pal.supgma
Interface SUPGMABase.PopulationParameters
- Enclosing class:
- SUPGMABase
public static interface SUPGMABase.PopulationParameters
Method Summary |
java.lang.String |
generateHTML()
|
Tree |
generateSUPGMATree(AlgorithmCallback callback,
ClusterTree.ClusteringMethod cm,
DistanceMatrixGenerator replicateSource,
int numberOfAlignmentBootstrapReplicates,
LMSSolver solver)
|
Tree |
generateSUPGMATree(ClusterTree.ClusteringMethod cm)
|
SUPGMABase.CISummary |
inferCI(AlgorithmCallback callback,
int numberOfReplicates,
SimulatedAlignment.Factory alignmentFactory,
SubstitutionModel evolutionaryModel,
LMSSolver solver)
|
boolean |
isCICompatible()
|
Tree |
simulateTree()
|
Tree[] |
simulateTrees(int numberOfTreesToSimulate,
AlgorithmCallback callback,
LMSSolver solver)
|
isCICompatible
boolean isCICompatible()
- Returns:
- true if it possible to do Confidence Interval stuff
inferCI
SUPGMABase.CISummary inferCI(AlgorithmCallback callback,
int numberOfReplicates,
SimulatedAlignment.Factory alignmentFactory,
SubstitutionModel evolutionaryModel,
LMSSolver solver)
generateSUPGMATree
Tree generateSUPGMATree(ClusterTree.ClusteringMethod cm)
generateSUPGMATree
Tree generateSUPGMATree(AlgorithmCallback callback,
ClusterTree.ClusteringMethod cm,
DistanceMatrixGenerator replicateSource,
int numberOfAlignmentBootstrapReplicates,
LMSSolver solver)
simulateTrees
Tree[] simulateTrees(int numberOfTreesToSimulate,
AlgorithmCallback callback,
LMSSolver solver)
simulateTree
Tree simulateTree()
generateHTML
java.lang.String generateHTML()