com.compomics.util.math.clustering

Class KMeansClustering

java.lang.Object

com.compomics.util.math.clustering.KMeansClustering

public class KMeansClustering
extends Object

K-means clustering.

Author:

Harald Barsnes

Constructor Summary

Constructors

Constructor and Description
KMeansClustering(double[][] samples, String[] sampleIds, int numClusters) Constructor.
KMeansClustering(File dataFile, int numClusters) Constructor.

Method Summary

Modifier and Type	Method and Description
ArrayList<String>	getClusterMembers(int clusterIndex) Get the sample names of all the members in the given cluster.
HashMap<String,ArrayList<Double>>	getClusterMembersData(int clusterIndex) Returns a hashmap with the values for the members in the given cluster.
int	getMaxIterations() Returns the maximum number of iterations.
int	getNumberOfClusters() Returns the number of clusters.
void	kMeanCluster(WaitingHandler waitingHandler) Run the k-means clustering.
static void	main(String[] args) Main method for testing purposes.
void	printCentroids() Print the centroids.
void	printClusters() Print the current clusters.
void	setMaxIterations(int maxIterations) Set the maximum number of iterations.

Methods inherited from class java.lang.Object

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

Constructor Detail

KMeansClustering

public KMeansClustering(double[][] samples,
                        String[] sampleIds,
                        int numClusters)

Constructor.

Parameters:

samples - the data

sampleIds - the sample identifiers

numClusters - the number of clusters

KMeansClustering

public KMeansClustering(File dataFile,
                        int numClusters)

Constructor.

Parameters:

dataFile - the file with the data

numClusters - the number of clusters

Method Detail

kMeanCluster

public void kMeanCluster(WaitingHandler waitingHandler)

Run the k-means clustering.

Parameters:

waitingHandler - the waiting handler

main

public static void main(String[] args)

Main method for testing purposes.

Parameters:

args - the command line arguments

printCentroids

public void printCentroids()

Print the centroids.

printClusters

public void printClusters()

Print the current clusters.

getClusterMembers

public ArrayList<String> getClusterMembers(int clusterIndex)

Get the sample names of all the members in the given cluster.

Parameters:

clusterIndex - the index of the cluster

Returns:

the sample names of all the members in the given cluster

getClusterMembersData

public HashMap<String,ArrayList<Double>> getClusterMembersData(int clusterIndex)

Returns a hashmap with the values for the members in the given cluster. Key: sample id, value: the data points.

Parameters:

clusterIndex - the index of the cluster

Returns:

the values for the members in the given cluster

getNumberOfClusters

public int getNumberOfClusters()

Returns the number of clusters.

Returns:

the number of clusters

getMaxIterations

public int getMaxIterations()

Returns the maximum number of iterations.

Returns:

the maximum number of iterations

setMaxIterations

public void setMaxIterations(int maxIterations)

Set the maximum number of iterations.

Parameters:

maxIterations - the maximum number of iterations