Reference

Bio::Cluster::FamilyI(3pm)

Family Interface

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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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 [email protected]

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

  We don't 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

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