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

package blastNResults;

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;


	sub generateHTMLFile{
	    my ($resultsFilePath, $blastM0File, $blastM6File, $queryPath) = @_;
#        print "Made it in here<Br>";
#         print Dumper(@_);
#        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 %options;
	    my $resultantfile;
	    my $parsed;
	    my $cgi = CGI->new;
	    my ($maxMin, $maxMinNoZero); #hash ref



	    open (FH, ">$resultsFilePath") or die "cant temp save file, error: $!";

#        print FH $cgi->header;

	    print FH $cgi->start_html(-title=>"Nucleotide Blast Results",
	            -script=>{-language=>'JAVASCRIPT', -src=>'/Javascripts/blastNResults.js'},
	            -style=>{-src=>'/StyleSheets/style.css'}, -onLoad=>'onLoad()');  #this is the window title
	    print FH $cgi->h1("Nucleotide Blast Results: \n");
	    print FH "<p  class='subTitle'>Save Blast Results: </p>\n";
	    print FH '<small>';
	    print FH $cgi->start_form(-target=>'_blank', -name=>"saveResults",
	        -action=>"/cgi-bin/BlastQuery/saveFile.cgi", -onSubmit=>"return validateMultipleForm()"),"\n";
	    print FH 'Folder name ',  $cgi->textfield(-name=>'saveFile',-size=>20,-maxlength=>50), ' (saved in C:\BlastQueries\)';
	    print FH '<br /><br />';
	    print FH $cgi->hidden(-name=>'queryPath', -value=>$queryPath);
	    print FH $cgi->hidden(-name=>'hidden', -value=>$blastM0File);
	    print FH $cgi->hidden(-name=>'hiddenM6', -value=>$blastM6File);
	    print FH $cgi->submit(-name=>'Save Results', -label=>'Save Results', -class=>"btn",
	        -onmouseover=>"this.className='btn btnhov'", -onmouseout=>"this.className='btn'",-onclick=>"return validateSaveResultsForm()" );
	    print FH $cgi->checkbox(-name=>'saveQuery', -value=>$cgi->param('queryFile'), -label=>'Save a copy of the query file/web query as well');
	    print FH $cgi->end_form();
	    print FH '</small>';

	    print FH "<p  class='subTitle'>Queries: </p>\n";
	#    return;

	    $parsed = new ParseBlastResults();
	    $resultantfile = $queryPath.$blastM0File;
	#        print FH $resultantfile;
	#        return;
	    open (my $fh, "<$resultantfile") or die "cant open , error: $!";
	    $parsed->readBlastNView0($fh);
	    close $fh;
	    $maxMin = $parsed->getMaxMinLite(0); #0 is whether to have gaps or not
	    my $hasZero=0;
	    my $maxMinDB = $parsed->getMaxMinDBLite();
	    #$parsed->print FHBlastPView0();
	#    print FH Dumper($maxMinDB);

	    my $queries = $parsed->getAllQueryInfo();

	    print FH '<small>';
	    print FH  $cgi->checkbox(-name=>'selectall',-checked=>0,-value=>'on',-label=>'Select/Deselect all queries for multiple viewing', -onclick=>'selectDeselect()');
	    print FH '<small>';
	    printIndividualQueryMenu($queries, $cgi, FH, $parsed, $resultantfile, $blastM6File);
	#        return;
	    print FH '</small></small>';

	    print FH "<p  class='subTitle'>Please select what data you wish to view: </p>\n";
	    print FH "<small>";
	    print FH $cgi->start_form(-target=>'_blank', -name=>"viewMultiple",
	        -action=>"/cgi-bin/BlastQuery/blastNVisualizationMany.cgi", -onSubmit=>"return validateMultipleForm()"),"\n";

	    print FH $cgi->table({-class=>'multipleMenu'}),
	        $cgi->Tr(), $cgi->td({-class=>'innerLeft'}), "\n";
	    print FH $cgi->hidden(-name=>'selectedQueries');
	    print FH $cgi->hidden(-name=>'hidden', -value=>$resultantfile);
	    print FH $cgi->hidden(-name=>'hiddenM6', -value=> $queryPath.$blastM6File);
	    print FH $cgi->hidden(-name=>'queryPath', -value=>$queryPath);

