#!/usr/local/bin/perl

#################################################################
#Copyright: University of Utah Genome Center, University of Utah
#Author:Andrew von Niederhausern
#Email: avonnied@genetics.utah.edu
#Created:01/02/2001
#Last Updated:07/14/2002
#Version: 1.3.2
#Purpose: Gene Model Image Distribution
#WebSite: http://www.genome.utah.edu/genesnps
#Unauthorized use is prohibited, this header may not be removed
# or edited
#################################################################


$genbank_dir = "genbank";  #### edit this to the path of the genbank files

$version = "1.3.2";
use Bio::Seq;
use Bio::SeqIO;
use Bio::SeqI;
use Bio::SeqFeatureI;
use Bio::Tools::CodonTable;
use CGI::Carp qw(carpout fatalsToBrowser);

######## Read parameters passed by web browser through QUERY_STRING
$buffer = $ENV{'QUERY_STRING'}; # Form Variables\
@pairs = split(/&/, $buffer);
foreach $pair (@pairs) {
    ($Fname, $Fvalue) = split(/=/, $pair);
    $Fvalue =~ tr/+/ /;
    #$Fvalue =~ s/%([a-fA-F0-9][a-fA-F0-9])/pack("C", hex($1))/eg;
    $FORM{$Fname} = $Fvalue;
}
if ( exists $FORM{organism} ) {
    $genbank_dir = "$FORM{organism}/$genbank_dir";
}
#### Security Data
###### NOTE: Feature currently not working
$refer_url = $ENV{"HTTP_REFERER"}; # Url of Referring page
(@refer_url) = split(/\//,$refer_url);
$refer_url= $refer_url[2];

$host=$ENV{"REMOTE_ADDR"}; # Address of remote computer
#################################

########## HTML HEADER DONOT REMOVE
print "Content-type: text/html\n\n";


if ($FORM{"gene"}) {  # gene name must be present

    $gene = $FORM{"gene"};
    $seqobj = &get_seqobj($gene);  # generate seqobj
    $dir="$genbank_dir/$gene"; #set working Directory

    use GD; ## Drawing Package

    $im = new GD::Image(750,150); # Initalize Image

    &color;  # initialize color_pool

########## Feature Colors ###########################
   
#### Set Gene Model Colors
    @exon_color = @realblue2;
    @intron_color = @cwhite;
    @utr_color = @green2;
    $background=$darkgrey;
    $im->filledRectangle(0,10,700,135,$background);

    
### Setting Colors of Legend Depending on Filters Chosen
    if ($FORM{"filter"} !~ "INTRON" 
	&& $FORM{"filter"} !~ "SYNON" 
	&& $FORM{"filter"} !~ "NONSYN" 
	&& $FORM{"filter"} !~ "EXON") {
	$flank_color = $black;
    } else {
	$flank_color = $lightgrey2;
    }
    if ($FORM{"filter"} !~ "NONSYN" 
	&& $FORM{"filter"} !~ "NONCODE" 
	&& $FORM{"filter"} !~ "INTRON") {
	  $syn_color =  $orange2;
	  $syn_color_label = $black;
    } else {
	 $syn_color = $lightgrey2;
	 $syn_color_label = $lightgrey2;
    }
    if ($FORM{"filter"} !~ "SYNON" 
	&& $FORM{"filter"} !~ "NONCODE" 
	&& $FORM{"filter"} !~ "INTRON") {
	  $nonsyn_color =  $pinky;
	  $nonsyn_color_label = $black;
    } else {
	 $nonsyn_color = $lightgrey2;
	 $nonsyn_color_label = $lightgrey2;
    } 
    if ($FORM{"filter"} !~ "EXON" 
	&& $FORM{"filter"} !~ "INTRON" 
	&& $FORM{"filter"} !~ "NONSYN") {
	
	  $utr_snp = $im->colorAllocate(0,100,0);
	  $utr_color_label = $black;
    } else {
	 $utr_snp = $lightgrey2;
	 $utr_color_label = $lightgrey2;
    } 
    if ($FORM{"filter"} !~ "SYNON" 
	&& $FORM{"filter"} !~ "EXON" 
	&& $FORM{"filter"} !~ "NONSYN") {
	  $intron_color = $pbrown;
	  $intron_color_label = $black;
    } else {
	 $intron_color = $lightgrey2;
	 $intron_color_label = $lightgrey2;
    } 
    $term_color=$firebrick1;
########## End Color Setting ##############################
 

    if ($FORM{"version"}) {
	$im->string(gdTinyFont,4,138,"v$version",$black); ### Displays Current revision of gene_model.cgi Not Really Needed
    }



#### Side Bar Lines and Labels ########################
    $im->string(gdMediumBoldFont,708,1,"Gene",$blue);
    $im->string(gdMediumBoldFont,703,15,"$gene",$blue);
### SNP Side Bars
    if ($FORM{"frequency"} == 1) { # Low Frequency Scale
	$freq_quarter = ".025";
	$freq_half = ".05";
	$freq_3quarter = ".075";
	$freq_full = ".1";
	$freq_label = "Low";
	$f_half_color = $red;
    } else { # High Frequency Scale
	$freq_quarter = ".12";
	$freq_half = ".25";
	$freq_3quarter = ".36";
	$f_half_color = $blue;
	$freq_label = "High";
	$freq_full = ".5";
    }
    $im->string(gdTinyFont,703,82,"SNP Freq.",$f_half_color); # Snp Label

