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1 package Bio::Graphics::Glyph::graded_segments;
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2 #$Id: graded_segments.pm,v 1.12.2.1 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::segments;
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6 use vars '@ISA';
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7 @ISA = 'Bio::Graphics::Glyph::segments';
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8
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9 # override draw method to calculate the min and max values for the components
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10 sub draw {
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11 my $self = shift;
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12
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13 # bail out if this isn't the right kind of feature
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14 # handle both das-style and Bio::SeqFeatureI style,
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15 # which use different names for subparts.
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16 my @parts = $self->parts;
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17 @parts = $self if !@parts && $self->level == 0;
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18 return $self->SUPER::draw(@_) unless @parts;
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19
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20 # figure out the colors
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21 my $max_score = $self->option('max_score');
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22 my $min_score = $self->option('min_score');
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23 unless (defined $max_score && defined $min_score) {
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24 for my $part (@parts) {
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25 my $s = eval { $part->feature->score };
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26 next unless defined $s;
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27 $max_score = $s if !defined $max_score or $s > $max_score;
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28 $min_score = $s if !defined $min_score or $s < $min_score;
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29 }
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30 }
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31
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32 return $self->SUPER::draw(@_)
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33 unless defined($max_score) && defined($min_score)
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34 && $min_score < $max_score;
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35
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36 my $span = $max_score - $min_score;
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37
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38 # allocate colors
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39 my $fill = $self->bgcolor;
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40 my ($red,$green,$blue) = $self->panel->rgb($fill);
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41
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42 foreach my $part (@parts) {
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43 my $s = eval { $part->feature->score };
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44 unless (defined $s) {
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45 $part->{partcolor} = $fill;
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46 next;
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47 }
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48 my ($r,$g,$b) = $self->calculate_color($s,[$red,$green,$blue],$min_score,$span);
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49 my $idx = $self->panel->translate_color($r,$g,$b);
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50 $part->{partcolor} = $idx;
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51 }
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52 $self->SUPER::draw(@_);
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53 }
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54
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55 sub calculate_color {
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56 my $self = shift;
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57 my ($s,$rgb,$min_score,$span) = @_;
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58 return map { 255 - (255-$_) * min(max( ($s-$min_score)/$span, 0), 1) } @$rgb;
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59 }
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60
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61 sub min { $_[0] < $_[1] ? $_[0] : $_[1] }
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62 sub max { $_[0] > $_[1] ? $_[0] : $_[1] }
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63
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64 sub subseq {
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65 my $class = shift;
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66 my $feature = shift;
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67 return $feature->segments if $feature->can('segments');
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68 return $feature->sub_SeqFeature if $feature->can('sub_SeqFeature');
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69 return;
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70 }
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71
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72 # synthesize a key glyph
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73 sub keyglyph {
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74 my $self = shift;
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75
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76 my $scale = 1/$self->scale; # base pairs/pixel
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77
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78 # two segments, at pixels 0->50, 60->80
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79 my $offset = $self->panel->offset;
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80
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81 my $feature =
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82 Bio::Graphics::Feature->new(
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83 -segments=>[ [ 0*$scale +$offset,20*$scale+$offset],
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84 [ 30*$scale +$offset,50*$scale+$offset],
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85 [60*$scale+$offset, 80*$scale+$offset]
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86 ],
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87 -name => $self->option('key'),
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88 -strand => '+1');
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89 ($feature->segments)[0]->score(10);
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90 ($feature->segments)[1]->score(50);
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91 ($feature->segments)[2]->score(100);
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92 my $factory = $self->factory->clone;
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93 $factory->set_option(label => 1);
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94 $factory->set_option(bump => 0);
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95 $factory->set_option(connector => 'solid');
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96 return $factory->make_glyph($feature);
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97 }
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98
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99 # component draws a shaded box
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100 sub bgcolor {
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101 my $self = shift;
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102 return $self->{partcolor} || $self->SUPER::bgcolor;
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103 }
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104 sub fgcolor {
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105 my $self = shift;
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106 return $self->{partcolor} || $self->SUPER::fgcolor;
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107 }
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108
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109 1;
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110
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111 =head1 NAME
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112
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113 Bio::Graphics::Glyph::graded_segments - The "graded_segments" glyph
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114
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115 =head1 SYNOPSIS
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116
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117 See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.
