Package pal.tree
Class TreeDistanceMatrix
- java.lang.Object
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- pal.distance.DistanceMatrix
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- pal.tree.TreeDistanceMatrix
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- 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
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Nested Class Summary
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Nested classes/interfaces inherited from interface pal.misc.IdGroup
IdGroup.Utils
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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 lengthsTreeDistanceMatrix(Tree t, IdGroup idGroup, boolean countEdges, double epsilon)
compute induced distance matrix
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
recompute(Tree t)
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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
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Constructor Detail
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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
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TreeDistanceMatrix
public TreeDistanceMatrix(Tree t, IdGroup idGroup)
compute induced distance matrix using actual branch lengths- Parameters:
idGroup
- sequence order for the matrixt
- tree
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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
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TreeDistanceMatrix
public TreeDistanceMatrix(Tree t)
compute induced distance matrix using actual branch lengths (using tree-induced order of sequences)- Parameters:
t
- tree
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Method Detail
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recompute
public void recompute(Tree t)
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