	    print FH $cgi->table(), $cgi->Tr(), $cgi->td();
	    print FH "<span class='sub'>From the hit annotation:</span><br />\n";
	    my @checked=('gene', 'location', 'length');
	    my $annotationTitles = $parsed->getAnnotationOrderInfo();
	    print FH $cgi->checkbox_group(-name=>'annotationTitles', -values=>$annotationTitles, -linebreak=>'true', -default=>\@checked), "<br />\n";
	    print FH $cgi->end_td(), $cgi->end_Tr(), $cgi->end_table();
	    print FH $cgi->end_td(), $cgi->td({-class=>'innerMiddle'}), "\n";
	    #alignment information
	    print FH $cgi->table(), $cgi->Tr(), $cgi->td();
	    print FH "<span class='sub'>From the alignment:</span><br>\n";
	    @checked = ('alignment','score','evalue','identity','alignment length');
	    my $alignmentTitles = ['alignment', 'score','evalue','identity','alignment length'];
	    print FH $cgi->checkbox_group(-name=>'alignmentTitles',-values=>$alignmentTitles, -linebreak=>'true', -default=>\@checked), "<br />\n";
	    #alignment filters
	    print FH "<span class='sub'>Filters:</span><br />\n";
	    print FH 'View top ', $cgi->textfield(-name=>'topXHit',-size=>5,-maxlength=>10, -default=>1), " hits (e value filtered)<br />\n";
	    print FH 'No E values > ', $cgi->textfield(-name=>'limitEvalue',-size=>5,-maxlength=>10),"<br />\n";
	    print FH 'No % Identity < ', $cgi->textfield(-name=>'limitIdentity',-size=>5,-maxlength=>10),"%<br />\n";
	    print FH $cgi->end_td(), $cgi->end_Tr(), $cgi->end_table();

	    print FH $cgi->end_td(), $cgi->td({-class=>'innerRight'}), "\n";
	    print FH $cgi->table(), $cgi->Tr(), $cgi->td();
	    print FH "<span class='sub'>From which database?</span><br />\n";
	    my $databases = $parsed->getAllDatabases();
	    print FH $cgi->checkbox_group(-name=>'databases',-values=>$databases,-linebreak=>'true', -default=>$databases), "<br />\n";

	    print FH "<span class='sub'>Order Results by:</span><br />\n";
	    my $orderBy = ['evalue', 'sourceDB'];
	    print FH  $cgi->radio_group(-name=>'orderBy',-value=>$orderBy, -default=>'evalue'), '<br />';
	    print FH '<br />';
	    print FH  $cgi->checkbox(-name=>'showQueryData',-checked=>1,-value=>'on',-label=>'Include query length in table');
	    print FH "<br /><br />\n";
	    print FH "</small>";
	    print FH $cgi->end_td(), $cgi->end_Tr(), $cgi->end_table();

	    print FH $cgi->end_td(), $cgi->end_Tr(), $cgi->end_table();


	    my %tempLabels =('regular'=>'Normal View', 'multiview'=>'Multi Database View');
	    print FH $cgi->table(), $cgi->Tr(), $cgi->td();
	    print FH "<span class='sub'>";
	    print FH $cgi->radio_group(-name=>'viewStyle',-value=>'regular', -default=>'regular', -labels=>\%tempLabels, -rel=>'regularview');
	    print FH "</span>", "&nbsp;&nbsp;&nbsp;&nbsp;","<span class='sub'>";
	    print FH $cgi->radio_group(-name=>'viewStyle',-value=>'multiview', -default=>'regular', -labels=>\%tempLabels, -rel=>'multiview');
	    print FH "</span>";
	    print FH $cgi->end_td(), $cgi->end_Tr(),$cgi->Tr({-rel=>'regularview'}),$cgi->td({-class=>'padded'});


	    #----- Single parameter visualization -----#
	    print FH "<span class='subsub'>Single Parameter Visualizations:</span><br />\n";
	    print FH $cgi->table({-class=>'multipleMenu'}), $cgi->Tr(), $cgi->td({-class=>'singleParam'});
	    my @visualizable = ('evalue','identity','alignment length');
	    my $i=0;
	    foreach my $element (@visualizable){
	        print FH $cgi->end_td(),$cgi->td({-class=>'singleParam'}) if ($i==2);
	        print FH '<br />';
	        print FH $cgi->checkbox(-name=>'visualize', -value=>$element, -label=>"Visualize $element", -rel=>"$element");
	        print FH "<small>";
	        if ($element eq 'evalue'){
	            print FH '<span class=\'red\'> max: ', $maxMin->{$element}->[0], ', min: ', $maxMin->{$element}->[1], '</span><br />';
	            print FH $cgi->hidden(-name=>$element.'Max', -value=>$maxMin->{$element}->[0]);
	            print FH $cgi->hidden(-name=>$element.'Min', -value=>$maxMin->{$element}->[1]);
	        }else{
	            print FH '<span class=\'red\'> max: ', $maxMin->{$element}->[0], ', min: ', $maxMin->{$element}->[1], '</span><br />';
	            print FH $cgi->hidden(-name=>$element.'Max', -value=>$maxMin->{$element}->[0]);
	            print FH $cgi->hidden(-name=>$element.'Min', -value=>$maxMin->{$element}->[1]);
	        }
	        print FH $cgi->table({-class=>'visualization'});
	        print FH $cgi->Tr({-rel=>"$element"}), $cgi->td();

	        print FH 'Visual colour: ',$cgi->popup_menu(-name=>$element.'displaycolour', -values=>['red','blue','green']);
	        if ($element eq 'evalue'){
	            my %labels = ('0,0,255'=>'blue','0,255,0'=>'green', '255,0,0'=>'red', '255,255,0'=>'yellow','0,255,255'=>'cyan','255,0,255'=>'magenta','255,255,255'=>'white','0,0,0'=>'black');
	            print FH ' Zero e value colour: ',$cgi->popup_menu(-name=>$element.'zero', -values=>[('0,0,255','0,255,0', '255,0,0', '255,255,0','0,255,255','255,0,255','255,255,255','0,0,0')], -labels=>\%labels);
	        }
	        print FH '<br />';

