Package pal.substmodel
Class CodonModel
- java.lang.Object
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- pal.substmodel.AbstractRateMatrix
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- pal.substmodel.CodonModel
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- All Implemented Interfaces:
java.io.Serializable
,java.lang.Cloneable
,ExternalParameterListener
,NamedParameterized
,Parameterized
,Report
,RateMatrix
- Direct Known Subclasses:
YangCodonModel
public abstract class CodonModel extends AbstractRateMatrix implements RateMatrix, java.io.Serializable
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:
- Serialized Form
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Nested Class Summary
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Nested classes/interfaces inherited from interface pal.misc.Parameterized
Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser, Parameterized.Utils
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Field Summary
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Fields inherited from class pal.substmodel.AbstractRateMatrix
format
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Constructor Summary
Constructors Modifier Constructor Description protected
CodonModel(double[] f)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description static CodonModel
getInstance(int modelID, double[] params, double[] freq)
Create codon substitution model according to model typeprotected void
printFrequencies(java.io.PrintWriter out)
protected void
printRatios(java.io.PrintWriter out)
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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
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Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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Methods inherited from interface pal.misc.NamedParameterized
getParameterName
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Methods inherited from interface pal.misc.Parameterized
getDefaultValue, getLowerLimit, getNumParameters, getParameter, getUpperLimit, setParameter, setParameterSE
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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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Method Detail
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getInstance
public static CodonModel getInstance(int modelID, double[] params, double[] freq)
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
protected void printFrequencies(java.io.PrintWriter out)
- Overrides:
printFrequencies
in classAbstractRateMatrix
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printRatios
protected void printRatios(java.io.PrintWriter out)
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