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1 package Bio::Graphics::Glyph::redgreen_segment;
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2 #$Id: redgreen_segment.pm,v 1.3.2.1 2003/07/05 00:32:04 lstein Exp $
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3
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4 use strict;
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5 use Bio::Graphics::Glyph::graded_segments;
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6 use vars '@ISA';
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7 @ISA = 'Bio::Graphics::Glyph::graded_segments';
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8
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9 sub calculate_color {
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10 my $self = shift;
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11 my $val = shift;
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12 return (0,0,0) unless $val =~ /^[\d.]+$/;
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13 return HSVtoRGB(120*(1-$val),1,255);
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14 }
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15
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16 sub HSVtoRGB ($$$) {
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17 my ($h,$s,$v)=@_;
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18 my ($r,$g,$b,$i,$f,$p,$q,$t);
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19
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20 if( $s == 0 ) {
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21 ## achromatic (grey)
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22 return ($v,$v,$v);
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23 }
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24
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25 $h /= 60; ## sector 0 to 5
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26 $i = int($h);
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27 $f = $h - $i; ## factorial part of h
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28 $p = $v * ( 1 - $s );
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29 $q = $v * ( 1 - $s * $f );
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30 $t = $v * ( 1 - $s * ( 1 - $f ) );
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31
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32 if($i<1) {
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33 $r = $v;
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34 $g = $t;
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35 $b = $p;
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36 } elsif($i<2){
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37 $r = $q;
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38 $g = $v;
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39 $b = $p;
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40 } elsif($i<3){
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41 $r = $p;
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42 $g = $v;
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43 $b = $t;
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44 } elsif($i<4){
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45 $r = $p;
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46 $g = $q;
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47 $b = $v;
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48 } elsif($i<5){
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49 $r = $t;
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50 $g = $p;
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51 $b = $v;
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52 } else {
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53 $r = $v;
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54 $g = $p;
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55 $b = $q;
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56 }
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57 return ($r,$g,$b);
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58 }
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59
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60 sub mMin {
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61 my $n=10000000000000;
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62 map { $n=($n>$_) ? $_ : $n } @_;
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63 return($n);
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64 }
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65
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66 sub mMax {
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67 my $n=0;
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68 map { $n=($n<$_) ? $_ : $n } @_;
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69 return($n);
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70 }
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71
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72
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73 1;
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74
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75 =head1 NAME
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76
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77 Bio::Graphics::Glyph::redgreen_segments - The "redgreen_segments" glyph
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78
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79 =head1 SYNOPSIS
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80
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81 See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.
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82
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83 =head1 DESCRIPTION
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84
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85 This glyph is similar to the graded_segments glyph except that it
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86 generates a green-E<gt>red gradient suitable for use with microarray data.
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87 A feature score of 0 is full green; a feature score of 1.0 is full
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88 red; intermediate scores are shades of yellow.
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89
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90 =head2 OPTIONS
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91
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92 The following options are standard among all Glyphs. See
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93 L<Bio::Graphics::Glyph> for a full explanation.
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94
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95 Option Description Default
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96 ------ ----------- -------
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97
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98 -fgcolor Foreground color black
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99
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100 -outlinecolor Synonym for -fgcolor
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101
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102 -bgcolor Background color turquoise
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103
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104 -fillcolor Synonym for -bgcolor
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105
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106 -linewidth Line width 1
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107
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108 -height Height of glyph 10
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109
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110 -font Glyph font gdSmallFont
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111
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112 -connector Connector type 0 (false)
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113
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114 -connector_color
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115 Connector color black
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116
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117 -label Whether to draw a label 0 (false)
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118
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119 -description Whether to draw a description 0 (false)
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120
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121 =head1 BUGS
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122
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123 Please report them.
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124
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125 =head1 SEE ALSO
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126
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127 L<Bio::Graphics::Panel>,
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128 L<Bio::Graphics::Glyph>,
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129 L<Bio::Graphics::Glyph::arrow>,
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130 L<Bio::Graphics::Glyph::cds>,
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131 L<Bio::Graphics::Glyph::crossbox>,
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132 L<Bio::Graphics::Glyph::diamond>,
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133 L<Bio::Graphics::Glyph::dna>,
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134 L<Bio::Graphics::Glyph::dot>,
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135 L<Bio::Graphics::Glyph::ellipse>,
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136 L<Bio::Graphics::Glyph::extending_arrow>,
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137 L<Bio::Graphics::Glyph::generic>,
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138 L<Bio::Graphics::Glyph::graded_segments>,
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139 L<Bio::Graphics::Glyph::heterogeneous_segments>,
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140 L<Bio::Graphics::Glyph::line>,
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141 L<Bio::Graphics::Glyph::pinsertion>,
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142 L<Bio::Graphics::Glyph::primers>,
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143 L<Bio::Graphics::Glyph::rndrect>,
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144 L<Bio::Graphics::Glyph::segments>,
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145 L<Bio::Graphics::Glyph::ruler_arrow>,
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146 L<Bio::Graphics::Glyph::toomany>,
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147 L<Bio::Graphics::Glyph::transcript>,
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148 L<Bio::Graphics::Glyph::transcript2>,
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149 L<Bio::Graphics::Glyph::translation>,
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150 L<Bio::Graphics::Glyph::triangle>,
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151 L<Bio::DB::GFF>,
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152 L<Bio::SeqI>,
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153 L<Bio::SeqFeatureI>,
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154 L<Bio::Das>,
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155 L<GD>
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156
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157 =head1 AUTHOR
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158
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159 Lincoln Stein E<lt>lstein@cshl.orgE<gt>
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160
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161 Copyright (c) 2001 Cold Spring Harbor Laboratory
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162
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163 This library is free software; you can redistribute it and/or modify
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164 it under the same terms as Perl itself. See DISCLAIMER.txt for
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165 disclaimers of warranty.
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166
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167 =cut
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