SoundSoftware Code Site

types="doxygen javadoc matlabdocs" # Do Doxygen first (it can be used for Java too)

#!/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"

<div style="clear: both; float: right"><small><i>Produced by mtree2html by Hartmut Pohlheim</i></small></div>

# 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

@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