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changeset 416:165e443660c4 live

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Merge
author Chris Cannam <chris.cannam@soundsoftware.ac.uk>
date Tue, 10 May 2011 10:09:14 +0100
parents e7c58b88e670 (current diff) 576a1dca2ee2 (diff)
children 6b3e9f512761
files
diffstat 7 files changed, 1807 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/app/helpers/projects_helper.rb	Mon Apr 11 18:01:57 2011 +0100
+++ b/app/helpers/projects_helper.rb	Tue May 10 10:09:14 2011 +0100
@@ -237,7 +237,9 @@
     s << "</tr>"
 
     project.children.each do |child|
-      s << render_project_in_table(child, oddeven, level + 1)
+      if child.is_public? or User.current.member_of?(child)
+        s << render_project_in_table(child, oddeven, level + 1)
+      end
     end
     
     s
--- a/extra/soundsoftware/extract-docs.sh	Mon Apr 11 18:01:57 2011 +0100
+++ b/extra/soundsoftware/extract-docs.sh	Tue May 10 10:09:14 2011 +0100
@@ -23,7 +23,7 @@
     *) progdir="$(pwd)/$progdir" ;;
 esac
 
-types="doxygen javadoc" # Do Doxygen first (it can be used for Java too)
+types="doxygen javadoc matlabdocs" # Do Doxygen first (it can be used for Java too)
 
 for x in $types; do
     if [ ! -x "$progdir/extract-$x.sh" ]; then
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/extra/soundsoftware/extract-matlabdocs.sh	Tue May 10 10:09:14 2011 +0100
@@ -0,0 +1,47 @@
+#!/bin/bash
+
+docdir="/var/doc"
+
+progdir=$(dirname $0)
+case "$progdir" in
+    /*) ;;
+    *) progdir="$(pwd)/$progdir" ;;
+esac
+
+project="$1"
+projectdir="$2"
+targetdir="$3"
+
+if [ -z "$project" ] || [ -z "$targetdir" ] || [ -z "$projectdir" ]; then
+    echo "Usage: $0 <project> <projectdir> <targetdir>"
+    exit 2
+fi
+
+if [ ! -d "$projectdir" ]; then
+    echo "Project directory $projectdir not found"
+    exit 1
+fi
+
+if [ ! -d "$targetdir" ]; then
+    echo "Target dir $targetdir not found"
+    exit 1
+fi
+
+if [ -f "$targetdir/index.html" ]; then
+    echo "Target dir $targetdir already contains index.html"
+    exit 1
+fi
+
+mfile=$(find "$projectdir" -type f -name \*.m -print0 | xargs -0 grep -l '^% ' | head -1)
+
+if [ -z "$mfile" ]; then
+    echo "No MATLAB files with comments found for project $project"
+    exit 1
+fi
+
+echo "Project $project contains at least one MATLAB file with comments"
+
+cd "$projectdir" || exit 1
+
+perl "$progdir/matlab-docs.pl" -c "$progdir/matlab-docs.conf" -d "$targetdir"
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/extra/soundsoftware/matlab-docs-credit.html	Tue May 10 10:09:14 2011 +0100
@@ -0,0 +1,1 @@
+<div style="clear: both; float: right"><small><i>Produced by mtree2html by Hartmut Pohlheim</i></small></div>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/extra/soundsoftware/matlab-docs.conf	Tue May 10 10:09:14 2011 +0100
@@ -0,0 +1,166 @@
+# configuration file for generation of html-docu from m-files
+#
+# Author:   Hartmut Pohlheim
+# History:  05.11.2000  file created (parameters for mtree2html2001)
+#
+# The following options/variables must be changed/adapted:
+#   dirmfiles
+#   dirhtml
+#   csslink
+#   texttitleframelayout
+#   texttitlefiles
+#
+# The following options/variables should be adapted:
+#   authorfile
+#   filenametopframe
+#   codeheadmeta
+
+#========================================================================
+# Variables (possible keywords: set)
+# to use the built-in settings, comment the line using # in first column
+#========================================================================
+
+#------------------------------------------------------------------------
+# dirmfiles: name of directory containing Matlab m-files
+# dirhtml: name of directory to place the html-files into
+# exthtml: extension used for the html files (.html or .htm)
+#          don't forget the point in front of the extension
+#------------------------------------------------------------------------
+set dirmfiles = .
+set dirhtml = doc-output
+set exthtml = .html
+
+#------------------------------------------------------------------------
+# authorfile:   name of file containing info about author (in html)
+#               if defined, this text is included at the bottom of the 
+#               html files
+#------------------------------------------------------------------------
+set authorfile = matlab-docs-credit.html
+
+#------------------------------------------------------------------------
+# csslink:   text for linking to css file (style sheets)
+#            the text defined here is directly included into the head 
+#            of the html file
+#------------------------------------------------------------------------
+#set csslink = <link rel=stylesheet type="text/css" href="CSSFILENAME.css" />
+
+#------------------------------------------------------------------------
+# links2filescase: this is a bit difficult
+#                  Matlab is case sensitive on UNIX, but case insensitive
+#                  on Windows. Under UNIX Matlab function calls work 
+#                  only, when the case of file name and function call are 
+#                  identical, under Windows you can do what you want.
+#                  This scripts help you, to keep an exact case in your 
+#                  project.
+#          exact - internal links are only generated, when case of file 
+#                  name and in source code are identical
+#            all - case doesn't matter
+#     exactupper - same as exact, additionally links are also vreated to 
+#                  all upper case function names in source code (often 
+#                  used by Mathworks)
+#      exactvery - same as exact, additionally info about not matching
+#                  case is written to screen (stdout), this can be very 
+#                  helpful in cleaning up the case in a project
+#------------------------------------------------------------------------
+set links2filescase = all
+
+#------------------------------------------------------------------------
+# texttitleframelayout:    text of title for frame layout file (whole docu)
+#------------------------------------------------------------------------
+set texttitleframelayout = MATLAB Function Documentation
+
+#------------------------------------------------------------------------
+# texttitle/headerindexalldirs: text of title and header for directory index
+#------------------------------------------------------------------------
+set texttitleindexalldirs = Index of Directories
+set textheaderindexalldirs = Index of Directories
+
+#------------------------------------------------------------------------
+# texttitle/headerindex:    text of title and header for index file
+#------------------------------------------------------------------------
+set texttitleindex = A-Z Index of Functions
+set textheaderindex = A-Z Index of Functions
+
+#------------------------------------------------------------------------
+# texttitle/headerfiles:    text of title and header for files
+#                           name of file will be added at the end
+#------------------------------------------------------------------------
+set texttitlefiles = Function
+set textheaderfiles = Documentation of
+
+#------------------------------------------------------------------------
+# frames: whether to use frames in layout (yes or no)
+#------------------------------------------------------------------------
+set frames = no
+
+#------------------------------------------------------------------------
+# filenametopframe: name of file including frame layout (highest level file)
+# [default: index]
+#------------------------------------------------------------------------
+set filenametopframe = index
+
+#------------------------------------------------------------------------
+# textjumpindexglobal: text displayed for jump to index of all files
+#                      (global)
+# textjumpindexlocal:  text displayed for jump to index of files in actual
+#                      directory (local)
+#------------------------------------------------------------------------
+set textjumpindexglobal = <b>Index of</b> all files:
+set textjumpindexlocal = this subdirectory only:
+
+#------------------------------------------------------------------------
+# includesource: include source of m-files in documentation [YES|no]
+#------------------------------------------------------------------------
+set includesource = yes
+
+#------------------------------------------------------------------------
+# usecontentsm: use contents.m files as well for structured
+#               (hopefully) index [YES|no]
+#------------------------------------------------------------------------
+set usecontentsm = no
+
+#------------------------------------------------------------------------
+# includesource: write/update contents.m files [yes|NO]
+#------------------------------------------------------------------------
+set writecontentsm = no
+
+#------------------------------------------------------------------------
+# processtree:  parse whole directory tree recursively [YES|no]
+#------------------------------------------------------------------------
+set processtree = yes
+
+#------------------------------------------------------------------------
+# producetree:  produce tree for html-files in same structure than
+#		          tree of m-files [yes|NO]
+#               if no, all files are saved in the same directory, often 
+#               easier for outside linking to files
+#------------------------------------------------------------------------
+set producetree = yes
+
+#------------------------------------------------------------------------
+# codebodyindex/files: HTML-code for adding to BODY tag
+#                      can be used for defining colors and
+#                      backgroundimages of the files
+#                      No longer recommended, use the css file
+#------------------------------------------------------------------------
+set codebodyindex =
+set codebodyfiles =
+
+#------------------------------------------------------------------------
+# codeheadmeta: HTML-code added in HEAD area, use for supplying META info
+#------------------------------------------------------------------------
+set codeheadmeta = 
+
+#------------------------------------------------------------------------
+# codehr: HTML-code used to define a <HR>, do what you want
+#------------------------------------------------------------------------
+set codehr = <hr>
+
+#------------------------------------------------------------------------
+# codeheader: HTML-code added to <H*> tags, use for centering header text
+#             or changing the colour/size/font of the header text
+#------------------------------------------------------------------------
+set codeheader = 
+
+
+# End of parameter file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/extra/soundsoftware/matlab-docs.pl	Tue May 10 10:09:14 2011 +0100
@@ -0,0 +1,1585 @@
+@rem = '--*-Perl-*--';
+@rem = '
+@echo off
+perl -w -S %0.bat %1 %2 %3 %4 %5 %6 %7 %8 %9
+goto endofperl
+@rem ';
+# perl -w -S %0.bat "$@"
+#!/usr/bin/perl
+#
+# mtree2html_2000 - produce html files from Matlab m-files.
+#                   use configuration file for flexibility
+#                   can process tree of directories
+#
+# Copyright (C) 1996-2000 Hartmut Pohlheim.  All rights reserved.
