.h  |  27 ++-
 .../DoxygenTranslator/src/DoxygenParser.cpp   |  72 +++----
 Source/DoxygenTranslator/src/DoxygenParser.h  |  75 +++++---
 .../src/DoxygenTranslator.cpp                 |  24 ++-
 .../DoxygenTranslator/src/DoxygenTranslator.h |  26 +--
 .../src/JavaDocConverter.cpp                  |   2 +-
 7 files changed, 155 insertions(+), 253 deletions(-)

diff --git a/Source/DoxygenTranslator/src/DoxygenEntity.cpp b/Source/DoxygenTranslator/src/DoxygenEntity.cpp
index 4039ccc99..7b0088e06 100644
--- a/Source/DoxygenTranslator/src/DoxygenEntity.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenEntity.cpp
@@ -14,182 +14,66 @@
 #include "DoxygenEntity.h"
 #include <iostream>
 
-DoxygenEntity::DoxygenEntity(std::string typeEnt) {
-  typeOfEntity = typeEnt;
-  data = "";
-  isLeaf = true;
-}
+using std::cout;
+
+DoxygenEntity::DoxygenEntity(const std::string &typeEnt) :
+  typeOfEntity(typeEnt),
+  isLeaf(true)
+{}
+
 
 /* Basic node for commands that have
- * only 1 thing after them
+ * only 1 item after them
  * example: \b word
  * OR holding a std::string
  */
-DoxygenEntity::DoxygenEntity(std::string typeEnt, std::string param1) {
-  typeOfEntity = typeEnt;
-  data = param1;
-  isLeaf = true;
-}
+DoxygenEntity::DoxygenEntity(const std::string &typeEnt,
+                                 const std::string &param1) :
+  typeOfEntity(typeEnt),
+  data(param1),
+  isLeaf(true)
+{}
+
 
 /* Nonterminal node
  * contains
  */
-DoxygenEntity::DoxygenEntity(std::string typeEnt, std::list < DoxygenEntity > &entList) {
-  typeOfEntity = typeEnt;
-  data = "";
-  isLeaf = false;
-  entityList = entList;
-}
+DoxygenEntity::DoxygenEntity(const std::string &typeEnt,
+                                 const DoxygenEntityList &entList) :
+  typeOfEntity(typeEnt),
+  isLeaf(false),
+  entityList(entList)
+{}
+
 
 void DoxygenEntity::printEntity(int level) const {
+
   int thisLevel = level;
+
   if (isLeaf) {
     for (int i = 0; i < thisLevel; i++) {
-      std::cout << "\t";
+      cout << "\t";
     }
 
-    std::cout << "Node Command: " << typeOfEntity << " ";
+    cout << "Node Command: " << typeOfEntity << " ";
 
-    if (data.compare("") != 0) {
-      std::cout << "Node Data: " << data;
+    if (!data.empty()) {
+      cout << "Node Data: " << data;
     }
-    std::cout << std::endl;
+    cout << std::endl;
 
   } else {
 
     for (int i = 0; i < thisLevel; i++) {
-      std::cout << "\t";
+      cout << "\t";
     }
 
-    std::cout << "Node Command : " << typeOfEntity << std::endl;
+    cout << "Node Command : " << typeOfEntity << std::endl;
 
-    std::list < DoxygenEntity >::const_iterator p = entityList.begin();
     thisLevel++;
 
-    while (p != entityList.end()) {
-      (*p).printEntity(thisLevel);
-      p++;
+    for (DoxygenEntityListCIt p = entityList.begin(); p != entityList.end(); p++) {
+      p->printEntity(thisLevel);
     }
   }
 }
-
-// not used, completely wrong - currently std lib reports 'invalid operator <'
-bool CompareDoxygenEntities::operator() (DoxygenEntity & first, DoxygenEntity & second) {
-
-  // return first.typeOfEntity < second.typeOfEntity;
-  if (first.typeOfEntity.compare("brief") == 0)
-    return true;
-  if (second.typeOfEntity.compare("brief") == 0)
-    return false;
-  if (first.typeOfEntity.compare("details") == 0)
-    return true;
-  if (second.typeOfEntity.compare("details") == 0)
-    return false;
-  if (first.typeOfEntity.compare("partofdescription") == 0)
-    return true;
-  if (second.typeOfEntity.compare("partofdescription") == 0)
-    return false;
-  if (first.typeOfEntity.compare("plainstd::string") == 0)
-    return true;
-  if (second.typeOfEntity.compare("plainstd::string") == 0)
-    return false;
-  if (first.typeOfEntity.compare("param") == 0) {
-    if (second.typeOfEntity.compare("param") == 0)
-      return true;
-    if (second.typeOfEntity.compare("return") == 0)
-      return true;
-    if (second.typeOfEntity.compare("exception") == 0)
-      return true;
-    if (second.typeOfEntity.compare("author") == 0)
-      return true;
-    if (second.typeOfEntity.compare("version") == 0)
-      return true;
-    if (second.typeOfEntity.compare("see") == 0)
-      return true;
-    if (second.typeOfEntity.compare("since") == 0)
-      return true;
-    if (second.typeOfEntity.compare("deprecated") == 0)
-      return true;
-    return false;
-  }
-  if (first.typeOfEntity.compare("return") == 0) {
-    if (second.typeOfEntity.compare("return") == 0)
-      return true;
-    if (second.typeOfEntity.compare("exception") == 0)
-      return true;
-    if (second.typeOfEntity.compare("author") == 0)
-      return true;
-    if (second.typeOfEntity.compare("version") == 0)
-      return true;
-    if (second.typeOfEntity.compare("see") == 0)
-      return true;
-    if (second.typeOfEntity.compare("since") == 0)
-      return true;
-    if (second.typeOfEntity.compare("deprecated") == 0)
-      return true;
-    return false;
-  }
-  if (first.typeOfEntity.compare("exception") == 0) {
-    if (second.typeOfEntity.compare("exception") == 0)
-      return true;
-    if (second.typeOfEntity.compare("author") == 0)
-      return true;
-    if (second.typeOfEntity.compare("version") == 0)
-      return true;
-    if (second.typeOfEntity.compare("see") == 0)
-      return true;
-    if (second.typeOfEntity.compare("since") == 0)
-      return true;
-    if (second.typeOfEntity.compare("deprecated") == 0)
-      return true;
-    return false;
-  }
-  if (first.typeOfEntity.compare("author") == 0) {
-    if (second.typeOfEntity.compare("author") == 0)
-      return true;
-    if (second.typeOfEntity.compare("version") == 0)
-      return true;
-    if (second.typeOfEntity.compare("see") == 0)
-      return true;
-    if (second.typeOfEntity.compare("since") == 0)
-      return true;
-    if (second.typeOfEntity.compare("deprecated") == 0)
-      return true;
-    return false;
-  }
-  if (first.typeOfEntity.compare("version") == 0) {
-    if (second.typeOfEntity.compare("version") == 0)
-      return true;
-    if (second.typeOfEntity.compare("see") == 0)
-      return true;
-    if (second.typeOfEntity.compare("since") == 0)
-      return true;
-    if (second.typeOfEntity.compare("deprecated") == 0)
-      return true;
-    return false;
-  }
-  if (first.typeOfEntity.compare("see") == 0 || first.typeOfEntity.compare("sa") == 0) {
-    if (second.typeOfEntity.compare("see") == 0)
-      return true;
-    if (second.typeOfEntity.compare("sa") == 0)
-      return true;
-    if (second.typeOfEntity.compare("since") == 0)
-      return true;
-    if (second.typeOfEntity.compare("deprecated") == 0)
-      return true;
-    return false;
-  }
-  if (first.typeOfEntity.compare("since") == 0) {
-    if (second.typeOfEntity.compare("since") == 0)
-      return true;
-    if (second.typeOfEntity.compare("deprecated") == 0)
-      return true;
-    return false;
-  }
-  if (first.typeOfEntity.compare("deprecated") == 0) {
-    if (second.typeOfEntity.compare("deprecated") == 0)
-      return true;
-    return false;
-  }
-  return true;
-}
diff --git a/Source/DoxygenTranslator/src/DoxygenEntity.h b/Source/DoxygenTranslator/src/DoxygenEntity.h
index 9e6fda4cb..cf03240d2 100644
--- a/Source/DoxygenTranslator/src/DoxygenEntity.h
+++ b/Source/DoxygenTranslator/src/DoxygenEntity.h
@@ -36,29 +36,28 @@ typedef enum {
   COMMAND
 } DoxyCommandEnum;
 
+class DoxygenEntity;
+
+typedef std::list <DoxygenEntity> DoxygenEntityList;
+typedef DoxygenEntityList::iterator DoxygenEntityListIt;
+typedef DoxygenEntityList::const_iterator DoxygenEntityListCIt;
+
+
 /*
  * Structure to represent a doxygen comment entry
  */
-struct DoxygenEntity {
+class DoxygenEntity {
+public:
   std::string typeOfEntity;
-  std::list < DoxygenEntity > entityList;
   std::string data;
   bool isLeaf;
+  DoxygenEntityList entityList;
 
-  DoxygenEntity(std::string typeEnt);
-  DoxygenEntity(std::string typeEnt, std::string param1);
-  DoxygenEntity(std::string typeEnt, std::list < DoxygenEntity > &entList);
+  DoxygenEntity(const std::string &typeEnt);
+  DoxygenEntity(const std::string &typeEnt, const std::string &param1);
+  DoxygenEntity(const std::string & typeEnt, const DoxygenEntityList &entList);
 
   void printEntity(int level) const;
 };
 
-/* 
- * Functor that sorts entities by javaDoc standard order for commands.
- * NOTE: will not behave entirely properly until "First level" comments
- * such as brief descriptions are TAGGED as such
- */
-struct CompareDoxygenEntities {
-  bool operator() (DoxygenEntity & first, DoxygenEntity & second);
-};
-
 #endif
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.cpp b/Source/DoxygenTranslator/src/DoxygenParser.cpp
index 10126808d..a66d66c28 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenParser.cpp
@@ -102,8 +102,8 @@ bool DoxygenParser::isSectionIndicator(const std::string &smallString) {
 }
 
 
-void DoxygenParser::printTree(const std::list <DoxygenEntity> &rootList) {
-	std::list < DoxygenEntity >::const_iterator p = rootList.begin();
+void DoxygenParser::printTree(const DoxygenEntityList &rootList) {
+	DoxygenEntityList::const_iterator p = rootList.begin();
 	while (p != rootList.end()) {
 		(*p).printEntity(0);
 		p++;
@@ -297,7 +297,7 @@ DoxygenParser::TokenListCIt DoxygenParser::getEndCommand(const std::string & the
 
 
 int DoxygenParser::addSimpleCommand(const std::string &theCommand,
-                                         std::list < DoxygenEntity > &doxyList) {
+                                         DoxygenEntityList &doxyList) {
 	if (noisy)
 		cout << "Parsing " << theCommand << endl;
 
@@ -308,13 +308,13 @@ int DoxygenParser::addSimpleCommand(const std::string &theCommand,
 
 int DoxygenParser::addCommandWord(const std::string &theCommand,
                                        const TokenList &tokList,
-                                       std::list < DoxygenEntity > &doxyList) {
+                                       DoxygenEntityList &doxyList) {
 	if (noisy)
 		cout << "Parsing " << theCommand << endl;
 
 	std::string name = getNextWord(tokList);
 	if (!name.empty()) {
-    std::list < DoxygenEntity > aNewList;
+    DoxygenEntityList aNewList;
     aNewList.push_back(DoxygenEntity("plainstd::string", name));
 		doxyList.push_back(DoxygenEntity(theCommand, aNewList));
 		return 1;
@@ -327,11 +327,11 @@ int DoxygenParser::addCommandWord(const std::string &theCommand,
 
 int DoxygenParser::addCommandLine(const std::string &theCommand,
                                        const TokenList &tokList,
-                                       std::list < DoxygenEntity > &doxyList) {
+                                       DoxygenEntityList &doxyList) {
 	if (noisy)
 		cout << "Parsing " << theCommand << endl;
 	TokenListCIt endOfLine = getOneLine(tokList);
-	std::list < DoxygenEntity > aNewList = parse(endOfLine, tokList);
+	DoxygenEntityList aNewList = parse(endOfLine, tokList);
 	doxyList.push_back(DoxygenEntity(theCommand, aNewList));
 	return 1;
 }
@@ -339,12 +339,12 @@ int DoxygenParser::addCommandLine(const std::string &theCommand,
 
 int DoxygenParser::addCommandParagraph(const std::string &theCommand,
                                             const TokenList &tokList,
-                                            std::list < DoxygenEntity > &doxyList) {
+                                            DoxygenEntityList &doxyList) {
 	if (noisy)
 		cout << "Parsing " << theCommand << endl;
 
 	TokenListCIt endOfParagraph = getEndOfParagraph(tokList);
-	std::list < DoxygenEntity > aNewList;
+	DoxygenEntityList aNewList;
 	aNewList = parse(endOfParagraph, tokList);
 	doxyList.push_back(DoxygenEntity(theCommand, aNewList));
 	return 1;
@@ -353,7 +353,7 @@ int DoxygenParser::addCommandParagraph(const std::string &theCommand,
 
 int DoxygenParser::addCommandEndCommand(const std::string &theCommand,
                                              const TokenList & tokList,
-                                             std::list < DoxygenEntity > &doxyList) {
+                                             DoxygenEntityList &doxyList) {
 	if (noisy)
 		cout << "Parsing " << theCommand << endl;
 	TokenListCIt endCommand = getEndCommand("end" + theCommand, tokList);
@@ -361,7 +361,7 @@ int DoxygenParser::addCommandEndCommand(const std::string &theCommand,
 	  printListError(WARN_DOXYGEN_COMMAND_EXPECTED, "Expected end" + theCommand);
 	  return 0;
 	}
-	std::list < DoxygenEntity > aNewList;
+	DoxygenEntityList aNewList;
 	aNewList = parse(endCommand, tokList);
 	m_tokenListIt++;
 	doxyList.push_back(DoxygenEntity(theCommand, aNewList));
@@ -371,7 +371,7 @@ int DoxygenParser::addCommandEndCommand(const std::string &theCommand,
 
 int DoxygenParser::addCommandWordParagraph(const std::string &theCommand,
                                                  const TokenList &tokList,
-                                                 std::list < DoxygenEntity > &doxyList) {
+                                                 DoxygenEntityList &doxyList) {
 	if (noisy)
 		cout << "Parsing " << theCommand << endl;
 
@@ -382,7 +382,7 @@ int DoxygenParser::addCommandWordParagraph(const std::string &theCommand,
 		return 0;
 	}
 	TokenListCIt endOfParagraph = getEndOfParagraph(tokList);
-	std::list < DoxygenEntity > aNewList;
+	DoxygenEntityList aNewList;
 	aNewList = parse(endOfParagraph, tokList);
 	aNewList.push_front(DoxygenEntity("plainstd::string", name));
 	doxyList.push_back(DoxygenEntity(theCommand, aNewList));
@@ -391,7 +391,7 @@ int DoxygenParser::addCommandWordParagraph(const std::string &theCommand,
 
 int DoxygenParser::addCommandWordLine(const std::string &theCommand,
                                            const TokenList & tokList,
-                                           std::list < DoxygenEntity > &doxyList) {
+                                           DoxygenEntityList &doxyList) {
 	if (noisy)
 		cout << "Parsing " << theCommand << endl;
 	std::string name = getNextWord(tokList);
@@ -401,7 +401,7 @@ int DoxygenParser::addCommandWordLine(const std::string &theCommand,
 	}
 
 	TokenListCIt endOfLine = getOneLine(tokList);
-	std::list < DoxygenEntity > aNewList;
+	DoxygenEntityList aNewList;
 	aNewList = parse(endOfLine, tokList);
 	aNewList.push_front(DoxygenEntity("plainstd::string", name));
 	doxyList.push_back(DoxygenEntity(theCommand, aNewList));
@@ -411,7 +411,7 @@ int DoxygenParser::addCommandWordLine(const std::string &theCommand,
 
 int DoxygenParser::addCommandWordOWordOWord(const std::string &theCommand,
                                                   const TokenList &tokList,
-                                                  std::list < DoxygenEntity > &doxyList) {
+                                                  DoxygenEntityList &doxyList) {
 	if (noisy)
 		cout << "Parsing " << theCommand << endl;
 
@@ -422,7 +422,7 @@ int DoxygenParser::addCommandWordOWordOWord(const std::string &theCommand,
 	}
 	std::string headerfile = getNextWord(tokList);
 	std::string headername = getNextWord(tokList);
-	std::list < DoxygenEntity > aNewList;
+	DoxygenEntityList aNewList;
 	aNewList.push_back(DoxygenEntity("plainstd::string", name));
 	if (!headerfile.empty())
 		aNewList.push_back(DoxygenEntity("plainstd::string", headerfile));
@@ -435,12 +435,12 @@ int DoxygenParser::addCommandWordOWordOWord(const std::string &theCommand,
 
 int DoxygenParser::addCommandOWord(const std::string &theCommand,
                                         const TokenList &tokList,
-                                        std::list < DoxygenEntity > &doxyList) {
+                                        DoxygenEntityList &doxyList) {
 	if (noisy)
 		cout << "Parsing " << theCommand << endl;
 
 	std::string name = getNextWord(tokList);
-	std::list < DoxygenEntity > aNewList;
+	DoxygenEntityList aNewList;
 	aNewList.push_back(DoxygenEntity("plainstd::string", name));
 	doxyList.push_back(DoxygenEntity(theCommand, aNewList));
 	return 1;
@@ -449,7 +449,7 @@ int DoxygenParser::addCommandOWord(const std::string &theCommand,
 
 int DoxygenParser::addCommandErrorThrow(const std::string &theCommand,
                                              const TokenList &tokList,
-                                             std::list < DoxygenEntity > &) {
+                                             DoxygenEntityList &) {
 
 	printListError(WARN_DOXYGEN_COMMAND_ERROR, "Encountered: " + theCommand +
 			"\nThis command should not have been encountered. Behaviour past this may be unpredictable");
@@ -460,13 +460,13 @@ int DoxygenParser::addCommandErrorThrow(const std::string &theCommand,
 
 int DoxygenParser::addCommandUnique(const std::string &theCommand,
                                          const TokenList &tokList,
-                                         std::list < DoxygenEntity > &doxyList) {
+                                         DoxygenEntityList &doxyList) {
 
     static std::map<std::string, std::string> endCommands;
-	std::list < DoxygenEntity > aNewList;
+	DoxygenEntityList aNewList;
 	if (theCommand == "arg" || theCommand == "li") {
 		TokenListCIt endOfSection = getEndOfSection(theCommand, tokList);
-		std::list < DoxygenEntity > aNewList;
+		DoxygenEntityList aNewList;
 		aNewList = parse(endOfSection, tokList);
 		doxyList.push_back(DoxygenEntity(theCommand, aNewList));
 	}
@@ -514,7 +514,7 @@ int DoxygenParser::addCommandUnique(const std::string &theCommand,
 	else if (theCommand == "par") {
 	    TokenListCIt endOfLine = getOneLine(tokList);
 		aNewList = parse(endOfLine, tokList);
-		std::list < DoxygenEntity > aNewList2;
+		DoxygenEntityList aNewList2;
 		TokenListCIt endOfParagraph = getEndOfParagraph(tokList);
 		aNewList2 = parse(endOfParagraph, tokList);
 		aNewList.splice(aNewList.end(), aNewList2);
@@ -523,7 +523,7 @@ int DoxygenParser::addCommandUnique(const std::string &theCommand,
 	}
 	// \headerfile <header-file> [<header-name>]
 	else if (theCommand == "headerfile") {
-		std::list < DoxygenEntity > aNewList;
+		DoxygenEntityList aNewList;
 		std::string name = getNextWord(tokList);
 		aNewList.push_back(DoxygenEntity("plainstd::string", name));
 		name = getNextWord(tokList);
@@ -536,7 +536,7 @@ int DoxygenParser::addCommandUnique(const std::string &theCommand,
 	else if (theCommand == "overload") {
 	    TokenListCIt endOfLine = getOneLine(tokList);
 		if (endOfLine != m_tokenListIt) {
-			std::list < DoxygenEntity > aNewList;
+			DoxygenEntityList aNewList;
 			aNewList = parse(endOfLine, tokList);
 			doxyList.push_back(DoxygenEntity(theCommand, aNewList));
 		} else
@@ -552,7 +552,7 @@ int DoxygenParser::addCommandUnique(const std::string &theCommand,
 			printListError(WARN_DOXYGEN_COMMAND_ERROR, "No word followed " + theCommand + " command. Not added");
 			return 0;
 		}
-		std::list < DoxygenEntity > aNewList;
+		DoxygenEntityList aNewList;
 		TokenListCIt endOfLine = getOneLine(tokList);
 		if (endOfLine != m_tokenListIt) {
 			aNewList = parse(endOfLine, tokList);
@@ -656,7 +656,7 @@ int DoxygenParser::addCommandUnique(const std::string &theCommand,
 		std::string caption = getNextWord(tokList);
 		std::string size = getNextWord(tokList);
 
-		std::list < DoxygenEntity > aNewList;
+		DoxygenEntityList aNewList;
 		aNewList.push_back(DoxygenEntity("plainstd::string", format));
 		aNewList.push_back(DoxygenEntity("plainstd::string", file));
 		if (!caption.empty())
@@ -674,7 +674,7 @@ int DoxygenParser::addCommandUnique(const std::string &theCommand,
 			printListError(WARN_DOXYGEN_COMMAND_ERROR, "No word followed " + theCommand + " command. Not added");
 			return 0;
 		}
-		std::list < DoxygenEntity > aNewList;
+		DoxygenEntityList aNewList;
 		TokenListCIt endOfLine = getOneLine(tokList);
 		if (endOfLine != m_tokenListIt) {
 			aNewList = parse(endOfLine, tokList);
@@ -726,7 +726,7 @@ int DoxygenParser::addCommandUnique(const std::string &theCommand,
 			return 0;
 		}
 
-		std::list < DoxygenEntity > aNewList;
+		DoxygenEntityList aNewList;
 		aNewList = parse(endCommand, tokList);
 		if (skipEndif)
 			m_tokenListIt++;
@@ -740,7 +740,7 @@ int DoxygenParser::addCommandUnique(const std::string &theCommand,
 
 int DoxygenParser::addCommand(const std::string &commandString,
                                   const TokenList &tokList,
-                                  std::list < DoxygenEntity > &doxyList) {
+                                  DoxygenEntityList &doxyList) {
 
 	std::string theCommand = stringToLower(commandString);
 	if (theCommand == "plainstd::string") {
@@ -778,12 +778,12 @@ int DoxygenParser::addCommand(const std::string &commandString,
 }
 
 
-std::list < DoxygenEntity > DoxygenParser::parse(TokenListCIt endParsingIndex,
+DoxygenEntityList DoxygenParser::parse(TokenListCIt endParsingIndex,
                                                        const TokenList &tokList,
                                                        bool root) {
 	// if we are root, than any strings should be added as 'partofdescription', else as 'plainstd::string'
 	std::string currPlainstringCommandType = root ? "partofdescription" : "plainstd::string";
-	std::list < DoxygenEntity > aNewList;
+	DoxygenEntityList aNewList;
 
 	while (m_tokenListIt != endParsingIndex) {
 
@@ -812,13 +812,13 @@ std::list < DoxygenEntity > DoxygenParser::parse(TokenListCIt endParsingIndex,
 }
 
 
-std::list < DoxygenEntity > DoxygenParser::createTree(const std::string &doxygenBlob, const std::string &fileName, int lineNumber) {
+DoxygenEntityList DoxygenParser::createTree(const std::string &doxygenBlob, const std::string &fileName, int lineNumber) {
 	TokenList tokList = tokenizeDoxygenComment(doxygenBlob, fileName, lineNumber);
 	if (noisy) {
 		cout << "---TOKEN LIST---" << endl;
 		printList();
 	}
-	std::list < DoxygenEntity > rootList;
+	DoxygenEntityList rootList;
 	rootList = parse(tokList.end(), tokList, true);
 	if (noisy) {
 		cout << "PARSED LIST" << endl;
@@ -856,7 +856,7 @@ DoxygenParser::TokenList DoxygenParser::tokenizeDoxygenComment(const std::string
         pos++;
       }
       // also strip the command till the first nonalpha char
-      for (int i = 2; i < currentWord.size(); i++) {
+      for (size_t i = 2; i < currentWord.size(); i++) {
         if (!isalpha(currentWord[i])) {
           currentWord = currentWord.substr(0, i);
           // set current parsing pos back, to parse the rest of the command
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.h b/Source/DoxygenTranslator/src/DoxygenParser.h
index 2dea05f6e..d015c1896 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.h
+++ b/Source/DoxygenTranslator/src/DoxygenParser.h
@@ -23,7 +23,6 @@ private:
     /** This class contains parts of Doxygen comment as a token. */
     class Token {
     public:
-        // typedef enum {COMMAND, PLAINSTRING, END_LINE, PARAGRAPH_END} ETokenType;
         DoxyCommandEnum m_tokenType;
         std::string m_tokenString;		/* the data , such as param for @param */
 
@@ -132,9 +131,9 @@ private:
   TokenListCIt getEndOfParagraph(const TokenList &tokList);
 
   /*
-   * Returns the end of a section, defined as the first blank line OR first encounter of the same 
-   * command. Example of this behaviour is \arg
-   * if no end is encountered, returns the last token of the std::list.
+   * Returns the end of a section, defined as the first blank line OR first
+   * encounter of the same command. Example of this behaviour is \arg.
+   * If no end is encountered, returns the last token of the std::list.
    */
   TokenListCIt getEndOfSection(const std::string &theCommand,
 		                         const TokenList &tokList);
@@ -149,7 +148,8 @@ private:
   TokenListCIt getEndCommand(const std::string &theCommand,
 		                       const TokenList &tokList);
   /*
-   * A specialty method for commands such as \arg that end at the end of a paragraph OR when another \arg is encountered
+   * A special method for commands such as \arg that end at the end of a
+   * paragraph OR when another \arg is encountered
   //TODO getTilAnyCommand
   TokenListCIt getTilAnyCommand(const std::string &theCommand,
                                   const TokenList &tokList);
@@ -162,47 +162,51 @@ private:
    *  \n \\ \@ \& \$ \# \< \> \%
    */
   int addSimpleCommand(const std::string &theCommand,
-		                 std::list < DoxygenEntity > &doxyList);
+		                 DoxygenEntityList &doxyList);
   /*
    * CommandWord
    * Format: @command <word>
    * Commands with a single WORD after then such as @b
    * "a", "b", "c", "e", "em", "p", "def", "enum", "example", "package", 
-   * "relates", "namespace", "relatesalso","anchor", "dontinclude", "include", "includelineno"
+   * "relates", "namespace", "relatesalso","anchor", "dontinclude", "include",
+   * "includelineno"
    */
   int addCommandWord(const std::string &theCommand,
 		               const TokenList &tokList,
-		               std::list < DoxygenEntity > &doxyList);
+		               DoxygenEntityList &doxyList);
   /*
    * CommandLine
    * Format: @command (line)
    * Commands with a single LINE after then such as @var
-   * "addindex", "fn", "name", "line", "var", "skipline", "typedef", "skip", "until", "property"
+   * "addindex", "fn", "name", "line", "var", "skipline", "typedef", "skip",
+   * "until", "property"
    */
   int addCommandLine(const std::string &theCommand,
 		               const TokenList &tokList,
-		               std::list < DoxygenEntity > &doxyList);
+		               DoxygenEntityList &doxyList);
   /*
    * CommandParagraph
    * Format: @command {paragraph}
    * Commands with a single paragraph after then such as @return
-   * "return", "remarks", "since", "test", "sa", "see", "pre", "post", "details", "invariant", 
-   * "deprecated", "date", "note", "warning", "version", "todo", "bug", "attention", "brief", "arg", "author"
+   * "return", "remarks", "since", "test", "sa", "see", "pre", "post",
+   * "details", "invariant", "deprecated", "date", "note", "warning",
+   * "version", "todo", "bug", "attention", "brief", "arg", "author"
    */
   int addCommandParagraph(const std::string &theCommand,
 		  	  	  	  	     const TokenList &tokList,
-		                     std::list < DoxygenEntity > &doxyList);
+		                     DoxygenEntityList &doxyList);
   /*
    * Command EndCommand
    * Format: @command and ends at @endcommand
-   * Commands that take in a block of text such as @code
-   * "code", "dot", "msc", "f$", "f[", "f{environment}{", "htmlonly", "latexonly", "manonly", 
-   * "verbatim", "xmlonly", "cond", "if", "ifnot", "link"
+   * Commands that take in a block of text such as @code:
+   * "code", "dot", "msc", "f$", "f[", "f{environment}{", "htmlonly",
+   * "latexonly", "manonly", "verbatim", "xmlonly", "cond", "if", "ifnot",
+   * "link"
    * Returns 1 if success, 0 if the endcommand is never encountered.
    */
   int addCommandEndCommand(const std::string &theCommand,
 		                      const TokenList & tokList,
-		                      std::list < DoxygenEntity > &doxyList);
+		                      DoxygenEntityList &doxyList);
   /*
    * CommandWordParagraph
    * Format: @command <word> {paragraph}
@@ -211,7 +215,7 @@ private:
    */
   int addCommandWordParagraph(const std::string &theCommand,
 		  	  	  	  	  	      const TokenList & tokList,
-		  	  	  	  	  	      std::list < DoxygenEntity > &doxyList);
+		  	  	  	  	  	      DoxygenEntityList &doxyList);
   /*
    * CommandWordLine
    * Format: @command <word> (line)
@@ -220,15 +224,16 @@ private:
    */
   int addCommandWordLine(const std::string &theCommand,
                             const TokenList &tokList,
-                            std::list < DoxygenEntity > &doxyList);
+                            DoxygenEntityList &doxyList);
   /*
    * Command Word Optional Word Optional Word
    * Format: @command <word> [<header-file>] [<header-name>]
    * Commands such as class
    * "category", "class", "protocol", "interface", "struct", "union"
    */
-  int addCommandWordOWordOWord(const std::string &theCommand, const TokenList &tokList,
-                                   std::list < DoxygenEntity > &doxyList);
+  int addCommandWordOWordOWord(const std::string &theCommand,
+                                   const TokenList &tokList,
+                                   DoxygenEntityList &doxyList);
   /*
    * Command Optional Word
    * Format: @command [<word>]
@@ -237,28 +242,34 @@ private:
    */
   int addCommandOWord(const std::string &theCommand,
                          const TokenList &tokList,
-                         std::list < DoxygenEntity > &doxyList);
+                         DoxygenEntityList &doxyList);
+
   /*
    * Commands that should not be encountered (such as PHP only)
    * goes til the end of line then returns
    */
   int addCommandErrorThrow(const std::string &theCommand,
                               const TokenList &tokList,
-                              std::list < DoxygenEntity > &doxyList);
+                              DoxygenEntityList &doxyList);
+
   /*
    *Adds the unique commands- different process for each unique command
    */
-  int addCommandUnique(const std::string &theCommand, const TokenList &tokList, std::list < DoxygenEntity > &doxyList);
+  int addCommandUnique(const std::string &theCommand,
+                          const TokenList &tokList,
+                          DoxygenEntityList &doxyList);
+
   /* 
-   * The actual "meat" of the doxygen parser. Calls the correct addCommand* function
+   * The actual "meat" of the doxygen parser. Calls the correct addCommand...()
+   * function.
    */
   int addCommand(const std::string &commandString,
                    const TokenList &tokList,
-                   std::list < DoxygenEntity > &doxyList);
+                   DoxygenEntityList &doxyList);
 
-  std::list < DoxygenEntity > parse(TokenListCIt endParsingIndex,
-		                                const TokenList &tokList,
-		                                bool root = false);
+  DoxygenEntityList parse(TokenListCIt endParsingIndex,
+                           const TokenList &tokList,
+                           bool root = false);
   
   /*
    * Fill static doxygenCommands and sectionIndicators containers
@@ -274,9 +285,9 @@ private:
 public:
   DoxygenParser(bool noisy = false);
   virtual ~DoxygenParser();
-  std::list < DoxygenEntity > createTree(const std::string &doxygen,
-		  	  	  	  	  	  	  	  	     const std::string &fileName,
-		  	  	  	  	  	  	  	  	     int lineNumber);
+  DoxygenEntityList createTree(const std::string &doxygen,
+                                const std::string &fileName,
+                                int lineNumber);
 };
 
 #endif
diff --git a/Source/DoxygenTranslator/src/DoxygenTranslator.cpp b/Source/DoxygenTranslator/src/DoxygenTranslator.cpp
index d9bf5f059..8175629d1 100644
--- a/Source/DoxygenTranslator/src/DoxygenTranslator.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenTranslator.cpp
@@ -14,16 +14,21 @@
 
 #include "DoxygenTranslator.h"
 
-DoxygenTranslator::DoxygenTranslator(bool debugTranslator, bool debugParser)
-: debug(debugTranslator), parser(debugParser) {
-}
+DoxygenTranslator::DoxygenTranslator(bool debugTranslator, bool debugParser) :
+  debug(debugTranslator),
+  parser(debugParser)
+{}
+
+
 DoxygenTranslator::~DoxygenTranslator() {
 }
 
+
 bool DoxygenTranslator::hasDocumentation(Node *node) {
   return getDoxygenComment(node);
 }
 
+
 String *DoxygenTranslator::getDoxygenComment(Node *node) {
   return Getattr(node, "doxygen");
 }
@@ -31,16 +36,17 @@ String *DoxygenTranslator::getDoxygenComment(Node *node) {
 
 String *DoxygenTranslator::getDocumentation(Node *node) {
   
-  if (!hasDocumentation(node))
+  if (!hasDocumentation(node)) {
     return NewString("");
+  }
   
   return makeDocumentation(node);
 }
 
-void DoxygenTranslator::printTree(std::list < DoxygenEntity > &entityList) {
-  std::list < DoxygenEntity >::iterator p = entityList.begin();
-  while (p != entityList.end()) {
-    (*p).printEntity(0);
-    p++;
+
+void DoxygenTranslator::printTree(const DoxygenEntityList &entityList) {
+
+  for (DoxygenEntityListCIt p = entityList.begin(); p != entityList.end(); p++) {
+    p->printEntity(0);
   }
 }
diff --git a/Source/DoxygenTranslator/src/DoxygenTranslator.h b/Source/DoxygenTranslator/src/DoxygenTranslator.h
index f24ad6c86..173bd58f0 100644
--- a/Source/DoxygenTranslator/src/DoxygenTranslator.h
+++ b/Source/DoxygenTranslator/src/DoxygenTranslator.h
@@ -23,8 +23,9 @@
 
 
 /*
- * A class to translate doxygen comments attached to parser nodes
- * into alternative formats for use in code generated for target languages.
+ * This is a base class for translator classes. It defines the basic interface
+ * for translators, which convert Doxygen comments into alternative formats for
+ * target languages.
  */
 class DoxygenTranslator {
 public:
@@ -32,41 +33,42 @@ public:
    * Constructor
    */
   DoxygenTranslator(bool debugTranslator = false, bool debugParser = false);
+
   /*
    * Virtual destructor.
    */
-  virtual ~ DoxygenTranslator();
+  virtual ~DoxygenTranslator();
+
   /*
    * Return the documentation for a given node formated for the correct 
    * documentation system.
    */
   String *getDocumentation(Node *node);
+
   /*
-   * Whether the specified node has comment or not
+   * Returns truem is the specified node has comment attached.
    */
   bool hasDocumentation(Node *node);
+
   /*
-   * Get original, Doxygen-format comment string
+   * Get original comment string in Doxygen-format.
    */
   String *getDoxygenComment(Node *node);
 
 protected:
   bool debug;
+  DoxygenParser parser;
+
   /*
-   * Overridden in subclasses to return the documentation formatted for a given
-   * documentation system.
+   * Returns the documentation formatted for a target language.
    */
   virtual String *makeDocumentation(Node *node) = 0;
   
   /*
    * Prints the details of a parsed entity list to stdout (for debugging).
    */
-  void printTree(std::list < DoxygenEntity > &entityList);
+  void printTree(const DoxygenEntityList &entityList);
   
-  /*
-   * Doxygen parser object
-   */
-  DoxygenParser parser;
 };
 
 #endif
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.cpp b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
index 20fc175da..171ef4dc7 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
@@ -458,7 +458,7 @@ int JavaDocConverter::cleanUpTree(DoxygenEntity &root, int level)
     return 0;
 
   int removedCount = 0;
-  while (root.entityList.rbegin()->typeOfEntity == "plainstd::endl") {
+  while (!root.entityList.empty()  &&  root.entityList.rbegin()->typeOfEntity == "plainstd::endl") {
     root.entityList.pop_back();
     removedCount++;
   }

From 46f2a16608576a11a94f552ef80bf2a712e4d361 Mon Sep 17 00:00:00 2001
From: Marko Klopcic <marko.klopcic@isystem.si>
Date: Sun, 26 Aug 2012 20:07:57 +0000
Subject: [PATCH 146/314] more refactoring, typedefs were introduced,
 DoxyCommandEnum moved to DoxygenParser

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13725 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Source/DoxygenTranslator/src/DoxygenEntity.h  |  18 ---
 .../DoxygenTranslator/src/DoxygenParser.cpp   |  89 ++++++-----
 Source/DoxygenTranslator/src/DoxygenParser.h  | 104 ++++++++-----
 .../src/JavaDocConverter.cpp                  | 146 +++++++++++++-----
 .../DoxygenTranslator/src/JavaDocConverter.h  |   2 +-
 5 files changed, 227 insertions(+), 132 deletions(-)

diff --git a/Source/DoxygenTranslator/src/DoxygenEntity.h b/Source/DoxygenTranslator/src/DoxygenEntity.h
index cf03240d2..d7df95e91 100644
--- a/Source/DoxygenTranslator/src/DoxygenEntity.h
+++ b/Source/DoxygenTranslator/src/DoxygenEntity.h
@@ -18,24 +18,6 @@
 #include <list>
 
 
-typedef enum {
-  SIMPLECOMMAND,
-  COMMANDWORD,
-  COMMANDLINE,
-  COMMANDPARAGRAPH,
-  COMMANDENDCOMMAND,
-  COMMANDWORDPARAGRAPH,
-  COMMANDWORDLINE,
-  COMMANDWORDOWORDWORD,
-  COMMANDOWORD,
-  COMMANDERRORTHROW,
-  COMMANDUNIQUE,
-  END_LINE,
-  PARAGRAPH_END,
-  PLAINSTRING,
-  COMMAND
-} DoxyCommandEnum;
-
 class DoxygenEntity;
 
 typedef std::list <DoxygenEntity> DoxygenEntityList;
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.cpp b/Source/DoxygenTranslator/src/DoxygenParser.cpp
index a66d66c28..fd1acdc78 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenParser.cpp
@@ -22,7 +22,7 @@ using std::cout;
 using std::endl;
 
 // Define static class members
-std::map<std::string, DoxyCommandEnum> DoxygenParser::doxygenCommands;
+DoxygenParser::DoxyCommandsMap DoxygenParser::doxygenCommands;
 std::set<std::string> DoxygenParser::doxygenSectionIndicators;
 
 const int TOKENSPERLINE = 8;    //change this to change the printing behaviour of the token list
@@ -110,16 +110,19 @@ void DoxygenParser::printTree(const DoxygenEntityList &rootList) {
 	}
 }
 
+
 int DoxygenParser::commandBelongs(const std::string &theCommand) {
 	std::string smallString = stringToLower(theCommand);
 	//cout << " Looking for command " << theCommand << endl;
-	std::map<std::string, DoxyCommandEnum>::iterator it;
-	it = doxygenCommands.find(smallString);
-	if (it!=doxygenCommands.end())
+	std::map<std::string, DoxyCommandEnum>::iterator it =
+	                                         doxygenCommands.find(smallString);
+	if (it != doxygenCommands.end()) {
 		return it->second;
+	}
 	return 0;
 }
 
+
 std::string DoxygenParser::getNextWord(const TokenList &tokList) {
 	// MK Token nextToken = tokList.peek();
     if (m_tokenListIt == m_tokenList.end()) {
@@ -703,7 +706,7 @@ int DoxygenParser::addCommandUnique(const std::string &theCommand,
 		TokenListCIt endCommand = tokList.end();
 
 		// go through the commands and find closing endif or else or elseif
-		for (TokenListCIt it = m_tokenListIt; it!=tokList.end(); it++) {
+		for (TokenListCIt it = m_tokenListIt; it != tokList.end(); it++) {
 			if (it->m_tokenType == COMMAND) {
 				if (it->m_tokenString == "if" || it->m_tokenString == "ifnot")
 					nestedCounter++;
@@ -742,9 +745,10 @@ int DoxygenParser::addCommand(const std::string &commandString,
                                   const TokenList &tokList,
                                   DoxygenEntityList &doxyList) {
 
-	std::string theCommand = stringToLower(commandString);
+	string theCommand = stringToLower(commandString);
+
 	if (theCommand == "plainstd::string") {
-		std::string nextPhrase = getStringTilCommand(tokList);
+		string nextPhrase = getStringTilCommand(tokList);
 		if (noisy)
 			cout << "Parsing plain std::string :" << nextPhrase << endl;
 		doxyList.push_back(DoxygenEntity("plainstd::string", nextPhrase));
@@ -778,9 +782,12 @@ int DoxygenParser::addCommand(const std::string &commandString,
 }
 
 
+/**
+ * This method converts TokenList to DoxygenEntryList.
+ */
 DoxygenEntityList DoxygenParser::parse(TokenListCIt endParsingIndex,
-                                                       const TokenList &tokList,
-                                                       bool root) {
+                                          const TokenList &tokList,
+                                          bool root) {
 	// if we are root, than any strings should be added as 'partofdescription', else as 'plainstd::string'
 	std::string currPlainstringCommandType = root ? "partofdescription" : "plainstd::string";
 	DoxygenEntityList aNewList;
@@ -812,22 +819,30 @@ DoxygenEntityList DoxygenParser::parse(TokenListCIt endParsingIndex,
 }
 
 
-DoxygenEntityList DoxygenParser::createTree(const std::string &doxygenBlob, const std::string &fileName, int lineNumber) {
-	TokenList tokList = tokenizeDoxygenComment(doxygenBlob, fileName, lineNumber);
-	if (noisy) {
-		cout << "---TOKEN LIST---" << endl;
-		printList();
-	}
-	DoxygenEntityList rootList;
-	rootList = parse(tokList.end(), tokList, true);
-	if (noisy) {
-		cout << "PARSED LIST" << endl;
-		printTree(rootList);
-	}
-	return rootList;
+DoxygenEntityList DoxygenParser::createTree(const std::string &doxygenBlob,
+                                               const std::string &fileName,
+                                               int lineNumber) {
+
+  TokenList tokList = tokenizeDoxygenComment(doxygenBlob, fileName, lineNumber);
+  if (noisy) {
+    cout << "---TOKEN LIST---" << endl;
+    printList();
+  }
+
+  DoxygenEntityList rootList = parse(tokList.end(), tokList, true);
+
+  if (noisy) {
+    cout << "PARSED LIST" << endl;
+    printTree(rootList);
+  }
+  return rootList;
 }
 
 
+/**
+ * This is one of the most important methods - it breaks the original
+ * doxygen comment into tokens.
+ */
 DoxygenParser::TokenList DoxygenParser::tokenizeDoxygenComment(const std::string &doxygenComment,
                                                                       const std::string &fileName,
                                                                       int fileLine) {
@@ -842,13 +857,17 @@ DoxygenParser::TokenList DoxygenParser::tokenizeDoxygenComment(const std::string
   while (true) {
     isPlainString = false;
     pos = doxygenComment.find_first_of("\\@\t\n ", lastPos);
-    if (pos == string::npos)
+    if (pos == string::npos) {
       pos = doxygenComment.size();
+    }
 
     currentWord = doxygenComment.substr(lastPos, pos-lastPos);
-    if (prevChar == '\n')
+
+    if (prevChar == '\n') {
+
       tokList.push_back(Token(END_LINE, "\n"));
-    else if (prevChar == '\\' || prevChar == '@') {
+
+    } else if (prevChar == '\\' || prevChar == '@') {
       // it's a doxygen command
       // hack to get commands like \\ or \@ or @\ or @@
       if (doxygenComment[pos] == '@' || doxygenComment[pos] == '\\') {
@@ -871,22 +890,24 @@ DoxygenParser::TokenList DoxygenParser::tokenizeDoxygenComment(const std::string
           // unknown commands are not translated - treated as literal string
           tokList.push_back(Token(PLAINSTRING, currentWord));
       }
-    }
-    else if (currentWord.size() && (currentWord[0] == '!' || currentWord[0] == '*' || currentWord[0] == '/')) {
+
+    } else if (currentWord.size() && (currentWord[0] == '!' || currentWord[0] == '*' || currentWord[0] == '/')) {
+
       // check if it's one of the '!!!', '***', '///' of any length
       char c = currentWord[0];
       isPlainString = false;
-      for (size_t i=0; i<currentWord.size(); i++)
+      for (size_t i = 0; i < currentWord.size(); i++)
         if (currentWord[i] != c) {
           isPlainString = true;
           break;
         }
-    }
-    else
+    } else {
       isPlainString = true;
+    }
 
-    if (isPlainString && currentWord.size())
+    if (isPlainString && currentWord.size()) {
       tokList.push_back(Token(PLAINSTRING, currentWord));
+    }
 
     prevChar = doxygenComment[pos];
     lastPos = pos + 1;
@@ -934,8 +955,6 @@ void DoxygenParser::printListError(int warningType,
     }
   }
 
-  Swig_warning(warningType, m_fileName.c_str(),
-                 curLine,
-                 "Doxygen parser warning: %s. \n",
-                 message.c_str());
+  Swig_warning(warningType, m_fileName.c_str(), curLine,
+                 "Doxygen parser warning: %s. \n", message.c_str());
 }
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.h b/Source/DoxygenTranslator/src/DoxygenParser.h
index d015c1896..e5fc5c06d 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.h
+++ b/Source/DoxygenTranslator/src/DoxygenParser.h
@@ -20,55 +20,79 @@
 class DoxygenParser {
 private:
 
-    /** This class contains parts of Doxygen comment as a token. */
-    class Token {
-    public:
-        DoxyCommandEnum m_tokenType;
-        std::string m_tokenString;		/* the data , such as param for @param */
-
-        Token(DoxyCommandEnum tType, std::string tString) :
-            m_tokenType(tType),
-            m_tokenString(tString) {}
-
-        std::string toString() const {
-
-            switch (m_tokenType) {
-            case END_LINE:
-                return "{END OF LINE}";
-            case PARAGRAPH_END:
-                return "{END OF PARAGRAPH}";
-            case PLAINSTRING:
-                return "{PLAINSTRING :" + m_tokenString + "}";
-            case COMMAND:
-                return "{COMMAND : " + m_tokenString + "}";
-            default:
-                return "";
-            }
-        }
-    };
+  typedef enum {
+    SIMPLECOMMAND,
+    COMMANDWORD,
+    COMMANDLINE,
+    COMMANDPARAGRAPH,
+    COMMANDENDCOMMAND,
+    COMMANDWORDPARAGRAPH,
+    COMMANDWORDLINE,
+    COMMANDWORDOWORDWORD,
+    COMMANDOWORD,
+    COMMANDERRORTHROW,
+    COMMANDUNIQUE,
+    END_LINE,
+    PARAGRAPH_END,
+    PLAINSTRING,
+    COMMAND
+  } DoxyCommandEnum;
 
 
-    typedef std::list<Token> TokenList;
-    typedef TokenList::const_iterator TokenListCIt;
-    typedef TokenList::iterator TokenListIt;
 
-    TokenList m_tokenList;
-    TokenListCIt m_tokenListIt;
-    std::string m_fileName;
-    int m_fileLineNo;
+  /** This class contains parts of Doxygen comment as a token. */
+  class Token {
+  public:
+    DoxyCommandEnum m_tokenType;
+    std::string m_tokenString;		/* the data , such as param for @param */
+
+    Token(DoxyCommandEnum tType, std::string tString) :
+      m_tokenType(tType),
+      m_tokenString(tString) {}
+
+    std::string toString() const {
+
+      switch (m_tokenType) {
+      case END_LINE:
+        return "{END OF LINE}";
+      case PARAGRAPH_END:
+        return "{END OF PARAGRAPH}";
+      case PLAINSTRING:
+        return "{PLAINSTRING :" + m_tokenString + "}";
+      case COMMAND:
+        return "{COMMAND : " + m_tokenString + "}";
+      default:
+        return "";
+      }
+    }
+  };
+
+
+  typedef std::list<Token> TokenList;
+  typedef TokenList::const_iterator TokenListCIt;
+  typedef TokenList::iterator TokenListIt;
+
+  TokenList m_tokenList;
+  TokenListCIt m_tokenListIt;
+
+  typedef std::map<std::string, DoxyCommandEnum> DoxyCommandsMap;
+  typedef DoxyCommandsMap::iterator DoxyCommandsMapIt;
+
+  /*
+   * Map of Doxygen commands to determine if a string is a
+   * command and how it needs to be parsed
+   */
+  static DoxyCommandsMap doxygenCommands;
+  static std::set<std::string> doxygenSectionIndicators;
+
+  std::string m_fileName;
+  int m_fileLineNo;
 
     /*
      * Whether to print lots of debug info during parsing
      */
     bool noisy;
 
-    /*
-     * Map of Doxygen commands to determine if a string is a
-     * command and how it needs to be parsed
-     */
-    static std::map<std::string, DoxyCommandEnum> doxygenCommands;
-    static std::set<std::string> doxygenSectionIndicators;
-
   /*
    *Changes a std::string to all lower case
    */
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.cpp b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
index 171ef4dc7..2c2aa8aa0 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
@@ -120,9 +120,19 @@ JavaDocConverter::JavaDocConverter(bool debugTranslator, bool debugParser)
   fillStaticTables();
 }
 
-std::string JavaDocConverter::formatCommand(std::string unformattedLine, int indent) {
+
+/**
+ * Formats comment lines by inserting '\n *' at to long lines and tabs for
+ * indent. Currently it is disabled, which means original comment format is
+ * preserved. Experience shows, that this is usually better than breaking
+ * lines automatically, especially because original line endings are not removed,
+ * which results in short lines. To be useful, this function should have much
+ * better algorithm.
+ */
+std::string JavaDocConverter::formatCommand(std::string unformattedLine,
+                                                int indent) {
   std::string formattedLines;
-  return unformattedLine;
+  return unformattedLine;  // currently disabled
   int lastPosition = 0;
   int i = 0;
   int isFirstLine = 1;
@@ -160,49 +170,70 @@ std::string JavaDocConverter::formatCommand(std::string unformattedLine, int ind
   return formattedLines;
 }
 
+
+/**
+ * Returns true, if the given parameter exists in the current node. If feature
+ * 'doxygen:nostripparams' is set, then this method always returns true.
+ */
 bool JavaDocConverter::paramExists(std::string param) {
-  if (GetFlag(currentNode, "feature:doxygen:nostripparams"))
+
+  if (GetFlag(currentNode, "feature:doxygen:nostripparams")) {
     return true;
+  }
+
   ParmList *plist = CopyParmList(Getattr(currentNode, "parms"));
-  Parm *p = NULL;
-  for (p = plist; p;) {
-    if (Getattr(p, "name") && Char(Getattr(p, "name")) == param)
+
+  for (Parm *p = plist; p;) {
+
+    if (Getattr(p, "name") && Char(Getattr(p, "name")) == param) {
       return true;
-    /*
-     * doesn't seem to work always: in some cases (especially for 'self' parameters)
+    }
+    /* doesn't seem to work always: in some cases (especially for 'self' parameters)
      * tmap:in is present, but tmap:in:next is not and so this code skips all the parameters
      */
     //p = Getattr(p, "tmap:in") ? Getattr(p, "tmap:in:next") : nextSibling(p);
     p = nextSibling(p);
   }
+
   Delete(plist);
+
   return false;
 }
 
-std::string JavaDocConverter::translateSubtree(DoxygenEntity & doxygenEntity) {
+
+std::string JavaDocConverter::translateSubtree(DoxygenEntity &doxygenEntity) {
   std::string translatedComment;
   
-  if (doxygenEntity.isLeaf)
+  if (doxygenEntity.isLeaf) {
     return translatedComment;
+  }
   
-  std::list < DoxygenEntity >::iterator p = doxygenEntity.entityList.begin();
-  while (p != doxygenEntity.entityList.end()) {
+  for (DoxygenEntityListIt p = doxygenEntity.entityList.begin();
+       p != doxygenEntity.entityList.end(); p++) {
+
     translateEntity(*p, translatedComment);
     translateSubtree(*p);
-    p++;
   }
   
   return translatedComment;
 }
 
-void JavaDocConverter::translateEntity(DoxygenEntity& tag, std::string& translatedComment) {
-  // check if we have needed handler and call it
+
+/**
+ * Checks if a handler for the given tag exists, and calls it.
+ */
+void JavaDocConverter::translateEntity(DoxygenEntity &tag,
+                                            std::string &translatedComment) {
+
   std::map<std::string, std::pair<tagHandler, std::string > >::iterator it;
   it = tagHandlers.find(tag.typeOfEntity);
-  if (it!=tagHandlers.end())
+
+  if (it != tagHandlers.end()) {
     (this->*(it->second.first))(tag, translatedComment, it->second.second);
+  }
 }
 
+
 void JavaDocConverter::handleTagHtml(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
   if (tag.entityList.size()) { // do not include empty tags
     std::string tagData = translateSubtree(tag);
@@ -214,9 +245,13 @@ void JavaDocConverter::handleTagHtml(DoxygenEntity& tag, std::string& translated
       translatedComment += "<" + arg + ">" + translateSubtree(tag) + "</" + arg + "> ";
   }
 }
+
+
 void JavaDocConverter::handleNewLine(DoxygenEntity&, std::string& translatedComment, std::string&) {
   translatedComment += "\n * ";
 }
+
+
 void JavaDocConverter::handleTagChar(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
   // escape it if we need to, else just print
   if (arg.size())
@@ -225,26 +260,35 @@ void JavaDocConverter::handleTagChar(DoxygenEntity& tag, std::string& translated
     translatedComment += tag.typeOfEntity;
   translatedComment += " ";
 }
+
+// handles tags which are the same in Doxygen and Javadoc.
 void JavaDocConverter::handleTagSame(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
   if (arg.size())
     tag.typeOfEntity = arg;
   translatedComment += formatCommand(std::string("@" + tag.typeOfEntity + " " + translateSubtree(tag)), 2);
 }
+
+
 void JavaDocConverter::handleParagraph(DoxygenEntity& tag, std::string& translatedComment, std::string&) {
   translatedComment += formatCommand(translateSubtree(tag), 0);
 }
+
+
 void JavaDocConverter::handlePlainString(DoxygenEntity& tag, std::string& translatedComment, std::string&) {
   translatedComment += tag.data;
   if (tag.data.size() && tag.data[tag.data.size()-1] != ' ')
   	translatedComment += " ";
 }
 
+
 void JavaDocConverter::handleTagExtended(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
   std::string dummy;
   translatedComment += "{@" + arg + " ";
   handleParagraph(tag, translatedComment, dummy);
   translatedComment += "}";
 }
+
+
 void JavaDocConverter::handleTagIf(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
   std::string dummy;
   translatedComment += arg;
@@ -254,11 +298,15 @@ void JavaDocConverter::handleTagIf(DoxygenEntity& tag, std::string& translatedCo
     translatedComment += " {" + translateSubtree(tag) + "}";
   }
 }
+
+
 void JavaDocConverter::handleTagMessage(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
   std::string dummy;
   translatedComment += formatCommand(arg, 0);
   handleParagraph(tag, translatedComment, dummy);
 }
+
+
 void JavaDocConverter::handleTagImage(DoxygenEntity& tag, std::string& translatedComment, std::string&) {
   if (tag.entityList.size() < 2)
     return;
@@ -282,6 +330,8 @@ void JavaDocConverter::handleTagImage(DoxygenEntity& tag, std::string& translate
     translatedComment += " alt=\"" + title +"\"";
   translatedComment += " />";
 }
+
+
 void JavaDocConverter::handleTagPar(DoxygenEntity& tag, std::string& translatedComment, std::string&) {
   std::string dummy;
   translatedComment += "<p";
@@ -294,6 +344,7 @@ void JavaDocConverter::handleTagPar(DoxygenEntity& tag, std::string& translatedC
   translatedComment += "</p>";
 }
 
+
 void JavaDocConverter::handleTagParam(DoxygenEntity& tag, std::string& translatedComment, std::string&) {
   std::string dummy;
   if (!tag.entityList.size())
@@ -307,6 +358,7 @@ void JavaDocConverter::handleTagParam(DoxygenEntity& tag, std::string& translate
   handleParagraph(tag, translatedComment, dummy);
 }
 
+
 string JavaDocConverter::convertLink(string linkObject) {
   if (GetFlag(currentNode, "feature:doxygen:nolinktranslate"))
     return linkObject;
@@ -394,6 +446,7 @@ string JavaDocConverter::convertLink(string linkObject) {
   return linkObject;
 }
 
+
 void JavaDocConverter::handleTagLink(DoxygenEntity& tag, std::string& translatedComment, std::string&) {
   std::string dummy;
   if (!tag.entityList.size())
@@ -410,6 +463,7 @@ void JavaDocConverter::handleTagLink(DoxygenEntity& tag, std::string& translated
   translatedComment += "}";
 }
 
+
 void JavaDocConverter::handleTagSee(DoxygenEntity& tag, std::string& translatedComment, std::string&) {
   std::string dummy;
   if (!tag.entityList.size())
@@ -429,33 +483,41 @@ void JavaDocConverter::handleTagSee(DoxygenEntity& tag, std::string& translatedC
   }
 }
 
-int JavaDocConverter::cleanUpTree(DoxygenEntity &root, int level)
-{
-  // this function should move all endlines out of the child entities
-  // for example:
-  // root
-  // -param
-  // --paramText
-  // --endline
-  // should be turned to
-  // root
-  // -param
-  // --paramText
-  // -endline
 
-  std::list < DoxygenEntity >::iterator it = root.entityList.begin();
+/* This function moves all endlines at the end of child entities
+ * out of the child entities to the parent.
+ * For example, entity tree:
+
+   -root
+    |-param
+      |-paramText
+      |-endline
+
+   should be turned to
+
+   -root
+    |-param
+      |-paramText
+    |-endline
+ *
+ */
+int JavaDocConverter::shiftEndlinesUpTree(DoxygenEntity &root, int level)
+{
+  DoxygenEntityListIt it = root.entityList.begin();
   while (it != root.entityList.end()) {
     // remove endlines
-    int ret = cleanUpTree(*it, level + 1);
+    int ret = shiftEndlinesUpTree(*it, level + 1);
     // insert them after this element
     it++;
-    for (int i=0; i<ret; i++)
+    for (int i = 0; i < ret; i++) {
       root.entityList.insert(it, DoxygenEntity("plainstd::endl"));
+    }
   }
 
   // continue only if we are not root
-  if (!level)
+  if (!level) {
     return 0;
+  }
 
   int removedCount = 0;
   while (!root.entityList.empty()  &&  root.entityList.rbegin()->typeOfEntity == "plainstd::endl") {
@@ -465,6 +527,7 @@ int JavaDocConverter::cleanUpTree(DoxygenEntity &root, int level)
   return removedCount;
 }
 
+
 String *JavaDocConverter::makeDocumentation(Node *node) {
 
   String *documentation = getDoxygenComment(node);
@@ -483,10 +546,11 @@ String *JavaDocConverter::makeDocumentation(Node *node) {
     return comment;
   }
 
-  std::list < DoxygenEntity > entityList = parser.createTree(Char(documentation), Char(Getfile(documentation)), Getline(documentation));
+  DoxygenEntityList entityList = parser.createTree(Char(documentation),
+                                                   Char(Getfile(documentation)),
+                                                   Getline(documentation));
 
   // entityList.sort(CompareDoxygenEntities()); sorting currently not used,
-  // see CompareDoxygenEntities::operator() in DoxygenEntity.cpp
 
   if (debug) {
     std::cout << "---RESORTED LIST---" << std::endl;
@@ -501,13 +565,19 @@ String *JavaDocConverter::makeDocumentation(Node *node) {
 
   DoxygenEntity root("root", entityList);
 
-  cleanUpTree(root);
+  shiftEndlinesUpTree(root);
+
   // strip endlines at the beginning
-  while (root.entityList.begin()->typeOfEntity == "plainstd::endl")
+  while (!root.entityList.empty()  &&
+          root.entityList.begin()->typeOfEntity == "plainstd::endl") {
     root.entityList.pop_front();
+  }
+
   // and at the end
-  while (root.entityList.rbegin()->typeOfEntity == "plainstd::endl")
+  while (!root.entityList.empty()  &&
+          root.entityList.rbegin()->typeOfEntity == "plainstd::endl") {
     root.entityList.pop_back();
+  }
 
   javaDocString += translateSubtree(root);
 
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.h b/Source/DoxygenTranslator/src/JavaDocConverter.h
index cad228038..1fab5e63b 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.h
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.h
@@ -42,7 +42,7 @@ protected:
   /*
    * Fix all endlines location, etc
    */
-  int cleanUpTree(DoxygenEntity &root, int level = 0);
+  int shiftEndlinesUpTree(DoxygenEntity &root, int level = 0);
   
   /*
    * Convert params in link-objects and references

From af74b4f96a244780b7c365b1bc7ff87665e3f0eb Mon Sep 17 00:00:00 2001
From: Marko Klopcic <marko.klopcic@isystem.si>
Date: Mon, 27 Aug 2012 20:25:00 +0000
Subject: [PATCH 147/314] renamed test case

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13726 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 ...constructs.i => doxygen_misc_constructs.i} |  0
 ...ava => doxygen_misc_constructs_runme.java} | 28 ++++++------
 ...me.py => doxygen_misc_constructs_runme.py} |  0
 .../DoxygenTranslator/src/DoxygenParser.cpp   | 45 ++++++++-----------
 Source/DoxygenTranslator/src/DoxygenParser.h  |  1 -
 5 files changed, 32 insertions(+), 42 deletions(-)
 rename Examples/test-suite/{doxygen_tricky_constructs.i => doxygen_misc_constructs.i} (100%)
 rename Examples/test-suite/java/{doxygen_tricky_constructs_runme.java => doxygen_misc_constructs_runme.java} (72%)
 rename Examples/test-suite/python/{doxygen_tricky_constructs_runme.py => doxygen_misc_constructs_runme.py} (100%)

diff --git a/Examples/test-suite/doxygen_tricky_constructs.i b/Examples/test-suite/doxygen_misc_constructs.i
similarity index 100%
rename from Examples/test-suite/doxygen_tricky_constructs.i
rename to Examples/test-suite/doxygen_misc_constructs.i
diff --git a/Examples/test-suite/java/doxygen_tricky_constructs_runme.java b/Examples/test-suite/java/doxygen_misc_constructs_runme.java
similarity index 72%
rename from Examples/test-suite/java/doxygen_tricky_constructs_runme.java
rename to Examples/test-suite/java/doxygen_misc_constructs_runme.java
index bb4f69839..696f8b609 100644
--- a/Examples/test-suite/java/doxygen_tricky_constructs_runme.java
+++ b/Examples/test-suite/java/doxygen_misc_constructs_runme.java
@@ -1,12 +1,12 @@
 
-import doxygen_tricky_constructs.*;
+import doxygen_misc_constructs.*;
 import com.sun.javadoc.*;
 import java.util.HashMap;
 
-public class doxygen_tricky_constructs_runme {
+public class doxygen_misc_constructs_runme {
   static {
     try {
-      System.loadLibrary("doxygen_tricky_constructs");
+      System.loadLibrary("doxygen_misc_constructs");
     } catch (UnsatisfiedLinkError e) {
       System.err.println("Native code library failed to load. See the chapter on Dynamic Linking Problems in the SWIG Java documentation for help.\n" + e);
       System.exit(1);
@@ -20,18 +20,18 @@ public class doxygen_tricky_constructs_runme {
       and calls the start() method of that class with parsed information.
     */
 	commentParser parser = new commentParser();
-    com.sun.tools.javadoc.Main.execute("doxygen_tricky_constructs runtime test",
-	"commentParser", new String[]{"-quiet", "doxygen_tricky_constructs"});
+    com.sun.tools.javadoc.Main.execute("doxygen_misc_constructs runtime test",
+	"commentParser", new String[]{"-quiet", "doxygen_misc_constructs"});
 
     HashMap<String, String> wantedComments = new HashMap<String, String>();
     
-    wantedComments.put("doxygen_tricky_constructs.doxygen_tricky_constructs.getConnection()",
+    wantedComments.put("doxygen_misc_constructs.doxygen_misc_constructs.getConnection()",
     		" \n" +
     		" \n" +
     		" This class manages connection. \n" +
     		" \n" +
     		"");
-    wantedComments.put("doxygen_tricky_constructs.doxygen_tricky_constructs.getAddress(doxygen_tricky_constructs.SWIGTYPE_p_int, int)",
+    wantedComments.put("doxygen_misc_constructs.doxygen_misc_constructs.getAddress(doxygen_misc_constructs.SWIGTYPE_p_int, int)",
     		" Returns address of file line. \n" +
     		" \n" +
     		" @param fileName name of the file, where the source line is located \n" +
@@ -39,7 +39,7 @@ public class doxygen_tricky_constructs_runme {
     		" {@link Connection::getId()  }<br> \n" +
     		" \n" +
     		"");
-    wantedComments.put("doxygen_tricky_constructs.doxygen_tricky_constructs.getG_zipCode()",
+    wantedComments.put("doxygen_misc_constructs.doxygen_misc_constructs.getG_zipCode()",
     		" Tag endlink must be recognized also when it is the last token \n" +
     		" in the commment. \n" +
     		" \n" +
@@ -47,7 +47,7 @@ public class doxygen_tricky_constructs_runme {
     		" {@link debugIdeTraceProfilerCoverageSample.py Python example.  }\n" +
     		" \n" +
     		"");
-    wantedComments.put("doxygen_tricky_constructs.doxygen_tricky_constructs.setG_zipCode(int)",
+    wantedComments.put("doxygen_misc_constructs.doxygen_misc_constructs.setG_zipCode(int)",
     		" Tag endlink must be recognized also when it is the last token \n" +
     		" in the commment. \n" +
     		" \n" +
@@ -55,19 +55,19 @@ public class doxygen_tricky_constructs_runme {
     		" {@link debugIdeTraceProfilerCoverageSample.py Python example.  }\n" +
     		" \n" +
     		"");
-    wantedComments.put("doxygen_tricky_constructs.doxygen_tricky_constructs.getG_counter()",
+    wantedComments.put("doxygen_misc_constructs.doxygen_misc_constructs.getG_counter()",
     		" Tag endlink must be recognized also when followed by nonspace charater. \n" +
     		" \n" +
     		" {@link Connection::getId()  }<br> \n" +
     		" \n" +
     		"");
-    wantedComments.put("doxygen_tricky_constructs.doxygen_tricky_constructs.waitTime(int)",
+    wantedComments.put("doxygen_misc_constructs.doxygen_misc_constructs.waitTime(int)",
     		" Determines how long the <code>isystem.connect</code> should wait for running \n" +
     		" instances to respond. Only one of <code>lfWaitXXX</code> flags from IConnect::ELaunchFlags \n" +
     		" may be specified. \n" +
     		" \n" +
     		"");
-    wantedComments.put("doxygen_tricky_constructs.CConnectionConfig",
+    wantedComments.put("doxygen_misc_constructs.CConnectionConfig",
     		" This class contains information for connection to winIDEA. Its methods \n" +
     		" return reference to self, so we can use it like this: \n" +
     		" <pre> \n" +
@@ -82,7 +82,7 @@ public class doxygen_tricky_constructs_runme {
     		" {@link advancedWinIDEALaunching.py Python example.  }<br> \n" +
     		" \n" +
     		"");
-    wantedComments.put("doxygen_tricky_constructs.doxygen_tricky_constructs.getAddress(doxygen_tricky_constructs.SWIGTYPE_p_int, int, boolean)",
+    wantedComments.put("doxygen_misc_constructs.doxygen_misc_constructs.getAddress(doxygen_misc_constructs.SWIGTYPE_p_int, int, boolean)",
     		" Returns address of file line. \n" +
     		" \n" +
     		" @param fileName name of the file, where the source line is located \n" +
@@ -92,7 +92,7 @@ public class doxygen_tricky_constructs_runme {
     		" {@link Connection::getId()  }<br> \n" +
     		" \n" +
     		"");
-    wantedComments.put("doxygen_tricky_constructs.doxygen_tricky_constructs.setG_counter(char)",
+    wantedComments.put("doxygen_misc_constructs.doxygen_misc_constructs.setG_counter(char)",
     		" Tag endlink must be recognized also when followed by nonspace charater. \n" +
     		" \n" +
     		" {@link Connection::getId()  }<br> \n" +
diff --git a/Examples/test-suite/python/doxygen_tricky_constructs_runme.py b/Examples/test-suite/python/doxygen_misc_constructs_runme.py
similarity index 100%
rename from Examples/test-suite/python/doxygen_tricky_constructs_runme.py
rename to Examples/test-suite/python/doxygen_misc_constructs_runme.py
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.cpp b/Source/DoxygenTranslator/src/DoxygenParser.cpp
index fd1acdc78..346e94cc2 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenParser.cpp
@@ -103,23 +103,24 @@ bool DoxygenParser::isSectionIndicator(const std::string &smallString) {
 
 
 void DoxygenParser::printTree(const DoxygenEntityList &rootList) {
-	DoxygenEntityList::const_iterator p = rootList.begin();
-	while (p != rootList.end()) {
-		(*p).printEntity(0);
-		p++;
-	}
+  DoxygenEntityList::const_iterator p = rootList.begin();
+  while (p != rootList.end()) {
+    (*p).printEntity(0);
+    p++;
+  }
 }
 
 
 int DoxygenParser::commandBelongs(const std::string &theCommand) {
-	std::string smallString = stringToLower(theCommand);
-	//cout << " Looking for command " << theCommand << endl;
-	std::map<std::string, DoxyCommandEnum>::iterator it =
-	                                         doxygenCommands.find(smallString);
-	if (it != doxygenCommands.end()) {
-		return it->second;
-	}
-	return 0;
+
+  std::string smallString = stringToLower(theCommand);
+  //cout << " Looking for command " << theCommand << endl;
+  DoxyCommandsMapIt it = doxygenCommands.find(smallString);
+
+  if (it != doxygenCommands.end()) {
+    return it->second;
+  }
+  return 0;
 }
 
 
@@ -922,22 +923,11 @@ DoxygenParser::TokenList DoxygenParser::tokenizeDoxygenComment(const std::string
 
 
 void DoxygenParser::printList() {
-  TokenListIt p = m_tokenList.begin();
-  int i = 1;
-  int b = 0;
-  while (p != m_tokenList.end()) {
-    cout << (*p).toString() << " ";
-    b = i % TOKENSPERLINE;
-    if (b == 0)
-      cout << endl;
-    p++;
-    i++;
-  }
-
-  TokenListCIt startIt = m_tokenList.begin();
 
   int tokNo = 0;
-  for (TokenListCIt it = startIt; it != m_tokenList.end(); it++, tokNo++) {
+  for (TokenListCIt it = m_tokenList.begin(); it != m_tokenList.end();
+                                                              it++, tokNo++) {
+
     cout << it->toString() << " ";
 
     if ((tokNo % TOKENSPERLINE) == 0) {
@@ -946,6 +936,7 @@ void DoxygenParser::printList() {
   }
 }
 
+
 void DoxygenParser::printListError(int warningType,
                                         const std::string &message) {
   int curLine = m_fileLineNo;
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.h b/Source/DoxygenTranslator/src/DoxygenParser.h
index e5fc5c06d..6e2c539ce 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.h
+++ b/Source/DoxygenTranslator/src/DoxygenParser.h
@@ -39,7 +39,6 @@ private:
   } DoxyCommandEnum;
 
 
-
   /** This class contains parts of Doxygen comment as a token. */
   class Token {
   public:

From faec66879a1852c6adc8e0061f770c9e3ca3951f Mon Sep 17 00:00:00 2001
From: Marko Klopcic <marko.klopcic@isystem.si>
Date: Tue, 28 Aug 2012 19:50:50 +0000
Subject: [PATCH 148/314] fixed doxygen tests after rename

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13727 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Examples/test-suite/common.mk                 | 2 +-
 Examples/test-suite/doxygen_misc_constructs.i | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/Examples/test-suite/common.mk b/Examples/test-suite/common.mk
index 729d04d66..f987a11d4 100644
--- a/Examples/test-suite/common.mk
+++ b/Examples/test-suite/common.mk
@@ -193,7 +193,7 @@ CPP_TEST_CASES += \
 	doxygen_translate \
 	doxygen_translate_all_tags \
 	doxygen_translate_links \
-	doxygen_tricky_constructs \
+	doxygen_misc_constructs \
 	dynamic_cast \
 	empty \
 	enum_rename \
diff --git a/Examples/test-suite/doxygen_misc_constructs.i b/Examples/test-suite/doxygen_misc_constructs.i
index 44cbb0426..03abbb116 100644
--- a/Examples/test-suite/doxygen_misc_constructs.i
+++ b/Examples/test-suite/doxygen_misc_constructs.i
@@ -1,7 +1,7 @@
 # This file contains tests for situations, which do not normally
 # appear in the code, but must neverthless be handled correctly.
 
-%module doxygen_tricky_constructs
+%module doxygen_misc_constructs
 
 %inline %{
 

From e62580acb82bc63e77bec251a43e09b3a9c99469 Mon Sep 17 00:00:00 2001
From: Marko Klopcic <marko.klopcic@isystem.si>
Date: Tue, 28 Aug 2012 20:59:32 +0000
Subject: [PATCH 149/314] fixed doxy documentation (also shortened lines),
 added test for discovered bug reltaed to nested enums

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13728 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Doc/Manual/Doxygen.html                       | 201 ++++++++++++------
 Examples/test-suite/doxygen_misc_constructs.i |  48 ++---
 .../java/doxygen_misc_constructs_runme.java   |  22 +-
 3 files changed, 181 insertions(+), 90 deletions(-)

diff --git a/Doc/Manual/Doxygen.html b/Doc/Manual/Doxygen.html
index d21c12d7e..d71c6dcba 100644
--- a/Doc/Manual/Doxygen.html
+++ b/Doc/Manual/Doxygen.html
@@ -43,33 +43,53 @@
 
 
 <p>
-This chapter describes SWIG's support for translating Doxygen comments found in interface and header files into a target language's normal documentation language.
-Currently only JavaDoc and PythonDoc is supported.
+This chapter describes SWIG's support for translating Doxygen comments
+found in interface and header files into a target language's normal
+documentation language.  Currently only JavaDoc and PythonDoc is
+supported.
 </p>
 
 <H2><a name="Doxygen_translation_overview"></a>39.1 Doxygen Translation Overview</H2>
 
 
 <p>
-The Doxygen Translation Module of SWIG is an ongoing effort from a <A HREF ="http://code.google.com/soc/2008/">Google Summer of Code</A> proposal from Summer 2008.
-It adds an extra layer of functionality to SWIG, allowing automated translation of <A HREF= "http://www.stack.nl/~dimitri/doxygen/">Doxygen</A> formatted comments from input files into a documentation language more suited for the target language.
-Currently this module only translates into JavaDoc and PythonDoc for the SWIG Java and Python Modules, but other extensions are to be added in time.
+The Doxygen Translation Module of SWIG is an ongoing effort from
+a <A HREF ="http://code.google.com/soc/2008/">Google Summer of
+Code</A> proposal from Summer 2008.  It adds an extra layer of
+functionality to SWIG, allowing automated translation of <A HREF=
+"http://www.stack.nl/~dimitri/doxygen/">Doxygen</A> formatted comments
+from input files into a documentation language more suited for the
+target language.  Currently this module only translates into JavaDoc
+and PythonDoc for the SWIG Java and Python Modules, but other
+extensions are to be added in time.
 </p>
 
 <p>
-Questions about running SWIG are best answered in the <a href="SWIG.html#SWIG">SWIG Basics</a> chapter as well as the target language modules. (For now, only <A href = "Java.html">Java</A> and <A href = "Python.html">Python</A>).
-The behaviour of this functionality is wildly unpredictable if the interface file is not proper to begin with!
+Questions about running SWIG are best answered in
+the <a href="SWIG.html#SWIG">SWIG Basics</a> chapter as well as the
+target language modules. (For now, only <A href = "Java.html">Java</A>
+and <A href = "Python.html">Python</A>).  The behaviour of this
+functionality is wildly unpredictable if the interface file is not
+proper to begin with!
 </p>
 
 <H2><a name="Doxygen_file_preparation"></a>39.2 Preparations</H2>
 
 
 <p>
-To make use of the comment translation system, your documentation comments must be in properly formatted <A HREF= "http://www.stack.nl/~dimitri/doxygen/">Doxygen.</A> They can be present in your main interface file or any header file that it imports.
-It is advised that you are certain your comments compile properly with Doxygen before you try to translate them.
-Doxygen itself is a deeper tool and can provide you better feedback for correcting any syntax errors that may be present.
-Please look at Doxygen's <A HREF = "http://www.stack.nl/~dimitri/doxygen/docblocks.html"> Documenting the code</A> for proper specificatons for comment format.
-However, SWIG's Doxygen parser will still point you most of errors and warnings found in comments (like unterminated strings or missing ending tags).
+To make use of the comment translation system, your documentation
+comments must be in properly formatted <A HREF=
+"http://www.stack.nl/~dimitri/doxygen/">Doxygen.</A> They can be
+present in your main interface file or any header file that it
+imports.  It is advised that you are certain your comments compile
+properly with Doxygen before you try to translate them.  Doxygen
+itself is a deeper tool and can provide you better feedback for
+correcting any syntax errors that may be present.  Please look at
+Doxygen's <A HREF =
+"http://www.stack.nl/~dimitri/doxygen/docblocks.html"> Documenting the
+code</A> for proper specificatons for comment format.  However, SWIG's
+Doxygen parser will still point you most of errors and warnings found
+in comments (like unterminated strings or missing ending tags).
 </p>
 
 <div class="code"><pre>
@@ -81,8 +101,10 @@ class Shape {
 </pre></div>
 
 <p>
-Currently, the whole subset of Doxygen comment styles is supported (See <A HREF = "http://www.stack.nl/~dimitri/doxygen/docblocks.html"> Documenting the code</A>)
-Here they are:
+Currently, the whole subset of Doxygen comment styles is supported
+(See <A HREF = "http://www.stack.nl/~dimitri/doxygen/docblocks.html">
+Documenting the code</A>). Here they are:
+
 <div class="code"><pre>
 /**
  * JavaDoc style comment, multiline
@@ -99,15 +121,21 @@ Here they are:
 </p>
 
 <p>
-Also any of the above with '<' added after comment-starting symbol, like <i>/**&lt;, /*!&lt;, ///&lt;, </i> or <i> //!&lt;</i>
-will be treated as post-comment and will be assigned to the node before the comment.
+Also any of the above with '<' added after comment-starting symbol,
+like <i>/**&lt;, /*!&lt;, ///&lt;, </i> or <i> //!&lt;</i> will be
+treated as post-comment and will be assigned to the node before the
+comment.
 <br>
-Any number of '*' or '/' in Doxygen comment is considered to be a separator and is not included in final comment, so you may safely use
+
+Any number of '*' or '/' in Doxygen comment is considered to be a
+separator and is not included in final comment, so you may safely use
 comments like <i>/*********/</i> or <i>//////////</i>.
 </p>
 
 <p>
-Please note, as SWIG parses input file by itself with strict grammar, there is only a limited support for various cases of comment placement in the file.
+Please note, as SWIG parses input file by itself with strict grammar,
+there is only a limited support for various cases of comment placement
+in the file.
 <br>
 Comments can be placed before C\C++ expressions on separate lines:
 </p>
@@ -163,21 +191,28 @@ enum E_NUMBERS
 </pre></div>
 
 <p>
-Just remember, if SWIG shows syntax error parsing the file because of your comment, try to move it in some other, 'safer' place as desribed above.
+Just remember, if SWIG shows syntax error parsing the file because of
+your comment, try to move it in some other, 'safer' place as desribed
+above.
 <br>
-Also, currently only the comments directly before or after the nodes are supported. Doxygen structural comments are stripped out and not assigned to anything.
+Also, currently only the comments directly before or after the nodes
+are supported. Doxygen structural comments are stripped out and not
+assigned to anything.
 </p>
 <H3><a name="Doxygen_running_swig"></a>39.2.1 Enabling Doxygen Translation</H3>
 
 
 <p>
 There is a switch '-doxygen' in every module that supports converting
-documentation comments. Some comments in some target languages can be manually overriden by specific
-swig's features, like <i>feature:docstring</i> or <i>feature:autodoc</i>, in this cases Doxygen comments
-have lowest priority.
+documentation comments. Some comments in some target languages can be
+manually overriden by specific swig's features,
+like <i>feature:docstring</i> or <i>feature:autodoc</i>, in this cases
+Doxygen comments have lowest priority.
 </p>
 <p>
-If Doxygen parsing is switched off, then all the comments are stripped out in parser and all the resources used by comment parser and translator are freed.
+If Doxygen parsing is switched off, then all the comments are stripped
+out in parser and all the resources used by comment parser and
+translator are freed.
 </p>
 
 <H3><a name="Doxygen_additional_options"></a>39.2.2 Additional Commandline Options</H3>
@@ -191,7 +226,9 @@ ALSO TO BE ADDED (JavaDoc Autobrief?)
 
 
 <p>
-If translation is enabled, JavaDoc formatted comments should be automatically placed in the correct locations in the resulting module and proxy files.
+If translation is enabled, JavaDoc formatted comments should be
+automatically placed in the correct locations in the resulting module
+and proxy files.
 </p>
 
 <H3><a name="Doxygen_basic_example"></a>39.3.1 Basic Example</H3>
@@ -276,24 +313,35 @@ public class Shape {
 </pre></div>
 
 <p>
-The code Java-wise should be identical to what would have been generated without this feature enabled.
-When the Doxygen Translator Module encounters a comment it finds nothing useful in or cannot parse, it should not effect the functionality of the SWIG generated code.
+The code Java-wise should be identical to what would have been
+generated without this feature enabled.  When the Doxygen Translator
+Module encounters a comment it finds nothing useful in or cannot
+parse, it should not effect the functionality of the SWIG generated
+code.
 </p>
 
 <p>
-JavaDoc translator will handle most of the tags conversions (see the table below). It will also automatically translate link-objects
-params, in \see and \link...\endlink commands. For example, 'someFunction(std::string)' will be converted to 'someFunction(String)'.
-If this works not really good for you, or if you don't want such behaviour, you could turn this off by using 'doxygen:nolinktranslate'
-feature. Also all '\param' and '\tparam' commands are stripped out, if specified parameter is not present in function. Use 'doxygen:nostripparams'
-to avoid.
+JavaDoc translator will handle most of the tags conversions (see the
+table below). It will also automatically translate link-objects
+params, in \see and \link...\endlink commands. For example,
+'someFunction(std::string)' will be converted to
+'someFunction(String)'.  If this works not really good for you, or if
+you don't want such behaviour, you could turn this off by using
+'doxygen:nolinktranslate' feature. Also all '\param' and '\tparam'
+commands are stripped out, if specified parameter is not present in
+function. Use 'doxygen:nostripparams' to avoid.
 <br>
-If you intend to use resulting proxy files with Doxygen docs generator, rather than JavaDoc, you may want to turn off translator completely
-(doxygen:notranslate feature).
-Then SWIG will just copy the comments to the proxy file and reformat them if needed, but all the comment content will be left as is.
+If you intend to use resulting proxy files with Doxygen docs
+generator, rather than JavaDoc, you may want to turn off translator
+completely (doxygen:notranslate feature).  Then SWIG will just copy
+the comments to the proxy file and reformat them if needed, but all
+the comment content will be left as is.
 </p>
 
 <p>
-JavaDoc translator features summary (see <a href="Customization.html#Customization_features">%feature directives</a>):
+JavaDoc translator features summary
+(see <a href="Customization.html#Customization_features">%feature
+directives</a>):
 <br>
 
 </p>
@@ -579,9 +627,14 @@ Here is the list of all Doxygen tags and the description of how they are transla
 
 
 <p>
-Doxygen has a wealth of tags such as @latexonly that have no equivalent in JavaDoc.
-As a result several tags that have no translation (or particular use, such as some linking and section tags) are supressed with their content just printed out (if it has any sense, typically text content).
-If you are interested in more of the specifics of JavaDoc, please visit <A HREF="http://java.sun.com/j2se/javadoc/writingdoccomments/">How to Write Doc Comments for the Javadoc Tool.</A>
+Doxygen has a wealth of tags such as @latexonly that have no
+equivalent in JavaDoc.  As a result several tags that have no
+translation (or particular use, such as some linking and section tags)
+are supressed with their content just printed out (if it has any
+sense, typically text content).  If you are interested in more of the
+specifics of JavaDoc, please
+visit <A HREF="http://java.sun.com/j2se/javadoc/writingdoccomments/">How
+to Write Doc Comments for the Javadoc Tool.</A>
 <br>
 Here is the list of these tags:
 </p>
@@ -751,8 +804,11 @@ TO BE ADDED.
 
 
 <p>
-If translation is enabled, PyDoc formatted comments should be automatically placed in the correct locations in the resulting module and proxy files.
-The problem is that PyDoc has no tag mechanism like Doxygen or JavaDoc, so most of Doxygen commands are translated as English plaintext pieces.
+If translation is enabled, PyDoc formatted comments should be
+automatically placed in the correct locations in the resulting module
+and proxy files.  The problem is that PyDoc has no tag mechanism like
+Doxygen or JavaDoc, so most of Doxygen commands are translated as
+English plaintext pieces.
 </p>
 
 <H3><a name="Doxygen_python_basic_example"></a>39.4.1 Basic Example</H3>
@@ -822,18 +878,25 @@ class Shape(_object):
 </pre></div>
 
 <p>
-Currently Doxygen comments assigned to vars are not present in proxy file, so they have no comment translated for them.
+Currently Doxygen comments assigned to vars are not present in proxy
+file, so they have no comment translated for them.
 </p>
 
 <p>
-Since all the overloaded functions in c++ are wrapped into one Python function, PyDoc translator will combine every comment of every
+Since all the overloaded functions in c++ are wrapped into one Python
+function, PyDoc translator will combine every comment of every
 overloaded function and put it in the comment for wrapping function.
 <br>
-If you intend to use resulting proxy files with Doxygen docs generator, rather than PyDoc, you may want to turn off translator completely
-(doxygen:notranslate feature).
-Then SWIG will just copy the comments to the proxy file and reformat them if needed, but all the comment content will be left as is. As Doxygen
-don't support special commands in Python comments (see <a href="http://www.stack.nl/~dimitri/doxygen/docblocks.html#pythonblocks">Doxygen docs</a>),
-you may want to use some tool like doxypy (<a href="http://code.foosel.org/doxypy">http://code.foosel.org/doxypy</a>) to do the work.
+If you intend to use resulting proxy files with Doxygen docs
+generator, rather than PyDoc, you may want to turn off translator
+completely (doxygen:notranslate feature).  Then SWIG will just copy
+the comments to the proxy file and reformat them if needed, but all
+the comment content will be left as is. As Doxygen don't support
+special commands in Python comments
+(see <a href="http://www.stack.nl/~dimitri/doxygen/docblocks.html#pythonblocks">Doxygen
+docs</a>), you may want to use some tool like doxypy
+(<a href="http://code.foosel.org/doxypy">http://code.foosel.org/doxypy</a>)
+to do the work.
 </p>
 
 <p>
@@ -1072,8 +1135,11 @@ Here is the list of all Doxygen tags and the description of how they are transla
 
 
 <p>
-Doxygen has a wealth of tags such as @latexonly that have no equivalent in PyDoc.
-As a result several tags that have no translation (or particular use, such as some linking and section tags) are supressed with their content just printed out (if it has any sense, typically text content).
+Doxygen has a wealth of tags such as @latexonly that have no
+equivalent in PyDoc.  As a result several tags that have no
+translation (or particular use, such as some linking and section tags)
+are supressed with their content just printed out (if it has any
+sense, typically text content).
 <br>
 Here is the list of these tags:
 </p>
@@ -1264,10 +1330,12 @@ TO BE ADDED.
 
 
 <p>
-If this functionality is turned on, SWIG places all comments found into the SWIG parse tree.
-Nodes contain an additional attribute called DoxygenComment when a comment is present.
-Individual nodes containing Doxygen with Structural Indicators, such as @file, as their first command, are also present in the parse tree.
-These individual "blobs" of Doxygen such as :
+If this functionality is turned on, SWIG places all comments found
+into the SWIG parse tree.  Nodes contain an additional attribute
+called DoxygenComment when a comment is present.  Individual nodes
+containing Doxygen with Structural Indicators, such as @file, as their
+first command, are also present in the parse tree.  These individual
+"blobs" of Doxygen such as :
 </p>
 <div class="code"><pre>
 /*! This is describing function Foo
@@ -1278,16 +1346,18 @@ These individual "blobs" of Doxygen such as :
 </pre></div>
 
 <p>
-are passed on individually to the DoxygenTranslator Module.
-This module builds its own private parse tree and hands it to a separate class for translation into the target documentation language.
-For example, <tt>JavaDocConverter</tt> is the JavaDoc module class.
+are passed on individually to the DoxygenTranslator Module.  This
+module builds its own private parse tree and hands it to a separate
+class for translation into the target documentation language.  For
+example, <tt>JavaDocConverter</tt> is the JavaDoc module class.
 </p>
 
 <H3><a name="Doxygen_debugging_commands"></a>39.5.2 Debugging Doxygen parser and translator</H3>
 
 
 <p>
-There are two handy command line switches, that enable lots of detailed debug information printing.
+There are two handy command line switches, that enable lots of
+detailed debug information printing.
 </p>
 
 <div class="shell"><pre>
@@ -1309,13 +1379,20 @@ This part of SWIG currently has 6 runtime tests in both Java and Python.
   doxygen_basic_translate
   doxygen_basic_notranslate
   doxygen_translate_links
-  doxygen_tricky_constructs
+  doxygen_misc_constructs
 </pre></div>
 
 <p>
-All this tests are included in common.mk and are build with the commands like 'make check-test-suite'
-or 'make check-python-test-suite'. To run them individually, type 'make <testname>.cpptest -s' in the
-language-specific subdir in Examples\test-suite.
+All this tests are included in common.mk and are build with the
+commands like 'make check-test-suite' or 'make
+check-python-test-suite'. To run them individually, type
+<code>make &lt;testname&gt;.cpptest -s</code> in the language-specific subdir in
+<code>Examples/test-suite</code> directory. For example:
+<pre>
+  Examples/test-suite/java $ make doxygen_misc_constructs.cpptest -s
+</pre>
+
+    
 <br>
 Runtime tests in Java are implemented using JavaDoc doclets. To make that work, you
 should have tools.jar from the JDK in your classpath. Or you should have JAVA_HOME
diff --git a/Examples/test-suite/doxygen_misc_constructs.i b/Examples/test-suite/doxygen_misc_constructs.i
index 03abbb116..bbec4c3ed 100644
--- a/Examples/test-suite/doxygen_misc_constructs.i
+++ b/Examples/test-suite/doxygen_misc_constructs.i
@@ -5,7 +5,7 @@
 
 %inline %{
 
-    // Bug 1: Tag '@endink' is not recognized becuse it is not
+    // Tag '@endink' must be recognized even if it is not
     // followed by whitespace.
 
     /** 
@@ -26,13 +26,8 @@
     int g_zipCode;
 
 
-    // Bug 2: Paramter 'isReportSize' is missing in comment of the overload, which
-    // has it. This bug disappears if @endlink is follwed by a space.
-    //
-    // Bug 3: Empty line before the link is missing,
-    // making the link text part of parameter description. This bug appears also
-    // when there is ordinary text in place of the link in case of overload
-    // with only 2 parameters.
+    // Paramter 'isReportSize' must appear in comment of the overload, which
+    // has it. Empty line before link must be preserved.
     /**
      * Returns address of file line.
      *
@@ -48,8 +43,7 @@
     {
     }
 
-    // Bug 4: The first comment is attached to the second in Python (wrong),
-    // but not in Java (correct).
+    // The first comment must be ignored.
     /** 
      * \defgroup icFacade isystem.connect Facade
      *
@@ -75,19 +69,7 @@
     {
     };
 
-    // Bug 5: Text after '\c' has no space following in Python.
-    // There are also to many empty lines in multiline comments in Python.
-    // Whitespaces are really a problem in Python (space and newlines),
-    // I like a parameter type added to each parameter description!
-    //    """
-    //    Determines how long the isystem.connectshould wait for running 
-    //
-    //    instances to respond. Only one of lfWaitXXXflags from IConnect::ELaunchFlags 
-    //
-    //    may be specified. 
-    //
-    //    """
-
+    // Text after '\c' must be kept unchanged in Python.
     /**
      * Determines how long the \c isystem.connect should wait for running 
      * instances to respond. Only one of \c lfWaitXXX flags from IConnect::ELaunchFlags
@@ -98,8 +80,7 @@
     }
 
 
-    // Bug 6: Text after tag \ingroup appears in Python comment (empty line in
-    // Java, which is acceptable):
+    // Line with tag \ingroup must not appear in translated comment:
     /** \ingroup icFacade
      *
      * This class manages connection.
@@ -107,6 +88,19 @@
     int getConnection()
     {
     }
-    
-    
+
+    /**
+     * Class description.
+     */
+    class ClassWithNestedEnum {
+    public:
+        /**
+         * Enum description.
+         */
+        typedef enum {ONE,  ///< desc of one
+                      TWO,  ///< desc of two
+                      THREE ///< desc of three
+        } ENested;
+
+    };
 %}
diff --git a/Examples/test-suite/java/doxygen_misc_constructs_runme.java b/Examples/test-suite/java/doxygen_misc_constructs_runme.java
index 696f8b609..7c0928a7a 100644
--- a/Examples/test-suite/java/doxygen_misc_constructs_runme.java
+++ b/Examples/test-suite/java/doxygen_misc_constructs_runme.java
@@ -98,7 +98,27 @@ public class doxygen_misc_constructs_runme {
     		" {@link Connection::getId()  }<br> \n" +
     		" \n" +
     		"");
-    
+
+    wantedComments.put("doxygen_misc_constructs.ClassWithNestedEnum",
+    		" Class description.\n" +
+    		" \n");
+
+    wantedComments.put("doxygen_misc_constructs.ClassWithNestedEnum.ENested",
+    		" Enum description.\n" +
+    		" \n");
+
+    wantedComments.put("doxygen_misc_constructs.ClassWithNestedEnum.ENested.ONE",
+    		" desc of one\n" +
+    		" \n");
+
+    wantedComments.put("doxygen_misc_constructs.ClassWithNestedEnum.ENested.TWO",
+    		" desc of two\n" +
+    		" \n");
+
+    wantedComments.put("doxygen_misc_constructs.ClassWithNestedEnum.ENested.THREE",
+    		" desc of three\n" +
+    		" \n");
+
     // and ask the parser to check comments for us
     System.exit(parser.check(wantedComments));
   }

From e50d37664f86ae31722826c40113a8662b3d899c Mon Sep 17 00:00:00 2001
From: Marko Klopcic <marko.klopcic@isystem.si>
Date: Wed, 29 Aug 2012 21:26:11 +0000
Subject: [PATCH 150/314] if feature doxygen:notranslate is used, comments are
 now properly decorated with '*'s.

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13730 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Examples/test-suite/doxygen_misc_constructs.i | 19 ++---
 .../src/JavaDocConverter.cpp                  | 84 +++++++++++++++++--
 .../DoxygenTranslator/src/JavaDocConverter.h  |  1 +
 3 files changed, 87 insertions(+), 17 deletions(-)

diff --git a/Examples/test-suite/doxygen_misc_constructs.i b/Examples/test-suite/doxygen_misc_constructs.i
index bbec4c3ed..80627559b 100644
--- a/Examples/test-suite/doxygen_misc_constructs.i
+++ b/Examples/test-suite/doxygen_misc_constructs.i
@@ -8,20 +8,19 @@
     // Tag '@endink' must be recognized even if it is not
     // followed by whitespace.
 
-    /** 
-     * Tag endlink must be recognized also when followed by nonspace charater.
+    /** Tag endlink must be recognized also when followed by nonspace charater.
      *
-     * @link Connection::getId() @endlink<br>
-     */
+     * @link Connection::getId() @endlink<br> */
+     
     char g_counter;
 
 
     /** 
-     * Tag endlink must be recognized also when it is the last token
-     * in the commment.
-     *
-     * @link Connection::getId() @endlink<br>
-     * @link debugIdeTraceProfilerCoverageSample.py Python example. @endlink
+      Tag endlink must be recognized also when it is the last token
+      in the commment.
+
+      @link Connection::getId() @endlink<br>
+      @link debugIdeTraceProfilerCoverageSample.py Python example. @endlink
      */
     int g_zipCode;
 
@@ -95,7 +94,7 @@
     class ClassWithNestedEnum {
     public:
         /**
-         * Enum description.
+         * Enum description.b
          */
         typedef enum {ONE,  ///< desc of one
                       TWO,  ///< desc of two
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.cpp b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
index 2c2aa8aa0..2144ffb9e 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
@@ -116,7 +116,7 @@ void JavaDocConverter::fillStaticTables() {
 
 
 JavaDocConverter::JavaDocConverter(bool debugTranslator, bool debugParser)
-: DoxygenTranslator(debugTranslator, debugParser) {
+: DoxygenTranslator(true, true) {
   fillStaticTables();
 }
 
@@ -528,6 +528,75 @@ int JavaDocConverter::shiftEndlinesUpTree(DoxygenEntity &root, int level)
 }
 
 
+/**
+ * This makes sure that all comment lines contain '*'. It is not mandatory in doxygen,
+ * but highly recommended for Javadoc. '*' in empty lines are indented according
+ * to indentation of the first line. Indentation of non-empty lines is not
+ * changed - garbage in garbage out.
+ */
+std::string JavaDocConverter::indentAndInsertAsterisks(const string &doc) {
+
+  size_t idx = doc.find('\n');
+  size_t indent = 0;
+  // Detect indentation.
+  //   The first line in comment is the one after '/**', which may be
+  //   spaces and '\n' or the text. In any case it is not suitable to detect
+  //   indentation, so we have to skip the first '\n'.
+  if (idx != string::npos) {
+    size_t nonspaceIdx = doc.find_first_not_of(' ', idx + 1);
+    if (nonspaceIdx != string::npos) {
+      indent = nonspaceIdx - idx;
+    }
+  }
+
+  // Create the first line of Javadoc comment.
+  string indentStr(indent - 1, ' ');
+  string translatedStr = indentStr + "/**";
+  if (indent > 1) {
+    // remove the first space, so that '*' will be aligned
+    translatedStr = translatedStr.substr(1);
+  }
+
+  translatedStr += doc;
+
+  // insert '*' before each comment line, if it does not have it
+  idx = translatedStr.find('\n');
+
+  while (idx != string::npos) {
+
+    size_t nonspaceIdx = translatedStr.find_first_not_of(' ', idx + 1);
+    if (nonspaceIdx != string::npos  &&  translatedStr[nonspaceIdx] != '*') {
+
+      // line without '*' found - is it empty?
+      if (translatedStr[nonspaceIdx] != '\n') {
+        // add '* ' to each line without it
+        translatedStr = translatedStr.substr(0, nonspaceIdx) + "* " +
+                translatedStr.substr(nonspaceIdx);
+      } else {
+        // we found empty line, replace it with indented '*'
+        translatedStr = translatedStr.substr(0, idx + 1) + indentStr +
+                "* " + translatedStr.substr(nonspaceIdx);
+      }
+    }
+    idx = translatedStr.find('\n', nonspaceIdx);
+  }
+
+  // Add the last comment line properly indented
+  size_t nonspaceEndIdx = translatedStr.find_last_not_of(' ');
+  if (nonspaceEndIdx != string::npos) {
+    if (translatedStr[nonspaceEndIdx] != '\n') {
+      translatedStr += '\n';
+    } else {
+      // remove trailing spaces
+      translatedStr = translatedStr.substr(0, nonspaceEndIdx + 1);
+    }
+  }
+  translatedStr += indentStr + "*/\n";
+
+  return translatedStr;
+}
+
+
 String *JavaDocConverter::makeDocumentation(Node *node) {
 
   String *documentation = getDoxygenComment(node);
@@ -537,12 +606,13 @@ String *JavaDocConverter::makeDocumentation(Node *node) {
   }
 
   if (GetFlag(node, "feature:doxygen:notranslate")) {
-    String *comment = NewString("/**\n");
-    Append(comment, documentation);
-    // reformat the comment
-    Replaceall(comment, "\n *", "\n");
-    Replaceall(comment, "\n", "\n * ");
-    Append(comment, "\n */\n");
+
+    string doc = Char(documentation);
+
+    string translatedStr = indentAndInsertAsterisks(doc);
+
+    String *comment = NewString(translatedStr.c_str());
+    // Append(comment, documentation); Replaceall(comment, "\n", "\n * ");
     return comment;
   }
 
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.h b/Source/DoxygenTranslator/src/JavaDocConverter.h
index 1fab5e63b..9715593c6 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.h
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.h
@@ -127,6 +127,7 @@ private:
   void fillStaticTables();
 
   bool paramExists(std::string param);
+  std::string indentAndInsertAsterisks(const std::string &doc);
 };
 
 #endif

From 2f77dbc7f4e2b406cb52aeaa10758dd35fffeca5 Mon Sep 17 00:00:00 2001
From: Marko Klopcic <marko.klopcic@isystem.si>
Date: Thu, 30 Aug 2012 20:35:23 +0000
Subject: [PATCH 151/314] fixed prepending '*' to nontranslated comments by
 taking also tabs into account

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13731 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Examples/test-suite/doxygen_misc_constructs.i     |  2 +-
 Source/DoxygenTranslator/src/JavaDocConverter.cpp | 10 +++++-----
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/Examples/test-suite/doxygen_misc_constructs.i b/Examples/test-suite/doxygen_misc_constructs.i
index 80627559b..0af22c72d 100644
--- a/Examples/test-suite/doxygen_misc_constructs.i
+++ b/Examples/test-suite/doxygen_misc_constructs.i
@@ -31,7 +31,7 @@
      * Returns address of file line.
      *
      * @param fileName name of the file, where the source line is located
-     * @param line line number
+	* @param line line number
      * @param isGetSize if set, for every object location both address and size are returned
      *
      * @link Connection::getId() @endlink <br>
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.cpp b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
index 2144ffb9e..667e4f74e 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
@@ -116,7 +116,7 @@ void JavaDocConverter::fillStaticTables() {
 
 
 JavaDocConverter::JavaDocConverter(bool debugTranslator, bool debugParser)
-: DoxygenTranslator(true, true) {
+: DoxygenTranslator(debugTranslator, debugParser) {
   fillStaticTables();
 }
 
@@ -543,7 +543,7 @@ std::string JavaDocConverter::indentAndInsertAsterisks(const string &doc) {
   //   spaces and '\n' or the text. In any case it is not suitable to detect
   //   indentation, so we have to skip the first '\n'.
   if (idx != string::npos) {
-    size_t nonspaceIdx = doc.find_first_not_of(' ', idx + 1);
+    size_t nonspaceIdx = doc.find_first_not_of(" \t", idx + 1);
     if (nonspaceIdx != string::npos) {
       indent = nonspaceIdx - idx;
     }
@@ -564,14 +564,14 @@ std::string JavaDocConverter::indentAndInsertAsterisks(const string &doc) {
 
   while (idx != string::npos) {
 
-    size_t nonspaceIdx = translatedStr.find_first_not_of(' ', idx + 1);
+    size_t nonspaceIdx = translatedStr.find_first_not_of(" \t", idx + 1);
     if (nonspaceIdx != string::npos  &&  translatedStr[nonspaceIdx] != '*') {
-
       // line without '*' found - is it empty?
       if (translatedStr[nonspaceIdx] != '\n') {
         // add '* ' to each line without it
         translatedStr = translatedStr.substr(0, nonspaceIdx) + "* " +
                 translatedStr.substr(nonspaceIdx);
+        //printf(translatedStr.c_str());
       } else {
         // we found empty line, replace it with indented '*'
         translatedStr = translatedStr.substr(0, idx + 1) + indentStr +
@@ -582,7 +582,7 @@ std::string JavaDocConverter::indentAndInsertAsterisks(const string &doc) {
   }
 
   // Add the last comment line properly indented
-  size_t nonspaceEndIdx = translatedStr.find_last_not_of(' ');
+  size_t nonspaceEndIdx = translatedStr.find_last_not_of(" \t");
   if (nonspaceEndIdx != string::npos) {
     if (translatedStr[nonspaceEndIdx] != '\n') {
       translatedStr += '\n';

From 8d61aae0fb913bd779b975645af12e12b3fa8565 Mon Sep 17 00:00:00 2001
From: Marko Klopcic <marko.klopcic@isystem.si>
Date: Thu, 6 Sep 2012 20:56:19 +0000
Subject: [PATCH 152/314] fixed handling of /******/ comments, added tests for
 backslash handling, which fail

git-svn-id: https://swig.svn.sourceforge.net/svnroot/swig/branches/gsoc2012-doxygen@13733 626c5289-ae23-0410-ae9c-e8d60b6d4f22
---
 Examples/test-suite/doxygen_misc_constructs.h | 52 +++++++++++++++++++
 Examples/test-suite/doxygen_misc_constructs.i | 27 +++++-----
 .../java/doxygen_misc_constructs_runme.java   | 28 +++++++++-
 Source/CParse/cscanner.c                      | 13 +++--
 .../src/JavaDocConverter.cpp                  |  4 ++
 5 files changed, 106 insertions(+), 18 deletions(-)
 create mode 100644 Examples/test-suite/doxygen_misc_constructs.h

diff --git a/Examples/test-suite/doxygen_misc_constructs.h b/Examples/test-suite/doxygen_misc_constructs.h
new file mode 100644
index 000000000..813e6ddcd
--- /dev/null
+++ b/Examples/test-suite/doxygen_misc_constructs.h
@@ -0,0 +1,52 @@
+/*
+ * This file contains comments which demonstrate details about Doxygen processing,
+ * so they can be emulated in SWIG doxy comment translation
+ */
+
+
+
+/**This comment without space after '*' is valid in Doxygen.
+ *
+ */
+void isNoSpaceValidA()
+{}
+
+/**.This comment without space after '*' is valid in Doxygen.
+ *
+ */
+void isNoSpaceValidB()
+{}
+
+
+/***This is not Doxygen comment.
+ *
+ */
+void isNoSpaceValidC()
+{}
+
+
+/**
+ * Backslash following\c word is valid doxygen command. Output contains
+ * 'followingword' with word in 'code' font.
+ */
+void backslashA()
+{}
+
+/**
+ * Doxy command without trailing \cspace space is ignored. Standalone
+ * \ and '\' get to output.  Commands not recognized by Doxygen \blah
+ * are ignored.  Backslashes in DOS paths d:\xyz\c\myfile and words
+ * following them do not appear on output, we must quote them with
+ * double quotes: "d:\xyz\c\myfile", single quotes do not help:
+ * 'd:\xyz\c\myfile'. Escaping works: d:\\xyz\\c\\myfile. Unix
+ * paths of course have no such problems: /xyz/c/myfile
+ */
+void backslashB()
+{}
+
+/**
+ *
+ */
+void htmlTags()
+{}
+
diff --git a/Examples/test-suite/doxygen_misc_constructs.i b/Examples/test-suite/doxygen_misc_constructs.i
index 0af22c72d..447e6b24e 100644
--- a/Examples/test-suite/doxygen_misc_constructs.i
+++ b/Examples/test-suite/doxygen_misc_constructs.i
@@ -37,10 +37,8 @@
      * @link Connection::getId() @endlink <br>
      */
     void getAddress(int &fileName, 
-                                  int line, 
-                                  bool isGetSize = false)
-    {
-    }
+                    int line,     
+                    bool isGetSize = false) {}
 
     // The first comment must be ignored.
     /** 
@@ -74,27 +72,28 @@
      * instances to respond. Only one of \c lfWaitXXX flags from IConnect::ELaunchFlags
      * may be specified.
      */
-    int waitTime(long waitTime)
-    {
-    }
+    int waitTime(long waitTime) {return 33;}
 
 
     // Line with tag \ingroup must not appear in translated comment:
     /** \ingroup icFacade
      *
-     * This class manages connection.
+     * This function returns connection id.
      */
-    int getConnection()
-    {
-    }
+    int getConnection() {return 3;}
 
+    // the follwing must produce no comment in wrapper
+    /*******************************************************************/
+    char getFirstLetter() {return 'a';}
+
+    
     /**
      * Class description.
      */
     class ClassWithNestedEnum {
     public:
         /**
-         * Enum description.b
+         * Enum description.
          */
         typedef enum {ONE,  ///< desc of one
                       TWO,  ///< desc of two
@@ -102,4 +101,8 @@
         } ENested;
 
     };
+
+    #include "doxygen_misc_constructs.h"
+    
 %}
+    %include "doxygen_misc_constructs.h"
diff --git a/Examples/test-suite/java/doxygen_misc_constructs_runme.java b/Examples/test-suite/java/doxygen_misc_constructs_runme.java
index 7c0928a7a..c7a14f91e 100644
--- a/Examples/test-suite/java/doxygen_misc_constructs_runme.java
+++ b/Examples/test-suite/java/doxygen_misc_constructs_runme.java
@@ -28,7 +28,7 @@ public class doxygen_misc_constructs_runme {
     wantedComments.put("doxygen_misc_constructs.doxygen_misc_constructs.getConnection()",
     		" \n" +
     		" \n" +
-    		" This class manages connection. \n" +
+    		" This function returns connection id. \n" +
     		" \n" +
     		"");
     wantedComments.put("doxygen_misc_constructs.doxygen_misc_constructs.getAddress(doxygen_misc_constructs.SWIGTYPE_p_int, int)",
@@ -119,6 +119,32 @@ public class doxygen_misc_constructs_runme {
     		" desc of three\n" +
     		" \n");
 
+    wantedComments.put("doxygen_misc_constructs.doxygen_misc_constructs.isNoSpaceValidA()",
+    		" This comment without space after '*' is valid in Doxygen. \n" +
+    		" \n" +
+    		"");
+ 
+    wantedComments.put("doxygen_misc_constructs.doxygen_misc_constructs.isNoSpaceValidB()",
+    		" .This comment without space after '*' is valid in Doxygen. \n" +
+    		" \n" +
+    		"");
+ 
+    wantedComments.put("doxygen_misc_constructs.doxygen_misc_constructs.backslashA()",
+    		" Backslash following<code>word</code> is valid doxygen command. Output contains \n" +
+    		" 'followingword' with word in 'code' font. \n" +
+    		" \n" +
+    		"");
+ 
+    wantedComments.put("doxygen_misc_constructs.doxygen_misc_constructs.backslashB()",
+                       " Doxy command without trailing cspace space is ignored. Standalone \n" +
+                       " \\ and '\\' get to output. Commands not recognized by Doxygen \n" +
+                       " are ignored. Backslashes in DOS paths d: and words \n" +
+                       " following them do not appear on output, we must quote them with \n" +
+                       " double quotes: \"d:\\xyz\\c\\myfile\", single quotes do not help: \n" +
+                       " 'd: '. Escaping works: d:\\xyz\\c\\myfile. Unix \n" +
+                       " paths of course have no such problems: /xyz/c/myfile \n" +
+    		" \n");
+ 
     // and ask the parser to check comments for us
     System.exit(parser.check(wantedComments));
   }
diff --git a/Source/CParse/cscanner.c b/Source/CParse/cscanner.c
index fb5754856..796281db9 100644
--- a/Source/CParse/cscanner.c
+++ b/Source/CParse/cscanner.c
@@ -349,11 +349,14 @@ static int yylook(void) {
 	    return DOXYGENPOSTSTRING;
 	  }
 	  if (strncmp(loc, "/**", 3) == 0 || strncmp(loc, "///", 3) == 0||strncmp(loc, "/*!", 3) == 0||strncmp(loc, "//!", 3) == 0) {
-	    /* printf("Doxygen Comment: %s lines %d-%d [%s]\n", Char(Scanner_file(scan)), Scanner_start_line(scan), Scanner_line(scan), loc);  */
-	    yylval.str =  NewString(loc);
-	    Setline(yylval.str, Scanner_start_line(scan));
-	    Setfile(yylval.str, Scanner_file(scan));
-	    return DOXYGENSTRING;
+	    /* printf("Doxygen Comment: %s lines %d-%d [%s]\n", Char(Scanner_file(scan)), Scanner_start_line(scan), Scanner_line(scan), loc); */
+	    /* ignore comments like / * * * and / * * /,  which are also ignored by Doxygen */
+	    if (loc[3] != '*'  &&  loc[3] != '/') {
+	      yylval.str =  NewString(loc);
+	      Setline(yylval.str, Scanner_start_line(scan));
+	      Setfile(yylval.str, Scanner_file(scan));
+	      return DOXYGENSTRING;
+	    }
 	  }
 	}
       }
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.cpp b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
index 667e4f74e..83b08ba39 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
@@ -549,6 +549,10 @@ std::string JavaDocConverter::indentAndInsertAsterisks(const string &doc) {
     }
   }
 
+  if (indent == 0) { // we can't indent the first line less than 0
+    indent = 1;
+  }
+
   // Create the first line of Javadoc comment.
   string indentStr(indent - 1, ' ');
   string translatedStr = indentStr + "/**";

From dd775a6ca96353533c2a33eb1ffa28c994c0ddb6 Mon Sep 17 00:00:00 2001
From: m <markok@ubuntu-ProBook-4710s.(none)>
Date: Thu, 10 Jan 2013 08:28:20 +0100
Subject: [PATCH 153/314] Files Token.cpp and TokenList.cpp removed from
 makefile. TokenList was replaced with std::vecor, Token is now nested class
 of DoxygenParser

---
 Source/Makefile.am | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/Source/Makefile.am b/Source/Makefile.am
index 6a5cb91b0..b3838ba75 100644
--- a/Source/Makefile.am
+++ b/Source/Makefile.am
@@ -98,11 +98,7 @@ eswig_SOURCES =	CParse/cscanner.c		\
 		DoxygenTranslator/src/JavaDocConverter.h\
 		DoxygenTranslator/src/JavaDocConverter.cpp\
 		DoxygenTranslator/src/PyDocConverter.h\
-		DoxygenTranslator/src/PyDocConverter.cpp\
-		DoxygenTranslator/src/Token.h\
-		DoxygenTranslator/src/Token.cpp\
-		DoxygenTranslator/src/TokenList.h\
-		DoxygenTranslator/src/TokenList.cpp
+		DoxygenTranslator/src/PyDocConverter.cpp
 
 bin_PROGRAMS = eswig
 eswig_LDADD   = @SWIGLIBS@

From a9ef35bc66d90e44694618451a7f464a9e67fa80 Mon Sep 17 00:00:00 2001
From: Marko Klopcic <markok3.14@gmail.com>
Date: Thu, 10 Jan 2013 08:45:00 +0100
Subject: [PATCH 154/314] Parsing of comments to tokens rewritten so that html
 entities and html tags are now treated as commands. Whitespaces are also
 preserved more acurately, so some doxygen tests fail at the moment

---
 .../DoxygenTranslator/src/DoxygenCommands.h   |  80 ++-
 .../DoxygenTranslator/src/DoxygenEntity.cpp   |   6 +-
 .../DoxygenTranslator/src/DoxygenParser.cpp   | 604 ++++++++++++++----
 Source/DoxygenTranslator/src/DoxygenParser.h  |  62 +-
 .../src/JavaDocConverter.cpp                  |  52 +-
 .../DoxygenTranslator/src/JavaDocConverter.h  |   2 +-
 6 files changed, 640 insertions(+), 166 deletions(-)

diff --git a/Source/DoxygenTranslator/src/DoxygenCommands.h b/Source/DoxygenTranslator/src/DoxygenCommands.h
index 10ebca862..154efc53f 100644
--- a/Source/DoxygenTranslator/src/DoxygenCommands.h
+++ b/Source/DoxygenTranslator/src/DoxygenCommands.h
@@ -2,10 +2,18 @@
 #ifndef DOXYGENCOMMANDS_H
 #define DOXYGENCOMMANDS_H
 
+const char *CMD_HTML_ONLY = "htmlonly";
+const char *CMD_VERBATIM = "verbatim";
+const char *CMD_END_HTML_ONLY = "endhtmlonly";
+const char *CMD_END_VERBATIM = "endverbatim";
+
 const char *sectionIndicators[] = {
-  "attention", "author", "authors", "brief", "bug", "cond", "date", "deprecated", "details",
-  "else", "elseif", "endcond", "endif", "exception", "if", "ifnot", "invariant", "note", "par", "param",
-  "tparam", "post", "pre", "remarks", "remark", "result", "return", "returns", "retval", "sa", "see", "since", "test", "throw", "throws", "todo", "version", "warning", "xrefitem"};
+  "attention", "author", "authors", "brief", "bug", "cond", "date",
+  "deprecated", "details", "else", "elseif", "endcond", "endif",
+  "exception", "if", "ifnot", "invariant", "note", "par", "param",
+  "tparam", "post", "pre", "remarks", "remark", "result", "return",
+  "returns", "retval", "sa", "see", "since", "test", "throw", "throws",
+  "todo", "version", "warning", "xrefitem"};
 const int sectionIndicatorsSize = sizeof(sectionIndicators) / sizeof(*sectionIndicators);
 
 /* All of the doxygen commands divided up by how they are parsed */
@@ -17,23 +25,27 @@ const char *simpleCommands[] = {
 const int simpleCommandsSize = sizeof(simpleCommands) / sizeof(*simpleCommands);
 
 const char *commandWords[] = {
-  "a", "b", "c", "e", "em", "p", "def", "enum", "package", "relates", "namespace", "relatesalso", "anchor", "dontinclude", "include",
-  "includelineno", "copydoc", "copybrief", "copydetails", "verbinclude", "htmlinclude", "extends", "implements", "memberof", "related",
-  "relatedalso", "cite"};
+  "a", "b", "c", "e", "em", "p", "def", "enum", "package", "relates",
+  "namespace", "relatesalso", "anchor", "dontinclude", "include",
+  "includelineno", "copydoc", "copybrief", "copydetails", "verbinclude",
+  "htmlinclude", "extends", "implements", "memberof", "related", "relatedalso",
+  "cite"};
 const int commandWordsSize = sizeof(commandWords) / sizeof(*commandWords);
 
 const char *commandLines[] = {
-  "addindex", "fn", "name", "line", "var", "skipline", "typedef", "skip", "until", "property"};
+  "addindex", "fn", "name", "line", "var", "skipline", "typedef", "skip",
+  "until", "property"};
 const int commandLinesSize = sizeof(commandLines) / sizeof(*commandLines);
 
 const char *commandParagraph[] = {
-  "partofdescription", "result", "return", "returns", "remarks", "remark", "since", "test", "sa", "see", "pre", "post", "details", "invariant",
-  "deprecated", "date", "note", "warning", "version", "todo", "bug", "attention", "brief", "author", "authors",
-  "copyright", "short"};
+  "partofdescription", "result", "return", "returns", "remarks", "remark",
+  "since", "test", "sa", "see", "pre", "post", "details", "invariant",
+  "deprecated", "date", "note", "warning", "version", "todo", "bug",
+  "attention", "brief", "author", "authors", "copyright", "short"};
 const int commandParagraphSize = sizeof(commandParagraph) / sizeof(*commandParagraph);
 
 const char *commandEndCommands[] = {
-  "htmlonly", "latexonly", "manonly", "xmlonly", "link", "rtfonly"};
+  CMD_HTML_ONLY, "latexonly", "manonly", "xmlonly", "link", "rtfonly"};
 const int commandEndCommandsSize = sizeof(commandEndCommands) / sizeof(*commandEndCommands);
 
 const char *commandWordParagraphs[] = {
@@ -41,7 +53,8 @@ const char *commandWordParagraphs[] = {
 const int commandWordParagraphsSize = sizeof(commandWordParagraphs) / sizeof(*commandWordParagraphs);
 
 const char *commandWordLines[] = {
-  "page", "subsection", "subsubsection", "section", "paragraph", "defgroup", "snippet", "mainpage"};
+  "page", "subsection", "subsubsection", "section", "paragraph", "defgroup",
+  "snippet", "mainpage"};
 const int commandWordLinesSize = sizeof(commandWordLines) / sizeof(*commandWordLines);
 
 const char *commandWordOWordOWords[] = {
@@ -61,7 +74,48 @@ const int commandErrorThrowingsSize = sizeof(commandErrorThrowings) / sizeof(*co
 
 const char *commandUniques[] = {
   "xrefitem", "arg", "ingroup", "par", "headerfile", "overload", "weakgroup", "ref", "subpage", "dotfile", "image", "addtogroup", "li",
-  "if", "ifnot", "elseif", "else", "mscfile", "code", "verbatim", "f{", "f[", "f$", "dot", "msc"};
+  "if", "ifnot", "elseif", "else", "mscfile", "code", CMD_VERBATIM, "f{", "f[", "f$", "dot", "msc"};
 const int commandUniquesSize = sizeof(commandUniques) / sizeof(*commandUniques);
 
+// These HTML commands are transformed when producing output in other formats.
+// Other commands are left intact, but '<' and '> are replaced with entities in HTML
+// output. So <varName> appears as &lt;varName&gt; in HTML output. The same
+// behavior must be repeated by SWIG. See Doxygen doc for the list of commands.
+// '<' and '>' are used to differentiate HTML commands from doxygen commands.
+const char *htmlCommands[] = {
+  "<A>", "<B>", "<BLOCKQUOTE>", "<BODY>", "<BR>", "<CENTER>", "<CAPTION>", "<CODE>", "<DFN>", "<DFN>",
+  "<DIV>", "<DL>", "<DT>", "<EM>", "<FORM>", "<HR>", "<H1>", "<H2>", "<H3>", "<I>", "<INPUT>", "<IMG>",
+  "<LI>", "<META>", "<MULTICOL>", "<OL>", "<P>", "<PRE>", "<SMALL>", "<SPAN>", "<STRONG>",
+  "<SUB>", "<SUP>", "<TABLE>", "<TD>", "<TH>", "<TR>", "<TT>", "<KBD>", "<UL>", "<VAR>"
+};
+
+const int htmlCommandsSize = sizeof(htmlCommands) / sizeof(*htmlCommands);
+
+// Only entities which are translatable to plain text are used here. Others
+// are copied unchanged to output.
+const char *htmlEntities[] = { "&copy", "&trade", "&reg", // (C), (TM), (R)
+"&lt",  // less-than symbol
+"&gt",  // greater-than symbol
+"&amp", // ampersand
+"&apos", // single quotation mark (straight)
+"&quot", // double quotation mark (straight)
+"&lsquo", // left single quotation mark
+"&rsquo", // right single quotation mark
+"&ldquo", // left double quotation mark
+"&rdquo", // right double quotation mark
+"&ndash", // n-dash (for numeric ranges, e.g. 2–8)
+"&mdash", // --
+"&nbsp", //
+"&times", // x
+"&minus", // -
+"&sdot", // .
+"&sim", // ~
+"&le", // <=
+"&ge", // >=
+"&larr", // <--
+"&rarr" // -->
+};
+
+const int htmlEntitiesSize = sizeof(htmlEntities) / sizeof(*htmlEntities);
+
 #endif
diff --git a/Source/DoxygenTranslator/src/DoxygenEntity.cpp b/Source/DoxygenTranslator/src/DoxygenEntity.cpp
index 7b0088e06..9e761c32b 100644
--- a/Source/DoxygenTranslator/src/DoxygenEntity.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenEntity.cpp
@@ -55,10 +55,10 @@ void DoxygenEntity::printEntity(int level) const {
       cout << "\t";
     }
 
-    cout << "Node Command: " << typeOfEntity << " ";
+    cout << "Node Leaf Command: '" << typeOfEntity << "',  ";
 
     if (!data.empty()) {
-      cout << "Node Data: " << data;
+      cout << "Node Data: '" << data << "'";
     }
     cout << std::endl;
 
@@ -68,7 +68,7 @@ void DoxygenEntity::printEntity(int level) const {
       cout << "\t";
     }
 
-    cout << "Node Command : " << typeOfEntity << std::endl;
+    cout << "Node Command: '" << typeOfEntity << "'" << std::endl;
 
     thisLevel++;
 
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.cpp b/Source/DoxygenTranslator/src/DoxygenParser.cpp
index 346e94cc2..7ec0ae261 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenParser.cpp
@@ -16,6 +16,7 @@
 
 #include <iostream>
 #include <algorithm>
+#include <vector>
 
 using std::string;
 using std::cout;
@@ -28,7 +29,8 @@ std::set<std::string> DoxygenParser::doxygenSectionIndicators;
 const int TOKENSPERLINE = 8;    //change this to change the printing behaviour of the token list
 
 
-DoxygenParser::DoxygenParser(bool noisy) : noisy(noisy) {
+DoxygenParser::DoxygenParser(bool noisy) : noisy(noisy)
+{
 	fillTables();
 }
 
@@ -36,37 +38,53 @@ DoxygenParser::~DoxygenParser() {
 }
 
 void DoxygenParser::fillTables() {
-	// run it only once
-	if (doxygenCommands.size())
-		return;
+    // run it only once
+    if (doxygenCommands.size())
+        return;
 
-	// fill in tables with data from DxygenCommands.h
-	for (int i = 0; i < simpleCommandsSize; i++)
-		doxygenCommands[simpleCommands[i]] = SIMPLECOMMAND;
-	for (int i = 0; i < commandWordsSize; i++)
-		doxygenCommands[commandWords[i]] = COMMANDWORD;
-	for (int i = 0; i < commandLinesSize; i++)
-		doxygenCommands[commandLines[i]] = COMMANDLINE;
-	for (int i = 0; i < commandParagraphSize; i++)
-		doxygenCommands[commandParagraph[i]] = COMMANDPARAGRAPH;
-	for (int i = 0; i < commandEndCommandsSize; i++)
-		doxygenCommands[commandEndCommands[i]] = COMMANDENDCOMMAND;
-	for (int i = 0; i < commandWordParagraphsSize; i++)
-		doxygenCommands[commandWordParagraphs[i]] = COMMANDWORDPARAGRAPH;
-	for (int i = 0; i < commandWordLinesSize; i++)
-		doxygenCommands[commandWordLines[i]] = COMMANDWORDLINE;
-	for (int i = 0; i < commandWordOWordOWordsSize; i++)
-		doxygenCommands[commandWordOWordOWords[i]] = COMMANDWORDOWORDWORD;
-	for (int i = 0; i < commandOWordsSize; i++)
-		doxygenCommands[commandOWords[i]] = COMMANDOWORD;
-	for (int i = 0; i < commandErrorThrowingsSize; i++)
-		doxygenCommands[commandErrorThrowings[i]] = COMMANDERRORTHROW;
-	for (int i = 0; i < commandUniquesSize; i++)
-		doxygenCommands[commandUniques[i]] = COMMANDUNIQUE;
+    // fill in tables with data from DxygenCommands.h
+    for (int i = 0; i < simpleCommandsSize; i++)
+        doxygenCommands[simpleCommands[i]] = SIMPLECOMMAND;
 
-	// fill section indicators command set
-	for (int i = 0; i < sectionIndicatorsSize; i++)
-		doxygenSectionIndicators.insert(sectionIndicators[i]);
+    for (int i = 0; i < commandWordsSize; i++)
+        doxygenCommands[commandWords[i]] = COMMANDWORD;
+
+    for (int i = 0; i < commandLinesSize; i++)
+        doxygenCommands[commandLines[i]] = COMMANDLINE;
+
+    for (int i = 0; i < commandParagraphSize; i++)
+        doxygenCommands[commandParagraph[i]] = COMMANDPARAGRAPH;
+
+    for (int i = 0; i < commandEndCommandsSize; i++)
+        doxygenCommands[commandEndCommands[i]] = COMMANDENDCOMMAND;
+
+    for (int i = 0; i < commandWordParagraphsSize; i++)
+        doxygenCommands[commandWordParagraphs[i]] = COMMANDWORDPARAGRAPH;
+
+    for (int i = 0; i < commandWordLinesSize; i++)
+        doxygenCommands[commandWordLines[i]] = COMMANDWORDLINE;
+
+    for (int i = 0; i < commandWordOWordOWordsSize; i++)
+        doxygenCommands[commandWordOWordOWords[i]] = COMMANDWORDOWORDWORD;
+
+    for (int i = 0; i < commandOWordsSize; i++)
+        doxygenCommands[commandOWords[i]] = COMMANDOWORD;
+
+    for (int i = 0; i < commandErrorThrowingsSize; i++)
+        doxygenCommands[commandErrorThrowings[i]] = COMMANDERRORTHROW;
+
+    for (int i = 0; i < commandUniquesSize; i++)
+        doxygenCommands[commandUniques[i]] = COMMANDUNIQUE;
+
+    for (int i = 0; i < htmlCommandsSize; i++)
+        doxygenCommands[htmlCommands[i]] = COMMANDUNIQUE;
+
+    for (int i = 0; i < commandUniquesSize; i++)
+        doxygenCommands[commandUniques[i]] = COMMANDUNIQUE;
+
+    // fill section indicators command set
+    for (int i = 0; i < sectionIndicatorsSize; i++)
+        doxygenSectionIndicators.insert(sectionIndicators[i]);
 }
 
 
@@ -124,22 +142,58 @@ int DoxygenParser::commandBelongs(const std::string &theCommand) {
 }
 
 
-std::string DoxygenParser::getNextWord(const TokenList &tokList) {
-	// MK Token nextToken = tokList.peek();
-    if (m_tokenListIt == m_tokenList.end()) {
+std::string DoxygenParser::trim(const std::string &text)
+{
+    size_t start = text.find_first_not_of(" \t");
+    size_t end = text.find_last_not_of(" \t");
+
+    if (start == string::npos  ||  start > end) {
         return "";
     }
-    Token nextToken = *m_tokenListIt;
-	if (nextToken.m_tokenType == PLAINSTRING) {
-		// handle quoted strings as words
-		if (nextToken.m_tokenString[0] == '"'
-				&& nextToken.m_tokenString[nextToken.m_tokenString.size() - 1] != '"') {
+    return text.substr(start, end - start + 1);
+}
 
-			string word = nextToken.m_tokenString + " ";
-			nextToken = *m_tokenListIt++;
+
+bool DoxygenParser::isEndOfLine()
+{
+    if (m_tokenListIt == m_tokenList.end()) {
+        return false;
+    }
+    Token nextToken = *m_tokenListIt;
+    return nextToken.m_tokenType == END_LINE;
+}
+
+
+void DoxygenParser::skipWhitespaceTokens()
+{
+    if (m_tokenListIt == m_tokenList.end()) {
+        return;
+    }
+
+    while (m_tokenListIt != m_tokenList.end()  &&
+            (m_tokenListIt->m_tokenType == END_LINE  ||  trim(m_tokenListIt->m_tokenString).empty())) {
+
+        m_tokenListIt++;
+    }
+}
+
+
+std::string DoxygenParser::getNextWord() {
+
+/*    if (m_tokenListIt == m_tokenList.end()) {
+        return "";
+    }
+*/
+	while (m_tokenListIt != m_tokenList.end()  &&  (m_tokenListIt->m_tokenType == PLAINSTRING)) {
+		// handle quoted strings as words
+		if (m_tokenListIt->m_tokenString[0] == '"'
+				&& m_tokenListIt->m_tokenString[m_tokenListIt->m_tokenString.size() - 1] != '"') {
+
+			string word = m_tokenListIt->m_tokenString + " ";
+			m_tokenListIt++;
 			while (true) {
-				string nextWord = getNextWord(tokList);
-				if (!nextWord.size()) {// maybe report unterminated string error
+				string nextWord = getNextWord();
+				if (nextWord.empty()) { // maybe report unterminated string error
 					return word;
 				}
 				word += nextWord;
@@ -150,12 +204,60 @@ std::string DoxygenParser::getNextWord(const TokenList &tokList) {
 			}
 		}
 
+        string tokenStr = trim(m_tokenListIt->m_tokenString);
 		m_tokenListIt++;
-		return nextToken.m_tokenString;
-	}
+		if (!tokenStr.empty()) {
+		    return tokenStr;
+		}
+	} /* else if (nextToken.m_tokenType == END_LINE) {
+	    // this handles cases when command is the last item in line, for example:
+	    // * This method returns line number \c
+	    // * relative to paragraph.
+        m_tokenListIt++;
+        return getNextWord();
+	} */
+
 	return "";
 }
 
+/* TODO remove this m.
+std::string DoxygenParser::getNextWordInComment() {
+
+    while (m_tokenListIt != m_tokenList.end()  &&  (m_tokenListIt->m_tokenType == PLAINSTRING  ||  m_tokenListIt->m_tokenType == END_LINE)) {
+        // handle quoted strings as words
+        if (m_tokenListIt->m_tokenString[0] == '"'
+                && m_tokenListIt->m_tokenString[m_tokenListIt->m_tokenString.size() - 1] != '"') {
+
+            string word = m_tokenListIt->m_tokenString + " ";
+            while (true) {
+                string nextWord = getNextWord();
+                if (nextWord.empty()) {// maybe report unterminated string error
+                    return word;
+                }
+                word += nextWord;
+                if (word[word.size() - 1] == '"') { // strip quotes
+                    return word.substr(1, word.size() - 2);
+                }
+                word += " ";
+            }
+        }
+
+        string tokenStr = trim(m_tokenListIt->m_tokenString);
+        m_tokenListIt++;
+        if (!tokenStr.empty()) {
+            return tokenStr;
+        }
+    } * else if (nextToken.m_tokenType == END_LINE) {
+        // this handles cases when command is the last item in line, for example:
+        // * This method returns line number \c
+        // * relative to paragraph.
+        m_tokenListIt++;
+        return getNextWord();
+    } *
+
+    return "";
+} */
+
 
 DoxygenParser::TokenListCIt DoxygenParser::getOneLine(const TokenList &tokList) {
 
@@ -183,7 +285,7 @@ std::string DoxygenParser::getStringTilCommand(const TokenList & tokList) {
     while (m_tokenListIt->m_tokenType == PLAINSTRING) {
 		const Token &currentToken = *m_tokenListIt++;
 		if (currentToken.m_tokenType == PLAINSTRING) {
-			description = description + currentToken.m_tokenString + " ";
+			description = description + currentToken.m_tokenString; // + " ";
 		}
 	}
 	return description;
@@ -201,12 +303,10 @@ std::string DoxygenParser::getStringTilEndCommand(const std::string & theCommand
 
 		//TODO: it won't output doxygen commands, need a way to fix it
 		if (m_tokenListIt->m_tokenType == PLAINSTRING) {
-			description += m_tokenListIt->m_tokenString + " ";
+			description += m_tokenListIt->m_tokenString;
 		} else if (m_tokenListIt->m_tokenType == END_LINE) {
 			description += "\n";
-	    }
-
-		if (m_tokenListIt->m_tokenString == theCommand) {
+	    } else if (m_tokenListIt->m_tokenString == theCommand) {
 		    m_tokenListIt++;
 			return description;
 		}
@@ -222,32 +322,33 @@ std::string DoxygenParser::getStringTilEndCommand(const std::string & theCommand
 
 DoxygenParser::TokenListCIt DoxygenParser::getEndOfParagraph(const TokenList & tokList) {
 
-	TokenListCIt endOfParagraph = m_tokenListIt;
+    TokenListCIt endOfParagraph = m_tokenListIt;
 
-	while (endOfParagraph != tokList.end()) {
-		if ((*endOfParagraph).m_tokenType == END_LINE) {
-			endOfParagraph++;
-			if (endOfParagraph != tokList.end() && (*endOfParagraph).m_tokenType == END_LINE) {
-				endOfParagraph++;
-				//cout << "ENCOUNTERED END OF PARA" << endl;
-				return endOfParagraph;
-			}
+    while (endOfParagraph != tokList.end()) {
+        if (endOfParagraph->m_tokenType == END_LINE) {
+            endOfParagraph++;
+            if (endOfParagraph != tokList.end() && endOfParagraph->m_tokenType == END_LINE) {
+                endOfParagraph++;
+                //cout << "ENCOUNTERED END OF PARA" << endl;
+                return endOfParagraph;
+            }
 
-		} else if ((*endOfParagraph).m_tokenType == COMMAND) {
+        } else if (endOfParagraph->m_tokenType == COMMAND) {
 
-			if (isSectionIndicator((*endOfParagraph).m_tokenString)) {
-				return endOfParagraph;
-			} else
-				endOfParagraph++;
+            if (isSectionIndicator(endOfParagraph->m_tokenString)) {
+                return endOfParagraph;
+            } else {
+                endOfParagraph++;
+            }
 
-		} else if ((*endOfParagraph).m_tokenType == PLAINSTRING) {
-			endOfParagraph++;
-		} else {
-			return tokList.end();
-		}
-	}
+        } else if (endOfParagraph->m_tokenType == PLAINSTRING) {
+            endOfParagraph++;
+        } else {
+            return tokList.end();
+        }
+    }
 
-	return tokList.end();
+    return tokList.end();
 }
 
 
@@ -257,16 +358,16 @@ DoxygenParser::TokenListCIt DoxygenParser::getEndOfSection(const std::string & t
     TokenListCIt endOfParagraph = m_tokenListIt;
 
 	while (endOfParagraph != tokList.end()) {
-		if ((*endOfParagraph).m_tokenType == COMMAND) {
-			if (theCommand == (*endOfParagraph).m_tokenString)
+		if (endOfParagraph->m_tokenType == COMMAND) {
+			if (theCommand == endOfParagraph->m_tokenString)
 				return endOfParagraph;
 			else
 				endOfParagraph++;
-		} else if ((*endOfParagraph).m_tokenType == PLAINSTRING) {
+		} else if (endOfParagraph->m_tokenType == PLAINSTRING) {
 			endOfParagraph++;
-		} else if ((*endOfParagraph).m_tokenType == END_LINE) {
+		} else if (endOfParagraph->m_tokenType == END_LINE) {
 			endOfParagraph++;
-			if ((*endOfParagraph).m_tokenType == END_LINE) {
+			if (endOfParagraph->m_tokenType == END_LINE) {
 				endOfParagraph++;
 				return endOfParagraph;
 			}
@@ -293,11 +394,14 @@ DoxygenParser::TokenListCIt DoxygenParser::getEndCommand(const std::string & the
 	return tokList.end();
 }
 
-/* DoxygenParser::TokenListIt DoxygenParser::getTilAnyCommand(const std::string &,
-                                                                  TokenList &) {
-    TokenListIt anIterator;
-	return anIterator;
-} */
+
+void DoxygenParser::skipEndOfLine()
+{
+    if (m_tokenListIt != m_tokenList.end()  &&
+                    m_tokenListIt->m_tokenType == END_LINE) {
+        m_tokenListIt++;
+    }
+}
 
 
 int DoxygenParser::addSimpleCommand(const std::string &theCommand,
@@ -311,19 +415,25 @@ int DoxygenParser::addSimpleCommand(const std::string &theCommand,
 
 
 int DoxygenParser::addCommandWord(const std::string &theCommand,
-                                       const TokenList &tokList,
+                                       const TokenList &,
                                        DoxygenEntityList &doxyList) {
 	if (noisy)
 		cout << "Parsing " << theCommand << endl;
 
-	std::string name = getNextWord(tokList);
-	if (!name.empty()) {
-    DoxygenEntityList aNewList;
-    aNewList.push_back(DoxygenEntity("plainstd::string", name));
-		doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-		return 1;
+	if (isEndOfLine()) {
+	    // handles cases when command is at the end of line (for example "\c\nreally"
+	    skipWhitespaceTokens();
+	    doxyList.push_back(DoxygenEntity("plainstd::endl"));
+	}
+	std::string name = getNextWord();
+    if (!name.empty()) {
+      DoxygenEntityList aNewList;
+      aNewList.push_back(DoxygenEntity("plainstd::string", name));
+      doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+      return 1;
 	} else {
-		printListError(WARN_DOXYGEN_COMMAND_ERROR, "No word followed " + theCommand + " command. Not added");
+		printListError(WARN_DOXYGEN_COMMAND_ERROR, "No word followed " +
+		                theCommand + " command. Not added");
 	}
 	return 0;
 }
@@ -337,6 +447,7 @@ int DoxygenParser::addCommandLine(const std::string &theCommand,
 	TokenListCIt endOfLine = getOneLine(tokList);
 	DoxygenEntityList aNewList = parse(endOfLine, tokList);
 	doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+	skipEndOfLine();
 	return 1;
 }
 
@@ -374,31 +485,32 @@ int DoxygenParser::addCommandEndCommand(const std::string &theCommand,
 
 
 int DoxygenParser::addCommandWordParagraph(const std::string &theCommand,
-                                                 const TokenList &tokList,
-                                                 DoxygenEntityList &doxyList) {
-	if (noisy)
-		cout << "Parsing " << theCommand << endl;
+                                           const TokenList &tokList,
+                                           DoxygenEntityList &doxyList) {
+    if (noisy)
+        cout << "Parsing " << theCommand << endl;
 
-	std::string name = getNextWord(tokList);
+    std::string name = getNextWord();
 
-	if (name.empty()) {
-		printListError(WARN_DOXYGEN_COMMAND_ERROR, "No word followed " + theCommand + " command. Not added");
-		return 0;
-	}
-	TokenListCIt endOfParagraph = getEndOfParagraph(tokList);
-	DoxygenEntityList aNewList;
-	aNewList = parse(endOfParagraph, tokList);
-	aNewList.push_front(DoxygenEntity("plainstd::string", name));
-	doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-	return 1;
+    if (name.empty()) {
+        printListError(WARN_DOXYGEN_COMMAND_ERROR, "No word followed " + theCommand + " command. Not added");
+        return 0;
+    }
+    TokenListCIt endOfParagraph = getEndOfParagraph(tokList);
+    DoxygenEntityList aNewList;
+    aNewList = parse(endOfParagraph, tokList);
+    aNewList.push_front(DoxygenEntity("plainstd::string", name));
+    doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+    return 1;
 }
 
+
 int DoxygenParser::addCommandWordLine(const std::string &theCommand,
                                            const TokenList & tokList,
                                            DoxygenEntityList &doxyList) {
 	if (noisy)
 		cout << "Parsing " << theCommand << endl;
-	std::string name = getNextWord(tokList);
+	std::string name = getNextWord();
 	if (name.empty()) {
 		printListError(WARN_DOXYGEN_COMMAND_ERROR, "No word followed " + theCommand + " command. Not added");
 		return 0;
@@ -413,19 +525,20 @@ int DoxygenParser::addCommandWordLine(const std::string &theCommand,
 	//else cout << "No line followed " << theCommand <<  " command. Not added" << endl;
 }
 
+
 int DoxygenParser::addCommandWordOWordOWord(const std::string &theCommand,
-                                                  const TokenList &tokList,
+                                                  const TokenList &,
                                                   DoxygenEntityList &doxyList) {
 	if (noisy)
 		cout << "Parsing " << theCommand << endl;
 
-	std::string name = getNextWord(tokList);
+	std::string name = getNextWord();
 	if (name.empty()) {
 		printListError(WARN_DOXYGEN_COMMAND_ERROR, "No word followed " + theCommand + " command. Not added");
 		return 0;
 	}
-	std::string headerfile = getNextWord(tokList);
-	std::string headername = getNextWord(tokList);
+	std::string headerfile = getNextWord();
+	std::string headername = getNextWord();
 	DoxygenEntityList aNewList;
 	aNewList.push_back(DoxygenEntity("plainstd::string", name));
 	if (!headerfile.empty())
@@ -438,12 +551,12 @@ int DoxygenParser::addCommandWordOWordOWord(const std::string &theCommand,
 
 
 int DoxygenParser::addCommandOWord(const std::string &theCommand,
-                                        const TokenList &tokList,
+                                        const TokenList &,
                                         DoxygenEntityList &doxyList) {
 	if (noisy)
 		cout << "Parsing " << theCommand << endl;
 
-	std::string name = getNextWord(tokList);
+	std::string name = getNextWord();
 	DoxygenEntityList aNewList;
 	aNewList.push_back(DoxygenEntity("plainstd::string", name));
 	doxyList.push_back(DoxygenEntity(theCommand, aNewList));
@@ -478,17 +591,17 @@ int DoxygenParser::addCommandUnique(const std::string &theCommand,
 	else if (theCommand == "xrefitem") {
 		if (noisy)
 			cout << "Parsing " << theCommand << endl;
-		std::string key = getNextWord(tokList);
+		std::string key = getNextWord();
 		if (key.empty()) {
 			printListError(WARN_DOXYGEN_COMMAND_ERROR, "No key followed " + theCommand + " command. Not added");
 			return 0;
 		}
-		std::string heading = getNextWord(tokList);
+		std::string heading = getNextWord();
 		if (key.empty()) {
 			printListError(WARN_DOXYGEN_COMMAND_ERROR, "No heading followed " + theCommand + " command. Not added");
 			return 0;
 		}
-		std::string title = getNextWord(tokList);
+		std::string title = getNextWord();
 		if (title.empty()) {
 			printListError(WARN_DOXYGEN_COMMAND_ERROR, "No title followed " + theCommand + " command. Not added");
 			return 0;
@@ -503,12 +616,12 @@ int DoxygenParser::addCommandUnique(const std::string &theCommand,
 	}
 	// \ingroup (<groupname> [<groupname> <groupname>])
 	else if (theCommand == "ingroup") {
-		std::string name = getNextWord(tokList);
+		std::string name = getNextWord();
 		aNewList.push_back(DoxygenEntity("plainstd::string", name));
-		name = getNextWord(tokList);
+		name = getNextWord();
 		if (!name.empty())
 			aNewList.push_back(DoxygenEntity("plainstd::string", name));
-		name = getNextWord(tokList);
+		name = getNextWord();
 		if (!name.empty())
 			aNewList.push_back(DoxygenEntity("plainstd::string", name));
 		doxyList.push_back(DoxygenEntity(theCommand, aNewList));
@@ -528,9 +641,9 @@ int DoxygenParser::addCommandUnique(const std::string &theCommand,
 	// \headerfile <header-file> [<header-name>]
 	else if (theCommand == "headerfile") {
 		DoxygenEntityList aNewList;
-		std::string name = getNextWord(tokList);
+		std::string name = getNextWord();
 		aNewList.push_back(DoxygenEntity("plainstd::string", name));
-		name = getNextWord(tokList);
+		name = getNextWord();
 		if (!name.empty())
 			aNewList.push_back(DoxygenEntity("plainstd::string", name));
 		doxyList.push_back(DoxygenEntity(theCommand, aNewList));
@@ -551,7 +664,7 @@ int DoxygenParser::addCommandUnique(const std::string &theCommand,
 	else if (theCommand == "weakgroup") {
 		if (noisy)
 			cout << "Parsing " << theCommand << endl;
-		std::string name = getNextWord(tokList);
+		std::string name = getNextWord();
 		if (name.empty()) {
 			printListError(WARN_DOXYGEN_COMMAND_ERROR, "No word followed " + theCommand + " command. Not added");
 			return 0;
@@ -568,12 +681,12 @@ int DoxygenParser::addCommandUnique(const std::string &theCommand,
 	else if (theCommand == "ref") {
 		if (noisy)
 			cout << "Parsing " << theCommand << endl;
-		std::string name = getNextWord(tokList);
+		std::string name = getNextWord();
 		if (name.empty()) {
 			printListError(WARN_DOXYGEN_COMMAND_ERROR, "No key followed " + theCommand + " command. Not added");
 			return 0;
 		}
-		std::string text = getNextWord(tokList);
+		std::string text = getNextWord();
 		aNewList.push_back(DoxygenEntity("plainstd::string", name));
 		if (!text.empty())
 			aNewList.push_back(DoxygenEntity("plainstd::string", text));
@@ -583,12 +696,12 @@ int DoxygenParser::addCommandUnique(const std::string &theCommand,
 	else if (theCommand == "subpage") {
 		if (noisy)
 			cout << "Parsing " << theCommand << endl;
-		std::string name = getNextWord(tokList);
+		std::string name = getNextWord();
 		if (name.empty()) {
 			printListError(WARN_DOXYGEN_COMMAND_ERROR, "No name followed " + theCommand + " command. Not added");
 			return 0;
 		}
-		std::string text = getNextWord(tokList);
+		std::string text = getNextWord();
 		aNewList.push_back(DoxygenEntity("plainstd::string", name));
 		if (!text.empty())
 			aNewList.push_back(DoxygenEntity("plainstd::string", text));
@@ -632,12 +745,12 @@ int DoxygenParser::addCommandUnique(const std::string &theCommand,
 	else if (theCommand == "dotfile" || theCommand == "mscfile") {
 		if (noisy)
 			cout << "Parsing " << theCommand << endl;
-		std::string file = getNextWord(tokList);
+		std::string file = getNextWord();
 		if (file.empty()) {
 			printListError(WARN_DOXYGEN_COMMAND_ERROR, "No file followed " + theCommand + " command. Not added");
 			return 0;
 		}
-		std::string caption = getNextWord(tokList);
+		std::string caption = getNextWord();
 		aNewList.push_back(DoxygenEntity("plainstd::string", file));
 		if (!caption.empty())
 			aNewList.push_back(DoxygenEntity("plainstd::string", caption));
@@ -647,18 +760,18 @@ int DoxygenParser::addCommandUnique(const std::string &theCommand,
 	else if (theCommand == "image") {
 		if (noisy)
 			cout << "Parsing " << theCommand << endl;
-		std::string format = getNextWord(tokList);
+		std::string format = getNextWord();
 		if (format.empty()) {
 			printListError(WARN_DOXYGEN_COMMAND_ERROR, "No format followed " + theCommand + " command. Not added");
 			return 0;
 		}
-		std::string file = getNextWord(tokList);
+		std::string file = getNextWord();
 		if (file.empty()) {
 			printListError(WARN_DOXYGEN_COMMAND_ERROR, "No name followed " + theCommand + " command. Not added");
 			return 0;
 		}
-		std::string caption = getNextWord(tokList);
-		std::string size = getNextWord(tokList);
+		std::string caption = getNextWord();
+		std::string size = getNextWord();
 
 		DoxygenEntityList aNewList;
 		aNewList.push_back(DoxygenEntity("plainstd::string", format));
@@ -673,9 +786,9 @@ int DoxygenParser::addCommandUnique(const std::string &theCommand,
 	else if (theCommand == "addtogroup") {
 		if (noisy)
 			cout << "Parsing " << theCommand << endl;
-		std::string name = getNextWord(tokList);
+		std::string name = getNextWord();
 		if (name.empty()) {
-			printListError(WARN_DOXYGEN_COMMAND_ERROR, "No word followed " + theCommand + " command. Not added");
+			printListError(WARN_DOXYGEN_COMMAND_ERROR, "There should be at least one word following the '" + theCommand + "' command. Command ignored.");
 			return 0;
 		}
 		DoxygenEntityList aNewList;
@@ -685,6 +798,7 @@ int DoxygenParser::addCommandUnique(const std::string &theCommand,
 		}
 		aNewList.push_front(DoxygenEntity("plainstd::string", name));
 		doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+		skipEndOfLine();
 	}
 	// \if <cond> [\else ...] [\elseif <cond> ...] \endif
 	else if (theCommand == "if" || theCommand == "ifnot" ||
@@ -696,7 +810,7 @@ int DoxygenParser::addCommandUnique(const std::string &theCommand,
 		bool skipEndif = false; // if true then we skip endif after parsing block of code
 		bool needsCond = (theCommand == "if" || theCommand == "ifnot" || theCommand == "elseif");
 		if (needsCond) {
-			cond = getNextWord(tokList);
+			cond = getNextWord();
 			if (cond.empty()) {
 				printListError(WARN_DOXYGEN_COMMAND_ERROR, "No word followed " + theCommand + " command. Not added");
 				return 0;
@@ -755,6 +869,7 @@ int DoxygenParser::addCommand(const std::string &commandString,
 		doxyList.push_back(DoxygenEntity("plainstd::string", nextPhrase));
 		return 1;
 	}
+
 	switch (commandBelongs(theCommand)) {
 		case SIMPLECOMMAND:
 			return addSimpleCommand(theCommand, doxyList);
@@ -824,13 +939,13 @@ DoxygenEntityList DoxygenParser::createTree(const std::string &doxygenBlob,
                                                const std::string &fileName,
                                                int lineNumber) {
 
-  TokenList tokList = tokenizeDoxygenComment(doxygenBlob, fileName, lineNumber);
+  tokenizeDoxygenComment(doxygenBlob, fileName, lineNumber);
   if (noisy) {
     cout << "---TOKEN LIST---" << endl;
     printList();
   }
 
-  DoxygenEntityList rootList = parse(tokList.end(), tokList, true);
+  DoxygenEntityList rootList = parse(m_tokenList.end(), m_tokenList, true);
 
   if (noisy) {
     cout << "PARSED LIST" << endl;
@@ -842,8 +957,8 @@ DoxygenEntityList DoxygenParser::createTree(const std::string &doxygenBlob,
 
 /**
  * This is one of the most important methods - it breaks the original
- * doxygen comment into tokens.
- */
+ * doxygen comment into tokens - one token per word.
+ * See replacement, which also handles html comments below.
 DoxygenParser::TokenList DoxygenParser::tokenizeDoxygenComment(const std::string &doxygenComment,
                                                                       const std::string &fileName,
                                                                       int fileLine) {
@@ -860,6 +975,14 @@ DoxygenParser::TokenList DoxygenParser::tokenizeDoxygenComment(const std::string
     pos = doxygenComment.find_first_of("\\@\t\n ", lastPos);
     if (pos == string::npos) {
       pos = doxygenComment.size();
+    // } else {
+      // preserve whitespaces
+    //  while (pos != string::npos  &&  (doxygenComment[pos] == ' ' ||  doxygenComment[pos] == '\t')) {
+    //    pos++;
+    //  }
+    //  if (pos == string::npos) {
+    //    pos = doxygenComment.size();
+    //  }
     }
 
     currentWord = doxygenComment.substr(lastPos, pos-lastPos);
@@ -875,7 +998,7 @@ DoxygenParser::TokenList DoxygenParser::tokenizeDoxygenComment(const std::string
         currentWord += doxygenComment[pos];
         pos++;
       }
-      // also strip the command till the first nonalpha char
+      // also strip the command till the first non-alpha char
       for (size_t i = 2; i < currentWord.size(); i++) {
         if (!isalpha(currentWord[i])) {
           currentWord = currentWord.substr(0, i);
@@ -920,6 +1043,213 @@ DoxygenParser::TokenList DoxygenParser::tokenizeDoxygenComment(const std::string
 
   return tokList;
 }
+ */
+
+
+// Splits 'text' on 'separator' chars. Separator chars are not part of the strings.
+DoxygenParser::StringVector DoxygenParser::split(const std::string &text, char separator)
+{
+    StringVector lines;
+    size_t prevPos = 0, pos = 0;
+
+    while (pos < string::npos) {
+        pos = text.find(separator, prevPos);
+        lines.push_back(text.substr(prevPos, pos - prevPos));
+        prevPos = pos + 1;
+    }
+
+    return lines;
+}
+
+
+bool DoxygenParser::isStartOfDoxyCommentChar(char c)
+{
+    return (strchr("*/!", c) != NULL);
+}
+
+
+void DoxygenParser::addDoxyCommand(DoxygenParser::TokenList &tokList,
+                                        const std::string &cmd) {
+    if (findCommand(cmd)) {
+        tokList.push_back(Token(COMMAND, cmd));
+    } else {
+        // Unknown commands are ignored, because they are
+        // also ignored by Doxygen - see test doxygen_misc_constructs.h, f. backslashB().
+        // This differs from original implementation in this class. Uncomment
+        // the line below to put unknown commands to output.
+        // tokList.push_back(Token(PLAINSTRING, cmd));
+    }
+}
+
+
+size_t DoxygenParser::processVerbatimText(size_t pos, const std::string &line)
+{
+    if (line[pos] == '\\'  ||  line[pos] == '@') {
+        pos++;
+        // characters '$[]{}' are used in commands \f$, \f[, ...
+        size_t endOfWordPos = line.find_first_not_of("abcdefghijklmnopqrstuvwxyz$[]{}", pos);
+        string cmd = line.substr(pos , endOfWordPos - pos);
+
+        if (cmd == CMD_END_HTML_ONLY  ||  cmd == CMD_END_VERBATIM) {
+            m_isVerbatimText = false;
+            addDoxyCommand(m_tokenList, cmd);
+        } else {
+            cmd = line[pos] + cmd; // prepend '\\' or '@'
+            m_tokenList.push_back(Token(PLAINSTRING,
+                                  line.substr(pos, endOfWordPos - pos)));
+        }
+        pos = endOfWordPos;
+    } else {
+        // whitespaces are stored as plain strings
+        size_t startOfPossibleEndCmd = line.find_first_of("\\@", pos);
+        m_tokenList.push_back(Token(PLAINSTRING,
+                              line.substr(pos, startOfPossibleEndCmd - pos)));
+        pos = startOfPossibleEndCmd;
+    }
+
+    return pos;
+}
+
+
+size_t DoxygenParser::processNormalComment(size_t pos, const std::string &line)
+{
+    switch (line[pos]) {
+    case '\\':  // process doxy command or escaped char
+       /* switch (line[pos + 1]) {
+        case '$':
+        case '@':
+        case '\':
+        case '&':
+        case '~':
+        case '<':
+        case '>':
+        case '#': \% \" \. \::
+        }
+        TODO break case if any of escaped chars */
+    case '@': {
+      pos++;
+      // characters '$[]{}' are used in commands \f$, \f[, ...
+      size_t endOfWordPos = line.find_first_not_of("abcdefghijklmnopqrstuvwxyz$[]{}", pos);
+      string cmd = line.substr(pos , endOfWordPos - pos);
+      addDoxyCommand(m_tokenList, cmd);
+      if (cmd == CMD_HTML_ONLY  ||  cmd == CMD_VERBATIM) {
+          m_isVerbatimText = true;
+      }
+      // skip any possible spaces after command, because some commands have parameters,
+      // and spaces between command and parameter must be ignored.
+      if (endOfWordPos != string::npos) {
+          pos = line.find_first_not_of(" \t", endOfWordPos);
+      } else {
+          pos = string::npos;
+      }
+    } break;
+
+    case ' ':  // whitespace
+    case '\t': {
+      // whitespaces are stored as plain strings
+      size_t startOfNextWordPos = line.find_first_not_of(" \t", pos + 1);
+      m_tokenList.push_back(Token(PLAINSTRING,
+                               line.substr(pos, startOfNextWordPos - pos)));
+      pos = startOfNextWordPos;
+    } break;
+
+    case '<': { // process html commands
+
+      size_t endHtmlPos = line.find_first_of("\t >", pos + 1);
+      if (endHtmlPos != string::npos) {
+        // will push plain string Token. If the command is not HTML supported by
+        // Doxygen, < and > will be replaced by HTML entities &lt; and &gt; respectively,
+        // but only if 'htmlOnly' flag == false. The flag is set/reset by \htmlonly \verbatim,
+        // \endhtmlonly \endverbatim Doxygen commands.
+        // handleHTMLCommand(line.substr(pos + 1), endHtmlPos - pos - 1);
+      }
+      pos = endHtmlPos;
+    } break;
+
+    case '&': { // process HTML entities
+        size_t endOfWordPos = line.find_first_not_of("abcdefghijklmnopqrstuvwxyz", pos + 1);
+        if (endOfWordPos != string::npos) {
+            if (line[endOfWordPos] == ';') {
+                addDoxyCommand(m_tokenList, line.substr(pos, endOfWordPos));
+            } else {
+                // it is not an entity - push plain string
+                m_tokenList.push_back(Token(PLAINSTRING,
+                                      line.substr(pos, endOfWordPos - pos)));
+                pos = endOfWordPos;
+            }
+        } else {
+            pos = string::npos;
+        }
+    }
+    break;
+    default:
+      printListError(WARN_DOXYGEN_COMMAND_ERROR, "Unknown special character: " + line[pos]);
+    }
+
+    return pos;
+}
+
+
+/**
+ * This method tokenizes Doxygen comment to words and doxygen commands.
+ */
+void DoxygenParser::tokenizeDoxygenComment(const std::string &doxygenComment,
+                                                 const std::string &fileName,
+                                                 int fileLine)
+{
+  m_isVerbatimText = false;
+  m_tokenList.clear();
+  m_fileLineNo = fileLine;
+  m_fileName = fileName;
+
+  StringVector lines = split(doxygenComment, '\n');
+
+  for (StringVectorCIt it = lines.begin(); it != lines.end(); it++) {
+    const string &line = *it;
+    size_t pos = line.find_first_not_of(" \t");
+
+    // skip sequences of '*', '/', and '!' of any length
+    while (pos != string::npos  &&  isStartOfDoxyCommentChar(line[pos])) {
+      pos++;
+    }
+
+    if (pos == string::npos) {
+        m_tokenList.push_back(Token(END_LINE, "\n"));
+      continue;
+    }
+
+    // line[pos] may be ' \t' or start of word, it there was no '*', '/' or '!'
+    // at beginning of the line. Make sure it points to start of the first word
+    // in the line.
+    pos = line.find_first_not_of(" \t", pos);
+    if (pos == string::npos) {
+      m_tokenList.push_back(Token(END_LINE, "\n"));
+      continue;
+    }
+
+    while (pos != string::npos) {
+      // find the end of the word
+      size_t doxyCmdOrHtmlTagPos = line.find_first_of("\\@< \t", pos);
+      if (doxyCmdOrHtmlTagPos != pos) {
+        // plain text found
+        m_tokenList.push_back(Token(PLAINSTRING,
+                                 line.substr(pos, doxyCmdOrHtmlTagPos - pos)));
+      }
+
+      pos = doxyCmdOrHtmlTagPos;
+      if (pos != string::npos) {
+        if (m_isVerbatimText) {
+            pos = processVerbatimText(pos, line);
+        } else {
+            pos = processNormalComment(pos, line);
+        }
+      }
+    }
+    m_tokenList.push_back(Token(END_LINE, "\n")); // add when pos == npos - end of line
+  }
+
+  m_tokenListIt = m_tokenList.begin();
+}
 
 
 void DoxygenParser::printList() {
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.h b/Source/DoxygenTranslator/src/DoxygenParser.h
index 6e2c539ce..019da8785 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.h
+++ b/Source/DoxygenTranslator/src/DoxygenParser.h
@@ -14,6 +14,7 @@
 #include <string>
 #include <list>
 #include <map>
+#include <vector>
 #include <set>
 #include "DoxygenEntity.h"
 
@@ -67,7 +68,7 @@ private:
   };
 
 
-  typedef std::list<Token> TokenList;
+  typedef std::vector<Token> TokenList;
   typedef TokenList::const_iterator TokenListCIt;
   typedef TokenList::iterator TokenListIt;
 
@@ -84,6 +85,8 @@ private:
   static DoxyCommandsMap doxygenCommands;
   static std::set<std::string> doxygenSectionIndicators;
 
+  bool m_isVerbatimText; // used to handle \htmlonly and \verbatim commands
+
   std::string m_fileName;
   int m_fileLineNo;
 
@@ -119,12 +122,34 @@ private:
    */
   void printTree(const std::list <DoxygenEntity> &rootList);
 
+  /**
+   * Returns true if the next token is end of line token. This is important
+   * when single word commands like \c are at the end of line.
+   */
+  bool isEndOfLine();
+
+  /**
+   * Skips spaces, tabs, and end of line tokens.
+   */
+  void skipWhitespaceTokens();
+
+  /**
+   * Removes all spaces and tabs from beginning end end of string.
+   */
+  std::string trim(const std::string &text);
+
   /*
    * Returns the next word ON THE CURRENT LINE ONLY
    * if a new line is encountered, returns a blank std::string.
-   * Updates the index it is given if success.
+   * Updates the iterator if successful.
    */
-  std::string getNextWord(const TokenList &tokList);
+  std::string getNextWord();
+
+  /*
+   * Returns the next word, which is not necessarily on the same line.
+   * Updates the iterator if successful.
+   */
+  std::string getNextWordInComment();
 
   /* 
    * Returns the location of the end of the line as
@@ -178,6 +203,16 @@ private:
                                   const TokenList &tokList);
    */
 
+  /**
+   * This methods skips end of line token, if it is the next token to be
+   * processed. It is called with comment commands which have args till the
+   * end of line, such as 'addtogroup' or 'addindex'.
+   * It is up to translator to specific language to decide whether
+   * to insert eol or not. For example, if a command is ignored in target
+   * language, new lines may make formatting ugly (Python).
+   */
+  void skipEndOfLine();
+
   /*
    * Method for Adding a Simple Command
    * Format: @command
@@ -298,13 +333,26 @@ private:
    * Fill static doxygenCommands and sectionIndicators containers
    */
   void fillTables();
-  
-  TokenList tokenizeDoxygenComment(const std::string &doxygenComment,
-		                              const std::string &fileName,
-		                              int fileLine);
+
+  /** Processes comment when \htmlonly and \verbatim commands are encountered. */
+  size_t processVerbatimText(size_t pos, const std::string &line);
+
+  /** Processes comment outside \htmlonly and \verbatim commands. */
+  size_t processNormalComment(size_t pos, const std::string &line);
+
+  void tokenizeDoxygenComment(const std::string &doxygenComment,
+                                 const std::string &fileName,
+                                 int fileLine);
   void printList();
   void printListError(int warningType, const std::string &message);
 
+  typedef std::vector<std::string> StringVector;
+  typedef StringVector::const_iterator StringVectorCIt;
+
+  StringVector split(const std::string &text, char separator);
+  bool isStartOfDoxyCommentChar(char c);
+  void addDoxyCommand(DoxygenParser::TokenList &tokList, const std::string &cmd);
+
 public:
   DoxygenParser(bool noisy = false);
   virtual ~DoxygenParser();
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.cpp b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
index 83b08ba39..8527ed689 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
@@ -30,6 +30,41 @@ void JavaDocConverter::fillStaticTables() {
   if (tagHandlers.size()) // fill only once
     return;
 
+  /*
+   * Some translation rules:
+   *
+   * @ and \ must be escaped for both Java and Python to appear on output: \@, \\,
+   *         while Doxygen produces output in both cases.
+   * Rule:   @ and \ with space on the right should get to output.
+   *
+   * :: remains intact, even in class::method(). But you can use class#method also
+   *    in C++ comment and it is properly translated to C++ output (changed by doxygen to ::)
+   *    and Java output (remains #).
+   * Rule: SWIG type system can't be used to convert C::m to C#m, because in Java it is C.m
+   *       Use string replacement :: --> # in tag see and links.
+   *
+   * HTML tags must be translated - remain in Java, to markdown in Python
+   *
+   * Unknown HTML tags, for example <x> is translated to &lt;x&gt; by doxygen, while
+   *     Java src is <x> and therefore invisible on output - browser ignores unknown command.
+   *     This is handy in syntax descriptions, for example: more <fileName>.
+   *
+   * Standlaone < and > need not to be translated, they are rendered properly in
+   *      all three outputs.
+   *
+   * ., %, and " need not to be translated
+   *
+   * entities must be translated - remain in Java, something meaningfull in Python (&lt, ...)
+   *
+   * \e at end of line freezes doxygen
+   *
+   * - enum inside class is missing comment
+   * - '\' not representing doxygen commands
+   * - add comments also to auto-generated methods lilke equals(), delete() in Java,
+   *   and methods for std::vector(), ...
+   */
+
+
   // these commands insert HTML tags
   tagHandlers["a"] = make_pair(&JavaDocConverter::handleTagHtml, "i");
   tagHandlers["arg"] = make_pair(&JavaDocConverter::handleTagHtml, "li");
@@ -172,8 +207,11 @@ std::string JavaDocConverter::formatCommand(std::string unformattedLine,
 
 
 /**
- * Returns true, if the given parameter exists in the current node. If feature
- * 'doxygen:nostripparams' is set, then this method always returns true.
+ * Returns true, if the given parameter exists in the current node
+ * (for example param is a name of function parameter). If feature
+ * 'doxygen:nostripparams' is set, then this method always returns
+ * true - parameters are copied to output regardless of presence in
+ * function params list.
  */
 bool JavaDocConverter::paramExists(std::string param) {
 
@@ -276,8 +314,8 @@ void JavaDocConverter::handleParagraph(DoxygenEntity& tag, std::string& translat
 
 void JavaDocConverter::handlePlainString(DoxygenEntity& tag, std::string& translatedComment, std::string&) {
   translatedComment += tag.data;
-  if (tag.data.size() && tag.data[tag.data.size()-1] != ' ')
-  	translatedComment += " ";
+ // if (tag.data.size() && tag.data[tag.data.size()-1] != ' ')
+ // 	translatedComment += " ";
 }
 
 
@@ -345,8 +383,11 @@ void JavaDocConverter::handleTagPar(DoxygenEntity& tag, std::string& translatedC
 }
 
 
-void JavaDocConverter::handleTagParam(DoxygenEntity& tag, std::string& translatedComment, std::string&) {
+void JavaDocConverter::handleTagParam(DoxygenEntity& tag,
+                                      std::string& translatedComment,
+                                      std::string&) {
   std::string dummy;
+
   if (!tag.entityList.size())
     return;
   if (!paramExists(tag.entityList.begin()->data))
@@ -356,6 +397,7 @@ void JavaDocConverter::handleTagParam(DoxygenEntity& tag, std::string& translate
   translatedComment += tag.entityList.begin()->data + " ";
   tag.entityList.pop_front();
   handleParagraph(tag, translatedComment, dummy);
+  printf("cmd: %s\n", translatedComment.c_str());
 }
 
 
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.h b/Source/DoxygenTranslator/src/JavaDocConverter.h
index 9715593c6..2c3ac72f0 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.h
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.h
@@ -35,7 +35,7 @@ protected:
    */
   std::string translateSubtree(DoxygenEntity & doxygenEntity);
   /*
-   * Translate one entity with the appropriate handler, acording
+   * Translate one entity with the appropriate handler, according
    * to the tagHandlers
    */
   void translateEntity(DoxygenEntity &tag, std::string &translatedComment);

From 20cc685e8aa64c0b802dcb3f7e2efc67498fb1ea Mon Sep 17 00:00:00 2001
From: Marko Klopcic <markok3.14@gmail.com>
Date: Thu, 10 Jan 2013 22:26:50 +0100
Subject: [PATCH 155/314] tests with escapes added, tests refactored - broken
 to smaller chunks

---
 Doc/Manual/Doxygen.html                       |  11 +-
 Examples/test-suite/doxygen_misc_constructs.h |  29 +++-
 Examples/test-suite/doxygen_misc_constructs.i |   2 +-
 .../test-suite/doxygen_translate_all_tags.i   |  79 +++++++--
 Examples/test-suite/java/commentParser.java   | 161 +++++++++---------
 .../doxygen_translate_all_tags_runme.java     |  76 +++++----
 6 files changed, 220 insertions(+), 138 deletions(-)

diff --git a/Doc/Manual/Doxygen.html b/Doc/Manual/Doxygen.html
index d71c6dcba..bc68ed15c 100644
--- a/Doc/Manual/Doxygen.html
+++ b/Doc/Manual/Doxygen.html
@@ -469,6 +469,10 @@ Here is the list of all Doxygen tags and the description of how they are transla
 <td>translated to @exception</td>
 </tr>
 <tr>
+<td>\f$, \f[, \f], \f{, \f}</td>
+<td>LateX formulas are left unchanged</td>
+</tr>
+<tr>
 <td>\if</td>
 <td>replaced with 'If: &lt;condition&gt; {'</td>
 </tr>
@@ -686,13 +690,6 @@ Here is the list of these tags:
 <td>\enum</td>
 <td>\example</td>
 <td>\extends</td>
-<td>\f$</td>
-</tr>
-<tr>
-<td>\f[</td>
-<td>\f]</td>
-<td>\f{</td>
-<td>\f}</td>
 </tr>
 <tr>
 <td>\file</td>
diff --git a/Examples/test-suite/doxygen_misc_constructs.h b/Examples/test-suite/doxygen_misc_constructs.h
index 813e6ddcd..e5d317fc2 100644
--- a/Examples/test-suite/doxygen_misc_constructs.h
+++ b/Examples/test-suite/doxygen_misc_constructs.h
@@ -26,24 +26,39 @@ void isNoSpaceValidC()
 
 
 /**
- * Backslash following\c word is valid doxygen command. Output contains
- * 'followingword' with word in 'code' font.
+ * Backslash following\c word is a valid doxygen command. Output contains
+ * 'followingword' with 'word' in 'code' font.
  */
 void backslashA()
 {}
 
+// Output of escaped symbols below in doxygen generated HTML:
+// Rendered: Escaped symbols: $ @ \ & < > # % " \. ::
+// HTML source: Escaped symbols: $ @ \ &amp; &lt; &gt; # % " \. :: 
+
 /**
- * Doxy command without trailing \cspace space is ignored. Standalone
- * \ and '\' get to output.  Commands not recognized by Doxygen \blah
- * are ignored.  Backslashes in DOS paths d:\xyz\c\myfile and words
- * following them do not appear on output, we must quote them with
- * double quotes: "d:\xyz\c\myfile", single quotes do not help:
+ * Doxy command without trailing \cspace space is ignored - nothing appears
+ * on output. Standalone \ and '\' get to output.
+ * Standalone @ and '@' get to output.
+ * Commands not recognized by Doxygen \blah @blah are ignored.
+ * Backslashes in DOS paths d:\xyz\c\myfile and
+ * words following them do not appear on output, we must quote them with
+ * double quotes: "d:\xyz\c\myfile", "@something". single quotes do not help:
  * 'd:\xyz\c\myfile'. Escaping works: d:\\xyz\\c\\myfile. Unix
  * paths of course have no such problems: /xyz/c/myfile
+ * Escaped symbols:
+ * \$ \@ \\ \& \~ \< \> \# \% \" \. \::
  */
 void backslashB()
 {}
 
+/**
+ * Backslash e at end of \e line froze SWIG \e
+ * with old comment parser.
+ */
+void backslashC()
+{}
+
 /**
  *
  */
diff --git a/Examples/test-suite/doxygen_misc_constructs.i b/Examples/test-suite/doxygen_misc_constructs.i
index 447e6b24e..0eee8aa9d 100644
--- a/Examples/test-suite/doxygen_misc_constructs.i
+++ b/Examples/test-suite/doxygen_misc_constructs.i
@@ -31,7 +31,7 @@
      * Returns address of file line.
      *
      * @param fileName name of the file, where the source line is located
-	* @param line line number
+     * @param line line number
      * @param isGetSize if set, for every object location both address and size are returned
      *
      * @link Connection::getId() @endlink <br>
diff --git a/Examples/test-suite/doxygen_translate_all_tags.i b/Examples/test-suite/doxygen_translate_all_tags.i
index cb3332179..f780b643a 100644
--- a/Examples/test-suite/doxygen_translate_all_tags.i
+++ b/Examples/test-suite/doxygen_translate_all_tags.i
@@ -17,7 +17,6 @@
  * You were warned!
  *
  * \authors lots of them
- * 
  * \author Zubr
  * 
  * \b boldword
@@ -26,21 +25,22 @@
  * extended to many lines.
  *
  * \bug Not everything works right now...
- *
  * \c codeword
  * 
  * \callgraph
- *
  * \callergraph
- *
  * \category someCategory headerFile.h headerName
  *
  * \cite citationword
- * 
  * \class someClass headerFile.h headerName
- *
  * \code some test code \endcode
- * 
+ */
+int func01(int a)
+{
+}
+
+ 
+/** 
  * \cond SOMECONDITION
  * Some conditional comment
  * \endcond
@@ -63,7 +63,13 @@
  * 
  * \details This is very large
  * and detailed description of some thing
- *
+ */
+int func02(int a)
+{
+}
+
+ 
+/**
  * \dir /somePath/someFolder
  *
  * \dontinclude someFile.h
@@ -87,6 +93,13 @@
  *
  * \example someFile.txt
  * Some details on using the example
+ */
+int func03(int a)
+{
+}
+
+ 
+/**
  * 
  * \exception SuperError
  * 
@@ -115,7 +128,13 @@
  * \htmlonly
  * This will only appear in hmtl
  * \endhtmlonly
- *
+ */
+int func04(int a)
+{
+}
+
+ 
+/**
  * \if ANOTHERCONDITION
  *   First part of comment
  *   \if SECONDCONDITION
@@ -150,7 +169,13 @@
  *
  * \invariant Some text
  * describing invariant.
- *
+ */
+int func05(int a)
+{
+}
+
+ 
+/**
  * \interface someInterface someHeader.h "Header name"
  *
  * \latexonly
@@ -186,7 +211,13 @@
  * \mscfile mscFile.msc "The caption"
  *
  * \n \n \n
- * 
+ */
+int func06(int a)
+{
+}
+
+ 
+/**
  * \name someHeader.h
  *
  * \namespace someNamespace
@@ -221,7 +252,13 @@
  * \privatesection
  *
  * \property someVar
- *
+ */
+int func07(int a)
+{
+}
+
+ 
+/**
  * \protected
  *
  * \protectedsection
@@ -253,7 +290,13 @@
  * \returns may return
  * 
  * \retval someValue Some description
- *
+ */
+int func08(int a)
+{
+}
+
+ 
+/**
  * \rtfonly
  * This will only appear in RTF
  * \endrtfonly
@@ -294,7 +337,13 @@
  * \throw superException
  * 
  * \throws RuntimeError
- * 
+ */
+int func09(int a)
+{
+}
+
+ 
+/**
  * \todo Some very important task
  * 
  * \tparam b B is mentioned again...
@@ -331,7 +380,7 @@
  * 
  * And here goes simple text
  */
-int function(int a, float b)
+int func10(int a, float b)
 {
 }
 
diff --git a/Examples/test-suite/java/commentParser.java b/Examples/test-suite/java/commentParser.java
index 94beb8c2f..581a862c8 100644
--- a/Examples/test-suite/java/commentParser.java
+++ b/Examples/test-suite/java/commentParser.java
@@ -5,97 +5,100 @@ import java.util.Map.Entry;
 import java.util.Iterator;
 
 public class commentParser {
-	static HashMap<String, String> parsedComments = new HashMap<String, String>();
+    static HashMap<String, String> parsedComments = new HashMap<String, String>();
 
-	public static boolean start(RootDoc root) {
+    public static boolean start(RootDoc root) {
 
-		/*
-		 * This method is called by 'javadoc' and gets the whole parsed java
-		 * file, we get comments and store them
-		 */
+        /*
+         * This method is called by 'javadoc' and gets the whole parsed java
+         * file, we get comments and store them
+         */
 
-		for (ClassDoc classDoc : root.classes()) {
+        for (ClassDoc classDoc : root.classes()) {
 
-			if (classDoc.getRawCommentText().length() > 0)
-				parsedComments.put(classDoc.qualifiedName(), classDoc.getRawCommentText());
+            if (classDoc.getRawCommentText().length() > 0)
+                parsedComments.put(classDoc.qualifiedName(), classDoc.getRawCommentText());
 
-			for (FieldDoc f : classDoc.enumConstants()) {
-				if (f.getRawCommentText().length() > 0)
-					parsedComments.put(f.qualifiedName(), f.getRawCommentText());
-			}
-			for (FieldDoc f : classDoc.fields()) {
-				if (f.getRawCommentText().length() > 0)
-					parsedComments.put(f.qualifiedName(), f.getRawCommentText());
-			}
-			for (MethodDoc m : classDoc.methods()) {
-				if (m.getRawCommentText().length() > 0)
-					parsedComments.put(m.toString(), m.getRawCommentText());
-			}
-		}
-		return true;
-	}
+            for (FieldDoc f : classDoc.enumConstants()) {
+                if (f.getRawCommentText().length() > 0)
+                    parsedComments.put(f.qualifiedName(), f.getRawCommentText());
+            }
+            for (FieldDoc f : classDoc.fields()) {
+                if (f.getRawCommentText().length() > 0)
+                    parsedComments.put(f.qualifiedName(), f.getRawCommentText());
+            }
+            for (MethodDoc m : classDoc.methods()) {
+                if (m.getRawCommentText().length() > 0)
+                    parsedComments.put(m.toString(), m.getRawCommentText());
+            }
+        }
+        return true;
+    }
 
-	public static int check(HashMap<String, String> wantedComments) {
-		int errorCount=0;
-		Iterator< Entry<String, String> > it = parsedComments.entrySet().iterator();
+    
+    public static int check(HashMap<String, String> wantedComments) {
+        int errorCount=0;
+        Iterator< Entry<String, String> > it = parsedComments.entrySet().iterator();
 
-		while (it.hasNext())
-		{
-			Entry<String, String> e = (Entry<String, String>) it.next();
-			String actualStr = e.getValue();
-			String wantedStr = wantedComments.get(e.getKey());
-			// this may be weird, but I don't know any more effective solution
-			actualStr = actualStr.replace(" ", "");
-			actualStr = actualStr.replace("\n", "");
-			actualStr = actualStr.replace("\t", "");
-			if (wantedStr != null) {
-				wantedStr = wantedStr.replace(" ", "");
-				wantedStr = wantedStr.replace("\n", "");
-				wantedStr = wantedStr.replace("\t", "");
-			}
+        while (it.hasNext())
+        {
+            Entry<String, String> e = (Entry<String, String>) it.next();
+            String actualStr = e.getValue();
+            String wantedStr = wantedComments.get(e.getKey());
+            // this may be weird, but I don't know any more effective solution
+            actualStr = actualStr.replace(" ", "");
+            actualStr = actualStr.replace("\n", "");
+            actualStr = actualStr.replace("\t", "");
+            if (wantedStr != null) {
+                wantedStr = wantedStr.replace(" ", "");
+                wantedStr = wantedStr.replace("\n", "");
+                wantedStr = wantedStr.replace("\t", "");
+            }
 
-			if (!actualStr.equals(wantedStr)) {
-				System.out.println("Documentation comments for " + e.getKey() + " does not match: ");
-				// here we print original strings, for nicer output
-				System.out.println("\texpected:"+wantedComments.get(e.getKey()));
-				System.out.println("\tgot:\t"+e.getValue());
-				errorCount++;
-			}
-		}
+            if (!actualStr.equals(wantedStr)) {
+                System.out.println("Documentation comments for " + e.getKey() + " do not match: ");
+                // here we print original strings, for nicer output
+                System.out.println("\n\n---\nexpected:\n" + wantedComments.get(e.getKey()));
+                System.out.println("\n\n---\ngot:\n" + e.getValue());
+                errorCount++;
+            }
+        }
 
-		if (parsedComments.size() < wantedComments.size()) {
-			System.out.println("Found " + (wantedComments.size()-parsedComments.size()) + " missed comment(s)!");
-			errorCount++;
-		}
+        if (parsedComments.size() < wantedComments.size()) {
+            System.out.println("Found " + (wantedComments.size()-parsedComments.size()) + " missed comment(s)!");
+            errorCount++;
+        }
 		
-		return errorCount;
-	}
-	
-	public static void printCommentListForJavaSource() {
-		Iterator< Entry<String, String> > it = parsedComments.entrySet().iterator();
-		while (it.hasNext())
-		{
-			Entry<String, String> e = (Entry<String, String>) it.next();
-			String commentText = e.getValue();
-			commentText = commentText.replace("\\", "\\\\");
-			commentText = commentText.replace("\"", "\\\"");
-			commentText = commentText.replace("\n", "\\n\" +\n\t\t\"");
-			System.out.format("wantedComments.put(\"%s\",\n\t\t\"%s\");\n", e.getKey(), commentText);
-		}
-	}
-	
-	public static void main(String argv[]) {
+        return errorCount > 0 ? 1 : 0;
+    }
+
+    
+    public static void printCommentListForJavaSource() {
+        Iterator< Entry<String, String> > it = parsedComments.entrySet().iterator();
+        while (it.hasNext())
+        {
+            Entry<String, String> e = (Entry<String, String>) it.next();
+            String commentText = e.getValue();
+            commentText = commentText.replace("\\", "\\\\");
+            commentText = commentText.replace("\"", "\\\"");
+            commentText = commentText.replace("\n", "\\n\" +\n\t\t\"");
+            System.out.format("wantedComments.put(\"%s\",\n\t\t\"%s\");\n", e.getKey(), commentText);
+        }
+    }
+
+    
+    public static void main(String argv[]) {
 		
-		if (argv.length<1) {
-			System.out.format("Usage:\n\tcommentParsing <package to parse>\n");
-			System.exit(1);
-		}
+        if (argv.length<1) {
+            System.out.format("Usage:\n\tcommentParsing <package to parse>\n");
+            System.exit(1);
+        }
 		
-		com.sun.tools.javadoc.Main.execute("The comment parser program",
-				"commentParser", new String[]{"-quiet", argv[0]});
+        com.sun.tools.javadoc.Main.execute("The comment parser program",
+                                           "commentParser", new String[]{"-quiet", argv[0]});
 		
-		// if we are run as standalone app, print the list of found comments as it would appear in java source
+        // if we are run as standalone app, print the list of found comments as it would appear in java source
 		
-		printCommentListForJavaSource();
-	}
+        printCommentListForJavaSource();
+    }
 }
diff --git a/Examples/test-suite/java/doxygen_translate_all_tags_runme.java b/Examples/test-suite/java/doxygen_translate_all_tags_runme.java
index 6db1f6686..9d9cec2b7 100644
--- a/Examples/test-suite/java/doxygen_translate_all_tags_runme.java
+++ b/Examples/test-suite/java/doxygen_translate_all_tags_runme.java
@@ -25,20 +25,22 @@ public class doxygen_translate_all_tags_runme {
 
     HashMap<String, String> wantedComments = new HashMap<String, String>();
     
-    wantedComments.put("doxygen_translate_all_tags.doxygen_translate_all_tags.function(int, float)",
-    		" <i>Hello </i>\n" +
-    		" <li>some list item \n" +
-    		" </li>This is attention! \n" +
-    		" You were warned! \n" +
-    		" @author lots of them \n" +
-    		" @author Zubr \n" +
-    		" <b>boldword </b>\n" +
-    		" Some brief description, \n" +
-    		" extended to many lines. \n" +
-    		" Not everything works right now... \n" +
-    		" <code>codeword </code>\n" +
-    		" <i>citationword </i>\n" +
-    		" {@code some test code }\n" +
+    wantedComments.put("doxygen_translate_all_tags.doxygen_translate_all_tags.func01(int)",
+    		" <i>Hello </i>\n\n\n\n\n\n" +
+    		" <li>some list item</li>\n\n" +
+    		" This is attention!\n" +
+    		" You were warned!\n" +
+    		" @author lots of them\n" +
+    		" @author Zubr\n\n" +
+    		" <b>boldword</b>\n\n" +
+    		" Some brief description,\n" +
+    		" extended to many lines.\n\n" +
+    		" Not everything works right now...\n" +
+    		" <code>codeword</code>\n\n\n\n\n\n" +
+    		" <i>citationword</i>\n" +
+                " {@code some test code }\n");
+    
+    wantedComments.put("doxygen_translate_all_tags.doxygen_translate_all_tags.func02(int)",
     		" Conditional comment: SOMECONDITION \n" +
     		" Some conditional comment \n" +
     		" End of conditional comment.\n" +
@@ -46,12 +48,18 @@ public class doxygen_translate_all_tags_runme {
     		" 1970 - 2012 \n" +
     		" @deprecated Now use another function \n" +
     		" This is very large \n" +
-    		" and detailed description of some thing \n" +
-    		" <i>italicword </i>\n" +
-    		" <i>emphazedWord </i>\n" +
-    		" @exception SuperError \n" +
-    		" This will only appear in hmtl \n" +
-    		" If: ANOTHERCONDITION {\n" +
+    		" and detailed description of some thing \n");
+    
+    wantedComments.put("doxygen_translate_all_tags.doxygen_translate_all_tags.func03(int)",
+                       " <i>italicword </i>\n" +
+    		" <i>emphazedWord </i>\n");
+    
+    wantedComments.put("doxygen_translate_all_tags.doxygen_translate_all_tags.func04(int)",
+                       " @exception SuperError \n" +
+    		" This will only appear in hmtl \n");
+    
+    wantedComments.put("doxygen_translate_all_tags.doxygen_translate_all_tags.func05(int)",
+                       " If: ANOTHERCONDITION {\n" +
     		" First part of comment \n" +
     		" If: SECONDCONDITION {\n" +
     		" Nested condition text \n" +
@@ -69,16 +77,20 @@ public class doxygen_translate_all_tags_runme {
     		" }\n" +
     		" <img src=testImage.bmp alt=\"Hello, world!\" />\n" +
     		" Some text \n" +
-    		" describing invariant. \n" +
-    		" This will only appear in LATeX \n" +
+    		" describing invariant. \n");
+    
+    wantedComments.put("doxygen_translate_all_tags.doxygen_translate_all_tags.func06(int)",
+                       " This will only appear in LATeX \n" +
     		" <ul> \n" +
     		" <li>Some unordered list \n" +
     		" </li><li>With lots of items \n" +
     		" </li><li>lots of lots of items \n" +
     		" </li></ul> \n" +
     		" {@link someMember Some description follows }\n" +
-    		" This will only appear in man \n" +
-    		" Note: Here \n" +
+    		" This will only appear in man\n");
+    
+    wantedComments.put("doxygen_translate_all_tags.doxygen_translate_all_tags.func07(int)",
+                       " Note: Here \n" +
     		" is the note! \n" +
     		" This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.\n" +
     		" <code>someword </code>\n" +
@@ -87,21 +99,27 @@ public class doxygen_translate_all_tags_runme {
     		" The paragraph text. \n" +
     		" Maybe even multiline \n" +
     		" </p>\n" +
-    		" @param a the first param \n" +
+                " @param a the first param\n");
+    
+    wantedComments.put("doxygen_translate_all_tags.doxygen_translate_all_tags.func08(int)",
     		" Remarks: Some remark text \n" +
     		" Remarks: Another remarks section \n" +
     		" @return Whatever \n" +
     		" @return it \n" +
-    		" @return may return \n" +
-    		" This will only appear in RTF \n" +
+    		" @return may return \n");
+    
+    wantedComments.put("doxygen_translate_all_tags.doxygen_translate_all_tags.func09(int)",
+                       " This will only appear in RTF \n" +
     		" @see someOtherMethod \n" +
     		" @see function \n" +
     		" Same as \n" +
     		" brief description \n" +
     		" @since version 0.0.0.1 \n" +
     		" @throws superException \n" +
-    		" @throws RuntimeError \n" +
-    		" TODO: Some very important task \n" +
+    		" @throws RuntimeError \n");
+    
+    wantedComments.put("doxygen_translate_all_tags.doxygen_translate_all_tags.func10(int, float)",
+                       " TODO: Some very important task \n" +
     		" @param b B is mentioned again... \n" +
     		" {@literal \n" +
     		"very long \n" +

From 32f34e16be96de1df8fa428f556ebf37b115fe87 Mon Sep 17 00:00:00 2001
From: Marko Klopcic <markok3.14@gmail.com>
Date: Sun, 13 Jan 2013 20:02:39 +0100
Subject: [PATCH 156/314] improved commands for escaped characters

---
 Examples/test-suite/doxygen_misc_constructs.h |  9 +++---
 Examples/test-suite/java/commentParser.java   | 26 +++++++++++++++-
 .../DoxygenTranslator/src/DoxygenCommands.h   |  4 ++-
 .../DoxygenTranslator/src/DoxygenParser.cpp   | 31 ++++++++++++-------
 .../src/JavaDocConverter.cpp                  |  4 +--
 5 files changed, 53 insertions(+), 21 deletions(-)

diff --git a/Examples/test-suite/doxygen_misc_constructs.h b/Examples/test-suite/doxygen_misc_constructs.h
index e5d317fc2..d22761a5e 100644
--- a/Examples/test-suite/doxygen_misc_constructs.h
+++ b/Examples/test-suite/doxygen_misc_constructs.h
@@ -33,8 +33,9 @@ void backslashA()
 {}
 
 // Output of escaped symbols below in doxygen generated HTML:
-// Rendered: Escaped symbols: $ @ \ & < > # % " \. ::
-// HTML source: Escaped symbols: $ @ \ &amp; &lt; &gt; # % " \. :: 
+// Rendered: Escaped symbols: $ @ \ & < > # % " \. :: @text ::text
+// HTML source: Escaped symbols: $ @ \ &amp; &lt; &gt; # % " \. :: @text ::text
+
 
 /**
  * Doxy command without trailing \cspace space is ignored - nothing appears
@@ -46,8 +47,8 @@ void backslashA()
  * double quotes: "d:\xyz\c\myfile", "@something". single quotes do not help:
  * 'd:\xyz\c\myfile'. Escaping works: d:\\xyz\\c\\myfile. Unix
  * paths of course have no such problems: /xyz/c/myfile
- * Escaped symbols:
- * \$ \@ \\ \& \~ \< \> \# \% \" \. \::
+ * Commands for escaped symbols:
+ * \$ \@ \\ \& \~ \< \> \# \% \" \. \:: \@text \::text
  */
 void backslashB()
 {}
diff --git a/Examples/test-suite/java/commentParser.java b/Examples/test-suite/java/commentParser.java
index 581a862c8..7ec9e1595 100644
--- a/Examples/test-suite/java/commentParser.java
+++ b/Examples/test-suite/java/commentParser.java
@@ -3,6 +3,11 @@ import com.sun.javadoc.*;
 import java.util.HashMap;
 import java.util.Map.Entry;
 import java.util.Iterator;
+import java.io.BufferedWriter;
+import java.io.OutputStreamWriter;
+import java.io.FileOutputStream;
+import java.io.IOException;
+
 
 public class commentParser {
     static HashMap<String, String> parsedComments = new HashMap<String, String>();
@@ -56,10 +61,29 @@ public class commentParser {
             }
 
             if (!actualStr.equals(wantedStr)) {
-                System.out.println("Documentation comments for " + e.getKey() + " do not match: ");
+                System.out.println("Documentation comments for " + e.getKey() + " do not match!");
+                String expectedFileName = "expected.txt";
+                String gotFileName = "got.txt";
+                System.out.println("Output is also saved to files '" + expectedFileName +
+                                   "' and '" + gotFileName + "'");
                 // here we print original strings, for nicer output
                 System.out.println("\n\n---\nexpected:\n" + wantedComments.get(e.getKey()));
                 System.out.println("\n\n---\ngot:\n" + e.getValue());
+
+                try {
+                    // write expected string to file
+                    BufferedWriter expectedFile = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(expectedFileName)));
+                    expectedFile.write(wantedComments.get(e.getKey()));
+                    expectedFile.close();
+
+                    // write translated string to file
+                    BufferedWriter gotFile = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(gotFileName)));
+                    gotFile.write(e.getValue());
+                    gotFile.close();
+                } catch (IOException ex) {
+                    System.out.println("Error when writing output to file: " + ex);
+                }
+                
                 errorCount++;
             }
         }
diff --git a/Source/DoxygenTranslator/src/DoxygenCommands.h b/Source/DoxygenTranslator/src/DoxygenCommands.h
index 154efc53f..5493e2f5f 100644
--- a/Source/DoxygenTranslator/src/DoxygenCommands.h
+++ b/Source/DoxygenTranslator/src/DoxygenCommands.h
@@ -18,7 +18,9 @@ const int sectionIndicatorsSize = sizeof(sectionIndicators) / sizeof(*sectionInd
 
 /* All of the doxygen commands divided up by how they are parsed */
 const char *simpleCommands[] = {
-  "n", "$", "@", "\\", "&", "~", "<", ">", "#", "%", "\"", ".", "::", "endcond",
+  // the first line are escaped chars, except \~, which is a language ID command.
+  "n", "$", "@", "\\", "&", "~", "<", ">", "#", "%", "\"", ".", "::",
+  "endcond",
   "callgraph", "callergraph", "showinitializer", "hideinitializer", "internal",
   "nosubgrouping", "public", "publicsection", "private", "privatesection",
   "protected", "protectedsection", "tableofcontents"};
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.cpp b/Source/DoxygenTranslator/src/DoxygenParser.cpp
index 7ec0ae261..baa453836 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenParser.cpp
@@ -1114,19 +1114,26 @@ size_t DoxygenParser::processVerbatimText(size_t pos, const std::string &line)
 size_t DoxygenParser::processNormalComment(size_t pos, const std::string &line)
 {
     switch (line[pos]) {
-    case '\\':  // process doxy command or escaped char
-       /* switch (line[pos + 1]) {
-        case '$':
-        case '@':
-        case '\':
-        case '&':
-        case '~':
-        case '<':
-        case '>':
-        case '#': \% \" \. \::
-        }
-        TODO break case if any of escaped chars */
+    case '\\':
     case '@': {
+      // process doxy commands for escaped characters - handling this separately
+      // supports documentation text like \@someText
+      if ((pos + 1) < line.size()) {
+        string escapedChars = "$@\\&~<>#%\".";
+        if (escapedChars.find(line[pos + 1]) != string::npos) {
+          addDoxyCommand(m_tokenList, line.substr(pos + 1, 1));
+          pos += 2;
+          break;
+        } else if ((pos + 2) < line.size()  &&
+                    line[pos + 1] == ':'  &&  line[pos + 2] == ':') {
+          // add command \:: - handling this separately supports documentation
+          // text like \::someText
+          addDoxyCommand(m_tokenList, line.substr(pos + 1, 2));
+          pos += 3;
+          break;
+        }
+      }
+      // handle word commands and \f[, \f$, ... commands
       pos++;
       // characters '$[]{}' are used in commands \f$, \f[, ...
       size_t endOfWordPos = line.find_first_not_of("abcdefghijklmnopqrstuvwxyz$[]{}", pos);
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.cpp b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
index 8527ed689..c94999e33 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
@@ -296,7 +296,6 @@ void JavaDocConverter::handleTagChar(DoxygenEntity& tag, std::string& translated
     translatedComment += arg;
   else
     translatedComment += tag.typeOfEntity;
-  translatedComment += " ";
 }
 
 // handles tags which are the same in Doxygen and Javadoc.
@@ -394,10 +393,9 @@ void JavaDocConverter::handleTagParam(DoxygenEntity& tag,
     return;
 
   translatedComment += "@param ";
-  translatedComment += tag.entityList.begin()->data + " ";
+  translatedComment += tag.entityList.begin()->data;
   tag.entityList.pop_front();
   handleParagraph(tag, translatedComment, dummy);
-  printf("cmd: %s\n", translatedComment.c_str());
 }
 
 

From 49dddb3bd19297e2078cb9a93055fed73e587cb0 Mon Sep 17 00:00:00 2001
From: Marko Klopcic <markok3.14@gmail.com>
Date: Sun, 13 Jan 2013 22:49:54 +0100
Subject: [PATCH 157/314] updated test doxygen_translate, but there is one bug
 with unordered list

---
 Examples/test-suite/doxygen_misc_constructs.h |  1 +
 .../java/doxygen_translate_runme.java         | 36 +++++++++----------
 2 files changed, 19 insertions(+), 18 deletions(-)

diff --git a/Examples/test-suite/doxygen_misc_constructs.h b/Examples/test-suite/doxygen_misc_constructs.h
index d22761a5e..ab97cc81d 100644
--- a/Examples/test-suite/doxygen_misc_constructs.h
+++ b/Examples/test-suite/doxygen_misc_constructs.h
@@ -56,6 +56,7 @@ void backslashB()
 /**
  * Backslash e at end of \e line froze SWIG \e
  * with old comment parser.
+ * \arg some list item
  */
 void backslashC()
 {}
diff --git a/Examples/test-suite/java/doxygen_translate_runme.java b/Examples/test-suite/java/doxygen_translate_runme.java
index 8aa80a6ed..5ab448694 100644
--- a/Examples/test-suite/java/doxygen_translate_runme.java
+++ b/Examples/test-suite/java/doxygen_translate_runme.java
@@ -28,9 +28,9 @@ public class doxygen_translate_runme {
     wantedComments.put("doxygen_translate.doxygen_translate.function(int, float)",
     		" <i>Hello </i>\n" +
     		" \n" +
-    		" <li>some list item \n" +
+    		" <li>some list item</li>\n" +
     		" \n" +
-    		" </li>@author lots of them \n" +
+    		" @author lots of them \n" +
     		" \n" +
     		" @author Zubr \n" +
     		" \n" +
@@ -57,28 +57,28 @@ public class doxygen_translate_runme {
     		" If: ANOTHERCONDITION {\n" +
     		" First part of comment \n" +
     		" If: SECONDCONDITION {\n" +
-    		" Nested condition text \n" +
-    		" }Else if: THIRDCONDITION {\n" +
-    		" The third condition text \n" +
-    		" }Else:  {The last text block \n" +
-    		" }\n" +
-    		" }Else:  {Second part of comment \n" +
+    		" Nested condition text}\n" +
+    		" Else if: THIRDCONDITION {\n" +
+    		" The third condition text}\n" +
+    		" Else:  {The last text block}}\n" +
+    		" \n" +
+    		" Else:  {Second part of comment \n" +
     		" If: CONDITION {\n" +
-    		" Second part extended \n" +
-    		" }\n" +
-    		" }\n" +
+    		" Second part extended}}\n" +
+    		" \n" +
+    		" \n" +
     		" \n" +
     		" If not: SOMECONDITION {\n" +
-    		" This is printed if not \n" +
-    		" }\n" +
+    		" This is printed if not}\n" +
+    		" \n" +
     		" \n" +
     		" <img src=testImage.bmp alt=\"Hello, world!\" />\n" +
     		" \n" +
     		" <ul> \n" +
     		" \n" +
-    		" <li>Some unordered list \n" +
-    		" </li><li>With lots of items \n" +
-    		" </li><li>lots of lots of items \n" +
+    		" <li>Some unordered list</li>\n" +
+    		" <li>With lots of items</li>\n" +
+    		" <li>lots of lots of items</li>\n" +
     		" \n" +
     		" </li></ul> \n" +
     		" \n" +
@@ -100,9 +100,9 @@ public class doxygen_translate_runme {
     		" \n" +
     		" <p alt=\"The paragraph title \">\n" +
     		" The paragraph text. \n" +
-    		" Maybe even multiline \n" +
+    		" Maybe even multiline</p>\n" +
     		" \n" +
-    		" </p>@param a the first param \n" +
+    		" @param a the first param \n" +
     		" \n" +
     		" Remarks: Some remark text \n" +
     		" \n" +

From 7984516b31a65d074cc77ac7443722924ecf02de Mon Sep 17 00:00:00 2001
From: Marko Klopcic <markok3.14@gmail.com>
Date: Wed, 16 Jan 2013 23:15:14 +0100
Subject: [PATCH 158/314] implemented translation of HTML tags - they are
 handled as a special class of commands

---
 .../java/doxygen_translate_runme.java         |  2 +-
 .../DoxygenTranslator/src/DoxygenCommands.h   | 18 ++--
 .../DoxygenTranslator/src/DoxygenParser.cpp   | 97 ++++++++++++++++---
 Source/DoxygenTranslator/src/DoxygenParser.h  | 24 +++--
 .../src/JavaDocConverter.cpp                  | 24 +++++
 .../DoxygenTranslator/src/JavaDocConverter.h  |  8 ++
 6 files changed, 143 insertions(+), 30 deletions(-)

diff --git a/Examples/test-suite/java/doxygen_translate_runme.java b/Examples/test-suite/java/doxygen_translate_runme.java
index 5ab448694..831dc4f83 100644
--- a/Examples/test-suite/java/doxygen_translate_runme.java
+++ b/Examples/test-suite/java/doxygen_translate_runme.java
@@ -80,7 +80,7 @@ public class doxygen_translate_runme {
     		" <li>With lots of items</li>\n" +
     		" <li>lots of lots of items</li>\n" +
     		" \n" +
-    		" </li></ul> \n" +
+    		" </ul> \n" +
     		" \n" +
     		" {@link someMember Some description follows }\n" +
     		" \n" +
diff --git a/Source/DoxygenTranslator/src/DoxygenCommands.h b/Source/DoxygenTranslator/src/DoxygenCommands.h
index 5493e2f5f..eb5f5d39f 100644
--- a/Source/DoxygenTranslator/src/DoxygenCommands.h
+++ b/Source/DoxygenTranslator/src/DoxygenCommands.h
@@ -83,19 +83,19 @@ const int commandUniquesSize = sizeof(commandUniques) / sizeof(*commandUniques);
 // Other commands are left intact, but '<' and '> are replaced with entities in HTML
 // output. So <varName> appears as &lt;varName&gt; in HTML output. The same
 // behavior must be repeated by SWIG. See Doxygen doc for the list of commands.
-// '<' and '>' are used to differentiate HTML commands from doxygen commands.
-const char *htmlCommands[] = {
-  "<A>", "<B>", "<BLOCKQUOTE>", "<BODY>", "<BR>", "<CENTER>", "<CAPTION>", "<CODE>", "<DFN>", "<DFN>",
-  "<DIV>", "<DL>", "<DT>", "<EM>", "<FORM>", "<HR>", "<H1>", "<H2>", "<H3>", "<I>", "<INPUT>", "<IMG>",
-  "<LI>", "<META>", "<MULTICOL>", "<OL>", "<P>", "<PRE>", "<SMALL>", "<SPAN>", "<STRONG>",
-  "<SUB>", "<SUP>", "<TABLE>", "<TD>", "<TH>", "<TR>", "<TT>", "<KBD>", "<UL>", "<VAR>"
+// '<' is prepended to distinguish HTML tags from Doxygen commands.
+const char *commandHtml[] = {
+  "<a", "<b", "<blockquote", "<body", "<br", "<center", "<caption", "<code", "<dfn",
+  "<div", "<dl", "<dt", "<em", "<form", "<hr", "<h1", "<h2", "<h3", "<i", "<input", "<img",
+  "<li", "<meta", "<multicol", "<ol", "<p", "<pre", "<small", "<span", "<strong",
+  "<sub", "<sup", "<table", "<td", "<th", "<tr", "<tt", "<kbd", "<ul", "<var"
 };
 
-const int htmlCommandsSize = sizeof(htmlCommands) / sizeof(*htmlCommands);
+const int commandHtmlSize = sizeof(commandHtml) / sizeof(*commandHtml);
 
 // Only entities which are translatable to plain text are used here. Others
 // are copied unchanged to output.
-const char *htmlEntities[] = { "&copy", "&trade", "&reg", // (C), (TM), (R)
+const char *commandHtmlEntities[] = { "&copy", "&trade", "&reg", // (C), (TM), (R)
 "&lt",  // less-than symbol
 "&gt",  // greater-than symbol
 "&amp", // ampersand
@@ -118,6 +118,6 @@ const char *htmlEntities[] = { "&copy", "&trade", "&reg", // (C), (TM), (R)
 "&rarr" // -->
 };
 
-const int htmlEntitiesSize = sizeof(htmlEntities) / sizeof(*htmlEntities);
+const int commandHtmlEntitiesSize = sizeof(commandHtmlEntities) / sizeof(*commandHtmlEntities);
 
 #endif
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.cpp b/Source/DoxygenTranslator/src/DoxygenParser.cpp
index baa453836..e9425b370 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenParser.cpp
@@ -27,7 +27,7 @@ DoxygenParser::DoxyCommandsMap DoxygenParser::doxygenCommands;
 std::set<std::string> DoxygenParser::doxygenSectionIndicators;
 
 const int TOKENSPERLINE = 8;    //change this to change the printing behaviour of the token list
-
+const std::string END_HTML_TAG_MARK("/");
 
 DoxygenParser::DoxygenParser(bool noisy) : noisy(noisy)
 {
@@ -76,11 +76,11 @@ void DoxygenParser::fillTables() {
     for (int i = 0; i < commandUniquesSize; i++)
         doxygenCommands[commandUniques[i]] = COMMANDUNIQUE;
 
-    for (int i = 0; i < htmlCommandsSize; i++)
-        doxygenCommands[htmlCommands[i]] = COMMANDUNIQUE;
+    for (int i = 0; i < commandHtmlSize; i++)
+        doxygenCommands[commandHtml[i]] = COMMAND_HTML;
 
-    for (int i = 0; i < commandUniquesSize; i++)
-        doxygenCommands[commandUniques[i]] = COMMANDUNIQUE;
+    for (int i = 0; i < commandHtmlEntitiesSize; i++)
+        doxygenCommands[commandHtmlEntities[i]] = COMMAND_HTML_ENTITY;
 
     // fill section indicators command set
     for (int i = 0; i < sectionIndicatorsSize; i++)
@@ -575,6 +575,32 @@ int DoxygenParser::addCommandErrorThrow(const std::string &theCommand,
 }
 
 
+int DoxygenParser::addCommandHtml(const std::string &theCommand,
+                                      const TokenList &,
+                                      DoxygenEntityList &doxyList)
+{
+    if (noisy)
+        cout << "Parsing " << theCommand << endl;
+
+    std::string htmlTagArgs = getNextWord();
+    doxyList.push_back(DoxygenEntity(theCommand, htmlTagArgs));
+    return 1;
+}
+
+
+int DoxygenParser::addCommandHtmlEntity(const std::string &theCommand,
+                                             const TokenList &,
+                                             DoxygenEntityList &doxyList)
+{
+    if (noisy)
+        cout << "Parsing " << theCommand << endl;
+
+    DoxygenEntityList aNewList;
+    doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+    return 1;
+}
+
+
 int DoxygenParser::addCommandUnique(const std::string &theCommand,
                                          const TokenList &tokList,
                                          DoxygenEntityList &doxyList) {
@@ -893,6 +919,10 @@ int DoxygenParser::addCommand(const std::string &commandString,
 			return addCommandErrorThrow(theCommand, tokList, doxyList);
 		case COMMANDUNIQUE:
 			return addCommandUnique(theCommand, tokList, doxyList);
+        case COMMAND_HTML:
+            return addCommandHtml(theCommand, tokList, doxyList);
+        case COMMAND_HTML_ENTITY:
+            return addCommandHtmlEntity(theCommand, tokList, doxyList);
 	}
 	return 0;
 }
@@ -1068,10 +1098,11 @@ bool DoxygenParser::isStartOfDoxyCommentChar(char c)
 }
 
 
-void DoxygenParser::addDoxyCommand(DoxygenParser::TokenList &tokList,
+bool DoxygenParser::addDoxyCommand(DoxygenParser::TokenList &tokList,
                                         const std::string &cmd) {
     if (findCommand(cmd)) {
         tokList.push_back(Token(COMMAND, cmd));
+        return true;
     } else {
         // Unknown commands are ignored, because they are
         // also ignored by Doxygen - see test doxygen_misc_constructs.h, f. backslashB().
@@ -1079,6 +1110,8 @@ void DoxygenParser::addDoxyCommand(DoxygenParser::TokenList &tokList,
         // the line below to put unknown commands to output.
         // tokList.push_back(Token(PLAINSTRING, cmd));
     }
+
+    return false;
 }
 
 
@@ -1156,21 +1189,58 @@ size_t DoxygenParser::processNormalComment(size_t pos, const std::string &line)
       // whitespaces are stored as plain strings
       size_t startOfNextWordPos = line.find_first_not_of(" \t", pos + 1);
       m_tokenList.push_back(Token(PLAINSTRING,
-                               line.substr(pos, startOfNextWordPos - pos)));
+                            line.substr(pos, startOfNextWordPos - pos)));
       pos = startOfNextWordPos;
     } break;
 
     case '<': { // process html commands
+      bool isEndHtmlTag = false;
+      pos++;
+      if (line.size() > pos &&  line[pos] == '/') {
+          isEndHtmlTag = true;
+          pos++;
+      }
 
-      size_t endHtmlPos = line.find_first_of("\t >", pos + 1);
-      if (endHtmlPos != string::npos) {
-        // will push plain string Token. If the command is not HTML supported by
-        // Doxygen, < and > will be replaced by HTML entities &lt; and &gt; respectively,
+      size_t endHtmlPos = line.find_first_of("\t\n >", pos);
+
+      // prepend '<' to distinguish HTML tags from doxygen commands
+      string cmd = line.substr(pos, endHtmlPos - pos);
+      pos = endHtmlPos;
+
+      if (addDoxyCommand(m_tokenList, '<' + cmd)) {
+          // it is a valid HTML command
+          if (line[pos] != '>') { // it should be HTML tag with args,
+                                   // for example <A ...>, <IMG ...>, ...
+              if (isEndHtmlTag) {
+                  m_tokenListIt = m_tokenList.end();
+                  printListError(WARN_DOXYGEN_COMMAND_ERROR, "Illegal end HTML tag without '>' found! Tag: " + cmd);
+              }
+              endHtmlPos = line.find(">", pos);
+              if (endHtmlPos == string::npos) {
+                  m_tokenListIt = m_tokenList.end();
+                  printListError(WARN_DOXYGEN_COMMAND_ERROR, "HTML tag without '>' found! Tag: " + cmd);
+              }
+              // add args of HTML command, like link URL, image URL, ...
+              m_tokenList.push_back(Token(PLAINSTRING,
+                                    line.substr(pos, endHtmlPos - pos)));
+          } else {
+              if (isEndHtmlTag) {
+                // it is a simple tag, so push empty string
+                m_tokenList.push_back(Token(PLAINSTRING, END_HTML_TAG_MARK));
+              } else {
+                // it is a simple tag, so push empty string
+                m_tokenList.push_back(Token(PLAINSTRING, ""));
+              }
+          }
+      } else {
+        // the command is not HTML supported by Doxygen, < and > will be
+        // replaced by HTML entities &lt; and &gt; respectively,
         // but only if 'htmlOnly' flag == false. The flag is set/reset by \htmlonly \verbatim,
         // \endhtmlonly \endverbatim Doxygen commands.
-        // handleHTMLCommand(line.substr(pos + 1), endHtmlPos - pos - 1);
+        m_tokenList.push_back(Token(PLAINSTRING, "&lt;"));
+        m_tokenList.push_back(Token(PLAINSTRING, cmd));
       }
-      pos = endHtmlPos;
+      pos++;
     } break;
 
     case '&': { // process HTML entities
@@ -1190,6 +1260,7 @@ size_t DoxygenParser::processNormalComment(size_t pos, const std::string &line)
     }
     break;
     default:
+      m_tokenListIt = m_tokenList.end();
       printListError(WARN_DOXYGEN_COMMAND_ERROR, "Unknown special character: " + line[pos]);
     }
 
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.h b/Source/DoxygenTranslator/src/DoxygenParser.h
index 019da8785..3417a59f4 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.h
+++ b/Source/DoxygenTranslator/src/DoxygenParser.h
@@ -33,6 +33,8 @@ private:
     COMMANDOWORD,
     COMMANDERRORTHROW,
     COMMANDUNIQUE,
+    COMMAND_HTML,
+    COMMAND_HTML_ENTITY,
     END_LINE,
     PARAGRAPH_END,
     PLAINSTRING,
@@ -299,23 +301,31 @@ private:
    * "dir", "file", "cond"
    */
   int addCommandOWord(const std::string &theCommand,
-                         const TokenList &tokList,
-                         DoxygenEntityList &doxyList);
+                      const TokenList &tokList,
+                      DoxygenEntityList &doxyList);
 
   /*
    * Commands that should not be encountered (such as PHP only)
    * goes til the end of line then returns
    */
   int addCommandErrorThrow(const std::string &theCommand,
-                              const TokenList &tokList,
-                              DoxygenEntityList &doxyList);
+                           const TokenList &tokList,
+                           DoxygenEntityList &doxyList);
+
+  int addCommandHtml(const std::string &theCommand,
+                     const TokenList &tokList,
+                     DoxygenEntityList &doxyList);
+
+  int addCommandHtmlEntity(const std::string &theCommand,
+                           const TokenList &tokList,
+                           DoxygenEntityList &doxyList);
 
   /*
    *Adds the unique commands- different process for each unique command
    */
   int addCommandUnique(const std::string &theCommand,
-                          const TokenList &tokList,
-                          DoxygenEntityList &doxyList);
+                       const TokenList &tokList,
+                       DoxygenEntityList &doxyList);
 
   /* 
    * The actual "meat" of the doxygen parser. Calls the correct addCommand...()
@@ -351,7 +361,7 @@ private:
 
   StringVector split(const std::string &text, char separator);
   bool isStartOfDoxyCommentChar(char c);
-  void addDoxyCommand(DoxygenParser::TokenList &tokList, const std::string &cmd);
+  bool addDoxyCommand(DoxygenParser::TokenList &tokList, const std::string &cmd);
 
 public:
   DoxygenParser(bool noisy = false);
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.cpp b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
index c94999e33..2a02af348 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
@@ -147,6 +147,10 @@ void JavaDocConverter::fillStaticTables() {
   tagHandlers["plainstd::string"] = make_pair(&JavaDocConverter::handlePlainString, "");
   tagHandlers["plainstd::endl"] = make_pair(&JavaDocConverter::handleNewLine, "");
   tagHandlers["n"] = make_pair(&JavaDocConverter::handleNewLine, "");
+
+  // HTML tags
+  tagHandlers["<ul"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<ul");
+
 }
 
 
@@ -268,6 +272,8 @@ void JavaDocConverter::translateEntity(DoxygenEntity &tag,
 
   if (it != tagHandlers.end()) {
     (this->*(it->second.first))(tag, translatedComment, it->second.second);
+  } else {
+      addError(WARN_DOXYGEN_COMMAND_ERROR, "Unknown doxygen or HTML tag: " + tag.typeOfEntity);
   }
 }
 
@@ -285,6 +291,17 @@ void JavaDocConverter::handleTagHtml(DoxygenEntity& tag, std::string& translated
 }
 
 
+void JavaDocConverter::handleDoxyHtmlTag(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
+    std::string htmlTagArgs = tag.data;
+    if (htmlTagArgs == "/") {
+        // end html tag, for example "</ul>
+        translatedComment += "</" + arg.substr(1) + ">";
+    } else {
+        translatedComment += arg + htmlTagArgs + ">";
+    }
+}
+
+
 void JavaDocConverter::handleNewLine(DoxygenEntity&, std::string& translatedComment, std::string&) {
   translatedComment += "\n * ";
 }
@@ -704,3 +721,10 @@ String *JavaDocConverter::makeDocumentation(Node *node) {
   
   return NewString(javaDocString.c_str());
 }
+
+
+void JavaDocConverter::addError(int warningType,
+                                     const std::string &message) {
+  Swig_warning(warningType, "", 0,
+               "Doxygen parser warning: %s. \n", message.c_str());
+}
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.h b/Source/DoxygenTranslator/src/JavaDocConverter.h
index 2c3ac72f0..1d757cf35 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.h
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.h
@@ -60,6 +60,12 @@ protected:
    * arg - html tag, with no braces
    */
   void handleTagHtml(DoxygenEntity &tag, std::string &translatedComment, std::string &arg);
+
+  /* Handles HTML tags recognized by Doxygen, like <A ...>, <ul>, <table>, ... */
+  void handleDoxyHtmlTag(DoxygenEntity& tag,
+                            std::string& translatedComment,
+                            std::string &arg);
+
   /*
    * Just prints new line
    */
@@ -128,6 +134,8 @@ private:
 
   bool paramExists(std::string param);
   std::string indentAndInsertAsterisks(const std::string &doc);
+
+  void addError(int warningType, const std::string &message);
 };
 
 #endif

From f25d03612b3bfc376f561a8b2d4dd4e6a6110cc0 Mon Sep 17 00:00:00 2001
From: Marko Klopcic <markok3.14@gmail.com>
Date: Thu, 17 Jan 2013 23:17:06 +0100
Subject: [PATCH 159/314] added the missing doxy command 'example'

---
 Examples/test-suite/java/doxygen_translate_runme.java | 5 ++++-
 Source/DoxygenTranslator/src/JavaDocConverter.cpp     | 3 +++
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/Examples/test-suite/java/doxygen_translate_runme.java b/Examples/test-suite/java/doxygen_translate_runme.java
index 831dc4f83..55342ef55 100644
--- a/Examples/test-suite/java/doxygen_translate_runme.java
+++ b/Examples/test-suite/java/doxygen_translate_runme.java
@@ -52,7 +52,10 @@ public class doxygen_translate_runme {
     		" \n" +
     		" <i>italicword </i>\n" +
     		" \n" +
-    		" @exception SuperError \n" +
+    		" @ example someFile.txt\n" +
+    		" Some details on using the example\n" +
+    		" \n" +
+                " @exception SuperError \n" +
     		" \n" +
     		" If: ANOTHERCONDITION {\n" +
     		" First part of comment \n" +
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.cpp b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
index 2a02af348..bd592adc2 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
@@ -126,6 +126,9 @@ void JavaDocConverter::fillStaticTables() {
   tagHandlers["else"] = make_pair(&JavaDocConverter::handleTagIf, "Else: ");
   tagHandlers["elseif"] = make_pair(&JavaDocConverter::handleTagIf, "Else if: ");
   tagHandlers["endcond"] = make_pair(&JavaDocConverter::handleTagMessage, "End of conditional comment.");
+  // space prevents Javadoc to treat '@ example' as command. File name of
+  // example is still informative to user.
+  tagHandlers["example"] = make_pair(&JavaDocConverter::handleTagSame, " example");
   tagHandlers["if"] = make_pair(&JavaDocConverter::handleTagIf, "If: ");
   tagHandlers["ifnot"] = make_pair(&JavaDocConverter::handleTagIf, "If not: ");
   tagHandlers["image"] = make_pair(&JavaDocConverter::handleTagImage, "");

From 13d2dad679c7635c4e7897ede354bc1f5037a134 Mon Sep 17 00:00:00 2001
From: Marko Klopcic <markok3.14@gmail.com>
Date: Fri, 18 Jan 2013 21:21:12 +0100
Subject: [PATCH 160/314] added tests for HTML tags, bugs in HTML tags fixed

---
 Examples/test-suite/doxygen_translate.i       | 86 +++++++++++++++++++
 .../java/doxygen_translate_runme.java         | 81 +++++++++++++++++
 .../DoxygenTranslator/src/DoxygenCommands.h   |  2 +-
 .../DoxygenTranslator/src/DoxygenParser.cpp   | 20 ++++-
 Source/DoxygenTranslator/src/DoxygenParser.h  |  6 ++
 .../src/JavaDocConverter.cpp                  | 43 +++++++++-
 6 files changed, 233 insertions(+), 5 deletions(-)

diff --git a/Examples/test-suite/doxygen_translate.i b/Examples/test-suite/doxygen_translate.i
index 8bfd3d250..6af66f0b1 100644
--- a/Examples/test-suite/doxygen_translate.i
+++ b/Examples/test-suite/doxygen_translate.i
@@ -125,4 +125,90 @@ int function(int a, float b)
 {
 }
 
+/**
+ * Test for html tags. See Doxygen doc for list of tags recognized by Doxygen.
+ *
+ * <a href = "http://acme.com/index.html">This is link</a>
+ * <b>bold</b>
+ * <BLOCKQUOTE>
+ * Quotation block.
+ * </BLOCKQUOTE>
+ * <br>
+ * <center>center</center>
+ * <code>this is code</code>
+ * <DD> Starts an item description.
+ * <DFN> Starts a piece of text displayed in a typewriter font.
+ * </DFN> 
+ * <DIV> Starts a section with a specific style (HTML only)
+ * </DIV> 
+ * <DL> Starts a description list.
+ * <DT> Starts an item title.</DT>
+ * </DL> 
+ * <EM> Starts a piece of text displayed in an italic font.
+ * </EM> 
+ * <FORM> 'Form' does not generate any output.
+ * </FORM>
+ * <HR> 
+ * <H1> Starts an unnumbered section.
+ * </H1>
+ * <H2> Starts an unnumbered subsection.
+ * </H2> 
+ * <H3> Starts an unnumbered subsubsection.
+ * </H3> 
+ * <I> Starts a piece of text displayed in an italic font.
+ * <INPUT> Does not generate any output.
+ * </I> 
+ * <IMG src="slika.png"> 
+ * <META> Does not generate any output.
+ * <MULTICOL> ignored by doxygen.
+ * </MULTICOL> ignored by doxygen.
+ *
+ * <OL> Starts a numbered item list.
+ * <LI> Starts a new list item.
+ * </LI> 
+ * </OL> Ends a numbered item list.
+ *
+ * <P> Starts a new paragraph.
+ * </P> 
+ * <PRE> Starts a preformatted fragment.
+ * </PRE>
+ * <SMALL> Starts a section of text displayed in a smaller font.
+ * </SMALL>
+ * <SPAN> Starts an inline text fragment with a specific style (HTML only)
+ * </SPAN>
+ * <STRONG> Starts a section of bold text.
+ * </STRONG>
+ * <SUB> Starts a piece of text displayed in subscript.
+ * </SUB>
+ * <SUP> Starts a piece of text displayed in superscript.
+ * </SUP>
+ *
+ * <table border = '1'>
+ * <caption>Animals</caption>
+ * <tr><th> cow   </th><th> dog    </th></tr>
+ * <tr><td> cow   </td><td> dog    </td></tr>
+ * <tr><td> cat   </td><td> mouse  </td></tr>
+ * <tr><td> horse </td><td> parrot </td></tr>
+ * </table>
+ *
+ * <TT> Starts a piece of text displayed in a typewriter font.
+ * </TT> 
+ * <KBD> Starts a piece of text displayed in a typewriter font.
+ * </KBD> 
+ *
+ * <UL> Starts an unnumbered item list.
+ * <LI> Starts a new list item 1.</LI> 
+ * <LI> Starts a new list item 2.</LI> 
+ * <LI> Starts a new list item 3.</LI> 
+ * </UL> Ends an unnumbered item list.
+ *
+ * <VAR> Starts a piece of text displayed in an italic font.
+ * </VAR>                                                                               
+ */
+int htmlFunction(int a, float b)
+{
+}
+
+
+ 
 %}
diff --git a/Examples/test-suite/java/doxygen_translate_runme.java b/Examples/test-suite/java/doxygen_translate_runme.java
index 55342ef55..40830a2f6 100644
--- a/Examples/test-suite/java/doxygen_translate_runme.java
+++ b/Examples/test-suite/java/doxygen_translate_runme.java
@@ -146,6 +146,87 @@ public class doxygen_translate_runme {
     		" And here goes simple text \n" +
     		" \n" +
     		"");
+
+        wantedComments.put("doxygen_translate.doxygen_translate.htmlFunction(int, float)",
+    		" Test for html tags. See Doxygen doc for list of tags recognized by Doxygen.          \n" +
+    		"                                                                                      \n" +
+    		" <a href = \"http://acme.com/index.html\">This is link</a>                               \n" +
+    		" <b>bold</b>                                                                          \n" +
+    		" <blockquote>                                                                         \n" +
+    		" Quotation block.                                                                     \n" +
+    		" </blockquote>                                                                        \n" +
+    		" <br>                                                                                 \n" +
+    		" <center>center</center>                                                              \n" +
+    		" <code>this is code</code>                                                            \n" +
+    		" <dd> Starts an item description.                                                     \n" +
+    		" <dfn> Starts a piece of text displayed in a typewriter font.                         \n" +
+    		" </dfn>                                                                               \n" +
+    		" <div> Starts a section with a specific style (HTML only)                             \n" +
+    		" </div>                                                                               \n" +
+    		" <dl> Starts a description list.                                                      \n" +
+    		" <dt> Starts an item title.</dt>                                                      \n" +
+    		" </dl>                                                                                \n" +
+    		" <em> Starts a piece of text displayed in an italic font.                             \n" +
+    		" </em>                                                                                \n" +
+    		" <form> 'Form' does not generate any output.                                          \n" +
+    		" </form>                                                                              \n" +
+    		" <hr>                                                                                 \n" +
+    		" <h1> Starts an unnumbered section.                                                   \n" +
+    		" </h1>                                                                                \n" +
+    		" <h2> Starts an unnumbered subsection.                                                \n" +
+    		" </h2>                                                                                \n" +
+    		" <h3> Starts an unnumbered subsubsection.                                             \n" +
+    		" </h3>                                                                                \n" +
+    		" <i> Starts a piece of text displayed in an italic font.                              \n" +
+    		" <input> Does not generate any output.                                                \n" +
+    		" </i>                                                                                 \n" +
+    		" <img src=\"slika.png\">                                                                \n" +
+    		" <meta> Does not generate any output.                                                 \n" +
+    		" <multicol> ignored by doxygen.                                                       \n" +
+    		" </multicol> ignored by doxygen.                                                      \n" +
+    		"                                                                                      \n" +
+    		" <ol> Starts a numbered item list.                                                    \n" +
+    		" <li> Starts a new list item.                                                         \n" +
+    		" </li>                                                                                \n" +
+    		" </ol> Ends a numbered item list.                                                     \n" +
+    		"                                                                                      \n" +
+    		" <p> Starts a new paragraph.                                                          \n" +
+    		" </p>                                                                                 \n" +
+    		" <pre> Starts a preformatted fragment.                                                \n" +
+    		" </pre>                                                                               \n" +
+    		" <small> Starts a section of text displayed in a smaller font.                        \n" +
+    		" </small>                                                                             \n" +
+    		" <span> Starts an inline text fragment with a specific style (HTML only)              \n" +
+    		" </span>                                                                              \n" +
+    		" <strong> Starts a section of bold text.                                              \n" +
+    		" </strong>                                                                            \n" +
+    		" <sub> Starts a piece of text displayed in subscript.                                 \n" +
+    		" </sub>                                                                               \n" +
+    		" <sup> Starts a piece of text displayed in superscript.                               \n" +
+    		" </sup>                                                                               \n" +
+    		"                                                                                      \n" +
+    		" <table border = '1'>                                                                 \n" +
+    		" <caption>Animals</caption>                                                           \n" +
+    		" <tr><th> cow   </th><th> dog    </th></tr>                                           \n" +
+    		" <tr><td> cow   </td><td> dog    </td></tr>                                           \n" +
+    		" <tr><td> cat   </td><td> mouse  </td></tr>                                           \n" +
+    		" <tr><td> horse </td><td> parrot </td></tr>                                           \n" +
+    		" </table>                                                                             \n" +
+    		"                                                                                      \n" +
+    		" <tt> Starts a piece of text displayed in a typewriter font.                          \n" +
+    		" </tt>                                                                                \n" +
+    		" <kbd> Starts a piece of text displayed in a typewriter font.                         \n" +
+    		" </kbd>                                                                               \n" +
+    		"                                                                                      \n" +
+    		" <ul> Starts an unnumbered item list.                                                 \n" +
+    		" <li> Starts a new list item 1.</li>                                                  \n" +
+    		" <li> Starts a new list item 2.</li>                                                  \n" +
+    		" <li> Starts a new list item 3.</li>                                                  \n" +
+    		" </ul> Ends an unnumbered item list.                                                  \n" +
+    		"                                                                                      \n" +
+    		" <var> Starts a piece of text displayed in an italic font.                            \n" +
+    		" </var>                                                                               \n" +
+                "");
     // and ask the parser to check comments for us
     System.exit(parser.check(wantedComments));
   }
diff --git a/Source/DoxygenTranslator/src/DoxygenCommands.h b/Source/DoxygenTranslator/src/DoxygenCommands.h
index eb5f5d39f..029c47550 100644
--- a/Source/DoxygenTranslator/src/DoxygenCommands.h
+++ b/Source/DoxygenTranslator/src/DoxygenCommands.h
@@ -85,7 +85,7 @@ const int commandUniquesSize = sizeof(commandUniques) / sizeof(*commandUniques);
 // behavior must be repeated by SWIG. See Doxygen doc for the list of commands.
 // '<' is prepended to distinguish HTML tags from Doxygen commands.
 const char *commandHtml[] = {
-  "<a", "<b", "<blockquote", "<body", "<br", "<center", "<caption", "<code", "<dfn",
+  "<a", "<b", "<blockquote", "<body", "<br", "<center", "<caption", "<code", "<dd", "<dfn",
   "<div", "<dl", "<dt", "<em", "<form", "<hr", "<h1", "<h2", "<h3", "<i", "<input", "<img",
   "<li", "<meta", "<multicol", "<ol", "<p", "<pre", "<small", "<span", "<strong",
   "<sub", "<sup", "<table", "<td", "<th", "<tr", "<tt", "<kbd", "<ul", "<var"
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.cpp b/Source/DoxygenTranslator/src/DoxygenParser.cpp
index e9425b370..46b8b6b4d 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenParser.cpp
@@ -178,6 +178,21 @@ void DoxygenParser::skipWhitespaceTokens()
 }
 
 
+std::string DoxygenParser::getNextToken() {
+
+    if (m_tokenListIt == m_tokenList.end()) {
+        return "";
+    }
+
+    if (m_tokenListIt->m_tokenType == PLAINSTRING) {
+        return (m_tokenListIt++)->m_tokenString;
+    }
+
+    return "";
+}
+
+
+
 std::string DoxygenParser::getNextWord() {
 
 /*    if (m_tokenListIt == m_tokenList.end()) {
@@ -582,7 +597,7 @@ int DoxygenParser::addCommandHtml(const std::string &theCommand,
     if (noisy)
         cout << "Parsing " << theCommand << endl;
 
-    std::string htmlTagArgs = getNextWord();
+    std::string htmlTagArgs = getNextToken();
     doxyList.push_back(DoxygenEntity(theCommand, htmlTagArgs));
     return 1;
 }
@@ -1201,7 +1216,7 @@ size_t DoxygenParser::processNormalComment(size_t pos, const std::string &line)
           pos++;
       }
 
-      size_t endHtmlPos = line.find_first_of("\t\n >", pos);
+      size_t endHtmlPos = line.find_first_of("\t >", pos);
 
       // prepend '<' to distinguish HTML tags from doxygen commands
       string cmd = line.substr(pos, endHtmlPos - pos);
@@ -1223,6 +1238,7 @@ size_t DoxygenParser::processNormalComment(size_t pos, const std::string &line)
               // add args of HTML command, like link URL, image URL, ...
               m_tokenList.push_back(Token(PLAINSTRING,
                                     line.substr(pos, endHtmlPos - pos)));
+              pos = endHtmlPos;
           } else {
               if (isEndHtmlTag) {
                 // it is a simple tag, so push empty string
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.h b/Source/DoxygenTranslator/src/DoxygenParser.h
index 3417a59f4..558a85ef3 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.h
+++ b/Source/DoxygenTranslator/src/DoxygenParser.h
@@ -140,6 +140,12 @@ private:
    */
   std::string trim(const std::string &text);
 
+  /*
+   * Returns string of the next token if the next token is PLAINSTRING. Returns
+   * empty string otherwise.
+   */
+  std::string getNextToken();
+
   /*
    * Returns the next word ON THE CURRENT LINE ONLY
    * if a new line is encountered, returns a blank std::string.
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.cpp b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
index bd592adc2..d070bbdad 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
@@ -152,8 +152,47 @@ void JavaDocConverter::fillStaticTables() {
   tagHandlers["n"] = make_pair(&JavaDocConverter::handleNewLine, "");
 
   // HTML tags
-  tagHandlers["<ul"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<ul");
-
+  tagHandlers["<a"      ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<a"      );
+  tagHandlers["<b"      ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<b"      );
+  tagHandlers["<blockquote"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<blockquote");
+  tagHandlers["<body"   ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<body"   );
+  tagHandlers["<br"     ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<br"     );
+  tagHandlers["<center" ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<center" );
+  tagHandlers["<caption"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<caption");
+  tagHandlers["<code"   ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<code"   );
+  tagHandlers["<dd"     ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<dd"     );
+  tagHandlers["<dfn"    ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<dfn"    );
+  tagHandlers["<div"    ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<div"    );
+  tagHandlers["<dl"     ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<dl"     );
+  tagHandlers["<dt"     ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<dt"     );
+  tagHandlers["<em"     ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<em"     );
+  tagHandlers["<form"   ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<form"   );
+  tagHandlers["<hr"     ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<hr"     );
+  tagHandlers["<h1"     ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<h1"     );
+  tagHandlers["<h2"     ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<h2"     );
+  tagHandlers["<h3"     ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<h3"     );
+  tagHandlers["<i"      ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<i"      );
+  tagHandlers["<input"  ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<input"  );
+  tagHandlers["<img"    ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<img"    );
+  tagHandlers["<li"     ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<li"     );
+  tagHandlers["<meta"   ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<meta"   );
+  tagHandlers["<multicol"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<multicol");
+  tagHandlers["<ol"     ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<ol"     );
+  tagHandlers["<p"      ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<p"      );
+  tagHandlers["<pre"    ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<pre"    );
+  tagHandlers["<small"  ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<small"  );
+  tagHandlers["<span"   ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<span"   );
+  tagHandlers["<strong" ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<strong" );
+  tagHandlers["<sub"    ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<sub"    );
+  tagHandlers["<sup"    ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<sup"    );
+  tagHandlers["<table"  ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<table"  );
+  tagHandlers["<td"     ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<td"     );
+  tagHandlers["<th"     ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<th"     );
+  tagHandlers["<tr"     ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<tr"     );
+  tagHandlers["<tt"     ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<tt"     );
+  tagHandlers["<kbd"    ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<kbd"    );
+  tagHandlers["<ul"     ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<ul"     );
+  tagHandlers["<var"    ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<var"    );
 }
 
 

From 4955cdaac6dbc54bfe493b46b92c2a275a556ffd Mon Sep 17 00:00:00 2001
From: Marko Klopcic <markok3.14@gmail.com>
Date: Fri, 18 Jan 2013 22:22:22 +0100
Subject: [PATCH 161/314] added handling of HTML entities

---
 Examples/test-suite/doxygen_translate.i       | 28 ++++++++++++++++
 .../java/doxygen_translate_runme.java         | 25 ++++++++++++++
 .../DoxygenTranslator/src/DoxygenParser.cpp   |  7 ++--
 .../src/JavaDocConverter.cpp                  | 33 +++++++++++++++++--
 .../DoxygenTranslator/src/JavaDocConverter.h  |  9 +++--
 5 files changed, 94 insertions(+), 8 deletions(-)

diff --git a/Examples/test-suite/doxygen_translate.i b/Examples/test-suite/doxygen_translate.i
index 6af66f0b1..ba787a140 100644
--- a/Examples/test-suite/doxygen_translate.i
+++ b/Examples/test-suite/doxygen_translate.i
@@ -210,5 +210,33 @@ int htmlFunction(int a, float b)
 }
 
 
+/**
+ * All entities are treated as commands &copy; &trade; &reg;
+ * should work also&lt;in text
+ * &gt;
+ * &amp;
+ * &apos;
+ * &quot;
+ * &lsquo;
+ * &rsquo;
+ * &ldquo;
+ * &rdaquo;
+ * &ndash;
+ * &mdash;
+ * &nbsp;
+ * &times;
+ * &minus;
+ * &sdot;
+ * &sim;
+ * &le;
+ * &ge;
+ * &larr;
+ * &rarr;
+ */
+int htmlEntitiesFunction(int a, float b)
+{
+}
+
+
  
 %}
diff --git a/Examples/test-suite/java/doxygen_translate_runme.java b/Examples/test-suite/java/doxygen_translate_runme.java
index 40830a2f6..6be2b2165 100644
--- a/Examples/test-suite/java/doxygen_translate_runme.java
+++ b/Examples/test-suite/java/doxygen_translate_runme.java
@@ -227,6 +227,31 @@ public class doxygen_translate_runme {
     		" <var> Starts a piece of text displayed in an italic font.                            \n" +
     		" </var>                                                                               \n" +
                 "");
+
+        wantedComments.put("doxygen_translate.doxygen_translate.htmlEntitiesFunction(int, float)",
+                "All entities are treated as commands &copy; &trade; &reg;\n" +
+                "should work also&lt;in text                              \n" +
+                "&gt;                                                     \n" +
+                "&amp;                                                    \n" +
+                "&apos;                                                   \n" +
+                "&quot;                                                   \n" +
+                "&lsquo;                                                  \n" +
+                "&rsquo;                                                  \n" +
+                "&ldquo;                                                  \n" +
+                "&rdquo;                                                  \n" +
+                "&ndash;                                                  \n" +
+                "&mdash;                                                  \n" +
+                "&nbsp;                                                   \n" +
+                "&times;                                                  \n" +
+                "&minus;                                                  \n" +
+                "&sdot;                                                   \n" +
+                "&sim;                                                    \n" +
+                "&le;                                                     \n" +
+                "&ge;                                                     \n" +
+                "&larr;                                                   \n" +
+                "&rarr;                                                   \n" +
+                "");
+        
     // and ask the parser to check comments for us
     System.exit(parser.check(wantedComments));
   }
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.cpp b/Source/DoxygenTranslator/src/DoxygenParser.cpp
index 46b8b6b4d..b514465ac 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenParser.cpp
@@ -1263,16 +1263,15 @@ size_t DoxygenParser::processNormalComment(size_t pos, const std::string &line)
         size_t endOfWordPos = line.find_first_not_of("abcdefghijklmnopqrstuvwxyz", pos + 1);
         if (endOfWordPos != string::npos) {
             if (line[endOfWordPos] == ';') {
-                addDoxyCommand(m_tokenList, line.substr(pos, endOfWordPos));
+                addDoxyCommand(m_tokenList, line.substr(pos, endOfWordPos - pos));
+                endOfWordPos++;  // skip ';'
             } else {
                 // it is not an entity - push plain string
                 m_tokenList.push_back(Token(PLAINSTRING,
                                       line.substr(pos, endOfWordPos - pos)));
-                pos = endOfWordPos;
             }
-        } else {
-            pos = string::npos;
         }
+        pos = endOfWordPos;
     }
     break;
     default:
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.cpp b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
index d070bbdad..44bd62016 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
@@ -56,8 +56,6 @@ void JavaDocConverter::fillStaticTables() {
    *
    * entities must be translated - remain in Java, something meaningfull in Python (&lt, ...)
    *
-   * \e at end of line freezes doxygen
-   *
    * - enum inside class is missing comment
    * - '\' not representing doxygen commands
    * - add comments also to auto-generated methods lilke equals(), delete() in Java,
@@ -193,6 +191,31 @@ void JavaDocConverter::fillStaticTables() {
   tagHandlers["<kbd"    ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<kbd"    );
   tagHandlers["<ul"     ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<ul"     );
   tagHandlers["<var"    ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<var"    );
+
+  // HTML entities
+  tagHandlers["&copy" ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "&copy");
+  tagHandlers["&trade"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "&trade");
+  tagHandlers["&reg"  ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "&reg");
+  tagHandlers["&lt"   ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "&lt");
+  tagHandlers["&gt"   ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "&gt");
+  tagHandlers["&amp"  ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "&amp");
+  tagHandlers["&apos" ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "&apos");
+  tagHandlers["&quot" ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "&quot");
+  tagHandlers["&lsquo"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "&lsquo");
+  tagHandlers["&rsquo"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "&rsquo");
+  tagHandlers["&ldquo"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "&ldquo");
+  tagHandlers["&rdquo"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "&rdquo");
+  tagHandlers["&ndash"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "&ndash");
+  tagHandlers["&mdash"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "&mdash");
+  tagHandlers["&nbsp" ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "&nbsp");
+  tagHandlers["&times"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "&times");
+  tagHandlers["&minus"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "&minus");
+  tagHandlers["&sdot" ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "&sdot");
+  tagHandlers["&sim"  ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "&sim");
+  tagHandlers["&le"   ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "&le");
+  tagHandlers["&ge"   ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "&ge");
+  tagHandlers["&larr" ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "&larr");
+  tagHandlers["&rarr" ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "&rarr");
 }
 
 
@@ -344,6 +367,12 @@ void JavaDocConverter::handleDoxyHtmlTag(DoxygenEntity& tag, std::string& transl
 }
 
 
+void JavaDocConverter::handleHtmlEntity(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
+    // html entities can be preserved for Java
+    translatedComment += arg + ';';
+}
+
+
 void JavaDocConverter::handleNewLine(DoxygenEntity&, std::string& translatedComment, std::string&) {
   translatedComment += "\n * ";
 }
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.h b/Source/DoxygenTranslator/src/JavaDocConverter.h
index 1d757cf35..c2e1251fc 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.h
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.h
@@ -63,8 +63,13 @@ protected:
 
   /* Handles HTML tags recognized by Doxygen, like <A ...>, <ul>, <table>, ... */
   void handleDoxyHtmlTag(DoxygenEntity& tag,
-                            std::string& translatedComment,
-                            std::string &arg);
+                         std::string& translatedComment,
+                         std::string &arg);
+
+  /* Handles HTML entities recognized by Doxygen, like &lt;, &copy;, ... */
+  void handleHtmlEntity(DoxygenEntity& tag,
+                        std::string& translatedComment,
+                        std::string &arg);
 
   /*
    * Just prints new line

From a2b0d42c32513afcb8e03dfcc01e2643a6677d8b Mon Sep 17 00:00:00 2001
From: Marko Klopcic <markok3.14@gmail.com>
Date: Fri, 18 Jan 2013 22:30:23 +0100
Subject: [PATCH 162/314] fixed tests for HTML entities and handling of HTML
 entities

---
 Examples/test-suite/doxygen_translate.i       |  2 +-
 .../DoxygenTranslator/src/DoxygenParser.cpp   |  2 +-
 .../src/JavaDocConverter.cpp                  | 48 +++++++++----------
 3 files changed, 26 insertions(+), 26 deletions(-)

diff --git a/Examples/test-suite/doxygen_translate.i b/Examples/test-suite/doxygen_translate.i
index ba787a140..43d01108f 100644
--- a/Examples/test-suite/doxygen_translate.i
+++ b/Examples/test-suite/doxygen_translate.i
@@ -220,7 +220,7 @@ int htmlFunction(int a, float b)
  * &lsquo;
  * &rsquo;
  * &ldquo;
- * &rdaquo;
+ * &rdquo;
  * &ndash;
  * &mdash;
  * &nbsp;
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.cpp b/Source/DoxygenTranslator/src/DoxygenParser.cpp
index b514465ac..80bd80876 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenParser.cpp
@@ -1322,7 +1322,7 @@ void DoxygenParser::tokenizeDoxygenComment(const std::string &doxygenComment,
 
     while (pos != string::npos) {
       // find the end of the word
-      size_t doxyCmdOrHtmlTagPos = line.find_first_of("\\@< \t", pos);
+      size_t doxyCmdOrHtmlTagPos = line.find_first_of("\\@<& \t", pos);
       if (doxyCmdOrHtmlTagPos != pos) {
         // plain text found
         m_tokenList.push_back(Token(PLAINSTRING,
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.cpp b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
index 44bd62016..86966afb7 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
@@ -193,29 +193,29 @@ void JavaDocConverter::fillStaticTables() {
   tagHandlers["<var"    ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<var"    );
 
   // HTML entities
-  tagHandlers["&copy" ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "&copy");
-  tagHandlers["&trade"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "&trade");
-  tagHandlers["&reg"  ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "&reg");
-  tagHandlers["&lt"   ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "&lt");
-  tagHandlers["&gt"   ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "&gt");
-  tagHandlers["&amp"  ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "&amp");
-  tagHandlers["&apos" ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "&apos");
-  tagHandlers["&quot" ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "&quot");
-  tagHandlers["&lsquo"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "&lsquo");
-  tagHandlers["&rsquo"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "&rsquo");
-  tagHandlers["&ldquo"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "&ldquo");
-  tagHandlers["&rdquo"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "&rdquo");
-  tagHandlers["&ndash"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "&ndash");
-  tagHandlers["&mdash"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "&mdash");
-  tagHandlers["&nbsp" ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "&nbsp");
-  tagHandlers["&times"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "&times");
-  tagHandlers["&minus"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "&minus");
-  tagHandlers["&sdot" ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "&sdot");
-  tagHandlers["&sim"  ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "&sim");
-  tagHandlers["&le"   ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "&le");
-  tagHandlers["&ge"   ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "&ge");
-  tagHandlers["&larr" ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "&larr");
-  tagHandlers["&rarr" ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "&rarr");
+  tagHandlers["&copy" ] = make_pair(&JavaDocConverter::handleHtmlEntity, "&copy");
+  tagHandlers["&trade"] = make_pair(&JavaDocConverter::handleHtmlEntity, "&trade");
+  tagHandlers["&reg"  ] = make_pair(&JavaDocConverter::handleHtmlEntity, "&reg");
+  tagHandlers["&lt"   ] = make_pair(&JavaDocConverter::handleHtmlEntity, "&lt");
+  tagHandlers["&gt"   ] = make_pair(&JavaDocConverter::handleHtmlEntity, "&gt");
+  tagHandlers["&amp"  ] = make_pair(&JavaDocConverter::handleHtmlEntity, "&amp");
+  tagHandlers["&apos" ] = make_pair(&JavaDocConverter::handleHtmlEntity, "&apos");
+  tagHandlers["&quot" ] = make_pair(&JavaDocConverter::handleHtmlEntity, "&quot");
+  tagHandlers["&lsquo"] = make_pair(&JavaDocConverter::handleHtmlEntity, "&lsquo");
+  tagHandlers["&rsquo"] = make_pair(&JavaDocConverter::handleHtmlEntity, "&rsquo");
+  tagHandlers["&ldquo"] = make_pair(&JavaDocConverter::handleHtmlEntity, "&ldquo");
+  tagHandlers["&rdquo"] = make_pair(&JavaDocConverter::handleHtmlEntity, "&rdquo");
+  tagHandlers["&ndash"] = make_pair(&JavaDocConverter::handleHtmlEntity, "&ndash");
+  tagHandlers["&mdash"] = make_pair(&JavaDocConverter::handleHtmlEntity, "&mdash");
+  tagHandlers["&nbsp" ] = make_pair(&JavaDocConverter::handleHtmlEntity, "&nbsp");
+  tagHandlers["&times"] = make_pair(&JavaDocConverter::handleHtmlEntity, "&times");
+  tagHandlers["&minus"] = make_pair(&JavaDocConverter::handleHtmlEntity, "&minus");
+  tagHandlers["&sdot" ] = make_pair(&JavaDocConverter::handleHtmlEntity, "&sdot");
+  tagHandlers["&sim"  ] = make_pair(&JavaDocConverter::handleHtmlEntity, "&sim");
+  tagHandlers["&le"   ] = make_pair(&JavaDocConverter::handleHtmlEntity, "&le");
+  tagHandlers["&ge"   ] = make_pair(&JavaDocConverter::handleHtmlEntity, "&ge");
+  tagHandlers["&larr" ] = make_pair(&JavaDocConverter::handleHtmlEntity, "&larr");
+  tagHandlers["&rarr" ] = make_pair(&JavaDocConverter::handleHtmlEntity, "&rarr");
 }
 
 
@@ -367,7 +367,7 @@ void JavaDocConverter::handleDoxyHtmlTag(DoxygenEntity& tag, std::string& transl
 }
 
 
-void JavaDocConverter::handleHtmlEntity(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
+void JavaDocConverter::handleHtmlEntity(DoxygenEntity&, std::string& translatedComment, std::string &arg) {
     // html entities can be preserved for Java
     translatedComment += arg + ';';
 }

From f6fc808534b28471394af88952a40270bb5779f1 Mon Sep 17 00:00:00 2001
From: Marko Klopcic <markok3.14@gmail.com>
Date: Mon, 21 Jan 2013 22:22:02 +0100
Subject: [PATCH 163/314] fixed handling of < and > when they are not used for
 html tag

---
 Examples/test-suite/doxygen_translate.i       |  9 ++++-
 .../java/doxygen_translate_runme.java         |  6 +++
 .../DoxygenTranslator/src/DoxygenCommands.h   |  2 +
 .../DoxygenTranslator/src/DoxygenParser.cpp   | 37 +++++++++++--------
 .../src/JavaDocConverter.cpp                  |  4 +-
 5 files changed, 41 insertions(+), 17 deletions(-)

diff --git a/Examples/test-suite/doxygen_translate.i b/Examples/test-suite/doxygen_translate.i
index 43d01108f..3a01deb22 100644
--- a/Examples/test-suite/doxygen_translate.i
+++ b/Examples/test-suite/doxygen_translate.i
@@ -203,7 +203,12 @@ int function(int a, float b)
  * </UL> Ends an unnumbered item list.
  *
  * <VAR> Starts a piece of text displayed in an italic font.
- * </VAR>                                                                               
+ * </VAR>
+ *
+ * \htmlonly
+ * <u>underlined \b bold text - doxy commands are ignored inside 'htmlonly' section </u>
+ * \endhtmlonly
+ * <u>underlined text</u>
  */
 int htmlFunction(int a, float b)
 {
@@ -232,6 +237,8 @@ int htmlFunction(int a, float b)
  * &ge;
  * &larr;
  * &rarr;
+ * Not an &text; html entity - ignored by Doxygen.
+ * Not an &text html entity - ampersand is replaced with entity.
  */
 int htmlEntitiesFunction(int a, float b)
 {
diff --git a/Examples/test-suite/java/doxygen_translate_runme.java b/Examples/test-suite/java/doxygen_translate_runme.java
index 6be2b2165..4ec0f0468 100644
--- a/Examples/test-suite/java/doxygen_translate_runme.java
+++ b/Examples/test-suite/java/doxygen_translate_runme.java
@@ -226,6 +226,10 @@ public class doxygen_translate_runme {
     		"                                                                                      \n" +
     		" <var> Starts a piece of text displayed in an italic font.                            \n" +
     		" </var>                                                                               \n" +
+                "\n" +
+                "<u>underlined \\b bold text - doxy commands are ignored inside 'htmlonly' section </u>\n" +
+                "\n" +
+                "&lt;u&gt;underlined text&lt;u&gt;\n" +
                 "");
 
         wantedComments.put("doxygen_translate.doxygen_translate.htmlEntitiesFunction(int, float)",
@@ -250,6 +254,8 @@ public class doxygen_translate_runme {
                 "&ge;                                                     \n" +
                 "&larr;                                                   \n" +
                 "&rarr;                                                   \n" +
+                "Not an  html entity - ignored by Doxygen.                \n" +
+                "Not an &amp;text html entity - ampersand is replaced with entity.\n" +
                 "");
         
     // and ask the parser to check comments for us
diff --git a/Source/DoxygenTranslator/src/DoxygenCommands.h b/Source/DoxygenTranslator/src/DoxygenCommands.h
index 029c47550..694e57b41 100644
--- a/Source/DoxygenTranslator/src/DoxygenCommands.h
+++ b/Source/DoxygenTranslator/src/DoxygenCommands.h
@@ -2,7 +2,9 @@
 #ifndef DOXYGENCOMMANDS_H
 #define DOXYGENCOMMANDS_H
 
+// doxy commands are not processed inside this block
 const char *CMD_HTML_ONLY = "htmlonly";
+// doxy commands are not processed inside this block
 const char *CMD_VERBATIM = "verbatim";
 const char *CMD_END_HTML_ONLY = "endhtmlonly";
 const char *CMD_END_VERBATIM = "endverbatim";
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.cpp b/Source/DoxygenTranslator/src/DoxygenParser.cpp
index 80bd80876..f32c7260f 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenParser.cpp
@@ -1136,15 +1136,15 @@ size_t DoxygenParser::processVerbatimText(size_t pos, const std::string &line)
         pos++;
         // characters '$[]{}' are used in commands \f$, \f[, ...
         size_t endOfWordPos = line.find_first_not_of("abcdefghijklmnopqrstuvwxyz$[]{}", pos);
-        string cmd = line.substr(pos , endOfWordPos - pos);
+        string cmd = line.substr(pos, endOfWordPos - pos);
 
         if (cmd == CMD_END_HTML_ONLY  ||  cmd == CMD_END_VERBATIM) {
             m_isVerbatimText = false;
             addDoxyCommand(m_tokenList, cmd);
         } else {
-            cmd = line[pos] + cmd; // prepend '\\' or '@'
             m_tokenList.push_back(Token(PLAINSTRING,
-                                  line.substr(pos, endOfWordPos - pos)));
+                                  // include '\' or '@'
+                                  line.substr(pos - 1, endOfWordPos - pos + 1)));
         }
         pos = endOfWordPos;
     } else {
@@ -1189,14 +1189,14 @@ size_t DoxygenParser::processNormalComment(size_t pos, const std::string &line)
       addDoxyCommand(m_tokenList, cmd);
       if (cmd == CMD_HTML_ONLY  ||  cmd == CMD_VERBATIM) {
           m_isVerbatimText = true;
-      }
-      // skip any possible spaces after command, because some commands have parameters,
-      // and spaces between command and parameter must be ignored.
-      if (endOfWordPos != string::npos) {
-          pos = line.find_first_not_of(" \t", endOfWordPos);
       } else {
-          pos = string::npos;
+          // skip any possible spaces after command, because some commands have parameters,
+          // and spaces between command and parameter must be ignored.
+          if (endOfWordPos != string::npos) {
+              endOfWordPos = line.find_first_not_of(" \t", endOfWordPos);
+          }
       }
+      pos = endOfWordPos;
     } break;
 
     case ' ':  // whitespace
@@ -1248,27 +1248,34 @@ size_t DoxygenParser::processNormalComment(size_t pos, const std::string &line)
                 m_tokenList.push_back(Token(PLAINSTRING, ""));
               }
           }
+          pos++; // skip '>'
       } else {
         // the command is not HTML supported by Doxygen, < and > will be
         // replaced by HTML entities &lt; and &gt; respectively,
         // but only if 'htmlOnly' flag == false. The flag is set/reset by \htmlonly \verbatim,
         // \endhtmlonly \endverbatim Doxygen commands.
-        m_tokenList.push_back(Token(PLAINSTRING, "&lt;"));
+        addDoxyCommand(m_tokenList, "&lt");
         m_tokenList.push_back(Token(PLAINSTRING, cmd));
       }
-      pos++;
     } break;
-
+    case '>': // this char is detected here only when it is not part of HTML tag
+        addDoxyCommand(m_tokenList, "&gt");
+        pos++;
+        break;
     case '&': { // process HTML entities
         size_t endOfWordPos = line.find_first_not_of("abcdefghijklmnopqrstuvwxyz", pos + 1);
         if (endOfWordPos != string::npos) {
             if (line[endOfWordPos] == ';') {
+                // if entity is not recognized by Doxygen (not in the list of
+                // commands) nothing is added (here and in Doxygen).
                 addDoxyCommand(m_tokenList, line.substr(pos, endOfWordPos - pos));
                 endOfWordPos++;  // skip ';'
             } else {
-                // it is not an entity - push plain string
+                // it is not an entity - add entity for ampersand and
+                // the rest of string
+                addDoxyCommand(m_tokenList, "&amp");
                 m_tokenList.push_back(Token(PLAINSTRING,
-                                      line.substr(pos, endOfWordPos - pos)));
+                                      line.substr(pos + 1, endOfWordPos - pos - 1)));
             }
         }
         pos = endOfWordPos;
@@ -1322,7 +1329,7 @@ void DoxygenParser::tokenizeDoxygenComment(const std::string &doxygenComment,
 
     while (pos != string::npos) {
       // find the end of the word
-      size_t doxyCmdOrHtmlTagPos = line.find_first_of("\\@<& \t", pos);
+      size_t doxyCmdOrHtmlTagPos = line.find_first_of("\\@<>& \t", pos);
       if (doxyCmdOrHtmlTagPos != pos) {
         // plain text found
         m_tokenList.push_back(Token(PLAINSTRING,
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.cpp b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
index 86966afb7..86736c8a7 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
@@ -49,7 +49,7 @@ void JavaDocConverter::fillStaticTables() {
    *     Java src is <x> and therefore invisible on output - browser ignores unknown command.
    *     This is handy in syntax descriptions, for example: more <fileName>.
    *
-   * Standlaone < and > need not to be translated, they are rendered properly in
+   * Standlaone < and > need not be translated, they are rendered properly in
    *      all three outputs.
    *
    * ., %, and " need not to be translated
@@ -92,6 +92,8 @@ void JavaDocConverter::fillStaticTables() {
   tagHandlers["bug"] = make_pair(&JavaDocConverter::handleParagraph, "");
   tagHandlers["date"] = make_pair(&JavaDocConverter::handleParagraph, "");
   tagHandlers["details"] = make_pair(&JavaDocConverter::handleParagraph, "");
+  // this command is inserts text accumulated after cmd htmlonly -
+  // see DoxygenParser - CMD_HTML_ONLY.
   tagHandlers["htmlonly"] = make_pair(&JavaDocConverter::handleParagraph, "");
   tagHandlers["invariant"] = make_pair(&JavaDocConverter::handleParagraph, "");
   tagHandlers["latexonly"] = make_pair(&JavaDocConverter::handleParagraph, "");

From 43eeb4528c801f69963015a74d252916f2146e3d Mon Sep 17 00:00:00 2001
From: Marko Klopcic <markok3.14@gmail.com>
Date: Tue, 22 Jan 2013 23:21:02 +0100
Subject: [PATCH 164/314] warnings eliminated, examples fixed, only
 doxygen_misc_constructs is not working now

---
 Doc/Manual/Doxygen.html                       | 69 +++++++++++++++++++
 .../test-suite/doxygen_translate_all_tags.i   | 18 +++++
 Examples/test-suite/java/commentParser.java   | 21 +++++-
 .../doxygen_translate_all_tags_runme.java     |  7 +-
 .../src/JavaDocConverter.cpp                  |  6 +-
 5 files changed, 116 insertions(+), 5 deletions(-)

diff --git a/Doc/Manual/Doxygen.html b/Doc/Manual/Doxygen.html
index bc68ed15c..d374a9c2f 100644
--- a/Doc/Manual/Doxygen.html
+++ b/Doc/Manual/Doxygen.html
@@ -790,6 +790,75 @@ Here is the list of these tags:
 </table>
 </pre></div>
 
+<p/>
+
+If one of the following Doxygen tags appears as the first tag in a
+comment, the whole comment block is ignored:
+<!-- see parser.y, function isStructuralDoxygen() -->
+
+</p>
+<div class="diagram"><pre>
+<table border="0">
+<tr>
+<td>\addtogroup</td>
+<td>\callgraph</td>
+<td>\callergraph</td>
+<td>\category</td>
+</tr>
+<tr>
+<td>\class</td>
+<td>\def</td>
+<td>\defgroup</td>
+<td>\dir</td>
+</tr>
+<tr>
+<td>\enum</td>
+<td>\example</td>
+<td>\file</td>
+<td>\fn</td>
+</tr>
+<tr>
+<td>\headerfile</td>
+<td>\hideinitializer</td>
+<td>\interface</td>
+<td>\internal</td>
+</tr>
+<tr>
+<td>\mainpage</td>
+<td>\name</td>
+<td>\namespace</td>
+<td>\nosubgrouping</td>
+</tr>
+<tr>
+<td>\overload</td>
+<td>\package</td>
+<td>\page</td>
+<td>\property</td>
+</tr>
+<tr>
+<td>\protocol</td>
+<td>\relates</td>
+<td>\relatesalso</td>
+<td>\showinitializer</td>
+</tr>
+<tr>
+<td>\struct</td>
+<td>\name</td>
+<td>\namespace</td>
+<td>\nosubgrouping</td>
+</tr>
+<tr>
+<td>\typedef</td>
+<td>\union</td>
+<td>\var</td>
+<td>\weakgroup</td>
+</tr>
+
+</table>
+</pre></div>
+
+
+
 <H3><a name="Doxygen_further_details"></a>39.3.4 Further Details</H3>
 
 
diff --git a/Examples/test-suite/doxygen_translate_all_tags.i b/Examples/test-suite/doxygen_translate_all_tags.i
index f780b643a..658fc92df 100644
--- a/Examples/test-suite/doxygen_translate_all_tags.i
+++ b/Examples/test-suite/doxygen_translate_all_tags.i
@@ -70,6 +70,8 @@ int func02(int a)
 
  
 /**
+ * Comment for \b func03().
+ *
  * \dir /somePath/someFolder
  *
  * \dontinclude someFile.h
@@ -176,6 +178,8 @@ int func05(int a)
 
  
 /**
+ * Comment for \b func06().
+ *
  * \interface someInterface someHeader.h "Header name"
  *
  * \latexonly
@@ -218,6 +222,8 @@ int func06(int a)
 
  
 /**
+ * Comment for \b func07().
+ *
  * \name someHeader.h
  *
  * \namespace someNamespace
@@ -384,4 +390,16 @@ int func10(int a, float b)
 {
 }
 
+
+/**
+ * \interface someInterface someHeader.h "Header name"
+ *
+ * Because of structural Doxygen command at the start of comment block,
+ * the whoile comment block is ignored. See parser.y, f. isStructuralDoxygen()
+ * or documentation for the list of commands.
+ */
+int func11(int a, float b)
+{
+}
+
 %}
diff --git a/Examples/test-suite/java/commentParser.java b/Examples/test-suite/java/commentParser.java
index 7ec9e1595..f410e889f 100644
--- a/Examples/test-suite/java/commentParser.java
+++ b/Examples/test-suite/java/commentParser.java
@@ -2,6 +2,8 @@
 import com.sun.javadoc.*;
 import java.util.HashMap;
 import java.util.Map.Entry;
+import java.util.Map;
+import java.util.Set;
 import java.util.Iterator;
 import java.io.BufferedWriter;
 import java.io.OutputStreamWriter;
@@ -88,8 +90,15 @@ public class commentParser {
             }
         }
 
-        if (parsedComments.size() < wantedComments.size()) {
-            System.out.println("Found " + (wantedComments.size()-parsedComments.size()) + " missed comment(s)!");
+        if (parsedComments.size() != wantedComments.size()) {
+            System.out.println("Mismatch in the number of comments!\n    Expected: " +
+                               wantedComments.size() + "\n    Parsed: " +
+                               parsedComments.size());
+            System.out.println("Expected keys: ");
+            printKeys(wantedComments);
+            System.out.println("Parsed keys: ");
+            printKeys(parsedComments);
+
             errorCount++;
         }
 		
@@ -97,6 +106,14 @@ public class commentParser {
     }
 
     
+    private static void printKeys(Map map) {
+        Set<String> keys = map.keySet();
+        for (String key : keys) {
+            System.out.println("    " + key);
+        }
+    }
+    
+    
     public static void printCommentListForJavaSource() {
         Iterator< Entry<String, String> > it = parsedComments.entrySet().iterator();
         while (it.hasNext())
diff --git a/Examples/test-suite/java/doxygen_translate_all_tags_runme.java b/Examples/test-suite/java/doxygen_translate_all_tags_runme.java
index 9d9cec2b7..aa6ed44ff 100644
--- a/Examples/test-suite/java/doxygen_translate_all_tags_runme.java
+++ b/Examples/test-suite/java/doxygen_translate_all_tags_runme.java
@@ -51,8 +51,11 @@ public class doxygen_translate_all_tags_runme {
     		" and detailed description of some thing \n");
     
     wantedComments.put("doxygen_translate_all_tags.doxygen_translate_all_tags.func03(int)",
+                       " Comment for <b>func03().</b>\n" +
                        " <i>italicword </i>\n" +
-    		" <i>emphazedWord </i>\n");
+    		" <i>emphazedWord </i>\n" +
+                " @ example someFile.txt\n" +
+                " Some details on using the example");
     
     wantedComments.put("doxygen_translate_all_tags.doxygen_translate_all_tags.func04(int)",
                        " @exception SuperError \n" +
@@ -80,6 +83,7 @@ public class doxygen_translate_all_tags_runme {
     		" describing invariant. \n");
     
     wantedComments.put("doxygen_translate_all_tags.doxygen_translate_all_tags.func06(int)",
+                       " Comment for <b>func06().</b>\n" +
                        " This will only appear in LATeX \n" +
     		" <ul> \n" +
     		" <li>Some unordered list \n" +
@@ -90,6 +94,7 @@ public class doxygen_translate_all_tags_runme {
     		" This will only appear in man\n");
     
     wantedComments.put("doxygen_translate_all_tags.doxygen_translate_all_tags.func07(int)",
+                       " Comment for <b>func07().</b>\n" +
                        " Note: Here \n" +
     		" is the note! \n" +
     		" This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.\n" +
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.cpp b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
index 86736c8a7..e5ad38008 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
@@ -126,7 +126,7 @@ void JavaDocConverter::fillStaticTables() {
   tagHandlers["else"] = make_pair(&JavaDocConverter::handleTagIf, "Else: ");
   tagHandlers["elseif"] = make_pair(&JavaDocConverter::handleTagIf, "Else if: ");
   tagHandlers["endcond"] = make_pair(&JavaDocConverter::handleTagMessage, "End of conditional comment.");
-  // space prevents Javadoc to treat '@ example' as command. File name of
+  // space in second arg prevents Javadoc to treat '@ example' as command. File name of
   // example is still informative to user.
   tagHandlers["example"] = make_pair(&JavaDocConverter::handleTagSame, " example");
   tagHandlers["if"] = make_pair(&JavaDocConverter::handleTagIf, "If: ");
@@ -340,7 +340,9 @@ void JavaDocConverter::translateEntity(DoxygenEntity &tag,
   if (it != tagHandlers.end()) {
     (this->*(it->second.first))(tag, translatedComment, it->second.second);
   } else {
-      addError(WARN_DOXYGEN_COMMAND_ERROR, "Unknown doxygen or HTML tag: " + tag.typeOfEntity);
+      // do NOT print warning, since there are many tags, which are not
+      // translatable - many warnings hide important ones
+      // addError(WARN_DOXYGEN_COMMAND_ERROR, "Unknown doxygen or HTML tag: " + tag.typeOfEntity);
   }
 }
 

From 8de06366cfc0533de38351400598d5af3cef1e02 Mon Sep 17 00:00:00 2001
From: Marko Klopcic <markok3.14@gmail.com>
Date: Wed, 23 Jan 2013 23:15:36 +0100
Subject: [PATCH 165/314] fixed handling of quoted text adn standalone
 backslash and @

---
 Examples/test-suite/doxygen_misc_constructs.h | 19 +++++-------
 Examples/test-suite/java/commentParser.java   |  3 +-
 .../java/doxygen_misc_constructs_runme.java   | 30 ++++++++++++-------
 .../doxygen_translate_all_tags_runme.java     |  3 ++
 .../DoxygenTranslator/src/DoxygenParser.cpp   | 27 +++++++++++++++--
 Source/DoxygenTranslator/src/DoxygenParser.h  |  1 +
 .../src/JavaDocConverter.cpp                  |  3 ++
 7 files changed, 61 insertions(+), 25 deletions(-)

diff --git a/Examples/test-suite/doxygen_misc_constructs.h b/Examples/test-suite/doxygen_misc_constructs.h
index ab97cc81d..75a5cbba2 100644
--- a/Examples/test-suite/doxygen_misc_constructs.h
+++ b/Examples/test-suite/doxygen_misc_constructs.h
@@ -27,7 +27,7 @@ void isNoSpaceValidC()
 
 /**
  * Backslash following\c word is a valid doxygen command. Output contains
- * 'followingword' with 'word' in 'code' font.
+ * 'followingword' with 'word' in code font.
  */
 void backslashA()
 {}
@@ -41,12 +41,13 @@ void backslashA()
  * Doxy command without trailing \cspace space is ignored - nothing appears
  * on output. Standalone \ and '\' get to output.
  * Standalone @ and '@' get to output.
+ * Commands "in quoted \b strings are treated as plain text".
  * Commands not recognized by Doxygen \blah @blah are ignored.
- * Backslashes in DOS paths d:\xyz\c\myfile and
- * words following them do not appear on output, we must quote them with
- * double quotes: "d:\xyz\c\myfile", "@something". single quotes do not help:
- * 'd:\xyz\c\myfile'. Escaping works: d:\\xyz\\c\\myfile. Unix
- * paths of course have no such problems: /xyz/c/myfile
+ * Backslashes in DOS paths d:\xyz\qwe\myfile and words 
+ * following them do not appear on output, we must quote them with
+ * double quotes: "d:\xyz\qwe\myfile", "@something". Single quotes do not help:
+ * 'd:\xyz\qwe\myfile'. Escaping works: d:\\xyz\\qwe\\myfile. Unix
+ * paths of course have no such problems: /xyz/qwe/myfile
  * Commands for escaped symbols:
  * \$ \@ \\ \& \~ \< \> \# \% \" \. \:: \@text \::text
  */
@@ -56,14 +57,8 @@ void backslashB()
 /**
  * Backslash e at end of \e line froze SWIG \e
  * with old comment parser.
- * \arg some list item
  */
 void backslashC()
 {}
 
-/**
- *
- */
-void htmlTags()
-{}
 
diff --git a/Examples/test-suite/java/commentParser.java b/Examples/test-suite/java/commentParser.java
index f410e889f..cc40c4ac8 100644
--- a/Examples/test-suite/java/commentParser.java
+++ b/Examples/test-suite/java/commentParser.java
@@ -63,7 +63,8 @@ public class commentParser {
             }
 
             if (!actualStr.equals(wantedStr)) {
-                System.out.println("Documentation comments for " + e.getKey() + " do not match!");
+                System.out.println("\n\n////////////////////////////////////////////////////////////////////////");
+                System.out.println("Documentation comments for '" + e.getKey() + "' do not match!");
                 String expectedFileName = "expected.txt";
                 String gotFileName = "got.txt";
                 System.out.println("Output is also saved to files '" + expectedFileName +
diff --git a/Examples/test-suite/java/doxygen_misc_constructs_runme.java b/Examples/test-suite/java/doxygen_misc_constructs_runme.java
index c7a14f91e..073460f05 100644
--- a/Examples/test-suite/java/doxygen_misc_constructs_runme.java
+++ b/Examples/test-suite/java/doxygen_misc_constructs_runme.java
@@ -72,7 +72,7 @@ public class doxygen_misc_constructs_runme {
     		" return reference to self, so we can use it like this: \n" +
     		" <pre> \n" +
     		" CConnectionConfig config = new CConnectionConfig(); \n" +
-    		" config.discoveryPort(5534).dllPath(\"C: \\ yWinIDEA \\ onnect.dll\").id(\"main\"); \n" +
+    		" config.discoveryPort(5534).dllPath(\"C:\\\\myWinIDEA\\\\connect.dll\").id(\"main\"); \n" +
     		" </pre> \n" +
     		" \n" +
     		" All parameters are optional. Set only what is required, default values are \n" +
@@ -130,21 +130,31 @@ public class doxygen_misc_constructs_runme {
     		"");
  
     wantedComments.put("doxygen_misc_constructs.doxygen_misc_constructs.backslashA()",
-    		" Backslash following<code>word</code> is valid doxygen command. Output contains \n" +
-    		" 'followingword' with word in 'code' font. \n" +
+    		" Backslash following<code>word</code> is a valid doxygen command. Output contains\n" +
+    		" 'followingword' with 'word' in code font. \n" +
     		" \n" +
     		"");
  
     wantedComments.put("doxygen_misc_constructs.doxygen_misc_constructs.backslashB()",
-                       " Doxy command without trailing cspace space is ignored. Standalone \n" +
-                       " \\ and '\\' get to output. Commands not recognized by Doxygen \n" +
-                       " are ignored. Backslashes in DOS paths d: and words \n" +
+                       " Doxy command without trailing space is ignored - nothing appears\n" +
+                       " on output. Standalone \\ and '\\' get to output. \n" +
+                       " Standalone @ and '@' get to output. \n" +
+                       " Commands \"in quoted \\b strings are treated as plain text\". \n" +
+                       " Commands not recognized by Doxygen are ignored. \n" +
+                       " Backslashes in DOS paths d: and words \n" +
                        " following them do not appear on output, we must quote them with \n" +
-                       " double quotes: \"d:\\xyz\\c\\myfile\", single quotes do not help: \n" +
-                       " 'd: '. Escaping works: d:\\xyz\\c\\myfile. Unix \n" +
-                       " paths of course have no such problems: /xyz/c/myfile \n" +
+                       " double quotes: \"d:\\xyz\\qwe\\myfile\", \"@something\". Single quotes do not help: \n" +
+                       " 'd: '. Escaping works: d:\\xyz\\qwe\\myfile. Unix \n" +
+                       " paths of course have no such problems: /xyz/qwe/myfile \n" +
+                       " Commands for escaped symbols:\n" +
+                       " $ @ \\ &amp; ~ &lt; &gt; # % &quot; . :: @text ::text" +
     		" \n");
- 
+
+   wantedComments.put("doxygen_misc_constructs.doxygen_misc_constructs.backslashC()",
+    		" Backslash e at end of <i>line</i> froze SWIG\n" +
+    		" <i>with</i> old comment parser.\n" +
+    		"");
+     
     // and ask the parser to check comments for us
     System.exit(parser.check(wantedComments));
   }
diff --git a/Examples/test-suite/java/doxygen_translate_all_tags_runme.java b/Examples/test-suite/java/doxygen_translate_all_tags_runme.java
index aa6ed44ff..6bb56c437 100644
--- a/Examples/test-suite/java/doxygen_translate_all_tags_runme.java
+++ b/Examples/test-suite/java/doxygen_translate_all_tags_runme.java
@@ -59,6 +59,9 @@ public class doxygen_translate_all_tags_runme {
     
     wantedComments.put("doxygen_translate_all_tags.doxygen_translate_all_tags.func04(int)",
                        " @exception SuperError \n" +
+                       " \sqrt{(x_2-x_1)^2+(y_2-y_1)^2} \n" +
+                       " \sqrt{(x_2-x_1)^2+(y_2-y_1)^2} \n" +
+                       " \sqrt{(x_2-x_1)^2+(y_2-y_1)^2} \n" +
     		" This will only appear in hmtl \n");
     
     wantedComments.put("doxygen_translate_all_tags.doxygen_translate_all_tags.func05(int)",
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.cpp b/Source/DoxygenTranslator/src/DoxygenParser.cpp
index f32c7260f..4a96fa922 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenParser.cpp
@@ -1167,6 +1167,16 @@ size_t DoxygenParser::processNormalComment(size_t pos, const std::string &line)
       // process doxy commands for escaped characters - handling this separately
       // supports documentation text like \@someText
       if ((pos + 1) < line.size()) {
+
+        // \ and @ with trailing whitespace or quoted get to output as plain string
+        string whitespaces = " '\t\n";
+        if (whitespaces.find(line[pos + 1]) != string::npos) {
+          m_tokenList.push_back(Token(PLAINSTRING, line.substr(pos, 1)));
+          pos++;
+          break;
+        }
+
+        // these chars can be escaped for doxygen
         string escapedChars = "$@\\&~<>#%\".";
         if (escapedChars.find(line[pos + 1]) != string::npos) {
           addDoxyCommand(m_tokenList, line.substr(pos + 1, 1));
@@ -1281,6 +1291,11 @@ size_t DoxygenParser::processNormalComment(size_t pos, const std::string &line)
         pos = endOfWordPos;
     }
     break;
+    case '"':
+        m_isInQuotedString = true;
+        m_tokenList.push_back(Token(PLAINSTRING, "\""));
+        pos++;
+        break;
     default:
       m_tokenListIt = m_tokenList.end();
       printListError(WARN_DOXYGEN_COMMAND_ERROR, "Unknown special character: " + line[pos]);
@@ -1298,6 +1313,7 @@ void DoxygenParser::tokenizeDoxygenComment(const std::string &doxygenComment,
                                                  int fileLine)
 {
   m_isVerbatimText = false;
+  m_isInQuotedString = false;
   m_tokenList.clear();
   m_fileLineNo = fileLine;
   m_fileName = fileName;
@@ -1329,17 +1345,24 @@ void DoxygenParser::tokenizeDoxygenComment(const std::string &doxygenComment,
 
     while (pos != string::npos) {
       // find the end of the word
-      size_t doxyCmdOrHtmlTagPos = line.find_first_of("\\@<>& \t", pos);
+      size_t doxyCmdOrHtmlTagPos = line.find_first_of("\\@<>&\" \t", pos);
       if (doxyCmdOrHtmlTagPos != pos) {
         // plain text found
         m_tokenList.push_back(Token(PLAINSTRING,
-                                 line.substr(pos, doxyCmdOrHtmlTagPos - pos)));
+                              line.substr(pos, doxyCmdOrHtmlTagPos - pos)));
       }
 
       pos = doxyCmdOrHtmlTagPos;
       if (pos != string::npos) {
         if (m_isVerbatimText) {
             pos = processVerbatimText(pos, line);
+        } else if (m_isInQuotedString) {
+            if (line[pos] == '"') {
+                m_isInQuotedString = false;
+            }
+            m_tokenList.push_back(Token(PLAINSTRING,
+                                     line.substr(pos, 1)));
+            pos++;
         } else {
             pos = processNormalComment(pos, line);
         }
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.h b/Source/DoxygenTranslator/src/DoxygenParser.h
index 558a85ef3..adc5c7f26 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.h
+++ b/Source/DoxygenTranslator/src/DoxygenParser.h
@@ -88,6 +88,7 @@ private:
   static std::set<std::string> doxygenSectionIndicators;
 
   bool m_isVerbatimText; // used to handle \htmlonly and \verbatim commands
+  bool m_isInQuotedString;
 
   std::string m_fileName;
   int m_fileLineNo;
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.cpp b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
index e5ad38008..ca83e9673 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
@@ -57,6 +57,9 @@ void JavaDocConverter::fillStaticTables() {
    * entities must be translated - remain in Java, something meaningfull in Python (&lt, ...)
    *
    * - enum inside class is missing comment
+   * - crash if link in @see tag is split to two lines
+   * - whitespaces in tests
+   * - Python
    * - '\' not representing doxygen commands
    * - add comments also to auto-generated methods lilke equals(), delete() in Java,
    *   and methods for std::vector(), ...

