Package pal.supgma
Class SUPGMABase
java.lang.Object
pal.supgma.SUPGMABase
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Nested Class Summary
Nested ClassesModifier and TypeClassDescriptionstatic interface
static interface
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Constructor Summary
ConstructorsConstructorDescriptionSUPGMABase
(DistanceMatrixAccess distanceAccess, DistanceMatrixGenerator replicateGenerator, TimeOrderCharacterData tocd) -
Method Summary
Modifier and TypeMethodDescriptiongenerateAlignmentBootstrappedSUPGMATree
(AlgorithmCallback callback, ClusterTree.ClusteringMethod cm, SUPGMABase.PopulationParameters pp, int numberOfReplicates, LMSSolver solver) pal.supgma.SUPGMABase.Analyser
Generates a suitable analyser.process
(DistanceMatrixAccess alternativeSource, AlgorithmCallback callback, LMSSolver solver) process
(AlgorithmCallback callback, LMSSolver solver) void
setRateHandler
(RateHandler rateHandler) Makes no difference if no time info availablevoid
setThetaHandler
(ThetaHandler handler) solve
(AlgorithmCallback callback, ClusterTree.ClusteringMethod cm, LMSSolver solver) toString()
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Constructor Details
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SUPGMABase
public SUPGMABase(DistanceMatrixAccess distanceAccess, DistanceMatrixGenerator replicateGenerator, TimeOrderCharacterData tocd)
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Method Details
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toString
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setThetaHandler
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setRateHandler
Makes no difference if no time info available -
solve
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process
public SUPGMABase.PopulationParameters process(DistanceMatrixAccess alternativeSource, AlgorithmCallback callback, LMSSolver solver) -
process
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generateAlignmentBootstrappedSUPGMATree
public Tree generateAlignmentBootstrappedSUPGMATree(AlgorithmCallback callback, ClusterTree.ClusteringMethod cm, SUPGMABase.PopulationParameters pp, int numberOfReplicates, LMSSolver solver) -
generateAnalyser
public pal.supgma.SUPGMABase.Analyser generateAnalyser()Generates a suitable analyser.
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