+# includes small parts of m2html from Jeffrey C. Kantor 1995
+#
+# Author:  Hartmut Pohlheim
+# History: 06.03.1996  file created
+#          07.03.1996  first working version
+#          08.03.1996  modularized, help text only once included
+#          11.03.1996  clean up, some functions rwritten
+#          18.04.1996  silent output with writing in one line only
+#                      version 0.20 fixed
+#          14.05.1996  start of adding tree structure, could create tree
+#          15.05.1996  creating of index files for every directory
+#          17.05.1996  first working version except compact A-Z index
+#          20.05.1996  cleanup of actual version, more variables and 
+#                      configurable settings
+#          21.05.1996  reading, update and creation of contents.m added 
+#          22.05.1996  creation of short index started
+#          28.05.1996  jump letters for short index,
+#                      3 different directory indexes (short/long/contents)
+#          29.05.1996  major cleanup, short and long index created from one function
+#                      links for HTML and Indexes from 1 function,
+#                      version 0.9
+#          30.05.1996  contents.m changed to Contents.m (because unix likes it)
+#                      function definition can be in first line of m file before comments
+#                      version 0.91 fixed
+#          03.06.1996  contents file can be written as wanted, the links will be correct
+#                      cross references in help block of m-file will be found and
+#                      converted, even if the name of the function is written upper case
+#                      version 0.92 fixed
+#          05.06.1996  construction of dependency matrix changed, is able now to process
+#                      even the whole matlab tree (previous version needed to much memory)
+#                      removed warning for contents files in different directories
+#                      version 0.94 fixed
+#          06.06.1996  new link name matrices for ConstructHTMLFile created,
+#                      everything is done in ConstructDependencyMatrix,
+#                      both dependencies (calls and called) and matrix 
+#                      with all mentioned names in this m-file, thus, much
+#                      less scanning in html construction
+#                      script is now (nearly) linear scalable, thus, matlab-toolbox
+#                      tree takes less than 1 hour on a Pentium120, with source
+#                      version 0.96 fixed
+#          10.06.1996  order of creation changed, first all indexes (includes 
+#                      update/creation of contents.m) and then ConstructDepency
+#                      thus, AutoAdd section will be linked as well
+#                      excludenames extended, some more common word function names added
+#                      version 0.97 fixed
+#          17.02.1998  writecontentsm as command line parameter added
+#                      error of file not found will even appear when silent
+#                      version 1.02
+#          21.05.2000  mark comments in source code specially (no fully correct, 
+#                      can't handle % in strings)
+#                      version 1.11
+#          05.11.2000  link also to upper and mixed case m-files
+#                      searching for .m files now really works (doesn't find grep.com any longer)
+#                      file renamed to mtree2html2001
+#                      generated html code now all lower case 
+#                      inclusion of meta-description and meta-keywords in html files
+#                      HTML4 compliance done (should be strict HTML4.0, quite near XHTML)
+#                      version 1.23
+#
+#	   29.03.2011  (Chris Cannam) add frames option.
+
+$VERSION  = '1.23';
+($PROGRAM = $0) =~ s@.*/@@; $PROGRAM = "\U$PROGRAM\E";
+$debug = 1;
+
+#------------------------------------------------------------------------
+# Define platform specific things
+#------------------------------------------------------------------------
+# suffix for files to search is defined twice
+# the first ($suffix) is for string creation and contains the . as well
+# the second ($suffixforsearch) is for regular expression, handling of . is quite special
+$suffix = ".m";
+$suffixforsearch = "m";
+# the directory separator
+$dirsep = "/";
+# what is the current directory
+$diract = ".";
+
+#------------------------------------------------------------------------
+#  Define all variables and their standard settings
+#  documentation of variables is contained in accompanying rc file
+#------------------------------------------------------------------------
+%var =
+(
+   'authorfile',                '',
+   'codebodyfiles',             '',
+   'codebodyindex',             '',
+   'codeheadmeta',              '<meta name="author of conversion perl script" content="Hartmut Pohlheim" />',
+   'codehr',                    '<hr size="3" noshade="noshade" />',
+   'codeheader',                '',
+   'configfile',                'matlab-docs.conf',
+   'csslink',                   '',
+   'dirmfiles',                 $diract,
+   'dirhtml',                   $diract,
+   'exthtml',                   '.html',
+   'frames',                    'yes',
+   'filenametopframe',          'index',
+   'filenameindexlongglobal',   'indexlg',
+   'filenameindexlonglocal',    'indexll',
+   'filenameindexshortglobal',  'indexsg',
+   'filenameindexshortlocal',   'indexsl',
+   'filenameextensionframe',    'f',
+   'filenameextensionindex',    'i',
+   'filenameextensionjump',     'j',
+   'filenamedirshort',          'dirtops',
+   'filenamedirlong',           'dirtopl',
+   'filenamedircontents',       'dirtopc',
+   'includesource',             'yes',
+   'links2filescase',           'all',
+   'processtree',               'yes',
+   'producetree',               'yes',
+   'textjumpindexlocal',        'Local Index',
+   'textjumpindexglobal',       'Global Index',
+   'texttitleframelayout',      'Documentation of Matlab Files',
+   'texttitleindexalldirs',     'Index of Directories',
+   'textheaderindexalldirs',    'Index of Directories',
+   'texttitleindex',            '',
+   'textheaderindex',           '',
+   'texttitlefiles',            'Documentation of ',
+   'textheaderfiles',           'Documentation of ',
+   'usecontentsm',              'yes',
+   'writecontentsm',            'no'
+);
+
+
+# define all m-file names, that should be excluded from linking
+# however, files will still be converted
+@excludenames = ( 'all','ans','any','are',
+                  'cs',
+                  'demo','dos',
+                  'echo','edit','else','elseif','end','exist',
+                  'flag','for','function',
+                  'global',
+                  'help',
+                  'i','if','inf','info',
+                  'j',
+                  'more',
+                  'null',
+                  'return',
+                  'script','strings',
+                  'what','which','while','who','whos','why',
+                );
+
+# Text for inclusion in created HTML/Frame files: Doctype and Charset
+$TextDocTypeHTML  = '<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd">';
+$TextDocTypeFrame = '<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Frameset//EN" "http://www.w3.org/TR/REC-html40/frameset.dtd">'; 
+$TextMetaCharset = '<meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1" />';
+
+#------------------------------------------------------------------------
+# Read the command line arguments
+#------------------------------------------------------------------------
+if (@ARGV == 0) {
+   &DisplayHelp()  if &CheckFileName($var{'configfile'}, 'configuration file');
+}
+
+# Print provided command line arguments on screen
+foreach (@ARGV) { print "   $_\n      "; }
+
+# Get the options
+use Getopt::Long;
+@options = ('help|h', 'todo|t', 'version|v',
+            'authorfile|a=s', 'configfile|c=s', 'dirhtml|html|d=s',
+            'dirmfiles|mfiles|m=s', 'includesource|i=s',
+            'processtree|r=s', 'producetree|p=s',
+            'silent|quiet|q', 'writecontentsm|w=s');
+&GetOptions(@options) || die "use -h switch to display help statement\n";
+
+
+# Display help or todo list, when requested
+&DisplayHelp()                         if $opt_help;
+&DisplayTodo()                         if $opt_todo;
+die "$PROGRAM v$VERSION\n"             if $opt_version;
+
+$exit_status = 0;
+
+#------------------------------------------------------------------------
+# Read the config file
+#------------------------------------------------------------------------
+$var{'configfile'} = $opt_configfile         if $opt_configfile;
+&GetConfigFile($var{'configfile'});
+
+
+#------------------------------------------------------------------------
+# Process/Check the command line otions
+#------------------------------------------------------------------------
+$var{'dirhtml'}   = $opt_dirhtml              if $opt_dirhtml;
+if (!(substr($var{'dirhtml'}, -1, 1) eq $dirsep)) { $var{'dirhtml'} = $var{'dirhtml'}.$dirsep; }
+$var{'dirmfiles'} = $opt_dirmfiles            if $opt_dirmfiles;
+if (!(substr($var{'dirmfiles'}, -1, 1) eq $dirsep)) { $var{'dirmfiles'} = $var{'dirmfiles'}.$dirsep; }
+
+$var{'authorfile'} = $opt_author              if $opt_author;
+$var{'includesource'} = $opt_includesource    if $opt_includesource;
+if ($var{'includesource'} ne 'no') { $var{'includesource'} = 'yes'; }
+$var{'processtree'} = $opt_processtree        if $opt_processtree;
+if ($var{'processtree'} ne 'no') { $var{'processtree'} = 'yes'; }
+$var{'producetree'} = $opt_producetree        if $opt_producetree;
+if ($var{'producetree'} ne 'no') { $var{'producetree'} = 'yes'; }
+if ($var{'processtree'} eq 'no') { $var{'producetree'} = 'no'; }
+if ($var{'frames'} ne 'no') { $var{'frames'} = 'yes'; }
+# if (($var{'processtree'} eq 'yes') && ($var{'producetree'} eq 'no')) { $var{'usecontentsm'} = 'no'; }
+
+$var{'writecontentsm'} = $opt_writecontentsm  if $opt_writecontentsm;
+
+#------------------------------------------------------------------------
+# Do the real stuff
+#------------------------------------------------------------------------
+
+# Print variables on screen, when not silent
+&ListVariables                          if !$opt_silent;
+
+# Check the author file
+if ($var{'authorfile'} ne '') {
+    if (!($var{'authorfile'} =~ m,^/,)) {
+	# relative path: treat as relative to config file
+	my $cfd = $var{'configfile'};
+	$cfd =~ s,/[^/]*$,/,;
+	$cfd =~ s,^[^/]*$,.,;
+	$var{'authorfile'} = "$cfd/" . $var{'authorfile'};
+    }
+    if (&CheckFileName($var{'authorfile'}, 'author file')) {
+	$var{'authorfile'} = '';
+	if (!$opt_silent) { print "   Proceeding without author information!\n"; }
+    }
+}
+
+# Call the function doing all the real work
+&ConstructNameMatrix;
+
+&ConstructDependencyMatrix;
+
+&ConstructAllIndexFiles;
+
+&ConstructHTMLFiles;
+
+exit $exit_status;
+
+#------------------------------------------------------------------------
+# Construct list of all mfile names and initialize various data arrays.
