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package Circos::URL;
=pod
=head1 NAME
Circos::URL - URL routines for PNG 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(
format_url
);
use Carp qw( carp confess croak );
use FindBin;
use GD;
use Params::Validate qw(:all);
use lib "$FindBin::RealBin";
use lib "$FindBin::RealBin/../lib";
use lib "$FindBin::RealBin/lib";
use Circos::Configuration;
#use Circos::Colors;
use Circos::Constants;
use Circos::Debug;
use Circos::Error;
#use Circos::Image qw(!draw_line);
use Circos::Utils;
use Memoize;
for my $f ( qw ( ) ) {
memoize($f);
}
sub format_url {
# given a url (although the function can be applied to any string)
# replace all instances of [PARAM] with the value of the parameter
# named PARAM extracted from the elements passed in the param_path
#
# e.g. format_url(url=>"www.domain.com/param=[ID]",param_path=>[$datum,$data]);
my %args = @_;
my $delim_left = "\Q[\E";
my $delim_right = "\Q]\E";
my $url = $args{url};
return unless defined $url;
my $ignore_param;
while ($url =~ /$delim_left([^$delim_right$delim_left]+)$delim_right/g) {
my $param = $1;
my $value;
if(exists $args{param_path}[0]{data}[0] &&
defined $args{param_path}[0]{data}[0]{$param}) {
$value = $args{param_path}[0]{data}[0]{$param};
} else {
$value = seek_parameter($param,@{$args{param_path}});
}
printdebug_group("url","format_url",$url,$1,$value);
if (! defined $value) {
if ($CONF{image}{image_map_missing_parameter} eq "exit") {
fatal_error("map","url_param_not_set",$url,$param);
} elsif ($CONF{image}{image_map_missing_parameter} =~ /removeurl/) {
# there is no value for this parameter, so return an empty url
return undef;
} elsif ($CONF{image}{image_map_missing_parameter} =~ /ignoreparam/) {
$ignore_param->{$param}++;
} elsif ($CONF{image}{image_map_missing_parameter} =~ /removeparam/ || 1) {
printdumper($args{param_path});exit;
# not defined - removeparam by default
error("warning","general","You have tried to use the URL $url for an image map, but the parameter in the url [$param] has no value defined for this data point or data set. This parameter is being removed from the URL of this element. Use the image_map_missing_parameter setting in the <image> block to adjust this behaviour.");
$url =~ s/$delim_left$param$delim_right//g;
}
} else {
$url =~ s/$delim_left$param$delim_right/$value/g;
}
}
printdebug_group("url","format_url_done",$url);
return $url;
}
1;
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