Uses of Class
com.actelion.research.calc.Matrix

Packages that use Matrix

Package	Description
com.actelion.research.calc
com.actelion.research.calc.graph
com.actelion.research.calc.histogram
com.actelion.research.calc.regression
com.actelion.research.calc.regression.gaussianprocess
com.actelion.research.calc.regression.knn
com.actelion.research.calc.regression.linear.pls
com.actelion.research.calc.regression.linear.pls.boxcox
com.actelion.research.calc.regression.median
com.actelion.research.calc.regression.neuralnetwork
com.actelion.research.calc.regression.randomforest
com.actelion.research.calc.regression.svm
com.actelion.research.calc.statistics
com.actelion.research.chem.alignment3d
com.actelion.research.chem.docking
com.actelion.research.chem.phesa
com.actelion.research.util.datamodel
com.actelion.research.util.datamodel.table

Uses of Matrix in com.actelion.research.calc

Methods in com.actelion.research.calc that return Matrix

Modifier and Type	Method	Description
Matrix	Matrix.add(double v)
Matrix	Matrix.add2CompleteCol(Matrix maRow)	The value in the col from the input matrix is added to all values in the corresponding col in the matrix.
static Matrix	MatrixFunctions.appendCols(Matrix ma0, Matrix ma1)
static Matrix	MatrixFunctions.appendRows(Matrix ma0, Matrix ma1)
static Matrix	MatrixFunctions.calculateSimilarityMatrixRowWise(Matrix X1, Matrix X2)
static Matrix	MatrixFunctions.cholesky(Matrix A)
static Matrix	MatrixFunctions.convert2Binary(Matrix A, double thresh)
Matrix	Matrix.correlation()	Generate a correlation matrix, each column contains values of a pulling.
static Matrix	MatrixFunctions.countFieldsBiggerThanThreshColWise(Matrix ma, double thresh)
Matrix	Matrix.covariance()	Generate a covariance matrix, each column contains values of a pulling.
static Matrix	MatrixFunctions.create(java.util.List<double[]> li)	List is already used as a constructor for Matrix.
Matrix	Matrix.devide(double dDivisor)
Matrix	Matrix.devide(Matrix maDivisor)
Matrix	Matrix.devideCols(Matrix maDivisor)
Matrix	Matrix.devideDivisorBigger(Matrix maDivisor)
Matrix	Matrix.diagonalize()
Matrix	Matrix.getAbs()
Matrix	Matrix.getCenteredMatrix()
Matrix	Matrix.getCenteredMatrix(Matrix maMean)
Matrix	Matrix.getCol(int col)
Matrix	Matrix.getColumns(java.util.List<java.lang.Integer> liIndex)
Matrix	Matrix.getColumns(java.util.Vector<java.lang.Integer> vecIndices)	Deprecated. use getColumns(List vecIndices) instead
Matrix	Matrix.getDeleteColsZeroVar(java.util.List<java.lang.Integer> vecIndices)	Deletes columns with zero variance.
Matrix	Matrix.getDiagonal()	Matrix diagonal extraction.
static Matrix	MatrixFunctions.getDistanceMatrix(java.util.List<java.awt.Point> li)
static Matrix	MatrixFunctions.getDistanceMatrixTanimotoInv(Matrix ma1, Matrix ma2)	Calculates the inverse Tanimoto coefficient from row wise comparison of the two input matrices.
static Matrix	MatrixFunctions.getDistTanimotoInvReduced(Matrix ma1, Matrix ma2)
Matrix	Matrix.getFlipped()	Opposite direction to transpose.
static Matrix	MatrixFunctions.getKMeanClusters(Matrix ma, int k)	03.10.04 MvK
Matrix	LUDecomposition.getL()	Return lower triangular factor
Matrix	Matrix.getLinedCol()
Matrix	Matrix.getMatrix(int[] r, int[] c)	Get a submatrix.
Matrix	Matrix.getMatrix(int[] r, int j0, int j1)	Get a submatrix.
Matrix	Matrix.getMatrix(int i0, int i1, int[] c)	Get a submatrix.
Matrix	Matrix.getMatrix(int i0, int i1, int j0, int j1)
Matrix	Matrix.getMaxMin()	max and min vals for all cols
Matrix	Matrix.getMeanCols()
Matrix	Matrix.getMeanCols(int[] rowIndex)
Matrix	Matrix.getMeanRows()
Matrix	Matrix.getMedianCols()
Matrix	Matrix.getMergeRows(Matrix ma)
Matrix	Matrix.getMinRows()
Matrix	Matrix.getMinRowsPosCol()
Matrix	Matrix.getNormalizedMatrix()
Matrix	Matrix.getNormalizedMatrix(Matrix maStandardDeviation)
static Matrix	Matrix.getParsed(java.util.Vector<java.lang.String> vecStringMatrix)	Parses an vector with Strings and converts it to a Matrix.
