Package pal.distance
Class JukesCantorDistanceMatrix
- java.lang.Object
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- pal.distance.DistanceMatrix
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- pal.distance.JukesCantorDistanceMatrix
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- All Implemented Interfaces:
java.io.Serializable
,IdGroup
public class JukesCantorDistanceMatrix extends DistanceMatrix
compute jukes-cantor corrected distance matrix- Version:
- $Id: JukesCantorDistanceMatrix.java,v 1.5 2002/12/05 04:27:28 matt Exp $
- Author:
- Alexei Drummond, Korbinian Strimmer
- 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 JukesCantorDistanceMatrix(Alignment alignment)
compute jukes-cantor corrected distancesJukesCantorDistanceMatrix(SitePattern sitePattern)
compute jukes-cantor corrected distancesJukesCantorDistanceMatrix(DistanceMatrix dist)
compute jukes-cantor corrected distances (assumes nucleotides as underlying data)JukesCantorDistanceMatrix(DistanceMatrix dist, int numStates)
compute jukes-cantor corrected distances
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Method Summary
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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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JukesCantorDistanceMatrix
public JukesCantorDistanceMatrix(DistanceMatrix dist)
compute jukes-cantor corrected distances (assumes nucleotides as underlying data)- Parameters:
dist
- distance matrix
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JukesCantorDistanceMatrix
public JukesCantorDistanceMatrix(DistanceMatrix dist, int numStates)
compute jukes-cantor corrected distances- Parameters:
dist
- distance matrixnumStates
- number of states of underlying data
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JukesCantorDistanceMatrix
public JukesCantorDistanceMatrix(Alignment alignment)
compute jukes-cantor corrected distances- Parameters:
alignment
- Alignment
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JukesCantorDistanceMatrix
public JukesCantorDistanceMatrix(SitePattern sitePattern)
compute jukes-cantor corrected distances- Parameters:
sitePattern
- SitePattern
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