java.io.Serializable
, java.lang.Cloneable
, ExternalParameterListener
, NamedParameterized
, Parameterized
, Report
, RateMatrix
YangCodonModel
public abstract class CodonModel extends AbstractRateMatrix implements RateMatrix, java.io.Serializable
Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser, Parameterized.Utils
format
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, updateMatrixExp
getParameterName
equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
getDefaultValue, getLowerLimit, getNumParameters, getParameter, getUpperLimit, setParameter, setParameterSE
addPalObjectListener, clone, getDataType, getDimension, getEquilibriumFrequencies, getEquilibriumFrequency, getModelID, getOrthogonalHints, getRelativeRates, getTransitionProbabilities, getTransitionProbability, getTypeID, getUniqueName, removePalObjectListener, scale, setDistance, setDistanceTranspose, setParametersNoScale
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)