    ## Side Lines
    $im->line(700,93.75,705,93.75,$darkgrey5); 
    $im->line(700,107.5,710,107.5,$darkgrey5);
    $im->line(700,120.5,705,120.5,$darkgrey5);

    $im->dashedLine(0,93.75,700,93.75, $darkgrey5); # 1/4 Line
    $im->dashedLine(0,107.5,700,107.5, $darkgrey5); # 1/2 Line
    $im->dashedLine(0,120.5,700,120.5, $darkgrey5); # 3/4 Line

    ## Scale Labels
    $im-> string(gdTinyFont,713,125,"$freq_full",$f_half_color);
    $im->string(gdTinyFont,713,103,"$freq_half",$f_half_color);

    ### Genomic Labels
    $im->line(700,40,750,40,$darkgrey5);
    $im->string(gdSmallFont,705,53,"Genomic",$blue);


##### Total Length ###################
    $start = 1;
    $end = $end = $seqobj->length();
    $total_l = $end;

    $end_orig = $end;
    $dna_length = $end;
    $dna_length /= 1000;
    $dna_length = sprintf("%.0f kb",$dna_length);
    $im->line(700,81,750,81,$black);


######## Moving ############
if($FORM{"move"}) { ### Parameter passed from browser, as nucleotides
    $move = $FORM{"move"};
    $start += $move;
    $end += $move;
}

####### Zooming ###########
if ($FORM{"zoom"} > 0) {  #passed as a percentage
    
    $zoom = sprintf("%.0f",(($end - $start) * $FORM{"zoom"})/2);
    
    $newstart = $start;
    $newend = $end;
#    $zoom = $FORM{"zoom"};
    $zoom_check = $end;
    $zoom_check -= $start;

    if ($zoom_check > $zoom) {
	$newstart += $zoom;
	$newend -= $zoom;
	if ($newstart < $newend) {
	    $start = $newstart;
	    $end = $newend;
	}
    } else {
	$im->arc(5,5,5,5,0,360,$red);
	$im-> fill(6,6,$red);
    }
}
 
######### Displayed Genomic Size ######
    $d_size = $end;
    $d_size -= $start;
    $dna_length = $d_size;
    if ($dna_length > 1000) {
	$dna_length /= 1000;
	$dna_length = sprintf("%.0fkb",$dna_length);
    }  else {
	$dna_length = sprintf("%.0f",$dna_length);
    }
    
    $im->string(gdTinyFont,705,70,"$dna_length",$black);


##### Division Factor, All other data is divided by Factor #########

$factor = $d_size;
$factor /= 700;
$imagestart = $start;
$imagestart /= $factor;
$drawfactor = $factor;
$factorcount = 0;
$drawfactinterval = $factor;
$drawfactinterval *= 4;
$drawfactor += $drawfactinterval;

######### Coordinate Bars #############
$im->line(0,0,0,30,$black);
$im->line(700,0,700,30,$black);
$im->line(0,10,700,10,$black);

### Genomic Sequence
    if ($start < 1) {
	$genomic_start = $start * -1;
	$genomic_start /= $factor;
	$im->dashedLine(0,73,$genomic_start,73,$white);
	$im->dashedLine(0,77,$genomic_start,77,$white);
	$im->line($genomic_start,10,$genomic_start,25,$black);
	$im->string(gdTinyFont,$genomic_start,25,"1",$white);
    } elsif ($start == 1) {
	$genomic_start = 0;
	
    } else {
	$genomic_start = 0;
    }
    if ($end > $end_orig) {
	$genomic_end = $end - $end_orig;
	$genomic_end /= $factor;
	$genomic_end = 700 - $genomic_end;
	$im->dashedLine($genomic_end,73,700,73,$white);
	$im->dashedLine($genomic_end,77,700,77,$white);
	$im->line($genomic_end,10,$genomic_end,25,$black);
	$im->string(gdTinyFont,$genomic_end,25,"$dna_length",$white)
    }  else {
	$genomic_end = "700";
    }


    $im->rectangle($genomic_start,72,$genomic_end,78,$black);

### Set Bar Spacing #########
    $firstfact = $factor;
    $firstfact += $start;
    $im->string(gdTinyFont,5,15,"$start",$white);
    $nol = $d_size;
    $nol /= $factor;
    $nol /= 10; # 10 Lines / image;
    $nolfactor = $nol;
    $grid = 100;

    while ($nol < 699) {
	$im->line($nol,0,$nol,10,$black);
	$factn = $nol;
	$factn *= $factor;
	$factn += $start;
	$factn = sprintf ("%.0f",$factn);
	$fontoff = $nol;
	$fontoff -= 30;
	$im->string(gdTinyFont,$fontoff,1,"$factn",$black);
	$nol += $nolfactor;
    }
    
    $im->string(gdTinyFont,670,1,"$end",$black);

####### Intron Coloring ########
    @exons = &feature_array('exon');
    my ($minstart, $maxend) = (0,0);
#    foreach my $exon (@exons) {
#	$minstart = $exon->start unless ($minstart < $exon->start);
#	$maxend = $exon->end unless ($maxend > $exon->end);
#    }
    $begin_int = $exons[0]->start;  # get exon 1
    $end_int = $exons[$#exons]->end; # get last exon
#    $begin_int = $minstart;
#    $end_int = $maxend;

