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)
           
 

Method Detail

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()