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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Graphics/Glyph/diamond.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,141 @@
+package Bio::Graphics::Glyph::diamond;
+# DAS-compatible package to use for drawing a colored diamond
+
+use strict;
+use vars '@ISA';
+use Bio::Graphics::Glyph::generic;
+@ISA = 'Bio::Graphics::Glyph::generic';
+
+sub draw_component {
+  my $self = shift;
+  my $gd = shift;
+  my $fg = $self->fgcolor;
+
+  # find the center and vertices
+  my ($x1,$y1,$x2,$y2) = $self->calculate_boundaries(@_);
+  my $xmid = ($x1+$x2)/2;
+  my $ymid = ($y1+$y2)/2;
+
+  my $h = $self->option('height')/2;
+  $y1 = $ymid - $h;
+  $y2 = $ymid + $h;
+
+  # if it's a point-like feature, then draw symmetrically
+  # around the midpoing
+  if ($self->option('point') || $x2 - $x1 < $h*2) {
+    $x1 = $xmid - $h;
+    $x2 = $xmid + $h;
+  }
+
+  elsif ($self->option('fallback_to_rectangle')) {
+    return $self->SUPER::draw_component($gd,@_);
+  }
+
+  $gd->line($x1,$ymid,$xmid,$y1,$fg);
+  $gd->line($xmid,$y1,$x2,$ymid,$fg);
+  $gd->line($x2,$ymid,$xmid,$y2,$fg);
+  $gd->line($xmid,$y2,$x1,$ymid,$fg);
+
+  if (my $c = $self->bgcolor) {
+    $gd->fillToBorder($xmid,$ymid,$fg,$c);
+  }
+}
+
+1;
+
+__END__
+
+=head1 NAME
+
+Bio::Graphics::Glyph::diamond - The "diamond" glyph
+
+=head1 SYNOPSIS
+
+  See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.
+
+=head1 DESCRIPTION
+
+This glyph draws a diamond of fixed size, positioned in the center of
+the feature.  The height and width of the diamond are set by the
+"height" option.
+
+=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
+
+If the feature is wider than a point, then the label and description
+are placed where the feature's boundary is, and not where the diamond
+is drawn.
+
+=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