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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Graphics/Glyph/redgreen_box.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,191 @@
+package Bio::Graphics::Glyph::redgreen_box;
+#$Id: redgreen_box.pm,v 1.4.2.1 2003/07/05 00:32:04 lstein Exp $
+
+use strict;
+use Bio::Graphics::Glyph::generic;
+use vars '@ISA';
+@ISA = 'Bio::Graphics::Glyph::generic';
+
+sub bgcolor {
+  my $self = shift;
+  $self->{force_bgcolor};
+}
+
+sub fgcolor {
+  my $self = shift;
+  return $self->option('border') ? $self->SUPER::fgcolor : $self->{force_bgcolor};
+}
+
+sub draw {
+  my $self = shift;
+  my $val  = $self->feature->score;
+
+  # we're going to force all our parts to share the same colors
+  # since the
+  my @parts = $self->parts;
+  @parts    = $self if !@parts && $self->level == 0;
+  my @rgb   = map {int($_)} HSVtoRGB(120*(1-$val),1,255);
+  my $color =  $self->panel->translate_color(@rgb);
+  $_->{force_bgcolor} = $color foreach @parts;
+
+  $self->SUPER::draw(@_);
+}
+
+sub HSVtoRGB ($$$) {
+  my ($h,$s,$v)=@_;
+  my ($r,$g,$b,$i,$f,$p,$q,$t);
+
+  if( $s == 0 ) {
+    ## achromatic (grey)
+    return ($v,$v,$v);
+  }
+
+  $h /= 60;                       ## sector 0 to 5
+  $i = int($h);
+  $f = $h - $i;                   ## factorial part of h
+  $p = $v * ( 1 - $s );
+  $q = $v * ( 1 - $s * $f );
+  $t = $v * ( 1 - $s * ( 1 - $f ) );
+  
+  if($i<1) {
+    $r = $v;
+    $g = $t;
+    $b = $p;
+  } elsif($i<2){
+    $r = $q;
+    $g = $v;
+    $b = $p;
+  } elsif($i<3){
+    $r = $p;
+    $g = $v;
+    $b = $t;
+  } elsif($i<4){
+    $r = $p;
+    $g = $q;
+    $b = $v;
+  } elsif($i<5){
+    $r = $t;
+    $g = $p;
+    $b = $v;
+  } else {
+    $r = $v;
+    $g = $p;
+    $b = $q;
+  }
+  return ($r,$g,$b);
+}
+
+sub mMin {
+        my $n=10000000000000;
+        map { $n=($n>$_) ? $_ : $n } @_;
+        return($n);     
+}
+
+sub mMax {
+        my $n=0;
+        map { $n=($n<$_) ? $_ : $n } @_;
+        return($n);     
+}
+
+
+1;
+
+=head1 NAME
+
+Bio::Graphics::Glyph::redgreen_box - The "redgreen_box" glyph
+
+=head1 SYNOPSIS
+
+  See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.
+
+=head1 DESCRIPTION
+
+This glyph is similar to the graded_segments glyph except that it
+generates a green-E<gt>red gradient suitable for use with microarray data.
+A feature score of 0 is full green; a feature score of 1.0 is full
+red; intermediate scores are shades of yellow.
+
+=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)
+
+The following glyph-specific option is recognized:
+
+  -border       Draw a fgcolor border around   0 (false)
+                the box
+
+
+=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