static Matrix	MatrixFunctions.getRandomMatrix(int rows, int cols)	generates a matrix with double values between 0 (inclusive) and 1 (exclusive).
static Matrix	Matrix.getRND(int rows, int cols)
static Matrix	MatrixFunctions.getRowMinUnique(Matrix ma)
static Matrix	MatrixFunctions.getScaled(Matrix ma)	Centers and divides by standard deviation.
static Matrix	MatrixFunctions.getScaledByFactor(Matrix ma, double fac)
Matrix	SimilarityMulticore.getSimilarityMatrix()
Matrix	Matrix.getSorted()	Sorts the row of the matrix according the compareTo(...) function in DoubleVec
Matrix	Matrix.getSQRT()
Matrix	Matrix.getStandardDeviationCols()
Matrix	Matrix.getStandardized()	Get the standard scores, also known as z-scores.
Matrix	Matrix.getSubMatrix(int indexRowStart, int indexRowEnd, int indexColStart, int indexColEnd)
Matrix	Matrix.getSubMatrix(java.util.List<java.lang.Integer> liIndexRow)
Matrix	Matrix.getSumCols()
Matrix	Matrix.getSumRows()
Matrix	Matrix.getTranspose()
Matrix	LUDecomposition.getU()	Return upper triangular factor
Matrix	Matrix.getVarianceCols()
static Matrix	MatrixFunctions.inv(Matrix A)	Returns the inverse of a matrix.
Matrix	Matrix.log()	Log function from the class Math .
Matrix	Matrix.multCols(Matrix maMuiltiplicant)
Matrix	Matrix.multiply(boolean transA, boolean transB, Matrix ma)	Multiplication of two matrices.
Matrix	Matrix.multiply(double dScalar)
Matrix	Matrix.multiply(Matrix ma)
Matrix	Matrix.multiplyValByVal(Matrix ma)	Value by value multiplication Matrices must have the same dimensions.
protected static Matrix	MatrixTests.pls(Matrix X, Matrix Y, java.lang.String sPatternHeaderX, int iNumPrincipalComponents, boolean bLogarithm, java.lang.String sFileDataSummaryOut)
Matrix	Matrix.plus(Matrix ma)
Matrix	Matrix.pow(double exp)
static Matrix	MatrixFunctions.read(java.io.File fiMatrix)
static Matrix	MatrixFunctions.read(java.io.File fiMatrix, boolean skipFirstLine)
static Matrix	MatrixFunctions.read(java.io.InputStream is)
static Matrix	MatrixFunctions.read(java.io.InputStream is, boolean skipFirstLine)
static Matrix	MatrixFunctions.read(java.lang.String s)
static Matrix	MatrixFunctions.readAsLineBase64Encoded(java.lang.String s)
static Matrix	MatrixFunctions.readCSV(java.io.File fi)
static Matrix	Matrix.readSerialized(java.io.File fiIn)
Matrix	Matrix.removeCol(int col2Remove)
static Matrix	BoxCox.reTransform(Matrix A, BoxCox boxCox)
static Matrix	MatrixFunctions.rnorm(int n, double mean, double sd)
Matrix	Matrix.row2Matrix(int row, int len)
Matrix	LUDecomposition.solve(Matrix B)	Solve A*X = B
static Matrix[]	MatrixFunctions.split(Matrix A, int row)	Splits the matrix row wise into two matrices.
static Matrix[]	MatrixFunctions.splitCol(Matrix A, int col)
Matrix	Matrix.subtract(double val)
Matrix	Matrix.subtract(Matrix ma)
Matrix	Matrix.subtractFromCols(Matrix maDivisor)
static Matrix	MatrixTests.test00()
static Matrix	MatrixTests.test01()
static Matrix	MatrixTests.test02()
static Matrix	MatrixTests.test03()
static Matrix	MatrixTests.test04()
static Matrix	MatrixTests.test05()
static Matrix	MatrixTests.test06()
static Matrix	MatrixTests.test07()
static Matrix	MatrixTests.test08()
static Matrix	MatrixTests.testDescriptor01X()
static Matrix	MatrixTests.testDescriptor01Y()
static Matrix	MatrixTests.testLonglyX()	http://itl.nist.gov/div898/strd/lls/data/LINKS/DATA/Longley.dat
static Matrix	MatrixTests.testLonglyY()	http://www.itl.nist.gov/div898/strd/lls/data/Longley.shtml Y Matrix
static Matrix	MatrixTests.testMatrix_XWine()
static Matrix	MatrixTests.testMatrix_YWine()	Validation data for PLS from Abdi, PLS, Encyclopedia of Social Sciences Reasearch Methods (2003).
static Matrix	MatrixTests.testMatrix02()
static Matrix	MatrixTests.testMatrixHenrion01()
static Matrix	MatrixTests.testSimple1X(int cols)
static Matrix	MatrixTests.testSimple1Y()
static Matrix	MatrixTests.testSimple2X(int cols)
Matrix	Matrix.toRow()
static Matrix	BoxCox.transform(Matrix A, BoxCox boxCox)

