Package pal.distance
Class AlignmentDistanceMatrix
java.lang.Object
pal.distance.DistanceMatrix
pal.distance.AlignmentDistanceMatrix
- All Implemented Interfaces:
Serializable
,IdGroup
compute distance matrix (observed and ML) from alignment (SitePattern)
- Version:
- $Id: AlignmentDistanceMatrix.java,v 1.10 2003/03/23 00:13:36 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 observed distancescompute maximum-likelihood distancesAlignmentDistanceMatrix
(SitePattern sp, SubstitutionModel m, AlgorithmCallback callback) compute maximum-likelihood distancesAlignmentDistanceMatrix
(SitePattern sp, AlgorithmCallback callback) compute observed distances -
Method Summary
Modifier and TypeMethodDescriptionvoid
recompute
(SitePattern sp, SubstitutionModel model) recompute maximum-likelihood distances under new site patternvoid
recompute
(SitePattern sp, SubstitutionModel model, AlgorithmCallback callback) recompute maximum-likelihood distances under new site patternvoid
recompute
(SitePattern sp, AlgorithmCallback callback) recompute observed distances under new site patternMethods 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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AlignmentDistanceMatrix
compute observed distances- Parameters:
sp
- site pattern
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AlignmentDistanceMatrix
compute observed distances- Parameters:
sp
- site patterncallback
- An algorithm callback to monitor progress
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AlignmentDistanceMatrix
compute maximum-likelihood distances- Parameters:
sp
- site patternm
- evolutionary modelimmediateCompute
- - signifies whether to calculate distances from within constructor (if no should call recompute() at some point!)
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AlignmentDistanceMatrix
compute maximum-likelihood distances- Parameters:
sp
- site patternm
- evolutionary modelcallback
- An algorithm callback to monitor progress
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Method Details
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recompute
recompute observed distances under new site pattern- Parameters:
sp
- site pattern
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recompute
recompute maximum-likelihood distances under new site pattern- Parameters:
sp
- site pattern
-
recompute
recompute maximum-likelihood distances under new site pattern- Parameters:
sp
- site pattern
-