File Coverage

Bio/ClusterI.pm
Criterion Covered Total %
statement 6 11 54.5
branch n/a
condition n/a
subroutine 2 7 28.5
pod 5 5 100.0
total 13 23 56.5


line stmt bran cond sub pod time code
1             #
2             # BioPerl module for Bio::ClusterI
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::ClusterI - Cluster 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              
28             =head1 DESCRIPTION
29              
30             This interface is the basic structure for a cluster of bioperl objects.
31             In this case it is up to the implementer to check arguments
32             and initialize whatever new object the implementing class is designed for.
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             # Let the code begin...
77              
78             package Bio::ClusterI;
79 4     4   17 use strict;
  4         5  
  4         95  
80              
81              
82 4     4   12 use base qw(Bio::Root::RootI);
  4         4  
  4         498  
83              
84             =head1 Implementation Specific Functions
85              
86             These functions are the ones that a specific implementation must
87             define.
88              
89             =head2 new
90              
91             We don't mandate but encourage implementors to support at least the
92             following named parameters upon object initialization.
93              
94             Argument Description
95             -------- -----------
96             -display_id the display ID or name for the cluster
97             -description the consensus description or name of the cluster
98             -members the array of objects belonging to the family
99              
100             =cut
101              
102             =head2 display_id
103              
104             Title : display_id
105             Usage :
106             Function: Get the display name or identifier for the cluster
107             Returns : a string
108             Args :
109              
110             =cut
111              
112             sub display_id{
113 0     0 1   shift->throw_not_implemented();
114             }
115              
116              
117             =head2 description
118              
119             Title : description
120             Usage : Bio::ClusterI->description("POLYUBIQUITIN")
121             Function: get/set for the consensus description of the cluster
122             Returns : the description string
123             Args : Optional the description string
124              
125             =cut
126              
127             sub description{
128 0     0 1   shift->throw_not_implemented();
129             }
130              
131             =head2 size
132              
133             Title : size
134             Usage : Bio::ClusterI->size();
135             Function: get/set for the size of the family,
136             calculated from the number of members
137             Returns : the size of the family
138             Args :
139              
140             =cut
141              
142             sub size {
143 0     0 1   shift->throw_not_implemented();
144             }
145              
146             =head2 cluster_score
147              
148             Title : cluster_score
149             Usage : $cluster ->cluster_score(100);
150             Function: get/set for cluster_score which
151             represent the score in which the clustering
152             algorithm assigns to this cluster.
153             Returns : a number
154              
155             =cut
156              
157             sub cluster_score{
158 0     0 1   shift->throw_not_implemented();
159             }
160              
161             =head2 get_members
162              
163             Title : get_members
164             Usage : Bio::ClusterI->get_members(($seq1, $seq2));
165             Function: retrieve the members of the family by some criteria, for
166             example :
167             $cluster->get_members(-species => 'homo sapiens');
168              
169             Will return all members if no criteria are provided.
170              
171             Returns : the array of members
172             Args :
173              
174             =cut
175              
176             sub get_members {
177 0     0 1   shift->throw_not_implemented();
178             }
179              
180             1;