Bio::Cluster::FamilyI - Family 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 if for a Family object representing a family of biological objects. A generic implementation for this may be found a Bio::Cluster::Family.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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
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
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
Title : display_id Usage : Function: Get the display name or identifier for the cluster Returns : a string Args :
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
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
Title : size Usage : Bio::Cluster::FamilyI->size(); Function: get/set for the description of the family Returns : size 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