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	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

All Methods Instance Methods Concrete Methods
Modifier and Type Method 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

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`recompute(Tree t)`

- 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)
```

Class TreeDistanceMatrix

Nested Class Summary

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

Constructor Summary

Method Summary

Methods inherited from class pal.distance.DistanceMatrix

Methods inherited from class java.lang.Object

Constructor Detail

TreeDistanceMatrix

TreeDistanceMatrix

TreeDistanceMatrix

TreeDistanceMatrix

Method Detail

recompute