Raw content of Bio::Graphics::Glyph::heterogeneous_segments
<![CDATA[package Bio::Graphics::Glyph::heterogeneous_segments;
# this glyph acts like graded_segments but the bgcolor of each segment is
# controlled by the source field of the feature. Use the source field name
# to set the background color:
# -waba_strong => 'blue'
# -waba_weak => 'red'
# -waba_coding => 'green'
# $Id: heterogeneous_segments.pm,v 1.5 2002/12/23 01:33:41 lstein Exp $
use strict;
use Bio::Graphics::Glyph::graded_segments;
use vars '@ISA';
@ISA = 'Bio::Graphics::Glyph::graded_segments';
# override draw method to calculate the min and max values for the components
sub draw {
my $self = shift;
# bail out if this isn't the right kind of feature
# handle both das-style and Bio::SeqFeatureI style,
# which use different names for subparts.
my @parts = $self->parts;
@parts = $self if !@parts && $self->level == 0;
return $self->SUPER::draw(@_) unless @parts;
# figure out the colors
$self->{source2color} ||= {};
my $fill = $self->bgcolor;
for my $part (@parts) {
my $s = eval { $part->feature->source_tag } or next;
$self->{source2color}{$s} ||= $self->color(lc($s)."_color") || $fill;
$part->{partcolor} = $self->{source2color}{$s};
}
$self->Bio::Graphics::Glyph::generic::draw(@_);
}
# synthesize a key glyph
sub keyglyph {
my $self = shift;
my $scale = 1/$self->scale; # base pairs/pixel
# two segments, at pixels 0->50, 60->80
my $offset = $self->panel->offset;
my $feature =
Bio::Graphics::Feature->new(
-segments=>[ [ 0*$scale +$offset,25*$scale+$offset],
[ 25*$scale +$offset,50*$scale+$offset],
[ 50*$scale+$offset, 75*$scale+$offset]
],
-name => $self->option('key'),
-strand => '+1');
my @sources = grep {/_color$/} $self->factory->options;
foreach (@sources) {s/_color$//}
($feature->segments)[0]->source_tag($sources[1]);
($feature->segments)[1]->source_tag($sources[0]);
($feature->segments)[2]->source_tag($sources[2]);
my $factory = $self->factory->clone;
$factory->set_option(label => 1);
$factory->set_option(bump => 0);
$factory->set_option(connector => 'solid');
my $glyph = $factory->make_glyph(0,$feature);
return $glyph;
}
1;
=head1 NAME
Bio::Graphics::Glyph::heterogeneous_segments - The "heterogeneous_segments" glyph
=head1 SYNOPSIS
See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.
=head1 DESCRIPTION
This glyph acts like graded_segments but the bgcolor of each segment (sub-feature)
can be individually set using the source field of the feature.
Each segment type color is specified using the following nomenclature:
-{source}_color => $color
For example, if the feature consists of a gene containing both
confirmed and unconfirmed exons, you can make the confirmed exons
green and the unconfirmed ones red this way:
-confirmed_color => 'green',
-unconfirmed_color => 'red'
=head2 OPTIONS
The following options are standard among all Glyphs. See
L<Bio::Graphics::Glyph> for a full explanation.
Option Description Default
------ ----------- -------
-fgcolor Foreground color black
-outlinecolor Synonym for -fgcolor
-bgcolor Background color turquoise
-fillcolor Synonym for -bgcolor
-linewidth Line width 1
-height Height of glyph 10
-font Glyph font gdSmallFont
-connector Connector type 0 (false)
-connector_color
Connector color black
-label Whether to draw a label 0 (false)
-description Whether to draw a description 0 (false)
=head1 BUGS
Please report them.
=head1 SEE ALSO
L<Bio::Graphics::Panel>,
L<Bio::Graphics::Glyph>,
L<Bio::Graphics::Glyph::arrow>,
L<Bio::Graphics::Glyph::cds>,
L<Bio::Graphics::Glyph::crossbox>,
L<Bio::Graphics::Glyph::diamond>,
L<Bio::Graphics::Glyph::dna>,
L<Bio::Graphics::Glyph::dot>,
L<Bio::Graphics::Glyph::ellipse>,
L<Bio::Graphics::Glyph::extending_arrow>,
L<Bio::Graphics::Glyph::generic>,
L<Bio::Graphics::Glyph::graded_segments>,
L<Bio::Graphics::Glyph::heterogeneous_segments>,
L<Bio::Graphics::Glyph::line>,
L<Bio::Graphics::Glyph::pinsertion>,
L<Bio::Graphics::Glyph::primers>,
L<Bio::Graphics::Glyph::rndrect>,
L<Bio::Graphics::Glyph::segments>,
L<Bio::Graphics::Glyph::ruler_arrow>,
L<Bio::Graphics::Glyph::toomany>,
L<Bio::Graphics::Glyph::transcript>,
L<Bio::Graphics::Glyph::transcript2>,
L<Bio::Graphics::Glyph::translation>,
L<Bio::Graphics::Glyph::triangle>,
L<Bio::DB::GFF>,
L<Bio::SeqI>,
L<Bio::SeqFeatureI>,
L<Bio::Das>,
L<GD>
=head1 AUTHOR
Lincoln Stein E<lt>lstein@cshl.orgE<gt>
Copyright (c) 2001 Cold Spring Harbor Laboratory
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.
=cut
]]>