	        my %temp =(auto=>'Auto range with ');
	        print FH  $cgi->radio_group(-name=>$element.'visualMethod',-value=>'auto',-onclick=>"enableOverwrite('".$element.'visualMethod'."','".$element.'bin'."', 0)", -default=>'auto', -labels=>\%temp, -rel=>'none');
	        print FH $cgi->textfield(-name=>$element.'bin',-size=>5,-maxlength=>5), ' bins or ';
	        %temp =(threshold=>'Set threshold');
	        print FH  $cgi->radio_group(-name=>$element.'visualMethod',-value=>'threshold', -onclick=>"enableOverwrite('".$element.'visualMethod'."','".$element.'bin'."',0)", -default=>'auto', -labels=>\%temp, -rel=>"range$element");

	        print FH $cgi->table({-class=>'threshold'});
	        print FH $cgi->Tr({-rel=>"range$element"}), $cgi->td();

	        print FH $cgi->table({-class=>'threshold', -id=>$element});
	        print FH $cgi->Tr(), $cgi->td();
	        %temp =(colour=>'Colour ', autorange=>'Auto Range with ');
	        print FH 'Range: [', $cgi->textfield(-name=>$element.'start1',-size=>5,-maxlength=>10), ', ',
	            $cgi->textfield(-name=>$element.'end1',-size=>5,-maxlength=>10), ')',
	            $cgi->radio_group(-name=>$element.'colour1',-value=>'colour', -default=>'colour', -labels=>\%temp, -onClick=>"enableOverwrite2('$element"."colour1', '$element"."bin1', 1,'$element"."specifiedcolour1')");
	        my %labels = ('0,0,255'=>'blue','0,255,0'=>'green', '255,0,0'=>'red', '255,255,0'=>'yellow','0,255,255'=>'cyan','255,0,255'=>'magenta','255,255,255'=>'white','0,0,0'=>'black');
	        print FH $cgi->popup_menu(-name=>$element.'specifiedcolour1', -values=>[('0,0,255','0,255,0', '255,0,0', '255,255,0','0,255,255','255,0,255','255,255,255','0,0,0')], -labels=>\%labels);
	        print FH ' ',$cgi->radio_group(-name=>$element.'colour1',-value=>'autorange',-default=>'colour', -labels=>\%temp, -onClick=>"enableOverwrite2('$element"."colour1', '$element"."bin1', 1,'$element"."specifiedcolour1')"),
	            $cgi->textfield(-name=>$element.'bin1',-size=>5,-maxlength=>5, -class=>'disabled'), ' bins';
	        print FH $cgi->end_td(), $cgi->end_Tr();
	        print FH $cgi->end_table();
	        print FH $cgi->button(-name=>'add', -value=>'Add another range', -onClick=>"addRow(\"$element\", \"$element\")");
	        print FH $cgi->button(-name=>'remove', -value=>'Remove last range', -onClick=>"removeRowFromTable(\"$element\")");
	        print FH $cgi->checkbox(-name=>$element.'overwrite', -value=>1, -label=>'Overwrite');
	        print FH $cgi->end_td(), $cgi->end_Tr();
	        print FH $cgi->end_table();

	        print FH $cgi->end_td(), $cgi->end_Tr();
	        print FH $cgi->end_table();
	        print FH "</small>";
	        $i++;
	    }
	    print FH $cgi->end_td(), $cgi->end_Tr(), $cgi->end_table();
	    print FH '<br />';

	    #----- Multiple parameter visualization -----#
	    print FH "<span class='subsub'>Multiple Parameter Visualizations:</span>",
	        $cgi->checkbox(-name=>'multiParam',-checked=>0,-value=>1,-label=>'', -rel=>'multiple'),"<br /><br />\n";
	    print FH $cgi->table({-class=>'multiVisual'}), $cgi->Tr({-rel=>'multiple'}), $cgi->td();
	    print FH '<small>';
	    print FH $cgi->table({-class=>'sets', -id=>'Multiple1'}), $cgi->Tr(), $cgi->td({-class=>'blue'});
	    print FH '<span class=\'bold\'>&nbsp;&nbsp;&nbsp;&nbsp;Visualization 1: </span>';
	    print FH 'Visual colour: ',$cgi->popup_menu(-name=>'Multiple1displaycolour', -values=>['red','blue','green']);
	    print FH $cgi->checkbox(-name=>'Multiple1overwrite', -value=>1, -label=>'Overwrite');
	    print FH $cgi->table({-class=>'ranges',-id=>'Multiple1Range1'}), $cgi->Tr(), $cgi->td({-class=>'ranges'});
	    print FH '<span class="green">Range 1: </span>';
	    my %temp =('auto'=>'Auto range with ');
	    print FH $cgi->radio_group(-name=>'Multiple1Range1Style',-value=>'auto', -default=>'auto', -labels=>\%temp, -rel=>'none', -onClick=>"enableOverwrite2('Multiple1Range1Style', 'Multiple1Range1bin', 0, 'Multiple1Range1specifiedcolour')");
	    print FH $cgi->textfield(-name=>'Multiple1Range1bin',-size=>5,-maxlength=>5), ' bins or ';
	    %temp =('colour'=>'Specify colour: ');
	    print FH  $cgi->radio_group(-name=>'Multiple1Range1Style',-value=>'colour', -default=>'auto', -labels=>\%temp, -onClick=>"enableOverwrite2('Multiple1Range1Style', 'Multiple1Range1bin', 0,'Multiple1Range1specifiedcolour')");
	    my %colourLabels = ('0,0,255'=>'blue','0,255,0'=>'green', '255,0,0'=>'red', '255,255,0'=>'yellow','0,255,255'=>'cyan','255,0,255'=>'magenta','255,255,255'=>'white','0,0,0'=>'black');
	    print FH $cgi->popup_menu(-name=>'Multiple1Range1specifiedcolour', -values=>[('0,0,255','0,255,0', '255,0,0', '255,255,0','0,255,255','255,0,255','255,255,255','0,0,0')], -labels=>\%colourLabels, -disabled=>'true');

