annotate variant_effect_predictor/Bio/Biblio/Proceeding.pm @ 0:2bc9b66ada89 draft default tip

Uploaded
author mahtabm
date Thu, 11 Apr 2013 06:29:17 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
1 # $Id: Proceeding.pm,v 1.6 2002/10/22 07:45:11 lapp Exp $
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
2 #
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
3 # BioPerl module for Bio::Biblio::Proceeding
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
4 #
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
5 # Cared for by Martin Senger <senger@ebi.ac.uk>
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
6 # For copyright and disclaimer see below.
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
7
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
8 # POD documentation - main docs before the code
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
9
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
10 =head1 NAME
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
11
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
12 Bio::Biblio::Proceeding - Representation of a conference proceeding
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
13
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
14 =head1 SYNOPSIS
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
15
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
16 $obj = new Bio::Biblio::Proceeding (-title => 'JavaONE');
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
17
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
18 --- OR ---
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
19
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
20 $obj = new Bio::Biblio::Proceeding;
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
21 $obj->title ('JavaONE');
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
22
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
23 =head1 DESCRIPTION
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
24
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
25 A storage object for a conference proceeding.
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
26 See its place in the class hierarchy in
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
27 http://industry.ebi.ac.uk/openBQS/images/bibobjects_perl.gif
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
28
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
29 =head2 Attributes
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
30
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
31 There are no specific attributes in this class
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
32 (however, you can set and get all attributes defined in the parent classes).
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
33
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
34 =head1 SEE ALSO
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
35
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
36 =over
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
37
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
38 =item *
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
39
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
40 OpenBQS home page: http://industry.ebi.ac.uk/openBQS
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
41
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
42 =item *
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
43
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
44 Comments to the Perl client: http://industry.ebi.ac.uk/openBQS/Client_perl.html
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
45
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
46 =back
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
47
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
48 =head1 FEEDBACK
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
49
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
50 =head2 Mailing Lists
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
51
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
52 User feedback is an integral part of the evolution of this and other
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
53 Bioperl modules. Send your comments and suggestions preferably to
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
54 the Bioperl mailing list. Your participation is much appreciated.
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
55
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
56 bioperl-l@bioperl.org - General discussion
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
57 http://bioperl.org/MailList.shtml - About the mailing lists
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
58
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
59 =head2 Reporting Bugs
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
60
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
61 Report bugs to the Bioperl bug tracking system to help us keep track
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
62 of the bugs and their resolution. Bug reports can be submitted via
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
63 email or the web:
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
64
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
65 bioperl-bugs@bioperl.org
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
66 http://bugzilla.bioperl.org/
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
67
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
68 =head1 AUTHORS
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
69
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
70 Heikki Lehvaslaiho (heikki@ebi.ac.uk),
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
71 Martin Senger (senger@ebi.ac.uk)
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
72
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
73 =head1 COPYRIGHT
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
74
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
75 Copyright (c) 2002 European Bioinformatics Institute. All Rights Reserved.
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
76
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
77 This module is free software; you can redistribute it and/or modify
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
78 it under the same terms as Perl itself.
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
79
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
80 =head1 DISCLAIMER
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
81
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
82 This software is provided "as is" without warranty of any kind.
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
83
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
84 =head1 BUGS AND LIMITATIONS
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
85
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
86 This class should be probably somewhere else in the class hierarchy
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
87 because a proceeding is actrually a collection of resources. Perhaps
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
88 this will be changed in the future.
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
89
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
90 =cut
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
91
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
92
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
93 # Let the code begin...
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
94
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
95
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
96 package Bio::Biblio::Proceeding;
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
97 use strict;
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
98 use vars qw(@ISA);
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
99
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
100 use Bio::Biblio::Ref;
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
101
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
102 @ISA = qw( Bio::Biblio::Ref);
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
103
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
104 #
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
105 # a closure with a list of allowed attribute names (these names
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
106 # correspond with the allowed 'get' and 'set' methods); each name also
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
107 # keep what type the attribute should be (use 'undef' if it is a
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
108 # simple scalar)
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
109 #
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
110 {
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
111 my %_allowed = (
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
112 );
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
113
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
114 # return 1 if $attr is allowed to be set/get in this class
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
115 sub _accessible {
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
116 my ($self, $attr) = @_;
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
117 exists $_allowed{$attr} or $self->SUPER::_accessible ($attr);
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
118 }
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
119
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
120 # return an expected type of given $attr
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
121 sub _attr_type {
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
122 my ($self, $attr) = @_;
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
123 if (exists $_allowed{$attr}) {
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
124 return $_allowed{$attr};
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
125 } else {
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
126 return $self->SUPER::_attr_type ($attr);
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
127 }
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
128 }
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
129 }
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
130
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
131
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
132 1;
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
133 __END__