Package pal.substmodel
Class CodonModel
java.lang.Object
pal.substmodel.AbstractRateMatrix
pal.substmodel.CodonModel
- All Implemented Interfaces:
Serializable
,Cloneable
,ExternalParameterListener
,NamedParameterized
,Parameterized
,Report
,RateMatrix
- Direct Known Subclasses:
YangCodonModel
base class for nucleotide rate matrices
- Version:
- $Id: CodonModel.java,v 1.5 2003/11/13 04:05:39 matt Exp $
- Author:
- Andrew Rambaut
- See Also:
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Nested Class Summary
Nested classes/interfaces inherited from interface pal.misc.Parameterized
Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser, Parameterized.Utils
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Field Summary
Fields inherited from class pal.substmodel.AbstractRateMatrix
format
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionstatic CodonModel
getInstance
(int modelID, double[] params, double[] freq) Create codon substitution model according to model typeprotected void
protected void
printRatios
(PrintWriter out) Methods inherited from class pal.substmodel.AbstractRateMatrix
addPalObjectListener, clone, fireParametersChangedEvent, fireParametersChangedEvent, getDataType, getDimension, getEquilibriumFrequencies, getEquilibriumFrequency, getFrequencies, getModelID, getOrthogonalHints, getParameter, getRelativeRates, getTransitionProbabilities, getTransitionProbability, getTypeID, parameterChanged, rebuild, rebuildRateMatrix, removePalObjectListener, scale, setDataType, setDistance, setDistanceTranspose, setFrequencies, setParameter, setParameters, setParametersNoScale, updateMatrixExp
Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
Methods inherited from interface pal.misc.NamedParameterized
getParameterName
Methods inherited from interface pal.misc.Parameterized
getDefaultValue, getLowerLimit, getNumParameters, getParameter, getUpperLimit, setParameter, setParameterSE
Methods inherited from interface pal.substmodel.RateMatrix
addPalObjectListener, clone, getDataType, getDimension, getEquilibriumFrequencies, getEquilibriumFrequency, getModelID, getOrthogonalHints, getRelativeRates, getTransitionProbabilities, getTransitionProbability, getTypeID, getUniqueName, removePalObjectListener, scale, setDistance, setDistanceTranspose, setParametersNoScale
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Constructor Details
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CodonModel
protected CodonModel(double[] f)
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Method Details
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getInstance
Create codon substitution model according to model type- Parameters:
modelID
- model codeparams
- model parametersfreq
- model frequencies- Returns:
- codon rate matrix
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printFrequencies
- Overrides:
printFrequencies
in classAbstractRateMatrix
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printRatios
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