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 bran cond 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   4 use strict;
  1         1  
  1         25  
78              
79              
80 1     1   3 use base qw(Bio::ClusterI);
  1         1  
  1         265  
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;