Bio/Biblio/MedlineArticle.pm

   1 # $Id$
   2 #
   3 # BioPerl module for Bio::Biblio::MedlineArticle
   4 #
   5 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   6 #
   7 # Cared for by Martin Senger <senger@ebi.ac.uk>
   8 # For copyright and disclaimer see below.
   9
  10 # POD documentation - main docs before the code
  11
  12 =head1 NAME
  13
  14 Bio::Biblio::MedlineArticle - Representation of a MEDLINE article
  15
  16 =head1 SYNOPSIS
  17
  18   $obj = Bio::Biblio::MedlineArticle->new(-mesh_headings =>
  19                                             #array ref of hashes
  20                                          );
  21
  22   # how are Mesh terms stored:
  23   use Data::Dumper;
  24   print Data::Dumper->Dump ( [$obj->mesh_headings], ['MeshHeadings']);
  25
  26   #It produces (something like) this:
  27   #'MeshHeadings' => [
  28   #       { 'descriptorName' => 'Adult' },
  29   #       { 'descriptorName' => 'Cardiovascular Diseases',
  30   #         'subHeadings'    => [ { 'subHeading' => 'etiology' },
  31   #                               { 'majorTopic' => 'Y',
  32   #                                 'subHeading' => 'mortality' } ] },
  33   #       { 'descriptorName' => 'Child Development',
  34   #         'subHeadings'    => [ { 'majorTopic' => 'Y',
  35   #                                 'subHeading' => 'physiology' } ] },
  36   #       { 'descriptorName' => 'Human' },
  37   #      ]
  38
  39 =head1 DESCRIPTION
  40
  41 A storage object for a MEDLINE article.
  42 See its place in the class hierarchy in
  43 http://www.ebi.ac.uk/~senger/openbqs/images/bibobjects_perl.gif
  44
  45 =head2 Attributes
  46
  47 The following attributes are specific to this class
  48 (however, you can also set and get all attributes defined in the parent classes):
  49
  50   affiliation
  51   chemicals                      type: array ref of hashes
  52   citation_owner
  53   comment_ins                    type: array ref of hashes
  54   comment_ons                    type: array ref of hashes
  55   date_of_electronic_publication
  56   erratum_fors                   type: array ref of hashes
  57   erratum_in                     type: array ref of hashes
  58   gene_symbols
  59   general_notes                  type: array ref of hashes
  60   grant_list_complete
  61   grants                         type: array ref of hashes
  62   medline_date
  63   medline_id
  64   medline_page
  65   mesh_headings                  type: array ref of hashes
  66   number_of_references
  67   original_report_ins            type: array ref of hashes
  68   other_abstracts                type: array ref of hashes
  69   other_ids                      type: array ref of hashes
  70   other_languages
  71   pmid
  72   republished_froms              type: array ref of hashes
  73   republished_ins                type: array ref of hashes
  74   retraction_ins                 type: array ref of hashes
  75   retraction_ofs                 type: array ref of hashes
  76   season
  77   status
  78   summary_for_patients_ins       type: array ref of hashes
  79   update_ins                     type: array ref of hashes
  80   update_ofs                     type: array ref of hashes
  81   vernacular_title
  82
  83 =head1 SEE ALSO
  84
  85 =over 4
  86
  87 =item *
  88
  89 OpenBQS home page: http://www.ebi.ac.uk/~senger/openbqs/
  90
  91 =item *
  92
  93 Comments to the Perl client: http://www.ebi.ac.uk/~senger/openbqs/Client_perl.html
  94
  95 =back
  96
  97 =head1 FEEDBACK
  98
  99 =head2 Mailing Lists
 100
 101 User feedback is an integral part of the evolution of this and other
 102 Bioperl modules. Send your comments and suggestions preferably to
 103 the Bioperl mailing list.  Your participation is much appreciated.
 104
 105   bioperl-l@bioperl.org                  - General discussion
 106   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
 107
 108 =head2 Support
 109
 110 Please direct usage questions or support issues to the mailing list:
 111
 112 L<bioperl-l@bioperl.org>
 113
 114 rather than to the module maintainer directly. Many experienced and
 115 reponsive experts will be able look at the problem and quickly
 116 address it. Please include a thorough description of the problem
 117 with code and data examples if at all possible.
 118
 119 =head2 Reporting Bugs
 120
 121 Report bugs to the Bioperl bug tracking system to help us keep track
 122 of the bugs and their resolution. Bug reports can be submitted via the
 123 web:
 124
 125   http://bugzilla.open-bio.org/
 126
 127 =head1 AUTHORS
 128
 129 Heikki Lehvaslaiho (heikki-at-bioperl-dot-org),
 130 Martin Senger (senger@ebi.ac.uk)
 131
 132 =head1 COPYRIGHT
 133
 134 Copyright (c) 2002 European Bioinformatics Institute. All Rights Reserved.
 135
 136 This module is free software; you can redistribute it and/or modify
 137 it under the same terms as Perl itself.
 138
 139 =head1 DISCLAIMER
 140
 141 This software is provided "as is" without warranty of any kind.
 142
 143 =cut
 144
 145
 146 # Let the code begin...
 147
 148
 149 package Bio::Biblio::MedlineArticle;
 150 use strict;
 151
 152
 153 use base qw(Bio::Biblio::Article);
 154
 155 #
 156 # a closure with a list of allowed attribute names (these names
 157 # correspond with the allowed 'get' and 'set' methods); each name also
 158 # keep what type the attribute should be (use 'undef' if it is a
 159 # simple scalar)
 160 #
 161 {
 162     my %_allowed =
 163         (
 164          _affiliation => undef,
 165          _chemicals => 'ARRAY',
 166          _citation_owner => undef,
 167          _comment_ins => 'ARRAY',
 168          _comment_ons => 'ARRAY',
 169          _date_of_electronic_publication => undef,
 170          _erratum_fors => 'ARRAY',
 171          _erratum_ins => 'ARRAY',
 172          _gene_symbols => undef,
 173          _general_notes => 'ARRAY',
 174          _grant_list_complete => undef,
 175          _grants => 'ARRAY',
 176          _medline_date => undef,
 177          _medline_id => undef,
 178          _medline_page => undef,
 179          _mesh_headings => 'ARRAY',
 180          _number_of_references => undef,
 181          _original_report_ins => 'ARRAY',
 182          _other_abstracts => 'ARRAY',
 183          _other_ids => 'ARRAY',
 184          _other_languages => undef,
 185          _pmid => undef,
 186          _republished_froms => 'ARRAY',
 187          _republished_ins => 'ARRAY',
 188          _retraction_ins => 'ARRAY',
 189          _retraction_ofs => 'ARRAY',
 190          _season => undef,
 191          _status => undef,
 192          _summary_for_patients_ins => 'ARRAY',
 193          _update_ins => 'ARRAY',
 194          _update_ofs => 'ARRAY',
 195          _vernacular_title => undef,
 196          );
 197
 198     # return 1 if $attr is allowed to be set/get in this class
 199     sub _accessible {
 200         my ($self, $attr) = @_;
 201         exists $_allowed{$attr} or $self->SUPER::_accessible ($attr);
 202     }
 203
 204     # return an expected type of given $attr
 205     sub _attr_type {
 206         my ($self, $attr) = @_;
 207         if (exists $_allowed{$attr}) {
 208             return $_allowed{$attr};
 209         } else {
 210             return $self->SUPER::_attr_type ($attr);
 211         }
 212     }
 213 }
 214
 215
 216 1;
 217 __END__