Package pal.supgma
Interface SUPGMABase.PopulationParameters
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- Enclosing class:
- SUPGMABase
public static interface SUPGMABase.PopulationParameters
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description java.lang.String
generateHTML()
Tree
generateSUPGMATree(ClusterTree.ClusteringMethod cm)
Tree
generateSUPGMATree(AlgorithmCallback callback, ClusterTree.ClusteringMethod cm, DistanceMatrixGenerator replicateSource, int numberOfAlignmentBootstrapReplicates, LMSSolver solver)
SUPGMABase.CISummary
inferCI(AlgorithmCallback callback, int numberOfReplicates, SimulatedAlignment.Factory alignmentFactory, SubstitutionModel evolutionaryModel, LMSSolver solver)
boolean
isCICompatible()
Tree
simulateTree()
Tree[]
simulateTrees(int numberOfTreesToSimulate, AlgorithmCallback callback, LMSSolver solver)
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Method Detail
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isCICompatible
boolean isCICompatible()
- Returns:
- true if it possible to do Confidence Interval stuff
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inferCI
SUPGMABase.CISummary inferCI(AlgorithmCallback callback, int numberOfReplicates, SimulatedAlignment.Factory alignmentFactory, SubstitutionModel evolutionaryModel, LMSSolver solver)
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generateSUPGMATree
Tree generateSUPGMATree(ClusterTree.ClusteringMethod cm)
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generateSUPGMATree
Tree generateSUPGMATree(AlgorithmCallback callback, ClusterTree.ClusteringMethod cm, DistanceMatrixGenerator replicateSource, int numberOfAlignmentBootstrapReplicates, LMSSolver solver)
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simulateTrees
Tree[] simulateTrees(int numberOfTreesToSimulate, AlgorithmCallback callback, LMSSolver solver)
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simulateTree
Tree simulateTree()
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generateHTML
java.lang.String generateHTML()
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