Methods in com.actelion.research.calc with parameters of type Matrix

Modifier and Type	Method	Description
Matrix	Matrix.add2CompleteCol(Matrix maRow)	The value in the col from the input matrix is added to all values in the corresponding col in the matrix.
void	Matrix.add2Row(int row, Matrix ma2, int row2)
static Matrix	MatrixFunctions.appendCols(Matrix ma0, Matrix ma1)
static Matrix	MatrixFunctions.appendRows(Matrix ma0, Matrix ma1)
void	Matrix.assignCol(int iCol, Matrix ma)
void	Matrix.assignCol(int iCol, Matrix ma, int iColMa)
static IntegerDouble	MatrixFunctions.calculateMaxSimilarity(Matrix X, double[] arr)
static IntegerDouble[]	MatrixFunctions.calculateMaxSimilarity(Matrix X, double[] arr, int nMostSimilar)
static double[]	MatrixFunctions.calculateMaxSimilarity(Matrix XTrain, Matrix Xtest)
static Matrix	MatrixFunctions.calculateSimilarityMatrixRowWise(Matrix X1, Matrix X2)
static Matrix	MatrixFunctions.cholesky(Matrix A)
static void	MatrixFunctions.columnIntoDoubleArray(Matrix A, int col, DoubleArray da)
static Matrix	MatrixFunctions.convert2Binary(Matrix A, double thresh)
void	Matrix.copy(Matrix maSource)	Copies a matrix ma into this, the pointer to ma1 is not changed.
void	Matrix.copyColumn(Matrix maSource, int colSource, int colDestination)
static int	MatrixFunctions.countFieldsBiggerThan(Matrix ma, int row, double thresh)
static Matrix	MatrixFunctions.countFieldsBiggerThanThreshColWise(Matrix ma, double thresh)
static int	MatrixFunctions.countFieldsBiggerThanThreshColWise(Matrix ma, int col, double thresh)
static java.util.List<IdentifiedObject<double[]>>	MatrixFunctions.createIdentifiedObject(Matrix A)
Matrix	Matrix.devide(Matrix maDivisor)
Matrix	Matrix.devideCols(Matrix maDivisor)
Matrix	Matrix.devideDivisorBigger(Matrix maDivisor)
boolean	Matrix.equal(Matrix ma)
boolean	Matrix.equal(Matrix ma, double dLimit)
boolean	Matrix.equalDimension(Matrix ma)	Checks two matrices for equal dimensions.
Matrix	Matrix.getCenteredMatrix(Matrix maMean)
static double	ArrayUtilsCalc.getCorrPearson(Matrix A, Matrix B)
static double	MatrixFunctions.getCorrPearson(Matrix A, int col1, int col2)
static double	MatrixFunctions.getCorrPearson(Matrix A, Matrix B)
static double	MatrixFunctions.getCorrSpearman(Matrix A, Matrix B)
static double	MatrixFunctions.getCovariance(Matrix A, Matrix B)
static double	MatrixFunctions.getCovarianceCentered(Matrix A, Matrix B)
static Matrix	MatrixFunctions.getDistanceMatrixTanimotoInv(Matrix ma1, Matrix ma2)	Calculates the inverse Tanimoto coefficient from row wise comparison of the two input matrices.
static double	MatrixFunctions.getDistanceTanimotoInv(Matrix ma1, int row1, Matrix ma2, int row2)
static double	MatrixFunctions.getDistTanimotoInvReduced(Matrix ma1, int row1, Matrix ma2, int row2)	Only fields are considered which are not nut 0 in both or in one of the rows we from where the distance is calculated.
static Matrix	MatrixFunctions.getDistTanimotoInvReduced(Matrix ma1, Matrix ma2)
