public abstract class CodonModel extends AbstractRateMatrix implements RateMatrix, java.io.Serializable
Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser, Parameterized.Utils
format
Modifier | Constructor and Description |
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protected |
CodonModel(double[] f) |
Modifier and Type | Method and Description |
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static CodonModel |
getInstance(int modelID,
double[] params,
double[] freq)
Create codon substitution model according to model type
|
protected void |
printFrequencies(java.io.PrintWriter out) |
protected void |
printRatios(java.io.PrintWriter out) |
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
equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
addPalObjectListener, clone, getDataType, getDimension, getEquilibriumFrequencies, getEquilibriumFrequency, getModelID, getOrthogonalHints, getRelativeRates, getTransitionProbabilities, getTransitionProbability, getTypeID, getUniqueName, removePalObjectListener, scale, setDistance, setDistanceTranspose, setParametersNoScale
getParameterName
getDefaultValue, getLowerLimit, getNumParameters, getParameter, getUpperLimit, setParameter, setParameterSE
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)