annotate variant_effect_predictor/Bio/Cluster/FamilyI.pm @ 0:2bc9b66ada89 draft default tip

Uploaded
author mahtabm
date Thu, 11 Apr 2013 06:29:17 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
1 #
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
2 # BioPerl module for Bio::Cluster::FamilyI
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
3 #
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
4 # Cared for by Shawn Hoon <shawnh@fugu-sg.org>
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
5 #
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
6 # Copyright Shawn Hoon
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
7 #
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
8 # You may distribute this module under the same terms as perl itself
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
9
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
10 # POD documentation - main docs before the code
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
11
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
12 =head1 NAME
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
13
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
14 Bio::Cluster::FamilyI - Family Interface
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
15
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
16 =head1 SYNOPSIS
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
17
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
18 # see the implementations of this interface for details but
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
19 # basically
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
20
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
21 my $cluster= $cluster->new(-description=>"POLYUBIQUITIN",
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
22 -members =>[$seq1,$seq2]);
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
23 my @members = $cluster->get_members();
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
24 my @sub_members = $cluster->get_members(-species=>"homo sapiens");
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
25
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
26
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
27
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
28 =head1 DESCRIPTION
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
29
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
30 This interface if for a Family object representing a family of
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
31 biological objects. A generic implementation for this may be
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
32 found a Bio::Cluster::Family.
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
33
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
34
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
35 =head1 FEEDBACK
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
36
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
37 =head2 Mailing Lists
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
38
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
39 User feedback is an integral part of the evolution of this and other
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
40 Bioperl modules. Send your comments and suggestions preferably to
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
41 the Bioperl mailing list. Your participation is much appreciated.
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
42
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
43 bioperl-l@bioperl.org - General discussion
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
44 http://bioperl.org/MailList.shtml - About the mailing lists
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
45
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
46 =head2 Reporting Bugs
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
47
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
48 Report bugs to the Bioperl bug tracking system to help us keep track
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
49 of the bugs and their resolution. Bug reports can be submitted via
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
50 email or the web:
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
51
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
52 bioperl-bugs@bioperl.org
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
53 http://bugzilla.bioperl.org/
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
54
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
55 =head1 AUTHOR - Shawn Hoon
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
56
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
57 Email shawnh@fugu-sg.org
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
58
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
59
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
60 =head1 CONTRIBUTORS
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
61
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
62 Additional contributors names and emails here
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
63
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
64 =head1 APPENDIX
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
65
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
66 The rest of the documentation details each of the object methods.
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
67 Internal methods are usually preceded with a _
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
68
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
69 =cut
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
70
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
71
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
72 package Bio::Cluster::FamilyI;
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
73 use vars qw(@ISA);
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
74 use strict;
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
75
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
76 use Bio::ClusterI;
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
77
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
78 @ISA = qw(Bio::ClusterI);
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
79
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
80 =head2 new
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
81
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
82 We dont mandate but encourage implementors to support at least the
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
83 following named parameters upon object initialization.
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
84
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
85 Arguments Description
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
86 --------- -----------
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
87 -family_id the name of the family
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
88 -description the consensus description of the family
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
89 -annotation_score the confidence by which the consensus description is
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
90 representative of the family
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
91 -members the members belonging to the family
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
92 -alignment the multiple alignment of the members
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
93
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
94 =cut
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
95
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
96
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
97 =head2 family_id
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
98
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
99 Title : family_id
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
100 Usage : Bio::Cluster::FamilyI->family_id("znfp");
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
101 Function: get/set for the family id
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
102 Returns : the family id
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
103 Args : the family id
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
104
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
105 =cut
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
106
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
107 sub family_id{
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
108 shift->throw_not_implemented();
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
109 }
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
110
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
111 =head2 family_score
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
112
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
113 Title : family_score
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
114 Usage : Bio::Cluster::FamilyI->family_score(95);
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
115 Function: get/set for the score of algorithm used to generate
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
116 the family if present
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
117 Returns : the score
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
118 Args : the score
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
119
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
120 =cut
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
121
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
122 sub family_score {
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
123 shift->throw_not_implemented();
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
124 }
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
125
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
126
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
127 =head1 Methods inherited from L<Bio::ClusterI>
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
128
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
129 =cut
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
130
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
131 =head2 display_id
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
132
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
133 Title : display_id
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
134 Usage :
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
135 Function: Get the display name or identifier for the cluster
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
136 Returns : a string
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
137 Args :
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
138
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
139 =cut
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
140
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
141 =head2 get_members
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
142
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
143 Title : get_members
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
144 Usage : Bio::Cluster::FamilyI->get_members();
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
145 Function: get the members of the family
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
146 Returns : the array of members
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
147 Args : the array of members
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
148
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
149 =cut
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
150
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
151 =head2 description
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
152
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
153 Title : description
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
154 Usage : Bio::Cluster::FamilyI->description("Zinc Finger Protein");
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
155 Function: get/set for the description of the family
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
156 Returns : the description
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
157 Args : the description
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
158
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
159 =cut
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
160
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
161
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
162 =head2 size
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
163
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
164 Title : size
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
165 Usage : Bio::Cluster::FamilyI->size();
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
166 Function: get/set for the description of the family
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
167 Returns : size
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
168 Args :
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
169
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
170 =cut
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
171
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
172 =head2 cluster_score
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
173
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
174 Title : cluster_score
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
175 Usage : $cluster ->cluster_score(100);
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
176 Function: get/set for cluster_score which
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
177 represent the score in which the clustering
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
178 algorithm assigns to this cluster.
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
179 Returns : a number
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
180
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
181 =cut
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
182
2bc9b66ada89 Uploaded
mahtabm
parents:
diff changeset
183 1;