Index

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All Classes and Interfaces|All Packages

A

Art2aEuclidKernel - Class in de.unijena.cheminf.clustering.art2a
ART-2a-Euclid algorithm implementation for unsupervised, open categorical clustering.
Art2aEuclidKernel(float[][], int, boolean) - Constructor for class de.unijena.cheminf.clustering.art2a.Art2aEuclidKernel
Constructor with default values for MAXIMUM_NUMBER_OF_EPOCHS (= 10), CONVERGENCE_THRESHOLD (= 0.1), LEARNING_PARAMETER (= 0.01), DEFAULT_OFFSET_FOR_CONTRAST_ENHANCEMENT (= 0.5) and RANDOM_SEED (= 1).
Art2aEuclidKernel(float[][], int, int, float, float, float, long, boolean) - Constructor for class de.unijena.cheminf.clustering.art2a.Art2aEuclidKernel
Constructor.
Art2aEuclidKernel(PreprocessedArt2aEuclidData, int) - Constructor for class de.unijena.cheminf.clustering.art2a.Art2aEuclidKernel
Constructor with default values for MAXIMUM_NUMBER_OF_EPOCHS (= 10), CONVERGENCE_THRESHOLD (= 0.1), LEARNING_PARAMETER (= 0.01) and RANDOM_SEED (= 1).
Art2aEuclidKernel(PreprocessedArt2aEuclidData, int, int, float, float, long) - Constructor for class de.unijena.cheminf.clustering.art2a.Art2aEuclidKernel
Constructor.
Art2aEuclidResult - Class in de.unijena.cheminf.clustering.art2a
Result of an ART-2a-Euclid clustering process.
Art2aEuclidResult(float, float, int, int, int[], float[][], boolean[], boolean, boolean, PreprocessedData) - Constructor for class de.unijena.cheminf.clustering.art2a.Art2aEuclidResult
Constructor.
Art2aEuclidTask - Class in de.unijena.cheminf.clustering.art2a
Callable that wraps an Art2aEuclidKernel instance where the call() method returns an Art2aEuclidResult object.
Art2aEuclidTask(float[][], float, int, boolean) - Constructor for class de.unijena.cheminf.clustering.art2a.Art2aEuclidTask
Constructor with default values for MAXIMUM_NUMBER_OF_EPOCHS (= 100), CONVERGENCE_THRESHOLD (= 0.1), LEARNING_PARAMETER (= 0.01), DEFAULT_OFFSET_FOR_CONTRAST_ENHANCEMENT (= 0.5) and RANDOM_SEED (= 1).
Art2aEuclidTask(float[][], float, int, int, float, float, float, long, boolean) - Constructor for class de.unijena.cheminf.clustering.art2a.Art2aEuclidTask
Constructor.
Art2aEuclidTask(PreprocessedArt2aEuclidData, float, int) - Constructor for class de.unijena.cheminf.clustering.art2a.Art2aEuclidTask
Constructor with default values for MAXIMUM_NUMBER_OF_EPOCHS (= 100), CONVERGENCE_THRESHOLD (= 0.1), LEARNING_PARAMETER (= 0.01) and RANDOM_SEED (= 1).
Art2aEuclidTask(PreprocessedArt2aEuclidData, float, int, int, float, float, long) - Constructor for class de.unijena.cheminf.clustering.art2a.Art2aEuclidTask
Constructor.
Art2aEuclidUtils - Class in de.unijena.cheminf.clustering.art2a
Library of static, thread-safe (stateless) utility methods for ART-2a-Euclid clustering.
Art2aEuclidUtils() - Constructor for class de.unijena.cheminf.clustering.art2a.Art2aEuclidUtils
Constructor
Art2aKernel - Class in de.unijena.cheminf.clustering.art2a
ART-2a algorithm implementation for unsupervised, open categorical clustering.
Art2aKernel(float[][], int, boolean) - Constructor for class de.unijena.cheminf.clustering.art2a.Art2aKernel
Constructor with default values for MAXIMUM_NUMBER_OF_EPOCHS (= 10), CONVERGENCE_THRESHOLD (= 0.99), LEARNING_PARAMETER (= 0.01), DEFAULT_OFFSET_FOR_CONTRAST_ENHANCEMENT (= 1.0) and RANDOM_SEED (= 1).
Art2aKernel(float[][], int, int, float, float, float, long, boolean) - Constructor for class de.unijena.cheminf.clustering.art2a.Art2aKernel
Constructor.
Art2aKernel(PreprocessedArt2aData, int) - Constructor for class de.unijena.cheminf.clustering.art2a.Art2aKernel
Constructor with default values for MAXIMUM_NUMBER_OF_EPOCHS (= 10), CONVERGENCE_THRESHOLD (= 0.99), LEARNING_PARAMETER (= 0.01) and RANDOM_SEED (= 1).
Art2aKernel(PreprocessedArt2aData, int, int, float, float, long) - Constructor for class de.unijena.cheminf.clustering.art2a.Art2aKernel
Constructor.
Art2aResult - Class in de.unijena.cheminf.clustering.art2a
Result of an ART-2a clustering process.
Art2aResult(float, float, int, int, int[], float[][], boolean[], boolean, boolean, PreprocessedData) - Constructor for class de.unijena.cheminf.clustering.art2a.Art2aResult
Constructor.
Art2aTask - Class in de.unijena.cheminf.clustering.art2a
Callable that wraps an Art2aKernel instance where the call() method returns an Art2aResult object.
Art2aTask(float[][], float, int, boolean) - Constructor for class de.unijena.cheminf.clustering.art2a.Art2aTask
Constructor with default values for MAXIMUM_NUMBER_OF_EPOCHS (= 100), CONVERGENCE_THRESHOLD (= 0.99), LEARNING_PARAMETER (= 0.01), DEFAULT_OFFSET_FOR_CONTRAST_ENHANCEMENT (= 1.0) and RANDOM_SEED (= 1).
Art2aTask(float[][], float, int, int, float, float, float, long, boolean) - Constructor for class de.unijena.cheminf.clustering.art2a.Art2aTask
Constructor.
Art2aTask(PreprocessedArt2aData, float, int) - Constructor for class de.unijena.cheminf.clustering.art2a.Art2aTask
Constructor with default values for MAXIMUM_NUMBER_OF_EPOCHS (= 100), CONVERGENCE_THRESHOLD (= 0.99), LEARNING_PARAMETER (= 0.01) and RANDOM_SEED (= 1).
Art2aTask(PreprocessedArt2aData, float, int, int, float, float, long) - Constructor for class de.unijena.cheminf.clustering.art2a.Art2aTask
Constructor.
Art2aUtils - Class in de.unijena.cheminf.clustering.art2a
Library of static, thread-safe (stateless) utility methods for ART-2a clustering.
Art2aUtils() - Constructor for class de.unijena.cheminf.clustering.art2a.Art2aUtils
Constructor

