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#!/usr/bin/perl -w
%author = ("ableasby" => "Bleasby",
"price" => "Rice",
"ilongden" => "Longden",
"mschuster" => "Schuster",
);
%types = ("Ione" => "Short",
"Ihtml" => "",
"Itable" => "Options",
"Usage" => "Example",
"Input" => "Input",
"Output" => "Output",
"History" => "History",
"Comment" => "Comment",
"Isee" => "Seealso"
);
%names = ("Alignformats" => "AlignFormats",
"Assemblyformats" => "AssemblyFormats",
"Codonformats" => "CodonFormats",
"Featformats" => "FeatFormats",
"Ontologyformats" => "OntologyFormats",
"Reportformats" => "ReportFormats",
"Resourceformats" => "ResourceFormats",
"Seqformats" => "SeqFormats",
"Seqfeatformats" => "SeqfeatFormats",
"Taxonformats" => "TaxonFormats",
"Textformats" => "TextFormats",
"Urlformats" => "UrlFormats",
"Variationformats" => "VariationFormats",
"Assemblyinformats" => "AssemblyInFormats",
"Codoninformats" => "CodonInFormats",
"Featinformats" => "FeatInFormats",
"Ontologyinformats" => "OntologyInFormats",
"Resourceinformats" => "ResourceInFormats",
"Seqinformats" => "SeqInFormats",
"Seqfeatinformats" => "SeqfeatInFormats",
"Taxoninformats" => "TaxonInFormats",
"Textinformats" => "TextInFormats",
"Urlinformats" => "UrlInFormats",
"Variationformats" => "VariationFormats",
"Gcfiles" => "GeneticCodeFiles",
"Localfiles" => "LocalFiles",
"Graphicsdevices" => "GraphicsDevices",
"Drcat" => "Drcat",
"Edam" => "Edam",
"Go" => "Go",
"Taxon" => "Taxon",
"Jaspfiles" => "JasparFiles",
"Refiles" => "RebaseFiles",
"Jison-programs" => "JonIsonPrograms",
);
use English;
$text = "";
while (<>) {
s/^[ \t]+//;
$text .= $_;
}
$text =~ s/^.*BEGIN MAIN CONTENT[^>]+>//gosm;
$text =~ s/(<\/?[Hh][Tt][Mm][Ll]>)//gosm;
$text =~ s/(<\/?[Bb][Oo][Dd][Yy][^>]*?>)//gosm;
$text =~ s/(<[Aa]\s+name\s*=\s*\"([^\"]+)[^>]+>)[^<]*<\/[Aa]>//gosm;
$text =~ s/<[Aa]\s+href\s*=\s*\"([^\".]+\.html)[^>]+>([^<]+)<\/[Aa]>/[http:\/\/evolution.genetics.washington.edu\/phylip\/doc\/$1 $2]/gosm;
$text =~ s/<[Aa]\s+href\s*=\s*\"([^\"]+)[^>]+>([^<]+)<\/[Aa]>/[$1| $2]/gosm;
$text =~ s/(<[Hh]\d>)\s*\n\s*/$1/gosm;
$text =~ s/\n(<\/[Hh]\d>)/$1/gosm;
$text =~ s/<\/[Dd][Ii][Vv]>//gosm;
$text =~ s/<[Hh][Rr]>//gosm;
$text =~ s/<[Hh]1>(.*?)<\/[Hh]1>/==$1==/gosm;
$text =~ s/<[Hh]2>(.*?)<\/[Hh]2>/==$1==/gosm;
$text =~ s/<[Hh]3>(.*?)<\/[Hh]3>/===$1===/gosm;
$text =~ s/<[Hh]4>(.*?)<\/[Hh]4>/====$1====/gosm;
$text =~ s/<[Pp]>/\n/gosm;
$text =~ s/<\/?[Tt][RrDd]>//gosm;
$text =~ s/<\/[Pp]>//gosm;
$text =~ s/(<\/?[Bb]>)/'''/gosm;
$text =~ s/(<\/?[Ee][Mm]>)/'''/gosm;
$text =~ s/(<\/?[Ii]>)/''/gosm;
$text =~ s/(<\/?[Ll][Ii]>)\n/$1/gosm;
$i=0;
$pre = 0;
$head=0;
$blank=0;
$table = 0;
$list = "";
while ($text =~ /.*?\n/gos) {
$t = $MATCH;
if($t =~ s/<[Hh][Ee][Aa][Dd]>//gosm) {$head=1}
if($t =~ s/<\/[Hh][Ee][Aa][Dd]>//gosm) {$head=0;next}
if($t =~ s/<!--#include file="header1.inc" -->//gosm) {$head=1}
if($t =~ s/<!--#include file="header2.inc" -->//gosm) {$head=0;next}
if($head) {next}
if($t =~ s/<\/[Tt][Aa][Bb][Ll][Ee][^>]*>//gosm) {$table = 0}
if($t =~ s/<[Tt][Aa][Bb][Ll][Ee][^>]*>//gosm) {$table = 1}
if($t =~ s/<\/[OoUu][Ll]>//gosm) {$list = ""}
if($t =~ s/<[Uu][Ll]>//gosm) {$list = "u";$nlist=0}
if($t =~ s/<[Oo][Ll]>//gosm) {$list = "o";$nlist=0}
if($t =~ s/<[Pp][Rr][Ee]>//gosm) {$pre = 1}
if($t =~ s/<\/[Pp][Rr][Ee]>//gosm) {$pre = 0}
if($t =~ /<[!]--[\#]include file=\"([^\"]+)\" -->/gosm){
$ifile = $1;
if($ifile =~ /inc\/([^.]+)[.]address/){
$aname = $1;
if(defined($author{$aname})){$aname = $author{$aname}}
else {$aname = ucfirst($aname)}
$t = "\{\{:Appinc:Address$aname\}\}\n";
}
elsif($ifile =~ /inc\/target([^.]*)[.]itxt/){
$tgtname = ucfirst($1);
$t = "\{\{:Appinc:Target$tgtname\}\}\n";
}
elsif($ifile =~ /inc\/([^.]+)[.]ihelp/){
$t = "";
}
elsif($ifile =~ /inc\/([^.]+)[.](.*)/){
$name = ucfirst($1);
$type=ucfirst($2);
if(defined($names{$name})){$name = $names{$name}}
if(defined($types{$type})){$type = $types{$type}}
if($type eq "Seealso") {
print "==See also==\n";
}
$t = "\{\{:Appinc:$type$name\}\}\n";
}
}
if(!$pre & $t =~ /^\n$/) {$blank++}
else{$blank=0}
$i++;
if($blank > 1){next}
if($blank == 1 && $list ne ""){next}
# print "$i:";
if($list ne "") {$t =~ s/\n/ /}
if($pre) {print " "}
if($t =~ s/<[Ll][Ii]>//gosm) {
if($nlist++){print "\n"}
if($list eq "u") {print "* "}
elsif($list eq "o") {print "# "}
}
if($nlist && $list eq "") {print "\n";$nlist=0;}
print "$t";
}
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