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# BioPerl module for Bio::Cluster::FamilyI
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Shawn Hoon <shawnh@fugu-sg.org>
#
# Copyright Shawn Hoon
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Cluster::FamilyI - Family Interface
=head1 SYNOPSIS
# see the implementations of this interface for details
my $cluster= $cluster->new(-description=>"POLYUBIQUITIN",
-members =>[$seq1,$seq2]);
my @members = $cluster->get_members();
my @sub_members = $cluster->get_members(-species=>"homo sapiens");
=head1 DESCRIPTION
This interface if for a Family object representing a family of
biological objects. A generic implementation for this may be
found a L<Bio::Cluster::Family>.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR - Shawn Hoon
Email shawnh@fugu-sg.org
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
package Bio::Cluster::FamilyI;
use strict;
use base qw(Bio::ClusterI);
=head2 new
We don't mandate but encourage implementors to support at least the
following named parameters upon object initialization.
Arguments Description
--------- -----------
-family_id the name of the family
-description the consensus description of the family
-annotation_score the confidence by which the consensus description is
representative of the family
-members the members belonging to the family
-alignment the multiple alignment of the members
=cut
=head2 family_id
Title : family_id
Usage : Bio::Cluster::FamilyI->family_id("znfp");
Function: get/set for the family id
Returns : the family id
Args : the family id
=cut
sub family_id{
shift->throw_not_implemented();
}
=head2 family_score
Title : family_score
Usage : Bio::Cluster::FamilyI->family_score(95);
Function: get/set for the score of algorithm used to generate
the family if present
Returns : the score
Args : the score
=cut
sub family_score {
shift->throw_not_implemented();
}
=head1 Methods inherited from L<Bio::ClusterI>
=cut
=head2 display_id
Title : display_id
Usage :
Function: Get the display name or identifier for the cluster
Returns : a string
Args :
=cut
=head2 get_members
Title : get_members
Usage : Bio::Cluster::FamilyI->get_members();
Function: get the members of the family
Returns : the array of members
Args : the array of members
=cut
=head2 description
Title : description
Usage : Bio::Cluster::FamilyI->description("Zinc Finger Protein");
Function: get/set for the description of the family
Returns : the description
Args : the description
=cut
=head2 size
Title : size
Usage : Bio::Cluster::FamilyI->size();
Function: get/set for the description of the family
Returns : size
Args :
=cut
=head2 cluster_score
Title : cluster_score
Usage : $cluster ->cluster_score(100);
Function: get/set for cluster_score which
represent the score in which the clustering
algorithm assigns to this cluster.
Returns : a number
=cut
1;
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