annotate variant_effect_predictor/Bio/Biblio/Article.pm @ 0:1f6dce3d34e0

Uploaded
author mahtabm
date Thu, 11 Apr 2013 02:01:53 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
1 # $Id: Article.pm,v 1.7 2002/10/22 07:45:11 lapp Exp $
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
2 #
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
3 # BioPerl module for Bio::Biblio::Article
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
4 #
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
5 # Cared for by Martin Senger <senger@ebi.ac.uk>
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
6 # For copyright and disclaimer see below.
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
7
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
8 # POD documentation - main docs before the code
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
9
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
10 =head1 NAME
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
11
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
12 Bio::Biblio::Article - Representation of a general article
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
13
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
14 =head1 SYNOPSIS
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
15
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
16 $obj = new Bio::Biblio::Article (-identifier => '123abc',
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
17 -first_page => 23,
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
18 -last_page => 68);
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
19 --- OR ---
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
20
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
21 $obj = new Bio::Biblio::Article;
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
22 $obj->identifier ('123abc');
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
23 $obj->first_page (23);
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
24 $obj->last_page (68);
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
25
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
26 =head1 DESCRIPTION
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
27
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
28 A storage object for a general article.
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
29 See its place in the class hierarchy in
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
30 http://industry.ebi.ac.uk/openBQS/images/bibobjects_perl.gif
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
31
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
32 =head2 Attributes
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
33
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
34 The following attributes are specific to this class
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
35 (however, you can also set and get all attributes defined in the parent classes):
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
36
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
37 first_page
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
38 last_page
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
39
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
40
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
41 =head1 SEE ALSO
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
42
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
43 =over
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
44
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
45 =item *
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
46
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
47 OpenBQS home page: http://industry.ebi.ac.uk/openBQS
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
48
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
49 =item *
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
50
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
51 Comments to the Perl client: http://industry.ebi.ac.uk/openBQS/Client_perl.html
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
52
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
53 =back
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
54
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
55 =head1 FEEDBACK
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
56
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
57 =head2 Mailing Lists
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
58
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
59 User feedback is an integral part of the evolution of this and other
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
60 Bioperl modules. Send your comments and suggestions preferably to
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
61 the Bioperl mailing list. Your participation is much appreciated.
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
62
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
63 bioperl-l@bioperl.org - General discussion
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
64 http://bioperl.org/MailList.shtml - About the mailing lists
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
65
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
66 =head2 Reporting Bugs
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
67
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
68 Report bugs to the Bioperl bug tracking system to help us keep track
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
69 of the bugs and their resolution. Bug reports can be submitted via
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
70 email or the web:
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
71
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
72 bioperl-bugs@bioperl.org
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
73 http://bugzilla.bioperl.org/
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
74
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
75 =head1 AUTHORS
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
76
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
77 Heikki Lehvaslaiho (heikki@ebi.ac.uk),
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
78 Martin Senger (senger@ebi.ac.uk)
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
79
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
80 =head1 COPYRIGHT
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
81
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
82 Copyright (c) 2002 European Bioinformatics Institute. All Rights Reserved.
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
83
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
84 This module is free software; you can redistribute it and/or modify
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
85 it under the same terms as Perl itself.
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
86
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
87 =head1 DISCLAIMER
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
88
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
89 This software is provided "as is" without warranty of any kind.
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
90
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
91 =cut
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
92
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
93
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
94 # Let the code begin...
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
95
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
96
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
97 package Bio::Biblio::Article;
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
98 use strict;
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
99 use vars qw(@ISA);
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
100
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
101 use Bio::Biblio::Ref;
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
102
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
103 @ISA = qw( Bio::Biblio::Ref);
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
104
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
105 #
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
106 # a closure with a list of allowed attribute names (these names
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
107 # correspond with the allowed 'get' and 'set' methods); each name also
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
108 # keep what type the attribute should be (use 'undef' if it is a
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
109 # simple scalar)
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
110 #
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
111 {
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
112 my %_allowed =
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
113 (
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
114 _first_page => undef,
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
115 _last_page => undef,
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
116 );
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
117
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
118 # return 1 if $attr is allowed to be set/get in this class
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
119 sub _accessible {
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
120 my ($self, $attr) = @_;
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
121 exists $_allowed{$attr} or $self->SUPER::_accessible ($attr);
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
122 }
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
123
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
124 # return an expected type of given $attr
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
125 sub _attr_type {
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
126 my ($self, $attr) = @_;
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
127 if (exists $_allowed{$attr}) {
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
128 return $_allowed{$attr};
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
129 } else {
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
130 return $self->SUPER::_attr_type ($attr);
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
131 }
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
132 }
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
133 }
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
134
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
135
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
136 1;
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
137 __END__