[Bio] / FigWebServices / ff.cgi Repository:
ViewVC logotype

View of /FigWebServices/ff.cgi

Parent Directory Parent Directory | Revision Log Revision Log


Revision 1.2 - (download) (annotate)
Sun May 20 02:53:33 2007 UTC (12 years, 6 months ago) by overbeek
Branch: MAIN
CVS Tags: mgrast_dev_08112011, rast_rel_2009_05_18, mgrast_dev_08022011, rast_rel_2014_0912, rast_rel_2008_06_18, myrast_rel40, rast_rel_2008_06_16, mgrast_dev_05262011, rast_rel_2008_12_18, mgrast_dev_04082011, rast_rel_2008_07_21, rast_rel_2010_0928, rast_2008_0924, mgrast_version_3_2, mgrast_dev_12152011, rast_rel_2008_04_23, mgrast_dev_06072011, rast_rel_2008_09_30, rast_rel_2009_0925, rast_rel_2010_0526, rast_rel_2014_0729, mgrast_dev_02212011, rast_rel_2010_1206, mgrast_release_3_0, mgrast_dev_03252011, rast_rel_2010_0118, mgrast_rel_2008_0924, mgrast_rel_2008_1110_v2, rast_rel_2009_02_05, rast_rel_2011_0119, mgrast_rel_2008_0625, mgrast_release_3_0_4, mgrast_release_3_0_2, mgrast_release_3_0_3, mgrast_release_3_0_1, mgrast_dev_03312011, mgrast_release_3_1_2, mgrast_release_3_1_1, mgrast_release_3_1_0, mgrast_dev_04132011, rast_rel_2008_10_09, mgrast_dev_04012011, rast_release_2008_09_29, mgrast_rel_2008_0806, mgrast_rel_2008_0923, mgrast_rel_2008_0919, rast_rel_2009_07_09, rast_rel_2010_0827, mgrast_rel_2008_1110, myrast_33, rast_rel_2011_0928, rast_rel_2008_09_29, mgrast_rel_2008_0917, rast_rel_2008_10_29, mgrast_dev_04052011, mgrast_dev_02222011, rast_rel_2009_03_26, mgrast_dev_10262011, rast_rel_2008_11_24, rast_rel_2008_08_07, HEAD
Changes since 1.1: +1 -1 lines
fix test for writable built in FigFam.pm

# -*- perl -*-
#
# Copyright (c) 2003-2006 University of Chicago and Fellowship
# for Interpretations of Genomes. All Rights Reserved.
#
# This file is part of the SEED Toolkit.
# 
# The SEED Toolkit is free software. You can redistribute
# it and/or modify it under the terms of the SEED Toolkit
# Public License. 
#
# You should have received a copy of the SEED Toolkit Public License
# along with this program; if not write to the University of Chicago
# at info@ci.uchicago.edu or the Fellowship for Interpretation of
# Genomes at veronika@thefig.info or download a copy from
# http://www.theseed.org/LICENSE.TXT.
#


use FIG;
my $fig = new FIG;

use FigFam;
use FigFams;

use Subsystem;

use HTML;
use strict;

use CGI;
my $cgi = new CGI;

my $user = $cgi->param('user'); 
$fig->set_user($user);

if (0)
{
    my $VAR1;
    eval(join("",`cat /tmp/ff_check_parms`));
    $cgi = $VAR1;
#   print STDERR &Dumper($cgi);
}

if (0)
{
    print $cgi->header;
    my @params = $cgi->param;
    print "<pre>\n";
    foreach $_ (@params)
    {
	print "$_\t:",join(",",$cgi->param($_)),":\n";
    }

    if (0)
    {
	if (open(TMP,">/tmp/ff_check_parms"))
	{
	    print TMP &Dumper($cgi);
	    close(TMP);
	}
    }
    exit;
}

my $html = [];
unshift @$html, "<TITLE>ff.cgi: check FIGfams</TITLE>\n";

my($request);
if (! $cgi->param('user'))
{
    push(@$html,$cgi->h1('You need to set a user'));
}
elsif (! ($request = $cgi->param('request')))
{
    &initial($fig,$cgi,$html);
}
elsif ($request eq "get_fams")
{
    &get_fams($fig,$cgi,$html);
}
elsif ($request eq "display_fam")
{
    &display_fam($fig,$cgi,$html);
}
else
{
    push(@$html,$cgi->h1("Invalid Request: $request"));
}