+#------------------------------------------------------------------------
+sub ConstructNameMatrix
+{
+   local(*MFILE);
+   local($file, $dirname);
+   local(@newdirectories);
+   local(%localnames);
+   
+   $RecDeep = 0;
+   &ParseTreeReadFiles($var{'dirmfiles'}, $RecDeep);
+
+   foreach $dirname (@directories) { 
+      if ($dirnumbermfiles{$dirname} > 0) {
+         push(@newdirectories, $dirname);
+         if (! defined($contentsname{$dirname})) {
+            $contentsname{$dirname} = 'Contents';
+            if (($var{'writecontentsm'} eq 'no') && ($var{'usecontentsm'} eq 'yes')) {
+               print "\r ParseTree - for directory  $dirname  no contents file found!\n";
+               print   "             create one or enable writing of contents file (writecontentsm = yes)!\n";
+            }
+         }
+      }
+   }
+   @alldirectories = @directories;
+   @directories = @newdirectories;
+
+   foreach $dirname (@directories) { 
+      if ($debug > 0) { print "Dir: $dirname \t\t $dirnumbermfiles{$dirname} \t$contentsname{$dirname}\n"; }
+   }
+   
+   @names = sort(keys %mfile);
+
+   # check, if name of directory is identical to name of file
+   @dirsinglenames = values(%dirnamesingle);
+   grep($localnames{$_}++, @dirsinglenames);
+   @dirandfilename = grep($localnames{$_}, @names);
+   if (@dirandfilename) { 
+      print "\r   Name clash between directory and file name: @dirandfilename\n";
+      print   "      These files will be excluded from linking!\n";
+      push(@excludenames, @dirandfilename);
+   }
+   
+   # construct names matrix for help text linking
+   #    exclude some common words (and at the same time m-functions) from linking in help text
+   grep($localnames{$_}++, @excludenames);
+   @linknames = grep(!$localnames{$_}, @names);
+
+   if ($debug > 2) { print "linknames (names of found m-files):\n    @linknames\n"; }
+   
+}
+
+#------------------------------------------------------------------------
+# Parse tree and collect all Files
+#------------------------------------------------------------------------
+sub ParseTreeReadFiles
+{
+   local($dirname, $localRecDeep) = @_;
+   local($file, $name, $filewosuffix);
+   local($dirhtmlname, $dirmode);
+   local($relpath, $relpathtoindex, $replacevardir);
+   local(*CHECKDIR, *AKTDIR);
+   local(@ALLEFILES);
+   
+   opendir(AKTDIR, $dirname) || die "ParseTree - Can't open directory $dirname: $!";
+   if ($debug > 1) { print "\nDirectory: $dirname\n"; }
+
+   # create relative path
+   $_ = $dirname; $replacevardir = $var{'dirmfiles'};
+   s/$replacevardir//; $relpath = $_;
+   s/[^\/]+/../g; $relpathtoindex = $_;
+
+   # producetree no
+   if ($var{'producetree'} eq 'no') { $relpath = ''; $relpathtoindex = ''; }
+
+   # names of directories (top-level and below top-level m-file-directory)
+   push(@directories, $dirname);
+   $dirnumbermfiles{$dirname} = 0;    # set number of m-files for this dir to zero
+   # relative path from top-level directory, depends on directory name
+   $dirnamerelpath{$dirname} = $relpath;
+   # relative path from actual directory to top-level directory, depends on directory name
+   $dirnamerelpathtoindex{$dirname} = $relpathtoindex;
+   # recursion level for directory, depends on directory name
+   $dirnamerecdeep{$dirname} = $localRecDeep;
+   
+   # only the name of the directory, without path
+   $rindexprint = rindex($dirname, $dirsep, length($dirname)-2);
+   $rindsub = substr($dirname, $rindexprint+1, length($dirname)-$rindexprint-2);
+   $dirnamesingle{$dirname} = $rindsub;
+
+   # create name of html-directories 
+   $_ = $dirname;
+   s/$var{'dirmfiles'}/$var{'dirhtml'}/;
+   $dirhtmlname = $_;
+   if ($var{'producetree'} eq 'no') { $dirhtmlname = $var{'dirhtml'}; }
+   # try to open html directory, if error, then create directory,
+   # use same mode as for corresponding m-file directory
+   opendir(CHECKDIR,"$dirhtmlname") || do {
+      $dirmode = (stat($dirname))[2]; # print "$dirmode\n";
+      mkdir("$dirhtmlname", $dirmode) || die ("Cannot create directory $dirhtmlname: $! !");
+   };
+   closedir(CHECKDIR);
+
+
+   # read everything from this directory and process them
+   @ALLEFILES = readdir(AKTDIR);
+
+   foreach $file (@ALLEFILES) {
+      # exclude . and .. directories
+      next if $file eq '.';  next if $file eq '..';
+
+      # test for existense of entry (redundant, used for debugging)
+      if (-e $dirname.$file) {
+         # if it's a directory, call this function recursively
+         if (-d $dirname.$file) {
+            if ($var{'processtree'} eq 'yes') {
+               &ParseTreeReadFiles($dirname.$file.$dirsep, $localRecDeep+1);
+            }
+         }
+         # if it's a file - test for m-file, save name and create some arrays
+         elsif (-f $dirname.$file) {
+            if ($file =~ /\.$suffixforsearch$/i) {
+               # Remove the file suffix to establish the matlab identifiers
+               $filewosuffix = $file;
+               $filewosuffix =~ s/\.$suffixforsearch$//i;
+               # $filename = $name;
+
+               # Contents file in unix must start with a capital letter (Contents.m)
+               # ensure, that m-file name is lower case, except the contents file
+               if (! ($filewosuffix =~ /^contents$/i)) {
+		   # if ($var{'links2filescase'}  eq 'low') { $filewosuffix = "\L$filewosuffix\E"; }
+                  $filewosuffixlow = "\L$filewosuffix\E";
+               }
+               else { $contentsname{$dirname} = $filewosuffix; }
+
+               # internal handle name is always lower case
+               $name     = $filewosuffixlow;
+               # file name is not lower case
+               $filename = $filewosuffix;
+
+               # if don't use C|contents.m, then forget all C|contents.m
+               if ($var{'usecontentsm'} eq 'no') { if ($name =~ /contents/i) { next; } }
+
+               # if m-file with this name already exists, use directory and name for name
+               # only the first occurence of name will be used for links
+               if (defined $mfile{$name}) { 
+                  if (! ($name =~ /^contents$/i) ) {
+                     print "\r ParseTree - Name conflict:  $name in $dirname already exists: $mfile{$name} !\n";
+                     print   "             $mfile{$name}  will be used for links!\n";
+                  }
+                  $name = $dirname.$name;
+               }
+               # mfile name with path
+               $mfile{$name} = $dirname.$file;
+               # mfile name (without path)
+               $mfilename{$name} = $filename;
+               # mfile directory
+               $mfiledir{$name} = $dirname;
+               
+               # html file name and full path, special extension of Contents files
+               if ($name =~ /contents/i) { $extrahtmlfilename = $dirnamesingle{$dirname}; }
+               else { $extrahtmlfilename = ''; }
+               $hfile{$name} = $dirhtmlname.$mfilename{$name}.$extrahtmlfilename.$var{'exthtml'};
+
+               # save relative html path
+               # if ($var{'producetree'} eq 'yes') {
+               $hfilerelpath{$name} = $relpath;
+               # } else { # if no tree to produce, relative path is empty
+               #    $hfilerelpath{$name} = '';
+               # }
+
+               # create relative path from html file to directory with global index file
+               $hfileindexpath{$name} = $relpathtoindex;
+
+               # Function declaration, if one exists, set default to script
+               $synopsis{$name} = "";
+               $mtype{$name} = "script";
+
+               # First comment line
+               $apropos{$name} = "";
+
+               # count number of m-files in directories
+               $dirnumbermfiles{$dirname}++;
+
+               if ($debug > 1) {
+                  if ($opt_silent) { print "\r"; }
+                  print "   ParseTree: $name \t\t $mfile{$name} \t\t $hfile{$name}\t\t";
+                  if (!$opt_silent) { print "\n"; }
+               }
+            }
+         }
+         else {
+            print "Unknown type of file in $dirname: $file\n";
+         }
+      }
+      else { print "Error: Not existing file in $dirname: $file\n"; }
+   }
+
+   closedir(AKTDIR)
+   
+}
+
+#------------------------------------------------------------------------
+# Construct Dependency matrix
+#    $dep{$x,$y} > 0 if $x includes a reference to $y.
+#------------------------------------------------------------------------
+sub ConstructDependencyMatrix
+{
+   &ConstructDependencyMatrixReadFiles('all');
+   &ConstructDependencyMatrixReally;
+}
+
+
+#------------------------------------------------------------------------
+# Construct Dependency matrix
+#    $dep{$x,$y} > 0 if $x includes a reference to $y.
+#------------------------------------------------------------------------
+sub ConstructDependencyMatrixReadFiles
+{
+   local($whatstring) = @_;
+   local(*MFILE);
+   local($name, $inames);
+   local(%symbolsdep, %symbolsall);
+
+   # Initialize as all zeros.
+   # foreach $name (@names) { grep($dep{$name,$_}=0,@names); if ($debug > 0) { print "\r   DepMatrix anlegen: $name\t$#names\t"; } }
+
+   # Compute the dependency matrix
+   $inames = -1;
+   foreach $name (@names) {
+      # Read each file and tabulate the distinct alphanumeric identifiers in
+      # an array of symbols. Also scan for:
+      #   synopsis: The function declaration line
+      #   apropos:  The first line of the help text
+
+      # look for whatstring, if all: process every file, if contents: process only contents files 
+      if ($whatstring eq 'contents') { if (! ($name =~ /contents$/i) ) { next; } }
+      elsif ($whatstring eq 'all') { }    # do nothing
+      else { print "\r   ConstructDependency: Unknown parameter whatstring: $whatstring \n"; }
+
+      undef %symbolsall; undef %symbolsdep;
+      open(MFILE,"<$mfile{$name}") || die("Can't open $mfile{$name}: $!\n");
+      while (<MFILE>) {
+         chop;
+
+         # Split on nonalphanumerics, then look for all words, used for links later
+         # this one for all references
+         @wordsall = grep(/[a-zA-Z]\w*/, split('\W',$_));
+         # set all words to lower case for link checking
+         undef @wordsall2;
+         # do case conversion not, case checking is done later
+         foreach (@wordsall) { push(@wordsall2, "\L$_\E"); }
+         # @wordsall2 = @wordsall;
+         grep($symbolsall{$_}++, @wordsall2);
+
+         # Store first comment line, skip all others.
