Bio::ClusterI.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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:
   http://bugzilla.open-bio.org/
 
 

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 dont 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    :