Release-1.7.4-20110727

INSTALL

-DOXYGEN Version 1.7.4-20110629
+DOXYGEN Version 1.7.4-20110727
 
 Please read the installation section of the manual 
 (http://www.doxygen.org/install.html) for instructions.
 
 --------
-Dimitri van Heesch (29 June 2011)
+Dimitri van Heesch (27 July 2011)

Makefile.in

@@ -10,7 +10,7 @@ clean: FORCE
 	cd qtools ; $(MAKE) clean
 	cd src ; $(MAKE) clean
 	cd libmd5 ; $(MAKE) clean
-	cd addon/doxywizard ; $(MAKE) clean
+	-cd addon/doxywizard ; $(MAKE) clean
 	cd addon/doxmlparser/src ; $(MAKE) clean
 	cd addon/doxmlparser/test ; $(MAKE) clean
 	cd addon/doxmlparser/examples/metrics ; $(MAKE) clean
@@ -20,7 +20,7 @@ clean: FORCE
 distclean: clean
 	cd src ; $(MAKE) distclean
 	cd libmd5 ; $(MAKE) distclean
-	cd addon/doxywizard ; $(MAKE) distclean
+	-cd addon/doxywizard ; $(MAKE) distclean
 	cd addon/doxmlparser/src ; $(MAKE) distclean
 	cd addon/doxmlparser/test ; $(MAKE) distclean
 	cd addon/doxmlparser/examples/metrics ; $(MAKE) distclean

README

-DOXYGEN Version 1.7.4_20110629
+DOXYGEN Version 1.7.4_20110727
 
 Please read INSTALL for compilation instructions.
 
@@ -26,4 +26,4 @@ forum.
 
 Enjoy,
 
-Dimitri van Heesch (dimitri@stack.nl) (29 June 2011)
+Dimitri van Heesch (dimitri@stack.nl) (27 July 2011)

configure

@@ -20,7 +20,7 @@ doxygen_version_minor=7
 doxygen_version_revision=4
 
 #NOTE: Setting version_mmn to "NO" will omit mmn info from the package.
-doxygen_version_mmn=20110629
+doxygen_version_mmn=20110727
 
 bin_dirs=`echo $PATH | sed -e "s/:/ /g"`
 

doc/commands.doc

@@ -51,6 +51,7 @@ documentation:
 \refitem cmdcallgraph \\callgraph
 \refitem cmdcallergraph \\callergraph
 \refitem cmdcategory \\category
+\refitem cmdcite \\cite
 \refitem cmdclass \\class
 \refitem cmdcode \\code
 \refitem cmdcond \\cond
@@ -1657,6 +1658,18 @@ Commands to create links
 
   \sa section \ref cmdref "\\ref".
 
+<hr>
+\section cmdcite \\cite <label>
+
+  \addindex \\cite
+  Adds a bibliographic reference in the text and in the list of bibliographic
+  references. The \<label\> must be a valid BibTeX label that can be found 
+  in one of the .bib files listed in \ref cfg_cite_bib_files "CITE_BIB_FILES".  
+  For the LaTeX output the formatting of the reference in the text can be 
+  configured with \ref cfg_latex_bib_style "LATEX_BIB_STYLE". For other
+  output formats a fixed representation is used. Note that using this
+  command requires the \c bibtex tool to be present in the search path.
+
 <hr>
 \section cmdendlink \\endlink
 
@@ -2399,11 +2412,13 @@ class Receiver
   \note The second { is optional and is only to help editors (such as Vim) to
   do proper syntax highlighting by making the number of opening and closing braces
   the same.
+  \sa section \ref cmdfcurlyclose "\\f}" and section \ref formulas "formulas".
 
 <hr>
 \section cmdfcurlyclose \\f}
 
   Marks the end of a formula that is in a specific environment.
+  \sa section \ref cmdfcurlyopen "\\f{" and section \ref formulas "formulas".
 
 <hr>
 \section cmdhtmlonly \\htmlonly

doc/config.doc

@@ -68,6 +68,7 @@ followed by the descriptions of the tags grouped by category.
 \refitem cfg_case_sense_names CASE_SENSE_NAMES 
 \refitem cfg_chm_file CHM_FILE
 \refitem cfg_chm_index_encoding CHM_INDEX_ENCODING
+\refitem cfg_cite_bib_files CITE_BIB_FILES
 \refitem cfg_class_diagrams CLASS_DIAGRAMS 
 \refitem cfg_class_graph CLASS_GRAPH
 \refitem cfg_collaboration_graph COLLABORATION_GRAPH
@@ -187,6 +188,7 @@ followed by the descriptions of the tags grouped by category.
 \refitem cfg_internal_docs INTERNAL_DOCS
 \refitem cfg_javadoc_autobrief JAVADOC_AUTOBRIEF
 \refitem cfg_latex_batchmode LATEX_BATCHMODE
+\refitem cfg_latex_bib_style LATEX_BIB_STYLE
 \refitem cfg_latex_cmd_name LATEX_CMD_NAME
 \refitem cfg_latex_footer LATEX_FOOTER
 \refitem cfg_latex_header LATEX_HEADER
@@ -199,6 +201,7 @@ followed by the descriptions of the tags grouped by category.
 \refitem cfg_man_extension MAN_EXTENSION
 \refitem cfg_man_links MAN_LINKS
 \refitem cfg_man_output MAN_OUTPUT
+\refitem cfg_mathjax_extensions MATHJAX_EXTENSIONS
 \refitem cfg_mathjax_relpath MATHJAX_RELPATH
 \refitem cfg_max_dot_graph_depth MAX_DOT_GRAPH_DEPTH
 \refitem cfg_max_initializer_lines MAX_INITIALIZER_LINES
@@ -951,6 +954,17 @@ FILE_VERSION_INFO = "cleartool desc -fmt \%Vn"
  a file called DoxygenLayout.xml, doxygen will parse it automatically even if 
  the \c LAYOUT_FILE tag is left empty.
 
+\anchor cfg_cite_bib_files
+<dt>\c CITE_BIB_FILES <dd>
+ \addindex CITE_BIB_FILES
+ The \c CITE_BIB_FILES tag can be used to specify one or more bib files 
+ containing the reference definitions. This must be a list of .bib files. The 
+ .bib extension is automatically appended if omitted. This requires the 
+ bibtex tool to be installed. See also http://en.wikipedia.org/wiki/BibTeX 
+ for more info. For LaTeX the style of the bibliography can be controlled 
+ using \ref cfg_latex_bib_style "LATEX_BIB_STYLE". See 
+ also \ref cmdcite "\\cite" for info how to create references.
+
 </dl>
 
 \section messages_input Options related to warning and progress messages 
@@ -1782,6 +1796,15 @@ and Class Hierarchy pages using a tree view instead of an ordered list.
  the http://www.mathjax.org site, so you can quickly see the result without installing 
  MathJax, but it is strongly recommended to install a local copy of MathJax 
  before deployment.
+
+\anchor cfg_mathjax_extensions
+<dt>\c MATHJAX_EXTENSIONS <dd>
+ \addindex MATHJAX_EXTENSIONS
+ The MATHJAX_EXTENSIONS tag can be used to specify one or MathJax extension 
+ names that should be enabled during MathJax rendering. For example
+\verbatim
+MATHJAX_EXTENSIONS     = TeX/AMSmath TeX/AMSsymbols
+\endverbatim
  
 </dl>
 \section latex_output LaTeX related options
@@ -1907,6 +1930,15 @@ EXTRA_PACKAGES = times
  asking the user for help. This option is also used when generating formulas 
  in HTML.
 
+\anchor cfg_latex_bib_style 
+<dt>\c LATEX_BIB_STYLE <dd>
+ \addindex LATEX_BIB_STYLE
+
+ The \c LATEX_BIB_STYLE tag can be used to specify the style to use for the 
+ bibliography, e.g. \c plainnat, or \c ieeetr. The default style is 
+ \c plain. See http://en.wikipedia.org/wiki/BibTeX and \ref cmdcite "\\cite"
+ for more info.
+
 \anchor cfg_latex_hide_indices
 <dt>\c LATEX_HIDE_INDICES <dd>
  \addindex LATEX_HIDE_INDICES
@@ -2426,7 +2458,7 @@ The default size is 10pt.
  visible in IE 9+ (other browsers do not have this requirement).
 
 \anchor cfg_interactive_svg
-<dt>\c INTERACTIVE_SVG
+<dt>\c INTERACTIVE_SVG <dd>
  If DOT_IMAGE_FORMAT is set to svg, then this option can be set to YES to
  enable generation of interactive SVG images that allow zooming and panning. 
  Note that this requires a modern browser other than Internet Explorer. 

doc/docblocks.doc

@@ -20,9 +20,9 @@
 
 A special documentation block is a C or C++ style comment block with some 
 additional markings, so doxygen knows it is a piece of documentation that
-needs to end up in the generated documentation. For Python and VHDL
-code there are a different comment conventions, which can be found in section 
-\ref pythonblocks and \ref vhdlblocks respectively.
+needs to end up in the generated documentation. For Python, VHDL, and Fortran
+code there are different comment conventions, which can be found in sections
+\ref pythonblocks, \ref vhdlblocks, and \ref fortranblocks respectively.
 
 For each code item there are two (or in some cases three) types of descriptions, 
 which together form the documentation: a \e brief description and \e detailed

qtools/Doxyfile

@@ -131,9 +131,9 @@ IGNORE_PREFIX          = Q
 #---------------------------------------------------------------------------
 GENERATE_HTML          = YES
 HTML_OUTPUT            =
-HTML_FILE_EXTENSION    = .xhtml
-HTML_HEADER            =
-HTML_FOOTER            =
+HTML_FILE_EXTENSION    = .html
+HTML_HEADER            = 
+HTML_FOOTER            = 
 HTML_STYLESHEET        =
 HTML_EXTRA_FILES       =
 HTML_COLORSTYLE_HUE    = 220
@@ -175,7 +175,7 @@ FORMULA_TRANSPARENT    = YES
 USE_MATHJAX            = NO
 MATHJAX_RELPATH        = http://www.mathjax.org/mathjax
 SEARCHENGINE           = YES
-SERVER_BASED_SEARCH    = NO
+SERVER_BASED_SEARCH    = YES
 #---------------------------------------------------------------------------
 # configuration options related to the LaTeX output
 #---------------------------------------------------------------------------

qtools/qthread_unix.cpp

@@ -53,6 +53,7 @@
 #include <sys/sysctl.h>
 #endif
 #include <unistd.h>
+#include <stdio.h>
 