static void	Matrix.getEigenvector(Matrix A, int n, Matrix D, Matrix E)	Householder reduction according num rec 11.2.
double	Matrix.getEuclideanDistanceFastRows(int iRow, Matrix A, int iRowA)	Skipping the sqrt.
static java.util.List<java.awt.Point>	MatrixFunctions.getIndicesUniqueMaxColumnWise(Matrix maIn)
static java.util.List<java.awt.Point>	MatrixFunctions.getIndicesUniqueMaxRowWise(Matrix maIn)
static Matrix	MatrixFunctions.getKMeanClusters(Matrix ma, int k)	03.10.04 MvK
Matrix	Matrix.getMergeRows(Matrix ma)
static java.util.List<java.awt.Point>	MatrixFunctions.getMooreNeighborhood(java.awt.Point p, int r, Matrix ma)
static java.util.List<java.awt.Point>	MatrixFunctions.getMooreNeighborhood(java.awt.Point p, Matrix ma)	A square-shaped neighborhood that can be used to define a set of cells surrounding a given point.
static IntVec	MatrixFunctions.getNonZeroCols(Matrix X)
Matrix	Matrix.getNormalizedMatrix(Matrix maStandardDeviation)
static java.util.List<java.awt.Point>	MatrixFunctions.getPoints(Matrix ma)
static Matrix	MatrixFunctions.getRowMinUnique(Matrix ma)
static Matrix	MatrixFunctions.getScaled(Matrix ma)	Centers and divides by standard deviation.
static Matrix	MatrixFunctions.getScaledByFactor(Matrix ma, double fac)
static double	MatrixFunctions.getSumSquaredDiff(Matrix ma1, int row1, Matrix ma2, int row2)
static double	MatrixFunctions.getTotalSumSquaredDiffRowWise(Matrix ma1, Matrix ma2)
static Matrix	MatrixFunctions.inv(Matrix A)	Returns the inverse of a matrix.
static boolean	MatrixFunctions.isEqualCol(Matrix A, int colA, Matrix B, int colB, double thresh)
static boolean	MatrixFunctions.isSquare(Matrix A)
static boolean	MatrixFunctions.isSymmetric(Matrix A)
Matrix	Matrix.multCols(Matrix maMuiltiplicant)
Matrix	Matrix.multiply(boolean transA, boolean transB, Matrix ma)	Multiplication of two matrices.
double	Matrix.multiply(int row1, Matrix ma2, int row2)
Matrix	Matrix.multiply(Matrix ma)
Matrix	Matrix.multiplyValByVal(Matrix ma)	Value by value multiplication Matrices must have the same dimensions.
protected static Matrix	MatrixTests.pls(Matrix X, Matrix Y, java.lang.String sPatternHeaderX, int iNumPrincipalComponents, boolean bLogarithm, java.lang.String sFileDataSummaryOut)
Matrix	Matrix.plus(Matrix ma)
static Matrix	BoxCox.reTransform(Matrix A, BoxCox boxCox)
void	Matrix.set(Matrix ma)
Matrix	LUDecomposition.solve(Matrix B)	Solve A*X = B
static Matrix[]	MatrixFunctions.split(Matrix A, int row)	Splits the matrix row wise into two matrices.
static Matrix[]	MatrixFunctions.splitCol(Matrix A, int col)
Matrix	Matrix.subtract(Matrix ma)
Matrix	Matrix.subtractFromCols(Matrix maDivisor)
static Matrix	BoxCox.transform(Matrix A, BoxCox boxCox)
static double[]	MatrixFunctions.upperTriangle(Matrix maQuadratic)
static void	MatrixFunctions.vecvec2Matrix(java.util.Vector<java.util.Vector<java.lang.Double>> vecvec, Matrix ma)	Converts a vector of vectors into doubles, each vector results in a row in the matrix.
static void	MatrixFunctions.writeQuadraticSymmetricMatrixPairwise(Matrix ma, java.io.File fiTxt)

