maltcms.commands.fragments.cluster
Class UPGMAAlgorithm

java.lang.Object
  cross.commands.fragments.AFragmentCommand
      maltcms.commands.fragments.cluster.ClusteringAlgorithm
          maltcms.commands.fragments.cluster.UPGMAAlgorithm

All Implemented Interfaces:

cross.commands.fragments.IFragmentCommand, cross.commands.ICommand<cross.datastructures.tuple.TupleND<cross.datastructures.fragments.IFileFragment>,cross.datastructures.tuple.TupleND<cross.datastructures.fragments.IFileFragment>>, cross.datastructures.workflow.IWorkflowElement, cross.event.IEventSource<cross.datastructures.workflow.IWorkflowResult>, cross.IConfigurable, cross.io.xml.IXMLSerializable, Serializable, Iterable<cross.datastructures.fragments.IFileFragment>, IClusteringAlgorithm

public class UPGMAAlgorithm
extends ClusteringAlgorithm

Implements UPGMA Algorithm by ? (cite ...) FIXME add citation

Author:

Nils.Hoffmann@cebitec.uni-bielefeld.de

See Also:

Serialized Form

Constructor Summary

UPGMAAlgorithm()

UPGMAAlgorithm(double[][] distances, String[] names)

UPGMAAlgorithm(double[][] distances, cross.datastructures.tuple.TupleND<cross.datastructures.fragments.IFileFragment> fragments, PairwiseFeatureSequenceSimilarity ld)

Method Summary

double[]	dmat(int i, int j, int k)
void	findBestD(int numclust)
void	joinIJtoK(int i, int j, int k, double[] dist)
static void	main(String[] args)

Methods inherited from class maltcms.commands.fragments.cluster.ClusteringAlgorithm

addNodeK, apply, configure, d, getChromatogramDistanceFunction, getChromatogramWarpCommand, getCluster, getCluster, getClusterNames, getClusters, getConsensus, getDescription, getDist, getFragments, getInputFiles, getL, getMinimizingArrayCompVariableName, getNames, getPairwiseDistanceMatrixVariableName, getPairwiseDistanceNamesVariableName, getUsedIndices, getWorkflowSlot, handleFileFragments, init, init, isMinimizeDist, isMinimizing, iterator, merge, printCluster, printDistanceToNewCluster, printDistMatrix, printNamesMatrix, putCluster, setChromatogramDistanceFunction, setChromatogramWarpCommand, setCluster, setClusterNames, setConsensus, setd, setDist, setFragments, setInputFiles, setL, setLDF, setMinimizeDist, setMinimizingArrayCompVariableName, setNames, setPairwiseDistanceMatrixVariableName, setPairwiseDistanceNamesVariableName, toGraphML, toString

Methods inherited from class cross.commands.fragments.AFragmentCommand

addListener, addWorkflowResult, addWorkflowResult, addWorkflowResult, addWorkflowResult, addWorkflowResults, addWorkflowResults, appendXML, canEqual, createBlockingCompletionService, createCompletionService, createNonBlockingCompletionService, createWorkFragment, createWorkFragments, equals, fireEvent, getWorkflow, hashCode, initSubCommand, mapToInput, postProcess, removeListener, setWorkflow

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

UPGMAAlgorithm

public UPGMAAlgorithm()

UPGMAAlgorithm

public UPGMAAlgorithm(double[][] distances,
                      String[] names)

UPGMAAlgorithm

public UPGMAAlgorithm(double[][] distances,
                      cross.datastructures.tuple.TupleND<cross.datastructures.fragments.IFileFragment> fragments,
                      PairwiseFeatureSequenceSimilarity ld)

Method Detail

main

public static void main(String[] args)

dmat

public double[] dmat(int i,
                     int j,
                     int k)

Specified by:

dmat in class ClusteringAlgorithm

findBestD

public void findBestD(int numclust)

Specified by:

findBestD in class ClusteringAlgorithm

joinIJtoK

public void joinIJtoK(int i,
                      int j,
                      int k,
                      double[] dist)

Specified by:

joinIJtoK in class ClusteringAlgorithm