pal.coalescent
Class SerialCoalescentGenerator
java.lang.Object
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)
|
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
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)
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)