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.