pal.tree
Class ClusterTree

java.lang.Object
  extended by pal.tree.SimpleTree
      extended by 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
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.tree.Tree
Tree.TreeBase
 
Nested classes/interfaces inherited from interface pal.misc.IdGroup
IdGroup.Utils
 
Field Summary
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
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
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

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)