Uses of Interface
pal.tree.ClusterTree.ClusteringMethod
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Packages that use ClusterTree.ClusteringMethod Package Description 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). -
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Uses of ClusterTree.ClusteringMethod in pal.supgma
Methods in pal.supgma with parameters of type ClusterTree.ClusteringMethod Modifier and Type Method Description Tree
SUPGMABase. generateAlignmentBootstrappedSUPGMATree(AlgorithmCallback callback, ClusterTree.ClusteringMethod cm, SUPGMABase.PopulationParameters pp, int numberOfReplicates, LMSSolver solver)
Tree
SUPGMABase.PopulationParameters. generateSUPGMATree(ClusterTree.ClusteringMethod cm)
Tree
SUPGMABase.PopulationParameters. generateSUPGMATree(AlgorithmCallback callback, ClusterTree.ClusteringMethod cm, DistanceMatrixGenerator replicateSource, int numberOfAlignmentBootstrapReplicates, LMSSolver solver)
Tree
SUPGMABase. solve(AlgorithmCallback callback, ClusterTree.ClusteringMethod cm, LMSSolver solver)
Constructors in pal.supgma with parameters of type ClusterTree.ClusteringMethod Constructor Description SUPGMATree(DistanceMatrix m, TimeOrderCharacterData tocd, double rate, ClusterTree.ClusteringMethod cm)
constructor SUPGMA treeSUPGMATree(DistanceMatrix m, TimeOrderCharacterData tocd, DeltaModel deltaModel, boolean allowNegatives, ClusterTree.ClusteringMethod cm)
constructor SUPGMA tree -
Uses of ClusterTree.ClusteringMethod in pal.tree
Fields in pal.tree declared as ClusterTree.ClusteringMethod Modifier and Type Field Description 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 Constructor Description ClusterTree(DistanceMatrix dm, ClusterTree.ClusteringMethod cm)
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