FastLikelihoodCalculator

java.lang.Object
- pal.eval.FastLikelihoodCalculator

All Implemented Interfaces:

LikelihoodCalculator, PalObjectListener
```
public class FastLikelihoodCalculator
extends java.lang.Object
implements PalObjectListener, LikelihoodCalculator
```
Title: Fast Likelihood Calculator
Description: A fast likelihood calculator
Original code by Matthew Goode. This calculates the likelihood of similar trees (or a single changing tree) on the same site pattern fast by remembering partial likelihoods of invariant subtrees. This class should be avoided if the underlying tree doesn't change (use GeneralLikelihoodCalculator). A new framework will be added one day to accomodate optimising tree topologies.

Version:

$Id: FastLikelihoodCalculator.java,v 1.11 2002/09/08 03:46:12 matt Exp $

Author:

Matthew Goode, Alexei Drummond

Nested Class Summary
- Nested classes/interfaces inherited from interface pal.misc.PalObjectListener
  PalObjectListener.EventGenerator

Constructor Summary

Constructors
Constructor and Description
`FastLikelihoodCalculator(SitePattern pattern)` Constructor taking only site pattern.
`FastLikelihoodCalculator(SitePattern pattern, Tree tree, RateMatrix model)` Constructor taking site pattern, tree and model.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`double`	`calculateLogLikelihood()`
`void`	`parametersChanged(PalObjectEvent pe)` Signifies that parametric valued governing the state of this Object have changed.
`void`	`release()` This method should be called when the user is through using this calculator to inform it to release any resources it has allocated.
`void`	`setRateMatrix(RateMatrix rateMatrix)`
`void`	`setTree(Tree t)`
`void`	`structureChanged(PalObjectEvent pe)` Signifies that the structure of the object has changed (for example in trees to topology has changed)
`void`	`updateSitePattern(SitePattern pattern)`

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

- Constructor Detail
  - FastLikelihoodCalculator
```
public FastLikelihoodCalculator(SitePattern pattern)
```
    Constructor taking only site pattern.
    NOTE: setTree and setRateMatrix must both be called (in that order) before computeLikelihood.
  - FastLikelihoodCalculator
```
public FastLikelihoodCalculator(SitePattern pattern,
                                Tree tree,
                                RateMatrix model)
```
    Constructor taking site pattern, tree and model.
- Method Detail
  - parametersChanged
```
public void parametersChanged(PalObjectEvent pe)
```
    Description copied from interface: PalObjectListener
    
    Signifies that parametric valued governing the state of this Object have changed. Parameters don't have to be visible ones For example, in trees the branch lengths have changed.
    
    Specified by:
    
    parametersChanged in interface PalObjectListener
  - structureChanged
```
public void structureChanged(PalObjectEvent pe)
```
    Description copied from interface: PalObjectListener
    
    Signifies that the structure of the object has changed (for example in trees to topology has changed)
    
    Specified by:
    
    structureChanged in interface PalObjectListener
  - setRateMatrix
```
public final void setRateMatrix(RateMatrix rateMatrix)
```
  - release
```
public void release()
```
    Description copied from interface: LikelihoodCalculator
    
    This method should be called when the user is through using this calculator to inform it to release any resources it has allocated.
    
    Specified by:
    
    release in interface LikelihoodCalculator
  - setTree
```
public final void setTree(Tree t)
```
  - updateSitePattern
```
public final void updateSitePattern(SitePattern pattern)
```
  - calculateLogLikelihood
```
public double calculateLogLikelihood()
```
    Specified by:
    
    calculateLogLikelihood in interface LikelihoodCalculator
    
    Returns:
    
    the likelihood of this tree under the given model and data.

Class FastLikelihoodCalculator

Nested Class Summary

Nested classes/interfaces inherited from interface pal.misc.PalObjectListener

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

FastLikelihoodCalculator

FastLikelihoodCalculator

Method Detail

parametersChanged

structureChanged

setRateMatrix

release

setTree

updateSitePattern

calculateLogLikelihood