pal.substmodel
public abstract class SimpleRateMatrixGroup extends java.lang.Object implements RateMatrixGroup
Constructor and Description |
---|
SimpleRateMatrixGroup(NeoRateMatrix[] baseMatrices,
double[] equilibriumFrequencies,
double[] initialClassProbabilities,
DataType dataType) |
Modifier and Type | Method and Description |
---|---|
DataType |
getDataType() |
double |
getDefaultValue(int n) |
double[] |
getEquilibriumFrequencies() |
double |
getLowerLimit(int n) |
int |
getNumberOfParameters() |
int |
getNumberOfTransitionCategories() |
java.lang.String |
getSummary(double[] parameters,
double[] categoryProbabilities) |
void |
getTransitionProbabilities(double branchLength,
double[][][] tableStore) |
void |
getTransitionProbabilities(double branchLength,
int category,
double[][] tableStore) |
void |
getTransitionProbabilitiesTranspose(double branchLength,
double[][][] tableStore) |
void |
getTransitionProbabilitiesTranspose(double branchLength,
int category,
double[][] tableStore) |
double |
getUpperLimit(int n) |
void |
setParameters(double[] parameters,
double[] categoryProbabilities) |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
getSummary, updateParameters
public SimpleRateMatrixGroup(NeoRateMatrix[] baseMatrices, double[] equilibriumFrequencies, double[] initialClassProbabilities, DataType dataType)
public int getNumberOfParameters()
public double getLowerLimit(int n)
public double getUpperLimit(int n)
public double getDefaultValue(int n)
public void setParameters(double[] parameters, double[] categoryProbabilities)
public double[] getEquilibriumFrequencies()
getEquilibriumFrequencies
in interface RateMatrixGroup
public DataType getDataType()
getDataType
in interface RateMatrixGroup
public int getNumberOfTransitionCategories()
getNumberOfTransitionCategories
in interface RateMatrixGroup
public void getTransitionProbabilities(double branchLength, double[][][] tableStore)
getTransitionProbabilities
in interface RateMatrixGroup
public void getTransitionProbabilitiesTranspose(double branchLength, double[][][] tableStore)
getTransitionProbabilitiesTranspose
in interface RateMatrixGroup
public void getTransitionProbabilities(double branchLength, int category, double[][] tableStore)
getTransitionProbabilities
in interface RateMatrixGroup
public void getTransitionProbabilitiesTranspose(double branchLength, int category, double[][] tableStore)
getTransitionProbabilitiesTranspose
in interface RateMatrixGroup
public java.lang.String getSummary(double[] parameters, double[] categoryProbabilities)