annotate variant_effect_predictor/Bio/Biblio/WebResource.pm @ 3:d30fa12e4cc5 default tip

Merge heads 2:a5976b2dce6f and 1:09613ce8151e which were created as a result of a recently fixed bug.
author devteam <devteam@galaxyproject.org>
date Mon, 13 Jan 2014 10:38:30 -0500
parents 1f6dce3d34e0
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
1 # $Id: WebResource.pm,v 1.6 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::WebResource
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::WebResource - Representation of a web resource
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::WebResource
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
17 (-url => 'http://resources/best.html',
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
18 -estimated_size => 45000);
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::WebResource;
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
22 $obj->cost ('0.3 EURO');
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
23
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
24 =head1 DESCRIPTION
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
25
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
26 A storage object for a citation quoting a web resource.
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
27 See its place in the class hierarchy in
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
28 http://industry.ebi.ac.uk/openBQS/images/bibobjects_perl.gif
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
29
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
30 =head2 Attributes
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
31
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
32 The following attributes are specific to this class
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
33 (however, you can also set and get all attributes defined in the parent classes):
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
34
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
35 url
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
36 estimated_size
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
37 cost
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
38
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
39 =head1 SEE ALSO
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
40
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
41 =over
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
42
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
43 =item *
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
44
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
45 OpenBQS home page: http://industry.ebi.ac.uk/openBQS
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
46
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
47 =item *
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
48
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
49 Comments to the Perl client: http://industry.ebi.ac.uk/openBQS/Client_perl.html
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
50
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
51 =back
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
52
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
53 =head1 FEEDBACK
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
54
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
55 =head2 Mailing Lists
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
56
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
57 User feedback is an integral part of the evolution of this and other
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
58 Bioperl modules. Send your comments and suggestions preferably to
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
59 the Bioperl mailing list. Your participation is much appreciated.
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
60
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
61 bioperl-l@bioperl.org - General discussion
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
62 http://bioperl.org/MailList.shtml - About the mailing lists
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
63
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
64 =head2 Reporting Bugs
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
65
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
66 Report bugs to the Bioperl bug tracking system to help us keep track
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
67 of the bugs and their resolution. Bug reports can be submitted via
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
68 email or the web:
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
69
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
70 bioperl-bugs@bioperl.org
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
71 http://bugzilla.bioperl.org/
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
72
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
73 =head1 AUTHORS
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
74
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
75 Heikki Lehvaslaiho (heikki@ebi.ac.uk),
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
76 Martin Senger (senger@ebi.ac.uk)
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
77
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
78 =head1 COPYRIGHT
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
79
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
80 Copyright (c) 2002 European Bioinformatics Institute. All Rights Reserved.
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
81
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
82 This module is free software; you can redistribute it and/or modify
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
83 it under the same terms as Perl itself.
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
84
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
85 =head1 DISCLAIMER
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
86
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
87 This software is provided "as is" without warranty of any kind.
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
88
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
89 =cut
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
90
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
91
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
92 # Let the code begin...
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
93
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
94
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
95 package Bio::Biblio::WebResource;
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
96 use strict;
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
97 use vars qw(@ISA);
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
98
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
99 use Bio::Biblio::Ref;
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
100
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
101 @ISA = qw( Bio::Biblio::Ref);
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
102
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
103 #
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
104 # a closure with a list of allowed attribute names (these names
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
105 # correspond with the allowed 'get' and 'set' methods); each name also
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
106 # keep what type the attribute should be (use 'undef' if it is a
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
107 # simple scalar)
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
108 #
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
109 {
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
110 my %_allowed = (
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
111 _url => undef,
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
112 _estimated_size => undef,
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
113 _cost => undef,
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
114 );
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
115
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
116 # return 1 if $attr is allowed to be set/get in this class
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
117 sub _accessible {
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
118 my ($self, $attr) = @_;
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
119 exists $_allowed{$attr} or $self->SUPER::_accessible ($attr);
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
120 }
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
121
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
122 # return an expected type of given $attr
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
123 sub _attr_type {
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
124 my ($self, $attr) = @_;
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
125 if (exists $_allowed{$attr}) {
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
126 return $_allowed{$attr};
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
127 } else {
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
128 return $self->SUPER::_attr_type ($attr);
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
129 }
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
130 }
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 1;
1f6dce3d34e0 Uploaded
mahtabm
parents:
diff changeset
135 __END__