 #include "qthread.h"
 #include "qthread_p.h"

src/cite.cpp

+/******************************************************************************
+ *
+ * Copyright (C) 2011 by Dimitri van Heesch
+ * Based on a patch by David Munger
+ *
+ * Permission to use, copy, modify, and distribute this software and its
+ * documentation under the terms of the GNU General Public License is hereby 
+ * granted. No representations are made about the suitability of this software 
+ * for any purpose. It is provided "as is" without express or implied warranty.
+ * See the GNU General Public License for more details.
+ *
+ * Documents produced by Doxygen are derivative works derived from the
+ * input used in their production; they are not affected by this license.
+ *
+ */
+
+#include "cite.h"
+#include "portable.h"
+#include "config.h"
+#include "message.h"
+#include "util.h"
+#include "language.h"
+#include "ftextstream.h"
+#include <qdir.h>
+
+//--------------------------------------------------------------------------
+
+static const char *doxygen_bst =
+#include "doxygen_bst.h"
+;
+
+//--------------------------------------------------------------------------
+
+const QCString CiteConsts::fileName("citelist");
+const QCString CiteConsts::anchorPrefix("CITEREF_");
+
+//--------------------------------------------------------------------------
+
+static bool writeBstFile(const QString &fileName)
+{
+  QCString bstData = doxygen_bst;
+  QFile f(fileName);
+  if (!f.open(IO_WriteOnly)) 
+  {
+    err("error: could not open file %s for writing\n",fileName.data());
+    return FALSE;
+  }
+  f.writeBlock(bstData, strlen(bstData));
+  return TRUE;
+}
+
+//--------------------------------------------------------------------------
+
+CiteDict::CiteDict(int size) : m_entries(size, FALSE)
+{ 
+  m_ordering.setAutoDelete(TRUE); 
+  m_entries.setAutoDelete(TRUE);
+}
+
+bool CiteDict::writeAux()
+{
+  //msg("..writing aux file\n");
+  QCString auxFileName(m_baseFileName + ".aux");
+  QFile auxFile(auxFileName);
+  if (!auxFile.open(IO_WriteOnly)) 
+    // point it to something valid, because warn() relies on it
+  {
+    err("Error opening file %s for output\n", auxFileName.data()); 
+    return FALSE;
+  }
+  FTextStream t(&auxFile);
+
+  QDictIterator<CiteInfo> cdi(m_entries);
+  for (CiteInfo *ci = 0; (ci=cdi.current()); ++cdi)
+  {
+    t << "\\citation{" << ci->label << "}\n";
+  }
+
+  t << "\\bibstyle{" << m_baseFileName << "}\n";
+
+  t << "\\bibdata{";
+  QStrList &citeDataList = Config_getList("CITE_BIB_FILES");
+  const char *bibdata = citeDataList.first();
+  while (bibdata)
+  {
+    QCString bibFile = bibdata;
+    if (!bibFile.isEmpty() && bibFile.right(4)!=".bib") bibFile+=".bib";
+    if (!bibFile.isEmpty())
+    {
+      QFileInfo fi(bibFile);
+      if (fi.exists())
+      {
+        if (!copyFile(bibFile,m_baseFileName+"_"+bibFile))
+        {
+          return FALSE;
+        }
+        t << m_baseFileName+"_"+bibFile;
+        bibdata = citeDataList.next();
+        if (bibdata)
+        {
+          t << ",";
+        }
+      }
+      else
+      {
+        err("The file %s specified at CITE_BIB_FILES could not be read!\n",bibdata);
+        return FALSE;
+      }
+    }
+    else
+    {
+      bibdata = citeDataList.next();
+    }
+  }
+  t << "}\n";
+  return TRUE;
+}
+
+bool CiteDict::writeBst()
+{
+  //msg("..writing bst file\n");
+  QCString bstFileName = m_baseFileName + ".bst";
+  return writeBstFile(bstFileName);
+}
+
+void CiteDict::writeDefaultBibStyle()
+{
+  writeBstFile("doxygen.bst");
+  msg("wrote doxygen.bst\n");
+}
+
+void CiteDict::writeLatexBibliography(FTextStream &t)
+{
+  if (m_entries.count()==0) return;
+  QCString style = Config_getString("LATEX_BIB_STYLE");
+  if (style.isEmpty()) style="plain";
+  t << "\\newpage \\bibliographystyle{" << style << "}" << endl;
+  t << "\\bibliography{";
+  QStrList &citeDataList = Config_getList("CITE_BIB_FILES");
+  const char *bibdata = citeDataList.first();
+  while (bibdata)
+  {
+    QCString bibFile = bibdata;
+    if (!bibFile.isEmpty())
+    {
+      t << bibFile;
+      bibdata = citeDataList.next();
+      if (bibdata)
+      {
+        t << ",";
+      }
+    }
+    else
+    {
+      bibdata = citeDataList.next();
+    }
+  }
+  t << "}" << endl;
+}
+
+void CiteDict::insert(const char *label)
+{
+  m_entries.insert(label,new CiteInfo(label));
+}
+
+CiteInfo *CiteDict::find(const char *label) const
+{
+  return label ? m_entries.find(label) : 0;
+}
+
+void CiteDict::clear()
+{
+  m_entries.clear();
+  m_ordering.clear();
+}
+
+bool CiteDict::execute()
+{
+  //msg("..running bibtex\n");
+  bool result=TRUE;
+  QCString auxFileName(m_baseFileName + ".aux");
+  int splitPoint = auxFileName.findRev('/');
+  QCString dirname = auxFileName.left(splitPoint);
+  QCString basename = auxFileName.mid(splitPoint + 1);
+  QCString oldDir = convertToQCString(QDir::currentDirPath());
+  QDir::setCurrent(dirname);
+  QCString args;
+  args += "-terse ";
+  args += basename;
+  portable_system("bibtex", args);
+  int exitCode;
+  if ((exitCode=portable_system("bibtex",args))!=0)
+  {
+    err("Problems running bibtex: exit code=%d, command='bibtex', arguments='%s'\n",
+      exitCode,args.data());
+    result=FALSE;
+  }
+  QDir::setCurrent(oldDir);
+  return result;
+}
+
+void CiteDict::parse()
+{
+  //msg("..parsing bbl file\n");
+  QCString bblFileName(m_baseFileName + ".bbl");
+  QFile f(bblFileName);
+  if (!f.open(IO_ReadOnly))
+  {
+    err("error: could not open file %s\n",bblFileName.data());
+    return;
+  }
+
+  m_ordering.clear();
+
+  QTextStream t(&f);
+  QCString label;
+  QCString line;
+  while (!t.eof())
+  {
+    label=t.readLine();
+    if (label.isEmpty())
+    {
+      continue;
+    }
+
+    CiteInfo* ci = m_entries.find(label);
+    if (!ci) insert(label); 
+
+    // BibTeX has its own way of sorting references,
+    // depending on the .bst file
+    m_ordering.append(new QCString(label));
+
+    ci->text=t.readLine();
+
+    while (!(line=t.readLine()).isEmpty())
+    {
+      ci->fullText += line + '\n';
+    }
+
+    // FIXME: process LaTeX-style accents properly
+    ci->fullText = substitute(substitute(substitute(ci->fullText,
+            "{", ""),
+          "}", ""),
+        "~", " ");
+    
+    //printf("BIB ENTRY: %s -> %s: %s\n", ci->label.data(), ci->text.data(), ci->fullText.data());
+  }
+}
+
+void CiteDict::clean()
+{
+  // clean
+  QDir thisDir;
+  QStrList &citeDataList = Config_getList("CITE_BIB_FILES");
+  const char *bibdata = citeDataList.first();
+  while (bibdata)
+  {
+    QCString bibFile = bibdata;
+    if (!bibFile.isEmpty() && bibFile.right(4)!=".bib") bibFile+=".bib";
+    if (!bibFile.isEmpty()) thisDir.remove(m_baseFileName+"_"+bibFile);
+    bibdata = citeDataList.next();
+  }
+
+  thisDir.remove(m_baseFileName + ".aux");
+  thisDir.remove(m_baseFileName + ".bbl");
+  thisDir.remove(m_baseFileName + ".blg");
+  thisDir.remove(m_baseFileName + ".tmp");
+  thisDir.remove(m_baseFileName + ".bst");
+
+  QCString &outputDirectory = Config_getString("OUTPUT_DIRECTORY");
+  if (outputDirectory.isEmpty()) 
+  {
+    outputDirectory=QDir::currentDirPath();
+  }
+  QDir d(outputDirectory);
+  d.rmdir("bib");
+}
+
+void CiteDict::resolve()
+{
+  QStrList &citeBibFiles = Config_getList("CITE_BIB_FILES");
+  if (citeBibFiles.count()==0 || m_entries.count()==0) return; // nothing to cite
+
+  QCString &outputDirectory = Config_getString("OUTPUT_DIRECTORY");
+  if (outputDirectory.isEmpty()) 
+  {
+    outputDirectory=QDir::currentDirPath();
+  }
+  QDir d(outputDirectory);
+  d.mkdir("bib");
+
+  uint pid = portable_pid();
+  m_baseFileName.sprintf("doxygen_bibtex_%d",pid);
+  m_baseFileName.prepend(outputDirectory+"/bib/");
+
+  if (writeAux() && writeBst() && execute()) 
+  {
+    parse();
+    clean();
+  }
+
+  if (Config_getBool("GENERATE_LATEX"))
+  {
+    // copy bib files to the latex output dir
+    QStrList &citeDataList = Config_getList("CITE_BIB_FILES");
+    QCString latexOutputDir = Config_getString("LATEX_OUTPUT")+"/";
+    const char *bibdata = citeDataList.first();
+    while (bibdata)
+    {
+      QCString bibFile = bibdata;
+      if (!bibFile.isEmpty() && bibFile.right(4)!=".bib") bibFile+=".bib";
+      if (!bibFile.isEmpty())
+      {
+        copyFile(bibFile,latexOutputDir+bibFile);
+      }
+      bibdata = citeDataList.next();
+    }
+  }
+}
+
+bool CiteDict::isEmpty() const
+{
+  QStrList &citeBibFiles = Config_getList("CITE_BIB_FILES");
+  return (citeBibFiles.count()==0 || m_ordering.isEmpty());
+}
+
+void CiteDict::generatePage() const
+{
+  //printf("** CiteDict::generatePage() count=%d\n",m_ordering.count());
+
+  // do not generate an empty citations page
+  if (isEmpty()) return; // nothing to cite
+
+  QCString doc;
+  doc += "<dl class=\"citelist\">";
+
+  QListIterator<QCString> it(m_ordering);
+  QCString *s;
+  for (it.toFirst();(s=it.current());++it)
+  {
+    CiteInfo* ci = m_entries.find(*s);
+    doc += " <dt>";
+    doc +=  "\\anchor ";
+    doc += CiteConsts::anchorPrefix + ci->label;
+    doc += "\n";
+    doc += ci->text;
+    doc += "</dt><dd> ";
+    doc += ci->fullText;
+    doc += "</dd>";
+  }
+  doc += "</dl>\n";
+  //printf("addRelatedPage with doc='%s'\n",doc.data());
+  addRelatedPage(CiteConsts::fileName,
+       theTranslator->trCiteReferences(),doc,0,CiteConsts::fileName,1,0,0,0);
+}
+

src/cite.h

+/******************************************************************************
+ *
+ * 
+ *
+ * Copyright (C) 2011 by Dimitri van Heesch
+ * Based on a patch by David Munger
+ *
+ * Permission to use, copy, modify, and distribute this software and its
+ * documentation under the terms of the GNU General Public License is hereby 
+ * granted. No representations are made about the suitability of this software 
+ * for any purpose. It is provided "as is" without express or implied warranty.
+ * See the GNU General Public License for more details.
+ *
+ * Documents produced by Doxygen are derivative works derived from the
+ * input used in their production; they are not affected by this license.
+ *
+ */
+
+#ifndef CITEDB_H
+#define CITEDB_H
+
+#include "qtbc.h"
+#include <qdict.h>
+#include <qlist.h>
+
+class FTextStream;
+
+/// String constants for citations
+struct CiteConsts
+{
+  static const QCString fileName;
+  static const QCString anchorPrefix;
+};
+
+/// Citation-related data.
+struct CiteInfo
+{
+  CiteInfo(const char *label_, const char *text_=0, const char *fullText_=0,
+      const char *ref_=0) :
+    label(label_), text(text_), fullText(fullText_), ref(ref_)
+  { }
+
+  CiteInfo(const CiteInfo &o)
+  { label=o.label.copy(); text=o.text.copy(); fullText=o.fullText.copy(); ref=o.ref.copy(); }
+
+  QCString label; 
+  QCString text;
+  QCString fullText;
+  QCString ref;
+
+};
+
+/**
+ * @brief Cite database access class.
+ * @details This class provides access do the database of bibliographic 
+ * references through the bibtex backend.
+ */
+class CiteDict 
+{
+  public:
+    /** Create the database, with an expected maximum of \a size entries */
+    CiteDict(int size);
+
+    /** Resolve references to citations */
+    void resolve();
+
+    /** Insert a citation identified by \a label into the database */
+    void insert(const char *label);
+
+    /** Return the citation info for a given \a label */
+    CiteInfo *find(const char *label) const;
+
+    /** Generate the citations page */
+    void generatePage() const;
+
+    /** clears the database */
+    void clear();
+
+    /** return TRUE if there are no citations. 
+     *  Only valid after calling resolve() 
+     */
+    bool isEmpty() const;
+
+    /** writes the latex code for the standard bibliography 
+     *  section to text stream \a t 
+     */
+    void writeLatexBibliography(FTextStream &t);
+
+    /** writes the default bibliography style to the output */
+    static void writeDefaultBibStyle();
+
+
+  private:
+    bool writeAux();
+    bool writeBst();
+    bool execute();
+    void parse();
+    void clean();
+    QDict<CiteInfo> m_entries;
+    QList<QCString> m_ordering;
+    QCString m_baseFileName;
+};
+
+#endif

src/classdef.h

@@ -265,10 +265,12 @@ class ClassDef : public Definition
     bool isUsedOnly() const;
 
