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1 package Bio::Graphics::Glyph::transcript;
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2 # $Id: transcript.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 = qw( Bio::Graphics::Glyph::segments);
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8
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9 sub pad_left {
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10 my $self = shift;
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11 my $pad = $self->SUPER::pad_left;
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12 return $pad if $self->{level} > 0;
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13 my $strand = $self->feature->strand;
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14 return $pad unless defined $strand && $strand < 0;
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15 return $self->arrow_length > $pad ? $self->arrow_length : $pad;
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16 }
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17
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18 sub pad_right {
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19 my $self = shift;
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20 my $pad = $self->SUPER::pad_right;
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21 return $pad if $self->{level} > 0;
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22 my $strand = $self->feature->strand;
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23 return $pad unless defined($strand) && $strand > 0;
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24 return $self->arrow_length > $pad ? $self->arrow_length : $pad;
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25 }
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26
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27 sub draw_component {
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28 my $self = shift;
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29 return unless $self->level > 0;
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30 $self->SUPER::draw_component(@_);
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31 }
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32
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33 sub draw_connectors {
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34 my $self = shift;
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35 my $gd = shift;
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36 my ($left,$top) = @_;
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37 $self->SUPER::draw_connectors($gd,$left,$top);
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38 my @parts = $self->parts;
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39
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40 # H'mmm. No parts. Must be in an intron, so draw intron
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41 # spanning entire range
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42 if (!@parts) {
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43 my($x1,$y1,$x2,$y2) = $self->bounds(0,0);
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44 $self->_connector($gd,$left,$top,$x1,$y1,$x1,$y2,$x2,$y1,$x2,$y2);
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45 @parts = $self;
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46 }
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47
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48 # flip argument makes this confusing
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49 # certainly there's a simpler way to express this idea
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50 my $strand = $self->feature->strand;
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51 my ($first,$last) = ($parts[0],$parts[-1]);
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52 ($first,$last) = ($last,$first) if exists $self->{flip};
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53
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54 if ($strand >= 0) {
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55 my($x1,$y1,$x2,$y2) = $last->bounds(@_);
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56 my $center = ($y2+$y1)/2;
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57 $self->{flip} ?
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58 $self->arrow($gd,$x1,$x1-$self->arrow_length,$center)
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59 :
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60 $self->arrow($gd,$x2,$x2+$self->arrow_length,$center);
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61 } else {
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62 my($x1,$y1,$x2,$y2) = $first->bounds(@_);
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63 my $center = ($y2+$y1)/2;
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64 $self->{flip } ?
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65 $self->arrow($gd,$x2,$x2+$self->arrow_length,$center)
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66 :
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67 $self->arrow($gd,$x1,$x1 - $self->arrow_length,$center);
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68 }
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69 }
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70
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71 sub arrow_length {
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72 my $self = shift;
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73 return $self->option('arrow_length') || 8;
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74 }
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75
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76 # override option() for force the "hat" type of connector
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77 sub connector {
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78 my $self = shift;
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79 return $self->SUPER::connector(@_) if $self->all_callbacks;
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80 return ($self->option('connector') || 'hat');
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81 }
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82
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83
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84 1;
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85
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86 __END__
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87
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88 =head1 NAME
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89
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90 Bio::Graphics::Glyph::transcript - The "transcript" glyph
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91
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92 =head1 SYNOPSIS
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93
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94 See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.
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95
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96 =head1 DESCRIPTION
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97
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98 This glyph is used for drawing transcripts. It is essentially a
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99 "segments" glyph in which the connecting segments are hats. The
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100 direction of the transcript is indicated by an arrow attached to the
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101 end of the glyph.
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102
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103 =head2 OPTIONS
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104
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105 The following options are standard among all Glyphs. See
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106 L<Bio::Graphics::Glyph> for a full explanation.
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107
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108 Option Description Default
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109 ------ ----------- -------
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110
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111 -fgcolor Foreground color black
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112
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113 -outlinecolor Synonym for -fgcolor
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114
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115 -bgcolor Background color turquoise
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116
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117 -fillcolor Synonym for -bgcolor
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118
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119 -linewidth Line width 1
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120
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121 -height Height of glyph 10
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122
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123 -font Glyph font gdSmallFont
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124
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125 -connector Connector type 0 (false)
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126
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127 -connector_color
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128 Connector color black
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129
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130 -label Whether to draw a label 0 (false)
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131
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132 -description Whether to draw a description 0 (false)
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133
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134 In addition, the alignment glyph recognizes the following
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135 glyph-specific options:
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136
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137 Option Description Default
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138 ------ ----------- -------
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139
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140 -arrow_length Length of the directional 8
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141 arrow.
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142
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143 =head1 BUGS
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144
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145 Please report them.
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146
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147 =head1 SEE ALSO
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148
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149
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150 L<Bio::Graphics::Panel>,
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151 L<Bio::Graphics::Glyph>,
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152 L<Bio::Graphics::Glyph::arrow>,
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153 L<Bio::Graphics::Glyph::cds>,
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154 L<Bio::Graphics::Glyph::crossbox>,
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155 L<Bio::Graphics::Glyph::diamond>,
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156 L<Bio::Graphics::Glyph::dna>,
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157 L<Bio::Graphics::Glyph::dot>,
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158 L<Bio::Graphics::Glyph::ellipse>,
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159 L<Bio::Graphics::Glyph::extending_arrow>,
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160 L<Bio::Graphics::Glyph::generic>,
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161 L<Bio::Graphics::Glyph::graded_segments>,
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162 L<Bio::Graphics::Glyph::heterogeneous_segments>,
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163 L<Bio::Graphics::Glyph::line>,
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164 L<Bio::Graphics::Glyph::pinsertion>,
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165 L<Bio::Graphics::Glyph::primers>,
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166 L<Bio::Graphics::Glyph::rndrect>,
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167 L<Bio::Graphics::Glyph::segments>,
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168 L<Bio::Graphics::Glyph::ruler_arrow>,
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169 L<Bio::Graphics::Glyph::toomany>,
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170 L<Bio::Graphics::Glyph::transcript>,
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171 L<Bio::Graphics::Glyph::transcript2>,
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172 L<Bio::Graphics::Glyph::translation>,
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173 L<Bio::Graphics::Glyph::triangle>,
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174 L<Bio::DB::GFF>,
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175 L<Bio::SeqI>,
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176 L<Bio::SeqFeatureI>,
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177 L<Bio::Das>,
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178 L<GD>
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179
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180 =head1 AUTHOR
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181
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182 Lincoln Stein E<lt>lstein@cshl.orgE<gt>
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183
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184 Copyright (c) 2001 Cold Spring Harbor Laboratory
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185
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186 This library is free software; you can redistribute it and/or modify
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187 it under the same terms as Perl itself. See DISCLAIMER.txt for
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188 disclaimers of warranty.
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189
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190 =cut
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