Bio::Cluster::FamilyI(3) 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 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


 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

Methods inherited from Bio::ClusterI


 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