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Revision 1.1 - (download) (annotate)
Tue May 15 21:13:53 2007 UTC (12 years, 9 months ago) by olson
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
Hope College  modifications.

use strict;
use integer;
use FIG;
use FIG_Config;
use CGI;
use HTML;
use CGI::Carp qw(fatalsToBrowser);
use model;

our $fig = new FIG;
my $cgi = new CGI;
my $html = [];

# There are six consecutive entries to this script:
# 1) from the Find reactions paths button on subsys.cgi.  This entry passes a particular
# subsystem name, scenario name and genome, and the script finds all possible paths
# from inputs to outputs for the subsystem scenario, given the genome's reactions.
# 2) Next, on the find_reaction_paths.cgi page, the user can select any combination
# of the presented paths for the subsystem/scenario, enter a name for the combination,
# and create FluxAnalyzer files for the named combination.

my $genome = $cgi->param("genome");
my $number_of_paths = $cgi->param("one_or_all");

#foreach my $elem($cgi->param){
#    push @$html, $cgi->p($elem),
#    $cgi->p($cgi->param($elem));

if ($genome eq "")
	$genome = "All";

# the following cgi params are used in entry 1 & 2
my $ssa = $cgi->param("ssa");
my $scenario = $cgi->param("scenario_name");

# the following cgi params are used in entry 2
my @checked = $cgi->param("checked");
my $paths_name = $cgi->param("paths_name");

push @$html, "<TITLE>Finding reaction paths for $ssa ($genome, $scenario)</TITLE>\n";

#We need to load up the superset file before we can use the module 
#this is so that it knows what superset to save the scenario under

if(!defined @checked)
    #Okay we first want to run path finding on the scenario and display the results
    push (@$html, $cgi->start_form(-method => 'post' , -action => 'find_reaction_paths.cgi',-name => 'write_paths'),
	  $cgi->hidden(-name => 'genome', -value => "$genome", -override => 1), "\n",
	  $cgi->hidden(-name => 'ssa', -value => "$ssa", -override => 1), "\n",
	  $cgi->hidden(-name => 'scenario_name', -value => "$scenario", -override => 1), "\n");

    model::show_path_results_two(model::internal_scenario($genome,$ssa,$scenario, $number_of_paths),$html,$cgi);

    push(@$html, $cgi->br, &HTML::java_buttons("write_paths","checked"), $cgi->br,
	 $cgi->submit(-name => 'batch_assign',
		 -label =>"Create FluxAnalyzer files for selected paths"),

else #here we want to write the selected paths out.
    my $path = model::write_selected_scenarios(\@checked,$genome,$ssa,$scenario);
    push(@$html,"<h2>Wrote $scenario paths to</h2> <h4>$path</h4>",$cgi->br,
	 "<a href=\"directoryRead.cgi?create_assembly_id=$genome\">View Scenarios</a>");


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