Manual Reference Pages - BIO::CLUSTERI (3)
Bio::ClusterI - Cluster Interface
# 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.
User feedback is an integral part of the evolution of this and other
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AUTHOR - Shawn Hoon
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
Implementation Specific Functions
These functions are the ones that a specific implementation must
We dont 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
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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