Interaction documentation.

sub substance_layout2 {
    &opt_default(output=>"show",filename=>"layout2.html", ptt=>"");

    my @args = opt_get(@_);
    my $gb = shift @args;
    my $filename = shift @args;
    my $output = opt_val("output");
    my $outfile = opt_val("filename");
    my $ptt = opt_val("ptt");

    set_gpac($gb, -ptt=>$ptt);

    my %gene2id;
    foreach my $cds ($gb->cds()){
	$gene2id{$gb->{$cds}->{gene}} = $cds;
    }
    
    mkdir("graph", 0777);
    open(FILE, '>graph/' . $outfile);
    print FILE qq(
		  <html>
		  <head>
		  <title>GENESYS: Substance Layout</title>
		  </head>
		  <body>
		  <applet code="GraphInteraction.class" width=800 height=600>
		  ); #"
    
    print FILE '<param name=functionkey value="';
    my $printcode = '';
    foreach my $code (keys %COG_fcode){
	$printcode .= sprintf("%s\#%s,", $code, $COG_fcode{$code});
    }
    print FILE $printcode . '">' . "\n";   #"
    
    my @contents;
    my %RuleHash;
    my $word;
    my $number=1;
    my ($s, $p, $e) = (1,1,1);
    my %Interaction;
    my %sum;

    open(ERI, $filename)|| die("ERROR: file does not exist\n");
    while(<ERI>){
	my @substrate=();
	my @product=();
	my @enzyme=();
	tr/\n//d;
	@contents=split /\t/;
	if($contents[0] eq 'REACTOR'){
	    $s=$p=$e=1;
	    $RuleHash{$number}{Type}=shift(@contents);
	    $RuleHash{$number}{Class}=shift(@contents);
	    
	    ($RuleHash{$number}{Paeth},$RuleHash{$number}{ID})=split(/:/,shift(@contents));
	    $RuleHash{$number}{Name}=shift(@contents);
	    $RuleHash{$number}{Enzyme}= (split(/-/,$RuleHash{$number}{ID}))[0];

	    foreach $word (@contents){
		if($word=~/Substrate/){
		    
		    ($RuleHash{$number}{"S_path$s"},$RuleHash{$number}{"S_ID$s"})=split(/:/,(split(/ /,$word))[1]);
		    $sum{$RuleHash{$number}{"S_ID$s"}}++;
		    push(@substrate,$RuleHash{$number}{"S_ID$s"});
		    $RuleHash{$number}{"S_Coeff$s"}=(split(/ /,$word))[2];
		    $s++;
		}elsif($word=~/Product/){
		    
		    ($RuleHash{$number}{"P_path$p"},$RuleHash{$number}{"P_ID$p"})=split(/:/,(split(/ /,$word))[1]);
		    $sum{$RuleHash{$number}{"P_ID$p"}}++;
		    push(@product,$RuleHash{$number}{"P_ID$p"});
		    $RuleHash{$number}{"P_Coeff$p"}=(split(/ /,$word))[2];
		    $p++;
		}elsif($word=~/Effector/){
		    
		    ($RuleHash{$number}{"E_path$e"},$RuleHash{$number}{"E_ID$e"})=split(/:/,(split(/ /,$word))[1]);
		    $RuleHash{$number}{"E_Coeff$e"}=(split(/ /,$word))[2];
		    $e++;
		}elsif($word=~/Catalyst/){
		    
		    ($RuleHash{$number}{C_path},$RuleHash{$number}{C_ID})=split(/:/,(split(/ /,$word))[1]);
		}else{
		    $RuleHash{$number}{Arg_tag}{(split(/ /,$word))[0]}=(split(/ /,$word))[1];
		}
	    }
	    $Interaction{$number}{substrate} =\@ substrate;
	    $Interaction{$number}{product} =\@ product;
	    $Interaction{$number}{enzyme} = $RuleHash{$number}{Enzyme};
	    $number++;
	}
	if($contents[0] eq 'Include'){
	    $RuleHash{$number}{Type}=shift(@contents);
	    $RuleHash{$number}{Class}=shift(@contents);
	}
    }
    close(ERI);
    
    my $printinter = '';
    print FILE qq(<param name=interaction value=");
    for(my $num=0; $num<$number-1; $num++){
	for(my $sub=0; $sub<=$#{$Interaction{$num}{substrate}}; $sub++){
	    my $substrate = ${$Interaction{$num}{substrate}}[$sub];
		 for(my $pro=0; $pro<=$#{$Interaction{$num}{product}}; $pro++){
		     my $product = ${$Interaction{$num}{product}}[$pro];
                     $printinter .= "$substrate-$product,";
	         }
       } 
    }
    substr($printinter, -1, 1) = '';
    print FILE $printinter . '">' , "\n";

    my $printinteraction = '';
    my %substance_list;
    print FILE qq(<param name=functionlist value=");
    for(my $num=0; $num<$number-1; $num++){
	for(my $sub=0; $sub<=$#{$Interaction{$num}{substrate}}; $sub++){
	    my $substrate = ${$Interaction{$num}{substrate}}[$sub];
                     if ($substance_list{$substrate} < 1){
                        $printinteraction .= sprintf("%s\#%s,", $substrate, $gb->{$gene2id{$Interaction{$num}{enzyme}}}->{code});
                     }
                     $substance_list{$substrate}++;
		     for(my $pro=0; $pro<=$#{$Interaction{$num}{product}}; $pro++){
		         my $product = ${$Interaction{$num}{product}}[$pro];

                         if ($substance_list{$product} < 1){
                               $printinteraction .= sprintf("%s\#%s,", 
                                   $product, $gb->{$gene2id{$Interaction{$num}{enzyme}}}->{code});
                         }
                         $substance_list{$product} ++;
	            }
       } 
    }
    substr($printinteraction, -1, 1) = '';
    print FILE $printinteraction . '">' , "\n";

    print FILE qq(
  	          </applet>
	          </body>
	          </html>
	         );

    return 1 unless ($output eq 'show');

    chdir("graph");
    system("wget http://www.charite.de/bioinformatics/interaction/Funk.class") unless(-M "Funk.class");
    system("wget http://www.charite.de/bioinformatics/interaction/GraphInteraction.class") unless(-M "GraphInteraction.class");
    system("wget http://www.charite.de/bioinformatics/interaction/GraphPanel.class") unless(-M "GraphPanel.class");
    system("wget http://www.charite.de/bioinformatics/interaction/Member.class") unless(-M "Member.class");
    system("wget http://www.charite.de/bioinformatics/interaction/Interaction.class") unless(-M "Interaction.class");
    system("wget http://www.charite.de/bioinformatics/interaction/Running.class") unless(-M "Running.class");
    system("appletviewer out.html &");
    chdir("../");

    return 1;
}