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1 package Bio::Graphics::Glyph::transcript2;
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2
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3 # $Id: transcript2.pm,v 1.15.2.1 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::transcript;
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7 use vars '@ISA';
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8 @ISA = 'Bio::Graphics::Glyph::transcript';
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9
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10 use constant MIN_WIDTH_FOR_ARROW => 8;
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11
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12 sub pad_left {
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13 my $self = shift;
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14 my $pad = $self->Bio::Graphics::Glyph::generic::pad_left;
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15 return $pad unless ($self->feature->strand||0) < 0; #uninitialized var warning
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16 my $first = ($self->parts)[0] || $self;
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17 my @rect = $first->bounds();
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18 my $width = abs($rect[2] - $rect[0]);
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19 return $self->SUPER::pad_left if $width < MIN_WIDTH_FOR_ARROW;
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20 return $pad;
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21 }
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22
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23 sub pad_right {
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24 my $self = shift;
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25 my $pad = $self->Bio::Graphics::Glyph::generic::pad_right;
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26 return $pad if $self->{level} > 0;
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27 my $last = ($self->parts)[-1] || $self;
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28 my @rect = $last->bounds();
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29 my $width = abs($rect[2] - $rect[0]);
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30 return $self->SUPER::pad_right if $width < MIN_WIDTH_FOR_ARROW;
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31 return $pad
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32 }
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33
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34 sub draw_component {
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35 my $self = shift;
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36 return unless $self->level > 0;
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37
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38 my $gd = shift;
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39 my ($left,$top) = @_;
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40 my @rect = $self->bounds(@_);
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41
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42 my $width = abs($rect[2] - $rect[0]);
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43 my $filled = defined($self->{partno}) && $width >= MIN_WIDTH_FOR_ARROW;
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44
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45 if ($filled) {
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46 my $f = $self->feature;
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47 my $strand = $f->strand;
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48 my ($first,$last) = ($self->{partno} == 0 , $self->{partno} == $self->{total_parts}-1);
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49 ($first,$last) = ($last,$first) if $self->{flip};
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50
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51 if ($strand < 0 && $first) { # first exon, minus strand transcript
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52 $self->filled_arrow($gd,-1,@rect);
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53 } elsif ($strand >= 0 && $last) { # last exon, plus strand
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54 $self->filled_arrow($gd,+1,@rect);
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55 } else {
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56 $self->SUPER::draw_component($gd,@_);
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57 }
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58 }
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59
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60 else {
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61 $self->SUPER::draw_component($gd,@_);
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62 }
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63
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64 }
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65
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66 sub draw_connectors {
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67 my $self = shift;
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68 my ($gd,$dx,$dy) = @_;
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69
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70 my $part;
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71 my $strand = $self->feature->strand;
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72 $strand *= -1 if $self->{flip}; #sigh
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73 if (my @parts = $self->parts) {
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74 $part = $strand >= 0 ? $parts[-1] : $parts[0];
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75 } else {
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76 # no parts -- so draw an intron spanning whole thing
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77 my($x1,$y1,$x2,$y2) = $self->bounds(0,0);
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78 $self->_connector($gd,$dx,$dy,$x1,$y1,$x1,$y2,$x2,$y1,$x2,$y2);
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79 $part = $self;
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80 }
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81 my @rect = $part->bounds();
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82 my $width = abs($rect[2] - $rect[0]);
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83 my $filled = $width >= MIN_WIDTH_FOR_ARROW;
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84
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85 if ($filled) {
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86 $self->Bio::Graphics::Glyph::generic::draw_connectors(@_);
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87 } else {
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88 $self->SUPER::draw_connectors(@_);
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89 }
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90 }
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91
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92 sub bump {
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93 my $self = shift;
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94 return $self->SUPER::bump(@_) if $self->all_callbacks;
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95 return 0; # never allow our components to bump
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96 }
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97
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98 1;
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99
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100
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101 __END__
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102
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103 =head1 NAME
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104
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105 Bio::Graphics::Glyph::transcript2 - The "transcript2" glyph
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106
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107 =head1 SYNOPSIS
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108
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109 See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.