From d52de0f36f570ff9aa0011a10ab6a9023cd8b56c Mon Sep 17 00:00:00 2001
From: Marko Klopcic <markok3.14@gmail.com>
Date: Sat, 26 Jan 2013 22:52:34 +0100
Subject: [PATCH 166/314] fixed comments for enum types in Java - they were
 missing before

---
 Source/Modules/java.cxx | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/Source/Modules/java.cxx b/Source/Modules/java.cxx
index 910d481ab..b584c9246 100644
--- a/Source/Modules/java.cxx
+++ b/Source/Modules/java.cxx
@@ -1252,6 +1252,16 @@ public:
       EnumFeature enum_feature = decodeEnumFeature(n);
       String *typemap_lookup_type = Getattr(n, "name");
 
+      if (doxygen && doxygenTranslator->hasDocumentation(n)){
+        String *doxygen_comments=doxygenTranslator->getDocumentation(n);
+        if(comment_creation_chatter) {
+          Printf(enum_code, "/* This was generated from enumvalueDeclaration() */");
+        }
+        Printv(enum_code, Char(doxygen_comments), NIL);
+        Delete(doxygen_comments);
+      }
+
+
       if ((enum_feature != SimpleEnum) && symname && typemap_lookup_type) {
 	// Wrap (non-anonymous) C/C++ enum within a typesafe, typeunsafe or proper Java enum
 

From 9a1bb671c10288b49677fdbc0f4b3e1afbe92006 Mon Sep 17 00:00:00 2001
From: Marko Klopcic <markok3.14@gmail.com>
Date: Sun, 27 Jan 2013 22:18:06 +0100
Subject: [PATCH 167/314] fixed bug with caption in command 'image'

---
 Examples/test-suite/doxygen_translate.i             |  2 +-
 .../test-suite/java/doxygen_translate_runme.java    |  2 +-
 Source/DoxygenTranslator/src/DoxygenParser.cpp      | 13 ++++++-------
 Source/DoxygenTranslator/src/JavaDocConverter.cpp   | 11 +++++++----
 4 files changed, 15 insertions(+), 13 deletions(-)

diff --git a/Examples/test-suite/doxygen_translate.i b/Examples/test-suite/doxygen_translate.i
index 3a01deb22..181c0799e 100644
--- a/Examples/test-suite/doxygen_translate.i
+++ b/Examples/test-suite/doxygen_translate.i
@@ -54,7 +54,7 @@
  *   This is printed if not
  * \endif
  * 
- * \image html testImage.bmp "Hello, world!" asd=10qwe
+ * \image html testImage.bmp "Hello, world!" width=10cm
  * 
  * <ul>
  * 
diff --git a/Examples/test-suite/java/doxygen_translate_runme.java b/Examples/test-suite/java/doxygen_translate_runme.java
index 4ec0f0468..10b5af28d 100644
--- a/Examples/test-suite/java/doxygen_translate_runme.java
+++ b/Examples/test-suite/java/doxygen_translate_runme.java
@@ -75,7 +75,7 @@ public class doxygen_translate_runme {
     		" This is printed if not}\n" +
     		" \n" +
     		" \n" +
-    		" <img src=testImage.bmp alt=\"Hello, world!\" />\n" +
+    		" <img src=testImage.bmp alt=\"Hello, world!\"/>\n" +
     		" \n" +
     		" <ul> \n" +
     		" \n" +
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.cpp b/Source/DoxygenTranslator/src/DoxygenParser.cpp
index 4a96fa922..eda17a7e9 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenParser.cpp
@@ -201,21 +201,20 @@ std::string DoxygenParser::getNextWord() {
 */
 	while (m_tokenListIt != m_tokenList.end()  &&  (m_tokenListIt->m_tokenType == PLAINSTRING)) {
 		// handle quoted strings as words
-		if (m_tokenListIt->m_tokenString[0] == '"'
-				&& m_tokenListIt->m_tokenString[m_tokenListIt->m_tokenString.size() - 1] != '"') {
+	    string token = m_tokenListIt->m_tokenString;
+		if (token == "\"") {
 
-			string word = m_tokenListIt->m_tokenString + " ";
+			string word = m_tokenListIt->m_tokenString;
 			m_tokenListIt++;
 			while (true) {
-				string nextWord = getNextWord();
+				string nextWord = getNextToken();
 				if (nextWord.empty()) { // maybe report unterminated string error
 					return word;
 				}
 				word += nextWord;
-				if (word[word.size() - 1] == '"') { // strip quotes
-					return word.substr(1, word.size() - 2);
+				if (nextWord == "\"") {
+					return word;
 				}
-				word += " ";
 			}
 		}
 
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.cpp b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
index ca83e9673..cc329e706 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
@@ -56,11 +56,11 @@ void JavaDocConverter::fillStaticTables() {
    *
    * entities must be translated - remain in Java, something meaningfull in Python (&lt, ...)
    *
-   * - enum inside class is missing comment
+   * - OK enum inside class is missing comment
    * - crash if link in @see tag is split to two lines
    * - whitespaces in tests
    * - Python
-   * - '\' not representing doxygen commands
+   * - OK '\' not representing doxygen commands
    * - add comments also to auto-generated methods lilke equals(), delete() in Java,
    *   and methods for std::vector(), ...
    */
@@ -459,8 +459,11 @@ void JavaDocConverter::handleTagImage(DoxygenEntity& tag, std::string& translate
 
   translatedComment += "<img src=" + file;
   if (title.size())
-    translatedComment += " alt=\"" + title +"\"";
-  translatedComment += " />";
+    translatedComment += " alt=" + title;
+
+  // the size indication is supported for Latex only in Doxygen, see manual
+
+  translatedComment += "/>";
 }
 
 

From 2df4449e3b233f5fd605bf188d8cf28803208b49 Mon Sep 17 00:00:00 2001
From: Marko Klopcic <markok3.14@gmail.com>
Date: Mon, 28 Jan 2013 20:07:36 +0100
Subject: [PATCH 168/314] commands \f? (LateX formulas) are no longer ignored -
 formulas are copied literally to Java comments

---
 .../doxygen_translate_all_tags_runme.java     |  6 +--
 .../DoxygenTranslator/src/DoxygenCommands.h   |  6 +++
 .../DoxygenTranslator/src/DoxygenParser.cpp   | 45 ++-----------------
 .../src/JavaDocConverter.cpp                  | 14 ++++++
 .../DoxygenTranslator/src/JavaDocConverter.h  |  6 +++
 5 files changed, 33 insertions(+), 44 deletions(-)

diff --git a/Examples/test-suite/java/doxygen_translate_all_tags_runme.java b/Examples/test-suite/java/doxygen_translate_all_tags_runme.java
index 6bb56c437..37d60ff81 100644
--- a/Examples/test-suite/java/doxygen_translate_all_tags_runme.java
+++ b/Examples/test-suite/java/doxygen_translate_all_tags_runme.java
@@ -59,9 +59,9 @@ public class doxygen_translate_all_tags_runme {
     
     wantedComments.put("doxygen_translate_all_tags.doxygen_translate_all_tags.func04(int)",
                        " @exception SuperError \n" +
-                       " \sqrt{(x_2-x_1)^2+(y_2-y_1)^2} \n" +
-                       " \sqrt{(x_2-x_1)^2+(y_2-y_1)^2} \n" +
-                       " \sqrt{(x_2-x_1)^2+(y_2-y_1)^2} \n" +
+                       " \\sqrt{(x_2-x_1)^2+(y_2-y_1)^2} \n" +
+                       " \\sqrt{(x_2-x_1)^2+(y_2-y_1)^2} \n" +
+                       " \\sqrt{(x_2-x_1)^2+(y_2-y_1)^2} \n" +
     		" This will only appear in hmtl \n");
     
     wantedComments.put("doxygen_translate_all_tags.doxygen_translate_all_tags.func05(int)",
diff --git a/Source/DoxygenTranslator/src/DoxygenCommands.h b/Source/DoxygenTranslator/src/DoxygenCommands.h
index 694e57b41..7fa1dbb54 100644
--- a/Source/DoxygenTranslator/src/DoxygenCommands.h
+++ b/Source/DoxygenTranslator/src/DoxygenCommands.h
@@ -6,8 +6,14 @@
 const char *CMD_HTML_ONLY = "htmlonly";
 // doxy commands are not processed inside this block
 const char *CMD_VERBATIM = "verbatim";
+const char *CMD_LATEX_1 = "f$";
+const char *CMD_LATEX_2 = "f{";
+const char *CMD_LATEX_3 = "f[";
 const char *CMD_END_HTML_ONLY = "endhtmlonly";
 const char *CMD_END_VERBATIM = "endverbatim";
+const char *CMD_END_LATEX_1 = "f$";
+const char *CMD_END_LATEX_2 = "f}";
+const char *CMD_END_LATEX_3 = "f]";
 
 const char *sectionIndicators[] = {
   "attention", "author", "authors", "brief", "bug", "cond", "date",
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.cpp b/Source/DoxygenTranslator/src/DoxygenParser.cpp
index eda17a7e9..59b47e46f 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenParser.cpp
@@ -234,44 +234,6 @@ std::string DoxygenParser::getNextWord() {
 	return "";
 }
 
-/* TODO remove this m.
-std::string DoxygenParser::getNextWordInComment() {
-
-    while (m_tokenListIt != m_tokenList.end()  &&  (m_tokenListIt->m_tokenType == PLAINSTRING  ||  m_tokenListIt->m_tokenType == END_LINE)) {
-        // handle quoted strings as words
-        if (m_tokenListIt->m_tokenString[0] == '"'
-                && m_tokenListIt->m_tokenString[m_tokenListIt->m_tokenString.size() - 1] != '"') {
-
-            string word = m_tokenListIt->m_tokenString + " ";
-            while (true) {
-                string nextWord = getNextWord();
-                if (nextWord.empty()) {// maybe report unterminated string error
-                    return word;
-                }
-                word += nextWord;
-                if (word[word.size() - 1] == '"') { // strip quotes
-                    return word.substr(1, word.size() - 2);
-                }
-                word += " ";
-            }
-        }
-
-        string tokenStr = trim(m_tokenListIt->m_tokenString);
-        m_tokenListIt++;
-        if (!tokenStr.empty()) {
-            return tokenStr;
-        }
-    } * else if (nextToken.m_tokenType == END_LINE) {
-        // this handles cases when command is the last item in line, for example:
-        // * This method returns line number \c
-        // * relative to paragraph.
-        m_tokenListIt++;
-        return getNextWord();
-    } *
-
-    return "";
-} */
-
 
 DoxygenParser::TokenListCIt DoxygenParser::getOneLine(const TokenList &tokList) {
 
@@ -315,7 +277,6 @@ std::string DoxygenParser::getStringTilEndCommand(const std::string & theCommand
 	string description;
 	while (m_tokenListIt != tokList.end()) {
 
-		//TODO: it won't output doxygen commands, need a way to fix it
 		if (m_tokenListIt->m_tokenType == PLAINSTRING) {
 			description += m_tokenListIt->m_tokenString;
 		} else if (m_tokenListIt->m_tokenType == END_LINE) {
@@ -1137,7 +1098,8 @@ size_t DoxygenParser::processVerbatimText(size_t pos, const std::string &line)
         size_t endOfWordPos = line.find_first_not_of("abcdefghijklmnopqrstuvwxyz$[]{}", pos);
         string cmd = line.substr(pos, endOfWordPos - pos);
 
-        if (cmd == CMD_END_HTML_ONLY  ||  cmd == CMD_END_VERBATIM) {
+        if (cmd == CMD_END_HTML_ONLY  ||  cmd == CMD_END_VERBATIM  ||
+            cmd == CMD_END_LATEX_1 ||  cmd == CMD_END_LATEX_2  ||  cmd == CMD_END_LATEX_3) {
             m_isVerbatimText = false;
             addDoxyCommand(m_tokenList, cmd);
         } else {
@@ -1196,7 +1158,8 @@ size_t DoxygenParser::processNormalComment(size_t pos, const std::string &line)
       size_t endOfWordPos = line.find_first_not_of("abcdefghijklmnopqrstuvwxyz$[]{}", pos);
       string cmd = line.substr(pos , endOfWordPos - pos);
       addDoxyCommand(m_tokenList, cmd);
-      if (cmd == CMD_HTML_ONLY  ||  cmd == CMD_VERBATIM) {
+      if (cmd == CMD_HTML_ONLY  ||  cmd == CMD_VERBATIM  ||
+          cmd == CMD_LATEX_1  ||  cmd == CMD_LATEX_2  ||  cmd == CMD_LATEX_3) {
           m_isVerbatimText = true;
       } else {
           // skip any possible spaces after command, because some commands have parameters,
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.cpp b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
index cc329e706..a815eb56b 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
@@ -147,6 +147,12 @@ void JavaDocConverter::fillStaticTables() {
   tagHandlers["remarks"] = make_pair(&JavaDocConverter::handleTagMessage, "Remarks: ");
   tagHandlers["todo"] = make_pair(&JavaDocConverter::handleTagMessage, "TODO: ");
   tagHandlers["verbatim"] = make_pair(&JavaDocConverter::handleTagExtended, "literal");
+
+  // \f commands output literal Latex formula, which is still better than nothing.
+  tagHandlers["f$"] = make_pair(&JavaDocConverter::handleTagVerbatim, "");
+  tagHandlers["f["] = make_pair(&JavaDocConverter::handleTagVerbatim, "");
+  tagHandlers["f{"] = make_pair(&JavaDocConverter::handleTagVerbatim, "");
+
   tagHandlers["warning"] = make_pair(&JavaDocConverter::handleTagMessage, "Warning: ");
   // this command just prints it's contents
   // (it is internal command of swig's parser, contains plain text)
@@ -413,6 +419,14 @@ void JavaDocConverter::handlePlainString(DoxygenEntity& tag, std::string& transl
 }
 
 
+void JavaDocConverter::handleTagVerbatim(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
+  translatedComment += arg + " ";
+  for (DoxygenEntityListCIt it = tag.entityList.begin(); it != tag.entityList.end(); it++) {
+      translatedComment += it->data;
+  }
+}
+
+
 void JavaDocConverter::handleTagExtended(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
   std::string dummy;
   translatedComment += "{@" + arg + " ";
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.h b/Source/DoxygenTranslator/src/JavaDocConverter.h
index c2e1251fc..abb6f2233 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.h
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.h
@@ -55,6 +55,12 @@ protected:
    */
   typedef void (JavaDocConverter::*tagHandler)(DoxygenEntity &tag,
       std::string &translatedComment, std::string &arg);
+
+  /**
+   * Copies verbatim args of the tag to output, used for commands like \f$, ...
+   */
+  void handleTagVerbatim(DoxygenEntity& tag, std::string& translatedComment, std::string &arg);
+
   /*
    * Wrap the command data with the html tag
    * arg - html tag, with no braces

From a2a345be39a688f77dfe1f020616400de395fa42 Mon Sep 17 00:00:00 2001
From: Marko Klopcic <markok3.14@gmail.com>
Date: Mon, 28 Jan 2013 22:25:40 +0100
Subject: [PATCH 169/314] improved handling of @see tags - SWIG no longer
 crashes if right brace is missing

---
 Examples/test-suite/doxygen_misc_constructs.h |  5 ++-
 .../java/doxygen_misc_constructs_runme.java   |  1 +
 .../src/JavaDocConverter.cpp                  | 45 ++++++++++++++-----
 3 files changed, 39 insertions(+), 12 deletions(-)

diff --git a/Examples/test-suite/doxygen_misc_constructs.h b/Examples/test-suite/doxygen_misc_constructs.h
index 75a5cbba2..dd345ca3a 100644
--- a/Examples/test-suite/doxygen_misc_constructs.h
+++ b/Examples/test-suite/doxygen_misc_constructs.h
@@ -56,7 +56,10 @@ void backslashB()
 
 /**
  * Backslash e at end of \e line froze SWIG \e
- * with old comment parser.
+ * with old comment parser. 
+ *
+ * @see MyClass::fun(char,
+ *  float)
  */
 void backslashC()
 {}
diff --git a/Examples/test-suite/java/doxygen_misc_constructs_runme.java b/Examples/test-suite/java/doxygen_misc_constructs_runme.java
index 073460f05..0879d26db 100644
--- a/Examples/test-suite/java/doxygen_misc_constructs_runme.java
+++ b/Examples/test-suite/java/doxygen_misc_constructs_runme.java
@@ -153,6 +153,7 @@ public class doxygen_misc_constructs_runme {
    wantedComments.put("doxygen_misc_constructs.doxygen_misc_constructs.backslashC()",
     		" Backslash e at end of <i>line</i> froze SWIG\n" +
     		" <i>with</i> old comment parser.\n" +
+                " @see MyClass#fun(char,float)\n" +
     		"");
      
     // and ask the parser to check comments for us
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.cpp b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
index a815eb56b..db024f302 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
@@ -56,11 +56,9 @@ void JavaDocConverter::fillStaticTables() {
    *
    * entities must be translated - remain in Java, something meaningfull in Python (&lt, ...)
    *
-   * - OK enum inside class is missing comment
    * - crash if link in @see tag is split to two lines
    * - whitespaces in tests
    * - Python
-   * - OK '\' not representing doxygen commands
    * - add comments also to auto-generated methods lilke equals(), delete() in Java,
    *   and methods for std::vector(), ...
    */
@@ -517,7 +515,7 @@ string JavaDocConverter::convertLink(string linkObject) {
   // find the params in function in linkObject (if any)
   size_t lbracePos = linkObject.find('(', 0);
   size_t rbracePos = linkObject.find(')', 0);
-  if (lbracePos == string::npos && rbracePos == string::npos && lbracePos >= rbracePos)
+  if (lbracePos == string::npos || rbracePos == string::npos || lbracePos >= rbracePos)
     return "";
 
   string paramsStr = linkObject.substr(lbracePos + 1, rbracePos - lbracePos - 1);
@@ -621,18 +619,43 @@ void JavaDocConverter::handleTagSee(DoxygenEntity& tag, std::string& translatedC
   if (!tag.entityList.size())
     return;
 
+  // tag.entity list contains contents of the @see paragraph. It should contain
+  // one link (references) to method with or without parameters. Doxygen supports
+  // arbitrary text and types mixed, but this feature is not supported here.
+  // :: or # may be used as a separator between class name and method name.
   list<DoxygenEntity>::iterator it;
+  string methodRef;
   for (it = tag.entityList.begin(); it!=tag.entityList.end(); it++) {
-    if (it->typeOfEntity == "plainstd::endl")
-      handleNewLine(*it, translatedComment, dummy);
-    if (it->typeOfEntity != "plainstd::string")
+    if (it->typeOfEntity == "plainstd::endl") {
+      // handleNewLine(*it, translatedComment, dummy);
       continue;
-    translatedComment += "@see ";
-    string linkObject = convertLink(it->data);
-    if (!linkObject.size())
-      linkObject = it->data;
-    translatedComment += linkObject;
+    }
+
+    // restore entities which may be used in C++ type declaration
+    if (it->typeOfEntity == "&amp") {
+        methodRef += '&';
+    } else if (it->typeOfEntity == "&lt") {
+        methodRef += '<';
+    } else if (it->typeOfEntity == "&gt") {
+        methodRef += '>';
+    } else {
+        methodRef += it->data;
+    }
   }
+
+  // replace :: with #, but only if it appears before left brace
+  size_t lbrace = methodRef.find('(');
+  size_t dblColon = methodRef.find("::");
+  if (dblColon < lbrace) {
+      methodRef = methodRef.substr(0, dblColon) + '#' + methodRef.substr(dblColon + 2);
+  }
+
+  translatedComment += "@see ";
+  string linkObject = convertLink(methodRef);
+  if (!linkObject.size()) {
+    linkObject = methodRef;
+  }
+  translatedComment += linkObject;
 }
 
 

From 289693887961909ca69b890246b0ad9c0259f602 Mon Sep 17 00:00:00 2001
From: Marko Klopcic <markok3.14@gmail.com>
Date: Tue, 29 Jan 2013 08:13:03 +0100
Subject: [PATCH 170/314] only whitespace cnhanges and code comment update

---
 Examples/test-suite/doxygen_misc_constructs.h |   2 +-
 Examples/test-suite/java/commentParser.java   |  15 +-
 .../java/doxygen_misc_constructs_runme.java   | 147 +++++++++---------
 .../src/JavaDocConverter.cpp                  |   1 -
 4 files changed, 86 insertions(+), 79 deletions(-)

diff --git a/Examples/test-suite/doxygen_misc_constructs.h b/Examples/test-suite/doxygen_misc_constructs.h
index dd345ca3a..d25b5af15 100644
--- a/Examples/test-suite/doxygen_misc_constructs.h
+++ b/Examples/test-suite/doxygen_misc_constructs.h
@@ -43,7 +43,7 @@ void backslashA()
  * Standalone @ and '@' get to output.
  * Commands "in quoted \b strings are treated as plain text".
  * Commands not recognized by Doxygen \blah @blah are ignored.
- * Backslashes in DOS paths d:\xyz\qwe\myfile and words 
+ * Backslashes in DOS paths d:\xyz\qwe\myfile and words
  * following them do not appear on output, we must quote them with
  * double quotes: "d:\xyz\qwe\myfile", "@something". Single quotes do not help:
  * 'd:\xyz\qwe\myfile'. Escaping works: d:\\xyz\\qwe\\myfile. Unix
diff --git a/Examples/test-suite/java/commentParser.java b/Examples/test-suite/java/commentParser.java
index cc40c4ac8..390bda8a8 100644
--- a/Examples/test-suite/java/commentParser.java
+++ b/Examples/test-suite/java/commentParser.java
@@ -54,13 +54,24 @@ public class commentParser {
             String wantedStr = wantedComments.get(e.getKey());
             // this may be weird, but I don't know any more effective solution
             actualStr = actualStr.replace(" ", "");
+            actualStr = actualStr.replaceAll("\t", "");
             actualStr = actualStr.replace("\n", "");
-            actualStr = actualStr.replace("\t", "");
             if (wantedStr != null) {
                 wantedStr = wantedStr.replace(" ", "");
-                wantedStr = wantedStr.replace("\n", "");
                 wantedStr = wantedStr.replace("\t", "");
+                wantedStr = wantedStr.replace("\n", "");
             }
+            /* The following lines replace multiple whitespaces with a single one.
+               Although this would be more exact testing, it would also require
+               more work on test maintenance.
+            actualStr = actualStr.replace('\t', ' ');
+            actualStr = actualStr.replaceAll(" +", " ");
+            // actualStr = actualStr.replace("\n", "");
+            if (wantedStr != null) {
+                wantedStr = wantedStr.replace('\t', ' ');
+                wantedStr = wantedStr.replaceAll(" +", " ");
+                // wantedStr = wantedStr.replace("\n", "");
+                } */
 
             if (!actualStr.equals(wantedStr)) {
                 System.out.println("\n\n////////////////////////////////////////////////////////////////////////");
diff --git a/Examples/test-suite/java/doxygen_misc_constructs_runme.java b/Examples/test-suite/java/doxygen_misc_constructs_runme.java
index 0879d26db..7f29f9b5f 100644
--- a/Examples/test-suite/java/doxygen_misc_constructs_runme.java
+++ b/Examples/test-suite/java/doxygen_misc_constructs_runme.java
@@ -26,129 +26,126 @@ public class doxygen_misc_constructs_runme {
     HashMap<String, String> wantedComments = new HashMap<String, String>();
     
     wantedComments.put("doxygen_misc_constructs.doxygen_misc_constructs.getConnection()",
-    		" \n" +
-    		" \n" +
-    		" This function returns connection id. \n" +
-    		" \n" +
+    		"\n" +
+    		"\n" +
+    		" This function returns connection id.\n" +
+    		"\n" +
     		"");
     wantedComments.put("doxygen_misc_constructs.doxygen_misc_constructs.getAddress(doxygen_misc_constructs.SWIGTYPE_p_int, int)",
-    		" Returns address of file line. \n" +
-    		" \n" +
-    		" @param fileName name of the file, where the source line is located \n" +
-    		" @param line line number \n" +
-    		" {@link Connection::getId()  }<br> \n" +
+    		" Returns address of file line.\n" +
     		" \n" +
+    		" @param fileName name of the file, where the source line is located\n" +
+    		" @param line line number\n" +
+    		" {@link Connection::getId()  }<br>\n" +
+    		"\n" +
     		"");
     wantedComments.put("doxygen_misc_constructs.doxygen_misc_constructs.getG_zipCode()",
-    		" Tag endlink must be recognized also when it is the last token \n" +
-    		" in the commment. \n" +
+    		" Tag endlink must be recognized also when it is the last token\n" +
+    		" in the commment.\n" +
     		" \n" +
-    		" {@link Connection::getId()  }<br> \n" +
+    		" {@link Connection::getId()  }<br>\n" +
     		" {@link debugIdeTraceProfilerCoverageSample.py Python example.  }\n" +
-    		" \n" +
+    		"\n" +
     		"");
     wantedComments.put("doxygen_misc_constructs.doxygen_misc_constructs.setG_zipCode(int)",
-    		" Tag endlink must be recognized also when it is the last token \n" +
-    		" in the commment. \n" +
-    		" \n" +
-    		" {@link Connection::getId()  }<br> \n" +
+    		" Tag endlink must be recognized also when it is the last token\n" +
+    		" in the commment.\n" +
+    		"\n" +
+    		" {@link Connection::getId()  }<br>\n" +
     		" {@link debugIdeTraceProfilerCoverageSample.py Python example.  }\n" +
-    		" \n" +
+    		"\n" +
     		"");
     wantedComments.put("doxygen_misc_constructs.doxygen_misc_constructs.getG_counter()",
-    		" Tag endlink must be recognized also when followed by nonspace charater. \n" +
-    		" \n" +
-    		" {@link Connection::getId()  }<br> \n" +
-    		" \n" +
+    		" Tag endlink must be recognized also when followed by nonspace charater.\n" +
+    		"\n" +
+    		" {@link Connection::getId()  }<br>\n" +
+    		"\n" +
     		"");
     wantedComments.put("doxygen_misc_constructs.doxygen_misc_constructs.waitTime(int)",
-    		" Determines how long the <code>isystem.connect</code> should wait for running \n" +
-    		" instances to respond. Only one of <code>lfWaitXXX</code> flags from IConnect::ELaunchFlags \n" +
-    		" may be specified. \n" +
-    		" \n" +
+    		" Determines how long the <code>isystem.connect</code> should wait for running\n" +
+    		" instances to respond. Only one of <code>lfWaitXXX</code> flags from IConnect::ELaunchFlags\n" +
+    		" may be specified.\n" +
+    		"\n" +
     		"");
     wantedComments.put("doxygen_misc_constructs.CConnectionConfig",
-    		" This class contains information for connection to winIDEA. Its methods \n" +
-    		" return reference to self, so we can use it like this: \n" +
-    		" <pre> \n" +
-    		" CConnectionConfig config = new CConnectionConfig(); \n" +
-    		" config.discoveryPort(5534).dllPath(\"C:\\\\myWinIDEA\\\\connect.dll\").id(\"main\"); \n" +
-    		" </pre> \n" +
-    		" \n" +
-    		" All parameters are optional. Set only what is required, default values are \n" +
-    		" used for unspecified parameters. \n" +
-    		" <p> \n" +
-    		" \n" +
-    		" {@link advancedWinIDEALaunching.py Python example.  }<br> \n" +
-    		" \n" +
+    		" This class contains information for connection to winIDEA. Its methods\n" +
+    		" return reference to self, so we can use it like this:\n" +
+    		" <pre>\n" +
+    		" CConnectionConfig config = new CConnectionConfig();\n" +
+    		" config.discoveryPort(5534).dllPath(\"C:\\\\myWinIDEA\\\\connect.dll\").id(\"main\");\n" +
+    		" </pre>\n" +
+    		"\n" +
+    		" All parameters are optional. Set only what is required, default values are\n" +
+    		" used for unspecified parameters.\n" +
+    		" <p>\n" +
+    		"\n" +
+    		" {@link advancedWinIDEALaunching.py Python example.  }<br>\n" +
+    		"\n" +
     		"");
     wantedComments.put("doxygen_misc_constructs.doxygen_misc_constructs.getAddress(doxygen_misc_constructs.SWIGTYPE_p_int, int, boolean)",
-    		" Returns address of file line. \n" +
-    		" \n" +
-    		" @param fileName name of the file, where the source line is located \n" +
-    		" @param line line number \n" +
-    		" @param isGetSize if set, for every object location both address and size are returned \n" +
-    		" \n" +
-    		" {@link Connection::getId()  }<br> \n" +
-    		" \n" +
+    		" Returns address of file line.\n" +
+    		"\n" +
+    		" @param fileName name of the file, where the source line is located\n" +
+    		" @param line line number\n" +
+    		" @param isGetSize if set, for every object location both address and size are returned\n" +
+    		"\n" +
+    		" {@link Connection::getId()  }<br>\n" +
+    		"\n" +
     		"");
     wantedComments.put("doxygen_misc_constructs.doxygen_misc_constructs.setG_counter(char)",
-    		" Tag endlink must be recognized also when followed by nonspace charater. \n" +
-    		" \n" +
-    		" {@link Connection::getId()  }<br> \n" +
-    		" \n" +
+    		" Tag endlink must be recognized also when followed by nonspace charater.\n" +
+    		"\n" +
+    		" {@link Connection::getId()  }<br>\n" +
+    		"\n" +
     		"");
 
     wantedComments.put("doxygen_misc_constructs.ClassWithNestedEnum",
     		" Class description.\n" +
-    		" \n");
+    		"\n");
 
     wantedComments.put("doxygen_misc_constructs.ClassWithNestedEnum.ENested",
     		" Enum description.\n" +
-    		" \n");
+    		"\n");
 
     wantedComments.put("doxygen_misc_constructs.ClassWithNestedEnum.ENested.ONE",
-    		" desc of one\n" +
-    		" \n");
+    		" desc of one\n");
 
     wantedComments.put("doxygen_misc_constructs.ClassWithNestedEnum.ENested.TWO",
-    		" desc of two\n" +
-    		" \n");
+    		" desc of two\n");
 
     wantedComments.put("doxygen_misc_constructs.ClassWithNestedEnum.ENested.THREE",
-    		" desc of three\n" +
-    		" \n");
+    		" desc of three\n");
 
     wantedComments.put("doxygen_misc_constructs.doxygen_misc_constructs.isNoSpaceValidA()",
-    		" This comment without space after '*' is valid in Doxygen. \n" +
-    		" \n" +
+    		" This comment without space after '*' is valid in Doxygen.\n" +
+    		"\n" +
     		"");
  
     wantedComments.put("doxygen_misc_constructs.doxygen_misc_constructs.isNoSpaceValidB()",
-    		" .This comment without space after '*' is valid in Doxygen. \n" +
-    		" \n" +
+    		" .This comment without space after '*' is valid in Doxygen.\n" +
+    		"\n" +
     		"");
  
     wantedComments.put("doxygen_misc_constructs.doxygen_misc_constructs.backslashA()",
     		" Backslash following<code>word</code> is a valid doxygen command. Output contains\n" +
-    		" 'followingword' with 'word' in code font. \n" +
-    		" \n" +
+    		" 'followingword' with 'word' in code font.\n" +
+    		"\n" +
     		"");
  
     wantedComments.put("doxygen_misc_constructs.doxygen_misc_constructs.backslashB()",
                        " Doxy command without trailing space is ignored - nothing appears\n" +
-                       " on output. Standalone \\ and '\\' get to output. \n" +
-                       " Standalone @ and '@' get to output. \n" +
-                       " Commands \"in quoted \\b strings are treated as plain text\". \n" +
-                       " Commands not recognized by Doxygen are ignored. \n" +
-                       " Backslashes in DOS paths d: and words \n" +
-                       " following them do not appear on output, we must quote them with \n" +
-                       " double quotes: \"d:\\xyz\\qwe\\myfile\", \"@something\". Single quotes do not help: \n" +
-                       " 'd: '. Escaping works: d:\\xyz\\qwe\\myfile. Unix \n" +
-                       " paths of course have no such problems: /xyz/qwe/myfile \n" +
+                       " on output. Standalone \\ and '\\' get to output.\n" +
+                       " Standalone @ and '@' get to output.\n" +
+                       " Commands \"in quoted \\b strings are treated as plain text\".\n" +
+                       " Commands not recognized by Doxygen are ignored.\n" +
+                       " Backslashes in DOS paths d:and words\n" +
+                       " following them do not appear on output, we must quote them with\n" +
+                       " double quotes: \"d:\\xyz\\qwe\\myfile\", \"@something\". Single quotes do not help:\n" +
+                       " 'd:'. Escaping works: d:\\xyz\\qwe\\myfile. Unix\n" +
+                       " paths of course have no such problems: /xyz/qwe/myfile\n" +
                        " Commands for escaped symbols:\n" +
                        " $ @ \\ &amp; ~ &lt; &gt; # % &quot; . :: @text ::text" +
-    		" \n");
+    		"\n");
 
    wantedComments.put("doxygen_misc_constructs.doxygen_misc_constructs.backslashC()",
     		" Backslash e at end of <i>line</i> froze SWIG\n" +
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.cpp b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
index db024f302..db5ba7e34 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
@@ -56,7 +56,6 @@ void JavaDocConverter::fillStaticTables() {
    *
    * entities must be translated - remain in Java, something meaningfull in Python (&lt, ...)
    *
-   * - crash if link in @see tag is split to two lines
    * - whitespaces in tests
    * - Python
    * - add comments also to auto-generated methods lilke equals(), delete() in Java,

From 0d66568ba38d7c3a8e4724ca0c2a64492179de2a Mon Sep 17 00:00:00 2001
From: Marko Klopcic <markok3.14@gmail.com>
Date: Tue, 29 Jan 2013 08:39:35 +0100
Subject: [PATCH 171/314] minor refactoring of CommentParser.java

---
 ...{commentParser.java => CommentParser.java} | 41 ++++++++++---------
 .../java/doxygen_basic_notranslate_runme.java |  5 ++-
 .../java/doxygen_basic_translate_runme.java   |  5 ++-
 .../java/doxygen_misc_constructs_runme.java   |  5 ++-
 .../doxygen_parsing_enums_proper_runme.java   |  5 ++-
 .../doxygen_parsing_enums_simple_runme.java   |  5 ++-
 .../doxygen_parsing_enums_typesafe_runme.java |  5 ++-
 ...oxygen_parsing_enums_typeunsafe_runme.java |  5 ++-
 .../java/doxygen_parsing_runme.java           |  5 ++-
 .../doxygen_translate_all_tags_runme.java     |  5 ++-
 .../java/doxygen_translate_links_runme.java   |  5 ++-
 .../java/doxygen_translate_runme.java         |  8 ++--
 12 files changed, 57 insertions(+), 42 deletions(-)
 rename Examples/test-suite/java/{commentParser.java => CommentParser.java} (82%)

diff --git a/Examples/test-suite/java/commentParser.java b/Examples/test-suite/java/CommentParser.java
similarity index 82%
rename from Examples/test-suite/java/commentParser.java
rename to Examples/test-suite/java/CommentParser.java
index 390bda8a8..1d61f16b1 100644
--- a/Examples/test-suite/java/commentParser.java
+++ b/Examples/test-suite/java/CommentParser.java
@@ -11,8 +11,8 @@ import java.io.FileOutputStream;
 import java.io.IOException;
 
 
-public class commentParser {
-    static HashMap<String, String> parsedComments = new HashMap<String, String>();
+public class CommentParser {
+    private static Map<String, String> m_parsedComments = new HashMap<String, String>();
 
     public static boolean start(RootDoc root) {
 
@@ -24,31 +24,31 @@ public class commentParser {
         for (ClassDoc classDoc : root.classes()) {
 
             if (classDoc.getRawCommentText().length() > 0)
-                parsedComments.put(classDoc.qualifiedName(), classDoc.getRawCommentText());
+                m_parsedComments.put(classDoc.qualifiedName(), classDoc.getRawCommentText());
 
             for (FieldDoc f : classDoc.enumConstants()) {
                 if (f.getRawCommentText().length() > 0)
-                    parsedComments.put(f.qualifiedName(), f.getRawCommentText());
+                    m_parsedComments.put(f.qualifiedName(), f.getRawCommentText());
             }
             for (FieldDoc f : classDoc.fields()) {
                 if (f.getRawCommentText().length() > 0)
-                    parsedComments.put(f.qualifiedName(), f.getRawCommentText());
+                    m_parsedComments.put(f.qualifiedName(), f.getRawCommentText());
             }
             for (MethodDoc m : classDoc.methods()) {
                 if (m.getRawCommentText().length() > 0)
-                    parsedComments.put(m.toString(), m.getRawCommentText());
+                    m_parsedComments.put(m.toString(), m.getRawCommentText());
             }
         }
         return true;
     }
 
     
-    public static int check(HashMap<String, String> wantedComments) {
+    public int check(Map<String, String> wantedComments) {
         int errorCount=0;
-        Iterator< Entry<String, String> > it = parsedComments.entrySet().iterator();
+        Iterator<Entry<String, String>> it = m_parsedComments.entrySet().iterator();
 
-        while (it.hasNext())
-        {
+        while (it.hasNext()) {
+            
             Entry<String, String> e = (Entry<String, String>) it.next();
             String actualStr = e.getValue();
             String wantedStr = wantedComments.get(e.getKey());
@@ -102,14 +102,14 @@ public class commentParser {
             }
         }
 
-        if (parsedComments.size() != wantedComments.size()) {
+        if (m_parsedComments.size() != wantedComments.size()) {
             System.out.println("Mismatch in the number of comments!\n    Expected: " +
                                wantedComments.size() + "\n    Parsed: " +
-                               parsedComments.size());
+                               m_parsedComments.size());
             System.out.println("Expected keys: ");
             printKeys(wantedComments);
             System.out.println("Parsed keys: ");
-            printKeys(parsedComments);
+            printKeys(m_parsedComments);
 
             errorCount++;
         }
@@ -118,7 +118,8 @@ public class commentParser {
     }
 
     
-    private static void printKeys(Map map) {
+    private void printKeys(Map<String, String> map) {
+        
         Set<String> keys = map.keySet();
         for (String key : keys) {
             System.out.println("    " + key);
@@ -127,9 +128,11 @@ public class commentParser {
     
     
     public static void printCommentListForJavaSource() {
-        Iterator< Entry<String, String> > it = parsedComments.entrySet().iterator();
-        while (it.hasNext())
-        {
+
+        Iterator< Entry<String, String> > it = m_parsedComments.entrySet().iterator();
+        
+        while (it.hasNext())  {
+            
             Entry<String, String> e = (Entry<String, String>) it.next();
             String commentText = e.getValue();
             commentText = commentText.replace("\\", "\\\\");
@@ -143,12 +146,12 @@ public class commentParser {
     public static void main(String argv[]) {
 		
         if (argv.length<1) {
-            System.out.format("Usage:\n\tcommentParsing <package to parse>\n");
+            System.out.format("Usage:\n\tCommentParser <package to parse>\n");
             System.exit(1);
         }
 		
         com.sun.tools.javadoc.Main.execute("The comment parser program",
-                                           "commentParser", new String[]{"-quiet", argv[0]});
+                                           "CommentParser", new String[]{"-quiet", argv[0]});
 		
         // if we are run as standalone app, print the list of found comments as it would appear in java source
 		
diff --git a/Examples/test-suite/java/doxygen_basic_notranslate_runme.java b/Examples/test-suite/java/doxygen_basic_notranslate_runme.java
index 711cfbb88..d1c433545 100644
--- a/Examples/test-suite/java/doxygen_basic_notranslate_runme.java
+++ b/Examples/test-suite/java/doxygen_basic_notranslate_runme.java
@@ -19,9 +19,10 @@ public class doxygen_basic_notranslate_runme {
       Here we are using internal javadoc tool, it accepts the name of the class as paramterer,
       and calls the start() method of that class with parsed information.
     */
-	commentParser parser = new commentParser();
+    CommentParser parser = new CommentParser();
     com.sun.tools.javadoc.Main.execute("doxygen_basic_notranslate runtime test",
-	"commentParser", new String[]{"-quiet", "doxygen_basic_notranslate"});
+                                       "CommentParser",
+                                       new String[]{"-quiet", "doxygen_basic_notranslate"});
 
     HashMap<String, String> wantedComments = new HashMap<String, String>();
     wantedComments.put("doxygen_basic_notranslate.doxygen_basic_notranslate.function3(int)",
diff --git a/Examples/test-suite/java/doxygen_basic_translate_runme.java b/Examples/test-suite/java/doxygen_basic_translate_runme.java
index 946988c57..395e61139 100644
--- a/Examples/test-suite/java/doxygen_basic_translate_runme.java
+++ b/Examples/test-suite/java/doxygen_basic_translate_runme.java
@@ -19,9 +19,10 @@ public class doxygen_basic_translate_runme {
       Here we are using internal javadoc tool, it accepts the name of the class as paramterer,
       and calls the start() method of that class with parsed information.
     */
-	commentParser parser = new commentParser();
+    CommentParser parser = new CommentParser();
     com.sun.tools.javadoc.Main.execute("doxygen_basic_translate runtime test",
-	"commentParser", new String[]{"-quiet", "doxygen_basic_translate"});
+                                       "CommentParser",
+                                       new String[]{"-quiet", "doxygen_basic_translate"});
 
     HashMap<String, String> wantedComments = new HashMap<String, String>();
     
diff --git a/Examples/test-suite/java/doxygen_misc_constructs_runme.java b/Examples/test-suite/java/doxygen_misc_constructs_runme.java
index 7f29f9b5f..ae9cc442f 100644
--- a/Examples/test-suite/java/doxygen_misc_constructs_runme.java
+++ b/Examples/test-suite/java/doxygen_misc_constructs_runme.java
@@ -19,9 +19,10 @@ public class doxygen_misc_constructs_runme {
       Here we are using internal javadoc tool, it accepts the name of the class as paramterer,
       and calls the start() method of that class with parsed information.
     */
-	commentParser parser = new commentParser();
+    CommentParser parser = new CommentParser();
     com.sun.tools.javadoc.Main.execute("doxygen_misc_constructs runtime test",
-	"commentParser", new String[]{"-quiet", "doxygen_misc_constructs"});
+                                       "CommentParser",
+                                       new String[]{"-quiet", "doxygen_misc_constructs"});
 
     HashMap<String, String> wantedComments = new HashMap<String, String>();
     
diff --git a/Examples/test-suite/java/doxygen_parsing_enums_proper_runme.java b/Examples/test-suite/java/doxygen_parsing_enums_proper_runme.java
index b96ee66ea..a8527e364 100644
--- a/Examples/test-suite/java/doxygen_parsing_enums_proper_runme.java
+++ b/Examples/test-suite/java/doxygen_parsing_enums_proper_runme.java
@@ -19,9 +19,10 @@ public class doxygen_parsing_enums_proper_runme {
       Here we are using internal javadoc tool, it accepts the name of the class as paramterer,
       and calls the start() method of that class with parsed information.
     */
-	commentParser parser = new commentParser();
+    CommentParser parser = new CommentParser();
     com.sun.tools.javadoc.Main.execute("doxygen_parsing_enums_proper runtime test",
-	"commentParser", new String[]{"-quiet", "doxygen_parsing_enums_proper"});
+                                       "CommentParser",
+                                       new String[]{"-quiet", "doxygen_parsing_enums_proper"});
 
     HashMap<String, String> wantedComments = new HashMap<String, String>();
     
diff --git a/Examples/test-suite/java/doxygen_parsing_enums_simple_runme.java b/Examples/test-suite/java/doxygen_parsing_enums_simple_runme.java
index cd97c9a4f..f68fff151 100644
--- a/Examples/test-suite/java/doxygen_parsing_enums_simple_runme.java
+++ b/Examples/test-suite/java/doxygen_parsing_enums_simple_runme.java
@@ -19,9 +19,10 @@ public class doxygen_parsing_enums_simple_runme {
       Here we are using internal javadoc tool, it accepts the name of the class as paramterer,
       and calls the start() method of that class with parsed information.
     */
-	commentParser parser = new commentParser();
+    CommentParser parser = new CommentParser();
     com.sun.tools.javadoc.Main.execute("doxygen_parsing_enums_simple runtime test",
-	"commentParser", new String[]{"-quiet", "doxygen_parsing_enums_simple"});
+                                       "CommentParser",
+                                       new String[]{"-quiet", "doxygen_parsing_enums_simple"});
 
     HashMap<String, String> wantedComments = new HashMap<String, String>();
     
diff --git a/Examples/test-suite/java/doxygen_parsing_enums_typesafe_runme.java b/Examples/test-suite/java/doxygen_parsing_enums_typesafe_runme.java
index 85ac15fe8..7c7f05ccc 100644
--- a/Examples/test-suite/java/doxygen_parsing_enums_typesafe_runme.java
+++ b/Examples/test-suite/java/doxygen_parsing_enums_typesafe_runme.java
@@ -19,9 +19,10 @@ public class doxygen_parsing_enums_typesafe_runme {
       Here we are using internal javadoc tool, it accepts the name of the class as paramterer,
       and calls the start() method of that class with parsed information.
     */
-	commentParser parser = new commentParser();
+    CommentParser parser = new CommentParser();
     com.sun.tools.javadoc.Main.execute("doxygen_parsing_enums_typesafe runtime test",
-	"commentParser", new String[]{"-quiet", "doxygen_parsing_enums_typesafe"});
+                                       "CommentParser",
+                                       new String[]{"-quiet", "doxygen_parsing_enums_typesafe"});
 
     HashMap<String, String> wantedComments = new HashMap<String, String>();
     
diff --git a/Examples/test-suite/java/doxygen_parsing_enums_typeunsafe_runme.java b/Examples/test-suite/java/doxygen_parsing_enums_typeunsafe_runme.java
index 6f453060d..8c7dfeda0 100644
--- a/Examples/test-suite/java/doxygen_parsing_enums_typeunsafe_runme.java
+++ b/Examples/test-suite/java/doxygen_parsing_enums_typeunsafe_runme.java
@@ -19,9 +19,10 @@ public class doxygen_parsing_enums_typeunsafe_runme {
       Here we are using internal javadoc tool, it accepts the name of the class as paramterer,
       and calls the start() method of that class with parsed information.
     */
-	commentParser parser = new commentParser();
+    CommentParser parser = new CommentParser();
     com.sun.tools.javadoc.Main.execute("doxygen_parsing_enums_typeunsafe runtime test",
-	"commentParser", new String[]{"-quiet", "doxygen_parsing_enums_typeunsafe"});
+                                       "CommentParser",
+                                       new String[]{"-quiet", "doxygen_parsing_enums_typeunsafe"});
 
     HashMap<String, String> wantedComments = new HashMap<String, String>();
     
diff --git a/Examples/test-suite/java/doxygen_parsing_runme.java b/Examples/test-suite/java/doxygen_parsing_runme.java
index 322a4e42c..ec9390849 100644
--- a/Examples/test-suite/java/doxygen_parsing_runme.java
+++ b/Examples/test-suite/java/doxygen_parsing_runme.java
@@ -19,9 +19,10 @@ public class doxygen_parsing_runme {
       Here we are using internal javadoc tool, it accepts the name of the class as paramterer,
       and calls the start() method of that class with parsed information.
     */
-	commentParser parser = new commentParser();
+    CommentParser parser = new CommentParser();
     com.sun.tools.javadoc.Main.execute("doxygen_parsing runtime test",
-	"commentParser", new String[]{"-quiet", "doxygen_parsing"});
+                                       "CommentParser",
+                                       new String[]{"-quiet", "doxygen_parsing"});
 
     HashMap<String, String> wantedComments = new HashMap<String, String>();
     
diff --git a/Examples/test-suite/java/doxygen_translate_all_tags_runme.java b/Examples/test-suite/java/doxygen_translate_all_tags_runme.java
index 37d60ff81..69a1169ca 100644
--- a/Examples/test-suite/java/doxygen_translate_all_tags_runme.java
+++ b/Examples/test-suite/java/doxygen_translate_all_tags_runme.java
@@ -19,9 +19,10 @@ public class doxygen_translate_all_tags_runme {
       Here we are using internal javadoc tool, it accepts the name of the class as paramterer,
       and calls the start() method of that class with parsed information.
     */
-	commentParser parser = new commentParser();
+    CommentParser parser = new CommentParser();
     com.sun.tools.javadoc.Main.execute("doxygen_translate_all_tags runtime test",
-	"commentParser", new String[]{"-quiet", "doxygen_translate_all_tags"});
+                                       "CommentParser",
+                                       new String[]{"-quiet", "doxygen_translate_all_tags"});
 
     HashMap<String, String> wantedComments = new HashMap<String, String>();
     
diff --git a/Examples/test-suite/java/doxygen_translate_links_runme.java b/Examples/test-suite/java/doxygen_translate_links_runme.java
index 080063430..6d74e16fe 100644
--- a/Examples/test-suite/java/doxygen_translate_links_runme.java
+++ b/Examples/test-suite/java/doxygen_translate_links_runme.java
@@ -19,9 +19,10 @@ public class doxygen_translate_links_runme {
       Here we are using internal javadoc tool, it accepts the name of the class as paramterer,
       and calls the start() method of that class with parsed information.
     */
-	commentParser parser = new commentParser();
+    CommentParser parser = new CommentParser();
     com.sun.tools.javadoc.Main.execute("doxygen_translate_links runtime test",
-	"commentParser", new String[]{"-quiet", "doxygen_translate_links"});
+                                       "CommentParser",
+                                       new String[]{"-quiet", "doxygen_translate_links"});
 
     HashMap<String, String> wantedComments = new HashMap<String, String>();
     
diff --git a/Examples/test-suite/java/doxygen_translate_runme.java b/Examples/test-suite/java/doxygen_translate_runme.java
index 10b5af28d..b93df89bf 100644
--- a/Examples/test-suite/java/doxygen_translate_runme.java
+++ b/Examples/test-suite/java/doxygen_translate_runme.java
@@ -2,6 +2,7 @@
 import doxygen_translate.*;
 import com.sun.javadoc.*;
 import java.util.HashMap;
+import java.util.Map;
 
 public class doxygen_translate_runme {
   static {
@@ -19,11 +20,12 @@ public class doxygen_translate_runme {
       Here we are using internal javadoc tool, it accepts the name of the class as paramterer,
       and calls the start() method of that class with parsed information.
     */
-	commentParser parser = new commentParser();
+    CommentParser parser = new CommentParser();
     com.sun.tools.javadoc.Main.execute("doxygen_translate runtime test",
-	"commentParser", new String[]{"-quiet", "doxygen_translate"});
+                                       "CommentParser",
+                                       new String[]{"-quiet", "doxygen_translate"});
 
-    HashMap<String, String> wantedComments = new HashMap<String, String>();
+    Map<String, String> wantedComments = new HashMap<String, String>();
     
     wantedComments.put("doxygen_translate.doxygen_translate.function(int, float)",
     		" <i>Hello </i>\n" +

From 18837977428c58cc54961ee2344ca60484cd9ad3 Mon Sep 17 00:00:00 2001
From: Marko Klopcic <markok3.14@gmail.com>
Date: Tue, 29 Jan 2013 22:58:10 +0100
Subject: [PATCH 172/314] refactored comment tokenizer

---
 .../DoxygenTranslator/src/DoxygenParser.cpp   | 456 ++++++++----------
 Source/DoxygenTranslator/src/DoxygenParser.h  |   6 +
 .../src/JavaDocConverter.cpp                  |   4 +-
 3 files changed, 221 insertions(+), 245 deletions(-)

diff --git a/Source/DoxygenTranslator/src/DoxygenParser.cpp b/Source/DoxygenTranslator/src/DoxygenParser.cpp
index 59b47e46f..846da261b 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenParser.cpp
@@ -960,98 +960,10 @@ DoxygenEntityList DoxygenParser::createTree(const std::string &doxygenBlob,
 }
 
 
-/**
- * This is one of the most important methods - it breaks the original
- * doxygen comment into tokens - one token per word.
- * See replacement, which also handles html comments below.
-DoxygenParser::TokenList DoxygenParser::tokenizeDoxygenComment(const std::string &doxygenComment,
-                                                                      const std::string &fileName,
-                                                                      int fileLine) {
-  TokenList tokList;
-  m_fileLineNo = fileLine;
-  m_fileName = fileName;
-
-  bool isPlainString = false;
-  string::size_type pos, lastPos = 0;
-  char prevChar = doxygenComment[lastPos];
-  string currentWord;
-  while (true) {
-    isPlainString = false;
-    pos = doxygenComment.find_first_of("\\@\t\n ", lastPos);
-    if (pos == string::npos) {
-      pos = doxygenComment.size();
-    // } else {
-      // preserve whitespaces
-    //  while (pos != string::npos  &&  (doxygenComment[pos] == ' ' ||  doxygenComment[pos] == '\t')) {
-    //    pos++;
-    //  }
-    //  if (pos == string::npos) {
-    //    pos = doxygenComment.size();
-    //  }
-    }
-
-    currentWord = doxygenComment.substr(lastPos, pos-lastPos);
-
-    if (prevChar == '\n') {
-
-      tokList.push_back(Token(END_LINE, "\n"));
-
-    } else if (prevChar == '\\' || prevChar == '@') {
-      // it's a doxygen command
-      // hack to get commands like \\ or \@ or @\ or @@
-      if (doxygenComment[pos] == '@' || doxygenComment[pos] == '\\') {
-        currentWord += doxygenComment[pos];
-        pos++;
-      }
-      // also strip the command till the first non-alpha char
-      for (size_t i = 2; i < currentWord.size(); i++) {
-        if (!isalpha(currentWord[i])) {
-          currentWord = currentWord.substr(0, i);
-          // set current parsing pos back, to parse the rest of the command
-          pos = lastPos + i - 1;
-          break;
-        }
-      }
-
-      if (findCommand(currentWord)) {
-          tokList.push_back(Token(COMMAND, currentWord));
-      } else {
-          // unknown commands are not translated - treated as literal string
-          tokList.push_back(Token(PLAINSTRING, currentWord));
-      }
-
-    } else if (currentWord.size() && (currentWord[0] == '!' || currentWord[0] == '*' || currentWord[0] == '/')) {
-
-      // check if it's one of the '!!!', '***', '///' of any length
-      char c = currentWord[0];
-      isPlainString = false;
-      for (size_t i = 0; i < currentWord.size(); i++)
-        if (currentWord[i] != c) {
-          isPlainString = true;
-          break;
-        }
-    } else {
-      isPlainString = true;
-    }
-
-    if (isPlainString && currentWord.size()) {
-      tokList.push_back(Token(PLAINSTRING, currentWord));
-    }
-
-    prevChar = doxygenComment[pos];
-    lastPos = pos + 1;
-    if (lastPos >= doxygenComment.size())
-      break;
-  }
-
-  m_tokenListIt = tokList.begin();
-
-  return tokList;
-}
+/*
+ * Splits 'text' on 'separator' chars. Separator chars are not part of the
+ * strings.
  */
-
-
-// Splits 'text' on 'separator' chars. Separator chars are not part of the strings.
 DoxygenParser::StringVector DoxygenParser::split(const std::string &text, char separator)
 {
     StringVector lines;
@@ -1067,12 +979,21 @@ DoxygenParser::StringVector DoxygenParser::split(const std::string &text, char s
 }
 
 
+/*
+ * Returns true, if 'c' is one of doxygen comment block start
+ * characters: *, /, or !
+ */
 bool DoxygenParser::isStartOfDoxyCommentChar(char c)
 {
     return (strchr("*/!", c) != NULL);
 }
 
 
+/*
+ * Adds token with Doxygen command to token list, but only if command is one of
+ * Doxygen commands. In that case true is returned. If the command is not
+ * recognized as a doxygen command, it is ignored and false is returned.
+ */
 bool DoxygenParser::addDoxyCommand(DoxygenParser::TokenList &tokList,
                                         const std::string &cmd) {
     if (findCommand(cmd)) {
@@ -1090,11 +1011,16 @@ bool DoxygenParser::addDoxyCommand(DoxygenParser::TokenList &tokList,
 }
 
 
+/*
+ * This method copies comment text to output as it is - no processing is
+ * done, Doxygen commands are ignored. It is used for commands \verbatim,
+ * \htmlonly, \f$, \f[, and \f{.
+ */
 size_t DoxygenParser::processVerbatimText(size_t pos, const std::string &line)
 {
-    if (line[pos] == '\\'  ||  line[pos] == '@') {
+    if (line[pos] == '\\'  ||  line[pos] == '@') { // check for end commands
         pos++;
-        // characters '$[]{}' are used in commands \f$, \f[, ...
+        // characters '$[]{}' are used in commands \f$, \f[, and \f{
         size_t endOfWordPos = line.find_first_not_of("abcdefghijklmnopqrstuvwxyz$[]{}", pos);
         string cmd = line.substr(pos, endOfWordPos - pos);
 
@@ -1120,155 +1046,194 @@ size_t DoxygenParser::processVerbatimText(size_t pos, const std::string &line)
 }
 
 
-size_t DoxygenParser::processNormalComment(size_t pos, const std::string &line)
+/*
+ * Processes doxy commands for escaped characters: \$ \@ \\ \& \~ \< \> \# \% \" \. \::
+ * Handling this separately supports documentation text like \@someText.
+ */
+bool DoxygenParser::processEscapedChars(size_t &pos, const std::string &line)
 {
-    switch (line[pos]) {
-    case '\\':
-    case '@': {
-      // process doxy commands for escaped characters - handling this separately
-      // supports documentation text like \@someText
-      if ((pos + 1) < line.size()) {
+  if ((pos + 1) < line.size()) {
 
-        // \ and @ with trailing whitespace or quoted get to output as plain string
-        string whitespaces = " '\t\n";
-        if (whitespaces.find(line[pos + 1]) != string::npos) {
-          m_tokenList.push_back(Token(PLAINSTRING, line.substr(pos, 1)));
-          pos++;
-          break;
-        }
-
-        // these chars can be escaped for doxygen
-        string escapedChars = "$@\\&~<>#%\".";
-        if (escapedChars.find(line[pos + 1]) != string::npos) {
-          addDoxyCommand(m_tokenList, line.substr(pos + 1, 1));
-          pos += 2;
-          break;
-        } else if ((pos + 2) < line.size()  &&
-                    line[pos + 1] == ':'  &&  line[pos + 2] == ':') {
-          // add command \:: - handling this separately supports documentation
-          // text like \::someText
-          addDoxyCommand(m_tokenList, line.substr(pos + 1, 2));
-          pos += 3;
-          break;
-        }
-      }
-      // handle word commands and \f[, \f$, ... commands
+    // \ and @ with trailing whitespace or quoted get to output as plain string
+    string whitespaces = " '\t\n";
+    if (whitespaces.find(line[pos + 1]) != string::npos) {
+      m_tokenList.push_back(Token(PLAINSTRING, line.substr(pos, 1)));
       pos++;
-      // characters '$[]{}' are used in commands \f$, \f[, ...
-      size_t endOfWordPos = line.find_first_not_of("abcdefghijklmnopqrstuvwxyz$[]{}", pos);
-      string cmd = line.substr(pos , endOfWordPos - pos);
-      addDoxyCommand(m_tokenList, cmd);
-      if (cmd == CMD_HTML_ONLY  ||  cmd == CMD_VERBATIM  ||
-          cmd == CMD_LATEX_1  ||  cmd == CMD_LATEX_2  ||  cmd == CMD_LATEX_3) {
-          m_isVerbatimText = true;
-      } else {
-          // skip any possible spaces after command, because some commands have parameters,
-          // and spaces between command and parameter must be ignored.
-          if (endOfWordPos != string::npos) {
-              endOfWordPos = line.find_first_not_of(" \t", endOfWordPos);
-          }
-      }
-      pos = endOfWordPos;
-    } break;
-
-    case ' ':  // whitespace
-    case '\t': {
-      // whitespaces are stored as plain strings
-      size_t startOfNextWordPos = line.find_first_not_of(" \t", pos + 1);
-      m_tokenList.push_back(Token(PLAINSTRING,
-                            line.substr(pos, startOfNextWordPos - pos)));
-      pos = startOfNextWordPos;
-    } break;
-
-    case '<': { // process html commands
-      bool isEndHtmlTag = false;
-      pos++;
-      if (line.size() > pos &&  line[pos] == '/') {
-          isEndHtmlTag = true;
-          pos++;
-      }
-
-      size_t endHtmlPos = line.find_first_of("\t >", pos);
-
-      // prepend '<' to distinguish HTML tags from doxygen commands
-      string cmd = line.substr(pos, endHtmlPos - pos);
-      pos = endHtmlPos;
-
-      if (addDoxyCommand(m_tokenList, '<' + cmd)) {
-          // it is a valid HTML command
-          if (line[pos] != '>') { // it should be HTML tag with args,
-                                   // for example <A ...>, <IMG ...>, ...
-              if (isEndHtmlTag) {
-                  m_tokenListIt = m_tokenList.end();
-                  printListError(WARN_DOXYGEN_COMMAND_ERROR, "Illegal end HTML tag without '>' found! Tag: " + cmd);
-              }
-              endHtmlPos = line.find(">", pos);
-              if (endHtmlPos == string::npos) {
-                  m_tokenListIt = m_tokenList.end();
-                  printListError(WARN_DOXYGEN_COMMAND_ERROR, "HTML tag without '>' found! Tag: " + cmd);
-              }
-              // add args of HTML command, like link URL, image URL, ...
-              m_tokenList.push_back(Token(PLAINSTRING,
-                                    line.substr(pos, endHtmlPos - pos)));
-              pos = endHtmlPos;
-          } else {
-              if (isEndHtmlTag) {
-                // it is a simple tag, so push empty string
-                m_tokenList.push_back(Token(PLAINSTRING, END_HTML_TAG_MARK));
-              } else {
-                // it is a simple tag, so push empty string
-                m_tokenList.push_back(Token(PLAINSTRING, ""));
-              }
-          }
-          pos++; // skip '>'
-      } else {
-        // the command is not HTML supported by Doxygen, < and > will be
-        // replaced by HTML entities &lt; and &gt; respectively,
-        // but only if 'htmlOnly' flag == false. The flag is set/reset by \htmlonly \verbatim,
-        // \endhtmlonly \endverbatim Doxygen commands.
-        addDoxyCommand(m_tokenList, "&lt");
-        m_tokenList.push_back(Token(PLAINSTRING, cmd));
-      }
-    } break;
-    case '>': // this char is detected here only when it is not part of HTML tag
-        addDoxyCommand(m_tokenList, "&gt");
-        pos++;
-        break;
-    case '&': { // process HTML entities
-        size_t endOfWordPos = line.find_first_not_of("abcdefghijklmnopqrstuvwxyz", pos + 1);
-        if (endOfWordPos != string::npos) {
-            if (line[endOfWordPos] == ';') {
-                // if entity is not recognized by Doxygen (not in the list of
-                // commands) nothing is added (here and in Doxygen).
-                addDoxyCommand(m_tokenList, line.substr(pos, endOfWordPos - pos));
-                endOfWordPos++;  // skip ';'
-            } else {
-                // it is not an entity - add entity for ampersand and
-                // the rest of string
-                addDoxyCommand(m_tokenList, "&amp");
-                m_tokenList.push_back(Token(PLAINSTRING,
-                                      line.substr(pos + 1, endOfWordPos - pos - 1)));
-            }
-        }
-        pos = endOfWordPos;
-    }
-    break;
-    case '"':
-        m_isInQuotedString = true;
-        m_tokenList.push_back(Token(PLAINSTRING, "\""));
-        pos++;
-        break;
-    default:
-      m_tokenListIt = m_tokenList.end();
-      printListError(WARN_DOXYGEN_COMMAND_ERROR, "Unknown special character: " + line[pos]);
+      return true;
     }
 
-    return pos;
+    // these chars can be escaped for doxygen
+    string escapedChars = "$@\\&~<>#%\".";
+    if (escapedChars.find(line[pos + 1]) != string::npos) {
+      addDoxyCommand(m_tokenList, line.substr(pos + 1, 1));
+      pos += 2;
+      return true;
+    } else if ((pos + 2) < line.size()  &&
+                line[pos + 1] == ':'  &&  line[pos + 2] == ':') {
+      // add command \:: - handling this separately supports documentation
+      // text like \::someText
+      addDoxyCommand(m_tokenList, line.substr(pos + 1, 2));
+      pos += 3;
+      return true;
+    }
+  }
+  return false;
 }
 
 
-/**
- * This method tokenizes Doxygen comment to words and doxygen commands.
+/*
+ * Processes word doxygen commands, like \arg, \c, \b, \return, ...
+ */
+void DoxygenParser::processWordCommands(size_t &pos, const std::string &line)
+{
+  pos++;
+  // characters '$[]{}' are used in commands \f$, \f[, ...
+  size_t endOfWordPos = line.find_first_not_of("abcdefghijklmnopqrstuvwxyz$[]{}", pos);
+  string cmd = line.substr(pos , endOfWordPos - pos);
+  addDoxyCommand(m_tokenList, cmd);
+  if (cmd == CMD_HTML_ONLY  ||  cmd == CMD_VERBATIM  ||
+    cmd == CMD_LATEX_1  ||  cmd == CMD_LATEX_2  ||  cmd == CMD_LATEX_3) {
+    m_isVerbatimText = true;
+  } else {
+    // skip any possible spaces after command, because some commands have parameters,
+    // and spaces between command and parameter must be ignored.
+    if (endOfWordPos != string::npos) {
+        endOfWordPos = line.find_first_not_of(" \t", endOfWordPos);
+    }
+  }
+  pos = endOfWordPos;
+}
+
+
+void DoxygenParser::processHtmlTags(size_t &pos, const std::string &line)
+{
+  bool isEndHtmlTag = false;
+  pos++;
+  if (line.size() > pos &&  line[pos] == '/') {
+    isEndHtmlTag = true;
+    pos++;
+  }
+
+  size_t endHtmlPos = line.find_first_of("\t >", pos);
+
+  string cmd = line.substr(pos, endHtmlPos - pos);
+  pos = endHtmlPos;
+
+  // prepend '<' to distinguish HTML tags from doxygen commands
+  if (addDoxyCommand(m_tokenList, '<' + cmd)) {
+    // it is a valid HTML command
+    if (line[pos] != '>') { // it should be HTML tag with args,
+                             // for example <A ...>, <IMG ...>, ...
+      if (isEndHtmlTag) {
+        m_tokenListIt = m_tokenList.end();
+        printListError(WARN_DOXYGEN_COMMAND_ERROR,
+                       "Illegal end HTML tag without '>' found! Tag: " + cmd);
+      }
+
+      endHtmlPos = line.find(">", pos);
+      if (endHtmlPos == string::npos) {
+        m_tokenListIt = m_tokenList.end();
+        printListError(WARN_DOXYGEN_COMMAND_ERROR,
+                       "HTML tag without '>' found! Tag: " + cmd);
+      }
+
+      // add args of HTML command, like link URL, image URL, ...
+      m_tokenList.push_back(Token(PLAINSTRING, line.substr(pos, endHtmlPos - pos)));
+      pos = endHtmlPos;
+    } else {
+      if (isEndHtmlTag) {
+        m_tokenList.push_back(Token(PLAINSTRING, END_HTML_TAG_MARK));
+      } else {
+        // it is a simple tag, so push empty string
+        m_tokenList.push_back(Token(PLAINSTRING, ""));
+      }
+    }
+    pos++; // skip '>'
+  } else {
+    // the command is not HTML supported by Doxygen, < and > will be
+    // replaced by HTML entities &lt; and &gt; respectively,
+    addDoxyCommand(m_tokenList, "&lt");
+    m_tokenList.push_back(Token(PLAINSTRING, cmd));
+  }
+}
+
+
+void DoxygenParser::processHtmlEntities(size_t &pos, const std::string &line)
+{
+  size_t endOfWordPos = line.find_first_not_of("abcdefghijklmnopqrstuvwxyz", pos + 1);
+
+  if (endOfWordPos != string::npos) {
+
+    if (line[endOfWordPos] == ';')
+    {
+      // if entity is not recognized by Doxygen (not in the list of
+      // commands) nothing is added (here and in Doxygen).
+      addDoxyCommand(m_tokenList, line.substr(pos, endOfWordPos - pos));
+      endOfWordPos++;  // skip ';'
+
+    } else {
+
+      // it is not an entity - add entity for ampersand and the rest of string
+      addDoxyCommand(m_tokenList, "&amp");
+      m_tokenList.push_back(Token(PLAINSTRING,
+                                   line.substr(pos + 1, endOfWordPos - pos - 1)));
+    }
+  }
+  pos = endOfWordPos;
+}
+
+
+/*
+ * This method processes normal comment, which has to be tokenized.
+ */
+size_t DoxygenParser::processNormalComment(size_t pos, const std::string &line)
+{
+  switch (line[pos]) {
+  case '\\':
+  case '@':
+    if (processEscapedChars(pos, line)) {
+      break;
+    }
+    // handle word commands \arg, \c, \return, ... and \f[, \f$, ... commands
+    processWordCommands(pos, line);
+    break;
+
+  case ' ':  // whitespace
+  case '\t': {
+    // whitespaces are stored as plain strings
+    size_t startOfNextWordPos = line.find_first_not_of(" \t", pos + 1);
+    m_tokenList.push_back(Token(PLAINSTRING,
+        line.substr(pos, startOfNextWordPos - pos)));
+    pos = startOfNextWordPos;
+  } break;
+
+  case '<':
+    processHtmlTags(pos, line);
+    break;
+  case '>': // this char is detected here only when it is not part of HTML tag
+    addDoxyCommand(m_tokenList, "&gt");
+    pos++;
+    break;
+  case '&':
+    processHtmlEntities(pos, line);
+    break;
+  case '"':
+    m_isInQuotedString = true;
+    m_tokenList.push_back(Token(PLAINSTRING, "\""));
+    pos++;
+    break;
+  default:
+    m_tokenListIt = m_tokenList.end();
+    printListError(WARN_DOXYGEN_COMMAND_ERROR, "Unknown special character: " + line[pos]);
+  }
+
+  return pos;
+}
+
+
+/*
+ * This is the main method, which tokenizes Doxygen comment to words and
+ * doxygen commands.
  */
 void DoxygenParser::tokenizeDoxygenComment(const std::string &doxygenComment,
                                                  const std::string &fileName,
@@ -1315,18 +1280,23 @@ void DoxygenParser::tokenizeDoxygenComment(const std::string &doxygenComment,
       }
 
       pos = doxyCmdOrHtmlTagPos;
-      if (pos != string::npos) {
-        if (m_isVerbatimText) {
-            pos = processVerbatimText(pos, line);
+      if (pos != string::npos)
+      {
+        if (m_isVerbatimText)
+        {
+          pos = processVerbatimText(pos, line);
+
         } else if (m_isInQuotedString) {
-            if (line[pos] == '"') {
-                m_isInQuotedString = false;
-            }
-            m_tokenList.push_back(Token(PLAINSTRING,
+
+          if (line[pos] == '"') {
+            m_isInQuotedString = false;
+          }
+          m_tokenList.push_back(Token(PLAINSTRING,
                                      line.substr(pos, 1)));
-            pos++;
+          pos++;
+
         } else {
-            pos = processNormalComment(pos, line);
+          pos = processNormalComment(pos, line);
         }
       }
     }
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.h b/Source/DoxygenTranslator/src/DoxygenParser.h
index adc5c7f26..06c14de04 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.h
+++ b/Source/DoxygenTranslator/src/DoxygenParser.h
@@ -354,6 +354,12 @@ private:
   /** Processes comment when \htmlonly and \verbatim commands are encountered. */
   size_t processVerbatimText(size_t pos, const std::string &line);
 
+  bool processEscapedChars(size_t &pos, const std::string &line);
+  void processWordCommands(size_t &pos, const std::string &line);
+  void processHtmlTags(size_t &pos, const std::string &line);
+  void processHtmlEntities(size_t &pos, const std::string &line);
+
+
   /** Processes comment outside \htmlonly and \verbatim commands. */
   size_t processNormalComment(size_t pos, const std::string &line);
 
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.cpp b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
index db5ba7e34..22a3ccc96 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
@@ -56,10 +56,10 @@ void JavaDocConverter::fillStaticTables() {
    *
    * entities must be translated - remain in Java, something meaningfull in Python (&lt, ...)
    *
-   * - whitespaces in tests
    * - Python
-   * - add comments also to auto-generated methods lilke equals(), delete() in Java,
+   * - add comments also to auto-generated methods like equals(), delete() in Java,
    *   and methods for std::vector(), ...
+   *   Commenting methods of std types is simple - add comment to std_*.i file.
    */
 
 

From 29d1bba70a3ff68928c8aa2f200db6af0e486284 Mon Sep 17 00:00:00 2001
From: Marko Klopcic <markok3.14@gmail.com>
Date: Sat, 2 Feb 2013 23:01:09 +0100
Subject: [PATCH 173/314] improved comment formatting for Python

---
 Examples/test-suite/doxygen_basic_translate.i |   6 +-
 Examples/test-suite/python/commentVerifier.py |  24 ++++
 .../python/doxygen_basic_translate_runme.py   | 124 +++++++++---------
 .../python/doxygen_misc_constructs_runme.py   |  86 ++++++------
 .../python/doxygen_parsing_runme.py           |   0
 .../doxygen_translate_all_tags_runme.py       |   0
 .../python/doxygen_translate_runme.py         |   0
 .../DoxygenTranslator/src/DoxygenParser.cpp   |  10 ++
 .../DoxygenTranslator/src/PyDocConverter.cpp  |  86 ++++++++----
 Source/Modules/python.cxx                     |  17 ++-
 10 files changed, 213 insertions(+), 140 deletions(-)
 create mode 100644 Examples/test-suite/python/commentVerifier.py
 mode change 100644 => 100755 Examples/test-suite/python/doxygen_basic_translate_runme.py
 mode change 100644 => 100755 Examples/test-suite/python/doxygen_misc_constructs_runme.py
 mode change 100644 => 100755 Examples/test-suite/python/doxygen_parsing_runme.py
 mode change 100644 => 100755 Examples/test-suite/python/doxygen_translate_all_tags_runme.py
 mode change 100644 => 100755 Examples/test-suite/python/doxygen_translate_runme.py

diff --git a/Examples/test-suite/doxygen_basic_translate.i b/Examples/test-suite/doxygen_basic_translate.i
index e8c21f452..02f5a1c14 100644
--- a/Examples/test-suite/doxygen_basic_translate.i
+++ b/Examples/test-suite/doxygen_basic_translate.i
@@ -8,9 +8,12 @@
  * \brief
  * Brief description.
  * 
- * The comment text
+ * The comment text.
+ *
  * \author Some author
+ *
  * \return Some number
+ *
  * \sa function2
  */
 int function()
@@ -51,7 +54,6 @@ int function3(int a, int b)
  * \arg it's null
  *
  * \warning This may not work as expected
- *
  * \code
  * int main() { while(true); }
  * \endcode
diff --git a/Examples/test-suite/python/commentVerifier.py b/Examples/test-suite/python/commentVerifier.py
new file mode 100644
index 000000000..8a73b1950
--- /dev/null
+++ b/Examples/test-suite/python/commentVerifier.py
@@ -0,0 +1,24 @@
+
+def check(got, expected):
+  #if got is Null
+  #  raise RuntimeError('Expected comment string\n')
+  #gotStr = string.replace(got, ' ', '')
+  #gotStr = string.replace(gotStr, '\n', '')
+  # gotStr = string.replace(gotStr, '\t', '')
+  #expectedStr = string.replace(expected, ' ', '')
+  #expectedStr = string.replace(expectedStr, '\n', '')
+  #expectedStr = string.replace(expectedStr, '\t', '')
+  if not got == expected:
+    print "\n\n////////////////////////////////////////////////////////////////////////"
+    expectedFileName = "expected.txt"
+    gotFileName = "got.txt"
+    print "Output is also saved to files '" + expectedFileName + \
+                                   "' and '" + gotFileName + "'";
+
+    expectedFile = open(expectedFileName, "w")
+    expectedFile.write(expected)
+    expectedFile.close()
+    gotFile = open(gotFileName, "w")
+    gotFile.write(got)
+    gotFile.close()    
+    raise RuntimeError("Expected: [" + str(expected) + "]\n" + "Got     : [" + str(got) + "]\n")
diff --git a/Examples/test-suite/python/doxygen_basic_translate_runme.py b/Examples/test-suite/python/doxygen_basic_translate_runme.py
old mode 100644
new mode 100755
index 4c1376f44..36ebea5d0
--- a/Examples/test-suite/python/doxygen_basic_translate_runme.py
+++ b/Examples/test-suite/python/doxygen_basic_translate_runme.py
@@ -3,71 +3,77 @@
 import doxygen_basic_translate
 import string
 import sys
+import commentVerifier
 
-def check(got, expected):
-  #if got is Null
-  #  raise RuntimeError('Expected comment string\n')
-  gotStr = string.replace(got, ' ', '')
-  gotStr = string.replace(gotStr, '\n', '')
-  gotStr = string.replace(gotStr, '\t', '')
-  expectedStr = string.replace(expected, ' ', '')
-  expectedStr = string.replace(expectedStr, '\n', '')
-  expectedStr = string.replace(expectedStr, '\t', '')
-  if not gotStr == expectedStr:
-    raise RuntimeError("Expected: [" + str(expected) + "]\n" + "Got     : [" + str(got) + "]\n")
+commentVerifier.check(doxygen_basic_translate.function.__doc__,
+  """
+  Brief description.
 
-check(doxygen_basic_translate.function.__doc__, ''
-'  Brief description.\n'
-'  The comment text\n'
-'  Authors:\n'
-'  Some author\n'
-'  Return:\n'
-'  Some number\n'
-'  See also:\n'
-'  function2\n'
+  The comment text.
+
+  Author: Some author
+
+  Return: Some number
+
+  See also: function2
+  """
 )
-check(doxygen_basic_translate.function2.__doc__, ''
-'  A test of a very very very very very very very very very very very'
-'  very very very very very'
-'  very very very very very long comment'
-'  string.'
+commentVerifier.check(doxygen_basic_translate.function2.__doc__,
+  """
+  A test of a very very very very very very very very very very very very very very very very
+  very very very very very long comment string.
+  """
 )
-check(doxygen_basic_translate.function3.__doc__, ''
-'  ----------------------------------------------------------------\n'
-'  Overload 1:\n'
-'  ----------------------------------------------------------------\n'
-'  A test for overloaded functions\n'
-'  This is function __one__\n'
-'  ----------------------------------------------------------------\n'
-'  Overload 2:\n'
-'  ----------------------------------------------------------------\n'
-'  A test for overloaded functions\n'
-'  This is function __two__\n'
+commentVerifier.check(doxygen_basic_translate.function3.__doc__,
+  """
+  ----------------------------------------------------------------
+  Overload 1:
+  ----------------------------------------------------------------
+  A test for overloaded functions
+  This is function __one__
+
+  ----------------------------------------------------------------
+  Overload 2:
+  ----------------------------------------------------------------
+  A test for overloaded functions
+  This is function __two__
+
+  """
 )
-check(doxygen_basic_translate.function4.__doc__, ''
-'  A test of some mixed tag usage\n' 
-'  If: CONDITION {\n'
-'  This _code_fragment shows us something .\n'
-'  Title: Minuses:\n'
-'   -it\'s senseless\n'
-'   -it\'s stupid\n'
-'   -it\'s null\n'
-'  Warning:\n'
-'  This may not work as expected\n'
-'  int main() { while(true); }\n'
-'  }'
+commentVerifier.check(doxygen_basic_translate.function4.__doc__,
+  """
+  A test of some mixed tag usage
+  If: CONDITION {
+  This _code_ fragment shows us something .
+  Title: Minuses:
+   -it\'s senseless
+   -it\'s stupid
+   -it\'s null
+
+  Warning: This may not work as expected
+
+  int main() { while(true); }
+
+  }
+  """
 )
-check(doxygen_basic_translate.function5.__doc__, ''
-'  This is a post comment. \n'
+commentVerifier.check(doxygen_basic_translate.function5.__doc__,
+  """
+  This is a post comment. 
+  """
 )
-check(doxygen_basic_translate.function6.__doc__, ''
-'  Test for default args \n'
-'  Arguments: \n'
-'  a (int) -- Some parameter, default is 42\n'
+commentVerifier.check(doxygen_basic_translate.function6.__doc__,
+  """
+  Test for default args
+  Arguments:
+    a (int) -- Some parameter, default is 42
+  """
 )
-check(doxygen_basic_translate.function7.__doc__, ''
-' Test for a parameter with difficult type \n'
-'  (mostly for python) \n'
-'  Arguments: \n'
-'  a (Shape::superType *[10])                              -- Very strange param \n'
+commentVerifier.check(doxygen_basic_translate.function7.__doc__,
+  """
+  Test for a parameter with difficult type
+  (mostly for python)
+  Arguments:
+    a (Shape::superType *[10]) -- Very strange param
+  """
 )
diff --git a/Examples/test-suite/python/doxygen_misc_constructs_runme.py b/Examples/test-suite/python/doxygen_misc_constructs_runme.py
old mode 100644
new mode 100755
index 156a279b7..55b4a7ef6
--- a/Examples/test-suite/python/doxygen_misc_constructs_runme.py
+++ b/Examples/test-suite/python/doxygen_misc_constructs_runme.py
@@ -1,54 +1,48 @@
 #!/usr/bin/python
 
-import doxygen_tricky_constructs
+import doxygen_misc_constructs
 import string
 import sys
+import commentVerifier
 
-def check(got, expected):
-  #if got is Null
-  #  raise RuntimeError('Expected comment string\n')
-  gotStr = string.replace(got, ' ', '')
-  gotStr = string.replace(gotStr, '\n', '')
-  gotStr = string.replace(gotStr, '\t', '')
-  expectedStr = string.replace(expected, ' ', '')
-  expectedStr = string.replace(expectedStr, '\n', '')
-  expectedStr = string.replace(expectedStr, '\t', '')
-  if not gotStr == expectedStr:
-    raise RuntimeError("Expected: [" + str(expected) + "]\n" + "Got     : [" + str(got) + "]\n")
 
-check(doxygen_tricky_constructs.getAddress.__doc__, ''
-'Returns address of file line.'
-''
-'   Arguments:'
-'  fileName (int &)                              -- name of the file, where the source'
-'                                line is located'
-'  line (int)                              -- line number'
-'  isGetSize (bool)                              -- if set, for every object location'
-'                                both address and size are returned'
-''
-''
-'  Connection::getId() <br>'
+commentVerifier.check(doxygen_misc_constructs.getAddress.__doc__,
+  r"""
+  Returns address of file line.
+
+  Arguments:
+    fileName (int &) -- name of the file, where the source line is located
+    line (int) -- line number
+    isGetSize (bool) -- if set, for every object location both address and size are returned
+
+  Connection::getId() 
+  """)
+
+commentVerifier.check(doxygen_misc_constructs.CConnectionConfig.__doc__,
+    r"""
+    This class contains information for connection to winIDEA. Its methods 
+    return reference to self, so we can use it like this:
+
+    CConnectionConfig config = new CConnectionConfig();
+    config.discoveryPort(5534).dllPath("C:\\myWinIDEA\\connect.dll").id("main");
+
+
+    All parameters are optional. Set only what is required, default values are
+    used for unspecified parameters.
+
+
+    advancedWinIDEALaunching.py Python example. 
+    """)
+
+commentVerifier.check(doxygen_misc_constructs.waitTime.__doc__,
+  r"""
+  Determines how long the 'isystem.connect' should wait for running 
+  instances to respond. Only one of 'lfWaitXXX' flags from IConnect::ELaunchFlags
+  may be specified.
+  """
 )
-check(doxygen_tricky_constructs.CConnectionConfig.__doc__, ''
-'    This class contains information for connection to winIDEA. Its methods'
-'    return reference to self, so we can use it like this:'
-'    <pre>'
-'    CConnectionConfig config = new CConnectionConfig();'
-'    config.discoveryPort(5534).dllPath("C: \yWinIDEA \onnect.dll").id("main");'
-'    </pre>'
-''
-'     All parameters are optional. Set only what is required, default values are'
-'    used for unspecified parameters.'
-'    <p>'
-''
-'     advancedWinIDEALaunching.py Python example. <br>'
-''
+commentVerifier.check(doxygen_misc_constructs.getConnection.__doc__,
+  r"""
+  This function returns connection id.
+  """
 )
-check(doxygen_tricky_constructs.waitTime.__doc__, ''
-'  Determines how long the isystem.connect should wait for running'
-'  instances to respond. Only one of lfWaitXXX flags from IConnect::ELaunchFlags'
-'  may be specified.'
-)
-check(doxygen_tricky_constructs.getConnection.__doc__, ''
-'This class manages connection.'
-)
\ No newline at end of file
diff --git a/Examples/test-suite/python/doxygen_parsing_runme.py b/Examples/test-suite/python/doxygen_parsing_runme.py
old mode 100644
new mode 100755
diff --git a/Examples/test-suite/python/doxygen_translate_all_tags_runme.py b/Examples/test-suite/python/doxygen_translate_all_tags_runme.py
old mode 100644
new mode 100755
diff --git a/Examples/test-suite/python/doxygen_translate_runme.py b/Examples/test-suite/python/doxygen_translate_runme.py
old mode 100644
new mode 100755
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.cpp b/Source/DoxygenTranslator/src/DoxygenParser.cpp
index 846da261b..9c07eb4cf 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenParser.cpp
@@ -1247,6 +1247,16 @@ void DoxygenParser::tokenizeDoxygenComment(const std::string &doxygenComment,
 
   StringVector lines = split(doxygenComment, '\n');
 
+  // remove trailing spaces, because they cause additional new line at the end
+  // comment, which is wrong, because these spaces are space preceding
+  // end of comment :  '  */'
+  if (!doxygenComment.empty()  &&  doxygenComment[doxygenComment.size() - 1] == ' ') {
+    string lastLine = lines[lines.size() - 1];
+    if (trim(lastLine).empty()) {
+      lines.pop_back(); // remove trailing empy line
+    }
+  }
+
   for (StringVectorCIt it = lines.begin(); it != lines.end(); it++) {
     const string &line = *it;
     size_t pos = line.find_first_not_of(" \t");
diff --git a/Source/DoxygenTranslator/src/PyDocConverter.cpp b/Source/DoxygenTranslator/src/PyDocConverter.cpp
index 4f3566635..675f2ae11 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/PyDocConverter.cpp
@@ -31,32 +31,33 @@ void PyDocConverter::fillStaticTables() {
 
   // table of section titles, they are printed only once
   // for each group of specified doxygen commands
-  sectionTitles["author"] = "Authors:";
-  sectionTitles["authors"] = "Authors:";
-  sectionTitles["copyright"] = "Copyright:";
-  sectionTitles["deprecated"] = "Deprecated:";
-  sectionTitles["example"] = "Example:";
-  sectionTitles["exception"] = "Throws:";
-  sectionTitles["param"] = "Arguments:";
-  sectionTitles["tparam"] = "Arguments:";
-  sectionTitles["note"] = "Notes:";
-  sectionTitles["remark"] = "Remarks:";
-  sectionTitles["remarks"] = "Remarks:";
-  sectionTitles["warning"] = "Warning:";
-  sectionTitles["result"] = "Return:";
-  sectionTitles["return"] = "Return:";
-  sectionTitles["returns"] = "Return:";
-  sectionTitles["sa"] = "See also:";
-  sectionTitles["see"] = "See also:";
-  sectionTitles["since"] = "Since:";
-  sectionTitles["throw"] = "Throws:";
-  sectionTitles["throws"] = "Throws:";
-  sectionTitles["todo"] = "TODO:";
-  sectionTitles["version"] = "Version:";
+  sectionTitles["author"] = "Author: ";
+  sectionTitles["authors"] = "Authors: ";
+  sectionTitles["copyright"] = "Copyright: ";
+  sectionTitles["deprecated"] = "Deprecated: ";
+  sectionTitles["example"] = "Example: ";
+  sectionTitles["exception"] = "Throws: ";
+  sectionTitles["param"] = "Arguments:\n";
+  sectionTitles["tparam"] = "Arguments:\n";
+  sectionTitles["note"] = "Notes: ";
+  sectionTitles["remark"] = "Remarks: ";
+  sectionTitles["remarks"] = "Remarks: ";
+  sectionTitles["warning"] = "Warning: ";
+  sectionTitles["result"] = "Return: ";
+  sectionTitles["return"] = "Return: ";
+  sectionTitles["returns"] = "Returns: ";
+  sectionTitles["sa"] = "See also: ";
+  sectionTitles["see"] = "See also: ";
+  sectionTitles["since"] = "Since: ";
+  sectionTitles["throw"] = "Throw: ";
+  sectionTitles["throws"] = "Throws: ";
+  sectionTitles["todo"] = "TODO: ";
+  sectionTitles["version"] = "Version: ";
 
-  // these commands insert HTML tags
   tagHandlers["a"] = make_pair(&PyDocConverter::handleTagWrap, "_");
   tagHandlers["b"] = make_pair(&PyDocConverter::handleTagWrap, "__");
+  // \c command is translated as single quotes around next word
+  tagHandlers["c"] = make_pair(&PyDocConverter::handleTagWrap, "'");
   tagHandlers["cite"] = make_pair(&PyDocConverter::handleTagWrap, "'");
   tagHandlers["e"] = make_pair(&PyDocConverter::handleTagWrap, "_");
   // these commands insert just a single char, some of them need to be escaped
@@ -78,7 +79,6 @@ void PyDocConverter::fillStaticTables() {
   tagHandlers["authors"] = make_pair(&PyDocConverter::handleParagraph, "");
   tagHandlers["brief"] = make_pair(&PyDocConverter::handleParagraph, "");
   tagHandlers["bug"] = make_pair(&PyDocConverter::handleParagraph, "");
-  tagHandlers["c"] = make_pair(&PyDocConverter::handleParagraph, " ");
   tagHandlers["code"] = make_pair(&PyDocConverter::handleParagraph, "");
   tagHandlers["copyright"] = make_pair(&PyDocConverter::handleParagraph, "");
   tagHandlers["date"] = make_pair(&PyDocConverter::handleParagraph, "");
@@ -196,7 +196,7 @@ std::string PyDocConverter::translateSubtree(DoxygenEntity & doxygenEntity) {
     if (it != sectionTitles.end()) {
       if (it->second != currentSection) {
         currentSection = it->second;
-        translatedComment += currentSection + "\n";
+        translatedComment += currentSection;
       }
     }
     translateEntity(*p, translatedComment);
@@ -215,22 +215,31 @@ void PyDocConverter::translateEntity(DoxygenEntity & doxyEntity, std::string &tr
     (this->*(it->second.first))(doxyEntity, translatedComment, it->second.second);
 }
 
+
 void PyDocConverter::handleParagraph(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
   translatedComment += translateSubtree(tag) + arg;
 }
+
+
 void PyDocConverter::handlePlainString(DoxygenEntity& tag, std::string& translatedComment, std::string&) {
   translatedComment += tag.data;
   if (tag.data.size() && tag.data[tag.data.size()-1] != ' ')
     translatedComment += "";
 }
+
+
 void PyDocConverter::handleTagMessage(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
   std::string dummy;
   translatedComment += arg;
   handleParagraph(tag, translatedComment, dummy);
 }
+
+
 void PyDocConverter::handleTagChar(DoxygenEntity& tag, std::string& translatedComment, std::string&) {
   translatedComment += tag.typeOfEntity;
 }
+
+
 void PyDocConverter::handleTagIf(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
   std::string dummy;
   translatedComment += arg;
@@ -240,6 +249,8 @@ void PyDocConverter::handleTagIf(DoxygenEntity& tag, std::string& translatedComm
     translatedComment += " {" + translateSubtree(tag) + "}";
   }
 }
+
+
 void PyDocConverter::handleTagPar(DoxygenEntity& tag, std::string& translatedComment, std::string&) {
   std::string dummy;
   translatedComment += "Title: ";
@@ -248,6 +259,8 @@ void PyDocConverter::handleTagPar(DoxygenEntity& tag, std::string& translatedCom
   tag.entityList.pop_front();
   handleParagraph(tag, translatedComment, dummy);
 }
+
+
 void PyDocConverter::handleTagImage(DoxygenEntity& tag, std::string& translatedComment, std::string&) {
   if (tag.entityList.size() < 2)
     return;
@@ -258,7 +271,11 @@ void PyDocConverter::handleTagImage(DoxygenEntity& tag, std::string& translatedC
   if (tag.entityList.size())
     translatedComment += "(" + tag.entityList.begin()->data + ")";
 }
-void PyDocConverter::handleTagParam(DoxygenEntity& tag, std::string& translatedComment, std::string&) {
+
+
+void PyDocConverter::handleTagParam(DoxygenEntity& tag,
+                                         std::string& translatedComment,
+                                         std::string&) {
   std::string dummy;
   if (tag.entityList.size() < 2)
     return;
@@ -270,9 +287,11 @@ void PyDocConverter::handleTagParam(DoxygenEntity& tag, std::string& translatedC
   if (!paramType.size())
     paramType = "none";
 
-  translatedComment += paramNameEntity.data + " (" + paramType + ") -- ";
+  translatedComment += "  " + paramNameEntity.data + " (" + paramType + ") --";
   handleParagraph(tag, translatedComment, dummy);
 }
+
+
 void PyDocConverter::handleTagWrap(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
   if (tag.entityList.size()) { // do not include empty tags
     std::string tagData = translateSubtree(tag);
@@ -281,13 +300,16 @@ void PyDocConverter::handleTagWrap(DoxygenEntity& tag, std::string& translatedCo
     if (wsPos != std::string::npos && wsPos != tagData.size() - 1)
       translatedComment += arg + tagData.substr(0, wsPos + 1) + arg + tagData.substr(wsPos + 1);
     else
-      translatedComment += arg + tagData + arg + " ";
+      translatedComment += arg + tagData + arg;
   }
 }
+
+
 void PyDocConverter::handleNewLine(DoxygenEntity&, std::string& translatedComment, std::string&) {
   translatedComment += "\n";
 }
 
+
 String *PyDocConverter::makeDocumentation(Node *n) {
   String *documentation;
   std::string pyDocString, result;
@@ -358,7 +380,13 @@ String *PyDocConverter::makeDocumentation(Node *n) {
   }
 
   // if we got something log the result and construct DOH string to return
-  if (pyDocString.length()) {
+  if (!pyDocString.empty()) {
+
+    // remove the last '\n' since additional one is added during writing to file
+    if (pyDocString[pyDocString.size() - 1] == '\n') {
+      pyDocString.erase(pyDocString.size() - 1);
+    }
+
     result = pyDocString;
 
     if (debug) {
diff --git a/Source/Modules/python.cxx b/Source/Modules/python.cxx
index 1d2096c81..f3f1df832 100644
--- a/Source/Modules/python.cxx
+++ b/Source/Modules/python.cxx
@@ -1257,26 +1257,35 @@ public:
     //
     // otherwise, put it all on a single line
     //
+    // All comments translated from doxygen are given as raw stringr (prefix "r"),
+    // because '\' is used often in comments, but may break Python module from
+    // loading. For example, in doxy comment one may write path in quotes:
+    //
+    //     This is path to file "C:\x\file.txt"
+    //
+    // Python will no load the module with such comment becaue of illegal
+    // escape '\x'. '\' may additionally appear in verbatim or htmlonly sections
+    // of doxygen doc, Latex expressions, ...
     if (have_auto && have_ds) {	// Both autodoc and docstring are present
       doc = NewString("");
-      Printv(doc, triple_double, "\n", pythoncode(autodoc, indent), "\n", pythoncode(str, indent), indent, triple_double, NIL);
+      Printv(doc, "r", triple_double, "\n", pythoncode(autodoc, indent), "\n", pythoncode(str, indent), indent, triple_double, NIL);
     } else if (!have_auto && have_ds) {	// only docstring
       if (Strchr(str, '\n') == 0) {
 	doc = NewStringf("%s%s%s", triple_double, str, triple_double);
       } else {
 	doc = NewString("");
-	Printv(doc, triple_double, "\n", pythoncode(str, indent), indent, triple_double, NIL);
+	Printv(doc, "r", triple_double, "\n", pythoncode(str, indent), indent, triple_double, NIL);
       }
     } else if (have_auto && !have_ds) {	// only autodoc
       if (Strchr(autodoc, '\n') == 0) {
 	doc = NewStringf("%s%s%s", triple_double, autodoc, triple_double);
       } else {
 	doc = NewString("");
-	Printv(doc, triple_double, "\n", pythoncode(autodoc, indent), indent, triple_double, NIL);
+	Printv(doc, "r", triple_double, "\n", pythoncode(autodoc, indent), indent, triple_double, NIL);
       }
     } else if (have_doxygen) { // the lowest priority
       doc = NewString("");
-      Printv(doc, triple_double, "\n", pythoncode(doxygen_comment, indent), indent, triple_double, NIL);
+      Printv(doc, "r", triple_double, "\n", pythoncode(doxygen_comment, indent), indent, triple_double, NIL);
     }
     else
       doc = NewString("");

From ee3e4024a6dcaeea1633fd3fd4b3b49f2cc55bdb Mon Sep 17 00:00:00 2001
From: Marko Klopcic <markok3.14@gmail.com>
Date: Tue, 5 Feb 2013 07:57:49 +0100
Subject: [PATCH 174/314] updated test doxygen_misc_constructs for Python

---
 Examples/test-suite/python/commentVerifier.py |  7 +-
 .../python/doxygen_misc_constructs_runme.py   | 64 +++++++++++++++++++
 2 files changed, 70 insertions(+), 1 deletion(-)

diff --git a/Examples/test-suite/python/commentVerifier.py b/Examples/test-suite/python/commentVerifier.py
index 8a73b1950..f7c0114ee 100644
--- a/Examples/test-suite/python/commentVerifier.py
+++ b/Examples/test-suite/python/commentVerifier.py
@@ -8,8 +8,13 @@ def check(got, expected):
   #expectedStr = string.replace(expected, ' ', '')
   #expectedStr = string.replace(expectedStr, '\n', '')
   #expectedStr = string.replace(expectedStr, '\t', '')
+
+  if got == None:  # when there is no commant attached to a class or function
+      got = ''
+
   if not got == expected:
     print "\n\n////////////////////////////////////////////////////////////////////////"
+
     expectedFileName = "expected.txt"
     gotFileName = "got.txt"
     print "Output is also saved to files '" + expectedFileName + \
@@ -20,5 +25,5 @@ def check(got, expected):
     expectedFile.close()
     gotFile = open(gotFileName, "w")
     gotFile.write(got)
-    gotFile.close()    
+    gotFile.close()
     raise RuntimeError("Expected: [" + str(expected) + "]\n" + "Got     : [" + str(got) + "]\n")
diff --git a/Examples/test-suite/python/doxygen_misc_constructs_runme.py b/Examples/test-suite/python/doxygen_misc_constructs_runme.py
index 55b4a7ef6..d2f04a874 100755
--- a/Examples/test-suite/python/doxygen_misc_constructs_runme.py
+++ b/Examples/test-suite/python/doxygen_misc_constructs_runme.py
@@ -41,8 +41,72 @@ commentVerifier.check(doxygen_misc_constructs.waitTime.__doc__,
   may be specified.
   """
 )
+
 commentVerifier.check(doxygen_misc_constructs.getConnection.__doc__,
   r"""
   This function returns connection id.
   """
 )
+
+
+commentVerifier.check(doxygen_misc_constructs.getFirstLetter.__doc__,
+  r''
+)
+
+commentVerifier.check(doxygen_misc_constructs.ClassWithNestedEnum.__doc__,
+  r"""
+    Class description.
+    """
+)
+
+commentVerifier.check(doxygen_misc_constructs.isNoSpaceValidA.__doc__,
+  r"""
+  This comment without space after '*' is valid in Doxygen.
+
+  """
+)
+
+commentVerifier.check(doxygen_misc_constructs.isNoSpaceValidB.__doc__,
+  r"""
+  .This comment without space after '*' is valid in Doxygen.
+
+  """
+)
+
+commentVerifier.check(doxygen_misc_constructs.isNoSpaceValidC.__doc__,
+  r''
+)
+
+commentVerifier.check(doxygen_misc_constructs.backslashA.__doc__,
+  r"""
+  Backslash following'word' is a valid doxygen command. Output contains
+  'followingword' with 'word' in code font.
+  """
+)
+
+commentVerifier.check(doxygen_misc_constructs.backslashB.__doc__,
+  r"""
+  Doxy command without trailing space is ignored - nothing appears
+  on output. Standalone \ and '\' get to output.
+  Standalone @ and '@' get to output.
+  Commands "in quoted \b strings are treated as plain text".
+  Commands not recognized by Doxygen are ignored.
+  Backslashes in DOS paths d:and words
+  following them do not appear on output, we must quote them with
+  double quotes: "d:\xyz\qwe\myfile", "@something". Single quotes do not help:
+  'd:'. Escaping works: d:\xyz\qwe\myfile. Unix
+  paths of course have no such problems: /xyz/qwe/myfile
+  Commands for escaped symbols:
+  $ @ \ & ~ < > # % " . :: @text ::text
+  """
+)
+
+commentVerifier.check(doxygen_misc_constructs.backslashC.__doc__,
+  r"""
+  Backslash e at end of _line_ froze SWIG 
+  _with_ old comment parser. 
+
+  See also: MyClass::fun(char,
+  float)
+  """
+)

From 08093ec17e1492826b70571d161b1c9a6a0e8385 Mon Sep 17 00:00:00 2001
From: Marko Klopcic <markok3.14@gmail.com>
Date: Wed, 6 Feb 2013 22:59:30 +0100
Subject: [PATCH 175/314] updated two additonal tests for python doxygen code
 comments

---
 .../python/doxygen_basic_notranslate_runme.py | 84 +++++++++++++++++
 .../python/doxygen_parsing_runme.py           | 89 +++++++++++--------
 2 files changed, 136 insertions(+), 37 deletions(-)
 create mode 100755 Examples/test-suite/python/doxygen_basic_notranslate_runme.py

diff --git a/Examples/test-suite/python/doxygen_basic_notranslate_runme.py b/Examples/test-suite/python/doxygen_basic_notranslate_runme.py
new file mode 100755
index 000000000..0be839c9d
--- /dev/null
+++ b/Examples/test-suite/python/doxygen_basic_notranslate_runme.py
@@ -0,0 +1,84 @@
+#!/usr/bin/python
+
+import doxygen_basic_notranslate
+import string
+import sys
+import commentVerifier
+
+commentVerifier.check(doxygen_basic_notranslate.function.__doc__,
+  r"""
+  \brief
+  Brief description.
+
+  The comment text
+  \author Some author
+  \return Some number
+  \sa function2
+
+  """
+)
+
+commentVerifier.check(doxygen_basic_notranslate.function2.__doc__,
+  r"""
+  A test of a very very very very very very very very very very very very very very very very
+  very very very very very long comment string.
+
+  """
+)
+
+commentVerifier.check(doxygen_basic_notranslate.function3.__doc__,
+  r"""
+  ----------------------------------------------------------------
+  Overload 1:
+  ----------------------------------------------------------------
+   A test for overloaded functions
+   This is function \b one
+   
+  ----------------------------------------------------------------
+  Overload 2:
+  ----------------------------------------------------------------
+   A test for overloaded functions
+   This is function \b two
+   
+  """
+)
+
+commentVerifier.check(doxygen_basic_notranslate.function4.__doc__,
+  r"""
+  A test of some mixed tag usage
+  \if CONDITION
+  This \a code fragment shows us something \.
+  \par Minuses:
+  \arg it's senseless
+  \arg it's stupid
+  \arg it's null
+
+  \warning This may not work as expected
+
+  \code
+  int main() { while(true); }
+  \endcode
+  \endif
+
+  """
+)
+commentVerifier.check(doxygen_basic_notranslate.function5.__doc__,
+  r"""
+  This is a post comment. 
+  """
+)
+commentVerifier.check(doxygen_basic_notranslate.function6.__doc__,
+  r"""
+  Test for default args
+  @param a Some parameter, default is 42
+
+  """
+)
+commentVerifier.check(doxygen_basic_notranslate.function7.__doc__,
+  r"""
+  Test for a parameter with difficult type
+  (mostly for python)
+  @param a Very strange param
+
+  """
+)
diff --git a/Examples/test-suite/python/doxygen_parsing_runme.py b/Examples/test-suite/python/doxygen_parsing_runme.py
index cb22bb369..ccf03797c 100755
--- a/Examples/test-suite/python/doxygen_parsing_runme.py
+++ b/Examples/test-suite/python/doxygen_parsing_runme.py
@@ -3,45 +3,60 @@
 import doxygen_parsing
 import string
 import sys
+import commentVerifier
 
-def check(got, expected):
-  #if got is Null
-  #  raise RuntimeError('Expected comment string\n')
-  gotStr = string.replace(got, ' ', '')
-  gotStr = string.replace(gotStr, '\n', '')
-  gotStr = string.replace(gotStr, '\t', '')
-  expectedStr = string.replace(expected, ' ', '')
-  expectedStr = string.replace(expectedStr, '\n', '')
-  expectedStr = string.replace(expectedStr, '\t', '')
-  if not gotStr == expectedStr:
-    raise RuntimeError("Expected: [" + str(expected) + "]\n" + "Got     : [" + str(got) + "]\n")
+commentVerifier.check(doxygen_parsing.someFunction.__doc__,
+r"""
+  The function comment
+  """)
+commentVerifier.check(doxygen_parsing.SomeClass.__doc__,
+r"""
+    The class comment
+    """)
+commentVerifier.check(doxygen_parsing.SomeStruct.__doc__,
+r"""
+    The struct comment
+    """)
+commentVerifier.check(doxygen_parsing.SomeAnotherClass.classMethod.__doc__,
+r"""
+        The class method comment
+        """)
+commentVerifier.check(doxygen_parsing.SomeAnotherClass.classMethodExtended.__doc__,
+r"""
+        The class method with parameter
 
-check(doxygen_parsing.someFunction.__doc__, 'The function comment')
-check(doxygen_parsing.SomeClass.__doc__, 'The class comment')
-check(doxygen_parsing.SomeStruct.__doc__, 'The struct comment')
-check(doxygen_parsing.SomeAnotherClass.classMethod.__doc__, 'The class method comment')
-check(doxygen_parsing.SomeAnotherClass.classMethodExtended.__doc__, ''
-'The class method with parameter\n'
-'Arguments:\n'
-'a (int) -- Parameter a\n'
-'b (int) -- Parameter b\n'
+        Arguments:
+          a (int) -- Parameter a
+          b (int) -- Parameter b
+        """
 )
-check(doxygen_parsing.SomeAnotherClass.classMethodExtended2.__doc__, ''
-'The class method with parameter\n'
-'Arguments:\n'
-'a (int)-- Parameter a\n'
-'b (int)-- Parameter b\n'
+commentVerifier.check(doxygen_parsing.SomeAnotherClass.classMethodExtended2.__doc__, 
+r"""
+        The class method with parameter
+
+        Arguments:
+          a (int) -- Parameter a
+          b (int) -- Parameter b
+        """
 )
-check(doxygen_parsing.SomeAnotherStruct.structMethod.__doc__, 'The struct method comment')
-check(doxygen_parsing.SomeAnotherStruct.structMethodExtended.__doc__, ''
-'The struct method with parameter\n'
-'Arguments:\n'
-'a (int)-- Parameter a\n'
-'b (int)-- Parameter b\n'
+commentVerifier.check(doxygen_parsing.SomeAnotherStruct.structMethod.__doc__,
+r"""
+        The struct method comment
+        """)
+commentVerifier.check(doxygen_parsing.SomeAnotherStruct.structMethodExtended.__doc__,
+r"""
+        The struct method with parameter
+
+        Arguments:
+          a (int) -- Parameter a
+          b (int) -- Parameter b
+        """
 )
-check(doxygen_parsing.SomeAnotherStruct.structMethodExtended2.__doc__, ''
-'The struct method with parameter\n'
-'Arguments:\n'
-'a (int)-- Parameter a\n'
-'b (int)-- Parameter b\n'
-)
\ No newline at end of file
+commentVerifier.check(doxygen_parsing.SomeAnotherStruct.structMethodExtended2.__doc__,
+r"""
+        The struct method with parameter
+
+        Arguments:
+          a (int) -- Parameter a
+          b (int) -- Parameter b
+        """)

From 77b6099c05f3d53b83cd4955e78744b03e9ffc99 Mon Sep 17 00:00:00 2001
From: Marko Klopcic <markok3.14@gmail.com>
Date: Thu, 7 Feb 2013 08:46:38 +0100
Subject: [PATCH 176/314] updated two additional python doxygen tests

---
 .../doxygen_translate_all_tags_runme.py       | 382 ++++++++++--------
 .../python/doxygen_translate_runme.py         | 265 ++++++------
 2 files changed, 336 insertions(+), 311 deletions(-)

diff --git a/Examples/test-suite/python/doxygen_translate_all_tags_runme.py b/Examples/test-suite/python/doxygen_translate_all_tags_runme.py
index f71cb7e11..058434cd2 100755
--- a/Examples/test-suite/python/doxygen_translate_all_tags_runme.py
+++ b/Examples/test-suite/python/doxygen_translate_all_tags_runme.py
@@ -3,176 +3,216 @@
 import doxygen_translate_all_tags
 import string
 import sys
+import commentVerifier
 
-def check(got, expected):
-  #if got is Null
-  #  raise RuntimeError('Expected comment string\n')
-  gotStr = string.replace(got, ' ', '')
-  gotStr = string.replace(gotStr, '\n', '')
-  gotStr = string.replace(gotStr, '\t', '')
-  expectedStr = string.replace(expected, ' ', '')
-  expectedStr = string.replace(expectedStr, '\n', '')
-  expectedStr = string.replace(expectedStr, '\t', '')
-  if not gotStr == expectedStr:
-    raise RuntimeError("Expected: [" + str(expected) + "]\n" + "Got     : [" + str(got) + "]\n")
 
-check(doxygen_translate_all_tags.function.__doc__, ''
-'  _Hello_'
-''
-'   -some list item '
-''
-'  This is attention! '
-'  You were warned! '
-''
-'  Authors:'
-'  lots of them '
-''
-'  Zubr '
-''
-'  __boldword__'
-''
-'  Some brief description, '
-'  extended to many lines. '
-''
-'  Not everything works right now... '
-''
-'  codeword'
-''
-'  \'citationword\''
-''
-'  some test code '
-''
-'  Conditional comment: SOMECONDITION'
-'  Some conditional comment '
-'  End of conditional comment.'
-''
-'  Copyright:'
-'  some copyright '
-''
-'  1970 - 2012 '
-''
-'  Deprecated:'
-'  Now use another function '
-''
-'  This is very large '
-'  and detailed description of some thing '
-''
-'  _italicword_'
-''
-'  emphazedWord'
-''
-'  Example:'
-'  someFile.txt'
-'  Some details on using the example '
-''
-'  Throws:'
-'  SuperError'
-''
-'  This will only appear in hmtl '
-''
-'  If: ANOTHERCONDITION {'
-'  First part of comment '
-'  If: SECONDCONDITION {'
-'  Nested condition text '
-'  }Else if: THIRDCONDITION {'
-'  The third condition text '
-'  }Else:  {The last text block '
-'  }'
-'  }Else:  {Second part of comment '
-'  If: CONDITION {'
-'  Second part extended '
-'  }'
-'  }'
-''
-'  If not: SOMECONDITION {'
-'  This is printed if not '
-'  }'
-''
-'  Image: testImage.bmp(Hello, world!)'
-''
-'  Some text '
-'  describing invariant. '
-''
-'  This will only appear in LATeX '
-''
-'  <ul> '
-''
-'   -Some unordered list '
-'   -With lots of items '
-'   -lots of lots of items '
-''
-'  </ul> '
-''
-'  someMember Some description follows '
-''
-'  This will only appear in man '
-''
-'  Notes:'
-'  Here '
-'  is the note! '
-''
-'  This is an overloaded member function, provided for convenience.'
-'  It differs from the above function only in what argument(s) it accepts.'
-''
-'  someword'
-''
-'  Title: The paragraph title '
-'  The paragraph text. '
-'  Maybe even multiline '
-''
-'  Arguments:'
-'  a (int)                              -- the first param '
-''
-'  Remarks:'
-'  Some remark text '
-''
-'  Another remarks section '
-''
-'  Return:'
-'  Whatever '
-''
-'  it '
-''
-'  may return '
-''
-'  This will only appear in RTF '
-''
-''
-'  See also:'
-'  someOtherMethod '
-''
-'  function '
-''
-'  Same as '
-'  brief description '
-''
-'  Since:'
-'  version 0.0.0.1 '
-''
-'  Throws:'
-'  superException'
-''
-'  RuntimeError'
-''
-'  TODO:'
-'  Some very important task '
-''
-'  Arguments:'
-'  b (float)                              -- B is mentioned again... '
-''
-'  very long '
-'  text with tags <sometag> '
-''
-'  Version:'
-'  0.0.0.2 '
-''
-'  Warning:'
-'  This is senseless! '
-''
-'  This will only appear in XML '
-''
-'  Here goes test of symbols: '
-'  $@\&~<>#%".::'
-''
-'  And here goes simple text '
-)
+commentVerifier.check(doxygen_translate_all_tags.func01.__doc__,
+r"""
+  _Hello_
+
+
+
+
+
+   -some list item
+
+  This is attention!
+  You were warned!
+
+  Authors: lots of them
+  Author: Zubr
+
+  __boldword__
+
+  Some brief description,
+  extended to many lines.
+
+  Not everything works right now...
+  'codeword'
+
+
+
+
+
+  'citationword'
+
+  some test code 
+  """)
+
+commentVerifier.check(doxygen_translate_all_tags.func02.__doc__,
+r"""
+  Conditional comment: SOMECONDITION
+  Some conditional comment
+  End of conditional comment.
+
+
+
+
+
+
+
+  Copyright: some copyright
+
+  1970 - 2012
+
+
+
+
+
+  Deprecated: Now use another function
+
+  This is very large
+  and detailed description of some thing
+  """)
+
+commentVerifier.check(doxygen_translate_all_tags.func03.__doc__,
+r"""
+  Comment for __func03().__
+
+
+
+
+
+
+
+
+
+  _italicword_
+
+  emphazedWord 
+
+
+
+  Example: someFile.txt
+  Some details on using the example
+  """)
+
+commentVerifier.check(doxygen_translate_all_tags.func04.__doc__,
+r"""
+  Throws: SuperError
+
+    \sqrt{(x_2-x_1)^2+(y_2-y_1)^2}
+ 
+    \sqrt{(x_2-x_1)^2+(y_2-y_1)^2}
+ 
+    \sqrt{(x_2-x_1)^2+(y_2-y_1)^2}
+
+  This will only appear in hmtl
+""")
+
+commentVerifier.check(doxygen_translate_all_tags.func05.__doc__,
+r"""
+  If: ANOTHERCONDITION {
+  First part of comment
+  If: SECONDCONDITION {
+  Nested condition text
+  }Else if: THIRDCONDITION {
+  The third condition text
+  }Else:  {The last text block
+  }
+  }Else:  {Second part of comment
+  If: CONDITION {
+  Second part extended
+  }
+  }
+
+  If not: SOMECONDITION {
+  This is printed if not
+  }
+
+  Image: testImage.bmp("Hello, world!")
+
+  Some text
+  describing invariant.
+""")
+
+commentVerifier.check(doxygen_translate_all_tags.func06.__doc__,
+r"""
+  This will only appear in LATeX
+
+
+
+   -Some unordered list
+   -With lots of items
+   -lots of lots of items
+
+
+
+  someMember Some description follows
+
+  This will only appear in man
+""")
+
+commentVerifier.check(doxygen_translate_all_tags.func07.__doc__,
+r"""
+  Notes: Here
+  is the note!
+
+  This is an overloaded member function, provided for convenience.
+  It differs from the above function only in what argument(s) it accepts.
+
+  someword
+
+  Title: The paragraph title
+  The paragraph text.
+  Maybe even multiline
+
+  Arguments:
+    a (int) -- the first param
+""")
+
+commentVerifier.check(doxygen_translate_all_tags.func08.__doc__,
+r"""
+  Remarks:
+  Some remark text
+
+  Another remarks section
+
+  Return: Whatever
+
+  it
+
+  may return
+""")
+
+commentVerifier.check(doxygen_translate_all_tags.func09.__doc__,
+r"""
+  This will only appear in RTF
+
+
+  See also: someOtherMethod
+
+  function
+
+  Same as
+  brief description
+
+  Since: version 0.0.0.1
+
+  Throws: superException
+
+  RuntimeError
+""")
+
+commentVerifier.check(doxygen_translate_all_tags.func10.__doc__,
+r"""
+  TODO:
+  Some very important task
+
+  Arguments:
+    b (float) -- B is mentioned again...
+
+  very long
+  text with tags <sometag>
+
+  Version: 0.0.0.2
+
+  Warning: This is senseless!
+
+  This will only appear in XML
+
+  Here goes test of symbols:
+  $ @ \ & ~ < > # % " . ::
+
+  And here goes simple text
+""")
diff --git a/Examples/test-suite/python/doxygen_translate_runme.py b/Examples/test-suite/python/doxygen_translate_runme.py
index e7d819199..506f338f7 100755
--- a/Examples/test-suite/python/doxygen_translate_runme.py
+++ b/Examples/test-suite/python/doxygen_translate_runme.py
@@ -3,146 +3,131 @@
 import doxygen_translate
 import string
 import sys
+import commentVerifier
 
-def check(got, expected):
-  #if got is Null
-  #  raise RuntimeError('Expected comment string\n')
-  gotStr = string.replace(got, ' ', '')
-  gotStr = string.replace(gotStr, '\n', '')
-  gotStr = string.replace(gotStr, '\t', '')
-  expectedStr = string.replace(expected, ' ', '')
-  expectedStr = string.replace(expectedStr, '\n', '')
-  expectedStr = string.replace(expectedStr, '\t', '')
-  if not gotStr == expectedStr:
-    raise RuntimeError("Expected: [" + str(expected) + "]\n" + "Got     : [" + str(got) + "]\n")
 
-check(doxygen_translate.function.__doc__, ''
-'  _Hello_'
-''
-'   -some list item '
-''
-'  Authors:'
-'  lots of them '
-''
-'  Zubr '
-''
-'  __boldword__'
-''
-'  codeword'
-''
-'  \'citationword\''
-''
-'  some test code '
-''
-'  Conditional comment: SOMECONDITION'
-'  Some conditional comment '
-'  End of conditional comment.'
-''
-'  Copyright:'
-'  some copyright '
-''
-'  Deprecated:'
-'  Now use another function '
-''
-'  _italicword_'
-''
-'  Example:'
-'  someFile.txt'
-'  Some details on using the example '
-''
-'  Throws:'
-'  SuperError'
-''
-'  If: ANOTHERCONDITION {'
-'  First part of comment '
-'  If: SECONDCONDITION {'
-'  Nested condition text '
-'  }Else if: THIRDCONDITION {'
-'  The third condition text '
-'  }Else:  {The last text block '
-'  }'
-'  }Else:  {Second part of comment '
-'  If: CONDITION {'
-'  Second part extended '
-'  }'
-'  }'
-''
-'  If not: SOMECONDITION {'
-'  This is printed if not '
-'  }'
-''
-'  Image: testImage.bmp(Hello, world!)'
-''
-'  <ul> '
-''
-'   -Some unordered list '
-'   -With lots of items '
-'   -lots of lots of items '
-''
-'  </ul> '
-''
-'  someMember Some description follows '
-''
-'  Notes:'
-'  Here '
-'  is the note! '
-''
-'  This is an overloaded member function, provided for convenience.'
-'  It differs from the above function only in what argument(s) it accepts.'
-''
-'  someword'
-''
-''
-''
-'  Title: The paragraph title '
-'  The paragraph text. '
-'  Maybe even multiline '
-''
-'  Arguments:'
-'  a (int)                              -- the first param '
-''
-'  Remarks:'
-'  Some remark text '
-''
-'  Another remarks section '
-''
-'  Return:'
-'  Whatever '
-''
-'  it '
-''
-'  may return '
-''
-'  See also:'
-'  someOtherMethod '
-''
-'  function '
-''
-'  Since:'
-'  version 0.0.0.1 '
-''
-'  Throws:'
-'  superException'
-''
-'  RuntimeError'
-''
-'  TODO:'
-'  Some very important task '
-''
-'  Arguments:'
-'  b (float)                              -- B is mentioned again... '
-''
-'  very long '
-'  text with tags <sometag> '
-''
-'  Version:'
-'  0.0.0.2 '
-''
-'  Warning:'
-'  This is senseless! '
-''
-'  Here goes test of symbols: '
-'  $@\&~<>#%".::'
-''
-'  And here goes simple text '
+commentVerifier.check(doxygen_translate.function.__doc__,
+r"""
+  _Hello_
+
+   -some list item
+
+  Authors: lots of them
+
+  Author: Zubr
+
+  __boldword__
+
+  'codeword'
+
+  'citationword'
+
+  some test code 
+
+  Conditional comment: SOMECONDITION
+  Some conditional comment
+  End of conditional comment.
+
+  Copyright: some copyright
+
+  Deprecated: Now use another function
+
+  _italicword_
+
+  Example: someFile.txt
+  Some details on using the example
+
+  Throws: SuperError
+
+  If: ANOTHERCONDITION {
+  First part of comment
+  If: SECONDCONDITION {
+  Nested condition text
+  }Else if: THIRDCONDITION {
+  The third condition text
+  }Else:  {The last text block
+  }
+  }Else:  {Second part of comment
+  If: CONDITION {
+  Second part extended
+  }
+  }
+
+  If not: SOMECONDITION {
+  This is printed if not
+  }
+
+  Image: testImage.bmp("Hello, world!")
+
+
+
+   -Some unordered list
+   -With lots of items
+   -lots of lots of items
+
+
+
+  someMember Some description follows 
+
+
+
+
+
+
+  Notes: Here
+  is the note!
+
+  This is an overloaded member function, provided for convenience.
+  It differs from the above function only in what argument(s) it accepts.
+
+  someword
+
+
+
+  Title: The paragraph title
+  The paragraph text.
+  Maybe even multiline
+
+  Arguments:
+    a (int) -- the first param
+
+  Remarks: Some remark text
+
+  Another remarks section
+
+  Return: Whatever
+
+  it
+
+  Returns: may return
+
+  See also: someOtherMethod
+
+  function
+
+  Since: version 0.0.0.1
+
+  Throw: superException
+
+  Throws: RuntimeError
+
+  TODO: Some very important task
+
+  Arguments:
+    b (float) -- B is mentioned again...
+
+
+  very long
+  text with tags <sometag>
+
+
+  Version: 0.0.0.2
+
+  Warning: This is senseless!
+
+  Here goes test of symbols:
+  $ @ \ & ~ < > # % " . ::
+
+  And here goes simple text
+  """
 )

From 560dedb6c0f5ed9bc208a836c14f917f2cfd0588 Mon Sep 17 00:00:00 2001
From: Marko Klopcic <markok3.14@gmail.com>
Date: Tue, 12 Feb 2013 22:58:50 +0100
Subject: [PATCH 177/314] added handling of HTML tags and HTML entities to
 PyDocConverter, updated tests

---
 .../test-suite/doxygen_translate_all_tags.i   |   6 +-
 .../doxygen_translate_all_tags_runme.py       | 137 +++++++++++--
 .../python/doxygen_translate_runme.py         | 119 +++++++++++-
 .../DoxygenTranslator/src/PyDocConverter.cpp  | 182 +++++++++++++++++-
 Source/DoxygenTranslator/src/PyDocConverter.h |  40 ++++
 5 files changed, 454 insertions(+), 30 deletions(-)

diff --git a/Examples/test-suite/doxygen_translate_all_tags.i b/Examples/test-suite/doxygen_translate_all_tags.i
index 658fc92df..0bc50f3a8 100644
--- a/Examples/test-suite/doxygen_translate_all_tags.i
+++ b/Examples/test-suite/doxygen_translate_all_tags.i
@@ -110,11 +110,11 @@ int func03(int a)
  * \f$ \sqrt{(x_2-x_1)^2+(y_2-y_1)^2} \f$
  *
  * \f[
- *   \sqrt{(x_2-x_1)^2+(y_2-y_1)^2}
+ *     \sqrt{(x_2-x_1)^2+(y_2-y_1)^2}
  * \f]
  *
  * \f{
- *   \sqrt{(x_2-x_1)^2+(y_2-y_1)^2}
+ *     \sqrt{(x_2-x_1)^2+(y_2-y_1)^2}
  * \f}
  *
  * \file file.h
@@ -395,7 +395,7 @@ int func10(int a, float b)
  * \interface someInterface someHeader.h "Header name"
  *
  * Because of structural Doxygen command at the start of comment block,
- * the whoile comment block is ignored. See parser.y, f. isStructuralDoxygen()
+ * the whole comment block is ignored. See parser.y, f. isStructuralDoxygen()
  * or documentation for the list of commands.
  */
 int func11(int a, float b)
diff --git a/Examples/test-suite/python/doxygen_translate_all_tags_runme.py b/Examples/test-suite/python/doxygen_translate_all_tags_runme.py
index 058434cd2..ecccc1fc5 100755
--- a/Examples/test-suite/python/doxygen_translate_all_tags_runme.py
+++ b/Examples/test-suite/python/doxygen_translate_all_tags_runme.py
@@ -91,14 +91,31 @@ commentVerifier.check(doxygen_translate_all_tags.func04.__doc__,
 r"""
   Throws: SuperError
 
-    \sqrt{(x_2-x_1)^2+(y_2-y_1)^2}
- 
-    \sqrt{(x_2-x_1)^2+(y_2-y_1)^2}
- 
-    \sqrt{(x_2-x_1)^2+(y_2-y_1)^2}
+
+
+    \sqrt{(x_2-x_1)^2+(y_2-y_1)^2} 
+
+   
+  \sqrt{(x_2-x_1)^2+(y_2-y_1)^2}
+
+
+   
+  \sqrt{(x_2-x_1)^2+(y_2-y_1)^2}
+
+
+
+
+
+
+
+
+
+
+
 
   This will only appear in hmtl
-""")
+
+  """)
 
 commentVerifier.check(doxygen_translate_all_tags.func05.__doc__,
 r"""
@@ -122,29 +139,68 @@ r"""
 
   Image: testImage.bmp("Hello, world!")
 
+
+
+
+
+
+
+
+
+
+
   Some text
   describing invariant.
-""")
+  """)
 
 commentVerifier.check(doxygen_translate_all_tags.func06.__doc__,
 r"""
+  Comment for __func06().__
+
+
+
+
   This will only appear in LATeX
 
 
 
+
    -Some unordered list
    -With lots of items
    -lots of lots of items
 
 
 
-  someMember Some description follows
+
+  someMember Some description follows 
+
+
+
 
   This will only appear in man
-""")
+
+
+
+
+
+
+
+
+
+
+
+
+  """)
 
 commentVerifier.check(doxygen_translate_all_tags.func07.__doc__,
 r"""
+  Comment for __func07().__
+
+
+
+
+
+
   Notes: Here
   is the note!
 
@@ -153,18 +209,28 @@ r"""
 
   someword
 
+
+
+
+
   Title: The paragraph title
   The paragraph text.
   Maybe even multiline
 
+
+
   Arguments:
     a (int) -- the first param
-""")
+
+
+
+
+
+  """)
 
 commentVerifier.check(doxygen_translate_all_tags.func08.__doc__,
 r"""
-  Remarks:
-  Some remark text
+  Remarks: Some remark text
 
   Another remarks section
 
@@ -172,8 +238,9 @@ r"""
 
   it
 
-  may return
-""")
+  Returns: may return
+
+  """)
 
 commentVerifier.check(doxygen_translate_all_tags.func09.__doc__,
 r"""
@@ -182,37 +249,67 @@ r"""
 
   See also: someOtherMethod
 
+
+
   function
 
   Same as
   brief description
 
+
+
   Since: version 0.0.0.1
 
-  Throws: superException
 
-  RuntimeError
-""")
+
+
+
+
+
+
+
+
+
+
+
+
+
+  Throw: superException
+
+  Throws: RuntimeError
+  """)
 
 commentVerifier.check(doxygen_translate_all_tags.func10.__doc__,
 r"""
-  TODO:
-  Some very important task
+  TODO: Some very important task
 
   Arguments:
     b (float) -- B is mentioned again...
 
+
+
+
+
+
+
   very long
   text with tags <sometag>
 
+
+
+
   Version: 0.0.0.2
 
   Warning: This is senseless!
 
+
+
+
   This will only appear in XML
 
+
   Here goes test of symbols:
   $ @ \ & ~ < > # % " . ::
 
   And here goes simple text
-""")
+  """)
diff --git a/Examples/test-suite/python/doxygen_translate_runme.py b/Examples/test-suite/python/doxygen_translate_runme.py
index 506f338f7..fe5b06a5b 100755
--- a/Examples/test-suite/python/doxygen_translate_runme.py
+++ b/Examples/test-suite/python/doxygen_translate_runme.py
@@ -103,7 +103,7 @@ r"""
 
   See also: someOtherMethod
 
-  function
+  See also: function
 
   Since: version 0.0.0.1
 
@@ -131,3 +131,120 @@ r"""
   And here goes simple text
   """
 )
+
+
+
+commentVerifier.check(doxygen_translate.htmlFunction.__doc__,
+r"""
+  Test for html tags. See Doxygen doc for list of tags recognized by Doxygen.
+ 
+  <a href = "http://acme.com/index.html">This is link</a>
+  <b>bold</b>
+  <BLOCKQUOTE>
+  Quotation block.
+  </BLOCKQUOTE>
+  <br>
+  <center>center</center>
+  <code>this is code</code>
+  <DD> Starts an item description.
+  <DFN> Starts a piece of text displayed in a typewriter font.
+  </DFN> 
+  <DIV> Starts a section with a specific style (HTML only)
+  </DIV> 
+  <DL> Starts a description list.
+  <DT> Starts an item title.</DT>
+  </DL> 
+  <EM> Starts a piece of text displayed in an italic font.
+  </EM> 
+  <FORM> 'Form' does not generate any output.
+  </FORM>
+  <HR> 
+  <H1> Starts an unnumbered section.
+  </H1>
+  <H2> Starts an unnumbered subsection.
+  </H2> 
+  <H3> Starts an unnumbered subsubsection.
+  </H3> 
+  <I> Starts a piece of text displayed in an italic font.
+  <INPUT> Does not generate any output.
+  </I> 
+  <IMG src="slika.png"> 
+  <META> Does not generate any output.
+  <MULTICOL> ignored by doxygen.
+  </MULTICOL> ignored by doxygen.
+ 
+  <OL> Starts a numbered item list.
+  <LI> Starts a new list item.
+  </LI> 
+  </OL> Ends a numbered item list.
+ 
+  <P> Starts a new paragraph.
+  </P> 
+  <PRE> Starts a preformatted fragment.
+  </PRE>
+  <SMALL> Starts a section of text displayed in a smaller font.
+  </SMALL>
+  <SPAN> Starts an inline text fragment with a specific style (HTML only)
+  </SPAN>
+  <STRONG> Starts a section of bold text.
+  </STRONG>
+  <SUB> Starts a piece of text displayed in subscript.
+  </SUB>
+  <SUP> Starts a piece of text displayed in superscript.
+  </SUP>
+ 
+  <table border = '1'>
+  <caption>Animals</caption>
+  <tr><th> cow   </th><th> dog    </th></tr>
+  <tr><td> cow   </td><td> dog    </td></tr>
+  <tr><td> cat   </td><td> mouse  </td></tr>
+  <tr><td> horse </td><td> parrot </td></tr>
+  </table>
+ 
+  <TT> Starts a piece of text displayed in a typewriter font.
+  </TT> 
+  <KBD> Starts a piece of text displayed in a typewriter font.
+  </KBD> 
+ 
+  <UL> Starts an unnumbered item list.
+  <LI> Starts a new list item 1.</LI> 
+  <LI> Starts a new list item 2.</LI> 
+  <LI> Starts a new list item 3.</LI> 
+  </UL> Ends an unnumbered item list.
+ 
+  <VAR> Starts a piece of text displayed in an italic font.
+  </VAR>
+ 
+  \htmlonly
+  <u>underlined \b bold text - doxy commands are ignored inside 'htmlonly' section </u>
+  \endhtmlonly
+  <u>underlined text</u>
+  """)
+
+
+commentVerifier.check(doxygen_translate.htmlEntitiesFunction.__doc__,
+r"""
+  All entities are treated as commands (C); TM  (R);
+  should work also<in text
+  >
+  &
+  '
+  "
+  '
+  '
+  "
+  "
+  -
+  --
+   
+  x
+  -
+  .
+  ~
+  <=
+  >=
+  <--
+  -->
+  Not an html entity - ignored by Doxygen.
+  Not an &text html entity - ampersand is replaced with entity.
+  """)
diff --git a/Source/DoxygenTranslator/src/PyDocConverter.cpp b/Source/DoxygenTranslator/src/PyDocConverter.cpp
index 675f2ae11..eed0645d2 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/PyDocConverter.cpp
@@ -46,8 +46,8 @@ void PyDocConverter::fillStaticTables() {
   sectionTitles["result"] = "Return: ";
   sectionTitles["return"] = "Return: ";
   sectionTitles["returns"] = "Returns: ";
-  sectionTitles["sa"] = "See also: ";
-  sectionTitles["see"] = "See also: ";
+//  sectionTitles["sa"] = "See also: ";
+//  sectionTitles["see"] = "See also: ";
   sectionTitles["since"] = "Since: ";
   sectionTitles["throw"] = "Throw: ";
   sectionTitles["throws"] = "Throws: ";
@@ -57,7 +57,7 @@ void PyDocConverter::fillStaticTables() {
   tagHandlers["a"] = make_pair(&PyDocConverter::handleTagWrap, "_");
   tagHandlers["b"] = make_pair(&PyDocConverter::handleTagWrap, "__");
   // \c command is translated as single quotes around next word
-  tagHandlers["c"] = make_pair(&PyDocConverter::handleTagWrap, "'");
+  tagHandlers["c"] = make_pair(&PyDocConverter::handleTagWrap, "'"); // see markdown support in doxy, section 'code wraps'
   tagHandlers["cite"] = make_pair(&PyDocConverter::handleTagWrap, "'");
   tagHandlers["e"] = make_pair(&PyDocConverter::handleTagWrap, "_");
   // these commands insert just a single char, some of them need to be escaped
@@ -101,8 +101,8 @@ void PyDocConverter::fillStaticTables() {
   tagHandlers["result"] = make_pair(&PyDocConverter::handleParagraph, "");
   tagHandlers["remark"] = make_pair(&PyDocConverter::handleParagraph, "");
   tagHandlers["remarks"] = make_pair(&PyDocConverter::handleParagraph, "");
-  tagHandlers["sa"] = make_pair(&PyDocConverter::handleParagraph, "");
-  tagHandlers["see"] = make_pair(&PyDocConverter::handleParagraph, "");
+  tagHandlers["sa"] = make_pair(&PyDocConverter::handleTagMessage, "See also: ");
+  tagHandlers["see"] = make_pair(&PyDocConverter::handleTagMessage, "See also: ");
   tagHandlers["since"] = make_pair(&PyDocConverter::handleParagraph, "");
   tagHandlers["short"] = make_pair(&PyDocConverter::handleParagraph, "");
   tagHandlers["throw"] = make_pair(&PyDocConverter::handleParagraph, "");
@@ -133,10 +133,87 @@ void PyDocConverter::fillStaticTables() {
   tagHandlers["plainstd::string"] = make_pair(&PyDocConverter::handlePlainString, "");
   tagHandlers["plainstd::endl"] = make_pair(&PyDocConverter::handleNewLine, "");
   tagHandlers["n"] = make_pair(&PyDocConverter::handleNewLine, "");
+
+  // \f commands output literal Latex formula, which is still better than nothing.
+  tagHandlers["f$"] = make_pair(&PyDocConverter::handleTagVerbatim, "");
+  tagHandlers["f["] = make_pair(&PyDocConverter::handleTagVerbatim, "");
+  tagHandlers["f{"] = make_pair(&PyDocConverter::handleTagVerbatim, "");
+
+  // HTML tags
+  tagHandlers["<a"      ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, ""      );
+  tagHandlers["<b"      ] = make_pair(&PyDocConverter::handleDoxyHtmlTag2, "__");
+  tagHandlers["<blockquote"] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "");
+  tagHandlers["<body"   ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, ""   );
+  tagHandlers["<br"     ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "\n"     );
+  tagHandlers["<center" ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "" );
+  tagHandlers["<caption"] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "");
+  tagHandlers["<code"   ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, ""   );
+  tagHandlers["<dd"     ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, ""     );
+  tagHandlers["<dfn"    ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, ""    );
+  tagHandlers["<div"    ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, ""    );
+  tagHandlers["<dl"     ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, ""     );
+  tagHandlers["<dt"     ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, ""     );
+  tagHandlers["<em"     ] = make_pair(&PyDocConverter::handleDoxyHtmlTag2, "_");
+  tagHandlers["<form"   ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, ""   );
+  tagHandlers["<hr"     ] = make_pair(&PyDocConverter::handleDoxyHtmlTag,
+              "--------------------------------------------------------------------\n"     );
+  tagHandlers["<h1"     ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "# "     );
+  tagHandlers["<h2"     ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "##"     );
+  tagHandlers["<h3"     ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "###"     );
+  tagHandlers["<i"      ] = make_pair(&PyDocConverter::handleDoxyHtmlTag2, "_");
+  tagHandlers["<input"  ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, ""  );
+  tagHandlers["<img"    ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "Image:"  );
+  tagHandlers["<li"     ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "- "     );
+  tagHandlers["<meta"   ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, ""   );
+  tagHandlers["<multicol"] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "");
+  tagHandlers["<ol"     ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, ""     );
+  tagHandlers["<p"      ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "\n\n"      );
+  tagHandlers["<pre"    ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, ""    );
+  tagHandlers["<small"  ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, ""  );
+  tagHandlers["<span"   ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, ""   );
+  tagHandlers["<strong" ] = make_pair(&PyDocConverter::handleDoxyHtmlTag2, "__");
+  tagHandlers["<sub"    ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, ""    );
+  tagHandlers["<sup"    ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, ""    );
+  tagHandlers["<table"  ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, ""  );
+  tagHandlers["<td"     ] = make_pair(&PyDocConverter::handleDoxyHtmlTag_td, "");
+  tagHandlers["<th"     ] = make_pair(&PyDocConverter::handleDoxyHtmlTag_th, "");
+  tagHandlers["<tr"     ] = make_pair(&PyDocConverter::handleDoxyHtmlTag_tr, "");
+  tagHandlers["<tt"     ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "");
+  tagHandlers["<kbd"    ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "");
+  tagHandlers["<ul"     ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "");
+  tagHandlers["<var"    ] = make_pair(&PyDocConverter::handleDoxyHtmlTag2, "_");
+
+  // HTML entities
+  tagHandlers["&copy" ] = make_pair(&PyDocConverter::handleHtmlEntity, "(C)");
+  tagHandlers["&trade"] = make_pair(&PyDocConverter::handleHtmlEntity, " TM");
+  tagHandlers["&reg"  ] = make_pair(&PyDocConverter::handleHtmlEntity, "(R)");
+  tagHandlers["&lt"   ] = make_pair(&PyDocConverter::handleHtmlEntity, "<");
+  tagHandlers["&gt"   ] = make_pair(&PyDocConverter::handleHtmlEntity, ">");
+  tagHandlers["&amp"  ] = make_pair(&PyDocConverter::handleHtmlEntity, "&");
+  tagHandlers["&apos" ] = make_pair(&PyDocConverter::handleHtmlEntity, "'");
+  tagHandlers["&quot" ] = make_pair(&PyDocConverter::handleHtmlEntity, "\"");
+  tagHandlers["&lsquo"] = make_pair(&PyDocConverter::handleHtmlEntity, "`");
+  tagHandlers["&rsquo"] = make_pair(&PyDocConverter::handleHtmlEntity, "'");
+  tagHandlers["&ldquo"] = make_pair(&PyDocConverter::handleHtmlEntity, "\"");
+  tagHandlers["&rdquo"] = make_pair(&PyDocConverter::handleHtmlEntity, "\"");
+  tagHandlers["&ndash"] = make_pair(&PyDocConverter::handleHtmlEntity, "-");
+  tagHandlers["&mdash"] = make_pair(&PyDocConverter::handleHtmlEntity, "--");
+  tagHandlers["&nbsp" ] = make_pair(&PyDocConverter::handleHtmlEntity, " ");
+  tagHandlers["&times"] = make_pair(&PyDocConverter::handleHtmlEntity, "x");
+  tagHandlers["&minus"] = make_pair(&PyDocConverter::handleHtmlEntity, "-");
+  tagHandlers["&sdot" ] = make_pair(&PyDocConverter::handleHtmlEntity, ".");
+  tagHandlers["&sim"  ] = make_pair(&PyDocConverter::handleHtmlEntity, "~");
+  tagHandlers["&le"   ] = make_pair(&PyDocConverter::handleHtmlEntity, "<=");
+  tagHandlers["&ge"   ] = make_pair(&PyDocConverter::handleHtmlEntity, ">=");
+  tagHandlers["&larr" ] = make_pair(&PyDocConverter::handleHtmlEntity, "<--");
+  tagHandlers["&rarr" ] = make_pair(&PyDocConverter::handleHtmlEntity, "-->");
 }
 
 PyDocConverter::PyDocConverter(bool debugTranslator, bool debugParser)
-: DoxygenTranslator(debugTranslator, debugParser) {
+: DoxygenTranslator(debugTranslator, debugParser),
+  m_tableLineLen(0),
+  m_prevRowIsTH(false)
+{
   fillStaticTables();
 }
 
@@ -228,6 +305,16 @@ void PyDocConverter::handlePlainString(DoxygenEntity& tag, std::string& translat
 }
 
 
+void PyDocConverter::handleTagVerbatim(DoxygenEntity& tag,
+                                            std::string& translatedComment,
+                                            std::string &arg) {
+  translatedComment += arg + " ";
+  for (DoxygenEntityListCIt it = tag.entityList.begin(); it != tag.entityList.end(); it++) {
+      translatedComment += it->data;
+  }
+}
+
+
 void PyDocConverter::handleTagMessage(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
   std::string dummy;
   translatedComment += arg;
@@ -305,6 +392,89 @@ void PyDocConverter::handleTagWrap(DoxygenEntity& tag, std::string& translatedCo
 }
 
 
+void PyDocConverter::handleDoxyHtmlTag(DoxygenEntity& tag,
+                                            std::string& translatedComment,
+                                            std::string &arg) {
+    std::string htmlTagArgs = tag.data;
+    if (htmlTagArgs == "/") {
+        // end html tag, for example "</ul>
+        // translatedComment += "</" + arg.substr(1) + ">";
+    } else {
+        translatedComment += arg + htmlTagArgs;
+    }
+}
+
+
+void PyDocConverter::handleDoxyHtmlTag2(DoxygenEntity& tag,
+                                             std::string& translatedComment,
+                                             std::string &arg) {
+    std::string htmlTagArgs = tag.data;
+    if (htmlTagArgs == "/") {
+        // end html tag, for example "</em>
+        translatedComment += arg;
+    } else {
+        translatedComment += arg;
+    }
+}
+
+void PyDocConverter::handleDoxyHtmlTag_tr(DoxygenEntity& tag,
+                                                std::string& translatedComment,
+                                                std::string &) {
+    std::string htmlTagArgs = tag.data;
+    if (htmlTagArgs == "/") {
+      // end tag, </tr> appends vertical table line '|'
+      translatedComment += '|';
+      size_t nlPos = translatedComment.rfind('\n');
+      if (nlPos != string::npos) {
+        size_t startOfTableLinePos = translatedComment.find_first_not_of(" \t", nlPos);
+        if (startOfTableLinePos != string::npos) {
+          m_tableLineLen = translatedComment.size() - startOfTableLinePos;
+        }
+      }
+    } else {
+      if (m_prevRowIsTH) {
+        // if previous row contained <th> tag, add horizontal separator
+        translatedComment += string('_', m_tableLineLen);
+        m_prevRowIsTH = false;
+      }
+    }
+}
+
+
+void PyDocConverter::handleDoxyHtmlTag_th(DoxygenEntity& tag,
+                                                std::string& translatedComment,
+                                                std::string &) {
+    std::string htmlTagArgs = tag.data;
+    if (htmlTagArgs == "/") {
+      // end tag, </th> is ignored
+    } else {
+        translatedComment += '|';
+        m_prevRowIsTH = true;
+    }
+}
+
+
+void PyDocConverter::handleDoxyHtmlTag_td(DoxygenEntity& tag,
+                                                std::string& translatedComment,
+                                                std::string &) {
+    std::string htmlTagArgs = tag.data;
+    if (htmlTagArgs == "/") {
+        // end tag, </td> is ignored
+    } else {
+      translatedComment += '|';
+    }
+}
+
+
+
+void PyDocConverter::handleHtmlEntity(DoxygenEntity&,
+                                           std::string& translatedComment,
+                                           std::string &arg) {
+    // html entities
+    translatedComment += arg;
+}
+
+
 void PyDocConverter::handleNewLine(DoxygenEntity&, std::string& translatedComment, std::string&) {
   translatedComment += "\n";
 }
diff --git a/Source/DoxygenTranslator/src/PyDocConverter.h b/Source/DoxygenTranslator/src/PyDocConverter.h
index ee4d436c3..97f742ff4 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.h
+++ b/Source/DoxygenTranslator/src/PyDocConverter.h
@@ -29,6 +29,10 @@ public:
   String *makeDocumentation(Node *node);
 
 protected:
+
+  size_t m_tableLineLen;
+  bool m_prevRowIsTH;
+
   /*
    * Format a string so it is justified and split over several lines 
    * not exeeding a given length.
@@ -74,6 +78,14 @@ protected:
    * Print only data part of code
    */
   void handlePlainString(DoxygenEntity &tag, std::string &translatedComment, std::string &arg);
+
+  /**
+   * Copies verbatim args of the tag to output, used for commands like \f$, ...
+   */
+  void handleTagVerbatim(DoxygenEntity& tag,
+                            std::string& translatedComment,
+                            std::string &arg);
+
   /*
    * Print the if-elseif-else-endif section
    */
@@ -96,6 +108,34 @@ protected:
    */
   void handleTagParam(DoxygenEntity &tag, std::string &translatedComment, std::string &arg);
 
+  /* Handles HTML tags recognized by Doxygen, like <A ...>, <ul>, <table>, ... */
+
+  void handleDoxyHtmlTag(DoxygenEntity& tag, std::string& translatedComment, std::string &arg);
+
+  /*
+   * Handles HTML tags, which are translated to markdown-like syntax, for example
+   * <i>text</i>  -->  _text_. Appends arg for start HTML tag and end HTML tag.
+   */
+  void handleDoxyHtmlTag2(DoxygenEntity& tag,
+                             std::string& translatedComment,
+                             std::string &arg);
+
+  /* Handles HTML table, tag <tr> */
+  void handleDoxyHtmlTag_tr(DoxygenEntity& tag, std::string& translatedComment,
+                               std::string &arg);
+
+  /* Handles HTML table, tag <th> */
+  void handleDoxyHtmlTag_th(DoxygenEntity& tag, std::string& translatedComment,
+                               std::string &arg);
+
+  /* Handles HTML table, tag <td> */
+  void handleDoxyHtmlTag_td(DoxygenEntity& tag, std::string& translatedComment,
+                                std::string &arg);
+
+  /* Handles HTML entities recognized by Doxygen, like &lt;, &copy;, ... */
+  void handleHtmlEntity(DoxygenEntity&, std::string& translatedComment, std::string &arg);
+
+
   /*
    * Utility method to generate a diving line for a documentation string.
    */

From 0b6bc8003846ff8cf1e38259297fcb7f1f60e063 Mon Sep 17 00:00:00 2001
From: Marko Klopcic <markok3.14@gmail.com>
Date: Wed, 13 Feb 2013 23:06:20 +0100
Subject: [PATCH 178/314] Translation of HTML tags to Python almost finished

---
 Examples/test-suite/doxygen_translate.i       |  83 +++++------
 .../python/doxygen_translate_links_runme.py   |  42 ++++++
 .../python/doxygen_translate_runme.py         | 138 ++++++++----------
 .../DoxygenTranslator/src/PyDocConverter.cpp  |  77 +++++++---
 Source/DoxygenTranslator/src/PyDocConverter.h |  13 ++
 5 files changed, 216 insertions(+), 137 deletions(-)
 create mode 100644 Examples/test-suite/python/doxygen_translate_links_runme.py

diff --git a/Examples/test-suite/doxygen_translate.i b/Examples/test-suite/doxygen_translate.i
index 181c0799e..e338e8a8c 100644
--- a/Examples/test-suite/doxygen_translate.i
+++ b/Examples/test-suite/doxygen_translate.i
@@ -128,67 +128,64 @@ int function(int a, float b)
 /**
  * Test for html tags. See Doxygen doc for list of tags recognized by Doxygen.
  *
- * <a href = "http://acme.com/index.html">This is link</a>
+ * <a href="http://acme.com/index.html">This is link</a>
  * <b>bold</b>
- * <BLOCKQUOTE>
+ * <BLOCKQUOTE cite="http://www.worldwildlife.org/who/index.html">
  * Quotation block.
  * </BLOCKQUOTE>
  * <br>
  * <center>center</center>
  * <code>this is code</code>
- * <DD> Starts an item description.
- * <DFN> Starts a piece of text displayed in a typewriter font.
+ *
+ * <DL>
+ * <DT>Starts an item title.</DT>
+ * <DD>Starts an item description.</dd>
+ * </dl>
+ *
+ * <DFN>Starts a piece of text displayed in a typewriter font.
  * </DFN> 
- * <DIV> Starts a section with a specific style (HTML only)
+ * <DIV>Starts a section with a specific style (HTML only)
  * </DIV> 
- * <DL> Starts a description list.
- * <DT> Starts an item title.</DT>
- * </DL> 
- * <EM> Starts a piece of text displayed in an italic font.
+ * <EM>Starts a piece of text displayed in an italic font.
  * </EM> 
- * <FORM> 'Form' does not generate any output.
+ * <FORM>'Form' does not generate any output.
  * </FORM>
  * <HR> 
- * <H1> Starts an unnumbered section.
+ * <H1>Heading 1
  * </H1>
- * <H2> Starts an unnumbered subsection.
+ * <H2>Heading 2
  * </H2> 
- * <H3> Starts an unnumbered subsubsection.
+ * <H3>Heading 3
  * </H3> 
- * <I> Starts a piece of text displayed in an italic font.
- * <INPUT> Does not generate any output.
- * </I> 
+ * <I>Starts a piece of text displayed in an italic font.</I>
+ * <INPUT>Input tag.
  * <IMG src="slika.png"> 
- * <META> Does not generate any output.
- * <MULTICOL> ignored by doxygen.
- * </MULTICOL> ignored by doxygen.
+ * <META>Meta tag.
+ * <MULTICOL>Multicol is ignored by doxygen.
+ * </MULTICOL>
  *
- * <OL> Starts a numbered item list.
- * <LI> Starts a new list item.
- * </LI> 
- * </OL> Ends a numbered item list.
+ * <OL>
+ * <LI>List item 1.</LI> 
+ * <LI>List item 2.</LI> 
+ * </OL> 
  *
- * <P> Starts a new paragraph.
+ * <P>Starts a new paragraph.
  * </P> 
- * <PRE> Starts a preformatted fragment.
+ * <PRE>Starts a preformatted fragment.
  * </PRE>
- * <SMALL> Starts a section of text displayed in a smaller font.
+ * <SMALL>Starts a section of text displayed in a smaller font.
  * </SMALL>
- * <SPAN> Starts an inline text fragment with a specific style (HTML only)
- * </SPAN>
- * <STRONG> Starts a section of bold text.
- * </STRONG>
- * <SUB> Starts a piece of text displayed in subscript.
- * </SUB>
- * <SUP> Starts a piece of text displayed in superscript.
- * </SUP>
+ * <SPAN>Starts an inline text fragment with a specific style.</SPAN>
+ * <STRONG>Starts a section of bold text.</STRONG>
+ * <SUB>Starts a piece of text displayed in subscript.</SUB>
+ * <SUP>Starts a piece of text displayed in superscript.</SUP>
  *
  * <table border = '1'>
  * <caption>Animals</caption>
- * <tr><th> cow   </th><th> dog    </th></tr>
- * <tr><td> cow   </td><td> dog    </td></tr>
- * <tr><td> cat   </td><td> mouse  </td></tr>
- * <tr><td> horse </td><td> parrot </td></tr>
+  <tr><th> Column 1 </th><th> Column 2 </th></tr>
+  <tr><td> cow      </td><td> dog      </td></tr>
+  <tr><td> cat      </td><td> mouse    </td></tr>
+  <tr><td> horse    </td><td> parrot   </td></tr>
  * </table>
  *
  * <TT> Starts a piece of text displayed in a typewriter font.
@@ -197,18 +194,16 @@ int function(int a, float b)
  * </KBD> 
  *
  * <UL> Starts an unnumbered item list.
- * <LI> Starts a new list item 1.</LI> 
- * <LI> Starts a new list item 2.</LI> 
- * <LI> Starts a new list item 3.</LI> 
+ * <LI> List item 1.</LI> 
+ * <LI> List item 2.</LI> 
+ * <LI> List item 3.</LI> 
  * </UL> Ends an unnumbered item list.
  *
- * <VAR> Starts a piece of text displayed in an italic font.
- * </VAR>
+ * <VAR>Starts a piece of text displayed in an italic font.</VAR>
  *
  * \htmlonly
  * <u>underlined \b bold text - doxy commands are ignored inside 'htmlonly' section </u>
  * \endhtmlonly
- * <u>underlined text</u>
  */
 int htmlFunction(int a, float b)
 {
diff --git a/Examples/test-suite/python/doxygen_translate_links_runme.py b/Examples/test-suite/python/doxygen_translate_links_runme.py
new file mode 100644
index 000000000..b56acf77c
--- /dev/null
+++ b/Examples/test-suite/python/doxygen_translate_links_runme.py
@@ -0,0 +1,42 @@
+#!/usr/bin/python
+
+import doxygen_translate_links
+import string
+import sys
+import commentVerifier
+
+
+commentVerifier.check(doxygen_translate_links.function.__doc__,
+r"""
+  Testing typenames converting in @ link
+
+  superFunc(int,std::string)
+  Test for std_string member
+
+
+  superFunc(int,long,void*)
+  Test for simple types
+
+
+  superFunc(Shape::superType*)
+  Test for custom types
+
+
+  superFunc(int**[13])
+  Test for complex types
+
+
+  same works for 'See also:' links:
+
+  See also: superFunc(int,std::string)
+  See also: superFunc(int,long,void*)
+  See also: superFunc(Shape::superType*)
+  See also: superFunc(int**[13])
+
+  some failing params:
+
+  See also: superFunc()
+  See also: superFunc()
+  See also: superFunc()
+
+  """)
diff --git a/Examples/test-suite/python/doxygen_translate_runme.py b/Examples/test-suite/python/doxygen_translate_runme.py
index fe5b06a5b..5f667f327 100755
--- a/Examples/test-suite/python/doxygen_translate_runme.py
+++ b/Examples/test-suite/python/doxygen_translate_runme.py
@@ -138,87 +138,77 @@ commentVerifier.check(doxygen_translate.htmlFunction.__doc__,
 r"""
   Test for html tags. See Doxygen doc for list of tags recognized by Doxygen.
  
-  <a href = "http://acme.com/index.html">This is link</a>
-  <b>bold</b>
-  <BLOCKQUOTE>
+  This is link (http://acme.com/index.html)
+  __bold__
+  Quote:
   Quotation block.
-  </BLOCKQUOTE>
-  <br>
-  <center>center</center>
-  <code>this is code</code>
-  <DD> Starts an item description.
-  <DFN> Starts a piece of text displayed in a typewriter font.
-  </DFN> 
-  <DIV> Starts a section with a specific style (HTML only)
-  </DIV> 
-  <DL> Starts a description list.
-  <DT> Starts an item title.</DT>
-  </DL> 
-  <EM> Starts a piece of text displayed in an italic font.
-  </EM> 
-  <FORM> 'Form' does not generate any output.
-  </FORM>
-  <HR> 
-  <H1> Starts an unnumbered section.
-  </H1>
-  <H2> Starts an unnumbered subsection.
-  </H2> 
-  <H3> Starts an unnumbered subsubsection.
-  </H3> 
-  <I> Starts a piece of text displayed in an italic font.
-  <INPUT> Does not generate any output.
-  </I> 
-  <IMG src="slika.png"> 
-  <META> Does not generate any output.
-  <MULTICOL> ignored by doxygen.
-  </MULTICOL> ignored by doxygen.
+   ("http://www.worldwildlife.org/who/index.html")
+
+
+  center
+  'this is code'
+
+
+  Starts an item title.
+      Starts an item description.
+
+
+  Starts a piece of text displayed in a typewriter font.
+                      
+  Starts a section with a specific style (HTML only)
+
+  __Starts a piece of text displayed in an italic font.__
+
+  'Form' does not generate any output.
+
+  --------------------------------------------------------------------
+  # Heading 1
+
+  ## Heading 2
+
+  ### Heading 3
+
+  _Starts a piece of text displayed in an italic font._
+  Input tag.
+  Image:src="slika.png"> 
+  Meta tag.
+  Multicol is ignored by doxygen.
+
+  - List item 1.
+  - List item 2.
+
+
+  Starts a new paragraph.
+
+  Starts a preformatted fragment.
+
+  Starts a section of text displayed in a smaller font.
+
+  'Starts an inline text fragment with a specific style.'
+
+  __Starts a section of bold text.__
+   Starts a piece of text displayed in subscript.
+   Starts a piece of text displayed in superscript.
+
  
-  <OL> Starts a numbered item list.
-  <LI> Starts a new list item.
-  </LI> 
-  </OL> Ends a numbered item list.
+  Animals
+  | Column 1 | Column 2 |
+  -----------------------
+  | cow      | dog      |
+  | cat      | mouse    |
+  | horse    | parrot   |
  
-  <P> Starts a new paragraph.
-  </P> 
-  <PRE> Starts a preformatted fragment.
-  </PRE>
-  <SMALL> Starts a section of text displayed in a smaller font.
-  </SMALL>
-  <SPAN> Starts an inline text fragment with a specific style (HTML only)
-  </SPAN>
-  <STRONG> Starts a section of bold text.
-  </STRONG>
-  <SUB> Starts a piece of text displayed in subscript.
-  </SUB>
-  <SUP> Starts a piece of text displayed in superscript.
-  </SUP>
+  Starts a piece of text displayed in a typewriter font.
+                      
+  Starts a piece of text displayed in a typewriter font.
  
-  <table border = '1'>
-  <caption>Animals</caption>
-  <tr><th> cow   </th><th> dog    </th></tr>
-  <tr><td> cow   </td><td> dog    </td></tr>
-  <tr><td> cat   </td><td> mouse  </td></tr>
-  <tr><td> horse </td><td> parrot </td></tr>
-  </table>
+  - List item 1.
+  - List item 2.
+  - List item 3.
  
-  <TT> Starts a piece of text displayed in a typewriter font.
-  </TT> 
-  <KBD> Starts a piece of text displayed in a typewriter font.
-  </KBD> 
+  _Starts a piece of text displayed in an italic font._
  
-  <UL> Starts an unnumbered item list.
-  <LI> Starts a new list item 1.</LI> 
-  <LI> Starts a new list item 2.</LI> 
-  <LI> Starts a new list item 3.</LI> 
-  </UL> Ends an unnumbered item list.
- 
-  <VAR> Starts a piece of text displayed in an italic font.
-  </VAR>
- 
-  \htmlonly
   <u>underlined \b bold text - doxy commands are ignored inside 'htmlonly' section </u>
-  \endhtmlonly
-  <u>underlined text</u>
   """)
 
 
diff --git a/Source/DoxygenTranslator/src/PyDocConverter.cpp b/Source/DoxygenTranslator/src/PyDocConverter.cpp
index eed0645d2..7200a2de6 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/PyDocConverter.cpp
@@ -140,41 +140,49 @@ void PyDocConverter::fillStaticTables() {
   tagHandlers["f{"] = make_pair(&PyDocConverter::handleTagVerbatim, "");
 
   // HTML tags
-  tagHandlers["<a"      ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, ""      );
+  tagHandlers["<a"      ] = make_pair(&PyDocConverter::handleDoxyHtmlTag_A, ""      );
   tagHandlers["<b"      ] = make_pair(&PyDocConverter::handleDoxyHtmlTag2, "__");
-  tagHandlers["<blockquote"] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "");
+  tagHandlers["<blockquote"] = make_pair(&PyDocConverter::handleDoxyHtmlTag_A, "Quote: ");
   tagHandlers["<body"   ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, ""   );
   tagHandlers["<br"     ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "\n"     );
+
+  // there is no formatting for this tag as it was deprecated in HTML 4.01 and
+  // not used in HTML 5
   tagHandlers["<center" ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "" );
   tagHandlers["<caption"] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "");
-  tagHandlers["<code"   ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, ""   );
-  tagHandlers["<dd"     ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, ""     );
+  tagHandlers["<code"   ] = make_pair(&PyDocConverter::handleDoxyHtmlTag2, "'"   );
+
+  tagHandlers["<dl"     ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "");
+  tagHandlers["<dd"     ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "    ");
+  tagHandlers["<dt"     ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "");
+
   tagHandlers["<dfn"    ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, ""    );
   tagHandlers["<div"    ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, ""    );
-  tagHandlers["<dl"     ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, ""     );
-  tagHandlers["<dt"     ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, ""     );
-  tagHandlers["<em"     ] = make_pair(&PyDocConverter::handleDoxyHtmlTag2, "_");
+  tagHandlers["<em"     ] = make_pair(&PyDocConverter::handleDoxyHtmlTag2, "__");
   tagHandlers["<form"   ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, ""   );
   tagHandlers["<hr"     ] = make_pair(&PyDocConverter::handleDoxyHtmlTag,
               "--------------------------------------------------------------------\n"     );
   tagHandlers["<h1"     ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "# "     );
-  tagHandlers["<h2"     ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "##"     );
-  tagHandlers["<h3"     ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "###"     );
+  tagHandlers["<h2"     ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "## "     );
+  tagHandlers["<h3"     ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "### "     );
   tagHandlers["<i"      ] = make_pair(&PyDocConverter::handleDoxyHtmlTag2, "_");
   tagHandlers["<input"  ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, ""  );
   tagHandlers["<img"    ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "Image:"  );
-  tagHandlers["<li"     ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "- "     );
-  tagHandlers["<meta"   ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, ""   );
+  tagHandlers["<li"     ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "- ");
+  tagHandlers["<meta"   ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "");
   tagHandlers["<multicol"] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "");
-  tagHandlers["<ol"     ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, ""     );
-  tagHandlers["<p"      ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "\n\n"      );
+  tagHandlers["<ol"     ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "");
+  tagHandlers["<p"      ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "\n");
   tagHandlers["<pre"    ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, ""    );
   tagHandlers["<small"  ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, ""  );
-  tagHandlers["<span"   ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, ""   );
+  tagHandlers["<span"   ] = make_pair(&PyDocConverter::handleDoxyHtmlTag2, "'"   );
   tagHandlers["<strong" ] = make_pair(&PyDocConverter::handleDoxyHtmlTag2, "__");
-  tagHandlers["<sub"    ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, ""    );
-  tagHandlers["<sup"    ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, ""    );
-  tagHandlers["<table"  ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, ""  );
+
+  // make a space between text and super/sub script.
+  tagHandlers["<sub"    ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, " ");
+  tagHandlers["<sup"    ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, " ");
+
+  tagHandlers["<table"  ] = make_pair(&PyDocConverter::handleDoxyHtmlTagNoParam, "");
   tagHandlers["<td"     ] = make_pair(&PyDocConverter::handleDoxyHtmlTag_td, "");
   tagHandlers["<th"     ] = make_pair(&PyDocConverter::handleDoxyHtmlTag_th, "");
   tagHandlers["<tr"     ] = make_pair(&PyDocConverter::handleDoxyHtmlTag_tr, "");
@@ -405,6 +413,37 @@ void PyDocConverter::handleDoxyHtmlTag(DoxygenEntity& tag,
 }
 
 
+void PyDocConverter::handleDoxyHtmlTagNoParam(DoxygenEntity& tag,
+                                                    std::string& translatedComment,
+                                                    std::string &arg) {
+    std::string htmlTagArgs = tag.data;
+    if (htmlTagArgs == "/") {
+        // end html tag, for example "</ul>
+    } else {
+        translatedComment += arg;
+    }
+}
+
+
+void PyDocConverter::handleDoxyHtmlTag_A(DoxygenEntity& tag,
+                                              std::string& translatedComment,
+                                              std::string &arg) {
+    std::string htmlTagArgs = tag.data;
+    if (htmlTagArgs == "/") {
+        // end html tag, "</a>
+        translatedComment += " (" + m_url + ')';
+        m_url.clear();
+    } else {
+      m_url.clear();
+      size_t pos = htmlTagArgs.find('=');
+      if (pos != string::npos) {
+        m_url = htmlTagArgs.substr(pos + 1);
+      }
+      translatedComment += arg;
+    }
+}
+
+
 void PyDocConverter::handleDoxyHtmlTag2(DoxygenEntity& tag,
                                              std::string& translatedComment,
                                              std::string &arg) {
@@ -428,13 +467,13 @@ void PyDocConverter::handleDoxyHtmlTag_tr(DoxygenEntity& tag,
       if (nlPos != string::npos) {
         size_t startOfTableLinePos = translatedComment.find_first_not_of(" \t", nlPos);
         if (startOfTableLinePos != string::npos) {
-          m_tableLineLen = translatedComment.size() - startOfTableLinePos;
+          m_tableLineLen = translatedComment.size() - startOfTableLinePos - 1;
         }
       }
     } else {
       if (m_prevRowIsTH) {
         // if previous row contained <th> tag, add horizontal separator
-        translatedComment += string('_', m_tableLineLen);
+        translatedComment += string(m_tableLineLen, '-') + '\n';
         m_prevRowIsTH = false;
       }
     }
diff --git a/Source/DoxygenTranslator/src/PyDocConverter.h b/Source/DoxygenTranslator/src/PyDocConverter.h
index 97f742ff4..ec831a1a2 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.h
+++ b/Source/DoxygenTranslator/src/PyDocConverter.h
@@ -32,6 +32,7 @@ protected:
 
   size_t m_tableLineLen;
   bool m_prevRowIsTH;
+  std::string m_url;
 
   /*
    * Format a string so it is justified and split over several lines 
@@ -112,6 +113,18 @@ protected:
 
   void handleDoxyHtmlTag(DoxygenEntity& tag, std::string& translatedComment, std::string &arg);
 
+  /** Does not ouput params of HTML tag, for example in <table border='1'>
+   * 'border=1' is not written to output.
+   */
+  void handleDoxyHtmlTagNoParam(DoxygenEntity& tag,
+                                    std::string& translatedComment,
+                                    std::string &arg);
+
+  /** TRanslates tag <a href = "url">text</a> to: text ("url"). */
+  void handleDoxyHtmlTag_A(DoxygenEntity& tag,
+                              std::string& translatedComment,
+                              std::string &arg);
+
   /*
    * Handles HTML tags, which are translated to markdown-like syntax, for example
    * <i>text</i>  -->  _text_. Appends arg for start HTML tag and end HTML tag.

From 9b52972c2431d64348ecb58d865839f43639127a Mon Sep 17 00:00:00 2001
From: Marko Klopcic <markok3.14@gmail.com>
Date: Thu, 14 Feb 2013 21:53:09 +0100
Subject: [PATCH 179/314] HTML tags and entities tests pass for Python

---
 Examples/test-suite/doxygen_translate.i       | 40 +++++++++----------
 .../python/doxygen_translate_runme.py         | 39 +++++++++++-------
 2 files changed, 44 insertions(+), 35 deletions(-)

diff --git a/Examples/test-suite/doxygen_translate.i b/Examples/test-suite/doxygen_translate.i
index e338e8a8c..03e9471f8 100644
--- a/Examples/test-suite/doxygen_translate.i
+++ b/Examples/test-suite/doxygen_translate.i
@@ -143,20 +143,20 @@ int function(int a, float b)
  * </dl>
  *
  * <DFN>Starts a piece of text displayed in a typewriter font.
- * </DFN> 
+ * </DFN>
  * <DIV>Starts a section with a specific style (HTML only)
- * </DIV> 
- * <EM>Starts a piece of text displayed in an italic font.
- * </EM> 
+ * </DIV>
+ * <EM>Starts a piece of text displayed in an italic font.</EM>
+ *
  * <FORM>'Form' does not generate any output.
  * </FORM>
- * <HR> 
+ * <HR>
  * <H1>Heading 1
  * </H1>
  * <H2>Heading 2
- * </H2> 
+ * </H2>
  * <H3>Heading 3
- * </H3> 
+ * </H3>
  * <I>Starts a piece of text displayed in an italic font.</I>
  * <INPUT>Input tag.
  * <IMG src="slika.png"> 
@@ -165,12 +165,12 @@ int function(int a, float b)
  * </MULTICOL>
  *
  * <OL>
- * <LI>List item 1.</LI> 
- * <LI>List item 2.</LI> 
- * </OL> 
+ * <LI>List item 1.</LI>
+ * <LI>List item 2.</LI>
+ * </OL>
  *
  * <P>Starts a new paragraph.
- * </P> 
+ * </P>
  * <PRE>Starts a preformatted fragment.
  * </PRE>
  * <SMALL>Starts a section of text displayed in a smaller font.
@@ -188,16 +188,16 @@ int function(int a, float b)
   <tr><td> horse    </td><td> parrot   </td></tr>
  * </table>
  *
- * <TT> Starts a piece of text displayed in a typewriter font.
- * </TT> 
- * <KBD> Starts a piece of text displayed in a typewriter font.
- * </KBD> 
+ * <TT>Starts a piece of text displayed in a typewriter font.
+ * </TT>
+ * <KBD>Starts a piece of text displayed in a typewriter font.
+ * </KBD>
  *
- * <UL> Starts an unnumbered item list.
- * <LI> List item 1.</LI> 
- * <LI> List item 2.</LI> 
- * <LI> List item 3.</LI> 
- * </UL> Ends an unnumbered item list.
+ * <UL>
+ * <LI>List item 1.</LI>
+ * <LI>List item 2.</LI>
+ * <LI>List item 3.</LI>
+ * </UL>
  *
  * <VAR>Starts a piece of text displayed in an italic font.</VAR>
  *
diff --git a/Examples/test-suite/python/doxygen_translate_runme.py b/Examples/test-suite/python/doxygen_translate_runme.py
index 5f667f327..183558415 100755
--- a/Examples/test-suite/python/doxygen_translate_runme.py
+++ b/Examples/test-suite/python/doxygen_translate_runme.py
@@ -137,10 +137,10 @@ r"""
 commentVerifier.check(doxygen_translate.htmlFunction.__doc__,
 r"""
   Test for html tags. See Doxygen doc for list of tags recognized by Doxygen.
- 
-  This is link (http://acme.com/index.html)
+
+  This is link ("http://acme.com/index.html")
   __bold__
-  Quote:
+  Quote: 
   Quotation block.
    ("http://www.worldwildlife.org/who/index.html")
 
@@ -154,7 +154,7 @@ r"""
 
 
   Starts a piece of text displayed in a typewriter font.
-                      
+
   Starts a section with a specific style (HTML only)
 
   __Starts a piece of text displayed in an italic font.__
@@ -162,6 +162,7 @@ r"""
   'Form' does not generate any output.
 
   --------------------------------------------------------------------
+
   # Heading 1
 
   ## Heading 2
@@ -170,14 +171,17 @@ r"""
 
   _Starts a piece of text displayed in an italic font._
   Input tag.
-  Image:src="slika.png"> 
+  Image: src="slika.png" 
   Meta tag.
   Multicol is ignored by doxygen.
 
+
+
   - List item 1.
   - List item 2.
 
 
+
   Starts a new paragraph.
 
   Starts a preformatted fragment.
@@ -185,42 +189,47 @@ r"""
   Starts a section of text displayed in a smaller font.
 
   'Starts an inline text fragment with a specific style.'
-
   __Starts a section of bold text.__
    Starts a piece of text displayed in subscript.
    Starts a piece of text displayed in superscript.
 
- 
+
   Animals
   | Column 1 | Column 2 |
   -----------------------
   | cow      | dog      |
   | cat      | mouse    |
   | horse    | parrot   |
- 
+
+
   Starts a piece of text displayed in a typewriter font.
-                      
+
   Starts a piece of text displayed in a typewriter font.
- 
+
+
+
   - List item 1.
   - List item 2.
   - List item 3.
- 
+
+
   _Starts a piece of text displayed in an italic font._
- 
+
+
   <u>underlined \b bold text - doxy commands are ignored inside 'htmlonly' section </u>
+
   """)
 
 
 commentVerifier.check(doxygen_translate.htmlEntitiesFunction.__doc__,
 r"""
-  All entities are treated as commands (C); TM  (R);
+  All entities are treated as commands (C)  TM (R)
   should work also<in text
   >
   &
   '
   "
-  '
+  `
   '
   "
   "
@@ -235,6 +244,6 @@ r"""
   >=
   <--
   -->
-  Not an html entity - ignored by Doxygen.
+  Not an  html entity - ignored by Doxygen.
   Not an &text html entity - ampersand is replaced with entity.
   """)

From fa8fc4baf3ccd75c19f2081ee750264c0aea7f72 Mon Sep 17 00:00:00 2001
From: Marko Klopcic <markok3.14@gmail.com>
Date: Fri, 15 Feb 2013 23:05:14 +0100
Subject: [PATCH 180/314] all doxygen tests pass

---
 Examples/test-suite/doxygen_misc_constructs.i |  2 +-
 .../java/doxygen_basic_translate_runme.java   | 10 +--
 .../java/doxygen_translate_runme.java         | 74 +++++++++----------
 .../python/doxygen_misc_constructs_runme.py   |  5 +-
 .../doxygen_translate_all_tags_runme.py       |  2 +-
 5 files changed, 47 insertions(+), 46 deletions(-)

diff --git a/Examples/test-suite/doxygen_misc_constructs.i b/Examples/test-suite/doxygen_misc_constructs.i
index 0eee8aa9d..9426b5909 100644
--- a/Examples/test-suite/doxygen_misc_constructs.i
+++ b/Examples/test-suite/doxygen_misc_constructs.i
@@ -60,7 +60,7 @@
      * used for unspecified parameters.
      * <p>
      *
-     * @link advancedWinIDEALaunching.py Python example. @endlink <br>
+     * @link advancedWinIDEALaunching.py Python example.@endlink <br>
      */
     class CConnectionConfig
     {
diff --git a/Examples/test-suite/java/doxygen_basic_translate_runme.java b/Examples/test-suite/java/doxygen_basic_translate_runme.java
index 395e61139..e6fbd0414 100644
--- a/Examples/test-suite/java/doxygen_basic_translate_runme.java
+++ b/Examples/test-suite/java/doxygen_basic_translate_runme.java
@@ -28,12 +28,12 @@ public class doxygen_basic_translate_runme {
     
     wantedComments.put("doxygen_basic_translate.doxygen_basic_translate.function()",
     		" \n" +
-    		" Brief description. \n" +
+    		" Brief description.\n" +
     		" \n" +
-    		" The comment text \n" +
-    		" @author Some author \n" +
-    		" @return Some number \n" +
-    		" @see function2 \n" +
+    		" The comment text.\n" +
+    		" @author Some author\n" +
+    		" @return Some number\n" +
+    		" @see function2\n" +
     		" \n" +
     		"");
     wantedComments.put("doxygen_basic_translate.doxygen_basic_translate.function2()",
diff --git a/Examples/test-suite/java/doxygen_translate_runme.java b/Examples/test-suite/java/doxygen_translate_runme.java
index b93df89bf..b3db6a816 100644
--- a/Examples/test-suite/java/doxygen_translate_runme.java
+++ b/Examples/test-suite/java/doxygen_translate_runme.java
@@ -152,45 +152,47 @@ public class doxygen_translate_runme {
         wantedComments.put("doxygen_translate.doxygen_translate.htmlFunction(int, float)",
     		" Test for html tags. See Doxygen doc for list of tags recognized by Doxygen.          \n" +
     		"                                                                                      \n" +
-    		" <a href = \"http://acme.com/index.html\">This is link</a>                               \n" +
+    		" <a href=\"http://acme.com/index.html\">This is link</a>                               \n" +
     		" <b>bold</b>                                                                          \n" +
-    		" <blockquote>                                                                         \n" +
+    		" <blockquote cite=\"http://www.worldwildlife.org/who/index.html\">                                                                         \n" +
     		" Quotation block.                                                                     \n" +
     		" </blockquote>                                                                        \n" +
     		" <br>                                                                                 \n" +
     		" <center>center</center>                                                              \n" +
     		" <code>this is code</code>                                                            \n" +
-    		" <dd> Starts an item description.                                                     \n" +
+                "\n" + 
+    		"  <dl>\n" + 
+    		"  <dt>Starts an item title.</dt>\n" + 
+    		"  <dd>Starts an item description.</dd>\n" + 
+    		"  </dl>\n" +
+                "\n" + 
     		" <dfn> Starts a piece of text displayed in a typewriter font.                         \n" +
     		" </dfn>                                                                               \n" +
     		" <div> Starts a section with a specific style (HTML only)                             \n" +
     		" </div>                                                                               \n" +
-    		" <dl> Starts a description list.                                                      \n" +
-    		" <dt> Starts an item title.</dt>                                                      \n" +
-    		" </dl>                                                                                \n" +
-    		" <em> Starts a piece of text displayed in an italic font.                             \n" +
-    		" </em>                                                                                \n" +
+    		" <em> Starts a piece of text displayed in an italic font.</em>                        \n" +
+    		"\n" +
     		" <form> 'Form' does not generate any output.                                          \n" +
     		" </form>                                                                              \n" +
     		" <hr>                                                                                 \n" +
-    		" <h1> Starts an unnumbered section.                                                   \n" +
+    		" <h1> Heading 1                                                   \n" +
     		" </h1>                                                                                \n" +
-    		" <h2> Starts an unnumbered subsection.                                                \n" +
+    		" <h2> Heading 2                                                \n" +
     		" </h2>                                                                                \n" +
-    		" <h3> Starts an unnumbered subsubsection.                                             \n" +
+    		" <h3> Heading 3                                             \n" +
     		" </h3>                                                                                \n" +
-    		" <i> Starts a piece of text displayed in an italic font.                              \n" +
-    		" <input> Does not generate any output.                                                \n" +
-    		" </i>                                                                                 \n" +
+    		" <i>Starts a piece of text displayed in an italic font.</i>                              \n" +
+    		" <input>Input tag.                                                \n" +
+    		"                                                                                  \n" +
     		" <img src=\"slika.png\">                                                                \n" +
-    		" <meta> Does not generate any output.                                                 \n" +
-    		" <multicol> ignored by doxygen.                                                       \n" +
-    		" </multicol> ignored by doxygen.                                                      \n" +
+    		" <meta>Meta tag.                                                 \n" +
+    		" <multicol>Multicol is ignored by doxygen.                                                       \n" +
+    		" </multicol>                                                      \n" +
     		"                                                                                      \n" +
-    		" <ol> Starts a numbered item list.                                                    \n" +
-    		" <li> Starts a new list item.                                                         \n" +
-    		" </li>                                                                                \n" +
-    		" </ol> Ends a numbered item list.                                                     \n" +
+    		" <ol>                                                      \n" +
+    		" <li>List item 1.</li>                                                      \n" +
+    		" <li>List item 2.</li>                                                      \n" +
+    		" </ol>                                                       \n" +
     		"                                                                                      \n" +
     		" <p> Starts a new paragraph.                                                          \n" +
     		" </p>                                                                                 \n" +
@@ -198,18 +200,15 @@ public class doxygen_translate_runme {
     		" </pre>                                                                               \n" +
     		" <small> Starts a section of text displayed in a smaller font.                        \n" +
     		" </small>                                                                             \n" +
-    		" <span> Starts an inline text fragment with a specific style (HTML only)              \n" +
-    		" </span>                                                                              \n" +
-    		" <strong> Starts a section of bold text.                                              \n" +
-    		" </strong>                                                                            \n" +
-    		" <sub> Starts a piece of text displayed in subscript.                                 \n" +
-    		" </sub>                                                                               \n" +
-    		" <sup> Starts a piece of text displayed in superscript.                               \n" +
-    		" </sup>                                                                               \n" +
+    		" <span> Starts an inline text fragment with a specific style.</span>              \n" +
+    		"                                                                               \n" +
+    		" <strong> Starts a section of bold text.</strong>                                              \n" +
+    		" <sub> Starts a piece of text displayed in subscript.</sub>                                 \n" +
+    		" <sup> Starts a piece of text displayed in superscript.</sup>                               \n" +
     		"                                                                                      \n" +
     		" <table border = '1'>                                                                 \n" +
     		" <caption>Animals</caption>                                                           \n" +
-    		" <tr><th> cow   </th><th> dog    </th></tr>                                           \n" +
+    		" <tr><th> Column 1   </th><th> Column 2   </th></tr>                                           \n" +
     		" <tr><td> cow   </td><td> dog    </td></tr>                                           \n" +
     		" <tr><td> cat   </td><td> mouse  </td></tr>                                           \n" +
     		" <tr><td> horse </td><td> parrot </td></tr>                                           \n" +
@@ -220,18 +219,17 @@ public class doxygen_translate_runme {
     		" <kbd> Starts a piece of text displayed in a typewriter font.                         \n" +
     		" </kbd>                                                                               \n" +
     		"                                                                                      \n" +
-    		" <ul> Starts an unnumbered item list.                                                 \n" +
-    		" <li> Starts a new list item 1.</li>                                                  \n" +
-    		" <li> Starts a new list item 2.</li>                                                  \n" +
-    		" <li> Starts a new list item 3.</li>                                                  \n" +
-    		" </ul> Ends an unnumbered item list.                                                  \n" +
+    		"  <ul>\n" +
+    		"  <li>List item 1.</li>\n" +
+    		"  <li>List item 2.</li>\n" +
+    		"  <li>List item 3.</li>\n" +
+    		"  </ul>\n" +
     		"                                                                                      \n" +
-    		" <var> Starts a piece of text displayed in an italic font.                            \n" +
-    		" </var>                                                                               \n" +
+    		" <var> Starts a piece of text displayed in an italic font.</var>                            \n" +
+    		"                                                                                \n" +
                 "\n" +
                 "<u>underlined \\b bold text - doxy commands are ignored inside 'htmlonly' section </u>\n" +
                 "\n" +
-                "&lt;u&gt;underlined text&lt;u&gt;\n" +
                 "");
 
         wantedComments.put("doxygen_translate.doxygen_translate.htmlEntitiesFunction(int, float)",
diff --git a/Examples/test-suite/python/doxygen_misc_constructs_runme.py b/Examples/test-suite/python/doxygen_misc_constructs_runme.py
index d2f04a874..1c2c55236 100755
--- a/Examples/test-suite/python/doxygen_misc_constructs_runme.py
+++ b/Examples/test-suite/python/doxygen_misc_constructs_runme.py
@@ -16,6 +16,7 @@ commentVerifier.check(doxygen_misc_constructs.getAddress.__doc__,
     isGetSize (bool) -- if set, for every object location both address and size are returned
 
   Connection::getId() 
+
   """)
 
 commentVerifier.check(doxygen_misc_constructs.CConnectionConfig.__doc__,
@@ -31,7 +32,9 @@ commentVerifier.check(doxygen_misc_constructs.CConnectionConfig.__doc__,
     used for unspecified parameters.
 
 
-    advancedWinIDEALaunching.py Python example. 
+
+    advancedWinIDEALaunching.py Python example.
+
     """)
 
 commentVerifier.check(doxygen_misc_constructs.waitTime.__doc__,
diff --git a/Examples/test-suite/python/doxygen_translate_all_tags_runme.py b/Examples/test-suite/python/doxygen_translate_all_tags_runme.py
index ecccc1fc5..3009caf64 100755
--- a/Examples/test-suite/python/doxygen_translate_all_tags_runme.py
+++ b/Examples/test-suite/python/doxygen_translate_all_tags_runme.py
@@ -251,7 +251,7 @@ r"""
 
 
 
-  function
+  See also: function
 
   Same as
   brief description

From 2a8b20785eebf5adb87a1e206b94eb1dedb9c380 Mon Sep 17 00:00:00 2001
From: Marko Klopcic <markok3.14@gmail.com>
Date: Tue, 19 Feb 2013 07:25:13 +0100
Subject: [PATCH 181/314] fixed bug in handling of HTML tags, test added

---
 Examples/test-suite/doxygen_misc_constructs.h         |  9 ++++++++-
 .../java/doxygen_misc_constructs_runme.java           | 11 ++++++++++-
 Source/DoxygenTranslator/src/DoxygenParser.cpp        |  9 ++++++---
 3 files changed, 24 insertions(+), 5 deletions(-)

diff --git a/Examples/test-suite/doxygen_misc_constructs.h b/Examples/test-suite/doxygen_misc_constructs.h
index d25b5af15..edbea3ed5 100644
--- a/Examples/test-suite/doxygen_misc_constructs.h
+++ b/Examples/test-suite/doxygen_misc_constructs.h
@@ -64,4 +64,11 @@ void backslashB()
 void backslashC()
 {}
 
-
+/**
+ * The next line contains expression:
+ * <pre>
+ * ['retVal < 10', 'g_counter == 23 && g_mode & 3']
+ *</pre>
+ */
+void cycle()
+{}
diff --git a/Examples/test-suite/java/doxygen_misc_constructs_runme.java b/Examples/test-suite/java/doxygen_misc_constructs_runme.java
index ae9cc442f..b14918a64 100644
--- a/Examples/test-suite/java/doxygen_misc_constructs_runme.java
+++ b/Examples/test-suite/java/doxygen_misc_constructs_runme.java
@@ -153,7 +153,16 @@ public class doxygen_misc_constructs_runme {
     		" <i>with</i> old comment parser.\n" +
                 " @see MyClass#fun(char,float)\n" +
     		"");
-     
+
+   wantedComments.put("doxygen_misc_constructs.doxygen_misc_constructs.cycle()",
+    		" The next line contains expression:\n" +
+                " <pre>\n" +
+    		" ['retVal &lt; 10', 'g_counter == 23 &amp;&amp; g_mode &amp; 3']\n" +
+                " </pre>\n" +
+    		"\n" +
+    		"");
+ 
+    
     // and ask the parser to check comments for us
     System.exit(parser.check(wantedComments));
   }
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.cpp b/Source/DoxygenTranslator/src/DoxygenParser.cpp
index 9c07eb4cf..d270631df 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenParser.cpp
@@ -1120,7 +1120,7 @@ void DoxygenParser::processHtmlTags(size_t &pos, const std::string &line)
   pos = endHtmlPos;
 
   // prepend '<' to distinguish HTML tags from doxygen commands
-  if (addDoxyCommand(m_tokenList, '<' + cmd)) {
+  if (!cmd.empty()  &&  addDoxyCommand(m_tokenList, '<' + cmd)) {
     // it is a valid HTML command
     if (line[pos] != '>') { // it should be HTML tag with args,
                              // for example <A ...>, <IMG ...>, ...
@@ -1148,7 +1148,10 @@ void DoxygenParser::processHtmlTags(size_t &pos, const std::string &line)
         m_tokenList.push_back(Token(PLAINSTRING, ""));
       }
     }
-    pos++; // skip '>'
+
+    if (pos != string::npos) {
+        pos++; // skip '>'
+    }
   } else {
     // the command is not HTML supported by Doxygen, < and > will be
     // replaced by HTML entities &lt; and &gt; respectively,
@@ -1164,7 +1167,7 @@ void DoxygenParser::processHtmlEntities(size_t &pos, const std::string &line)
 
   if (endOfWordPos != string::npos) {
 
-    if (line[endOfWordPos] == ';')
+    if (line[endOfWordPos] == ';'  &&  (endOfWordPos - pos) > 1)
     {
       // if entity is not recognized by Doxygen (not in the list of
       // commands) nothing is added (here and in Doxygen).

From b5dea7456b37232472ff985ae841b3774ef446e5 Mon Sep 17 00:00:00 2001
From: Marko Klopcic <markok3.14@gmail.com>
Date: Thu, 21 Feb 2013 09:05:11 +0100
Subject: [PATCH 182/314] improved handling of word commands if puntuation is
 following the word, preserved spaces at start of comment line

---
 Examples/test-suite/doxygen_misc_constructs.h |  22 ++-
 .../java/doxygen_misc_constructs_runme.java   |  20 ++-
 .../doxygen_translate_all_tags_runme.java     |   6 +-
 Examples/test-suite/python/autodoc_runme.py   |  64 ++++----
 .../python/doxygen_misc_constructs_runme.py   |  31 +++-
 .../doxygen_translate_all_tags_runme.py       |  34 ++--
 .../python/doxygen_translate_runme.py         |  24 +--
 .../DoxygenTranslator/src/DoxygenParser.cpp   | 153 +++++++++++-------
 8 files changed, 224 insertions(+), 130 deletions(-)

diff --git a/Examples/test-suite/doxygen_misc_constructs.h b/Examples/test-suite/doxygen_misc_constructs.h
index edbea3ed5..98856ac9a 100644
--- a/Examples/test-suite/doxygen_misc_constructs.h
+++ b/Examples/test-suite/doxygen_misc_constructs.h
@@ -69,6 +69,26 @@ void backslashC()
  * <pre>
  * ['retVal < 10', 'g_counter == 23 && g_mode & 3']
  *</pre>
+ *
+ * Both words should be emphasized \b isystem.connect.
+ * But not the last period. For \b example, comma should not be emphasized.
+ * Similar \b for: double colon.
+ *
+ * Spaces at the start of line should be taken into account:
+ * @param id used as prefix in log
+ *     statements. The default value is empty string, which is OK if
+ *     there is only one app. instance. Example:
+ *     <pre>
+ *         ctrl.setBP("func1");
+ *     </pre>
+ *     If we set the id to \c main_, we get:
+ *     <pre>
+ *         main_ctrl.setBP("func1");
+ *     </pre>
+ *
+ * @param fileName name of the log file
  */
-void cycle()
+void cycle(int id, char *fileName)
 {}
+
+
diff --git a/Examples/test-suite/java/doxygen_misc_constructs_runme.java b/Examples/test-suite/java/doxygen_misc_constructs_runme.java
index b14918a64..ba0f2b265 100644
--- a/Examples/test-suite/java/doxygen_misc_constructs_runme.java
+++ b/Examples/test-suite/java/doxygen_misc_constructs_runme.java
@@ -154,13 +154,29 @@ public class doxygen_misc_constructs_runme {
                 " @see MyClass#fun(char,float)\n" +
     		"");
 
-   wantedComments.put("doxygen_misc_constructs.doxygen_misc_constructs.cycle()",
+   wantedComments.put("doxygen_misc_constructs.doxygen_misc_constructs.cycle(int, java.lang.String)",
     		" The next line contains expression:\n" +
                 " <pre>\n" +
     		" ['retVal &lt; 10', 'g_counter == 23 &amp;&amp; g_mode &amp; 3']\n" +
                 " </pre>\n" +
     		"\n" +
-    		"");
+                " Both words should be emphasized <b>isystem.connect</b>.\n" +
+                " But not the last period. For <b>example</b>, comma should not be emphasized.\n" +
+                " Similar <b>for</b>: double colon.\n" +
+    		"\n" +
+                " Spaces at the start of line should be taken into account:\n" +
+                " @param id used as prefix in log\n" +
+                "     statements. The default value is empty string, which is OK if\n" +
+                "     there is only one app. instance. Example:\n" +
+                "     <pre>\n" +
+                "         ctrl.setBP(\"func1\");\n" +
+                "     </pre>\n" +
+                "     If we set the id to <code>main_</code>, we get:\n" +
+                "     <pre>\n" +
+                "         main_ctrl.setBP(\"func1\");\n" +
+                "     </pre>\n" +
+                "\n" +
+                " @param fileName name of the log file\n");
  
     
     // and ask the parser to check comments for us
diff --git a/Examples/test-suite/java/doxygen_translate_all_tags_runme.java b/Examples/test-suite/java/doxygen_translate_all_tags_runme.java
index 69a1169ca..5374d97c4 100644
--- a/Examples/test-suite/java/doxygen_translate_all_tags_runme.java
+++ b/Examples/test-suite/java/doxygen_translate_all_tags_runme.java
@@ -52,7 +52,7 @@ public class doxygen_translate_all_tags_runme {
     		" and detailed description of some thing \n");
     
     wantedComments.put("doxygen_translate_all_tags.doxygen_translate_all_tags.func03(int)",
-                       " Comment for <b>func03().</b>\n" +
+                       " Comment for <b>func03()</b>.\n" +
                        " <i>italicword </i>\n" +
     		" <i>emphazedWord </i>\n" +
                 " @ example someFile.txt\n" +
@@ -87,7 +87,7 @@ public class doxygen_translate_all_tags_runme {
     		" describing invariant. \n");
     
     wantedComments.put("doxygen_translate_all_tags.doxygen_translate_all_tags.func06(int)",
-                       " Comment for <b>func06().</b>\n" +
+                       " Comment for <b>func06()</b>.\n" +
                        " This will only appear in LATeX \n" +
     		" <ul> \n" +
     		" <li>Some unordered list \n" +
@@ -98,7 +98,7 @@ public class doxygen_translate_all_tags_runme {
     		" This will only appear in man\n");
     
     wantedComments.put("doxygen_translate_all_tags.doxygen_translate_all_tags.func07(int)",
-                       " Comment for <b>func07().</b>\n" +
+                       " Comment for <b>func07()</b>.\n" +
                        " Note: Here \n" +
     		" is the note! \n" +
     		" This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.\n" +
diff --git a/Examples/test-suite/python/autodoc_runme.py b/Examples/test-suite/python/autodoc_runme.py
index b0359f2e0..4c28f7f7e 100644
--- a/Examples/test-suite/python/autodoc_runme.py
+++ b/Examples/test-suite/python/autodoc_runme.py
@@ -1,14 +1,12 @@
 from autodoc import *
+import commentVerifier
 
-def check(got, expected):
-  if expected != got:
-    raise RuntimeError("\n" + "Expected: [" + str(expected) + "]\n" + "Got     : [" + str(got) + "]")
 
-check(A.__doc__, "Proxy of C++ A class")
-check(A.funk.__doc__, "just a string")
-check(A.func0.__doc__, "func0(self, arg2, hello) -> int")
-check(A.func1.__doc__, "func1(A self, short arg2, Tuple hello) -> int")
-check(A.func2.__doc__,  "\n"
+commentVerifier.check(A.__doc__, "Proxy of C++ A class")
+commentVerifier.check(A.funk.__doc__, "just a string")
+commentVerifier.check(A.func0.__doc__, "func0(self, arg2, hello) -> int")
+commentVerifier.check(A.func1.__doc__, "func1(A self, short arg2, Tuple hello) -> int")
+commentVerifier.check(A.func2.__doc__,  "\n"
 "        func2(self, arg2, hello) -> int\n"
 "\n"
 "        Parameters:\n"
@@ -17,7 +15,7 @@ check(A.func2.__doc__,  "\n"
 "\n"
 "        "
 )
-check(A.func3.__doc__,  "\n"
+commentVerifier.check(A.func3.__doc__,  "\n"
 "        func3(A self, short arg2, Tuple hello) -> int\n"
 "\n"
 "        Parameters:\n"
@@ -27,17 +25,17 @@ check(A.func3.__doc__,  "\n"
 "        "
 )
 
-check(A.func0default.__doc__, "\n"
+commentVerifier.check(A.func0default.__doc__, "\n"
 "        func0default(self, e, arg3, hello, f=2) -> int\n"
 "        func0default(self, e, arg3, hello) -> int\n"
 "        "
 )
-check(A.func1default.__doc__, "\n"
+commentVerifier.check(A.func1default.__doc__, "\n"
 "        func1default(A self, A e, short arg3, Tuple hello, double f=2) -> int\n"
 "        func1default(A self, A e, short arg3, Tuple hello) -> int\n"
 "        "
 )
-check(A.func2default.__doc__,  "\n"
+commentVerifier.check(A.func2default.__doc__,  "\n"
 "        func2default(self, e, arg3, hello, f=2) -> int\n"
 "\n"
 "        Parameters:\n"
@@ -55,7 +53,7 @@ check(A.func2default.__doc__,  "\n"
 "\n"
 "        "
 )
-check(A.func3default.__doc__,  "\n"
+commentVerifier.check(A.func3default.__doc__,  "\n"
 "        func3default(A self, A e, short arg3, Tuple hello, double f=2) -> int\n"
 "\n"
 "        Parameters:\n"
@@ -74,17 +72,17 @@ check(A.func3default.__doc__,  "\n"
 "        "
 )
 
-check(A.func0static.__doc__, "\n"
+commentVerifier.check(A.func0static.__doc__, "\n"
 "        func0static(e, arg2, hello, f=2) -> int\n"
 "        func0static(e, arg2, hello) -> int\n"
 "        "
 )
-check(A.func1static.__doc__, "\n"
+commentVerifier.check(A.func1static.__doc__, "\n"
 "        func1static(A e, short arg2, Tuple hello, double f=2) -> int\n"
 "        func1static(A e, short arg2, Tuple hello) -> int\n"
 "        "
 )
-check(A.func2static.__doc__,  "\n"
+commentVerifier.check(A.func2static.__doc__,  "\n"
 "        func2static(e, arg2, hello, f=2) -> int\n"
 "\n"
 "        Parameters:\n"
@@ -102,7 +100,7 @@ check(A.func2static.__doc__,  "\n"
 "\n"
 "        "
 )
-check(A.func3static.__doc__,  "\n"
+commentVerifier.check(A.func3static.__doc__,  "\n"
 "        func3static(A e, short arg2, Tuple hello, double f=2) -> int\n"
 "\n"
 "        Parameters:\n"
@@ -121,16 +119,16 @@ check(A.func3static.__doc__,  "\n"
 "        "
 )
 
-check(A.variable_a.__doc__, "A_variable_a_get(self) -> int")
-check(A.variable_b.__doc__, "A_variable_b_get(A self) -> int")
-check(A.variable_c.__doc__, "\n"
+commentVerifier.check(A.variable_a.__doc__, "A_variable_a_get(self) -> int")
+commentVerifier.check(A.variable_b.__doc__, "A_variable_b_get(A self) -> int")
+commentVerifier.check(A.variable_c.__doc__, "\n"
 "A_variable_c_get(self) -> int\n"
 "\n"
 "Parameters:\n"
 "    self: A *\n"
 "\n"
 )
-check(A.variable_d.__doc__, "\n"
+commentVerifier.check(A.variable_d.__doc__, "\n"
 "A_variable_d_get(A self) -> int\n"
 "\n"
 "Parameters:\n"
@@ -138,10 +136,10 @@ check(A.variable_d.__doc__, "\n"
 "\n"
 )
 
-check(B.__doc__, "Proxy of C++ B class")
-check(C.__init__.__doc__, "__init__(self, a, b, h) -> C")
-check(D.__init__.__doc__, "__init__(D self, int a, int b, Hola h) -> D")
-check(E.__init__.__doc__, "\n"
+commentVerifier.check(B.__doc__, "Proxy of C++ B class")
+commentVerifier.check(C.__init__.__doc__, "__init__(self, a, b, h) -> C")
+commentVerifier.check(D.__init__.__doc__, "__init__(D self, int a, int b, Hola h) -> D")
+commentVerifier.check(E.__init__.__doc__, "\n"
 "        __init__(self, a, b, h) -> E\n"
 "\n"
 "        Parameters:\n"
@@ -151,7 +149,7 @@ check(E.__init__.__doc__, "\n"
 "\n"
 "        "
 )
-check(F.__init__.__doc__, "\n"
+commentVerifier.check(F.__init__.__doc__, "\n"
 "        __init__(F self, int a, int b, Hola h) -> F\n"
 "\n"
 "        Parameters:\n"
@@ -162,15 +160,15 @@ check(F.__init__.__doc__, "\n"
 "        "
 )
 
-check(B.funk.__doc__, "funk(B self, int c, int d) -> int")
-check(funk.__doc__, "funk(A e, short arg2, int c, int d) -> int")
-check(funkdefaults.__doc__, "\n"
+commentVerifier.check(B.funk.__doc__, "funk(B self, int c, int d) -> int")
+commentVerifier.check(funk.__doc__, "funk(A e, short arg2, int c, int d) -> int")
+commentVerifier.check(funkdefaults.__doc__, "\n"
 "  funkdefaults(A e, short arg2, int c, int d, double f=2) -> int\n"
 "  funkdefaults(A e, short arg2, int c, int d) -> int\n"
 "  "
 )
 
-check(func_input.__doc__, "func_input(int * INPUT) -> int")
-check(func_output.__doc__, "func_output() -> int")
-check(func_inout.__doc__, "func_inout(int * INOUT) -> int")
-check(banana.__doc__, "banana(S a, S b, int c, Integer d)")
+commentVerifier.check(func_input.__doc__, "func_input(int * INPUT) -> int")
+commentVerifier.check(func_output.__doc__, "func_output() -> int")
+commentVerifier.check(func_inout.__doc__, "func_inout(int * INOUT) -> int")
+commentVerifier.check(banana.__doc__, "banana(S a, S b, int c, Integer d)")
diff --git a/Examples/test-suite/python/doxygen_misc_constructs_runme.py b/Examples/test-suite/python/doxygen_misc_constructs_runme.py
index 1c2c55236..61060e6be 100755
--- a/Examples/test-suite/python/doxygen_misc_constructs_runme.py
+++ b/Examples/test-suite/python/doxygen_misc_constructs_runme.py
@@ -110,6 +110,35 @@ commentVerifier.check(doxygen_misc_constructs.backslashC.__doc__,
   _with_ old comment parser. 
 
   See also: MyClass::fun(char,
-  float)
+   float)
   """
 )
+
+
+commentVerifier.check(doxygen_misc_constructs.cycle.__doc__,
+  r"""
+  The next line contains expression:
+
+  ['retVal < 10', 'g_counter == 23 && g_mode & 3']
+
+
+  Both words should be emphasized __isystem.connect__.
+  But not the last period. For __example__, comma should not be emphasized.
+  Similar __for__: double colon.
+
+  Spaces at the start of line should be taken into account:
+  Arguments:
+    id (int) -- used as prefix in log
+      statements. The default value is empty string, which is OK if
+      there is only one app. instance. Example:
+      
+          ctrl.setBP("func1");
+      
+      If we set the id to 'main_', we get:
+      
+          main_ctrl.setBP("func1");
+      
+
+    fileName (char *) -- name of the log file
+  """
+);
diff --git a/Examples/test-suite/python/doxygen_translate_all_tags_runme.py b/Examples/test-suite/python/doxygen_translate_all_tags_runme.py
index 3009caf64..051a9a51e 100755
--- a/Examples/test-suite/python/doxygen_translate_all_tags_runme.py
+++ b/Examples/test-suite/python/doxygen_translate_all_tags_runme.py
@@ -67,7 +67,7 @@ r"""
 
 commentVerifier.check(doxygen_translate_all_tags.func03.__doc__,
 r"""
-  Comment for __func03().__
+  Comment for __func03()__.
 
 
 
@@ -96,11 +96,11 @@ r"""
     \sqrt{(x_2-x_1)^2+(y_2-y_1)^2} 
 
    
-  \sqrt{(x_2-x_1)^2+(y_2-y_1)^2}
+      \sqrt{(x_2-x_1)^2+(y_2-y_1)^2}
 
 
    
-  \sqrt{(x_2-x_1)^2+(y_2-y_1)^2}
+      \sqrt{(x_2-x_1)^2+(y_2-y_1)^2}
 
 
 
@@ -120,21 +120,21 @@ r"""
 commentVerifier.check(doxygen_translate_all_tags.func05.__doc__,
 r"""
   If: ANOTHERCONDITION {
-  First part of comment
-  If: SECONDCONDITION {
-  Nested condition text
-  }Else if: THIRDCONDITION {
-  The third condition text
-  }Else:  {The last text block
-  }
-  }Else:  {Second part of comment
-  If: CONDITION {
-  Second part extended
-  }
+    First part of comment
+    If: SECONDCONDITION {
+      Nested condition text
+    }Else if: THIRDCONDITION {
+      The third condition text
+    }Else:  {    The last text block
+    }
+  }Else:  {  Second part of comment
+    If: CONDITION {
+      Second part extended
+    }
   }
 
   If not: SOMECONDITION {
-  This is printed if not
+    This is printed if not
   }
 
   Image: testImage.bmp("Hello, world!")
@@ -155,7 +155,7 @@ r"""
 
 commentVerifier.check(doxygen_translate_all_tags.func06.__doc__,
 r"""
-  Comment for __func06().__
+  Comment for __func06()__.
 
 
 
@@ -194,7 +194,7 @@ r"""
 
 commentVerifier.check(doxygen_translate_all_tags.func07.__doc__,
 r"""
-  Comment for __func07().__
+  Comment for __func07()__.
 
 
 
diff --git a/Examples/test-suite/python/doxygen_translate_runme.py b/Examples/test-suite/python/doxygen_translate_runme.py
index 183558415..9365d1ce6 100755
--- a/Examples/test-suite/python/doxygen_translate_runme.py
+++ b/Examples/test-suite/python/doxygen_translate_runme.py
@@ -40,21 +40,21 @@ r"""
   Throws: SuperError
 
   If: ANOTHERCONDITION {
-  First part of comment
-  If: SECONDCONDITION {
-  Nested condition text
-  }Else if: THIRDCONDITION {
-  The third condition text
-  }Else:  {The last text block
-  }
-  }Else:  {Second part of comment
-  If: CONDITION {
-  Second part extended
-  }
+    First part of comment
+    If: SECONDCONDITION {
+      Nested condition text
+    }Else if: THIRDCONDITION {
+      The third condition text
+    }Else:  {    The last text block
+    }
+  }Else:  {  Second part of comment
+    If: CONDITION {
+      Second part extended
+    }
   }
 
   If not: SOMECONDITION {
-  This is printed if not
+    This is printed if not
   }
 
   Image: testImage.bmp("Hello, world!")
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.cpp b/Source/DoxygenTranslator/src/DoxygenParser.cpp
index d270631df..07839f5d7 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenParser.cpp
@@ -199,39 +199,33 @@ std::string DoxygenParser::getNextWord() {
         return "";
     }
 */
-	while (m_tokenListIt != m_tokenList.end()  &&  (m_tokenListIt->m_tokenType == PLAINSTRING)) {
-		// handle quoted strings as words
-	    string token = m_tokenListIt->m_tokenString;
-		if (token == "\"") {
+  while (m_tokenListIt != m_tokenList.end()  &&  (m_tokenListIt->m_tokenType == PLAINSTRING)) {
+    // handle quoted strings as words
+    string token = m_tokenListIt->m_tokenString;
+    if (token == "\"") {
 
-			string word = m_tokenListIt->m_tokenString;
-			m_tokenListIt++;
-			while (true) {
-				string nextWord = getNextToken();
-				if (nextWord.empty()) { // maybe report unterminated string error
-					return word;
-				}
-				word += nextWord;
-				if (nextWord == "\"") {
-					return word;
-				}
-			}
-		}
+      string word = m_tokenListIt->m_tokenString;
+      m_tokenListIt++;
+      while (true) {
+        string nextWord = getNextToken();
+        if (nextWord.empty()) { // maybe report unterminated string error
+          return word;
+        }
+        word += nextWord;
+        if (nextWord == "\"") {
+          return word;
+        }
+      }
+    }
 
-        string tokenStr = trim(m_tokenListIt->m_tokenString);
-		m_tokenListIt++;
-		if (!tokenStr.empty()) {
-		    return tokenStr;
-		}
-	} /* else if (nextToken.m_tokenType == END_LINE) {
-	    // this handles cases when command is the last item in line, for example:
-	    // * This method returns line number \c
-	    // * relative to paragraph.
-        m_tokenListIt++;
-        return getNextWord();
-	} */
+    string tokenStr = trim(m_tokenListIt->m_tokenString);
+    m_tokenListIt++;
+    if (!tokenStr.empty()) {
+      return tokenStr;
+    }
+  }
 
-	return "";
+  return "";
 }
 
 
@@ -381,36 +375,36 @@ void DoxygenParser::skipEndOfLine()
 
 int DoxygenParser::addSimpleCommand(const std::string &theCommand,
                                          DoxygenEntityList &doxyList) {
-	if (noisy)
-		cout << "Parsing " << theCommand << endl;
+  if (noisy)
+    cout << "Parsing " << theCommand << endl;
 
-	doxyList.push_back(DoxygenEntity(theCommand));
-	return 1;
+  doxyList.push_back(DoxygenEntity(theCommand));
+  return 1;
 }
 
 
 int DoxygenParser::addCommandWord(const std::string &theCommand,
                                        const TokenList &,
                                        DoxygenEntityList &doxyList) {
-	if (noisy)
-		cout << "Parsing " << theCommand << endl;
+  if (noisy)
+    cout << "Parsing " << theCommand << endl;
 
-	if (isEndOfLine()) {
-	    // handles cases when command is at the end of line (for example "\c\nreally"
-	    skipWhitespaceTokens();
-	    doxyList.push_back(DoxygenEntity("plainstd::endl"));
-	}
-	std::string name = getNextWord();
-    if (!name.empty()) {
-      DoxygenEntityList aNewList;
-      aNewList.push_back(DoxygenEntity("plainstd::string", name));
-      doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-      return 1;
-	} else {
-		printListError(WARN_DOXYGEN_COMMAND_ERROR, "No word followed " +
-		                theCommand + " command. Not added");
-	}
-	return 0;
+  if (isEndOfLine()) {
+    // handles cases when command is at the end of line (for example "\c\nreally"
+    skipWhitespaceTokens();
+    doxyList.push_back(DoxygenEntity("plainstd::endl"));
+  }
+  std::string name = getNextWord();
+  if (!name.empty()) {
+    DoxygenEntityList aNewList;
+    aNewList.push_back(DoxygenEntity("plainstd::string", name));
+    doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+    return 1;
+  } else {
+    printListError(WARN_DOXYGEN_COMMAND_ERROR, "No word followed " +
+        theCommand + " command. Not added");
+  }
+  return 0;
 }
 
 
@@ -1264,32 +1258,69 @@ void DoxygenParser::tokenizeDoxygenComment(const std::string &doxygenComment,
     const string &line = *it;
     size_t pos = line.find_first_not_of(" \t");
 
-    // skip sequences of '*', '/', and '!' of any length
-    while (pos != string::npos  &&  isStartOfDoxyCommentChar(line[pos])) {
-      pos++;
+    if (pos == string::npos) {
+      m_tokenList.push_back(Token(END_LINE, "\n"));
+      continue;
     }
 
-    if (pos == string::npos) {
-        m_tokenList.push_back(Token(END_LINE, "\n"));
+    // skip sequences of '*', '/', and '!' of any length
+    bool isStartOfCommentLineCharFound = false;
+    while (pos < line.size()  &&  isStartOfDoxyCommentChar(line[pos])) {
+      pos++;
+      isStartOfCommentLineCharFound = true;
+    }
+
+    if (pos == line.size()) {
+      m_tokenList.push_back(Token(END_LINE, "\n"));
       continue;
     }
 
+    // if 'isStartOfCommentLineCharFound' then preserve leading spaces, so
+    // ' *    comment' gets translated to ' *    comment', not ' * comment'
+    // This is important to keep formatting for comments translated to Python.
+    if (isStartOfCommentLineCharFound  &&  line[pos] == ' ') {
+      pos++; // points to char after ' * '
+      if (pos == line.size()) {
+        m_tokenList.push_back(Token(END_LINE, "\n"));
+        continue;
+      }
+    }
+
     // line[pos] may be ' \t' or start of word, it there was no '*', '/' or '!'
     // at beginning of the line. Make sure it points to start of the first word
     // in the line.
-    pos = line.find_first_not_of(" \t", pos);
-    if (pos == string::npos) {
+    size_t firstWordPos = line.find_first_not_of(" \t", pos);
+    if (firstWordPos == string::npos) {
       m_tokenList.push_back(Token(END_LINE, "\n"));
       continue;
     }
 
+    if (isStartOfCommentLineCharFound  &&  firstWordPos > pos) {
+      m_tokenList.push_back(Token(PLAINSTRING, line.substr(pos, firstWordPos - pos)));
+    }
+
+    pos = firstWordPos;
+
     while (pos != string::npos) {
       // find the end of the word
       size_t doxyCmdOrHtmlTagPos = line.find_first_of("\\@<>&\" \t", pos);
       if (doxyCmdOrHtmlTagPos != pos) {
         // plain text found
-        m_tokenList.push_back(Token(PLAINSTRING,
-                              line.substr(pos, doxyCmdOrHtmlTagPos - pos)));
+        // if the last char is punctuation, make it a separate word, otherwise
+        // it may be included with word also when not appropriate, for example:
+        //   colors are \b red, green, and blue --> colors are <b>red,</b> green, and blue
+        // instead of (comma not bold):
+        //   colors are \b red, green, and blue --> colors are <b>red</b>, green, and blue
+        // In Python it looks even worse:
+        //   colors are \b red, green, and blue --> colors are 'red,' green, and blue
+        string text = line.substr(pos, doxyCmdOrHtmlTagPos - pos);
+        string punctuations(".,:");
+        if (!text.empty()  &&  punctuations.find(text[text.size() - 1]) != string::npos) {
+          m_tokenList.push_back(Token(PLAINSTRING, text.substr(0, text.size() - 1)));
+          m_tokenList.push_back(Token(PLAINSTRING, text.substr(text.size() - 1)));
+        } else {
+          m_tokenList.push_back(Token(PLAINSTRING, text));
+        }
       }
 
       pos = doxyCmdOrHtmlTagPos;

From 9cd379b800adbd2ea5f3619ad2c7a475e943ca2a Mon Sep 17 00:00:00 2001
From: Marko Klopcic <markok3.14@gmail.com>
Date: Thu, 21 Feb 2013 22:50:15 +0100
Subject: [PATCH 183/314] fixed bug with autodoc, manual updated with table
 description and tests description

---
 Doc/Manual/Doxygen.html                 | 46 ++++++++++++++++++++++++-
 Examples/test-suite/doxygen_translate.i |  8 ++---
 Source/Modules/python.cxx               |  6 ++--
 3 files changed, 52 insertions(+), 8 deletions(-)

diff --git a/Doc/Manual/Doxygen.html b/Doc/Manual/Doxygen.html
index d374a9c2f..d530218a3 100644
--- a/Doc/Manual/Doxygen.html
+++ b/Doc/Manual/Doxygen.html
@@ -949,6 +949,40 @@ file, so they have no comment translated for them.
 </p>
 
 <p>
+  <b>Whitespaces and tables</b><br>
+  Whitespaces are preserved when translating comments, so it makes
+  sense to have Doxygen comments formatted in a readable way. This
+  includes tables, where tags &lt;th&gt;, &lt;td&gt; and &lt;/tr&gt;are translated
+  to '|'. The line after line with &lt;th&gt; tags contains dashes.
+  If we take care about whitespaces, comments in Python are much more
+  readable. Example:
+
+<div class="code"><pre>
+/**
+ * &lt;table border = '1'&gt;
+ * &lt;caption&gt;Animals&lt;/caption&gt;
+ * &lt;tr&gt;&lt;th&gt; Column 1 &lt;/th&gt;&lt;th&gt; Column 2 &lt;/th&gt;&lt;/tr&gt;
+ * &lt;tr&gt;&lt;td&gt; cow      &lt;/td&gt;&lt;td&gt; dog      &lt;/td&gt;&lt;/tr&gt;
+ * &lt;tr&gt;&lt;td&gt; cat      &lt;/td&gt;&lt;td&gt; mouse    &lt;/td&gt;&lt;/tr&gt;
+ * &lt;tr&gt;&lt;td&gt; horse    &lt;/td&gt;&lt;td&gt; parrot   &lt;/td&gt;&lt;/tr&gt;
+ * &lt;/table&gt;
+ */
+</pre></div>
+<p/>
+translates to Python as:
+<p/>
+<div class="targetlang"><pre>
+  Animals
+  | Column 1 | Column 2 |
+  -----------------------
+  | cow      | dog      |
+  | cat      | mouse    |
+  | horse    | parrot   |
+</pre></div>
+</p>
+
+<p>
+  <b>Overloaded functions</b><br>
 Since all the overloaded functions in c++ are wrapped into one Python
 function, PyDoc translator will combine every comment of every
 overloaded function and put it in the comment for wrapping function.
@@ -957,7 +991,7 @@ If you intend to use resulting proxy files with Doxygen docs
 generator, rather than PyDoc, you may want to turn off translator
 completely (doxygen:notranslate feature).  Then SWIG will just copy
 the comments to the proxy file and reformat them if needed, but all
-the comment content will be left as is. As Doxygen don't support
+the comment content will be left as is. As Doxygen doesn't support
 special commands in Python comments
 (see <a href="http://www.stack.nl/~dimitri/doxygen/docblocks.html#pythonblocks">Doxygen
 docs</a>), you may want to use some tool like doxypy
@@ -1458,6 +1492,16 @@ check-python-test-suite'. To run them individually, type
   Examples/test-suite/java $ make doxygen_misc_constructs.cpptest -s
 </pre>
 
+If test fails, both expected and translated comments are printed to
+std out, but also written to files <i>expected.txt</i>
+and <I>got.txt</I>. Since it is often difficult to find a single
+character difference in several lines of text, we can use some diff
+tool, for example:
+<pre>
+  Examples/test-suite/java $ kdiff3 expected.txt got.txt
+</pre>
+
+
     
 <br>
 Runtime tests in Java are implemented using JavaDoc doclets. To make that work, you
diff --git a/Examples/test-suite/doxygen_translate.i b/Examples/test-suite/doxygen_translate.i
index 03e9471f8..a41391dc9 100644
--- a/Examples/test-suite/doxygen_translate.i
+++ b/Examples/test-suite/doxygen_translate.i
@@ -182,10 +182,10 @@ int function(int a, float b)
  *
  * <table border = '1'>
  * <caption>Animals</caption>
-  <tr><th> Column 1 </th><th> Column 2 </th></tr>
-  <tr><td> cow      </td><td> dog      </td></tr>
-  <tr><td> cat      </td><td> mouse    </td></tr>
-  <tr><td> horse    </td><td> parrot   </td></tr>
+ * <tr><th> Column 1 </th><th> Column 2 </th></tr>
+ * <tr><td> cow      </td><td> dog      </td></tr>
+ * <tr><td> cat      </td><td> mouse    </td></tr>
+ * <tr><td> horse    </td><td> parrot   </td></tr>
  * </table>
  *
  * <TT>Starts a piece of text displayed in a typewriter font.
diff --git a/Source/Modules/python.cxx b/Source/Modules/python.cxx
index f3f1df832..5292e8462 100644
--- a/Source/Modules/python.cxx
+++ b/Source/Modules/python.cxx
@@ -1257,13 +1257,13 @@ public:
     //
     // otherwise, put it all on a single line
     //
-    // All comments translated from doxygen are given as raw stringr (prefix "r"),
+    // All comments translated from doxygen are given as raw strings (prefix "r"),
     // because '\' is used often in comments, but may break Python module from
     // loading. For example, in doxy comment one may write path in quotes:
     //
     //     This is path to file "C:\x\file.txt"
     //
-    // Python will no load the module with such comment becaue of illegal
+    // Python will no load the module with such comment because of illegal
     // escape '\x'. '\' may additionally appear in verbatim or htmlonly sections
     // of doxygen doc, Latex expressions, ...
     if (have_auto && have_ds) {	// Both autodoc and docstring are present
@@ -1281,7 +1281,7 @@ public:
 	doc = NewStringf("%s%s%s", triple_double, autodoc, triple_double);
       } else {
 	doc = NewString("");
-	Printv(doc, "r", triple_double, "\n", pythoncode(autodoc, indent), indent, triple_double, NIL);
+	Printv(doc, triple_double, "\n", pythoncode(autodoc, indent), indent, triple_double, NIL);
       }
     } else if (have_doxygen) { // the lowest priority
       doc = NewString("");

From 3b7908fa6eaab58a4e5e438655a85907acf17b69 Mon Sep 17 00:00:00 2001
From: Marko Klopcic <markok3.14@gmail.com>
Date: Sat, 23 Feb 2013 15:20:27 +0100
Subject: [PATCH 184/314] fixed leading spaces for the second row of table in
 pydoc, sources formatted

---
 Examples/test-suite/doxygen_translate.i       |  17 +
 .../java/doxygen_translate_runme.java         |  15 +
 .../python/doxygen_translate_runme.py         |  18 +
 .../DoxygenTranslator/src/DoxygenCommands.h   |  40 +-
 .../src/JavaDocConverter.cpp                  | 513 ++++++++++--------
 .../DoxygenTranslator/src/PyDocConverter.cpp  | 488 +++++++++--------
 6 files changed, 639 insertions(+), 452 deletions(-)

diff --git a/Examples/test-suite/doxygen_translate.i b/Examples/test-suite/doxygen_translate.i
index a41391dc9..3c2930ff1 100644
--- a/Examples/test-suite/doxygen_translate.i
+++ b/Examples/test-suite/doxygen_translate.i
@@ -209,6 +209,23 @@ int htmlFunction(int a, float b)
 {
 }
 
+/** 
+ * The meaning of flags:
+ *
+ * @param byFlags bits marking required items:
+ *   <table>
+ *   <tr><th> Size in bits</th><th> Items Required </th></tr>
+ *   <tr><td> 1 - 8       </td><td>      1         </td></tr>
+ *   <tr><td> 9 - 16      </td><td>      2         </td></tr>
+ *   <tr><td> 17 - 32     </td><td>      4         </td></tr>
+ *   </table>
+ *   Almost all combinations of above flags are supported by
+ *   \c htmlTable... functions.
+ */
+int htmlTableFunction(int byFlags)
+{
+}
+
 
 /**
  * All entities are treated as commands &copy; &trade; &reg;
diff --git a/Examples/test-suite/java/doxygen_translate_runme.java b/Examples/test-suite/java/doxygen_translate_runme.java
index b3db6a816..55e5d23d3 100644
--- a/Examples/test-suite/java/doxygen_translate_runme.java
+++ b/Examples/test-suite/java/doxygen_translate_runme.java
@@ -232,6 +232,21 @@ public class doxygen_translate_runme {
                 "\n" +
                 "");
 
+        wantedComments.put("doxygen_translate.doxygen_translate.htmlTableFunction(int)",
+                "The meaning of flags:\n" +
+                "\n" +
+                " @param byFlags bits marking required items:\n" +
+                "   <table>\n" +
+                "   <tr><th> Size in bits</th><th> Items Required </th></tr>\n" +
+                "   <tr><td> 1 - 8       </td><td>      1         </td></tr>\n" +
+                "   <tr><td> 9 - 16      </td><td>      2         </td></tr>\n" +
+                "   <tr><td> 17 - 32     </td><td>      4         </td></tr>\n" +
+                "   </table>\n" +
+                "   Almost all combinations of above flags are supported by\n" +
+                "   <code>htmlTable...</code> functions.\n" +
+                   "");
+
+        
         wantedComments.put("doxygen_translate.doxygen_translate.htmlEntitiesFunction(int, float)",
                 "All entities are treated as commands &copy; &trade; &reg;\n" +
                 "should work also&lt;in text                              \n" +
diff --git a/Examples/test-suite/python/doxygen_translate_runme.py b/Examples/test-suite/python/doxygen_translate_runme.py
index 9365d1ce6..48d2971a5 100755
--- a/Examples/test-suite/python/doxygen_translate_runme.py
+++ b/Examples/test-suite/python/doxygen_translate_runme.py
@@ -221,6 +221,24 @@ r"""
   """)
 
 
+commentVerifier.check(doxygen_translate.htmlTableFunction.__doc__,
+r"""
+  The meaning of flags:
+
+  Arguments:
+    byFlags (int) -- bits marking required items:
+    
+    | Size in bits| Items Required |
+    --------------------------------
+    | 1 - 8       |      1         |
+    | 9 - 16      |      2         |
+    | 17 - 32     |      4         |
+    
+    Almost all combinations of above flags are supported by
+    'htmlTable...' functions.
+  """)                      
+
+
 commentVerifier.check(doxygen_translate.htmlEntitiesFunction.__doc__,
 r"""
   All entities are treated as commands (C)  TM (R)
diff --git a/Source/DoxygenTranslator/src/DoxygenCommands.h b/Source/DoxygenTranslator/src/DoxygenCommands.h
index 7fa1dbb54..ff2527ace 100644
--- a/Source/DoxygenTranslator/src/DoxygenCommands.h
+++ b/Source/DoxygenTranslator/src/DoxygenCommands.h
@@ -104,26 +104,26 @@ const int commandHtmlSize = sizeof(commandHtml) / sizeof(*commandHtml);
 // Only entities which are translatable to plain text are used here. Others
 // are copied unchanged to output.
 const char *commandHtmlEntities[] = { "&copy", "&trade", "&reg", // (C), (TM), (R)
-"&lt",  // less-than symbol
-"&gt",  // greater-than symbol
-"&amp", // ampersand
-"&apos", // single quotation mark (straight)
-"&quot", // double quotation mark (straight)
-"&lsquo", // left single quotation mark
-"&rsquo", // right single quotation mark
-"&ldquo", // left double quotation mark
-"&rdquo", // right double quotation mark
-"&ndash", // n-dash (for numeric ranges, e.g. 2–8)
-"&mdash", // --
-"&nbsp", //
-"&times", // x
-"&minus", // -
-"&sdot", // .
-"&sim", // ~
-"&le", // <=
-"&ge", // >=
-"&larr", // <--
-"&rarr" // -->
+  "&lt",  // less-than symbol
+  "&gt",  // greater-than symbol
+  "&amp", // ampersand
+  "&apos", // single quotation mark (straight)
+  "&quot", // double quotation mark (straight)
+  "&lsquo", // left single quotation mark
+  "&rsquo", // right single quotation mark
+  "&ldquo", // left double quotation mark
+  "&rdquo", // right double quotation mark
+  "&ndash", // n-dash (for numeric ranges, e.g. 2–8)
+  "&mdash", // --
+  "&nbsp", //
+  "&times", // x
+  "&minus", // -
+  "&sdot", // .
+  "&sim", // ~
+  "&le", // <=
+  "&ge", // >=
+  "&larr", // <--
+  "&rarr" // -->
 };
 
 const int commandHtmlEntitiesSize = sizeof(commandHtmlEntities) / sizeof(*commandHtmlEntities);
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.cpp b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
index 22a3ccc96..f14fefafd 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
@@ -20,13 +20,14 @@
 //TODO {@link} {@linkplain} {@docRoot}, and other useful doxy commands that are not a javadoc tag
 
 // define static tables, they are filled in JavaDocConverter's constructor
-std::map<std::string, std::pair<JavaDocConverter::tagHandler, std::string > > JavaDocConverter::tagHandlers;
+std::map<std::string, std::pair<JavaDocConverter::tagHandler, std::string> > JavaDocConverter::tagHandlers;
 
 using std::string;
 using std::list;
 using std::vector;
 
-void JavaDocConverter::fillStaticTables() {
+void JavaDocConverter::fillStaticTables()
+{
   if (tagHandlers.size()) // fill only once
     return;
 
@@ -62,7 +63,6 @@ void JavaDocConverter::fillStaticTables() {
    *   Commenting methods of std types is simple - add comment to std_*.i file.
    */
 
-
   // these commands insert HTML tags
   tagHandlers["a"] = make_pair(&JavaDocConverter::handleTagHtml, "i");
   tagHandlers["arg"] = make_pair(&JavaDocConverter::handleTagHtml, "li");
@@ -98,13 +98,15 @@ void JavaDocConverter::fillStaticTables() {
   tagHandlers["invariant"] = make_pair(&JavaDocConverter::handleParagraph, "");
   tagHandlers["latexonly"] = make_pair(&JavaDocConverter::handleParagraph, "");
   tagHandlers["manonly"] = make_pair(&JavaDocConverter::handleParagraph, "");
-  tagHandlers["partofdescription"] = make_pair(&JavaDocConverter::handleParagraph, "");
+  tagHandlers["partofdescription"] = make_pair(
+      &JavaDocConverter::handleParagraph, "");
   tagHandlers["rtfonly"] = make_pair(&JavaDocConverter::handleParagraph, "");
   tagHandlers["short"] = make_pair(&JavaDocConverter::handleParagraph, "");
   tagHandlers["xmlonly"] = make_pair(&JavaDocConverter::handleParagraph, "");
   // these commands are kept as-is, they are supported by JavaDoc
   tagHandlers["author"] = make_pair(&JavaDocConverter::handleTagSame, "");
-  tagHandlers["authors"] = make_pair(&JavaDocConverter::handleTagSame, "author");
+  tagHandlers["authors"] = make_pair(&JavaDocConverter::handleTagSame,
+      "author");
   tagHandlers["deprecated"] = make_pair(&JavaDocConverter::handleTagSame, "");
   tagHandlers["exception"] = make_pair(&JavaDocConverter::handleTagSame, "");
   tagHandlers["package"] = make_pair(&JavaDocConverter::handleTagSame, "");
@@ -112,7 +114,8 @@ void JavaDocConverter::fillStaticTables() {
   tagHandlers["tparam"] = make_pair(&JavaDocConverter::handleTagParam, "");
   tagHandlers["result"] = make_pair(&JavaDocConverter::handleTagSame, "return");
   tagHandlers["return"] = make_pair(&JavaDocConverter::handleTagSame, "");
-  tagHandlers["returns"] = make_pair(&JavaDocConverter::handleTagSame, "return");
+  tagHandlers["returns"] = make_pair(&JavaDocConverter::handleTagSame,
+      "return");
   //tagHandlers["see"] = make_pair(&JavaDocConverter::handleTagSame, "");
   //tagHandlers["sa"] = make_pair(&JavaDocConverter::handleTagSame, "see");
   tagHandlers["since"] = make_pair(&JavaDocConverter::handleTagSame, "");
@@ -121,118 +124,160 @@ void JavaDocConverter::fillStaticTables() {
   tagHandlers["version"] = make_pair(&JavaDocConverter::handleTagSame, "");
   // these commands have special handlers
   tagHandlers["code"] = make_pair(&JavaDocConverter::handleTagExtended, "code");
-  tagHandlers["cond"] = make_pair(&JavaDocConverter::handleTagMessage, "Conditional comment: ");
-  tagHandlers["copyright"] = make_pair(&JavaDocConverter::handleTagMessage, "Copyright: ");
+  tagHandlers["cond"] = make_pair(&JavaDocConverter::handleTagMessage,
+      "Conditional comment: ");
+  tagHandlers["copyright"] = make_pair(&JavaDocConverter::handleTagMessage,
+      "Copyright: ");
   tagHandlers["else"] = make_pair(&JavaDocConverter::handleTagIf, "Else: ");
-  tagHandlers["elseif"] = make_pair(&JavaDocConverter::handleTagIf, "Else if: ");
-  tagHandlers["endcond"] = make_pair(&JavaDocConverter::handleTagMessage, "End of conditional comment.");
+  tagHandlers["elseif"] = make_pair(&JavaDocConverter::handleTagIf,
+      "Else if: ");
+  tagHandlers["endcond"] = make_pair(&JavaDocConverter::handleTagMessage,
+      "End of conditional comment.");
   // space in second arg prevents Javadoc to treat '@ example' as command. File name of
   // example is still informative to user.
-  tagHandlers["example"] = make_pair(&JavaDocConverter::handleTagSame, " example");
+  tagHandlers["example"] = make_pair(&JavaDocConverter::handleTagSame,
+      " example");
   tagHandlers["if"] = make_pair(&JavaDocConverter::handleTagIf, "If: ");
   tagHandlers["ifnot"] = make_pair(&JavaDocConverter::handleTagIf, "If not: ");
   tagHandlers["image"] = make_pair(&JavaDocConverter::handleTagImage, "");
   tagHandlers["link"] = make_pair(&JavaDocConverter::handleTagLink, "");
   tagHandlers["see"] = make_pair(&JavaDocConverter::handleTagSee, "");
   tagHandlers["sa"] = make_pair(&JavaDocConverter::handleTagSee, "");
-  tagHandlers["note"] = make_pair(&JavaDocConverter::handleTagMessage, "Note: ");
-  tagHandlers["overload"] = make_pair(&JavaDocConverter::handleTagMessage, "This is an overloaded member function, provided for"
-      " convenience. It differs from the above function only in what"
-      " argument(s) it accepts.");
+  tagHandlers["note"] = make_pair(&JavaDocConverter::handleTagMessage,
+      "Note: ");
+  tagHandlers["overload"] = make_pair(&JavaDocConverter::handleTagMessage,
+      "This is an overloaded member function, provided for"
+          " convenience. It differs from the above function only in what"
+          " argument(s) it accepts.");
   tagHandlers["par"] = make_pair(&JavaDocConverter::handleTagPar, "");
-  tagHandlers["remark"] = make_pair(&JavaDocConverter::handleTagMessage, "Remarks: ");
-  tagHandlers["remarks"] = make_pair(&JavaDocConverter::handleTagMessage, "Remarks: ");
-  tagHandlers["todo"] = make_pair(&JavaDocConverter::handleTagMessage, "TODO: ");
-  tagHandlers["verbatim"] = make_pair(&JavaDocConverter::handleTagExtended, "literal");
+  tagHandlers["remark"] = make_pair(&JavaDocConverter::handleTagMessage,
+      "Remarks: ");
+  tagHandlers["remarks"] = make_pair(&JavaDocConverter::handleTagMessage,
+      "Remarks: ");
+  tagHandlers["todo"] = make_pair(&JavaDocConverter::handleTagMessage,
+      "TODO: ");
+  tagHandlers["verbatim"] = make_pair(&JavaDocConverter::handleTagExtended,
+      "literal");
 
   // \f commands output literal Latex formula, which is still better than nothing.
   tagHandlers["f$"] = make_pair(&JavaDocConverter::handleTagVerbatim, "");
   tagHandlers["f["] = make_pair(&JavaDocConverter::handleTagVerbatim, "");
   tagHandlers["f{"] = make_pair(&JavaDocConverter::handleTagVerbatim, "");
 
-  tagHandlers["warning"] = make_pair(&JavaDocConverter::handleTagMessage, "Warning: ");
+  tagHandlers["warning"] = make_pair(&JavaDocConverter::handleTagMessage,
+      "Warning: ");
   // this command just prints it's contents
   // (it is internal command of swig's parser, contains plain text)
-  tagHandlers["plainstd::string"] = make_pair(&JavaDocConverter::handlePlainString, "");
-  tagHandlers["plainstd::endl"] = make_pair(&JavaDocConverter::handleNewLine, "");
+  tagHandlers["plainstd::string"] = make_pair(
+      &JavaDocConverter::handlePlainString, "");
+  tagHandlers["plainstd::endl"] = make_pair(&JavaDocConverter::handleNewLine,
+      "");
   tagHandlers["n"] = make_pair(&JavaDocConverter::handleNewLine, "");
 
   // HTML tags
-  tagHandlers["<a"      ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<a"      );
-  tagHandlers["<b"      ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<b"      );
-  tagHandlers["<blockquote"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<blockquote");
-  tagHandlers["<body"   ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<body"   );
-  tagHandlers["<br"     ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<br"     );
-  tagHandlers["<center" ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<center" );
-  tagHandlers["<caption"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<caption");
-  tagHandlers["<code"   ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<code"   );
-  tagHandlers["<dd"     ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<dd"     );
-  tagHandlers["<dfn"    ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<dfn"    );
-  tagHandlers["<div"    ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<div"    );
-  tagHandlers["<dl"     ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<dl"     );
-  tagHandlers["<dt"     ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<dt"     );
-  tagHandlers["<em"     ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<em"     );
-  tagHandlers["<form"   ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<form"   );
-  tagHandlers["<hr"     ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<hr"     );
-  tagHandlers["<h1"     ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<h1"     );
-  tagHandlers["<h2"     ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<h2"     );
-  tagHandlers["<h3"     ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<h3"     );
-  tagHandlers["<i"      ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<i"      );
-  tagHandlers["<input"  ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<input"  );
-  tagHandlers["<img"    ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<img"    );
-  tagHandlers["<li"     ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<li"     );
-  tagHandlers["<meta"   ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<meta"   );
-  tagHandlers["<multicol"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<multicol");
-  tagHandlers["<ol"     ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<ol"     );
-  tagHandlers["<p"      ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<p"      );
-  tagHandlers["<pre"    ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<pre"    );
-  tagHandlers["<small"  ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<small"  );
-  tagHandlers["<span"   ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<span"   );
-  tagHandlers["<strong" ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<strong" );
-  tagHandlers["<sub"    ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<sub"    );
-  tagHandlers["<sup"    ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<sup"    );
-  tagHandlers["<table"  ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<table"  );
-  tagHandlers["<td"     ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<td"     );
-  tagHandlers["<th"     ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<th"     );
-  tagHandlers["<tr"     ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<tr"     );
-  tagHandlers["<tt"     ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<tt"     );
-  tagHandlers["<kbd"    ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<kbd"    );
-  tagHandlers["<ul"     ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<ul"     );
-  tagHandlers["<var"    ] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<var"    );
+  tagHandlers["<a"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<a");
+  tagHandlers["<b"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<b");
+  tagHandlers["<blockquote"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag,
+      "<blockquote");
+  tagHandlers["<body"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag,
+      "<body");
+  tagHandlers["<br"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<br");
+  tagHandlers["<center"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag,
+      "<center");
+  tagHandlers["<caption"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag,
+      "<caption");
+  tagHandlers["<code"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag,
+      "<code");
+  tagHandlers["<dd"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<dd");
+  tagHandlers["<dfn"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<dfn");
+  tagHandlers["<div"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<div");
+  tagHandlers["<dl"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<dl");
+  tagHandlers["<dt"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<dt");
+  tagHandlers["<em"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<em");
+  tagHandlers["<form"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag,
+      "<form");
+  tagHandlers["<hr"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<hr");
+  tagHandlers["<h1"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<h1");
+  tagHandlers["<h2"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<h2");
+  tagHandlers["<h3"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<h3");
+  tagHandlers["<i"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<i");
+  tagHandlers["<input"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag,
+      "<input");
+  tagHandlers["<img"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<img");
+  tagHandlers["<li"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<li");
+  tagHandlers["<meta"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag,
+      "<meta");
+  tagHandlers["<multicol"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag,
+      "<multicol");
+  tagHandlers["<ol"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<ol");
+  tagHandlers["<p"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<p");
+  tagHandlers["<pre"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<pre");
+  tagHandlers["<small"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag,
+      "<small");
+  tagHandlers["<span"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag,
+      "<span");
+  tagHandlers["<strong"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag,
+      "<strong");
+  tagHandlers["<sub"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<sub");
+  tagHandlers["<sup"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<sup");
+  tagHandlers["<table"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag,
+      "<table");
+  tagHandlers["<td"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<td");
+  tagHandlers["<th"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<th");
+  tagHandlers["<tr"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<tr");
+  tagHandlers["<tt"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<tt");
+  tagHandlers["<kbd"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<kbd");
+  tagHandlers["<ul"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<ul");
+  tagHandlers["<var"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<var");
 
   // HTML entities
-  tagHandlers["&copy" ] = make_pair(&JavaDocConverter::handleHtmlEntity, "&copy");
-  tagHandlers["&trade"] = make_pair(&JavaDocConverter::handleHtmlEntity, "&trade");
-  tagHandlers["&reg"  ] = make_pair(&JavaDocConverter::handleHtmlEntity, "&reg");
-  tagHandlers["&lt"   ] = make_pair(&JavaDocConverter::handleHtmlEntity, "&lt");
-  tagHandlers["&gt"   ] = make_pair(&JavaDocConverter::handleHtmlEntity, "&gt");
-  tagHandlers["&amp"  ] = make_pair(&JavaDocConverter::handleHtmlEntity, "&amp");
-  tagHandlers["&apos" ] = make_pair(&JavaDocConverter::handleHtmlEntity, "&apos");
-  tagHandlers["&quot" ] = make_pair(&JavaDocConverter::handleHtmlEntity, "&quot");
-  tagHandlers["&lsquo"] = make_pair(&JavaDocConverter::handleHtmlEntity, "&lsquo");
-  tagHandlers["&rsquo"] = make_pair(&JavaDocConverter::handleHtmlEntity, "&rsquo");
-  tagHandlers["&ldquo"] = make_pair(&JavaDocConverter::handleHtmlEntity, "&ldquo");
-  tagHandlers["&rdquo"] = make_pair(&JavaDocConverter::handleHtmlEntity, "&rdquo");
-  tagHandlers["&ndash"] = make_pair(&JavaDocConverter::handleHtmlEntity, "&ndash");
-  tagHandlers["&mdash"] = make_pair(&JavaDocConverter::handleHtmlEntity, "&mdash");
-  tagHandlers["&nbsp" ] = make_pair(&JavaDocConverter::handleHtmlEntity, "&nbsp");
-  tagHandlers["&times"] = make_pair(&JavaDocConverter::handleHtmlEntity, "&times");
-  tagHandlers["&minus"] = make_pair(&JavaDocConverter::handleHtmlEntity, "&minus");
-  tagHandlers["&sdot" ] = make_pair(&JavaDocConverter::handleHtmlEntity, "&sdot");
-  tagHandlers["&sim"  ] = make_pair(&JavaDocConverter::handleHtmlEntity, "&sim");
-  tagHandlers["&le"   ] = make_pair(&JavaDocConverter::handleHtmlEntity, "&le");
-  tagHandlers["&ge"   ] = make_pair(&JavaDocConverter::handleHtmlEntity, "&ge");
-  tagHandlers["&larr" ] = make_pair(&JavaDocConverter::handleHtmlEntity, "&larr");
-  tagHandlers["&rarr" ] = make_pair(&JavaDocConverter::handleHtmlEntity, "&rarr");
+  tagHandlers["&copy"] = make_pair(&JavaDocConverter::handleHtmlEntity,
+      "&copy");
+  tagHandlers["&trade"] = make_pair(&JavaDocConverter::handleHtmlEntity,
+      "&trade");
+  tagHandlers["&reg"] = make_pair(&JavaDocConverter::handleHtmlEntity, "&reg");
+  tagHandlers["&lt"] = make_pair(&JavaDocConverter::handleHtmlEntity, "&lt");
+  tagHandlers["&gt"] = make_pair(&JavaDocConverter::handleHtmlEntity, "&gt");
+  tagHandlers["&amp"] = make_pair(&JavaDocConverter::handleHtmlEntity, "&amp");
+  tagHandlers["&apos"] = make_pair(&JavaDocConverter::handleHtmlEntity,
+      "&apos");
+  tagHandlers["&quot"] = make_pair(&JavaDocConverter::handleHtmlEntity,
+      "&quot");
+  tagHandlers["&lsquo"] = make_pair(&JavaDocConverter::handleHtmlEntity,
+      "&lsquo");
+  tagHandlers["&rsquo"] = make_pair(&JavaDocConverter::handleHtmlEntity,
+      "&rsquo");
+  tagHandlers["&ldquo"] = make_pair(&JavaDocConverter::handleHtmlEntity,
+      "&ldquo");
+  tagHandlers["&rdquo"] = make_pair(&JavaDocConverter::handleHtmlEntity,
+      "&rdquo");
+  tagHandlers["&ndash"] = make_pair(&JavaDocConverter::handleHtmlEntity,
+      "&ndash");
+  tagHandlers["&mdash"] = make_pair(&JavaDocConverter::handleHtmlEntity,
+      "&mdash");
+  tagHandlers["&nbsp"] = make_pair(&JavaDocConverter::handleHtmlEntity,
+      "&nbsp");
+  tagHandlers["&times"] = make_pair(&JavaDocConverter::handleHtmlEntity,
+      "&times");
+  tagHandlers["&minus"] = make_pair(&JavaDocConverter::handleHtmlEntity,
+      "&minus");
+  tagHandlers["&sdot"] = make_pair(&JavaDocConverter::handleHtmlEntity,
+      "&sdot");
+  tagHandlers["&sim"] = make_pair(&JavaDocConverter::handleHtmlEntity, "&sim");
+  tagHandlers["&le"] = make_pair(&JavaDocConverter::handleHtmlEntity, "&le");
+  tagHandlers["&ge"] = make_pair(&JavaDocConverter::handleHtmlEntity, "&ge");
+  tagHandlers["&larr"] = make_pair(&JavaDocConverter::handleHtmlEntity,
+      "&larr");
+  tagHandlers["&rarr"] = make_pair(&JavaDocConverter::handleHtmlEntity,
+      "&rarr");
 }
 
-
-JavaDocConverter::JavaDocConverter(bool debugTranslator, bool debugParser)
-: DoxygenTranslator(debugTranslator, debugParser) {
+JavaDocConverter::JavaDocConverter(bool debugTranslator, bool debugParser) :
+    DoxygenTranslator(debugTranslator, debugParser)
+{
   fillStaticTables();
 }
 
-
 /**
  * Formats comment lines by inserting '\n *' at to long lines and tabs for
  * indent. Currently it is disabled, which means original comment format is
@@ -242,7 +287,8 @@ JavaDocConverter::JavaDocConverter(bool debugTranslator, bool debugParser)
  * better algorithm.
  */
 std::string JavaDocConverter::formatCommand(std::string unformattedLine,
-                                                int indent) {
+                                            int indent)
+{
   std::string formattedLines;
   return unformattedLine;  // currently disabled
   int lastPosition = 0;
@@ -262,10 +308,12 @@ std::string JavaDocConverter::formatCommand(std::string unformattedLine,
       if (!isFirstLine)
         for (int j = 0; j < indent; j++) {
           formattedLines.append("\t");
-        } else {
-          isFirstLine = 0;
         }
-      formattedLines.append(unformattedLine.substr(lastPosition, i - lastPosition + 1));
+      else {
+        isFirstLine = 0;
+      }
+      formattedLines.append(
+          unformattedLine.substr(lastPosition, i - lastPosition + 1));
       formattedLines.append("\n *");
 
     }
@@ -276,13 +324,14 @@ std::string JavaDocConverter::formatCommand(std::string unformattedLine,
         formattedLines.append("\t");
       }
     }
-    formattedLines.append(unformattedLine.substr(lastPosition, unformattedLine.length() - lastPosition));
+    formattedLines.append(
+        unformattedLine.substr(lastPosition,
+            unformattedLine.length() - lastPosition));
   }
 
   return formattedLines;
 }
 
-
 /**
  * Returns true, if the given parameter exists in the current node
  * (for example param is a name of function parameter). If feature
@@ -290,7 +339,8 @@ std::string JavaDocConverter::formatCommand(std::string unformattedLine,
  * true - parameters are copied to output regardless of presence in
  * function params list.
  */
-bool JavaDocConverter::paramExists(std::string param) {
+bool JavaDocConverter::paramExists(std::string param)
+{
 
   if (GetFlag(currentNode, "feature:doxygen:nostripparams")) {
     return true;
@@ -300,7 +350,7 @@ bool JavaDocConverter::paramExists(std::string param) {
 
   for (Parm *p = plist; p;) {
 
-    if (Getattr(p, "name") && Char(Getattr(p, "name")) == param) {
+    if (Getattr(p, "name") && Char (Getattr(p, "name")) == param) {
       return true;
     }
     /* doesn't seem to work always: in some cases (especially for 'self' parameters)
@@ -315,80 +365,92 @@ bool JavaDocConverter::paramExists(std::string param) {
   return false;
 }
 
-
-std::string JavaDocConverter::translateSubtree(DoxygenEntity &doxygenEntity) {
+std::string JavaDocConverter::translateSubtree(DoxygenEntity &doxygenEntity)
+{
   std::string translatedComment;
-  
+
   if (doxygenEntity.isLeaf) {
     return translatedComment;
   }
-  
+
   for (DoxygenEntityListIt p = doxygenEntity.entityList.begin();
-       p != doxygenEntity.entityList.end(); p++) {
+      p != doxygenEntity.entityList.end(); p++) {
 
     translateEntity(*p, translatedComment);
     translateSubtree(*p);
   }
-  
+
   return translatedComment;
 }
 
-
 /**
  * Checks if a handler for the given tag exists, and calls it.
  */
 void JavaDocConverter::translateEntity(DoxygenEntity &tag,
-                                            std::string &translatedComment) {
+                                       std::string &translatedComment)
+{
 
-  std::map<std::string, std::pair<tagHandler, std::string > >::iterator it;
+  std::map<std::string, std::pair<tagHandler, std::string> >::iterator it;
   it = tagHandlers.find(tag.typeOfEntity);
 
   if (it != tagHandlers.end()) {
     (this->*(it->second.first))(tag, translatedComment, it->second.second);
   } else {
-      // do NOT print warning, since there are many tags, which are not
-      // translatable - many warnings hide important ones
-      // addError(WARN_DOXYGEN_COMMAND_ERROR, "Unknown doxygen or HTML tag: " + tag.typeOfEntity);
+    // do NOT print warning, since there are many tags, which are not
+    // translatable - many warnings hide important ones
+    // addError(WARN_DOXYGEN_COMMAND_ERROR, "Unknown doxygen or HTML tag: " + tag.typeOfEntity);
   }
 }
 
-
-void JavaDocConverter::handleTagHtml(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
+void JavaDocConverter::handleTagHtml(DoxygenEntity& tag,
+                                     std::string& translatedComment,
+                                     std::string &arg)
+{
   if (tag.entityList.size()) { // do not include empty tags
     std::string tagData = translateSubtree(tag);
     // wrap the thing, ignoring whitespaces
     size_t wsPos = tagData.find_last_not_of("\n\t ");
     if (wsPos != std::string::npos)
-      translatedComment += "<" + arg + ">" + tagData.substr(0, wsPos + 1) + "</" + arg + ">" + tagData.substr(wsPos + 1);
+      translatedComment += "<" + arg + ">" + tagData.substr(0, wsPos + 1) + "</"
+          + arg + ">" + tagData.substr(wsPos + 1);
     else
-      translatedComment += "<" + arg + ">" + translateSubtree(tag) + "</" + arg + "> ";
+      translatedComment += "<" + arg + ">" + translateSubtree(tag) + "</" + arg
+          + "> ";
   }
 }
 
-
-void JavaDocConverter::handleDoxyHtmlTag(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
-    std::string htmlTagArgs = tag.data;
-    if (htmlTagArgs == "/") {
-        // end html tag, for example "</ul>
-        translatedComment += "</" + arg.substr(1) + ">";
-    } else {
-        translatedComment += arg + htmlTagArgs + ">";
-    }
+void JavaDocConverter::handleDoxyHtmlTag(DoxygenEntity& tag,
+                                         std::string& translatedComment,
+                                         std::string &arg)
+{
+  std::string htmlTagArgs = tag.data;
+  if (htmlTagArgs == "/") {
+    // end html tag, for example "</ul>
+    translatedComment += "</" + arg.substr(1) + ">";
+  } else {
+    translatedComment += arg + htmlTagArgs + ">";
+  }
 }
 
-
-void JavaDocConverter::handleHtmlEntity(DoxygenEntity&, std::string& translatedComment, std::string &arg) {
-    // html entities can be preserved for Java
-    translatedComment += arg + ';';
+void JavaDocConverter::handleHtmlEntity(DoxygenEntity&,
+                                        std::string& translatedComment,
+                                        std::string &arg)
+{
+  // html entities can be preserved for Java
+  translatedComment += arg + ';';
 }
 
-
-void JavaDocConverter::handleNewLine(DoxygenEntity&, std::string& translatedComment, std::string&) {
+void JavaDocConverter::handleNewLine(DoxygenEntity&,
+                                     std::string& translatedComment,
+                                     std::string&)
+{
   translatedComment += "\n * ";
 }
 
-
-void JavaDocConverter::handleTagChar(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
+void JavaDocConverter::handleTagChar(DoxygenEntity& tag,
+                                     std::string& translatedComment,
+                                     std::string &arg)
+{
   // escape it if we need to, else just print
   if (arg.size())
     translatedComment += arg;
@@ -397,42 +459,57 @@ void JavaDocConverter::handleTagChar(DoxygenEntity& tag, std::string& translated
 }
 
 // handles tags which are the same in Doxygen and Javadoc.
-void JavaDocConverter::handleTagSame(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
+void JavaDocConverter::handleTagSame(DoxygenEntity& tag,
+                                     std::string& translatedComment,
+                                     std::string &arg)
+{
   if (arg.size())
     tag.typeOfEntity = arg;
-  translatedComment += formatCommand(std::string("@" + tag.typeOfEntity + " " + translateSubtree(tag)), 2);
+  translatedComment += formatCommand(
+      std::string("@" + tag.typeOfEntity + " " + translateSubtree(tag)), 2);
 }
 
-
-void JavaDocConverter::handleParagraph(DoxygenEntity& tag, std::string& translatedComment, std::string&) {
+void JavaDocConverter::handleParagraph(DoxygenEntity& tag,
+                                       std::string& translatedComment,
+                                       std::string&)
+{
   translatedComment += formatCommand(translateSubtree(tag), 0);
 }
 
-
-void JavaDocConverter::handlePlainString(DoxygenEntity& tag, std::string& translatedComment, std::string&) {
+void JavaDocConverter::handlePlainString(DoxygenEntity& tag,
+                                         std::string& translatedComment,
+                                         std::string&)
+{
   translatedComment += tag.data;
- // if (tag.data.size() && tag.data[tag.data.size()-1] != ' ')
- // 	translatedComment += " ";
+  // if (tag.data.size() && tag.data[tag.data.size()-1] != ' ')
+  // 	translatedComment += " ";
 }
 
-
-void JavaDocConverter::handleTagVerbatim(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
+void JavaDocConverter::handleTagVerbatim(DoxygenEntity& tag,
+                                         std::string& translatedComment,
+                                         std::string &arg)
+{
   translatedComment += arg + " ";
-  for (DoxygenEntityListCIt it = tag.entityList.begin(); it != tag.entityList.end(); it++) {
-      translatedComment += it->data;
+  for (DoxygenEntityListCIt it = tag.entityList.begin();
+      it != tag.entityList.end(); it++) {
+    translatedComment += it->data;
   }
 }
 
-
-void JavaDocConverter::handleTagExtended(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
+void JavaDocConverter::handleTagExtended(DoxygenEntity& tag,
+                                         std::string& translatedComment,
+                                         std::string &arg)
+{
   std::string dummy;
   translatedComment += "{@" + arg + " ";
   handleParagraph(tag, translatedComment, dummy);
   translatedComment += "}";
 }
 
