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Bio::Cluster::FamilyI(3pm) User Contributed Perl Documentation Bio::Cluster::FamilyI(3pm) 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: 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 _ 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 perl v5.14.2 2012-03-02 Bio::Cluster::FamilyI(3pm)
HA Cluster solution for Linux - which one to use?