net.maizegenetics.matrixalgebra.Matrix

Class BlasDoubleMatrix

net.maizegenetics.matrixalgebra.Matrix.BlasDoubleMatrix

All Implemented Interfaces:

DoubleMatrix

public class BlasDoubleMatrix
implements DoubleMatrix

Field Detail

myMatrix

protected kotlin.Array[] myMatrix

nrows

protected int nrows

ncols

protected int ncols

size

protected int size

Constructor Detail

BlasDoubleMatrix

public BlasDoubleMatrix()

BlasDoubleMatrix

public BlasDoubleMatrix(kotlin.Array[] values)

BlasDoubleMatrix

public BlasDoubleMatrix(DistanceMatrix values)

BlasDoubleMatrix

public BlasDoubleMatrix(int nrows,
                        int ncols)

Method Detail

multMatrices

public static void multMatrices(kotlin.Array[] A,
                                int nrowsA,
                                int ncolsA,
                                kotlin.Array[] B,
                                int nrowsB,
                                int ncolsB,
                                kotlin.Array[] C,
                                double alpha,
                                double beta,
                                boolean transA,
                                boolean transB)

solveLSdgelsd

public static int solveLSdgelsd(kotlin.Array[] A,
                                int Arows,
                                int Acols,
                                kotlin.Array[] B,
                                int Bcols,
                                double rcond,
                                kotlin.Array[] rank)

solveLSdgelsy

public static int solveLSdgelsy(kotlin.Array[] A,
                                int Arows,
                                int Acols,
                                kotlin.Array[] B,
                                int Bcols,
                                double rcond,
                                kotlin.Array[] rank)

singularValueDecompositionDgesvd

public static int singularValueDecompositionDgesvd(char jobu,
                                                   char jobvt,
                                                   int m,
                                                   int n,
                                                   kotlin.Array[] A,
                                                   int lda,
                                                   kotlin.Array[] S,
                                                   kotlin.Array[] U,
                                                   int ldu,
                                                   kotlin.Array[] VT,
                                                   int ldvt)

singularValueDecompositionDgesdd

public static int singularValueDecompositionDgesdd(char jobz,
                                                   int m,
                                                   int n,
                                                   kotlin.Array[] A,
                                                   int lda,
                                                   kotlin.Array[] S,
                                                   kotlin.Array[] U,
                                                   int ldu,
                                                   kotlin.Array[] VT,
                                                   int ldvt)

eigenValueSymmetricDecomposition

public static int eigenValueSymmetricDecomposition(int order,
                                                   kotlin.Array[] A,
                                                   kotlin.Array[] eigval,
                                                   kotlin.Array[] eigvector)

getInstance

public static BlasDoubleMatrix getInstance(int nrows,
                                           int ncols,
                                           kotlin.Array[] values,
                                           boolean columnMajor)

getInstance

public static BlasDoubleMatrix getInstance(int nrows,
                                           int ncols,
                                           double dblValue)

get

public double get(int row,
                  int col)

getChecked

public double getChecked(int row,
                         int col)

set

public void set(int row,
                int col,
                double value)

setChecked

public void setChecked(int row,
                       int col,
                       double value)

transpose

public DoubleMatrix transpose()

transposeInPlace

public void transposeInPlace()

mult

public DoubleMatrix mult(DoubleMatrix dm,
                         boolean transpose,
                         boolean transposedm)

multadd

public DoubleMatrix multadd(DoubleMatrix A,
                            DoubleMatrix B,
                            double alpha,
                            double beta,
                            boolean transpose,
                            boolean transposeA)

mult

public DoubleMatrix mult(DoubleMatrix dm)

crossproduct

public DoubleMatrix crossproduct()

crossproduct

public DoubleMatrix crossproduct(DoubleMatrix dm)

tcrossproduct

public DoubleMatrix tcrossproduct()

tcrossproduct

public DoubleMatrix tcrossproduct(DoubleMatrix dm)

concatenate

public DoubleMatrix concatenate(DoubleMatrix dm,
                                boolean rows)

inverse

public DoubleMatrix inverse()

invert

public boolean invert()

generalizedInverse

public DoubleMatrix generalizedInverse()

generalizedInverseWithRank

public DoubleMatrix generalizedInverseWithRank(kotlin.Array[] rank)

solve

public DoubleMatrix solve(DoubleMatrix Y)

numberOfRows

public int numberOfRows()

numberOfColumns

public int numberOfColumns()

row

public DoubleMatrix row(int i)

column

public DoubleMatrix column(int j)

getXtXGM

public DoubleMatrix[] getXtXGM()

copy

public DoubleMatrix copy()

getEigenvalueDecomposition

public EigenvalueDecomposition getEigenvalueDecomposition()

getSingularValueDecomposition

public SingularValueDecomposition getSingularValueDecomposition()

getQRDecomposition

public QRDecomposition getQRDecomposition()

minus

public DoubleMatrix minus(DoubleMatrix dm)

minusEquals

public void minusEquals(DoubleMatrix dm)

plus

public DoubleMatrix plus(DoubleMatrix dm)

plusEquals

public void plusEquals(DoubleMatrix dm)

scalarAdd

public DoubleMatrix scalarAdd(double s)

scalarAddEquals

public void scalarAddEquals(double s)

scalarMult

public DoubleMatrix scalarMult(double s)

scalarMultEquals

public void scalarMultEquals(double s)

getSelection

public DoubleMatrix getSelection(kotlin.Array[] rows,
                                 kotlin.Array[] columns)

getSelectionFromDoubleArray

public static kotlin.Array[] getSelectionFromDoubleArray(kotlin.Array[] original,
                                                         int nrows,
                                                         int ncols,
                                                         kotlin.Array[] rows,
                                                         kotlin.Array[] columns)

Parameters:

original - the original matrix as a one dimensional double array in column-major order

nrows - the number of rows in the original matrix

ncols - the number of columns in the original matrix

rows - an int array of the selected rows

columns - an int array of the selected columns

Returns:

org.jetbrains.dokka.NodeRenderContent@1f16a489: the resulting double array, column-major order

rowSum

public double rowSum(int row)

columnSum

public double columnSum(int column)

columnRank

public int columnRank()

getMatrix

public kotlin.Array[] getMatrix()

getMatrixCopy

public kotlin.Array[] getMatrixCopy()

getSize

public int getSize()

getDiagonalMatrix

public static BlasDoubleMatrix getDiagonalMatrix(kotlin.Array[] diag)

getIdentityMatrix

public static BlasDoubleMatrix getIdentityMatrix(int dim)

compose

public static DoubleMatrix compose(DoubleMatrix[] input)

to1DArray

public kotlin.Array[] to1DArray()

toArray

public kotlin.Array[] toArray()

toString

public java.lang.String toString()