jebl.evolution.substmodel
Class WAG

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

All Implemented Interfaces:

Serializable, Cloneable, RateMatrix

public class WAG
extends AminoAcidModel

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

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
String	getUniqueName()
protected void	rebuildRateMatrix(double[][] rate, double[] parameters)

Methods inherited from class jebl.evolution.substmodel.AbstractRateMatrix

getDimension, getEquilibriumFrequencies, getEquilibriumFrequency, getFrequencies, getRelativeRates, getSequenceType, getTransitionProbabilities, getTransitionProbability, rebuild, scale, setDistance, setDistanceTranspose, setFrequencies, setParametersNoScale, setSequenceType, updateMatrixExp

Methods inherited from class java.lang.Object

clone, equals, finalize, 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

rebuildRateMatrix

protected void rebuildRateMatrix(double[][] rate,
                                 double[] parameters)

Specified by:

rebuildRateMatrix in class AbstractRateMatrix

getUniqueName

public String getUniqueName()

Returns:

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