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java.lang.Objectpal.distance.DistanceMatrix
pal.distance.JukesCantorDistanceMatrix
public class JukesCantorDistanceMatrix
compute jukes-cantor corrected distance matrix
Nested Class Summary |
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Nested classes/interfaces inherited from interface pal.misc.IdGroup |
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IdGroup.Utils |
Constructor Summary | |
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JukesCantorDistanceMatrix(Alignment alignment)
compute jukes-cantor corrected distances |
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JukesCantorDistanceMatrix(DistanceMatrix dist)
compute jukes-cantor corrected distances (assumes nucleotides as underlying data) |
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JukesCantorDistanceMatrix(DistanceMatrix dist,
int numStates)
compute jukes-cantor corrected distances |
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JukesCantorDistanceMatrix(SitePattern sitePattern)
compute jukes-cantor corrected distances |
Method Summary |
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Methods inherited from class pal.distance.DistanceMatrix |
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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 |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Constructor Detail |
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public JukesCantorDistanceMatrix(DistanceMatrix dist)
dist
- distance matrixpublic JukesCantorDistanceMatrix(DistanceMatrix dist, int numStates)
dist
- distance matrixnumStates
- number of states of underlying datapublic JukesCantorDistanceMatrix(Alignment alignment)
alignment
- Alignmentpublic JukesCantorDistanceMatrix(SitePattern sitePattern)
sitePattern
- SitePattern
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