Bio::ClusterI(3pm) User Contributed Perl Documentation Bio::ClusterI(3pm)
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:
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 _
Implementation Specific Functions
These functions are the ones that a specific implementation must define.
new
We don't 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 :
perl v5.14.2 2012-03-02 Bio::ClusterI(3pm)