Summary

Bio::Graphics::Glyph::redgreen_box - The "redgreen_box" glyph

Package variables

Included modules

Inherit

Bio::Graphics::Glyph::generic

Synopsis

  See Bio::Graphics::Panel and Bio::Graphics::Glyph.

Description

This glyph is similar to the graded_segments glyph except that it
generates a green->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. The following options are standard among all Glyphs. See
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

Methods

Methods description

None available.

Methods code

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);

}

General documentation

Please report them.

Bio::Graphics::Panel,
Bio::Graphics::Glyph,
Bio::Graphics::Glyph::arrow,
Bio::Graphics::Glyph::cds,
Bio::Graphics::Glyph::crossbox,
Bio::Graphics::Glyph::diamond,
Bio::Graphics::Glyph::dna,
Bio::Graphics::Glyph::dot,
Bio::Graphics::Glyph::ellipse,
Bio::Graphics::Glyph::extending_arrow,
Bio::Graphics::Glyph::generic,
Bio::Graphics::Glyph::graded_segments,
Bio::Graphics::Glyph::heterogeneous_segments,
Bio::Graphics::Glyph::line,
Bio::Graphics::Glyph::pinsertion,
Bio::Graphics::Glyph::primers,
Bio::Graphics::Glyph::rndrect,
Bio::Graphics::Glyph::segments,
Bio::Graphics::Glyph::ruler_arrow,
Bio::Graphics::Glyph::toomany,
Bio::Graphics::Glyph::transcript,
Bio::Graphics::Glyph::transcript2,
Bio::Graphics::Glyph::translation,
Bio::Graphics::Glyph::triangle,
Bio::DB::GFF,
Bio::SeqI,
Bio::SeqFeatureI,
Bio::Das,
GD

Lincoln Stein <lstein@cshl.org>
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.