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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Graphics/Glyph/transcript.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,190 @@
+package Bio::Graphics::Glyph::transcript;
+# $Id: transcript.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 = qw( Bio::Graphics::Glyph::segments);
+
+sub pad_left  {
+  my $self = shift;
+  my $pad  = $self->SUPER::pad_left;
+  return $pad if $self->{level} > 0;
+  my $strand = $self->feature->strand;
+  return $pad unless defined $strand && $strand < 0;
+  return $self->arrow_length > $pad ? $self->arrow_length : $pad;
+}
+
+sub pad_right {
+  my $self = shift;
+  my $pad  = $self->SUPER::pad_right;
+  return $pad if $self->{level} > 0;
+  my $strand = $self->feature->strand;
+  return $pad unless defined($strand) && $strand > 0;
+  return $self->arrow_length > $pad ? $self->arrow_length : $pad;
+}
+
+sub draw_component {
+  my $self = shift;
+  return unless $self->level > 0;
+  $self->SUPER::draw_component(@_);
+}
+
+sub draw_connectors {
+  my $self = shift;
+  my $gd = shift;
+  my ($left,$top) = @_;
+  $self->SUPER::draw_connectors($gd,$left,$top);
+  my @parts = $self->parts;
+
+  # H'mmm.  No parts.  Must be in an intron, so draw intron
+  # spanning entire range
+  if (!@parts) {
+    my($x1,$y1,$x2,$y2) = $self->bounds(0,0);
+    $self->_connector($gd,$left,$top,$x1,$y1,$x1,$y2,$x2,$y1,$x2,$y2);
+    @parts = $self;
+  }
+
+  # flip argument makes this confusing
+  # certainly there's a simpler way to express this idea
+  my $strand    = $self->feature->strand;
+  my ($first,$last) = ($parts[0],$parts[-1]);
+  ($first,$last) = ($last,$first) if exists $self->{flip};
+
+  if ($strand >= 0) {
+    my($x1,$y1,$x2,$y2) = $last->bounds(@_);
+    my $center = ($y2+$y1)/2;
+    $self->{flip} ?
+	$self->arrow($gd,$x1,$x1-$self->arrow_length,$center)
+      :
+	$self->arrow($gd,$x2,$x2+$self->arrow_length,$center);
+  } else {
+    my($x1,$y1,$x2,$y2) = $first->bounds(@_);
+    my $center = ($y2+$y1)/2;
+    $self->{flip } ?
+	$self->arrow($gd,$x2,$x2+$self->arrow_length,$center)
+      :
+	$self->arrow($gd,$x1,$x1 - $self->arrow_length,$center);
+  }
+}
+
+sub arrow_length {
+  my $self = shift;
+  return $self->option('arrow_length') || 8;
+}
+
+# override option() for force the "hat" type of connector
+sub connector {
+  my $self = shift;
+  return $self->SUPER::connector(@_) if $self->all_callbacks;
+  return ($self->option('connector') || 'hat');
+}
+
+
+1;
+
+__END__
+
+=head1 NAME
+
+Bio::Graphics::Glyph::transcript - The "transcript" glyph
+
+=head1 SYNOPSIS
+
+  See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.
+
+=head1 DESCRIPTION
+
+This glyph is used for drawing transcripts.  It is essentially a
+"segments" glyph in which the connecting segments are hats.  The
+direction of the transcript is indicated by an arrow attached to the
+end of the glyph.
+
+=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
+  ------         -----------                  -------
+
+  -arrow_length  Length of the directional   8
+                 arrow.
+
+=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