Package pal.tree
Class TreeDistanceMatrix
java.lang.Object
pal.distance.DistanceMatrix
pal.tree.TreeDistanceMatrix
- All Implemented Interfaces:
Serializable
,IdGroup
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:
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Nested Class Summary
Nested classes/interfaces inherited from interface pal.misc.IdGroup
IdGroup.Utils
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Constructor Summary
ConstructorsConstructorDescriptioncompute 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 -
Method Summary
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 Details
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TreeDistanceMatrix
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
compute induced distance matrix using actual branch lengths- Parameters:
idGroup
- sequence order for the matrixt
- tree
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TreeDistanceMatrix
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
compute induced distance matrix using actual branch lengths (using tree-induced order of sequences)- Parameters:
t
- tree
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Method Details
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recompute
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