jebl.evolution.substmodel
Class WAG

java.lang.Object
  jebl.evolution.substmodel.AbstractRateMatrix
      jebl.evolution.substmodel.AminoAcidModel
          jebl.evolution.substmodel.WAG

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, RateMatrix

public class WAG
extends AminoAcidModel

WAG model of amino acid evolution (S. Whelan and N. Goldman 2000)

Version:

$Id: WAG.java 185 2006-01-23 23:03:18Z rambaut $

Author:

Korbinian Strimmer, Alexei Drummond

See Also:

Serialized Form

Constructor Summary

WAG(double[] f)
constructor

Method Summary

static double[]	getOriginalFrequencies()
static void	getOriginalFrequencies(double[] f) get the frequencies of the original data set that formed the basis for the estimation of the rate matrix
java.lang.String	getUniqueName()

Methods inherited from class jebl.evolution.substmodel.AbstractRateMatrix

getDimension, getEquilibriumFrequencies, getEquilibriumFrequency, getRelativeRates, getSequenceType, getTransitionProbabilities, getTransitionProbability, rebuild, scale, setDistance, setDistanceTranspose, setParametersNoScale

Methods inherited from class java.lang.Object

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

Constructor Detail

WAG

public WAG(double[] f)

constructor

Parameters:

f - amino acid frequencies

Method Detail

getOriginalFrequencies

public static void getOriginalFrequencies(double[] f)

get the frequencies of the original data set that formed the basis for the estimation of the rate matrix

Parameters:

f - array where amino acid frequencies will be stored

getOriginalFrequencies

public static double[] getOriginalFrequencies()

Returns:

the frequencies of the original data set that formed the basis for the estimation of the rate matrix

getUniqueName

public java.lang.String getUniqueName()

Returns:

a short unique human-readable identifier for this rate matrix.