/usr/share/perl5/Circos/Track/Link.pm is in circos 0.64-1.
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 | package Circos::Track::Link;
=pod
=head1 NAME
Circos::Track::Link - routines for link handling in Circos
=head1 SYNOPSIS
This module is not meant to be used directly.
=head1 DESCRIPTION
Circos is an application for the generation of publication-quality,
circularly composited renditions of genomic data and related
annotations.
Circos is particularly suited for visualizing alignments, conservation
and intra and inter-chromosomal relationships. However, Circos can be
used to plot any kind of 2D data in a circular layout - its use is not
limited to genomics. Circos' use of lines to relate position pairs
(ribbons add a thickness parameter to each end) is effective to
display relationships between objects or positions on one or more
scales.
All documentation is in the form of tutorials at L<http://www.circos.ca>.
=cut
# -------------------------------------------------------------------
use strict;
use warnings;
use base 'Exporter';
our @EXPORT = qw();
use Carp qw( carp confess croak );
use FindBin;
use GD::Image;
use Params::Validate qw(:all);
use lib "$FindBin::RealBin";
use lib "$FindBin::RealBin/../lib";
use lib "$FindBin::RealBin/lib";
use Circos::Configuration; # qw(%CONF $DIMS);
use Circos::Constants;
#use Circos::Colors;
use Circos::Debug;
use Circos::Error;
#use Circos::Font;
#use Circos::Geometry;
#use Circos::SVG;
#use Circos::Image;
use Circos::Utils;
use Memoize;
for my $f ( qw ( ) ) {
memoize($f);
}
sub make_tracks {
my $conf_leaf = shift;
my @link_tracks;
# If the links are stored in the old form (named block), associate the
# name with the __id parameter for each link. Otherwise, generate __id
# automatically using an index
if(ref $conf_leaf eq "HASH") {
# Could be one or more named blocks, or a single unnamed block.
# If each value is a hash, then assume that we have named blocks
my @values = values %$conf_leaf;
my $values_hash = grep(ref $_ eq "HASH", @values);
if($values_hash == @values) {
# likely one or more named blocks
printdebug_group("conf","found multiple named link blocks");
for my $link_name (keys %$conf_leaf) {
printdebug_group("conf","adding named link block [$link_name]");
my $link_track = $conf_leaf->{$link_name};
if ( ref $link_track eq "ARRAY" ) {
fatal_error("links","duplicate_names",$link_name);
}
if(defined $link_track->{id}) {
$link_track->{__id} = $link_track->{id};
} else {
$link_track->{id} = $link_track->{__id} = $link_name;
}
push @link_tracks, $link_track;
}
} else {
# likely a single unnamed block
printdebug_group("conf","found single unnamed link block");
push @link_tracks, $CONF{links}{link};
}
} elsif(ref $conf_leaf eq "ARRAY") {
# Multiple unnamed/named blocks. A named block will be a
# hash with a single key.
printdebug_group("conf","found multiple unnamed/named link blocks");
for my $link_track (@$conf_leaf) {
if(ref $link_track eq "HASH" && keys %$link_track == 1) {
my ($link_name) = keys %$link_track;
$link_track = $link_track->{$link_name};
if(defined $link_track->{id}) {
$link_track->{__id} = $link_track->{id};
} else {
$link_track->{id} = $link_track->{__id} = $link_name;
}
printdebug_group("conf","adding named link block [$link_name]");
push @link_tracks, $link_track;
} else {
printdebug_group("conf","adding unnamed link block");
push @link_tracks, $link_track;
}
}
}
for my $i (0..@link_tracks-1) {
my $id = first_defined($link_tracks[$i]{id}, $link_tracks[$i]{__id});
if(! defined $id) {
$id = sprintf("link_%d",$i);
printdebug_group("conf","adding automatic link id [$id]");
}
$link_tracks[$i]{id} = $link_tracks[$i]{__id} = $id;
}
return @link_tracks;
}
1;
|