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java.lang.Objectpal.substmodel.AbstractRateMatrix
pal.substmodel.NucleotideModel
public abstract class NucleotideModel
base class for nucleotide rate matrices
Nested Class Summary |
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Nested classes/interfaces inherited from interface pal.misc.Parameterized |
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Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser, Parameterized.Utils |
Field Summary |
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Fields inherited from class pal.substmodel.AbstractRateMatrix |
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format |
Constructor Summary | |
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protected |
NucleotideModel(double[] f)
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Method Summary | |
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static NucleotideModel |
getInstance(int modelID,
double[] params,
double[] freq)
Create nucleotide substitution model according to model type |
protected void |
printFrequencies(java.io.PrintWriter out)
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protected void |
printRatios(java.io.PrintWriter out)
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Methods inherited from class java.lang.Object |
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equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Methods inherited from interface pal.substmodel.RateMatrix |
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addPalObjectListener, clone, getDataType, getDimension, getEquilibriumFrequencies, getEquilibriumFrequency, getModelID, getOrthogonalHints, getRelativeRates, getTransitionProbabilities, getTransitionProbability, getTypeID, getUniqueName, removePalObjectListener, scale, setDistance, setDistanceTranspose, setParametersNoScale |
Methods inherited from interface pal.misc.NamedParameterized |
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getParameterName |
Methods inherited from interface pal.misc.Parameterized |
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getDefaultValue, getLowerLimit, getNumParameters, getParameter, getUpperLimit, setParameter, setParameterSE |
Methods inherited from interface pal.misc.Report |
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report |
Constructor Detail |
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protected NucleotideModel(double[] f)
Method Detail |
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public static NucleotideModel getInstance(int modelID, double[] params, double[] freq)
modelID
- model codeparams
- model parametersfreq
- model frequencies
protected void printFrequencies(java.io.PrintWriter out)
printFrequencies
in class AbstractRateMatrix
protected void printRatios(java.io.PrintWriter out)
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