#!/usr/bin/perl -w

%names = ("alignformats" => "AlignFormats",
	  "assemblyformats" => "AssemblyFormats",
	  "codonformats" => "CodonFormats",
	  "featformats" => "FeatFormats",
	  "ontologyformats" => "OntologyFormats",
	  "refseqformats" => "RefseqFormats",
	  "reportformats" => "ReportFormats",
	  "resourceformats" => "ResourceFormats",
	  "seqformats" => "SeqFormats",
	  "seqfeatformats" => "SeqfeatFormats",
	  "taxonformats" => "TaxonFormats",
	  "textformats" => "TextFormats",
	  "urlformats" => "UrlFormats",
	  "variationformats" => "VariationFormats",
	  "xmlformats" => "XmlFormats",
	  "assemblyinformats" => "AssemblyInFormats",
	  "codoninformats" => "CodonInFormats",
	  "featinformats" => "FeatInFormats",
	  "ontologyinformats" => "OntologyInFormats",
	  "refseqinformats" => "RefseqInFormats",
	  "resourceinformats" => "ResourceInFormats",
	  "seqinformats" => "SeqInFormats",
	  "seqfeatinformats" => "SeqfeatInFormats",
	  "taxoninformats" => "TaxonInFormats",
	  "textinformats" => "TextInFormats",
	  "urlinformats" => "UrlInFormats",
	  "variationinformats" => "VariationInFormats",
	  "xmlinformats" => "XmlInFormats",
	  "gcfiles" => "GeneticCodeFiles",
	  "localfiles" => "LocalFiles",
	  "graphicsdevices" => "GraphicsDevices",
	  "drcat" => "Drcat",
	  "edam" => "Edam",
	  "go" => "Go",
	  "taxon" => "Taxon",
	  "jaspfiles" => "JasparFiles",
	  "refiles" => "RebaseFiles",
	  "jison-programs" => "JonIsonPrograms",
     );

open (VERS, "embossversion -full -auto|") || die "Cannot run embossversion";
while (<VERS>) {
    if(/InstallDirectory: +(\S+)/) {
	$installtop = $1;
	$installtop =~ s/\/$//;
    }
    if(/BaseDirectory: +(\S+)/) {
	$distribtop = $1;
	$distribtop =~ s/\/$//;
    }
}
close VERS;

$docdir = "$distribtop/doc/programs/master/emboss/apps";
$docinc = "$docdir/inc";

opendir(INC, $docinc);

while ($file = readdir(INC)) {
    if($file =~ /(^[^.]+)[.]ione$/) {
	$newname = "Short".ucfirst($1);
	system "cp $docinc/$file $newname";
	$newname = "Options".ucfirst($1);
	system "acdtable $1 -verbose 2> x.x";
	system "wikifytable.pl x.x > $newname";
	system "rm x.x";
	$newname = ucfirst($1);
	system "wikifyhtml.pl $docdir/$1.html > $newname.wiki";
    }
    if($file =~ /(^[^.]+)[.]isee$/) {
	$newname = "Seealso".ucfirst($1);
	system "wikifyseealso.pl $docinc/$file > $newname";
    }
    if($file =~ /(^[^.]+)[.]usage$/) {
	$newname = "Example".ucfirst($1);
	system "wikifyusage.pl $docinc/$file > $newname";
    }
    if($file =~ /(^[^.]+)[.]input$/) {
	$newname = "Input".ucfirst($1);
	system "wikifyusage.pl $docinc/$file > $newname";
    }
    if($file =~ /(^[^.]+)[.]output$/) {
	$newname = "Output".ucfirst($1);
	system "wikifyusage.pl $docinc/$file > $newname";
    }
    if($file =~ /(^[^.]+)[.]comment$/) {
	$newname = "Comment".ucfirst($1);
	system "wikifyhtml.pl $docinc/$file > $newname";
    }
    if($file =~ /(^[^.]+)[.]history$/) {
	$newname = "History".ucfirst($1);
	system "wikifyhtml.pl $docinc/$file > $newname";
    }
    if($file =~ /(^[^.]+)[.]ihtml$/) {
	if(defined($names{$1})) {$newname = $names{$1}}
	else{
	    print "ihtml file $1 has no name\n";
	    $newname = ucfirst($1);
	    next;
	}
	system "wikifyhtml.pl $docinc/$file > $newname";
    }
}