G::SystemsBiology

EcellReader

G::Ecell::Reader - Perl extension for blah blah blah

  use G::Ecell::Reader;
  blah blah blah

Stub documentation for G::Ecell::Reader was created by h2xs. It looks like the
author of the extension was negligent enough to leave the stub
unedited.

Blah blah blah.

Methods description

Methods code

    my $self = shift;

    my $Result=&_eri_reader(shift @_);
    my @ID=@_;
    my @key;
    my @key2;
    my @key3;
    my $tmp;
    my $tmp2;
    my $tmp3;
    my $ID;
    my $switch;
    my $type;
    my $tmp_ID;
    
    $ID[0]=".*" if($ID[0] eq '');

    @key=sort{$a <=> $b} keys(%{$Result});
    foreach $tmp (@key){
	$switch=0;
	$type=0;
	foreach(@ID){
	    if($Result->{$tmp}->{Type}=~/$_/){
		$switch=1;
	    }
	    if($_ eq 'REACTOR' || $_ eq 'SUBSTANCE' || $_ eq 'SYSTEM'){
		$type=1;
	    }
	}
	if($switch==1 || $type==0){
	    if($##ID==0){
		$tmp_ID=$ID[0];
		$ID[0]=".*";
	    }
	    @key2=sort{$a <=> $b} keys(%{$Result->{$tmp}});
	    foreach $tmp2 (sort @key2){
		foreach $ID (@ID){
		    if($tmp2=~/$ID/){
			if($tmp2 eq "Arg_tag"){
			    @key3=sort keys(%{$Result->{$tmp}->{Arg_tag}});
			    foreach $tmp3 (@key3){
				&msg_send($tmp,' -> ',$tmp2,' -> ',$tmp3,' -> ',$Result->{$tmp}->{$tmp2}->{$tmp3},"\n");
			    }
			}
			else{
			    &msg_send($tmp,' -> ',$tmp2,' -> ',$Result->{$tmp}->{$tmp2},"\n");
			}
		    }
		}
	    }
	    if($##ID == 0){
		$ID[0]=$tmp_ID;
		$tmp_ID='';
	    }

    my $filename=shift;
    my @contents;
    my %RuleHash;
    my $word;
    my $number=1;
    my $s=1;
    my $p=1;
    my $e=1;
    
    
    open(FILE, $filename)|| die("ERROR: file does not exist\n"); 
    &msg_error("open data file $filename\n");

    while(<FILE>){
	tr/\n//d;
	@contents=split /\t/;
	if($contents[0] eq 'SYSTEM'){
	    $RuleHash{$number}{Type}=shift(@contents);
	    $RuleHash{$number}{Class}=shift(@contents);
	    $RuleHash{$number}{Path}=shift(@contents);
	    $RuleHash{$number}{Name}=shift(@contents);
	    foreach $word (@contents){
		$RuleHash{$number}{(split(/ /,$word))[0]}=(split(/ /,$word))[1];
	    }
	    $number++;
	}
	if($contents[0] eq 'SUBSTANCE'){
	    $RuleHash{$number}{Type}=shift(@contents);
	    $RuleHash{$number}{Class}=shift(@contents);
	    ($RuleHash{$number}{Path},$RuleHash{$number}{ID})=split(/:/,shift(@contents));
	    $RuleHash{$number}{Name}=shift(@contents);
	    foreach $word (@contents){
		$RuleHash{$number}{(split(/ /,$word))[0]}=(split(/ /,$word))[1];
	    }
	    $number++;
	}
	if($contents[0] eq 'FIX'){
	    ($RuleHash{$number-1}{FIX_path},$RuleHash{$number-1}{FIX})=split(/:/,$contents[1]);
	}
	if($contents[0] eq 'REACTOR'){
	    $s=$p=$e=1;
	    $RuleHash{$number}{Type}=shift(@contents);
	    $RuleHash{$number}{Class}=shift(@contents);
	    ($RuleHash{$number}{Path},$RuleHash{$number}{ID})=split(/:/,shift(@contents));
	    $RuleHash{$number}{Name}=shift(@contents);
	    foreach $word (@contents){
		if($word=~/Substrate/){
		    ($RuleHash{$number}{"S_path$s"},$RuleHash{$number}{"S_ID$s"})=split(/:/,(split(/ /,$word))[1]);
		    $RuleHash{$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]);
		    $RuleHash{$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];
		}
	    }
	    $number++;
	}
	if($contents[0] eq 'Include'){
	    $RuleHash{$number}{Type}=shift(@contents);
	    $RuleHash{$number}{Class}=shift(@contents);    
	}
    }
    return\% RuleHash;

    my $pkg = shift;
    my $filename = shift;
    my $option = shift;
    my $this;

    return $this;

General documentation

A. U. Thor, a.u.thor@a.galaxy.far.far.away

perl(1).