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110
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111 =head1 DESCRIPTION
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112
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113 This glyph is used for drawing transcripts. It is like "transcript"
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114 except that if there is sufficient room the terminal exon is shaped
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115 like an arrow in order to indicate the direction of transcription. If
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116 there isn't enough room, a small arrow is drawn.
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117
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118 =head2 OPTIONS
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119
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120 The following options are standard among all Glyphs. See
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121 L<Bio::Graphics::Glyph> for a full explanation.
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122
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123 Option Description Default
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124 ------ ----------- -------
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125
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126 -fgcolor Foreground color black
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127
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128 -outlinecolor Synonym for -fgcolor
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129
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130 -bgcolor Background color turquoise
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131
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132 -fillcolor Synonym for -bgcolor
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133
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134 -linewidth Line width 1
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135
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136 -height Height of glyph 10
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137
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138 -font Glyph font gdSmallFont
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139
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140 -connector Connector type 0 (false)
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141
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142 -connector_color
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143 Connector color black
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144
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145 -label Whether to draw a label 0 (false)
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146
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147 -description Whether to draw a description 0 (false)
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148
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149 -strand_arrow Whether to indicate 0 (false)
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150 strandedness
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151
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152 In addition, the alignment glyph recognizes the following
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153 glyph-specific options:
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154
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155 Option Description Default
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156 ------ ----------- -------
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157
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158 -arrow_length Length of the directional 8
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159 arrow.
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160
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161 =head1 BUGS
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162
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163 Please report them.
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164
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165 =head1 SEE ALSO
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166
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167
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168 L<Bio::Graphics::Panel>,
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169 L<Bio::Graphics::Glyph>,
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170 L<Bio::Graphics::Glyph::arrow>,
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171 L<Bio::Graphics::Glyph::cds>,
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172 L<Bio::Graphics::Glyph::crossbox>,
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173 L<Bio::Graphics::Glyph::diamond>,
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174 L<Bio::Graphics::Glyph::dna>,
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175 L<Bio::Graphics::Glyph::dot>,
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176 L<Bio::Graphics::Glyph::ellipse>,
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177 L<Bio::Graphics::Glyph::extending_arrow>,
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178 L<Bio::Graphics::Glyph::generic>,
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179 L<Bio::Graphics::Glyph::graded_segments>,
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180 L<Bio::Graphics::Glyph::heterogeneous_segments>,
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181 L<Bio::Graphics::Glyph::line>,
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182 L<Bio::Graphics::Glyph::pinsertion>,
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183 L<Bio::Graphics::Glyph::primers>,
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184 L<Bio::Graphics::Glyph::rndrect>,
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185 L<Bio::Graphics::Glyph::segments>,
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186 L<Bio::Graphics::Glyph::ruler_arrow>,
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187 L<Bio::Graphics::Glyph::toomany>,
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188 L<Bio::Graphics::Glyph::transcript>,
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189 L<Bio::Graphics::Glyph::transcript2>,
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190 L<Bio::Graphics::Glyph::translation>,
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191 L<Bio::Graphics::Glyph::triangle>,
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192 L<Bio::DB::GFF>,
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193 L<Bio::SeqI>,
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194 L<Bio::SeqFeatureI>,
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195 L<Bio::Das>,
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196 L<GD>
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197
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198 =head1 AUTHOR
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199
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200 Lincoln Stein E<lt>lstein@cshl.orgE<gt>
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201
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202 Copyright (c) 2001 Cold Spring Harbor Laboratory
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203
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204 This library is free software; you can redistribute it and/or modify
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205 it under the same terms as Perl itself. See DISCLAIMER.txt for
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206 disclaimers of warranty.
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207
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208 =cut
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