Bio::ClusterI - Cluster Interface # 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"); 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.

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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/ Email shawnh@fugu-sg.org Additional contributors names and emails here The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ These functions are the ones that a specific implementation must define.

new
We dont 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 :