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
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 |
TreeDistanceMatrix
public TreeDistanceMatrix(Tree t,
IdGroup idGroup,
boolean countEdges,
double epsilon)
- compute induced distance matrix
- Parameters:
idGroup
- sequence order for the matrixt
- treecountEdges
- 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 matrixt
- tree
TreeDistanceMatrix
public TreeDistanceMatrix(Tree t,
boolean countEdges,
double epsilon)
- compute induced distance matrix
(using tree-induced order of sequences)
- Parameters:
t
- treecountEdges
- 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
recompute
public void recompute(Tree t)