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://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 _

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    :