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java.lang.Objectpal.distance.DistanceMatrix
pal.distance.AlignmentDistanceMatrix
public class AlignmentDistanceMatrix
compute distance matrix (observed and ML) from alignment (SitePattern)
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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AlignmentDistanceMatrix(SitePattern sp)
compute observed distances |
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AlignmentDistanceMatrix(SitePattern sp,
AlgorithmCallback callback)
compute observed distances |
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AlignmentDistanceMatrix(SitePattern sp,
SubstitutionModel m)
compute maximum-likelihood distances |
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AlignmentDistanceMatrix(SitePattern sp,
SubstitutionModel m,
AlgorithmCallback callback)
compute maximum-likelihood distances |
Method Summary | |
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void |
recompute(SitePattern sp,
AlgorithmCallback callback)
recompute observed distances under new site pattern |
void |
recompute(SitePattern sp,
SubstitutionModel model)
recompute maximum-likelihood distances under new site pattern |
void |
recompute(SitePattern sp,
SubstitutionModel model,
AlgorithmCallback callback)
recompute maximum-likelihood distances under new site pattern |
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 AlignmentDistanceMatrix(SitePattern sp)
sp
- site patternpublic AlignmentDistanceMatrix(SitePattern sp, AlgorithmCallback callback)
sp
- site patterncallback
- An algorithm callback to monitor progresspublic AlignmentDistanceMatrix(SitePattern sp, SubstitutionModel m)
sp
- site patternm
- evolutionary modelimmediateCompute
- - signifies whether to calculate distances from within constructor
(if no should call recompute() at some point!)public AlignmentDistanceMatrix(SitePattern sp, SubstitutionModel m, AlgorithmCallback callback)
sp
- site patternm
- evolutionary modelcallback
- An algorithm callback to monitor progressMethod Detail |
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public void recompute(SitePattern sp, AlgorithmCallback callback)
sp
- site patternpublic void recompute(SitePattern sp, SubstitutionModel model)
sp
- site patternpublic void recompute(SitePattern sp, SubstitutionModel model, AlgorithmCallback callback)
sp
- site pattern
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