File Coverage

blib/lib/OBO/APO/APO_ID.pm

Criterion	Covered	Total	%
statement	40	40	100.0
branch	5	6	83.3
condition	7	12	58.3
subroutine	9	9	100.0
pod	5	6	83.3
total	66	73	90.4

# $Id: APO_ID.pm 2010-09-29 erick.antezana $
#
# Module  : APO_ID.pm
# Purpose : A APO_ID.
# License : Copyright (c) 2006-2014 by Erick Antezana. All rights reserved.
#           This program is free software; you can redistribute it and/or
#           modify it under the same terms as Perl itself.
# Contact : Erick Antezana
#

package OBO::APO::APO_ID;

=head1 NAME

OBO::APO::APO_ID - A module for describing Application Ontology (APO) identifiers. Its idspace, subnamespace and localID are stored.

=head1 SYNOPSIS

use OBO::APO::APO_ID;

$id = APO_ID->new();

$id->idspace("APO");

$id->subnamespace("X");

$id->localID("0000001");

$idspace = $id->idspace();

$subnamespace = $id->subnamespace();

$localID = $id->localID();

print $id->id_as_string();

$id->id_as_string("APO:P1234567");

=head1 DESCRIPTION

The OBO::APO::APO_ID class implements an Application Ontology identifier.

A APO ID holds: IDSPACE, SUBNAMESPACE and a NUMBER in the following form:

	APO:[A-Z][a-z]?nnnnnnn

For instance: APO:Pa1234567

The SUBNAMESPACE may be one of the following:

	C	Cellular component
	F	Molecular Function
	P	Biological Process
	B	Protein
	G	Gene
	I	Interaction
	R	Reference
	T	Taxon
	N	Instance
	U	Upper Level Ontology (APO)
	L	Relationship type (e.g. is_a)
	Y	Interaction type
	Z	Unknown

plus an extra (optional) qualifier could be added to explicitly capture the organism:

	a	Arabidopsis thaliana
	h	Homo sapiens
	y	Saccharomyces cerevisiae
	s	Schizosaccharomyces pombe
	c	Caenorhabditis elegans
	d	Drosophila melanogaster
	m	Mus musculus

=head1 AUTHOR

Erick Antezana, Eerick.antezana -@- gmail.comE

=head1 COPYRIGHT AND LICENSE

Copyright (c) 2006-2014 by Erick Antezana

This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself, either Perl version 5.8.7 or,
at your option, any later version of Perl 5 you may have available.

=cut

our @ISA = qw(OBO::XO::OBO_ID);
use OBO::XO::OBO_ID;
use strict;
use Carp;

sub new {
	my $class = shift;
	my $self  = {};

	$self->{IDSPACE}      = undef; # string
	$self->{SUBNAMESPACE} = undef; # subnamespace
	$self->{LOCALID}      = undef; # 7 digits

	bless ($self, $class);
	return $self;
}

=head2 subnamespace

  Usage    - print $id->subnamespace() or $id->subnamespace($name)
  Returns  - the subnamespace (string)
  Args     - the subnamespace (string)
  Function - gets/sets the subnamespace

=cut

sub subnamespace {
	my ($self, $sns) = @_;
	if ($sns) { $self->{SUBNAMESPACE} = $sns }
	return $self->{SUBNAMESPACE};
}

=head2 id_as_string

  Usage    - print $id->id_as_string() or $id->id_as_string("APO:X0000001")
  Returns  - the id as string (scalar)
  Args     - the id as string
  Function - gets/sets the id as string

=cut

sub id_as_string () {
	my ($self, $id_as_string) = @_;
	if ( defined $id_as_string && $id_as_string =~ /(APO):([A-Z][a-z]?)([0-9]{7})/ ) {
		$self->{IDSPACE} = $1;
		$self->{SUBNAMESPACE} = $2;
		$self->{LOCALID} = substr($3 + 10000000, 1, 7); # trick: forehead zeros
	} elsif ($self->{IDSPACE} && $self->{SUBNAMESPACE} && $self->{LOCALID}) {
		return $self->{IDSPACE}.':'.$self->{SUBNAMESPACE}.$self->{LOCALID};
	}
}
*id = \&id_as_string;

=head2 equals

  Usage    - print $id->equals($id)
  Returns  - 1 (true) or 0 (false)
  Args     - the other ID (OBO::APO::APO_ID)
  Function - tells if two IDs are equal

=cut

sub equals () {
	my ($self, $target) = @_;
	return (($self->{IDSPACE} eq $target->{IDSPACE}) &&
			($self->{SUBNAMESPACE} eq $target->{SUBNAMESPACE}) &&
			($self->{LOCALID} == $target->{LOCALID}));
}

=head2 next_id

  Usage    - $id->next_id()
  Returns  - the next ID (OBO::APO::APO_ID)
  Args     - none
  Function - returns the next ID, which is new

=cut

sub next_id () {
	my $self = shift;
	my $next_id = OBO::APO::APO_ID->new();
	$next_id->{IDSPACE} = $self->{IDSPACE};
	$next_id->{SUBNAMESPACE} = $self->{SUBNAMESPACE};
	$next_id->{LOCALID} = substr(10000001 + $self->{LOCALID}, 1, 7); # trick: forehead zeros
	return $next_id;
}

=head2 previous_id

  Usage    - $id->previous_id()
  Returns  - the previous ID (OBO::APO::APO_ID)
  Args     - none
  Function - returns the previous ID, which is new

=cut

sub previous_id () {
	my $self = shift;
	my $previous_id = OBO::APO::APO_ID->new ();
	$previous_id->{IDSPACE} = $self->{IDSPACE};
	$previous_id->{SUBNAMESPACE} = $self->{SUBNAMESPACE};
	$previous_id->{LOCALID} = substr((10000000 + $self->{LOCALID}) - 1, 1, 7); # trick: forehead zeros
	return $previous_id;
}

1;