	    print FH $cgi->end_td(), $cgi->end_Tr(), $cgi->Tr(), $cgi->td();
	    print FH $cgi->table({-class =>'parameters',-id=>'Multiple1Range1Param1'}), $cgi->Tr(), $cgi->td();
	    my %paramLabels = ('evalue'=>'E Value','identity'=>'Identity', 'alignment length'=>'Alignment Length');
	    #my %paramAttrs = ('evalue'=>{'rel'=>'includeZero'},'identity'=>{'rel'=>'none'}, 'gaps'=>{'rel'=>'none'}, 'alignment length'=>{'rel'=>'none'});
	    print FH '<span class="brown"> Parameter:</span> ',$cgi->popup_menu(-name=>'Multiple1Range1Param1', -values=>\@visualizable, -labels=>\%paramLabels);
	    print FH ' Range: [',$cgi->textfield(-name=>'Multiple1Range1Param1Start',-size=>5,-maxlength=>10), ',',
	        $cgi->textfield(-name=>'Multiple1Range1Param1End',-size=>5,-maxlength=>10),')';
	    print FH $cgi->end_td(), $cgi->td();
	    print FH $cgi->checkbox(-name=>'Multiple1Range1Param1Zero', -value=>1, -label=>"Include zero e values");
	    print FH $cgi->end_td(), $cgi->end_Tr();
	    print FH $cgi->end_table();
	    print FH '&nbsp;&nbsp;&nbsp;&nbsp;';
	    print FH $cgi->button(-name=>'addParam', -value=>'Add another parameter', -onClick=>"addParamRow('Multiple1Range1Param1','Multiple1Range1' )",
	        -class=>"btn2",-onmouseout=>"this.className='btn2'");
	    print FH $cgi->button(-name=>'removeParam', -value=>'Remove last parameter', -onClick=>"removeRowFromTable('Multiple1Range1Param1')",
	        -class=>"btn2",-onmouseout=>"this.className='btn2'");
	    print FH $cgi->end_td(), $cgi->end_Tr();
	    print FH $cgi->end_table();
	    print FH '&nbsp;&nbsp;&nbsp;&nbsp;';
	    print FH $cgi->button(-name=>'addRange', -value=>'Add another range', -onClick=>"addRangeRow('Multiple1Range1','Multiple1' )",
	        -class=>"btn3", -onmouseout=>"this.className='btn3'");
	    print FH $cgi->button(-name=>'removeRange', -value=>'Remove last range', -onClick=>"remove2RowsFromTable('Multiple1Range1')",
	        -class=>"btn3", -onmouseout=>"this.className='btn3'");
	    print FH $cgi->end_td(), $cgi->end_Tr();
	    print FH '</small>';
	    print FH $cgi->end_table();

	    print FH $cgi->button(-name=>'addSet', -value=>'Add another visualization', -onClick=>"addSetRow(\"Multiple1\", \"Multiple\")",
	        -class=>"btn4", -onmouseout=>"this.className='btn4'");
	    print FH $cgi->button(-name=>'removeSet', -value=>'Remove last visualization', -onClick=>"remove2RowsFromTable(\"Multiple1\")",
	        -class=>"btn4", -onmouseout=>"this.className='btn4'");
	    print FH $cgi->end_td(), $cgi->td({-class=>'bottom'});
	    print FH '<small>';
	    #print FH the max and min infos
	    foreach my $element (@visualizable){
	        if ($element eq 'evalue'){
	            print FH $element,':<span class=\'red\'> max: ', $maxMin->{$element}->[0], ', min: ', $maxMin->{$element}->[1], '</span><br />';
	        }else{
	            print FH $element, ':<span class=\'red\'> max: ', $maxMin->{$element}->[0], ', min: ', $maxMin->{$element}->[1], '</span><br />';
	        }
	    }
	    print FH '<br /><br /><br />';
	    print FH '</small>';
	    print FH $cgi->end_td(),$cgi->end_Tr();
	    print FH $cgi->end_table();

	    print FH $cgi->end_td(), $cgi->end_Tr(),$cgi->Tr({-rel=>'multiview'}),$cgi->td({-class=>'padded'});