Constructors in com.actelion.research.calc with parameters of type Matrix

Constructor	Description
LUDecomposition(Matrix A)	LU Decomposition Structure to access L, U and piv.
Matrix(Matrix ma)

Uses of Matrix in com.actelion.research.calc.graph

Methods in com.actelion.research.calc.graph that return Matrix

Modifier and Type	Method	Description
Matrix	MinimumSpanningTree.getMST()

Constructors in com.actelion.research.calc.graph with parameters of type Matrix

Constructor	Description
MinimumSpanningTree(Matrix maAdjacency)

Uses of Matrix in com.actelion.research.calc.histogram

Methods in com.actelion.research.calc.histogram that return Matrix

Modifier and Type	Method	Description
Matrix	Histogram.getHistogram()
static Matrix	MatrixBasedHistogram.getHistogram(double[] arrValues, Matrix maHistogramBins)
static Matrix	MatrixBasedHistogram.getHistogram(float[][] ma, int col, Matrix maHistogramBins)
static Matrix	MatrixBasedHistogram.getHistogram(float[] ma, Matrix maHistogramBins)
static Matrix	MatrixBasedHistogram.getHistogram(Matrix maHistogramBins)
static Matrix	MatrixBasedHistogram.getHistogram(Matrix ma, int numBins)
static Matrix	MatrixBasedHistogram.getHistogram(Matrix ma, Matrix maHistogramBins)
static Matrix	MatrixBasedHistogram.getHistogramBins(double dMin, double dMax, int iNumBins)

Methods in com.actelion.research.calc.histogram with parameters of type Matrix

Modifier and Type	Method	Description
static double[]	MatrixBasedHistogram.getBordersMostFreqOccBin(Matrix maHistogram, int radius)	Gets the upper and lower limit of the most occupied bin.
static Histogram	MatrixBasedHistogram.getFromQuadraticMatrix(Matrix ma, double min, double max, int bins)
static Matrix	MatrixBasedHistogram.getHistogram(double[] arrValues, Matrix maHistogramBins)
static Matrix	MatrixBasedHistogram.getHistogram(float[][] ma, int col, Matrix maHistogramBins)
static Matrix	MatrixBasedHistogram.getHistogram(float[] ma, Matrix maHistogramBins)
static Matrix	MatrixBasedHistogram.getHistogram(Matrix maHistogramBins)
static Matrix	MatrixBasedHistogram.getHistogram(Matrix ma, int numBins)
static Matrix	MatrixBasedHistogram.getHistogram(Matrix ma, Matrix maHistogramBins)
static double	MatrixBasedHistogram.getMaxOccBin(Matrix maHist)
static double	MatrixBasedHistogram.getMinOccBin(Matrix maHist)
static java.lang.String	MatrixBasedHistogram.histogram2String(Matrix hist, int digits, int totalWidth)
static void	MatrixBasedHistogram.writeHistogram(java.lang.String sFile, Matrix hist, boolean bApppend, int digits, int totalWidth)

