java.io.Serializable, java.lang.Cloneable, ExternalParameterListener, NamedParameterized, Parameterized, Report, RateMatrixYangCodonModelpublic abstract class CodonModel extends AbstractRateMatrix implements RateMatrix, java.io.Serializable
Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser, Parameterized.Utilsformat| Modifier | Constructor | Description |
|---|---|---|
protected |
CodonModel(double[] f) |
| Modifier and Type | Method | Description |
|---|---|---|
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, updateMatrixExpgetParameterNameequals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, waitgetDefaultValue, getLowerLimit, getNumParameters, getParameter, getUpperLimit, setParameter, setParameterSEaddPalObjectListener, clone, getDataType, getDimension, getEquilibriumFrequencies, getEquilibriumFrequency, getModelID, getOrthogonalHints, getRelativeRates, getTransitionProbabilities, getTransitionProbability, getTypeID, getUniqueName, removePalObjectListener, scale, setDistance, setDistanceTranspose, setParametersNoScalepublic 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 AbstractRateMatrixprotected void printRatios(java.io.PrintWriter out)