C

call() - Method in class de.unijena.cheminf.clustering.art2a.Art2aEuclidTask
Performs the clustering process.
call() - Method in class de.unijena.cheminf.clustering.art2a.Art2aTask
Performs the clustering process.
ClusterRemovalInfo() - Constructor for class de.unijena.cheminf.clustering.art2a.Utils.ClusterRemovalInfo
Constructor
copyMatrix(float[][], float[][]) - Static method in class de.unijena.cheminf.clustering.art2a.Utils
(Deep) Copies source matrix to destination matrix.
copyRows(float[][], float[][], int) - Static method in class de.unijena.cheminf.clustering.art2a.Utils
(Deep) Copies specified number of rows of source matrix to destination matrix.
copyVector(float[], float[]) - Static method in class de.unijena.cheminf.clustering.art2a.Utils
(Deep) Copies source vector to destination vector.

D

de.unijena.cheminf.clustering.art2a - package de.unijena.cheminf.clustering.art2a
 

E

enhanceContrast(float[], float) - Static method in class de.unijena.cheminf.clustering.art2a.Utils
Calculates contrast enhanced vector.
equals(Object) - Method in record class de.unijena.cheminf.clustering.art2a.Utils.MinMaxValue
Indicates whether some other object is "equal to" this one.

F

fillMatrix(float[][], float) - Static method in class de.unijena.cheminf.clustering.art2a.Utils
Fills matrix with value.
fillVector(boolean[], boolean) - Static method in class de.unijena.cheminf.clustering.art2a.Utils
Fills vector with value.
fillVector(float[], float) - Static method in class de.unijena.cheminf.clustering.art2a.Utils
Fills vector with value.
fillVector(int[], int) - Static method in class de.unijena.cheminf.clustering.art2a.Utils
Fills vector with value.

