net.maizegenetics.matrixalgebra.Matrix

Interface DoubleMatrix

All Known Implementing Classes:

BlasDoubleMatrix, ColtDoubleMatrix, EJMLDoubleMatrix

public DoubleMatrix

Method Detail

get

double get(int row,
           int col)

The row and column coordinates are not checked to make sure they are in the matrix

Parameters:

row - the zero-based row index

col - the zero-based column index

Returns:

org.jetbrains.dokka.NodeRenderContent@1036a50b: the value at row, col

getChecked

double getChecked(int row,
                  int col)

The row and column coordinates are checked to make sure they fall in the matrix. If not an error is generated.

Parameters:

row - the zero-based row index

col - the zero-based column index

Returns:

org.jetbrains.dokka.NodeRenderContent@1cd656d9: the value at row, col

set

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

Sets the matrix value at row, col. The coordinates are not checked to make sure they fall in the matrix.

Parameters:

row - the zero-based row index

col - the zero-based column index

value - the value to be set at row, col

setChecked

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

Sets the matrix value at row, col. The coordinates are checked to make sure they fall in the matrix.

Parameters:

row - the zero-based row index

col - the zero-based column index

value - the value to be set at row, col

transpose

DoubleMatrix transpose()

Returns:

org.jetbrains.dokka.NodeRenderContent@cb8d444: the transpose of this matrix

mult

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

Multiply this matrix times another.

Parameters:

dm - a double matrix

transpose - if true, this matrix will be transposed before multiplying

transposedm - if true, dm will be transposed before multiplying

multadd

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

Using this function for combining multiplication and addition allows the implementing library to optimize the operations. Performs: alpha * XA + beta*B, where X is this matrix

Parameters:

A - the matrix to be multiplied

B - the matrix to be added, can be null

alpha - scalar multiplier for A

beta - scalar multiplier for B

transpose - if true, X is transposed

transposeA - if true, A is transposed

Returns:

org.jetbrains.dokka.NodeRenderContent@3a900ce4: the matrix resulting from the specified operations

mult

DoubleMatrix mult(DoubleMatrix dm)

Parameters:

dm - a double matrix

Returns:

org.jetbrains.dokka.NodeRenderContent@1fabf840: this matrix times dm

crossproduct

DoubleMatrix crossproduct()

Returns:

org.jetbrains.dokka.NodeRenderContent@31e515f2: X'X, where X is this matrix

crossproduct

DoubleMatrix crossproduct(DoubleMatrix dm)

Parameters:

dm - a double matrix

Returns:

org.jetbrains.dokka.NodeRenderContent@7b35ed7e: X'dm, where X is this matrix

tcrossproduct

DoubleMatrix tcrossproduct()

Returns:

org.jetbrains.dokka.NodeRenderContent@41f839d0: XX', where X is this matrix

tcrossproduct

DoubleMatrix tcrossproduct(DoubleMatrix dm)

Parameters:

dm - a double matrix

Returns:

org.jetbrains.dokka.NodeRenderContent@151a057: Xdm', where X is this matrix

concatenate

DoubleMatrix concatenate(DoubleMatrix dm,
                         boolean rows)

Parameters:

dm - a DoubleMatrix

rows - true if rows are to concatenated, false if columns are to be concatenated

Returns:

org.jetbrains.dokka.NodeRenderContent@18827f0a: returns X with dm appended, where X is this matrix

inverse

DoubleMatrix inverse()

This returns the inverse or a square matrix, without modifying the original matrix.

Returns:

org.jetbrains.dokka.NodeRenderContent@4c083f79: the inverse of a square matrix if it is non-singular, null otherwise

invert

void invert()

This returns the inverse or a square matrix, replacing the original with the inverse.

generalizedInverse

DoubleMatrix generalizedInverse()

Returns:

org.jetbrains.dokka.NodeRenderContent@4cbea991: the generalized inverse of a square matrix

generalizedInverseWithRank

DoubleMatrix generalizedInverseWithRank(kotlin.Array[] rank)

inverts the matrix and returns the rank as the first element in rank[]. The original matrix is not modified.

