Provided by: libbio-perl-perl_1.6.901-2_all bug

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    :