Bio/Biblio/PubmedArticle.pm

   1 # $Id$
   2 #
   3 # BioPerl module for Bio::Biblio::PubmedArticle
   4 #
   5 # Cared for by Martin Senger <senger@ebi.ac.uk>
   6 # For copyright and disclaimer see below.
   7
   8 # POD documentation - main docs before the code
   9
  10 =head1 NAME
  11
  12 Bio::Biblio::PubmedArticle - Representation of a PUBMED article
  13
  14 =head1 SYNOPSIS
  15
  16     $obj = new Bio::Biblio::PubmedArticle
  17                   (-pubmed_history_list =>
  18                        [ { 'pub_status' => 'pubmed',
  19                            'date' => '2001-12-1T10:0:00Z' },
  20                          { 'pub_status' => 'medline',
  21                            'date' => '2002-1-5T10:1:00Z' } ],
  22                    -pubmed_status => 'ppublish');
  23  --- OR ---
  24
  25     $obj = new Bio::Biblio::PubmedArticle;
  26     $obj->pubmed_status ('ppublish');
  27
  28 =head1 DESCRIPTION
  29
  30 A storage object for a general PUBMED article.
  31 See its place in the class hierarchy in
  32 http://industry.ebi.ac.uk/openBQS/images/bibobjects_perl.gif
  33
  34 =head2 Attributes
  35
  36 The following attributes are specific to this class
  37 (however, you can also set and get all attributes defined in the parent classes):
  38
  39   pubmed_status
  40   pubmed_provider_id
  41   pubmed_history_list       type: array ref of hashes
  42   pubmed_article_id_list    type: array ref of hashes
  43   pubmed_url_list           type: array ref of hashes
  44
  45 =head1 SEE ALSO
  46
  47 =over
  48
  49 =item *
  50
  51 OpenBQS home page: http://industry.ebi.ac.uk/openBQS
  52
  53 =item *
  54
  55 Comments to the Perl client: http://industry.ebi.ac.uk/openBQS/Client_perl.html
  56
  57 =back
  58
  59 =head1 FEEDBACK
  60
  61 =head2 Mailing Lists
  62
  63 User feedback is an integral part of the evolution of this and other
  64 Bioperl modules. Send your comments and suggestions preferably to
  65 the Bioperl mailing list.  Your participation is much appreciated.
  66
  67   bioperl-l@bioperl.org              - General discussion
  68   http://bioperl.org/MailList.shtml  - About the mailing lists
  69
  70 =head2 Reporting Bugs
  71
  72 Report bugs to the Bioperl bug tracking system to help us keep track
  73 of the bugs and their resolution. Bug reports can be submitted via
  74 email or the web:
  75
  76   bioperl-bugs@bioperl.org
  77   http://bugzilla.bioperl.org/
  78
  79 =head1 AUTHOR
  80
  81 Martin Senger (senger@ebi.ac.uk)
  82
  83 =head1 COPYRIGHT
  84
  85 Copyright (c) 2002 European Bioinformatics Institute. All Rights Reserved.
  86
  87 This module is free software; you can redistribute it and/or modify
  88 it under the same terms as Perl itself.
  89
  90 =head1 DISCLAIMER
  91
  92 This software is provided "as is" without warranty of any kind.
  93
  94 =cut
  95
  96
  97 # Let the code begin...
  98
  99
 100 package Bio::Biblio::PubmedArticle;
 101 use strict;
 102 use vars qw(@ISA);
 103
 104 use Bio::Biblio::MedlineArticle;
 105 @ISA = qw(Bio::Biblio::MedlineArticle);
 106
 107 #
 108 # a closure with a list of allowed attribute names (these names
 109 # correspond with the allowed 'get' and 'set' methods); each name also
 110 # keep what type the attribute should be (use 'undef' if it is a
 111 # simple scalar)
 112 #
 113 {
 114     my %_allowed =
 115         (
 116          _pubmed_status => undef,
 117          _pubmed_provider_id => undef,
 118          _pubmed_history_list => 'ARRAY',
 119          _pubmed_article_id_list => 'ARRAY',
 120          _pubmed_url_list => 'ARRAY',
 121          );
 122
 123     # return 1 if $attr is allowed to be set/get in this class
 124     sub _accessible {
 125         my ($self, $attr) = @_;
 126         return 1 if exists $_allowed{$attr};
 127         foreach my $parent (@ISA) {
 128             return 1 if $parent->_accessible ($attr);
 129         }
 130     }
 131
 132     # return an expected type of given $attr
 133     sub _attr_type {
 134         my ($self, $attr) = @_;
 135         if (exists $_allowed{$attr}) {
 136             return $_allowed{$attr};
 137         } else {
 138             foreach my $parent (@ISA) {
 139                 if ($parent->_accessible ($attr)) {
 140                     return $parent->_attr_type ($attr);
 141                 }
 142             }
 143         }
 144         return 'unknown';
 145     }
 146 }
 147
 148 1;
 149 __END__