# 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


    # 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();


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






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


=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:


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


=head1 AUTHOR - Ewan Birney

Email birney@ebi.ac.uk


package Bio::IdentifiableI;
$Bio::IdentifiableI::VERSION = '1.7.8';
use strict;

use base qw(Bio::Root::RootI);

=head1 Implementation Specific Functions

These functions are the ones that a specific implementation must

=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


sub object_id {
   my ($self) = @_;

=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


sub version {
   my ($self) = @_;

=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


sub authority {
   my ($self) = @_;

=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


sub namespace {
   my ($self) = @_;

=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


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
 Returns : A scalar


sub namespace_string {
  my ($self) = @_;

  return $self->namespace.":".$self->object_id .
      (defined($self->version()) ? ".".$self->version : '');