-
-void JavaDocConverter::handleTagIf(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
+void JavaDocConverter::handleTagIf(DoxygenEntity& tag,
+                                   std::string& translatedComment,
+                                   std::string &arg)
+{
   std::string dummy;
   translatedComment += arg;
   if (tag.entityList.size()) {
@@ -442,22 +519,26 @@ void JavaDocConverter::handleTagIf(DoxygenEntity& tag, std::string& translatedCo
   }
 }
 
-
-void JavaDocConverter::handleTagMessage(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
+void JavaDocConverter::handleTagMessage(DoxygenEntity& tag,
+                                        std::string& translatedComment,
+                                        std::string &arg)
+{
   std::string dummy;
   translatedComment += formatCommand(arg, 0);
   handleParagraph(tag, translatedComment, dummy);
 }
 
-
-void JavaDocConverter::handleTagImage(DoxygenEntity& tag, std::string& translatedComment, std::string&) {
+void JavaDocConverter::handleTagImage(DoxygenEntity& tag,
+                                      std::string& translatedComment,
+                                      std::string&)
+{
   if (tag.entityList.size() < 2)
     return;
 
   std::string file;
   std::string title;
 
-  std::list <DoxygenEntity>::iterator it = tag.entityList.begin();
+  std::list<DoxygenEntity>::iterator it = tag.entityList.begin();
   if (it->data != "html")
     return;
 
@@ -477,8 +558,10 @@ void JavaDocConverter::handleTagImage(DoxygenEntity& tag, std::string& translate
   translatedComment += "/>";
 }
 
-
-void JavaDocConverter::handleTagPar(DoxygenEntity& tag, std::string& translatedComment, std::string&) {
+void JavaDocConverter::handleTagPar(DoxygenEntity& tag,
+                                    std::string& translatedComment,
+                                    std::string&)
+{
   std::string dummy;
   translatedComment += "<p";
   if (tag.entityList.size()) {
@@ -490,10 +573,10 @@ void JavaDocConverter::handleTagPar(DoxygenEntity& tag, std::string& translatedC
   translatedComment += "</p>";
 }
 
-
 void JavaDocConverter::handleTagParam(DoxygenEntity& tag,
                                       std::string& translatedComment,
-                                      std::string&) {
+                                      std::string&)
+{
   std::string dummy;
 
   if (!tag.entityList.size())
@@ -507,17 +590,19 @@ void JavaDocConverter::handleTagParam(DoxygenEntity& tag,
   handleParagraph(tag, translatedComment, dummy);
 }
 
-
-string JavaDocConverter::convertLink(string linkObject) {
+string JavaDocConverter::convertLink(string linkObject)
+{
   if (GetFlag(currentNode, "feature:doxygen:nolinktranslate"))
     return linkObject;
   // find the params in function in linkObject (if any)
   size_t lbracePos = linkObject.find('(', 0);
   size_t rbracePos = linkObject.find(')', 0);
-  if (lbracePos == string::npos || rbracePos == string::npos || lbracePos >= rbracePos)
+  if (lbracePos == string::npos || rbracePos == string::npos
+      || lbracePos >= rbracePos)
     return "";
 
-  string paramsStr = linkObject.substr(lbracePos + 1, rbracePos - lbracePos - 1);
+  string paramsStr = linkObject.substr(lbracePos + 1,
+      rbracePos - lbracePos - 1);
   // strip the params, to fill them later
   linkObject = linkObject.substr(0, lbracePos);
 
@@ -539,7 +624,7 @@ string JavaDocConverter::convertLink(string linkObject) {
   }
 
   linkObject += "(";
-  for (size_t i=0; i<params.size(); i++) {
+  for (size_t i = 0; i < params.size(); i++) {
     // translate c/c++ type string to swig's type
     // i e 'int **arr[100][10]' -> 'a(100).a(10).p.p.int'
     // also converting arrays to pointers
@@ -551,18 +636,17 @@ string JavaDocConverter::convertLink(string linkObject) {
       SwigType_add_qualifier(swigType, "const");
 
     // handle pointers, references and arrays
-    for (int j=(int)params[i].size() - 1; j>=0; j--) {
+    for (int j = (int) params[i].size() - 1; j >= 0; j--) {
       // skip all the [...] blocks, write 'p.' for every of it
       if (paramStr[j] == ']') {
-        while (j>=0 && paramStr[j] != '[')
+        while (j >= 0 && paramStr[j] != '[')
           j--;
         // no closing brace
         if (j < 0)
           return "";
         SwigType_add_pointer(swigType);
         continue;
-      }
-      else if (paramStr[j] == '*')
+      } else if (paramStr[j] == '*')
         SwigType_add_pointer(swigType);
       else if (paramStr[j] == '&')
         SwigType_add_reference(swigType);
@@ -572,7 +656,8 @@ string JavaDocConverter::convertLink(string linkObject) {
           typeNameStart = 0;
         else
           typeNameStart++;
-        Append(swigType, paramStr.substr(typeNameStart, j - typeNameStart + 1).c_str());
+        Append(swigType,
+            paramStr.substr(typeNameStart, j - typeNameStart + 1).c_str());
         break;
       }
     }
@@ -580,10 +665,11 @@ string JavaDocConverter::convertLink(string linkObject) {
     // make dummy param list, to lookup typemaps for it
     Parm *dummyParam = NewParm(swigType, "", 0);
     Swig_typemap_attach_parms("jstype", dummyParam, NULL);
-    Language::instance()->replaceSpecialVariables(0, Getattr(dummyParam, "tmap:jstype"), dummyParam);
+    Language::instance()->replaceSpecialVariables(0,
+        Getattr(dummyParam, "tmap:jstype"), dummyParam);
 
     //Swig_print(dummyParam, 1);
-    linkObject += Char(Getattr(dummyParam, "tmap:jstype"));
+    linkObject += Char (Getattr(dummyParam, "tmap:jstype"));
     if (i != params.size() - 1)
       linkObject += ",";
 
@@ -595,8 +681,10 @@ string JavaDocConverter::convertLink(string linkObject) {
   return linkObject;
 }
 
-
-void JavaDocConverter::handleTagLink(DoxygenEntity& tag, std::string& translatedComment, std::string&) {
+void JavaDocConverter::handleTagLink(DoxygenEntity& tag,
+                                     std::string& translatedComment,
+                                     std::string&)
+{
   std::string dummy;
   if (!tag.entityList.size())
     return;
@@ -612,8 +700,10 @@ void JavaDocConverter::handleTagLink(DoxygenEntity& tag, std::string& translated
   translatedComment += "}";
 }
 
-
-void JavaDocConverter::handleTagSee(DoxygenEntity& tag, std::string& translatedComment, std::string&) {
+void JavaDocConverter::handleTagSee(DoxygenEntity& tag,
+                                    std::string& translatedComment,
+                                    std::string&)
+{
   std::string dummy;
   if (!tag.entityList.size())
     return;
@@ -624,7 +714,7 @@ void JavaDocConverter::handleTagSee(DoxygenEntity& tag, std::string& translatedC
   // :: or # may be used as a separator between class name and method name.
   list<DoxygenEntity>::iterator it;
   string methodRef;
-  for (it = tag.entityList.begin(); it!=tag.entityList.end(); it++) {
+  for (it = tag.entityList.begin(); it != tag.entityList.end(); it++) {
     if (it->typeOfEntity == "plainstd::endl") {
       // handleNewLine(*it, translatedComment, dummy);
       continue;
@@ -632,13 +722,13 @@ void JavaDocConverter::handleTagSee(DoxygenEntity& tag, std::string& translatedC
 
     // restore entities which may be used in C++ type declaration
     if (it->typeOfEntity == "&amp") {
-        methodRef += '&';
+      methodRef += '&';
     } else if (it->typeOfEntity == "&lt") {
-        methodRef += '<';
+      methodRef += '<';
     } else if (it->typeOfEntity == "&gt") {
-        methodRef += '>';
+      methodRef += '>';
     } else {
-        methodRef += it->data;
+      methodRef += it->data;
     }
   }
 
@@ -646,7 +736,8 @@ void JavaDocConverter::handleTagSee(DoxygenEntity& tag, std::string& translatedC
   size_t lbrace = methodRef.find('(');
   size_t dblColon = methodRef.find("::");
   if (dblColon < lbrace) {
-      methodRef = methodRef.substr(0, dblColon) + '#' + methodRef.substr(dblColon + 2);
+    methodRef = methodRef.substr(0, dblColon) + '#'
+        + methodRef.substr(dblColon + 2);
   }
 
   translatedComment += "@see ";
@@ -657,22 +748,21 @@ void JavaDocConverter::handleTagSee(DoxygenEntity& tag, std::string& translatedC
   translatedComment += linkObject;
 }
 
-
 /* This function moves all endlines at the end of child entities
  * out of the child entities to the parent.
  * For example, entity tree:
 
-   -root
-    |-param
-      |-paramText
-      |-endline
+ -root
+ |-param
+ |-paramText
+ |-endline
 
-   should be turned to
+ should be turned to
 
-   -root
-    |-param
-      |-paramText
-    |-endline
+ -root
+ |-param
+ |-paramText
+ |-endline
  *
  */
 int JavaDocConverter::shiftEndlinesUpTree(DoxygenEntity &root, int level)
@@ -694,21 +784,22 @@ int JavaDocConverter::shiftEndlinesUpTree(DoxygenEntity &root, int level)
   }
 
   int removedCount = 0;
-  while (!root.entityList.empty()  &&  root.entityList.rbegin()->typeOfEntity == "plainstd::endl") {
+  while (!root.entityList.empty()
+      && root.entityList.rbegin()->typeOfEntity == "plainstd::endl") {
     root.entityList.pop_back();
     removedCount++;
   }
   return removedCount;
 }
 
-
 /**
  * This makes sure that all comment lines contain '*'. It is not mandatory in doxygen,
  * but highly recommended for Javadoc. '*' in empty lines are indented according
  * to indentation of the first line. Indentation of non-empty lines is not
  * changed - garbage in garbage out.
  */
-std::string JavaDocConverter::indentAndInsertAsterisks(const string &doc) {
+std::string JavaDocConverter::indentAndInsertAsterisks(const string &doc)
+{
 
   size_t idx = doc.find('\n');
   size_t indent = 0;
@@ -743,17 +834,17 @@ std::string JavaDocConverter::indentAndInsertAsterisks(const string &doc) {
   while (idx != string::npos) {
 
     size_t nonspaceIdx = translatedStr.find_first_not_of(" \t", idx + 1);
-    if (nonspaceIdx != string::npos  &&  translatedStr[nonspaceIdx] != '*') {
+    if (nonspaceIdx != string::npos && translatedStr[nonspaceIdx] != '*') {
       // line without '*' found - is it empty?
       if (translatedStr[nonspaceIdx] != '\n') {
         // add '* ' to each line without it
-        translatedStr = translatedStr.substr(0, nonspaceIdx) + "* " +
-                translatedStr.substr(nonspaceIdx);
+        translatedStr = translatedStr.substr(0, nonspaceIdx) + "* "
+            + translatedStr.substr(nonspaceIdx);
         //printf(translatedStr.c_str());
       } else {
         // we found empty line, replace it with indented '*'
-        translatedStr = translatedStr.substr(0, idx + 1) + indentStr +
-                "* " + translatedStr.substr(nonspaceIdx);
+        translatedStr = translatedStr.substr(0, idx + 1) + indentStr + "* "
+            + translatedStr.substr(nonspaceIdx);
       }
     }
     idx = translatedStr.find('\n', nonspaceIdx);
@@ -774,8 +865,8 @@ std::string JavaDocConverter::indentAndInsertAsterisks(const string &doc) {
   return translatedStr;
 }
 
-
-String *JavaDocConverter::makeDocumentation(Node *node) {
+String *JavaDocConverter::makeDocumentation(Node *node)
+{
 
   String *documentation = getDoxygenComment(node);
 
@@ -785,7 +876,7 @@ String *JavaDocConverter::makeDocumentation(Node *node) {
 
   if (GetFlag(node, "feature:doxygen:notranslate")) {
 
-    string doc = Char(documentation);
+    string doc = Char (documentation);
 
     string translatedStr = indentAndInsertAsterisks(doc);
 
@@ -794,9 +885,8 @@ String *JavaDocConverter::makeDocumentation(Node *node) {
     return comment;
   }
 
-  DoxygenEntityList entityList = parser.createTree(Char(documentation),
-                                                   Char(Getfile(documentation)),
-                                                   Getline(documentation));
+  DoxygenEntityList entityList = parser.createTree(Char (documentation),
+      Char (Getfile(documentation)), Getline(documentation));
 
   // entityList.sort(CompareDoxygenEntities()); sorting currently not used,
 
@@ -816,14 +906,14 @@ String *JavaDocConverter::makeDocumentation(Node *node) {
   shiftEndlinesUpTree(root);
 
   // strip endlines at the beginning
-  while (!root.entityList.empty()  &&
-          root.entityList.begin()->typeOfEntity == "plainstd::endl") {
+  while (!root.entityList.empty()
+      && root.entityList.begin()->typeOfEntity == "plainstd::endl") {
     root.entityList.pop_front();
   }
 
   // and at the end
-  while (!root.entityList.empty()  &&
-          root.entityList.rbegin()->typeOfEntity == "plainstd::endl") {
+  while (!root.entityList.empty()
+      && root.entityList.rbegin()->typeOfEntity == "plainstd::endl") {
     root.entityList.pop_back();
   }
 
@@ -835,13 +925,12 @@ String *JavaDocConverter::makeDocumentation(Node *node) {
     std::cout << "\n---RESULT IN JAVADOC---" << std::endl;
     std::cout << javaDocString;
   }
-  
+
   return NewString(javaDocString.c_str());
 }
 
-
-void JavaDocConverter::addError(int warningType,
-                                     const std::string &message) {
-  Swig_warning(warningType, "", 0,
-               "Doxygen parser warning: %s. \n", message.c_str());
+void JavaDocConverter::addError(int warningType, const std::string &message)
+{
+  Swig_warning(warningType, "", 0, "Doxygen parser warning: %s. \n",
+      message.c_str());
 }
diff --git a/Source/DoxygenTranslator/src/PyDocConverter.cpp b/Source/DoxygenTranslator/src/PyDocConverter.cpp
index 7200a2de6..4346fb99c 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/PyDocConverter.cpp
@@ -19,13 +19,13 @@
 #include <iostream>
 
 // define static tables, they are filled in PyDocConverter's constructor
-std::map<std::string, std::pair<PyDocConverter::tagHandler, std::string > > PyDocConverter::tagHandlers;
+std::map<std::string, std::pair<PyDocConverter::tagHandler, std::string> > PyDocConverter::tagHandlers;
 std::map<std::string, std::string> PyDocConverter::sectionTitles;
 
 using std::string;
 
-
-void PyDocConverter::fillStaticTables() {
+void PyDocConverter::fillStaticTables()
+{
   if (tagHandlers.size()) // fill only once
     return;
 
@@ -94,15 +94,18 @@ void PyDocConverter::fillStaticTables() {
   tagHandlers["manonly"] = make_pair(&PyDocConverter::handleParagraph, "");
   tagHandlers["note"] = make_pair(&PyDocConverter::handleParagraph, "");
   tagHandlers["p"] = make_pair(&PyDocConverter::handleParagraph, "");
-  tagHandlers["partofdescription"] = make_pair(&PyDocConverter::handleParagraph, "");
+  tagHandlers["partofdescription"] = make_pair(&PyDocConverter::handleParagraph,
+      "");
   tagHandlers["rtfonly"] = make_pair(&PyDocConverter::handleParagraph, "");
   tagHandlers["return"] = make_pair(&PyDocConverter::handleParagraph, "");
   tagHandlers["returns"] = make_pair(&PyDocConverter::handleParagraph, "");
   tagHandlers["result"] = make_pair(&PyDocConverter::handleParagraph, "");
   tagHandlers["remark"] = make_pair(&PyDocConverter::handleParagraph, "");
   tagHandlers["remarks"] = make_pair(&PyDocConverter::handleParagraph, "");
-  tagHandlers["sa"] = make_pair(&PyDocConverter::handleTagMessage, "See also: ");
-  tagHandlers["see"] = make_pair(&PyDocConverter::handleTagMessage, "See also: ");
+  tagHandlers["sa"] = make_pair(&PyDocConverter::handleTagMessage,
+      "See also: ");
+  tagHandlers["see"] = make_pair(&PyDocConverter::handleTagMessage,
+      "See also: ");
   tagHandlers["since"] = make_pair(&PyDocConverter::handleParagraph, "");
   tagHandlers["short"] = make_pair(&PyDocConverter::handleParagraph, "");
   tagHandlers["throw"] = make_pair(&PyDocConverter::handleParagraph, "");
@@ -114,23 +117,27 @@ void PyDocConverter::fillStaticTables() {
   tagHandlers["xmlonly"] = make_pair(&PyDocConverter::handleParagraph, "");
   // these commands have special handlers
   tagHandlers["arg"] = make_pair(&PyDocConverter::handleTagMessage, " -");
-  tagHandlers["cond"] = make_pair(&PyDocConverter::handleTagMessage, "Conditional comment: ");
+  tagHandlers["cond"] = make_pair(&PyDocConverter::handleTagMessage,
+      "Conditional comment: ");
   tagHandlers["else"] = make_pair(&PyDocConverter::handleTagIf, "Else: ");
   tagHandlers["elseif"] = make_pair(&PyDocConverter::handleTagIf, "Else if: ");
-  tagHandlers["endcond"] = make_pair(&PyDocConverter::handleTagMessage, "End of conditional comment.");
+  tagHandlers["endcond"] = make_pair(&PyDocConverter::handleTagMessage,
+      "End of conditional comment.");
   tagHandlers["if"] = make_pair(&PyDocConverter::handleTagIf, "If: ");
   tagHandlers["ifnot"] = make_pair(&PyDocConverter::handleTagIf, "If not: ");
   tagHandlers["image"] = make_pair(&PyDocConverter::handleTagImage, "");
   tagHandlers["li"] = make_pair(&PyDocConverter::handleTagMessage, " -");
-  tagHandlers["overload"] = make_pair(&PyDocConverter::handleTagMessage, "This is an overloaded member function, provided for"
-      " convenience.\nIt differs from the above function only in what"
-      " argument(s) it accepts.");
+  tagHandlers["overload"] = make_pair(&PyDocConverter::handleTagMessage,
+      "This is an overloaded member function, provided for"
+          " convenience.\nIt differs from the above function only in what"
+          " argument(s) it accepts.");
   tagHandlers["par"] = make_pair(&PyDocConverter::handleTagPar, "");
   tagHandlers["param"] = make_pair(&PyDocConverter::handleTagParam, "");
   tagHandlers["tparam"] = make_pair(&PyDocConverter::handleTagParam, "");
   // this command just prints it's contents
   // (it is internal command of swig's parser, contains plain text)
-  tagHandlers["plainstd::string"] = make_pair(&PyDocConverter::handlePlainString, "");
+  tagHandlers["plainstd::string"] = make_pair(
+      &PyDocConverter::handlePlainString, "");
   tagHandlers["plainstd::endl"] = make_pair(&PyDocConverter::handleNewLine, "");
   tagHandlers["n"] = make_pair(&PyDocConverter::handleNewLine, "");
 
@@ -140,97 +147,99 @@ void PyDocConverter::fillStaticTables() {
   tagHandlers["f{"] = make_pair(&PyDocConverter::handleTagVerbatim, "");
 
   // HTML tags
-  tagHandlers["<a"      ] = make_pair(&PyDocConverter::handleDoxyHtmlTag_A, ""      );
-  tagHandlers["<b"      ] = make_pair(&PyDocConverter::handleDoxyHtmlTag2, "__");
-  tagHandlers["<blockquote"] = make_pair(&PyDocConverter::handleDoxyHtmlTag_A, "Quote: ");
-  tagHandlers["<body"   ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, ""   );
-  tagHandlers["<br"     ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "\n"     );
+  tagHandlers["<a"] = make_pair(&PyDocConverter::handleDoxyHtmlTag_A, "");
+  tagHandlers["<b"] = make_pair(&PyDocConverter::handleDoxyHtmlTag2, "__");
+  tagHandlers["<blockquote"] = make_pair(&PyDocConverter::handleDoxyHtmlTag_A,
+      "Quote: ");
+  tagHandlers["<body"] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "");
+  tagHandlers["<br"] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "\n");
 
   // there is no formatting for this tag as it was deprecated in HTML 4.01 and
   // not used in HTML 5
-  tagHandlers["<center" ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "" );
+  tagHandlers["<center"] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "");
   tagHandlers["<caption"] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "");
-  tagHandlers["<code"   ] = make_pair(&PyDocConverter::handleDoxyHtmlTag2, "'"   );
+  tagHandlers["<code"] = make_pair(&PyDocConverter::handleDoxyHtmlTag2, "'");
 
-  tagHandlers["<dl"     ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "");
-  tagHandlers["<dd"     ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "    ");
-  tagHandlers["<dt"     ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "");
+  tagHandlers["<dl"] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "");
+  tagHandlers["<dd"] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "    ");
+  tagHandlers["<dt"] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "");
 
-  tagHandlers["<dfn"    ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, ""    );
-  tagHandlers["<div"    ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, ""    );
-  tagHandlers["<em"     ] = make_pair(&PyDocConverter::handleDoxyHtmlTag2, "__");
-  tagHandlers["<form"   ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, ""   );
-  tagHandlers["<hr"     ] = make_pair(&PyDocConverter::handleDoxyHtmlTag,
-              "--------------------------------------------------------------------\n"     );
-  tagHandlers["<h1"     ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "# "     );
-  tagHandlers["<h2"     ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "## "     );
-  tagHandlers["<h3"     ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "### "     );
-  tagHandlers["<i"      ] = make_pair(&PyDocConverter::handleDoxyHtmlTag2, "_");
-  tagHandlers["<input"  ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, ""  );
-  tagHandlers["<img"    ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "Image:"  );
-  tagHandlers["<li"     ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "- ");
-  tagHandlers["<meta"   ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "");
+  tagHandlers["<dfn"] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "");
+  tagHandlers["<div"] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "");
+  tagHandlers["<em"] = make_pair(&PyDocConverter::handleDoxyHtmlTag2, "__");
+  tagHandlers["<form"] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "");
+  tagHandlers["<hr"] = make_pair(&PyDocConverter::handleDoxyHtmlTag,
+      "--------------------------------------------------------------------\n");
+  tagHandlers["<h1"] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "# ");
+  tagHandlers["<h2"] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "## ");
+  tagHandlers["<h3"] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "### ");
+  tagHandlers["<i"] = make_pair(&PyDocConverter::handleDoxyHtmlTag2, "_");
+  tagHandlers["<input"] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "");
+  tagHandlers["<img"] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "Image:");
+  tagHandlers["<li"] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "- ");
+  tagHandlers["<meta"] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "");
   tagHandlers["<multicol"] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "");
-  tagHandlers["<ol"     ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "");
-  tagHandlers["<p"      ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "\n");
-  tagHandlers["<pre"    ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, ""    );
-  tagHandlers["<small"  ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, ""  );
-  tagHandlers["<span"   ] = make_pair(&PyDocConverter::handleDoxyHtmlTag2, "'"   );
-  tagHandlers["<strong" ] = make_pair(&PyDocConverter::handleDoxyHtmlTag2, "__");
+  tagHandlers["<ol"] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "");
+  tagHandlers["<p"] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "\n");
+  tagHandlers["<pre"] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "");
+  tagHandlers["<small"] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "");
+  tagHandlers["<span"] = make_pair(&PyDocConverter::handleDoxyHtmlTag2, "'");
+  tagHandlers["<strong"] = make_pair(&PyDocConverter::handleDoxyHtmlTag2, "__");
 
   // make a space between text and super/sub script.
-  tagHandlers["<sub"    ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, " ");
-  tagHandlers["<sup"    ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, " ");
+  tagHandlers["<sub"] = make_pair(&PyDocConverter::handleDoxyHtmlTag, " ");
+  tagHandlers["<sup"] = make_pair(&PyDocConverter::handleDoxyHtmlTag, " ");
 
-  tagHandlers["<table"  ] = make_pair(&PyDocConverter::handleDoxyHtmlTagNoParam, "");
-  tagHandlers["<td"     ] = make_pair(&PyDocConverter::handleDoxyHtmlTag_td, "");
-  tagHandlers["<th"     ] = make_pair(&PyDocConverter::handleDoxyHtmlTag_th, "");
-  tagHandlers["<tr"     ] = make_pair(&PyDocConverter::handleDoxyHtmlTag_tr, "");
-  tagHandlers["<tt"     ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "");
-  tagHandlers["<kbd"    ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "");
-  tagHandlers["<ul"     ] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "");
-  tagHandlers["<var"    ] = make_pair(&PyDocConverter::handleDoxyHtmlTag2, "_");
+  tagHandlers["<table"] = make_pair(&PyDocConverter::handleDoxyHtmlTagNoParam,
+      "");
+  tagHandlers["<td"] = make_pair(&PyDocConverter::handleDoxyHtmlTag_td, "");
+  tagHandlers["<th"] = make_pair(&PyDocConverter::handleDoxyHtmlTag_th, "");
+  tagHandlers["<tr"] = make_pair(&PyDocConverter::handleDoxyHtmlTag_tr, "");
+  tagHandlers["<tt"] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "");
+  tagHandlers["<kbd"] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "");
+  tagHandlers["<ul"] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "");
+  tagHandlers["<var"] = make_pair(&PyDocConverter::handleDoxyHtmlTag2, "_");
 
   // HTML entities
-  tagHandlers["&copy" ] = make_pair(&PyDocConverter::handleHtmlEntity, "(C)");
+  tagHandlers["&copy"] = make_pair(&PyDocConverter::handleHtmlEntity, "(C)");
   tagHandlers["&trade"] = make_pair(&PyDocConverter::handleHtmlEntity, " TM");
-  tagHandlers["&reg"  ] = make_pair(&PyDocConverter::handleHtmlEntity, "(R)");
-  tagHandlers["&lt"   ] = make_pair(&PyDocConverter::handleHtmlEntity, "<");
-  tagHandlers["&gt"   ] = make_pair(&PyDocConverter::handleHtmlEntity, ">");
-  tagHandlers["&amp"  ] = make_pair(&PyDocConverter::handleHtmlEntity, "&");
-  tagHandlers["&apos" ] = make_pair(&PyDocConverter::handleHtmlEntity, "'");
-  tagHandlers["&quot" ] = make_pair(&PyDocConverter::handleHtmlEntity, "\"");
+  tagHandlers["&reg"] = make_pair(&PyDocConverter::handleHtmlEntity, "(R)");
+  tagHandlers["&lt"] = make_pair(&PyDocConverter::handleHtmlEntity, "<");
+  tagHandlers["&gt"] = make_pair(&PyDocConverter::handleHtmlEntity, ">");
+  tagHandlers["&amp"] = make_pair(&PyDocConverter::handleHtmlEntity, "&");
+  tagHandlers["&apos"] = make_pair(&PyDocConverter::handleHtmlEntity, "'");
+  tagHandlers["&quot"] = make_pair(&PyDocConverter::handleHtmlEntity, "\"");
   tagHandlers["&lsquo"] = make_pair(&PyDocConverter::handleHtmlEntity, "`");
   tagHandlers["&rsquo"] = make_pair(&PyDocConverter::handleHtmlEntity, "'");
   tagHandlers["&ldquo"] = make_pair(&PyDocConverter::handleHtmlEntity, "\"");
   tagHandlers["&rdquo"] = make_pair(&PyDocConverter::handleHtmlEntity, "\"");
   tagHandlers["&ndash"] = make_pair(&PyDocConverter::handleHtmlEntity, "-");
   tagHandlers["&mdash"] = make_pair(&PyDocConverter::handleHtmlEntity, "--");
-  tagHandlers["&nbsp" ] = make_pair(&PyDocConverter::handleHtmlEntity, " ");
+  tagHandlers["&nbsp"] = make_pair(&PyDocConverter::handleHtmlEntity, " ");
   tagHandlers["&times"] = make_pair(&PyDocConverter::handleHtmlEntity, "x");
   tagHandlers["&minus"] = make_pair(&PyDocConverter::handleHtmlEntity, "-");
-  tagHandlers["&sdot" ] = make_pair(&PyDocConverter::handleHtmlEntity, ".");
-  tagHandlers["&sim"  ] = make_pair(&PyDocConverter::handleHtmlEntity, "~");
-  tagHandlers["&le"   ] = make_pair(&PyDocConverter::handleHtmlEntity, "<=");
-  tagHandlers["&ge"   ] = make_pair(&PyDocConverter::handleHtmlEntity, ">=");
-  tagHandlers["&larr" ] = make_pair(&PyDocConverter::handleHtmlEntity, "<--");
-  tagHandlers["&rarr" ] = make_pair(&PyDocConverter::handleHtmlEntity, "-->");
+  tagHandlers["&sdot"] = make_pair(&PyDocConverter::handleHtmlEntity, ".");
+  tagHandlers["&sim"] = make_pair(&PyDocConverter::handleHtmlEntity, "~");
+  tagHandlers["&le"] = make_pair(&PyDocConverter::handleHtmlEntity, "<=");
+  tagHandlers["&ge"] = make_pair(&PyDocConverter::handleHtmlEntity, ">=");
+  tagHandlers["&larr"] = make_pair(&PyDocConverter::handleHtmlEntity, "<--");
+  tagHandlers["&rarr"] = make_pair(&PyDocConverter::handleHtmlEntity, "-->");
 }
 
-PyDocConverter::PyDocConverter(bool debugTranslator, bool debugParser)
-: DoxygenTranslator(debugTranslator, debugParser),
-  m_tableLineLen(0),
-  m_prevRowIsTH(false)
+PyDocConverter::PyDocConverter(bool debugTranslator, bool debugParser) :
+    DoxygenTranslator(debugTranslator, debugParser), m_tableLineLen(0), m_prevRowIsTH(
+        false)
 {
   fillStaticTables();
 }
 
-std::string PyDocConverter::getParamType(std::string param) {
+std::string PyDocConverter::getParamType(std::string param)
+{
   ParmList *plist = CopyParmList(Getattr(currentNode, "parms"));
   Parm *p = NULL;
   for (p = plist; p;) {
-    if (Char(Getattr(p, "name")) == param) {
-      std::string type = Char(SwigType_str(Getattr(p, "type"), ""));
+    if (Char (Getattr(p, "name")) == param) {
+      std::string type = Char (SwigType_str(Getattr(p, "type"), ""));
       return type;
     }
     /*
@@ -244,17 +253,21 @@ std::string PyDocConverter::getParamType(std::string param) {
   return "";
 }
 
-std::string PyDocConverter::justifyString(std::string documentString, int indent, int maxWidth) {
+std::string PyDocConverter::justifyString(std::string documentString,
+                                          int indent, int maxWidth)
+{
   std::string formattedString;
   std::string currentLine;
 
-  for (std::string::iterator stringPosition = documentString.begin(); stringPosition != documentString.end(); ++stringPosition) {
+  for (std::string::iterator stringPosition = documentString.begin();
+      stringPosition != documentString.end(); ++stringPosition) {
     if (currentLine.length() == 0)
       currentLine.resize(indent, ' ');
 
     currentLine += *stringPosition;
 
-    if ((iswspace(*stringPosition) && (int) currentLine.size() >= maxWidth) || (stringPosition + 1) == documentString.end()) {
+    if ((iswspace(*stringPosition) && (int) currentLine.size() >= maxWidth)
+        || (stringPosition + 1) == documentString.end()) {
       formattedString += currentLine + "\n";
       currentLine = "";
     }
@@ -267,14 +280,15 @@ std::string PyDocConverter::justifyString(std::string documentString, int indent
   return formattedString;
 }
 
-std::string PyDocConverter::translateSubtree(DoxygenEntity & doxygenEntity) {
+std::string PyDocConverter::translateSubtree(DoxygenEntity & doxygenEntity)
+{
   std::string translatedComment;
 
   if (doxygenEntity.isLeaf)
     return translatedComment;
 
   std::string currentSection;
-  std::list < DoxygenEntity >::iterator p = doxygenEntity.entityList.begin();
+  std::list<DoxygenEntity>::iterator p = doxygenEntity.entityList.begin();
   while (p != doxygenEntity.entityList.end()) {
     std::map<std::string, std::string>::iterator it;
     it = sectionTitles.find(p->typeOfEntity);
@@ -292,50 +306,63 @@ std::string PyDocConverter::translateSubtree(DoxygenEntity & doxygenEntity) {
   return translatedComment;
 }
 
-void PyDocConverter::translateEntity(DoxygenEntity & doxyEntity, std::string &translatedComment) {
+void PyDocConverter::translateEntity(DoxygenEntity & doxyEntity,
+                                     std::string &translatedComment)
+{
   // check if we have needed handler and call it
-  std::map<std::string, std::pair<tagHandler, std::string > >::iterator it;
+  std::map<std::string, std::pair<tagHandler, std::string> >::iterator it;
   it = tagHandlers.find(doxyEntity.typeOfEntity);
-  if (it!=tagHandlers.end())
-    (this->*(it->second.first))(doxyEntity, translatedComment, it->second.second);
+  if (it != tagHandlers.end())
+    (this->*(it->second.first))(doxyEntity, translatedComment,
+        it->second.second);
 }
 
-
-void PyDocConverter::handleParagraph(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
+void PyDocConverter::handleParagraph(DoxygenEntity& tag,
+                                     std::string& translatedComment,
+                                     std::string &arg)
+{
   translatedComment += translateSubtree(tag) + arg;
 }
 
-
-void PyDocConverter::handlePlainString(DoxygenEntity& tag, std::string& translatedComment, std::string&) {
+void PyDocConverter::handlePlainString(DoxygenEntity& tag,
+                                       std::string& translatedComment,
+                                       std::string&)
+{
   translatedComment += tag.data;
-  if (tag.data.size() && tag.data[tag.data.size()-1] != ' ')
+  if (tag.data.size() && tag.data[tag.data.size() - 1] != ' ')
     translatedComment += "";
 }
 
-
 void PyDocConverter::handleTagVerbatim(DoxygenEntity& tag,
-                                            std::string& translatedComment,
-                                            std::string &arg) {
+                                       std::string& translatedComment,
+                                       std::string &arg)
+{
   translatedComment += arg + " ";
-  for (DoxygenEntityListCIt it = tag.entityList.begin(); it != tag.entityList.end(); it++) {
-      translatedComment += it->data;
+  for (DoxygenEntityListCIt it = tag.entityList.begin();
+      it != tag.entityList.end(); it++) {
+    translatedComment += it->data;
   }
 }
 
-
-void PyDocConverter::handleTagMessage(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
+void PyDocConverter::handleTagMessage(DoxygenEntity& tag,
+                                      std::string& translatedComment,
+                                      std::string &arg)
+{
   std::string dummy;
   translatedComment += arg;
   handleParagraph(tag, translatedComment, dummy);
 }
 
-
-void PyDocConverter::handleTagChar(DoxygenEntity& tag, std::string& translatedComment, std::string&) {
+void PyDocConverter::handleTagChar(DoxygenEntity& tag,
+                                   std::string& translatedComment, std::string&)
+{
   translatedComment += tag.typeOfEntity;
 }
 
-
-void PyDocConverter::handleTagIf(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
+void PyDocConverter::handleTagIf(DoxygenEntity& tag,
+                                 std::string& translatedComment,
+                                 std::string &arg)
+{
   std::string dummy;
   translatedComment += arg;
   if (tag.entityList.size()) {
@@ -345,8 +372,9 @@ void PyDocConverter::handleTagIf(DoxygenEntity& tag, std::string& translatedComm
   }
 }
 
-
-void PyDocConverter::handleTagPar(DoxygenEntity& tag, std::string& translatedComment, std::string&) {
+void PyDocConverter::handleTagPar(DoxygenEntity& tag,
+                                  std::string& translatedComment, std::string&)
+{
   std::string dummy;
   translatedComment += "Title: ";
   if (tag.entityList.size())
@@ -355,8 +383,10 @@ void PyDocConverter::handleTagPar(DoxygenEntity& tag, std::string& translatedCom
   handleParagraph(tag, translatedComment, dummy);
 }
 
-
-void PyDocConverter::handleTagImage(DoxygenEntity& tag, std::string& translatedComment, std::string&) {
+void PyDocConverter::handleTagImage(DoxygenEntity& tag,
+                                    std::string& translatedComment,
+                                    std::string&)
+{
   if (tag.entityList.size() < 2)
     return;
   tag.entityList.pop_front();
@@ -367,10 +397,10 @@ void PyDocConverter::handleTagImage(DoxygenEntity& tag, std::string& translatedC
     translatedComment += "(" + tag.entityList.begin()->data + ")";
 }
 
-
 void PyDocConverter::handleTagParam(DoxygenEntity& tag,
-                                         std::string& translatedComment,
-                                         std::string&) {
+                                    std::string& translatedComment,
+                                    std::string&)
+{
   std::string dummy;
   if (tag.entityList.size() < 2)
     return;
@@ -386,140 +416,152 @@ void PyDocConverter::handleTagParam(DoxygenEntity& tag,
   handleParagraph(tag, translatedComment, dummy);
 }
 
-
-void PyDocConverter::handleTagWrap(DoxygenEntity& tag, std::string& translatedComment, std::string &arg) {
+void PyDocConverter::handleTagWrap(DoxygenEntity& tag,
+                                   std::string& translatedComment,
+                                   std::string &arg)
+{
   if (tag.entityList.size()) { // do not include empty tags
     std::string tagData = translateSubtree(tag);
     // wrap the thing, ignoring whitespaces
     size_t wsPos = tagData.find_last_not_of("\n\t ");
     if (wsPos != std::string::npos && wsPos != tagData.size() - 1)
-      translatedComment += arg + tagData.substr(0, wsPos + 1) + arg + tagData.substr(wsPos + 1);
+      translatedComment += arg + tagData.substr(0, wsPos + 1) + arg
+          + tagData.substr(wsPos + 1);
     else
       translatedComment += arg + tagData + arg;
   }
 }
 
-
 void PyDocConverter::handleDoxyHtmlTag(DoxygenEntity& tag,
-                                            std::string& translatedComment,
-                                            std::string &arg) {
-    std::string htmlTagArgs = tag.data;
-    if (htmlTagArgs == "/") {
-        // end html tag, for example "</ul>
-        // translatedComment += "</" + arg.substr(1) + ">";
-    } else {
-        translatedComment += arg + htmlTagArgs;
-    }
+                                       std::string& translatedComment,
+                                       std::string &arg)
+{
+  std::string htmlTagArgs = tag.data;
+  if (htmlTagArgs == "/") {
+    // end html tag, for example "</ul>
+    // translatedComment += "</" + arg.substr(1) + ">";
+  } else {
+    translatedComment += arg + htmlTagArgs;
+  }
 }
 
-
 void PyDocConverter::handleDoxyHtmlTagNoParam(DoxygenEntity& tag,
-                                                    std::string& translatedComment,
-                                                    std::string &arg) {
-    std::string htmlTagArgs = tag.data;
-    if (htmlTagArgs == "/") {
-        // end html tag, for example "</ul>
-    } else {
-        translatedComment += arg;
-    }
+                                              std::string& translatedComment,
+                                              std::string &arg)
+{
+  std::string htmlTagArgs = tag.data;
+  if (htmlTagArgs == "/") {
+    // end html tag, for example "</ul>
+  } else {
+    translatedComment += arg;
+  }
 }
 
-
 void PyDocConverter::handleDoxyHtmlTag_A(DoxygenEntity& tag,
-                                              std::string& translatedComment,
-                                              std::string &arg) {
-    std::string htmlTagArgs = tag.data;
-    if (htmlTagArgs == "/") {
-        // end html tag, "</a>
-        translatedComment += " (" + m_url + ')';
-        m_url.clear();
-    } else {
-      m_url.clear();
-      size_t pos = htmlTagArgs.find('=');
-      if (pos != string::npos) {
-        m_url = htmlTagArgs.substr(pos + 1);
-      }
-      translatedComment += arg;
+                                         std::string& translatedComment,
+                                         std::string &arg)
+{
+  std::string htmlTagArgs = tag.data;
+  if (htmlTagArgs == "/") {
+    // end html tag, "</a>
+    translatedComment += " (" + m_url + ')';
+    m_url.clear();
+  } else {
+    m_url.clear();
+    size_t pos = htmlTagArgs.find('=');
+    if (pos != string::npos) {
+      m_url = htmlTagArgs.substr(pos + 1);
     }
+    translatedComment += arg;
+  }
 }
 
-
 void PyDocConverter::handleDoxyHtmlTag2(DoxygenEntity& tag,
-                                             std::string& translatedComment,
-                                             std::string &arg) {
-    std::string htmlTagArgs = tag.data;
-    if (htmlTagArgs == "/") {
-        // end html tag, for example "</em>
-        translatedComment += arg;
-    } else {
-        translatedComment += arg;
-    }
+                                        std::string& translatedComment,
+                                        std::string &arg)
+{
+  std::string htmlTagArgs = tag.data;
+  if (htmlTagArgs == "/") {
+    // end html tag, for example "</em>
+    translatedComment += arg;
+  } else {
+    translatedComment += arg;
+  }
 }
 
 void PyDocConverter::handleDoxyHtmlTag_tr(DoxygenEntity& tag,
-                                                std::string& translatedComment,
-                                                std::string &) {
-    std::string htmlTagArgs = tag.data;
-    if (htmlTagArgs == "/") {
-      // end tag, </tr> appends vertical table line '|'
-      translatedComment += '|';
-      size_t nlPos = translatedComment.rfind('\n');
-      if (nlPos != string::npos) {
-        size_t startOfTableLinePos = translatedComment.find_first_not_of(" \t", nlPos);
-        if (startOfTableLinePos != string::npos) {
-          m_tableLineLen = translatedComment.size() - startOfTableLinePos - 1;
-        }
-      }
-    } else {
-      if (m_prevRowIsTH) {
-        // if previous row contained <th> tag, add horizontal separator
-        translatedComment += string(m_tableLineLen, '-') + '\n';
-        m_prevRowIsTH = false;
+                                          std::string& translatedComment,
+                                          std::string &)
+{
+  std::string htmlTagArgs = tag.data;
+  size_t nlPos = translatedComment.rfind('\n');
+  if (htmlTagArgs == "/") {
+    // end tag, </tr> appends vertical table line '|'
+    translatedComment += '|';
+    if (nlPos != string::npos) {
+      size_t startOfTableLinePos = translatedComment.find_first_not_of(" \t",
+          nlPos + 1);
+      if (startOfTableLinePos != string::npos) {
+        m_tableLineLen = translatedComment.size() - startOfTableLinePos;
       }
     }
-}
+  } else {
+    if (m_prevRowIsTH) {
+      // if previous row contained <th> tag, add horizontal separator
+      // but first get leading spaces, because they'll be needed for the next row
+      size_t numLeadingSpaces = translatedComment.size() - nlPos - 1;
 
+      translatedComment += string(m_tableLineLen, '-') + '\n';
+
+      if (nlPos != string::npos) {
+        translatedComment += string(numLeadingSpaces, ' ');
+      }
+      m_prevRowIsTH = false;
+    }
+  }
+}
 
 void PyDocConverter::handleDoxyHtmlTag_th(DoxygenEntity& tag,
-                                                std::string& translatedComment,
-                                                std::string &) {
-    std::string htmlTagArgs = tag.data;
-    if (htmlTagArgs == "/") {
-      // end tag, </th> is ignored
-    } else {
-        translatedComment += '|';
-        m_prevRowIsTH = true;
-    }
+                                          std::string& translatedComment,
+                                          std::string &)
+{
+  std::string htmlTagArgs = tag.data;
+  if (htmlTagArgs == "/") {
+    // end tag, </th> is ignored
+  } else {
+    translatedComment += '|';
+    m_prevRowIsTH = true;
+  }
 }
 
-
 void PyDocConverter::handleDoxyHtmlTag_td(DoxygenEntity& tag,
-                                                std::string& translatedComment,
-                                                std::string &) {
-    std::string htmlTagArgs = tag.data;
-    if (htmlTagArgs == "/") {
-        // end tag, </td> is ignored
-    } else {
-      translatedComment += '|';
-    }
+                                          std::string& translatedComment,
+                                          std::string &)
+{
+  std::string htmlTagArgs = tag.data;
+  if (htmlTagArgs == "/") {
+    // end tag, </td> is ignored
+  } else {
+    translatedComment += '|';
+  }
 }
 
-
-
 void PyDocConverter::handleHtmlEntity(DoxygenEntity&,
-                                           std::string& translatedComment,
-                                           std::string &arg) {
-    // html entities
-    translatedComment += arg;
+                                      std::string& translatedComment,
+                                      std::string &arg)
+{
+  // html entities
+  translatedComment += arg;
 }
 
-
-void PyDocConverter::handleNewLine(DoxygenEntity&, std::string& translatedComment, std::string&) {
+void PyDocConverter::handleNewLine(DoxygenEntity&,
+                                   std::string& translatedComment, std::string&)
+{
   translatedComment += "\n";
 }
 
-
-String *PyDocConverter::makeDocumentation(Node *n) {
+String *PyDocConverter::makeDocumentation(Node *n)
+{
   String *documentation;
   std::string pyDocString, result;
 
@@ -532,25 +574,26 @@ String *PyDocConverter::makeDocumentation(Node *n) {
     while (Getattr(n, "sym:previousSibling"))
       n = Getattr(n, "sym:previousSibling");
 
-    std::vector < std::string > allDocumentation;
+    std::vector<std::string> allDocumentation;
 
     // for each real method (not a generated overload) append the documentation
     while (n) {
       documentation = getDoxygenComment(n);
       if (!Swig_is_generated_overload(n) && documentation) {
-	currentNode = n;
-	if (GetFlag(n, "feature:doxygen:notranslate")) {
-	  String *comment = NewString("");
-	  Append(comment, documentation);
-	  Replaceall(comment, "\n *", "\n");
-	  allDocumentation.push_back(Char(comment));
-	  Delete(comment);
-	}
-	else {
-	  std::list < DoxygenEntity > entityList = parser.createTree(Char(documentation), Char(Getfile(documentation)), Getline(documentation));
-	  DoxygenEntity root("root", entityList);
-	  allDocumentation.push_back(translateSubtree(root));
-	}
+        currentNode = n;
+        if (GetFlag(n, "feature:doxygen:notranslate")) {
+          String *comment = NewString("");
+          Append(comment, documentation);
+          Replaceall(comment, "\n *", "\n");
+          allDocumentation.push_back(Char (comment));
+          Delete(comment);
+        } else {
+          std::list<DoxygenEntity> entityList = parser.createTree(
+              Char (documentation), Char (Getfile(documentation)),
+              Getline(documentation));
+          DoxygenEntity root("root", entityList);
+          allDocumentation.push_back(translateSubtree(root));
+        }
       }
       n = Getattr(n, "sym:nextSibling");
     }
@@ -558,9 +601,12 @@ String *PyDocConverter::makeDocumentation(Node *n) {
     // construct final documentation string
     if (allDocumentation.size() > 1) {
       std::ostringstream concatDocString;
-      for (int realOverloadCount = 0; realOverloadCount < (int) allDocumentation.size(); realOverloadCount++) {
+      for (int realOverloadCount = 0;
+          realOverloadCount < (int) allDocumentation.size();
+          realOverloadCount++) {
         concatDocString << generateDivider() << std::endl;
-        concatDocString << "Overload " << (realOverloadCount + 1) << ":" << std::endl;
+        concatDocString << "Overload " << (realOverloadCount + 1) << ":"
+            << std::endl;
         concatDocString << generateDivider();
         concatDocString << allDocumentation[realOverloadCount] << std::endl;
       }
@@ -577,11 +623,12 @@ String *PyDocConverter::makeDocumentation(Node *n) {
         String *comment = NewString("");
         Append(comment, documentation);
         Replaceall(comment, "\n *", "\n");
-        pyDocString = Char(comment);
+        pyDocString = Char (comment);
         Delete(comment);
-      }
-      else {
-        std::list < DoxygenEntity > entityList = parser.createTree(Char(documentation), Char(Getfile(documentation)), Getline(documentation));
+      } else {
+        std::list<DoxygenEntity> entityList = parser.createTree(
+            Char (documentation), Char (Getfile(documentation)),
+            Getline(documentation));
         DoxygenEntity root("root", entityList);
         pyDocString = translateSubtree(root);
       }
@@ -610,7 +657,8 @@ String *PyDocConverter::makeDocumentation(Node *n) {
   return NewString("");
 }
 
-std::string PyDocConverter::generateDivider() {
+std::string PyDocConverter::generateDivider()
+{
   static string dividerString(DOC_STRING_LENGTH, '-');
   return dividerString;
 }

From 530d65a98c6efa0af31ca73c7060791f6bcb2a8d Mon Sep 17 00:00:00 2001
From: Marko Klopcic <markok3.14@gmail.com>
Date: Sat, 23 Feb 2013 16:44:09 +0100
Subject: [PATCH 185/314] added fix for word commands aqnd ellipsis

---
 Source/DoxygenTranslator/src/DoxygenParser.cpp | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/Source/DoxygenTranslator/src/DoxygenParser.cpp b/Source/DoxygenTranslator/src/DoxygenParser.cpp
index 07839f5d7..c597a7e36 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenParser.cpp
@@ -1315,7 +1315,11 @@ void DoxygenParser::tokenizeDoxygenComment(const std::string &doxygenComment,
         //   colors are \b red, green, and blue --> colors are 'red,' green, and blue
         string text = line.substr(pos, doxyCmdOrHtmlTagPos - pos);
         string punctuations(".,:");
-        if (!text.empty()  &&  punctuations.find(text[text.size() - 1]) != string::npos) {
+        size_t textSize = text.size();
+
+        if (!text.empty()  &&  punctuations.find(text[text.size() - 1]) != string::npos  &&
+            // but do not break ellipsis (...)
+            !(textSize > 1 && text[textSize - 2] == '.')) {
           m_tokenList.push_back(Token(PLAINSTRING, text.substr(0, text.size() - 1)));
           m_tokenList.push_back(Token(PLAINSTRING, text.substr(text.size() - 1)));
         } else {

From 00ff8886c6ca53c16d5a6dd7c8177059f30a9503 Mon Sep 17 00:00:00 2001
From: Marko Klopcic <markok3.14@gmail.com>
Date: Sat, 23 Feb 2013 16:46:14 +0100
Subject: [PATCH 186/314] formatting updated

---
 .../DoxygenTranslator/src/DoxygenParser.cpp   | 1595 +++++++++--------
 1 file changed, 814 insertions(+), 781 deletions(-)

diff --git a/Source/DoxygenTranslator/src/DoxygenParser.cpp b/Source/DoxygenTranslator/src/DoxygenParser.cpp
index c597a7e36..995e0c7ab 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenParser.cpp
@@ -26,101 +26,104 @@ using std::endl;
 DoxygenParser::DoxyCommandsMap DoxygenParser::doxygenCommands;
 std::set<std::string> DoxygenParser::doxygenSectionIndicators;
 
-const int TOKENSPERLINE = 8;    //change this to change the printing behaviour of the token list
+const int TOKENSPERLINE = 8; //change this to change the printing behaviour of the token list
 const std::string END_HTML_TAG_MARK("/");
 
-DoxygenParser::DoxygenParser(bool noisy) : noisy(noisy)
+DoxygenParser::DoxygenParser(bool noisy) :
+    noisy(noisy)
 {
-	fillTables();
+  fillTables();
 }
 
-DoxygenParser::~DoxygenParser() {
+DoxygenParser::~DoxygenParser()
+{
 }
 
-void DoxygenParser::fillTables() {
-    // run it only once
-    if (doxygenCommands.size())
-        return;
+void DoxygenParser::fillTables()
+{
+  // run it only once
+  if (doxygenCommands.size())
+    return;
 
-    // fill in tables with data from DxygenCommands.h
-    for (int i = 0; i < simpleCommandsSize; i++)
-        doxygenCommands[simpleCommands[i]] = SIMPLECOMMAND;
+  // fill in tables with data from DxygenCommands.h
+  for (int i = 0; i < simpleCommandsSize; i++)
+    doxygenCommands[simpleCommands[i]] = SIMPLECOMMAND;
 
-    for (int i = 0; i < commandWordsSize; i++)
-        doxygenCommands[commandWords[i]] = COMMANDWORD;
+  for (int i = 0; i < commandWordsSize; i++)
+    doxygenCommands[commandWords[i]] = COMMANDWORD;
 
-    for (int i = 0; i < commandLinesSize; i++)
-        doxygenCommands[commandLines[i]] = COMMANDLINE;
+  for (int i = 0; i < commandLinesSize; i++)
+    doxygenCommands[commandLines[i]] = COMMANDLINE;
 
-    for (int i = 0; i < commandParagraphSize; i++)
-        doxygenCommands[commandParagraph[i]] = COMMANDPARAGRAPH;
+  for (int i = 0; i < commandParagraphSize; i++)
+    doxygenCommands[commandParagraph[i]] = COMMANDPARAGRAPH;
 
-    for (int i = 0; i < commandEndCommandsSize; i++)
-        doxygenCommands[commandEndCommands[i]] = COMMANDENDCOMMAND;
+  for (int i = 0; i < commandEndCommandsSize; i++)
+    doxygenCommands[commandEndCommands[i]] = COMMANDENDCOMMAND;
 
-    for (int i = 0; i < commandWordParagraphsSize; i++)
-        doxygenCommands[commandWordParagraphs[i]] = COMMANDWORDPARAGRAPH;
+  for (int i = 0; i < commandWordParagraphsSize; i++)
+    doxygenCommands[commandWordParagraphs[i]] = COMMANDWORDPARAGRAPH;
 
-    for (int i = 0; i < commandWordLinesSize; i++)
-        doxygenCommands[commandWordLines[i]] = COMMANDWORDLINE;
+  for (int i = 0; i < commandWordLinesSize; i++)
+    doxygenCommands[commandWordLines[i]] = COMMANDWORDLINE;
 
-    for (int i = 0; i < commandWordOWordOWordsSize; i++)
-        doxygenCommands[commandWordOWordOWords[i]] = COMMANDWORDOWORDWORD;
+  for (int i = 0; i < commandWordOWordOWordsSize; i++)
+    doxygenCommands[commandWordOWordOWords[i]] = COMMANDWORDOWORDWORD;
 
-    for (int i = 0; i < commandOWordsSize; i++)
-        doxygenCommands[commandOWords[i]] = COMMANDOWORD;
+  for (int i = 0; i < commandOWordsSize; i++)
+    doxygenCommands[commandOWords[i]] = COMMANDOWORD;
 
-    for (int i = 0; i < commandErrorThrowingsSize; i++)
-        doxygenCommands[commandErrorThrowings[i]] = COMMANDERRORTHROW;
+  for (int i = 0; i < commandErrorThrowingsSize; i++)
+    doxygenCommands[commandErrorThrowings[i]] = COMMANDERRORTHROW;
 
-    for (int i = 0; i < commandUniquesSize; i++)
-        doxygenCommands[commandUniques[i]] = COMMANDUNIQUE;
+  for (int i = 0; i < commandUniquesSize; i++)
+    doxygenCommands[commandUniques[i]] = COMMANDUNIQUE;
 
-    for (int i = 0; i < commandHtmlSize; i++)
-        doxygenCommands[commandHtml[i]] = COMMAND_HTML;
+  for (int i = 0; i < commandHtmlSize; i++)
+    doxygenCommands[commandHtml[i]] = COMMAND_HTML;
 
-    for (int i = 0; i < commandHtmlEntitiesSize; i++)
-        doxygenCommands[commandHtmlEntities[i]] = COMMAND_HTML_ENTITY;
+  for (int i = 0; i < commandHtmlEntitiesSize; i++)
+    doxygenCommands[commandHtmlEntities[i]] = COMMAND_HTML_ENTITY;
 
-    // fill section indicators command set
-    for (int i = 0; i < sectionIndicatorsSize; i++)
-        doxygenSectionIndicators.insert(sectionIndicators[i]);
+  // fill section indicators command set
+  for (int i = 0; i < sectionIndicatorsSize; i++)
+    doxygenSectionIndicators.insert(sectionIndicators[i]);
 }
 
+std::string DoxygenParser::stringToLower(const std::string &stringToConvert)
+{
 
-std::string DoxygenParser::stringToLower(const std::string &stringToConvert) {
+  string result(stringToConvert.size(), ' ');
 
-	string result(stringToConvert.size(), ' ');
+  for (size_t i = 0; i < result.size(); i++) {
+    result[i] = tolower(stringToConvert[i]);
+  }
 
-	for (size_t i = 0; i < result.size(); i++) {
-	    result[i] = tolower(stringToConvert[i]);
-	}
-
-	return result;
+  return result;
 }
 
+bool DoxygenParser::findCommand(const std::string &smallString)
+{
+  // I'm not sure if we can really do so, because there are different commands
+  // in doxygenCommands and original commandArray
 
-bool DoxygenParser::findCommand(const std::string &smallString) {
-    // I'm not sure if we can really do so, because there are different commands
-    // in doxygenCommands and original commandArray
+  std::map<std::string, DoxyCommandEnum>::iterator it = doxygenCommands.find(
+      stringToLower(smallString));
 
-    std::map<std::string, DoxyCommandEnum>::iterator it =
-                    doxygenCommands.find(stringToLower(smallString));
-
-	return it != doxygenCommands.end(); // returns true if command was found
+  return it != doxygenCommands.end(); // returns true if command was found
 }
 
+bool DoxygenParser::isSectionIndicator(const std::string &smallString)
+{
 
-bool DoxygenParser::isSectionIndicator(const std::string &smallString) {
+  std::set<std::string>::iterator it = doxygenSectionIndicators.find(
+      stringToLower(smallString));
 
-    std::set<std::string>::iterator it =
-                    doxygenSectionIndicators.find(stringToLower(smallString));
-
-	return it != doxygenSectionIndicators.end();
+  return it != doxygenSectionIndicators.end();
 }
 
-
-void DoxygenParser::printTree(const DoxygenEntityList &rootList) {
+void DoxygenParser::printTree(const DoxygenEntityList &rootList)
+{
   DoxygenEntityList::const_iterator p = rootList.begin();
   while (p != rootList.end()) {
     (*p).printEntity(0);
@@ -128,8 +131,8 @@ void DoxygenParser::printTree(const DoxygenEntityList &rootList) {
   }
 }
 
-
-int DoxygenParser::commandBelongs(const std::string &theCommand) {
+int DoxygenParser::commandBelongs(const std::string &theCommand)
+{
 
   std::string smallString = stringToLower(theCommand);
   //cout << " Looking for command " << theCommand << endl;
@@ -141,65 +144,63 @@ int DoxygenParser::commandBelongs(const std::string &theCommand) {
   return 0;
 }
 
-
 std::string DoxygenParser::trim(const std::string &text)
 {
-    size_t start = text.find_first_not_of(" \t");
-    size_t end = text.find_last_not_of(" \t");
+  size_t start = text.find_first_not_of(" \t");
+  size_t end = text.find_last_not_of(" \t");
 
-    if (start == string::npos  ||  start > end) {
-        return "";
-    }
-    return text.substr(start, end - start + 1);
+  if (start == string::npos || start > end) {
+    return "";
+  }
+  return text.substr(start, end - start + 1);
 }
 
-
 bool DoxygenParser::isEndOfLine()
 {
-    if (m_tokenListIt == m_tokenList.end()) {
-        return false;
-    }
-    Token nextToken = *m_tokenListIt;
-    return nextToken.m_tokenType == END_LINE;
+  if (m_tokenListIt == m_tokenList.end()) {
+    return false;
+  }
+  Token nextToken = *m_tokenListIt;
+  return nextToken.m_tokenType == END_LINE;
 }
 
-
 void DoxygenParser::skipWhitespaceTokens()
 {
-    if (m_tokenListIt == m_tokenList.end()) {
-        return;
-    }
+  if (m_tokenListIt == m_tokenList.end()) {
+    return;
+  }
 
-    while (m_tokenListIt != m_tokenList.end()  &&
-            (m_tokenListIt->m_tokenType == END_LINE  ||  trim(m_tokenListIt->m_tokenString).empty())) {
+  while (m_tokenListIt != m_tokenList.end()
+      && (m_tokenListIt->m_tokenType == END_LINE
+          || trim(m_tokenListIt->m_tokenString).empty())) {
 
-        m_tokenListIt++;
-    }
+    m_tokenListIt++;
+  }
 }
 
+std::string DoxygenParser::getNextToken()
+{
 
-std::string DoxygenParser::getNextToken() {
-
-    if (m_tokenListIt == m_tokenList.end()) {
-        return "";
-    }
-
-    if (m_tokenListIt->m_tokenType == PLAINSTRING) {
-        return (m_tokenListIt++)->m_tokenString;
-    }
-
+  if (m_tokenListIt == m_tokenList.end()) {
     return "";
+  }
+
+  if (m_tokenListIt->m_tokenType == PLAINSTRING) {
+    return (m_tokenListIt++)->m_tokenString;
+  }
+
+  return "";
 }
 
+std::string DoxygenParser::getNextWord()
+{
 
-
-std::string DoxygenParser::getNextWord() {
-
-/*    if (m_tokenListIt == m_tokenList.end()) {
-        return "";
-    }
-*/
-  while (m_tokenListIt != m_tokenList.end()  &&  (m_tokenListIt->m_tokenType == PLAINSTRING)) {
+  /*    if (m_tokenListIt == m_tokenList.end()) {
+   return "";
+   }
+   */
+  while (m_tokenListIt != m_tokenList.end()
+      && (m_tokenListIt->m_tokenType == PLAINSTRING)) {
     // handle quoted strings as words
     string token = m_tokenListIt->m_tokenString;
     if (token == "\"") {
@@ -228,153 +229,156 @@ std::string DoxygenParser::getNextWord() {
   return "";
 }
 
+DoxygenParser::TokenListCIt DoxygenParser::getOneLine(const TokenList &tokList)
+{
 
-DoxygenParser::TokenListCIt DoxygenParser::getOneLine(const TokenList &tokList) {
+  TokenListCIt endOfLineIt = m_tokenListIt;
 
-	TokenListCIt endOfLineIt = m_tokenListIt;
+  while (endOfLineIt != tokList.end()) {
+    if (endOfLineIt->m_tokenType == END_LINE) {
+      return endOfLineIt;
+    }
+    endOfLineIt++;
+  }
 
-	while (endOfLineIt != tokList.end()) {
-		if (endOfLineIt->m_tokenType == END_LINE) {
-			return endOfLineIt;
-		}
-		endOfLineIt++;
-	}
-
-	return tokList.end();
+  return tokList.end();
 }
 
+std::string DoxygenParser::getStringTilCommand(const TokenList & tokList)
+{
 
-std::string DoxygenParser::getStringTilCommand(const TokenList & tokList) {
+  if (m_tokenListIt == tokList.end()) {
+    return "";
+  }
 
-	if (m_tokenListIt == tokList.end()) {
-		return "";
-	}
+  string description;
 
-    string description;
-
-    while (m_tokenListIt->m_tokenType == PLAINSTRING) {
-		const Token &currentToken = *m_tokenListIt++;
-		if (currentToken.m_tokenType == PLAINSTRING) {
-			description = description + currentToken.m_tokenString; // + " ";
-		}
-	}
-	return description;
+  while (m_tokenListIt->m_tokenType == PLAINSTRING) {
+    const Token &currentToken = *m_tokenListIt++;
+    if (currentToken.m_tokenType == PLAINSTRING) {
+      description = description + currentToken.m_tokenString; // + " ";
+    }
+  }
+  return description;
 }
 
+std::string DoxygenParser::getStringTilEndCommand(
+    const std::string & theCommand, const TokenList & tokList)
+{
 
-std::string DoxygenParser::getStringTilEndCommand(const std::string & theCommand, const TokenList & tokList) {
+  if (m_tokenListIt == tokList.end()) {
+    return "";
+  }
 
-    if (m_tokenListIt == tokList.end()) {
-        return "";
+  string description;
+  while (m_tokenListIt != tokList.end()) {
+
+    if (m_tokenListIt->m_tokenType == PLAINSTRING) {
+      description += m_tokenListIt->m_tokenString;
+    } else if (m_tokenListIt->m_tokenType == END_LINE) {
+      description += "\n";
+    } else if (m_tokenListIt->m_tokenString == theCommand) {
+      m_tokenListIt++;
+      return description;
     }
 
-	string description;
-	while (m_tokenListIt != tokList.end()) {
+    m_tokenListIt++;
+  }
 
-		if (m_tokenListIt->m_tokenType == PLAINSTRING) {
-			description += m_tokenListIt->m_tokenString;
-		} else if (m_tokenListIt->m_tokenType == END_LINE) {
-			description += "\n";
-	    } else if (m_tokenListIt->m_tokenString == theCommand) {
-		    m_tokenListIt++;
-			return description;
-		}
+  printListError(WARN_DOXYGEN_COMMAND_EXPECTED,
+      theCommand + " command expected");
 
-		m_tokenListIt++;
-	}
-
-	printListError(WARN_DOXYGEN_COMMAND_EXPECTED, theCommand + " command expected");
-
-	return description;
+  return description;
 }
 
+DoxygenParser::TokenListCIt DoxygenParser::getEndOfParagraph(
+    const TokenList & tokList)
+{
 
-DoxygenParser::TokenListCIt DoxygenParser::getEndOfParagraph(const TokenList & tokList) {
+  TokenListCIt endOfParagraph = m_tokenListIt;
 
-    TokenListCIt endOfParagraph = m_tokenListIt;
+  while (endOfParagraph != tokList.end()) {
+    if (endOfParagraph->m_tokenType == END_LINE) {
+      endOfParagraph++;
+      if (endOfParagraph != tokList.end()
+          && endOfParagraph->m_tokenType == END_LINE) {
+        endOfParagraph++;
+        //cout << "ENCOUNTERED END OF PARA" << endl;
+        return endOfParagraph;
+      }
 
-    while (endOfParagraph != tokList.end()) {
-        if (endOfParagraph->m_tokenType == END_LINE) {
-            endOfParagraph++;
-            if (endOfParagraph != tokList.end() && endOfParagraph->m_tokenType == END_LINE) {
-                endOfParagraph++;
-                //cout << "ENCOUNTERED END OF PARA" << endl;
-                return endOfParagraph;
-            }
+    } else if (endOfParagraph->m_tokenType == COMMAND) {
 
-        } else if (endOfParagraph->m_tokenType == COMMAND) {
+      if (isSectionIndicator(endOfParagraph->m_tokenString)) {
+        return endOfParagraph;
+      } else {
+        endOfParagraph++;
+      }
 
-            if (isSectionIndicator(endOfParagraph->m_tokenString)) {
-                return endOfParagraph;
-            } else {
-                endOfParagraph++;
-            }
-
-        } else if (endOfParagraph->m_tokenType == PLAINSTRING) {
-            endOfParagraph++;
-        } else {
-            return tokList.end();
-        }
+    } else if (endOfParagraph->m_tokenType == PLAINSTRING) {
+      endOfParagraph++;
+    } else {
+      return tokList.end();
     }
+  }
 
-    return tokList.end();
+  return tokList.end();
 }
 
+DoxygenParser::TokenListCIt DoxygenParser::getEndOfSection(
+    const std::string & theCommand, const TokenList & tokList)
+{
 
-DoxygenParser::TokenListCIt DoxygenParser::getEndOfSection(const std::string & theCommand,
-                                                                 const TokenList & tokList) {
+  TokenListCIt endOfParagraph = m_tokenListIt;
 
-    TokenListCIt endOfParagraph = m_tokenListIt;
-
-	while (endOfParagraph != tokList.end()) {
-		if (endOfParagraph->m_tokenType == COMMAND) {
-			if (theCommand == endOfParagraph->m_tokenString)
-				return endOfParagraph;
-			else
-				endOfParagraph++;
-		} else if (endOfParagraph->m_tokenType == PLAINSTRING) {
-			endOfParagraph++;
-		} else if (endOfParagraph->m_tokenType == END_LINE) {
-			endOfParagraph++;
-			if (endOfParagraph->m_tokenType == END_LINE) {
-				endOfParagraph++;
-				return endOfParagraph;
-			}
-		}
-	}
-	return tokList.end();
+  while (endOfParagraph != tokList.end()) {
+    if (endOfParagraph->m_tokenType == COMMAND) {
+      if (theCommand == endOfParagraph->m_tokenString)
+        return endOfParagraph;
+      else
+        endOfParagraph++;
+    } else if (endOfParagraph->m_tokenType == PLAINSTRING) {
+      endOfParagraph++;
+    } else if (endOfParagraph->m_tokenType == END_LINE) {
+      endOfParagraph++;
+      if (endOfParagraph->m_tokenType == END_LINE) {
+        endOfParagraph++;
+        return endOfParagraph;
+      }
+    }
+  }
+  return tokList.end();
 }
 
+DoxygenParser::TokenListCIt DoxygenParser::getEndCommand(
+    const std::string & theCommand, const TokenList & tokList)
+{
 
-DoxygenParser::TokenListCIt DoxygenParser::getEndCommand(const std::string & theCommand,
-                                                              const TokenList & tokList) {
+  TokenListCIt endOfCommand = m_tokenListIt;
 
-    TokenListCIt endOfCommand = m_tokenListIt;
-
-	while (endOfCommand != tokList.end()) {
-        endOfCommand++;
-		if ((*endOfCommand).m_tokenType == COMMAND) {
-			if (theCommand == (*endOfCommand).m_tokenString) {
-				return endOfCommand;
-			}
-		}
-	}
-	//End command not found
-	return tokList.end();
+  while (endOfCommand != tokList.end()) {
+    endOfCommand++;
+    if ((*endOfCommand).m_tokenType == COMMAND) {
+      if (theCommand == (*endOfCommand).m_tokenString) {
+        return endOfCommand;
+      }
+    }
+  }
+  //End command not found
+  return tokList.end();
 }
 
-
 void DoxygenParser::skipEndOfLine()
 {
-    if (m_tokenListIt != m_tokenList.end()  &&
-                    m_tokenListIt->m_tokenType == END_LINE) {
-        m_tokenListIt++;
-    }
+  if (m_tokenListIt != m_tokenList.end()
+      && m_tokenListIt->m_tokenType == END_LINE) {
+    m_tokenListIt++;
+  }
 }
 
-
 int DoxygenParser::addSimpleCommand(const std::string &theCommand,
-                                         DoxygenEntityList &doxyList) {
+                                    DoxygenEntityList &doxyList)
+{
   if (noisy)
     cout << "Parsing " << theCommand << endl;
 
@@ -382,10 +386,10 @@ int DoxygenParser::addSimpleCommand(const std::string &theCommand,
   return 1;
 }
 
-
 int DoxygenParser::addCommandWord(const std::string &theCommand,
-                                       const TokenList &,
-                                       DoxygenEntityList &doxyList) {
+                                  const TokenList &,
+                                  DoxygenEntityList &doxyList)
+{
   if (noisy)
     cout << "Parsing " << theCommand << endl;
 
@@ -401,542 +405,559 @@ int DoxygenParser::addCommandWord(const std::string &theCommand,
     doxyList.push_back(DoxygenEntity(theCommand, aNewList));
     return 1;
   } else {
-    printListError(WARN_DOXYGEN_COMMAND_ERROR, "No word followed " +
-        theCommand + " command. Not added");
+    printListError(WARN_DOXYGEN_COMMAND_ERROR,
+        "No word followed " + theCommand + " command. Not added");
   }
   return 0;
 }
 
-
 int DoxygenParser::addCommandLine(const std::string &theCommand,
-                                       const TokenList &tokList,
-                                       DoxygenEntityList &doxyList) {
-	if (noisy)
-		cout << "Parsing " << theCommand << endl;
-	TokenListCIt endOfLine = getOneLine(tokList);
-	DoxygenEntityList aNewList = parse(endOfLine, tokList);
-	doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-	skipEndOfLine();
-	return 1;
+                                  const TokenList &tokList,
+                                  DoxygenEntityList &doxyList)
+{
+  if (noisy)
+    cout << "Parsing " << theCommand << endl;
+  TokenListCIt endOfLine = getOneLine(tokList);
+  DoxygenEntityList aNewList = parse(endOfLine, tokList);
+  doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+  skipEndOfLine();
+  return 1;
 }
 
-
 int DoxygenParser::addCommandParagraph(const std::string &theCommand,
-                                            const TokenList &tokList,
-                                            DoxygenEntityList &doxyList) {
-	if (noisy)
-		cout << "Parsing " << theCommand << endl;
+                                       const TokenList &tokList,
+                                       DoxygenEntityList &doxyList)
+{
+  if (noisy)
+    cout << "Parsing " << theCommand << endl;
 
-	TokenListCIt endOfParagraph = getEndOfParagraph(tokList);
-	DoxygenEntityList aNewList;
-	aNewList = parse(endOfParagraph, tokList);
-	doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-	return 1;
+  TokenListCIt endOfParagraph = getEndOfParagraph(tokList);
+  DoxygenEntityList aNewList;
+  aNewList = parse(endOfParagraph, tokList);
+  doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+  return 1;
 }
 
-
 int DoxygenParser::addCommandEndCommand(const std::string &theCommand,
-                                             const TokenList & tokList,
-                                             DoxygenEntityList &doxyList) {
-	if (noisy)
-		cout << "Parsing " << theCommand << endl;
-	TokenListCIt endCommand = getEndCommand("end" + theCommand, tokList);
-	if (endCommand == tokList.end()) {
-	  printListError(WARN_DOXYGEN_COMMAND_EXPECTED, "Expected end" + theCommand);
-	  return 0;
-	}
-	DoxygenEntityList aNewList;
-	aNewList = parse(endCommand, tokList);
-	m_tokenListIt++;
-	doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-	return 1;
+                                        const TokenList & tokList,
+                                        DoxygenEntityList &doxyList)
+{
+  if (noisy)
+    cout << "Parsing " << theCommand << endl;
+  TokenListCIt endCommand = getEndCommand("end" + theCommand, tokList);
+  if (endCommand == tokList.end()) {
+    printListError(WARN_DOXYGEN_COMMAND_EXPECTED, "Expected end" + theCommand);
+    return 0;
+  }
+  DoxygenEntityList aNewList;
+  aNewList = parse(endCommand, tokList);
+  m_tokenListIt++;
+  doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+  return 1;
 }
 
-
 int DoxygenParser::addCommandWordParagraph(const std::string &theCommand,
                                            const TokenList &tokList,
-                                           DoxygenEntityList &doxyList) {
-    if (noisy)
-        cout << "Parsing " << theCommand << endl;
+                                           DoxygenEntityList &doxyList)
+{
+  if (noisy)
+    cout << "Parsing " << theCommand << endl;
 
-    std::string name = getNextWord();
+  std::string name = getNextWord();
 
-    if (name.empty()) {
-        printListError(WARN_DOXYGEN_COMMAND_ERROR, "No word followed " + theCommand + " command. Not added");
-        return 0;
-    }
-    TokenListCIt endOfParagraph = getEndOfParagraph(tokList);
-    DoxygenEntityList aNewList;
-    aNewList = parse(endOfParagraph, tokList);
-    aNewList.push_front(DoxygenEntity("plainstd::string", name));
-    doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-    return 1;
+  if (name.empty()) {
+    printListError(WARN_DOXYGEN_COMMAND_ERROR,
+        "No word followed " + theCommand + " command. Not added");
+    return 0;
+  }
+  TokenListCIt endOfParagraph = getEndOfParagraph(tokList);
+  DoxygenEntityList aNewList;
+  aNewList = parse(endOfParagraph, tokList);
+  aNewList.push_front(DoxygenEntity("plainstd::string", name));
+  doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+  return 1;
 }
 
-
 int DoxygenParser::addCommandWordLine(const std::string &theCommand,
-                                           const TokenList & tokList,
-                                           DoxygenEntityList &doxyList) {
-	if (noisy)
-		cout << "Parsing " << theCommand << endl;
-	std::string name = getNextWord();
-	if (name.empty()) {
-		printListError(WARN_DOXYGEN_COMMAND_ERROR, "No word followed " + theCommand + " command. Not added");
-		return 0;
-	}
-
-	TokenListCIt endOfLine = getOneLine(tokList);
-	DoxygenEntityList aNewList;
-	aNewList = parse(endOfLine, tokList);
-	aNewList.push_front(DoxygenEntity("plainstd::string", name));
-	doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-	return 1;
-	//else cout << "No line followed " << theCommand <<  " command. Not added" << endl;
-}
-
-
-int DoxygenParser::addCommandWordOWordOWord(const std::string &theCommand,
-                                                  const TokenList &,
-                                                  DoxygenEntityList &doxyList) {
-	if (noisy)
-		cout << "Parsing " << theCommand << endl;
-
-	std::string name = getNextWord();
-	if (name.empty()) {
-		printListError(WARN_DOXYGEN_COMMAND_ERROR, "No word followed " + theCommand + " command. Not added");
-		return 0;
-	}
-	std::string headerfile = getNextWord();
-	std::string headername = getNextWord();
-	DoxygenEntityList aNewList;
-	aNewList.push_back(DoxygenEntity("plainstd::string", name));
-	if (!headerfile.empty())
-		aNewList.push_back(DoxygenEntity("plainstd::string", headerfile));
-	if (!headername.empty())
-		aNewList.push_back(DoxygenEntity("plainstd::string", headername));
-	doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-	return 1;
-}
-
-
-int DoxygenParser::addCommandOWord(const std::string &theCommand,
-                                        const TokenList &,
-                                        DoxygenEntityList &doxyList) {
-	if (noisy)
-		cout << "Parsing " << theCommand << endl;
-
-	std::string name = getNextWord();
-	DoxygenEntityList aNewList;
-	aNewList.push_back(DoxygenEntity("plainstd::string", name));
-	doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-	return 1;
-}
-
-
-int DoxygenParser::addCommandErrorThrow(const std::string &theCommand,
-                                             const TokenList &tokList,
-                                             DoxygenEntityList &) {
-
-	printListError(WARN_DOXYGEN_COMMAND_ERROR, "Encountered: " + theCommand +
-			"\nThis command should not have been encountered. Behaviour past this may be unpredictable");
-	m_tokenListIt = getOneLine(tokList);
-	return 0;
-}
-
-
-int DoxygenParser::addCommandHtml(const std::string &theCommand,
-                                      const TokenList &,
+                                      const TokenList & tokList,
                                       DoxygenEntityList &doxyList)
 {
-    if (noisy)
-        cout << "Parsing " << theCommand << endl;
+  if (noisy)
+    cout << "Parsing " << theCommand << endl;
+  std::string name = getNextWord();
+  if (name.empty()) {
+    printListError(WARN_DOXYGEN_COMMAND_ERROR,
+        "No word followed " + theCommand + " command. Not added");
+    return 0;
+  }
 
-    std::string htmlTagArgs = getNextToken();
-    doxyList.push_back(DoxygenEntity(theCommand, htmlTagArgs));
-    return 1;
+  TokenListCIt endOfLine = getOneLine(tokList);
+  DoxygenEntityList aNewList;
+  aNewList = parse(endOfLine, tokList);
+  aNewList.push_front(DoxygenEntity("plainstd::string", name));
+  doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+  return 1;
+  //else cout << "No line followed " << theCommand <<  " command. Not added" << endl;
 }
 
+int DoxygenParser::addCommandWordOWordOWord(const std::string &theCommand,
+                                            const TokenList &,
+                                            DoxygenEntityList &doxyList)
+{
+  if (noisy)
+    cout << "Parsing " << theCommand << endl;
+
+  std::string name = getNextWord();
+  if (name.empty()) {
+    printListError(WARN_DOXYGEN_COMMAND_ERROR,
+        "No word followed " + theCommand + " command. Not added");
+    return 0;
+  }
+  std::string headerfile = getNextWord();
+  std::string headername = getNextWord();
+  DoxygenEntityList aNewList;
+  aNewList.push_back(DoxygenEntity("plainstd::string", name));
+  if (!headerfile.empty())
+    aNewList.push_back(DoxygenEntity("plainstd::string", headerfile));
+  if (!headername.empty())
+    aNewList.push_back(DoxygenEntity("plainstd::string", headername));
+  doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+  return 1;
+}
+
+int DoxygenParser::addCommandOWord(const std::string &theCommand,
+                                   const TokenList &,
+                                   DoxygenEntityList &doxyList)
+{
+  if (noisy)
+    cout << "Parsing " << theCommand << endl;
+
+  std::string name = getNextWord();
+  DoxygenEntityList aNewList;
+  aNewList.push_back(DoxygenEntity("plainstd::string", name));
+  doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+  return 1;
+}
+
+int DoxygenParser::addCommandErrorThrow(const std::string &theCommand,
+                                        const TokenList &tokList,
+                                        DoxygenEntityList &)
+{
+
+  printListError(WARN_DOXYGEN_COMMAND_ERROR,
+      "Encountered: " + theCommand
+          + "\nThis command should not have been encountered. Behaviour past this may be unpredictable");
+  m_tokenListIt = getOneLine(tokList);
+  return 0;
+}
+
+int DoxygenParser::addCommandHtml(const std::string &theCommand,
+                                  const TokenList &,
+                                  DoxygenEntityList &doxyList)
+{
+  if (noisy)
+    cout << "Parsing " << theCommand << endl;
+
+  std::string htmlTagArgs = getNextToken();
+  doxyList.push_back(DoxygenEntity(theCommand, htmlTagArgs));
+  return 1;
+}
 
 int DoxygenParser::addCommandHtmlEntity(const std::string &theCommand,
-                                             const TokenList &,
-                                             DoxygenEntityList &doxyList)
+                                        const TokenList &,
+                                        DoxygenEntityList &doxyList)
 {
-    if (noisy)
-        cout << "Parsing " << theCommand << endl;
+  if (noisy)
+    cout << "Parsing " << theCommand << endl;
 
-    DoxygenEntityList aNewList;
-    doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-    return 1;
+  DoxygenEntityList aNewList;
+  doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+  return 1;
 }
 
-
 int DoxygenParser::addCommandUnique(const std::string &theCommand,
-                                         const TokenList &tokList,
-                                         DoxygenEntityList &doxyList) {
+                                    const TokenList &tokList,
+                                    DoxygenEntityList &doxyList)
+{
 
-    static std::map<std::string, std::string> endCommands;
-	DoxygenEntityList aNewList;
-	if (theCommand == "arg" || theCommand == "li") {
-		TokenListCIt endOfSection = getEndOfSection(theCommand, tokList);
-		DoxygenEntityList aNewList;
-		aNewList = parse(endOfSection, tokList);
-		doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-	}
-	// \xrefitem <key> "(heading)" "(std::list title)" {text}
-	else if (theCommand == "xrefitem") {
-		if (noisy)
-			cout << "Parsing " << theCommand << endl;
-		std::string key = getNextWord();
-		if (key.empty()) {
-			printListError(WARN_DOXYGEN_COMMAND_ERROR, "No key followed " + theCommand + " command. Not added");
-			return 0;
-		}
-		std::string heading = getNextWord();
-		if (key.empty()) {
-			printListError(WARN_DOXYGEN_COMMAND_ERROR, "No heading followed " + theCommand + " command. Not added");
-			return 0;
-		}
-		std::string title = getNextWord();
-		if (title.empty()) {
-			printListError(WARN_DOXYGEN_COMMAND_ERROR, "No title followed " + theCommand + " command. Not added");
-			return 0;
-		}
-		TokenListCIt endOfParagraph = getEndOfParagraph(tokList);
-		aNewList = parse(endOfParagraph, tokList);
-		aNewList.push_front(DoxygenEntity("plainstd::string", title));
-		aNewList.push_front(DoxygenEntity("plainstd::string", heading));
-		aNewList.push_front(DoxygenEntity("plainstd::string", key));
-		doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-		return 1;
-	}
-	// \ingroup (<groupname> [<groupname> <groupname>])
-	else if (theCommand == "ingroup") {
-		std::string name = getNextWord();
-		aNewList.push_back(DoxygenEntity("plainstd::string", name));
-		name = getNextWord();
-		if (!name.empty())
-			aNewList.push_back(DoxygenEntity("plainstd::string", name));
-		name = getNextWord();
-		if (!name.empty())
-			aNewList.push_back(DoxygenEntity("plainstd::string", name));
-		doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-		return 1;
-	}
-	// \par [(paragraph title)] { paragraph }
-	else if (theCommand == "par") {
-	    TokenListCIt endOfLine = getOneLine(tokList);
-		aNewList = parse(endOfLine, tokList);
-		DoxygenEntityList aNewList2;
-		TokenListCIt endOfParagraph = getEndOfParagraph(tokList);
-		aNewList2 = parse(endOfParagraph, tokList);
-		aNewList.splice(aNewList.end(), aNewList2);
-		doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-		return 1;
-	}
-	// \headerfile <header-file> [<header-name>]
-	else if (theCommand == "headerfile") {
-		DoxygenEntityList aNewList;
-		std::string name = getNextWord();
-		aNewList.push_back(DoxygenEntity("plainstd::string", name));
-		name = getNextWord();
-		if (!name.empty())
-			aNewList.push_back(DoxygenEntity("plainstd::string", name));
-		doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-		return 1;
-	}
-	// \overload [(function declaration)]
-	else if (theCommand == "overload") {
-	    TokenListCIt endOfLine = getOneLine(tokList);
-		if (endOfLine != m_tokenListIt) {
-			DoxygenEntityList aNewList;
-			aNewList = parse(endOfLine, tokList);
-			doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-		} else
-			doxyList.push_back(DoxygenEntity(theCommand));
-		return 1;
-	}
-	// \weakgroup <name> [(title)]
-	else if (theCommand == "weakgroup") {
-		if (noisy)
-			cout << "Parsing " << theCommand << endl;
-		std::string name = getNextWord();
-		if (name.empty()) {
-			printListError(WARN_DOXYGEN_COMMAND_ERROR, "No word followed " + theCommand + " command. Not added");
-			return 0;
-		}
-		DoxygenEntityList aNewList;
-		TokenListCIt endOfLine = getOneLine(tokList);
-		if (endOfLine != m_tokenListIt) {
-			aNewList = parse(endOfLine, tokList);
-		}
-		aNewList.push_front(DoxygenEntity("plainstd::string", name));
-		doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-	}
-	// \ref <name> ["(text)"]
-	else if (theCommand == "ref") {
-		if (noisy)
-			cout << "Parsing " << theCommand << endl;
-		std::string name = getNextWord();
-		if (name.empty()) {
-			printListError(WARN_DOXYGEN_COMMAND_ERROR, "No key followed " + theCommand + " command. Not added");
-			return 0;
-		}
-		std::string text = getNextWord();
-		aNewList.push_back(DoxygenEntity("plainstd::string", name));
-		if (!text.empty())
-			aNewList.push_back(DoxygenEntity("plainstd::string", text));
-		doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-	}
-	// \subpage <name> ["(text)"]
-	else if (theCommand == "subpage") {
-		if (noisy)
-			cout << "Parsing " << theCommand << endl;
-		std::string name = getNextWord();
-		if (name.empty()) {
-			printListError(WARN_DOXYGEN_COMMAND_ERROR, "No name followed " + theCommand + " command. Not added");
-			return 0;
-		}
-		std::string text = getNextWord();
-		aNewList.push_back(DoxygenEntity("plainstd::string", name));
-		if (!text.empty())
-			aNewList.push_back(DoxygenEntity("plainstd::string", text));
-		doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-	}
-    // \code ... \endcode
-    // \verbatim ... \endverbatim
-	// \dot dotcode \enddot
-	// \msc msccode \endmsc
-	// \f[ ... \f]
-	// \f{ ... \f}
-	// \f{env}{ ... \f}
-	// \f$ ... \f$
-    else if (theCommand == "code" || theCommand == "verbatim"
-        || theCommand == "dot" || theCommand == "msc"
-        || theCommand == "f[" || theCommand == "f{"
-        || theCommand == "f$") {
-        if (!endCommands.size()) {
-          // fill in static table of end commands
-          endCommands["f["] = "f]";
-          endCommands["f{"] = "f}";
-          endCommands["f$"] = "f$";
-        }
-        if (noisy)
-            cout << "Parsing " << theCommand << endl;
-
-        std::string endCommand;
-        std::map <std::string, std::string>::iterator it;
-        it = endCommands.find(theCommand);
-        if (it != endCommands.end())
-          endCommand = it->second;
-        else
-          endCommand = "end" + theCommand;
-
-        std::string content = getStringTilEndCommand(endCommand, tokList);
-        aNewList.push_back(DoxygenEntity("plainstd::string", content));
-        doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+  static std::map<std::string, std::string> endCommands;
+  DoxygenEntityList aNewList;
+  if (theCommand == "arg" || theCommand == "li") {
+    TokenListCIt endOfSection = getEndOfSection(theCommand, tokList);
+    DoxygenEntityList aNewList;
+    aNewList = parse(endOfSection, tokList);
+    doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+  }
+  // \xrefitem <key> "(heading)" "(std::list title)" {text}
+  else if (theCommand == "xrefitem") {
+    if (noisy)
+      cout << "Parsing " << theCommand << endl;
+    std::string key = getNextWord();
+    if (key.empty()) {
+      printListError(WARN_DOXYGEN_COMMAND_ERROR,
+          "No key followed " + theCommand + " command. Not added");
+      return 0;
     }
-	// \dotfile <file> ["caption"]
-	// \mscfile <file> ["caption"]
-	else if (theCommand == "dotfile" || theCommand == "mscfile") {
-		if (noisy)
-			cout << "Parsing " << theCommand << endl;
-		std::string file = getNextWord();
-		if (file.empty()) {
-			printListError(WARN_DOXYGEN_COMMAND_ERROR, "No file followed " + theCommand + " command. Not added");
-			return 0;
-		}
-		std::string caption = getNextWord();
-		aNewList.push_back(DoxygenEntity("plainstd::string", file));
-		if (!caption.empty())
-			aNewList.push_back(DoxygenEntity("plainstd::string", caption));
-		doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-	}
-	// \image <format> <file> ["caption"] [<sizeindication>=<size>]
-	else if (theCommand == "image") {
-		if (noisy)
-			cout << "Parsing " << theCommand << endl;
-		std::string format = getNextWord();
-		if (format.empty()) {
-			printListError(WARN_DOXYGEN_COMMAND_ERROR, "No format followed " + theCommand + " command. Not added");
-			return 0;
-		}
-		std::string file = getNextWord();
-		if (file.empty()) {
-			printListError(WARN_DOXYGEN_COMMAND_ERROR, "No name followed " + theCommand + " command. Not added");
-			return 0;
-		}
-		std::string caption = getNextWord();
-		std::string size = getNextWord();
+    std::string heading = getNextWord();
+    if (key.empty()) {
+      printListError(WARN_DOXYGEN_COMMAND_ERROR,
+          "No heading followed " + theCommand + " command. Not added");
+      return 0;
+    }
+    std::string title = getNextWord();
+    if (title.empty()) {
+      printListError(WARN_DOXYGEN_COMMAND_ERROR,
+          "No title followed " + theCommand + " command. Not added");
+      return 0;
+    }
+    TokenListCIt endOfParagraph = getEndOfParagraph(tokList);
+    aNewList = parse(endOfParagraph, tokList);
+    aNewList.push_front(DoxygenEntity("plainstd::string", title));
+    aNewList.push_front(DoxygenEntity("plainstd::string", heading));
+    aNewList.push_front(DoxygenEntity("plainstd::string", key));
+    doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+    return 1;
+  }
+  // \ingroup (<groupname> [<groupname> <groupname>])
+  else if (theCommand == "ingroup") {
+    std::string name = getNextWord();
+    aNewList.push_back(DoxygenEntity("plainstd::string", name));
+    name = getNextWord();
+    if (!name.empty())
+      aNewList.push_back(DoxygenEntity("plainstd::string", name));
+    name = getNextWord();
+    if (!name.empty())
+      aNewList.push_back(DoxygenEntity("plainstd::string", name));
+    doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+    return 1;
+  }
+  // \par [(paragraph title)] { paragraph }
+  else if (theCommand == "par") {
+    TokenListCIt endOfLine = getOneLine(tokList);
+    aNewList = parse(endOfLine, tokList);
+    DoxygenEntityList aNewList2;
+    TokenListCIt endOfParagraph = getEndOfParagraph(tokList);
+    aNewList2 = parse(endOfParagraph, tokList);
+    aNewList.splice(aNewList.end(), aNewList2);
+    doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+    return 1;
+  }
+  // \headerfile <header-file> [<header-name>]
+  else if (theCommand == "headerfile") {
+    DoxygenEntityList aNewList;
+    std::string name = getNextWord();
+    aNewList.push_back(DoxygenEntity("plainstd::string", name));
+    name = getNextWord();
+    if (!name.empty())
+      aNewList.push_back(DoxygenEntity("plainstd::string", name));
+    doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+    return 1;
+  }
+  // \overload [(function declaration)]
+  else if (theCommand == "overload") {
+    TokenListCIt endOfLine = getOneLine(tokList);
+    if (endOfLine != m_tokenListIt) {
+      DoxygenEntityList aNewList;
+      aNewList = parse(endOfLine, tokList);
+      doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+    } else
+      doxyList.push_back(DoxygenEntity(theCommand));
+    return 1;
+  }
+  // \weakgroup <name> [(title)]
+  else if (theCommand == "weakgroup") {
+    if (noisy)
+      cout << "Parsing " << theCommand << endl;
+    std::string name = getNextWord();
+    if (name.empty()) {
+      printListError(WARN_DOXYGEN_COMMAND_ERROR,
+          "No word followed " + theCommand + " command. Not added");
+      return 0;
+    }
+    DoxygenEntityList aNewList;
+    TokenListCIt endOfLine = getOneLine(tokList);
+    if (endOfLine != m_tokenListIt) {
+      aNewList = parse(endOfLine, tokList);
+    }
+    aNewList.push_front(DoxygenEntity("plainstd::string", name));
+    doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+  }
+  // \ref <name> ["(text)"]
+  else if (theCommand == "ref") {
+    if (noisy)
+      cout << "Parsing " << theCommand << endl;
+    std::string name = getNextWord();
+    if (name.empty()) {
+      printListError(WARN_DOXYGEN_COMMAND_ERROR,
+          "No key followed " + theCommand + " command. Not added");
+      return 0;
+    }
+    std::string text = getNextWord();
+    aNewList.push_back(DoxygenEntity("plainstd::string", name));
+    if (!text.empty())
+      aNewList.push_back(DoxygenEntity("plainstd::string", text));
+    doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+  }
+  // \subpage <name> ["(text)"]
+  else if (theCommand == "subpage") {
+    if (noisy)
+      cout << "Parsing " << theCommand << endl;
+    std::string name = getNextWord();
+    if (name.empty()) {
+      printListError(WARN_DOXYGEN_COMMAND_ERROR,
+          "No name followed " + theCommand + " command. Not added");
+      return 0;
+    }
+    std::string text = getNextWord();
+    aNewList.push_back(DoxygenEntity("plainstd::string", name));
+    if (!text.empty())
+      aNewList.push_back(DoxygenEntity("plainstd::string", text));
+    doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+  }
+  // \code ... \endcode
+  // \verbatim ... \endverbatim
+  // \dot dotcode \enddot
+  // \msc msccode \endmsc
+  // \f[ ... \f]
+  // \f{ ... \f}
+  // \f{env}{ ... \f}
+  // \f$ ... \f$
+  else if (theCommand == "code" || theCommand == "verbatim"
+      || theCommand == "dot" || theCommand == "msc" || theCommand == "f["
+      || theCommand == "f{" || theCommand == "f$") {
+    if (!endCommands.size()) {
+      // fill in static table of end commands
+      endCommands["f["] = "f]";
+      endCommands["f{"] = "f}";
+      endCommands["f$"] = "f$";
+    }
+    if (noisy)
+      cout << "Parsing " << theCommand << endl;
 
-		DoxygenEntityList aNewList;
-		aNewList.push_back(DoxygenEntity("plainstd::string", format));
-		aNewList.push_back(DoxygenEntity("plainstd::string", file));
-		if (!caption.empty())
-			aNewList.push_back(DoxygenEntity("plainstd::string", caption));
-		if (!size.empty())
-			aNewList.push_back(DoxygenEntity("plainstd::string", size));
-		doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-	}
-	// \addtogroup <name> [(title)]
-	else if (theCommand == "addtogroup") {
-		if (noisy)
-			cout << "Parsing " << theCommand << endl;
-		std::string name = getNextWord();
-		if (name.empty()) {
-			printListError(WARN_DOXYGEN_COMMAND_ERROR, "There should be at least one word following the '" + theCommand + "' command. Command ignored.");
-			return 0;
-		}
-		DoxygenEntityList aNewList;
-		TokenListCIt endOfLine = getOneLine(tokList);
-		if (endOfLine != m_tokenListIt) {
-			aNewList = parse(endOfLine, tokList);
-		}
-		aNewList.push_front(DoxygenEntity("plainstd::string", name));
-		doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-		skipEndOfLine();
-	}
-	// \if <cond> [\else ...] [\elseif <cond> ...] \endif
-	else if (theCommand == "if" || theCommand == "ifnot" ||
-					 theCommand == "else" || theCommand == "elseif") {
-		if (noisy)
-			cout << "Parsing " << theCommand << endl;
+    std::string endCommand;
+    std::map<std::string, std::string>::iterator it;
+    it = endCommands.find(theCommand);
+    if (it != endCommands.end())
+      endCommand = it->second;
+    else
+      endCommand = "end" + theCommand;
 
-		std::string cond;
-		bool skipEndif = false; // if true then we skip endif after parsing block of code
-		bool needsCond = (theCommand == "if" || theCommand == "ifnot" || theCommand == "elseif");
-		if (needsCond) {
-			cond = getNextWord();
-			if (cond.empty()) {
-				printListError(WARN_DOXYGEN_COMMAND_ERROR, "No word followed " + theCommand + " command. Not added");
-				return 0;
-			}
-		}
+    std::string content = getStringTilEndCommand(endCommand, tokList);
+    aNewList.push_back(DoxygenEntity("plainstd::string", content));
+    doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+  }
+  // \dotfile <file> ["caption"]
+  // \mscfile <file> ["caption"]
+  else if (theCommand == "dotfile" || theCommand == "mscfile") {
+    if (noisy)
+      cout << "Parsing " << theCommand << endl;
+    std::string file = getNextWord();
+    if (file.empty()) {
+      printListError(WARN_DOXYGEN_COMMAND_ERROR,
+          "No file followed " + theCommand + " command. Not added");
+      return 0;
+    }
+    std::string caption = getNextWord();
+    aNewList.push_back(DoxygenEntity("plainstd::string", file));
+    if (!caption.empty())
+      aNewList.push_back(DoxygenEntity("plainstd::string", caption));
+    doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+  }
+  // \image <format> <file> ["caption"] [<sizeindication>=<size>]
+  else if (theCommand == "image") {
+    if (noisy)
+      cout << "Parsing " << theCommand << endl;
+    std::string format = getNextWord();
+    if (format.empty()) {
+      printListError(WARN_DOXYGEN_COMMAND_ERROR,
+          "No format followed " + theCommand + " command. Not added");
+      return 0;
+    }
+    std::string file = getNextWord();
+    if (file.empty()) {
+      printListError(WARN_DOXYGEN_COMMAND_ERROR,
+          "No name followed " + theCommand + " command. Not added");
+      return 0;
+    }
+    std::string caption = getNextWord();
+    std::string size = getNextWord();
 
-		int nestedCounter = 1;
-		TokenListCIt endCommand = tokList.end();
+    DoxygenEntityList aNewList;
+    aNewList.push_back(DoxygenEntity("plainstd::string", format));
+    aNewList.push_back(DoxygenEntity("plainstd::string", file));
+    if (!caption.empty())
+      aNewList.push_back(DoxygenEntity("plainstd::string", caption));
+    if (!size.empty())
+      aNewList.push_back(DoxygenEntity("plainstd::string", size));
+    doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+  }
+  // \addtogroup <name> [(title)]
+  else if (theCommand == "addtogroup") {
+    if (noisy)
+      cout << "Parsing " << theCommand << endl;
+    std::string name = getNextWord();
+    if (name.empty()) {
+      printListError(WARN_DOXYGEN_COMMAND_ERROR,
+          "There should be at least one word following the '" + theCommand
+              + "' command. Command ignored.");
+      return 0;
+    }
+    DoxygenEntityList aNewList;
+    TokenListCIt endOfLine = getOneLine(tokList);
+    if (endOfLine != m_tokenListIt) {
+      aNewList = parse(endOfLine, tokList);
+    }
+    aNewList.push_front(DoxygenEntity("plainstd::string", name));
+    doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+    skipEndOfLine();
+  }
+  // \if <cond> [\else ...] [\elseif <cond> ...] \endif
+  else if (theCommand == "if" || theCommand == "ifnot" || theCommand == "else"
+      || theCommand == "elseif") {
+    if (noisy)
+      cout << "Parsing " << theCommand << endl;
 
-		// go through the commands and find closing endif or else or elseif
-		for (TokenListCIt it = m_tokenListIt; it != tokList.end(); it++) {
-			if (it->m_tokenType == COMMAND) {
-				if (it->m_tokenString == "if" || it->m_tokenString == "ifnot")
-					nestedCounter++;
-				else if (it->m_tokenString == "endif")
-					nestedCounter--;
-				if (nestedCounter == 1 && (it->m_tokenString == "else" || it->m_tokenString == "elseif")) { // else found
-					endCommand = it;
-					break;
-				}
-				if (nestedCounter == 0) { // endif found
-					endCommand = it;
-					skipEndif = true;
-					break;
-				}
-			}
-		}
+    std::string cond;
+    bool skipEndif = false; // if true then we skip endif after parsing block of code
+    bool needsCond = (theCommand == "if" || theCommand == "ifnot"
+        || theCommand == "elseif");
+    if (needsCond) {
+      cond = getNextWord();
+      if (cond.empty()) {
+        printListError(WARN_DOXYGEN_COMMAND_ERROR,
+            "No word followed " + theCommand + " command. Not added");
+        return 0;
+      }
+    }
 
-		if (endCommand == tokList.end()) {
-			printListError(WARN_DOXYGEN_COMMAND_EXPECTED, "No corresponding endif found");
-			return 0;
-		}
+    int nestedCounter = 1;
+    TokenListCIt endCommand = tokList.end();
 
-		DoxygenEntityList aNewList;
-		aNewList = parse(endCommand, tokList);
-		if (skipEndif)
-			m_tokenListIt++;
-		if (needsCond)
-			aNewList.push_front(DoxygenEntity("plainstd::string", cond));
-		doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-	}
-	return 0;
+    // go through the commands and find closing endif or else or elseif
+    for (TokenListCIt it = m_tokenListIt; it != tokList.end(); it++) {
+      if (it->m_tokenType == COMMAND) {
+        if (it->m_tokenString == "if" || it->m_tokenString == "ifnot")
+          nestedCounter++;
+        else if (it->m_tokenString == "endif")
+          nestedCounter--;
+        if (nestedCounter == 1
+            && (it->m_tokenString == "else" || it->m_tokenString == "elseif")) { // else found
+          endCommand = it;
+          break;
+        }
+        if (nestedCounter == 0) { // endif found
+          endCommand = it;
+          skipEndif = true;
+          break;
+        }
+      }
+    }
+
+    if (endCommand == tokList.end()) {
+      printListError(WARN_DOXYGEN_COMMAND_EXPECTED,
+          "No corresponding endif found");
+      return 0;
+    }
+
+    DoxygenEntityList aNewList;
+    aNewList = parse(endCommand, tokList);
+    if (skipEndif)
+      m_tokenListIt++;
+    if (needsCond)
+      aNewList.push_front(DoxygenEntity("plainstd::string", cond));
+    doxyList.push_back(DoxygenEntity(theCommand, aNewList));
+  }
+  return 0;
 }
 
-
 int DoxygenParser::addCommand(const std::string &commandString,
-                                  const TokenList &tokList,
-                                  DoxygenEntityList &doxyList) {
+                              const TokenList &tokList,
+                              DoxygenEntityList &doxyList)
+{
 
-	string theCommand = stringToLower(commandString);
+  string theCommand = stringToLower(commandString);
 
-	if (theCommand == "plainstd::string") {
-		string nextPhrase = getStringTilCommand(tokList);
-		if (noisy)
-			cout << "Parsing plain std::string :" << nextPhrase << endl;
-		doxyList.push_back(DoxygenEntity("plainstd::string", nextPhrase));
-		return 1;
-	}
+  if (theCommand == "plainstd::string") {
+    string nextPhrase = getStringTilCommand(tokList);
+    if (noisy)
+      cout << "Parsing plain std::string :" << nextPhrase << endl;
+    doxyList.push_back(DoxygenEntity("plainstd::string", nextPhrase));
+    return 1;
+  }
 
-	switch (commandBelongs(theCommand)) {
-		case SIMPLECOMMAND:
-			return addSimpleCommand(theCommand, doxyList);
-		case COMMANDWORD:
-			return addCommandWord(theCommand, tokList, doxyList);
-		case COMMANDLINE:
-			return addCommandLine(theCommand, tokList, doxyList);
-		case COMMANDPARAGRAPH:
-			return addCommandParagraph(theCommand, tokList, doxyList);
-		case COMMANDENDCOMMAND:
-			return addCommandEndCommand(theCommand, tokList, doxyList);
-		case COMMANDWORDPARAGRAPH:
-			return addCommandWordParagraph(theCommand, tokList, doxyList);
-		case COMMANDWORDLINE:
-			return addCommandWordLine(theCommand, tokList, doxyList);
-		case COMMANDWORDOWORDWORD:
-			return addCommandWordOWordOWord(theCommand, tokList, doxyList);
-		case COMMANDOWORD:
-			return addCommandOWord(theCommand, tokList, doxyList);
-		case COMMANDERRORTHROW:
-			return addCommandErrorThrow(theCommand, tokList, doxyList);
-		case COMMANDUNIQUE:
-			return addCommandUnique(theCommand, tokList, doxyList);
-        case COMMAND_HTML:
-            return addCommandHtml(theCommand, tokList, doxyList);
-        case COMMAND_HTML_ENTITY:
-            return addCommandHtmlEntity(theCommand, tokList, doxyList);
-	}
-	return 0;
+  switch (commandBelongs(theCommand)) {
+  case SIMPLECOMMAND:
+    return addSimpleCommand(theCommand, doxyList);
+  case COMMANDWORD:
+    return addCommandWord(theCommand, tokList, doxyList);
+  case COMMANDLINE:
+    return addCommandLine(theCommand, tokList, doxyList);
+  case COMMANDPARAGRAPH:
+    return addCommandParagraph(theCommand, tokList, doxyList);
+  case COMMANDENDCOMMAND:
+    return addCommandEndCommand(theCommand, tokList, doxyList);
+  case COMMANDWORDPARAGRAPH:
+    return addCommandWordParagraph(theCommand, tokList, doxyList);
+  case COMMANDWORDLINE:
+    return addCommandWordLine(theCommand, tokList, doxyList);
+  case COMMANDWORDOWORDWORD:
+    return addCommandWordOWordOWord(theCommand, tokList, doxyList);
+  case COMMANDOWORD:
+    return addCommandOWord(theCommand, tokList, doxyList);
+  case COMMANDERRORTHROW:
+    return addCommandErrorThrow(theCommand, tokList, doxyList);
+  case COMMANDUNIQUE:
+    return addCommandUnique(theCommand, tokList, doxyList);
+  case COMMAND_HTML:
+    return addCommandHtml(theCommand, tokList, doxyList);
+  case COMMAND_HTML_ENTITY:
+    return addCommandHtmlEntity(theCommand, tokList, doxyList);
+  }
+  return 0;
 }
 
-
 /**
  * This method converts TokenList to DoxygenEntryList.
  */
 DoxygenEntityList DoxygenParser::parse(TokenListCIt endParsingIndex,
-                                          const TokenList &tokList,
-                                          bool root) {
-	// if we are root, than any strings should be added as 'partofdescription', else as 'plainstd::string'
-	std::string currPlainstringCommandType = root ? "partofdescription" : "plainstd::string";
-	DoxygenEntityList aNewList;
+                                       const TokenList &tokList, bool root)
+{
+  // if we are root, than any strings should be added as 'partofdescription', else as 'plainstd::string'
+  std::string currPlainstringCommandType =
+      root ? "partofdescription" : "plainstd::string";
+  DoxygenEntityList aNewList;
 
-	while (m_tokenListIt != endParsingIndex) {
+  while (m_tokenListIt != endParsingIndex) {
 
-		Token currToken = *m_tokenListIt;
+    Token currToken = *m_tokenListIt;
 
-		if (noisy)
-			cout << "Parsing for phrase starting in:" << currToken.toString() << endl;
+    if (noisy)
+      cout << "Parsing for phrase starting in:" << currToken.toString() << endl;
 
-		if (currToken.m_tokenType == END_LINE) {
-		    aNewList.push_back(DoxygenEntity("plainstd::endl"));
-		    m_tokenListIt++;
-		} else if (currToken.m_tokenType == COMMAND) {
-		    m_tokenListIt++;
-		    addCommand(currToken.m_tokenString, tokList, aNewList);
-		} else if (currToken.m_tokenType == PLAINSTRING) {
-			addCommand(currPlainstringCommandType, tokList, aNewList);
-		}
+    if (currToken.m_tokenType == END_LINE) {
+      aNewList.push_back(DoxygenEntity("plainstd::endl"));
+      m_tokenListIt++;
+    } else if (currToken.m_tokenType == COMMAND) {
+      m_tokenListIt++;
+      addCommand(currToken.m_tokenString, tokList, aNewList);
+    } else if (currToken.m_tokenType == PLAINSTRING) {
+      addCommand(currPlainstringCommandType, tokList, aNewList);
+    }
 
-		if (endParsingIndex != tokList.end() && m_tokenListIt == tokList.end()) {
-		  // this could happen if we can't reach the original endParsingIndex
-		  printListError(WARN_DOXYGEN_UNEXPECTED_END_OF_COMMENT, "Unexpected end of comment encountered");
-		  break;
-		}
-	}
-	return aNewList;
+    if (endParsingIndex != tokList.end() && m_tokenListIt == tokList.end()) {
+      // this could happen if we can't reach the original endParsingIndex
+      printListError(WARN_DOXYGEN_UNEXPECTED_END_OF_COMMENT,
+          "Unexpected end of comment encountered");
+      break;
+    }
+  }
+  return aNewList;
 }
 
-
 DoxygenEntityList DoxygenParser::createTree(const std::string &doxygenBlob,
-                                               const std::string &fileName,
-                                               int lineNumber) {
+                                            const std::string &fileName,
+                                            int lineNumber)
+{
 
   tokenizeDoxygenComment(doxygenBlob, fileName, lineNumber);
   if (noisy) {
@@ -953,58 +974,56 @@ DoxygenEntityList DoxygenParser::createTree(const std::string &doxygenBlob,
   return rootList;
 }
 
-
 /*
  * Splits 'text' on 'separator' chars. Separator chars are not part of the
  * strings.
  */
-DoxygenParser::StringVector DoxygenParser::split(const std::string &text, char separator)
+DoxygenParser::StringVector DoxygenParser::split(const std::string &text,
+                                                 char separator)
 {
-    StringVector lines;
-    size_t prevPos = 0, pos = 0;
+  StringVector lines;
+  size_t prevPos = 0, pos = 0;
 
-    while (pos < string::npos) {
-        pos = text.find(separator, prevPos);
-        lines.push_back(text.substr(prevPos, pos - prevPos));
-        prevPos = pos + 1;
-    }
+  while (pos < string::npos) {
+    pos = text.find(separator, prevPos);
+    lines.push_back(text.substr(prevPos, pos - prevPos));
+    prevPos = pos + 1;
+  }
 
-    return lines;
+  return lines;
 }
 
-
 /*
  * Returns true, if 'c' is one of doxygen comment block start
  * characters: *, /, or !
  */
 bool DoxygenParser::isStartOfDoxyCommentChar(char c)
 {
-    return (strchr("*/!", c) != NULL);
+  return (strchr("*/!", c) != NULL);
 }
 
-
 /*
  * Adds token with Doxygen command to token list, but only if command is one of
  * Doxygen commands. In that case true is returned. If the command is not
  * recognized as a doxygen command, it is ignored and false is returned.
  */
 bool DoxygenParser::addDoxyCommand(DoxygenParser::TokenList &tokList,
-                                        const std::string &cmd) {
-    if (findCommand(cmd)) {
-        tokList.push_back(Token(COMMAND, cmd));
-        return true;
-    } else {
-        // Unknown commands are ignored, because they are
-        // also ignored by Doxygen - see test doxygen_misc_constructs.h, f. backslashB().
-        // This differs from original implementation in this class. Uncomment
-        // the line below to put unknown commands to output.
-        // tokList.push_back(Token(PLAINSTRING, cmd));
-    }
+                                   const std::string &cmd)
+{
+  if (findCommand(cmd)) {
+    tokList.push_back(Token(COMMAND, cmd));
+    return true;
+  } else {
+    // Unknown commands are ignored, because they are
+    // also ignored by Doxygen - see test doxygen_misc_constructs.h, f. backslashB().
+    // This differs from original implementation in this class. Uncomment
+    // the line below to put unknown commands to output.
+    // tokList.push_back(Token(PLAINSTRING, cmd));
+  }
 
-    return false;
+  return false;
 }
 
-
 /*
  * This method copies comment text to output as it is - no processing is
  * done, Doxygen commands are ignored. It is used for commands \verbatim,
@@ -1012,33 +1031,41 @@ bool DoxygenParser::addDoxyCommand(DoxygenParser::TokenList &tokList,
  */
 size_t DoxygenParser::processVerbatimText(size_t pos, const std::string &line)
 {
-    if (line[pos] == '\\'  ||  line[pos] == '@') { // check for end commands
-        pos++;
-        // characters '$[]{}' are used in commands \f$, \f[, and \f{
-        size_t endOfWordPos = line.find_first_not_of("abcdefghijklmnopqrstuvwxyz$[]{}", pos);
-        string cmd = line.substr(pos, endOfWordPos - pos);
+  if (line[pos] == '\\' || line[pos] == '@') { // check for end commands
+
+    pos++;
+    // characters '$[]{}' are used in commands \f$, \f[, and \f{
+    size_t endOfWordPos = line.find_first_not_of(
+        "abcdefghijklmnopqrstuvwxyz$[]{}", pos);
+    string cmd = line.substr(pos, endOfWordPos - pos);
+
+    if (cmd == CMD_END_HTML_ONLY || cmd == CMD_END_VERBATIM
+        || cmd == CMD_END_LATEX_1 || cmd == CMD_END_LATEX_2
+        || cmd == CMD_END_LATEX_3) {
+
+      m_isVerbatimText = false;
+      addDoxyCommand(m_tokenList, cmd);
 
-        if (cmd == CMD_END_HTML_ONLY  ||  cmd == CMD_END_VERBATIM  ||
-            cmd == CMD_END_LATEX_1 ||  cmd == CMD_END_LATEX_2  ||  cmd == CMD_END_LATEX_3) {
-            m_isVerbatimText = false;
-            addDoxyCommand(m_tokenList, cmd);
-        } else {
-            m_tokenList.push_back(Token(PLAINSTRING,
-                                  // include '\' or '@'
-                                  line.substr(pos - 1, endOfWordPos - pos + 1)));
-        }
-        pos = endOfWordPos;
     } else {
-        // whitespaces are stored as plain strings
-        size_t startOfPossibleEndCmd = line.find_first_of("\\@", pos);
-        m_tokenList.push_back(Token(PLAINSTRING,
-                              line.substr(pos, startOfPossibleEndCmd - pos)));
-        pos = startOfPossibleEndCmd;
+
+      m_tokenList.push_back(Token(PLAINSTRING,
+      // include '\' or '@'
+          line.substr(pos - 1, endOfWordPos - pos + 1)));
     }
 
-    return pos;
-}
+    pos = endOfWordPos;
 
+  } else {
+
+    // whitespaces are stored as plain strings
+    size_t startOfPossibleEndCmd = line.find_first_of("\\@", pos);
+    m_tokenList.push_back(
+        Token(PLAINSTRING, line.substr(pos, startOfPossibleEndCmd - pos)));
+    pos = startOfPossibleEndCmd;
+  }
+
+  return pos;
+}
 
 /*
  * Processes doxy commands for escaped characters: \$ \@ \\ \& \~ \< \> \# \% \" \. \::
@@ -1059,11 +1086,14 @@ bool DoxygenParser::processEscapedChars(size_t &pos, const std::string &line)
     // these chars can be escaped for doxygen
     string escapedChars = "$@\\&~<>#%\".";
     if (escapedChars.find(line[pos + 1]) != string::npos) {
+
       addDoxyCommand(m_tokenList, line.substr(pos + 1, 1));
       pos += 2;
       return true;
-    } else if ((pos + 2) < line.size()  &&
-                line[pos + 1] == ':'  &&  line[pos + 2] == ':') {
+
+    } else if ((pos + 2) < line.size() && line[pos + 1] == ':'
+        && line[pos + 2] == ':') {
+
       // add command \:: - handling this separately supports documentation
       // text like \::someText
       addDoxyCommand(m_tokenList, line.substr(pos + 1, 2));
@@ -1074,7 +1104,6 @@ bool DoxygenParser::processEscapedChars(size_t &pos, const std::string &line)
   return false;
 }
 
-
 /*
  * Processes word doxygen commands, like \arg, \c, \b, \return, ...
  */
@@ -1082,28 +1111,32 @@ void DoxygenParser::processWordCommands(size_t &pos, const std::string &line)
 {
   pos++;
   // characters '$[]{}' are used in commands \f$, \f[, ...
+
   size_t endOfWordPos = line.find_first_not_of("abcdefghijklmnopqrstuvwxyz$[]{}", pos);
-  string cmd = line.substr(pos , endOfWordPos - pos);
+
+  string cmd = line.substr(pos, endOfWordPos - pos);
   addDoxyCommand(m_tokenList, cmd);
-  if (cmd == CMD_HTML_ONLY  ||  cmd == CMD_VERBATIM  ||
-    cmd == CMD_LATEX_1  ||  cmd == CMD_LATEX_2  ||  cmd == CMD_LATEX_3) {
+
+  if (cmd == CMD_HTML_ONLY || cmd == CMD_VERBATIM || cmd == CMD_LATEX_1
+      || cmd == CMD_LATEX_2 || cmd == CMD_LATEX_3) {
+
     m_isVerbatimText = true;
+
   } else {
     // skip any possible spaces after command, because some commands have parameters,
     // and spaces between command and parameter must be ignored.
     if (endOfWordPos != string::npos) {
-        endOfWordPos = line.find_first_not_of(" \t", endOfWordPos);
+      endOfWordPos = line.find_first_not_of(" \t", endOfWordPos);
     }
   }
   pos = endOfWordPos;
 }
 
-
 void DoxygenParser::processHtmlTags(size_t &pos, const std::string &line)
 {
   bool isEndHtmlTag = false;
   pos++;
-  if (line.size() > pos &&  line[pos] == '/') {
+  if (line.size() > pos && line[pos] == '/') {
     isEndHtmlTag = true;
     pos++;
   }
@@ -1114,25 +1147,26 @@ void DoxygenParser::processHtmlTags(size_t &pos, const std::string &line)
   pos = endHtmlPos;
 
   // prepend '<' to distinguish HTML tags from doxygen commands
-  if (!cmd.empty()  &&  addDoxyCommand(m_tokenList, '<' + cmd)) {
+  if (!cmd.empty() && addDoxyCommand(m_tokenList, '<' + cmd)) {
     // it is a valid HTML command
     if (line[pos] != '>') { // it should be HTML tag with args,
-                             // for example <A ...>, <IMG ...>, ...
+                            // for example <A ...>, <IMG ...>, ...
       if (isEndHtmlTag) {
         m_tokenListIt = m_tokenList.end();
         printListError(WARN_DOXYGEN_COMMAND_ERROR,
-                       "Illegal end HTML tag without '>' found! Tag: " + cmd);
+            "Illegal end HTML tag without '>' found! Tag: " + cmd);
       }
 
       endHtmlPos = line.find(">", pos);
       if (endHtmlPos == string::npos) {
         m_tokenListIt = m_tokenList.end();
         printListError(WARN_DOXYGEN_COMMAND_ERROR,
-                       "HTML tag without '>' found! Tag: " + cmd);
+            "HTML tag without '>' found! Tag: " + cmd);
       }
 
       // add args of HTML command, like link URL, image URL, ...
-      m_tokenList.push_back(Token(PLAINSTRING, line.substr(pos, endHtmlPos - pos)));
+      m_tokenList.push_back(
+          Token(PLAINSTRING, line.substr(pos, endHtmlPos - pos)));
       pos = endHtmlPos;
     } else {
       if (isEndHtmlTag) {
@@ -1144,7 +1178,7 @@ void DoxygenParser::processHtmlTags(size_t &pos, const std::string &line)
     }
 
     if (pos != string::npos) {
-        pos++; // skip '>'
+      pos++; // skip '>'
     }
   } else {
     // the command is not HTML supported by Doxygen, < and > will be
@@ -1154,15 +1188,14 @@ void DoxygenParser::processHtmlTags(size_t &pos, const std::string &line)
   }
 }
 
-
 void DoxygenParser::processHtmlEntities(size_t &pos, const std::string &line)
 {
-  size_t endOfWordPos = line.find_first_not_of("abcdefghijklmnopqrstuvwxyz", pos + 1);
+  size_t endOfWordPos = line.find_first_not_of("abcdefghijklmnopqrstuvwxyz",
+      pos + 1);
 
   if (endOfWordPos != string::npos) {
 
-    if (line[endOfWordPos] == ';'  &&  (endOfWordPos - pos) > 1)
-    {
+    if (line[endOfWordPos] == ';' && (endOfWordPos - pos) > 1) {
       // if entity is not recognized by Doxygen (not in the list of
       // commands) nothing is added (here and in Doxygen).
       addDoxyCommand(m_tokenList, line.substr(pos, endOfWordPos - pos));
@@ -1172,14 +1205,13 @@ void DoxygenParser::processHtmlEntities(size_t &pos, const std::string &line)
 
       // it is not an entity - add entity for ampersand and the rest of string
       addDoxyCommand(m_tokenList, "&amp");
-      m_tokenList.push_back(Token(PLAINSTRING,
-                                   line.substr(pos + 1, endOfWordPos - pos - 1)));
+      m_tokenList.push_back(
+          Token(PLAINSTRING, line.substr(pos + 1, endOfWordPos - pos - 1)));
     }
   }
   pos = endOfWordPos;
 }
 
-
 /*
  * This method processes normal comment, which has to be tokenized.
  */
@@ -1199,10 +1231,11 @@ size_t DoxygenParser::processNormalComment(size_t pos, const std::string &line)
   case '\t': {
     // whitespaces are stored as plain strings
     size_t startOfNextWordPos = line.find_first_not_of(" \t", pos + 1);
-    m_tokenList.push_back(Token(PLAINSTRING,
-        line.substr(pos, startOfNextWordPos - pos)));
+    m_tokenList.push_back(
+        Token(PLAINSTRING, line.substr(pos, startOfNextWordPos - pos)));
     pos = startOfNextWordPos;
-  } break;
+  }
+    break;
 
   case '<':
     processHtmlTags(pos, line);
@@ -1221,20 +1254,20 @@ size_t DoxygenParser::processNormalComment(size_t pos, const std::string &line)
     break;
   default:
     m_tokenListIt = m_tokenList.end();
-    printListError(WARN_DOXYGEN_COMMAND_ERROR, "Unknown special character: " + line[pos]);
+    printListError(WARN_DOXYGEN_COMMAND_ERROR,
+        "Unknown special character: " + line[pos]);
   }
 
   return pos;
 }
 
-
 /*
  * This is the main method, which tokenizes Doxygen comment to words and
  * doxygen commands.
  */
 void DoxygenParser::tokenizeDoxygenComment(const std::string &doxygenComment,
-                                                 const std::string &fileName,
-                                                 int fileLine)
+                                           const std::string &fileName,
+                                           int fileLine)
 {
   m_isVerbatimText = false;
   m_isInQuotedString = false;
@@ -1247,8 +1280,10 @@ void DoxygenParser::tokenizeDoxygenComment(const std::string &doxygenComment,
   // remove trailing spaces, because they cause additional new line at the end
   // comment, which is wrong, because these spaces are space preceding
   // end of comment :  '  */'
-  if (!doxygenComment.empty()  &&  doxygenComment[doxygenComment.size() - 1] == ' ') {
+  if (!doxygenComment.empty() && doxygenComment[doxygenComment.size() - 1] == ' ') {
+
     string lastLine = lines[lines.size() - 1];
+
     if (trim(lastLine).empty()) {
       lines.pop_back(); // remove trailing empy line
     }
@@ -1265,7 +1300,7 @@ void DoxygenParser::tokenizeDoxygenComment(const std::string &doxygenComment,
 
     // skip sequences of '*', '/', and '!' of any length
     bool isStartOfCommentLineCharFound = false;
-    while (pos < line.size()  &&  isStartOfDoxyCommentChar(line[pos])) {
+    while (pos < line.size() && isStartOfDoxyCommentChar(line[pos])) {
       pos++;
       isStartOfCommentLineCharFound = true;
     }
@@ -1278,7 +1313,7 @@ void DoxygenParser::tokenizeDoxygenComment(const std::string &doxygenComment,
     // if 'isStartOfCommentLineCharFound' then preserve leading spaces, so
     // ' *    comment' gets translated to ' *    comment', not ' * comment'
     // This is important to keep formatting for comments translated to Python.
-    if (isStartOfCommentLineCharFound  &&  line[pos] == ' ') {
+    if (isStartOfCommentLineCharFound && line[pos] == ' ') {
       pos++; // points to char after ' * '
       if (pos == line.size()) {
         m_tokenList.push_back(Token(END_LINE, "\n"));
@@ -1295,8 +1330,9 @@ void DoxygenParser::tokenizeDoxygenComment(const std::string &doxygenComment,
       continue;
     }
 
-    if (isStartOfCommentLineCharFound  &&  firstWordPos > pos) {
-      m_tokenList.push_back(Token(PLAINSTRING, line.substr(pos, firstWordPos - pos)));
+    if (isStartOfCommentLineCharFound && firstWordPos > pos) {
+      m_tokenList.push_back(
+          Token(PLAINSTRING, line.substr(pos, firstWordPos - pos)));
     }
 
     pos = firstWordPos;
@@ -1317,7 +1353,8 @@ void DoxygenParser::tokenizeDoxygenComment(const std::string &doxygenComment,
         string punctuations(".,:");
         size_t textSize = text.size();
 
-        if (!text.empty()  &&  punctuations.find(text[text.size() - 1]) != string::npos  &&
+        if (!text.empty()
+            && punctuations.find(text[text.size() - 1]) != string::npos &&
             // but do not break ellipsis (...)
             !(textSize > 1 && text[textSize - 2] == '.')) {
           m_tokenList.push_back(Token(PLAINSTRING, text.substr(0, text.size() - 1)));
@@ -1328,10 +1365,8 @@ void DoxygenParser::tokenizeDoxygenComment(const std::string &doxygenComment,
       }
 
       pos = doxyCmdOrHtmlTagPos;
-      if (pos != string::npos)
-      {
-        if (m_isVerbatimText)
-        {
+      if (pos != string::npos) {
+        if (m_isVerbatimText) {
           pos = processVerbatimText(pos, line);
 
         } else if (m_isInQuotedString) {
@@ -1339,8 +1374,7 @@ void DoxygenParser::tokenizeDoxygenComment(const std::string &doxygenComment,
           if (line[pos] == '"') {
             m_isInQuotedString = false;
           }
-          m_tokenList.push_back(Token(PLAINSTRING,
-                                     line.substr(pos, 1)));
+          m_tokenList.push_back(Token(PLAINSTRING, line.substr(pos, 1)));
           pos++;
 
         } else {
@@ -1354,12 +1388,12 @@ void DoxygenParser::tokenizeDoxygenComment(const std::string &doxygenComment,
   m_tokenListIt = m_tokenList.begin();
 }
 
-
-void DoxygenParser::printList() {
+void DoxygenParser::printList()
+{
 
   int tokNo = 0;
   for (TokenListCIt it = m_tokenList.begin(); it != m_tokenList.end();
-                                                              it++, tokNo++) {
+      it++, tokNo++) {
 
     cout << it->toString() << " ";
 
@@ -1369,9 +1403,8 @@ void DoxygenParser::printList() {
   }
 }
 
-
-void DoxygenParser::printListError(int warningType,
-                                        const std::string &message) {
+void DoxygenParser::printListError(int warningType, const std::string &message)
+{
   int curLine = m_fileLineNo;
   for (TokenListCIt it = m_tokenList.begin(); it != m_tokenListIt; it++) {
     if (it->m_tokenType == END_LINE) {
@@ -1380,5 +1413,5 @@ void DoxygenParser::printListError(int warningType,
   }
 
   Swig_warning(warningType, m_fileName.c_str(), curLine,
-                 "Doxygen parser warning: %s. \n", message.c_str());
+      "Doxygen parser warning: %s. \n", message.c_str());
 }

From 4e2c1e3ac36b5750c1bc84ceeb6af146e0987595 Mon Sep 17 00:00:00 2001
From: Marko Klopcic <markok3.14@gmail.com>
Date: Sat, 16 Mar 2013 10:53:48 +0100
Subject: [PATCH 187/314] added handling for tag ref in Java

---
 .../test-suite/doxygen_translate_all_tags.i   |  4 ++
 .../doxygen_translate_all_tags_runme.java     | 14 ++++---
 .../DoxygenTranslator/src/DoxygenParser.cpp   | 10 +++--
 .../src/JavaDocConverter.cpp                  | 41 +++++++++++++++++++
 .../DoxygenTranslator/src/JavaDocConverter.h  | 11 +++++
 5 files changed, 71 insertions(+), 9 deletions(-)

diff --git a/Examples/test-suite/doxygen_translate_all_tags.i b/Examples/test-suite/doxygen_translate_all_tags.i
index 0bc50f3a8..9fc25416f 100644
--- a/Examples/test-suite/doxygen_translate_all_tags.i
+++ b/Examples/test-suite/doxygen_translate_all_tags.i
@@ -269,12 +269,16 @@ int func07(int a)
  *
  * \protectedsection
  *
+ * \anchor someAnchor
+ * Text after anchor.
  * \protocol someProtocol header.h "Header name"
  *
  * \public
  *
  * \publicsection
  *
+ * \ref someAnchor Anchor description
+ *
  * \ref someAnchor
  *
  * \related toSomething
diff --git a/Examples/test-suite/java/doxygen_translate_all_tags_runme.java b/Examples/test-suite/java/doxygen_translate_all_tags_runme.java
index 5374d97c4..50c36b6f7 100644
--- a/Examples/test-suite/java/doxygen_translate_all_tags_runme.java
+++ b/Examples/test-suite/java/doxygen_translate_all_tags_runme.java
@@ -111,11 +111,15 @@ public class doxygen_translate_all_tags_runme {
                 " @param a the first param\n");
     
     wantedComments.put("doxygen_translate_all_tags.doxygen_translate_all_tags.func08(int)",
-    		" Remarks: Some remark text \n" +
-    		" Remarks: Another remarks section \n" +
-    		" @return Whatever \n" +
-    		" @return it \n" +
-    		" @return may return \n");
+                       "<a id=\"#someAnchor\"></a>\n" +
+                       "Text after anchor.\n" + 
+                       "<i>Anchor description</i>\n" +
+                       "<i>someAnchor</i>\n" +
+                       " Remarks: Some remark text \n" +
+                       " Remarks: Another remarks section \n" +
+                       " @return Whatever \n" +
+                       " @return it \n" +
+                       " @return may return \n");
     
     wantedComments.put("doxygen_translate_all_tags.doxygen_translate_all_tags.func09(int)",
                        " This will only appear in RTF \n" +
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.cpp b/Source/DoxygenTranslator/src/DoxygenParser.cpp
index 995e0c7ab..08dae5a86 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenParser.cpp
@@ -692,10 +692,12 @@ int DoxygenParser::addCommandUnique(const std::string &theCommand,
           "No key followed " + theCommand + " command. Not added");
       return 0;
     }
-    std::string text = getNextWord();
-    aNewList.push_back(DoxygenEntity("plainstd::string", name));
-    if (!text.empty())
-      aNewList.push_back(DoxygenEntity("plainstd::string", text));
+    DoxygenEntityList aNewList;
+    TokenListCIt endOfLine = getOneLine(tokList);
+    if (endOfLine != m_tokenListIt) {
+      aNewList = parse(endOfLine, tokList);
+    }
+    aNewList.push_front(DoxygenEntity("plainstd::string", name));
     doxyList.push_back(DoxygenEntity(theCommand, aNewList));
   }
   // \subpage <name> ["(text)"]
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.cpp b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
index f14fefafd..f9d27c84c 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
@@ -88,6 +88,7 @@ void JavaDocConverter::fillStaticTables()
   tagHandlers["::"] = make_pair(&JavaDocConverter::handleTagChar, "");
   // these commands are stripped out
   tagHandlers["attention"] = make_pair(&JavaDocConverter::handleParagraph, "");
+  tagHandlers["anchor"] = make_pair(&JavaDocConverter::handleTagAnchor, "");
   tagHandlers["brief"] = make_pair(&JavaDocConverter::handleParagraph, "");
   tagHandlers["bug"] = make_pair(&JavaDocConverter::handleParagraph, "");
   tagHandlers["date"] = make_pair(&JavaDocConverter::handleParagraph, "");
@@ -112,6 +113,7 @@ void JavaDocConverter::fillStaticTables()
   tagHandlers["package"] = make_pair(&JavaDocConverter::handleTagSame, "");
   tagHandlers["param"] = make_pair(&JavaDocConverter::handleTagParam, "");
   tagHandlers["tparam"] = make_pair(&JavaDocConverter::handleTagParam, "");
+  tagHandlers["ref"] = make_pair(&JavaDocConverter::handleTagRef, "");
   tagHandlers["result"] = make_pair(&JavaDocConverter::handleTagSame, "return");
   tagHandlers["return"] = make_pair(&JavaDocConverter::handleTagSame, "");
   tagHandlers["returns"] = make_pair(&JavaDocConverter::handleTagSame,
@@ -402,6 +404,15 @@ void JavaDocConverter::translateEntity(DoxygenEntity &tag,
   }
 }
 
+
+void JavaDocConverter::handleTagAnchor(DoxygenEntity& tag,
+                                       std::string& translatedComment,
+                                       std::string &)
+{
+  translatedComment += "<a id=\"#" + translateSubtree(tag) + "\"></a>";
+}
+
+
 void JavaDocConverter::handleTagHtml(DoxygenEntity& tag,
                                      std::string& translatedComment,
                                      std::string &arg)
@@ -573,6 +584,7 @@ void JavaDocConverter::handleTagPar(DoxygenEntity& tag,
   translatedComment += "</p>";
 }
 
+
 void JavaDocConverter::handleTagParam(DoxygenEntity& tag,
                                       std::string& translatedComment,
                                       std::string&)
@@ -590,6 +602,35 @@ void JavaDocConverter::handleTagParam(DoxygenEntity& tag,
   handleParagraph(tag, translatedComment, dummy);
 }
 
+
+void JavaDocConverter::handleTagRef(DoxygenEntity& tag,
+                                    std::string& translatedComment,
+                                    std::string&)
+{
+  std::string dummy;
+//  translatedComment += "1111";
+  if (!tag.entityList.size())
+    return;
+//  translatedComment += "2222";
+  //if (!paramExists(tag.entityList.begin()->data))
+//    return;
+
+  // we don't translate to link, since \page is not supported in Java, but we
+  // make text in italic, so that reader at least knows what to look at.
+  // translatedComment += "<i>";
+  //  tag.entityList.pop_front();
+  //  translatedComment += translateSubtree(tag);
+  //  translatedComment += "</i>";
+  string anchor = tag.entityList.begin()->data;
+  tag.entityList.pop_front();
+  string anchorText = translateSubtree(tag);
+  if (anchorText.find_first_not_of(" \t") == string::npos) {
+    anchorText = anchor;
+  }
+  translatedComment += "<a href=\"#" + anchor + "\">" + anchorText + "</a>";
+}
+
+
 string JavaDocConverter::convertLink(string linkObject)
 {
   if (GetFlag(currentNode, "feature:doxygen:nolinktranslate"))
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.h b/Source/DoxygenTranslator/src/JavaDocConverter.h
index abb6f2233..b0355e9c2 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.h
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.h
@@ -61,6 +61,11 @@ protected:
    */
   void handleTagVerbatim(DoxygenEntity& tag, std::string& translatedComment, std::string &arg);
 
+  /** Creates anchor link. */
+  void handleTagAnchor(DoxygenEntity& tag,
+                       std::string& translatedComment,
+                       std::string &arg);
+
   /*
    * Wrap the command data with the html tag
    * arg - html tag, with no braces
@@ -125,6 +130,12 @@ protected:
    * Insert \@param command, if it is really a function param
    */
   void handleTagParam(DoxygenEntity &tag, std::string &translatedComment, std::string &arg);
+  /*
+   * Writes text of \ref tag in italic. Does not produce link, because javadoc
+   * does not support page and section tags.
+   */
+  void handleTagRef(DoxygenEntity& tag, std::string& translatedComment,
+                    std::string&);
   /*
    * Insert {@link...} command, and handle all the <link-object>s correctly
    * (like converting types of params, etc)

From 4663fce63cc9a4a0222f80304f7acc15ed695c30 Mon Sep 17 00:00:00 2001
From: Marko Klopcic <markok3.14@gmail.com>
Date: Sun, 17 Mar 2013 20:09:34 +0100
Subject: [PATCH 188/314] fixed bug in handling of ref tag in Java, added
 handling in Python

---
 .../test-suite/doxygen_translate_all_tags.i   |  4 ++-
 .../doxygen_translate_all_tags_runme.java     |  7 +++--
 .../doxygen_translate_all_tags_runme.py       |  6 ++++
 .../DoxygenTranslator/src/DoxygenParser.cpp   | 20 +++++++++---
 .../src/JavaDocConverter.cpp                  | 31 ++++++++++---------
 .../DoxygenTranslator/src/JavaDocConverter.h  |  3 +-
 .../DoxygenTranslator/src/PyDocConverter.cpp  | 20 ++++++++++++
 Source/DoxygenTranslator/src/PyDocConverter.h |  6 +++-
 8 files changed, 71 insertions(+), 26 deletions(-)

diff --git a/Examples/test-suite/doxygen_translate_all_tags.i b/Examples/test-suite/doxygen_translate_all_tags.i
index 9fc25416f..d1319840f 100644
--- a/Examples/test-suite/doxygen_translate_all_tags.i
+++ b/Examples/test-suite/doxygen_translate_all_tags.i
@@ -277,7 +277,9 @@ int func07(int a)
  *
  * \publicsection
  *
- * \ref someAnchor Anchor description
+ * \ref someAnchor "Anchor description"
+ *
+ * \ref someAnchor not quoted text is not part of ref tag
  *
  * \ref someAnchor
  *
diff --git a/Examples/test-suite/java/doxygen_translate_all_tags_runme.java b/Examples/test-suite/java/doxygen_translate_all_tags_runme.java
index 50c36b6f7..da05d51f6 100644
--- a/Examples/test-suite/java/doxygen_translate_all_tags_runme.java
+++ b/Examples/test-suite/java/doxygen_translate_all_tags_runme.java
@@ -111,10 +111,11 @@ public class doxygen_translate_all_tags_runme {
                 " @param a the first param\n");
     
     wantedComments.put("doxygen_translate_all_tags.doxygen_translate_all_tags.func08(int)",
-                       "<a id=\"#someAnchor\"></a>\n" +
+                       "<a id=\"someAnchor\"></a>\n" +
                        "Text after anchor.\n" + 
-                       "<i>Anchor description</i>\n" +
-                       "<i>someAnchor</i>\n" +
+                       "<a href="someAnchor">Anchor description</a>\n" +
+                       "<a href="someAnchor">someAnchor</a>\n" +
+                       "<a href="someAnchor">someAnchor</a>\n" +
                        " Remarks: Some remark text \n" +
                        " Remarks: Another remarks section \n" +
                        " @return Whatever \n" +
diff --git a/Examples/test-suite/python/doxygen_translate_all_tags_runme.py b/Examples/test-suite/python/doxygen_translate_all_tags_runme.py
index 051a9a51e..65c74b2ba 100755
--- a/Examples/test-suite/python/doxygen_translate_all_tags_runme.py
+++ b/Examples/test-suite/python/doxygen_translate_all_tags_runme.py
@@ -230,6 +230,12 @@ r"""
 
 commentVerifier.check(doxygen_translate_all_tags.func08.__doc__,
 r"""
+  Text after anchor.
+
+  'Anchor description'
+  'someAnchor'
+  'someAnchor'
+
   Remarks: Some remark text
 
   Another remarks section
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.cpp b/Source/DoxygenTranslator/src/DoxygenParser.cpp
index 08dae5a86..57a0c5bd0 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenParser.cpp
@@ -693,11 +693,23 @@ int DoxygenParser::addCommandUnique(const std::string &theCommand,
       return 0;
     }
     DoxygenEntityList aNewList;
-    TokenListCIt endOfLine = getOneLine(tokList);
-    if (endOfLine != m_tokenListIt) {
-      aNewList = parse(endOfLine, tokList);
-    }
     aNewList.push_front(DoxygenEntity("plainstd::string", name));
+    // TokenListCIt endOfLine = getOneLine(tokList);
+    // if (endOfLine != m_tokenListIt) {
+    //   aNewList = parse(endOfLine, tokList);
+    //}
+    TokenListCIt tmpIt = m_tokenListIt;
+    std::string refTitle = getNextWord();
+    // If title is following the ref tag, it must be quoted. Otherwise
+    // doxy puts link on ref id.
+    if (refTitle.size() > 1  &&  refTitle[0] == '"') {
+        // remove quotes
+        refTitle = refTitle.substr(1, refTitle.size() - 2);
+        aNewList.push_back(DoxygenEntity("plainstd::string", refTitle));
+    } else {
+        // no quoted string is following, so we have to restore iterator
+        m_tokenListIt = tmpIt;
+    }
     doxyList.push_back(DoxygenEntity(theCommand, aNewList));
   }
   // \subpage <name> ["(text)"]
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.cpp b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
index f9d27c84c..b0a18b991 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
@@ -409,7 +409,7 @@ void JavaDocConverter::handleTagAnchor(DoxygenEntity& tag,
                                        std::string& translatedComment,
                                        std::string &)
 {
-  translatedComment += "<a id=\"#" + translateSubtree(tag) + "\"></a>";
+  translatedComment += "<a id=\"" + translateSubtree(tag) + "\"></a>";
 }
 
 
@@ -455,7 +455,15 @@ void JavaDocConverter::handleNewLine(DoxygenEntity&,
                                      std::string& translatedComment,
                                      std::string&)
 {
-  translatedComment += "\n * ";
+  // <br> tag is added, because otherwise to much text is joined
+  // into same paragraph by javadoc. For example, doxy list:
+  // - item one
+  // - item two
+  // becomes one paragraph with surrounding text without newlines.
+  // This way we get to many empty lines in javadoc output, but this
+  // is still better than joined lines. Possibility for improvements
+  // exists.
+  translatedComment += "<br>\n * ";
 }
 
 void JavaDocConverter::handleTagChar(DoxygenEntity& tag,
@@ -608,24 +616,17 @@ void JavaDocConverter::handleTagRef(DoxygenEntity& tag,
                                     std::string&)
 {
   std::string dummy;
-//  translatedComment += "1111";
   if (!tag.entityList.size())
     return;
-//  translatedComment += "2222";
-  //if (!paramExists(tag.entityList.begin()->data))
-//    return;
 
-  // we don't translate to link, since \page is not supported in Java, but we
-  // make text in italic, so that reader at least knows what to look at.
-  // translatedComment += "<i>";
-  //  tag.entityList.pop_front();
-  //  translatedComment += translateSubtree(tag);
-  //  translatedComment += "</i>";
+  // we translate to link, although \page is not supported in Java, but 
+  // reader at least knows what to look at. Also for \anchor tag on the same
+  // page this link works.
   string anchor = tag.entityList.begin()->data;
   tag.entityList.pop_front();
-  string anchorText = translateSubtree(tag);
-  if (anchorText.find_first_not_of(" \t") == string::npos) {
-    anchorText = anchor;
+  string anchorText = anchor;
+  if (!tag.entityList.empty()) {
+    anchorText = tag.entityList.begin()->data;
   }
   translatedComment += "<a href=\"#" + anchor + "\">" + anchorText + "</a>";
 }
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.h b/Source/DoxygenTranslator/src/JavaDocConverter.h
index b0355e9c2..78bf6bb88 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.h
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.h
@@ -131,8 +131,7 @@ protected:
    */
   void handleTagParam(DoxygenEntity &tag, std::string &translatedComment, std::string &arg);
   /*
-   * Writes text of \ref tag in italic. Does not produce link, because javadoc
-   * does not support page and section tags.
+   * Writes link for \ref tag. 
    */
   void handleTagRef(DoxygenEntity& tag, std::string& translatedComment,
                     std::string&);
diff --git a/Source/DoxygenTranslator/src/PyDocConverter.cpp b/Source/DoxygenTranslator/src/PyDocConverter.cpp
index 4346fb99c..5a1bbbc6f 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/PyDocConverter.cpp
@@ -134,6 +134,7 @@ void PyDocConverter::fillStaticTables()
   tagHandlers["par"] = make_pair(&PyDocConverter::handleTagPar, "");
   tagHandlers["param"] = make_pair(&PyDocConverter::handleTagParam, "");
   tagHandlers["tparam"] = make_pair(&PyDocConverter::handleTagParam, "");
+  tagHandlers["ref"] = make_pair(&PyDocConverter::handleTagRef, "");
   // this command just prints it's contents
   // (it is internal command of swig's parser, contains plain text)
   tagHandlers["plainstd::string"] = make_pair(
@@ -416,6 +417,25 @@ void PyDocConverter::handleTagParam(DoxygenEntity& tag,
   handleParagraph(tag, translatedComment, dummy);
 }
 
+
+void PyDocConverter::handleTagRef(DoxygenEntity& tag,
+                                  std::string& translatedComment,
+                                  std::string&)
+{
+  std::string dummy;
+  if (!tag.entityList.size())
+    return;
+
+  string anchor = tag.entityList.begin()->data;
+  tag.entityList.pop_front();
+  string anchorText = anchor;
+  if (!tag.entityList.empty()) {
+    anchorText = tag.entityList.begin()->data;
+  }
+  translatedComment += "'" + anchorText + "'";
+}
+
+
 void PyDocConverter::handleTagWrap(DoxygenEntity& tag,
                                    std::string& translatedComment,
                                    std::string &arg)
diff --git a/Source/DoxygenTranslator/src/PyDocConverter.h b/Source/DoxygenTranslator/src/PyDocConverter.h
index ec831a1a2..e0ac9cbc0 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.h
+++ b/Source/DoxygenTranslator/src/PyDocConverter.h
@@ -108,7 +108,11 @@ protected:
    * Format nice param description with type information
    */
   void handleTagParam(DoxygenEntity &tag, std::string &translatedComment, std::string &arg);
-
+  /*
+   * Writes text for \ref tag. 
+   */
+  void handleTagRef(DoxygenEntity& tag, std::string& translatedComment, std::string&);
+    
   /* Handles HTML tags recognized by Doxygen, like <A ...>, <ul>, <table>, ... */
 
   void handleDoxyHtmlTag(DoxygenEntity& tag, std::string& translatedComment, std::string &arg);

From 02d0acfbb3625875bc8a4bd5c2ac3ed1e8459c5f Mon Sep 17 00:00:00 2001
From: Marko Klopcic <markok3.14@gmail.com>
Date: Sun, 17 Mar 2013 21:42:22 +0100
Subject: [PATCH 189/314] doxygen translation tests updated for tags 'anchor'
 and 'ref'

---
 Examples/test-suite/java/CommentParser.java     | 10 +++++++++-
 .../java/doxygen_translate_all_tags_runme.java  |  9 +++++----
 .../python/doxygen_translate_all_tags_runme.py  | 17 ++++++++++++++++-
 3 files changed, 30 insertions(+), 6 deletions(-)

diff --git a/Examples/test-suite/java/CommentParser.java b/Examples/test-suite/java/CommentParser.java
index 1d61f16b1..c8adc1d1e 100644
--- a/Examples/test-suite/java/CommentParser.java
+++ b/Examples/test-suite/java/CommentParser.java
@@ -56,10 +56,18 @@ public class CommentParser {
             actualStr = actualStr.replace(" ", "");
             actualStr = actualStr.replaceAll("\t", "");
             actualStr = actualStr.replace("\n", "");
+            
+            // Removing of <br> is temporary solution, since adding of
+            // <br> tag requires changes in all tests. However, <br>
+            // tag should be added more selectively and when this is
+            // implemented, tests should be updated.
+            actualStr = actualStr.replace("<br>", "");
+            
             if (wantedStr != null) {
                 wantedStr = wantedStr.replace(" ", "");
                 wantedStr = wantedStr.replace("\t", "");
                 wantedStr = wantedStr.replace("\n", "");
+                wantedStr = wantedStr.replace("<br>", "");
             }
             /* The following lines replace multiple whitespaces with a single one.
                Although this would be more exact testing, it would also require
@@ -92,7 +100,7 @@ public class CommentParser {
 
                     // write translated string to file
                     BufferedWriter gotFile = new BufferedWriter(new OutputStreamWriter(new FileOutputStream(gotFileName)));
-                    gotFile.write(e.getValue());
+                    gotFile.write(e.getValue().replace("<br>", ""));
                     gotFile.close();
                 } catch (IOException ex) {
                     System.out.println("Error when writing output to file: " + ex);
diff --git a/Examples/test-suite/java/doxygen_translate_all_tags_runme.java b/Examples/test-suite/java/doxygen_translate_all_tags_runme.java
index da05d51f6..8bd65224f 100644
--- a/Examples/test-suite/java/doxygen_translate_all_tags_runme.java
+++ b/Examples/test-suite/java/doxygen_translate_all_tags_runme.java
@@ -27,7 +27,8 @@ public class doxygen_translate_all_tags_runme {
     HashMap<String, String> wantedComments = new HashMap<String, String>();
     
     wantedComments.put("doxygen_translate_all_tags.doxygen_translate_all_tags.func01(int)",
-    		" <i>Hello </i>\n\n\n\n\n\n" +
+    		" <i>Hello </i>\n\n\n" +
+                " <a id=\"theAnchor\"></a>\n\n\n" +
     		" <li>some list item</li>\n\n" +
     		" This is attention!\n" +
     		" You were warned!\n" +
@@ -113,9 +114,9 @@ public class doxygen_translate_all_tags_runme {
     wantedComments.put("doxygen_translate_all_tags.doxygen_translate_all_tags.func08(int)",
                        "<a id=\"someAnchor\"></a>\n" +
                        "Text after anchor.\n" + 
-                       "<a href="someAnchor">Anchor description</a>\n" +
-                       "<a href="someAnchor">someAnchor</a>\n" +
-                       "<a href="someAnchor">someAnchor</a>\n" +
+                       "<a href=\"#someAnchor\">Anchor description</a>\n" +
+                       "<a href=\"#someAnchor\">someAnchor</a> not quoted text is not part of ref tag\n" +
+                       "<a href=\"#someAnchor\">someAnchor</a>\n" +
                        " Remarks: Some remark text \n" +
                        " Remarks: Another remarks section \n" +
                        " @return Whatever \n" +
diff --git a/Examples/test-suite/python/doxygen_translate_all_tags_runme.py b/Examples/test-suite/python/doxygen_translate_all_tags_runme.py
index 65c74b2ba..053ebc7ec 100755
--- a/Examples/test-suite/python/doxygen_translate_all_tags_runme.py
+++ b/Examples/test-suite/python/doxygen_translate_all_tags_runme.py
@@ -232,9 +232,24 @@ commentVerifier.check(doxygen_translate_all_tags.func08.__doc__,
 r"""
   Text after anchor.
 
+
+
+
+
+
   'Anchor description'
+
+  'someAnchor' not quoted text is not part of ref tag
+
   'someAnchor'
-  'someAnchor'
+
+
+
+
+
+
+
+
 
   Remarks: Some remark text
 

From 9549a960b8049d59c18934516ea7a4c9ef8a0874 Mon Sep 17 00:00:00 2001
From: William S Fulton <wsf@fultondesigns.co.uk>
Date: Sat, 16 Mar 2013 17:43:08 +0000
Subject: [PATCH 190/314] First attempt at Travis Continuous integration builds

---
 .travis.yml | 5 +++++
 1 file changed, 5 insertions(+)
 create mode 100644 .travis.yml

diff --git a/.travis.yml b/.travis.yml
new file mode 100644
index 000000000..ecd39ab85
--- /dev/null
+++ b/.travis.yml
@@ -0,0 +1,5 @@
+language: cpp
+compiler:
+  - gcc
+  - clang
+script: ./autogen.sh && ./configure && make

From d8e7b09323b304235ad34b9d117406ea99fb7f7a Mon Sep 17 00:00:00 2001
From: William S Fulton <wsf@fultondesigns.co.uk>
Date: Sun, 17 Mar 2013 19:44:28 +0000
Subject: [PATCH 191/314] Travis CI only on master and silent builds

---
 .travis.yml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index ecd39ab85..c41027bc0 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -2,4 +2,7 @@ language: cpp
 compiler:
   - gcc
   - clang
-script: ./autogen.sh && ./configure && make
+script: ./autogen.sh && ./configure && make -s
+branches:
+  only:
+    - master

From b2c5c70f1b7bd3cd4626ba045fdf2ac37278b267 Mon Sep 17 00:00:00 2001
From: Yann Diorcet <yann.diorcet@belledonne-communications.com>
Date: Mon, 22 Apr 2013 14:22:35 +0200
Subject: [PATCH 192/314] Fix link additional text in doxygen

---
 Source/DoxygenTranslator/src/JavaDocConverter.cpp | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.cpp b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
index b0a18b991..7f12af96d 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
@@ -646,6 +646,7 @@ string JavaDocConverter::convertLink(string linkObject)
   string paramsStr = linkObject.substr(lbracePos + 1,
       rbracePos - lbracePos - 1);
   // strip the params, to fill them later
+  string additionalObject = linkObject.substr(rbracePos + 1, string::npos);
   linkObject = linkObject.substr(0, lbracePos);
 
   // find all the params
@@ -720,7 +721,7 @@ string JavaDocConverter::convertLink(string linkObject)
   }
   linkObject += ")";
 
-  return linkObject;
+  return linkObject + additionalObject;
 }
 
 void JavaDocConverter::handleTagLink(DoxygenEntity& tag,

From 1bf26f216d5333ff29a083bed3ce95b57cc201f0 Mon Sep 17 00:00:00 2001
From: Marko Klopcic <markok3.14@gmail.com>
Date: Mon, 22 Apr 2013 23:08:50 +0200
Subject: [PATCH 193/314] tests updated according to fix for the link tag'

---
 Examples/test-suite/doxygen_parsing.i               | 4 +++-
 Examples/test-suite/java/doxygen_parsing_runme.java | 5 +++--
 Examples/test-suite/python/doxygen_parsing_runme.py | 4 +++-
 3 files changed, 9 insertions(+), 4 deletions(-)

diff --git a/Examples/test-suite/doxygen_parsing.i b/Examples/test-suite/doxygen_parsing.i
index b4579c886..d94c60222 100644
--- a/Examples/test-suite/doxygen_parsing.i
+++ b/Examples/test-suite/doxygen_parsing.i
@@ -51,7 +51,9 @@ public:
 									//!< with details
 
 	/**
-	 * The class method comment
+	 * The class method comment.
+         *
+         * \link SomeAnotherClass#classMethodExtended(int, int) a link text \endlink
 	 */
 	void classMethod()
 	{
diff --git a/Examples/test-suite/java/doxygen_parsing_runme.java b/Examples/test-suite/java/doxygen_parsing_runme.java
index ec9390849..7a8b0fae9 100644
--- a/Examples/test-suite/java/doxygen_parsing_runme.java
+++ b/Examples/test-suite/java/doxygen_parsing_runme.java
@@ -111,8 +111,9 @@ public class doxygen_parsing_runme {
     		"The class attribute post-comment with details \n" +
     		"");
     wantedComments.put("doxygen_parsing.SomeAnotherClass.classMethod()",
-    		" The class method comment \n" +
-    		" \n" +
+    		" The class method comment.<br>\n" +
+                " <br>\n" +
+                " {@link SomeAnotherClass#classMethodExtended(int,int) a link text  }\n" +
     		"");
     wantedComments.put("doxygen_parsing.SomeAnotherStruct.structMethodExtended2(int, int)",
     		" The struct method with parameter \n" +
diff --git a/Examples/test-suite/python/doxygen_parsing_runme.py b/Examples/test-suite/python/doxygen_parsing_runme.py
index ccf03797c..1ad95ff75 100755
--- a/Examples/test-suite/python/doxygen_parsing_runme.py
+++ b/Examples/test-suite/python/doxygen_parsing_runme.py
@@ -19,7 +19,9 @@ r"""
     """)
 commentVerifier.check(doxygen_parsing.SomeAnotherClass.classMethod.__doc__,
 r"""
-        The class method comment
+        The class method comment.
+
+        SomeAnotherClass#classMethodExtended(int, int) a link text 
         """)
 commentVerifier.check(doxygen_parsing.SomeAnotherClass.classMethodExtended.__doc__,
 r"""

From a1c539ed26f5fa4b86feff6a037be982c3a0af2f Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Wed, 7 May 2014 18:32:28 +0200
Subject: [PATCH 194/314] Avoid crash in the parser for two consecutive Doxygen
 comments.

This change fixes the crash which happened when parsing the following code:

	/// Description of the section.
	//@{
	...
	//@}

As the second Doxygen item didn't have any associated text in this case.
---
 Source/CParse/parser.y | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/Source/CParse/parser.y b/Source/CParse/parser.y
index bf77b952e..b5791a49e 100644
--- a/Source/CParse/parser.y
+++ b/Source/CParse/parser.y
@@ -3546,10 +3546,13 @@ doxygen_comment_item : DOXYGENSTRING {
 		  $$ = $1;
 		}
 		| doxygen_comment_item doxygen_comment_item {
-		  if ($1)
-		    Append($1, $2);
-		  else
+		  if ($1) {
+		    if ($2)
+		      Append($1, $2);
+		  }
+		  else {
 		    $1 = $2;
+		  }
 		  $$ = $1;
 		}
 		;

From 46a375a135be131caea706a1b4e2d305df27f62b Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Wed, 7 May 2014 18:43:01 +0200
Subject: [PATCH 195/314] Avoid unnecessary compilation dependency on
 DoxygenTranslator.h.

Use forward declaration instead of including this header in the common header
used by all languages (and not just the two of them that actually use
DoxygenTranslator currently).
---
 Source/Modules/swigmod.h | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/Source/Modules/swigmod.h b/Source/Modules/swigmod.h
index 8f39ad1c2..2922a6057 100644
--- a/Source/Modules/swigmod.h
+++ b/Source/Modules/swigmod.h
@@ -17,7 +17,6 @@
 #include "swig.h"
 #include "preprocessor.h"
 #include "swigwarn.h"
-#include "../DoxygenTranslator/src/DoxygenTranslator.h"
 
 #if !defined(HAVE_BOOL)
 typedef int bool;
@@ -345,8 +344,9 @@ protected:
   /* Director language module */
   int director_language;
 
-  // Class instance to translate comments
-  DoxygenTranslator *doxygenTranslator;
+  /* Used to translate Doxygen comments to target documentation format */
+  class DoxygenTranslator *doxygenTranslator;
+
 private:
   Hash *symtabs; /* symbol tables */
   Hash *classtypes;

From ed40190fe1755ff83b17689cba0a92408af465bb Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Wed, 7 May 2014 18:43:50 +0200
Subject: [PATCH 196/314] Remove unused and apparently unnecessary file.

This is probably another Eclipse (?) leftover.
---
 Source/DoxygenTranslator/src/.dirstamp | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 delete mode 100644 Source/DoxygenTranslator/src/.dirstamp

diff --git a/Source/DoxygenTranslator/src/.dirstamp b/Source/DoxygenTranslator/src/.dirstamp
deleted file mode 100644
index e69de29bb..000000000

From 984d5fa299a9cf992f9499065751789b6727e94b Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Wed, 7 May 2014 18:46:30 +0200
Subject: [PATCH 197/314] Initialize doxygenTranslator pointer to NULL when it
 is unused.

No real changes, but avoid having pointer with junk contents, even if it's
unused.

This also avoid the need for checking whether it's used before deleting it.
---
 Source/Modules/java.cxx | 3 +--
 Source/Modules/lang.cxx | 2 ++
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/Source/Modules/java.cxx b/Source/Modules/java.cxx
index be045b9fb..18e6cb71c 100644
--- a/Source/Modules/java.cxx
+++ b/Source/Modules/java.cxx
@@ -171,8 +171,7 @@ public:
   }
   
   ~JAVA() {
-    if (doxygen)
-      delete doxygenTranslator;
+    delete doxygenTranslator;
   }
 
   /* -----------------------------------------------------------------------------
diff --git a/Source/Modules/lang.cxx b/Source/Modules/lang.cxx
index 0afdafe77..824018c4a 100644
--- a/Source/Modules/lang.cxx
+++ b/Source/Modules/lang.cxx
@@ -340,6 +340,8 @@ directors(0) {
   director_language = 0;
   assert(!this_);
   this_ = this;
+
+  doxygenTranslator = NULL;
 }
 
 Language::~Language() {

From c6ef433b9b4547d468645d9788da14728de5dd8b Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Wed, 7 May 2014 18:57:14 +0200
Subject: [PATCH 198/314] Don't leak doxygenTranslator in Python module.

Delete the pointer we allocate, just as in Java module.
---
 Source/Modules/python.cxx | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/Source/Modules/python.cxx b/Source/Modules/python.cxx
index 9429b4989..f6af3d84a 100644
--- a/Source/Modules/python.cxx
+++ b/Source/Modules/python.cxx
@@ -259,6 +259,11 @@ public:
     director_multiple_inheritance = 1;
     director_language = 1;
   }
+
+  ~PYTHON() {
+    delete doxygenTranslator;
+  }
+
   /* ------------------------------------------------------------
    * Thread Implementation
    * ------------------------------------------------------------ */

From 5c0ed6c63584f6dd5c756a1ed43199623e7a475c Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Wed, 7 May 2014 19:10:43 +0200
Subject: [PATCH 199/314] No changes, just spelling fixes in Doxygen branch
 changes.

Most are just typos, but also s/JavaDoc/Javadoc/ and s/PythonDoc/Pydoc/ as
this is how they are officially called.
---
 Doc/Manual/Doxygen.html                       | 102 +++++++++---------
 .../DoxygenTranslator/src/DoxygenParser.cpp   |   2 +-
 .../src/JavaDocConverter.cpp                  |  12 +--
 .../DoxygenTranslator/src/PyDocConverter.cpp  |   2 +-
 Source/DoxygenTranslator/src/PyDocConverter.h |  10 +-
 5 files changed, 64 insertions(+), 64 deletions(-)

diff --git a/Doc/Manual/Doxygen.html b/Doc/Manual/Doxygen.html
index d530218a3..9e0b3d813 100644
--- a/Doc/Manual/Doxygen.html
+++ b/Doc/Manual/Doxygen.html
@@ -13,19 +13,19 @@
 <li><a href="#Doxygen_file_preparation">Preparations</a>
 <ul>
 <li><a href="#Doxygen_running_swig">Enabling Doxygen Translation</a>
-<li><a href="#Doxygen_additional_options">Additional Commandline Options</a>
+<li><a href="#Doxygen_additional_options">Additional Command Line Options</a>
 </ul>
-<li><a href="#Doxygen_to_javadoc">Doxygen To JavaDoc</a>
+<li><a href="#Doxygen_to_javadoc">Doxygen To Javadoc</a>
 <ul>
 <li><a href="#Doxygen_basic_example">Basic Example</a>
-<li><a href="#Doxygen_javadoc_tags">JavaDoc Tags</a>
+<li><a href="#Doxygen_javadoc_tags">Javadoc Tags</a>
 <li><a href="#Doxygen_unsupported_tags">Unsupported tags</a>
 <li><a href="#Doxygen_further_details">Further Details</a>
 </ul>
-<li><a href="#Doxygen_to_pydoc">Doxygen To PythonDoc</a>
+<li><a href="#Doxygen_to_pydoc">Doxygen To Pydoc</a>
 <ul>
 <li><a href="#Doxygen_python_basic_example">Basic Example</a>
-<li><a href="#Doxygen_pydoc_tags">PyDoc translator</a>
+<li><a href="#Doxygen_pydoc_tags">Pydoc translator</a>
 <li><a href="#Doxygen_python_unsupported_tags">Unsupported tags</a>
 <li><a href="#Doxygen_python_further_details">Further Details</a>
 </ul>
@@ -45,7 +45,7 @@
 <p>
 This chapter describes SWIG's support for translating Doxygen comments
 found in interface and header files into a target language's normal
-documentation language.  Currently only JavaDoc and PythonDoc is
+documentation language.  Currently only Javadoc and Pydoc is
 supported.
 </p>
 
@@ -59,8 +59,8 @@ Code</A> proposal from Summer 2008.  It adds an extra layer of
 functionality to SWIG, allowing automated translation of <A HREF=
 "http://www.stack.nl/~dimitri/doxygen/">Doxygen</A> formatted comments
 from input files into a documentation language more suited for the
-target language.  Currently this module only translates into JavaDoc
-and PythonDoc for the SWIG Java and Python Modules, but other
+target language.  Currently this module only translates into Javadoc
+and Pydoc for the SWIG Java and Python Modules, but other
 extensions are to be added in time.
 </p>
 
@@ -87,7 +87,7 @@ itself is a deeper tool and can provide you better feedback for
 correcting any syntax errors that may be present.  Please look at
 Doxygen's <A HREF =
 "http://www.stack.nl/~dimitri/doxygen/docblocks.html"> Documenting the
-code</A> for proper specificatons for comment format.  However, SWIG's
+code</A> for proper specifications for comment format.  However, SWIG's
 Doxygen parser will still point you most of errors and warnings found
 in comments (like unterminated strings or missing ending tags).
 </p>
@@ -107,7 +107,7 @@ Documenting the code</A>). Here they are:
 
 <div class="code"><pre>
 /**
- * JavaDoc style comment, multiline
+ * Javadoc style comment, multiline
  */
 /*!
  * QT-style comment, multiline
@@ -192,7 +192,7 @@ enum E_NUMBERS
 
 <p>
 Just remember, if SWIG shows syntax error parsing the file because of
-your comment, try to move it in some other, 'safer' place as desribed
+your comment, try to move it in some other, 'safer' place as described
 above.
 <br>
 Also, currently only the comments directly before or after the nodes
@@ -205,7 +205,7 @@ assigned to anything.
 <p>
 There is a switch '-doxygen' in every module that supports converting
 documentation comments. Some comments in some target languages can be
-manually overriden by specific swig's features,
+manually overridden by specific swig's features,
 like <i>feature:docstring</i> or <i>feature:autodoc</i>, in this cases
 Doxygen comments have lowest priority.
 </p>
@@ -215,18 +215,18 @@ out in parser and all the resources used by comment parser and
 translator are freed.
 </p>
 
-<H3><a name="Doxygen_additional_options"></a>39.2.2 Additional Commandline Options</H3>
+<H3><a name="Doxygen_additional_options"></a>39.2.2 Additional Command Line Options</H3>
 
 
 <p>
-ALSO TO BE ADDED (JavaDoc Autobrief?)
+ALSO TO BE ADDED (Javadoc auto brief?)
 </p>
 
-<H2><a name="Doxygen_to_javadoc"></a>39.3 Doxygen To JavaDoc</H2>
+<H2><a name="Doxygen_to_javadoc"></a>39.3 Doxygen To Javadoc</H2>
 
 
 <p>
-If translation is enabled, JavaDoc formatted comments should be
+If translation is enabled, Javadoc formatted comments should be
 automatically placed in the correct locations in the resulting module
 and proxy files.
 </p>
@@ -321,7 +321,7 @@ code.
 </p>
 
 <p>
-JavaDoc translator will handle most of the tags conversions (see the
+Javadoc translator will handle most of the tags conversions (see the
 table below). It will also automatically translate link-objects
 params, in \see and \link...\endlink commands. For example,
 'someFunction(std::string)' will be converted to
@@ -332,14 +332,14 @@ commands are stripped out, if specified parameter is not present in
 function. Use 'doxygen:nostripparams' to avoid.
 <br>
 If you intend to use resulting proxy files with Doxygen docs
-generator, rather than JavaDoc, you may want to turn off translator
+generator, rather than Javadoc, you may want to turn off translator
 completely (doxygen:notranslate feature).  Then SWIG will just copy
 the comments to the proxy file and reformat them if needed, but all
 the comment content will be left as is.
 </p>
 
 <p>
-JavaDoc translator features summary
+Javadoc translator features summary
 (see <a href="Customization.html#Customization_features">%feature
 directives</a>):
 <br>
@@ -349,7 +349,7 @@ directives</a>):
 <div class="shell"><pre>
 <table>
 <tr>
-<td>doxygen:noranslate</td>
+<td>doxygen:notranslate</td>
 <td>
 Turn off the whole Doxygen translator.
 The Doxygen comment will be attached to the right node,
@@ -358,7 +358,7 @@ but all the commands and text will be left as-is
 </tr>
 
 <tr>
-<td>doxygen:notlinkranslate</td>
+<td>doxygen:nolinkranslate</td>
 <td>Turn off automatic link-objects translation</td>
 </tr>
 
@@ -373,11 +373,11 @@ Doxygen commands if such parameter is not found
 </pre></div>
 
 
-<H3><a name="Doxygen_javadoc_tags"></a>39.3.2 JavaDoc Tags</H3>
+<H3><a name="Doxygen_javadoc_tags"></a>39.3.2 Javadoc Tags</H3>
 
 
 <p>
-Here is the list of all Doxygen tags and the description of how they are translated to JavaDoc
+Here is the list of all Doxygen tags and the description of how they are translated to Javadoc
 <br>
 <b>Doxygen tags:</b>
 </p>
@@ -422,7 +422,7 @@ Here is the list of all Doxygen tags and the description of how they are transla
 </tr>
 <tr>
 <td>\copyright</td>
-<td>replaced with 'Copyrigth:'</td>
+<td>replaced with 'Copyright:'</td>
 </tr>
 <tr>
 <td>\deprecated</td>
@@ -554,7 +554,7 @@ Here is the list of all Doxygen tags and the description of how they are transla
 </tr>
 <tr>
 <td>\throws</td>
-<td>translated to @thtows</td>
+<td>translated to @throws</td>
 </tr>
 <tr>
 <td>\todo</td>
@@ -632,11 +632,11 @@ Here is the list of all Doxygen tags and the description of how they are transla
 
 <p>
 Doxygen has a wealth of tags such as @latexonly that have no
-equivalent in JavaDoc.  As a result several tags that have no
+equivalent in Javadoc.  As a result several tags that have no
 translation (or particular use, such as some linking and section tags)
-are supressed with their content just printed out (if it has any
+are suppressed with their content just printed out (if it has any
 sense, typically text content).  If you are interested in more of the
-specifics of JavaDoc, please
+specifics of Javadoc, please
 visit <A HREF="http://java.sun.com/j2se/javadoc/writingdoccomments/">How
 to Write Doc Comments for the Javadoc Tool.</A>
 <br>
@@ -866,15 +866,15 @@ comment, the whole comment block is ignored:
 TO BE ADDED.
 </p>
 
-<H2><a name="Doxygen_to_pydoc"></a>39.4 Doxygen To PythonDoc</H2>
+<H2><a name="Doxygen_to_pydoc"></a>39.4 Doxygen To Pydoc</H2>
 
 
 <p>
-If translation is enabled, PyDoc formatted comments should be
+If translation is enabled, Pydoc formatted comments should be
 automatically placed in the correct locations in the resulting module
-and proxy files.  The problem is that PyDoc has no tag mechanism like
-Doxygen or JavaDoc, so most of Doxygen commands are translated as
-English plaintext pieces.
+and proxy files.  The problem is that Pydoc has no tag mechanism like
+Doxygen or Javadoc, so most of Doxygen commands are translated as
+English plain text pieces.
 </p>
 
 <H3><a name="Doxygen_python_basic_example"></a>39.4.1 Basic Example</H3>
@@ -949,12 +949,12 @@ file, so they have no comment translated for them.
 </p>
 
 <p>
-  <b>Whitespaces and tables</b><br>
-  Whitespaces are preserved when translating comments, so it makes
+  <b>Whitespace and tables</b><br>
+  Whitespace is preserved when translating comments, so it makes
   sense to have Doxygen comments formatted in a readable way. This
   includes tables, where tags &lt;th&gt;, &lt;td&gt; and &lt;/tr&gt;are translated
   to '|'. The line after line with &lt;th&gt; tags contains dashes.
-  If we take care about whitespaces, comments in Python are much more
+  If we take care about whitespace, comments in Python are much more
   readable. Example:
 
 <div class="code"><pre>
@@ -984,11 +984,11 @@ translates to Python as:
 <p>
   <b>Overloaded functions</b><br>
 Since all the overloaded functions in c++ are wrapped into one Python
-function, PyDoc translator will combine every comment of every
+function, Pydoc translator will combine every comment of every
 overloaded function and put it in the comment for wrapping function.
 <br>
 If you intend to use resulting proxy files with Doxygen docs
-generator, rather than PyDoc, you may want to turn off translator
+generator, rather than Pydoc, you may want to turn off translator
 completely (doxygen:notranslate feature).  Then SWIG will just copy
 the comments to the proxy file and reformat them if needed, but all
 the comment content will be left as is. As Doxygen doesn't support
@@ -1000,7 +1000,7 @@ to do the work.
 </p>
 
 <p>
-PyDoc translator features summary (see <a href="Customization.html#Customization_features">%feature directives</a>):
+Pydoc translator features summary (see <a href="Customization.html#Customization_features">%feature directives</a>):
 <br>
 
 </p>
@@ -1008,7 +1008,7 @@ PyDoc translator features summary (see <a href="Customization.html#Customization
 <div class="shell"><pre>
 <table>
 <tr>
-<td>doxygen:noranslate</td>
+<td>doxygen:notranslate</td>
 <td>
 Turn off the whole Doxygen translator.
 The Doxygen comment will be attached to the right node,
@@ -1018,11 +1018,11 @@ but all the commands and text will be left as-is
 </table>
 </pre></div>
 
-<H3><a name="Doxygen_pydoc_tags"></a>39.4.2 PyDoc translator</H3>
+<H3><a name="Doxygen_pydoc_tags"></a>39.4.2 Pydoc translator</H3>
 
 
 <p>
-Here is the list of all Doxygen tags and the description of how they are translated to PyDoc
+Here is the list of all Doxygen tags and the description of how they are translated to Pydoc
 <br>
 <b>Doxygen tags:</b>
 </p>
@@ -1058,7 +1058,7 @@ Here is the list of all Doxygen tags and the description of how they are transla
 </tr>
 <tr>
 <td>\copyright</td>
-<td>prints'Copyrigth:'</td>
+<td>prints 'Copyright:'</td>
 </tr>
 <tr>
 <td>\deprecated</td>
@@ -1222,7 +1222,7 @@ Here is the list of all Doxygen tags and the description of how they are transla
 </tr>
 <tr>
 <td>\.</td>
-<td>prints . char</td>
+<td>prints . character</td>
 </tr>
 <tr>
 <td>\::</td>
@@ -1236,9 +1236,9 @@ Here is the list of all Doxygen tags and the description of how they are transla
 
 <p>
 Doxygen has a wealth of tags such as @latexonly that have no
-equivalent in PyDoc.  As a result several tags that have no
+equivalent in Pydoc.  As a result several tags that have no
 translation (or particular use, such as some linking and section tags)
-are supressed with their content just printed out (if it has any
+are suppressed with their content just printed out (if it has any
 sense, typically text content).
 <br>
 Here is the list of these tags:
@@ -1449,7 +1449,7 @@ first command, are also present in the parse tree.  These individual
 are passed on individually to the DoxygenTranslator Module.  This
 module builds its own private parse tree and hands it to a separate
 class for translation into the target documentation language.  For
-example, <tt>JavaDocConverter</tt> is the JavaDoc module class.
+example, <tt>JavaDocConverter</tt> is the Javadoc module class.
 </p>
 
 <H3><a name="Doxygen_debugging_commands"></a>39.5.2 Debugging Doxygen parser and translator</H3>
@@ -1483,7 +1483,7 @@ This part of SWIG currently has 6 runtime tests in both Java and Python.
 </pre></div>
 
 <p>
-All this tests are included in common.mk and are build with the
+All this tests are included in common.mk and are built with the
 commands like 'make check-test-suite' or 'make
 check-python-test-suite'. To run them individually, type
 <code>make &lt;testname&gt;.cpptest -s</code> in the language-specific subdir in
@@ -1492,7 +1492,7 @@ check-python-test-suite'. To run them individually, type
   Examples/test-suite/java $ make doxygen_misc_constructs.cpptest -s
 </pre>
 
-If test fails, both expected and translated comments are printed to
+If the test fails, both expected and translated comments are printed to
 std out, but also written to files <i>expected.txt</i>
 and <I>got.txt</I>. Since it is often difficult to find a single
 character difference in several lines of text, we can use some diff
@@ -1504,14 +1504,14 @@ tool, for example:
 
     
 <br>
-Runtime tests in Java are implemented using JavaDoc doclets. To make that work, you
+Runtime tests in Java are implemented using Javadoc doclets. To make that work, you
 should have tools.jar from the JDK in your classpath. Or you should have JAVA_HOME
 environmental var defined and pointing to the JDK location.
 <br>
 The Java's comment parsing code (the testing part) is located in commentParser.java.
 You may see it to understand how the checking process works. There is also a possibility
 to run that file as stand-alone program, with 'java commentParser <some java package>',
-and it will print the list of comments found in the specified dir (in the format it's used
+and it will print the list of comments found in the specified directory (in the format it's used
 in runtime tests). So, when you want to create the new test of Doxygen comment translator,
 just copy any existing one, and replace the actual comment content (section of entries in
 form 'wantedComments.put(...)' with the output of the above command.
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.cpp b/Source/DoxygenTranslator/src/DoxygenParser.cpp
index 57a0c5bd0..22f391b36 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenParser.cpp
@@ -45,7 +45,7 @@ void DoxygenParser::fillTables()
   if (doxygenCommands.size())
     return;
 
-  // fill in tables with data from DxygenCommands.h
+  // fill in tables with data from DoxygenCommands.h
   for (int i = 0; i < simpleCommandsSize; i++)
     doxygenCommands[simpleCommands[i]] = SIMPLECOMMAND;
 
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.cpp b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
index 7f12af96d..b5edcb8a2 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
@@ -50,12 +50,12 @@ void JavaDocConverter::fillStaticTables()
    *     Java src is <x> and therefore invisible on output - browser ignores unknown command.
    *     This is handy in syntax descriptions, for example: more <fileName>.
    *
-   * Standlaone < and > need not be translated, they are rendered properly in
+   * Standalone < and > need not be translated, they are rendered properly in
    *      all three outputs.
    *
    * ., %, and " need not to be translated
    *
-   * entities must be translated - remain in Java, something meaningfull in Python (&lt, ...)
+   * entities must be translated - remain in Java, something meaningful in Python (&lt, ...)
    *
    * - Python
    * - add comments also to auto-generated methods like equals(), delete() in Java,
@@ -419,7 +419,7 @@ void JavaDocConverter::handleTagHtml(DoxygenEntity& tag,
 {
   if (tag.entityList.size()) { // do not include empty tags
     std::string tagData = translateSubtree(tag);
-    // wrap the thing, ignoring whitespaces
+    // wrap the thing, ignoring whitespace
     size_t wsPos = tagData.find_last_not_of("\n\t ");
     if (wsPos != std::string::npos)
       translatedComment += "<" + arg + ">" + tagData.substr(0, wsPos + 1) + "</"
@@ -791,7 +791,7 @@ void JavaDocConverter::handleTagSee(DoxygenEntity& tag,
   translatedComment += linkObject;
 }
 
-/* This function moves all endlines at the end of child entities
+/* This function moves all line endings at the end of child entities
  * out of the child entities to the parent.
  * For example, entity tree:
 
@@ -812,7 +812,7 @@ int JavaDocConverter::shiftEndlinesUpTree(DoxygenEntity &root, int level)
 {
   DoxygenEntityListIt it = root.entityList.begin();
   while (it != root.entityList.end()) {
-    // remove endlines
+    // remove line endings
     int ret = shiftEndlinesUpTree(*it, level + 1);
     // insert them after this element
     it++;
@@ -948,7 +948,7 @@ String *JavaDocConverter::makeDocumentation(Node *node)
 
   shiftEndlinesUpTree(root);
 
-  // strip endlines at the beginning
+  // strip line endings at the beginning
   while (!root.entityList.empty()
       && root.entityList.begin()->typeOfEntity == "plainstd::endl") {
     root.entityList.pop_front();
diff --git a/Source/DoxygenTranslator/src/PyDocConverter.cpp b/Source/DoxygenTranslator/src/PyDocConverter.cpp
index 5a1bbbc6f..5320ce7f9 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/PyDocConverter.cpp
@@ -442,7 +442,7 @@ void PyDocConverter::handleTagWrap(DoxygenEntity& tag,
 {
   if (tag.entityList.size()) { // do not include empty tags
     std::string tagData = translateSubtree(tag);
-    // wrap the thing, ignoring whitespaces
+    // wrap the thing, ignoring whitespace
     size_t wsPos = tagData.find_last_not_of("\n\t ");
     if (wsPos != std::string::npos && wsPos != tagData.size() - 1)
       translatedComment += arg + tagData.substr(0, wsPos + 1) + arg
diff --git a/Source/DoxygenTranslator/src/PyDocConverter.h b/Source/DoxygenTranslator/src/PyDocConverter.h
index e0ac9cbc0..262772e7b 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.h
+++ b/Source/DoxygenTranslator/src/PyDocConverter.h
@@ -36,7 +36,7 @@ protected:
 
   /*
    * Format a string so it is justified and split over several lines 
-   * not exeeding a given length.
+   * not exceeding a given length.
    */
   std::string justifyString(std::string unformattedLine, int indent = 0, int maxWidth = DOC_STRING_LENGTH);
   /*
@@ -46,7 +46,7 @@ protected:
    */
   std::string translateSubtree(DoxygenEntity & doxygenEntity);
   /*
-   * Translate one entity with the appropriate handler, acording
+   * Translate one entity with the appropriate handler, according
    * to the tagHandlers
    */
   void translateEntity(DoxygenEntity & doxyEntity, std::string &translatedComment);
@@ -117,14 +117,14 @@ protected:
 
   void handleDoxyHtmlTag(DoxygenEntity& tag, std::string& translatedComment, std::string &arg);
 
-  /** Does not ouput params of HTML tag, for example in <table border='1'>
+  /** Does not output params of HTML tag, for example in <table border='1'>
    * 'border=1' is not written to output.
    */
   void handleDoxyHtmlTagNoParam(DoxygenEntity& tag,
                                     std::string& translatedComment,
                                     std::string &arg);
 
-  /** TRanslates tag <a href = "url">text</a> to: text ("url"). */
+  /** Translates tag <a href = "url">text</a> to: text ("url"). */
   void handleDoxyHtmlTag_A(DoxygenEntity& tag,
                               std::string& translatedComment,
                               std::string &arg);
@@ -170,7 +170,7 @@ private:
   Node *currentNode;
   // this contains the handler pointer and one string argument
   static std::map<std::string, std::pair<tagHandler, std::string> > tagHandlers;
-  // this cointains the sectins titiles, like 'Arguments:' or 'Notes:', that are printed only once
+  // this contains the sections tittles, like 'Arguments:' or 'Notes:', that are printed only once
   static std::map<std::string, std::string> sectionTitles;
   void fillStaticTables();
 };

From 2e553caf353646a9620b0b61c05f519cb8fe2ea2 Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Wed, 7 May 2014 23:03:31 +0200
Subject: [PATCH 200/314] Fix test suite for languages without Doxygen support.

"-doxygen" can't be used in SWIGOPT for the languages other than Java and
Python, this results in immediate error as it's not supported by SWIG when
using any other language.

Use this switch -- and run the Doxygen tests -- only for the languages that do
support it and, to avoid slowing down the test suite even more, only for the
tests that need it.

Also allow running only the Doxygen tests using check-doxygen target.
---
 Examples/test-suite/common.mk | 34 ++++++++++++++++++++++++++--------
 1 file changed, 26 insertions(+), 8 deletions(-)

diff --git a/Examples/test-suite/common.mk b/Examples/test-suite/common.mk
index a670e1fb1..d0463badd 100644
--- a/Examples/test-suite/common.mk
+++ b/Examples/test-suite/common.mk
@@ -64,7 +64,7 @@ CXXSRCS    =
 CSRCS      = 
 TARGETPREFIX = 
 TARGETSUFFIX = 
-SWIGOPT    = -doxygen -outcurrentdir -I$(top_srcdir)/$(EXAMPLES)/$(TEST_SUITE)
+SWIGOPT    = -outcurrentdir -I$(top_srcdir)/$(EXAMPLES)/$(TEST_SUITE)
 INCLUDES   = -I$(top_srcdir)/$(EXAMPLES)/$(TEST_SUITE)
 LIBS       = -L.
 LIBPREFIX  = lib
@@ -195,13 +195,6 @@ CPP_TEST_CASES += \
 	director_using \
 	director_wombat \
 	disown \
-	doxygen_parsing \
-	doxygen_basic_translate \
-	doxygen_basic_notranslate \
-	doxygen_translate \
-	doxygen_translate_all_tags \
-	doxygen_translate_links \
-	doxygen_misc_constructs \
 	dynamic_cast \
 	empty \
 	enum_ignore \
@@ -541,6 +534,27 @@ CPP11_TEST_BROKEN = \
 #	cpp11_variadic_templates \    # Broken for some languages (such as Java)
 #	cpp11_reference_wrapper \     # No typemaps
 
+# Doxygen support test cases: can only be used with languages supporting
+# Doxygen comment translation, currently only Python and Java.
+python_HAS_DOXYGEN := 1
+java_HAS_DOXYGEN := 1
+
+$(eval HAS_DOXYGEN := $($(LANGUAGE)_HAS_DOXYGEN))
+
+ifdef HAS_DOXYGEN
+DOXYGEN_TEST_CASES := \
+	doxygen_parsing \
+	doxygen_basic_translate \
+	doxygen_basic_notranslate \
+	doxygen_translate \
+	doxygen_translate_all_tags \
+	doxygen_translate_links \
+	doxygen_misc_constructs \
+
+$(DOXYGEN_TEST_CASES:=.cpptest): SWIGOPT += -doxygen
+
+CPP_TEST_CASES += $(DOXYGEN_TEST_CASES)
+endif
 
 #
 # Put all the heavy STD/STL cases here, where they can be skipped if needed
@@ -680,6 +694,10 @@ check-cpp: $(CPP_TEST_CASES:=.cpptest)
 
 check-cpp11: $(CPP11_TEST_CASES:=.cpptest)
 
+ifdef HAS_DOXYGEN
+check-doxygen: $(DOXYGEN_TEST_CASES:=.cpptest)
+endif
+
 endif
 
 # partialcheck target runs SWIG only, ie no compilation or running of tests (for a subset of languages)

From 6d0d6758e0d4317a336d4ea7a302d32fe2a5f2e5 Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Thu, 15 May 2014 00:28:33 +0200
Subject: [PATCH 201/314] Fix Java-specific Doxygen unit tests.

Put these tests in DOXYGEN_TEST_CASES and not just CPP_TEST_CASES as the
"-doxygen" switch is only used for those in the former and not the latter.
---
 Examples/test-suite/common.mk        |  2 +-
 Examples/test-suite/java/Makefile.in | 10 ++++++----
 2 files changed, 7 insertions(+), 5 deletions(-)

diff --git a/Examples/test-suite/common.mk b/Examples/test-suite/common.mk
index 3614f0467..745f61e0b 100644
--- a/Examples/test-suite/common.mk
+++ b/Examples/test-suite/common.mk
@@ -542,7 +542,7 @@ java_HAS_DOXYGEN := 1
 $(eval HAS_DOXYGEN := $($(LANGUAGE)_HAS_DOXYGEN))
 
 ifdef HAS_DOXYGEN
-DOXYGEN_TEST_CASES := \
+DOXYGEN_TEST_CASES += \
 	doxygen_parsing \
 	doxygen_basic_translate \
 	doxygen_basic_notranslate \
diff --git a/Examples/test-suite/java/Makefile.in b/Examples/test-suite/java/Makefile.in
index c708c5c09..5c11c89b5 100644
--- a/Examples/test-suite/java/Makefile.in
+++ b/Examples/test-suite/java/Makefile.in
@@ -16,10 +16,6 @@ C_TEST_CASES = \
 	java_lib_various
 
 CPP_TEST_CASES = \
-	doxygen_parsing_enums_simple \
-	doxygen_parsing_enums_proper \
-	doxygen_parsing_enums_typesafe \
-	doxygen_parsing_enums_typeunsafe \
 	enum_thorough_proper \
 	enum_thorough_simple \
 	enum_thorough_typeunsafe \
@@ -43,6 +39,12 @@ CPP_TEST_CASES = \
 	java_typemaps_typewrapper
 #	li_boost_intrusive_ptr
 
+DOXYGEN_TEST_CASES := \
+	doxygen_parsing_enums_simple \
+	doxygen_parsing_enums_proper \
+	doxygen_parsing_enums_typesafe \
+	doxygen_parsing_enums_typeunsafe \
+
 include $(srcdir)/../common.mk
 
 # Overridden variables here

From cd64ad2a71021e32ccc05d64eace1c988a28e7ad Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Thu, 15 May 2014 00:29:44 +0200
Subject: [PATCH 202/314] Fix running Doxygen Java unit tests from separate
 build directory.

Use full path for CommentsParser.java instead of relying on it being found by
"find . -name *.java".

Also use tools.jar from the JDL for the Doxygen-specific tests only, the other
ones don't need it.
---
 Examples/test-suite/java/Makefile.in | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/Examples/test-suite/java/Makefile.in b/Examples/test-suite/java/Makefile.in
index 5c11c89b5..7759979e5 100644
--- a/Examples/test-suite/java/Makefile.in
+++ b/Examples/test-suite/java/Makefile.in
@@ -87,14 +87,20 @@ setup = \
 	  mkdir $(JAVA_PACKAGE);							  \
 	fi
 
+# Doxygen test cases need to be compiled together with the CommentsParser class
+# which depends on com.sun.javadoc package which is located in this JAR.
+JAVA_CLASSPATH := .
+$(DOXYGEN_TEST_CASES:=.cpptest): JAVA_CLASSPATH := $(JAVA_HOME)/lib/tools.jar:.
+$(DOXYGEN_TEST_CASES:=.cpptest): DOXYGEN_COMMENT_PARSER := $(srcdir)/CommentParser.java
+
 # Compiles java files then runs the testcase. A testcase is only run if
 # a file is found which has _runme.java appended after the testcase name.
 # Note Java uses LD_LIBRARY_PATH under Unix, PATH under Cygwin/Windows, SHLIB_PATH on HPUX and DYLD_LIBRARY_PATH on Mac OS X.
 run_testcase = \
 	cd $(JAVA_PACKAGE) && $(COMPILETOOL) $(JAVAC) -classpath . `find . -name "*.java"` && cd .. && \
 	if [ -f $(srcdir)/$(SCRIPTPREFIX)$*$(SCRIPTSUFFIX) ]; then \
-	  $(COMPILETOOL) $(JAVAC) -classpath $(JAVA_HOME)/lib/tools.jar:. -d . $(srcdir)/$(SCRIPTPREFIX)$*$(SCRIPTSUFFIX) && \
-	  env LD_LIBRARY_PATH="$(JAVA_PACKAGE):$$LD_LIBRARY_PATH" PATH="$(JAVA_PACKAGE):$$PATH" SHLIB_PATH="$(JAVA_PACKAGE):$$SHLIB_PATH" DYLD_LIBRARY_PATH="$(JAVA_PACKAGE):$$DYLD_LIBRARY_PATH" $(RUNTOOL) $(JAVA) $(JAVAFLAGS) -classpath $(JAVA_HOME)/lib/tools.jar:. $*_runme; \
+	  $(COMPILETOOL) $(JAVAC) -classpath $(JAVA_CLASSPATH) -d . $(DOXYGEN_COMMENT_PARSER) $(srcdir)/$(SCRIPTPREFIX)$*$(SCRIPTSUFFIX) && \
+	  env LD_LIBRARY_PATH="$(JAVA_PACKAGE):$$LD_LIBRARY_PATH" PATH="$(JAVA_PACKAGE):$$PATH" SHLIB_PATH="$(JAVA_PACKAGE):$$SHLIB_PATH" DYLD_LIBRARY_PATH="$(JAVA_PACKAGE):$$DYLD_LIBRARY_PATH" $(RUNTOOL) $(JAVA) $(JAVAFLAGS) -classpath $(JAVA_CLASSPATH) $*_runme; \
 	fi
 
 # Clean: remove testcase directories

From 4f032332c9e9bd692fc6addee7653fe4e76279c4 Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Thu, 15 May 2014 00:42:09 +0200
Subject: [PATCH 203/314] Work around apparent clang bug.

Clang seems to be confused by "tm" being the name both of a local variable and
a struct tm from the standard <time.h> header, included indirectly in the
doxygen branch from java.cxx via "swig.h" and <stdlin.h>.

Just removing the unnecessary cast helps to clear the confusion.
---
 Source/Modules/java.cxx | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/Source/Modules/java.cxx b/Source/Modules/java.cxx
index 18e6cb71c..a2687ab6e 100644
--- a/Source/Modules/java.cxx
+++ b/Source/Modules/java.cxx
@@ -2556,7 +2556,7 @@ public:
     }
 
     generateThrowsClause(n, function_code);
-    Printf(function_code, " %s\n\n", tm ? (const String *) tm : empty_string);
+    Printf(function_code, " %s\n\n", tm ? tm : empty_string);
     Printv(proxy_class_code, function_code, NIL);
 
     Delete(pre_code);
@@ -3032,7 +3032,7 @@ public:
     }
 
     generateThrowsClause(n, function_code);
-    Printf(function_code, " %s\n\n", tm ? (const String *) tm : empty_string);
+    Printf(function_code, " %s\n\n", tm ? tm : empty_string);
     Printv(module_class_code, function_code, NIL);
 
     Delete(pre_code);

From f6ba7b91487fec619a75d3421619bae90ce0fc94 Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Thu, 15 May 2014 01:00:33 +0200
Subject: [PATCH 204/314] Make Doxygen unit test supporting module
 Python3-friendly.

Add parentheses around print argument to make the same code work in both
Python2 and Python3.
---
 Examples/test-suite/python/commentVerifier.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/Examples/test-suite/python/commentVerifier.py b/Examples/test-suite/python/commentVerifier.py
index f7c0114ee..e231565c2 100644
--- a/Examples/test-suite/python/commentVerifier.py
+++ b/Examples/test-suite/python/commentVerifier.py
@@ -13,12 +13,12 @@ def check(got, expected):
       got = ''
 
   if not got == expected:
-    print "\n\n////////////////////////////////////////////////////////////////////////"
+    print("\n\n////////////////////////////////////////////////////////////////////////")
 
     expectedFileName = "expected.txt"
     gotFileName = "got.txt"
-    print "Output is also saved to files '" + expectedFileName + \
-                                   "' and '" + gotFileName + "'";
+    print("Output is also saved to files '" + expectedFileName + \
+                                   "' and '" + gotFileName + "'")
 
     expectedFile = open(expectedFileName, "w")
     expectedFile.write(expected)

From f684242467239a446ef049c05f6c1cd60572050a Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Wed, 11 Jun 2014 19:36:49 +0200
Subject: [PATCH 205/314] Replace DoxygenTranslator debug parameters with a
 single flags one.

This makes the code more readable and more extensible as more flags are easier
to add in the future than more boolean parameters.

No user-visible changes.
---
 .../src/DoxygenTranslator.cpp                 |  6 +++---
 .../DoxygenTranslator/src/DoxygenTranslator.h | 19 +++++++++++++++++--
 .../src/JavaDocConverter.cpp                  |  8 ++++----
 .../DoxygenTranslator/src/JavaDocConverter.h  |  2 +-
 .../DoxygenTranslator/src/PyDocConverter.cpp  |  6 +++---
 Source/DoxygenTranslator/src/PyDocConverter.h |  2 +-
 Source/Modules/java.cxx                       | 17 ++++++++---------
 Source/Modules/python.cxx                     | 17 ++++++++---------
 8 files changed, 45 insertions(+), 32 deletions(-)

diff --git a/Source/DoxygenTranslator/src/DoxygenTranslator.cpp b/Source/DoxygenTranslator/src/DoxygenTranslator.cpp
index 8175629d1..3ea92e03b 100644
--- a/Source/DoxygenTranslator/src/DoxygenTranslator.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenTranslator.cpp
@@ -14,9 +14,9 @@
 
 #include "DoxygenTranslator.h"
 
-DoxygenTranslator::DoxygenTranslator(bool debugTranslator, bool debugParser) :
-  debug(debugTranslator),
-  parser(debugParser)
+DoxygenTranslator::DoxygenTranslator(int flags) :
+  m_flags(flags),
+  parser((flags & debug_parser) != 0)
 {}
 
 
diff --git a/Source/DoxygenTranslator/src/DoxygenTranslator.h b/Source/DoxygenTranslator/src/DoxygenTranslator.h
index 173bd58f0..7d908ee1f 100644
--- a/Source/DoxygenTranslator/src/DoxygenTranslator.h
+++ b/Source/DoxygenTranslator/src/DoxygenTranslator.h
@@ -29,10 +29,23 @@
  */
 class DoxygenTranslator {
 public:
+  /*
+   * Bit flags for the translator ctor.
+   *
+   * Derived classes may define additional flags.
+   */
+  enum {
+    // Use DoxygenParser in "noisy" mode.
+    debug_parser = 1,
+
+    // Output results of translating Doxygen comments.
+    debug_translator = 2
+  };
+
   /*
    * Constructor
    */
-  DoxygenTranslator(bool debugTranslator = false, bool debugParser = false);
+  DoxygenTranslator(int flags = 0);
 
   /*
    * Virtual destructor.
@@ -56,7 +69,9 @@ public:
   String *getDoxygenComment(Node *node);
 
 protected:
-  bool debug;
+  // The flags passed to the ctor.
+  const int m_flags;
+
   DoxygenParser parser;
 
   /*
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.cpp b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
index b5edcb8a2..c7c601b9b 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
@@ -274,8 +274,8 @@ void JavaDocConverter::fillStaticTables()
       "&rarr");
 }
 
-JavaDocConverter::JavaDocConverter(bool debugTranslator, bool debugParser) :
-    DoxygenTranslator(debugTranslator, debugParser)
+JavaDocConverter::JavaDocConverter(int flags) :
+    DoxygenTranslator(flags)
 {
   fillStaticTables();
 }
@@ -933,7 +933,7 @@ String *JavaDocConverter::makeDocumentation(Node *node)
 
   // entityList.sort(CompareDoxygenEntities()); sorting currently not used,
 
-  if (debug) {
+  if (m_flags & debug_translator) {
     std::cout << "---RESORTED LIST---" << std::endl;
     printTree(entityList);
   }
@@ -964,7 +964,7 @@ String *JavaDocConverter::makeDocumentation(Node *node)
 
   javaDocString += "\n */\n";
 
-  if (debug) {
+  if (m_flags & debug_translator) {
     std::cout << "\n---RESULT IN JAVADOC---" << std::endl;
     std::cout << javaDocString;
   }
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.h b/Source/DoxygenTranslator/src/JavaDocConverter.h
index 78bf6bb88..eff00590c 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.h
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.h
@@ -22,7 +22,7 @@
  */
 class JavaDocConverter : public DoxygenTranslator {
 public:
-  JavaDocConverter(bool debugTranslator = false, bool debugParser = false);
+  JavaDocConverter(int flags = 0);
   String *makeDocumentation(Node *node);
 
 protected:
diff --git a/Source/DoxygenTranslator/src/PyDocConverter.cpp b/Source/DoxygenTranslator/src/PyDocConverter.cpp
index 5320ce7f9..740eb6de2 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/PyDocConverter.cpp
@@ -227,8 +227,8 @@ void PyDocConverter::fillStaticTables()
   tagHandlers["&rarr"] = make_pair(&PyDocConverter::handleHtmlEntity, "-->");
 }
 
-PyDocConverter::PyDocConverter(bool debugTranslator, bool debugParser) :
-    DoxygenTranslator(debugTranslator, debugParser), m_tableLineLen(0), m_prevRowIsTH(
+PyDocConverter::PyDocConverter(int flags) :
+    DoxygenTranslator(flags), m_tableLineLen(0), m_prevRowIsTH(
         false)
 {
   fillStaticTables();
@@ -665,7 +665,7 @@ String *PyDocConverter::makeDocumentation(Node *n)
 
     result = pyDocString;
 
-    if (debug) {
+    if (m_flags & debug_translator) {
       std::cout << "\n---RESULT IN PYDOC---" << std::endl;
       std::cout << result;
       std::cout << std::endl;
diff --git a/Source/DoxygenTranslator/src/PyDocConverter.h b/Source/DoxygenTranslator/src/PyDocConverter.h
index 262772e7b..e037db9ce 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.h
+++ b/Source/DoxygenTranslator/src/PyDocConverter.h
@@ -25,7 +25,7 @@
 
 class PyDocConverter : public DoxygenTranslator {
 public:
-  PyDocConverter(bool debugTranslator = false, bool debugParser = false);
+  PyDocConverter(int flags = 0);
   String *makeDocumentation(Node *node);
 
 protected:
diff --git a/Source/Modules/java.cxx b/Source/Modules/java.cxx
index a2687ab6e..4059ce9c7 100644
--- a/Source/Modules/java.cxx
+++ b/Source/Modules/java.cxx
@@ -261,8 +261,7 @@ public:
 
     SWIG_library_directory("java");
 
-    bool debug_doxygen_translator = false;
-    bool debug_doxygen_parser = false;
+    int doxygen_translator_flags = 0;
 
     // Look for certain command line options
     for (int i = 1; i < argc; i++) {
@@ -289,12 +288,12 @@ public:
 	  Swig_mark_arg(i);
 	  doxygen = true;
 	  scan_doxygen_comments = true;
-  } else if ((strcmp(argv[i], "-debug-doxygen-translator") == 0)) {
-    Swig_mark_arg(i);
-    debug_doxygen_translator = true;
-  } else if ((strcmp(argv[i], "-debug-doxygen-parser") == 0)) {
-    Swig_mark_arg(i);
-    debug_doxygen_parser = true;
+	} else if ((strcmp(argv[i], "-debug-doxygen-translator") == 0)) {
+	  Swig_mark_arg(i);
+	  doxygen_translator_flags |= DoxygenTranslator::debug_translator;
+	} else if ((strcmp(argv[i], "-debug-doxygen-parser") == 0)) {
+	  Swig_mark_arg(i);
+	  doxygen_translator_flags |= DoxygenTranslator::debug_parser;
 	} else if ((strcmp(argv[i], "-noproxy") == 0)) {
 	  Swig_mark_arg(i);
 	  proxy_flag = false;
@@ -320,7 +319,7 @@ public:
     }
     
     if (doxygen)
-      doxygenTranslator = new JavaDocConverter(debug_doxygen_translator, debug_doxygen_parser);
+      doxygenTranslator = new JavaDocConverter(doxygen_translator_flags);
 
     // Add a symbol to the parser for conditional compilation
     Preprocessor_define("SWIGJAVA 1", 0);
diff --git a/Source/Modules/python.cxx b/Source/Modules/python.cxx
index 7a7c63733..e9675a8a7 100644
--- a/Source/Modules/python.cxx
+++ b/Source/Modules/python.cxx
@@ -339,8 +339,7 @@ public:
 
     SWIG_library_directory("python");
 
-    bool debug_doxygen_parser = false;
-    bool debug_doxygen_translator = false;
+    int doxygen_translator_flags = 0;
 
     for (int i = 1; i < argc; i++) {
       if (argv[i]) {
@@ -436,12 +435,12 @@ public:
 	  doxygen = 1;
 	  scan_doxygen_comments = 1;
 	  Swig_mark_arg(i);
-  } else if (strcmp(argv[i], "-debug-doxygen-translator") == 0) {
-    debug_doxygen_translator = true;
-    Swig_mark_arg(i);
-  } else if (strcmp(argv[i], "-debug-doxygen-parser") == 0) {
-    debug_doxygen_parser = true;
-    Swig_mark_arg(i);
+	} else if (strcmp(argv[i], "-debug-doxygen-translator") == 0) {
+	  doxygen_translator_flags |= DoxygenTranslator::debug_translator;
+	  Swig_mark_arg(i);
+	} else if (strcmp(argv[i], "-debug-doxygen-parser") == 0) {
+	  doxygen_translator_flags |= DoxygenTranslator::debug_parser;
+	  Swig_mark_arg(i);
 	} else if (strcmp(argv[i], "-fastunpack") == 0) {
 	  fastunpack = 1;
 	  Swig_mark_arg(i);
@@ -564,7 +563,7 @@ public:
     }
     
     if (doxygen)
-      doxygenTranslator = new PyDocConverter(debug_doxygen_translator, debug_doxygen_parser);
+      doxygenTranslator = new PyDocConverter(doxygen_translator_flags);
 
     if (!global_name)
       global_name = NewString("cvar");

From a76c1343b712c4d619922d4e7a9695cf8337ddf4 Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Sun, 15 Jun 2014 17:55:45 +0200
Subject: [PATCH 206/314] Simplify management of tag handlers in
 PyDocConverter.

Avoid having to pass dummy empty string arguments, just use default value for
the unused last parameter of handleParagraph().

Also get rid of dozens of "" occurrences in the tag map initialization code,
use a helper function instead.

No real changes.
---
 .../DoxygenTranslator/src/PyDocConverter.cpp  | 354 +++++++++---------
 Source/DoxygenTranslator/src/PyDocConverter.h |  55 +--
 2 files changed, 213 insertions(+), 196 deletions(-)

diff --git a/Source/DoxygenTranslator/src/PyDocConverter.cpp b/Source/DoxygenTranslator/src/PyDocConverter.cpp
index 740eb6de2..dee98a873 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/PyDocConverter.cpp
@@ -19,11 +19,25 @@
 #include <iostream>
 
 // define static tables, they are filled in PyDocConverter's constructor
-std::map<std::string, std::pair<PyDocConverter::tagHandler, std::string> > PyDocConverter::tagHandlers;
+PyDocConverter::TagHandlersMap PyDocConverter::tagHandlers;
 std::map<std::string, std::string> PyDocConverter::sectionTitles;
 
 using std::string;
 
+/* static */
+PyDocConverter::TagHandlersMap::mapped_type
+PyDocConverter::make_handler(tagHandler handler)
+{
+  return make_pair(handler, std::string());
+}
+
+/* static */
+PyDocConverter::TagHandlersMap::mapped_type
+PyDocConverter::make_handler(tagHandler handler, const char* arg)
+{
+  return make_pair(handler, arg);
+}
+
 void PyDocConverter::fillStaticTables()
 {
   if (tagHandlers.size()) // fill only once
@@ -54,177 +68,173 @@ void PyDocConverter::fillStaticTables()
   sectionTitles["todo"] = "TODO: ";
   sectionTitles["version"] = "Version: ";
 
-  tagHandlers["a"] = make_pair(&PyDocConverter::handleTagWrap, "_");
-  tagHandlers["b"] = make_pair(&PyDocConverter::handleTagWrap, "__");
+  tagHandlers["a"] = make_handler(&PyDocConverter::handleTagWrap, "_");
+  tagHandlers["b"] = make_handler(&PyDocConverter::handleTagWrap, "__");
   // \c command is translated as single quotes around next word
-  tagHandlers["c"] = make_pair(&PyDocConverter::handleTagWrap, "'"); // see markdown support in doxy, section 'code wraps'
-  tagHandlers["cite"] = make_pair(&PyDocConverter::handleTagWrap, "'");
-  tagHandlers["e"] = make_pair(&PyDocConverter::handleTagWrap, "_");
+  tagHandlers["c"] = make_handler(&PyDocConverter::handleTagWrap, "'"); // see markdown support in doxy, section 'code wraps'
+  tagHandlers["cite"] = make_handler(&PyDocConverter::handleTagWrap, "'");
+  tagHandlers["e"] = make_handler(&PyDocConverter::handleTagWrap, "_");
   // these commands insert just a single char, some of them need to be escaped
-  tagHandlers["$"] = make_pair(&PyDocConverter::handleTagChar, "");
-  tagHandlers["@"] = make_pair(&PyDocConverter::handleTagChar, "");
-  tagHandlers["\\"] = make_pair(&PyDocConverter::handleTagChar, "");
-  tagHandlers["<"] = make_pair(&PyDocConverter::handleTagChar, "");
-  tagHandlers[">"] = make_pair(&PyDocConverter::handleTagChar, "");
-  tagHandlers["&"] = make_pair(&PyDocConverter::handleTagChar, "");
-  tagHandlers["#"] = make_pair(&PyDocConverter::handleTagChar, "");
-  tagHandlers["%"] = make_pair(&PyDocConverter::handleTagChar, "");
-  tagHandlers["~"] = make_pair(&PyDocConverter::handleTagChar, "");
-  tagHandlers["\""] = make_pair(&PyDocConverter::handleTagChar, "");
-  tagHandlers["."] = make_pair(&PyDocConverter::handleTagChar, "");
-  tagHandlers["::"] = make_pair(&PyDocConverter::handleTagChar, "");
+  tagHandlers["$"] = make_handler(&PyDocConverter::handleTagChar);
+  tagHandlers["@"] = make_handler(&PyDocConverter::handleTagChar);
+  tagHandlers["\\"] = make_handler(&PyDocConverter::handleTagChar);
+  tagHandlers["<"] = make_handler(&PyDocConverter::handleTagChar);
+  tagHandlers[">"] = make_handler(&PyDocConverter::handleTagChar);
+  tagHandlers["&"] = make_handler(&PyDocConverter::handleTagChar);
+  tagHandlers["#"] = make_handler(&PyDocConverter::handleTagChar);
+  tagHandlers["%"] = make_handler(&PyDocConverter::handleTagChar);
+  tagHandlers["~"] = make_handler(&PyDocConverter::handleTagChar);
+  tagHandlers["\""] = make_handler(&PyDocConverter::handleTagChar);
+  tagHandlers["."] = make_handler(&PyDocConverter::handleTagChar);
+  tagHandlers["::"] = make_handler(&PyDocConverter::handleTagChar);
   // these commands are stripped out, and only their content is printed
-  tagHandlers["attention"] = make_pair(&PyDocConverter::handleParagraph, "");
-  tagHandlers["author"] = make_pair(&PyDocConverter::handleParagraph, "");
-  tagHandlers["authors"] = make_pair(&PyDocConverter::handleParagraph, "");
-  tagHandlers["brief"] = make_pair(&PyDocConverter::handleParagraph, "");
-  tagHandlers["bug"] = make_pair(&PyDocConverter::handleParagraph, "");
-  tagHandlers["code"] = make_pair(&PyDocConverter::handleParagraph, "");
-  tagHandlers["copyright"] = make_pair(&PyDocConverter::handleParagraph, "");
-  tagHandlers["date"] = make_pair(&PyDocConverter::handleParagraph, "");
-  tagHandlers["deprecated"] = make_pair(&PyDocConverter::handleParagraph, "");
-  tagHandlers["details"] = make_pair(&PyDocConverter::handleParagraph, "");
-  tagHandlers["em"] = make_pair(&PyDocConverter::handleParagraph, " ");
-  tagHandlers["example"] = make_pair(&PyDocConverter::handleParagraph, "");
-  tagHandlers["exception"] = make_pair(&PyDocConverter::handleParagraph, "");
-  tagHandlers["htmlonly"] = make_pair(&PyDocConverter::handleParagraph, "");
-  tagHandlers["invariant"] = make_pair(&PyDocConverter::handleParagraph, "");
-  tagHandlers["latexonly"] = make_pair(&PyDocConverter::handleParagraph, "");
-  tagHandlers["link"] = make_pair(&PyDocConverter::handleParagraph, "");
-  tagHandlers["manonly"] = make_pair(&PyDocConverter::handleParagraph, "");
-  tagHandlers["note"] = make_pair(&PyDocConverter::handleParagraph, "");
-  tagHandlers["p"] = make_pair(&PyDocConverter::handleParagraph, "");
-  tagHandlers["partofdescription"] = make_pair(&PyDocConverter::handleParagraph,
-      "");
-  tagHandlers["rtfonly"] = make_pair(&PyDocConverter::handleParagraph, "");
-  tagHandlers["return"] = make_pair(&PyDocConverter::handleParagraph, "");
-  tagHandlers["returns"] = make_pair(&PyDocConverter::handleParagraph, "");
-  tagHandlers["result"] = make_pair(&PyDocConverter::handleParagraph, "");
-  tagHandlers["remark"] = make_pair(&PyDocConverter::handleParagraph, "");
-  tagHandlers["remarks"] = make_pair(&PyDocConverter::handleParagraph, "");
-  tagHandlers["sa"] = make_pair(&PyDocConverter::handleTagMessage,
+  tagHandlers["attention"] = make_handler(&PyDocConverter::handleParagraph);
+  tagHandlers["author"] = make_handler(&PyDocConverter::handleParagraph);
+  tagHandlers["authors"] = make_handler(&PyDocConverter::handleParagraph);
+  tagHandlers["brief"] = make_handler(&PyDocConverter::handleParagraph);
+  tagHandlers["bug"] = make_handler(&PyDocConverter::handleParagraph);
+  tagHandlers["code"] = make_handler(&PyDocConverter::handleParagraph);
+  tagHandlers["copyright"] = make_handler(&PyDocConverter::handleParagraph);
+  tagHandlers["date"] = make_handler(&PyDocConverter::handleParagraph);
+  tagHandlers["deprecated"] = make_handler(&PyDocConverter::handleParagraph);
+  tagHandlers["details"] = make_handler(&PyDocConverter::handleParagraph);
+  tagHandlers["em"] = make_handler(&PyDocConverter::handleParagraph, " ");
+  tagHandlers["example"] = make_handler(&PyDocConverter::handleParagraph);
+  tagHandlers["exception"] = make_handler(&PyDocConverter::handleParagraph);
+  tagHandlers["htmlonly"] = make_handler(&PyDocConverter::handleParagraph);
+  tagHandlers["invariant"] = make_handler(&PyDocConverter::handleParagraph);
+  tagHandlers["latexonly"] = make_handler(&PyDocConverter::handleParagraph);
+  tagHandlers["link"] = make_handler(&PyDocConverter::handleParagraph);
+  tagHandlers["manonly"] = make_handler(&PyDocConverter::handleParagraph);
+  tagHandlers["note"] = make_handler(&PyDocConverter::handleParagraph);
+  tagHandlers["p"] = make_handler(&PyDocConverter::handleParagraph);
+  tagHandlers["partofdescription"] = make_handler(&PyDocConverter::handleParagraph);
+  tagHandlers["rtfonly"] = make_handler(&PyDocConverter::handleParagraph);
+  tagHandlers["return"] = make_handler(&PyDocConverter::handleParagraph);
+  tagHandlers["returns"] = make_handler(&PyDocConverter::handleParagraph);
+  tagHandlers["result"] = make_handler(&PyDocConverter::handleParagraph);
+  tagHandlers["remark"] = make_handler(&PyDocConverter::handleParagraph);
+  tagHandlers["remarks"] = make_handler(&PyDocConverter::handleParagraph);
+  tagHandlers["sa"] = make_handler(&PyDocConverter::handleTagMessage, "See also: ");
+  tagHandlers["see"] = make_handler(&PyDocConverter::handleTagMessage,
       "See also: ");
-  tagHandlers["see"] = make_pair(&PyDocConverter::handleTagMessage,
-      "See also: ");
-  tagHandlers["since"] = make_pair(&PyDocConverter::handleParagraph, "");
-  tagHandlers["short"] = make_pair(&PyDocConverter::handleParagraph, "");
-  tagHandlers["throw"] = make_pair(&PyDocConverter::handleParagraph, "");
-  tagHandlers["throws"] = make_pair(&PyDocConverter::handleParagraph, "");
-  tagHandlers["todo"] = make_pair(&PyDocConverter::handleParagraph, "");
-  tagHandlers["version"] = make_pair(&PyDocConverter::handleParagraph, "");
-  tagHandlers["verbatim"] = make_pair(&PyDocConverter::handleParagraph, "");
-  tagHandlers["warning"] = make_pair(&PyDocConverter::handleParagraph, "");
-  tagHandlers["xmlonly"] = make_pair(&PyDocConverter::handleParagraph, "");
+  tagHandlers["since"] = make_handler(&PyDocConverter::handleParagraph);
+  tagHandlers["short"] = make_handler(&PyDocConverter::handleParagraph);
+  tagHandlers["throw"] = make_handler(&PyDocConverter::handleParagraph);
+  tagHandlers["throws"] = make_handler(&PyDocConverter::handleParagraph);
+  tagHandlers["todo"] = make_handler(&PyDocConverter::handleParagraph);
+  tagHandlers["version"] = make_handler(&PyDocConverter::handleParagraph);
+  tagHandlers["verbatim"] = make_handler(&PyDocConverter::handleParagraph);
+  tagHandlers["warning"] = make_handler(&PyDocConverter::handleParagraph);
+  tagHandlers["xmlonly"] = make_handler(&PyDocConverter::handleParagraph);
   // these commands have special handlers
-  tagHandlers["arg"] = make_pair(&PyDocConverter::handleTagMessage, " -");
-  tagHandlers["cond"] = make_pair(&PyDocConverter::handleTagMessage,
+  tagHandlers["arg"] = make_handler(&PyDocConverter::handleTagMessage, " -");
+  tagHandlers["cond"] = make_handler(&PyDocConverter::handleTagMessage,
       "Conditional comment: ");
-  tagHandlers["else"] = make_pair(&PyDocConverter::handleTagIf, "Else: ");
-  tagHandlers["elseif"] = make_pair(&PyDocConverter::handleTagIf, "Else if: ");
-  tagHandlers["endcond"] = make_pair(&PyDocConverter::handleTagMessage,
+  tagHandlers["else"] = make_handler(&PyDocConverter::handleTagIf, "Else: ");
+  tagHandlers["elseif"] = make_handler(&PyDocConverter::handleTagIf, "Else if: ");
+  tagHandlers["endcond"] = make_handler(&PyDocConverter::handleTagMessage,
       "End of conditional comment.");
-  tagHandlers["if"] = make_pair(&PyDocConverter::handleTagIf, "If: ");
-  tagHandlers["ifnot"] = make_pair(&PyDocConverter::handleTagIf, "If not: ");
-  tagHandlers["image"] = make_pair(&PyDocConverter::handleTagImage, "");
-  tagHandlers["li"] = make_pair(&PyDocConverter::handleTagMessage, " -");
-  tagHandlers["overload"] = make_pair(&PyDocConverter::handleTagMessage,
+  tagHandlers["if"] = make_handler(&PyDocConverter::handleTagIf, "If: ");
+  tagHandlers["ifnot"] = make_handler(&PyDocConverter::handleTagIf, "If not: ");
+  tagHandlers["image"] = make_handler(&PyDocConverter::handleTagImage);
+  tagHandlers["li"] = make_handler(&PyDocConverter::handleTagMessage, " -");
+  tagHandlers["overload"] = make_handler(&PyDocConverter::handleTagMessage,
       "This is an overloaded member function, provided for"
           " convenience.\nIt differs from the above function only in what"
           " argument(s) it accepts.");
-  tagHandlers["par"] = make_pair(&PyDocConverter::handleTagPar, "");
-  tagHandlers["param"] = make_pair(&PyDocConverter::handleTagParam, "");
-  tagHandlers["tparam"] = make_pair(&PyDocConverter::handleTagParam, "");
-  tagHandlers["ref"] = make_pair(&PyDocConverter::handleTagRef, "");
+  tagHandlers["par"] = make_handler(&PyDocConverter::handleTagPar);
+  tagHandlers["param"] = make_handler(&PyDocConverter::handleTagParam);
+  tagHandlers["tparam"] = make_handler(&PyDocConverter::handleTagParam);
+  tagHandlers["ref"] = make_handler(&PyDocConverter::handleTagRef);
   // this command just prints it's contents
   // (it is internal command of swig's parser, contains plain text)
-  tagHandlers["plainstd::string"] = make_pair(
-      &PyDocConverter::handlePlainString, "");
-  tagHandlers["plainstd::endl"] = make_pair(&PyDocConverter::handleNewLine, "");
-  tagHandlers["n"] = make_pair(&PyDocConverter::handleNewLine, "");
+  tagHandlers["plainstd::string"] = make_handler(&PyDocConverter::handlePlainString);
+  tagHandlers["plainstd::endl"] = make_handler(&PyDocConverter::handleNewLine);
+  tagHandlers["n"] = make_handler(&PyDocConverter::handleNewLine);
 
   // \f commands output literal Latex formula, which is still better than nothing.
-  tagHandlers["f$"] = make_pair(&PyDocConverter::handleTagVerbatim, "");
-  tagHandlers["f["] = make_pair(&PyDocConverter::handleTagVerbatim, "");
-  tagHandlers["f{"] = make_pair(&PyDocConverter::handleTagVerbatim, "");
+  tagHandlers["f$"] = make_handler(&PyDocConverter::handleTagVerbatim);
+  tagHandlers["f["] = make_handler(&PyDocConverter::handleTagVerbatim);
+  tagHandlers["f{"] = make_handler(&PyDocConverter::handleTagVerbatim);
 
   // HTML tags
-  tagHandlers["<a"] = make_pair(&PyDocConverter::handleDoxyHtmlTag_A, "");
-  tagHandlers["<b"] = make_pair(&PyDocConverter::handleDoxyHtmlTag2, "__");
-  tagHandlers["<blockquote"] = make_pair(&PyDocConverter::handleDoxyHtmlTag_A,
+  tagHandlers["<a"] = make_handler(&PyDocConverter::handleDoxyHtmlTag_A);
+  tagHandlers["<b"] = make_handler(&PyDocConverter::handleDoxyHtmlTag2, "__");
+  tagHandlers["<blockquote"] = make_handler(&PyDocConverter::handleDoxyHtmlTag_A,
       "Quote: ");
-  tagHandlers["<body"] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "");
-  tagHandlers["<br"] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "\n");
+  tagHandlers["<body"] = make_handler(&PyDocConverter::handleDoxyHtmlTag);
+  tagHandlers["<br"] = make_handler(&PyDocConverter::handleDoxyHtmlTag, "\n");
 
   // there is no formatting for this tag as it was deprecated in HTML 4.01 and
   // not used in HTML 5
-  tagHandlers["<center"] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "");
-  tagHandlers["<caption"] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "");
-  tagHandlers["<code"] = make_pair(&PyDocConverter::handleDoxyHtmlTag2, "'");
+  tagHandlers["<center"] = make_handler(&PyDocConverter::handleDoxyHtmlTag);
+  tagHandlers["<caption"] = make_handler(&PyDocConverter::handleDoxyHtmlTag);
+  tagHandlers["<code"] = make_handler(&PyDocConverter::handleDoxyHtmlTag2, "'");
 
-  tagHandlers["<dl"] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "");
-  tagHandlers["<dd"] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "    ");
-  tagHandlers["<dt"] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "");
+  tagHandlers["<dl"] = make_handler(&PyDocConverter::handleDoxyHtmlTag);
+  tagHandlers["<dd"] = make_handler(&PyDocConverter::handleDoxyHtmlTag, "    ");
+  tagHandlers["<dt"] = make_handler(&PyDocConverter::handleDoxyHtmlTag);
 
-  tagHandlers["<dfn"] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "");
-  tagHandlers["<div"] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "");
-  tagHandlers["<em"] = make_pair(&PyDocConverter::handleDoxyHtmlTag2, "__");
-  tagHandlers["<form"] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "");
-  tagHandlers["<hr"] = make_pair(&PyDocConverter::handleDoxyHtmlTag,
+  tagHandlers["<dfn"] = make_handler(&PyDocConverter::handleDoxyHtmlTag);
+  tagHandlers["<div"] = make_handler(&PyDocConverter::handleDoxyHtmlTag);
+  tagHandlers["<em"] = make_handler(&PyDocConverter::handleDoxyHtmlTag2, "__");
+  tagHandlers["<form"] = make_handler(&PyDocConverter::handleDoxyHtmlTag);
+  tagHandlers["<hr"] = make_handler(&PyDocConverter::handleDoxyHtmlTag,
       "--------------------------------------------------------------------\n");
-  tagHandlers["<h1"] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "# ");
-  tagHandlers["<h2"] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "## ");
-  tagHandlers["<h3"] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "### ");
-  tagHandlers["<i"] = make_pair(&PyDocConverter::handleDoxyHtmlTag2, "_");
-  tagHandlers["<input"] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "");
-  tagHandlers["<img"] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "Image:");
-  tagHandlers["<li"] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "- ");
-  tagHandlers["<meta"] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "");
-  tagHandlers["<multicol"] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "");
-  tagHandlers["<ol"] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "");
-  tagHandlers["<p"] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "\n");
-  tagHandlers["<pre"] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "");
-  tagHandlers["<small"] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "");
-  tagHandlers["<span"] = make_pair(&PyDocConverter::handleDoxyHtmlTag2, "'");
-  tagHandlers["<strong"] = make_pair(&PyDocConverter::handleDoxyHtmlTag2, "__");
+  tagHandlers["<h1"] = make_handler(&PyDocConverter::handleDoxyHtmlTag, "# ");
+  tagHandlers["<h2"] = make_handler(&PyDocConverter::handleDoxyHtmlTag, "## ");
+  tagHandlers["<h3"] = make_handler(&PyDocConverter::handleDoxyHtmlTag, "### ");
+  tagHandlers["<i"] = make_handler(&PyDocConverter::handleDoxyHtmlTag2, "_");
+  tagHandlers["<input"] = make_handler(&PyDocConverter::handleDoxyHtmlTag);
+  tagHandlers["<img"] = make_handler(&PyDocConverter::handleDoxyHtmlTag, "Image:");
+  tagHandlers["<li"] = make_handler(&PyDocConverter::handleDoxyHtmlTag, "- ");
+  tagHandlers["<meta"] = make_handler(&PyDocConverter::handleDoxyHtmlTag);
+  tagHandlers["<multicol"] = make_handler(&PyDocConverter::handleDoxyHtmlTag);
+  tagHandlers["<ol"] = make_handler(&PyDocConverter::handleDoxyHtmlTag);
+  tagHandlers["<p"] = make_handler(&PyDocConverter::handleDoxyHtmlTag, "\n");
+  tagHandlers["<pre"] = make_handler(&PyDocConverter::handleDoxyHtmlTag);
+  tagHandlers["<small"] = make_handler(&PyDocConverter::handleDoxyHtmlTag);
+  tagHandlers["<span"] = make_handler(&PyDocConverter::handleDoxyHtmlTag2, "'");
+  tagHandlers["<strong"] = make_handler(&PyDocConverter::handleDoxyHtmlTag2, "__");
 
   // make a space between text and super/sub script.
-  tagHandlers["<sub"] = make_pair(&PyDocConverter::handleDoxyHtmlTag, " ");
-  tagHandlers["<sup"] = make_pair(&PyDocConverter::handleDoxyHtmlTag, " ");
+  tagHandlers["<sub"] = make_handler(&PyDocConverter::handleDoxyHtmlTag, " ");
+  tagHandlers["<sup"] = make_handler(&PyDocConverter::handleDoxyHtmlTag, " ");
 
-  tagHandlers["<table"] = make_pair(&PyDocConverter::handleDoxyHtmlTagNoParam,
-      "");
-  tagHandlers["<td"] = make_pair(&PyDocConverter::handleDoxyHtmlTag_td, "");
-  tagHandlers["<th"] = make_pair(&PyDocConverter::handleDoxyHtmlTag_th, "");
-  tagHandlers["<tr"] = make_pair(&PyDocConverter::handleDoxyHtmlTag_tr, "");
-  tagHandlers["<tt"] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "");
-  tagHandlers["<kbd"] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "");
-  tagHandlers["<ul"] = make_pair(&PyDocConverter::handleDoxyHtmlTag, "");
-  tagHandlers["<var"] = make_pair(&PyDocConverter::handleDoxyHtmlTag2, "_");
+  tagHandlers["<table"] = make_handler(&PyDocConverter::handleDoxyHtmlTagNoParam);
+  tagHandlers["<td"] = make_handler(&PyDocConverter::handleDoxyHtmlTag_td);
+  tagHandlers["<th"] = make_handler(&PyDocConverter::handleDoxyHtmlTag_th);
+  tagHandlers["<tr"] = make_handler(&PyDocConverter::handleDoxyHtmlTag_tr);
+  tagHandlers["<tt"] = make_handler(&PyDocConverter::handleDoxyHtmlTag);
+  tagHandlers["<kbd"] = make_handler(&PyDocConverter::handleDoxyHtmlTag);
+  tagHandlers["<ul"] = make_handler(&PyDocConverter::handleDoxyHtmlTag);
+  tagHandlers["<var"] = make_handler(&PyDocConverter::handleDoxyHtmlTag2, "_");
 
   // HTML entities
-  tagHandlers["&copy"] = make_pair(&PyDocConverter::handleHtmlEntity, "(C)");
-  tagHandlers["&trade"] = make_pair(&PyDocConverter::handleHtmlEntity, " TM");
-  tagHandlers["&reg"] = make_pair(&PyDocConverter::handleHtmlEntity, "(R)");
-  tagHandlers["&lt"] = make_pair(&PyDocConverter::handleHtmlEntity, "<");
-  tagHandlers["&gt"] = make_pair(&PyDocConverter::handleHtmlEntity, ">");
-  tagHandlers["&amp"] = make_pair(&PyDocConverter::handleHtmlEntity, "&");
-  tagHandlers["&apos"] = make_pair(&PyDocConverter::handleHtmlEntity, "'");
-  tagHandlers["&quot"] = make_pair(&PyDocConverter::handleHtmlEntity, "\"");
-  tagHandlers["&lsquo"] = make_pair(&PyDocConverter::handleHtmlEntity, "`");
-  tagHandlers["&rsquo"] = make_pair(&PyDocConverter::handleHtmlEntity, "'");
-  tagHandlers["&ldquo"] = make_pair(&PyDocConverter::handleHtmlEntity, "\"");
-  tagHandlers["&rdquo"] = make_pair(&PyDocConverter::handleHtmlEntity, "\"");
-  tagHandlers["&ndash"] = make_pair(&PyDocConverter::handleHtmlEntity, "-");
-  tagHandlers["&mdash"] = make_pair(&PyDocConverter::handleHtmlEntity, "--");
-  tagHandlers["&nbsp"] = make_pair(&PyDocConverter::handleHtmlEntity, " ");
-  tagHandlers["&times"] = make_pair(&PyDocConverter::handleHtmlEntity, "x");
-  tagHandlers["&minus"] = make_pair(&PyDocConverter::handleHtmlEntity, "-");
-  tagHandlers["&sdot"] = make_pair(&PyDocConverter::handleHtmlEntity, ".");
-  tagHandlers["&sim"] = make_pair(&PyDocConverter::handleHtmlEntity, "~");
-  tagHandlers["&le"] = make_pair(&PyDocConverter::handleHtmlEntity, "<=");
-  tagHandlers["&ge"] = make_pair(&PyDocConverter::handleHtmlEntity, ">=");
-  tagHandlers["&larr"] = make_pair(&PyDocConverter::handleHtmlEntity, "<--");
-  tagHandlers["&rarr"] = make_pair(&PyDocConverter::handleHtmlEntity, "-->");
+  tagHandlers["&copy"] = make_handler(&PyDocConverter::handleHtmlEntity, "(C)");
+  tagHandlers["&trade"] = make_handler(&PyDocConverter::handleHtmlEntity, " TM");
+  tagHandlers["&reg"] = make_handler(&PyDocConverter::handleHtmlEntity, "(R)");
+  tagHandlers["&lt"] = make_handler(&PyDocConverter::handleHtmlEntity, "<");
+  tagHandlers["&gt"] = make_handler(&PyDocConverter::handleHtmlEntity, ">");
+  tagHandlers["&amp"] = make_handler(&PyDocConverter::handleHtmlEntity, "&");
+  tagHandlers["&apos"] = make_handler(&PyDocConverter::handleHtmlEntity, "'");
+  tagHandlers["&quot"] = make_handler(&PyDocConverter::handleHtmlEntity, "\"");
+  tagHandlers["&lsquo"] = make_handler(&PyDocConverter::handleHtmlEntity, "`");
+  tagHandlers["&rsquo"] = make_handler(&PyDocConverter::handleHtmlEntity, "'");
+  tagHandlers["&ldquo"] = make_handler(&PyDocConverter::handleHtmlEntity, "\"");
+  tagHandlers["&rdquo"] = make_handler(&PyDocConverter::handleHtmlEntity, "\"");
+  tagHandlers["&ndash"] = make_handler(&PyDocConverter::handleHtmlEntity, "-");
+  tagHandlers["&mdash"] = make_handler(&PyDocConverter::handleHtmlEntity, "--");
+  tagHandlers["&nbsp"] = make_handler(&PyDocConverter::handleHtmlEntity, " ");
+  tagHandlers["&times"] = make_handler(&PyDocConverter::handleHtmlEntity, "x");
+  tagHandlers["&minus"] = make_handler(&PyDocConverter::handleHtmlEntity, "-");
+  tagHandlers["&sdot"] = make_handler(&PyDocConverter::handleHtmlEntity, ".");
+  tagHandlers["&sim"] = make_handler(&PyDocConverter::handleHtmlEntity, "~");
+  tagHandlers["&le"] = make_handler(&PyDocConverter::handleHtmlEntity, "<=");
+  tagHandlers["&ge"] = make_handler(&PyDocConverter::handleHtmlEntity, ">=");
+  tagHandlers["&larr"] = make_handler(&PyDocConverter::handleHtmlEntity, "<--");
+  tagHandlers["&rarr"] = make_handler(&PyDocConverter::handleHtmlEntity, "-->");
 }
 
 PyDocConverter::PyDocConverter(int flags) :
@@ -320,14 +330,14 @@ void PyDocConverter::translateEntity(DoxygenEntity & doxyEntity,
 
 void PyDocConverter::handleParagraph(DoxygenEntity& tag,
                                      std::string& translatedComment,
-                                     std::string &arg)
+                                     const std::string&)
 {
-  translatedComment += translateSubtree(tag) + arg;
+  translatedComment += translateSubtree(tag);
 }
 
 void PyDocConverter::handlePlainString(DoxygenEntity& tag,
                                        std::string& translatedComment,
-                                       std::string&)
+                                       const std::string&)
 {
   translatedComment += tag.data;
   if (tag.data.size() && tag.data[tag.data.size() - 1] != ' ')
@@ -336,7 +346,7 @@ void PyDocConverter::handlePlainString(DoxygenEntity& tag,
 
 void PyDocConverter::handleTagVerbatim(DoxygenEntity& tag,
                                        std::string& translatedComment,
-                                       std::string &arg)
+                                       const std::string &arg)
 {
   translatedComment += arg + " ";
   for (DoxygenEntityListCIt it = tag.entityList.begin();
@@ -347,24 +357,23 @@ void PyDocConverter::handleTagVerbatim(DoxygenEntity& tag,
 
 void PyDocConverter::handleTagMessage(DoxygenEntity& tag,
                                       std::string& translatedComment,
-                                      std::string &arg)
+                                      const std::string &arg)
 {
-  std::string dummy;
   translatedComment += arg;
-  handleParagraph(tag, translatedComment, dummy);
+  handleParagraph(tag, translatedComment);
 }
 
 void PyDocConverter::handleTagChar(DoxygenEntity& tag,
-                                   std::string& translatedComment, std::string&)
+                                   std::string& translatedComment,
+                                   const std::string&)
 {
   translatedComment += tag.typeOfEntity;
 }
 
 void PyDocConverter::handleTagIf(DoxygenEntity& tag,
                                  std::string& translatedComment,
-                                 std::string &arg)
+                                 const std::string &arg)
 {
-  std::string dummy;
   translatedComment += arg;
   if (tag.entityList.size()) {
     translatedComment += tag.entityList.begin()->data;
@@ -374,19 +383,19 @@ void PyDocConverter::handleTagIf(DoxygenEntity& tag,
 }
 
 void PyDocConverter::handleTagPar(DoxygenEntity& tag,
-                                  std::string& translatedComment, std::string&)
+                                  std::string& translatedComment,
+                                  const std::string&)
 {
-  std::string dummy;
   translatedComment += "Title: ";
   if (tag.entityList.size())
     translatedComment += tag.entityList.begin()->data;
   tag.entityList.pop_front();
-  handleParagraph(tag, translatedComment, dummy);
+  handleParagraph(tag, translatedComment);
 }
 
 void PyDocConverter::handleTagImage(DoxygenEntity& tag,
                                     std::string& translatedComment,
-                                    std::string&)
+                                    const std::string&)
 {
   if (tag.entityList.size() < 2)
     return;
@@ -400,9 +409,8 @@ void PyDocConverter::handleTagImage(DoxygenEntity& tag,
 
 void PyDocConverter::handleTagParam(DoxygenEntity& tag,
                                     std::string& translatedComment,
-                                    std::string&)
+                                    const std::string&)
 {
-  std::string dummy;
   if (tag.entityList.size() < 2)
     return;
 
@@ -414,15 +422,14 @@ void PyDocConverter::handleTagParam(DoxygenEntity& tag,
     paramType = "none";
 
   translatedComment += "  " + paramNameEntity.data + " (" + paramType + ") --";
-  handleParagraph(tag, translatedComment, dummy);
+  handleParagraph(tag, translatedComment);
 }
 
 
 void PyDocConverter::handleTagRef(DoxygenEntity& tag,
                                   std::string& translatedComment,
-                                  std::string&)
+                                  const std::string&)
 {
-  std::string dummy;
   if (!tag.entityList.size())
     return;
 
@@ -438,7 +445,7 @@ void PyDocConverter::handleTagRef(DoxygenEntity& tag,
 
 void PyDocConverter::handleTagWrap(DoxygenEntity& tag,
                                    std::string& translatedComment,
-                                   std::string &arg)
+                                   const std::string &arg)
 {
   if (tag.entityList.size()) { // do not include empty tags
     std::string tagData = translateSubtree(tag);
@@ -454,7 +461,7 @@ void PyDocConverter::handleTagWrap(DoxygenEntity& tag,
 
 void PyDocConverter::handleDoxyHtmlTag(DoxygenEntity& tag,
                                        std::string& translatedComment,
-                                       std::string &arg)
+                                       const std::string &arg)
 {
   std::string htmlTagArgs = tag.data;
   if (htmlTagArgs == "/") {
@@ -467,7 +474,7 @@ void PyDocConverter::handleDoxyHtmlTag(DoxygenEntity& tag,
 
 void PyDocConverter::handleDoxyHtmlTagNoParam(DoxygenEntity& tag,
                                               std::string& translatedComment,
-                                              std::string &arg)
+                                              const std::string &arg)
 {
   std::string htmlTagArgs = tag.data;
   if (htmlTagArgs == "/") {
@@ -479,7 +486,7 @@ void PyDocConverter::handleDoxyHtmlTagNoParam(DoxygenEntity& tag,
 
 void PyDocConverter::handleDoxyHtmlTag_A(DoxygenEntity& tag,
                                          std::string& translatedComment,
-                                         std::string &arg)
+                                         const std::string &arg)
 {
   std::string htmlTagArgs = tag.data;
   if (htmlTagArgs == "/") {
@@ -498,7 +505,7 @@ void PyDocConverter::handleDoxyHtmlTag_A(DoxygenEntity& tag,
 
 void PyDocConverter::handleDoxyHtmlTag2(DoxygenEntity& tag,
                                         std::string& translatedComment,
-                                        std::string &arg)
+                                        const std::string &arg)
 {
   std::string htmlTagArgs = tag.data;
   if (htmlTagArgs == "/") {
@@ -511,7 +518,7 @@ void PyDocConverter::handleDoxyHtmlTag2(DoxygenEntity& tag,
 
 void PyDocConverter::handleDoxyHtmlTag_tr(DoxygenEntity& tag,
                                           std::string& translatedComment,
-                                          std::string &)
+                                          const std::string &)
 {
   std::string htmlTagArgs = tag.data;
   size_t nlPos = translatedComment.rfind('\n');
@@ -543,7 +550,7 @@ void PyDocConverter::handleDoxyHtmlTag_tr(DoxygenEntity& tag,
 
 void PyDocConverter::handleDoxyHtmlTag_th(DoxygenEntity& tag,
                                           std::string& translatedComment,
-                                          std::string &)
+                                          const std::string &)
 {
   std::string htmlTagArgs = tag.data;
   if (htmlTagArgs == "/") {
@@ -556,7 +563,7 @@ void PyDocConverter::handleDoxyHtmlTag_th(DoxygenEntity& tag,
 
 void PyDocConverter::handleDoxyHtmlTag_td(DoxygenEntity& tag,
                                           std::string& translatedComment,
-                                          std::string &)
+                                          const std::string &)
 {
   std::string htmlTagArgs = tag.data;
   if (htmlTagArgs == "/") {
@@ -568,14 +575,15 @@ void PyDocConverter::handleDoxyHtmlTag_td(DoxygenEntity& tag,
 
 void PyDocConverter::handleHtmlEntity(DoxygenEntity&,
                                       std::string& translatedComment,
-                                      std::string &arg)
+                                      const std::string &arg)
 {
   // html entities
   translatedComment += arg;
 }
 
 void PyDocConverter::handleNewLine(DoxygenEntity&,
-                                   std::string& translatedComment, std::string&)
+                                   std::string& translatedComment,
+                                   const std::string&)
 {
   translatedComment += "\n";
 }
diff --git a/Source/DoxygenTranslator/src/PyDocConverter.h b/Source/DoxygenTranslator/src/PyDocConverter.h
index e037db9ce..921e1c09e 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.h
+++ b/Source/DoxygenTranslator/src/PyDocConverter.h
@@ -56,78 +56,79 @@ protected:
    * arg - some string argument to easily pass it through lookup table
    */
   typedef void (PyDocConverter::*tagHandler)(DoxygenEntity &tag,
-      std::string &translatedComment, std::string &arg);
+      std::string &translatedComment, const std::string &arg);
 
   /*
    * Wrap the command data with the some string
    * arg - string to wrap with, like '_' or '*'
    */
-  void handleTagWrap(DoxygenEntity &tag, std::string &translatedComment, std::string &arg);
+  void handleTagWrap(DoxygenEntity &tag, std::string &translatedComment, const std::string &arg);
   /*
    * Just prints new line
    */
-  void handleNewLine(DoxygenEntity &tag, std::string &translatedComment, std::string &arg);
+  void handleNewLine(DoxygenEntity &tag, std::string &translatedComment, const std::string &arg);
   /*
    * Print the name of tag to the output, used for escape-commands
    */
-  void handleTagChar(DoxygenEntity &tag, std::string &translatedComment, std::string &arg);
+  void handleTagChar(DoxygenEntity &tag, std::string &translatedComment, const std::string &arg);
   /*
    * Print only the content and strip original tag
    */
-  void handleParagraph(DoxygenEntity &tag, std::string &translatedComment, std::string &arg);
+  void handleParagraph(DoxygenEntity &tag, std::string &translatedComment,
+                       const std::string &arg = std::string());
   /*
    * Print only data part of code
    */
-  void handlePlainString(DoxygenEntity &tag, std::string &translatedComment, std::string &arg);
+  void handlePlainString(DoxygenEntity &tag, std::string &translatedComment, const std::string &arg);
 
   /**
    * Copies verbatim args of the tag to output, used for commands like \f$, ...
    */
   void handleTagVerbatim(DoxygenEntity& tag,
                             std::string& translatedComment,
-                            std::string &arg);
+                            const std::string &arg);
 
   /*
    * Print the if-elseif-else-endif section
    */
-  void handleTagIf(DoxygenEntity &tag, std::string &translatedComment, std::string &arg);
+  void handleTagIf(DoxygenEntity &tag, std::string &translatedComment, const std::string &arg);
   /*
    * Prints the specified message, than the contents of the tag
    * arg - message
    */
-  void handleTagMessage(DoxygenEntity &tag, std::string &translatedComment, std::string &arg);
+  void handleTagMessage(DoxygenEntity &tag, std::string &translatedComment, const std::string &arg);
   /*
    * Insert 'Title: ...'
    */
-  void handleTagPar(DoxygenEntity &tag, std::string &translatedComment, std::string &arg);
+  void handleTagPar(DoxygenEntity &tag, std::string &translatedComment, const std::string &arg);
   /*
    * Insert 'Image: ...'
    */
-  void handleTagImage(DoxygenEntity &tag, std::string &translatedComment, std::string &arg);
+  void handleTagImage(DoxygenEntity &tag, std::string &translatedComment, const std::string &arg);
   /*
    * Format nice param description with type information
    */
-  void handleTagParam(DoxygenEntity &tag, std::string &translatedComment, std::string &arg);
+  void handleTagParam(DoxygenEntity &tag, std::string &translatedComment, const std::string &arg);
   /*
    * Writes text for \ref tag. 
    */
-  void handleTagRef(DoxygenEntity& tag, std::string& translatedComment, std::string&);
-    
+  void handleTagRef(DoxygenEntity& tag, std::string& translatedComment, const std::string &arg);
+
   /* Handles HTML tags recognized by Doxygen, like <A ...>, <ul>, <table>, ... */
 
-  void handleDoxyHtmlTag(DoxygenEntity& tag, std::string& translatedComment, std::string &arg);
+  void handleDoxyHtmlTag(DoxygenEntity& tag, std::string& translatedComment, const std::string &arg);
 
   /** Does not output params of HTML tag, for example in <table border='1'>
    * 'border=1' is not written to output.
    */
   void handleDoxyHtmlTagNoParam(DoxygenEntity& tag,
                                     std::string& translatedComment,
-                                    std::string &arg);
+                                    const std::string &arg);
 
   /** Translates tag <a href = "url">text</a> to: text ("url"). */
   void handleDoxyHtmlTag_A(DoxygenEntity& tag,
                               std::string& translatedComment,
-                              std::string &arg);
+                              const std::string &arg);
 
   /*
    * Handles HTML tags, which are translated to markdown-like syntax, for example
@@ -135,22 +136,22 @@ protected:
    */
   void handleDoxyHtmlTag2(DoxygenEntity& tag,
                              std::string& translatedComment,
-                             std::string &arg);
+                             const std::string &arg);
 
   /* Handles HTML table, tag <tr> */
   void handleDoxyHtmlTag_tr(DoxygenEntity& tag, std::string& translatedComment,
-                               std::string &arg);
+                               const std::string &arg);
 
   /* Handles HTML table, tag <th> */
   void handleDoxyHtmlTag_th(DoxygenEntity& tag, std::string& translatedComment,
-                               std::string &arg);
+                               const std::string &arg);
 
   /* Handles HTML table, tag <td> */
   void handleDoxyHtmlTag_td(DoxygenEntity& tag, std::string& translatedComment,
-                                std::string &arg);
+                                const std::string &arg);
 
   /* Handles HTML entities recognized by Doxygen, like &lt;, &copy;, ... */
-  void handleHtmlEntity(DoxygenEntity&, std::string& translatedComment, std::string &arg);
+  void handleHtmlEntity(DoxygenEntity&, std::string& translatedComment, const std::string &arg);
 
 
   /*
@@ -168,10 +169,18 @@ protected:
 private:
   // temporary thing, should be refactored somehow
   Node *currentNode;
+
   // this contains the handler pointer and one string argument
-  static std::map<std::string, std::pair<tagHandler, std::string> > tagHandlers;
+  typedef std::map<std::string, std::pair<tagHandler, std::string> > TagHandlersMap;
+  static TagHandlersMap tagHandlers;
+
   // this contains the sections tittles, like 'Arguments:' or 'Notes:', that are printed only once
   static std::map<std::string, std::string> sectionTitles;
+
+  // Helper functions for fillStaticTables(): make a new tag handler object.
+  TagHandlersMap::mapped_type make_handler(tagHandler handler);
+  TagHandlersMap::mapped_type make_handler(tagHandler handler, const char* arg);
+
   void fillStaticTables();
 };
 

From 329d64bb044d9248eeb0b692c87426826a57f2b4 Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Sun, 15 Jun 2014 23:40:34 +0200
Subject: [PATCH 207/314] Show the diff when a Doxygen test fails.

This is much more readable than just dumping the expected output and the
actual result produced by SWIG, especially for longer Doxygen comments.

Remove the bunch of commented out code and also do not save the results
in the file, this is not very useful as it's not even clear which test the
files correspond to and annoying when these files are left over later. If
anybody really uses this functionality, it ought to be optional.
---
 Examples/test-suite/python/commentVerifier.py | 31 +++----------------
 1 file changed, 5 insertions(+), 26 deletions(-)

diff --git a/Examples/test-suite/python/commentVerifier.py b/Examples/test-suite/python/commentVerifier.py
index e231565c2..ea840935a 100644
--- a/Examples/test-suite/python/commentVerifier.py
+++ b/Examples/test-suite/python/commentVerifier.py
@@ -1,29 +1,8 @@
-
 def check(got, expected):
-  #if got is Null
-  #  raise RuntimeError('Expected comment string\n')
-  #gotStr = string.replace(got, ' ', '')
-  #gotStr = string.replace(gotStr, '\n', '')
-  # gotStr = string.replace(gotStr, '\t', '')
-  #expectedStr = string.replace(expected, ' ', '')
-  #expectedStr = string.replace(expectedStr, '\n', '')
-  #expectedStr = string.replace(expectedStr, '\t', '')
-
-  if got == None:  # when there is no commant attached to a class or function
+  if got is None:  # Absence of comment is equivalent to empty comment.
       got = ''
 
-  if not got == expected:
-    print("\n\n////////////////////////////////////////////////////////////////////////")
-
-    expectedFileName = "expected.txt"
-    gotFileName = "got.txt"
-    print("Output is also saved to files '" + expectedFileName + \
-                                   "' and '" + gotFileName + "'")
-
-    expectedFile = open(expectedFileName, "w")
-    expectedFile.write(expected)
-    expectedFile.close()
-    gotFile = open(gotFileName, "w")
-    gotFile.write(got)
-    gotFile.close()
-    raise RuntimeError("Expected: [" + str(expected) + "]\n" + "Got     : [" + str(got) + "]\n")
+  if got != expected:
+    from difflib import unified_diff
+    diff = unified_diff(expected.splitlines(True), got.splitlines(True), "expected", "got")
+    raise RuntimeError("Comments don't match:\n" + "".join(diff))

From b374aad0da6d219f892bb153b6bd4e55010dd1dd Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Sun, 15 Jun 2014 23:42:41 +0200
Subject: [PATCH 208/314] Use Sphinx-compatible docstring format in
 PyDocConverter.

Use the more or less standard :param:, :type:, :return: and :raises: in the
function/methods descriptions.

Update the output expected from the Python tests accordingly.
---
 .../python/doxygen_basic_translate_runme.py   | 10 ++--
 .../python/doxygen_misc_constructs_runme.py   | 17 ++++---
 .../python/doxygen_parsing_runme.py           | 28 +++++-----
 .../doxygen_translate_all_tags_runme.py       | 22 ++++----
 .../python/doxygen_translate_runme.py         | 24 ++++-----
 .../DoxygenTranslator/src/PyDocConverter.cpp  | 51 ++++++++++++-------
 Source/DoxygenTranslator/src/PyDocConverter.h |  8 +++
 7 files changed, 94 insertions(+), 66 deletions(-)

diff --git a/Examples/test-suite/python/doxygen_basic_translate_runme.py b/Examples/test-suite/python/doxygen_basic_translate_runme.py
index dfc6688d0..080f47c92 100644
--- a/Examples/test-suite/python/doxygen_basic_translate_runme.py
+++ b/Examples/test-suite/python/doxygen_basic_translate_runme.py
@@ -13,7 +13,7 @@ commentVerifier.check(doxygen_basic_translate.function.__doc__,
 
     Author: Some author
 
-    Return: Some number
+    :return: Some number
 
     See also: function2
     """
@@ -65,15 +65,15 @@ commentVerifier.check(doxygen_basic_translate.function5.__doc__,
 commentVerifier.check(doxygen_basic_translate.function6.__doc__,
     """
     Test for default args
-    Arguments:
-      a (int) -- Some parameter, default is 42
+    :type a: int
+    :param a: Some parameter, default is 42
     """
 )
 commentVerifier.check(doxygen_basic_translate.function7.__doc__,
     """
     Test for a parameter with difficult type
     (mostly for python)
-    Arguments:
-      a (Shape::superType *[10]) -- Very strange param
+    :type a: Shape::superType *[10]
+    :param a: Very strange param
     """
 )
diff --git a/Examples/test-suite/python/doxygen_misc_constructs_runme.py b/Examples/test-suite/python/doxygen_misc_constructs_runme.py
index 1517a7279..38a2baf2b 100644
--- a/Examples/test-suite/python/doxygen_misc_constructs_runme.py
+++ b/Examples/test-suite/python/doxygen_misc_constructs_runme.py
@@ -10,10 +10,12 @@ commentVerifier.check(doxygen_misc_constructs.getAddress.__doc__,
     r"""
     Returns address of file line.
 
-    Arguments:
-      fileName (int &) -- name of the file, where the source line is located
-      line (int) -- line number
-      isGetSize (bool) -- if set, for every object location both address and size are returned
+    :type fileName: int &
+    :param fileName: name of the file, where the source line is located
+    :type line: int
+    :param line: line number
+    :type isGetSize: bool
+    :param isGetSize: if set, for every object location both address and size are returned
 
     Connection::getId() 
 
@@ -127,8 +129,8 @@ commentVerifier.check(doxygen_misc_constructs.cycle.__doc__,
     Similar __for__: double colon.
 
     Spaces at the start of line should be taken into account:
-    Arguments:
-      id (int) -- used as prefix in log
+    :type id: int
+    :param id: used as prefix in log
         statements. The default value is empty string, which is OK if
         there is only one app. instance. Example:
         
@@ -139,6 +141,7 @@ commentVerifier.check(doxygen_misc_constructs.cycle.__doc__,
             main_ctrl.setBP("func1");
         
 
-      fileName (char *) -- name of the log file
+    :type fileName: char *
+    :param fileName: name of the log file
     """
 );
diff --git a/Examples/test-suite/python/doxygen_parsing_runme.py b/Examples/test-suite/python/doxygen_parsing_runme.py
index 7b4e03424..1e5dd7e00 100644
--- a/Examples/test-suite/python/doxygen_parsing_runme.py
+++ b/Examples/test-suite/python/doxygen_parsing_runme.py
@@ -27,18 +27,20 @@ commentVerifier.check(doxygen_parsing.SomeAnotherClass.classMethodExtended.__doc
     r"""
         The class method with parameter
 
-        Arguments:
-          a (int) -- Parameter a
-          b (int) -- Parameter b
+        :type a: int
+        :param a: Parameter a
+        :type b: int
+        :param b: Parameter b
         """
 )
 commentVerifier.check(doxygen_parsing.SomeAnotherClass.classMethodExtended2.__doc__, 
     r"""
         The class method with parameter
 
-        Arguments:
-          a (int) -- Parameter a
-          b (int) -- Parameter b
+        :type a: int
+        :param a: Parameter a
+        :type b: int
+        :param b: Parameter b
         """
 )
 commentVerifier.check(doxygen_parsing.SomeAnotherStruct.structMethod.__doc__,
@@ -49,16 +51,18 @@ commentVerifier.check(doxygen_parsing.SomeAnotherStruct.structMethodExtended.__d
     r"""
         The struct method with parameter
 
-        Arguments:
-          a (int) -- Parameter a
-          b (int) -- Parameter b
+        :type a: int
+        :param a: Parameter a
+        :type b: int
+        :param b: Parameter b
         """
 )
 commentVerifier.check(doxygen_parsing.SomeAnotherStruct.structMethodExtended2.__doc__,
     r"""
         The struct method with parameter
 
-        Arguments:
-          a (int) -- Parameter a
-          b (int) -- Parameter b
+        :type a: int
+        :param a: Parameter a
+        :type b: int
+        :param b: Parameter b
         """)
diff --git a/Examples/test-suite/python/doxygen_translate_all_tags_runme.py b/Examples/test-suite/python/doxygen_translate_all_tags_runme.py
index f1263f39e..0128ca5aa 100644
--- a/Examples/test-suite/python/doxygen_translate_all_tags_runme.py
+++ b/Examples/test-suite/python/doxygen_translate_all_tags_runme.py
@@ -79,7 +79,7 @@ r"""
 
     _italicword_
 
-    emphazedWord 
+    emphazedWord
 
 
 
@@ -89,7 +89,7 @@ r"""
 
 commentVerifier.check(doxygen_translate_all_tags.func04.__doc__,
 r"""
-    Throws: SuperError
+    :raises: SuperError
 
 
 
@@ -219,8 +219,8 @@ r"""
 
 
 
-    Arguments:
-      a (int) -- the first param
+    :type a: int
+    :param a: the first param
 
 
 
@@ -255,11 +255,11 @@ r"""
 
     Another remarks section
 
-    Return: Whatever
+    :return: Whatever
 
-    it
+    :return: it
 
-    Returns: may return
+    :return: may return
 
     """)
 
@@ -295,17 +295,17 @@ r"""
 
 
 
-    Throw: superException
+    :raises: superException
 
-    Throws: RuntimeError
+    :raises: RuntimeError
     """)
 
 commentVerifier.check(doxygen_translate_all_tags.func10.__doc__,
 r"""
     TODO: Some very important task
 
-    Arguments:
-      b (float) -- B is mentioned again...
+    :type b: float
+    :param b: B is mentioned again...
 
 
 
diff --git a/Examples/test-suite/python/doxygen_translate_runme.py b/Examples/test-suite/python/doxygen_translate_runme.py
index 4e2338124..2b22c7380 100644
--- a/Examples/test-suite/python/doxygen_translate_runme.py
+++ b/Examples/test-suite/python/doxygen_translate_runme.py
@@ -37,7 +37,7 @@ r"""
     Example: someFile.txt
     Some details on using the example
 
-    Throws: SuperError
+    :raises: SuperError
 
     If: ANOTHERCONDITION {
       First part of comment
@@ -88,18 +88,18 @@ r"""
     The paragraph text.
     Maybe even multiline
 
-    Arguments:
-      a (int) -- the first param
+    :type a: int
+    :param a: the first param
 
     Remarks: Some remark text
 
     Another remarks section
 
-    Return: Whatever
+    :return: Whatever
 
-    it
+    :return: it
 
-    Returns: may return
+    :return: may return
 
     See also: someOtherMethod
 
@@ -107,14 +107,14 @@ r"""
 
     Since: version 0.0.0.1
 
-    Throw: superException
+    :raises: superException
 
-    Throws: RuntimeError
+    :raises: RuntimeError
 
     TODO: Some very important task
 
-    Arguments:
-      b (float) -- B is mentioned again...
+    :type b: float
+    :param b: B is mentioned again...
 
 
     very long
@@ -225,8 +225,8 @@ commentVerifier.check(doxygen_translate.htmlTableFunction.__doc__,
 r"""
     The meaning of flags:
 
-    Arguments:
-      byFlags (int) -- bits marking required items:
+    :type byFlags: int
+    :param byFlags: bits marking required items:
       
       | Size in bits| Items Required |
       --------------------------------
diff --git a/Source/DoxygenTranslator/src/PyDocConverter.cpp b/Source/DoxygenTranslator/src/PyDocConverter.cpp
index dee98a873..ee9535953 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/PyDocConverter.cpp
@@ -50,21 +50,13 @@ void PyDocConverter::fillStaticTables()
   sectionTitles["copyright"] = "Copyright: ";
   sectionTitles["deprecated"] = "Deprecated: ";
   sectionTitles["example"] = "Example: ";
-  sectionTitles["exception"] = "Throws: ";
-  sectionTitles["param"] = "Arguments:\n";
-  sectionTitles["tparam"] = "Arguments:\n";
   sectionTitles["note"] = "Notes: ";
   sectionTitles["remark"] = "Remarks: ";
   sectionTitles["remarks"] = "Remarks: ";
   sectionTitles["warning"] = "Warning: ";
-  sectionTitles["result"] = "Return: ";
-  sectionTitles["return"] = "Return: ";
-  sectionTitles["returns"] = "Returns: ";
 //  sectionTitles["sa"] = "See also: ";
 //  sectionTitles["see"] = "See also: ";
   sectionTitles["since"] = "Since: ";
-  sectionTitles["throw"] = "Throw: ";
-  sectionTitles["throws"] = "Throws: ";
   sectionTitles["todo"] = "TODO: ";
   sectionTitles["version"] = "Version: ";
 
@@ -100,7 +92,9 @@ void PyDocConverter::fillStaticTables()
   tagHandlers["details"] = make_handler(&PyDocConverter::handleParagraph);
   tagHandlers["em"] = make_handler(&PyDocConverter::handleParagraph, " ");
   tagHandlers["example"] = make_handler(&PyDocConverter::handleParagraph);
-  tagHandlers["exception"] = make_handler(&PyDocConverter::handleParagraph);
+  tagHandlers["exception"] =
+  tagHandlers["throw"] =
+  tagHandlers["throws"] = make_handler(&PyDocConverter::handleTagException);
   tagHandlers["htmlonly"] = make_handler(&PyDocConverter::handleParagraph);
   tagHandlers["invariant"] = make_handler(&PyDocConverter::handleParagraph);
   tagHandlers["latexonly"] = make_handler(&PyDocConverter::handleParagraph);
@@ -110,9 +104,6 @@ void PyDocConverter::fillStaticTables()
   tagHandlers["p"] = make_handler(&PyDocConverter::handleParagraph);
   tagHandlers["partofdescription"] = make_handler(&PyDocConverter::handleParagraph);
   tagHandlers["rtfonly"] = make_handler(&PyDocConverter::handleParagraph);
-  tagHandlers["return"] = make_handler(&PyDocConverter::handleParagraph);
-  tagHandlers["returns"] = make_handler(&PyDocConverter::handleParagraph);
-  tagHandlers["result"] = make_handler(&PyDocConverter::handleParagraph);
   tagHandlers["remark"] = make_handler(&PyDocConverter::handleParagraph);
   tagHandlers["remarks"] = make_handler(&PyDocConverter::handleParagraph);
   tagHandlers["sa"] = make_handler(&PyDocConverter::handleTagMessage, "See also: ");
@@ -120,8 +111,6 @@ void PyDocConverter::fillStaticTables()
       "See also: ");
   tagHandlers["since"] = make_handler(&PyDocConverter::handleParagraph);
   tagHandlers["short"] = make_handler(&PyDocConverter::handleParagraph);
-  tagHandlers["throw"] = make_handler(&PyDocConverter::handleParagraph);
-  tagHandlers["throws"] = make_handler(&PyDocConverter::handleParagraph);
   tagHandlers["todo"] = make_handler(&PyDocConverter::handleParagraph);
   tagHandlers["version"] = make_handler(&PyDocConverter::handleParagraph);
   tagHandlers["verbatim"] = make_handler(&PyDocConverter::handleParagraph);
@@ -144,9 +133,13 @@ void PyDocConverter::fillStaticTables()
           " convenience.\nIt differs from the above function only in what"
           " argument(s) it accepts.");
   tagHandlers["par"] = make_handler(&PyDocConverter::handleTagPar);
-  tagHandlers["param"] = make_handler(&PyDocConverter::handleTagParam);
+  tagHandlers["param"] =
   tagHandlers["tparam"] = make_handler(&PyDocConverter::handleTagParam);
   tagHandlers["ref"] = make_handler(&PyDocConverter::handleTagRef);
+  tagHandlers["result"] =
+  tagHandlers["return"] =
+  tagHandlers["returns"] = make_handler(&PyDocConverter::handleTagReturn);
+
   // this command just prints it's contents
   // (it is internal command of swig's parser, contains plain text)
   tagHandlers["plainstd::string"] = make_handler(&PyDocConverter::handlePlainString);
@@ -417,11 +410,31 @@ void PyDocConverter::handleTagParam(DoxygenEntity& tag,
   DoxygenEntity paramNameEntity = *tag.entityList.begin();
   tag.entityList.pop_front();
 
-  std::string paramType = getParamType(paramNameEntity.data);
-  if (!paramType.size())
-    paramType = "none";
+  const std::string& paramName = paramNameEntity.data;
 
-  translatedComment += "  " + paramNameEntity.data + " (" + paramType + ") --";
+  const std::string paramType = getParamType(paramName);
+  if (!paramType.empty())
+    translatedComment += ":type " + paramName + ": " + paramType + "\n";
+
+  translatedComment += ":param " + paramName + ":";
+  handleParagraph(tag, translatedComment);
+}
+
+
+void PyDocConverter::handleTagReturn(DoxygenEntity &tag,
+                                     std::string &translatedComment,
+                                     const std::string &)
+{
+  translatedComment += ":return: ";
+  handleParagraph(tag, translatedComment);
+}
+
+
+void PyDocConverter::handleTagException(DoxygenEntity &tag,
+                                        std::string &translatedComment,
+                                        const std::string &)
+{
+  translatedComment += ":raises: ";
   handleParagraph(tag, translatedComment);
 }
 
diff --git a/Source/DoxygenTranslator/src/PyDocConverter.h b/Source/DoxygenTranslator/src/PyDocConverter.h
index 921e1c09e..435c18c28 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.h
+++ b/Source/DoxygenTranslator/src/PyDocConverter.h
@@ -71,6 +71,10 @@ protected:
    * Print the name of tag to the output, used for escape-commands
    */
   void handleTagChar(DoxygenEntity &tag, std::string &translatedComment, const std::string &arg);
+  /*
+   * Format the contents of the \exception tag or its synonyms.
+   */
+  void handleTagException(DoxygenEntity &tag, std::string &translatedComment, const std::string &arg);
   /*
    * Print only the content and strip original tag
    */
@@ -109,6 +113,10 @@ protected:
    * Format nice param description with type information
    */
   void handleTagParam(DoxygenEntity &tag, std::string &translatedComment, const std::string &arg);
+  /*
+   * Format the contents of the \return tag or its synonyms.
+   */
+  void handleTagReturn(DoxygenEntity &tag, std::string &translatedComment, const std::string &arg);
   /*
    * Writes text for \ref tag. 
    */

From 7d2743a0bb93b5b9fff597368216ad2163108719 Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Mon, 16 Jun 2014 00:01:36 +0200
Subject: [PATCH 209/314] Use reST inline markup in PyDocConverter instead of
 Markdown.

reST is standard Python markup, so use *...*, ``...`` and so on instead of
_..._, '...' etc.

