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1 package Bio::Graphics::Glyph::redgreen_box;
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2 #$Id: redgreen_box.pm,v 1.4.2.1 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::generic;
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6 use vars '@ISA';
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7 @ISA = 'Bio::Graphics::Glyph::generic';
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8
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9 sub bgcolor {
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10 my $self = shift;
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11 $self->{force_bgcolor};
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12 }
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13
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14 sub fgcolor {
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15 my $self = shift;
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16 return $self->option('border') ? $self->SUPER::fgcolor : $self->{force_bgcolor};
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17 }
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18
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19 sub draw {
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20 my $self = shift;
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21 my $val = $self->feature->score;
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22
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23 # we're going to force all our parts to share the same colors
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24 # since the
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25 my @parts = $self->parts;
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26 @parts = $self if !@parts && $self->level == 0;
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27 my @rgb = map {int($_)} HSVtoRGB(120*(1-$val),1,255);
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28 my $color = $self->panel->translate_color(@rgb);
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29 $_->{force_bgcolor} = $color foreach @parts;
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30
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31 $self->SUPER::draw(@_);
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32 }
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33
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34 sub HSVtoRGB ($$$) {
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35 my ($h,$s,$v)=@_;
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36 my ($r,$g,$b,$i,$f,$p,$q,$t);
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37
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38 if( $s == 0 ) {
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39 ## achromatic (grey)
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40 return ($v,$v,$v);
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41 }
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42
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43 $h /= 60; ## sector 0 to 5
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44 $i = int($h);
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45 $f = $h - $i; ## factorial part of h
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46 $p = $v * ( 1 - $s );
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47 $q = $v * ( 1 - $s * $f );
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48 $t = $v * ( 1 - $s * ( 1 - $f ) );
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49
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50 if($i<1) {
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51 $r = $v;
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52 $g = $t;
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53 $b = $p;
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54 } elsif($i<2){
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55 $r = $q;
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56 $g = $v;
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57 $b = $p;
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58 } elsif($i<3){
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59 $r = $p;
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60 $g = $v;
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61 $b = $t;
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62 } elsif($i<4){
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63 $r = $p;
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64 $g = $q;
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65 $b = $v;
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66 } elsif($i<5){
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67 $r = $t;
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68 $g = $p;
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69 $b = $v;
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70 } else {
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71 $r = $v;
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72 $g = $p;
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73 $b = $q;
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74 }
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75 return ($r,$g,$b);
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76 }
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77
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78 sub mMin {
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79 my $n=10000000000000;
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80 map { $n=($n>$_) ? $_ : $n } @_;
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81 return($n);
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82 }
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83
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84 sub mMax {
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85 my $n=0;
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86 map { $n=($n<$_) ? $_ : $n } @_;
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87 return($n);
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88 }
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89
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90
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91 1;
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92
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93 =head1 NAME
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94
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95 Bio::Graphics::Glyph::redgreen_box - The "redgreen_box" glyph
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96
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97 =head1 SYNOPSIS
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98
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99 See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.
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100
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101 =head1 DESCRIPTION
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102
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103 This glyph is similar to the graded_segments glyph except that it
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104 generates a green-E<gt>red gradient suitable for use with microarray data.
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105 A feature score of 0 is full green; a feature score of 1.0 is full
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106 red; intermediate scores are shades of yellow.
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107
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108 =head2 OPTIONS
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109
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110 The following options are standard among all Glyphs. See
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111 L<Bio::Graphics::Glyph> for a full explanation.
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112
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113 Option Description Default
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114 ------ ----------- -------
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115
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116 -fgcolor Foreground color black
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117
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118 -outlinecolor Synonym for -fgcolor
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119
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120 -bgcolor Background color turquoise
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121
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122 -fillcolor Synonym for -bgcolor
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123
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124 -linewidth Line width 1
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125
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126 -height Height of glyph 10
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127
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128 -font Glyph font gdSmallFont
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129
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130 -connector Connector type 0 (false)
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131
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132 -connector_color
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133 Connector color black
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134
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135 -label Whether to draw a label 0 (false)
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136
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137 -description Whether to draw a description 0 (false)
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138
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139 The following glyph-specific option is recognized:
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140
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141 -border Draw a fgcolor border around 0 (false)
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142 the box
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143
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144
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145 =head1 BUGS
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146
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147 Please report them.
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148
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149 =head1 SEE ALSO
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150
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151 L<Bio::Graphics::Panel>,
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152 L<Bio::Graphics::Glyph>,
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153 L<Bio::Graphics::Glyph::arrow>,
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154 L<Bio::Graphics::Glyph::cds>,
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155 L<Bio::Graphics::Glyph::crossbox>,
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156 L<Bio::Graphics::Glyph::diamond>,
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157 L<Bio::Graphics::Glyph::dna>,
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158 L<Bio::Graphics::Glyph::dot>,
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159 L<Bio::Graphics::Glyph::ellipse>,
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160 L<Bio::Graphics::Glyph::extending_arrow>,
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161 L<Bio::Graphics::Glyph::generic>,
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162 L<Bio::Graphics::Glyph::graded_segments>,
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163 L<Bio::Graphics::Glyph::heterogeneous_segments>,
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164 L<Bio::Graphics::Glyph::line>,
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165 L<Bio::Graphics::Glyph::pinsertion>,
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166 L<Bio::Graphics::Glyph::primers>,
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167 L<Bio::Graphics::Glyph::rndrect>,
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168 L<Bio::Graphics::Glyph::segments>,
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169 L<Bio::Graphics::Glyph::ruler_arrow>,
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170 L<Bio::Graphics::Glyph::toomany>,
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171 L<Bio::Graphics::Glyph::transcript>,
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172 L<Bio::Graphics::Glyph::transcript2>,
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173 L<Bio::Graphics::Glyph::translation>,
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174 L<Bio::Graphics::Glyph::triangle>,
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175 L<Bio::DB::GFF>,
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176 L<Bio::SeqI>,
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177 L<Bio::SeqFeatureI>,
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178 L<Bio::Das>,
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179 L<GD>
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180
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181 =head1 AUTHOR
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182
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183 Lincoln Stein E<lt>lstein@cshl.orgE<gt>
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184
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185 Copyright (c) 2001 Cold Spring Harbor Laboratory
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186
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187 This library is free software; you can redistribute it and/or modify
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188 it under the same terms as Perl itself. See DISCLAIMER.txt for
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189 disclaimers of warranty.
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190
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191 =cut
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