pal.supgma.SUPGMABase

public class SUPGMABase extends Object

Constructor Details
- SUPGMABase
  
  public SUPGMABase(DistanceMatrixAccess distanceAccess, DistanceMatrixGenerator replicateGenerator, TimeOrderCharacterData tocd)
Method Details
- toString
  
  public String toString()
  
  Overrides:
  
  toString in class 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.

Class SUPGMABase

Nested Class Summary