maltcms.commands.fragments.cluster

Class NeighborJoinAlgorithm

java.lang.Object

cross.commands.fragments.AFragmentCommand

maltcms.commands.fragments.cluster.ClusteringAlgorithm

maltcms.commands.fragments.cluster.NeighborJoinAlgorithm

All Implemented Interfaces:

IFragmentCommand, ICommand<TupleND<IFileFragment>,TupleND<IFileFragment>>, IWorkflowElement, IEventSource<IWorkflowResult>, IConfigurable, IXMLSerializable, Serializable, Iterable<IFileFragment>, IClusteringAlgorithm

public class NeighborJoinAlgorithm
extends ClusteringAlgorithm

Implementation of NeighborJoining by Saitou and Nei (cite...) FIXME add citation

Author:

Nils.Hoffmann@cebitec.uni-bielefeld.de

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
NeighborJoinAlgorithm()
NeighborJoinAlgorithm(double[][] distances, String[] names)
NeighborJoinAlgorithm(double[][] distances, TupleND<IFileFragment> fragments, PairwiseFeatureSequenceSimilarity ld)

Method Summary

Methods

Modifier and Type	Method and Description
void	calcR(int numclust)
double[]	dmat(int i, int j, int k)
void	findBestD(int numclust)
void	init(double[][] distances, String[] names, TupleND<IFileFragment> fragments)
void	joinIJtoK(int i, int j, int k, double[] dist)
static void	main(String[] args)
void	printRMatrix()

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, 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, getCvResolver, getProgress, getWorkflow, hashCode, initProgress, initSubCommand, mapToInput, mapToInputUri, postProcess, postProcessUri, removeListener, resolve, save, setCvResolver, setProgress, setWorkflow

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

NeighborJoinAlgorithm

public NeighborJoinAlgorithm()

NeighborJoinAlgorithm

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

NeighborJoinAlgorithm

public NeighborJoinAlgorithm(double[][] distances,
                     TupleND<IFileFragment> fragments,
                     PairwiseFeatureSequenceSimilarity ld)

Method Detail

main

public static void main(String[] args)

calcR

public void calcR(int numclust)

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

init

public void init(double[][] distances,
        String[] names,
        TupleND<IFileFragment> fragments)

Overrides:

init in class ClusteringAlgorithm

joinIJtoK

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

Specified by:

joinIJtoK in class ClusteringAlgorithm

printRMatrix

public void printRMatrix()