Package ubic.basecode.dataStructure.matrix

Class SparseRaggedDoubleMatrix<R,C>

java.lang.Object

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

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

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

All Implemented Interfaces:

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

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

A sparse matrix class where the rows are ragged and compressed.

Author:

pavlidis

See Also:

Serialized Form

Field Summary

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

MAX_ROWS_TO_PRINT

Constructor Summary

Constructors

Constructor	Description
SparseRaggedDoubleMatrix()

Method Summary

Modifier and Type	Method	Description
void	addRow(R name, cern.colt.list.IntArrayList indexes, cern.colt.list.DoubleArrayList values)
void	addRow(R name, cern.colt.matrix.DoubleMatrix1D matrix1D)
double[][]	asArray()
int	columns()	Returns the size of the widest row.
DoubleMatrix<R,C>	copy()	Create a deep copy of this
double	get(int i, int j)
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 i)
cern.colt.list.DoubleArrayList	getRowArrayList(int row)	This gives just the list of values in the row - make sure this is what you want.
Double[]	getRowObj(int i)
DoubleMatrix<R,C>	getRowRange(int startRow, int endRow)
boolean	isMissing(int i, int j)	(non-Javadoc) Note that in a sparse matrix, zero values are considered "missing"!
int	rows()	Get the number of rows the matrix has
void	set(int i, int j, Double d)
int	size()
DoubleMatrix<R,C>	subsetColumns(List<C> c)	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()
cern.colt.matrix.DoubleMatrix1D	viewColumn(int column)
cern.colt.matrix.DoubleMatrix1D	viewRow(int i)

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

getByKeys, getColumnByName, getEntry, getRawMatrix, getRowByName, 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

SparseRaggedDoubleMatrix

public SparseRaggedDoubleMatrix()

Method Detail

addRow

public void addRow(R name,
                   cern.colt.matrix.DoubleMatrix1D matrix1D)

Parameters:

matrix1D -

addRow

public void addRow(R name,
                   cern.colt.list.IntArrayList indexes,
                   cern.colt.list.DoubleArrayList values)

Parameters:

name -

indexes -

values -

asArray

public double[][] asArray()

Specified by:

asArray in class DoubleMatrix<R,C>

Returns:

double[][]

columns

public int columns()

Returns the size of the widest row.

Returns:

int

See Also:

basecode.dataStructure.matrix.Matrix2D#columns()

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 i,
                  int j)

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 i)

Specified by:

getRow in class DoubleMatrix<R,C>

getRowArrayList

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

This gives just the list of values in the row - make sure this is what you want. It does not include the zero values.

Specified by:

getRowArrayList in class DoubleMatrix<R,C>

Parameters:

row -

Returns:

getRowObj

public Double[] getRowObj(int i)

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)

(non-Javadoc) Note that in a sparse matrix, zero values are considered "missing"!

Parameters:

i - row

j - column

Returns:

true if the value is missing, false otherwise.

See Also:

basecode.dataStructure.matrix.Matrix2D#isMissing(int, int)

rows

public int rows()

Description copied from interface: Matrix2D

Get the number of rows the matrix has

Returns:

int

set

public void set(int i,
                int j,
                Double d)

size

public int size()

Specified by:

size in class AbstractMatrix<R,C,Double>

subsetColumns

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

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>

viewColumn

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

Specified by:

viewColumn in class DoubleMatrix<R,C>

viewRow

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

Specified by:

viewRow in class DoubleMatrix<R,C>

Returns: