public class MultiRateMatrixHandler extends java.lang.Object implements NeoParameterized, java.io.Serializable
Constructor and Description |
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MultiRateMatrixHandler(NeoRateMatrix[] rateMatrices,
double[] equilibriumFrequencies,
double[] initialClassProportions) |
Modifier and Type | Method and Description |
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MultiRateMatrixHandler |
getCopy() |
double |
getDefaultValue(int n) |
void |
getDefaultValues(double[] store,
int startIndex)
get default value parameter values
|
double[] |
getEquilibriumFrequencies() |
double |
getLowerLimit(int n)
get lower parameter limit
|
int |
getNumberOfParameters()
get number of parameters
|
int |
getNumberOfSubstitutionClasses() |
void |
getParameters(double[] parameterStore,
int startIndex)
get model parameter
|
double |
getSubstitutionClassDefaultValue() |
double |
getSubstitutionClassLowerLimit() |
double |
getSubstitutionClassUpperLimit() |
void |
getTransitionProbabilities(double distance,
double[][][] store) |
void |
getTransitionProbabilities(double distance,
int category,
double[][] store) |
void |
getTransitionProbabilitiesTranspose(double distance,
double[][][] store) |
void |
getTransitionProbabilitiesTranspose(double distance,
int category,
double[][] store) |
double |
getUpperLimit(int n)
get upper parameter limit
|
void |
report(java.io.PrintWriter out)
Reporting stuff
|
void |
setAllParameters(double[] rateParameters,
double[] classProportions) |
void |
setParameters(double[] parameters,
int startIndex)
set model parameter
|
void |
setSubstitutionClassProbabilities(double[] classProportions) |
void |
setSubstitutionClassProbabilities(double[] classProportions,
int startIndex) |
public MultiRateMatrixHandler(NeoRateMatrix[] rateMatrices, double[] equilibriumFrequencies, double[] initialClassProportions)
public void setSubstitutionClassProbabilities(double[] classProportions)
public void setSubstitutionClassProbabilities(double[] classProportions, int startIndex)
public final int getNumberOfSubstitutionClasses()
public final MultiRateMatrixHandler getCopy()
public final double[] getEquilibriumFrequencies()
public void getTransitionProbabilities(double distance, double[][][] store)
public void getTransitionProbabilities(double distance, int category, double[][] store)
public void getTransitionProbabilitiesTranspose(double distance, double[][][] store)
public void getTransitionProbabilitiesTranspose(double distance, int category, double[][] store)
public void report(java.io.PrintWriter out)
out
- where to report toopublic final double getSubstitutionClassLowerLimit()
public final double getSubstitutionClassUpperLimit()
public final double getSubstitutionClassDefaultValue()
public double getLowerLimit(int n)
NeoParameterized
getLowerLimit
in interface NeoParameterized
n
- parameter numberpublic double getUpperLimit(int n)
NeoParameterized
getUpperLimit
in interface NeoParameterized
n
- parameter numberpublic double getDefaultValue(int n)
public int getNumberOfParameters()
NeoParameterized
getNumberOfParameters
in interface NeoParameterized
public void setAllParameters(double[] rateParameters, double[] classProportions)
public void setParameters(double[] parameters, int startIndex)
NeoParameterized
setParameters
in interface NeoParameterized
parameters
- the array holding the parametersstartIndex
- the index into the array that the related parameters start atpublic void getParameters(double[] parameterStore, int startIndex)
NeoParameterized
getParameters
in interface NeoParameterized
startIndex
- the index into the array that the related parameters start atpublic void getDefaultValues(double[] store, int startIndex)
NeoParameterized
getDefaultValues
in interface NeoParameterized