/usr/share/perl5/Circos/DataPoint.pm is in circos 0.69.6+dfsg-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 | package Circos::DataPoint;
=pod
=head1 NAME
Circos::DataPoint - routines for handling data points 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 Data::Dumper;
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::Debug;
use Circos::Error;
use Circos::Expression;
use Circos::Utils;
use Memoize;
for my $f ( qw() ) { }
sub apply_filter {
my ($filter,@args) = @_;
if($filter eq "minsize") {
_apply_filter_minsize(@args);
}
}
sub _apply_filter_minsize {
my ($value,$datum) = @_;
for my $point (@{$datum->{data}}) {
my $size = $point->{end}-$point->{start}+1;
my $d = $value-$size;
if($d > 0) {
$point->{start} -= int($d/2);
if($point->{start} > 0) {
$point->{end} = $point->{start}+$value-1;
} else {
$point->{start} = 0;
$point->{end} = $value-1;
}
if($point->{set}) {
$point->{set} = make_set( @{$point}{qw(start end)});
}
}
}
}
1;
|