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java.lang.Object | +--pal.substmodel.AbstractRateMatrix | +--pal.substmodel.CodonModel
base class for nucleotide rate matrices
Fields inherited from class pal.substmodel.AbstractRateMatrix |
dataType, dimension, format, frequency, rate |
Constructor Summary | |
protected |
CodonModel(double[] f)
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Method Summary | |
static CodonModel |
getInstance(int modelID,
double[] params,
double[] freq)
Create codon 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 |
equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Methods inherited from interface pal.substmodel.RateMatrix |
addPalObjectListener, clone, getDataType, getDimension, getEquilibriumFrequencies, getEquilibriumFrequency, getModelID, getRelativeRates, getTransitionProbabilities, getTransitionProbability, getTypeID, getUniqueName, removePalObjectListener, setDistance |
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.misc.Report |
report |
Constructor Detail |
protected CodonModel(double[] f)
Method Detail |
public static CodonModel getInstance(int modelID, double[] params, double[] freq)
modelID
- model codeparams
- model parametersfreq
- model frequenciesprotected void printFrequencies(java.io.PrintWriter out)
printFrequencies
in class AbstractRateMatrix
protected void printRatios(java.io.PrintWriter out)
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