jebl.evolution.distances

Class JukesCantorDistanceMatrix

java.lang.Object

jebl.evolution.distances.BasicDistanceMatrix

jebl.evolution.distances.JukesCantorDistanceMatrix

All Implemented Interfaces:

DistanceMatrix

public class JukesCantorDistanceMatrix
extends BasicDistanceMatrix

Compute jukes-cantor corrected distance matrix for a set of aligned sequences. Adapted from BEAST code by joseph.

Version:

$Id: JukesCantorDistanceMatrix.java 998 2009-04-09 03:06:19Z richardmoir $

Author:

Andrew Rambaut, Korbinian Strimmer, Joseph Heled

Constructor Summary

Constructors

Constructor and Description
JukesCantorDistanceMatrix(Alignment alignment, ProgressListener progress)
JukesCantorDistanceMatrix(Alignment alignment, ProgressListener progress, boolean useTwiceMaximumDistanceWhenPairwiseDistanceNotCalculatable)

Method Summary

Methods inherited from class jebl.evolution.distances.BasicDistanceMatrix

getDistance, getDistance, getDistances, getSize, getSubmatrix, getTaxa

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

JukesCantorDistanceMatrix

public JukesCantorDistanceMatrix(Alignment alignment,
                         ProgressListener progress)
                          throws CannotBuildDistanceMatrixException

Throws:

CannotBuildDistanceMatrixException

JukesCantorDistanceMatrix

public JukesCantorDistanceMatrix(Alignment alignment,
                         ProgressListener progress,
                         boolean useTwiceMaximumDistanceWhenPairwiseDistanceNotCalculatable)
                          throws CannotBuildDistanceMatrixException

Throws:

CannotBuildDistanceMatrixException