Bio::Cluster::FamilyI.3pm

Langue: en

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

Section: 3 (Bibliothèques de fonctions)

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:
   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 _

new

   We dont 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