public class GeneralTopologyPool extends java.lang.Object implements TopologyTestEngine.TopologyPool
Constructor and Description |
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GeneralTopologyPool(Tree[] topologies,
LikelihoodEvaluator baseCalculator,
ReplicateLikelihoodEvaluator replicateCalculator,
Alignment baseAlignment,
AlignmentGenerator replicateGenerator) |
Modifier and Type | Method and Description |
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double[] |
getNewReplicateLogLikelihoods(AlgorithmCallback callback) |
int |
getNumberOfTopologies() |
double[] |
getOriginalOptimisedLogLikelihoods() |
Tree[] |
getOriginalOptimisedTrees() |
void |
optimiseOriginalTopologies(AlgorithmCallback callback) |
public GeneralTopologyPool(Tree[] topologies, LikelihoodEvaluator baseCalculator, ReplicateLikelihoodEvaluator replicateCalculator, Alignment baseAlignment, AlignmentGenerator replicateGenerator)
public void optimiseOriginalTopologies(AlgorithmCallback callback)
public int getNumberOfTopologies()
getNumberOfTopologies
in interface TopologyTestEngine.TopologyPool
public Tree[] getOriginalOptimisedTrees()
public double[] getOriginalOptimisedLogLikelihoods()
getOriginalOptimisedLogLikelihoods
in interface TopologyTestEngine.TopologyPool
public double[] getNewReplicateLogLikelihoods(AlgorithmCallback callback)
getNewReplicateLogLikelihoods
in interface TopologyTestEngine.TopologyPool