    $begin_int -= $start;
    $end_int -= $start;
    
    $begin_int /= $factor;
    $end_int /= $factor;

    if ($begin_int < 0) {
	$bein_int = 0;
    }

    if ($end_int > 700) {
	$end_int = 700;
    }

    if ($begin_int < 0 && $end_int < 0) {
	$draw_intron = 1;
    }

    if ($begin_int > 700 && $end_int > 700) {
	$draw_intron = 1
    }

    $i_start = 71; ## Start of Genomic

    if (!$draw_intron) {
	foreach (@intron_color) {
	    $im->line($begin_int,$i_start,$end_int,$i_start,$_);
	    $i_start++;
	}
    }
########## End Intron Coloring ##########



############## Gene Bar ##############
    @gene_tag = &feature_array("gene");
    $ts = 0;
    if ($gene_tag[0] != -1) {
	foreach $g (@gene_tag) {
	    my ($newgene) = $g->get_tag_values ("gene");
	    if ($newgene eq $gene) {
		if ($g->length >= $ts) {
		    $ts = $g->length();
		    $gstart = $g->start();
		    $gend = $g->end();
		}
	    }
	}
    
	$gene_length = $gend;
	$gene_length -= $gstart;
	$gstart -= $start;
	$gend -= $start;
	
	$gstart /= $factor;
	$gend /= $factor;
	
	if ($gend > 700) {
	    $gend = 700;
	}
	
	if ($gend > 700 && $gstart > 700) {
	    $g_d = 1;
	}
	
	if ($gend < 0 && $gstart < 0) {
	    $g_d = 1;
	}
	
	if (!$g_d) {
	    $im->filledRectangle($gstart,10,$gend,13,$green);
	}
	
	$gene_length /= 1000;
	$gene_length = sprintf ("%.0f kb",$gene_length);
	$im->string(gdTinyFont,715,30,"$gene_length",$black);
    }
########### End Gene Bar ########################

########### Zoom Pointer ##########
$im->line(350,10,350,18,$black);
$im->line(347,15,350,18,$black);
$im->line(350,18,353,15,$black);
##################################


###################### Exon Info ####################
    my $isnewgene = 0;
    my $color = $white;
    my ($gene, $newgene) = ('', '');
    if ($exons[0] != -1) {
	foreach my $ex (@exons) {
	    $estart = $ex->start();
	    $eend = $ex->end();
	    my ($exoncount) = $ex->get_tag_values ("number");
	    my ($newgene) = $ex->get_tag_values ("gene");
	    if ($gene ne $newgene) {
		$color = ($color == $white) ? $black : $white;
		$gene = $newgene;
	    }
	    $estart -= 1;
	    
	    if ($estart > $end && $eend > $end) {
		next;
	    }
	    
	    if ($estart < $start && $eend < $start) {
		next;
	    }
	    
	    if ($eend > $end) {
		$eend = $end;
	    }
	    
	    $elength = $eend;
	    $estart -= $start;
	    $eend -= $start;
	    $estart /= $factor;
	    $eend /= $factor;
	    
	    if ($eend > 700) {
		$eend = 700;
	    }
	    
	    $np = $eend; # for printing exon number
	    $ne = $estart;
	    $np -= $ne;
	    $np /= 2;
	    $ne += $np;
	    $exon_print_test = $ne;
	    $exon_print_test -= $last_exon_end;
	    if ($exon_print_test > 15 || $exon_print_test < -15 ) { ### If Spacing is OK print Number ( avoids number crowding)
		$im->string(gdTinyFont,$ne,45,$exoncount,$color);
		$last_exon_end = $ne;
	    }
	
	    ### Print the Exon itself ####
	    $i_start = 68;
	    foreach (@exon_color) {
		$im->line($estart,$i_start,$eend,$i_start,$_);
		$i_start++;
	    }
	}
    }
################ End Exon Information ###########################

######################### UTR Info ########################
    @utrs = &feature_array("UTR");
    if ($utrs[0] != -1) {
	foreach $utr (@utrs) {
	    ($utrs,$utre) = split(/,/,$utr);
	    eval{
		$location = $utr->location();
		if ($location =~ /Simple/) {
		    &draw_utr($utr->start(),$utr->end());
		} elsif ($location =~ /Split/) {
		    @subloc = $location->sub_Location();
		    if (@subloc) {
			foreach $sl (@subloc) {
			    &draw_utr($sl->start(),$sl->end());
			}
		    }
		}
	    };
	}
    }
############### End UTR Info ##############################################


########### MASKED #######################
    @masked = &feature_array("misc_feature","note","RepeatMask");
    if ($FORM{"masked"} =~ /SHOW/ && $masked[0] != -1) {
	
	foreach (@masked) {
#	    ($m_start,$m_end) = split(/,/,$_);
	    $m_start = $_->start();
	    $m_end = $_->end();
	    $m_start -= $start;
	    $m_end -= $start;
	    $m_start /= $factor;
	    $m_end /= $factor;
	    if ($m_start <= 0 && $m_end >=0) {
		$m_start=0;
	    }
	    if ($m_start < 700 && $m_end >= 700) {
		$m_end = 700;
	    }
	    if ($m_end <= 0 || $m_start >= 700) {next;}
	    $im->filledRectangle($m_start,73,$m_end,77,$purple);
	    $m_start+=5;
	    $m_end -= 2;
	    
