pal.statistics
Class GeneralTopologyPool

java.lang.Object
  extended by pal.statistics.GeneralTopologyPool
All Implemented Interfaces:
TopologyTestEngine.TopologyPool

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


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