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118
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119 =head1 DESCRIPTION
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120
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121 This is identical to the "alignment" glyph, and is used for
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122 drawing features that consist of discontinuous segments. The
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123 color intensity of each segment is proportionate to the score.
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124
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125 =head2 OPTIONS
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126
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127 The following options are standard among all Glyphs. See
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128 L<Bio::Graphics::Glyph> for a full explanation.
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129
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130 Option Description Default
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131 ------ ----------- -------
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132
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133 -fgcolor Foreground color black
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134
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135 -outlinecolor Synonym for -fgcolor
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136
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137 -bgcolor Background color turquoise
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138
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139 -fillcolor Synonym for -bgcolor
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140
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141 -linewidth Line width 1
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142
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143 -height Height of glyph 10
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144
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145 -font Glyph font gdSmallFont
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146
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147 -connector Connector type 0 (false)
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148
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149 -connector_color
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150 Connector color black
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151
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152 -label Whether to draw a label 0 (false)
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153
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154 -description Whether to draw a description 0 (false)
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155
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156 In addition, the alignment glyph recognizes the following
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157 glyph-specific options:
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158
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159 Option Description Default
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160 ------ ----------- -------
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161
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162 -max_score Maximum value of the Calculated
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163 feature's "score" attribute
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164
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165 -min_score Minimum value of the Calculated
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166 feature's "score" attribute
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167
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168 If max_score and min_score are not specified, then the glyph will
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169 calculate the local maximum and minimum scores at run time.
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170
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171
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172 =head1 BUGS
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173
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174 Please report them.
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175
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176 =head1 SEE ALSO
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177
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178 L<Bio::Graphics::Panel>,
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179 L<Bio::Graphics::Glyph>,
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180 L<Bio::Graphics::Glyph::arrow>,
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181 L<Bio::Graphics::Glyph::cds>,
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182 L<Bio::Graphics::Glyph::crossbox>,
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183 L<Bio::Graphics::Glyph::diamond>,
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184 L<Bio::Graphics::Glyph::dna>,
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185 L<Bio::Graphics::Glyph::dot>,
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186 L<Bio::Graphics::Glyph::ellipse>,
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187 L<Bio::Graphics::Glyph::extending_arrow>,
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188 L<Bio::Graphics::Glyph::generic>,
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189 L<Bio::Graphics::Glyph::graded_segments>,
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190 L<Bio::Graphics::Glyph::heterogeneous_segments>,
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191 L<Bio::Graphics::Glyph::line>,
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192 L<Bio::Graphics::Glyph::pinsertion>,
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193 L<Bio::Graphics::Glyph::primers>,
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194 L<Bio::Graphics::Glyph::rndrect>,
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195 L<Bio::Graphics::Glyph::segments>,
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196 L<Bio::Graphics::Glyph::ruler_arrow>,
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197 L<Bio::Graphics::Glyph::toomany>,
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198 L<Bio::Graphics::Glyph::transcript>,
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199 L<Bio::Graphics::Glyph::transcript2>,
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200 L<Bio::Graphics::Glyph::translation>,
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201 L<Bio::Graphics::Glyph::triangle>,
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202 L<Bio::DB::GFF>,
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203 L<Bio::SeqI>,
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204 L<Bio::SeqFeatureI>,
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205 L<Bio::Das>,
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206 L<GD>
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207
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208 =head1 AUTHOR
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209
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210 Lincoln Stein E<lt>lstein@cshl.orgE<gt>
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211
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212 Copyright (c) 2001 Cold Spring Harbor Laboratory
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213
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214 This library is free software; you can redistribute it and/or modify
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215 it under the same terms as Perl itself. See DISCLAIMER.txt for
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216 disclaimers of warranty.
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217
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218 =cut
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