java.io.Serializable
, IdGroup
, Report
, Units
, UnitsProvider
, Tree
public class SUPGMATree extends ClusterTree
ClusterTree.ClusteringMethod
IdGroup.Utils
Tree.TreeBase
COMPLETE_LINKAGE, SINGLE_LINKAGE, UPGMA, WPGMA
DAYS, EXPECTED_SUBSTITUTIONS, GENERATIONS, MONTHS, SAMPLE, SHORT_UNIT_NAMES, UNIT_NAMES, UNKNOWN, YEARS
Constructor | Description |
---|---|
SUPGMATree(DistanceMatrix m,
TimeOrderCharacterData tocd,
double rate,
ClusterTree.ClusteringMethod cm) |
constructor SUPGMA tree
|
SUPGMATree(DistanceMatrix m,
TimeOrderCharacterData tocd,
DeltaModel deltaModel,
boolean allowNegatives,
ClusterTree.ClusteringMethod cm) |
constructor SUPGMA tree
|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
createNodeList, findNode, getAttribute, getCopy, getExternalNode, getExternalNodeCount, getIdCount, getIdentifier, getInternalNode, getInternalNodeCount, getRoot, getUnits, report, reroot, reroot, setAttribute, setIdentifier, setRoot, setUnits, toString, whichIdNumber
public SUPGMATree(DistanceMatrix m, TimeOrderCharacterData tocd, double rate, ClusterTree.ClusteringMethod cm)
m
- *uncorrected* distance matrixpublic SUPGMATree(DistanceMatrix m, TimeOrderCharacterData tocd, DeltaModel deltaModel, boolean allowNegatives, ClusterTree.ClusteringMethod cm)
m
- *uncorrected* distance matrix