Raw content of Bio::Ontology::OntologyStore
<![CDATA[# $Id: OntologyStore.pm,v 1.1.2.2 2003/03/27 10:07:56 lapp Exp $
#
# BioPerl module for Bio::Ontology::OntologyStore
#
# Cared for by Hilmar Lapp <hlapp at gmx.net>
#
# Copyright Hilmar Lapp
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Ontology::OntologyStore - A repository of ontologies
=head1 SYNOPSIS
# see documentation of methods
=head1 DESCRIPTION
The primary purpose of this module is that of a singleton repository
of L<Bio::Ontology::OntologyI> instances from which an Ontology
instance can be retrieved by name or identifier. This enables TermI
implementations to return their corresponding OntologyI through using
this singleton store instead of storing a direct reference to the
Ontology object. The latter would almost inevitably lead to memory
cycles, and would therefore potentially blow up an application.
As a user of Ontology objects and Term objects you almost certainly
will not need to deal with this module.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/MailList.shtml - About the mailing lists
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
the web:
http://bugzilla.bioperl.org/
=head1 AUTHOR - Hilmar Lapp
Email hlapp at gmx.net
=head1 CONTRIBUTORS
Additional contributors names and emails here
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Ontology::OntologyStore;
use vars qw(@ISA);
use strict;
# Object preamble - inherits from Bio::Root::Root
use Bio::Root::Root;
@ISA = qw(Bio::Root::Root );
# these are the static ontology stores by name and by identifier - there is
# only one of each in any application
my %ont_store_by_name = ();
my %ont_store_by_id = ();
# also, this is really meant as a singleton object, so we try to enforce it
my $instance = undef;
=head2 new
Title : new
Usage : my $obj = new Bio::Ontology::OntologyStore();
Function: Returns the Bio::Ontology::OntologyStore object.
Unlike usual implementations of new, this implementation
will try to return a previously instantiated store, if
there is any. It is just a synonym for get_instance. In
order to avoid ambiguities in your code, you may rather
want to call rather get_instance explicitly, which also
usually is better associated with this kind of behaviour.
Returns : an instance of Bio::Ontology::OntologyStore
Args :
=cut
sub new {
return shift->get_instance(@_);
}
=head2 get_instance
Title : get_instance
Usage :
Function: Get an instance of this class for perusal.
Since by design this class is meant to be used as a
singleton, the implementation will return a previously
instantianted store if there is one, and instantiate a new
one otherwise. In order to use this class by means of an
instance, call this method for added code clarity, not
new().
Example :
Returns : an instance of this class
Args : named parameters, if any (currently, there are no
class-specific parameters other than those accepted by
L<Bio::Root::Root>.
=cut
sub get_instance{
my ($self,@args) = @_;
if(! $instance) {
$instance = $self->SUPER::new(@args);
}
return $instance;
}
=head2 get_ontology
Title : get_ontology
Usage :
Function: Get a previously instantiated and registered instance of
this class by name or by identifier.
One of the main purposes of this class is to enable TermI
implementations to return their respective ontology without
keeping a strong reference to the respective ontology
object. Only objects previously registered objects can be
retrieved.
This is a class method, hence you can call it on the class
name, without dereferencing an object.
Example :
Returns : a L<Bio::Ontology::OntologyI> implementing object, or undef
if the query could not be satisfied
Args : Named parameters specifying the query. The following parameters
are recognized:
-name query the store for an ontology with the given name
-id query for an ontology with the given identifier
If both are specified, an implicit AND logical operator is
assumed.
=cut
sub get_ontology{
my ($self,@args) = @_;
my $ont;
my ($name,$id) = $self->_rearrange([qw(NAME ID)], @args);
if($id) {
$ont = $ont_store_by_id{$id};
return unless $ont; # no AND can be satisfied in this case
}
if($name) {
my $o = $ont_store_by_name{$name};
if((! $ont) || ($ont->identifier() eq $o->identifier())) {
$ont = $o;
} else {
$ont = undef;
}
}
return $ont;
}
=head2 register_ontology
Title : register_ontology
Usage :
Function: Registers the given Ontology object for later retrieval
by name and identifier.
Example :
Returns : TRUE on success and FALSE otherwise
Args : the L<Bio::Ontology::OntologyI> object(s) to register
=cut
sub register_ontology{
my ($self,@args) = @_;
my $ret = 1;
foreach my $ont (@args) {
if(! (ref($ont) && $ont->isa("Bio::Ontology::OntologyI"))) {
$self->throw((ref($ont) ? ref($ont) : $ont)." does not implement ".
"Bio::Ontology::OntologyI or is not an object");
}
if($self->get_ontology(-name => $ont->name())) {
$self->warn("ontology with name \"".$ont->name().
"\" already exists in the store, ignoring new one");
$ret = 0;
next;
}
if($self->get_ontology(-id => $ont->identifier())) {
$self->warn("ontology with id \"".$ont->identifier().
"\" already exists in the store, ignoring new one");
$ret = 0;
next;
}
$ont_store_by_name{$ont->name()} = $ont;
$ont_store_by_id{$ont->identifier()} = $ont;
}
return $ret;
}
=head2 remove_ontology
Title : remove_ontology
Usage :
Function: Remove the specified ontology from the store.
Example :
Returns : TRUE on success and FALSE otherwise
Args : the L<Bio::Ontology::OntologyI> implementing object(s)
to be removed from the store
=cut
sub remove_ontology{
my $self = shift;
my $ret = 1;
foreach my $ont (@_) {
$self->throw(ref($ont)." does not implement Bio::Ontology::OntologyI")
unless $ont && ref($ont) && $ont->isa("Bio::Ontology::OntologyI");
# remove it from both the id hash and the name hash
delete $ont_store_by_id{$ont->identifier()};
delete $ont_store_by_name{$ont->name()} if $ont->name();
}
return 1;
}
1;
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