Package ubic.basecode.dataStructure.matrix

Class RCDoubleMatrix1D

java.lang.Object

cern.colt.PersistentObject

cern.colt.matrix.impl.AbstractMatrix

cern.colt.matrix.impl.AbstractMatrix1D

cern.colt.matrix.DoubleMatrix1D

ubic.basecode.dataStructure.matrix.RCDoubleMatrix1D

All Implemented Interfaces:

Serializable, Cloneable

public class RCDoubleMatrix1D
extends DoubleMatrix1D

A row-compressed 1D matrix. The only deviation from the contract of DoubleMatrix1D is in apply(), which only operates on the non-empty (0) elements. This implementation has a highly optimized dot product computer. If you need to compute the dot product of a RCDoubleMatrix1D with another DoubleMatrix1D, call zDotProduct on this, not on the other. This is because getQuick() and setQuick() are not very fast for this.

Author:

pavlidis

See Also:

• Serialized Form

Field Summary

Fields

Modifier and Type	Field	Description
protected IntArrayList	indexes
protected DoubleArrayList	values

Fields inherited from class cern.colt.matrix.impl.AbstractMatrix1D

size, stride, zero

Fields inherited from class cern.colt.matrix.impl.AbstractMatrix

isNoView

Constructor Summary

Constructors

Constructor	Description
RCDoubleMatrix1D(double[] values)
RCDoubleMatrix1D(int length)
RCDoubleMatrix1D(IntArrayList indexes, DoubleArrayList values)

Method Summary

Modifier and Type	Method	Description
DoubleMatrix1D	assign(double[] v)
DoubleMatrix1D	assign(DoubleFunction function)	WARNING this only assigns to the non-empty values, for performance reasons.
double	get(int index)
double	getQuick(int index)
DoubleMatrix1D	like(int s)
DoubleMatrix2D	like2D(int rows, int columns)
void	setQuick(int column, double value)
String	toString()
protected DoubleMatrix1D	viewSelectionLike(int[] offsets)
double	zDotProduct(DoubleMatrix1D y)
double	zSum()

Methods inherited from class cern.colt.matrix.DoubleMatrix1D

aggregate, aggregate, assign, assign, assign, assign, cardinality, cardinality, copy, equals, equals, getContent, getNonZeros, getNonZeros, haveSharedCells, haveSharedCellsRaw, like, set, swap, toArray, toArray, view, viewFlip, viewPart, viewSelection, viewSelection, viewSorted, viewStrides, zDotProduct, zDotProduct, zDotProduct

Methods inherited from class cern.colt.matrix.impl.AbstractMatrix1D

_offset, _rank, checkIndex, checkIndexes, checkRange, checkSize, checkSize, index, setUp, setUp, size, stride, toStringShort, vFlip, vPart, vStrides

Methods inherited from class cern.colt.matrix.impl.AbstractMatrix

ensureCapacity, isView, trimToSize

Methods inherited from class cern.colt.PersistentObject

clone

Methods inherited from class java.lang.Object

finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Details

indexes

protected IntArrayList indexes

values

protected DoubleArrayList values

Constructor Details

RCDoubleMatrix1D

public RCDoubleMatrix1D(double[] values)

Parameters:

values -

RCDoubleMatrix1D

public RCDoubleMatrix1D(int length)

Parameters:

length -

RCDoubleMatrix1D

public RCDoubleMatrix1D(IntArrayList indexes,
 DoubleArrayList values)

Parameters:

indexes - These MUST be in sorted order.

values - These MuST be in the same order as the indexes, meaning that indexes[0] is the column for values[0].

Method Details

assign

public DoubleMatrix1D assign(double[] v)

Overrides:

assign in class DoubleMatrix1D

assign

public DoubleMatrix1D assign(DoubleFunction function)

WARNING this only assigns to the non-empty values, for performance reasons. If you need to assign to any index, you have to use another way.

Overrides:

assign in class DoubleMatrix1D

See Also:

• DoubleMatrix1D.assign(cern.colt.function.DoubleFunction)

get

public double get(int index)

Overrides:

get in class DoubleMatrix1D

getQuick

public double getQuick(int index)

Specified by:

getQuick in class DoubleMatrix1D

like

public DoubleMatrix1D like(int s)

Specified by:

like in class DoubleMatrix1D

like2D

public DoubleMatrix2D like2D(int rows,
 int columns)

Specified by:

like2D in class DoubleMatrix1D

setQuick

public void setQuick(int column,
 double value)

Specified by:

setQuick in class DoubleMatrix1D

toString

public String toString()

Overrides:

toString in class DoubleMatrix1D

zDotProduct

public double zDotProduct(DoubleMatrix1D y)

Overrides:

zDotProduct in class DoubleMatrix1D

zSum

public double zSum()

Overrides:

zSum in class DoubleMatrix1D

viewSelectionLike

protected DoubleMatrix1D viewSelectionLike(int[] offsets)

Specified by:

viewSelectionLike in class DoubleMatrix1D