pal.supgma
public class SUPGMABase extends java.lang.Object
Modifier and Type | Class and Description |
---|---|
static interface |
SUPGMABase.CISummary |
static interface |
SUPGMABase.PopulationParameters |
Constructor and Description |
---|
SUPGMABase(DistanceMatrixAccess distanceAccess,
DistanceMatrixGenerator replicateGenerator,
TimeOrderCharacterData tocd) |
Modifier and Type | Method and Description |
---|---|
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() |
public SUPGMABase(DistanceMatrixAccess distanceAccess, DistanceMatrixGenerator replicateGenerator, TimeOrderCharacterData tocd)
public java.lang.String toString()
toString
in class java.lang.Object
public void setThetaHandler(ThetaHandler handler)
public void setRateHandler(RateHandler rateHandler)
public Tree solve(AlgorithmCallback callback, ClusterTree.ClusteringMethod cm, LMSSolver solver)
public SUPGMABase.PopulationParameters process(DistanceMatrixAccess alternativeSource, AlgorithmCallback callback, LMSSolver solver)
public SUPGMABase.PopulationParameters process(AlgorithmCallback callback, LMSSolver solver)
public Tree generateAlignmentBootstrappedSUPGMATree(AlgorithmCallback callback, ClusterTree.ClusteringMethod cm, SUPGMABase.PopulationParameters pp, int numberOfReplicates, LMSSolver solver)
public pal.supgma.SUPGMABase.Analyser generateAnalyser()