No other changes even though the mapping of some Doxygen tags to markup used
for them seems suspicions (e.g. \var almost certainly should be the same as
\em).
---
 .../python/doxygen_basic_translate_runme.py   | 12 +++---
 .../python/doxygen_misc_constructs_runme.py   | 18 ++++----
 .../doxygen_translate_all_tags_runme.py       | 22 +++++-----
 .../python/doxygen_translate_runme.py         | 42 +++++++++----------
 .../DoxygenTranslator/src/PyDocConverter.cpp  | 26 ++++++------
 5 files changed, 60 insertions(+), 60 deletions(-)

diff --git a/Examples/test-suite/python/doxygen_basic_translate_runme.py b/Examples/test-suite/python/doxygen_basic_translate_runme.py
index 080f47c92..a0c921829 100644
--- a/Examples/test-suite/python/doxygen_basic_translate_runme.py
+++ b/Examples/test-suite/python/doxygen_basic_translate_runme.py
@@ -30,13 +30,13 @@ commentVerifier.check(doxygen_basic_translate.function3.__doc__,
     Overload 1:
     ----------------------------------------------------------------
     A test for overloaded functions
-    This is function __one__
+    This is function **one**
 
     ----------------------------------------------------------------
     Overload 2:
     ----------------------------------------------------------------
     A test for overloaded functions
-    This is function __two__
+    This is function **two**
 
     """
 )
@@ -44,11 +44,11 @@ commentVerifier.check(doxygen_basic_translate.function4.__doc__,
     """
     A test of some mixed tag usage
     If: CONDITION {
-    This _code_ fragment shows us something .
+    This *code* fragment shows us something .
     Title: Minuses:
-     -it\'s senseless
-     -it\'s stupid
-     -it\'s null
+    * it\'s senseless
+    * it\'s stupid
+    * it\'s null
 
     Warning: This may not work as expected
 
diff --git a/Examples/test-suite/python/doxygen_misc_constructs_runme.py b/Examples/test-suite/python/doxygen_misc_constructs_runme.py
index 38a2baf2b..2c68fd65d 100644
--- a/Examples/test-suite/python/doxygen_misc_constructs_runme.py
+++ b/Examples/test-suite/python/doxygen_misc_constructs_runme.py
@@ -41,8 +41,8 @@ commentVerifier.check(doxygen_misc_constructs.CConnectionConfig.__doc__,
 
 commentVerifier.check(doxygen_misc_constructs.waitTime.__doc__,
     r"""
-    Determines how long the 'isystem.connect' should wait for running 
-    instances to respond. Only one of 'lfWaitXXX' flags from IConnect::ELaunchFlags
+    Determines how long the ``isystem.connect`` should wait for running 
+    instances to respond. Only one of ``lfWaitXXX`` flags from IConnect::ELaunchFlags
     may be specified.
     """
 )
@@ -84,7 +84,7 @@ commentVerifier.check(doxygen_misc_constructs.isNoSpaceValidC.__doc__,
 
 commentVerifier.check(doxygen_misc_constructs.backslashA.__doc__,
     r"""
-    Backslash following'word' is a valid doxygen command. Output contains
+    Backslash following``word`` is a valid doxygen command. Output contains
     'followingword' with 'word' in code font.
     """
 )
@@ -108,8 +108,8 @@ commentVerifier.check(doxygen_misc_constructs.backslashB.__doc__,
 
 commentVerifier.check(doxygen_misc_constructs.backslashC.__doc__,
     r"""
-    Backslash e at end of _line_ froze SWIG 
-    _with_ old comment parser. 
+    Backslash e at end of *line* froze SWIG 
+    *with* old comment parser. 
 
     See also: MyClass::fun(char,
      float)
@@ -124,9 +124,9 @@ commentVerifier.check(doxygen_misc_constructs.cycle.__doc__,
     ['retVal < 10', 'g_counter == 23 && g_mode & 3']
 
 
-    Both words should be emphasized __isystem.connect__.
-    But not the last period. For __example__, comma should not be emphasized.
-    Similar __for__: double colon.
+    Both words should be emphasized **isystem.connect**.
+    But not the last period. For **example**, comma should not be emphasized.
+    Similar **for**: double colon.
 
     Spaces at the start of line should be taken into account:
     :type id: int
@@ -136,7 +136,7 @@ commentVerifier.check(doxygen_misc_constructs.cycle.__doc__,
         
             ctrl.setBP("func1");
         
-        If we set the id to 'main_', we get:
+        If we set the id to ``main_``, we get:
         
             main_ctrl.setBP("func1");
         
diff --git a/Examples/test-suite/python/doxygen_translate_all_tags_runme.py b/Examples/test-suite/python/doxygen_translate_all_tags_runme.py
index 0128ca5aa..1913eaf42 100644
--- a/Examples/test-suite/python/doxygen_translate_all_tags_runme.py
+++ b/Examples/test-suite/python/doxygen_translate_all_tags_runme.py
@@ -8,13 +8,13 @@ import commentVerifier
 
 commentVerifier.check(doxygen_translate_all_tags.func01.__doc__,
 r"""
-    _Hello_
+    *Hello*
 
 
 
 
 
-     -some list item
+    * some list item
 
     This is attention!
     You were warned!
@@ -22,13 +22,13 @@ r"""
     Authors: lots of them
     Author: Zubr
 
-    __boldword__
+    **boldword**
 
     Some brief description,
     extended to many lines.
 
     Not everything works right now...
-    'codeword'
+    ``codeword``
 
 
 
@@ -67,7 +67,7 @@ r"""
 
 commentVerifier.check(doxygen_translate_all_tags.func03.__doc__,
 r"""
-    Comment for __func03()__.
+    Comment for **func03()**.
 
 
 
@@ -77,7 +77,7 @@ r"""
 
 
 
-    _italicword_
+    *italicword*
 
     emphazedWord
 
@@ -155,7 +155,7 @@ r"""
 
 commentVerifier.check(doxygen_translate_all_tags.func06.__doc__,
 r"""
-    Comment for __func06()__.
+    Comment for **func06()**.
 
 
 
@@ -165,9 +165,9 @@ r"""
 
 
 
-     -Some unordered list
-     -With lots of items
-     -lots of lots of items
+    * Some unordered list
+    * With lots of items
+    * lots of lots of items
 
 
 
@@ -194,7 +194,7 @@ r"""
 
 commentVerifier.check(doxygen_translate_all_tags.func07.__doc__,
 r"""
-    Comment for __func07()__.
+    Comment for **func07()**.
 
 
 
diff --git a/Examples/test-suite/python/doxygen_translate_runme.py b/Examples/test-suite/python/doxygen_translate_runme.py
index 2b22c7380..028bf32fd 100644
--- a/Examples/test-suite/python/doxygen_translate_runme.py
+++ b/Examples/test-suite/python/doxygen_translate_runme.py
@@ -8,17 +8,17 @@ import commentVerifier
 
 commentVerifier.check(doxygen_translate.function.__doc__,
 r"""
-    _Hello_
+    *Hello*
 
-     -some list item
+    * some list item
 
     Authors: lots of them
 
     Author: Zubr
 
-    __boldword__
+    **boldword**
 
-    'codeword'
+    ``codeword``
 
     'citationword'
 
@@ -32,7 +32,7 @@ r"""
 
     Deprecated: Now use another function
 
-    _italicword_
+    *italicword*
 
     Example: someFile.txt
     Some details on using the example
@@ -61,9 +61,9 @@ r"""
 
 
 
-     -Some unordered list
-     -With lots of items
-     -lots of lots of items
+    * Some unordered list
+    * With lots of items
+    * lots of lots of items
 
 
 
@@ -139,14 +139,14 @@ r"""
     Test for html tags. See Doxygen doc for list of tags recognized by Doxygen.
 
     This is link ("http://acme.com/index.html")
-    __bold__
-    Quote: 
+    **bold**
+    Quote:
     Quotation block.
      ("http://www.worldwildlife.org/who/index.html")
 
 
     center
-    'this is code'
+    ``this is code``
 
 
     Starts an item title.
@@ -157,7 +157,7 @@ r"""
 
     Starts a section with a specific style (HTML only)
 
-    __Starts a piece of text displayed in an italic font.__
+    **Starts a piece of text displayed in an italic font.**
 
     'Form' does not generate any output.
 
@@ -169,7 +169,7 @@ r"""
 
     ### Heading 3
 
-    _Starts a piece of text displayed in an italic font._
+    *Starts a piece of text displayed in an italic font.*
     Input tag.
     Image: src="slika.png" 
     Meta tag.
@@ -177,8 +177,8 @@ r"""
 
 
 
-    - List item 1.
-    - List item 2.
+    * List item 1.
+    * List item 2.
 
 
 
@@ -189,7 +189,7 @@ r"""
     Starts a section of text displayed in a smaller font.
 
     'Starts an inline text fragment with a specific style.'
-    __Starts a section of bold text.__
+    **Starts a section of bold text.**
      Starts a piece of text displayed in subscript.
      Starts a piece of text displayed in superscript.
 
@@ -208,12 +208,12 @@ r"""
 
 
 
-    - List item 1.
-    - List item 2.
-    - List item 3.
+    * List item 1.
+    * List item 2.
+    * List item 3.
 
 
-    _Starts a piece of text displayed in an italic font._
+    *Starts a piece of text displayed in an italic font.*
 
 
     <u>underlined \b bold text - doxy commands are ignored inside 'htmlonly' section </u>
@@ -235,7 +235,7 @@ r"""
       | 17 - 32     |      4         |
       
       Almost all combinations of above flags are supported by
-      'htmlTable...' functions.
+      ``htmlTable...`` functions.
     """)                      
 
 
diff --git a/Source/DoxygenTranslator/src/PyDocConverter.cpp b/Source/DoxygenTranslator/src/PyDocConverter.cpp
index ee9535953..edeb056c1 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/PyDocConverter.cpp
@@ -60,12 +60,12 @@ void PyDocConverter::fillStaticTables()
   sectionTitles["todo"] = "TODO: ";
   sectionTitles["version"] = "Version: ";
 
-  tagHandlers["a"] = make_handler(&PyDocConverter::handleTagWrap, "_");
-  tagHandlers["b"] = make_handler(&PyDocConverter::handleTagWrap, "__");
+  tagHandlers["a"] = make_handler(&PyDocConverter::handleTagWrap, "*");
+  tagHandlers["b"] = make_handler(&PyDocConverter::handleTagWrap, "**");
   // \c command is translated as single quotes around next word
-  tagHandlers["c"] = make_handler(&PyDocConverter::handleTagWrap, "'"); // see markdown support in doxy, section 'code wraps'
+  tagHandlers["c"] = make_handler(&PyDocConverter::handleTagWrap, "``");
   tagHandlers["cite"] = make_handler(&PyDocConverter::handleTagWrap, "'");
-  tagHandlers["e"] = make_handler(&PyDocConverter::handleTagWrap, "_");
+  tagHandlers["e"] = make_handler(&PyDocConverter::handleTagWrap, "*");
   // these commands insert just a single char, some of them need to be escaped
   tagHandlers["$"] = make_handler(&PyDocConverter::handleTagChar);
   tagHandlers["@"] = make_handler(&PyDocConverter::handleTagChar);
@@ -117,7 +117,7 @@ void PyDocConverter::fillStaticTables()
   tagHandlers["warning"] = make_handler(&PyDocConverter::handleParagraph);
   tagHandlers["xmlonly"] = make_handler(&PyDocConverter::handleParagraph);
   // these commands have special handlers
-  tagHandlers["arg"] = make_handler(&PyDocConverter::handleTagMessage, " -");
+  tagHandlers["arg"] = make_handler(&PyDocConverter::handleTagMessage, "* ");
   tagHandlers["cond"] = make_handler(&PyDocConverter::handleTagMessage,
       "Conditional comment: ");
   tagHandlers["else"] = make_handler(&PyDocConverter::handleTagIf, "Else: ");
@@ -127,7 +127,7 @@ void PyDocConverter::fillStaticTables()
   tagHandlers["if"] = make_handler(&PyDocConverter::handleTagIf, "If: ");
   tagHandlers["ifnot"] = make_handler(&PyDocConverter::handleTagIf, "If not: ");
   tagHandlers["image"] = make_handler(&PyDocConverter::handleTagImage);
-  tagHandlers["li"] = make_handler(&PyDocConverter::handleTagMessage, " -");
+  tagHandlers["li"] = make_handler(&PyDocConverter::handleTagMessage, "* ");
   tagHandlers["overload"] = make_handler(&PyDocConverter::handleTagMessage,
       "This is an overloaded member function, provided for"
           " convenience.\nIt differs from the above function only in what"
@@ -153,7 +153,7 @@ void PyDocConverter::fillStaticTables()
 
   // HTML tags
   tagHandlers["<a"] = make_handler(&PyDocConverter::handleDoxyHtmlTag_A);
-  tagHandlers["<b"] = make_handler(&PyDocConverter::handleDoxyHtmlTag2, "__");
+  tagHandlers["<b"] = make_handler(&PyDocConverter::handleDoxyHtmlTag2, "**");
   tagHandlers["<blockquote"] = make_handler(&PyDocConverter::handleDoxyHtmlTag_A,
       "Quote: ");
   tagHandlers["<body"] = make_handler(&PyDocConverter::handleDoxyHtmlTag);
@@ -163,7 +163,7 @@ void PyDocConverter::fillStaticTables()
   // not used in HTML 5
   tagHandlers["<center"] = make_handler(&PyDocConverter::handleDoxyHtmlTag);
   tagHandlers["<caption"] = make_handler(&PyDocConverter::handleDoxyHtmlTag);
-  tagHandlers["<code"] = make_handler(&PyDocConverter::handleDoxyHtmlTag2, "'");
+  tagHandlers["<code"] = make_handler(&PyDocConverter::handleDoxyHtmlTag2, "``");
 
   tagHandlers["<dl"] = make_handler(&PyDocConverter::handleDoxyHtmlTag);
   tagHandlers["<dd"] = make_handler(&PyDocConverter::handleDoxyHtmlTag, "    ");
@@ -171,17 +171,17 @@ void PyDocConverter::fillStaticTables()
 
   tagHandlers["<dfn"] = make_handler(&PyDocConverter::handleDoxyHtmlTag);
   tagHandlers["<div"] = make_handler(&PyDocConverter::handleDoxyHtmlTag);
-  tagHandlers["<em"] = make_handler(&PyDocConverter::handleDoxyHtmlTag2, "__");
+  tagHandlers["<em"] = make_handler(&PyDocConverter::handleDoxyHtmlTag2, "**");
   tagHandlers["<form"] = make_handler(&PyDocConverter::handleDoxyHtmlTag);
   tagHandlers["<hr"] = make_handler(&PyDocConverter::handleDoxyHtmlTag,
       "--------------------------------------------------------------------\n");
   tagHandlers["<h1"] = make_handler(&PyDocConverter::handleDoxyHtmlTag, "# ");
   tagHandlers["<h2"] = make_handler(&PyDocConverter::handleDoxyHtmlTag, "## ");
   tagHandlers["<h3"] = make_handler(&PyDocConverter::handleDoxyHtmlTag, "### ");
-  tagHandlers["<i"] = make_handler(&PyDocConverter::handleDoxyHtmlTag2, "_");
+  tagHandlers["<i"] = make_handler(&PyDocConverter::handleDoxyHtmlTag2, "*");
   tagHandlers["<input"] = make_handler(&PyDocConverter::handleDoxyHtmlTag);
   tagHandlers["<img"] = make_handler(&PyDocConverter::handleDoxyHtmlTag, "Image:");
-  tagHandlers["<li"] = make_handler(&PyDocConverter::handleDoxyHtmlTag, "- ");
+  tagHandlers["<li"] = make_handler(&PyDocConverter::handleDoxyHtmlTag, "* ");
   tagHandlers["<meta"] = make_handler(&PyDocConverter::handleDoxyHtmlTag);
   tagHandlers["<multicol"] = make_handler(&PyDocConverter::handleDoxyHtmlTag);
   tagHandlers["<ol"] = make_handler(&PyDocConverter::handleDoxyHtmlTag);
@@ -189,7 +189,7 @@ void PyDocConverter::fillStaticTables()
   tagHandlers["<pre"] = make_handler(&PyDocConverter::handleDoxyHtmlTag);
   tagHandlers["<small"] = make_handler(&PyDocConverter::handleDoxyHtmlTag);
   tagHandlers["<span"] = make_handler(&PyDocConverter::handleDoxyHtmlTag2, "'");
-  tagHandlers["<strong"] = make_handler(&PyDocConverter::handleDoxyHtmlTag2, "__");
+  tagHandlers["<strong"] = make_handler(&PyDocConverter::handleDoxyHtmlTag2, "**");
 
   // make a space between text and super/sub script.
   tagHandlers["<sub"] = make_handler(&PyDocConverter::handleDoxyHtmlTag, " ");
@@ -202,7 +202,7 @@ void PyDocConverter::fillStaticTables()
   tagHandlers["<tt"] = make_handler(&PyDocConverter::handleDoxyHtmlTag);
   tagHandlers["<kbd"] = make_handler(&PyDocConverter::handleDoxyHtmlTag);
   tagHandlers["<ul"] = make_handler(&PyDocConverter::handleDoxyHtmlTag);
-  tagHandlers["<var"] = make_handler(&PyDocConverter::handleDoxyHtmlTag2, "_");
+  tagHandlers["<var"] = make_handler(&PyDocConverter::handleDoxyHtmlTag2, "*");
 
   // HTML entities
   tagHandlers["&copy"] = make_handler(&PyDocConverter::handleHtmlEntity, "(C)");

From acc5bb60a196a39e230f4e278fedb3bdfcb9aeb9 Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Sat, 12 Jul 2014 15:31:35 +0200
Subject: [PATCH 210/314] Attach Doxygen comments to enum elements in Python
 output.

Sphinx is smart enough to use the docstrings following the constant definition
in Python code as its documentation, so doing this is still useful even if
Python itself doesn't support having docstrings for the variables (and this is
why it's impractical to write a unit test for the changes of this commit: we
can't easily extract the generated docstrings).
---
 Source/Modules/python.cxx | 45 ++++++++++++++++++++++++++-------------
 1 file changed, 30 insertions(+), 15 deletions(-)

diff --git a/Source/Modules/python.cxx b/Source/Modules/python.cxx
index e9675a8a7..b76b83ebb 100644
--- a/Source/Modules/python.cxx
+++ b/Source/Modules/python.cxx
@@ -106,7 +106,8 @@ enum autodoc_t {
   AUTODOC_DTOR,
   AUTODOC_STATICFUNC,
   AUTODOC_FUNC,
-  AUTODOC_METHOD
+  AUTODOC_METHOD,
+  AUTODOC_CONST
 };
 
 
@@ -1817,17 +1818,24 @@ public:
 	  break;
 
 	case AUTODOC_METHOD:
-	  String *paramList = make_autodocParmList(n, showTypes);
-	  Printf(doc, "%s(", symname);
-	  if (showTypes)
-	    Printf(doc, "%s ", class_name);
-	  if (Len(paramList))
-	    Printf(doc, "self, %s)", paramList);
-	  else
-	    Printf(doc, "self)");
-	  if (type_str)
-	    Printf(doc, " -> %s", type_str);
+	  {
+	    String *paramList = make_autodocParmList(n, showTypes);
+	    Printf(doc, "%s(", symname);
+	    if (showTypes)
+	      Printf(doc, "%s ", class_name);
+	    if (Len(paramList))
+	      Printf(doc, "self, %s)", paramList);
+	    else
+	      Printf(doc, "self)");
+	    if (type_str)
+	      Printf(doc, " -> %s", type_str);
+	  }
 	  break;
+
+	case AUTODOC_CONST:
+	  // There is no autodoc support for constants currently, this enum
+	  // element only exists to allow calling docstring() with it.
+	  return NULL;
 	}
 	Delete(type_str);
       }
@@ -3215,12 +3223,17 @@ public:
     }
 
     if (!builtin && (shadow) && (!(shadow & PYSHADOW_MEMBER))) {
+      String *f_s;
       if (!in_class) {
-	Printv(f_shadow, iname, " = ", module, ".", iname, "\n", NIL);
+	f_s = f_shadow;
       } else {
-	if (!(Getattr(n, "feature:python:callback"))) {
-	  Printv(f_shadow_stubs, iname, " = ", module, ".", iname, "\n", NIL);
-	}
+	f_s = Getattr(n, "feature:python:callback") ? NIL : f_shadow_stubs;
+      }
+
+      if (f_s) {
+	Printv(f_s, iname, " = ", module, ".", iname, "\n", NIL);
+	if (have_docstring(n))
+	  Printv(f_s, docstring(n, AUTODOC_CONST, ""), "\n", NIL);
       }
     }
     return SWIG_OK;
@@ -4750,6 +4763,8 @@ public:
       Swig_restore(n);
     } else if (shadow) {
       Printv(f_shadow, tab4, symname, " = ", module, ".", Swig_name_member(NSPACE_TODO, class_name, symname), "\n", NIL);
+      if (have_docstring(n))
+	Printv(f_shadow, tab4, docstring(n, AUTODOC_CONST, tab4), "\n", NIL);
     }
     return SWIG_OK;
   }

From b96dd8bb97110598763a5cd502dfeb8396d21b26 Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Sat, 12 Jul 2014 19:26:29 +0200
Subject: [PATCH 211/314] Implement translation of Doxygen formulae to Sphinx
 notation.

This allows to automatically have nicely looking formulae in HTML output when
using Sphinx with e.g. sphinx.ext.mathjax extension.
---
 .../doxygen_translate_all_tags_runme.py       | 10 ++--
 .../DoxygenTranslator/src/PyDocConverter.cpp  | 47 +++++++++++++++++--
 Source/DoxygenTranslator/src/PyDocConverter.h |  6 +++
 3 files changed, 57 insertions(+), 6 deletions(-)

diff --git a/Examples/test-suite/python/doxygen_translate_all_tags_runme.py b/Examples/test-suite/python/doxygen_translate_all_tags_runme.py
index 1913eaf42..44b4f536d 100644
--- a/Examples/test-suite/python/doxygen_translate_all_tags_runme.py
+++ b/Examples/test-suite/python/doxygen_translate_all_tags_runme.py
@@ -93,13 +93,16 @@ r"""
 
 
 
-      \sqrt{(x_2-x_1)^2+(y_2-y_1)^2} 
+    :math:`\sqrt{(x_2-x_1)^2+(y_2-y_1)^2}`
+
+    .. math::
 
-     
         \sqrt{(x_2-x_1)^2+(y_2-y_1)^2}
 
 
-     
+
+    .. math::
+
         \sqrt{(x_2-x_1)^2+(y_2-y_1)^2}
 
 
@@ -113,6 +116,7 @@ r"""
 
 
 
+
     This will only appear in hmtl
 
     """)
diff --git a/Source/DoxygenTranslator/src/PyDocConverter.cpp b/Source/DoxygenTranslator/src/PyDocConverter.cpp
index edeb056c1..883bc9bd9 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/PyDocConverter.cpp
@@ -147,9 +147,9 @@ void PyDocConverter::fillStaticTables()
   tagHandlers["n"] = make_handler(&PyDocConverter::handleNewLine);
 
   // \f commands output literal Latex formula, which is still better than nothing.
-  tagHandlers["f$"] = make_handler(&PyDocConverter::handleTagVerbatim);
-  tagHandlers["f["] = make_handler(&PyDocConverter::handleTagVerbatim);
-  tagHandlers["f{"] = make_handler(&PyDocConverter::handleTagVerbatim);
+  tagHandlers["f$"] =
+  tagHandlers["f["] =
+  tagHandlers["f{"] = make_handler(&PyDocConverter::handleMath);
 
   // HTML tags
   tagHandlers["<a"] = make_handler(&PyDocConverter::handleDoxyHtmlTag_A);
@@ -328,6 +328,47 @@ void PyDocConverter::handleParagraph(DoxygenEntity& tag,
   translatedComment += translateSubtree(tag);
 }
 
+void PyDocConverter::handleMath(DoxygenEntity &tag,
+                                std::string &translatedComment,
+                                const std::string& arg)
+{
+  // Only \f$ is translated to inline formulae, \f[ and \f{ are for the block ones.
+  const bool inlineFormula = tag.typeOfEntity == "f$";
+
+  if (inlineFormula) {
+    translatedComment += ":math:`";
+  } else {
+    translatedComment += ".. math::\n\n    ";
+  }
+
+  std::string formula;
+  handleTagVerbatim(tag, formula, arg);
+
+  // It is important to ensure that we have no spaces around the inline math
+  // contents, so strip them.
+  const size_t start = formula.find_first_not_of(" \t\n");
+  const size_t end = formula.find_last_not_of(" \t\n");
+  if (start != std::string::npos) {
+    for (size_t n = start; n <= end; n++) {
+      if (formula[n] == '\n') {
+        // New lines must be suppressed in inline maths and indented in the
+        // block ones.
+        if (!inlineFormula)
+          translatedComment += "\n    ";
+      } else {
+        // Just copy everything else.
+        translatedComment += formula[n];
+      }
+    }
+  }
+
+  if (inlineFormula) {
+    translatedComment += "`";
+  } else {
+    translatedComment += "\n\n";
+  }
+}
+
 void PyDocConverter::handlePlainString(DoxygenEntity& tag,
                                        std::string& translatedComment,
                                        const std::string&)
diff --git a/Source/DoxygenTranslator/src/PyDocConverter.h b/Source/DoxygenTranslator/src/PyDocConverter.h
index 435c18c28..7f7dd53f9 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.h
+++ b/Source/DoxygenTranslator/src/PyDocConverter.h
@@ -80,6 +80,12 @@ protected:
    */
   void handleParagraph(DoxygenEntity &tag, std::string &translatedComment,
                        const std::string &arg = std::string());
+
+  /*
+   * Handle one of the Doxygen formula-related tags.
+   */
+  void handleMath(DoxygenEntity &tag, std::string &translatedComment, const std::string &arg);
+
   /*
    * Print only data part of code
    */

From 3db8c1fca23a74292f4b1777255f846c6cb046b7 Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Sat, 12 Jul 2014 19:42:57 +0200
Subject: [PATCH 212/314] Fix memory leaks in Doxygen to PyDoc parameter types
 conversion code.

Don't forget to delete the local copy of parameter list and the temporary
string.
---
 Source/DoxygenTranslator/src/PyDocConverter.cpp | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/Source/DoxygenTranslator/src/PyDocConverter.cpp b/Source/DoxygenTranslator/src/PyDocConverter.cpp
index 883bc9bd9..39a0ea587 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/PyDocConverter.cpp
@@ -239,12 +239,16 @@ PyDocConverter::PyDocConverter(int flags) :
 
 std::string PyDocConverter::getParamType(std::string param)
 {
+  std::string type;
+
   ParmList *plist = CopyParmList(Getattr(currentNode, "parms"));
   Parm *p = NULL;
   for (p = plist; p;) {
     if (Char (Getattr(p, "name")) == param) {
-      std::string type = Char (SwigType_str(Getattr(p, "type"), ""));
-      return type;
+      String *s = SwigType_str(Getattr(p, "type"), "");
+      type = Char (s);
+      Delete(s);
+      break;
     }
     /*
      * doesn't seem to work always: in some cases (especially for 'self' parameters)
@@ -254,7 +258,7 @@ std::string PyDocConverter::getParamType(std::string param)
     p = nextSibling(p);
   }
   Delete(plist);
-  return "";
+  return type;
 }
 
 std::string PyDocConverter::justifyString(std::string documentString,

From d677321323163fab9c4d8e3149988fe08c7d06bd Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Sat, 12 Jul 2014 20:03:26 +0200
Subject: [PATCH 213/314] No real changes, just rewrite the parameter iteration
 loop to be more clear.

Also remove unused commented out code.
---
 .../DoxygenTranslator/src/PyDocConverter.cpp  | 22 +++++++------------
 1 file changed, 8 insertions(+), 14 deletions(-)

diff --git a/Source/DoxygenTranslator/src/PyDocConverter.cpp b/Source/DoxygenTranslator/src/PyDocConverter.cpp
index 39a0ea587..607e339b6 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/PyDocConverter.cpp
@@ -242,20 +242,14 @@ std::string PyDocConverter::getParamType(std::string param)
   std::string type;
 
   ParmList *plist = CopyParmList(Getattr(currentNode, "parms"));
-  Parm *p = NULL;
-  for (p = plist; p;) {
-    if (Char (Getattr(p, "name")) == param) {
-      String *s = SwigType_str(Getattr(p, "type"), "");
-      type = Char (s);
-      Delete(s);
-      break;
-    }
-    /*
-     * doesn't seem to work always: in some cases (especially for 'self' parameters)
-     * tmap:in is present, but tmap:in:next is not and so this code skips all the parameters
-     */
-    //p = Getattr(p, "tmap:in") ? Getattr(p, "tmap:in:next") : nextSibling(p);
-    p = nextSibling(p);
+  for (Parm *p = plist; p;p = nextSibling(p)) {
+    if (Char (Getattr(p, "name")) != param)
+      continue;
+
+    String *s = SwigType_str(Getattr(p, "type"), "");
+    type = Char (s);
+    Delete(s);
+    break;
   }
   Delete(plist);
   return type;

From dd4c680a02b53c813d5d6d7270f0a758449f07fc Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Sun, 13 Jul 2014 00:46:31 +0200
Subject: [PATCH 214/314] Use Python-ish, not C++, parameter types in Python
 documentation.

Using C++ types in documentation for Python users is more harmful than
useless, so use Python types whenever possible and allow defining "doctype"
typemap to customize this for the user-defined types.
---
 Doc/Manual/Doxygen.html                       | 37 +++++++++++++++++++
 .../python/doxygen_basic_translate_runme.py   |  2 +-
 .../python/doxygen_misc_constructs_runme.py   |  6 +--
 Lib/python/boost_shared_ptr.i                 |  3 ++
 Lib/python/pydocs.swg                         | 21 +++++++++++
 .../DoxygenTranslator/src/PyDocConverter.cpp  | 10 ++++-
 6 files changed, 74 insertions(+), 5 deletions(-)

diff --git a/Doc/Manual/Doxygen.html b/Doc/Manual/Doxygen.html
index 9e0b3d813..d927593ab 100644
--- a/Doc/Manual/Doxygen.html
+++ b/Doc/Manual/Doxygen.html
@@ -943,6 +943,43 @@ class Shape(_object):
         return _Shapes.Shape_perimeter(self)
 </pre></div>
 
+<p>
+If any parameters of a function or a method are documented in the Doxygen comment,
+their description is copied into the generated output using
+<a href="http://sphinx-doc.org/">Sphinx </a> documentation conventions. For example
+</p>
+<div class="code"><pre>
+/**
+    Set a breakpoint at the given location.
+
+    @param filename The full path to the file.
+    @param line_number The line number in the file.
+ */
+bool SetBreakpoint(const char* filename, int line_number);
+</pre></div>
+would be translated to
+<div class="targetlang"><pre>
+def SetBreakpoint(*args):
+    r"""
+    Set a breakpoint at the given location.
+
+    :type filename: string
+    :param filename: The full path to the file.
+    :type line_number: int
+    :param line_number: The line number in the file.
+    """
+</pre></div>
+<p>
+The types used for the parameter documentation come from <tt>doctype</tt> typemap which
+is defined for all the primitive types and a few others (e.g. <tt>std::string</tt> and
+<tt>shared_ptr&lt;T&gt;</tt>) but for non-primitive types is taken to be just the C++
+name of the type with namespace scope delimiters (<tt>::</tt>) replaced with a dot. To
+change this, you can define your own typemaps for the custom types, e.g:
+</p>
+<div class="code"><pre>
+%typemap(doctype) MyDate "datetime.date";
+</pre></div>
+
 <p>
 Currently Doxygen comments assigned to vars are not present in proxy
 file, so they have no comment translated for them.
diff --git a/Examples/test-suite/python/doxygen_basic_translate_runme.py b/Examples/test-suite/python/doxygen_basic_translate_runme.py
index a0c921829..303b81a45 100644
--- a/Examples/test-suite/python/doxygen_basic_translate_runme.py
+++ b/Examples/test-suite/python/doxygen_basic_translate_runme.py
@@ -73,7 +73,7 @@ commentVerifier.check(doxygen_basic_translate.function7.__doc__,
     """
     Test for a parameter with difficult type
     (mostly for python)
-    :type a: Shape::superType *[10]
+    :type a: Shape
     :param a: Very strange param
     """
 )
diff --git a/Examples/test-suite/python/doxygen_misc_constructs_runme.py b/Examples/test-suite/python/doxygen_misc_constructs_runme.py
index 2c68fd65d..183fc870f 100644
--- a/Examples/test-suite/python/doxygen_misc_constructs_runme.py
+++ b/Examples/test-suite/python/doxygen_misc_constructs_runme.py
@@ -10,11 +10,11 @@ commentVerifier.check(doxygen_misc_constructs.getAddress.__doc__,
     r"""
     Returns address of file line.
 
-    :type fileName: int &
+    :type fileName: int
     :param fileName: name of the file, where the source line is located
     :type line: int
     :param line: line number
-    :type isGetSize: bool
+    :type isGetSize: boolean
     :param isGetSize: if set, for every object location both address and size are returned
 
     Connection::getId() 
@@ -141,7 +141,7 @@ commentVerifier.check(doxygen_misc_constructs.cycle.__doc__,
             main_ctrl.setBP("func1");
         
 
-    :type fileName: char *
+    :type fileName: string
     :param fileName: name of the log file
     """
 );
diff --git a/Lib/python/boost_shared_ptr.i b/Lib/python/boost_shared_ptr.i
index 100ed3e82..560a49f81 100644
--- a/Lib/python/boost_shared_ptr.i
+++ b/Lib/python/boost_shared_ptr.i
@@ -314,6 +314,9 @@
 #error "typemaps for $1_type not available"
 %}
 
+%typemap(doctype) SWIG_SHARED_PTR_QNAMESPACE::shared_ptr< CONST TYPE >,
+                  SWIG_SHARED_PTR_QNAMESPACE::shared_ptr< CONST TYPE >& %{TYPE%}
+
 
 %template() SWIG_SHARED_PTR_QNAMESPACE::shared_ptr< CONST TYPE >;
 
diff --git a/Lib/python/pydocs.swg b/Lib/python/pydocs.swg
index 969af92aa..1eea41b8d 100644
--- a/Lib/python/pydocs.swg
+++ b/Lib/python/pydocs.swg
@@ -22,3 +22,24 @@
 %typemap(doc) SWIGTYPE *INPUT, SWIGTYPE &INPUT "$1_name: $1_type (input)";
 %typemap(doc) SWIGTYPE *OUTPUT, SWIGTYPE &OUTPUT "$1_name: $1_type (output)";
 #endif
+
+
+// Types to use in Python documentation for the parameters of the given C++ type.
+%typemap(doctype) bool "boolean";
+
+%define int_doctype_for_cppint_type(cppint_type)
+    %typemap(doctype) cppint_type, unsigned cppint_type "int";
+%enddef
+%formacro(int_doctype_for_cppint_type, short, int, long, long long)
+
+%typemap(doctype) size_t "int";
+
+%typemap(doctype) enum SWIGTYPE "int";
+
+%typemap(doctype) float, double, long double "float";
+
+%typemap(doctype) char*, std::string "string";
+
+%typemap(doctype) SWIGTYPE "$1_basetype"
+%typemap(doctype) SWIGTYPE * "$typemap(doctype, $*1_ltype)"
+%typemap(doctype) SWIGTYPE & "$typemap(doctype, $*1_ltype)"
diff --git a/Source/DoxygenTranslator/src/PyDocConverter.cpp b/Source/DoxygenTranslator/src/PyDocConverter.cpp
index 607e339b6..05df48c0f 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/PyDocConverter.cpp
@@ -246,8 +246,16 @@ std::string PyDocConverter::getParamType(std::string param)
     if (Char (Getattr(p, "name")) != param)
       continue;
 
-    String *s = SwigType_str(Getattr(p, "type"), "");
+    String *s = Swig_typemap_lookup("doctype", p, Getattr(p, "name"), 0);
+    if (!s)
+      s = SwigType_str(Getattr(p, "type"), "");
+
+    // In Python C++ namespaces are flattened, so remove all but last component
+    // of the name.
+    String * const last = Swig_scopename_last(s);
+
     type = Char (s);
+    Delete(last);
     Delete(s);
     break;
   }

From eaf63ba47d68767633c472c1faa857ba8e670877 Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Sun, 13 Jul 2014 20:31:43 +0200
Subject: [PATCH 215/314] Add poor man trailing white space detection to
 Doxygen Python tests.

Show that there is trailing white space in the output in an ugly but
functional way, as without this it's impossible to determine what is the
actual change at all.
---
 Examples/test-suite/python/commentVerifier.py | 22 +++++++++++++++++--
 1 file changed, 20 insertions(+), 2 deletions(-)

diff --git a/Examples/test-suite/python/commentVerifier.py b/Examples/test-suite/python/commentVerifier.py
index ea840935a..a49539ed1 100644
--- a/Examples/test-suite/python/commentVerifier.py
+++ b/Examples/test-suite/python/commentVerifier.py
@@ -3,6 +3,24 @@ def check(got, expected):
       got = ''
 
   if got != expected:
+    import re
+    p = re.compile(r'^[+-]([^+-].*\S)?(\s+)$', re.M)
+
+    def make_trailing_spaces_visible(str):
+        def replace_trailing_spaces(match):
+            res = match.group(0)
+            spaces = match.group(2)
+            if spaces is not None:
+                res = res + "{+%d trailing spaces}" % len(spaces)
+            return res
+        return re.sub(p, replace_trailing_spaces, str)
+
     from difflib import unified_diff
-    diff = unified_diff(expected.splitlines(True), got.splitlines(True), "expected", "got")
-    raise RuntimeError("Comments don't match:\n" + "".join(diff))
+    diff = unified_diff(expected.splitlines(True),
+                        got.splitlines(True), "expected", "got")
+    lines = []
+    for line in diff:
+        line = make_trailing_spaces_visible(line.strip("\r\n"))
+        lines.append(line + "\n")
+
+    raise RuntimeError("Comments don't match:\n" + "".join(lines))

From ea1d56da6793facfb97e92bf05c640f7d3d43192 Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Sun, 13 Jul 2014 20:47:00 +0200
Subject: [PATCH 216/314] Use Sphinx-friendly formatting for overloaded
 functions documentation.

Sphinx doesn't allow sections inside the function documentation and gives tons
of SEVERE warnings for them, so while just emphasizing the "Overload" header
is not ideal, it is better than before because at least the string "Overload"
itself appears in the Sphinx-generated output.
---
 .../python/doxygen_basic_notranslate_runme.py          | 10 ++++------
 .../test-suite/python/doxygen_basic_translate_runme.py | 10 ++++------
 Source/DoxygenTranslator/src/PyDocConverter.cpp        | 10 +---------
 Source/DoxygenTranslator/src/PyDocConverter.h          |  5 -----
 4 files changed, 9 insertions(+), 26 deletions(-)

diff --git a/Examples/test-suite/python/doxygen_basic_notranslate_runme.py b/Examples/test-suite/python/doxygen_basic_notranslate_runme.py
index 54baf2e1e..bb2fae0f5 100644
--- a/Examples/test-suite/python/doxygen_basic_notranslate_runme.py
+++ b/Examples/test-suite/python/doxygen_basic_notranslate_runme.py
@@ -28,15 +28,13 @@ commentVerifier.check(doxygen_basic_notranslate.function2.__doc__,
 
 commentVerifier.check(doxygen_basic_notranslate.function3.__doc__,
     r"""
-    ----------------------------------------------------------------
-    Overload 1:
-    ----------------------------------------------------------------
+    *Overload 1:*
+
      A test for overloaded functions
      This is function \b one
      
-    ----------------------------------------------------------------
-    Overload 2:
-    ----------------------------------------------------------------
+    *Overload 2:*
+
      A test for overloaded functions
      This is function \b two
      
diff --git a/Examples/test-suite/python/doxygen_basic_translate_runme.py b/Examples/test-suite/python/doxygen_basic_translate_runme.py
index 303b81a45..0910ea8ea 100644
--- a/Examples/test-suite/python/doxygen_basic_translate_runme.py
+++ b/Examples/test-suite/python/doxygen_basic_translate_runme.py
@@ -26,15 +26,13 @@ commentVerifier.check(doxygen_basic_translate.function2.__doc__,
 )
 commentVerifier.check(doxygen_basic_translate.function3.__doc__,
     """
-    ----------------------------------------------------------------
-    Overload 1:
-    ----------------------------------------------------------------
+    *Overload 1:*
+
     A test for overloaded functions
     This is function **one**
 
-    ----------------------------------------------------------------
-    Overload 2:
-    ----------------------------------------------------------------
+    *Overload 2:*
+
     A test for overloaded functions
     This is function **two**
 
diff --git a/Source/DoxygenTranslator/src/PyDocConverter.cpp b/Source/DoxygenTranslator/src/PyDocConverter.cpp
index 05df48c0f..dec4fc0e5 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/PyDocConverter.cpp
@@ -692,10 +692,8 @@ String *PyDocConverter::makeDocumentation(Node *n)
       for (int realOverloadCount = 0;
           realOverloadCount < (int) allDocumentation.size();
           realOverloadCount++) {
-        concatDocString << generateDivider() << std::endl;
-        concatDocString << "Overload " << (realOverloadCount + 1) << ":"
+        concatDocString << "*Overload " << (realOverloadCount + 1) << ":*"
             << std::endl;
-        concatDocString << generateDivider();
         concatDocString << allDocumentation[realOverloadCount] << std::endl;
       }
       pyDocString = concatDocString.str();
@@ -744,9 +742,3 @@ String *PyDocConverter::makeDocumentation(Node *n)
 
   return NewString("");
 }
-
-std::string PyDocConverter::generateDivider()
-{
-  static string dividerString(DOC_STRING_LENGTH, '-');
-  return dividerString;
-}
diff --git a/Source/DoxygenTranslator/src/PyDocConverter.h b/Source/DoxygenTranslator/src/PyDocConverter.h
index 7f7dd53f9..a4214e49c 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.h
+++ b/Source/DoxygenTranslator/src/PyDocConverter.h
@@ -168,11 +168,6 @@ protected:
   void handleHtmlEntity(DoxygenEntity&, std::string& translatedComment, const std::string &arg);
 
 
-  /*
-   * Utility method to generate a diving line for a documentation string.
-   */
-  std::string generateDivider();
-
   /*
    * Simple helper function that calculates correct parameter type
    * of the node stored in 'currentNode'

From 14ba3b8dd4acf2babad92fd33e3d989a8cc25fd2 Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Mon, 14 Jul 2014 02:29:49 +0200
Subject: [PATCH 217/314] Preserve relative indentation when parsing Doxygen
 comments.

This is important to preserve the structure of the lists which appear
correctly in Python output without any additional effort if the indentation is
lost.

It is also makes the behaviour consistent for

	/**
	 *
	 *
	 */

comments and those without the asterisks in the middle lines, as now the
indentation is preserved in both cases while it was only preserved when the
asterisks were present previously.
---
 Examples/test-suite/doxygen_misc_constructs.i | 14 +++++++++++
 .../java/doxygen_misc_constructs_runme.java   | 14 ++++++++++-
 .../python/doxygen_misc_constructs_runme.py   | 15 ++++++++++++
 .../DoxygenTranslator/src/DoxygenParser.cpp   | 24 +++++++++++--------
 4 files changed, 56 insertions(+), 11 deletions(-)

diff --git a/Examples/test-suite/doxygen_misc_constructs.i b/Examples/test-suite/doxygen_misc_constructs.i
index 9426b5909..78c72fe6d 100644
--- a/Examples/test-suite/doxygen_misc_constructs.i
+++ b/Examples/test-suite/doxygen_misc_constructs.i
@@ -102,6 +102,20 @@
 
     };
 
+    /**
+        An example of a list in a documentation comment.
+
+            - The first item of the list.
+            - The second list item, on
+              several indented lines,
+              showing that the indentation
+              is preserved.
+            - And the final list item after it.
+
+        And this is not a list item any more.
+     */
+    void showList() { }
+
     #include "doxygen_misc_constructs.h"
     
 %}
diff --git a/Examples/test-suite/java/doxygen_misc_constructs_runme.java b/Examples/test-suite/java/doxygen_misc_constructs_runme.java
index ba0f2b265..7c799412e 100644
--- a/Examples/test-suite/java/doxygen_misc_constructs_runme.java
+++ b/Examples/test-suite/java/doxygen_misc_constructs_runme.java
@@ -117,6 +117,18 @@ public class doxygen_misc_constructs_runme {
     wantedComments.put("doxygen_misc_constructs.ClassWithNestedEnum.ENested.THREE",
     		" desc of three\n");
 
+    wantedComments.put("doxygen_misc_constructs.doxygen_misc_constructs.showList()",
+"         An example of a list in a documentation comment.<br>\n" +
+" <br>\n" +
+"             - The first item of the list.<br>\n" +
+"             - The second list item, on<br>\n" +
+"               several indented lines,<br>\n" +
+"               showing that the indentation<br>\n" +
+"               is preserved.<br>\n" +
+"             - And the final list item after it.<br>\n" +
+" <br>\n" +
+"        And this is not a list item any more.\n" +
+    		"");
     wantedComments.put("doxygen_misc_constructs.doxygen_misc_constructs.isNoSpaceValidA()",
     		" This comment without space after '*' is valid in Doxygen.\n" +
     		"\n" +
@@ -182,4 +194,4 @@ public class doxygen_misc_constructs_runme {
     // and ask the parser to check comments for us
     System.exit(parser.check(wantedComments));
   }
-}
\ No newline at end of file
+}
diff --git a/Examples/test-suite/python/doxygen_misc_constructs_runme.py b/Examples/test-suite/python/doxygen_misc_constructs_runme.py
index 183fc870f..742c19b16 100644
--- a/Examples/test-suite/python/doxygen_misc_constructs_runme.py
+++ b/Examples/test-suite/python/doxygen_misc_constructs_runme.py
@@ -64,6 +64,21 @@ commentVerifier.check(doxygen_misc_constructs.ClassWithNestedEnum.__doc__,
     """
 )
 
+commentVerifier.check(doxygen_misc_constructs.showList.__doc__,
+    r"""
+    An example of a list in a documentation comment.
+
+        - The first item of the list.
+        - The second list item, on
+          several indented lines,
+          showing that the indentation
+          is preserved.
+        - And the final list item after it.
+
+    And this is not a list item any more.
+    """
+)
+
 commentVerifier.check(doxygen_misc_constructs.isNoSpaceValidA.__doc__,
     r"""
     This comment without space after '*' is valid in Doxygen.
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.cpp b/Source/DoxygenTranslator/src/DoxygenParser.cpp
index 22f391b36..8523b51f4 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenParser.cpp
@@ -1338,19 +1338,23 @@ void DoxygenParser::tokenizeDoxygenComment(const std::string &doxygenComment,
     // line[pos] may be ' \t' or start of word, it there was no '*', '/' or '!'
     // at beginning of the line. Make sure it points to start of the first word
     // in the line.
-    size_t firstWordPos = line.find_first_not_of(" \t", pos);
-    if (firstWordPos == string::npos) {
-      m_tokenList.push_back(Token(END_LINE, "\n"));
-      continue;
-    }
+    if (isStartOfCommentLineCharFound) {
+      size_t firstWordPos = line.find_first_not_of(" \t", pos);
+      if (firstWordPos == string::npos) {
+        m_tokenList.push_back(Token(END_LINE, "\n"));
+        continue;
+      }
 
-    if (isStartOfCommentLineCharFound && firstWordPos > pos) {
-      m_tokenList.push_back(
-          Token(PLAINSTRING, line.substr(pos, firstWordPos - pos)));
+      if (firstWordPos > pos) {
+        m_tokenList.push_back(
+            Token(PLAINSTRING, line.substr(pos, firstWordPos - pos)));
+        pos = firstWordPos;
+      }
+    } else {
+        m_tokenList.push_back(
+            Token(PLAINSTRING, line.substr(0, pos)));
     }
 
-    pos = firstWordPos;
-
     while (pos != string::npos) {
       // find the end of the word
       size_t doxyCmdOrHtmlTagPos = line.find_first_of("\\@<>&\" \t", pos);

From b833dbe302e15b8e450e03bdf4d51abc234e0063 Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Mon, 14 Jul 2014 14:22:35 +0200
Subject: [PATCH 218/314] No real changes, just remove an unnecessary variable.

Avoid copying "pyDocString" to "result" completely unnecessary, just use
"pyDocString" itself directly.
---
 Source/DoxygenTranslator/src/PyDocConverter.cpp | 12 ++++--------
 1 file changed, 4 insertions(+), 8 deletions(-)

diff --git a/Source/DoxygenTranslator/src/PyDocConverter.cpp b/Source/DoxygenTranslator/src/PyDocConverter.cpp
index dec4fc0e5..beb351d24 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/PyDocConverter.cpp
@@ -651,7 +651,7 @@ void PyDocConverter::handleNewLine(DoxygenEntity&,
 String *PyDocConverter::makeDocumentation(Node *n)
 {
   String *documentation;
-  std::string pyDocString, result;
+  std::string pyDocString;
 
   // store the node, we may need it later
   currentNode = n;
@@ -721,7 +721,7 @@ String *PyDocConverter::makeDocumentation(Node *n)
     }
   }
 
-  // if we got something log the result and construct DOH string to return
+  // if we got something log the result
   if (!pyDocString.empty()) {
 
     // remove the last '\n' since additional one is added during writing to file
@@ -729,16 +729,12 @@ String *PyDocConverter::makeDocumentation(Node *n)
       pyDocString.erase(pyDocString.size() - 1);
     }
 
-    result = pyDocString;
-
     if (m_flags & debug_translator) {
       std::cout << "\n---RESULT IN PYDOC---" << std::endl;
-      std::cout << result;
+      std::cout << pyDocString;
       std::cout << std::endl;
     }
-
-    return NewString(result.c_str());
   }
 
-  return NewString("");
+  return NewString(pyDocString.c_str());
 }

From 70d3533e12cbc624ca78c72247e542de550fc895 Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Mon, 14 Jul 2014 19:16:18 +0200
Subject: [PATCH 219/314] Remove unused method from PyDocConverter.

justifyString() was unused and doesn't seem to be useful as there are no
particular constraints on the line length in Python documentation, so just
preserve whatever is used in the original C++ code.
---
 .../DoxygenTranslator/src/PyDocConverter.cpp  | 27 -------------------
 Source/DoxygenTranslator/src/PyDocConverter.h |  5 ----
 2 files changed, 32 deletions(-)

diff --git a/Source/DoxygenTranslator/src/PyDocConverter.cpp b/Source/DoxygenTranslator/src/PyDocConverter.cpp
index beb351d24..afe979e10 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/PyDocConverter.cpp
@@ -263,33 +263,6 @@ std::string PyDocConverter::getParamType(std::string param)
   return type;
 }
 
-std::string PyDocConverter::justifyString(std::string documentString,
-                                          int indent, int maxWidth)
-{
-  std::string formattedString;
-  std::string currentLine;
-
-  for (std::string::iterator stringPosition = documentString.begin();
-      stringPosition != documentString.end(); ++stringPosition) {
-    if (currentLine.length() == 0)
-      currentLine.resize(indent, ' ');
-
-    currentLine += *stringPosition;
-
-    if ((iswspace(*stringPosition) && (int) currentLine.size() >= maxWidth)
-        || (stringPosition + 1) == documentString.end()) {
-      formattedString += currentLine + "\n";
-      currentLine = "";
-    }
-  }
-
-  // strip the last endl
-  if (formattedString.size())
-    formattedString = formattedString.substr(0, formattedString.size() - 1);
-
-  return formattedString;
-}
-
 std::string PyDocConverter::translateSubtree(DoxygenEntity & doxygenEntity)
 {
   std::string translatedComment;
diff --git a/Source/DoxygenTranslator/src/PyDocConverter.h b/Source/DoxygenTranslator/src/PyDocConverter.h
index a4214e49c..9257e14a8 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.h
+++ b/Source/DoxygenTranslator/src/PyDocConverter.h
@@ -34,11 +34,6 @@ protected:
   bool m_prevRowIsTH;
   std::string m_url;
 
-  /*
-   * Format a string so it is justified and split over several lines 
-   * not exceeding a given length.
-   */
-  std::string justifyString(std::string unformattedLine, int indent = 0, int maxWidth = DOC_STRING_LENGTH);
   /*
    * Translate every entity in a tree, also manages sections
    * display. Prints title for every group of tags that have

From 8b83976f4cbec5a7fdaf504e8705df10ff2a164d Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Sun, 13 Jul 2014 20:27:52 +0200
Subject: [PATCH 220/314] Fix arguments of @param, @return etc translations to
 Python.

For the parameter documentation to be really taken as such, in its entirety,
by Sphinx, it must be indented relative to the :param: tag. Do this by
appending an extra indent after every line of the output and work around the
unnecessary indent of the last line by removing the trailing whitespace.

This required updating the existing tests and removing the expected but not
present any more whitespace from them, but as trailing whitespace in the
documentation is at best insignificant (and at worst harmful) anyhow, this is
not a big price to pay for simpler translator code.
---
 .../python/doxygen_basic_translate_runme.py   |   2 +-
 .../python/doxygen_misc_constructs_runme.py   |  26 ++---
 .../python/doxygen_parsing_runme.py           |   4 +-
 .../doxygen_translate_all_tags_runme.py       |   6 +-
 .../python/doxygen_translate_runme.py         |  28 ++---
 .../DoxygenTranslator/src/PyDocConverter.cpp  | 104 +++++++++++++++++-
 Source/DoxygenTranslator/src/PyDocConverter.h |   4 +
 7 files changed, 135 insertions(+), 39 deletions(-)

diff --git a/Examples/test-suite/python/doxygen_basic_translate_runme.py b/Examples/test-suite/python/doxygen_basic_translate_runme.py
index 0910ea8ea..3018b72de 100644
--- a/Examples/test-suite/python/doxygen_basic_translate_runme.py
+++ b/Examples/test-suite/python/doxygen_basic_translate_runme.py
@@ -57,7 +57,7 @@ commentVerifier.check(doxygen_basic_translate.function4.__doc__,
 )
 commentVerifier.check(doxygen_basic_translate.function5.__doc__,
     """
-    This is a post comment. 
+    This is a post comment.
     """
 )
 commentVerifier.check(doxygen_basic_translate.function6.__doc__,
diff --git a/Examples/test-suite/python/doxygen_misc_constructs_runme.py b/Examples/test-suite/python/doxygen_misc_constructs_runme.py
index 742c19b16..ac439ceb4 100644
--- a/Examples/test-suite/python/doxygen_misc_constructs_runme.py
+++ b/Examples/test-suite/python/doxygen_misc_constructs_runme.py
@@ -23,7 +23,7 @@ commentVerifier.check(doxygen_misc_constructs.getAddress.__doc__,
 
 commentVerifier.check(doxygen_misc_constructs.CConnectionConfig.__doc__,
     r"""
-    This class contains information for connection to winIDEA. Its methods 
+    This class contains information for connection to winIDEA. Its methods
     return reference to self, so we can use it like this:
 
     CConnectionConfig config = new CConnectionConfig();
@@ -41,7 +41,7 @@ commentVerifier.check(doxygen_misc_constructs.CConnectionConfig.__doc__,
 
 commentVerifier.check(doxygen_misc_constructs.waitTime.__doc__,
     r"""
-    Determines how long the ``isystem.connect`` should wait for running 
+    Determines how long the ``isystem.connect`` should wait for running
     instances to respond. Only one of ``lfWaitXXX`` flags from IConnect::ELaunchFlags
     may be specified.
     """
@@ -123,8 +123,8 @@ commentVerifier.check(doxygen_misc_constructs.backslashB.__doc__,
 
 commentVerifier.check(doxygen_misc_constructs.backslashC.__doc__,
     r"""
-    Backslash e at end of *line* froze SWIG 
-    *with* old comment parser. 
+    Backslash e at end of *line* froze SWIG
+    *with* old comment parser.
 
     See also: MyClass::fun(char,
      float)
@@ -146,15 +146,15 @@ commentVerifier.check(doxygen_misc_constructs.cycle.__doc__,
     Spaces at the start of line should be taken into account:
     :type id: int
     :param id: used as prefix in log
-        statements. The default value is empty string, which is OK if
-        there is only one app. instance. Example:
-        
-            ctrl.setBP("func1");
-        
-        If we set the id to ``main_``, we get:
-        
-            main_ctrl.setBP("func1");
-        
+            statements. The default value is empty string, which is OK if
+            there is only one app. instance. Example:
+
+                ctrl.setBP("func1");
+
+            If we set the id to ``main_``, we get:
+
+                main_ctrl.setBP("func1");
+
 
     :type fileName: string
     :param fileName: name of the log file
diff --git a/Examples/test-suite/python/doxygen_parsing_runme.py b/Examples/test-suite/python/doxygen_parsing_runme.py
index 1e5dd7e00..c850e419d 100644
--- a/Examples/test-suite/python/doxygen_parsing_runme.py
+++ b/Examples/test-suite/python/doxygen_parsing_runme.py
@@ -21,7 +21,7 @@ commentVerifier.check(doxygen_parsing.SomeAnotherClass.classMethod.__doc__,
     r"""
         The class method comment.
 
-        SomeAnotherClass#classMethodExtended(int, int) a link text 
+        SomeAnotherClass#classMethodExtended(int, int) a link text
         """)
 commentVerifier.check(doxygen_parsing.SomeAnotherClass.classMethodExtended.__doc__,
     r"""
@@ -33,7 +33,7 @@ commentVerifier.check(doxygen_parsing.SomeAnotherClass.classMethodExtended.__doc
         :param b: Parameter b
         """
 )
-commentVerifier.check(doxygen_parsing.SomeAnotherClass.classMethodExtended2.__doc__, 
+commentVerifier.check(doxygen_parsing.SomeAnotherClass.classMethodExtended2.__doc__,
     r"""
         The class method with parameter
 
diff --git a/Examples/test-suite/python/doxygen_translate_all_tags_runme.py b/Examples/test-suite/python/doxygen_translate_all_tags_runme.py
index 44b4f536d..c74ba4828 100644
--- a/Examples/test-suite/python/doxygen_translate_all_tags_runme.py
+++ b/Examples/test-suite/python/doxygen_translate_all_tags_runme.py
@@ -36,7 +36,7 @@ r"""
 
     'citationword'
 
-    some test code 
+    some test code
     """)
 
 commentVerifier.check(doxygen_translate_all_tags.func02.__doc__,
@@ -95,6 +95,7 @@ r"""
 
     :math:`\sqrt{(x_2-x_1)^2+(y_2-y_1)^2}`
 
+
     .. math::
 
         \sqrt{(x_2-x_1)^2+(y_2-y_1)^2}
@@ -116,7 +117,6 @@ r"""
 
 
 
-
     This will only appear in hmtl
 
     """)
@@ -176,7 +176,7 @@ r"""
 
 
 
-    someMember Some description follows 
+    someMember Some description follows
 
 
 
diff --git a/Examples/test-suite/python/doxygen_translate_runme.py b/Examples/test-suite/python/doxygen_translate_runme.py
index 028bf32fd..55c5d8c9a 100644
--- a/Examples/test-suite/python/doxygen_translate_runme.py
+++ b/Examples/test-suite/python/doxygen_translate_runme.py
@@ -22,7 +22,7 @@ r"""
 
     'citationword'
 
-    some test code 
+    some test code
 
     Conditional comment: SOMECONDITION
     Some conditional comment
@@ -67,7 +67,7 @@ r"""
 
 
 
-    someMember Some description follows 
+    someMember Some description follows
 
 
 
@@ -171,7 +171,7 @@ r"""
 
     *Starts a piece of text displayed in an italic font.*
     Input tag.
-    Image: src="slika.png" 
+    Image: src="slika.png"
     Meta tag.
     Multicol is ignored by doxygen.
 
@@ -227,16 +227,16 @@ r"""
 
     :type byFlags: int
     :param byFlags: bits marking required items:
-      
-      | Size in bits| Items Required |
-      --------------------------------
-      | 1 - 8       |      1         |
-      | 9 - 16      |      2         |
-      | 17 - 32     |      4         |
-      
-      Almost all combinations of above flags are supported by
-      ``htmlTable...`` functions.
-    """)                      
+
+          | Size in bits| Items Required |
+          --------------------------------
+          | 1 - 8       |      1         |
+          | 9 - 16      |      2         |
+          | 17 - 32     |      4         |
+
+          Almost all combinations of above flags are supported by
+          ``htmlTable...`` functions.
+    """)
 
 
 commentVerifier.check(doxygen_translate.htmlEntitiesFunction.__doc__,
@@ -253,7 +253,7 @@ r"""
     "
     -
     --
-     
+
     x
     -
     .
diff --git a/Source/DoxygenTranslator/src/PyDocConverter.cpp b/Source/DoxygenTranslator/src/PyDocConverter.cpp
index afe979e10..d27a677d3 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/PyDocConverter.cpp
@@ -24,6 +24,72 @@ std::map<std::string, std::string> PyDocConverter::sectionTitles;
 
 using std::string;
 
+// Helper class increasing the provided indent string in its ctor and decreasing
+// it in its dtor.
+class IndentGuard
+{
+public:
+  // One indent level.
+  static const char* Level() { return "    "; }
+
+  // Ctor takes the output to determine the current indent and to remove the
+  // extra indent added to it in the dtor and the variable containing the indent
+  // to use, which must be used after every new line by the code actually
+  // updating the output.
+  explicit IndentGuard(string& output, string& indent) :
+    m_output(output),
+    m_indent(indent)
+  {
+    const size_t lastNonSpace = m_output.find_last_not_of(' ');
+    if (lastNonSpace == string::npos) {
+      m_firstLineIndent = m_output.length();
+    } else if (m_output[lastNonSpace] == '\n') {
+      m_firstLineIndent = m_output.length() - (lastNonSpace + 1);
+    } else {
+      m_firstLineIndent = 0;
+    }
+
+    // Notice that the indent doesn't include the first line indent because it's
+    // implicit, i.e. it is present in the input and so is copied into the
+    // output anyhow.
+    m_indent = Level();
+  }
+
+  // Get the indent for the first line of the paragraph, which is smaller than
+  // the indent for the subsequent lines.
+  string getFirstLineIndent() const { return string(m_firstLineIndent, ' '); }
+
+  ~IndentGuard()
+  {
+    m_indent.clear();
+
+    // Get rid of possible remaining extra indent, e.g. if there were any trailing
+    // new lines: we shouldn't add the extra indent level to whatever follows
+    // this paragraph.
+    static const size_t lenIndentLevel = strlen(Level());
+    if (m_output.length() > lenIndentLevel) {
+      const size_t start = m_output.length() - lenIndentLevel;
+      if (m_output.compare(start, string::npos, Level()) == 0)
+          m_output.erase(start);
+    }
+  }
+
+private:
+  string& m_output;
+  string& m_indent;
+  unsigned m_firstLineIndent;
+
+  IndentGuard(const IndentGuard&);
+  IndentGuard& operator=(const IndentGuard&);
+};
+
+static void trimWhitespace(string& s)
+{
+  const size_t lastNonSpace = s.find_last_not_of(' ');
+  if (lastNonSpace != string::npos)
+    s.erase(lastNonSpace + 1);
+}
+
 /* static */
 PyDocConverter::TagHandlersMap::mapped_type
 PyDocConverter::make_handler(tagHandler handler)
@@ -311,13 +377,27 @@ void PyDocConverter::handleMath(DoxygenEntity &tag,
                                 std::string &translatedComment,
                                 const std::string& arg)
 {
+  IndentGuard indent(translatedComment, m_indent);
+
   // Only \f$ is translated to inline formulae, \f[ and \f{ are for the block ones.
   const bool inlineFormula = tag.typeOfEntity == "f$";
 
+  string formulaNL;
+
   if (inlineFormula) {
     translatedComment += ":math:`";
   } else {
-    translatedComment += ".. math::\n\n    ";
+    trimWhitespace(translatedComment);
+    translatedComment += '\n';
+
+    const string formulaIndent = indent.getFirstLineIndent();
+    translatedComment += formulaIndent;
+    translatedComment += ".. math::\n";
+
+    formulaNL = '\n';
+    formulaNL += formulaIndent;
+    formulaNL += m_indent;
+    translatedComment += formulaNL;
   }
 
   std::string formula;
@@ -330,10 +410,9 @@ void PyDocConverter::handleMath(DoxygenEntity &tag,
   if (start != std::string::npos) {
     for (size_t n = start; n <= end; n++) {
       if (formula[n] == '\n') {
-        // New lines must be suppressed in inline maths and indented in the
-        // block ones.
+        // New lines must be suppressed in inline maths and indented in the block ones.
         if (!inlineFormula)
-          translatedComment += "\n    ";
+          translatedComment += formulaNL;
       } else {
         // Just copy everything else.
         translatedComment += formula[n];
@@ -344,7 +423,7 @@ void PyDocConverter::handleMath(DoxygenEntity &tag,
   if (inlineFormula) {
     translatedComment += "`";
   } else {
-    translatedComment += "\n\n";
+    translatedComment += '\n';
   }
 }
 
@@ -427,16 +506,21 @@ void PyDocConverter::handleTagParam(DoxygenEntity& tag,
   if (tag.entityList.size() < 2)
     return;
 
+  IndentGuard indent(translatedComment, m_indent);
+
   DoxygenEntity paramNameEntity = *tag.entityList.begin();
   tag.entityList.pop_front();
 
   const std::string& paramName = paramNameEntity.data;
 
   const std::string paramType = getParamType(paramName);
-  if (!paramType.empty())
+  if (!paramType.empty()) {
     translatedComment += ":type " + paramName + ": " + paramType + "\n";
+    translatedComment += indent.getFirstLineIndent();
+  }
 
   translatedComment += ":param " + paramName + ":";
+
   handleParagraph(tag, translatedComment);
 }
 
@@ -445,6 +529,8 @@ void PyDocConverter::handleTagReturn(DoxygenEntity &tag,
                                      std::string &translatedComment,
                                      const std::string &)
 {
+  IndentGuard indent(translatedComment, m_indent);
+
   translatedComment += ":return: ";
   handleParagraph(tag, translatedComment);
 }
@@ -454,6 +540,8 @@ void PyDocConverter::handleTagException(DoxygenEntity &tag,
                                         std::string &translatedComment,
                                         const std::string &)
 {
+  IndentGuard indent(translatedComment, m_indent);
+
   translatedComment += ":raises: ";
   handleParagraph(tag, translatedComment);
 }
@@ -618,7 +706,11 @@ void PyDocConverter::handleNewLine(DoxygenEntity&,
                                    std::string& translatedComment,
                                    const std::string&)
 {
+  trimWhitespace(translatedComment);
+
   translatedComment += "\n";
+  if (!m_indent.empty())
+    translatedComment += m_indent;
 }
 
 String *PyDocConverter::makeDocumentation(Node *n)
diff --git a/Source/DoxygenTranslator/src/PyDocConverter.h b/Source/DoxygenTranslator/src/PyDocConverter.h
index 9257e14a8..dae0ec62c 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.h
+++ b/Source/DoxygenTranslator/src/PyDocConverter.h
@@ -174,6 +174,10 @@ private:
   // temporary thing, should be refactored somehow
   Node *currentNode;
 
+  // Extra indent for the current paragraph, must be output after each new line.
+  std::string m_indent;
+
+
   // this contains the handler pointer and one string argument
   typedef std::map<std::string, std::pair<tagHandler, std::string> > TagHandlersMap;
   static TagHandlersMap tagHandlers;

From 0d4f0683be2cadc04de867f8e1e0a95ac9530a94 Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Mon, 11 Aug 2014 00:37:19 +0200
Subject: [PATCH 221/314] Make Language::classLookup() and enumLookup() static.

This will allow to reuse them in the code that doesn't have access to a
Language object, such as DoxygenTranslator implementation.

These methods didn't really use any of Language object non-static fields
anyhow, the only one they did use (classtypes or enumtypes, respectively), was
only used for caching and can just as well be made local to the function
itself as long as we use other global variables anyhow.
---
 Source/Modules/lang.cxx  | 18 +++++++++++-------
 Source/Modules/swigmod.h |  6 ++----
 2 files changed, 13 insertions(+), 11 deletions(-)

diff --git a/Source/Modules/lang.cxx b/Source/Modules/lang.cxx
index 824018c4a..aa0f7d949 100644
--- a/Source/Modules/lang.cxx
+++ b/Source/Modules/lang.cxx
@@ -318,8 +318,6 @@ none_comparison(NewString("$arg != 0")),
 director_ctor_code(NewString("")),
 director_prot_ctor_code(0),
 symtabs(NewHash()),
-classtypes(NewHash()),
-enumtypes(NewHash()),
 overloading(0),
 multiinput(0),
 cplus_runtime(0),
@@ -346,8 +344,6 @@ directors(0) {
 
 Language::~Language() {
   Delete(symtabs);
-  Delete(classtypes);
-  Delete(enumtypes);
   Delete(director_ctor_code);
   Delete(none_comparison);
   this_ = 0;
@@ -3209,11 +3205,13 @@ Node *Language::symbolLookup(String *s, const_String_or_char_ptr scope) {
  * Tries to locate a class from a type definition
  * ----------------------------------------------------------------------------- */
 
-Node *Language::classLookup(const SwigType *s) const {
+Node *Language::classLookup(const SwigType *s) {
+  static Hash *classtypes = 0;
+
   Node *n = 0;
 
   /* Look in hash of cached values */
-  n = Getattr(classtypes, s);
+  n = classtypes ? Getattr(classtypes, s) : 0;
   if (!n) {
     Symtab *stab = 0;
     SwigType *ty1 = SwigType_typedef_resolve_all(s);
@@ -3268,6 +3266,8 @@ Node *Language::classLookup(const SwigType *s) const {
       }
       if (acceptable_prefix) {
 	SwigType *cs = Copy(s);
+	if (!classtypes)
+	  classtypes = NewHash();
 	Setattr(classtypes, cs, n);
 	Delete(cs);
       } else {
@@ -3294,10 +3294,12 @@ Node *Language::classLookup(const SwigType *s) const {
  * ----------------------------------------------------------------------------- */
 
 Node *Language::enumLookup(SwigType *s) {
+  static Hash *enumtypes = 0;
+
   Node *n = 0;
 
   /* Look in hash of cached values */
-  n = Getattr(enumtypes, s);
+  n = enumtypes ? Getattr(enumtypes, s) : 0;
   if (!n) {
     Symtab *stab = 0;
     SwigType *lt = SwigType_ltype(s);
@@ -3338,6 +3340,8 @@ Node *Language::enumLookup(SwigType *s) {
     if (n) {
       /* Found a match.  Look at the prefix.  We only allow simple types. */
       if (Len(prefix) == 0) {	/* Simple type */
+	if (!enumtypes)
+	  enumtypes = NewHash();
 	Setattr(enumtypes, Copy(s), n);
       } else {
 	n = 0;
diff --git a/Source/Modules/swigmod.h b/Source/Modules/swigmod.h
index 2922a6057..84a15b0d1 100644
--- a/Source/Modules/swigmod.h
+++ b/Source/Modules/swigmod.h
@@ -225,8 +225,8 @@ public:
   virtual Hash* symbolAddScope(const_String_or_char_ptr scope);
   virtual Hash* symbolScopeLookup(const_String_or_char_ptr scope);
   virtual Hash* symbolScopePseudoSymbolLookup(const_String_or_char_ptr scope);
-  virtual Node *classLookup(const SwigType *s) const; /* Class lookup      */
-  virtual Node *enumLookup(SwigType *s);	/* Enum lookup       */
+  static Node *classLookup(const SwigType *s); /* Class lookup      */
+  static Node *enumLookup(SwigType *s);	/* Enum lookup       */
   virtual int abstractClassTest(Node *n);	/* Is class really abstract? */
   virtual int is_assignable(Node *n);	/* Is variable assignable? */
   virtual String *runtimeCode();	/* returns the language specific runtime code */
@@ -349,8 +349,6 @@ protected:
 
 private:
   Hash *symtabs; /* symbol tables */
-  Hash *classtypes;
-  Hash *enumtypes;
   int overloading;
   int multiinput;
   int cplus_runtime;

From bb01e06a6af9d793f66c890e4638a641ab5fad57 Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Tue, 5 Aug 2014 16:21:09 +0200
Subject: [PATCH 222/314] Make Python parameters types hyperlinks in the doc
 strings.

It is very useful to be able to click on the parameter types in a function
documentation to go to this parameter description, so always use hyperlink
markup for the parameters of class types, even if not all of them are
necessarily documented -- Sphinx doesn't seem to complain about links to
unknown classes.
---
 .../python/doxygen_basic_translate_runme.py   |  2 +-
 .../DoxygenTranslator/src/PyDocConverter.cpp  | 28 ++++++++++++++-----
 2 files changed, 22 insertions(+), 8 deletions(-)

diff --git a/Examples/test-suite/python/doxygen_basic_translate_runme.py b/Examples/test-suite/python/doxygen_basic_translate_runme.py
index 3018b72de..eb9886ac9 100644
--- a/Examples/test-suite/python/doxygen_basic_translate_runme.py
+++ b/Examples/test-suite/python/doxygen_basic_translate_runme.py
@@ -71,7 +71,7 @@ commentVerifier.check(doxygen_basic_translate.function7.__doc__,
     """
     Test for a parameter with difficult type
     (mostly for python)
-    :type a: Shape
+    :type a: :py:class:`Shape`
     :param a: Very strange param
     """
 )
diff --git a/Source/DoxygenTranslator/src/PyDocConverter.cpp b/Source/DoxygenTranslator/src/PyDocConverter.cpp
index d27a677d3..7571038d9 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/PyDocConverter.cpp
@@ -18,6 +18,8 @@
 #include <vector>
 #include <iostream>
 
+#include "swigmod.h"
+
 // define static tables, they are filled in PyDocConverter's constructor
 PyDocConverter::TagHandlersMap PyDocConverter::tagHandlers;
 std::map<std::string, std::string> PyDocConverter::sectionTitles;
@@ -309,19 +311,31 @@ std::string PyDocConverter::getParamType(std::string param)
 
   ParmList *plist = CopyParmList(Getattr(currentNode, "parms"));
   for (Parm *p = plist; p;p = nextSibling(p)) {
-    if (Char (Getattr(p, "name")) != param)
+    String* pname = Getattr(p, "name");
+    if (Char (pname) != param)
       continue;
 
-    String *s = Swig_typemap_lookup("doctype", p, Getattr(p, "name"), 0);
+    String *s = Swig_typemap_lookup("doctype", p, pname, 0);
     if (!s)
       s = SwigType_str(Getattr(p, "type"), "");
 
-    // In Python C++ namespaces are flattened, so remove all but last component
-    // of the name.
-    String * const last = Swig_scopename_last(s);
+    if (Language::classLookup(s)) {
+      // In Python C++ namespaces are flattened, so remove all but last component
+      // of the name.
+      String * const last = Swig_scopename_last(s);
+
+      // We are not actually sure whether it's a documented class or not, but
+      // there doesn't seem to be any harm in making it a reference if it isn't,
+      // while there is a lot of benefit in having a hyperlink if it is.
+      type = ":py:class:`";
+      type += Char (last);
+      type += "`";
+
+      Delete(last);
+    } else {
+      type = Char(s);
+    }
 
-    type = Char (s);
-    Delete(last);
     Delete(s);
     break;
   }

From 0f21adf3f933149198069f314d913fe32ef8d6d9 Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Tue, 5 Aug 2014 01:48:49 +0200
Subject: [PATCH 223/314] Add a simple test of multiple parameters to Doxygen
 test suite.

Ensure that translating more than one @param tag works correctly.
---
 Examples/test-suite/doxygen_basic_translate.i        | 12 ++++++++++++
 .../java/doxygen_basic_translate_runme.java          | 11 +++++++++--
 .../python/doxygen_basic_translate_runme.py          | 12 ++++++++++++
 3 files changed, 33 insertions(+), 2 deletions(-)

diff --git a/Examples/test-suite/doxygen_basic_translate.i b/Examples/test-suite/doxygen_basic_translate.i
index 02f5a1c14..b8bd7668a 100644
--- a/Examples/test-suite/doxygen_basic_translate.i
+++ b/Examples/test-suite/doxygen_basic_translate.i
@@ -92,6 +92,18 @@ void function7(Shape::superType *a[10])
 {
 }
 
+/**
+    Multiple parameters test.
+
+    @param y Vertical coordinate.
+    @param x Horizontal coordinate.
+    @return Arc tangent of @c y/x.
+ */
+double Atan2(double y, double x)
+{
+    return 0;
+}
+
 /**
  * Comment at the end of file should be ignored.
  */
diff --git a/Examples/test-suite/java/doxygen_basic_translate_runme.java b/Examples/test-suite/java/doxygen_basic_translate_runme.java
index e6fbd0414..f307b3abc 100644
--- a/Examples/test-suite/java/doxygen_basic_translate_runme.java
+++ b/Examples/test-suite/java/doxygen_basic_translate_runme.java
@@ -85,8 +85,15 @@ public class doxygen_basic_translate_runme {
     		" This is function <b>two </b>\n" +
     		" \n" +
     		"");
-    
+    wantedComments.put("doxygen_basic_translate.doxygen_basic_translate.Atan2(double, double)",
+    		" Multiple parameters test.\n" +
+    		" \n" +
+    		" @param y Vertical coordinate.\n" +
+    		" @param x Horizontal coordinate.\n" +
+    		" @return Arc tangent of <code>y/x</code>.\n" +
+    		"");
+
     // and ask the parser to check comments for us
     System.exit(parser.check(wantedComments));
   }
-}
\ No newline at end of file
+}
diff --git a/Examples/test-suite/python/doxygen_basic_translate_runme.py b/Examples/test-suite/python/doxygen_basic_translate_runme.py
index eb9886ac9..1275d11cf 100644
--- a/Examples/test-suite/python/doxygen_basic_translate_runme.py
+++ b/Examples/test-suite/python/doxygen_basic_translate_runme.py
@@ -75,3 +75,15 @@ commentVerifier.check(doxygen_basic_translate.function7.__doc__,
     :param a: Very strange param
     """
 )
+
+commentVerifier.check(doxygen_basic_translate.Atan2.__doc__,
+"""
+    Multiple parameters test.
+
+    :type y: float
+    :param y: Vertical coordinate.
+    :type x: float
+    :param x: Horizontal coordinate.
+    :return: Arc tangent of ``y/x``.
+    """
+)

From d678891e43816ab39fcfb08694627fc814f596e8 Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Wed, 6 Aug 2014 18:18:20 +0200
Subject: [PATCH 224/314] Translate Doxygen code blocks to Sphinx code blocks.

This ensures they are formatted correctly and syntax highlighted (currently
always as C++ code).
---
 .../python/doxygen_basic_translate_runme.py   |  5 +-
 .../doxygen_translate_all_tags_runme.py       |  6 ++-
 .../python/doxygen_translate_runme.py         |  6 ++-
 .../DoxygenTranslator/src/PyDocConverter.cpp  | 47 ++++++++++++++++++-
 Source/DoxygenTranslator/src/PyDocConverter.h |  5 ++
 5 files changed, 65 insertions(+), 4 deletions(-)

diff --git a/Examples/test-suite/python/doxygen_basic_translate_runme.py b/Examples/test-suite/python/doxygen_basic_translate_runme.py
index 1275d11cf..1e017fb74 100644
--- a/Examples/test-suite/python/doxygen_basic_translate_runme.py
+++ b/Examples/test-suite/python/doxygen_basic_translate_runme.py
@@ -50,7 +50,10 @@ commentVerifier.check(doxygen_basic_translate.function4.__doc__,
 
     Warning: This may not work as expected
 
-    int main() { while(true); }
+    .. code-block:: c++
+
+
+        int main() { while(true); }
 
     }
     """
diff --git a/Examples/test-suite/python/doxygen_translate_all_tags_runme.py b/Examples/test-suite/python/doxygen_translate_all_tags_runme.py
index c74ba4828..9df2df593 100644
--- a/Examples/test-suite/python/doxygen_translate_all_tags_runme.py
+++ b/Examples/test-suite/python/doxygen_translate_all_tags_runme.py
@@ -36,7 +36,11 @@ r"""
 
     'citationword'
 
-    some test code
+
+    .. code-block:: c++
+
+         some test code
+
     """)
 
 commentVerifier.check(doxygen_translate_all_tags.func02.__doc__,
diff --git a/Examples/test-suite/python/doxygen_translate_runme.py b/Examples/test-suite/python/doxygen_translate_runme.py
index 55c5d8c9a..788bc90eb 100644
--- a/Examples/test-suite/python/doxygen_translate_runme.py
+++ b/Examples/test-suite/python/doxygen_translate_runme.py
@@ -22,7 +22,11 @@ r"""
 
     'citationword'
 
-    some test code
+
+    .. code-block:: c++
+
+         some test code
+
 
     Conditional comment: SOMECONDITION
     Some conditional comment
diff --git a/Source/DoxygenTranslator/src/PyDocConverter.cpp b/Source/DoxygenTranslator/src/PyDocConverter.cpp
index 7571038d9..e7a55e1ba 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/PyDocConverter.cpp
@@ -153,7 +153,7 @@ void PyDocConverter::fillStaticTables()
   tagHandlers["authors"] = make_handler(&PyDocConverter::handleParagraph);
   tagHandlers["brief"] = make_handler(&PyDocConverter::handleParagraph);
   tagHandlers["bug"] = make_handler(&PyDocConverter::handleParagraph);
-  tagHandlers["code"] = make_handler(&PyDocConverter::handleParagraph);
+  tagHandlers["code"] = make_handler(&PyDocConverter::handleCode);
   tagHandlers["copyright"] = make_handler(&PyDocConverter::handleParagraph);
   tagHandlers["date"] = make_handler(&PyDocConverter::handleParagraph);
   tagHandlers["deprecated"] = make_handler(&PyDocConverter::handleParagraph);
@@ -441,6 +441,51 @@ void PyDocConverter::handleMath(DoxygenEntity &tag,
   }
 }
 
+void PyDocConverter::handleCode(DoxygenEntity &tag,
+                                std::string &translatedComment,
+                                const std::string &arg)
+{
+  IndentGuard indent(translatedComment, m_indent);
+
+  trimWhitespace(translatedComment);
+  translatedComment += '\n';
+
+  // Use the current indent for the code-block line itself.
+  string codeIndent = indent.getFirstLineIndent();
+  translatedComment += codeIndent;
+
+  // Go out on a limb and assume that examples in the C or C++ sources use C++.
+  // In the worst case, we'll highlight C code using C++ syntax which is not a
+  // big deal (TODO: handle Doxygen code command language argument).
+  translatedComment += ".. code-block:: c++\n\n";
+
+  // For now on, use extra indent level for all the subsequent lines.
+  codeIndent += m_indent;
+
+  std::string code;
+  handleTagVerbatim(tag, code, arg);
+
+  translatedComment += codeIndent;
+  for (size_t n = 0; n < code.length(); n++) {
+    if (code[n] == '\n') {
+      // Don't leave trailing white space, this results in PEP8 validation
+      // errors in Python code (which are performed by our own unit tests).
+      trimWhitespace(translatedComment);
+      translatedComment += '\n';
+
+      // Ensure that we indent all the lines by the code indent.
+      translatedComment += codeIndent;
+    } else {
+      // Just copy everything else.
+      translatedComment += code[n];
+    }
+  }
+
+  trimWhitespace(translatedComment);
+  if (*translatedComment.rbegin() != '\n')
+    translatedComment += '\n';
+}
+
 void PyDocConverter::handlePlainString(DoxygenEntity& tag,
                                        std::string& translatedComment,
                                        const std::string&)
diff --git a/Source/DoxygenTranslator/src/PyDocConverter.h b/Source/DoxygenTranslator/src/PyDocConverter.h
index dae0ec62c..338b1fed9 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.h
+++ b/Source/DoxygenTranslator/src/PyDocConverter.h
@@ -81,6 +81,11 @@ protected:
    */
   void handleMath(DoxygenEntity &tag, std::string &translatedComment, const std::string &arg);
 
+  /*
+   * Handle a code snippet.
+   */
+  void handleCode(DoxygenEntity &tag, std::string &translatedComment, const std::string &arg);
+
   /*
    * Print only data part of code
    */

From 16548cced02882e82e02012b28b38219e350abf2 Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Thu, 7 Aug 2014 00:25:06 +0200
Subject: [PATCH 225/314] Simplify and make more efficient building Python
 docstrings.

Make the rules for combining explicitly specified docstring, autodoc one and
the one obtained by translating Doxygen comments implicit in the structure of
the code itself instead of writing complicated conditions checking them.

This results in small changes to the whitespace in the generated Python code
when using autodoc, but this makes it PEP 8-compliant, so it is the right
thing to do anyhow.

Also cache the docstring built from translated Doxygen comments. The existing
code seemed to intend to do it, but didn't, really. This helps with
performance generally speaking (-10% for a relatively big library using a lot
of Doxygen comments) and also makes debugging Doxygen translation code less
painful as it's executed only once instead of twice for each comment.

Finally, avoid putting "r", used for Python raw strings, into docstrings in C
code, it is really not needed there.
---
 Examples/test-suite/python/autodoc_runme.py   |  12 +-
 .../python/doxygen_basic_notranslate_runme.py |   4 +-
 .../python/doxygen_basic_translate_runme.py   |   4 +-
 Source/Modules/python.cxx                     | 137 +++++++++++-------
 4 files changed, 88 insertions(+), 69 deletions(-)

diff --git a/Examples/test-suite/python/autodoc_runme.py b/Examples/test-suite/python/autodoc_runme.py
index 03a01960b..5312802f6 100644
--- a/Examples/test-suite/python/autodoc_runme.py
+++ b/Examples/test-suite/python/autodoc_runme.py
@@ -124,19 +124,17 @@ if sys.version_info[0:2] > (2, 4):
   # Python 2.4 does not seem to work
   commentVerifier.check(A.variable_a.__doc__, "A_variable_a_get(self) -> int")
   commentVerifier.check(A.variable_b.__doc__, "A_variable_b_get(A self) -> int")
-  commentVerifier.check(A.variable_c.__doc__, "\n"
+  commentVerifier.check(A.variable_c.__doc__,
   "A_variable_c_get(self) -> int\n"
   "\n"
   "Parameters:\n"
   "    self: A *\n"
-  "\n"
   )
-  commentVerifier.check(A.variable_d.__doc__, "\n"
+  commentVerifier.check(A.variable_d.__doc__,
   "A_variable_d_get(A self) -> int\n"
   "\n"
   "Parameters:\n"
   "    self: A *\n"
-  "\n"
   )
 
 commentVerifier.check(B.__doc__, "Proxy of C++ B class")
@@ -166,9 +164,9 @@ commentVerifier.check(F.__init__.__doc__, "\n"
 commentVerifier.check(B.funk.__doc__, "funk(B self, int c, int d) -> int")
 commentVerifier.check(funk.__doc__, "funk(A e, short arg2, int c, int d) -> int")
 commentVerifier.check(funkdefaults.__doc__, "\n"
-"  funkdefaults(A e, short arg2, int c, int d, double f=2) -> int\n"
-"  funkdefaults(A e, short arg2, int c, int d) -> int\n"
-"  "
+"    funkdefaults(A e, short arg2, int c, int d, double f=2) -> int\n"
+"    funkdefaults(A e, short arg2, int c, int d) -> int\n"
+"    "
 )
 
 commentVerifier.check(func_input.__doc__, "func_input(int * INPUT) -> int")
diff --git a/Examples/test-suite/python/doxygen_basic_notranslate_runme.py b/Examples/test-suite/python/doxygen_basic_notranslate_runme.py
index bb2fae0f5..27dcb4a7e 100644
--- a/Examples/test-suite/python/doxygen_basic_notranslate_runme.py
+++ b/Examples/test-suite/python/doxygen_basic_notranslate_runme.py
@@ -61,9 +61,7 @@ commentVerifier.check(doxygen_basic_notranslate.function4.__doc__,
     """
 )
 commentVerifier.check(doxygen_basic_notranslate.function5.__doc__,
-    r"""
-    This is a post comment. 
-    """
+    r""" This is a post comment. """
 )
 commentVerifier.check(doxygen_basic_notranslate.function6.__doc__,
     r"""
diff --git a/Examples/test-suite/python/doxygen_basic_translate_runme.py b/Examples/test-suite/python/doxygen_basic_translate_runme.py
index 1e017fb74..b5ba162e2 100644
--- a/Examples/test-suite/python/doxygen_basic_translate_runme.py
+++ b/Examples/test-suite/python/doxygen_basic_translate_runme.py
@@ -59,9 +59,7 @@ commentVerifier.check(doxygen_basic_translate.function4.__doc__,
     """
 )
 commentVerifier.check(doxygen_basic_translate.function5.__doc__,
-    """
-    This is a post comment.
-    """
+    """ This is a post comment."""
 )
 commentVerifier.check(doxygen_basic_translate.function6.__doc__,
     """
diff --git a/Source/Modules/python.cxx b/Source/Modules/python.cxx
index b76b83ebb..39703bc7e 100644
--- a/Source/Modules/python.cxx
+++ b/Source/Modules/python.cxx
@@ -1476,38 +1476,76 @@ public:
   }
 
   /* ------------------------------------------------------------
-   * docstring()
-   *    Get the docstring text, stripping off {} if neccessary,
-   *    and enclose in triple double quotes.  If autodoc is also
-   *    set then it will build a combined docstring.
+   * build_combined_docstring()
+   *    Build the full docstring which may be a combination of the
+   *    explicit docstring and autodoc string or, if none of them
+   *    is specified, obtained by translating Doxygen comment to
+   *    Python.
+   *
+   *    Return new string to be deleted by caller (never NIL but
+   *    may be empty if there is no docstring).
    * ------------------------------------------------------------ */
-
-  String *docstring(Node *n, autodoc_t ad_type, const String *indent, bool use_triple = true) {
-    String *str = Getattr(n, "feature:docstring");
-    String *doxygen_comment = 0;
-    bool have_ds = (str && Len(str) > 0);
-    bool have_auto = (Getattr(n, "feature:autodoc") && !GetFlag(n, "feature:noautodoc"));
-    bool have_doxygen = doxygen && doxygenTranslator->hasDocumentation(n);
-    const char *triple_double = use_triple ? "\"\"\"" : "";
-    String *autodoc = NULL;
-    String *doc = NULL;
-
-    if (have_ds) {
-      char *t = Char(str);
+  String *build_combined_docstring(Node *n, autodoc_t ad_type) {
+    String *docstr = Getattr(n, "feature:docstring");
+    if (docstr && Len(docstr)) {
+      docstr = Copy(docstr);
+      char *t = Char(docstr);
       if (*t == '{') {
-	Delitem(str, 0);
-	Delitem(str, DOH_END);
+	Delitem(docstr, 0);
+	Delitem(docstr, DOH_END);
       }
     }
 
-    if (have_auto) {
-      autodoc = make_autodoc(n, ad_type);
-      have_auto = (autodoc && Len(autodoc) > 0);
+    if (Getattr(n, "feature:autodoc") && !GetFlag(n, "feature:noautodoc")) {
+      String* autodoc = make_autodoc(n, ad_type);
+      if (autodoc && Len(autodoc) > 0) {
+	if (docstr && Len(docstr)) {
+	  Append(autodoc, "\n");
+	  Append(autodoc, docstr);
+	}
+
+	String* tmp = autodoc;
+	autodoc = docstr;
+	docstr = tmp;
+      }
+
+      Delete(autodoc);
     }
-    if (have_doxygen) {
-      doxygen_comment = doxygenTranslator->getDocumentation(n);
-      have_doxygen = (doxygen_comment && Len(doxygen_comment) > 0);
+
+    if (!docstr || !Len(docstr)) {
+      if (doxygen) {
+	docstr = Getattr(n, "python:docstring");
+	if (!docstr && doxygenTranslator->hasDocumentation(n)) {
+	  docstr = doxygenTranslator->getDocumentation(n);
+
+	  // Avoid rebuilding it again the next time: notice that we can't do
+	  // this for the combined doc string as autodoc part of it depends on
+	  // the sym:name of the node and it is changed while handling it, so
+	  // the cached results become incorrect. But Doxygen docstring only
+	  // depends on the comment which is not going to change, so we can
+	  // safely cache it.
+	  Setattr(n, "python:docstring", Copy(docstr));
+	}
+      }
     }
+
+    if (!docstr)
+      docstr = NewString("");
+
+    return docstr;
+  }
+
+  /* ------------------------------------------------------------
+   * docstring()
+   *    Get the docstring text enclosed in triple double quotes.
+   * ------------------------------------------------------------ */
+
+  String *docstring(Node *n, autodoc_t ad_type, const String *indent) {
+    String *docstr = build_combined_docstring(n, ad_type);
+    if (!Len(docstr))
+      return docstr;
+
+
     // If there is more than one line then make docstrings like this:
     //
     //      """
@@ -1517,45 +1555,32 @@ public:
     //
     // otherwise, put it all on a single line
     //
-    // All comments translated from doxygen are given as raw strings (prefix "r"),
+    // Notice that all comments are created as raw strings (prefix "r"),
     // because '\' is used often in comments, but may break Python module from
     // loading. For example, in doxy comment one may write path in quotes:
     //
     //     This is path to file "C:\x\file.txt"
     //
-    // Python will no load the module with such comment because of illegal
+    // Python will not load the module with such comment because of illegal
     // escape '\x'. '\' may additionally appear in verbatim or htmlonly sections
     // of doxygen doc, Latex expressions, ...
-    if (have_auto && have_ds) {	// Both autodoc and docstring are present
-      doc = NewString("");
-      Printv(doc, "r", triple_double, "\n", pythoncode(autodoc, indent), "\n", pythoncode(str, indent), indent, triple_double, NIL);
-    } else if (!have_auto && have_ds) {	// only docstring
-      if (Strchr(str, '\n') == 0) {
-	doc = NewStringf("%s%s%s", triple_double, str, triple_double);
-      } else {
-	doc = NewString("");
-	Printv(doc, "r", triple_double, "\n", pythoncode(str, indent), indent, triple_double, NIL);
-      }
-    } else if (have_auto && !have_ds) {	// only autodoc
-      if (Strchr(autodoc, '\n') == 0) {
-	doc = NewStringf("%s%s%s", triple_double, autodoc, triple_double);
-      } else {
-	doc = NewString("");
-	Printv(doc, triple_double, "\n", pythoncode(autodoc, indent), indent, triple_double, NIL);
-      }
-    } else if (have_doxygen) { // the lowest priority
-      doc = NewString("");
-      Printv(doc, "r", triple_double, "\n", pythoncode(doxygen_comment, indent), indent, triple_double, NIL);
-    }
-    else
-      doc = NewString("");
+    String *doc = NewString("");
+    Append(doc, "r\"\"\"");
+
+    if (Strchr(docstr, '\n') == 0) {
+      Append(doc, docstr);
+    } else {
+      Append(doc, "\n");
+      Append(doc, pythoncode(docstr, indent));
+      Append(doc, indent);
+    }
+
+    Append(doc, "\"\"\"");
+
+    Delete(docstr);
 
-    // Save the generated strings in the parse tree in case they are used later
-    // by post processing tools
-    Setattr(n, "python:docstring", doc);
-    Setattr(n, "python:autodoc", autodoc);
     return doc;
-  }   
+  }
 
   /* ------------------------------------------------------------
    * cdocstring()
@@ -1565,7 +1590,7 @@ public:
 
   String *cdocstring(Node *n, autodoc_t ad_type)
   {
-    String *ds = docstring(n, ad_type, "", false);
+    String *ds = build_combined_docstring(n, ad_type);
     Replaceall(ds, "\\", "\\\\");
     Replaceall(ds, "\"", "\\\"");
     Replaceall(ds, "\n", "\\n\"\n\t\t\"");

From 9a511f1a33daa30e4edb659cdcf04fa23adaa14b Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Sun, 10 Aug 2014 14:40:35 +0200
Subject: [PATCH 226/314] Remove long line wrapping from Python parameter list
 generation code.

This doesn't play well with PEP8 checks which imposes very strict continuation
line indentation rules which need to be _visually_ aligned, i.e. the subsequent
lines must be indented by the position of the opening bracket in the function
declaration line, but the code generating the parameter lists doesn't have
this information and so it's impossible to do it while avoiding either E128 or
E123 ("continuation line {under,over}-indented for visual indent" respectively)
error from pep8.

Moreover, the wrapping code didn't work correctly anyhow as it only took into
account the length of the parameter list itself and not the total line length,
which should include the function name as well.

So just disable wrapping entirely, long lines shouldn't be a problem anyhow in
auto-generated code.
---
 Source/Modules/python.cxx | 8 --------
 1 file changed, 8 deletions(-)

diff --git a/Source/Modules/python.cxx b/Source/Modules/python.cxx
index 39703bc7e..825072269 100644
--- a/Source/Modules/python.cxx
+++ b/Source/Modules/python.cxx
@@ -1637,9 +1637,7 @@ public:
     Parm *pnext;
 
 
-    int lines = 0;
     int start_arg_num = is_wrapping_class() ? 1 : 0;
-    const int maxwidth = 80;
 
     if (calling)
       func_annotation = false;
@@ -1689,12 +1687,6 @@ public:
       if (Len(doc)) {
 	// add a comma to the previous one if any
 	Append(doc, ", ");
-
-	// Do we need to wrap a long line?
-	if ((Len(doc) - lines * maxwidth) > maxwidth) {
-	  Printf(doc, "\n%s", tab4);
-	  lines += 1;
-	}
       }
 
       // Do the param type too?

From 8c762706194d6becdf4835e5a3e3037b1c34149b Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Sat, 16 Aug 2014 00:21:33 +0200
Subject: [PATCH 227/314] Refactor: move makeParameterName() to common Language
 base class.

This method was duplicated more or less identically for 4 languages and will
be needed for another one soon, so put it in the base class from which it can
be simply reused instead.

No changes in the program behaviour whatsoever.
---
 Source/Modules/csharp.cxx  | 37 -------------------------------------
 Source/Modules/d.cxx       | 34 +---------------------------------
 Source/Modules/java.cxx    | 38 --------------------------------------
 Source/Modules/lang.cxx    | 38 ++++++++++++++++++++++++++++++++++++++
 Source/Modules/modula3.cxx | 29 -----------------------------
 Source/Modules/swigmod.h   |  3 +++
 6 files changed, 42 insertions(+), 137 deletions(-)

diff --git a/Source/Modules/csharp.cxx b/Source/Modules/csharp.cxx
index d30bd18c5..e2dd66c03 100644
--- a/Source/Modules/csharp.cxx
+++ b/Source/Modules/csharp.cxx
@@ -3198,43 +3198,6 @@ public:
     Delete(replacementname);
   }
 
-  /* -----------------------------------------------------------------------------
-   * makeParameterName()
-   *
-   * Inputs: 
-   *   n - Node
-   *   p - parameter node
-   *   arg_num - parameter argument number
-   *   setter  - set this flag when wrapping variables
-   * Return:
-   *   arg - a unique parameter name
-   * ----------------------------------------------------------------------------- */
-
-  String *makeParameterName(Node *n, Parm *p, int arg_num, bool setter) {
-
-    String *arg = 0;
-    String *pn = Getattr(p, "name");
-
-    // Use C parameter name unless it is a duplicate or an empty parameter name
-    int count = 0;
-    ParmList *plist = Getattr(n, "parms");
-    while (plist) {
-      if ((Cmp(pn, Getattr(plist, "name")) == 0))
-        count++;
-      plist = nextSibling(plist);
-    }
-    String *wrn = pn ? Swig_name_warning(p, 0, pn, 0) : 0;
-    arg = (!pn || (count > 1) || wrn) ? NewStringf("arg%d", arg_num) : Copy(pn);
-
-    if (setter && Cmp(arg, "self") != 0) {
-      // Note that in C# properties, the input variable name is always called 'value'
-      Delete(arg);      
-      arg = NewString("value");
-    }
-
-    return arg;
-  }
-
   /* -----------------------------------------------------------------------------
    * emitTypeWrapperClass()
    * ----------------------------------------------------------------------------- */
diff --git a/Source/Modules/d.cxx b/Source/Modules/d.cxx
index 419828ea1..364a2bbee 100644
--- a/Source/Modules/d.cxx
+++ b/Source/Modules/d.cxx
@@ -4299,40 +4299,8 @@ private:
     return proxyname;
   }
 
-  /* ---------------------------------------------------------------------------
-   * D::makeParameterName()
-   *
-   * Inputs:
-   *   n - Node
-   *   p - parameter node
-   *   arg_num - parameter argument number
-   *   setter  - set this flag when wrapping variables
-   * Return:
-   *   arg - a unique parameter name
-   * --------------------------------------------------------------------------- */
   String *makeParameterName(Node *n, Parm *p, int arg_num, bool setter) const {
-    String *arg = 0;
-    String *pn = Getattr(p, "name");
-
-    // Use C parameter name unless it is a duplicate or an empty parameter name
-    int count = 0;
-    ParmList *plist = Getattr(n, "parms");
-    while (plist) {
-      if ((Cmp(pn, Getattr(plist, "name")) == 0))
-	count++;
-      plist = nextSibling(plist);
-    }
-    String *wrn = pn ? Swig_name_warning(p, 0, pn, 0) : 0;
-    arg = (!pn || (count > 1) || wrn) ? NewStringf("arg%d", arg_num) : Copy(pn);
-
-    if (setter && Cmp(arg, "self") != 0) {
-      // In theory, we could use the normal parameter name for setter functions.
-      // Unfortunately, it is set to "Class::VariableName" for static public
-      // members by the parser, which is not legal D syntax. Thus, we just force
-      // it to "value".
-      Delete(arg);
-      arg = NewString("value");
-    }
+    String *arg = Language::makeParameterName(n, p, arg_num, setter);
 
     if (split_proxy_dmodule && Strncmp(arg, package, Len(arg)) == 0) {
       // If we are in split proxy mode and the argument is named like the target
diff --git a/Source/Modules/java.cxx b/Source/Modules/java.cxx
index 4059ce9c7..c6947a37e 100644
--- a/Source/Modules/java.cxx
+++ b/Source/Modules/java.cxx
@@ -3256,44 +3256,6 @@ public:
     Delete(replacementname);
   }
 
-  /* -----------------------------------------------------------------------------
-   * makeParameterName()
-   *
-   * Inputs: 
-   *   n - Node
-   *   p - parameter node
-   *   arg_num - parameter argument number
-   *   setter  - set this flag when wrapping variables
-   * Return:
-   *   arg - a unique parameter name
-   * ----------------------------------------------------------------------------- */
-
-  String *makeParameterName(Node *n, Parm *p, int arg_num, bool setter) {
-
-    String *arg = 0;
-    String *pn = Getattr(p, "name");
-
-    // Use C parameter name unless it is a duplicate or an empty parameter name
-    int count = 0;
-    ParmList *plist = Getattr(n, "parms");
-    while (plist) {
-      if ((Cmp(pn, Getattr(plist, "name")) == 0))
-        count++;
-      plist = nextSibling(plist);
-    }
-    String *wrn = pn ? Swig_name_warning(p, 0, pn, 0) : 0;
-    arg = (!pn || (count > 1) || wrn) ? NewStringf("arg%d", arg_num) : Copy(pn);
-
-    if (setter && Cmp(arg, "self") != 0) {
-      // Note that for setters the parameter name is always set but sometimes includes C++ 
-      // scope resolution, so we need to strip off the scope resolution to make a valid name.
-      Delete(arg);
-      arg = NewString("value");	//Swig_scopename_last(pn);
-    }
-
-    return arg;
-  }
-
   /* -----------------------------------------------------------------------------
    * emitTypeWrapperClass()
    * ----------------------------------------------------------------------------- */
diff --git a/Source/Modules/lang.cxx b/Source/Modules/lang.cxx
index aa0f7d949..be6968407 100644
--- a/Source/Modules/lang.cxx
+++ b/Source/Modules/lang.cxx
@@ -3522,6 +3522,44 @@ int Language::is_smart_pointer() const {
   return SmartPointer;
 }
 
+/* -----------------------------------------------------------------------------
+ * Language::makeParameterName()
+ *
+ * Inputs: 
+ *   n - Node
+ *   p - parameter node
+ *   arg_num - parameter argument number
+ *   setter  - set this flag when wrapping variables
+ * Return:
+ *   arg - a unique parameter name
+ * ----------------------------------------------------------------------------- */
+String *Language::makeParameterName(Node *n, Parm *p, int arg_num, bool setter) const {
+
+  String *arg = 0;
+  String *pn = Getattr(p, "name");
+
+  // Use C parameter name unless it is a duplicate or an empty parameter name
+  int count = 0;
+  ParmList *plist = Getattr(n, "parms");
+  while (plist) {
+    if ((Cmp(pn, Getattr(plist, "name")) == 0))
+      count++;
+    plist = nextSibling(plist);
+  }
+  String *wrn = pn ? Swig_name_warning(p, 0, pn, 0) : 0;
+  arg = (!pn || (count > 1) || wrn) ? NewStringf("arg%d", arg_num) : Copy(pn);
+
+  if (setter && Cmp(arg, "self") != 0) {
+    // Some languages (C#) insist on calling the input variable "value" while
+    // others (D, Java) could, in principle, use something different but this
+    // would require more work, and so we just use "value" for them too.
+    Delete(arg);
+    arg = NewString("value");
+  }
+
+  return arg;
+}
+
 /* -----------------------------------------------------------------------------
  * Language::()
  * ----------------------------------------------------------------------------- */
diff --git a/Source/Modules/modula3.cxx b/Source/Modules/modula3.cxx
index db5d0981b..2d6f26108 100644
--- a/Source/Modules/modula3.cxx
+++ b/Source/Modules/modula3.cxx
@@ -3621,35 +3621,6 @@ MODULA3():
     return substitution_performed;
   }
 
-  /* -----------------------------------------------------------------------------
-   * makeParameterName()
-   *
-   * Inputs: 
-   *   n - Node
-   *   p - parameter node
-   *   arg_num - parameter argument number
-   * Return:
-   *   arg - a unique parameter name
-   * ----------------------------------------------------------------------------- */
-
-  String *makeParameterName(Node *n, Parm *p, int arg_num) {
-
-    // Use C parameter name unless it is a duplicate or an empty parameter name
-    String *pn = Getattr(p, "name");
-    int count = 0;
-    ParmList *plist = Getattr(n, "parms");
-    while (plist) {
-      if ((Cmp(pn, Getattr(plist, "name")) == 0))
-	count++;
-      plist = nextSibling(plist);
-    }
-    String *arg = (!pn || (count > 1)) ? NewStringf("arg%d",
-						    arg_num) : Copy(Getattr(p,
-									    "name"));
-
-    return arg;
-  }
-
   /* -----------------------------------------------------------------------------
    * attachParameterNames()
    *
diff --git a/Source/Modules/swigmod.h b/Source/Modules/swigmod.h
index 84a15b0d1..806295a78 100644
--- a/Source/Modules/swigmod.h
+++ b/Source/Modules/swigmod.h
@@ -303,6 +303,9 @@ protected:
   /* Return true if the current method is part of a smart-pointer */
   int is_smart_pointer() const;
 
+  /* Return the name to use for the given parameter. */
+  virtual String *makeParameterName(Node *n, Parm *p, int arg_num, bool setter = false) const;
+
   /* Some language modules require additional wrappers for virtual methods not declared in sub-classes */
   virtual bool extraDirectorProtectedCPPMethodsRequired() const;
 

From 1f41850e34e0d6004162f8a3ee298c4f69f41ae9 Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Sat, 16 Aug 2014 13:08:46 +0200
Subject: [PATCH 228/314] No real changes, just make PYTHON::check_kwargs()
 const.

This will allow calling it from const methods too.
---
 Source/Modules/python.cxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Source/Modules/python.cxx b/Source/Modules/python.cxx
index 825072269..79d1ec9b5 100644
--- a/Source/Modules/python.cxx
+++ b/Source/Modules/python.cxx
@@ -2125,7 +2125,7 @@ public:
    *    check if using kwargs is allowed for this Node
    * ------------------------------------------------------------ */
 
-  int check_kwargs(Node *n) {
+  int check_kwargs(Node *n) const {
     return (use_kw || GetFlag(n, "feature:kwargs"))
 	&& !GetFlag(n, "memberset") && !GetFlag(n, "memberget");
   }

From 8734c658d7765aa9b1829a12ddd4b9bf0deaf445 Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Sat, 9 Aug 2014 16:33:23 +0200
Subject: [PATCH 229/314] Don't always use "*args" for all Python wrapper
 functions.

Due to what seems like a bug introduced during Python 3 support merge, all the
generated Python functions used the general "*args" signature instead of using
the named parameters when possible.

This happened due to is_primitive_defaultargs() always returning false for the
functions without any default arguments as "value" passed to convertValue()
was NULL in this case and convertValue() always returns false for NULL.

Fix this by checking for value being non-NULL before calling convertValue().

Doing this exposed several problems with the handling of unnamed, duplicate
(happens for parameters called INOUT, for example) or clashing with keywords
parameter names, so the code dealing with them had to be fixed too. Basically
just use makeParameterName() consistently everywhere.
---
 Source/Modules/python.cxx | 83 ++++++++++++++++++++++++---------------
 1 file changed, 51 insertions(+), 32 deletions(-)

diff --git a/Source/Modules/python.cxx b/Source/Modules/python.cxx
index 79d1ec9b5..327a3bb16 100644
--- a/Source/Modules/python.cxx
+++ b/Source/Modules/python.cxx
@@ -1597,6 +1597,21 @@ public:
     return ds;
   }
 
+  virtual String *makeParameterName(Node *n, Parm *p, int arg_num, bool = false) const {
+    // For the keyword arguments, we want to preserve the names as much as possible,
+    // so we only minimally rename them in Swig_name_make(), e.g. replacing "keyword"
+    // with "_keyword" if they have any name at all.
+    if (check_kwargs(n)) {
+      String* name = Getattr(p, "name");
+      if (name)
+	return Swig_name_make(p, 0, name, 0, 0);
+    }
+
+    // For the other cases use the general function which replaces arguments whose
+    // names clash with keywords with (less useful) "argN".
+    return Language::makeParameterName(n, p, arg_num);
+  }
+
   /* -----------------------------------------------------------------------------
    * addMissingParameterNames()
    *  For functions that have not had nameless parameters set in the Language class.
@@ -1608,13 +1623,14 @@ public:
    *   The "lname" attribute in each parameter in plist will be contain a parameter name
    * ----------------------------------------------------------------------------- */
 
-  void addMissingParameterNames(ParmList *plist, int arg_offset) {
+  void addMissingParameterNames(Node* n, ParmList *plist, int arg_offset) {
     Parm *p = plist;
     int i = arg_offset;
     while (p) {
       if (!Getattr(p, "lname")) {
-	String *pname = Swig_cparm_name(p, i);
-	Delete(pname);
+	String *name = makeParameterName(n, p, i);
+	Setattr(p, "lname", name);
+	Delete(name);
       }
       i++;
       p = nextSibling(p);
@@ -1637,12 +1653,18 @@ public:
     Parm *pnext;
 
 
-    int start_arg_num = is_wrapping_class() ? 1 : 0;
+    // Normally we start counting auto-generated argument names from 1, but we should do it from 2
+    // if the first argument is "self", i.e. if we're handling a non-static member function.
+    int arg_num = 1;
+    if (is_wrapping_class()) {
+      if (Cmp(Getattr(n, "storage"), "static") != 0)
+	arg_num++;
+    }
 
     if (calling)
       func_annotation = false;
 
-    addMissingParameterNames(plist, start_arg_num); // for $1_name substitutions done in Swig_typemap_attach_parms
+    addMissingParameterNames(n, plist, arg_num); // for $1_name substitutions done in Swig_typemap_attach_parms
     Swig_typemap_attach_parms("in", plist, 0);
     Swig_typemap_attach_parms("doc", plist, 0);
 
@@ -1651,7 +1673,7 @@ public:
       return doc;
     }
 
-    for (p = plist; p; p = pnext) {
+    for (p = plist; p; p = pnext, arg_num++) {
 
       String *tm = Getattr(p, "tmap:in");
       if (tm) {
@@ -1674,15 +1696,18 @@ public:
       }
 
       // Note: the generated name should be consistent with that in kwnames[]
-      name = name ? name : Getattr(p, "name");
-      name = name ? name : Getattr(p, "lname");
-      name = Swig_name_make(p, 0, name, 0, 0); // rename parameter if a keyword
+      String *made_name = 0;
+      if (!name) {
+	name = made_name = makeParameterName(n, p, arg_num);
+      }
 
       type = type ? type : Getattr(p, "type");
       value = value ? value : Getattr(p, "value");
 
-      if (SwigType_isvarargs(type))
+      if (SwigType_isvarargs(type)) {
+	Delete(made_name);
 	break;
+      }
 
       if (Len(doc)) {
 	// add a comma to the previous one if any
@@ -1718,7 +1743,7 @@ public:
 	Printf(doc, "=%s", value);
       }
       Delete(type_str);
-      Delete(name);
+      Delete(made_name);
     }
     if (pdocs)
       Setattr(n, "feature:pdocs", pdocs);
@@ -1897,16 +1922,19 @@ public:
   }
   /* ------------------------------------------------------------
    * is_primitive_defaultargs()
-   *    Check if all the default args have primitive type.
-   *    (So we can generate proper parameter list with default 
-   *    values..)
+   *    Check if the function parameters default argument values
+   *    have primitive types, so that their default values could be
+   *    used in Python code.
+   *
+   *    If this method returns false, the parameters will be translated
+   *    to a generic "*args" which allows us to deal with default values
+   *    at C++ code level where they can always be handled.
    * ------------------------------------------------------------ */
   bool is_primitive_defaultargs(Node *n) {
     ParmList *plist = CopyParmList(Getattr(n, "parms"));
     Parm *p;
     Parm *pnext;
 
-    Swig_typemap_attach_parms("in", plist, 0);
     for (p = plist; p; p = pnext) {
       String *tm = Getattr(p, "tmap:in");
       if (tm) {
@@ -1917,10 +1945,11 @@ public:
       } else {
 	pnext = nextSibling(p);
       }
-      String *type = Getattr(p, "type");
-      String *value = Getattr(p, "value");
-      if (!convertValue(value, type))
-	return false;
+      if (String *value = Getattr(p, "value")) {
+	String *type = Getattr(p, "type");
+	if (!convertValue(value, type))
+	  return false;
+      }
     }
     return true;
   }
@@ -2504,7 +2533,6 @@ public:
       }
 
       SwigType *pt = Getattr(p, "type");
-      String *pn = Getattr(p, "name");
       String *ln = Getattr(p, "lname");
       bool parse_from_tuple = (i > 0 || !add_self);
       if (SwigType_type(pt) == T_VARARGS) {
@@ -2526,18 +2554,9 @@ public:
 
       /* Keyword argument handling */
       if (allow_kwargs && parse_from_tuple) {
-	if (Len(pn)) {
-	  String *tmp = 0;
-	  String *name = pn;
-	  if (!Getattr(p, "hidden")) {
-	    name = tmp = Swig_name_make(p, 0, pn, 0, 0); // rename parameter if a keyword
-	  }
-	  Printf(kwargs, "(char *) \"%s\",", name);
-	  if (tmp)
-	    Delete(tmp);
-	} else {
-	  Printf(kwargs, "(char *)\"arg%d\",", i + 1);
-	}
+	String *name = makeParameterName(n, p, i + 1);
+	Printf(kwargs, "(char *) \"%s\",", name);
+	Delete(name);
       }
 
       /* Look for an input typemap */

From 52bd2a1921667b3ba191165e890c71d699fde045 Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Sun, 10 Aug 2014 03:56:04 +0200
Subject: [PATCH 230/314] Allow using enum elements as default values for
 Python functions.

Enum values are just (integer) constants in Python and so can be used as the
function default values just as well as literal numbers, account for this when
checking whether function parameters can be represented in Python.

Also rename is_primitive_defaultargs() to is_representable_as_pyargs() to
describe better what this function does.
---
 .../test-suite/python/default_args_runme.py   |  3 +
 Source/Modules/python.cxx                     | 63 ++++++++++---------
 2 files changed, 35 insertions(+), 31 deletions(-)

diff --git a/Examples/test-suite/python/default_args_runme.py b/Examples/test-suite/python/default_args_runme.py
index 091a92376..ad5e03d11 100644
--- a/Examples/test-suite/python/default_args_runme.py
+++ b/Examples/test-suite/python/default_args_runme.py
@@ -1,5 +1,8 @@
 import default_args 
 
+ec = default_args.EnumClass()
+if not ec.blah():
+  raise RuntimeError,"EnumClass::blah() default arguments don't work"
 
 if default_args.Statics_staticMethod() != 60:
   raise RuntimeError
diff --git a/Source/Modules/python.cxx b/Source/Modules/python.cxx
index 327a3bb16..8a9b5c917 100644
--- a/Source/Modules/python.cxx
+++ b/Source/Modules/python.cxx
@@ -1733,14 +1733,8 @@ public:
       // Write default value
       if (value && !calling) {
 	String *new_value = convertValue(value, Getattr(p, "type"));
-	if (new_value) {
-	  value = new_value;
-	} else {
-	  Node *lookup = Swig_symbol_clookup(value, 0);
-	  if (lookup)
-	    value = Getattr(lookup, "sym:name");
-	}
-	Printf(doc, "=%s", value);
+	if (new_value)
+	  Printf(doc, "=%s", new_value);
       }
       Delete(type_str);
       Delete(made_name);
@@ -1898,39 +1892,46 @@ public:
 
   /* ------------------------------------------------------------
    * convertValue()
-   *    Check if string v can be a Python value literal,
-   *    (eg. number or string), or translate it to a Python literal.
+   *    Check if string v can be a Python value literal or a
+   *    constant. Return NIL if it isn't.
    * ------------------------------------------------------------ */
   String *convertValue(String *v, SwigType *t) {
-    if (v && Len(v) > 0) {
-      char fc = (Char(v))[0];
-      if (('0' <= fc && fc <= '9') || '\'' == fc || '"' == fc) {
-	/* number or string (or maybe NULL pointer) */
-	if (SwigType_ispointer(t) && Strcmp(v, "0") == 0)
-	  return NewString("None");
-	else
-	  return v;
-      }
-      if (Strcmp(v, "true") == 0 || Strcmp(v, "TRUE") == 0)
-	return NewString("True");
-      if (Strcmp(v, "false") == 0 || Strcmp(v, "FALSE") == 0)
-	return NewString("False");
-      if (Strcmp(v, "NULL") == 0 || Strcmp(v, "nullptr") == 0)
-	return SwigType_ispointer(t) ? NewString("None") : NewString("0");
+    char fc = (Char(v))[0];
+    if (('0' <= fc && fc <= '9') || '\'' == fc || '"' == fc) {
+      /* number or string (or maybe NULL pointer) */
+      if (SwigType_ispointer(t) && Strcmp(v, "0") == 0)
+	return NewString("None");
+      else
+	return v;
     }
-    return 0;
+    if (Strcmp(v, "true") == 0 || Strcmp(v, "TRUE") == 0)
+      return NewString("True");
+    if (Strcmp(v, "false") == 0 || Strcmp(v, "FALSE") == 0)
+      return NewString("False");
+    if (Strcmp(v, "NULL") == 0 || Strcmp(v, "nullptr") == 0)
+      return SwigType_ispointer(t) ? NewString("None") : NewString("0");
+
+    // This could also be an enum type, default value of which is perfectly
+    // representable in Python.
+    Node *lookup = Swig_symbol_clookup(v, 0);
+    if (lookup) {
+      if (Cmp(Getattr(lookup, "nodeType"), "enumitem") == 0)
+	return Getattr(lookup, "sym:name");
+    }
+
+    return NIL;
   }
+
   /* ------------------------------------------------------------
-   * is_primitive_defaultargs()
+   * is_representable_as_pyargs()
    *    Check if the function parameters default argument values
-   *    have primitive types, so that their default values could be
-   *    used in Python code.
+   *    can be represented in Python.
    *
    *    If this method returns false, the parameters will be translated
    *    to a generic "*args" which allows us to deal with default values
    *    at C++ code level where they can always be handled.
    * ------------------------------------------------------------ */
-  bool is_primitive_defaultargs(Node *n) {
+  bool is_representable_as_pyargs(Node *n) {
     ParmList *plist = CopyParmList(Getattr(n, "parms"));
     Parm *p;
     Parm *pnext;
@@ -1994,7 +1995,7 @@ public:
       n = nn;
 
     /* For overloaded function, just use *args */
-    if (is_real_overloaded(n) || GetFlag(n, "feature:compactdefaultargs") || !is_primitive_defaultargs(n)) {
+    if (is_real_overloaded(n) || GetFlag(n, "feature:compactdefaultargs") || !is_representable_as_pyargs(n)) {
       String *parms = NewString("");
       if (in_class)
 	Printf(parms, "self, ");

From 73f6971931d9e60d56dd575a4274c8e447ff799e Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Mon, 11 Aug 2014 00:34:30 +0200
Subject: [PATCH 231/314] Also merge Doxygen comments for overloaded
 constructors in Python.

This was done for plain functions/methods but not constructors, which don't
have "kind=function" attribute.

Just don't check for "kind" at all, the presence of "sym:overloaded" should be
good enough to indicate that it's an overloaded something.

Also add a test for overloaded constructors documentation.
---
 Examples/test-suite/doxygen_parsing.i               | 6 ++++++
 Examples/test-suite/python/doxygen_parsing_runme.py | 9 +++++++++
 Source/DoxygenTranslator/src/PyDocConverter.cpp     | 2 +-
 3 files changed, 16 insertions(+), 1 deletion(-)

diff --git a/Examples/test-suite/doxygen_parsing.i b/Examples/test-suite/doxygen_parsing.i
index d94c60222..670d8699b 100644
--- a/Examples/test-suite/doxygen_parsing.i
+++ b/Examples/test-suite/doxygen_parsing.i
@@ -39,6 +39,12 @@ int someVar=42;
 class SomeAnotherClass
 {
 public:
+	/// First overloaded constructor.
+	SomeAnotherClass(int) { }
+
+	/// Second overloaded constructor.
+	SomeAnotherClass(const char*) { }
+
 
 	/**
 	 * The class attribute comment
diff --git a/Examples/test-suite/python/doxygen_parsing_runme.py b/Examples/test-suite/python/doxygen_parsing_runme.py
index c850e419d..54e2667b3 100644
--- a/Examples/test-suite/python/doxygen_parsing_runme.py
+++ b/Examples/test-suite/python/doxygen_parsing_runme.py
@@ -17,6 +17,15 @@ commentVerifier.check(doxygen_parsing.SomeStruct.__doc__,
     r"""
     The struct comment
     """)
+commentVerifier.check(doxygen_parsing.SomeAnotherClass.__init__.__doc__,
+    r"""
+        *Overload 1:*
+         First overloaded constructor.
+
+        *Overload 2:*
+         Second overloaded constructor.
+
+        """)
 commentVerifier.check(doxygen_parsing.SomeAnotherClass.classMethod.__doc__,
     r"""
         The class method comment.
diff --git a/Source/DoxygenTranslator/src/PyDocConverter.cpp b/Source/DoxygenTranslator/src/PyDocConverter.cpp
index e7a55e1ba..6d904f6c4 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/PyDocConverter.cpp
@@ -781,7 +781,7 @@ String *PyDocConverter::makeDocumentation(Node *n)
   currentNode = n;
 
   // for overloaded functions we must concat documentation for underlying overloads
-  if (Checkattr(n, "kind", "function") && Getattr(n, "sym:overloaded")) {
+  if (Getattr(n, "sym:overloaded")) {
     // rewind to the first overload
     while (Getattr(n, "sym:previousSibling"))
       n = Getattr(n, "sym:previousSibling");

From 1f826b0925c2e282160da1950aca7826e48d1c2c Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Mon, 11 Aug 2014 15:17:29 +0200
Subject: [PATCH 232/314] Fix translated Doxygen comments for overloaded
 functions in Python.

The most important change is to ensure that the "Overload" headers added by
PyDocConverter code are indented correctly, i.e. using the same indent level
as the comment itself, otherwise Sphinx directives such as :param: were not
parsed correctly.

Also add a vertical separator using reST "|" formatting character to increase
separation between the overloads.
---
 .../python/doxygen_basic_notranslate_runme.py | 13 ++--
 .../python/doxygen_basic_translate_runme.py   |  3 +-
 .../python/doxygen_parsing_runme.py           |  7 +-
 .../DoxygenTranslator/src/PyDocConverter.cpp  | 67 +++++++++++++++++--
 4 files changed, 73 insertions(+), 17 deletions(-)

diff --git a/Examples/test-suite/python/doxygen_basic_notranslate_runme.py b/Examples/test-suite/python/doxygen_basic_notranslate_runme.py
index 27dcb4a7e..e7c9ea1b8 100644
--- a/Examples/test-suite/python/doxygen_basic_notranslate_runme.py
+++ b/Examples/test-suite/python/doxygen_basic_notranslate_runme.py
@@ -30,14 +30,15 @@ commentVerifier.check(doxygen_basic_notranslate.function3.__doc__,
     r"""
     *Overload 1:*
 
-     A test for overloaded functions
-     This is function \b one
-     
+    A test for overloaded functions
+    This is function \b one
+
+    |
+
     *Overload 2:*
 
-     A test for overloaded functions
-     This is function \b two
-     
+    A test for overloaded functions
+    This is function \b two
     """
 )
 
diff --git a/Examples/test-suite/python/doxygen_basic_translate_runme.py b/Examples/test-suite/python/doxygen_basic_translate_runme.py
index b5ba162e2..4f8505e24 100644
--- a/Examples/test-suite/python/doxygen_basic_translate_runme.py
+++ b/Examples/test-suite/python/doxygen_basic_translate_runme.py
@@ -31,11 +31,12 @@ commentVerifier.check(doxygen_basic_translate.function3.__doc__,
     A test for overloaded functions
     This is function **one**
 
+    |
+
     *Overload 2:*
 
     A test for overloaded functions
     This is function **two**
-
     """
 )
 commentVerifier.check(doxygen_basic_translate.function4.__doc__,
diff --git a/Examples/test-suite/python/doxygen_parsing_runme.py b/Examples/test-suite/python/doxygen_parsing_runme.py
index 54e2667b3..5ff5cf5c7 100644
--- a/Examples/test-suite/python/doxygen_parsing_runme.py
+++ b/Examples/test-suite/python/doxygen_parsing_runme.py
@@ -20,11 +20,12 @@ commentVerifier.check(doxygen_parsing.SomeStruct.__doc__,
 commentVerifier.check(doxygen_parsing.SomeAnotherClass.__init__.__doc__,
     r"""
         *Overload 1:*
-         First overloaded constructor.
+        First overloaded constructor.
+
+        |
 
         *Overload 2:*
-         Second overloaded constructor.
-
+        Second overloaded constructor.
         """)
 commentVerifier.check(doxygen_parsing.SomeAnotherClass.classMethod.__doc__,
     r"""
diff --git a/Source/DoxygenTranslator/src/PyDocConverter.cpp b/Source/DoxygenTranslator/src/PyDocConverter.cpp
index 6d904f6c4..065c8f4da 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/PyDocConverter.cpp
@@ -85,6 +85,35 @@ private:
   IndentGuard& operator=(const IndentGuard&);
 };
 
+// Return the indent of the given multiline string, i.e. the maximal number of
+// spaces present in the beginning of all its non-empty lines.
+static size_t determineIndent(const string& s)
+{
+  size_t minIndent = static_cast<size_t>(-1);
+
+  for (size_t lineStart = 0; lineStart < s.length();) {
+    const size_t lineEnd = s.find('\n', lineStart);
+    const size_t firstNonSpace = s.find_first_not_of(' ', lineStart);
+
+    // If inequality doesn't hold, it means that this line contains only spaces
+    // (notice that this works whether lineEnd is valid or string::npos), in
+    // which case it doesn't matter when determining the indent.
+    if (firstNonSpace < lineEnd) {
+      // Here we can be sure firstNonSpace != string::npos.
+      const size_t lineIndent = firstNonSpace - lineStart;
+      if (lineIndent < minIndent)
+        minIndent = lineIndent;
+    }
+
+    if (lineEnd == string::npos)
+      break;
+
+    lineStart = lineEnd + 1;
+  }
+
+  return minIndent;
+}
+
 static void trimWhitespace(string& s)
 {
   const size_t lastNonSpace = s.find_last_not_of(' ');
@@ -788,7 +817,11 @@ String *PyDocConverter::makeDocumentation(Node *n)
 
     std::vector<std::string> allDocumentation;
 
+    // minimal indent of any documentation comments, not initialized yet
+    size_t minIndent = static_cast<size_t>(-1);
+
     // for each real method (not a generated overload) append the documentation
+    string oneDoc;
     while (n) {
       documentation = getDoxygenComment(n);
       if (!Swig_is_generated_overload(n) && documentation) {
@@ -797,28 +830,48 @@ String *PyDocConverter::makeDocumentation(Node *n)
           String *comment = NewString("");
           Append(comment, documentation);
           Replaceall(comment, "\n *", "\n");
-          allDocumentation.push_back(Char (comment));
+          oneDoc = Char (comment);
           Delete(comment);
         } else {
           std::list<DoxygenEntity> entityList = parser.createTree(
               Char (documentation), Char (Getfile(documentation)),
               Getline(documentation));
           DoxygenEntity root("root", entityList);
-          allDocumentation.push_back(translateSubtree(root));
+
+          oneDoc = translateSubtree(root);
         }
+
+        // find the minimal indent of this documentation comment, we need to
+        // ensure that the entire comment is indented by it to avoid the leading
+        // parts of the other lines being simply discarded later
+        const size_t oneIndent = determineIndent(oneDoc);
+        if (oneIndent < minIndent)
+          minIndent = oneIndent;
+
+        allDocumentation.push_back(oneDoc);
       }
       n = Getattr(n, "sym:nextSibling");
     }
 
     // construct final documentation string
     if (allDocumentation.size() > 1) {
+      string indentStr;
+      if (minIndent != static_cast<size_t>(-1))
+        indentStr.assign(minIndent, ' ');
+
       std::ostringstream concatDocString;
-      for (int realOverloadCount = 0;
-          realOverloadCount < (int) allDocumentation.size();
+      for (size_t realOverloadCount = 0;
+          realOverloadCount < allDocumentation.size();
           realOverloadCount++) {
-        concatDocString << "*Overload " << (realOverloadCount + 1) << ":*"
-            << std::endl;
-        concatDocString << allDocumentation[realOverloadCount] << std::endl;
+        if (realOverloadCount != 0) {
+          // separate it from the preceding one.
+          concatDocString << "\n" << indentStr << "|\n\n";
+        }
+
+        oneDoc = allDocumentation[realOverloadCount];
+        trimWhitespace(oneDoc);
+        concatDocString << indentStr << "*Overload " << (realOverloadCount + 1) << ":*\n"
+                        << oneDoc;
       }
       pyDocString = concatDocString.str();
     } else if (allDocumentation.size() == 1) {

From 6aa9cd37a5aae7134cd65e72c9c98551ae15ec5a Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Mon, 11 Aug 2014 16:22:48 +0200
Subject: [PATCH 233/314] Document the return type when translating Doxygen
 @return to Python.

In addition to translating the comment itself, also document the type of the
object returned. This is consistent with generating not only :param: but also
:type: for the parameters documented using @param.
---
 .../python/doxygen_basic_translate_runme.py   |  2 +
 .../doxygen_translate_all_tags_runme.py       |  3 +
 .../python/doxygen_translate_runme.py         |  3 +
 .../DoxygenTranslator/src/PyDocConverter.cpp  | 63 ++++++++++++-------
 4 files changed, 49 insertions(+), 22 deletions(-)

diff --git a/Examples/test-suite/python/doxygen_basic_translate_runme.py b/Examples/test-suite/python/doxygen_basic_translate_runme.py
index 4f8505e24..87010ee39 100644
--- a/Examples/test-suite/python/doxygen_basic_translate_runme.py
+++ b/Examples/test-suite/python/doxygen_basic_translate_runme.py
@@ -13,6 +13,7 @@ commentVerifier.check(doxygen_basic_translate.function.__doc__,
 
     Author: Some author
 
+    :rtype: int
     :return: Some number
 
     See also: function2
@@ -86,6 +87,7 @@ commentVerifier.check(doxygen_basic_translate.Atan2.__doc__,
     :param y: Vertical coordinate.
     :type x: float
     :param x: Horizontal coordinate.
+    :rtype: float
     :return: Arc tangent of ``y/x``.
     """
 )
diff --git a/Examples/test-suite/python/doxygen_translate_all_tags_runme.py b/Examples/test-suite/python/doxygen_translate_all_tags_runme.py
index 9df2df593..d0bd43980 100644
--- a/Examples/test-suite/python/doxygen_translate_all_tags_runme.py
+++ b/Examples/test-suite/python/doxygen_translate_all_tags_runme.py
@@ -263,10 +263,13 @@ r"""
 
     Another remarks section
 
+    :rtype: int
     :return: Whatever
 
+    :rtype: int
     :return: it
 
+    :rtype: int
     :return: may return
 
     """)
diff --git a/Examples/test-suite/python/doxygen_translate_runme.py b/Examples/test-suite/python/doxygen_translate_runme.py
index 788bc90eb..92850aa19 100644
--- a/Examples/test-suite/python/doxygen_translate_runme.py
+++ b/Examples/test-suite/python/doxygen_translate_runme.py
@@ -99,10 +99,13 @@ r"""
 
     Another remarks section
 
+    :rtype: int
     :return: Whatever
 
+    :rtype: int
     :return: it
 
+    :rtype: int
     :return: may return
 
     See also: someOtherMethod
diff --git a/Source/DoxygenTranslator/src/PyDocConverter.cpp b/Source/DoxygenTranslator/src/PyDocConverter.cpp
index 065c8f4da..9203904c5 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/PyDocConverter.cpp
@@ -334,6 +334,38 @@ PyDocConverter::PyDocConverter(int flags) :
   fillStaticTables();
 }
 
+// Return the type as it should appear in the output documentation.
+static
+std::string getPyDocType(Node* n, const_String_or_char_ptr lname = "")
+{
+  std::string type;
+
+  String *s = Swig_typemap_lookup("doctype", n, lname, 0);
+  if (!s)
+    s = SwigType_str(Getattr(n, "type"), "");
+
+  if (Language::classLookup(s)) {
+    // In Python C++ namespaces are flattened, so remove all but last component
+    // of the name.
+    String * const last = Swig_scopename_last(s);
+
+    // We are not actually sure whether it's a documented class or not, but
+    // there doesn't seem to be any harm in making it a reference if it isn't,
+    // while there is a lot of benefit in having a hyperlink if it is.
+    type = ":py:class:`";
+    type += Char (last);
+    type += "`";
+
+    Delete(last);
+  } else {
+    type = Char(s);
+  }
+
+  Delete(s);
+
+  return type;
+}
+
 std::string PyDocConverter::getParamType(std::string param)
 {
   std::string type;
@@ -344,28 +376,7 @@ std::string PyDocConverter::getParamType(std::string param)
     if (Char (pname) != param)
       continue;
 
-    String *s = Swig_typemap_lookup("doctype", p, pname, 0);
-    if (!s)
-      s = SwigType_str(Getattr(p, "type"), "");
-
-    if (Language::classLookup(s)) {
-      // In Python C++ namespaces are flattened, so remove all but last component
-      // of the name.
-      String * const last = Swig_scopename_last(s);
-
-      // We are not actually sure whether it's a documented class or not, but
-      // there doesn't seem to be any harm in making it a reference if it isn't,
-      // while there is a lot of benefit in having a hyperlink if it is.
-      type = ":py:class:`";
-      type += Char (last);
-      type += "`";
-
-      Delete(last);
-    } else {
-      type = Char(s);
-    }
-
-    Delete(s);
+    type = getPyDocType(p, pname);
     break;
   }
   Delete(plist);
@@ -619,6 +630,14 @@ void PyDocConverter::handleTagReturn(DoxygenEntity &tag,
 {
   IndentGuard indent(translatedComment, m_indent);
 
+  const std::string pytype = getPyDocType(currentNode);
+  if (!pytype.empty()) {
+    translatedComment += ":rtype: ";
+    translatedComment += pytype;
+    translatedComment += "\n";
+    translatedComment += indent.getFirstLineIndent();
+  }
+
   translatedComment += ":return: ";
   handleParagraph(tag, translatedComment);
 }

From a1d79308350eef20ced130b15fb313595b7303e3 Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Fri, 22 Aug 2014 22:44:55 +0200
Subject: [PATCH 234/314] Give warnings for unknown Doxygen commands in Doxygen
 parser.

Silently ignoring unknown Doxygen commands is not a reasonable default
behaviour, it's simple enough to turn off the warning if the command is really
supposed to be just ignored, but it's too easy to not notice a real problem if
it isn't.

Turn WARN_DOXYGEN_UNKNOWN_COMMAND on by default and add a test to the errors
test suite checking that it is indeed given.
---
 Examples/test-suite/doxygen_misc_constructs.i |  2 ++
 Examples/test-suite/errors/Makefile.in        | 14 ++++++++++-
 .../errors/doxygen_unknown_command.i          |  6 +++++
 .../errors/doxygen_unknown_command.stderr     |  1 +
 .../DoxygenTranslator/src/DoxygenParser.cpp   | 23 ++++++++++++++-----
 5 files changed, 39 insertions(+), 7 deletions(-)
 create mode 100644 Examples/test-suite/errors/doxygen_unknown_command.i
 create mode 100644 Examples/test-suite/errors/doxygen_unknown_command.stderr

diff --git a/Examples/test-suite/doxygen_misc_constructs.i b/Examples/test-suite/doxygen_misc_constructs.i
index 78c72fe6d..04c063e64 100644
--- a/Examples/test-suite/doxygen_misc_constructs.i
+++ b/Examples/test-suite/doxygen_misc_constructs.i
@@ -3,6 +3,8 @@
 
 %module doxygen_misc_constructs
 
+%warnfilter(SWIGWARN_DOXYGEN_UNKNOWN_COMMAND) backslashB;
+
 %inline %{
 
     // Tag '@endink' must be recognized even if it is not
diff --git a/Examples/test-suite/errors/Makefile.in b/Examples/test-suite/errors/Makefile.in
index 4c61001e7..09f5bc8c7 100644
--- a/Examples/test-suite/errors/Makefile.in
+++ b/Examples/test-suite/errors/Makefile.in
@@ -24,12 +24,24 @@ top_builddir = @top_builddir@
 ALL_ERROR_TEST_CASES := $(patsubst %.i,%, $(notdir $(wildcard $(srcdir)/*.i)))
 CPP_ERROR_TEST_CASES := $(filter cpp_%, $(ALL_ERROR_TEST_CASES))
 C_ERROR_TEST_CASES := $(filter-out $(CPP_ERROR_TEST_CASES), $(ALL_ERROR_TEST_CASES))
+DOXYGEN_ERROR_TEST_CASES := $(filter doxygen_%, $(C_ERROR_TEST_CASES))
+C_ERROR_TEST_CASES := $(filter-out $(DOXYGEN_ERROR_TEST_CASES), $(C_ERROR_TEST_CASES))
+
+# Always use C++ for Doxygen tests, there doesn't seem to be any need to
+# distinguish between C and C++ Doxygen tests.
+DOXYGEN_ERROR_TEST_CASES := $(DOXYGEN_ERROR_TEST_CASES:=.cpptest)
 
 ERROR_TEST_CASES := $(CPP_ERROR_TEST_CASES:=.cpptest) \
-		    $(C_ERROR_TEST_CASES:=.ctest)
+		    $(C_ERROR_TEST_CASES:=.ctest) \
+		    $(DOXYGEN_ERROR_TEST_CASES)
 
 include $(srcdir)/../common.mk
 
+# This is tricky: we need to let common.mk define SWIGOPT before appending to
+# it, if we do it before including it, its defining of SWIGOPT would override
+# whatever we do here.
+$(DOXYGEN_ERROR_TEST_CASES): SWIGOPT += -doxygen
+
 # Portable dos2unix / todos for stripping CR
 TODOS        = tr -d '\r'
 #TODOS        = sed -e 's/\r$$//' # On OSX behaves as if written 's/r$$//'
diff --git a/Examples/test-suite/errors/doxygen_unknown_command.i b/Examples/test-suite/errors/doxygen_unknown_command.i
new file mode 100644
index 000000000..0f32ee966
--- /dev/null
+++ b/Examples/test-suite/errors/doxygen_unknown_command.i
@@ -0,0 +1,6 @@
+%module xxx
+
+/**
+    There is an \unknown Doxygen comment here.
+ */
+void foo();
diff --git a/Examples/test-suite/errors/doxygen_unknown_command.stderr b/Examples/test-suite/errors/doxygen_unknown_command.stderr
new file mode 100644
index 000000000..263d9cca2
--- /dev/null
+++ b/Examples/test-suite/errors/doxygen_unknown_command.stderr
@@ -0,0 +1 @@
+doxygen_unknown_command.i:4: Warning 720: Doxygen parser warning: unknown command "unknown".
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.cpp b/Source/DoxygenTranslator/src/DoxygenParser.cpp
index 8523b51f4..0cb27c1af 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenParser.cpp
@@ -1028,11 +1028,22 @@ bool DoxygenParser::addDoxyCommand(DoxygenParser::TokenList &tokList,
     tokList.push_back(Token(COMMAND, cmd));
     return true;
   } else {
-    // Unknown commands are ignored, because they are
-    // also ignored by Doxygen - see test doxygen_misc_constructs.h, f. backslashB().
-    // This differs from original implementation in this class. Uncomment
-    // the line below to put unknown commands to output.
-    // tokList.push_back(Token(PLAINSTRING, cmd));
+    // This function is called for the special Doxygen commands, but also for
+    // HTML commands (or anything that looks like them, actually) and entities.
+    // We don't recognize all of those, so just ignore them and pass them
+    // through, but warn about unknown Doxygen commands as ignoring them will
+    // often result in wrong output being generated.
+    const char ch = *cmd.begin();
+    if (ch != '<' && ch != '&') {
+      // Before calling printListError() we must ensure that m_tokenListIt used
+      // by it is valid.
+      const TokenListCIt itSave = m_tokenListIt;
+      m_tokenListIt = m_tokenList.end();
+
+      printListError(WARN_DOXYGEN_UNKNOWN_COMMAND, "unknown command \"" + cmd + '"');
+
+      m_tokenListIt = itSave;
+    }
   }
 
   return false;
@@ -1431,5 +1442,5 @@ void DoxygenParser::printListError(int warningType, const std::string &message)
   }
 
   Swig_warning(warningType, m_fileName.c_str(), curLine,
-      "Doxygen parser warning: %s. \n", message.c_str());
+      "Doxygen parser warning: %s.\n", message.c_str());
 }

From a1ae3a4344b0ded88ee490ae0cbe2871dfcdf619 Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Fri, 22 Aug 2014 23:06:46 +0200
Subject: [PATCH 235/314] Describe Doxygen-specific %features in a single
 place.

Put them all in a single table instead of describing doxygen:notranslate
separately for Java and Python when it does the same thing for both.

And while doxygen:nolinkranslate and doxygen:nostripparams are currently
Java-specific, it probably won't remain this way and these features would
either be made to work for Python as well or, perhaps, removed entirely.
---
 Doc/Manual/Doxygen.html | 102 +++++++++++++++-------------------------
 1 file changed, 38 insertions(+), 64 deletions(-)

diff --git a/Doc/Manual/Doxygen.html b/Doc/Manual/Doxygen.html
index d927593ab..916bd5e87 100644
--- a/Doc/Manual/Doxygen.html
+++ b/Doc/Manual/Doxygen.html
@@ -14,6 +14,7 @@
 <ul>
 <li><a href="#Doxygen_running_swig">Enabling Doxygen Translation</a>
 <li><a href="#Doxygen_additional_options">Additional Command Line Options</a>
+<li><a href="#Doxygen_features">Doxygen-specific %feature Directives</a>
 </ul>
 <li><a href="#Doxygen_to_javadoc">Doxygen To Javadoc</a>
 <ul>
@@ -201,21 +202,46 @@ assigned to anything.
 </p>
 <H3><a name="Doxygen_running_swig"></a>39.2.1 Enabling Doxygen Translation</H3>
 
-
 <p>
-There is a switch '-doxygen' in every module that supports converting
-documentation comments. Some comments in some target languages can be
-manually overridden by specific swig's features,
-like <i>feature:docstring</i> or <i>feature:autodoc</i>, in this cases
-Doxygen comments have lowest priority.
-</p>
-<p>
-If Doxygen parsing is switched off, then all the comments are stripped
-out in parser and all the resources used by comment parser and
-translator are freed.
+Doxygen comments translation is disabled by default and needs to be explicitly
+enabled using the command line <tt>-doxygen</tt> switch for the languages that
+do support it (currently Java and Python).
 </p>
 
-<H3><a name="Doxygen_additional_options"></a>39.2.2 Additional Command Line Options</H3>
+<H3><a name="Doxygen_features"></a>39.2.2 Doxygen-specific %feature Directives</H3>
+
+<p>
+Translation of Doxygen comments is influenced by the following <a
+href="Customization.html#Customization_features">%feature directives</a>:
+</p>
+
+<h4>doxygen:notranslate</h4>
+
+<p>
+Turns off translation of Doxygen comments to the target language syntax: the
+original comment will be copied to the output unchanged. This is useful if you
+want to use Doxygen itself to generate documentation for the target language
+instead of the corresponding language tool (<tt>javadoc</tt>, <tt>sphinx</tt>,
+...).
+</p>
+
+
+<h4>doxygen:nolinkranslate (Java-only currently)</h4>
+
+<p>
+Turn off automatic link-objects translation.
+</p>
+
+
+<h4>doxygen:nostripparams (Java-only currently)</h4>
+
+<p>
+Turn off stripping of <tt>@param</tt> and <tt>@tparam</tt>
+Doxygen commands if the parameter is not found in the function signature.
+</p>
+
+
+<H3><a name="Doxygen_additional_options"></a>39.2.3 Additional Command Line Options</H3>
 
 
 <p>
@@ -330,12 +356,6 @@ you don't want such behaviour, you could turn this off by using
 'doxygen:nolinktranslate' feature. Also all '\param' and '\tparam'
 commands are stripped out, if specified parameter is not present in
 function. Use 'doxygen:nostripparams' to avoid.
-<br>
-If you intend to use resulting proxy files with Doxygen docs
-generator, rather than Javadoc, you may want to turn off translator
-completely (doxygen:notranslate feature).  Then SWIG will just copy
-the comments to the proxy file and reformat them if needed, but all
-the comment content will be left as is.
 </p>
 
 <p>
@@ -346,33 +366,6 @@ directives</a>):
 
 </p>
 
-<div class="shell"><pre>
-<table>
-<tr>
-<td>doxygen:notranslate</td>
-<td>
-Turn off the whole Doxygen translator.
-The Doxygen comment will be attached to the right node,
-but all the commands and text will be left as-is
-</td>
-</tr>
-
-<tr>
-<td>doxygen:nolinkranslate</td>
-<td>Turn off automatic link-objects translation</td>
-</tr>
-
-<tr>
-<td>doxygen:nostripparams</td>
-<td>
-Turn off stripping of @param and @tparam
-Doxygen commands if such parameter is not found
-</td>
-</tr>
-</table>
-</pre></div>
-
-
 <H3><a name="Doxygen_javadoc_tags"></a>39.3.2 Javadoc Tags</H3>
 
 
@@ -1036,25 +1029,6 @@ docs</a>), you may want to use some tool like doxypy
 to do the work.
 </p>
 
-<p>
-Pydoc translator features summary (see <a href="Customization.html#Customization_features">%feature directives</a>):
-<br>
-
-</p>
-
-<div class="shell"><pre>
-<table>
-<tr>
-<td>doxygen:notranslate</td>
-<td>
-Turn off the whole Doxygen translator.
-The Doxygen comment will be attached to the right node,
-but all the commands and text will be left as-is
-</td>
-</tr>
-</table>
-</pre></div>
-
 <H3><a name="Doxygen_pydoc_tags"></a>39.4.2 Pydoc translator</H3>
 
 

From f0ed5e90d7714f81c43d2fa6275f0c8d360451fc Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Mon, 25 Aug 2014 16:45:28 +0200
Subject: [PATCH 236/314] No real changes, just pass original command to
 commandBelongs().

Don't transform commandBelongs() argument to lower case as it's done inside
the function itself anyhow -- and it will need the original case soon.
---
 Source/DoxygenTranslator/src/DoxygenParser.cpp | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/Source/DoxygenTranslator/src/DoxygenParser.cpp b/Source/DoxygenTranslator/src/DoxygenParser.cpp
index 0cb27c1af..ef3997cf7 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenParser.cpp
@@ -133,10 +133,7 @@ void DoxygenParser::printTree(const DoxygenEntityList &rootList)
 
 int DoxygenParser::commandBelongs(const std::string &theCommand)
 {
-
-  std::string smallString = stringToLower(theCommand);
-  //cout << " Looking for command " << theCommand << endl;
-  DoxyCommandsMapIt it = doxygenCommands.find(smallString);
+  DoxyCommandsMapIt it = doxygenCommands.find(stringToLower(theCommand));
 
   if (it != doxygenCommands.end()) {
     return it->second;
@@ -899,7 +896,7 @@ int DoxygenParser::addCommand(const std::string &commandString,
     return 1;
   }
 
-  switch (commandBelongs(theCommand)) {
+  switch (commandBelongs(commandString)) {
   case SIMPLECOMMAND:
     return addSimpleCommand(theCommand, doxyList);
   case COMMANDWORD:

From f256f0107e3d25f978ddff943df03a99dd33d41f Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Mon, 25 Aug 2014 16:57:24 +0200
Subject: [PATCH 237/314] Recognize unknown Doxygen tags correctly.

DoxygenParser::commandBelongs() returned the same value (0) for simple
commands and unrecognized commands. Fix this by returning a different NONE
value for the latter.
---
 Source/DoxygenTranslator/src/DoxygenParser.cpp | 2 +-
 Source/DoxygenTranslator/src/DoxygenParser.h   | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/Source/DoxygenTranslator/src/DoxygenParser.cpp b/Source/DoxygenTranslator/src/DoxygenParser.cpp
index ef3997cf7..5b235f91e 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenParser.cpp
@@ -138,7 +138,7 @@ int DoxygenParser::commandBelongs(const std::string &theCommand)
   if (it != doxygenCommands.end()) {
     return it->second;
   }
-  return 0;
+  return NONE;
 }
 
 std::string DoxygenParser::trim(const std::string &text)
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.h b/Source/DoxygenTranslator/src/DoxygenParser.h
index 06c14de04..0b1212d4b 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.h
+++ b/Source/DoxygenTranslator/src/DoxygenParser.h
@@ -22,6 +22,7 @@ class DoxygenParser {
 private:
 
   typedef enum {
+    NONE = -1,
     SIMPLECOMMAND,
     COMMANDWORD,
     COMMANDLINE,

From a7b67a2cac8546a8184ba360a9da29f3f084d154 Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Mon, 25 Aug 2014 17:00:24 +0200
Subject: [PATCH 238/314] Get rid of findCommand() which duplicaed
 commandBelongs().

There is no need for two functions for finding the value of a key in the map.
---
 Source/DoxygenTranslator/src/DoxygenParser.cpp | 13 +------------
 Source/DoxygenTranslator/src/DoxygenParser.h   |  5 -----
 2 files changed, 1 insertion(+), 17 deletions(-)

diff --git a/Source/DoxygenTranslator/src/DoxygenParser.cpp b/Source/DoxygenTranslator/src/DoxygenParser.cpp
index 5b235f91e..13c40dee1 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenParser.cpp
@@ -102,17 +102,6 @@ std::string DoxygenParser::stringToLower(const std::string &stringToConvert)
   return result;
 }
 
-bool DoxygenParser::findCommand(const std::string &smallString)
-{
-  // I'm not sure if we can really do so, because there are different commands
-  // in doxygenCommands and original commandArray
-
-  std::map<std::string, DoxyCommandEnum>::iterator it = doxygenCommands.find(
-      stringToLower(smallString));
-
-  return it != doxygenCommands.end(); // returns true if command was found
-}
-
 bool DoxygenParser::isSectionIndicator(const std::string &smallString)
 {
 
@@ -1021,7 +1010,7 @@ bool DoxygenParser::isStartOfDoxyCommentChar(char c)
 bool DoxygenParser::addDoxyCommand(DoxygenParser::TokenList &tokList,
                                    const std::string &cmd)
 {
-  if (findCommand(cmd)) {
+  if (commandBelongs(cmd) != NONE) {
     tokList.push_back(Token(COMMAND, cmd));
     return true;
   } else {
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.h b/Source/DoxygenTranslator/src/DoxygenParser.h
index 0b1212d4b..4df978fc7 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.h
+++ b/Source/DoxygenTranslator/src/DoxygenParser.h
@@ -104,11 +104,6 @@ private:
    */
   std::string stringToLower(const std::string &stringToConvert);
 
-  /* 
-   * Finds out if a command exists (is a possible command)
-   * returns -1 if no match is found
-   */
-  bool findCommand(const std::string &smallString);
   /* 
    * isSectionIndicator returns a boolean if the command is a section indicator
    * This is a helper method for finding the end of a paragraph

From dc3102a535b404f074a3b21be7cb0b1315d69bec Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Tue, 26 Aug 2014 17:45:59 +0200
Subject: [PATCH 239/314] Pass the node the Doxygen comment is attached to to
 DoxygenParser.

This will be needed to take into account various Doxygen-specific features
that can be attached to this node.
---
 Source/DoxygenTranslator/src/DoxygenParser.cpp    | 12 ++++++++----
 Source/DoxygenTranslator/src/DoxygenParser.h      |  8 +++++---
 Source/DoxygenTranslator/src/JavaDocConverter.cpp |  3 +--
 Source/DoxygenTranslator/src/PyDocConverter.cpp   |  8 ++------
 4 files changed, 16 insertions(+), 15 deletions(-)

diff --git a/Source/DoxygenTranslator/src/DoxygenParser.cpp b/Source/DoxygenTranslator/src/DoxygenParser.cpp
index 13c40dee1..0f6e18943 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenParser.cpp
@@ -954,12 +954,16 @@ DoxygenEntityList DoxygenParser::parse(TokenListCIt endParsingIndex,
   return aNewList;
 }
 
-DoxygenEntityList DoxygenParser::createTree(const std::string &doxygenBlob,
-                                            const std::string &fileName,
-                                            int lineNumber)
+DoxygenEntityList DoxygenParser::createTree(Node* node, String* documentation)
 {
+  m_node = node;
+
+  tokenizeDoxygenComment(
+      Char(documentation),
+      Char(Getfile(documentation)),
+      Getline(documentation)
+    );
 
-  tokenizeDoxygenComment(doxygenBlob, fileName, lineNumber);
   if (noisy) {
     cout << "---TOKEN LIST---" << endl;
     printList();
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.h b/Source/DoxygenTranslator/src/DoxygenParser.h
index 4df978fc7..f86f94f44 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.h
+++ b/Source/DoxygenTranslator/src/DoxygenParser.h
@@ -16,6 +16,9 @@
 #include <map>
 #include <vector>
 #include <set>
+
+#include "swig.h"
+
 #include "DoxygenEntity.h"
 
 class DoxygenParser {
@@ -91,6 +94,7 @@ private:
   bool m_isVerbatimText; // used to handle \htmlonly and \verbatim commands
   bool m_isInQuotedString;
 
+  Node* m_node;
   std::string m_fileName;
   int m_fileLineNo;
 
@@ -375,9 +379,7 @@ private:
 public:
   DoxygenParser(bool noisy = false);
   virtual ~DoxygenParser();
-  DoxygenEntityList createTree(const std::string &doxygen,
-                                const std::string &fileName,
-                                int lineNumber);
+  DoxygenEntityList createTree(Node* node, String* documentation);
 };
 
 #endif
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.cpp b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
index c7c601b9b..c2b47a796 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
@@ -928,8 +928,7 @@ String *JavaDocConverter::makeDocumentation(Node *node)
     return comment;
   }
 
-  DoxygenEntityList entityList = parser.createTree(Char (documentation),
-      Char (Getfile(documentation)), Getline(documentation));
+  DoxygenEntityList entityList = parser.createTree(node, documentation);
 
   // entityList.sort(CompareDoxygenEntities()); sorting currently not used,
 
diff --git a/Source/DoxygenTranslator/src/PyDocConverter.cpp b/Source/DoxygenTranslator/src/PyDocConverter.cpp
index 9203904c5..d7dbabe35 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/PyDocConverter.cpp
@@ -852,9 +852,7 @@ String *PyDocConverter::makeDocumentation(Node *n)
           oneDoc = Char (comment);
           Delete(comment);
         } else {
-          std::list<DoxygenEntity> entityList = parser.createTree(
-              Char (documentation), Char (Getfile(documentation)),
-              Getline(documentation));
+          std::list<DoxygenEntity> entityList = parser.createTree(n, documentation);
           DoxygenEntity root("root", entityList);
 
           oneDoc = translateSubtree(root);
@@ -908,9 +906,7 @@ String *PyDocConverter::makeDocumentation(Node *n)
         pyDocString = Char (comment);
         Delete(comment);
       } else {
-        std::list<DoxygenEntity> entityList = parser.createTree(
-            Char (documentation), Char (Getfile(documentation)),
-            Getline(documentation));
+        std::list<DoxygenEntity> entityList = parser.createTree(n, documentation);
         DoxygenEntity root("root", entityList);
         pyDocString = translateSubtree(root);
       }

From 6629d93481d437ffb3dfcd9d17a0bef310c6b718 Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Wed, 27 Aug 2014 00:05:06 +0200
Subject: [PATCH 240/314] Allow upper case letters and digits in Doxygen words.

Although all standard Doxygen commands are composed from lower case letters
and some special symbols only, custom commands can include upper case letters
and digits too.

Also use a symbolic constant defined once instead of repeating the same set of
characters twice.
---
 Source/DoxygenTranslator/src/DoxygenParser.cpp | 16 ++++++++++------
 1 file changed, 10 insertions(+), 6 deletions(-)

diff --git a/Source/DoxygenTranslator/src/DoxygenParser.cpp b/Source/DoxygenTranslator/src/DoxygenParser.cpp
index 0f6e18943..5e1f3a5d3 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenParser.cpp
@@ -22,6 +22,14 @@ using std::string;
 using std::cout;
 using std::endl;
 
+// This constant defines the (only) characters valid inside a Doxygen "word".
+// It includes some unusual ones because of the commands such as \f[, \f{, \f],
+// \f} and \f$.
+static const char* DOXYGEN_WORD_CHARS = "abcdefghijklmnopqrstuvwxyz"
+                                        "ABCDEFGHIJKLMNOPQRSTUVWXYZ"
+                                        "0123456789"
+                                        "$[]{}";
+
 // Define static class members
 DoxygenParser::DoxyCommandsMap DoxygenParser::doxygenCommands;
 std::set<std::string> DoxygenParser::doxygenSectionIndicators;
@@ -1049,9 +1057,7 @@ size_t DoxygenParser::processVerbatimText(size_t pos, const std::string &line)
   if (line[pos] == '\\' || line[pos] == '@') { // check for end commands
 
     pos++;
-    // characters '$[]{}' are used in commands \f$, \f[, and \f{
-    size_t endOfWordPos = line.find_first_not_of(
-        "abcdefghijklmnopqrstuvwxyz$[]{}", pos);
+    size_t endOfWordPos = line.find_first_not_of( DOXYGEN_WORD_CHARS, pos);
     string cmd = line.substr(pos, endOfWordPos - pos);
 
     if (cmd == CMD_END_HTML_ONLY || cmd == CMD_END_VERBATIM
@@ -1125,9 +1131,7 @@ bool DoxygenParser::processEscapedChars(size_t &pos, const std::string &line)
 void DoxygenParser::processWordCommands(size_t &pos, const std::string &line)
 {
   pos++;
-  // characters '$[]{}' are used in commands \f$, \f[, ...
-
-  size_t endOfWordPos = line.find_first_not_of("abcdefghijklmnopqrstuvwxyz$[]{}", pos);
+  size_t endOfWordPos = line.find_first_not_of(DOXYGEN_WORD_CHARS, pos);
 
   string cmd = line.substr(pos, endOfWordPos - pos);
   addDoxyCommand(m_tokenList, cmd);

From 846a90f8d769ab6ee56102e28b52ab0c9ad78005 Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Wed, 3 Sep 2014 17:27:13 +0200
Subject: [PATCH 241/314] Use "//", not "#", for comments in SWIG input.

One Doxygen test file used "#" for comments for some reason, this doesn't work
with the latest SWIG trunk where a lone "#" is considered to be an unknown
preprocessor directive.
---
 Examples/test-suite/doxygen_misc_constructs.i | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/Examples/test-suite/doxygen_misc_constructs.i b/Examples/test-suite/doxygen_misc_constructs.i
index 04c063e64..ed5fa4326 100644
--- a/Examples/test-suite/doxygen_misc_constructs.i
+++ b/Examples/test-suite/doxygen_misc_constructs.i
@@ -1,5 +1,5 @@
-# This file contains tests for situations, which do not normally
-# appear in the code, but must neverthless be handled correctly.
+// This file contains tests for situations, which do not normally
+// appear in the code, but must nevertheless be handled correctly.
 
 %module doxygen_misc_constructs
 

From 306d99f7d6d937ddfdb2c9f33f6bd80db7930c5d Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Thu, 4 Sep 2014 18:53:14 +0200
Subject: [PATCH 242/314] No changes, just make checking for Doxygen structural
 tags more sane.

Replace an if statement with 33 conditions in it with a table and a loop.
---
 Source/CParse/parser.y | 61 ++++++++++++++++++++++++++++++++----------
 1 file changed, 47 insertions(+), 14 deletions(-)

diff --git a/Source/CParse/parser.y b/Source/CParse/parser.y
index dee839b73..678b4b3ac 100644
--- a/Source/CParse/parser.y
+++ b/Source/CParse/parser.y
@@ -68,24 +68,57 @@ static Node *previousNode = NULL; /* Pointer to the previous node (for post comm
 static Node *currentNode = NULL; /* Pointer to the current node (for post comments) */
 
 int isStructuralDoxygen(String *s){
+	static const char* const structuralTags[] = {
+	  "addtogroup",
+	  "callgraph",
+	  "callergraph",
+	  "category",
+	  "class",
+	  "def",
+	  "defgroup",
+	  "dir",
+	  "enum",
+	  "example",
+	  "file",
+	  "fn",
+	  "headerfile",
+	  "hideinitializer",
+	  "interface",
+	  "internal",
+	  "mainpage",
+	  "name",
+	  "namespace",
+	  "nosubgrouping",
+	  "overload",
+	  "package",
+	  "page",
+	  "property",
+	  "protocol",
+	  "relates",
+	  "relatesalso",
+	  "showinitializer",
+	  "struct",
+	  "typedef",
+	  "union",
+	  "var",
+	  "weakgroup",
+	};
+
+	unsigned n;
 	char *slashPointer = Strchr(s, '\\');
 	char *atPointer = Strchr(s,'@');
 	if (slashPointer == NULL && atPointer == NULL) return 0;
 	else if( slashPointer == NULL) slashPointer = atPointer;
-	/* Perhaps a better solution exists... */
-	slashPointer++;
-	if (strncmp(slashPointer, "addtogroup", 10) == 0 || strncmp(slashPointer, "callgraph", 9) == 0 || strncmp(slashPointer, "callergraph", 11) == 0 
-	      || strncmp(slashPointer, "category", 8) == 0 || strncmp(slashPointer, "class", 5) == 0 || strncmp(slashPointer, "def", 3) == 0
-	      || strncmp(slashPointer, "defgroup", 8) == 0 || strncmp(slashPointer, "dir", 3) == 0 || strncmp(slashPointer, "enum", 4) == 0
-	      || strncmp(slashPointer, "example", 7) == 0 || strncmp(slashPointer, "file", 4) == 0 || strncmp(slashPointer, "fn", 2) == 0
-	      || strncmp(slashPointer, "headerfile", 9) == 0 || strncmp(slashPointer, "hideinitializer", 12) == 0
-	      || strncmp(slashPointer, "interface", 9) == 0 || strncmp(slashPointer, "internal", 8) == 0 || strncmp(slashPointer, "mainpage", 8) == 0
-	      || strncmp(slashPointer, "name", 4) == 0 || strncmp(slashPointer, "namespace", 9) == 0 || strncmp(slashPointer, "nosubgrouping", 13) == 0
-	      || strncmp(slashPointer, "overload", 8) == 0 || strncmp(slashPointer, "package", 7) == 0 || strncmp(slashPointer, "page", 4) == 0
-	      || strncmp(slashPointer, "property", 8) == 0 || strncmp(slashPointer, "protocol", 8) == 0 || strncmp(slashPointer, "relates", 7) == 0
-	      || strncmp(slashPointer, "relatesalso", 5) == 0 || strncmp(slashPointer, "showinitializer", 5) == 0 || strncmp(slashPointer, "struct", 5) == 0
-	      || strncmp(slashPointer, "typedef", 7) == 0 || strncmp(slashPointer, "union", 5) == 0 || strncmp(slashPointer, "var", 3) == 0
-	      || strncmp(slashPointer, "weakgroup", 9) == 0){ return 1;}
+
+	slashPointer++; /* skip backslash or at sign */
+
+	for (n = 0; n < sizeof(structuralTags)/sizeof(structuralTags[0]); n++) {
+	  const size_t len = strlen(structuralTags[n]);
+	  if (strncmp(slashPointer, structuralTags[n], len) == 0) {
+	    return 1;
+	  }
+	}
+
 	return 0;
 }
 

From dcdc5fb42165474067bdbc91fe2cf816d0f22c81 Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Thu, 4 Sep 2014 18:59:55 +0200
Subject: [PATCH 243/314] Fix structural Doxygen comment recognition in the
 parser.

The code wrongly recognized something like "@direction" as a structural "@dir"
comment (why is the latter structural is another question).

Add a check that we've really found the entire tag and not just a prefix of
some other tag.
---
 Source/CParse/parser.y | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/Source/CParse/parser.y b/Source/CParse/parser.y
index 678b4b3ac..9347ef1fd 100644
--- a/Source/CParse/parser.y
+++ b/Source/CParse/parser.y
@@ -115,7 +115,9 @@ int isStructuralDoxygen(String *s){
 	for (n = 0; n < sizeof(structuralTags)/sizeof(structuralTags[0]); n++) {
 	  const size_t len = strlen(structuralTags[n]);
 	  if (strncmp(slashPointer, structuralTags[n], len) == 0) {
-	    return 1;
+	    /* Take care to avoid false positives with prefixes of other tags. */
+	    if (slashPointer[len] == '\0' || isspace(slashPointer[len]))
+	      return 1;
 	  }
 	}
 

From cd1f4619d2948a4d49eb86e166c465f1740dd7fe Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Thu, 4 Sep 2014 19:01:26 +0200
Subject: [PATCH 244/314] Stop completely ignoring many Doxygen comments.

For some reason, Doxygen comments such as @class or @enum were considered to
be "structural" (whatever this means) and completely removed during the
parsing time. This is wrong as such comments can be attached to their
corresponding declarations and while it would be arguably better to check that
this is indeed the case (e.g. "@class Foo" really appears before or after the
declaration of this class), throwing them away is definitely not the right
thing to do and keeping them without any further checks is a better alternative.
---
 Examples/test-suite/doxygen_translate_all_tags.i | 12 ------------
 Source/CParse/parser.y                           | 11 -----------
 2 files changed, 23 deletions(-)

diff --git a/Examples/test-suite/doxygen_translate_all_tags.i b/Examples/test-suite/doxygen_translate_all_tags.i
index d1319840f..84b0531d5 100644
--- a/Examples/test-suite/doxygen_translate_all_tags.i
+++ b/Examples/test-suite/doxygen_translate_all_tags.i
@@ -396,16 +396,4 @@ int func10(int a, float b)
 {
 }
 
-
-/**
- * \interface someInterface someHeader.h "Header name"
- *
- * Because of structural Doxygen command at the start of comment block,
- * the whole comment block is ignored. See parser.y, f. isStructuralDoxygen()
- * or documentation for the list of commands.
- */
-int func11(int a, float b)
-{
-}
-
 %}
diff --git a/Source/CParse/parser.y b/Source/CParse/parser.y
index 9347ef1fd..cdaab6b1c 100644
--- a/Source/CParse/parser.y
+++ b/Source/CParse/parser.y
@@ -73,34 +73,23 @@ int isStructuralDoxygen(String *s){
 	  "callgraph",
 	  "callergraph",
 	  "category",
-	  "class",
 	  "def",
 	  "defgroup",
 	  "dir",
-	  "enum",
 	  "example",
 	  "file",
-	  "fn",
 	  "headerfile",
-	  "hideinitializer",
-	  "interface",
 	  "internal",
 	  "mainpage",
 	  "name",
-	  "namespace",
 	  "nosubgrouping",
 	  "overload",
 	  "package",
 	  "page",
-	  "property",
 	  "protocol",
 	  "relates",
 	  "relatesalso",
 	  "showinitializer",
-	  "struct",
-	  "typedef",
-	  "union",
-	  "var",
 	  "weakgroup",
 	};
 

From 05b5ed11bc726c24d878b2ea44850975f7414ff2 Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Wed, 3 Sep 2014 15:57:56 +0200
Subject: [PATCH 245/314] Add a possibility to flexibly ignore custom Doxygen
 tags.

Add %feature("doxygen:ignore:<command>") implementation, documentation and
test case.

This feature allows to use custom tags in C++ Doxygen comments for
C++-specific things that don't make sense in the context of the target
language and also allows to insert contents specific to the target language in
the C++ comments using (different) custom commands, which is very useful in
practice to explain the particularities of the API wrappers.
---
 Doc/Manual/Doxygen.html                       | 120 ++++++++++++++++++
 Examples/test-suite/common.mk                 |   1 +
 Examples/test-suite/doxygen_ignore.i          |  41 ++++++
 .../test-suite/java/doxygen_ignore_runme.java |  44 +++++++
 .../test-suite/python/doxygen_ignore_runme.py |  21 +++
 .../DoxygenTranslator/src/DoxygenParser.cpp   | 113 +++++++++++++++++
 Source/DoxygenTranslator/src/DoxygenParser.h  |  20 +++
 7 files changed, 360 insertions(+)
 create mode 100644 Examples/test-suite/doxygen_ignore.i
 create mode 100644 Examples/test-suite/java/doxygen_ignore_runme.java
 create mode 100644 Examples/test-suite/python/doxygen_ignore_runme.py

diff --git a/Doc/Manual/Doxygen.html b/Doc/Manual/Doxygen.html
index 916bd5e87..8b63d5b2b 100644
--- a/Doc/Manual/Doxygen.html
+++ b/Doc/Manual/Doxygen.html
@@ -226,6 +226,126 @@ instead of the corresponding language tool (<tt>javadoc</tt>, <tt>sphinx</tt>,
 </p>
 
 
+<h4>doxygen:ignore:&lt;command-name&gt;</h4>
+
+<p>
+Specify that the Doxygen command with the given name should be ignored. This is
+useful for custom Doxygen commands which can be defined using <tt>ALIASES</tt>
+option for Doxygen itself but which are unknown to SWIG. <tt>"command-name"</tt>
+is the real name of the command, e.g. you could use
+</p>
+
+<div class="code"><pre>
+%feature("doxygen:ignore:transferfull");
+</pre></div>
+
+<p>
+if you use a custom Doxygen <tt>transferfull</tt> command to indicate that the
+return value ownership is transferred to the caller, as this information doesn't
+make much sense for the other languages without explicit ownership management.
+</p>
+
+<p>
+Doxygen syntax is rather rich and, in addition to simple commands such as
+<tt>@transferfull</tt>, it is also possible to define commands with arguments.
+As explained in <a href="http://www.stack.nl/~dimitri/doxygen/manual/commands.html">Doxygen documentation</a>,
+the arguments can have a range of a single word, everything until the end of
+line or everything until the end of the next paragraph. Currently, only the "end
+of line" case is supported using the <tt>range="line"</tt> argument of the
+feature directive:
+</p>
+
+<div class="code"><pre>
+// Ignore occurrences of
+//
+//    @compiler-options Some special C++ compiler options.
+//
+// in Doxygen comments as C++ options are not interested for the target language
+// developers.
+%feature("doxygen:ignore:compileroptions", range="line");
+</pre></div>
+
+<p>
+In addition, it is also possible to have custom pairs of begin/end tags,
+similarly to the standard Doxygen <tt>@code/@endcode</tt>, for example. Such
+tags can also be ignored using the special value of <tt>range</tt> starting with
+<tt>end</tt> to indicate that the range is an interval, for example:
+</p>
+
+<div class="code"><pre>
+%feature("doxygen:ignore:forcpponly", range="end"); // same as "end:endforcpponly"
+</pre></div>
+
+<p>
+would ignore everything between <tt>@forcpponly</tt> and <tt>@endforcpponly</tt>
+commands in Doxygen comments. By default, the name of the end command is the
+same as of the start one with "end" prefix, following Doxygen conventions, but
+this can be overridden by providing the end command name after the colon.
+</p>
+<p>
+This example shows how custom tags can be used to bracket anything specific to
+C++ and prevent it from appearing in the target language documentation.
+Conversely, another pair of custom tags could be used to put target language
+specific information in the C++ comments. In this case, only the custom tags
+themselves should be ignored, but their contents should be parsed as usual and
+<tt>contents="parse"</tt> can be used for this:
+</p>
+
+<div class="code"><pre>
+%feature("doxygen:ignore:beginPythonOnly", range="end:endPythonOnly", contents="parse");
+</pre></div>
+
+<p>
+Putting everything together, if these directives are in effect:
+</p>
+
+<div class="code"><pre>
+%feature("doxygen:ignore:transferfull");
+%feature("doxygen:ignore:compileroptions", range="line");
+%feature("doxygen:ignore:forcpponly", range="end");
+%feature("doxygen:ignore:beginPythonOnly", range="end:endPythonOnly", contents="parse");
+</pre></div>
+
+<p>
+then the following C++ Doxygen comment:
+</p>
+
+<div class="code"><pre>
+/**
+    A contrived example of ignoring too many commands in one comment.
+
+    @forcpponly
+    This is C++-specific.
+    @endforcpponly
+
+    @beginPythonOnly
+    This is specific to @b Python.
+    @endPythonOnly
+
+    @transferfull Command ignored, but anything here is still included.
+
+    @compileroptions This function must be compiled with /EHa when using MSVC.
+ */
+void func();
+</pre></div>
+
+<p>
+would be translated to this comment in Python:
+</p>
+
+<div class="code"><pre>
+def func():
+    r"""
+    A contrived example of ignoring too many commands in one comment.
+
+    This is specific to **Python**.
+
+    Command ignored, but anything here is still included.
+    """
+    ...
+</pre></div>
+
+
 <h4>doxygen:nolinkranslate (Java-only currently)</h4>
 
 <p>
diff --git a/Examples/test-suite/common.mk b/Examples/test-suite/common.mk
index 39ad4c012..76c088cf7 100644
--- a/Examples/test-suite/common.mk
+++ b/Examples/test-suite/common.mk
@@ -551,6 +551,7 @@ $(eval HAS_DOXYGEN := $($(LANGUAGE)_HAS_DOXYGEN))
 ifdef HAS_DOXYGEN
 DOXYGEN_TEST_CASES += \
 	doxygen_parsing \
+	doxygen_ignore \
 	doxygen_basic_translate \
 	doxygen_basic_notranslate \
 	doxygen_translate \
diff --git a/Examples/test-suite/doxygen_ignore.i b/Examples/test-suite/doxygen_ignore.i
new file mode 100644
index 000000000..d15110257
--- /dev/null
+++ b/Examples/test-suite/doxygen_ignore.i
@@ -0,0 +1,41 @@
+%module doxygen_ignore
+
+%feature("doxygen:ignore:transferfull");
+%feature("doxygen:ignore:compileroptions", range="line");
+%feature("doxygen:ignore:forcpponly", range="end");
+
+#ifdef SWIGJAVA
+%feature("doxygen:ignore:beginJavaOnly", range="end:endJavaOnly", contents="parse");
+%feature("doxygen:ignore:beginPythonOnly", range="end:endPythonOnly");
+#elif defined(SWIGPYTHON)
+%feature("doxygen:ignore:beginJavaOnly", range="end:endJavaOnly");
+%feature("doxygen:ignore:beginPythonOnly", range="end:endPythonOnly", contents="parse");
+#else
+%feature("doxygen:ignore:beginJavaOnly", range="end:endJavaOnly");
+%feature("doxygen:ignore:beginPythonOnly", range="end:endPythonOnly");
+#endif
+
+%inline %{
+
+/**
+    A contrived example of ignoring too many commands in one comment.
+
+    @forcpponly
+    This is C++-specific.
+    @endforcpponly
+
+    @beginJavaOnly
+    This is specific to @e Java.
+    @endJavaOnly
+
+    @beginPythonOnly
+    This is specific to @b Python.
+    @endPythonOnly
+
+    @transferfull Command ignored, but anything here is still included.
+
+    @compileroptions This function must be compiled with /EHa when using MSVC.
+ */
+void func() { }
+
+%}
diff --git a/Examples/test-suite/java/doxygen_ignore_runme.java b/Examples/test-suite/java/doxygen_ignore_runme.java
new file mode 100644
index 000000000..d6a4d8c8d
--- /dev/null
+++ b/Examples/test-suite/java/doxygen_ignore_runme.java
@@ -0,0 +1,44 @@
+
+import doxygen_ignore.*;
+import com.sun.javadoc.*;
+import java.util.HashMap;
+
+public class doxygen_ignore_runme {
+  static {
+    try {
+      System.loadLibrary("doxygen_ignore");
+    } catch (UnsatisfiedLinkError e) {
+      System.err.println("Native code library failed to load. See the chapter on Dynamic Linking Problems in the SWIG Java documentation for help.\n" + e);
+      System.exit(1);
+    }
+  }
+
+  public static void main(String argv[]) 
+  {
+    CommentParser parser = new CommentParser();
+    com.sun.tools.javadoc.Main.execute("doxygen_ignore runtime test",
+                                       "CommentParser",
+                                       new String[]{"-quiet", "doxygen_ignore"});
+
+    HashMap<String, String> wantedComments = new HashMap<String, String>();
+    wantedComments.put("doxygen_ignore.doxygen_ignore.func()",
+      "     A contrived example of ignoring too many commands in one comment.<br>\n" +
+      " <br>\n" +
+      "     <br>\n" +
+      " <br>\n" +
+      "     <br>\n" +
+      "     This is specific to <i>Java</i>.<br>\n" +
+      "     <br>\n" +
+      " <br>\n" +
+      "     <br>\n" +
+      " <br>\n" +
+      "     Command ignored, but anything here is still included.<br>\n" +
+      " <br>\n" +
+      "\n" +
+      "\n" +
+      "\n" +
+      "");
+
+    System.exit(parser.check(wantedComments));
+  }
+}
diff --git a/Examples/test-suite/python/doxygen_ignore_runme.py b/Examples/test-suite/python/doxygen_ignore_runme.py
new file mode 100644
index 000000000..7fe2667d3
--- /dev/null
+++ b/Examples/test-suite/python/doxygen_ignore_runme.py
@@ -0,0 +1,21 @@
+#!/usr/bin/python
+
+import doxygen_ignore
+import commentVerifier
+
+commentVerifier.check(doxygen_ignore.func.__doc__,
+    r"""
+    A contrived example of ignoring too many commands in one comment.
+
+
+
+
+
+
+    This is specific to **Python**.
+
+
+    Command ignored, but anything here is still included.
+
+
+    """)
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.cpp b/Source/DoxygenTranslator/src/DoxygenParser.cpp
index 5e1f3a5d3..c8cb40ab8 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenParser.cpp
@@ -135,6 +135,28 @@ int DoxygenParser::commandBelongs(const std::string &theCommand)
   if (it != doxygenCommands.end()) {
     return it->second;
   }
+
+  // Check if this command should be ignored.
+  if (String* const ignore = getIgnoreFeature(theCommand)) {
+    // Check that no value is specified for this feature ("1" is the implicit
+    // one given to it by SWIG itself), we may use the value in the future, but
+    // for now we only use the attributes.
+    if (Strcmp(ignore, "1") != 0) {
+      Swig_warning(WARN_PP_UNEXPECTED_TOKENS, m_fileName.c_str(), m_fileLineNo,
+          "Feature \"doxygen:ignore\" value ignored for Doxygen command \"%s\".\n",
+          theCommand.c_str());
+    }
+
+    // Also ensure that the matching end command, if any, will be recognized.
+    const string endCommand = getIgnoreFeatureEndCommand(theCommand);
+    if (!endCommand.empty()) {
+      Setattr(m_node, ("feature:doxygen:ignore:" + endCommand).c_str(),
+          NewString("1"));
+    }
+
+    return COMMAND_IGNORE;
+  }
+
   return NONE;
 }
 
@@ -878,6 +900,95 @@ int DoxygenParser::addCommandUnique(const std::string &theCommand,
   return 0;
 }
 
+String* DoxygenParser::getIgnoreFeature(const std::string& theCommand,
+                                        const char* argument) const
+{
+  string feature_name = "feature:doxygen:ignore:" + theCommand;
+  if (argument) {
+    feature_name += ':';
+    feature_name += argument;
+  }
+
+  return Getattr(m_node, feature_name.c_str());
+}
+
+string DoxygenParser::getIgnoreFeatureEndCommand(const std::string& theCommand) const
+{
+  // We may be dealing either with a simple command or with the starting command
+  // of a block, as indicated by the value of "range" starting with "end".
+  string endCommand;
+  if (String* const range = getIgnoreFeature(theCommand, "range")) {
+    const char* const p = Char(range);
+    if (strncmp(p, "end", 3) == 0) {
+      if (p[3] == ':') {
+        // Normally the end command name follows after the colon.
+        endCommand = p + 4;
+      } else if (p[3] == '\0') {
+        // But it may be omitted in which case the default Doxygen convention of
+        // using "something"/"endsomething" is used.
+        endCommand = "end" + theCommand;
+      }
+    }
+  }
+
+  return endCommand;
+}
+
+int DoxygenParser::ignoreCommand(const std::string& theCommand,
+                                 const TokenList &tokList,
+                                 DoxygenEntityList &doxyList)
+{
+  const string endCommand = getIgnoreFeatureEndCommand(theCommand);
+  if (!endCommand.empty()) {
+    TokenListCIt itEnd = getEndCommand(endCommand, tokList);
+    if (itEnd == tokList.end()) {
+      printListError(WARN_DOXYGEN_COMMAND_EXPECTED, "Expected " + endCommand);
+      return 0;
+    }
+
+    // Determine what to do with the part of the comment between the start and
+    // end commands: by default, we simply throw it away, but "contents"
+    // attribute may be used to change this.
+    if (String* const contents = getIgnoreFeature(theCommand, "contents")) {
+      // Currently only "parse" is supported but we may need to add "copy" to
+      // handle custom tags which contain text that is supposed to be copied
+      // verbatim in the future.
+      if (Strcmp(contents, "parse") == 0) {
+        DoxygenEntityList aNewList = parse(itEnd, tokList);
+        doxyList.splice(doxyList.end(), aNewList);
+      } else {
+        Swig_error(m_fileName.c_str(), m_fileLineNo,
+            "Invalid \"doxygen:ignore\" feature \"contents\" attribute \"%s\".\n",
+            Char(contents)
+          );
+        return 0;
+      }
+    }
+
+    m_tokenListIt = itEnd;
+    m_tokenListIt++;
+  } else if (String* const range = getIgnoreFeature(theCommand, "range")) {
+    // Currently we only support "line" but, in principle, we should also
+    // support "word" and "paragraph" for consistency with the built-in Doxygen
+    // commands which can have either of these three ranges (which are indicated
+    // using <word-arg>, (line-arg) and {para-arg} respectively in Doxygen
+    // documentation).
+    if (Strcmp(range, "line") == 0) {
+      // Consume everything until the end of line.
+      m_tokenListIt = getOneLine(tokList);
+      skipEndOfLine();
+    } else {
+      Swig_error(m_fileName.c_str(), m_fileLineNo,
+          "Invalid \"doxygen:ignore\" feature \"range\" attribute \"%s\".\n",
+          Char(range)
+        );
+      return 0;
+    }
+  }
+
+  return 1;
+}
+
 int DoxygenParser::addCommand(const std::string &commandString,
                               const TokenList &tokList,
                               DoxygenEntityList &doxyList)
@@ -920,6 +1031,8 @@ int DoxygenParser::addCommand(const std::string &commandString,
     return addCommandHtml(theCommand, tokList, doxyList);
   case COMMAND_HTML_ENTITY:
     return addCommandHtmlEntity(theCommand, tokList, doxyList);
+  case COMMAND_IGNORE:
+    return ignoreCommand(commandString, tokList, doxyList);
   }
   return 0;
 }
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.h b/Source/DoxygenTranslator/src/DoxygenParser.h
index f86f94f44..c1e4994c0 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.h
+++ b/Source/DoxygenTranslator/src/DoxygenParser.h
@@ -39,6 +39,7 @@ private:
     COMMANDUNIQUE,
     COMMAND_HTML,
     COMMAND_HTML_ENTITY,
+    COMMAND_IGNORE,
     END_LINE,
     PARAGRAPH_END,
     PLAINSTRING,
@@ -98,6 +99,17 @@ private:
   std::string m_fileName;
   int m_fileLineNo;
 
+  /*
+   * Return the end command for a command appearing in "ignore" feature or empty
+   * string if this is a simple command and not a block one.
+   */
+  std::string getIgnoreFeatureEndCommand(const std::string& theCommand) const;
+
+  /*
+   * Helper for getting the value of doxygen:ignore feature or its argument.
+   */
+  String* getIgnoreFeature(const std::string& theCommand, const char* argument = NULL) const;
+
     /*
      * Whether to print lots of debug info during parsing
      */
@@ -334,6 +346,14 @@ private:
                        const TokenList &tokList,
                        DoxygenEntityList &doxyList);
 
+  /*
+   * Simply ignore the given command, possibly with the word following it or
+   * until the matching end command.
+   */
+  int ignoreCommand(const std::string& theCommand,
+                    const TokenList &tokList,
+                    DoxygenEntityList &doxyList);
+
   /* 
    * The actual "meat" of the doxygen parser. Calls the correct addCommand...()
    * function.

From 410b508e9a2a6d2f34170ef7f33cc755ba72b941 Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Mon, 15 Dec 2014 12:58:03 +0100
Subject: [PATCH 246/314] Don't indent Doxygen doc strings in generated Python
 code.

This is unnecessary and inconsistent with "builtin" case in which the
docstrings are not indented in the generated C++ code, thus making it
impossible to write tests working in both cases.

Most of the changes in this commit simply remove the extra whitespace from the
expected values in the tests.
---
 .../python/doxygen_basic_notranslate_runme.py |  83 +++--
 .../python/doxygen_basic_translate_runme.py   |  79 +++--
 .../test-suite/python/doxygen_ignore_runme.py |   7 +-
 .../python/doxygen_misc_constructs_runme.py   | 151 ++++-----
 .../python/doxygen_parsing_runme.py           |  73 ++---
 .../doxygen_translate_all_tags_runme.py       | 231 +++++++------
 .../python/doxygen_translate_links_runme.py   |  39 ++-
 .../python/doxygen_translate_runme.py         | 304 +++++++++---------
 Source/Modules/python.cxx                     |  39 +--
 9 files changed, 471 insertions(+), 535 deletions(-)

diff --git a/Examples/test-suite/python/doxygen_basic_notranslate_runme.py b/Examples/test-suite/python/doxygen_basic_notranslate_runme.py
index e7c9ea1b8..5559e38bc 100644
--- a/Examples/test-suite/python/doxygen_basic_notranslate_runme.py
+++ b/Examples/test-suite/python/doxygen_basic_notranslate_runme.py
@@ -7,75 +7,68 @@ import commentVerifier
 
 commentVerifier.check(doxygen_basic_notranslate.function.__doc__,
     r"""
-    \brief
-    Brief description.
-
-    The comment text
-    \author Some author
-    \return Some number
-    \sa function2
-
-    """
+ \brief
+ Brief description.
+ 
+ The comment text
+ \author Some author
+ \return Some number
+ \sa function2
+ """
 )
 
 commentVerifier.check(doxygen_basic_notranslate.function2.__doc__,
     r"""
-    A test of a very very very very very very very very very very very very very very very very
-    very very very very very long comment string.
-
-    """
+ A test of a very very very very very very very very very very very very very very very very
+ very very very very very long comment string.
+ """
 )
 
 commentVerifier.check(doxygen_basic_notranslate.function3.__doc__,
-    r"""
-    *Overload 1:*
+    r""" *Overload 1:*
 
-    A test for overloaded functions
-    This is function \b one
+ A test for overloaded functions
+ This is function \b one
 
-    |
+ |
 
-    *Overload 2:*
+ *Overload 2:*
 
-    A test for overloaded functions
-    This is function \b two
-    """
+ A test for overloaded functions
+ This is function \b two"""
 )
 
 commentVerifier.check(doxygen_basic_notranslate.function4.__doc__,
     r"""
-    A test of some mixed tag usage
-    \if CONDITION
-    This \a code fragment shows us something \.
-    \par Minuses:
-    \arg it's senseless
-    \arg it's stupid
-    \arg it's null
+ A test of some mixed tag usage
+ \if CONDITION
+ This \a code fragment shows us something \.
+ \par Minuses:
+ \arg it's senseless
+ \arg it's stupid
+ \arg it's null
 
-    \warning This may not work as expected
+ \warning This may not work as expected
 
-    \code
-    int main() { while(true); }
-    \endcode
-    \endif
-
-    """
+ \code
+ int main() { while(true); }
+ \endcode
+ \endif
+ """
 )
 commentVerifier.check(doxygen_basic_notranslate.function5.__doc__,
     r""" This is a post comment. """
 )
 commentVerifier.check(doxygen_basic_notranslate.function6.__doc__,
     r"""
-    Test for default args
-    @param a Some parameter, default is 42
-
-    """
+ Test for default args
+ @param a Some parameter, default is 42
+ """
 )
 commentVerifier.check(doxygen_basic_notranslate.function7.__doc__,
     r"""
-    Test for a parameter with difficult type
-    (mostly for python)
-    @param a Very strange param
-
-    """
+ Test for a parameter with difficult type
+ (mostly for python)
+ @param a Very strange param
+ """
 )
diff --git a/Examples/test-suite/python/doxygen_basic_translate_runme.py b/Examples/test-suite/python/doxygen_basic_translate_runme.py
index 87010ee39..a93f75e6f 100644
--- a/Examples/test-suite/python/doxygen_basic_translate_runme.py
+++ b/Examples/test-suite/python/doxygen_basic_translate_runme.py
@@ -7,80 +7,74 @@ import commentVerifier
 
 commentVerifier.check(doxygen_basic_translate.function.__doc__,
     """
-    Brief description.
 
-    The comment text.
+Brief description.
 
-    Author: Some author
+The comment text.
 
-    :rtype: int
-    :return: Some number
+Author: Some author
 
-    See also: function2
-    """
+:rtype: int
+:return: Some number
+
+See also: function2"""
 )
 commentVerifier.check(doxygen_basic_translate.function2.__doc__,
     """
-    A test of a very very very very very very very very very very very very very very very very
-    very very very very very long comment string.
-    """
+A test of a very very very very very very very very very very very very very very very very
+very very very very very long comment string."""
 )
 commentVerifier.check(doxygen_basic_translate.function3.__doc__,
-    """
-    *Overload 1:*
+    """*Overload 1:*
 
-    A test for overloaded functions
-    This is function **one**
+A test for overloaded functions
+This is function **one**
 
-    |
+|
 
-    *Overload 2:*
+*Overload 2:*
 
-    A test for overloaded functions
-    This is function **two**
-    """
+A test for overloaded functions
+This is function **two**"""
 )
 commentVerifier.check(doxygen_basic_translate.function4.__doc__,
     """
-    A test of some mixed tag usage
-    If: CONDITION {
-    This *code* fragment shows us something .
-    Title: Minuses:
-    * it\'s senseless
-    * it\'s stupid
-    * it\'s null
+A test of some mixed tag usage
+If: CONDITION {
+This *code* fragment shows us something .
+Title: Minuses:
+* it\'s senseless
+* it\'s stupid
+* it\'s null
 
-    Warning: This may not work as expected
+Warning: This may not work as expected
 
-    .. code-block:: c++
+.. code-block:: c++
 
 
-        int main() { while(true); }
+    int main() { while(true); }
 
-    }
-    """
+}"""
 )
 commentVerifier.check(doxygen_basic_translate.function5.__doc__,
     """ This is a post comment."""
 )
 commentVerifier.check(doxygen_basic_translate.function6.__doc__,
     """
-    Test for default args
-    :type a: int
-    :param a: Some parameter, default is 42
-    """
+Test for default args
+:type a: int
+:param a: Some parameter, default is 42"""
 )
 commentVerifier.check(doxygen_basic_translate.function7.__doc__,
     """
-    Test for a parameter with difficult type
-    (mostly for python)
-    :type a: :py:class:`Shape`
-    :param a: Very strange param
-    """
+Test for a parameter with difficult type
+(mostly for python)
+:type a: :py:class:`Shape`
+:param a: Very strange param"""
 )
 
 commentVerifier.check(doxygen_basic_translate.Atan2.__doc__,
-"""
+    """
     Multiple parameters test.
 
     :type y: float
@@ -88,6 +82,5 @@ commentVerifier.check(doxygen_basic_translate.Atan2.__doc__,
     :type x: float
     :param x: Horizontal coordinate.
     :rtype: float
-    :return: Arc tangent of ``y/x``.
-    """
+    :return: Arc tangent of ``y/x``."""
 )
diff --git a/Examples/test-suite/python/doxygen_ignore_runme.py b/Examples/test-suite/python/doxygen_ignore_runme.py
index 7fe2667d3..84ef0ddab 100644
--- a/Examples/test-suite/python/doxygen_ignore_runme.py
+++ b/Examples/test-suite/python/doxygen_ignore_runme.py
@@ -7,15 +7,14 @@ commentVerifier.check(doxygen_ignore.func.__doc__,
     r"""
     A contrived example of ignoring too many commands in one comment.
 
+    
 
+    
 
-
-
-
+    
     This is specific to **Python**.
 
 
     Command ignored, but anything here is still included.
 
-
     """)
diff --git a/Examples/test-suite/python/doxygen_misc_constructs_runme.py b/Examples/test-suite/python/doxygen_misc_constructs_runme.py
index ac439ceb4..81e0ee0a9 100644
--- a/Examples/test-suite/python/doxygen_misc_constructs_runme.py
+++ b/Examples/test-suite/python/doxygen_misc_constructs_runme.py
@@ -8,49 +8,46 @@ import commentVerifier
 
 commentVerifier.check(doxygen_misc_constructs.getAddress.__doc__,
     r"""
-    Returns address of file line.
+Returns address of file line.
 
-    :type fileName: int
-    :param fileName: name of the file, where the source line is located
-    :type line: int
-    :param line: line number
-    :type isGetSize: boolean
-    :param isGetSize: if set, for every object location both address and size are returned
+:type fileName: int
+:param fileName: name of the file, where the source line is located
+:type line: int
+:param line: line number
+:type isGetSize: boolean
+:param isGetSize: if set, for every object location both address and size are returned
 
-    Connection::getId() 
-
-    """)
+Connection::getId() 
+""")
 
 commentVerifier.check(doxygen_misc_constructs.CConnectionConfig.__doc__,
     r"""
-    This class contains information for connection to winIDEA. Its methods
-    return reference to self, so we can use it like this:
+This class contains information for connection to winIDEA. Its methods
+return reference to self, so we can use it like this:
 
-    CConnectionConfig config = new CConnectionConfig();
-    config.discoveryPort(5534).dllPath("C:\\myWinIDEA\\connect.dll").id("main");
+CConnectionConfig config = new CConnectionConfig();
+config.discoveryPort(5534).dllPath("C:\\myWinIDEA\\connect.dll").id("main");
 
 
-    All parameters are optional. Set only what is required, default values are
-    used for unspecified parameters.
+All parameters are optional. Set only what is required, default values are
+used for unspecified parameters.
 
 
 
-    advancedWinIDEALaunching.py Python example.
-
-    """)
+advancedWinIDEALaunching.py Python example.
+""")
 
 commentVerifier.check(doxygen_misc_constructs.waitTime.__doc__,
     r"""
-    Determines how long the ``isystem.connect`` should wait for running
-    instances to respond. Only one of ``lfWaitXXX`` flags from IConnect::ELaunchFlags
-    may be specified.
-    """
+Determines how long the ``isystem.connect`` should wait for running
+instances to respond. Only one of ``lfWaitXXX`` flags from IConnect::ELaunchFlags
+may be specified."""
 )
 
 commentVerifier.check(doxygen_misc_constructs.getConnection.__doc__,
-    r"""
-    This function returns connection id.
-    """
+    r""" 
+
+This function returns connection id."""
 )
 
 
@@ -60,37 +57,31 @@ commentVerifier.check(doxygen_misc_constructs.getFirstLetter.__doc__,
 
 commentVerifier.check(doxygen_misc_constructs.ClassWithNestedEnum.__doc__,
     r"""
-    Class description.
-    """
+Class description."""
 )
 
 commentVerifier.check(doxygen_misc_constructs.showList.__doc__,
     r"""
-    An example of a list in a documentation comment.
+        An example of a list in a documentation comment.
 
-        - The first item of the list.
-        - The second list item, on
-          several indented lines,
-          showing that the indentation
-          is preserved.
-        - And the final list item after it.
+            - The first item of the list.
+            - The second list item, on
+              several indented lines,
+              showing that the indentation
+              is preserved.
+            - And the final list item after it.
 
-    And this is not a list item any more.
-    """
+        And this is not a list item any more."""
 )
 
 commentVerifier.check(doxygen_misc_constructs.isNoSpaceValidA.__doc__,
-    r"""
-    This comment without space after '*' is valid in Doxygen.
-
-    """
+    r"""This comment without space after '*' is valid in Doxygen.
+"""
 )
 
 commentVerifier.check(doxygen_misc_constructs.isNoSpaceValidB.__doc__,
-    r"""
-    .This comment without space after '*' is valid in Doxygen.
-
-    """
+    r""".This comment without space after '*' is valid in Doxygen.
+"""
 )
 
 commentVerifier.check(doxygen_misc_constructs.isNoSpaceValidC.__doc__,
@@ -99,64 +90,60 @@ commentVerifier.check(doxygen_misc_constructs.isNoSpaceValidC.__doc__,
 
 commentVerifier.check(doxygen_misc_constructs.backslashA.__doc__,
     r"""
-    Backslash following``word`` is a valid doxygen command. Output contains
-    'followingword' with 'word' in code font.
-    """
+Backslash following``word`` is a valid doxygen command. Output contains
+'followingword' with 'word' in code font."""
 )
 
 commentVerifier.check(doxygen_misc_constructs.backslashB.__doc__,
     r"""
-    Doxy command without trailing space is ignored - nothing appears
-    on output. Standalone \ and '\' get to output.
-    Standalone @ and '@' get to output.
-    Commands "in quoted \b strings are treated as plain text".
-    Commands not recognized by Doxygen are ignored.
-    Backslashes in DOS paths d:and words
-    following them do not appear on output, we must quote them with
-    double quotes: "d:\xyz\qwe\myfile", "@something". Single quotes do not help:
-    'd:'. Escaping works: d:\xyz\qwe\myfile. Unix
-    paths of course have no such problems: /xyz/qwe/myfile
-    Commands for escaped symbols:
-    $ @ \ & ~ < > # % " . :: @text ::text
-    """
+Doxy command without trailing space is ignored - nothing appears
+on output. Standalone \ and '\' get to output.
+Standalone @ and '@' get to output.
+Commands "in quoted \b strings are treated as plain text".
+Commands not recognized by Doxygen are ignored.
+Backslashes in DOS paths d:and words
+following them do not appear on output, we must quote them with
+double quotes: "d:\xyz\qwe\myfile", "@something". Single quotes do not help:
+'d:'. Escaping works: d:\xyz\qwe\myfile. Unix
+paths of course have no such problems: /xyz/qwe/myfile
+Commands for escaped symbols:
+$ @ \ & ~ < > # % " . :: @text ::text"""
 )
 
 commentVerifier.check(doxygen_misc_constructs.backslashC.__doc__,
     r"""
-    Backslash e at end of *line* froze SWIG
-    *with* old comment parser.
+Backslash e at end of *line* froze SWIG
+*with* old comment parser.
 
-    See also: MyClass::fun(char,
-     float)
-    """
+See also: MyClass::fun(char,
+ float)"""
 )
 
 
 commentVerifier.check(doxygen_misc_constructs.cycle.__doc__,
     r"""
-    The next line contains expression:
+The next line contains expression:
 
-    ['retVal < 10', 'g_counter == 23 && g_mode & 3']
+['retVal < 10', 'g_counter == 23 && g_mode & 3']
 
 
-    Both words should be emphasized **isystem.connect**.
-    But not the last period. For **example**, comma should not be emphasized.
-    Similar **for**: double colon.
+Both words should be emphasized **isystem.connect**.
+But not the last period. For **example**, comma should not be emphasized.
+Similar **for**: double colon.
 
-    Spaces at the start of line should be taken into account:
-    :type id: int
-    :param id: used as prefix in log
-            statements. The default value is empty string, which is OK if
-            there is only one app. instance. Example:
+Spaces at the start of line should be taken into account:
+:type id: int
+:param id: used as prefix in log
+        statements. The default value is empty string, which is OK if
+        there is only one app. instance. Example:
 
-                ctrl.setBP("func1");
+            ctrl.setBP("func1");
 
-            If we set the id to ``main_``, we get:
+        If we set the id to ``main_``, we get:
 
-                main_ctrl.setBP("func1");
+            main_ctrl.setBP("func1");
 
 
-    :type fileName: string
-    :param fileName: name of the log file
-    """
+:type fileName: string
+:param fileName: name of the log file"""
 );
diff --git a/Examples/test-suite/python/doxygen_parsing_runme.py b/Examples/test-suite/python/doxygen_parsing_runme.py
index 5ff5cf5c7..d89a1741a 100644
--- a/Examples/test-suite/python/doxygen_parsing_runme.py
+++ b/Examples/test-suite/python/doxygen_parsing_runme.py
@@ -7,72 +7,61 @@ import commentVerifier
 
 commentVerifier.check(doxygen_parsing.someFunction.__doc__,
     r"""
-    The function comment
-    """)
+The function comment""")
 commentVerifier.check(doxygen_parsing.SomeClass.__doc__,
     r"""
-    The class comment
-    """)
+The class comment""")
 commentVerifier.check(doxygen_parsing.SomeStruct.__doc__,
     r"""
-    The struct comment
-    """)
+The struct comment""")
 commentVerifier.check(doxygen_parsing.SomeAnotherClass.__init__.__doc__,
-    r"""
-        *Overload 1:*
-        First overloaded constructor.
+    r""" *Overload 1:*
+ First overloaded constructor.
 
-        |
+ |
 
-        *Overload 2:*
-        Second overloaded constructor.
-        """)
+ *Overload 2:*
+ Second overloaded constructor.""")
 commentVerifier.check(doxygen_parsing.SomeAnotherClass.classMethod.__doc__,
     r"""
-        The class method comment.
+The class method comment.
 
-        SomeAnotherClass#classMethodExtended(int, int) a link text
-        """)
+SomeAnotherClass#classMethodExtended(int, int) a link text""")
 commentVerifier.check(doxygen_parsing.SomeAnotherClass.classMethodExtended.__doc__,
     r"""
-        The class method with parameter
+The class method with parameter
 
-        :type a: int
-        :param a: Parameter a
-        :type b: int
-        :param b: Parameter b
-        """
+:type a: int
+:param a: Parameter a
+:type b: int
+:param b: Parameter b"""
 )
 commentVerifier.check(doxygen_parsing.SomeAnotherClass.classMethodExtended2.__doc__,
     r"""
-        The class method with parameter
+The class method with parameter
 
-        :type a: int
-        :param a: Parameter a
-        :type b: int
-        :param b: Parameter b
-        """
+:type a: int
+:param a: Parameter a
+:type b: int
+:param b: Parameter b"""
 )
 commentVerifier.check(doxygen_parsing.SomeAnotherStruct.structMethod.__doc__,
     r"""
-        The struct method comment
-        """)
+The struct method comment""")
 commentVerifier.check(doxygen_parsing.SomeAnotherStruct.structMethodExtended.__doc__,
     r"""
-        The struct method with parameter
+The struct method with parameter
 
-        :type a: int
-        :param a: Parameter a
-        :type b: int
-        :param b: Parameter b
-        """
+:type a: int
+:param a: Parameter a
+:type b: int
+:param b: Parameter b"""
 )
 commentVerifier.check(doxygen_parsing.SomeAnotherStruct.structMethodExtended2.__doc__,
     r"""
-        The struct method with parameter
+The struct method with parameter
 
-        :type a: int
-        :param a: Parameter a
-        :type b: int
-        :param b: Parameter b
-        """)
+:type a: int
+:param a: Parameter a
+:type b: int
+:param b: Parameter b""")
diff --git a/Examples/test-suite/python/doxygen_translate_all_tags_runme.py b/Examples/test-suite/python/doxygen_translate_all_tags_runme.py
index d0bd43980..838ea3210 100644
--- a/Examples/test-suite/python/doxygen_translate_all_tags_runme.py
+++ b/Examples/test-suite/python/doxygen_translate_all_tags_runme.py
@@ -8,46 +8,45 @@ import commentVerifier
 
 commentVerifier.check(doxygen_translate_all_tags.func01.__doc__,
 r"""
-    *Hello*
+*Hello*
 
 
 
 
 
-    * some list item
+* some list item
 
-    This is attention!
-    You were warned!
+This is attention!
+You were warned!
 
-    Authors: lots of them
-    Author: Zubr
+Authors: lots of them
+Author: Zubr
 
-    **boldword**
+**boldword**
 
-    Some brief description,
-    extended to many lines.
+Some brief description,
+extended to many lines.
 
-    Not everything works right now...
-    ``codeword``
+Not everything works right now...
+``codeword``
 
 
 
 
 
-    'citationword'
+'citationword'
 
 
-    .. code-block:: c++
+.. code-block:: c++
 
-         some test code
-
-    """)
+     some test code
+""")
 
 commentVerifier.check(doxygen_translate_all_tags.func02.__doc__,
 r"""
-    Conditional comment: SOMECONDITION
-    Some conditional comment
-    End of conditional comment.
+Conditional comment: SOMECONDITION
+Some conditional comment
+End of conditional comment.
 
 
 
@@ -55,23 +54,22 @@ r"""
 
 
 
-    Copyright: some copyright
+Copyright: some copyright
 
-    1970 - 2012
+1970 - 2012
 
 
 
 
 
-    Deprecated: Now use another function
+Deprecated: Now use another function
 
-    This is very large
-    and detailed description of some thing
-    """)
+This is very large
+and detailed description of some thing""")
 
 commentVerifier.check(doxygen_translate_all_tags.func03.__doc__,
 r"""
-    Comment for **func03()**.
+Comment for **func03()**.
 
 
 
@@ -81,34 +79,34 @@ r"""
 
 
 
-    *italicword*
+*italicword*
 
-    emphazedWord
+emphazedWord
 
 
 
-    Example: someFile.txt
-    Some details on using the example
-    """)
+Example: someFile.txt
+Some details on using the example""")
 
 commentVerifier.check(doxygen_translate_all_tags.func04.__doc__,
 r"""
-    :raises: SuperError
+
+:raises: SuperError
 
 
 
-    :math:`\sqrt{(x_2-x_1)^2+(y_2-y_1)^2}`
+:math:`\sqrt{(x_2-x_1)^2+(y_2-y_1)^2}`
 
 
-    .. math::
+.. math::
 
-        \sqrt{(x_2-x_1)^2+(y_2-y_1)^2}
+    \sqrt{(x_2-x_1)^2+(y_2-y_1)^2}
 
 
 
-    .. math::
+.. math::
 
-        \sqrt{(x_2-x_1)^2+(y_2-y_1)^2}
+    \sqrt{(x_2-x_1)^2+(y_2-y_1)^2}
 
 
 
@@ -121,31 +119,30 @@ r"""
 
 
 
-    This will only appear in hmtl
-
-    """)
+This will only appear in hmtl
+""")
 
 commentVerifier.check(doxygen_translate_all_tags.func05.__doc__,
 r"""
-    If: ANOTHERCONDITION {
-      First part of comment
-      If: SECONDCONDITION {
-        Nested condition text
-      }Else if: THIRDCONDITION {
-        The third condition text
-      }Else:  {    The last text block
-      }
-    }Else:  {  Second part of comment
-      If: CONDITION {
-        Second part extended
-      }
-    }
+If: ANOTHERCONDITION {
+  First part of comment
+  If: SECONDCONDITION {
+    Nested condition text
+  }Else if: THIRDCONDITION {
+    The third condition text
+  }Else:  {    The last text block
+  }
+}Else:  {  Second part of comment
+  If: CONDITION {
+    Second part extended
+  }
+}
 
-    If not: SOMECONDITION {
-      This is printed if not
-    }
+If not: SOMECONDITION {
+  This is printed if not
+}
 
-    Image: testImage.bmp("Hello, world!")
+Image: testImage.bmp("Hello, world!")
 
 
 
@@ -157,35 +154,34 @@ r"""
 
 
 
-    Some text
-    describing invariant.
-    """)
+Some text
+describing invariant.""")
 
 commentVerifier.check(doxygen_translate_all_tags.func06.__doc__,
 r"""
-    Comment for **func06()**.
+Comment for **func06()**.
 
 
 
 
-    This will only appear in LATeX
+This will only appear in LATeX
 
 
 
 
-    * Some unordered list
-    * With lots of items
-    * lots of lots of items
+* Some unordered list
+* With lots of items
+* lots of lots of items
 
 
 
 
-    someMember Some description follows
+someMember Some description follows
 
 
 
 
-    This will only appear in man
+This will only appear in man
 
 
 
@@ -197,59 +193,62 @@ r"""
 
 
 
-
-    """)
+""")
 
 commentVerifier.check(doxygen_translate_all_tags.func07.__doc__,
 r"""
-    Comment for **func07()**.
+Comment for **func07()**.
 
 
 
 
 
 
-    Notes: Here
-    is the note!
+Notes: Here
+is the note!
 
-    This is an overloaded member function, provided for convenience.
-    It differs from the above function only in what argument(s) it accepts.
+This is an overloaded member function, provided for convenience.
+It differs from the above function only in what argument(s) it accepts.
 
-    someword
+someword
 
 
 
 
 
-    Title: The paragraph title
-    The paragraph text.
-    Maybe even multiline
+Title: The paragraph title
+The paragraph text.
+Maybe even multiline
 
 
 
-    :type a: int
-    :param a: the first param
+:type a: int
+:param a: the first param
 
 
 
 
-
-    """)
+""")
 
 commentVerifier.check(doxygen_translate_all_tags.func08.__doc__,
 r"""
-    Text after anchor.
+
+
+
+
+
+Text after anchor.
 
 
 
 
 
 
-    'Anchor description'
+'Anchor description'
 
-    'someAnchor' not quoted text is not part of ref tag
+'someAnchor' not quoted text is not part of ref tag
 
-    'someAnchor'
+'someAnchor'
 
 
 
@@ -259,38 +258,38 @@ r"""
 
 
 
-    Remarks: Some remark text
+Remarks: Some remark text
 
-    Another remarks section
+Another remarks section
 
-    :rtype: int
-    :return: Whatever
+:rtype: int
+:return: Whatever
 
-    :rtype: int
-    :return: it
+:rtype: int
+:return: it
 
-    :rtype: int
-    :return: may return
-
-    """)
+:rtype: int
+:return: may return
+""")
 
 commentVerifier.check(doxygen_translate_all_tags.func09.__doc__,
 r"""
-    This will only appear in RTF
+
+This will only appear in RTF
 
 
-    See also: someOtherMethod
+See also: someOtherMethod
 
 
 
-    See also: function
+See also: function
 
-    Same as
-    brief description
+Same as
+brief description
 
 
 
-    Since: version 0.0.0.1
+Since: version 0.0.0.1
 
 
 
@@ -306,17 +305,16 @@ r"""
 
 
 
-    :raises: superException
+:raises: superException
 
-    :raises: RuntimeError
-    """)
+:raises: RuntimeError""")
 
 commentVerifier.check(doxygen_translate_all_tags.func10.__doc__,
 r"""
-    TODO: Some very important task
+TODO: Some very important task
 
-    :type b: float
-    :param b: B is mentioned again...
+:type b: float
+:param b: B is mentioned again...
 
 
 
@@ -324,24 +322,23 @@ r"""
 
 
 
-    very long
-    text with tags <sometag>
+very long
+text with tags <sometag>
 
 
 
 
-    Version: 0.0.0.2
+Version: 0.0.0.2
 
-    Warning: This is senseless!
+Warning: This is senseless!
 
 
 
 
-    This will only appear in XML
+This will only appear in XML
 
 
-    Here goes test of symbols:
-    $ @ \ & ~ < > # % " . ::
+Here goes test of symbols:
+$ @ \ & ~ < > # % " . ::
 
-    And here goes simple text
-    """)
+And here goes simple text""")
diff --git a/Examples/test-suite/python/doxygen_translate_links_runme.py b/Examples/test-suite/python/doxygen_translate_links_runme.py
index 9c83cae99..bad1d36ee 100644
--- a/Examples/test-suite/python/doxygen_translate_links_runme.py
+++ b/Examples/test-suite/python/doxygen_translate_links_runme.py
@@ -8,35 +8,34 @@ import commentVerifier
 
 commentVerifier.check(doxygen_translate_links.function.__doc__,
 r"""
-    Testing typenames converting in @ link
+Testing typenames converting in @ link
 
-    superFunc(int,std::string)
-    Test for std_string member
+superFunc(int,std::string)
+Test for std_string member
 
 
-    superFunc(int,long,void*)
-    Test for simple types
+superFunc(int,long,void*)
+Test for simple types
 
 
-    superFunc(Shape::superType*)
-    Test for custom types
+superFunc(Shape::superType*)
+Test for custom types
 
 
-    superFunc(int**[13])
-    Test for complex types
+superFunc(int**[13])
+Test for complex types
 
 
-    same works for 'See also:' links:
+same works for 'See also:' links:
 
-    See also: superFunc(int,std::string)
-    See also: superFunc(int,long,void*)
-    See also: superFunc(Shape::superType*)
-    See also: superFunc(int**[13])
+See also: superFunc(int,std::string)
+See also: superFunc(int,long,void*)
+See also: superFunc(Shape::superType*)
+See also: superFunc(int**[13])
 
-    some failing params:
+some failing params:
 
-    See also: superFunc()
-    See also: superFunc()
-    See also: superFunc()
-
-    """)
+See also: superFunc()
+See also: superFunc()
+See also: superFunc()
+""")
diff --git a/Examples/test-suite/python/doxygen_translate_runme.py b/Examples/test-suite/python/doxygen_translate_runme.py
index 92850aa19..8ccacc35f 100644
--- a/Examples/test-suite/python/doxygen_translate_runme.py
+++ b/Examples/test-suite/python/doxygen_translate_runme.py
@@ -8,267 +8,263 @@ import commentVerifier
 
 commentVerifier.check(doxygen_translate.function.__doc__,
 r"""
-    *Hello*
+*Hello*
 
-    * some list item
+* some list item
 
-    Authors: lots of them
+Authors: lots of them
 
-    Author: Zubr
+Author: Zubr
 
-    **boldword**
+**boldword**
 
-    ``codeword``
+``codeword``
 
-    'citationword'
+'citationword'
 
 
-    .. code-block:: c++
+.. code-block:: c++
 
-         some test code
+     some test code
 
 
-    Conditional comment: SOMECONDITION
-    Some conditional comment
-    End of conditional comment.
+Conditional comment: SOMECONDITION
+Some conditional comment
+End of conditional comment.
 
-    Copyright: some copyright
+Copyright: some copyright
 
-    Deprecated: Now use another function
+Deprecated: Now use another function
 
-    *italicword*
+*italicword*
 
-    Example: someFile.txt
-    Some details on using the example
+Example: someFile.txt
+Some details on using the example
 
-    :raises: SuperError
+:raises: SuperError
 
-    If: ANOTHERCONDITION {
-      First part of comment
-      If: SECONDCONDITION {
-        Nested condition text
-      }Else if: THIRDCONDITION {
-        The third condition text
-      }Else:  {    The last text block
-      }
-    }Else:  {  Second part of comment
-      If: CONDITION {
-        Second part extended
-      }
-    }
+If: ANOTHERCONDITION {
+  First part of comment
+  If: SECONDCONDITION {
+    Nested condition text
+  }Else if: THIRDCONDITION {
+    The third condition text
+  }Else:  {    The last text block
+  }
+}Else:  {  Second part of comment
+  If: CONDITION {
+    Second part extended
+  }
+}
 
-    If not: SOMECONDITION {
-      This is printed if not
-    }
+If not: SOMECONDITION {
+  This is printed if not
+}
 
-    Image: testImage.bmp("Hello, world!")
+Image: testImage.bmp("Hello, world!")
 
 
 
-    * Some unordered list
-    * With lots of items
-    * lots of lots of items
+* Some unordered list
+* With lots of items
+* lots of lots of items
 
 
 
-    someMember Some description follows
+someMember Some description follows
 
 
 
 
 
 
-    Notes: Here
-    is the note!
+Notes: Here
+is the note!
 
-    This is an overloaded member function, provided for convenience.
-    It differs from the above function only in what argument(s) it accepts.
+This is an overloaded member function, provided for convenience.
+It differs from the above function only in what argument(s) it accepts.
 
-    someword
+someword
 
 
 
-    Title: The paragraph title
-    The paragraph text.
-    Maybe even multiline
+Title: The paragraph title
+The paragraph text.
+Maybe even multiline
 
-    :type a: int
-    :param a: the first param
+:type a: int
+:param a: the first param
 
-    Remarks: Some remark text
+Remarks: Some remark text
 
-    Another remarks section
+Another remarks section
 
-    :rtype: int
-    :return: Whatever
+:rtype: int
+:return: Whatever
 
-    :rtype: int
-    :return: it
+:rtype: int
+:return: it
 
-    :rtype: int
-    :return: may return
+:rtype: int
+:return: may return
 
-    See also: someOtherMethod
+See also: someOtherMethod
 
-    See also: function
+See also: function
 
-    Since: version 0.0.0.1
+Since: version 0.0.0.1
 
-    :raises: superException
+:raises: superException
 
-    :raises: RuntimeError
+:raises: RuntimeError
 
-    TODO: Some very important task
+TODO: Some very important task
 
-    :type b: float
-    :param b: B is mentioned again...
+:type b: float
+:param b: B is mentioned again...
 
 
-    very long
-    text with tags <sometag>
+very long
+text with tags <sometag>
 
 
-    Version: 0.0.0.2
+Version: 0.0.0.2
 
-    Warning: This is senseless!
+Warning: This is senseless!
 
-    Here goes test of symbols:
-    $ @ \ & ~ < > # % " . ::
+Here goes test of symbols:
+$ @ \ & ~ < > # % " . ::
 
-    And here goes simple text
-    """
+And here goes simple text"""
 )
 
 
 
 commentVerifier.check(doxygen_translate.htmlFunction.__doc__,
 r"""
-    Test for html tags. See Doxygen doc for list of tags recognized by Doxygen.
+Test for html tags. See Doxygen doc for list of tags recognized by Doxygen.
 
-    This is link ("http://acme.com/index.html")
-    **bold**
-    Quote:
-    Quotation block.
-     ("http://www.worldwildlife.org/who/index.html")
+This is link ("http://acme.com/index.html")
+**bold**
+Quote:
+Quotation block.
+ ("http://www.worldwildlife.org/who/index.html")
 
 
-    center
-    ``this is code``
+center
+``this is code``
 
 
-    Starts an item title.
-        Starts an item description.
+Starts an item title.
+    Starts an item description.
 
 
-    Starts a piece of text displayed in a typewriter font.
+Starts a piece of text displayed in a typewriter font.
 
-    Starts a section with a specific style (HTML only)
+Starts a section with a specific style (HTML only)
 
-    **Starts a piece of text displayed in an italic font.**
+**Starts a piece of text displayed in an italic font.**
 
-    'Form' does not generate any output.
+'Form' does not generate any output.
 
-    --------------------------------------------------------------------
+--------------------------------------------------------------------
 
-    # Heading 1
+# Heading 1
 
-    ## Heading 2
+## Heading 2
 
-    ### Heading 3
+### Heading 3
 
-    *Starts a piece of text displayed in an italic font.*
-    Input tag.
-    Image: src="slika.png"
-    Meta tag.
-    Multicol is ignored by doxygen.
+*Starts a piece of text displayed in an italic font.*
+Input tag.
+Image: src="slika.png"
+Meta tag.
+Multicol is ignored by doxygen.
 
 
 
-    * List item 1.
-    * List item 2.
+* List item 1.
+* List item 2.
 
 
 
-    Starts a new paragraph.
+Starts a new paragraph.
 
-    Starts a preformatted fragment.
+Starts a preformatted fragment.
 
-    Starts a section of text displayed in a smaller font.
+Starts a section of text displayed in a smaller font.
 
-    'Starts an inline text fragment with a specific style.'
-    **Starts a section of bold text.**
-     Starts a piece of text displayed in subscript.
-     Starts a piece of text displayed in superscript.
+'Starts an inline text fragment with a specific style.'
+**Starts a section of bold text.**
+ Starts a piece of text displayed in subscript.
+ Starts a piece of text displayed in superscript.
 
 
-    Animals
-    | Column 1 | Column 2 |
-    -----------------------
-    | cow      | dog      |
-    | cat      | mouse    |
-    | horse    | parrot   |
+Animals
+| Column 1 | Column 2 |
+-----------------------
+| cow      | dog      |
+| cat      | mouse    |
+| horse    | parrot   |
 
 
-    Starts a piece of text displayed in a typewriter font.
+Starts a piece of text displayed in a typewriter font.
 
-    Starts a piece of text displayed in a typewriter font.
+Starts a piece of text displayed in a typewriter font.
 
 
 
-    * List item 1.
-    * List item 2.
-    * List item 3.
+* List item 1.
+* List item 2.
+* List item 3.
 
 
-    *Starts a piece of text displayed in an italic font.*
+*Starts a piece of text displayed in an italic font.*
 
 
-    <u>underlined \b bold text - doxy commands are ignored inside 'htmlonly' section </u>
-
-    """)
+<u>underlined \b bold text - doxy commands are ignored inside 'htmlonly' section </u>
+""")
 
 
 commentVerifier.check(doxygen_translate.htmlTableFunction.__doc__,
 r"""
-    The meaning of flags:
+The meaning of flags:
 
-    :type byFlags: int
-    :param byFlags: bits marking required items:
+:type byFlags: int
+:param byFlags: bits marking required items:
 
-          | Size in bits| Items Required |
-          --------------------------------
-          | 1 - 8       |      1         |
-          | 9 - 16      |      2         |
-          | 17 - 32     |      4         |
+      | Size in bits| Items Required |
+      --------------------------------
+      | 1 - 8       |      1         |
+      | 9 - 16      |      2         |
+      | 17 - 32     |      4         |
 
-          Almost all combinations of above flags are supported by
-          ``htmlTable...`` functions.
-    """)
+      Almost all combinations of above flags are supported by
+      ``htmlTable...`` functions.""")
 
 
 commentVerifier.check(doxygen_translate.htmlEntitiesFunction.__doc__,
 r"""
-    All entities are treated as commands (C)  TM (R)
-    should work also<in text
-    >
-    &
-    '
-    "
-    `
-    '
-    "
-    "
-    -
-    --
+All entities are treated as commands (C)  TM (R)
+should work also<in text
+>
+&
+'
+"
+`
+'
+"
+"
+-
+--
 
-    x
-    -
-    .
-    ~
-    <=
-    >=
-    <--
-    -->
-    Not an  html entity - ignored by Doxygen.
-    Not an &text html entity - ampersand is replaced with entity.
-    """)
+x
+-
+.
+~
+<=
+>=
+<--
+-->
+Not an  html entity - ignored by Doxygen.
+Not an &text html entity - ampersand is replaced with entity.""")
diff --git a/Source/Modules/python.cxx b/Source/Modules/python.cxx
index 9a461d28b..1342f8204 100644
--- a/Source/Modules/python.cxx
+++ b/Source/Modules/python.cxx
@@ -1545,21 +1545,12 @@ public:
    *    Get the docstring text enclosed in triple double quotes.
    * ------------------------------------------------------------ */
 
-  String *docstring(Node *n, autodoc_t ad_type, const String *indent) {
+  String *docstring(Node *n, autodoc_t ad_type) {
     String *docstr = build_combined_docstring(n, ad_type);
     if (!Len(docstr))
       return docstr;
 
 
-    // If there is more than one line then make docstrings like this:
-    //
-    //      """
-    //      This is line1
-    //      And here is line2 followed by the rest of them
-    //      """
-    //
-    // otherwise, put it all on a single line
-    //
     // Notice that all comments are created as raw strings (prefix "r"),
     // because '\' is used often in comments, but may break Python module from
     // loading. For example, in doxy comment one may write path in quotes:
@@ -1571,15 +1562,7 @@ public:
     // of doxygen doc, Latex expressions, ...
     String *doc = NewString("");
     Append(doc, "r\"\"\"");
-
-    if (Strchr(docstr, '\n') == 0) {
-      Append(doc, docstr);
-    } else {
-      Append(doc, "\n");
-      Append(doc, pythoncode(docstr, indent));
-      Append(doc, indent);
-    }
-
+    Append(doc, docstr);
     Append(doc, "\"\"\"");
 
     Delete(docstr);
@@ -2137,7 +2120,7 @@ public:
     /* Make a wrapper function to insert the code into */
     Printv(f_dest, "\ndef ", name, "(", parms, ")", returnTypeAnnotation(n), ":\n", NIL);
     if (have_docstring(n))
-      Printv(f_dest, tab4, docstring(n, AUTODOC_FUNC, tab4), "\n", NIL);
+      Printv(f_dest, tab4, docstring(n, AUTODOC_FUNC), "\n", NIL);
     if (have_pythonprepend(n))
       Printv(f_dest, pythoncode(pythonprepend(n), tab4), "\n", NIL);
     if (have_pythonappend(n)) {
@@ -3274,7 +3257,7 @@ public:
       if (f_s) {
 	Printv(f_s, iname, " = ", module, ".", iname, "\n", NIL);
 	if (have_docstring(n))
-	  Printv(f_s, docstring(n, AUTODOC_CONST, ""), "\n", NIL);
+	  Printv(f_s, docstring(n, AUTODOC_CONST), "\n", NIL);
       }
     }
     return SWIG_OK;
@@ -4053,7 +4036,7 @@ public:
 
 	// write docstrings if requested
 	if (have_docstring(n)) {
-	  String *str = docstring(n, AUTODOC_CLASS, tab4);
+	  String *str = docstring(n, AUTODOC_CLASS);
 	  if (str && Len(str))
 	    Printv(f_shadow, tab4, str, "\n", NIL);
 	}
@@ -4333,7 +4316,7 @@ public:
 	  } else {
 	    Printv(f_shadow, "\n", tab4, "def ", symname, "(", parms, ")", returnTypeAnnotation(n), ":\n", NIL);
 	    if (have_docstring(n))
-	      Printv(f_shadow, tab8, docstring(n, AUTODOC_METHOD, tab8), "\n", NIL);
+	      Printv(f_shadow, tab8, docstring(n, AUTODOC_METHOD), "\n", NIL);
 	    if (have_pythonprepend(n)) {
 	      fproxy = 0;
 	      Printv(f_shadow, pythoncode(pythonprepend(n), tab8), "\n", NIL);
@@ -4419,7 +4402,7 @@ public:
 	String *callParms = make_pyParmList(n, false, true, kw);
 	Printv(f_shadow, "\n", tab4, "def ", symname, "(", parms, ")", returnTypeAnnotation(n), ":\n", NIL);
 	if (have_docstring(n))
-	  Printv(f_shadow, tab8, docstring(n, AUTODOC_STATICFUNC, tab8), "\n", NIL);
+	  Printv(f_shadow, tab8, docstring(n, AUTODOC_STATICFUNC), "\n", NIL);
 	if (have_pythonprepend(n))
 	  Printv(f_shadow, pythoncode(pythonprepend(n), tab8), "\n", NIL);
 	if (have_pythonappend(n)) {
@@ -4536,7 +4519,7 @@ public:
 
 	      Printv(f_shadow, "\n", tab4, "def __init__(", parms, ")", returnTypeAnnotation(n), ":\n", NIL);
 	      if (have_docstring(n))
-		Printv(f_shadow, tab8, docstring(n, AUTODOC_CTOR, tab8), "\n", NIL);
+		Printv(f_shadow, tab8, docstring(n, AUTODOC_CTOR), "\n", NIL);
 	      if (have_pythonprepend(n))
 		Printv(f_shadow, pythoncode(pythonprepend(n), tab8), "\n", NIL);
 	      Printv(f_shadow, pass_self, NIL);
@@ -4569,7 +4552,7 @@ public:
 
 	    Printv(f_shadow_stubs, "\ndef ", symname, "(", parms, ")", returnTypeAnnotation(n), ":\n", NIL);
 	    if (have_docstring(n))
-	      Printv(f_shadow_stubs, tab4, docstring(n, AUTODOC_CTOR, tab4), "\n", NIL);
+	      Printv(f_shadow_stubs, tab4, docstring(n, AUTODOC_CTOR), "\n", NIL);
 	    if (have_pythonprepend(n))
 	      Printv(f_shadow_stubs, pythoncode(pythonprepend(n), tab4), "\n", NIL);
 	    String *subfunc = NULL;
@@ -4637,7 +4620,7 @@ public:
 	}
 	Printv(f_shadow, tab4, "def __del__(self):\n", NIL);
 	if (have_docstring(n))
-	  Printv(f_shadow, tab8, docstring(n, AUTODOC_DTOR, tab8), "\n", NIL);
+	  Printv(f_shadow, tab8, docstring(n, AUTODOC_DTOR), "\n", NIL);
 	if (have_pythonprepend(n))
 	  Printv(f_shadow, pythoncode(pythonprepend(n), tab8), "\n", NIL);
 #ifdef USE_THISOWN
@@ -4811,7 +4794,7 @@ public:
     } else if (shadow) {
       Printv(f_shadow, tab4, symname, " = ", module, ".", Swig_name_member(NSPACE_TODO, class_name, symname), "\n", NIL);
       if (have_docstring(n))
-	Printv(f_shadow, tab4, docstring(n, AUTODOC_CONST, tab4), "\n", NIL);
+	Printv(f_shadow, tab4, docstring(n, AUTODOC_CONST), "\n", NIL);
     }
     return SWIG_OK;
   }

From d5c5cd4521842481b4958f0a9dd036c429eeb1d5 Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Mon, 15 Dec 2014 13:32:23 +0100
Subject: [PATCH 247/314] Use class docstrings in "-builtin" Python case.

Put the docstring into tp_doc slot which exists exactly for this purpose.
---
 Source/Modules/python.cxx | 23 +++++++++++++----------
 1 file changed, 13 insertions(+), 10 deletions(-)

diff --git a/Source/Modules/python.cxx b/Source/Modules/python.cxx
index 1342f8204..a59e29dc9 100644
--- a/Source/Modules/python.cxx
+++ b/Source/Modules/python.cxx
@@ -1573,7 +1573,7 @@ public:
   /* ------------------------------------------------------------
    * cdocstring()
    *    Get the docstring text as it would appear in C-language
-   *	source code.
+   *	source code (but without quotes around it).
    * ------------------------------------------------------------ */
 
   String *cdocstring(Node *n, autodoc_t ad_type)
@@ -1581,7 +1581,7 @@ public:
     String *ds = build_combined_docstring(n, ad_type);
     Replaceall(ds, "\\", "\\\\");
     Replaceall(ds, "\"", "\\\"");
-    Replaceall(ds, "\n", "\\n\"\n\t\t\"");
+    Replaceall(ds, "\n", "\\n\"\n\t\"");
     return ds;
   }
 
@@ -3734,7 +3734,16 @@ public:
     Printv(f, "#else\n", NIL);
     printSlot(f, tp_flags, "tp_flags");
     Printv(f, "#endif\n", NIL);
-    printSlot(f, quoted_rname, "tp_doc");
+    if (have_docstring(n)) {
+      String *ds = cdocstring(n, AUTODOC_CLASS);
+      String *tp_doc = NewString("");
+      Printf(tp_doc, "\"%s\"", ds);
+      Delete(ds);
+      printSlot(f, tp_doc, "tp_doc");
+      Delete(tp_doc);
+    } else {
+      printSlot(f, quoted_rname, "tp_doc");
+    }
     printSlot(f, getSlot(n, "feature:python:tp_traverse"), "tp_traverse", "traverseproc");
     printSlot(f, getSlot(n, "feature:python:tp_clear"), "tp_clear", "inquiry");
     printSlot(f, richcompare_func, "feature:python:tp_richcompare", "richcmpfunc");
@@ -4012,13 +4021,7 @@ public:
 	Printv(base_class, abcs, NIL);
       }
 
-      if (builtin) {
-	if (have_docstring(n)) {
-	  String *str = cdocstring(n, AUTODOC_CLASS);
-	  Setattr(n, "feature:python:tp_doc", str);
-	  Delete(str);
-	}
-      } else {
+      if (!builtin) {
 	Printv(f_shadow, "class ", class_name, NIL);
 
 	if (Len(base_class)) {

From 8316f08aec9b1a99cd1819f087f28bda22024c01 Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Mon, 15 Dec 2014 14:05:15 +0100
Subject: [PATCH 248/314] Fix Doxygen unit test in Python "-builtin" case.

Unfortunately there doesn't seem to be any way to use docstrings for __init__
methods when using "-builtin", so just disable this particular test then.
---
 Examples/test-suite/python/doxygen_parsing_runme.py | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/Examples/test-suite/python/doxygen_parsing_runme.py b/Examples/test-suite/python/doxygen_parsing_runme.py
index d89a1741a..883fbd83b 100644
--- a/Examples/test-suite/python/doxygen_parsing_runme.py
+++ b/Examples/test-suite/python/doxygen_parsing_runme.py
@@ -2,6 +2,7 @@
 
 import doxygen_parsing
 import string
+import os
 import sys
 import commentVerifier
 
@@ -14,7 +15,12 @@ The class comment""")
 commentVerifier.check(doxygen_parsing.SomeStruct.__doc__,
     r"""
 The struct comment""")
-commentVerifier.check(doxygen_parsing.SomeAnotherClass.__init__.__doc__,
+
+# There doesn't seem to be any way to specify the doc string for __init__ when
+# using "-builtin" (see http://stackoverflow.com/q/11913492/15275), so skip
+# this test in this case.
+if str(os.environ.get('SWIG_FEATURES')).find('-builtin') == -1:
+    commentVerifier.check(doxygen_parsing.SomeAnotherClass.__init__.__doc__,
     r""" *Overload 1:*
  First overloaded constructor.
 
@@ -22,6 +28,7 @@ commentVerifier.check(doxygen_parsing.SomeAnotherClass.__init__.__doc__,
 
  *Overload 2:*
  Second overloaded constructor.""")
+
 commentVerifier.check(doxygen_parsing.SomeAnotherClass.classMethod.__doc__,
     r"""
 The class method comment.

From fd47e6870ef1281879c9ce6de9f54a7de101c55d Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Mon, 15 Dec 2014 20:27:46 +0100
Subject: [PATCH 249/314] Fix autodoc strings generated in Python builtin case
 and the test.

Use the proper AUTODOC_METHOD for autodoc strings generation when using
"-builtin", there is no reason to use AUTODOC_FUNC here when AUTODOC_METHOD is
used by default (i.e. without "-builtin").

This allows to (almost) stop differentiating between the two cases in the
autodoc unit test, allowing to simplify it significantly.

Also fix this test to pass after the recent changes removing docstring
indentation in the generated code.
---
 Examples/test-suite/python/autodoc_runme.py | 255 +++++---------------
 Source/Modules/python.cxx                   |   2 +-
 2 files changed, 58 insertions(+), 199 deletions(-)

diff --git a/Examples/test-suite/python/autodoc_runme.py b/Examples/test-suite/python/autodoc_runme.py
index 55e54cd07..8c3ca56fa 100644
--- a/Examples/test-suite/python/autodoc_runme.py
+++ b/Examples/test-suite/python/autodoc_runme.py
@@ -1,51 +1,20 @@
 from autodoc import *
-import commentVerifier
+from commentVerifier import check
 import sys
 
-def check(got, expected, expected_builtin = None, skip = False):
-  if not skip:
-    expect = expected
-    if is_python_builtin() and expected_builtin != None:
-      expect = expected_builtin
-    commentVerifier.check(got, expect)
-
-skip = True # skip builtin check - the autodoc is missing, but it probably should not be
-
-check(A.__doc__, "Proxy of C++ A class", "::A")
+check(A.__doc__, "Proxy of C++ A class")
 check(A.funk.__doc__, "just a string")
-check(A.func0.__doc__,
-"func0(self, arg2, hello) -> int",
-"func0(arg2, hello) -> int")
-check(A.func1.__doc__,
-"func1(A self, short arg2, Tuple hello) -> int",
-"func1(short arg2, Tuple hello) -> int")
+check(A.func0.__doc__, "func0(self, arg2, hello) -> int")
+check(A.func1.__doc__, "func1(A self, short arg2, Tuple hello) -> int")
 check(A.func2.__doc__,
-"\n"
-"        func2(self, arg2, hello) -> int\n"
-"\n"
-"        Parameters:\n"
-"            arg2: short\n"
-"            hello: int tuple[2]\n"
-"\n"
-"        "
-,
-"func2(arg2, hello) -> int\n"
+"func2(self, arg2, hello) -> int\n"
 "\n"
 "Parameters:\n"
 "    arg2: short\n"
 "    hello: int tuple[2]\n"
 )
 check(A.func3.__doc__,
-"\n"
-"        func3(A self, short arg2, Tuple hello) -> int\n"
-"\n"
-"        Parameters:\n"
-"            arg2: short\n"
-"            hello: int tuple[2]\n"
-"\n"
-"        "
-,
-"func3(short arg2, Tuple hello) -> int\n"
+"func3(A self, short arg2, Tuple hello) -> int\n"
 "\n"
 "Parameters:\n"
 "    arg2: short\n"
@@ -53,43 +22,15 @@ check(A.func3.__doc__,
 )
 
 check(A.func0default.__doc__,
-"\n"
-"        func0default(self, e, arg3, hello, f=2) -> int\n"
-"        func0default(self, e, arg3, hello) -> int\n"
-"        "
-,
-"func0default(e, arg3, hello, f=2) -> int\n"
-"func0default(e, arg3, hello) -> int"
+"func0default(self, e, arg3, hello, f=2) -> int\n"
+"func0default(self, e, arg3, hello) -> int"
 )
 check(A.func1default.__doc__,
-"\n"
-"        func1default(A self, A e, short arg3, Tuple hello, double f=2) -> int\n"
-"        func1default(A self, A e, short arg3, Tuple hello) -> int\n"
-"        "
-,
-"func1default(A e, short arg3, Tuple hello, double f=2) -> int\n"
-"func1default(A e, short arg3, Tuple hello) -> int"
+"func1default(A self, A e, short arg3, Tuple hello, double f=2) -> int\n"
+"func1default(A self, A e, short arg3, Tuple hello) -> int"
 )
 check(A.func2default.__doc__,
-"\n"
-"        func2default(self, e, arg3, hello, f=2) -> int\n"
-"\n"
-"        Parameters:\n"
-"            e: A *\n"
-"            arg3: short\n"
-"            hello: int tuple[2]\n"
-"            f: double\n"
-"\n"
-"        func2default(self, e, arg3, hello) -> int\n"
-"\n"
-"        Parameters:\n"
-"            e: A *\n"
-"            arg3: short\n"
-"            hello: int tuple[2]\n"
-"\n"
-"        "
-,
-"func2default(e, arg3, hello, f=2) -> int\n"
+"func2default(self, e, arg3, hello, f=2) -> int\n"
 "\n"
 "Parameters:\n"
 "    e: A *\n"
@@ -97,7 +38,7 @@ check(A.func2default.__doc__,
 "    hello: int tuple[2]\n"
 "    f: double\n"
 "\n"
-"func2default(e, arg3, hello) -> int\n"
+"func2default(self, e, arg3, hello) -> int\n"
 "\n"
 "Parameters:\n"
 "    e: A *\n"
@@ -105,25 +46,7 @@ check(A.func2default.__doc__,
 "    hello: int tuple[2]\n"
 )
 check(A.func3default.__doc__,
-"\n"
-"        func3default(A self, A e, short arg3, Tuple hello, double f=2) -> int\n"
-"\n"
-"        Parameters:\n"
-"            e: A *\n"
-"            arg3: short\n"
-"            hello: int tuple[2]\n"
-"            f: double\n"
-"\n"
-"        func3default(A self, A e, short arg3, Tuple hello) -> int\n"
-"\n"
-"        Parameters:\n"
-"            e: A *\n"
-"            arg3: short\n"
-"            hello: int tuple[2]\n"
-"\n"
-"        "
-,
-"func3default(A e, short arg3, Tuple hello, double f=2) -> int\n"
+"func3default(A self, A e, short arg3, Tuple hello, double f=2) -> int\n"
 "\n"
 "Parameters:\n"
 "    e: A *\n"
@@ -131,7 +54,7 @@ check(A.func3default.__doc__,
 "    hello: int tuple[2]\n"
 "    f: double\n"
 "\n"
-"func3default(A e, short arg3, Tuple hello) -> int\n"
+"func3default(A self, A e, short arg3, Tuple hello) -> int\n"
 "\n"
 "Parameters:\n"
 "    e: A *\n"
@@ -140,42 +63,14 @@ check(A.func3default.__doc__,
 )
 
 check(A.func0static.__doc__,
-"\n"
-"        func0static(e, arg2, hello, f=2) -> int\n"
-"        func0static(e, arg2, hello) -> int\n"
-"        "
-,
 "func0static(e, arg2, hello, f=2) -> int\n"
 "func0static(e, arg2, hello) -> int"
 )
 check(A.func1static.__doc__,
-"\n"
-"        func1static(A e, short arg2, Tuple hello, double f=2) -> int\n"
-"        func1static(A e, short arg2, Tuple hello) -> int\n"
-"        "
-,
 "func1static(A e, short arg2, Tuple hello, double f=2) -> int\n"
 "func1static(A e, short arg2, Tuple hello) -> int"
 )
 check(A.func2static.__doc__,
-"\n"
-"        func2static(e, arg2, hello, f=2) -> int\n"
-"\n"
-"        Parameters:\n"
-"            e: A *\n"
-"            arg2: short\n"
-"            hello: int tuple[2]\n"
-"            f: double\n"
-"\n"
-"        func2static(e, arg2, hello) -> int\n"
-"\n"
-"        Parameters:\n"
-"            e: A *\n"
-"            arg2: short\n"
-"            hello: int tuple[2]\n"
-"\n"
-"        "
-,
 "func2static(e, arg2, hello, f=2) -> int\n"
 "\n"
 "Parameters:\n"
@@ -192,24 +87,6 @@ check(A.func2static.__doc__,
 "    hello: int tuple[2]\n"
 )
 check(A.func3static.__doc__,
-"\n"
-"        func3static(A e, short arg2, Tuple hello, double f=2) -> int\n"
-"\n"
-"        Parameters:\n"
-"            e: A *\n"
-"            arg2: short\n"
-"            hello: int tuple[2]\n"
-"            f: double\n"
-"\n"
-"        func3static(A e, short arg2, Tuple hello) -> int\n"
-"\n"
-"        Parameters:\n"
-"            e: A *\n"
-"            arg2: short\n"
-"            hello: int tuple[2]\n"
-"\n"
-"        "
-,
 "func3static(A e, short arg2, Tuple hello, double f=2) -> int\n"
 "\n"
 "Parameters:\n"
@@ -228,77 +105,59 @@ check(A.func3static.__doc__,
 
 if sys.version_info[0:2] > (2, 4):
   # Python 2.4 does not seem to work
-  check(A.variable_a.__doc__,
-  "A_variable_a_get(self) -> int",
-  "A.variable_a"
-  )
-  check(A.variable_b.__doc__,
-  "A_variable_b_get(A self) -> int",
-  "A.variable_b"
-  )
-  check(A.variable_c.__doc__,
-  "A_variable_c_get(self) -> int\n"
+  if is_python_builtin():
+    check(A.variable_a.__doc__, "A.variable_a")
+    check(A.variable_b.__doc__, "A.variable_b")
+    check(A.variable_c.__doc__, "A.variable_c")
+    check(A.variable_d.__doc__, "A.variable_d")
+  else:
+    check(A.variable_a.__doc__, "A_variable_a_get(self) -> int"
+    )
+    check(A.variable_b.__doc__, "A_variable_b_get(A self) -> int")
+    check(A.variable_c.__doc__,
+    "A_variable_c_get(self) -> int\n"
+    "\n"
+    "Parameters:\n"
+    "    self: A *\n"
+    )
+    check(A.variable_d.__doc__,
+    "A_variable_d_get(A self) -> int\n"
+    "\n"
+    "Parameters:\n"
+    "    self: A *\n"
+    )
+
+check(B.__doc__, "Proxy of C++ B class")
+
+# skip builtin check - the autodoc is missing, but it probably should not be
+if not is_python_builtin():
+  check(C.__init__.__doc__, "__init__(self, a, b, h) -> C")
+  check(D.__init__.__doc__, "__init__(D self, int a, int b, Hola h) -> D")
+  check(E.__init__.__doc__,
+  "__init__(self, a, b, h) -> E\n"
   "\n"
   "Parameters:\n"
-  "    self: A *\n"
-  ,
-  "A.variable_c"
+  "    a: special comment for parameter a\n"
+  "    b: another special comment for parameter b\n"
+  "    h: enum Hola\n"
   )
-  check(A.variable_d.__doc__,
-  "A_variable_d_get(A self) -> int\n"
+  check(F.__init__.__doc__,
+  "__init__(F self, int a, int b, Hola h) -> F\n"
   "\n"
   "Parameters:\n"
-  "    self: A *\n"
-  ,
-  "A.variable_d"
+  "    a: special comment for parameter a\n"
+  "    b: another special comment for parameter b\n"
+  "    h: enum Hola\n"
   )
 
-check(B.__doc__,
-"Proxy of C++ B class",
-"::B"
-)
-check(C.__init__.__doc__, "__init__(self, a, b, h) -> C", None, skip)
-check(D.__init__.__doc__, "__init__(D self, int a, int b, Hola h) -> D", None, skip)
-check(E.__init__.__doc__,
-"\n"
-"        __init__(self, a, b, h) -> E\n"
-"\n"
-"        Parameters:\n"
-"            a: special comment for parameter a\n"
-"            b: another special comment for parameter b\n"
-"            h: enum Hola\n"
-"\n"
-"        "
-, None, skip
-)
-check(F.__init__.__doc__,
-"\n"
-"        __init__(F self, int a, int b, Hola h) -> F\n"
-"\n"
-"        Parameters:\n"
-"            a: special comment for parameter a\n"
-"            b: another special comment for parameter b\n"
-"            h: enum Hola\n"
-"\n"
-"        "
-, None, skip
-)
-
-check(B.funk.__doc__,
-"funk(B self, int c, int d) -> int",
-"funk(int c, int d) -> int")
+check(B.funk.__doc__, "funk(B self, int c, int d) -> int")
 check(funk.__doc__, "funk(A e, short arg2, int c, int d) -> int")
 check(funkdefaults.__doc__,
-"\n"
-"    funkdefaults(A e, short arg2, int c, int d, double f=2) -> int\n"
-"    funkdefaults(A e, short arg2, int c, int d) -> int\n"
-"    "
-,
 "funkdefaults(A e, short arg2, int c, int d, double f=2) -> int\n"
 "funkdefaults(A e, short arg2, int c, int d) -> int"
 )
 
-commentVerifier.check(func_input.__doc__, "func_input(int * INPUT) -> int")
-commentVerifier.check(func_output.__doc__, "func_output() -> int")
-commentVerifier.check(func_inout.__doc__, "func_inout(int * INOUT) -> int")
-commentVerifier.check(banana.__doc__, "banana(S a, S b, int c, Integer d)")
+check(func_input.__doc__, "func_input(int * INPUT) -> int")
+check(func_output.__doc__, "func_output() -> int")
+check(func_inout.__doc__, "func_inout(int * INOUT) -> int")
+check(banana.__doc__, "banana(S a, S b, int c, Integer d)")
diff --git a/Source/Modules/python.cxx b/Source/Modules/python.cxx
index a59e29dc9..cd0ec2b44 100644
--- a/Source/Modules/python.cxx
+++ b/Source/Modules/python.cxx
@@ -4273,7 +4273,7 @@ public:
 	String *wname = Swig_name_wrapper(fullname);
 	Setattr(class_members, symname, n);
 	int argcount = Getattr(n, "python:argcount") ? atoi(Char(Getattr(n, "python:argcount"))) : 2;
-	String *ds = have_docstring(n) ? cdocstring(n, AUTODOC_FUNC) : NewString("");
+	String *ds = have_docstring(n) ? cdocstring(n, AUTODOC_METHOD) : NewString("");
 	if (check_kwargs(n)) {
 	  Printf(builtin_methods, "  { \"%s\", (PyCFunction) %s, METH_VARARGS|METH_KEYWORDS, (char*) \"%s\" },\n", symname, wname, ds);
 	} else if (argcount == 0) {

From ad67f4ab4ddf8d0e828ffabb247b9ad307102ece Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Tue, 16 Dec 2014 17:27:15 +0100
Subject: [PATCH 250/314] Remove trailing space from one of Doxygen tests.

This resulted in a warning (treated as error) from pep8 1.5.7 when running
Doxygen test suite for Python.
---
 Examples/test-suite/doxygen_basic_notranslate.i               | 2 +-
 Examples/test-suite/python/doxygen_basic_notranslate_runme.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/Examples/test-suite/doxygen_basic_notranslate.i b/Examples/test-suite/doxygen_basic_notranslate.i
index 8699e3289..e97cc589f 100644
--- a/Examples/test-suite/doxygen_basic_notranslate.i
+++ b/Examples/test-suite/doxygen_basic_notranslate.i
@@ -14,7 +14,7 @@
 /**
  * \brief
  * Brief description.
- * 
+ *
  * The comment text
  * \author Some author
  * \return Some number
diff --git a/Examples/test-suite/python/doxygen_basic_notranslate_runme.py b/Examples/test-suite/python/doxygen_basic_notranslate_runme.py
index 5559e38bc..90a0897c3 100644
--- a/Examples/test-suite/python/doxygen_basic_notranslate_runme.py
+++ b/Examples/test-suite/python/doxygen_basic_notranslate_runme.py
@@ -9,7 +9,7 @@ commentVerifier.check(doxygen_basic_notranslate.function.__doc__,
     r"""
  \brief
  Brief description.
- 
+
  The comment text
  \author Some author
  \return Some number

From b7160d92c9323fc6585c511f369c41e06e0c5865 Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Wed, 17 Dec 2014 04:57:17 +0100
Subject: [PATCH 251/314] Remove any whitespace before ignored Doxygen
 commands.

This is done mainly to avoid problems with trailing whitespace in the
generated Python code as this provokes pep8 problems, but is also, arguably,
more logical, as if a command which is on its own on a line is ignored, we
shouldn't leave any whitespace neither (and perhaps should even suppress the
line entirely, in fact).
---
 Examples/test-suite/java/doxygen_ignore_runme.java |  6 +++---
 Examples/test-suite/python/doxygen_ignore_runme.py |  6 +++---
 Source/DoxygenTranslator/src/DoxygenParser.cpp     | 13 +++++++++++++
 3 files changed, 19 insertions(+), 6 deletions(-)

diff --git a/Examples/test-suite/java/doxygen_ignore_runme.java b/Examples/test-suite/java/doxygen_ignore_runme.java
index d6a4d8c8d..6250ce525 100644
--- a/Examples/test-suite/java/doxygen_ignore_runme.java
+++ b/Examples/test-suite/java/doxygen_ignore_runme.java
@@ -24,13 +24,13 @@ public class doxygen_ignore_runme {
     wantedComments.put("doxygen_ignore.doxygen_ignore.func()",
       "     A contrived example of ignoring too many commands in one comment.<br>\n" +
       " <br>\n" +
-      "     <br>\n" +
       " <br>\n" +
-      "     <br>\n" +
+      " <br>\n" +
+      " <br>\n" +
       "     This is specific to <i>Java</i>.<br>\n" +
       "     <br>\n" +
       " <br>\n" +
-      "     <br>\n" +
+      " <br>\n" +
       " <br>\n" +
       "     Command ignored, but anything here is still included.<br>\n" +
       " <br>\n" +
diff --git a/Examples/test-suite/python/doxygen_ignore_runme.py b/Examples/test-suite/python/doxygen_ignore_runme.py
index 84ef0ddab..3d407021d 100644
--- a/Examples/test-suite/python/doxygen_ignore_runme.py
+++ b/Examples/test-suite/python/doxygen_ignore_runme.py
@@ -7,11 +7,11 @@ commentVerifier.check(doxygen_ignore.func.__doc__,
     r"""
     A contrived example of ignoring too many commands in one comment.
 
-    
 
-    
 
-    
+
+
+
     This is specific to **Python**.
 
 
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.cpp b/Source/DoxygenTranslator/src/DoxygenParser.cpp
index c8cb40ab8..f60113ccf 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenParser.cpp
@@ -946,6 +946,19 @@ int DoxygenParser::ignoreCommand(const std::string& theCommand,
       return 0;
     }
 
+    // If we ignore the command, also ignore any whitespace preceding it as we
+    // want to avoid having lines consisting of whitespace only or trailing
+    // whitespace in general (at least Python, with its pep8 tool, really
+    // doesn't like it).
+    if (!doxyList.empty()) {
+      DoxygenEntityList::iterator i = doxyList.end();
+      --i;
+      if (i->typeOfEntity == "plainstd::string" &&
+          i->data.find_first_not_of(" \t") == std::string::npos) {
+        doxyList.erase(i);
+      }
+    }
+
     // Determine what to do with the part of the comment between the start and
     // end commands: by default, we simply throw it away, but "contents"
     // attribute may be used to change this.

From e546dfd85680eff19bf027fc7108a688fea191da Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Mon, 16 Feb 2015 23:50:12 +0100
Subject: [PATCH 252/314] Remove unused Swig_warn() function.

This was removed in master by 1e8fa8fee022de3151209d0719aa30aa0fdb4e65 but
somehow left here.
---
 Source/Swig/swig.h | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/Source/Swig/swig.h b/Source/Swig/swig.h
index 731e02d2d..ea30dceba 100644
--- a/Source/Swig/swig.h
+++ b/Source/Swig/swig.h
@@ -335,8 +335,7 @@ extern int        ParmList_is_compactdefargs(ParmList *p);
   extern void Swig_offset_string(String *s, int number);
   extern String *Swig_pcre_version(void);
   extern void Swig_init(void);
-  extern void Swig_warn(const char *filename, int line, const char *msg);
-  
+
   extern int Swig_value_wrapper_mode(int mode);
   extern int Swig_is_generated_overload(Node *n);
 

From 56a6f296b8da1c960d0a1e6aef135152341d4295 Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Mon, 16 Feb 2015 23:51:57 +0100
Subject: [PATCH 253/314] Remove unreferenced struct declaration.

This was introduced by 774cbc3ef216d9428620c0076dd569af61107da3, apparently
accidentally.
---
 Source/CParse/parser.y | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/Source/CParse/parser.y b/Source/CParse/parser.y
index f24fbcc78..44af84923 100644
--- a/Source/CParse/parser.y
+++ b/Source/CParse/parser.y
@@ -6888,7 +6888,3 @@ ParmList *Swig_cparse_parms(String *s, Node *file_line_node) {
    /*   Printf(stdout,"typeparse: '%s' ---> '%s'\n", s, top); */
    return top;
 }
-
-
-
-struct S;

From d92bc54662281e1b49968e5ff04de010672260c9 Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Mon, 16 Feb 2015 23:55:01 +0100
Subject: [PATCH 254/314] Remove unused <sstream> header.

std::stringstream is not used in this file, so it is unneeded.
---
 Source/Modules/python.cxx | 1 -
 1 file changed, 1 deletion(-)

diff --git a/Source/Modules/python.cxx b/Source/Modules/python.cxx
index 3244d9ea6..c1b2b1415 100644
--- a/Source/Modules/python.cxx
+++ b/Source/Modules/python.cxx
@@ -19,7 +19,6 @@ static int treduce = SWIG_cparse_template_reduce(0);
 #include <ctype.h>
 #include <errno.h>
 #include <stdlib.h>
-#include <sstream>
 #include "../DoxygenTranslator/src/PyDocConverter.h"
 
 #define PYSHADOW_MEMBER  0x2

From 6fe4c0707bc5b8758fb951302ea4960e82ef8e70 Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Mon, 16 Feb 2015 23:59:46 +0100
Subject: [PATCH 255/314] Remove code not doing anything from PyDocConverter.

There is really no need to append empty string.
---
 Source/DoxygenTranslator/src/PyDocConverter.cpp | 2 --
 1 file changed, 2 deletions(-)

diff --git a/Source/DoxygenTranslator/src/PyDocConverter.cpp b/Source/DoxygenTranslator/src/PyDocConverter.cpp
index d7dbabe35..5bcf8f174 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/PyDocConverter.cpp
@@ -531,8 +531,6 @@ void PyDocConverter::handlePlainString(DoxygenEntity& tag,
                                        const std::string&)
 {
   translatedComment += tag.data;
-  if (tag.data.size() && tag.data[tag.data.size() - 1] != ' ')
-    translatedComment += "";
 }
 
 void PyDocConverter::handleTagVerbatim(DoxygenEntity& tag,

From 45ecc9cb84cf8d894c57832f893350cfdf7eb3f6 Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Tue, 17 Feb 2015 00:10:37 +0100
Subject: [PATCH 256/314] Fix trimming whitespace from Doxygen comments.

Also trim the string (making it empty) if it consists solely of whitespace.
---
 Examples/test-suite/python/doxygen_misc_constructs_runme.py | 2 +-
 Source/DoxygenTranslator/src/PyDocConverter.cpp             | 4 +++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/Examples/test-suite/python/doxygen_misc_constructs_runme.py b/Examples/test-suite/python/doxygen_misc_constructs_runme.py
index 81e0ee0a9..3dc083b6b 100644
--- a/Examples/test-suite/python/doxygen_misc_constructs_runme.py
+++ b/Examples/test-suite/python/doxygen_misc_constructs_runme.py
@@ -45,7 +45,7 @@ may be specified."""
 )
 
 commentVerifier.check(doxygen_misc_constructs.getConnection.__doc__,
-    r""" 
+    r"""
 
 This function returns connection id."""
 )
diff --git a/Source/DoxygenTranslator/src/PyDocConverter.cpp b/Source/DoxygenTranslator/src/PyDocConverter.cpp
index 5bcf8f174..e1bae2792 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/PyDocConverter.cpp
@@ -117,7 +117,9 @@ static size_t determineIndent(const string& s)
 static void trimWhitespace(string& s)
 {
   const size_t lastNonSpace = s.find_last_not_of(' ');
-  if (lastNonSpace != string::npos)
+  if (lastNonSpace == string::npos)
+    s.clear();
+  else
     s.erase(lastNonSpace + 1);
 }
 

From 2e5017c6efa6ca746be32935a905c91b66ab8642 Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Tue, 17 Feb 2015 18:32:56 +0100
Subject: [PATCH 257/314] Fix missing returns in the Doxygen test suite code.

Missing returns resulted in test suite failures now that it is built with
-Wreturn-type, so avoid them by simply making most of the functions void and
adding explicit return statements to a couple of them that used Doxygen
\return command in their documentation, which doesn't make sense for the void
functions.
---
 .../test-suite/doxygen_basic_notranslate.i    | 13 ++++++------
 Examples/test-suite/doxygen_basic_translate.i | 13 ++++++------
 Examples/test-suite/doxygen_translate.i       |  7 ++++---
 .../test-suite/doxygen_translate_all_tags.i   | 20 +++++++++----------
 Examples/test-suite/doxygen_translate_links.i |  2 +-
 .../doxygen_translate_all_tags_runme.py       |  6 +++---
 6 files changed, 32 insertions(+), 29 deletions(-)

diff --git a/Examples/test-suite/doxygen_basic_notranslate.i b/Examples/test-suite/doxygen_basic_notranslate.i
index e97cc589f..45e36c6e3 100644
--- a/Examples/test-suite/doxygen_basic_notranslate.i
+++ b/Examples/test-suite/doxygen_basic_notranslate.i
@@ -22,13 +22,14 @@
  */
 int function()
 {
+    return 0;
 }
 
 /**
  * A test of a very very very very very very very very very very very very very very very very
  * very very very very very long comment string.
  */
-int function2()
+void function2()
 {
 }
 
@@ -36,7 +37,7 @@ int function2()
  * A test for overloaded functions
  * This is function \b one
  */
-int function3(int a)
+void function3(int a)
 {
 }
 
@@ -44,7 +45,7 @@ int function3(int a)
  * A test for overloaded functions
  * This is function \b two
  */
-int function3(int a, int b)
+void function3(int a, int b)
 {
 }
 
@@ -64,12 +65,12 @@ int function3(int a, int b)
  * \endcode
  * \endif
  */
-int function4()
+void function4()
 {
 }
 
 
-int function5(int a)
+void function5(int a)
 {
 }
 /**< This is a post comment. */
@@ -78,7 +79,7 @@ int function5(int a)
  * Test for default args
  * @param a Some parameter, default is 42
  */
-int function6(int a=42)
+void function6(int a=42)
 {
 }
 
diff --git a/Examples/test-suite/doxygen_basic_translate.i b/Examples/test-suite/doxygen_basic_translate.i
index b8bd7668a..0a8b0474f 100644
--- a/Examples/test-suite/doxygen_basic_translate.i
+++ b/Examples/test-suite/doxygen_basic_translate.i
@@ -18,13 +18,14 @@
  */
 int function()
 {
+    return 0;
 }
 
 /**
  * A test of a very very very very very very very very very very very very very very very very
  * very very very very very long comment string.
  */
-int function2()
+void function2()
 {
 }
 
@@ -32,7 +33,7 @@ int function2()
  * A test for overloaded functions
  * This is function \b one
  */
-int function3(int a)
+void function3(int a)
 {
 }
 
@@ -40,7 +41,7 @@ int function3(int a)
  * A test for overloaded functions
  * This is function \b two
  */
-int function3(int a, int b)
+void function3(int a, int b)
 {
 }
 
@@ -59,12 +60,12 @@ int function3(int a, int b)
  * \endcode
  * \endif
  */
-int function4()
+void function4()
 {
 }
 
 
-int function5(int a)
+void function5(int a)
 {
 }
 /**< This is a post comment. */
@@ -73,7 +74,7 @@ int function5(int a)
  * Test for default args
  * @param a Some parameter, default is 42
  */
-int function6(int a=42)
+void function6(int a=42)
 {
 }
 
diff --git a/Examples/test-suite/doxygen_translate.i b/Examples/test-suite/doxygen_translate.i
index 3c2930ff1..348b2e9a8 100644
--- a/Examples/test-suite/doxygen_translate.i
+++ b/Examples/test-suite/doxygen_translate.i
@@ -123,6 +123,7 @@
  */
 int function(int a, float b)
 {
+    return 0;
 }
 
 /**
@@ -205,7 +206,7 @@ int function(int a, float b)
  * <u>underlined \b bold text - doxy commands are ignored inside 'htmlonly' section </u>
  * \endhtmlonly
  */
-int htmlFunction(int a, float b)
+void htmlFunction(int a, float b)
 {
 }
 
@@ -222,7 +223,7 @@ int htmlFunction(int a, float b)
  *   Almost all combinations of above flags are supported by
  *   \c htmlTable... functions.
  */
-int htmlTableFunction(int byFlags)
+void htmlTableFunction(int byFlags)
 {
 }
 
@@ -252,7 +253,7 @@ int htmlTableFunction(int byFlags)
  * Not an &text; html entity - ignored by Doxygen.
  * Not an &text html entity - ampersand is replaced with entity.
  */
-int htmlEntitiesFunction(int a, float b)
+void htmlEntitiesFunction(int a, float b)
 {
 }
 
diff --git a/Examples/test-suite/doxygen_translate_all_tags.i b/Examples/test-suite/doxygen_translate_all_tags.i
index 84b0531d5..ba348fd50 100644
--- a/Examples/test-suite/doxygen_translate_all_tags.i
+++ b/Examples/test-suite/doxygen_translate_all_tags.i
@@ -35,7 +35,7 @@
  * \class someClass headerFile.h headerName
  * \code some test code \endcode
  */
-int func01(int a)
+void func01(int a)
 {
 }
 
@@ -64,7 +64,7 @@ int func01(int a)
  * \details This is very large
  * and detailed description of some thing
  */
-int func02(int a)
+void func02(int a)
 {
 }
 
@@ -96,7 +96,7 @@ int func02(int a)
  * \example someFile.txt
  * Some details on using the example
  */
-int func03(int a)
+void func03(int a)
 {
 }
 
@@ -131,7 +131,7 @@ int func03(int a)
  * This will only appear in hmtl
  * \endhtmlonly
  */
-int func04(int a)
+void func04(int a)
 {
 }
 
@@ -172,7 +172,7 @@ int func04(int a)
  * \invariant Some text
  * describing invariant.
  */
-int func05(int a)
+void func05(int a)
 {
 }
 
@@ -216,7 +216,7 @@ int func05(int a)
  *
  * \n \n \n
  */
-int func06(int a)
+void func06(int a)
 {
 }
 
@@ -259,7 +259,7 @@ int func06(int a)
  *
  * \property someVar
  */
-int func07(int a)
+void func07(int a)
 {
 }
 
@@ -303,7 +303,7 @@ int func07(int a)
  * 
  * \retval someValue Some description
  */
-int func08(int a)
+void func08(int a)
 {
 }
 
@@ -350,7 +350,7 @@ int func08(int a)
  * 
  * \throws RuntimeError
  */
-int func09(int a)
+void func09(int a)
 {
 }
 
@@ -392,7 +392,7 @@ int func09(int a)
  * 
  * And here goes simple text
  */
-int func10(int a, float b)
+void func10(int a, float b)
 {
 }
 
diff --git a/Examples/test-suite/doxygen_translate_links.i b/Examples/test-suite/doxygen_translate_links.i
index 5eee1d67f..769a4f4e7 100644
--- a/Examples/test-suite/doxygen_translate_links.i
+++ b/Examples/test-suite/doxygen_translate_links.i
@@ -44,7 +44,7 @@ public:
  * \sa superFunc()
  *
  */
-int function()
+void function()
 {
 }
 
diff --git a/Examples/test-suite/python/doxygen_translate_all_tags_runme.py b/Examples/test-suite/python/doxygen_translate_all_tags_runme.py
index 838ea3210..c9620040f 100644
--- a/Examples/test-suite/python/doxygen_translate_all_tags_runme.py
+++ b/Examples/test-suite/python/doxygen_translate_all_tags_runme.py
@@ -262,13 +262,13 @@ Remarks: Some remark text
 
 Another remarks section
 
-:rtype: int
+:rtype: void
 :return: Whatever
 
-:rtype: int
+:rtype: void
 :return: it
 
-:rtype: int
+:rtype: void
 :return: may return
 """)
 

From 751dbf2bb73af93500662e3ac82c328e6c2bb6be Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Mon, 20 Jul 2015 01:01:27 +0200
Subject: [PATCH 258/314] Remove unused C_COMMENT_STRING terminal from the
 grammar.

This was a leftover from the initial Doxygen GSoC work in 2008 and should have
been removed by 4951d4a9007a0a64ed67b56e4d0d12a56097fe97 (GSoC 2012).
---
 Source/CParse/parser.y | 1 -
 1 file changed, 1 deletion(-)

diff --git a/Source/CParse/parser.y b/Source/CParse/parser.y
index c6e15bc32..7afccea01 100644
--- a/Source/CParse/parser.y
+++ b/Source/CParse/parser.y
@@ -1472,7 +1472,6 @@ static void mark_nodes_as_extend(Node *n) {
 %token PARSETYPE PARSEPARM PARSEPARMS
 %token <str> DOXYGENSTRING 
 %token <str> DOXYGENPOSTSTRING 
-%token <str> C_COMMENT_STRING 
 
 %left  CAST
 %left  QUESTIONMARK

From b908a9b43096403f687746c21133181fe8393707 Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Mon, 20 Jul 2015 15:43:23 +0200
Subject: [PATCH 259/314] Quote JAVA_HOME variable value in Java test suite
 makefile.