	    $im->string(gdTinyFont,260,138,"(Repeats)",$blue);

	}
    }
#########################################





######################### SNP Info ######################################

    $snpcount = 0;
    
    if ($FORM{"submitter"}) {
	$im->string(gdSmallFont,500,20,"Submitter:$FORM{submitter}",$white);
    }

    @snps = &feature_array("variation");
    $snpcount++;
    
    if ($snps[0] != -1) {
	foreach (@snps) {
	    undef($snp_frequency);
	    undef($snp_chromosomes);
	    undef($snp_implication);
	    undef($snp_alleles);
	    undef($snp_submitter);
	    undef($snp_heterozygosity);
	    undef($snp_ssnumber);
	    undef($snp_position);
	    eval{
		$snp_position = $_->start();
	    };
	    if ($snp_position < $start || $snp_position > $end) {next;};
	    eval{
		($snp_implication) = $_->each_tag_value("implication");
	    };
	    eval{
		($snp_ssnumber) = $_->each_tag_value("standard_name");
	    };
	    eval{
		($snp_alleles) = $_->each_tag_value("allele");
	    };
	    eval{
		($snp_submitter) = $_->each_tag_value("submitter");
	    };
	    eval{
		($snp_frequency) = $_->each_tag_value("frequency");
	    };
	    eval{
		($snp_chromosomes) = $_->each_tag_value("chromosomes");
	    };
	    eval{
		($snp_heterozygosity) = $_->each_tag_value("heterozygosity");
	    };
	

	    if ($FORM{"submitter"}) {
		if ($FORM{"submitter"} !~ /^$snp_submitter$/) {
		    next;
		}
	    }
	    
	    $asnp = $snpp;
	    $snp_position -= $start;
	    $snp_position /= $factor;
	    
	    if ($snp_position > 700 || $snp < 0) {next;}
	    
	    
	    ######### Confirmed SNP filter
	    if ($FORM{"validate"} =~ "VERIFIED") {
		if ($snp_frequency == 0 && $snp_heterozygosity == 0) {
		    next;
		}
	    }
	    
	    if ($snp_frequency == 0 && $snp_heterozygosity != 0) {
		$snp_frequency = $snp_heterozygosity;
	    }
	    
	##### Frequency Scaling ######
	    
	    if ($FORM{"frequency"} == 1) {
		$freq_factor = 550;
	    } else {
		$freq_factor = 110;
	    }
	    
	    if ($FORM{"frequency"} == 1) {
		$snp_cutoff = .01;
	    } else {
		$snp_cutoff = .05;
	    }
	    
	    if ($snp_frequency < $snp_cutoff && $snp_frequency != 0) {
		$snp_frequency = $snp_cutoff;
	    }
	    $f2 = $snp_frequency;
	    if ($snp_frequency != 0) {
		$snp_frequency *= $freq_factor;
		$snp_frequency += 80;
	    } else {
		$snp_frequency = 85;
	    }
	    if ($FORM{"frequency"} && $snp_frequency > 130) {
		$snp_frequency = 130;
	    }
	    
	    ########### SNP Implication Filters ##########
	    if ($snp_implication =~ /nonsyn/) {
		if ($FORM{"filter"} =~ "INTRON" 
		    || $FORM{"filter"} =~ "SYNON" 
		    || $FORM{"filter"} =~ "NONCODE") {next;}
		$snpcolor = $nonsyn_color;
	    } elsif ($snp_implication =~ "term") {
		if ($FORM{"filter"} =~ "INTRON"
		    || $FORM{"filter"} =~ "NONSYN" 
		    || $FORM{"filter"} =~ "SYNON" 
		    || $FORM{"filter"} =~ "NONCODE"){next;}
		$snpcolor = $term_color;
	    } elsif ($snp_implication =~ /synon/) {
		if ($FORM{"filter"} =~ "INTRON" 
		    || $FORM{"filter"} =~ "NONSYN" 
		    || $FORM{"filter"} =~ "NONCODE"){next;}
		$snpcolor = $syn_color;
	    } elsif ($snp_implication =~ /intron/) {
		if ($FORM{"filter"} =~ "SYNON" 
		    || $FORM{"filter"} =~ "NONSYN" 
		    ||  $FORM{"filter"} =~ "EXON"){next;}
		$snpcolor = $intron_color;
	    } elsif ($snp_implication =~ /UTR/) {
		if ($FORM{"filter"} =~ "NONSYN" 
		    || $FORM{"filter"} =~ "INTRON" 
		    || $FORM{"filter"} =~ "EXON") {
		    next;
		}
		$snpcolor = $utr_snp;
	    } else {
		if ($FORM{"filter"} =~ "SYNON" 
		    || $FORM{"filter"} =~ "NONSYN" 
		    ||  $FORM{"filter"} =~ "EXON" 
		    ||  $FORM{"filter"} =~ "INTRON"){next;}
		$snpcolor = $black;
	    }
	    

