Bio/IdCollectionI.pm

   1 # $Id$
   2
   3 #
   4 # This module is licensed under the same terms as Perl itself. You use,
   5 # modify, and redistribute it under the terms of the Perl Artistic License.
   6 #
   7
   8 =head1 NAME
   9
  10 Bio::IdCollectionI - interface for objects with multiple identifiers
  11
  12 =head1 SYNOPSIS
  13
  14
  15     # to test this is an identifiable collection object
  16
  17     $obj->isa("Bio::IdCollectionI") ||
  18       $obj->throw("$obj does not implement the Bio::IdCollectionI interface");
  19
  20     # accessors
  21     @authorities = $obj->id_authorities();
  22     @ids         = $obj->ids();
  23     $id          = $obj->ids($authority);
  24
  25 =head1 DESCRIPTION
  26
  27 This interface describes methods expected on objects that have
  28 multiple identifiers, each of which is controlled by a different
  29 authority.
  30
  31 =head1 FEEDBACK
  32
  33 =head2 Mailing Lists
  34
  35 User feedback is an integral part of the evolution of this and other
  36 Bioperl modules. Send your comments and suggestions preferably to one
  37 of the Bioperl mailing lists.  Your participation is much appreciated.
  38
  39   bioperl-l@bioperl.org                  - General discussion
  40   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  41
  42 =head2 Reporting Bugs
  43
  44 Report bugs to the Bioperl bug tracking system to help us keep track
  45 the bugs and their resolution.  Bug reports can be submitted via the
  46 web:
  47
  48   http://bugzilla.open-bio.org/
  49
  50 =head1 AUTHOR - Lincoln Stein
  51
  52 Email lstein@cshl.org
  53
  54 =cut
  55
  56 package Bio::IdCollectionI;
  57 use strict;
  58
  59
  60 use base qw(Bio::Root::RootI);
  61
  62 =head1 Implementation Specific Functions
  63
  64 These functions are the ones that a specific implementation must
  65 define.
  66
  67 =head2 id_authorities
  68
  69  Title   : id_authorities
  70  Usage   : @array    = $obj->id_authorities()
  71  Function: Return the authorities which have names for this object.
  72            The authorities can then be used to select ids.
  73
  74  Returns : An array
  75  Status  : Virtual
  76
  77 =cut
  78
  79 sub id_authorities {
  80    my ($self) = @_;
  81    $self->throw_not_implemented();
  82 }
  83
  84 =head2 ids
  85
  86  Title   : ids
  87  Usage   : @ids    = $obj->ids([$authority1,$authority2...])
  88  Function: return a list of Bio::IdentifiableI objects, optionally
  89            filtered by the list of authorities.
  90
  91  Returns : A list of Bio::IdentifiableI objects.
  92  Status  : Virtual
  93
  94 =cut
  95
  96 sub ids {
  97    my ($self) = @_;
  98    my @authorities = @_;
  99    $self->throw_not_implemented();
 100 }
 101
 102 1;