NAME

Bio::Cluster::FamilyI - Family Interface

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");

DESCRIPTION

This interface if for a Family object representing a family of biological objects. A generic implementation for this may be found a Bio::Cluster::Family.

FEEDBACK

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

Support

Please direct usage questions or support issues to the mailing list:

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.

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://github.com/bioperl/bioperl-live/issues

AUTHOR - Shawn Hoon

Email shawnh@fugu-sg.org

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

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

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

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

Methods inherited from Bio::ClusterI

display_id

Title   : display_id
Usage   :
Function: Get the display name or identifier for the cluster
Returns : a string
Args    :

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

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

size

Title   : size
Usage   : Bio::Cluster::FamilyI->size();
Function: get/set for the description of the family
Returns : size
Args    :

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

cpanm Bio::Cluster

perl -MCPAN -e shell
install Bio::Cluster