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1 package Bio::Graphics::Glyph::heterogeneous_segments;
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2
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3 # this glyph acts like graded_segments but the bgcolor of each segment is
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4 # controlled by the source field of the feature. Use the source field name
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5 # to set the background color:
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6 # -waba_strong => 'blue'
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7 # -waba_weak => 'red'
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8 # -waba_coding => 'green'
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9
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10 # $Id: heterogeneous_segments.pm,v 1.5 2002/12/23 01:33:41 lstein Exp $
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11
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12 use strict;
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13 use Bio::Graphics::Glyph::graded_segments;
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14 use vars '@ISA';
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15 @ISA = 'Bio::Graphics::Glyph::graded_segments';
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16
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17 # override draw method to calculate the min and max values for the components
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18 sub draw {
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19 my $self = shift;
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20
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21 # bail out if this isn't the right kind of feature
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22 # handle both das-style and Bio::SeqFeatureI style,
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23 # which use different names for subparts.
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24 my @parts = $self->parts;
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25 @parts = $self if !@parts && $self->level == 0;
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26 return $self->SUPER::draw(@_) unless @parts;
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27
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28 # figure out the colors
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29 $self->{source2color} ||= {};
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30 my $fill = $self->bgcolor;
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31 for my $part (@parts) {
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32 my $s = eval { $part->feature->source_tag } or next;
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33 $self->{source2color}{$s} ||= $self->color(lc($s)."_color") || $fill;
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34 $part->{partcolor} = $self->{source2color}{$s};
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35 }
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36
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37 $self->Bio::Graphics::Glyph::generic::draw(@_);
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38 }
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39
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40
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41 # synthesize a key glyph
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42 sub keyglyph {
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43 my $self = shift;
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44
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45 my $scale = 1/$self->scale; # base pairs/pixel
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46
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47 # two segments, at pixels 0->50, 60->80
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48 my $offset = $self->panel->offset;
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49
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50 my $feature =
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51 Bio::Graphics::Feature->new(
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52 -segments=>[ [ 0*$scale +$offset,25*$scale+$offset],
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53 [ 25*$scale +$offset,50*$scale+$offset],
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54 [ 50*$scale+$offset, 75*$scale+$offset]
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55 ],
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56 -name => $self->option('key'),
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57 -strand => '+1');
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58 my @sources = grep {/_color$/} $self->factory->options;
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59 foreach (@sources) {s/_color$//}
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60 ($feature->segments)[0]->source_tag($sources[1]);
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61 ($feature->segments)[1]->source_tag($sources[0]);
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62 ($feature->segments)[2]->source_tag($sources[2]);
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63 my $factory = $self->factory->clone;
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64 $factory->set_option(label => 1);
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65 $factory->set_option(bump => 0);
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66 $factory->set_option(connector => 'solid');
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67 my $glyph = $factory->make_glyph(0,$feature);
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68 return $glyph;
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69 }
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70
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71 1;
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72
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73 =head1 NAME
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74
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75 Bio::Graphics::Glyph::heterogeneous_segments - The "heterogeneous_segments" glyph
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76
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77 =head1 SYNOPSIS
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78
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79 See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.
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80
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81 =head1 DESCRIPTION
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82
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83 This glyph acts like graded_segments but the bgcolor of each segment (sub-feature)
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84 can be individually set using the source field of the feature.
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85
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86 Each segment type color is specified using the following nomenclature:
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87
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88 -{source}_color => $color
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89
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90 For example, if the feature consists of a gene containing both
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91 confirmed and unconfirmed exons, you can make the confirmed exons
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92 green and the unconfirmed ones red this way:
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93
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94 -confirmed_color => 'green',
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95 -unconfirmed_color => 'red'
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96
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97 =head2 OPTIONS
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98
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99 The following options are standard among all Glyphs. See
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100 L<Bio::Graphics::Glyph> for a full explanation.
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101
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102 Option Description Default
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103 ------ ----------- -------
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104
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105 -fgcolor Foreground color black
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106
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107 -outlinecolor Synonym for -fgcolor
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108
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109 -bgcolor Background color turquoise
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110
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111 -fillcolor Synonym for -bgcolor
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112
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113 -linewidth Line width 1
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114
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115 -height Height of glyph 10
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116
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117 -font Glyph font gdSmallFont
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118
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119 -connector Connector type 0 (false)
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120
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121 -connector_color
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122 Connector color black
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123
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124 -label Whether to draw a label 0 (false)
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125
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126 -description Whether to draw a description 0 (false)
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127
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128 =head1 BUGS
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129
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130 Please report them.
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131
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132 =head1 SEE ALSO
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133
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134 L<Bio::Graphics::Panel>,
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135 L<Bio::Graphics::Glyph>,
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136 L<Bio::Graphics::Glyph::arrow>,
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137 L<Bio::Graphics::Glyph::cds>,
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138 L<Bio::Graphics::Glyph::crossbox>,
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139 L<Bio::Graphics::Glyph::diamond>,
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140 L<Bio::Graphics::Glyph::dna>,
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141 L<Bio::Graphics::Glyph::dot>,
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142 L<Bio::Graphics::Glyph::ellipse>,
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143 L<Bio::Graphics::Glyph::extending_arrow>,
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144 L<Bio::Graphics::Glyph::generic>,
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145 L<Bio::Graphics::Glyph::graded_segments>,
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146 L<Bio::Graphics::Glyph::heterogeneous_segments>,
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147 L<Bio::Graphics::Glyph::line>,
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148 L<Bio::Graphics::Glyph::pinsertion>,
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149 L<Bio::Graphics::Glyph::primers>,
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150 L<Bio::Graphics::Glyph::rndrect>,
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151 L<Bio::Graphics::Glyph::segments>,
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152 L<Bio::Graphics::Glyph::ruler_arrow>,
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153 L<Bio::Graphics::Glyph::toomany>,
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154 L<Bio::Graphics::Glyph::transcript>,
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155 L<Bio::Graphics::Glyph::transcript2>,
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156 L<Bio::Graphics::Glyph::translation>,
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157 L<Bio::Graphics::Glyph::triangle>,
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158 L<Bio::DB::GFF>,
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159 L<Bio::SeqI>,
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160 L<Bio::SeqFeatureI>,
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161 L<Bio::Das>,
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162 L<GD>
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163
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164 =head1 AUTHOR
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165
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166 Lincoln Stein E<lt>lstein@cshl.orgE<gt>
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167
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168 Copyright (c) 2001 Cold Spring Harbor Laboratory
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169
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170 This library is free software; you can redistribute it and/or modify
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171 it under the same terms as Perl itself. See DISCLAIMER.txt for
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172 disclaimers of warranty.
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173
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174 =cut
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