	    %tempLabels =('single'=>'Single Parameter Visualizations', 'multi'=>'Multiple Parameters Visualizations');
	    print FH $cgi->table(), $cgi->Tr(), $cgi->td();
	    print FH "<span class='subsub'>";
	    print FH $cgi->radio_group(-name=>'paramStyle',-value=>'single', -default=>'single', -labels=>\%tempLabels, -rel=>'singleParamStyle');
	    print FH "</span>", "&nbsp;&nbsp;&nbsp;&nbsp;", "<span class='subsub'>";
	    print FH $cgi->radio_group(-name=>'paramStyle',-value=>'multi', -default=>'single', -labels=>\%tempLabels, -rel=>'multiParamStyle');
	    print FH $cgi->end_td(),$cgi->end_Tr(), $cgi->Tr({-rel=>'singleParamStyle'}), $cgi->td({-class=>'padded'});
	    print FH "</span>";
	    #----- Single parameter visualization -----#

	    print FH $cgi->table(), $cgi->Tr(), $cgi->td();
	    print FH '<small>';

	    print FH $cgi->table({-class=>'visualization'}), $cgi->Tr(), $cgi->td();
	    %paramLabels = ('evalue'=>'E Value','identity'=>'Identity', 'alignment length'=>'Alignment Length');
	    print FH '<span class="brown"> Parameter:</span> ',$cgi->popup_menu(-name=>'visualtype', -values=>\@visualizable, -labels=>\%paramLabels , -onchange=>"enableEvalue()");

	    print FH 'Visual colour: ',$cgi->popup_menu(-name=>'singledisplaycolour', -values=>['red','blue','green']);

	    my %labels = ('0,0,255'=>'blue','0,255,0'=>'green', '255,0,0'=>'red', '255,255,0'=>'yellow','0,255,255'=>'cyan','255,0,255'=>'magenta','255,255,255'=>'white','0,0,0'=>'black');
	    print FH ' Zero e value colour: ',$cgi->popup_menu(-name=>'singlezero',-values=>[('0,0,255','0,255,0', '255,0,0', '255,255,0','0,255,255','255,0,255','255,255,255','0,0,0')], -labels=>\%labels);

	    print FH '<br />';

	    %temp =(auto=>'Auto range with ');
	    print FH  $cgi->radio_group(-name=>'singlevisualMethod',-value=>'auto', -default=>'auto', -labels=>\%temp, -rel=>'none', -onclick=>"enableOverwrite('singlevisualMethod','singlebin',0)");
	    print FH $cgi->textfield(-name=>'singlebin',-size=>5,-maxlength=>5), ' bins or ';
	    %temp =(threshold=>'Set threshold');
	    print FH  $cgi->radio_group(-name=>'singlevisualMethod',-value=>'threshold', -default=>'auto', -labels=>\%temp, -rel=>'singleRange', -onclick=>"enableOverwrite('singlevisualMethod','singlebin',0)");
	    print FH $cgi->table({-class=>'threshold'}), $cgi->Tr({-rel=>'singleRange'}), $cgi->td();

	    print FH $cgi->table({-class=>'threshold', -id=>'single'}), $cgi->Tr(), $cgi->td();
	    %temp =(colour=>'Colour ', autorange=>'Auto Range with ');
	    print FH 'Range: [', $cgi->textfield(-name=>'singlestart1',-size=>5,-maxlength=>10), ', ',
	        $cgi->textfield(-name=>'singleend1',-size=>5,-maxlength=>10), ')',
	        $cgi->radio_group(-name=>'singlecolour1',-value=>'colour', -default=>'colour', -labels=>\%temp, -onClick=>"enableOverwrite2('singlecolour1','singlebin1',1,'singlespecifiedcolour1' )");
	    %labels = ('0,0,255'=>'blue','0,255,0'=>'green', '255,0,0'=>'red', '255,255,0'=>'yellow','0,255,255'=>'cyan','255,0,255'=>'magenta','255,255,255'=>'white','0,0,0'=>'black');
	    print FH $cgi->popup_menu(-name=>'singlespecifiedcolour1', -values=>[('0,0,255','0,255,0', '255,0,0', '255,255,0','0,255,255','255,0,255','255,255,255','0,0,0')], -labels=>\%labels);
	    print FH ' ',$cgi->radio_group(-name=>'singlecolour1',-value=>'autorange',-default=>'colour', -labels=>\%temp, -onClick=>"enableOverwrite2('singlecolour1','singlebin1',1,'singlespecifiedcolour1' )"),
	        $cgi->textfield(-name=>'singlebin1',-size=>5,-maxlength=>5,-disabled=>'true', -class=>'disabled'), ' bins';
	    print FH $cgi->end_td(), $cgi->end_Tr(), $cgi->end_table();
	    print FH $cgi->button(-name=>'add', -value=>'Add another range', -onClick=>"addRow(\"single\", \"single\")");
	    print FH $cgi->button(-name=>'remove', -value=>'Remove last range', -onClick=>"removeRowFromTable(\"single\")");
	    print FH $cgi->checkbox(-name=>'singleoverwrite', -value=>1, -label=>'Overwrite');
	    print FH $cgi->end_td(), $cgi->end_Tr(), $cgi->end_table();

