SuffixTreeKernel (biojava-legacy 1.9.5 API)

SuffixTreeKernel (biojava-legacy 1.9.5 API)

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	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 Description

SuffixTreeKernel()

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	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
  - toString
```
public String toString()
```
    Overrides:
    
    toString in class Object