pal.coalescent
Class SerialCoalescentGenerator

java.lang.Object
  extended by pal.coalescent.SerialCoalescentGenerator
All Implemented Interfaces:
java.io.Serializable

public class SerialCoalescentGenerator
extends java.lang.Object
implements java.io.Serializable

See Also:
Serialized Form

Nested Class Summary
static 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
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
 SerialCoalescentGenerator.Results generateResults(AlgorithmCallback callback)
           
 Tree generateTree()
           
 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 Detail

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 Detail

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)