File Coverage

Bio/Cluster/FamilyI.pm

Criterion	Covered	Total	%
statement	6	8	75.0
branch			n/a
condition			n/a
subroutine	2	4	50.0
pod	2	2	100.0
total	10	14	71.4

line	stmt	sub	pod	time	code
1					#
2					# BioPerl module for Bio::Cluster::FamilyI
3					#
4					# Please direct questions and support issues to
5					#
6					# Cared for by Shawn Hoon
7					#
8					# Copyright Shawn Hoon
9					#
10					# You may distribute this module under the same terms as perl itself
11
12					# POD documentation - main docs before the code
13
14					=head1 NAME
15
16					Bio::Cluster::FamilyI - Family Interface
17
18					=head1 SYNOPSIS
19
20					# see the implementations of this interface for details
21
22					my $cluster= $cluster->new(-description=>"POLYUBIQUITIN",
23					-members =>[$seq1,$seq2]);
24					my @members = $cluster->get_members();
25					my @sub_members = $cluster->get_members(-species=>"homo sapiens");
26
27					=head1 DESCRIPTION
28
29					This interface if for a Family object representing a family of
30					biological objects. A generic implementation for this may be
31					found a L.
32
33
34					=head1 FEEDBACK
35
36					=head2 Mailing Lists
37
38					User feedback is an integral part of the evolution of this and other
39					Bioperl modules. Send your comments and suggestions preferably to
40					the Bioperl mailing list. Your participation is much appreciated.
41
42					bioperl-l@bioperl.org - General discussion
43					http://bioperl.org/wiki/Mailing_lists - About the mailing lists
44
45					=head2 Support
46
47					Please direct usage questions or support issues to the mailing list:
48
49					I
50
51					rather than to the module maintainer directly. Many experienced and
52					reponsive experts will be able look at the problem and quickly
53					address it. Please include a thorough description of the problem
54					with code and data examples if at all possible.
55
56					=head2 Reporting Bugs
57
58					Report bugs to the Bioperl bug tracking system to help us keep track
59					of the bugs and their resolution. Bug reports can be submitted via the
60					web:
61
62					https://github.com/bioperl/bioperl-live/issues
63
64					=head1 AUTHOR - Shawn Hoon
65
66					Email shawnh@fugu-sg.org
67
68					=head1 APPENDIX
69
70					The rest of the documentation details each of the object methods.
71					Internal methods are usually preceded with a _
72
73					=cut
74
75
76					package Bio::Cluster::FamilyI;
77	1	1		5	use strict;
	1			1
	1			26
78
79
80	1	1		3	use base qw(Bio::ClusterI);
	1			2
	1			238
81
82					=head2 new
83
84					We don't mandate but encourage implementors to support at least the
85					following named parameters upon object initialization.
86
87					Arguments Description
88					--------- -----------
89					-family_id the name of the family
90					-description the consensus description of the family
91					-annotation_score the confidence by which the consensus description is
92					representative of the family
93					-members the members belonging to the family
94					-alignment the multiple alignment of the members
95
96					=cut
97
98
99					=head2 family_id
100
101					Title : family_id
102					Usage : Bio::Cluster::FamilyI->family_id("znfp");
103					Function: get/set for the family id
104					Returns : the family id
105					Args : the family id
106
107					=cut
108
109					sub family_id{
110	0	0	1		shift->throw_not_implemented();
111					}
112
113					=head2 family_score
114
115					Title : family_score
116					Usage : Bio::Cluster::FamilyI->family_score(95);
117					Function: get/set for the score of algorithm used to generate
118					the family if present
119					Returns : the score
120					Args : the score
121
122					=cut
123
124					sub family_score {
125	0	0	1		shift->throw_not_implemented();
126					}
127
128
129					=head1 Methods inherited from L
130
131					=cut
132
133					=head2 display_id
134
135					Title : display_id
136					Usage :
137					Function: Get the display name or identifier for the cluster
138					Returns : a string
139					Args :
140
141					=cut
142
143					=head2 get_members
144
145					Title : get_members
146					Usage : Bio::Cluster::FamilyI->get_members();
147					Function: get the members of the family
148					Returns : the array of members
149					Args : the array of members
150
151					=cut
152
153					=head2 description
154
155					Title : description
156					Usage : Bio::Cluster::FamilyI->description("Zinc Finger Protein");
157					Function: get/set for the description of the family
158					Returns : the description
159					Args : the description
160
161					=cut
162
163
164					=head2 size
165
166					Title : size
167					Usage : Bio::Cluster::FamilyI->size();
168					Function: get/set for the description of the family
169					Returns : size
170					Args :
171
172					=cut
173
174					=head2 cluster_score
175
176					Title : cluster_score
177					Usage : $cluster ->cluster_score(100);
178					Function: get/set for cluster_score which
179					represent the score in which the clustering
180					algorithm assigns to this cluster.
181					Returns : a number
182
183					=cut
184
185					1;