Bio/Biblio/PubmedJournalArticle.pm

   1 #
   2 # BioPerl module for Bio::Biblio::PubmedJournalArticle
   3 #
   4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   5 #
   6 # Cared for by Martin Senger <senger@ebi.ac.uk>
   7 # For copyright and disclaimer see below.
   8
   9 # POD documentation - main docs before the code
  10
  11 =head1 NAME
  12
  13 Bio::Biblio::PubmedJournalArticle - Representation of a PUBMED journal article
  14
  15 =head1 SYNOPSIS
  16
  17     $obj = Bio::Biblio::PubmedJournalArticle->new(
  18
  19                   # some attributes from MedlineJournalArticle
  20                   -title => 'Thermal adaptation analyzed by comparison of protein sequences from mesophilic and extremely thermophilic Methanococcus species.',
  21                   -journal => Bio::Biblio::MedlineJournal->new(-issn => '0027-8424'),
  22                   -volume => 96,
  23                   -issue => 7,
  24
  25                   # and some from PubmedArticle
  26                   -pubmed_history_list =>
  27                        [ { 'pub_status' => 'pubmed',
  28                            'date' => '2001-12-1T10:0:00Z' },
  29                          { 'pub_status' => 'medline',
  30                            'date' => '2002-1-5T10:1:00Z' } ],
  31                    -pubmed_status => 'ppublish');
  32   #--- OR ---
  33
  34     $obj = Bio::Biblio::PubmedJournalArticle->new();
  35     $obj->title ('...');
  36     $obj->journal (Bio::Biblio::MedlineJournal->new(-issn => '0027-8424'));
  37     $obj->pubmed_status ('ppublish');
  38
  39
  40 =head1 DESCRIPTION
  41
  42 A storage object for a PUBMED journal article.
  43 See its place in the class hierarchy in
  44 http://www.ebi.ac.uk/~senger/openbqs/images/bibobjects_perl.gif
  45
  46 =head2 Attributes
  47
  48 There are no specific attributes in this class
  49 (however, you can set and get all attributes defined in the parent classes).
  50
  51 =head1 SEE ALSO
  52
  53 =over 4
  54
  55 =item *
  56
  57 OpenBQS home page: http://www.ebi.ac.uk/~senger/openbqs/
  58
  59 =item *
  60
  61 Comments to the Perl client: http://www.ebi.ac.uk/~senger/openbqs/Client_perl.html
  62
  63 =back
  64
  65 =head1 FEEDBACK
  66
  67 =head2 Mailing Lists
  68
  69 User feedback is an integral part of the evolution of this and other
  70 Bioperl modules. Send your comments and suggestions preferably to
  71 the Bioperl mailing list.  Your participation is much appreciated.
  72
  73   bioperl-l@bioperl.org                  - General discussion
  74   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  75
  76 =head2 Support
  77
  78 Please direct usage questions or support issues to the mailing list:
  79
  80 I<bioperl-l@bioperl.org>
  81
  82 rather than to the module maintainer directly. Many experienced and
  83 reponsive experts will be able look at the problem and quickly
  84 address it. Please include a thorough description of the problem
  85 with code and data examples if at all possible.
  86
  87 =head2 Reporting Bugs
  88
  89 Report bugs to the Bioperl bug tracking system to help us keep track
  90 of the bugs and their resolution. Bug reports can be submitted via the
  91 web:
  92
  93   http://bugzilla.open-bio.org/
  94
  95 =head1 AUTHOR
  96
  97 Martin Senger (senger@ebi.ac.uk)
  98
  99 =head1 COPYRIGHT
 100
 101 Copyright (c) 2002 European Bioinformatics Institute. All Rights Reserved.
 102
 103 This module is free software; you can redistribute it and/or modify
 104 it under the same terms as Perl itself.
 105
 106 =head1 DISCLAIMER
 107
 108 This software is provided "as is" without warranty of any kind.
 109
 110 =cut
 111
 112
 113 # Let the code begin...
 114
 115
 116 package Bio::Biblio::PubmedJournalArticle;
 117 use strict;
 118 use vars qw(@ISA);
 119
 120 use base qw(Bio::Biblio::PubmedArticle Bio::Biblio::MedlineJournalArticle);
 121
 122 #
 123 # a closure with a list of allowed attribute names (these names
 124 # correspond with the allowed 'get' and 'set' methods); each name also
 125 # keep what type the attribute should be (use 'undef' if it is a
 126 # simple scalar)
 127 #
 128 {
 129     my %_allowed =
 130         (
 131          );
 132
 133     # return 1 if $attr is allowed to be set/get in this class
 134     sub _accessible {
 135         my ($self, $attr) = @_;
 136         return 1 if exists $_allowed{$attr};
 137         foreach my $parent (@ISA) {
 138             return 1 if $parent->_accessible ($attr);
 139         }
 140     }
 141
 142     # return an expected type of given $attr
 143     sub _attr_type {
 144         my ($self, $attr) = @_;
 145         if (exists $_allowed{$attr}) {
 146             return $_allowed{$attr};
 147         } else {
 148             foreach my $parent (@ISA) {
 149                 if ($parent->_accessible ($attr)) {
 150                     return $parent->_attr_type ($attr);
 151                 }
 152             }
 153         }
 154         return 'unknown';
 155     }
 156 }
 157
 158
 159 1;
 160 __END__