pal.supgma
Class SUPGMADistanceMatrix

java.lang.Object
  pal.distance.DistanceMatrix
      pal.supgma.SUPGMADistanceMatrix

All Implemented Interfaces:

java.io.Serializable, IdGroup

public class SUPGMADistanceMatrix
extends DistanceMatrix

Corrects distances in a distance matrix such that all tips appear contemporaneous, given a time/date and rate information for the taxa.

Version:

$Id: SUPGMADistanceMatrix.java,v 1.1 2003/10/19 02:35:26 matt Exp $

Author:

Alexei Drummond, Matthew Goode

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from interface pal.misc.IdGroup

IdGroup.Utils

Constructor Summary

SUPGMADistanceMatrix(DistanceMatrix raw, TimeOrderCharacterData tocd, DeltaModel deltaModel)
Uses date/time information and a constant rate to correct distance matrices.

Method Summary

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

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

SUPGMADistanceMatrix

public SUPGMADistanceMatrix(DistanceMatrix raw,
                            TimeOrderCharacterData tocd,
                            DeltaModel deltaModel)

Uses date/time information and a constant rate to correct distance matrices.