Uses of Interface
pal.tree.ClusterTree.ClusteringMethod

Packages that use ClusterTree.ClusteringMethod
pal.supgma   
pal.tree Classes for providing the data structure of trees, for constructing and modifying trees, and for parameterizing trees (e.g., clock constraint). 
 

Uses of ClusterTree.ClusteringMethod in pal.supgma
 

Methods in pal.supgma with parameters of type ClusterTree.ClusteringMethod
 Tree SUPGMABase.generateAlignmentBootstrappedSUPGMATree(AlgorithmCallback callback, ClusterTree.ClusteringMethod cm, SUPGMABase.PopulationParameters pp, int numberOfReplicates, LMSSolver solver)
           
 Tree SUPGMABase.PopulationParameters.generateSUPGMATree(AlgorithmCallback callback, ClusterTree.ClusteringMethod cm, DistanceMatrixGenerator replicateSource, int numberOfAlignmentBootstrapReplicates, LMSSolver solver)
           
 Tree SUPGMABase.PopulationParameters.generateSUPGMATree(ClusterTree.ClusteringMethod cm)
           
 Tree SUPGMABase.solve(AlgorithmCallback callback, ClusterTree.ClusteringMethod cm, LMSSolver solver)
           
 

Constructors in pal.supgma with parameters of type ClusterTree.ClusteringMethod
SUPGMATree(DistanceMatrix m, TimeOrderCharacterData tocd, DeltaModel deltaModel, boolean allowNegatives, ClusterTree.ClusteringMethod cm)
          constructor SUPGMA tree
SUPGMATree(DistanceMatrix m, TimeOrderCharacterData tocd, double rate, ClusterTree.ClusteringMethod cm)
          constructor SUPGMA tree
 

Uses of ClusterTree.ClusteringMethod in pal.tree
 

Fields in pal.tree declared as ClusterTree.ClusteringMethod
static ClusterTree.ClusteringMethod ClusterTree.COMPLETE_LINKAGE
           
static ClusterTree.ClusteringMethod ClusterTree.SINGLE_LINKAGE
           
static ClusterTree.ClusteringMethod ClusterTree.UPGMA
           
static ClusterTree.ClusteringMethod ClusterTree.WPGMA
           
 

Constructors in pal.tree with parameters of type ClusterTree.ClusteringMethod
ClusterTree(DistanceMatrix dm, ClusterTree.ClusteringMethod cm)