	    $im->line($snp_position, 80, $snp_position, $snp_frequency, $snpcolor); ### Draw SNP Line

	    $snpt = $snpp;
	    $snpl = $snpp;
	    $snpt -=1;
	    $snpl +=1;
	}
    }
###################### END SNP Info ################################

####################### Sequence Gaps  #############################
    @part = &feature_array("misc_feature","note","SequenceGap");

    if ($part[0] != -1) {
	foreach (@part) {
	    $p_start = $_->start();
	    $p_end = $_->end();
	    $p_size = $p_end;
	    $p_size -= $p_start;

	    if ($p_size < 20) {next;}

	    if ($p_start < $start && $p_end < $start) {next;}
	    if ($p_start > $end && $p_end > $end) {next;}
	    if ($p_start < $start && $p_end > $end) {
		$p_draw = 1;
	    } else {
		$p_draw = 0;
	    }

	    if ($p_start < $start) {
		$p_start = $start;
	    }

	    if ($p_end > $end) {
		$p_end = $end;
	    }

	    $p_start -= $start;
	    $p_end -= $start;
	    $p_start /= $factor;
	    $p_end /= $factor;

	    $im->filledRectangle($p_start,70,$p_end,80,$background); ### clear Area
	    $im->line($p_start,70,$p_start,80,$black); # Cap End
	    $im->line($p_end,70,$p_end,80,$black); ### cap end
    }
}
############### End Sequence Holes ######################################

############################### Legend ###################################

    $im->line(0,135,750,135,$black);
    $im->string(gdSmallFont,710,135,"Legend", $black);

#################### Gene Legend #######################

    $im->string(gdTinyFont,50,138,"Gene",$black);

 ####### Exons ######
    $im->line(75,135,75,150,$black);
    $im->string (gdTinyFont,84,138,"CDS",$black);

    $i_start = 137;
    foreach (@exon_color) {
	if ($i_start > 147) {
	    next;
	}
	$im->line(105,$i_start,115,$i_start,$_);
	$i_start++;
	
    }

    ###### UTRS ####
    $im->line(125,135,125,150,$black);
    $im->string(gdTinyFont,130,138,"UTR",$utr_color_label);

    $i_start = 137;
    foreach (@utr_color) {
	$im->line(150,$i_start,160,$i_start,$_);
	$i_start++;
    }

    ###### Introns #######
    $im->line(165,135,165,150,$black);
    $im->string(gdTinyFont,170,138,"Intron",$black);

    $i_start = 138;
    foreach (@intron_color) {
	$im->line(205,$i_start,215,$i_start,$_);
	$i_start++;
    }

####################### SNPs Legend ####################

    if ($FORM{"validate"} =~ "VERIFIED") {
	$im->string(gdTinyFont,325,138,"(Validated)",$blue);
    }

    $im->string(gdTinyFont,385,138,"SNPs",$black);

    #flank
    $im->line(412,135,412,150,$black);
    $im->string(gdTinyFont,417,138,"Flank",$flank_color);
    $im->filledRectangle(447,137,457,147,$flank_color);
    
   
    

    #intron
    $im->line(462,135,462,150,$black);
    $im->string(gdTinyFont,467,138,"Intron",$intron_color_label);
    $im->filledRectangle(500,137,510,147,$intron_color);

    #nonsyn
   $im->line(515,135,515,150,$black);
    $im->string(gdTinyFont,520,138,"Nonsyn",$nonsyn_color_label);
    $im->filledRectangle(553,137,563,147,$nonsyn_color);

    #Syn
    $im->line(568,135,568,150,$black);
    $im->string(gdTinyFont,573,138,"Synon",$syn_color_label);
    $im->filledRectangle(600,137,610,147,$syn_color);
    
    #UTR
    $im->line(615,135,615,150,$black);
    $im->string(gdTinyFont,620,138,"UTR",$utr_color_label);
    $im->filledRectangle(640,137,650,147,$utr_snp);

    #Border Image
    $im->rectangle(0,0,749,149,$black);
    $im->line(700,0,700,150, $black);


    binmode STDOUT; ### Binmode ( For DOS mainly)

    print $im->gif; ### Print the Image Dynamically ( not to file handle)   
}

################################## End Gene Model Image #########################






###############################################################
##################### SUB ROUTINES ############################
###############################################################

sub draw_utr {
    ($utrs,$utre) = @_;
    $utrs -= 1;
    if ($utrs > $end && $utre > $end) {
	next;
    }

    if ($utrs < $start && $utre < $start) {
	next;
    }
    
    if ($utrs < $start) {
	$utrs = $start;
    }
    
    if ($utre > $end) {
	$utre = $end;
    }
    
    $utrs -= $start;
    $utre -= $start;
    $utre /= $factor;
    $utrs /= $factor;
    
    $im->filledRectangle($utrs, 66, $utre, 84, $background); ### clear anything already drawn at that position
    
    $i_start = 70;
    foreach (@utr_color) {
	$im->line($utrs,$i_start,$utre,$i_start,$_);
	$i_start++;
    }
}

 
sub get_seqobj {
    $in = Bio::SeqIO->new("-file"=>"$genbank_dir/$gene.gb","-format"=>"Genbank");
    $seqobj = $in->next_seq();
}
sub feature_array {
    undef(@returns);
    ($tag) = $_[0];
    ($subtag) = $_[1];
    ($subvalue) = $_[2];
    @all = $seqobj->all_SeqFeatures();
    foreach (@all) {
	if ($_->primary_tag =~ /$tag/) {
	    if ($subtag && $subvalue) {
		eval{
		    ($cvalue) = $_->each_tag_value("$subtag");
		    if ($cvalue =~ /$subvalue/) {
			push(@returns,$_);
		    }
		  
