Package pal.statistics
Class GeneralTopologyPool
- java.lang.Object
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- pal.statistics.GeneralTopologyPool
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- All Implemented Interfaces:
TopologyTestEngine.TopologyPool
public class GeneralTopologyPool extends java.lang.Object implements TopologyTestEngine.TopologyPool
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Constructor Summary
Constructors Constructor Description GeneralTopologyPool(Tree[] topologies, LikelihoodEvaluator baseCalculator, ReplicateLikelihoodEvaluator replicateCalculator, Alignment baseAlignment, AlignmentGenerator replicateGenerator)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description double[]
getNewReplicateLogLikelihoods(AlgorithmCallback callback)
int
getNumberOfTopologies()
double[]
getOriginalOptimisedLogLikelihoods()
Tree[]
getOriginalOptimisedTrees()
void
optimiseOriginalTopologies(AlgorithmCallback callback)
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Constructor Detail
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GeneralTopologyPool
public GeneralTopologyPool(Tree[] topologies, LikelihoodEvaluator baseCalculator, ReplicateLikelihoodEvaluator replicateCalculator, Alignment baseAlignment, AlignmentGenerator replicateGenerator)
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Method Detail
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optimiseOriginalTopologies
public void optimiseOriginalTopologies(AlgorithmCallback callback)
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getNumberOfTopologies
public int getNumberOfTopologies()
- Specified by:
getNumberOfTopologies
in interfaceTopologyTestEngine.TopologyPool
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getOriginalOptimisedTrees
public Tree[] getOriginalOptimisedTrees()
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getOriginalOptimisedLogLikelihoods
public double[] getOriginalOptimisedLogLikelihoods()
- Specified by:
getOriginalOptimisedLogLikelihoods
in interfaceTopologyTestEngine.TopologyPool
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getNewReplicateLogLikelihoods
public double[] getNewReplicateLogLikelihoods(AlgorithmCallback callback)
- Specified by:
getNewReplicateLogLikelihoods
in interfaceTopologyTestEngine.TopologyPool
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