+         if (/^\s*%/) {
+            if (!$apropos{$name}) {
+               s/^\s*%\s*//;   # remove % and leading white spaces on line
+               $_ = &SubstituteHTMLEntities($_);
+               $apropos{$name} = $_;
+            }
+            next;
+         }
+
+         # If it's the function declaration line, then store it and skip
+         # but only, when first function definition (multiple function lines when private subfunctions in file
+         if ($synopsis{$name} eq '') {
+            if (/^\s*function/) {
+               s/^\s*function\s*//;
+               $synopsis{$name} = $_;
+               $mtype{$name} = "function";
+               next;
+            }
+         }
+
+         # Split off any trailing comments
+         if ($_ ne '') {
+            # this one for references in program code only
+            # when syntax parsing, here is a working place
+            ($statement) = split('%',$_,1);
+            @wordsdep = grep(/[a-zA-Z]\w*/,split('\W',$statement));
+            # do case conversion not, case checking is done later
+            undef @wordsdep2;
+            foreach (@wordsdep) { push(@wordsdep2, "\L$_\E"); }
+            grep($symbolsdep{$_}++, @wordsdep2);
+         }
+      }
+      close MFILE;
+
+      # compute intersection between %symbolsall and @linknames
+      delete($symbolsall{$name});
+      # foreach $localsumall ($symbolsall) {
+      #    $localsumall = "\L$localsumall\E";
+      # }
+      @{'all'.$name} = grep($symbolsall{$_}, @linknames);
+
+      # compute intersection between %symbolsdep and @linknames
+      delete($symbolsdep{$name});
+      @{'depcalls'.$name} = grep($symbolsdep{$_}, @linknames);
+
+      $inames++; print "\r   DepCallsMatrix: $inames/$#names\t $name\t";
+      if ($debug > 2) { print "\n      depnames: @{'depcalls'.$name}\n      all: @{'all'.$name}\n"; } 
+   }
+}
+
+
+#------------------------------------------------------------------------
+# Construct Dependency matrix
+#    $dep{$x,$y} > 0 if $x includes a reference to $y.
+#------------------------------------------------------------------------
+sub ConstructDependencyMatrixReally
+{
+   local($inames, $name);
+
+   $inames = -1;
+   foreach $name (@names) { undef %{'depint'.$name}; }
+   foreach $name (@names) {
+      grep(${'depint'.$_}{$name}++, @{'depcalls'.$name});
+      $inames++; print "\r   DepCalledMatrix1: $inames/$#names\t $name\t";
+   }
+   $inames = -1;
+   foreach $name (@names) {
+      # compute intersection between %depint.name{$_} and @linknames
+      if (defined (%{'depint'.$name})) { @{'depcalled'.$name} = grep(${'depint'.$name}{$_}, @linknames); }
+      $inames++; print "\r   DepCalledMatrix2: $inames/$#names\t $name\t";
+      if ($debug > 2) { print "\n      depcalled: @{'depcalled'.$name}\n"; }
+   }
+
+}
+
+
+#========================================================================
+# Construct all index files
+#========================================================================
+sub ConstructAllIndexFiles
+{
+   local(@localnames);
+   local($ActDir);
+   local($name);
+   
+   # define variables and names for frame target
+   $GlobalNameFrameMainLeft = 'Cont_Main';
+   $GlobalNameFrameMainRight = 'Cont_Lower';
+   $GlobalNameFrameAZIndexsmall = 'IndexAZindex';
+   $GlobalNameFrameAZIndexjump = 'IndexAZjump';
+
+   $indexcreated = 0;
+
+   &ConstructHighestIndexFile;
+   $indexcreated++;
+
+   # if ($var{'producetree'} eq 'yes') {
+      # moved next 2 lines out of if for producetree no
+      # &ConstructHighestIndexFile;
+      # $indexcreated++;
+   
+      foreach $ActDir (@directories) {
+         undef @localnames;
+         foreach $name (@names) {
+            local($pathsubstr) = substr($mfile{$name}, 0, rindex($mfile{$name}, "/")+1);
+            if ($ActDir eq $pathsubstr) {
+               if ($debug > 1) { print "IndexFile: $pathsubstr    ActDir: $ActDir   Hfilerelpath: $hfilerelpath{$name}\n"; }
+               push(@localnames, $name);
+            }
+         }
+         if ($debug > 2) { print "localnames: @localnames\n"; }
+         # create contents file and short|long index of files in local directory
+         &ConstructContentsmFile($ActDir, @localnames);
+         &ConstructAZIndexFile($ActDir, 'short', 'local', @localnames);
+         &ConstructAZIndexFile($ActDir, 'long', 'local', @localnames);
+         $indexcreated+=2;
+      }   
+   # } else {
+   #    &ConstructContentsmFile($var{'dirmfiles'}, @names);
+   # }
+
+   # create short|long index of files in all directory
+   &ConstructAZIndexFile($var{'dirmfiles'}, 'short', 'global', @names);
+   &ConstructAZIndexFile($var{'dirmfiles'}, 'long', 'global', @names);
+   $indexcreated+=2;
+
+   # if contents.m were created or updated, the dependency matrices should 
+   # be updated as well
+   if ($var{'writecontentsm'} eq 'yes') { &ConstructDependencyMatrixReadFiles('contents');; }
+}
+
+
+#========================================================================
+# Construct the highest level index file
+#========================================================================
+sub ConstructHighestIndexFile
+{
+   local(*IFILE);
+   local($indexfile, $filename);
+
+   # Build the frame layout file, this files includes the layout of the frames
+   # Build the frame layout file name (highest one)
+   $indexfile = $var{'dirhtml'}.$var{'filenametopframe'}.$var{'exthtml'};
+
+   if ($var{'frames'} eq 'yes') {
+
+       open(IFILE,">$indexfile") || die("Cannot open frame layout file $indexfile\n");
+
+       # Write the header of frame file
+       print IFILE "$TextDocTypeFrame\n<html>\n<head>\n$var{'codeheadmeta'}\n$TextMetaCharset\n";
+       print IFILE "   <title>$var{'texttitleframelayout'}</title>\n";
+       print IFILE "</head>\n";
+
+       # definition of 2 frames, left the tree of directories,
+       # right the index of that directory or the docu of a file
+       print IFILE "<frameset  cols=\"25%,75%\">\n";
+       print IFILE "   <frame src=\"$var{'filenamedirshort'}$var{'exthtml'}\" name=\"$GlobalNameFrameMainLeft\" />\n";
+       print IFILE "   <frame src=\"$var{'filenameindexshortglobal'}$var{'filenameextensionframe'}$var{'exthtml'}\" name=\"$GlobalNameFrameMainRight\" />\n";   print IFILE "</frameset>\n";
+
+       print IFILE "</html>\n";
+
+       close(IFILE);
+
+       if ($opt_silent) { print "\r"; }
+       print "   Frame layout file created: $indexfile\t";
+       if (!$opt_silent) { print "\n"; }
+   }
+
+   for($irun=0; $irun <= 2; $irun++) {
+      # Build the top directory index file, these files include the directory tree
+      # Build the directory tree index file name
+      
+      # Create no directory file for contents, when no contents to use
+      if (($irun == 2) && ($var{'usecontentsm'} eq 'no')) { next; }
+
+      # Assign the correct index file name
+      if ($irun == 0) { $filename = $var{'filenamedirshort'}; }
+      elsif ($irun == 1) { $filename = $var{'filenamedirlong'}; }
+      elsif ($irun == 2) { $filename = $var{'filenamedircontents'}; }
+      
+      $indexfile = $var{'dirhtml'}.$filename.$var{'exthtml'};
+
+      open(IFILE,">$indexfile") || die("Cannot open directory tree index file $indexfile\n");
+      # Write header of HTML file
+      print IFILE "$TextDocTypeHTML\n<html>\n<head>\n$var{'codeheadmeta'}\n$TextMetaCharset\n$var{'csslink'}\n";
+
+      if ($var{'texttitleindexalldirs'} eq '') {
+         print IFILE "<title>Index of Directories of $var{'dirmfiles'}</title>\n";
+      } else {
+         print IFILE "<title>$var{'texttitleindexalldirs'}</title>\n";
+      }
+      
+      if ($var{'frames'} eq 'yes') {
+	  print IFILE "<base target=\"$GlobalNameFrameMainRight\" />\n";
+      }
+
+      print IFILE "</head>\n";
+      print IFILE "<body $var{'codebodyindex'}>\n";
+      print IFILE "<div id=\"matlabdoc\">\n";
+      if ($var{'textheaderindexalldirs'} eq '') {
+         print IFILE "<h1 $var{'codeheader'}>Index of Directories of <em>$var{'dirmfiles'}</em></h1>\n";
+      } else {
+         print IFILE "<h1 $var{'codeheader'}>$var{'textheaderindexalldirs'}</h1>\n";
+      }
+      print IFILE "<p>\n";
+
+      if ($var{'frames'} eq 'yes') {
+	  if ($irun == 0) { print IFILE "<strong>short</strong>\n"; }
+	  else { print IFILE "<a href=\"$var{'filenamedirshort'}$var{'exthtml'}\" target=\"$GlobalNameFrameMainLeft\">short</a>\n"; }
+	  if ($irun == 1) { print IFILE " | <strong>long</strong>\n"; }
+	  else { print IFILE " | <a href=\"$var{'filenamedirlong'}$var{'exthtml'}\" target=\"$GlobalNameFrameMainLeft\">long</a>\n"; }
+	  if ($var{'usecontentsm'} eq 'yes') {
+	      if ($irun == 2) { print IFILE " | <strong>contents</strong>\n"; }
+	      else { print IFILE " | <a href=\"$var{'filenamedircontents'}$var{'exthtml'}\" target=\"$GlobalNameFrameMainLeft\">contents</a>\n"; }
+	  }
+      } else {
+	  if ($irun == 0) { print IFILE "<strong>short</strong>\n"; }
+	  else { print IFILE "<a href=\"$var{'filenamedirshort'}$var{'exthtml'}\">short</a>\n"; }
+	  if ($irun == 1) { print IFILE " | <strong>long</strong>\n"; }
+	  else { print IFILE " | <a href=\"$var{'filenamedirlong'}$var{'exthtml'}\">long</a>\n"; }
+	  if ($var{'usecontentsm'} eq 'yes') {
+	      if ($irun == 2) { print IFILE " | <strong>contents</strong>\n"; }