Uses of Matrix in com.actelion.research.calc.regression

Methods in com.actelion.research.calc.regression that return Matrix

Modifier and Type	Method	Description
Matrix	ICalculateYHat.calculateYHat(Matrix X)
Matrix	RegressionMethodContainer.calculateYHat(Matrix X)
Matrix	ICalculateModel.createModel(ModelXYIndex modelXYIndexTrain)
Matrix	RegressionMethodContainer.createModel(ModelXYIndex modelXYIndexTrain)

Methods in com.actelion.research.calc.regression with parameters of type Matrix

Modifier and Type	Method	Description
static ModelError	ModelError.calculateError(Matrix Y, Matrix YHat)	Calculates the absolute and the relative error.
static ModelError	ModelError.calculateError(Matrix Y, Matrix YHat, double threshold, boolean above)
Matrix	ICalculateYHat.calculateYHat(Matrix X)
Matrix	RegressionMethodContainer.calculateYHat(Matrix X)

Uses of Matrix in com.actelion.research.calc.regression.gaussianprocess

Methods in com.actelion.research.calc.regression.gaussianprocess that return Matrix

Modifier and Type	Method	Description
Matrix	GaussianProcessRegression.calculateYHat(Matrix X)
Matrix	GaussianProcessRegression.createModel(ModelXYIndex modelXYIndexTrain)

Methods in com.actelion.research.calc.regression.gaussianprocess with parameters of type Matrix

Modifier and Type	Method	Description
Matrix	GaussianProcessRegression.calculateYHat(Matrix X)

Uses of Matrix in com.actelion.research.calc.regression.knn

Methods in com.actelion.research.calc.regression.knn that return Matrix

Modifier and Type	Method	Description
Matrix	KNNRegression.calculateYHat(Matrix X)
Matrix	KNNRegression.createModel(ModelXYIndex modelXYIndexTrain)

Methods in com.actelion.research.calc.regression.knn with parameters of type Matrix

Modifier and Type	Method	Description
Matrix	KNNRegression.calculateYHat(Matrix X)

Uses of Matrix in com.actelion.research.calc.regression.linear.pls

Fields in com.actelion.research.calc.regression.linear.pls declared as Matrix

Modifier and Type	Field	Description
protected Matrix	SimPLS.B
protected Matrix	SimPLS.ES
protected Matrix	SimPLS.EX
protected Matrix	SimPLS.EY
protected Matrix	SimPLS.P
protected Matrix	SimPLS.Q
protected Matrix	SimPLS.R
protected Matrix	SimPLS.T
protected Matrix	SimPLS.U
protected Matrix	SimPLS.V

