procope.methods.clustering
Class HierarchicalClusterer

java.lang.Object
  extended by procope.methods.clustering.HierarchicalClusterer
All Implemented Interfaces:
Clusterer

public class HierarchicalClusterer
extends Object
implements Clusterer

Wrapper for HierarchicalClusteringTrees which implements the Clusterer interface. Here you directly have to specify the threshold for the minimum similarity needed for two clusters in order to be merged.

Author:
Jan Krumsiek

Constructor Summary
HierarchicalClusterer(HierarchicalLinkage linkage, float threshold)
          Creates a hierarchical clusterer with given the given linkage and cutoff threshold.
 
Method Summary
 ComplexSet cluster(ProteinNetwork net)
          Performs hierarchical agglomerative clustering on given similarity network.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

HierarchicalClusterer

public HierarchicalClusterer(HierarchicalLinkage linkage,
                             float threshold)
Creates a hierarchical clusterer with given the given linkage and cutoff threshold.

Parameters:
linkage - linkage method
threshold - cutoff threshold, minimum similarity needed between two clusters in order for them to be merged
Method Detail

cluster

public ComplexSet cluster(ProteinNetwork net)
Performs hierarchical agglomerative clustering on given similarity network. Missing edges get an implicit weight of zero.

Specified by:
cluster in interface Clusterer
Parameters:
net - similarity network which will be clustered
Returns:
the resulting clustering