     QCString anchor() const;
-    bool isEmbeddedInGroupDocs() const;
+    bool isEmbeddedInOuterScope() const;
 
     SrcLangExt getLanguage() const;
 
+    bool isSimple() const;
+
     //-----------------------------------------------------------------------------------
     // --- setters ----
     //-----------------------------------------------------------------------------------
@@ -345,6 +347,7 @@ class ClassDef : public Definition
     void writeMemberDeclarations(OutputList &ol,MemberList::ListType lt,const QCString &title,
                                  const char *subTitle=0,bool showInline=FALSE);
     void writeMemberDocumentation(OutputList &ol,MemberList::ListType lt,const QCString &title,bool showInline=FALSE);
+    void writeSimpleMemberDocumentation(OutputList &ol,MemberList::ListType lt);
     void writePlainMemberDeclaration(OutputList &ol,MemberList::ListType lt,bool inGroup);
     void writeBriefDescription(OutputList &ol,bool exampleFlag);
     void writeDetailedDescription(OutputList &ol,const QCString &pageType,bool exampleFlag,
@@ -355,6 +358,7 @@ class ClassDef : public Definition
     void writeCollaborationGraph(OutputList &ol);
     void writeMemberGroups(OutputList &ol,bool showInline=FALSE);
     void writeNestedClasses(OutputList &ol,const QCString &title);
+    void writeInlineClasses(OutputList &ol);
     void startMemberDeclarations(OutputList &ol);
     void endMemberDeclarations(OutputList &ol);
     void startMemberDocumentation(OutputList &ol);

src/classlist.cpp

@@ -96,8 +96,6 @@ bool ClassSDict::declVisible(const ClassDef::CompoundType *filter) const
 void ClassSDict::writeDeclaration(OutputList &ol,const ClassDef::CompoundType *filter,
                                   const char *header,bool localNames)
 {
-//  static bool inlineGroupedClasses = Config_getBool("INLINE_GROUPED_CLASSES");
-//  bool first=TRUE;
   if (count()>0)
   {
     ClassSDict::Iterator sdi(*this);
@@ -110,45 +108,48 @@ void ClassSDict::writeDeclaration(OutputList &ol,const ClassDef::CompoundType *f
           (filter==0 || *filter==cd->compoundType())
          )
       {
-//        //bool isLink = cd->isLinkable();
-//        if (inlineGroupedClasses && cd->partOfGroups()->count()>0)
-//        {
-//          cd->writeInlineDeclaration(ol,first);
-//          first=FALSE;
-//        }
-//        else // show link's only
-//        {
-          cd->writeDeclarationLink(ol,found,header,localNames);
-//        }
+        cd->writeDeclarationLink(ol,found,header,localNames);
       }
     }
     if (found) ol.endMemberList();
   }
 }
   
-void ClassSDict::writeDocumentation(OutputList &ol)
+void ClassSDict::writeDocumentation(OutputList &ol,Definition *container)
 {
   static bool fortranOpt = Config_getBool("OPTIMIZE_FOR_FORTRAN");
 
   static bool inlineGroupedClasses = Config_getBool("INLINE_GROUPED_CLASSES");
-  if (!inlineGroupedClasses) return;
+  static bool inlineSimpleClasses = Config_getBool("INLINE_SIMPLE_STRUCTS");
+  if (!inlineGroupedClasses && !inlineSimpleClasses) return;
 
   if (count()>0)
   {
-    ol.writeRuler();
-    ol.startGroupHeader();
-    ol.parseText(fortranOpt?theTranslator->trTypeDocumentation():
-        theTranslator->trClassDocumentation());
-    ol.endGroupHeader();
+    bool found=FALSE;
 
     ClassSDict::Iterator sdi(*this);
     ClassDef *cd=0;
     for (sdi.toFirst();(cd=sdi.current());++sdi)
     {
-      if (cd->name().find('@')==-1 && 
-          cd->partOfGroups()->count()==1
+      //printf("%s:writeDocumentation() %p=%p embedded=%d\n",
+      //  cd->name().data(),container,cd->getOuterScope(),cd->isEmbeddedInOuterScope());
+
+      if (cd->name().find('@')==-1 && cd->isEmbeddedInOuterScope() &&
+          (container==0 || // no container -> used for groups
+           cd->getOuterScope()==container || // correct container -> used for namespaces and classes
+           (container->definitionType()==Definition::TypeFile && cd->getOuterScope()==Doxygen::globalScope && cd->partOfGroups()==0) // non grouped class with file scope -> used for files
+          )
          )
       {
+        if (!found)
+        {
+          ol.writeRuler();
+          ol.startGroupHeader();
+          ol.parseText(fortranOpt?theTranslator->trTypeDocumentation():
+              theTranslator->trClassDocumentation());
+          ol.endGroupHeader();
+          found=TRUE;
+        }
         cd->writeInlineDocumentation(ol);
       }
     }

src/classlist.h

@@ -24,6 +24,8 @@
 #include "classdef.h"
 #include "sortdict.h"
 
+class Definition;
+
 class ClassList : public QList<ClassDef>
 { 
   public:
@@ -54,7 +56,7 @@ class ClassSDict : public SDict<ClassDef>
    int compareItems(GCI item1,GCI item2);
    void writeDeclaration(OutputList &ol,const ClassDef::CompoundType *filter=0,
                          const char *header=0,bool localNames=FALSE);
-   void writeDocumentation(OutputList &ol);
+   void writeDocumentation(OutputList &ol,Definition *container=0);
    bool declVisible(const ClassDef::CompoundType *filter=0) const;
 };
 

src/cmdmapper.cpp

@@ -29,6 +29,7 @@ CommandMap cmdMap[] =
   { "authors",       CMD_AUTHORS },
   { "b",             CMD_BOLD },
   { "c",             CMD_CODE },
+  { "cite",          CMD_CITE },
   { "code",          CMD_STARTCODE },
   { "copydoc",       CMD_COPYDOC },
   { "copybrief",     CMD_COPYBRIEF },

src/cmdmapper.h

@@ -117,6 +117,7 @@ enum CommandType
   CMD_MSCFILE      = 83,
   CMD_DCOLON       = 84,
   CMD_COPYRIGHT    = 85 | SIMPLESECT_BIT,
+  CMD_CITE         = 86,
 };
 
 enum HtmlTagType

src/commentscan.l

@@ -44,6 +44,7 @@
 #include "reflist.h"
 #include "debug.h"
 #include "parserintf.h"
+#include "cite.h"
 
 // forward declarations
 static bool handleBrief(const QCString &);
@@ -83,6 +84,7 @@ static bool handleMemberOf(const QCString &);
 static bool handleRefItem(const QCString &);
 static bool handleSection(const QCString &);
 static bool handleAnchor(const QCString &);
+static bool handleCite(const QCString &);
 static bool handleFormatBlock(const QCString &);
 static bool handleAddIndex(const QCString &);
 static bool handleIf(const QCString &);
@@ -161,6 +163,7 @@ static DocCmdMap docCmdMap[] =
   { "relatedalso",     &handleRelatedAlso,      TRUE  },
   { "relatesalso",     &handleRelatedAlso,      TRUE  },
   { "refitem",         &handleRefItem,          TRUE  },
+  { "cite",            &handleCite,             TRUE  },
   { "subpage",         &handleSubpage,          TRUE  },
   { "section",         &handleSection,          TRUE  },
   { "subsection",      &handleSection,          TRUE  },
@@ -602,6 +605,13 @@ static void addSection()
 
 //-----------------------------------------------------------------------------
 
+static void addCite()
+{
+  Doxygen::citeDict->insert(yytext);
+}
+
+//-----------------------------------------------------------------------------
+
 // strip trailing whitespace (excluding newlines) from string s
 static void stripTrailingWhiteSpace(QCString &s)
 {
@@ -780,7 +790,7 @@ static int yyread(char *buf,int max_size)
 
        /* start command character */
 CMD	  ("\\"|"@")
-DCMD1     ("arg"|"attention"|"author"|"code")
+DCMD1     ("arg"|"attention"|"author"|"cite"|"code")
 DCMD2     ("date"|"dot"|"msc"|"dotfile"|"example")
 DCMD3     ("htmlinclude"|"htmlonly"|"image"|"include")
 DCMD4     ("includelineno"|"internal"|"invariant")
@@ -861,6 +871,7 @@ RCSTAG    "$"{ID}":"[^\n$]+"$"
 %x	AnchorLabel
 %x      HtmlComment
 %x      SkipLang
+%x	CiteLabel
 
 %%
 
@@ -1953,6 +1964,29 @@ RCSTAG    "$"{ID}":"[^\n$]+"$"
 <SkipLang>.			   { /* any other character */
                                    }
 
+  /* ----- handle arguments of the cite command ------- */
+
+<CiteLabel>{LABELID}			{ // found argyment
+  					  addCite();
+                                          addOutput(yytext);
+					  BEGIN(Comment);
+  					}
+<CiteLabel>{DOCNL}			{ // missing argument
+  					  warn(yyFileName,yyLineNr,
+					      "warning: \\cite command has no label"
+					      );
+  					  if (*yytext=='\n') yyLineNr++;
+					  addOutput('\n');
+					  BEGIN( Comment );
+  					}
+<CiteLabel>.				{ // invalid character for cite label
+  					  warn(yyFileName,yyLineNr,
+					      "warning: Invalid or missing cite label"
+					      );
+					  BEGIN(Comment);
+  					}
+
+
 
 %%
 
@@ -2259,6 +2293,13 @@ static bool handleAnchor(const QCString &s)
   return FALSE;
 }
 
