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1 package Bio::Graphics::Glyph::processed_transcript;
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2
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3 # $Id: processed_transcript.pm,v 1.3.2.1 2003/07/05 00:32:04 lstein Exp $
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4
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5 use strict;
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6 use Bio::Graphics::Glyph::transcript2;
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7 use vars '@ISA';
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8 @ISA = 'Bio::Graphics::Glyph::transcript2';
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9 use constant DEFAULT_UTR_COLOR => '#D0D0D0';
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10
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11 sub is_utr {
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12 my $self = shift;
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13 return $self->feature->primary_tag =~ /UTR|untranslated_region/i;
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14 }
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15
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16 sub thin_utr {
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17 my $self = shift;
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18 $self->option('thin_utr');
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19 }
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20
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21 sub utr_color {
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22 my $self = shift;
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23 return $self->color('utr_color') if $self->option('utr_color');
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24 return $self->factory->translate_color(DEFAULT_UTR_COLOR);
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25 }
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26
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27 sub height {
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28 my $self = shift;
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29 my $height = $self->SUPER::height;
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30 return $height unless $self->thin_utr;
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31 return $self->is_utr ? int($height/1.5+0.5) : $height;
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32 }
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33
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34 sub pad_top {
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35 my $self = shift;
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36 my $pad_top = $self->SUPER::pad_top;
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37 return $pad_top unless $self->thin_utr && $self->is_utr;
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38 return $pad_top + int(0.167*$self->SUPER::height + 0.5);
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39 }
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40
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41 sub bgcolor {
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42 my $self = shift;
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43 return $self->SUPER::bgcolor unless $self->is_utr;
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44 return $self->utr_color;
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45 }
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46
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47 sub connector {
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48 my $self = shift;
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49 return 'quill' if $self->option('decorate_introns');
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50 return $self->SUPER::connector(@_);
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51 }
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52
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53
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54 1;
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55
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56
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57 __END__
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58
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59 =head1 NAME
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60
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61 Bio::Graphics::Glyph::processed_transcript - The sequence ontology transcript glyph
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62
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63 =head1 SYNOPSIS
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64
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65 See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.
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66
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67 =head1 DESCRIPTION
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68
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69 This glyph is used for drawing processed transcripts that have both
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70 CDS and UTR segments. The CDS is drawn in the background color, and
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71 the UTRs are drawn in an alternate color selected by the utr_color
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72 option. In addition, you can make the UTRs thinner than the CDS by
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73 setting the "thin_utr" option.
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74
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75 For this glyph to produce the desired results, you should pass it a
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76 compound Bio::SeqFeature that has subfeatures of primary_tag "CDS" and
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77 "UTR". In fact, you may give it more specific types of UTR, including
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78 5'-UTR, 3'-UTR, or the Sequence Ontology terms "untranslated_region,"
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79 "five_prime_untranslated_region," and
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80 "three_prime_untranslated_region."
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81
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82 =head2 OPTIONS
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83
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84 The following options are standard among all Glyphs. See
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85 L<Bio::Graphics::Glyph> for a full explanation.
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86
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87 Option Description Default
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88 ------ ----------- -------
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89
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90 -fgcolor Foreground color black
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91
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92 -outlinecolor Synonym for -fgcolor
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93
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94 -bgcolor Background color turquoise
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95
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96 -fillcolor Synonym for -bgcolor
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97
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98 -linewidth Line width 1
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99
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100 -height Height of glyph 10
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101
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102 -font Glyph font gdSmallFont
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103
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104 -connector Connector type undef (false)
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105
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106 -connector_color
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107 Connector color black
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108
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109 -label Whether to draw a label undef (false)
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110
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111 -description Whether to draw a description undef (false)
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112
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113 -strand_arrow Whether to indicate undef (false)
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114 strandedness
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115
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116 In addition, the alignment glyph recognizes the following
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117 glyph-specific options:
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118
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119 Option Description Default
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120 ------ ----------- -------
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121
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122 -thin_utr Flag. If true, UTRs will undef (false)
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123 be drawn at 2/3 of the
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124 height of CDS segments.
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125
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126 -utr_color Color of UTR segments. Gray #D0D0D0
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127
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128 -decorate_introns
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129 Draw strand with little arrows undef (false)
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130 on the intron.
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131
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132 =head1 BUGS
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133
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134 Please report them.
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135
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136 =head1 SEE ALSO
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137
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138
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139 L<Bio::Graphics::Panel>,
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140 L<Bio::Graphics::Glyph>,
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141 L<Bio::Graphics::Glyph::arrow>,
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142 L<Bio::Graphics::Glyph::cds>,
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143 L<Bio::Graphics::Glyph::crossbox>,
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144 L<Bio::Graphics::Glyph::diamond>,
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145 L<Bio::Graphics::Glyph::dna>,
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146 L<Bio::Graphics::Glyph::dot>,
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147 L<Bio::Graphics::Glyph::ellipse>,
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148 L<Bio::Graphics::Glyph::extending_arrow>,
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149 L<Bio::Graphics::Glyph::generic>,
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150 L<Bio::Graphics::Glyph::graded_segments>,
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151 L<Bio::Graphics::Glyph::heterogeneous_segments>,
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152 L<Bio::Graphics::Glyph::line>,
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153 L<Bio::Graphics::Glyph::pinsertion>,
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154 L<Bio::Graphics::Glyph::primers>,
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155 L<Bio::Graphics::Glyph::rndrect>,
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156 L<Bio::Graphics::Glyph::segments>,
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157 L<Bio::Graphics::Glyph::ruler_arrow>,
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158 L<Bio::Graphics::Glyph::toomany>,
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159 L<Bio::Graphics::Glyph::transcript>,
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160 L<Bio::Graphics::Glyph::transcript2>,
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161 L<Bio::Graphics::Glyph::translation>,
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162 L<Bio::Graphics::Glyph::triangle>,
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163 L<Bio::DB::GFF>,
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164 L<Bio::SeqI>,
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165 L<Bio::SeqFeatureI>,
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166 L<Bio::Das>,
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167 L<GD>
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168
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169 =head1 AUTHOR
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170
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171 Lincoln Stein E<lt>lstein@cshl.orgE<gt>
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172
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173 Copyright (c) 2001 Cold Spring Harbor Laboratory
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174
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175 This library is free software; you can redistribute it and/or modify
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176 it under the same terms as Perl itself. See DISCLAIMER.txt for
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177 disclaimers of warranty.
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178
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179 =cut
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