java.io.Serializable
, Parameterized
, Report
, SubstitutionModel
public class GeneralRateDistributionSubstitutionModel extends Parameterized.ParameterizedUser implements SubstitutionModel
Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser
SubstitutionModel.Utils
Constructor | Description |
---|---|
GeneralRateDistributionSubstitutionModel(NeoRateMatrix base,
RateDistribution rateDistribution,
DataType dt,
double[] frequencies) |
Modifier and Type | Method | Description |
---|---|---|
void |
addPalObjectListener(PalObjectListener l) |
|
java.lang.Object |
clone() |
|
SubstitutionModel |
getCopy() |
|
DataType |
getDataType() |
|
double[] |
getEquilibriumFrequencies() |
Should return a double[] array of the related equilibrium frequencies.
|
double[] |
getMatrixParameters() |
|
int |
getNumberOfTransitionCategories() |
|
OrthogonalHints |
getOrthogonalHints() |
May return null
|
double[] |
getRateDistributionParameters() |
|
double[] |
getTransitionCategoryProbabilities() |
|
double |
getTransitionCategoryProbability(int category) |
|
void |
getTransitionProbabilities(double branchLength,
double[][][] store) |
Table is organized as [transition_group][from][to]
|
void |
getTransitionProbabilities(double branchLength,
int category,
double[][] store) |
Table is organized as [transition_group][from][to]
|
void |
getTransitionProbabilitiesTranspose(double branchLength,
double[][][] store) |
Table is organized as [transition_group][to][from]
|
void |
getTransitionProbabilitiesTranspose(double branchLength,
int category,
double[][] store) |
Table is organized as [transition_group][to][from]
|
void |
removePalObjectListener(PalObjectListener l) |
|
void |
report(java.io.PrintWriter out) |
print human readable report (e.g., on parameters and associated model)
|
java.lang.String |
toString() |
equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
fireParametersChangedEvent, fireParametersChangedEvent, fireStructureChangedEvent, fireStructureChangedEvent
getDefaultValue, getLowerLimit, getNumParameters, getParameter, getUpperLimit, setParameter, setParameterSE
getAllParameters, getDefaultValue, getLowerLimit, getNumParameters, getParameter, getRandomParameterValue, getUpperLimit, randomiseParameters, setParameter, setParameterizedBase, setParameterSE
public GeneralRateDistributionSubstitutionModel(NeoRateMatrix base, RateDistribution rateDistribution, DataType dt, double[] frequencies)
public double[] getMatrixParameters()
public double[] getRateDistributionParameters()
public DataType getDataType()
getDataType
in interface SubstitutionModel
public int getNumberOfTransitionCategories()
getNumberOfTransitionCategories
in interface SubstitutionModel
public double getTransitionCategoryProbability(int category)
getTransitionCategoryProbability
in interface SubstitutionModel
public double[] getTransitionCategoryProbabilities()
getTransitionCategoryProbabilities
in interface SubstitutionModel
public double[] getEquilibriumFrequencies()
SubstitutionModel
getEquilibriumFrequencies
in interface SubstitutionModel
public void getTransitionProbabilities(double branchLength, double[][][] store)
SubstitutionModel
getTransitionProbabilities
in interface SubstitutionModel
public void getTransitionProbabilities(double branchLength, int category, double[][] store)
SubstitutionModel
getTransitionProbabilities
in interface SubstitutionModel
public void getTransitionProbabilitiesTranspose(double branchLength, double[][][] store)
SubstitutionModel
getTransitionProbabilitiesTranspose
in interface SubstitutionModel
public void getTransitionProbabilitiesTranspose(double branchLength, int category, double[][] store)
SubstitutionModel
getTransitionProbabilitiesTranspose
in interface SubstitutionModel
public void addPalObjectListener(PalObjectListener l)
addPalObjectListener
in interface SubstitutionModel
addPalObjectListener
in class PalObjectListener.EventGenerator
public void removePalObjectListener(PalObjectListener l)
removePalObjectListener
in interface SubstitutionModel
removePalObjectListener
in class PalObjectListener.EventGenerator
public OrthogonalHints getOrthogonalHints()
SubstitutionModel
getOrthogonalHints
in interface SubstitutionModel
public void report(java.io.PrintWriter out)
Report
public java.lang.String toString()
toString
in class java.lang.Object
public java.lang.Object clone()
clone
in interface SubstitutionModel
clone
in class java.lang.Object
public SubstitutionModel getCopy()