This should fix problem with JAVA_HOME containing spaces, as it happens in
the AppVeyor build.
---
 Examples/test-suite/java/Makefile.in | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Examples/test-suite/java/Makefile.in b/Examples/test-suite/java/Makefile.in
index 3e0c4a8c4..3b2e1e0d9 100644
--- a/Examples/test-suite/java/Makefile.in
+++ b/Examples/test-suite/java/Makefile.in
@@ -96,7 +96,7 @@ setup = \
 # Doxygen test cases need to be compiled together with the CommentsParser class
 # which depends on com.sun.javadoc package which is located in this JAR.
 JAVA_CLASSPATH := .
-$(DOXYGEN_TEST_CASES:=.cpptest): JAVA_CLASSPATH := $(JAVA_HOME)/lib/tools.jar:.
+$(DOXYGEN_TEST_CASES:=.cpptest): JAVA_CLASSPATH := "$(JAVA_HOME)/lib/tools.jar":.
 $(DOXYGEN_TEST_CASES:=.cpptest): DOXYGEN_COMMENT_PARSER := $(srcdir)/CommentParser.java
 
 # Compiles java files then runs the testcase. A testcase is only run if

From e191360c9f54863230f68c4bf8b062689f1d354d Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Mon, 20 Jul 2015 16:17:06 +0200
Subject: [PATCH 260/314] Merge "-builtin" autodoc bugs workarounds from master
 into test.

Although some of the bugs (e.g. missing "self") in the autodoc doc strings
when using "-builtin" option were fixed in the Doxygen branch, others are
still present, so we still need to skip some of the tests in "-builtin" case.
---
 Examples/test-suite/python/autodoc_runme.py   | 42 ++++++++++++++-----
 Examples/test-suite/python/commentVerifier.py |  2 +-
 2 files changed, 32 insertions(+), 12 deletions(-)

diff --git a/Examples/test-suite/python/autodoc_runme.py b/Examples/test-suite/python/autodoc_runme.py
index 6a490d1b4..9629ef011 100644
--- a/Examples/test-suite/python/autodoc_runme.py
+++ b/Examples/test-suite/python/autodoc_runme.py
@@ -1,7 +1,14 @@
 from autodoc import *
-from commentVerifier import check
+import commentVerifier
 import sys
 
+def check(got, expected, expected_builtin=None, skip=False):
+    if not skip:
+        expect = expected
+        if is_python_builtin() and expected_builtin != None:
+            expect = expected_builtin
+        commentVerifier.check(got, expect)
+
 def is_new_style_class(cls):
     return hasattr(cls, "__class__")
 
@@ -10,7 +17,10 @@ if not is_new_style_class(A):
     # used!
     sys.exit(0)
 
-check(A.__doc__, "Proxy of C++ A class")
+# skip builtin check - the autodoc is missing, but it probably should not be
+skip = True
+
+check(A.__doc__, "Proxy of C++ A class", "::A")
 check(A.funk.__doc__, "just a string")
 check(A.func0.__doc__, "func0(self, arg2, hello) -> int")
 check(A.func1.__doc__, "func1(A self, short arg2, Tuple hello) -> int")
@@ -114,34 +124,43 @@ check(A.func3static.__doc__,
 if sys.version_info[0:2] > (2, 4):
     # Python 2.4 does not seem to work
     check(A.variable_a.__doc__,
-          "A_variable_a_get(self) -> int"
+          "A_variable_a_get(self) -> int",
+          "A.variable_a"
           )
     check(A.variable_b.__doc__,
-          "A_variable_b_get(A self) -> int"
+          "A_variable_b_get(A self) -> int",
+          "A.variable_b"
           )
     check(A.variable_c.__doc__,
           "A_variable_c_get(self) -> int\n"
           "\n"
           "Parameters:\n"
-          "    self: A *\n"
+          "    self: A *\n",
+          "A.variable_c"
           )
     check(A.variable_d.__doc__,
           "A_variable_d_get(A self) -> int\n"
           "\n"
           "Parameters:\n"
-          "    self: A *\n"
+          "    self: A *\n",
+          "A.variable_d"
           )
 
-check(B.__doc__, "Proxy of C++ B class")
-check(C.__init__.__doc__, "__init__(self, a, b, h) -> C")
-check(D.__init__.__doc__, "__init__(D self, int a, int b, Hola h) -> D")
+check(B.__doc__,
+      "Proxy of C++ B class",
+      "::B"
+      )
+check(C.__init__.__doc__, "__init__(self, a, b, h) -> C", None, skip)
+check(D.__init__.__doc__,
+      "__init__(D self, int a, int b, Hola h) -> D", None, skip)
 check(E.__init__.__doc__,
       "__init__(self, a, b, h) -> E\n"
       "\n"
       "Parameters:\n"
       "    a: special comment for parameter a\n"
       "    b: another special comment for parameter b\n"
-      "    h: enum Hola\n"
+      "    h: enum Hola\n",
+      None, skip
       )
 check(F.__init__.__doc__,
       "__init__(F self, int a, int b, Hola h) -> F\n"
@@ -149,7 +168,8 @@ check(F.__init__.__doc__,
       "Parameters:\n"
       "    a: special comment for parameter a\n"
       "    b: another special comment for parameter b\n"
-      "    h: enum Hola\n"
+      "    h: enum Hola\n",
+      None, skip
       )
 
 check(B.funk.__doc__, "funk(B self, int c, int d) -> int")
diff --git a/Examples/test-suite/python/commentVerifier.py b/Examples/test-suite/python/commentVerifier.py
index a49539ed1..57ac0b721 100644
--- a/Examples/test-suite/python/commentVerifier.py
+++ b/Examples/test-suite/python/commentVerifier.py
@@ -1,4 +1,4 @@
-def check(got, expected):
+def check(got, expected, expected_builtin=None):
   if got is None:  # Absence of comment is equivalent to empty comment.
       got = ''
 

From dc9cecb9435fc5e69c78629443da062b1907a67d Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Wed, 22 Jul 2015 17:39:04 +0200
Subject: [PATCH 261/314] Move Doxygen comment mangling from the parser to the
 lexer.

This is a more logical place to do this and it also simplifies the parser
code, e.g. the parser doesn't get the ignored (called "structural" for some
reason in the code) Doxygen comments from the lexer at all any more instead of
having to ignore them on its own. It also allows to define doxygen_comment and
doxygen_post_comment rules in a simpler way and avoid shift/reduce conflicts
for the sequences of Doxygen [post] comments by specifying their associativity.

In principle, the lexer could also take care of concatenating the subsequent
Doxygen comments in a single one, as this would also seem to belong to it
rather than the parser, but this doesn't seem to provide any immediate gains
and so isn't done by this commit.
---
 Source/CParse/cscanner.c |  78 +++++++++++++++++++++++-----
 Source/CParse/parser.y   | 108 ++++++---------------------------------
 2 files changed, 80 insertions(+), 106 deletions(-)

diff --git a/Source/CParse/cscanner.c b/Source/CParse/cscanner.c
index a987c4fd2..bc7463589 100644
--- a/Source/CParse/cscanner.c
+++ b/Source/CParse/cscanner.c
@@ -53,6 +53,52 @@ static int rename_active = 0;
 /* Doxygen comments scanning */
 int scan_doxygen_comments = 0;
 
+int isStructuralDoxygen(String *s){
+	static const char* const structuralTags[] = {
+	  "addtogroup",
+	  "callgraph",
+	  "callergraph",
+	  "category",
+	  "def",
+	  "defgroup",
+	  "dir",
+	  "example",
+	  "file",
+	  "headerfile",
+	  "internal",
+	  "mainpage",
+	  "name",
+	  "nosubgrouping",
+	  "overload",
+	  "package",
+	  "page",
+	  "protocol",
+	  "relates",
+	  "relatesalso",
+	  "showinitializer",
+	  "weakgroup",
+	};
+
+	unsigned n;
+	char *slashPointer = Strchr(s, '\\');
+	char *atPointer = Strchr(s,'@');
+	if (slashPointer == NULL && atPointer == NULL) return 0;
+	else if( slashPointer == NULL) slashPointer = atPointer;
+
+	slashPointer++; /* skip backslash or at sign */
+
+	for (n = 0; n < sizeof(structuralTags)/sizeof(structuralTags[0]); n++) {
+	  const size_t len = strlen(structuralTags[n]);
+	  if (strncmp(slashPointer, structuralTags[n], len) == 0) {
+	    /* Take care to avoid false positives with prefixes of other tags. */
+	    if (slashPointer[len] == '\0' || isspace(slashPointer[len]))
+	      return 1;
+	  }
+	}
+
+	return 0;
+}
+
 /* -----------------------------------------------------------------------------
  * Swig_cparse_cplusplus()
  * ----------------------------------------------------------------------------- */
@@ -376,21 +422,25 @@ static int yylook(void) {
 	  Scanner_locator(scan, cmt);
 	}
 	if (scan_doxygen_comments) { /* else just skip this node, to avoid crashes in parser module*/
-	  if (strncmp(loc, "/**<", 4) == 0 || strncmp(loc, "///<", 4) == 0||strncmp(loc, "/*!<", 4) == 0||strncmp(loc, "//!<", 4) == 0) {
-	    /* printf("Doxygen Post Comment: %s lines %d-%d [%s]\n", Char(Scanner_file(scan)), Scanner_start_line(scan), Scanner_line(scan), loc); */
-	    yylval.str =  NewString(loc);
-	    Setline(yylval.str, Scanner_start_line(scan));
-	    Setfile(yylval.str, Scanner_file(scan));
-	    return DOXYGENPOSTSTRING;
-	  }
-	  if (strncmp(loc, "/**", 3) == 0 || strncmp(loc, "///", 3) == 0||strncmp(loc, "/*!", 3) == 0||strncmp(loc, "//!", 3) == 0) {
-	    /* printf("Doxygen Comment: %s lines %d-%d [%s]\n", Char(Scanner_file(scan)), Scanner_start_line(scan), Scanner_line(scan), loc); */
-	    /* ignore comments like / * * * and / * * /,  which are also ignored by Doxygen */
-	    if (loc[3] != '*'  &&  loc[3] != '/') {
-	      yylval.str =  NewString(loc);
+	  /* Check for all possible Doxygen comment start markers while ignoring
+	     comments starting with a row of asterisks or slashes just as
+	     Doxygen itself does. */
+	  if (Len(cmt) > 3 && loc[0] == '/' &&
+	      ((loc[1] == '/' && ((loc[2] == '/' && loc[3] != '/') || loc[2] == '!')) ||
+	       (loc[1] == '*' && ((loc[2] == '*' && loc[3] != '*') || loc[2] == '!')))) {
+	    int is_post_comment = loc[3] == '<';
+
+	    if (is_post_comment || !isStructuralDoxygen(loc)) {
+	      int begin = is_post_comment ? 4 : 3;
+	      int end = Len(cmt);
+	      if (loc[end - 1] == '/' && loc[end - 2] == '*') {
+		end -= 2;
+	      }
+
+	      yylval.str =  NewStringWithSize(loc + begin, end - begin);
 	      Setline(yylval.str, Scanner_start_line(scan));
 	      Setfile(yylval.str, Scanner_file(scan));
-	      return DOXYGENSTRING;
+	      return is_post_comment ? DOXYGENPOSTSTRING : DOXYGENSTRING;
 	    }
 	  }
 	}
@@ -930,7 +980,7 @@ int yylex(void) {
   case POUND:
     return yylex();
   case SWIG_TOKEN_COMMENT:
-	  return yylex();
+    return yylex();
   default:
     return (l);
   }
diff --git a/Source/CParse/parser.y b/Source/CParse/parser.y
index 7afccea01..30928f73f 100644
--- a/Source/CParse/parser.y
+++ b/Source/CParse/parser.y
@@ -61,58 +61,12 @@ static int      cparse_externc = 0;
 int		ignore_nested_classes = 0;
 int		kwargs_supported = 0;
 /* -----------------------------------------------------------------------------
- *                            Doxygen Comment Globals and Assist Functions
+ *                            Doxygen Comment Globals
  * ----------------------------------------------------------------------------- */
 static String *currentDeclComment = NULL; /* Comment of C/C++ declaration. */
 static Node *previousNode = NULL; /* Pointer to the previous node (for post comments) */
 static Node *currentNode = NULL; /* Pointer to the current node (for post comments) */
 
-int isStructuralDoxygen(String *s){
-	static const char* const structuralTags[] = {
-	  "addtogroup",
-	  "callgraph",
-	  "callergraph",
-	  "category",
-	  "def",
-	  "defgroup",
-	  "dir",
-	  "example",
-	  "file",
-	  "headerfile",
-	  "internal",
-	  "mainpage",
-	  "name",
-	  "nosubgrouping",
-	  "overload",
-	  "package",
-	  "page",
-	  "protocol",
-	  "relates",
-	  "relatesalso",
-	  "showinitializer",
-	  "weakgroup",
-	};
-
-	unsigned n;
-	char *slashPointer = Strchr(s, '\\');
-	char *atPointer = Strchr(s,'@');
-	if (slashPointer == NULL && atPointer == NULL) return 0;
-	else if( slashPointer == NULL) slashPointer = atPointer;
-
-	slashPointer++; /* skip backslash or at sign */
-
-	for (n = 0; n < sizeof(structuralTags)/sizeof(structuralTags[0]); n++) {
-	  const size_t len = strlen(structuralTags[n]);
-	  if (strncmp(slashPointer, structuralTags[n], len) == 0) {
-	    /* Take care to avoid false positives with prefixes of other tags. */
-	    if (slashPointer[len] == '\0' || isspace(slashPointer[len]))
-	      return 1;
-	  }
-	}
-
-	return 0;
-}
-
 /* -----------------------------------------------------------------------------
  *                            Assist Functions
  * ----------------------------------------------------------------------------- */
@@ -1470,8 +1424,14 @@ static void mark_nodes_as_extend(Node *n) {
 %token <str> OPERATOR
 %token <str> CONVERSIONOPERATOR
 %token PARSETYPE PARSEPARM PARSEPARMS
-%token <str> DOXYGENSTRING 
-%token <str> DOXYGENPOSTSTRING 
+
+/* Make Doxygen comment left associative to avoid shift/reduce conflicts for
+   several of them in a row, it doesn't really matter in which order we
+   concatenate them but this order must be defined. */
+%token <str> DOXYGENSTRING
+%left DOXYGENSTRING
+%token <str> DOXYGENPOSTSTRING
+%left DOXYGENPOSTSTRING
 
 %left  CAST
 %left  QUESTIONMARK
@@ -1546,9 +1506,7 @@ static void mark_nodes_as_extend(Node *n) {
 %type <node>     fname stringtype;
 %type <node>     featattr;
 %type <str>	 doxygen_comment;
-%type <str>	 doxygen_comment_item;
 %type <str>	 doxygen_post_comment;
-%type <str>	 doxygen_post_comment_item;
 %type <node>     lambda_introducer lambda_body;
 %type <pl>       lambda_tail;
 %type <node>     optional_constant_directive;
@@ -3474,56 +3432,22 @@ c_constructor_decl : storage_class type LPAREN parms RPAREN ctor_end {
    A Doxygen Comment (a string in Doxygen Format)
    ------------------------------------------------------------ */
 
-doxygen_comment_item : DOXYGENSTRING {
-		  DohReplace($1, "/**", "", 0);
-		  DohReplace($1, "/*!", "", 0);
-		  DohReplace($1, "///", "", 0);
-		  DohReplace($1, "//!", "", 0);
-		  DohReplace($1, "*/", "", 0);
-
-		  /* Throw out all structural comments */
-		  if (isStructuralDoxygen($1)) {
-		    Delete($1);
-		    $1 = 0;
-		  }
-		  $$ = $1;
-		}
-		| doxygen_comment_item doxygen_comment_item {
-		  if ($1) {
-		    if ($2)
-		      Append($1, $2);
-		  }
-		  else {
-		    $1 = $2;
-		  }
-		  $$ = $1;
-		}
-		;
-
-doxygen_comment : doxygen_comment_item {
+doxygen_comment : DOXYGENSTRING {
                   $$ = $1;
 		}
-		;
-
-
-doxygen_post_comment_item : DOXYGENPOSTSTRING {
-		  DohReplace($1, "///<", "", 0);
-		  DohReplace($1, "/**<", "", 0);
-		  DohReplace($1, "/*!<", "", 0);
-		  DohReplace($1, "//!<", "", 0);
-		  DohReplace($1, "*/", "", 0);
-		  
-		  $$ = $1;
-		}
-		| doxygen_post_comment_item doxygen_post_comment_item {
+		| DOXYGENSTRING doxygen_comment {
 		  Append($1, $2);
 		  $$ = $1;
 		}
 		;
 
-doxygen_post_comment : doxygen_post_comment_item {
+doxygen_post_comment : DOXYGENPOSTSTRING {
                   $$ = $1;
 		}
+		| DOXYGENPOSTSTRING doxygen_post_comment {
+		  Append($1, $2);
+		  $$ = $1;
+		}
 		;
 
 /* ======================================================================

From 9ab3f2e232d8d45e6a6f2dcb33b8c856d773640a Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Wed, 22 Jul 2015 18:43:50 +0200
Subject: [PATCH 262/314] No changes, just remove spurious white space only
 differences.

Whitespace-only changes to decrease the diff with master.
---
 Source/CParse/parser.y | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/Source/CParse/parser.y b/Source/CParse/parser.y
index 30928f73f..15e88d89d 100644
--- a/Source/CParse/parser.y
+++ b/Source/CParse/parser.y
@@ -4390,8 +4390,8 @@ cpp_members  : cpp_member cpp_members {
 	       appendChild($$,$4);
 	       set_nextSibling($$,$7);
 	     }
-         | include_directive { $$ = $1; }
-         | empty { $$ = 0;}
+             | include_directive { $$ = $1; }
+             | empty { $$ = 0;}
 	     | error {
 	       int start_line = cparse_line;
 	       skip_decl();
@@ -4806,10 +4806,10 @@ parms          : rawparms {
                  Parm *p;
 		 $$ = $1;
 		 p = $1;
-		 while (p) {
+                 while (p) {
 		   Replace(Getattr(p,"type"),"typename ", "", DOH_REPLACE_ANY);
 		   p = nextSibling(p);
-		 }
+                 }
                }
     	       ;
 
@@ -4823,7 +4823,7 @@ rawparms          : parm ptail {
 ptail          : COMMA parm ptail {
                  set_nextSibling($2,$3);
 		 $$ = $2;
-               }
+                }
 	       | COMMA doxygen_post_comment parm ptail {
 		 set_comment(previousNode, $2);
                  set_nextSibling($3,$4);

From bc2ee1b1309b3dc27773e73a27ca42507604eec3 Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Sat, 25 Jul 2015 16:58:07 +0200
Subject: [PATCH 263/314] Rewrote part of the grammar dealing with Doxygen
 comments for enums.

This brings down the number of yacc shift/reduce conflicts from 16 to 8 and
eliminates all 4 of the previously existing reduce/reduce conflicts.
---
 Source/CParse/parser.y | 97 +++++++++++++++++++++++++++---------------
 1 file changed, 62 insertions(+), 35 deletions(-)

diff --git a/Source/CParse/parser.y b/Source/CParse/parser.y
index 15e88d89d..ae7625c62 100644
--- a/Source/CParse/parser.y
+++ b/Source/CParse/parser.y
@@ -1459,7 +1459,7 @@ static void mark_nodes_as_extend(Node *n) {
 
 /* C declarations */
 %type <node>     c_declaration c_decl c_decl_tail c_enum_key c_enum_inherit c_enum_decl c_enum_forward_decl c_constructor_decl;
-%type <node>     enumlist edecl;
+%type <node>     enumlist enumlist_tail enumlist_item edecl_with_dox edecl;
 
 /* C++ declarations */
 %type <node>     cpp_declaration cpp_class_decl cpp_forward_class_decl cpp_template_decl cpp_alternate_rettype;
@@ -1509,7 +1509,6 @@ static void mark_nodes_as_extend(Node *n) {
 %type <str>	 doxygen_post_comment;
 %type <node>     lambda_introducer lambda_body;
 %type <pl>       lambda_tail;
-%type <node>     optional_constant_directive;
 %type <str>      virt_specifier_seq;
 
 %%
@@ -5946,28 +5945,69 @@ ename          :  identifier { $$ = $1; }
 	       |  empty { $$ = (char *) 0;}
 	       ;
 
-optional_constant_directive : constant_directive { $$ = $1; }
-		           | empty { $$ = 0; }
-		           ;
+optional_ignored_define
+		: constant_directive
+		| empty
+		;
+
+optional_ignored_define_after_comma
+		: empty
+		| COMMA
+		| COMMA constant_directive
+		;
 
 /* Enum lists - any #define macros (constant directives) within the enum list are ignored. Trailing commas accepted. */
-enumlist       :  enumlist COMMA optional_constant_directive edecl optional_constant_directive {
-		 Node *leftSibling = Getattr($1,"_last");
-		 set_nextSibling(leftSibling,$4);
-		 Setattr($1,"_last",$4);
-		 $$ = $1;
-	       }
-	       | enumlist COMMA optional_constant_directive {
-		 $$ = $1;
-	       }
-	       | optional_constant_directive edecl optional_constant_directive {
-		 Setattr($2,"_last",$2);
-		 $$ = $2;
-	       }
-	       | optional_constant_directive {
-		 $$ = 0;
-	       }
-	       ;
+enumlist	: enumlist_item optional_ignored_define_after_comma {
+		  Setattr($1,"_last",$1);
+		  $$ = $1;
+		}
+		| enumlist_item enumlist_tail optional_ignored_define_after_comma {
+		  set_nextSibling($1, $2);
+		  Setattr($1,"_last",Getattr($2,"_last"));
+		  $$ = $1;
+		}
+		| optional_ignored_define {
+		  $$ = 0;
+		}
+		;
+
+enumlist_tail	: COMMA enumlist_item {
+		  Setattr($2,"_last",$2);
+		  $$ = $2;
+		}
+		| enumlist_tail COMMA enumlist_item {
+		  set_nextSibling(Getattr($1,"_last"), $3);
+		  Setattr($1,"_last",$3);
+		  $$ = $1;
+		}
+		;
+
+enumlist_item	: optional_ignored_define edecl_with_dox optional_ignored_define {
+		  $$ = $2;
+		}
+		;
+
+edecl_with_dox	: edecl {
+		  $$ = $1;
+		}
+		| doxygen_comment edecl {
+		  $$ = $2;
+		  set_comment($2, $1);
+		}
+		| edecl doxygen_post_comment {
+		  $$ = $1;
+		  set_comment($1, $2);
+		}
+		| doxygen_post_comment edecl {
+		  $$ = $2;
+		  set_comment(previousNode, $1);
+		}
+		| doxygen_post_comment edecl doxygen_post_comment {
+		  $$ = $2;
+		  set_comment(previousNode, $1);
+		  set_comment($2, $3);
+		}
+		;
 
 edecl          :  identifier {
 		   SwigType *type = NewSwigType(T_INT);
@@ -5987,19 +6027,6 @@ edecl          :  identifier {
 		   Setattr($$,"value",$1);
 		   Delete(type);
                  }
-		 | doxygen_comment edecl {
-		   $$ = $2;
-		   set_comment($2, $1);
-		 }
-		 | doxygen_post_comment edecl {
-		   $$ = $2;
-		   set_comment(previousNode, $1);
-		 }
-		 | edecl doxygen_post_comment {
-		   $$ = $1;
-		   set_comment($1, $2);
-		 }
-                 | empty { $$ = 0; previousNode = currentNode; currentNode = 0; }
                  ;
 
 etype            : expr {

From 864945ba2e00954b44e194c55d170b6986680579 Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Sat, 25 Jul 2015 19:02:31 +0200
Subject: [PATCH 264/314] Fix shift/reduce conflicts in Doxygen pre/post
 comment parsing.

Don't accept both pre- and post-comments for the same declaration (a function
parameter or a class member), this didn't work before neither as the
pre-comment overrode the post-one due to the default shift/reduce resolution
preferring to shift, but it happened silently whereas now it will result in a
parse error.

In the future we could complicate the grammar to detect this and give a
warning about one of the comments being ignored instead, but for now keep
things simple.
---
 Source/CParse/parser.y | 25 +++++++++++++++++--------
 1 file changed, 17 insertions(+), 8 deletions(-)

diff --git a/Source/CParse/parser.y b/Source/CParse/parser.y
index ae7625c62..fa19c1638 100644
--- a/Source/CParse/parser.y
+++ b/Source/CParse/parser.y
@@ -1463,7 +1463,7 @@ static void mark_nodes_as_extend(Node *n) {
 
 /* C++ declarations */
 %type <node>     cpp_declaration cpp_class_decl cpp_forward_class_decl cpp_template_decl cpp_alternate_rettype;
-%type <node>     cpp_members cpp_member;
+%type <node>     cpp_members cpp_member cpp_member_no_dox;
 %type <node>     cpp_constructor_decl cpp_destructor_decl cpp_protection_decl cpp_conversion_operator cpp_static_assert;
 %type <node>     cpp_swig_directive cpp_temp_possible cpp_opt_declarators ;
 %type <node>     cpp_using_decl cpp_namespace_decl cpp_catch_decl cpp_lambda_decl;
@@ -1475,7 +1475,7 @@ static void mark_nodes_as_extend(Node *n) {
 %type <id>       storage_class extern_string;
 %type <pl>       parms  ptail rawparms varargs_parms ;
 %type <pl>       templateparameters templateparameterstail;
-%type <p>        parm valparm rawvalparms valparms valptail ;
+%type <p>        parm_no_dox parm valparm rawvalparms valparms valptail ;
 %type <p>        typemap_parm tm_list tm_tail ;
 %type <p>        templateparameter ;
 %type <id>       templcpptype cpptype access_specifier;
@@ -4407,7 +4407,7 @@ cpp_members  : cpp_member cpp_members {
 
 /* A class member.  May be data or a function. Static or virtual as well */
 
-cpp_member   : c_declaration { $$ = $1; }
+cpp_member_no_dox : c_declaration { $$ = $1; }
              | cpp_constructor_decl { 
                  $$ = $1; 
 		 if (extendmode && current_class) {
@@ -4442,11 +4442,15 @@ cpp_member   : c_declaration { $$ = $1; }
              | fragment_directive {$$ = $1; }
              | types_directive {$$ = $1; }
              | SEMI { $$ = 0; }
-             | doxygen_comment cpp_member {
+
+cpp_member   : cpp_member_no_dox {
+		$$ = $1;
+	     }
+             | doxygen_comment cpp_member_no_dox {
 	         $$ = $2;
 		 set_comment($2, $1);
 	     }
-             | cpp_member doxygen_post_comment {
+             | cpp_member_no_dox doxygen_post_comment {
 	         $$ = $1;
 		 set_comment($1, $2);
 	     }
@@ -4832,7 +4836,7 @@ ptail          : COMMA parm ptail {
                ;
 
 
-parm           : rawtype parameter_declarator {
+parm_no_dox	: rawtype parameter_declarator {
                    SwigType_push($1,$2.type);
 		   $$ = NewParmWithoutFileLineInfo($1,$2.id);
 		   previousNode = currentNode;
@@ -4862,11 +4866,16 @@ parm           : rawtype parameter_declarator {
 		  Setfile($$,cparse_file);
 		  Setline($$,cparse_line);
 		}
-		| doxygen_comment parm {
+		;
+
+parm		: parm_no_dox {
+		  $$ = $1;
+		}
+		| doxygen_comment parm_no_dox {
 		  $$ = $2;
 		  set_comment($2, $1);
 		}
-		| parm doxygen_post_comment {
+		| parm_no_dox doxygen_post_comment {
 		  $$ = $1;
 		  set_comment($1, $2);
 		}

From 4884f8cb3c8d2c2a30b2d3f2be10d8f148b36f67 Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Sun, 26 Jul 2015 20:55:07 +0200
Subject: [PATCH 265/314] Move Doxygen comments concatenation from the parser
 to the lexer.

This allows to write the grammar in a simpler way without running into
shift/reduce conflicts all the time because a Doxygen post comment can often
be either reduced with the preceding token or shifted if there is another
Doxygen post comment after it.

Just take care of concatenating the comments in the lexer, which makes it
handling of comment tokens slightly more complex as it now needs to look ahead
at the next tokens, but it's worse the simplifications in the parser.

No changes in behaviour.
---
 Source/CParse/cscanner.c | 83 +++++++++++++++++++++++++++++-----------
 Source/CParse/parser.y   | 51 ++++++------------------
 2 files changed, 72 insertions(+), 62 deletions(-)

diff --git a/Source/CParse/cscanner.c b/Source/CParse/cscanner.c
index bc7463589..f1390e283 100644
--- a/Source/CParse/cscanner.c
+++ b/Source/CParse/cscanner.c
@@ -416,33 +416,72 @@ static int yylook(void) {
       
     case SWIG_TOKEN_COMMENT:
       {
-	String *cmt = Scanner_text(scan);
-	char *loc = Char(cmt);
-	if ((strncmp(loc,"/*@SWIG",7) == 0) && (loc[Len(cmt)-3] == '@')) {
-	  Scanner_locator(scan, cmt);
-	}
-	if (scan_doxygen_comments) { /* else just skip this node, to avoid crashes in parser module*/
-	  /* Check for all possible Doxygen comment start markers while ignoring
-	     comments starting with a row of asterisks or slashes just as
-	     Doxygen itself does. */
-	  if (Len(cmt) > 3 && loc[0] == '/' &&
-	      ((loc[1] == '/' && ((loc[2] == '/' && loc[3] != '/') || loc[2] == '!')) ||
-	       (loc[1] == '*' && ((loc[2] == '*' && loc[3] != '*') || loc[2] == '!')))) {
-	    int is_post_comment = loc[3] == '<';
+	typedef enum {
+	  DOX_COMMENT_PRE = -1,
+	  DOX_COMMENT_NONE,
+	  DOX_COMMENT_POST
+	} comment_kind_t;
+	comment_kind_t existing_comment = DOX_COMMENT_NONE;
 
-	    if (is_post_comment || !isStructuralDoxygen(loc)) {
-	      int begin = is_post_comment ? 4 : 3;
-	      int end = Len(cmt);
-	      if (loc[end - 1] == '/' && loc[end - 2] == '*') {
-		end -= 2;
+	/* Concatenate or skip all consecutive comments at once. */
+	do {
+	  String *cmt = Scanner_text(scan);
+	  char *loc = Char(cmt);
+	  if ((strncmp(loc,"/*@SWIG",7) == 0) && (loc[Len(cmt)-3] == '@')) {
+	    Scanner_locator(scan, cmt);
+	  }
+	  if (scan_doxygen_comments) { /* else just skip this node, to avoid crashes in parser module*/
+	    /* Check for all possible Doxygen comment start markers while ignoring
+	       comments starting with a row of asterisks or slashes just as
+	       Doxygen itself does. */
+	    if (Len(cmt) > 3 && loc[0] == '/' &&
+		((loc[1] == '/' && ((loc[2] == '/' && loc[3] != '/') || loc[2] == '!')) ||
+		 (loc[1] == '*' && ((loc[2] == '*' && loc[3] != '*') || loc[2] == '!')))) {
+	      comment_kind_t this_comment = loc[3] == '<' ? DOX_COMMENT_POST
+							  : DOX_COMMENT_PRE;
+
+	      if (existing_comment != DOX_COMMENT_NONE && this_comment != existing_comment) {
+		/* We can't concatenate together Doxygen pre- and post-comments. */
+		break;
 	      }
 
-	      yylval.str =  NewStringWithSize(loc + begin, end - begin);
-	      Setline(yylval.str, Scanner_start_line(scan));
-	      Setfile(yylval.str, Scanner_file(scan));
-	      return is_post_comment ? DOXYGENPOSTSTRING : DOXYGENSTRING;
+	      if (this_comment == DOX_COMMENT_POST || !isStructuralDoxygen(loc)) {
+		String *str;
+
+		int begin = this_comment == DOX_COMMENT_POST ? 4 : 3;
+		int end = Len(cmt);
+		if (loc[end - 1] == '/' && loc[end - 2] == '*') {
+		  end -= 2;
+		}
+
+		str = NewStringWithSize(loc + begin, end - begin);
+
+		if (existing_comment == DOX_COMMENT_NONE) {
+		  yylval.str = str;
+		  Setline(yylval.str, Scanner_start_line(scan));
+		  Setfile(yylval.str, Scanner_file(scan));
+		} else {
+		  Append(yylval.str, str);
+		}
+
+		existing_comment = this_comment;
+	      }
 	    }
 	  }
+	  do {
+	    tok = Scanner_token(scan);
+	  } while (tok == SWIG_TOKEN_ENDLINE);
+	} while (tok == SWIG_TOKEN_COMMENT);
+
+	Scanner_pushtoken(scan, tok, Scanner_text(scan));
+
+	switch (existing_comment) {
+	  case DOX_COMMENT_PRE:
+	    return DOXYGENSTRING;
+	  case DOX_COMMENT_NONE:
+	    break;
+	  case DOX_COMMENT_POST:
+	    return DOXYGENPOSTSTRING;
 	}
       }
       break;
diff --git a/Source/CParse/parser.y b/Source/CParse/parser.y
index fa19c1638..2051b8ff4 100644
--- a/Source/CParse/parser.y
+++ b/Source/CParse/parser.y
@@ -1425,13 +1425,8 @@ static void mark_nodes_as_extend(Node *n) {
 %token <str> CONVERSIONOPERATOR
 %token PARSETYPE PARSEPARM PARSEPARMS
 
-/* Make Doxygen comment left associative to avoid shift/reduce conflicts for
-   several of them in a row, it doesn't really matter in which order we
-   concatenate them but this order must be defined. */
 %token <str> DOXYGENSTRING
-%left DOXYGENSTRING
 %token <str> DOXYGENPOSTSTRING
-%left DOXYGENPOSTSTRING
 
 %left  CAST
 %left  QUESTIONMARK
@@ -1505,8 +1500,6 @@ static void mark_nodes_as_extend(Node *n) {
 %type <ptype>    type_specifier primitive_type_list ;
 %type <node>     fname stringtype;
 %type <node>     featattr;
-%type <str>	 doxygen_comment;
-%type <str>	 doxygen_post_comment;
 %type <node>     lambda_introducer lambda_body;
 %type <pl>       lambda_tail;
 %type <str>      virt_specifier_seq;
@@ -1562,11 +1555,11 @@ interface      : interface declaration {
                    appendChild($1,$2);
                    $$ = $1;
                }
-               | interface doxygen_comment {
+               | interface DOXYGENSTRING {
                    currentDeclComment = $2; 
                    $$ = $1;
                }
-               | interface doxygen_post_comment {
+               | interface DOXYGENPOSTSTRING {
                    Node *node = lastChild($1);
                    if (node) {
                        set_comment(node, $2);
@@ -3427,28 +3420,6 @@ c_constructor_decl : storage_class type LPAREN parms RPAREN ctor_end {
                 }
                 ;
 
-/* ------------------------------------------------------------
-   A Doxygen Comment (a string in Doxygen Format)
-   ------------------------------------------------------------ */
-
-doxygen_comment : DOXYGENSTRING {
-                  $$ = $1;
-		}
-		| DOXYGENSTRING doxygen_comment {
-		  Append($1, $2);
-		  $$ = $1;
-		}
-		;
-
-doxygen_post_comment : DOXYGENPOSTSTRING {
-                  $$ = $1;
-		}
-		| DOXYGENPOSTSTRING doxygen_post_comment {
-		  Append($1, $2);
-		  $$ = $1;
-		}
-		;
-
 /* ======================================================================
  *                       C++ Support
  * ====================================================================== */
@@ -4446,11 +4417,11 @@ cpp_member_no_dox : c_declaration { $$ = $1; }
 cpp_member   : cpp_member_no_dox {
 		$$ = $1;
 	     }
-             | doxygen_comment cpp_member_no_dox {
+             | DOXYGENSTRING cpp_member_no_dox {
 	         $$ = $2;
 		 set_comment($2, $1);
 	     }
-             | cpp_member_no_dox doxygen_post_comment {
+             | cpp_member_no_dox DOXYGENPOSTSTRING {
 	         $$ = $1;
 		 set_comment($1, $2);
 	     }
@@ -4827,7 +4798,7 @@ ptail          : COMMA parm ptail {
                  set_nextSibling($2,$3);
 		 $$ = $2;
                 }
-	       | COMMA doxygen_post_comment parm ptail {
+	       | COMMA DOXYGENPOSTSTRING parm ptail {
 		 set_comment(previousNode, $2);
                  set_nextSibling($3,$4);
 		 $$ = $3;
@@ -4871,11 +4842,11 @@ parm_no_dox	: rawtype parameter_declarator {
 parm		: parm_no_dox {
 		  $$ = $1;
 		}
-		| doxygen_comment parm_no_dox {
+		| DOXYGENSTRING parm_no_dox {
 		  $$ = $2;
 		  set_comment($2, $1);
 		}
-		| parm_no_dox doxygen_post_comment {
+		| parm_no_dox DOXYGENPOSTSTRING {
 		  $$ = $1;
 		  set_comment($1, $2);
 		}
@@ -5999,19 +5970,19 @@ enumlist_item	: optional_ignored_define edecl_with_dox optional_ignored_define {
 edecl_with_dox	: edecl {
 		  $$ = $1;
 		}
-		| doxygen_comment edecl {
+		| DOXYGENSTRING edecl {
 		  $$ = $2;
 		  set_comment($2, $1);
 		}
-		| edecl doxygen_post_comment {
+		| edecl DOXYGENPOSTSTRING {
 		  $$ = $1;
 		  set_comment($1, $2);
 		}
-		| doxygen_post_comment edecl {
+		| DOXYGENPOSTSTRING edecl {
 		  $$ = $2;
 		  set_comment(previousNode, $1);
 		}
-		| doxygen_post_comment edecl doxygen_post_comment {
+		| DOXYGENPOSTSTRING edecl DOXYGENPOSTSTRING {
 		  $$ = $2;
 		  set_comment(previousNode, $1);
 		  set_comment($2, $3);

From dc23904408555b94732443b24cd1be3138eb0075 Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Sun, 26 Jul 2015 18:48:57 +0200
Subject: [PATCH 266/314] Don't duplicate Javadoc from global enum Doxygen
 comments twice.

The commit d52de0f36f570ff9aa0011a10ab6a9023cd8b56c did fix the bug with
missing Javadoc comments for the nested enums, but it also resulted in the
Javadoc being generated twice for global enums, remove the code outputting the
same Javadoc for the second time to fix this.
---
 Source/Modules/java.cxx | 11 +----------
 1 file changed, 1 insertion(+), 10 deletions(-)

diff --git a/Source/Modules/java.cxx b/Source/Modules/java.cxx
index 7af93b589..95348f234 100644
--- a/Source/Modules/java.cxx
+++ b/Source/Modules/java.cxx
@@ -1278,7 +1278,7 @@ public:
       if (doxygen && doxygenTranslator->hasDocumentation(n)){
         String *doxygen_comments=doxygenTranslator->getDocumentation(n);
         if(comment_creation_chatter) {
-          Printf(enum_code, "/* This was generated from enumvalueDeclaration() */");
+          Printf(enum_code, "/* This was generated from enumDeclaration() */");
         }
         Printv(enum_code, Char(doxygen_comments), NIL);
         Delete(doxygen_comments);
@@ -1377,15 +1377,6 @@ public:
 	  Printv(f_enum, typemapLookup(n, "javaimports", typemap_lookup_type, WARN_NONE), // Import statements
 		 "\n\n", NIL);
 	  
-	  //translate and write javadoc comment if flagged
-	  if (doxygen && doxygenTranslator->hasDocumentation(n)){
-	    String *doxygen_comments=doxygenTranslator->getDocumentation(n);
-	    if(comment_creation_chatter)
-	      Printf(f_enum, "/* This was generated from enumDeclaration() */");
-	    Printv(f_enum, Char(doxygen_comments), NIL);
-	    Delete(doxygen_comments);
-	  }
-	  
 	  Printv(f_enum, enum_code, "\n", NIL);
 
 	  Printf(f_enum, "\n");

From 68492869fdef7736509da73a1f8543539d1e3ac3 Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Mon, 27 Jul 2015 04:25:48 +0200
Subject: [PATCH 267/314] Reset "_last" for all but first enum elements.

There is an implicit assumption (see TypePass::enumvalueDeclaration()) that
only the first enum element has a non-null "_last" attribute, but this was
broken by the latest enum-related grammar changes as the second enum element
also had "_last" set, coming from the new "enumlist_tail" production. This
resulted in wrong values being used for the second (only) element.

Fix this by explicitly resetting "_last" of enumlist_tail to NULL when
building the semantic value associated with it.
---
 Source/CParse/parser.y | 1 +
 1 file changed, 1 insertion(+)

diff --git a/Source/CParse/parser.y b/Source/CParse/parser.y
index 2051b8ff4..8ef9af198 100644
--- a/Source/CParse/parser.y
+++ b/Source/CParse/parser.y
@@ -5944,6 +5944,7 @@ enumlist	: enumlist_item optional_ignored_define_after_comma {
 		| enumlist_item enumlist_tail optional_ignored_define_after_comma {
 		  set_nextSibling($1, $2);
 		  Setattr($1,"_last",Getattr($2,"_last"));
+		  Setattr($2,"_last",NULL);
 		  $$ = $1;
 		}
 		| optional_ignored_define {

From 86531935b5cb36c38a22cd0826318ce20f5c2c75 Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Mon, 27 Jul 2015 04:29:46 +0200
Subject: [PATCH 268/314] Fix harmless MSVC warning in DoxygenTranslator code.

Explicitly compare pointer with NULL instead of implicitly converting it to
bool as this resulted in MSVS "warning C4800: forcing value to bool 'true' or
'false' (performance warning)".
---
 Source/DoxygenTranslator/src/DoxygenTranslator.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Source/DoxygenTranslator/src/DoxygenTranslator.cpp b/Source/DoxygenTranslator/src/DoxygenTranslator.cpp
index 3ea92e03b..93314b19d 100644
--- a/Source/DoxygenTranslator/src/DoxygenTranslator.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenTranslator.cpp
@@ -25,7 +25,7 @@ DoxygenTranslator::~DoxygenTranslator() {
 
 
 bool DoxygenTranslator::hasDocumentation(Node *node) {
-  return getDoxygenComment(node);
+  return getDoxygenComment(node) != NULL;
 }
 
 

From e80d9eead6417b5dedb3b8f04ebd476e6b148e1f Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Mon, 27 Jul 2015 04:35:31 +0200
Subject: [PATCH 269/314] Display JAVA_HOME value in "make java_version".

This can be useful for diagnostic purposes when using automated build systems.
---
 Examples/Makefile.in | 1 +
 1 file changed, 1 insertion(+)

diff --git a/Examples/Makefile.in b/Examples/Makefile.in
index 6ba9dac12..aea834625 100644
--- a/Examples/Makefile.in
+++ b/Examples/Makefile.in
@@ -616,6 +616,7 @@ java_run:
 java_version:
 	$(JAVA) -version
 	$(JAVAC) -version || echo "Unknown javac version"
+	echo "JAVA_HOME=\"$(JAVA_HOME)\""
 
 # -----------------------------------------------------------------
 # Cleaning the java examples

From 03d5ea426a8a035a4ff44b2e77954b6076d3c586 Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Mon, 27 Jul 2015 16:12:17 +0200
Subject: [PATCH 270/314] Use JAVA_HOME value in configure to detect Java.

This is simpler than having to use --with-java, --with-javac and
--with-javaincl options and, even more importantly, will usually just work by
default.
---
 appveyor.yml |  2 +-
 configure.ac | 65 +++++++++++++++++++++++++++++++++++++++-------------
 2 files changed, 50 insertions(+), 17 deletions(-)

diff --git a/appveyor.yml b/appveyor.yml
index 25abcb342..dc96d0bca 100755
--- a/appveyor.yml
+++ b/appveyor.yml
@@ -65,7 +65,7 @@ build_script:
 - set CCCL_OPTIONS=--cccl-muffle /W3
 - set CHECK_OPTIONS=CSHARPOPTIONS=-platform:%Platform%
   # Open dummy file descriptor to fix error on cygwin: ./configure: line 560: 0: Bad file descriptor
-- bash -c "exec 0</dev/null && ./autogen.sh && time ./configure --disable-dependency-tracking --disable-ccache CC=cccl CXX=cccl CFLAGS='-O2' CXXFLAGS='-O2' LDFLAGS='--cccl-link /LTCG' PCRE_CFLAGS='-I%PCRE_ROOT%/include -DPCRE_STATIC' PCRE_LIBS='-L%PCRE_ROOT%/lib/v110/%PCRE_PLATFORM%/Release/static/utf8 -lpcre8' --with-java='%JAVA_HOME%/bin/java.exe' --with-javac='%JAVA_HOME%/bin/javac.exe' --with-javaincl='%JAVA_HOME%/include' --without-perl5 --without-go --with-boost=C:/Libraries/boost || cat config.log"
+- bash -c "exec 0</dev/null && ./autogen.sh && time ./configure --disable-dependency-tracking --disable-ccache CC=cccl CXX=cccl CFLAGS='-O2' CXXFLAGS='-O2' LDFLAGS='--cccl-link /LTCG' PCRE_CFLAGS='-I%PCRE_ROOT%/include -DPCRE_STATIC' PCRE_LIBS='-L%PCRE_ROOT%/lib/v110/%PCRE_PLATFORM%/Release/static/utf8 -lpcre8' --without-perl5 --without-go --with-boost=C:/Libraries/boost || cat config.log"
 - bash -c "time make -s"
 
 test_script:
diff --git a/configure.ac b/configure.ac
index 713680f59..8326cf514 100644
--- a/configure.ac
+++ b/configure.ac
@@ -1193,14 +1193,42 @@ AC_MSG_NOTICE([Disabling Java])
 JAVA=
 else
 
+dnl Platform-specific Java detection logic.
+case $host in
+  *-*-cygwin*)
+    dnl Ensure that JAVA_HOME is in the form we can use, it's typically set to Windows path by the installer.
+    if test -n "$JAVA_HOME"; then
+      JAVA_HOME=`cygpath --mixed "$JAVA_HOME"`
+    fi
+    ;;
+  *-*-darwin*)
+    dnl Under OS X JAVA_HOME is not set by default, try to set it to the default value.
+    if test -z "$JAVA_HOME"; then
+      JAVA_HOME=`/usr/libexec/java_home`
+    fi
+    ;;
+esac
+
 if test "x$JAVABIN" = xyes; then
-  AC_CHECK_PROGS(JAVA, java kaffe guavac)
+  if test -x "$JAVA_HOME/bin/java"; then
+    AC_MSG_CHECKING(for java)
+    JAVA="$JAVA_HOME/bin/java"
+    AC_MSG_RESULT($JAVA)
+  else
+    AC_CHECK_PROGS(JAVA, java kaffe guavac)
+  fi
 else
   JAVA="$JAVABIN"
 fi
 
 if test -z "$JAVACBIN"; then
-  AC_CHECK_PROGS(JAVAC, javac)
+  if test -x "$JAVA_HOME/bin/javac"; then
+    AC_MSG_CHECKING(for javac)
+    JAVAC="$JAVA_HOME/bin/javac"
+    AC_MSG_RESULT($JAVAC)
+  else
+    AC_CHECK_PROGS(JAVAC, javac)
+  fi
 else
   JAVAC="$JAVACBIN"
 fi
@@ -1210,22 +1238,27 @@ AC_ARG_WITH(javaincl, [  --with-javaincl=path    Set location of Java include di
 
 JAVAINC=""
 if test -z "$JAVAINCDIR" ; then
-  JAVAINCDIR="/usr/j2sdk*/include /usr/local/j2sdk*/include /usr/jdk*/include /usr/local/jdk*/include /opt/j2sdk*/include /opt/jdk*/include /usr/java/include /usr/java/j2sdk*/include /usr/java/jdk*/include /usr/local/java/include /opt/java/include /usr/include/java /usr/local/include/java /usr/lib/java/include /usr/lib/jvm/java*/include /usr/lib64/jvm/java*/include /usr/include/kaffe /usr/local/include/kaffe /usr/include"
+  if test -r "$JAVA_HOME/include/jni.h"; then
+    JAVAINCDIR="$JAVA_HOME/include"
+    JAVAINC=-I\"$JAVAINCDIR\"
+  else
+    JAVAINCDIR="/usr/j2sdk*/include /usr/local/j2sdk*/include /usr/jdk*/include /usr/local/jdk*/include /opt/j2sdk*/include /opt/jdk*/include /usr/java/include /usr/java/j2sdk*/include /usr/java/jdk*/include /usr/local/java/include /opt/java/include /usr/include/java /usr/local/include/java /usr/lib/java/include /usr/lib/jvm/java*/include /usr/lib64/jvm/java*/include /usr/include/kaffe /usr/local/include/kaffe /usr/include"
 
-  # Add in default installation directory on Windows for Cygwin
-  case $host in
-  *-*-cygwin* | *-*-mingw*) JAVAINCDIR="c:/Program*Files*/Java/jdk*/include d:/Program*Files*/Java/jdk*/include c:/j2sdk*/include d:/j2sdk*/include c:/jdk*/include d:/jdk*/include $JAVAINCDIR";;
-  *-*-darwin*) JAVAINCDIR="/System/Library/Frameworks/JavaVM.framework/Headers $JAVAINCDIR";;
-  *);;
-  esac
+    # Add in default installation directory on Windows for Cygwin
+    case $host in
+    *-*-cygwin* | *-*-mingw*) JAVAINCDIR="c:/Program*Files*/Java/jdk*/include d:/Program*Files*/Java/jdk*/include c:/j2sdk*/include d:/j2sdk*/include c:/jdk*/include d:/jdk*/include $JAVAINCDIR";;
+    *-*-darwin*) JAVAINCDIR="/System/Library/Frameworks/JavaVM.framework/Headers $JAVAINCDIR";;
+    *);;
+    esac
 
-  for d in $JAVAINCDIR ; do
-    if test -r "$d/jni.h" ; then
-      JAVAINCDIR=$d
-      JAVAINC=-I\"$d\"
-      break
-    fi
-  done
+    for d in $JAVAINCDIR ; do
+      if test -r "$d/jni.h" ; then
+	JAVAINCDIR=$d
+	JAVAINC=-I\"$d\"
+	break
+      fi
+    done
+  fi
 else
   if test -r "$JAVAINCDIR/jni.h" ; then
     JAVAINC=-I\"$JAVAINCDIR\"

From b472a01ae89e7b697188e215a6505cfeb81e9b75 Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Mon, 27 Jul 2015 17:19:36 +0200
Subject: [PATCH 271/314] Remove executable permission from appveyor.yml.

This is not an executable file.
---
 appveyor.yml | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 mode change 100755 => 100644 appveyor.yml

diff --git a/appveyor.yml b/appveyor.yml
old mode 100755
new mode 100644

From 658f92a993a3c831f73cbc0a79dfc1ce7dd0dc7f Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Mon, 27 Jul 2015 17:17:16 +0200
Subject: [PATCH 272/314] Use correct separator in Java class path under
 Windows.

A semicolon must be used there and not a colon as under Unix.
---
 Examples/test-suite/java/Makefile.in |  3 ++-
 configure.ac                         | 11 +++++++++++
 2 files changed, 13 insertions(+), 1 deletion(-)

diff --git a/Examples/test-suite/java/Makefile.in b/Examples/test-suite/java/Makefile.in
index 3b2e1e0d9..6dcc62f26 100644
--- a/Examples/test-suite/java/Makefile.in
+++ b/Examples/test-suite/java/Makefile.in
@@ -6,6 +6,7 @@ LANGUAGE     = java
 JAVA         = @JAVA@
 JAVAC        = @JAVAC@
 JAVAFLAGS    = -Xcheck:jni
+JAVA_CLASSPATH_SEP := @JAVA_CLASSPATH_SEP@
 SCRIPTSUFFIX = _runme.java
 
 srcdir       = @srcdir@
@@ -96,7 +97,7 @@ setup = \
 # Doxygen test cases need to be compiled together with the CommentsParser class
 # which depends on com.sun.javadoc package which is located in this JAR.
 JAVA_CLASSPATH := .
-$(DOXYGEN_TEST_CASES:=.cpptest): JAVA_CLASSPATH := "$(JAVA_HOME)/lib/tools.jar":.
+$(DOXYGEN_TEST_CASES:=.cpptest): JAVA_CLASSPATH := "$(JAVA_HOME)/lib/tools.jar$(JAVA_CLASSPATH_SEP)."
 $(DOXYGEN_TEST_CASES:=.cpptest): DOXYGEN_COMMENT_PARSER := $(srcdir)/CommentParser.java
 
 # Compiles java files then runs the testcase. A testcase is only run if
diff --git a/configure.ac b/configure.ac
index 8326cf514..3c4d192dd 100644
--- a/configure.ac
+++ b/configure.ac
@@ -1200,12 +1200,22 @@ case $host in
     if test -n "$JAVA_HOME"; then
       JAVA_HOME=`cygpath --mixed "$JAVA_HOME"`
     fi
+    dnl Java uses semicolons and not colons as separators in its classes search path under Windows.
+    JAVA_CLASSPATH_SEP=";"
+    ;;
+  *-*-mingw*)
+    JAVA_CLASSPATH_SEP=";"
     ;;
   *-*-darwin*)
     dnl Under OS X JAVA_HOME is not set by default, try to set it to the default value.
     if test -z "$JAVA_HOME"; then
       JAVA_HOME=`/usr/libexec/java_home`
     fi
+    JAVA_CLASSPATH_SEP=":"
+    ;;
+  *)
+    dnl Assume generic Unix.
+    JAVA_CLASSPATH_SEP=":"
     ;;
 esac
 
@@ -1344,6 +1354,7 @@ fi
 AC_SUBST(JAVA)
 AC_SUBST(JAVAC)
 AC_SUBST(JAVAINC)
+AC_SUBST(JAVA_CLASSPATH_SEP)
 AC_SUBST(JAVADYNAMICLINKING)
 AC_SUBST(JAVALIBRARYPREFIX)
 AC_SUBST(JAVASO)

From 148bcab7a0d25ce92b97b3030b801acc13268b45 Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Mon, 12 Dec 2016 01:20:55 +0100
Subject: [PATCH 273/314] Switch Python Doxygen unit tests to use
 inspect.getdoc()

Using the standard inspect module instead of accessing __doc__ directly allows
the tests to pass both when using and not using -builtin, as whitespace-only
differences between the docstrings don't matter then because inspect.getdoc()
removes the indentation and the leading and trailing spaces.

This is similar to what had been already done for python_docstring unit test
in fa282b3540c87927fc3562bd0f0863accf6a853f.
---
 .../python/doxygen_basic_notranslate_runme.py | 91 +++++++++----------
 .../python/doxygen_basic_translate_runme.py   | 46 +++++-----
 .../test-suite/python/doxygen_ignore_runme.py | 13 ++-
 .../python/doxygen_misc_constructs_runme.py   | 86 ++++++++----------
 .../python/doxygen_parsing_runme.py           | 58 +++++-------
 .../doxygen_translate_all_tags_runme.py       | 88 ++++++------------
 .../python/doxygen_translate_links_runme.py   |  9 +-
 .../python/doxygen_translate_runme.py         | 24 ++---
 8 files changed, 171 insertions(+), 244 deletions(-)

diff --git a/Examples/test-suite/python/doxygen_basic_notranslate_runme.py b/Examples/test-suite/python/doxygen_basic_notranslate_runme.py
index 90a0897c3..bf2703c21 100644
--- a/Examples/test-suite/python/doxygen_basic_notranslate_runme.py
+++ b/Examples/test-suite/python/doxygen_basic_notranslate_runme.py
@@ -1,74 +1,65 @@
 #!/usr/bin/python
 
 import doxygen_basic_notranslate
+import inspect
 import string
 import sys
 import commentVerifier
 
-commentVerifier.check(doxygen_basic_notranslate.function.__doc__,
-    r"""
- \brief
- Brief description.
+commentVerifier.check(inspect.getdoc(doxygen_basic_notranslate.function),
+    r"""\brief
+Brief description.
 
- The comment text
- \author Some author
- \return Some number
- \sa function2
- """
+The comment text
+\author Some author
+\return Some number
+\sa function2"""
 )
 
-commentVerifier.check(doxygen_basic_notranslate.function2.__doc__,
-    r"""
- A test of a very very very very very very very very very very very very very very very very
- very very very very very long comment string.
- """
+commentVerifier.check(inspect.getdoc(doxygen_basic_notranslate.function2),
+    r"""A test of a very very very very very very very very very very very very very very very very
+very very very very very long comment string."""
 )
 
-commentVerifier.check(doxygen_basic_notranslate.function3.__doc__,
-    r""" *Overload 1:*
+commentVerifier.check(inspect.getdoc(doxygen_basic_notranslate.function3),
+    r"""*Overload 1:*
 
- A test for overloaded functions
- This is function \b one
+A test for overloaded functions
+This is function \b one
 
- |
+|
 
- *Overload 2:*
+*Overload 2:*
 
- A test for overloaded functions
- This is function \b two"""
+A test for overloaded functions
+This is function \b two"""
 )
 
-commentVerifier.check(doxygen_basic_notranslate.function4.__doc__,
-    r"""
- A test of some mixed tag usage
- \if CONDITION
- This \a code fragment shows us something \.
- \par Minuses:
- \arg it's senseless
- \arg it's stupid
- \arg it's null
+commentVerifier.check(inspect.getdoc(doxygen_basic_notranslate.function4),
+    r"""A test of some mixed tag usage
+\if CONDITION
+This \a code fragment shows us something \.
+\par Minuses:
+\arg it's senseless
+\arg it's stupid
+\arg it's null
 
- \warning This may not work as expected
+\warning This may not work as expected
 
- \code
- int main() { while(true); }
- \endcode
- \endif
- """
+\code
+int main() { while(true); }
+\endcode
+\endif"""
 )
-commentVerifier.check(doxygen_basic_notranslate.function5.__doc__,
-    r""" This is a post comment. """
+commentVerifier.check(inspect.getdoc(doxygen_basic_notranslate.function5),
+    r"""This is a post comment. """
 )
-commentVerifier.check(doxygen_basic_notranslate.function6.__doc__,
-    r"""
- Test for default args
- @param a Some parameter, default is 42
- """
+commentVerifier.check(inspect.getdoc(doxygen_basic_notranslate.function6),
+    r"""Test for default args
+@param a Some parameter, default is 42"""
 )
-commentVerifier.check(doxygen_basic_notranslate.function7.__doc__,
-    r"""
- Test for a parameter with difficult type
- (mostly for python)
- @param a Very strange param
- """
+commentVerifier.check(inspect.getdoc(doxygen_basic_notranslate.function7),
+    r"""Test for a parameter with difficult type
+(mostly for python)
+@param a Very strange param"""
 )
diff --git a/Examples/test-suite/python/doxygen_basic_translate_runme.py b/Examples/test-suite/python/doxygen_basic_translate_runme.py
index a93f75e6f..f566086e1 100644
--- a/Examples/test-suite/python/doxygen_basic_translate_runme.py
+++ b/Examples/test-suite/python/doxygen_basic_translate_runme.py
@@ -1,13 +1,13 @@
 #!/usr/bin/python
 
 import doxygen_basic_translate
+import inspect
 import string
 import sys
 import commentVerifier
 
-commentVerifier.check(doxygen_basic_translate.function.__doc__,
-    """
-
+commentVerifier.check(inspect.getdoc(doxygen_basic_translate.function),
+    """\
 Brief description.
 
 The comment text.
@@ -19,12 +19,12 @@ Author: Some author
 
 See also: function2"""
 )
-commentVerifier.check(doxygen_basic_translate.function2.__doc__,
-    """
+commentVerifier.check(inspect.getdoc(doxygen_basic_translate.function2),
+    """\
 A test of a very very very very very very very very very very very very very very very very
 very very very very very long comment string."""
 )
-commentVerifier.check(doxygen_basic_translate.function3.__doc__,
+commentVerifier.check(inspect.getdoc(doxygen_basic_translate.function3),
     """*Overload 1:*
 
 A test for overloaded functions
@@ -37,8 +37,8 @@ This is function **one**
 A test for overloaded functions
 This is function **two**"""
 )
-commentVerifier.check(doxygen_basic_translate.function4.__doc__,
-    """
+commentVerifier.check(inspect.getdoc(doxygen_basic_translate.function4),
+    """\
 A test of some mixed tag usage
 If: CONDITION {
 This *code* fragment shows us something .
@@ -56,31 +56,31 @@ Warning: This may not work as expected
 
 }"""
 )
-commentVerifier.check(doxygen_basic_translate.function5.__doc__,
-    """ This is a post comment."""
+commentVerifier.check(inspect.getdoc(doxygen_basic_translate.function5),
+    """This is a post comment."""
 )
-commentVerifier.check(doxygen_basic_translate.function6.__doc__,
-    """
+commentVerifier.check(inspect.getdoc(doxygen_basic_translate.function6),
+    """\
 Test for default args
 :type a: int
 :param a: Some parameter, default is 42"""
 )
-commentVerifier.check(doxygen_basic_translate.function7.__doc__,
-    """
+commentVerifier.check(inspect.getdoc(doxygen_basic_translate.function7),
+    """\
 Test for a parameter with difficult type
 (mostly for python)
 :type a: :py:class:`Shape`
 :param a: Very strange param"""
 )
 
-commentVerifier.check(doxygen_basic_translate.Atan2.__doc__,
-    """
-    Multiple parameters test.
+commentVerifier.check(inspect.getdoc(doxygen_basic_translate.Atan2),
+    """\
+Multiple parameters test.
 
-    :type y: float
-    :param y: Vertical coordinate.
-    :type x: float
-    :param x: Horizontal coordinate.
-    :rtype: float
-    :return: Arc tangent of ``y/x``."""
+:type y: float
+:param y: Vertical coordinate.
+:type x: float
+:param x: Horizontal coordinate.
+:rtype: float
+:return: Arc tangent of ``y/x``."""
 )
diff --git a/Examples/test-suite/python/doxygen_ignore_runme.py b/Examples/test-suite/python/doxygen_ignore_runme.py
index 3d407021d..9e2e73da7 100644
--- a/Examples/test-suite/python/doxygen_ignore_runme.py
+++ b/Examples/test-suite/python/doxygen_ignore_runme.py
@@ -1,20 +1,19 @@
 #!/usr/bin/python
 
 import doxygen_ignore
+import inspect
 import commentVerifier
 
-commentVerifier.check(doxygen_ignore.func.__doc__,
-    r"""
-    A contrived example of ignoring too many commands in one comment.
+commentVerifier.check(inspect.getdoc(doxygen_ignore.func),
+    """\
+A contrived example of ignoring too many commands in one comment.
 
 
 
 
 
 
-    This is specific to **Python**.
+This is specific to **Python**.
 
 
-    Command ignored, but anything here is still included.
-
-    """)
+Command ignored, but anything here is still included.""")
diff --git a/Examples/test-suite/python/doxygen_misc_constructs_runme.py b/Examples/test-suite/python/doxygen_misc_constructs_runme.py
index 3dc083b6b..316d7e69b 100644
--- a/Examples/test-suite/python/doxygen_misc_constructs_runme.py
+++ b/Examples/test-suite/python/doxygen_misc_constructs_runme.py
@@ -1,14 +1,14 @@
 #!/usr/bin/python
 
 import doxygen_misc_constructs
+import inspect
 import string
 import sys
 import commentVerifier
 
 
-commentVerifier.check(doxygen_misc_constructs.getAddress.__doc__,
-    r"""
-Returns address of file line.
+commentVerifier.check(inspect.getdoc(doxygen_misc_constructs.getAddress),
+    r"""Returns address of file line.
 
 :type fileName: int
 :param fileName: name of the file, where the source line is located
@@ -17,12 +17,10 @@ Returns address of file line.
 :type isGetSize: boolean
 :param isGetSize: if set, for every object location both address and size are returned
 
-Connection::getId() 
-""")
+Connection::getId() """)
 
-commentVerifier.check(doxygen_misc_constructs.CConnectionConfig.__doc__,
-    r"""
-This class contains information for connection to winIDEA. Its methods
+commentVerifier.check(inspect.getdoc(doxygen_misc_constructs.CConnectionConfig),
+    r"""This class contains information for connection to winIDEA. Its methods
 return reference to self, so we can use it like this:
 
 CConnectionConfig config = new CConnectionConfig();
@@ -34,69 +32,59 @@ used for unspecified parameters.
 
 
 
-advancedWinIDEALaunching.py Python example.
-""")
+advancedWinIDEALaunching.py Python example.""")
 
-commentVerifier.check(doxygen_misc_constructs.waitTime.__doc__,
-    r"""
-Determines how long the ``isystem.connect`` should wait for running
+commentVerifier.check(inspect.getdoc(doxygen_misc_constructs.waitTime),
+    r"""Determines how long the ``isystem.connect`` should wait for running
 instances to respond. Only one of ``lfWaitXXX`` flags from IConnect::ELaunchFlags
 may be specified."""
 )
 
-commentVerifier.check(doxygen_misc_constructs.getConnection.__doc__,
-    r"""
-
-This function returns connection id."""
+commentVerifier.check(inspect.getdoc(doxygen_misc_constructs.getConnection),
+    r"""This function returns connection id."""
 )
 
 
-commentVerifier.check(doxygen_misc_constructs.getFirstLetter.__doc__,
+commentVerifier.check(inspect.getdoc(doxygen_misc_constructs.getFirstLetter),
     r''
 )
 
-commentVerifier.check(doxygen_misc_constructs.ClassWithNestedEnum.__doc__,
-    r"""
-Class description."""
+commentVerifier.check(inspect.getdoc(doxygen_misc_constructs.ClassWithNestedEnum),
+    r"""Class description."""
 )
 
-commentVerifier.check(doxygen_misc_constructs.showList.__doc__,
-    r"""
-        An example of a list in a documentation comment.
+commentVerifier.check(inspect.getdoc(doxygen_misc_constructs.showList),
+    r"""An example of a list in a documentation comment.
 
-            - The first item of the list.
-            - The second list item, on
-              several indented lines,
-              showing that the indentation
-              is preserved.
-            - And the final list item after it.
+    - The first item of the list.
+    - The second list item, on
+      several indented lines,
+      showing that the indentation
+      is preserved.
+    - And the final list item after it.
 
-        And this is not a list item any more."""
+And this is not a list item any more."""
 )
 
-commentVerifier.check(doxygen_misc_constructs.isNoSpaceValidA.__doc__,
-    r"""This comment without space after '*' is valid in Doxygen.
-"""
+commentVerifier.check(inspect.getdoc(doxygen_misc_constructs.isNoSpaceValidA),
+    r"""This comment without space after '*' is valid in Doxygen."""
 )
 
-commentVerifier.check(doxygen_misc_constructs.isNoSpaceValidB.__doc__,
-    r""".This comment without space after '*' is valid in Doxygen.
-"""
+commentVerifier.check(inspect.getdoc(doxygen_misc_constructs.isNoSpaceValidB),
+    r""".This comment without space after '*' is valid in Doxygen."""
 )
 
-commentVerifier.check(doxygen_misc_constructs.isNoSpaceValidC.__doc__,
+commentVerifier.check(inspect.getdoc(doxygen_misc_constructs.isNoSpaceValidC),
     r''
 )
 
-commentVerifier.check(doxygen_misc_constructs.backslashA.__doc__,
-    r"""
-Backslash following``word`` is a valid doxygen command. Output contains
+commentVerifier.check(inspect.getdoc(doxygen_misc_constructs.backslashA),
+    r"""Backslash following``word`` is a valid doxygen command. Output contains
 'followingword' with 'word' in code font."""
 )
 
-commentVerifier.check(doxygen_misc_constructs.backslashB.__doc__,
-    r"""
-Doxy command without trailing space is ignored - nothing appears
+commentVerifier.check(inspect.getdoc(doxygen_misc_constructs.backslashB),
+    r"""Doxy command without trailing space is ignored - nothing appears
 on output. Standalone \ and '\' get to output.
 Standalone @ and '@' get to output.
 Commands "in quoted \b strings are treated as plain text".
@@ -110,9 +98,8 @@ Commands for escaped symbols:
 $ @ \ & ~ < > # % " . :: @text ::text"""
 )
 
-commentVerifier.check(doxygen_misc_constructs.backslashC.__doc__,
-    r"""
-Backslash e at end of *line* froze SWIG
+commentVerifier.check(inspect.getdoc(doxygen_misc_constructs.backslashC),
+    r"""Backslash e at end of *line* froze SWIG
 *with* old comment parser.
 
 See also: MyClass::fun(char,
@@ -120,9 +107,8 @@ See also: MyClass::fun(char,
 )
 
 
-commentVerifier.check(doxygen_misc_constructs.cycle.__doc__,
-    r"""
-The next line contains expression:
+commentVerifier.check(inspect.getdoc(doxygen_misc_constructs.cycle),
+    r"""The next line contains expression:
 
 ['retVal < 10', 'g_counter == 23 && g_mode & 3']
 
diff --git a/Examples/test-suite/python/doxygen_parsing_runme.py b/Examples/test-suite/python/doxygen_parsing_runme.py
index 883fbd83b..22ad83020 100644
--- a/Examples/test-suite/python/doxygen_parsing_runme.py
+++ b/Examples/test-suite/python/doxygen_parsing_runme.py
@@ -1,72 +1,64 @@
 #!/usr/bin/python
 
 import doxygen_parsing
+import inspect
 import string
 import os
 import sys
 import commentVerifier
 
-commentVerifier.check(doxygen_parsing.someFunction.__doc__,
-    r"""
-The function comment""")
-commentVerifier.check(doxygen_parsing.SomeClass.__doc__,
-    r"""
-The class comment""")
-commentVerifier.check(doxygen_parsing.SomeStruct.__doc__,
-    r"""
-The struct comment""")
+commentVerifier.check(inspect.getdoc(doxygen_parsing.someFunction),
+    "The function comment")
+commentVerifier.check(inspect.getdoc(doxygen_parsing.SomeClass),
+    "The class comment")
+commentVerifier.check(inspect.getdoc(doxygen_parsing.SomeStruct),
+    "The struct comment")
 
 # There doesn't seem to be any way to specify the doc string for __init__ when
 # using "-builtin" (see http://stackoverflow.com/q/11913492/15275), so skip
 # this test in this case.
 if str(os.environ.get('SWIG_FEATURES')).find('-builtin') == -1:
-    commentVerifier.check(doxygen_parsing.SomeAnotherClass.__init__.__doc__,
-    r""" *Overload 1:*
- First overloaded constructor.
+    commentVerifier.check(inspect.getdoc(doxygen_parsing.SomeAnotherClass.__init__),
+    r"""*Overload 1:*
+First overloaded constructor.
 
- |
+|
 
- *Overload 2:*
- Second overloaded constructor.""")
+*Overload 2:*
+Second overloaded constructor.""")
 
-commentVerifier.check(doxygen_parsing.SomeAnotherClass.classMethod.__doc__,
-    r"""
-The class method comment.
+commentVerifier.check(inspect.getdoc(doxygen_parsing.SomeAnotherClass.classMethod),
+    r"""The class method comment.
 
 SomeAnotherClass#classMethodExtended(int, int) a link text""")
-commentVerifier.check(doxygen_parsing.SomeAnotherClass.classMethodExtended.__doc__,
-    r"""
-The class method with parameter
+commentVerifier.check(inspect.getdoc(doxygen_parsing.SomeAnotherClass.classMethodExtended),
+    r"""The class method with parameter
 
 :type a: int
 :param a: Parameter a
 :type b: int
 :param b: Parameter b"""
 )
-commentVerifier.check(doxygen_parsing.SomeAnotherClass.classMethodExtended2.__doc__,
-    r"""
-The class method with parameter
+commentVerifier.check(inspect.getdoc(doxygen_parsing.SomeAnotherClass.classMethodExtended2),
+    r"""The class method with parameter
 
 :type a: int
 :param a: Parameter a
 :type b: int
 :param b: Parameter b"""
 )
-commentVerifier.check(doxygen_parsing.SomeAnotherStruct.structMethod.__doc__,
-    r"""
-The struct method comment""")
-commentVerifier.check(doxygen_parsing.SomeAnotherStruct.structMethodExtended.__doc__,
-    r"""
-The struct method with parameter
+commentVerifier.check(inspect.getdoc(doxygen_parsing.SomeAnotherStruct.structMethod),
+    r"""The struct method comment""")
+commentVerifier.check(inspect.getdoc(doxygen_parsing.SomeAnotherStruct.structMethodExtended),
+    r"""The struct method with parameter
 
 :type a: int
 :param a: Parameter a
 :type b: int
 :param b: Parameter b"""
 )
-commentVerifier.check(doxygen_parsing.SomeAnotherStruct.structMethodExtended2.__doc__,
-    r"""
-The struct method with parameter
+commentVerifier.check(inspect.getdoc(doxygen_parsing.SomeAnotherStruct.structMethodExtended2),
+    r"""The struct method with parameter
 
 :type a: int
 :param a: Parameter a
diff --git a/Examples/test-suite/python/doxygen_translate_all_tags_runme.py b/Examples/test-suite/python/doxygen_translate_all_tags_runme.py
index c9620040f..f26c44328 100644
--- a/Examples/test-suite/python/doxygen_translate_all_tags_runme.py
+++ b/Examples/test-suite/python/doxygen_translate_all_tags_runme.py
@@ -1,14 +1,14 @@
 #!/usr/bin/python
 
 import doxygen_translate_all_tags
+import inspect
 import string
 import sys
 import commentVerifier
 
 
-commentVerifier.check(doxygen_translate_all_tags.func01.__doc__,
-r"""
-*Hello*
+commentVerifier.check(inspect.getdoc(doxygen_translate_all_tags.func01),
+r"""*Hello*
 
 
 
@@ -39,12 +39,10 @@ Not everything works right now...
 
 .. code-block:: c++
 
-     some test code
-""")
+     some test code""")
 
-commentVerifier.check(doxygen_translate_all_tags.func02.__doc__,
-r"""
-Conditional comment: SOMECONDITION
+commentVerifier.check(inspect.getdoc(doxygen_translate_all_tags.func02),
+r"""Conditional comment: SOMECONDITION
 Some conditional comment
 End of conditional comment.
 
@@ -67,9 +65,8 @@ Deprecated: Now use another function
 This is very large
 and detailed description of some thing""")
 
-commentVerifier.check(doxygen_translate_all_tags.func03.__doc__,
-r"""
-Comment for **func03()**.
+commentVerifier.check(inspect.getdoc(doxygen_translate_all_tags.func03),
+r"""Comment for **func03()**.
 
 
 
@@ -88,10 +85,8 @@ emphazedWord
 Example: someFile.txt
 Some details on using the example""")
 
-commentVerifier.check(doxygen_translate_all_tags.func04.__doc__,
-r"""
-
-:raises: SuperError
+commentVerifier.check(inspect.getdoc(doxygen_translate_all_tags.func04),
+r""":raises: SuperError
 
 
 
@@ -119,12 +114,10 @@ r"""
 
 
 
-This will only appear in hmtl
-""")
+This will only appear in hmtl""")
 
-commentVerifier.check(doxygen_translate_all_tags.func05.__doc__,
-r"""
-If: ANOTHERCONDITION {
+commentVerifier.check(inspect.getdoc(doxygen_translate_all_tags.func05),
+r"""If: ANOTHERCONDITION {
   First part of comment
   If: SECONDCONDITION {
     Nested condition text
@@ -157,9 +150,8 @@ Image: testImage.bmp("Hello, world!")
 Some text
 describing invariant.""")
 
-commentVerifier.check(doxygen_translate_all_tags.func06.__doc__,
-r"""
-Comment for **func06()**.
+commentVerifier.check(inspect.getdoc(doxygen_translate_all_tags.func06),
+r"""Comment for **func06()**.
 
 
 
@@ -181,23 +173,10 @@ someMember Some description follows
 
 
 
-This will only appear in man
+This will only appear in man""")
 
-
-
-
-
-
-
-
-
-
-
-""")
-
-commentVerifier.check(doxygen_translate_all_tags.func07.__doc__,
-r"""
-Comment for **func07()**.
+commentVerifier.check(inspect.getdoc(doxygen_translate_all_tags.func07),
+r"""Comment for **func07()**.
 
 
 
@@ -223,21 +202,10 @@ Maybe even multiline
 
 
 :type a: int
-:param a: the first param
+:param a: the first param""")
 
-
-
-
-""")
-
-commentVerifier.check(doxygen_translate_all_tags.func08.__doc__,
-r"""
-
-
-
-
-
-Text after anchor.
+commentVerifier.check(inspect.getdoc(doxygen_translate_all_tags.func08),
+r"""Text after anchor.
 
 
 
@@ -269,13 +237,10 @@ Another remarks section
 :return: it
 
 :rtype: void
-:return: may return
-""")
+:return: may return""")
 
-commentVerifier.check(doxygen_translate_all_tags.func09.__doc__,
-r"""
-
-This will only appear in RTF
+commentVerifier.check(inspect.getdoc(doxygen_translate_all_tags.func09),
+r"""This will only appear in RTF
 
 
 See also: someOtherMethod
@@ -309,9 +274,8 @@ Since: version 0.0.0.1
 
 :raises: RuntimeError""")
 
-commentVerifier.check(doxygen_translate_all_tags.func10.__doc__,
-r"""
-TODO: Some very important task
+commentVerifier.check(inspect.getdoc(doxygen_translate_all_tags.func10),
+r"""TODO: Some very important task
 
 :type b: float
 :param b: B is mentioned again...
diff --git a/Examples/test-suite/python/doxygen_translate_links_runme.py b/Examples/test-suite/python/doxygen_translate_links_runme.py
index bad1d36ee..f0df1ebc1 100644
--- a/Examples/test-suite/python/doxygen_translate_links_runme.py
+++ b/Examples/test-suite/python/doxygen_translate_links_runme.py
@@ -1,14 +1,14 @@
 #!/usr/bin/python
 
 import doxygen_translate_links
+import inspect
 import string
 import sys
 import commentVerifier
 
 
-commentVerifier.check(doxygen_translate_links.function.__doc__,
-r"""
-Testing typenames converting in @ link
+commentVerifier.check(inspect.getdoc(doxygen_translate_links.function),
+r"""Testing typenames converting in @ link
 
 superFunc(int,std::string)
 Test for std_string member
@@ -37,5 +37,4 @@ some failing params:
 
 See also: superFunc()
 See also: superFunc()
-See also: superFunc()
-""")
+See also: superFunc()""")
diff --git a/Examples/test-suite/python/doxygen_translate_runme.py b/Examples/test-suite/python/doxygen_translate_runme.py
index 8ccacc35f..9a2ce53a2 100644
--- a/Examples/test-suite/python/doxygen_translate_runme.py
+++ b/Examples/test-suite/python/doxygen_translate_runme.py
@@ -1,14 +1,14 @@
 #!/usr/bin/python
 
 import doxygen_translate
+import inspect
 import string
 import sys
 import commentVerifier
 
 
-commentVerifier.check(doxygen_translate.function.__doc__,
-r"""
-*Hello*
+commentVerifier.check(inspect.getdoc(doxygen_translate.function),
+r"""*Hello*
 
 * some list item
 
@@ -140,9 +140,8 @@ And here goes simple text"""
 
 
 
-commentVerifier.check(doxygen_translate.htmlFunction.__doc__,
-r"""
-Test for html tags. See Doxygen doc for list of tags recognized by Doxygen.
+commentVerifier.check(inspect.getdoc(doxygen_translate.htmlFunction),
+r"""Test for html tags. See Doxygen doc for list of tags recognized by Doxygen.
 
 This is link ("http://acme.com/index.html")
 **bold**
@@ -222,13 +221,11 @@ Starts a piece of text displayed in a typewriter font.
 *Starts a piece of text displayed in an italic font.*
 
 
-<u>underlined \b bold text - doxy commands are ignored inside 'htmlonly' section </u>
-""")
+<u>underlined \b bold text - doxy commands are ignored inside 'htmlonly' section </u>""")
 
 
-commentVerifier.check(doxygen_translate.htmlTableFunction.__doc__,
-r"""
-The meaning of flags:
+commentVerifier.check(inspect.getdoc(doxygen_translate.htmlTableFunction),
+r"""The meaning of flags:
 
 :type byFlags: int
 :param byFlags: bits marking required items:
@@ -243,9 +240,8 @@ The meaning of flags:
       ``htmlTable...`` functions.""")
 
 
-commentVerifier.check(doxygen_translate.htmlEntitiesFunction.__doc__,
-r"""
-All entities are treated as commands (C)  TM (R)
+commentVerifier.check(inspect.getdoc(doxygen_translate.htmlEntitiesFunction),
+r"""All entities are treated as commands (C)  TM (R)
 should work also<in text
 >
 &

From 31fcda945c1f1b104ac4c5bb8bb61bbdcf3e97bf Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Mon, 12 Dec 2016 22:13:25 +0100
Subject: [PATCH 274/314] Fix error reporting for special characters in Doxygen
 parsing code

Don't use "+" with a "const char*" and "char", this doesn't do what the code
intended to happen.

Thanks clang for the -Wstring-plus-int warning.
---
 Source/DoxygenTranslator/src/DoxygenParser.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Source/DoxygenTranslator/src/DoxygenParser.cpp b/Source/DoxygenTranslator/src/DoxygenParser.cpp
index f60113ccf..ba8882404 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenParser.cpp
@@ -1400,7 +1400,7 @@ size_t DoxygenParser::processNormalComment(size_t pos, const std::string &line)
   default:
     m_tokenListIt = m_tokenList.end();
     printListError(WARN_DOXYGEN_COMMAND_ERROR,
-        "Unknown special character: " + line[pos]);
+        std::string("Unknown special character: ") + line[pos]);
   }
 
   return pos;

From 04a5215665f0320271f6c969678d5818aee48b68 Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Mon, 12 Dec 2016 22:28:57 +0100
Subject: [PATCH 275/314] Fix using com.sun.tools.javadoc package under macOS

Export JAVA_HOME found by configure, so that the Java test suite makefile
could find this package under this directory.
---
 Examples/test-suite/java/Makefile.in | 4 +++-
 configure.ac                         | 1 +
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/Examples/test-suite/java/Makefile.in b/Examples/test-suite/java/Makefile.in
index 986c230cc..ee6011ff8 100644
--- a/Examples/test-suite/java/Makefile.in
+++ b/Examples/test-suite/java/Makefile.in
@@ -6,9 +6,11 @@ LANGUAGE     = java
 JAVA         = @JAVA@
 JAVAC        = @JAVAC@
 JAVAFLAGS    = @JAVAFLAGS@
-JAVA_CLASSPATH_SEP := @JAVA_CLASSPATH_SEP@
+JAVA_CLASSPATH_SEP = @JAVA_CLASSPATH_SEP@
 SCRIPTSUFFIX = _runme.java
 
+JAVA_HOME ?= @JAVA_HOME@
+
 srcdir       = @srcdir@
 top_srcdir   = ../@top_srcdir@
 top_builddir = ../@top_builddir@
diff --git a/configure.ac b/configure.ac
index 7313dbd3f..7b9e8433a 100644
--- a/configure.ac
+++ b/configure.ac
@@ -1391,6 +1391,7 @@ fi
 # Turned off due to spurious warnings in later versions of openjdk-1.8
 # JAVAFLAGS=-Xcheck:jni
 
+AC_SUBST(JAVA_HOME)
 AC_SUBST(JAVA)
 AC_SUBST(JAVAC)
 AC_SUBST(JAVAINC)

From 2b7bf3c85017bcd8817c72fcbba25d36a258fde7 Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Mon, 9 Jan 2017 13:29:03 +0100
Subject: [PATCH 276/314] Fix broken link to java.sun.com in Doxygen
 documentation

Link to the reference documentation of Javadoc at oracle.com instead, it is
more useful than the overview article (which can still be found on Oracle web
site searching for its title).
---
 Doc/Manual/Doxygen.html | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/Doc/Manual/Doxygen.html b/Doc/Manual/Doxygen.html
index 8b63d5b2b..310374358 100644
--- a/Doc/Manual/Doxygen.html
+++ b/Doc/Manual/Doxygen.html
@@ -745,13 +745,12 @@ Here is the list of all Doxygen tags and the description of how they are transla
 
 <p>
 Doxygen has a wealth of tags such as @latexonly that have no
-equivalent in Javadoc.  As a result several tags that have no
+equivalent in Javadoc (all supported tags are listed in
+<a href="http://docs.oracle.com/javase/7/docs/technotes/tools/windows/javadoc.html">Javadoc documentation</a>).
+As a result several tags that have no
 translation (or particular use, such as some linking and section tags)
 are suppressed with their content just printed out (if it has any
-sense, typically text content).  If you are interested in more of the
-specifics of Javadoc, please
-visit <A HREF="http://java.sun.com/j2se/javadoc/writingdoccomments/">How
-to Write Doc Comments for the Javadoc Tool.</A>
+sense, typically text content).
 <br>
 Here is the list of these tags:
 </p>

From 0fa55e4e8080b31b10f24f912b3d0cb44f70e773 Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Fri, 20 Jan 2017 17:06:20 +0100
Subject: [PATCH 277/314] Replace literal "<" with "&lt;" in HTML documentation

Even though browsers manage to display unpaired "<"s correctly, using them is
still wrong and they confuse other tools, e.g. syntax highlighting in the
editors.
---
 Doc/Manual/Doxygen.html | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/Doc/Manual/Doxygen.html b/Doc/Manual/Doxygen.html
index 310374358..c5b50e040 100644
--- a/Doc/Manual/Doxygen.html
+++ b/Doc/Manual/Doxygen.html
@@ -122,7 +122,7 @@ Documenting the code</A>). Here they are:
 </p>
 
 <p>
-Also any of the above with '<' added after comment-starting symbol,
+Also any of the above with '&lt;' added after comment-starting symbol,
 like <i>/**&lt;, /*!&lt;, ///&lt;, </i> or <i> //!&lt;</i> will be
 treated as post-comment and will be assigned to the node before the
 comment.
@@ -164,8 +164,8 @@ After C\C++ expressions at the end of the line:
 </p>
 
 <div class="code"><pre>
-int someVariable = 9; ///< This is a var holding magic number 9
-void doNothing(); ///< This does nothing, nop
+int someVariable = 9; ///&lt; This is a var holding magic number 9
+void doNothing(); ///&lt; This does nothing, nop
 </pre></div>
 
 <p>
@@ -174,7 +174,7 @@ and in some special cases, like function parameter comments:
 
 <div class="code"><pre>
 void someFunction(
-         int a ///< Some parameter 
+         int a ///&lt; Some parameter 
      );
 </pre></div>
 
@@ -185,8 +185,8 @@ or enum element comments:
 <div class="code"><pre>
 enum E_NUMBERS
 {
-    EN_ZERO, ///< The first enum item, gets zero as it's value
-    EN_ONE, ///< The second, EN_ONE=1
+    EN_ZERO, ///&lt; The first enum item, gets zero as it's value
+    EN_ONE, ///&lt; The second, EN_ONE=1
     EN_THREE
 };
 </pre></div>
@@ -623,7 +623,7 @@ Here is the list of all Doxygen tags and the description of how they are transla
 </tr>
 <tr>
 <td>\par</td>
-<td>replaced with &lt;p alt='title'&gt;...&lt/p&gt;</td>
+<td>replaced with &lt;p alt='title'&gt;...&lt;/p&gt;</td>
 </tr>
 <tr>
 <td>\param</td>

From 14b28f592315ffa5340a516babb5b36390265036 Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Fri, 20 Jan 2017 17:08:38 +0100
Subject: [PATCH 278/314] Use slash, not backslash, in "C/C++" in the
 documentation

No real changes, but using backslashes here was really too weird.
---
 Doc/Manual/Doxygen.html | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/Doc/Manual/Doxygen.html b/Doc/Manual/Doxygen.html
index c5b50e040..faea2c7d9 100644
--- a/Doc/Manual/Doxygen.html
+++ b/Doc/Manual/Doxygen.html
@@ -138,7 +138,7 @@ Please note, as SWIG parses input file by itself with strict grammar,
 there is only a limited support for various cases of comment placement
 in the file.
 <br>
-Comments can be placed before C\C++ expressions on separate lines:
+Comments can be placed before C/C++ expressions on separate lines:
 </p>
 
 <div class="code"><pre>
@@ -160,7 +160,7 @@ class Shape {
 </pre></div>
 
 <p>
-After C\C++ expressions at the end of the line:
+After C/C++ expressions at the end of the line:
 </p>
 
 <div class="code"><pre>

From 87ae580d7595367b8ab8e3a9f62c0dbe5e0ad267 Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Wed, 1 Feb 2017 01:38:43 +0100
Subject: [PATCH 279/314] Get rid of unnecessary "typedef enum" in C++ code

No real changes, just remove this C-ism from C++ DoxygenParser class code.
---
 Source/DoxygenTranslator/src/DoxygenParser.h | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/Source/DoxygenTranslator/src/DoxygenParser.h b/Source/DoxygenTranslator/src/DoxygenParser.h
index c1e4994c0..bbb519092 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.h
+++ b/Source/DoxygenTranslator/src/DoxygenParser.h
@@ -24,7 +24,7 @@
 class DoxygenParser {
 private:
 
-  typedef enum {
+  enum DoxyCommandEnum {
     NONE = -1,
     SIMPLECOMMAND,
     COMMANDWORD,
@@ -44,7 +44,7 @@ private:
     PARAGRAPH_END,
     PLAINSTRING,
     COMMAND
-  } DoxyCommandEnum;
+  };
 
 
   /** This class contains parts of Doxygen comment as a token. */

From 71c4e55fd955d6dd405a12bed293034e14fb1afc Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Wed, 1 Feb 2017 01:43:11 +0100
Subject: [PATCH 280/314] Return enum, not untyped int, when classifying
 Doxygen commands

This makes the purpose of DoxygenParser::commandBelongs() more clear and also
allows the compiler to check that we handle all of its possible return values.
And it actually turns out that we didn't, so add the missing values now to
avoid changing the behaviour in any way in this commit, but they will be dealt
with later.
---
 Source/DoxygenTranslator/src/DoxygenParser.cpp | 10 +++++++++-
 Source/DoxygenTranslator/src/DoxygenParser.h   |  2 +-
 2 files changed, 10 insertions(+), 2 deletions(-)

diff --git a/Source/DoxygenTranslator/src/DoxygenParser.cpp b/Source/DoxygenTranslator/src/DoxygenParser.cpp
index ba8882404..dce394798 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenParser.cpp
@@ -128,7 +128,8 @@ void DoxygenParser::printTree(const DoxygenEntityList &rootList)
   }
 }
 
-int DoxygenParser::commandBelongs(const std::string &theCommand)
+DoxygenParser::DoxyCommandEnum
+DoxygenParser::commandBelongs(const std::string &theCommand)
 {
   DoxyCommandsMapIt it = doxygenCommands.find(stringToLower(theCommand));
 
@@ -1046,6 +1047,13 @@ int DoxygenParser::addCommand(const std::string &commandString,
     return addCommandHtmlEntity(theCommand, tokList, doxyList);
   case COMMAND_IGNORE:
     return ignoreCommand(commandString, tokList, doxyList);
+  case NONE:
+  case END_LINE:
+  case PARAGRAPH_END:
+  case PLAINSTRING:
+  case COMMAND:
+    // TODO: Ensure that these values either are correctly ignored here or can't happen.
+    break;
   }
   return 0;
 }
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.h b/Source/DoxygenTranslator/src/DoxygenParser.h
index bbb519092..753b996d8 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.h
+++ b/Source/DoxygenTranslator/src/DoxygenParser.h
@@ -130,7 +130,7 @@ private:
    * Determines how a command should be handled (what group it belongs to
    * for parsing rules
    */
-  int commandBelongs(const std::string &theCommand);
+  DoxyCommandEnum commandBelongs(const std::string &theCommand);
 
   /*
    *prints the parse tree

From 4e7dad2b76cda59e9970720965faafff6ac09935 Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Wed, 1 Feb 2017 01:53:31 +0100
Subject: [PATCH 281/314] Get rid of meaningless return type of DoxygenParser
 methods

The return value of methods handling various Doxygen commands was never
actually used, so just get rid of it and don't return anything, this makes the
code slightly simpler without any change of functionality.

It also makes the question about why all these functions return "int" (which
should have been "bool" from the beginning) obsolete.
---
 .../DoxygenTranslator/src/DoxygenParser.cpp   | 207 +++++++++---------
 Source/DoxygenTranslator/src/DoxygenParser.h  |  30 +--
 2 files changed, 122 insertions(+), 115 deletions(-)

diff --git a/Source/DoxygenTranslator/src/DoxygenParser.cpp b/Source/DoxygenTranslator/src/DoxygenParser.cpp
index dce394798..88b2863cf 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenParser.cpp
@@ -393,19 +393,20 @@ void DoxygenParser::skipEndOfLine()
   }
 }
 
-int DoxygenParser::addSimpleCommand(const std::string &theCommand,
-                                    DoxygenEntityList &doxyList)
+void
+DoxygenParser::addSimpleCommand(const std::string &theCommand,
+                                DoxygenEntityList &doxyList)
 {
   if (noisy)
     cout << "Parsing " << theCommand << endl;
 
   doxyList.push_back(DoxygenEntity(theCommand));
-  return 1;
 }
 
-int DoxygenParser::addCommandWord(const std::string &theCommand,
-                                  const TokenList &,
-                                  DoxygenEntityList &doxyList)
+void
+DoxygenParser::addCommandWord(const std::string &theCommand,
+                              const TokenList &,
+                              DoxygenEntityList &doxyList)
 {
   if (noisy)
     cout << "Parsing " << theCommand << endl;
@@ -420,17 +421,16 @@ int DoxygenParser::addCommandWord(const std::string &theCommand,
     DoxygenEntityList aNewList;
     aNewList.push_back(DoxygenEntity("plainstd::string", name));
     doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-    return 1;
   } else {
     printListError(WARN_DOXYGEN_COMMAND_ERROR,
         "No word followed " + theCommand + " command. Not added");
   }
-  return 0;
 }
 
-int DoxygenParser::addCommandLine(const std::string &theCommand,
-                                  const TokenList &tokList,
-                                  DoxygenEntityList &doxyList)
+void
+DoxygenParser::addCommandLine(const std::string &theCommand,
+                              const TokenList &tokList,
+                              DoxygenEntityList &doxyList)
 {
   if (noisy)
     cout << "Parsing " << theCommand << endl;
@@ -438,12 +438,12 @@ int DoxygenParser::addCommandLine(const std::string &theCommand,
   DoxygenEntityList aNewList = parse(endOfLine, tokList);
   doxyList.push_back(DoxygenEntity(theCommand, aNewList));
   skipEndOfLine();
-  return 1;
 }
 
-int DoxygenParser::addCommandParagraph(const std::string &theCommand,
-                                       const TokenList &tokList,
-                                       DoxygenEntityList &doxyList)
+void
+DoxygenParser::addCommandParagraph(const std::string &theCommand,
+                                   const TokenList &tokList,
+                                   DoxygenEntityList &doxyList)
 {
   if (noisy)
     cout << "Parsing " << theCommand << endl;
@@ -452,30 +452,30 @@ int DoxygenParser::addCommandParagraph(const std::string &theCommand,
   DoxygenEntityList aNewList;
   aNewList = parse(endOfParagraph, tokList);
   doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-  return 1;
 }
 
-int DoxygenParser::addCommandEndCommand(const std::string &theCommand,
-                                        const TokenList & tokList,
-                                        DoxygenEntityList &doxyList)
+void
+DoxygenParser::addCommandEndCommand(const std::string &theCommand,
+                                    const TokenList & tokList,
+                                    DoxygenEntityList &doxyList)
 {
   if (noisy)
     cout << "Parsing " << theCommand << endl;
   TokenListCIt endCommand = getEndCommand("end" + theCommand, tokList);
   if (endCommand == tokList.end()) {
     printListError(WARN_DOXYGEN_COMMAND_EXPECTED, "Expected end" + theCommand);
-    return 0;
+    return;
   }
   DoxygenEntityList aNewList;
   aNewList = parse(endCommand, tokList);
   m_tokenListIt++;
   doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-  return 1;
 }
 
-int DoxygenParser::addCommandWordParagraph(const std::string &theCommand,
-                                           const TokenList &tokList,
-                                           DoxygenEntityList &doxyList)
+void
+DoxygenParser::addCommandWordParagraph(const std::string &theCommand,
+                                       const TokenList &tokList,
+                                       DoxygenEntityList &doxyList)
 {
   if (noisy)
     cout << "Parsing " << theCommand << endl;
@@ -485,19 +485,19 @@ int DoxygenParser::addCommandWordParagraph(const std::string &theCommand,
   if (name.empty()) {
     printListError(WARN_DOXYGEN_COMMAND_ERROR,
         "No word followed " + theCommand + " command. Not added");
-    return 0;
+    return;
   }
   TokenListCIt endOfParagraph = getEndOfParagraph(tokList);
   DoxygenEntityList aNewList;
   aNewList = parse(endOfParagraph, tokList);
   aNewList.push_front(DoxygenEntity("plainstd::string", name));
   doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-  return 1;
 }
 
-int DoxygenParser::addCommandWordLine(const std::string &theCommand,
-                                      const TokenList & tokList,
-                                      DoxygenEntityList &doxyList)
+void
+DoxygenParser::addCommandWordLine(const std::string &theCommand,
+                                  const TokenList & tokList,
+                                  DoxygenEntityList &doxyList)
 {
   if (noisy)
     cout << "Parsing " << theCommand << endl;
@@ -505,7 +505,7 @@ int DoxygenParser::addCommandWordLine(const std::string &theCommand,
   if (name.empty()) {
     printListError(WARN_DOXYGEN_COMMAND_ERROR,
         "No word followed " + theCommand + " command. Not added");
-    return 0;
+    return;
   }
 
   TokenListCIt endOfLine = getOneLine(tokList);
@@ -513,13 +513,13 @@ int DoxygenParser::addCommandWordLine(const std::string &theCommand,
   aNewList = parse(endOfLine, tokList);
   aNewList.push_front(DoxygenEntity("plainstd::string", name));
   doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-  return 1;
   //else cout << "No line followed " << theCommand <<  " command. Not added" << endl;
 }
 
-int DoxygenParser::addCommandWordOWordOWord(const std::string &theCommand,
-                                            const TokenList &,
-                                            DoxygenEntityList &doxyList)
+void
+DoxygenParser::addCommandWordOWordOWord(const std::string &theCommand,
+                                        const TokenList &,
+                                        DoxygenEntityList &doxyList)
 {
   if (noisy)
     cout << "Parsing " << theCommand << endl;
@@ -528,7 +528,7 @@ int DoxygenParser::addCommandWordOWordOWord(const std::string &theCommand,
   if (name.empty()) {
     printListError(WARN_DOXYGEN_COMMAND_ERROR,
         "No word followed " + theCommand + " command. Not added");
-    return 0;
+    return;
   }
   std::string headerfile = getNextWord();
   std::string headername = getNextWord();
@@ -539,12 +539,12 @@ int DoxygenParser::addCommandWordOWordOWord(const std::string &theCommand,
   if (!headername.empty())
     aNewList.push_back(DoxygenEntity("plainstd::string", headername));
   doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-  return 1;
 }
 
-int DoxygenParser::addCommandOWord(const std::string &theCommand,
-                                   const TokenList &,
-                                   DoxygenEntityList &doxyList)
+void
+DoxygenParser::addCommandOWord(const std::string &theCommand,
+                               const TokenList &,
+                               DoxygenEntityList &doxyList)
 {
   if (noisy)
     cout << "Parsing " << theCommand << endl;
@@ -553,48 +553,48 @@ int DoxygenParser::addCommandOWord(const std::string &theCommand,
   DoxygenEntityList aNewList;
   aNewList.push_back(DoxygenEntity("plainstd::string", name));
   doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-  return 1;
 }
 
-int DoxygenParser::addCommandErrorThrow(const std::string &theCommand,
-                                        const TokenList &tokList,
-                                        DoxygenEntityList &)
+void
+DoxygenParser::addCommandErrorThrow(const std::string &theCommand,
+                                    const TokenList &tokList,
+                                    DoxygenEntityList &)
 {
 
   printListError(WARN_DOXYGEN_COMMAND_ERROR,
       "Encountered: " + theCommand
           + "\nThis command should not have been encountered. Behaviour past this may be unpredictable");
   m_tokenListIt = getOneLine(tokList);
-  return 0;
 }
 
-int DoxygenParser::addCommandHtml(const std::string &theCommand,
-                                  const TokenList &,
-                                  DoxygenEntityList &doxyList)
+void
+DoxygenParser::addCommandHtml(const std::string &theCommand,
+                              const TokenList &,
+                              DoxygenEntityList &doxyList)
 {
   if (noisy)
     cout << "Parsing " << theCommand << endl;
 
   std::string htmlTagArgs = getNextToken();
   doxyList.push_back(DoxygenEntity(theCommand, htmlTagArgs));
-  return 1;
 }
 
-int DoxygenParser::addCommandHtmlEntity(const std::string &theCommand,
-                                        const TokenList &,
-                                        DoxygenEntityList &doxyList)
+void
+DoxygenParser::addCommandHtmlEntity(const std::string &theCommand,
+                                    const TokenList &,
+                                    DoxygenEntityList &doxyList)
 {
   if (noisy)
     cout << "Parsing " << theCommand << endl;
 
   DoxygenEntityList aNewList;
   doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-  return 1;
 }
 
-int DoxygenParser::addCommandUnique(const std::string &theCommand,
-                                    const TokenList &tokList,
-                                    DoxygenEntityList &doxyList)
+void
+DoxygenParser::addCommandUnique(const std::string &theCommand,
+                                const TokenList &tokList,
+                                DoxygenEntityList &doxyList)
 {
 
   static std::map<std::string, std::string> endCommands;
@@ -613,19 +613,19 @@ int DoxygenParser::addCommandUnique(const std::string &theCommand,
     if (key.empty()) {
       printListError(WARN_DOXYGEN_COMMAND_ERROR,
           "No key followed " + theCommand + " command. Not added");
-      return 0;
+      return;
     }
     std::string heading = getNextWord();
     if (key.empty()) {
       printListError(WARN_DOXYGEN_COMMAND_ERROR,
           "No heading followed " + theCommand + " command. Not added");
-      return 0;
+      return;
     }
     std::string title = getNextWord();
     if (title.empty()) {
       printListError(WARN_DOXYGEN_COMMAND_ERROR,
           "No title followed " + theCommand + " command. Not added");
-      return 0;
+      return;
     }
     TokenListCIt endOfParagraph = getEndOfParagraph(tokList);
     aNewList = parse(endOfParagraph, tokList);
@@ -633,7 +633,6 @@ int DoxygenParser::addCommandUnique(const std::string &theCommand,
     aNewList.push_front(DoxygenEntity("plainstd::string", heading));
     aNewList.push_front(DoxygenEntity("plainstd::string", key));
     doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-    return 1;
   }
   // \ingroup (<groupname> [<groupname> <groupname>])
   else if (theCommand == "ingroup") {
@@ -646,7 +645,6 @@ int DoxygenParser::addCommandUnique(const std::string &theCommand,
     if (!name.empty())
       aNewList.push_back(DoxygenEntity("plainstd::string", name));
     doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-    return 1;
   }
   // \par [(paragraph title)] { paragraph }
   else if (theCommand == "par") {
@@ -657,7 +655,6 @@ int DoxygenParser::addCommandUnique(const std::string &theCommand,
     aNewList2 = parse(endOfParagraph, tokList);
     aNewList.splice(aNewList.end(), aNewList2);
     doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-    return 1;
   }
   // \headerfile <header-file> [<header-name>]
   else if (theCommand == "headerfile") {
@@ -668,7 +665,6 @@ int DoxygenParser::addCommandUnique(const std::string &theCommand,
     if (!name.empty())
       aNewList.push_back(DoxygenEntity("plainstd::string", name));
     doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-    return 1;
   }
   // \overload [(function declaration)]
   else if (theCommand == "overload") {
@@ -679,7 +675,6 @@ int DoxygenParser::addCommandUnique(const std::string &theCommand,
       doxyList.push_back(DoxygenEntity(theCommand, aNewList));
     } else
       doxyList.push_back(DoxygenEntity(theCommand));
-    return 1;
   }
   // \weakgroup <name> [(title)]
   else if (theCommand == "weakgroup") {
@@ -689,7 +684,7 @@ int DoxygenParser::addCommandUnique(const std::string &theCommand,
     if (name.empty()) {
       printListError(WARN_DOXYGEN_COMMAND_ERROR,
           "No word followed " + theCommand + " command. Not added");
-      return 0;
+      return;
     }
     DoxygenEntityList aNewList;
     TokenListCIt endOfLine = getOneLine(tokList);
@@ -707,7 +702,7 @@ int DoxygenParser::addCommandUnique(const std::string &theCommand,
     if (name.empty()) {
       printListError(WARN_DOXYGEN_COMMAND_ERROR,
           "No key followed " + theCommand + " command. Not added");
-      return 0;
+      return;
     }
     DoxygenEntityList aNewList;
     aNewList.push_front(DoxygenEntity("plainstd::string", name));
@@ -737,7 +732,7 @@ int DoxygenParser::addCommandUnique(const std::string &theCommand,
     if (name.empty()) {
       printListError(WARN_DOXYGEN_COMMAND_ERROR,
           "No name followed " + theCommand + " command. Not added");
-      return 0;
+      return;
     }
     std::string text = getNextWord();
     aNewList.push_back(DoxygenEntity("plainstd::string", name));
@@ -786,7 +781,7 @@ int DoxygenParser::addCommandUnique(const std::string &theCommand,
     if (file.empty()) {
       printListError(WARN_DOXYGEN_COMMAND_ERROR,
           "No file followed " + theCommand + " command. Not added");
-      return 0;
+      return;
     }
     std::string caption = getNextWord();
     aNewList.push_back(DoxygenEntity("plainstd::string", file));
@@ -802,13 +797,13 @@ int DoxygenParser::addCommandUnique(const std::string &theCommand,
     if (format.empty()) {
       printListError(WARN_DOXYGEN_COMMAND_ERROR,
           "No format followed " + theCommand + " command. Not added");
-      return 0;
+      return;
     }
     std::string file = getNextWord();
     if (file.empty()) {
       printListError(WARN_DOXYGEN_COMMAND_ERROR,
           "No name followed " + theCommand + " command. Not added");
-      return 0;
+      return;
     }
     std::string caption = getNextWord();
     std::string size = getNextWord();
@@ -831,7 +826,7 @@ int DoxygenParser::addCommandUnique(const std::string &theCommand,
       printListError(WARN_DOXYGEN_COMMAND_ERROR,
           "There should be at least one word following the '" + theCommand
               + "' command. Command ignored.");
-      return 0;
+      return;
     }
     DoxygenEntityList aNewList;
     TokenListCIt endOfLine = getOneLine(tokList);
@@ -857,7 +852,7 @@ int DoxygenParser::addCommandUnique(const std::string &theCommand,
       if (cond.empty()) {
         printListError(WARN_DOXYGEN_COMMAND_ERROR,
             "No word followed " + theCommand + " command. Not added");
-        return 0;
+        return;
       }
     }
 
@@ -887,7 +882,7 @@ int DoxygenParser::addCommandUnique(const std::string &theCommand,
     if (endCommand == tokList.end()) {
       printListError(WARN_DOXYGEN_COMMAND_EXPECTED,
           "No corresponding endif found");
-      return 0;
+      return;
     }
 
     DoxygenEntityList aNewList;
@@ -898,7 +893,6 @@ int DoxygenParser::addCommandUnique(const std::string &theCommand,
       aNewList.push_front(DoxygenEntity("plainstd::string", cond));
     doxyList.push_back(DoxygenEntity(theCommand, aNewList));
   }
-  return 0;
 }
 
 String* DoxygenParser::getIgnoreFeature(const std::string& theCommand,
@@ -935,16 +929,17 @@ string DoxygenParser::getIgnoreFeatureEndCommand(const std::string& theCommand)
   return endCommand;
 }
 
-int DoxygenParser::ignoreCommand(const std::string& theCommand,
-                                 const TokenList &tokList,
-                                 DoxygenEntityList &doxyList)
+void
+DoxygenParser::ignoreCommand(const std::string& theCommand,
+                             const TokenList &tokList,
+                             DoxygenEntityList &doxyList)
 {
   const string endCommand = getIgnoreFeatureEndCommand(theCommand);
   if (!endCommand.empty()) {
     TokenListCIt itEnd = getEndCommand(endCommand, tokList);
     if (itEnd == tokList.end()) {
       printListError(WARN_DOXYGEN_COMMAND_EXPECTED, "Expected " + endCommand);
-      return 0;
+      return;
     }
 
     // If we ignore the command, also ignore any whitespace preceding it as we
@@ -975,7 +970,7 @@ int DoxygenParser::ignoreCommand(const std::string& theCommand,
             "Invalid \"doxygen:ignore\" feature \"contents\" attribute \"%s\".\n",
             Char(contents)
           );
-        return 0;
+        return;
       }
     }
 
@@ -996,16 +991,15 @@ int DoxygenParser::ignoreCommand(const std::string& theCommand,
           "Invalid \"doxygen:ignore\" feature \"range\" attribute \"%s\".\n",
           Char(range)
         );
-      return 0;
+      return;
     }
   }
-
-  return 1;
 }
 
-int DoxygenParser::addCommand(const std::string &commandString,
-                              const TokenList &tokList,
-                              DoxygenEntityList &doxyList)
+void
+DoxygenParser::addCommand(const std::string &commandString,
+                          const TokenList &tokList,
+                          DoxygenEntityList &doxyList)
 {
 
   string theCommand = stringToLower(commandString);
@@ -1015,38 +1009,52 @@ int DoxygenParser::addCommand(const std::string &commandString,
     if (noisy)
       cout << "Parsing plain std::string :" << nextPhrase << endl;
     doxyList.push_back(DoxygenEntity("plainstd::string", nextPhrase));
-    return 1;
+    return;
   }
 
   switch (commandBelongs(commandString)) {
   case SIMPLECOMMAND:
-    return addSimpleCommand(theCommand, doxyList);
+    addSimpleCommand(theCommand, doxyList);
+    break;
   case COMMANDWORD:
-    return addCommandWord(theCommand, tokList, doxyList);
+    addCommandWord(theCommand, tokList, doxyList);
+    break;
   case COMMANDLINE:
-    return addCommandLine(theCommand, tokList, doxyList);
+    addCommandLine(theCommand, tokList, doxyList);
+    break;
   case COMMANDPARAGRAPH:
-    return addCommandParagraph(theCommand, tokList, doxyList);
+    addCommandParagraph(theCommand, tokList, doxyList);
+    break;
   case COMMANDENDCOMMAND:
-    return addCommandEndCommand(theCommand, tokList, doxyList);
+    addCommandEndCommand(theCommand, tokList, doxyList);
+    break;
   case COMMANDWORDPARAGRAPH:
-    return addCommandWordParagraph(theCommand, tokList, doxyList);
+    addCommandWordParagraph(theCommand, tokList, doxyList);
+    break;
   case COMMANDWORDLINE:
-    return addCommandWordLine(theCommand, tokList, doxyList);
+    addCommandWordLine(theCommand, tokList, doxyList);
+    break;
   case COMMANDWORDOWORDWORD:
-    return addCommandWordOWordOWord(theCommand, tokList, doxyList);
+    addCommandWordOWordOWord(theCommand, tokList, doxyList);
+    break;
   case COMMANDOWORD:
-    return addCommandOWord(theCommand, tokList, doxyList);
+    addCommandOWord(theCommand, tokList, doxyList);
+    break;
   case COMMANDERRORTHROW:
-    return addCommandErrorThrow(theCommand, tokList, doxyList);
+    addCommandErrorThrow(theCommand, tokList, doxyList);
+    break;
   case COMMANDUNIQUE:
-    return addCommandUnique(theCommand, tokList, doxyList);
+    addCommandUnique(theCommand, tokList, doxyList);
+    break;
   case COMMAND_HTML:
-    return addCommandHtml(theCommand, tokList, doxyList);
+    addCommandHtml(theCommand, tokList, doxyList);
+    break;
   case COMMAND_HTML_ENTITY:
-    return addCommandHtmlEntity(theCommand, tokList, doxyList);
+    addCommandHtmlEntity(theCommand, tokList, doxyList);
+    break;
   case COMMAND_IGNORE:
-    return ignoreCommand(commandString, tokList, doxyList);
+    ignoreCommand(commandString, tokList, doxyList);
+    break;
   case NONE:
   case END_LINE:
   case PARAGRAPH_END:
@@ -1055,7 +1063,6 @@ int DoxygenParser::addCommand(const std::string &commandString,
     // TODO: Ensure that these values either are correctly ignored here or can't happen.
     break;
   }
-  return 0;
 }
 
 /**
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.h b/Source/DoxygenTranslator/src/DoxygenParser.h
index 753b996d8..521d2a02f 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.h
+++ b/Source/DoxygenTranslator/src/DoxygenParser.h
@@ -240,7 +240,7 @@ private:
    * Plain commands, such as newline etc, they contain no other data
    *  \n \\ \@ \& \$ \# \< \> \%
    */
-  int addSimpleCommand(const std::string &theCommand,
+  void addSimpleCommand(const std::string &theCommand,
 		                 DoxygenEntityList &doxyList);
   /*
    * CommandWord
@@ -250,7 +250,7 @@ private:
    * "relates", "namespace", "relatesalso","anchor", "dontinclude", "include",
    * "includelineno"
    */
-  int addCommandWord(const std::string &theCommand,
+  void addCommandWord(const std::string &theCommand,
 		               const TokenList &tokList,
 		               DoxygenEntityList &doxyList);
   /*
@@ -260,7 +260,7 @@ private:
    * "addindex", "fn", "name", "line", "var", "skipline", "typedef", "skip",
    * "until", "property"
    */
-  int addCommandLine(const std::string &theCommand,
+  void addCommandLine(const std::string &theCommand,
 		               const TokenList &tokList,
 		               DoxygenEntityList &doxyList);
   /*
@@ -271,7 +271,7 @@ private:
    * "details", "invariant", "deprecated", "date", "note", "warning",
    * "version", "todo", "bug", "attention", "brief", "arg", "author"
    */
-  int addCommandParagraph(const std::string &theCommand,
+  void addCommandParagraph(const std::string &theCommand,
 		  	  	  	  	     const TokenList &tokList,
 		                     DoxygenEntityList &doxyList);
   /*
@@ -283,7 +283,7 @@ private:
    * "link"
    * Returns 1 if success, 0 if the endcommand is never encountered.
    */
-  int addCommandEndCommand(const std::string &theCommand,
+  void addCommandEndCommand(const std::string &theCommand,
 		                      const TokenList & tokList,
 		                      DoxygenEntityList &doxyList);
   /*
@@ -292,7 +292,7 @@ private:
    * Commands such as param
    * "param", "tparam", "throw", "throws", "retval", "exception"
    */
-  int addCommandWordParagraph(const std::string &theCommand,
+  void addCommandWordParagraph(const std::string &theCommand,
 		  	  	  	  	  	      const TokenList & tokList,
 		  	  	  	  	  	      DoxygenEntityList &doxyList);
   /*
@@ -301,7 +301,7 @@ private:
    * Commands such as param
    * "page", "subsection", "subsubsection", "section", "paragraph", "defgroup"
    */
-  int addCommandWordLine(const std::string &theCommand,
+  void addCommandWordLine(const std::string &theCommand,
                             const TokenList &tokList,
                             DoxygenEntityList &doxyList);
   /*
@@ -310,7 +310,7 @@ private:
    * Commands such as class
    * "category", "class", "protocol", "interface", "struct", "union"
    */
-  int addCommandWordOWordOWord(const std::string &theCommand,
+  void addCommandWordOWordOWord(const std::string &theCommand,
                                    const TokenList &tokList,
                                    DoxygenEntityList &doxyList);
   /*
@@ -319,7 +319,7 @@ private:
    * Commands such as dir
    * "dir", "file", "cond"
    */
-  int addCommandOWord(const std::string &theCommand,
+  void addCommandOWord(const std::string &theCommand,
                       const TokenList &tokList,
                       DoxygenEntityList &doxyList);
 
@@ -327,22 +327,22 @@ private:
    * Commands that should not be encountered (such as PHP only)
    * goes til the end of line then returns
    */
-  int addCommandErrorThrow(const std::string &theCommand,
+  void addCommandErrorThrow(const std::string &theCommand,
                            const TokenList &tokList,
                            DoxygenEntityList &doxyList);
 
-  int addCommandHtml(const std::string &theCommand,
+  void addCommandHtml(const std::string &theCommand,
                      const TokenList &tokList,
                      DoxygenEntityList &doxyList);
 
-  int addCommandHtmlEntity(const std::string &theCommand,
+  void addCommandHtmlEntity(const std::string &theCommand,
                            const TokenList &tokList,
                            DoxygenEntityList &doxyList);
 
   /*
    *Adds the unique commands- different process for each unique command
    */
-  int addCommandUnique(const std::string &theCommand,
+  void addCommandUnique(const std::string &theCommand,
                        const TokenList &tokList,
                        DoxygenEntityList &doxyList);
 
@@ -350,7 +350,7 @@ private:
    * Simply ignore the given command, possibly with the word following it or
    * until the matching end command.
    */
-  int ignoreCommand(const std::string& theCommand,
+  void ignoreCommand(const std::string& theCommand,
                     const TokenList &tokList,
                     DoxygenEntityList &doxyList);
 
@@ -358,7 +358,7 @@ private:
    * The actual "meat" of the doxygen parser. Calls the correct addCommand...()
    * function.
    */
-  int addCommand(const std::string &commandString,
+  void addCommand(const std::string &commandString,
                    const TokenList &tokList,
                    DoxygenEntityList &doxyList);
 

From 751f617aac000ea1cddc0d52d58ba5ed3a6318a3 Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Wed, 1 Feb 2017 02:06:16 +0100
Subject: [PATCH 282/314] Add support for doxygen:alias feature

This allows to replace non-standard Doxygen commands with some (fixed) text
instead of just ignoring them, as was already possible with the feature
doxygen:ignore.
---
 Doc/Manual/Doxygen.html                       | 53 +++++++++++++++++--
 Examples/test-suite/common.mk                 |  1 +
 Examples/test-suite/doxygen_alias.i           | 22 ++++++++
 .../test-suite/java/doxygen_alias_runme.java  | 32 +++++++++++
 .../test-suite/python/doxygen_alias_runme.py  | 12 +++++
 .../DoxygenTranslator/src/DoxygenParser.cpp   | 20 +++++++
 Source/DoxygenTranslator/src/DoxygenParser.h  |  8 +++
 7 files changed, 144 insertions(+), 4 deletions(-)
 create mode 100644 Examples/test-suite/doxygen_alias.i
 create mode 100644 Examples/test-suite/java/doxygen_alias_runme.java
 create mode 100644 Examples/test-suite/python/doxygen_alias_runme.py

diff --git a/Doc/Manual/Doxygen.html b/Doc/Manual/Doxygen.html
index faea2c7d9..5fa4b820e 100644
--- a/Doc/Manual/Doxygen.html
+++ b/Doc/Manual/Doxygen.html
@@ -226,13 +226,58 @@ instead of the corresponding language tool (<tt>javadoc</tt>, <tt>sphinx</tt>,
 </p>
 
 
+<h4>doxygen:alias:&lt;command-name&gt;</h4>
+
+<p>
+Specify an alias for a Doxygen command with the given name. This can be useful
+for custom Doxygen commands which can be defined using <tt>ALIASES</tt> option
+for Doxygen itself but which are unknown to SWIG. <tt>"command-name"</tt> is the
+name of the command in the Doxyfile, e.g. if it contains
+</p>
+
+<div class="code"><pre>
+ALIASES = "sideeffect=\par Side Effects:\n"
+</pre></div>
+
+<p>
+Then you could also the same expansion for SWIG with:
+</p>
+
+<div class="code"><pre>
+%feature("doxygen:alias:sideeffect") "\par Side Effects:\n"
+</pre></div>
+
+<p>
+Please note that command arguments are not currently supported with this
+feature.
+</p>
+
+<p>
+Notice that it is perfectly possible and potentially useful to define the alias
+expansion differently depending on the target language, e.g. with
+</p>
+
+<div class="code"><pre>
+#ifdef SWIGJAVA
+%feature("doxygen:alias:not_for_java") "This functionality is not available for Java"
+#else
+%feature("doxygen:alias:not_for_java") ""
+#endif
+</pre></div>
+
+<p>
+you could use <tt>@not_for_java</tt> in the documentation comments of all
+functions which can't, for whatever reason, be currently exposed in Java
+wrappers of the C++ API.
+</p>
+
+
 <h4>doxygen:ignore:&lt;command-name&gt;</h4>
 
 <p>
-Specify that the Doxygen command with the given name should be ignored. This is
-useful for custom Doxygen commands which can be defined using <tt>ALIASES</tt>
-option for Doxygen itself but which are unknown to SWIG. <tt>"command-name"</tt>
-is the real name of the command, e.g. you could use
+This feature allows to just ignore an unknown Doxygen command, instead of
+replacing it with a predefined text as <tt>doxygen:alias</tt> features allows to
+do. For example, you could use
 </p>
 
 <div class="code"><pre>
diff --git a/Examples/test-suite/common.mk b/Examples/test-suite/common.mk
index c8670801c..806be3da3 100644
--- a/Examples/test-suite/common.mk
+++ b/Examples/test-suite/common.mk
@@ -583,6 +583,7 @@ $(eval HAS_DOXYGEN := $($(LANGUAGE)_HAS_DOXYGEN))
 ifdef HAS_DOXYGEN
 DOXYGEN_TEST_CASES += \
 	doxygen_parsing \
+	doxygen_alias \
 	doxygen_ignore \
 	doxygen_basic_translate \
 	doxygen_basic_notranslate \
diff --git a/Examples/test-suite/doxygen_alias.i b/Examples/test-suite/doxygen_alias.i
new file mode 100644
index 000000000..79cb7964b
--- /dev/null
+++ b/Examples/test-suite/doxygen_alias.i
@@ -0,0 +1,22 @@
+%module doxygen_alias
+
+#ifdef SWIGJAVA
+%feature("doxygen:alias:nullptr") "null"
+#elif defined(SWIGPYTHON)
+%feature("doxygen:alias:nullptr") "None"
+#else
+%feature("doxygen:alias:nullptr") "NULL"
+#endif
+
+%inline %{
+
+class Something {};
+
+/**
+    A function returning something.
+
+    @returns A new object which may be @nullptr.
+ */
+Something* make_something() { return 0; }
+
+%}
diff --git a/Examples/test-suite/java/doxygen_alias_runme.java b/Examples/test-suite/java/doxygen_alias_runme.java
new file mode 100644
index 000000000..e21ed6d19
--- /dev/null
+++ b/Examples/test-suite/java/doxygen_alias_runme.java
@@ -0,0 +1,32 @@
+
+import doxygen_alias.*;
+import com.sun.javadoc.*;
+import java.util.HashMap;
+
+public class doxygen_alias_runme {
+  static {
+    try {
+      System.loadLibrary("doxygen_alias");
+    } catch (UnsatisfiedLinkError e) {
+      System.err.println("Native code library failed to load. See the chapter on Dynamic Linking Problems in the SWIG Java documentation for help.\n" + e);
+      System.exit(1);
+    }
+  }
+
+  public static void main(String argv[])
+  {
+    CommentParser parser = new CommentParser();
+    com.sun.tools.javadoc.Main.execute("doxygen_alias runtime test",
+                                       "CommentParser",
+                                       new String[]{"-quiet", "doxygen_alias"});
+
+    HashMap<String, String> wantedComments = new HashMap<String, String>();
+    wantedComments.put("doxygen_alias.doxygen_alias.make_something()",
+      "     A function returning something.<br>\n" +
+      " <br>\n" +
+      "     @return A new object which may be null.\n" +
+      "");
+
+    System.exit(parser.check(wantedComments));
+  }
+}
diff --git a/Examples/test-suite/python/doxygen_alias_runme.py b/Examples/test-suite/python/doxygen_alias_runme.py
new file mode 100644
index 000000000..4117f00e5
--- /dev/null
+++ b/Examples/test-suite/python/doxygen_alias_runme.py
@@ -0,0 +1,12 @@
+#!/usr/bin/python
+
+import doxygen_alias
+import inspect
+import commentVerifier
+
+commentVerifier.check(inspect.getdoc(doxygen_alias.make_something),
+    """\
+A function returning something.
+
+:rtype: :py:class:`Something`
+:return: A new object which may be None.""")
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.cpp b/Source/DoxygenTranslator/src/DoxygenParser.cpp
index 88b2863cf..e42f7400a 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenParser.cpp
@@ -137,6 +137,11 @@ DoxygenParser::commandBelongs(const std::string &theCommand)
     return it->second;
   }
 
+  // Check if this command is defined as an alias.
+  if (String* const alias = Getattr(m_node, ("feature:doxygen:alias:" + theCommand).c_str())) {
+    return COMMAND_ALIAS;
+  }
+
   // Check if this command should be ignored.
   if (String* const ignore = getIgnoreFeature(theCommand)) {
     // Check that no value is specified for this feature ("1" is the implicit
@@ -895,6 +900,18 @@ DoxygenParser::addCommandUnique(const std::string &theCommand,
   }
 }
 
+void
+DoxygenParser::aliasCommand(const std::string& theCommand,
+                            const TokenList& /* tokList */,
+                            DoxygenEntityList &doxyList)
+{
+  String* const alias = Getattr(m_node, ("feature:doxygen:alias:" + theCommand).c_str());
+  if (!alias)
+    return;
+
+  doxyList.push_back(DoxygenEntity("plainstd::string", Char(alias)));
+}
+
 String* DoxygenParser::getIgnoreFeature(const std::string& theCommand,
                                         const char* argument) const
 {
@@ -1052,6 +1069,9 @@ DoxygenParser::addCommand(const std::string &commandString,
   case COMMAND_HTML_ENTITY:
     addCommandHtmlEntity(theCommand, tokList, doxyList);
     break;
+  case COMMAND_ALIAS:
+    aliasCommand(commandString, tokList, doxyList);
+    break;
   case COMMAND_IGNORE:
     ignoreCommand(commandString, tokList, doxyList);
     break;
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.h b/Source/DoxygenTranslator/src/DoxygenParser.h
index 521d2a02f..82550465d 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.h
+++ b/Source/DoxygenTranslator/src/DoxygenParser.h
@@ -39,6 +39,7 @@ private:
     COMMANDUNIQUE,
     COMMAND_HTML,
     COMMAND_HTML_ENTITY,
+    COMMAND_ALIAS,
     COMMAND_IGNORE,
     END_LINE,
     PARAGRAPH_END,
@@ -346,6 +347,13 @@ private:
                        const TokenList &tokList,
                        DoxygenEntityList &doxyList);
 
+  /*
+   * Replace the given command with its predefined alias expansion.
+   */
+  void aliasCommand(const std::string& theCommand,
+		    const TokenList &tokList,
+		    DoxygenEntityList &doxyList);
+
   /*
    * Simply ignore the given command, possibly with the word following it or
    * until the matching end command.

From d42a5f2ce332103731a01fc4c5f93e9bb4be53f3 Mon Sep 17 00:00:00 2001
From: Vadim Zeitlin <vz-swig@zeitlins.org>
Date: Mon, 19 Mar 2018 21:52:47 +0100
Subject: [PATCH 283/314] Fix wrongly resetting indent after formulae in
 Doxygen comments

Don't use IndentGuard unconditionally in handleMath(), it should only be
used for display (or block) formulae, but not for the inline ones.

This fixes "losing" the correct indent after a paragraph containing any
inline formulae in the generated Python comments.
---
 .../DoxygenTranslator/src/PyDocConverter.cpp  | 56 +++++++++++++------
 1 file changed, 40 insertions(+), 16 deletions(-)

diff --git a/Source/DoxygenTranslator/src/PyDocConverter.cpp b/Source/DoxygenTranslator/src/PyDocConverter.cpp
index e1bae2792..76431af54 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/PyDocConverter.cpp
@@ -34,19 +34,35 @@ public:
   // One indent level.
   static const char* Level() { return "    "; }
 
+  // Default ctor doesn't do anything and prevents the dtor from doing anything
+  // too and should only be used when the guard needs to be initialized
+  // conditionally as Init() can then be called after checking some condition.
+  // Otherwise, prefer to use the non default ctor below.
+  IndentGuard()
+  {
+    m_initialized = false;
+  }
+
   // Ctor takes the output to determine the current indent and to remove the
   // extra indent added to it in the dtor and the variable containing the indent
   // to use, which must be used after every new line by the code actually
   // updating the output.
-  explicit IndentGuard(string& output, string& indent) :
-    m_output(output),
-    m_indent(indent)
+  IndentGuard(string& output, string& indent)
   {
-    const size_t lastNonSpace = m_output.find_last_not_of(' ');
+    Init(output, indent);
+  }
+
+  // Really initializes the object created using the default ctor.
+  void Init(string& output, string& indent)
+  {
+    m_output = &output;
+    m_indent = &indent;
+
+    const size_t lastNonSpace = m_output->find_last_not_of(' ');
     if (lastNonSpace == string::npos) {
-      m_firstLineIndent = m_output.length();
-    } else if (m_output[lastNonSpace] == '\n') {
-      m_firstLineIndent = m_output.length() - (lastNonSpace + 1);
+      m_firstLineIndent = m_output->length();
+    } else if ((*m_output)[lastNonSpace] == '\n') {
+      m_firstLineIndent = m_output->length() - (lastNonSpace + 1);
     } else {
       m_firstLineIndent = 0;
     }
@@ -54,7 +70,9 @@ public:
     // Notice that the indent doesn't include the first line indent because it's
     // implicit, i.e. it is present in the input and so is copied into the
     // output anyhow.
-    m_indent = Level();
+    *m_indent = Level();
+
+    m_initialized = true;
   }
 
   // Get the indent for the first line of the paragraph, which is smaller than
@@ -63,23 +81,27 @@ public:
 
   ~IndentGuard()
   {
-    m_indent.clear();
+    if (!m_initialized)
+      return;
+
+    m_indent->clear();
 
     // Get rid of possible remaining extra indent, e.g. if there were any trailing
     // new lines: we shouldn't add the extra indent level to whatever follows
     // this paragraph.
     static const size_t lenIndentLevel = strlen(Level());
-    if (m_output.length() > lenIndentLevel) {
-      const size_t start = m_output.length() - lenIndentLevel;
-      if (m_output.compare(start, string::npos, Level()) == 0)
-          m_output.erase(start);
+    if (m_output->length() > lenIndentLevel) {
+      const size_t start = m_output->length() - lenIndentLevel;
+      if (m_output->compare(start, string::npos, Level()) == 0)
+          m_output->erase(start);
     }
   }
 
 private:
-  string& m_output;
-  string& m_indent;
+  string* m_output;
+  string* m_indent;
   unsigned m_firstLineIndent;
+  bool m_initialized;
 
   IndentGuard(const IndentGuard&);
   IndentGuard& operator=(const IndentGuard&);
@@ -433,7 +455,7 @@ void PyDocConverter::handleMath(DoxygenEntity &tag,
                                 std::string &translatedComment,
                                 const std::string& arg)
 {
-  IndentGuard indent(translatedComment, m_indent);
+  IndentGuard indent;
 
   // Only \f$ is translated to inline formulae, \f[ and \f{ are for the block ones.
   const bool inlineFormula = tag.typeOfEntity == "f$";
@@ -443,6 +465,8 @@ void PyDocConverter::handleMath(DoxygenEntity &tag,
   if (inlineFormula) {
     translatedComment += ":math:`";
   } else {
+    indent.Init(translatedComment, m_indent);
+
     trimWhitespace(translatedComment);
     translatedComment += '\n';
 

From aa9691b1a81e3262f3ef6e7d9d81ecc105e84cf7 Mon Sep 17 00:00:00 2001
From: William S Fulton <wsf@fultondesigns.co.uk>
Date: Fri, 18 May 2018 19:34:48 +0100
Subject: [PATCH 284/314] Unused variable warning fix

---
 Source/DoxygenTranslator/src/DoxygenParser.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Source/DoxygenTranslator/src/DoxygenParser.cpp b/Source/DoxygenTranslator/src/DoxygenParser.cpp
index e42f7400a..faed5b931 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenParser.cpp
@@ -138,7 +138,7 @@ DoxygenParser::commandBelongs(const std::string &theCommand)
   }
 
   // Check if this command is defined as an alias.
-  if (String* const alias = Getattr(m_node, ("feature:doxygen:alias:" + theCommand).c_str())) {
+  if (Getattr(m_node, ("feature:doxygen:alias:" + theCommand).c_str())) {
     return COMMAND_ALIAS;
   }
 

From abfc304740669fa3a963574846f0ec6422f2c17a Mon Sep 17 00:00:00 2001
From: William S Fulton <wsf@fultondesigns.co.uk>
Date: Sat, 19 May 2018 08:12:10 +0100
Subject: [PATCH 285/314] Various merge fixes in doxygen branches

---
 Examples/test-suite/li_std_queue.i                  | 11 +----------
 Examples/test-suite/li_std_stack.i                  | 11 +----------
 Examples/test-suite/ruby/ruby_li_std_speed_runme.rb |  3 ---
 Examples/test-suite/ruby_li_std_speed.i             | 11 +----------
 Lib/csharp/arrays_csharp.i                          |  3 ---
 Lib/php/director.swg                                |  3 ---
 6 files changed, 3 insertions(+), 39 deletions(-)

diff --git a/Examples/test-suite/li_std_queue.i b/Examples/test-suite/li_std_queue.i
index 2d322b4d9..6bf71afca 100644
--- a/Examples/test-suite/li_std_queue.i
+++ b/Examples/test-suite/li_std_queue.i
@@ -1,13 +1,4 @@
-/**
- * @file   std_queue.i
- * @author gga
- * @date   Sun May  6 01:52:44 2007
- * 
- * @brief  test of std::queue
- * 
- * 
- */
-
+// test of std::queue
 %module li_std_queue
 
 %include std_queue.i
diff --git a/Examples/test-suite/li_std_stack.i b/Examples/test-suite/li_std_stack.i
index d29254089..19b45d46f 100644
--- a/Examples/test-suite/li_std_stack.i
+++ b/Examples/test-suite/li_std_stack.i
@@ -1,13 +1,4 @@
-/**
- * @file   std_stack.i
- * @author gga
- * @date   Sun May  6 01:52:44 2007
- * 
- * @brief  test of std::stack
- * 
- * 
- */
-
+// test of std::stack
 %module li_std_stack
 
 %include std_stack.i
diff --git a/Examples/test-suite/ruby/ruby_li_std_speed_runme.rb b/Examples/test-suite/ruby/ruby_li_std_speed_runme.rb
index 825f3c593..e79cb46a8 100644
--- a/Examples/test-suite/ruby/ruby_li_std_speed_runme.rb
+++ b/Examples/test-suite/ruby/ruby_li_std_speed_runme.rb
@@ -3,9 +3,6 @@
 # This is a simple speed benchmark suite for std containers,
 # to verify their O(n) performance.
 # It is not part of the standard tests.
-#
-# License::   SWIG
-#
 
 
 require 'benchmark'
diff --git a/Examples/test-suite/ruby_li_std_speed.i b/Examples/test-suite/ruby_li_std_speed.i
index 3c8e60643..bfb0b2776 100644
--- a/Examples/test-suite/ruby_li_std_speed.i
+++ b/Examples/test-suite/ruby_li_std_speed.i
@@ -1,13 +1,4 @@
-/**
- * @file   ruby_li_std_speed.i
- * @author gga
- * @date   Fri May 18 18:03:15 2007
- * 
- * @brief  A speed test of the ruby stl
- * 
- * 
- */
-
+// A speed test of the ruby stl
 %module ruby_li_std_speed
 
 %include <std_list.i>
diff --git a/Lib/csharp/arrays_csharp.i b/Lib/csharp/arrays_csharp.i
index 534fca40f..237067a88 100644
--- a/Lib/csharp/arrays_csharp.i
+++ b/Lib/csharp/arrays_csharp.i
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * arrays_csharp.i
  *
  * This file contains a two approaches to marshaling arrays. The first uses
diff --git a/Lib/php/director.swg b/Lib/php/director.swg
index 082b03604..ea0eba8ac 100644
--- a/Lib/php/director.swg
+++ b/Lib/php/director.swg
@@ -1,7 +1,4 @@
 /* -----------------------------------------------------------------------------
- * See the LICENSE file for information on copyright, usage and redistribution
- * of SWIG, and the README file for authors - http://www.swig.org/release.html.
- *
  * director.swg
  *
  * This file contains support for director classes so that PHP proxy

From 9deaa6ff2465af11122916a438ae9d3112d18b24 Mon Sep 17 00:00:00 2001
From: William S Fulton <wsf@fultondesigns.co.uk>
Date: Sat, 19 May 2018 09:00:06 +0100
Subject: [PATCH 286/314] new_node refactor

Reduce code duplication for doxygen to match code in master prior to
merge to master
---
 Source/CParse/cparse.h |  1 +
 Source/CParse/parser.y |  5 +----
 Source/CParse/util.c   | 13 +++++++++++++
 Source/Swig/extend.c   | 18 ++----------------
 4 files changed, 17 insertions(+), 20 deletions(-)

diff --git a/Source/CParse/cparse.h b/Source/CParse/cparse.h
index ed0cfdb38..c67ffeaba 100644
--- a/Source/CParse/cparse.h
+++ b/Source/CParse/cparse.h
@@ -62,6 +62,7 @@ extern "C" {
   extern void cparse_normalize_void(Node *);
   extern Parm *Swig_cparse_parm(String *s);
   extern ParmList *Swig_cparse_parms(String *s, Node *file_line_node);
+  extern Node *Swig_cparse_new_node(const_String_or_char_ptr tag);
 
 /* templ.c */
   extern int Swig_cparse_template_expand(Node *n, String *rname, ParmList *tparms, Symtab *tscope);
diff --git a/Source/CParse/parser.y b/Source/CParse/parser.y
index 46a106c47..2e13b0ae4 100644
--- a/Source/CParse/parser.y
+++ b/Source/CParse/parser.y
@@ -83,10 +83,7 @@ static void yyerror (const char *e) {
 }
 
 static Node *new_node(const_String_or_char_ptr tag) {
-  Node *n = NewHash();
-  set_nodeType(n,tag);
-  Setfile(n,cparse_file);
-  Setline(n,cparse_line);
+  Node *n = Swig_cparse_new_node(tag);
   /* Remember the previous node in case it will need a post-comment */
   previousNode = currentNode;
   currentNode = n;
diff --git a/Source/CParse/util.c b/Source/CParse/util.c
index 6bf20efc4..714bb2972 100644
--- a/Source/CParse/util.c
+++ b/Source/CParse/util.c
@@ -111,3 +111,16 @@ void cparse_normalize_void(Node *n) {
   }
 }
 
+/* -----------------------------------------------------------------------------
+ * Swig_cparse_new_node()
+ *
+ * Create an empty parse node, setting file and line number information
+ * ----------------------------------------------------------------------------- */
+
+Node *Swig_cparse_new_node(const_String_or_char_ptr tag) {
+  Node *n = NewHash();
+  set_nodeType(n,tag);
+  Setfile(n,cparse_file);
+  Setline(n,cparse_line);
+  return n;
+}
diff --git a/Source/Swig/extend.c b/Source/Swig/extend.c
index b95989237..70355a245 100644
--- a/Source/Swig/extend.c
+++ b/Source/Swig/extend.c
@@ -16,20 +16,6 @@
 
 static Hash *extendhash = 0;     /* Hash table of added methods */
 
-/* -----------------------------------------------------------------------------
- * new_node()
- *
- * Create an empty parse node, setting file and line number information
- * ----------------------------------------------------------------------------- */
-
-static Node *new_node(const_String_or_char_ptr tag) {
-  Node *n = NewHash();
-  set_nodeType(n,tag);
-  Setfile(n,cparse_file);
-  Setline(n,cparse_line);
-  return n;
-}
-
 /* -----------------------------------------------------------------------------
  * Swig_extend_hash()
  *
@@ -120,10 +106,10 @@ void Swig_extend_append_previous(Node *cls, Node *am) {
     set_nextSibling(n,0);
     /* typemaps and fragments need to be prepended */
     if (((Cmp(nodeType(n),"typemap") == 0) || (Cmp(nodeType(n),"fragment") == 0)))  {
-      if (!pe) pe = new_node("extend");
+      if (!pe) pe = Swig_cparse_new_node("extend");
       appendChild(pe, n);
     } else {
-      if (!ae) ae = new_node("extend");
+      if (!ae) ae = Swig_cparse_new_node("extend");
       appendChild(ae, n);
     }    
     n = ne;

From 0483caaed5d392723f1e4dcee8528603ad28f255 Mon Sep 17 00:00:00 2001
From: William S Fulton <wsf@fultondesigns.co.uk>
Date: Sat, 19 May 2018 12:24:43 +0100
Subject: [PATCH 287/314] Remove unused doxygen code

---
 Source/Modules/java.cxx  | 26 +-------------------------
 Source/Modules/lang.cxx  | 18 ------------------
 Source/Modules/swigmod.h |  6 ------
 3 files changed, 1 insertion(+), 49 deletions(-)

diff --git a/Source/Modules/java.cxx b/Source/Modules/java.cxx
index 74649ef1f..936fdd62d 100644
--- a/Source/Modules/java.cxx
+++ b/Source/Modules/java.cxx
@@ -81,7 +81,6 @@ class JAVA:public Language {
   String *imclass_cppcasts_code;	//C++ casts up inheritance hierarchies intermediary class code
   String *imclass_directors;	// Intermediate class director code
   String *destructor_call;	//C++ destructor call if any
-  String *structuralComments;
   String *destructor_throws_clause;	//C++ destructor throws clause if any
 
   // Director method stuff:
@@ -157,7 +156,6 @@ public:
       imclass_cppcasts_code(NULL),
       imclass_directors(NULL),
       destructor_call(NULL),
-      structuralComments(NULL),
       destructor_throws_clause(NULL),
       dmethods_seq(NULL),
       dmethods_table(NULL),
@@ -448,7 +446,6 @@ public:
     imclass_imports = NewString("");
     imclass_cppcasts_code = NewString("");
     imclass_directors = NewString("");
-    structuralComments = NewString("");
     upcasts_code = NewString("");
     dmethods_seq = NewList();
     dmethods_table = NewHash();
@@ -587,10 +584,7 @@ public:
 
       // Start writing out the module class file
       emitBanner(f_module);
-      //Add any structural comments to the top
-      if(doxygen && structuralComments){
-    	  Printf(f_module, "%s", structuralComments);
-      }
+
       if (package)
 	Printf(f_module, "package %s;\n", package);
 
@@ -735,8 +729,6 @@ public:
     module_imports = NULL;
     Delete(module_class_modifiers);
     module_class_modifiers = NULL;
-    Delete(structuralComments);
-    structuralComments = NULL;
     Delete(imclass_imports);
     imclass_imports = NULL;
     Delete(imclass_cppcasts_code);
@@ -1546,22 +1538,6 @@ public:
     return SWIG_OK;
   }
 
-  /* -----------------------------------------------------------------------
-   * doxygenComment()
-   * Simply translates the doxygen comment and places it into the appropriate
-   * file
-   * ------------------------------------------------------------------------ */
-  virtual int doxygenComment(Node *n){
-    if (doxygen && doxygenTranslator->hasDocumentation(n)){
-      String *doxygen_comments=doxygenTranslator->getDocumentation(n);
-      if(comment_creation_chatter)
-	Printf(structuralComments, "/* This was generated from doxygenComment() */");
-      Printv(structuralComments, Char(doxygen_comments), NIL);
-      Delete(doxygen_comments);
-    }
-    return SWIG_OK;
-  }
-  
   /* -----------------------------------------------------------------------
    * constantWrapper()
    * Used for wrapping constants - #define or %constant.
diff --git a/Source/Modules/lang.cxx b/Source/Modules/lang.cxx
index 8663df6b3..05ecead9c 100644
--- a/Source/Modules/lang.cxx
+++ b/Source/Modules/lang.cxx
@@ -138,9 +138,6 @@ int Dispatcher::emit_one(Node *n) {
     ret = namespaceDeclaration(n);
   } else if (strcmp(tag, "template") == 0) {
     ret = templateDeclaration(n);
-  }
-  else if (strcmp(tag, "doxycomm") == 0) {
-    ret = doxygenComment(n);
   } else if (strcmp(tag, "lambda") == 0) {
     ret = lambdaDeclaration(n);
   }
@@ -309,9 +306,6 @@ int Dispatcher::usingDeclaration(Node *n) {
 int Dispatcher::namespaceDeclaration(Node *n) {
   return defaultHandler(n);
 }
-int Dispatcher::doxygenComment(Node *n){
-  return defaultHandler(n);
-}
 
 /* Allocators */
 Language::Language():
@@ -2980,18 +2974,6 @@ int Language::usingDeclaration(Node *n) {
 
 /* Stubs. Language modules need to implement these */
 
-/* ----------------------------------------------------------------------
- * Language::doxygenComment()
- * ---------------------------------------------------------------------- */
-int Language::doxygenComment(Node *n){
-	
-  String *comment = Getattr(n, "comment");
-  Printf(stdout, "doxygenComment   : %s\n", comment);
-
-  return SWIG_OK;
-	
-}
-
 /* ----------------------------------------------------------------------
  * Language::constantWrapper()
  * ---------------------------------------------------------------------- */
diff --git a/Source/Modules/swigmod.h b/Source/Modules/swigmod.h
index d5e59b203..1e49993bf 100644
--- a/Source/Modules/swigmod.h
+++ b/Source/Modules/swigmod.h
@@ -78,9 +78,6 @@ public:
   virtual int typemapcopyDirective(Node *n);
   virtual int typesDirective(Node *n);
 
-  /* Doxygen Comment */
-  virtual int doxygenComment(Node *n);
-  
   /* C/C++ parsing */
 
   virtual int cDeclaration(Node *n);
@@ -161,9 +158,6 @@ public:
   virtual int namespaceDeclaration(Node *n);
   virtual int usingDeclaration(Node *n);
 
-  /* C/C++ parsing */
-  virtual int doxygenComment(Node *n);
-  
   /* Function handlers */
 
   virtual int functionHandler(Node *n);

From 73c585b994754c130b6751d56d3bb22244f990e6 Mon Sep 17 00:00:00 2001
From: William S Fulton <wsf@fultondesigns.co.uk>
Date: Sat, 19 May 2018 20:52:39 +0100
Subject: [PATCH 288/314] Code formatting fixes in doxygen code

---
 Source/CParse/cscanner.c  | 88 ++++++++++++++++++------------------
 Source/CParse/parser.y    | 14 +++---
 Source/Modules/java.cxx   | 95 ++++++++++++++++++---------------------
 Source/Modules/python.cxx | 23 +++++-----
 4 files changed, 109 insertions(+), 111 deletions(-)

diff --git a/Source/CParse/cscanner.c b/Source/CParse/cscanner.c
index f1390e283..4566817a0 100644
--- a/Source/CParse/cscanner.c
+++ b/Source/CParse/cscanner.c
@@ -53,50 +53,52 @@ static int rename_active = 0;
 /* Doxygen comments scanning */
 int scan_doxygen_comments = 0;
 
-int isStructuralDoxygen(String *s){
-	static const char* const structuralTags[] = {
-	  "addtogroup",
-	  "callgraph",
-	  "callergraph",
-	  "category",
-	  "def",
-	  "defgroup",
-	  "dir",
-	  "example",
-	  "file",
-	  "headerfile",
-	  "internal",
-	  "mainpage",
-	  "name",
-	  "nosubgrouping",
-	  "overload",
-	  "package",
-	  "page",
-	  "protocol",
-	  "relates",
-	  "relatesalso",
-	  "showinitializer",
-	  "weakgroup",
-	};
+int isStructuralDoxygen(String *s) {
+  static const char* const structuralTags[] = {
+    "addtogroup",
+    "callgraph",
+    "callergraph",
+    "category",
+    "def",
+    "defgroup",
+    "dir",
+    "example",
+    "file",
+    "headerfile",
+    "internal",
+    "mainpage",
+    "name",
+    "nosubgrouping",
+    "overload",
+    "package",
+    "page",
+    "protocol",
+    "relates",
+    "relatesalso",
+    "showinitializer",
+    "weakgroup",
+  };
 
-	unsigned n;
-	char *slashPointer = Strchr(s, '\\');
-	char *atPointer = Strchr(s,'@');
-	if (slashPointer == NULL && atPointer == NULL) return 0;
-	else if( slashPointer == NULL) slashPointer = atPointer;
+  unsigned n;
+  char *slashPointer = Strchr(s, '\\');
+  char *atPointer = Strchr(s,'@');
+  if (slashPointer == NULL && atPointer == NULL)
+    return 0;
+  else if(slashPointer == NULL)
+    slashPointer = atPointer;
 
-	slashPointer++; /* skip backslash or at sign */
+  slashPointer++; /* skip backslash or at sign */
 
-	for (n = 0; n < sizeof(structuralTags)/sizeof(structuralTags[0]); n++) {
-	  const size_t len = strlen(structuralTags[n]);
-	  if (strncmp(slashPointer, structuralTags[n], len) == 0) {
-	    /* Take care to avoid false positives with prefixes of other tags. */
-	    if (slashPointer[len] == '\0' || isspace(slashPointer[len]))
-	      return 1;
-	  }
-	}
+  for (n = 0; n < sizeof(structuralTags)/sizeof(structuralTags[0]); n++) {
+    const size_t len = strlen(structuralTags[n]);
+    if (strncmp(slashPointer, structuralTags[n], len) == 0) {
+      /* Take care to avoid false positives with prefixes of other tags. */
+      if (slashPointer[len] == '\0' || isspace(slashPointer[len]))
+	return 1;
+    }
+  }
 
-	return 0;
+  return 0;
 }
 
 /* -----------------------------------------------------------------------------
@@ -427,7 +429,7 @@ static int yylook(void) {
 	do {
 	  String *cmt = Scanner_text(scan);
 	  char *loc = Char(cmt);
-	  if ((strncmp(loc,"/*@SWIG",7) == 0) && (loc[Len(cmt)-3] == '@')) {
+	  if ((strncmp(loc, "/*@SWIG", 7) == 0) && (loc[Len(cmt)-3] == '@')) {
 	    Scanner_locator(scan, cmt);
 	  }
 	  if (scan_doxygen_comments) { /* else just skip this node, to avoid crashes in parser module*/
@@ -437,9 +439,7 @@ static int yylook(void) {
 	    if (Len(cmt) > 3 && loc[0] == '/' &&
 		((loc[1] == '/' && ((loc[2] == '/' && loc[3] != '/') || loc[2] == '!')) ||
 		 (loc[1] == '*' && ((loc[2] == '*' && loc[3] != '*') || loc[2] == '!')))) {
-	      comment_kind_t this_comment = loc[3] == '<' ? DOX_COMMENT_POST
-							  : DOX_COMMENT_PRE;
-
+	      comment_kind_t this_comment = loc[3] == '<' ? DOX_COMMENT_POST : DOX_COMMENT_PRE;
 	      if (existing_comment != DOX_COMMENT_NONE && this_comment != existing_comment) {
 		/* We can't concatenate together Doxygen pre- and post-comments. */
 		break;
diff --git a/Source/CParse/parser.y b/Source/CParse/parser.y
index 2e13b0ae4..bbc536109 100644
--- a/Source/CParse/parser.y
+++ b/Source/CParse/parser.y
@@ -1723,8 +1723,8 @@ program        :  interface {
 interface      : interface declaration {  
                    /* add declaration to end of linked list (the declaration isn't always a single declaration, sometimes it is a linked list itself) */
                    if (currentDeclComment != NULL) {
-                       set_comment($2, currentDeclComment);
-                       currentDeclComment = NULL;
+		     set_comment($2, currentDeclComment);
+		     currentDeclComment = NULL;
                    }                                      
                    appendChild($1,$2);
                    $$ = $1;
@@ -1736,7 +1736,7 @@ interface      : interface declaration {
                | interface DOXYGENPOSTSTRING {
                    Node *node = lastChild($1);
                    if (node) {
-                       set_comment(node, $2);
+                     set_comment(node, $2);
                    }
                    $$ = $1;
                }
@@ -5048,7 +5048,11 @@ rawparms          : parm ptail {
                   set_nextSibling($1,$2);
                   $$ = $1;
 		}
-               | empty { $$ = 0; previousNode = currentNode; currentNode=0; }
+               | empty {
+		  $$ = 0;
+		  previousNode = currentNode;
+		  currentNode=0;
+	       }
                ;
 
 ptail          : COMMA parm ptail {
@@ -5057,7 +5061,7 @@ ptail          : COMMA parm ptail {
                 }
 	       | COMMA DOXYGENPOSTSTRING parm ptail {
 		 set_comment(previousNode, $2);
-                 set_nextSibling($3,$4);
+                 set_nextSibling($3, $4);
 		 $$ = $3;
                }
                | empty { $$ = 0; }
diff --git a/Source/Modules/java.cxx b/Source/Modules/java.cxx
index 936fdd62d..4a895f308 100644
--- a/Source/Modules/java.cxx
+++ b/Source/Modules/java.cxx
@@ -590,10 +590,10 @@ public:
 
       if (module_imports)
 	Printf(f_module, "%s\n", module_imports);
-      
-      if (doxygen && doxygenTranslator->hasDocumentation(n)){
-	String *doxygen_comments=doxygenTranslator->getDocumentation(n);
-	if(comment_creation_chatter)
+
+      if (doxygen && doxygenTranslator->hasDocumentation(n)) {
+	String *doxygen_comments = doxygenTranslator->getDocumentation(n);
+	if (comment_creation_chatter)
 	  Printf(f_module, "/* This was generated from top() */");
 	Printv(f_module, Char(doxygen_comments), NIL);
 	Delete(doxygen_comments);
@@ -1019,7 +1019,7 @@ public:
       Delete(c_param_type);
       Delete(arg);
     }
-    
+
     Printv(f->code, nondir_args, NIL);
     Delete(nondir_args);
 
@@ -1274,16 +1274,15 @@ public:
       EnumFeature enum_feature = decodeEnumFeature(n);
       String *typemap_lookup_type = Getattr(n, "name");
 
-      if (doxygen && doxygenTranslator->hasDocumentation(n)){
-        String *doxygen_comments=doxygenTranslator->getDocumentation(n);
-        if(comment_creation_chatter) {
+      if (doxygen && doxygenTranslator->hasDocumentation(n)) {
+        String *doxygen_comments = doxygenTranslator->getDocumentation(n);
+        if (comment_creation_chatter) {
           Printf(enum_code, "/* This was generated from enumDeclaration() */");
         }
         Printv(enum_code, Char(doxygen_comments), NIL);
         Delete(doxygen_comments);
       }
 
-
       if ((enum_feature != SimpleEnum) && symname && typemap_lookup_type) {
 	// Wrap (non-anonymous) C/C++ enum within a typesafe, typeunsafe or proper Java enum
 
@@ -1306,18 +1305,16 @@ public:
 	  Replaceall(enum_code, "$static ", "");
 	Delete(scope);
       } else {
-	//translate and write javadoc comment for the enum itself if flagged
-	if (doxygen && doxygenTranslator->hasDocumentation(n)){
-	  String *doxygen_comments=doxygenTranslator->getDocumentation(n);
-	  if(comment_creation_chatter)
+	// Translate and write javadoc comment for the enum itself if flagged
+	if (doxygen && doxygenTranslator->hasDocumentation(n)) {
+	  String *doxygen_comments = doxygenTranslator->getDocumentation(n);
+	  if (comment_creation_chatter)
 	    Printf(constants_code, "/* This was generated from enumDeclaration() */");
-	  Printf(constants_code, "/* Comment for enum %s */\n",
-		 Getattr(n, "unnamedinstance") ? "" : symname);
+	  Printf(constants_code, "/* Comment for enum %s */\n", Getattr(n, "unnamedinstance") ? "" : symname);
 	  Printf(constants_code, Char(doxygen_comments));
 	  Printf(constants_code, "\n");
 	  Delete(doxygen_comments);
-	}
-	else if (symname && !Getattr(n, "unnamedinstance"))
+	} else if (symname && !Getattr(n, "unnamedinstance"))
 	  Printf(constants_code, "  // %s \n", symname);
       }
 
@@ -1430,7 +1427,7 @@ public:
       tmpValue = NewString(name);
     // Note that this is used in enumValue() amongst other places
     Setattr(n, "value", tmpValue);
-    
+
     // Deal with enum values that are not int
     int swigtype = SwigType_type(Getattr(n, "type"));
     if (swigtype == T_BOOL) {
@@ -1472,10 +1469,10 @@ public:
       if (!addSymbol(symname, n, scope))
 	return SWIG_ERROR;
       
-      //translate and write javadoc comment if flagged
-      if (doxygen && doxygenTranslator->hasDocumentation(n)){
-	String *doxygen_comments=doxygenTranslator->getDocumentation(n);
-	if(comment_creation_chatter)
+      // Translate and write javadoc comment if flagged
+      if (doxygen && doxygenTranslator->hasDocumentation(n)) {
+	String *doxygen_comments = doxygenTranslator->getDocumentation(n);
+	if (comment_creation_chatter)
 	  Printf(enum_code, "/* This was generated from enumvalueDeclaration() */");
 	Printv(enum_code, Char(doxygen_comments), NIL);
 	Delete(doxygen_comments);
@@ -1557,13 +1554,12 @@ public:
     String *tm;
     String *return_type = NewString("");
     String *constants_code = NewString("");
-    
     Swig_save("constantWrapper", n, "value", NIL);
 
-    //translate and write javadoc comment if flagged
-    if (doxygen && doxygenTranslator->hasDocumentation(n)){
-      String *doxygen_comments=doxygenTranslator->getDocumentation(n);
-      if(comment_creation_chatter)
+    // Translate and write javadoc comment if flagged
+    if (doxygen && doxygenTranslator->hasDocumentation(n)) {
+      String *doxygen_comments = doxygenTranslator->getDocumentation(n);
+      if (comment_creation_chatter)
 	Printf(constants_code, "/* This was generated from constantWrapper() */");
       Printv(constants_code, Char(doxygen_comments), NIL);
       Delete(doxygen_comments);
@@ -2008,11 +2004,11 @@ public:
 
     // Pure Java interfaces
     const String *pure_interfaces = typemapLookup(n, "javainterfaces", typemap_lookup_type, WARN_NONE);
-    
-    //translate and write javadoc comment if flagged
-    if (doxygen && doxygenTranslator->hasDocumentation(n)){
-      String *doxygen_comments=doxygenTranslator->getDocumentation(n);
-      if(comment_creation_chatter)
+
+    // Translate and write javadoc comment if flagged
+    if (doxygen && doxygenTranslator->hasDocumentation(n)) {
+      String *doxygen_comments = doxygenTranslator->getDocumentation(n);
+      if (comment_creation_chatter)
 	Printf(proxy_class_def, "/* This was generated from emitProxyClassDefAndCPPCasts() */");
       Printv(proxy_class_def, Char(doxygen_comments), NIL);
       Delete(doxygen_comments);
@@ -2021,7 +2017,6 @@ public:
     if (*Char(interface_list) && *Char(pure_interfaces))
       Append(interface_list, ", ");
     Append(interface_list, pure_interfaces);
-
     // Start writing the proxy class
     if (!has_outerclass) // Import statements
       Printv(proxy_class_def, typemapLookup(n, "javaimports", typemap_lookup_type, WARN_NONE),"\n", NIL);
@@ -2506,11 +2501,11 @@ public:
       // For wrapping member variables (Javabean setter)
       setter_flag = (Cmp(Getattr(n, "sym:name"), Swig_name_set(getNSpace(), Swig_name_member(0, getClassPrefix(), variable_name))) == 0);
     }
-    
-    //translate and write javadoc comment if flagged
-    if (doxygen && doxygenTranslator->hasDocumentation(n)){
-      String *doxygen_comments=doxygenTranslator->getDocumentation(n);
-      if(comment_creation_chatter)
+
+    // Translate and write javadoc comment if flagged
+    if (doxygen && doxygenTranslator->hasDocumentation(n)) {
+      String *doxygen_comments = doxygenTranslator->getDocumentation(n);
+      if (comment_creation_chatter)
 	Printf(function_code, "/* This was generated from proxyclassfunctionhandler() */");
       Printv(function_code, Char(doxygen_comments), NIL);
       Delete(doxygen_comments);
@@ -2750,16 +2745,16 @@ public:
 
       tm = Getattr(n, "tmap:jtype"); // typemaps were attached earlier to the node
       Printf(im_return_type, "%s", tm);
-      
-      //translate and write javadoc comment if flagged
-    if (doxygen && doxygenTranslator->hasDocumentation(n)){
-      String *doxygen_comments=doxygenTranslator->getDocumentation(n);
-	if(comment_creation_chatter)
+
+    // Translate and write javadoc comment if flagged
+    if (doxygen && doxygenTranslator->hasDocumentation(n)) {
+      String *doxygen_comments = doxygenTranslator->getDocumentation(n);
+	if (comment_creation_chatter)
 	  Printf(function_code, "/* This was generated from constructionhandler() */");
 	Printv(function_code, Char(doxygen_comments), NIL);
 	Delete(doxygen_comments);
       }
-	    
+
       Printf(function_code, "  %s %s(", methodmods, proxy_class_name);
       Printf(helper_code, "  static private %s SwigConstruct%s(", im_return_type, proxy_class_name);
 
@@ -3024,11 +3019,11 @@ public:
     bool setter_flag = false;
     String *pre_code = NewString("");
     String *post_code = NewString("");
-    
-    // translate and write javadoc comment if flagged
-    if (doxygen && doxygenTranslator->hasDocumentation(n)){
-      String *doxygen_comments=doxygenTranslator->getDocumentation(n);
-      if(comment_creation_chatter)
+
+    // Translate and write javadoc comment if flagged
+    if (doxygen && doxygenTranslator->hasDocumentation(n)) {
+      String *doxygen_comments = doxygenTranslator->getDocumentation(n);
+      if (comment_creation_chatter)
 	Printf(function_code, "/* This was generated from moduleClassFunctionHandler() */");
       Printv(function_code, doxygen_comments, NIL);
       Delete(doxygen_comments);
@@ -3514,7 +3509,6 @@ public:
     const String *pure_baseclass = typemapLookup(n, "javabase", type, WARN_NONE);
     const String *pure_interfaces = typemapLookup(n, "javainterfaces", type, WARN_NONE);
 
-    
     // Emit the class
     Printv(swigtype, typemapLookup(n, "javaimports", type, WARN_NONE),	// Import statements
 	   "\n", typemapLookup(n, "javaclassmodifiers", type, WARN_JAVA_TYPEMAP_CLASSMOD_UNDEF),	// Class modifiers
@@ -4993,4 +4987,3 @@ Java Options (available with -java)\n\
      -oldvarnames    - Old intermediary method names for variable wrappers\n\
      -package <name> - Set name of the Java package to <name>\n\
 \n";
-
diff --git a/Source/Modules/python.cxx b/Source/Modules/python.cxx
index 4fe1dd516..036124837 100644
--- a/Source/Modules/python.cxx
+++ b/Source/Modules/python.cxx
@@ -1688,14 +1688,16 @@ public:
 
   /* ------------------------------------------------------------
    * build_combined_docstring()
-   *    Build the full docstring which may be a combination of the
-   *    explicit docstring and autodoc string or, if none of them
-   *    is specified, obtained by translating Doxygen comment to
-   *    Python.
    *
-   *    Return new string to be deleted by caller (never NIL but
-   *    may be empty if there is no docstring).
+   * Build the full docstring which may be a combination of the
+   * explicit docstring and autodoc string or, if none of them
+   * is specified, obtained by translating Doxygen comment to
+   * Python.
+   *
+   * Return new string to be deleted by caller (never NIL but
+   * may be empty if there is no docstring).
    * ------------------------------------------------------------ */
+
   String *build_combined_docstring(Node *n, autodoc_t ad_type, const String *indent = "") {
     String *docstr = Getattr(n, "feature:docstring");
     if (docstr && Len(docstr)) {
@@ -1708,14 +1710,14 @@ public:
     }
 
     if (Getattr(n, "feature:autodoc") && !GetFlag(n, "feature:noautodoc")) {
-      String* autodoc = make_autodoc(n, ad_type);
+      String *autodoc = make_autodoc(n, ad_type);
       if (autodoc && Len(autodoc) > 0) {
 	if (docstr && Len(docstr)) {
 	  Append(autodoc, "\n");
 	  Append(autodoc, docstr);
 	}
 
-	String* tmp = autodoc;
+	String *tmp = autodoc;
 	autodoc = docstr;
 	docstr = tmp;
       }
@@ -1751,8 +1753,7 @@ public:
     //      """
     //
     // otherwise, put it all on a single line
-    if (Strchr(docstr, '\n'))
-    {
+    if (Strchr(docstr, '\n')) {
       String *tmp = NewString("");
       Append(tmp, "\n");
       Append(tmp, indent_docstring(docstr, indent));
@@ -3728,7 +3729,7 @@ public:
       }
 
       if (f_s) {
-	if(needs_swigconstant(n)) {
+	if (needs_swigconstant(n)) {
 	  Printv(f_s, "\n",NIL);
 	  Printv(f_s, module, ".", iname, "_swigconstant(",module,")\n", NIL);
 	}

From 658eb26e191de338248a375637ee34a2ab00370f Mon Sep 17 00:00:00 2001
From: William S Fulton <wsf@fultondesigns.co.uk>
Date: Sun, 20 May 2018 21:24:31 +0100
Subject: [PATCH 289/314] Beautify doxygen source code

Just whitespace changes
---
 .../DoxygenTranslator/src/DoxygenCommands.h   |  93 ++--
 .../DoxygenTranslator/src/DoxygenEntity.cpp   |  22 +-
 Source/DoxygenTranslator/src/DoxygenEntity.h  |   4 +-
 .../DoxygenTranslator/src/DoxygenParser.cpp   | 435 ++++++------------
 Source/DoxygenTranslator/src/DoxygenParser.h  | 114 ++---
 .../src/DoxygenTranslator.cpp                 |  10 +-
 .../DoxygenTranslator/src/DoxygenTranslator.h |   4 +-
 .../src/JavaDocConverter.cpp                  | 346 +++++---------
 .../DoxygenTranslator/src/JavaDocConverter.h  |  41 +-
 .../DoxygenTranslator/src/PyDocConverter.cpp  | 273 ++++-------
 Source/DoxygenTranslator/src/PyDocConverter.h |  60 ++-
 11 files changed, 477 insertions(+), 925 deletions(-)

diff --git a/Source/DoxygenTranslator/src/DoxygenCommands.h b/Source/DoxygenTranslator/src/DoxygenCommands.h
index ff2527ace..0be6a1851 100644
--- a/Source/DoxygenTranslator/src/DoxygenCommands.h
+++ b/Source/DoxygenTranslator/src/DoxygenCommands.h
@@ -21,7 +21,9 @@ const char *sectionIndicators[] = {
   "exception", "if", "ifnot", "invariant", "note", "par", "param",
   "tparam", "post", "pre", "remarks", "remark", "result", "return",
   "returns", "retval", "sa", "see", "since", "test", "throw", "throws",
-  "todo", "version", "warning", "xrefitem"};
+  "todo", "version", "warning", "xrefitem"
+};
+
 const int sectionIndicatorsSize = sizeof(sectionIndicators) / sizeof(*sectionIndicators);
 
 /* All of the doxygen commands divided up by how they are parsed */
@@ -31,7 +33,9 @@ const char *simpleCommands[] = {
   "endcond",
   "callgraph", "callergraph", "showinitializer", "hideinitializer", "internal",
   "nosubgrouping", "public", "publicsection", "private", "privatesection",
-  "protected", "protectedsection", "tableofcontents"};
+  "protected", "protectedsection", "tableofcontents"
+};
+
 const int simpleCommandsSize = sizeof(simpleCommands) / sizeof(*simpleCommands);
 
 const char *commandWords[] = {
@@ -39,52 +43,72 @@ const char *commandWords[] = {
   "namespace", "relatesalso", "anchor", "dontinclude", "include",
   "includelineno", "copydoc", "copybrief", "copydetails", "verbinclude",
   "htmlinclude", "extends", "implements", "memberof", "related", "relatedalso",
-  "cite"};
+  "cite"
+};
+
 const int commandWordsSize = sizeof(commandWords) / sizeof(*commandWords);
 
 const char *commandLines[] = {
   "addindex", "fn", "name", "line", "var", "skipline", "typedef", "skip",
-  "until", "property"};
+  "until", "property"
+};
+
 const int commandLinesSize = sizeof(commandLines) / sizeof(*commandLines);
 
 const char *commandParagraph[] = {
   "partofdescription", "result", "return", "returns", "remarks", "remark",
   "since", "test", "sa", "see", "pre", "post", "details", "invariant",
   "deprecated", "date", "note", "warning", "version", "todo", "bug",
-  "attention", "brief", "author", "authors", "copyright", "short"};
+  "attention", "brief", "author", "authors", "copyright", "short"
+};
+
 const int commandParagraphSize = sizeof(commandParagraph) / sizeof(*commandParagraph);
 
 const char *commandEndCommands[] = {
-  CMD_HTML_ONLY, "latexonly", "manonly", "xmlonly", "link", "rtfonly"};
+  CMD_HTML_ONLY, "latexonly", "manonly", "xmlonly", "link", "rtfonly"
+};
+
 const int commandEndCommandsSize = sizeof(commandEndCommands) / sizeof(*commandEndCommands);
 
 const char *commandWordParagraphs[] = {
-  "param", "tparam", "throw", "throws", "retval", "exception", "example"};
+  "param", "tparam", "throw", "throws", "retval", "exception", "example"
+};
+
 const int commandWordParagraphsSize = sizeof(commandWordParagraphs) / sizeof(*commandWordParagraphs);
 
 const char *commandWordLines[] = {
   "page", "subsection", "subsubsection", "section", "paragraph", "defgroup",
-  "snippet", "mainpage"};
+  "snippet", "mainpage"
+};
+
 const int commandWordLinesSize = sizeof(commandWordLines) / sizeof(*commandWordLines);
 
 const char *commandWordOWordOWords[] = {
-  "category", "class", "protocol", "interface", "struct", "union"};
+  "category", "class", "protocol", "interface", "struct", "union"
+};
+
 const int commandWordOWordOWordsSize = sizeof(commandWordOWordOWords) / sizeof(*commandWordOWordOWords);
 
 const char *commandOWords[] = {
-  "dir", "file", "cond"};
+  "dir", "file", "cond"
+};
+
 const int commandOWordsSize = sizeof(commandOWords) / sizeof(*commandOWords);
 
 const char *commandErrorThrowings[] = {
   "annotatedclassstd::list", "classhierarchy", "define", "functionindex", "header",
   "headerfilestd::list", "inherit", "l", "postheader", "endcode", "enddot", "endmsc", "endhtmlonly",
   "endlatexonly", "endmanonly", "endlink", "endverbatim", "endxmlonly", "f]", "f}", "endif", "else",
-  "endrtfonly"};
+  "endrtfonly"
+};
+
 const int commandErrorThrowingsSize = sizeof(commandErrorThrowings) / sizeof(*commandErrorThrowings);
 
 const char *commandUniques[] = {
   "xrefitem", "arg", "ingroup", "par", "headerfile", "overload", "weakgroup", "ref", "subpage", "dotfile", "image", "addtogroup", "li",
-  "if", "ifnot", "elseif", "else", "mscfile", "code", CMD_VERBATIM, "f{", "f[", "f$", "dot", "msc"};
+  "if", "ifnot", "elseif", "else", "mscfile", "code", CMD_VERBATIM, "f{", "f[", "f$", "dot", "msc"
+};
+
 const int commandUniquesSize = sizeof(commandUniques) / sizeof(*commandUniques);
 
 // These HTML commands are transformed when producing output in other formats.
@@ -103,27 +127,30 @@ const int commandHtmlSize = sizeof(commandHtml) / sizeof(*commandHtml);
 
 // Only entities which are translatable to plain text are used here. Others
 // are copied unchanged to output.
-const char *commandHtmlEntities[] = { "&copy", "&trade", "&reg", // (C), (TM), (R)
-  "&lt",  // less-than symbol
-  "&gt",  // greater-than symbol
-  "&amp", // ampersand
-  "&apos", // single quotation mark (straight)
-  "&quot", // double quotation mark (straight)
-  "&lsquo", // left single quotation mark
-  "&rsquo", // right single quotation mark
-  "&ldquo", // left double quotation mark
-  "&rdquo", // right double quotation mark
-  "&ndash", // n-dash (for numeric ranges, e.g. 2–8)
-  "&mdash", // --
-  "&nbsp", //
-  "&times", // x
-  "&minus", // -
-  "&sdot", // .
-  "&sim", // ~
-  "&le", // <=
-  "&ge", // >=
-  "&larr", // <--
-  "&rarr" // -->
+const char *commandHtmlEntities[] = {
+  "&copy",                  // (C)
+  "&trade",                 // (TM)
+  "&reg",                   // (R)
+  "&lt",                    // less-than symbol
+  "&gt",                    // greater-than symbol
+  "&amp",                   // ampersand
+  "&apos",                  // single quotation mark (straight)
+  "&quot",                  // double quotation mark (straight)
+  "&lsquo",                 // left single quotation mark
+  "&rsquo",                 // right single quotation mark
+  "&ldquo",                 // left double quotation mark
+  "&rdquo",                 // right double quotation mark
+  "&ndash",                 // n-dash (for numeric ranges, e.g. 2–8)
+  "&mdash",                 // --
+  "&nbsp",                  //
+  "&times",                 // x
+  "&minus",                 // -
+  "&sdot",                  // .
+  "&sim",                   // ~
+  "&le",                    // <=
+  "&ge",                    // >=
+  "&larr",                  // <--
+  "&rarr"                   // -->
 };
 
 const int commandHtmlEntitiesSize = sizeof(commandHtmlEntities) / sizeof(*commandHtmlEntities);
diff --git a/Source/DoxygenTranslator/src/DoxygenEntity.cpp b/Source/DoxygenTranslator/src/DoxygenEntity.cpp
index 9e761c32b..98329e84f 100644
--- a/Source/DoxygenTranslator/src/DoxygenEntity.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenEntity.cpp
@@ -16,10 +16,8 @@
 
 using std::cout;
 
-DoxygenEntity::DoxygenEntity(const std::string &typeEnt) :
-  typeOfEntity(typeEnt),
-  isLeaf(true)
-{}
+DoxygenEntity::DoxygenEntity(const std::string &typeEnt):typeOfEntity(typeEnt), isLeaf(true) {
+}
 
 
 /* Basic node for commands that have
@@ -27,23 +25,15 @@ DoxygenEntity::DoxygenEntity(const std::string &typeEnt) :
  * example: \b word
  * OR holding a std::string
  */
-DoxygenEntity::DoxygenEntity(const std::string &typeEnt,
-                                 const std::string &param1) :
-  typeOfEntity(typeEnt),
-  data(param1),
-  isLeaf(true)
-{}
+DoxygenEntity::DoxygenEntity(const std::string &typeEnt, const std::string &param1) : typeOfEntity(typeEnt), data(param1), isLeaf(true) {
+}
 
 
 /* Nonterminal node
  * contains
  */
-DoxygenEntity::DoxygenEntity(const std::string &typeEnt,
-                                 const DoxygenEntityList &entList) :
-  typeOfEntity(typeEnt),
-  isLeaf(false),
-  entityList(entList)
-{}
+DoxygenEntity::DoxygenEntity(const std::string &typeEnt, const DoxygenEntityList &entList) : typeOfEntity(typeEnt), isLeaf(false), entityList(entList) {
+}
 
 
 void DoxygenEntity::printEntity(int level) const {
diff --git a/Source/DoxygenTranslator/src/DoxygenEntity.h b/Source/DoxygenTranslator/src/DoxygenEntity.h
index d7df95e91..29a0e2076 100644
--- a/Source/DoxygenTranslator/src/DoxygenEntity.h
+++ b/Source/DoxygenTranslator/src/DoxygenEntity.h
@@ -20,7 +20,7 @@
 
 class DoxygenEntity;
 
-typedef std::list <DoxygenEntity> DoxygenEntityList;
+typedef std::list<DoxygenEntity> DoxygenEntityList;
 typedef DoxygenEntityList::iterator DoxygenEntityListIt;
 typedef DoxygenEntityList::const_iterator DoxygenEntityListCIt;
 
@@ -37,7 +37,7 @@ public:
 
   DoxygenEntity(const std::string &typeEnt);
   DoxygenEntity(const std::string &typeEnt, const std::string &param1);
-  DoxygenEntity(const std::string & typeEnt, const DoxygenEntityList &entList);
+  DoxygenEntity(const std::string &typeEnt, const DoxygenEntityList &entList);
 
   void printEntity(int level) const;
 };
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.cpp b/Source/DoxygenTranslator/src/DoxygenParser.cpp
index faed5b931..c14cdb9fd 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenParser.cpp
@@ -25,10 +25,7 @@ using std::endl;
 // This constant defines the (only) characters valid inside a Doxygen "word".
 // It includes some unusual ones because of the commands such as \f[, \f{, \f],
 // \f} and \f$.
-static const char* DOXYGEN_WORD_CHARS = "abcdefghijklmnopqrstuvwxyz"
-                                        "ABCDEFGHIJKLMNOPQRSTUVWXYZ"
-                                        "0123456789"
-                                        "$[]{}";
+static const char *DOXYGEN_WORD_CHARS = "abcdefghijklmnopqrstuvwxyz" "ABCDEFGHIJKLMNOPQRSTUVWXYZ" "0123456789" "$[]{}";
 
 // Define static class members
 DoxygenParser::DoxyCommandsMap DoxygenParser::doxygenCommands;
@@ -37,18 +34,14 @@ std::set<std::string> DoxygenParser::doxygenSectionIndicators;
 const int TOKENSPERLINE = 8; //change this to change the printing behaviour of the token list
 const std::string END_HTML_TAG_MARK("/");
 
-DoxygenParser::DoxygenParser(bool noisy) :
-    noisy(noisy)
-{
+DoxygenParser::DoxygenParser(bool noisy) : noisy(noisy) {
   fillTables();
 }
 
-DoxygenParser::~DoxygenParser()
-{
+DoxygenParser::~DoxygenParser() {
 }
 
-void DoxygenParser::fillTables()
-{
+void DoxygenParser::fillTables() {
   // run it only once
   if (doxygenCommands.size())
     return;
@@ -98,8 +91,7 @@ void DoxygenParser::fillTables()
     doxygenSectionIndicators.insert(sectionIndicators[i]);
 }
 
-std::string DoxygenParser::stringToLower(const std::string &stringToConvert)
-{
+std::string DoxygenParser::stringToLower(const std::string &stringToConvert) {
 
   string result(stringToConvert.size(), ' ');
 
@@ -110,17 +102,14 @@ std::string DoxygenParser::stringToLower(const std::string &stringToConvert)
   return result;
 }
 
-bool DoxygenParser::isSectionIndicator(const std::string &smallString)
-{
+bool DoxygenParser::isSectionIndicator(const std::string &smallString) {
 
-  std::set<std::string>::iterator it = doxygenSectionIndicators.find(
-      stringToLower(smallString));
+  std::set<std::string>::iterator it = doxygenSectionIndicators.find(stringToLower(smallString));
 
   return it != doxygenSectionIndicators.end();
 }
 
-void DoxygenParser::printTree(const DoxygenEntityList &rootList)
-{
+void DoxygenParser::printTree(const DoxygenEntityList &rootList) {
   DoxygenEntityList::const_iterator p = rootList.begin();
   while (p != rootList.end()) {
     (*p).printEntity(0);
@@ -128,36 +117,29 @@ void DoxygenParser::printTree(const DoxygenEntityList &rootList)
   }
 }
 
-DoxygenParser::DoxyCommandEnum
-DoxygenParser::commandBelongs(const std::string &theCommand)
-{
+DoxygenParser::DoxyCommandEnum DoxygenParser::commandBelongs(const std::string &theCommand) {
   DoxyCommandsMapIt it = doxygenCommands.find(stringToLower(theCommand));
 
   if (it != doxygenCommands.end()) {
     return it->second;
   }
-
   // Check if this command is defined as an alias.
   if (Getattr(m_node, ("feature:doxygen:alias:" + theCommand).c_str())) {
     return COMMAND_ALIAS;
   }
-
   // Check if this command should be ignored.
-  if (String* const ignore = getIgnoreFeature(theCommand)) {
+  if (String *const ignore = getIgnoreFeature(theCommand)) {
     // Check that no value is specified for this feature ("1" is the implicit
     // one given to it by SWIG itself), we may use the value in the future, but
     // for now we only use the attributes.
     if (Strcmp(ignore, "1") != 0) {
       Swig_warning(WARN_PP_UNEXPECTED_TOKENS, m_fileName.c_str(), m_fileLineNo,
-          "Feature \"doxygen:ignore\" value ignored for Doxygen command \"%s\".\n",
-          theCommand.c_str());
+                   "Feature \"doxygen:ignore\" value ignored for Doxygen command \"%s\".\n", theCommand.c_str());
     }
-
     // Also ensure that the matching end command, if any, will be recognized.
     const string endCommand = getIgnoreFeatureEndCommand(theCommand);
     if (!endCommand.empty()) {
-      Setattr(m_node, ("feature:doxygen:ignore:" + endCommand).c_str(),
-          NewString("1"));
+      Setattr(m_node, ("feature:doxygen:ignore:" + endCommand).c_str(), NewString("1"));
     }
 
     return COMMAND_IGNORE;
@@ -166,8 +148,7 @@ DoxygenParser::commandBelongs(const std::string &theCommand)
   return NONE;
 }
 
-std::string DoxygenParser::trim(const std::string &text)
-{
+std::string DoxygenParser::trim(const std::string &text) {
   size_t start = text.find_first_not_of(" \t");
   size_t end = text.find_last_not_of(" \t");
 
@@ -177,8 +158,7 @@ std::string DoxygenParser::trim(const std::string &text)
   return text.substr(start, end - start + 1);
 }
 
-bool DoxygenParser::isEndOfLine()
-{
+bool DoxygenParser::isEndOfLine() {
   if (m_tokenListIt == m_tokenList.end()) {
     return false;
   }
@@ -186,22 +166,19 @@ bool DoxygenParser::isEndOfLine()
   return nextToken.m_tokenType == END_LINE;
 }
 
-void DoxygenParser::skipWhitespaceTokens()
-{
+void DoxygenParser::skipWhitespaceTokens() {
   if (m_tokenListIt == m_tokenList.end()) {
     return;
   }
 
   while (m_tokenListIt != m_tokenList.end()
-      && (m_tokenListIt->m_tokenType == END_LINE
-          || trim(m_tokenListIt->m_tokenString).empty())) {
+         && (m_tokenListIt->m_tokenType == END_LINE || trim(m_tokenListIt->m_tokenString).empty())) {
 
     m_tokenListIt++;
   }
 }
 
-std::string DoxygenParser::getNextToken()
-{
+std::string DoxygenParser::getNextToken() {
 
   if (m_tokenListIt == m_tokenList.end()) {
     return "";
@@ -214,15 +191,14 @@ std::string DoxygenParser::getNextToken()
   return "";
 }
 
-std::string DoxygenParser::getNextWord()
-{
+std::string DoxygenParser::getNextWord() {
 
   /*    if (m_tokenListIt == m_tokenList.end()) {
-   return "";
-   }
+     return "";
+     }
    */
   while (m_tokenListIt != m_tokenList.end()
-      && (m_tokenListIt->m_tokenType == PLAINSTRING)) {
+         && (m_tokenListIt->m_tokenType == PLAINSTRING)) {
     // handle quoted strings as words
     string token = m_tokenListIt->m_tokenString;
     if (token == "\"") {
@@ -251,8 +227,7 @@ std::string DoxygenParser::getNextWord()
   return "";
 }
 
-DoxygenParser::TokenListCIt DoxygenParser::getOneLine(const TokenList &tokList)
-{
+DoxygenParser::TokenListCIt DoxygenParser::getOneLine(const TokenList &tokList) {
 
   TokenListCIt endOfLineIt = m_tokenListIt;
 
@@ -266,8 +241,7 @@ DoxygenParser::TokenListCIt DoxygenParser::getOneLine(const TokenList &tokList)
   return tokList.end();
 }
 
-std::string DoxygenParser::getStringTilCommand(const TokenList & tokList)
-{
+std::string DoxygenParser::getStringTilCommand(const TokenList &tokList) {
 
   if (m_tokenListIt == tokList.end()) {
     return "";
@@ -284,9 +258,7 @@ std::string DoxygenParser::getStringTilCommand(const TokenList & tokList)
   return description;
 }
 
-std::string DoxygenParser::getStringTilEndCommand(
-    const std::string & theCommand, const TokenList & tokList)
-{
+std::string DoxygenParser::getStringTilEndCommand(const std::string &theCommand, const TokenList &tokList) {
 
   if (m_tokenListIt == tokList.end()) {
     return "";
@@ -307,15 +279,12 @@ std::string DoxygenParser::getStringTilEndCommand(
     m_tokenListIt++;
   }
 
-  printListError(WARN_DOXYGEN_COMMAND_EXPECTED,
-      theCommand + " command expected");
+  printListError(WARN_DOXYGEN_COMMAND_EXPECTED, theCommand + " command expected");
 
   return description;
 }
 
-DoxygenParser::TokenListCIt DoxygenParser::getEndOfParagraph(
-    const TokenList & tokList)
-{
+DoxygenParser::TokenListCIt DoxygenParser::getEndOfParagraph(const TokenList &tokList) {
 
   TokenListCIt endOfParagraph = m_tokenListIt;
 
@@ -347,9 +316,7 @@ DoxygenParser::TokenListCIt DoxygenParser::getEndOfParagraph(
   return tokList.end();
 }
 
-DoxygenParser::TokenListCIt DoxygenParser::getEndOfSection(
-    const std::string & theCommand, const TokenList & tokList)
-{
+DoxygenParser::TokenListCIt DoxygenParser::getEndOfSection(const std::string &theCommand, const TokenList &tokList) {
 
   TokenListCIt endOfParagraph = m_tokenListIt;
 
@@ -372,9 +339,7 @@ DoxygenParser::TokenListCIt DoxygenParser::getEndOfSection(
   return tokList.end();
 }
 
-DoxygenParser::TokenListCIt DoxygenParser::getEndCommand(
-    const std::string & theCommand, const TokenList & tokList)
-{
+DoxygenParser::TokenListCIt DoxygenParser::getEndCommand(const std::string &theCommand, const TokenList &tokList) {
 
   TokenListCIt endOfCommand = m_tokenListIt;
 
@@ -390,29 +355,21 @@ DoxygenParser::TokenListCIt DoxygenParser::getEndCommand(
   return tokList.end();
 }
 
-void DoxygenParser::skipEndOfLine()
-{
+void DoxygenParser::skipEndOfLine() {
   if (m_tokenListIt != m_tokenList.end()
       && m_tokenListIt->m_tokenType == END_LINE) {
     m_tokenListIt++;
   }
 }
 
-void
-DoxygenParser::addSimpleCommand(const std::string &theCommand,
-                                DoxygenEntityList &doxyList)
-{
+void DoxygenParser::addSimpleCommand(const std::string &theCommand, DoxygenEntityList &doxyList) {
   if (noisy)
     cout << "Parsing " << theCommand << endl;
 
   doxyList.push_back(DoxygenEntity(theCommand));
 }
 
-void
-DoxygenParser::addCommandWord(const std::string &theCommand,
-                              const TokenList &,
-                              DoxygenEntityList &doxyList)
-{
+void DoxygenParser::addCommandWord(const std::string &theCommand, const TokenList &, DoxygenEntityList &doxyList) {
   if (noisy)
     cout << "Parsing " << theCommand << endl;
 
@@ -427,16 +384,11 @@ DoxygenParser::addCommandWord(const std::string &theCommand,
     aNewList.push_back(DoxygenEntity("plainstd::string", name));
     doxyList.push_back(DoxygenEntity(theCommand, aNewList));
   } else {
-    printListError(WARN_DOXYGEN_COMMAND_ERROR,
-        "No word followed " + theCommand + " command. Not added");
+    printListError(WARN_DOXYGEN_COMMAND_ERROR, "No word followed " + theCommand + " command. Not added");
   }
 }
 
-void
-DoxygenParser::addCommandLine(const std::string &theCommand,
-                              const TokenList &tokList,
-                              DoxygenEntityList &doxyList)
-{
+void DoxygenParser::addCommandLine(const std::string &theCommand, const TokenList &tokList, DoxygenEntityList &doxyList) {
   if (noisy)
     cout << "Parsing " << theCommand << endl;
   TokenListCIt endOfLine = getOneLine(tokList);
@@ -445,11 +397,7 @@ DoxygenParser::addCommandLine(const std::string &theCommand,
   skipEndOfLine();
 }
 
-void
-DoxygenParser::addCommandParagraph(const std::string &theCommand,
-                                   const TokenList &tokList,
-                                   DoxygenEntityList &doxyList)
-{
+void DoxygenParser::addCommandParagraph(const std::string &theCommand, const TokenList &tokList, DoxygenEntityList &doxyList) {
   if (noisy)
     cout << "Parsing " << theCommand << endl;
 
@@ -459,11 +407,7 @@ DoxygenParser::addCommandParagraph(const std::string &theCommand,
   doxyList.push_back(DoxygenEntity(theCommand, aNewList));
 }
 
-void
-DoxygenParser::addCommandEndCommand(const std::string &theCommand,
-                                    const TokenList & tokList,
-                                    DoxygenEntityList &doxyList)
-{
+void DoxygenParser::addCommandEndCommand(const std::string &theCommand, const TokenList &tokList, DoxygenEntityList &doxyList) {
   if (noisy)
     cout << "Parsing " << theCommand << endl;
   TokenListCIt endCommand = getEndCommand("end" + theCommand, tokList);
@@ -477,19 +421,14 @@ DoxygenParser::addCommandEndCommand(const std::string &theCommand,
   doxyList.push_back(DoxygenEntity(theCommand, aNewList));
 }
 
-void
-DoxygenParser::addCommandWordParagraph(const std::string &theCommand,
-                                       const TokenList &tokList,
-                                       DoxygenEntityList &doxyList)
-{
+void DoxygenParser::addCommandWordParagraph(const std::string &theCommand, const TokenList &tokList, DoxygenEntityList &doxyList) {
   if (noisy)
     cout << "Parsing " << theCommand << endl;
 
   std::string name = getNextWord();
 
   if (name.empty()) {
-    printListError(WARN_DOXYGEN_COMMAND_ERROR,
-        "No word followed " + theCommand + " command. Not added");
+    printListError(WARN_DOXYGEN_COMMAND_ERROR, "No word followed " + theCommand + " command. Not added");
     return;
   }
   TokenListCIt endOfParagraph = getEndOfParagraph(tokList);
@@ -499,17 +438,12 @@ DoxygenParser::addCommandWordParagraph(const std::string &theCommand,
   doxyList.push_back(DoxygenEntity(theCommand, aNewList));
 }
 
-void
-DoxygenParser::addCommandWordLine(const std::string &theCommand,
-                                  const TokenList & tokList,
-                                  DoxygenEntityList &doxyList)
-{
+void DoxygenParser::addCommandWordLine(const std::string &theCommand, const TokenList &tokList, DoxygenEntityList &doxyList) {
   if (noisy)
     cout << "Parsing " << theCommand << endl;
   std::string name = getNextWord();
   if (name.empty()) {
-    printListError(WARN_DOXYGEN_COMMAND_ERROR,
-        "No word followed " + theCommand + " command. Not added");
+    printListError(WARN_DOXYGEN_COMMAND_ERROR, "No word followed " + theCommand + " command. Not added");
     return;
   }
 
@@ -521,18 +455,13 @@ DoxygenParser::addCommandWordLine(const std::string &theCommand,
   //else cout << "No line followed " << theCommand <<  " command. Not added" << endl;
 }
 
-void
-DoxygenParser::addCommandWordOWordOWord(const std::string &theCommand,
-                                        const TokenList &,
-                                        DoxygenEntityList &doxyList)
-{
+void DoxygenParser::addCommandWordOWordOWord(const std::string &theCommand, const TokenList &, DoxygenEntityList &doxyList) {
   if (noisy)
     cout << "Parsing " << theCommand << endl;
 
   std::string name = getNextWord();
   if (name.empty()) {
-    printListError(WARN_DOXYGEN_COMMAND_ERROR,
-        "No word followed " + theCommand + " command. Not added");
+    printListError(WARN_DOXYGEN_COMMAND_ERROR, "No word followed " + theCommand + " command. Not added");
     return;
   }
   std::string headerfile = getNextWord();
@@ -546,11 +475,7 @@ DoxygenParser::addCommandWordOWordOWord(const std::string &theCommand,
   doxyList.push_back(DoxygenEntity(theCommand, aNewList));
 }
 
-void
-DoxygenParser::addCommandOWord(const std::string &theCommand,
-                               const TokenList &,
-                               DoxygenEntityList &doxyList)
-{
+void DoxygenParser::addCommandOWord(const std::string &theCommand, const TokenList &, DoxygenEntityList &doxyList) {
   if (noisy)
     cout << "Parsing " << theCommand << endl;
 
@@ -560,23 +485,14 @@ DoxygenParser::addCommandOWord(const std::string &theCommand,
   doxyList.push_back(DoxygenEntity(theCommand, aNewList));
 }
 
-void
-DoxygenParser::addCommandErrorThrow(const std::string &theCommand,
-                                    const TokenList &tokList,
-                                    DoxygenEntityList &)
-{
+void DoxygenParser::addCommandErrorThrow(const std::string &theCommand, const TokenList &tokList, DoxygenEntityList &) {
 
   printListError(WARN_DOXYGEN_COMMAND_ERROR,
-      "Encountered: " + theCommand
-          + "\nThis command should not have been encountered. Behaviour past this may be unpredictable");
+                 "Encountered: " + theCommand + "\nThis command should not have been encountered. Behaviour past this may be unpredictable");
   m_tokenListIt = getOneLine(tokList);
 }
 
-void
-DoxygenParser::addCommandHtml(const std::string &theCommand,
-                              const TokenList &,
-                              DoxygenEntityList &doxyList)
-{
+void DoxygenParser::addCommandHtml(const std::string &theCommand, const TokenList &, DoxygenEntityList &doxyList) {
   if (noisy)
     cout << "Parsing " << theCommand << endl;
 
@@ -584,11 +500,7 @@ DoxygenParser::addCommandHtml(const std::string &theCommand,
   doxyList.push_back(DoxygenEntity(theCommand, htmlTagArgs));
 }
 
-void
-DoxygenParser::addCommandHtmlEntity(const std::string &theCommand,
-                                    const TokenList &,
-                                    DoxygenEntityList &doxyList)
-{
+void DoxygenParser::addCommandHtmlEntity(const std::string &theCommand, const TokenList &, DoxygenEntityList &doxyList) {
   if (noisy)
     cout << "Parsing " << theCommand << endl;
 
@@ -596,11 +508,7 @@ DoxygenParser::addCommandHtmlEntity(const std::string &theCommand,
   doxyList.push_back(DoxygenEntity(theCommand, aNewList));
 }
 
-void
-DoxygenParser::addCommandUnique(const std::string &theCommand,
-                                const TokenList &tokList,
-                                DoxygenEntityList &doxyList)
-{
+void DoxygenParser::addCommandUnique(const std::string &theCommand, const TokenList &tokList, DoxygenEntityList &doxyList) {
 
   static std::map<std::string, std::string> endCommands;
   DoxygenEntityList aNewList;
@@ -616,20 +524,17 @@ DoxygenParser::addCommandUnique(const std::string &theCommand,
       cout << "Parsing " << theCommand << endl;
     std::string key = getNextWord();
     if (key.empty()) {
-      printListError(WARN_DOXYGEN_COMMAND_ERROR,
-          "No key followed " + theCommand + " command. Not added");
+      printListError(WARN_DOXYGEN_COMMAND_ERROR, "No key followed " + theCommand + " command. Not added");
       return;
     }
     std::string heading = getNextWord();
     if (key.empty()) {
-      printListError(WARN_DOXYGEN_COMMAND_ERROR,
-          "No heading followed " + theCommand + " command. Not added");
+      printListError(WARN_DOXYGEN_COMMAND_ERROR, "No heading followed " + theCommand + " command. Not added");
       return;
     }
     std::string title = getNextWord();
     if (title.empty()) {
-      printListError(WARN_DOXYGEN_COMMAND_ERROR,
-          "No title followed " + theCommand + " command. Not added");
+      printListError(WARN_DOXYGEN_COMMAND_ERROR, "No title followed " + theCommand + " command. Not added");
       return;
     }
     TokenListCIt endOfParagraph = getEndOfParagraph(tokList);
@@ -687,8 +592,7 @@ DoxygenParser::addCommandUnique(const std::string &theCommand,
       cout << "Parsing " << theCommand << endl;
     std::string name = getNextWord();
     if (name.empty()) {
-      printListError(WARN_DOXYGEN_COMMAND_ERROR,
-          "No word followed " + theCommand + " command. Not added");
+      printListError(WARN_DOXYGEN_COMMAND_ERROR, "No word followed " + theCommand + " command. Not added");
       return;
     }
     DoxygenEntityList aNewList;
@@ -705,8 +609,7 @@ DoxygenParser::addCommandUnique(const std::string &theCommand,
       cout << "Parsing " << theCommand << endl;
     std::string name = getNextWord();
     if (name.empty()) {
-      printListError(WARN_DOXYGEN_COMMAND_ERROR,
-          "No key followed " + theCommand + " command. Not added");
+      printListError(WARN_DOXYGEN_COMMAND_ERROR, "No key followed " + theCommand + " command. Not added");
       return;
     }
     DoxygenEntityList aNewList;
@@ -719,13 +622,13 @@ DoxygenParser::addCommandUnique(const std::string &theCommand,
     std::string refTitle = getNextWord();
     // If title is following the ref tag, it must be quoted. Otherwise
     // doxy puts link on ref id.
-    if (refTitle.size() > 1  &&  refTitle[0] == '"') {
-        // remove quotes
-        refTitle = refTitle.substr(1, refTitle.size() - 2);
-        aNewList.push_back(DoxygenEntity("plainstd::string", refTitle));
+    if (refTitle.size() > 1 && refTitle[0] == '"') {
+      // remove quotes
+      refTitle = refTitle.substr(1, refTitle.size() - 2);
+      aNewList.push_back(DoxygenEntity("plainstd::string", refTitle));
     } else {
-        // no quoted string is following, so we have to restore iterator
-        m_tokenListIt = tmpIt;
+      // no quoted string is following, so we have to restore iterator
+      m_tokenListIt = tmpIt;
     }
     doxyList.push_back(DoxygenEntity(theCommand, aNewList));
   }
@@ -735,8 +638,7 @@ DoxygenParser::addCommandUnique(const std::string &theCommand,
       cout << "Parsing " << theCommand << endl;
     std::string name = getNextWord();
     if (name.empty()) {
-      printListError(WARN_DOXYGEN_COMMAND_ERROR,
-          "No name followed " + theCommand + " command. Not added");
+      printListError(WARN_DOXYGEN_COMMAND_ERROR, "No name followed " + theCommand + " command. Not added");
       return;
     }
     std::string text = getNextWord();
@@ -754,8 +656,7 @@ DoxygenParser::addCommandUnique(const std::string &theCommand,
   // \f{env}{ ... \f}
   // \f$ ... \f$
   else if (theCommand == "code" || theCommand == "verbatim"
-      || theCommand == "dot" || theCommand == "msc" || theCommand == "f["
-      || theCommand == "f{" || theCommand == "f$") {
+           || theCommand == "dot" || theCommand == "msc" || theCommand == "f[" || theCommand == "f{" || theCommand == "f$") {
     if (!endCommands.size()) {
       // fill in static table of end commands
       endCommands["f["] = "f]";
@@ -784,8 +685,7 @@ DoxygenParser::addCommandUnique(const std::string &theCommand,
       cout << "Parsing " << theCommand << endl;
     std::string file = getNextWord();
     if (file.empty()) {
-      printListError(WARN_DOXYGEN_COMMAND_ERROR,
-          "No file followed " + theCommand + " command. Not added");
+      printListError(WARN_DOXYGEN_COMMAND_ERROR, "No file followed " + theCommand + " command. Not added");
       return;
     }
     std::string caption = getNextWord();
@@ -800,14 +700,12 @@ DoxygenParser::addCommandUnique(const std::string &theCommand,
       cout << "Parsing " << theCommand << endl;
     std::string format = getNextWord();
     if (format.empty()) {
-      printListError(WARN_DOXYGEN_COMMAND_ERROR,
-          "No format followed " + theCommand + " command. Not added");
+      printListError(WARN_DOXYGEN_COMMAND_ERROR, "No format followed " + theCommand + " command. Not added");
       return;
     }
     std::string file = getNextWord();
     if (file.empty()) {
-      printListError(WARN_DOXYGEN_COMMAND_ERROR,
-          "No name followed " + theCommand + " command. Not added");
+      printListError(WARN_DOXYGEN_COMMAND_ERROR, "No name followed " + theCommand + " command. Not added");
       return;
     }
     std::string caption = getNextWord();
@@ -828,9 +726,7 @@ DoxygenParser::addCommandUnique(const std::string &theCommand,
       cout << "Parsing " << theCommand << endl;
     std::string name = getNextWord();
     if (name.empty()) {
-      printListError(WARN_DOXYGEN_COMMAND_ERROR,
-          "There should be at least one word following the '" + theCommand
-              + "' command. Command ignored.");
+      printListError(WARN_DOXYGEN_COMMAND_ERROR, "There should be at least one word following the '" + theCommand + "' command. Command ignored.");
       return;
     }
     DoxygenEntityList aNewList;
@@ -843,20 +739,17 @@ DoxygenParser::addCommandUnique(const std::string &theCommand,
     skipEndOfLine();
   }
   // \if <cond> [\else ...] [\elseif <cond> ...] \endif
-  else if (theCommand == "if" || theCommand == "ifnot" || theCommand == "else"
-      || theCommand == "elseif") {
+  else if (theCommand == "if" || theCommand == "ifnot" || theCommand == "else" || theCommand == "elseif") {
     if (noisy)
       cout << "Parsing " << theCommand << endl;
 
     std::string cond;
     bool skipEndif = false; // if true then we skip endif after parsing block of code
-    bool needsCond = (theCommand == "if" || theCommand == "ifnot"
-        || theCommand == "elseif");
+    bool needsCond = (theCommand == "if" || theCommand == "ifnot" || theCommand == "elseif");
     if (needsCond) {
       cond = getNextWord();
       if (cond.empty()) {
-        printListError(WARN_DOXYGEN_COMMAND_ERROR,
-            "No word followed " + theCommand + " command. Not added");
+        printListError(WARN_DOXYGEN_COMMAND_ERROR, "No word followed " + theCommand + " command. Not added");
         return;
       }
     }
@@ -871,8 +764,7 @@ DoxygenParser::addCommandUnique(const std::string &theCommand,
           nestedCounter++;
         else if (it->m_tokenString == "endif")
           nestedCounter--;
-        if (nestedCounter == 1
-            && (it->m_tokenString == "else" || it->m_tokenString == "elseif")) { // else found
+        if (nestedCounter == 1 && (it->m_tokenString == "else" || it->m_tokenString == "elseif")) { // else found
           endCommand = it;
           break;
         }
@@ -885,8 +777,7 @@ DoxygenParser::addCommandUnique(const std::string &theCommand,
     }
 
     if (endCommand == tokList.end()) {
-      printListError(WARN_DOXYGEN_COMMAND_EXPECTED,
-          "No corresponding endif found");
+      printListError(WARN_DOXYGEN_COMMAND_EXPECTED, "No corresponding endif found");
       return;
     }
 
@@ -900,21 +791,15 @@ DoxygenParser::addCommandUnique(const std::string &theCommand,
   }
 }
 
-void
-DoxygenParser::aliasCommand(const std::string& theCommand,
-                            const TokenList& /* tokList */,
-                            DoxygenEntityList &doxyList)
-{
-  String* const alias = Getattr(m_node, ("feature:doxygen:alias:" + theCommand).c_str());
+void DoxygenParser::aliasCommand(const std::string &theCommand, const TokenList &/* tokList */ , DoxygenEntityList &doxyList) {
+  String *const alias = Getattr(m_node, ("feature:doxygen:alias:" + theCommand).c_str());
   if (!alias)
     return;
 
   doxyList.push_back(DoxygenEntity("plainstd::string", Char(alias)));
 }
 
-String* DoxygenParser::getIgnoreFeature(const std::string& theCommand,
-                                        const char* argument) const
-{
+String *DoxygenParser::getIgnoreFeature(const std::string &theCommand, const char *argument) const {
   string feature_name = "feature:doxygen:ignore:" + theCommand;
   if (argument) {
     feature_name += ':';
@@ -924,13 +809,12 @@ String* DoxygenParser::getIgnoreFeature(const std::string& theCommand,
   return Getattr(m_node, feature_name.c_str());
 }
 
-string DoxygenParser::getIgnoreFeatureEndCommand(const std::string& theCommand) const
-{
+string DoxygenParser::getIgnoreFeatureEndCommand(const std::string &theCommand) const {
   // We may be dealing either with a simple command or with the starting command
   // of a block, as indicated by the value of "range" starting with "end".
   string endCommand;
-  if (String* const range = getIgnoreFeature(theCommand, "range")) {
-    const char* const p = Char(range);
+  if (String *const range = getIgnoreFeature(theCommand, "range")) {
+    const char *const p = Char(range);
     if (strncmp(p, "end", 3) == 0) {
       if (p[3] == ':') {
         // Normally the end command name follows after the colon.
@@ -946,11 +830,7 @@ string DoxygenParser::getIgnoreFeatureEndCommand(const std::string& theCommand)
   return endCommand;
 }
 
-void
-DoxygenParser::ignoreCommand(const std::string& theCommand,
-                             const TokenList &tokList,
-                             DoxygenEntityList &doxyList)
-{
+void DoxygenParser::ignoreCommand(const std::string &theCommand, const TokenList &tokList, DoxygenEntityList &doxyList) {
   const string endCommand = getIgnoreFeatureEndCommand(theCommand);
   if (!endCommand.empty()) {
     TokenListCIt itEnd = getEndCommand(endCommand, tokList);
@@ -958,7 +838,6 @@ DoxygenParser::ignoreCommand(const std::string& theCommand,
       printListError(WARN_DOXYGEN_COMMAND_EXPECTED, "Expected " + endCommand);
       return;
     }
-
     // If we ignore the command, also ignore any whitespace preceding it as we
     // want to avoid having lines consisting of whitespace only or trailing
     // whitespace in general (at least Python, with its pep8 tool, really
@@ -966,16 +845,14 @@ DoxygenParser::ignoreCommand(const std::string& theCommand,
     if (!doxyList.empty()) {
       DoxygenEntityList::iterator i = doxyList.end();
       --i;
-      if (i->typeOfEntity == "plainstd::string" &&
-          i->data.find_first_not_of(" \t") == std::string::npos) {
+      if (i->typeOfEntity == "plainstd::string" && i->data.find_first_not_of(" \t") == std::string::npos) {
         doxyList.erase(i);
       }
     }
-
     // Determine what to do with the part of the comment between the start and
     // end commands: by default, we simply throw it away, but "contents"
     // attribute may be used to change this.
-    if (String* const contents = getIgnoreFeature(theCommand, "contents")) {
+    if (String *const contents = getIgnoreFeature(theCommand, "contents")) {
       // Currently only "parse" is supported but we may need to add "copy" to
       // handle custom tags which contain text that is supposed to be copied
       // verbatim in the future.
@@ -983,17 +860,14 @@ DoxygenParser::ignoreCommand(const std::string& theCommand,
         DoxygenEntityList aNewList = parse(itEnd, tokList);
         doxyList.splice(doxyList.end(), aNewList);
       } else {
-        Swig_error(m_fileName.c_str(), m_fileLineNo,
-            "Invalid \"doxygen:ignore\" feature \"contents\" attribute \"%s\".\n",
-            Char(contents)
-          );
+        Swig_error(m_fileName.c_str(), m_fileLineNo, "Invalid \"doxygen:ignore\" feature \"contents\" attribute \"%s\".\n", Char(contents));
         return;
       }
     }
 
     m_tokenListIt = itEnd;
     m_tokenListIt++;
-  } else if (String* const range = getIgnoreFeature(theCommand, "range")) {
+  } else if (String *const range = getIgnoreFeature(theCommand, "range")) {
     // Currently we only support "line" but, in principle, we should also
     // support "word" and "paragraph" for consistency with the built-in Doxygen
     // commands which can have either of these three ranges (which are indicated
@@ -1004,20 +878,13 @@ DoxygenParser::ignoreCommand(const std::string& theCommand,
       m_tokenListIt = getOneLine(tokList);
       skipEndOfLine();
     } else {
-      Swig_error(m_fileName.c_str(), m_fileLineNo,
-          "Invalid \"doxygen:ignore\" feature \"range\" attribute \"%s\".\n",
-          Char(range)
-        );
+      Swig_error(m_fileName.c_str(), m_fileLineNo, "Invalid \"doxygen:ignore\" feature \"range\" attribute \"%s\".\n", Char(range));
       return;
     }
   }
 }
 
-void
-DoxygenParser::addCommand(const std::string &commandString,
-                          const TokenList &tokList,
-                          DoxygenEntityList &doxyList)
-{
+void DoxygenParser::addCommand(const std::string &commandString, const TokenList &tokList, DoxygenEntityList &doxyList) {
 
   string theCommand = stringToLower(commandString);
 
@@ -1088,12 +955,9 @@ DoxygenParser::addCommand(const std::string &commandString,
 /**
  * This method converts TokenList to DoxygenEntryList.
  */
-DoxygenEntityList DoxygenParser::parse(TokenListCIt endParsingIndex,
-                                       const TokenList &tokList, bool root)
-{
+DoxygenEntityList DoxygenParser::parse(TokenListCIt endParsingIndex, const TokenList &tokList, bool root) {
   // if we are root, than any strings should be added as 'partofdescription', else as 'plainstd::string'
-  std::string currPlainstringCommandType =
-      root ? "partofdescription" : "plainstd::string";
+  std::string currPlainstringCommandType = root ? "partofdescription" : "plainstd::string";
   DoxygenEntityList aNewList;
 
   while (m_tokenListIt != endParsingIndex) {
@@ -1115,23 +979,17 @@ DoxygenEntityList DoxygenParser::parse(TokenListCIt endParsingIndex,
 
     if (endParsingIndex != tokList.end() && m_tokenListIt == tokList.end()) {
       // this could happen if we can't reach the original endParsingIndex
-      printListError(WARN_DOXYGEN_UNEXPECTED_END_OF_COMMENT,
-          "Unexpected end of comment encountered");
+      printListError(WARN_DOXYGEN_UNEXPECTED_END_OF_COMMENT, "Unexpected end of comment encountered");
       break;
     }
   }
   return aNewList;
 }
 
-DoxygenEntityList DoxygenParser::createTree(Node* node, String* documentation)
-{
+DoxygenEntityList DoxygenParser::createTree(Node *node, String *documentation) {
   m_node = node;
 
-  tokenizeDoxygenComment(
-      Char(documentation),
-      Char(Getfile(documentation)),
-      Getline(documentation)
-    );
+  tokenizeDoxygenComment(Char(documentation), Char(Getfile(documentation)), Getline(documentation));
 
   if (noisy) {
     cout << "---TOKEN LIST---" << endl;
@@ -1151,9 +1009,7 @@ DoxygenEntityList DoxygenParser::createTree(Node* node, String* documentation)
  * Splits 'text' on 'separator' chars. Separator chars are not part of the
  * strings.
  */
-DoxygenParser::StringVector DoxygenParser::split(const std::string &text,
-                                                 char separator)
-{
+DoxygenParser::StringVector DoxygenParser::split(const std::string &text, char separator) {
   StringVector lines;
   size_t prevPos = 0, pos = 0;
 
@@ -1170,8 +1026,7 @@ DoxygenParser::StringVector DoxygenParser::split(const std::string &text,
  * Returns true, if 'c' is one of doxygen comment block start
  * characters: *, /, or !
  */
-bool DoxygenParser::isStartOfDoxyCommentChar(char c)
-{
+bool DoxygenParser::isStartOfDoxyCommentChar(char c) {
   return (strchr("*/!", c) != NULL);
 }
 
@@ -1180,9 +1035,7 @@ bool DoxygenParser::isStartOfDoxyCommentChar(char c)
  * Doxygen commands. In that case true is returned. If the command is not
  * recognized as a doxygen command, it is ignored and false is returned.
  */
-bool DoxygenParser::addDoxyCommand(DoxygenParser::TokenList &tokList,
-                                   const std::string &cmd)
-{
+bool DoxygenParser::addDoxyCommand(DoxygenParser::TokenList &tokList, const std::string &cmd) {
   if (commandBelongs(cmd) != NONE) {
     tokList.push_back(Token(COMMAND, cmd));
     return true;
@@ -1213,17 +1066,14 @@ bool DoxygenParser::addDoxyCommand(DoxygenParser::TokenList &tokList,
  * done, Doxygen commands are ignored. It is used for commands \verbatim,
  * \htmlonly, \f$, \f[, and \f{.
  */
-size_t DoxygenParser::processVerbatimText(size_t pos, const std::string &line)
-{
+size_t DoxygenParser::processVerbatimText(size_t pos, const std::string &line) {
   if (line[pos] == '\\' || line[pos] == '@') { // check for end commands
 
     pos++;
-    size_t endOfWordPos = line.find_first_not_of( DOXYGEN_WORD_CHARS, pos);
+    size_t endOfWordPos = line.find_first_not_of(DOXYGEN_WORD_CHARS, pos);
     string cmd = line.substr(pos, endOfWordPos - pos);
 
-    if (cmd == CMD_END_HTML_ONLY || cmd == CMD_END_VERBATIM
-        || cmd == CMD_END_LATEX_1 || cmd == CMD_END_LATEX_2
-        || cmd == CMD_END_LATEX_3) {
+    if (cmd == CMD_END_HTML_ONLY || cmd == CMD_END_VERBATIM || cmd == CMD_END_LATEX_1 || cmd == CMD_END_LATEX_2 || cmd == CMD_END_LATEX_3) {
 
       m_isVerbatimText = false;
       addDoxyCommand(m_tokenList, cmd);
@@ -1231,8 +1081,8 @@ size_t DoxygenParser::processVerbatimText(size_t pos, const std::string &line)
     } else {
 
       m_tokenList.push_back(Token(PLAINSTRING,
-      // include '\' or '@'
-          line.substr(pos - 1, endOfWordPos - pos + 1)));
+                                  // include '\' or '@'
+                                  line.substr(pos - 1, endOfWordPos - pos + 1)));
     }
 
     pos = endOfWordPos;
@@ -1241,8 +1091,7 @@ size_t DoxygenParser::processVerbatimText(size_t pos, const std::string &line)
 
     // whitespaces are stored as plain strings
     size_t startOfPossibleEndCmd = line.find_first_of("\\@", pos);
-    m_tokenList.push_back(
-        Token(PLAINSTRING, line.substr(pos, startOfPossibleEndCmd - pos)));
+    m_tokenList.push_back(Token(PLAINSTRING, line.substr(pos, startOfPossibleEndCmd - pos)));
     pos = startOfPossibleEndCmd;
   }
 
@@ -1253,8 +1102,7 @@ size_t DoxygenParser::processVerbatimText(size_t pos, const std::string &line)
  * Processes doxy commands for escaped characters: \$ \@ \\ \& \~ \< \> \# \% \" \. \::
  * Handling this separately supports documentation text like \@someText.
  */
-bool DoxygenParser::processEscapedChars(size_t &pos, const std::string &line)
-{
+bool DoxygenParser::processEscapedChars(size_t &pos, const std::string &line) {
   if ((pos + 1) < line.size()) {
 
     // \ and @ with trailing whitespace or quoted get to output as plain string
@@ -1264,7 +1112,6 @@ bool DoxygenParser::processEscapedChars(size_t &pos, const std::string &line)
       pos++;
       return true;
     }
-
     // these chars can be escaped for doxygen
     string escapedChars = "$@\\&~<>#%\".";
     if (escapedChars.find(line[pos + 1]) != string::npos) {
@@ -1273,8 +1120,7 @@ bool DoxygenParser::processEscapedChars(size_t &pos, const std::string &line)
       pos += 2;
       return true;
 
-    } else if ((pos + 2) < line.size() && line[pos + 1] == ':'
-        && line[pos + 2] == ':') {
+    } else if ((pos + 2) < line.size() && line[pos + 1] == ':' && line[pos + 2] == ':') {
 
       // add command \:: - handling this separately supports documentation
       // text like \::someText
@@ -1289,16 +1135,14 @@ bool DoxygenParser::processEscapedChars(size_t &pos, const std::string &line)
 /*
  * Processes word doxygen commands, like \arg, \c, \b, \return, ...
  */
-void DoxygenParser::processWordCommands(size_t &pos, const std::string &line)
-{
+void DoxygenParser::processWordCommands(size_t &pos, const std::string &line) {
   pos++;
   size_t endOfWordPos = line.find_first_not_of(DOXYGEN_WORD_CHARS, pos);
 
   string cmd = line.substr(pos, endOfWordPos - pos);
   addDoxyCommand(m_tokenList, cmd);
 
-  if (cmd == CMD_HTML_ONLY || cmd == CMD_VERBATIM || cmd == CMD_LATEX_1
-      || cmd == CMD_LATEX_2 || cmd == CMD_LATEX_3) {
+  if (cmd == CMD_HTML_ONLY || cmd == CMD_VERBATIM || cmd == CMD_LATEX_1 || cmd == CMD_LATEX_2 || cmd == CMD_LATEX_3) {
 
     m_isVerbatimText = true;
 
@@ -1312,8 +1156,7 @@ void DoxygenParser::processWordCommands(size_t &pos, const std::string &line)
   pos = endOfWordPos;
 }
 
-void DoxygenParser::processHtmlTags(size_t &pos, const std::string &line)
-{
+void DoxygenParser::processHtmlTags(size_t &pos, const std::string &line) {
   bool isEndHtmlTag = false;
   pos++;
   if (line.size() > pos && line[pos] == '/') {
@@ -1329,24 +1172,21 @@ void DoxygenParser::processHtmlTags(size_t &pos, const std::string &line)
   // prepend '<' to distinguish HTML tags from doxygen commands
   if (!cmd.empty() && addDoxyCommand(m_tokenList, '<' + cmd)) {
     // it is a valid HTML command
-    if (line[pos] != '>') { // it should be HTML tag with args,
-                            // for example <A ...>, <IMG ...>, ...
+    if (line[pos] != '>') {
+      // it should be HTML tag with args,
+      // for example <A ...>, <IMG ...>, ...
       if (isEndHtmlTag) {
         m_tokenListIt = m_tokenList.end();
-        printListError(WARN_DOXYGEN_COMMAND_ERROR,
-            "Illegal end HTML tag without '>' found! Tag: " + cmd);
+        printListError(WARN_DOXYGEN_COMMAND_ERROR, "Illegal end HTML tag without '>' found! Tag: " + cmd);
       }
 
       endHtmlPos = line.find(">", pos);
       if (endHtmlPos == string::npos) {
         m_tokenListIt = m_tokenList.end();
-        printListError(WARN_DOXYGEN_COMMAND_ERROR,
-            "HTML tag without '>' found! Tag: " + cmd);
+        printListError(WARN_DOXYGEN_COMMAND_ERROR, "HTML tag without '>' found! Tag: " + cmd);
       }
-
       // add args of HTML command, like link URL, image URL, ...
-      m_tokenList.push_back(
-          Token(PLAINSTRING, line.substr(pos, endHtmlPos - pos)));
+      m_tokenList.push_back(Token(PLAINSTRING, line.substr(pos, endHtmlPos - pos)));
       pos = endHtmlPos;
     } else {
       if (isEndHtmlTag) {
@@ -1368,10 +1208,8 @@ void DoxygenParser::processHtmlTags(size_t &pos, const std::string &line)
   }
 }
 
-void DoxygenParser::processHtmlEntities(size_t &pos, const std::string &line)
-{
-  size_t endOfWordPos = line.find_first_not_of("abcdefghijklmnopqrstuvwxyz",
-      pos + 1);
+void DoxygenParser::processHtmlEntities(size_t &pos, const std::string &line) {
+  size_t endOfWordPos = line.find_first_not_of("abcdefghijklmnopqrstuvwxyz", pos + 1);
 
   if (endOfWordPos != string::npos) {
 
@@ -1379,14 +1217,11 @@ void DoxygenParser::processHtmlEntities(size_t &pos, const std::string &line)
       // if entity is not recognized by Doxygen (not in the list of
       // commands) nothing is added (here and in Doxygen).
       addDoxyCommand(m_tokenList, line.substr(pos, endOfWordPos - pos));
-      endOfWordPos++;  // skip ';'
-
+      endOfWordPos++; // skip ';'
     } else {
-
       // it is not an entity - add entity for ampersand and the rest of string
       addDoxyCommand(m_tokenList, "&amp");
-      m_tokenList.push_back(
-          Token(PLAINSTRING, line.substr(pos + 1, endOfWordPos - pos - 1)));
+      m_tokenList.push_back(Token(PLAINSTRING, line.substr(pos + 1, endOfWordPos - pos - 1)));
     }
   }
   pos = endOfWordPos;
@@ -1395,8 +1230,7 @@ void DoxygenParser::processHtmlEntities(size_t &pos, const std::string &line)
 /*
  * This method processes normal comment, which has to be tokenized.
  */
-size_t DoxygenParser::processNormalComment(size_t pos, const std::string &line)
-{
+size_t DoxygenParser::processNormalComment(size_t pos, const std::string &line) {
   switch (line[pos]) {
   case '\\':
   case '@':
@@ -1407,14 +1241,14 @@ size_t DoxygenParser::processNormalComment(size_t pos, const std::string &line)
     processWordCommands(pos, line);
     break;
 
-  case ' ':  // whitespace
-  case '\t': {
-    // whitespaces are stored as plain strings
-    size_t startOfNextWordPos = line.find_first_not_of(" \t", pos + 1);
-    m_tokenList.push_back(
-        Token(PLAINSTRING, line.substr(pos, startOfNextWordPos - pos)));
-    pos = startOfNextWordPos;
-  }
+  case ' ': // whitespace
+  case '\t':
+    {
+      // whitespaces are stored as plain strings
+      size_t startOfNextWordPos = line.find_first_not_of(" \t", pos + 1);
+      m_tokenList.push_back(Token(PLAINSTRING, line.substr(pos, startOfNextWordPos - pos)));
+      pos = startOfNextWordPos;
+    }
     break;
 
   case '<':
@@ -1434,8 +1268,7 @@ size_t DoxygenParser::processNormalComment(size_t pos, const std::string &line)
     break;
   default:
     m_tokenListIt = m_tokenList.end();
-    printListError(WARN_DOXYGEN_COMMAND_ERROR,
-        std::string("Unknown special character: ") + line[pos]);
+    printListError(WARN_DOXYGEN_COMMAND_ERROR, std::string("Unknown special character: ") + line[pos]);
   }
 
   return pos;
@@ -1445,10 +1278,7 @@ size_t DoxygenParser::processNormalComment(size_t pos, const std::string &line)
  * This is the main method, which tokenizes Doxygen comment to words and
  * doxygen commands.
  */
-void DoxygenParser::tokenizeDoxygenComment(const std::string &doxygenComment,
-                                           const std::string &fileName,
-                                           int fileLine)
-{
+void DoxygenParser::tokenizeDoxygenComment(const std::string &doxygenComment, const std::string &fileName, int fileLine) {
   m_isVerbatimText = false;
   m_isInQuotedString = false;
   m_tokenList.clear();
@@ -1477,7 +1307,6 @@ void DoxygenParser::tokenizeDoxygenComment(const std::string &doxygenComment,
       m_tokenList.push_back(Token(END_LINE, "\n"));
       continue;
     }
-
     // skip sequences of '*', '/', and '!' of any length
     bool isStartOfCommentLineCharFound = false;
     while (pos < line.size() && isStartOfDoxyCommentChar(line[pos])) {
@@ -1489,7 +1318,6 @@ void DoxygenParser::tokenizeDoxygenComment(const std::string &doxygenComment,
       m_tokenList.push_back(Token(END_LINE, "\n"));
       continue;
     }
-
     // if 'isStartOfCommentLineCharFound' then preserve leading spaces, so
     // ' *    comment' gets translated to ' *    comment', not ' * comment'
     // This is important to keep formatting for comments translated to Python.
@@ -1500,7 +1328,6 @@ void DoxygenParser::tokenizeDoxygenComment(const std::string &doxygenComment,
         continue;
       }
     }
-
     // line[pos] may be ' \t' or start of word, it there was no '*', '/' or '!'
     // at beginning of the line. Make sure it points to start of the first word
     // in the line.
@@ -1512,13 +1339,11 @@ void DoxygenParser::tokenizeDoxygenComment(const std::string &doxygenComment,
       }
 
       if (firstWordPos > pos) {
-        m_tokenList.push_back(
-            Token(PLAINSTRING, line.substr(pos, firstWordPos - pos)));
+        m_tokenList.push_back(Token(PLAINSTRING, line.substr(pos, firstWordPos - pos)));
         pos = firstWordPos;
       }
     } else {
-        m_tokenList.push_back(
-            Token(PLAINSTRING, line.substr(0, pos)));
+      m_tokenList.push_back(Token(PLAINSTRING, line.substr(0, pos)));
     }
 
     while (pos != string::npos) {
@@ -1572,12 +1397,10 @@ void DoxygenParser::tokenizeDoxygenComment(const std::string &doxygenComment,
   m_tokenListIt = m_tokenList.begin();
 }
 
-void DoxygenParser::printList()
-{
+void DoxygenParser::printList() {
 
   int tokNo = 0;
-  for (TokenListCIt it = m_tokenList.begin(); it != m_tokenList.end();
-      it++, tokNo++) {
+  for (TokenListCIt it = m_tokenList.begin(); it != m_tokenList.end(); it++, tokNo++) {
 
     cout << it->toString() << " ";
 
@@ -1587,8 +1410,7 @@ void DoxygenParser::printList()
   }
 }
 
-void DoxygenParser::printListError(int warningType, const std::string &message)
-{
+void DoxygenParser::printListError(int warningType, const std::string &message) {
   int curLine = m_fileLineNo;
   for (TokenListCIt it = m_tokenList.begin(); it != m_tokenListIt; it++) {
     if (it->m_tokenType == END_LINE) {
@@ -1596,6 +1418,5 @@ void DoxygenParser::printListError(int warningType, const std::string &message)
     }
   }
 
-  Swig_warning(warningType, m_fileName.c_str(), curLine,
-      "Doxygen parser warning: %s.\n", message.c_str());
+  Swig_warning(warningType, m_fileName.c_str(), curLine, "Doxygen parser warning: %s.\n", message.c_str());
 }
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.h b/Source/DoxygenTranslator/src/DoxygenParser.h
index 82550465d..35204e670 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.h
+++ b/Source/DoxygenTranslator/src/DoxygenParser.h
@@ -52,14 +52,12 @@ private:
   class Token {
   public:
     DoxyCommandEnum m_tokenType;
-    std::string m_tokenString;		/* the data , such as param for @param */
-
-    Token(DoxyCommandEnum tType, std::string tString) :
-      m_tokenType(tType),
-      m_tokenString(tString) {}
+    std::string m_tokenString; /* the data , such as param for @param */
 
+    Token(DoxyCommandEnum tType, std::string tString) : m_tokenType(tType), m_tokenString(tString) {
+    }
+    
     std::string toString() const {
-
       switch (m_tokenType) {
       case END_LINE:
         return "{END OF LINE}";
@@ -96,7 +94,7 @@ private:
   bool m_isVerbatimText; // used to handle \htmlonly and \verbatim commands
   bool m_isInQuotedString;
 
-  Node* m_node;
+  Node *m_node;
   std::string m_fileName;
   int m_fileLineNo;
 
@@ -104,17 +102,17 @@ private:
    * Return the end command for a command appearing in "ignore" feature or empty
    * string if this is a simple command and not a block one.
    */
-  std::string getIgnoreFeatureEndCommand(const std::string& theCommand) const;
+  std::string getIgnoreFeatureEndCommand(const std::string &theCommand) const;
 
   /*
    * Helper for getting the value of doxygen:ignore feature or its argument.
    */
-  String* getIgnoreFeature(const std::string& theCommand, const char* argument = NULL) const;
+  String *getIgnoreFeature(const std::string &theCommand, const char *argument = NULL) const;
 
-    /*
-     * Whether to print lots of debug info during parsing
-     */
-    bool noisy;
+  /*
+   * Whether to print lots of debug info during parsing
+   */
+  bool noisy;
 
   /*
    *Changes a std::string to all lower case
@@ -136,7 +134,7 @@ private:
   /*
    *prints the parse tree
    */
-  void printTree(const std::list <DoxygenEntity> &rootList);
+  void printTree(const std::list<DoxygenEntity> &rootList);
 
   /**
    * Returns true if the next token is end of line token. This is important
@@ -190,8 +188,7 @@ private:
    * up til the command specified is encountered
    */
   //TODO check that this behaves properly for formulas
-  std::string getStringTilEndCommand(const std::string &theCommand,
-		  	  	  	  	  	  	  	  	const TokenList &tokList);
+  std::string getStringTilEndCommand(const std::string &theCommand, const TokenList &tokList);
 
   /*
    * Returns the end of a Paragraph as an iterator-
@@ -205,8 +202,7 @@ private:
    * encounter of the same command. Example of this behaviour is \arg.
    * If no end is encountered, returns the last token of the std::list.
    */
-  TokenListCIt getEndOfSection(const std::string &theCommand,
-		                         const TokenList &tokList);
+  TokenListCIt getEndOfSection(const std::string &theCommand, const TokenList &tokList);
 
   /*
    * This method is for returning the end of a specific form of doxygen command
@@ -215,14 +211,12 @@ private:
    * progressTilEndCommand("endcode", tokenList);
    * If the end is never encountered, it returns the end of the std::list.
    */
-  TokenListCIt getEndCommand(const std::string &theCommand,
-		                       const TokenList &tokList);
+  TokenListCIt getEndCommand(const std::string &theCommand, const TokenList &tokList);
   /*
    * A special method for commands such as \arg that end at the end of a
    * paragraph OR when another \arg is encountered
   //TODO getTilAnyCommand
-  TokenListCIt getTilAnyCommand(const std::string &theCommand,
-                                  const TokenList &tokList);
+  TokenListCIt getTilAnyCommand(const std::string &theCommand, const TokenList &tokList);
    */
 
   /**
@@ -241,8 +235,7 @@ private:
    * Plain commands, such as newline etc, they contain no other data
    *  \n \\ \@ \& \$ \# \< \> \%
    */
-  void addSimpleCommand(const std::string &theCommand,
-		                 DoxygenEntityList &doxyList);
+  void addSimpleCommand(const std::string &theCommand, DoxygenEntityList &doxyList);
   /*
    * CommandWord
    * Format: @command <word>
@@ -251,9 +244,7 @@ private:
    * "relates", "namespace", "relatesalso","anchor", "dontinclude", "include",
    * "includelineno"
    */
-  void addCommandWord(const std::string &theCommand,
-		               const TokenList &tokList,
-		               DoxygenEntityList &doxyList);
+  void addCommandWord(const std::string &theCommand, const TokenList &tokList, DoxygenEntityList &doxyList);
   /*
    * CommandLine
    * Format: @command (line)
@@ -261,9 +252,7 @@ private:
    * "addindex", "fn", "name", "line", "var", "skipline", "typedef", "skip",
    * "until", "property"
    */
-  void addCommandLine(const std::string &theCommand,
-		               const TokenList &tokList,
-		               DoxygenEntityList &doxyList);
+  void addCommandLine(const std::string &theCommand, const TokenList &tokList, DoxygenEntityList &doxyList);
   /*
    * CommandParagraph
    * Format: @command {paragraph}
@@ -272,9 +261,7 @@ private:
    * "details", "invariant", "deprecated", "date", "note", "warning",
    * "version", "todo", "bug", "attention", "brief", "arg", "author"
    */
-  void addCommandParagraph(const std::string &theCommand,
-		  	  	  	  	     const TokenList &tokList,
-		                     DoxygenEntityList &doxyList);
+  void addCommandParagraph(const std::string &theCommand, const TokenList &tokList, DoxygenEntityList &doxyList);
   /*
    * Command EndCommand
    * Format: @command and ends at @endcommand
@@ -284,96 +271,70 @@ private:
    * "link"
    * Returns 1 if success, 0 if the endcommand is never encountered.
    */
-  void addCommandEndCommand(const std::string &theCommand,
-		                      const TokenList & tokList,
-		                      DoxygenEntityList &doxyList);
+  void addCommandEndCommand(const std::string &theCommand, const TokenList &tokList, DoxygenEntityList &doxyList);
   /*
    * CommandWordParagraph
    * Format: @command <word> {paragraph}
    * Commands such as param
    * "param", "tparam", "throw", "throws", "retval", "exception"
    */
-  void addCommandWordParagraph(const std::string &theCommand,
-		  	  	  	  	  	      const TokenList & tokList,
-		  	  	  	  	  	      DoxygenEntityList &doxyList);
+  void addCommandWordParagraph(const std::string &theCommand, const TokenList &tokList, DoxygenEntityList &doxyList);
   /*
    * CommandWordLine
    * Format: @command <word> (line)
    * Commands such as param
    * "page", "subsection", "subsubsection", "section", "paragraph", "defgroup"
    */
-  void addCommandWordLine(const std::string &theCommand,
-                            const TokenList &tokList,
-                            DoxygenEntityList &doxyList);
+  void addCommandWordLine(const std::string &theCommand, const TokenList &tokList, DoxygenEntityList &doxyList);
   /*
    * Command Word Optional Word Optional Word
    * Format: @command <word> [<header-file>] [<header-name>]
    * Commands such as class
    * "category", "class", "protocol", "interface", "struct", "union"
    */
-  void addCommandWordOWordOWord(const std::string &theCommand,
-                                   const TokenList &tokList,
-                                   DoxygenEntityList &doxyList);
+  void addCommandWordOWordOWord(const std::string &theCommand, const TokenList &tokList, DoxygenEntityList &doxyList);
   /*
    * Command Optional Word
    * Format: @command [<word>]
    * Commands such as dir
    * "dir", "file", "cond"
    */
-  void addCommandOWord(const std::string &theCommand,
-                      const TokenList &tokList,
-                      DoxygenEntityList &doxyList);
+  void addCommandOWord(const std::string &theCommand, const TokenList &tokList, DoxygenEntityList &doxyList);
 
   /*
    * Commands that should not be encountered (such as PHP only)
    * goes til the end of line then returns
    */
-  void addCommandErrorThrow(const std::string &theCommand,
-                           const TokenList &tokList,
-                           DoxygenEntityList &doxyList);
+  void addCommandErrorThrow(const std::string &theCommand, const TokenList &tokList, DoxygenEntityList &doxyList);
 
-  void addCommandHtml(const std::string &theCommand,
-                     const TokenList &tokList,
-                     DoxygenEntityList &doxyList);
+  void addCommandHtml(const std::string &theCommand, const TokenList &tokList, DoxygenEntityList &doxyList);
 
-  void addCommandHtmlEntity(const std::string &theCommand,
-                           const TokenList &tokList,
-                           DoxygenEntityList &doxyList);
+  void addCommandHtmlEntity(const std::string &theCommand, const TokenList &tokList, DoxygenEntityList &doxyList);
 
   /*
    *Adds the unique commands- different process for each unique command
    */
-  void addCommandUnique(const std::string &theCommand,
-                       const TokenList &tokList,
-                       DoxygenEntityList &doxyList);
+  void addCommandUnique(const std::string &theCommand, const TokenList &tokList, DoxygenEntityList &doxyList);
 
   /*
    * Replace the given command with its predefined alias expansion.
    */
-  void aliasCommand(const std::string& theCommand,
-		    const TokenList &tokList,
-		    DoxygenEntityList &doxyList);
+  void aliasCommand(const std::string &theCommand, const TokenList &tokList, DoxygenEntityList &doxyList);
 
   /*
    * Simply ignore the given command, possibly with the word following it or
    * until the matching end command.
    */
-  void ignoreCommand(const std::string& theCommand,
-                    const TokenList &tokList,
-                    DoxygenEntityList &doxyList);
+  void ignoreCommand(const std::string &theCommand, const TokenList &tokList, DoxygenEntityList &doxyList);
 
   /* 
    * The actual "meat" of the doxygen parser. Calls the correct addCommand...()
    * function.
    */
-  void addCommand(const std::string &commandString,
-                   const TokenList &tokList,
-                   DoxygenEntityList &doxyList);
+  void addCommand(const std::string &commandString, const TokenList &tokList, DoxygenEntityList &doxyList);
+
+  DoxygenEntityList parse(TokenListCIt endParsingIndex, const TokenList &tokList, bool root = false);
 
-  DoxygenEntityList parse(TokenListCIt endParsingIndex,
-                           const TokenList &tokList,
-                           bool root = false);
-  
   /*
    * Fill static doxygenCommands and sectionIndicators containers
    */
@@ -391,9 +352,7 @@ private:
   /** Processes comment outside \htmlonly and \verbatim commands. */
   size_t processNormalComment(size_t pos, const std::string &line);
 
-  void tokenizeDoxygenComment(const std::string &doxygenComment,
-                                 const std::string &fileName,
-                                 int fileLine);
+  void tokenizeDoxygenComment(const std::string &doxygenComment, const std::string &fileName, int fileLine);
   void printList();
   void printListError(int warningType, const std::string &message);
 
@@ -407,8 +366,7 @@ private:
 public:
   DoxygenParser(bool noisy = false);
   virtual ~DoxygenParser();
-  DoxygenEntityList createTree(Node* node, String* documentation);
+  DoxygenEntityList createTree(Node *node, String *documentation);
 };
 
 #endif
-
diff --git a/Source/DoxygenTranslator/src/DoxygenTranslator.cpp b/Source/DoxygenTranslator/src/DoxygenTranslator.cpp
index 93314b19d..111822660 100644
--- a/Source/DoxygenTranslator/src/DoxygenTranslator.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenTranslator.cpp
@@ -14,10 +14,8 @@
 
 #include "DoxygenTranslator.h"
 
-DoxygenTranslator::DoxygenTranslator(int flags) :
-  m_flags(flags),
-  parser((flags & debug_parser) != 0)
-{}
+DoxygenTranslator::DoxygenTranslator(int flags) : m_flags(flags), parser((flags &debug_parser) != 0) {
+}
 
 
 DoxygenTranslator::~DoxygenTranslator() {
@@ -35,11 +33,11 @@ String *DoxygenTranslator::getDoxygenComment(Node *node) {
 
 
 String *DoxygenTranslator::getDocumentation(Node *node) {
-  
+
   if (!hasDocumentation(node)) {
     return NewString("");
   }
-  
+
   return makeDocumentation(node);
 }
 
diff --git a/Source/DoxygenTranslator/src/DoxygenTranslator.h b/Source/DoxygenTranslator/src/DoxygenTranslator.h
index 7d908ee1f..ae7c211ba 100644
--- a/Source/DoxygenTranslator/src/DoxygenTranslator.h
+++ b/Source/DoxygenTranslator/src/DoxygenTranslator.h
@@ -78,12 +78,12 @@ protected:
    * Returns the documentation formatted for a target language.
    */
   virtual String *makeDocumentation(Node *node) = 0;
-  
+
   /*
    * Prints the details of a parsed entity list to stdout (for debugging).
    */
   void printTree(const DoxygenEntityList &entityList);
-  
+
 };
 
 #endif
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.cpp b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
index c2b47a796..90da0eb1a 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
@@ -15,8 +15,8 @@
 #include <vector>
 #include <list>
 #include "../../Modules/swigmod.h"
-#define APPROX_LINE_LENGTH 64	//characters per line allowed
-#define TAB_SIZE 8		//current tab size in spaces
+#define APPROX_LINE_LENGTH 64   // characters per line allowed
+#define TAB_SIZE 8              // current tab size in spaces
 //TODO {@link} {@linkplain} {@docRoot}, and other useful doxy commands that are not a javadoc tag
 
 // define static tables, they are filled in JavaDocConverter's constructor
@@ -26,8 +26,7 @@ using std::string;
 using std::list;
 using std::vector;
 
-void JavaDocConverter::fillStaticTables()
-{
+void JavaDocConverter::fillStaticTables() {
   if (tagHandlers.size()) // fill only once
     return;
 
@@ -99,15 +98,13 @@ void JavaDocConverter::fillStaticTables()
   tagHandlers["invariant"] = make_pair(&JavaDocConverter::handleParagraph, "");
   tagHandlers["latexonly"] = make_pair(&JavaDocConverter::handleParagraph, "");
   tagHandlers["manonly"] = make_pair(&JavaDocConverter::handleParagraph, "");
-  tagHandlers["partofdescription"] = make_pair(
-      &JavaDocConverter::handleParagraph, "");
+  tagHandlers["partofdescription"] = make_pair(&JavaDocConverter::handleParagraph, "");
   tagHandlers["rtfonly"] = make_pair(&JavaDocConverter::handleParagraph, "");
   tagHandlers["short"] = make_pair(&JavaDocConverter::handleParagraph, "");
   tagHandlers["xmlonly"] = make_pair(&JavaDocConverter::handleParagraph, "");
   // these commands are kept as-is, they are supported by JavaDoc
   tagHandlers["author"] = make_pair(&JavaDocConverter::handleTagSame, "");
-  tagHandlers["authors"] = make_pair(&JavaDocConverter::handleTagSame,
-      "author");
+  tagHandlers["authors"] = make_pair(&JavaDocConverter::handleTagSame, "author");
   tagHandlers["deprecated"] = make_pair(&JavaDocConverter::handleTagSame, "");
   tagHandlers["exception"] = make_pair(&JavaDocConverter::handleTagSame, "");
   tagHandlers["package"] = make_pair(&JavaDocConverter::handleTagSame, "");
@@ -116,8 +113,7 @@ void JavaDocConverter::fillStaticTables()
   tagHandlers["ref"] = make_pair(&JavaDocConverter::handleTagRef, "");
   tagHandlers["result"] = make_pair(&JavaDocConverter::handleTagSame, "return");
   tagHandlers["return"] = make_pair(&JavaDocConverter::handleTagSame, "");
-  tagHandlers["returns"] = make_pair(&JavaDocConverter::handleTagSame,
-      "return");
+  tagHandlers["returns"] = make_pair(&JavaDocConverter::handleTagSame, "return");
   //tagHandlers["see"] = make_pair(&JavaDocConverter::handleTagSame, "");
   //tagHandlers["sa"] = make_pair(&JavaDocConverter::handleTagSame, "see");
   tagHandlers["since"] = make_pair(&JavaDocConverter::handleTagSame, "");
@@ -126,104 +122,77 @@ void JavaDocConverter::fillStaticTables()
   tagHandlers["version"] = make_pair(&JavaDocConverter::handleTagSame, "");
   // these commands have special handlers
   tagHandlers["code"] = make_pair(&JavaDocConverter::handleTagExtended, "code");
-  tagHandlers["cond"] = make_pair(&JavaDocConverter::handleTagMessage,
-      "Conditional comment: ");
-  tagHandlers["copyright"] = make_pair(&JavaDocConverter::handleTagMessage,
-      "Copyright: ");
+  tagHandlers["cond"] = make_pair(&JavaDocConverter::handleTagMessage, "Conditional comment: ");
+  tagHandlers["copyright"] = make_pair(&JavaDocConverter::handleTagMessage, "Copyright: ");
   tagHandlers["else"] = make_pair(&JavaDocConverter::handleTagIf, "Else: ");
-  tagHandlers["elseif"] = make_pair(&JavaDocConverter::handleTagIf,
-      "Else if: ");
-  tagHandlers["endcond"] = make_pair(&JavaDocConverter::handleTagMessage,
-      "End of conditional comment.");
+  tagHandlers["elseif"] = make_pair(&JavaDocConverter::handleTagIf, "Else if: ");
+  tagHandlers["endcond"] = make_pair(&JavaDocConverter::handleTagMessage, "End of conditional comment.");
   // space in second arg prevents Javadoc to treat '@ example' as command. File name of
   // example is still informative to user.
-  tagHandlers["example"] = make_pair(&JavaDocConverter::handleTagSame,
-      " example");
+  tagHandlers["example"] = make_pair(&JavaDocConverter::handleTagSame, " example");
   tagHandlers["if"] = make_pair(&JavaDocConverter::handleTagIf, "If: ");
   tagHandlers["ifnot"] = make_pair(&JavaDocConverter::handleTagIf, "If not: ");
   tagHandlers["image"] = make_pair(&JavaDocConverter::handleTagImage, "");
   tagHandlers["link"] = make_pair(&JavaDocConverter::handleTagLink, "");
   tagHandlers["see"] = make_pair(&JavaDocConverter::handleTagSee, "");
   tagHandlers["sa"] = make_pair(&JavaDocConverter::handleTagSee, "");
-  tagHandlers["note"] = make_pair(&JavaDocConverter::handleTagMessage,
-      "Note: ");
+  tagHandlers["note"] = make_pair(&JavaDocConverter::handleTagMessage, "Note: ");
   tagHandlers["overload"] = make_pair(&JavaDocConverter::handleTagMessage,
-      "This is an overloaded member function, provided for"
-          " convenience. It differs from the above function only in what"
-          " argument(s) it accepts.");
+                                      "This is an overloaded member function, provided for"
+                                      " convenience. It differs from the above function only in what" " argument(s) it accepts.");
   tagHandlers["par"] = make_pair(&JavaDocConverter::handleTagPar, "");
-  tagHandlers["remark"] = make_pair(&JavaDocConverter::handleTagMessage,
-      "Remarks: ");
-  tagHandlers["remarks"] = make_pair(&JavaDocConverter::handleTagMessage,
-      "Remarks: ");
-  tagHandlers["todo"] = make_pair(&JavaDocConverter::handleTagMessage,
-      "TODO: ");
-  tagHandlers["verbatim"] = make_pair(&JavaDocConverter::handleTagExtended,
-      "literal");
+  tagHandlers["remark"] = make_pair(&JavaDocConverter::handleTagMessage, "Remarks: ");
+  tagHandlers["remarks"] = make_pair(&JavaDocConverter::handleTagMessage, "Remarks: ");
+  tagHandlers["todo"] = make_pair(&JavaDocConverter::handleTagMessage, "TODO: ");
+  tagHandlers["verbatim"] = make_pair(&JavaDocConverter::handleTagExtended, "literal");
 
   // \f commands output literal Latex formula, which is still better than nothing.
   tagHandlers["f$"] = make_pair(&JavaDocConverter::handleTagVerbatim, "");
   tagHandlers["f["] = make_pair(&JavaDocConverter::handleTagVerbatim, "");
   tagHandlers["f{"] = make_pair(&JavaDocConverter::handleTagVerbatim, "");
 
-  tagHandlers["warning"] = make_pair(&JavaDocConverter::handleTagMessage,
-      "Warning: ");
+  tagHandlers["warning"] = make_pair(&JavaDocConverter::handleTagMessage, "Warning: ");
   // this command just prints it's contents
   // (it is internal command of swig's parser, contains plain text)
-  tagHandlers["plainstd::string"] = make_pair(
-      &JavaDocConverter::handlePlainString, "");
-  tagHandlers["plainstd::endl"] = make_pair(&JavaDocConverter::handleNewLine,
-      "");
+  tagHandlers["plainstd::string"] = make_pair(&JavaDocConverter::handlePlainString, "");
+  tagHandlers["plainstd::endl"] = make_pair(&JavaDocConverter::handleNewLine, "");
   tagHandlers["n"] = make_pair(&JavaDocConverter::handleNewLine, "");
 
   // HTML tags
   tagHandlers["<a"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<a");
   tagHandlers["<b"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<b");
-  tagHandlers["<blockquote"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag,
-      "<blockquote");
-  tagHandlers["<body"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag,
-      "<body");
+  tagHandlers["<blockquote"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<blockquote");
+  tagHandlers["<body"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<body");
   tagHandlers["<br"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<br");
-  tagHandlers["<center"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag,
-      "<center");
-  tagHandlers["<caption"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag,
-      "<caption");
-  tagHandlers["<code"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag,
-      "<code");
+  tagHandlers["<center"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<center");
+  tagHandlers["<caption"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<caption");
+  tagHandlers["<code"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<code");
   tagHandlers["<dd"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<dd");
   tagHandlers["<dfn"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<dfn");
   tagHandlers["<div"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<div");
   tagHandlers["<dl"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<dl");
   tagHandlers["<dt"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<dt");
   tagHandlers["<em"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<em");
-  tagHandlers["<form"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag,
-      "<form");
+  tagHandlers["<form"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<form");
   tagHandlers["<hr"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<hr");
   tagHandlers["<h1"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<h1");
   tagHandlers["<h2"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<h2");
   tagHandlers["<h3"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<h3");
   tagHandlers["<i"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<i");
-  tagHandlers["<input"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag,
-      "<input");
+  tagHandlers["<input"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<input");
   tagHandlers["<img"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<img");
   tagHandlers["<li"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<li");
-  tagHandlers["<meta"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag,
-      "<meta");
-  tagHandlers["<multicol"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag,
-      "<multicol");
+  tagHandlers["<meta"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<meta");
+  tagHandlers["<multicol"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<multicol");
   tagHandlers["<ol"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<ol");
   tagHandlers["<p"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<p");
   tagHandlers["<pre"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<pre");
-  tagHandlers["<small"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag,
-      "<small");
-  tagHandlers["<span"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag,
-      "<span");
-  tagHandlers["<strong"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag,
-      "<strong");
+  tagHandlers["<small"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<small");
+  tagHandlers["<span"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<span");
+  tagHandlers["<strong"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<strong");
   tagHandlers["<sub"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<sub");
   tagHandlers["<sup"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<sup");
-  tagHandlers["<table"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag,
-      "<table");
+  tagHandlers["<table"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<table");
   tagHandlers["<td"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<td");
   tagHandlers["<th"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<th");
   tagHandlers["<tr"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<tr");
@@ -233,50 +202,33 @@ void JavaDocConverter::fillStaticTables()
   tagHandlers["<var"] = make_pair(&JavaDocConverter::handleDoxyHtmlTag, "<var");
 
   // HTML entities
-  tagHandlers["&copy"] = make_pair(&JavaDocConverter::handleHtmlEntity,
-      "&copy");
-  tagHandlers["&trade"] = make_pair(&JavaDocConverter::handleHtmlEntity,
-      "&trade");
+  tagHandlers["&copy"] = make_pair(&JavaDocConverter::handleHtmlEntity, "&copy");
+  tagHandlers["&trade"] = make_pair(&JavaDocConverter::handleHtmlEntity, "&trade");
   tagHandlers["&reg"] = make_pair(&JavaDocConverter::handleHtmlEntity, "&reg");
   tagHandlers["&lt"] = make_pair(&JavaDocConverter::handleHtmlEntity, "&lt");
   tagHandlers["&gt"] = make_pair(&JavaDocConverter::handleHtmlEntity, "&gt");
   tagHandlers["&amp"] = make_pair(&JavaDocConverter::handleHtmlEntity, "&amp");
-  tagHandlers["&apos"] = make_pair(&JavaDocConverter::handleHtmlEntity,
-      "&apos");
-  tagHandlers["&quot"] = make_pair(&JavaDocConverter::handleHtmlEntity,
-      "&quot");
-  tagHandlers["&lsquo"] = make_pair(&JavaDocConverter::handleHtmlEntity,
-      "&lsquo");
-  tagHandlers["&rsquo"] = make_pair(&JavaDocConverter::handleHtmlEntity,
-      "&rsquo");
-  tagHandlers["&ldquo"] = make_pair(&JavaDocConverter::handleHtmlEntity,
-      "&ldquo");
-  tagHandlers["&rdquo"] = make_pair(&JavaDocConverter::handleHtmlEntity,
-      "&rdquo");
-  tagHandlers["&ndash"] = make_pair(&JavaDocConverter::handleHtmlEntity,
-      "&ndash");
-  tagHandlers["&mdash"] = make_pair(&JavaDocConverter::handleHtmlEntity,
-      "&mdash");
-  tagHandlers["&nbsp"] = make_pair(&JavaDocConverter::handleHtmlEntity,
-      "&nbsp");
-  tagHandlers["&times"] = make_pair(&JavaDocConverter::handleHtmlEntity,
-      "&times");
-  tagHandlers["&minus"] = make_pair(&JavaDocConverter::handleHtmlEntity,
-      "&minus");
-  tagHandlers["&sdot"] = make_pair(&JavaDocConverter::handleHtmlEntity,
-      "&sdot");
+  tagHandlers["&apos"] = make_pair(&JavaDocConverter::handleHtmlEntity, "&apos");
+  tagHandlers["&quot"] = make_pair(&JavaDocConverter::handleHtmlEntity, "&quot");
+  tagHandlers["&lsquo"] = make_pair(&JavaDocConverter::handleHtmlEntity, "&lsquo");
+  tagHandlers["&rsquo"] = make_pair(&JavaDocConverter::handleHtmlEntity, "&rsquo");
+  tagHandlers["&ldquo"] = make_pair(&JavaDocConverter::handleHtmlEntity, "&ldquo");
+  tagHandlers["&rdquo"] = make_pair(&JavaDocConverter::handleHtmlEntity, "&rdquo");
+  tagHandlers["&ndash"] = make_pair(&JavaDocConverter::handleHtmlEntity, "&ndash");
+  tagHandlers["&mdash"] = make_pair(&JavaDocConverter::handleHtmlEntity, "&mdash");
+  tagHandlers["&nbsp"] = make_pair(&JavaDocConverter::handleHtmlEntity, "&nbsp");
+  tagHandlers["&times"] = make_pair(&JavaDocConverter::handleHtmlEntity, "&times");
+  tagHandlers["&minus"] = make_pair(&JavaDocConverter::handleHtmlEntity, "&minus");
+  tagHandlers["&sdot"] = make_pair(&JavaDocConverter::handleHtmlEntity, "&sdot");
   tagHandlers["&sim"] = make_pair(&JavaDocConverter::handleHtmlEntity, "&sim");
   tagHandlers["&le"] = make_pair(&JavaDocConverter::handleHtmlEntity, "&le");
   tagHandlers["&ge"] = make_pair(&JavaDocConverter::handleHtmlEntity, "&ge");
-  tagHandlers["&larr"] = make_pair(&JavaDocConverter::handleHtmlEntity,
-      "&larr");
-  tagHandlers["&rarr"] = make_pair(&JavaDocConverter::handleHtmlEntity,
-      "&rarr");
+  tagHandlers["&larr"] = make_pair(&JavaDocConverter::handleHtmlEntity, "&larr");
+  tagHandlers["&rarr"] = make_pair(&JavaDocConverter::handleHtmlEntity, "&rarr");
 }
 
 JavaDocConverter::JavaDocConverter(int flags) :
-    DoxygenTranslator(flags)
-{
+  DoxygenTranslator(flags) {
   fillStaticTables();
 }
 
@@ -288,11 +240,9 @@ JavaDocConverter::JavaDocConverter(int flags) :
  * which results in short lines. To be useful, this function should have much
  * better algorithm.
  */
-std::string JavaDocConverter::formatCommand(std::string unformattedLine,
-                                            int indent)
-{
+std::string JavaDocConverter::formatCommand(std::string unformattedLine, int indent) {
   std::string formattedLines;
-  return unformattedLine;  // currently disabled
+  return unformattedLine; // currently disabled
   int lastPosition = 0;
   int i = 0;
   int isFirstLine = 1;
@@ -310,12 +260,10 @@ std::string JavaDocConverter::formatCommand(std::string unformattedLine,
       if (!isFirstLine)
         for (int j = 0; j < indent; j++) {
           formattedLines.append("\t");
-        }
-      else {
+      } else {
         isFirstLine = 0;
       }
-      formattedLines.append(
-          unformattedLine.substr(lastPosition, i - lastPosition + 1));
+      formattedLines.append(unformattedLine.substr(lastPosition, i - lastPosition + 1));
       formattedLines.append("\n *");
 
     }
@@ -326,9 +274,7 @@ std::string JavaDocConverter::formatCommand(std::string unformattedLine,
         formattedLines.append("\t");
       }
     }
-    formattedLines.append(
-        unformattedLine.substr(lastPosition,
-            unformattedLine.length() - lastPosition));
+    formattedLines.append(unformattedLine.substr(lastPosition, unformattedLine.length() - lastPosition));
   }
 
   return formattedLines;
@@ -341,8 +287,7 @@ std::string JavaDocConverter::formatCommand(std::string unformattedLine,
  * true - parameters are copied to output regardless of presence in
  * function params list.
  */
-bool JavaDocConverter::paramExists(std::string param)
-{
+bool JavaDocConverter::paramExists(std::string param) {
 
   if (GetFlag(currentNode, "feature:doxygen:nostripparams")) {
     return true;
@@ -352,7 +297,7 @@ bool JavaDocConverter::paramExists(std::string param)
 
   for (Parm *p = plist; p;) {
 
-    if (Getattr(p, "name") && Char (Getattr(p, "name")) == param) {
+    if (Getattr(p, "name") && Char(Getattr(p, "name")) == param) {
       return true;
     }
     /* doesn't seem to work always: in some cases (especially for 'self' parameters)
@@ -367,16 +312,14 @@ bool JavaDocConverter::paramExists(std::string param)
   return false;
 }
 
-std::string JavaDocConverter::translateSubtree(DoxygenEntity &doxygenEntity)
-{
+std::string JavaDocConverter::translateSubtree(DoxygenEntity &doxygenEntity) {
   std::string translatedComment;
 
   if (doxygenEntity.isLeaf) {
     return translatedComment;
   }
 
-  for (DoxygenEntityListIt p = doxygenEntity.entityList.begin();
-      p != doxygenEntity.entityList.end(); p++) {
+  for (DoxygenEntityListIt p = doxygenEntity.entityList.begin(); p != doxygenEntity.entityList.end(); p++) {
 
     translateEntity(*p, translatedComment);
     translateSubtree(*p);
@@ -388,9 +331,7 @@ std::string JavaDocConverter::translateSubtree(DoxygenEntity &doxygenEntity)
 /**
  * Checks if a handler for the given tag exists, and calls it.
  */
-void JavaDocConverter::translateEntity(DoxygenEntity &tag,
-                                       std::string &translatedComment)
-{
+void JavaDocConverter::translateEntity(DoxygenEntity &tag, std::string &translatedComment) {
 
   std::map<std::string, std::pair<tagHandler, std::string> >::iterator it;
   it = tagHandlers.find(tag.typeOfEntity);
@@ -405,35 +346,24 @@ void JavaDocConverter::translateEntity(DoxygenEntity &tag,
 }
 
 
-void JavaDocConverter::handleTagAnchor(DoxygenEntity& tag,
-                                       std::string& translatedComment,
-                                       std::string &)
-{
+void JavaDocConverter::handleTagAnchor(DoxygenEntity &tag, std::string &translatedComment, std::string &) {
   translatedComment += "<a id=\"" + translateSubtree(tag) + "\"></a>";
 }
 
 
-void JavaDocConverter::handleTagHtml(DoxygenEntity& tag,
-                                     std::string& translatedComment,
-                                     std::string &arg)
-{
+void JavaDocConverter::handleTagHtml(DoxygenEntity &tag, std::string &translatedComment, std::string &arg) {
   if (tag.entityList.size()) { // do not include empty tags
     std::string tagData = translateSubtree(tag);
     // wrap the thing, ignoring whitespace
     size_t wsPos = tagData.find_last_not_of("\n\t ");
     if (wsPos != std::string::npos)
-      translatedComment += "<" + arg + ">" + tagData.substr(0, wsPos + 1) + "</"
-          + arg + ">" + tagData.substr(wsPos + 1);
+      translatedComment += "<" + arg + ">" + tagData.substr(0, wsPos + 1) + "</" + arg + ">" + tagData.substr(wsPos + 1);
     else
-      translatedComment += "<" + arg + ">" + translateSubtree(tag) + "</" + arg
-          + "> ";
+      translatedComment += "<" + arg + ">" + translateSubtree(tag) + "</" + arg + "> ";
   }
 }
 
-void JavaDocConverter::handleDoxyHtmlTag(DoxygenEntity& tag,
-                                         std::string& translatedComment,
-                                         std::string &arg)
-{
+void JavaDocConverter::handleDoxyHtmlTag(DoxygenEntity &tag, std::string &translatedComment, std::string &arg) {
   std::string htmlTagArgs = tag.data;
   if (htmlTagArgs == "/") {
     // end html tag, for example "</ul>
@@ -443,18 +373,12 @@ void JavaDocConverter::handleDoxyHtmlTag(DoxygenEntity& tag,
   }
 }
 
-void JavaDocConverter::handleHtmlEntity(DoxygenEntity&,
-                                        std::string& translatedComment,
-                                        std::string &arg)
-{
+void JavaDocConverter::handleHtmlEntity(DoxygenEntity &, std::string &translatedComment, std::string &arg) {
   // html entities can be preserved for Java
   translatedComment += arg + ';';
 }
 
-void JavaDocConverter::handleNewLine(DoxygenEntity&,
-                                     std::string& translatedComment,
-                                     std::string&)
-{
+void JavaDocConverter::handleNewLine(DoxygenEntity &, std::string &translatedComment, std::string &) {
   // <br> tag is added, because otherwise to much text is joined
   // into same paragraph by javadoc. For example, doxy list:
   // - item one
@@ -466,10 +390,7 @@ void JavaDocConverter::handleNewLine(DoxygenEntity&,
   translatedComment += "<br>\n * ";
 }
 
-void JavaDocConverter::handleTagChar(DoxygenEntity& tag,
-                                     std::string& translatedComment,
-                                     std::string &arg)
-{
+void JavaDocConverter::handleTagChar(DoxygenEntity &tag, std::string &translatedComment, std::string &arg) {
   // escape it if we need to, else just print
   if (arg.size())
     translatedComment += arg;
@@ -478,57 +399,37 @@ void JavaDocConverter::handleTagChar(DoxygenEntity& tag,
 }
 
 // handles tags which are the same in Doxygen and Javadoc.
-void JavaDocConverter::handleTagSame(DoxygenEntity& tag,
-                                     std::string& translatedComment,
-                                     std::string &arg)
-{
+void JavaDocConverter::handleTagSame(DoxygenEntity &tag, std::string &translatedComment, std::string &arg) {
   if (arg.size())
     tag.typeOfEntity = arg;
-  translatedComment += formatCommand(
-      std::string("@" + tag.typeOfEntity + " " + translateSubtree(tag)), 2);
+  translatedComment += formatCommand(std::string("@" + tag.typeOfEntity + " " + translateSubtree(tag)), 2);
 }
 
-void JavaDocConverter::handleParagraph(DoxygenEntity& tag,
-                                       std::string& translatedComment,
-                                       std::string&)
-{
+void JavaDocConverter::handleParagraph(DoxygenEntity &tag, std::string &translatedComment, std::string &) {
   translatedComment += formatCommand(translateSubtree(tag), 0);
 }
 
-void JavaDocConverter::handlePlainString(DoxygenEntity& tag,
-                                         std::string& translatedComment,
-                                         std::string&)
-{
+void JavaDocConverter::handlePlainString(DoxygenEntity &tag, std::string &translatedComment, std::string &) {
   translatedComment += tag.data;
   // if (tag.data.size() && tag.data[tag.data.size()-1] != ' ')
-  // 	translatedComment += " ";
+  //    translatedComment += " ";
 }
 
-void JavaDocConverter::handleTagVerbatim(DoxygenEntity& tag,
-                                         std::string& translatedComment,
-                                         std::string &arg)
-{
+void JavaDocConverter::handleTagVerbatim(DoxygenEntity &tag, std::string &translatedComment, std::string &arg) {
   translatedComment += arg + " ";
-  for (DoxygenEntityListCIt it = tag.entityList.begin();
-      it != tag.entityList.end(); it++) {
+  for (DoxygenEntityListCIt it = tag.entityList.begin(); it != tag.entityList.end(); it++) {
     translatedComment += it->data;
   }
 }
 
-void JavaDocConverter::handleTagExtended(DoxygenEntity& tag,
-                                         std::string& translatedComment,
-                                         std::string &arg)
-{
+void JavaDocConverter::handleTagExtended(DoxygenEntity &tag, std::string &translatedComment, std::string &arg) {
   std::string dummy;
   translatedComment += "{@" + arg + " ";
   handleParagraph(tag, translatedComment, dummy);
   translatedComment += "}";
 }
 
-void JavaDocConverter::handleTagIf(DoxygenEntity& tag,
-                                   std::string& translatedComment,
-                                   std::string &arg)
-{
+void JavaDocConverter::handleTagIf(DoxygenEntity &tag, std::string &translatedComment, std::string &arg) {
   std::string dummy;
   translatedComment += arg;
   if (tag.entityList.size()) {
@@ -538,19 +439,13 @@ void JavaDocConverter::handleTagIf(DoxygenEntity& tag,
   }
 }
 
-void JavaDocConverter::handleTagMessage(DoxygenEntity& tag,
-                                        std::string& translatedComment,
-                                        std::string &arg)
-{
+void JavaDocConverter::handleTagMessage(DoxygenEntity &tag, std::string &translatedComment, std::string &arg) {
   std::string dummy;
   translatedComment += formatCommand(arg, 0);
   handleParagraph(tag, translatedComment, dummy);
 }
 
-void JavaDocConverter::handleTagImage(DoxygenEntity& tag,
-                                      std::string& translatedComment,
-                                      std::string&)
-{
+void JavaDocConverter::handleTagImage(DoxygenEntity &tag, std::string &translatedComment, std::string &) {
   if (tag.entityList.size() < 2)
     return;
 
@@ -577,10 +472,7 @@ void JavaDocConverter::handleTagImage(DoxygenEntity& tag,
   translatedComment += "/>";
 }
 
-void JavaDocConverter::handleTagPar(DoxygenEntity& tag,
-                                    std::string& translatedComment,
-                                    std::string&)
-{
+void JavaDocConverter::handleTagPar(DoxygenEntity &tag, std::string &translatedComment, std::string &) {
   std::string dummy;
   translatedComment += "<p";
   if (tag.entityList.size()) {
@@ -593,10 +485,7 @@ void JavaDocConverter::handleTagPar(DoxygenEntity& tag,
 }
 
 
-void JavaDocConverter::handleTagParam(DoxygenEntity& tag,
-                                      std::string& translatedComment,
-                                      std::string&)
-{
+void JavaDocConverter::handleTagParam(DoxygenEntity &tag, std::string &translatedComment, std::string &) {
   std::string dummy;
 
   if (!tag.entityList.size())
@@ -611,10 +500,7 @@ void JavaDocConverter::handleTagParam(DoxygenEntity& tag,
 }
 
 
-void JavaDocConverter::handleTagRef(DoxygenEntity& tag,
-                                    std::string& translatedComment,
-                                    std::string&)
-{
+void JavaDocConverter::handleTagRef(DoxygenEntity &tag, std::string &translatedComment, std::string &) {
   std::string dummy;
   if (!tag.entityList.size())
     return;
@@ -632,19 +518,17 @@ void JavaDocConverter::handleTagRef(DoxygenEntity& tag,
 }
 
