Bio::Graphics::Glyph::operon - The "polycistronic operon" glyph

Bio-Graphics documentation Contained in the Bio-Graphics distribution.

Index

Code Index:

NAME

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Bio::Graphics::Glyph::operon - The "polycistronic operon" glyph

SYNOPSIS

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  See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.

DESCRIPTION

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This glyph is used for drawing polycistronic operons. It is essentially a "segments" glyph in which subfeatures of specific types "TSS" and "terminator" are displayed as line+arrow and a red lollipop, respectively. Note that these are hardcoded SO types

OPTIONS

accepts standard options so far. This version does not yet allow user configuration of things like terminator color, promoter arrow size etc.

BUGS

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Please report them.

SEE ALSO

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AUTHOR

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Jim Hu <jimhu@tamu.edu>

Copyright (c) 2011 Texas A&M Univ.

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See DISCLAIMER.txt for disclaimers of warranty.

Bio-Graphics documentation Contained in the Bio-Graphics distribution. 
package Bio::Graphics::Glyph::operon;
 
use strict;
use base 'Bio::Graphics::Glyph::segments';
#use Data::Dumper;

sub draw_component {
  my $self = shift;
  my ($gd,$dx,$dy) = @_;
  my ($left,$top,$right,$bottom) = $self->bounds($dx,$dy);
 
 my $feature = $self->feature;

	 $feature->type =~ /^([\S_]+):/; 
 
	if ($1 eq 'TSS') {

		# draw the promoter as an arrow
		if ($feature->strand == 1){
			$self->vline($gd, $left, $top-5, ($top+$bottom)/2);
  			$self->arrow($gd,$left,$left+5,$top-5);
		}
		if ($feature->strand == -1){
			$self->vline($gd, $right, $top-5, ($top+$bottom)/2);
  			$self->arrow($gd,$right,$right-5,$top-5);
		}
		return;
 		
	}
	if ($1 eq 'terminator') {

		# draw the terminator as an lollipop
		if ($feature->strand >= 0){
			$self->vline($gd, $right, $top-5, ($top+$bottom)/2);
		    $gd->filledEllipse($right,$top-4,6,6,$self->translate_color('red'));
		}
		if ($feature->strand < 0){
			$self->vline($gd, $left, $top-5, ($top+$bottom)/2);
		    $gd->filledEllipse($left,$top-4,6,6,$self->translate_color('red'));
		}
		return;
 		
	}
	$self->SUPER::draw_component(@_);
 
}

sub pad_top{
	return 10;
}

sub pad_right{
	return 10;
}

sub pad_left{
	return 10;
}
 
sub default_width{
  return 20;  
}
 
sub vline {
  my $self  = shift;
  my $image = shift;
  my ($x,$y1,$y2) = @_;
  my $fg     = $self->set_pen;

  $image->line($x,$y1,$x,$y2,$fg);
}
 
1;