Ok here is the code for the main script. It is accessed by by another script that passes in a form variable that has its name starting with 'view'. A folder name is also passed in where the files to be read are located.

I had shortened the file, so if there's useless variables please ignore :-) 

#!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 blas
+t 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 t
+he 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\\h
+tdocs\\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=>'/Javasc
+ripts/blastNResultsPre.js'},
#                    -style=>{-src=>'/StyleSheets/style.css'});
#            print $cgi->start_form( -name=>'checkBlast', -action=>"/c
+gi-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=>'/Javasc
+ripts/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=>'/Javascr
+ipts/blastNResultsPre.js'},
                    -style=>{-src=>'/StyleSheets/style.css'});
            print $cgi->start_form( -name=>'checkBlast', -action=>"/cg
+i-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, $blastM0Fil
+e, $blastM6File, $queryPath);
        my $thr = threads->new(\&blastNResults::generateHTMLFile, $res
+ultsFilePath, $blastM0File,$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 t
+he window title
        print $cgi->h1("Nucleotide Blast Results: \n");
        print $cgi->start_form( -name=>'checkBlast', -action=>"/cgi-bi
+n/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, $re
+sultsFilePath, $blastM0File,$blastM6File, $queryPath);
#            $thr->detach;


    }



}

[download]


and here is the module code for the actual reading and writing of the html file 

#!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 blas
+t 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 h
+old 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\\Apach
+e2\\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, er
+ror: $!";

#        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=>'on
+Load()');  #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=>"saveResul
+ts",
            -action=>"/cgi-bin/BlastQuery/saveFile.cgi", -onSubmit=>"r
+eturn validateMultipleForm()"),"\n";
        print FH 'Folder name ',  $cgi->textfield(-name=>'saveFile',-s
+ize=>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 Res
+ults', -class=>"btn",
            -onmouseover=>"this.className='btn btnhov'", -onmouseout=>
+"this.className='btn'",-onclick=>"return validateSaveResultsForm()" )
+;
        print FH $cgi->checkbox(-name=>'saveQuery', -value=>$cgi->para
+m('queryFile'), -label=>'Save a copy of the query file/web query as w
+ell');
        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 gap
+s 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  $cgi->checkbox(-name=>'selectall',-checked=>0,-value
+=>'on',-label=>'Select/Deselect all queries for multiple viewing', -o
+nclick=>'selectDeselect()');
        print FH '<small>';
        printIndividualQueryMenu($queries, $cgi, FH, $parsed, $resulta
+ntfile, $blastM6File);
    #        return;
        print FH '</small></small>';

