2 # BioPerl module for Bio::Cluster::FamilyI
4 # Cared for by Shawn Hoon <shawnh@fugu-sg.org>
8 # You may distribute this module under the same terms as perl itself
10 # POD documentation - main docs before the code
14 Bio::Cluster::FamilyI - Family Interface
18 # see the implementations of this interface for details
20 my $cluster= $cluster->new(-description=>"POLYUBIQUITIN",
21 -members =>[$seq1,$seq2]);
22 my @members = $cluster->get_members();
23 my @sub_members = $cluster->get_members(-species=>"homo sapiens");
27 This interface if for a Family object representing a family of
28 biological objects. A generic implementation for this may be
29 found a L<Bio::Cluster::Family>.
36 User feedback is an integral part of the evolution of this and other
37 Bioperl modules. Send your comments and suggestions preferably to
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40 bioperl-l@bioperl.org - General discussion
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45 Report bugs to the Bioperl bug tracking system to help us keep track
46 of the bugs and their resolution. Bug reports can be submitted via the
49 http://bugzilla.open-bio.org/
51 =head1 AUTHOR - Shawn Hoon
53 Email shawnh@fugu-sg.org
57 The rest of the documentation details each of the object methods.
58 Internal methods are usually preceded with a _
63 package Bio
::Cluster
::FamilyI
;
67 use base
qw(Bio::ClusterI);
71 We dont mandate but encourage implementors to support at least the
72 following named parameters upon object initialization.
76 -family_id the name of the family
77 -description the consensus description of the family
78 -annotation_score the confidence by which the consensus description is
79 representative of the family
80 -members the members belonging to the family
81 -alignment the multiple alignment of the members
89 Usage : Bio::Cluster::FamilyI->family_id("znfp");
90 Function: get/set for the family id
91 Returns : the family id
97 shift->throw_not_implemented();
103 Usage : Bio::Cluster::FamilyI->family_score(95);
104 Function: get/set for the score of algorithm used to generate
105 the family if present
112 shift->throw_not_implemented();
116 =head1 Methods inherited from L<Bio::ClusterI>
124 Function: Get the display name or identifier for the cluster
133 Usage : Bio::Cluster::FamilyI->get_members();
134 Function: get the members of the family
135 Returns : the array of members
136 Args : the array of members
143 Usage : Bio::Cluster::FamilyI->description("Zinc Finger Protein");
144 Function: get/set for the description of the family
145 Returns : the description
146 Args : the description
154 Usage : Bio::Cluster::FamilyI->size();
155 Function: get/set for the description of the family
163 Title : cluster_score
164 Usage : $cluster ->cluster_score(100);
165 Function: get/set for cluster_score which
166 represent the score in which the clustering
167 algorithm assigns to this cluster.