		};
	    } else {
		push(@returns,$_);
	    }
	}
    }
    if ($returns[0]) {
	return(@returns);
    } else {
	return(-1);
	
    }

}



sub color {

################### Color Pool #####################
    $white = $im->colorAllocate(255,255,255);
    $black = $im->colorAllocate(0,0,0);
    $lightgrey = $im->colorAllocate(240,240,240);
    $lightgrey2 = $im->colorAllocate(180,180,180);
    $darkgrey = $im->colorAllocate(165,165,165);
    $darkgrey2 = $im->colorAllocate(150,150,150);
    $darkgrey3 = $im->colorAllocate(140,140,140);
    $darkgrey4 = $im->colorAllocate(130,130,130);
    $darkgrey5 = $im->colorAllocate(120,120,120);
    $darkgrey6 = $im->colorAllocate(180,180,180);
    ########## Browns ############
    $saddle = $im->colorAllocate(200, 140, 105);
    $tan = $im->colorAllocate(238,154,73);
    $lightgoldenrod4=$im->colorAllocate(139,129,76);
    $peru=$im->colorAllocate(205,133,63);
    $bisque3=$im->colorAllocate(205,183,158);
    $sienna4=$im->colorAllocate(139,71,38);
    $khaki2=$im->colorAllocate(238,230,133);
    $beige=$im->colorAllocate(245,245,220);
    $pbrown=$im->colorAllocate(120,80,70);
    ########## Reds ##############
    $red = $im->colorAllocate(255,0,0);
    $lightred = $im->colorAllocate(255,0,0);
    $red4=$im->colorAllocate(139,0,0);
    $darkjedired=$im->colorAllocate(150,100,70);
    $red3=$im->colorAllocate(205,0,0);
    $orange3=$im->colorAllocate(205,133,0);
    $darkorange4=$im->colorAllocate(139,69,0);
    $maroon = $im->colorAllocate(180,100,100);
    $mediumvioletred=$im->colorAllocate(199,21,133);
    $indianred4=$im->colorAllocate(139,58,58);
    $orangered2=$im->colorAllocate(238,64,0);
    $indianred1=$im->colorAllocate(255,106,106);
    $firebrick1=$im->colorAllocate(255,48,48);
    $pinky =$im->colorAllocate(255,0,120); 
    $orange2=$im->colorAllocate(255,215,0);
    ########## Blues #############
    $blue =  $im->colorAllocate(0,0,200);
    $azure1=$im->colorAllocate(240,255,255);
    $lightsteelblue=$im->colorAllocate(176,196,222);
    $royalblue1=$im->colorAllocate(72,118,255);
    $royalblue2=$im->colorAllocate(67,110,238);
    $slateblue3=$im->colorAllocate(105,89,205);
    $slateblue2=$im->colorAllocate(122,103,238);
    $blueviolet=$im->colorAllocate(138,43,226);
    $dodgerblue=$im->colorAllocate(30,144,255);
    $midnightblue=$im->colorAllocate(25,25,112);
    $snpblue = $im->colorAllocate(100,200,255);
    $darkjedigreen=$im->colorAllocate(30,100,70);
    $dgreen2=$im->colorAllocate(70,150,60);
    $utrc1 = $im->colorAllocate(200,100,255);
    ########## Greens ############
    $lightgreen = $im->colorAllocate(100,180,100);
    $green = $im->colorAllocate(0,255,0);
    $darkgreen = $im->colorAllocate(180,100,100);
    $green_yellow=$im->colorAllocate(173,255,47);
    $darkseagreen1=$im->colorAllocate(193,255,193);
    $darkolivegreen2=$im->colorAllocate(188,238,104);
    $olive_drab=$im->colorAllocate(107,142,35);
    $forest_green=$im->colorAllocate(34,139,34);
    $lawngreen=$im->colorAllocate(124,252,0);
    $bgreen = $im->colorAllocate(50,255,150);
    ########## Yellows ###########
    $gold2=$im->colorAllocate(255,240,0);
    $gold = $im->colorAllocate(240,194,0);
    $yellow=$im->colorAllocate(255,255,0);
    $lemon_chiffon=$im->colorAllocate(255,250,205);
    ########## Purples ###########
    $lightviolet=$im->colorAllocate(240,200,255);
    $purple = $im->colorAllocate(139,123,139);
    $darkviolet=$im->colorAllocate(148,0,211);
    $violetred4=$im->colorAllocate(139,34,82);
    $violetred2=$im->colorAllocate(200,60,120);
    $darkjedipurple=$im->colorAllocate(150,70,170);
##################### Scaled Colors #########
    $darkblue1 =  $im->colorAllocate(65, 145, 172);    #          8998
    $darkblue2 =  $im->colorAllocate(64, 143, 171);    #          8668 
    $darkblue4 =  $im->colorAllocate(60, 134, 160);    #          5445 
    $darkblue6 =  $im->colorAllocate(53, 121, 143);    #           22
    $darkblue9 =  $im->colorAllocate(63, 141, 166);    #          1111           
    $darkblue10 =  $im->colorAllocate(45, 88, 103);    #          66
    @darkblue = ("$darkblue10","$darkblue9","$darkblue6","$darkblue6","$darkblue4","$darkblue2","$darkblue1","$darkblue6","$darkblue10",);

