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.chem.phesa
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.
Matrix	Matrix.correlation()	Generate a correlation matrix, each column contains values of a pulling.
Matrix	Matrix.covariance()	Generate a covariance matrix, each column contains values of a pulling.
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.
Matrix	Matrix.getFlipped()	Opposite direction to transpose.
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	Matrix.getRND(int rows, int cols)
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()
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.
Matrix	Matrix.plus(Matrix ma)
Matrix	Matrix.pow(double exp)
static Matrix	Matrix.readSerialized(java.io.File fiIn)
Matrix	Matrix.removeCol(int col2Remove)
Matrix	Matrix.row2Matrix(int row, int len)
Matrix	LUDecomposition.solve(Matrix B)	Solve A*X = B
Matrix	Matrix.subtract(double val)
Matrix	Matrix.subtract(Matrix ma)
Matrix	Matrix.subtractFromCols(Matrix maDivisor)
Matrix	Matrix.toRow()

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)
void	Matrix.assignCol(int iCol, Matrix ma)
void	Matrix.assignCol(int iCol, Matrix ma, int iColMa)
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)
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 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.
Matrix	Matrix.getMergeRows(Matrix ma)
Matrix	Matrix.getNormalizedMatrix(Matrix maStandardDeviation)
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.
Matrix	Matrix.plus(Matrix ma)
void	Matrix.set(Matrix ma)
Matrix	LUDecomposition.solve(Matrix B)	Solve A*X = B
Matrix	Matrix.subtract(Matrix ma)
Matrix	Matrix.subtractFromCols(Matrix maDivisor)

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.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()	convert Quaternion to a rotation matrix
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.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)