Methods in com.actelion.research.calc.regression.linear.pls that return Matrix

Modifier and Type	Method	Description
Matrix	PLSRegressionModelCalculator.calculateYHat(Matrix Xtest)	With centering of Xtest with Xtrain.
Matrix	PLSRegressionModelCalculator.calculateYHatWithoutDeCentering(Matrix Xtest)
Matrix	PLSRegressionModelCalculator.createModel(ModelXYIndex dataXYTrain)
Matrix	PLSRegressionModelCalculator.getB()
Matrix	RegressionModelCalculatorOptimumFactors.getB()
Matrix	SimPLS.getExplainedVarS()
Matrix	SimPLS.getExplainedVarX()
Matrix	SimPLS.getExplainedVarY()
Matrix	SimPLS.getP()
Matrix	SimPLS.getQ()
Matrix	SimPLS.getR()
Matrix	PLSRegressionModelCalculator.getT(Matrix XPreprocessed)
Matrix	SimPLS.getT()
Matrix	SimPLS.getT(Matrix XPreprocessed)
Matrix	SimPLS.getU()
Matrix	SimPLS.getV()
Matrix	PLSRegressionModelCalculator.getXvar()
Matrix	PLSRegressionModelCalculator.getYHat()
Matrix	RegressionModelCalculatorOptimumFactors.getYHat()
static Matrix	SimPLS.invLinReg_Yhat(Matrix BFromCentered, Matrix Xtest)
static Matrix	SimPLS.invLinReg_Yhat(Matrix B, Matrix Xtrain, Matrix Xtest, Matrix Ytrain)

Methods in com.actelion.research.calc.regression.linear.pls with parameters of type Matrix

Modifier and Type	Method	Description
ModelError	PLSRegressionModelCalculator.calculateModelErrorTest(Matrix Xtest, Matrix Ytest)
Matrix	PLSRegressionModelCalculator.calculateYHat(Matrix Xtest)	With centering of Xtest with Xtrain.
Matrix	PLSRegressionModelCalculator.calculateYHatWithoutDeCentering(Matrix Xtest)
Matrix	PLSRegressionModelCalculator.getT(Matrix XPreprocessed)
Matrix	SimPLS.getT(Matrix XPreprocessed)
static Matrix	SimPLS.invLinReg_Yhat(Matrix BFromCentered, Matrix Xtest)
static Matrix	SimPLS.invLinReg_Yhat(Matrix B, Matrix Xtrain, Matrix Xtest, Matrix Ytrain)
void	SimPLS.simPlsSave(Matrix Xtrain, Matrix Ytrain, int facmax)	No explained variance is calculated.
void	SimPLS.simPlsSave(Matrix Xtrain, Matrix Ytrain, Matrix Xtest, Matrix Ytest, int facmax)
void	SimPLS.simPlsSaveExplainedVariance(Matrix Xtrain, Matrix Ytrain, int facmax)	The explained variance is calculated.

Constructors in com.actelion.research.calc.regression.linear.pls with parameters of type Matrix

Constructor	Description
SimPLSLMOValidation(Matrix X, Matrix Y)	Deprecated.

Uses of Matrix in com.actelion.research.calc.regression.linear.pls.boxcox

Methods in com.actelion.research.calc.regression.linear.pls.boxcox that return Matrix

Modifier and Type	Method	Description
Matrix	PLSBoxCoxY.calculateYHat(Matrix Xtest)
Matrix	PLSBoxCoxY.createModel(ModelXYIndex modelXYIndexTrain)

Methods in com.actelion.research.calc.regression.linear.pls.boxcox with parameters of type Matrix

Modifier and Type	Method	Description
Matrix	PLSBoxCoxY.calculateYHat(Matrix Xtest)

Uses of Matrix in com.actelion.research.calc.regression.median

Methods in com.actelion.research.calc.regression.median that return Matrix

Modifier and Type	Method	Description
Matrix	MedianRegression.calculateYHat(Matrix X)
Matrix	MedianRegression.createModel(ModelXYIndex modelXYIndexTrain)

Methods in com.actelion.research.calc.regression.median with parameters of type Matrix

Modifier and Type	Method	Description
Matrix	MedianRegression.calculateYHat(Matrix X)

Uses of Matrix in com.actelion.research.calc.regression.neuralnetwork

Methods in com.actelion.research.calc.regression.neuralnetwork that return Matrix

Modifier and Type	Method	Description
Matrix	NeuralNetworkRegression.calculateYHat(Matrix X)
Matrix	NeuralNetworkRegression.createModel(ModelXYIndex modelXYIndexTrain)

Methods in com.actelion.research.calc.regression.neuralnetwork with parameters of type Matrix