        print FH "<p  class='subTitle'>Please select what data you wis
+h to view: </p>\n";
        print FH "<small>";
        print FH $cgi->start_form(-target=>'_blank', -name=>"viewMulti
+ple",
            -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 $cgi->checkbox_group(-name=>'annotationTitles', -valu
+es=>$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=>'limitIden
+tity',-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 $cgi->checkbox_group(-name=>'databases',-values=>$dat
+abases,-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,-v
+alue=>'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='s
+ub'>";
        print FH $cgi->radio_group(-name=>'viewStyle',-value=>'multivi
+ew', -default=>'regular', -labels=>\%tempLabels, -rel=>'multiview');
        print FH "</span>";
        print FH $cgi->end_td(), $cgi->end_Tr(),$cgi->Tr({-rel=>'regul
+arview'}),$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(), $c
+gi->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 $cgi->checkbox(-name=>'visualize', -value=>$eleme
+nt, -label=>"Visualize $element", -rel=>"$element");
            print FH "<small>";
            if ($element eq 'evalue'){
                print FH '<span class=\'red\'> max: ', $maxMin->{$elem
+ent}->[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: ', $maxMin->{$elem
+ent}->[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: ',$cgi->popup_menu(-name=>$elemen
+t.'displaycolour', -values=>['red','blue','green']);
            if ($element eq 'evalue'){
                my %labels = ('0,0,255'=>'blue','0,255,0'=>'green', '2
+55,0,0'=>'red', '255,255,0'=>'yellow','0,255,255'=>'cyan','255,0,255'
+=>'magenta','255,255,255'=>'white','0,0,0'=>'black');
                print FH ' Zero e value colour: ',$cgi->popup_menu(-na
+me=>$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=>\%la
+bels);
            }
            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, -re
+l=>'none');
            print FH $cgi->textfield(-name=>$element.'bin',-size=>5,-m
+axlength=>5), ' bins or ';
            %temp =(threshold=>'Set threshold');
            print FH  $cgi->radio_group(-name=>$element.'visualMethod'
+,-value=>'threshold', -onclick=>"enableOverwrite('".$element.'visualM
+ethod'."','".$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.'star
+t1',-size=>5,-maxlength=>10), ', ',
                $cgi->textfield(-name=>$element.'end1',-size=>5,-maxle
+ngth=>10), ')',
                $cgi->radio_group(-name=>$element.'colour1',-value=>'c
+olour', -default=>'colour', -labels=>\%temp, -onClick=>"enableOverwri
+te2('$element"."colour1', '$element"."bin1', 1,'$element"."specifiedc
+olour1')");
            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'=>'m
+agenta','255,255,255'=>'white','0,0,0'=>'black');
            print FH $cgi->popup_menu(-name=>$element.'specifiedcolour
+1', -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=>"en
+ableOverwrite2('$element"."colour1', '$element"."bin1', 1,'$element".
+"specifiedcolour1')"),
                $cgi->textfield(-name=>$element.'bin1',-size=>5,-maxle
+ngth=>5, -class=>'disabled'), ' bins';
            print FH $cgi->end_td(), $cgi->end_Tr();
            print FH $cgi->end_table();
            print FH $cgi->button(-name=>'add', -value=>'Add another r
+ange', -onClick=>"addRow(\"$element\", \"$element\")");
            print FH $cgi->button(-name=>'remove', -value=>'Remove las
+t range', -onClick=>"removeRowFromTable(\"$element\")");
            print FH $cgi->checkbox(-name=>$element.'overwrite', -valu
+e=>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 Visualizatio
+ns:</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(), $cgi->td({-class=>'blue'});
        print FH '<span class=\'bold\'>&nbsp;&nbsp;&nbsp;&nbsp;Visuali
+zation 1: </span>';
        print FH 'Visual colour: ',$cgi->popup_menu(-name=>'Multiple1d
+isplaycolour', -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',-valu
+e=>'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',-val
+ue=>'colour', -default=>'auto', -labels=>\%temp, -onClick=>"enableOve
+rwrite2('Multiple1Range1Style', 'Multiple1Range1bin', 0,'Multiple1Ran
+ge1specifiedcolour')");
        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=>'Multiple1Range1specifiedcolo
+ur', -values=>[('0,0,255','0,255,0', '255,0,0', '255,255,0','0,255,25
+5','255,0,255','255,255,255','0,0,0')], -labels=>\%colourLabels, -dis
+abled=>'true');

        print FH $cgi->end_td(), $cgi->end_Tr(), $cgi->Tr(), $cgi->td(
+);
        print FH $cgi->table({-class =>'parameters',-id=>'Multiple1Ran
+ge1Param1'}), $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, -label
+s=>\%paramLabels);
        print FH ' Range: [',$cgi->textfield(-name=>'Multiple1Range1Pa
+ram1Start',-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', -v
+alue=>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','Multiple1
+Range1' )",
            -class=>"btn2",-onmouseout=>"this.className='btn2'");
        print FH $cgi->button(-name=>'removeParam', -value=>'Remove la
+st 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 la
+st 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 vi
+sualization', -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: ', $maxM
+in->{$element}->[0], ', min: ', $maxMin->{$element}->[1], '</span><br
+ />';
            }else{
                print FH $element, ':<span class=\'red\'> max: ', $max
+Min->{$element}->[0], ', min: ', $maxMin->{$element}->[1], '</span><b
+r />';
            }
        }
        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=>'multi
+view'}),$cgi->td({-class=>'padded'});