    $blue1 =  $im->colorAllocate(112, 204, 227);    #          1111
    $blue2 =  $im->colorAllocate(110, 202, 225);    #           66 
    $blue4 =  $im->colorAllocate(102, 188, 210);    #           
    $blue6 =  $im->colorAllocate(89, 167, 186);    #           
    $blue9 =  $im->colorAllocate(109, 198, 222);    #           
    $blue10 =  $im->colorAllocate(68, 115, 125);    #
    @blue = ("$blue10", "$blue9", "$blue6", "$blue6", "$blue4", "$blue2", "$blue1", "$blue6", "$blue10");

    $deepblue1 =  $im->colorAllocate(150, 150, 255);    #          1111
    $deepblue2 =  $im->colorAllocate(120, 120, 225);    #           66 
    $deepblue4 =  $im->colorAllocate(100,100, 200);    #           
    $deepblue6 =  $im->colorAllocate(100, 100, 150);    #           
    $deepblue9 =  $im->colorAllocate(70, 70, 125);    #           
    $deepblue10 =  $im->colorAllocate(50, 50, 100);    #
    @deepblue = ("$deepblue10", "$deepblue9", "$deepblue6", "$deepblue6", "$deepblue4", "$deepblue2", "$deepblue1", "$deepblue6", "$deepblue10");
    
    $cblue1 =  $im->colorAllocate(200, 200, 255);    #          1111
    $cblue2 =  $im->colorAllocate(180, 180, 240);    #           66 
    $cblue3 =  $im->colorAllocate(180, 180, 230);    #           
    $cblue4 =  $im->colorAllocate(180, 180, 220);    #           
    $cblue5 =  $im->colorAllocate(180, 180, 210);    #           
    $cblue6 =  $im->colorAllocate(170, 170, 200);    #
    $cblue7 =  $im->colorAllocate(150, 150, 190);    #           66 
    $cblue8 =  $im->colorAllocate(150,150, 180);    #           
    $cblue9 =  $im->colorAllocate(130, 130, 170);    #           
    $cblue10 =  $im->colorAllocate(120, 120, 160);    #           
    $cblue11 =  $im->colorAllocate(120, 120, 150);    #
    $cblue12 =  $im->colorAllocate(100, 100, 140);    #           66 
    $cblue13 =  $im->colorAllocate(100,100, 130);    #           
    $cblue14 =  $im->colorAllocate(90, 90, 120);    #           
    $cblue15 =  $im->colorAllocate(70, 70, 110);    #           
    $cblue16 =  $im->colorAllocate(70, 70, 100);    #
    $cblue17 =  $im->colorAllocate(30, 30, 90);    #           66 
    $cblue18 =  $im->colorAllocate(30,30, 80);    #           
    $cblue19 =  $im->colorAllocate(30, 30, 70);    #           
    @cblue = ("$cblue1","$cblue2","$cblue3","$cblue4","$cblue5","$cblue6","$cblue7","$cblue8","$cblue9","$cblue10","$cblue11","$cblue12","$cblue13","$cblue14","$cblue15","$cblue16","$cblue17");
   @cblue = reverse(@cblue);
    $sblue1 =  $im->colorAllocate(100, 180, 240);    #          1111
    $sblue2 =  $im->colorAllocate(99, 180, 225);    #           66 
    $sblue4 =  $im->colorAllocate(80, 160, 240);    #           
    $sblue6 =  $im->colorAllocate(50, 140, 180);    #           
    $sblue9 =  $im->colorAllocate(95, 150, 225);    #           
    $sblue10 =  $im->colorAllocate(50, 90, 118);    #
    @sblue = ("$sblue10", "$sblue9", "$sblue6", "$sblue6", "$sblue4", "$sblue2", "$sblue1", "$sblue6", "$sblue10");

    $white1 =  $im->colorAllocate(248, 248, 248);    #          8998
    $white2 =  $im->colorAllocate(245, 245, 245);    #          8668 
    $white4 =  $im->colorAllocate(227, 227, 227);    #          5445 
    $white6 =  $im->colorAllocate(203, 203, 203);    #           22 
    $white9 =  $im->colorAllocate(237, 237, 237);    #          1111           
    $white10 =  $im->colorAllocate(121, 121, 121);    #
    @white = ("$white10", "$white9", " $white6", " $white6", " $white4", " $white2", " $white1", " $white6", " $white10");

    $cwhite1 =  $im->colorAllocate(255, 255, 255);    #          8998
    $cwhite2 =  $im->colorAllocate(230, 230, 230);    #          8668 
    $cwhite4 =  $im->colorAllocate(200, 200, 200);    #          5445 
    $cwhite6 =  $im->colorAllocate(175, 175, 175);    #           22 
    $cwhite9 =  $im->colorAllocate(150, 150, 150);    #          1111           
    $cwhite10 =  $im->colorAllocate(125, 125, 125);    #
    @cwhite = ("$cwhite9", "$cwhite4", " $cwhite1", " $cwhite2", " $cwhite4", " $cwhite4", " $cwhite6", " $cwhite6", " $cwhite10");
    @cwhite = reverse(@cwhite);
    