	    print FH $cgi->end_td(), $cgi->end_Tr(), $cgi->end_table();
	    print FH '</small>';
	    print FH $cgi->end_td(), $cgi->td();
	    print FH '<small>';
	    #print FH the max and min infos
	    foreach my $element (@visualizable){
	        if ($element eq 'evalue'){
	            print FH $element,':<span class=\'red\'> max: ', $maxMinDB->{$element}->[0], ', min: ', $maxMinDB->{$element}->[1], '</span><br />';
	            print FH $cgi->hidden(-name=>$element.'Max', -value=>$maxMinDB->{$element}->[0]);
	            print FH $cgi->hidden(-name=>$element.'Min', -value=>$maxMinDB->{$element}->[1]);
	            print FH 'Zero e value exists<br>' if $hasZero;
	            print FH "haszero $hasZero<br>";
	        }else{
	            print FH $element, ':<span class=\'red\'> max: ', $maxMinDB->{$element}->[0], ', min: ', $maxMinDB->{$element}->[1], '</span><br />';
	            print FH $cgi->hidden(-name=>$element.'Max', -value=>$maxMinDB->{$element}->[0]);
	            print FH $cgi->hidden(-name=>$element.'Min', -value=>$maxMinDB->{$element}->[1]);
	        }
	    }

	    print FH '</small>';
	    print FH $cgi->end_td(),$cgi->end_Tr(), $cgi->end_table(); #end single param table
	    #ends single parameter visualization

	    print FH $cgi->end_td(),$cgi->end_Tr(), $cgi->Tr({-rel=>'multiParamStyle'}), $cgi->td({-class=>'padded'});

	    #----- Multiple parameter visualization -----#
	    print FH $cgi->table(), $cgi->Tr(), $cgi->td();
	    print FH '<small>';

	    print FH $cgi->table({-class=>'sets', -id=>'Multiple1'}), $cgi->Tr(), $cgi->td({-class=>'blue'});
	    print FH '<span class=\'bold\'>&nbsp;&nbsp;&nbsp;&nbsp;Visualization 1: </span>';
	    print FH 'Visual colour: ',$cgi->popup_menu(-name=>'Multiple1displaycolour', -values=>['red','blue','green']);
	    print FH $cgi->checkbox(-name=>'Multiple1overwrite', -value=>1, -label=>'Overwrite');

	    print FH $cgi->table({-class=>'ranges',-id=>'Multiple1Range1'}), $cgi->Tr(), $cgi->td({-class=>'ranges'});
	    print FH '<span class="green">Range 1: </span>';
	    %temp =('auto'=>'Auto range with ');
	    print FH $cgi->radio_group(-name=>'Multiple1Range1Style',-value=>'auto', -default=>'auto', -labels=>\%temp, -rel=>'none', -onClick=>"enableOverwrite2('Multiple1Range1Style','Multiple1Range1bin',0, 'Multiple1Range1specifiedcolour')");
	    print FH $cgi->textfield(-name=>'Multiple1Range1bin',-size=>5,-maxlength=>5), ' bins or ';
	    %temp =(threshold=>'Specify colour: ');
	    print FH  $cgi->radio_group(-name=>'Multiple1Range1Style',-value=>'colour', -default=>'auto', -labels=>\%temp, -onClick=>"enableOverwrite2('Multiple1Range1Style','Multiple1Range1bin',0, 'Multiple1Range1specifiedcolour')");
	    %colourLabels = ('0,0,255'=>'blue','0,255,0'=>'green', '255,0,0'=>'red', '255,255,0'=>'yellow','0,255,255'=>'cyan','255,0,255'=>'magenta','255,255,255'=>'white','0,0,0'=>'black');
	    print FH $cgi->popup_menu(-name=>'Multiple1Range1specifiedcolour', -values=>[('0,0,255','0,255,0', '255,0,0', '255,255,0','0,255,255','255,0,255','255,255,255','0,0,0')], -labels=>\%colourLabels, -disabled=>'true');
	    print FH $cgi->end_td(), $cgi->end_Tr(), $cgi->Tr(), $cgi->td();