        %tempLabels =('single'=>'Single Parameter Visualizations', 'mu
+lti'=>'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=>'singl
+eParamStyle'}), $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', 'a
+lignment length'=>'Alignment Length');
        print FH '<span class="brown"> Parameter:</span> ',$cgi->popup
+_menu(-name=>'visualtype', -values=>\@visualizable, -labels=>\%paramL
+abels , -onchange=>"enableEvalue()");

        print FH 'Visual colour: ',$cgi->popup_menu(-name=>'singledisp
+laycolour', -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'=>'magen
+ta','255,255,255'=>'white','0,0,0'=>'black');
        print FH ' Zero e value colour: ',$cgi->popup_menu(-name=>'sin
+glezero',-values=>[('0,0,255','0,255,0', '255,0,0', '255,255,0','0,25
+5,255','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,-maxlengt
+h=>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'}), $c
+gi->Tr(), $cgi->td();
        %temp =(colour=>'Colour ', autorange=>'Auto Range with ');
        print FH 'Range: [', $cgi->textfield(-name=>'singlestart1',-si
+ze=>5,-maxlength=>10), ', ',
            $cgi->textfield(-name=>'singleend1',-size=>5,-maxlength=>1
+0), ')',
            $cgi->radio_group(-name=>'singlecolour1',-value=>'colour',
+ -default=>'colour', -labels=>\%temp, -onClick=>"enableOverwrite2('si
+nglecolour1','singlebin1',1,'singlespecifiedcolour1' )");
        %labels = ('0,0,255'=>'blue','0,255,0'=>'green', '255,0,0'=>'r
+ed', '255,255,0'=>'yellow','0,255,255'=>'cyan','255,0,255'=>'magenta'
+,'255,255,255'=>'white','0,0,0'=>'black');
        print FH $cgi->popup_menu(-name=>'singlespecifiedcolour1', -va
+lues=>[('0,0,255','0,255,0', '255,0,0', '255,255,0','0,255,255','255,
+0,255','255,255,255','0,0,0')], -labels=>\%labels);
        print FH ' ',$cgi->radio_group(-name=>'singlecolour1',-value=>
+'autorange',-default=>'colour', -labels=>\%temp, -onClick=>"enableOve
+rwrite2('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 ra
+nge', -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: ', $maxM
+inDB->{$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: ', $max
+MinDB->{$element}->[0], ', min: ', $maxMinDB->{$element}->[1], '</spa
+n><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(); #en
+d single param table
        #ends single parameter visualization

        print FH $cgi->end_td(),$cgi->end_Tr(), $cgi->Tr({-rel=>'multi
+ParamStyle'}), $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(), $cgi->td({-class=>'blue'});
        print FH '<span class=\'bold\'>&nbsp;&nbsp;&nbsp;&nbsp;Visuali
+zation 1: </span>';
        print FH 'Visual colour: ',$cgi->popup_menu(-name=>'Multiple1d
+isplaycolour', -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',-valu
+e=>'auto', -default=>'auto', -labels=>\%temp, -rel=>'none', -onClick=
+>"enableOverwrite2('Multiple1Range1Style','Multiple1Range1bin',0, 'Mu
+ltiple1Range1specifiedcolour')");
        print FH $cgi->textfield(-name=>'Multiple1Range1bin',-size=>5,
+-maxlength=>5), ' bins or ';
        %temp =(threshold=>'Specify colour: ');
        print FH  $cgi->radio_group(-name=>'Multiple1Range1Style',-val
+ue=>'colour', -default=>'auto', -labels=>\%temp, -onClick=>"enableOve
+rwrite2('Multiple1Range1Style','Multiple1Range1bin',0, 'Multiple1Rang
+e1specifiedcolour')");
        %colourLabels = ('0,0,255'=>'blue','0,255,0'=>'green', '255,0,
+0'=>'red', '255,255,0'=>'yellow','0,255,255'=>'cyan','255,0,255'=>'ma
+genta','255,255,255'=>'white','0,0,0'=>'black');
        print FH $cgi->popup_menu(-name=>'Multiple1Range1specifiedcolo
+ur', -values=>[('0,0,255','0,255,0', '255,0,0', '255,255,0','0,255,25
+5','255,0,255','255,255,255','0,0,0')], -labels=>\%colourLabels, -dis
+abled=>'true');
        print FH $cgi->end_td(), $cgi->end_Tr(), $cgi->Tr(), $cgi->td(
+);

