Package pal.tree
Class ClusterTree
- java.lang.Object
-
- pal.tree.SimpleTree
-
- pal.tree.ClusterTree
-
- All Implemented Interfaces:
java.io.Serializable
,IdGroup
,Report
,Units
,UnitsProvider
,Tree
- Direct Known Subclasses:
SUPGMATree
public class ClusterTree extends SimpleTree
- See Also:
- Serialized Form
-
-
Nested Class Summary
Nested Classes Modifier and Type Class Description static interface
ClusterTree.ClusteringMethod
An interface for describing Clustering methods To be updated to cope with Ward's method and others...-
Nested classes/interfaces inherited from interface pal.misc.IdGroup
IdGroup.Utils
-
Nested classes/interfaces inherited from interface pal.tree.Tree
Tree.TreeBase
-
-
Field Summary
Fields Modifier and Type Field Description static ClusterTree.ClusteringMethod
COMPLETE_LINKAGE
static ClusterTree.ClusteringMethod
SINGLE_LINKAGE
static ClusterTree.ClusteringMethod
UPGMA
static ClusterTree.ClusteringMethod
WPGMA
-
Fields inherited from interface pal.misc.Units
DAYS, EXPECTED_SUBSTITUTIONS, GENERATIONS, MONTHS, SAMPLE, SHORT_UNIT_NAMES, UNIT_NAMES, UNKNOWN, YEARS
-
-
Constructor Summary
Constructors Constructor Description ClusterTree(DistanceMatrix dm, ClusterTree.ClusteringMethod cm)
-
Method Summary
-
Methods inherited from class pal.tree.SimpleTree
createNodeList, findNode, getAttribute, getCopy, getExternalNode, getExternalNodeCount, getIdCount, getIdentifier, getInternalNode, getInternalNodeCount, getRoot, getUnits, report, reroot, reroot, setAttribute, setIdentifier, setRoot, setUnits, toString, whichIdNumber
-
-
-
-
Field Detail
-
UPGMA
public static final ClusterTree.ClusteringMethod UPGMA
-
WPGMA
public static final ClusterTree.ClusteringMethod WPGMA
-
SINGLE_LINKAGE
public static final ClusterTree.ClusteringMethod SINGLE_LINKAGE
-
COMPLETE_LINKAGE
public static final ClusterTree.ClusteringMethod COMPLETE_LINKAGE
-
-
Constructor Detail
-
ClusterTree
public ClusterTree(DistanceMatrix dm, ClusterTree.ClusteringMethod cm)
-
-