File Coverage

Bio/Ontology/RelationshipFactory.pm
Criterion Covered Total %
statement 14 14 100.0
branch n/a
condition 1 2 50.0
subroutine 4 4 100.0
pod 1 1 100.0
total 20 21 95.2


line stmt bran cond sub pod time code
1             #
2             # BioPerl module for Bio::Ontology::RelationshipFactory
3             #
4             # Please direct questions and support issues to
5             #
6             # Cared for by Hilmar Lapp
7             #
8             # Copyright Hilmar Lapp
9             #
10             # You may distribute this module under the same terms as perl itself
11              
12             #
13             # (c) Hilmar Lapp, hlapp at gmx.net, 2002.
14             # (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002.
15             #
16             # You may distribute this module under the same terms as perl itself.
17             # Refer to the Perl Artistic License (see the license accompanying this
18             # software package, or see http://www.perl.com/language/misc/Artistic.html)
19             # for the terms under which you may use, modify, and redistribute this module.
20             #
21             # THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
22             # WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
23             # MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
24             #
25              
26             # POD documentation - main docs before the code
27              
28             =head1 NAME
29              
30             Bio::Ontology::RelationshipFactory - Instantiates a new
31             Bio::Ontology::RelationshipI (or derived class) through a factory
32              
33             =head1 SYNOPSIS
34              
35             use Bio::Ontology::RelationshipFactory;
36              
37             # the default type is Bio::Ontology::Relationship
38             my $factory = Bio::Ontology::RelationshipFactory->new(
39             -type => 'Bio::Ontology::GOterm');
40             my $clu = $factory->create_object(-name => 'peroxisome',
41             -ontology => 'Gene Ontology',
42             -identifier => 'GO:0005777');
43              
44              
45             =head1 DESCRIPTION
46              
47             This object will build L objects generically.
48              
49             =head1 FEEDBACK
50              
51             =head2 Mailing Lists
52              
53             User feedback is an integral part of the evolution of this and other
54             Bioperl modules. Send your comments and suggestions preferably to
55             the Bioperl mailing list. Your participation is much appreciated.
56              
57             bioperl-l@bioperl.org - General discussion
58             http://bioperl.org/wiki/Mailing_lists - About the mailing lists
59              
60             =head2 Support
61              
62             Please direct usage questions or support issues to the mailing list:
63              
64             I
65              
66             rather than to the module maintainer directly. Many experienced and
67             reponsive experts will be able look at the problem and quickly
68             address it. Please include a thorough description of the problem
69             with code and data examples if at all possible.
70              
71             =head2 Reporting Bugs
72              
73             Report bugs to the Bioperl bug tracking system to help us keep track
74             of the bugs and their resolution. Bug reports can be submitted via
75             the web:
76              
77             https://github.com/bioperl/bioperl-live/issues
78              
79             =head1 AUTHOR - Hilmar Lapp
80              
81             Email hlapp at gmx.net
82              
83              
84             =head1 APPENDIX
85              
86             The rest of the documentation details each of the object methods.
87             Internal methods are usually preceded with a _
88              
89             =cut
90              
91              
92             # Let the code begin...
93              
94              
95             package Bio::Ontology::RelationshipFactory;
96 4     4   23 use strict;
  4         7  
  4         97  
97              
98 4     4   17 use Bio::Root::Root;
  4         6  
  4         80  
99              
100 4     4   16 use base qw(Bio::Factory::ObjectFactory);
  4         8  
  4         764  
101              
102             =head2 new
103              
104             Title : new
105             Usage : my $obj = Bio::Ontology::RelationshipFactory->new();
106             Function: Builds a new Bio::Ontology::RelationshipFactory object
107             Returns : Bio::Ontology::RelationshipFactory
108             Args : -type => string, name of a Bio::Ontology::RelationshipI
109             derived class.
110             The default is Bio::Ontology::Relationship.
111              
112             See L, L.
113              
114             =cut
115              
116             sub new {
117 8     8 1 27 my($class,@args) = @_;
118              
119 8         51 my $self = $class->SUPER::new(@args);
120            
121             # make sure this matches our requirements
122 8         25 $self->interface("Bio::Ontology::RelationshipI");
123 8   50     20 $self->type($self->type() || "Bio::Ontology::Relationship");
124              
125 8         35 return $self;
126             }
127              
128             1;