/usr/lib/perl5/Ace/Graphics/Glyph/segments.pm is in libace-perl 1.92-2build3.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 | package Ace::Graphics::Glyph::segments;
# package to use for drawing anything that is interrupted
# (has the segment() method)
use strict;
use vars '@ISA';
use GD;
@ISA = 'Ace::Graphics::Glyph';
use constant GRAY => 'lightgrey';
my %BRUSHES;
# override right to allow for label
sub calculate_right {
my $self = shift;
my $left = $self->left;
my $val = $self->SUPER::calculate_right(@_);
if ($self->option('label') && (my $description = $self->description)) {
my $description_width = $self->font->width * length $self->description;
$val = $left + $description_width if $left + $description_width > $val;
}
$val;
}
# override draw method
sub draw {
my $self = shift;
# bail out if this isn't the right kind of feature
# handle both das-style and Bio::SeqFeatureI style,
# which use different names for subparts.
my @segments;
my $f = $self->feature;
if ($f->can('merged_segments')) {
@segments = $f->merged_segments;
} elsif ($f->can('segments')) {
@segments = $f->segments;
} elsif ($f->can('sub_SeqFeature')) {
@segments = $f->sub_SeqFeature;
} else {
return $self->SUPER::draw(@_);
}
# get parameters
my $gd = shift;
my ($x1,$y1,$x2,$y2) = $self->calculate_boundaries(@_);
my ($left,$top) = @_;
my $gray = $self->color(GRAY);
my (@boxes,@skips);
my $stranded = $self->option('stranded');
for (my $i=0; $i < @segments; $i++) {
my ($start,$stop) = ($left + $self->map_pt($segments[$i]->start),
$left + $self->map_pt($segments[$i]->end));
my $strand = 0;
my $target;
if ($stranded
&& $segments[$i]->can('target')
&& ($target = $segments[$i]->target)
&& $target->can('start')) {
$strand = $target->start < $target->end ? 1 : -1;
}
# probably unnecessary, but we do it out of paranaoia
($start,$stop) = ($stop,$start) if $start > $stop;
push @boxes,[$start,$stop,$strand];
if (my $next_segment = $segments[$i+1]) {
my ($next_start,$next_stop) = ($left + $self->map_pt($next_segment->start),
$left + $self->map_pt($next_segment->end));
# probably unnecessary, but we do it out of paranaoia
($next_start,$next_stop) = ($next_stop,$next_start) if $next_start > $next_stop;
# fudge boxes that are within two pixels of each other
if ($next_start - $stop < 2) {
$boxes[-1][1] = $next_start;
}
push @skips,[$stop+1,$next_start-1];
}
}
my $fg = $self->fgcolor;
my $fill = $self->fillcolor;
my $center = ($y1 + $y2)/2;
# each segment becomes a box
for my $e (@boxes) {
my @rect = ($e->[0],$y1,$e->[1],$y2);
if ($e->[2] == 0 || !$stranded) {
$self->filled_box($gd,@rect);
} else {
# $self->filled_arrow($gd,1,@rect);
$self->oriented_box($gd,$e->[2],@rect);
}
}
# each skip becomes a simple line
for my $i (@skips) {
next unless $i->[1] - $i->[0] >= 1;
$gd->line($i->[0],$center,$i->[1],$center,$gray);
}
# draw label
$self->draw_label($gd,@_) if $self->option('label');
}
sub oriented_box {
my $self = shift;
my $gd = shift;
my $orientation = shift;
my ($x1,$y1,$x2,$y2) = @_;
$self->filled_box($gd,@_);
return unless $x2 - $x1 >= 4;
$BRUSHES{$orientation} ||= $self->make_brush($orientation);
my $top = int(1.5 + $y1 + ($y2 - $y1 - ($BRUSHES{$orientation}->getBounds)[1])/2);
$gd->setBrush($BRUSHES{$orientation});
$gd->setStyle(0,0,0,1);
$gd->line($x1+2,$top,$x2-2,$top,gdStyledBrushed);
}
sub make_brush {
my $self = shift;
my $orientation = shift;
my $brush = GD::Image->new(3,3);
my $bgcolor = $brush->colorAllocate(255,255,255); #white
$brush->transparent($bgcolor);
my $fgcolor = $brush->colorAllocate($self->factory->panel->rgb($self->fgcolor));
if ($orientation > 0) {
$brush->setPixel(0,0,$fgcolor);
$brush->setPixel(1,1,$fgcolor);
$brush->setPixel(0,2,$fgcolor);
} else {
$brush->setPixel(1,0,$fgcolor);
$brush->setPixel(0,1,$fgcolor);
$brush->setPixel(1,2,$fgcolor);
}
$brush;
}
sub description {
my $self = shift;
$self->feature->info;
}
1;
__END__
=head1 NAME
Ace::Graphics::Glyph::segments - The "discontinuous segments" glyph
=head1 SYNOPSIS
See L<Ace::Graphics::Panel> and L<Ace::Graphics::Glyph>.
=head1 DESCRIPTION
This glyph draws a sequence feature that consists of multiple
discontinuous segments, such as the exons on a transcript or a gapped
alignment. The representation is a series of filled rectangles
connected by line segments.
The features passed to it must either respond to the
Bio::SequenceFeatureI-style subSeqFeatures() method, or the
AcePerl/Das-style segments() or merged_segments() methods.
=head2 OPTIONS
In addition to the common options, this glyph recognizes the
b<-stranded> argument. If b<-stranded> is true and the feature is an
alignment (has the target() method) then the glyph will draw little
arrows in the segment boxes to indicate the direction of the
alignment.
=head1 BUGS
Please report them.
=head1 SEE ALSO
L<Ace::Sequence>, L<Ace::Sequence::Feature>, L<Ace::Graphics::Panel>,
L<Ace::Graphics::Track>,
L<Ace::Graphics::Glyph::anchored_arrow>,
L<Ace::Graphics::Glyph::arrow>,
L<Ace::Graphics::Glyph::box>,
L<Ace::Graphics::Glyph::primers>,
L<Ace::Graphics::Glyph::segments>,
L<Ace::Graphics::Glyph::toomany>,
L<Ace::Graphics::Glyph::transcript>,
=head1 AUTHOR
Lincoln Stein <lstein@cshl.org>.
Copyright (c) 2001 Cold Spring Harbor Laboratory
This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself. See DISCLAIMER.txt for
disclaimers of warranty.
=cut
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