Package pal.coalescent
Class SerialCoalescentGenerator
java.lang.Object
pal.coalescent.SerialCoalescentGenerator
- All Implemented Interfaces:
Serializable
- See Also:
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Nested Class Summary
Nested ClassesModifier and TypeClassDescriptionstatic final class
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
ConstructorsConstructorDescriptionSerialCoalescentGenerator
(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
Modifier and TypeMethodDescriptiongenerateResults
(AlgorithmCallback callback) final Tree
final Tree[]
generateTrees
(AlgorithmCallback callback) If callback request stop then returns trees creating thus far
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Constructor Details
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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)
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Method Details
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generateTree
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generateTrees
If callback request stop then returns trees creating thus far -
generateResults
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