#!c:/perl/bin/perl.exe -w

use lib 'C:\Program Files\Apache Group\Apache2\cgi-bin\MyModules';

use strict "vars";
use CGI;
use BlastQueries; # self created package for handling creation of blast db
use ParseBlastResults;
use CreateBlastDB;
use CGI::Carp qw( fatalsToBrowser);
use Data::Dumper;
use threads;
use ParseBlastResults;
use blastNResults;

BEGIN{
	my $queryPath = "C:\\BlastQueries\\";  #path where all query files should be placed by user
	my $dbFilePath = "C:\\BlastDBs\\";
	my $tempQueryFile = $queryPath."_webQuery.txt"; #temporaily hold the query from webpage
	my $blastall= "C:\\Genomes\\bin\\blastall.exe";
    my $blastM0File = "blastNResultsM0.ffn";
    my $blastM6File = "blastNResultsM6.ffn";
    my $resultsFilePath = "C:\\Program Files\\Apache Group\\Apache2\\htdocs\\results.html";
    my $resultsFile =  "/results.html";

	my %options;
	my $resultantfile;
	my $cgi = CGI->new;
    my @params = $cgi->param;
#   print $cgi->header;
	my $folder = '';
    my ($view, $wait, $runBlast, $running) = 0;
    my $iteration = 1;
    $iteration = $cgi->param('iteration');
    $iteration ++ if ($iteration == 1);
    foreach (@params){
	if($_ =~/^view/){
            $folder = $cgi->param($_) if $cgi->param($_);
            $runBlast = 0;
            $running = 0;
            $view = 1;
            $wait = 0;
            last;
        }elsif($_ eq 'wait'){
            $runBlast = 0;
            $running = 0;
            $wait = 1;
            last;
        }
    }

	if($wait){ #still waiting for html file to be done
#            print $cgi->start_html(-title=>"Nucleotide Blast Results",
#                    -script=>{-language=>'JAVASCRIPT', -src=>'/Javascripts/blastNResultsPre.js'},
#                    -style=>{-src=>'/StyleSheets/style.css'});
#            print $cgi->start_form( -name=>'checkBlast', -action=>"/cgi-bin/BlastQuery/blastNResultsPre.cgi"),"\n";
#            print $cgi->hidden(-name=>'wait', -value=>1);
        my $display = BlastQueries::checkHTMLFile($resultsFilePath);
#        print "display 2 : $display <br>";
        if($display){
#            print $cgi->start_html(-title=>"Nucleotide Blast Results",
#                    -script=>{-language=>'JAVASCRIPT', -src=>'/Javascripts/blastNResultsPre.js'},
#                    -style=>{-src=>'/StyleSheets/style.css'});
            print $cgi->redirect( -URL => $resultsFile);
      #      print "FINISHED!<BR>";
        }else{ #finished and now can see file
        	print $cgi->header;
            print $cgi->start_html(-title=>"Nucleotide Blast Results",
                    -script=>{-language=>'JAVASCRIPT', -src=>'/Javascripts/blastNResultsPre.js'},
                    -style=>{-src=>'/StyleSheets/style.css'});
	        print $cgi->start_form( -name=>'checkBlast', -action=>"/cgi-bin/BlastQuery/blastNResultsPre.cgi"),"\n";
            print $cgi->hidden(-name=>'wait', -value=>1);
#            $iteration ++;
            print $cgi->hidden(-name=>'iteration', -value=>"$iteration");
            print "Still creating display file. Please wait.<br>";
            print "This page has been refreshed $iteration times<br />";
            print $cgi->end_form();
        }
        print $cgi->end_form()
    }elsif($view){
        $queryPath = $queryPath.$folder.'\\';
#        blastNResults::generateHTMLFile($resultsFilePath, $blastM0File, $blastM6File, $queryPath);
        my $thr = threads->new(\&blastNResults::generateHTMLFile, $resultsFilePath, $blastM0File,$blastM6File, $queryPath);
        sleep(4);
        $thr->detach;
        print $cgi->header;
	    print $cgi->start_html(-title=>"Nucleotide Blast Results",
	            -script=>{-language=>'JAVASCRIPT', -src=>'/Javascripts/blastNResultsPre.js'},
	            -style=>{-src=>'/StyleSheets/style.css'});  #this is the window title
	    print $cgi->h1("Nucleotide Blast Results: \n");
        print $cgi->start_form( -name=>'checkBlast', -action=>"/cgi-bin/BlastQuery/blastNResultsPre.cgi"),"\n";
        print $cgi->hidden(-name=>'wait', -value=>1);
        print $cgi->hidden(-name=>'iteration', -value=>'1');
        print "Creating display file. Please wait.<br>";
        print $cgi->end_form();
#        my $thr = threads->new(\&blastNResults::generateHTMLFile, $resultsFilePath, $blastM0File,$blastM6File, $queryPath);
#            $thr->detach;


	}



}