view release on metacpan or  search on metacpan

lib/Bio/GeneDesign/Graph.pm  view on Meta::CPAN

{
  my ($seq1, $seq2, $winsize, $stringency, $outfile) = @_;
  my $Lseq1 = length($seq1);
  my $Lseq2 = length($seq2);

  my $BitMap = GD::Image->new($Lseq1, $Lseq2);

  my $white = $BitMap->colorAllocate(255,255,255);
  my $black = $BitMap->colorAllocate(0,0,0);

  $BitMap->transparent($white);

  for (my $i = 0; $i < $Lseq1 - $winsize; $i++)
  {
    for (my $j = 0; $j < $Lseq2 - $winsize; $j++)
    {
      my $match = 0;
      for (my $w = 0; $w < $winsize; $w++)
      {
        if (substr($seq1, $i + $w, 1) eq substr($seq2, $j + $w, 1))
        {