Returns:

org.jetbrains.dokka.NodeRenderContent@40e1eb49: a generalized inverse of this matrix

solve

DoubleMatrix solve(DoubleMatrix Y)

Parameters:

Y - a DoubleMatrix

Returns:

org.jetbrains.dokka.NodeRenderContent@4b90b670: the least squares solutions for B, where XB = Y and X is this matrix

numberOfRows

int numberOfRows()

Returns:

org.jetbrains.dokka.NodeRenderContent@46eebb8c: the number of rows in this matrix

numberOfColumns

int numberOfColumns()

Returns:

org.jetbrains.dokka.NodeRenderContent@7fa570e1: the number of columns in this matrix

row

DoubleMatrix row(int i)

Parameters:

i - a row index

Returns:

org.jetbrains.dokka.NodeRenderContent@305167ff: the ith row of this matrix as a column vector

column

DoubleMatrix column(int j)

Parameters:

j - a column index

Returns:

org.jetbrains.dokka.NodeRenderContent@7ebc74b3: the jth column of this matrix as a column vector

getXtXGM

DoubleMatrix[] getXtXGM()

Returns:

org.jetbrains.dokka.NodeRenderContent@4d3d8233: an array of three DoubleMatrix's. Where X is this matrix, the first is X'X, the second is the inverse of X'X, and the third is I - XGX'.

copy

DoubleMatrix copy()

Returns:

org.jetbrains.dokka.NodeRenderContent@194bd10d: a copy of this matrix

getEigenvalueDecomposition

EigenvalueDecomposition getEigenvalueDecomposition()

Returns:

org.jetbrains.dokka.NodeRenderContent@229e2344: an Eigenvalue Decomposition of this matrix

getSingularValueDecomposition

SingularValueDecomposition getSingularValueDecomposition()

Returns:

org.jetbrains.dokka.NodeRenderContent@3f9ac248: a Singular Value Decomposition of this matrix

getQRDecomposition

QRDecomposition getQRDecomposition()

Returns:

org.jetbrains.dokka.NodeRenderContent@1e17e392: a QR Decomposition of this matrix

minus

DoubleMatrix minus(DoubleMatrix dm)

Parameters:

dm - a DoubleMatrix

Returns:

org.jetbrains.dokka.NodeRenderContent@59939ae4: a new DoubleMatrix created by subtracting dm from this matrix

minusEquals

void minusEquals(DoubleMatrix dm)

This function subtracts dm, modifying the original matrix

Parameters:

dm - a DoubleMatrix

plus

DoubleMatrix plus(DoubleMatrix dm)

Parameters:

dm - a DoubleMatrix

Returns:

org.jetbrains.dokka.NodeRenderContent@a441691: a new DoubleMatrix created by adding dm to this matrix

plusEquals

void plusEquals(DoubleMatrix dm)

This function adds dm, modifying the original matrix

Parameters:

dm - a DoubleMatrix

scalarAdd

DoubleMatrix scalarAdd(double s)

Adds a scalar to this matrix and returns a new matrix. The original is not modified.

Parameters:

s - a scalar

Returns:

org.jetbrains.dokka.NodeRenderContent@63a51d13: the sum of this matrix and a scalar s

scalarAddEquals

void scalarAddEquals(double s)

Adds a scalar s to this matrix, replacing the original matrix with the result.

Parameters:

s - a scalar

scalarMult

DoubleMatrix scalarMult(double s)

Multiplies this matrix times a scalar and returns a new matrix. The original is not modified.

Parameters:

s - a scalar

Returns:

org.jetbrains.dokka.NodeRenderContent@420f6986: the product of this matrix and a scalar s

scalarMultEquals

void scalarMultEquals(double s)

Multiplies this matrix times a scalar s, replacing the original matrix with the result.

Parameters:

s - a scalar

getSelection

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

Creates a new matrix consisting or the rows and columns of this matrix in the order specified. If rows or columns is null then all rows or columns, respectively, will be included

Parameters:

rows - the rows to be included in the new matrix

columns - the columns to be included in the new matrix

Returns:

org.jetbrains.dokka.NodeRenderContent@78e8f99: a new matrix consisting of the specified rows and columns

rowSum

double rowSum(int row)

Parameters:

row -

Returns:

org.jetbrains.dokka.NodeRenderContent@2d54e167: the sum of elements in this row

columnSum

double columnSum(int column)

Parameters:

column -

Returns:

org.jetbrains.dokka.NodeRenderContent@66522c5b: the sum of elements in this column

columnRank

int columnRank()

Returns:

org.jetbrains.dokka.NodeRenderContent@5fa83a4e: the column rank of this matrix

to1DArray

kotlin.Array[] to1DArray()

Returns:

org.jetbrains.dokka.NodeRenderContent@2c299465: the matrix as a one dimensional, row-major primitive array

toArray

kotlin.Array[] toArray()

Returns:

org.jetbrains.dokka.NodeRenderContent@26fc075e: the matrix as a primitive array