+	      else { print IFILE " | <a href=\"$var{'filenamedircontents'}$var{'exthtml'}\">contents</a>\n"; }
+	  }
+      }
+   
+      print IFILE "</p><br />\n\n";
+      print IFILE "<ul>\n";
+
+      # go through all directories and create a list entry for each one,
+      # depending on recursion level create sublists
+      $prevrecdeeplevel = 0;
+      foreach $name (@alldirectories) {
+         $actrecdeeplevel = $dirnamerecdeep{$name};
+         for( ; $prevrecdeeplevel < $actrecdeeplevel; $prevrecdeeplevel++ ) { print IFILE "<ul>\n"; }
+         for( ; $prevrecdeeplevel > $actrecdeeplevel; $prevrecdeeplevel-- ) { print IFILE "</ul>\n"; }
+         if ($irun == 0) { $indexfilenameused = $var{'filenameindexshortlocal'}.$var{'filenameextensionframe'}; }
+         elsif ($irun == 1) { $indexfilenameused = $var{'filenameindexlonglocal'}.$var{'filenameextensionframe'}; }
+         elsif ($irun == 2) { $indexfilenameused = $contentsname{$name}; }
+         else { die "ConstructHighestIndexFile: Unknown value of irun"; }
+         if ($dirnumbermfiles{$name} > 0) {
+            # producetree no
+            # if ($var{'producetree'} eq 'no') { $dirnamehere = ''; }
+            # else { $dirnamehere = '$dirnamerelpath{$name}'; }
+            # print IFILE "<LI><A HREF=\"$dirnamehere$indexfilenameused_$dirnamesingle{$name}$var{'exthtml'}\">$dirnamesingle{$name}</A>\n";
+            print IFILE "<li><a href=\"$dirnamerelpath{$name}$indexfilenameused$dirnamesingle{$name}$var{'exthtml'}\">$dirnamesingle{$name}</a></li>\n";
+         } else { 
+            # print directories with no m-files inside not
+            # print IFILE "<li>$dirnamesingle{$name}</li>\n";
+         }
+      }
+      $actrecdeeplevel = 0;
+      for( ; $prevrecdeeplevel > $actrecdeeplevel; $prevrecdeeplevel-- ) { print IFILE "</ul>\n"; }
+      print IFILE "</ul>\n<br />$var{'codehr'}\n";
+
+      # Include info about author from authorfile
+      &WriteFile2Handle($var{'authorfile'}, IFILE);
+
+      print IFILE "<!--navigate-->\n";
+      print IFILE "<!--copyright-->\n";
+      print IFILE "</div>\n</body>\n</html>\n";
+
+      close(IFILE);
+
+      if ($opt_silent) { print "\r"; }
+      print "   Directory - Indexfile created: $indexfile\t";
+      if (!$opt_silent) { print "\n"; }
+   }
+}
+
+
+#========================================================================
+# Construct the A-Z index file (global/local and/or short/long)
+#========================================================================
+sub ConstructAZIndexFile
+{
+   local($LocalActDir, $LocalShortLong, $LocalGlobalLocal, @localnames) = @_;
+   local(*IFILE);
+   local($name, $indexfilename, $dirpath);
+   local($firstletter, $firstone);
+   
+   if ($debug > 2) { print "localnames in AZ small: @localnames\n"; print "     ActDir in A-Z: $LocalActDir\n"; }
+   
+   # extract filename of index file from parameters of function
+   if ($LocalShortLong eq 'short') {
+      if ($LocalGlobalLocal eq 'global') { $indexfilename = $var{'filenameindexshortglobal'}; }
+      elsif ($LocalGlobalLocal eq 'local') { $indexfilename = $var{'filenameindexshortlocal'}; }
+      else { die "wrong parameter for LocalGlobalLocal in ConstructAZIndexFile: $LocalGlobalLocal."; }
+   } elsif ($LocalShortLong eq 'long') {
+      if ($LocalGlobalLocal eq 'global') { $indexfilename = $var{'filenameindexlongglobal'}; }
+      elsif ($LocalGlobalLocal eq 'local') { $indexfilename = $var{'filenameindexlonglocal'}; }
+      else { die "wrong parameter for LocalGlobalLocal in ConstructAZIndexFile: $LocalGlobalLocal."; }
+   } else { die "wrong parameter for LocalShortLong in ConstructAZIndexFile: $LocalShortLong."; }
+   
+   # producetree no
+   # if ($var{'producetree'} eq 'no') { $dirnamehere = ''; }
+   # else { $dirnamehere = '$dirnamerelpath{$LocalActDir}'; }
+   # Build the index file name
+   # handle the global index file case separately (no extra directory name in file)
+   #    the local index file name must be extended by the name of the directory
+   if ($LocalGlobalLocal eq 'global') { $extradirfilename = ''; }
+   else { $extradirfilename = $dirnamesingle{$LocalActDir}; }
+   $indexfile = $var{'dirhtml'}.$dirnamerelpath{$LocalActDir}.$indexfilename.$var{'filenameextensionindex'}.$extradirfilename.$var{'exthtml'};
+
+   if ($LocalShortLong eq 'short' and $extradirfilename eq '' and $var{'frames'} ne 'yes') {
+       # With no frames and no subdir path, this must go in the
+       # top-level index file instead
+       $indexfile = $var{'dirhtml'}.$var{'filenametopframe'}.$var{'exthtml'};
+   }
+
+   if ($debug > 2) { print "   indexfilename (a-z small): $indexfile\n"; }
+
+   open(IFILE,">$indexfile") || die("Cannot open index file $indexfile: $!\n");
+
+   # Write the header of HTML file
+   print IFILE "$TextDocTypeHTML\n<html>\n<head>\n$var{'codeheadmeta'}\n$TextMetaCharset\n$var{'csslink'}\n";
+   
+   my $dirToPrint = $LocalActDir;
+   $dirToPrint =~ s,^./,,;
+
+   if ($var{'texttitleindex'} eq '') {
+      print IFILE "<title>Index of Matlab Files in Directory $dirToPrint</title>\n";
+   } else {
+      if ($LocalGlobalLocal eq 'global') { print IFILE "<title>$var{'texttitleindex'}</title>\n"; }
+      else { print IFILE "<title>$var{'texttitleindex'} in Directory $dirToPrint</title>\n"; }
+   }
+
+   if ($var{'frames'} eq 'yes') {
+       print IFILE "<base target=\"$GlobalNameFrameMainRight\" />\n";
+   }
+   print IFILE "</head>\n";
+
+   print IFILE "<body $var{'codebodyindex'}>\n";
+   print IFILE "<div id=\"matlabdoc\">\n";
+   if ($var{'textheaderindex'} eq '') {
+      print IFILE "<h1 $var{'codeheader'}>Index of Matlab Files in Directory $dirToPrint</h1>\n";
+   } else {
+      if ($LocalGlobalLocal eq 'global') { print IFILE "<h1 $var{'codeheader'}>$var{'textheaderindex'}</h1>\n"; }
+      else { print IFILE "<h1 $var{'codeheader'}>$var{'textheaderindex'} in Directory $dirToPrint</h1>\n"; }
+   }
+
+   # include links to indexes
+   &ConstructLinks2Index(IFILE, $dirnamerelpathtoindex{$LocalActDir}, $LocalActDir, $LocalGlobalLocal);
+
+   # Collect the starting letters of m files in this directory or all m-files
+   for('a'..'z') { undef @{$_}; }
+   foreach $name (@localnames) {
+      if (! ($mfilename{$name} =~ /contents/i)) {
+         $firstletter = substr($mfilename{$name}, 0, 1);
+         # convert first letter always to lower case
+         # needed for reference to lower and upper case m-files
+         $firstletter = "\L$firstletter\E";
+         push(@{$firstletter}, $name);
+      }
+   }
+   
+   if ($LocalShortLong eq 'short') {
+      # begin create short index
+      print IFILE "<table width=\"100%\">\n";
+
+      for('a'..'z') {
+         # print "   $_: @{$_}\n";
+         $numberofletter = $#{$_}+1;
+	 $cols = 3;
+         if ($numberofletter > 0) {
+            print IFILE "\n<tr><td><br/><strong><a name=\"\U$_\E$_\"></a><span class=\"an\">\U$_\E</span></strong></td></tr>\n";
+            for ($count = 0; $count < $numberofletter; $count++) {
+		if (($count % $cols) == 0) {
+		    if ($count > 0) {
+			print IFILE "</tr><tr>\n";
+		    }
+		    print IFILE "<tr><td></td>";
+		}
+		$name = @{$_}[$count];
+		if ($LocalGlobalLocal eq 'global') { $dirpath = $hfilerelpath{$name}; } else { $dirpath = ""; }
+		print IFILE "<td><a href=\"$dirpath$mfilename{$name}$var{'exthtml'}\">$mfilename{$name}</a></td>";
+	    }
+
+	    print IFILE "</tr>\n";
+		    
+            # $numberhalf = ($numberofletter + 1 - (($numberofletter+1) % 2))/2;
+            # if ($debug > 2) { print "   $_: @{$_} \t $numberhalf \t $numberofletter\n"; }
+            # for($count = 0; $count < $numberhalf; $count++) {
+            #    $name = @{$_}[$count];
+            #    if ($LocalGlobalLocal eq 'global') { $dirpath = $hfilerelpath{$name}; } else { $dirpath = ""; }
+            #    print IFILE "<tr><td width=\"50%\"><a href=\"$dirpath$mfilename{$name}$var{'exthtml'}\">$mfilename{$name}</a></td>";
+            #    if (($count + $numberhalf) < $numberofletter) {
+            #       $name = @{$_}[$count + $numberhalf];
+            #       if ($LocalGlobalLocal eq 'global') { $dirpath = $hfilerelpath{$name}; } else { $dirpath = ""; }
+            #       print IFILE "<td width=\"50%\"><a href=\"$dirpath$mfilename{$name}$var{'exthtml'}\">$mfilename{$name}</a></td></tr>\n";
+            #    } else {
+            #       print IFILE "<td width=\"50%\"></td></tr>\n";
+            #    }
+            # }
+         }
+      }
+      print IFILE "</table>\n<br />$var{'codehr'}\n";
+
+   } elsif ($LocalShortLong eq 'long') {
+      # begin create long index
+      print IFILE "<table width=\"100%\">\n";
+      print IFILE "<tr><th>Name</th><th>Synopsis</th></tr>\n";
+
+      for('a'..'z') {
+         # print "   $_: @{$_}\n";
+         $numberofletter = $#{$_}+1;
+         if ($numberofletter > 0) {
+            $firstone = 1;
+            foreach $name (@{$_}) {
+               if ($debug > 1) { print "   AZinforeach1: $name \t\t $hfilerelpath{$name} \t\t $dirnamerelpath{$LocalActDir}\n"; }
+               if ($LocalGlobalLocal eq 'global') { $dirpath = $hfilerelpath{$name}; } else { $dirpath = ""; }
+               if (! ($mfilename{$name} =~ /contents/i)) {
+                  if ($firstone == 1) { print IFILE "\n<tr><td colspan=\"2\"><br /><strong><a name=\"\U$_\E$_\"></a><span class=\"an\">\U$_\E</span></strong></td></tr>\n"; $firstone = 0; } 