	    print FH $cgi->table({-class =>'parameters',-id=>'Multiple1Range1Param1'}), $cgi->Tr(), $cgi->td();
		%paramLabels = ('evalue'=>'E Value','identity'=>'Identity', 'alignment length'=>'Alignment Length');
	    #my %paramAttrs = ('evalue'=>{'rel'=>'includeZero'},'identity'=>{'rel'=>'none'}, 'gap'=>{'rel'=>'none'}, 'alignment length'=>{'rel'=>'none'});
	    print FH '<span class="brown"> Parameter:</span> ',$cgi->popup_menu(-name=>'Multiple1Range1Param1', -values=>\@visualizable, -labels=>\%paramLabels);
	    print FH ' Range: [',$cgi->textfield(-name=>'Multiple1Range1Param1Start',-size=>5,-maxlength=>10), ',',
	        $cgi->textfield(-name=>'Multiple1Range1Param1End',-size=>5,-maxlength=>10),')';
	    print FH $cgi->end_td(), $cgi->td();
	    print FH $cgi->checkbox(-name=>'Multiple1Range1Param1Zero', -value=>1, -label=>"Include zero e values");
	    print FH $cgi->end_td(), $cgi->end_Tr(), $cgi->end_table(); #end parameters table

	    print FH '&nbsp;&nbsp;&nbsp;&nbsp;';
	    print FH $cgi->button(-name=>'addParam', -value=>'Add another parameter', -onClick=>"addParamRow('Multiple1Range1Param1','Multiple1Range1' )",
	        -class=>"btn2",-onmouseout=>"this.className='btn2'");
	    print FH $cgi->button(-name=>'removeParam', -value=>'Remove last parameter', -onClick=>"removeRowFromTable('Multiple1Range1Param1')",
	        -class=>"btn2",-onmouseout=>"this.className='btn2'");
	    print FH $cgi->end_td(), $cgi->end_Tr(), $cgi->end_table(); #end ranges table

	    print FH '&nbsp;&nbsp;&nbsp;&nbsp;';
	    print FH $cgi->button(-name=>'addRange', -value=>'Add another range', -onClick=>"addRangeRow('Multiple1Range1','Multiple1' )",
	        -class=>"btn3", -onmouseout=>"this.className='btn3'");
	    print FH $cgi->button(-name=>'removeRange', -value=>'Remove last range', -onClick=>"remove2RowsFromTable('Multiple1Range1')",
	        -class=>"btn3", -onmouseout=>"this.className='btn3'");
	    print FH '</small>';
	    print FH $cgi->end_td(), $cgi->end_Tr(), $cgi->end_table();#end multiple table

	    print FH $cgi->end_td(), $cgi->td({-class=>'bottom'});
	    print FH '<small>';
	    #print FH the max and min infos
	    foreach my $element (@visualizable){
	        if ($element eq 'evalue'){
	            print FH $element,':<span class=\'red\'> max: ', $maxMinDB->{$element}->[0], ', min: ', $maxMinDB->{$element}->[1], '</span><br />';
	            print FH 'Zero e value exists<br>' if $hasZero;
	        }else{
	            print FH $element, ':<span class=\'red\'> max: ', $maxMinDB->{$element}->[0], ', min: ', $maxMinDB->{$element}->[1], '</span><br />';
	        }
	    }
	    print FH '<br /><br /><br />';
	    print FH '</small>';
	    print FH $cgi->end_td(),$cgi->end_Tr(), $cgi->end_table(); #end multiparam table

	    print FH $cgi->end_td(), $cgi->end_Tr(),$cgi->end_table();
	    print FH $cgi->end_td(), $cgi->end_Tr(),$cgi->end_table();

	#        print FH '<br />';
	    print FH '<br />';
	#        print FH "<p  class='subTitle'>  </p>\n";
	    #form buttons
	    print FH $cgi->button(-name=>'Cancel', -label=>'Cancel', -class=>"btn", -onClick=>"parent.location='/cgi-bin/BlastQuery/blastPMain.cgi'",
	        -onmouseover=>"this.className='btn btnhov'", -onmouseout=>"this.className='btn'"), '&nbsp;&nbsp;&nbsp;&nbsp;';
	    print FH $cgi->submit(-name=>'Perform Blast', -label=>'View Results', -class=>"btn",
	        -onmouseover=>"this.className='btn btnhov'", -onmouseout=>"this.className='btn'", -onclick=>"return changeSubmit()");
	    print FH $cgi->hidden(-name=>'queryPath', -value=>$queryPath);
	    print FH $cgi->end_form();


	    print FH "<p>",$cgi->hr(), $cgi->a({-href=>"/"}, "<p>Back to Main");
        print FH "<br>\nthis is the end";
	    close FH;
	}


	sub querySummary{
		my ($query, $FH) = @_;
	    my $total = 0;
        my @dbs = keys %{ $query->[2]};
	    foreach my $db (@dbs){
	       	$total +=  $query->[2]->{$db};
	   	}
	    print $FH "<br />&nbsp;&nbsp;&nbsp;&nbsp;<span class='blue'>Total hits: $total</span>, from databases: ";
        foreach my $db (@dbs){
			print $FH "<span class='orange'>$db</span>($query->[2]->{$db}) ";
	   	}
        print $FH '<br />';

	}

	sub printIndividualQueryMenu{
		my ($queries, $cgi, $FH, $parsed, $resultantfile, $blastM6File) = @_;
        my @qNames = keys %{$queries};
        my $size = @qNames;
        print $FH "**query total: ",$size, "<br>";
#        print FH Dumper($queries);
    	my $i = 0;
    	foreach my $query (@qNames){
        	$i++;
            my @dbs = keys %{ $queries->{$query}->[2]};
     		print $FH $cgi->table({-class=>'individual'}), "\n";

