org.biojava.stats.svm

Class SparseVector

java.lang.Object

org.biojava.stats.svm.SparseVector

All Implemented Interfaces:

Serializable

public class SparseVector
extends Object
implements Serializable

An implementation of a sparse vector.

Memory is only allocated for dimensions that have non-zero values.

Author:

Thomas Down, Matthew Pocock

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	SparseVector.NormalizingKernel A version of the standard dot-product kernel that scales each column independently.

Field Summary

Fields

Modifier and Type	Field and Description
static SVMKernel	kernel

Constructor Summary

Constructors

Constructor and Description
SparseVector()
SparseVector(int capacity)

Method Summary

Methods

Modifier and Type	Method and Description
double	get(int dim) Retrieve the value at dimension dim.
int	getDimAtIndex(int indx) Retrieve the dimension at a specific index.
double	getValueAtIndex(int indx) Retrieve the value at a specific index.
int	maxIndex()
static SparseVector	normalLengthVector(SparseVector v, double length)
void	put(int dim, double value) Set the value at a particular dimension.
int	size() The number of used dimensions.

Methods inherited from class java.lang.Object

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

Field Detail

kernel

public static final SVMKernel kernel

Constructor Detail

SparseVector

public SparseVector()

SparseVector

public SparseVector(int capacity)

Method Detail

size

public int size()

The number of used dimensions.

This is the total number of non-zero dimensions. It is not equal to the number of the highest indexed dimension.

Returns:

the number of non-zero dimensions

put

public void put(int dim,
       double value)

Set the value at a particular dimension.

This silently handles the case when previously there was no value at dim. It does not contract the sparse array if you set a value to zero.

Parameters:

dim - the dimension to alter

value - the new value

get

public double get(int dim)

Retrieve the value at dimension dim.

Parameters:

dim - the dimension to retrieve a value for

Returns:

the value at that dimension

getDimAtIndex

public int getDimAtIndex(int indx)

Retrieve the dimension at a specific index.

E.g., if the sparse vector had dimensions 5, 11, 12, 155 set to non-zero values then sv.getDimAtIndex(2) would return 12.

Parameters:

indx - the index

Returns:

the dimension stoored at that index

Throws:

ArrayIndexOutOfBoundsException - if index >= size.

getValueAtIndex

public double getValueAtIndex(int indx)

Retrieve the value at a specific index.

E.g., if the sparse vector contained the data 5->0.1, 11->100, 12->8.5, 155->-10 then sv.geValueAtIndex(2) would return 8.5.

Parameters:

indx - the index

Returns:

the value stoored at that index

Throws:

ArrayIndexOutOfBoundsException - if index >= size.

maxIndex

public int maxIndex()

normalLengthVector

public static SparseVector normalLengthVector(SparseVector v,
                              double length)