pal.statistics

Class GeneralTopologyPool

java.lang.Object

pal.statistics.GeneralTopologyPool

All Implemented Interfaces:

TopologyTestEngine.TopologyPool

public class GeneralTopologyPool
extends java.lang.Object
implements TopologyTestEngine.TopologyPool

Constructor Summary

Constructors

Constructor and Description
GeneralTopologyPool(Tree[] topologies, LikelihoodEvaluator baseCalculator, ReplicateLikelihoodEvaluator replicateCalculator, Alignment baseAlignment, AlignmentGenerator replicateGenerator)

Method Summary

Methods

Modifier and Type	Method and Description
double[]	getNewReplicateLogLikelihoods(AlgorithmCallback callback)
int	getNumberOfTopologies()
double[]	getOriginalOptimisedLogLikelihoods()
Tree[]	getOriginalOptimisedTrees()
void	optimiseOriginalTopologies(AlgorithmCallback callback)

Methods inherited from class java.lang.Object

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

Constructor Detail

GeneralTopologyPool

public GeneralTopologyPool(Tree[] topologies,
                   LikelihoodEvaluator baseCalculator,
                   ReplicateLikelihoodEvaluator replicateCalculator,
                   Alignment baseAlignment,
                   AlignmentGenerator replicateGenerator)

Method Detail

optimiseOriginalTopologies

public void optimiseOriginalTopologies(AlgorithmCallback callback)

getNumberOfTopologies

public int getNumberOfTopologies()

Specified by:

getNumberOfTopologies in interface TopologyTestEngine.TopologyPool

getOriginalOptimisedTrees

public Tree[] getOriginalOptimisedTrees()

getOriginalOptimisedLogLikelihoods

public double[] getOriginalOptimisedLogLikelihoods()

Specified by:

getOriginalOptimisedLogLikelihoods in interface TopologyTestEngine.TopologyPool

getNewReplicateLogLikelihoods

public double[] getNewReplicateLogLikelihoods(AlgorithmCallback callback)

Specified by:

getNewReplicateLogLikelihoods in interface TopologyTestEngine.TopologyPool