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