branch-1-6/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 Support
  43
  44 Please direct usage questions or support issues to the mailing list:
  45
  46 I<bioperl-l@bioperl.org>
  47
  48 rather than to the module maintainer directly. Many experienced and
  49 reponsive experts will be able look at the problem and quickly
  50 address it. Please include a thorough description of the problem
  51 with code and data examples if at all possible.
  52
  53 =head2 Reporting Bugs
  54
  55 Report bugs to the Bioperl bug tracking system to help us keep track
  56 the bugs and their resolution.  Bug reports can be submitted via the
  57 web:
  58
  59   http://bugzilla.open-bio.org/
  60
  61 =head1 AUTHOR - Lincoln Stein
  62
  63 Email lstein@cshl.org
  64
  65 =cut
  66
  67 package Bio::IdCollectionI;
  68 use strict;
  69
  70
  71 use base qw(Bio::Root::RootI);
  72
  73 =head1 Implementation Specific Functions
  74
  75 These functions are the ones that a specific implementation must
  76 define.
  77
  78 =head2 id_authorities
  79
  80  Title   : id_authorities
  81  Usage   : @array    = $obj->id_authorities()
  82  Function: Return the authorities which have names for this object.
  83            The authorities can then be used to select ids.
  84
  85  Returns : An array
  86  Status  : Virtual
  87
  88 =cut
  89
  90 sub id_authorities {
  91    my ($self) = @_;
  92    $self->throw_not_implemented();
  93 }
  94
  95 =head2 ids
  96
  97  Title   : ids
  98  Usage   : @ids    = $obj->ids([$authority1,$authority2...])
  99  Function: return a list of Bio::IdentifiableI objects, optionally
 100            filtered by the list of authorities.
 101
 102  Returns : A list of Bio::IdentifiableI objects.
 103  Status  : Virtual
 104
 105 =cut
 106
 107 sub ids {
 108    my ($self) = @_;
 109    my @authorities = @_;
 110    $self->throw_not_implemented();
 111 }
 112
 113 1;