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://github.com/bioperl/bioperl-live/issues
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