+static bool handleCite(const QCString &s)
+{
+  addOutput(" @"+s+" ");
+  BEGIN(CiteLabel);
+  return FALSE;
+}
+
 static bool handleFormatBlock(const QCString &s)
 {
   addOutput(" @"+s+" ");

src/config.xml

@@ -8,8 +8,9 @@ iconv built into libc) for the transcoding. See
 http://www.gnu.org/software/libiconv for the list of possible encodings. 
 ' defval='UTF-8'/>
     <option type='string' id='PROJECT_NAME' format='string' docs='
-The PROJECT_NAME tag is a single word (or a sequence of words surrounded 
-by quotes) that should identify the project. ' defval=''/>
+The PROJECT_NAME tag is a single word (or sequence of words) that should 
+identify the project. Note that if you do not use Doxywizard you need 
+to put quotes around the project name if it contains spaces.' defval=''/>
     <option type='string' id='PROJECT_NUMBER' format='string' docs='
 The PROJECT_NUMBER tag can be used to enter a project or revision number. 
 This could be handy for archiving the generated documentation or 
@@ -288,6 +289,13 @@ unions are shown inside the group in which they are included (e.g. using
 @ingroup) instead of on a separate page (for HTML and Man pages) or 
 section (for LaTeX and RTF).
 ' defval='0'/>
+    <option type='bool' id='INLINE_SIMPLE_STRUCTS' docs='
+When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and 
+unions with only public data fields will be shown inline in the documentation 
+of the scope in which they are defined (i.e. file, namespace, or group 
+documentation), provided this scope is documented. If set to NO (the default), 
+structs, classes, and unions are shown on a separate page (for HTML and Man 
+pages) or section (for LaTeX and RTF).' defval='0'/>
     <option type='bool' id='TYPEDEF_HIDES_STRUCT' docs='
 When TYPEDEF_HIDES_STRUCT is enabled, a typedef of a struct, union, or enum 
 is documented as struct, union, or enum with the name of the typedef. So 
@@ -515,6 +523,14 @@ output files in an output format independent way. The create the layout file
 that represents doxygen&apos;s defaults, run doxygen with the -l option. 
 You can optionally specify a file name after the option, if omitted 
 DoxygenLayout.xml will be used as the name of the layout file. 
+' defval=''/>
+    <option type='list' id='CITE_BIB_FILES' format='file' docs='
+The CITE_BIB_FILES tag can be used to specify one or more bib files 
+containing the references data. This must be a list of .bib files. The 
+.bib extension is automatically appended if omitted. Using this command 
+requires the bibtex tool to be installed. See also 
+http://en.wikipedia.org/wiki/BibTeX for more info. For LaTeX the style 
+of the bibliography can be controlled using LATEX_BIB_STYLE. 
 ' defval=''/>
   </group>
   <group name='Messages' docs='configuration options related to warning and progress messages'>
@@ -789,13 +805,13 @@ doxygen will generate files with .html extension.
     <option type='string' id='HTML_HEADER' format='file' docs='
 The HTML_HEADER tag can be used to specify a personal HTML header for 
 each generated HTML page. If it is left blank doxygen will generate a 
-standard header. Note that when using a custom header you are responsible 
+standard header. Note that when using a custom header you are responsible  
 for the proper inclusion of any scripts and style sheets that doxygen 
 needs, which is dependent on the configuration options used. 
 It is adviced to generate a default header using "doxygen -w html 
 header.html footer.html stylesheet.css YourConfigFile" and then modify 
 that header. Note that the header is subject to change so you typically 
-have to redo this when upgrading to a newer version of doxygen or when
+have to redo this when upgrading to a newer version of doxygen or when 
 changing the value of configuration settings such as GENERATE_TREEVIEW!
 ' defval='' depends='GENERATE_HTML'/>
     <option type='string' id='HTML_FOOTER' format='file' docs='
@@ -1052,6 +1068,11 @@ mathjax.org site, so you can quickly see the result without installing
 MathJax, but it is strongly recommended to install a local copy of MathJax 
 before deployment.
 ' defval='http://www.mathjax.org/mathjax'/>
+    <option type='list' id='MATHJAX_EXTENSIONS' format='string' docs='
+The MATHJAX_EXTENSIONS tag can be used to specify one or MathJax extension 
+names that should be enabled during MathJax rendering. 
+' depends='USE_MATHJAX'>
+    </option>
     <option type='bool' id='SEARCHENGINE' docs='
 When the SEARCHENGINE tag is enabled doxygen will generate a search box 
 for the HTML output. The underlying search engine uses javascript 
@@ -1154,6 +1175,11 @@ source code with syntax highlighting in the LaTeX output.
 Note that which sources are shown also depends on other settings 
 such as SOURCE_BROWSER.
 ' defval='0' depends='GENERATE_LATEX'/>
+    <option type='string' id='LATEX_BIB_STYLE' format='string' docs='
+The LATEX_BIB_STYLE tag can be used to specify the style to use for the 
+bibliography, e.g. plainnat, or ieeetr. The default style is &quot;plain&quot;. See 
+http://en.wikipedia.org/wiki/BibTeX for more info.
+' defval='plain'/>
   </group>
   <group name='RTF' docs='configuration options related to the RTF output'>
     <option type='bool' id='GENERATE_RTF' docs='
@@ -1405,7 +1431,7 @@ explicitly to a value larger than 0 to get control over the balance
 between CPU load and processing speed.  
 ' defval='0' minval='0' maxval='32'/>
     <option type='string' id='DOT_FONTNAME' format='string' docs='
-By default doxygen will use the Helvetica font for all dot files that
+By default doxygen will use the Helvetica font for all dot files that 
 doxygen generates. When you want a differently looking font you can specify 
 the font name using DOT_FONTNAME. You need to make sure dot is able to find 
 the font, which can be done by putting it in a standard location or by setting 
@@ -1418,7 +1444,7 @@ The default size is 10pt.
 ' minval='4' maxval='24' defval='10' depends='HAVE_DOT'/>
     <option type='string' id='DOT_FONTPATH' format='string' docs='
 By default doxygen will tell dot to use the Helvetica font. 
-If you specify a different font using DOT_FONTNAME you can use DOT_FONTPATH to
+If you specify a different font using DOT_FONTNAME you can use DOT_FONTPATH to 
 set the path where dot can find it.
 ' defval='' depends='HAVE_DOT'/>
     <option type='bool' id='CLASS_GRAPH' docs='
@@ -1486,7 +1512,7 @@ relations between the files in the directories.
 The DOT_IMAGE_FORMAT tag can be used to set the image format of the images 
 generated by dot. Possible values are svg, png, jpg, or gif. 
 If left blank png will be used. If you choose svg you need to set 
-HTML_FILE_EXTENSION to xhtml in order to make the SVG files
+HTML_FILE_EXTENSION to xhtml in order to make the SVG files 
 visible in IE 9+ (other browsers do not have this requirement).
 ' depends='HAVE_DOT'>
       <value name='png'/>
@@ -1494,13 +1520,13 @@ visible in IE 9+ (other browsers do not have this requirement).
       <value name='gif'/>
       <value name='svg'/>
     </option>
-    <option type='bool' id='INTERACTIVE_SVG' doc='
-If DOT_IMAGE_FORMAT is set to svg, then this option can be set to YES to
+    <option type='bool' id='INTERACTIVE_SVG' docs='
+If DOT_IMAGE_FORMAT is set to svg, then this option can be set to YES to 
 enable generation of interactive SVG images that allow zooming and panning. 
 Note that this requires a modern browser other than Internet Explorer. 
-Tested and working are Firefox, Chrome, Safari, and Opera. For IE 9+ you
-need to set HTML_FILE_EXTENSION to xhtml in order to make the SVG files
-visible. Older versions of IE do not have SVG support.
+Tested and working are Firefox, Chrome, Safari, and Opera. For IE 9+ you 
+need to set HTML_FILE_EXTENSION to xhtml in order to make the SVG files 
+visible. Older versions of IE do not have SVG support. 
 ' defval='0' depends='HAVE_DOT'/>
     <option type='string' id='DOT_PATH' format='dir' docs='
 The tag DOT_PATH can be used to specify the path where the dot tool can be 

src/configoptions.cpp

@@ -32,8 +32,9 @@ void addConfigOptions(Config *cfg)
   //----
   cs = cfg->addString(
                  "PROJECT_NAME",
-                 "The PROJECT_NAME tag is a single word (or a sequence of words surrounded\n"
-                 "by quotes) that should identify the project."
+                 "The PROJECT_NAME tag is a single word (or sequence of words) that should\n"
+                 "identify the project. Note that if you do not use Doxywizard you need\n"
+                 "to put quotes around the project name if it contains spaces."
                 );
   //----
   cs = cfg->addString(
@@ -404,6 +405,17 @@ void addConfigOptions(Config *cfg)
                  FALSE
                 );
   //----
+  cb = cfg->addBool(
+                 "INLINE_SIMPLE_STRUCTS",
+                 "When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and\n"
+                 "unions with only public data fields will be shown inline in the documentation\n"
+                 "of the scope in which they are defined (i.e. file, namespace, or group\n"
+                 "documentation), provided this scope is documented. If set to NO (the default),\n"
+                 "structs, classes, and unions are shown on a separate page (for HTML and Man\n"
+                 "pages) or section (for LaTeX and RTF).",
+                 FALSE
+                );
+  //----
   cb = cfg->addBool(
                  "TYPEDEF_HIDES_STRUCT",
                  "When TYPEDEF_HIDES_STRUCT is enabled, a typedef of a struct, union, or enum\n"
@@ -741,6 +753,17 @@ void addConfigOptions(Config *cfg)
                  "DoxygenLayout.xml will be used as the name of the layout file."
                 );
   cs->setWidgetType(ConfigString::File);
+  //----
+  cl = cfg->addList(
+                 "CITE_BIB_FILES",
+                 "The CITE_BIB_FILES tag can be used to specify one or more bib files\n"
+                 "containing the references data. This must be a list of .bib files. The\n"
+                 ".bib extension is automatically appended if omitted. Using this command\n"
+                 "requires the bibtex tool to be installed. See also\n"
+                 "http://en.wikipedia.org/wiki/BibTeX for more info. For LaTeX the style\n"
+                 "of the bibliography can be controlled using LATEX_BIB_STYLE."
+                );
+  cl->setWidgetType(ConfigList::File);
   //---------------------------------------------------------------------------
   cfg->addInfo("Messages","configuration options related to warning and progress messages");
   //---------------------------------------------------------------------------
@@ -1130,12 +1153,13 @@ void addConfigOptions(Config *cfg)
                  "The HTML_HEADER tag can be used to specify a personal HTML header for\n"
                  "each generated HTML page. If it is left blank doxygen will generate a\n"
                  "standard header. Note that when using a custom header you are responsible\n"
-                 "for the proper inclusion of any scripts and style sheets that doxygen\n"
+                 " for the proper inclusion of any scripts and style sheets that doxygen\n"
                  "needs, which is dependent on the configuration options used.\n"
                  "It is adviced to generate a default header using \"doxygen -w html\n"
                  "header.html footer.html stylesheet.css YourConfigFile\" and then modify\n"
                  "that header. Note that the header is subject to change so you typically\n"
-                 "have to redo this when upgrading to a newer version of doxygen or when changing the value of configuration settings such as GENERATE_TREEVIEW!"
+                 "have to redo this when upgrading to a newer version of doxygen or when\n"
+                 "changing the value of configuration settings such as GENERATE_TREEVIEW!"
                 );
   cs->setWidgetType(ConfigString::File);
   cs->addDependency("GENERATE_HTML");
@@ -1551,6 +1575,13 @@ void addConfigOptions(Config *cfg)
                 );
   cs->setDefaultValue("http://www.mathjax.org/mathjax");
   //----
+  cl = cfg->addList(
+                 "MATHJAX_EXTENSIONS",
+                 "The MATHJAX_EXTENSIONS tag can be used to specify one or MathJax extension\n"
+                 "names that should be enabled during MathJax rendering."
+                );
+  cl->addDependency("USE_MATHJAX");
+  //----
   cb = cfg->addBool(
                  "SEARCHENGINE",
                  "When the SEARCHENGINE tag is enabled doxygen will generate a search box\n"
@@ -1717,6 +1748,14 @@ void addConfigOptions(Config *cfg)
                  FALSE
                 );
   cb->addDependency("GENERATE_LATEX");
+  //----
+  cs = cfg->addString(
+                 "LATEX_BIB_STYLE",
+                 "The LATEX_BIB_STYLE tag can be used to specify the style to use for the\n"
+                 "bibliography, e.g. plainnat, or ieeetr. The default style is \"plain\". See\n"
+                 "http://en.wikipedia.org/wiki/BibTeX for more info."
+                );
+  cs->setDefaultValue("plain");
   //---------------------------------------------------------------------------
   cfg->addInfo("RTF","configuration options related to the RTF output");
   //---------------------------------------------------------------------------
@@ -2123,7 +2162,8 @@ void addConfigOptions(Config *cfg)
   //----
   cs = cfg->addString(
                  "DOT_FONTNAME",
-                 "By default doxygen will use the Helvetica font for all dot files that doxygen generates. When you want a differently looking font you can specify\n"
+                 "By default doxygen will use the Helvetica font for all dot files that\n"
+                 "doxygen generates. When you want a differently looking font you can specify\n"
                  "the font name using DOT_FONTNAME. You need to make sure dot is able to find\n"
                  "the font, which can be done by putting it in a standard location or by setting\n"
                  "the DOTFONTPATH environment variable or by setting DOT_FONTPATH to the\n"
@@ -2143,7 +2183,8 @@ void addConfigOptions(Config *cfg)
   cs = cfg->addString(
                  "DOT_FONTPATH",
                  "By default doxygen will tell dot to use the Helvetica font.\n"
-                 "If you specify a different font using DOT_FONTNAME you can use DOT_FONTPATH to set the path where dot can find it."
+                 "If you specify a different font using DOT_FONTNAME you can use DOT_FONTPATH to\n"
+                 "set the path where dot can find it."
                 );
   cs->addDependency("HAVE_DOT");
   //----
@@ -2257,7 +2298,8 @@ void addConfigOptions(Config *cfg)
                  "The DOT_IMAGE_FORMAT tag can be used to set the image format of the images\n"
                  "generated by dot. Possible values are svg, png, jpg, or gif.\n"
                  "If left blank png will be used. If you choose svg you need to set\n"
-                 "HTML_FILE_EXTENSION to xhtml in order to make the SVG files visible in IE 9+ (other browsers do not have this requirement).",
+                 "HTML_FILE_EXTENSION to xhtml in order to make the SVG files\n"
+                 "visible in IE 9+ (other browsers do not have this requirement).",
                  "png"
                 );
   ce->addValue("png");
@@ -2268,7 +2310,12 @@ void addConfigOptions(Config *cfg)
   //----
   cb = cfg->addBool(
                  "INTERACTIVE_SVG",
-                 "",
+                 "If DOT_IMAGE_FORMAT is set to svg, then this option can be set to YES to\n"
+                 "enable generation of interactive SVG images that allow zooming and panning.\n"
+                 "Note that this requires a modern browser other than Internet Explorer.\n"
+                 "Tested and working are Firefox, Chrome, Safari, and Opera. For IE 9+ you\n"
+                 "need to set HTML_FILE_EXTENSION to xhtml in order to make the SVG files\n"
+                 "visible. Older versions of IE do not have SVG support.",
                  FALSE
                 );
   cb->addDependency("HAVE_DOT");

