java.io.Serializable
public class SerialCoalescentGenerator
extends java.lang.Object
implements java.io.Serializable
Modifier and Type | Class | Description |
---|---|---|
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 | 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) |
Modifier and Type | Method | Description |
---|---|---|
SerialCoalescentGenerator.Results |
generateResults(AlgorithmCallback callback) |
|
Tree |
generateTree() |
|
Tree[] |
generateTrees(AlgorithmCallback callback) |
If callback request stop then returns trees creating thus far
|
public SerialCoalescentGenerator(TimeOrderCharacterData tocd, DemographicModel demographicModel, int numberOfTreesToGenerate)
public SerialCoalescentGenerator(TimeOrderCharacterData tocd, DemographicModel demographicModel, int numberOfTreesToGenerate, TreeOperation treeFinisher)
public SerialCoalescentGenerator(TimeOrderCharacterData tocd, DemographicModel demographicModel, TreeOperation treeFinisher, SimulatedAlignment.Factory alignmentFactory)
public SerialCoalescentGenerator(TimeOrderCharacterData tocd, DemographicModel demographicModel, int numberOfTreesToGenerate, TreeOperation treeFinisher, SimulatedAlignment.Factory alignmentFactory)
alignmentFactory
- Can be null if no alignments to be generated (otherwise results will contain alignments as well as trees)public final Tree generateTree()
public final Tree[] generateTrees(AlgorithmCallback callback)
public final SerialCoalescentGenerator.Results generateResults(AlgorithmCallback callback)