        print FH $cgi->table({-class =>'parameters',-id=>'Multiple1Ran
+ge1Param1'}), $cgi->Tr(), $cgi->td();
        %paramLabels = ('evalue'=>'E Value','identity'=>'Identity', 'a
+lignment length'=>'Alignment Length');
        #my %paramAttrs = ('evalue'=>{'rel'=>'includeZero'},'identity'
+=>{'rel'=>'none'}, 'gap'=>{'rel'=>'none'}, 'alignment length'=>{'rel'
+=>'none'});
        print FH '<span class="brown"> Parameter:</span> ',$cgi->popup
+_menu(-name=>'Multiple1Range1Param1', -values=>\@visualizable, -label
+s=>\%paramLabels);
        print FH ' Range: [',$cgi->textfield(-name=>'Multiple1Range1Pa
+ram1Start',-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', -v
+alue=>1, -label=>"Include zero e values");
        print FH $cgi->end_td(), $cgi->end_Tr(), $cgi->end_table(); #e
+nd parameters table

        print FH '&nbsp;&nbsp;&nbsp;&nbsp;';
        print FH $cgi->button(-name=>'addParam', -value=>'Add another 
+parameter', -onClick=>"addParamRow('Multiple1Range1Param1','Multiple1
+Range1' )",
            -class=>"btn2",-onmouseout=>"this.className='btn2'");
        print FH $cgi->button(-name=>'removeParam', -value=>'Remove la
+st parameter', -onClick=>"removeRowFromTable('Multiple1Range1Param1')
+",
            -class=>"btn2",-onmouseout=>"this.className='btn2'");
        print FH $cgi->end_td(), $cgi->end_Tr(), $cgi->end_table(); #e
+nd 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 la
+st range', -onClick=>"remove2RowsFromTable('Multiple1Range1')",
            -class=>"btn3", -onmouseout=>"this.className='btn3'");
        print FH '</small>';
        print FH $cgi->end_td(), $cgi->end_Tr(), $cgi->end_table();#en
+d 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: ', $maxM
+inDB->{$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: ', $max
+MinDB->{$element}->[0], ', min: ', $maxMinDB->{$element}->[1], '</spa
+n><br />';
            }
        }
        print FH '<br /><br /><br />';
        print FH '</small>';
        print FH $cgi->end_td(),$cgi->end_Tr(), $cgi->end_table(); #en
+d 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', -clas
+s=>"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 Re
+sults', -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 M
+ain");
        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'>To
+tal 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 $cgi->checkbox(-name=>'selectedQueries',-chec
+ked=>0,-value=>"$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=>'in
+dividual'}), "\n";
               print $FH $cgi->start_form(-target=>'_blank', -name=>"v
+iewOne", -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:</spa
+n><br />\n";
            my @checked=('gene', 'location', 'length');
               my $annotationTitles = $parsed->getAnnotationOrderInfo(
+);
               print $FH $cgi->checkbox_group(-name=>'annotationTitles
+', -values=>$annotationTitles, -linebreak=>'true', -default=>\@checke
+d), "<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','alig
+nment length');
            my $alignmentTitles = ['alignment','score', 'evalue','iden
+tity','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',-s
+ize=>5,-maxlength=>10, -default=>10), " hits (e value filtered)<br />
+\n";
            print $FH 'No E values > ', $cgi->textfield(-name=>'limitE
+value',-size=>5,-maxlength=>10),"<br />\n";
            print $FH 'No % Identity < ', $cgi->textfield(-name=>'limi
+tIdentity',-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><b
+r />\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  $cgi->radio_group(-name=>'orderBy',-value=>$ord
+erBy, -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=>'Vi
+ew 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;

[download]
Thanks! Like i said, it works fine if i wait for the thread to finish first..

In reply to Re: detached thread not working?? by bluegirl123
in thread detached thread not working?? by bluegirl123

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