maltcms.commands.fragments.cluster
Class SingleLinkageAlgorithm

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

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 SingleLinkageAlgorithm
extends ClusteringAlgorithm

Implements SingleLinkage clustering.

Author:

Nils.Hoffmann@cebitec.uni-bielefeld.de

See Also:

Serialized Form

Constructor Summary

SingleLinkageAlgorithm()

Method Summary

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

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

SingleLinkageAlgorithm

public SingleLinkageAlgorithm()

Method Detail

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