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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Graphics/Glyph/splice_site.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,115 @@
+package Bio::Graphics::Glyph::splice_site;
+
+use strict;
+use vars '@ISA';
+@ISA = 'Bio::Graphics::Glyph::generic';
+use Bio::Graphics::Glyph::generic;
+
+use constant PWIDTH => 3;
+
+sub draw_component {
+  my $self = shift;
+  my $gd = shift;
+  my ($left,$top) = @_;
+  my($x1,$y1,$x2,$y2) = $self->bounds(@_); 
+
+  my $center = int(0.5+($x1+$x2)/2);
+  my $direction = $self->option('direction');
+  
+  my $height    = $y2 - $y1;
+  my $fraction  = $self->option('height_fraction') || 1.0;
+  my $bottom    = $y2;
+  $top          = $y2 - $fraction * $height;
+  
+  # draw the base
+  my $fgcolor = $self->fgcolor;
+  $gd->line($center,$bottom,$center,$top,$fgcolor);
+
+  if ($direction eq 'right') {
+    $gd->line($center,$top,$center + PWIDTH,$top,$fgcolor);
+  } elsif ($direction eq 'left') {
+    $gd->line($center,$top,$center - PWIDTH,$top,$fgcolor);
+  }
+    
+}
+
+1;
+
+
+=head1 NAME
+
+Bio::Graphics::Glyph::splice_site - The "splice_site" glyph
+
+=head1 SYNOPSIS
+
+  See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.
+
+=head1 DESCRIPTION
+
+This glyph was designed to show an inverted "L" representing splice
+donors and acceptors.  The vertical part of the L points downwards and
+is positioned in the center of the range (even if the range is quite
+large).  
+
+In addition to the usual glyph options, this glyph recognizes:
+
+   Option            Value              Description
+   ------            -----              -----------
+
+   direction         "left" or "right"  direction the short part of the L
+                                        points
+
+   height_fraction   0.0 - 1.0          fractional height of the glyph,
+                                        usually a callback that uses the
+                                        feature's score to determine its
+                                        height
+
+=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::chromosome>,
+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
+
+Xiaokang Pan E<lt>[e-mail]<gt>
+
+Copyright (c) 2001 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