+                  print IFILE "<tr><td valign=\"top\"><a href=\"$dirpath$mfilename{$name}$var{'exthtml'}\">$mfilename{$name}</a></td><td>$apropos{$name}</td></tr>\n";
+               }
+            }
+         }
+      }
+      print IFILE "</table>\n<br />$var{'codehr'}\n";
+   } else { die "wrong parameter for LocalShortLong in ConstructAZIndexFile: $LocalShortLong."; }
+
+   # Include info about author from authorfile
+   &WriteFile2Handle($var{'authorfile'}, IFILE);
+
+   print IFILE "<!--navigate-->\n";
+   print IFILE "<!--copyright-->\n";
+   print IFILE "</div>\n</body>\n</html>\n";
+
+   close(IFILE);
+
+   if ($opt_silent) { print "\r"; }
+   print "   Indexfile small (A-Z) created: $indexfile\t";
+   if (!$opt_silent) { print "\n"; }
+
+
+   # Build the A-Z jump index file name
+   # handle the global index file case separately (no extra directory name in file)
+   if ($LocalGlobalLocal eq 'global') { $extradirfilename = ''; }
+   else { $extradirfilename = $dirnamesingle{$LocalActDir}; }
+
+   if ($var{'frames'} eq 'yes') {
+
+       $indexfile = $var{'dirhtml'}.$dirnamerelpath{$LocalActDir}.$indexfilename.$var{'filenameextensionjump'}.$extradirfilename.$var{'exthtml'};
+       if ($debug > 2) { print "   indexfilename (a-z jump): $indexfile\n"; }
+       open(IFILE,">$indexfile") || die("Cannot open jump index file $indexfile: $!\n");
+
+       # Write the header of HTML file
+       print IFILE "$TextDocTypeHTML\n<html>\n<head>\n$var{'codeheadmeta'}\n$TextMetaCharset\n$var{'csslink'}\n";
+       
+       if ($var{'texttitleindex'} eq '') {
+	   print IFILE "<title>A-Z jump index in directory $dirToPrint</title>\n";
+       } else {
+	   if ($LocalGlobalLocal eq 'global') { print IFILE "<title>$var{'texttitleindex'}</title>\n"; }
+	   else { print IFILE "<title>$var{'texttitleindex'} in Directory $dirToPrint</title>\n"; }
+       }
+
+       if ($var{'frames'} eq 'yes') {
+	   print IFILE "<base target=\"$GlobalNameFrameAZIndexsmall\" />\n";
+       }
+       print IFILE "</head>\n";
+       print IFILE "<body $var{'codebodyindex'}>\n";
+       print IFILE "<div id=\"matlabdoc\">\n";
+
+       # Write the A-Z jump line, generate link for letters with files starting with this letter
+       # and only letters for no files starting with this letter
+       # use previously generated arrays with names of files sorted by starting letter
+       for('a'..'z') {
+	   $numberofletter = $#{$_}+1;
+	   if ($numberofletter > 0) {
+	       print IFILE "<strong><a href=\"$indexfilename$var{'filenameextensionindex'}$extradirfilename$var{'exthtml'}#\U$_\E$_\">\U$_\E</a> </strong>\n";
+	   } else {
+	       print IFILE "\U$_\E \n";
+	   }
+       }
+
+       print IFILE "</div></body>\n</html>\n";
+
+       close(IFILE);
+
+       if ($opt_silent) { print "\r"; }
+       print "   Indexfile small (A-Z jump) created: $indexfile\t";
+       if (!$opt_silent) { print "\n"; }
+   }
+
+
+   # Build the frame layout file, this file includes the layout of the frames
+   # Build the frame layout file name (for small/compact A-Z index)
+   # handle the global index file case separately (no extra directory name in file)
+   if ($LocalGlobalLocal eq 'global') { $extradirfilename = ''; }
+   else { $extradirfilename = $dirnamesingle{$LocalActDir}; }
+
+   if ($var{'frames'} eq 'yes') {
+
+       $indexfile = $var{'dirhtml'}.$dirnamerelpath{$LocalActDir}.$indexfilename.$var{'filenameextensionframe'}.$extradirfilename.$var{'exthtml'};
+       if ($debug > 2) { print "   indexfilename (a-z frame): $indexfile\n"; }
+
+       open(IFILE,">$indexfile") || die("Cannot open jump index frame file $indexfile: $!\n");
+
+       # Write the header of Frame file
+       print IFILE "$TextDocTypeHTML\n<html>\n<head>\n$var{'codeheadmeta'}\n$TextMetaCharset\n$var{'csslink'}\n";
+
+       if ($var{'texttitleindex'} eq '') {
+	   print IFILE "<title>Index of Matlab Files in Directory $dirToPrint</title>\n";
+       } else {
+	   if ($LocalGlobalLocal eq 'global') { print IFILE "<title>$var{'texttitleindex'}</title>\n"; }
+	   else { print IFILE "<title>$var{'texttitleindex'} in Directory $dirToPrint</title>\n"; }
+       }
+       print IFILE "</head>\n";
+
+       # definition of 2 frames, top the A-Z index, below the jump letter line
+       print IFILE "<frameset  rows=\"90%,10%\">\n";
+       print IFILE "   <frame src=\"$indexfilename$var{'filenameextensionindex'}$extradirfilename$var{'exthtml'}\" name=\"$GlobalNameFrameAZIndexsmall\" />\n";
+       print IFILE "   <frame src=\"$indexfilename$var{'filenameextensionjump'}$extradirfilename$var{'exthtml'}\" name=\"$GlobalNameFrameAZIndexjump\" />\n";
+       print IFILE "</frameset>\n";
+
+       print IFILE "</html>\n";
+
+       close(IFILE);
+
+       if ($opt_silent) { print "\r"; }
+       print "   Frame layout file created: $indexfile\t";
+       if (!$opt_silent) { print "\n"; }
+   }
+}
+   
+
+#========================================================================
+# Construct the links to all indexes
+#========================================================================
+sub ConstructLinks2Index
+{
+   local(*WRITEFILE, $LocalPath2Index, $PathContents, $LocalGlobalLocal) = @_;
+   
+   # include links to short/long - local/global index and C|contents.m
+   print WRITEFILE "\n<p>";
+   print WRITEFILE "$var{'textjumpindexglobal'} ";
+
+   if ($var{'frames'} eq 'yes') {
+       print WRITEFILE "<a href=\"$LocalPath2Index$var{'filenameindexshortglobal'}$var{'filenameextensionframe'}$var{'exthtml'}\">short</a> | ";
+       print WRITEFILE "<a href=\"$LocalPath2Index$var{'filenameindexlongglobal'}$var{'filenameextensionframe'}$var{'exthtml'}\">long</a>\n";
+   } else {
+       print WRITEFILE "<a href=\"$LocalPath2Index$var{'filenametopframe'}$var{'exthtml'}\">short</a> | ";
+       print WRITEFILE "<a href=\"$LocalPath2Index$var{'filenameindexlongglobal'}$var{'filenameextensionindex'}$var{'exthtml'}\">long</a>\n";
+   }
+
+   if ($LocalGlobalLocal eq 'local') {
+      if ($var{'usecontentsm'} eq 'yes') {
+         print WRITEFILE " | <a href=\"$contentsname{$PathContents}$dirnamesingle{$PathContents}$var{'exthtml'}\">Local contents</a>\n";
+      }
+      if ($var{'frames'} eq 'yes') {
+         print WRITEFILE " | $var{'textjumpindexlocal'} ";
+         print WRITEFILE "<a href=\"$var{'filenameindexshortlocal'}$var{'filenameextensionframe'}$dirnamesingle{$PathContents}$var{'exthtml'}\">short</a> | ";
+         print WRITEFILE "<a href=\"$var{'filenameindexlonglocal'}$var{'filenameextensionframe'}$dirnamesingle{$PathContents}$var{'exthtml'}\">long</a>\n";
+      } else {
+         print WRITEFILE " | $var{'textjumpindexlocal'} ";
+         print WRITEFILE "<a href=\"$var{'filenameindexshortlocal'}$var{'filenameextensionindex'}$dirnamesingle{$PathContents}$var{'exthtml'}\">short</a> | ";
+         print WRITEFILE "<a href=\"$var{'filenameindexlonglocal'}$var{'filenameextensionindex'}$dirnamesingle{$PathContents}$var{'exthtml'}\">long</a>\n";
+      }
+   }
+   print WRITEFILE "</p>\n\n";
+   print WRITEFILE "$var{'codehr'}\n";
+}
+
+
+#========================================================================
+# Construct the contents.m files or update
+#========================================================================
+sub ConstructContentsmFile
+{
+   local($LocalActDir, @localnames) = @_;
+   local(*CFILE, $name,$newline);
+   local($contentsfile, $isincontentsonly);
+   local(@lines, @autoaddlines, @emptylines);
+   local($autoadd) = 'AutoAdd';
+   local($autoaddsection) = 0;
+   local($emptylineflag) = 0;
+   local(%nameincontents);
+   
+   # Build the contents file name
+   $contentsfile = $LocalActDir.$contentsname{$LocalActDir}.$suffix;
+   
+   if (-e $contentsfile) {
+      open(CFILE,"<$contentsfile") || die("Cannot open contents file $contentsfile: $!\n");
+      while (<CFILE>) {
+         # Search for the specified string pattern
+         @words = split;
+         if ((@words >= 3) && ($words[2] eq '-')) {
+            $isincontentsonly = 0;
+            foreach $name (@localnames) {
+               if ($name eq $words[1]) {    # old
+               # if ($mfilename{$name} eq $words[1]) {
+                  $isincontentsonly = 1;
+                  $nameincontents{$name} = 1;
+                  $newline = sprintf("%% %-13s - %s\n", $mfilename{$name}, $apropos{$name});
+                  push(@lines, $newline);
+               }
+            }
+            # issue a warning, if file is in contents, but not as file in the directory
+            if ($isincontentsonly == 0) {
+               print "\rConstructContents: Obsolete entry  $words[1]  in  $contentsfile ! Entry not used.\n";
+            }
+         } else {
+            # look for the AutoAdd section, should be the second word
+            if ((@words >= 2) && ($words[1] eq $autoadd)) { $autoaddsection = 1; }
+            # push the red line in an array
+            push(@lines, $_); 
+         }
+      }   
+      close(CFILE);
+   } else {
+      $newline = "% MATLAB Files in directory  $LocalActDir\n%\n";
+      push(@lines, $newline);
+      
+   }
+   
+   # collect the file names, that were not included in original C|contents.m
+   foreach $name (@localnames) {
