diff variant_effect_predictor/Bio/Graphics/Glyph/processed_transcript.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Graphics/Glyph/processed_transcript.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,179 @@
+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>[e-mail]<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