File Coverage

blib/lib/GO/OntologyProvider.pm

Criterion	Covered	Total	%
statement	12	21	57.1
branch			n/a
condition			n/a
subroutine	4	9	44.4
pod	4	4	100.0
total	20	34	58.8

line	stmt	sub	pod	time	code
1					package GO::OntologyProvider;
2
3					# File : OntologyProvider.pm
4					# Author : Gavin Sherlock
5					# Date Begun : September 23rd 2002
6
7					# $Id: OntologyProvider.pm,v 1.7 2004/05/05 22:12:33 sherlock Exp $
8
9					# License information (the MIT license)
10
11					# Copyright (c) 2003 Gavin Sherlock; Stanford University
12
13					# Permission is hereby granted, free of charge, to any person
14					# obtaining a copy of this software and associated documentation files
15					# (the "Software"), to deal in the Software without restriction,
16					# including without limitation the rights to use, copy, modify, merge,
17					# publish, distribute, sublicense, and/or sell copies of the Software,
18					# and to permit persons to whom the Software is furnished to do so,
19					# subject to the following conditions:
20
21					# The above copyright notice and this permission notice shall be
22					# included in all copies or substantial portions of the Software.
23
24					# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
25					# EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
26					# MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
27					# NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
28					# BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
29					# ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
30					# CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
31					# SOFTWARE.
32
33					=pod
34
35					=head1 NAME
36
37					GO::OntologyProvider - abstract base class providing API for the provision on Gene Ontology information
38
39					=head1 DESCRIPTION
40
41					GO::OntologyProvider is an abstract class that defines an
42					interface that should be implemented by specific subclasses, which may
43					read ontology information from databases, flatfiles, XML files etc.
44
45					All of the methods return either one or many GO::Node(s), and any
46					concrete subclass is expected to fully flesh out the such Node objects
47					with all the parents, children and paths to the root, such that any
48					node should return a true value when the isValid method is invoked on
49					it.
50
51					=head1 Constructor
52
53					Because this is an abstract class, there is no constructor. A
54					constructor must be implemented by concrete subclasses.
55
56					=head1 Public instance methods
57
58					All of these public instance methods must be implemented by concrete
59					subclasses.
60
61					=cut
62
63	2	2		15	use strict;
	2			4
	2			69
64	2	2		11	use warnings;
	2			5
	2			53
65	2	2		11	use diagnostics;
	2			5
	2			12
66
67	2	2		61	use vars qw ($VERSION);
	2			5
	2			506
68
69					$VERSION = 0.12;
70
71					############################################################################
72					sub allNodes{
73					############################################################################
74					=pod
75
76					=head2 allNodes
77
78					This method returns an array of all the GO::Nodes that have been
79					created.
80
81					Usage:
82
83					my @nodes = $ontologyProvider->allNodes;
84
85					=cut
86					############################################################################
87
88	0	0	1		$_[0]->__complainStubMethod;
89
90					}
91
92					############################################################################
93					sub rootNode{
94					############################################################################
95					=pod
96
97					=head2 rootNode
98
99					This method returns the root node in the ontology.
100
101					Usage:
102
103					my $rootNode = $ontologyProvider->rootNode;
104
105					=cut
106					############################################################################
107
108	0	0	1		$_[0]->__complainStubMethod;
109
110					}
111
112					############################################################################
113					sub nodeFromId{
114					############################################################################
115					=pod
116
117					=head2 nodeFromId
118
119					This method returns a GO::Node corresponding to the provided
120					GOID, should one exist. Otherwise it returns undef.
121
122					Usage:
123
124					my $node = $ontologyProvider->nodeFromId("GO:0003673");
125
126					=cut
127					############################################################################
128
129	0	0	1		$_[0]->__complainStubMethod;
130
131					}
132
133					############################################################################
134					sub numNodes{
135					############################################################################
136					=pod
137
138					=head2 numNodes
139
140					This method returns the number of nodes that exist within the
141					ontology.
142
143					Usage:
144
145					my $numNodes = $ontologyProvider->numNodes;
146
147					=cut
148
149					############################################################################
150
151	0	0	1		$_[0]->__complainStubMethod;
152
153					}
154
155					############################################################################
156					sub __complainStubMethod{
157					############################################################################
158
159	0	0			my ($self) = @_;
160
161	0				my $subroutine = (caller(1))[3];
162
163	0				$subroutine =~ s/.+:://;
164
165	0				my $package = ref $self;
166
167	0				die "The package $package has not implemented the required method $subroutine().\n";
168
169					}
170
171					1; # to keep Perl happy
172
173					=pod
174
175					=head1 AUTHOR
176
177					Gavin Sherlock, sherlock@genome.stanford.edu
178
179					=cut