Raw content of Bio::Ontology::OntologyStore # $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;