src/definition.cpp

@@ -1343,7 +1343,6 @@ void Definition::writePathFragment(OutputList &ol) const
 void Definition::writeNavigationPath(OutputList &ol) const
 {
   static bool generateTreeView = Config_getBool("GENERATE_TREEVIEW");
-  static bool hasCustomFooter = !Config_getString("HTML_FOOTER").isEmpty();
 
   ol.pushGeneratorState();
   ol.disableAllBut(OutputGenerator::Html);
@@ -1356,13 +1355,7 @@ void Definition::writeNavigationPath(OutputList &ol) const
   ol.writeString("  <div id=\"nav-path\" class=\"navpath\">\n");
   ol.writeString("    <ul>\n");
   writePathFragment(ol);
-  if (!hasCustomFooter && generateTreeView) // write the doxygen logo as part of the navigation bar
-  {
-    ol.writeString("      <li class=\"footer\">");
-    ol.writeLogo();
-    ol.writeString("</li>\n");
-  }
-  if (!hasCustomFooter || !generateTreeView)
+  if (!generateTreeView)
   {
     ol.writeString("    </ul>\n");
     ol.writeString("  </div>\n");

src/dirdef.cpp

@@ -193,8 +193,7 @@ void DirDef::writeDirectoryGraph(OutputList &ol)
       ol.disable(OutputGenerator::Man);
       //ol.startParagraph();
       ol.startDirDepGraph();
-      //TODO: ol.parseText(theTranslator->trDirDepGraph());
-      ol.parseText((QCString)"Directory dependency graph for "+displayName()+":");
+      ol.parseText(theTranslator->trDirDepGraph(displayName()));
       ol.endDirDepGraph(dirDep);
       //ol.endParagraph();
       ol.enableAll();
@@ -381,6 +380,7 @@ void DirDef::writeDocumentation(OutputList &ol)
         }
         break;
       case LayoutDocEntry::ClassIncludes:
+      case LayoutDocEntry::ClassInlineClasses:
       case LayoutDocEntry::ClassInheritanceGraph:
       case LayoutDocEntry::ClassNestedClasses:
       case LayoutDocEntry::ClassCollaborationGraph:
@@ -388,12 +388,14 @@ void DirDef::writeDocumentation(OutputList &ol)
       case LayoutDocEntry::ClassUsedFiles:
       case LayoutDocEntry::NamespaceNestedNamespaces:
       case LayoutDocEntry::NamespaceClasses:
+      case LayoutDocEntry::NamespaceInlineClasses:
       case LayoutDocEntry::FileClasses:
       case LayoutDocEntry::FileNamespaces:
       case LayoutDocEntry::FileIncludes:
       case LayoutDocEntry::FileIncludeGraph:
       case LayoutDocEntry::FileIncludedByGraph: 
       case LayoutDocEntry::FileSourceLink:
+      case LayoutDocEntry::FileInlineClasses:
       case LayoutDocEntry::GroupClasses: 
       case LayoutDocEntry::GroupInlineClasses: 
       case LayoutDocEntry::GroupNamespaces:

src/docparser.cpp

@@ -41,6 +41,7 @@
 #include "searchindex.h"
 #include "language.h"
 #include "portable.h"
+#include "cite.h"
 
 // debug off
 #define DBG(x) do {} while(0)
@@ -1163,11 +1164,10 @@ static DocInternalRef *handleInternalRef(DocNode *parent)
 static DocAnchor *handleAnchor(DocNode *parent)
 {
   int tok=doctokenizerYYlex();
-  QCString tokenName = g_token->name;
   if (tok!=TK_WHITESPACE)
   {
     warn_doc_error(g_fileName,doctokenizerYYlineno,"warning: expected whitespace after %s command",
-        qPrint(tokenName));
+        qPrint(g_token->name));
     return 0;
   }
   doctokenizerYYsetStateAnchor();
@@ -1175,13 +1175,13 @@ static DocAnchor *handleAnchor(DocNode *parent)
   if (tok==0)
   {
     warn_doc_error(g_fileName,doctokenizerYYlineno,"warning: unexpected end of comment block while parsing the "
-        "argument of command %s",qPrint(tokenName));
+        "argument of command %s",qPrint(g_token->name));
     return 0;
   }
   else if (tok!=TK_WORD && tok!=TK_LNKWORD)
   {
     warn_doc_error(g_fileName,doctokenizerYYlineno,"warning: unexpected token %s as the argument of %s",
-        tokToString(tok),qPrint(tokenName));
+        tokToString(tok),qPrint(g_token->name));
     return 0;
   }
   doctokenizerYYsetStatePara();
@@ -1689,6 +1689,21 @@ DocAnchor::DocAnchor(DocNode *parent,const QCString &id,bool newAnchor)
   {
     m_anchor = id;
   }
+  else if (id.left(CiteConsts::anchorPrefix.length()) == CiteConsts::anchorPrefix) 
+  {
+    CiteInfo *cite = Doxygen::citeDict->find(id.mid(CiteConsts::anchorPrefix.length()));
+    if (cite) 
+    {
+      m_file = CiteConsts::fileName;
+      m_anchor = id;
+    }
+    else 
+    {
+      warn_doc_error(g_fileName,doctokenizerYYlineno,"warning: Invalid cite anchor id `%s'",qPrint(id));
+      m_anchor = "invalid";
+      m_file = "invalid";
+    }
+  }
   else // found \anchor label
   {
     SectionInfo *sec = Doxygen::sectionDict[id];
@@ -2385,6 +2400,33 @@ void DocRef::parse()
 
 //---------------------------------------------------------------------------
 
+DocCite::DocCite(DocNode *parent,const QCString &target,const QCString &) //context)
+{
+  static uint numBibFiles = Config_getList("CITE_BIB_FILES").count();
+  m_parent = parent; 
+  QCString     anchor;
+  //printf("DocCite::DocCite(target=%s,context=%s\n",target.data(),context.data());
+  ASSERT(!target.isEmpty());
+  m_relPath = g_relPath;
+  CiteInfo *cite = Doxygen::citeDict->find(target);
+  if (numBibFiles>0 && cite) // ref to citation
+  {
+    m_text         = cite->text;
+    if (m_text.isEmpty()) m_text = cite->label;
+    m_ref          = cite->ref;
+    m_anchor       = CiteConsts::anchorPrefix+cite->label;
+    m_file         = CiteConsts::fileName;
+    //printf("CITE ==> m_text=%s,m_ref=%s,m_file=%s,m_anchor=%s\n",
+    //    m_text.data(),m_ref.data(),m_file.data(),m_anchor.data());
+    return;
+  }
+  m_text = linkToText(target,FALSE);
+  warn_doc_error(g_fileName,doctokenizerYYlineno,"warning: unable to resolve reference to `%s' for \\cite command",
+           qPrint(target)); 
+}
+
+//---------------------------------------------------------------------------
+
 DocLink::DocLink(DocNode *parent,const QCString &target) 
 {
   m_parent = parent; 
@@ -4420,6 +4462,38 @@ int DocPara::handleParamSection(const QCString &cmdName,
   return (rv!=TK_NEWPARA) ? rv : RetVal_OK;
 }
 
+void DocPara::handleCite()
+{
+  // get the argument of the cite command.
+  int tok=doctokenizerYYlex();
+  if (tok!=TK_WHITESPACE)
+  {
+    warn_doc_error(g_fileName,doctokenizerYYlineno,"warning: expected whitespace after %s command",
+        qPrint("cite"));
+    return;
+  }
+  tok=doctokenizerYYlex();
+  if (tok==0)
+  {
+    warn_doc_error(g_fileName,doctokenizerYYlineno,"warning: unexpected end of comment block while parsing the "
+        "argument of command %s\n", qPrint("cite"));
+    return;
+  }
+  else if (tok!=TK_WORD && tok!=TK_LNKWORD)
+  {
+    warn_doc_error(g_fileName,doctokenizerYYlineno,"warning: unexpected token %s as the argument of %s",
+        tokToString(tok),qPrint("cite"));
+    return;
+  }
+  g_token->sectionId = g_token->name;
+  doctokenizerYYsetStateCite();
+  DocCite *cite = new DocCite(this,g_token->name,g_context);
+  m_children.append(cite);
+  //cite->parse();
+
+  doctokenizerYYsetStatePara();
+}
+
 int DocPara::handleXRefItem()
 {
   int retval=doctokenizerYYlex();
@@ -5103,6 +5177,9 @@ int DocPara::handleCommand(const QCString &cmdName)
     case CMD_JAVALINK:
       handleLink(cmdName,TRUE);
       break;
+    case CMD_CITE:
+      handleCite();
+      break;
     case CMD_REF: // fall through
     case CMD_SUBPAGE:
       handleRef(cmdName);

src/docparser.h

@@ -272,8 +272,8 @@ class DocAnchor : public DocNode
   public:
     DocAnchor(DocNode *parent,const QCString &id,bool newAnchor);
     Kind kind() const          { return Kind_Anchor; }
-    QCString anchor() const     { return m_anchor; }
-    QCString file() const       { return m_file; }
+    QCString anchor() const    { return m_anchor; }
+    QCString file() const      { return m_file; }
     void accept(DocVisitor *v) { v->visit(this); }
 
   private:
@@ -281,6 +281,28 @@ class DocAnchor : public DocNode
     QCString  m_file;
 };
 
