Package ubic.basecode.dataStructure.matrix

Class DenseDouble3dMatrix<R,C,S>

java.lang.Object

ubic.basecode.dataStructure.matrix.AbstractMatrix3D<R,C,S,Double>

ubic.basecode.dataStructure.matrix.DoubleMatrix3D<R,C,S>

ubic.basecode.dataStructure.matrix.DenseDouble3dMatrix<R,C,S>

All Implemented Interfaces:

Matrix3D<R,C,S,Double>

public class DenseDouble3dMatrix<R,C,S>
extends DoubleMatrix3D<R,C,S>

Author:

Xwan

Field Summary

Fields inherited from class ubic.basecode.dataStructure.matrix.DoubleMatrix3D

MAX_ROWS_TO_PRINT, MAX_SLICES_TO_PRINT

Fields inherited from class ubic.basecode.dataStructure.matrix.AbstractMatrix3D

colMap, colNames, rowMap, rowNames, sliceMap, sliceNames

Constructor Summary

Constructors

Constructor	Description
DenseDouble3dMatrix(double[][][] data)
DenseDouble3dMatrix(double[][][] data, List<S> sliceNames, List<R> rowNames, List<C> colNames)
DenseDouble3dMatrix(int slices, int rows, int columns)
DenseDouble3dMatrix(List<S> sliceNames, List<R> rowNames, List<C> colNames)

Method Summary

Modifier and Type	Method	Description
int	columns()	Get the number of columns the matrix has.
double	get(int i, int j, int k)
Double[][]	getColObj(int col)
double[][]	getColumn(int col)
Double	getObject(int slice, int row, int col)
double[][]	getRow(int row)
Double[][]	getRowObj(int row)
double[][]	getSlice(int slice)
Double[][]	getSliceObj(int slice)
boolean	isMissing(int slice, int row, int col)	Check if the value at a given index is missing.
int	numMissing()	Return the number of missing values in the matrix.
int	rows()	Get the number of rows the matrix has
void	set(int slice, int row, int col, double val)
void	setQuick(int slice, int row, int column, double c)
int	slices()
cern.colt.matrix.DoubleMatrix2D	viewColumn(int column)
cern.colt.matrix.DoubleMatrix2D	viewRow(int row)
cern.colt.matrix.DoubleMatrix2D	viewSlice(int slice)

Methods inherited from class ubic.basecode.dataStructure.matrix.DoubleMatrix3D

getColumnByName, getRowByName, getSliceByName, toString

Methods inherited from class ubic.basecode.dataStructure.matrix.AbstractMatrix3D

addColumnName, addRowName, addSliceName, containsColumnName, containsRowName, containsSliceName, getColIndexByName, getColName, getColNameIterator, getColNames, getRowIndexByName, getRowName, getRowNameIterator, getRowNames, getSliceIndexByName, getSliceName, getSliceNameIterator, getSliceNames, hasColNames, hasRow, hasRowNames, hasSliceNames, setColumnNames, setRowNames, setSliceNames

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

DenseDouble3dMatrix

public DenseDouble3dMatrix(double[][][] data)

DenseDouble3dMatrix

public DenseDouble3dMatrix(double[][][] data,
                           List<S> sliceNames,
                           List<R> rowNames,
                           List<C> colNames)

DenseDouble3dMatrix

public DenseDouble3dMatrix(int slices,
                           int rows,
                           int columns)

DenseDouble3dMatrix

public DenseDouble3dMatrix(List<S> sliceNames,
                           List<R> rowNames,
                           List<C> colNames)

Method Detail

columns

public int columns()

Description copied from interface: Matrix3D

Get the number of columns the matrix has.

Specified by:

columns in interface Matrix3D<R,C,S,Double>

Specified by:

columns in class AbstractMatrix3D<R,C,S,Double>

Returns:

int

get

public double get(int i,
                  int j,
                  int k)

Specified by:

get in class DoubleMatrix3D<R,C,S>

getColObj

public Double[][] getColObj(int col)

Specified by:

getColObj in class DoubleMatrix3D<R,C,S>

getColumn

public double[][] getColumn(int col)

Specified by:

getColumn in class DoubleMatrix3D<R,C,S>

getObject

public Double getObject(int slice,
                        int row,
                        int col)

getRow

public double[][] getRow(int row)

Specified by:

getRow in class DoubleMatrix3D<R,C,S>

getRowObj

public Double[][] getRowObj(int row)

Specified by:

getRowObj in class DoubleMatrix3D<R,C,S>

getSlice

public double[][] getSlice(int slice)

Specified by:

getSlice in class DoubleMatrix3D<R,C,S>

getSliceObj

public Double[][] getSliceObj(int slice)

Specified by:

getSliceObj in class DoubleMatrix3D<R,C,S>

isMissing

public boolean isMissing(int slice,
                         int row,
                         int col)

Description copied from interface: Matrix3D

Check if the value at a given index is missing.

Specified by:

isMissing in interface Matrix3D<R,C,S,Double>

Specified by:

isMissing in class DoubleMatrix3D<R,C,S>

Returns:

true if the value is missing, false otherwise.

numMissing

public int numMissing()

Description copied from interface: Matrix3D

Return the number of missing values in the matrix.

Specified by:

numMissing in interface Matrix3D<R,C,S,Double>

Specified by:

numMissing in class AbstractMatrix3D<R,C,S,Double>

Returns:

number missing

rows

public int rows()

Description copied from interface: Matrix3D

Get the number of rows the matrix has

Specified by:

rows in interface Matrix3D<R,C,S,Double>

Specified by:

rows in class DoubleMatrix3D<R,C,S>

Returns:

int

set

public void set(int slice,
                int row,
                int col,
                double val)

Specified by:

set in class DoubleMatrix3D<R,C,S>

setQuick

public void setQuick(int slice,
                     int row,
                     int column,
                     double c)

Specified by:

setQuick in class DoubleMatrix3D<R,C,S>

slices

public int slices()

Specified by:

slices in interface Matrix3D<R,C,S,Double>

Specified by:

slices in class DoubleMatrix3D<R,C,S>

viewColumn

public cern.colt.matrix.DoubleMatrix2D viewColumn(int column)

Specified by:

viewColumn in class DoubleMatrix3D<R,C,S>

viewRow

public cern.colt.matrix.DoubleMatrix2D viewRow(int row)

Specified by:

viewRow in class DoubleMatrix3D<R,C,S>

Returns:

viewSlice

public cern.colt.matrix.DoubleMatrix2D viewSlice(int slice)

Specified by:

viewSlice in class DoubleMatrix3D<R,C,S>