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, waitgetSummary, updateParameterspublic 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 RateMatrixGrouppublic DataType getDataType()
getDataType in interface RateMatrixGrouppublic int getNumberOfTransitionCategories()
getNumberOfTransitionCategories in interface RateMatrixGrouppublic void getTransitionProbabilities(double branchLength,
double[][][] tableStore)
getTransitionProbabilities in interface RateMatrixGrouppublic void getTransitionProbabilitiesTranspose(double branchLength,
double[][][] tableStore)
getTransitionProbabilitiesTranspose in interface RateMatrixGrouppublic void getTransitionProbabilities(double branchLength,
int category,
double[][] tableStore)
getTransitionProbabilities in interface RateMatrixGrouppublic void getTransitionProbabilitiesTranspose(double branchLength,
int category,
double[][] tableStore)
getTransitionProbabilitiesTranspose in interface RateMatrixGrouppublic java.lang.String getSummary(double[] parameters,
double[] categoryProbabilities)