+/*! @brief Node representing a citation of some bibliographic reference */
+class DocCite : public DocNode
+{
+  public:
+    DocCite(DocNode *parent,const QCString &target,const QCString &context);
+    Kind kind() const            { return Kind_Ref; }
+    QCString file() const        { return m_file; }
+    QCString relPath() const     { return m_relPath; }
+    QCString ref() const         { return m_ref; }
+    QCString anchor() const      { return m_anchor; }
+    QCString text() const        { return m_text; }
+    void accept(DocVisitor *v) { v->visit(this); }
+
+  private:
+    QCString   m_file;
+    QCString   m_relPath;
+    QCString   m_ref;
+    QCString   m_anchor;
+    QCString   m_text;
+};
+
+
 /*! @brief Node representing a style change */
 class DocStyleChange : public DocNode
 {
@@ -980,6 +1002,7 @@ class DocPara : public CompAccept<DocPara>, public DocNode
     void handleMscFile(const QCString &cmdName);
     void handleInclude(const QCString &cmdName,DocInclude::Type t);
     void handleLink(const QCString &cmdName,bool isJavaLink);
+    void handleCite();
     void handleRef(const QCString &cmdName);
     void handleSection(const QCString &cmdName);
     void handleInheritDoc();

src/doctokenizer.h

@@ -141,6 +141,7 @@ void doctokenizerYYsetStateXRefItem();
 void doctokenizerYYsetStateFile();
 void doctokenizerYYsetStatePattern();
 void doctokenizerYYsetStateLink();
+void doctokenizerYYsetStateCite();
 void doctokenizerYYsetStateRef();
 void doctokenizerYYsetStateInternalRef();
 void doctokenizerYYsetStateText();

src/doctokenizer.l

@@ -337,7 +337,7 @@ CHARWORDQ [^ \t\n\r\\@<>()\[\]:;\?{}&%$#,."=]
 ESCWORD   "%"{ID}(("::"|"."){ID})*
 WORD1     {ESCWORD}|{CHARWORDQ}+|"{"|"}"|"'\"'"|("\""[^"\n]*\n?[^"\n]*"\"")
 WORD2     "."|","|"("|")"|"["|"]"|":"|";"|"\?"|"="
-WORD1NQ   {ESCWORD}|{CHARWORDQ}+
+WORD1NQ   {ESCWORD}|{CHARWORDQ}+|"{"|"}"
 WORD2NQ   "."|","|"("|")"|"["|"]"|":"|";"|"\?"|"="
 HTMLTAG   "<"(("/")?){ID}({WS}+{ATTRIB})*{WS}*(("/")?)">" 
 HTMLKEYL  "strong"|"center"|"table"|"caption"|"small"|"code"|"dfn"|"var"|"img"|"pre"|"sub"|"sup"|"tr"|"td"|"th"|"ol"|"ul"|"li"|"tt"|"kbd"|"em"|"hr"|"dl"|"dt"|"dd"|"br"|"i"|"a"|"b"|"p"
@@ -372,6 +372,7 @@ REFWORD   {LABELID}|{REFWORD2}|{REFWORD3}
 %x St_File
 %x St_Pattern
 %x St_Link
+%x St_Cite
 %x St_Ref
 %x St_Ref2
 %x St_IntRef
@@ -733,6 +734,22 @@ REFWORD   {LABELID}|{REFWORD2}|{REFWORD3}
   			 unput(*yytext);
 			 return 0;
   		       }
+<St_Cite>{LABELID}     { // label to cite
+  			 g_token->name=yytext;
+			 return TK_WORD;
+  		       }
+<St_Cite>{BLANK}       { // white space
+  			 unput(' ');
+  			 return 0;
+                       }
+<St_Cite>\n	       { // new line
+                         unput(*yytext);
+  			 return 0;
+  		       }
+<St_Cite>.	       { // any other character
+                         unput(*yytext);
+  			 return 0;
+  		       }
 <St_Ref>{REFWORD}      { // label to refer to
   			 g_token->name=yytext;
 			 return TK_WORD;
@@ -1079,6 +1096,11 @@ void doctokenizerYYsetStateLink()
   BEGIN(St_Link);
 }
 
+void doctokenizerYYsetStateCite()
+{
+  BEGIN(St_Cite);
+}
+
 void doctokenizerYYsetStateRef()
 {
   BEGIN(St_Ref);

src/docvisitor.h

@@ -67,6 +67,7 @@ class DocImage;
 class DocDotFile;
 class DocMscFile;
 class DocLink;
+class DocCite;
 class DocRef;
 class DocFormula;
 class DocSecRefItem;
@@ -108,6 +109,7 @@ class DocVisitor
     virtual void visit(DocLinkedWord *) = 0;
     virtual void visit(DocIndexEntry *) = 0;
     virtual void visit(DocSimpleSectSep *) = 0;
+    virtual void visit(DocCite *) = 0;
     /*! @} */
 
     /*! @name Visitor functions for internal nodes 

src/dot.cpp

@@ -3808,6 +3808,7 @@ void writeDotGraphFromFile(const char *inFile,const char *outDir,
  *  \param relPath relative path the to root of the output dir
  *  \param baseName the base name of the output files
  *  \param context the scope in which this graph is found (for resolving links)
+ *  \param graphId a unique id for this graph, use for dynamic sections
  */
 void writeDotImageMapFromFile(FTextStream &t,
                             const QCString &inFile, const QCString &outDir,

src/doxygen.cpp

@@ -78,6 +78,7 @@
 #include "vhdlscanner.h"
 #include "vhdldocgen.h"
 #include "eclipsehelp.h"
+#include "cite.h"
 
 #include "layout.h"
 
@@ -108,6 +109,7 @@ FormulaDict      Doxygen::formulaNameDict(1009);   // the label name of all form
 PageSDict       *Doxygen::pageSDict = 0;
 PageSDict       *Doxygen::exampleSDict = 0;
 SectionDict      Doxygen::sectionDict(257);        // all page sections
+CiteDict        *Doxygen::citeDict=0;              // database of bibliographic references
 StringDict       Doxygen::aliasDict(257);          // aliases
 FileNameDict    *Doxygen::includeNameDict = 0;     // include names
 FileNameDict    *Doxygen::exampleNameDict = 0;     // examples
@@ -180,6 +182,7 @@ void clearAll()
   Doxygen::formulaDict.clear();      
   Doxygen::formulaNameDict.clear();  
   Doxygen::tagDestinationDict.clear();
+  delete Doxygen::citeDict;
   delete Doxygen::mainPage; Doxygen::mainPage=0;
 }
 
@@ -7408,7 +7411,7 @@ static void generateClassList(ClassSDict &classSDict)
     //printf("cd=%s getOuterScope=%p global=%p\n",cd->name().data(),cd->getOuterScope(),Doxygen::globalScope);
     if ((cd->getOuterScope()==0 || // <-- should not happen, but can if we read an old tag file
          cd->getOuterScope()==Doxygen::globalScope // only look at global classes
-        ) && !cd->isHidden() && !cd->isEmbeddedInGroupDocs()
+        ) && !cd->isHidden() && !cd->isEmbeddedInOuterScope()
        ) 
     {
       // skip external references, anonymous compounds and 
@@ -8177,6 +8180,7 @@ static void resolveUserReferences()
 }
 
 
+
 //----------------------------------------------------------------------------
 // generate all separate documentation pages
 
@@ -8348,7 +8352,7 @@ static void generateNamespaceDocs()
              cd->templateMaster()==0
            ) // skip external references, anonymous compounds and 
              // template instances and nested classes
-           && !cd->isHidden()
+           && !cd->isHidden() && !cd->isEmbeddedInOuterScope()
          )
       {
         msg("Generating docs for compound %s...\n",cd->name().data());
@@ -8609,36 +8613,9 @@ static void readTagFile(Entry *root,const char *tl)
     msg("Reading tag file `%s'...\n",fileName.data());
 
   parseTagFile(root,fi.absFilePath(),fi.fileName());
-
 }
 
 //----------------------------------------------------------------------------
-static void copyFile(const QCString &src,const QCString &dest)
-{
-  QFile sf(src);
-  if (sf.open(IO_ReadOnly))
-  {
-    QFileInfo fi(src);
-    QFile df(dest);
-    if (df.open(IO_WriteOnly))
-    {
-      char *buffer = new char[fi.size()];
-      sf.readBlock(buffer,fi.size());
-      df.writeBlock(buffer,fi.size());
-      df.flush();
-      delete[] buffer;
-    }
-    else
-    {
-      err("error: could not write to file %s\n",dest.data());
-    }
-  }
-  else
-  {
-    err("error: could not open user specified file %s\n",src.data());
-  }
-}
-
 static void copyStyleSheet()
 {
   QCString &htmlStyleSheet = Config_getString("HTML_STYLESHEET");
@@ -9231,9 +9208,9 @@ static void usage(const char *name)
   msg("   generated documentation:\n");
   msg("    %s -l layoutFileName.xml\n\n",name);
   msg("5) Use doxygen to generate a template style sheet file for RTF, HTML or Latex.\n");
-  msg("    RTF:   %s -w rtf styleSheetFile\n",name);
-  msg("    HTML:  %s -w html headerFile footerFile styleSheetFile [configFile]\n",name);
-  msg("    LaTeX: %s -w latex headerFile footerFile styleSheetFile [configFile]\n\n",name);
+  msg("    RTF:        %s -w rtf styleSheetFile\n",name);
+  msg("    HTML:       %s -w html headerFile footerFile styleSheetFile [configFile]\n",name);
+  msg("    LaTeX:      %s -w latex headerFile footerFile styleSheetFile [configFile]\n\n",name);
   msg("6) Use doxygen to generate an rtf extensions file\n");
   msg("    RTF:   %s -e rtf extensionsFile\n\n",name);
   msg("If -s is specified the comments in the config file will be omitted.\n");
@@ -9320,6 +9297,7 @@ void initDoxygen()
   Doxygen::tagDestinationDict.setAutoDelete(TRUE);
   Doxygen::lookupCache.setAutoDelete(TRUE);
   Doxygen::dirRelations.setAutoDelete(TRUE);
+  Doxygen::citeDict = new CiteDict(256);
 }
 
 void cleanUpDoxygen()
@@ -9578,9 +9556,9 @@ void readConfiguration(int argc, char **argv)
           cleanUpDoxygen();
           exit(0);
         }
-        else 
+        else
         {
-          err("error: Illegal format specifier %s: should be one of rtf, html, or latex\n",formatName);
+          err("error: Illegal format specifier %s: should be one of rtf, html, latex, or bst\n",formatName);
           cleanUpDoxygen();
           exit(1);
         }
@@ -10399,6 +10377,12 @@ void parseInput()
     computeDirDependencies();
   }
 
+  msg("Resolving citations...\n");
+  Doxygen::citeDict->resolve();
+
+  msg("Generating citations page...\n");
+  Doxygen::citeDict->generatePage();
+
   msg("Counting data structures...\n");
   countDataStructures();
  
@@ -10569,7 +10553,7 @@ void generateOutput()
   }
 
   //statistics();
-  
+
   // count the number of documented elements in the lists we have built. 
   // If the result is 0 we do not generate the lists and omit the 
   // corresponding links in the index.