G

getAngleBetweenClusters(int, int) - Method in class de.unijena.cheminf.clustering.art2a.Art2aResult
Return angle in degree between specified clusters with aClusterIndex1 and aClusterIndex2.
getClusterRepresentativeIndex(int) - Method in class de.unijena.cheminf.clustering.art2a.Art2aEuclidResult
Calculates index of representative data vector which is closest to the specified cluster vector with index aClusterIndex.
getClusterRepresentativeIndex(int) - Method in class de.unijena.cheminf.clustering.art2a.Art2aResult
Calculates index of representative data vector which is closest to the specified cluster vector with index aClusterIndex.
getClusterRepresentativeIndices(int) - Method in class de.unijena.cheminf.clustering.art2a.Art2aEuclidResult
Calculates array of indices of sorted representative data vectors of the specified cluster with index aClusterIndex.
getClusterRepresentativeIndices(int) - Method in class de.unijena.cheminf.clustering.art2a.Art2aResult
Calculates an array of indices of sorted representative data vectors of the specified cluster with index aClusterIndex.
getClusterResult(float, boolean) - Method in class de.unijena.cheminf.clustering.art2a.Art2aEuclidKernel
Performs ART-2a-Euclid clustering and returns corresponding Art2aEuclidResult.
getClusterResult(float, boolean) - Method in class de.unijena.cheminf.clustering.art2a.Art2aKernel
Performs ART-2a clustering and returns corresponding Art2aResult.
getClusterResults(float[], boolean) - Method in class de.unijena.cheminf.clustering.art2a.Art2aEuclidKernel
Performs ART-2a-Euclid clustering for specified vigilance parameters and returns corresponding Art2aEuclidResult objects.
getClusterResults(float[], boolean) - Method in class de.unijena.cheminf.clustering.art2a.Art2aKernel
Performs ART-2a clustering for specified vigilance parameters and returns corresponding Art2aResult objects.
getClusterSize(int) - Method in class de.unijena.cheminf.clustering.art2a.Art2aEuclidResult
Returns size of the specified cluster with index aClusterIndex, i.e.
getClusterSize(int) - Method in class de.unijena.cheminf.clustering.art2a.Art2aResult
Returns size of the specified cluster with index aClusterIndex, i.e., the number of data vectors of the original data matrix that belong to the cluster.
getClusterVector(int) - Method in class de.unijena.cheminf.clustering.art2a.Art2aEuclidResult
Returns specified cluster vector with index aClusterIndex in clusterMatrix.
getClusterVector(int) - Method in class de.unijena.cheminf.clustering.art2a.Art2aResult
Returns specified cluster vector with index aClusterIndex in clusterMatrix.
getDataMatrix() - Method in class de.unijena.cheminf.clustering.art2a.PreprocessedData
Original data matrix with data row vectors
getDataVectorIndicesOfCluster(int) - Method in class de.unijena.cheminf.clustering.art2a.Art2aEuclidResult
Returns indices of data vectors in original data matrix that belong to the specified cluster with index aClusterIndex.
getDataVectorIndicesOfCluster(int) - Method in class de.unijena.cheminf.clustering.art2a.Art2aResult
Returns indices of data vectors in the original data matrix that belong to the specified cluster with index aClusterIndex.
getDataVectorZeroLengthFlags() - Method in class de.unijena.cheminf.clustering.art2a.PreprocessedData
Flags array that indicates if scaled data row vectors have a length of zero (i.e.
getDistanceBetweenClusters(int, int) - Method in class de.unijena.cheminf.clustering.art2a.Art2aEuclidResult
Return distance between specified clusters with aClusterIndex1 and aClusterIndex2.
getIndexOfCluster() - Method in class de.unijena.cheminf.clustering.art2a.Utils.RhoWinner
Index of cluster
getMeanDistance(float[][], int[]) - Static method in class de.unijena.cheminf.clustering.art2a.Utils
Returns mean distance of all specified row vectors.
getMinMaxComponents(float[][]) - Static method in class de.unijena.cheminf.clustering.art2a.Utils
Returns min-max components for matrix where MinMaxValue[j] corresponds to column j of the row vectors of the matrix.
getMinMaxComponentsOfDataMatrix() - Method in class de.unijena.cheminf.clustering.art2a.PreprocessedData
Min-max components of original data matrix (see method Utils.getMinMaxComponents() for data structure)
getNumberOfDetectedClusters() - Method in class de.unijena.cheminf.clustering.art2a.Art2aEuclidResult
Number of detected clusters
getNumberOfDetectedClusters() - Method in class de.unijena.cheminf.clustering.art2a.Art2aResult
Number of detected clusters
getNumberOfDetectedClusters() - Method in class de.unijena.cheminf.clustering.art2a.Utils.ClusterRemovalInfo
Number of detected clusters
getNumberOfEpochs() - Method in class de.unijena.cheminf.clustering.art2a.Art2aEuclidResult
Number of epochs
getNumberOfEpochs() - Method in class de.unijena.cheminf.clustering.art2a.Art2aResult
