pal.statistics.GeneralTopologyPool

public class GeneralTopologyPool extends Object implements TopologyTestEngine.TopologyPool

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

Class GeneralTopologyPool

Constructor Summary