DiagonalCachingKernel (biojava-legacy 1.9.5 API)

java.lang.Object
- org.biojava.stats.svm.NestedKernel
- - org.biojava.stats.svm.DiagonalCachingKernel

All Implemented Interfaces:

Serializable, SVMKernel
```
public class DiagonalCachingKernel
extends NestedKernel
```
Caches the leading diagonal of a kernel matrix.
Several kernels need to repeatedly access k(x,x) to do things like normalization, or to calculate distances. This kernel wraps k so that these leading diagonal elements do not need to be calculated each time.
This kernel is thread-safe. However, care must be taken when setting the nested kernel that no other thread is retrieving values at the same time. This would cause a race condition in which the newly flushed cache may contain a value from the previous kernel.

Author:

Matthew Pocock, Thomas Down

See Also:

Serialized Form

Constructor Summary

Constructors
Constructor Description

DiagonalCachingKernel()
Create a new CachingKernel.

DiagonalCachingKernel(SVMKernel k)
Creates a new DiagonalCachingKernel that nests k.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`double`	`evaluate(Object x, Object y)`	Returns the kernel product of two Objects.
`void`	`setNestedKernel(SVMKernel k)`	Set the kernel to nest.
`String`	`toString()`

Methods inherited from class org.biojava.stats.svm.NestedKernel
getNestedKernel

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Constructor Detail
  - DiagonalCachingKernel
```
public DiagonalCachingKernel()
```
    Create a new CachingKernel.
  - DiagonalCachingKernel
```
public DiagonalCachingKernel(SVMKernel k)
```
    Creates a new DiagonalCachingKernel that nests k.
- Method Detail
  - setNestedKernel
```
public void setNestedKernel(SVMKernel k)
```
    Set the kernel to nest.
    
    This will flush the cache.
    
    Overrides:
    
    setNestedKernel in class NestedKernel
    
    Parameters:
    
    k - the kernel to nest.
  - evaluate
```
public double evaluate(Object x,
                       Object y)
```
    Returns the kernel product of two Objects.
    
    This returns getNestedKernel.evaluate(x, y). If x.equals(y) then it will cache the result first time, and do a hash table look up to retrieve the value in subsequent calls.
  - toString
```
public String toString()
```
    Overrides:
    
    toString in class Object