jebl.evolution.substmodel
Class AminoAcidModel

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

All Implemented Interfaces:

Serializable, Cloneable, RateMatrix

Direct Known Subclasses:

WAG

public abstract class AminoAcidModel
extends AbstractRateMatrix

base class of rate matrices for amino acids

Author:

Korbinian Strimmer

See Also:

Serialized Form

Constructor Summary

protected

AminoAcidModel(double[] f)

Method Summary

Methods inherited from class jebl.evolution.substmodel.AbstractRateMatrix

getDimension, getEquilibriumFrequencies, getEquilibriumFrequency, getFrequencies, getRelativeRates, getSequenceType, getTransitionProbabilities, getTransitionProbability, rebuild, rebuildRateMatrix, 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

Methods inherited from interface jebl.evolution.substmodel.RateMatrix

getUniqueName

Constructor Detail

AminoAcidModel

protected AminoAcidModel(double[] f)