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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Graphics/Glyph/heterogeneous_segments.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,174 @@
+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>[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