pal.supgma
Class SUPGMABase
java.lang.Object
pal.supgma.SUPGMABase
public class SUPGMABase
- extends java.lang.Object
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
SUPGMABase
public SUPGMABase(DistanceMatrixAccess distanceAccess,
DistanceMatrixGenerator replicateGenerator,
TimeOrderCharacterData tocd)
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.