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#
# 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();
# Gets authority:namespace:object_id
$lsid = $obj->lsid_string();
# Gets namespace:object_id.version
$ns_string = $obj->namespace_string();
=head1 DESCRIPTION
This interface describes methods expected on identifiable objects, i.e.
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
Example:
swissprot:P012334.2
or:
GO:0007048
The object will also work with LSID proposals which adds the concept of an
authority, being the DNS name of the organisation assigning the namespace.
See L<http://lsid.sourceforge.net/>.
Helper functions are provided to make useful strings:
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://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=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 the
web:
https://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR - Ewan Birney
Email birney@ebi.ac.uk
=cut
package Bio::IdentifiableI;
use strict;
use base 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;
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