&HTML::show_page($cgi,$html);

sub initial {
    my($fig,$cgi,$html) = @_;

    my $user = $cgi->param('user');
    push(@$html,$cgi->start_form(-action => "ff.cgi",
				  -method => 'post'),
	         $cgi->hidden(-name => 'request', -value => 'get_fams', -override => 1),
                 $cgi->hidden(-name => 'user', -value=>$user),
	         $cgi->h1('Paste in Some PEGs that Represent Families to Work on'),
	         $cgi->textarea(-name => 'pegtext', -rows => 40, -cols => 80, -value => ''),
	         $cgi->br,
	         $cgi->submit( 'Process' ),
	         $cgi->end_form
	 );
}

sub get_fams {
    my($fig,$cgi,$html) = @_;

    my $figfams = new FigFams($fig);
    my $text = $cgi->param('pegtext');
    my @pegs = ($text =~ /fig\|\d+\.\d+\.peg\.\d+/g);
    my $col_hdrs = ['Family','Family Function','PEG','Function','Subsystems'];
    my $tab = [];

    my(%hit_fam,$fam,$peg);
    foreach $peg (@pegs)
    {
	foreach $fam ($figfams->families_containing_peg($peg))
	{
	    $hit_fam{$fam}->{$peg} = 1;
	}
    }

    foreach $fam (sort keys(%hit_fam))
    {
	my $famO  = new FigFam($fig,$fam);
	my $ffunc = $famO->family_function;
	my @peg_func_tuples  = map { [$_,scalar $fig->function_of($_),&subs($fig,$_)] } keys(%{$hit_fam{$fam}});
	my $i;
	for ($i=0; ($i < @peg_func_tuples); $i++)
	{
	    if ($i == 0)
	    {
		push(@$tab,[&fam_link($cgi,$fam),
			    $ffunc,
			    &HTML::fid_link($cgi,$peg_func_tuples[$i]->[0]),
			    $peg_func_tuples[$i]->[1],
			    $peg_func_tuples[$i]->[2]]
		     );
	    }
	    else
	    {
		push(@$tab,['&nbsp;',
			    '&nbsp;',
			    &HTML::fid_link($cgi,$peg_func_tuples[$i]->[0]),
			    $peg_func_tuples[$i]->[1],
			    $peg_func_tuples[$i]->[2]]
		     );
	    }
	}
    }
    push(@$html,&HTML::make_table($col_hdrs,$tab,'Families to Check'));
}

sub fam_link {
    my($cgi,$fam) = @_;

    my $user = $cgi->param('user');
    my $url = &FIG::cgi_url . "/ff.cgi?user=$user&request=display_fam&fam=$fam";
    return "<a href=$url>$fam</>";
}

sub display_fam {
    my($fig,$cgi,$html) = @_;

    my $fam   = $cgi->param('fam');
    my $famO  = new FigFam($fig,$fam);
    my $ffunc = $famO->family_function;
    my @pegs  = $famO->list_members;
    my $col_hdrs = ['PEG','Length','Function','Subsystems'];
    my $tab = [];
    foreach my $peg (@pegs)
    {
	push(@$tab,[&HTML::fid_link($cgi,$peg),
		    $fig->translation_length($peg),
		    scalar $fig->function_of($peg),
		    &subs($fig,$peg)
		   ]);
    }
    $tab = [sort { $a->[2] cmp $b->[2] } @$tab];
    push(@$html,&HTML::make_table($col_hdrs,$tab,"$fam: $ffunc"));
}

sub subs {
    my($fig,$peg) = @_;

    return join("<br>",$fig->peg_to_subsystems($peg));
}

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3