SerialCoalescentGenerator

java.lang.Object

pal.coalescent.SerialCoalescentGenerator

All Implemented Interfaces:: Serializable

public class SerialCoalescentGenerator extends Object implements Serializable

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type

Class

Description

static final class

SerialCoalescentGenerator.Results

A simple wrapper class for containing the results which may either be a number of trees, or a number of trees and alignments (in parallel arrays)
Constructor Summary

Constructors

Constructor

Description

SerialCoalescentGenerator(TimeOrderCharacterData tocd, DemographicModel demographicModel, int numberOfTreesToGenerate)

Results will not contain alignments

SerialCoalescentGenerator(TimeOrderCharacterData tocd, DemographicModel demographicModel, int numberOfTreesToGenerate, TreeOperation treeFinisher)

Results will not contain alignments

SerialCoalescentGenerator(TimeOrderCharacterData tocd, DemographicModel demographicModel, int numberOfTreesToGenerate, TreeOperation treeFinisher, SimulatedAlignment.Factory alignmentFactory)

SerialCoalescentGenerator(TimeOrderCharacterData tocd, DemographicModel demographicModel, TreeOperation treeFinisher, SimulatedAlignment.Factory alignmentFactory)
Method Summary

Modifier and Type

Method

Description

final SerialCoalescentGenerator.Results

generateResults(AlgorithmCallback callback)

final Tree

generateTree()

final Tree[]

generateTrees(AlgorithmCallback callback)

If callback request stop then returns trees creating thus far

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details
- SerialCoalescentGenerator
  
  public SerialCoalescentGenerator(TimeOrderCharacterData tocd, DemographicModel demographicModel, int numberOfTreesToGenerate)
  
  Results will not contain alignments
- SerialCoalescentGenerator
  
  public SerialCoalescentGenerator(TimeOrderCharacterData tocd, DemographicModel demographicModel, int numberOfTreesToGenerate, TreeOperation treeFinisher)
  
  Results will not contain alignments
- SerialCoalescentGenerator
  
  public SerialCoalescentGenerator(TimeOrderCharacterData tocd, DemographicModel demographicModel, TreeOperation treeFinisher, SimulatedAlignment.Factory alignmentFactory)
- SerialCoalescentGenerator
  
  public SerialCoalescentGenerator(TimeOrderCharacterData tocd, DemographicModel demographicModel, int numberOfTreesToGenerate, TreeOperation treeFinisher, SimulatedAlignment.Factory alignmentFactory)
  
  Parameters:
  
  alignmentFactory - Can be null if no alignments to be generated (otherwise results will contain alignments as well as trees)
Method Details
- generateTree
  
  public final Tree generateTree()
- generateTrees
  
  public final Tree[] generateTrees(AlgorithmCallback callback)
  
  If callback request stop then returns trees creating thus far
- generateResults
  
  public final SerialCoalescentGenerator.Results generateResults(AlgorithmCallback callback)