pal.distance
Class JukesCantorDistanceMatrix
java.lang.Object
|
+--pal.distance.DistanceMatrix
|
+--pal.distance.JukesCantorDistanceMatrix
- All Implemented Interfaces:
- IdGroup, java.io.Serializable
- public class JukesCantorDistanceMatrix
- extends DistanceMatrix
compute jukes-cantor corrected distance matrix
- 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 |
JukesCantorDistanceMatrix
public JukesCantorDistanceMatrix(DistanceMatrix dist)
- compute jukes-cantor corrected distances
(assumes nucleotides as underlying data)
- Parameters:
dist
- distance matrix
JukesCantorDistanceMatrix
public JukesCantorDistanceMatrix(DistanceMatrix dist,
int numStates)
- compute jukes-cantor corrected distances
- Parameters:
dist
- distance matrixnumStates
- number of states of underlying data
JukesCantorDistanceMatrix
public JukesCantorDistanceMatrix(Alignment alignment)
- compute jukes-cantor corrected distances
- Parameters:
alignment
- Alignment
JukesCantorDistanceMatrix
public JukesCantorDistanceMatrix(SitePattern sitePattern)
- compute jukes-cantor corrected distances
- Parameters:
sitePattern
- SitePattern