Package pal.distance
Class AlignmentDistanceMatrix
- java.lang.Object
-
- pal.distance.DistanceMatrix
-
- pal.distance.AlignmentDistanceMatrix
-
- All Implemented Interfaces:
java.io.Serializable
,IdGroup
public class AlignmentDistanceMatrix extends DistanceMatrix implements java.io.Serializable
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:
- Serialized Form
-
-
Nested Class Summary
-
Nested classes/interfaces inherited from interface pal.misc.IdGroup
IdGroup.Utils
-
-
Constructor Summary
Constructors Constructor Description AlignmentDistanceMatrix(SitePattern sp)
compute observed distancesAlignmentDistanceMatrix(SitePattern sp, SubstitutionModel m)
compute maximum-likelihood distancesAlignmentDistanceMatrix(SitePattern sp, SubstitutionModel m, AlgorithmCallback callback)
compute maximum-likelihood distancesAlignmentDistanceMatrix(SitePattern sp, AlgorithmCallback callback)
compute observed distances
-
Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
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 pattern-
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
-
-
-
-
Constructor Detail
-
AlignmentDistanceMatrix
public AlignmentDistanceMatrix(SitePattern sp)
compute observed distances- Parameters:
sp
- site pattern
-
AlignmentDistanceMatrix
public AlignmentDistanceMatrix(SitePattern sp, AlgorithmCallback callback)
compute observed distances- Parameters:
sp
- site patterncallback
- An algorithm callback to monitor progress
-
AlignmentDistanceMatrix
public AlignmentDistanceMatrix(SitePattern sp, SubstitutionModel m)
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!)
-
AlignmentDistanceMatrix
public AlignmentDistanceMatrix(SitePattern sp, SubstitutionModel m, AlgorithmCallback callback)
compute maximum-likelihood distances- Parameters:
sp
- site patternm
- evolutionary modelcallback
- An algorithm callback to monitor progress
-
-
Method Detail
-
recompute
public void recompute(SitePattern sp, AlgorithmCallback callback)
recompute observed distances under new site pattern- Parameters:
sp
- site pattern
-
recompute
public void recompute(SitePattern sp, SubstitutionModel model)
recompute maximum-likelihood distances under new site pattern- Parameters:
sp
- site pattern
-
recompute
public void recompute(SitePattern sp, SubstitutionModel model, AlgorithmCallback callback)
recompute maximum-likelihood distances under new site pattern- Parameters:
sp
- site pattern
-
-