#use GD;
use strict;
use warnings;

my @x1;
my @y1;
my $max1;
my $min1;
my $lines = LoadFile ("fwd.stb", \@x1, \@y1, \$min1, \$max1);

# Define constants
my    $X1start = 50+20;  # X-axis
my    $Y1start = 300;    #  X-axis
my    $X1end   = 450+$lines-400; # X-axis
my    $Y1end   = 300;  # X-axis
my    $X2start = 50+20;
my    $Y2start = 100;
my    $X2end   = 50+20;
my    $Y2end   = 300;

# create a new image
my  $im = new GD::Image($X1end+50,$Y2end+100);

# allocate some colors
my  $white = $im->colorAllocate(255,255,255);
my  $green = $im->colorAllocate(0,255,0);
my  $black = $im->colorAllocate(0,0,0);
my  $red = $im->colorAllocate(255,0,0);
my  $blue = $im->colorAllocate(0,0,255);

# set the caption for the graph
$im->string(gdLargeFont,int($lines/2)-50,20,"ENERGY GRAPH",$black);

# draw the y-axis & x-axis
$im->line($X2start,$Y2start,$X2end,$Y2end,$black);
$im->line($X1start,$Y1start,$X1end,$Y1end,$black);

# set the caption for x-axis and y-axis
$im->string(gdLargeFont,int($lines/2)-50,335,"NUCLEOTIDE POSITION",$bl
+ack);
$im->stringUp(gdLargeFont,5,260,"FREE ENERGY(delta G)",$black);

$im->string(gdSmallFont,int($lines/2)+100,20," Genomic  Sequence -----
+--",$red);
$im->string(gdSmallFont,int($lines/2)+100,40," Shuffled Sequence -----
+--",$blue);

my @x2;
my @y2; ## Was @Y2 - probably a bug. Caught by use strict
my $min2;
my $max2;

$lines = LoadFile ("total_shuffle.stb", \@x1, \@y1, \$min2, \$max2);

my $min = $min1 <= $min2 ? $min1 : $min2;
my $max = $max1 >= $max2 ? $max1 : $max2;

my @y = @y1;
my @x = @x1;
graph();

@y = @y2;
@x = @x2;
my  $png_data = $im->png;

open (DISPLAY,"| display -") || die;
#open (DISPLAY,">image.jpg") || die;
binmode DISPLAY;
print DISPLAY $png_data;
close DISPLAY;

sub graph {
    # set min and max energy
    my $minEnergy = $min;
    my $maxEnergy = $max;
    
    # set the length of x-axis and y-axis
    my $xLen = $X1end-$X1start;
    my $yLen = $Y2end-$Y2start;
    
    # Scaling the values
    my $Yscale = $yLen/(abs($minEnergy)-abs($maxEnergy));
    my $scale = ($minEnergy-$maxEnergy)/5;
    my $incEnergy = $maxEnergy;
    
    while ($incEnergy > $minEnergy) { ##### Prob loop####
        my $x1 = $X1start-2;
        my $y1 = int(((abs($incEnergy)-abs($maxEnergy))*$Yscale)+$Y2st
+art);
        my $x2 = $X1start+2;
        
        $im->line($x1,$y1,$x2,$y1,$black);
        my $displayEnergy = sprintf("%2.1f",$incEnergy);
        $im->string(gdSmallFont,$x1-35,$y1-10,$displayEnergy,$black);
        $incEnergy = $incEnergy+$scale;
    }
    
    my $count = 0; ## $count was not declared
    my $len = @x; # set the length of nucleotide
    my $posSkip = int(@x/10); # mark 10 points on the position axis
    my $skipPixel = $xLen/$len; # If the length of the fragment is les
+ser than the x-axis
    
    for(my $i=0;$i<$len-1;$i++) {
        my $x1 = int(($i*$skipPixel)+$X1start);
        my $y1 = int(((abs($y[$i])-abs($maxEnergy))*$Yscale)+$Y2start)
+;
        my $x2 = int((($i+1)*$skipPixel)+$X1start);
        my $y2 = int(((abs($y[$i+1])-abs($maxEnergy))*$Yscale)+$Y2star
+t);
        
        ## graph is only called once in this code so $call can only ev
+er be undef
        ##if($call == 0) {
            $im->line($x1,$y1,$x2,$y2,$red);
        ##} else {
        ##    $im->line($x1,$y1,$x2,$y2,$blue);
        ##}
        $count++;
        
        if($count == $posSkip) {
            $x1 = int(($i*$skipPixel)+$X1start);
            $y1 = $Y1end-2;
            $x2 = int(($i*$skipPixel)+$X1start);
            $y2 = $Y1end+2;
            
            ## graph is only called once in this code so $call can onl
+y ever be undef
            ##if($call == 0) {
                $im->line($x1,$y1,$x2,$y2,$black);
                $im->string(gdSmallFont,$x1,$y1+10,$i+1,$black);
            ##}
            $count = 0;
        }
    }
    
    ## graph is only called once in this code so $call can only ever b
+e undef
    ## $call++;
}


## Common file reading code in sub
sub LoadFile {
    my ($filename, $x, $y, $min, $max) = @_;
    
    ## Three parameter open and check result
    open FILE1,'<', $filename or die "Failed to open $filename: $!"; 
    
    ## Remove $i from while loop - [-1] is last element
    while(<FILE1>) {
        my @value = split(/\s+/,$_);
    
        next if 2 != @value; # Skip if bad input line - could die or w
+arn
        
        push @x, $value[0]-7;
        push @y, $value[1];
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        if(@$x1) {
            $$max = $y->[-1] if $y->[-1] > $max;
            $$min = $y->[-1] if $y->[-1] < $min;
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        if(@$x) {
            $$max = $y->[-1] if $y->[-1] > $$max;
            $$min = $y->[-1] if $y->[-1] < $$min;
        } else {
            $$min = $$max = $y->[-1];
        }
    }
    
    return $.; ## Number of lines
}
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