Package ubic.basecode.dataStructure.matrix

Class CompressedSparseDoubleMatrix<R,C>

java.lang.Object

ubic.basecode.dataStructure.matrix.AbstractMatrix<R,C,Double>

ubic.basecode.dataStructure.matrix.DoubleMatrix<R,C>

ubic.basecode.dataStructure.matrix.CompressedSparseDoubleMatrix<R,C>

All Implemented Interfaces:

Serializable, Matrix2D<R,C,Double>, PrimitiveMatrix<R,C,Double>

public class CompressedSparseDoubleMatrix<R,C>
extends DoubleMatrix<R,C>

Supports sparse matrices (where sparse means most values are zero, not that they are missing).

Author:

xwan

See Also:

for how this is implemented under the hood., Serialized Form

Field Summary

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

MAX_ROWS_TO_PRINT

Constructor Summary

Constructors

Constructor	Description
CompressedSparseDoubleMatrix(double[][] mat)
CompressedSparseDoubleMatrix(int rows, int cols)

Method Summary

Modifier and Type	Method	Description
double[][]	asArray()
int	cardinality()
int	columns()	Get the number of columns the matrix has.
DoubleMatrix<R,C>	copy()	Create a deep copy of this
double	get(int row, int column)
Double[]	getColObj(int col)
DoubleMatrix<R,C>	getColRange(int startCol, int endCol)
double[]	getColumn(int col)
Double	getObject(int row, int col)
double[]	getRow(int row)	Return a reference to a specific row.
cern.colt.list.DoubleArrayList	getRowArrayList(int i)
double[]	getRowByName(R s)
Double[]	getRowObj(int row)
DoubleMatrix<R,C>	getRowRange(int startRow, int endRow)
boolean	isMissing(int i, int j)	Check if the value at a given index is missing.
int	rows()	Get the number of rows the matrix has
void	set(int row, int column, Double value)
int	size()
DoubleMatrix<R,C>	subsetColumns(List<C> columns)	Create a copy of this matrix with only the selected columns, in the selected order.
DoubleMatrix<R,C>	subsetRows(List<R> rowNames)	Create a copy of this matrix with only the selected rows, in the selected order.
DoubleMatrix<C,R>	transpose()
void	trimToSize()
cern.colt.matrix.DoubleMatrix1D	viewColumn(int column)
cern.colt.matrix.DoubleMatrix1D	viewRow(int row)

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

getByKeys, getColumnByName, getEntry, getRawMatrix, setByKeys, sortByColumnAbsoluteValues, toString

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

addColumnName, addRowName, asDoubles, assign, checkColRange, checkRowRange, containsColumnName, containsRowName, getColIndexByName, getColName, getColNames, getRowIndexByName, getRowName, getRowNameMapIterator, getRowNames, hasColNames, hasMissingValues, hasRow, hasRowNames, numMissing, setColumnName, setColumnNames, setRowName, setRowNames

Methods inherited from class java.lang.Object

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

Methods inherited from interface ubic.basecode.dataStructure.matrix.Matrix2D

addColumnName, asDoubles, assign, containsColumnName, containsRowName, getColIndexByName, getColName, getColNames, getRowIndexByName, getRowName, getRowNameMapIterator, getRowNames, hasColNames, hasRow, hasRowNames, numMissing, setColumnName, setColumnNames, setRowName, setRowNames

Constructor Detail

CompressedSparseDoubleMatrix

public CompressedSparseDoubleMatrix(double[][] mat)

Parameters:

mat -

CompressedSparseDoubleMatrix

public CompressedSparseDoubleMatrix(int rows,
                                    int cols)

Parameters:

rows - int

cols - int

Method Detail

asArray

public double[][] asArray()

Specified by:

asArray in class DoubleMatrix<R,C>

Returns:

double[][]

cardinality

public int cardinality()

Returns:

columns

public int columns()

Description copied from interface: Matrix2D

Get the number of columns the matrix has.

Returns:

copy

public DoubleMatrix<R,C> copy()

Description copied from class: DoubleMatrix

Create a deep copy of this

Specified by:

copy in class DoubleMatrix<R,C>

Returns:

a deep copy of this

get

public double get(int row,
                  int column)

Specified by:

get in class DoubleMatrix<R,C>

Parameters:

row -

column -

Returns:

getColObj

public Double[] getColObj(int col)

Returns:

getColRange

public DoubleMatrix<R,C> getColRange(int startCol,
                                           int endCol)

Specified by:

getColRange in class DoubleMatrix<R,C>

Parameters:

startCol - inclusive, numbered from zero

endCol - inclusive, numbered from zero

Returns:

new matrix with just the requested range of columns from this

getColumn

public double[] getColumn(int col)

Specified by:

getColumn in class DoubleMatrix<R,C>

getObject

public Double getObject(int row,
                        int col)

Returns:

getRow

public double[] getRow(int row)

Return a reference to a specific row.

Specified by:

getRow in class DoubleMatrix<R,C>

Parameters:

row - int

Returns:

double[]

getRowArrayList

public cern.colt.list.DoubleArrayList getRowArrayList(int i)

Specified by:

getRowArrayList in class DoubleMatrix<R,C>

getRowByName

public double[] getRowByName(R s)

Overrides:

getRowByName in class DoubleMatrix<R,C>

Parameters:

s - String

Returns:

double[]

getRowObj

public Double[] getRowObj(int row)

Returns:

getRowRange

public DoubleMatrix<R,C> getRowRange(int startRow,
                                           int endRow)

Specified by:

getRowRange in class DoubleMatrix<R,C>

Parameters:

startRow - inclusive, numbered from zero

endRow - inclusive

Returns:

isMissing

public boolean isMissing(int i,
                         int j)

Description copied from interface: Matrix2D

Check if the value at a given index is missing.

Parameters:

i - row

j - column

Returns:

true if the value is missing, false otherwise.

rows

public int rows()

Description copied from interface: Matrix2D

Get the number of rows the matrix has

Returns:

int

set

public void set(int row,
                int column,
                Double value)

Parameters:

row -

column -

value -

size

public int size()

Specified by:

size in class AbstractMatrix<R,C,Double>

Returns:

subsetColumns

public DoubleMatrix<R,C> subsetColumns(List<C> columns)

Description copied from class: DoubleMatrix

Create a copy of this matrix with only the selected columns, in the selected order.

Specified by:

subsetColumns in class DoubleMatrix<R,C>

Returns:

subsetRows

public DoubleMatrix<R,C> subsetRows(List<R> rowNames)

Description copied from class: DoubleMatrix

Create a copy of this matrix with only the selected rows, in the selected order.

Specified by:

subsetRows in class DoubleMatrix<R,C>

Returns:

transpose

public DoubleMatrix<C,R> transpose()

Specified by:

transpose in class DoubleMatrix<R,C>

trimToSize

public void trimToSize()

viewColumn

public cern.colt.matrix.DoubleMatrix1D viewColumn(int column)

Specified by:

viewColumn in class DoubleMatrix<R,C>

Parameters:

column -

Returns:

viewRow

public cern.colt.matrix.DoubleMatrix1D viewRow(int row)

Specified by:

viewRow in class DoubleMatrix<R,C>

Parameters:

row -

Returns: