Raw content of Bio::IdentifiableI # $Id: IdentifiableI.pm,v 1.6 2002/10/23 18:07:49 lapp Exp $ # # This module is licensed under the same terms as Perl itself. You use, # modify, and redistribute it under the terms of the Perl Artistic License. # =head1 NAME Bio::IdentifiableI - interface for objects with identifiers =head1 SYNOPSIS # to test this is an identifiable object $obj->isa("Bio::IdentifiableI") || $obj->throw("$obj does not implement the Bio::IdentifiableI interface"); # accessors $object_id = $obj->object_id(); $namespace = $obj->namespace(); $authority = $obj->authority(); $version = $obj->version(); # utility function $lsid = $obj->lsid_string(); # gives authority:namespace:object_id $ns_string = $obj->namespace_string(); # gives namespace:object_id.version =head1 DESCRIPTION This interface describes methods expected on identifiable objects, ie ones which have identifiers expected to make sense across a number of instances and/or domains. This interface is modeled after pretty much ubiquitous ideas for names in bioinformatics being databasename:object_id.version examples being swissprot:P012334.2 or GO:0007048 We also work well with LSID proposals which adds in the concept of an authority, being the DNS name of the organisation assigning the namespace. Helper functions are provided to make useful strings being lsid_string - string complying to the LSID standard namespace_string - string complying to the usual convention of namespace:object_id.version =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 one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bio.perl.org/MailList.html - About the mailing lists =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ =head1 AUTHOR - Ewan Birney Email birney@sanger.ac.uk =cut package Bio::IdentifiableI; use vars qw(@ISA ); use strict; use Bio::Root::RootI; @ISA = qw(Bio::Root::RootI); =head1 Implementation Specific Functions These functions are the ones that a specific implementation must define. =head2 object_id Title : object_id Usage : $string = $obj->object_id() Function: a string which represents the stable primary identifier in this namespace of this object. For DNA sequences this is its accession_number, similarly for protein sequences Returns : A scalar Status : Virtual =cut sub object_id { my ($self) = @_; $self->throw_not_implemented(); } =head2 version Title : version Usage : $version = $obj->version() Function: a number which differentiates between versions of the same object. Higher numbers are considered to be later and more relevant, but a single object described the same identifier should represent the same concept Returns : A number Status : Virtual =cut sub version { my ($self) = @_; $self->throw_not_implemented(); } =head2 authority Title : authority Usage : $authority = $obj->authority() Function: a string which represents the organisation which granted the namespace, written as the DNS name for organisation (eg, wormbase.org) Returns : A scalar Status : Virtual =cut sub authority { my ($self) = @_; $self->throw_not_implemented(); } =head2 namespace Title : namespace Usage : $string = $obj->namespace() Function: A string representing the name space this identifier is valid in, often the database name or the name describing the collection Returns : A scalar Status : Virtual =cut sub namespace { my ($self) = @_; $self->throw_not_implemented(); } =head1 Implementation optional functions These functions are helper functions that are provided by the interface but can be overridden if so wished =head2 lsid_string Title : lsid_string Usage : $string = $obj->lsid_string() Function: a string which gives the LSID standard notation for the identifier of interest Returns : A scalar =cut sub lsid_string { my ($self) = @_; return $self->authority.":".$self->namespace.":".$self->object_id; } =head2 namespace_string Title : namespace_string Usage : $string = $obj->namespace_string() Function: a string which gives the common notation of namespace:object_id.version Returns : A scalar =cut sub namespace_string { my ($self) = @_; return $self->namespace.":".$self->object_id . (defined($self->version()) ? ".".$self->version : ''); } 1;