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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Graphics/Glyph/dot.pm	Fri Aug 03 10:04:48 2012 -0400
@@ -0,0 +1,150 @@
+package Bio::Graphics::Glyph::dot;
+# DAS-compatible package to use for drawing a ring or filled circle
+
+use strict;
+use vars '@ISA';
+use Bio::Graphics::Glyph::generic;
+@ISA = 'Bio::Graphics::Glyph::generic';
+use constant PI => 3.14159;
+
+sub draw {
+  my $self = shift;
+#  $self->SUPER::draw(@_);
+  my $gd = shift;
+  my $fg = $self->fgcolor;
+
+  # now draw a circle
+  my ($x1,$y1,$x2,$y2) = $self->calculate_boundaries(@_);
+  my $xmid   = (($x1+$x2)/2);  my $width  = abs($x2-$x1);
+  my $ymid   = (($y1+$y2)/2);  my $height = abs($y2-$y1);
+
+  #only point ovals allowed now
+  my $r = $self->height ;
+    $gd->arc($xmid,$ymid,$r,$r,0,360,$fg);
+
+
+  if ($self->option('bgcolor')){
+    my $c = $self->color('bgcolor');
+    $gd->fill($xmid,$ymid,$c);
+  }
+
+  #how about a fuse for the bomb?
+  #work in degrees, not radians.  So we define PI above
+  if(defined $self->option('stem')){
+    my $angle = $self->option('stem');
+
+    $gd->line($xmid+($r/PI*sin($angle*PI/180)),
+	      $ymid+($r/PI*cos($angle*PI/180)),
+	      $xmid+($r*sin($angle*PI/180)),
+	      $ymid+($r*cos($angle*PI/180)),$fg);
+  }
+
+  $self->draw_label($gd,@_) if $self->option('label');
+}
+
+1;
+
+__END__
+
+=head1 NAME
+
+Bio::Graphics::Glyph::dot - The "dot" glyph
+
+=head1 SYNOPSIS
+
+  See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.
+
+=head1 DESCRIPTION
+
+This glyph draws an ellipse the width of the scaled feature passed,
+and height a possibly configured height (See Bio::Graphics::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 to the common options, the following glyph-specific
+options are recognized:
+
+  Option      Description                  Default
+  ------      -----------                  -------
+
+  -point      Whether to draw an ellipse   feature width
+              the scaled width of the
+              feature or with radius
+              point.
+
+=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>.
+
+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