    $grey11 =  $im->colorAllocate(180, 180, 180);
    $grey1 =  $im->colorAllocate(150, 150, 150);    #          8998c
    $grey2 =  $im->colorAllocate(130, 130, 130);    #          8668 
    $grey4 =  $im->colorAllocate(100, 100, 100);    #          5445 
    $grey6 =  $im->colorAllocate(70, 70, 70);    #           22 
    $grey9 =  $im->colorAllocate(30, 30, 30);    #          1111           
    $grey10 =  $im->colorAllocate(0, 0, 0);    #
    @grey = ("$grey9", " $grey6", " $grey4", " $grey2", " $grey1", " $grey1", "$grey2");
#    @grey = reverse(@grey);

    $green1 =  $im->colorAllocate(147, 219, 151);    #          8998
    $green2 =  $im->colorAllocate(145, 218, 149);    #          8668 
    $green4 =  $im->colorAllocate(135, 204, 140);    #          5445 
    $green6 =  $im->colorAllocate(121, 182, 124);    #           22
    $green9 =  $im->colorAllocate(143, 212, 147);    #          1111           
    $green10 =  $im->colorAllocate(89, 126, 91);    #          66
    @green = ("$green10", " $green9", " $green6", " $green6", " $green4", " $green2", " $green1", " $green1", "$green2");

    $green1 =  $im->colorAllocate(100, 255, 100);    #          8998
    $green2 =  $im->colorAllocate(100, 225, 100);    #          8668 
    $green4 =  $im->colorAllocate(100, 200, 100);    #          5445 
    $green6 =  $im->colorAllocate(100, 175, 100);    #           22
    $green9 =  $im->colorAllocate(100, 150, 100);    #          1111           
    $green10 =  $im->colorAllocate(89, 125, 91);    #          66
    @green2 = ("$green10", " $green10", " $green9", " $green9", " $green6", " $green4", " $green2", "$green2", "$green1", "$green1", "$green4");
#    @green2 = reverse(@green2);
    $purple1 =  $im->colorAllocate(200, 150, 200);    #          8998
    $purple2 =  $im->colorAllocate(180, 140, 180);    #          8668 
    $purple4 =  $im->colorAllocate(160, 130, 160);    #          5445 
    $purple6 =  $im->colorAllocate(140, 120, 140);    #           22
    $purple9 =  $im->colorAllocate(120, 75, 120);    #          1111           
    $purple10 =  $im->colorAllocate(100, 50, 100);    #          66
    @purple = ("$purple10", " $purple9", " $purple6", " $purple6", " $purple4", " $purple2", " $purple1", " $purple6", " $purple10");

    $realblue1 =  $im->colorAllocate(55, 63, 138);    #
      $realblue2 = $im->colorAllocate(140,150,180);
#    $realblue2 =  $im->colorAllocate(124, 132, 207);    #
    $realblue3 =  $im->colorAllocate(158, 185, 202);    #
    $realblue4 =  $im->colorAllocate(174, 201, 218);    #
    $realblue5 =  $im->colorAllocate(186, 216, 227);    #
    $realblue6 =  $im->colorAllocate(177, 208, 254);    #
    $realblue7 =  $im->colorAllocate(161, 192, 238);    #
    $realblue8 =  $im->colorAllocate(149, 183, 220);    #
    $realblue7 =  $im->colorAllocate(161, 192, 238);    #
    $realblue9 =  $im->colorAllocate(170, 202, 249);    #
    $realblue10 =  $im->colorAllocate(188, 224, 246);    #
    $realblue11 =  $im->colorAllocate(203, 241, 254);    #
    $realblue12 =  $im->colorAllocate(210, 250, 255);    #
    $realblue13 =  $im->colorAllocate(204, 241, 249);    #
    $realblue14 =  $im->colorAllocate(192, 229, 237);    #
    $realblue15 =  $im->colorAllocate(120, 143, 151);
    $realblue16 =  $im->colorAllocate(146, 169, 177);    #
    $realblue17 =  $im->colorAllocate(187, 189, 201);    #
    $realblue18 =  $im->colorAllocate(213, 215, 227);    #
    #
@realblue = ("$realblue1","$realblue2","$realblue3","$realblue4","$realblue5","$realblue6","$realblue7","$realblue8","$realblue7","$realblue9","$realblue10","$realblue11","$realblue12","$realblue13","$realblue14","$realblue15","$realblue16","$realblue17","$realblue18");
#@realblue2 = ("$realblue1","$realblue2","$realblue3","$realblue4","$realblue5","$realblue6","$realblue7","$realblue8","$realblue7","$realblue9","$realblue10","$realblue11","$realblue12","$realblue13","$realblue14");
@realblue2 = ("$realblue2","$realblue2","$realblue2","$realblue3","$realblue8","$realblue7","$realblue6","$realblue10","$realblue10","$realblue11","$realblue11","$realblue12","$realblue13","$realblue18","$realblue8");

    $greyblue = $im->colorAllocate(140,150,180);

}