Number of epochs
getOffsetForContrastEnhancement() - Method in class de.unijena.cheminf.clustering.art2a.PreprocessedData
Returns offset for contrast enhancement
getPreprocessedArt2aData(float[][]) - Static method in class de.unijena.cheminf.clustering.art2a.Art2aKernel
Creates PreprocessedData object with preprocessed ART-2a data for maximum speed of the clustering process.
getPreprocessedArt2aData(float[][], float) - Static method in class de.unijena.cheminf.clustering.art2a.Art2aKernel
Creates PreprocessedData object with preprocessed ART-2a data for maximum speed of the clustering process.
getPreprocessedArt2aEuclidData(float[][]) - Static method in class de.unijena.cheminf.clustering.art2a.Art2aEuclidKernel
Creates PreprocessedData object with preprocessed ART-2a-Euclid data for maximum speed of the clustering process.
getPreprocessedArt2aEuclidData(float[][], float) - Static method in class de.unijena.cheminf.clustering.art2a.Art2aEuclidKernel
Creates PreprocessedData object with preprocessed ART-2a-Euclid data for maximum speed of the clustering process.
getPreprocessedMatrix() - Method in class de.unijena.cheminf.clustering.art2a.PreprocessedData
Matrix of contrast enhanced unit vectors
getRepresentativeIndicesOfClusters() - Method in class de.unijena.cheminf.clustering.art2a.Art2aEuclidResult
Returns data vector indices which are closest to their cluster vectors.
getRepresentativeIndicesOfClusters() - Method in class de.unijena.cheminf.clustering.art2a.Art2aResult
Returns data vector indices which are closest to their cluster vectors.
getRepresentatives(int, float, float, int, boolean) - Method in class de.unijena.cheminf.clustering.art2a.Art2aEuclidKernel
Nearest (smaller) indices of approximants to the desired number of representatives.
getRepresentatives(int, float, float, int, boolean) - Method in class de.unijena.cheminf.clustering.art2a.Art2aKernel
Nearest (smaller) indices of approximates to the desired number of representatives.
getRhoValue() - Method in class de.unijena.cheminf.clustering.art2a.Utils.RhoWinner
Rho value
getScalarProduct(float[], float[]) - Static method in class de.unijena.cheminf.clustering.art2a.Utils
Calculates the scalar product (dot product) of aVector1 and aVector2.
getScaledClusterVector(int) - Method in class de.unijena.cheminf.clustering.art2a.Art2aEuclidResult
Returns specified cluster vector with index aClusterIndex in cluster matrix with components being scaled to interval [0,1].
getScaledClusterVector(int) - Method in class de.unijena.cheminf.clustering.art2a.Art2aResult
Returns specified cluster vector with index aClusterIndex in cluster matrix with components being scaled to interval [0,1].
getScaledVector(float[]) - Static method in class de.unijena.cheminf.clustering.art2a.Utils
Scales components of aVectorToBeScaled to interval [0,1].
getSquaredDistance(float[], float[]) - Static method in class de.unijena.cheminf.clustering.art2a.Utils
Calculates the squared distance between aVector1 and aVector2.
getSumOfComponents(float[]) - Static method in class de.unijena.cheminf.clustering.art2a.Utils
Calculates the sum of components of aVector.
getSumOfSquaredDifferences(float[], float) - Static method in class de.unijena.cheminf.clustering.art2a.Utils
Calculates the sum of squared differences between the components of the specified vector and a value.
getThresholdForContrastEnhancement(int, float) - Static method in class de.unijena.cheminf.clustering.art2a.Utils
Threshold for contrast enhancement
getTrainingAndTestIndices(float) - Method in class de.unijena.cheminf.clustering.art2a.Art2aResult
Creates clustering-based training and test data vector indices that cover a similar space.
getTrainingAndTestIndices(float, float, float, int, boolean) - Method in class de.unijena.cheminf.clustering.art2a.Art2aKernel
Creates clustering-based training and test data vector indices that cover a similar space.
getTrainingAndTestIndices(Art2aResult) - Static method in class de.unijena.cheminf.clustering.art2a.Utils
Creates clustering-based training and test data vector indices that cover a similar space.
getVectorLength(float[]) - Static method in class de.unijena.cheminf.clustering.art2a.Utils
Calculates the length of aVector.
getVigilance() - Method in class de.unijena.cheminf.clustering.art2a.Art2aEuclidResult
Vigilance parameter
getVigilance() - Method in class de.unijena.cheminf.clustering.art2a.Art2aResult
Vigilance parameter
getZeroLengthDataVectorIndices() - Method in class de.unijena.cheminf.clustering.art2a.Art2aEuclidResult
Returns all indices of (scaled) data vectors that have a length of zero.
getZeroLengthDataVectorIndices() - Method in class de.unijena.cheminf.clustering.art2a.Art2aResult
Returns all indices of (scaled) data vectors that have a length of zero.

