Bio/IdCollectionI.pm

   1
   2 #
   3 # This module is licensed under the same terms as Perl itself. You use,
   4 # modify, and redistribute it under the terms of the Perl Artistic License.
   5 #
   6
   7 =head1 NAME
   8
   9 Bio::IdCollectionI - interface for objects with multiple identifiers
  10
  11 =head1 SYNOPSIS
  12
  13
  14     # to test this is an identifiable collection object
  15
  16     $obj->isa("Bio::IdCollectionI") ||
  17       $obj->throw("$obj does not implement the Bio::IdCollectionI interface");
  18
  19     # accessors
  20     @authorities = $obj->id_authorities();
  21     @ids         = $obj->ids();
  22     $id          = $obj->ids($authority);
  23
  24 =head1 DESCRIPTION
  25
  26 This interface describes methods expected on objects that have
  27 multiple identifiers, each of which is controlled by a different
  28 authority.
  29
  30 =head1 FEEDBACK
  31
  32 =head2 Mailing Lists
  33
  34 User feedback is an integral part of the evolution of this and other
  35 Bioperl modules. Send your comments and suggestions preferably to one
  36 of the Bioperl mailing lists.  Your participation is much appreciated.
  37
  38   bioperl-l@bioperl.org                  - General discussion
  39   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  40
  41 =head2 Support
  42
  43 Please direct usage questions or support issues to the mailing list:
  44
  45 I<bioperl-l@bioperl.org>
  46
  47 rather than to the module maintainer directly. Many experienced and
  48 reponsive experts will be able look at the problem and quickly
  49 address it. Please include a thorough description of the problem
  50 with code and data examples if at all possible.
  51
  52 =head2 Reporting Bugs
  53
  54 Report bugs to the Bioperl bug tracking system to help us keep track
  55 the bugs and their resolution.  Bug reports can be submitted via the
  56 web:
  57
  58   https://redmine.open-bio.org/projects/bioperl/
  59
  60 =head1 AUTHOR - Lincoln Stein
  61
  62 Email lstein@cshl.org
  63
  64 =cut
  65
  66 package Bio::IdCollectionI;
  67 use strict;
  68
  69
  70 use base qw(Bio::Root::RootI);
  71
  72 =head1 Implementation Specific Functions
  73
  74 These functions are the ones that a specific implementation must
  75 define.
  76
  77 =head2 id_authorities
  78
  79  Title   : id_authorities
  80  Usage   : @array    = $obj->id_authorities()
  81  Function: Return the authorities which have names for this object.
  82            The authorities can then be used to select ids.
  83
  84  Returns : An array
  85  Status  : Virtual
  86
  87 =cut
  88
  89 sub id_authorities {
  90    my ($self) = @_;
  91    $self->throw_not_implemented();
  92 }
  93
  94 =head2 ids
  95
  96  Title   : ids
  97  Usage   : @ids    = $obj->ids([$authority1,$authority2...])
  98  Function: return a list of Bio::IdentifiableI objects, optionally
  99            filtered by the list of authorities.
 100
 101  Returns : A list of Bio::IdentifiableI objects.
 102  Status  : Virtual
 103
 104 =cut
 105
 106 sub ids {
 107    my ($self) = @_;
 108    my @authorities = @_;
 109    $self->throw_not_implemented();
 110 }
 111
 112 1;