#!/usr/bin/perl
use strict;
use warnings;
use Data::Dumper;
use Bio::Graphics::DrawTransmembrane;

my $topology_final = 'IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII0IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIMMMMMMMMMOOOOOOOOOOOOOOOMMMMMMMIIIMMMMMMMMMOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOMMMMMMMMMIIIMMMMMMMMMOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOMMMMMMMMMIIIIIIIMMMMMMMMMMMOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOMMMMMMMMMMMIIIMMMMMMMMMMMOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOMMMMMMMMMMMIIIIIMMMMMMMMMOOOOOOOMMMMMMMMMMMIIIMMMMMMMMMMMOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOMMMMMMMMMMMIIIIMMMMMMMOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOMMMMMMMMMIIIMMMMMMMMMMMOOOOOOOOOOOOOOMMMMMMMMMMMIIIIIMMMMMMMMMOOOOOOOOOOOOOOOOOOOOOOOOOOOMMMMMMMMMMMIIIMMMMMMMOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOMMMMMMMMM';

my @total_top = ();
if($topology_final=~/M/) {
    while ($topology_final =~/(.)\1*/g) {
	if ($1 eq "M") {
	    my $start_TM = $-[0] + 1;
	    my $end_TM = $+[0];
	    
	    push @total_top, $start_TM;
	    push @total_top, $end_TM;
	}
    }
}

print Dumper(\@total_top);

## More advanced use
my %labels = ( 176 => '5 - Sulphation Site',
	       206 => '1st Helix',
	       256 => '40 - Mutation',
	       276 => 'Voltage Sensor',
	       316 => '72 - Mutation 2',
	       392 => '73 - Mutation 3',
	       489 => '138 - Glycosylation Site',
	       539 => '170 - Phosphorylation Site',
	       747 => 'Last Helix' );

my $image = Bio::Graphics::DrawTransmembrane->new( 
    -title=>"topology prediction image",
    -n_terminal=>'in',
    -topology=>\@total_top,
    -bold_helices=> 1,
    -labels=> \%labels,
    -bold_labels => 1,
    -text_offset=>-25,
    -helix_label=>'b',
    -outside_label=>'Extracellular',
    -inside_label=>'Periplasm',
    -membrane_label=>'Membrane',
    -helix_width=>30,
    -vertical_padding=>150,
    -horizontal_padding=>120,
    -n_terminal_offset=>50,
    -n_terminal_height=>220,
    -c_terminal_offset=>30,
    -c_terminal_height=>220,
    -helix_label=>'Sheet',
    -colour_scheme=>'yellow');    

open (OUTPUT, '>', 'test.png');
binmode OUTPUT;
print OUTPUT $image->png; 
close (OUTPUT);