H

hashCode() - Method in record class de.unijena.cheminf.clustering.art2a.Utils.MinMaxValue
Returns a hash code value for this object.
hasLengthOfZero(float[]) - Static method in class de.unijena.cheminf.clustering.art2a.Utils
Checks if vector has a length of zero (i.e.
hasNonFiniteComponent(float[][]) - Static method in class de.unijena.cheminf.clustering.art2a.Utils
Checks if data matrix has a non-finite component.
hasPreprocessedData() - Method in class de.unijena.cheminf.clustering.art2a.PreprocessedData
Returns if Art2aData object has preprocessed data, i.e.

I

isClusterOverflow() - Method in class de.unijena.cheminf.clustering.art2a.Art2aEuclidResult
Returns if cluster overflow occurred.
isClusterOverflow() - Method in class de.unijena.cheminf.clustering.art2a.Art2aResult
Returns if cluster overflow occurred.
isClusterRemoved() - Method in class de.unijena.cheminf.clustering.art2a.Utils.ClusterRemovalInfo
True: Cluster is removed, false: Otherwise
isContrastEnhanced(float[], float) - Static method in class de.unijena.cheminf.clustering.art2a.Utils
Calculates contrast enhanced vector.
isConverged() - Method in class de.unijena.cheminf.clustering.art2a.Art2aEuclidResult
Returns if clustering process converged.
isConverged() - Method in class de.unijena.cheminf.clustering.art2a.Art2aResult
Returns if clustering process converged.
isDataMatrixValid(float[][]) - Static method in class de.unijena.cheminf.clustering.art2a.Utils
Checks if aDataMatrix is valid.
isMatrixValid(float[][]) - Static method in class de.unijena.cheminf.clustering.art2a.Utils
Checks if matrix is valid.
isNonFiniteComponentRemoval(float[][]) - Static method in class de.unijena.cheminf.clustering.art2a.Utils
Removes columns from data matrix with non-finite components.

M

maxValue() - Method in record class de.unijena.cheminf.clustering.art2a.Utils.MinMaxValue
Returns the value of the maxValue record component.
MinMaxValue(float, float) - Constructor for record class de.unijena.cheminf.clustering.art2a.Utils.MinMaxValue
Constructor
minValue() - Method in record class de.unijena.cheminf.clustering.art2a.Utils.MinMaxValue
Returns the value of the minValue record component.

