Package 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
Nested Classes 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 Summary
Constructors Constructor Description SerialCoalescentGenerator(TimeOrderCharacterData tocd, DemographicModel demographicModel, int numberOfTreesToGenerate)
Results will not contain alignmentsSerialCoalescentGenerator(TimeOrderCharacterData tocd, DemographicModel demographicModel, int numberOfTreesToGenerate, TreeOperation treeFinisher)
Results will not contain alignmentsSerialCoalescentGenerator(TimeOrderCharacterData tocd, DemographicModel demographicModel, int numberOfTreesToGenerate, TreeOperation treeFinisher, SimulatedAlignment.Factory alignmentFactory)
SerialCoalescentGenerator(TimeOrderCharacterData tocd, DemographicModel demographicModel, TreeOperation treeFinisher, SimulatedAlignment.Factory alignmentFactory)
-
Method Summary
All Methods Instance Methods Concrete Methods 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
-
-
-
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)
-
-