Modifier and Type	Method	Description
Matrix	NeuralNetworkRegression.calculateYHat(Matrix X)

Uses of Matrix in com.actelion.research.calc.regression.randomforest

Methods in com.actelion.research.calc.regression.randomforest that return Matrix

Modifier and Type	Method	Description
Matrix	RandomForestRegression.calculateYHat(Matrix X)
Matrix	RandomForestRegression.createModel(ModelXYIndex modelXYIndexTrain)

Methods in com.actelion.research.calc.regression.randomforest with parameters of type Matrix

Modifier and Type	Method	Description
Matrix	RandomForestRegression.calculateYHat(Matrix X)

Uses of Matrix in com.actelion.research.calc.regression.svm

Methods in com.actelion.research.calc.regression.svm that return Matrix

Modifier and Type	Method	Description
Matrix	SVMRegression.calculateYHat(Matrix X)
Matrix	SVMRegression.createModel(ModelXYIndex modelXYIndex)

Methods in com.actelion.research.calc.regression.svm with parameters of type Matrix

Modifier and Type	Method	Description
Matrix	SVMRegression.calculateYHat(Matrix X)
static svm_node[][]	Matrix2SVMNodeConverter.convert(Matrix A)

Uses of Matrix in com.actelion.research.calc.statistics

Methods in com.actelion.research.calc.statistics that return Matrix

Modifier and Type	Method	Description
Matrix	StatisticsOverview.getHistogram()

Uses of Matrix in com.actelion.research.chem.alignment3d

Methods in com.actelion.research.chem.alignment3d with parameters of type Matrix

Modifier and Type	Method	Description
void	KabschAlignment.align(Coordinates trans1, Matrix rot, Coordinates trans2)

Uses of Matrix in com.actelion.research.chem.docking

Methods in com.actelion.research.chem.docking that return Matrix

Modifier and Type	Method	Description
static Matrix	DockingUtils.calculateMassCovarianceMatrix(Conformer conf)
static Matrix	DockingUtils.createInitialOrientation(Conformer conf)

Uses of Matrix in com.actelion.research.chem.phesa

Methods in com.actelion.research.chem.phesa that return Matrix

Modifier and Type	Method	Description
static Matrix	PheSAAlignment.createCanonicalOrientation(Conformer conf, MolecularVolume molGauss)
Matrix	Quaternion.getRotMatrix()
static Matrix	PheSAAlignment.preProcess(Conformer conf, MolecularVolume molVol)	Move COM of the molecular volume to the origin of the lab-frame and orient molecules so that their principal moments of inertia coincide with the 3 axis of the coordinate system

Methods in com.actelion.research.chem.phesa with parameters of type Matrix

Modifier and Type	Method	Description
static void	PheSAAlignment.rotateMol(Conformer conf, Matrix rotMat)
static void	PheSAAlignment.rotateMol(StereoMolecule mol, Matrix rotMat)
void	VolumeGaussian.rotateShift(Matrix rotMat)

Uses of Matrix in com.actelion.research.util.datamodel

Fields in com.actelion.research.util.datamodel declared as Matrix

Modifier and Type	Field	Description
Matrix	ModelXY.X
Matrix	ModelXY.Y

Methods in com.actelion.research.util.datamodel that return Matrix

Modifier and Type	Method	Description
Matrix	ModelXYCrossValidation.getXtest()	Deprecated.
Matrix	ModelXYCrossValidation.getXtrain()	Deprecated.
Matrix	ModelXYCrossValidation.getYtest()	Deprecated.
Matrix	ModelXYCrossValidation.getYtrain()	Deprecated.

Constructors in com.actelion.research.util.datamodel with parameters of type Matrix

Constructor	Description
ModelXY(Matrix x, Matrix y)
ModelXYIndex(Matrix x, Matrix y)

Uses of Matrix in com.actelion.research.util.datamodel.table

Methods in com.actelion.research.util.datamodel.table with parameters of type Matrix

Modifier and Type	Method	Description
void	TableModelString.set(Matrix m, int digits)