Package pal.supgma
Class SUPGMABase
- java.lang.Object
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- pal.supgma.SUPGMABase
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public class SUPGMABase extends java.lang.Object
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Nested Class Summary
Nested Classes Modifier and Type Class Description static interface
SUPGMABase.CISummary
static interface
SUPGMABase.PopulationParameters
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Constructor Summary
Constructors Constructor Description SUPGMABase(DistanceMatrixAccess distanceAccess, DistanceMatrixGenerator replicateGenerator, TimeOrderCharacterData tocd)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description Tree
generateAlignmentBootstrappedSUPGMATree(AlgorithmCallback callback, ClusterTree.ClusteringMethod cm, SUPGMABase.PopulationParameters pp, int numberOfReplicates, LMSSolver solver)
pal.supgma.SUPGMABase.Analyser
generateAnalyser()
Generates a suitable analyser.SUPGMABase.PopulationParameters
process(DistanceMatrixAccess alternativeSource, AlgorithmCallback callback, LMSSolver solver)
SUPGMABase.PopulationParameters
process(AlgorithmCallback callback, LMSSolver solver)
void
setRateHandler(RateHandler rateHandler)
Makes no difference if no time info availablevoid
setThetaHandler(ThetaHandler handler)
Tree
solve(AlgorithmCallback callback, ClusterTree.ClusteringMethod cm, LMSSolver solver)
java.lang.String
toString()
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Constructor Detail
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SUPGMABase
public SUPGMABase(DistanceMatrixAccess distanceAccess, DistanceMatrixGenerator replicateGenerator, TimeOrderCharacterData tocd)
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Method Detail
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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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setThetaHandler
public void setThetaHandler(ThetaHandler handler)
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setRateHandler
public void setRateHandler(RateHandler rateHandler)
Makes no difference if no time info available
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solve
public Tree solve(AlgorithmCallback callback, ClusterTree.ClusteringMethod cm, LMSSolver solver)
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process
public SUPGMABase.PopulationParameters process(DistanceMatrixAccess alternativeSource, AlgorithmCallback callback, LMSSolver solver)
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process
public SUPGMABase.PopulationParameters process(AlgorithmCallback callback, LMSSolver solver)
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generateAlignmentBootstrappedSUPGMATree
public Tree generateAlignmentBootstrappedSUPGMATree(AlgorithmCallback callback, ClusterTree.ClusteringMethod cm, SUPGMABase.PopulationParameters pp, int numberOfReplicates, LMSSolver solver)
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generateAnalyser
public pal.supgma.SUPGMABase.Analyser generateAnalyser()
Generates a suitable analyser.
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