Package pal.substmodel
Class NucleotideModel
- java.lang.Object
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- pal.substmodel.AbstractRateMatrix
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- pal.substmodel.NucleotideModel
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- All Implemented Interfaces:
java.io.Serializable
,java.lang.Cloneable
,ExternalParameterListener
,NamedParameterized
,Parameterized
,Report
,RateMatrix
public abstract class NucleotideModel extends AbstractRateMatrix implements RateMatrix, java.io.Serializable
base class for nucleotide rate matrices- Version:
- $Id: NucleotideModel.java,v 1.10 2003/11/30 05:29:22 matt Exp $
- Author:
- Korbinian Strimmer
- 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
NucleotideModel(double[] f)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description static NucleotideModel
getInstance(int modelID, double[] params, double[] freq)
Create nucleotide 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 NucleotideModel getInstance(int modelID, double[] params, double[] freq)
Create nucleotide substitution model according to model type- Parameters:
modelID
- model codeparams
- model parametersfreq
- model frequencies- Returns:
- nucleotide 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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