 
-string JavaDocConverter::convertLink(string linkObject)
-{
+string JavaDocConverter::convertLink(string linkObject) {
   if (GetFlag(currentNode, "feature:doxygen:nolinktranslate"))
     return linkObject;
   // find the params in function in linkObject (if any)
   size_t lbracePos = linkObject.find('(', 0);
   size_t rbracePos = linkObject.find(')', 0);
-  if (lbracePos == string::npos || rbracePos == string::npos
-      || lbracePos >= rbracePos)
+  if (lbracePos == string::npos || rbracePos == string::npos || lbracePos >= rbracePos)
     return "";
 
   string paramsStr = linkObject.substr(lbracePos + 1,
-      rbracePos - lbracePos - 1);
+                                       rbracePos - lbracePos - 1);
   // strip the params, to fill them later
   string additionalObject = linkObject.substr(rbracePos + 1, string::npos);
   linkObject = linkObject.substr(0, lbracePos);
@@ -679,7 +563,7 @@ string JavaDocConverter::convertLink(string linkObject)
       SwigType_add_qualifier(swigType, "const");
 
     // handle pointers, references and arrays
-    for (int j = (int) params[i].size() - 1; j >= 0; j--) {
+    for (int j = (int)params[i].size() - 1; j >= 0; j--) {
       // skip all the [...] blocks, write 'p.' for every of it
       if (paramStr[j] == ']') {
         while (j >= 0 && paramStr[j] != '[')
@@ -699,8 +583,7 @@ string JavaDocConverter::convertLink(string linkObject)
           typeNameStart = 0;
         else
           typeNameStart++;
-        Append(swigType,
-            paramStr.substr(typeNameStart, j - typeNameStart + 1).c_str());
+        Append(swigType, paramStr.substr(typeNameStart, j - typeNameStart + 1).c_str());
         break;
       }
     }
@@ -708,11 +591,10 @@ string JavaDocConverter::convertLink(string linkObject)
     // make dummy param list, to lookup typemaps for it
     Parm *dummyParam = NewParm(swigType, "", 0);
     Swig_typemap_attach_parms("jstype", dummyParam, NULL);
-    Language::instance()->replaceSpecialVariables(0,
-        Getattr(dummyParam, "tmap:jstype"), dummyParam);
+    Language::instance()->replaceSpecialVariables(0, Getattr(dummyParam, "tmap:jstype"), dummyParam);
 
     //Swig_print(dummyParam, 1);
-    linkObject += Char (Getattr(dummyParam, "tmap:jstype"));
+    linkObject += Char(Getattr(dummyParam, "tmap:jstype"));
     if (i != params.size() - 1)
       linkObject += ",";
 
@@ -724,10 +606,7 @@ string JavaDocConverter::convertLink(string linkObject)
   return linkObject + additionalObject;
 }
 
-void JavaDocConverter::handleTagLink(DoxygenEntity& tag,
-                                     std::string& translatedComment,
-                                     std::string&)
-{
+void JavaDocConverter::handleTagLink(DoxygenEntity &tag, std::string &translatedComment, std::string &) {
   std::string dummy;
   if (!tag.entityList.size())
     return;
@@ -743,10 +622,7 @@ void JavaDocConverter::handleTagLink(DoxygenEntity& tag,
   translatedComment += "}";
 }
 
-void JavaDocConverter::handleTagSee(DoxygenEntity& tag,
-                                    std::string& translatedComment,
-                                    std::string&)
-{
+void JavaDocConverter::handleTagSee(DoxygenEntity &tag, std::string &translatedComment, std::string &) {
   std::string dummy;
   if (!tag.entityList.size())
     return;
@@ -762,7 +638,6 @@ void JavaDocConverter::handleTagSee(DoxygenEntity& tag,
       // handleNewLine(*it, translatedComment, dummy);
       continue;
     }
-
     // restore entities which may be used in C++ type declaration
     if (it->typeOfEntity == "&amp") {
       methodRef += '&';
@@ -779,8 +654,7 @@ void JavaDocConverter::handleTagSee(DoxygenEntity& tag,
   size_t lbrace = methodRef.find('(');
   size_t dblColon = methodRef.find("::");
   if (dblColon < lbrace) {
-    methodRef = methodRef.substr(0, dblColon) + '#'
-        + methodRef.substr(dblColon + 2);
+    methodRef = methodRef.substr(0, dblColon) + '#' + methodRef.substr(dblColon + 2);
   }
 
   translatedComment += "@see ";
@@ -808,8 +682,7 @@ void JavaDocConverter::handleTagSee(DoxygenEntity& tag,
  |-endline
  *
  */
-int JavaDocConverter::shiftEndlinesUpTree(DoxygenEntity &root, int level)
-{
+int JavaDocConverter::shiftEndlinesUpTree(DoxygenEntity &root, int level) {
   DoxygenEntityListIt it = root.entityList.begin();
   while (it != root.entityList.end()) {
     // remove line endings
@@ -828,7 +701,7 @@ int JavaDocConverter::shiftEndlinesUpTree(DoxygenEntity &root, int level)
 
   int removedCount = 0;
   while (!root.entityList.empty()
-      && root.entityList.rbegin()->typeOfEntity == "plainstd::endl") {
+         && root.entityList.rbegin()->typeOfEntity == "plainstd::endl") {
     root.entityList.pop_back();
     removedCount++;
   }
@@ -841,8 +714,7 @@ int JavaDocConverter::shiftEndlinesUpTree(DoxygenEntity &root, int level)
  * to indentation of the first line. Indentation of non-empty lines is not
  * changed - garbage in garbage out.
  */
-std::string JavaDocConverter::indentAndInsertAsterisks(const string &doc)
-{
+std::string JavaDocConverter::indentAndInsertAsterisks(const string &doc) {
 
   size_t idx = doc.find('\n');
   size_t indent = 0;
@@ -857,10 +729,10 @@ std::string JavaDocConverter::indentAndInsertAsterisks(const string &doc)
     }
   }
 
-  if (indent == 0) { // we can't indent the first line less than 0
+  if (indent == 0) {
+    // we can't indent the first line less than 0
     indent = 1;
   }
-
   // Create the first line of Javadoc comment.
   string indentStr(indent - 1, ' ');
   string translatedStr = indentStr + "/**";
@@ -881,13 +753,11 @@ std::string JavaDocConverter::indentAndInsertAsterisks(const string &doc)
       // line without '*' found - is it empty?
       if (translatedStr[nonspaceIdx] != '\n') {
         // add '* ' to each line without it
-        translatedStr = translatedStr.substr(0, nonspaceIdx) + "* "
-            + translatedStr.substr(nonspaceIdx);
+        translatedStr = translatedStr.substr(0, nonspaceIdx) + "* " + translatedStr.substr(nonspaceIdx);
         //printf(translatedStr.c_str());
       } else {
         // we found empty line, replace it with indented '*'
-        translatedStr = translatedStr.substr(0, idx + 1) + indentStr + "* "
-            + translatedStr.substr(nonspaceIdx);
+        translatedStr = translatedStr.substr(0, idx + 1) + indentStr + "* " + translatedStr.substr(nonspaceIdx);
       }
     }
     idx = translatedStr.find('\n', nonspaceIdx);
@@ -908,8 +778,7 @@ std::string JavaDocConverter::indentAndInsertAsterisks(const string &doc)
   return translatedStr;
 }
 
-String *JavaDocConverter::makeDocumentation(Node *node)
-{
+String *JavaDocConverter::makeDocumentation(Node *node) {
 
   String *documentation = getDoxygenComment(node);
 
@@ -919,7 +788,7 @@ String *JavaDocConverter::makeDocumentation(Node *node)
 
   if (GetFlag(node, "feature:doxygen:notranslate")) {
 
-    string doc = Char (documentation);
+    string doc = Char(documentation);
 
     string translatedStr = indentAndInsertAsterisks(doc);
 
@@ -936,7 +805,6 @@ String *JavaDocConverter::makeDocumentation(Node *node)
     std::cout << "---RESORTED LIST---" << std::endl;
     printTree(entityList);
   }
-
   // store the current node
   // (currently just to handle params)
   currentNode = node;
@@ -949,13 +817,13 @@ String *JavaDocConverter::makeDocumentation(Node *node)
 
   // strip line endings at the beginning
   while (!root.entityList.empty()
-      && root.entityList.begin()->typeOfEntity == "plainstd::endl") {
+         && root.entityList.begin()->typeOfEntity == "plainstd::endl") {
     root.entityList.pop_front();
   }
 
   // and at the end
   while (!root.entityList.empty()
-      && root.entityList.rbegin()->typeOfEntity == "plainstd::endl") {
+         && root.entityList.rbegin()->typeOfEntity == "plainstd::endl") {
     root.entityList.pop_back();
   }
 
@@ -971,8 +839,6 @@ String *JavaDocConverter::makeDocumentation(Node *node)
   return NewString(javaDocString.c_str());
 }
 
-void JavaDocConverter::addError(int warningType, const std::string &message)
-{
-  Swig_warning(warningType, "", 0, "Doxygen parser warning: %s. \n",
-      message.c_str());
+void JavaDocConverter::addError(int warningType, const std::string &message) {
+  Swig_warning(warningType, "", 0, "Doxygen parser warning: %s. \n", message.c_str());
 }
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.h b/Source/DoxygenTranslator/src/JavaDocConverter.h
index eff00590c..df579e625 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.h
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.h
@@ -30,20 +30,23 @@ protected:
    * Used to properly format JavaDoc-style command
    */
   std::string formatCommand(std::string unformattedLine, int indent);
+
   /*
    * Translate every entity in a tree.
    */
-  std::string translateSubtree(DoxygenEntity & doxygenEntity);
+  std::string translateSubtree(DoxygenEntity &doxygenEntity);
+
   /*
    * Translate one entity with the appropriate handler, according
    * to the tagHandlers
    */
   void translateEntity(DoxygenEntity &tag, std::string &translatedComment);
+
   /*
    * Fix all endlines location, etc
    */
   int shiftEndlinesUpTree(DoxygenEntity &root, int level = 0);
-  
+
   /*
    * Convert params in link-objects and references
    */
@@ -53,18 +56,15 @@ protected:
    * Typedef for the function that handles one tag
    * arg - some string argument to easily pass it through lookup table
    */
-  typedef void (JavaDocConverter::*tagHandler)(DoxygenEntity &tag,
-      std::string &translatedComment, std::string &arg);
+  typedef void (JavaDocConverter::*tagHandler) (DoxygenEntity &tag, std::string &translatedComment, std::string &arg);
 
   /**
    * Copies verbatim args of the tag to output, used for commands like \f$, ...
    */
-  void handleTagVerbatim(DoxygenEntity& tag, std::string& translatedComment, std::string &arg);
+  void handleTagVerbatim(DoxygenEntity &tag, std::string &translatedComment, std::string &arg);
 
   /** Creates anchor link. */
-  void handleTagAnchor(DoxygenEntity& tag,
-                       std::string& translatedComment,
-                       std::string &arg);
+  void handleTagAnchor(DoxygenEntity &tag, std::string &translatedComment, std::string &arg);
 
   /*
    * Wrap the command data with the html tag
@@ -73,80 +73,87 @@ protected:
   void handleTagHtml(DoxygenEntity &tag, std::string &translatedComment, std::string &arg);
 
   /* Handles HTML tags recognized by Doxygen, like <A ...>, <ul>, <table>, ... */
-  void handleDoxyHtmlTag(DoxygenEntity& tag,
-                         std::string& translatedComment,
-                         std::string &arg);
+  void handleDoxyHtmlTag(DoxygenEntity &tag, std::string &translatedComment, std::string &arg);
 
   /* Handles HTML entities recognized by Doxygen, like &lt;, &copy;, ... */
-  void handleHtmlEntity(DoxygenEntity& tag,
-                        std::string& translatedComment,
-                        std::string &arg);
+  void handleHtmlEntity(DoxygenEntity &tag, std::string &translatedComment, std::string &arg);
 
   /*
    * Just prints new line
    */
   void handleNewLine(DoxygenEntity &tag, std::string &translatedComment, std::string &arg);
+
   /*
    * Print the name of tag to the output, used for escape-commands
    * arg - html-escaped variant, if not provided the command data is used
    */
   void handleTagChar(DoxygenEntity &tag, std::string &translatedComment, std::string &arg);
+
   /*
    * Do not translate and print as-is
    * arg - the new tag name, if it needs to be renamed
    */
   void handleTagSame(DoxygenEntity &tag, std::string &translatedComment, std::string &arg);
+
   /*
    * Print only the content and strip original tag
    */
   void handleParagraph(DoxygenEntity &tag, std::string &translatedComment, std::string &arg);
+
   /*
    * Print only data part of code
    */
   void handlePlainString(DoxygenEntity &tag, std::string &translatedComment, std::string &arg);
+
   /*
    * Print extended Javadoc command, like {@code ...} or {@literal ...}
    * arg - command name
    */
   void handleTagExtended(DoxygenEntity &tag, std::string &translatedComment, std::string &arg);
+
   /*
    * Print the if-elseif-else-endif section
    */
   void handleTagIf(DoxygenEntity &tag, std::string &translatedComment, std::string &arg);
+
   /*
    * Prints the specified message, than the contents of the tag
    * arg - message
    */
   void handleTagMessage(DoxygenEntity &tag, std::string &translatedComment, std::string &arg);
+
   /*
    * Insert <img src=... /> tag if the 'format' field is specified as 'html'
    */
   void handleTagImage(DoxygenEntity &tag, std::string &translatedComment, std::string &arg);
+
   /*
    * Insert <p alt='title'>...</p>
    */
   void handleTagPar(DoxygenEntity &tag, std::string &translatedComment, std::string &arg);
+
   /*
    * Insert \@param command, if it is really a function param
    */
   void handleTagParam(DoxygenEntity &tag, std::string &translatedComment, std::string &arg);
+
   /*
    * Writes link for \ref tag. 
    */
-  void handleTagRef(DoxygenEntity& tag, std::string& translatedComment,
-                    std::string&);
+  void handleTagRef(DoxygenEntity &tag, std::string &translatedComment, std::string &);
+
   /*
    * Insert {@link...} command, and handle all the <link-object>s correctly
    * (like converting types of params, etc)
    */
   void handleTagLink(DoxygenEntity &tag, std::string &translatedComment, std::string &arg);
+
   /*
    * Insert @see command, and handle all the <link-object>s correctly
    * (like converting types of params, etc)
    */
   void handleTagSee(DoxygenEntity &tag, std::string &translatedComment, std::string &arg);
 
-
 private:
   Node *currentNode;
   // this contains the handler pointer and one string argument
diff --git a/Source/DoxygenTranslator/src/PyDocConverter.cpp b/Source/DoxygenTranslator/src/PyDocConverter.cpp
index 76431af54..b6aaa2d91 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/PyDocConverter.cpp
@@ -28,18 +28,14 @@ using std::string;
 
 // Helper class increasing the provided indent string in its ctor and decreasing
 // it in its dtor.
-class IndentGuard
-{
+class IndentGuard {
 public:
   // One indent level.
-  static const char* Level() { return "    "; }
-
-  // Default ctor doesn't do anything and prevents the dtor from doing anything
-  // too and should only be used when the guard needs to be initialized
-  // conditionally as Init() can then be called after checking some condition.
-  // Otherwise, prefer to use the non default ctor below.
-  IndentGuard()
-  {
+  static const char *Level() {
+    return "    ";
+  }
+  // Default ctor doesn't do anything and prevents the dtor from doing anything// too and should only be used when the guard needs to be initialized// conditionally as Init() can then be called after checking some condition.// Otherwise, prefer to use the non default ctor below.
+      IndentGuard() {
     m_initialized = false;
   }
 
@@ -47,14 +43,12 @@ public:
   // extra indent added to it in the dtor and the variable containing the indent
   // to use, which must be used after every new line by the code actually
   // updating the output.
-  IndentGuard(string& output, string& indent)
-  {
+  IndentGuard(string &output, string &indent) {
     Init(output, indent);
   }
 
   // Really initializes the object created using the default ctor.
-  void Init(string& output, string& indent)
-  {
+  void Init(string &output, string &indent) {
     m_output = &output;
     m_indent = &indent;
 
@@ -77,10 +71,11 @@ public:
 
   // Get the indent for the first line of the paragraph, which is smaller than
   // the indent for the subsequent lines.
-  string getFirstLineIndent() const { return string(m_firstLineIndent, ' '); }
-
-  ~IndentGuard()
-  {
+  string getFirstLineIndent() const {
+    return string(m_firstLineIndent, ' ');
+  }
+ 
+  ~IndentGuard() {
     if (!m_initialized)
       return;
 
@@ -93,24 +88,23 @@ public:
     if (m_output->length() > lenIndentLevel) {
       const size_t start = m_output->length() - lenIndentLevel;
       if (m_output->compare(start, string::npos, Level()) == 0)
-          m_output->erase(start);
+        m_output->erase(start);
     }
   }
 
 private:
-  string* m_output;
-  string* m_indent;
+  string *m_output;
+  string *m_indent;
   unsigned m_firstLineIndent;
   bool m_initialized;
 
-  IndentGuard(const IndentGuard&);
-  IndentGuard& operator=(const IndentGuard&);
+  IndentGuard(const IndentGuard &);
+  IndentGuard &operator=(const IndentGuard &);
 };
 
 // Return the indent of the given multiline string, i.e. the maximal number of
 // spaces present in the beginning of all its non-empty lines.
-static size_t determineIndent(const string& s)
-{
+static size_t determineIndent(const string &s) {
   size_t minIndent = static_cast<size_t>(-1);
 
   for (size_t lineStart = 0; lineStart < s.length();) {
@@ -136,8 +130,7 @@ static size_t determineIndent(const string& s)
   return minIndent;
 }
 
-static void trimWhitespace(string& s)
-{
+static void trimWhitespace(string &s) {
   const size_t lastNonSpace = s.find_last_not_of(' ');
   if (lastNonSpace == string::npos)
     s.clear();
@@ -146,21 +139,16 @@ static void trimWhitespace(string& s)
 }
 
 /* static */
-PyDocConverter::TagHandlersMap::mapped_type
-PyDocConverter::make_handler(tagHandler handler)
-{
+PyDocConverter::TagHandlersMap::mapped_type PyDocConverter::make_handler(tagHandler handler) {
   return make_pair(handler, std::string());
 }
 
 /* static */
-PyDocConverter::TagHandlersMap::mapped_type
-PyDocConverter::make_handler(tagHandler handler, const char* arg)
-{
+PyDocConverter::TagHandlersMap::mapped_type PyDocConverter::make_handler(tagHandler handler, const char *arg) {
   return make_pair(handler, arg);
 }
 
-void PyDocConverter::fillStaticTables()
-{
+void PyDocConverter::fillStaticTables() {
   if (tagHandlers.size()) // fill only once
     return;
 
@@ -213,9 +201,7 @@ void PyDocConverter::fillStaticTables()
   tagHandlers["details"] = make_handler(&PyDocConverter::handleParagraph);
   tagHandlers["em"] = make_handler(&PyDocConverter::handleParagraph, " ");
   tagHandlers["example"] = make_handler(&PyDocConverter::handleParagraph);
-  tagHandlers["exception"] =
-  tagHandlers["throw"] =
-  tagHandlers["throws"] = make_handler(&PyDocConverter::handleTagException);
+  tagHandlers["exception"] = tagHandlers["throw"] = tagHandlers["throws"] = make_handler(&PyDocConverter::handleTagException);
   tagHandlers["htmlonly"] = make_handler(&PyDocConverter::handleParagraph);
   tagHandlers["invariant"] = make_handler(&PyDocConverter::handleParagraph);
   tagHandlers["latexonly"] = make_handler(&PyDocConverter::handleParagraph);
@@ -228,8 +214,7 @@ void PyDocConverter::fillStaticTables()
   tagHandlers["remark"] = make_handler(&PyDocConverter::handleParagraph);
   tagHandlers["remarks"] = make_handler(&PyDocConverter::handleParagraph);
   tagHandlers["sa"] = make_handler(&PyDocConverter::handleTagMessage, "See also: ");
-  tagHandlers["see"] = make_handler(&PyDocConverter::handleTagMessage,
-      "See also: ");
+  tagHandlers["see"] = make_handler(&PyDocConverter::handleTagMessage, "See also: ");
   tagHandlers["since"] = make_handler(&PyDocConverter::handleParagraph);
   tagHandlers["short"] = make_handler(&PyDocConverter::handleParagraph);
   tagHandlers["todo"] = make_handler(&PyDocConverter::handleParagraph);
@@ -239,27 +224,21 @@ void PyDocConverter::fillStaticTables()
   tagHandlers["xmlonly"] = make_handler(&PyDocConverter::handleParagraph);
   // these commands have special handlers
   tagHandlers["arg"] = make_handler(&PyDocConverter::handleTagMessage, "* ");
-  tagHandlers["cond"] = make_handler(&PyDocConverter::handleTagMessage,
-      "Conditional comment: ");
+  tagHandlers["cond"] = make_handler(&PyDocConverter::handleTagMessage, "Conditional comment: ");
   tagHandlers["else"] = make_handler(&PyDocConverter::handleTagIf, "Else: ");
   tagHandlers["elseif"] = make_handler(&PyDocConverter::handleTagIf, "Else if: ");
-  tagHandlers["endcond"] = make_handler(&PyDocConverter::handleTagMessage,
-      "End of conditional comment.");
+  tagHandlers["endcond"] = make_handler(&PyDocConverter::handleTagMessage, "End of conditional comment.");
   tagHandlers["if"] = make_handler(&PyDocConverter::handleTagIf, "If: ");
   tagHandlers["ifnot"] = make_handler(&PyDocConverter::handleTagIf, "If not: ");
   tagHandlers["image"] = make_handler(&PyDocConverter::handleTagImage);
   tagHandlers["li"] = make_handler(&PyDocConverter::handleTagMessage, "* ");
   tagHandlers["overload"] = make_handler(&PyDocConverter::handleTagMessage,
-      "This is an overloaded member function, provided for"
-          " convenience.\nIt differs from the above function only in what"
-          " argument(s) it accepts.");
+                                         "This is an overloaded member function, provided for"
+                                         " convenience.\nIt differs from the above function only in what" " argument(s) it accepts.");
   tagHandlers["par"] = make_handler(&PyDocConverter::handleTagPar);
-  tagHandlers["param"] =
-  tagHandlers["tparam"] = make_handler(&PyDocConverter::handleTagParam);
+  tagHandlers["param"] = tagHandlers["tparam"] = make_handler(&PyDocConverter::handleTagParam);
   tagHandlers["ref"] = make_handler(&PyDocConverter::handleTagRef);
-  tagHandlers["result"] =
-  tagHandlers["return"] =
-  tagHandlers["returns"] = make_handler(&PyDocConverter::handleTagReturn);
+  tagHandlers["result"] = tagHandlers["return"] = tagHandlers["returns"] = make_handler(&PyDocConverter::handleTagReturn);
 
   // this command just prints it's contents
   // (it is internal command of swig's parser, contains plain text)
@@ -268,15 +247,12 @@ void PyDocConverter::fillStaticTables()
   tagHandlers["n"] = make_handler(&PyDocConverter::handleNewLine);
 
   // \f commands output literal Latex formula, which is still better than nothing.
-  tagHandlers["f$"] =
-  tagHandlers["f["] =
-  tagHandlers["f{"] = make_handler(&PyDocConverter::handleMath);
+  tagHandlers["f$"] = tagHandlers["f["] = tagHandlers["f{"] = make_handler(&PyDocConverter::handleMath);
 
   // HTML tags
   tagHandlers["<a"] = make_handler(&PyDocConverter::handleDoxyHtmlTag_A);
   tagHandlers["<b"] = make_handler(&PyDocConverter::handleDoxyHtmlTag2, "**");
-  tagHandlers["<blockquote"] = make_handler(&PyDocConverter::handleDoxyHtmlTag_A,
-      "Quote: ");
+  tagHandlers["<blockquote"] = make_handler(&PyDocConverter::handleDoxyHtmlTag_A, "Quote: ");
   tagHandlers["<body"] = make_handler(&PyDocConverter::handleDoxyHtmlTag);
   tagHandlers["<br"] = make_handler(&PyDocConverter::handleDoxyHtmlTag, "\n");
 
@@ -294,8 +270,7 @@ void PyDocConverter::fillStaticTables()
   tagHandlers["<div"] = make_handler(&PyDocConverter::handleDoxyHtmlTag);
   tagHandlers["<em"] = make_handler(&PyDocConverter::handleDoxyHtmlTag2, "**");
   tagHandlers["<form"] = make_handler(&PyDocConverter::handleDoxyHtmlTag);
-  tagHandlers["<hr"] = make_handler(&PyDocConverter::handleDoxyHtmlTag,
-      "--------------------------------------------------------------------\n");
+  tagHandlers["<hr"] = make_handler(&PyDocConverter::handleDoxyHtmlTag, "--------------------------------------------------------------------\n");
   tagHandlers["<h1"] = make_handler(&PyDocConverter::handleDoxyHtmlTag, "# ");
   tagHandlers["<h2"] = make_handler(&PyDocConverter::handleDoxyHtmlTag, "## ");
   tagHandlers["<h3"] = make_handler(&PyDocConverter::handleDoxyHtmlTag, "### ");
@@ -351,17 +326,13 @@ void PyDocConverter::fillStaticTables()
   tagHandlers["&rarr"] = make_handler(&PyDocConverter::handleHtmlEntity, "-->");
 }
 
-PyDocConverter::PyDocConverter(int flags) :
-    DoxygenTranslator(flags), m_tableLineLen(0), m_prevRowIsTH(
-        false)
-{
+PyDocConverter::PyDocConverter(int flags):
+DoxygenTranslator(flags), m_tableLineLen(0), m_prevRowIsTH(false) {
   fillStaticTables();
 }
 
 // Return the type as it should appear in the output documentation.
-static
-std::string getPyDocType(Node* n, const_String_or_char_ptr lname = "")
-{
+static std::string getPyDocType(Node *n, const_String_or_char_ptr lname = "") {
   std::string type;
 
   String *s = Swig_typemap_lookup("doctype", n, lname, 0);
@@ -371,13 +342,13 @@ std::string getPyDocType(Node* n, const_String_or_char_ptr lname = "")
   if (Language::classLookup(s)) {
     // In Python C++ namespaces are flattened, so remove all but last component
     // of the name.
-    String * const last = Swig_scopename_last(s);
+    String *const last = Swig_scopename_last(s);
 
     // We are not actually sure whether it's a documented class or not, but
     // there doesn't seem to be any harm in making it a reference if it isn't,
     // while there is a lot of benefit in having a hyperlink if it is.
     type = ":py:class:`";
-    type += Char (last);
+    type += Char(last);
     type += "`";
 
     Delete(last);
@@ -390,14 +361,13 @@ std::string getPyDocType(Node* n, const_String_or_char_ptr lname = "")
   return type;
 }
 
-std::string PyDocConverter::getParamType(std::string param)
-{
+std::string PyDocConverter::getParamType(std::string param) {
   std::string type;
 
   ParmList *plist = CopyParmList(Getattr(currentNode, "parms"));
-  for (Parm *p = plist; p;p = nextSibling(p)) {
-    String* pname = Getattr(p, "name");
-    if (Char (pname) != param)
+  for (Parm *p = plist; p; p = nextSibling(p)) {
+    String *pname = Getattr(p, "name");
+    if (Char(pname) != param)
       continue;
 
     type = getPyDocType(p, pname);
@@ -407,8 +377,7 @@ std::string PyDocConverter::getParamType(std::string param)
   return type;
 }
 
-std::string PyDocConverter::translateSubtree(DoxygenEntity & doxygenEntity)
-{
+std::string PyDocConverter::translateSubtree(DoxygenEntity &doxygenEntity) {
   std::string translatedComment;
 
   if (doxygenEntity.isLeaf)
@@ -433,28 +402,19 @@ std::string PyDocConverter::translateSubtree(DoxygenEntity & doxygenEntity)
   return translatedComment;
 }
 
-void PyDocConverter::translateEntity(DoxygenEntity & doxyEntity,
-                                     std::string &translatedComment)
-{
+void PyDocConverter::translateEntity(DoxygenEntity &doxyEntity, std::string &translatedComment) {
   // check if we have needed handler and call it
   std::map<std::string, std::pair<tagHandler, std::string> >::iterator it;
   it = tagHandlers.find(doxyEntity.typeOfEntity);
   if (it != tagHandlers.end())
-    (this->*(it->second.first))(doxyEntity, translatedComment,
-        it->second.second);
+    (this->*(it->second.first)) (doxyEntity, translatedComment, it->second.second);
 }
 
-void PyDocConverter::handleParagraph(DoxygenEntity& tag,
-                                     std::string& translatedComment,
-                                     const std::string&)
-{
+void PyDocConverter::handleParagraph(DoxygenEntity &tag, std::string &translatedComment, const std::string &) {
   translatedComment += translateSubtree(tag);
 }
 
-void PyDocConverter::handleMath(DoxygenEntity &tag,
-                                std::string &translatedComment,
-                                const std::string& arg)
-{
+void PyDocConverter::handleMath(DoxygenEntity &tag, std::string &translatedComment, const std::string &arg) {
   IndentGuard indent;
 
   // Only \f$ is translated to inline formulae, \f[ and \f{ are for the block ones.
@@ -507,10 +467,7 @@ void PyDocConverter::handleMath(DoxygenEntity &tag,
   }
 }
 
-void PyDocConverter::handleCode(DoxygenEntity &tag,
-                                std::string &translatedComment,
-                                const std::string &arg)
-{
+void PyDocConverter::handleCode(DoxygenEntity &tag, std::string &translatedComment, const std::string &arg) {
   IndentGuard indent(translatedComment, m_indent);
 
   trimWhitespace(translatedComment);
@@ -552,43 +509,27 @@ void PyDocConverter::handleCode(DoxygenEntity &tag,
     translatedComment += '\n';
 }
 
-void PyDocConverter::handlePlainString(DoxygenEntity& tag,
-                                       std::string& translatedComment,
-                                       const std::string&)
-{
+void PyDocConverter::handlePlainString(DoxygenEntity &tag, std::string &translatedComment, const std::string &) {
   translatedComment += tag.data;
 }
 
-void PyDocConverter::handleTagVerbatim(DoxygenEntity& tag,
-                                       std::string& translatedComment,
-                                       const std::string &arg)
-{
+void PyDocConverter::handleTagVerbatim(DoxygenEntity &tag, std::string &translatedComment, const std::string &arg) {
   translatedComment += arg + " ";
-  for (DoxygenEntityListCIt it = tag.entityList.begin();
-      it != tag.entityList.end(); it++) {
+  for (DoxygenEntityListCIt it = tag.entityList.begin(); it != tag.entityList.end(); it++) {
     translatedComment += it->data;
   }
 }
 
-void PyDocConverter::handleTagMessage(DoxygenEntity& tag,
-                                      std::string& translatedComment,
-                                      const std::string &arg)
-{
+void PyDocConverter::handleTagMessage(DoxygenEntity &tag, std::string &translatedComment, const std::string &arg) {
   translatedComment += arg;
   handleParagraph(tag, translatedComment);
 }
 
-void PyDocConverter::handleTagChar(DoxygenEntity& tag,
-                                   std::string& translatedComment,
-                                   const std::string&)
-{
+void PyDocConverter::handleTagChar(DoxygenEntity &tag, std::string &translatedComment, const std::string &) {
   translatedComment += tag.typeOfEntity;
 }
 
-void PyDocConverter::handleTagIf(DoxygenEntity& tag,
-                                 std::string& translatedComment,
-                                 const std::string &arg)
-{
+void PyDocConverter::handleTagIf(DoxygenEntity &tag, std::string &translatedComment, const std::string &arg) {
   translatedComment += arg;
   if (tag.entityList.size()) {
     translatedComment += tag.entityList.begin()->data;
@@ -597,10 +538,7 @@ void PyDocConverter::handleTagIf(DoxygenEntity& tag,
   }
 }
 
-void PyDocConverter::handleTagPar(DoxygenEntity& tag,
-                                  std::string& translatedComment,
-                                  const std::string&)
-{
+void PyDocConverter::handleTagPar(DoxygenEntity &tag, std::string &translatedComment, const std::string &) {
   translatedComment += "Title: ";
   if (tag.entityList.size())
     translatedComment += tag.entityList.begin()->data;
@@ -608,10 +546,7 @@ void PyDocConverter::handleTagPar(DoxygenEntity& tag,
   handleParagraph(tag, translatedComment);
 }
 
-void PyDocConverter::handleTagImage(DoxygenEntity& tag,
-                                    std::string& translatedComment,
-                                    const std::string&)
-{
+void PyDocConverter::handleTagImage(DoxygenEntity &tag, std::string &translatedComment, const std::string &) {
   if (tag.entityList.size() < 2)
     return;
   tag.entityList.pop_front();
@@ -622,10 +557,7 @@ void PyDocConverter::handleTagImage(DoxygenEntity& tag,
     translatedComment += "(" + tag.entityList.begin()->data + ")";
 }
 
-void PyDocConverter::handleTagParam(DoxygenEntity& tag,
-                                    std::string& translatedComment,
-                                    const std::string&)
-{
+void PyDocConverter::handleTagParam(DoxygenEntity &tag, std::string &translatedComment, const std::string &) {
   if (tag.entityList.size() < 2)
     return;
 
@@ -634,7 +566,7 @@ void PyDocConverter::handleTagParam(DoxygenEntity& tag,
   DoxygenEntity paramNameEntity = *tag.entityList.begin();
   tag.entityList.pop_front();
 
-  const std::string& paramName = paramNameEntity.data;
+  const std::string &paramName = paramNameEntity.data;
 
   const std::string paramType = getParamType(paramName);
   if (!paramType.empty()) {
@@ -648,10 +580,7 @@ void PyDocConverter::handleTagParam(DoxygenEntity& tag,
 }
 
 
-void PyDocConverter::handleTagReturn(DoxygenEntity &tag,
-                                     std::string &translatedComment,
-                                     const std::string &)
-{
+void PyDocConverter::handleTagReturn(DoxygenEntity &tag, std::string &translatedComment, const std::string &) {
   IndentGuard indent(translatedComment, m_indent);
 
   const std::string pytype = getPyDocType(currentNode);
@@ -667,10 +596,7 @@ void PyDocConverter::handleTagReturn(DoxygenEntity &tag,
 }
 
 
-void PyDocConverter::handleTagException(DoxygenEntity &tag,
-                                        std::string &translatedComment,
-                                        const std::string &)
-{
+void PyDocConverter::handleTagException(DoxygenEntity &tag, std::string &translatedComment, const std::string &) {
   IndentGuard indent(translatedComment, m_indent);
 
   translatedComment += ":raises: ";
@@ -678,10 +604,7 @@ void PyDocConverter::handleTagException(DoxygenEntity &tag,
 }
 
 
-void PyDocConverter::handleTagRef(DoxygenEntity& tag,
-                                  std::string& translatedComment,
-                                  const std::string&)
-{
+void PyDocConverter::handleTagRef(DoxygenEntity &tag, std::string &translatedComment, const std::string &) {
   if (!tag.entityList.size())
     return;
 
@@ -695,26 +618,19 @@ void PyDocConverter::handleTagRef(DoxygenEntity& tag,
 }
 
 
-void PyDocConverter::handleTagWrap(DoxygenEntity& tag,
-                                   std::string& translatedComment,
-                                   const std::string &arg)
-{
+void PyDocConverter::handleTagWrap(DoxygenEntity &tag, std::string &translatedComment, const std::string &arg) {
   if (tag.entityList.size()) { // do not include empty tags
     std::string tagData = translateSubtree(tag);
     // wrap the thing, ignoring whitespace
     size_t wsPos = tagData.find_last_not_of("\n\t ");
     if (wsPos != std::string::npos && wsPos != tagData.size() - 1)
-      translatedComment += arg + tagData.substr(0, wsPos + 1) + arg
-          + tagData.substr(wsPos + 1);
+      translatedComment += arg + tagData.substr(0, wsPos + 1) + arg + tagData.substr(wsPos + 1);
     else
       translatedComment += arg + tagData + arg;
   }
 }
 
-void PyDocConverter::handleDoxyHtmlTag(DoxygenEntity& tag,
-                                       std::string& translatedComment,
-                                       const std::string &arg)
-{
+void PyDocConverter::handleDoxyHtmlTag(DoxygenEntity &tag, std::string &translatedComment, const std::string &arg) {
   std::string htmlTagArgs = tag.data;
   if (htmlTagArgs == "/") {
     // end html tag, for example "</ul>
@@ -724,10 +640,7 @@ void PyDocConverter::handleDoxyHtmlTag(DoxygenEntity& tag,
   }
 }
 
-void PyDocConverter::handleDoxyHtmlTagNoParam(DoxygenEntity& tag,
-                                              std::string& translatedComment,
-                                              const std::string &arg)
-{
+void PyDocConverter::handleDoxyHtmlTagNoParam(DoxygenEntity &tag, std::string &translatedComment, const std::string &arg) {
   std::string htmlTagArgs = tag.data;
   if (htmlTagArgs == "/") {
     // end html tag, for example "</ul>
@@ -736,10 +649,7 @@ void PyDocConverter::handleDoxyHtmlTagNoParam(DoxygenEntity& tag,
   }
 }
 
-void PyDocConverter::handleDoxyHtmlTag_A(DoxygenEntity& tag,
-                                         std::string& translatedComment,
-                                         const std::string &arg)
-{
+void PyDocConverter::handleDoxyHtmlTag_A(DoxygenEntity &tag, std::string &translatedComment, const std::string &arg) {
   std::string htmlTagArgs = tag.data;
   if (htmlTagArgs == "/") {
     // end html tag, "</a>
@@ -755,10 +665,7 @@ void PyDocConverter::handleDoxyHtmlTag_A(DoxygenEntity& tag,
   }
 }
 
-void PyDocConverter::handleDoxyHtmlTag2(DoxygenEntity& tag,
-                                        std::string& translatedComment,
-                                        const std::string &arg)
-{
+void PyDocConverter::handleDoxyHtmlTag2(DoxygenEntity &tag, std::string &translatedComment, const std::string &arg) {
   std::string htmlTagArgs = tag.data;
   if (htmlTagArgs == "/") {
     // end html tag, for example "</em>
@@ -768,18 +675,14 @@ void PyDocConverter::handleDoxyHtmlTag2(DoxygenEntity& tag,
   }
 }
 
-void PyDocConverter::handleDoxyHtmlTag_tr(DoxygenEntity& tag,
-                                          std::string& translatedComment,
-                                          const std::string &)
-{
+void PyDocConverter::handleDoxyHtmlTag_tr(DoxygenEntity &tag, std::string &translatedComment, const std::string &) {
   std::string htmlTagArgs = tag.data;
   size_t nlPos = translatedComment.rfind('\n');
   if (htmlTagArgs == "/") {
     // end tag, </tr> appends vertical table line '|'
     translatedComment += '|';
     if (nlPos != string::npos) {
-      size_t startOfTableLinePos = translatedComment.find_first_not_of(" \t",
-          nlPos + 1);
+      size_t startOfTableLinePos = translatedComment.find_first_not_of(" \t", nlPos + 1);
       if (startOfTableLinePos != string::npos) {
         m_tableLineLen = translatedComment.size() - startOfTableLinePos;
       }
@@ -800,10 +703,7 @@ void PyDocConverter::handleDoxyHtmlTag_tr(DoxygenEntity& tag,
   }
 }
 
-void PyDocConverter::handleDoxyHtmlTag_th(DoxygenEntity& tag,
-                                          std::string& translatedComment,
-                                          const std::string &)
-{
+void PyDocConverter::handleDoxyHtmlTag_th(DoxygenEntity &tag, std::string &translatedComment, const std::string &) {
   std::string htmlTagArgs = tag.data;
   if (htmlTagArgs == "/") {
     // end tag, </th> is ignored
@@ -813,10 +713,7 @@ void PyDocConverter::handleDoxyHtmlTag_th(DoxygenEntity& tag,
   }
 }
 
-void PyDocConverter::handleDoxyHtmlTag_td(DoxygenEntity& tag,
-                                          std::string& translatedComment,
-                                          const std::string &)
-{
+void PyDocConverter::handleDoxyHtmlTag_td(DoxygenEntity &tag, std::string &translatedComment, const std::string &) {
   std::string htmlTagArgs = tag.data;
   if (htmlTagArgs == "/") {
     // end tag, </td> is ignored
@@ -825,18 +722,12 @@ void PyDocConverter::handleDoxyHtmlTag_td(DoxygenEntity& tag,
   }
 }
 
-void PyDocConverter::handleHtmlEntity(DoxygenEntity&,
-                                      std::string& translatedComment,
-                                      const std::string &arg)
-{
+void PyDocConverter::handleHtmlEntity(DoxygenEntity &, std::string &translatedComment, const std::string &arg) {
   // html entities
   translatedComment += arg;
 }
 
-void PyDocConverter::handleNewLine(DoxygenEntity&,
-                                   std::string& translatedComment,
-                                   const std::string&)
-{
+void PyDocConverter::handleNewLine(DoxygenEntity &, std::string &translatedComment, const std::string &) {
   trimWhitespace(translatedComment);
 
   translatedComment += "\n";
@@ -844,8 +735,7 @@ void PyDocConverter::handleNewLine(DoxygenEntity&,
     translatedComment += m_indent;
 }
 
-String *PyDocConverter::makeDocumentation(Node *n)
-{
+String *PyDocConverter::makeDocumentation(Node *n) {
   String *documentation;
   std::string pyDocString;
 
@@ -873,7 +763,7 @@ String *PyDocConverter::makeDocumentation(Node *n)
           String *comment = NewString("");
           Append(comment, documentation);
           Replaceall(comment, "\n *", "\n");
-          oneDoc = Char (comment);
+          oneDoc = Char(comment);
           Delete(comment);
         } else {
           std::list<DoxygenEntity> entityList = parser.createTree(n, documentation);
@@ -898,12 +788,10 @@ String *PyDocConverter::makeDocumentation(Node *n)
     if (allDocumentation.size() > 1) {
       string indentStr;
       if (minIndent != static_cast<size_t>(-1))
-        indentStr.assign(minIndent, ' ');
+       indentStr.assign(minIndent, ' ');
 
       std::ostringstream concatDocString;
-      for (size_t realOverloadCount = 0;
-          realOverloadCount < allDocumentation.size();
-          realOverloadCount++) {
+      for (size_t realOverloadCount = 0; realOverloadCount < allDocumentation.size(); realOverloadCount++) {
         if (realOverloadCount != 0) {
           // separate it from the preceding one.
           concatDocString << "\n" << indentStr << "|\n\n";
@@ -911,8 +799,7 @@ String *PyDocConverter::makeDocumentation(Node *n)
 
         oneDoc = allDocumentation[realOverloadCount];
         trimWhitespace(oneDoc);
-        concatDocString << indentStr << "*Overload " << (realOverloadCount + 1) << ":*\n"
-                        << oneDoc;
+        concatDocString << indentStr << "*Overload " << (realOverloadCount + 1) << ":*\n" << oneDoc;
       }
       pyDocString = concatDocString.str();
     } else if (allDocumentation.size() == 1) {
@@ -927,7 +814,7 @@ String *PyDocConverter::makeDocumentation(Node *n)
         String *comment = NewString("");
         Append(comment, documentation);
         Replaceall(comment, "\n *", "\n");
-        pyDocString = Char (comment);
+        pyDocString = Char(comment);
         Delete(comment);
       } else {
         std::list<DoxygenEntity> entityList = parser.createTree(n, documentation);
diff --git a/Source/DoxygenTranslator/src/PyDocConverter.h b/Source/DoxygenTranslator/src/PyDocConverter.h
index 338b1fed9..b78d81ed3 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.h
+++ b/Source/DoxygenTranslator/src/PyDocConverter.h
@@ -20,8 +20,8 @@
 #include "DoxygenEntity.h"
 #include "DoxygenTranslator.h"
 
-#define DOC_STRING_LENGTH	  64	// characters per line allowed
-#define DOC_PARAM_STRING_LENGTH	  30	// characters reserved for param name / type
+#define DOC_STRING_LENGTH         64 // characters per line allowed
+#define DOC_PARAM_STRING_LENGTH   30 // characters reserved for param name / type
 
 class PyDocConverter : public DoxygenTranslator {
 public:
@@ -39,42 +39,45 @@ protected:
    * display. Prints title for every group of tags that have
    * a section title associated with them
    */
-  std::string translateSubtree(DoxygenEntity & doxygenEntity);
+  std::string translateSubtree(DoxygenEntity &doxygenEntity);
+
   /*
    * Translate one entity with the appropriate handler, according
    * to the tagHandlers
    */
-  void translateEntity(DoxygenEntity & doxyEntity, std::string &translatedComment);
+  void translateEntity(DoxygenEntity &doxyEntity, std::string &translatedComment);
 
   /*
    * Typedef for the function that handles one tag
    * arg - some string argument to easily pass it through lookup table
    */
-  typedef void (PyDocConverter::*tagHandler)(DoxygenEntity &tag,
-      std::string &translatedComment, const std::string &arg);
+  typedef void (PyDocConverter::*tagHandler) (DoxygenEntity &tag, std::string &translatedComment, const std::string &arg);
 
   /*
    * Wrap the command data with the some string
    * arg - string to wrap with, like '_' or '*'
    */
   void handleTagWrap(DoxygenEntity &tag, std::string &translatedComment, const std::string &arg);
+
   /*
    * Just prints new line
    */
   void handleNewLine(DoxygenEntity &tag, std::string &translatedComment, const std::string &arg);
+
   /*
    * Print the name of tag to the output, used for escape-commands
    */
   void handleTagChar(DoxygenEntity &tag, std::string &translatedComment, const std::string &arg);
+
   /*
    * Format the contents of the \exception tag or its synonyms.
    */
   void handleTagException(DoxygenEntity &tag, std::string &translatedComment, const std::string &arg);
+
   /*
    * Print only the content and strip original tag
    */
-  void handleParagraph(DoxygenEntity &tag, std::string &translatedComment,
-                       const std::string &arg = std::string());
+  void handleParagraph(DoxygenEntity &tag, std::string &translatedComment, const std::string &arg = std::string());
 
   /*
    * Handle one of the Doxygen formula-related tags.
@@ -94,78 +97,73 @@ protected:
   /**
    * Copies verbatim args of the tag to output, used for commands like \f$, ...
    */
-  void handleTagVerbatim(DoxygenEntity& tag,
-                            std::string& translatedComment,
-                            const std::string &arg);
+  void handleTagVerbatim(DoxygenEntity &tag, std::string &translatedComment, const std::string &arg);
 
   /*
    * Print the if-elseif-else-endif section
    */
   void handleTagIf(DoxygenEntity &tag, std::string &translatedComment, const std::string &arg);
+
   /*
    * Prints the specified message, than the contents of the tag
    * arg - message
    */
   void handleTagMessage(DoxygenEntity &tag, std::string &translatedComment, const std::string &arg);
+
   /*
    * Insert 'Title: ...'
    */
   void handleTagPar(DoxygenEntity &tag, std::string &translatedComment, const std::string &arg);
+
   /*
    * Insert 'Image: ...'
    */
   void handleTagImage(DoxygenEntity &tag, std::string &translatedComment, const std::string &arg);
+
   /*
    * Format nice param description with type information
    */
   void handleTagParam(DoxygenEntity &tag, std::string &translatedComment, const std::string &arg);
+
   /*
    * Format the contents of the \return tag or its synonyms.
    */
   void handleTagReturn(DoxygenEntity &tag, std::string &translatedComment, const std::string &arg);
+
   /*
    * Writes text for \ref tag. 
    */
-  void handleTagRef(DoxygenEntity& tag, std::string& translatedComment, const std::string &arg);
+  void handleTagRef(DoxygenEntity &tag, std::string &translatedComment, const std::string &arg);
 
   /* Handles HTML tags recognized by Doxygen, like <A ...>, <ul>, <table>, ... */
 
-  void handleDoxyHtmlTag(DoxygenEntity& tag, std::string& translatedComment, const std::string &arg);
+  void handleDoxyHtmlTag(DoxygenEntity &tag, std::string &translatedComment, const std::string &arg);
 
   /** Does not output params of HTML tag, for example in <table border='1'>
    * 'border=1' is not written to output.
    */
-  void handleDoxyHtmlTagNoParam(DoxygenEntity& tag,
-                                    std::string& translatedComment,
-                                    const std::string &arg);
+  void handleDoxyHtmlTagNoParam(DoxygenEntity &tag, std::string &translatedComment, const std::string &arg);
 
   /** Translates tag <a href = "url">text</a> to: text ("url"). */
-  void handleDoxyHtmlTag_A(DoxygenEntity& tag,
-                              std::string& translatedComment,
-                              const std::string &arg);
+  void handleDoxyHtmlTag_A(DoxygenEntity &tag, std::string &translatedComment, const std::string &arg);
 
   /*
    * Handles HTML tags, which are translated to markdown-like syntax, for example
    * <i>text</i>  -->  _text_. Appends arg for start HTML tag and end HTML tag.
    */
-  void handleDoxyHtmlTag2(DoxygenEntity& tag,
-                             std::string& translatedComment,
-                             const std::string &arg);
+  void handleDoxyHtmlTag2(DoxygenEntity &tag, std::string &translatedComment, const std::string &arg);
 
   /* Handles HTML table, tag <tr> */
-  void handleDoxyHtmlTag_tr(DoxygenEntity& tag, std::string& translatedComment,
-                               const std::string &arg);
+  void handleDoxyHtmlTag_tr(DoxygenEntity &tag, std::string &translatedComment, const std::string &arg);
 
   /* Handles HTML table, tag <th> */
-  void handleDoxyHtmlTag_th(DoxygenEntity& tag, std::string& translatedComment,
-                               const std::string &arg);
+  void handleDoxyHtmlTag_th(DoxygenEntity &tag, std::string &translatedComment, const std::string &arg);
 
   /* Handles HTML table, tag <td> */
-  void handleDoxyHtmlTag_td(DoxygenEntity& tag, std::string& translatedComment,
-                                const std::string &arg);
+  void handleDoxyHtmlTag_td(DoxygenEntity &tag, std::string &translatedComment, const std::string &arg);
 
   /* Handles HTML entities recognized by Doxygen, like &lt;, &copy;, ... */
-  void handleHtmlEntity(DoxygenEntity&, std::string& translatedComment, const std::string &arg);
+  void handleHtmlEntity(DoxygenEntity &, std::string &translatedComment, const std::string &arg);
 
 
   /*
@@ -184,7 +182,7 @@ private:
 
 
   // this contains the handler pointer and one string argument
-  typedef std::map<std::string, std::pair<tagHandler, std::string> > TagHandlersMap;
+  typedef std::map<std::string, std::pair<tagHandler, std::string> >TagHandlersMap;
   static TagHandlersMap tagHandlers;
 
   // this contains the sections tittles, like 'Arguments:' or 'Notes:', that are printed only once
@@ -192,7 +190,7 @@ private:
 
   // Helper functions for fillStaticTables(): make a new tag handler object.
   TagHandlersMap::mapped_type make_handler(tagHandler handler);
-  TagHandlersMap::mapped_type make_handler(tagHandler handler, const char* arg);
+  TagHandlersMap::mapped_type make_handler(tagHandler handler, const char *arg);
 
   void fillStaticTables();
 };

From ef8d68c0ab4a5699c6d3166d24b922d2df65d71f Mon Sep 17 00:00:00 2001
From: William S Fulton <wsf@fultondesigns.co.uk>
Date: Mon, 21 May 2018 20:07:26 +0100
Subject: [PATCH 290/314] Remove doxygen Examples subdirectory

Doesn't seem to be used or useful now.
---
 .../src/Examples/DoxygenTransWTokenizer.cpp   | 1013 -----------------
 .../src/Examples/DoxygenTransWTokenizer.h     |   21 -
 .../DoxygenTranslator/src/Examples/Example1   |    6 -
 .../DoxygenTranslator/src/Examples/Example2   |    7 -
 .../DoxygenTranslator/src/Examples/Example3   |   10 -
 .../DoxygenTranslator/src/Examples/Example4   |    5 -
 .../DoxygenTranslator/src/Examples/Example5   |    0
 .../DoxygenTranslator/src/Examples/Example6   |    0
 .../src/Examples/translator.h                 |  155 ---
 9 files changed, 1217 deletions(-)
 delete mode 100644 Source/DoxygenTranslator/src/Examples/DoxygenTransWTokenizer.cpp
 delete mode 100644 Source/DoxygenTranslator/src/Examples/DoxygenTransWTokenizer.h
 delete mode 100644 Source/DoxygenTranslator/src/Examples/Example1
 delete mode 100644 Source/DoxygenTranslator/src/Examples/Example2
 delete mode 100644 Source/DoxygenTranslator/src/Examples/Example3
 delete mode 100644 Source/DoxygenTranslator/src/Examples/Example4
 delete mode 100644 Source/DoxygenTranslator/src/Examples/Example5
 delete mode 100644 Source/DoxygenTranslator/src/Examples/Example6
 delete mode 100644 Source/DoxygenTranslator/src/Examples/translator.h

diff --git a/Source/DoxygenTranslator/src/Examples/DoxygenTransWTokenizer.cpp b/Source/DoxygenTranslator/src/Examples/DoxygenTransWTokenizer.cpp
deleted file mode 100644
index dd803b75f..000000000
--- a/Source/DoxygenTranslator/src/Examples/DoxygenTransWTokenizer.cpp
+++ /dev/null
@@ -1,1013 +0,0 @@
-/* ----------------------------------------------------------------------------- 
- * This file is part of SWIG, which is licensed as a whole under version 3 
- * (or any later version) of the GNU General Public License. Some additional
- * terms also apply to certain portions of SWIG. The full details of the SWIG
- * license and copyrights can be found in the LICENSE and COPYRIGHT files
- * included with the SWIG source code as distributed by the SWIG developers
- * and at http://www.swig.org/legal.html.
- *
- * DoxygenTransWTokenizer.cpp
- *
- * The main class for translating blobs of Doxygen for SWIG
- * ----------------------------------------------------------------------------- */
-
-//TODO DOH instead of STL?
-//TODO Most commands are not fully implemented
-
-#include <cstdlib>
-#include <iostream>
-#include <fstream>
-#include <string>
-#include <list>
-#include "DoxygenEntity.h"
-#include "TokenList.h"
-#define SIMPLECOMMAND 1
-#define IGNOREDSIMPLECOMMAND 2
-#define COMMANDWORD 3
-#define IGNOREDCOMMANDWORD 4
-#define COMMANDLINE 5
-#define IGNOREDCOMMANDLINE 6
-#define COMMANDPARAGRAPH 7
-#define IGNORECOMMANDPARAGRAPH 8
-#define COMMANDENDCOMMAND 9
-#define COMMANDWORDPARAGRAPH 10
-#define COMMANDWORDLINE 11
-#define COMMANDWORDOWORDWORD 12
-#define COMMANDOWORD 13
-#define COMMANDERRORTHROW 14
-#define COMMANDUNIQUE 15
-using namespace std;
-
-
-//////////////////////////////////////////
-/*Set these to pick what internal functions
-to test. */
-
-//int testCommandParsingFunctions = 1;// not implemented
-
-int testCodeCrawlingFunctions = 0;
-int demonstrateParsing = 0;
-int runExamples = 0;
-int noisy = 0;			// set this to 1 for extra chatter from the parsing stage.
-int addCommand(string commandName, int &startInd, list < DoxygenEntity > &doxyList, string doxygenString);
-//////////////////////////////////////////
-
-
-
-/* Globals*/
-
-
-// An array of all the commands and my generic description tag, plaindescription
-
-string commandArray[] = { "a", "addindex", "addtogroup", "anchor", "arg", "attention",
-  "author", "b", "brief", "bug", "c", "callgraph", "callergraph", "category",
-  "class", "code", "cond", "copybrief", "copydetails", "copydoc", "date", "def",
-  "defgroup", "deprecated", "details", "dir", "dontinclude", "dot", "dotfile", "e",
-  "else", "elseif", "em", "endcode", "endcond", "enddot", "endhtmlonly", "endif",
-  "endlatexonly", "endlink", "endmanonly", "endmsc", "endverbatim", "endxmlonly",
-  "enum", "example", "exception", "f$", "f[", "f]", "f{", "f}", "file", "fn", "headerfile",
-  "hideinitializer", "htmlinclude", "htmlonly", "if", "ifnot", "image", "include",
-  "includelineno", "ingroup", "internal", "invariant", "interface", "latexonly", "li",
-  "line", "link", "mainpage", "manonly", "msc", "n", "name", "namespace", "nosubgrouping",
-  "note", "overload", "p", "package", "page", "par", "paragraph", "param", "post", "pre",
-  "private", "privatesection", "property", "protected", "protectedsection", "protocol",
-  "public", "publicsection", "ref", "relates", "relatesalso", "remarks", "return", "retval",
-  "sa", "section", "see", "showinitializer", "since", "skip", "skipline", "struct", "subpage",
-  "subsection", "subsubsection", "test", "throw", "todo", "tparam", "typedef", "union", "until",
-  "var", "verbatim", "verbinclude", "version", "warning", "weakgroup", "xmlonly", "xrefitem",
-  "$", "@", "//", "&", "~", "<", ">", "#", "%"
-};
-
-
-string sectionIndicators[] = { "attention", "author", "brief", "bug", "cond", "date", "deprecated", "details",
-  "else", "elseif", "endcond", "endif", "exception", "if", "ifnot", "invariant", "note", "par", "param",
-  "tparam", "post", "pre", "remarks", "return", "retval", "sa", "see", "since", "test", "throw", "todo",
-  "version", "warning", "xrefitem"
-};
-
-/* All of the doxygen commands divided up by how they are parsed */
-string simpleCommands[] = { "n", "$", "@", "//", "&", "~", "<", ">", "#", "%" };
-string ignoredSimpleCommands[] = { "nothing at the moment" };
-
-string commandWords[] = { "a", "b", "c", "e", "em", "p", "def", "enum", "example", "package",
-  "relates", "namespace", "relatesalso", "anchor", "dontinclude", "include", "includelineno"
-};
-string ignoredCommandWords[] = { "copydoc", "copybrief", "copydetails", "verbinclude", "htmlinclude" };
-string commandLines[] = { "addindex", "fn", "name", "line", "var", "skipline", "typedef", "skip", "until", "property" };
-string ignoreCommandLines[] = { "nothing at the moment" };
-
-string commandParagraph[] = { "return", "remarks", "since", "test", "sa", "see", "pre", "post", "details", "invariant",
-  "deprecated", "date", "note", "warning", "version", "todo", "bug", "attention", "brief", "arg", "author"
-};
-string ignoreCommandParagraphs[] = { "nothing at the moment" };
-
-string commandEndCommands[] = { "code", "dot", "msc", "f$", "f[", "f{environment}{", "htmlonly", "latexonly", "manonly",
-  "verbatim", "xmlonly", "cond", "if", "ifnot", "link"
-};
-string commandWordParagraphs[] = { "param", "tparam", "throw", "retval", "exception" };
-string commandWordLines[] = { "page", "subsection", "subsubsection", "section", "paragraph", "defgroup" };
-string commandWordOWordOWords[] = { "category", "class", "protocol", "interface", "struct", "union" };
-string commandOWords[] = { "dir", "file", "cond" };
-
-string commandErrorThrowings[] = { "annotatedclasslist", "classhierarchy", "define", "functionindex", "header",
-  "headerfilelist", "inherit", "l", "postheader", "private", "privatesection", "protected",
-  "protectedsection", "public", "publicsection", "endcode", "enddot", "endmsc", "endhtmlonly",
-  "endlatexonly", "endmanonly", "endlink", "endverbatim", "endxmlonly", "f]", "f}", "endcond",
-  "endif"
-};
-
-string commandUniques[] = { "xrefitem", "ingroup", "par", "headerfile", "overload", "weakgroup", "ref",
-  "subpage", "dotfile", "image", "addtogroup", "li"
-};
-
- //int startIndex = 0;
-int isNewLine = 0;
-int briefDescExists = 0;
-
- /* Entity list is the root list.
-  * it is arranged this way to help documentation modules,
-  * such as the javaDoc one, "sort" entities where they need to.
-  */
-
-list < DoxygenEntity > rootList;
-
-/* General (untested) assist methods */
-
-string StringToLower(string stringToConvert)
-{
-  //change each element of the string to lower case
-
-  for (unsigned int i = 0; i < stringToConvert.length(); i++) {
-    stringToConvert[i] = tolower(stringToConvert[i]);
-  }
-  return stringToConvert;	//return the converted string
-}
-
-int findCommand(string smallString) {
-
-  smallString = StringToLower(smallString);
-  int a;
-  for (int i = 0; i < sizeof(commandArray) / sizeof(*commandArray); i++) {
-    if ((a = smallString.compare(commandArray[i])) == 0) {
-      return 101 + i;
-    }
-
-
-  }
-  return -1;
-}
-
-int commandBelongs(string theCommand) {
-  string smallString = StringToLower(theCommand);
-  //cout << " Looking for command " << theCommand << endl;
-  int i = 0;
-  for (i = 0; i < sizeof(simpleCommands) / sizeof(*simpleCommands); i++) {
-    if (smallString.compare(simpleCommands[i]) == 0) {
-      return SIMPLECOMMAND;
-    }
-  }
-  for (i = 0; i < sizeof(ignoredSimpleCommands) / sizeof(*ignoredSimpleCommands); i++) {
-    if (smallString.compare(ignoredSimpleCommands[i]) == 0) {
-      return IGNOREDSIMPLECOMMAND;
-    }
-  }
-  for (i = 0; i < sizeof(commandWords) / sizeof(*commandWords); i++) {
-    if (smallString.compare(commandWords[i]) == 0) {
-      return COMMANDWORD;
-    }
-  }
-  for (i = 0; i < sizeof(ignoredCommandWords) / sizeof(*ignoredCommandWords); i++) {
-    if (smallString.compare(ignoredCommandWords[i]) == 0) {
-      return IGNOREDCOMMANDWORD;
-    }
-  }
-  for (i = 0; i < sizeof(commandLines) / sizeof(*commandLines); i++) {
-    if (smallString.compare(commandLines[i]) == 0) {
-      return COMMANDLINE;
-    }
-  }
-  for (i = 0; i < sizeof(ignoreCommandLines) / sizeof(*ignoreCommandLines); i++) {
-    if (smallString.compare(ignoreCommandLines[i]) == 0) {
-      return IGNOREDCOMMANDLINE;
-    }
-  }
-  for (i = 0; i < sizeof(commandParagraph) / sizeof(*commandParagraph); i++) {
-    if (smallString.compare(commandParagraph[i]) == 0) {
-      return COMMANDPARAGRAPH;
-    }
-  }
-  /* IgnoreCommandParagraph */
-  for (i = 0; i < sizeof(ignoreCommandParagraphs) / sizeof(*ignoreCommandParagraphs); i++) {
-    if (smallString.compare(ignoreCommandParagraphs[i]) == 0) {
-      return IGNORECOMMANDPARAGRAPH;
-    }
-  }
-  for (i = 0; i < sizeof(commandEndCommands) / sizeof(*commandEndCommands); i++) {
-    if (smallString.compare(commandEndCommands[i]) == 0) {
-      return COMMANDENDCOMMAND;
-    }
-  }
-  for (i = 0; i < sizeof(commandWordParagraphs) / sizeof(*commandWordParagraphs); i++) {
-    if (smallString.compare(commandWordParagraphs[i]) == 0) {
-      return COMMANDWORDPARAGRAPH;
-    }
-  }
-  for (i = 0; i < sizeof(commandWordLines) / sizeof(*commandWordLines); i++) {
-    if (smallString.compare(commandWordLines[i]) == 0) {
-      return COMMANDWORDLINE;
-    }
-  }
-  for (i = 0; i < sizeof(commandWordOWordOWords) / sizeof(*commandWordOWordOWords); i++) {
-    if (smallString.compare(commandWordOWordOWords[i]) == 0) {
-      return COMMANDWORDOWORDWORD;
-    }
-  }
-  for (i = 0; i < sizeof(commandOWords) / sizeof(*commandOWords); i++) {
-    if (smallString.compare(commandOWords[i]) == 0) {
-      return COMMANDOWORD;
-    }
-  }
-  for (i = 0; i < sizeof(commandErrorThrowings) / sizeof(*commandErrorThrowings); i++) {
-    if (smallString.compare(commandErrorThrowings[i]) == 0) {
-      return COMMANDERRORTHROW;
-    }
-  }
-  for (i = 0; i < sizeof(commandUniques) / sizeof(*commandUniques); i++) {
-    if (smallString.compare(commandUniques[i]) == 0) {
-      return COMMANDUNIQUE;
-    }
-  }
-
-  return 0;
-
-}
-
- /* isSectionIndicator returns a boolean if the command is a section indicator
-  * This is a helper method for finding the end of a paragraph
-  * by Doxygen's terms
-  */
-int isSectionIndicator(string smallString) {
-  smallString = StringToLower(smallString);
-
-  for (int i = 0; i < sizeof(sectionIndicators) / sizeof(*sectionIndicators); i++) {
-    if (smallString.compare(sectionIndicators[i]) == 0) {
-      return 1;
-    }
-  }
-  return 0;
-}
-
-
- /* HELPER METHODS
-  * To test these, change the flags at the top of this class
-  */
-
- /* Tiny method to compartmentalise the removal of all optional comment fluff such as ///
-  * or **** that often occurs before commment blobs.
-  */
-int clearFluff(int &startInd, string doxygenString) {
-  int startIndex = startInd;
-  int amountRemoved = 0;
-
-  while (doxygenString[startIndex] == '/' || doxygenString[startIndex] == '!' || doxygenString[startIndex] == '*'
-	 || doxygenString[startIndex] == '\n' || doxygenString[startIndex] == ' ' || doxygenString[startIndex] == '\t') {
-    startIndex++;
-    amountRemoved++;
-  }
-  startInd = startIndex;
-  return startIndex;
-}
-
- /* Returns the next word ON THE CURRENT LINE ONLY
-  * if a new line is encountered, returns a blank string.
-  * Updates the index it is given after completion.
-  */
-
-string getNextWord(int &startInd, string doxygenString) {
-  int startIndex = startInd;
-  string nextWord;
-  while (startIndex < doxygenString.length() && (doxygenString[startIndex] == '/' || doxygenString[startIndex] == ' '
-						 || doxygenString[startIndex] == '*' || doxygenString[startIndex] == '\n' || doxygenString[startIndex] == '\t'
-						 || doxygenString[startIndex] == '!')) {
-    if (doxygenString[startIndex] == '\n') {
-      startInd = startIndex;
-      return nextWord;
-    }
-    startIndex++;
-    //cout << "Start Index" << startIndex << endl;
-  }
-  //cout << doxygenString[startIndex] << endl;
-  int endIndex = startIndex;
-
-  while (endIndex < doxygenString.length() && (doxygenString[endIndex] != '\n' && doxygenString[endIndex] != ' ')) {
-    endIndex++;
-    //cout << "End Index " << endIndex << endl;
-  }
-  nextWord = doxygenString.substr(startIndex, endIndex - startIndex);
-  startInd = endIndex;
-  //cout << "Next Word :" << nextWord << ":" << endl;
-  return nextWord;
-}
-
- /* Returns the string remaining on a line
-  * and moved the index to the NEXT line
-  * returns "" if nothing on the current line.
-  */
-string getOneLine(int &startInd, string doxygenString) {
-  int startIndex = startInd;
-  while (doxygenString[startIndex] == '/' || doxygenString[startIndex] == ' '
-	 || doxygenString[startIndex] == '*' || doxygenString[startIndex] == '\n' || doxygenString[startIndex] == '!' || doxygenString[startIndex] == '\t') {
-    if (doxygenString[startIndex] == '\n')
-      return "";
-    startIndex++;
-  }
-
-  int endIndex = startIndex;
-  while ((endIndex != doxygenString.length()) && (doxygenString[endIndex] != '\n')) {
-    endIndex++;
-    //cout << doxygenString[endIndex] << "End Index: " << endIndex << endl;
-  }
-  string returnedLine = doxygenString.substr(startIndex, endIndex - startIndex);
-  if (doxygenString[endIndex] == '\n' && (endIndex < doxygenString.length()))
-    endIndex++;
-  startInd = endIndex;
-  return returnedLine;
-}
-
-/* Returns a properly formatted (all doxygen *, //! etc removed)
- * up til ANY command or end of paragraph is encountered. Has all the same issues as
- * getStringTilEndOfParagraph formatting wise.
- */
-string getStringTilCommand(int &startInd, string doxygenString) {
-  if (startInd >= doxygenString.length())
-    return "";
-  int startIndex = startInd;
-  int endIndex = startInd;
-  string description;
-  /* Find the End of the description */
-  int keepLooping = 1;
-  int spareIndex = 0;
-  int counter;
-  int finalIndex;
-  while (keepLooping) {
-    if (endIndex >= doxygenString.length()) {
-      finalIndex = endIndex;
-      keepLooping = 0;
-    } else if (doxygenString[endIndex] == '\n') {
-      //cout << "1 ";
-      counter = endIndex;
-      if (keepLooping && endIndex < doxygenString.length() - 1) {
-	counter++;
-	//cout << "Counter :" << counter << endl;
-	while (keepLooping && endIndex < doxygenString.length() && (doxygenString[counter] == ' ' ||
-								    doxygenString[counter] == '*' || doxygenString[counter] == '\n'
-								    || doxygenString[counter] == '/' || doxygenString[counter] == '!'
-								    || doxygenString[startIndex] == '\t')) {
-	  if (doxygenString[counter] == '\n') {
-	    //cout << "Blank line found" << endl;
-	    keepLooping = 0;
-	    finalIndex = counter;
-	  } else {
-	    counter++;
-	  }
-	}
-
-      }
-      //endIndex = counter;
-    } else if (doxygenString[endIndex] == '\\' || doxygenString[endIndex] == '@') {
-      finalIndex = endIndex;
-      keepLooping = 0;
-    } else if (endIndex < doxygenString.length() - 2 && string("**/").compare(doxygenString.substr(endIndex, endIndex + 2)) == 0) {
-      finalIndex = endIndex;
-      //cout << "3 ";
-      keepLooping = 0;
-    }
-    if (keepLooping) {
-      //cout << "4 ";
-      endIndex++;
-    }
-  }
-  //cout << "Done with EndIndex" << endl;
-  while (doxygenString[startIndex] == '!' || doxygenString[startIndex] == ' '
-	 || doxygenString[startIndex] == '/' || doxygenString[startIndex] == '*' || doxygenString[startIndex] == '\t')
-    startIndex++;
-
-  for (int i = startIndex; i < endIndex; i++) {
-
-    if (doxygenString[i] == '\n') {
-
-      while ((doxygenString[i] == '\n' || doxygenString[startIndex] == '\t' || doxygenString[i] == ' '
-	      || doxygenString[i] == '*' || doxygenString[i] == '/') && endIndex < doxygenString.length() - 1) {
-	i++;
-      }
-      description.append(" ");
-    }
-    description.push_back(doxygenString[i]);
-    //cout << doxygenString[i];
-  }
-  //if(noisy) cout << "Final Index is: " << finalIndex << endl;
-  startInd = finalIndex;
-  return description;
-}
-
-
-/* Returns a Paragraph- defined in Doxygen to be a paragraph of text
- * seperate by either a structural command or a blank line
- * This method is VERY messy currently
- */
- //TODO fix getStringTilEndOfParagraph to be more forgiving, work on ' ' characters
-string getStringTilEndOfParagraph(int &startInd, string doxygenString) {
-  if (startInd >= doxygenString.length())
-    return "";
-  int startIndex = startInd;
-  int endIndex = startInd;
-  string description;
-  /* Find the End of the description */
-  int keepLooping = 1;
-  int spareIndex = 0;
-  int counter;
-  int finalIndex;
-  while (keepLooping) {
-    if (endIndex >= doxygenString.length()) {
-      finalIndex = endIndex;
-      keepLooping = 0;
-    } else if (doxygenString[endIndex] == '\n') {
-      //cout << "1 ";
-      counter = endIndex;
-      if (keepLooping && endIndex < doxygenString.length() - 1) {
-	counter++;
-	//cout << "Counter :" << counter << endl;
-	while (keepLooping && endIndex < doxygenString.length() && (doxygenString[counter] == ' ' ||
-								    doxygenString[counter] == '*' || doxygenString[startIndex] == '\t'
-								    || doxygenString[counter] == '\n' || doxygenString[counter] == '/'
-								    || doxygenString[counter] == '!')) {
-	  if (doxygenString[counter] == '\n') {
-	    //cout << "Blank line found" << endl;
-	    keepLooping = 0;
-	    finalIndex = counter;
-	  } else {
-	    counter++;
-	  }
-	}
-
-      }
-      //endIndex = counter;
-    }
-    //todo this fix for not immediately exciting while parsing a paragraph seems somewhat cheap
-    else if (endIndex != startInd && doxygenString[endIndex] == '\\' || doxygenString[endIndex] == '@') {
-      spareIndex = endIndex + 1;
-
-      if (isSectionIndicator(getNextWord(spareIndex, doxygenString))) {
-	keepLooping = 0;
-	finalIndex = endIndex;
-      }
-    } else if (endIndex < doxygenString.length() - 1 && string("*/").compare(doxygenString.substr(endIndex, endIndex + 1)) == 0) {
-      keepLooping = 0;
-      finalIndex = endIndex;
-    }
-    if (keepLooping) {
-      endIndex++;
-    }
-  }
-  //cout << "Done with EndIndex" << endl;
-  while (doxygenString[startIndex] == '!' || doxygenString[startIndex] == ' ' || doxygenString[startIndex] == '\t'
-	 || doxygenString[startIndex] == '/' || doxygenString[startIndex] == '*')
-    startIndex++;
-
-  for (int i = startIndex; i < endIndex; i++) {
-
-    if (doxygenString[i] == '\n') {
-
-      while ((doxygenString[i] == '\n' || doxygenString[startIndex] == '\t' || doxygenString[i] == ' ' || doxygenString[startIndex] == '!'
-	      || doxygenString[i] == '*' || doxygenString[i] == '/') && endIndex < doxygenString.length() - 1) {
-	i++;
-      }
-      description.append(" ");
-    }
-    description.push_back(doxygenString[i]);
-    //cout << doxygenString[i];
-  }
-  startInd = finalIndex;
-  return description;
-}
-
- /* This method is for a specific form of doxygen command
-  * that begins with a \command and ends in \endcommand
-  * such as \code and \endcode. The proper usage is
-  * progressTilEndCommand("endcode", index)
-  * currently this method does NOT process what is in between the two commands
-  */
- //TODO Make progressTilCommand return a formatted string
-int progressTilEndCommand(string theCommand, int &startInd, string doxygenString) {
-  int endIndex = startInd;
-  while (endIndex < doxygenString.length()) {
-    if (doxygenString[endIndex] == '\\' || doxygenString[endIndex] == '@') {
-      //cout << doxygenString.substr(endIndex + 1 , theCommand.length())<< endl;
-      if (theCommand.compare(doxygenString.substr(endIndex + 1, theCommand.length())) == 0) {
-	startInd = endIndex + theCommand.length() + 1;
-	return 1;
-      }
-    }
-    endIndex++;
-  }
-  //End command not found
-  return 0;
-}
-
- /* A specialty method for commands such as \arg that end at the end of a paragraph OR when another \arg is encountered
-  */
-
-string getStringTilAnyCommand(string theCommand, int &startInd, string doxygenString) {
-  if (startInd >= doxygenString.length())
-    return "";
-  int startIndex = startInd;
-  int endIndex = startInd;
-  string description;
-  /* Find the End of the description */
-  int keepLooping = 1;
-  int spareIndex = 0;
-  int counter;
-  int finalIndex;
-  while (keepLooping) {
-    if (endIndex >= theCommand.length()) {
-      finalIndex = endIndex;
-      keepLooping = 0;
-    } else if (doxygenString[endIndex] == '\n') {
-      //cout << "1 ";
-      counter = endIndex;
-      if (keepLooping && endIndex < doxygenString.length() - 1) {
-	counter++;
-	//cout << "Counter :" << counter << endl;
-	while (keepLooping && endIndex < doxygenString.length() && (doxygenString[counter] == ' ' ||
-								    doxygenString[counter] == '*' || doxygenString[counter] == '\n'
-								    || doxygenString[counter] == '/' || doxygenString[counter] == '!'
-								    || doxygenString[startIndex] == '\t')) {
-	  if (doxygenString[counter] == '\n') {
-	    //cout << "Blank line found" << endl;
-	    keepLooping = 0;
-	    finalIndex = counter;
-	  } else {
-	    counter++;
-	  }
-	}
-
-      }
-      //endIndex = counter;
-    } else if (doxygenString[endIndex] == '\\' || doxygenString[endIndex] == '@') {
-      //cout << "2 ";
-      spareIndex = endIndex;
-      if (endIndex + theCommand.length() < theCommand.length()
-	  && theCommand.compare(doxygenString.substr(endIndex, theCommand.length())) == 0)
-	keepLooping = 0;
-    } else if (endIndex < doxygenString.length() - 1 && string("*/").compare(doxygenString.substr(endIndex, endIndex + 1)) == 0) {
-      //cout << "3 ";
-      keepLooping = 0;
-    }
-    if (keepLooping) {
-      //cout << "4 ";
-      endIndex++;
-    }
-  }
-  //cout << "Done with EndIndex" << endl;
-  while (doxygenString[startIndex] == '!' || doxygenString[startIndex] == ' '
-	 || doxygenString[startIndex] == '/' || doxygenString[startIndex] == '*' || doxygenString[startIndex] == '\t')
-    startIndex++;
-
-  for (int i = startIndex; i < endIndex; i++) {
-
-    if (doxygenString[i] == '\n') {
-
-      while ((doxygenString[i] == '\n' || doxygenString[i] == ' ' || doxygenString[startIndex] == '\t'
-	      || doxygenString[i] == '*' || doxygenString[i] == '/') && endIndex < doxygenString.length() - 1) {
-	i++;
-      }
-      description.append(" ");
-    }
-    description.push_back(doxygenString[i]);
-    //cout << doxygenString[i];
-  }
-  startInd = finalIndex;
-  return description;
-}
-
-
- /* prints the parse tree
-  *
-  */
-void printTree() {
-
-  list < DoxygenEntity >::iterator p = rootList.begin();
-  while (p != rootList.end()) {
-    (*p).printEntity(0);
-    p++;
-  }
-
-}
-
-
-
-list < DoxygenEntity > parse(int startInd, string doxygenString) {
-  string currWord;
-  int startIndex = startInd;
-  int savedIndex;
-  list < DoxygenEntity > aNewList;
-  int endIndex = doxygenString.length();
-  int currCommand;
-  while (startIndex < endIndex) {
-    savedIndex = startIndex;
-    currWord = getNextWord(startIndex, doxygenString);
-    if (noisy)
-      cout << "Parsing for phrase starting in:" << currWord << endl;
-    if (currWord == "") {
-      if (startIndex < endIndex)
-	startIndex++;
-    } else if (currWord[0] == '\\' || currWord[0] == '@') {
-      currWord = currWord.substr(1, currWord.length() - 1);
-      currCommand = findCommand(currWord);
-      if (currCommand < 0) {
-	if (noisy)
-	  cout << "BAD COMMAND: " << currWord << endl;
-      }
-      //cout << "Command: " << currWord << " " << currCommand << endl;
-      else
-	addCommand(currWord, startIndex, aNewList, doxygenString);
-    } else {
-      startIndex = savedIndex;
-      addCommand(string("plainstd::string"), startIndex, aNewList, doxygenString);
-
-    }
-  }
-
-  return aNewList;
-}
-
- /*  Method for Adding a Simple Command
-  * Format: @command
-  * Plain commands, such as newline etc, they contain no other data
-  *  \n \\ \@ \& \$ \# \< \> \%
-  */
-int addSimpleCommand(string theCommand, int &startInd, list < DoxygenEntity > &doxyList, string doxygenString) {
-
-  if (noisy)
-    cout << "Parsing " << theCommand << endl;
-  doxyList.push_back(DoxygenEntity(theCommand));
-  return 1;
-}
-
-  /* NOT INCLUDED Simple Commands
-   * Format: @command
-   * Plain commands, such as newline etc, they contain no other data
-   */
-int ignoreSimpleCommand(string theCommand, int &startInd, list < DoxygenEntity > &doxyList, string doxygenString) {
-
-  if (noisy)
-    cout << "Not Adding " << theCommand << endl;
-  return 1;
-}
-
-  /* CommandWord
-   * Format: @command <word>
-   * Commands with a single WORD after then such as @b
-   * "a", "b", "c", "e", "em", "p", "def", "enum", "example", "package", 
-   * "relates", "namespace", "relatesalso","anchor", "dontinclude", "include", "includelineno"
-   */
-int addCommandWord(string theCommand, int &startInd, list < DoxygenEntity > &doxyList, string doxygenString) {
-  if (noisy)
-    cout << "Parsing " << theCommand << endl;
-  string name = getNextWord(startInd, doxygenString);
-  if (!name.empty()) {
-    doxyList.push_back(DoxygenEntity(theCommand, name));
-    return 1;
-  } else
-    cout << "No word followed " << theCommand << " command. Not added" << endl;
-  return 0;
-}
-
-  /* NOT INCLUDED CommandWord
-   * Format: @command <word>
-   * Commands with a single WORD after then such as @b
-   * "copydoc", "copybrief", "copydetails", "verbinclude", "htmlinclude"
-   */
-int ignoreCommandWord(string theCommand, int &startInd, list < DoxygenEntity > &doxyList, string doxygenString) {
-  if (noisy)
-    cout << "Not Adding " << theCommand << endl;
-  string name = getNextWord(startInd, doxygenString);
-  if (!name.empty()) {
-    return 1;
-  } else
-    cout << "WARNING: No word followed " << theCommand << " command." << endl;
-  return 0;
-}
-
-  /* CommandLine
-   * Format: @command (line)
-   * Commands with a single LINE after then such as @var
-   * "addindex", "fn", "name", "line", "var", "skipline", "typedef", "skip", "until", "property"
-   */
-int addCommandLine(string theCommand, int &startInd, list < DoxygenEntity > &doxyList, string doxygenString) {
-  if (noisy)
-    cout << "Parsing " << theCommand << endl;
-  string line = getOneLine(startInd, doxygenString);
-  if (!line.empty()) {
-    int placement = 0;
-    list < DoxygenEntity > aNewList;
-    aNewList = parse(placement, line);
-    doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-    return 1;
-  } else
-    cout << "No line followed " << theCommand << " command. Not added" << endl;
-  return 0;
-}
-
-  /* NOT INCLUDED CommandLine
-   * Format: @command (line)
-   * Commands with a single LINE after then such as @var
-   * 
-   */
-int ignoreCommandLine(string theCommand, int &startInd, list < DoxygenEntity > &doxyList, string doxygenString) {
-  if (noisy)
-    cout << "Not Adding " << theCommand << endl;
-  string line = getOneLine(startInd, doxygenString);
-  if (!line.empty()) {
-    return 1;
-  } else
-    cout << "WARNING: No line followed " << theCommand << " command." << endl;
-  return 0;
-}
-
-  /* CommandParagraph
-   * Format: @command {paragraph}
-   * Commands with a single paragraph after then such as @return
-   * "return", "remarks", "since", "test", "sa", "see", "pre", "post", "details", "invariant", 
-   * "deprecated", "date", "note", "warning", "version", "todo", "bug", "attention", "brief", "arg", "author"
-   */
-int addCommandParagraph(string theCommand, int &startInd, list < DoxygenEntity > &doxyList, string doxygenString) {
-  if (noisy)
-    cout << "Parsing " << theCommand << endl;
-  string restOfParagraph = getStringTilEndOfParagraph(startInd, doxygenString);
-  if (!restOfParagraph.empty()) {
-    int placement = 0;
-    list < DoxygenEntity > aNewList;
-    aNewList = parse(placement, restOfParagraph);
-    doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-    return 1;
-  } else
-    cout << "No line followed " << theCommand << " command. Not added" << endl;
-  return 0;
-}
-
-  /* CommandParagraph
-   * Format: @command {paragraph}
-   * Commands with a single LINE after then such as @var
-   * 
-   */
-int ignoreCommandParagraph(string theCommand, int &startInd, list < DoxygenEntity > &doxyList, string doxygenString) {
-  if (noisy)
-    cout << "Not Adding " << theCommand << endl;
-  string restOfParagraph = getStringTilEndOfParagraph(startInd, doxygenString);
-  if (!restOfParagraph.empty()) {
-    return 1;
-  } else
-    cout << "WARNING: No line followed " << theCommand << " command." << endl;
-  return 0;
-}
-
-  /* Command EndCommand
-   * Format: @command and ends at @endcommand
-   * Commands that take in a block of text such as @code
-   * "code", "dot", "msc", "f$", "f[", "f{environment}{", "htmlonly", "latexonly", "manonly", 
-   * "verbatim", "xmlonly", "cond", "if", "ifnot", "link"
-   * Returns 1 if success, 0 if the endcommand is never encountered.
-   */
-
-int ignoreCommandEndCommand(string theCommand, int &startInd, list < DoxygenEntity > &doxyList, string doxygenString) {
-  if (noisy)
-    cout << "Not Adding " << theCommand << endl;
-  return progressTilEndCommand("end" + theCommand, startInd, doxygenString);
-
-}
-
-  /* CommandWordParagraph
-   * Format: @command <word> {paragraph}
-   * Commands such as param
-   * "param", "tparam", "throw", "retval", "exception"
-   */
-int addCommandWordParagraph(string theCommand, int &startInd, list < DoxygenEntity > &doxyList, string doxygenString) {
-  if (noisy)
-    cout << "Parsing " << theCommand << endl;
-  string name = getNextWord(startInd, doxygenString);
-  if (name.empty()) {
-    cout << "No word followed " << theCommand << " command. Not added" << endl;
-    return 0;
-  }
-  string restOfParagraph = getStringTilEndOfParagraph(startInd, doxygenString);
-  int placement = 0;
-  if (!restOfParagraph.empty()) {
-    list < DoxygenEntity > aNewList;
-    aNewList = parse(placement, restOfParagraph);
-    aNewList.push_front(DoxygenEntity("plainstd::string", name));
-    doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-    return 1;
-  } else
-    cout << "No paragraph followed " << theCommand << " command. Not added" << endl;
-  return 0;
-}
-
-  /* CommandWordLine
-   * Format: @command <word> (line)
-   * Commands such as param
-   * "page", "subsection", "subsubsection", "section", "paragraph", "defgroup"
-   */
-int addCommandWordLine(string theCommand, int &startInd, list < DoxygenEntity > &doxyList, string doxygenString) {
-  if (noisy)
-    cout << "Parsing " << theCommand << endl;
-  string name = getNextWord(startInd, doxygenString);
-  if (name.empty()) {
-    cout << "No word followed " << theCommand << " command. Not added" << endl;
-    return 0;
-  }
-  string restOfLine = getStringTilEndOfParagraph(startInd, doxygenString);
-  int placement = 0;
-  if (!restOfLine.empty()) {
-    list < DoxygenEntity > aNewList;
-    aNewList = parse(placement, restOfLine);
-    aNewList.push_front(DoxygenEntity("plainstd::string", name));
-    doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-    return 1;
-  } else
-    cout << "No line followed " << theCommand << " command. Not added" << endl;
-  return 0;
-}
-
-  /* Command Word Optional Word Optional Word
-   * Format: @command <word> [<header-file>] [<header-name>]
-   * Commands such as class
-   * "category", "class", "protocol", "interface", "struct", "union"
-   */
-int addCommandWordOWordOWord(string theCommand, int &startInd, list < DoxygenEntity > &doxyList, string doxygenString) {
-  if (noisy)
-    cout << "Parsing " << theCommand << endl;
-  string name = getNextWord(startInd, doxygenString);
-  if (name.empty()) {
-    cout << "No word followed " << theCommand << " command. Not added" << endl;
-    return 0;
-  }
-  string headerfile = getNextWord(startInd, doxygenString);
-  string headername = getNextWord(startInd, doxygenString);
-  list < DoxygenEntity > aNewList;
-  aNewList.push_back(DoxygenEntity("plainstd::string", name));
-  if (!headerfile.empty())
-    aNewList.push_back(DoxygenEntity("plainstd::string", headerfile));
-  if (!headername.empty())
-    aNewList.push_back(DoxygenEntity("plainstd::string", headername));
-  doxyList.push_back(DoxygenEntity(theCommand, aNewList));
-  return 1;
-}
-
-  /* Command Optional Word
-   * Format: @command [<word>]
-   * Commands such as dir
-   * "dir", "file", "cond"
-   */
-int addCommandOWord(string theCommand, int &startInd, list < DoxygenEntity > &doxyList, string doxygenString) {
-  if (noisy)
-    cout << "Parsing " << theCommand << endl;
-  string name = getNextWord(startInd, doxygenString);
-  doxyList.push_back(DoxygenEntity(theCommand, name));
-  return 1;
-}
-
- /* The actual "meat" of the doxygen parser. This is not yet fully implemented
-  * with my current design- however the skeletal outline is contained in
-  * the file Skeleton
-  */
-
-
-int addCommand(string commandString, int &startInd, list < DoxygenEntity > &doxyList, string doxygenString) {
-  string theCommand = StringToLower(commandString);
-  string voidArray[] = { "" };
-  /* @command */
-
-
-  if (theCommand.compare("plainstd::string") == 0) {
-    string nextPhrase = getStringTilCommand(startInd, doxygenString);
-    if (noisy)
-      cout << "Parsing plain string :" << nextPhrase << endl;
-    doxyList.push_back(DoxygenEntity("plainstd::string", nextPhrase));
-    return 1;
-  }
-  int commandNumber = commandBelongs(theCommand);
-  if (commandNumber == SIMPLECOMMAND) {
-    return addSimpleCommand(theCommand, startInd, doxyList, doxygenString);
-  }
-  if (commandNumber == IGNOREDSIMPLECOMMAND) {
-    return ignoreSimpleCommand(theCommand, startInd, doxyList, doxygenString);
-  }
-  if (commandNumber == COMMANDWORD) {
-    return addCommandWord(theCommand, startInd, doxyList, doxygenString);
-  }
-  if (commandNumber == IGNOREDCOMMANDWORD) {
-    return ignoreCommandWord(theCommand, startInd, doxyList, doxygenString);
-  }
-  if (commandNumber == COMMANDLINE) {
-    return addCommandLine(theCommand, startInd, doxyList, doxygenString);
-  }
-  if (commandNumber == IGNOREDCOMMANDLINE) {
-    return ignoreCommandLine(theCommand, startInd, doxyList, doxygenString);
-  }
-  if (commandNumber == COMMANDPARAGRAPH) {
-    return addCommandParagraph(theCommand, startInd, doxyList, doxygenString);
-  }
-  if (commandNumber == IGNORECOMMANDPARAGRAPH) {
-    return ignoreCommandParagraph(theCommand, startInd, doxyList, doxygenString);
-  }
-  if (commandNumber == COMMANDENDCOMMAND) {
-    return ignoreCommandEndCommand(theCommand, startInd, doxyList, doxygenString);
-  }
-  if (commandNumber == COMMANDWORDPARAGRAPH) {
-    return addCommandWordParagraph(theCommand, startInd, doxyList, doxygenString);
-  }
-  if (commandNumber == COMMANDWORDLINE) {
-    return addCommandWordLine(theCommand, startInd, doxyList, doxygenString);
-  }
-  if (commandNumber == COMMANDWORDOWORDWORD) {
-    return addCommandWordOWordOWord(theCommand, startInd, doxyList, doxygenString);
-  }
-  if (commandNumber == COMMANDOWORD) {
-    return addCommandOWord(theCommand, startInd, doxyList, doxygenString);
-  }
-  if (commandNumber == COMMANDERRORTHROW) {
-    return 0;
-  }
-  if (commandNumber == COMMANDUNIQUE) {
-    return 0;
-  }
-
-  return 0;
-}
-
-int weirdTest() {
-  string doxygenString = "this is a test.";
-  string restOfParagraph;
-  int startIndex = 0;
-  restOfParagraph = getStringTilEndOfParagraph(startIndex, doxygenString);
-  cout << restOfParagraph << " " << startIndex << endl;
-
-  startIndex = 0;
-  restOfParagraph = getStringTilCommand(startIndex, doxygenString);
-  cout << restOfParagraph << " " << startIndex << endl;
-}
-
-
-
-int doRunExamples() {
-  string line;
-  string filename;
-  string exampleNames[] = { "Examples/Example1", "Examples/Example2", "Examples/Example3", "Examples/Example4", "Examples/Example5" };
-  int placement;
-  string doxygenString;
-  ifstream doxCommentFile;
-  for (int i = 0; i < 5; i++) {
-    doxCommentFile.open(exampleNames[i].c_str());
-    doxCommentFile >> doxygenString;
-    while (getline(doxCommentFile, line)) {
-      doxygenString += line + "\n";
-    }
-    doxCommentFile.close();
-    placement = 0;
-    cout << "---RAW CODE---" << endl << doxygenString << endl << endl;
-    //clearFluff(placement, doxygenString);
-    //rootList = parse(placement, doxygenString);
-    TokenList tokList = TokenList(doxygenString);
-    tokList.printList();
-    cout << "---THE TREE---" << endl;
-    printTree();
-  }
-  return 1;
-}
-
-
- /* Returns a parse tree for a string */
-int main(int argc, char *argv[]) {
-  //weirdTest();
-  if (testCodeCrawlingFunctions)
-    testCCF();
-  if (runExamples)
-    doRunExamples();
-  if (demonstrateParsing) {
-    string doxygenString =
-	"//! A normal member taking two arguments and returning an integer value.\n/*!\n \\param a an integer argument. \\param s a constant character pointer\n \\return The test results\n  \\sa Test(), ~Test(), testMeToo() and publicVar()\n */";
-    //string doxygenString = " /** This is a small sentence.\n *\n@param x this is a parameter. \n \n This is a line with a @b bold letter \n * \n  @brief small @b description. \n\n * **/";
-    //string doxygenString = "This is a description.";
-    int placement = 0;
-    clearFluff(placement, doxygenString);
-    rootList = parse(placement, doxygenString);
-    cout << "---THE TREE---" << endl;
-    printTree();
-  }
-  string doxygenString2 =
-      "//! A normal member taking two arguments and returning an integer value.\n/*!\n \\param a an integer argument. \\param s a constant character pointer\n\n\n\n \\return The test results\n  \\sa Test(), ~Test(), testMeToo() and publicVar()\n */";
-  TokenList tokList = TokenList(doxygenString2);
-  tokList.printList();
-  return 1;
-}
diff --git a/Source/DoxygenTranslator/src/Examples/DoxygenTransWTokenizer.h b/Source/DoxygenTranslator/src/Examples/DoxygenTransWTokenizer.h
deleted file mode 100644
index 8a51b4d02..000000000
--- a/Source/DoxygenTranslator/src/Examples/DoxygenTransWTokenizer.h
+++ /dev/null
@@ -1,21 +0,0 @@
-/* -----------------------------------------------------------------------------
- * This file is part of SWIG, which is licensed as a whole under version 3 
- * (or any later version) of the GNU General Public License. Some additional
- * terms also apply to certain portions of SWIG. The full details of the SWIG
- * license and copyrights can be found in the LICENSE and COPYRIGHT files
- * included with the SWIG source code as distributed by the SWIG developers
- * and at http://www.swig.org/legal.html.
- *
- * DoxygenTransWTokenizer.h
- * ----------------------------------------------------------------------------- */
-
-#ifndef DOXYGENTRANSWTOKENIZER_H_
-#define DOXYGENTRANSWTOKENIZER_H_
-
-class DoxygenTransWTokenizer {
-public:
-  DoxygenTransWTokenizer();
-  virtual ~DoxygenTransWTokenizer();
-};
-
-#endif
diff --git a/Source/DoxygenTranslator/src/Examples/Example1 b/Source/DoxygenTranslator/src/Examples/Example1
deleted file mode 100644
index 03aac4921..000000000
--- a/Source/DoxygenTranslator/src/Examples/Example1
+++ /dev/null
@@ -1,6 +0,0 @@
-/*! \brief Brief description.
- *         Brief description continued.
- *
- *  Detailed description starts here.
- */
-
diff --git a/Source/DoxygenTranslator/src/Examples/Example2 b/Source/DoxygenTranslator/src/Examples/Example2
deleted file mode 100644
index 27f915e4a..000000000
--- a/Source/DoxygenTranslator/src/Examples/Example2
+++ /dev/null
@@ -1,7 +0,0 @@
-//! A normal member taking two arguments and returning an integer value.
-/*!
- \param a an integer argument.
- \param s a constant character pointer.
- \return The test results
- \sa Test(), ~Test(), testMeToo() and publicVar()
- */
diff --git a/Source/DoxygenTranslator/src/Examples/Example3 b/Source/DoxygenTranslator/src/Examples/Example3
deleted file mode 100644
index 8e24ba005..000000000
--- a/Source/DoxygenTranslator/src/Examples/Example3
+++ /dev/null
@@ -1,10 +0,0 @@
-      /**
-       * a normal member taking two arguments and returning an integer value.
-       * @param a an integer argument.
-       * @param s a constant character pointer.
-       * @see Test()
-       * @see ~Test()
-       * @see testMeToo()
-       * @see publicVar()
-       * @return The test results
-       */
diff --git a/Source/DoxygenTranslator/src/Examples/Example4 b/Source/DoxygenTranslator/src/Examples/Example4
deleted file mode 100644
index 55b68da18..000000000
--- a/Source/DoxygenTranslator/src/Examples/Example4
+++ /dev/null
@@ -1,5 +0,0 @@
-//! Brief descripion.
-
-//! Detailed description 
-//! starts here.
-
diff --git a/Source/DoxygenTranslator/src/Examples/Example5 b/Source/DoxygenTranslator/src/Examples/Example5
deleted file mode 100644
index e69de29bb..000000000
diff --git a/Source/DoxygenTranslator/src/Examples/Example6 b/Source/DoxygenTranslator/src/Examples/Example6
deleted file mode 100644
index e69de29bb..000000000
diff --git a/Source/DoxygenTranslator/src/Examples/translator.h b/Source/DoxygenTranslator/src/Examples/translator.h
deleted file mode 100644
index f9da98180..000000000
--- a/Source/DoxygenTranslator/src/Examples/translator.h
+++ /dev/null
@@ -1,155 +0,0 @@
-/* -----------------------------------------------------------------------------
- * This file is part of SWIG, which is licensed as a whole under version 3 
- * (or any later version) of the GNU General Public License. Some additional
- * terms also apply to certain portions of SWIG. The full details of the SWIG
- * license and copyrights can be found in the LICENSE and COPYRIGHT files
- * included with the SWIG source code as distributed by the SWIG developers
- * and at http://www.swig.org/legal.html.
- *
- * translator.h
- * ----------------------------------------------------------------------------- */
-
-#ifndef TRANSLATOR_H_
-#define TRANSLATOR_H_
-
-#define BRIEFDESCRIPTION       99
-#define LONGDESCRIPTION        100
-#define A_COMMAND              101  /* \a */
-#define ADDINDEX               102  /* \addindex */
-#define ADDTOGROUP             103  /* \addtogroup */
-#define ANCHOR                 104  /* \anchor */
-#define ARG_COMMAND            105  /* \arg */
-#define ATTENTION              106  /* \attention */
-#define AUTHOR                 107  /* \author */
-#define B_COMMAND              108  /* \b */
-#define BRIEF                  109  /* \brief */
-#define BUG                    110  /* \bug */
-#define C_COMMAND              111  /* \c */
-#define CALLGRAPH              112  /* \callgraph */
-#define CALLERGRAPH            113  /* \callergraph */
-#define CATEGORY               114  /* \category */
-#define CLASS_COMMAND          115  /* \class */
-#define CODE                   116  /* \code */
-#define COND                   117  /* \cond */
-#define COPYBRIEF              118  /* \copybrief */
-#define COPYDETAILS            119  /* \copydetails */
-#define COPYDOC                120  /* \copydoc */
-#define DATE                   121  /* \date */
-#define DEF                    122  /* \def */
-#define DEFGROUP               123  /* \defgroup */
-#define DEPRECATED             124  /* \deprecated */
-#define DETAILS                125  /* \details */
-#define DIR_COMMAND            126  /* \dir */
-#define DONTINCLUDE            127  /* \dontinclude */
-#define DOT                    128  /* \dot */
-#define DOTFILE                129  /* \dotfile */
-#define E_COMMAND              130  /* \e */
-#define ELSE_COMMAND           131  /* \else */
-#define ELSEIF_COMMAND         132  /* \elseif */
-#define EM                     133  /* \em */
-#define ENDCODE                134  /* \endcode  */
-#define ENDCOND                135  /* \endcond */
-#define ENDDOT                 136  /* \enddot */
-#define ENDHTMLONLY            137  /* \endhtmlonly  */
-#define ENDIF                  138  /* \endif */
-#define ENDLATEXONLY           139  /* \endlatexonly  */
-#define ENDLINK                140  /* \endlink */
-#define ENDMANONLY             141  /* \endmanonly */
-#define ENDMSC                 142  /* \endmsc */
-#define ENDVERBATIM            143  /* \endverbatim */
-#define ENDXMLONLY             144  /* \endxmlonly */
-#define ENUM                   145  /* \enum */
-#define EXAMPLE                146  /* \example */
-#define EXCEPTION              147  /* \exception */
-#define FDOLLAR                148  /* \f$ */
-#define FLEFTSQUAREBRACKET     149  /* \f[ */
-#define FRIGHTSQUAREBRACKET    150  /* \f] */
-#define FLEFTBRACKET           151  /* \f{ */
-#define FRIGHTBRACKET          152  /* \f} */
-#define FILE_COMMAND           153  /* \file */
-#define FN_COMMAND             154  /* \fn */
-#define HEADERFILE             155  /* \headerfile */
-#define HIDEINITIALIZER        156  /* \hideinitializer */
-#define HTMLINCLUDE            157  /* \htmlinclude */
-#define HTMLONLY               158  /* \htmlonly */
-#define IF_COMMAND             159  /* \if */
-#define IFNOT_COMMAND          160  /* \ifnot */
-#define IMAGE                  161  /* \image */
-#define INCLUDE_COMMAND        162  /* \include */
-#define INCLUDELINENO          163  /* \includelineno */
-#define INGROUP                164  /* \ingroup */
-#define INTERNAL               165  /* \internal */
-#define INVARIANT              166  /* \invariant */
-#define INTERFACE_COMMAND      167  /* \interface */
-#define LATEXONLY              168  /* \latexonly */
-#define LI                     169  /* \li */
-#define LINE                   170  /* \line */
-#define LINK                   171  /* \link */
-#define MAINPAGE               172  /* \mainpage */
-#define MANONLY                173  /* \manonly */
-#define MSC                    174  /* \msc */
-#define N                      175  /* \n */
-#define NAME                   176  /* \name */
-#define NAMESPACE              177  /* \namespace */
-#define NOSUBGROUPING          178  /* \nosubgrouping */
-#define NOTE                   179  /* \note */
-#define OVERLOAD               180  /* \overload */
-#define P                      181  /* \p */
-#define PACKAGE                182  /* \package */
-#define PAGE                   183  /* \page */
-#define PAR                    184  /* \par */
-#define PARAGRAPH              185  /* \paragraph */
-#define PARAM                  186  /* \param */
-#define POST                   187  /* \post */
-#define PRE                    188  /* \pre */
-#define PRIVATE                189  /* \private (PHP only) */
-#define PRIVATESECTION         190  /* \privatesection (PHP only) */
-#define PROPERTY               191  /* \property */
-#define PROTECTED              192  /* \protected (PHP only) */
-#define PROTECTEDSECTION       193  /* \protectedsection (PHP only) */
-#define PROTOCOL               194  /* \protocol */
-#define PUBLIC                 195  /* \public (PHP only) */
-#define PUBLICSECTION          196  /* \publicsection (PHP only) */
-#define REF                    197  /* \ref */
-#define RELATES                198  /* \relates */
-#define RELATESALSO            199  /* \relatesalso */
-#define REMARKS                200  /* \remarks */
-#define RETURN_COMMAND         201  /* \return */
-#define RETVAL                 202  /* \retval */
-#define SA                     203  /* \sa */
-#define SECTION                204  /* \section */
-#define SEE                    205  /* \see */
-#define SHOWINITIALIZER        206  /* \showinitializer */
-#define SINCE                  207  /* \since */
-#define SKIP                   208  /* \skip */
-#define SKIPLINE               209  /* \skipline */
-#define STRUCT                 210  /* \struct */
-#define SUBPAGE                211  /* \subpage */
-#define SUBSECTION             212  /* \subsection */
-#define SUBSUBSECTION          213  /* \subsubsection */
-#define TEST                   214  /* \test */
-#define THROW_COMMAND          215  /* \throw */
-#define TODO_COMMAND           216  /* \todo */
-#define TPARAM_COMMAND         217  /* \tparam */
-#define TYPEDEF_COMMAND        218  /* \typedef */
-#define UNION_COMMAND          219  /* \union */
-#define UNTIL_COMMAND          220  /* \until */
-#define VAR_COMMAND            221  /* \var */
-#define VERBATIM               222  /* \verbatim */
-#define VERBININCLUDE          223  /* \verbinclude */
-#define VERSION                224  /* \version */
-#define WARNING                225  /* \warning */
-#define WEAKGROUP              226  /* \weakgroup */
-#define XMLONLY                227  /* \xmlonly */
-#define XREFITEM               228  /* \xrefitem */
-#define DOLLAR_COMMAND         229  /* \$ */
-#define AT_COMMAND             230  /* \@ */
-#define SLASH_COMMAND          231  /* \\ */
-#define AND_COMMAND            232  /* \& */
-#define TILDE_COMMAND          233  /* \~ */
-#define LEFTANGLEBRACKET       234  /* \< */
-#define RIGHTANGLEBRACKET      235  /* \> */
-#define POUND_COMMAND          236  /* \# */
-#define PERCENT_COMMAND        237  /* \%  */
-
-#endif

From 73736c3b89c9d1147d59bffde8dfd260289ab3e4 Mon Sep 17 00:00:00 2001
From: William S Fulton <wsf@fultondesigns.co.uk>
Date: Tue, 22 May 2018 19:31:31 +0100
Subject: [PATCH 291/314] Doxygen html documentation updates and corrections

---
 Doc/Manual/Doxygen.html | 300 +++++++++++++++++++++-------------------
 1 file changed, 161 insertions(+), 139 deletions(-)

diff --git a/Doc/Manual/Doxygen.html b/Doc/Manual/Doxygen.html
index 5fa4b820e..886391972 100644
--- a/Doc/Manual/Doxygen.html
+++ b/Doc/Manual/Doxygen.html
@@ -32,7 +32,7 @@
 </ul>
 <li><a href="#Doxygen_developer_details">Developer Information</a>
 <ul>
-<li><a href="#Doxygen_module_design">Module Design</a>
+<li><a href="#Doxygen_translator_design">Doxygen Translator Design</a>
 <li><a href="#Doxygen_debugging_commands">Debugging Doxygen parser and translator</a>
 <li><a href="#Doxygen_debugging_commands">Tests</a>
 </ul>
@@ -50,28 +50,20 @@ documentation language.  Currently only Javadoc and Pydoc is
 supported.
 </p>
 
-<H2><a name="Doxygen_translation_overview"></a>39.1 Doxygen Translation Overview</H2>
+<H2><a name="Doxygen_translation_overview"></a>39.1 Doxygen translation overview</H2>
 
 
 <p>
-The Doxygen Translation Module of SWIG is an ongoing effort from
-a <A HREF ="http://code.google.com/soc/2008/">Google Summer of
-Code</A> proposal from Summer 2008.  It adds an extra layer of
-functionality to SWIG, allowing automated translation of <A HREF=
-"http://www.stack.nl/~dimitri/doxygen/">Doxygen</A> formatted comments
+The Doxygen Translation module of SWIG adds an extra layer of
+functionality to SWIG, allowing automated translation of <a href=
+"http://www.stack.nl/~dimitri/doxygen/">Doxygen</a> formatted comments
 from input files into a documentation language more suited for the
 target language.  Currently this module only translates into Javadoc
-and Pydoc for the SWIG Java and Python Modules, but other
-extensions are to be added in time.
-</p>
-
-<p>
-Questions about running SWIG are best answered in
-the <a href="SWIG.html#SWIG">SWIG Basics</a> chapter as well as the
-target language modules. (For now, only <A href = "Java.html">Java</A>
-and <A href = "Python.html">Python</A>).  The behaviour of this
-functionality is wildly unpredictable if the interface file is not
-proper to begin with!
+and Pydoc for the SWIG Java and Python modules.
+Other extensions could be added at a later date.
+The Doxygen Translation module originally started as
+a <a href="http://code.google.com/soc/2008/">Google Summer of
+Code</a> proposal from Summer 2008.  
 </p>
 
 <H2><a name="Doxygen_file_preparation"></a>39.2 Preparations</H2>
@@ -79,32 +71,24 @@ proper to begin with!
 
 <p>
 To make use of the comment translation system, your documentation
-comments must be in properly formatted <A HREF=
-"http://www.stack.nl/~dimitri/doxygen/">Doxygen.</A> They can be
-present in your main interface file or any header file that it
-imports.  It is advised that you are certain your comments compile
+comments must be in properly formatted <a href=
+"http://www.stack.nl/~dimitri/doxygen/">Doxygen.</a> Doxygen comments can be
+present in your main SWIG interface file or any header file that it
+imports.  You are advised to be validate that your comments compile
 properly with Doxygen before you try to translate them.  Doxygen
-itself is a deeper tool and can provide you better feedback for
+itself is a more comprehensive tool and can provide you better feedback for
 correcting any syntax errors that may be present.  Please look at
-Doxygen's <A HREF =
+Doxygen's <a href=
 "http://www.stack.nl/~dimitri/doxygen/docblocks.html"> Documenting the
-code</A> for proper specifications for comment format.  However, SWIG's
-Doxygen parser will still point you most of errors and warnings found
+code</a> for the full comment format specifications.  However, SWIG's
+Doxygen parser will still report many errors and warnings found
 in comments (like unterminated strings or missing ending tags).
 </p>
 
-<div class="code"><pre>
-/*! This is describing class Shape
- \author Bob
- */
-
-class Shape {
-</pre></div>
-
 <p>
 Currently, the whole subset of Doxygen comment styles is supported
-(See <A HREF = "http://www.stack.nl/~dimitri/doxygen/docblocks.html">
-Documenting the code</A>). Here they are:
+(See <a href="http://www.stack.nl/~dimitri/doxygen/docblocks.html">
+Documenting the code</a>). Here they are:
 
 <div class="code"><pre>
 /**
@@ -124,20 +108,20 @@ Documenting the code</A>). Here they are:
 <p>
 Also any of the above with '&lt;' added after comment-starting symbol,
 like <i>/**&lt;, /*!&lt;, ///&lt;, </i> or <i> //!&lt;</i> will be
-treated as post-comment and will be assigned to the node before the
+treated as a post-comment and will be assigned to the code before the
 comment.
-<br>
 
-Any number of '*' or '/' in Doxygen comment is considered to be a
-separator and is not included in final comment, so you may safely use
+Any number of '*' or '/' within a Doxygen comment is considered to be a
+separator and is not included in the final comment, so you may safely use
 comments like <i>/*********/</i> or <i>//////////</i>.
 </p>
 
 <p>
-Please note, as SWIG parses input file by itself with strict grammar,
+Please note, as SWIG parses the input file by itself with strict grammar,
 there is only a limited support for various cases of comment placement
 in the file.
-<br>
+<p>
+</p>
 Comments can be placed before C/C++ expressions on separate lines:
 </p>
 
@@ -192,15 +176,13 @@ enum E_NUMBERS
 </pre></div>
 
 <p>
-Just remember, if SWIG shows syntax error parsing the file because of
-your comment, try to move it in some other, 'safer' place as described
-above.
-<br>
-Also, currently only the comments directly before or after the nodes
-are supported. Doxygen structural comments are stripped out and not
-assigned to anything.
+Currently only comments directly before or after the code items
+are supported. Doxygen also supports comments containing structural commands,
+where the comments for a code item are not put directly before or after the code item.
+These structural commands are stripped out by SWIG and are not assigned to anything.
 </p>
-<H3><a name="Doxygen_running_swig"></a>39.2.1 Enabling Doxygen Translation</H3>
+
+<H3><a name="Doxygen_running_swig"></a>39.2.1 Enabling Doxygen translation</H3>
 
 <p>
 Doxygen comments translation is disabled by default and needs to be explicitly
@@ -208,7 +190,7 @@ enabled using the command line <tt>-doxygen</tt> switch for the languages that
 do support it (currently Java and Python).
 </p>
 
-<H3><a name="Doxygen_features"></a>39.2.2 Doxygen-specific %feature Directives</H3>
+<H3><a name="Doxygen_features"></a>39.2.2 Doxygen-specific %feature directives</H3>
 
 <p>
 Translation of Doxygen comments is influenced by the following <a
@@ -240,7 +222,7 @@ ALIASES = "sideeffect=\par Side Effects:\n"
 </pre></div>
 
 <p>
-Then you could also the same expansion for SWIG with:
+Then you could also specify the same expansion for SWIG with:
 </p>
 
 <div class="code"><pre>
@@ -275,13 +257,19 @@ wrappers of the C++ API.
 <h4>doxygen:ignore:&lt;command-name&gt;</h4>
 
 <p>
-This feature allows to just ignore an unknown Doxygen command, instead of
-replacing it with a predefined text as <tt>doxygen:alias</tt> features allows to
-do. For example, you could use
+This feature makes it possible to just ignore an unknown Doxygen command, instead of
+replacing it with the predefined text that <tt>doxygen:alias</tt> does.
+For example, you could use
 </p>
 
 <div class="code"><pre>
-%feature("doxygen:ignore:transferfull");
+%feature("doxygen:ignore:transferfull") Fantastic();
+/**
+    A fantastic function.
+
+    @transferfull Command ignored, but anything here is still included.
+ */
+int * Fantastic() { }
 </pre></div>
 
 <p>
@@ -303,11 +291,19 @@ feature directive:
 <div class="code"><pre>
 // Ignore occurrences of
 //
-//    @compiler-options Some special C++ compiler options.
+//    @compileroptions Some special C++ compiler options.
 //
-// in Doxygen comments as C++ options are not interested for the target language
+// in Doxygen comments as C++ options are not interesting for the target language
 // developers.
-%feature("doxygen:ignore:compileroptions", range="line");
+%feature("doxygen:ignore:compileroptions", range="line") Amazing();
+
+/**
+    An amazing function.
+
+    @compileroptions This function must be compiled with /EHa when using MSVC.
+ */
+void Amazing();
+
 </pre></div>
 
 <p>
@@ -319,6 +315,14 @@ tags can also be ignored using the special value of <tt>range</tt> starting with
 
 <div class="code"><pre>
 %feature("doxygen:ignore:forcpponly", range="end"); // same as "end:endforcpponly"
+/**
+    An incredible function.
+
+    @forcpponly
+    This is C++-specific.
+    @endforcpponly
+ */
+void Incredible();
 </pre></div>
 
 <p>
@@ -338,6 +342,15 @@ themselves should be ignored, but their contents should be parsed as usual and
 
 <div class="code"><pre>
 %feature("doxygen:ignore:beginPythonOnly", range="end:endPythonOnly", contents="parse");
+/**
+    A splendid function.
+
+    @beginPythonOnly
+    This is specific to @b Python.
+    @endPythonOnly
+ */
+void Splendid();
+
 </pre></div>
 
 <p>
@@ -371,7 +384,7 @@ then the following C++ Doxygen comment:
 
     @compileroptions This function must be compiled with /EHa when using MSVC.
  */
-void func();
+int * Contrived();
 </pre></div>
 
 <p>
@@ -391,7 +404,7 @@ def func():
 </pre></div>
 
 
-<h4>doxygen:nolinkranslate (Java-only currently)</h4>
+<h4>doxygen:nolinktranslate (Java-only currently)</h4>
 
 <p>
 Turn off automatic link-objects translation.
@@ -406,14 +419,14 @@ Doxygen commands if the parameter is not found in the function signature.
 </p>
 
 
-<H3><a name="Doxygen_additional_options"></a>39.2.3 Additional Command Line Options</H3>
+<H3><a name="Doxygen_additional_options"></a>39.2.3 Additional command line options</H3>
 
 
 <p>
 ALSO TO BE ADDED (Javadoc auto brief?)
 </p>
 
-<H2><a name="Doxygen_to_javadoc"></a>39.3 Doxygen To Javadoc</H2>
+<H2><a name="Doxygen_to_javadoc"></a>39.3 Doxygen to Javadoc</H2>
 
 
 <p>
@@ -422,7 +435,7 @@ automatically placed in the correct locations in the resulting module
 and proxy files.
 </p>
 
-<H3><a name="Doxygen_basic_example"></a>39.3.1 Basic Example</H3>
+<H3><a name="Doxygen_basic_example"></a>39.3.1 Basic example</H3>
 
 
 <p>
@@ -505,42 +518,41 @@ public class Shape {
 
 <p>
 The code Java-wise should be identical to what would have been
-generated without this feature enabled.  When the Doxygen Translator
-Module encounters a comment it finds nothing useful in or cannot
-parse, it should not effect the functionality of the SWIG generated
+generated without the doxygen functionality enabled.  When the Doxygen Translator
+module encounters a comment that contains nothing useful or a doxygen comment that it cannot
+parse, it will not affect the functionality of the SWIG generated
 code.
 </p>
 
 <p>
-Javadoc translator will handle most of the tags conversions (see the
+The Javadoc translator will handle most of the tags conversions (see the
 table below). It will also automatically translate link-objects
 params, in \see and \link...\endlink commands. For example,
 'someFunction(std::string)' will be converted to
-'someFunction(String)'.  If this works not really good for you, or if
-you don't want such behaviour, you could turn this off by using
+'someFunction(String)'.  If 
+you don't want such behaviour, you could turn this off by using the
 'doxygen:nolinktranslate' feature. Also all '\param' and '\tparam'
-commands are stripped out, if specified parameter is not present in
-function. Use 'doxygen:nostripparams' to avoid.
+commands are stripped out, if the specified parameter is not present in
+the function. Use 'doxygen:nostripparams' to avoid.
 </p>
 
 <p>
 Javadoc translator features summary
 (see <a href="Customization.html#Customization_features">%feature
 directives</a>):
-<br>
-
 </p>
 
-<H3><a name="Doxygen_javadoc_tags"></a>39.3.2 Javadoc Tags</H3>
+<H3><a name="Doxygen_javadoc_tags"></a>39.3.2 Javadoc tags</H3>
 
 
 <p>
 Here is the list of all Doxygen tags and the description of how they are translated to Javadoc
-<br>
-<b>Doxygen tags:</b>
 </p>
 <div class="diagram"><pre>
 <table border="0">
+<tr>
+  <th id="Doxygen Tags Java" align="left">Doxygen tags</th>
+</tr>
 <tr>
 <td>\a</td>
 <td>wrapped with &lt;i&gt; html tag</td>
@@ -792,15 +804,17 @@ Here is the list of all Doxygen tags and the description of how they are transla
 Doxygen has a wealth of tags such as @latexonly that have no
 equivalent in Javadoc (all supported tags are listed in
 <a href="http://docs.oracle.com/javase/7/docs/technotes/tools/windows/javadoc.html">Javadoc documentation</a>).
-As a result several tags that have no
-translation (or particular use, such as some linking and section tags)
-are suppressed with their content just printed out (if it has any
+As a result several tags have no
+translation or particular use, such as some linking and section tags.
+These are suppressed with their content just printed out (if the tag has any
 sense, typically text content).
-<br>
 Here is the list of these tags:
 </p>
 <div class="diagram"><pre>
 <table border="0">
+<tr>
+  <th id="Unsupported Doxygen Tags Java" align="left">Unsupported Doxygen tags</th>
+</tr>
 <tr>
 <td>\addindex</td>
 <td>\addtogroup</td>
@@ -956,6 +970,9 @@ comment, the whole comment block is ignored:
 </p>
 <div class="diagram"><pre>
 <table border="0">
+<tr>
+  <th id="Ignored Doxygen Tags" align="left">Ignored Doxygen tags</th>
+</tr>
 <tr>
 <td>\addtogroup</td>
 <td>\callgraph</td>
@@ -1016,25 +1033,25 @@ comment, the whole comment block is ignored:
 
 
 
-<H3><a name="Doxygen_further_details"></a>39.3.4 Further Details</H3>
+<H3><a name="Doxygen_further_details"></a>39.3.4 Further details</H3>
 
 
 <p>
 TO BE ADDED.
 </p>
 
-<H2><a name="Doxygen_to_pydoc"></a>39.4 Doxygen To Pydoc</H2>
+<H2><a name="Doxygen_to_pydoc"></a>39.4 Doxygen to Pydoc</H2>
 
 
 <p>
 If translation is enabled, Pydoc formatted comments should be
 automatically placed in the correct locations in the resulting module
 and proxy files.  The problem is that Pydoc has no tag mechanism like
-Doxygen or Javadoc, so most of Doxygen commands are translated as
-English plain text pieces.
+Doxygen or Javadoc, so most of Doxygen commands are translated by merely
+copying the appropriate command text.
 </p>
 
-<H3><a name="Doxygen_python_basic_example"></a>39.4.1 Basic Example</H3>
+<H3><a name="Doxygen_python_basic_example"></a>39.4.1 Basic example</H3>
 
 
 <p>
@@ -1114,9 +1131,13 @@ their description is copied into the generated output using
  */
 bool SetBreakpoint(const char* filename, int line_number);
 </pre></div>
+
+<p>
 would be translated to
+</p>
+
 <div class="targetlang"><pre>
-def SetBreakpoint(*args):
+def SetBreakpoint(filename, line_number):
     r"""
     Set a breakpoint at the given location.
 
@@ -1127,7 +1148,7 @@ def SetBreakpoint(*args):
     """
 </pre></div>
 <p>
-The types used for the parameter documentation come from <tt>doctype</tt> typemap which
+The types used for the parameter documentation come from the "doctype" typemap which
 is defined for all the primitive types and a few others (e.g. <tt>std::string</tt> and
 <tt>shared_ptr&lt;T&gt;</tt>) but for non-primitive types is taken to be just the C++
 name of the type with namespace scope delimiters (<tt>::</tt>) replaced with a dot. To
@@ -1138,12 +1159,12 @@ change this, you can define your own typemaps for the custom types, e.g:
 </pre></div>
 
 <p>
-Currently Doxygen comments assigned to vars are not present in proxy
-file, so they have no comment translated for them.
+Currently Doxygen comments assigned to global variables and static member variables
+are not present in generated code, so they have no comment translated for them.
 </p>
 
 <p>
-  <b>Whitespace and tables</b><br>
+  <b>Whitespace and tables</b>
   Whitespace is preserved when translating comments, so it makes
   sense to have Doxygen comments formatted in a readable way. This
   includes tables, where tags &lt;th&gt;, &lt;td&gt; and &lt;/tr&gt;are translated
@@ -1176,13 +1197,14 @@ translates to Python as:
 </p>
 
 <p>
-  <b>Overloaded functions</b><br>
+  <b>Overloaded functions</b>
 Since all the overloaded functions in c++ are wrapped into one Python
 function, Pydoc translator will combine every comment of every
-overloaded function and put it in the comment for wrapping function.
-<br>
-If you intend to use resulting proxy files with Doxygen docs
-generator, rather than Pydoc, you may want to turn off translator
+overloaded function and put it into the comment for the one wrapper function.
+</p>
+<p>
+If you intend to use resulting generated Python file with the Doxygen docs
+generator, rather than Pydoc, you may want to turn off translation
 completely (doxygen:notranslate feature).  Then SWIG will just copy
 the comments to the proxy file and reformat them if needed, but all
 the comment content will be left as is. As Doxygen doesn't support
@@ -1198,11 +1220,12 @@ to do the work.
 
 <p>
 Here is the list of all Doxygen tags and the description of how they are translated to Pydoc
-<br>
-<b>Doxygen tags:</b>
 </p>
 <div class="diagram"><pre>
 <table border="0">
+<tr>
+  <th id="Doxygen Tags Python" align="left">Doxygen tags</th>
+</tr>
 <tr>
 <td>\a</td>
 <td>wrapped with '_'</td>
@@ -1415,11 +1438,13 @@ equivalent in Pydoc.  As a result several tags that have no
 translation (or particular use, such as some linking and section tags)
 are suppressed with their content just printed out (if it has any
 sense, typically text content).
-<br>
 Here is the list of these tags:
 </p>
 <div class="diagram"><pre>
 <table border="0">
+<tr>
+  <th id="Unsupported Doxygen Tags Python" align="left">Unsupported Doxygen tags</th>
+</tr>
 <tr>
 <td>\addindex</td>
 <td>\addtogroup</td>
@@ -1588,26 +1613,26 @@ Here is the list of these tags:
 </table>
 </pre></div>
 
-<H3><a name="Doxygen_python_further_details"></a>39.4.4 Further Details</H3>
+<H3><a name="Doxygen_python_further_details"></a>39.4.4 Further details</H3>
 
 
 <p>
 TO BE ADDED.
 </p>
 
-<H2><a name="Doxygen_developer_details"></a>39.5 Developer Information</H2>
+<H2><a name="Doxygen_developer_details"></a>39.5 Developer information</H2>
 
 
 <p>
 </p>
 
-<H3><a name="Doxygen_module_design"></a>39.5.1 Module Design</H3>
+<H3><a name="Doxygen_translator_design"></a>39.5.1 Doxygen translator design</H3>
 
 
 <p>
 If this functionality is turned on, SWIG places all comments found
 into the SWIG parse tree.  Nodes contain an additional attribute
-called DoxygenComment when a comment is present.  Individual nodes
+called <tt>doxygen</tt> when a comment is present.  Individual nodes
 containing Doxygen with Structural Indicators, such as @file, as their
 first command, are also present in the parse tree.  These individual
 "blobs" of Doxygen such as :
@@ -1621,13 +1646,13 @@ first command, are also present in the parse tree.  These individual
 </pre></div>
 
 <p>
-are passed on individually to the DoxygenTranslator Module.  This
+are passed on individually to the Doxygen Translator module.  This
 module builds its own private parse tree and hands it to a separate
 class for translation into the target documentation language.  For
 example, <tt>JavaDocConverter</tt> is the Javadoc module class.
 </p>
 
-<H3><a name="Doxygen_debugging_commands"></a>39.5.2 Debugging Doxygen parser and translator</H3>
+<H3><a name="Doxygen_debugging_commands"></a>39.5.2 Debugging the Doxygen parser and translator</H3>
 
 
 <p>
@@ -1644,58 +1669,55 @@ detailed debug information printing.
 
 
 <p>
-This part of SWIG currently has 6 runtime tests in both Java and Python.
+Doxygen tests have been added to the regular SWIG test-suite.
+There are a number of tests beginning <tt>doxygen_</tt> in the Examples/test-suite sub-directory.
+</p>
+
+<p>
+Like any other SWIG test case, the tests are included in Examples/test-suite/common.mk and can be tested with
+commands like <tt>make check-test-suite</tt> or <tt>make check-python-test-suite</tt>.
+To run them individually, type
+<tt>make -s &lt;testname&gt;.cpptest</tt> in the language-specific sub-directory in
+<tt>Examples/test-suite</tt> directory. For example:
 </p>
 
 <div class="shell"><pre>
-  doxygen_parsing
-  doxygen_translate
-  doxygen_translate_all_tags
-  doxygen_basic_translate
-  doxygen_basic_notranslate
-  doxygen_translate_links
-  doxygen_misc_constructs
+  Examples/test-suite/java $ make -s doxygen_parsing.cpptest
 </pre></div>
 
 <p>
-All this tests are included in common.mk and are built with the
-commands like 'make check-test-suite' or 'make
-check-python-test-suite'. To run them individually, type
-<code>make &lt;testname&gt;.cpptest -s</code> in the language-specific subdir in
-<code>Examples/test-suite</code> directory. For example:
-<pre>
-  Examples/test-suite/java $ make doxygen_misc_constructs.cpptest -s
-</pre>
-
 If the test fails, both expected and translated comments are printed to
 std out, but also written to files <i>expected.txt</i>
-and <I>got.txt</I>. Since it is often difficult to find a single
+and <i>got.txt</i>. Since it is often difficult to find a single
 character difference in several lines of text, we can use some diff
 tool, for example:
-<pre>
-  Examples/test-suite/java $ kdiff3 expected.txt got.txt
-</pre>
+</p>
 
+<div class="shell"><pre>
+  Examples/test-suite/java $ kdiff3 expected.txt got.txt
+</pre></div>
 
     
-<br>
+<p>
 Runtime tests in Java are implemented using Javadoc doclets. To make that work, you
 should have tools.jar from the JDK in your classpath. Or you should have JAVA_HOME
-environmental var defined and pointing to the JDK location.
-<br>
+environment variable defined and pointing to the JDK location.
+</p>
+<p>
 The Java's comment parsing code (the testing part) is located in commentParser.java.
-You may see it to understand how the checking process works. There is also a possibility
-to run that file as stand-alone program, with 'java commentParser <some java package>',
-and it will print the list of comments found in the specified directory (in the format it's used
-in runtime tests). So, when you want to create the new test of Doxygen comment translator,
-just copy any existing one, and replace the actual comment content (section of entries in
+It checks the generated code. It is possible
+to run this file as a stand-alone program, with <tt>java commentParser &lt;some java package&gt;</tt>,
+and it will print the list of comments found in the specified directory (in the format it has used
+in the runtime tests). So, when you want to create a new Doxygen test case,
+just copy an existing one and replace the actual comment content (section of entries in
 form 'wantedComments.put(...)' with the output of the above command.
-<br>
-Runtime tests in Python are just plain strings comparison with the use of __doc__
+</p>
+<p>
+Runtime tests in Python are just plain string comparisons of the __doc__
 properties.
 </p>
 
-<H2><a name="Doxygen_language_extension"></a>39.6 Extending to Other Languages</H2>
+<H2><a name="Doxygen_language_extension"></a>39.6 Extending to other languages</H2>
 
 
 <p>
@@ -1705,7 +1727,7 @@ The basic gist is that anywhere a comment may reside on a node, there needs to b
 The other half of extension is building a target documentation language comment generator that handles one blob at a time.
 However, this is relatively simple and nowhere near as complex as the wrapper generating modules in SWIG.
 See DoxygenTranslator/JavaDocConverter.cpp for a good example.
-The target language module hands the DoxygenTranslator the blob to translate, and receives back a translated text.
+The target language module passes the Doxygen Translator the blob to translate, and receives back the translated text.
 </p>
 <p>
 <b> What is given to the Doxygen Translator</b>
@@ -1728,7 +1750,7 @@ The target language module hands the DoxygenTranslator the blob to translate, an
  * @return Foo
  */
 </pre></div>
-<p> Development of the comment translator itself is simplified by the fact that the DoxygenTranslator module can easily include a <tt>main</tt> function and thus be developed, compiled, and tested independently of SWIG.
+<p> Development of the comment translator itself is simplified by the fact that the Doxygen Translator module can easily include a <tt>main</tt> function and thus be developed, compiled, and tested independently of SWIG.
 </p>
 
 </body>

From 6bad5ca3a119291d0fd8179d4306f7027cf81bbb Mon Sep 17 00:00:00 2001
From: William S Fulton <wsf@fultondesigns.co.uk>
Date: Tue, 22 May 2018 19:32:47 +0100
Subject: [PATCH 292/314] Doxygen testcase tweak to match that in the html docs

---
 Examples/test-suite/doxygen_ignore.i | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Examples/test-suite/doxygen_ignore.i b/Examples/test-suite/doxygen_ignore.i
index d15110257..ce83470b6 100644
--- a/Examples/test-suite/doxygen_ignore.i
+++ b/Examples/test-suite/doxygen_ignore.i
@@ -36,6 +36,6 @@
 
     @compileroptions This function must be compiled with /EHa when using MSVC.
  */
-void func() { }
+int * func() { }
 
 %}

From caccb20491c3c7e437525c81e8b399be6427fac7 Mon Sep 17 00:00:00 2001
From: William S Fulton <wsf@fultondesigns.co.uk>
Date: Tue, 22 May 2018 19:50:33 +0100
Subject: [PATCH 293/314] Format files to unix format

---
 Examples/test-suite/doxygen_misc_constructs.h | 188 ++++++-------
 Examples/test-suite/doxygen_misc_constructs.i | 248 +++++++++---------
 2 files changed, 218 insertions(+), 218 deletions(-)

diff --git a/Examples/test-suite/doxygen_misc_constructs.h b/Examples/test-suite/doxygen_misc_constructs.h
index 98856ac9a..d677dc3d3 100644
--- a/Examples/test-suite/doxygen_misc_constructs.h
+++ b/Examples/test-suite/doxygen_misc_constructs.h
@@ -1,94 +1,94 @@
-/*
- * This file contains comments which demonstrate details about Doxygen processing,
- * so they can be emulated in SWIG doxy comment translation
- */
-
-
-
-/**This comment without space after '*' is valid in Doxygen.
- *
- */
-void isNoSpaceValidA()
-{}
-
-/**.This comment without space after '*' is valid in Doxygen.
- *
- */
-void isNoSpaceValidB()
-{}
-
-
-/***This is not Doxygen comment.
- *
- */
-void isNoSpaceValidC()
-{}
-
-
-/**
- * Backslash following\c word is a valid doxygen command. Output contains
- * 'followingword' with 'word' in code font.
- */
-void backslashA()
-{}
-
-// Output of escaped symbols below in doxygen generated HTML:
-// Rendered: Escaped symbols: $ @ \ & < > # % " \. :: @text ::text
-// HTML source: Escaped symbols: $ @ \ &amp; &lt; &gt; # % " \. :: @text ::text
-
-
-/**
- * Doxy command without trailing \cspace space is ignored - nothing appears
- * on output. Standalone \ and '\' get to output.
- * Standalone @ and '@' get to output.
- * Commands "in quoted \b strings are treated as plain text".
- * Commands not recognized by Doxygen \blah @blah are ignored.
- * Backslashes in DOS paths d:\xyz\qwe\myfile and words
- * following them do not appear on output, we must quote them with
- * double quotes: "d:\xyz\qwe\myfile", "@something". Single quotes do not help:
- * 'd:\xyz\qwe\myfile'. Escaping works: d:\\xyz\\qwe\\myfile. Unix
- * paths of course have no such problems: /xyz/qwe/myfile
- * Commands for escaped symbols:
- * \$ \@ \\ \& \~ \< \> \# \% \" \. \:: \@text \::text
- */
-void backslashB()
-{}
-
-/**
- * Backslash e at end of \e line froze SWIG \e
- * with old comment parser. 
- *
- * @see MyClass::fun(char,
- *  float)
- */
-void backslashC()
-{}
-
-/**
- * The next line contains expression:
- * <pre>
- * ['retVal < 10', 'g_counter == 23 && g_mode & 3']
- *</pre>
- *
- * Both words should be emphasized \b isystem.connect.
- * But not the last period. For \b example, comma should not be emphasized.
- * Similar \b for: double colon.
- *
- * Spaces at the start of line should be taken into account:
- * @param id used as prefix in log
- *     statements. The default value is empty string, which is OK if
- *     there is only one app. instance. Example:
- *     <pre>
- *         ctrl.setBP("func1");
- *     </pre>
- *     If we set the id to \c main_, we get:
- *     <pre>
- *         main_ctrl.setBP("func1");
- *     </pre>
- *
- * @param fileName name of the log file
- */
-void cycle(int id, char *fileName)
-{}
-
-
+/*
+ * This file contains comments which demonstrate details about Doxygen processing,
+ * so they can be emulated in SWIG doxy comment translation
+ */
+
+
+
+/**This comment without space after '*' is valid in Doxygen.
+ *
+ */
+void isNoSpaceValidA()
+{}
+
+/**.This comment without space after '*' is valid in Doxygen.
+ *
+ */
+void isNoSpaceValidB()
+{}
+
+
+/***This is not Doxygen comment.
+ *
+ */
+void isNoSpaceValidC()
+{}
+
+
+/**
+ * Backslash following\c word is a valid doxygen command. Output contains
+ * 'followingword' with 'word' in code font.
+ */
+void backslashA()
+{}
+
+// Output of escaped symbols below in doxygen generated HTML:
+// Rendered: Escaped symbols: $ @ \ & < > # % " \. :: @text ::text
+// HTML source: Escaped symbols: $ @ \ &amp; &lt; &gt; # % " \. :: @text ::text
+
+
+/**
+ * Doxy command without trailing \cspace space is ignored - nothing appears
+ * on output. Standalone \ and '\' get to output.
+ * Standalone @ and '@' get to output.
+ * Commands "in quoted \b strings are treated as plain text".
+ * Commands not recognized by Doxygen \blah @blah are ignored.
+ * Backslashes in DOS paths d:\xyz\qwe\myfile and words
+ * following them do not appear on output, we must quote them with
+ * double quotes: "d:\xyz\qwe\myfile", "@something". Single quotes do not help:
+ * 'd:\xyz\qwe\myfile'. Escaping works: d:\\xyz\\qwe\\myfile. Unix
+ * paths of course have no such problems: /xyz/qwe/myfile
+ * Commands for escaped symbols:
+ * \$ \@ \\ \& \~ \< \> \# \% \" \. \:: \@text \::text
+ */
+void backslashB()
+{}
+
+/**
+ * Backslash e at end of \e line froze SWIG \e
+ * with old comment parser. 
+ *
+ * @see MyClass::fun(char,
+ *  float)
+ */
+void backslashC()
+{}
+
+/**
+ * The next line contains expression:
+ * <pre>
+ * ['retVal < 10', 'g_counter == 23 && g_mode & 3']
+ *</pre>
+ *
+ * Both words should be emphasized \b isystem.connect.
+ * But not the last period. For \b example, comma should not be emphasized.
+ * Similar \b for: double colon.
+ *
+ * Spaces at the start of line should be taken into account:
+ * @param id used as prefix in log
+ *     statements. The default value is empty string, which is OK if
+ *     there is only one app. instance. Example:
+ *     <pre>
+ *         ctrl.setBP("func1");
+ *     </pre>
+ *     If we set the id to \c main_, we get:
+ *     <pre>
+ *         main_ctrl.setBP("func1");
+ *     </pre>
+ *
+ * @param fileName name of the log file
+ */
+void cycle(int id, char *fileName)
+{}
+
+
diff --git a/Examples/test-suite/doxygen_misc_constructs.i b/Examples/test-suite/doxygen_misc_constructs.i
index ed5fa4326..461415316 100644
--- a/Examples/test-suite/doxygen_misc_constructs.i
+++ b/Examples/test-suite/doxygen_misc_constructs.i
@@ -1,124 +1,124 @@
-// This file contains tests for situations, which do not normally
-// appear in the code, but must nevertheless be handled correctly.
-
-%module doxygen_misc_constructs
-
-%warnfilter(SWIGWARN_DOXYGEN_UNKNOWN_COMMAND) backslashB;
-
-%inline %{
-
-    // Tag '@endink' must be recognized even if it is not
-    // followed by whitespace.
-
-    /** Tag endlink must be recognized also when followed by nonspace charater.
-     *
-     * @link Connection::getId() @endlink<br> */
-     
-    char g_counter;
-
-
-    /** 
-      Tag endlink must be recognized also when it is the last token
-      in the commment.
-
-      @link Connection::getId() @endlink<br>
-      @link debugIdeTraceProfilerCoverageSample.py Python example. @endlink
-     */
-    int g_zipCode;
-
-
-    // Paramter 'isReportSize' must appear in comment of the overload, which
-    // has it. Empty line before link must be preserved.
-    /**
-     * Returns address of file line.
-     *
-     * @param fileName name of the file, where the source line is located
-     * @param line line number
-     * @param isGetSize if set, for every object location both address and size are returned
-     *
-     * @link Connection::getId() @endlink <br>
-     */
-    void getAddress(int &fileName, 
-                    int line,     
-                    bool isGetSize = false) {}
-
-    // The first comment must be ignored.
-    /** 
-     * \defgroup icFacade isystem.connect Facade
-     *
-     * This page shows the core classes, which can be used to control
-     * all aspects of winIDEA, for example: debugging, analyzers, IO module, ...
-     */
-
-    /** 
-     * This class contains information for connection to winIDEA. Its methods 
-     * return reference to self, so we can use it like this:
-     * <pre>
-     * CConnectionConfig config = new CConnectionConfig();
-     * config.discoveryPort(5534).dllPath("C:\\myWinIDEA\\connect.dll").id("main");
-     * </pre>
-     *
-     * All parameters are optional. Set only what is required, default values are
-     * used for unspecified parameters.
-     * <p>
-     *
-     * @link advancedWinIDEALaunching.py Python example.@endlink <br>
-     */
-    class CConnectionConfig
-    {
-    };
-
-    // Text after '\c' must be kept unchanged in Python.
-    /**
-     * Determines how long the \c isystem.connect should wait for running 
-     * instances to respond. Only one of \c lfWaitXXX flags from IConnect::ELaunchFlags
-     * may be specified.
-     */
-    int waitTime(long waitTime) {return 33;}
-
-
-    // Line with tag \ingroup must not appear in translated comment:
-    /** \ingroup icFacade
-     *
-     * This function returns connection id.
-     */
-    int getConnection() {return 3;}
-
-    // the follwing must produce no comment in wrapper
-    /*******************************************************************/
-    char getFirstLetter() {return 'a';}
-
-    
-    /**
-     * Class description.
-     */
-    class ClassWithNestedEnum {
-    public:
-        /**
-         * Enum description.
-         */
-        typedef enum {ONE,  ///< desc of one
-                      TWO,  ///< desc of two
-                      THREE ///< desc of three
-        } ENested;
-
-    };
-
-    /**
-        An example of a list in a documentation comment.
-
-            - The first item of the list.
-            - The second list item, on
-              several indented lines,
-              showing that the indentation
-              is preserved.
-            - And the final list item after it.
-
-        And this is not a list item any more.
-     */
-    void showList() { }
-
-    #include "doxygen_misc_constructs.h"
-    
-%}
-    %include "doxygen_misc_constructs.h"
+// This file contains tests for situations, which do not normally
+// appear in the code, but must nevertheless be handled correctly.
+
+%module doxygen_misc_constructs
+
+%warnfilter(SWIGWARN_DOXYGEN_UNKNOWN_COMMAND) backslashB;
+
+%inline %{
+
+    // Tag '@endink' must be recognized even if it is not
+    // followed by whitespace.
+
+    /** Tag endlink must be recognized also when followed by nonspace charater.
+     *
+     * @link Connection::getId() @endlink<br> */
+     
+    char g_counter;
+
+
+    /** 
+      Tag endlink must be recognized also when it is the last token
+      in the commment.
+
+      @link Connection::getId() @endlink<br>
+      @link debugIdeTraceProfilerCoverageSample.py Python example. @endlink
+     */
+    int g_zipCode;
+
+
+    // Paramter 'isReportSize' must appear in comment of the overload, which
+    // has it. Empty line before link must be preserved.
+    /**
+     * Returns address of file line.
+     *
+     * @param fileName name of the file, where the source line is located
+     * @param line line number
+     * @param isGetSize if set, for every object location both address and size are returned
+     *
+     * @link Connection::getId() @endlink <br>
+     */
+    void getAddress(int &fileName, 
+                    int line,     
+                    bool isGetSize = false) {}
+
+    // The first comment must be ignored.
+    /** 
+     * \defgroup icFacade isystem.connect Facade
+     *
+     * This page shows the core classes, which can be used to control
+     * all aspects of winIDEA, for example: debugging, analyzers, IO module, ...
+     */
+
+    /** 
+     * This class contains information for connection to winIDEA. Its methods 
+     * return reference to self, so we can use it like this:
+     * <pre>
+     * CConnectionConfig config = new CConnectionConfig();
+     * config.discoveryPort(5534).dllPath("C:\\myWinIDEA\\connect.dll").id("main");
+     * </pre>
+     *
+     * All parameters are optional. Set only what is required, default values are
+     * used for unspecified parameters.
+     * <p>
+     *
+     * @link advancedWinIDEALaunching.py Python example.@endlink <br>
+     */
+    class CConnectionConfig
+    {
+    };
+
+    // Text after '\c' must be kept unchanged in Python.
+    /**
+     * Determines how long the \c isystem.connect should wait for running 
+     * instances to respond. Only one of \c lfWaitXXX flags from IConnect::ELaunchFlags
+     * may be specified.
+     */
+    int waitTime(long waitTime) {return 33;}
+
+
+    // Line with tag \ingroup must not appear in translated comment:
+    /** \ingroup icFacade
+     *
+     * This function returns connection id.
+     */
+    int getConnection() {return 3;}
+
+    // the follwing must produce no comment in wrapper
+    /*******************************************************************/
+    char getFirstLetter() {return 'a';}
+
+    
+    /**
+     * Class description.
+     */
+    class ClassWithNestedEnum {
+    public:
+        /**
+         * Enum description.
+         */
+        typedef enum {ONE,  ///< desc of one
+                      TWO,  ///< desc of two
+                      THREE ///< desc of three
+        } ENested;
+
+    };
+
+    /**
+        An example of a list in a documentation comment.
+
+            - The first item of the list.
+            - The second list item, on
+              several indented lines,
+              showing that the indentation
+              is preserved.
+            - And the final list item after it.
+
+        And this is not a list item any more.
+     */
+    void showList() { }
+
+    #include "doxygen_misc_constructs.h"
+    
+%}
+    %include "doxygen_misc_constructs.h"

From 419e850ea0239c32548a944947a3d58952f3b37b Mon Sep 17 00:00:00 2001
From: William S Fulton <wsf@fultondesigns.co.uk>
Date: Thu, 24 May 2018 07:02:21 +0100
Subject: [PATCH 294/314] Add missing CPlusPlus17.html file

Mistakenly omitted from 066c396ad6c1656a477997561def5a6131bafda5
---
 Doc/Manual/CPlusPlus17.html | 78 +++++++++++++++++++++++++++++++++++++
 1 file changed, 78 insertions(+)
 create mode 100644 Doc/Manual/CPlusPlus17.html

diff --git a/Doc/Manual/CPlusPlus17.html b/Doc/Manual/CPlusPlus17.html
new file mode 100644
index 000000000..690173e6e
--- /dev/null
+++ b/Doc/Manual/CPlusPlus17.html
@@ -0,0 +1,78 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<html>
+<head>
+<title>SWIG and C++17</title>
+<link rel="stylesheet" type="text/css" href="style.css">
+<meta http-equiv="content-type" content="text/html; charset=UTF-8">
+</head>
+
+<body bgcolor="#ffffff">
+<H1><a name="CPlusPlus17">8 SWIG and C++17</a></H1>
+<!-- INDEX -->
+<div class="sectiontoc">
+<ul>
+<li><a href="#CPlusPlus17_introduction">Introduction</a>
+<li><a href="#CPlusPlus17_core_language_changes">Core language changes</a>
+<ul>
+<li><a href="#CPlusPlus17_nested_namespaces">Nested namespace definitions</a>
+</ul>
+<li><a href="#CPlusPlus17_standard_library_changes">Standard library changes</a>
+</ul>
+</div>
+<!-- INDEX -->
+
+
+
+<H2><a name="CPlusPlus17_introduction">8.1 Introduction</a></H2>
+
+
+<p>This chapter gives you a brief overview about the SWIG
+implementation of the C++17 standard.
+There isn't much in C++17 that affects SWIG, however, work has only just begun on adding
+C++17 support.
+</p>
+
+<H2><a name="CPlusPlus17_core_language_changes">8.2 Core language changes</a></H2>
+
+
+<H3><a name="CPlusPlus17_nested_namespaces">8.2.1 Nested namespace definitions</a></H3>
+
+
+<p>
+C++17 offers a more concise syntax for defining namespaces.
+SWIG has support for nested namespace definitions such as:
+</p>
+
+<div class="code">
+<pre>
+namespace A::B::C {
+  ...
+}
+</pre>
+</div>
+
+<p>
+This is the equivalent to the C++98 namespace definitions:
+</p>
+
+<div class="code">
+<pre>
+namespace A {
+  namespace B {
+    namespace C {
+      ...
+    }
+  }
+}
+</pre>
+</div>
+
+<p>
+<b>Compatibility note:</b> SWIG-4.0.0 was the first version to support nested namespace definitions.
+</p>
+
+<H2><a name="CPlusPlus17_standard_library_changes">8.3 Standard library changes</a></H2>
+
+
+</body>
+</html>

From a1b1ba105b0fd98da91a9b51653357e50150fa43 Mon Sep 17 00:00:00 2001
From: William S Fulton <wsf@fultondesigns.co.uk>
Date: Thu, 24 May 2018 07:30:02 +0100
Subject: [PATCH 295/314] html fixes for Doxygen

---
 Doc/Manual/Doxygen.html | 55 ++++++++++++++++++++---------------------
 1 file changed, 27 insertions(+), 28 deletions(-)

diff --git a/Doc/Manual/Doxygen.html b/Doc/Manual/Doxygen.html
index 886391972..9e92d31be 100644
--- a/Doc/Manual/Doxygen.html
+++ b/Doc/Manual/Doxygen.html
@@ -89,6 +89,7 @@ in comments (like unterminated strings or missing ending tags).
 Currently, the whole subset of Doxygen comment styles is supported
 (See <a href="http://www.stack.nl/~dimitri/doxygen/docblocks.html">
 Documenting the code</a>). Here they are:
+</p>
 
 <div class="code"><pre>
 /**
@@ -103,7 +104,6 @@ Documenting the code</a>). Here they are:
 /// Single-line comment
 //! Another single-line comment
 </pre></div>
-</p>
 
 <p>
 Also any of the above with '&lt;' added after comment-starting symbol,
@@ -120,8 +120,8 @@ comments like <i>/*********/</i> or <i>//////////</i>.
 Please note, as SWIG parses the input file by itself with strict grammar,
 there is only a limited support for various cases of comment placement
 in the file.
-<p>
 </p>
+<p>
 Comments can be placed before C/C++ expressions on separate lines:
 </p>
 
@@ -548,10 +548,10 @@ directives</a>):
 <p>
 Here is the list of all Doxygen tags and the description of how they are translated to Javadoc
 </p>
-<div class="diagram"><pre>
-<table border="0">
+<div class="diagram">
+<table border="0" summary="Java Doxygen tags">
 <tr>
-  <th id="Doxygen Tags Java" align="left">Doxygen tags</th>
+  <th align="left">Doxygen tags</th>
 </tr>
 <tr>
 <td>\a</td>
@@ -578,7 +578,6 @@ Here is the list of all Doxygen tags and the description of how they are transla
 <td>wrapped with &lt;code&gt; html tag</td>
 </tr>
 <tr>
-<tr>
 <td>\cite</td>
 <td>wrapped with &lt;i&gt; html tag</td>
 </tr>
@@ -795,7 +794,7 @@ Here is the list of all Doxygen tags and the description of how they are transla
 <td>prints ::</td>
 </tr>
 </table>
-</pre></div>
+</div>
 
 <H3><a name="Doxygen_unsupported_tags"></a>39.3.3 Unsupported tags</H3>
 
@@ -810,10 +809,10 @@ These are suppressed with their content just printed out (if the tag has any
 sense, typically text content).
 Here is the list of these tags:
 </p>
-<div class="diagram"><pre>
-<table border="0">
+<div class="diagram">
+<table border="0" summary="Unsupported Java Doxygen Tags">
 <tr>
-  <th id="Unsupported Doxygen Tags Java" align="left">Unsupported Doxygen tags</th>
+  <th align="left">Unsupported Doxygen tags</th>
 </tr>
 <tr>
 <td>\addindex</td>
@@ -959,19 +958,19 @@ Here is the list of these tags:
 <td>\category</td>
 </tr>
 </table>
-</pre></div>
+</div>
 
-<p/>
+<p>
 
 If one of the following Doxygen tags appears as the first tag in a
 comment, the whole comment block is ignored:
 <!-- see parser.y, function isStructuralDoxygen() -->
 
 </p>
-<div class="diagram"><pre>
-<table border="0">
+<div class="diagram">
+<table border="0" summary="Ignored Java Doxygen Tags">
 <tr>
-  <th id="Ignored Doxygen Tags" align="left">Ignored Doxygen tags</th>
+  <th align="left">Ignored Doxygen tags</th>
 </tr>
 <tr>
 <td>\addtogroup</td>
@@ -1029,7 +1028,7 @@ comment, the whole comment block is ignored:
 </tr>
 
 </table>
-</pre></div>
+</div>
 
 
 
@@ -1183,10 +1182,10 @@ are not present in generated code, so they have no comment translated for them.
  * &lt;/table&gt;
  */
 </pre></div>
-<p/>
+<p>
 translates to Python as:
-<p/>
-<div class="targetlang"><pre>
+</p>
+<div class="diagram"><pre>
   Animals
   | Column 1 | Column 2 |
   -----------------------
@@ -1194,7 +1193,6 @@ translates to Python as:
   | cat      | mouse    |
   | horse    | parrot   |
 </pre></div>
-</p>
 
 <p>
   <b>Overloaded functions</b>
@@ -1221,10 +1219,10 @@ to do the work.
 <p>
 Here is the list of all Doxygen tags and the description of how they are translated to Pydoc
 </p>
-<div class="diagram"><pre>
-<table border="0">
+<div class="diagram">
+<table border="0" summary="Python Doxygen tags">
 <tr>
-  <th id="Doxygen Tags Python" align="left">Doxygen tags</th>
+  <th align="left">Doxygen tags</th>
 </tr>
 <tr>
 <td>\a</td>
@@ -1427,7 +1425,7 @@ Here is the list of all Doxygen tags and the description of how they are transla
 <td>prints ::</td>
 </tr>
 </table>
-</pre></div>
+</div>
 
 <H3><a name="Doxygen_python_unsupported_tags"></a>39.4.3 Unsupported tags</H3>
 
@@ -1440,10 +1438,10 @@ are suppressed with their content just printed out (if it has any
 sense, typically text content).
 Here is the list of these tags:
 </p>
-<div class="diagram"><pre>
-<table border="0">
+<div class="diagram">
+<table border="0" summary="Unsupported Python Doxygen Tags">
 <tr>
-  <th id="Unsupported Doxygen Tags Python" align="left">Unsupported Doxygen tags</th>
+  <th align="left">Unsupported Doxygen tags</th>
 </tr>
 <tr>
 <td>\addindex</td>
@@ -1611,7 +1609,7 @@ Here is the list of these tags:
 <td>\c</td>
 </tr>
 </table>
-</pre></div>
+</div>
 
 <H3><a name="Doxygen_python_further_details"></a>39.4.4 Further details</H3>
 
@@ -1624,6 +1622,7 @@ TO BE ADDED.
 
 
 <p>
+This section contains information for developers enhancing the Doxygen translator.
 </p>
 
 <H3><a name="Doxygen_translator_design"></a>39.5.1 Doxygen translator design</H3>

From 62814e4ab73e49865234a418a560e27d7ac5eb0b Mon Sep 17 00:00:00 2001
From: William S Fulton <wsf@fultondesigns.co.uk>
Date: Thu, 24 May 2018 18:32:53 +0100
Subject: [PATCH 296/314] Fixes to makechap.py to detect ill-formed headers

---
 Doc/Manual/Doxygen.html | 10 +++++-----
 Doc/Manual/makechap.py  |  4 +++-
 2 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/Doc/Manual/Doxygen.html b/Doc/Manual/Doxygen.html
index 9e92d31be..a736fb6a4 100644
--- a/Doc/Manual/Doxygen.html
+++ b/Doc/Manual/Doxygen.html
@@ -197,7 +197,7 @@ Translation of Doxygen comments is influenced by the following <a
 href="Customization.html#Customization_features">%feature directives</a>:
 </p>
 
-<h4>doxygen:notranslate</h4>
+<h4><a name="Doxygen_notranslate"></a>doxygen:notranslate</h4>
 
 <p>
 Turns off translation of Doxygen comments to the target language syntax: the
@@ -208,7 +208,7 @@ instead of the corresponding language tool (<tt>javadoc</tt>, <tt>sphinx</tt>,
 </p>
 
 
-<h4>doxygen:alias:&lt;command-name&gt;</h4>
+<h4><a name="Doxygen_alias"></a>doxygen:alias:&lt;command-name&gt;</h4>
 
 <p>
 Specify an alias for a Doxygen command with the given name. This can be useful
@@ -254,7 +254,7 @@ wrappers of the C++ API.
 </p>
 
 
-<h4>doxygen:ignore:&lt;command-name&gt;</h4>
+<h4><a name="Doxygen_ignore"></a>doxygen:ignore:&lt;command-name&gt;</h4>
 
 <p>
 This feature makes it possible to just ignore an unknown Doxygen command, instead of
@@ -404,14 +404,14 @@ def func():
 </pre></div>
 
 
-<h4>doxygen:nolinktranslate (Java-only currently)</h4>
+<h4><a name="Doxygen_nolinktranslate"></a>doxygen:nolinktranslate (Java-only currently)</h4>
 
 <p>
 Turn off automatic link-objects translation.
 </p>
 
 
-<h4>doxygen:nostripparams (Java-only currently)</h4>
+<h4><a name="Doxygen_nostripparams"></a>doxygen:nostripparams (Java-only currently)</h4>
 
 <p>
 Turn off stripping of <tt>@param</tt> and <tt>@tparam</tt>
diff --git a/Doc/Manual/makechap.py b/Doc/Manual/makechap.py
index 61994e2a0..e30d14e0f 100644
--- a/Doc/Manual/makechap.py
+++ b/Doc/Manual/makechap.py
@@ -44,6 +44,8 @@ def getheadingname(m):
 def getheadingtext(m, s):
     prevheadingtext_newstyle = m.group(2)
     prevheadingtext_oldstyle = m.group(3)
+    if prevheadingtext_oldstyle is None or prevheadingtext_newstyle is None:
+        raise RuntimeError("Ill-formed heading in line:\n%s" % s)
     if len(prevheadingtext_oldstyle) == 0 and len(prevheadingtext_newstyle) == 0:
         raise RuntimeError("No heading text in line:\n%s" % s)
     if len(prevheadingtext_oldstyle) > 0 and len(prevheadingtext_newstyle) > 0:
@@ -72,7 +74,7 @@ name = ""
 
 # Regexs for <h1>,... <h5> sections
 
-h1 = re.compile(r".*?<H1>(<a.*?>\s*[\d\s]*(.*?)</a>)*[\d\s]*(.*?)</H1>", re.IGNORECASE)
+h1 = re.compile(r".*?<H1>(<a.*?>\s*[\d\.\s]*(.*?)</a>)*[\d\.\s]*(.*?)</H1>", re.IGNORECASE)
 h2 = re.compile(r".*?<H2>(<a.*?>\s*[\d\.\s]*(.*?)</a>)*[\d\.\s]*(.*?)</H2>", re.IGNORECASE)
 h3 = re.compile(r".*?<H3>(<a.*?>\s*[\d\.\s]*(.*?)</a>)*[\d\.\s]*(.*?)</H3>", re.IGNORECASE)
 h4 = re.compile(r".*?<H4>(<a.*?>\s*[\d\.\s]*(.*?)</a>)*[\d\.\s]*(.*?)</H4>", re.IGNORECASE)

From 4cdca98709a4a722245005890269a7c4af887288 Mon Sep 17 00:00:00 2001
From: William S Fulton <wsf@fultondesigns.co.uk>
Date: Thu, 24 May 2018 18:36:20 +0100
Subject: [PATCH 297/314] Update html chapter numbering for added Doxygen
 chapter

---
 Doc/Manual/Allegrocl.html  | 108 +++++++++---------
 Doc/Manual/Android.html    |  16 +--
 Doc/Manual/CCache.html     |  36 +++---
 Doc/Manual/CSharp.html     |  60 +++++-----
 Doc/Manual/Chicken.html    |  40 +++----
 Doc/Manual/Contents.html   | 134 +++++++++++-----------
 Doc/Manual/D.html          |  44 ++++----
 Doc/Manual/Doxygen.html    | 100 +++++++++--------
 Doc/Manual/Extending.html  | 100 ++++++++---------
 Doc/Manual/Go.html         |  56 +++++-----
 Doc/Manual/Guile.html      |  44 ++++----
 Doc/Manual/Java.html       | 220 ++++++++++++++++++-------------------
 Doc/Manual/Javascript.html |  44 ++++----
 Doc/Manual/Lisp.html       |  22 ++--
 Doc/Manual/Lua.html        |  88 +++++++--------
 Doc/Manual/Modula3.html    |  40 +++----
 Doc/Manual/Modules.html    |  16 +--
 Doc/Manual/Mzscheme.html   |   8 +-
 Doc/Manual/Ocaml.html      |  62 +++++------
 Doc/Manual/Octave.html     |  52 ++++-----
 Doc/Manual/Perl5.html      | 108 +++++++++---------
 Doc/Manual/Php.html        |  50 ++++-----
 Doc/Manual/Pike.html       |  24 ++--
 Doc/Manual/Python.html     | 192 ++++++++++++++++----------------
 Doc/Manual/R.html          |  16 +--
 Doc/Manual/Ruby.html       | 200 ++++++++++++++++-----------------
 Doc/Manual/Scilab.html     |  90 +++++++--------
 Doc/Manual/Sections.html   |   1 +
 Doc/Manual/Tcl.html        |  92 ++++++++--------
 Doc/Manual/Warnings.html   |  36 +++---
 Doc/Manual/chapters        |   2 +-
 31 files changed, 1062 insertions(+), 1039 deletions(-)

diff --git a/Doc/Manual/Allegrocl.html b/Doc/Manual/Allegrocl.html
index f8e5d013e..aaa2ec5f1 100644
--- a/Doc/Manual/Allegrocl.html
+++ b/Doc/Manual/Allegrocl.html
@@ -8,7 +8,7 @@
 
 <body bgcolor="#ffffff">
 
-<H1><a name="Allegrocl">19 SWIG and Allegro Common Lisp</a></H1>
+<H1><a name="Allegrocl">20 SWIG and Allegro Common Lisp</a></H1>
 <!-- INDEX -->
 <div class="sectiontoc">
 <ul>
@@ -135,10 +135,10 @@ be unhappy to see some enterprising folk use this work to add
 to it.
 </p>
 
-<H2><a name="Allegrocl_nn2">19.1 Basics</a></H2>
+<H2><a name="Allegrocl_nn2">20.1 Basics</a></H2>
 
 
-<H3><a name="Allegrocl_nn3">19.1.1 Running SWIG</a></H3>
+<H3><a name="Allegrocl_nn3">20.1.1 Running SWIG</a></H3>
 
 
 <p>
@@ -360,7 +360,7 @@ need to link in the Allegro shared library. The library you create from
 the C++ wrapper will be what you then load into Allegro CL.
 </p>
 
-<H3><a name="Allegrocl_nn4">19.1.2 Command Line Options</a></H3>
+<H3><a name="Allegrocl_nn4">20.1.2 Command Line Options</a></H3>
 
 
 <p>
@@ -396,7 +396,7 @@ See <a href="#Allegrocl_nn47">Section 17.5 Identifier converter
 functions</a> for more details.
 </p>
 
-<H3><a name="Allegrocl_nn5">19.1.3 Inserting user code into generated files</a></H3>
+<H3><a name="Allegrocl_nn5">20.1.3 Inserting user code into generated files</a></H3>
 
 
 <p>
@@ -436,7 +436,7 @@ Note that the block <tt>%{ ... %}</tt> is effectively a shortcut for
 </p>
 
 
-<H2><a name="Allegrocl_nn6">19.2 Wrapping Overview</a></H2>
+<H2><a name="Allegrocl_nn6">20.2 Wrapping Overview</a></H2>
 
 
 <p>
@@ -446,7 +446,7 @@ New users to SWIG are encouraged to read
 interested in generating an interface to C++.
 </p>
 
-<H3><a name="Allegrocl_nn7">19.2.1 Function Wrapping</a></H3>
+<H3><a name="Allegrocl_nn7">20.2.1 Function Wrapping</a></H3>
 
 
   <p>
@@ -499,7 +499,7 @@ interested in generating an interface to C++.
   </pre>
   </div>
 
-<H3><a name="Allegrocl_nn8">19.2.2 Foreign Wrappers</a></H3>
+<H3><a name="Allegrocl_nn8">20.2.2 Foreign Wrappers</a></H3>
 
 
   <p>
@@ -512,7 +512,7 @@ interested in generating an interface to C++.
     typemap. 
   </p>
 
-<H3><a name="Allegrocl_nn9">19.2.3 FFI Wrappers</a></H3>
+<H3><a name="Allegrocl_nn9">20.2.3 FFI Wrappers</a></H3>
 
 
   <p>
@@ -593,7 +593,7 @@ char *xxx();
     ff:def-foreign-call's.
   </p>
 
-<H3><a name="Allegrocl_nn10">19.2.4 Non-overloaded Defuns</a></H3>
+<H3><a name="Allegrocl_nn10">20.2.4 Non-overloaded Defuns</a></H3>
 
 
   <p>
@@ -606,7 +606,7 @@ char *xxx();
     this function can be manipulated via the <tt>lout</tt> typemap.
   </p>
 
-<H3><a name="Allegrocl_nn11">19.2.5 Overloaded Defuns</a></H3>
+<H3><a name="Allegrocl_nn11">20.2.5 Overloaded Defuns</a></H3>
 
 
   <p>
@@ -622,7 +622,7 @@ char *xxx();
     can be manipulated via the <tt>lout</tt> typemap.
   </p>
 
-<H3><a name="Allegrocl_nn12">19.2.6 What about constant and variable access?</a></H3>
+<H3><a name="Allegrocl_nn12">20.2.6 What about constant and variable access?</a></H3>
 
 
   <p>
@@ -635,7 +635,7 @@ char *xxx();
     into the foreign module.
   </p>
 
-<H3><a name="Allegrocl_nn13">19.2.7 Object Wrapping</a></H3>
+<H3><a name="Allegrocl_nn13">20.2.7 Object Wrapping</a></H3>
 
 
   <p>
@@ -657,7 +657,7 @@ char *xxx();
   foreign function interface.
   </p>
 
-<H2><a name="Allegrocl_nn14">19.3 Wrapping Details</a></H2>
+<H2><a name="Allegrocl_nn14">20.3 Wrapping Details</a></H2>
 
 
   <p>
@@ -665,7 +665,7 @@ char *xxx();
     translated into lisp.
   </p>
 
-<H3><a name="Allegrocl_nn15">19.3.1 Namespaces</a></H3>
+<H3><a name="Allegrocl_nn15">20.3.1 Namespaces</a></H3>
 
 
   <p>
@@ -742,7 +742,7 @@ namespace car {
       function such as <tt>(car '(1 2 3)</tt>.
     </p>
 
-<H3><a name="Allegrocl_nn16">19.3.2 Constants</a></H3>
+<H3><a name="Allegrocl_nn16">20.3.2 Constants</a></H3>
 
 
     
@@ -803,7 +803,7 @@ namespace car {
       not use the <tt>-nocwrap</tt> command-line option.
       </p>
 
-<H3><a name="Allegrocl_nn17">19.3.3 Variables</a></H3>
+<H3><a name="Allegrocl_nn17">20.3.3 Variables</a></H3>
 
 
     <p>
@@ -881,7 +881,7 @@ globalvar&gt; (globalvar.nnn::glob_float)
     </pre>
     </div>
 
-<H3><a name="Allegrocl_nn18">19.3.4 Enumerations</a></H3>
+<H3><a name="Allegrocl_nn18">20.3.4 Enumerations</a></H3>
 
 
     <p>
@@ -957,7 +957,7 @@ EXPORT const int ACL_ENUM___FOO3__SWIG_0 = FOO3;
       </pre>
       </div>
 
-<H3><a name="Allegrocl_nn19">19.3.5 Arrays</a></H3>
+<H3><a name="Allegrocl_nn19">20.3.5 Arrays</a></H3>
 
 
     <p>
@@ -1105,10 +1105,10 @@ namespace BAR {
     </pre>
     </div>
 
-<H3><a name="Allegrocl_nn20">19.3.6 Classes and Structs and Unions (oh my!)</a></H3>
+<H3><a name="Allegrocl_nn20">20.3.6 Classes and Structs and Unions (oh my!)</a></H3>
 
 
-<H4><a name="Allegrocl_nn21">19.3.6.1 CLOS wrapping of</a></H4>
+<H4><a name="Allegrocl_nn21">20.3.6.1 CLOS wrapping of</a></H4>
 
 
     <p>
@@ -1123,7 +1123,7 @@ namespace BAR {
       integer values.
     </p>
 
-<H4><a name="Allegrocl_nn22">19.3.6.2 CLOS Inheritance</a></H4>
+<H4><a name="Allegrocl_nn22">20.3.6.2 CLOS Inheritance</a></H4>
 
 
     <p>
@@ -1136,7 +1136,7 @@ namespace BAR {
       parameter.
     </p>
 
-<H4><a name="Allegrocl_nn23">19.3.6.3 Member fields and functions</a></H4>
+<H4><a name="Allegrocl_nn23">20.3.6.3 Member fields and functions</a></H4>
 
 
     <p>
@@ -1152,7 +1152,7 @@ namespace BAR {
       the interface does nothing for <tt>friend</tt> directives, 
     </p>
 
-<H4><a name="Allegrocl_nn24">19.3.6.4 Why not directly access C++ classes using foreign types?</a></H4>
+<H4><a name="Allegrocl_nn24">20.3.6.4 Why not directly access C++ classes using foreign types?</a></H4>
 
 
     <p>
@@ -1170,11 +1170,11 @@ namespace BAR {
       use the more robust wrapper functions. 
     </p>
 
-<H3><a name="Allegrocl_nn25">19.3.7 Templates</a></H3>
+<H3><a name="Allegrocl_nn25">20.3.7 Templates</a></H3>
 
 
     
-<H4><a name="Allegrocl_nn26">19.3.7.1 Generating wrapper code for templates</a></H4>
+<H4><a name="Allegrocl_nn26">20.3.7.1 Generating wrapper code for templates</a></H4>
 
 
 <p>
@@ -1187,7 +1187,7 @@ them. This is done via the
 directive.
 </p>
 
-<H4><a name="Allegrocl_nn27">19.3.7.2 Implicit Template instantiation</a></H4>
+<H4><a name="Allegrocl_nn27">20.3.7.2 Implicit Template instantiation</a></H4>
 
 
 <p>
@@ -1197,7 +1197,7 @@ to include these templated classes in the foreign-type and CLOS
 class schema.
 </p>
 
-<H3><a name="Allegrocl_nn28">19.3.8 Typedef, Templates, and Synonym Types</a></H3>
+<H3><a name="Allegrocl_nn28">20.3.8 Typedef, Templates, and Synonym Types</a></H3>
 
 
     <p>
@@ -1277,7 +1277,7 @@ synonym&gt;
     </pre>
     </div>
 
-<H4><a name="Allegrocl_nn29">19.3.8.1 Choosing a primary type</a></H4>
+<H4><a name="Allegrocl_nn29">20.3.8.1 Choosing a primary type</a></H4>
 
 
     <p>
@@ -1298,7 +1298,7 @@ synonym&gt;
         </li>
       </ul>
 
-<H3><a name="Allegrocl_nn30">19.3.9 Function overloading/Parameter defaulting</a></H3>
+<H3><a name="Allegrocl_nn30">20.3.9 Function overloading/Parameter defaulting</a></H3>
 
 
     <p>
@@ -1461,7 +1461,7 @@ overload&gt;
     </pre>
     </div>
 
-<H3><a name="Allegrocl_nn31">19.3.10 Operator wrapping and Operator overloading</a></H3>
+<H3><a name="Allegrocl_nn31">20.3.10 Operator wrapping and Operator overloading</a></H3>
 
 
     <p>
@@ -1607,7 +1607,7 @@ opoverload&gt;
     </pre>
     </div>
 
-<H3><a name="Allegrocl_nn32">19.3.11 Varargs</a></H3>
+<H3><a name="Allegrocl_nn32">20.3.11 Varargs</a></H3>
 
 
     <p>
@@ -1628,7 +1628,7 @@ opoverload&gt;
       with other ways such functions can be wrapped.
     </p>
 
-<H3><a name="Allegrocl_nn33">19.3.12 C++ Exceptions</a></H3>
+<H3><a name="Allegrocl_nn33">20.3.12 C++ Exceptions</a></H3>
 
 
     <p>
@@ -1640,7 +1640,7 @@ opoverload&gt;
       implemented.
     </p>
 
-<H3><a name="Allegrocl_nn34">19.3.13 Pass by value, pass by reference</a></H3>
+<H3><a name="Allegrocl_nn34">20.3.13 Pass by value, pass by reference</a></H3>
 
 
     <p>
@@ -1652,7 +1652,7 @@ opoverload&gt;
       newly defined types.
     </p>
 
-<H2><a name="Allegrocl_nn35">19.4 Typemaps</a></H2>
+<H2><a name="Allegrocl_nn35">20.4 Typemaps</a></H2>
 
 
 <p>
@@ -1663,7 +1663,7 @@ opoverload&gt;
   on <a href="Typemaps.html#Typemaps">Typemaps</a> for more information.
 </p>
 
-<H3><a name="Allegrocl_nn36">19.4.1 Code Generation in the C++ Wrapper</a></H3>
+<H3><a name="Allegrocl_nn36">20.4.1 Code Generation in the C++ Wrapper</a></H3>
 
 
     
@@ -1693,7 +1693,7 @@ return-val wrapper-name(parm0, parm1, ..., parmN)
     </pre>
     </div>
 
-<H4><a name="Allegrocl_nn37">19.4.1.1 IN Typemap</a></H4>
+<H4><a name="Allegrocl_nn37">20.4.1.1 IN Typemap</a></H4>
 
 
     <p>
@@ -1728,7 +1728,7 @@ return-val wrapper-name(parm0, parm1, ..., parmN)
     </pre>
     </div>
 
-<H4><a name="Allegrocl_nn38">19.4.1.2 OUT Typemap</a></H4>
+<H4><a name="Allegrocl_nn38">20.4.1.2 OUT Typemap</a></H4>
 
 
     <p>
@@ -1752,7 +1752,7 @@ return-val wrapper-name(parm0, parm1, ..., parmN)
     </pre>
     </div>
 
-<H4><a name="Allegrocl_nn39">19.4.1.3 CTYPE Typemap</a></H4>
+<H4><a name="Allegrocl_nn39">20.4.1.3 CTYPE Typemap</a></H4>
 
 
     <p>
@@ -1784,7 +1784,7 @@ return-val wrapper-name(parm0, parm1, ..., parmN)
       these <a href="Typemaps.html#Typemaps_nn25">common typemaps</a> here.
     </p>
 
-<H3><a name="Allegrocl_nn40">19.4.2 Code generation in Lisp wrappers</a></H3>
+<H3><a name="Allegrocl_nn40">20.4.2 Code generation in Lisp wrappers</a></H3>
 
 
     <p>
@@ -1803,7 +1803,7 @@ return-val wrapper-name(parm0, parm1, ..., parmN)
       <a href="#Allegrocl_nn15">16.3.1 Namespaces</a> for details.
     </p>
 
-<H4><a name="Allegrocl_nn41">19.4.2.1 LIN Typemap</a></H4>
+<H4><a name="Allegrocl_nn41">20.4.2.1 LIN Typemap</a></H4>
 
 
     <p>
@@ -1846,7 +1846,7 @@ return-val wrapper-name(parm0, parm1, ..., parmN)
     </pre>
     </div>
 
-<H4><a name="Allegrocl_nn42">19.4.2.2 LOUT Typemap</a></H4>
+<H4><a name="Allegrocl_nn42">20.4.2.2 LOUT Typemap</a></H4>
 
 
     <p>
@@ -1889,7 +1889,7 @@ return-val wrapper-name(parm0, parm1, ..., parmN)
     </pre>
     </div>
 
-<H4><a name="Allegrocl_nn43">19.4.2.3 FFITYPE Typemap</a></H4>
+<H4><a name="Allegrocl_nn43">20.4.2.3 FFITYPE Typemap</a></H4>
 
 
     
@@ -1939,7 +1939,7 @@ return-val wrapper-name(parm0, parm1, ..., parmN)
     </pre>
     </div>
 
-<H4><a name="Allegrocl_nn44">19.4.2.4 LISPTYPE Typemap</a></H4>
+<H4><a name="Allegrocl_nn44">20.4.2.4 LISPTYPE Typemap</a></H4>
 
 
     <p>
@@ -1959,7 +1959,7 @@ return-val wrapper-name(parm0, parm1, ..., parmN)
     </pre>
     </div>
 
-<H4><a name="Allegrocl_nn45">19.4.2.5 LISPCLASS Typemap</a></H4>
+<H4><a name="Allegrocl_nn45">20.4.2.5 LISPCLASS Typemap</a></H4>
 
 
     <p>
@@ -1983,7 +1983,7 @@ return-val wrapper-name(parm0, parm1, ..., parmN)
     </pre>
     </div>
 
-<H3><a name="Allegrocl_nn46">19.4.3 Modifying SWIG behavior using typemaps</a></H3>
+<H3><a name="Allegrocl_nn46">20.4.3 Modifying SWIG behavior using typemaps</a></H3>
 
 
     <p>
@@ -2017,10 +2017,10 @@ return-val wrapper-name(parm0, parm1, ..., parmN)
     </pre>
     </div>
 
-<H2><a name="Allegrocl_nn47">19.5 Identifier Converter functions</a></H2>
+<H2><a name="Allegrocl_nn47">20.5 Identifier Converter functions</a></H2>
 
 
-<H3><a name="Allegrocl_nn48">19.5.1 Creating symbols in the lisp environment</a></H3>
+<H3><a name="Allegrocl_nn48">20.5.1 Creating symbols in the lisp environment</a></H3>
 
 
 <p>
@@ -2041,11 +2041,11 @@ return-val wrapper-name(parm0, parm1, ..., parmN)
   of arguments.
 </p>
 
-<H3><a name="Allegrocl_nn49">19.5.2 Existing identifier-converter functions</a></H3>
+<H3><a name="Allegrocl_nn49">20.5.2 Existing identifier-converter functions</a></H3>
 
 
   <p>Two basic identifier routines have been defined.
-<H4><a name="Allegrocl_nn50">19.5.2.1 identifier-convert-null</a></H4>
+<H4><a name="Allegrocl_nn50">20.5.2.1 identifier-convert-null</a></H4>
 
 
     <p>
@@ -2054,7 +2054,7 @@ return-val wrapper-name(parm0, parm1, ..., parmN)
       strings, from which a symbol will be created.
     </p>
 
-<H4><a name="Allegrocl_nn51">19.5.2.2 identifier-convert-lispify</a></H4>
+<H4><a name="Allegrocl_nn51">20.5.2.2 identifier-convert-lispify</a></H4>
 
 
     <p>
@@ -2063,7 +2063,7 @@ return-val wrapper-name(parm0, parm1, ..., parmN)
       same symbol transformations.
     </p>
 
-<H4><a name="Allegrocl_nn52">19.5.2.3 Default identifier to symbol conversions</a></H4>
+<H4><a name="Allegrocl_nn52">20.5.2.3 Default identifier to symbol conversions</a></H4>
 
 
     <p>
@@ -2072,7 +2072,7 @@ return-val wrapper-name(parm0, parm1, ..., parmN)
       default naming conventions.
     </p>
 
-<H3><a name="Allegrocl_nn53">19.5.3 Defining your own identifier-converter</a></H3>
+<H3><a name="Allegrocl_nn53">20.5.3 Defining your own identifier-converter</a></H3>
 
 
 <p>
@@ -2128,7 +2128,7 @@ indicating the number of arguments passed to the routine indicated by
 this identifier.
 </p>
 
-<H3><a name="Allegrocl_nn54">19.5.4 Instructing SWIG to use a particular identifier-converter</a></H3>
+<H3><a name="Allegrocl_nn54">20.5.4 Instructing SWIG to use a particular identifier-converter</a></H3>
 
 
 <p>
diff --git a/Doc/Manual/Android.html b/Doc/Manual/Android.html
index cc11ec26e..894724188 100644
--- a/Doc/Manual/Android.html
+++ b/Doc/Manual/Android.html
@@ -6,7 +6,7 @@
 <meta http-equiv="content-type" content="text/html; charset=UTF-8">
 </head>
 <body bgcolor="#FFFFFF">
-<H1><a name="Android">20 SWIG and Android</a></H1>
+<H1><a name="Android">21 SWIG and Android</a></H1>
 <!-- INDEX -->
 <div class="sectiontoc">
 <ul>
@@ -31,7 +31,7 @@ This chapter describes SWIG's support of Android.
 
 
 
-<H2><a name="Android_overview">20.1 Overview</a></H2>
+<H2><a name="Android_overview">21.1 Overview</a></H2>
 
 
 <p>
@@ -41,10 +41,10 @@ Everything in the <a href="Java.html#Java">Java chapter</a> applies to generatin
 This chapter contains a few Android specific notes and examples.
 </p>
 
-<H2><a name="Android_examples">20.2 Android examples</a></H2>
+<H2><a name="Android_examples">21.2 Android examples</a></H2>
 
 
-<H3><a name="Android_examples_intro">20.2.1 Examples introduction</a></H3>
+<H3><a name="Android_examples_intro">21.2.1 Examples introduction</a></H3>
 
 
 <p>
@@ -77,7 +77,7 @@ $ android list targets
 The following examples are shipped with SWIG under the Examples/android directory and include a Makefile to build and install each example.
 </p>
 
-<H3><a name="Android_example_simple">20.2.2 Simple C example</a></H3>
+<H3><a name="Android_example_simple">21.2.2 Simple C example</a></H3>
 
 
 <p>
@@ -399,7 +399,7 @@ Run the app again and this time you will see the output pictured below, showing
 <center><img src="android-simple.png" alt="Android screenshot of SwigSimple example"></center>
 
 
-<H3><a name="Android_example_class">20.2.3 C++ class example</a></H3>
+<H3><a name="Android_example_class">21.2.3 C++ class example</a></H3>
 
 
 <p>
@@ -747,7 +747,7 @@ Run the app to see the result of calling the C++ code from Java:
 
 <center><img src="android-class.png" alt="Android screenshot of SwigClass example"></center>
 
-<H3><a name="Android_examples_other">20.2.4 Other examples</a></H3>
+<H3><a name="Android_examples_other">21.2.4 Other examples</a></H3>
 
 
 <p>
@@ -759,7 +759,7 @@ Note that the 'extend' example is demonstrates the directors feature.
 Normally C++ exception handling and the STL is not available by default in the version of g++ shipped with Android, but this example turns these features on as described in the next section.
 </p>
 
-<H2><a name="Android_stl">20.3 C++ STL</a></H2>
+<H2><a name="Android_stl">21.3 C++ STL</a></H2>
 
 
 <p>
diff --git a/Doc/Manual/CCache.html b/Doc/Manual/CCache.html
index 77b54e31a..6923b2e95 100644
--- a/Doc/Manual/CCache.html
+++ b/Doc/Manual/CCache.html
@@ -7,7 +7,7 @@
 </head>
 
 <body bgcolor="#ffffff">
-<H1><a name="CCache">18 Using SWIG with ccache - ccache-swig(1) manpage</a></H1>
+<H1><a name="CCache">19 Using SWIG with ccache - ccache-swig(1) manpage</a></H1>
 <!-- INDEX -->
 <div class="sectiontoc">
 <ul>
@@ -35,7 +35,7 @@
 
 
 <p>
-<H2><a name="CCache_nn2">18.1 NAME</a></H2>
+<H2><a name="CCache_nn2">19.1 NAME</a></H2>
 
 
 <p>
@@ -43,7 +43,7 @@
 ccache-swig - a fast compiler cache
 
 <p>
-<H2><a name="CCache_nn3">18.2 SYNOPSIS</a></H2>
+<H2><a name="CCache_nn3">19.2 SYNOPSIS</a></H2>
 
 
 <p>
@@ -53,7 +53,7 @@ ccache-swig &lt;compiler&gt; [COMPILER OPTIONS]
 <p>
 &lt;compiler&gt; [COMPILER OPTIONS]
 <p>
-<H2><a name="CCache_nn4">18.3 DESCRIPTION</a></H2>
+<H2><a name="CCache_nn4">19.3 DESCRIPTION</a></H2>
 
 
 <p>
@@ -62,7 +62,7 @@ by caching previous compiles and detecting when the same compile is
 being done again. ccache-swig is ccache plus support for SWIG. ccache
 and ccache-swig are used interchangeably in this document.
 <p>
-<H2><a name="CCache_nn5">18.4 OPTIONS SUMMARY</a></H2>
+<H2><a name="CCache_nn5">19.4 OPTIONS SUMMARY</a></H2>
 
 
 <p>
@@ -82,7 +82,7 @@ Here is a summary of the options to ccache-swig.
 </pre>
 
 <p>
-<H2><a name="CCache_nn6">18.5 OPTIONS</a></H2>
+<H2><a name="CCache_nn6">19.5 OPTIONS</a></H2>
 
 
 <p>
@@ -124,7 +124,7 @@ rounded down to the nearest multiple of 16 kilobytes.
 <p>
 </dl>
 <p>
-<H2><a name="CCache_nn7">18.6 INSTALLATION</a></H2>
+<H2><a name="CCache_nn7">19.6 INSTALLATION</a></H2>
 
 
 <p>
@@ -156,7 +156,7 @@ This will work as long as /usr/local/bin comes before the path to gcc
 Note! Do not use a hard link, use a symbolic link. A hardlink will
 cause "interesting" problems.
 <p>
-<H2><a name="CCache_nn8">18.7 EXTRA OPTIONS</a></H2>
+<H2><a name="CCache_nn8">19.7 EXTRA OPTIONS</a></H2>
 
 
 <p>
@@ -176,7 +176,7 @@ file). By using --ccache-skip you can force an option to not be
 treated as an input file name and instead be passed along to the
 compiler as a command line option.
 <p>
-<H2><a name="CCache_nn9">18.8 ENVIRONMENT VARIABLES</a></H2>
+<H2><a name="CCache_nn9">19.8 ENVIRONMENT VARIABLES</a></H2>
 
 
 <p>
@@ -315,7 +315,7 @@ the use of '#pragma SWIG'.
 <p>
 </dl>
 <p>
-<H2><a name="CCache_nn10">18.9 CACHE SIZE MANAGEMENT</a></H2>
+<H2><a name="CCache_nn10">19.9 CACHE SIZE MANAGEMENT</a></H2>
 
 
 <p>
@@ -328,7 +328,7 @@ When these limits are reached ccache will reduce the cache to 20%
 below the numbers you specified in order to avoid doing the cache
 clean operation too often.
 <p>
-<H2><a name="CCache_nn11">18.10 CACHE COMPRESSION</a></H2>
+<H2><a name="CCache_nn11">19.10 CACHE COMPRESSION</a></H2>
 
 
 <p>
@@ -339,7 +339,7 @@ performance slowdown, it significantly increases the number of files
 that fit in the cache. You can turn off compression setting the
 CCACHE_NOCOMPRESS environment variable.
 <p>
-<H2><a name="CCache_nn12">18.11 HOW IT WORKS</a></H2>
+<H2><a name="CCache_nn12">19.11 HOW IT WORKS</a></H2>
 
 
 <p>
@@ -364,7 +364,7 @@ compiler output that you would get without the cache. If you ever
 discover a case where ccache changes the output of your compiler then
 please let me know.
 <p>
-<H2><a name="CCache_nn13">18.12 USING CCACHE WITH DISTCC</a></H2>
+<H2><a name="CCache_nn13">19.12 USING CCACHE WITH DISTCC</a></H2>
 
 
 <p>
@@ -378,7 +378,7 @@ option. You just need to set the environment variable CCACHE_PREFIX to
 'distcc' and ccache will prefix the command line used with the
 compiler with the command 'distcc'.
 <p>
-<H2><a name="CCache_nn14">18.13 SHARING A CACHE</a></H2>
+<H2><a name="CCache_nn14">19.13 SHARING A CACHE</a></H2>
 
 
 <p>
@@ -407,7 +407,7 @@ following conditions need to be met:
   versions of ccache that do not support compression.
 </ul>
 <p>
-<H2><a name="CCache_nn15">18.14 HISTORY</a></H2>
+<H2><a name="CCache_nn15">19.14 HISTORY</a></H2>
 
 
 <p>
@@ -423,7 +423,7 @@ I wrote ccache because I wanted to get a bit more speed out of a
 compiler cache and I wanted to remove some of the limitations of the
 shell-script version.
 <p>
-<H2><a name="CCache_nn16">18.15 DIFFERENCES FROM COMPILERCACHE</a></H2>
+<H2><a name="CCache_nn16">19.15 DIFFERENCES FROM COMPILERCACHE</a></H2>
 
 
 <p>
@@ -441,7 +441,7 @@ are:
 <li> ccache avoids a double call to cpp on a cache miss
 </ul>
 <p>
-<H2><a name="CCache_nn17">18.16 CREDITS</a></H2>
+<H2><a name="CCache_nn17">19.16 CREDITS</a></H2>
 
 
 <p>
@@ -453,7 +453,7 @@ Thanks to the following people for their contributions to ccache
  <li> Paul Russell for many suggestions and the debian packaging
 </ul>
 <p>
-<H2><a name="CCache_nn18">18.17 AUTHOR</a></H2>
+<H2><a name="CCache_nn18">19.17 AUTHOR</a></H2>
 
 
 <p>
diff --git a/Doc/Manual/CSharp.html b/Doc/Manual/CSharp.html
index 85d651fd1..58d058a19 100644
--- a/Doc/Manual/CSharp.html
+++ b/Doc/Manual/CSharp.html
@@ -6,7 +6,7 @@
 <meta http-equiv="content-type" content="text/html; charset=UTF-8">
 </head>
 <body bgcolor="#FFFFFF">
-<H1><a name="CSharp">21 SWIG and C#</a></H1>
+<H1><a name="CSharp">22 SWIG and C#</a></H1>
 <!-- INDEX -->
 <div class="sectiontoc">
 <ul>
@@ -55,7 +55,7 @@
 
 
 
-<H2><a name="CSharp_introduction">21.1 Introduction</a></H2>
+<H2><a name="CSharp_introduction">22.1 Introduction</a></H2>
 
 
 <p>
@@ -75,7 +75,7 @@ The <a href="http://msdn.microsoft.com">Microsoft Developer Network (MSDN)</a> h
 Monodoc, available from the Mono project, has a very useful section titled <a href="http://www.mono-project.com/docs/advanced/pinvoke/">Interop with native libraries</a>.
 </p>
 
-<H3><a name="CSharp_introduction_swig2_compatibility">21.1.1 SWIG 2 Compatibility</a></H3>
+<H3><a name="CSharp_introduction_swig2_compatibility">22.1.1 SWIG 2 Compatibility</a></H3>
 
 
 <p>
@@ -83,7 +83,7 @@ In order to minimize name collisions between names generated based on input to S
 </p>
 
 
-<H3><a name="CSharp_commandline">21.1.2 Additional command line options</a></H3>
+<H3><a name="CSharp_commandline">22.1.2 Additional command line options</a></H3>
 
 
 <p>
@@ -135,7 +135,7 @@ Note that the file extension (.cs) will not be automatically added and needs to
 Due to possible compiler limits it is not advisable to use <tt>-outfile</tt> for large projects.
 </p>
 
-<H2><a name="CSharp_differences_java">21.2 Differences to the Java module</a></H2>
+<H2><a name="CSharp_differences_java">22.2 Differences to the Java module</a></H2>
 
 
 <p>
@@ -556,7 +556,7 @@ Windows users can also get the examples working using a
 <a href="http://www.cygwin.com">Cygwin</a> or <a href="http://www.mingw.org">MinGW</a> environment for automatic configuration of the example makefiles.
 Any one of the C# compilers (Mono or Microsoft) can be detected from within a Cygwin or Mingw environment if installed in your path. 
 
-<H2><a name="CSharp_void_pointers">21.3 Void pointers</a></H2>
+<H2><a name="CSharp_void_pointers">22.3 Void pointers</a></H2>
 
 
 <p>
@@ -574,7 +574,7 @@ void * f(void *v);
 </pre>
 </div>
 
-<H2><a name="CSharp_arrays">21.4 C# Arrays</a></H2>
+<H2><a name="CSharp_arrays">22.4 C# Arrays</a></H2>
 
 
 <p>
@@ -586,7 +586,7 @@ with one of the following three approaches; namely the SWIG C arrays library, P/
 pinned arrays.
 </p>
 
-<H3><a name="CSharp_arrays_swig_library">21.4.1 The SWIG C arrays library</a></H3>
+<H3><a name="CSharp_arrays_swig_library">22.4.1 The SWIG C arrays library</a></H3>
 
 
 <p>
@@ -623,7 +623,7 @@ example.print_array(c.cast());          // Pass to C
 </div>
 
 
-<H3><a name="CSharp_arrays_pinvoke_default_array_marshalling">21.4.2 Managed arrays using P/Invoke default array marshalling</a></H3>
+<H3><a name="CSharp_arrays_pinvoke_default_array_marshalling">22.4.2 Managed arrays using P/Invoke default array marshalling</a></H3>
 
 
 <p>
@@ -750,7 +750,7 @@ and intermediary class method
 </div>
 
 
-<H3><a name="CSharp_arrays_pinning">21.4.3 Managed arrays using pinning</a></H3>
+<H3><a name="CSharp_arrays_pinning">22.4.3 Managed arrays using pinning</a></H3>
 
 
 <p>
@@ -845,7 +845,7 @@ public static extern void myArrayCopy(global::System.IntPtr jarg1, global::Syste
 
 
 
-<H2><a name="CSharp_exceptions">21.5 C# Exceptions</a></H2>
+<H2><a name="CSharp_exceptions">22.5 C# Exceptions</a></H2>
 
 
 <p>
@@ -942,7 +942,7 @@ set so should only be used when a C# exception is not created.
 </p>
 
 
-<H3><a name="CSharp_exception_example_check_typemap">21.5.1 C# exception example using "check" typemap</a></H3>
+<H3><a name="CSharp_exception_example_check_typemap">22.5.1 C# exception example using "check" typemap</a></H3>
 
 
 <p>
@@ -1124,7 +1124,7 @@ method and C# code does not handle pending exceptions via the canthrow attribute
 Actually it will issue this warning for any function beginning with <tt>SWIG_CSharpSetPendingException</tt>.
 </P>
 
-<H3><a name="CSharp_exception_example_percent_exception">21.5.2 C# exception example using %exception</a></H3>
+<H3><a name="CSharp_exception_example_percent_exception">22.5.2 C# exception example using %exception</a></H3>
 
 
 <p>
@@ -1189,7 +1189,7 @@ The managed code generated does check for the pending exception as mentioned ear
 </pre>
 </div>
 
-<H3><a name="CSharp_exception_example_exception_specifications">21.5.3 C# exception example using exception specifications</a></H3>
+<H3><a name="CSharp_exception_example_exception_specifications">22.5.3 C# exception example using exception specifications</a></H3>
 
 
 <p>
@@ -1245,7 +1245,7 @@ SWIGEXPORT void SWIGSTDCALL CSharp_evensonly(int jarg1) {
 Multiple catch handlers are generated should there be more than one exception specifications declared.
 </p>
 
-<H3><a name="CSharp_custom_application_exception">21.5.4 Custom C# ApplicationException example</a></H3>
+<H3><a name="CSharp_custom_application_exception">22.5.4 Custom C# ApplicationException example</a></H3>
 
 
 <p>
@@ -1379,7 +1379,7 @@ try {
 </pre>
 </div>
 
-<H2><a name="CSharp_directors">21.6 C# Directors</a></H2>
+<H2><a name="CSharp_directors">22.6 C# Directors</a></H2>
 
 
 <p>
@@ -1392,7 +1392,7 @@ The following sections provide information on the C# director implementation and
 However, the <a href="Java.html#Java_directors">Java directors</a> section should also be read in order to gain more insight into directors.
 </p>
 
-<H3><a name="CSharp_directors_example">21.6.1 Directors example</a></H3>
+<H3><a name="CSharp_directors_example">22.6.1 Directors example</a></H3>
 
 
 <p>
@@ -1513,7 +1513,7 @@ CSharpDerived - UIntMethod(123)
 </pre>
 </div>
 
-<H3><a name="CSharp_directors_implementation">21.6.2 Directors implementation</a></H3>
+<H3><a name="CSharp_directors_implementation">22.6.2 Directors implementation</a></H3>
 
 
 <p>
@@ -1721,7 +1721,7 @@ before SWIG parses the Base class will change all the delegates to <tt>internal<
 </pre>
 </div>
 
-<H3><a name="CSharp_director_caveats">21.6.3 Director caveats</a></H3>
+<H3><a name="CSharp_director_caveats">22.6.3 Director caveats</a></H3>
 
 
 <p>
@@ -1769,7 +1769,7 @@ However, a call from C# to <tt>CSharpDefaults.DefaultMethod()</tt> will of cours
 should pass the call on to <tt>CSharpDefaults.DefaultMethod(int)</tt>using the C++ default value, as shown above.
 </p>
 
-<H2><a name="CSharp_multiple_modules">21.7 Multiple modules</a></H2>
+<H2><a name="CSharp_multiple_modules">22.7 Multiple modules</a></H2>
 
 
 <p>
@@ -1804,7 +1804,7 @@ the <tt>[System.ComponentModel.EditorBrowsable(System.ComponentModel.EditorBrows
 if you don't want users to easily stumble upon these so called 'internal workings' of the wrappers.
 </p>
 
-<H2><a name="CSharp_typemap_examples">21.8 C# Typemap examples</a></H2>
+<H2><a name="CSharp_typemap_examples">22.8 C# Typemap examples</a></H2>
 
 
 This section includes a few examples of typemaps.  For more examples, you
@@ -1812,7 +1812,7 @@ might look at the files "<tt>csharp.swg</tt>" and "<tt>typemaps.i</tt>" in
 the SWIG library.
 
 
-<H3><a name="CSharp_memory_management_member_variables">21.8.1 Memory management when returning references to member variables</a></H3>
+<H3><a name="CSharp_memory_management_member_variables">22.8.1 Memory management when returning references to member variables</a></H3>
 
 
 <p>
@@ -1936,7 +1936,7 @@ public class Bike : global::System.IDisposable {
 Note the <tt>addReference</tt> call.
 </p>
 
-<H3><a name="CSharp_memory_management_objects">21.8.2 Memory management for objects passed to the C++ layer</a></H3>
+<H3><a name="CSharp_memory_management_objects">22.8.2 Memory management for objects passed to the C++ layer</a></H3>
 
 
 <p>
@@ -2068,7 +2068,7 @@ as mentioned earlier, <tt>setElement</tt> is actually:
 </div>
 
 
-<H3><a name="CSharp_date_marshalling">21.8.3 Date marshalling using the csin typemap and associated attributes</a></H3>
+<H3><a name="CSharp_date_marshalling">22.8.3 Date marshalling using the csin typemap and associated attributes</a></H3>
 
 
 <p>
@@ -2354,7 +2354,7 @@ public class example {
 </pre>
 </div>
 
-<H3><a name="CSharp_date_properties">21.8.4 A date example demonstrating marshalling of C# properties</a></H3>
+<H3><a name="CSharp_date_properties">22.8.4 A date example demonstrating marshalling of C# properties</a></H3>
 
 
 <p>
@@ -2454,7 +2454,7 @@ Some points to note:
   <li>The 'csin' typemap has 'pre', 'post' and 'cshin' attributes, and these are all ignored in the property set. The code in these attributes must instead be replicated within the 'csvarin' typemap. The line creating the <tt>temp$csinput</tt> variable is such an example; it is identical to what is in the 'pre' attribute.
 </ul>
 
-<H3><a name="CSharp_date_pre_post_directors">21.8.5 Date example demonstrating the 'pre' and 'post' typemap attributes for directors</a></H3>
+<H3><a name="CSharp_date_pre_post_directors">22.8.5 Date example demonstrating the 'pre' and 'post' typemap attributes for directors</a></H3>
 
 
 <p>
@@ -2516,7 +2516,7 @@ Pay special attention to the memory management issues, using these attributes.
 </p>
 
 
-<H3><a name="CSharp_partial_classes">21.8.6 Turning proxy classes into partial classes</a></H3>
+<H3><a name="CSharp_partial_classes">22.8.6 Turning proxy classes into partial classes</a></H3>
 
 
 <p>
@@ -2616,7 +2616,7 @@ demonstrating that the class contains methods calling both unmanaged code - <tt>
 The following example is an alternative approach to adding managed code to the generated proxy class.
 </p>
 
-<H3><a name="CSharp_sealed_proxy_class">21.8.7 Turning proxy classes into sealed classes</a></H3>
+<H3><a name="CSharp_sealed_proxy_class">22.8.7 Turning proxy classes into sealed classes</a></H3>
 
 
 <p>
@@ -2706,7 +2706,7 @@ Either suppress the warning or modify the generated code by copying and tweaking
 'csbody' typemap code in csharp.swg by modifying swigCMemOwn to not be protected.
 </p>
 
-<H3><a name="CSharp_extending_proxy_class">21.8.8 Extending proxy classes with additional C# code</a></H3>
+<H3><a name="CSharp_extending_proxy_class">22.8.8 Extending proxy classes with additional C# code</a></H3>
 
 
 <p>
@@ -2745,7 +2745,7 @@ public class ExtendMe : global::System.IDisposable {
 </pre>
 </div>
 
-<H3><a name="CSharp_enum_underlying_type">21.8.9 Underlying type for enums</a></H3>
+<H3><a name="CSharp_enum_underlying_type">22.8.9 Underlying type for enums</a></H3>
 
 
 <P>
diff --git a/Doc/Manual/Chicken.html b/Doc/Manual/Chicken.html
index bf34ae507..3a80811bd 100644
--- a/Doc/Manual/Chicken.html
+++ b/Doc/Manual/Chicken.html
@@ -8,7 +8,7 @@
 
 <body bgcolor="#ffffff">
 
-<H1><a name="Chicken">22 SWIG and Chicken</a></H1>
+<H1><a name="Chicken">23 SWIG and Chicken</a></H1>
 <!-- INDEX -->
 <div class="sectiontoc">
 <ul>
@@ -72,7 +72,7 @@
 
     </p>
 
-<H2><a name="Chicken_nn2">22.1 Preliminaries</a></H2>
+<H2><a name="Chicken_nn2">23.1 Preliminaries</a></H2>
 
 
     <p>
@@ -89,7 +89,7 @@
       directory for the basic steps to run SWIG CHICKEN.
       </p>
 
-<H3><a name="Chicken_nn3">22.1.1 Running SWIG in C mode</a></H3>
+<H3><a name="Chicken_nn3">23.1.1 Running SWIG in C mode</a></H3>
 
 
       <p>
@@ -122,7 +122,7 @@
       object files and linked into your project.
       </p>
 
-<H3><a name="Chicken_nn4">22.1.2 Running SWIG in C++ mode</a></H3>
+<H3><a name="Chicken_nn4">23.1.2 Running SWIG in C++ mode</a></H3>
 
 
       <p>
@@ -151,10 +151,10 @@
       object files and linked into your project.
       </p>
 
-<H2><a name="Chicken_nn5">22.2 Code Generation</a></H2>
+<H2><a name="Chicken_nn5">23.2 Code Generation</a></H2>
 
 
-<H3><a name="Chicken_nn6">22.2.1 Naming Conventions</a></H3>
+<H3><a name="Chicken_nn6">23.2.1 Naming Conventions</a></H3>
 
 
     <p>
@@ -170,7 +170,7 @@
       <tt>%rename</tt> SWIG directive in the SWIG interface file.
     </p>
 
-<H3><a name="Chicken_nn7">22.2.2 Modules</a></H3>
+<H3><a name="Chicken_nn7">23.2.2 Modules</a></H3>
 
 
       <p>
@@ -192,7 +192,7 @@
         (uses <i>modulename</i>))</code> CHICKEN Scheme form.
     </p>
 
-<H3><a name="Chicken_nn8">22.2.3 Constants and Variables</a></H3>
+<H3><a name="Chicken_nn8">23.2.3 Constants and Variables</a></H3>
 
 
     <p>
@@ -229,7 +229,7 @@
       for info on how to apply the %feature.
     </p>
 
-<H3><a name="Chicken_nn9">22.2.4 Functions</a></H3>
+<H3><a name="Chicken_nn9">23.2.4 Functions</a></H3>
 
 
     <p>
@@ -248,7 +248,7 @@
       parameters).  The return values can then be accessed with <code>(call-with-values)</code>.
     </p>
 
-<H3><a name="Chicken_nn10">22.2.5 Exceptions</a></H3>
+<H3><a name="Chicken_nn10">23.2.5 Exceptions</a></H3>
 
 
      <p>The SWIG chicken module has support for exceptions thrown from
@@ -290,7 +290,7 @@
 </pre></div>
 
 
-<H2><a name="Chicken_nn11">22.3 TinyCLOS</a></H2>
+<H2><a name="Chicken_nn11">23.3 TinyCLOS</a></H2>
 
 
       <p>
@@ -333,7 +333,7 @@
       
       </p>
 
-<H2><a name="Chicken_nn12">22.4 Linkage</a></H2>
+<H2><a name="Chicken_nn12">23.4 Linkage</a></H2>
 
 
     <p>
@@ -354,7 +354,7 @@
    </p>
 
 
-<H3><a name="Chicken_nn13">22.4.1 Static binary or shared library linked at compile time</a></H3>
+<H3><a name="Chicken_nn13">23.4.1 Static binary or shared library linked at compile time</a></H3>
 
 
    <p>We can easily use csc to build a static binary.</p>
@@ -395,7 +395,7 @@ in which case the test script does not need to be linked with example.so.  The t
 be run with <tt>csi</tt>.
 </p>
 
-<H3><a name="Chicken_nn14">22.4.2 Building chicken extension libraries</a></H3>
+<H3><a name="Chicken_nn14">23.4.2 Building chicken extension libraries</a></H3>
 
 
 <p>Building a shared library like in the above section only works if the library
@@ -453,7 +453,7 @@ distributed and used by anyone, even if SWIG is not installed.</p>
 <p>See the <tt>Examples/chicken/egg</tt> directory in the SWIG source for an example that builds
 two eggs, one using the first method and one using the second method.</p>
 
-<H3><a name="Chicken_nn15">22.4.3 Linking multiple SWIG modules with TinyCLOS</a></H3>
+<H3><a name="Chicken_nn15">23.4.3 Linking multiple SWIG modules with TinyCLOS</a></H3>
 
 
 <p>Linking together multiple modules that share type information using the <code>%import</code>
@@ -477,7 +477,7 @@ with <code>(declare (uses ...))</code>.
 To create an extension library or an egg, just create a <tt>module_load.scm</tt> file that <code>(declare (uses ...))</code>
 all the modules.</p>
 
-<H2><a name="Chicken_nn16">22.5 Typemaps</a></H2>
+<H2><a name="Chicken_nn16">23.5 Typemaps</a></H2>
 
 
     <p>
@@ -486,7 +486,7 @@ all the modules.</p>
       <code>Lib/chicken/chicken.swg</code>.
     </p>
 
-<H2><a name="Chicken_nn17">22.6 Pointers</a></H2>
+<H2><a name="Chicken_nn17">23.6 Pointers</a></H2>
 
 
     <p>
@@ -519,7 +519,7 @@ all the modules.</p>
       type. flags is either zero or SWIG_POINTER_DISOWN (see below).
     </p>
 
-<H3><a name="Chicken_collection">22.6.1 Garbage collection</a></H3>
+<H3><a name="Chicken_collection">23.6.1 Garbage collection</a></H3>
 
 
   <p>If the owner flag passed to <code>SWIG_NewPointerObj</code> is 1, <code>NewPointerObj</code> will add a
@@ -550,7 +550,7 @@ all the modules.</p>
   must be called manually.
   </p>
 
-<H2><a name="Chicken_nn18">22.7 Unsupported features and known problems</a></H2>
+<H2><a name="Chicken_nn18">23.7 Unsupported features and known problems</a></H2>
 
 
     <ul>
@@ -560,7 +560,7 @@ all the modules.</p>
           <a href="SWIGPlus.html#SWIGPlus_default_args">%feature(compactdefaultargs)</a>.</li>
     </ul>
 
-<H3><a name="Chicken_nn19">22.7.1 TinyCLOS problems with Chicken version &lt;= 1.92</a></H3>
+<H3><a name="Chicken_nn19">23.7.1 TinyCLOS problems with Chicken version &lt;= 1.92</a></H3>
 
 
     <p>In Chicken versions equal to or below 1.92, TinyCLOS has a limitation such that generic methods do not properly work on methods
diff --git a/Doc/Manual/Contents.html b/Doc/Manual/Contents.html
index b8909322c..b7de00077 100644
--- a/Doc/Manual/Contents.html
+++ b/Doc/Manual/Contents.html
@@ -591,7 +591,51 @@
 </div>
 <!-- INDEX -->
 
-<h3><a href="Warnings.html#Warnings">16 Warning Messages</a></h3>
+<h3><a href="Doxygen.html#Doxygen">16 SWIG and Doxygen Translation</a></h3>
+
+<!-- INDEX -->
+<div class="sectiontoc">
+<ul>
+<li><a href="Doxygen.html#Doxygen_translation_overview">Doxygen translation overview</a>
+<li><a href="Doxygen.html#Doxygen_file_preparation">Preparations</a>
+<ul>
+<li><a href="Doxygen.html#Doxygen_running_swig">Enabling Doxygen translation</a>
+<li><a href="Doxygen.html#Doxygen_features">Doxygen-specific %feature directives</a>
+<ul>
+<li><a href="Doxygen.html#Doxygen_notranslate">doxygen:notranslate</a>
+<li><a href="Doxygen.html#Doxygen_alias">doxygen:alias:&lt;command-name&gt;</a>
+<li><a href="Doxygen.html#Doxygen_ignore">doxygen:ignore:&lt;command-name&gt;</a>
+<li><a href="Doxygen.html#Doxygen_nolinktranslate">doxygen:nolinktranslate (Java-only currently)</a>
+<li><a href="Doxygen.html#Doxygen_nostripparams">doxygen:nostripparams (Java-only currently)</a>
+</ul>
+<li><a href="Doxygen.html#Doxygen_additional_options">Additional command line options</a>
+</ul>
+<li><a href="Doxygen.html#Doxygen_to_javadoc">Doxygen to Javadoc</a>
+<ul>
+<li><a href="Doxygen.html#Doxygen_basic_example">Basic example</a>
+<li><a href="Doxygen.html#Doxygen_javadoc_tags">Javadoc tags</a>
+<li><a href="Doxygen.html#Doxygen_unsupported_tags">Unsupported tags</a>
+<li><a href="Doxygen.html#Doxygen_further_details">Further details</a>
+</ul>
+<li><a href="Doxygen.html#Doxygen_to_pydoc">Doxygen to Pydoc</a>
+<ul>
+<li><a href="Doxygen.html#Doxygen_python_basic_example">Basic example</a>
+<li><a href="Doxygen.html#Doxygen_pydoc_tags">Pydoc translator</a>
+<li><a href="Doxygen.html#Doxygen_python_unsupported_tags">Unsupported tags</a>
+<li><a href="Doxygen.html#Doxygen_python_further_details">Further details</a>
+</ul>
+<li><a href="Doxygen.html#Doxygen_developer_details">Developer information</a>
+<ul>
+<li><a href="Doxygen.html#Doxygen_translator_design">Doxygen translator design</a>
+<li><a href="Doxygen.html#Doxygen_debugging_commands">Debugging the Doxygen parser and translator</a>
+<li><a href="Doxygen.html#Doxygen_tests">Tests</a>
+</ul>
+<li><a href="Doxygen.html#Doxygen_language_extension">Extending to other languages</a>
+</ul>
+</div>
+<!-- INDEX -->
+
+<h3><a href="Warnings.html#Warnings">17 Warning Messages</a></h3>
 
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-<h3><a href="Modules.html#Modules">17 Working with Modules</a></h3>
+<h3><a href="Modules.html#Modules">18 Working with Modules</a></h3>
 
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-<h3><a href="CCache.html#CCache">18 Using SWIG with ccache - ccache-swig(1) manpage</a></h3>
+<h3><a href="CCache.html#CCache">19 Using SWIG with ccache - ccache-swig(1) manpage</a></h3>
 
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-<h3><a href="Allegrocl.html#Allegrocl">19 SWIG and Allegro Common Lisp</a></h3>
+<h3><a href="Allegrocl.html#Allegrocl">20 SWIG and Allegro Common Lisp</a></h3>
 
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-<h3><a href="Android.html#Android">20 SWIG and Android</a></h3>
+<h3><a href="Android.html#Android">21 SWIG and Android</a></h3>
 
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-<h3><a href="CSharp.html#CSharp">21 SWIG and C#</a></h3>
+<h3><a href="CSharp.html#CSharp">22 SWIG and C#</a></h3>
 
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-<h3><a href="Chicken.html#Chicken">22 SWIG and Chicken</a></h3>
+<h3><a href="Chicken.html#Chicken">23 SWIG and Chicken</a></h3>
 
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-<h3><a href="D.html#D">23 SWIG and D</a></h3>
+<h3><a href="D.html#D">24 SWIG and D</a></h3>
 
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-<h3><a href="Go.html#Go">24 SWIG and Go</a></h3>
+<h3><a href="Go.html#Go">25 SWIG and Go</a></h3>
 
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-<h3><a href="Guile.html#Guile">25 SWIG and Guile</a></h3>
+<h3><a href="Guile.html#Guile">26 SWIG and Guile</a></h3>
 
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-<h3><a href="Java.html#Java">26 SWIG and Java</a></h3>
+<h3><a href="Java.html#Java">27 SWIG and Java</a></h3>
 
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-<h3><a href="Javascript.html#Javascript">27 SWIG and Javascript</a></h3>
+<h3><a href="Javascript.html#Javascript">28 SWIG and Javascript</a></h3>
 
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-<h3><a href="Lisp.html#Lisp">28 SWIG and Common Lisp</a></h3>
+<h3><a href="Lisp.html#Lisp">29 SWIG and Common Lisp</a></h3>
 
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-<h3><a href="Lua.html#Lua">29 SWIG and Lua</a></h3>
+<h3><a href="Lua.html#Lua">30 SWIG and Lua</a></h3>
 
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-<h3><a href="Modula3.html#Modula3">30 SWIG and Modula-3</a></h3>
+<h3><a href="Modula3.html#Modula3">31 SWIG and Modula-3</a></h3>
 
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-<h3><a href="Mzscheme.html#Mzscheme">31 SWIG and MzScheme/Racket</a></h3>
+<h3><a href="Mzscheme.html#Mzscheme">32 SWIG and MzScheme/Racket</a></h3>
 
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-<h3><a href="Ocaml.html#Ocaml">32 SWIG and Ocaml</a></h3>
+<h3><a href="Ocaml.html#Ocaml">33 SWIG and Ocaml</a></h3>
 
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-<h3><a href="Octave.html#Octave">33 SWIG and Octave</a></h3>
+<h3><a href="Octave.html#Octave">34 SWIG and Octave</a></h3>
 
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-<h3><a href="Perl5.html#Perl5">34 SWIG and Perl5</a></h3>
+<h3><a href="Perl5.html#Perl5">35 SWIG and Perl5</a></h3>
 
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-<h3><a href="Php.html#Php">35 SWIG and PHP</a></h3>
+<h3><a href="Php.html#Php">36 SWIG and PHP</a></h3>
 
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-<h3><a href="Pike.html#Pike">36 SWIG and Pike</a></h3>
+<h3><a href="Pike.html#Pike">37 SWIG and Pike</a></h3>
 
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-<h3><a href="Python.html#Python">37 SWIG and Python</a></h3>
+<h3><a href="Python.html#Python">38 SWIG and Python</a></h3>
 
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-<h3><a href="R.html#R">38 SWIG and R</a></h3>
+<h3><a href="R.html#R">39 SWIG and R</a></h3>
 
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@@ -1684,7 +1728,7 @@
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-<h3><a href="Ruby.html#Ruby">39 SWIG and Ruby</a></h3>
+<h3><a href="Ruby.html#Ruby">40 SWIG and Ruby</a></h3>
 
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@@ -1822,7 +1866,7 @@
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-<h3><a href="Scilab.html#Scilab">40 SWIG and Scilab</a></h3>
+<h3><a href="Scilab.html#Scilab">41 SWIG and Scilab</a></h3>
 
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-<h3><a href="Tcl.html#Tcl">41 SWIG and Tcl</a></h3>
+<h3><a href="Tcl.html#Tcl">42 SWIG and Tcl</a></h3>
 
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-<h3><a href="Extending.html#Extending">42 Extending SWIG to support new languages</a></h3>
+<h3><a href="Extending.html#Extending">43 Extending SWIG to support new languages</a></h3>
 
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@@ -2025,42 +2069,6 @@
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-<h3><a href="Doxygen.html#Doxygen">40 SWIG and Doxygen Translation</a></h3>
-
-<!-- INDEX -->
-<div class="sectiontoc">
-<ul>
-<li><a href="Doxygen.html#Doxygen_translation_overview">Doxygen Translation Overview</a>
-<li><a href="Doxygen.html#Doxygen_file_preparation">Preparations</a>
-<ul>
-<li><a href="Doxygen.html#Doxygen_running_swig">Enabling Doxygen Translation</a>
-<li><a href="Doxygen.html#Doxygen_additional_options">Additional Commandline Options</a>
-</ul>
-<li><a href="Doxygen.html#Doxygen_to_javadoc">Doxygen To JavaDoc</a>
-<ul>
-<li><a href="Doxygen.html#Doxygen_basic_example">Basic Example</a>
-<li><a href="Doxygen.html#Doxygen_javadoc_tags">JavaDoc Tags</a>
-<li><a href="Doxygen.html#Doxygen_unsupported_tags">Unsupported tags</a>
-<li><a href="Doxygen.html#Doxygen_further_details">Further Details</a>
-</ul>
-<li><a href="Doxygen.html#Doxygen_to_pydoc">Doxygen To PythonDoc</a>
-<ul>
-<li><a href="Doxygen.html#Doxygen_python_basic_example">Basic Example</a>
-<li><a href="Doxygen.html#Doxygen_pydoc_tags">PyDoc translator</a>
-<li><a href="Doxygen.html#Doxygen_python_unsupported_tags">Unsupported tags</a>
-<li><a href="Doxygen.html#Doxygen_python_further_details">Further Details</a>
-</ul>
-<li><a href="Doxygen.html#Doxygen_developer_details">Developer Information</a>
-<ul>
-<li><a href="Doxygen.html#Doxygen_module_design">Module Design</a>
-<li><a href="Doxygen.html#Doxygen_debugging_commands">Debugging Doxygen parser and translator</a>
-<li><a href="Doxygen.html#Doxygen_debugging_commands">Tests</a>
-</ul>
-<li><a href="Doxygen.html#Doxygen_language_extension">Extending to Other Languages</a>
-</ul>
-</div>
-<!-- INDEX -->
-
 
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diff --git a/Doc/Manual/D.html b/Doc/Manual/D.html
index a252650ff..5a6ee8f28 100644
--- a/Doc/Manual/D.html
+++ b/Doc/Manual/D.html
@@ -6,7 +6,7 @@
 <meta http-equiv="content-type" content="text/html; charset=UTF-8">
 </head>
 <body bgcolor="#FFFFFF">
-<H1><a name="D">23 SWIG and D</a></H1>
+<H1><a name="D">24 SWIG and D</a></H1>
 <!-- INDEX -->
 <div class="sectiontoc">
 <ul>
@@ -41,7 +41,7 @@
 
 
 
-<H2><a name="D_introduction">23.1 Introduction</a></H2>
+<H2><a name="D_introduction">24.1 Introduction</a></H2>
 
 
 <p>From the <a href="http://www.digitalmars.com/d/">D Programming Language</a> web site: <em>D is a systems programming language. Its focus is on combining the power and high performance of C and C++ with the programmer productivity of modern languages like Ruby and Python. [...] The D language is statically typed and compiles directly to machine code.</em> As such, it is not very surprising that D is able to directly <a href="http://www.digitalmars.com/d/1.0/interfaceToC.html">interface with C libraries</a>. Why would a SWIG module for D be needed then in the first place?</p>
@@ -53,7 +53,7 @@
 <p>To help addressing these issues, the SWIG C# module has been forked to support D. Is has evolved quite a lot since then, but there are still many similarities, so if you do not find what you are looking for on this page, it might be worth having a look at the chapter on <a href="CSharp.html#CSharp">C#</a> (and also on <a href="Java.html#Java">Java</a>, since the C# module was in turn forked from it).</p>
 
 
-<H2><a name="D_command_line_invocation">23.2 Command line invocation</a></H2>
+<H2><a name="D_command_line_invocation">24.2 Command line invocation</a></H2>
 
 
 <p>To activate the D module, pass the <tt>-d</tt> option to SWIG at the command line. The same standard command line switches as with any other language module are available, plus the following D specific ones:</p>
@@ -83,10 +83,10 @@
 </dl>
 
 
-<H2><a name="D_typemaps">23.3 Typemaps</a></H2>
+<H2><a name="D_typemaps">24.3 Typemaps</a></H2>
 
 
-<H3><a name="D_typemap_name_comparison">23.3.1 C# &lt;-&gt; D name comparison</a></H3>
+<H3><a name="D_typemap_name_comparison">24.3.1 C# &lt;-&gt; D name comparison</a></H3>
 
 
 <p>If you already know the SWIG C# module, you might find the following name comparison table useful:</p>
@@ -112,7 +112,7 @@
 </pre></div>
 
 
-<H3><a name="D_ctype_imtype_dtype">23.3.2 ctype, imtype, dtype</a></H3>
+<H3><a name="D_ctype_imtype_dtype">24.3.2 ctype, imtype, dtype</a></H3>
 
 
 <p>Mapping of types between the C/C++ library, the C/C++ library wrapper exposing the C functions, the D wrapper module importing these functions and the D proxy code.</p>
@@ -120,7 +120,7 @@
 <p>The <tt>ctype</tt> typemap is used to determine the types to use in the C wrapper functions. The types from the <tt>imtype</tt> typemap are used in the extern(C) declarations of these functions in the intermediary D module. The <tt>dtype</tt> typemap contains the D types used in the D proxy module/class.</p>
 
 
-<H3><a name="D_in_out_directorin_direcetorout">23.3.3 in, out, directorin, directorout</a></H3>
+<H3><a name="D_in_out_directorin_direcetorout">24.3.3 in, out, directorin, directorout</a></H3>
 
 
 <p>Used for converting between the types for C/C++ and D when generating the code for the wrapper functions (on the C++ side).</p>
@@ -130,7 +130,7 @@
 <p>The <tt>directorin</tt> typemap is used to convert parameters to the type used in the D director callback function, its return value is processed by <tt>directorout</tt> (see below).</p>
 
 
-<H3><a name="D_din_dout_ddirectorin_ddirectorout">23.3.4 din, dout, ddirectorin, ddirectorout</a></H3>
+<H3><a name="D_din_dout_ddirectorin_ddirectorout">24.3.4 din, dout, ddirectorin, ddirectorout</a></H3>
 
 
 <p>Typemaps for code generation in D proxy and type wrapper classes.</p>
@@ -157,13 +157,13 @@
       dtype             DClass.method(dtype a)</pre></div>
 
 
-<H3><a name="D_typecheck_typemaps">23.3.5 typecheck typemaps</a></H3>
+<H3><a name="D_typecheck_typemaps">24.3.5 typecheck typemaps</a></H3>
 
 
 <p>Because, unlike many scripting languages supported by SWIG, D does not need any dynamic dispatch helper to access an overloaded function, the purpose of these is merely to issue a warning for overloaded C++ functions that cannot be overloaded in D (as more than one C++ type maps to a single D type).</p>
 
 
-<H3><a name="D_code_injection_typemaps">23.3.6 Code injection typemaps</a></H3>
+<H3><a name="D_code_injection_typemaps">24.3.6 Code injection typemaps</a></H3>
 
 
 <p>These typemaps are used for generating the skeleton of proxy classes for C++ types.</p>
@@ -178,7 +178,7 @@
 Code can also be injected into the D proxy class using <tt>%proxycode</tt>.
 </p>
 
-<H3><a name="D_special_variables">23.3.7 Special variable macros</a></H3>
+<H3><a name="D_special_variables">24.3.7 Special variable macros</a></H3>
 
 
 <p>The standard SWIG special variables are available for use within typemaps as described in the <a href="Typemaps.html#Typemaps">Typemaps documentation</a>, for example <tt>$1</tt>, <tt>$input</tt>, <tt>$result</tt> etc.</p>
@@ -299,7 +299,7 @@ $importtype(AnotherInterface)
 </dl>
 
 
-<H2><a name="D_features">23.4 D and %feature</a></H2>
+<H2><a name="D_features">24.4 D and %feature</a></H2>
 
 
 <p>The D module defines a number of directives which modify the <a href="Customization.html#Customization_features">SWIG features</a> set globally or for a specific declaration:</p>
@@ -329,7 +329,7 @@ struct A {
 </dl>
 
 
-<H2><a name="D_pragmas">23.5 Pragmas</a></H2>
+<H2><a name="D_pragmas">24.5 Pragmas</a></H2>
 
 
 <p>There are a few SWIG pragmas specific to the D module, which you can use to influence the D code SWIG generates:</p>
@@ -368,7 +368,7 @@ struct A {
 </dl>
 
 
-<H2><a name="D_exceptions">23.6 D Exceptions</a></H2>
+<H2><a name="D_exceptions">24.6 D Exceptions</a></H2>
 
 
 <p>Out of the box, C++ exceptions are fundamentally incompatible to their equivalent in the D world and cannot simply be propagated to a calling D method. There is, however, an easy way to solve this problem: Just catch the exception in the C/C++ wrapper layer, pass the contents to D, and make the wrapper code rethrow the exception in the D world.</p>
@@ -378,7 +378,7 @@ struct A {
 <p>As this feature is implemented in exactly the same way it is for C#, please see the <a href="CSharp.html#CSharp_exceptions">C# documentation</a> for a more detailed explanation.</p>
 
 
-<H2><a name="D_directors">23.7 D Directors</a></H2>
+<H2><a name="D_directors">24.7 D Directors</a></H2>
 
 
 <p>When the directors feature is activated, SWIG generates extra code on both the C++ and the D side to enable cross-language polymorphism. Essentially, this means that if you subclass a proxy class in D, C++ code can access any overridden virtual methods just as if you created a derived class in C++.</p>
@@ -387,16 +387,16 @@ struct A {
 </p>
 
 
-<H2><a name="D_other_features">23.8 Other features</a></H2>
+<H2><a name="D_other_features">24.8 Other features</a></H2>
 
 
-<H3><a name="D_nspace">23.8.1 Extended namespace support (nspace)</a></H3>
+<H3><a name="D_nspace">24.8.1 Extended namespace support (nspace)</a></H3>
 
 
 <p>By default, SWIG flattens all C++ namespaces into a single target language namespace, but as for Java and C#, the <a href="SWIGPlus.html#SWIGPlus_nspace"><tt>nspace</tt></a> feature is supported for D. If it is active, C++ namespaces are mapped to D packages/modules. Note, however, that like for the other languages, <em>free</em> variables and functions are not supported yet; currently, they are all allows written to the main proxy D module.</p>
 
 
-<H3><a name="D_native_pointer_support">23.8.2 Native pointer support</a></H3>
+<H3><a name="D_native_pointer_support">24.8.2 Native pointer support</a></H3>
 
 
 <p>Contrary to many of the scripting languages supported by SWIG, D fully supports C-style pointers. The D module thus includes a custom mechanism to wrap C pointers directly as D pointers where applicable, that is, if the type that is pointed to is represented the same in C and D (on the bit-level), dubbed a <em>primitive type</em> below.</p>
@@ -408,7 +408,7 @@ struct A {
 <p>To determine if a type should be considered primitive, the <tt>cprimitive</tt> attribute on its <tt>dtype</tt> attribute is used. For example, the <tt>dtype</tt> typemap for <tt>float</tt> has <tt>cprimitive="1"</tt>, so the code from the <tt>nativepointer</tt> attribute is taken into account e.g. for <tt>float **</tt> or the function pointer <tt>float (*)(float *)</tt>.</p>
 
 
-<H3><a name="D_operator_overloading">23.8.3 Operator overloading</a></H3>
+<H3><a name="D_operator_overloading">24.8.3 Operator overloading</a></H3>
 
 
 <p>The D module comes with basic operator overloading support for both D1 and D2. There are, however, a few limitations arising from conceptual differences between C++ and D:</p>
@@ -420,7 +420,7 @@ struct A {
 <p>There are also some cases where the operators can be translated to D, but the differences in the implementation details are big enough that a rather involved scheme would be required for automatic wrapping them, which has not been implemented yet. This affects, for example, the array subscript operator, <tt>[]</tt>, in combination with assignments - while <tt>operator []</tt> in C++ simply returns a reference which is then written to, D resorts to a separate <tt>opIndexAssign</tt> method -, or implicit casting (which was introduced in D2 via <tt>alias this</tt>). Despite the lack of automatic support, manually handling these cases should be perfectly possible.</p>
 
 
-<H3><a name="D_test_suite">23.8.4 Running the test-suite</a></H3>
+<H3><a name="D_test_suite">24.8.4 Running the test-suite</a></H3>
 
 
 <p>As with any other language, the SWIG test-suite can be built for D using the <tt>*-d-test-suite</tt> targets of the top-level Makefile. By default, D1 is targeted, to build it with D2, use the optional <tt>D_VERSION</tt> variable, e.g. <tt>make check-d-test-suite D_VERSION=2</tt>.</p>
@@ -428,14 +428,14 @@ struct A {
 <p>Note: If you want to use GDC on Linux or another platform which requires you to link <tt>libdl</tt> for dynamically loading the shared library, you might have to add <tt>-ldl</tt> manually to the <tt>d_compile</tt> target in <tt>Examples/Makefile</tt>, because GDC does not currently honor the <tt>pragma(lib, ...)</tt> statement.</p>
 
 
-<H2><a name="D_typemap_examples">23.9 D Typemap examples</a></H2>
+<H2><a name="D_typemap_examples">24.9 D Typemap examples</a></H2>
 
 
 <p>There are no D-specific typemap examples yet. However, with the above <a href="D.html#D_typemap_name_comparison">name comparison table</a>, you should be able to get an idea what can be done by looking at the <a href="CSharp.html#CSharp_typemap_examples">corresponding C# section</a>.</p>
 
 
 
-<H2><a name="D_planned_features">23.10 Work in progress and planned features</a></H2>
+<H2><a name="D_planned_features">24.10 Work in progress and planned features</a></H2>
 
 
 <p>There are a couple of features which are not implemented yet, but would be very useful and might be added in the near future:</p>
diff --git a/Doc/Manual/Doxygen.html b/Doc/Manual/Doxygen.html
index a736fb6a4..de9ff5841 100644
--- a/Doc/Manual/Doxygen.html
+++ b/Doc/Manual/Doxygen.html
@@ -5,38 +5,45 @@
 <link rel="stylesheet" type="text/css" href="style.css">
 </head>
 <body bgcolor="#FFFFFF">
-<H1><a name="Doxygen"></a>39 SWIG and Doxygen Translation</H1>
+<H1><a name="Doxygen">16 SWIG and Doxygen Translation</a></H1>
 <!-- INDEX -->
 <div class="sectiontoc">
 <ul>
-<li><a href="#Doxygen_translation_overview">Doxygen Translation Overview</a>
+<li><a href="#Doxygen_translation_overview">Doxygen translation overview</a>
 <li><a href="#Doxygen_file_preparation">Preparations</a>
 <ul>
-<li><a href="#Doxygen_running_swig">Enabling Doxygen Translation</a>
-<li><a href="#Doxygen_additional_options">Additional Command Line Options</a>
-<li><a href="#Doxygen_features">Doxygen-specific %feature Directives</a>
-</ul>
-<li><a href="#Doxygen_to_javadoc">Doxygen To Javadoc</a>
+<li><a href="#Doxygen_running_swig">Enabling Doxygen translation</a>
+<li><a href="#Doxygen_features">Doxygen-specific %feature directives</a>
 <ul>
-<li><a href="#Doxygen_basic_example">Basic Example</a>
-<li><a href="#Doxygen_javadoc_tags">Javadoc Tags</a>
+<li><a href="#Doxygen_notranslate">doxygen:notranslate</a>
+<li><a href="#Doxygen_alias">doxygen:alias:&lt;command-name&gt;</a>
+<li><a href="#Doxygen_ignore">doxygen:ignore:&lt;command-name&gt;</a>
+<li><a href="#Doxygen_nolinktranslate">doxygen:nolinktranslate (Java-only currently)</a>
+<li><a href="#Doxygen_nostripparams">doxygen:nostripparams (Java-only currently)</a>
+</ul>
+<li><a href="#Doxygen_additional_options">Additional command line options</a>
+</ul>
+<li><a href="#Doxygen_to_javadoc">Doxygen to Javadoc</a>
+<ul>
+<li><a href="#Doxygen_basic_example">Basic example</a>
+<li><a href="#Doxygen_javadoc_tags">Javadoc tags</a>
 <li><a href="#Doxygen_unsupported_tags">Unsupported tags</a>
-<li><a href="#Doxygen_further_details">Further Details</a>
+<li><a href="#Doxygen_further_details">Further details</a>
 </ul>
-<li><a href="#Doxygen_to_pydoc">Doxygen To Pydoc</a>
+<li><a href="#Doxygen_to_pydoc">Doxygen to Pydoc</a>
 <ul>
-<li><a href="#Doxygen_python_basic_example">Basic Example</a>
+<li><a href="#Doxygen_python_basic_example">Basic example</a>
 <li><a href="#Doxygen_pydoc_tags">Pydoc translator</a>
 <li><a href="#Doxygen_python_unsupported_tags">Unsupported tags</a>
-<li><a href="#Doxygen_python_further_details">Further Details</a>
+<li><a href="#Doxygen_python_further_details">Further details</a>
 </ul>
-<li><a href="#Doxygen_developer_details">Developer Information</a>
+<li><a href="#Doxygen_developer_details">Developer information</a>
 <ul>
-<li><a href="#Doxygen_translator_design">Doxygen Translator Design</a>
-<li><a href="#Doxygen_debugging_commands">Debugging Doxygen parser and translator</a>
-<li><a href="#Doxygen_debugging_commands">Tests</a>
+<li><a href="#Doxygen_translator_design">Doxygen translator design</a>
+<li><a href="#Doxygen_debugging_commands">Debugging the Doxygen parser and translator</a>
+<li><a href="#Doxygen_tests">Tests</a>
 </ul>
-<li><a href="#Doxygen_language_extension">Extending to Other Languages</a>
+<li><a href="#Doxygen_language_extension">Extending to other languages</a>
 </ul>
 </div>
 <!-- INDEX -->
@@ -50,7 +57,7 @@ documentation language.  Currently only Javadoc and Pydoc is
 supported.
 </p>
 
-<H2><a name="Doxygen_translation_overview"></a>39.1 Doxygen translation overview</H2>
+<H2><a name="Doxygen_translation_overview">16.1 Doxygen translation overview</a></H2>
 
 
 <p>
@@ -66,7 +73,7 @@ a <a href="http://code.google.com/soc/2008/">Google Summer of
 Code</a> proposal from Summer 2008.  
 </p>
 
-<H2><a name="Doxygen_file_preparation"></a>39.2 Preparations</H2>
+<H2><a name="Doxygen_file_preparation">16.2 Preparations</a></H2>
 
 
 <p>
@@ -182,7 +189,8 @@ where the comments for a code item are not put directly before or after the code
 These structural commands are stripped out by SWIG and are not assigned to anything.
 </p>
 
-<H3><a name="Doxygen_running_swig"></a>39.2.1 Enabling Doxygen translation</H3>
+<H3><a name="Doxygen_running_swig">16.2.1 Enabling Doxygen translation</a></H3>
+
 
 <p>
 Doxygen comments translation is disabled by default and needs to be explicitly
@@ -190,14 +198,16 @@ enabled using the command line <tt>-doxygen</tt> switch for the languages that
 do support it (currently Java and Python).
 </p>
 
-<H3><a name="Doxygen_features"></a>39.2.2 Doxygen-specific %feature directives</H3>
+<H3><a name="Doxygen_features">16.2.2 Doxygen-specific %feature directives</a></H3>
+
 
 <p>
 Translation of Doxygen comments is influenced by the following <a
 href="Customization.html#Customization_features">%feature directives</a>:
 </p>
 
-<h4><a name="Doxygen_notranslate"></a>doxygen:notranslate</h4>
+<H4><a name="Doxygen_notranslate">16.2.2.1 doxygen:notranslate</a></H4>
+
 
 <p>
 Turns off translation of Doxygen comments to the target language syntax: the
@@ -208,7 +218,8 @@ instead of the corresponding language tool (<tt>javadoc</tt>, <tt>sphinx</tt>,
 </p>
 
 
-<h4><a name="Doxygen_alias"></a>doxygen:alias:&lt;command-name&gt;</h4>
+<H4><a name="Doxygen_alias">16.2.2.2 doxygen:alias:&lt;command-name&gt;</a></H4>
+
 
 <p>
 Specify an alias for a Doxygen command with the given name. This can be useful
@@ -254,7 +265,8 @@ wrappers of the C++ API.
 </p>
 
 
-<h4><a name="Doxygen_ignore"></a>doxygen:ignore:&lt;command-name&gt;</h4>
+<H4><a name="Doxygen_ignore">16.2.2.3 doxygen:ignore:&lt;command-name&gt;</a></H4>
+
 
 <p>
 This feature makes it possible to just ignore an unknown Doxygen command, instead of
@@ -404,14 +416,16 @@ def func():
 </pre></div>
 
 
-<h4><a name="Doxygen_nolinktranslate"></a>doxygen:nolinktranslate (Java-only currently)</h4>
+<H4><a name="Doxygen_nolinktranslate">16.2.2.4 doxygen:nolinktranslate (Java-only currently)</a></H4>
+
 
 <p>
 Turn off automatic link-objects translation.
 </p>
 
 
-<h4><a name="Doxygen_nostripparams"></a>doxygen:nostripparams (Java-only currently)</h4>
+<H4><a name="Doxygen_nostripparams">16.2.2.5 doxygen:nostripparams (Java-only currently)</a></H4>
+
 
 <p>
 Turn off stripping of <tt>@param</tt> and <tt>@tparam</tt>
@@ -419,14 +433,14 @@ Doxygen commands if the parameter is not found in the function signature.
 </p>
 
 
-<H3><a name="Doxygen_additional_options"></a>39.2.3 Additional command line options</H3>
+<H3><a name="Doxygen_additional_options">16.2.3 Additional command line options</a></H3>
 
 
 <p>
 ALSO TO BE ADDED (Javadoc auto brief?)
 </p>
 
-<H2><a name="Doxygen_to_javadoc"></a>39.3 Doxygen to Javadoc</H2>
+<H2><a name="Doxygen_to_javadoc">16.3 Doxygen to Javadoc</a></H2>
 
 
 <p>
@@ -435,7 +449,7 @@ automatically placed in the correct locations in the resulting module
 and proxy files.
 </p>
 
-<H3><a name="Doxygen_basic_example"></a>39.3.1 Basic example</H3>
+<H3><a name="Doxygen_basic_example">16.3.1 Basic example</a></H3>
 
 
 <p>
@@ -542,7 +556,7 @@ Javadoc translator features summary
 directives</a>):
 </p>
 
-<H3><a name="Doxygen_javadoc_tags"></a>39.3.2 Javadoc tags</H3>
+<H3><a name="Doxygen_javadoc_tags">16.3.2 Javadoc tags</a></H3>
 
 
 <p>
@@ -796,7 +810,7 @@ Here is the list of all Doxygen tags and the description of how they are transla
 </table>
 </div>
 
-<H3><a name="Doxygen_unsupported_tags"></a>39.3.3 Unsupported tags</H3>
+<H3><a name="Doxygen_unsupported_tags">16.3.3 Unsupported tags</a></H3>
 
 
 <p>
@@ -1032,14 +1046,14 @@ comment, the whole comment block is ignored:
 
 
 
-<H3><a name="Doxygen_further_details"></a>39.3.4 Further details</H3>
+<H3><a name="Doxygen_further_details">16.3.4 Further details</a></H3>
 
 
 <p>
 TO BE ADDED.
 </p>
 
-<H2><a name="Doxygen_to_pydoc"></a>39.4 Doxygen to Pydoc</H2>
+<H2><a name="Doxygen_to_pydoc">16.4 Doxygen to Pydoc</a></H2>
 
 
 <p>
@@ -1050,7 +1064,7 @@ Doxygen or Javadoc, so most of Doxygen commands are translated by merely
 copying the appropriate command text.
 </p>
 
-<H3><a name="Doxygen_python_basic_example"></a>39.4.1 Basic example</H3>
+<H3><a name="Doxygen_python_basic_example">16.4.1 Basic example</a></H3>
 
 
 <p>
@@ -1213,7 +1227,7 @@ docs</a>), you may want to use some tool like doxypy
 to do the work.
 </p>
 
-<H3><a name="Doxygen_pydoc_tags"></a>39.4.2 Pydoc translator</H3>
+<H3><a name="Doxygen_pydoc_tags">16.4.2 Pydoc translator</a></H3>
 
 
 <p>
@@ -1427,7 +1441,7 @@ Here is the list of all Doxygen tags and the description of how they are transla
 </table>
 </div>
 
-<H3><a name="Doxygen_python_unsupported_tags"></a>39.4.3 Unsupported tags</H3>
+<H3><a name="Doxygen_python_unsupported_tags">16.4.3 Unsupported tags</a></H3>
 
 
 <p>
@@ -1611,21 +1625,21 @@ Here is the list of these tags:
 </table>
 </div>
 
-<H3><a name="Doxygen_python_further_details"></a>39.4.4 Further details</H3>
+<H3><a name="Doxygen_python_further_details">16.4.4 Further details</a></H3>
 
 
 <p>
 TO BE ADDED.
 </p>
 
-<H2><a name="Doxygen_developer_details"></a>39.5 Developer information</H2>
+<H2><a name="Doxygen_developer_details">16.5 Developer information</a></H2>
 
 
 <p>
 This section contains information for developers enhancing the Doxygen translator.
 </p>
 
-<H3><a name="Doxygen_translator_design"></a>39.5.1 Doxygen translator design</H3>
+<H3><a name="Doxygen_translator_design">16.5.1 Doxygen translator design</a></H3>
 
 
 <p>
@@ -1651,7 +1665,7 @@ class for translation into the target documentation language.  For
 example, <tt>JavaDocConverter</tt> is the Javadoc module class.
 </p>
 
-<H3><a name="Doxygen_debugging_commands"></a>39.5.2 Debugging the Doxygen parser and translator</H3>
+<H3><a name="Doxygen_debugging_commands">16.5.2 Debugging the Doxygen parser and translator</a></H3>
 
 
 <p>
@@ -1664,7 +1678,7 @@ detailed debug information printing.
   -debug-doxygen-translator - Display Doxygen translator module debugging information
 </pre></div>
 
-<H3><a name="Doxygen_tests"></a>39.5.3 Tests</H3>
+<H3><a name="Doxygen_tests">16.5.3 Tests</a></H3>
 
 
 <p>
@@ -1716,7 +1730,7 @@ Runtime tests in Python are just plain string comparisons of the __doc__
 properties.
 </p>
 
-<H2><a name="Doxygen_language_extension"></a>39.6 Extending to other languages</H2>
+<H2><a name="Doxygen_language_extension">16.6 Extending to other languages</a></H2>
 
 
 <p>
diff --git a/Doc/Manual/Extending.html b/Doc/Manual/Extending.html
index aafc650f6..8769aa36e 100644
--- a/Doc/Manual/Extending.html
+++ b/Doc/Manual/Extending.html
@@ -7,7 +7,7 @@
 </head>
 
 <body bgcolor="#ffffff">
-<H1><a name="Extending">42 Extending SWIG to support new languages</a></H1>
+<H1><a name="Extending">43 Extending SWIG to support new languages</a></H1>
 <!-- INDEX -->
 <div class="sectiontoc">
 <ul>
@@ -76,7 +76,7 @@
 
 
 
-<H2><a name="Extending_nn2">42.1 Introduction</a></H2>
+<H2><a name="Extending_nn2">43.1 Introduction</a></H2>
 
 
 <p>
@@ -92,7 +92,7 @@ Also, this chapter is not meant to be a hand-holding tutorial.  As a starting po
 you should probably look at one of SWIG's existing modules.
 </p>
 
-<H2><a name="Extending_nn3">42.2 Prerequisites</a></H2>
+<H2><a name="Extending_nn3">43.2 Prerequisites</a></H2>
 
 
 <p>
@@ -122,7 +122,7 @@ obvious, but almost all SWIG directives as well as the low-level generation of
 wrapper code are driven by C++ datatypes.
 </p>
 
-<H2><a name="Extending_nn4">42.3 The Big Picture</a></H2>
+<H2><a name="Extending_nn4">43.3 The Big Picture</a></H2>
 
 
 <p>
@@ -159,7 +159,7 @@ role in making the system work.  For example, both typemaps and declaration anno
 based on pattern matching and interact heavily with the underlying type system.
 </p>
 
-<H2><a name="Extending_nn5">42.4 Execution Model</a></H2>
+<H2><a name="Extending_nn5">43.4 Execution Model</a></H2>
 
 
 <p>
@@ -204,7 +204,7 @@ latter stage of compilation.
 The next few sections briefly describe some of these stages.
 </p>
 
-<H3><a name="Extending_nn6">42.4.1 Preprocessing</a></H3>
+<H3><a name="Extending_nn6">43.4.1 Preprocessing</a></H3>
 
 
 <p>
@@ -285,7 +285,7 @@ been expanded as well as everything else that goes into the low-level
 construction of the wrapper code.
 </p>
 
-<H3><a name="Extending_nn7">42.4.2 Parsing</a></H3>
+<H3><a name="Extending_nn7">43.4.2 Parsing</a></H3>
 
 
 <p>
@@ -386,7 +386,7 @@ returning a <tt>foo</tt> and taking types <tt>a</tt> and <tt>b</tt> as
 arguments).
 </p>
 
-<H3><a name="Extending_nn8">42.4.3 Parse Trees</a></H3>
+<H3><a name="Extending_nn8">43.4.3 Parse Trees</a></H3>
 
 
 <p>
@@ -641,7 +641,7 @@ $ swig -c++ -python -debug-module 4 example.i
 </pre>
 </div>
 
-<H3><a name="Extending_nn9">42.4.4 Attribute namespaces</a></H3>
+<H3><a name="Extending_nn9">43.4.4 Attribute namespaces</a></H3>
 
 
 <p>
@@ -660,7 +660,7 @@ that matches the name of the target language.  For example, <tt>python:foo</tt>
 <tt>perl:foo</tt>.
 </p>
 
-<H3><a name="Extending_nn10">42.4.5 Symbol Tables</a></H3>
+<H3><a name="Extending_nn10">43.4.5 Symbol Tables</a></H3>
 
 
 <p>
@@ -751,7 +751,7 @@ example.i:5. Previous declaration is foo_i(int )
 </pre>
 </div>
 
-<H3><a name="Extending_nn11">42.4.6 The %feature directive</a></H3>
+<H3><a name="Extending_nn11">43.4.6 The %feature directive</a></H3>
 
 
 <p>
@@ -807,7 +807,7 @@ For example, the exception code above is simply
 stored without any modifications.
 </p>
 
-<H3><a name="Extending_nn12">42.4.7 Code Generation</a></H3>
+<H3><a name="Extending_nn12">43.4.7 Code Generation</a></H3>
 
 
 <p>
@@ -929,7 +929,7 @@ public :
 The role of these functions is described shortly.
 </p>
 
-<H3><a name="Extending_nn13">42.4.8 SWIG and XML</a></H3>
+<H3><a name="Extending_nn13">43.4.8 SWIG and XML</a></H3>
 
 
 <p>
@@ -942,7 +942,7 @@ internal data structures, it may be useful to keep XML in the back of
 your mind as a model.
 </p>
 
-<H2><a name="Extending_nn14">42.5 Primitive Data Structures</a></H2>
+<H2><a name="Extending_nn14">43.5 Primitive Data Structures</a></H2>
 
 
 <p>
@@ -988,7 +988,7 @@ typedef Hash   Typetab;
 </pre>
 </div>
 
-<H3><a name="Extending_nn15">42.5.1 Strings</a></H3>
+<H3><a name="Extending_nn15">43.5.1 Strings</a></H3>
 
 
 <p>
@@ -1129,7 +1129,7 @@ Returns the number of replacements made (if any).
 
 </div>
 
-<H3><a name="Extending_nn16">42.5.2 Hashes</a></H3>
+<H3><a name="Extending_nn16">43.5.2 Hashes</a></H3>
 
 
 <p>
@@ -1206,7 +1206,7 @@ Returns the list of hash table keys.
 </div>
 
 
-<H3><a name="Extending_nn17">42.5.3 Lists</a></H3>
+<H3><a name="Extending_nn17">43.5.3 Lists</a></H3>
 
 
 <p>
@@ -1295,7 +1295,7 @@ If <tt>t</tt> is not a standard object, it is assumed to be a <tt>char *</tt>
 and is used to create a String object.
 </div>
 
-<H3><a name="Extending_nn18">42.5.4 Common operations</a></H3>
+<H3><a name="Extending_nn18">43.5.4 Common operations</a></H3>
 
 
 The following operations are applicable to all datatypes.
@@ -1350,7 +1350,7 @@ objects and report errors.
 Gets the line number associated with <tt>x</tt>.
 </div>
 
-<H3><a name="Extending_nn19">42.5.5 Iterating over Lists and Hashes</a></H3>
+<H3><a name="Extending_nn19">43.5.5 Iterating over Lists and Hashes</a></H3>
 
 
 To iterate over the elements of a list or a hash table, the following functions are used:
@@ -1395,7 +1395,7 @@ for (j = First(j); j.item; j= Next(j)) {
 
 </div>
 
-<H3><a name="Extending_nn20">42.5.6 I/O</a></H3>
+<H3><a name="Extending_nn20">43.5.6 I/O</a></H3>
 
 
 Special I/O functions are used for all internal I/O.  These operations
@@ -1529,7 +1529,7 @@ Printf(f, "%s\n", s);
 Similarly, the preprocessor and parser all operate on string-files.
 </p>
 
-<H2><a name="Extending_nn21">42.6 Navigating and manipulating parse trees</a></H2>
+<H2><a name="Extending_nn21">43.6 Navigating and manipulating parse trees</a></H2>
 
 
 Parse trees are built as collections of hash tables.   Each node is a hash table in which
@@ -1663,7 +1663,7 @@ Deletes a node from the parse tree.  Deletion reconnects siblings and properly u
 the parent so that sibling nodes are unaffected.
 </div>
 
-<H2><a name="Extending_nn22">42.7 Working with attributes</a></H2>
+<H2><a name="Extending_nn22">43.7 Working with attributes</a></H2>
 
 
 <p>
@@ -1780,7 +1780,7 @@ the attribute is optional.   <tt>Swig_restore()</tt> must always be called after
 function.
 </div>
 
-<H2><a name="Extending_nn23">42.8 Type system</a></H2>
+<H2><a name="Extending_nn23">43.8 Type system</a></H2>
 
 
 <p>
@@ -1789,7 +1789,7 @@ pointers, references, and pointers to members.   A detailed discussion of
 type theory is impossible here.   However, let's cover the highlights.
 </p>
 
-<H3><a name="Extending_nn24">42.8.1 String encoding of types</a></H3>
+<H3><a name="Extending_nn24">43.8.1 String encoding of types</a></H3>
 
 
 <p>
@@ -1890,7 +1890,7 @@ make the final type, the two parts are just joined together using
 string concatenation.
 </p>
 
-<H3><a name="Extending_nn25">42.8.2 Type construction</a></H3>
+<H3><a name="Extending_nn25">43.8.2 Type construction</a></H3>
 
 
 <p>
@@ -2059,7 +2059,7 @@ Returns the prefix of a type. For example, if <tt>ty</tt> is
 <tt>ty</tt> is unmodified.
 </div>
 
-<H3><a name="Extending_nn26">42.8.3 Type tests</a></H3>
+<H3><a name="Extending_nn26">43.8.3 Type tests</a></H3>
 
 
 <p>
@@ -2146,7 +2146,7 @@ Checks if <tt>ty</tt> is a varargs type.
 Checks if <tt>ty</tt> is a templatized type.
 </div>
 
-<H3><a name="Extending_nn27">42.8.4 Typedef and inheritance</a></H3>
+<H3><a name="Extending_nn27">43.8.4 Typedef and inheritance</a></H3>
 
 
 <p>
@@ -2248,7 +2248,7 @@ Fully reduces <tt>ty</tt> according to typedef rules.  Resulting datatype
 will consist only of primitive typenames.
 </div>
 
-<H3><a name="Extending_nn28">42.8.5 Lvalues</a></H3>
+<H3><a name="Extending_nn28">43.8.5 Lvalues</a></H3>
 
 
 <p>
@@ -2285,7 +2285,7 @@ Literal y;    // type = 'Literal', ltype='p.char'
 </pre>
 </div>
 
-<H3><a name="Extending_nn29">42.8.6 Output functions</a></H3>
+<H3><a name="Extending_nn29">43.8.6 Output functions</a></H3>
 
 
 <p>
@@ -2347,7 +2347,7 @@ SWIG, but is most commonly associated with type-descriptor objects
 that appear in wrappers (e.g., <tt>SWIGTYPE_p_double</tt>).
 </div>
 
-<H2><a name="Extending_nn30">42.9 Parameters</a></H2>
+<H2><a name="Extending_nn30">43.9 Parameters</a></H2>
 
 
 <p>
@@ -2446,7 +2446,7 @@ included.  Used to emit prototypes.
 Returns the number of required (non-optional) arguments in <tt>p</tt>.
 </div>
 
-<H2><a name="Extending_nn31">42.10 Writing a Language Module</a></H2>
+<H2><a name="Extending_nn31">43.10 Writing a Language Module</a></H2>
 
 
 <p>
@@ -2461,7 +2461,7 @@ describes the creation of a minimal Python module.   You should be able to extra
 this to other languages.
 </p>
 
-<H3><a name="Extending_nn32">42.10.1 Execution model</a></H3>
+<H3><a name="Extending_nn32">43.10.1 Execution model</a></H3>
 
 
 <p>
@@ -2471,7 +2471,7 @@ the parsing of command line options, all aspects of code generation are controll
 different methods of the <tt>Language</tt> that must be defined by your module.
 </p>
 
-<H3><a name="Extending_starting_out">42.10.2 Starting out</a></H3>
+<H3><a name="Extending_starting_out">43.10.2 Starting out</a></H3>
 
 
 <p>
@@ -2579,7 +2579,7 @@ that activates your module. For example, <tt>swig -python foo.i</tt>. The
 messages from your new module should appear.
 </p>
 
-<H3><a name="Extending_nn34">42.10.3 Command line options</a></H3>
+<H3><a name="Extending_nn34">43.10.3 Command line options</a></H3>
 
 
 <p>
@@ -2638,7 +2638,7 @@ to mark the option as valid.   If you forget to do this, SWIG will terminate wit
 unrecognized command line option error.
 </p>
 
-<H3><a name="Extending_nn35">42.10.4 Configuration and preprocessing</a></H3>
+<H3><a name="Extending_nn35">43.10.4 Configuration and preprocessing</a></H3>
 
 
 <p>
@@ -2687,7 +2687,7 @@ an implementation file <tt>python.cxx</tt> and a configuration file
 <tt>python.swg</tt>.
 </p>
 
-<H3><a name="Extending_nn36">42.10.5 Entry point to code generation</a></H3>
+<H3><a name="Extending_nn36">43.10.5 Entry point to code generation</a></H3>
 
 
 <p>
@@ -2745,7 +2745,7 @@ int Python::top(Node *n) {
 </pre>
 </div>
 
-<H3><a name="Extending_nn37">42.10.6 Module I/O and wrapper skeleton</a></H3>
+<H3><a name="Extending_nn37">43.10.6 Module I/O and wrapper skeleton</a></H3>
 
 
 <!-- please report bugs in this section to mgossage -->
@@ -2893,7 +2893,7 @@ functionWrapper   : void Shape_y_set(Shape *self, double y)
 </pre>
 </div>
 
-<H3><a name="Extending_nn38">42.10.7 Low-level code generators</a></H3>
+<H3><a name="Extending_nn38">43.10.7 Low-level code generators</a></H3>
 
 
 <!-- please report bugs in this section to mgossage -->
@@ -3047,7 +3047,7 @@ but without the typemaps, there is still work to do.
 </p>
 
 
-<H3><a name="Extending_configuration_files">42.10.8 Configuration files</a></H3>
+<H3><a name="Extending_configuration_files">43.10.8 Configuration files</a></H3>
 
 
 <!-- please report bugs in this section to ttn -->
@@ -3191,7 +3191,7 @@ politely displays the ignoring language message.
 </dl>
 
 
-<H3><a name="Extending_nn40">42.10.9 Runtime support</a></H3>
+<H3><a name="Extending_nn40">43.10.9 Runtime support</a></H3>
 
 
 <p>
@@ -3200,7 +3200,7 @@ Discuss the kinds of functions typically needed for SWIG runtime support (e.g.
 the SWIG files that implement those functions.
 </p>
 
-<H3><a name="Extending_nn41">42.10.10 Standard library files</a></H3>
+<H3><a name="Extending_nn41">43.10.10 Standard library files</a></H3>
 
 
 <p>
@@ -3219,7 +3219,7 @@ The following are the minimum that are usually supported:
 Please copy these and modify for any new language.
 </p>
 
-<H3><a name="Extending_nn42">42.10.11 User examples</a></H3>
+<H3><a name="Extending_nn42">43.10.11 User examples</a></H3>
 
 
 <p>
@@ -3248,7 +3248,7 @@ during this process, see the section on <a href="#Extending_configuration_files"
 files</a>.
 </p>
 
-<H3><a name="Extending_test_suite">42.10.12 Test driven development and the test-suite</a></H3>
+<H3><a name="Extending_test_suite">43.10.12 Test driven development and the test-suite</a></H3>
 
 
 <p>
@@ -3307,7 +3307,7 @@ It is therefore essential that the runtime tests are written in a manner that di
 but error/exception out with an error message on stderr on failure.
 </p>
 
-<H4><a name="Extending_running_test_suite">42.10.12.1 Running the test-suite</a></H4>
+<H4><a name="Extending_running_test_suite">43.10.12.1 Running the test-suite</a></H4>
 
 
 <p>
@@ -3499,7 +3499,7 @@ It can be run in the same way as the other language test-suites, replacing [lang
 The test cases used and the way it works is described in <tt>Examples/test-suite/errors/Makefile.in</tt>.
 </p>
 
-<H3><a name="Extending_nn43">42.10.13 Documentation</a></H3>
+<H3><a name="Extending_nn43">43.10.13 Documentation</a></H3>
 
 
 <p>
@@ -3531,7 +3531,7 @@ Some topics that you'll want to be sure to address include:
      if available.
 </ul>
 
-<H3><a name="Extending_prerequisites">42.10.14 Prerequisites for adding a new language module to the SWIG distribution</a></H3>
+<H3><a name="Extending_prerequisites">43.10.14 Prerequisites for adding a new language module to the SWIG distribution</a></H3>
 
 
 <p>
@@ -3588,7 +3588,7 @@ should be added should there be an area not already covered by
 the existing tests.
 </p>
 
-<H3><a name="Extending_coding_style_guidelines">42.10.15 Coding style guidelines</a></H3>
+<H3><a name="Extending_coding_style_guidelines">43.10.15 Coding style guidelines</a></H3>
 
 
 <p>
@@ -3612,7 +3612,7 @@ The generated C/C++ code should also follow this style as close as possible. How
 should be avoided as unlike the SWIG developers, users will never have consistent tab settings.
 </p>
 
-<H2><a name="Extending_debugging_options">42.11 Debugging Options</a></H2>
+<H2><a name="Extending_debugging_options">43.11 Debugging Options</a></H2>
 
 
 <p>
@@ -3639,7 +3639,7 @@ There are various command line options which can aid debugging a SWIG interface
 The complete list of command line options for SWIG are available by running <tt>swig -help</tt>.
 </p>
 
-<H2><a name="Extending_nn46">42.12 Guide to parse tree nodes</a></H2>
+<H2><a name="Extending_nn46">43.12 Guide to parse tree nodes</a></H2>
 
 
 <p>
@@ -4047,7 +4047,7 @@ extern "X" { ... } declaration.
 </pre>
 </div>
 
-<H2><a name="Extending_further_info">42.13 Further Development Information</a></H2>
+<H2><a name="Extending_further_info">43.13 Further Development Information</a></H2>
 
 
 <p>
diff --git a/Doc/Manual/Go.html b/Doc/Manual/Go.html
index 432f932ad..750a62514 100644
--- a/Doc/Manual/Go.html
+++ b/Doc/Manual/Go.html
@@ -6,7 +6,7 @@
 <meta http-equiv="content-type" content="text/html; charset=UTF-8">
 </head>
 <body bgcolor="#FFFFFF">
-<H1><a name="Go">24 SWIG and Go</a></H1>
+<H1><a name="Go">25 SWIG and Go</a></H1>
 <!-- INDEX -->
 <div class="sectiontoc">
 <ul>
@@ -57,7 +57,7 @@ the Go programming language
 see <a href="http://golang.org/">golang.org</a>.
 </p>
 
-<H2><a name="Go_overview">24.1 Overview</a></H2>
+<H2><a name="Go_overview">25.1 Overview</a></H2>
 
 
 <p>
@@ -86,7 +86,7 @@ type-safe as well.  In case of type issues the build will fail and hence SWIG's
 are not used.
 </p>
 
-<H2><a name="Go_examples">24.2 Examples</a></H2>
+<H2><a name="Go_examples">25.2 Examples</a></H2>
 
 
 <p>
@@ -101,7 +101,7 @@ SWIG interface file extension for backwards compatibility with Go 1.
 </p>
 
 
-<H2><a name="Go_running_swig">24.3 Running SWIG with Go</a></H2>
+<H2><a name="Go_running_swig">25.3 Running SWIG with Go</a></H2>
 
 
 <p>
@@ -181,7 +181,7 @@ sequence for this approach would look like this:
 </pre></div>
 
 
-<H3><a name="Go_commandline">24.3.1 Go-specific Commandline Options</a></H3>
+<H3><a name="Go_commandline">25.3.1 Go-specific Commandline Options</a></H3>
 
 
 <p>
@@ -264,7 +264,7 @@ swig -go -help
 </table>
 
 
-<H3><a name="Go_outputs">24.3.2 Generated Wrapper Files</a></H3>
+<H3><a name="Go_outputs">25.3.2 Generated Wrapper Files</a></H3>
 
 
 <p>There are two different approaches to generating wrapper files,
@@ -308,7 +308,7 @@ combined with the compiled MODULE.go using go tool pack.
 </ul>
 
 
-<H2><a name="Go_basic_tour">24.4 A tour of basic C/C++ wrapping</a></H2>
+<H2><a name="Go_basic_tour">25.4 A tour of basic C/C++ wrapping</a></H2>
 
 
 <p>
@@ -318,7 +318,7 @@ modifications have to occur.  This section briefly covers the
 essential aspects of this wrapping.
 </p>
 
-<H3><a name="Go_package">24.4.1 Go Package Name</a></H3>
+<H3><a name="Go_package">25.4.1 Go Package Name</a></H3>
 
 
 <p>
@@ -328,7 +328,7 @@ directive.  You may override this by using SWIG's <tt>-package</tt>
 command line option.
 </p>
 
-<H3><a name="Go_names">24.4.2 Go Names</a></H3>
+<H3><a name="Go_names">25.4.2 Go Names</a></H3>
 
 
 <p>
@@ -360,7 +360,7 @@ followed by that name, and the destructor will be
 named <tt>Delete</tt> followed by that name.
 </p>
 
-<H3><a name="Go_constants">24.4.3 Go Constants</a></H3>
+<H3><a name="Go_constants">25.4.3 Go Constants</a></H3>
 
 
 <p>
@@ -368,7 +368,7 @@ C/C++ constants created via <tt>#define</tt> or the <tt>%constant</tt>
 directive become Go constants, declared with a <tt>const</tt>
 declaration.
 
-<H3><a name="Go_enumerations">24.4.4 Go Enumerations</a></H3>
+<H3><a name="Go_enumerations">25.4.4 Go Enumerations</a></H3>
 
 
 <p>
@@ -378,7 +378,7 @@ usual).  The values of the enumeration will become variables in Go;
 code should avoid modifying those variables.
 </p>
 
-<H3><a name="Go_classes">24.4.5 Go Classes</a></H3>
+<H3><a name="Go_classes">25.4.5 Go Classes</a></H3>
 
 
 <p>
@@ -456,7 +456,7 @@ returns a go interface.  If the returned pointer can be null, you can check
 for this by calling the Swigcptr() method.
 </p>
 
-<H4><a name="Go_class_memory">24.4.5.1 Go Class Memory Management</a></H4>
+<H4><a name="Go_class_memory">25.4.5.1 Go Class Memory Management</a></H4>
 
 
 <p>
@@ -578,7 +578,7 @@ func (o *GoClassName) Close() {
 </pre>
 </div>
 
-<H4><a name="Go_class_inheritance">24.4.5.2 Go Class Inheritance</a></H4>
+<H4><a name="Go_class_inheritance">25.4.5.2 Go Class Inheritance</a></H4>
 
 
 <p>
@@ -590,7 +590,7 @@ Doing the reverse will require an explicit type assertion, which will
 be checked dynamically.
 </p>
 
-<H3><a name="Go_templates">24.4.6 Go Templates</a></H3>
+<H3><a name="Go_templates">25.4.6 Go Templates</a></H3>
 
 
 <p>
@@ -599,7 +599,7 @@ wrappers for a particular template instantation.  To do this, use
 the <tt>%template</tt> directive.
 
