OBO::CCO::CCO_ID_Term_Map - A map between CCO IDs and term names.

  Usage    - $map->get_new_id("CCO", "P", "cell cycle") or $map->get_new_id("CCO", "Pa", "cell cycle")
  Returns  - a new CCO ID (string)
  Args     - idspace (string), subnamespace (string), term (string)
  Function - get a new CCO ID and insert it (put) into this map

# $Id: CCO_ID_Term_Map.pm 2010-12-02 erick.antezana $
#
# Module  : CCO_ID_Term_Map.pm
# Purpose : A (birectional) map CCO_ID vs Term name.
# License : Copyright (c) 2006-2011 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 <erick.antezana -@- gmail.com>
#
package OBO::CCO::CCO_ID_Term_Map;

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

use OBO::CCO::CCO_ID_Set;

sub new {
    my $class = shift;
    my $self  = {};
    $self->{FILE} = shift;

    %{ $self->{MAP_BY_ID} }   = ();    # key=cco_id; value=term name
    %{ $self->{MAP_BY_TERM} } = ();    # key=term name; value=cco_id
    $self->{KEYS} = OBO::CCO::CCO_ID_Set->new();

    bless( $self, $class );

    confess if ( !defined $self->{FILE} );

    # if the file exists:
    if ( -e $self->{FILE} && -r $self->{FILE} ) {
        open( CCO_ID_MAP_IN_FH, "<$self->{FILE}" );
        while (<CCO_ID_MAP_IN_FH>) {
            chomp;
            if ( $_ =~ /(CCO:[A-Z][a-z]?[0-9]{7})\s+(.*)/ ) { ### vlmir
            my ( $key, $value ) = ( $1, $2 );                 # e.g.: CCO:I1234567		test
				$self->{MAP_BY_ID}->{$key}     = $value;      # put
				$self->{MAP_BY_TERM}->{$value} = $key;        # put
            } else {
            	warn "\nThe following entry: '", $_, "' found in '", $self->{FILE}, "' is not recognized as a valid CCO key-value pair!";
            }
        }
        close CCO_ID_MAP_IN_FH;
    }
    else {
        open( CCO_ID_MAP_IN_FH, "$self->{FILE}" );
        # TODO Should I include a date?
        close CCO_ID_MAP_IN_FH;
    }

    $self->{KEYS}->add_all_as_string( keys( %{ $self->{MAP_BY_ID} } ) );
    return $self;
}

sub _is_valid_id () {
	my $new_name = $_[0];
	return ($new_name =~ /CCO:[A-Z]\d{7}/)?1:0;
}

sub get_new_id () {
	my ( $self, $idspace, $subnamespace, $term ) = @_;
	my $result;
	if ( $idspace && $subnamespace && $term ) {
		if ( $self->is_empty() ) {
			$result = $idspace.':'.$subnamespace.'0000001';
		} else {
			$result = $self->{KEYS}->get_new_id($idspace, $subnamespace);
		}
		$self->put( $result, $term );    # put
	}
	return $result;
}

1;