pal.supgma
Class SUPGMABase

java.lang.Object
  extended by 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.