N

normalizeVector(float[]) - Static method in class de.unijena.cheminf.clustering.art2a.Utils
Calculates normalized (unit) vector of length 1.

P

PreprocessedArt2aData - Class in de.unijena.cheminf.clustering.art2a
Class for preprocessed ART-2a data
PreprocessedArt2aData(float[][], boolean[], Utils.MinMaxValue[], float) - Constructor for class de.unijena.cheminf.clustering.art2a.PreprocessedArt2aData
Constructor
PreprocessedArt2aEuclidData - Class in de.unijena.cheminf.clustering.art2a
Class for preprocessed ART-2a-Euclid data
PreprocessedArt2aEuclidData(float[][], boolean[], Utils.MinMaxValue[], float) - Constructor for class de.unijena.cheminf.clustering.art2a.PreprocessedArt2aEuclidData
Constructor
PreprocessedData - Class in de.unijena.cheminf.clustering.art2a
Class for preprocessed data.
PreprocessedData(float[][], boolean[], Utils.MinMaxValue[], float) - Constructor for class de.unijena.cheminf.clustering.art2a.PreprocessedData
Constructor
PreprocessedData(float[][], Utils.MinMaxValue[], float) - Constructor for class de.unijena.cheminf.clustering.art2a.PreprocessedData
Constructor

R

removeEmptyClusters(boolean[], float[][], int, Utils.ClusterRemovalInfo) - Static method in class de.unijena.cheminf.clustering.art2a.Utils
Removes empty clusters from cluster matrix
RhoWinner() - Constructor for class de.unijena.cheminf.clustering.art2a.Utils.RhoWinner
Constructor

S

scaleVector(float[], Utils.MinMaxValue[]) - Static method in class de.unijena.cheminf.clustering.art2a.Utils
Scales components of aVectorToBeScaled according to min-max components to interval [0,1] (see code and method getMinMaxComponents()).
setClusterRemovalInfo(boolean, int) - Method in class de.unijena.cheminf.clustering.art2a.Utils.ClusterRemovalInfo
Set cluster removal info
setContrastEnhancedUnitVector(float[], float[], Utils.MinMaxValue[], float) - Static method in class de.unijena.cheminf.clustering.art2a.Art2aUtils
Transforms original data vector into corresponding contrast enhanced unit vector (see code).
setContrastEnhancedVector(float[], float[], Utils.MinMaxValue[], float) - Static method in class de.unijena.cheminf.clustering.art2a.Art2aEuclidUtils
Transforms original data vector into corresponding contrast enhanced unit vector (see code).
setContrastEnhancement(float[], float) - Static method in class de.unijena.cheminf.clustering.art2a.Utils
Calculates contrast enhanced vector.
setRhoWinner(float, int) - Method in class de.unijena.cheminf.clustering.art2a.Utils.RhoWinner
Set rho winner
setRowVector(float[][], float[], int) - Static method in class de.unijena.cheminf.clustering.art2a.Utils
Sets copied (!) row vector at index in matrix.
shuffleIndices(int[], Random) - Static method in class de.unijena.cheminf.clustering.art2a.Utils
Randomly shuffles indices from 0 to (anIndices.Length - 1) in anIndexArray using Fisher-Yates shuffling (i.e.

T

toString() - Method in record class de.unijena.cheminf.clustering.art2a.Utils.MinMaxValue
Returns a string representation of this record class.

U

Utils - Class in de.unijena.cheminf.clustering.art2a
Library of helper records, static helper classes and static, thread-safe (stateless) utility methods for ART-2a and ART-2a-Euclid clustering.
Utils() - Constructor for class de.unijena.cheminf.clustering.art2a.Utils
Constructor
Utils.ClusterRemovalInfo - Class in de.unijena.cheminf.clustering.art2a
Helper class: Cluster removal info.
Utils.MinMaxValue - Record Class in de.unijena.cheminf.clustering.art2a
Helper record: Minimum and maximum value.
Utils.RhoWinner - Class in de.unijena.cheminf.clustering.art2a
Helper class: Rho winner.
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