pal.distance
Class AlignmentDistanceMatrix
java.lang.Object
|
+--pal.distance.DistanceMatrix
|
+--pal.distance.AlignmentDistanceMatrix
- All Implemented Interfaces:
- IdGroup, java.io.Serializable
- public class AlignmentDistanceMatrix
- extends DistanceMatrix
- implements java.io.Serializable
compute distance matrix (observed and ML) from alignment (SitePattern)
- See Also:
- Serialized Form
Methods inherited from class pal.distance.DistanceMatrix |
absoluteDistance, addDistance, getDistances, getIdCount, getIdentifier, getIdGroup, getSize, isSymmetric, meanDistance, printPHYLIP, setDistance, setIdentifier, squaredDistance, toString, whichIdNumber |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
AlignmentDistanceMatrix
public AlignmentDistanceMatrix(SitePattern sp)
- compute observed distances
- Parameters:
sp
- site pattern
AlignmentDistanceMatrix
public AlignmentDistanceMatrix(SitePattern sp,
boolean immediateCompute)
- compute observed distances
- Parameters:
sp
- site patternimmediateCompute
- - signifies whether to calculate distances from within constructor
(if no should call recompute() at some point!)
AlignmentDistanceMatrix
public AlignmentDistanceMatrix(SitePattern sp,
SubstitutionModel m)
- compute maximum-likelihood distances
- Parameters:
sp
- site patternm
- evolutionary model
AlignmentDistanceMatrix
protected AlignmentDistanceMatrix(SitePattern sp,
SubstitutionModel m,
boolean immediateCompute)
- 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!)
recompute
public void recompute(SubstitutionModel m)
- recompute maximum-likelihood distances under new model
- Parameters:
m
- evolutionary model
recompute
public void recompute(SitePattern sp)
- recompute maximum-likelihood distances under new site pattern
- Parameters:
sp
- site pattern
getProgress
public final double getProgress()
- Returns -1 if not doing anything, or a number between 0 and 1