pal.tree

Class TreeDistanceMatrix

java.lang.Object

pal.distance.DistanceMatrix

pal.tree.TreeDistanceMatrix

All Implemented Interfaces:

java.io.Serializable, IdGroup

public class TreeDistanceMatrix
extends DistanceMatrix

computes distance matrix induced by a tree (needs only O(n^2) time, following algorithm DistanceInTree by D.Bryant and P. Wadell. 1998. MBE 15:1346-1359)

Version:

$Id: TreeDistanceMatrix.java,v 1.9 2002/12/05 04:27:28 matt Exp $

Author:

Korbinian Strimmer, Alexei Drummond

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from interface pal.misc.IdGroup

IdGroup.Utils

Constructor Summary

Constructors

Constructor and Description
TreeDistanceMatrix(Tree t) compute induced distance matrix using actual branch lengths (using tree-induced order of sequences)
TreeDistanceMatrix(Tree t, boolean countEdges, double epsilon) compute induced distance matrix (using tree-induced order of sequences)
TreeDistanceMatrix(Tree t, IdGroup idGroup) compute induced distance matrix using actual branch lengths
TreeDistanceMatrix(Tree t, IdGroup idGroup, boolean countEdges, double epsilon) compute induced distance matrix

Method Summary

Methods

Modifier and Type	Method and Description
void	recompute(Tree t)

Methods inherited from class pal.distance.DistanceMatrix

absoluteDistance, addDistance, getClonedDistances, getClosestIndex, getClosestIndex, getDistance, getDistances, getIdCount, getIdentifier, getIdGroup, getSize, isSymmetric, meanDistance, printPHYLIP, setDistance, setDistances, setIdentifier, setIdGroup, squaredDistance, toString, whichIdNumber

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

TreeDistanceMatrix

public TreeDistanceMatrix(Tree t,
                  IdGroup idGroup,
                  boolean countEdges,
                  double epsilon)

compute induced distance matrix

Parameters:

idGroup - sequence order for the matrix

t - tree

countEdges - boolean variable deciding whether the actual branch lengths are used in computing the distance or whether simply all edges larger or equal a certain threshold length are counted (each with weight 1.0)

epsilon - minimum branch length for a which an edge is counted

TreeDistanceMatrix

public TreeDistanceMatrix(Tree t,
                  IdGroup idGroup)

compute induced distance matrix using actual branch lengths

Parameters:

idGroup - sequence order for the matrix

t - tree

TreeDistanceMatrix

public TreeDistanceMatrix(Tree t,
                  boolean countEdges,
                  double epsilon)

compute induced distance matrix (using tree-induced order of sequences)

Parameters:

t - tree

countEdges - boolean variable deciding whether the actual branch lengths are used in computing the distance or whether simply all edges larger or equal a certain threshold length are counted (each with weight 1.0)

epsilon - minimum branch length for a which an edge is counted

TreeDistanceMatrix

public TreeDistanceMatrix(Tree t)

compute induced distance matrix using actual branch lengths (using tree-induced order of sequences)

Parameters:

t - tree

Method Detail

recompute

public void recompute(Tree t)