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