org.biojava.stats.svm.tools

Class SuffixTreeKernel

java.lang.Object

org.biojava.stats.svm.tools.SuffixTreeKernel

All Implemented Interfaces:

Serializable, SVMKernel

public class SuffixTreeKernel
extends Object
implements SVMKernel, Serializable

Computes the dot-product of two suffix-trees as the sum of the products of the counts of all nodes they have in common.

This implementation allows you to scale the sub-space for each word length independently.

Author:

Matthew Pocock

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static interface	SuffixTreeKernel.DepthScaler Encapsulates the scale factor to apply at a given depth.
static class	SuffixTreeKernel.MultipleScalar Scale using a multiple of two DepthScalers.
static class	SuffixTreeKernel.NullModelScaler Scales by 4^depth - equivalent to dividing by a probablistic flatt prior null model
static class	SuffixTreeKernel.SelectionScalar Scale using a BitSet to allow/disallow depths.
static class	SuffixTreeKernel.UniformScaler Scale all depths by 1.0

Constructor Summary

Constructors

Constructor and Description
SuffixTreeKernel()

Method Summary

Methods

Modifier and Type	Method and Description
double	evaluate(Object a, Object b) Calculate the dot product between the SuffixTrees a and b.
SuffixTreeKernel.DepthScaler	getDepthScaler() Retrieve the current DepthScaler.
void	setDepthScaler(SuffixTreeKernel.DepthScaler depthScaler) Change the current DepthScaler to depthScaler.
String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

SuffixTreeKernel

public SuffixTreeKernel()

Method Detail

getDepthScaler

public SuffixTreeKernel.DepthScaler getDepthScaler()

Retrieve the current DepthScaler.

Returns:

the current DepthScaler

setDepthScaler

public void setDepthScaler(SuffixTreeKernel.DepthScaler depthScaler)

Change the current DepthScaler to depthScaler.

Parameters:

depthScaler - the new DepthScaler to use

evaluate

public double evaluate(Object a,
              Object b)

Calculate the dot product between the SuffixTrees a and b.

This is the sum of the dot products of each subspace for a given word length. Each subspace is scaled using the DepthScaler returned by getDepthScaler.

Specified by:

evaluate in interface SVMKernel

Parameters:

a - the first Object

b - the second Object

Returns:

a.b

Throws:

- class="type">ClassCastException if either a or b are not castable to SuffixTree

toString

public String toString()

Overrides:

toString in class Object