Package jebl.evolution.substmodel
Class WAG
- java.lang.Object
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- jebl.evolution.substmodel.AbstractRateMatrix
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- jebl.evolution.substmodel.AminoAcidModel
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- jebl.evolution.substmodel.WAG
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- 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
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Constructor Summary
Constructors Constructor Description WAG(double[] f)
constructor
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description 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 matrixjava.lang.String
getUniqueName()
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Methods inherited from class jebl.evolution.substmodel.AbstractRateMatrix
getDimension, getEquilibriumFrequencies, getEquilibriumFrequency, getRelativeRates, getSequenceType, getTransitionProbabilities, getTransitionProbability, rebuild, scale, setDistance, setDistanceTranspose, setParametersNoScale
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Method Detail
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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
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getOriginalFrequencies
public static double[] getOriginalFrequencies()
- Returns:
- the frequencies of the original data set that formed the basis for the estimation of the rate matrix
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getUniqueName
public java.lang.String getUniqueName()
- Returns:
- a short unique human-readable identifier for this rate matrix.
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