pal.eval
Class SimpleLikelihoodCalculator

java.lang.Object
  pal.eval.SimpleLikelihoodCalculator

All Implemented Interfaces:

LikelihoodCalculator

public class SimpleLikelihoodCalculator
extends java.lang.Object
implements LikelihoodCalculator

Constructor Summary

SimpleLikelihoodCalculator(SitePattern pattern)
Need to use setTree(), and setModel() before using compute() if you use this constructor

SimpleLikelihoodCalculator(SitePattern pattern, Tree tree, RateMatrix model)

Method Summary

double	calculateLogLikelihood() compute log-likelihood for current tree (fixed branch lengths and model) return log-likelihood
protected Node	getNextBranch(Node branch, Node center) get next branch around a center node (center may be root, but root is never returned)
protected double[][]	getPartial(Node branch) get partial likelihood of a branch
SitePattern	getSitePattern()
Tree	getTree()
void	modelUpdated()
protected void	partialsExternal(Node branch) compute partials for external branch
protected void	partialsInternal(Node center) compute partials for branch around center node (it is assumed that multiplied partials are available in the neighbor branch)
protected void	productPartials(Node center) multiply partials into the neighbour of branch
void	release() Doesn't do anything...
void	setRateMatrix(RateMatrix m) define model (a site pattern must have been set before calling this method)
void	setTree(Tree t) define tree ,(must only be called only after a site pattern has been defined).
void	treeUpdated()

Methods inherited from class java.lang.Object

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

Constructor Detail

SimpleLikelihoodCalculator

public SimpleLikelihoodCalculator(SitePattern pattern)

Need to use setTree(), and setModel() before using compute() if you use this constructor

SimpleLikelihoodCalculator

public SimpleLikelihoodCalculator(SitePattern pattern,
                                  Tree tree,
                                  RateMatrix model)

Method Detail

release

public void release()

Doesn't do anything...

Specified by:

release in interface LikelihoodCalculator

calculateLogLikelihood

public double calculateLogLikelihood()

compute log-likelihood for current tree (fixed branch lengths and model) return log-likelihood

Specified by:

calculateLogLikelihood in interface LikelihoodCalculator

getSitePattern

public SitePattern getSitePattern()

getTree

public Tree getTree()

setRateMatrix

public void setRateMatrix(RateMatrix m)

define model (a site pattern must have been set before calling this method)

Parameters:

m - model of substitution (rate matrix + rate distribution)

setTree

public void setTree(Tree t)

define tree ,(must only be called only after a site pattern has been defined).

Parameters:

t - tree

modelUpdated

public final void modelUpdated()

treeUpdated

public final void treeUpdated()

getPartial

protected double[][] getPartial(Node branch)

get partial likelihood of a branch

getNextBranch

protected Node getNextBranch(Node branch,
                             Node center)

get next branch around a center node (center may be root, but root is never returned)

productPartials

protected void productPartials(Node center)

multiply partials into the neighbour of branch

partialsInternal

protected void partialsInternal(Node center)

compute partials for branch around center node (it is assumed that multiplied partials are available in the neighbor branch)

partialsExternal

protected void partialsExternal(Node branch)

compute partials for external branch