Bio::ClusterI - Cluster Interface
# 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");
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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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.
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
Title : display_id Usage : Function: Get the display name or identifier for the cluster Returns : a string Args :
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
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 :
Title : cluster_score Usage : $cluster ->cluster_score(100); Function: get/set for cluster_score which represent the score in which the clustering algorithm assigns to this cluster. Returns : a number
Title : get_members Usage : Bio::ClusterI->get_members(($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 :