pal.supgma
Class SUPGMABase

java.lang.Object
  pal.supgma.SUPGMABase

public class SUPGMABase
extends java.lang.Object

Nested Class Summary

static interface	SUPGMABase.CISummary
static interface	SUPGMABase.PopulationParameters

Constructor Summary

SUPGMABase(DistanceMatrixAccess distanceAccess, DistanceMatrixGenerator replicateGenerator, TimeOrderCharacterData tocd)

Method Summary

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(AlgorithmCallback callback, LMSSolver solver)
SUPGMABase.PopulationParameters	process(DistanceMatrixAccess alternativeSource, AlgorithmCallback callback, LMSSolver solver)
void	setRateHandler(RateHandler rateHandler) Makes no difference if no time info available
void	setThetaHandler(ThetaHandler handler)
Tree	solve(AlgorithmCallback callback, ClusterTree.ClusteringMethod cm, LMSSolver solver)
java.lang.String	toString()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

SUPGMABase

public SUPGMABase(DistanceMatrixAccess distanceAccess,
                  DistanceMatrixGenerator replicateGenerator,
                  TimeOrderCharacterData tocd)

Method Detail

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

setThetaHandler

public void setThetaHandler(ThetaHandler handler)

setRateHandler

public void setRateHandler(RateHandler rateHandler)

Makes no difference if no time info available

solve

public Tree solve(AlgorithmCallback callback,
                  ClusterTree.ClusteringMethod cm,
                  LMSSolver solver)

process

public SUPGMABase.PopulationParameters process(DistanceMatrixAccess alternativeSource,
                                               AlgorithmCallback callback,
                                               LMSSolver solver)

process

public SUPGMABase.PopulationParameters process(AlgorithmCallback callback,
                                               LMSSolver solver)

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.