package Bio::Graphics::Glyph::redgreen_box;
use strict;
use base qw(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 color_subparts { shift->option('color_subparts') }
sub bump {
my $self = shift;
return 0 if $self->color_subparts;
return $self->SUPER::bump;
}
sub draw {
my $self = shift;
my $val = $self->feature->score;
# we're going to force all our parts to share the same colors
# unless otherwise requested
my @parts = $self->parts;
@parts = $self if !@parts && $self->level == 0;
unless ($self->color_subparts) {
my @rgb = map {int($_)} HSVtoRGB(120*(1-$val),1,255);
my $color = $self->panel->translate_color(@rgb);
$_->{force_bgcolor} = $color foreach @parts;
} else {
foreach (@parts) {
my $val = $_->feature->score;
my @rgb = map {int($_)} HSVtoRGB(120*(1-$val),1,255);
my $color = $self->panel->translate_color(@rgb);
$_->{force_bgcolor} = $color;
}
}
$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)
-hilite Highlight color undef (no color)
The following glyph-specific option is recognized:
-border Draw a fgcolor border around 0 (false)
the box
-color_subparts
Give each subpart a separate 0 (false)
color based on its score
If the B<-color_subparts> option is true, then the glyph will
individually coloriz each of its subparts. In addition, internal
bumping of features will be turned off. This will produce an effect
similar to graded_segments.
=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>lstein@cshl.orgE<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