Raw content of Bio::Graphics::Glyph::processed_transcript
<![CDATA[package Bio::Graphics::Glyph::processed_transcript;
# $Id: processed_transcript.pm,v 1.3.2.1 2003/07/05 00:32:04 lstein Exp $
use strict;
use Bio::Graphics::Glyph::transcript2;
use vars '@ISA';
@ISA = 'Bio::Graphics::Glyph::transcript2';
use constant DEFAULT_UTR_COLOR => '#D0D0D0';
sub is_utr {
my $self = shift;
return $self->feature->primary_tag =~ /UTR|untranslated_region/i;
}
sub thin_utr {
my $self = shift;
$self->option('thin_utr');
}
sub utr_color {
my $self = shift;
return $self->color('utr_color') if $self->option('utr_color');
return $self->factory->translate_color(DEFAULT_UTR_COLOR);
}
sub height {
my $self = shift;
my $height = $self->SUPER::height;
return $height unless $self->thin_utr;
return $self->is_utr ? int($height/1.5+0.5) : $height;
}
sub pad_top {
my $self = shift;
my $pad_top = $self->SUPER::pad_top;
return $pad_top unless $self->thin_utr && $self->is_utr;
return $pad_top + int(0.167*$self->SUPER::height + 0.5);
}
sub bgcolor {
my $self = shift;
return $self->SUPER::bgcolor unless $self->is_utr;
return $self->utr_color;
}
sub connector {
my $self = shift;
return 'quill' if $self->option('decorate_introns');
return $self->SUPER::connector(@_);
}
1;
__END__
=head1 NAME
Bio::Graphics::Glyph::processed_transcript - The sequence ontology transcript glyph
=head1 SYNOPSIS
See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.
=head1 DESCRIPTION
This glyph is used for drawing processed transcripts that have both
CDS and UTR segments. The CDS is drawn in the background color, and
the UTRs are drawn in an alternate color selected by the utr_color
option. In addition, you can make the UTRs thinner than the CDS by
setting the "thin_utr" option.
For this glyph to produce the desired results, you should pass it a
compound Bio::SeqFeature that has subfeatures of primary_tag "CDS" and
"UTR". In fact, you may give it more specific types of UTR, including
5'-UTR, 3'-UTR, or the Sequence Ontology terms "untranslated_region,"
"five_prime_untranslated_region," and
"three_prime_untranslated_region."
=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 undef (false)
-connector_color
Connector color black
-label Whether to draw a label undef (false)
-description Whether to draw a description undef (false)
-strand_arrow Whether to indicate undef (false)
strandedness
In addition, the alignment glyph recognizes the following
glyph-specific options:
Option Description Default
------ ----------- -------
-thin_utr Flag. If true, UTRs will undef (false)
be drawn at 2/3 of the
height of CDS segments.
-utr_color Color of UTR segments. Gray #D0D0D0
-decorate_introns
Draw strand with little arrows undef (false)
on the intron.
=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
]]>