 
-<H3><a name="Go_director_classes">24.4.7 Go Director Classes</a></H3>
+<H3><a name="Go_director_classes">25.4.7 Go Director Classes</a></H3>
 
 
 <p>
@@ -617,7 +617,7 @@ completely to avoid common pitfalls with directors in Go.
 </p>
 
 
-<H4><a name="Go_director_example_cpp_code">24.4.7.1 Example C++ code</a></H4>
+<H4><a name="Go_director_example_cpp_code">25.4.7.1 Example C++ code</a></H4>
 
 
 <p>
@@ -689,7 +689,7 @@ be found in <a href="#Go_director_foobargo_class">the end of the guide</a>.
 </p>
 
 
-<H4><a name="Go_director_enable">24.4.7.2 Enable director feature</a></H4>
+<H4><a name="Go_director_enable">25.4.7.2 Enable director feature</a></H4>
 
 
 <p>
@@ -724,7 +724,7 @@ documentation on directors.
 </p>
 
 
-<H4><a name="Go_director_ctor_dtor">24.4.7.3 Constructor and destructor</a></H4>
+<H4><a name="Go_director_ctor_dtor">25.4.7.3 Constructor and destructor</a></H4>
 
 
 <p>
@@ -777,7 +777,7 @@ embedding</a>.
 </p>
 
 
-<H4><a name="Go_director_overriding">24.4.7.4 Override virtual methods</a></H4>
+<H4><a name="Go_director_overriding">25.4.7.4 Override virtual methods</a></H4>
 
 
 <p>
@@ -843,7 +843,7 @@ the Go methods.
 </p>
 
 
-<H4><a name="Go_director_base_methods">24.4.7.5 Call base methods</a></H4>
+<H4><a name="Go_director_base_methods">25.4.7.5 Call base methods</a></H4>
 
 
 <p>
@@ -880,7 +880,7 @@ be found in <a href="#Go_director_foobargo_class">the end of the guide</a>.
 </p>
 
 
-<H4><a name="Go_director_subclass">24.4.7.6 Subclass via embedding</a></H4>
+<H4><a name="Go_director_subclass">25.4.7.6 Subclass via embedding</a></H4>
 
 
 <p>
@@ -948,7 +948,7 @@ class.
 </p>
 
 
-<H4><a name="Go_director_finalizer">24.4.7.7 Memory management with runtime.SetFinalizer</a></H4>
+<H4><a name="Go_director_finalizer">25.4.7.7 Memory management with runtime.SetFinalizer</a></H4>
 
 
 <p>
@@ -1013,7 +1013,7 @@ before using <tt>runtime.SetFinalizer</tt> to know all of its gotchas.
 </p>
 
 
-<H4><a name="Go_director_foobargo_class">24.4.7.8 Complete FooBarGo example class</a></H4>
+<H4><a name="Go_director_foobargo_class">25.4.7.8 Complete FooBarGo example class</a></H4>
 
 
 <p>
@@ -1142,7 +1142,7 @@ SWIG/Examples/go/director/</a>.
 </p>
 
 
-<H3><a name="Go_primitive_type_mappings">24.4.8 Default Go primitive type mappings</a></H3>
+<H3><a name="Go_primitive_type_mappings">25.4.8 Default Go primitive type mappings</a></H3>
 
 
 <p>
@@ -1249,7 +1249,7 @@ that typemap, or add new values, to control how C/C++ types are mapped
 into Go types.
 </p>
 
-<H3><a name="Go_output_arguments">24.4.9 Output arguments</a></H3>
+<H3><a name="Go_output_arguments">25.4.9 Output arguments</a></H3>
 
 
 <p>Because of limitations in the way output arguments are processed in swig,
@@ -1302,7 +1302,7 @@ void f(char *output);
 </pre>
 </div>
 
-<H3><a name="Go_adding_additional_code">24.4.10 Adding additional go code</a></H3>
+<H3><a name="Go_adding_additional_code">25.4.10 Adding additional go code</a></H3>
 
 
 <p>Often the APIs generated by swig are not very natural in go, especially if
@@ -1397,7 +1397,7 @@ func bar() {
 </pre>
 </div>
 
-<H3><a name="Go_typemaps">24.4.11 Go typemaps</a></H3>
+<H3><a name="Go_typemaps">25.4.11 Go typemaps</a></H3>
 
 
 <p>
diff --git a/Doc/Manual/Guile.html b/Doc/Manual/Guile.html
index 31d822599..9d55b632b 100644
--- a/Doc/Manual/Guile.html
+++ b/Doc/Manual/Guile.html
@@ -8,7 +8,7 @@
 
 <body bgcolor="#ffffff">
 
-<H1><a name="Guile">25 SWIG and Guile</a></H1>
+<H1><a name="Guile">26 SWIG and Guile</a></H1>
 <!-- INDEX -->
 <div class="sectiontoc">
 <ul>
@@ -48,7 +48,7 @@
 <p>
 This section details guile-specific support in SWIG.
 
-<H2><a name="Guile_nn1">25.1 Supported Guile Versions</a></H2>
+<H2><a name="Guile_nn1">26.1 Supported Guile Versions</a></H2>
 
 
 <p>
@@ -62,7 +62,7 @@ improved performance. This is currently not tested with swig
 so your mileage may vary. To be safe set environment variable
 GUILE_AUTO_COMPILE to 0 when using swig generated guile code.
 
-<H2><a name="Guile_nn2">25.2 Meaning of "Module"</a></H2>
+<H2><a name="Guile_nn2">26.2 Meaning of "Module"</a></H2>
 
 
 <p>
@@ -70,7 +70,7 @@ There are three different concepts of "module" involved, defined
 separately for SWIG, Guile, and Libtool.  To avoid horrible confusion,
 we explicitly prefix the context, e.g., "guile-module".
 
-<H2><a name="Guile_nn3">25.3 Old GH Guile API</a></H2>
+<H2><a name="Guile_nn3">26.3 Old GH Guile API</a></H2>
 
 
 <p>Guile 1.8 and older could be interfaced using two different api's, the SCM
@@ -81,7 +81,7 @@ or the GH API. The GH interface to guile is deprecated.  Read more about why in
 version of SWIG that can still generate guile GH wrapper code is 2.0.9. Please
 use that version if you really need the GH wrapper code.
 
-<H2><a name="Guile_nn4">25.4 Linkage</a></H2>
+<H2><a name="Guile_nn4">26.4 Linkage</a></H2>
 
 
 <p>
@@ -89,7 +89,7 @@ Guile support is complicated by a lack of user community cohesiveness,
 which manifests in multiple shared-library usage conventions.  A set of
 policies implementing a usage convention is called a <b>linkage</b>.
 
-<H3><a name="Guile_nn5">25.4.1 Simple Linkage</a></H3>
+<H3><a name="Guile_nn5">26.4.1 Simple Linkage</a></H3>
 
 
 <p>
@@ -194,7 +194,7 @@ placed between the <code>define-module</code> form and the
 <code>SWIG_init</code> via a preprocessor define to avoid symbol
 clashes. For this case, however, passive linkage is available.
 
-<H3><a name="Guile_nn6">25.4.2 Passive Linkage</a></H3>
+<H3><a name="Guile_nn6">26.4.2 Passive Linkage</a></H3>
 
 
 <p>Passive linkage is just like simple linkage, but it generates an
@@ -204,7 +204,7 @@ package name (see below).
 <p>You should use passive linkage rather than simple linkage when you
 are using multiple modules.
 
-<H3><a name="Guile_nn7">25.4.3 Native Guile Module Linkage</a></H3>
+<H3><a name="Guile_nn7">26.4.3 Native Guile Module Linkage</a></H3>
 
 
 <p>SWIG can also generate wrapper code that does all the Guile module
@@ -245,7 +245,7 @@ Newer Guile versions have a shorthand procedure for this:
 </div>
 </ul>
 
-<H3><a name="Guile_nn8">25.4.4 Old Auto-Loading Guile Module Linkage</a></H3>
+<H3><a name="Guile_nn8">26.4.4 Old Auto-Loading Guile Module Linkage</a></H3>
 
 
 <p>Guile used to support an autoloading facility for object-code
@@ -271,7 +271,7 @@ option, SWIG generates an exported module initialization function with
 an appropriate name. 
 
 
-<H3><a name="Guile_nn9">25.4.5 Hobbit4D Linkage</a></H3>
+<H3><a name="Guile_nn9">26.4.5 Hobbit4D Linkage</a></H3>
 
 
 <p>
@@ -296,7 +296,7 @@ my/lib/libfoo.so.X.Y.Z and friends.  This scheme is still very
 experimental; the (hobbit4d link) conventions are not well understood.
 </p>
 
-<H2><a name="Guile_nn10">25.5 Underscore Folding</a></H2>
+<H2><a name="Guile_nn10">26.5 Underscore Folding</a></H2>
 
 
 <p>
@@ -308,7 +308,7 @@ complained so far.
 <code>%rename</code> to specify the Guile name of the wrapped
 functions and variables (see CHANGES).
 
-<H2><a name="Guile_nn11">25.6 Typemaps</a></H2>
+<H2><a name="Guile_nn11">26.6 Typemaps</a></H2>
 
 
 <p>
@@ -400,7 +400,7 @@ constant will appear as a scheme variable. See
 <a href="Customization.html#Customization_features">Features and the %feature directive</a>
 for info on how to apply the %feature.</p>
 
-<H2><a name="Guile_nn12">25.7 Representation of pointers as smobs</a></H2>
+<H2><a name="Guile_nn12">26.7 Representation of pointers as smobs</a></H2>
 
 
 <p>
@@ -421,7 +421,7 @@ representing the expected pointer type.  See also
 If the Scheme object passed was not a SWIG smob representing a compatible
 pointer, a <code>wrong-type-arg</code> exception is raised.
 
-<H3><a name="Guile_nn14">25.7.1 Smobs</a></H3>
+<H3><a name="Guile_nn14">26.7.1 Smobs</a></H3>
 
 
 <p>
@@ -440,7 +440,7 @@ structure describing this type.  If a generated GOOPS module has been loaded, sm
 the corresponding GOOPS class.</p>
 
 
-<H3><a name="Guile_nn15">25.7.2 Garbage Collection</a></H3>
+<H3><a name="Guile_nn15">26.7.2 Garbage Collection</a></H3>
 
 
 <p>Garbage collection is a feature of Guile since version 1.6. As SWIG now requires Guile &gt; 1.8,
@@ -454,14 +454,14 @@ is exactly like described in <a href="Customization.html#Customization_ownership
 Object ownership and %newobject</a> in the SWIG manual.  All typemaps use an $owner var, and
 the guile module replaces $owner with 0 or 1 depending on feature:new.</p>
 
-<H2><a name="Guile_nn16">25.8 Native Guile pointers</a></H2>
+<H2><a name="Guile_nn16">26.8 Native Guile pointers</a></H2>
 
 
 <p>
 In addition to SWIG smob pointers, <a href="https://www.gnu.org/software/guile/manual/html_node/Foreign-Pointers.html">Guile's native pointer type</a> are accepted as arguments to wrapped SWIG functions. This can be useful for passing <a href="https://www.gnu.org/software/guile/manual/html_node/Void-Pointers-and-Byte-Access.html#">pointers to bytevector data</a> to wrapped functions.
 </p>
 
-<H2><a name="Guile_nn17">25.9 Exception Handling</a></H2>
+<H2><a name="Guile_nn17">26.9 Exception Handling</a></H2>
 
 
 <p>
@@ -487,7 +487,7 @@ mapping:
 The default when not specified here is to use "swig-error".
 See Lib/exception.i for details.
 
-<H2><a name="Guile_nn18">25.10 Procedure documentation</a></H2>
+<H2><a name="Guile_nn18">26.10 Procedure documentation</a></H2>
 
 
 <p>If invoked with the command-line option <code>-procdoc
@@ -522,7 +522,7 @@ like this:
 typemap argument <code>doc</code>. See <code>Lib/guile/typemaps.i</code> for
 details.
 
-<H2><a name="Guile_nn19">25.11 Procedures with setters</a></H2>
+<H2><a name="Guile_nn19">26.11 Procedures with setters</a></H2>
 
 
 <p>For global variables, SWIG creates a single wrapper procedure
@@ -550,7 +550,7 @@ struct members, the procedures <code>(<var>struct</var>-<var>member</var>-get
 pointer)</code> and <code>(<var>struct-member</var>-set pointer
 value)</code> are <em>not</em> generated.
 
-<H2><a name="Guile_nn20">25.12 GOOPS Proxy Classes</a></H2>
+<H2><a name="Guile_nn20">26.12 GOOPS Proxy Classes</a></H2>
 
 
 <p>SWIG can also generate classes and generic functions for use with
@@ -696,7 +696,7 @@ Notice that &lt;Foo&gt; is used before it is defined.  The fix is to just put th
 <code>%import "foo.h"</code> before the <code>%inline</code> block.
 </p>
 
-<H3><a name="Guile_nn21">25.12.1 Naming Issues</a></H3>
+<H3><a name="Guile_nn21">26.12.1 Naming Issues</a></H3>
 
 
 <p>As you can see in the example above, there are potential naming conflicts.  The default exported
@@ -733,7 +733,7 @@ guile-modules.  For example,</p>
 (use-modules ((Test) #:renamer (symbol-prefix-proc 'goops:)))
 </pre></div>
 
-<H3><a name="Guile_nn22">25.12.2 Linking</a></H3>
+<H3><a name="Guile_nn22">26.12.2 Linking</a></H3>
 
 
 <p>The guile-modules generated above all need to be linked together.  GOOPS support requires
diff --git a/Doc/Manual/Java.html b/Doc/Manual/Java.html
index 9dfaa1fd4..f1ca6667e 100644
--- a/Doc/Manual/Java.html
+++ b/Doc/Manual/Java.html
@@ -6,7 +6,7 @@
 <meta http-equiv="content-type" content="text/html; charset=UTF-8">
 </head>
 <body bgcolor="#FFFFFF">
-<H1><a name="Java">26 SWIG and Java</a></H1>
+<H1><a name="Java">27 SWIG and Java</a></H1>
 <!-- INDEX -->
 <div class="sectiontoc">
 <ul>
@@ -167,7 +167,7 @@ It covers most SWIG features, but certain low-level details are covered in less
 </p>
 
 
-<H2><a name="Java_overview">26.1 Overview</a></H2>
+<H2><a name="Java_overview">27.1 Overview</a></H2>
 
 
 <p>
@@ -202,7 +202,7 @@ Various customisation tips and techniques using SWIG directives are covered.
 The latter sections cover the advanced techniques of using typemaps for complete control of the wrapping process.
 </p>
 
-<H2><a name="Java_preliminaries">26.2 Preliminaries</a></H2>
+<H2><a name="Java_preliminaries">27.2 Preliminaries</a></H2>
 
 
 <p>
@@ -222,7 +222,7 @@ This is the commonly used method to load JNI code so your system will more than
 Android uses Java JNI and also works with SWIG. Please read the <a href="Android.html#Android">Android chapter</a> in conjunction with this one if you are targeting Android.
 </p>
 
-<H3><a name="Java_running_swig">26.2.1 Running SWIG</a></H3>
+<H3><a name="Java_running_swig">27.2.1 Running SWIG</a></H3>
 
 
 <p>
@@ -281,7 +281,7 @@ The following sections have further practical examples and details on how you mi
 compiling and using the generated files.
 </p>
 
-<H3><a name="Java_commandline">26.2.2 Additional Commandline Options</a></H3>
+<H3><a name="Java_commandline">27.2.2 Additional Commandline Options</a></H3>
 
 
 <p>
@@ -318,7 +318,7 @@ swig -java -help
 Their use will become clearer by the time you have finished reading this section on SWIG and Java.
 </p>
 
-<H3><a name="Java_getting_right_headers">26.2.3 Getting the right header files</a></H3>
+<H3><a name="Java_getting_right_headers">27.2.3 Getting the right header files</a></H3>
 
 
 <p>
@@ -333,7 +333,7 @@ They are usually in directories like this:</p>
 <p>
 The exact location may vary on your machine, but the above locations are typical. </p>
 
-<H3><a name="Java_compiling_dynamic">26.2.4 Compiling a dynamic module</a></H3>
+<H3><a name="Java_compiling_dynamic">27.2.4 Compiling a dynamic module</a></H3>
 
 
 <p>
@@ -368,7 +368,7 @@ The name of the shared library output file is important.
 If the name of your SWIG module is "<tt>example</tt>", the name of the corresponding shared library file should be "<tt>libexample.so</tt>" (or equivalent depending on your machine, see <a href="#Java_dynamic_linking_problems">Dynamic linking problems</a> for more information). 
 The name of the module is specified using the <tt>%module</tt> directive or <tt>-module</tt> command line option.</p>
 
-<H3><a name="Java_using_module">26.2.5 Using your module</a></H3>
+<H3><a name="Java_using_module">27.2.5 Using your module</a></H3>
 
 
 <p>
@@ -403,7 +403,7 @@ $
 If it doesn't work have a look at the following section which discusses problems loading the shared library.
 </p>
 
-<H3><a name="Java_dynamic_linking_problems">26.2.6 Dynamic linking problems</a></H3>
+<H3><a name="Java_dynamic_linking_problems">27.2.6 Dynamic linking problems</a></H3>
 
 
 <p>
@@ -490,7 +490,7 @@ The following section also contains some C++ specific linking problems and solut
 </p>
 
 
-<H3><a name="Java_compilation_problems_cpp">26.2.7 Compilation problems and compiling with C++</a></H3>
+<H3><a name="Java_compilation_problems_cpp">27.2.7 Compilation problems and compiling with C++</a></H3>
 
 
 <p>
@@ -542,7 +542,7 @@ Finally make sure the version of JDK header files matches the version of Java th
 </p>
 
 
-<H3><a name="Java_building_windows">26.2.8 Building on Windows</a></H3>
+<H3><a name="Java_building_windows">27.2.8 Building on Windows</a></H3>
 
 
 <p>
@@ -551,7 +551,7 @@ You will want to produce a DLL that can be loaded by the Java Virtual Machine.
 This section covers the process of using SWIG with Microsoft Visual C++ 6 although the procedure may be similar with other compilers.  
 In order for everything to work, you will need to have a JDK installed on your machine in order to read the JNI header files.</p>
 
-<H4><a name="Java_visual_studio">26.2.8.1 Running SWIG from Visual Studio</a></H4>
+<H4><a name="Java_visual_studio">27.2.8.1 Running SWIG from Visual Studio</a></H4>
 
 
 <p>
@@ -590,7 +590,7 @@ To run the native code in the DLL (example.dll), make sure that it is in your pa
 If the library fails to load have a look at <a href="#Java_dynamic_linking_problems">Dynamic linking problems</a>.
 </p>
 
-<H4><a name="Java_nmake">26.2.8.2 Using NMAKE</a></H4>
+<H4><a name="Java_nmake">27.2.8.2 Using NMAKE</a></H4>
 
 
 <p>
@@ -649,7 +649,7 @@ Of course you may want to make changes for it to work for C++ by adding in the -
 </p>
 
 
-<H2><a name="Java_basic_tour">26.3 A tour of basic C/C++ wrapping</a></H2>
+<H2><a name="Java_basic_tour">27.3 A tour of basic C/C++ wrapping</a></H2>
 
 
 <p>
@@ -659,7 +659,7 @@ variables are wrapped with JavaBean type getters and setters and so forth.
 This section briefly covers the essential aspects of this wrapping.
 </p>
 
-<H3><a name="Java_module_packages_classes">26.3.1 Modules, packages and generated Java classes</a></H3>
+<H3><a name="Java_module_packages_classes">27.3.1 Modules, packages and generated Java classes</a></H3>
 
 
 <p>
@@ -695,7 +695,7 @@ swig -java -package com.bloggs.swig -outdir com/bloggs/swig example.i
 SWIG won't create the directory, so make sure it exists beforehand.
 </p>
 
-<H3><a name="Java_functions">26.3.2 Functions</a></H3>
+<H3><a name="Java_functions">27.3.2 Functions</a></H3>
 
 
 <p>
@@ -729,7 +729,7 @@ System.out.println(example.fact(4));
 </pre></div>
 
 
-<H3><a name="Java_global_variables">26.3.3 Global variables</a></H3>
+<H3><a name="Java_global_variables">27.3.3 Global variables</a></H3>
 
 
 <p>
@@ -816,7 +816,7 @@ extern char *path;      // Read-only (due to %immutable)
 </div>
 
 
-<H3><a name="Java_constants">26.3.4 Constants</a></H3>
+<H3><a name="Java_constants">27.3.4 Constants</a></H3>
 
 
 <p>
@@ -956,7 +956,7 @@ Or if you decide this practice isn't so bad and your own class implements <tt>ex
 </p>
 
 
-<H3><a name="Java_enumerations">26.3.5 Enumerations</a></H3>
+<H3><a name="Java_enumerations">27.3.5 Enumerations</a></H3>
 
 
 <p>
@@ -970,7 +970,7 @@ The final two approaches use simple integers for each enum item.
 Before looking at the various approaches for wrapping named C/C++ enums, anonymous enums are considered.
 </p>
 
-<H4><a name="Java_anonymous_enums">26.3.5.1 Anonymous enums</a></H4>
+<H4><a name="Java_anonymous_enums">27.3.5.1 Anonymous enums</a></H4>
 
 
 <p>
@@ -1033,7 +1033,7 @@ As in the case of constants, you can access them through either the module class
 </p>
 
 
-<H4><a name="Java_typesafe_enums">26.3.5.2 Typesafe enums</a></H4>
+<H4><a name="Java_typesafe_enums">27.3.5.2 Typesafe enums</a></H4>
 
 
 <p>
@@ -1127,7 +1127,7 @@ When upgrading to JDK 1.5 or later, proper Java enums could be used instead, wit
 The following section details proper Java enum generation.
 </p>
 
-<H4><a name="Java_proper_enums">26.3.5.3 Proper Java enums</a></H4>
+<H4><a name="Java_proper_enums">27.3.5.3 Proper Java enums</a></H4>
 
 
 <p>
@@ -1180,7 +1180,7 @@ The additional support methods need not be generated if none of the enum items h
 <a href="#Java_simpler_enum_classes">Simpler Java enums for enums without initializers</a> section.
 </p>
 
-<H4><a name="Java_typeunsafe_enums">26.3.5.4 Type unsafe enums</a></H4>
+<H4><a name="Java_typeunsafe_enums">27.3.5.4 Type unsafe enums</a></H4>
 
 
 <p>
@@ -1228,7 +1228,7 @@ Note that unlike typesafe enums, this approach requires users to mostly use diff
 Thus the upgrade path to proper enums provided in JDK 1.5 is more painful.
 </p>
 
-<H4><a name="Java_simple_enums">26.3.5.5 Simple enums</a></H4>
+<H4><a name="Java_simple_enums">27.3.5.5 Simple enums</a></H4>
 
 
 <p>
@@ -1247,7 +1247,7 @@ SWIG-1.3.21 and earlier versions wrapped all enums using this approach.
 The type unsafe approach is preferable to this one and this simple approach is only included for backwards compatibility with these earlier versions of SWIG.
 </p>
 
-<H3><a name="Java_pointers">26.3.6 Pointers</a></H3>
+<H3><a name="Java_pointers">27.3.6 Pointers</a></H3>
 
 
 <p>
@@ -1335,7 +1335,7 @@ C-style cast may return a bogus result whereas as the C++-style cast will return
 a NULL pointer if the conversion can't be performed.
 </p>
 
-<H3><a name="Java_structures">26.3.7 Structures</a></H3>
+<H3><a name="Java_structures">27.3.7 Structures</a></H3>
 
 
 <p>
@@ -1503,7 +1503,7 @@ x.setA(3);          // Modify x.a - this is the same as b.f.a
 </div>
 
 
-<H3><a name="Java_classes">26.3.8 C++ classes</a></H3>
+<H3><a name="Java_classes">27.3.8 C++ classes</a></H3>
 
 
 <p>
@@ -1566,7 +1566,7 @@ int bar = Spam.getBar();
 </div>
 
 
-<H3><a name="Java_inheritance">26.3.9 C++ inheritance</a></H3>
+<H3><a name="Java_inheritance">27.3.9 C++ inheritance</a></H3>
 
 
 <p>
@@ -1627,7 +1627,7 @@ Note that Java does not support multiple inheritance so any multiple inheritance
 A warning is given when multiple inheritance is detected and only the first base class is used. 
 </p>
 
-<H3><a name="Java_pointers_refs_arrays">26.3.10 Pointers, references, arrays and pass by value</a></H3>
+<H3><a name="Java_pointers_refs_arrays">27.3.10 Pointers, references, arrays and pass by value</a></H3>
 
 
 <p>
@@ -1682,7 +1682,7 @@ to hold the result and a pointer is returned (Java will release this memory
 when the returned object's finalizer is run by the garbage collector).
 </p>
 
-<H4><a name="Java_null_pointers">26.3.10.1 Null pointers</a></H4>
+<H4><a name="Java_null_pointers">27.3.10.1 Null pointers</a></H4>
 
 
 <p>
@@ -1706,7 +1706,7 @@ For <tt>spam1</tt> and <tt>spam4</tt> above the Java <tt>null</tt> gets translat
 The converse also occurs, that is, NULL pointers are translated into <tt>null</tt> Java objects when returned from a C/C++ function.
 </p>
 
-<H3><a name="Java_overloaded_functions">26.3.11 C++ overloaded functions</a></H3>
+<H3><a name="Java_overloaded_functions">27.3.11 C++ overloaded functions</a></H3>
 
 
 <p>
@@ -1821,7 +1821,7 @@ void spam(unsigned short);   // Ignored
 </pre>
 </div>
 
-<H3><a name="Java_default_arguments">26.3.12 C++ default arguments</a></H3>
+<H3><a name="Java_default_arguments">27.3.12 C++ default arguments</a></H3>
 
 
 <p>
@@ -1864,7 +1864,7 @@ Further details on default arguments and how to restore this approach are given
 </p>
 
 
-<H3><a name="Java_namespaces">26.3.13 C++ namespaces</a></H3>
+<H3><a name="Java_namespaces">27.3.13 C++ namespaces</a></H3>
 
 
 <p>
@@ -1954,7 +1954,7 @@ If the resulting use of the nspace feature and hence packages results in a proxy
 you will need to open up the visibility for the pointer constructor and <tt>getCPtr</tt> method from the default 'protected' to 'public' with the <tt>SWIG_JAVABODY_PROXY</tt> macro. See <a href="#Java_code_typemaps">Java code typemaps</a>.
 </p>
 
-<H3><a name="Java_templates">26.3.14 C++ templates</a></H3>
+<H3><a name="Java_templates">27.3.14 C++ templates</a></H3>
 
 
 <p>
@@ -2003,10 +2003,10 @@ Obviously, there is more to template wrapping than shown in this example.
 More details can be found in the <a href="SWIGPlus.html#SWIGPlus">SWIG and C++</a> chapter.   
 </p>
 
-<H3><a name="Java_smart_pointers">26.3.15 C++ Smart Pointers</a></H3>
+<H3><a name="Java_smart_pointers">27.3.15 C++ Smart Pointers</a></H3>
 
 
-<H4><a name="Java_smart_pointers_shared_ptr">26.3.15.1 The shared_ptr Smart Pointer</a></H4>
+<H4><a name="Java_smart_pointers_shared_ptr">27.3.15.1 The shared_ptr Smart Pointer</a></H4>
 
 
 <p>
@@ -2017,7 +2017,7 @@ in the <a href="Library.html#Library_std_shared_ptr">shared_ptr smart pointer</a
 </p>
 
 
-<H4><a name="Java_smart_pointers_generic">26.3.15.2 Generic Smart Pointers</a></H4>
+<H4><a name="Java_smart_pointers_generic">27.3.15.2 Generic Smart Pointers</a></H4>
 
 
 <p>
@@ -2101,7 +2101,7 @@ Foo f = p.__deref__();               // Returns underlying Foo *
 </pre>
 </div>
 
-<H2><a name="Java_further_details">26.4 Further details on the generated Java classes</a></H2>
+<H2><a name="Java_further_details">27.4 Further details on the generated Java classes</a></H2>
 
 
 <p>
@@ -2116,7 +2116,7 @@ Finally enum classes are covered.
 First, the crucial intermediary JNI class is considered.
 </p>
 
-<H3><a name="Java_imclass">26.4.1 The intermediary JNI class</a></H3>
+<H3><a name="Java_imclass">27.4.1 The intermediary JNI class</a></H3>
 
 
 <p>
@@ -2236,7 +2236,7 @@ If <tt>name</tt> is the same as <tt>modulename</tt> then the module class name g
 from <tt>modulename</tt> to <tt>modulenameModule</tt>.
 </p>
 
-<H4><a name="Java_imclass_pragmas">26.4.1.1 The intermediary JNI class pragmas</a></H4>
+<H4><a name="Java_imclass_pragmas">27.4.1.1 The intermediary JNI class pragmas</a></H4>
 
 
 <p>
@@ -2318,7 +2318,7 @@ For example, let's change the intermediary JNI class access to just the default
 All the methods in the intermediary JNI class will then not be callable outside of the package as the method modifiers have been changed from public access to default access. This is useful if you want to prevent users calling these low level functions.
 </p>
 
-<H3><a name="Java_module_class">26.4.2 The Java module class</a></H3>
+<H3><a name="Java_module_class">27.4.2 The Java module class</a></H3>
 
 
 <p>
@@ -2349,7 +2349,7 @@ example.egg(new Foo());
 The primary reason for having the module class wrapping the calls in the intermediary JNI class is to implement static type checking. In this case only a <tt>Foo</tt> can be passed to the <tt>egg</tt> function, whereas any <tt>long</tt> can be passed to the <tt>egg</tt> function in the intermediary JNI class.
 </p>
 
-<H4><a name="Java_module_class_pragmas">26.4.2.1 The Java module class pragmas</a></H4>
+<H4><a name="Java_module_class_pragmas">27.4.2.1 The Java module class pragmas</a></H4>
 
 
 <p>
@@ -2400,7 +2400,7 @@ See <a href="#Java_imclass_pragmas">The intermediary JNI class pragmas</a> secti
 </p>
 
 
-<H3><a name="Java_proxy_classes">26.4.3 Java proxy classes</a></H3>
+<H3><a name="Java_proxy_classes">27.4.3 Java proxy classes</a></H3>
 
 
 <p>
@@ -2476,7 +2476,7 @@ int y = f.spam(5, new Foo());
 </pre>
 </div>
 
-<H4><a name="Java_memory_management">26.4.3.1 Memory management</a></H4>
+<H4><a name="Java_memory_management">27.4.3.1 Memory management</a></H4>
 
 
 <p>
@@ -2638,7 +2638,7 @@ and
 </p>
 
 
-<H4><a name="Java_inheritance_mirroring">26.4.3.2 Inheritance</a></H4>
+<H4><a name="Java_inheritance_mirroring">27.4.3.2 Inheritance</a></H4>
 
 
 <p>
@@ -2754,7 +2754,7 @@ However, true cross language polymorphism can be achieved using the <a href="#Ja
 </p>
 
 
-<H4><a name="Java_proxy_classes_gc">26.4.3.3 Proxy classes and garbage collection</a></H4>
+<H4><a name="Java_proxy_classes_gc">27.4.3.3 Proxy classes and garbage collection</a></H4>
 
 
 <p>
@@ -2837,7 +2837,7 @@ The section on <a href="#Java_typemaps">Java typemaps</a> details how to specify
 See the <a href="http://www.devx.com/Java/Article/30192">How to Handle Java Finalization's Memory-Retention Issues</a> article for alternative approaches to managing memory by avoiding finalizers altogether.
 </p>
 
-<H4><a name="Java_pgcpp">26.4.3.4 The premature garbage collection prevention parameter for proxy class marshalling</a></H4>
+<H4><a name="Java_pgcpp">27.4.3.4 The premature garbage collection prevention parameter for proxy class marshalling</a></H4>
 
 
 <p>
@@ -2959,7 +2959,7 @@ For example:
 <b>Compatibility note:</b> The generation of this additional parameter did not occur in versions prior to SWIG-1.3.30.
 </p>
 
-<H4><a name="Java_multithread_libraries">26.4.3.5 Single threaded applications and thread safety</a></H4>
+<H4><a name="Java_multithread_libraries">27.4.3.5 Single threaded applications and thread safety</a></H4>
 
 
 <p>
@@ -3047,7 +3047,7 @@ for (int i=0; i&lt;100000; i++) {
 </pre></div>
  
 
-<H3><a name="Java_type_wrapper_classes">26.4.4 Type wrapper classes</a></H3>
+<H3><a name="Java_type_wrapper_classes">27.4.4 Type wrapper classes</a></H3>
 
 
 <p>
@@ -3134,7 +3134,7 @@ public static void spam(SWIGTYPE_p_int x, SWIGTYPE_p_int y, int z) { ... }
 </div>
 
 
-<H3><a name="Java_enum_classes">26.4.5 Enum classes</a></H3>
+<H3><a name="Java_enum_classes">27.4.5 Enum classes</a></H3>
 
 
 <p>
@@ -3143,7 +3143,7 @@ The <a href="#Java_enumerations">Enumerations</a> section discussed these but om
 The following sub-sections detail the various types of enum classes that can be generated.
 </p>
 
-<H4><a name="Java_typesafe_enums_classes">26.4.5.1 Typesafe enum classes</a></H4>
+<H4><a name="Java_typesafe_enums_classes">27.4.5.1 Typesafe enum classes</a></H4>
 
 
 <p>
@@ -3227,7 +3227,7 @@ The <tt>swigValue</tt> method is used for marshalling in the other direction.
 The <tt>toString</tt> method is overridden so that the enum name is available.
 </p>
 
-<H4><a name="Java_proper_enums_classes">26.4.5.2 Proper Java enum classes</a></H4>
+<H4><a name="Java_proper_enums_classes">27.4.5.2 Proper Java enum classes</a></H4>
 
 
 <p>
@@ -3305,7 +3305,7 @@ These needn't be generated if the enum being wrapped does not have any initializ
 <a href="#Java_simpler_enum_classes">Simpler Java enums for enums without initializers</a> section describes how typemaps can be used to achieve this.
 </p>
 
-<H4><a name="Java_typeunsafe_enums_classes">26.4.5.3 Type unsafe enum classes</a></H4>
+<H4><a name="Java_typeunsafe_enums_classes">27.4.5.3 Type unsafe enum classes</a></H4>
 
 
 <p>
@@ -3336,7 +3336,7 @@ public final class Beverage {
 </pre>
 </div>
 
-<H3><a name="Java_interfaces">26.4.6 Interfaces</a></H3>
+<H3><a name="Java_interfaces">27.4.6 Interfaces</a></H3>
 
 
 <p>
@@ -3581,7 +3581,7 @@ typemap which is only used when a class is marked with the <tt>interface</tt> fe
 See <a href="Java.html#Java_code_typemaps">Java code typemaps</a> for details.
 </p>
 
-<H2><a name="Java_directors">26.5 Cross language polymorphism using directors</a></H2>
+<H2><a name="Java_directors">27.5 Cross language polymorphism using directors</a></H2>
 
 
 <p>
@@ -3603,7 +3603,7 @@ The upshot is that C++ classes can be extended in Java and from C++ these extens
 Neither C++ code nor Java code needs to know where a particular method is implemented: the combination of proxy classes, director classes, and C wrapper functions transparently takes care of all the cross-language method routing.
 </p>
 
-<H3><a name="Java_enabling_directors">26.5.1 Enabling directors</a></H3>
+<H3><a name="Java_enabling_directors">27.5.1 Enabling directors</a></H3>
 
 
 <p>
@@ -3671,7 +3671,7 @@ public:
 </pre>
 </div>
 
-<H3><a name="Java_directors_classes">26.5.2 Director classes</a></H3>
+<H3><a name="Java_directors_classes">27.5.2 Director classes</a></H3>
 
 
 <p>
@@ -3698,7 +3698,7 @@ If the correct implementation is in Java, the Java API is used to call the metho
 </p>
 
 
-<H3><a name="Java_directors_overhead">26.5.3 Overhead and code bloat</a></H3>
+<H3><a name="Java_directors_overhead">27.5.3 Overhead and code bloat</a></H3>
 
 
 <p>
@@ -3716,7 +3716,7 @@ This situation can be optimized by selectively enabling director methods (using
 </p>
 
 
-<H3><a name="Java_directors_example">26.5.4 Simple directors example</a></H3>
+<H3><a name="Java_directors_example">27.5.4 Simple directors example</a></H3>
 
 
 <p>
@@ -3779,7 +3779,7 @@ DirectorDerived.upcall_method() invoked.
 </pre>
 </div>
 
-<H3><a name="Java_directors_threading">26.5.5 Director threading issues</a></H3>
+<H3><a name="Java_directors_threading">27.5.5 Director threading issues</a></H3>
 
 
 <p>
@@ -3799,7 +3799,7 @@ Macros can be defined on the commandline when compiling your C++ code, or altern
 </pre>
 </div>
 
-<H3><a name="Java_directors_performance">26.5.6 Director performance tuning</a></H3>
+<H3><a name="Java_directors_performance">27.5.6 Director performance tuning</a></H3>
 
 
 <p>
@@ -3820,7 +3820,7 @@ However, if all director methods are expected to usually be overridden by Java s
 The disadvantage is that invocation of director methods from C++ when Java doesn't actually override the method will require an additional call up into Java and back to C++.  As such, this option is only useful when overrides are extremely common and instantiation is frequent enough that its performance is critical.
 </p>
 
-<H3><a name="Java_exceptions_from_directors">26.5.7 Java exceptions from directors</a></H3>
+<H3><a name="Java_exceptions_from_directors">27.5.7 Java exceptions from directors</a></H3>
 
 
 <p>
@@ -3896,7 +3896,7 @@ Exception in thread "main" java.lang.RuntimeException: There was a problem!
 More on the <tt>Swig::DirectorException</tt> class can be found in the next section which details how to customize the handling of director exceptions.
 </p>
 
-<H4><a name="Java_customizing_director_exceptions">26.5.7.1 Customizing director exceptions</a></H4>
+<H4><a name="Java_customizing_director_exceptions">27.5.7.1 Customizing director exceptions</a></H4>
 
 
 <p>
@@ -4454,7 +4454,7 @@ Exception in thread "main" java.lang.IndexOutOfBoundsException: Index is negativ
 </pre>
 </div>
 
-<H2><a name="Java_allprotected">26.6 Accessing protected members</a></H2>
+<H2><a name="Java_allprotected">27.6 Accessing protected members</a></H2>
 
 
 <p>
@@ -4550,7 +4550,7 @@ class MyProtectedBase extends ProtectedBase
 
 
 
-<H2><a name="Java_common_customization">26.7 Common customization features</a></H2>
+<H2><a name="Java_common_customization">27.7 Common customization features</a></H2>
 
 
 <p>
@@ -4562,7 +4562,7 @@ be awkward.  This section describes some common SWIG features that are used
 to improve the interface to existing C/C++ code.
 </p>
 
-<H3><a name="Java_helper_functions">26.7.1 C/C++ helper functions</a></H3>
+<H3><a name="Java_helper_functions">27.7.1 C/C++ helper functions</a></H3>
 
 
 <p>
@@ -4628,7 +4628,7 @@ hard to implement.  It is possible to improve on this using Java code, typemaps,
 customization features as covered in later sections, but sometimes helper functions are a quick and easy solution to difficult cases.  
 </p>
 
-<H3><a name="Java_class_extension">26.7.2 Class extension with %extend</a></H3>
+<H3><a name="Java_class_extension">27.7.2 Class extension with %extend</a></H3>
 
 
 <p>
@@ -4691,7 +4691,7 @@ Vector(2, 3, 4)
 in any way---the extensions only show up in the Java interface.
 </p>
 
-<H3><a name="Java_proxycode">26.7.3 Class extension with %proxycode</a></H3>
+<H3><a name="Java_proxycode">27.7.3 Class extension with %proxycode</a></H3>
 
 
 <p>
@@ -4828,7 +4828,7 @@ public class ValueUnsignedInt {
 </pre>
 </div>
 
-<H3><a name="Java_exception_handling">26.7.4 Exception handling with %exception and %javaexception</a></H3>
+<H3><a name="Java_exception_handling">27.7.4 Exception handling with %exception and %javaexception</a></H3>
 
 
 <p>
@@ -4987,7 +4987,7 @@ to raise exceptions.  See the <a href="Library.html#Library">SWIG Library</a> ch
 The typemap example <a href="#Java_exception_typemap">Handling C++ exception specifications as Java exceptions</a> provides further exception handling capabilities.
 </p>
 
-<H3><a name="Java_method_access">26.7.5 Method access with %javamethodmodifiers</a></H3>
+<H3><a name="Java_method_access">27.7.5 Method access with %javamethodmodifiers</a></H3>
 
 
 <p>
@@ -5013,7 +5013,7 @@ protected static void protect_me() {
 </pre>
 </div>
 
-<H2><a name="Java_tips_techniques">26.8 Tips and techniques</a></H2>
+<H2><a name="Java_tips_techniques">27.8 Tips and techniques</a></H2>
 
 
 <p>
@@ -5023,7 +5023,7 @@ strings and arrays.   This chapter discusses the common techniques for
 solving these problems.
 </p>
 
-<H3><a name="Java_input_output_parameters">26.8.1 Input and output parameters using primitive pointers and references</a></H3>
+<H3><a name="Java_input_output_parameters">27.8.1 Input and output parameters using primitive pointers and references</a></H3>
 
 
 <p>
@@ -5197,7 +5197,7 @@ void foo(Bar *OUTPUT);
 will not have the intended effect since <tt>typemaps.i</tt> does not define an OUTPUT rule for <tt>Bar</tt>.
 </p>
 
-<H3><a name="Java_simple_pointers">26.8.2 Simple pointers</a></H3>
+<H3><a name="Java_simple_pointers">27.8.2 Simple pointers</a></H3>
 
 
 <p>
@@ -5263,7 +5263,7 @@ System.out.println("3 + 4 = " + result);
 See the <a href="Library.html#Library">SWIG Library</a> chapter for further details.
 </p>
 
-<H3><a name="Java_c_arrays">26.8.3 Wrapping C arrays with Java arrays</a></H3>
+<H3><a name="Java_c_arrays">27.8.3 Wrapping C arrays with Java arrays</a></H3>
 
 
 <p>
@@ -5330,7 +5330,7 @@ Please be aware that the typemaps in this library are not efficient as all the e
 There is an alternative approach using the SWIG array library and this is covered in the next section.
 </p>
 
-<H3><a name="Java_unbounded_c_arrays">26.8.4 Unbounded C Arrays</a></H3>
+<H3><a name="Java_unbounded_c_arrays">27.8.4 Unbounded C Arrays</a></H3>
 
 
 <p>
@@ -5475,7 +5475,7 @@ well suited for applications in which you need to create buffers,
 package binary data, etc.
 </p>
 
-<H3><a name="Java_binary_char">26.8.5 Binary data vs Strings</a></H3>
+<H3><a name="Java_binary_char">27.8.5 Binary data vs Strings</a></H3>
 
 
 <p>
@@ -5519,7 +5519,7 @@ len: 5 data: 68 69 0 6a 6b
 </pre></div>
 
 
-<H3><a name="Java_heap_allocations">26.8.6 Overriding new and delete to allocate from Java heap</a></H3>
+<H3><a name="Java_heap_allocations">27.8.6 Overriding new and delete to allocate from Java heap</a></H3>
 
 
 <p>
@@ -5636,7 +5636,7 @@ model and use these functions in place of malloc and free in your own
 code.
 </p>
 
-<H2><a name="Java_typemaps">26.9 Java typemaps</a></H2>
+<H2><a name="Java_typemaps">27.9 Java typemaps</a></H2>
 
 
 <p>
@@ -5657,7 +5657,7 @@ Before proceeding, it should be stressed that typemaps are not a required
 part of using SWIG---the default wrapping behavior is enough in most cases.
 Typemaps are only used if you want to change some aspect of the generated code.
 
-<H3><a name="Java_default_primitive_type_mappings">26.9.1 Default primitive type mappings</a></H3>
+<H3><a name="Java_default_primitive_type_mappings">27.9.1 Default primitive type mappings</a></H3>
 
 
 <p>
@@ -5809,7 +5809,7 @@ However, the mappings allow the full range of values for each C type from Java.
 </p>
 
 
-<H3><a name="Java_default_non_primitive_typemaps">26.9.2 Default typemaps for non-primitive types</a></H3>
+<H3><a name="Java_default_non_primitive_typemaps">27.9.2 Default typemaps for non-primitive types</a></H3>
 
 
 <p>
@@ -5824,7 +5824,7 @@ So in summary, the C/C++ pointer to non-primitive types is cast into the 64 bit
 The Java type is either the proxy class or type wrapper class.
 </p>
 
-<H3><a name="Java_jvm64">26.9.3 Sixty four bit JVMs</a></H3>
+<H3><a name="Java_jvm64">27.9.3 Sixty four bit JVMs</a></H3>
 
 
 <p>
@@ -5837,7 +5837,7 @@ Unfortunately it won't of course hold true for JNI code.
 </p>
 
 
-<H3><a name="Java_what_is_typemap">26.9.4 What is a typemap?</a></H3>
+<H3><a name="Java_what_is_typemap">27.9.4 What is a typemap?</a></H3>
 
 
 <p>
@@ -5960,7 +5960,7 @@ int c = example.count('e', "Hello World");
 </pre>
 </div>
 
-<H3><a name="Java_typemaps_c_to_java_types">26.9.5 Typemaps for mapping C/C++ types to Java types</a></H3>
+<H3><a name="Java_typemaps_c_to_java_types">27.9.5 Typemaps for mapping C/C++ types to Java types</a></H3>
 
 
 <p>
@@ -6240,7 +6240,7 @@ These are listed below:
 
 </table>
 
-<H3><a name="Java_typemap_attributes">26.9.6 Java typemap attributes</a></H3>
+<H3><a name="Java_typemap_attributes">27.9.6 Java typemap attributes</a></H3>
 
 
 <p>
@@ -6286,7 +6286,7 @@ The "javain" typemap has the optional 'pre', 'post' and 'pgcppname' attributes.
 Note that when the 'pre' or 'post' attributes are specified and the associated type is used in a constructor, a constructor helper function is generated. This is necessary as the Java proxy constructor wrapper makes a call to a support constructor using a <i>this</i> call. In Java the <i>this</i> call must be the first statement in the constructor body. The constructor body thus calls the helper function and the helper function instead makes the JNI call, ensuring the 'pre' code is called before the JNI call is made. There is a <a href="#Java_date_marshalling">Date marshalling</a> example showing 'pre', 'post' and 'pgcppname' attributes in action.
 </p>
 
-<H3><a name="Java_special_variables">26.9.7 Java special variables</a></H3>
+<H3><a name="Java_special_variables">27.9.7 Java special variables</a></H3>
 
 
 <p>
@@ -6468,7 +6468,7 @@ in that it is not fully qualified with the package name when using the
 <a href="SWIGPlus.html#SWIGPlus_nspace">nspace feature</a>.
 </p>
 
-<H3><a name="Java_typemaps_for_c_and_cpp">26.9.8 Typemaps for both C and C++ compilation</a></H3>
+<H3><a name="Java_typemaps_for_c_and_cpp">27.9.8 Typemaps for both C and C++ compilation</a></H3>
 
 
 <p>
@@ -6505,7 +6505,7 @@ If you do not intend your code to be targeting both C and C++ then your typemaps
 </p>
 
 
-<H3><a name="Java_code_typemaps">26.9.9 Java code typemaps</a></H3>
+<H3><a name="Java_code_typemaps">27.9.9 Java code typemaps</a></H3>
 
 
 <p>
@@ -6801,7 +6801,7 @@ to make the method and constructor public:
 </pre>
 </div>
 
-<H3><a name="Java_directors_typemaps">26.9.10 Director specific typemaps</a></H3>
+<H3><a name="Java_directors_typemaps">27.9.10 Director specific typemaps</a></H3>
 
 
 <p>
@@ -7078,7 +7078,7 @@ The basic strategy here is to provide a default package typemap for the majority
 
 </div>
 
-<H2><a name="Java_typemap_examples">26.10 Typemap Examples</a></H2>
+<H2><a name="Java_typemap_examples">27.10 Typemap Examples</a></H2>
 
 
 <p>
@@ -7088,7 +7088,7 @@ the SWIG library.
 </p>
 
 
-<H3><a name="Java_simpler_enum_classes">26.10.1 Simpler Java enums for enums without initializers</a></H3>
+<H3><a name="Java_simpler_enum_classes">27.10.1 Simpler Java enums for enums without initializers</a></H3>
 
 
 <p>
@@ -7167,7 +7167,7 @@ This would be done by using the original versions of these typemaps in "enums.sw
 </p>
 
 
-<H3><a name="Java_exception_typemap">26.10.2 Handling C++ exception specifications as Java exceptions</a></H3>
+<H3><a name="Java_exception_typemap">27.10.2 Handling C++ exception specifications as Java exceptions</a></H3>
 
 
 <p>
@@ -7292,7 +7292,7 @@ We could alternatively have used <tt>%rename</tt> to rename <tt>what()</tt> into
 </p>
 
 
-<H3><a name="Java_nan_exception_typemap">26.10.3 NaN Exception - exception handling for a particular type</a></H3>
+<H3><a name="Java_nan_exception_typemap">27.10.3 NaN Exception - exception handling for a particular type</a></H3>
 
 
 <p>
@@ -7447,7 +7447,7 @@ If we were a martyr to the JNI cause, we could replace the succinct code within
 If we had, we would have put it in the "in" typemap which, like all JNI and Java typemaps, also supports the 'throws' attribute.
 </p>
 
-<H3><a name="Java_converting_java_string_arrays">26.10.4 Converting Java String arrays to char ** </a></H3>
+<H3><a name="Java_converting_java_string_arrays">27.10.4 Converting Java String arrays to char ** </a></H3>
 
 
 <p>
@@ -7591,7 +7591,7 @@ Lastly the "jni", "jtype" and "jstype" typemaps are also required to specify
 what Java types to use.
 </p>
 
-<H3><a name="Java_expanding_java_object">26.10.5 Expanding a Java object to multiple arguments</a></H3>
+<H3><a name="Java_expanding_java_object">27.10.5 Expanding a Java object to multiple arguments</a></H3>
 
 
 <p>
@@ -7673,7 +7673,7 @@ example.foo(new String[]{"red", "green", "blue", "white"});
 </div>
 
 
-<H3><a name="Java_using_typemaps_return_arguments">26.10.6 Using typemaps to return arguments</a></H3>
+<H3><a name="Java_using_typemaps_return_arguments">27.10.6 Using typemaps to return arguments</a></H3>
 
 
 <p>
@@ -7791,7 +7791,7 @@ $ java runme
 1 12.0  340.0
 </pre></div>
 
-<H3><a name="Java_adding_downcasts">26.10.7 Adding Java downcasts to polymorphic return types</a></H3>
+<H3><a name="Java_adding_downcasts">27.10.7 Adding Java downcasts to polymorphic return types</a></H3>
 
 
 <p>
@@ -7997,7 +7997,7 @@ SWIG usually generates code which constructs the proxy classes using Java code a
 Note that the JNI code above uses a number of string lookups to call a constructor, whereas this would not occur using byte compiled Java code.
 </p>
 
-<H3><a name="Java_adding_equals_method">26.10.8 Adding an equals method to the Java classes</a></H3>
+<H3><a name="Java_adding_equals_method">27.10.8 Adding an equals method to the Java classes</a></H3>
 
 
 <p>
@@ -8041,7 +8041,7 @@ System.out.println("foo1? " + foo1.equals(foo2));
 </div>
 
 
-<H3><a name="Java_void_pointers">26.10.9 Void pointers and a common Java base class</a></H3>
+<H3><a name="Java_void_pointers">27.10.9 Void pointers and a common Java base class</a></H3>
 
 
 <p>
@@ -8100,7 +8100,7 @@ This example contains some useful functionality which you may want in your code.
     <li> It also has a function which effectively implements a cast from the type of the proxy/type wrapper class to a void pointer. This is necessary for passing a proxy class or a type wrapper class to a function that takes a void pointer.
 </ul>
 
-<H3><a name="Java_struct_pointer_pointer">26.10.10 Struct pointer to pointer</a></H3>
+<H3><a name="Java_struct_pointer_pointer">27.10.10 Struct pointer to pointer</a></H3>
 
 
 <p>
@@ -8280,7 +8280,7 @@ The C functional interface has been completely morphed into an object-oriented i
 the Butler class would behave much like any pure Java class and feel more natural to Java users.
 </p>
 
-<H3><a name="Java_memory_management_member_variables">26.10.11 Memory management when returning references to member variables</a></H3>
+<H3><a name="Java_memory_management_member_variables">27.10.11 Memory management when returning references to member variables</a></H3>
 
 
 <p>
@@ -8403,7 +8403,7 @@ public class Bike {
 Note the <tt>addReference</tt> call.
 </p>
 
-<H3><a name="Java_memory_management_objects">26.10.12 Memory management for objects passed to the C++ layer</a></H3>
+<H3><a name="Java_memory_management_objects">27.10.12 Memory management for objects passed to the C++ layer</a></H3>
 
 
 <p>
@@ -8531,7 +8531,7 @@ as mentioned earlier, <tt>setElement</tt> is actually:
 </pre>
 </div>
 
-<H3><a name="Java_date_marshalling">26.10.13 Date marshalling using the javain typemap and associated attributes</a></H3>
+<H3><a name="Java_date_marshalling">27.10.13 Date marshalling using the javain typemap and associated attributes</a></H3>
 
 
 <p>
@@ -8708,7 +8708,7 @@ A few things to note:
 
 
 
-<H2><a name="Java_directors_faq">26.11 Living with Java Directors</a></H2>
+<H2><a name="Java_directors_faq">27.11 Living with Java Directors</a></H2>
 
 
 <p>
@@ -8887,10 +8887,10 @@ public abstract class UserVisibleFoo extends Foo {
   </li>
 </ol>
 
-<H2><a name="Java_odds_ends">26.12 Odds and ends</a></H2>
+<H2><a name="Java_odds_ends">27.12 Odds and ends</a></H2>
 
 
-<H3><a name="Java_javadoc_comments">26.12.1 JavaDoc comments</a></H3>
+<H3><a name="Java_javadoc_comments">27.12.1 JavaDoc comments</a></H3>
 
 
 <p>
@@ -8946,7 +8946,7 @@ public class Barmy {
 
 
 
-<H3><a name="Java_functional_interface">26.12.2 Functional interface without proxy classes</a></H3>
+<H3><a name="Java_functional_interface">27.12.2 Functional interface without proxy classes</a></H3>
 
 
 <p>
@@ -9007,7 +9007,7 @@ All destructors have to be called manually for example the <tt>delete_Foo(foo)</
 </p>
 
 
-<H3><a name="Java_using_own_jni_functions">26.12.3 Using your own JNI functions</a></H3>
+<H3><a name="Java_using_own_jni_functions">27.12.3 Using your own JNI functions</a></H3>
 
 
 <p>
@@ -9057,7 +9057,7 @@ This directive is only really useful if you want to mix your own hand crafted JN
 </p>
 
 
-<H3><a name="Java_performance">26.12.4 Performance concerns and hints</a></H3>
+<H3><a name="Java_performance">27.12.4 Performance concerns and hints</a></H3>
 
 
 <p>
@@ -9078,7 +9078,7 @@ However, you will have to be careful about memory management and make sure that
 This method normally calls the C++ destructor or <tt>free()</tt> for C code.
 </p>
 
-<H3><a name="Java_debugging">26.12.5 Debugging</a></H3>
+<H3><a name="Java_debugging">27.12.5 Debugging</a></H3>
 
 
 <p>
@@ -9100,7 +9100,7 @@ The -verbose:jni and -verbose:gc are also useful options for monitoring code beh
 </p>
 
 
-<H2><a name="Java_examples">26.13 Java Examples</a></H2>
+<H2><a name="Java_examples">27.13 Java Examples</a></H2>
 
 
 <p>
diff --git a/Doc/Manual/Javascript.html b/Doc/Manual/Javascript.html
index 10612f001..2a18aed8c 100644
--- a/Doc/Manual/Javascript.html
+++ b/Doc/Manual/Javascript.html
@@ -7,7 +7,7 @@
 </head>
 <body>
 
-<H1><a name="Javascript">27 SWIG and Javascript</a></H1>
+<H1><a name="Javascript">28 SWIG and Javascript</a></H1>
 <!-- INDEX -->
 <div class="sectiontoc">
 <ul>
@@ -52,7 +52,7 @@
 
 <p>This chapter describes SWIG's support of Javascript. It does not cover SWIG basics, but only information that is specific to this module.</p>
 
-<H2><a name="Javascript_overview">27.1 Overview</a></H2>
+<H2><a name="Javascript_overview">28.1 Overview</a></H2>
 
 
 <p>Javascript is a prototype-based scripting language that is dynamic, weakly typed and has first-class functions. Its arguably the most popular language for web development.
@@ -63,10 +63,10 @@ Javascript has gone beyond being a browser-based scripting language and with <a
 With <a href="https://github.com/rogerwang/node-webkit">node-webkit</a> there is a platform which uses Google's <code>Chromium</code> as Web-Browser widget and <code>node.js</code> for javascript extensions.
 </p>
 
-<H2><a name="Javascript_preliminaries">27.2 Preliminaries</a></H2>
+<H2><a name="Javascript_preliminaries">28.2 Preliminaries</a></H2>
 
 
-<H3><a name="Javascript_running_swig">27.2.1 Running SWIG</a></H3>
+<H3><a name="Javascript_running_swig">28.2.1 Running SWIG</a></H3>
 
 
 <p>Suppose that you defined a SWIG module such as the following:</p>
@@ -121,7 +121,7 @@ void example_initialize(v8::Handle&lt;v8::Object&gt; exports)</pre>
 <b>Note</b>: be aware that <code>v8</code> has a C++ API, and thus, the generated modules must be compiled as C++.
 </p>
 
-<H3><a name="Javascript_running_tests_examples">27.2.2 Running Tests and Examples</a></H3>
+<H3><a name="Javascript_running_tests_examples">28.2.2 Running Tests and Examples</a></H3>
 
 
 <p>The configuration for tests and examples currently supports Linux and Mac only and not MinGW (Windows) yet.</p>
@@ -153,7 +153,7 @@ $ make check-javascript-test-suite ENGINE=jsc</pre>
 $ make check-javascript-examples V8_VERSION=0x032530 ENGINE=v8</pre>
 </div>
 
-<H3><a name="Javascript_known_issues">27.2.3 Known Issues</a></H3>
+<H3><a name="Javascript_known_issues">28.2.3 Known Issues</a></H3>
 
 
 <p>At the moment, the Javascript generators pass all tests syntactically, i.e., the generated source code compiles. However, there are still remaining runtime issues.</p>
@@ -170,12 +170,12 @@ $ make check-javascript-examples V8_VERSION=0x032530 ENGINE=v8</pre>
 
 <p>The primary development environment has been Linux (Ubuntu 12.04). Windows and Mac OS X have been tested sporadically. Therefore, the generators might have more issues on those platforms. Please report back any problem you observe to help us improving this module quickly.</p>
 
-<H2><a name="Javascript_integration">27.3 Integration</a></H2>
+<H2><a name="Javascript_integration">28.3 Integration</a></H2>
 
 
 <p>This chapter gives a short introduction how to use a native Javascript extension: as a <code>node.js</code> module, and as an extension for an embedded Webkit.</p>
 
-<H3><a name="Javascript_node_extensions">27.3.1 Creating node.js Extensions</a></H3>
+<H3><a name="Javascript_node_extensions">28.3.1 Creating node.js Extensions</a></H3>
 
 
 <p>To install <code>node.js</code> you can download an installer from their <a href="https://launchpad.net/~chris-lea/+archive/node.js">web-site</a> for Mac OS X and Windows. For Linux you can either build the source yourself and run <code>sudo checkinstall</code> or keep to the (probably stone-age) packaged version. For Ubuntu there is a <a href="https://launchpad.net/~chris-lea/+archive/ubuntu/node.js/">PPA</a> available.</p>
@@ -221,7 +221,7 @@ require("./build/Release/example")</pre>
 </div>
 <p>A more detailed explanation is given in the <a href="#Javascript_examples">Examples</a> section.</p>
 
-<H4><a name="Javascript_troubleshooting">27.3.1.1 Troubleshooting</a></H4>
+<H4><a name="Javascript_troubleshooting">28.3.1.1 Troubleshooting</a></H4>
 
 
 <ul>
@@ -233,12 +233,12 @@ require("./build/Release/example")</pre>
 $ sudo apt-get remove gyp</pre>
 </div>
 
-<H3><a name="Javascript_embedded_webkit">27.3.2 Embedded Webkit</a></H3>
+<H3><a name="Javascript_embedded_webkit">28.3.2 Embedded Webkit</a></H3>
 
 
 <p>Webkit is pre-installed on Mac OS X and available as a library for GTK.</p>
 
-<H4><a name="Javascript_osx">27.3.2.1 Mac OS X</a></H4>
+<H4><a name="Javascript_osx">28.3.2.1 Mac OS X</a></H4>
 
 
 <p>There is general information about programming with WebKit on <a href="https://developer.apple.com/library/mac/documentation/cocoa/conceptual/DisplayWebContent/DisplayWebContent.html">Apple Developer Documentation</a>. Details about <code>Cocoa</code> programming are not covered here.</p>
@@ -286,7 +286,7 @@ extern bool example_initialize(JSGlobalContextRef context, JSObjectRef* exports)
 @end</pre>
 </div>
 
-<H4><a name="Javascript_gtk">27.3.2.2 GTK</a></H4>
+<H4><a name="Javascript_gtk">28.3.2.2 GTK</a></H4>
 
 
 <p>There is general information about programming GTK at <a href="https://developer.gnome.org/gtk2/">GTK documentation</a> and in the <a href="https://developer.gnome.org/gtk-tutorial">GTK tutorial</a>, and for Webkit there is a <a href="http://webkitgtk.org/reference/webkitgtk/stable/index.html">Webkit GTK+ API Reference</a>.</p>
@@ -331,7 +331,7 @@ int main(int argc, char* argv[])
 }</pre>
 </div>
 
-<H3><a name="Javascript_applications_webkit">27.3.3 Creating Applications with node-webkit</a></H3>
+<H3><a name="Javascript_applications_webkit">28.3.3 Creating Applications with node-webkit</a></H3>
 
 
 <p>To get started with <code>node-webkit</code> there is a very informative set of <a href="https://github.com/rogerwang/node-webkit/wiki">wiki pages</a>.</p>
@@ -422,12 +422,12 @@ open new windows, and many more things.
 };</pre>
 </div>
 
-<H2><a name="Javascript_examples">27.4 Examples</a></H2>
+<H2><a name="Javascript_examples">28.4 Examples</a></H2>
 
 
 <p>Some basic examples are shown here in more detail.</p>
 
-<H3><a name="Javascript_simple_example">27.4.1 Simple</a></H3>
+<H3><a name="Javascript_simple_example">28.4.1 Simple</a></H3>
 
 
 <p>The common example <code>simple</code> looks like this:</p>
@@ -477,7 +477,7 @@ example.Foo = 3.1415926;</pre>
 
 <p><b>Note</b>: ECMAScript 5, the currently implemented Javascript standard, does not have modules. <code>node.js</code> and other implementations provide this mechanism defined by the <a href="http://wiki.commonjs.org/wiki/CommonJS">CommonJS</a> group. For browsers this is provided by <a href="http://browserify.org">Browserify</a>, for instance.</p>
 
-<H3><a name="Javascript_class_example">27.4.2 Class</a></H3>
+<H3><a name="Javascript_class_example">28.4.2 Class</a></H3>
 
 
 <p>The common example <code>class</code> defines three classes, <code>Shape</code>, <code>Circle</code>, and <code>Square</code>:</p>
@@ -607,12 +607,12 @@ at emitKey (readline.js:1095:12)</pre>
 <b>Note</b>: In ECMAScript 5 there is no concept for classes. Instead each function can be used as a constructor function which is executed by the 'new' operator. Furthermore, during construction the key property <code>prototype</code> of the constructor function is used to attach a prototype instance to the created object. A prototype is essentially an object itself that is the first-class delegate of a class used whenever the access to a property of an object fails. The very same prototype instance is shared among all instances of one type. Prototypal inheritance is explained in more detail on in <a href="https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Inheritance_and_the_prototype_chain">Inheritance and the prototype chain</a>, for instance.
 </p>
 
-<H2><a name="Javascript_implementation">27.5 Implementation</a></H2>
+<H2><a name="Javascript_implementation">28.5 Implementation</a></H2>
 
 
 <p>The Javascript Module implementation has taken a very different approach compared to other language modules in order to support different Javascript interpreters.</p>
 
-<H3><a name="Javascript_source_code">27.5.1 Source Code</a></H3>
+<H3><a name="Javascript_source_code">28.5.1 Source Code</a></H3>
 
 
 <p>The Javascript module is implemented in <code>Source/Modules/javascript.cxx</code>. It dispatches the code generation to a <code>JSEmitter</code> instance, <code>V8Emitter</code> or <code>JSCEmitter</code>. Additionally there are some helpers: <code>Template</code>, for templated code generation, and <code>JSEmitterState</code>, which is used to manage state information during AST traversal. This rough map shall make it easier to find a way through this huge source file:</p>
@@ -713,7 +713,7 @@ Template::Template(const String *code_) { ... }
 ...</pre>
 </div>
 
-<H3><a name="Javascript_code_templates">27.5.2 Code Templates</a></H3>
+<H3><a name="Javascript_code_templates">28.5.2 Code Templates</a></H3>
 
 
 <p>All generated code is created on the basis of code templates. The templates for <em>JavascriptCore</em> can be found in <code>Lib/javascript/jsc/javascriptcode.swg</code>, for <em>v8</em> in <code>Lib/javascript/v8/javascriptcode.swg</code>.</p>
@@ -752,7 +752,7 @@ t_register.replace("$jsparent", state.clazz(NAME_MANGLED))
 </div>
 <p><code>Template</code> creates a copy of that string and <code>Template::replace</code> uses Swig's <code>Replaceall</code> to replace variables in the template. <code>Template::trim</code> can be used to eliminate leading and trailing whitespaces. <code>Template::print</code> is used to write the final template string to a Swig <code>DOH</code> (based on <code>Printv</code>). All methods allow chaining.</p>
 
-<H3><a name="Javascript_emitter">27.5.3 Emitter</a></H3>
+<H3><a name="Javascript_emitter">28.5.3 Emitter</a></H3>
 
 
 <p>The Javascript module delegates code generation to a <code>JSEmitter</code> instance. The following extract shows the essential interface:</p>
@@ -871,7 +871,7 @@ int JAVASCRIPT::classHandler(Node *n) {
 </div>
 <p>In <code>enterClass</code> the emitter stores state information that is necessary when processing class members. In <code>exitClass</code> the wrapper code for the whole class is generated.</p>
 
-<H3><a name="Javascript_emitter_states">27.5.4 Emitter states</a></H3>
+<H3><a name="Javascript_emitter_states">28.5.4 Emitter states</a></H3>
 
 
 <p>For storing information during the AST traversal the emitter provides a <code>JSEmitterState</code> with different slots to store data representing the scopes global, class, function, and variable.</p>
@@ -915,7 +915,7 @@ state.clazz(NAME, Getattr(n, "sym:name"));</pre>
 <p>State information can be retrieved using <code>state.clazz(NAME)</code> or with <code>Getattr</code> on <code>state.clazz()</code> which actually returns a <code>Hash</code> instance.</p>
 
 
-<H3><a name="Javascript_jsc_exceptions">27.5.5 Handling Exceptions in JavascriptCore</a></H3>
+<H3><a name="Javascript_jsc_exceptions">28.5.5 Handling Exceptions in JavascriptCore</a></H3>
 
 
 <p>Applications with an embedded JavascriptCore should be able to present detailed exception messages that occur in the Javascript engine. Below is an example derived from code provided by Brian Barnes on how these exception details can be extracted.</p>
diff --git a/Doc/Manual/Lisp.html b/Doc/Manual/Lisp.html
index 0d9e3dc4f..7ea6fb1b9 100644
--- a/Doc/Manual/Lisp.html
+++ b/Doc/Manual/Lisp.html
@@ -7,7 +7,7 @@
 </head>
 
 <body bgcolor="#ffffff">
-<H1><a name="Lisp">28 SWIG and Common Lisp</a></H1>
+<H1><a name="Lisp">29 SWIG and Common Lisp</a></H1>
 <!-- INDEX -->
 <div class="sectiontoc">
 <ul>
@@ -42,7 +42,7 @@
       Lisp, Common Foreign Function Interface(CFFI), CLisp and UFFI
       foreign function interfaces.  
 </p>
-<H2><a name="Lisp_nn2">28.1 Allegro Common Lisp</a></H2>
+<H2><a name="Lisp_nn2">29.1 Allegro Common Lisp</a></H2>
 
 
 <p>
@@ -51,7 +51,7 @@
   <a href="Allegrocl.html#Allegrocl">here</a>
 </p>
 
-<H2><a name="Lisp_nn3">28.2 Common Foreign Function Interface(CFFI)</a></H2>
+<H2><a name="Lisp_nn3">29.2 Common Foreign Function Interface(CFFI)</a></H2>
 
 
 <p>
@@ -78,7 +78,7 @@ swig -cffi -module <i>module-name</i>   <i>file-name</i>
       files and the various things which you can do with them.
 </p>
 
-<H3><a name="Lisp_nn4">28.2.1 Additional Commandline Options </a></H3>
+<H3><a name="Lisp_nn4">29.2.1 Additional Commandline Options </a></H3>
 
 
 <p>
@@ -119,7 +119,7 @@ swig -cffi -help
 
 </table>
 
-<H3><a name="Lisp_nn5">28.2.2 Generating CFFI bindings</a></H3>
+<H3><a name="Lisp_nn5">29.2.2 Generating CFFI bindings</a></H3>
 
 
 <p>
@@ -403,7 +403,7 @@ The feature <i>intern_function</i> ensures that all C names are
 
 </pre></div>
 
-<H3><a name="Lisp_nn6">28.2.3 Generating CFFI bindings for C++ code</a></H3>
+<H3><a name="Lisp_nn6">29.2.3 Generating CFFI bindings for C++ code</a></H3>
 
 
 <p>This feature to SWIG (for CFFI) is very new and still far from
@@ -582,7 +582,7 @@ If you have any questions, suggestions, patches, etc., related to CFFI
       module feel free to contact us on the SWIG mailing list, and
       also please add a "[CFFI]" tag in the subject line.
 
-<H3><a name="Lisp_nn7">28.2.4 Inserting user code into generated files</a></H3>
+<H3><a name="Lisp_nn7">29.2.4 Inserting user code into generated files</a></H3>
 
 
 <p>
@@ -622,7 +622,7 @@ Note that the block <tt>%{ ... %}</tt> is effectively a shortcut for
 </p>
 
 
-<H2><a name="Lisp_nn8">28.3 CLISP</a></H2>
+<H2><a name="Lisp_nn8">29.3 CLISP</a></H2>
 
 
 <p>
@@ -652,7 +652,7 @@ swig -clisp -module <i>module-name</i>   <i>file-name</i>
     interface file for the CLISP module. The CLISP module tries to
     produce code which is both human readable and easily modifyable.
 </p>
-<H3><a name="Lisp_nn9">28.3.1 Additional Commandline Options </a></H3>
+<H3><a name="Lisp_nn9">29.3.1 Additional Commandline Options </a></H3>
 
 
 <p>
@@ -685,7 +685,7 @@ shortcuts according to the typedefs in the input.
 
 </table>
 
-<H3><a name="Lisp_nn10">28.3.2 Details on CLISP bindings</a></H3>
+<H3><a name="Lisp_nn10">29.3.2 Details on CLISP bindings</a></H3>
 
 
 <p>
@@ -809,7 +809,7 @@ struct bar {
 
 </pre></div>
 
-<H2><a name="Lisp_nn11">28.4 UFFI </a></H2>
+<H2><a name="Lisp_nn11">29.4 UFFI </a></H2>
 
 
 </body>
diff --git a/Doc/Manual/Lua.html b/Doc/Manual/Lua.html
index 8e545776f..944223f3c 100644
--- a/Doc/Manual/Lua.html
+++ b/Doc/Manual/Lua.html
@@ -7,7 +7,7 @@
 </head>
 
 <body bgcolor="#ffffff">
-<H1><a name="Lua">29 SWIG and Lua</a></H1>
+<H1><a name="Lua">30 SWIG and Lua</a></H1>
 <!-- INDEX -->
 <div class="sectiontoc">
 <ul>
@@ -83,14 +83,14 @@ Lua is an extension programming language designed to support general procedural
 eLua stands for Embedded Lua (can be thought of as a flavor of Lua) and offers the full implementation of the Lua programming language to the embedded world, extending it with specific features for efficient and portable software embedded development. eLua runs on smaller devices like microcontrollers and provides the full features of the regular Lua desktop version. More information on eLua can be found here: <a href="http://www.eluaproject.net">http://www.eluaproject.net</a>
 </p>
 
-<H2><a name="Lua_nn2">29.1 Preliminaries</a></H2>
+<H2><a name="Lua_nn2">30.1 Preliminaries</a></H2>
 
 
 <p>
 The current SWIG implementation is designed to work with Lua 5.0.x, 5.1.x and 5.2.x. It should work with later versions of Lua, but certainly not with Lua 4.0 due to substantial API changes. It is possible to either static link or dynamic link a Lua module into the interpreter (normally Lua static links its libraries, as dynamic linking is not available on all platforms). SWIG also has support for eLua starting from eLua 0.8. Due to substantial changes between SWIG 2.x and SWIG 3.0 and unavailability of testing platform, eLua status was downgraded to 'experimental'.
 </p>
 
-<H2><a name="Lua_nn3">29.2 Running SWIG</a></H2>
+<H2><a name="Lua_nn3">30.2 Running SWIG</a></H2>
 
 
 <p>
@@ -138,7 +138,7 @@ $ swig -lua -eluac example.i
 The <tt>-elua</tt> option puts all the C function wrappers and variable get/set wrappers in rotables. It also generates a metatable which will control the access to these variables from eLua. It also offers a significant amount of module size compression. On the other hand, the <tt>-eluac</tt> option puts all the wrappers in a single rotable. With this option, no matter how huge the module, it will consume no additional microcontroller SRAM (crass compression). There is a catch though: Metatables are not generated with <tt>-eluac</tt>. To access any value from eLua, one must directly call the wrapper function associated with that value.
 </p>
 
-<H3><a name="Lua_commandline">29.2.1 Additional command line options</a></H3>
+<H3><a name="Lua_commandline">30.2.1 Additional command line options</a></H3>
 
 
 <p>
@@ -179,7 +179,7 @@ swig -lua -help
 </tr>
 </table>
 
-<H3><a name="Lua_nn4">29.2.2 Compiling and Linking and Interpreter</a></H3>
+<H3><a name="Lua_nn4">30.2.2 Compiling and Linking and Interpreter</a></H3>
 
 
 <p>
@@ -250,7 +250,7 @@ LUALIB_API int ( luaopen_mod )(lua_State *L );
 More information on building and configuring eLua can be found here: <a href="http://www.eluaproject.net/doc/v0.8/en_building.html">http://www.eluaproject.net/doc/v0.8/en_building.html</a>
 </p>
 
-<H3><a name="Lua_nn5">29.2.3 Compiling a dynamic module</a></H3>
+<H3><a name="Lua_nn5">30.2.3 Compiling a dynamic module</a></H3>
 
 
 <p>
@@ -318,7 +318,7 @@ Is quite obvious (Go back and consult the Lua documents on how to enable loadlib
 
 
 
-<H3><a name="Lua_nn6">29.2.4 Using your module</a></H3>
+<H3><a name="Lua_nn6">30.2.4 Using your module</a></H3>
 
 
 <p>
@@ -336,19 +336,19 @@ $ ./my_lua
 &gt;
 </pre></div>
 
-<H2><a name="Lua_nn7">29.3 A tour of basic C/C++ wrapping</a></H2>
+<H2><a name="Lua_nn7">30.3 A tour of basic C/C++ wrapping</a></H2>
 
 
 <p>
 By default, SWIG tries to build a very natural Lua interface to your C/C++ code. This section briefly covers the essential aspects of this wrapping.
 </p>
-<H3><a name="Lua_nn8">29.3.1 Modules</a></H3>
+<H3><a name="Lua_nn8">30.3.1 Modules</a></H3>
 
 
 <p>
 The SWIG module directive specifies the name of the Lua module. If you specify `module example', then everything is wrapped into a Lua table 'example' containing all the functions and variables. When choosing a module name, make sure you don't use the same name as a built-in Lua command or standard module name.
 </p>
-<H3><a name="Lua_nn9">29.3.2 Functions</a></H3>
+<H3><a name="Lua_nn9">30.3.2 Functions</a></H3>
 
 
 <p>
@@ -389,7 +389,7 @@ It is also possible to rename the module with an assignment.
 24
 </pre></div>
 
-<H3><a name="Lua_nn10">29.3.3 Global variables</a></H3>
+<H3><a name="Lua_nn10">30.3.3 Global variables</a></H3>
 
 
 <p>
@@ -477,7 +477,7 @@ If you have used the <tt>-eluac</tt> option for your eLua module, you will have
 In general, functions of the form <tt>"variable_get()"</tt> and <tt>"variable_set()"</tt> are automatically generated by SWIG for use with <tt>-eluac</tt>.
 </p>
 
-<H3><a name="Lua_nn11">29.3.4 Constants and enums</a></H3>
+<H3><a name="Lua_nn11">30.3.4 Constants and enums</a></H3>
 
 
 <p>
@@ -512,7 +512,7 @@ If you're using eLua and have used <tt>-elua</tt> or <tt>-eluac</tt> to generate
 Hello World
 </pre></div>
 
-<H4><a name="Lua_nn13">29.3.4.1 Constants/enums and classes/structures</a></H4>
+<H4><a name="Lua_nn13">30.3.4.1 Constants/enums and classes/structures</a></H4>
 
 
 <p>
@@ -568,7 +568,7 @@ If the <tt>-no-old-metatable-bindings</tt> option is used, then these old-style
 It is worth mentioning, that <tt>example.Test.TEST1</tt> and <tt>example.Test_TEST1</tt> are different entities and changing one does not change the other. 
 Given the fact that these are constantes and they are not supposed to be changed, it is up to you to avoid such issues.
 </p>
-<H3><a name="Lua_nn12">29.3.5 Pointers</a></H3>
+<H3><a name="Lua_nn12">30.3.5 Pointers</a></H3>
 
 
 <p>
@@ -606,7 +606,7 @@ Lua enforces the integrity of its userdata, so it is virtually impossible to cor
 nil
 </pre></div>
 
-<H3><a name="Lua_structures">29.3.6 Structures</a></H3>
+<H3><a name="Lua_structures">30.3.6 Structures</a></H3>
 
 
 <p>
@@ -710,7 +710,7 @@ For eLua with the <tt>-eluac</tt> option, structure manipulation has to be perfo
 In general, functions of the form <tt>"new_struct()"</tt>, <tt>"struct_member_get()"</tt>, <tt>"struct_member_set()"</tt> and <tt>"free_struct()"</tt> are automatically generated by SWIG for each structure defined in C. (Please note: This doesn't apply for modules generated with the <tt>-elua</tt> option)
 </p>
 
-<H3><a name="Lua_nn14">29.3.7 C++ classes</a></H3>
+<H3><a name="Lua_nn14">30.3.7 C++ classes</a></H3>
 
 
 <p>
@@ -785,7 +785,7 @@ Both style names are generated by default now.
 However, if the <tt>-no-old-metatable-bindings</tt> option is used, then the backward compatible names are not generated in addition to ordinary ones.
 </p>
 
-<H3><a name="Lua_nn15">29.3.8 C++ inheritance</a></H3>
+<H3><a name="Lua_nn15">30.3.8 C++ inheritance</a></H3>
 
 
 <p>
@@ -810,7 +810,7 @@ then the function <tt>spam()</tt> accepts a Foo pointer or a pointer to any clas
 <p>
 It is safe to use multiple inheritance with SWIG.
 </p>
-<H3><a name="Lua_nn16">29.3.9 Pointers, references, values, and arrays</a></H3>
+<H3><a name="Lua_nn16">30.3.9 Pointers, references, values, and arrays</a></H3>
 
 
 <p>
@@ -841,7 +841,7 @@ Foo  spam7();
 <p>
 then all three functions will return a pointer to some Foo object. Since the third function (spam7) returns a value, newly allocated memory is used to hold the result and a pointer is returned (Lua will release this memory when the return value is garbage collected). The other two are pointers which are assumed to be managed by the C code and so will not be garbage collected.
 </p>
-<H3><a name="Lua_nn17">29.3.10 C++ overloaded functions</a></H3>
+<H3><a name="Lua_nn17">30.3.10 C++ overloaded functions</a></H3>
 
 
 <p>
@@ -927,7 +927,7 @@ Please refer to the "SWIG and C++" chapter for more information about overloadin
 <p>
 Dealing with the Lua coercion mechanism, the priority is roughly (integers, floats, strings, userdata). But it is better to rename the functions rather than rely upon the ordering.
 </p>
-<H3><a name="Lua_nn18">29.3.11 C++ operators</a></H3>
+<H3><a name="Lua_nn18">30.3.11 C++ operators</a></H3>
 
 
 <p>
@@ -1059,7 +1059,7 @@ operators and pseudo-operators):</p>
 </ul>
 <p>No other lua metafunction is inherited. For example, __gc is not inherited and must be redefined in every class. <tt>__tostring</tt> is subject to a special handling. If absent in class and in class bases, a default one will be provided by SWIG.
 </p>
-<H3><a name="Lua_nn19">29.3.12 Class extension with %extend</a></H3>
+<H3><a name="Lua_nn19">30.3.12 Class extension with %extend</a></H3>
 
 
 <p>
@@ -1116,7 +1116,7 @@ true
 Extend works with both C and C++ code, on classes and structs. It does not modify the underlying object in any way---the extensions only show up in the Lua interface. The only item to take note of is the code has to use the '$self' instead of 'this', and that you cannot access protected/private members of the code (as you are not officially part of the class).
 </p>
 
-<H3><a name="Lua_nn20">29.3.13 Using %newobject to release memory</a></H3>
+<H3><a name="Lua_nn20">30.3.13 Using %newobject to release memory</a></H3>
 
 
 <p> If you have a function that allocates memory like this,</p>
@@ -1140,7 +1140,7 @@ char *foo();
 </div>
 <p> This will release the allocated memory.</p>
 
-<H3><a name="Lua_nn21">29.3.14 C++ templates</a></H3>
+<H3><a name="Lua_nn21">30.3.14 C++ templates</a></H3>
 
 
 <p>
@@ -1175,7 +1175,7 @@ In Lua:
 <p>
 Obviously, there is more to template wrapping than shown in this example. More details can be found in the SWIG and C++ chapter. Some more complicated examples will appear later.
 </p>
-<H3><a name="Lua_nn22">29.3.15 C++ Smart Pointers</a></H3>
+<H3><a name="Lua_nn22">30.3.15 C++ Smart Pointers</a></H3>
 
 
 <p>
@@ -1227,7 +1227,7 @@ If you ever need to access the underlying pointer returned by <tt>operator-&gt;(
 &gt; f = p:__deref__()     -- Returns underlying Foo *
 </pre></div>
 
-<H3><a name="Lua_nn23">29.3.16 C++ Exceptions</a></H3>
+<H3><a name="Lua_nn23">30.3.16 C++ Exceptions</a></H3>
 
 
 <p>
@@ -1370,7 +1370,7 @@ and the "<a href="Customization.html#Customization_exception">Exception handling
 add exception specification to functions or globally (respectively).
 </p>
 
-<H3><a name="Lua_namespaces">29.3.17 Namespaces </a></H3>
+<H3><a name="Lua_namespaces">30.3.17 Namespaces </a></H3>
 
 
 <p>
@@ -1421,7 +1421,7 @@ Now, from Lua usage is as follows:
 19
 &gt;
 </pre></div>
-<H4><a name="Lua_nn27">29.3.17.1 Compatibility Note </a></H4>
+<H4><a name="Lua_nn27">30.3.17.1 Compatibility Note </a></H4>
 
 
 <p>
@@ -1437,7 +1437,7 @@ If SWIG is running in a backwards compatible way, i.e. without the <tt>-no-old-m
 </pre></div>
 
 
-<H4><a name="Lua_nn29">29.3.17.2 Names </a></H4>
+<H4><a name="Lua_nn29">30.3.17.2 Names </a></H4>
 
 
 <p> If SWIG is launched without <tt>-no-old-metatable-bindings</tt> option, then it enters backward-compatible mode. While in this mode, it tries
@@ -1481,7 +1481,7 @@ surrounding scope without any prefixing. Pretending that Test2 is a struct, not
 &gt;
 </pre></div>
 
-<H4><a name="Lua_nn30">29.3.17.3 Inheritance </a></H4>
+<H4><a name="Lua_nn30">30.3.17.3 Inheritance </a></H4>
 
 
 <p> The internal organization of inheritance has changed. 
@@ -1522,12 +1522,12 @@ function
 &gt;
 </pre></div>
 
-<H2><a name="Lua_nn24">29.4 Typemaps</a></H2>
+<H2><a name="Lua_nn24">30.4 Typemaps</a></H2>
 
 
 <p>This section explains what typemaps are and how to use them. The default wrapping behaviour of SWIG is enough in most cases. However sometimes SWIG may need a little additional assistance to know which typemap to apply to provide the best wrapping. This section will be explaining how to use typemaps to best effect</p>
 
-<H3><a name="Lua_nn25">29.4.1 What is a typemap?</a></H3>
+<H3><a name="Lua_nn25">30.4.1 What is a typemap?</a></H3>
 
 
 <p>A typemap is nothing more than a code generation rule that is attached to a specific C datatype. For example, to convert integers from Lua to C, you might define a typemap like this:</p>
@@ -1555,7 +1555,7 @@ Received an integer : 6
 720
 </pre></div>
 
-<H3><a name="Lua_nn26">29.4.2 Using typemaps</a></H3>
+<H3><a name="Lua_nn26">30.4.2 Using typemaps</a></H3>
 
 
 <p>There are many ready written typemaps built into SWIG for all common types (int, float, short, long, char*, enum and more), which SWIG uses automatically, with no effort required on your part.</p>
@@ -1608,7 +1608,7 @@ void swap(int *sx, int *sy);
 
 <p>Note: C++ references must be handled exactly the same way. However SWIG will automatically wrap a <tt>const int&amp;</tt>  as an input parameter (since that it obviously input).</p>
 
-<H3><a name="Lua_typemap_arrays">29.4.3 Typemaps and arrays</a></H3>
+<H3><a name="Lua_typemap_arrays">30.4.3 Typemaps and arrays</a></H3>
 
 
 <p>Arrays present a challenge for SWIG, because like pointers SWIG does not know whether these are input or output values, nor
@@ -1672,7 +1672,7 @@ and Lua tables to be 1..N, (the indexing follows the norm for the language). In
 
 <p>Note: SWIG also can support arrays of pointers in a similar manner.</p>
 
-<H3><a name="Lua_typemaps_ptr_ptr_functions">29.4.4 Typemaps and pointer-pointer functions</a></H3>
+<H3><a name="Lua_typemaps_ptr_ptr_functions">30.4.4 Typemaps and pointer-pointer functions</a></H3>
 
 
 <p>Several C++ libraries use a pointer-pointer functions to create its objects. These functions require a pointer to a pointer which is then filled with the pointer to the new object. Microsoft's COM and DirectX as well as many other libraries have this kind of function. An example is given below:</p>
@@ -1706,7 +1706,7 @@ int Create_Math(iMath** pptr); // its creator (assume it mallocs)
 ptr=nil -- the iMath* will be GC'ed as normal
 </pre></div>
 
-<H2><a name="Lua_writing_typemaps">29.5 Writing typemaps</a></H2>
+<H2><a name="Lua_writing_typemaps">30.5 Writing typemaps</a></H2>
 
 
 <p>This section describes how you can modify SWIG's default wrapping behavior for various C/C++ datatypes using the <tt>%typemap</tt> directive. This is an advanced topic that assumes familiarity with the Lua C API as well as the material in the "<a href="Typemaps.html#Typemaps">Typemaps</a>" chapter.</p>
@@ -1715,7 +1715,7 @@ ptr=nil -- the iMath* will be GC'ed as normal
 
 <p>Before proceeding, you should read the previous section on using typemaps, and look at the existing typemaps found in luatypemaps.swg and typemaps.i. These are both well documented and fairly easy to read. You should not attempt to write your own typemaps until you have read and can understand both of these files (they may well also give you an idea to base your work on).</p>
 
-<H3><a name="Lua_typemaps_write">29.5.1 Typemaps you can write</a></H3>
+<H3><a name="Lua_typemaps_write">30.5.1 Typemaps you can write</a></H3>
 
 
 <p>There are many different types of typemap that can be written, the full list can be found in the "<a href="Typemaps.html#Typemaps">Typemaps</a>" chapter. However the following are the most commonly used ones.</p>
@@ -1728,7 +1728,7 @@ ptr=nil -- the iMath* will be GC'ed as normal
 (the syntax for the typecheck is different from the typemap, see typemaps for details).</li>
 </ul>
 
-<H3><a name="Lua_nn31">29.5.2 SWIG's Lua-C API</a></H3>
+<H3><a name="Lua_nn31">30.5.2 SWIG's Lua-C API</a></H3>
 
 
 <p>This section explains the SWIG specific Lua-C API. It does not cover the main Lua-C api, as this is well documented and not worth covering.</p>
@@ -1777,7 +1777,7 @@ This macro, when called within the context of a SWIG wrapped function, will disp
 <div class="indent">
 Similar to SWIG_fail_arg, except that it will display the swig_type_info information instead.</div>
 
-<H2><a name="Lua_nn32">29.6 Customization of your Bindings</a></H2>
+<H2><a name="Lua_nn32">30.6 Customization of your Bindings</a></H2>
 
 
 <p>
@@ -1786,7 +1786,7 @@ This section covers adding of some small extra bits to your module to add the la
 
 
 
-<H3><a name="Lua_nn33">29.6.1 Writing your own custom wrappers</a></H3>
+<H3><a name="Lua_nn33">30.6.1 Writing your own custom wrappers</a></H3>
 
 
 <p>
@@ -1805,7 +1805,7 @@ int native_function(lua_State*L) // my native code
 The <tt>%native</tt> directive in the above example, tells SWIG that there is a function <tt>int native_function(lua_State*L);</tt> which is to be added into the module under the name '<tt>my_func</tt>'. SWIG will not add any wrapper for this function, beyond adding it into the function table. How you write your code is entirely up to you.
 </p>
 
-<H3><a name="Lua_nn34">29.6.2 Adding additional Lua code</a></H3>
+<H3><a name="Lua_nn34">30.6.2 Adding additional Lua code</a></H3>
 
 
 <p>
@@ -1843,7 +1843,7 @@ Good uses for this feature is adding of new code, or writing helper functions to
 See Examples/lua/arrays for an example of this code.
 </p>
 
-<H2><a name="Lua_nn35">29.7 Details on the Lua binding</a></H2>
+<H2><a name="Lua_nn35">30.7 Details on the Lua binding</a></H2>
 
 
 <p>
@@ -1854,7 +1854,7 @@ See Examples/lua/arrays for an example of this code.
  </i>
 </p>
 
-<H3><a name="Lua_nn36">29.7.1 Binding global data into the module.</a></H3>
+<H3><a name="Lua_nn36">30.7.1 Binding global data into the module.</a></H3>
 
 
 <p>
@@ -1914,7 +1914,7 @@ end
 <p>
 That way when you call '<tt>a=example.Foo</tt>', the interpreter looks at the table 'example' sees that there is no field 'Foo' and calls __index. This will in turn check in '.get' table and find the existence of 'Foo' and then return the value of the C function call 'Foo_get()'. Similarly for the code '<tt>example.Foo=10</tt>', the interpreter will check the table, then call the __newindex which will then check the '.set' table and call the C function 'Foo_set(10)'.
 </p>
-<H3><a name="Lua_nn37">29.7.2 Userdata and Metatables</a></H3>
+<H3><a name="Lua_nn37">30.7.2 Userdata and Metatables</a></H3>
 
 
 <p>
@@ -1994,7 +1994,7 @@ Note: Both the opaque structures (like the FILE*) and normal wrapped classes/str
 <p>
 Note: Operator overloads are basically done in the same way, by adding functions such as '__add' &amp; '__call' to the class' metatable. The current implementation is a bit rough as it will add any member function beginning with '__' into the metatable too, assuming its an operator overload.
 </p>
-<H3><a name="Lua_nn38">29.7.3 Memory management</a></H3>
+<H3><a name="Lua_nn38">30.7.3 Memory management</a></H3>
 
 
 <p>
diff --git a/Doc/Manual/Modula3.html b/Doc/Manual/Modula3.html
index bdfc5992d..fc4ffa03c 100644
--- a/Doc/Manual/Modula3.html
+++ b/Doc/Manual/Modula3.html
@@ -6,7 +6,7 @@
 <meta http-equiv="content-type" content="text/html; charset=UTF-8">
 </head>
 <body bgcolor="#FFFFFF">
-<H1><a name="Modula3">30 SWIG and Modula-3</a></H1>
+<H1><a name="Modula3">31 SWIG and Modula-3</a></H1>
 <!-- INDEX -->
 <div class="sectiontoc">
 <ul>
@@ -55,7 +55,7 @@ especially
 <a href="Typemaps.html#Typemaps">typemaps</a>.
 </p>
 
-<H2><a name="Modula3_modula3_overview">30.1 Overview</a></H2>
+<H2><a name="Modula3_modula3_overview">31.1 Overview</a></H2>
 
 
 <p>
@@ -85,7 +85,7 @@ FFTW
 </li>
 </ol>
 
-<H3><a name="Modula3_motivation">30.1.1 Motivation</a></H3>
+<H3><a name="Modula3_motivation">31.1.1 Motivation</a></H3>
 
 
 <p>
@@ -132,10 +132,10 @@ functions), but it doesn't allow you to easily integrate a Modula-3 module into
 a C/C++ project.
 </p>
 
-<H2><a name="Modula3_conception">30.2 Conception</a></H2>
+<H2><a name="Modula3_conception">31.2 Conception</a></H2>
 
 
-<H3><a name="Modula3_cinterface">30.2.1 Interfaces to C libraries</a></H3>
+<H3><a name="Modula3_cinterface">31.2.1 Interfaces to C libraries</a></H3>
 
 
 <p>
@@ -284,7 +284,7 @@ and the principal type must be renamed (<tt>%typemap</tt>).
 </p>
 
 
-<H3><a name="Modula3_cppinterface">30.2.2 Interfaces to C++ libraries</a></H3>
+<H3><a name="Modula3_cppinterface">31.2.2 Interfaces to C++ libraries</a></H3>
 
 
 <p>
@@ -385,10 +385,10 @@ There is no C++ library I wrote a SWIG interface for,
 so I'm not sure if this is possible or sensible, yet.
 </p>
 
-<H2><a name="Modula3_preliminaries">30.3 Preliminaries</a></H2>
+<H2><a name="Modula3_preliminaries">31.3 Preliminaries</a></H2>
 
 
-<H3><a name="Modula3_compilers">30.3.1 Compilers</a></H3>
+<H3><a name="Modula3_compilers">31.3.1 Compilers</a></H3>
 
 
 <p>
@@ -401,7 +401,7 @@ For testing examples I use Critical Mass cm3.
 </p>
 
 
-<H3><a name="Modula3_commandline">30.3.2 Additional Commandline Options</a></H3>
+<H3><a name="Modula3_commandline">31.3.2 Additional Commandline Options</a></H3>
 
 
 <p>
@@ -478,10 +478,10 @@ Instead generate templates for some basic typemaps.
 </tr>
 </table>
 
-<H2><a name="Modula3_typemaps">30.4 Modula-3 typemaps</a></H2>
+<H2><a name="Modula3_typemaps">31.4 Modula-3 typemaps</a></H2>
 
 
-<H3><a name="Modula3_inoutparam">30.4.1 Inputs and outputs</a></H3>
+<H3><a name="Modula3_inoutparam">31.4.1 Inputs and outputs</a></H3>
 
 
 <p>
@@ -695,7 +695,7 @@ consist of the following parts:
 </table>
 
 
-<H3><a name="Modula3_ordinals">30.4.2 Subranges, Enumerations, Sets</a></H3>
+<H3><a name="Modula3_ordinals">31.4.2 Subranges, Enumerations, Sets</a></H3>
 
 
 <p>
@@ -747,7 +747,7 @@ that I'd like to automate.
 </p>
 
 
-<H3><a name="Modula3_class">30.4.3 Objects</a></H3>
+<H3><a name="Modula3_class">31.4.3 Objects</a></H3>
 
 
 <p>
@@ -760,7 +760,7 @@ is not really useful, yet.
 </p>
 
 
-<H3><a name="Modula3_imports">30.4.4 Imports</a></H3>
+<H3><a name="Modula3_imports">31.4.4 Imports</a></H3>
 
 
 <p>
@@ -793,7 +793,7 @@ IMPORT M3toC;
 </pre></div>
 
 
-<H3><a name="Modula3_exceptions">30.4.5 Exceptions</a></H3>
+<H3><a name="Modula3_exceptions">31.4.5 Exceptions</a></H3>
 
 
 <p>
@@ -817,7 +817,7 @@ you should declare
 <tt>%typemap("m3wrapinconv:throws") blah * %{OSError.E%}</tt>.
 </p>
 
-<H3><a name="Modula3_typemap_example">30.4.6 Example</a></H3>
+<H3><a name="Modula3_typemap_example">31.4.6 Example</a></H3>
 
 
 <p>
@@ -864,10 +864,10 @@ where almost everything is generated by a typemap:
 </pre></div>
 
 
-<H2><a name="Modula3_hints">30.5 More hints to the generator</a></H2>
+<H2><a name="Modula3_hints">31.5 More hints to the generator</a></H2>
 
 
-<H3><a name="Modula3_features">30.5.1 Features</a></H3>
+<H3><a name="Modula3_features">31.5.1 Features</a></H3>
 
 
 <table border summary="Modula-3 features">
@@ -904,7 +904,7 @@ where almost everything is generated by a typemap:
 </tr>
 </table>
 
-<H3><a name="Modula3_pragmas">30.5.2 Pragmas</a></H3>
+<H3><a name="Modula3_pragmas">31.5.2 Pragmas</a></H3>
 
 
 <table border summary="Modula-3 pragmas">
@@ -927,7 +927,7 @@ where almost everything is generated by a typemap:
 </tr>
 </table>
 
-<H2><a name="Modula3_remarks">30.6 Remarks</a></H2>
+<H2><a name="Modula3_remarks">31.6 Remarks</a></H2>
 
 
 <ul>
diff --git a/Doc/Manual/Modules.html b/Doc/Manual/Modules.html
index 682e549e0..19b69e5f4 100644
--- a/Doc/Manual/Modules.html
+++ b/Doc/Manual/Modules.html
@@ -7,7 +7,7 @@
 </head>
 
 <body bgcolor="#ffffff">
-<H1><a name="Modules">17 Working with Modules</a></H1>
+<H1><a name="Modules">18 Working with Modules</a></H1>
 <!-- INDEX -->
 <div class="sectiontoc">
 <ul>
@@ -24,7 +24,7 @@
 
 
 
-<H2><a name="Modules_introduction">17.1 Modules Introduction</a></H2>
+<H2><a name="Modules_introduction">18.1 Modules Introduction</a></H2>
 
 
 <p>
@@ -78,7 +78,7 @@ where you want to create a collection of modules.
 Each module in the collection is created via separate invocations of SWIG.
 </p>
 
-<H2><a name="Modules_nn1">17.2 Basics</a></H2>
+<H2><a name="Modules_nn1">18.2 Basics</a></H2>
 
 
 <p>
@@ -177,7 +177,7 @@ in parallel from multiple threads as SWIG provides no locking - for more on that
 issue, read on.
 </p>
 
-<H2><a name="Modules_nn2">17.3 The SWIG runtime code</a></H2>
+<H2><a name="Modules_nn2">18.3 The SWIG runtime code</a></H2>
 
 
 <p>
@@ -243,7 +243,7 @@ can peacefully coexist. So the type structures are separated by the
 is empty. Only modules compiled with the same pair will share type information.
 </p>
 
-<H2><a name="Modules_external_run_time">17.4 External access to the runtime</a></H2>
+<H2><a name="Modules_external_run_time">18.4 External access to the runtime</a></H2>
 
 
 <p>As described in <a href="Typemaps.html#Typemaps_runtime_type_checker">The run-time type checker</a>,
@@ -282,7 +282,7 @@ SWIG_TYPE_TABLE to be the same as the module whose types you are trying to
 access.
 </p>
 
-<H2><a name="Modules_nn4">17.5 A word of caution about static libraries</a></H2>
+<H2><a name="Modules_nn4">18.5 A word of caution about static libraries</a></H2>
 
 
 <p>
@@ -293,7 +293,7 @@ into it. This is very often <b>NOT</b> what you want and it can lead to unexpect
 behavior. When working with dynamically loadable modules, you should try to work exclusively with shared libraries.
 </p>
 
-<H2><a name="Modules_nn5">17.6 References</a></H2>
+<H2><a name="Modules_nn5">18.6 References</a></H2>
 
 
 <p>
@@ -301,7 +301,7 @@ Due to the complexity of working with shared libraries and multiple modules, it
 an outside reference.  John Levine's "Linkers and Loaders" is highly recommended.
 </p>
 
-<H2><a name="Modules_nn6">17.7 Reducing the wrapper file size</a></H2>
+<H2><a name="Modules_nn6">18.7 Reducing the wrapper file size</a></H2>
 
 
 <p>
diff --git a/Doc/Manual/Mzscheme.html b/Doc/Manual/Mzscheme.html
index 0e85fdbfa..c3af5c49e 100644
--- a/Doc/Manual/Mzscheme.html
+++ b/Doc/Manual/Mzscheme.html
@@ -8,7 +8,7 @@
 
 <body bgcolor="#ffffff">
 
-<H1><a name="Mzscheme">31 SWIG and MzScheme/Racket</a></H1>
+<H1><a name="Mzscheme">32 SWIG and MzScheme/Racket</a></H1>
 <!-- INDEX -->
 <div class="sectiontoc">
 <ul>
@@ -24,7 +24,7 @@
 <p>
 This section contains information on SWIG's support of Racket, formally known as MzScheme.
 
-<H2><a name="MzScheme_nn2">31.1 Creating native structures</a></H2>
+<H2><a name="MzScheme_nn2">32.1 Creating native structures</a></H2>
 
 
 <p>
@@ -65,7 +65,7 @@ Then in scheme, you can use regular struct access procedures like
 </pre>
 </div>
 
-<H2><a name="MzScheme_simple">31.2 Simple example</a></H2>
+<H2><a name="MzScheme_simple">32.2 Simple example</a></H2>
 
 
 <p>
@@ -166,7 +166,7 @@ Some points of interest:
   <li> The above requests mzc to create an extension using the CGC garbage-collector. The alternative -- the 3m collector -- has generally better performance, but work is still required for SWIG to emit code which is compatible with it.
 </ul>
 
-<H2><a name="MzScheme_external_docs">31.3 External documentation</a></H2>
+<H2><a name="MzScheme_external_docs">32.3 External documentation</a></H2>
 
 
 <p>
diff --git a/Doc/Manual/Ocaml.html b/Doc/Manual/Ocaml.html
index 2466fc5bc..70504cf15 100644
--- a/Doc/Manual/Ocaml.html
+++ b/Doc/Manual/Ocaml.html
@@ -7,7 +7,7 @@
 </head>
 
 <body bgcolor="#ffffff">
-<H1><a name="Ocaml">32 SWIG and Ocaml</a></H1>
+<H1><a name="Ocaml">33 SWIG and Ocaml</a></H1>
 <!-- INDEX -->
 <div class="sectiontoc">
 <ul>
@@ -84,7 +84,7 @@ If you're not familiar with the Objective Caml language, you can visit
 <a href="http://ocaml.org/">The Ocaml Website</a>.
 </p>
 
-<H2><a name="Ocaml_nn2">32.1 Preliminaries</a></H2>
+<H2><a name="Ocaml_nn2">33.1 Preliminaries</a></H2>
 
 
 <p>
@@ -102,7 +102,7 @@ file Examples/Makefile illustrate how to compile and link SWIG modules that
 will be loaded dynamically.  This has only been tested on Linux so far.
 </p>
 
-<H3><a name="Ocaml_nn3">32.1.1 Running SWIG</a></H3>
+<H3><a name="Ocaml_nn3">33.1.1 Running SWIG</a></H3>
 
 
 <p>
@@ -125,7 +125,7 @@ you will compile the file <tt>example_wrap.c</tt> with <tt>ocamlc</tt> or
 the resulting .ml and .mli files as well, and do the final link with -custom
 (not needed for native link).</p>
 
-<H3><a name="Ocaml_nn4">32.1.2 Compiling the code</a></H3>
+<H3><a name="Ocaml_nn4">33.1.2 Compiling the code</a></H3>
 
 
 <p>
@@ -162,7 +162,7 @@ in C++ mode, you must:</p>
 </pre>
 </div>
 
-<H3><a name="Ocaml_nn5">32.1.3 The camlp4 module</a></H3>
+<H3><a name="Ocaml_nn5">33.1.3 The camlp4 module</a></H3>
 
 
 <p>
@@ -238,7 +238,7 @@ let b = C_string (getenv "PATH")
 </td></tr>
 </table>
 
-<H3><a name="Ocaml_nn6">32.1.4 Using your module</a></H3>
+<H3><a name="Ocaml_nn6">33.1.4 Using your module</a></H3>
 
 
 <p>
@@ -252,7 +252,7 @@ option to build your functions into the primitive list. This
 option is not needed when you build native code.
 </p>
 
-<H3><a name="Ocaml_nn7">32.1.5 Compilation problems and compiling with C++</a></H3>
+<H3><a name="Ocaml_nn7">33.1.5 Compilation problems and compiling with C++</a></H3>
 
 
 <p>
@@ -263,7 +263,7 @@ liberal with pointer types may not compile under the C++ compiler.
 Most code meant to be compiled as C++ will not have problems.
 </p>
 
-<H2><a name="Ocaml_nn8">32.2 The low-level Ocaml/C interface</a></H2>
+<H2><a name="Ocaml_nn8">33.2 The low-level Ocaml/C interface</a></H2>
 
 
 <p>
@@ -363,7 +363,7 @@ value items pass through directly, but you must make your own type
 signature for a function that uses value in this way.
 </p>
 
-<H3><a name="Ocaml_nn9">32.2.1 The generated module</a></H3>
+<H3><a name="Ocaml_nn9">33.2.1 The generated module</a></H3>
 
 
 <p>
@@ -397,7 +397,7 @@ it describes the output SWIG will generate for class definitions.
 </td></tr>
 </table>
 
-<H3><a name="Ocaml_nn10">32.2.2 Enums</a></H3>
+<H3><a name="Ocaml_nn10">33.2.2 Enums</a></H3>
 
 
 <p>
@@ -460,7 +460,7 @@ val x : Enum_test.c_obj = C_enum `a
 </pre>
 </div>
 
-<H4><a name="Ocaml_nn11">32.2.2.1 Enum typing in Ocaml</a></H4>
+<H4><a name="Ocaml_nn11">33.2.2.1 Enum typing in Ocaml</a></H4>
 
 
 <p>
@@ -473,10 +473,10 @@ functions imported from different modules.  You must convert values to master
 values using the swig_val function before sharing them with another module.
 </p>
 
-<H3><a name="Ocaml_nn12">32.2.3 Arrays</a></H3>
+<H3><a name="Ocaml_nn12">33.2.3 Arrays</a></H3>
 
 
-<H4><a name="Ocaml_nn13">32.2.3.1 Simple types of bounded arrays</a></H4>
+<H4><a name="Ocaml_nn13">33.2.3.1 Simple types of bounded arrays</a></H4>
 
 
 <p>
@@ -497,7 +497,7 @@ arrays of simple types with known bounds in your code, but this only works
 for arrays whose bounds are completely specified.
 </p>
 
-<H4><a name="Ocaml_nn14">32.2.3.2 Complex and unbounded arrays</a></H4>
+<H4><a name="Ocaml_nn14">33.2.3.2 Complex and unbounded arrays</a></H4>
 
 
 <p>
@@ -510,7 +510,7 @@ SWIG can't predict which of these methods will be used in the array,
 so you have to specify it for yourself in the form of a typemap.
 </p>
 
-<H4><a name="Ocaml_nn15">32.2.3.3 Using an object</a></H4>
+<H4><a name="Ocaml_nn15">33.2.3.3 Using an object</a></H4>
 
 
 <p>
@@ -524,7 +524,7 @@ Consider writing an object when the ending condition of your array is complex,
 such as using a required sentinel, etc.
 </p>
 
-<H4><a name="Ocaml_nn16">32.2.3.4 Example typemap for a function taking float * and int</a></H4>
+<H4><a name="Ocaml_nn16">33.2.3.4 Example typemap for a function taking float * and int</a></H4>
 
 
 <p>
@@ -575,7 +575,7 @@ void printfloats( float *tab, int len );
 </pre></td></tr></table>
 
 
-<H3><a name="Ocaml_nn17">32.2.4 C++ Classes</a></H3>
+<H3><a name="Ocaml_nn17">33.2.4 C++ Classes</a></H3>
 
 
 <p>
@@ -618,7 +618,7 @@ the underlying pointer, so using create_[x]_from_ptr alters the
 returned value for the same object.
 </p>
 
-<H4><a name="Ocaml_nn18">32.2.4.1 STL vector and string Example</a></H4>
+<H4><a name="Ocaml_nn18">33.2.4.1 STL vector and string Example</a></H4>
 
 
 <p>
@@ -698,7 +698,7 @@ baz
 #
 </pre></div>
 
-<H4><a name="Ocaml_nn19">32.2.4.2 C++ Class Example</a></H4>
+<H4><a name="Ocaml_nn19">33.2.4.2 C++ Class Example</a></H4>
 
 
 <p>
@@ -728,7 +728,7 @@ public:
 };
 </pre></td></tr></table>
 
-<H4><a name="Ocaml_nn20">32.2.4.3 Compiling the example</a></H4>
+<H4><a name="Ocaml_nn20">33.2.4.3 Compiling the example</a></H4>
 
 
 <div class="code"><pre>
@@ -746,7 +746,7 @@ bash-2.05a$ ocamlmktop -custom swig.cmo -I `camlp4 -where` \
   -L$QTPATH/lib -cclib -lqt
 </pre></div>
 
-<H4><a name="Ocaml_nn21">32.2.4.4 Sample Session</a></H4>
+<H4><a name="Ocaml_nn21">33.2.4.4 Sample Session</a></H4>
 
 
 <div class="code"><pre>
@@ -773,10 +773,10 @@ Assuming you have a working installation of QT, you will see a window
 containing the string "hi" in a button.
 </p>
 
-<H3><a name="Ocaml_nn22">32.2.5 Director Classes</a></H3>
+<H3><a name="Ocaml_nn22">33.2.5 Director Classes</a></H3>
 
 
-<H4><a name="Ocaml_nn23">32.2.5.1 Director Introduction</a></H4>
+<H4><a name="Ocaml_nn23">33.2.5.1 Director Introduction</a></H4>
 
 
 <p>
@@ -803,7 +803,7 @@ class foo {
 };
 </pre></div>
 
-<H4><a name="Ocaml_nn24">32.2.5.2 Overriding Methods in Ocaml</a></H4>
+<H4><a name="Ocaml_nn24">33.2.5.2 Overriding Methods in Ocaml</a></H4>
 
 
 <p>
@@ -831,7 +831,7 @@ In this example, I'll examine the objective caml code involved in providing
 an overloaded class.  This example is contained in Examples/ocaml/shapes.
 </p>
 
-<H4><a name="Ocaml_nn25">32.2.5.3 Director Usage Example</a></H4>
+<H4><a name="Ocaml_nn25">33.2.5.3 Director Usage Example</a></H4>
 
 
 <table border="1" bgcolor="#dddddd" summary="Director usage example">
@@ -890,7 +890,7 @@ in a more effortless style in ocaml, while leaving the "engine" part of the
 program in C++.
 </p>
 
-<H4><a name="Ocaml_nn26">32.2.5.4 Creating director objects</a></H4>
+<H4><a name="Ocaml_nn26">33.2.5.4 Creating director objects</a></H4>
 
 
 <p>
@@ -931,7 +931,7 @@ object from causing a core dump, as long as the object is destroyed
 properly.
 </p>
 
-<H4><a name="Ocaml_nn27">32.2.5.5 Typemaps for directors, directorin, directorout, directorargout</a></H4>
+<H4><a name="Ocaml_nn27">33.2.5.5 Typemaps for directors, directorin, directorout, directorargout</a></H4>
 
 
 <p>
@@ -942,7 +942,7 @@ well as a function return value in the same way you provide function arguments,
 and to receive arguments the same way you normally receive function returns.
 </p>
 
-<H4><a name="Ocaml_nn28">32.2.5.6 typemap</a></H4>
+<H4><a name="Ocaml_nn28">33.2.5.6 typemap</a></H4>
 
 
 <p>
@@ -953,7 +953,7 @@ code receives when you are called.  In general, a simple <tt>directorin</tt> typ
 can use the same body as a simple <tt>out</tt> typemap.
 </p>
 
-<H4><a name="Ocaml_nn29">32.2.5.7 directorout typemap</a></H4>
+<H4><a name="Ocaml_nn29">33.2.5.7 directorout typemap</a></H4>
 
 
 <p>
@@ -964,7 +964,7 @@ for the same type, except when there are special requirements for object
 ownership, etc.
 </p>
 
-<H4><a name="Ocaml_nn30">32.2.5.8 directorargout typemap</a></H4>
+<H4><a name="Ocaml_nn30">33.2.5.8 directorargout typemap</a></H4>
 
 
 <p>
@@ -981,7 +981,7 @@ In the event that you don't specify all of the necessary values, integral
 values will read zero, and struct or object returns have undefined results.
 </p>
 
-<H3><a name="Ocaml_nn31">32.2.6 Exceptions</a></H3>
+<H3><a name="Ocaml_nn31">33.2.6 Exceptions</a></H3>
 
 
 <p>
diff --git a/Doc/Manual/Octave.html b/Doc/Manual/Octave.html
index 606ca820c..1295966bd 100644
--- a/Doc/Manual/Octave.html
+++ b/Doc/Manual/Octave.html
@@ -9,7 +9,7 @@
 
 <body bgcolor="#ffffff">
 
-<H1><a name="Octave">33 SWIG and Octave</a></H1>
+<H1><a name="Octave">34 SWIG and Octave</a></H1>
 <!-- INDEX -->
 <div class="sectiontoc">
 <ul>
@@ -60,7 +60,7 @@ This chapter is intended to give an introduction to using the module. You should
 Also, there are a dozen or so examples in the Examples/octave directory, and hundreds in the test suite (Examples/test-suite and Examples/test-suite/octave).
 </p>
 
-<H2><a name="Octave_nn2">33.1 Preliminaries</a></H2>
+<H2><a name="Octave_nn2">34.1 Preliminaries</a></H2>
 
 
 <p>
@@ -76,7 +76,7 @@ This cannot be guaranteed however, as in recent times new Octave releases have r
 The SWIG runtime exports the function <tt>swig_octave_prereq()</tt> for checking the version of Octave.
 </p>
 
-<H2><a name="Octave_nn3">33.2 Running SWIG</a></H2>
+<H2><a name="Octave_nn3">34.2 Running SWIG</a></H2>
 
 
 <p>
@@ -108,7 +108,7 @@ The <tt>-c++</tt> option is also required when wrapping C++ code:
 This creates a C++ source file "example_wrap.cpp". A C++ file is generated even when wrapping C code as Octave is itself written in C++ and requires wrapper code to be in the same language. The generated C++ source file contains the low-level wrappers that need to be compiled and linked with the rest of your C/C++ application (in this case, the gcd implementation) to create an extension module.
 </p>
 
-<H3><a name="Octave_nn4">33.2.1 Command-line options</a></H3>
+<H3><a name="Octave_nn4">34.2.1 Command-line options</a></H3>
 
 
 <p>
@@ -131,7 +131,7 @@ The special name "." loads C global variables into the module namespace, i.e. al
 The <em>-opprefix</em> options sets the prefix of the names of global/friend <a href="#Octave_nn18">operator</a> functions.
 </p>
 
-<H3><a name="Octave_nn5">33.2.2 Compiling a dynamic module</a></H3>
+<H3><a name="Octave_nn5">34.2.2 Compiling a dynamic module</a></H3>
 
 
 <p>
@@ -158,7 +158,7 @@ $ mkoctfile example_wrap.cpp example.c
 
           <div class="targetlang"><pre>octave:1&gt; swigexample</pre></div>
 
-<H3><a name="Octave_nn6">33.2.3 Using your module</a></H3>
+<H3><a name="Octave_nn6">34.2.3 Using your module</a></H3>
 
 
 <p>
@@ -176,10 +176,10 @@ octave:4&gt; swigexample.cvar.Foo=4;
 octave:5&gt; swigexample.cvar.Foo
 ans =  4 </pre></div>
 
-<H2><a name="Octave_nn7">33.3 A tour of basic C/C++ wrapping</a></H2>
+<H2><a name="Octave_nn7">34.3 A tour of basic C/C++ wrapping</a></H2>
 
 
-<H3><a name="Octave_nn8">33.3.1 Modules</a></H3>
+<H3><a name="Octave_nn8">34.3.1 Modules</a></H3>
 
 
 <p>
@@ -224,7 +224,7 @@ octave:4&gt; swigexample.gcd(4, 6)
 ans =  2
 </pre></div>
 
-<H3><a name="Octave_nn9">33.3.2 Functions</a></H3>
+<H3><a name="Octave_nn9">34.3.2 Functions</a></H3>
 
 
 <p>
@@ -241,7 +241,7 @@ int fact(int n); </pre></div>
     <div class="targetlang"><pre>octave:1&gt; swigexample.fact(4)
 24 </pre></div>
 
-<H3><a name="Octave_nn10">33.3.3 Global variables</a></H3>
+<H3><a name="Octave_nn10">34.3.3 Global variables</a></H3>
 
 
 <p>
@@ -294,7 +294,7 @@ octave:2&gt; swigexample.PI=3.142;
 octave:3&gt; swigexample.PI
 ans =  3.1420 </pre></div>
 
-<H3><a name="Octave_nn11">33.3.4 Constants and enums</a></H3>
+<H3><a name="Octave_nn11">34.3.4 Constants and enums</a></H3>
 
 
 <p>
@@ -316,7 +316,7 @@ swigexample.SCONST="Hello World"
 swigexample.SUNDAY=0
 .... </pre></div>
 
-<H3><a name="Octave_nn12">33.3.5 Pointers</a></H3>
+<H3><a name="Octave_nn12">34.3.5 Pointers</a></H3>
 
 
 <p>
@@ -363,7 +363,7 @@ octave:2&gt; f=swigexample.fopen("not there", "r");
 error: value on right hand side of assignment is undefined
 error: evaluating assignment expression near line 2, column 2 </pre></div>
 
-<H3><a name="Octave_nn13">33.3.6 Structures and C++ classes</a></H3>
+<H3><a name="Octave_nn13">34.3.6 Structures and C++ classes</a></H3>
 
 
 <p>
@@ -498,7 +498,7 @@ ans =  1
 Depending on the ownership setting of a <tt>swig_ref</tt>, it may call C++ destructors when its reference count goes to zero. See the section on memory management below for details.
 </p>
 
-<H3><a name="Octave_nn15">33.3.7 C++ inheritance</a></H3>
+<H3><a name="Octave_nn15">34.3.7 C++ inheritance</a></H3>
 
 
 <p>
@@ -507,7 +507,7 @@ This information contains the full class hierarchy. When an indexing operation (
 the tree is walked to find a match in the current class as well as any of its bases. The lookup is then cached in the <tt>swig_ref</tt>.
 </p>
 
-<H3><a name="Octave_nn17">33.3.8 C++ overloaded functions</a></H3>
+<H3><a name="Octave_nn17">34.3.8 C++ overloaded functions</a></H3>
 
 
 <p>
@@ -517,7 +517,7 @@ The dispatch function selects which overload to call (if any) based on the passe
 <tt>typecheck</tt> typemaps are used to analyze each argument, as well as assign precedence. See the chapter on typemaps for details.
 </p>
 
-<H3><a name="Octave_nn18">33.3.9 C++ operators</a></H3>
+<H3><a name="Octave_nn18">34.3.9 C++ operators</a></H3>
 
 
 <p>
@@ -621,7 +621,7 @@ On the C++ side, the default mappings are as follows:
 Octave can also utilise friend (i.e. non-member) operators with a simple %rename: see the example in the Examples/octave/operator directory.
 </p>
 
-<H3><a name="Octave_nn19">33.3.10 Class extension with %extend</a></H3>
+<H3><a name="Octave_nn19">34.3.10 Class extension with %extend</a></H3>
 
 
 <p>
@@ -660,7 +660,7 @@ Similarly, Octave can use the <tt>__float__</tt> method to convert an object to
 Octave 3.8.0 and later versions will also map unary functions X() to the corresponding <tt>__X__</tt> method, where X includes: abs(), acos(), acosh(), angle(), arg(), asin(), asinh(), atan(), atanh(), cbrt(), ceil(), conj(), cos(), cosh(), dawson(), erf(), erfc(), erfcinv(), erfcx(), erfi(), erfinv(), exp(), expm1(), finite(), fix(), floor(), gamma(), imag(), isalnum(), isalpha(), isascii(), iscntrl(), isdigit(), isgraph(), isinf(), islower(), isna(), isnan(), isprint(), ispunct(), isspace(), isupper(), isxdigit(), lgamma(), log(), log10(), log1p(), log2(), real(), round(), roundb(), signbit(), signum(), sin(), sinh(), sqrt(), tan(), tanh(), toascii(), tolower(), toupper()
 </p>
 
-<H3><a name="Octave_nn20">33.3.11 C++ templates</a></H3>
+<H3><a name="Octave_nn20">34.3.11 C++ templates</a></H3>
 
 
 <p>
@@ -737,10 +737,10 @@ ans =
 </pre></div>
 
 
-<H3><a name="Octave_nn21">33.3.12 C++ Smart Pointers</a></H3>
+<H3><a name="Octave_nn21">34.3.12 C++ Smart Pointers</a></H3>
 
 
-<H4><a name="Octave_smart_pointers_shared_ptr">33.3.12.1 The shared_ptr Smart Pointer</a></H4>
+<H4><a name="Octave_smart_pointers_shared_ptr">34.3.12.1 The shared_ptr Smart Pointer</a></H4>
 
 
 <p>
@@ -751,14 +751,14 @@ in the <a href="Library.html#Library_std_shared_ptr">shared_ptr smart pointer</a
 </p>
 
 
-<H4><a name="Octave_smart_pointers_generic">33.3.12.2 Generic Smart Pointers</a></H4>
+<H4><a name="Octave_smart_pointers_generic">34.3.12.2 Generic Smart Pointers</a></H4>
 
 
 <p>
 C++ smart pointers are fully supported as in other modules.
 </p>
 
-<H3><a name="Octave_nn22">33.3.13 Directors (calling Octave from C++ code)</a></H3>
+<H3><a name="Octave_nn22">34.3.13 Directors (calling Octave from C++ code)</a></H3>
 
 
 <p>
@@ -839,14 +839,14 @@ c-side routine called
 octave-side routine called
 </pre></div>
 
-<H3><a name="Octave_nn23">33.3.14 Threads</a></H3>
+<H3><a name="Octave_nn23">34.3.14 Threads</a></H3>
 
 
 <p>
 The use of threads in wrapped Director code is not supported; i.e., an Octave-side implementation of a C++ class must be called from the Octave interpreter's thread. Anything fancier (apartment/queue model, whatever) is left to the user. Without anything fancier, this amounts to the limitation that Octave must drive the module... like, for example, an optimization package that calls Octave to evaluate an objective function.
 </p>
 
-<H3><a name="Octave_nn24">33.3.15 Memory management</a></H3>
+<H3><a name="Octave_nn24">34.3.15 Memory management</a></H3>
 
 
 <p>
@@ -880,14 +880,14 @@ The %newobject directive may be used to control this behavior for pointers retur
 In the case where one wishes for the C++ side to own an object that was created in Octave (especially a Director object), one can use the __disown() method to invert this logic. Then letting the Octave reference count go to zero will not destroy the object, but destroying the object will invalidate the Octave-side object if it still exists (and call destructors of other C++ bases in the case of multiple inheritance/<tt>subclass()</tt>'ing).
 </p>
 
-<H3><a name="Octave_nn25">33.3.16 STL support</a></H3>
+<H3><a name="Octave_nn25">34.3.16 STL support</a></H3>
 
 
 <p>
 Various STL library files are provided for wrapping STL containers.
 </p>
 
-<H3><a name="Octave_nn26">33.3.17 Matrix typemaps</a></H3>
+<H3><a name="Octave_nn26">34.3.17 Matrix typemaps</a></H3>
 
 
 <p>
diff --git a/Doc/Manual/Perl5.html b/Doc/Manual/Perl5.html
index 61a08a545..8bb65ec66 100644
--- a/Doc/Manual/Perl5.html
+++ b/Doc/Manual/Perl5.html
@@ -7,7 +7,7 @@
 </head>
 
 <body bgcolor="#ffffff">
-<H1><a name="Perl5">34 SWIG and Perl5</a></H1>
+<H1><a name="Perl5">35 SWIG and Perl5</a></H1>
 <!-- INDEX -->
 <div class="sectiontoc">
 <ul>
@@ -97,7 +97,7 @@ later. We're no longer testing regularly with older versions, but
 Perl 5.6 seems to mostly work, while older versions don't.
 </p>
 
-<H2><a name="Perl5_nn2">34.1 Overview</a></H2>
+<H2><a name="Perl5_nn2">35.1 Overview</a></H2>
 
 
 <p>
@@ -118,7 +118,7 @@ described.  Advanced customization features, typemaps, and other
 options are found near the end of the chapter.
 </p>
 
-<H2><a name="Perl5_nn3">34.2 Preliminaries</a></H2>
+<H2><a name="Perl5_nn3">35.2 Preliminaries</a></H2>
 
 
 <p>
@@ -143,7 +143,7 @@ To build the module, you will need to compile the file
 <tt>example_wrap.c</tt> and link it with the rest of your program.
 </p>
 
-<H3><a name="Perl5_nn4">34.2.1 Getting the right header files</a></H3>
+<H3><a name="Perl5_nn4">35.2.1 Getting the right header files</a></H3>
 
 
 <p>
@@ -175,7 +175,7 @@ $ perl -e 'use Config; print "$Config{archlib}\n";'
 </pre>
 </div>
 
-<H3><a name="Perl5_nn5">34.2.2 Compiling a dynamic module</a></H3>
+<H3><a name="Perl5_nn5">35.2.2 Compiling a dynamic module</a></H3>
 
 
 <p>
@@ -208,7 +208,7 @@ the target should be named `<tt>example.so</tt>',
 `<tt>example.sl</tt>', or the appropriate dynamic module name on your system.
 </p>
 
-<H3><a name="Perl5_nn6">34.2.3 Building a dynamic module with MakeMaker</a></H3>
+<H3><a name="Perl5_nn6">35.2.3 Building a dynamic module with MakeMaker</a></H3>
 
 
 <p>
@@ -242,7 +242,7 @@ the preferred approach to compilation.  More information about MakeMaker can be
 found in "Programming Perl, 2nd ed." by Larry Wall, Tom Christiansen,
 and Randal Schwartz.</p>
 
-<H3><a name="Perl5_nn7">34.2.4 Building a static version of Perl</a></H3>
+<H3><a name="Perl5_nn7">35.2.4 Building a static version of Perl</a></H3>
 
 
 <p>
@@ -311,7 +311,7 @@ added to it.  Depending on your machine, you may need to link with
 additional libraries such as <tt>-lsocket, -lnsl, -ldl</tt>, etc.
 </p>
 
-<H3><a name="Perl5_nn8">34.2.5 Using the module</a></H3>
+<H3><a name="Perl5_nn8">35.2.5 Using the module</a></H3>
 
 
 <p>
@@ -464,7 +464,7 @@ system configuration (this requires root access and you will need to
 read the man pages).
 </p>
 
-<H3><a name="Perl5_nn9">34.2.6 Compilation problems and compiling with C++</a></H3>
+<H3><a name="Perl5_nn9">35.2.6 Compilation problems and compiling with C++</a></H3>
 
 
 <p>
@@ -607,7 +607,7 @@ have to find the macro that conflicts and add an #undef into the .i file.  Pleas
 any conflicting macros you find to <a href="http://www.swig.org/mail.html">swig-user mailing list</a>.
 </p>
 
-<H3><a name="Perl5_nn10">34.2.7 Compiling for 64-bit platforms</a></H3>
+<H3><a name="Perl5_nn10">35.2.7 Compiling for 64-bit platforms</a></H3>
 
 
 <p>
@@ -634,7 +634,7 @@ also introduce problems on platforms that support more than one
 linking standard (e.g., -o32 and -n32 on Irix).
 </p>
 
-<H2><a name="Perl5_nn11">34.3 Building Perl Extensions under Windows</a></H2>
+<H2><a name="Perl5_nn11">35.3 Building Perl Extensions under Windows</a></H2>
 
 
 <p>
@@ -645,7 +645,7 @@ section assumes you are using SWIG with Microsoft Visual C++
 although the procedure may be similar with other compilers.  
 </p>
 
-<H3><a name="Perl5_nn12">34.3.1 Running SWIG from Developer Studio</a></H3>
+<H3><a name="Perl5_nn12">35.3.1 Running SWIG from Developer Studio</a></H3>
 
 
 <p>
@@ -708,7 +708,7 @@ print "$a\n";
 
 </pre></div>
 
-<H3><a name="Perl5_nn13">34.3.2 Using other compilers</a></H3>
+<H3><a name="Perl5_nn13">35.3.2 Using other compilers</a></H3>
 
 
 <p>
@@ -716,7 +716,7 @@ SWIG is known to work with Cygwin and may work with other compilers on Windows.
 For general hints and suggestions refer to the <a href="Windows.html#Windows">Windows</a> chapter.
 </p>
 
-<H2><a name="Perl5_nn14">34.4 The low-level interface</a></H2>
+<H2><a name="Perl5_nn14">35.4 The low-level interface</a></H2>
 
 
 <p>
@@ -726,7 +726,7 @@ can be used to control your application.  However, it is also used to
 construct more user-friendly proxy classes as described in the next section.
 </p>
 
-<H3><a name="Perl5_nn15">34.4.1 Functions</a></H3>
+<H3><a name="Perl5_nn15">35.4.1 Functions</a></H3>
 
 
 <p>
@@ -749,7 +749,7 @@ use example;
 $a = &amp;example::fact(2);
 </pre></div>
 
-<H3><a name="Perl5_nn16">34.4.2 Global variables</a></H3>
+<H3><a name="Perl5_nn16">35.4.2 Global variables</a></H3>
 
 
 <p>
@@ -819,7 +819,7 @@ extern char *path;       // Declared later in the input
 </pre>
 </div>
 
-<H3><a name="Perl5_nn17">34.4.3 Constants</a></H3>
+<H3><a name="Perl5_nn17">35.4.3 Constants</a></H3>
 
 
 <p>
@@ -859,7 +859,7 @@ print example::FOO, "\n";
 </pre>
 </div>
 
-<H3><a name="Perl5_nn18">34.4.4 Pointers</a></H3>
+<H3><a name="Perl5_nn18">35.4.4 Pointers</a></H3>
 
 
 <p>
@@ -968,7 +968,7 @@ as XS and <tt>xsubpp</tt>.  Given the advancement of the SWIG typesystem and the
 SWIG and XS, this is no longer supported.
 </p>
 
-<H3><a name="Perl5_nn19">34.4.5 Structures</a></H3>
+<H3><a name="Perl5_nn19">35.4.5 Structures</a></H3>
 
 
 <p>
@@ -1102,7 +1102,7 @@ void Bar_f_set(Bar *b, Foo *val) {
 </div>
 
 
-<H3><a name="Perl5_nn20">34.4.6 C++ classes</a></H3>
+<H3><a name="Perl5_nn20">35.4.6 C++ classes</a></H3>
 
 
 <p>
@@ -1167,7 +1167,7 @@ provides direct access to C++ objects.  A higher level interface using Perl prox
 can be built using these low-level accessors.  This is described shortly.
 </p>
 
-<H3><a name="Perl5_nn21">34.4.7 C++ classes and type-checking</a></H3>
+<H3><a name="Perl5_nn21">35.4.7 C++ classes and type-checking</a></H3>
 
 
 <p>
@@ -1203,7 +1203,7 @@ If necessary, the type-checker also adjusts the value of the pointer (as is nece
 multiple inheritance is used).
 </p>
 
-<H3><a name="Perl5_nn22">34.4.8 C++ overloaded functions</a></H3>
+<H3><a name="Perl5_nn22">35.4.8 C++ overloaded functions</a></H3>
 
 
 <p>
@@ -1247,7 +1247,7 @@ example::Spam_foo_d($s, 3.14);
 Please refer to the "SWIG Basics" chapter for more information. 
 </p>
 
-<H3><a name="Perl5_nn23">34.4.9 Operators</a></H3>
+<H3><a name="Perl5_nn23">35.4.9 Operators</a></H3>
 
 
     <p>
@@ -1274,7 +1274,7 @@ The following C++ operators are currently supported by the Perl module:
 <li>operator or  </li>
     </ul>
 
-<H3><a name="Perl5_nn24">34.4.10 Modules and packages</a></H3>
+<H3><a name="Perl5_nn24">35.4.10 Modules and packages</a></H3>
 
 
 <p>
@@ -1369,7 +1369,7 @@ print Foo::fact(4), "\n";        # Call a function in package FooBar
 </pre></div>
 -->
 
-<H2><a name="Perl5_nn25">34.5 Input and output parameters</a></H2>
+<H2><a name="Perl5_nn25">35.5 Input and output parameters</a></H2>
 
 
 <p>
@@ -1588,7 +1588,7 @@ print "$c\n";
 <b>Note:</b> The <tt>REFERENCE</tt> feature is only currently supported for numeric types (integers and floating point).
 </p>
 
-<H2><a name="Perl5_nn26">34.6 Exception handling</a></H2>
+<H2><a name="Perl5_nn26">35.6 Exception handling</a></H2>
 
 
 <p>
@@ -1752,7 +1752,7 @@ This is still supported, but it is deprecated.  The newer <tt>%exception</tt> di
 functionality, but it has additional capabilities that make it more powerful.
 </p>
 
-<H2><a name="Perl5_nn27">34.7 Remapping datatypes with typemaps</a></H2>
+<H2><a name="Perl5_nn27">35.7 Remapping datatypes with typemaps</a></H2>
 
 
 <p>
@@ -1769,7 +1769,7 @@ Typemaps are only used if you want to change some aspect of the primitive
 C-Perl interface.
 </p>
 
-<H3><a name="Perl5_nn28">34.7.1 A simple typemap example</a></H3>
+<H3><a name="Perl5_nn28">35.7.1 A simple typemap example</a></H3>
 
 
 <p>
@@ -1873,7 +1873,7 @@ example::count("e", "Hello World");
 </div>
 
 
-<H3><a name="Perl5_nn29">34.7.2 Perl5 typemaps</a></H3>
+<H3><a name="Perl5_nn29">35.7.2 Perl5 typemaps</a></H3>
 
 
 <p>
@@ -1978,7 +1978,7 @@ Return of C++ member data (all languages).
 Check value of input parameter.
 </div>
 
-<H3><a name="Perl5_nn30">34.7.3 Typemap variables</a></H3>
+<H3><a name="Perl5_nn30">35.7.3 Typemap variables</a></H3>
 
 
 <p>
@@ -2049,7 +2049,7 @@ properly assigned.
 The Perl name of the wrapper function being created.
 </div>
 
-<H3><a name="Perl5_nn31">34.7.4 Useful functions</a></H3>
+<H3><a name="Perl5_nn31">35.7.4 Useful functions</a></H3>
 
 
 <p>
@@ -2118,7 +2118,7 @@ int       sv_isa(SV *, char *0;
 </div>
 
 
-<H2><a name="Perl5_nn32">34.8 Typemap Examples</a></H2>
+<H2><a name="Perl5_nn32">35.8 Typemap Examples</a></H2>
 
 
 <p>
@@ -2127,7 +2127,7 @@ might look at the files "<tt>perl5.swg</tt>" and "<tt>typemaps.i</tt>" in
 the SWIG library.
 </p>
 
-<H3><a name="Perl5_nn33">34.8.1 Converting a Perl5 array to a char **</a></H3>
+<H3><a name="Perl5_nn33">35.8.1 Converting a Perl5 array to a char **</a></H3>
 
 
 <p>
@@ -2219,7 +2219,7 @@ print @$b, "\n";                                 # Print it out
 </pre></div>
 
 
-<H3><a name="Perl5_nn34">34.8.2 Return values</a></H3>
+<H3><a name="Perl5_nn34">35.8.2 Return values</a></H3>
 
 
 <p>
@@ -2248,7 +2248,7 @@ can be done using the <tt>EXTEND()</tt> macro as in:
 }
 </pre></div>
 
-<H3><a name="Perl5_nn35">34.8.3 Returning values from arguments</a></H3>
+<H3><a name="Perl5_nn35">35.8.3 Returning values from arguments</a></H3>
 
 
 <p>
@@ -2302,7 +2302,7 @@ print "multout(7, 13) = @r\n";
 ($x, $y) = multout(7, 13);
 </pre></div>
 
-<H3><a name="Perl5_nn36">34.8.4 Accessing array structure members</a></H3>
+<H3><a name="Perl5_nn36">35.8.4 Accessing array structure members</a></H3>
 
 
 <p>
@@ -2365,7 +2365,7 @@ the "in" typemap in the previous section would be used to convert an
 to copy the converted array into a C data structure.
 </p>
 
-<H3><a name="Perl5_nn37">34.8.5 Turning Perl references into C pointers</a></H3>
+<H3><a name="Perl5_nn37">35.8.5 Turning Perl references into C pointers</a></H3>
 
 
 <p>
@@ -2430,7 +2430,7 @@ print "$c\n";
 
 </pre></div>
 
-<H3><a name="Perl5_nn38">34.8.6 Pointer handling</a></H3>
+<H3><a name="Perl5_nn38">35.8.6 Pointer handling</a></H3>
 
 
 <p>
@@ -2515,7 +2515,7 @@ For example:
 </pre>
 </div>
 
-<H2><a name="Perl5_nn39">34.9 Proxy classes</a></H2>
+<H2><a name="Perl5_nn39">35.9 Proxy classes</a></H2>
 
 
 <p>
@@ -2531,7 +2531,7 @@ to the underlying code.  This section describes the implementation
 details of the proxy interface.
 </p>
 
-<H3><a name="Perl5_nn40">34.9.1 Preliminaries</a></H3>
+<H3><a name="Perl5_nn40">35.9.1 Preliminaries</a></H3>
 
 
 <p>
@@ -2553,7 +2553,7 @@ SWIG creates a collection of high-level Perl wrappers.  In your scripts, you wil
 high level wrappers.  The wrappers, in turn, interact with the low-level procedural module.
 </p>
 
-<H3><a name="Perl5_nn41">34.9.2 Structure and class wrappers</a></H3>
+<H3><a name="Perl5_nn41">35.9.2 Structure and class wrappers</a></H3>
 
 
 <p>
@@ -2680,7 +2680,7 @@ $v-&gt;DESTROY();
 
 </pre></div>
 
-<H3><a name="Perl5_nn42">34.9.3 Object Ownership</a></H3>
+<H3><a name="Perl5_nn42">35.9.3 Object Ownership</a></H3>
 
 
 <p>
@@ -2767,7 +2767,7 @@ counting, garbage collection, or advanced features one might find in
 sophisticated languages.
 </p>
 
-<H3><a name="Perl5_nn43">34.9.4 Nested Objects</a></H3>
+<H3><a name="Perl5_nn43">35.9.4 Nested Objects</a></H3>
 
 
 <p>
@@ -2820,7 +2820,7 @@ $p-&gt;{f}-&gt;{x} = 0.0;
 %${$p-&gt;{v}} = ( x=&gt;0, y=&gt;0, z=&gt;0);         
 </pre></div>
 
-<H3><a name="Perl5_nn44">34.9.5 Proxy Functions</a></H3>
+<H3><a name="Perl5_nn44">35.9.5 Proxy Functions</a></H3>
 
 
 <p>
@@ -2854,7 +2854,7 @@ This function replaces the original function, but operates in an
 identical manner.
 </p>
 
-<H3><a name="Perl5_nn45">34.9.6 Inheritance</a></H3>
+<H3><a name="Perl5_nn45">35.9.6 Inheritance</a></H3>
 
 
 <p>
@@ -2930,7 +2930,7 @@ particular, inheritance of data members is extremely tricky (and I'm
 not even sure if it really works).
 </p>
 
-<H3><a name="Perl5_nn46">34.9.7 Modifying the proxy methods</a></H3>
+<H3><a name="Perl5_nn46">35.9.7 Modifying the proxy methods</a></H3>
 
 
 <p>
@@ -2958,7 +2958,7 @@ public:
 };
 </pre></div>
 
-<H2><a name="Perl5_nn47">34.10 Adding additional Perl code</a></H2>
+<H2><a name="Perl5_nn47">35.10 Adding additional Perl code</a></H2>
 
 
 <p>
@@ -3009,7 +3009,7 @@ set_transform($im, $a);
 </pre>
 </div>
 
-<H2><a name="Perl5_directors">34.11 Cross language polymorphism</a></H2>
+<H2><a name="Perl5_directors">35.11 Cross language polymorphism</a></H2>
 
 
 <p>
@@ -3043,7 +3043,7 @@ proxy classes, director classes, and C wrapper functions takes care of
 all the cross-language method routing transparently.
 </p>
 
-<H3><a name="Perl5_nn48">34.11.1 Enabling directors</a></H3>
+<H3><a name="Perl5_nn48">35.11.1 Enabling directors</a></H3>
 
 
 <p>
@@ -3133,7 +3133,7 @@ sub one {
 </div>
 
 
-<H3><a name="Perl5_nn49">34.11.2 Director classes</a></H3>
+<H3><a name="Perl5_nn49">35.11.2 Director classes</a></H3>
 
 
  
@@ -3213,7 +3213,7 @@ so there is no need for the extra overhead involved with routing the
 calls through Perl.
 </p>
 
-<H3><a name="Perl5_nn50">34.11.3 Ownership and object destruction</a></H3>
+<H3><a name="Perl5_nn50">35.11.3 Ownership and object destruction</a></H3>
 
 
 <p>
@@ -3262,7 +3262,7 @@ sub DESTROY {
 </div>
 
 
-<H3><a name="Perl5_nn51">34.11.4 Exception unrolling</a></H3>
+<H3><a name="Perl5_nn51">35.11.4 Exception unrolling</a></H3>
 
 
 <p>
@@ -3318,7 +3318,7 @@ Swig::DirectorMethodException is thrown, Perl will register the
 exception as soon as the C wrapper function returns.
 </p>
 
-<H3><a name="Perl5_nn52">34.11.5 Overhead and code bloat</a></H3>
+<H3><a name="Perl5_nn52">35.11.5 Overhead and code bloat</a></H3>
 
 
 <p>
@@ -3352,7 +3352,7 @@ directive) for only those methods that are likely to be extended in
 Perl.
 </p>
 
-<H3><a name="Perl5_nn53">34.11.6 Typemaps</a></H3>
+<H3><a name="Perl5_nn53">35.11.6 Typemaps</a></H3>
 
 
 <p>
diff --git a/Doc/Manual/Php.html b/Doc/Manual/Php.html
index 8d2c3e8e4..e061690a9 100644
--- a/Doc/Manual/Php.html
+++ b/Doc/Manual/Php.html
@@ -7,7 +7,7 @@
 </head>
 
 <body bgcolor="#ffffff">
-<H1><a name="Php">35 SWIG and PHP</a></H1>
+<H1><a name="Php">36 SWIG and PHP</a></H1>
 <!-- INDEX -->
 <div class="sectiontoc">
 <ul>
@@ -77,7 +77,7 @@ your extension into php directly, you will need the complete PHP source tree
 available.
 </p>
 
-<H2><a name="Php_nn1">35.1 Generating PHP Extensions</a></H2>
+<H2><a name="Php_nn1">36.1 Generating PHP Extensions</a></H2>
 
 
 <p>
@@ -128,7 +128,7 @@ and it doesn't play nicely with package system.  We don't recommend
 this approach, or provide explicit support for it.
 </p>
 
-<H3><a name="Php_nn1_1">35.1.1 Building a loadable extension</a></H3>
+<H3><a name="Php_nn1_1">36.1.1 Building a loadable extension</a></H3>
 
 
 <p>
@@ -143,7 +143,7 @@ least work for Linux though):
         gcc -shared example_wrap.o example.o -o example.so
 </pre></div>
 
-<H3><a name="Php_nn1_3">35.1.2 Using PHP Extensions</a></H3>
+<H3><a name="Php_nn1_3">36.1.2 Using PHP Extensions</a></H3>
 
 
 <p>
@@ -191,7 +191,7 @@ This PHP module also defines the PHP classes for the wrapped API, so you'll
 almost certainly want to include it anyway.
 </p>
 
-<H2><a name="Php_nn2">35.2 Basic PHP interface</a></H2>
+<H2><a name="Php_nn2">36.2 Basic PHP interface</a></H2>
 
 
 <p>
@@ -202,7 +202,7 @@ other symbols unless care is taken to <tt>%rename</tt> them.  At present
 SWIG doesn't have support for the namespace feature added in PHP 5.3.
 </p>
 
-<H3><a name="Php_nn2_1">35.2.1 Constants</a></H3>
+<H3><a name="Php_nn2_1">36.2.1 Constants</a></H3>
 
 
 <p>
@@ -280,7 +280,7 @@ would be treated as false!  Modern versions of PHP will at least issue
 a PHP notice by default when this happens.
 </p>
 
-<H3><a name="Php_nn2_2">35.2.2 Global Variables</a></H3>
+<H3><a name="Php_nn2_2">36.2.2 Global Variables</a></H3>
 
 
 <p>
@@ -329,7 +329,7 @@ undefined.
 At this time SWIG does not support custom accessor methods.
 </p>
 
-<H3><a name="Php_nn2_3">35.2.3 Functions</a></H3>
+<H3><a name="Php_nn2_3">36.2.3 Functions</a></H3>
 
 
 <p>
@@ -382,7 +382,7 @@ print $s;      # The value of $s was not changed.
 -->
 
 
-<H3><a name="Php_nn2_4">35.2.4 Overloading</a></H3>
+<H3><a name="Php_nn2_4">36.2.4 Overloading</a></H3>
 
 
 <p>
@@ -437,7 +437,7 @@ taking the integer argument.
 </p>
 -->
 
-<H3><a name="Php_nn2_5">35.2.5 Pointers and References</a></H3>
+<H3><a name="Php_nn2_5">36.2.5 Pointers and References</a></H3>
 
 
 <p>
@@ -582,7 +582,7 @@ PHP in a number of ways: by using <tt>unset</tt> on an existing
 variable, or assigning <tt>NULL</tt> to a variable.
 </p>
 
-<H3><a name="Php_nn2_6">35.2.6 Structures and C++ classes</a></H3>
+<H3><a name="Php_nn2_6">36.2.6 Structures and C++ classes</a></H3>
 
 
 <p>
@@ -643,7 +643,7 @@ Would be used in the following way from PHP:
 Member variables and methods are accessed using the <tt>-&gt;</tt> operator.
 </p>
 
-<H4><a name="Php_nn2_6_1">35.2.6.1 Using -noproxy</a></H4>
+<H4><a name="Php_nn2_6_1">36.2.6.1 Using -noproxy</a></H4>
 
 
 <p>
@@ -669,7 +669,7 @@ Complex_im_set($obj, $d);
 Complex_im_get($obj);
 </pre></div>
 
-<H4><a name="Php_nn2_6_2">35.2.6.2 Constructors and Destructors</a></H4>
+<H4><a name="Php_nn2_6_2">36.2.6.2 Constructors and Destructors</a></H4>
 
 
 <p>
@@ -710,7 +710,7 @@ the programmer can either reassign the variable or call
 <tt>unset($v)</tt>
 </p>
 
-<H4><a name="Php_nn2_6_3">35.2.6.3 Static Member Variables</a></H4>
+<H4><a name="Php_nn2_6_3">36.2.6.3 Static Member Variables</a></H4>
 
 
 <p>
@@ -753,7 +753,7 @@ Ko::threats(10);
 echo "There have now been " . Ko::threats() . " threats\n";
 
 </pre></div>
-<H4><a name="Php_nn2_6_4">35.2.6.4 Static Member Functions</a></H4>
+<H4><a name="Php_nn2_6_4">36.2.6.4 Static Member Functions</a></H4>
 
 
 <p>
@@ -775,7 +775,7 @@ Ko::threats();
 </pre></div>
 
 
-<H4><a name="Php_nn2_6_5">35.2.6.5 Specifying Implemented Interfaces</a></H4>
+<H4><a name="Php_nn2_6_5">36.2.6.5 Specifying Implemented Interfaces</a></H4>
 
 
 <p>
@@ -793,7 +793,7 @@ so:
 If there are multiple interfaces, just list them separated by commas.
 </p>
 
-<H3><a name="Php_nn2_7">35.2.7 PHP Pragmas, Startup and Shutdown code</a></H3>
+<H3><a name="Php_nn2_7">36.2.7 PHP Pragmas, Startup and Shutdown code</a></H3>
 
 
 <p>
@@ -890,7 +890,7 @@ The <tt>%rinit</tt> and <tt>%rshutdown</tt> statements are very similar but inse
 into the request init (PHP_RINIT_FUNCTION) and request shutdown (PHP_RSHUTDOWN_FUNCTION) code respectively.
 </p>
 
-<H2><a name="Php_nn3">35.3 Cross language polymorphism</a></H2>
+<H2><a name="Php_nn3">36.3 Cross language polymorphism</a></H2>
 
 
 <p>
@@ -925,7 +925,7 @@ wrapper functions takes care of all the cross-language method routing
 transparently.
 </p>
 
-<H3><a name="Php_nn3_1">35.3.1 Enabling directors</a></H3>
+<H3><a name="Php_nn3_1">36.3.1 Enabling directors</a></H3>
 
 
 <p>
@@ -1014,7 +1014,7 @@ class MyFoo extends Foo {
 </div>
 
 
-<H3><a name="Php_nn3_2">35.3.2 Director classes</a></H3>
+<H3><a name="Php_nn3_2">36.3.2 Director classes</a></H3>
 
 
  
@@ -1094,7 +1094,7 @@ so there is no need for the extra overhead involved with routing the
 calls through PHP.
 </p>
 
-<H3><a name="Php_nn3_3">35.3.3 Ownership and object destruction</a></H3>
+<H3><a name="Php_nn3_3">36.3.3 Ownership and object destruction</a></H3>
 
 
 <p>
@@ -1150,7 +1150,7 @@ In this example, we are assuming that FooContainer will take care of
 deleting all the Foo pointers it contains at some point.
 </p>
 
-<H3><a name="Php_nn3_4">35.3.4 Exception unrolling</a></H3>
+<H3><a name="Php_nn3_4">36.3.4 Exception unrolling</a></H3>
 
 
 <p>
@@ -1217,7 +1217,7 @@ Swig::DirectorMethodException is thrown, PHP will register the exception
 as soon as the C wrapper function returns.
 </p>
 
-<H3><a name="Php_nn3_5">35.3.5 Overhead and code bloat</a></H3>
+<H3><a name="Php_nn3_5">36.3.5 Overhead and code bloat</a></H3>
 
 
 <p>
@@ -1250,7 +1250,7 @@ optimized by selectively enabling director methods (using the %feature
 directive) for only those methods that are likely to be extended in PHP.
 </p>
 
-<H3><a name="Php_nn3_6">35.3.6 Typemaps</a></H3>
+<H3><a name="Php_nn3_6">36.3.6 Typemaps</a></H3>
 
 
 <p>
@@ -1264,7 +1264,7 @@ need to be supported.
 </p>
 
 
-<H3><a name="Php_nn3_7">35.3.7 Miscellaneous</a></H3>
+<H3><a name="Php_nn3_7">36.3.7 Miscellaneous</a></H3>
 
 
 <p> Director typemaps for STL classes are mostly in place, and hence you
diff --git a/Doc/Manual/Pike.html b/Doc/Manual/Pike.html
index 59af01227..2b8432399 100644
--- a/Doc/Manual/Pike.html
+++ b/Doc/Manual/Pike.html
@@ -7,7 +7,7 @@
 </head>
 
 <body bgcolor="#ffffff">
-<H1><a name="Pike">36 SWIG and Pike</a></H1>
+<H1><a name="Pike">37 SWIG and Pike</a></H1>
 <!-- INDEX -->
 <div class="sectiontoc">
 <ul>
@@ -47,10 +47,10 @@ least, make sure you read the "<a href="SWIG.html#SWIG">SWIG Basics</a>"
 chapter.<br>
 </p>
 
-<H2><a name="Pike_nn2">36.1 Preliminaries</a></H2>
+<H2><a name="Pike_nn2">37.1 Preliminaries</a></H2>
 
 
-<H3><a name="Pike_nn3">36.1.1 Running SWIG</a></H3>
+<H3><a name="Pike_nn3">37.1.1 Running SWIG</a></H3>
 
 
 <p>
@@ -95,7 +95,7 @@ can use the <tt>-o</tt> option:
 <div class="code">
   <pre>$ <b>swig -pike -o pseudonym.c example.i</b><br></pre>
 </div>
-<H3><a name="Pike_nn4">36.1.2 Getting the right header files</a></H3>
+<H3><a name="Pike_nn4">37.1.2 Getting the right header files</a></H3>
 
 
 <p>
@@ -115,7 +115,7 @@ You're looking for files with the names <tt>global.h</tt>, <tt>program.h</tt>
 and so on.
 </p>
 
-<H3><a name="Pike_nn5">36.1.3 Using your module</a></H3>
+<H3><a name="Pike_nn5">37.1.3 Using your module</a></H3>
 
 
 <p>
@@ -130,10 +130,10 @@ Pike v7.4 release 10 running Hilfe v3.5 (Incremental Pike Frontend)
 (1) Result: 24
 </pre></div>
 
-<H2><a name="Pike_nn6">36.2 Basic C/C++ Mapping</a></H2>
+<H2><a name="Pike_nn6">37.2 Basic C/C++ Mapping</a></H2>
 
 
-<H3><a name="Pike_nn7">36.2.1 Modules</a></H3>
+<H3><a name="Pike_nn7">37.2.1 Modules</a></H3>
 
 
 <p>
@@ -144,7 +144,7 @@ concerned), SWIG's <tt>%module</tt> directive doesn't really have any
 significance.
 </p>
 
-<H3><a name="Pike_nn8">36.2.2 Functions</a></H3>
+<H3><a name="Pike_nn8">37.2.2 Functions</a></H3>
 
 
 <p>
@@ -169,7 +169,7 @@ exactly as you'd expect it to:
 (1) Result: 24
 </pre></div>
 
-<H3><a name="Pike_nn9">36.2.3 Global variables</a></H3>
+<H3><a name="Pike_nn9">37.2.3 Global variables</a></H3>
 
 
 <p>
@@ -198,7 +198,7 @@ will result in two functions, <tt>Foo_get()</tt> and <tt>Foo_set()</tt>:
 (3) Result: 3.141590
 </pre></div>
 
-<H3><a name="Pike_nn10">36.2.4 Constants and enumerated types</a></H3>
+<H3><a name="Pike_nn10">37.2.4 Constants and enumerated types</a></H3>
 
 
 <p>
@@ -206,7 +206,7 @@ Enumerated types in C/C++ declarations are wrapped as Pike constants,
 not as Pike enums.
 </p>
 
-<H3><a name="Pike_nn11">36.2.5 Constructors and Destructors</a></H3>
+<H3><a name="Pike_nn11">37.2.5 Constructors and Destructors</a></H3>
 
 
 <p>
@@ -214,7 +214,7 @@ Constructors are wrapped as <tt>create()</tt> methods, and destructors are
 wrapped as <tt>destroy()</tt> methods, for Pike classes.
 </p>
 
-<H3><a name="Pike_nn12">36.2.6 Static Members</a></H3>
+<H3><a name="Pike_nn12">37.2.6 Static Members</a></H3>
 
 
 <p>
diff --git a/Doc/Manual/Python.html b/Doc/Manual/Python.html
index d387b9a77..10c82e152 100644
--- a/Doc/Manual/Python.html
+++ b/Doc/Manual/Python.html
@@ -7,7 +7,7 @@
 </head>
 
 <body bgcolor="#ffffff">
-<H1><a name="Python">37 SWIG and Python</a></H1>
+<H1><a name="Python">38 SWIG and Python</a></H1>
 <!-- INDEX -->
 <div class="sectiontoc">
 <ul>
@@ -162,7 +162,7 @@ very least, make sure you read the "<a href="SWIG.html#SWIG">SWIG
 Basics</a>" chapter.
 </p>
 
-<H2><a name="Python_nn2">37.1 Overview</a></H2>
+<H2><a name="Python_nn2">38.1 Overview</a></H2>
 
 
 <p>
@@ -189,10 +189,10 @@ described followed by a discussion of low-level implementation
 details.
 </p>
 
-<H2><a name="Python_nn3">37.2 Preliminaries</a></H2>
+<H2><a name="Python_nn3">38.2 Preliminaries</a></H2>
 
 
-<H3><a name="Python_nn4">37.2.1 Running SWIG</a></H3>
+<H3><a name="Python_nn4">38.2.1 Running SWIG</a></H3>
 
 
 <p>
@@ -289,7 +289,7 @@ The following sections have further practical examples and details on
 how you might go about compiling and using the generated files.
 </p>
 
-<H3><a name="Python_nn6">37.2.2 Using distutils</a></H3>
+<H3><a name="Python_nn6">38.2.2 Using distutils</a></H3>
 
 
 <p>
@@ -381,7 +381,7 @@ This same approach works on all platforms if the appropriate compiler is install
 can even build extensions to the standard Windows Python using MingGW)
 </p>
 
-<H3><a name="Python_nn7">37.2.3 Hand compiling a dynamic module</a></H3>
+<H3><a name="Python_nn7">38.2.3 Hand compiling a dynamic module</a></H3>
 
 
 <p>
@@ -429,7 +429,7 @@ module actually consists of two files; <tt>socket.py</tt> and
 </p>
 
 
-<H3><a name="Python_nn8">37.2.4 Static linking</a></H3>
+<H3><a name="Python_nn8">38.2.4 Static linking</a></H3>
 
 
 <p>
@@ -508,7 +508,7 @@ If using static linking, you might want to rely on a different approach
 (perhaps using distutils).
 </p>
 
-<H3><a name="Python_nn9">37.2.5 Using your module</a></H3>
+<H3><a name="Python_nn9">38.2.5 Using your module</a></H3>
 
 
 <p>
@@ -665,7 +665,7 @@ system configuration (this requires root access and you will need to
 read the man pages).
 </p>
 
-<H3><a name="Python_nn10">37.2.6 Compilation of C++ extensions</a></H3>
+<H3><a name="Python_nn10">38.2.6 Compilation of C++ extensions</a></H3>
 
 
 <p>
@@ -757,7 +757,7 @@ erratic program behavior.   If working with lots of software components, you
 might want to investigate using a more formal standard such as COM.
 </p>
 
-<H3><a name="Python_nn11">37.2.7 Compiling for 64-bit platforms</a></H3>
+<H3><a name="Python_nn11">38.2.7 Compiling for 64-bit platforms</a></H3>
 
 
 <p>
@@ -794,7 +794,7 @@ and -m64 allow you to choose the desired binary format for your python
 extension.
 </p>
 
-<H3><a name="Python_nn12">37.2.8 Building Python Extensions under Windows</a></H3>
+<H3><a name="Python_nn12">38.2.8 Building Python Extensions under Windows</a></H3>
 
 
 <p>
@@ -923,7 +923,7 @@ SWIG Wiki</a>.
 </p>
 
 
-<H2><a name="Python_nn13">37.3 A tour of basic C/C++ wrapping</a></H2>
+<H2><a name="Python_nn13">38.3 A tour of basic C/C++ wrapping</a></H2>
 
 
 <p>
@@ -932,7 +932,7 @@ to your C/C++ code.  Functions are wrapped as functions, classes are wrapped as
 This section briefly covers the essential aspects of this wrapping.
 </p>
 
-<H3><a name="Python_nn14">37.3.1 Modules</a></H3>
+<H3><a name="Python_nn14">38.3.1 Modules</a></H3>
 
 
 <p>
@@ -945,7 +945,7 @@ module name, make sure you don't use the same name as a built-in
 Python command or standard module name.
 </p>
 
-<H3><a name="Python_nn15">37.3.2 Functions</a></H3>
+<H3><a name="Python_nn15">38.3.2 Functions</a></H3>
 
 
 <p>
@@ -969,7 +969,7 @@ like you think it does:
 &gt;&gt;&gt;
 </pre></div>
 
-<H3><a name="Python_nn16">37.3.3 Global variables</a></H3>
+<H3><a name="Python_nn16">38.3.3 Global variables</a></H3>
 
 
 <p>
@@ -1107,7 +1107,7 @@ that starts with a leading underscore. SWIG does not create <tt>cvar</tt>
 if there are no global variables in a module.
 </p>
 
-<H3><a name="Python_nn17">37.3.4 Constants and enums</a></H3>
+<H3><a name="Python_nn17">38.3.4 Constants and enums</a></H3>
 
 
 <p>
@@ -1147,7 +1147,7 @@ other object.  Unfortunately, there is no easy way for SWIG to
 generate code that prevents this.  You will just have to be careful.
 </p>
 
-<H3><a name="Python_nn18">37.3.5 Pointers</a></H3>
+<H3><a name="Python_nn18">38.3.5 Pointers</a></H3>
 
 
 <p>
@@ -1288,7 +1288,7 @@ C-style cast may return a bogus result whereas as the C++-style cast will return
 <tt>None</tt> if the conversion can't be performed.
 </p>
 
-<H3><a name="Python_nn19">37.3.6 Structures</a></H3>
+<H3><a name="Python_nn19">38.3.6 Structures</a></H3>
 
 
 <p>
@@ -1477,7 +1477,7 @@ everything works just like you would expect. For example:
 </pre>
 </div>
 
-<H3><a name="Python_nn20">37.3.7 C++ classes</a></H3>
+<H3><a name="Python_nn20">38.3.7 C++ classes</a></H3>
 
 
 <p>
@@ -1565,7 +1565,7 @@ they are accessed through <tt>cvar</tt> like this:
 </pre>
 </div>
 
-<H3><a name="Python_nn21">37.3.8 C++ inheritance</a></H3>
+<H3><a name="Python_nn21">38.3.8 C++ inheritance</a></H3>
 
 
 <p>
@@ -1620,7 +1620,7 @@ then the function <tt>spam()</tt> accepts <tt>Foo *</tt> or a pointer to any cla
 It is safe to use multiple inheritance with SWIG.
 </p>
 
-<H3><a name="Python_nn22">37.3.9 Pointers, references, values, and arrays</a></H3>
+<H3><a name="Python_nn22">38.3.9 Pointers, references, values, and arrays</a></H3>
 
 
 <p>
@@ -1681,7 +1681,7 @@ treated as a returning value, and it will follow the same
 allocation/deallocation process.
 </p>
 
-<H3><a name="Python_nn23">37.3.10 C++ overloaded functions</a></H3>
+<H3><a name="Python_nn23">38.3.10 C++ overloaded functions</a></H3>
 
 
 <p>
@@ -1804,7 +1804,7 @@ first declaration takes precedence.
 Please refer to the "SWIG and C++" chapter for more information about overloading.
 </p>
 
-<H3><a name="Python_nn24">37.3.11 C++ operators</a></H3>
+<H3><a name="Python_nn24">38.3.11 C++ operators</a></H3>
 
 
 <p>
@@ -1901,7 +1901,7 @@ instead of raising an exception when the comparison fails, that is, on any kind
 This follows the guidelines in <a href="https://www.python.org/dev/peps/pep-0207/">PEP 207 - Rich Comparisons</a> and <a href="https://docs.python.org/3/library/constants.html#NotImplemented">NotImplemented Python constant</a>.
 </p>
 
-<H3><a name="Python_nn25">37.3.12 C++ namespaces</a></H3>
+<H3><a name="Python_nn25">38.3.12 C++ namespaces</a></H3>
 
 
 <p>
@@ -1968,7 +1968,7 @@ utilizes thousands of small deeply nested namespaces each with
 identical symbol names, well, then you get what you deserve.
 </p>
 
-<H3><a name="Python_nn26">37.3.13 C++ templates</a></H3>
+<H3><a name="Python_nn26">38.3.13 C++ templates</a></H3>
 
 
 <p>
@@ -2022,10 +2022,10 @@ Some more complicated
 examples will appear later.
 </p>
 
-<H3><a name="Python_nn27">37.3.14 C++ Smart Pointers</a></H3>
+<H3><a name="Python_nn27">38.3.14 C++ Smart Pointers</a></H3>
 
 
-<H4><a name="Python_smart_pointers_shared_ptr">37.3.14.1 The shared_ptr Smart Pointer</a></H4>
+<H4><a name="Python_smart_pointers_shared_ptr">38.3.14.1 The shared_ptr Smart Pointer</a></H4>
 
 
 <p>
@@ -2036,7 +2036,7 @@ in the <a href="Library.html#Library_std_shared_ptr">shared_ptr smart pointer</a
 </p>
 
 
-<H4><a name="Python_smart_pointers_generic">37.3.14.2 Generic Smart Pointers</a></H4>
+<H4><a name="Python_smart_pointers_generic">38.3.14.2 Generic Smart Pointers</a></H4>
 
 
 <p>
@@ -2120,7 +2120,7 @@ simply use the <tt>__deref__()</tt> method.  For example:
 </pre>
 </div>
 
-<H3><a name="Python_nn27a">37.3.15 C++ reference counted objects</a></H3>
+<H3><a name="Python_nn27a">38.3.15 C++ reference counted objects</a></H3>
 
 
 <p>
@@ -2129,7 +2129,7 @@ Python examples of memory management using referencing counting.
 </p>
 
 
-<H2><a name="Python_nn28">37.4 Further details on the Python class interface</a></H2>
+<H2><a name="Python_nn28">38.4 Further details on the Python class interface</a></H2>
 
 
 <p>
@@ -2152,7 +2152,7 @@ the <tt>-builtin</tt> option are in the <a href="#Python_builtin_types">Built-in
 section.
 </p>
 
-<H3><a name="Python_nn29">37.4.1 Proxy classes</a></H3>
+<H3><a name="Python_nn29">38.4.1 Proxy classes</a></H3>
 
 
 <p>
@@ -2241,7 +2241,7 @@ you can attach new Python methods to the class and you can even inherit from it
 by Python built-in types until Python 2.2).
 </p>
 
-<H3><a name="Python_builtin_types">37.4.2 Built-in Types</a></H3>
+<H3><a name="Python_builtin_types">38.4.2 Built-in Types</a></H3>
 
 
 <p>
@@ -2285,7 +2285,7 @@ please refer to the python documentation:</p>
 
 <p><a href="http://docs.python.org/extending/newtypes.html">http://docs.python.org/extending/newtypes.html</a></p>
 
-<H4><a name="Python_builtin_limitations">37.4.2.1 Limitations</a></H4>
+<H4><a name="Python_builtin_limitations">38.4.2.1 Limitations</a></H4>
 
 
 <p>Use of the <tt>-builtin</tt> option implies a couple of limitations:
@@ -2453,7 +2453,7 @@ assert(issubclass(B.Derived, A.Base))
 </li>
 </ul>
 
-<H4><a name="Python_builtin_overloads">37.4.2.2 Operator overloads and slots -- use them!</a></H4>
+<H4><a name="Python_builtin_overloads">38.4.2.2 Operator overloads and slots -- use them!</a></H4>
 
 
 <p>The entire justification for the <tt>-builtin</tt> option is improved
@@ -2613,7 +2613,7 @@ in the file <tt>python/pyopers.swig</tt> in the SWIG library.
 </p>
 
 
-<H3><a name="Python_nn30">37.4.3 Memory management</a></H3>
+<H3><a name="Python_nn30">38.4.3 Memory management</a></H3>
 
 
 <p>NOTE: Although this section refers to proxy objects, everything here also applies
@@ -2808,7 +2808,7 @@ It is also possible to deal with situations like this using
 typemaps--an advanced topic discussed later.
 </p>
 
-<H3><a name="Python_nn31">37.4.4 Python 2.2 and classic classes</a></H3>
+<H3><a name="Python_nn31">38.4.4 Python 2.2 and classic classes</a></H3>
 
 
 <p>
@@ -2845,7 +2845,7 @@ class itself.  In Python-2.1 and earlier, they have to be accessed as a global
 function or through an instance (see the earlier section).
 </p>
 
-<H2><a name="Python_directors">37.5 Cross language polymorphism</a></H2>
+<H2><a name="Python_directors">38.5 Cross language polymorphism</a></H2>
 
 
 <p>
@@ -2879,7 +2879,7 @@ proxy classes, director classes, and C wrapper functions takes care of
 all the cross-language method routing transparently.
 </p>
 
-<H3><a name="Python_nn33">37.5.1 Enabling directors</a></H3>
+<H3><a name="Python_nn33">38.5.1 Enabling directors</a></H3>
 
 
 <p>
@@ -2971,7 +2971,7 @@ class MyFoo(mymodule.Foo):
 </div>
 
 
-<H3><a name="Python_nn34">37.5.2 Director classes</a></H3>
+<H3><a name="Python_nn34">38.5.2 Director classes</a></H3>
 
 
 <p>
@@ -3050,7 +3050,7 @@ so there is no need for the extra overhead involved with routing the
 calls through Python.
 </p>
 
-<H3><a name="Python_nn35">37.5.3 Ownership and object destruction</a></H3>
+<H3><a name="Python_nn35">38.5.3 Ownership and object destruction</a></H3>
 
 
 <p>
@@ -3117,7 +3117,7 @@ deleting all the Foo pointers it contains at some point.  Note that no hard
 references to the Foo objects remain in Python.
 </p>
 
-<H3><a name="Python_nn36">37.5.4 Exception unrolling</a></H3>
+<H3><a name="Python_nn36">38.5.4 Exception unrolling</a></H3>
 
 
 <p>
@@ -3176,7 +3176,7 @@ Swig::DirectorMethodException is thrown, Python will register the
 exception as soon as the C wrapper function returns.
 </p>
 
-<H3><a name="Python_nn37">37.5.5 Overhead and code bloat</a></H3>
+<H3><a name="Python_nn37">38.5.5 Overhead and code bloat</a></H3>
 
 
 <p>
@@ -3210,7 +3210,7 @@ directive) for only those methods that are likely to be extended in
 Python.
 </p>
 
-<H3><a name="Python_nn38">37.5.6 Typemaps</a></H3>
+<H3><a name="Python_nn38">38.5.6 Typemaps</a></H3>
 
 
 <p>
@@ -3224,7 +3224,7 @@ need to be supported.
 </p>
 
 
-<H3><a name="Python_nn39">37.5.7 Miscellaneous</a></H3>
+<H3><a name="Python_nn39">38.5.7 Miscellaneous</a></H3>
 
 
 <p>
@@ -3271,7 +3271,7 @@ methods that return const references.
 </p>
 
 
-<H2><a name="Python_nn40">37.6 Common customization features</a></H2>
+<H2><a name="Python_nn40">38.6 Common customization features</a></H2>
 
 
 <p>
@@ -3284,7 +3284,7 @@ This section describes some common SWIG features that are used to
 improve your the interface to an extension module.
 </p>
 
-<H3><a name="Python_nn41">37.6.1 C/C++ helper functions</a></H3>
+<H3><a name="Python_nn41">38.6.1 C/C++ helper functions</a></H3>
 
 
 <p>
@@ -3365,7 +3365,7 @@ hard to implement.  It is possible to clean this up using Python code, typemaps,
 customization features as covered in later sections.
 </p>
 
-<H3><a name="Python_nn42">37.6.2 Adding additional Python code</a></H3>
+<H3><a name="Python_nn42">38.6.2 Adding additional Python code</a></H3>
 
 
 <p>
@@ -3617,7 +3617,7 @@ The same applies for overloaded constructors.
 </p>
 
 
-<H3><a name="Python_nn43">37.6.3 Class extension with %extend</a></H3>
+<H3><a name="Python_nn43">38.6.3 Class extension with %extend</a></H3>
 
 
 <p>
@@ -3706,7 +3706,7 @@ Vector(12, 14, 16)
 in any way---the extensions only show up in the Python interface.
 </p>
 
-<H3><a name="Python_nn44">37.6.4 Exception handling with %exception</a></H3>
+<H3><a name="Python_nn44">38.6.4 Exception handling with %exception</a></H3>
 
 
 <p>
@@ -3840,7 +3840,7 @@ The language-independent <tt>exception.i</tt> library file can also be used
 to raise exceptions.  See the <a href="Library.html#Library">SWIG Library</a> chapter.
 </p>
 
-<H2><a name="Python_nn45">37.7 Tips and techniques</a></H2>
+<H2><a name="Python_nn45">38.7 Tips and techniques</a></H2>
 
 
 <p>
@@ -3850,7 +3850,7 @@ strings, binary data, and arrays.   This chapter discusses the common techniques
 solving these problems.
 </p>
 
-<H3><a name="Python_nn46">37.7.1 Input and output parameters</a></H3>
+<H3><a name="Python_nn46">38.7.1 Input and output parameters</a></H3>
 
 
 <p>
@@ -4063,7 +4063,7 @@ void foo(Bar *OUTPUT);
 may not have the intended effect since <tt>typemaps.i</tt> does not define an OUTPUT rule for <tt>Bar</tt>.
 </p>
 
-<H3><a name="Python_nn47">37.7.2 Simple pointers</a></H3>
+<H3><a name="Python_nn47">38.7.2 Simple pointers</a></H3>
 
 
 <p>
@@ -4132,7 +4132,7 @@ If you replace <tt>%pointer_functions()</tt> by <tt>%pointer_class(type, name)</
 See the <a href="Library.html#Library">SWIG Library</a> chapter for further details.
 </p>
 
-<H3><a name="Python_nn48">37.7.3 Unbounded C Arrays</a></H3>
+<H3><a name="Python_nn48">38.7.3 Unbounded C Arrays</a></H3>
 
 
 <p>
@@ -4194,7 +4194,7 @@ well suited for applications in which you need to create buffers,
 package binary data, etc.
 </p>
 
-<H3><a name="Python_nn49">37.7.4 String handling</a></H3>
+<H3><a name="Python_nn49">38.7.4 String handling</a></H3>
 
 
 <p>
@@ -4264,7 +4264,7 @@ also be used to extra binary data from arbitrary pointers.
 </p>
 
 
-<H3><a name="Python_default_args">37.7.5 Default arguments</a></H3>
+<H3><a name="Python_default_args">38.7.5 Default arguments</a></H3>
 
 
 <p>
@@ -4363,7 +4363,7 @@ Versions of SWIG prior to this varied in their ability to convert C++ default va
 equivalent Python default argument values.
 </p>
 
-<H2><a name="Python_nn53">37.8 Typemaps</a></H2>
+<H2><a name="Python_nn53">38.8 Typemaps</a></H2>
 
 
 <p>
@@ -4380,7 +4380,7 @@ Typemaps are only used if you want to change some aspect of the primitive
 C-Python interface or if you want to elevate your guru status.
 </p>
 
-<H3><a name="Python_nn54">37.8.1 What is a typemap?</a></H3>
+<H3><a name="Python_nn54">38.8.1 What is a typemap?</a></H3>
 
 
 <p>
@@ -4496,7 +4496,7 @@ parameter is omitted):
 </pre>
 </div>
 
-<H3><a name="Python_nn55">37.8.2 Python typemaps</a></H3>
+<H3><a name="Python_nn55">38.8.2 Python typemaps</a></H3>
 
 
 <p>
@@ -4537,7 +4537,7 @@ a look at the SWIG library version 1.3.20 or so.
 </p>
 
 
-<H3><a name="Python_nn56">37.8.3 Typemap variables</a></H3>
+<H3><a name="Python_nn56">38.8.3 Typemap variables</a></H3>
 
 
 <p>
@@ -4608,7 +4608,7 @@ properly assigned.
 The Python name of the wrapper function being created.
 </div>
 
-<H3><a name="Python_nn57">37.8.4 Useful Python Functions</a></H3>
+<H3><a name="Python_nn57">38.8.4 Useful Python Functions</a></H3>
 
 
 <p>
@@ -4736,7 +4736,7 @@ write me
 </pre>
 </div>
 
-<H2><a name="Python_nn58">37.9 Typemap Examples</a></H2>
+<H2><a name="Python_nn58">38.9 Typemap Examples</a></H2>
 
 
 <p>
@@ -4745,7 +4745,7 @@ might look at the files "<tt>python.swg</tt>" and "<tt>typemaps.i</tt>" in
 the SWIG library.
 </p>
 
-<H3><a name="Python_nn59">37.9.1 Converting  Python list to a char ** </a></H3>
+<H3><a name="Python_nn59">38.9.1 Converting  Python list to a char ** </a></H3>
 
 
 <p>
@@ -4825,7 +4825,7 @@ memory allocation is used to allocate memory for the array, the
 the C function.
 </p>
 
-<H3><a name="Python_nn60">37.9.2 Expanding a Python object into multiple arguments</a></H3>
+<H3><a name="Python_nn60">38.9.2 Expanding a Python object into multiple arguments</a></H3>
 
 
 <p>
@@ -4944,7 +4944,7 @@ NotImplementedError: Wrong number or type of arguments for overloaded function '
 </pre>
 </div>
 
-<H3><a name="Python_nn61">37.9.3 Using typemaps to return arguments</a></H3>
+<H3><a name="Python_nn61">38.9.3 Using typemaps to return arguments</a></H3>
 
 
 <p>
@@ -5032,7 +5032,7 @@ function can now be used as follows:
 &gt;&gt;&gt;
 </pre></div>
 
-<H3><a name="Python_nn62">37.9.4 Mapping Python tuples into small arrays</a></H3>
+<H3><a name="Python_nn62">38.9.4 Mapping Python tuples into small arrays</a></H3>
 
 
 <p>
@@ -5081,7 +5081,7 @@ array, such an approach would not be recommended for huge arrays, but
 for small structures, this approach works fine.
 </p>
 
-<H3><a name="Python_nn63">37.9.5 Mapping sequences to C arrays</a></H3>
+<H3><a name="Python_nn63">38.9.5 Mapping sequences to C arrays</a></H3>
 
 
 <p>
@@ -5170,7 +5170,7 @@ static int convert_darray(PyObject *input, double *ptr, int size) {
 </pre>
 </div>
 
-<H3><a name="Python_nn64">37.9.6 Pointer handling</a></H3>
+<H3><a name="Python_nn64">38.9.6 Pointer handling</a></H3>
 
 
 <p>
@@ -5269,7 +5269,7 @@ class object (if applicable).
 
 
 
-<H2><a name="Python_nn65">37.10 Docstring Features</a></H2>
+<H2><a name="Python_nn65">38.10 Docstring Features</a></H2>
 
 
 <p>
@@ -5297,7 +5297,7 @@ of your users much simpler.
 </p>
 
 
-<H3><a name="Python_nn66">37.10.1 Module docstring</a></H3>
+<H3><a name="Python_nn66">38.10.1 Module docstring</a></H3>
 
 
 <p>
@@ -5331,7 +5331,7 @@ layout of controls on a panel, etc. to be loaded from an XML file."
 </div>
 
 
-<H3><a name="Python_nn67">37.10.2 %feature("autodoc")</a></H3>
+<H3><a name="Python_nn67">38.10.2 %feature("autodoc")</a></H3>
 
 
 <p>
@@ -5359,7 +5359,7 @@ four levels for autodoc controlled by the value given to the
 feature, <tt>%feature("autodoc", "<i>level</i>")</tt>.
 The four values for <i>level</i> are covered in the following sub-sections.
 
-<H4><a name="Python_nn68">37.10.2.1 %feature("autodoc", "0")</a></H4>
+<H4><a name="Python_nn68">38.10.2.1 %feature("autodoc", "0")</a></H4>
 
 
 <p>
@@ -5388,7 +5388,7 @@ def function_name(*args, **kwargs):
 </div>
 
 
-<H4><a name="Python_nn69">37.10.2.2 %feature("autodoc", "1")</a></H4>
+<H4><a name="Python_nn69">38.10.2.2 %feature("autodoc", "1")</a></H4>
 
 
 <p>
@@ -5413,7 +5413,7 @@ def function_name(*args, **kwargs):
 </div>
 
 
-<H4><a name="Python_autodoc2">37.10.2.3 %feature("autodoc", "2")</a></H4>
+<H4><a name="Python_autodoc2">38.10.2.3 %feature("autodoc", "2")</a></H4>
 
 
 <p>
@@ -5475,7 +5475,7 @@ def function_name(*args, **kwargs):
 </pre>
 </div>
 
-<H4><a name="Python_autodoc3">37.10.2.4 %feature("autodoc", "3")</a></H4>
+<H4><a name="Python_autodoc3">38.10.2.4 %feature("autodoc", "3")</a></H4>
 
 
 <p>
@@ -5501,7 +5501,7 @@ def function_name(*args, **kwargs):
 </div>
 
 
-<H4><a name="Python_nn70">37.10.2.5 %feature("autodoc", "docstring")</a></H4>
+<H4><a name="Python_nn70">38.10.2.5 %feature("autodoc", "docstring")</a></H4>
 
 
 <p>
@@ -5520,7 +5520,7 @@ void GetPosition(int* OUTPUT, int* OUTPUT);
 </div>
 
 
-<H3><a name="Python_nn71">37.10.3 %feature("docstring")</a></H3>
+<H3><a name="Python_nn71">38.10.3 %feature("docstring")</a></H3>
 
 
 <p>
@@ -5552,7 +5552,7 @@ with more than one line.
 </pre>
 </div>
 
-<H2><a name="Python_nn72">37.11 Python Packages</a></H2>
+<H2><a name="Python_nn72">38.11 Python Packages</a></H2>
 
 
 <p>Python has concepts of modules and packages. Modules are separate units of
@@ -5627,7 +5627,7 @@ users may need to use special features such as the <tt>package</tt> option in th
 <tt>%module</tt> directive or import related command line options. These are
 explained in the following sections.</p>
 
-<H3><a name="Python_modulepackage">37.11.1 Setting the Python package</a></H3>
+<H3><a name="Python_modulepackage">38.11.1 Setting the Python package</a></H3>
 
 
 <p>
@@ -5681,7 +5681,7 @@ pkg1/pkg2/_foo.so       # (shared library built from C/C++ code generated by SWI
 </pre>
 </div>
 
-<H3><a name="Python_absrelimports">37.11.2 Absolute and relative imports</a></H3>
+<H3><a name="Python_absrelimports">38.11.2 Absolute and relative imports</a></H3>
 
 
 <p>Suppose, we have the following hierarchy of files:</p>
@@ -5816,7 +5816,7 @@ uses relative imports. Second case is, when one puts import directives in
 <tt>__init__.py</tt> to import symbols from submodules or subpackages and the
 submodule depends on other submodules (discussed later).</p>
 
-<H3><a name="Python_absimport">37.11.3 Enforcing absolute import semantics</a></H3>
+<H3><a name="Python_absimport">38.11.3 Enforcing absolute import semantics</a></H3>
 
 
 <p>As you may know, there is an incompatibility in import semantics (for the
@@ -5853,7 +5853,7 @@ from __future__ import absolute_import
 </pre>
 </div>
 
-<H3><a name="Python_importfrominit">37.11.4 Importing from __init__.py</a></H3>
+<H3><a name="Python_importfrominit">38.11.4 Importing from __init__.py</a></H3>
 
 
 <p>Imports in <tt>__init__.py</tt> are handy when you want to populate a
@@ -5963,7 +5963,7 @@ class Bar(pkg3.foo.Foo): pass
 effect (note, that the Python 2 case also needs the <tt>-relativeimport</tt>
 workaround).</p>
 
-<H3><a name="Python_implicit_namespace_packages">37.11.5 Implicit Namespace Packages</a></H3>
+<H3><a name="Python_implicit_namespace_packages">38.11.5 Implicit Namespace Packages</a></H3>
 
 
 <p> Python 3.3 introduced
@@ -6041,7 +6041,7 @@ zipimporter requires python-3.5.1 or newer to work with subpackages.
 </p>
 
 
-<H3><a name="Python_package_search">37.11.6 Searching for the wrapper module</a></H3>
+<H3><a name="Python_package_search">38.11.6 Searching for the wrapper module</a></H3>
 
 
 <p>
@@ -6116,7 +6116,7 @@ following ways:
 </p>
 
 
-<H4><a name="Python_package_search_both_package_modules">37.11.6.1 Both modules in the same package</a></H4>
+<H4><a name="Python_package_search_both_package_modules">38.11.6.1 Both modules in the same package</a></H4>
 
 
 <p>Both modules are in one package:</p>
@@ -6135,7 +6135,7 @@ from package import foo
 </div>
 
 
-<H4><a name="Python_package_search_wrapper_split">37.11.6.2 Split modules</a></H4>
+<H4><a name="Python_package_search_wrapper_split">38.11.6.2 Split modules</a></H4>
 
 
 <p>The pure python module is in a package and the C/C++ module is global:</p>
@@ -6154,7 +6154,7 @@ from package import foo
 </div>
 
 
-<H4><a name="Python_package_search_both_global_modules">37.11.6.3 Both modules are global</a></H4>
+<H4><a name="Python_package_search_both_global_modules">38.11.6.3 Both modules are global</a></H4>
 
 
 <p>Both modules are global:</p>
@@ -6179,7 +6179,7 @@ loaded modules.  So, one may place the module either globally or in a package
 as desired.
 </p>
 
-<H4><a name="Python_package_search_static">37.11.6.4 Statically linked C modules</a></H4>
+<H4><a name="Python_package_search_static">38.11.6.4 Statically linked C modules</a></H4>
 
 
 <p>It is strongly recommended to use dynamically linked modules for the C
@@ -6251,7 +6251,7 @@ module then you will either need to refer to the Python documentation on how
 to do this (remember you are now the Python importer) or use dynamic linking.
 </p>
 
-<H2><a name="Python_python3support">37.12 Python 3 Support</a></H2>
+<H2><a name="Python_python3support">38.12 Python 3 Support</a></H2>
 
 
 <p>
@@ -6278,7 +6278,7 @@ The following are Python 3.0 new features that are currently supported by
 SWIG.
 </p>
 
-<H3><a name="Python_nn74">37.12.1 Function annotation</a></H3>
+<H3><a name="Python_nn74">38.12.1 Function annotation</a></H3>
 
 
 <p>
@@ -6311,7 +6311,7 @@ For detailed usage of function annotation, see
 <a href="https://www.python.org/dev/peps/pep-3107/">PEP 3107</a>.
 </p>
 
-<H3><a name="Python_nn75">37.12.2 Buffer interface</a></H3>
+<H3><a name="Python_nn75">38.12.2 Buffer interface</a></H3>
 
 
 <p>
@@ -6463,7 +6463,7 @@ modify the buffer.
 </div>
 
 
-<H3><a name="Python_nn76">37.12.3 Abstract base classes</a></H3>
+<H3><a name="Python_nn76">38.12.3 Abstract base classes</a></H3>
 
 
 <p>
@@ -6504,7 +6504,7 @@ For details of abstract base class, please see
 <a href="https://www.python.org/dev/peps/pep-3119/">PEP 3119</a>.
 </p>
 
-<H3><a name="Python_nn77">37.12.4 Byte string output conversion</a></H3>
+<H3><a name="Python_nn77">38.12.4 Byte string output conversion</a></H3>
 
 
 <p>
@@ -6684,7 +6684,7 @@ overloads taking both std::string (as Python bytes) and std::wstring
 (as Python unicode).
 </p>
 
-<H3><a name="Python_2_unicode">37.12.5 Python 2 Unicode</a></H3>
+<H3><a name="Python_2_unicode">38.12.5 Python 2 Unicode</a></H3>
 
 
 <p>
@@ -6756,7 +6756,7 @@ the first is allowing unicode conversion and the second is explicitly
 prohibiting it.
 </p>
 
-<H2><a name="Python_multithreaded">37.13 Support for Multithreaded Applications</a></H2>
+<H2><a name="Python_multithreaded">38.13 Support for Multithreaded Applications</a></H2>
 
 
 <p>By default, SWIG does not enable support for multithreaded Python applications.  More
@@ -6771,7 +6771,7 @@ will not be able to run any other threads, even if the wrapped C/C++ code is wai
     interface for this is described in the next section.
 </p>
 
-<H3><a name="Python_thread_UI">37.13.1 UI for Enabling Multithreading Support</a></H3>
+<H3><a name="Python_thread_UI">38.13.1 UI for Enabling Multithreading Support</a></H3>
 
 
 <p>The user interface is as follows:</p>
@@ -6814,7 +6814,7 @@ will not be able to run any other threads, even if the wrapped C/C++ code is wai
   </li>
 </ol>
 
-<H3><a name="Python_thread_performance">37.13.2 Multithread Performance</a></H3>
+<H3><a name="Python_thread_performance">38.13.2 Multithread Performance</a></H3>
 
 
 <p>
diff --git a/Doc/Manual/R.html b/Doc/Manual/R.html
index b6cf2d879..3a6aaeb3c 100644
--- a/Doc/Manual/R.html
+++ b/Doc/Manual/R.html
@@ -7,7 +7,7 @@
 </head>
 
 <body bgcolor="#ffffff">
-<H1><a name="R">38 SWIG and R</a></H1>
+<H1><a name="R">39 SWIG and R</a></H1>
 <!-- INDEX -->
 <div class="sectiontoc">
 <ul>
@@ -34,7 +34,7 @@ compile and run an R interface to QuantLib running on Mandriva Linux
 with gcc. The R bindings also work on Microsoft Windows using Visual C++.
 </p>
 
-<H2><a name="R_nn2">38.1 Bugs</a></H2>
+<H2><a name="R_nn2">39.1 Bugs</a></H2>
 
 
 <p>
@@ -46,7 +46,7 @@ Currently the following features are not implemented or broken:
 <li>C Array wrappings
 </ul>
 
-<H2><a name="R_nn3">38.2 Using R and SWIG</a></H2>
+<H2><a name="R_nn3">39.2 Using R and SWIG</a></H2>
 
 
 <p>
@@ -137,7 +137,7 @@ Error in .Call("R_swig_fact", s_arg1, as.logical(.copy), PACKAGE = "example") :
 <li>Make sure the architecture of the shared library(x64 for instance), matches the architecture of the R program you want to load your shared library into
 </ul>
 
-<H2><a name="R_nn4">38.3 Precompiling large R files</a></H2>
+<H2><a name="R_nn4">39.3 Precompiling large R files</a></H2>
 
 
 In cases where the R file is large, one make save a lot of loading
@@ -155,7 +155,7 @@ will save a large amount of loading time.
 
 
 
-<H2><a name="R_nn5">38.4 General policy</a></H2>
+<H2><a name="R_nn5">39.4 General policy</a></H2>
 
 
 <p>
@@ -164,7 +164,7 @@ wrapping over the underlying functions and rely on the R type system
 to provide R syntax.
 </p>
 
-<H2><a name="R_language_conventions">38.5 Language conventions</a></H2>
+<H2><a name="R_language_conventions">39.5 Language conventions</a></H2>
 
 
 <p>
@@ -173,7 +173,7 @@ and [ are overloaded to allow for R syntax (one based indices and
 slices)
 </p>
 
-<H2><a name="R_nn6">38.6 C++ classes</a></H2>
+<H2><a name="R_nn6">39.6 C++ classes</a></H2>
 
 
 <p>
@@ -185,7 +185,7 @@ keep track of the pointer object which removes the necessity for a lot
 of the proxy class baggage you see in other languages.
 </p>
 
-<H2><a name="R_nn7">38.7 Enumerations</a></H2>
+<H2><a name="R_nn7">39.7 Enumerations</a></H2>
 
 
 <p>
diff --git a/Doc/Manual/Ruby.html b/Doc/Manual/Ruby.html
index 051a40518..9b9b49d07 100644
--- a/Doc/Manual/Ruby.html
+++ b/Doc/Manual/Ruby.html
@@ -8,7 +8,7 @@
 
 <body bgcolor="#ffffff">
 
-<H1><a name="Ruby">39 SWIG and Ruby</a></H1>
+<H1><a name="Ruby">40 SWIG and Ruby</a></H1>
 <!-- INDEX -->
 <div class="sectiontoc">
 <ul>
@@ -149,7 +149,7 @@
 
 <p>This chapter describes SWIG's support of Ruby.</p>
 
-<H2><a name="Ruby_nn2">39.1 Preliminaries</a></H2>
+<H2><a name="Ruby_nn2">40.1 Preliminaries</a></H2>
 
 
 <p> SWIG 3.0 is known to work with Ruby versions 1.8 and later.
@@ -164,7 +164,7 @@ read the "<a href="SWIG.html#SWIG">SWIG Basics</a>"
 chapter. It is also assumed that the reader has a basic understanding
 of Ruby. </p>
 
-<H3><a name="Ruby_nn3">39.1.1 Running SWIG</a></H3>
+<H3><a name="Ruby_nn3">40.1.1 Running SWIG</a></H3>
 
 
 <p> To build a Ruby module, run SWIG using the <tt>-ruby</tt>
@@ -188,7 +188,7 @@ if compiling a C++ extension) that contains all of the code needed to
 build a Ruby extension module. To finish building the module, you need
 to compile this file and link it with the rest of your program. </p>
 
-<H3><a name="Ruby_nn4">39.1.2 Getting the right header files</a></H3>
+<H3><a name="Ruby_nn4">40.1.2 Getting the right header files</a></H3>
 
 
 <p> In order to compile the wrapper code, the compiler needs the <tt>ruby.h</tt>
@@ -202,7 +202,7 @@ the compiler options needed to compile the code is to ask Ruby itself:</p>
 </pre>
 </div>
 
-<H3><a name="Ruby_nn5">39.1.3 Compiling a dynamic module</a></H3>
+<H3><a name="Ruby_nn5">40.1.3 Compiling a dynamic module</a></H3>
 
 
 <p> Ruby extension modules are typically compiled into shared
@@ -275,7 +275,7 @@ manual pages for your compiler and linker to determine the correct set
 of options. You might also check the <a href="https://github.com/swig/swig/wiki">SWIG Wiki</a>
 for additional information. </p>
 
-<H3><a name="Ruby_nn6">39.1.4 Using your module</a></H3>
+<H3><a name="Ruby_nn6">40.1.4 Using your module</a></H3>
 
 
 <p> Ruby <i>module</i> names must be capitalized,
@@ -305,7 +305,7 @@ begins with: </p>
 <p> will result in an extension module using the feature name
 "example" and Ruby module name "Example". </p>
 
-<H3><a name="Ruby_nn7">39.1.5 Static linking</a></H3>
+<H3><a name="Ruby_nn7">40.1.5 Static linking</a></H3>
 
 
 <p> An alternative approach to dynamic linking is to rebuild the
@@ -320,7 +320,7 @@ finding the Ruby source, adding an entry to the <tt>ext/Setup</tt>
 file, adding your directory to the list of extensions in the file, and
 finally rebuilding Ruby. </p>
 
-<H3><a name="Ruby_nn8">39.1.6 Compilation of C++ extensions</a></H3>
+<H3><a name="Ruby_nn8">40.1.6 Compilation of C++ extensions</a></H3>
 
 
 <p> On most machines, C++ extension modules should be linked
@@ -352,7 +352,7 @@ $libs = append_library($libs, "supc++")
 create_makefile('example')</pre>
 </div>
 
-<H2><a name="Ruby_nn9">39.2 Building Ruby Extensions under Windows 95/NT</a></H2>
+<H2><a name="Ruby_nn9">40.2 Building Ruby Extensions under Windows 95/NT</a></H2>
 
 
 <p> Building a SWIG extension to Ruby under Windows 95/NT is
@@ -377,7 +377,7 @@ order to build extensions, you may need to download the source
 distribution to the Ruby package, as you will need the Ruby header
 files. </p>
 
-<H3><a name="Ruby_nn10">39.2.1 Running SWIG from Developer Studio</a></H3>
+<H3><a name="Ruby_nn10">40.2.1 Running SWIG from Developer Studio</a></H3>
 
 
 <p> If you are developing your application within Microsoft
@@ -441,13 +441,13 @@ Foo = 3.0
 </pre>
 </div>
 
-<H2><a name="Ruby_nn11">39.3 The Ruby-to-C/C++ Mapping</a></H2>
+<H2><a name="Ruby_nn11">40.3 The Ruby-to-C/C++ Mapping</a></H2>
 
 
 <p> This section describes the basics of how SWIG maps C or C++
 declarations in your SWIG interface files to Ruby constructs. </p>
 
-<H3><a name="Ruby_nn12">39.3.1 Modules</a></H3>
+<H3><a name="Ruby_nn12">40.3.1 Modules</a></H3>
 
 
 <p> The SWIG <tt>%module</tt> directive specifies
@@ -519,7 +519,7 @@ option to wrap everything into the global module, take care that the
 names of your constants, classes and methods don't conflict with any of
 Ruby's built-in names. </p>
 
-<H3><a name="Ruby_nn13">39.3.2 Functions</a></H3>
+<H3><a name="Ruby_nn13">40.3.2 Functions</a></H3>
 
 
 <p> Global functions are wrapped as Ruby module methods. For
@@ -553,7 +553,7 @@ irb(main):002:0&gt; <b>Example.fact(4)</b>
 24</pre>
 </div>
 
-<H3><a name="Ruby_nn14">39.3.3 Variable Linking</a></H3>
+<H3><a name="Ruby_nn14">40.3.3 Variable Linking</a></H3>
 
 
 <p> C/C++ global variables are wrapped as a pair of singleton
@@ -615,7 +615,7 @@ directive. For example: </p>
 effect until it is explicitly disabled using <tt>%mutable</tt>.
 </p>
 
-<H3><a name="Ruby_nn15">39.3.4 Constants</a></H3>
+<H3><a name="Ruby_nn15">40.3.4 Constants</a></H3>
 
 
 <p> C/C++ constants are wrapped as module constants initialized
@@ -643,7 +643,7 @@ irb(main):002:0&gt; <b>Example::PI</b>
 3.14159</pre>
 </div>
 
-<H3><a name="Ruby_nn16">39.3.5 Pointers</a></H3>
+<H3><a name="Ruby_nn16">40.3.5 Pointers</a></H3>
 
 
 <p> "Opaque" pointers to arbitrary C/C++ types (i.e. types that
@@ -667,7 +667,7 @@ returns an instance of an internally generated Ruby class: </p>
 <p> A <tt>NULL</tt> pointer is always represented by
 the Ruby <tt>nil</tt> object. </p>
 
-<H3><a name="Ruby_nn17">39.3.6 Structures</a></H3>
+<H3><a name="Ruby_nn17">40.3.6 Structures</a></H3>
 
 
 <p> C/C++ structs are wrapped as Ruby classes, with accessor
@@ -772,7 +772,7 @@ void Bar_f_set(Bar *b, Foo *val) {
 }</pre>
 </div>
 
-<H3><a name="Ruby_nn18">39.3.7 C++ classes</a></H3>
+<H3><a name="Ruby_nn18">40.3.7 C++ classes</a></H3>
 
 
 <p> Like structs, C++ classes are wrapped by creating a new Ruby
@@ -827,7 +827,7 @@ Ale
 3</pre>
 </div>
 
-<H3><a name="Ruby_nn19">39.3.8 C++ Inheritance</a></H3>
+<H3><a name="Ruby_nn19">40.3.8 C++ Inheritance</a></H3>
 
 
 <p> The SWIG type-checker is fully aware of C++ inheritance.
@@ -980,7 +980,7 @@ inherit from both <tt>Base1</tt> and <tt>Base2</tt>
 (i.e. they exhibit <a href="http://c2.com/cgi/wiki?DuckTyping">"Duck
 Typing"</a>). </p>
 
-<H3><a name="Ruby_nn20">39.3.9 C++ Overloaded Functions</a></H3>
+<H3><a name="Ruby_nn20">40.3.9 C++ Overloaded Functions</a></H3>
 
 
 <p> C++ overloaded functions, methods, and constructors are
@@ -1070,7 +1070,7 @@ arises--in this case, the first declaration takes precedence. </p>
 <p>Please refer to the <a href="SWIGPlus.html#SWIGPlus">"SWIG
 and C++"</a> chapter for more information about overloading. </p>
 
-<H3><a name="Ruby_nn21">39.3.10 C++ Operators</a></H3>
+<H3><a name="Ruby_nn21">40.3.10 C++ Operators</a></H3>
 
 
 <p> For the most part, overloaded operators are handled
@@ -1112,7 +1112,7 @@ c = Example.add_complex(a, b)</pre>
 is discussed in the <a href="#Ruby_operator_overloading">section
 on operator overloading</a>. </p>
 
-<H3><a name="Ruby_nn22">39.3.11 C++ namespaces</a></H3>
+<H3><a name="Ruby_nn22">40.3.11 C++ namespaces</a></H3>
 
 
 <p> SWIG is aware of C++ namespaces, but namespace names do not
@@ -1169,7 +1169,7 @@ and create extension modules for each namespace separately. If your
 program utilizes thousands of small deeply nested namespaces each with
 identical symbol names, well, then you get what you deserve. </p>
 
-<H3><a name="Ruby_nn23">39.3.12 C++ templates</a></H3>
+<H3><a name="Ruby_nn23">40.3.12 C++ templates</a></H3>
 
 
 <p> C++ templates don't present a huge problem for SWIG. However,
@@ -1211,7 +1211,7 @@ irb(main):004:0&gt; <b>p.second</b>
 4</pre>
 </div>
 
-<H3><a name="Ruby_nn23_1">39.3.13 C++ Standard Template Library (STL)</a></H3>
+<H3><a name="Ruby_nn23_1">40.3.13 C++ Standard Template Library (STL)</a></H3>
 
 
 <p> On a related note, the standard SWIG library contains a
@@ -1304,7 +1304,7 @@ puts v
 shown in these examples. More details can be found in the <a href="SWIGPlus.html#SWIGPlus">SWIG and C++</a>
 chapter.</p>
 
-<H3><a name="Ruby_C_STL_Functors">39.3.14 C++ STL Functors</a></H3>
+<H3><a name="Ruby_C_STL_Functors">40.3.14 C++ STL Functors</a></H3>
 
 
 <p>Some containers in the STL allow you to modify their default
@@ -1365,7 +1365,7 @@ b
 </pre>
 </div>
 
-<H3><a name="Ruby_C_Iterators">39.3.15 C++ STL Iterators</a></H3>
+<H3><a name="Ruby_C_Iterators">40.3.15 C++ STL Iterators</a></H3>
 
 
 <p>The STL is well known for the use of iterators. There
@@ -1448,10 +1448,10 @@ i
 
 <p>If you'd rather have STL classes without any iterators, you should define <tt>-DSWIG_NO_EXPORT_ITERATOR_METHODS</tt> when running swig.</p>
 
-<H3><a name="Ruby_nn24">39.3.16 C++ Smart Pointers</a></H3>
+<H3><a name="Ruby_nn24">40.3.16 C++ Smart Pointers</a></H3>
 
 
-<H4><a name="Ruby_smart_pointers_shared_ptr">39.3.16.1 The shared_ptr Smart Pointer</a></H4>
+<H4><a name="Ruby_smart_pointers_shared_ptr">40.3.16.1 The shared_ptr Smart Pointer</a></H4>
 
 
 <p>
@@ -1462,7 +1462,7 @@ in the <a href="Library.html#Library_std_shared_ptr">shared_ptr smart pointer</a
 </p>
 
 
-<H4><a name="Ruby_smart_pointers_generic">39.3.16.2 Generic Smart Pointers</a></H4>
+<H4><a name="Ruby_smart_pointers_generic">40.3.16.2 Generic Smart Pointers</a></H4>
 
 
 <p> In certain C++ programs, it is common to use classes that
@@ -1527,7 +1527,7 @@ method. For example: </p>
 <pre>irb(main):004:0&gt; <b>f = p.__deref__()</b> # Returns underlying Foo *</pre>
 </div>
 
-<H3><a name="Ruby_nn25">39.3.17 Cross-Language Polymorphism</a></H3>
+<H3><a name="Ruby_nn25">40.3.17 Cross-Language Polymorphism</a></H3>
 
 
 <p> SWIG's Ruby module supports cross-language polymorphism
@@ -1536,7 +1536,7 @@ module. Rather than duplicate the information presented in the <a href="Python.h
 section just notes the differences that you need to be aware of when
 using this feature with Ruby. </p>
 
-<H4><a name="Ruby_nn26">39.3.17.1 Exception Unrolling</a></H4>
+<H4><a name="Ruby_nn26">40.3.17.1 Exception Unrolling</a></H4>
 
 
 <p> Whenever a C++ director class routes one of its virtual
@@ -1559,7 +1559,7 @@ method is "wrapped" using the <tt>rb_rescue2()</tt>
 function from Ruby's C API. If any Ruby exception is raised, it will be
 caught here and a C++ exception is raised in its place. </p>
 
-<H2><a name="Ruby_nn27">39.4 Naming</a></H2>
+<H2><a name="Ruby_nn27">40.4 Naming</a></H2>
 
 
 <p>Ruby has several common naming conventions. Constants are
@@ -1597,7 +1597,7 @@ generated
 by SWIG, it is turned off by default in SWIG 1.3.28. However, it is
 planned to become the default option in future releases.</p>
 
-<H3><a name="Ruby_nn28">39.4.1 Defining Aliases</a></H3>
+<H3><a name="Ruby_nn28">40.4.1 Defining Aliases</a></H3>
 
 
 <p> It's a fairly common practice in the Ruby built-ins and
@@ -1667,7 +1667,7 @@ matching rules used for other kinds of features apply (see the chapter
 on <a href="Customization.html#Customization">"Customization
 Features"</a>) for more details).</p>
 
-<H3><a name="Ruby_nn29">39.4.2 Predicate Methods</a></H3>
+<H3><a name="Ruby_nn29">40.4.2 Predicate Methods</a></H3>
 
 
 <p> Ruby methods that return a boolean value and end in a
@@ -1716,7 +1716,7 @@ using SWIG's "features" mechanism and so the same name matching rules
 used for other kinds of features apply (see the chapter on <a href="Customization.html#Customization">"Customization
 Features"</a>) for more details). </p>
 
-<H3><a name="Ruby_nn30">39.4.3 Bang Methods</a></H3>
+<H3><a name="Ruby_nn30">40.4.3 Bang Methods</a></H3>
 
 
 <p> Ruby methods that modify an object in-place and end in an
@@ -1748,7 +1748,7 @@ using SWIG's "features" mechanism and so the same name matching rules
 used for other kinds of features apply (see the chapter on <a href="Customization.html#Customization">"Customization
 Features"</a>) for more details). </p>
 
-<H3><a name="Ruby_nn31">39.4.4 Getters and Setters</a></H3>
+<H3><a name="Ruby_nn31">40.4.4 Getters and Setters</a></H3>
 
 
 <p> Often times a C++ library will expose properties through
@@ -1783,7 +1783,7 @@ irb(main):003:0&gt; <b>puts foo.value</b></pre>
 %rename("value=") Foo::setValue(int value);</pre>
 </div>
 
-<H2><a name="Ruby_nn32">39.5 Input and output parameters</a></H2>
+<H2><a name="Ruby_nn32">40.5 Input and output parameters</a></H2>
 
 
 <p> A common problem in some C programs is handling parameters
@@ -1922,10 +1922,10 @@ void get_dimensions(Matrix *m, int *rows, int*columns);</pre>
 <pre>r, c = Example.get_dimensions(m)</pre>
 </div>
 
-<H2><a name="Ruby_nn33">39.6 Exception handling </a></H2>
+<H2><a name="Ruby_nn33">40.6 Exception handling </a></H2>
 
 
-<H3><a name="Ruby_nn34">39.6.1 Using the %exception directive </a></H3>
+<H3><a name="Ruby_nn34">40.6.1 Using the %exception directive </a></H3>
 
 
 <p>The SWIG <tt>%exception</tt> directive can be
@@ -2034,7 +2034,7 @@ methods and functions named <tt>getitem</tt> and <tt>setitem</tt>.
 limited to C++ exception handling. See the chapter on <a href="Customization.html#Customization">Customization
 Features</a> for more examples.</p>
 
-<H3><a name="Ruby_nn34_2">39.6.2 Handling Ruby Blocks </a></H3>
+<H3><a name="Ruby_nn34_2">40.6.2 Handling Ruby Blocks </a></H3>
 
 
 <p>One of the highlights of Ruby and most of its standard library
@@ -2101,7 +2101,7 @@ a special in typemap, like:</p>
 
 <p>For more information on typemaps, see <a href="#Ruby_nn37">Typemaps</a>.</p>
 
-<H3><a name="Ruby_nn35">39.6.3 Raising exceptions </a></H3>
+<H3><a name="Ruby_nn35">40.6.3 Raising exceptions </a></H3>
 
 
 <p>There are three ways to raise exceptions from C++ code to
@@ -2258,7 +2258,7 @@ function. The first argument passed to <tt>rb_raise()</tt>
 is the exception type. You can raise a custom exception type or one of
 the built-in Ruby exception types.</p>
 
-<H3><a name="Ruby_nn36">39.6.4 Exception classes </a></H3>
+<H3><a name="Ruby_nn36">40.6.4 Exception classes </a></H3>
 
 
 <p>Starting with SWIG 1.3.28, the Ruby module supports the <tt>%exceptionclass</tt>
@@ -2295,7 +2295,7 @@ end </pre>
 <p>For another example look at swig/Examples/ruby/exception_class.
 </p>
 
-<H2><a name="Ruby_nn37">39.7 Typemaps</a></H2>
+<H2><a name="Ruby_nn37">40.7 Typemaps</a></H2>
 
 
 <p> This section describes how you can modify SWIG's default
@@ -2310,7 +2310,7 @@ a required part of using SWIG---the default wrapping behavior is enough
 in most cases. Typemaps are only used if you want to change some aspect
 of the primitive C-Ruby interface.</p>
 
-<H3><a name="Ruby_nn38">39.7.1 What is a typemap?</a></H3>
+<H3><a name="Ruby_nn38">40.7.1 What is a typemap?</a></H3>
 
 
 <p> A typemap is nothing more than a code generation rule that is
@@ -2467,7 +2467,7 @@ to be used as follows (notice how the length parameter is omitted): </p>
 2</pre>
 </div>
 
-<H3><a name="Ruby_Typemap_scope">39.7.2 Typemap scope</a></H3>
+<H3><a name="Ruby_Typemap_scope">40.7.2 Typemap scope</a></H3>
 
 
 <p> Once defined, a typemap remains in effect for all of the
@@ -2513,7 +2513,7 @@ where the class itself is defined. For example:</p>
 };</pre>
 </div>
 
-<H3><a name="Ruby_Copying_a_typemap">39.7.3 Copying a typemap</a></H3>
+<H3><a name="Ruby_Copying_a_typemap">40.7.3 Copying a typemap</a></H3>
 
 
 <p> A typemap is copied by using assignment. For example:</p>
@@ -2555,7 +2555,7 @@ rules as for <tt>
 %apply (char *buf, int len) { (char *buffer, int size) }; // Multiple arguments</pre>
 </div>
 
-<H3><a name="Ruby_Deleting_a_typemap">39.7.4 Deleting a typemap</a></H3>
+<H3><a name="Ruby_Deleting_a_typemap">40.7.4 Deleting a typemap</a></H3>
 
 
 <p> A typemap can be deleted by simply defining no code. For
@@ -2580,7 +2580,7 @@ defined by typemaps, clearing a fundamental type like <tt>int</tt>
 will make that type unusable unless you also define a new set of
 typemaps immediately after the clear operation.</p>
 
-<H3><a name="Ruby_Placement_of_typemaps">39.7.5 Placement of typemaps</a></H3>
+<H3><a name="Ruby_Placement_of_typemaps">40.7.5 Placement of typemaps</a></H3>
 
 
 <p> Typemap declarations can be declared in the global scope,
@@ -2651,13 +2651,13 @@ In this example, this is done using the class declaration <tt>class
 string</tt>
 .</p>
 
-<H3><a name="Ruby_nn39">39.7.6 Ruby typemaps</a></H3>
+<H3><a name="Ruby_nn39">40.7.6 Ruby typemaps</a></H3>
 
 
 <p>The following list details all of the typemap methods that
 can be used by the Ruby module: </p>
 
-<H4><a name="Ruby_in_typemap">39.7.6.1 "in" typemap</a></H4>
+<H4><a name="Ruby_in_typemap">40.7.6.1 "in" typemap</a></H4>
 
 
 <p>Converts Ruby objects to input
@@ -2724,7 +2724,7 @@ arguments to be specified. For example:</p>
 
 <p> At this time, only zero or one arguments may be converted.</p>
 
-<H4><a name="Ruby_typecheck_typemap">39.7.6.2 "typecheck" typemap</a></H4>
+<H4><a name="Ruby_typecheck_typemap">40.7.6.2 "typecheck" typemap</a></H4>
 
 
 <p> The "typecheck" typemap is used to support overloaded
@@ -2746,7 +2746,7 @@ program uses overloaded methods, you should also define a collection of
 "typecheck" typemaps. More details about this follow in a later section
 on "Typemaps and Overloading."</p>
 
-<H4><a name="Ruby_out_typemap">39.7.6.3 "out" typemap</a></H4>
+<H4><a name="Ruby_out_typemap">40.7.6.3 "out" typemap</a></H4>
 
 
 <p>Converts return value of a C function
@@ -2797,7 +2797,7 @@ version of the C datatype matched by the typemap.</td>
 </table>
 </div>
 
-<H4><a name="Ruby_arginit_typemap">39.7.6.4 "arginit" typemap</a></H4>
+<H4><a name="Ruby_arginit_typemap">40.7.6.4 "arginit" typemap</a></H4>
 
 
 <p> The "arginit" typemap is used to set the initial value of a
@@ -2812,7 +2812,7 @@ applications. For example:</p>
 }</pre>
 </div>
 
-<H4><a name="Ruby_default_typemap">39.7.6.5 "default" typemap</a></H4>
+<H4><a name="Ruby_default_typemap">40.7.6.5 "default" typemap</a></H4>
 
 
 <p> The "default" typemap is used to turn an argument into a
@@ -2837,7 +2837,7 @@ arguments that follow must have default values. See the <a href="SWIG.html#SWIG_
 Default/optional arguments</a> section for further information on
 default argument wrapping.</p>
 
-<H4><a name="Ruby_check_typemap">39.7.6.6 "check" typemap</a></H4>
+<H4><a name="Ruby_check_typemap">40.7.6.6 "check" typemap</a></H4>
 
 
 <p> The "check" typemap is used to supply value checking code
@@ -2852,7 +2852,7 @@ arguments have been converted. For example:</p>
 }</pre>
 </div>
 
-<H4><a name="Ruby_argout_typemap_">39.7.6.7 "argout" typemap</a></H4>
+<H4><a name="Ruby_argout_typemap_">40.7.6.7 "argout" typemap</a></H4>
 
 
 <p> The "argout" typemap is used to return values from arguments.
@@ -2906,7 +2906,7 @@ some function like SWIG_Ruby_AppendOutput.</p>
 
 <p> See the <tt>typemaps.i</tt> library for examples.</p>
 
-<H4><a name="Ruby_freearg_typemap_">39.7.6.8 "freearg" typemap</a></H4>
+<H4><a name="Ruby_freearg_typemap_">40.7.6.8 "freearg" typemap</a></H4>
 
 
 <p> The "freearg" typemap is used to cleanup argument data. It is
@@ -2933,7 +2933,7 @@ This code is also placed into a special variable <tt>$cleanup</tt>
 that may be used in other typemaps whenever a wrapper function needs to
 abort prematurely.</p>
 
-<H4><a name="Ruby_newfree_typemap">39.7.6.9 "newfree" typemap</a></H4>
+<H4><a name="Ruby_newfree_typemap">40.7.6.9 "newfree" typemap</a></H4>
 
 
 <p> The "newfree" typemap is used in conjunction with the <tt>%newobject</tt>
@@ -2957,7 +2957,7 @@ string *foo();</pre>
 <p> See <a href="Customization.html#Customization_ownership">Object
 ownership and %newobject</a> for further details.</p>
 
-<H4><a name="Ruby_memberin_typemap">39.7.6.10 "memberin" typemap</a></H4>
+<H4><a name="Ruby_memberin_typemap">40.7.6.10 "memberin" typemap</a></H4>
 
 
 <p> The "memberin" typemap is used to copy data from<em> an
@@ -2975,21 +2975,21 @@ example:</p>
 already provides a default implementation for arrays, strings, and
 other objects.</p>
 
-<H4><a name="Ruby_varin_typemap">39.7.6.11 "varin" typemap</a></H4>
+<H4><a name="Ruby_varin_typemap">40.7.6.11 "varin" typemap</a></H4>
 
 
 <p> The "varin" typemap is used to convert objects in the target
 language to C for the purposes of assigning to a C/C++ global variable.
 This is implementation specific.</p>
 
-<H4><a name="Ruby_varout_typemap_">39.7.6.12 "varout" typemap</a></H4>
+<H4><a name="Ruby_varout_typemap_">40.7.6.12 "varout" typemap</a></H4>
 
 
 <p> The "varout" typemap is used to convert a C/C++ object to an
 object in the target language when reading a C/C++ global variable.
 This is implementation specific.</p>
 
-<H4><a name="Ruby_throws_typemap">39.7.6.13 "throws" typemap</a></H4>
+<H4><a name="Ruby_throws_typemap">40.7.6.13 "throws" typemap</a></H4>
 
 
 <p> The "throws" typemap is only used when SWIG parses a C++
@@ -3030,7 +3030,7 @@ specification yet they do throw exceptions, SWIG cannot know how to
 deal with them. For a neat way to handle these, see the <a href="Customization.html#Customization_exception">Exception
 handling with %exception</a> section.</p>
 
-<H4><a name="Ruby_directorin_typemap">39.7.6.14 directorin typemap</a></H4>
+<H4><a name="Ruby_directorin_typemap">40.7.6.14 directorin typemap</a></H4>
 
 
 <p>Converts C++ objects in director
@@ -3089,7 +3089,7 @@ referring to the class itself.</td>
 </table>
 </div>
 
-<H4><a name="Ruby_directorout_typemap">39.7.6.15 directorout typemap</a></H4>
+<H4><a name="Ruby_directorout_typemap">40.7.6.15 directorout typemap</a></H4>
 
 
 <p>Converts Ruby objects in director
@@ -3162,7 +3162,7 @@ exception.
 
 </p>
 
-<H4><a name="Ruby_directorargout_typemap">39.7.6.16 directorargout typemap</a></H4>
+<H4><a name="Ruby_directorargout_typemap">40.7.6.16 directorargout typemap</a></H4>
 
 
 <p>Output argument processing in director
@@ -3220,19 +3220,19 @@ referring to the instance of the class itself</td>
 </table>
 </div>
 
-<H4><a name="Ruby_ret_typemap">39.7.6.17 ret typemap</a></H4>
+<H4><a name="Ruby_ret_typemap">40.7.6.17 ret typemap</a></H4>
 
 
 <p>Cleanup of function return values
 </p>
 
-<H4><a name="Ruby_globalin_typemap">39.7.6.18 globalin typemap</a></H4>
+<H4><a name="Ruby_globalin_typemap">40.7.6.18 globalin typemap</a></H4>
 
 
 <p>Setting of C global variables
 </p>
 
-<H3><a name="Ruby_nn40">39.7.7 Typemap variables</a></H3>
+<H3><a name="Ruby_nn40">40.7.7 Typemap variables</a></H3>
 
 
 <p>
@@ -3282,7 +3282,7 @@ so that their values can be properly assigned. </div>
 <div class="indent">The Ruby name of the wrapper function
 being created. </div>
 
-<H3><a name="Ruby_nn41">39.7.8 Useful Functions</a></H3>
+<H3><a name="Ruby_nn41">40.7.8 Useful Functions</a></H3>
 
 
 <p> When you write a typemap, you usually have to work directly
@@ -3297,7 +3297,7 @@ stick to the swig functions instead of the native Ruby functions.
 That should help you avoid having to rewrite a lot of typemaps
 across multiple languages.</p>
 
-<H4><a name="Ruby_nn42">39.7.8.1 C Datatypes to Ruby Objects</a></H4>
+<H4><a name="Ruby_nn42">40.7.8.1 C Datatypes to Ruby Objects</a></H4>
 
 
 <div class="diagram">
@@ -3339,7 +3339,7 @@ SWIG_From_float(float)</td>
 </table>
 </div>
 
-<H4><a name="Ruby_nn43">39.7.8.2 Ruby Objects to C Datatypes</a></H4>
+<H4><a name="Ruby_nn43">40.7.8.2 Ruby Objects to C Datatypes</a></H4>
 
 
 <p>Here, while the Ruby versions return the value directly, the SWIG
@@ -3407,7 +3407,7 @@ versions do not, but return a status value to indicate success (<tt>SWIG_OK</tt>
 </table>
 </div>
 
-<H4><a name="Ruby_nn44">39.7.8.3 Macros for VALUE</a></H4>
+<H4><a name="Ruby_nn44">40.7.8.3 Macros for VALUE</a></H4>
 
 
 <p> <tt>RSTRING_LEN(str)</tt> </p>
@@ -3430,7 +3430,7 @@ versions do not, but return a status value to indicate success (<tt>SWIG_OK</tt>
 
 <div class="indent">pointer to array storage</div>
 
-<H4><a name="Ruby_nn45">39.7.8.4 Exceptions</a></H4>
+<H4><a name="Ruby_nn45">40.7.8.4 Exceptions</a></H4>
 
 
 <p> <tt>void rb_raise(VALUE exception, const char *fmt,
@@ -3509,7 +3509,7 @@ message to standard error if Ruby was invoked with the <tt>-w</tt>
 flag. The given format string <i>fmt</i> and remaining
 arguments are interpreted as with <tt>printf()</tt>. </div>
 
-<H4><a name="Ruby_nn46">39.7.8.5 Iterators</a></H4>
+<H4><a name="Ruby_nn46">40.7.8.5 Iterators</a></H4>
 
 
 <p> <tt>void rb_iter_break()</tt> </p>
@@ -3555,14 +3555,14 @@ VALUE), VALUE value)</tt></p>
 <div class="indent"> Equivalent to Ruby's <tt>throw</tt>.
 </div>
 
-<H3><a name="Ruby_nn47">39.7.9 Typemap Examples</a></H3>
+<H3><a name="Ruby_nn47">40.7.9 Typemap Examples</a></H3>
 
 
 <p> This section includes a few examples of typemaps. For more
 examples, you might look at the examples in the <tt>Example/ruby</tt>
 directory. </p>
 
-<H3><a name="Ruby_nn48">39.7.10 Converting a Ruby array to a char **</a></H3>
+<H3><a name="Ruby_nn48">40.7.10 Converting a Ruby array to a char **</a></H3>
 
 
 <p> A common problem in many C programs is the processing of
@@ -3627,7 +3627,7 @@ array. Since dynamic memory allocation is used to allocate memory for
 the array, the "freearg" typemap is used to later release this memory
 after the execution of the C function. </p>
 
-<H3><a name="Ruby_nn49">39.7.11 Collecting arguments in a hash</a></H3>
+<H3><a name="Ruby_nn49">40.7.11 Collecting arguments in a hash</a></H3>
 
 
 <p> Ruby's solution to the "keyword arguments" capability of some
@@ -3841,7 +3841,7 @@ memory leak. Fortunately, this typemap is a lot easier to write: </p>
 program that uses the extension, can be found in the <tt>Examples/ruby/hashargs</tt>
 directory of the SWIG distribution. </p>
 
-<H3><a name="Ruby_nn50">39.7.12 Pointer handling</a></H3>
+<H3><a name="Ruby_nn50">40.7.12 Pointer handling</a></H3>
 
 
 <p> Occasionally, it might be necessary to convert pointer values
@@ -3900,7 +3900,7 @@ For example: </p>
 }</pre>
 </div>
 
-<H4><a name="Ruby_nn51">39.7.12.1 Ruby Datatype Wrapping</a></H4>
+<H4><a name="Ruby_nn51">40.7.12.1 Ruby Datatype Wrapping</a></H4>
 
 
 <p> <tt>VALUE Data_Wrap_Struct(VALUE class, void
@@ -3927,7 +3927,7 @@ as above. </div>
 type <i>c-type</i> from the data object <i>obj</i>
 and assigns that pointer to <i>ptr</i>. </div>
 
-<H3><a name="Ruby_nn52">39.7.13 Example: STL Vector to Ruby Array</a></H3>
+<H3><a name="Ruby_nn52">40.7.13 Example: STL Vector to Ruby Array</a></H3>
 
 
 <p>Another use for macros and type maps is to create a Ruby array
@@ -4019,7 +4019,7 @@ STL with ruby, you are advised to use the standard swig STL library,
 which does much more than this. Refer to the section called
 the<a href="#Ruby_nn23_1"> C++ Standard Template Library</a>.
 
-<H2><a name="Ruby_nn65">39.8 Docstring Features</a></H2>
+<H2><a name="Ruby_nn65">40.8 Docstring Features</a></H2>
 
 
 <p>
@@ -4053,7 +4053,7 @@ generate ri documentation from a c wrap file, you could do:</p>
 $ rdoc -r file_wrap.c
 </pre></div>
 
-<H3><a name="Ruby_nn66">39.8.1 Module docstring</a></H3>
+<H3><a name="Ruby_nn66">40.8.1 Module docstring</a></H3>
 
 
 <p>
@@ -4083,7 +4083,7 @@ layout of controls on a panel, etc. to be loaded from an XML file."
 %module(docstring=DOCSTRING) xrc</pre>
 </div>
 
-<H3><a name="Ruby_nn67">39.8.2 %feature("autodoc")</a></H3>
+<H3><a name="Ruby_nn67">40.8.2 %feature("autodoc")</a></H3>
 
 
 <p>Since SWIG does know everything about the function it wraps,
@@ -4104,7 +4104,7 @@ several options for autodoc controlled by the value given to the
 feature, described below.
 </p>
 
-<H4><a name="Ruby_nn68">39.8.2.1 %feature("autodoc", "0")</a></H4>
+<H4><a name="Ruby_nn68">40.8.2.1 %feature("autodoc", "0")</a></H4>
 
 
 <p>
@@ -4128,7 +4128,7 @@ Then Ruby code like this will be generated:
   ...</pre>
 </div>
 
-<H4><a name="Ruby_autodoc1">39.8.2.2 %feature("autodoc", "1")</a></H4>
+<H4><a name="Ruby_autodoc1">40.8.2.2 %feature("autodoc", "1")</a></H4>
 
 
 <p>
@@ -4148,7 +4148,7 @@ this:
   ...</pre>
 </div>
 
-<H4><a name="Ruby_autodoc2">39.8.2.3 %feature("autodoc", "2")</a></H4>
+<H4><a name="Ruby_autodoc2">40.8.2.3 %feature("autodoc", "2")</a></H4>
 
 
 <p>
@@ -4160,7 +4160,7 @@ parameter types with the "2" option will result in Ruby code like
 this:
 </p>
 
-<H4><a name="Ruby_feature_autodoc3">39.8.2.4 %feature("autodoc", "3")</a></H4>
+<H4><a name="Ruby_feature_autodoc3">40.8.2.4 %feature("autodoc", "3")</a></H4>
 
 
 <p>
@@ -4181,7 +4181,7 @@ Parameters:
         bar - Bar</pre>
 </div>
 
-<H4><a name="Ruby_nn70">39.8.2.5 %feature("autodoc", "docstring")</a></H4>
+<H4><a name="Ruby_nn70">40.8.2.5 %feature("autodoc", "docstring")</a></H4>
 
 
 <p>
@@ -4197,7 +4197,7 @@ generated string. For example:
 void GetPosition(int* OUTPUT, int* OUTPUT);</pre>
 </div>
 
-<H3><a name="Ruby_nn71">39.8.3 %feature("docstring")</a></H3>
+<H3><a name="Ruby_nn71">40.8.3 %feature("docstring")</a></H3>
 
 
 <p>
@@ -4208,10 +4208,10 @@ docstring associated with classes, function or methods are output.
 If an item already has an autodoc string then it is combined with the
 docstring and they are output together. </p>
 
-<H2><a name="Ruby_nn53">39.9 Advanced Topics</a></H2>
+<H2><a name="Ruby_nn53">40.9 Advanced Topics</a></H2>
 
 
-<H3><a name="Ruby_operator_overloading">39.9.1 Operator overloading</a></H3>
+<H3><a name="Ruby_operator_overloading">40.9.1 Operator overloading</a></H3>
 
 
 <p> SWIG allows operator overloading with, by using the <tt>%extend</tt>
@@ -4392,7 +4392,7 @@ separate method for handling <i>inequality</i> since Ruby
 parses the expression <i>a != b</i> as <i>!(a == b)</i>.
 </p>
 
-<H3><a name="Ruby_nn55">39.9.2 Creating Multi-Module Packages</a></H3>
+<H3><a name="Ruby_nn55">40.9.2 Creating Multi-Module Packages</a></H3>
 
 
 <p> The chapter on <a href="Modules.html#Modules">Working
@@ -4518,7 +4518,7 @@ irb(main):005:0&gt; <b>c.getX()</b>
 5.0</pre>
 </div>
 
-<H3><a name="Ruby_nn56">39.9.3 Specifying Mixin Modules</a></H3>
+<H3><a name="Ruby_nn56">40.9.3 Specifying Mixin Modules</a></H3>
 
 
 <p> The Ruby language doesn't support multiple inheritance, but
@@ -4585,7 +4585,7 @@ matching rules used for other kinds of features apply (see the chapter
 on <a href="Customization.html#Customization">"Customization
 Features"</a>) for more details). </p>
 
-<H2><a name="Ruby_nn57">39.10 Memory Management</a></H2>
+<H2><a name="Ruby_nn57">40.10 Memory Management</a></H2>
 
 
 <p>One of the most common issues in generating SWIG bindings for
@@ -4608,7 +4608,7 @@ to C++ (or vice versa) depending on what function or methods are
 invoked. Clearly, developing a SWIG wrapper requires a thorough
 understanding of how the underlying library manages memory.</p>
 
-<H3><a name="Ruby_nn58">39.10.1 Mark and Sweep Garbage Collector </a></H3>
+<H3><a name="Ruby_nn58">40.10.1 Mark and Sweep Garbage Collector </a></H3>
 
 
 <p>Ruby uses a mark and sweep garbage collector. When the garbage
@@ -4639,7 +4639,7 @@ any memory has been allocated in creating the underlying C struct or
 C++ struct, then a "free" function must be defined that deallocates
 this memory. </p>
 
-<H3><a name="Ruby_nn59">39.10.2 Object Ownership</a></H3>
+<H3><a name="Ruby_nn59">40.10.2 Object Ownership</a></H3>
 
 
 <p>As described above, memory management depends on clearly
@@ -4784,7 +4784,7 @@ public:
 
 <p> This code can be seen in swig/examples/ruby/tracking.</p>
 
-<H3><a name="Ruby_nn60">39.10.3 Object Tracking</a></H3>
+<H3><a name="Ruby_nn60">40.10.3 Object Tracking</a></H3>
 
 
 <p>The remaining parts of this section will use the class library
@@ -5010,7 +5010,7 @@ However, if you implement your own free functions (see below) you may
 also have to call the <tt>SWIG_RubyRemoveTracking</tt> and <tt>RubyUnlinkObjects</tt>
 methods.</p>
 
-<H3><a name="Ruby_nn61">39.10.4 Mark Functions</a></H3>
+<H3><a name="Ruby_nn61">40.10.4 Mark Functions</a></H3>
 
 
 <p>With a bit more testing, we see that our class library still
@@ -5139,7 +5139,7 @@ irb(main):016:0&gt;</pre>
 
 <p>This code can be seen in swig/examples/ruby/mark_function.</p>
 
-<H3><a name="Ruby_nn62">39.10.5 Free Functions</a></H3>
+<H3><a name="Ruby_nn62">40.10.5 Free Functions</a></H3>
 
 
 <p>By default, SWIG creates a "free" function that is called when
@@ -5307,7 +5307,7 @@ been freed, and thus raises a runtime exception.</p>
 
 <p>This code can be seen in swig/examples/ruby/free_function.</p>
 
-<H3><a name="Ruby_nn63">39.10.6 Embedded Ruby and the C++ Stack</a></H3>
+<H3><a name="Ruby_nn63">40.10.6 Embedded Ruby and the C++ Stack</a></H3>
 
 
 <p>As has been said, the Ruby GC runs and marks objects before
diff --git a/Doc/Manual/Scilab.html b/Doc/Manual/Scilab.html
index 9c8e4b71b..662a8227a 100644
--- a/Doc/Manual/Scilab.html
+++ b/Doc/Manual/Scilab.html
@@ -9,7 +9,7 @@
 
 <body bgcolor="#ffffff">
 
-<H1><a name="Scilab">40 SWIG and Scilab</a></H1>
+<H1><a name="Scilab">41 SWIG and Scilab</a></H1>
 <!-- INDEX -->
 <div class="sectiontoc">
 <ul>
@@ -88,7 +88,7 @@ This chapter explains how to use SWIG for Scilab. After this introduction, you s
 </p>
 
 
-<H2><a name="Scilab_preliminaries">40.1 Preliminaries</a></H2>
+<H2><a name="Scilab_preliminaries">41.1 Preliminaries</a></H2>
 
 
 <p>
@@ -105,7 +105,7 @@ SWIG for Scilab supports C language. C++ is partially supported. See <a href="#S
 </p>
 
 
-<H2><a name="Scilab_running_swig">40.2 Running SWIG</a></H2>
+<H2><a name="Scilab_running_swig">41.2 Running SWIG</a></H2>
 
 
 <p>
@@ -139,7 +139,7 @@ Note: a code in an <tt>%inline</tt> section is both parsed and wrapped by SWIG,
 </p>
 
 
-<H3><a name="Scilab_running_swig_generating_module">40.2.1 Generating the module</a></H3>
+<H3><a name="Scilab_running_swig_generating_module">41.2.1 Generating the module</a></H3>
 
 
 <p>
@@ -182,7 +182,7 @@ The <tt>swig</tt> executable has several other command line options you can use.
 </p>
 
 
-<H3><a name="Scilab_running_swig_building_module">40.2.2 Building the module</a></H3>
+<H3><a name="Scilab_running_swig_building_module">41.2.2 Building the module</a></H3>
 
 
 <p>
@@ -202,7 +202,7 @@ $ gcc -shared example_wrap.o -o libexample.so
 Note: we supposed in this example that the path to the Scilab include directory is <tt>/usr/local/include/scilab</tt> (which is the case in a Debian environment), this should be changed for another environment.
 </p>
 
-<H3><a name="Scilab_running_swig_loading_module">40.2.3 Loading the module</a></H3>
+<H3><a name="Scilab_running_swig_loading_module">41.2.3 Loading the module</a></H3>
 
 
 <p>
@@ -226,7 +226,7 @@ Link done.
 which means that Scilab has successfully loaded the shared library. The module functions and other symbols are now available in Scilab.
 </p>
 
-<H3><a name="Scilab_running_swig_using_module">40.2.4 Using the module</a></H3>
+<H3><a name="Scilab_running_swig_using_module">41.2.4 Using the module</a></H3>
 
 
 <p>
@@ -260,7 +260,7 @@ ans  =
 Note: for conciseness, we assume in the subsequent Scilab code examples that the modules have been beforehand built and loaded in Scilab.
 </p>
 
-<H3><a name="Scilab_running_swig_options">40.2.5 Scilab command line options</a></H3>
+<H3><a name="Scilab_running_swig_options">41.2.5 Scilab command line options</a></H3>
 
 
 <p>
@@ -320,10 +320,10 @@ $ swig -scilab -help
 </pre></div>
 
 
-<H2><a name="Scilab_wrapping">40.3 A basic tour of C/C++ wrapping</a></H2>
+<H2><a name="Scilab_wrapping">41.3 A basic tour of C/C++ wrapping</a></H2>
 
 
-<H3><a name="Scilab_wrapping_overview">40.3.1 Overview</a></H3>
+<H3><a name="Scilab_wrapping_overview">41.3.1 Overview</a></H3>
 
 
 <p>
@@ -332,7 +332,7 @@ This means that functions, structs, classes, variables, etc... are interfaced th
 There are a few exceptions, such as constants and enumerations, which can be wrapped directly as Scilab variables.
 </p>
 
-<H3><a name="Scilab_wrapping_identifiers">40.3.2 Identifiers</a></H3>
+<H3><a name="Scilab_wrapping_identifiers">41.3.2 Identifiers</a></H3>
 
 
 <p>
@@ -347,7 +347,7 @@ In these cases, the <a href="SWIG.html#SWIG_rename_ignore">%rename directive</a>
 Note: truncations can be disabled by specifying the target version 6 of Scilab in the <tt>targetversion</tt> argument (i.e. <tt>-targetversion 6</tt>).
 </p>
 
-<H3><a name="Scilab_wrapping_functions">40.3.3 Functions</a></H3>
+<H3><a name="Scilab_wrapping_functions">41.3.3 Functions</a></H3>
 
 
 <p>
@@ -378,7 +378,7 @@ ans  =
     24.
 </pre></div>
 
-<H4><a name="Scilab_nn13">40.3.3.1 Argument passing</a></H4>
+<H4><a name="Scilab_nn13">41.3.3.1 Argument passing</a></H4>
 
 
 <p>
@@ -431,7 +431,7 @@ In Scilab, parameters are passed by value. The output (and inout) parameters are
     7.
 </pre></div>
 
-<H4><a name="Scilab_nn14">40.3.3.2 Multiple output arguments</a></H4>
+<H4><a name="Scilab_nn14">41.3.3.2 Multiple output arguments</a></H4>
 
 
 <p>
@@ -480,7 +480,7 @@ int divide(int n, int d, int *OUTPUT, int *OUTPUT);
 </pre></div>
 
 
-<H3><a name="Scilab_wrapping_global_variables">40.3.4 Global variables</a></H3>
+<H3><a name="Scilab_wrapping_global_variables">41.3.4 Global variables</a></H3>
 
 
 <p>
@@ -549,10 +549,10 @@ It works the same:</p>
 </pre></div>
 
 
-<H3><a name="Scilab_wrapping_constants_and_enums">40.3.5 Constants and enumerations</a></H3>
+<H3><a name="Scilab_wrapping_constants_and_enums">41.3.5 Constants and enumerations</a></H3>
 
 
-<H4><a name="Scilab_wrapping_constants">40.3.5.1 Constants</a></H4>
+<H4><a name="Scilab_wrapping_constants">41.3.5.1 Constants</a></H4>
 
 
 <p>
@@ -693,7 +693,7 @@ are mapped to Scilab variables, with the same name:
     3.14
 </pre></div>
 
-<H4><a name="Scilab_wrapping_enums">40.3.5.2 Enumerations</a></H4>
+<H4><a name="Scilab_wrapping_enums">41.3.5.2 Enumerations</a></H4>
 
 
 <p>
@@ -758,7 +758,7 @@ typedef enum { RED, BLUE, GREEN } color;
 
 </pre></div>
 
-<H3><a name="Scilab_wrapping_pointers">40.3.6 Pointers</a></H3>
+<H3><a name="Scilab_wrapping_pointers">41.3.6 Pointers</a></H3>
 
 
 <p>
@@ -820,7 +820,7 @@ Note: the type name <tt>_p_FILE</tt> which means "pointer to FILE".
 The user of a pointer is responsible for freeing it or, like in the example, closing any resources associated with it (just as is required in a C program).
 </p>
 
-<H4><a name="Scilab_wrapping_pointers_pointer_adresses">40.3.6.1 Utility functions</a></H4>
+<H4><a name="Scilab_wrapping_pointers_pointer_adresses">41.3.6.1 Utility functions</a></H4>
 
 
 <p>
@@ -861,7 +861,7 @@ ans  =
 </pre></div>
 
 
-<H4><a name="Scilab_wrapping_pointers_null_pointers">40.3.6.2 Null pointers:</a></H4>
+<H4><a name="Scilab_wrapping_pointers_null_pointers">41.3.6.2 Null pointers:</a></H4>
 
 
 <p>
@@ -877,7 +877,7 @@ Using the previous <tt>SWIG_this()</tt> and <tt>SWIG_ptr()</tt>, it is possible
 </pre></div>
 
 
-<H3><a name="Scilab_wrapping_structs">40.3.7 Structures</a></H3>
+<H3><a name="Scilab_wrapping_structs">41.3.7 Structures</a></H3>
 
 
 <p>
@@ -986,7 +986,7 @@ Note: the pointer to the struct works as described in <a href="Scilab_wrapping_p
 --&gt; delete_Bar(b);
 </pre></div>
 
-<H3><a name="Scilab_wrapping_cpp_classes">40.3.8 C++ classes</a></H3>
+<H3><a name="Scilab_wrapping_cpp_classes">41.3.8 C++ classes</a></H3>
 
 
 <p>
@@ -1054,7 +1054,7 @@ Note: like structs, class pointers are mapped as described in <a href="Scilab_wr
 --&gt; delete_Point(p);
 </pre></div>
 
-<H3><a name="Scilab_wrapping_cpp_inheritance">40.3.9 C++ inheritance</a></H3>
+<H3><a name="Scilab_wrapping_cpp_inheritance">41.3.9 C++ inheritance</a></H3>
 
 
 <p>
@@ -1129,7 +1129,7 @@ But we can use either use the <tt>get_perimeter()</tt> function of the parent cl
     18.84
 </pre></div>
 
-<H3><a name="Scilab_wrapping_cpp_overloading">40.3.10 C++ overloading</a></H3>
+<H3><a name="Scilab_wrapping_cpp_overloading">41.3.10 C++ overloading</a></H3>
 
 
 <p>
@@ -1169,7 +1169,7 @@ void magnify(Circle *circle, double factor) {
 </pre></div>
 
 
-<H3><a name="Scilab_wrapping_pointers_references_values_arrays">40.3.11 Pointers, references, values, and arrays</a></H3>
+<H3><a name="Scilab_wrapping_pointers_references_values_arrays">41.3.11 Pointers, references, values, and arrays</a></H3>
 
 
 <p>
@@ -1227,7 +1227,7 @@ All these functions will return a pointer to an instance of <tt>Foo</tt>.
 As the function <tt>spam7</tt> returns a value, new instance of <tt>Foo</tt> has to be allocated, and a pointer on this instance is returned.
 </p>
 
-<H3><a name="Scilab_wrapping_cpp_templates">40.3.12 C++ templates</a></H3>
+<H3><a name="Scilab_wrapping_cpp_templates">41.3.12 C++ templates</a></H3>
 
 
 <p>
@@ -1286,7 +1286,7 @@ Then in Scilab:
 More details on template support can be found in the <a href="SWIGPlus.html#SWIGPlus_nn30">templates</a> documentation.
 </p>
 
-<H3><a name="Scilab_wrapping_cpp_operators">40.3.13 C++ operators</a></H3>
+<H3><a name="Scilab_wrapping_cpp_operators">41.3.13 C++ operators</a></H3>
 
 
 <p>
@@ -1339,7 +1339,7 @@ private:
 </pre></div>
 
 
-<H3><a name="Scilab_wrapping_cpp_namespaces">40.3.14 C++ namespaces</a></H3>
+<H3><a name="Scilab_wrapping_cpp_namespaces">41.3.14 C++ namespaces</a></H3>
 
 
 <p>
@@ -1417,7 +1417,7 @@ Note: the <a href="SWIGPlus.html#SWIGPlus_nspace">nspace</a> feature is not supp
 </p>
 
 
-<H3><a name="Scilab_wrapping_cpp_exceptions">40.3.15 C++ exceptions</a></H3>
+<H3><a name="Scilab_wrapping_cpp_exceptions">41.3.15 C++ exceptions</a></H3>
 
 
 <p>
@@ -1500,17 +1500,17 @@ More complex or custom exception types require specific exception typemaps to be
 See the <a href="SWIGPlus.html#SWIGPlus">SWIG C++ documentation</a> for more details.
 </p>
 
-<H3><a name="Scilab_wrapping_cpp_stl">40.3.16 C++ STL</a></H3>
+<H3><a name="Scilab_wrapping_cpp_stl">41.3.16 C++ STL</a></H3>
 
 
 <p>
 The Standard Template Library (STL) is partially supported. See <a href="#Scilab_typemaps_stl">STL</a> for more details.
 </p>
 
-<H2><a name="Scilab_typemaps">40.4 Type mappings and libraries</a></H2>
+<H2><a name="Scilab_typemaps">41.4 Type mappings and libraries</a></H2>
 
 
-<H3><a name="Scilab_typemaps_primitive_types">40.4.1 Default primitive type mappings</a></H3>
+<H3><a name="Scilab_typemaps_primitive_types">41.4.1 Default primitive type mappings</a></H3>
 
 
 <p>
@@ -1561,7 +1561,7 @@ The default behaviour is for SWIG to generate code that will give a runtime erro
 
 
 
-<H3><a name="Scilab_typemaps_arrays">40.4.2 Arrays</a></H3>
+<H3><a name="Scilab_typemaps_arrays">41.4.2 Arrays</a></H3>
 
 
 <p>
@@ -1616,7 +1616,7 @@ void printArray(int values[], int len) {
 [ 0  1  2  3 ]
 </pre></div>
 
-<H3><a name="Scilab_typemaps_pointer-to-pointers">40.4.3 Pointer-to-pointers</a></H3>
+<H3><a name="Scilab_typemaps_pointer-to-pointers">41.4.3 Pointer-to-pointers</a></H3>
 
 
 <p>
@@ -1689,7 +1689,7 @@ void print_matrix(double **M, int nbRows, int nbCols) {
 </pre></div>
 
 
-<H3><a name="Scilab_typemaps_matrices">40.4.4 Matrices</a></H3>
+<H3><a name="Scilab_typemaps_matrices">41.4.4 Matrices</a></H3>
 
 
 <p>
@@ -1782,7 +1782,7 @@ The remarks made earlier for arrays also apply here:
 <li>There is no control while converting <tt>double</tt> values to integers, <tt>double</tt> values are truncated without any checking or warning.</li>
 </ul>
 
-<H3><a name="Scilab_typemaps_stl">40.4.5 STL</a></H3>
+<H3><a name="Scilab_typemaps_stl">41.4.5 STL</a></H3>
 
 
 <p>
@@ -1982,7 +1982,7 @@ ans  =
 --&gt; delete_PersonPtrSet(p);
 </pre></div>
 
-<H2><a name="Scilab_module_initialization">40.5 Module initialization</a></H2>
+<H2><a name="Scilab_module_initialization">41.5 Module initialization</a></H2>
 
 
 <p>
@@ -2006,7 +2006,7 @@ For example, to initialize the module <tt>example</tt>:
 --&gt; example_Init();
 </pre></div>
 
-<H2><a name="Scilab_building_modes">40.6 Building modes</a></H2>
+<H2><a name="Scilab_building_modes">41.6 Building modes</a></H2>
 
 
 <p>
@@ -2021,7 +2021,7 @@ To produce a dynamic module, when generating the wrapper, there are two possibil
 <li>the <tt>builder</tt> mode. In this mode, Scilab is responsible of building.
 </ul>
 
-<H3><a name="Scilab_building_modes_nobuilder_mode">40.6.1 No-builder mode</a></H3>
+<H3><a name="Scilab_building_modes_nobuilder_mode">41.6.1 No-builder mode</a></H3>
 
 
 <p>
@@ -2034,7 +2034,7 @@ This mode is the best option to use when you have to integrate the module build
 </p>
 
 
-<H3><a name="Scilab_building_modes_builder_mode">40.6.2 Builder mode</a></H3>
+<H3><a name="Scilab_building_modes_builder_mode">41.6.2 Builder mode</a></H3>
 
 
 <p>
@@ -2074,14 +2074,14 @@ The command is:
 $ swig -scilab -builder -buildercflags -I/opt/foo/include -builderldflags "-L/opt/foo/lib -lfoo" -buildersources baa1.cxx, baa2.cxx example.i
 </pre></div>
 
-<H2><a name="Scilab_generated_scripts">40.7 Generated scripts</a></H2>
+<H2><a name="Scilab_generated_scripts">41.7 Generated scripts</a></H2>
 
 
 <p>
 In this part we give some details about the generated Scilab scripts.
 </p>
 
-<H3><a name="Scilab_generated_scripts_builder_script">40.7.1 Builder script</a></H3>
+<H3><a name="Scilab_generated_scripts_builder_script">41.7.1 Builder script</a></H3>
 
 
 <p>
@@ -2106,7 +2106,7 @@ ilib_build(ilib_name, table, files, libs);
 <li><tt><b>table</b></tt>: two column string matrix containing a table of pairs of 'scilab function name', 'C function name'.</li>
 </ul>
 
-<H3><a name="Scilab_generated_scripts_loader_script">40.7.2 Loader script</a></H3>
+<H3><a name="Scilab_generated_scripts_loader_script">41.7.2 Loader script</a></H3>
 
 
 <p>
@@ -2145,7 +2145,7 @@ clear get_file_path;
 </ul>
 
 
-<H2><a name="Scilab_other_resources">40.8 Other resources</a></H2>
+<H2><a name="Scilab_other_resources">41.8 Other resources</a></H2>
 
 
 <ul>
diff --git a/Doc/Manual/Sections.html b/Doc/Manual/Sections.html
index b75706de5..547faf0cf 100644
--- a/Doc/Manual/Sections.html
+++ b/Doc/Manual/Sections.html
@@ -30,6 +30,7 @@ Last update : SWIG-4.0.0 (in progress)
 <li><a href="Customization.html#Customization">Customization features</a></li>
 <li><a href="Contract.html#Contract">Contracts</a></li>
 <li><a href="Varargs.html#Varargs">Variable length arguments</a></li>
+<li><a href="Doxygen.html#Doxygen">Doxygen documentation comments</a></li>
 <li><a href="Warnings.html#Warnings">Warning messages</a></li>
 <li><a href="Modules.html#Modules">Working with Modules</a></li>
 <li><a href="CCache.html#CCache">Using SWIG with ccache</a></li>
diff --git a/Doc/Manual/Tcl.html b/Doc/Manual/Tcl.html
index b6a7edcd4..7e7cd5f87 100644
--- a/Doc/Manual/Tcl.html
+++ b/Doc/Manual/Tcl.html
@@ -7,7 +7,7 @@
 </head>
 
 <body bgcolor="#ffffff">
-<H1><a name="Tcl">41 SWIG and Tcl</a></H1>
+<H1><a name="Tcl">42 SWIG and Tcl</a></H1>
 <!-- INDEX -->
 <div class="sectiontoc">
 <ul>
@@ -84,7 +84,7 @@ Tcl 8.0 or a later release.   Earlier releases of SWIG supported Tcl 7.x, but
 this is no longer supported.
 </p>
 
-<H2><a name="Tcl_nn2">41.1 Preliminaries</a></H2>
+<H2><a name="Tcl_nn2">42.1 Preliminaries</a></H2>
 
 
 <p>
@@ -110,7 +110,7 @@ build a Tcl extension module.  To finish building the module, you
 need to compile this file and link it with the rest of your program.
 </p>
 
-<H3><a name="Tcl_nn3">41.1.1 Getting the right header files</a></H3>
+<H3><a name="Tcl_nn3">42.1.1 Getting the right header files</a></H3>
 
 
 <p>
@@ -128,7 +128,7 @@ this is the case, you should probably make a symbolic link so that <tt>tcl.h</tt
 header file.
 </p>
 
-<H3><a name="Tcl_nn4">41.1.2 Compiling a dynamic module</a></H3>
+<H3><a name="Tcl_nn4">42.1.2 Compiling a dynamic module</a></H3>
 
 
 <p>
@@ -164,7 +164,7 @@ The name of the module is specified using the <tt>%module</tt> directive or the
  <tt>-module</tt> command line option.
 </p>
 
-<H3><a name="Tcl_nn5">41.1.3 Static linking</a></H3>
+<H3><a name="Tcl_nn5">42.1.3 Static linking</a></H3>
 
 
 <p>
@@ -230,7 +230,7 @@ minimal in most situations (and quite frankly not worth the extra
 hassle in the opinion of this author). 
 </p>
 
-<H3><a name="Tcl_nn6">41.1.4 Using your module</a></H3>
+<H3><a name="Tcl_nn6">42.1.4 Using your module</a></H3>
 
 
 <p>
@@ -358,7 +358,7 @@ to the default system configuration (this requires root access and you will need
 the man pages). 
 </p>
 
-<H3><a name="Tcl_nn7">41.1.5 Compilation of C++ extensions</a></H3>
+<H3><a name="Tcl_nn7">42.1.5 Compilation of C++ extensions</a></H3>
 
 
 <p>
@@ -441,7 +441,7 @@ erratic program behavior.   If working with lots of software components, you
 might want to investigate using a more formal standard such as COM.
 </p>
 
-<H3><a name="Tcl_nn8">41.1.6 Compiling for 64-bit platforms</a></H3>
+<H3><a name="Tcl_nn8">42.1.6 Compiling for 64-bit platforms</a></H3>
 
 
 <p>
@@ -468,7 +468,7 @@ also introduce problems on platforms that support more than one
 linking standard (e.g., -o32 and -n32 on Irix).
 </p>
 
-<H3><a name="Tcl_nn9">41.1.7 Setting a package prefix</a></H3>
+<H3><a name="Tcl_nn9">42.1.7 Setting a package prefix</a></H3>
 
 
 <p>
@@ -487,7 +487,7 @@ option will append the prefix to the name when creating a command and
 call it "<tt>Foo_bar</tt>".
 </p>
 
-<H3><a name="Tcl_nn10">41.1.8 Using namespaces</a></H3>
+<H3><a name="Tcl_nn10">42.1.8 Using namespaces</a></H3>
 
 
 <p>
@@ -509,7 +509,7 @@ When the <tt>-namespace</tt> option is used, objects in the module
 are always accessed with the namespace name such as <tt>Foo::bar</tt>.
 </p>
 
-<H2><a name="Tcl_nn11">41.2 Building Tcl/Tk Extensions under Windows 95/NT</a></H2>
+<H2><a name="Tcl_nn11">42.2 Building Tcl/Tk Extensions under Windows 95/NT</a></H2>
 
 
 <p>
@@ -520,7 +520,7 @@ covers the process of using SWIG with Microsoft Visual C++.
 although the procedure may be similar with other compilers.
 </p>
 
-<H3><a name="Tcl_nn12">41.2.1 Running SWIG from Developer Studio</a></H3>
+<H3><a name="Tcl_nn12">42.2.1 Running SWIG from Developer Studio</a></H3>
 
 
 <p>
@@ -578,7 +578,7 @@ MSDOS &gt; tclsh80
 %
 </pre></div>
 
-<H3><a name="Tcl_nn13">41.2.2 Using NMAKE</a></H3>
+<H3><a name="Tcl_nn13">42.2.2 Using NMAKE</a></H3>
 
 
 <p>
@@ -641,7 +641,7 @@ to get you started.  With a little practice, you'll be making lots of
 Tcl extensions.
 </p>
 
-<H2><a name="Tcl_nn14">41.3 A tour of basic C/C++ wrapping</a></H2>
+<H2><a name="Tcl_nn14">42.3 A tour of basic C/C++ wrapping</a></H2>
 
 
 <p>
@@ -652,7 +652,7 @@ classes.  This section briefly covers the essential aspects of this
 wrapping.
 </p>
 
-<H3><a name="Tcl_nn15">41.3.1 Modules</a></H3>
+<H3><a name="Tcl_nn15">42.3.1 Modules</a></H3>
 
 
 <p>
@@ -686,7 +686,7 @@ To fix this, supply an extra argument to <tt>load</tt> like this:
 </pre>
 </div>
 
-<H3><a name="Tcl_nn16">41.3.2 Functions</a></H3>
+<H3><a name="Tcl_nn16">42.3.2 Functions</a></H3>
 
 
 <p>
@@ -711,7 +711,7 @@ like you think it does:
 %
 </pre></div>
 
-<H3><a name="Tcl_nn17">41.3.3 Global variables</a></H3>
+<H3><a name="Tcl_nn17">42.3.3 Global variables</a></H3>
 
 
 <p>
@@ -791,7 +791,7 @@ extern char *path;      // Read-only (due to %immutable)
 </pre>
 </div>
 
-<H3><a name="Tcl_nn18">41.3.4 Constants and enums</a></H3>
+<H3><a name="Tcl_nn18">42.3.4 Constants and enums</a></H3>
 
 
 <p>
@@ -875,7 +875,7 @@ When an identifier name is given, it is used to perform an implicit hash-table l
 conversion.  This allows the <tt>global</tt> statement to be omitted.
 </p>
 
-<H3><a name="Tcl_nn19">41.3.5 Pointers</a></H3>
+<H3><a name="Tcl_nn19">42.3.5 Pointers</a></H3>
 
 
 <p>
@@ -971,7 +971,7 @@ C-style cast may return a bogus result whereas as the C++-style cast will return
 <tt>None</tt> if the conversion can't be performed.
 </p>
 
-<H3><a name="Tcl_nn20">41.3.6 Structures</a></H3>
+<H3><a name="Tcl_nn20">42.3.6 Structures</a></H3>
 
 
 <p>
@@ -1253,7 +1253,7 @@ Note: Tcl only destroys the underlying object if it has ownership.  See the
 memory management section that appears shortly.
 </p>
 
-<H3><a name="Tcl_nn21">41.3.7 C++ classes</a></H3>
+<H3><a name="Tcl_nn21">42.3.7 C++ classes</a></H3>
 
 
 <p>
@@ -1319,7 +1319,7 @@ In Tcl, the static member is accessed as follows:
 </pre>
 </div>
 
-<H3><a name="Tcl_nn22">41.3.8 C++ inheritance</a></H3>
+<H3><a name="Tcl_nn22">42.3.8 C++ inheritance</a></H3>
 
 
 <p>
@@ -1368,7 +1368,7 @@ For instance:
 It is safe to use multiple inheritance with SWIG.
 </p>
 
-<H3><a name="Tcl_nn23">41.3.9 Pointers, references, values, and arrays</a></H3>
+<H3><a name="Tcl_nn23">42.3.9 Pointers, references, values, and arrays</a></H3>
 
 
 <p>
@@ -1422,7 +1422,7 @@ to hold the result and a pointer is returned (Tcl will release this memory
 when the return value is garbage collected).
 </p>
 
-<H3><a name="Tcl_nn24">41.3.10 C++ overloaded functions</a></H3>
+<H3><a name="Tcl_nn24">42.3.10 C++ overloaded functions</a></H3>
 
 
 <p>
@@ -1545,7 +1545,7 @@ first declaration takes precedence.
 Please refer to the "SWIG and C++" chapter for more information about overloading. 
 </p>
 
-<H3><a name="Tcl_nn25">41.3.11 C++ operators</a></H3>
+<H3><a name="Tcl_nn25">42.3.11 C++ operators</a></H3>
 
 
 <p>
@@ -1647,7 +1647,7 @@ There are ways to make this operator appear as part of the class using the <tt>%
 Keep reading.
 </p>
 
-<H3><a name="Tcl_nn26">41.3.12 C++ namespaces</a></H3>
+<H3><a name="Tcl_nn26">42.3.12 C++ namespaces</a></H3>
 
 
 <p>
@@ -1711,7 +1711,7 @@ utilizes thousands of small deeply nested namespaces each with
 identical symbol names, well, then you get what you deserve.
 </p>
 
-<H3><a name="Tcl_nn27">41.3.13 C++ templates</a></H3>
+<H3><a name="Tcl_nn27">42.3.13 C++ templates</a></H3>
 
 
 <p>
@@ -1763,7 +1763,7 @@ More details can be found in the <a href="SWIGPlus.html#SWIGPlus">SWIG and C++</
 examples will appear later.
 </p>
 
-<H3><a name="Tcl_nn28">41.3.14 C++ Smart Pointers</a></H3>
+<H3><a name="Tcl_nn28">42.3.14 C++ Smart Pointers</a></H3>
 
 
 <p>
@@ -1847,7 +1847,7 @@ simply use the <tt>__deref__()</tt> method.  For example:
 </pre>
 </div>
 
-<H2><a name="Tcl_nn29">41.4 Further details on the Tcl class interface</a></H2>
+<H2><a name="Tcl_nn29">42.4 Further details on the Tcl class interface</a></H2>
 
 
 <p>
@@ -1860,7 +1860,7 @@ of low-level details were omitted.  This section provides a brief overview
 of how the proxy classes work.
 </p>
 
-<H3><a name="Tcl_nn30">41.4.1 Proxy classes</a></H3>
+<H3><a name="Tcl_nn30">42.4.1 Proxy classes</a></H3>
 
 
 <p>
@@ -1925,7 +1925,7 @@ function.   This allows objects to be encapsulated objects that look a lot like
 as shown in the last section.
 </p>
 
-<H3><a name="Tcl_nn31">41.4.2 Memory management</a></H3>
+<H3><a name="Tcl_nn31">42.4.2 Memory management</a></H3>
 
 
 <p>
@@ -2113,7 +2113,7 @@ typemaps--an advanced topic discussed later.
 </p>
 
 
-<H2><a name="Tcl_nn32">41.5 Input and output parameters</a></H2>
+<H2><a name="Tcl_nn32">42.5 Input and output parameters</a></H2>
 
 
 <p>
@@ -2301,7 +2301,7 @@ set c  [lindex $dim 1]
 </pre>
 </div>
 
-<H2><a name="Tcl_nn33">41.6 Exception handling </a></H2>
+<H2><a name="Tcl_nn33">42.6 Exception handling </a></H2>
 
 
 <p>
@@ -2435,7 +2435,7 @@ Since SWIG's exception handling is user-definable, you are not limited to C++ ex
 See the chapter on "<a href="Customization.html#Customization">Customization Features</a>" for more examples.
 </p>
 
-<H2><a name="Tcl_nn34">41.7 Typemaps</a></H2>
+<H2><a name="Tcl_nn34">42.7 Typemaps</a></H2>
 
 
 <p>
@@ -2452,7 +2452,7 @@ Typemaps are only used if you want to change some aspect of the primitive
 C-Tcl interface.
 </p>
 
-<H3><a name="Tcl_nn35">41.7.1 What is a typemap?</a></H3>
+<H3><a name="Tcl_nn35">42.7.1 What is a typemap?</a></H3>
 
 
 <p>
@@ -2572,7 +2572,7 @@ parameter is omitted):
 </pre>
 </div>
 
-<H3><a name="Tcl_nn36">41.7.2 Tcl typemaps</a></H3>
+<H3><a name="Tcl_nn36">42.7.2 Tcl typemaps</a></H3>
 
 
 <p>
@@ -2710,7 +2710,7 @@ Initialize an argument to a value before any conversions occur.
 Examples of these methods will appear shortly.
 </p>
 
-<H3><a name="Tcl_nn37">41.7.3 Typemap variables</a></H3>
+<H3><a name="Tcl_nn37">42.7.3 Typemap variables</a></H3>
 
 
 <p>
@@ -2781,7 +2781,7 @@ properly assigned.
 The Tcl name of the wrapper function being created.
 </div>
 
-<H3><a name="Tcl_nn38">41.7.4 Converting  a Tcl list to a char ** </a></H3>
+<H3><a name="Tcl_nn38">42.7.4 Converting  a Tcl list to a char ** </a></H3>
 
 
 <p>
@@ -2843,7 +2843,7 @@ argv[2] = Larry
 3
 </pre></div>
 
-<H3><a name="Tcl_nn39">41.7.5 Returning values in arguments</a></H3>
+<H3><a name="Tcl_nn39">42.7.5 Returning values in arguments</a></H3>
 
 
 <p>
@@ -2885,7 +2885,7 @@ result, a Tcl function using these typemaps will work like this :
 %
 </pre></div>
 
-<H3><a name="Tcl_nn40">41.7.6 Useful functions</a></H3>
+<H3><a name="Tcl_nn40">42.7.6 Useful functions</a></H3>
 
 
 <p>
@@ -2961,7 +2961,7 @@ int      Tcl_IsShared(Tcl_Obj *obj);
 </pre>
 </div>
 
-<H3><a name="Tcl_nn41">41.7.7 Standard  typemaps</a></H3>
+<H3><a name="Tcl_nn41">42.7.7 Standard  typemaps</a></H3>
 
 
 <p>
@@ -3045,7 +3045,7 @@ work)
 </pre>
 </div>
 
-<H3><a name="Tcl_nn42">41.7.8 Pointer handling</a></H3>
+<H3><a name="Tcl_nn42">42.7.8 Pointer handling</a></H3>
 
 
 <p>
@@ -3127,7 +3127,7 @@ For example:
 </pre>
 </div>
 
-<H2><a name="Tcl_nn43">41.8 Turning a SWIG module into a Tcl Package.</a></H2>
+<H2><a name="Tcl_nn43">42.8 Turning a SWIG module into a Tcl Package.</a></H2>
 
 
 <p>
@@ -3199,7 +3199,7 @@ As a final note, most SWIG examples do not yet use the
 to use the <tt>load</tt> command instead.
 </p>
 
-<H2><a name="Tcl_nn44">41.9 Building new kinds of Tcl interfaces (in Tcl)</a></H2>
+<H2><a name="Tcl_nn44">42.9 Building new kinds of Tcl interfaces (in Tcl)</a></H2>
 
 
 <p>
@@ -3298,7 +3298,7 @@ danger of blowing something up (although it is easily accomplished
 with an out of bounds array access).
 </p>
 
-<H3><a name="Tcl_nn45">41.9.1 Proxy classes</a></H3>
+<H3><a name="Tcl_nn45">42.9.1 Proxy classes</a></H3>
 
 
 <p>
@@ -3419,7 +3419,7 @@ short, but clever Tcl script can be combined with SWIG to do many
 interesting things.
 </p>
 
-<H2><a name="Tcl_nn46">41.10 Tcl/Tk Stubs</a></H2>
+<H2><a name="Tcl_nn46">42.10 Tcl/Tk Stubs</a></H2>
 
 
 <p>
diff --git a/Doc/Manual/Warnings.html b/Doc/Manual/Warnings.html
index 75ca11561..4fdff486b 100644
--- a/Doc/Manual/Warnings.html
+++ b/Doc/Manual/Warnings.html
@@ -7,7 +7,7 @@
 </head>
 
 <body bgcolor="#ffffff">
-<H1><a name="Warnings">16 Warning Messages</a></H1>
+<H1><a name="Warnings">17 Warning Messages</a></H1>
 <!-- INDEX -->
 <div class="sectiontoc">
 <ul>
@@ -36,7 +36,7 @@
 
 
 
-<H2><a name="Warnings_nn2">16.1 Introduction</a></H2>
+<H2><a name="Warnings_nn2">17.1 Introduction</a></H2>
 
 
 <p>
@@ -56,7 +56,7 @@ where the generated wrapper code will probably compile, but it may not
 work like you expect.
 </p>
 
-<H2><a name="Warnings_suppression">16.2 Warning message suppression</a></H2>
+<H2><a name="Warnings_suppression">17.2 Warning message suppression</a></H2>
 
 
 <p>
@@ -148,7 +148,7 @@ your interface.  Ignore the warning messages at your own peril.
 </p>
 
 
-<H2><a name="Warnings_nn4">16.3 Enabling extra warnings</a></H2>
+<H2><a name="Warnings_nn4">17.3 Enabling extra warnings</a></H2>
 
 
 <p>
@@ -221,7 +221,7 @@ that is, any warnings suppressed or added in <tt>%warnfilter</tt>, <tt>#pragma S
 or the <tt>-w</tt> option.
 </p>
 
-<H2><a name="Warnings_nn5">16.4 Issuing a warning message</a></H2>
+<H2><a name="Warnings_nn5">17.4 Issuing a warning message</a></H2>
 
 
 <p>
@@ -275,7 +275,7 @@ example.i:24: Warning 901: You are really going to regret this usage of blah * s
 </pre>
 </div>
 
-<H2><a name="Warnings_symbolic_symbols">16.5 Symbolic symbols</a></H2>
+<H2><a name="Warnings_symbolic_symbols">17.5 Symbolic symbols</a></H2>
 
 
 <p>
@@ -310,7 +310,7 @@ or
 </pre>
 </div>
 
-<H2><a name="Warnings_nn6">16.6 Commentary</a></H2>
+<H2><a name="Warnings_nn6">17.6 Commentary</a></H2>
 
 
 <p>
@@ -327,7 +327,7 @@ no obvious recovery.  There is no mechanism for suppressing error
 messages.
 </p>
 
-<H2><a name="Warnings_nn7">16.7 Warnings as errors</a></H2>
+<H2><a name="Warnings_nn7">17.7 Warnings as errors</a></H2>
 
 
 <p>
@@ -336,7 +336,7 @@ option. This will cause SWIG to exit with a non successful exit code if a
 warning is encountered.
 </p>
 
-<H2><a name="Warnings_nn8">16.8 Message output format</a></H2>
+<H2><a name="Warnings_nn8">17.8 Message output format</a></H2>
 
 
 <p>
@@ -355,10 +355,10 @@ $ swig -python -Fmicrosoft example.i
 example.i(4) : Syntax error in input(1).
 </pre></div>
 
-<H2><a name="Warnings_nn9">16.9 Warning number reference</a></H2>
+<H2><a name="Warnings_nn9">17.9 Warning number reference</a></H2>
 
 
-<H3><a name="Warnings_nn10">16.9.1 Deprecated features (100-199)</a></H3>
+<H3><a name="Warnings_nn10">17.9.1 Deprecated features (100-199)</a></H3>
 
 
 <ul>
@@ -386,7 +386,7 @@ example.i(4) : Syntax error in input(1).
 <li>126. The 'nestedworkaround' feature is deprecated.
 </ul>
 
-<H3><a name="Warnings_nn11">16.9.2 Preprocessor (200-299)</a></H3>
+<H3><a name="Warnings_nn11">17.9.2 Preprocessor (200-299)</a></H3>
 
 
 <ul>
@@ -398,7 +398,7 @@ example.i(4) : Syntax error in input(1).
 <li>206. Unexpected tokens after #<em>directive</em> directive.
 </ul>
 
-<H3><a name="Warnings_nn12">16.9.3 C/C++ Parser (300-399)</a></H3>
+<H3><a name="Warnings_nn12">17.9.3 C/C++ Parser (300-399)</a></H3>
 
 
 <ul>
@@ -475,7 +475,7 @@ example.i(4) : Syntax error in input(1).
 <li>395. operator delete[] ignored.
 </ul>
 
-<H3><a name="Warnings_nn13">16.9.4 Types and typemaps (400-499) </a></H3>
+<H3><a name="Warnings_nn13">17.9.4 Types and typemaps (400-499) </a></H3>
 
 
 <ul>
@@ -506,7 +506,7 @@ example.i(4) : Syntax error in input(1).
 
