Package 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 Details

    • KMeansClustering

      public KMeansClustering()
      Empty default constructor

    • 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 Details

    • 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