Raw content of Bio::Graphics::Glyph::graded_segments
<![CDATA[package Bio::Graphics::Glyph::graded_segments;
#$Id: graded_segments.pm,v 1.12.2.1 2003/07/05 00:32:04 lstein Exp $
use strict;
use Bio::Graphics::Glyph::segments;
use vars '@ISA';
@ISA = 'Bio::Graphics::Glyph::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
my $max_score = $self->option('max_score');
my $min_score = $self->option('min_score');
unless (defined $max_score && defined $min_score) {
for my $part (@parts) {
my $s = eval { $part->feature->score };
next unless defined $s;
$max_score = $s if !defined $max_score or $s > $max_score;
$min_score = $s if !defined $min_score or $s < $min_score;
}
}
return $self->SUPER::draw(@_)
unless defined($max_score) && defined($min_score)
&& $min_score < $max_score;
my $span = $max_score - $min_score;
# allocate colors
my $fill = $self->bgcolor;
my ($red,$green,$blue) = $self->panel->rgb($fill);
foreach my $part (@parts) {
my $s = eval { $part->feature->score };
unless (defined $s) {
$part->{partcolor} = $fill;
next;
}
my ($r,$g,$b) = $self->calculate_color($s,[$red,$green,$blue],$min_score,$span);
my $idx = $self->panel->translate_color($r,$g,$b);
$part->{partcolor} = $idx;
}
$self->SUPER::draw(@_);
}
sub calculate_color {
my $self = shift;
my ($s,$rgb,$min_score,$span) = @_;
return map { 255 - (255-$_) * min(max( ($s-$min_score)/$span, 0), 1) } @$rgb;
}
sub min { $_[0] < $_[1] ? $_[0] : $_[1] }
sub max { $_[0] > $_[1] ? $_[0] : $_[1] }
sub subseq {
my $class = shift;
my $feature = shift;
return $feature->segments if $feature->can('segments');
return $feature->sub_SeqFeature if $feature->can('sub_SeqFeature');
return;
}
# 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 +$offset,20*$scale+$offset],
[ 30*$scale +$offset,50*$scale+$offset],
[60*$scale+$offset, 80*$scale+$offset]
],
-name => $self->option('key'),
-strand => '+1');
($feature->segments)[0]->score(10);
($feature->segments)[1]->score(50);
($feature->segments)[2]->score(100);
my $factory = $self->factory->clone;
$factory->set_option(label => 1);
$factory->set_option(bump => 0);
$factory->set_option(connector => 'solid');
return $factory->make_glyph($feature);
}
# component draws a shaded box
sub bgcolor {
my $self = shift;
return $self->{partcolor} || $self->SUPER::bgcolor;
}
sub fgcolor {
my $self = shift;
return $self->{partcolor} || $self->SUPER::fgcolor;
}
1;
=head1 NAME
Bio::Graphics::Glyph::graded_segments - The "graded_segments" glyph
=head1 SYNOPSIS
See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.
=head1 DESCRIPTION
This is identical to the "alignment" glyph, and is used for
drawing features that consist of discontinuous segments. The
color intensity of each segment is proportionate to the score.
=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)
In addition, the alignment glyph recognizes the following
glyph-specific options:
Option Description Default
------ ----------- -------
-max_score Maximum value of the Calculated
feature's "score" attribute
-min_score Minimum value of the Calculated
feature's "score" attribute
If max_score and min_score are not specified, then the glyph will
calculate the local maximum and minimum scores at run time.
=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
]]>