diff variant_effect_predictor/Bio/Biblio/MedlineArticle.pm @ 0:2bc9b66ada89 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Biblio/MedlineArticle.pm	Thu Apr 11 06:29:17 2013 -0400
@@ -0,0 +1,205 @@
+# $Id: MedlineArticle.pm,v 1.5 2002/10/22 07:45:11 lapp Exp $
+#
+# BioPerl module for Bio::Biblio::MedlineArticle
+#
+# Cared for by Martin Senger <[e-mail]>
+# For copyright and disclaimer see below.
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::Biblio::MedlineArticle - Representation of a MEDLINE article
+
+=head1 SYNOPSIS
+
+  $obj = new Bio::Biblio::MedlineArticle (-mesh_headings => ...);
+
+  # how are Mesh terms stored:
+  use Data::Dumper;
+  print Data::Dumper->Dump ( [$obj->mesh_headings], ['MeshHeadings']);
+
+  It produces (something like) this:
+  'MeshHeadings' => [
+	 { 'descriptorName' => 'Adult' },
+         { 'descriptorName' => 'Cardiovascular Diseases',
+           'subHeadings'    => [ { 'subHeading' => 'etiology' },
+			         { 'majorTopic' => 'Y',
+			           'subHeading' => 'mortality' } ] },
+	 { 'descriptorName' => 'Child Development',
+	   'subHeadings'    => [ { 'majorTopic' => 'Y',
+				   'subHeading' => 'physiology' } ] },
+	 { 'descriptorName' => 'Human' },
+	]
+
+=head1 DESCRIPTION
+
+A storage object for a MEDLINE article.
+See its place in the class hierarchy in
+http://industry.ebi.ac.uk/openBQS/images/bibobjects_perl.gif
+
+=head2 Attributes
+
+The following attributes are specific to this class
+(however, you can also set and get all attributes defined in the parent classes):
+
+  affiliation
+  chemicals                      type: array ref of hashes
+  citation_owner
+  comment_ins                    type: array ref of hashes
+  comment_ons                    type: array ref of hashes
+  date_of_electronic_publication
+  erratum_fors                   type: array ref of hashes
+  erratum_in                     type: array ref of hashes
+  gene_symbols
+  general_notes                  type: array ref of hashes
+  grant_list_complete
+  grants                         type: array ref of hashes
+  medline_date
+  medline_id
+  medline_page
+  mesh_headings                  type: array ref of hashes
+  number_of_references
+  original_report_ins            type: array ref of hashes
+  other_abstracts                type: array ref of hashes
+  other_ids                      type: array ref of hashes
+  other_languages
+  pmid
+  republished_froms              type: array ref of hashes
+  republished_ins                type: array ref of hashes
+  retraction_ins                 type: array ref of hashes
+  retraction_ofs                 type: array ref of hashes
+  season
+  status
+  summary_for_patients_ins       type: array ref of hashes
+  update_ins                     type: array ref of hashes
+  update_ofs                     type: array ref of hashes
+  vernacular_title
+
+=head1 SEE ALSO
+
+=over
+
+=item *
+
+OpenBQS home page: http://industry.ebi.ac.uk/openBQS
+
+=item *
+
+Comments to the Perl client: http://industry.ebi.ac.uk/openBQS/Client_perl.html
+
+=back
+
+=head1 FEEDBACK
+
+=head2 Mailing Lists
+
+User feedback is an integral part of the evolution of this and other
+Bioperl modules. Send your comments and suggestions preferably to
+the Bioperl mailing list.  Your participation is much appreciated.
+
+  [e-mail]              - General discussion
+  http://bioperl.org/MailList.shtml  - About the mailing lists
+
+=head2 Reporting Bugs
+
+Report bugs to the Bioperl bug tracking system to help us keep track
+of the bugs and their resolution. Bug reports can be submitted via
+email or the web:
+
+  [e-mail]
+  http://bugzilla.bioperl.org/
+
+=head1 AUTHORS
+
+Heikki Lehvaslaiho ([e-mail]),
+Martin Senger ([e-mail])
+
+=head1 COPYRIGHT
+
+Copyright (c) 2002 European Bioinformatics Institute. All Rights Reserved.
+
+This module is free software; you can redistribute it and/or modify
+it under the same terms as Perl itself.
+
+=head1 DISCLAIMER
+
+This software is provided "as is" without warranty of any kind.
+
+=cut
+
+
+# Let the code begin...
+
+
+package Bio::Biblio::MedlineArticle;
+use strict;
+use vars qw(@ISA);
+
+use Bio::Biblio::Article;
+
+@ISA = qw(Bio::Biblio::Article);
+
+#
+# a closure with a list of allowed attribute names (these names
+# correspond with the allowed 'get' and 'set' methods); each name also
+# keep what type the attribute should be (use 'undef' if it is a
+# simple scalar)
+#
+{
+    my %_allowed =
+	(
+	 _affiliation => undef,
+	 _chemicals => 'ARRAY',
+	 _citation_owner => undef,
+	 _comment_ins => 'ARRAY',
+	 _comment_ons => 'ARRAY',
+	 _date_of_electronic_publication => undef,
+	 _erratum_fors => 'ARRAY',
+	 _erratum_ins => 'ARRAY',
+	 _gene_symbols => undef,
+	 _general_notes => 'ARRAY',
+	 _grant_list_complete => undef,
+	 _grants => 'ARRAY',
+	 _medline_date => undef,
+	 _medline_id => undef,
+	 _medline_page => undef,
+	 _mesh_headings => 'ARRAY',
+	 _number_of_references => undef,
+	 _original_report_ins => 'ARRAY',
+	 _other_abstracts => 'ARRAY',
+	 _other_ids => 'ARRAY',
+	 _other_languages => undef,
+	 _pmid => undef,
+	 _republished_froms => 'ARRAY',
+	 _republished_ins => 'ARRAY',
+	 _retraction_ins => 'ARRAY',
+	 _retraction_ofs => 'ARRAY',
+	 _season => undef,
+	 _status => undef,
+	 _summary_for_patients_ins => 'ARRAY',
+	 _update_ins => 'ARRAY',
+	 _update_ofs => 'ARRAY',
+	 _vernacular_title => undef,
+	 );
+
+    # return 1 if $attr is allowed to be set/get in this class
+    sub _accessible {
+	my ($self, $attr) = @_;
+	exists $_allowed{$attr} or $self->SUPER::_accessible ($attr);
+    }
+
+    # return an expected type of given $attr
+    sub _attr_type {
+	my ($self, $attr) = @_;
+	if (exists $_allowed{$attr}) {
+	    return $_allowed{$attr};
+	} else {
+	    return $self->SUPER::_attr_type ($attr);
+	}
+    }
+}
+
+
+1;
+__END__