+      if (! defined $nameincontents{$name}) {
+         if (! ($mfilename{$name} =~ /contents/i)) {
+            $newline = sprintf("%% %-13s - %s\n", $mfilename{$name}, $apropos{$name});
+            push(@autoaddlines, $newline);
+         }   
+      }
+   }
+
+   # write/update C|contents.m only if variable is set
+   if ($var{'writecontentsm'} eq 'yes') {
+      unlink($contentsfile);
+      open(CFILE,">$contentsfile") || die("Cannot open contents file $contentsfile: $!\n");
+      # write old C|contents.m or header of new file, as long as comment lines
+      foreach $line (@lines) {
+         if ($emptylineflag == 0) {
+            if ($line =~ /^\s*%/) { print CFILE $line; }
+            else { $emptylineflag = 1; push(@emptylines, $line); }
+         } else { push(@emptylines, $line); }
+      }
+      # add header of AutoAdd section
+      if (($autoaddsection == 0) && (@autoaddlines > 0)) { print CFILE "%\n% $autoadd\n"; }
+      # add autoadd section lines (previously undocumented files
+      foreach $line (@autoaddlines) { print CFILE $line; }
+      # add tail of original C|contents.m (everything behind first non-comment line)
+      foreach $line (@emptylines)   { print CFILE $line; }
+      print CFILE "\n";
+      close CFILE;
+      if ($opt_silent) { print "\r"; }
+      print "   Contents file created/updated: $contentsfile\t";
+      if (!$opt_silent) { print "\n"; }
+   }
+}
+
+
+#========================================================================
+# Replace found special characters with their HTMl Entities
+#========================================================================
+sub SubstituteHTMLEntities {
+   local($_) = @_;
+   
+   # Replace & <-> &amp;  < <-> &lt;  > <-> &gt;  " <-> &quot;
+   s/&/&amp;/g; s/\</&lt;/g; s/\>/&gt;/g; s/\"/&quot;/g;
+   return $_;
+}
+
+#========================================================================
+# Replace found m-filenamestring with full link.
+#========================================================================
+sub SubstituteName2Link {
+   local($_, $funname) = @_;
+   local($refstr1, $refstr2, $reffound);
+   
+   # Look for something matching in the line
+   if ( /(\W+)($funname)(\W+)/i ) {
+      $reffound = $2;
+      $refstr1 = "<a class=\"mfun\" href=\"$hfileindexpath{$name}$hfilerelpath{$funname}$mfilename{$funname}$var{'exthtml'}\">";
+      $refstr2 = "<\/a>";
+      # Do links only for exact case match
+      if ( ($var{'links2filescase'}  eq 'exact') || ($var{'links2filescase'}  eq 'exactvery') ) {
+         if ( /(\W+)($funname)(\W+)/g ) {
+            s/(\W+)($funname)(\W+)/$1$refstr1$funname$refstr2$3/g;
+         }
+         else {
+            # Print info for not matching case in references, good for check up of files
+            if ( ($var{'links2filescase'}  eq 'exactvery') ) {
+               print "Diff in case found: $funname  (case of file name)   <->  $reffound  (case in source code)\n";  
+               print "     (source line)  $_ \n";
+            }
+         }
+      }
+      # Do links for exact match and additionally for all upper case (often used in original matlab help text)
+      elsif ( ($var{'links2filescase'}  eq 'exactupper') ) {
+         s/(\W+)($funname)(\W+)/$1$refstr1$2$refstr2$3/g;
+         $funname2 = "\U$funname\E";
+         s/(\W+)($funname2)(\W+)/$1$refstr1$2$refstr2$3/g;
+      }
+      # Do links for all case mixes, this calls for trouble under LINUX/UNIX
+      else {  #elsif ( ($var{'links2filescase'}  eq 'all') )
+         s/(\W+)($funname)(\W+)/$1$refstr1$2$refstr2$3/ig;
+      }
+   }
+   
+   return $_;
+}
+
+#========================================================================
+# Construct the html files for each matlab file.
+#    Need to reread each matlab file to find the help text.
+#    Note that we can't do this in a single loop because sometimes
+#    the help text maybe before the function declaration.
+#========================================================================
+sub ConstructHTMLFiles
+{
+   local(*MFILE);
+   local(*HFILE);
+
+   local($filescreated) = 0;
+   local($functionline);
+   
+   foreach $name (@names) {
+      # Create cross reference information already here, used for keywords as well
+      # Construct list of referenced functions
+      @xref = @{'depcalls'.$name};    # the functions, that this m-file calls
+      @yref = @{'depcalled'.$name};   # the functions, that this m-file is called from
+      # print "   depcalls: @{'depcalls'.$name}\n   depcalled: @{'depcalled'.$name}\n";
+      # foreach $cname (@names) { next if $cname eq $name; push(@yref,$cname) if grep(/$name/,@{'depcalls'.$cname}); }
+
+
+      # Open m-file and html-file
+      open(MFILE,"<$mfile{$name}");
+      open(HFILE,">$hfile{$name}");
+
+      # Write the header of HTML file
+      print HFILE "$TextDocTypeHTML\n<html>\n<head>\n$var{'codeheadmeta'}\n$TextMetaCharset\n$var{'csslink'}\n";
+
+      # Write meta tags: use apropos (one line function description) for description
+      # and cross reference function names for keywords (any better ideas?)
+      print HFILE "<meta name=\"description\" content=\" $apropos{$name} \" />\n";
+      print HFILE "<meta name=\"keywords\" content=\" @xref @yref \" />\n";
+
+      # Write Title and start body of html-file
+      print HFILE "<title>$var{'texttitlefiles'} $mfilename{$name}</title>\n</head>\n";
+      print HFILE "<body $var{'codebodyfiles'}>\n";
+      print HFILE "<div id=\"matlabdoc\">\n";
+      print HFILE "<h1 $var{'codeheader'}>$var{'textheaderfiles'} $mfilename{$name}</h1>\n";
+
+# http://test.soundsoftware.ac.uk/cannam/projects/smallbox/repository/annotate/DL/RLS-DLA/SolveFISTA.m
+#      print HFILE "<a href=\"" . $hfileindexpath{$name} . "../../projects/smallbox/repository/annotate/" . $mfiledir{$name}  . $mfilename{$name} . ".m\">View in repository</a>\n";
+
+      print HFILE "$var{'codehr'}\n";
+
+      # include links to short/long - local/global index and C|contents.m
+      &ConstructLinks2Index(HFILE, $hfileindexpath{$name}, $mfiledir{$name}, 'local');
+
+      # If this is a function, then write out the first line as a synopsis
+      if ($mtype{$name} eq "function") {
+         print HFILE "<h2 $var{'codeheader'}>Function Synopsis</h2>\n";
+         print HFILE "<pre>$synopsis{$name}</pre>\n$var{'codehr'}\n";
+      }
+
+      # Look for the matlab help text block
+      $functionline = "\n";
+      do {
+         $_ = <MFILE>;
+         # remember functionline, if before help text block
+         if (/^\s*function/) { $functionline = $_; }
+      } until (/^\s*%/ || eof);
+      if (! (eof(MFILE))) {
+         print HFILE "<h2 $var{'codeheader'}>Help text</h2>\n";
+         print HFILE "<pre>\n";
+         while (/^\s*%/) {
+            # First remove leading % and white space, then Substitute special characlers
+            s/^\s*%//;
+            $_ = &SubstituteHTMLEntities($_);
+
+            # check/create cross references
+            foreach $funname (@{'all'.$name}) {
+               if ($funname =~ /simulink/) { print "\n Simulink - Filename: $name;  scanname: $funname\n"; }
+               next if $funname eq $name;
+               $_ = &SubstituteName2Link($_, $funname);
+            }
+            print HFILE $_;
+            if (! eof) { $_ = <MFILE>; }
+         }
+         print HFILE "</pre>\n$var{'codehr'}\n";
+      }
+
+      # Write the cross reference information
+      if (@xref || @yref) {
+         print HFILE "<h2 $var{'codeheader'}>Cross-Reference Information</H2>\n";
+         print HFILE "<table border=\"0\" width=\"100%\">\n<tr align=\"left\">\n<th width=\"50%\">";
+         if (@xref) {
+            print HFILE "This $mtype{$name} calls";
+         }
+         print HFILE "</th>\n<th width=\"50%\">";
+         if (@yref) {
+            print HFILE "This $mtype{$name} is called by";
+         }
+         print HFILE "</th>\n</tr>\n<tr valign=\"top\"><td>";
+         if (@xref) {
+            print HFILE "\n<ul>\n";
+            foreach $cname (sort @xref) {
+               print HFILE "<li><a class=\"mfun\" href=\"$hfileindexpath{$name}$hfilerelpath{$cname}$mfilename{$cname}$var{'exthtml'}\">$mfilename{$cname}</a></li>\n";
+            }
+            print HFILE "</ul>\n";
+         }
+         print HFILE "</td><td>";
+         if (@yref) {
+            print HFILE "\n<ul>\n";
+            foreach $cname (sort @yref) {
+               print HFILE "<li><a class=\"mfun\" href=\"$hfileindexpath{$name}$hfilerelpath{$cname}$mfilename{$cname}$var{'exthtml'}\">$mfilename{$cname}</a></li>\n";
+            }
+            print HFILE "</ul>\n";
+         }
+         print HFILE "</td>\n</tr>\n</table>\n";
+         print HFILE "$var{'codehr'}\n";
+      }
+
+      # Include source text if requested
+      if (($var{'includesource'} eq 'yes') && (! ($mfilename{$name} =~ /^contents$/i))) {
+         print HFILE "<h2 $var{'codeheader'}>Listing of $mtype{$name} $mfilename{$name}</h2>\n";
+         seek(MFILE,0,0);
+         print HFILE "<pre>\n";
+         $IsStillHelp = 2;
+         print HFILE $functionline;    # functionline from scanning of help
+         while (<MFILE>) {
+            if ($IsStillHelp == 2) {
+               next     if (/^\s*$/);
+               next     if (/^\s*function/);
+               if (/^\s*%/) { $IsStillHelp = 1; next; }