src/doxygen.css

@@ -629,6 +629,58 @@ table.doxtable th {
 	text-align:left;
 }
 
+table.fieldtable {
+        width: 100%;
+        margin-bottom: 10px;
+        border: 1px solid ##B4;
+        border-spacing: 0px;
+        -moz-border-radius: 4px;
+        -webkit-border-radius: 4px;
+        border-radius: 4px;
+        -moz-box-shadow: rgba(0, 0, 0, 0.15) 2px 2px 2px;
+        -webkit-box-shadow: 2px 2px 2px rgba(0, 0, 0, 0.15);
+        box-shadow: 2px 2px 2px rgba(0, 0, 0, 0.15);
+}
+
+.fieldtable td, .fieldtable th {
+        padding: 3px 7px 2px;
+}
+
+.fieldtable td.fieldtype, .fieldtable td.fieldname {
+        white-space: nowrap;
+        border-right: 1px solid ##B4;
+        border-bottom: 1px solid ##B4;
+        vertical-align: top;
+}
+
+.fieldtable td.fielddoc {
+        border-bottom: 1px solid ##B4;
+        width: 100%;
+}
+
+.fieldtable tr:last-child td {
+        border-bottom: none;
+}
+
+.fieldtable th {
+        background-image:url('nav_f.png');
+        background-repeat:repeat-x;
+        background-color: ##E6;
+        font-size: 90%;
+        color: ##2B;
+        padding-bottom: 4px;
+        padding-top: 5px;
+        text-align:left;
+        -moz-border-radius-topleft: 4px;
+        -moz-border-radius-topright: 4px;
+        -webkit-border-top-left-radius: 4px;
+        -webkit-border-top-right-radius: 4px;
+        border-top-left-radius: 4px;
+        border-top-right-radius: 4px;
+        border-bottom: 1px solid ##B4;
+}
+
+
 .tabsearch {
 	top: 0px;
 	left: 10px;
@@ -846,6 +898,23 @@ div.zoom
 	border: 1px solid ##A0;
 }
 
+dl.citelist {
+        margin-bottom:50px;
+}
+
+dl.citelist dt {
+        color:##40;
+        float:left;
+        font-weight:bold;
+        margin-right:10px;
+        padding:5px;
+}
+
+dl.citelist dd {
+        margin:2px 0;
+        padding:5px 0;
+}
+
 @media print
 {
   #top { display: none; }

src/doxygen.h

@@ -48,6 +48,7 @@ class ObjCache;
 class Store;
 class QFileInfo;
 class BufStr;
+class CiteDict;
 
 typedef QList<QCString>    StringList;
 typedef QDict<FileDef>     FileDict;
@@ -126,6 +127,7 @@ class Doxygen
     static Store                    *symbolStorage;
     static QCString                  objDBFileName;
     static QCString                  entryDBFileName;
+    static CiteDict                 *citeDict;
     static bool                      gatherDefines;
     static bool                      userComments;
     static IndexList                 indexList;

src/doxygen_css.h

@@ -629,6 +629,58 @@
 "	text-align:left;\n"
 "}\n"
 "\n"
+"table.fieldtable {\n"
+"        width: 100%;\n"
+"        margin-bottom: 10px;\n"
+"        border: 1px solid ##B4;\n"
+"        border-spacing: 0px;\n"
+"        -moz-border-radius: 4px;\n"
+"        -webkit-border-radius: 4px;\n"
+"        border-radius: 4px;\n"
+"        -moz-box-shadow: rgba(0, 0, 0, 0.15) 2px 2px 2px;\n"
+"        -webkit-box-shadow: 2px 2px 2px rgba(0, 0, 0, 0.15);\n"
+"        box-shadow: 2px 2px 2px rgba(0, 0, 0, 0.15);\n"
+"}\n"
+"\n"
+".fieldtable td, .fieldtable th {\n"
+"        padding: 3px 7px 2px;\n"
+"}\n"
+"\n"
+".fieldtable td.fieldtype, .fieldtable td.fieldname {\n"
+"        white-space: nowrap;\n"
+"        border-right: 1px solid ##B4;\n"
+"        border-bottom: 1px solid ##B4;\n"
+"        vertical-align: top;\n"
+"}\n"
+"\n"
+".fieldtable td.fielddoc {\n"
+"        border-bottom: 1px solid ##B4;\n"
+"        width: 100%;\n"
+"}\n"
+"\n"
+".fieldtable tr:last-child td {\n"
+"        border-bottom: none;\n"
+"}\n"
+"\n"
+".fieldtable th {\n"
+"        background-image:url('nav_f.png');\n"
+"        background-repeat:repeat-x;\n"
+"        background-color: ##E6;\n"
+"        font-size: 90%;\n"
+"        color: ##2B;\n"
+"        padding-bottom: 4px;\n"
+"        padding-top: 5px;\n"
+"        text-align:left;\n"
+"        -moz-border-radius-topleft: 4px;\n"
+"        -moz-border-radius-topright: 4px;\n"
+"        -webkit-border-top-left-radius: 4px;\n"
+"        -webkit-border-top-right-radius: 4px;\n"
+"        border-top-left-radius: 4px;\n"
+"        border-top-right-radius: 4px;\n"
+"        border-bottom: 1px solid ##B4;\n"
+"}\n"
+"\n"
+"\n"
 ".tabsearch {\n"
 "	top: 0px;\n"
 "	left: 10px;\n"
@@ -846,6 +898,23 @@
 "	border: 1px solid ##A0;\n"
 "}\n"
 "\n"
+"dl.citelist {\n"
+"        margin-bottom:50px;\n"
+"}\n"
+"\n"
+"dl.citelist dt {\n"
+"        color:##40;\n"
+"        float:left;\n"
+"        font-weight:bold;\n"
+"        margin-right:10px;\n"
+"        padding:5px;\n"
+"}\n"
+"\n"
+"dl.citelist dd {\n"
+"        margin:2px 0;\n"
+"        padding:5px 0;\n"
+"}\n"
+"\n"
 "@media print\n"
 "{\n"
 "  #top { display: none; }\n"

src/entry.cpp

@@ -360,6 +360,12 @@ void Entry::addSpecialListItem(const char *listName,int itemId)
   sli->append(ili);
 }
 
+Entry *Entry::removeSubEntry(Entry *e)
+{
+ int i = m_sublist->find(e);
+ return i!=-1 ? m_sublist->take(i) : 0;
+}
+
 //------------------------------------------------------------------
 
 

src/entry.h

@@ -289,23 +289,43 @@ class Entry
 
     Entry();
     Entry(const Entry &);
-    ~Entry();
+   ~Entry();
+
+    /*! Returns the static size of the Entry (so excluding any dynamic memory) */
     int getSize();
+
     void addSpecialListItem(const char *listName,int index);
     void createNavigationIndex(EntryNav *rootNav,FileStorage *storage,FileDef *fd);
 
     // while parsing a file these function can be used to navigate/build the tree
     void setParent(Entry *parent) { m_parent = parent; }
+
+    /*! Returns the parent for this Entry or 0 if this entry has no parent. */
     Entry *parent() const { return m_parent; }
+
+    /*! Returns the list of children for this Entry 
+     *  @see addSubEntry() and removeSubEntry()
+     */
     const QList<Entry> *children() const { return m_sublist; }
 
-    /*! Adds entry \e as a child to this entry */
-    void	addSubEntry (Entry* e) ;
+    /*! Adds entry \a e as a child to this entry */
+    void addSubEntry (Entry* e) ;
+
+    /*! Removes entry \a e from the list of children. 
+     *  Returns a pointer to the entry or 0 if the entry was not a child. 
+     *  Note the entry will not be deleted.
+     */ 
+    Entry *removeSubEntry(Entry *e);
+
     /*! Restore the state of this Entry to the default value it has
      *  at construction time. 
      */
     void reset();
+
+    /*! Serialize this entry to a persistent storage stream. */
     void marshall(StorageIntf *);
+
+    /*! Reinitialize this entry from a persistent storage stream. */
     void unmarshall(StorageIntf *);
 
   public:
@@ -366,6 +386,7 @@ class Entry
     bool        artificial;   //!< Artificially introduced item
     GroupDocType groupDocType;
 
+
     static int  num;          //!< counts the total number of entries
 
     /// return the command name used to define GROUPDOC_SEC

src/filedef.cpp

@@ -398,6 +398,11 @@ void FileDef::writeClassDeclarations(OutputList &ol,const QCString &title)
   if (classSDict) classSDict->writeDeclaration(ol,0,title,FALSE);
 }
 
+void FileDef::writeInlineClasses(OutputList &ol)
+{
+  if (classSDict) classSDict->writeDocumentation(ol,this);
+}
+
 void FileDef::startMemberDeclarations(OutputList &ol)
 {
   ol.startMemberSections();
@@ -636,6 +641,9 @@ void FileDef::writeDocumentation(OutputList &ol)
       case LayoutDocEntry::MemberDefStart: 
         startMemberDocumentation(ol);
         break; 
+      case LayoutDocEntry::FileInlineClasses:
+        writeInlineClasses(ol);
+        break;
       case LayoutDocEntry::MemberDef: 
         {
           LayoutDocEntryMemberDef *lmd = (LayoutDocEntryMemberDef*)lde;
@@ -654,8 +662,10 @@ void FileDef::writeDocumentation(OutputList &ol)
       case LayoutDocEntry::ClassCollaborationGraph:
       case LayoutDocEntry::ClassAllMembersLink:
       case LayoutDocEntry::ClassUsedFiles:
+      case LayoutDocEntry::ClassInlineClasses:
       case LayoutDocEntry::NamespaceNestedNamespaces:
       case LayoutDocEntry::NamespaceClasses:
+      case LayoutDocEntry::NamespaceInlineClasses:
       case LayoutDocEntry::GroupClasses: 
       case LayoutDocEntry::GroupInlineClasses: 
       case LayoutDocEntry::GroupNamespaces:

src/filedef.h

@@ -198,6 +198,7 @@ class FileDef : public Definition
     void writeSourceLink(OutputList &ol);
     void writeNamespaceDeclarations(OutputList &ol,const QCString &title);
     void writeClassDeclarations(OutputList &ol,const QCString &title);
+    void writeInlineClasses(OutputList &ol);
     void startMemberDeclarations(OutputList &ol);
     void endMemberDeclarations(OutputList &ol);
     void startMemberDocumentation(OutputList &ol);

src/footer.html

+<!--BEGIN GENERATE_TREEVIEW-->
+    <li class="footer">$generatedby
+    <a href="http://www.doxygen.org/index.html">
+    <img class="footer" src="doxygen.png" alt="doxygen"/></a> $doxygenversion </li>
+   </ul>
+ </div>
+<!--END GENERATE_TREEVIEW-->
+<!--BEGIN !GENERATE_TREEVIEW-->
+<hr class="footer"/><address class="footer"><small>
+$generatedby &#160;<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="$relpath$doxygen.png" alt="doxygen"/>
+</a> $doxygenversion
+</small></address>
+<!--END !GENERATE_TREEVIEW-->
+</body>
+</html>
\ No newline at end of file

src/footer_html.h

+"<!--BEGIN GENERATE_TREEVIEW-->\n"
+"    <li class=\"footer\">$generatedby\n"
+"    <a href=\"http://www.doxygen.org/index.html\">\n"
+"    <img class=\"footer\" src=\"doxygen.png\" alt=\"doxygen\"/></a> $doxygenversion </li>\n"
+"   </ul>\n"
+" </div>\n"
+"<!--END GENERATE_TREEVIEW-->\n"
+"<!--BEGIN !GENERATE_TREEVIEW-->\n"
+"<hr class=\"footer\"/><address class=\"footer\"><small>\n"
+"$generatedby &#160;<a href=\"http://www.doxygen.org/index.html\">\n"
+"<img class=\"footer\" src=\"$relpath$doxygen.png\" alt=\"doxygen\"/>\n"
+"</a> $doxygenversion\n"
+"</small></address>\n"
+"<!--END !GENERATE_TREEVIEW-->\n"
+"</body>\n"
+"</html>\n"
\ No newline at end of file

src/fortranscanner.l

@@ -496,6 +496,7 @@ PREFIX    (RECURSIVE{BS_}|PURE{BS_}|ELEMENTAL{BS_}){0,2}(RECURSIVE|PURE|ELEMENTA
 
  /*------ module handling ------------------------------------------------------------*/ 
 <Start>module|program{BS_}             {  //
+                                         v_type = V_IGNORE;
 					    if(yytext[0]=='m' || yytext[0]=='M')
 					      yy_push_state(Module);
 					    else
@@ -903,6 +904,7 @@ private                                 {
 
