view variant_effect_predictor/Bio/Graphics/Glyph/redgreen_box.pm @ 3:d30fa12e4cc5 default tip

Merge heads 2:a5976b2dce6f and 1:09613ce8151e which were created as a result of a recently fixed bug.

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