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)