Package de.unijena.cheminf.clustering.art2a.results

Class Art2aDoubleClusteringResult

java.lang.Object

de.unijena.cheminf.clustering.art2a.abstractResult.Art2aAbstractResult

de.unijena.cheminf.clustering.art2a.results.Art2aDoubleClusteringResult

All Implemented Interfaces:

IArt2aClusteringResult

public class Art2aDoubleClusteringResult
extends Art2aAbstractResult

Result class for the double clustering.

Constructor Summary

Constructors

Constructor	Description
Art2aDoubleClusteringResult(double aVigilanceParameter, int aNumberOfEpochs, int aNumberOfDetectedClusters, int[] aClusterView, double[][] aClusterMatrix, double[][] aDataMatrix)	Constructor.
Art2aDoubleClusteringResult(double aVigilanceParameter, int aNumberOfEpochs, int aNumberOfDetectedClusters, int[] aClusterView, double[][] aClusterMatrix, double[][] aDataMatrix, ConcurrentLinkedQueue<String> aClusteringProcessQueue, ConcurrentLinkedQueue<String> aClusteringResultQueue)	Constructor.

Method Summary

Modifier and Type	Method	Description
Double	getAngleBetweenClusters(int aFirstCluster, int aSecondCluster)	Calculates the angle between two clusters.
int	getClusterRepresentatives(int aClusterNumber)	Calculates the cluster representative.
Double	getVigilanceParameter()	Returns the vigilance parameter of the clustering algorithm.

Methods inherited from class de.unijena.cheminf.clustering.art2a.abstractResult.Art2aAbstractResult

exportClusteringResultsToTextFiles, getClusterIndices, getNumberOfDetectedClusters, getNumberOfEpochs

Methods inherited from class java.lang.Object

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

Constructor Details

Art2aDoubleClusteringResult

public Art2aDoubleClusteringResult(double aVigilanceParameter,
 int aNumberOfEpochs,
 int aNumberOfDetectedClusters,
 int[] aClusterView,
 double[][] aClusterMatrix,
 double[][] aDataMatrix,
 ConcurrentLinkedQueue<String> aClusteringProcessQueue,
 ConcurrentLinkedQueue<String> aClusteringResultQueue)
                            throws NullPointerException,
IllegalArgumentException

Constructor.

Parameters:

aVigilanceParameter - parameter to influence the number of clusters.

aNumberOfEpochs - final epoch number.

aNumberOfDetectedClusters - final number of detected clusters.

aClusteringProcessQueue - clustering result (process) queue of ty String. The queue is required to be able to export the cluster results. If it is not specified, they are set to null and export is not possible.

aClusteringResultQueue - clustering result queue of typ String. See #aClusteringProcessQueue

aClusterView - array for cluster assignment of each input vector.

aClusterMatrix - cluster vector matrix. All cluster vectors created after double ART-2a clustering are stored in this matrix.

aDataMatrix - matrix with all input vectors/fingerprints. Each row in the matrix corresponds to an input vector.

Throws:

NullPointerException - is thrown, if the specified matrices are null.

IllegalArgumentException - is thrown, if the specified vigilance parameter is invalid.

Art2aDoubleClusteringResult

public Art2aDoubleClusteringResult(double aVigilanceParameter,
 int aNumberOfEpochs,
 int aNumberOfDetectedClusters,
 int[] aClusterView,
 double[][] aClusterMatrix,
 double[][] aDataMatrix)
                            throws NullPointerException

Constructor.

Parameters:

aVigilanceParameter - parameter to influence the number of clusters.

aNumberOfEpochs - final epoch number.

aNumberOfDetectedClusters - final number of detected clusters.

aClusterView - array for cluster assignment of each input vector.

aClusterMatrix - double cluster vector matrix. All cluster vectors created after double ART-2a clustering are stored in this matrix.

aDataMatrix - double matrix with all input vectors/fingerprints. Each row in the matrix corresponds to an input vector.

Throws:

NullPointerException - is thrown, if the specified matrices are null.

IllegalArgumentException - is thrown, if the specified vigilance parameter is invalid.

See Also:

• Art2aDoubleClusteringResult(double, int, int, int[], double[][], double[][], ConcurrentLinkedQueue, ConcurrentLinkedQueue)

Method Details

getVigilanceParameter

public Double getVigilanceParameter()

Returns the vigilance parameter of the clustering algorithm.

Returns:

float vigilance parameter

getClusterRepresentatives

public int getClusterRepresentatives(int aClusterNumber)
                              throws IllegalArgumentException

Calculates the cluster representative. This means that the input that is most similar to the cluster vector is determined.

Parameters:

aClusterNumber - Cluster number for which the representative is to be calculated.

Returns:

int input indices of the representative input in the cluster.

Throws:

IllegalArgumentException - is thrown if the given cluster number is invalid.

getAngleBetweenClusters

public Double getAngleBetweenClusters(int aFirstCluster,
 int aSecondCluster)
                               throws IllegalArgumentException

Calculates the angle between two clusters. The angle between the clusters defines the distance between them. Since all vectors are normalized to unit vectors in the first step of clustering and only positive components are allowed, they all lie in the positive quadrant of the unit sphere, so the maximum distance between two clusters can be 90 degrees.

Parameters:

aFirstCluster - first cluster

aSecondCluster - second cluster

Returns:

generic angle double or float.

Throws:

IllegalArgumentException - if the given parameters are invalid.