 
 
-<H3><a name="Warnings_nn14">16.9.5 Code generation (500-599)</a></H3>
+<H3><a name="Warnings_nn14">17.9.5 Code generation (500-599)</a></H3>
 
 
 <ul>
@@ -535,7 +535,7 @@ example.i(4) : Syntax error in input(1).
 <li>523. Use of an illegal destructor name '<em>name</em>' in %extend is deprecated, the destructor name should be '<em>name</em>'.
 </ul>
 
-<H3><a name="Warnings_nn15">16.9.6 Language module specific (700-899) </a></H3>
+<H3><a name="Warnings_nn15">17.9.6 Language module specific (700-899) </a></H3>
 
 
 <ul>
@@ -586,14 +586,14 @@ example.i(4) : Syntax error in input(1).
 <li>871. Unrecognized pragma <em>pragma</em>.   (Php).
 </ul>
 
-<H3><a name="Warnings_nn16">16.9.7 User defined (900-999)</a></H3>
+<H3><a name="Warnings_nn16">17.9.7 User defined (900-999)</a></H3>
 
 
 <p>
 These numbers can be used by your own application.
 </p>
 
-<H2><a name="Warnings_nn17">16.10 History</a></H2>
+<H2><a name="Warnings_nn17">17.10 History</a></H2>
 
 
 <p>
diff --git a/Doc/Manual/chapters b/Doc/Manual/chapters
index 0b9f9bdda..056f6136c 100644
--- a/Doc/Manual/chapters
+++ b/Doc/Manual/chapters
@@ -13,6 +13,7 @@ Typemaps.html
 Customization.html
 Contract.html
 Varargs.html
+Doxygen.html
 Warnings.html
 Modules.html
 CCache.html
@@ -40,4 +41,3 @@ Ruby.html
 Scilab.html
 Tcl.html
 Extending.html
-Doxygen.html

From fdade90ac85e1568dc8a588f9bfd0b18ef1efdfb Mon Sep 17 00:00:00 2001
From: William S Fulton <wsf@fultondesigns.co.uk>
Date: Thu, 24 May 2018 18:38:52 +0100
Subject: [PATCH 298/314] Doxygen html tweaks

---
 Doc/Manual/Contents.html |  4 ++--
 Doc/Manual/Doxygen.html  | 10 ++++++----
 2 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/Doc/Manual/Contents.html b/Doc/Manual/Contents.html
index b7de00077..98481537a 100644
--- a/Doc/Manual/Contents.html
+++ b/Doc/Manual/Contents.html
@@ -605,8 +605,8 @@
 <li><a href="Doxygen.html#Doxygen_notranslate">doxygen:notranslate</a>
 <li><a href="Doxygen.html#Doxygen_alias">doxygen:alias:&lt;command-name&gt;</a>
 <li><a href="Doxygen.html#Doxygen_ignore">doxygen:ignore:&lt;command-name&gt;</a>
-<li><a href="Doxygen.html#Doxygen_nolinktranslate">doxygen:nolinktranslate (Java-only currently)</a>
-<li><a href="Doxygen.html#Doxygen_nostripparams">doxygen:nostripparams (Java-only currently)</a>
+<li><a href="Doxygen.html#Doxygen_nolinktranslate">doxygen:nolinktranslate</a>
+<li><a href="Doxygen.html#Doxygen_nostripparams">doxygen:nostripparams</a>
 </ul>
 <li><a href="Doxygen.html#Doxygen_additional_options">Additional command line options</a>
 </ul>
diff --git a/Doc/Manual/Doxygen.html b/Doc/Manual/Doxygen.html
index de9ff5841..08d1aef94 100644
--- a/Doc/Manual/Doxygen.html
+++ b/Doc/Manual/Doxygen.html
@@ -18,8 +18,8 @@
 <li><a href="#Doxygen_notranslate">doxygen:notranslate</a>
 <li><a href="#Doxygen_alias">doxygen:alias:&lt;command-name&gt;</a>
 <li><a href="#Doxygen_ignore">doxygen:ignore:&lt;command-name&gt;</a>
-<li><a href="#Doxygen_nolinktranslate">doxygen:nolinktranslate (Java-only currently)</a>
-<li><a href="#Doxygen_nostripparams">doxygen:nostripparams (Java-only currently)</a>
+<li><a href="#Doxygen_nolinktranslate">doxygen:nolinktranslate</a>
+<li><a href="#Doxygen_nostripparams">doxygen:nostripparams</a>
 </ul>
 <li><a href="#Doxygen_additional_options">Additional command line options</a>
 </ul>
@@ -416,20 +416,22 @@ def func():
 </pre></div>
 
 
-<H4><a name="Doxygen_nolinktranslate">16.2.2.4 doxygen:nolinktranslate (Java-only currently)</a></H4>
+<H4><a name="Doxygen_nolinktranslate">16.2.2.4 doxygen:nolinktranslate</a></H4>
 
 
 <p>
 Turn off automatic link-objects translation.
+This is only applicable to Java at the moment.
 </p>
 
 
-<H4><a name="Doxygen_nostripparams">16.2.2.5 doxygen:nostripparams (Java-only currently)</a></H4>
+<H4><a name="Doxygen_nostripparams">16.2.2.5 doxygen:nostripparams</a></H4>
 
 
 <p>
 Turn off stripping of <tt>@param</tt> and <tt>@tparam</tt>
 Doxygen commands if the parameter is not found in the function signature.
+This is only applicable to Java at the moment.
 </p>
 
 

From cbaf6eb2b3b04fd75b152d94f9baa806aa698ab9 Mon Sep 17 00:00:00 2001
From: William S Fulton <wsf@fultondesigns.co.uk>
Date: Thu, 24 May 2018 19:18:55 +0100
Subject: [PATCH 299/314] Clean up merge problem

---
 Examples/test-suite/java/Makefile.in | 1 -
 1 file changed, 1 deletion(-)

diff --git a/Examples/test-suite/java/Makefile.in b/Examples/test-suite/java/Makefile.in
index e3333692c..f1717b81b 100644
--- a/Examples/test-suite/java/Makefile.in
+++ b/Examples/test-suite/java/Makefile.in
@@ -76,7 +76,6 @@ java_nspacewithoutpackage.%: JAVA_PACKAGEOPT =
 multiple_inheritance_nspace.%: JAVA_PACKAGE = $*Package
 nspace.%: JAVA_PACKAGE = $*Package
 nspace_extend.%: JAVA_PACKAGE = $*Package
-doxygen_misc_constructs.%: INCLUDES = -I../$(srcdir)/..
 
 # Rules for the different types of tests
 %.cpptest:

From 95caf875960d53adf4e79fcb5e157760d94ecfb8 Mon Sep 17 00:00:00 2001
From: William S Fulton <wsf@fultondesigns.co.uk>
Date: Thu, 24 May 2018 19:28:15 +0100
Subject: [PATCH 300/314] PEP8 conformance for comment verifier module

---
 Examples/test-suite/python/autodoc_runme.py   |  4 +--
 ...commentVerifier.py => comment_verifier.py} |  0
 .../test-suite/python/doxygen_alias_runme.py  |  4 +--
 .../python/doxygen_basic_notranslate_runme.py | 16 +++++-----
 .../python/doxygen_basic_translate_runme.py   | 18 +++++------
 .../test-suite/python/doxygen_ignore_runme.py |  4 +--
 .../python/doxygen_misc_constructs_runme.py   | 30 +++++++++----------
 .../python/doxygen_parsing_runme.py           | 22 +++++++-------
 .../doxygen_translate_all_tags_runme.py       | 22 +++++++-------
 .../python/doxygen_translate_links_runme.py   |  4 +--
 .../python/doxygen_translate_runme.py         | 10 +++----
 11 files changed, 67 insertions(+), 67 deletions(-)
 rename Examples/test-suite/python/{commentVerifier.py => comment_verifier.py} (100%)

diff --git a/Examples/test-suite/python/autodoc_runme.py b/Examples/test-suite/python/autodoc_runme.py
index 7635f6c4a..11e499d25 100644
--- a/Examples/test-suite/python/autodoc_runme.py
+++ b/Examples/test-suite/python/autodoc_runme.py
@@ -1,5 +1,5 @@
 from autodoc import *
-import commentVerifier
+import comment_verifier
 import inspect
 import sys
 
@@ -8,7 +8,7 @@ def check(got, expected, expected_builtin=None, skip=False):
         expect = expected
         if is_python_builtin() and expected_builtin != None:
             expect = expected_builtin
-        commentVerifier.check(got, expect)
+        comment_verifier.check(got, expect)
 
 def is_new_style_class(cls):
     return hasattr(cls, "__class__")
diff --git a/Examples/test-suite/python/commentVerifier.py b/Examples/test-suite/python/comment_verifier.py
similarity index 100%
rename from Examples/test-suite/python/commentVerifier.py
rename to Examples/test-suite/python/comment_verifier.py
diff --git a/Examples/test-suite/python/doxygen_alias_runme.py b/Examples/test-suite/python/doxygen_alias_runme.py
index 4117f00e5..ad580f719 100644
--- a/Examples/test-suite/python/doxygen_alias_runme.py
+++ b/Examples/test-suite/python/doxygen_alias_runme.py
@@ -2,9 +2,9 @@
 
 import doxygen_alias
 import inspect
-import commentVerifier
+import comment_verifier
 
-commentVerifier.check(inspect.getdoc(doxygen_alias.make_something),
+comment_verifier.check(inspect.getdoc(doxygen_alias.make_something),
     """\
 A function returning something.
 
diff --git a/Examples/test-suite/python/doxygen_basic_notranslate_runme.py b/Examples/test-suite/python/doxygen_basic_notranslate_runme.py
index bf2703c21..17c03e32d 100644
--- a/Examples/test-suite/python/doxygen_basic_notranslate_runme.py
+++ b/Examples/test-suite/python/doxygen_basic_notranslate_runme.py
@@ -4,9 +4,9 @@ import doxygen_basic_notranslate
 import inspect
 import string
 import sys
-import commentVerifier
+import comment_verifier
 
-commentVerifier.check(inspect.getdoc(doxygen_basic_notranslate.function),
+comment_verifier.check(inspect.getdoc(doxygen_basic_notranslate.function),
     r"""\brief
 Brief description.
 
@@ -16,12 +16,12 @@ The comment text
 \sa function2"""
 )
 
-commentVerifier.check(inspect.getdoc(doxygen_basic_notranslate.function2),
+comment_verifier.check(inspect.getdoc(doxygen_basic_notranslate.function2),
     r"""A test of a very very very very very very very very very very very very very very very very
 very very very very very long comment string."""
 )
 
-commentVerifier.check(inspect.getdoc(doxygen_basic_notranslate.function3),
+comment_verifier.check(inspect.getdoc(doxygen_basic_notranslate.function3),
     r"""*Overload 1:*
 
 A test for overloaded functions
@@ -35,7 +35,7 @@ A test for overloaded functions
 This is function \b two"""
 )
 
-commentVerifier.check(inspect.getdoc(doxygen_basic_notranslate.function4),
+comment_verifier.check(inspect.getdoc(doxygen_basic_notranslate.function4),
     r"""A test of some mixed tag usage
 \if CONDITION
 This \a code fragment shows us something \.
@@ -51,14 +51,14 @@ int main() { while(true); }
 \endcode
 \endif"""
 )
-commentVerifier.check(inspect.getdoc(doxygen_basic_notranslate.function5),
+comment_verifier.check(inspect.getdoc(doxygen_basic_notranslate.function5),
     r"""This is a post comment. """
 )
-commentVerifier.check(inspect.getdoc(doxygen_basic_notranslate.function6),
+comment_verifier.check(inspect.getdoc(doxygen_basic_notranslate.function6),
     r"""Test for default args
 @param a Some parameter, default is 42"""
 )
-commentVerifier.check(inspect.getdoc(doxygen_basic_notranslate.function7),
+comment_verifier.check(inspect.getdoc(doxygen_basic_notranslate.function7),
     r"""Test for a parameter with difficult type
 (mostly for python)
 @param a Very strange param"""
diff --git a/Examples/test-suite/python/doxygen_basic_translate_runme.py b/Examples/test-suite/python/doxygen_basic_translate_runme.py
index f566086e1..1be6b6b07 100644
--- a/Examples/test-suite/python/doxygen_basic_translate_runme.py
+++ b/Examples/test-suite/python/doxygen_basic_translate_runme.py
@@ -4,9 +4,9 @@ import doxygen_basic_translate
 import inspect
 import string
 import sys
-import commentVerifier
+import comment_verifier
 
-commentVerifier.check(inspect.getdoc(doxygen_basic_translate.function),
+comment_verifier.check(inspect.getdoc(doxygen_basic_translate.function),
     """\
 Brief description.
 
@@ -19,12 +19,12 @@ Author: Some author
 
 See also: function2"""
 )
-commentVerifier.check(inspect.getdoc(doxygen_basic_translate.function2),
+comment_verifier.check(inspect.getdoc(doxygen_basic_translate.function2),
     """\
 A test of a very very very very very very very very very very very very very very very very
 very very very very very long comment string."""
 )
-commentVerifier.check(inspect.getdoc(doxygen_basic_translate.function3),
+comment_verifier.check(inspect.getdoc(doxygen_basic_translate.function3),
     """*Overload 1:*
 
 A test for overloaded functions
@@ -37,7 +37,7 @@ This is function **one**
 A test for overloaded functions
 This is function **two**"""
 )
-commentVerifier.check(inspect.getdoc(doxygen_basic_translate.function4),
+comment_verifier.check(inspect.getdoc(doxygen_basic_translate.function4),
     """\
 A test of some mixed tag usage
 If: CONDITION {
@@ -56,16 +56,16 @@ Warning: This may not work as expected
 
 }"""
 )
-commentVerifier.check(inspect.getdoc(doxygen_basic_translate.function5),
+comment_verifier.check(inspect.getdoc(doxygen_basic_translate.function5),
     """This is a post comment."""
 )
-commentVerifier.check(inspect.getdoc(doxygen_basic_translate.function6),
+comment_verifier.check(inspect.getdoc(doxygen_basic_translate.function6),
     """\
 Test for default args
 :type a: int
 :param a: Some parameter, default is 42"""
 )
-commentVerifier.check(inspect.getdoc(doxygen_basic_translate.function7),
+comment_verifier.check(inspect.getdoc(doxygen_basic_translate.function7),
     """\
 Test for a parameter with difficult type
 (mostly for python)
@@ -73,7 +73,7 @@ Test for a parameter with difficult type
 :param a: Very strange param"""
 )
 
-commentVerifier.check(inspect.getdoc(doxygen_basic_translate.Atan2),
+comment_verifier.check(inspect.getdoc(doxygen_basic_translate.Atan2),
     """\
 Multiple parameters test.
 
diff --git a/Examples/test-suite/python/doxygen_ignore_runme.py b/Examples/test-suite/python/doxygen_ignore_runme.py
index 9e2e73da7..33329d2de 100644
--- a/Examples/test-suite/python/doxygen_ignore_runme.py
+++ b/Examples/test-suite/python/doxygen_ignore_runme.py
@@ -2,9 +2,9 @@
 
 import doxygen_ignore
 import inspect
-import commentVerifier
+import comment_verifier
 
-commentVerifier.check(inspect.getdoc(doxygen_ignore.func),
+comment_verifier.check(inspect.getdoc(doxygen_ignore.func),
     """\
 A contrived example of ignoring too many commands in one comment.
 
diff --git a/Examples/test-suite/python/doxygen_misc_constructs_runme.py b/Examples/test-suite/python/doxygen_misc_constructs_runme.py
index 316d7e69b..32ee912fd 100644
--- a/Examples/test-suite/python/doxygen_misc_constructs_runme.py
+++ b/Examples/test-suite/python/doxygen_misc_constructs_runme.py
@@ -4,10 +4,10 @@ import doxygen_misc_constructs
 import inspect
 import string
 import sys
-import commentVerifier
+import comment_verifier
 
 
-commentVerifier.check(inspect.getdoc(doxygen_misc_constructs.getAddress),
+comment_verifier.check(inspect.getdoc(doxygen_misc_constructs.getAddress),
     r"""Returns address of file line.
 
 :type fileName: int
@@ -19,7 +19,7 @@ commentVerifier.check(inspect.getdoc(doxygen_misc_constructs.getAddress),
 
 Connection::getId() """)
 
-commentVerifier.check(inspect.getdoc(doxygen_misc_constructs.CConnectionConfig),
+comment_verifier.check(inspect.getdoc(doxygen_misc_constructs.CConnectionConfig),
     r"""This class contains information for connection to winIDEA. Its methods
 return reference to self, so we can use it like this:
 
@@ -34,26 +34,26 @@ used for unspecified parameters.
 
 advancedWinIDEALaunching.py Python example.""")
 
-commentVerifier.check(inspect.getdoc(doxygen_misc_constructs.waitTime),
+comment_verifier.check(inspect.getdoc(doxygen_misc_constructs.waitTime),
     r"""Determines how long the ``isystem.connect`` should wait for running
 instances to respond. Only one of ``lfWaitXXX`` flags from IConnect::ELaunchFlags
 may be specified."""
 )
 
-commentVerifier.check(inspect.getdoc(doxygen_misc_constructs.getConnection),
+comment_verifier.check(inspect.getdoc(doxygen_misc_constructs.getConnection),
     r"""This function returns connection id."""
 )
 
 
-commentVerifier.check(inspect.getdoc(doxygen_misc_constructs.getFirstLetter),
+comment_verifier.check(inspect.getdoc(doxygen_misc_constructs.getFirstLetter),
     r''
 )
 
-commentVerifier.check(inspect.getdoc(doxygen_misc_constructs.ClassWithNestedEnum),
+comment_verifier.check(inspect.getdoc(doxygen_misc_constructs.ClassWithNestedEnum),
     r"""Class description."""
 )
 
-commentVerifier.check(inspect.getdoc(doxygen_misc_constructs.showList),
+comment_verifier.check(inspect.getdoc(doxygen_misc_constructs.showList),
     r"""An example of a list in a documentation comment.
 
     - The first item of the list.
@@ -66,24 +66,24 @@ commentVerifier.check(inspect.getdoc(doxygen_misc_constructs.showList),
 And this is not a list item any more."""
 )
 
-commentVerifier.check(inspect.getdoc(doxygen_misc_constructs.isNoSpaceValidA),
+comment_verifier.check(inspect.getdoc(doxygen_misc_constructs.isNoSpaceValidA),
     r"""This comment without space after '*' is valid in Doxygen."""
 )
 
-commentVerifier.check(inspect.getdoc(doxygen_misc_constructs.isNoSpaceValidB),
+comment_verifier.check(inspect.getdoc(doxygen_misc_constructs.isNoSpaceValidB),
     r""".This comment without space after '*' is valid in Doxygen."""
 )
 
-commentVerifier.check(inspect.getdoc(doxygen_misc_constructs.isNoSpaceValidC),
+comment_verifier.check(inspect.getdoc(doxygen_misc_constructs.isNoSpaceValidC),
     r''
 )
 
-commentVerifier.check(inspect.getdoc(doxygen_misc_constructs.backslashA),
+comment_verifier.check(inspect.getdoc(doxygen_misc_constructs.backslashA),
     r"""Backslash following``word`` is a valid doxygen command. Output contains
 'followingword' with 'word' in code font."""
 )
 
-commentVerifier.check(inspect.getdoc(doxygen_misc_constructs.backslashB),
+comment_verifier.check(inspect.getdoc(doxygen_misc_constructs.backslashB),
     r"""Doxy command without trailing space is ignored - nothing appears
 on output. Standalone \ and '\' get to output.
 Standalone @ and '@' get to output.
@@ -98,7 +98,7 @@ Commands for escaped symbols:
 $ @ \ & ~ < > # % " . :: @text ::text"""
 )
 
-commentVerifier.check(inspect.getdoc(doxygen_misc_constructs.backslashC),
+comment_verifier.check(inspect.getdoc(doxygen_misc_constructs.backslashC),
     r"""Backslash e at end of *line* froze SWIG
 *with* old comment parser.
 
@@ -107,7 +107,7 @@ See also: MyClass::fun(char,
 )
 
 
-commentVerifier.check(inspect.getdoc(doxygen_misc_constructs.cycle),
+comment_verifier.check(inspect.getdoc(doxygen_misc_constructs.cycle),
     r"""The next line contains expression:
 
 ['retVal < 10', 'g_counter == 23 && g_mode & 3']
diff --git a/Examples/test-suite/python/doxygen_parsing_runme.py b/Examples/test-suite/python/doxygen_parsing_runme.py
index 22ad83020..20e840df5 100644
--- a/Examples/test-suite/python/doxygen_parsing_runme.py
+++ b/Examples/test-suite/python/doxygen_parsing_runme.py
@@ -5,20 +5,20 @@ import inspect
 import string
 import os
 import sys
-import commentVerifier
+import comment_verifier
 
-commentVerifier.check(inspect.getdoc(doxygen_parsing.someFunction),
+comment_verifier.check(inspect.getdoc(doxygen_parsing.someFunction),
     "The function comment")
-commentVerifier.check(inspect.getdoc(doxygen_parsing.SomeClass),
+comment_verifier.check(inspect.getdoc(doxygen_parsing.SomeClass),
     "The class comment")
-commentVerifier.check(inspect.getdoc(doxygen_parsing.SomeStruct),
+comment_verifier.check(inspect.getdoc(doxygen_parsing.SomeStruct),
     "The struct comment")
 
 # There doesn't seem to be any way to specify the doc string for __init__ when
 # using "-builtin" (see http://stackoverflow.com/q/11913492/15275), so skip
 # this test in this case.
 if str(os.environ.get('SWIG_FEATURES')).find('-builtin') == -1:
-    commentVerifier.check(inspect.getdoc(doxygen_parsing.SomeAnotherClass.__init__),
+    comment_verifier.check(inspect.getdoc(doxygen_parsing.SomeAnotherClass.__init__),
     r"""*Overload 1:*
 First overloaded constructor.
 
@@ -27,11 +27,11 @@ First overloaded constructor.
 *Overload 2:*
 Second overloaded constructor.""")
 
-commentVerifier.check(inspect.getdoc(doxygen_parsing.SomeAnotherClass.classMethod),
+comment_verifier.check(inspect.getdoc(doxygen_parsing.SomeAnotherClass.classMethod),
     r"""The class method comment.
 
 SomeAnotherClass#classMethodExtended(int, int) a link text""")
-commentVerifier.check(inspect.getdoc(doxygen_parsing.SomeAnotherClass.classMethodExtended),
+comment_verifier.check(inspect.getdoc(doxygen_parsing.SomeAnotherClass.classMethodExtended),
     r"""The class method with parameter
 
 :type a: int
@@ -39,7 +39,7 @@ commentVerifier.check(inspect.getdoc(doxygen_parsing.SomeAnotherClass.classMetho
 :type b: int
 :param b: Parameter b"""
 )
-commentVerifier.check(inspect.getdoc(doxygen_parsing.SomeAnotherClass.classMethodExtended2),
+comment_verifier.check(inspect.getdoc(doxygen_parsing.SomeAnotherClass.classMethodExtended2),
     r"""The class method with parameter
 
 :type a: int
@@ -47,9 +47,9 @@ commentVerifier.check(inspect.getdoc(doxygen_parsing.SomeAnotherClass.classMetho
 :type b: int
 :param b: Parameter b"""
 )
-commentVerifier.check(inspect.getdoc(doxygen_parsing.SomeAnotherStruct.structMethod),
+comment_verifier.check(inspect.getdoc(doxygen_parsing.SomeAnotherStruct.structMethod),
     r"""The struct method comment""")
-commentVerifier.check(inspect.getdoc(doxygen_parsing.SomeAnotherStruct.structMethodExtended),
+comment_verifier.check(inspect.getdoc(doxygen_parsing.SomeAnotherStruct.structMethodExtended),
     r"""The struct method with parameter
 
 :type a: int
@@ -57,7 +57,7 @@ commentVerifier.check(inspect.getdoc(doxygen_parsing.SomeAnotherStruct.structMet
 :type b: int
 :param b: Parameter b"""
 )
-commentVerifier.check(inspect.getdoc(doxygen_parsing.SomeAnotherStruct.structMethodExtended2),
+comment_verifier.check(inspect.getdoc(doxygen_parsing.SomeAnotherStruct.structMethodExtended2),
     r"""The struct method with parameter
 
 :type a: int
diff --git a/Examples/test-suite/python/doxygen_translate_all_tags_runme.py b/Examples/test-suite/python/doxygen_translate_all_tags_runme.py
index f26c44328..ed66f4bcd 100644
--- a/Examples/test-suite/python/doxygen_translate_all_tags_runme.py
+++ b/Examples/test-suite/python/doxygen_translate_all_tags_runme.py
@@ -4,10 +4,10 @@ import doxygen_translate_all_tags
 import inspect
 import string
 import sys
-import commentVerifier
+import comment_verifier
 
 
-commentVerifier.check(inspect.getdoc(doxygen_translate_all_tags.func01),
+comment_verifier.check(inspect.getdoc(doxygen_translate_all_tags.func01),
 r"""*Hello*
 
 
@@ -41,7 +41,7 @@ Not everything works right now...
 
      some test code""")
 
-commentVerifier.check(inspect.getdoc(doxygen_translate_all_tags.func02),
+comment_verifier.check(inspect.getdoc(doxygen_translate_all_tags.func02),
 r"""Conditional comment: SOMECONDITION
 Some conditional comment
 End of conditional comment.
@@ -65,7 +65,7 @@ Deprecated: Now use another function
 This is very large
 and detailed description of some thing""")
 
-commentVerifier.check(inspect.getdoc(doxygen_translate_all_tags.func03),
+comment_verifier.check(inspect.getdoc(doxygen_translate_all_tags.func03),
 r"""Comment for **func03()**.
 
 
@@ -85,7 +85,7 @@ emphazedWord
 Example: someFile.txt
 Some details on using the example""")
 
-commentVerifier.check(inspect.getdoc(doxygen_translate_all_tags.func04),
+comment_verifier.check(inspect.getdoc(doxygen_translate_all_tags.func04),
 r""":raises: SuperError
 
 
@@ -116,7 +116,7 @@ r""":raises: SuperError
 
 This will only appear in hmtl""")
 
-commentVerifier.check(inspect.getdoc(doxygen_translate_all_tags.func05),
+comment_verifier.check(inspect.getdoc(doxygen_translate_all_tags.func05),
 r"""If: ANOTHERCONDITION {
   First part of comment
   If: SECONDCONDITION {
@@ -150,7 +150,7 @@ Image: testImage.bmp("Hello, world!")
 Some text
 describing invariant.""")
 
-commentVerifier.check(inspect.getdoc(doxygen_translate_all_tags.func06),
+comment_verifier.check(inspect.getdoc(doxygen_translate_all_tags.func06),
 r"""Comment for **func06()**.
 
 
@@ -175,7 +175,7 @@ someMember Some description follows
 
 This will only appear in man""")
 
-commentVerifier.check(inspect.getdoc(doxygen_translate_all_tags.func07),
+comment_verifier.check(inspect.getdoc(doxygen_translate_all_tags.func07),
 r"""Comment for **func07()**.
 
 
@@ -204,7 +204,7 @@ Maybe even multiline
 :type a: int
 :param a: the first param""")
 
-commentVerifier.check(inspect.getdoc(doxygen_translate_all_tags.func08),
+comment_verifier.check(inspect.getdoc(doxygen_translate_all_tags.func08),
 r"""Text after anchor.
 
 
@@ -239,7 +239,7 @@ Another remarks section
 :rtype: void
 :return: may return""")
 
-commentVerifier.check(inspect.getdoc(doxygen_translate_all_tags.func09),
+comment_verifier.check(inspect.getdoc(doxygen_translate_all_tags.func09),
 r"""This will only appear in RTF
 
 
@@ -274,7 +274,7 @@ Since: version 0.0.0.1
 
 :raises: RuntimeError""")
 
-commentVerifier.check(inspect.getdoc(doxygen_translate_all_tags.func10),
+comment_verifier.check(inspect.getdoc(doxygen_translate_all_tags.func10),
 r"""TODO: Some very important task
 
 :type b: float
diff --git a/Examples/test-suite/python/doxygen_translate_links_runme.py b/Examples/test-suite/python/doxygen_translate_links_runme.py
index f0df1ebc1..b7e2b73fa 100644
--- a/Examples/test-suite/python/doxygen_translate_links_runme.py
+++ b/Examples/test-suite/python/doxygen_translate_links_runme.py
@@ -4,10 +4,10 @@ import doxygen_translate_links
 import inspect
 import string
 import sys
-import commentVerifier
+import comment_verifier
 
 
-commentVerifier.check(inspect.getdoc(doxygen_translate_links.function),
+comment_verifier.check(inspect.getdoc(doxygen_translate_links.function),
 r"""Testing typenames converting in @ link
 
 superFunc(int,std::string)
diff --git a/Examples/test-suite/python/doxygen_translate_runme.py b/Examples/test-suite/python/doxygen_translate_runme.py
index 9a2ce53a2..cbdde5fec 100644
--- a/Examples/test-suite/python/doxygen_translate_runme.py
+++ b/Examples/test-suite/python/doxygen_translate_runme.py
@@ -4,10 +4,10 @@ import doxygen_translate
 import inspect
 import string
 import sys
-import commentVerifier
+import comment_verifier
 
 
-commentVerifier.check(inspect.getdoc(doxygen_translate.function),
+comment_verifier.check(inspect.getdoc(doxygen_translate.function),
 r"""*Hello*
 
 * some list item
@@ -140,7 +140,7 @@ And here goes simple text"""
 
 
 
-commentVerifier.check(inspect.getdoc(doxygen_translate.htmlFunction),
+comment_verifier.check(inspect.getdoc(doxygen_translate.htmlFunction),
 r"""Test for html tags. See Doxygen doc for list of tags recognized by Doxygen.
 
 This is link ("http://acme.com/index.html")
@@ -224,7 +224,7 @@ Starts a piece of text displayed in a typewriter font.
 <u>underlined \b bold text - doxy commands are ignored inside 'htmlonly' section </u>""")
 
 
-commentVerifier.check(inspect.getdoc(doxygen_translate.htmlTableFunction),
+comment_verifier.check(inspect.getdoc(doxygen_translate.htmlTableFunction),
 r"""The meaning of flags:
 
 :type byFlags: int
@@ -240,7 +240,7 @@ r"""The meaning of flags:
       ``htmlTable...`` functions.""")
 
 
-commentVerifier.check(inspect.getdoc(doxygen_translate.htmlEntitiesFunction),
+comment_verifier.check(inspect.getdoc(doxygen_translate.htmlEntitiesFunction),
 r"""All entities are treated as commands (C)  TM (R)
 should work also<in text
 >

From 7d1578e58cd57199e5f9c48b38afefaa2ac89bf5 Mon Sep 17 00:00:00 2001
From: William S Fulton <wsf@fultondesigns.co.uk>
Date: Thu, 24 May 2018 20:00:03 +0100
Subject: [PATCH 301/314] Add omitted doxygen_parsing_enums testcase

Still needs a Python runtime test
---
 Examples/test-suite/common.mk | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/Examples/test-suite/common.mk b/Examples/test-suite/common.mk
index e94ff7b02..520c1bbfe 100644
--- a/Examples/test-suite/common.mk
+++ b/Examples/test-suite/common.mk
@@ -607,15 +607,16 @@ $(eval HAS_DOXYGEN := $($(LANGUAGE)_HAS_DOXYGEN))
 
 ifdef HAS_DOXYGEN
 DOXYGEN_TEST_CASES += \
-	doxygen_parsing \
 	doxygen_alias \
-	doxygen_ignore \
-	doxygen_basic_translate \
 	doxygen_basic_notranslate \
+	doxygen_basic_translate \
+	doxygen_ignore \
+	doxygen_misc_constructs \
+	doxygen_parsing \
+	doxygen_parsing_enums \
 	doxygen_translate \
 	doxygen_translate_all_tags \
 	doxygen_translate_links \
-	doxygen_misc_constructs \
 
 $(DOXYGEN_TEST_CASES:=.cpptest): SWIGOPT += -doxygen
 

From 8344aec3a3cd999636f7908667024d5e13de8338 Mon Sep 17 00:00:00 2001
From: William S Fulton <wsf@fultondesigns.co.uk>
Date: Fri, 25 May 2018 08:27:47 +0100
Subject: [PATCH 302/314] Java enums output format fixes

Restore generated Java enum code output to what it was pre-doxygen code changes.
Improves code with doxygen comments too.
---
 Source/Modules/java.cxx | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/Source/Modules/java.cxx b/Source/Modules/java.cxx
index 4a895f308..7a4bc8214 100644
--- a/Source/Modules/java.cxx
+++ b/Source/Modules/java.cxx
@@ -1373,9 +1373,7 @@ public:
 	  }
 
 	  Printv(f_enum, typemapLookup(n, "javaimports", typemap_lookup_type, WARN_NONE), // Import statements
-		 "\n\n", NIL);
-	  
-	  Printv(f_enum, enum_code, "\n", NIL);
+		 "\n", enum_code, "\n", NIL);
 
 	  Printf(f_enum, "\n");
 	  Delete(f_enum);
@@ -1469,6 +1467,11 @@ public:
       if (!addSymbol(symname, n, scope))
 	return SWIG_ERROR;
       
+      if ((enum_feature == ProperEnum) && parent_name && !unnamedinstance) {
+	if (!GetFlag(n, "firstenumitem"))
+	  Printf(enum_code, ",\n");
+      }
+
       // Translate and write javadoc comment if flagged
       if (doxygen && doxygenTranslator->hasDocumentation(n)) {
 	String *doxygen_comments = doxygenTranslator->getDocumentation(n);
@@ -1481,14 +1484,12 @@ public:
       if ((enum_feature == ProperEnum) && parent_name && !unnamedinstance) {
 	// Wrap (non-anonymous) C/C++ enum with a proper Java enum
 	// Emit the enum item.
-	
 	Printf(enum_code, "  %s", symname);
 	if (Getattr(n, "enumvalue")) {
 	  String *value = enumValue(n);
 	  Printf(enum_code, "(%s)", value);
 	  Delete(value);
 	}
-	Printf(enum_code, ",\n");
       } else {
 	// Wrap C/C++ enums with constant integers or use the typesafe enum pattern
 	SwigType *typemap_lookup_type = parent_name ? parent_name : NewString("enum ");

From 448691cfa8bc408bb7b38aba59ad2d66f5f48579 Mon Sep 17 00:00:00 2001
From: William S Fulton <wsf@fultondesigns.co.uk>
Date: Fri, 25 May 2018 23:18:57 +0100
Subject: [PATCH 303/314] Another merge fix from doxygen branches

---
 Examples/test-suite/python/Makefile.in | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Examples/test-suite/python/Makefile.in b/Examples/test-suite/python/Makefile.in
index b26253329..e2aad7c8b 100644
--- a/Examples/test-suite/python/Makefile.in
+++ b/Examples/test-suite/python/Makefile.in
@@ -167,7 +167,7 @@ convert_testcase = \
 	  $(MAKE) $(SCRIPTDIR)/$(py_runme); \
 	fi
 
-$(SCRIPTDIR)/$(SCRIPTPREFIX)%$(SCRIPTSUFFIX): $(abspath $(srcdir)/$(SCRIPTPREFIX)%$(PY2SCRIPTSUFFIX))
+$(SCRIPTDIR)/$(SCRIPTPREFIX)%$(SCRIPTSUFFIX): $(srcdir)/$(SCRIPTPREFIX)%$(PY2SCRIPTSUFFIX)
 	test x$< = x$@ || cp $< $@ || exit 1
 	test x$(PY3) = x || $(PY2TO3) -w $@ >/dev/null 2>&1 || exit 1
 

From d1e0912ac0397bd0c2be697799069c5a6c581ea5 Mon Sep 17 00:00:00 2001
From: William S Fulton <wsf@fultondesigns.co.uk>
Date: Fri, 25 May 2018 23:35:06 +0100
Subject: [PATCH 304/314] Correct source code headers

---
 Source/DoxygenTranslator/src/DoxygenCommands.h     | 12 ++++++++++++
 Source/DoxygenTranslator/src/DoxygenEntity.cpp     |  4 ++--
 Source/DoxygenTranslator/src/DoxygenEntity.h       |  2 +-
 Source/DoxygenTranslator/src/DoxygenParser.cpp     |  4 ++--
 Source/DoxygenTranslator/src/DoxygenParser.h       |  2 +-
 Source/DoxygenTranslator/src/DoxygenTranslator.cpp |  4 ++--
 Source/DoxygenTranslator/src/DoxygenTranslator.h   |  2 +-
 Source/DoxygenTranslator/src/JavaDocConverter.cpp  |  4 ++--
 Source/DoxygenTranslator/src/JavaDocConverter.h    |  2 +-
 Source/DoxygenTranslator/src/PyDocConverter.cpp    |  4 ++--
 Source/DoxygenTranslator/src/PyDocConverter.h      |  2 +-
 11 files changed, 27 insertions(+), 15 deletions(-)

diff --git a/Source/DoxygenTranslator/src/DoxygenCommands.h b/Source/DoxygenTranslator/src/DoxygenCommands.h
index 0be6a1851..eca148a50 100644
--- a/Source/DoxygenTranslator/src/DoxygenCommands.h
+++ b/Source/DoxygenTranslator/src/DoxygenCommands.h
@@ -1,3 +1,15 @@
+/* -----------------------------------------------------------------------------
+ * This file is part of SWIG, which is licensed as a whole under version 3
+ * (or any later version) of the GNU General Public License. Some additional
+ * terms also apply to certain portions of SWIG. The full details of the SWIG
+ * license and copyrights can be found in the LICENSE and COPYRIGHT files
+ * included with the SWIG source code as distributed by the SWIG developers
+ * and at http://www.swig.org/legal.html.
+ *
+ * DoxygenCommands.h
+ *
+ * Part of the Doxygen comment translation module of SWIG.
+ * ----------------------------------------------------------------------------- */
 
 #ifndef DOXYGENCOMMANDS_H
 #define DOXYGENCOMMANDS_H
diff --git a/Source/DoxygenTranslator/src/DoxygenEntity.cpp b/Source/DoxygenTranslator/src/DoxygenEntity.cpp
index 98329e84f..7e977ee9b 100644
--- a/Source/DoxygenTranslator/src/DoxygenEntity.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenEntity.cpp
@@ -1,5 +1,5 @@
-/* ----------------------------------------------------------------------------- 
- * This file is part of SWIG, which is licensed as a whole under version 3 
+/* -----------------------------------------------------------------------------
+ * This file is part of SWIG, which is licensed as a whole under version 3
  * (or any later version) of the GNU General Public License. Some additional
  * terms also apply to certain portions of SWIG. The full details of the SWIG
  * license and copyrights can be found in the LICENSE and COPYRIGHT files
diff --git a/Source/DoxygenTranslator/src/DoxygenEntity.h b/Source/DoxygenTranslator/src/DoxygenEntity.h
index 29a0e2076..3c243462c 100644
--- a/Source/DoxygenTranslator/src/DoxygenEntity.h
+++ b/Source/DoxygenTranslator/src/DoxygenEntity.h
@@ -1,5 +1,5 @@
 /* -----------------------------------------------------------------------------
- * This file is part of SWIG, which is licensed as a whole under version 3 
+ * This file is part of SWIG, which is licensed as a whole under version 3
  * (or any later version) of the GNU General Public License. Some additional
  * terms also apply to certain portions of SWIG. The full details of the SWIG
  * license and copyrights can be found in the LICENSE and COPYRIGHT files
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.cpp b/Source/DoxygenTranslator/src/DoxygenParser.cpp
index c14cdb9fd..4c7bcdd1c 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenParser.cpp
@@ -1,5 +1,5 @@
-/* ----------------------------------------------------------------------------- 
- * This file is part of SWIG, which is licensed as a whole under version 3 
+/* -----------------------------------------------------------------------------
+ * This file is part of SWIG, which is licensed as a whole under version 3
  * (or any later version) of the GNU General Public License. Some additional
  * terms also apply to certain portions of SWIG. The full details of the SWIG
  * license and copyrights can be found in the LICENSE and COPYRIGHT files
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.h b/Source/DoxygenTranslator/src/DoxygenParser.h
index 35204e670..ec5e24cc2 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.h
+++ b/Source/DoxygenTranslator/src/DoxygenParser.h
@@ -1,5 +1,5 @@
 /* -----------------------------------------------------------------------------
- * This file is part of SWIG, which is licensed as a whole under version 3 
+ * This file is part of SWIG, which is licensed as a whole under version 3
  * (or any later version) of the GNU General Public License. Some additional
  * terms also apply to certain portions of SWIG. The full details of the SWIG
  * license and copyrights can be found in the LICENSE and COPYRIGHT files
diff --git a/Source/DoxygenTranslator/src/DoxygenTranslator.cpp b/Source/DoxygenTranslator/src/DoxygenTranslator.cpp
index 111822660..bd5963973 100644
--- a/Source/DoxygenTranslator/src/DoxygenTranslator.cpp
+++ b/Source/DoxygenTranslator/src/DoxygenTranslator.cpp
@@ -1,5 +1,5 @@
-/* ----------------------------------------------------------------------------- 
- * This file is part of SWIG, which is licensed as a whole under version 3 
+/* -----------------------------------------------------------------------------
+ * This file is part of SWIG, which is licensed as a whole under version 3
  * (or any later version) of the GNU General Public License. Some additional
  * terms also apply to certain portions of SWIG. The full details of the SWIG
  * license and copyrights can be found in the LICENSE and COPYRIGHT files
diff --git a/Source/DoxygenTranslator/src/DoxygenTranslator.h b/Source/DoxygenTranslator/src/DoxygenTranslator.h
index ae7c211ba..35e521898 100644
--- a/Source/DoxygenTranslator/src/DoxygenTranslator.h
+++ b/Source/DoxygenTranslator/src/DoxygenTranslator.h
@@ -1,5 +1,5 @@
 /* -----------------------------------------------------------------------------
- * This file is part of SWIG, which is licensed as a whole under version 3 
+ * This file is part of SWIG, which is licensed as a whole under version 3
  * (or any later version) of the GNU General Public License. Some additional
  * terms also apply to certain portions of SWIG. The full details of the SWIG
  * license and copyrights can be found in the LICENSE and COPYRIGHT files
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.cpp b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
index 90da0eb1a..c2fd8577e 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.cpp
@@ -1,5 +1,5 @@
-/* ----------------------------------------------------------------------------- 
- * This file is part of SWIG, which is licensed as a whole under version 3 
+/* -----------------------------------------------------------------------------
+ * This file is part of SWIG, which is licensed as a whole under version 3
  * (or any later version) of the GNU General Public License. Some additional
  * terms also apply to certain portions of SWIG. The full details of the SWIG
  * license and copyrights can be found in the LICENSE and COPYRIGHT files
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.h b/Source/DoxygenTranslator/src/JavaDocConverter.h
index df579e625..100a77818 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.h
+++ b/Source/DoxygenTranslator/src/JavaDocConverter.h
@@ -1,5 +1,5 @@
 /* -----------------------------------------------------------------------------
- * This file is part of SWIG, which is licensed as a whole under version 3 
+ * This file is part of SWIG, which is licensed as a whole under version 3
  * (or any later version) of the GNU General Public License. Some additional
  * terms also apply to certain portions of SWIG. The full details of the SWIG
  * license and copyrights can be found in the LICENSE and COPYRIGHT files
diff --git a/Source/DoxygenTranslator/src/PyDocConverter.cpp b/Source/DoxygenTranslator/src/PyDocConverter.cpp
index b6aaa2d91..5edf7fa18 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.cpp
+++ b/Source/DoxygenTranslator/src/PyDocConverter.cpp
@@ -1,5 +1,5 @@
-/* ----------------------------------------------------------------------------- 
- * This file is part of SWIG, which is licensed as a whole under version 3 
+/* -----------------------------------------------------------------------------
+ * This file is part of SWIG, which is licensed as a whole under version 3
  * (or any later version) of the GNU General Public License. Some additional
  * terms also apply to certain portions of SWIG. The full details of the SWIG
  * license and copyrights can be found in the LICENSE and COPYRIGHT files
diff --git a/Source/DoxygenTranslator/src/PyDocConverter.h b/Source/DoxygenTranslator/src/PyDocConverter.h
index b78d81ed3..88e8f1f91 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.h
+++ b/Source/DoxygenTranslator/src/PyDocConverter.h
@@ -1,5 +1,5 @@
 /* -----------------------------------------------------------------------------
- * This file is part of SWIG, which is licensed as a whole under version 3 
+ * This file is part of SWIG, which is licensed as a whole under version 3
  * (or any later version) of the GNU General Public License. Some additional
  * terms also apply to certain portions of SWIG. The full details of the SWIG
  * license and copyrights can be found in the LICENSE and COPYRIGHT files

From 823465649714f37b6e929c239542f43d950bea4c Mon Sep 17 00:00:00 2001
From: William S Fulton <wsf@fultondesigns.co.uk>
Date: Fri, 25 May 2018 23:35:28 +0100
Subject: [PATCH 305/314] Correct python example headers

---
 Examples/test-suite/python/doxygen_alias_runme.py              | 2 --
 Examples/test-suite/python/doxygen_basic_notranslate_runme.py  | 2 --
 Examples/test-suite/python/doxygen_basic_translate_runme.py    | 2 --
 Examples/test-suite/python/doxygen_ignore_runme.py             | 2 --
 Examples/test-suite/python/doxygen_misc_constructs_runme.py    | 2 --
 Examples/test-suite/python/doxygen_parsing_runme.py            | 2 --
 Examples/test-suite/python/doxygen_translate_all_tags_runme.py | 2 --
 Examples/test-suite/python/doxygen_translate_links_runme.py    | 2 --
 Examples/test-suite/python/doxygen_translate_runme.py          | 2 --
 9 files changed, 18 deletions(-)

diff --git a/Examples/test-suite/python/doxygen_alias_runme.py b/Examples/test-suite/python/doxygen_alias_runme.py
index ad580f719..505261bcd 100644
--- a/Examples/test-suite/python/doxygen_alias_runme.py
+++ b/Examples/test-suite/python/doxygen_alias_runme.py
@@ -1,5 +1,3 @@
-#!/usr/bin/python
-
 import doxygen_alias
 import inspect
 import comment_verifier
diff --git a/Examples/test-suite/python/doxygen_basic_notranslate_runme.py b/Examples/test-suite/python/doxygen_basic_notranslate_runme.py
index 17c03e32d..81ac99975 100644
--- a/Examples/test-suite/python/doxygen_basic_notranslate_runme.py
+++ b/Examples/test-suite/python/doxygen_basic_notranslate_runme.py
@@ -1,5 +1,3 @@
-#!/usr/bin/python
-
 import doxygen_basic_notranslate
 import inspect
 import string
diff --git a/Examples/test-suite/python/doxygen_basic_translate_runme.py b/Examples/test-suite/python/doxygen_basic_translate_runme.py
index 1be6b6b07..e664e06f6 100644
--- a/Examples/test-suite/python/doxygen_basic_translate_runme.py
+++ b/Examples/test-suite/python/doxygen_basic_translate_runme.py
@@ -1,5 +1,3 @@
-#!/usr/bin/python
-
 import doxygen_basic_translate
 import inspect
 import string
diff --git a/Examples/test-suite/python/doxygen_ignore_runme.py b/Examples/test-suite/python/doxygen_ignore_runme.py
index 33329d2de..9a7b2e5df 100644
--- a/Examples/test-suite/python/doxygen_ignore_runme.py
+++ b/Examples/test-suite/python/doxygen_ignore_runme.py
@@ -1,5 +1,3 @@
-#!/usr/bin/python
-
 import doxygen_ignore
 import inspect
 import comment_verifier
diff --git a/Examples/test-suite/python/doxygen_misc_constructs_runme.py b/Examples/test-suite/python/doxygen_misc_constructs_runme.py
index 32ee912fd..c441c3dfe 100644
--- a/Examples/test-suite/python/doxygen_misc_constructs_runme.py
+++ b/Examples/test-suite/python/doxygen_misc_constructs_runme.py
@@ -1,5 +1,3 @@
-#!/usr/bin/python
-
 import doxygen_misc_constructs
 import inspect
 import string
diff --git a/Examples/test-suite/python/doxygen_parsing_runme.py b/Examples/test-suite/python/doxygen_parsing_runme.py
index 20e840df5..14579281d 100644
--- a/Examples/test-suite/python/doxygen_parsing_runme.py
+++ b/Examples/test-suite/python/doxygen_parsing_runme.py
@@ -1,5 +1,3 @@
-#!/usr/bin/python
-
 import doxygen_parsing
 import inspect
 import string
diff --git a/Examples/test-suite/python/doxygen_translate_all_tags_runme.py b/Examples/test-suite/python/doxygen_translate_all_tags_runme.py
index ed66f4bcd..53d087e69 100644
--- a/Examples/test-suite/python/doxygen_translate_all_tags_runme.py
+++ b/Examples/test-suite/python/doxygen_translate_all_tags_runme.py
@@ -1,5 +1,3 @@
-#!/usr/bin/python
-
 import doxygen_translate_all_tags
 import inspect
 import string
diff --git a/Examples/test-suite/python/doxygen_translate_links_runme.py b/Examples/test-suite/python/doxygen_translate_links_runme.py
index b7e2b73fa..89f276f6e 100644
--- a/Examples/test-suite/python/doxygen_translate_links_runme.py
+++ b/Examples/test-suite/python/doxygen_translate_links_runme.py
@@ -1,5 +1,3 @@
-#!/usr/bin/python
-
 import doxygen_translate_links
 import inspect
 import string
diff --git a/Examples/test-suite/python/doxygen_translate_runme.py b/Examples/test-suite/python/doxygen_translate_runme.py
index cbdde5fec..2d0840a1f 100644
--- a/Examples/test-suite/python/doxygen_translate_runme.py
+++ b/Examples/test-suite/python/doxygen_translate_runme.py
@@ -1,5 +1,3 @@
-#!/usr/bin/python
-
 import doxygen_translate
 import inspect
 import string

From 0ae73a67ff4ceed3a70991fbd05c7f93305f31be Mon Sep 17 00:00:00 2001
From: William S Fulton <wsf@fultondesigns.co.uk>
Date: Fri, 25 May 2018 23:36:24 +0100
Subject: [PATCH 306/314] More merge fixes from doxygen branches

---
 Examples/php/reference/runme-proxy.php4 | 79 ------------------------
 Examples/php/variables/runme.php4.old   | 80 -------------------------
 2 files changed, 159 deletions(-)
 delete mode 100644 Examples/php/reference/runme-proxy.php4
 delete mode 100644 Examples/php/variables/runme.php4.old

diff --git a/Examples/php/reference/runme-proxy.php4 b/Examples/php/reference/runme-proxy.php4
deleted file mode 100644
index 9d216f78b..000000000
--- a/Examples/php/reference/runme-proxy.php4
+++ /dev/null
@@ -1,79 +0,0 @@
-<?php
-
-# This file illustrates the manipulation of C++ references in Php.
-# This uses the low-level interface.  Proxy classes work differently.
-
-require "example.php";
-
-# ----- Object creation -----
-
-print "Creating some objects:\n";
-$a = new Vector(3,4,5);
-$b = new Vector(10,11,12);
-
-print "    Created a: $a " . $a->print() . "\n";
-print "    Created b: $b " . $b->print() . "\n";
-
-# ----- Call an overloaded operator -----
-
-# This calls the wrapper we placed around
-#
-#      operator+(const Vector &a, const Vector &) 
-#
-# It returns a new allocated object.
-
-print "Adding a+b\n";
-$c = addv($a,$b);
-print "    a+b =". $c->print()."\n";
-
-# Note: Unless we free the result, a memory leak will occur
-$c = 0;
-
-# ----- Create a vector array -----
-
-# Note: Using the high-level interface here
-print "Creating an array of vectors\n";
-$va = new VectorArray(10);
-
-print "    va: $va size=".$va->size()."\n";
-
-# ----- Set some values in the array -----
-
-# These operators copy the value of $a and $b to the vector array
-$va->set(0,$a);
-$va->set(1,$b);
-
-$va->get(0);
-# This will work, but it will cause a memory leak!
-
-$va->set(2,addv($a,$b));
-
-# The non-leaky way to do it
-
-$c = addv($a,$b);
-$va->set(3,$c);
-$c = NULL;
-
-# Get some values from the array
-
-print "Getting some array values\n";
-for ($i = 0; $i < 5; $i++) {
-print "do $i\n";
-    $v = $va->get($i);
-    print "    va($i) = ". $v->print(). "\n";
-}
-
-# Watch under resource meter to check on this
-#print "Making sure we don't leak memory.\n";
-#for ($i = 0; $i < 1000000; $i++) {
-#    $c = VectorArray_get($va,$i % 10);
-#}
-
-# ----- Clean up -----
-print "Cleaning up\n";
-# wants fixing FIXME
-#delete_VectorArray($va);
-#delete_Vector($a);
-#delete_Vector($b);
-
-?>
diff --git a/Examples/php/variables/runme.php4.old b/Examples/php/variables/runme.php4.old
deleted file mode 100644
index 9a6bfb386..000000000
--- a/Examples/php/variables/runme.php4.old
+++ /dev/null
@@ -1,80 +0,0 @@
-<?php
-### THIS VERSION was written for when php global vars fakingly mirrored
-### the wrapped global vars, but it was very inefficient.
-### For now we don't do this (pending some changes to php itself) so
-### we use accessor functions instead; WE KEEP THIS version around ready
-### for when those php changes are made and we can switch back.
-### Specifically we want $_GLOBALS variable overloading like object 
-### property overloading
-
-	require "example.php";
-
-	/* Try to set the values of some global variables */
-
-	$ivar = 42;
-	$svar = -31000;
-	$lvar = 65537;
-	$uivar = 123456;
-	$usvar = 61000;
-	$ulvar = 654321;
-	$scvar = -13;
-	$ucvar = 251;
-	$cvar = "S";
-	$fvar = 3.14159;
-	$dvar = 2.1828;
-	$strvar = "Hello World";
-	$cstrvar = "Goodbye";
-	$iptrvar = new_int(37);
-	$ptptr = new_point(37,42);
-	$name = "Bill";
-
-	echo "Variables (values printed from PHP)\n";
-
-	echo "ivar	= $ivar\n";
-	echo "svar	= $svar\n";
-	echo "lvar	= $lvar\n";
-	echo "uivar	= $uivar\n";
-	echo "usvar	= $usvar\n";
-	echo "ulvar	= $ulvar\n";
-	echo "scvar	= $scvar\n";
-	echo "ucvar	= $ucvar\n";
-	echo "cvar	= $cvar\n";
-	echo "fvar	= $fvar\n";
-	echo "dvar	= $dvar\n";
-	echo "strvar	= $strvar\n";
-	echo "cstrvar	= $cstrvar\n";
-	echo "iptrvar	= $iptrvar\n";
-	echo "name	= $name\n";
-	echo "ptptr	= $ptptr" , point_print($ptptr) , "\n";
-	echo "pt	= $pt" , point_print($pt) , "\n";
-
-	echo "\nVariables (values printed from C)\n";
-
-	print_vars();
-
-	echo "\nI'm going to try and update a structure variable.\n";
-
-	$pt = $ptptr;
-
-	echo "The new value is \n";
-
-	pt_print();
-
-	echo "You should see the value", point_print($ptptr), "\n";
-
-	echo "\nNow I'm going to try and modify some read only variables\n";
-
-	echo "Trying to set 'path'\n";
-
-	/* Sadly this works */
-	$path = "Whoa!";
-	echo "Path = $path\n";
-
-	echo "Trying to set 'status'\n";
-
-	/* And this */
-	$status = 0;
-	echo "Status = $status\n";
-
-?>
-

From ac85784a76066870b47ea624ccd155098ec0c4ee Mon Sep 17 00:00:00 2001
From: William S Fulton <wsf@fultondesigns.co.uk>
Date: Sat, 26 May 2018 12:52:52 +0100
Subject: [PATCH 307/314] Doxygen source rename

Source/DoxygenTranslator/src directory is renamed Source/Doxygen
Renamed files in this directory to short names using lowercase as is the
convention for the rest of the SWIG source.
C++ extension is also .cxx like other SWIG source code.

I used doxy as the prefix for most file renames because without this
Doxygen/parser.* would be easily confused with CParse/parser.* so
Doxygen/doxyparser.* is renamed from DoxygenTranslator/src/DoxygenParser.*
---
 Doc/Devel/plan-gsoc-2012.txt                  |  2 +-
 Doc/Manual/Doxygen.html                       |  2 +-
 .../doxycommands.h}                           |  2 +-
 .../doxyentity.cxx}                           |  4 ++--
 .../DoxygenEntity.h => Doxygen/doxyentity.h}  |  2 +-
 .../doxyparser.cxx}                           |  8 +++----
 .../DoxygenParser.h => Doxygen/doxyparser.h}  |  4 ++--
 .../doxytranslator.cxx}                       |  4 ++--
 .../doxytranslator.h}                         |  6 ++---
 .../javadoc.cxx}                              |  8 +++----
 .../JavaDocConverter.h => Doxygen/javadoc.h}  |  4 ++--
 .../PyDocConverter.cpp => Doxygen/pydoc.cxx}  |  6 ++---
 .../src/PyDocConverter.h => Doxygen/pydoc.h}  |  6 ++---
 Source/Makefile.am                            | 24 +++++++++----------
 Source/Modules/java.cxx                       |  2 +-
 Source/Modules/python.cxx                     |  2 +-
 16 files changed, 43 insertions(+), 43 deletions(-)
 rename Source/{DoxygenTranslator/src/DoxygenCommands.h => Doxygen/doxycommands.h} (99%)
 rename Source/{DoxygenTranslator/src/DoxygenEntity.cpp => Doxygen/doxyentity.cxx} (97%)
 rename Source/{DoxygenTranslator/src/DoxygenEntity.h => Doxygen/doxyentity.h} (98%)
 rename Source/{DoxygenTranslator/src/DoxygenParser.cpp => Doxygen/doxyparser.cxx} (99%)
 rename Source/{DoxygenTranslator/src/DoxygenParser.h => Doxygen/doxyparser.h} (99%)
 rename Source/{DoxygenTranslator/src/DoxygenTranslator.cpp => Doxygen/doxytranslator.cxx} (96%)
 rename Source/{DoxygenTranslator/src/DoxygenTranslator.h => Doxygen/doxytranslator.h} (96%)
 rename Source/{DoxygenTranslator/src/JavaDocConverter.cpp => Doxygen/javadoc.cxx} (99%)
 rename Source/{DoxygenTranslator/src/JavaDocConverter.h => Doxygen/javadoc.h} (99%)
 rename Source/{DoxygenTranslator/src/PyDocConverter.cpp => Doxygen/pydoc.cxx} (99%)
 rename Source/{DoxygenTranslator/src/PyDocConverter.h => Doxygen/pydoc.h} (98%)

diff --git a/Doc/Devel/plan-gsoc-2012.txt b/Doc/Devel/plan-gsoc-2012.txt
index 51d387d3c..ac764fb2a 100644
--- a/Doc/Devel/plan-gsoc-2012.txt
+++ b/Doc/Devel/plan-gsoc-2012.txt
@@ -321,7 +321,7 @@ make doxygen_tricky_constructs.cpptest -s
 Refactoring
 ===========
 
-All the code in directory _DoxygenTranslator_ should be refactored:
+All the code in directory _Doxygen_ should be refactored:
 -OK- all methods should be class members
 -OK- most static methods should be normal members
 -OK- replace C arrays of strings and sequential searches with STL data
diff --git a/Doc/Manual/Doxygen.html b/Doc/Manual/Doxygen.html
index 08d1aef94..842f146d8 100644
--- a/Doc/Manual/Doxygen.html
+++ b/Doc/Manual/Doxygen.html
@@ -1741,7 +1741,7 @@ Searching for "doxygen" in the java.cxx module can give you a good idea of the p
 The basic gist is that anywhere a comment may reside on a node, there needs to be a catch for it in front of where that function, class, or other object is written out to a target language file.
 The other half of extension is building a target documentation language comment generator that handles one blob at a time.
 However, this is relatively simple and nowhere near as complex as the wrapper generating modules in SWIG.
-See DoxygenTranslator/JavaDocConverter.cpp for a good example.
+See Source/Doxygen/javadoc.cxx for a good example.
 The target language module passes the Doxygen Translator the blob to translate, and receives back the translated text.
 </p>
 <p>
diff --git a/Source/DoxygenTranslator/src/DoxygenCommands.h b/Source/Doxygen/doxycommands.h
similarity index 99%
rename from Source/DoxygenTranslator/src/DoxygenCommands.h
rename to Source/Doxygen/doxycommands.h
index eca148a50..1f7b5fa5b 100644
--- a/Source/DoxygenTranslator/src/DoxygenCommands.h
+++ b/Source/Doxygen/doxycommands.h
@@ -6,7 +6,7 @@
  * included with the SWIG source code as distributed by the SWIG developers
  * and at http://www.swig.org/legal.html.
  *
- * DoxygenCommands.h
+ * doxycommands.h
  *
  * Part of the Doxygen comment translation module of SWIG.
  * ----------------------------------------------------------------------------- */
diff --git a/Source/DoxygenTranslator/src/DoxygenEntity.cpp b/Source/Doxygen/doxyentity.cxx
similarity index 97%
rename from Source/DoxygenTranslator/src/DoxygenEntity.cpp
rename to Source/Doxygen/doxyentity.cxx
index 7e977ee9b..8b9f65736 100644
--- a/Source/DoxygenTranslator/src/DoxygenEntity.cpp
+++ b/Source/Doxygen/doxyentity.cxx
@@ -6,12 +6,12 @@
  * included with the SWIG source code as distributed by the SWIG developers
  * and at http://www.swig.org/legal.html.
  *
- * DoxygenEntity.cpp
+ * doxyentity.cxx
  *
  * Part of the Doxygen comment translation module of SWIG.
  * ----------------------------------------------------------------------------- */
 
-#include "DoxygenEntity.h"
+#include "doxyentity.h"
 #include <iostream>
 
 using std::cout;
diff --git a/Source/DoxygenTranslator/src/DoxygenEntity.h b/Source/Doxygen/doxyentity.h
similarity index 98%
rename from Source/DoxygenTranslator/src/DoxygenEntity.h
rename to Source/Doxygen/doxyentity.h
index 3c243462c..93737e604 100644
--- a/Source/DoxygenTranslator/src/DoxygenEntity.h
+++ b/Source/Doxygen/doxyentity.h
@@ -6,7 +6,7 @@
  * included with the SWIG source code as distributed by the SWIG developers
  * and at http://www.swig.org/legal.html.
  *
- * DoxygenEntity.h
+ * doxyentity.h
  *
  * Part of the Doxygen comment translation module of SWIG.
  * ----------------------------------------------------------------------------- */
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.cpp b/Source/Doxygen/doxyparser.cxx
similarity index 99%
rename from Source/DoxygenTranslator/src/DoxygenParser.cpp
rename to Source/Doxygen/doxyparser.cxx
index 4c7bcdd1c..558b0401f 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.cpp
+++ b/Source/Doxygen/doxyparser.cxx
@@ -6,11 +6,11 @@
  * included with the SWIG source code as distributed by the SWIG developers
  * and at http://www.swig.org/legal.html.
  *
- * DoxygenParser.cpp
+ * doxyparser.cxx
  * ----------------------------------------------------------------------------- */
 
-#include "DoxygenParser.h"
-#include "DoxygenCommands.h"
+#include "doxyparser.h"
+#include "doxycommands.h"
 #include "swig.h"
 #include "swigwarn.h"
 
@@ -46,7 +46,7 @@ void DoxygenParser::fillTables() {
   if (doxygenCommands.size())
     return;
 
-  // fill in tables with data from DoxygenCommands.h
+  // fill in tables with data from doxycommands.h
   for (int i = 0; i < simpleCommandsSize; i++)
     doxygenCommands[simpleCommands[i]] = SIMPLECOMMAND;
 
diff --git a/Source/DoxygenTranslator/src/DoxygenParser.h b/Source/Doxygen/doxyparser.h
similarity index 99%
rename from Source/DoxygenTranslator/src/DoxygenParser.h
rename to Source/Doxygen/doxyparser.h
index ec5e24cc2..96c71d22f 100644
--- a/Source/DoxygenTranslator/src/DoxygenParser.h
+++ b/Source/Doxygen/doxyparser.h
@@ -6,7 +6,7 @@
  * included with the SWIG source code as distributed by the SWIG developers
  * and at http://www.swig.org/legal.html.
  *
- * DoxygenParser.h
+ * doxyparser.h
  * ----------------------------------------------------------------------------- */
 
 #ifndef DOXYGENPARSER_H_
@@ -19,7 +19,7 @@
 
 #include "swig.h"
 
-#include "DoxygenEntity.h"
+#include "doxyentity.h"
 
 class DoxygenParser {
 private:
diff --git a/Source/DoxygenTranslator/src/DoxygenTranslator.cpp b/Source/Doxygen/doxytranslator.cxx
similarity index 96%
rename from Source/DoxygenTranslator/src/DoxygenTranslator.cpp
rename to Source/Doxygen/doxytranslator.cxx
index bd5963973..2684adcea 100644
--- a/Source/DoxygenTranslator/src/DoxygenTranslator.cpp
+++ b/Source/Doxygen/doxytranslator.cxx
@@ -6,13 +6,13 @@
  * included with the SWIG source code as distributed by the SWIG developers
  * and at http://www.swig.org/legal.html.
  *
- * DoxygenTranslator.cpp
+ * doxytranslator.cxx
  *
  * Module to return documentation for nodes formatted for various documentation
  * systems.
  * ----------------------------------------------------------------------------- */
 
-#include "DoxygenTranslator.h"
+#include "doxytranslator.h"
 
 DoxygenTranslator::DoxygenTranslator(int flags) : m_flags(flags), parser((flags &debug_parser) != 0) {
 }
diff --git a/Source/DoxygenTranslator/src/DoxygenTranslator.h b/Source/Doxygen/doxytranslator.h
similarity index 96%
rename from Source/DoxygenTranslator/src/DoxygenTranslator.h
rename to Source/Doxygen/doxytranslator.h
index 35e521898..ffc378a7b 100644
--- a/Source/DoxygenTranslator/src/DoxygenTranslator.h
+++ b/Source/Doxygen/doxytranslator.h
@@ -6,7 +6,7 @@
  * included with the SWIG source code as distributed by the SWIG developers
  * and at http://www.swig.org/legal.html.
  *
- * DoxygenTranslator.h
+ * doxytranslator.h
  *
  * Module to return documentation for nodes formatted for various documentation
  * systems.
@@ -16,8 +16,8 @@
 #define DOXYGENTRANSLATOR_H_
 
 #include "swig.h"
-#include "DoxygenEntity.h"
-#include "DoxygenParser.h"
+#include "doxyentity.h"
+#include "doxyparser.h"
 #include <list>
 #include <string>
 
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.cpp b/Source/Doxygen/javadoc.cxx
similarity index 99%
rename from Source/DoxygenTranslator/src/JavaDocConverter.cpp
rename to Source/Doxygen/javadoc.cxx
index c2fd8577e..3b81c55a5 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.cpp
+++ b/Source/Doxygen/javadoc.cxx
@@ -6,15 +6,15 @@
  * included with the SWIG source code as distributed by the SWIG developers
  * and at http://www.swig.org/legal.html.
  *
- * JavaDocConverter.cpp
+ * javadoc.cxx
  * ----------------------------------------------------------------------------- */
 
-#include "JavaDocConverter.h"
-#include "DoxygenParser.h"
+#include "javadoc.h"
+#include "doxyparser.h"
 #include <iostream>
 #include <vector>
 #include <list>
-#include "../../Modules/swigmod.h"
+#include "swigmod.h"
 #define APPROX_LINE_LENGTH 64   // characters per line allowed
 #define TAB_SIZE 8              // current tab size in spaces
 //TODO {@link} {@linkplain} {@docRoot}, and other useful doxy commands that are not a javadoc tag
diff --git a/Source/DoxygenTranslator/src/JavaDocConverter.h b/Source/Doxygen/javadoc.h
similarity index 99%
rename from Source/DoxygenTranslator/src/JavaDocConverter.h
rename to Source/Doxygen/javadoc.h
index 100a77818..6feff5295 100644
--- a/Source/DoxygenTranslator/src/JavaDocConverter.h
+++ b/Source/Doxygen/javadoc.h
@@ -6,7 +6,7 @@
  * included with the SWIG source code as distributed by the SWIG developers
  * and at http://www.swig.org/legal.html.
  *
- * JavaDocConverter.h
+ * javadoc.h
  *
  * Module to return documentation for nodes formatted for JavaDoc
  * ----------------------------------------------------------------------------- */
@@ -14,7 +14,7 @@
 #ifndef JAVADOCCONVERTER_H_
 #define JAVADOCCONVERTER_H_
 
-#include "DoxygenTranslator.h"
+#include "doxytranslator.h"
 #include <map>
 
 /*
diff --git a/Source/DoxygenTranslator/src/PyDocConverter.cpp b/Source/Doxygen/pydoc.cxx
similarity index 99%
rename from Source/DoxygenTranslator/src/PyDocConverter.cpp
rename to Source/Doxygen/pydoc.cxx
index 5edf7fa18..0f8484d6b 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.cpp
+++ b/Source/Doxygen/pydoc.cxx
@@ -6,13 +6,13 @@
  * included with the SWIG source code as distributed by the SWIG developers
  * and at http://www.swig.org/legal.html.
  *
- * PyDocConverter.cpp
+ * pydoc.cxx
  *
  * Module to return documentation for nodes formatted for PyDoc
  * ----------------------------------------------------------------------------- */
 
-#include "PyDocConverter.h"
-#include "DoxygenParser.h"
+#include "pydoc.h"
+#include "doxyparser.h"
 #include <sstream>
 #include <string>
 #include <vector>
diff --git a/Source/DoxygenTranslator/src/PyDocConverter.h b/Source/Doxygen/pydoc.h
similarity index 98%
rename from Source/DoxygenTranslator/src/PyDocConverter.h
rename to Source/Doxygen/pydoc.h
index 88e8f1f91..8f432fd18 100644
--- a/Source/DoxygenTranslator/src/PyDocConverter.h
+++ b/Source/Doxygen/pydoc.h
@@ -6,7 +6,7 @@
  * included with the SWIG source code as distributed by the SWIG developers
  * and at http://www.swig.org/legal.html.
  *
- * PyDocConverter.h
+ * pydoc.h
  *
  * Module to return documentation for nodes formatted for PyDoc
  * ----------------------------------------------------------------------------- */
@@ -17,8 +17,8 @@
 #include <list>
 #include <string>
 #include "swig.h"
-#include "DoxygenEntity.h"
-#include "DoxygenTranslator.h"
+#include "doxyentity.h"
+#include "doxytranslator.h"
 
 #define DOC_STRING_LENGTH         64 // characters per line allowed
 #define DOC_PARAM_STRING_LENGTH   30 // characters reserved for param name / type
diff --git a/Source/Makefile.am b/Source/Makefile.am
index b1d6359b0..df3d4b75f 100644
--- a/Source/Makefile.am
+++ b/Source/Makefile.am
@@ -34,6 +34,16 @@ eswig_SOURCES =	CParse/cscanner.c		\
 		DOH/memory.c			\
 		DOH/string.c			\
 		DOH/void.c			\
+		Doxygen/doxyentity.cxx		\
+		Doxygen/doxyentity.h		\
+		Doxygen/doxyparser.cxx		\
+		Doxygen/doxyparser.h		\
+		Doxygen/doxytranslator.cxx	\
+		Doxygen/doxytranslator.h	\
+		Doxygen/javadoc.cxx		\
+		Doxygen/javadoc.h		\
+		Doxygen/pydoc.cxx		\
+		Doxygen/pydoc.h			\
 		Modules/allegrocl.cxx		\
 		Modules/allocate.cxx		\
 		Modules/browser.cxx		\
@@ -91,20 +101,10 @@ eswig_SOURCES =	CParse/cscanner.c		\
 		Swig/stype.c			\
 		Swig/symbol.c			\
 		Swig/tree.c			\
-		Swig/typeobj.c			\
 		Swig/typemap.c			\
+		Swig/typeobj.c			\
 		Swig/typesys.c			\
-		Swig/wrapfunc.c			\
-		DoxygenTranslator/src/DoxygenEntity.h\
-		DoxygenTranslator/src/DoxygenEntity.cpp\
-		DoxygenTranslator/src/DoxygenParser.h\
-		DoxygenTranslator/src/DoxygenParser.cpp\
-		DoxygenTranslator/src/DoxygenTranslator.h\
-		DoxygenTranslator/src/DoxygenTranslator.cpp\
-		DoxygenTranslator/src/JavaDocConverter.h\
-		DoxygenTranslator/src/JavaDocConverter.cpp\
-		DoxygenTranslator/src/PyDocConverter.h\
-		DoxygenTranslator/src/PyDocConverter.cpp
+		Swig/wrapfunc.c
 
 bin_PROGRAMS = eswig
 eswig_LDADD   = @SWIGLIBS@
diff --git a/Source/Modules/java.cxx b/Source/Modules/java.cxx
index 7a4bc8214..12da307cf 100644
--- a/Source/Modules/java.cxx
+++ b/Source/Modules/java.cxx
@@ -15,7 +15,7 @@
 #include <limits.h>		// for INT_MAX
 #include "cparse.h"
 #include <ctype.h>
-#include "../DoxygenTranslator/src/JavaDocConverter.h"
+#include "../Doxygen/javadoc.h"
 
 /* Hash type used for upcalls from C/C++ */
 typedef DOH UpcallData;
diff --git a/Source/Modules/python.cxx b/Source/Modules/python.cxx
index 036124837..79edb6532 100644
--- a/Source/Modules/python.cxx
+++ b/Source/Modules/python.cxx
@@ -17,7 +17,7 @@
 #include <ctype.h>
 #include <errno.h>
 #include <stdlib.h>
-#include "../DoxygenTranslator/src/PyDocConverter.h"
+#include "../Doxygen/pydoc.h"
 
 #include <iostream>
 #include <stdint.h>

From ec2cb809cd57b26ad2468894d7266c2ff7ddadc1 Mon Sep 17 00:00:00 2001
From: William S Fulton <wsf@fultondesigns.co.uk>
Date: Tue, 29 May 2018 06:59:26 +0100
Subject: [PATCH 308/314] Add Doxygen to include paths

---
 Source/Makefile.am        | 1 +
 Source/Modules/java.cxx   | 2 +-
 Source/Modules/python.cxx | 2 +-
 3 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/Source/Makefile.am b/Source/Makefile.am
index df3d4b75f..845fc33fd 100644
--- a/Source/Makefile.am
+++ b/Source/Makefile.am
@@ -13,6 +13,7 @@ AM_CPPFLAGS =	-I$(BUILD_SOURCE_DIR)/Include	\
 		-I$(SOURCE_DIR)/Include		\
 		-I$(SOURCE_DIR)/DOH		\
 		-I$(SOURCE_DIR)/CParse		\
+		-I$(SOURCE_DIR)/Doxygen		\
 		-I$(SOURCE_DIR)/Preprocessor	\
 		-I$(SOURCE_DIR)/Swig		\
 		-I$(SOURCE_DIR)/Modules
diff --git a/Source/Modules/java.cxx b/Source/Modules/java.cxx
index 12da307cf..0d42ba7d5 100644
--- a/Source/Modules/java.cxx
+++ b/Source/Modules/java.cxx
@@ -15,7 +15,7 @@
 #include <limits.h>		// for INT_MAX
 #include "cparse.h"
 #include <ctype.h>
-#include "../Doxygen/javadoc.h"
+#include "javadoc.h"
 
 /* Hash type used for upcalls from C/C++ */
 typedef DOH UpcallData;
diff --git a/Source/Modules/python.cxx b/Source/Modules/python.cxx
index 79edb6532..fae1f66e1 100644
--- a/Source/Modules/python.cxx
+++ b/Source/Modules/python.cxx
@@ -17,7 +17,7 @@
 #include <ctype.h>
 #include <errno.h>
 #include <stdlib.h>
-#include "../Doxygen/pydoc.h"
+#include "pydoc.h"
 
 #include <iostream>
 #include <stdint.h>

From 12e7926ee29d8749545bd2b5a17e5eda72f7ab14 Mon Sep 17 00:00:00 2001
From: William S Fulton <wsf@fultondesigns.co.uk>
Date: Thu, 31 May 2018 20:13:52 +0100
Subject: [PATCH 309/314] Doxygen example

Replace the unnecessarily large number of doxygen examples with one
doxygen example.
---
 .../doxygencomments/java/callback/Makefile    |  18 --
 .../doxygencomments/java/callback/example.cxx |   4 -
 .../doxygencomments/java/callback/example.h   |  27 ---
 .../doxygencomments/java/callback/example.i   |  14 --
 .../doxygencomments/java/callback/index.html  |  20 --
 .../doxygencomments/java/callback/main.java   |  56 -----
 Examples/doxygencomments/java/check.list      |  15 --
 Examples/doxygencomments/java/class/Makefile  |  18 --
 .../doxygencomments/java/class/example.cxx    |  28 ---
 Examples/doxygencomments/java/class/example.h |  51 -----
 Examples/doxygencomments/java/class/example.i |  10 -
 .../doxygencomments/java/class/index.html     | 197 ------------------
 Examples/doxygencomments/java/class/main.java |  70 -------
 .../doxygencomments/java/constants/Makefile   |  18 --
 .../doxygencomments/java/constants/example.i  |  30 ---
 .../doxygencomments/java/constants/index.html |  52 -----
 .../doxygencomments/java/constants/main.java  |  44 ----
 Examples/doxygencomments/java/enum/Makefile   |  18 --
 .../doxygencomments/java/enum/example.cxx     |  37 ----
 Examples/doxygencomments/java/enum/example.h  |  23 --
 Examples/doxygencomments/java/enum/example.i  |  14 --
 Examples/doxygencomments/java/enum/index.html |  29 ---
 Examples/doxygencomments/java/enum/main.java  |  38 ----
 Examples/doxygencomments/java/extend/Makefile |  18 --
 .../doxygencomments/java/extend/example.cxx   |   4 -
 .../doxygencomments/java/extend/example.h     |  67 ------
 .../doxygencomments/java/extend/example.i     |  15 --
 .../doxygencomments/java/extend/index.html    |  19 --
 .../doxygencomments/java/extend/main.java     |  88 --------
 .../doxygencomments/java/funcptr/Makefile     |  18 --
 .../doxygencomments/java/funcptr/example.c    |  19 --
 .../doxygencomments/java/funcptr/example.h    |  10 -
 .../doxygencomments/java/funcptr/example.i    |  16 --
 .../doxygencomments/java/funcptr/index.html   |  91 --------
 .../doxygencomments/java/funcptr/main.java    |  33 ---
 Examples/doxygencomments/java/index.html      |  65 ------
 .../doxygencomments/java/multimap/Makefile    |  18 --
 .../doxygencomments/java/multimap/example.c   |  53 -----
 .../doxygencomments/java/multimap/example.dsp | 158 --------------
 .../doxygencomments/java/multimap/example.i   | 109 ----------
 .../doxygencomments/java/multimap/main.java   |  40 ----
 Examples/doxygencomments/java/native/Makefile |  18 --
 .../doxygencomments/java/native/example.i     |  67 ------
 .../doxygencomments/java/native/index.html    |  33 ---
 .../doxygencomments/java/native/main.java     |  19 --
 .../doxygencomments/java/pointer/Makefile     |  18 --
 .../doxygencomments/java/pointer/example.c    |  16 --
 .../doxygencomments/java/pointer/example.i    |  38 ----
 .../doxygencomments/java/pointer/index.html   | 165 ---------------
 .../doxygencomments/java/pointer/main.java    |  55 -----
 .../doxygencomments/java/reference/Makefile   |  18 --
 .../java/reference/example.cxx                |  46 ----
 .../doxygencomments/java/reference/example.h  |  26 ---
 .../doxygencomments/java/reference/example.i  |  58 ------
 .../doxygencomments/java/reference/index.html | 147 -------------
 .../doxygencomments/java/reference/main.java  |  79 -------
 Examples/doxygencomments/java/simple/Makefile |  18 --
 .../doxygencomments/java/simple/example.c     |  18 --
 .../doxygencomments/java/simple/example.dsp   | 158 --------------
 .../doxygencomments/java/simple/example.i     |  11 -
 .../doxygencomments/java/simple/index.html    | 108 ----------
 .../doxygencomments/java/simple/main.java     |  32 ---
 .../doxygencomments/java/template/Makefile    |  18 --
 .../doxygencomments/java/template/example.h   |  39 ----
 .../doxygencomments/java/template/example.i   |  17 --
 .../doxygencomments/java/template/index.html  | 102 ---------
 .../doxygencomments/java/template/main.java   |  45 ----
 .../doxygencomments/java/typemap/Makefile     |  18 --
 .../doxygencomments/java/typemap/example.i    | 101 ---------
 .../doxygencomments/java/typemap/index.html   |  32 ---
 .../doxygencomments/java/typemap/main.java    |  26 ---
 .../doxygencomments/java/variables/Makefile   |  18 --
 .../doxygencomments/java/variables/example.c  |  91 --------
 .../doxygencomments/java/variables/example.h  |   6 -
 .../doxygencomments/java/variables/example.i  |  57 -----
 .../doxygencomments/java/variables/index.html |  85 --------
 .../doxygencomments/java/variables/main.java  |  97 ---------
 Examples/java/check.list                      |   1 +
 Examples/java/doxygen/Makefile                |  21 ++
 Examples/java/doxygen/example.cxx             |  48 +++++
 .../java/class => java/doxygen}/example.dsp   |   4 +-
 Examples/java/doxygen/example.h               | 107 ++++++++++
 Examples/java/doxygen/example.i               |  17 ++
 Examples/java/doxygen/runme.java              |  63 ++++++
 84 files changed, 259 insertions(+), 3574 deletions(-)
 delete mode 100644 Examples/doxygencomments/java/callback/Makefile
 delete mode 100644 Examples/doxygencomments/java/callback/example.cxx
 delete mode 100644 Examples/doxygencomments/java/callback/example.h
 delete mode 100644 Examples/doxygencomments/java/callback/example.i
 delete mode 100644 Examples/doxygencomments/java/callback/index.html
 delete mode 100644 Examples/doxygencomments/java/callback/main.java
 delete mode 100644 Examples/doxygencomments/java/check.list
 delete mode 100644 Examples/doxygencomments/java/class/Makefile
 delete mode 100644 Examples/doxygencomments/java/class/example.cxx
 delete mode 100644 Examples/doxygencomments/java/class/example.h
 delete mode 100644 Examples/doxygencomments/java/class/example.i
 delete mode 100644 Examples/doxygencomments/java/class/index.html
 delete mode 100644 Examples/doxygencomments/java/class/main.java
 delete mode 100644 Examples/doxygencomments/java/constants/Makefile
 delete mode 100644 Examples/doxygencomments/java/constants/example.i
 delete mode 100644 Examples/doxygencomments/java/constants/index.html
 delete mode 100644 Examples/doxygencomments/java/constants/main.java
 delete mode 100644 Examples/doxygencomments/java/enum/Makefile
 delete mode 100644 Examples/doxygencomments/java/enum/example.cxx
 delete mode 100644 Examples/doxygencomments/java/enum/example.h
 delete mode 100644 Examples/doxygencomments/java/enum/example.i
 delete mode 100644 Examples/doxygencomments/java/enum/index.html
 delete mode 100644 Examples/doxygencomments/java/enum/main.java
 delete mode 100644 Examples/doxygencomments/java/extend/Makefile
 delete mode 100644 Examples/doxygencomments/java/extend/example.cxx
 delete mode 100644 Examples/doxygencomments/java/extend/example.h
 delete mode 100644 Examples/doxygencomments/java/extend/example.i
 delete mode 100644 Examples/doxygencomments/java/extend/index.html
 delete mode 100644 Examples/doxygencomments/java/extend/main.java
 delete mode 100644 Examples/doxygencomments/java/funcptr/Makefile
 delete mode 100644 Examples/doxygencomments/java/funcptr/example.c
 delete mode 100644 Examples/doxygencomments/java/funcptr/example.h
 delete mode 100644 Examples/doxygencomments/java/funcptr/example.i
 delete mode 100644 Examples/doxygencomments/java/funcptr/index.html
 delete mode 100644 Examples/doxygencomments/java/funcptr/main.java
 delete mode 100644 Examples/doxygencomments/java/index.html
 delete mode 100644 Examples/doxygencomments/java/multimap/Makefile
 delete mode 100644 Examples/doxygencomments/java/multimap/example.c
 delete mode 100644 Examples/doxygencomments/java/multimap/example.dsp
 delete mode 100644 Examples/doxygencomments/java/multimap/example.i
 delete mode 100644 Examples/doxygencomments/java/multimap/main.java
 delete mode 100644 Examples/doxygencomments/java/native/Makefile
 delete mode 100644 Examples/doxygencomments/java/native/example.i
 delete mode 100644 Examples/doxygencomments/java/native/index.html
 delete mode 100644 Examples/doxygencomments/java/native/main.java
 delete mode 100644 Examples/doxygencomments/java/pointer/Makefile
 delete mode 100644 Examples/doxygencomments/java/pointer/example.c
 delete mode 100644 Examples/doxygencomments/java/pointer/example.i
 delete mode 100644 Examples/doxygencomments/java/pointer/index.html
 delete mode 100644 Examples/doxygencomments/java/pointer/main.java
 delete mode 100644 Examples/doxygencomments/java/reference/Makefile
 delete mode 100644 Examples/doxygencomments/java/reference/example.cxx
 delete mode 100644 Examples/doxygencomments/java/reference/example.h
 delete mode 100644 Examples/doxygencomments/java/reference/example.i
 delete mode 100644 Examples/doxygencomments/java/reference/index.html
 delete mode 100644 Examples/doxygencomments/java/reference/main.java
 delete mode 100644 Examples/doxygencomments/java/simple/Makefile
 delete mode 100644 Examples/doxygencomments/java/simple/example.c
 delete mode 100644 Examples/doxygencomments/java/simple/example.dsp
 delete mode 100644 Examples/doxygencomments/java/simple/example.i
 delete mode 100644 Examples/doxygencomments/java/simple/index.html
 delete mode 100644 Examples/doxygencomments/java/simple/main.java
 delete mode 100644 Examples/doxygencomments/java/template/Makefile
 delete mode 100644 Examples/doxygencomments/java/template/example.h
 delete mode 100644 Examples/doxygencomments/java/template/example.i
 delete mode 100644 Examples/doxygencomments/java/template/index.html
 delete mode 100644 Examples/doxygencomments/java/template/main.java
 delete mode 100644 Examples/doxygencomments/java/typemap/Makefile
 delete mode 100644 Examples/doxygencomments/java/typemap/example.i
 delete mode 100644 Examples/doxygencomments/java/typemap/index.html
 delete mode 100644 Examples/doxygencomments/java/typemap/main.java
 delete mode 100644 Examples/doxygencomments/java/variables/Makefile
 delete mode 100644 Examples/doxygencomments/java/variables/example.c
 delete mode 100644 Examples/doxygencomments/java/variables/example.h
 delete mode 100644 Examples/doxygencomments/java/variables/example.i
 delete mode 100644 Examples/doxygencomments/java/variables/index.html
 delete mode 100644 Examples/doxygencomments/java/variables/main.java
 create mode 100644 Examples/java/doxygen/Makefile
 create mode 100644 Examples/java/doxygen/example.cxx
 rename Examples/{doxygencomments/java/class => java/doxygen}/example.dsp (95%)
 create mode 100644 Examples/java/doxygen/example.h
 create mode 100644 Examples/java/doxygen/example.i
 create mode 100644 Examples/java/doxygen/runme.java

diff --git a/Examples/doxygencomments/java/callback/Makefile b/Examples/doxygencomments/java/callback/Makefile
deleted file mode 100644
index 14c301703..000000000
--- a/Examples/doxygencomments/java/callback/Makefile
+++ /dev/null
@@ -1,18 +0,0 @@
-TOP        = ../..
-SWIG       = $(TOP)/../preinst-swig
-CXXSRCS    = example.cxx
-TARGET     = example
-INTERFACE  = example.i
-SWIGOPT    =
-
-all::	java
-
-java::
-	$(MAKE) -f $(TOP)/Makefile CXXSRCS='$(CXXSRCS)' SWIG='$(SWIG)' \
-	SWIGOPT='$(SWIGOPT)' TARGET='$(TARGET)' INTERFACE='$(INTERFACE)' java_cpp
-	javac *.java
-
-clean::
-	$(MAKE) -f $(TOP)/Makefile java_clean
-
-check: all
diff --git a/Examples/doxygencomments/java/callback/example.cxx b/Examples/doxygencomments/java/callback/example.cxx
deleted file mode 100644
index 450d75608..000000000
--- a/Examples/doxygencomments/java/callback/example.cxx
+++ /dev/null
@@ -1,4 +0,0 @@
-/* File : example.cxx */
-
-#include "example.h"
-
diff --git a/Examples/doxygencomments/java/callback/example.h b/Examples/doxygencomments/java/callback/example.h
deleted file mode 100644
index a0c5fc4d2..000000000
--- a/Examples/doxygencomments/java/callback/example.h
+++ /dev/null
@@ -1,27 +0,0 @@
-/* File : example.h */
-
-#include <cstdio>
-#include <iostream>
-
-/*! Let's document class CALLBACK! 
- /author Alfred
- */
-class Callback {
-public:
-	/** Information about Callback */
-	virtual ~Callback() { std::cout << "Callback::~Callback()" << std:: endl; }
-	virtual void run() { std::cout << "Callback::run()" << std::endl; }
-};
-
-/** Let's document class Caller! */
-class Caller {
-private:
-	Callback *_callback;
-public:
-	Caller(): _callback(0) {}
-	~Caller() { delCallback(); }/**< Deletes Callback */
-	void delCallback() { delete _callback; _callback = 0; }
-	void setCallback(Callback *cb) { delCallback(); _callback = cb; }
-	void call() { if (_callback) _callback->run(); }
-};
-
diff --git a/Examples/doxygencomments/java/callback/example.i b/Examples/doxygencomments/java/callback/example.i
deleted file mode 100644
index 5dae4e7c1..000000000
--- a/Examples/doxygencomments/java/callback/example.i
+++ /dev/null
@@ -1,14 +0,0 @@
-/* File : example.i */
-/** Let's document module Example! */
-%module(directors="1") example
-%{
-#include "example.h"
-%}
-
-%include "std_string.i"
-
-/* turn on director wrapping Callback */
-%feature("director") Callback;
-
-%include "example.h"
-
diff --git a/Examples/doxygencomments/java/callback/index.html b/Examples/doxygencomments/java/callback/index.html
deleted file mode 100644
index c25452018..000000000
--- a/Examples/doxygencomments/java/callback/index.html
+++ /dev/null
@@ -1,20 +0,0 @@
-<html>
-<head>
-<title>SWIG:Examples:java:callback</title>
-</head>
-
-<body bgcolor="#ffffff">
-
-
-<tt>SWIG/Examples/python/extend/</tt>
-<hr>
-
-<H2>Implementing C++ callbacks in Java</H2>
-
-<p>
-This example illustrates how to use directors to implement C++ callbacks in Java.
-</p>
-
-<hr>
-</body>
-</html>
diff --git a/Examples/doxygencomments/java/callback/main.java b/Examples/doxygencomments/java/callback/main.java
deleted file mode 100644
index 4800f8cc9..000000000
--- a/Examples/doxygencomments/java/callback/main.java
+++ /dev/null
@@ -1,56 +0,0 @@
-public class main
-{
-  static {
-    try {
-        System.loadLibrary("example");
-    } catch (UnsatisfiedLinkError e) {
-      System.err.println("Native code library failed to load. See the chapter on Dynamic Linking Problems in the SWIG Java documentation for help.\n" + e);
-      System.exit(1);
-    }
-  }
-
-  public static void main(String[] args)
-  {
-    System.out.println("Adding and calling a normal C++ callback");
-    System.out.println("----------------------------------------");
-
-    Caller              caller = new Caller();
-    Callback            callback = new Callback();
-    
-    caller.setCallback(callback);
-    caller.call();
-    caller.delCallback();
-
-    callback = new JavaCallback();
-
-    System.out.println();
-    System.out.println("Adding and calling a Java callback");
-    System.out.println("------------------------------------");
-
-    caller.setCallback(callback);
-    caller.call();
-    caller.delCallback();
-
-    // Test that a double delete does not occur as the object has already been deleted from the C++ layer.
-    // Note that the garbage collector can also call the delete() method via the finalizer (callback.finalize())
-    // at any point after here.
-    callback.delete();
-
-    System.out.println();
-    System.out.println("java exit");
-  }
-}
-
-class JavaCallback extends Callback
-{
-  public JavaCallback()
-  {
-    super();
-  }
-
-  public void run()
-  {
-    System.out.println("JavaCallback.run()");
-  }
-}
-
diff --git a/Examples/doxygencomments/java/check.list b/Examples/doxygencomments/java/check.list
deleted file mode 100644
index 9728342f2..000000000
--- a/Examples/doxygencomments/java/check.list
+++ /dev/null
@@ -1,15 +0,0 @@
-# see top-level Makefile.in
-callback
-class
-constants
-enum
-extend
-funcptr
-multimap
-native
-pointer
-reference
-simple
-template
-typemap
-variables
diff --git a/Examples/doxygencomments/java/class/Makefile b/Examples/doxygencomments/java/class/Makefile
deleted file mode 100644
index 14c301703..000000000
--- a/Examples/doxygencomments/java/class/Makefile
+++ /dev/null
@@ -1,18 +0,0 @@
-TOP        = ../..
-SWIG       = $(TOP)/../preinst-swig
-CXXSRCS    = example.cxx
-TARGET     = example
-INTERFACE  = example.i
-SWIGOPT    =
-
-all::	java
-
-java::
-	$(MAKE) -f $(TOP)/Makefile CXXSRCS='$(CXXSRCS)' SWIG='$(SWIG)' \
-	SWIGOPT='$(SWIGOPT)' TARGET='$(TARGET)' INTERFACE='$(INTERFACE)' java_cpp
-	javac *.java
-
-clean::
-	$(MAKE) -f $(TOP)/Makefile java_clean
-
-check: all
diff --git a/Examples/doxygencomments/java/class/example.cxx b/Examples/doxygencomments/java/class/example.cxx
deleted file mode 100644
index 1e8e203dd..000000000
--- a/Examples/doxygencomments/java/class/example.cxx
+++ /dev/null
@@ -1,28 +0,0 @@
-/* File : example.c */
-
-#include "example.h"
-#define M_PI 3.14159265358979323846
-
-/* Move the shape to a new location */
-void Shape::move(double dx, double dy) {
-  x += dx;
-  y += dy;
-}
-
-int Shape::nshapes = 0;
-
-double Circle::area(void) {
-  return M_PI*radius*radius;
-}
-
-double Circle::perimeter(void) {
-  return 2*M_PI*radius;
-}
-
-double Square::area(void) {
-  return width*width;
-}
-
-double Square::perimeter(void) {
-  return 4*width;
-}
diff --git a/Examples/doxygencomments/java/class/example.h b/Examples/doxygencomments/java/class/example.h
deleted file mode 100644
index ce9af23d3..000000000
--- a/Examples/doxygencomments/java/class/example.h
+++ /dev/null
@@ -1,51 +0,0 @@
-/*! \file example.h 
-comments on example.h */
-
-/*! This is describing class Shape
- \author Bob
- \exception some sort of exception
- \see OtherShapes()
- */
-
-class Shape {
-public:
-  Shape() {
-    nshapes++;
-  }
-  virtual ~Shape() {
-    nshapes--;
-  };
-  double  x, y; /*!< Important variables  */
-  void    move(double dx, double dy);
-  virtual double area(void) = 0; /*!< \return the area \exception exception description */
-  virtual double perimeter(void) = 0; /*!< \exception exception description 
-					\return the perimeter */
-  static  int nshapes; /*!< Details about nshapes. */
-};
-/*! This is describing class Circle */
-class Circle : public Shape {
-private:
-  double radius;
-public:
-  Circle(double r) : radius(r) { };
-  virtual double area(void); /*!< \return the area \exception exception description */
-  virtual double perimeter(void); /*!< \exception exception description 
-					\return the perimeter */
-};
-
-/*! This is describing class square */
-class Square : public Shape {
-private:
-  double width;
-public:
-  Square(double w) : width(w) { }; /*!< Create square
-					/param w the width
-					/exception some description */
-  virtual double area(void);
-  virtual double perimeter(void);
-};
-
-
-
-
-  
diff --git a/Examples/doxygencomments/java/class/example.i b/Examples/doxygencomments/java/class/example.i
deleted file mode 100644
index 05c0ca2ab..000000000
--- a/Examples/doxygencomments/java/class/example.i
+++ /dev/null
@@ -1,10 +0,0 @@
-/** File : example.i */
-%module example
-
-%{
-#include "example.h"
-%}
-
-/* Let's just grab the original header file here */
-%include "example.h"
-
diff --git a/Examples/doxygencomments/java/class/index.html b/Examples/doxygencomments/java/class/index.html
deleted file mode 100644
index e9db7e94a..000000000
--- a/Examples/doxygencomments/java/class/index.html
+++ /dev/null
@@ -1,197 +0,0 @@
-<html>
-<head>
-<title>SWIG:Examples:java:class</title>
-</head>
-
-<body bgcolor="#ffffff">
-
-
-<tt>SWIG/Examples/java/class/</tt>
-<hr>
-
-<H2>Wrapping a simple C++ class</H2>
-
-<p>
-This example illustrates the high level form of C++ class wrapping performed
-by SWIG.  In this case, a C++ class has a proxy Java class, which 
-provides access to C++ class members.
-
-<h2>The C++ Code</h2>
-
-Suppose you have some C++ classes described by the following (and admittedly lame) 
-header file:
-
-<blockquote>
-<pre>
-/* File : example.h */
-
-class Shape {
-public:
-  Shape() {
-    nshapes++;
-  }
-  virtual ~Shape() {
-    nshapes--;
-  };
-  double  x, y;   
-  void    move(double dx, double dy);
-  virtual double area() = 0;
-  virtual double perimeter() = 0;
-  static  int nshapes;
-};
-
-class Circle : public Shape {
-private:
-  double radius;
-public:
-  Circle(double r) : radius(r) { };
-  virtual double area();
-  virtual double perimeter();
-};
-
-class Square : public Shape {
-private:
-  double width;
-public:
-  Square(double w) : width(w) { };
-  virtual double area();
-  virtual double perimeter();
-};
-</pre>
-</blockquote>
-
-<h2>The SWIG interface</h2>
-
-A simple SWIG interface for this can be built by simply grabbing the header file
-like this:
-
-<blockquote>
-<pre>
-/* File : example.i */
-%module example
-
-%{
-#include "example.h"
-%}
-
-/* Let's just grab the original header file here */
-%include "example.h"
-</pre>
-</blockquote>
-
-Note: when creating a C++ extension, you must run SWIG with the <tt>-c++</tt> option like this:
-<blockquote>
-<pre>
-% swig -c++ -java example.i
-</pre>
-</blockquote>
-
-<h2>A sample Java program</h2>
-
-Click <a href="main.java">here</a> to see a Java program that calls the C++ functions from Java.
-
-<h2>Key points</h2>
-
-<ul>
-<li>To create a new object, you call a constructor like this:
-
-<blockquote>
-<pre>
-Circle c = new Circle(10);
-</pre>
-</blockquote>
-
-<p>
-<li>To access member data, a pair of accessor functions are used.
-For example:
-
-<blockquote>
-<pre>
-c.setX(15);        // Set member data
-x = c.getX();      // Get member data
-</pre>
-</blockquote>
-
-<p>
-<li>To invoke a member function, you simply do this
-
-<blockquote>
-<pre>
-System.out.println( "The area is " + c.area() );
-</pre>
-</blockquote>
-
-<p>
-<li>To invoke a destructor, simply do this
-
-<blockquote>
-<pre>
-c.delete();     // Deletes a shape
-</pre>
-</blockquote>
-
-<p>
-<li>Static member variables are wrapped with java static get and set access functions.  For example:
-
-<blockquote>
-<pre>
-n = Shape.getNshapes();     // Get a static data member
-Shape.setNshapes(13);       // Set a static data member
-</pre>
-</blockquote>
-
-</ul>
-
-<h2>General Comments</h2>
-
-<ul>
-<li>This high-level interface using proxy classes is not the only way to handle C++ code. 
-A low level interface using c functions to access member variables and member functions is the alternative SWIG
-approach. This entails passing around the c pointer or c++ 'this' pointer and as such it is not difficult to crash the JVM. 
-The abstraction of the underlying pointer by the java proxy classes far better fits the java programming paradigm.
-
-<p>
-<li>SWIG *does* know how to properly perform upcasting of objects in an inheritance
-hierarchy (including multiple inheritance).  However Java classes can only derive from one base class so multiple inheritance
-is not implemented. Java classes can implement more than one interface so there is scope for improvement in the future. 
-
-<p>
-<li>A wide variety of C++ features are not currently supported by SWIG.  Here is the
-short and incomplete list:
-
-<p>
-<ul>
-<li>Overloaded methods and functions.  SWIG wrappers don't know how to resolve name
-conflicts so you must give an alternative name to any overloaded method name using the
-%name directive like this:
-
-<blockquote>
-<pre>
-void foo(int a);  
-%name(foo2) void foo(double a, double b);
-</pre>
-</blockquote>
-
-<p>
-<li>Overloaded operators.  Not supported at all. The only workaround for this is
-to write a helper function. For example:
-
-<blockquote>
-<pre>
-%inline %{
-    Vector *vector_add(Vector *a, Vector *b) {
-          ... whatever ...
-    }
-%}
-</pre>
-</blockquote>
-
-<p>
-<li>Namespaces.  Not supported at all. Won't be supported until SWIG2.0 (if at all).
-
-</ul>
-</ul>
-
-<hr>
-</body>
-</html>
diff --git a/Examples/doxygencomments/java/class/main.java b/Examples/doxygencomments/java/class/main.java
deleted file mode 100644
index 8ef35db6d..000000000
--- a/Examples/doxygencomments/java/class/main.java
+++ /dev/null
@@ -1,70 +0,0 @@
-// This example illustrates how C++ classes can be used from Java using SWIG.
-// The Java class gets mapped onto the C++ class and behaves as if it is a Java class.
-
-public class main {
-  static {
-    try {
-        System.loadLibrary("example");
-    } catch (UnsatisfiedLinkError e) {
-      System.err.println("Native code library failed to load. See the chapter on Dynamic Linking Problems in the SWIG Java documentation for help.\n" + e);
-      System.exit(1);
-    }
-  }
-
-  public static void main(String argv[]) 
-  {
-    // ----- Object creation -----
-    
-    System.out.println( "Creating some objects:" );
-    Circle c = new Circle(10);
-    System.out.println( "    Created circle " + c );
-    Square s = new Square(10);
-    System.out.println( "    Created square " + s );
-    
-    // ----- Access a static member -----
-    
-    System.out.println( "\nA total of " + Shape.getNshapes() + " shapes were created" );
-    
-    // ----- Member data access -----
-    
-    // Notice how we can do this using functions specific to
-    // the 'Circle' class.
-    c.setX(20);
-    c.setY(30);
-    
-    // Now use the same functions in the base class
-    Shape shape = s;
-    shape.setX(-10);
-    shape.setY(5);
-    
-    System.out.println( "\nHere is their current position:" );
-    System.out.println( "    Circle = (" + c.getX() + " " + c.getY() + ")" );
-    System.out.println( "    Square = (" + s.getX() + " " + s.getY() + ")" );
-    
-    // ----- Call some methods -----
-    
-    System.out.println( "\nHere are some properties of the shapes:" );
-    Shape[] shapes = {c,s};
-    for (int i=0; i<shapes.length; i++)
-    {
-          System.out.println( "   " + shapes[i].toString() );
-          System.out.println( "        area      = " + shapes[i].area() );
-          System.out.println( "        perimeter = " + shapes[i].perimeter() );
-    }
-    
-    // Notice how the area() and perimeter() functions really
-    // invoke the appropriate virtual method on each object.
-    
-    // ----- Delete everything -----
-    
-    System.out.println( "\nGuess I'll clean up now" );
-    
-    // Note: this invokes the virtual destructor
-    // You could leave this to the garbage collector
-    c.delete();
-    s.delete();
-    
-    System.out.println( Shape.getNshapes() + " shapes remain" );
-    System.out.println( "Goodbye" );
-  }
-}
diff --git a/Examples/doxygencomments/java/constants/Makefile b/Examples/doxygencomments/java/constants/Makefile
deleted file mode 100644
index 2b3d35c6a..000000000
--- a/Examples/doxygencomments/java/constants/Makefile
+++ /dev/null
@@ -1,18 +0,0 @@
-TOP        = ../..
-SWIG       = $(TOP)/../preinst-swig
-CXXSRCS    = 
-TARGET     = example
-INTERFACE  = example.i
-SWIGOPT    =
-
-all::	java
-
-java::
-	$(MAKE) -f $(TOP)/Makefile CXXSRCS='$(CXXSRCS)' SWIG='$(SWIG)' \
-	SWIGOPT='$(SWIGOPT)' TARGET='$(TARGET)' INTERFACE='$(INTERFACE)' java_cpp
-	javac *.java
-
-clean::
-	$(MAKE) -f $(TOP)/Makefile java_clean
-
-check: all
diff --git a/Examples/doxygencomments/java/constants/example.i b/Examples/doxygencomments/java/constants/example.i
deleted file mode 100644
index 5cbcf2463..000000000
--- a/Examples/doxygencomments/java/constants/example.i
+++ /dev/null
@@ -1,30 +0,0 @@
-/*! File : example.i */
-%module example
-
-/* Force the generated Java code to use the C constant values rather than making a JNI call */
-%javaconst(1);
-
-/*! A few preprocessor macros */
-
-#define    ICONST      42
-#define    FCONST      2.1828
-#define    CCONST      'x'
-#define    CCONST2     '\n'
-#define    SCONST      "Hello World"
-#define    SCONST2     "\"Hello World\""
-
-/*! This should work just fine */
-#define    EXPR        ICONST + 3*(FCONST)
-
-/*! This shouldn't do anything */
-#define    EXTERN      extern
-
-/*! Neither should this (BAR isn't defined) */
-#define    FOO         (ICONST + BAR)
-
-/*! The following directives also produce constants */
-
-%constant int iconst = 37;
-%constant double fconst = 3.14;
-
-
diff --git a/Examples/doxygencomments/java/constants/index.html b/Examples/doxygencomments/java/constants/index.html
deleted file mode 100644
index 8367d0571..000000000
--- a/Examples/doxygencomments/java/constants/index.html
+++ /dev/null
@@ -1,52 +0,0 @@
-<html>
-<head>
-<title>SWIG:Examples:java:constants</title>
-</head>
-
-<body bgcolor="#ffffff">
-
-<tt>SWIG/Examples/java/constants/</tt>
-<hr>
-
-<H2>Wrapping C Constants</H2>
-
-<p>
-When SWIG encounters C preprocessor macros and C declarations that look like constants,
-it creates Java constant with an identical value.  Click <a href="example.i">here</a>
-to see a SWIG interface with some constant declarations in it.
-
-
-<h2>Accessing Constants from Java</h2>
-Click <a href="../../../Doc/Manual/Java.html#constants">here</a> for the section on constants in the SWIG and Java documentation.
-<p>
-
-Click <a href="main.java">here</a> to see a Java program that prints out the values
-of the constants contained in the above file.</p>
-<h2>Key points</h2>
-<ul>
-<li>The values of preprocessor macros are converted into Java constants.
-<li>Types are inferred by syntax (e.g., "3" is an integer and "3.5" is a float).
-<li>Character constants such as 'x' are converted into Java strings.
-<li>C string literals such as "Hello World" are converted into Java strings.
-<li>Macros that are not fully defined are simply ignored.  For example:
-<blockquote>
-<pre>
-#define EXTERN extern
-</pre>
-</blockquote>
-is ignored because SWIG has no idea what type of variable this would be.
-
-<p>
-<li>Expressions are allowed provided that all of their components are defined. Otherwise, the constant is ignored.
-
-<li>Certain C declarations involving 'const' are also turned into Java constants. 
-<li>The constants that appear in a SWIG interface file do not have to appear in any sort
-of matching C source file since the creation of a constant does not require linkage
-to a stored value (i.e., a value held in a C global variable or memory location).
-</ul>
-
-<hr>
-
-
-</body>
-</html>
diff --git a/Examples/doxygencomments/java/constants/main.java b/Examples/doxygencomments/java/constants/main.java
deleted file mode 100644
index 7130c3d70..000000000
--- a/Examples/doxygencomments/java/constants/main.java
+++ /dev/null
@@ -1,44 +0,0 @@
-import java.lang.reflect.*;
-
-public class main {
-  static {
-    try {
-        System.loadLibrary("example");
-    } catch (UnsatisfiedLinkError e) {
-      System.err.println("Native code library failed to load. See the chapter on Dynamic Linking Problems in the SWIG Java documentation for help.\n" + e);
-      System.exit(1);
-    }
-  }
-
-  public static void main(String argv[]) 
-  {
-    System.out.println("ICONST  = " + example.ICONST + " (should be 42)");
-    System.out.println("FCONST  = " + example.FCONST + " (should be 2.1828)");
-    System.out.println("CCONST  = " + example.CCONST + " (should be 'x')");
-    System.out.println("CCONST2 = " + example.CCONST2 + " (this should be on a new line)");
-    System.out.println("SCONST  = " + example.SCONST + " (should be 'Hello World')");
-    System.out.println("SCONST2 = " + example.SCONST2 + " (should be '\"Hello World\"')");
-    System.out.println("EXPR    = " + example.EXPR +   " (should be 48.5484)");
-    System.out.println("iconst  = " + example.iconst + " (should be 37)");
-    System.out.println("fconst  = " + example.fconst + " (should be 3.14)");
-
-// Use reflection to check if these variables are defined:
-    try
-    {
-        System.out.println("EXTERN = " + example.class.getField("EXTERN") + " (Arg! This shouldn't print anything)");
-    }
-    catch (NoSuchFieldException e)
-    {
-        System.out.println("EXTERN isn't defined (good)");
-    }
-
-    try
-    {
-        System.out.println("FOO    = " + example.class.getField("FOO") + " (Arg! This shouldn't print anything)");
-    }
-    catch (NoSuchFieldException e)
-    {
-        System.out.println("FOO isn't defined (good)");
-    }
-  }
-}
diff --git a/Examples/doxygencomments/java/enum/Makefile b/Examples/doxygencomments/java/enum/Makefile
deleted file mode 100644
index 14c301703..000000000
--- a/Examples/doxygencomments/java/enum/Makefile
+++ /dev/null
@@ -1,18 +0,0 @@
-TOP        = ../..
-SWIG       = $(TOP)/../preinst-swig
-CXXSRCS    = example.cxx
-TARGET     = example
-INTERFACE  = example.i
-SWIGOPT    =
-
-all::	java
-
-java::
-	$(MAKE) -f $(TOP)/Makefile CXXSRCS='$(CXXSRCS)' SWIG='$(SWIG)' \
-	SWIGOPT='$(SWIGOPT)' TARGET='$(TARGET)' INTERFACE='$(INTERFACE)' java_cpp
-	javac *.java
-
-clean::
-	$(MAKE) -f $(TOP)/Makefile java_clean
-
-check: all
diff --git a/Examples/doxygencomments/java/enum/example.cxx b/Examples/doxygencomments/java/enum/example.cxx
deleted file mode 100644
index df7bb6328..000000000
--- a/Examples/doxygencomments/java/enum/example.cxx
+++ /dev/null
@@ -1,37 +0,0 @@
-/* File : example.cxx */
-
-#include "example.h"
-#include <stdio.h>
-
-void Foo::enum_test(speed s) {
-  if (s == IMPULSE) {
-    printf("IMPULSE speed\n");
-  } else if (s == WARP) {
-    printf("WARP speed\n");
-  } else if (s == LUDICROUS) {
-    printf("LUDICROUS speed\n");
-  } else {
-    printf("Unknown speed\n");
-  }
-}
-
-void enum_test(color c, Foo::speed s) {
-  if (c == RED) {
-    printf("color = RED, ");
-  } else if (c == BLUE) {
-    printf("color = BLUE, ");
-  } else if (c == GREEN) {
-    printf("color = GREEN, ");
-  } else {
-    printf("color = Unknown color!, ");
-  }
-  if (s == Foo::IMPULSE) {
-    printf("speed = IMPULSE speed\n");
-  } else if (s == Foo::WARP) {
-    printf("speed = WARP speed\n");
-  } else if (s == Foo::LUDICROUS) {
-    printf("speed = LUDICROUS speed\n");
-  } else {
-    printf("speed = Unknown speed!\n");
-  }
-}
diff --git a/Examples/doxygencomments/java/enum/example.h b/Examples/doxygencomments/java/enum/example.h
deleted file mode 100644
index 2142d8240..000000000
--- a/Examples/doxygencomments/java/enum/example.h
+++ /dev/null
@@ -1,23 +0,0 @@
-
-
-/** This is a block describing enum
- */
-
-enum color { RED, BLUE, GREEN };
-
-/*! This is describing class foo
- */
-
-class Foo {
- public:
-  Foo() { }
-  enum speed { IMPULSE=10, WARP=20, LUDICROUS=30 };
-  void enum_test(speed s);
-};
-
-/*! This is describing enum test
-//! \param c the color c
-//! \param s the speed
- */
-
-void enum_test(color c, Foo::speed s);
diff --git a/Examples/doxygencomments/java/enum/example.i b/Examples/doxygencomments/java/enum/example.i
deleted file mode 100644
index 1f1f9d526..000000000
--- a/Examples/doxygencomments/java/enum/example.i
+++ /dev/null
@@ -1,14 +0,0 @@
-/** File : example.i */
-%module example
-
-%{
-#include "example.h"
-%}
-
-/** Force the generated Java code to use the C enum values rather than making a JNI call */
-%javaconst(1);
-
-/** Let's just grab the original header file here */
-
-%include "example.h"
-
diff --git a/Examples/doxygencomments/java/enum/index.html b/Examples/doxygencomments/java/enum/index.html
deleted file mode 100644
index 52c06c5d1..000000000
--- a/Examples/doxygencomments/java/enum/index.html
+++ /dev/null
@@ -1,29 +0,0 @@
-<html>
-<head>
-<title>SWIG:Examples:java:enum</title>
-</head>
-
-<body bgcolor="#ffffff">
-
-
-<tt>SWIG/Examples/java/enum/</tt>
-<hr>
-
-<H2>Wrapping enumerations</H2>
-
-<p>
-This example tests SWIG's ability to wrap enumerations. 
-SWIG wraps enums in numerous different ways. The default approach is to wrap
-each enum with the typesafe enum pattern. Enums are handled as integers in the JNI layer.
-See the documentation for the other approaches for wrapping enums.
-
-
-<ul>
-<li><a href="example.h">example.h</a>.  Header file containing some enums.
-<li><a href="example.i">example.i</a>.  Interface file.
-<li><a href="main.java">main.java</a>. Sample Java program.
-</ul>
-
-<hr>
-</body>
-</html>
diff --git a/Examples/doxygencomments/java/enum/main.java b/Examples/doxygencomments/java/enum/main.java
deleted file mode 100644
index 8646e0087..000000000
--- a/Examples/doxygencomments/java/enum/main.java
+++ /dev/null
@@ -1,38 +0,0 @@
-
-public class main {
-  static {
-    try {
-        System.loadLibrary("example");
-    } catch (UnsatisfiedLinkError e) {
-      System.err.println("Native code library failed to load. See the chapter on Dynamic Linking Problems in the SWIG Java documentation for help.\n" + e);
-      System.exit(1);
-    }
-  }
-
-  public static void main(String argv[]) 
-  {
-    // Print out the value of some enums
-    System.out.println("*** color ***");
-    System.out.println("    " + color.RED + " = " + color.RED.swigValue());
-    System.out.println("    " + color.BLUE + " = " + color.BLUE.swigValue());
-    System.out.println("    " + color.GREEN + " = " + color.GREEN.swigValue());
-
-    System.out.println("\n*** Foo::speed ***");
-    System.out.println("    Foo::" + Foo.speed.IMPULSE + " = " + Foo.speed.IMPULSE.swigValue());
-    System.out.println("    Foo::" + Foo.speed.WARP + " = " + Foo.speed.WARP.swigValue());
-    System.out.println("    Foo::" + Foo.speed.LUDICROUS + " = " + Foo.speed.LUDICROUS.swigValue());
-
-    System.out.println("\nTesting use of enums with functions\n");
-
-    example.enum_test(color.RED, Foo.speed.IMPULSE);
-    example.enum_test(color.BLUE, Foo.speed.WARP);
-    example.enum_test(color.GREEN, Foo.speed.LUDICROUS);
-
-    System.out.println( "\nTesting use of enum with class method" );
-    Foo f = new Foo();
-
-    f.enum_test(Foo.speed.IMPULSE);
-    f.enum_test(Foo.speed.WARP);
-    f.enum_test(Foo.speed.LUDICROUS);
-  }
-}
diff --git a/Examples/doxygencomments/java/extend/Makefile b/Examples/doxygencomments/java/extend/Makefile
deleted file mode 100644
index 14c301703..000000000
--- a/Examples/doxygencomments/java/extend/Makefile
+++ /dev/null
@@ -1,18 +0,0 @@
-TOP        = ../..
-SWIG       = $(TOP)/../preinst-swig
-CXXSRCS    = example.cxx
-TARGET     = example
-INTERFACE  = example.i
-SWIGOPT    =
-
-all::	java
-
-java::
-	$(MAKE) -f $(TOP)/Makefile CXXSRCS='$(CXXSRCS)' SWIG='$(SWIG)' \
-	SWIGOPT='$(SWIGOPT)' TARGET='$(TARGET)' INTERFACE='$(INTERFACE)' java_cpp
-	javac *.java
-
-clean::
-	$(MAKE) -f $(TOP)/Makefile java_clean
-
-check: all
diff --git a/Examples/doxygencomments/java/extend/example.cxx b/Examples/doxygencomments/java/extend/example.cxx
deleted file mode 100644
index 450d75608..000000000
--- a/Examples/doxygencomments/java/extend/example.cxx
+++ /dev/null
@@ -1,4 +0,0 @@
-/* File : example.cxx */
-
-#include "example.h"
-
diff --git a/Examples/doxygencomments/java/extend/example.h b/Examples/doxygencomments/java/extend/example.h
deleted file mode 100644
index 9b882fd59..000000000
--- a/Examples/doxygencomments/java/extend/example.h
+++ /dev/null
@@ -1,67 +0,0 @@
-/* File : example.h */
-
-#include <cstdio>
-#include <iostream>
-#include <vector>
-#include <string>
-#include <cmath>
-
-/**This is describiing class Employee 
- /author Bob */
-class Employee {
-private:
-	std::string name;
-public:
-	/** Employee
-	 \param n name of Employee
-	 \throws some exception */
-	Employee(const char* n): name(n) {}
-/**This is describing method getTitle */
-	virtual std::string getTitle() { return getPosition() + " " + getName(); }
-	virtual std::string getName() { return name; }
-	virtual std::string getPosition() const { return "Employee"; }
-	virtual ~Employee() { printf("~Employee() @ %p\n", this); }
-};
-
-/**This is describing class Manager */
-class Manager: public Employee {
-public:
-	Manager(const char* n): Employee(n) {}
-	virtual std::string getPosition() const { return "Manager"; }
-};
-
-
-class EmployeeList {
-	std::vector<Employee*> list;
-public:
-	/** Initialises Employee List */
-	EmployeeList() {
-		list.push_back(new Employee("Bob"));
-		list.push_back(new Employee("Jane"));
-		list.push_back(new Manager("Ted"));
-	}
-	/** Add employee
-	 * \param p employee p
-	 * \return void */
-	void addEmployee(Employee *p) {
-		list.push_back(p);
-		std::cout << "New employee added.   Current employees are:" << std::endl;
-		std::vector<Employee*>::iterator i;
-		for (i=list.begin(); i!=list.end(); i++) {
-			std::cout << "  " << (*i)->getTitle() << std::endl;
-		}
-	}
-/**This is describing class get item */
-	const Employee *get_item(int i) {
-		return list[i];
-	}
-	~EmployeeList() { 
-		std::vector<Employee*>::iterator i;
-		std::cout << "~EmployeeList, deleting " << list.size() << " employees." << std::endl;
-		for (i=list.begin(); i!=list.end(); i++) {
-			delete *i;
-		}
-		std::cout << "~EmployeeList empty." << std::endl;
-	}
-};
-
diff --git a/Examples/doxygencomments/java/extend/example.i b/Examples/doxygencomments/java/extend/example.i
deleted file mode 100644
index c8ec32e09..000000000
--- a/Examples/doxygencomments/java/extend/example.i
+++ /dev/null
@@ -1,15 +0,0 @@
-/* File : example.i */
-%module(directors="1") example
-%{
-#include "example.h"
-%}
-
-%include "std_vector.i"
-%include "std_string.i"
-
-/* turn on director wrapping for Manager */
-%feature("director") Employee;
-%feature("director") Manager;
-
-%include "example.h"
-
diff --git a/Examples/doxygencomments/java/extend/index.html b/Examples/doxygencomments/java/extend/index.html
deleted file mode 100644
index c7c2c127d..000000000
--- a/Examples/doxygencomments/java/extend/index.html
+++ /dev/null
@@ -1,19 +0,0 @@
-<html>
-<head>
-<title>SWIG:Examples:java:extend</title>
-</head>
-
-<body bgcolor="#ffffff">
-
-
-<tt>SWIG/Examples/java/extend/</tt>
-<hr>
-
-<H2>Extending a simple C++ class in Java</H2>
-
-<p>
-This example illustrates the extending of a C++ class with cross language polymorphism.
-
-<hr>
-</body>
-</html>
diff --git a/Examples/doxygencomments/java/extend/main.java b/Examples/doxygencomments/java/extend/main.java
deleted file mode 100644
index ee3a94ed0..000000000
--- a/Examples/doxygencomments/java/extend/main.java
+++ /dev/null
@@ -1,88 +0,0 @@
-// This file illustrates the cross language polymorphism using directors.
-
-
-// CEO class, which overrides Employee::getPosition().
-
-class CEO extends Manager {
-  public CEO(String name) {
-    super(name);
-    }
-  public String getPosition() {
-    return "CEO";
-    }
-  // Public method to stop the SWIG proxy base class from thinking it owns the underlying C++ memory.
-  public void disownMemory() {
-    swigCMemOwn = false; 
-  } 
-}
-
-
-public class main {
-  static {
-    try {
-        System.loadLibrary("example");
-    } catch (UnsatisfiedLinkError e) {
-      System.err.println("Native code library failed to load. See the chapter on Dynamic Linking Problems in the SWIG Java documentation for help.\n" + e);
-      System.exit(1);
-    }
-  }
-
-  public static void main(String argv[]) 
-  {
-
-    // Create an instance of CEO, a class derived from the Java proxy of the 
-    // underlying C++ class. The calls to getName() and getPosition() are standard,
-    // the call to getTitle() uses the director wrappers to call CEO.getPosition().
-
-    CEO e = new CEO("Alice");
-    System.out.println( e.getName() + " is a " + e.getPosition() );
-    System.out.println( "Just call her \"" + e.getTitle() + "\"" );
-    System.out.println( "----------------------" );
-
-
-    // Create a new EmployeeList instance.  This class does not have a C++
-    // director wrapper, but can be used freely with other classes that do.
-
-    EmployeeList list = new EmployeeList();
-
-    // EmployeeList owns its items, so we must surrender ownership of objects we add.
-    e.disownMemory();
-    list.addEmployee(e);
-    System.out.println( "----------------------" );
-
-    // Now we access the first four items in list (three are C++ objects that
-    // EmployeeList's constructor adds, the last is our CEO). The virtual
-    // methods of all these instances are treated the same. For items 0, 1, and
-    // 2, all methods resolve in C++. For item 3, our CEO, getTitle calls
-    // getPosition which resolves in Java. The call to getPosition is
-    // slightly different, however, because of the overidden getPosition() call, since
-    // now the object reference has been "laundered" by passing through
-    // EmployeeList as an Employee*. Previously, Java resolved the call
-    // immediately in CEO, but now Java thinks the object is an instance of
-    // class Employee. So the call passes through the
-    // Employee proxy class and on to the C wrappers and C++ director,
-    // eventually ending up back at the Java CEO implementation of getPosition().
-    // The call to getTitle() for item 3 runs the C++ Employee::getTitle()
-    // method, which in turn calls getPosition(). This virtual method call
-    // passes down through the C++ director class to the Java implementation
-    // in CEO. All this routing takes place transparently.
-
-    System.out.println( "(position, title) for items 0-3:" );
-
-    System.out.println( "  " + list.get_item(0).getPosition() + ", \"" + list.get_item(0).getTitle() + "\"" );
-    System.out.println( "  " + list.get_item(1).getPosition() + ", \"" + list.get_item(1).getTitle() + "\"" );
-    System.out.println( "  " + list.get_item(2).getPosition() + ", \"" + list.get_item(2).getTitle() + "\"" );
-    System.out.println( "  " + list.get_item(3).getPosition() + ", \"" + list.get_item(3).getTitle() + "\"" );
-    System.out.println( "----------------------" );
-
-    // Time to delete the EmployeeList, which will delete all the Employee*
-    // items it contains. The last item is our CEO, which gets destroyed as well.
-    list.delete();
-    System.out.println( "----------------------" );
-
-    // All done.
-
-    System.out.println( "java exit" );
-
-  }
-}
diff --git a/Examples/doxygencomments/java/funcptr/Makefile b/Examples/doxygencomments/java/funcptr/Makefile
deleted file mode 100644
index 968c92c6c..000000000
--- a/Examples/doxygencomments/java/funcptr/Makefile
+++ /dev/null
@@ -1,18 +0,0 @@
-TOP        = ../..
-SWIG       = $(TOP)/../preinst-swig
-SRCS       = example.c
-TARGET     = example
-INTERFACE  = example.i
-SWIGOPT    =
-
-all::	java
-
-java::
-	$(MAKE) -f $(TOP)/Makefile SRCS='$(SRCS)' SWIG='$(SWIG)' \
-	SWIGOPT='$(SWIGOPT)' TARGET='$(TARGET)' INTERFACE='$(INTERFACE)' java
-	javac *.java
-
-clean::
-	$(MAKE) -f $(TOP)/Makefile java_clean
-
-check: all
diff --git a/Examples/doxygencomments/java/funcptr/example.c b/Examples/doxygencomments/java/funcptr/example.c
deleted file mode 100644
index 5c4a3dabf..000000000
--- a/Examples/doxygencomments/java/funcptr/example.c
+++ /dev/null
@@ -1,19 +0,0 @@
-/* File : example.c */
-
-int do_op(int a, int b, int (*op)(int,int)) {
-  return (*op)(a,b);
-}
-
-int add(int a, int b) {
-  return a+b;
-}
-
-int sub(int a, int b) {
-  return a-b;
-}
-
-int mul(int a, int b) {
-  return a*b;
-}
-
-int (*funcvar)(int,int) = add;
diff --git a/Examples/doxygencomments/java/funcptr/example.h b/Examples/doxygencomments/java/funcptr/example.h
deleted file mode 100644
index 5285737a3..000000000
--- a/Examples/doxygencomments/java/funcptr/example.h
+++ /dev/null
@@ -1,10 +0,0 @@
-/* file: example.h */
-
-extern int do_op(int,int, int (*op)(int,int));
-/*! Describing function add */
-extern int add(int,int);
-extern int sub(int,int);
-extern int mul(int,int);
-
-extern int (*funcvar)(int,int);
-
diff --git a/Examples/doxygencomments/java/funcptr/example.i b/Examples/doxygencomments/java/funcptr/example.i
deleted file mode 100644
index 82c3c2201..000000000
--- a/Examples/doxygencomments/java/funcptr/example.i
+++ /dev/null
@@ -1,16 +0,0 @@
-/* File : example.i */
-%module example
-%{
-#include "example.h"
-%}
-
-/** Wrap a function taking a pointer to a function */
-extern int  do_op(int a, int b, int (*op)(int, int));
-
-/** Now install a bunch of "ops" as constants */
-%constant int (*ADD)(int,int) = add;
-%constant int (*SUB)(int,int) = sub;
-%constant int (*MUL)(int,int) = mul;
-
-extern int (*funcvar)(int,int);
-
diff --git a/Examples/doxygencomments/java/funcptr/index.html b/Examples/doxygencomments/java/funcptr/index.html
deleted file mode 100644
index 0ad2be1cf..000000000
--- a/Examples/doxygencomments/java/funcptr/index.html
+++ /dev/null
@@ -1,91 +0,0 @@
-<html>
-<head>
-<title>SWIG:Examples:java:funcptr</title>
-</head>
-
-<body bgcolor="#ffffff">
-
-
-<tt>SWIG/Examples/java/funcptr/</tt>
-<hr>
-
-<H2>Pointers to Functions</H2>
-
-<p>
-Okay, just what in the heck does SWIG do with a declaration like this?
-
-<blockquote>
-<pre>
-int do_op(int a, int b, int (*op)(int, int));
-</pre>
-</blockquote>
-
-Well, it creates a wrapper as usual.  Of course, that does raise some
-questions about the third argument (the pointer to a function). 
-
-<p>
-In this case, SWIG will wrap the function pointer as it does for all other
-pointers.  However, in order to actually call this function from a Java program,
-you will need to pass some kind of C function pointer object.  In C,
-this is easy, you just supply a function name as an argument like this:
-
-<blockquote>
-<pre>
-/* Some callback function */
-int add(int a, int b) {
-   return a+b;
-} 
-...
-int r = do_op(x,y,add);
-</pre>
-</blockquote>
-
-To make this work with SWIG, you will need to do a little extra work.  Specifically,
-you need to create some function pointer objects using the %constant directive like this:
-
-<blockquote>
-<pre>
-%constant(int (*)(int,int)) ADD = add;
-</pre>
-</blockquote>
-
-Now, in a Java program, you would do this:
-
-<blockquote>
-<pre>
-int r = do_op(x,y, example.ADD)
-</pre>
-</blockquote>
-where <tt>example</tt> is the module name.
-
-<h2>An Example</h2>
-
-Here are some files that illustrate this with a simple example:
-
-<ul>
-<li><a href="example.c">example.c</a>
-<li><a href="example.h">example.h</a>
-<li><a href="example.i">example.i</a> (SWIG interface)
-<li><a href="main.java">main.java</a> (Sample program)
-</ul>
-
-<h2>Notes</h2>
-
-<ul>
-<li>The value of a function pointer must correspond to a function written in C or C++.
-It is not possible to pass an arbitrary Java function in as a substitute for a C 
-function pointer.
-
-<p>
-<li>A Java function can be used as a C/C++ callback if you write some
-clever typemaps and are very careful about how you create your extension.
-This is an advanced topic not covered here.
-</ul>
-
-<hr>
-</body>
-</html>
-
-
-
-
diff --git a/Examples/doxygencomments/java/funcptr/main.java b/Examples/doxygencomments/java/funcptr/main.java
deleted file mode 100644
index cf81f92b4..000000000
--- a/Examples/doxygencomments/java/funcptr/main.java
+++ /dev/null
@@ -1,33 +0,0 @@
-
-public class main {
-
-  static {
-    try {
-	System.loadLibrary("example");
-    } catch (UnsatisfiedLinkError e) {
-      System.err.println("Native code library failed to load. See the chapter on Dynamic Linking Problems in the SWIG Java documentation for help.\n" + e);
-      System.exit(1);
-    }
-  }
-
-  public static void main(String argv[]) {
-
-
-    int a = 37;
-    int b = 42;
-
-    // Now call our C function with a bunch of callbacks
-
-    System.out.println( "Trying some C callback functions" );
-    System.out.println( "    a        = " + a );
-    System.out.println( "    b        = " + b );
-    System.out.println( "    ADD(a,b) = " + example.do_op(a,b,example.ADD) );
-    System.out.println( "    SUB(a,b) = " + example.do_op(a,b,example.SUB) );
-    System.out.println( "    MUL(a,b) = " + example.do_op(a,b,example.MUL) );
-
-    System.out.println( "Here is what the C callback function classes are called in Java" );
-    System.out.println( "    ADD      = " + example.ADD.getClass().getName() );
-    System.out.println( "    SUB      = " + example.SUB.getClass().getName() );
-    System.out.println( "    MUL      = " + example.MUL.getClass().getName() );
-  }
-}
diff --git a/Examples/doxygencomments/java/index.html b/Examples/doxygencomments/java/index.html
deleted file mode 100644
index d98f9a393..000000000
--- a/Examples/doxygencomments/java/index.html
+++ /dev/null
@@ -1,65 +0,0 @@
-<html>
-<head>
-<title>SWIG:Examples:java</title>
-</head>
-
-<body bgcolor="#ffffff">
-<H1>SWIG Java Examples</H1>
-
-<p>
-The following examples illustrate the use of SWIG with Java.
-
-<ul>
-<li><a href="simple/index.html">simple</a>.  A minimal example showing how SWIG can
-be used to wrap a C function, a global variable, and a constant.
-<li><a href="native/index.html">native</a>. Comparing the manual and the SWIG approach to calling native code.
-<li><a href="typemap/index.html">typemap</a>. Modifying the Java module's default behaviour by using typemaps.
-<li><a href="constants/index.html">constants</a>.  This shows how preprocessor macros and
-certain C declarations are turned into constants.
-<li><a href="variables/index.html">variables</a>. An example showing how to access C global variables.
-<li><a href="enum/index.html">enum</a>. Wrapping enumerations.
-<li><a href="class/index.html">class</a>. How to wrap a simple C++ class.
-<li><a href="reference/index.html">reference</a>. C++ references.
-<li><a href="pointer/index.html">pointer</a>. Simple pointer handling.
-<li><a href="template/index.html">template</a>. C++ templates.
-<li><a href="funcptr/index.html">funcptr</a>. Pointers to functions.
-<li><a href="callback/index.html">callback</a>. C++ callbacks using directors.
-<li><a href="extend/index.html">extend</a>. Polymorphism using directors.
-</ul>
-
-<h2>Running the examples</h2>
-Please see the <a href="../../Doc/Manual/Windows.html">Windows</a> page in the main manual for information on using the examples on Windows. <p>
-
-On Unix most of the examples work by making the Makefile before executing the program main.java. The Makefile will output the swig generated JNI c code as well as the Java wrapper classes. Additionally the JNI c/c++ code is compiled into the shared object (dynamic link library) which is needed for dynamic linking to the native code. The Makefiles also compile the Java files using javac. 
-<p>
-Ensure that the dynamic link library file is in the appropriate path before executing the Java program. For example in Unix, libexample.so must be in the LD_LIBRARY_PATH. 
-<p>
-A Unix example:
-<blockquote>
-<pre>
-$ make
-$ export LD_LIBRARY_PATH=. #ksh 
-$ java main
-</pre>
-</blockquote>
-<p>
-
-</ul>
-
-<h2>Compatibility</h2>
-
-The examples have been extensively tested on the following platforms:
-
-<ul>
-<li>Solaris
-<li>Linux
-<li>Cygwin
-<li>Windows
-</ul>
-
-Your mileage may vary.  If you experience a problem, please let us know by 
-contacting us on the <a href="http://www.swig.org/mail.html">mailing lists</a>.
-</body>
-</html>
-
-
diff --git a/Examples/doxygencomments/java/multimap/Makefile b/Examples/doxygencomments/java/multimap/Makefile
deleted file mode 100644
index 968c92c6c..000000000
--- a/Examples/doxygencomments/java/multimap/Makefile
+++ /dev/null
@@ -1,18 +0,0 @@
-TOP        = ../..
-SWIG       = $(TOP)/../preinst-swig
-SRCS       = example.c
-TARGET     = example
-INTERFACE  = example.i
-SWIGOPT    =
-
-all::	java
-
-java::
-	$(MAKE) -f $(TOP)/Makefile SRCS='$(SRCS)' SWIG='$(SWIG)' \
-	SWIGOPT='$(SWIGOPT)' TARGET='$(TARGET)' INTERFACE='$(INTERFACE)' java
-	javac *.java
-
-clean::
-	$(MAKE) -f $(TOP)/Makefile java_clean
-
-check: all
diff --git a/Examples/doxygencomments/java/multimap/example.c b/Examples/doxygencomments/java/multimap/example.c
deleted file mode 100644
index b8360fa8a..000000000
--- a/Examples/doxygencomments/java/multimap/example.c
+++ /dev/null
@@ -1,53 +0,0 @@
-/* File : example.c */
-#include <stdio.h>
-#include <stdlib.h>
-#include <ctype.h>
-
-/* Compute the greatest common divisor of positive integers */
-int gcd(int x, int y) {
-  int g;
-  g = y;
-  while (x > 0) {
-    g = x;
-    x = y % x;
-    y = g;
-  }
-  return g;
-}
-
-int gcdmain(int argc, char *argv[]) {
-  int x,y;
-  if (argc != 3) {
-    printf("usage: gcd x y\n");
-    return -1;
-  }
-  x = atoi(argv[1]);
-  y = atoi(argv[2]);
-  printf("gcd(%d,%d) = %d\n", x,y,gcd(x,y));
-  return 0;
-}
-
-int count(char *bytes, int len, char c) {
-  int i;
-  int count = 0;
-  for (i = 0; i < len; i++) {
-    if (bytes[i] == c) count++;
-  }
-  return count;
-}
-
-void capitalize(char *str, int len) {
-  int i;
-  for (i = 0; i < len; i++) {
-    str[i] = (char)toupper(str[i]);
-  }
-}
-
-void circle(double x, double y) {
-  double a = x*x + y*y;
-  if (a > 1.0) {
-    printf("Bad points %g, %g\n", x,y);
-  } else {
-    printf("Good points %g, %g\n", x,y);
-  }
-}
diff --git a/Examples/doxygencomments/java/multimap/example.dsp b/Examples/doxygencomments/java/multimap/example.dsp
deleted file mode 100644
index 8e1f8415e..000000000
--- a/Examples/doxygencomments/java/multimap/example.dsp
+++ /dev/null
@@ -1,158 +0,0 @@
-# Microsoft Developer Studio Project File - Name="example" - Package Owner=<4>
-# Microsoft Developer Studio Generated Build File, Format Version 6.00
-# ** DO NOT EDIT **
-
-# TARGTYPE "Win32 (x86) Dynamic-Link Library" 0x0102
-
-CFG=example - Win32 Release
-!MESSAGE This is not a valid makefile. To build this project using NMAKE,
-!MESSAGE use the Export Makefile command and run
-!MESSAGE 
-!MESSAGE NMAKE /f "example.mak".
-!MESSAGE 
-!MESSAGE You can specify a configuration when running NMAKE
-!MESSAGE by defining the macro CFG on the command line. For example:
-!MESSAGE 
-!MESSAGE NMAKE /f "example.mak" CFG="example - Win32 Release"
-!MESSAGE 
-!MESSAGE Possible choices for configuration are:
-!MESSAGE 
-!MESSAGE "example - Win32 Debug" (based on "Win32 (x86) Dynamic-Link Library")
-!MESSAGE "example - Win32 Release" (based on "Win32 (x86) Dynamic-Link Library")
-!MESSAGE 
-
-# Begin Project
-# PROP AllowPerConfigDependencies 0
-# PROP Scc_ProjName ""
-# PROP Scc_LocalPath ""
-CPP=cl.exe
-MTL=midl.exe
-RSC=rc.exe
-
-!IF  "$(CFG)" == "example - Win32 Debug"
-
-# PROP BASE Use_MFC 0
-# PROP BASE Use_Debug_Libraries 1
-# PROP BASE Output_Dir "Debug"
-# PROP BASE Intermediate_Dir "Debug"
-# PROP BASE Target_Dir ""
-# PROP Use_MFC 0
-# PROP Use_Debug_Libraries 1
-# PROP Output_Dir "Debug"
-# PROP Intermediate_Dir "Debug"
-# PROP Ignore_Export_Lib 0
-# PROP Target_Dir ""
-# ADD BASE CPP /nologo /MTd /W3 /Gm /GX /ZI /Od /D "WIN32" /D "_DEBUG" /D "_WINDOWS" /D "_MBCS" /D "_USRDLL" /D "EXAMPLE_EXPORTS" /YX /FD /GZ /c
-# ADD CPP /nologo /MTd /W3 /Gm /GX /ZI /Od /I "$(JAVA_INCLUDE)" /I "$(JAVA_INCLUDE)\win32" /D "WIN32" /D "_DEBUG" /D "_WINDOWS" /D "_MBCS" /D "_USRDLL" /D "EXAMPLE_EXPORTS" /YX /FD /GZ /c
-# ADD BASE MTL /nologo /D "_DEBUG" /mktyplib203 /win32
-# ADD MTL /nologo /D "_DEBUG" /mktyplib203 /win32
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-# ADD RSC /l 0x809 /d "_DEBUG"
-BSC32=bscmake.exe
-# ADD BASE BSC32 /nologo
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-LINK32=link.exe
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-# Begin Special Build Tool
-SOURCE="$(InputPath)"
-PostBuild_Desc=Java compile post-build step
-PostBuild_Cmds=echo on	"%JAVA_BIN%\javac" *.java
-# End Special Build Tool
-
-!ELSEIF  "$(CFG)" == "example - Win32 Release"
-
-# PROP BASE Use_MFC 0
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-# PROP BASE Intermediate_Dir "Release"
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-# ADD BASE CPP /nologo /MT /W3 /GX /O2 /D "WIN32" /D "NDEBUG" /D "_WINDOWS" /D "_MBCS" /D "_USRDLL" /D "EXAMPLE_EXPORTS" /YX /FD /c
-# ADD CPP /nologo /MT /W3 /GX /O2 /I "$(JAVA_INCLUDE)" /I "$(JAVA_INCLUDE)\win32" /D "WIN32" /D "NDEBUG" /D "_WINDOWS" /D "_MBCS" /D "_USRDLL" /D "EXAMPLE_EXPORTS" /YX /FD /c
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-LINK32=link.exe
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-PostBuild_Cmds=echo on	"%JAVA_BIN%\javac" *.java
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-
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-
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-# Name "example - Win32 Release"
-# Begin Group "Source Files"
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-# Begin Source File
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-SOURCE=.\example.c
-# End Source File
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-!IF  "$(CFG)" == "example - Win32 Debug"
-
-# Begin Custom Build
-InputPath=.\example.i
-InputName=example
-
-"$(InputName)_wrap.c" : $(SOURCE) "$(INTDIR)" "$(OUTDIR)"
-	echo In order to function correctly, please ensure the following environment variables are correctly set: 
-	echo JAVA_INCLUDE: %JAVA_INCLUDE% 
-	echo JAVA_BIN: %JAVA_BIN% 
-	echo on 
-	..\..\..\swig.exe -java $(InputPath) 
-	
-# End Custom Build
-
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-	echo on 
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-	
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-
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diff --git a/Examples/doxygencomments/java/multimap/example.i b/Examples/doxygencomments/java/multimap/example.i
deleted file mode 100644
index 8d67282a5..000000000
--- a/Examples/doxygencomments/java/multimap/example.i
+++ /dev/null
@@ -1,109 +0,0 @@
-/* File : example.i */
-%module example
-
-%{
-extern int gcd(int x, int y);
-extern int gcdmain(int argc, char *argv[]);
-extern int count(char *bytes, int len, char c);
-extern void capitalize (char *str, int len);
-extern void circle (double cx, double cy);
-extern int squareCubed (int n, int *OUTPUT);
-%}
-
-extern int    gcd(int x, int y);
-
-%typemap(jni) (int argc, char *argv[]) "jobjectArray"
-%typemap(jtype) (int argc, char *argv[]) "String[]"
-%typemap(jstype) (int argc, char *argv[]) "String[]"
-
-%typemap(javain) (int argc, char *argv[]) "$javainput"
-
-%typemap(in) (int argc, char *argv[]) (jstring *jsarray) {
-int i;
-
-  $1 = (*jenv)->GetArrayLength(jenv, $input);
-  if ($1 == 0) {
-    SWIG_JavaThrowException(jenv, SWIG_JavaIndexOutOfBoundsException, "Array must contain at least 1 element");
-    return $null;
-  }
-  $2 = (char **) malloc(($1+1)*sizeof(char *));
-  jsarray = (jstring *) malloc($1*sizeof(jstring));
-  for (i = 0; i < $1; i++) {
-    jsarray[i] = (jstring) (*jenv)->GetObjectArrayElement(jenv, $input, i);
-    $2[i] = (char *) (*jenv)->GetStringUTFChars(jenv, jsarray[i], 0);
-  }
-  $2[i] = 0;
-}
-
-%typemap(argout) (int argc, char *argv[]) "" /* override char *[] default */
-
-%typemap(freearg) (int argc, char *argv[]) {
-int i;
-  for (i = 0; i < $1; i++) {
-    (*jenv)->ReleaseStringUTFChars(jenv, jsarray$argnum[i], $2[i]);
-  }
-  free($2);
-}
-
-extern int gcdmain(int argc, char *argv[]);
-
-%typemap(jni) (char *bytes, int len) "jstring"
-%typemap(jtype) (char *bytes, int len) "String"
-%typemap(jstype) (char *bytes, int len) "String"
-
-%typemap(javain) (char *bytes, int len) "$javainput"
-
-%typemap(in) (char *bytes, int len) {
-  $1 = ($1_type)(*jenv)->GetStringUTFChars(jenv, $input, 0);
-  $2 = (*jenv)->GetStringUTFLength(jenv, $input);
-}
-
-%typemap(freearg) (char *bytes, int len) %{
-  (*jenv)->ReleaseStringUTFChars(jenv, $input, $1);
-%}
-
-extern int count(char *bytes, int len, char c);
-
-/* This example shows how to wrap a function that mutates a c string. A one
- * element Java string array is used so that the string can be returned modified.*/
-
-%typemap(jni) (char *str, int len) "jobjectArray"
-%typemap(jtype) (char *str, int len) "String[]"
-%typemap(jstype) (char *str, int len) "String[]"
-
-%typemap(javain) (char *str, int len) "$javainput"
-
-%typemap(in) (char *str, int len) (jstring js) {
-  int index = 0;
-  js = (jstring) (*jenv)->GetObjectArrayElement(jenv, $input, index);
-  $1 = (char *) (*jenv)->GetStringUTFChars(jenv, js, 0);
-  $2 = (*jenv)->GetStringUTFLength(jenv, js);
-}
-
-/* Return the mutated string as a modified element in the array. */
-%typemap(argout) (char *str, int len) {
-  jstring newstring = (*jenv)->NewStringUTF(jenv, $1);
-  (*jenv)->SetObjectArrayElement(jenv, $input, 0, newstring);
-}
-
-/* Release memory */
-%typemap(freearg) (char *str, int len) {
-  (*jenv)->ReleaseStringUTFChars(jenv, js$argnum, $1);
-}
-
-extern void capitalize(char *str, int len);
-
-/* A multi-valued constraint.  Force two arguments to lie
-   inside the unit circle */
-
-%typemap(check) (double cx, double cy) {
-   double a = $1*$1 + $2*$2;
-   if (a > 1.0) {
-    SWIG_JavaThrowException(jenv, SWIG_JavaIllegalArgumentException, "$1_name and $2_name must be in unit circle");
-    return;
-   }
-}
-
-extern void circle(double cx, double cy);
-
-
diff --git a/Examples/doxygencomments/java/multimap/main.java b/Examples/doxygencomments/java/multimap/main.java
deleted file mode 100644
index 331ac6b89..000000000
--- a/Examples/doxygencomments/java/multimap/main.java
+++ /dev/null
@@ -1,40 +0,0 @@
-
-public class main {
-
-  static {
-    try {
-      System.loadLibrary("example");
-    } catch (UnsatisfiedLinkError e) {
-      System.err.println("Native code library failed to load. See the chapter on Dynamic Linking Problems in the SWIG Java documentation for help.\n" + e);
-      System.exit(1);
-    }
-  }
-
-  public static void main(String argv[]) {
-
-    // Call our gcd() function
-    int x = 42;
-    int y = 105;
-    int g = example.gcd(x,y);
-    System.out.println("The gcd of " + x + " and " + y + " is " + g);
-    
-    // Call the gcdmain() function
-    String[] args = {"gcdmain","42","105"};
-    example.gcdmain(args);
-    
-    // Call the count function
-    System.out.println(example.count("Hello World", 'l'));
-    
-    // Call the capitalize function
-    String[] capitalizeMe = {"hello world"};
-    example.capitalize(capitalizeMe);
-    System.out.println(capitalizeMe[0]);
-  }
-}
-
-
-
-
-
-
-
diff --git a/Examples/doxygencomments/java/native/Makefile b/Examples/doxygencomments/java/native/Makefile
deleted file mode 100644
index 92afbd4d0..000000000
--- a/Examples/doxygencomments/java/native/Makefile
+++ /dev/null
@@ -1,18 +0,0 @@
-TOP        = ../..
-SWIG       = $(TOP)/../preinst-swig
-SRCS       = 
-TARGET     = example
-INTERFACE  = example.i
-SWIGOPT    =
-
-all::	java
-
-java::
-	$(MAKE) -f $(TOP)/Makefile SRCS='$(SRCS)' SWIG='$(SWIG)' \
-	SWIGOPT='$(SWIGOPT)' TARGET='$(TARGET)' INTERFACE='$(INTERFACE)' java
-	javac *.java
-
-clean::
-	$(MAKE) -f $(TOP)/Makefile java_clean
-
-check: all
diff --git a/Examples/doxygencomments/java/native/example.i b/Examples/doxygencomments/java/native/example.i
deleted file mode 100644
index 21bcf528c..000000000
--- a/Examples/doxygencomments/java/native/example.i
+++ /dev/null
@@ -1,67 +0,0 @@
-/* File : example.i */
-%module example
-
-%{
-#include <string.h>
-
-/*! Structure Point */
-typedef struct point {
-  int x;
-  int y;
-} Point;
-
-/*! Point_create Description
- /param x integer x
- /param y some integer y
- /return a point */
-
-Point *point_create(int x, int y) {
-  Point *p = (Point *) malloc(sizeof(Point));
-  p->x = x;
-  p->y = y;
-
-  return p;
-}
-
-/*! Point_create Description
- /param format the format 
- /param p some p
- /return a character string of the point p */
-
-static char *point_toString(char *format, Point *p) {
-  static char buf[80];
-
-  sprintf(buf, format, p->x, p->y);
-
-  return buf;
-}
-
-/* this function will be wrapped by SWIG */
-char *point_toString1(Point *p) {
-  return point_toString("(%d,%d)", p);
-}
-
-/* this one we wrapped manually*/
-JNIEXPORT jstring JNICALL Java_exampleJNI_point_1toString2(JNIEnv *jenv, jclass jcls, jlong jpoint) {
-    Point * p;
-    jstring result;
-
-    (void)jcls;
-
-    p = *(Point **)&jpoint;
-
-    result = (*jenv)->NewStringUTF(jenv, point_toString("[%d,%d]", p));
-
-    return result;
-}
-%}
-
-
-Point *point_create(int x, int y);
-char *point_toString1(Point *p);
-
-/* give access to free() for memory cleanup of the malloc'd Point */
-extern void free(void *memblock);
-
-%native(point_toString2) char *point_toString2(Point *p);
-
diff --git a/Examples/doxygencomments/java/native/index.html b/Examples/doxygencomments/java/native/index.html
deleted file mode 100644
index 7ecf129ce..000000000
--- a/Examples/doxygencomments/java/native/index.html
+++ /dev/null
@@ -1,33 +0,0 @@
-<html>
-<head>
-<title>SWIG:Examples:java:native</title>
-</head>
-
-<body bgcolor="#ffffff">
-
-
-<tt>SWIG/Examples/java/native/</tt>
-<hr>
-
-<H2>SWIG wrapped and manually wrapped functions in Java</H2>
-
-Click <a href="../../../Doc/Manual/Java.html#using_own_jni_functions">here</a> for the relevant section in the SWIG and Java documentation.
-<p>
-This example compares wrapping a c global function using the manual way and the SWIG way.
-</p>
-
-<ul>
-<li><a href="example.i">example.i</a>. Interface file comparing code wrapped by SWIG and wrapped manually. 
-<li><a href="main.java">main.java</a>. Sample Java program showing calls to both manually wrapped and SWIG wrapped c functions.
-</ul>
-
-<h2>Notes</h2>
-
-<ul>
-<li>SWIG writes all the awkward JNI code for you. You just have to tell SWIG which functions to wrap.
-<li>If memory is allocated in c it needs to be free'd. A function, such as free(), can be provided with access from Java to free the memory.
-</ul>
-
-<hr>
-</body>
-</html>
diff --git a/Examples/doxygencomments/java/native/main.java b/Examples/doxygencomments/java/native/main.java
deleted file mode 100644
index f4760bb3d..000000000
--- a/Examples/doxygencomments/java/native/main.java
+++ /dev/null
@@ -1,19 +0,0 @@
-
-public class main {
-
-  static {
-    try {
-	System.loadLibrary("example");
-    } catch (UnsatisfiedLinkError e) {
-      System.err.println("Native code library failed to load. See the chapter on Dynamic Linking Problems in the SWIG Java documentation for help.\n" + e);
-      System.exit(1);
-    }
-  }
-
-  public static void main(String argv[]) {
-    SWIGTYPE_p_Point p = example.point_create(1, 2);
-    System.out.println("auto wrapped  : " + example.point_toString1(p));
-    System.out.println("manual wrapped: " + example.point_toString2(p));
-    example.free(new SWIGTYPE_p_void(SWIGTYPE_p_Point.getCPtr(p), false)); //clean up c allocated memory
-  }
-}
diff --git a/Examples/doxygencomments/java/pointer/Makefile b/Examples/doxygencomments/java/pointer/Makefile
deleted file mode 100644
index 968c92c6c..000000000
--- a/Examples/doxygencomments/java/pointer/Makefile
+++ /dev/null
@@ -1,18 +0,0 @@
-TOP        = ../..
-SWIG       = $(TOP)/../preinst-swig
-SRCS       = example.c
-TARGET     = example
-INTERFACE  = example.i
-SWIGOPT    =
-
-all::	java
-
-java::
-	$(MAKE) -f $(TOP)/Makefile SRCS='$(SRCS)' SWIG='$(SWIG)' \
-	SWIGOPT='$(SWIGOPT)' TARGET='$(TARGET)' INTERFACE='$(INTERFACE)' java
-	javac *.java
-
-clean::
-	$(MAKE) -f $(TOP)/Makefile java_clean
-
-check: all
diff --git a/Examples/doxygencomments/java/pointer/example.c b/Examples/doxygencomments/java/pointer/example.c
deleted file mode 100644
index b877d9a5b..000000000
--- a/Examples/doxygencomments/java/pointer/example.c
+++ /dev/null
@@ -1,16 +0,0 @@
-/* File : example.c */
-
-void add(int *x, int *y, int *result) {
-  *result = *x + *y;
-}
-
-void sub(int *x, int *y, int *result) {
-  *result = *x - *y;
-}
-
-int divide(int n, int d, int *r) {
-   int q;
-   q = n/d;
-   *r = n - q*d;
-   return q;
-}
diff --git a/Examples/doxygencomments/java/pointer/example.i b/Examples/doxygencomments/java/pointer/example.i
deleted file mode 100644
index 7ac3b8cf8..000000000
--- a/Examples/doxygencomments/java/pointer/example.i
+++ /dev/null
@@ -1,38 +0,0 @@
-/* File : example.i */
-%module example
-
-%{
-extern void add(int *, int *, int *);
-extern void sub(int *, int *, int *);
-extern int divide(int, int, int *);
-%}
-
-/** This example illustrates a couple of different techniques
-   for manipulating C pointers */
-
-/* First we'll use the pointer library */
-
-/*! function add
- \param x some int x
- \param y some int y
- \param result some result
- */
-extern void add(int *x, int *y, int *result);
-%include cpointer.i
-%pointer_functions(int, intp);
-
-/* Next we'll use some typemaps */
-
-%include typemaps.i
-extern void sub(int *INPUT, int *INPUT, int *OUTPUT);
-
-/* Next we'll use typemaps and the %apply directive */
-
-%apply int *OUTPUT { int *r };
-extern int divide(int n, int d, int *r);
-
-
-
-
-
-
diff --git a/Examples/doxygencomments/java/pointer/index.html b/Examples/doxygencomments/java/pointer/index.html
deleted file mode 100644
index c30d549e6..000000000
--- a/Examples/doxygencomments/java/pointer/index.html
+++ /dev/null
@@ -1,165 +0,0 @@
-<html>
-<head>
-<title>SWIG:Examples:java:pointer</title>
-</head>
-
-<body bgcolor="#ffffff">
-
-<tt>SWIG/Examples/java/pointer/</tt>
-<hr>
-
-<H2>Simple Pointer Handling</H2>
-
-<p>
-This example illustrates a couple of techniques for handling
-simple pointers in SWIG.  The prototypical example is a C function
-that operates on pointers such as this:
-
-<blockquote>
-<pre>
-void add(int *x, int *y, int *r) { 
-    *r = *x + *y;
-}
-</pre>
-</blockquote>
-
-By default, SWIG wraps this function exactly as specified and creates
-an interface that expects pointer objects for arguments.  
-SWIG wraps a C pointer with a type wrapper class, for example, SWIGTYPE_p_int for an int*.
-The only problem is how does one go about creating these objects from a Java program?
-<p>
-
-
-<h2>Possible Solutions</h2>
-
-<ul>
-<li>Write some helper functions to explicitly create objects.  For
-example:
-
-<blockquote>
-<pre>
-int *new_int(int ivalue) {
-  int *i = (int *) malloc(sizeof(ivalue));
-  *i = ivalue;
-  return i;
-}
-int get_int(int *i) {
-  return *i;
-}
-
-void delete_int(int *i) {
-  free(i);
-}
-</pre>
-</blockquote>
-
-<p>
-<li>The SWIG pointer library provides an easier way. <br> 
-For example, in the interface file 
-you would do this:
-
-<blockquote>
-<pre>
-%include cpointer.i
-%pointer_functions(int, intp);
-</pre>
-</blockquote>
-
-and from Java you would use pointers like this:
-
-<blockquote>
-<pre>
-SWIGTYPE_p_int a = example.new_intp();
-SWIGTYPE_p_int b = example.new_intp();
-SWIGTYPE_p_int c = example.new_intp();
-example.intp_assign(a,37);
-example.intp_assign(b,42);
-
-// Note that getCPtr() has package access by default
-System.out.println("     a =" + Long.toHexString(SWIGTYPE_p_int.getCPtr(a)));
-System.out.println("     b =" + Long.toHexString(SWIGTYPE_p_int.getCPtr(b)));
-System.out.println("     c =" + Long.toHexString(SWIGTYPE_p_int.getCPtr(c)));
-
-// Call the add() function with some pointers
-example.add(a,b,c);
-
-// Now get the result
-int res = example.intp_value(c);
-System.out.println("     37 + 42 =" + res);
-
-// Clean up the pointers
-example.delete_intp(a);
-example.delete_intp(b);
-example.delete_intp(c);
-</pre>
-</blockquote>
-
-<p>
-<li>Use the SWIG typemap library.  This library allows you to completely
-change the way arguments are processed by SWIG.  For example:
-
-<blockquote>
-<pre>
-%include "typemaps.i"
-void add(int *INPUT, int *INPUT, int *OUTPUT);
-</pre>
-</blockquote>
-
-And in a Java program:
-
-<blockquote>
-<pre>
-int[] r = {0};
-example.sub(37,42,r);
-System.out.println("Result =" + r[0]);
-</pre>
-</blockquote>
-Needless to say, this is substantially easier although a bit unusual.
-
-<p>
-<li>A final alternative is to use the typemaps library in combination
-with the %apply directive.  This allows you to change the names of parameters
-that behave as input or output parameters. For example:
-
-<blockquote>
-<pre>
-%include "typemaps.i"
-%apply int *INPUT {int *x, int *y};
-%apply int *OUTPUT {int *r};
-
-void add(int *x, int *y, int *r);
-void sub(int *x, int *y, int *r);
-void mul(int *x, int *y, int *r);
-... etc ...
-</pre>
-</blockquote>
-
-</ul>
-
-<h2>Example</h2>
-
-The following example illustrates the use of these features for pointer
-extraction.
-
-<ul>
-<li> <a href="example.c">example.c</a>  (C Source)
-<li> <a href="example.i">example.i</a>  (Swig interface)
-<li> <a href="main.java">main.java</a>  (Java program)
-</ul>
-
-<h2>Notes</h2>
-
-<ul>
-<li>Since pointers are used for so many different things (arrays, output values,
-etc...) the complexity of pointer handling can be as complicated as you want to
-make it.
-
-<p>
-<li>More documentation on the typemaps.i and cpointer.i library files can be
-found in the SWIG user manual.  The files also contain documentation.
-
-</ul>
-
-<hr>
-</body>
-</html>
diff --git a/Examples/doxygencomments/java/pointer/main.java b/Examples/doxygencomments/java/pointer/main.java
deleted file mode 100644
index e96e02eaa..000000000
--- a/Examples/doxygencomments/java/pointer/main.java
+++ /dev/null
@@ -1,55 +0,0 @@
-
-public class main {
-
-  static {
-    try {
-	System.loadLibrary("example");
-    } catch (UnsatisfiedLinkError e) {
-      System.err.println("Native code library failed to load. See the chapter on Dynamic Linking Problems in the SWIG Java documentation for help.\n" + e);
-      System.exit(1);
-    }
-  }
-
-  public static void main(String argv[]) {
-
-    // First create some objects using the pointer library.
-    System.out.println("Testing the pointer library");
-    SWIGTYPE_p_int a = example.new_intp();
-    SWIGTYPE_p_int b = example.new_intp();
-    SWIGTYPE_p_int c = example.new_intp();
-    example.intp_assign(a,37);
-    example.intp_assign(b,42);
-
-    // Note that getCPtr() has package access by default
-    System.out.println("     a =" + Long.toHexString(SWIGTYPE_p_int.getCPtr(a)));
-    System.out.println("     b =" + Long.toHexString(SWIGTYPE_p_int.getCPtr(b)));
-    System.out.println("     c =" + Long.toHexString(SWIGTYPE_p_int.getCPtr(c)));
-
-    // Call the add() function with some pointers
-    example.add(a,b,c);
-
-    // Now get the result
-    int res = example.intp_value(c);
-    System.out.println("     37 + 42 =" + res);
-
-    // Clean up the pointers
-    example.delete_intp(a);
-    example.delete_intp(b);
-    example.delete_intp(c);
-
-    // Now try the typemap library
-    // Now it is no longer necessary to manufacture pointers.
-    // Instead we use a single element array which in Java is modifiable.
-
-    System.out.println("Trying the typemap library");
-    int[] r = {0};
-    example.sub(37,42,r);
-    System.out.println("     37 - 42 = " + r[0]);
-
-    // Now try the version with return value
-
-    System.out.println("Testing return value");
-    int q = example.divide(42,37,r);
-    System.out.println("     42/37 = " + q + " remainder " + r[0]);
-  }
-}
diff --git a/Examples/doxygencomments/java/reference/Makefile b/Examples/doxygencomments/java/reference/Makefile
deleted file mode 100644
index 14c301703..000000000
--- a/Examples/doxygencomments/java/reference/Makefile
+++ /dev/null
@@ -1,18 +0,0 @@
-TOP        = ../..
-SWIG       = $(TOP)/../preinst-swig
-CXXSRCS    = example.cxx
-TARGET     = example
-INTERFACE  = example.i
-SWIGOPT    =
-
-all::	java
-
-java::
-	$(MAKE) -f $(TOP)/Makefile CXXSRCS='$(CXXSRCS)' SWIG='$(SWIG)' \
-	SWIGOPT='$(SWIGOPT)' TARGET='$(TARGET)' INTERFACE='$(INTERFACE)' java_cpp
-	javac *.java
-
-clean::
-	$(MAKE) -f $(TOP)/Makefile java_clean
-
-check: all
diff --git a/Examples/doxygencomments/java/reference/example.cxx b/Examples/doxygencomments/java/reference/example.cxx
deleted file mode 100644
index 8a513bf49..000000000
--- a/Examples/doxygencomments/java/reference/example.cxx
+++ /dev/null
@@ -1,46 +0,0 @@
-/* File : example.cxx */
-
-/* Deal with Microsoft's attempt at deprecating C standard runtime functions */
-#if !defined(SWIG_NO_CRT_SECURE_NO_DEPRECATE) && defined(_MSC_VER)
-# define _CRT_SECURE_NO_DEPRECATE
-#endif
-
-#include "example.h"
-#include <stdio.h>
-#include <stdlib.h>
-
-Vector operator+(const Vector &a, const Vector &b) {
-  Vector r;
-  r.x = a.x + b.x;
-  r.y = a.y + b.y;
-  r.z = a.z + b.z;
-  return r;
-}
-
-char *Vector::print() {
-  static char temp[512];
-  sprintf(temp,"Vector %p (%g,%g,%g)", this, x,y,z);
-  return temp;
-}
-
-VectorArray::VectorArray(int size) {
-  items = new Vector[size];
-  maxsize = size;
-}
-
-VectorArray::~VectorArray() {
-  delete [] items;
-}
-
-Vector &VectorArray::operator[](int index) {
-  if ((index < 0) || (index >= maxsize)) {
-    printf("Panic! Array index out of bounds.\n");
-    exit(1);
-  }
-  return items[index];
-}
-
-int VectorArray::size() {
-  return maxsize;
-}
-
diff --git a/Examples/doxygencomments/java/reference/example.h b/Examples/doxygencomments/java/reference/example.h
deleted file mode 100644
index 4915adb1b..000000000
--- a/Examples/doxygencomments/java/reference/example.h
+++ /dev/null
@@ -1,26 +0,0 @@
-/* File : example.h */
-
-class Vector {
-private:
-  double x,y,z;
-public:
-  Vector() : x(0), y(0), z(0) { };
-  Vector(double x, double y, double z) : x(x), y(y), z(z) { };
-  friend Vector operator+(const Vector &a, const Vector &b);
-  char *print();
-};
-
-class VectorArray {
-private:
-  Vector *items;
-  int     maxsize;
-public:
-  VectorArray(int maxsize);
-  ~VectorArray();
-  Vector &operator[](int);
-  int size();
-};
-
-
-
-  
diff --git a/Examples/doxygencomments/java/reference/example.i b/Examples/doxygencomments/java/reference/example.i
deleted file mode 100644
index 8e4d05239..000000000
--- a/Examples/doxygencomments/java/reference/example.i
+++ /dev/null
@@ -1,58 +0,0 @@
-/* File : example.i */
-
-/* This file has a few "typical" uses of C++ references. */
-
-%module example
-
-%{
-#include "example.h"
-%}
-
-/*! Class vector description
- \author Fred
- \exception something random 
- \since 1.0
- \name ignoreme
- \see something */
-class Vector {
-public:
-    Vector(double x, double y, double z);
-   ~Vector();
-    char *print();
-};
-
-/** This helper function calls an overloaded operator */
-%inline %{
-Vector addv(Vector &a, Vector &b) {
-  return a+b;
-}
-%}
-
-/*! Class Vector Array
- \exception something random 
- \since 1.3
- \see something
- \author Fred */
-class VectorArray {
-public:
-  VectorArray(int maxsize);
-  ~VectorArray();
-  int size();
-  
-  /* This wrapper provides an alternative to the [] operator */
-  %extend {
-    Vector &get(int index) {
-      return (*$self)[index];
-    }
-    void set(int index, Vector &a) {
-      (*$self)[index] = a;
-    }
-  }
-};
-
-
-
-
-
-
-
diff --git a/Examples/doxygencomments/java/reference/index.html b/Examples/doxygencomments/java/reference/index.html
deleted file mode 100644
index 64b129cbb..000000000
--- a/Examples/doxygencomments/java/reference/index.html
+++ /dev/null
@@ -1,147 +0,0 @@
-<html>
-<head>
-<title>SWIG:Examples:java:reference</title>
-</head>
-
-<body bgcolor="#ffffff">
-
-
-<tt>SWIG/Examples/java/reference/</tt>
-<hr>
-
-<H2>C++ Reference Handling</H2>
-
-<p>
-This example tests SWIG's handling of C++ references.  Since C++
-references are closely related to pointers (as both refer to a
-location in memory), SWIG simply collapses all references into
-pointers when creating wrappers.
-
-<h2>Some examples</h2>
-
-References are most commonly used as function parameter.  For example,
-you might have an operator like this:
-
-<blockquote>
-<pre>
-Vector operator+(const Vector &amp;a, const Vector &amp;b) {
-   Vector result;
-   result.x = a.x + b.x;
-   result.y = a.y + b.y;
-   result.z = a.z + b.z;
-   return result;
-}
-</pre>
-</blockquote>
-
-or a function:
-
-<blockquote>
-<pre>
-Vector addv(const Vector &amp;a, const Vector &amp;b) {
-   Vector result;
-   result.x = a.x + b.x;
-   result.y = a.y + b.y;
-   result.z = a.z + b.z;
-   return result;
-}
-</pre>
-</blockquote>
-
-In these cases, SWIG transforms everything into a pointer and creates a wrapper
-that looks like this:
-
-<blockquote>
-<pre>
-Vector wrap_addv(Vector *a, Vector *b) {
-    return addv(*a,*b);
-}
-</pre>
-</blockquote>
-
-Occasionally, a reference is used as a return value of a function
-when the return result is to be used as an lvalue in an expression.
-The prototypical example is an operator like this:
-
-<blockquote>
-<pre>
-Vector &amp;operator[](int index);
-</pre>
-</blockquote>
-
-or a method:
-
-<blockquote>
-<pre>
-Vector &amp;get(int index);
-</pre>
-</blockquote>
-
-For functions returning references, a wrapper like this is created:
-
-<blockquote>
-<pre>
-Vector *wrap_Object_get(Object *self, int index) {
-    Vector &amp;result = self-&gt;get(index);
-    return &amp;result;
-}
-</pre>
-</blockquote>
-
-The following <a href="example.h">header file</a> contains some class
-definitions with some operators and use of references.
-
-<h2>SWIG Interface</h2>
-
-SWIG does NOT support overloaded operators so it can not directly build
-an interface to the classes in the above file.   However, a number of workarounds
-can be made.  For example, an overloaded operator can be stuck behind a function
-call such as the <tt>addv()</tt> function above.  Array access can be handled
-with a pair of set/get functions like this:
-
-<blockquote>
-<pre>
-class VectorArray {
-public:
- ...
-   %addmethods {
-    Vector &amp;get(int index) {
-      return (*self)[index];
-    }
-    void set(int index, Vector &amp;a) {
-      (*self)[index] = a;
-    }
-   }
-   ...
-}
-</pre>
-</blockquote>
-
-Click <a href="example.i">here</a> to see a SWIG interface file with these additions.
-
-<h2>Sample Java program</h2>
-
-Click <a href="main.java">here</a> to see a Java program that manipulates some C++ references.
-
-<h2>Notes:</h2>
-
-<ul>
-<li>C++ references primarily provide notational convenience for C++
-source code.  However, Java only supports the 'x.a' 
-notation so it doesn't much matter.
-
-<p>
-<li>When a program returns a reference, a pointer is returned.
-Unlike return by value, memory is not allocated to hold the
-return result.
-
-<p>
-<li>SWIG has particular trouble handling various combinations of references
-and pointers.  This is side effect of an old parsing scheme and
-type representation that will be replaced in future versions.
-
-</ul>
-
-<hr>
-</body>
-</html>
diff --git a/Examples/doxygencomments/java/reference/main.java b/Examples/doxygencomments/java/reference/main.java
deleted file mode 100644
index 4fd354761..000000000
--- a/Examples/doxygencomments/java/reference/main.java
+++ /dev/null
@@ -1,79 +0,0 @@
-// This example illustrates the manipulation of C++ references in Java.
-
-public class main {
-  static {
-    try {
-        System.loadLibrary("example");
-    } catch (UnsatisfiedLinkError e) {
-      System.err.println("Native code library failed to load. See the chapter on Dynamic Linking Problems in the SWIG Java documentation for help.\n" + e);
-      System.exit(1);
-    }
-  }
-
-  public static void main(String argv[]) 
-  {
-    System.out.println( "Creating some objects:" );
-    Vector a = new Vector(3,4,5);
-    Vector b = new Vector(10,11,12);
-    
-    System.out.println( "    Created " + a.print() );
-    System.out.println( "    Created " + b.print() );
-    
-    // ----- Call an overloaded operator -----
-    
-    // This calls the wrapper we placed around
-    //
-    //      operator+(const Vector &a, const Vector &) 
-    //
-    // It returns a new allocated object.
-    
-    System.out.println( "Adding a+b" );
-    Vector c = example.addv(a,b);
-    System.out.println( "    a+b = " + c.print() );
-    
-    // Note: Unless we free the result, a memory leak will occur if the -noproxy commandline
-    // is used as the proxy classes define finalizers which call the delete() method. When
-    // -noproxy is not specified the memory management is controlled by the garbage collector.
-    // You can still call delete(). It will free the c++ memory immediately, but not the 
-    // Java memory! You then must be careful not to call any member functions as it will 
-    // use a NULL c pointer on the underlying c++ object. We set the Java object to null
-    // which will then throw a Java exception should we attempt to use it again.
-    c.delete();
-    c = null;
-    
-    // ----- Create a vector array -----
-    
-    System.out.println( "Creating an array of vectors" );
-    VectorArray va = new VectorArray(10);
-    System.out.println( "    va = " + va.toString() );
-    
-    // ----- Set some values in the array -----
-    
-    // These operators copy the value of Vector a and Vector b to the vector array
-    va.set(0,a);
-    va.set(1,b);
-    
-    // This works, but it would cause a memory leak if -noproxy was used!
-    
-    va.set(2,example.addv(a,b));
-    
-
-    // Get some values from the array
-    
-    System.out.println( "Getting some array values" );
-    for (int i=0; i<5; i++)
-        System.out.println( "    va(" + i + ") = " + va.get(i).print() );
-    
-    // Watch under resource meter to check on this
-    System.out.println( "Making sure we don't leak memory." );
-    for (int i=0; i<1000000; i++)
-        c = va.get(i%10);
-    
-    // ----- Clean up -----
-    // This could be omitted. The garbage collector would then clean up for us.
-    System.out.println( "Cleaning up" );
-    va.delete();
-    a.delete();
-    b.delete();
-  }
-}
diff --git a/Examples/doxygencomments/java/simple/Makefile b/Examples/doxygencomments/java/simple/Makefile
deleted file mode 100644
index 968c92c6c..000000000
--- a/Examples/doxygencomments/java/simple/Makefile
+++ /dev/null
@@ -1,18 +0,0 @@
-TOP        = ../..
-SWIG       = $(TOP)/../preinst-swig
-SRCS       = example.c
-TARGET     = example
-INTERFACE  = example.i
-SWIGOPT    =
-
-all::	java
-
-java::
-	$(MAKE) -f $(TOP)/Makefile SRCS='$(SRCS)' SWIG='$(SWIG)' \
-	SWIGOPT='$(SWIGOPT)' TARGET='$(TARGET)' INTERFACE='$(INTERFACE)' java
-	javac *.java
-
-clean::
-	$(MAKE) -f $(TOP)/Makefile java_clean
-
-check: all
diff --git a/Examples/doxygencomments/java/simple/example.c b/Examples/doxygencomments/java/simple/example.c
deleted file mode 100644
index 1c2af789c..000000000
--- a/Examples/doxygencomments/java/simple/example.c
+++ /dev/null
@@ -1,18 +0,0 @@
-/* File : example.c */
-
-/* A global variable */
-double Foo = 3.0;
-
-/* Compute the greatest common divisor of positive integers */
-int gcd(int x, int y) {
-  int g;
-  g = y;
-  while (x > 0) {
-    g = x;
-    x = y % x;
-    y = g;
-  }
-  return g;
-}
-
-
diff --git a/Examples/doxygencomments/java/simple/example.dsp b/Examples/doxygencomments/java/simple/example.dsp
deleted file mode 100644
index 8e1f8415e..000000000
--- a/Examples/doxygencomments/java/simple/example.dsp
+++ /dev/null
@@ -1,158 +0,0 @@
-# Microsoft Developer Studio Project File - Name="example" - Package Owner=<4>
-# Microsoft Developer Studio Generated Build File, Format Version 6.00
-# ** DO NOT EDIT **
-
-# TARGTYPE "Win32 (x86) Dynamic-Link Library" 0x0102
-
-CFG=example - Win32 Release
-!MESSAGE This is not a valid makefile. To build this project using NMAKE,
-!MESSAGE use the Export Makefile command and run
-!MESSAGE 
-!MESSAGE NMAKE /f "example.mak".
-!MESSAGE 
-!MESSAGE You can specify a configuration when running NMAKE
-!MESSAGE by defining the macro CFG on the command line. For example:
-!MESSAGE 
-!MESSAGE NMAKE /f "example.mak" CFG="example - Win32 Release"
-!MESSAGE 
-!MESSAGE Possible choices for configuration are:
-!MESSAGE 
-!MESSAGE "example - Win32 Debug" (based on "Win32 (x86) Dynamic-Link Library")
-!MESSAGE "example - Win32 Release" (based on "Win32 (x86) Dynamic-Link Library")
-!MESSAGE 
-
-# Begin Project
-# PROP AllowPerConfigDependencies 0
-# PROP Scc_ProjName ""
-# PROP Scc_LocalPath ""
-CPP=cl.exe
-MTL=midl.exe
-RSC=rc.exe
-
-!IF  "$(CFG)" == "example - Win32 Debug"
-
-# PROP BASE Use_MFC 0
-# PROP BASE Use_Debug_Libraries 1
-# PROP BASE Output_Dir "Debug"
-# PROP BASE Intermediate_Dir "Debug"
-# PROP BASE Target_Dir ""
-# PROP Use_MFC 0
-# PROP Use_Debug_Libraries 1
-# PROP Output_Dir "Debug"
-# PROP Intermediate_Dir "Debug"
-# PROP Ignore_Export_Lib 0
-# PROP Target_Dir ""
-# ADD BASE CPP /nologo /MTd /W3 /Gm /GX /ZI /Od /D "WIN32" /D "_DEBUG" /D "_WINDOWS" /D "_MBCS" /D "_USRDLL" /D "EXAMPLE_EXPORTS" /YX /FD /GZ /c
-# ADD CPP /nologo /MTd /W3 /Gm /GX /ZI /Od /I "$(JAVA_INCLUDE)" /I "$(JAVA_INCLUDE)\win32" /D "WIN32" /D "_DEBUG" /D "_WINDOWS" /D "_MBCS" /D "_USRDLL" /D "EXAMPLE_EXPORTS" /YX /FD /GZ /c
-# ADD BASE MTL /nologo /D "_DEBUG" /mktyplib203 /win32
-# ADD MTL /nologo /D "_DEBUG" /mktyplib203 /win32
-# ADD BASE RSC /l 0x809 /d "_DEBUG"
-# ADD RSC /l 0x809 /d "_DEBUG"
-BSC32=bscmake.exe
-# ADD BASE BSC32 /nologo
-# ADD BSC32 /nologo
-LINK32=link.exe
-# ADD BASE LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib /nologo /dll /debug /machine:I386 /pdbtype:sept
-# ADD LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib /nologo /dll /debug /machine:I386 /out:"example.dll" /pdbtype:sept
-# Begin Special Build Tool
-SOURCE="$(InputPath)"
-PostBuild_Desc=Java compile post-build step
-PostBuild_Cmds=echo on	"%JAVA_BIN%\javac" *.java
-# End Special Build Tool
-
-!ELSEIF  "$(CFG)" == "example - Win32 Release"
-
-# PROP BASE Use_MFC 0
-# PROP BASE Use_Debug_Libraries 0
-# PROP BASE Output_Dir "Release"
-# PROP BASE Intermediate_Dir "Release"
-# PROP BASE Target_Dir ""
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-# PROP Output_Dir "Release"
-# PROP Intermediate_Dir "Release"
-# PROP Ignore_Export_Lib 0
-# PROP Target_Dir ""
-# ADD BASE CPP /nologo /MT /W3 /GX /O2 /D "WIN32" /D "NDEBUG" /D "_WINDOWS" /D "_MBCS" /D "_USRDLL" /D "EXAMPLE_EXPORTS" /YX /FD /c
-# ADD CPP /nologo /MT /W3 /GX /O2 /I "$(JAVA_INCLUDE)" /I "$(JAVA_INCLUDE)\win32" /D "WIN32" /D "NDEBUG" /D "_WINDOWS" /D "_MBCS" /D "_USRDLL" /D "EXAMPLE_EXPORTS" /YX /FD /c
-# ADD BASE MTL /nologo /D "NDEBUG" /mktyplib203 /win32
-# ADD MTL /nologo /D "NDEBUG" /mktyplib203 /win32
-# ADD BASE RSC /l 0x809 /d "NDEBUG"
-# ADD RSC /l 0x809 /d "NDEBUG"
-BSC32=bscmake.exe
-# ADD BASE BSC32 /nologo
-# ADD BSC32 /nologo
-LINK32=link.exe
-# ADD BASE LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib /nologo /dll /machine:I386
-# ADD LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib /nologo /dll /machine:I386 /out:"example.dll"
-# Begin Special Build Tool
-SOURCE="$(InputPath)"
-PostBuild_Desc=Java compile post-build step
-PostBuild_Cmds=echo on	"%JAVA_BIN%\javac" *.java
-# End Special Build Tool
-
-!ENDIF 
-
-# Begin Target
-
-# Name "example - Win32 Debug"
-# Name "example - Win32 Release"
-# Begin Group "Source Files"
-
-# PROP Default_Filter "cpp;c;cxx;rc;def;r;odl;idl;hpj;bat"
-# Begin Source File
-
-SOURCE=.\example.c
-# End Source File
-# Begin Source File
-
-SOURCE=.\example_wrap.c
-# End Source File
-# End Group
-# Begin Group "Header Files"
-
-# PROP Default_Filter "h;hpp;hxx;hm;inl"
-# End Group
-# Begin Group "Resource Files"
-
-# PROP Default_Filter "ico;cur;bmp;dlg;rc2;rct;bin;rgs;gif;jpg;jpeg;jpe"
-# End Group
-# Begin Source File
-
-SOURCE=.\example.i
-
-!IF  "$(CFG)" == "example - Win32 Debug"
-
-# Begin Custom Build
-InputPath=.\example.i
-InputName=example
-
-"$(InputName)_wrap.c" : $(SOURCE) "$(INTDIR)" "$(OUTDIR)"
-	echo In order to function correctly, please ensure the following environment variables are correctly set: 
-	echo JAVA_INCLUDE: %JAVA_INCLUDE% 
-	echo JAVA_BIN: %JAVA_BIN% 
-	echo on 
-	..\..\..\swig.exe -java $(InputPath) 
-	
-# End Custom Build
-
-!ELSEIF  "$(CFG)" == "example - Win32 Release"
-
-# Begin Custom Build
-InputPath=.\example.i
-InputName=example
-
-"$(InputName)_wrap.c" : $(SOURCE) "$(INTDIR)" "$(OUTDIR)"
-	echo In order to function correctly, please ensure the following environment variables are correctly set: 
-	echo JAVA_INCLUDE: %JAVA_INCLUDE% 
-	echo JAVA_BIN: %JAVA_BIN% 
-	echo on 
-	..\..\..\swig.exe -java $(InputPath) 
-	
-# End Custom Build
-
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-
-# End Source File
-# End Target
-# End Project
diff --git a/Examples/doxygencomments/java/simple/example.i b/Examples/doxygencomments/java/simple/example.i
deleted file mode 100644
index d10fe5e19..000000000
--- a/Examples/doxygencomments/java/simple/example.i
+++ /dev/null
@@ -1,11 +0,0 @@
-/* File : example.i */
-%module example
-
-%inline %{
-/*! Function foo
- \param x int x
- \param y int y
- \return the gcd */
-extern int    gcd(int x, int y);
-extern double Foo; /*!< description of double foo */
-%}
diff --git a/Examples/doxygencomments/java/simple/index.html b/Examples/doxygencomments/java/simple/index.html
deleted file mode 100644
index a363327fe..000000000
--- a/Examples/doxygencomments/java/simple/index.html
+++ /dev/null
@@ -1,108 +0,0 @@
-<html>
-<head>
-<title>SWIG:Examples:java:simple</title>
-</head>
-
-<body bgcolor="#ffffff">
-
-
-<tt>SWIG/Examples/java/simple/</tt>
-<hr>
-
-<H2>Simple Java Example</H2>
-
-<p>
-This example illustrates how you can hook Java to a very simple C program containing
-a function and a global variable.
-
-<h2>The C Code</h2>
-
-Suppose you have the following C code:
-
-<blockquote>
-<pre>
-/* File : example.c */
-
-/* A global variable */
-double Foo = 3.0;
-
-/* Compute the greatest common divisor of positive integers */
-int gcd(int x, int y) {
-  int g;
-  g = y;
-  while (x &gt; 0) {
-    g = x;
-    x = y % x;
-    y = g;
-  }
-  return g;
-}
-</pre>
-</blockquote>
-
-<h2>The SWIG interface</h2>
-
-Here is a simple SWIG interface file:
-
-<blockquote>
-<pre>
-/* File: example.i */
-%module example
-
-extern int gcd(int x, int y);
-extern double Foo;
-</pre>
-</blockquote>
-
-<h2>Compilation</h2>
-
-<ol>
-<li><tt>swig -java <a href="example.i">example.i</a></tt>
-<p>
-<li>Compile <tt><a href="example_wrap.c">example_wrap.c</a></tt> and <tt><a href="example.c">example.c</a></tt>
-to create the extension <tt>libexample.so (unix)</tt>. 
-</ol>
-
-<h2>Using the extension</h2>
-
-Click <a href="main.java">here</a> to see a program that calls our C functions from Java.
-<p>
-Compile the java files <tt><a href="example.java">example.java</a></tt> and <tt><a href="main.java">main.java</a></tt>
-to create the class files example.class and main.class before running main in the JVM.  Ensure that the libexample.so file is in your LD_LIBRARY_PATH before running. For example:
-<blockquote>
-<pre>
-export LD_LIBRARY_PATH=. #ksh 
-javac *.java
-java main
-</pre>
-</blockquote>
-
-<h2>Key points</h2>
-
-<ul>
-<li>Use the <tt>loadLibrary</tt> statement from java to load and access the generated java classes. For example:
-<blockquote>
-<pre>
-System.loadLibrary("example");
-</pre>
-</blockquote>
-
-<li>C functions work just like Java functions. For example:
-<blockquote>
-<pre>
-int g = example.gcd(42,105);
-</pre>
-</blockquote>
-
-<li>C global variables are accessed through get and set functions in the module class. For example:
-<blockquote>
-<pre>
-double a = example.get_Foo();
-example.set_Foo(20.0);
-</pre>
-</blockquote>
-</ul>
-
-<hr>
-</body>
-</html>
diff --git a/Examples/doxygencomments/java/simple/main.java b/Examples/doxygencomments/java/simple/main.java
deleted file mode 100644
index 6d224a4dc..000000000
--- a/Examples/doxygencomments/java/simple/main.java
+++ /dev/null
@@ -1,32 +0,0 @@
-
-public class main {
-
-  static {
-    try {
-	System.loadLibrary("example");
-    } catch (UnsatisfiedLinkError e) {
-      System.err.println("Native code library failed to load. See the chapter on Dynamic Linking Problems in the SWIG Java documentation for help.\n" + e);
-      System.exit(1);
-    }
-  }
-
-  public static void main(String argv[]) {
-    // Call our gcd() function
-    
-    int x = 42;
-    int y = 105;
-    int g = example.gcd(x,y);
-    System.out.println("The gcd of " + x + " and " + y + " is " + g);
-    
-    // Manipulate the Foo global variable
-    
-    // Output its current value
-    System.out.println("Foo = " + example.getFoo());
-    
-    // Change its value
-    example.setFoo(3.1415926);
-    
-    // See if the change took effect
-    System.out.println("Foo = " + example.getFoo());
-  }
-}
diff --git a/Examples/doxygencomments/java/template/Makefile b/Examples/doxygencomments/java/template/Makefile
deleted file mode 100644
index 2b3d35c6a..000000000
--- a/Examples/doxygencomments/java/template/Makefile
+++ /dev/null
@@ -1,18 +0,0 @@
-TOP        = ../..
-SWIG       = $(TOP)/../preinst-swig
-CXXSRCS    = 
-TARGET     = example
-INTERFACE  = example.i
-SWIGOPT    =
-
-all::	java
-
-java::
-	$(MAKE) -f $(TOP)/Makefile CXXSRCS='$(CXXSRCS)' SWIG='$(SWIG)' \
-	SWIGOPT='$(SWIGOPT)' TARGET='$(TARGET)' INTERFACE='$(INTERFACE)' java_cpp
-	javac *.java
-
-clean::
-	$(MAKE) -f $(TOP)/Makefile java_clean
-
-check: all
diff --git a/Examples/doxygencomments/java/template/example.h b/Examples/doxygencomments/java/template/example.h
deleted file mode 100644
index 9ec711391..000000000
--- a/Examples/doxygencomments/java/template/example.h
+++ /dev/null
@@ -1,39 +0,0 @@
-/* File : example.h */
-
-// Some template definitions
-
-/*! Template class T 
- \author cmfoil 
- \sa something something */
-
-template<class T> T max(T a, T b) { return  a>b ? a : b; }
-
-/*! Template class Vector 
- \author cmfoil 
- \sa something something */
-template<class T> class vector {
-  T *v;
-  int sz;
- public:
-  vector(int _sz) {
-    v = new T[_sz];
-    sz = _sz;
-  }
-  T &get(int index) {
-    return v[index];
-  }
-  void set(int index, T &val) {
-    v[index] = val;
-  } /*!< Something about set */
-#ifdef SWIG
-  %extend {
-    T getitem(int index) {
-      return $self->get(index);
-    }/*!< Something about get item */
-    void setitem(int index, T val) {
-      $self->set(index,val);
-    }
-  }
-#endif
-};
-
diff --git a/Examples/doxygencomments/java/template/example.i b/Examples/doxygencomments/java/template/example.i
deleted file mode 100644
index 8f94c4da1..000000000
--- a/Examples/doxygencomments/java/template/example.i
+++ /dev/null
@@ -1,17 +0,0 @@
-/* File : example.i */
-%module example
-
-%{
-#include "example.h"
-%}
-
-/* Let's just grab the original header file here */
-%include "example.h"
-
-/* Now instantiate some specific template declarations */
-
-%template(maxint) max<int>;
-%template(maxdouble) max<double>;
-%template(vecint) vector<int>;
-%template(vecdouble) vector<double>;
-
diff --git a/Examples/doxygencomments/java/template/index.html b/Examples/doxygencomments/java/template/index.html
deleted file mode 100644
index 1aebd4c2a..000000000
--- a/Examples/doxygencomments/java/template/index.html
+++ /dev/null
@@ -1,102 +0,0 @@
-<html>
-<head>
-<title>SWIG:Examples:java:template</title>
-</head>
-
-<body bgcolor="#ffffff">
-
-
-<tt>SWIG/Examples/java/template/</tt>
-<hr>
-
-<H2>C++ template support</H2>
-
-<p>
-This example illustrates how C++ templates can be used from Java using SWIG.
-
-<h2>The C++ Code</h2>
-
-Lets take a templated function and a templated class as follows:
-
-<blockquote>
-<pre>
-/* File : example.h */
-
-// Some template definitions
-
-template<class T> T max(T a, T b) { return  a&gt;b ? a : b; }
-
-template<class T> class vector {
-  T *v;
-  int sz;
- public:
-  vector(int _sz) {
-    v = new T[_sz];
-    sz = _sz;
-  }
-  T &amp;get(int index) {
-    return v[index];
-  }
-  void set(int index, T &amp;val) {
-    v[index] = val;
-  }
-#ifdef SWIG
-  %addmethods {
-    T getitem(int index) {
-      return self-&gt;get(index);
-    }
-    void setitem(int index, T val) {
-      self-&gt;set(index,val);
-    }
-  }
-#endif
-};
-</pre>
-</blockquote>
-The %addmethods is used for a neater interface from Java as the functions <tt>get</tt> and <tt>set</tt> use C++ references to primitive types. These are tricky to use from Java as they end up as a pointer in Java (Java long).
-
-<h2>The SWIG interface</h2>
-
-A simple SWIG interface for this can be built by simply grabbing the header file
-like this:
-
-<blockquote>
-<pre>
-/* File : example.i */
-%module example
-
-%{
-#include "example.h"
-%}
-
-/* Let's just grab the original header file here */
-%include "example.h"
-
-/* Now instantiate some specific template declarations */
-
-%template(maxint) max<int>;
-%template(maxdouble) max<double>;
-%template(vecint) vector<int>;
-%template(vecdouble) vector<double>;
-</pre>
-</blockquote>
-
-Note that SWIG parses the templated function <tt>max</tt> and templated class <tt>vector</tt> and so knows about them. However to generate code for use from Java, SWIG has to be told which class/type to use as the template parameter. The SWIG directive %template is used for this.
-
-<h2>A sample Java program</h2>
-
-Click <a href="main.java">here</a> to see a Java program that calls the C++ functions from Java.
-
-<h2>Notes</h2>
-Use templated classes just like you would any other SWIG generated Java class. Use the classnames specified by the %template directive.
-
-<blockquote>
-<pre>
-vecdouble dv = new vecdouble(1000);
-dv.setitem(i, 12.34));
-</pre>
-</blockquote>
-
-<hr>
-</body>
-</html>
diff --git a/Examples/doxygencomments/java/template/main.java b/Examples/doxygencomments/java/template/main.java
deleted file mode 100644
index 9129fcf2a..000000000
--- a/Examples/doxygencomments/java/template/main.java
+++ /dev/null
@@ -1,45 +0,0 @@
-// This example illustrates how C++ templates can be used from Java.
-
-public class main {
-  static {
-    try {
-        System.loadLibrary("example");
-    } catch (UnsatisfiedLinkError e) {
-      System.err.println("Native code library failed to load. See the chapter on Dynamic Linking Problems in the SWIG Java documentation for help.\n" + e);
-      System.exit(1);
-    }
-  }
-
-  public static void main(String argv[]) 
-  {
-    // Call some templated functions
-    System.out.println(example.maxint(3,7));
-    System.out.println(example.maxdouble(3.14,2.18));
-    
-    // Create some class
-    
-    vecint iv = new vecint(100);
-    vecdouble dv = new vecdouble(1000);
-    
-    for (int i=0; i<100; i++)
-        iv.setitem(i,2*i);
-    
-    for (int i=0; i<1000; i++)
-          dv.setitem(i, 1.0/(i+1));
-    
-    {
-    int sum = 0;
-    for (int i=0; i<100; i++)
-          sum = sum + iv.getitem(i);
-    
-    System.out.println(sum);
-    }
-    
-    {
-    double sum = 0.0;
-    for (int i=0; i<1000; i++)
-          sum = sum + dv.getitem(i);
-    System.out.println(sum);
-    }
-  }
-}
diff --git a/Examples/doxygencomments/java/typemap/Makefile b/Examples/doxygencomments/java/typemap/Makefile
deleted file mode 100644
index 92afbd4d0..000000000
--- a/Examples/doxygencomments/java/typemap/Makefile
+++ /dev/null
@@ -1,18 +0,0 @@
-TOP        = ../..
-SWIG       = $(TOP)/../preinst-swig
-SRCS       = 
-TARGET     = example
-INTERFACE  = example.i
-SWIGOPT    =
-
-all::	java
-
-java::
-	$(MAKE) -f $(TOP)/Makefile SRCS='$(SRCS)' SWIG='$(SWIG)' \
-	SWIGOPT='$(SWIGOPT)' TARGET='$(TARGET)' INTERFACE='$(INTERFACE)' java
-	javac *.java
-
-clean::
-	$(MAKE) -f $(TOP)/Makefile java_clean
-
-check: all
diff --git a/Examples/doxygencomments/java/typemap/example.i b/Examples/doxygencomments/java/typemap/example.i
deleted file mode 100644
index 7c97e6673..000000000
--- a/Examples/doxygencomments/java/typemap/example.i
+++ /dev/null
@@ -1,101 +0,0 @@
-/* File : example.i */
-%module example
-%{
-/*
-   example of a function that returns a value in the char * argument
-   normally used like:
-
-   char buf[bigenough];
-   f1(buf);
-*/
-
-void f1(char *s) {
-  if(s != NULL) {
-    sprintf(s, "hello world");
-  }
-}
-
-void f2(char *s) {
-  f1(s);
-}
-
-void f3(char *s) {
-  f1(s);
-}
-
-%}
-
-/* default behaviour is that of input arg, Java cannot return a value in a 
- * string argument, so any changes made by f1(char*) will not be seen in the Java
- * string passed to the f1 function.
-*/
-void f1(char *s);
-
-%include various.i
-
-/* use the BYTE argout typemap to get around this. Changes in the string by 
- * f2 can be seen in Java. */
-void f2(char *BYTE);
-
-
-
-/* Alternative approach uses a StringBuffer typemap for argout */
-
-/* Define the types to use in the generated JNI C code and Java code */
-%typemap(jni) char *SBUF "jobject"
-%typemap(jtype) char *SBUF "StringBuffer"
-%typemap(jstype) char *SBUF "StringBuffer"
-
-/* How to convert Java(JNI) type to requested C type */
-%typemap(in) char *SBUF {
-
-  $1 = NULL;
-  if($input != NULL) {
-    /* Get the String from the StringBuffer */
-    jmethodID setLengthID;
-    jclass sbufClass = (*jenv)->GetObjectClass(jenv, $input);
-    jmethodID toStringID = (*jenv)->GetMethodID(jenv, sbufClass, "toString", "()Ljava/lang/String;");
-    jstring js = (jstring) (*jenv)->CallObjectMethod(jenv, $input, toStringID);
-
-    /* Convert the String to a C string */
-    const char *pCharStr = (*jenv)->GetStringUTFChars(jenv, js, 0);
-
-    /* Take a copy of the C string as the typemap is for a non const C string */
-    jmethodID capacityID = (*jenv)->GetMethodID(jenv, sbufClass, "capacity", "()I");
-    jint capacity = (*jenv)->CallIntMethod(jenv, $input, capacityID);
-    $1 = (char *) malloc(capacity+1);
-    strcpy($1, pCharStr);
-
-    /* Release the UTF string we obtained with GetStringUTFChars */
-    (*jenv)->ReleaseStringUTFChars(jenv,  js, pCharStr);
-
-    /* Zero the original StringBuffer, so we can replace it with the result */
-    setLengthID = (*jenv)->GetMethodID(jenv, sbufClass, "setLength", "(I)V");
-    (*jenv)->CallVoidMethod(jenv, $input, setLengthID, (jint) 0);
-  }
-}
-
-/* How to convert the C type to the Java(JNI) type */
-%typemap(argout) char *SBUF {
-
-  if($1 != NULL) {
-    /* Append the result to the empty StringBuffer */
-    jstring newString = (*jenv)->NewStringUTF(jenv, $1);
-    jclass sbufClass = (*jenv)->GetObjectClass(jenv, $input);
-    jmethodID appendStringID = (*jenv)->GetMethodID(jenv, sbufClass, "append", "(Ljava/lang/String;)Ljava/lang/StringBuffer;");
-    (*jenv)->CallObjectMethod(jenv, $input, appendStringID, newString);
-
-    /* Clean up the string object, no longer needed */
-    free($1);
-    $1 = NULL;
-  }  
-}
-/* Prevent the default freearg typemap from being used */
-%typemap(freearg) char *SBUF ""
-
-/* Convert the jstype to jtype typemap type */
-%typemap(javain) char *SBUF "$javainput"
-
-/* apply the new typemap to our function */
-void f3(char *SBUF);
-
diff --git a/Examples/doxygencomments/java/typemap/index.html b/Examples/doxygencomments/java/typemap/index.html
deleted file mode 100644
index 486aa8e79..000000000
--- a/Examples/doxygencomments/java/typemap/index.html
+++ /dev/null
@@ -1,32 +0,0 @@
-<html>
-<head>
-<title>SWIG:Examples:java:typemap</title>
-</head>
-
-<body bgcolor="#ffffff">
-
-
-<tt>SWIG/Examples/java/typemap/</tt>
-<hr>
-
-<H2>Typemaps in Java</H2>
-
-<p>
-This example shows how typemaps can be used to modify the default behaviour of the Java SWIG module.
-
-<ul>
-<li><a href="example.i">example.i</a>. Interface file. 
-<li><a href="main.java">main.java</a>. Sample Java program.
-</ul>
-
-<h2>Notes</h2>
-
-<ul>
-<li>Shows how to pass strings to Java from c and visa versa.
-<li>Typemaps can modify the default behaviour of the Java SWIG module.
-<li>The default c to java mapping can be modified using typemaps.
-</ul>
-
-<hr>
-</body>
-</html>
diff --git a/Examples/doxygencomments/java/typemap/main.java b/Examples/doxygencomments/java/typemap/main.java
deleted file mode 100644
index bd9a4e1b6..000000000
--- a/Examples/doxygencomments/java/typemap/main.java
+++ /dev/null
@@ -1,26 +0,0 @@
-
-public class main {
-
-  static {
-    try {
-	System.loadLibrary("example");
-    } catch (UnsatisfiedLinkError e) {
-      System.err.println("Native code library failed to load. See the chapter on Dynamic Linking Problems in the SWIG Java documentation for help.\n" + e);
-      System.exit(1);
-    }
-  }
-
-  public static void main(String argv[]) {
-    String s = "brave new world";
-    example.f1(s);
-    System.out.println("f1(String): " + s);
-
-    byte b[] = new byte[25];
-    example.f2(b);
-    System.out.println("f2(byte[]): " + new String(b));
-
-    StringBuffer sb = new StringBuffer(20);
-    example.f3(sb);
-    System.out.println("f3(StringBuffer): " + sb);
-  }
-}
diff --git a/Examples/doxygencomments/java/variables/Makefile b/Examples/doxygencomments/java/variables/Makefile
deleted file mode 100644
index 968c92c6c..000000000
--- a/Examples/doxygencomments/java/variables/Makefile
+++ /dev/null
@@ -1,18 +0,0 @@
-TOP        = ../..
-SWIG       = $(TOP)/../preinst-swig
-SRCS       = example.c
-TARGET     = example
-INTERFACE  = example.i
-SWIGOPT    =
-
-all::	java
-
-java::
-	$(MAKE) -f $(TOP)/Makefile SRCS='$(SRCS)' SWIG='$(SWIG)' \
-	SWIGOPT='$(SWIGOPT)' TARGET='$(TARGET)' INTERFACE='$(INTERFACE)' java
-	javac *.java
-
-clean::
-	$(MAKE) -f $(TOP)/Makefile java_clean
-
-check: all
diff --git a/Examples/doxygencomments/java/variables/example.c b/Examples/doxygencomments/java/variables/example.c
deleted file mode 100644
index aa4ffe9b3..000000000
--- a/Examples/doxygencomments/java/variables/example.c
+++ /dev/null
@@ -1,91 +0,0 @@
-/* File : example.c */
-
-/* I'm a file containing some C global variables */
-
-/* Deal with Microsoft's attempt at deprecating C standard runtime functions */
-#if !defined(SWIG_NO_CRT_SECURE_NO_DEPRECATE) && defined(_MSC_VER)
-# define _CRT_SECURE_NO_DEPRECATE
-#endif
-
-#include <stdio.h>
-#include <stdlib.h>
-#include "example.h"
-
-int              ivar = 0;                    
-short            svar = 0;
-long             lvar = 0;
-unsigned int     uivar = 0;
-unsigned short   usvar = 0;
-unsigned long    ulvar = 0;
-signed char      scvar = 0;
-unsigned char    ucvar = 0;
-char             cvar = 0;
-float            fvar = 0;
-double           dvar = 0;
-char            *strvar = 0;
-const char       cstrvar[] = "Goodbye";
-int             *iptrvar = 0;
-char             name[256] = "Dave";
-char             path[256] = "/home/beazley";
-
-
-/* Global variables involving a structure */
-Point           *ptptr = 0;
-Point            pt = { 10, 20 };
-
-/* A variable that we will make read-only in the interface */
-int              status = 1;
-
-/* A debugging function to print out their values */
-
-void print_vars() {
-  printf("ivar      = %d\n", ivar);
-  printf("svar      = %d\n", svar);
-  printf("lvar      = %ld\n", lvar);
-  printf("uivar     = %u\n", uivar);
-  printf("usvar     = %u\n", usvar);
-  printf("ulvar     = %lu\n", ulvar);
-  printf("scvar     = %d\n", scvar);
-  printf("ucvar     = %u\n", ucvar);
-  printf("fvar      = %g\n", fvar);
-  printf("dvar      = %g\n", dvar);
-  printf("cvar      = %c\n", cvar);
-  printf("strvar    = %s\n", strvar ? strvar : "(null)");
-  printf("cstrvar   = %s\n", cstrvar ? cstrvar : "(null)");
-  printf("iptrvar   = %p\n", iptrvar);
-  printf("name      = %s\n", name);
-  printf("ptptr     = %p (%d, %d)\n", ptptr, ptptr ? ptptr->x : 0, ptptr ? ptptr->y : 0);
-  printf("pt        = (%d, %d)\n", pt.x, pt.y);
-  printf("status    = %d\n", status);
-}
-
-/* A function to create an integer (to test iptrvar) */
-
-int *new_int(int value) {
-  int *ip = (int *) malloc(sizeof(int));
-  *ip = value;
-  return ip;
-}
-
-/* A function to create a point */
-
-Point *new_Point(int x, int y) {
-  Point *p = (Point *) malloc(sizeof(Point));
-  p->x = x;
-  p->y = y;
-  return p;
-}
-
-char * Point_print(Point *p) {
-  static char buffer[256];
-  if (p) {
-    sprintf(buffer,"(%d,%d)", p->x,p->y);
-  } else {
-    sprintf(buffer,"null");
-  }
-  return buffer;
-}
-
-void pt_print() {
-  printf("(%d, %d)\n", pt.x, pt.y);
-}
diff --git a/Examples/doxygencomments/java/variables/example.h b/Examples/doxygencomments/java/variables/example.h
deleted file mode 100644
index 2265a45f3..000000000
--- a/Examples/doxygencomments/java/variables/example.h
+++ /dev/null
@@ -1,6 +0,0 @@
-/* File: example.h */
-
-typedef struct {
-  int x,y;
-} Point; /*!< Description of struct Point */
-
diff --git a/Examples/doxygencomments/java/variables/example.i b/Examples/doxygencomments/java/variables/example.i
deleted file mode 100644
index b9794f0cf..000000000
--- a/Examples/doxygencomments/java/variables/example.i
+++ /dev/null
@@ -1,57 +0,0 @@
-/* File : example.i */
-%module example
-%{
-#include "example.h"
-%}
-
-/* Some global variable declarations */
-%inline %{
-extern int              ivar; /*!< Description of ivar */
-extern short            svar; /*!< Description of svar */
-extern long             lvar; /*!< Description of lvar */
-extern unsigned int     uivar; /*!< Description of uivar */
-extern unsigned short   usvar; /*!< Description of usvar */
-extern unsigned long    ulvar; /*!< Description of ulvar */
-extern signed char      scvar; /*!< Description of scvar */
-extern unsigned char    ucvar; /*!< Description of ucvar */
-extern char             cvar; /*!< Description of cvar */
-extern float            fvar; /*!< Description of fvar */
-extern double           dvar; /*!< Description of dvar */
-extern char            *strvar; /*!< Description of strvar */
-extern const char       cstrvar[]; /*!< Description of cstrvar */
-extern int             *iptrvar;  /*!< Description of iptrvar */
-extern char             name[256];  /*!< Description of name */
-
-extern Point           *ptptr;  /*!< Description of ptrptr */
-extern Point            pt;  /*!< Description of pt */
-%}
-
-
-/* Some read-only variables */
-
-%immutable;
-
-%inline %{
-extern int  status;
-extern char path[256];
-%}
-
-%mutable;
-
-/* Some helper functions to make it easier to test */
-%inline %{
-/*! this function prints variables
- \author someone */
-extern void  print_vars();
-extern int  *new_int(int value);  /*!< Description of new_int
-				   \param value the value
-				   \return a new int */
-/*! Description of new_point
-  \param x the value x
-  \param y the value y
- \return a new point */
-extern Point *new_Point(int x, int y);
-extern char  *Point_print(Point *p);
-extern void  pt_print();
-%}
-
diff --git a/Examples/doxygencomments/java/variables/index.html b/Examples/doxygencomments/java/variables/index.html
deleted file mode 100644
index 05aaa2d6e..000000000
--- a/Examples/doxygencomments/java/variables/index.html
+++ /dev/null
@@ -1,85 +0,0 @@
-<html>
-<head>
-<title>SWIG:Examples:java:variables</title>
-</head>
-
-<body bgcolor="#ffffff">
-
-<tt>SWIG/Examples/java/variables/</tt>
-<hr>
-
-<H2>Wrapping C Global Variables</H2>
-
-<p>
-When a C global variable appears in an interface file, SWIG tries to
-wrap it using a technique known as "variable linking."  The idea is
-pretty simple---we try to create a Java variable that magically
-retrieves or updates the value of the underlying C variable when it is
-accessed.  Click <a href="example.i">here</a> to see a SWIG interface with some variable
-declarations in it.
-
-
-<p>Click <a href="../../../Doc/Manual/Java.html#global_variables">here</a> for the section on global variables in the SWIG and Java documentation.</p>
-<h2>Manipulating Variables from Java</h2>
-
-C variables are accessed through getters and setters from Java. Unfortunately this is the only way to get current values from variables because it is not possible to overload the dot operator in Java. All global variables are accessible from the module class. For example if the module class is called 'example', the global variable
-
-<blockquote>
-<pre>
-double foo;
-</pre>
-</blockquote>
-
-will be accessed in the Java module as
-<blockquote>
-<pre>
-example.get_foo();
-example.set_foo(12.3);
-</pre>
-</blockquote>
-
-Click <a href="main.java">here</a> to see the example program that updates and prints
-out the values of the variables using this technique.
-
-<h2>Key points</h2>
-
-<ul>
-<li>When a global variable has the type "<tt>char *</tt>", SWIG manages it as a character
-string.   However, whenever the value of such a variable is set from Java, the old
-value is destroyed using <tt>free()</tt> or <tt>delete</tt> (the choice of which depends
-on whether or not SWIG was run with the -c++ option).
-<li><tt>signed char</tt> and <tt>unsigned char</tt> are handled as small 8-bit integers.
-<li>String array variables such as '<tt>char name[256]</tt>' are managed as Java strings, but
-when setting the value, the result is truncated to the maximum length of the array.  Furthermore, the string is assumed to be null-terminated.
-<li>When structures and classes are used as global variables, they are mapped into pointers.
-Getting the "value" returns a pointer to the global variable.  Setting the value of a structure results in a memory copy from a pointer to the global.
-</ul>
-
-<h2>Creating read-only variables</h2>
-
-The <tt>%immutable</tt> and <tt>%mutable</tt> directives can be used to
-specify a collection of read-only variables.  For example:
-
-<blockquote>
-<pre>
-%immutable;
-int    status;
-double blah;
-...
-%mutable;
-</pre>
-</blockquote>
-
-The <tt>%immutable</tt> directive remains in effect until it is explicitly disabled
-using the <tt>%mutable</tt> directive.
-
-<h2>Comments</h2>
-<ul>
-<li>Management of global variables is one of the most problematic aspects 
-of C/C++ wrapping because the Java interface and resulting memory management
-is much trickier than simply creating a wrapper function.
-</ul>
-
-</body>
-</html>
-<hr>
diff --git a/Examples/doxygencomments/java/variables/main.java b/Examples/doxygencomments/java/variables/main.java
deleted file mode 100644
index 92745db99..000000000
--- a/Examples/doxygencomments/java/variables/main.java
+++ /dev/null
@@ -1,97 +0,0 @@
-// This example illustrates global variable access from Java.
-
-import java.lang.reflect.*;
-
-public class main {
-  static {
-    try {
-        System.loadLibrary("example");
-    } catch (UnsatisfiedLinkError e) {
-      System.err.println("Native code library failed to load. See the chapter on Dynamic Linking Problems in the SWIG Java documentation for help.\n" + e);
-      System.exit(1);
-    }
-  }
-
-  public static void main(String argv[]) {
-
-// Try to set the values of some global variables
-
-    example.setIvar(42);
-    example.setSvar((short)-31000);
-    example.setLvar(65537);
-    example.setUivar(123456);
-    example.setUsvar(61000);
-    example.setUlvar(654321);
-    example.setScvar((byte)-13);
-    example.setUcvar((short)251);
-    example.setCvar('S');
-    example.setFvar((float)3.14159);
-    example.setDvar(2.1828);
-    example.setStrvar("Hello World");
-    example.setIptrvar(example.new_int(37));
-    example.setPtptr(example.new_Point(37,42));
-    example.setName("Bill");
-
-    // Now print out the values of the variables
-
-    System.out.println( "Variables (values printed from Java)" );
-
-    System.out.println( "ivar      =" + example.getIvar() );
-    System.out.println( "svar      =" + example.getSvar() );
-    System.out.println( "lvar      =" + example.getLvar() );
-    System.out.println( "uivar     =" + example.getUivar() );
-    System.out.println( "usvar     =" + example.getUsvar() );
-    System.out.println( "ulvar     =" + example.getUlvar() );
-    System.out.println( "scvar     =" + example.getScvar() );
-    System.out.println( "ucvar     =" + example.getUcvar() );
-    System.out.println( "fvar      =" + example.getFvar() );
-    System.out.println( "dvar      =" + example.getDvar() );
-    System.out.println( "cvar      =" + (char)example.getCvar() );
-    System.out.println( "strvar    =" + example.getStrvar() );
-    System.out.println( "cstrvar   =" + example.getCstrvar() );
-    System.out.println( "iptrvar   =" + Long.toHexString(SWIGTYPE_p_int.getCPtr(example.getIptrvar())) );
-    System.out.println( "name      =" + example.getName() );
-    System.out.println( "ptptr     =" + Long.toHexString(SWIGTYPE_p_Point.getCPtr(example.getPtptr())) + example.Point_print(example.getPtptr()) );
-    System.out.println( "pt        =" + Long.toHexString(SWIGTYPE_p_Point.getCPtr(example.getPt())) + example.Point_print(example.getPt()) );
-
-    System.out.println( "\nVariables (values printed from C)" );
-
-    example.print_vars();
-
-    System.out.println( "\nNow I'm going to try and modify some read only variables" );
-
-    System.out.println( "     Trying to set 'path'" );
-    try {
-        Method m = example.class.getDeclaredMethod("setPath", new Class[] {String.class});
-        m.invoke(example.class, new Object[] {"Whoa!"} );
-        System.out.println( "Hey, what's going on?!?! This shouldn't work" );
-    }
-    catch (NoSuchMethodException e) {
-        System.out.println( "Good." );
-    }
-    catch (Throwable t) {
-        System.out.println( "You shouldn't see this!" );
-    }
-
-    System.out.println( "     Trying to set 'status'" );
-    try {
-        Method m = example.class.getDeclaredMethod("setStatus", new Class[] {Integer.class});
-        m.invoke(example.class, new Object[] {new Integer(0)} );
-        System.out.println( "Hey, what's going on?!?! This shouldn't work" );
-    }
-    catch (NoSuchMethodException e) {
-        System.out.println( "Good." );
-    }
-    catch (Throwable t) {
-        System.out.println( "You shouldn't see this!" );
-    }
-
-    System.out.println( "\nI'm going to try and update a structure variable.\n" );
-
-    example.setPt(example.getPtptr());
-
-    System.out.println( "The new value is" );
-    example.pt_print();
-    System.out.println( "You should see the value" + example.Point_print(example.getPtptr()) );
-  }
-}
diff --git a/Examples/java/check.list b/Examples/java/check.list
index 825d04a6d..c30550a1c 100644
--- a/Examples/java/check.list
+++ b/Examples/java/check.list
@@ -2,6 +2,7 @@
 callback
 class
 constants
+doxygen
 enum
 extend
 funcptr
diff --git a/Examples/java/doxygen/Makefile b/Examples/java/doxygen/Makefile
new file mode 100644
index 000000000..9f471746e
--- /dev/null
+++ b/Examples/java/doxygen/Makefile
@@ -0,0 +1,21 @@
+TOP        = ../..
+SWIGEXE    = $(TOP)/../swig
+SWIG_LIB_DIR = $(TOP)/../$(TOP_BUILDDIR_TO_TOP_SRCDIR)Lib
+CXXSRCS    = example.cxx
+TARGET     = example
+INTERFACE  = example.i
+SWIGOPT    = -doxygen
+JAVASRCS   = *.java
+
+check: build
+	$(MAKE) -f $(TOP)/Makefile SRCDIR='$(SRCDIR)' java_run
+
+build:
+	$(MAKE) -f $(TOP)/Makefile SRCDIR='$(SRCDIR)' CXXSRCS='$(CXXSRCS)' \
+	SWIG_LIB_DIR='$(SWIG_LIB_DIR)' SWIGEXE='$(SWIGEXE)' \
+	SWIGOPT='$(SWIGOPT)' TARGET='$(TARGET)' INTERFACE='$(INTERFACE)' java_cpp
+	$(MAKE) -f $(TOP)/Makefile SRCDIR='$(SRCDIR)' JAVASRCS='$(JAVASRCS)' JAVAFLAGS='$(JAVAFLAGS)' java_compile
+
+clean:
+	$(MAKE) -f $(TOP)/Makefile SRCDIR='$(SRCDIR)' java_clean
+	rm -rf javadocs
diff --git a/Examples/java/doxygen/example.cxx b/Examples/java/doxygen/example.cxx
new file mode 100644
index 000000000..ccdb87dfe
--- /dev/null
+++ b/Examples/java/doxygen/example.cxx
@@ -0,0 +1,48 @@
+/* File : example.cxx */
+
+#include "example.h"
+#define M_PI 3.14159265358979323846
+
+/* Move the shape to a new location */
+void Shape::move(double dx, double dy) {
+  x += dx;
+  y += dy;
+}
+
+int Shape::nshapes = 0;
+
+Circle::Circle(double r) : radius(r) {
+  NumCircles++;
+}
+
+double Circle::area() {
+  return M_PI*radius*radius;
+}
+
+double Circle::perimeter() {
+  return 2*M_PI*radius;
+}
+
+Square::Square(double w) : width(w) {
+  NumSquares++;
+}
+
+double Square::area() {
+  return width*width;
+}
+
+double Square::perimeter() {
+  return 4*width;
+}
+
+int NumSquares = 0;
+int NumCircles = 0;
+
+Square MakeSquare(double r) {
+  return Square(r);
+}
+
+Circle MakeCircle(double w) {
+  return Circle(w);
+}
+
diff --git a/Examples/doxygencomments/java/class/example.dsp b/Examples/java/doxygen/example.dsp
similarity index 95%
rename from Examples/doxygencomments/java/class/example.dsp
rename to Examples/java/doxygen/example.dsp
index fbe87e7a4..f52544b95 100644
--- a/Examples/doxygencomments/java/class/example.dsp
+++ b/Examples/java/doxygen/example.dsp
@@ -136,7 +136,7 @@ InputName=example
 	echo JAVA_INCLUDE: %JAVA_INCLUDE% 
 	echo JAVA_BIN: %JAVA_BIN% 
 	echo on 
-	..\..\..\swig.exe -c++ -java $(InputPath) 
+	..\..\..\swig.exe -c++ -java "$(InputPath)" 
 	
 # End Custom Build
 
@@ -151,7 +151,7 @@ InputName=example
 	echo JAVA_INCLUDE: %JAVA_INCLUDE% 
 	echo JAVA_BIN: %JAVA_BIN% 
 	echo on 
-	..\..\..\swig.exe -c++ -java $(InputPath) 
+	..\..\..\swig.exe -c++ -java "$(InputPath)" 
 	
 # End Custom Build
 
diff --git a/Examples/java/doxygen/example.h b/Examples/java/doxygen/example.h
new file mode 100644
index 000000000..203348ae4
--- /dev/null
+++ b/Examples/java/doxygen/example.h
@@ -0,0 +1,107 @@
+/*! \file example.h 
+This file provides a simple set of Shape classes. */
+
+/*! Base class for all shapes.
+ \author Bob
+ */
+class Shape {
+public:
+  /*! Default constructor for creating a Shape */
+  Shape() {
+    nshapes++;
+  }
+  /*! Destructor for destroying a Shape */
+  virtual ~Shape() {
+    nshapes--;
+  }
+  double x; /*!< x co-ordinate */
+  double y; /*!< y co-ordinate */
+  void    move(double dx, double dy); /*!< Move a shape to a new co-ordinate
+  \param dx x co-ordinate
+  \param dy y co-ordinate */
+  virtual double area() = 0; /*!< \return the area */
+  virtual double perimeter() = 0; /*!< \return the perimeter */
+  static  int nshapes; /*!< Number of shapes currently in existence */
+};
+
+/*! A class for representing a circle.
+ \author Jack
+ */
+class Circle : public Shape {
+private:
+  double radius;
+public:
+  /*! Construct a circle
+   *  \param r radius of the circle */
+  Circle(double r);
+  /*! Calculate the area of the circle
+   *  \return calculated area */
+  virtual double area();
+  /*! Calculate the perimeter of the circle
+   *  \return calculated perimeter of the circle */
+  virtual double perimeter();
+};
+
+/// A class for representing a square.
+class Square : public Shape {
+private:
+  double width;
+public:
+  /** Construct a square
+   *  \param w width of the square */
+  Square(double w);
+  /** Calculate the area of the square
+   *  \return calculated area */
+  virtual double area();
+  /** Calculate the perimeter of the square
+   *  \return calculated perimeter of the square */
+  virtual double perimeter();
+};
+
+/// A class for representing a rectangle, templated on the type for the rectangle dimensions
+template<typename T>
+class Rectangle : public Shape {
+private:
+  T height;
+  T width;
+public:
+  /** Construct a rectangle
+   *  \param h height of the rectangle
+   *  \param w width of the rectangle */
+  Rectangle(T h, T w) : height(h), width(w) {}
+  /** Calculate the area of the rectangle
+   *  \return calculated area */
+  virtual double area() { return width*height; }
+  /** Calculate the perimeter of the rectangle
+   *  \return calculated perimeter of the rectangle */
+  virtual double perimeter() { return 2*height + 2*width; }
+};
+
+
+/*! Factory function for creating a square
+ *  \param r width of the square
+ *  \return a fully constructed square */
+Square MakeSquare(double r);
+
+/*! Factory function for creating a circle
+ *  \param w radius of the circle
+ *  \return a fully constructed circle */
+Circle MakeCircle(double w);
+
+/*! Factory function for creating a rectangle
+ *  \param h height of the rectangle
+ *  \param w width of the rectangle
+ *  \return a fully constructed rectangle */
+template<typename T>
+Rectangle<T> MakeRectangle(T h, T w) {
+  return Rectangle<T>(h, w);
+}
+
+
+
+/*! Total number of circles ever created */
+extern int NumCircles;
+
+/// Total number of squares ever created
+extern int NumSquares;
+
diff --git a/Examples/java/doxygen/example.i b/Examples/java/doxygen/example.i
new file mode 100644
index 000000000..803563dd9
--- /dev/null
+++ b/Examples/java/doxygen/example.i
@@ -0,0 +1,17 @@
+%module example
+
+%{
+#include "example.h"
+%}
+
+%immutable NumSquares;
+%immutable NumCircles;
+
+%include "example.h"
+
+/*! - this instantiation uses type int */
+%template(RectangleInt) Rectangle<int>;
+
+/*! - this instantiation uses type int */
+%template(MakeRectangleInt) MakeRectangle<int>;
+
diff --git a/Examples/java/doxygen/runme.java b/Examples/java/doxygen/runme.java
new file mode 100644
index 000000000..6b7bb3d01
--- /dev/null
+++ b/Examples/java/doxygen/runme.java
@@ -0,0 +1,63 @@
+// This example shows simple usage of the wrapped Shape classes.
+// The main purpose of this example is to show the doxygen comments translation to JavaDoc comments.
+// Users should look at the generated .java files and if javadoc is installed and working on your system,
+// the generated Java docs can be viewed in a browser by opening the javadocs/index.html file.
+
+import java.io.*;
+
+public class runme {
+  static {
+    try {
+        System.loadLibrary("example");
+    } catch (UnsatisfiedLinkError e) {
+      System.err.println("Native code library failed to load. See the chapter on Dynamic Linking Problems in the SWIG Java documentation for help.\n" + e);
+      System.exit(1);
+    }
+  }
+
+  public static void main(String argv[]) throws InterruptedException, IOException
+  {
+    System.out.println("Creating some objects:");
+    Circle c = example.MakeCircle(10);
+    System.out.println("    Created circle " + c);
+    Square s = example.MakeSquare(10);
+    System.out.println("    Created square " + s);
+    RectangleInt r = example.MakeRectangleInt(10, 20);
+    System.out.println("    Created rectangle " + r);
+
+    System.out.println("\nHere are some properties of the shapes:");
+    Shape[] shapes = {c, s, r};
+    for (int i=0; i<shapes.length; i++) {
+      System.out.println("   " + shapes[i].toString());
+      System.out.println("        area      = " + shapes[i].area());
+      System.out.println("        perimeter = " + shapes[i].perimeter());
+    }
+
+    String command = "javadoc -quiet -public -d javadocs example.java Shape.java Circle.java Square.java RectangleInt.java";
+    System.out.println("\nRunning: " + command);
+    Process p = Runtime.getRuntime().exec(command);
+    int exitCode = p.waitFor();
+    System.out.println("javadoc exited with code " + exitCode);
+
+    BufferedReader stdout = new BufferedReader(new InputStreamReader(p.getInputStream()));
+    BufferedReader stderr = new BufferedReader(new InputStreamReader(p.getErrorStream()));
+
+    String line = null;
+
+    System.out.println("stdout from javadoc:\n");
+    while ((line = stdout.readLine()) != null) {
+      System.out.println(line);
+    }
+
+    System.out.println("\nstderr from javadoc:\n");
+    while ((line = stderr.readLine()) != null) {
+      System.out.println(line);
+    }
+
+    if (exitCode != 0) {
+      System.out.println("No java docs were generated!\n");
+    } else {
+      System.out.println("javadoc ran successfully, open javadocs/index.html in your browser to view the generated java docs.");
+    }
+  }
+}

From 89a25055d9162b38a9e3af968d70a33a3a142ceb Mon Sep 17 00:00:00 2001
From: William S Fulton <wsf@fultondesigns.co.uk>
Date: Thu, 31 May 2018 20:48:02 +0100
Subject: [PATCH 310/314] Add Python doxygen example

---
 Examples/python/check.list          |   1 +
 Examples/python/doxygen/Makefile    |  27 +++++
 Examples/python/doxygen/example.cxx |  48 +++++++++
 Examples/python/doxygen/example.dsp | 152 ++++++++++++++++++++++++++++
 Examples/python/doxygen/example.h   | 107 ++++++++++++++++++++
 Examples/python/doxygen/example.i   |  17 ++++
 Examples/python/doxygen/runme.py    |  28 +++++
 7 files changed, 380 insertions(+)
 create mode 100644 Examples/python/doxygen/Makefile
 create mode 100644 Examples/python/doxygen/example.cxx
 create mode 100644 Examples/python/doxygen/example.dsp
 create mode 100644 Examples/python/doxygen/example.h
 create mode 100644 Examples/python/doxygen/example.i
 create mode 100644 Examples/python/doxygen/runme.py

diff --git a/Examples/python/check.list b/Examples/python/check.list
index 73182025d..0798b5f7e 100644
--- a/Examples/python/check.list
+++ b/Examples/python/check.list
@@ -4,6 +4,7 @@ class
 constants
 contract
 docstrings
+doxygen
 enum
 exception
 exceptproxy
diff --git a/Examples/python/doxygen/Makefile b/Examples/python/doxygen/Makefile
new file mode 100644
index 000000000..1a0e3d7c5
--- /dev/null
+++ b/Examples/python/doxygen/Makefile
@@ -0,0 +1,27 @@
+TOP        = ../..
+SWIGEXE    = $(TOP)/../swig
+SWIG_LIB_DIR = $(TOP)/../$(TOP_BUILDDIR_TO_TOP_SRCDIR)Lib
+CXXSRCS    = example.cxx
+TARGET     = example
+INTERFACE  = example.i
+LIBS       = -lm
+SWIGOPT    = -doxygen
+
+check: build
+	$(MAKE) -f $(TOP)/Makefile SRCDIR='$(SRCDIR)' python_run
+
+build:
+	$(MAKE) -f $(TOP)/Makefile SRCDIR='$(SRCDIR)' CXXSRCS='$(CXXSRCS)' \
+	SWIG_LIB_DIR='$(SWIG_LIB_DIR)' SWIGEXE='$(SWIGEXE)' \
+	SWIGOPT='$(SWIGOPT)' \
+	TARGET='$(TARGET)' INTERFACE='$(INTERFACE)' python_cpp
+
+static:
+	$(MAKE) -f $(TOP)/Makefile SRCDIR='$(SRCDIR)' CXXSRCS='$(CXXSRCS)' \
+	SWIG_LIB_DIR='$(SWIG_LIB_DIR)' SWIGEXE='$(SWIGEXE)' \
+	SWIGOPT='$(SWIGOPT)' \
+	TARGET='mypython' INTERFACE='$(INTERFACE)' python_cpp_static
+
+clean:
+	$(MAKE) -f $(TOP)/Makefile SRCDIR='$(SRCDIR)' TARGET='$(TARGET)' python_clean
+	rm -f example.html
diff --git a/Examples/python/doxygen/example.cxx b/Examples/python/doxygen/example.cxx
new file mode 100644
index 000000000..ccdb87dfe
--- /dev/null
+++ b/Examples/python/doxygen/example.cxx
@@ -0,0 +1,48 @@
+/* File : example.cxx */
+
+#include "example.h"
+#define M_PI 3.14159265358979323846
+
+/* Move the shape to a new location */
+void Shape::move(double dx, double dy) {
+  x += dx;
+  y += dy;
+}
+
+int Shape::nshapes = 0;
+
+Circle::Circle(double r) : radius(r) {
+  NumCircles++;
+}
+
+double Circle::area() {
+  return M_PI*radius*radius;
+}
+
+double Circle::perimeter() {
+  return 2*M_PI*radius;
+}
+
+Square::Square(double w) : width(w) {
+  NumSquares++;
+}
+
+double Square::area() {
+  return width*width;
+}
+
+double Square::perimeter() {
+  return 4*width;
+}
+
+int NumSquares = 0;
+int NumCircles = 0;
+
+Square MakeSquare(double r) {
+  return Square(r);
+}
+
+Circle MakeCircle(double w) {
+  return Circle(w);
+}
+
diff --git a/Examples/python/doxygen/example.dsp b/Examples/python/doxygen/example.dsp
new file mode 100644
index 000000000..95ad8f173
--- /dev/null
+++ b/Examples/python/doxygen/example.dsp
@@ -0,0 +1,152 @@
+# Microsoft Developer Studio Project File - Name="example" - Package Owner=<4>
+# Microsoft Developer Studio Generated Build File, Format Version 6.00
+# ** DO NOT EDIT **
+
+# TARGTYPE "Win32 (x86) Dynamic-Link Library" 0x0102
+
+CFG=example - Win32 Release
+!MESSAGE This is not a valid makefile. To build this project using NMAKE,
+!MESSAGE use the Export Makefile command and run
+!MESSAGE 
+!MESSAGE NMAKE /f "example.mak".
+!MESSAGE 
+!MESSAGE You can specify a configuration when running NMAKE
+!MESSAGE by defining the macro CFG on the command line. For example:
+!MESSAGE 
+!MESSAGE NMAKE /f "example.mak" CFG="example - Win32 Release"
+!MESSAGE 
+!MESSAGE Possible choices for configuration are:
+!MESSAGE 
+!MESSAGE "example - Win32 Debug" (based on "Win32 (x86) Dynamic-Link Library")
+!MESSAGE "example - Win32 Release" (based on "Win32 (x86) Dynamic-Link Library")
+!MESSAGE 
+
+# Begin Project
+# PROP AllowPerConfigDependencies 0
+# PROP Scc_ProjName ""
+# PROP Scc_LocalPath ""
+CPP=cl.exe
+MTL=midl.exe
+RSC=rc.exe
+
+!IF  "$(CFG)" == "example - Win32 Debug"
+
+# PROP BASE Use_MFC 0
+# PROP BASE Use_Debug_Libraries 1
+# PROP BASE Output_Dir "Debug"
+# PROP BASE Intermediate_Dir "Debug"
+# PROP BASE Target_Dir ""
+# PROP Use_MFC 0
+# PROP Use_Debug_Libraries 1
+# PROP Output_Dir "Debug"
+# PROP Intermediate_Dir "Debug"
+# PROP Ignore_Export_Lib 0
+# PROP Target_Dir ""
+# ADD BASE CPP /nologo /MTd /W3 /Gm /GX /ZI /Od /D "WIN32" /D "_DEBUG" /D "_WINDOWS" /D "_MBCS" /D "_USRDLL" /D "EXAMPLE_EXPORTS" /YX /FD /GZ /c
+# ADD CPP /nologo /MTd /W3 /Gm /GX /ZI /Od /I "$(PYTHON_INCLUDE)" /D "SWIG_PYTHON_INTERPRETER_NO_DEBUG" /D "WIN32" /D "_DEBUG" /D "_WINDOWS" /D "_MBCS" /D "_USRDLL" /D "EXAMPLE_EXPORTS" /YX /FD /GZ /c
+# ADD BASE MTL /nologo /D "_DEBUG" /mktyplib203 /win32
+# ADD MTL /nologo /D "_DEBUG" /mktyplib203 /win32
+# ADD BASE RSC /l 0x809 /d "_DEBUG"
+# ADD RSC /l 0x809 /d "_DEBUG"
+BSC32=bscmake.exe
+# ADD BASE BSC32 /nologo
+# ADD BSC32 /nologo
+LINK32=link.exe
+# ADD BASE LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib /nologo /dll /debug /machine:I386 /pdbtype:sept
+# ADD LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib "$(PYTHON_LIB)" /nologo /dll /debug /machine:I386 /out:"_example.pyd" /pdbtype:sept
+
+!ELSEIF  "$(CFG)" == "example - Win32 Release"
+
+# PROP BASE Use_MFC 0
+# PROP BASE Use_Debug_Libraries 0
+# PROP BASE Output_Dir "Release"
+# PROP BASE Intermediate_Dir "Release"
+# PROP BASE Target_Dir ""
+# PROP Use_MFC 0
+# PROP Use_Debug_Libraries 0
+# PROP Output_Dir "Release"
+# PROP Intermediate_Dir "Release"
+# PROP Ignore_Export_Lib 0
+# PROP Target_Dir ""
+# ADD BASE CPP /nologo /MT /W3 /GX /O2 /D "WIN32" /D "NDEBUG" /D "_WINDOWS" /D "_MBCS" /D "_USRDLL" /D "EXAMPLE_EXPORTS" /YX /FD /c
+# ADD CPP /nologo /MT /W3 /GX /O2 /I "$(PYTHON_INCLUDE)" /D "WIN32" /D "NDEBUG" /D "_WINDOWS" /D "_MBCS" /D "_USRDLL" /D "EXAMPLE_EXPORTS" /YX /FD /c
+# ADD BASE MTL /nologo /D "NDEBUG" /mktyplib203 /win32
+# ADD MTL /nologo /D "NDEBUG" /mktyplib203 /win32
+# ADD BASE RSC /l 0x809 /d "NDEBUG"
+# ADD RSC /l 0x809 /d "NDEBUG"
+BSC32=bscmake.exe
+# ADD BASE BSC32 /nologo
+# ADD BSC32 /nologo
+LINK32=link.exe
+# ADD BASE LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib /nologo /dll /machine:I386
+# ADD LINK32 kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib advapi32.lib shell32.lib ole32.lib oleaut32.lib uuid.lib "$(PYTHON_LIB)" /nologo /dll /machine:I386 /out:"_example.pyd"
+
+!ENDIF 
+
+# Begin Target
+
+# Name "example - Win32 Debug"
+# Name "example - Win32 Release"
+# Begin Group "Source Files"
+
+# PROP Default_Filter "cpp;c;cxx;rc;def;r;odl;idl;hpj;bat"
+# Begin Source File
+
+SOURCE=.\example.cxx
+# End Source File
+# Begin Source File
+
+SOURCE=.\example_wrap.cxx
+# End Source File
+# End Group
+# Begin Group "Header Files"
+
+# PROP Default_Filter "h;hpp;hxx;hm;inl"
+# Begin Source File
+
+SOURCE=.\example.h
+# End Source File
+# End Group
+# Begin Group "Resource Files"
+
+# PROP Default_Filter "ico;cur;bmp;dlg;rc2;rct;bin;rgs;gif;jpg;jpeg;jpe"
+# End Group
+# Begin Source File
+
+SOURCE=.\example.i
+
+!IF  "$(CFG)" == "example - Win32 Debug"
+
+# Begin Custom Build
+InputPath=.\example.i
+InputName=example
+
+"$(InputName)_wrap.cxx" : $(SOURCE) "$(INTDIR)" "$(OUTDIR)"
+	echo In order to function correctly, please ensure the following environment variables are correctly set: 
+	echo PYTHON_INCLUDE: %PYTHON_INCLUDE% 
+	echo PYTHON_LIB: %PYTHON_LIB% 
+	echo on 
+	..\..\..\swig.exe -c++ -python "$(InputPath)" 
+	
+# End Custom Build
+
+!ELSEIF  "$(CFG)" == "example - Win32 Release"
+
+# Begin Custom Build
+InputPath=.\example.i
+InputName=example
+
+"$(InputName)_wrap.cxx" : $(SOURCE) "$(INTDIR)" "$(OUTDIR)"
+	echo In order to function correctly, please ensure the following environment variables are correctly set: 
+	echo PYTHON_INCLUDE: %PYTHON_INCLUDE% 
+	echo PYTHON_LIB: %PYTHON_LIB% 
+	echo on 
+	..\..\..\swig.exe -c++ -python "$(InputPath)" 
+	
+# End Custom Build
+
+!ENDIF 
+
+# End Source File
+# End Target
+# End Project
diff --git a/Examples/python/doxygen/example.h b/Examples/python/doxygen/example.h
new file mode 100644
index 000000000..203348ae4
--- /dev/null
+++ b/Examples/python/doxygen/example.h
@@ -0,0 +1,107 @@
+/*! \file example.h 
+This file provides a simple set of Shape classes. */
+
+/*! Base class for all shapes.
+ \author Bob
+ */
+class Shape {
+public:
+  /*! Default constructor for creating a Shape */
+  Shape() {
+    nshapes++;
+  }
+  /*! Destructor for destroying a Shape */
+  virtual ~Shape() {
+    nshapes--;
+  }
+  double x; /*!< x co-ordinate */
+  double y; /*!< y co-ordinate */
+  void    move(double dx, double dy); /*!< Move a shape to a new co-ordinate
+  \param dx x co-ordinate
+  \param dy y co-ordinate */
+  virtual double area() = 0; /*!< \return the area */
+  virtual double perimeter() = 0; /*!< \return the perimeter */
+  static  int nshapes; /*!< Number of shapes currently in existence */
+};
+
+/*! A class for representing a circle.
+ \author Jack
+ */
+class Circle : public Shape {
+private:
+  double radius;
+public:
+  /*! Construct a circle
+   *  \param r radius of the circle */
+  Circle(double r);
+  /*! Calculate the area of the circle
+   *  \return calculated area */
+  virtual double area();
+  /*! Calculate the perimeter of the circle
+   *  \return calculated perimeter of the circle */
+  virtual double perimeter();
+};
+
+/// A class for representing a square.
+class Square : public Shape {
+private:
+  double width;
+public:
+  /** Construct a square
+   *  \param w width of the square */
+  Square(double w);
+  /** Calculate the area of the square
+   *  \return calculated area */
+  virtual double area();
+  /** Calculate the perimeter of the square
+   *  \return calculated perimeter of the square */
+  virtual double perimeter();
+};
+
+/// A class for representing a rectangle, templated on the type for the rectangle dimensions
+template<typename T>
+class Rectangle : public Shape {
+private:
+  T height;
+  T width;
+public:
+  /** Construct a rectangle
+   *  \param h height of the rectangle
+   *  \param w width of the rectangle */
+  Rectangle(T h, T w) : height(h), width(w) {}
+  /** Calculate the area of the rectangle
+   *  \return calculated area */
+  virtual double area() { return width*height; }
+  /** Calculate the perimeter of the rectangle
+   *  \return calculated perimeter of the rectangle */
+  virtual double perimeter() { return 2*height + 2*width; }
+};
+
+
+/*! Factory function for creating a square
+ *  \param r width of the square
+ *  \return a fully constructed square */
+Square MakeSquare(double r);
+
+/*! Factory function for creating a circle
+ *  \param w radius of the circle
+ *  \return a fully constructed circle */
+Circle MakeCircle(double w);
+
+/*! Factory function for creating a rectangle
+ *  \param h height of the rectangle
+ *  \param w width of the rectangle
+ *  \return a fully constructed rectangle */
+template<typename T>
+Rectangle<T> MakeRectangle(T h, T w) {
+  return Rectangle<T>(h, w);
+}
+
+
+
+/*! Total number of circles ever created */
+extern int NumCircles;
+
+/// Total number of squares ever created
+extern int NumSquares;
+
diff --git a/Examples/python/doxygen/example.i b/Examples/python/doxygen/example.i
new file mode 100644
index 000000000..803563dd9
--- /dev/null
+++ b/Examples/python/doxygen/example.i
@@ -0,0 +1,17 @@
+%module example
+
+%{
+#include "example.h"
+%}
+
+%immutable NumSquares;
+%immutable NumCircles;
+
+%include "example.h"
+
+/*! - this instantiation uses type int */
+%template(RectangleInt) Rectangle<int>;
+
+/*! - this instantiation uses type int */
+%template(MakeRectangleInt) MakeRectangle<int>;
+
diff --git a/Examples/python/doxygen/runme.py b/Examples/python/doxygen/runme.py
new file mode 100644
index 000000000..e23528874
--- /dev/null
+++ b/Examples/python/doxygen/runme.py
@@ -0,0 +1,28 @@
+# This example shows simple usage of the wrapped Shape classes.
+# The main purpose of this example is to show the doxygen comments translation to PyDoc comments.
+# Users should look at the generated example.py file.
+# The generated PyDoc can be viewed in a browser by opening the example.html file.
+
+import example
+
+print "Creating some objects:"
+c = example.MakeCircle(10)
+print "    Created circle", c
+s = example.MakeSquare(10)
+print "    Created square", s
+r = example.MakeRectangleInt(10, 20)
+print "    Created rectangle", r
+
+print "\nHere are some properties of the shapes:"
+for o in [c, s, r]:
+    print "   ", o
+    print "        area      = ", o.area()
+    print "        perimeter = ", o.perimeter()
+
+print "\nRunning pydoc, this is the equivalent to executing: pydoc -w ./example.py"
+
+import pydoc
+
+pydoc.writedoc("example")
+
+print "Open example.html in your browser to view the generated python docs"

From 15f16155f2f3f4c82726e27dd77c219ba6c4732d Mon Sep 17 00:00:00 2001
From: William S Fulton <wsf@fultondesigns.co.uk>
Date: Fri, 1 Jun 2018 21:00:06 +0100
Subject: [PATCH 311/314] Move doxygen warning numbers

Move out of the range reserved for language modules
---
 .../errors/doxygen_unknown_command.stderr        |  2 +-
 Source/Include/swigwarn.h                        | 16 ++++++++--------
 2 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/Examples/test-suite/errors/doxygen_unknown_command.stderr b/Examples/test-suite/errors/doxygen_unknown_command.stderr
index 1ac00d6b0..e92da6e6c 100644
--- a/Examples/test-suite/errors/doxygen_unknown_command.stderr
+++ b/Examples/test-suite/errors/doxygen_unknown_command.stderr
@@ -1 +1 @@
-doxygen_unknown_command.i:4: Warning 760: Doxygen parser warning: unknown command "unknown".
+doxygen_unknown_command.i:4: Warning 560: Doxygen parser warning: unknown command "unknown".
diff --git a/Source/Include/swigwarn.h b/Source/Include/swigwarn.h
index c0921530f..a7f9526e1 100644
--- a/Source/Include/swigwarn.h
+++ b/Source/Include/swigwarn.h
@@ -209,6 +209,14 @@
 #define WARN_LANG_EXTEND_CONSTRUCTOR  522
 #define WARN_LANG_EXTEND_DESTRUCTOR   523
 
+/* -- Doxygen comments -- */
+
+#define WARN_DOXYGEN_UNKNOWN_COMMAND          560
+#define WARN_DOXYGEN_UNEXPECTED_END_OF_COMMENT  561
+#define WARN_DOXYGEN_COMMAND_EXPECTED         562
+#define WARN_DOXYGEN_UNTERMINATED_STRING      563
+#define WARN_DOXYGEN_COMMAND_ERROR            564
+
 /* -- Reserved (600-799) -- */
 
 /* -- Language module specific warnings (700 - 899) -- */
@@ -241,14 +249,6 @@
 
 /* please leave 740-759 free for Python */
 
-#define WARN_DOXYGEN_UNKNOWN_COMMAND          760
-#define WARN_DOXYGEN_UNEXPECTED_END_OF_COMMENT   761
-#define WARN_DOXYGEN_COMMAND_EXPECTED         762
-#define WARN_DOXYGEN_UNTERMINATED_STRING      763
-#define WARN_DOXYGEN_COMMAND_ERROR            764
-
-/* please leave 760-779 free for Doxygen */
-
 #define WARN_RUBY_WRONG_NAME                  801
 #define WARN_RUBY_MULTIPLE_INHERITANCE        802
 

From 396910c100cd4d50167ce5aa78a2fd110adbbb81 Mon Sep 17 00:00:00 2001
From: William S Fulton <wsf@fultondesigns.co.uk>
Date: Tue, 5 Jun 2018 18:40:30 +0100
Subject: [PATCH 312/314] Doxygen warnings cleanup

- Remove unused warnings.
- Refactor some warnings.
- Document all Doxygen warnings.
---
 Doc/Manual/Warnings.html                      | 12 ++++-
 .../errors/doxygen_unknown_command.stderr     |  2 +-
 Source/Doxygen/doxyparser.cxx                 | 53 +++++++++----------
 Source/Include/swigwarn.h                     |  3 +-
 4 files changed, 40 insertions(+), 30 deletions(-)

diff --git a/Doc/Manual/Warnings.html b/Doc/Manual/Warnings.html
index 4fdff486b..853ab691e 100644
--- a/Doc/Manual/Warnings.html
+++ b/Doc/Manual/Warnings.html
@@ -506,7 +506,7 @@ example.i(4) : Syntax error in input(1).
 
 
 
-<H3><a name="Warnings_nn14">17.9.5 Code generation (500-599)</a></H3>
+<H3><a name="Warnings_nn14">17.9.5 Code generation (500-559)</a></H3>
 
 
 <ul>
@@ -535,6 +535,16 @@ example.i(4) : Syntax error in input(1).
 <li>523. Use of an illegal destructor name '<em>name</em>' in %extend is deprecated, the destructor name should be '<em>name</em>'.
 </ul>
 
+<H3><a name="Warnings_doxygen">Doxygen comments (560-599)</a></H3>
+
+<ul>
+  <li>560: Unknown Doxygen command: <em>command</em>.</li>
+  <li>561: Unexpected end of Doxygen comment encountered.</li>
+  <li>562: Expected Doxygen command: <em>command</em></li>
+  <li>563: Doxygen HTML error for tag <em>tag</em>: <em>error text</em>.</li>
+  <li>564: Error parsing Doxygen command <em>command</em>: <em>error text</em>. Command ignored."</li>
+</ul>
+
 <H3><a name="Warnings_nn15">17.9.6 Language module specific (700-899) </a></H3>
 
 
diff --git a/Examples/test-suite/errors/doxygen_unknown_command.stderr b/Examples/test-suite/errors/doxygen_unknown_command.stderr
index e92da6e6c..e5c32cc4b 100644
--- a/Examples/test-suite/errors/doxygen_unknown_command.stderr
+++ b/Examples/test-suite/errors/doxygen_unknown_command.stderr
@@ -1 +1 @@
-doxygen_unknown_command.i:4: Warning 560: Doxygen parser warning: unknown command "unknown".
+doxygen_unknown_command.i:4: Warning 560: Unknown Doxygen command: unknown.
diff --git a/Source/Doxygen/doxyparser.cxx b/Source/Doxygen/doxyparser.cxx
index 558b0401f..7286adeb0 100644
--- a/Source/Doxygen/doxyparser.cxx
+++ b/Source/Doxygen/doxyparser.cxx
@@ -279,7 +279,7 @@ std::string DoxygenParser::getStringTilEndCommand(const std::string &theCommand,
     m_tokenListIt++;
   }
 
-  printListError(WARN_DOXYGEN_COMMAND_EXPECTED, theCommand + " command expected");
+  printListError(WARN_DOXYGEN_COMMAND_EXPECTED, "Expected Doxygen command: " + theCommand + ".");
 
   return description;
 }
@@ -384,7 +384,7 @@ void DoxygenParser::addCommandWord(const std::string &theCommand, const TokenLis
     aNewList.push_back(DoxygenEntity("plainstd::string", name));
     doxyList.push_back(DoxygenEntity(theCommand, aNewList));
   } else {
-    printListError(WARN_DOXYGEN_COMMAND_ERROR, "No word followed " + theCommand + " command. Not added");
+    printListError(WARN_DOXYGEN_COMMAND_ERROR, "Error parsing Doxygen command " + theCommand + ": No word followed the command. Command ignored.");
   }
 }
 
@@ -412,7 +412,7 @@ void DoxygenParser::addCommandEndCommand(const std::string &theCommand, const To
     cout << "Parsing " << theCommand << endl;
   TokenListCIt endCommand = getEndCommand("end" + theCommand, tokList);
   if (endCommand == tokList.end()) {
-    printListError(WARN_DOXYGEN_COMMAND_EXPECTED, "Expected end" + theCommand);
+    printListError(WARN_DOXYGEN_COMMAND_EXPECTED, "Expected Doxygen command: end" + theCommand + ".");
     return;
   }
   DoxygenEntityList aNewList;
@@ -428,7 +428,7 @@ void DoxygenParser::addCommandWordParagraph(const std::string &theCommand, const
   std::string name = getNextWord();
 
   if (name.empty()) {
-    printListError(WARN_DOXYGEN_COMMAND_ERROR, "No word followed " + theCommand + " command. Not added");
+    printListError(WARN_DOXYGEN_COMMAND_ERROR, "Error parsing Doxygen command " + theCommand + ": No word followed the command. Command ignored.");
     return;
   }
   TokenListCIt endOfParagraph = getEndOfParagraph(tokList);
@@ -443,7 +443,7 @@ void DoxygenParser::addCommandWordLine(const std::string &theCommand, const Toke
     cout << "Parsing " << theCommand << endl;
   std::string name = getNextWord();
   if (name.empty()) {
-    printListError(WARN_DOXYGEN_COMMAND_ERROR, "No word followed " + theCommand + " command. Not added");
+    printListError(WARN_DOXYGEN_COMMAND_ERROR, "Error parsing Doxygen command " + theCommand + ": No word followed the command. Command ignored.");
     return;
   }
 
@@ -461,7 +461,7 @@ void DoxygenParser::addCommandWordOWordOWord(const std::string &theCommand, cons
 
   std::string name = getNextWord();
   if (name.empty()) {
-    printListError(WARN_DOXYGEN_COMMAND_ERROR, "No word followed " + theCommand + " command. Not added");
+    printListError(WARN_DOXYGEN_COMMAND_ERROR, "Error parsing Doxygen command " + theCommand + ": No word followed the command. Command ignored.");
     return;
   }
   std::string headerfile = getNextWord();
@@ -487,8 +487,7 @@ void DoxygenParser::addCommandOWord(const std::string &theCommand, const TokenLi
 
 void DoxygenParser::addCommandErrorThrow(const std::string &theCommand, const TokenList &tokList, DoxygenEntityList &) {
 
-  printListError(WARN_DOXYGEN_COMMAND_ERROR,
-                 "Encountered: " + theCommand + "\nThis command should not have been encountered. Behaviour past this may be unpredictable");
+  printListError(WARN_DOXYGEN_COMMAND_ERROR, "Error parsing Doxygen command " + theCommand + ": Unexpectedly encountered this command.");
   m_tokenListIt = getOneLine(tokList);
 }
 
@@ -524,17 +523,17 @@ void DoxygenParser::addCommandUnique(const std::string &theCommand, const TokenL
       cout << "Parsing " << theCommand << endl;
     std::string key = getNextWord();
     if (key.empty()) {
-      printListError(WARN_DOXYGEN_COMMAND_ERROR, "No key followed " + theCommand + " command. Not added");
+      printListError(WARN_DOXYGEN_COMMAND_ERROR, "Error parsing Doxygen command " + theCommand + ": No key followed the command. Command ignored.");
       return;
     }
     std::string heading = getNextWord();
     if (key.empty()) {
-      printListError(WARN_DOXYGEN_COMMAND_ERROR, "No heading followed " + theCommand + " command. Not added");
+      printListError(WARN_DOXYGEN_COMMAND_ERROR, "Error parsing Doxygen command " + theCommand + ": No heading followed the command. Command ignored.");
       return;
     }
     std::string title = getNextWord();
     if (title.empty()) {
-      printListError(WARN_DOXYGEN_COMMAND_ERROR, "No title followed " + theCommand + " command. Not added");
+      printListError(WARN_DOXYGEN_COMMAND_ERROR, "Error parsing Doxygen command " + theCommand + ": No title followed the command. Command ignored.");
       return;
     }
     TokenListCIt endOfParagraph = getEndOfParagraph(tokList);
@@ -592,7 +591,7 @@ void DoxygenParser::addCommandUnique(const std::string &theCommand, const TokenL
       cout << "Parsing " << theCommand << endl;
     std::string name = getNextWord();
     if (name.empty()) {
-      printListError(WARN_DOXYGEN_COMMAND_ERROR, "No word followed " + theCommand + " command. Not added");
+      printListError(WARN_DOXYGEN_COMMAND_ERROR, "Error parsing Doxygen command " + theCommand + ": No word followed the command. Command ignored.");
       return;
     }
     DoxygenEntityList aNewList;
@@ -609,7 +608,7 @@ void DoxygenParser::addCommandUnique(const std::string &theCommand, const TokenL
       cout << "Parsing " << theCommand << endl;
     std::string name = getNextWord();
     if (name.empty()) {
-      printListError(WARN_DOXYGEN_COMMAND_ERROR, "No key followed " + theCommand + " command. Not added");
+      printListError(WARN_DOXYGEN_COMMAND_ERROR, "Error parsing Doxygen command " + theCommand + ": No key followed the command. Command ignored.");
       return;
     }
     DoxygenEntityList aNewList;
@@ -638,7 +637,7 @@ void DoxygenParser::addCommandUnique(const std::string &theCommand, const TokenL
       cout << "Parsing " << theCommand << endl;
     std::string name = getNextWord();
     if (name.empty()) {
-      printListError(WARN_DOXYGEN_COMMAND_ERROR, "No name followed " + theCommand + " command. Not added");
+      printListError(WARN_DOXYGEN_COMMAND_ERROR, "Error parsing Doxygen command " + theCommand + ": No name followed the command. Command ignored.");
       return;
     }
     std::string text = getNextWord();
@@ -685,7 +684,7 @@ void DoxygenParser::addCommandUnique(const std::string &theCommand, const TokenL
       cout << "Parsing " << theCommand << endl;
     std::string file = getNextWord();
     if (file.empty()) {
-      printListError(WARN_DOXYGEN_COMMAND_ERROR, "No file followed " + theCommand + " command. Not added");
+      printListError(WARN_DOXYGEN_COMMAND_ERROR, "Error parsing Doxygen command " + theCommand + ": No file followed the command. Command ignored.");
       return;
     }
     std::string caption = getNextWord();
@@ -700,12 +699,12 @@ void DoxygenParser::addCommandUnique(const std::string &theCommand, const TokenL
       cout << "Parsing " << theCommand << endl;
     std::string format = getNextWord();
     if (format.empty()) {
-      printListError(WARN_DOXYGEN_COMMAND_ERROR, "No format followed " + theCommand + " command. Not added");
+      printListError(WARN_DOXYGEN_COMMAND_ERROR, "Error parsing Doxygen command " + theCommand + ": No format followed the command. Command ignored.");
       return;
     }
     std::string file = getNextWord();
     if (file.empty()) {
-      printListError(WARN_DOXYGEN_COMMAND_ERROR, "No name followed " + theCommand + " command. Not added");
+      printListError(WARN_DOXYGEN_COMMAND_ERROR, "Error parsing Doxygen command " + theCommand + ": No name followed the command. Command ignored.");
       return;
     }
     std::string caption = getNextWord();
@@ -726,7 +725,7 @@ void DoxygenParser::addCommandUnique(const std::string &theCommand, const TokenL
       cout << "Parsing " << theCommand << endl;
     std::string name = getNextWord();
     if (name.empty()) {
-      printListError(WARN_DOXYGEN_COMMAND_ERROR, "There should be at least one word following the '" + theCommand + "' command. Command ignored.");
+      printListError(WARN_DOXYGEN_COMMAND_ERROR, "Error parsing Doxygen command " + theCommand + ": There should be at least one word following the command. Command ignored.");
       return;
     }
     DoxygenEntityList aNewList;
@@ -749,7 +748,7 @@ void DoxygenParser::addCommandUnique(const std::string &theCommand, const TokenL
     if (needsCond) {
       cond = getNextWord();
       if (cond.empty()) {
-        printListError(WARN_DOXYGEN_COMMAND_ERROR, "No word followed " + theCommand + " command. Not added");
+        printListError(WARN_DOXYGEN_COMMAND_ERROR, "Error parsing Doxygen command " + theCommand + ": No word followed the command. Command ignored.");
         return;
       }
     }
@@ -777,7 +776,7 @@ void DoxygenParser::addCommandUnique(const std::string &theCommand, const TokenL
     }
 
     if (endCommand == tokList.end()) {
-      printListError(WARN_DOXYGEN_COMMAND_EXPECTED, "No corresponding endif found");
+      printListError(WARN_DOXYGEN_COMMAND_EXPECTED, "Expected Doxygen command: endif.");
       return;
     }
 
@@ -835,7 +834,7 @@ void DoxygenParser::ignoreCommand(const std::string &theCommand, const TokenList
   if (!endCommand.empty()) {
     TokenListCIt itEnd = getEndCommand(endCommand, tokList);
     if (itEnd == tokList.end()) {
-      printListError(WARN_DOXYGEN_COMMAND_EXPECTED, "Expected " + endCommand);
+      printListError(WARN_DOXYGEN_COMMAND_EXPECTED, "Expected Doxygen command: " + endCommand + ".");
       return;
     }
     // If we ignore the command, also ignore any whitespace preceding it as we
@@ -979,7 +978,7 @@ DoxygenEntityList DoxygenParser::parse(TokenListCIt endParsingIndex, const Token
 
     if (endParsingIndex != tokList.end() && m_tokenListIt == tokList.end()) {
       // this could happen if we can't reach the original endParsingIndex
-      printListError(WARN_DOXYGEN_UNEXPECTED_END_OF_COMMENT, "Unexpected end of comment encountered");
+      printListError(WARN_DOXYGEN_UNEXPECTED_END_OF_COMMENT, "Unexpected end of Doxygen comment encountered.");
       break;
     }
   }
@@ -1052,7 +1051,7 @@ bool DoxygenParser::addDoxyCommand(DoxygenParser::TokenList &tokList, const std:
       const TokenListCIt itSave = m_tokenListIt;
       m_tokenListIt = m_tokenList.end();
 
-      printListError(WARN_DOXYGEN_UNKNOWN_COMMAND, "unknown command \"" + cmd + '"');
+      printListError(WARN_DOXYGEN_UNKNOWN_COMMAND, "Unknown Doxygen command: " + cmd + ".");
 
       m_tokenListIt = itSave;
     }
@@ -1177,13 +1176,13 @@ void DoxygenParser::processHtmlTags(size_t &pos, const std::string &line) {
       // for example <A ...>, <IMG ...>, ...
       if (isEndHtmlTag) {
         m_tokenListIt = m_tokenList.end();
-        printListError(WARN_DOXYGEN_COMMAND_ERROR, "Illegal end HTML tag without '>' found! Tag: " + cmd);
+        printListError(WARN_DOXYGEN_HTML_ERROR, "Doxygen HTML error for tag " + cmd + ": Illegal end HTML tag without '>' found.");
       }
 
       endHtmlPos = line.find(">", pos);
       if (endHtmlPos == string::npos) {
         m_tokenListIt = m_tokenList.end();
-        printListError(WARN_DOXYGEN_COMMAND_ERROR, "HTML tag without '>' found! Tag: " + cmd);
+        printListError(WARN_DOXYGEN_HTML_ERROR, "Doxygen HTML error for tag " + cmd + ": HTML tag without '>' found.");
       }
       // add args of HTML command, like link URL, image URL, ...
       m_tokenList.push_back(Token(PLAINSTRING, line.substr(pos, endHtmlPos - pos)));
@@ -1268,7 +1267,7 @@ size_t DoxygenParser::processNormalComment(size_t pos, const std::string &line)
     break;
   default:
     m_tokenListIt = m_tokenList.end();
-    printListError(WARN_DOXYGEN_COMMAND_ERROR, std::string("Unknown special character: ") + line[pos]);
+    printListError(WARN_DOXYGEN_UNKNOWN_CHARACTER, std::string("Unknown special character in Doxygen comment: ") + line[pos] + ".");
   }
 
   return pos;
@@ -1418,5 +1417,5 @@ void DoxygenParser::printListError(int warningType, const std::string &message)
     }
   }
 
-  Swig_warning(warningType, m_fileName.c_str(), curLine, "Doxygen parser warning: %s.\n", message.c_str());
+  Swig_warning(warningType, m_fileName.c_str(), curLine, "%s\n", message.c_str());
 }
diff --git a/Source/Include/swigwarn.h b/Source/Include/swigwarn.h
index a7f9526e1..9f863f194 100644
--- a/Source/Include/swigwarn.h
+++ b/Source/Include/swigwarn.h
@@ -214,8 +214,9 @@
 #define WARN_DOXYGEN_UNKNOWN_COMMAND          560
 #define WARN_DOXYGEN_UNEXPECTED_END_OF_COMMENT  561
 #define WARN_DOXYGEN_COMMAND_EXPECTED         562
-#define WARN_DOXYGEN_UNTERMINATED_STRING      563
+#define WARN_DOXYGEN_HTML_ERROR               563
 #define WARN_DOXYGEN_COMMAND_ERROR            564
+#define WARN_DOXYGEN_UNKNOWN_CHARACTER        565
 
 /* -- Reserved (600-799) -- */
 

From 088d7c7773e4395a0246dd90bbc85c7d27d2a7b5 Mon Sep 17 00:00:00 2001
From: William S Fulton <wsf@fultondesigns.co.uk>
Date: Tue, 5 Jun 2018 18:52:30 +0100
Subject: [PATCH 313/314] Add some missing doctype tyemaps

---
 Lib/python/boost_shared_ptr.i | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/Lib/python/boost_shared_ptr.i b/Lib/python/boost_shared_ptr.i
index 8aeae5be5..709e7811d 100644
--- a/Lib/python/boost_shared_ptr.i
+++ b/Lib/python/boost_shared_ptr.i
@@ -399,7 +399,10 @@
 %}
 
 %typemap(doctype) SWIG_SHARED_PTR_QNAMESPACE::shared_ptr< CONST TYPE >,
-                  SWIG_SHARED_PTR_QNAMESPACE::shared_ptr< CONST TYPE >& %{TYPE%}
+                  SWIG_SHARED_PTR_QNAMESPACE::shared_ptr< CONST TYPE > &,
+                  SWIG_SHARED_PTR_QNAMESPACE::shared_ptr< CONST TYPE > *,
+                  SWIG_SHARED_PTR_QNAMESPACE::shared_ptr< CONST TYPE > *&
+  %{TYPE%}
 
 
 %template() SWIG_SHARED_PTR_QNAMESPACE::shared_ptr< CONST TYPE >;

From ac80a0ed265984492918f9ea4c89c87264028498 Mon Sep 17 00:00:00 2001
From: William S Fulton <wsf@fultondesigns.co.uk>
Date: Thu, 7 Jun 2018 07:42:08 +0100
Subject: [PATCH 314/314] Add changes entry for Doxygen support

---
 CHANGES.current | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/CHANGES.current b/CHANGES.current
index 2e1934cce..3a3487e15 100644
--- a/CHANGES.current
+++ b/CHANGES.current
@@ -7,6 +7,11 @@ the issue number to the end of the URL: https://github.com/swig/swig/issues/
 Version 4.0.0 (in progress)
 ===========================
 
+2018-06-07: cmfoil, kabbi, Jamie Kirkpatrick, markok314, vadz, wsfulton, Yann Diorcet
+            #170 Doxygen documentation support added. This allows translation of Doxygen comments
+            into JavaDoc and PyDoc documentation. It is enabled via the -doxygen command line
+            option. See the Doxygen.html chapter in the documentation for further information.
+
 2018-05-15: kwwette
             [Octave] add support for version 4.4
             - Should not introduce any user-visible incompatibilities