Raw content of Bio::Cluster::FamilyI # # BioPerl module for Bio::Cluster::FamilyI # # Cared for by Shawn Hoon <shawnh@fugu-sg.org> # # Copyright Shawn Hoon # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Cluster::FamilyI - Family Interface =head1 SYNOPSIS # see the implementations of this interface for details but # basically my $cluster= $cluster->new(-description=>"POLYUBIQUITIN", -members =>[$seq1,$seq2]); my @members = $cluster->get_members(); my @sub_members = $cluster->get_members(-species=>"homo sapiens"); =head1 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. =head1 FEEDBACK =head2 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/MailList.shtml - About the mailing lists =head2 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 email or the web: bioperl-bugs@bioperl.org http://bugzilla.bioperl.org/ =head1 AUTHOR - Shawn Hoon Email shawnh@fugu-sg.org =head1 CONTRIBUTORS Additional contributors names and emails here =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::Cluster::FamilyI; use vars qw(@ISA); use strict; use Bio::ClusterI; @ISA = qw(Bio::ClusterI); =head2 new We dont 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 =cut =head2 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 =cut sub family_id{ shift->throw_not_implemented(); } =head2 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 =cut sub family_score { shift->throw_not_implemented(); } =head1 Methods inherited from L<Bio::ClusterI> =cut =head2 display_id Title : display_id Usage : Function: Get the display name or identifier for the cluster Returns : a string Args : =cut =head2 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 =cut =head2 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 =cut =head2 size Title : size Usage : Bio::Cluster::FamilyI->size(); Function: get/set for the description of the family Returns : size Args : =cut =head2 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 =cut 1;