+            } elsif ($IsStillHelp == 1) {
+               next     if (/^\s*%/);
+               $IsStillHelp = 0;
+            }
+            
+            # Substritute special characters
+            $_ = &SubstituteHTMLEntities($_);
+            
+            # check for comment in line and format with css em
+            s/^(.*)%(.*?)([\s\r\n]+)$/$1<em class=\"mcom\">%$2<\/em>$3/;
+
+            # check/create cross references
+            foreach $funname (@{'all'.$name}) {
+               next if $funname eq $name;
+               $_ = &SubstituteName2Link($_, $funname);
+            }
+            print HFILE $_;
+         }
+         print HFILE "</pre>\n$var{'codehr'}\n";
+      }
+
+      # Include info about author from authorfile
+      &WriteFile2Handle($var{'authorfile'}, HFILE)   ;
+
+      print HFILE "<!--navigate-->\n";
+      print HFILE "<!--copyright-->\n";
+      print HFILE "</div>\n</body>\n</html>\n";
+      close(MFILE);
+      close(HFILE);
+
+      # Print name of finished file
+      if ($opt_silent) { print "\r"; }
+      print "   HTML-File created: $hfile{$name}\t";
+      if (!$opt_silent) { print "\n"; }
+      $filescreated++;
+   }
+
+   print "\n$PROGRAM: $indexcreated index and $filescreated files created.\n"; 
+}
+
+#========================================================================
+# Function:	CheckFileName
+# Purpose:	.
+#========================================================================
+sub CheckFileName {
+   local($filename, $description) = @_;
+   local(*CHECKFILE);
+   
+   open(CHECKFILE,"<$filename") || do {
+      if ($description eq '') {$description = 'file';}
+      # if (!$opt_silent) { print "Cannot open $description $filename: $!\n"; }
+      print "Cannot open $description $filename: $!\n";
+      return 1;
+   };
+   close(CHECKFILE);
+   return 0;
+
+}
+
+#========================================================================
+# Function:	CheckDirName
+# Purpose:	.
+#========================================================================
+sub CheckDirName {
+   local($dirname, $description) = @_;
+   local(*CHECKDIR);
+   
+   opendir(CHECKDIR,"$dirname") || die ("Cannot open $description directory $dirname: $!\n");
+   closedir(CHECKDIR);
+}
+
+#========================================================================
+# Function:	WriteFile2Handle
+# Purpose:	.
+#========================================================================
+sub WriteFile2Handle {
+   local($filename, *WRITEFILE) = @_;
+   local(*READFILE);
+   
+   if ($filename ne '') {
+      open(READFILE,"<$filename");  
+      @filecontents = <READFILE>;
+      close(READFILE);
+      print WRITEFILE "@filecontents\n";
+      # if (!$opt_silent) {print "      Contents of $filename added\n"};
+   }
+}
+
+
+#========================================================================
+# Function:	GetConfigFile
+# Purpose:	Read user's configuration file, if such exists.
+#========================================================================
+sub GetConfigFile
+{
+   local($filename) = @_;
+   local(*CONFIG);
+   local($value);
+
+   if (&CheckFileName($filename, 'configuration file')) {
+      # if (!$opt_silent) { print "   Proceeding using built-in defaults for configuration.\n"; }
+      print "   Proceeding using built-in defaults for configuration.\n";
+      return 0;
+   };
+
+   open(CONFIG,"< $filename");
+   while (<CONFIG>) {
+      s/#.*$//;
+      next if /^\s*$/o;
+
+      # match keyword: process one or more arguments
+      # keyword set
+      if (/^\s*set\s+(\S+)\s*=\s*(.*)/) {
+         # setting a configuration variable
+         if (defined $var{$1}) {
+            $var{$1} = $2;
+            if ($debug > 3) { print "$1:   $var{$1}\n"; }
+         }
+         else {
+            print "$PROGRAM: unknown variable `$1' in configuration file\n"
+         }
+      } else {
+         chop($_);
+         print "$PROGRAM: unknown keyword in configuration file in line: `$_'\n"
+      }
+   }
+   close CONFIG;
+   1;
+}
+
+
+#------------------------------------------------------------------------
+# DisplayHelp - display help text using -h or -help command-line switch
+#------------------------------------------------------------------------
+sub DisplayHelp
+{
+   $help=<<EofHelp;
+   $PROGRAM v$VERSION - generate html documentation from Matlab m-files
+
+   Usage: $PROGRAM [-h] [-c config_file] [-m|dirmfiles matlab_dir] [-d|dirhtml html_dir]
+                   [-i yes|no] [-r yes|no] [-p yes|no] [-quiet|q] [-a authorfile]
+
+   $PROGRAM is a perl script that reads each matlab .m file in a directory
+   to produce a corresponding .html file of help documentation and cross
+   reference information. An index file is written with links to all of 
+   the html files produced. The options are:
+
+      -quiet         or -q : be silent, no status information during generation
+      -help          or -h : display this help message
+      -todo          or -t : print the todo list for $PROGRAM
+      -version       or -v : display version
+
+      -configfile    or -c : name of configuration file (default to $var{'configfile'}).
+      -dirmfiles     or -m : top level directory containing matlab files to generate html for;
+                             default to actual directory.
+      -dirhtml       or -d : top level directory for generated html files;
+                             default to actual directory.
+
+      -includesource or -i : Include matlab source in the html documentation [yes|no]
+                             default to yes.
+      -processtree   or -r : create docu for m-file directory and all subdirectories [yes|no];
+                             default to yes.
+      -producetree   or -p : create multi-level docu identical to directory structure
+                             of m-files [yes|no]; default to yes.
+      -writecontentsm or -w: update or write contents.m files into the matlab source
+                             directories [yes|no]; default to no.
+
+      -authorfile    or -a : name of file including author information, last element in html;
+                             default to empty.
+      
+   The command line setting overwrite all other settings (built-in and configuration file).
+   The configuration file settings overwrite the built-in settings (and not the command
+   line settings).
+
+   Typical usages are:
+     $PROGRAM   
+        (use default parameters from perl script, if configuration 
+         file is found -> generation of docu, else display of help)
+
+     $PROGRAM -dirmfiles matlab -dirhtml html
+        (generate html documentation for all m-files in directory matlab,
+         place html files in directory html, use built-in defaults for
+         all other parameters, this way all m-files in the directory
+         matlab and below are converted and the generated html-files are
+         placed in the directory html and below producing the same 
+         directory structure than below matlab)
+
+     $PROGRAM -quiet
+        (use built-in parameters from perl script, if configuration 
+         file is found use these settings as well, do generation,
+         no display except critical errors, status of conversion and result)
+         
+     $PROGRAM -m toolbox -dirhtml doc/html -r yes -p no
+        (convert all m-files in directory toolbox and below and place
+         the generated html files in directory doc/html, read all m-files
+         recursively, however, the generated html files are placed in one
+         directory)
+
+     $PROGRAM -m toolbox -dirhtml doc/html -i no -r no
+        (convert all m-files in directory toolbox and place
+         the generated html files in directory doc/html, do not read m-files
+         recursively, do not include source code in documentation)
+
+EofHelp
+
+   die "$help";
+}
+
+#------------------------------------------------------------------------
+# DisplayTodo - display ToDo list using -t or -todo command-line switch
+#------------------------------------------------------------------------
+sub DisplayTodo
+{
+   $todo=<<EofToDo;
+      $PROGRAM v$VERSION - ToDo list
+
+       o	use more than one high level directory
+       
+       o	what should/could be done here???
+
+EofToDo
+
+   die "$todo";
+}
+
+
+#------------------------------------------------------------------------
+# ListVariables - list all defined variables and their values
+#------------------------------------------------------------------------
+sub ListVariables
+{
+   local($value);
+   
+   if ($debug > 0) {
+      print "List of all variables and their values\n";
+      foreach (sort keys %var)
+      {
+         if ($var{$_} eq '') {
+            $value = "empty";
+         } else {
+            $value = $var{$_};
+         }
+         print "   $_\n      $value\n";
+      }
+      print "\n\n";
+   }
+}
+
+
+__END__
+:endofperl
--- a/public/themes/soundsoftware/stylesheets/application.css	Mon Apr 11 18:01:57 2011 +0100
+++ b/public/themes/soundsoftware/stylesheets/application.css	Tue May 10 10:09:14 2011 +0100
@@ -231,5 +231,9 @@
 
 .embedded .contents .center { text-align: center; } /* undo javadoc hack above */
 
+/* For MATLAB documentation */
 
+.embedded #matlabdoc th { text-align: left; }
 
+
+