Bio/Biblio/PubmedJournalArticle.pm

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