alun.mcld
Class JointScheme

java.lang.Object
  alun.mcld.JointScheme

Direct Known Subclasses:

WindowingScheme

public class JointScheme
extends java.lang.Object

Constructor Summary

JointScheme(DataHaplotypeSource s, GraphMHScheme m)

Method Summary

void	addRemoveAnalysis(java.io.PrintWriter w)
Graph<Locus,java.lang.Object>	getBestGraph()
LogLikelihood	getBestLogLike()
double	getBestScore()
LikelihoodCalculator	getCalculator()
Graph<Locus,java.lang.Object>	getCurrentGraph()
LogLikelihood	getCurrentLogLike()
double	getCurrentScore()
HaplotypeSource	getHaplotypeSource()
double	getParameterPenalty()
GraphMHScheme	getSearchScheme()
boolean	gibbsUpdate()
boolean	gibbsUpdate(double temp)
boolean	metropolisUpdate()
boolean	metropolisUpdate(double temp)
void	reconstruct()
void	setCopyBest(boolean b)
void	setDistancePenalty(double d)
void	setParameterPenalty(double x)

Methods inherited from class java.lang.Object

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

Constructor Detail

JointScheme

public JointScheme(DataHaplotypeSource s,
                   GraphMHScheme m)

Method Detail

getSearchScheme

public GraphMHScheme getSearchScheme()

getHaplotypeSource

public HaplotypeSource getHaplotypeSource()

getCalculator

public LikelihoodCalculator getCalculator()

reconstruct

public void reconstruct()

gibbsUpdate

public boolean gibbsUpdate()

gibbsUpdate

public boolean gibbsUpdate(double temp)

metropolisUpdate

public boolean metropolisUpdate()

metropolisUpdate

public boolean metropolisUpdate(double temp)

setParameterPenalty

public void setParameterPenalty(double x)

getParameterPenalty

public double getParameterPenalty()

getBestScore

public double getBestScore()

getBestGraph

public Graph<Locus,java.lang.Object> getBestGraph()

getCurrentGraph

public Graph<Locus,java.lang.Object> getCurrentGraph()

getCurrentScore

public double getCurrentScore()

getCurrentLogLike

public LogLikelihood getCurrentLogLike()

getBestLogLike

public LogLikelihood getBestLogLike()

addRemoveAnalysis

public void addRemoveAnalysis(java.io.PrintWriter w)

setCopyBest

public void setCopyBest(boolean b)

setDistancePenalty

public void setDistancePenalty(double d)