pal.supgma
Class SUPGMATree

java.lang.Object
  extended by pal.tree.SimpleTree
      extended by pal.tree.ClusterTree
          extended by pal.supgma.SUPGMATree
All Implemented Interfaces:
java.io.Serializable, IdGroup, Report, Units, UnitsProvider, Tree

public class SUPGMATree
extends ClusterTree

constructs an SUPGMA tree from pairwise distances.
Reference:
Alexei Drummond and Allen G. Rodrigo (2000). Reconstructing Genealogies of Serial Samples Under the Assumption of a Molecular Clock Using Serial-Sample UPGMA. Molecular Biology and Evolution 17:1807-1815

Version:
$Id: SUPGMATree.java,v 1.1 2003/10/19 02:35:26 matt Exp $
Author:
Alexei Drummond, Matthew Goode
See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from class pal.tree.ClusterTree
ClusterTree.ClusteringMethod
 
Nested classes/interfaces inherited from interface pal.tree.Tree
Tree.TreeBase
 
Nested classes/interfaces inherited from interface pal.misc.IdGroup
IdGroup.Utils
 
Field Summary
 
Fields inherited from class pal.tree.ClusterTree
COMPLETE_LINKAGE, SINGLE_LINKAGE, UPGMA, WPGMA
 
Fields inherited from interface pal.misc.Units
DAYS, EXPECTED_SUBSTITUTIONS, GENERATIONS, MONTHS, SAMPLE, SHORT_UNIT_NAMES, UNIT_NAMES, UNKNOWN, YEARS
 
Constructor Summary
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
 
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
 

Constructor Detail

SUPGMATree

public SUPGMATree(DistanceMatrix m,
                  TimeOrderCharacterData tocd,
                  double rate,
                  ClusterTree.ClusteringMethod cm)
constructor SUPGMA tree

Parameters:
m - *uncorrected* distance matrix

SUPGMATree

public SUPGMATree(DistanceMatrix m,
                  TimeOrderCharacterData tocd,
                  DeltaModel deltaModel,
                  boolean allowNegatives,
                  ClusterTree.ClusteringMethod cm)
constructor SUPGMA tree

Parameters:
m - *uncorrected* distance matrix