java.lang.Object
- pal.statistics.GeneralTopologyPool

All Implemented Interfaces:: TopologyTestEngine.TopologyPool

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

Constructor Summary

Constructors
Constructor	Description
`GeneralTopologyPool(Tree[] topologies, LikelihoodEvaluator baseCalculator, ReplicateLikelihoodEvaluator replicateCalculator, Alignment baseAlignment, AlignmentGenerator replicateGenerator)`

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)`

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

Class GeneralTopologyPool

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

GeneralTopologyPool

Method Detail

optimiseOriginalTopologies

getNumberOfTopologies

getOriginalOptimisedTrees

getOriginalOptimisedLogLikelihoods

getNewReplicateLogLikelihoods