org.biojava.nbio.core.util

Class SingleLinkageClusterer

java.lang.Object

org.biojava.nbio.core.util.SingleLinkageClusterer

public class SingleLinkageClusterer
extends Object

An implementation of a single linkage clusterer See http://en.wikipedia.org/wiki/Single-linkage_clustering

Author:

Jose Duarte

Constructor Summary

Constructors

Constructor and Description
SingleLinkageClusterer(double[][] matrix, boolean isScoreMatrix) Constructs a new SingleLinkageClusterer Subsequently use getDendrogram() to get the full tree or getClusters(double) to get the clusters at a certain cutoff in the tree Please note that the matrix will be altered during the clustering procedure.

Method Summary

Modifier and Type	Method and Description
Map<Integer,Set<Integer>>	getClusters(double cutoff) Get the clusters by cutting the dendrogram at given cutoff
org.biojava.nbio.core.util.SingleLinkageClusterer.LinkedPair[]	getDendrogram() Get the full dendrogram (size n-1) result of the hierarchical clustering

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SingleLinkageClusterer

public SingleLinkageClusterer(double[][] matrix,
                              boolean isScoreMatrix)

Constructs a new SingleLinkageClusterer Subsequently use getDendrogram() to get the full tree or getClusters(double) to get the clusters at a certain cutoff in the tree Please note that the matrix will be altered during the clustering procedure. A copy must be made before by the user if needing to use the original matrix further.

Parameters:

matrix - the distance matrix with distance values in j>i half, all other values will be ignored

isScoreMatrix - if false the matrix will be considered a distance matrix: lower values (distances) mean closer objects, if true the matrix will be considered a score matrix: larger values (scores) mean closer objects

Throws:

IllegalArgumentException - if matrix not square

Method Detail

getDendrogram

public org.biojava.nbio.core.util.SingleLinkageClusterer.LinkedPair[] getDendrogram()

Get the full dendrogram (size n-1) result of the hierarchical clustering

Returns:

getClusters

public Map<Integer,Set<Integer>> getClusters(double cutoff)

Get the clusters by cutting the dendrogram at given cutoff

Parameters:

cutoff -

Returns:

Map from cluster numbers to indices of the cluster members