Bio::ClusterI - Cluster Interface
No package variables defined.
# see the implementations of this interface for details
my $cluster= $cluster->new(-description=>"POLYUBIQUITIN",
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.
Title : display_id
Function: Get the display name or identifier for the cluster
Returns : a string
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
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
$cluster->get_members(-species => 'homo sapiens');
Will return all members if no criteria are provided.
Returns : the array of members
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The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
|Implementation Specific Functions||Top|
These functions are the ones that a specific implementation must
We don't mandate but encourage implementors to support at least the
following named parameters upon object initialization.
-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