 <SubprogPrefix>{BS}{SUBPROG}{BS_}     {
                                          // Fortran subroutine or function found
+                                         v_type = V_IGNORE;
                                          result=yytext;
                                          result=result.stripWhiteSpace();
                                          addSubprogram(result);
@@ -1572,84 +1574,84 @@ static QCString applyModifiers(QCString typeName, SymbolModifiers& mdfs)
 {
   if (!mdfs.dimension.isNull()) 
   {
-    typeName += ",";
+    typeName += ", ";
     typeName += mdfs.dimension;
   }
   if (mdfs.direction!=SymbolModifiers::NONE_D) 
   {
-    typeName += ",";
+    typeName += ", ";
     typeName += directionStrs[mdfs.direction];
   }
   if (mdfs.optional) 
   {
-    typeName += ",";
+    typeName += ", ";
     typeName += "optional";
   }
   if (mdfs.allocatable) 
   {
-    typeName += ",";
+    typeName += ", ";
     typeName += "allocatable";
   }
   if (mdfs.external) 
   {
-    typeName += ",";
+    typeName += ", ";
     typeName += "external";
   }
   if (mdfs.intrinsic) 
   {
-    typeName += ",";
+    typeName += ", ";
     typeName += "intrinsic";
   }
   if (mdfs.parameter) 
   {
-    typeName += ",";
+    typeName += ", ";
     typeName += "parameter";
   }
   if (mdfs.pointer) 
   {
-    typeName += ",";
+    typeName += ", ";
     typeName += "pointer";
   }
   if (mdfs.target) 
   {
-    typeName += ",";
+    typeName += ", ";
     typeName += "target";
   }
   if (mdfs.save) 
   {
-    typeName += ",";
+    typeName += ", ";
     typeName += "save";
   }
   if (mdfs.deferred) 
   {
-    typeName += ",";
+    typeName += ", ";
     typeName += "deferred";
   }
   if (mdfs.nonoverridable) 
   {
-    typeName += ",";
+    typeName += ", ";
     typeName += "non_overridable";
   }
   if (mdfs.nopass) 
   {
-    typeName += ",";
+    typeName += ", ";
     typeName += "nopass";
   }
   if (mdfs.pass) 
   {
-    typeName += ",";
+    typeName += ", ";
     typeName += "pass";
     if (!mdfs.passVar.isEmpty())
       typeName += "(" + mdfs.passVar + ")";
   }
   if (mdfs.protection == SymbolModifiers::PUBLIC)
   {
-    typeName += ",";
+    typeName += ", ";
     typeName += "public";
   }
   else if (mdfs.protection == SymbolModifiers::PRIVATE)
   {
-    typeName += ",";
+    typeName += ", ";
     typeName += "private";
   }
 
@@ -1739,8 +1741,11 @@ static bool endScope(Entry *scope, bool isGlobalRoot)
       //cout<<"Search in "<<scope->name<<endl;
       EntryListIterator eli(*scope->children());
       Entry *ce;
+      int count = 0;
+      int found = FALSE;
       for (;(ce=eli.current());++eli) 
       {
+        count++;
         if (ce->section != Entry::FUNCTION_SEC)
           continue;
 
@@ -1751,6 +1756,15 @@ static bool endScope(Entry *scope, bool isGlobalRoot)
 	  arg->name = arg->type;
           arg->type = scope->name;
         }
+        if (ce->name.lower() == scope->name.lower()) found = TRUE;
+      }
+      if ((count == 1) && found)
+      {
+        // clear all modifiers of the scope
+        modifiers.remove(scope);
+        delete scope->parent()->removeSubEntry(scope);
+        scope = 0;
+        return TRUE;
       }
     }
   } 

src/header.html

+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<!--BEGIN PROJECT_NAME--><title>$projectname: $title</title><!--END PROJECT_NAME-->
+<!--BEGIN !PROJECT_NAME--><title>$title</title><!--END !PROJECT_NAME-->
+<link href="$relpath$tabs.css" rel="stylesheet" type="text/css"/>
+<link href="$relpath$$stylesheet" rel="stylesheet" type="text/css" />
+$treeview
+$search
+$mathjax
+</head>
+<body>
+<div id="top"><!-- do not remove this div! -->
+
+<!--BEGIN TITLEAREA-->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+  <!--BEGIN PROJECT_LOGO-->
+  <td id="projectlogo"><img alt="Logo" src="$relpath$$projectlogo"/></td>
+  <!--END PROJECT_LOGO-->
+  <!--BEGIN PROJECT_NAME-->
+  <td style="padding-left: 0.5em;">
+   <div id="projectname">$projectname
+   <!--BEGIN PROJECT_NUMBER-->&#160;<span id="projectnumber">$projectnumber</span><!--END PROJECT_NUMBER-->
+   </div>
+   <!--BEGIN PROJECT_BRIEF--><div id="projectbrief">$projectbrief</div><!--END PROJECT_BRIEF-->
+  </td>
+  <!--END PROJECT_NAME-->
+  <!--BEGIN !PROJECT_NAME-->
+   <!--BEGIN PROJECT_BRIEF-->
+    <td style="padding-left: 0.5em;">
+    <div id="projectbrief">$projectbrief</div>
+    </td>
+   <!--END PROJECT_BRIEF-->
+  <!--END !PROJECT_NAME-->
+  <!--BEGIN DISABLE_INDEX-->
+   <!--BEGIN SEARCHENGINE-->
+   <td>$searchbox</td>
+   <!--END SEARCHENGINE-->
+  <!--END DISABLE_INDEX-->
+ </tr>
+ </tbody>
+</table>
+</div>
+<!--END TITLEAREA-->

src/header_html.h

+"<!DOCTYPE html PUBLIC \"-//W3C//DTD XHTML 1.0 Transitional//EN\" \"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd\">\n"
+"<html xmlns=\"http://www.w3.org/1999/xhtml\">\n"
+"<head>\n"
+"<meta http-equiv=\"Content-Type\" content=\"text/xhtml;charset=UTF-8\"/>\n"
+"<!--BEGIN PROJECT_NAME--><title>$projectname: $title</title><!--END PROJECT_NAME-->\n"
+"<!--BEGIN !PROJECT_NAME--><title>$title</title><!--END !PROJECT_NAME-->\n"
+"<link href=\"$relpath$tabs.css\" rel=\"stylesheet\" type=\"text/css\"/>\n"
+"<link href=\"$relpath$$stylesheet\" rel=\"stylesheet\" type=\"text/css\" />\n"
+"$treeview\n"
+"$search\n"
+"$mathjax\n"
+"</head>\n"
+"<body>\n"
+"<div id=\"top\"><!-- do not remove this div! -->\n"
+"\n"
+"<!--BEGIN TITLEAREA-->\n"
+"<div id=\"titlearea\">\n"
+"<table cellspacing=\"0\" cellpadding=\"0\">\n"
+" <tbody>\n"
+" <tr style=\"height: 56px;\">\n"
+"  <!--BEGIN PROJECT_LOGO-->\n"
+"  <td id=\"projectlogo\"><img alt=\"Logo\" src=\"$relpath$$projectlogo\"/></td>\n"
+"  <!--END PROJECT_LOGO-->\n"
+"  <!--BEGIN PROJECT_NAME-->\n"
+"  <td style=\"padding-left: 0.5em;\">\n"
+"   <div id=\"projectname\">$projectname\n"
+"   <!--BEGIN PROJECT_NUMBER-->&#160;<span id=\"projectnumber\">$projectnumber</span><!--END PROJECT_NUMBER-->\n"
+"   </div>\n"
+"   <!--BEGIN PROJECT_BRIEF--><div id=\"projectbrief\">$projectbrief</div><!--END PROJECT_BRIEF-->\n"
+"  </td>\n"
+"  <!--END PROJECT_NAME-->\n"
+"  <!--BEGIN !PROJECT_NAME-->\n"
+"   <!--BEGIN PROJECT_BRIEF-->\n"
+"    <td style=\"padding-left: 0.5em;\">\n"
+"    <div id=\"projectbrief\">$projectbrief</div>\n"
+"    </td>\n"
+"   <!--END PROJECT_BRIEF-->\n"
+"  <!--END !PROJECT_NAME-->\n"
+"  <!--BEGIN DISABLE_INDEX-->\n"
+"   <!--BEGIN SEARCHENGINE-->\n"
+"   <td>$searchbox</td>\n"
+"   <!--END SEARCHENGINE-->\n"
+"  <!--END DISABLE_INDEX-->\n"
+" </tr>\n"
+" </tbody>\n"
+"</table>\n"
+"</div>\n"
+"<!--END TITLEAREA-->\n"

src/htmldocvisitor.cpp

@@ -551,6 +551,29 @@ void HtmlDocVisitor::visit(DocSimpleSectSep *)
   m_t << "<dd>" << endl;
 }
 
+void HtmlDocVisitor::visit(DocCite *cite)
+{
+  if (m_hide) return;
+  if (!cite->file().isEmpty()) 
+  {
+    startLink(cite->ref(),cite->file(),cite->relPath(),cite->anchor());
+  }
+  else
+  {
+    m_t << "<b>[";
+  }
+  filter(cite->text());
+  if (!cite->file().isEmpty()) 
+  {
+    endLink();
+  }
+  else
+  {
+    m_t << "]</b>";
+  }
+}
+
+
 //--------------------------------------
 // visitor functions for compound nodes
 //--------------------------------------
@@ -913,7 +936,7 @@ void HtmlDocVisitor::visitPre(DocSimpleSect *s)
     case DocSimpleSect::Post:
       m_t << theTranslator->trPostcondition(); break;
     case DocSimpleSect::Copyright:
-      m_t << "Copyright" /* TODO: theTranslator->trCopyright() */; break;
+      m_t << theTranslator->trCopyright(); break;
     case DocSimpleSect::Invar:
       m_t << theTranslator->trInvariant(); break;
     case DocSimpleSect::Remark:

src/htmldocvisitor.h

@@ -52,6 +52,7 @@ class HtmlDocVisitor : public DocVisitor
     void visit(DocFormula *);
     void visit(DocIndexEntry *);
     void visit(DocSimpleSectSep *);
+    void visit(DocCite *);
 
     //--------------------------------------
     // visitor functions for compound nodes

src/language.cpp

@@ -176,7 +176,7 @@ bool setTranslator(const char *langName)
   }
 #endif
 #ifdef LANG_AM
-  else if (L_EQUAL("amerenian"))
+  else if (L_EQUAL("armenian"))
   {
     theTranslator=new TranslatorArmenian;
   }

src/latexdocvisitor.h

@@ -53,6 +53,7 @@ class LatexDocVisitor : public DocVisitor
     void visit(DocFormula *);
     void visit(DocIndexEntry *);
     void visit(DocSimpleSectSep *);
+    void visit(DocCite *);
 
     //--------------------------------------
     // visitor functions for compound nodes