            #----- summary of query -----#
			print $FH $cgi->Tr(), $cgi->td({-class=>'individual'}), "\n";
            print $FH '<span class="red">';
       		print $FH $cgi->checkbox(-name=>'selectedQueries',-checked=>0,-value=>"$query", -label=>"$query", -onClick=>"checkValue(this)");
            print $FH '</span>';
            querySummary($queries->{$query}, $FH);
            print $FH '&nbsp;&nbsp;&nbsp;&nbsp;';
	        print $FH $cgi->checkbox(-name=>"$i", -checked=>0, -value=>"", -label=>"View this query separately", -rel=>"$i");
	       	print $FH $cgi->end_td(), $cgi->end_Tr(), "\n";

            #----- form starts -----#
	       	print $FH $cgi->Tr({-rel=>"$i"}), $cgi->td({-class=>'individual'}), "\n";
	       	print $FH $cgi->start_form(-target=>'_blank', -name=>"viewOne", -action=>"/cgi-bin/BlastQuery/blastNVisualizationOne.cgi"),"\n";

       	   	print $FH $cgi->table({-class=>'individualMenu'});

            #----- Hit annotation info -----#
            print $FH $cgi->Tr(), $cgi->td({-class=>'innerLeft'}), "\n";
            print $FH $cgi->table(), $cgi->Tr(), $cgi->td();
	        print $FH "<span class='sub'>From the hit annotation:</span><br />\n";
	        my @checked=('gene', 'location', 'length');
       		my $annotationTitles = $parsed->getAnnotationOrderInfo();
       		print $FH $cgi->checkbox_group(-name=>'annotationTitles', -values=>$annotationTitles, -linebreak=>'true', -default=>\@checked), "<br />\n";
            print $FH $cgi->end_td(), $cgi->end_Tr(), $cgi->end_table();

            print $FH $cgi->end_td(), $cgi->td({-class=>'innerMiddle'}), "\n";
	        #alignment information
	        print $FH $cgi->table(), $cgi->Tr(), $cgi->td();
	        print $FH "<span class='sub'>From the alignment:</span><br>\n";
	        @checked = ('alignment','score', 'evalue','identity','alignment length');
	        my $alignmentTitles = ['alignment','score', 'evalue','identity','alignment length'];
	            print $FH $cgi->checkbox_group(-name=>'alignmentTitles', -values=>$alignmentTitles, -linebreak=>'true', -default=>\@checked), "<br>\n";

	        #alignment filters
	        print $FH "<span class='sub'>Filters:</span><br />\n";
	        print $FH 'View top ', $cgi->textfield(-name=>'topXHit',-size=>5,-maxlength=>10, -default=>10), " hits (e value filtered)<br />\n";
	        print $FH 'No E values > ', $cgi->textfield(-name=>'limitEvalue',-size=>5,-maxlength=>10),"<br />\n";
	        print $FH 'No % Identity < ', $cgi->textfield(-name=>'limitIdentity',-size=>5,-maxlength=>10),"%<br />\n";
	        print $FH $cgi->end_td(), $cgi->end_Tr(), $cgi->end_table();

        	#last column
	        print $FH $cgi->end_td(), $cgi->td({-class=>'innerRight'}), "\n";
	        print $FH $cgi->table(), $cgi->Tr(), $cgi->td();
	        print $FH "<span class='sub'>From which database?</span><br />\n";
	        print $FH $cgi->checkbox_group(-name=>'databases',-values=>\@dbs,-linebreak=>'true', -default=>\@dbs), "<br />\n";

	        print $FH "<span class='sub'>Order Results by:</span><br />\n";
	        my $orderBy = ['evalue', 'sourceDB'];
	        print $FH  $cgi->radio_group(-name=>'orderBy',-value=>$orderBy, -default=>'evalue'), '<br />';
            print $FH '<br />';
	        print $FH  $cgi->checkbox(-name=>'showQueryData',-checked=>1,-value=>'on',-label=>'Include query length and ID in table');
	        print $FH "<br /><br />\n";
	        print $FH "</small>";


            #----- submit button -----#
            print $FH $cgi->submit(-name=>'Perform Blast', -label=>'View Results', -class=>"btn",
        	-onmouseover=>"this.className='btn btnhov'", -onmouseout=>"this.className='btn'");
    		print $FH $cgi->end_td(), $cgi->end_Tr(), $cgi->end_table();
            print $FH $cgi->hidden(-name=>'hidden', -default=>[$query, $resultantfile, $blastM6File]);
            print $FH $cgi->end_td(), $cgi->end_Tr(), $cgi->end_table();
    		print $FH $cgi->end_form();
       		print $FH $cgi->end_td(), $cgi->end_Tr(), "\n";
       		print $FH $cgi->end_table();
            print $FH "<br />";
    	}

	}

	sub isInArray{
	    my ($element, $array) = @_;
	    foreach (@$array){
        	return 1 if ($element eq $_);
	    }
		return 0;
	}
1;