annotate variant_effect_predictor/Bio/Biblio/MedlineBook.pm @ 1:d6778b5d8382 draft default tip

Deleted selected files
author willmclaren
date Fri, 03 Aug 2012 10:05:43 -0400
parents 21066c0abaf5
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
1 # $Id: MedlineBook.pm,v 1.3 2002/10/22 07:45:11 lapp Exp $
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
2 #
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
3 # BioPerl module for Bio::Biblio::MedlineBook
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
4 #
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
5 # Cared for by Martin Senger <senger@ebi.ac.uk>
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
6 # For copyright and disclaimer see below.
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
7
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
8 # POD documentation - main docs before the code
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
9
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
10 =head1 NAME
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
11
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
12 Bio::Biblio::MedlineBook - Representation of a MEDLINE book
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
13
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
14 =head1 SYNOPSIS
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
15
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
16 $obj = new Bio::Biblio::MedlineBook
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
17 (-editor => new Bio::Biblio::Person
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
18 (-lastname => 'Loukides'),
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
19 -isbn => '0-596-00068-5');
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
20 --- OR ---
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
21
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
22 $obj = new Bio::Biblio::MedlineBook;
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
23 $obj->isbn ('0-596-00068-5');
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
24
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
25 =head1 DESCRIPTION
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
26
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
27 A storage object for a MEDLINE book.
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
28 See its place in the class hierarchy in
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
29 http://industry.ebi.ac.uk/openBQS/images/bibobjects_perl.gif
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
30
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
31 =head2 Attributes
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
32
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
33 There are no specific attributes in this class
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
34 (however, you can set and get all attributes defined in the parent classes).
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
35 The main raison d'etre of this class is to be associated with MEDLINE book articles.
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
36
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
37 =head1 SEE ALSO
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
38
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
39 =over
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
40
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
41 =item *
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
42
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
43 OpenBQS home page: http://industry.ebi.ac.uk/openBQS
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
44
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
45 =item *
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
46
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
47 Comments to the Perl client: http://industry.ebi.ac.uk/openBQS/Client_perl.html
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
48
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
49 =back
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
50
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
51 =head1 FEEDBACK
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
52
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
53 =head2 Mailing Lists
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
54
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
55 User feedback is an integral part of the evolution of this and other
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
56 Bioperl modules. Send your comments and suggestions preferably to
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
57 the Bioperl mailing list. Your participation is much appreciated.
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
58
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
59 bioperl-l@bioperl.org - General discussion
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
60 http://bioperl.org/MailList.shtml - About the mailing lists
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
61
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
62 =head2 Reporting Bugs
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
63
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
64 Report bugs to the Bioperl bug tracking system to help us keep track
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
65 of the bugs and their resolution. Bug reports can be submitted via
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
66 email or the web:
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
67
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
68 bioperl-bugs@bioperl.org
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
69 http://bugzilla.bioperl.org/
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
70
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
71 =head1 AUTHORS
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
72
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
73 Heikki Lehvaslaiho (heikki@ebi.ac.uk),
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
74 Martin Senger (senger@ebi.ac.uk)
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
75
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
76 =head1 COPYRIGHT
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
77
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
78 Copyright (c) 2002 European Bioinformatics Institute. All Rights Reserved.
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
79
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
80 This module is free software; you can redistribute it and/or modify
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
81 it under the same terms as Perl itself.
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
82
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
83 =head1 DISCLAIMER
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
84
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
85 This software is provided "as is" without warranty of any kind.
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
86
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
87 =cut
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
88
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
89
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
90 # Let the code begin...
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
91
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
92
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
93 package Bio::Biblio::MedlineBook;
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
94 use strict;
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
95 use vars qw(@ISA);
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
96
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
97 use Bio::Biblio::Book;
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
98
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
99 @ISA = qw(Bio::Biblio::Book);
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
100
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
101 #
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
102 # a closure with a list of allowed attribute names (these names
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
103 # correspond with the allowed 'get' and 'set' methods); each name also
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
104 # keep what type the attribute should be (use 'undef' if it is a
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
105 # simple scalar)
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
106 #
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
107 {
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
108 my %_allowed =
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
109 (
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
110 );
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
111
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
112 # return 1 if $attr is allowed to be set/get in this class
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
113 sub _accessible {
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
114 my ($self, $attr) = @_;
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
115 exists $_allowed{$attr} or $self->SUPER::_accessible ($attr);
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
116 }
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
117
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
118 # return an expected type of given $attr
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
119 sub _attr_type {
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
120 my ($self, $attr) = @_;
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
121 if (exists $_allowed{$attr}) {
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
122 return $_allowed{$attr};
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
123 } else {
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
124 return $self->SUPER::_attr_type ($attr);
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
125 }
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
126 }
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
127 }
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
128
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
129
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
130 1;
21066c0abaf5 Uploaded
willmclaren
parents:
diff changeset
131 __END__