Bio::ClusterI(3pm)					User Contributed Perl Documentation					Bio::ClusterI(3pm)

NAME

       Bio::ClusterI - Cluster 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 is the basic structure for a cluster of bioperl objects.	In this case it is up to the implementer to check arguments and
       initialize whatever new object the implementing class is designed for.

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://redmine.open-bio.org/projects/bioperl/

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 _

Implementation Specific Functions
       These functions are the ones that a specific implementation must define.

   new
	 We don't mandate but encourage implementors to support at least the
	 following named parameters upon object initialization.

	 Argument	 Description
	 --------	 -----------
	 -display_id	 the display ID or name for the cluster
	 -description	 the consensus description or name of the cluster
	 -members	 the array of objects belonging to the family

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

   description
	Title	: description
	Usage	: Bio::ClusterI->description("POLYUBIQUITIN")
	Function: get/set for the consensus description of the cluster
	Returns : the description string
	Args	: Optional the description string

   size
	Title	: size
	Usage	: Bio::ClusterI->size();
	Function: get/set for the size of the family,
		  calculated from the number of members
	Returns : the size of the family
	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

   get_members
	Title	: get_members
	Usage	: Bio::ClusterI->get_members(($seq1, $seq2));
	Function: retrieve the members of the family by some criteria, for
		  example :
		  $cluster->get_members(-species => 'homo sapiens');

		  Will return all members if no criteria are provided.

	Returns : the array of members
	Args	:

perl v5.14.2							    2012-03-02							Bio::ClusterI(3pm)