Bio/Biblio/MedlineArticle.pm

   1 # $Id$
   2 #
   3 # BioPerl module for Bio::Biblio::MedlineArticle
   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::MedlineArticle - Representation of a MEDLINE article
  13
  14 =head1 SYNOPSIS
  15
  16   $obj = Bio::Biblio::MedlineArticle->new(-mesh_headings =>
  17                                             #array ref of hashes
  18                                          );
  19
  20   # how are Mesh terms stored:
  21   use Data::Dumper;
  22   print Data::Dumper->Dump ( [$obj->mesh_headings], ['MeshHeadings']);
  23
  24   #It produces (something like) this:
  25   #'MeshHeadings' => [
  26   #       { 'descriptorName' => 'Adult' },
  27   #       { 'descriptorName' => 'Cardiovascular Diseases',
  28   #         'subHeadings'    => [ { 'subHeading' => 'etiology' },
  29   #                               { 'majorTopic' => 'Y',
  30   #                                 'subHeading' => 'mortality' } ] },
  31   #       { 'descriptorName' => 'Child Development',
  32   #         'subHeadings'    => [ { 'majorTopic' => 'Y',
  33   #                                 'subHeading' => 'physiology' } ] },
  34   #       { 'descriptorName' => 'Human' },
  35   #      ]
  36
  37 =head1 DESCRIPTION
  38
  39 A storage object for a MEDLINE article.
  40 See its place in the class hierarchy in
  41 http://www.ebi.ac.uk/~senger/openbqs/images/bibobjects_perl.gif
  42
  43 =head2 Attributes
  44
  45 The following attributes are specific to this class
  46 (however, you can also set and get all attributes defined in the parent classes):
  47
  48   affiliation
  49   chemicals                      type: array ref of hashes
  50   citation_owner
  51   comment_ins                    type: array ref of hashes
  52   comment_ons                    type: array ref of hashes
  53   date_of_electronic_publication
  54   erratum_fors                   type: array ref of hashes
  55   erratum_in                     type: array ref of hashes
  56   gene_symbols
  57   general_notes                  type: array ref of hashes
  58   grant_list_complete
  59   grants                         type: array ref of hashes
  60   medline_date
  61   medline_id
  62   medline_page
  63   mesh_headings                  type: array ref of hashes
  64   number_of_references
  65   original_report_ins            type: array ref of hashes
  66   other_abstracts                type: array ref of hashes
  67   other_ids                      type: array ref of hashes
  68   other_languages
  69   pmid
  70   republished_froms              type: array ref of hashes
  71   republished_ins                type: array ref of hashes
  72   retraction_ins                 type: array ref of hashes
  73   retraction_ofs                 type: array ref of hashes
  74   season
  75   status
  76   summary_for_patients_ins       type: array ref of hashes
  77   update_ins                     type: array ref of hashes
  78   update_ofs                     type: array ref of hashes
  79   vernacular_title
  80
  81 =head1 SEE ALSO
  82
  83 =over 4
  84
  85 =item *
  86
  87 OpenBQS home page: http://www.ebi.ac.uk/~senger/openbqs/
  88
  89 =item *
  90
  91 Comments to the Perl client: http://www.ebi.ac.uk/~senger/openbqs/Client_perl.html
  92
  93 =back
  94
  95 =head1 FEEDBACK
  96
  97 =head2 Mailing Lists
  98
  99 User feedback is an integral part of the evolution of this and other
 100 Bioperl modules. Send your comments and suggestions preferably to
 101 the Bioperl mailing list.  Your participation is much appreciated.
 102
 103   bioperl-l@bioperl.org                  - General discussion
 104   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
 105
 106 =head2 Reporting Bugs
 107
 108 Report bugs to the Bioperl bug tracking system to help us keep track
 109 of the bugs and their resolution. Bug reports can be submitted via the
 110 web:
 111
 112   http://bugzilla.open-bio.org/
 113
 114 =head1 AUTHORS
 115
 116 Heikki Lehvaslaiho (heikki-at-bioperl-dot-org),
 117 Martin Senger (senger@ebi.ac.uk)
 118
 119 =head1 COPYRIGHT
 120
 121 Copyright (c) 2002 European Bioinformatics Institute. All Rights Reserved.
 122
 123 This module is free software; you can redistribute it and/or modify
 124 it under the same terms as Perl itself.
 125
 126 =head1 DISCLAIMER
 127
 128 This software is provided "as is" without warranty of any kind.
 129
 130 =cut
 131
 132
 133 # Let the code begin...
 134
 135
 136 package Bio::Biblio::MedlineArticle;
 137 use strict;
 138
 139
 140 use base qw(Bio::Biblio::Article);
 141
 142 #
 143 # a closure with a list of allowed attribute names (these names
 144 # correspond with the allowed 'get' and 'set' methods); each name also
 145 # keep what type the attribute should be (use 'undef' if it is a
 146 # simple scalar)
 147 #
 148 {
 149     my %_allowed =
 150         (
 151          _affiliation => undef,
 152          _chemicals => 'ARRAY',
 153          _citation_owner => undef,
 154          _comment_ins => 'ARRAY',
 155          _comment_ons => 'ARRAY',
 156          _date_of_electronic_publication => undef,
 157          _erratum_fors => 'ARRAY',
 158          _erratum_ins => 'ARRAY',
 159          _gene_symbols => undef,
 160          _general_notes => 'ARRAY',
 161          _grant_list_complete => undef,
 162          _grants => 'ARRAY',
 163          _medline_date => undef,
 164          _medline_id => undef,
 165          _medline_page => undef,
 166          _mesh_headings => 'ARRAY',
 167          _number_of_references => undef,
 168          _original_report_ins => 'ARRAY',
 169          _other_abstracts => 'ARRAY',
 170          _other_ids => 'ARRAY',
 171          _other_languages => undef,
 172          _pmid => undef,
 173          _republished_froms => 'ARRAY',
 174          _republished_ins => 'ARRAY',
 175          _retraction_ins => 'ARRAY',
 176          _retraction_ofs => 'ARRAY',
 177          _season => undef,
 178          _status => undef,
 179          _summary_for_patients_ins => 'ARRAY',
 180          _update_ins => 'ARRAY',
 181          _update_ofs => 'ARRAY',
 182          _vernacular_title => undef,
 183          );
 184
 185     # return 1 if $attr is allowed to be set/get in this class
 186     sub _accessible {
 187         my ($self, $attr) = @_;
 188         exists $_allowed{$attr} or $self->SUPER::_accessible ($attr);
 189     }
 190
 191     # return an expected type of given $attr
 192     sub _attr_type {
 193         my ($self, $attr) = @_;
 194         if (exists $_allowed{$attr}) {
 195             return $_allowed{$attr};
 196         } else {
 197             return $self->SUPER::_attr_type ($attr);
 198         }
 199     }
 200 }
 201
 202
 203 1;
 204 __END__