diff variant_effect_predictor/Bio/Graphics/Glyph/pinsertion.pm @ 0:21066c0abaf5 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Graphics/Glyph/pinsertion.pm	Fri Aug 03 10:04:48 2012 -0400
@@ -0,0 +1,127 @@
+package Bio::Graphics::Glyph::pinsertion;
+# package to use for drawing P insertion as a triangle
+# p insertion is a point (one base).
+
+use strict;
+use GD;
+use vars '@ISA';
+@ISA = 'Bio::Graphics::Glyph::generic';
+use Bio::Graphics::Glyph::generic;
+
+sub box {
+  my $self = shift;
+  my $half = $self->insertion_width/2;
+  return ($self->left-$half,$self->top,$self->right+$half,$self->bottom);
+}
+
+sub insertion_width {
+  my $self = shift;
+  return $self->option('insertion_width') || 6;
+}
+
+# override draw method
+sub draw {
+  my $self = shift;
+
+  my $gd = shift;
+  my ($left,$top) = @_;
+  my ($x1,$y1,$x2,$y2) = $self->calculate_boundaries(@_);
+
+  my $height = $self->height;
+
+  my $half = $self->insertion_width/2;
+
+  my $fill = $self->bgcolor;
+
+  my $poly = GD::Polygon->new;
+
+  if ($self->feature->strand > 0) { #plus strand
+      $poly->addPt($x1 - $half, $y1);
+      $poly->addPt($x1 + ($half), $y1);
+      $poly->addPt($x1, $y2); #pointer down
+  } else {
+      $poly->addPt($x1, $y1); #pointer up
+      $poly->addPt($x1 - $half, $y2);
+      $poly->addPt($x1 + ($half), $y2);
+  }
+  $gd->filledPolygon($poly, $fill);
+  $gd->polygon($poly, $fill);
+
+  # add a label if requested
+  $self->draw_label($gd,$left,$top)       if $self->option('label');
+  $self->draw_description($gd,$left,$top) if $self->option('description');
+}
+
+
+1;
+
+=head1 NAME
+
+Bio::Graphics::Glyph::pinsertion - The "Drosophila P-element Insertion" glyph
+
+=head1 SYNOPSIS
+
+  See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.
+
+=head1 DESCRIPTION
+
+This glyph was designed to show P-element insertions in the Drosophila
+genome, but in fact is suitable for any type of zero-width feature.
+Also see the triangle glyph.
+
+=head2 OPTIONS
+
+In addition to the generic options, this glyph recognizes:
+
+ Option Name       Description              Default
+ -----------       -----------              -------
+
+ -insertion_width  Width of glyph in pixels    3
+
+=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
+
+Allen Day E<lt>[e-mail]<gt>, Shengqiang Shu E<lt>[e-mail]<gt>
+
+Copyright (c) 2001 Cold Spring Harbor Laboratory, BDGP
+
+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