public class AlignmentDistanceMatrix extends DistanceMatrix implements java.io.Serializable
IdGroup.Utils| Constructor and Description |
|---|
AlignmentDistanceMatrix(SitePattern sp)
compute observed distances
|
AlignmentDistanceMatrix(SitePattern sp,
AlgorithmCallback callback)
compute observed distances
|
AlignmentDistanceMatrix(SitePattern sp,
SubstitutionModel m)
compute maximum-likelihood distances
|
AlignmentDistanceMatrix(SitePattern sp,
SubstitutionModel m,
AlgorithmCallback callback)
compute maximum-likelihood distances
|
| Modifier and Type | Method and Description |
|---|---|
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
|
absoluteDistance, addDistance, getClonedDistances, getClosestIndex, getClosestIndex, getDistance, getDistances, getIdCount, getIdentifier, getIdGroup, getSize, isSymmetric, meanDistance, printPHYLIP, setDistance, setDistances, setIdentifier, setIdGroup, squaredDistance, toString, whichIdNumberpublic 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 progresspublic 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