pal.substmodel
Class MultiRateMatrixHandler

java.lang.Object
  pal.substmodel.MultiRateMatrixHandler

All Implemented Interfaces:

java.io.Serializable, NeoParameterized

public class MultiRateMatrixHandler
extends java.lang.Object
implements NeoParameterized, java.io.Serializable

See Also:

Serialized Form

Constructor Summary

MultiRateMatrixHandler(NeoRateMatrix[] rateMatrices, double[] equilibriumFrequencies, double[] initialClassProportions)

Method Summary

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)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

MultiRateMatrixHandler

public MultiRateMatrixHandler(NeoRateMatrix[] rateMatrices,
                              double[] equilibriumFrequencies,
                              double[] initialClassProportions)

Method Detail

setSubstitutionClassProbabilities

public void setSubstitutionClassProbabilities(double[] classProportions)

setSubstitutionClassProbabilities

public void setSubstitutionClassProbabilities(double[] classProportions,
                                              int startIndex)

getNumberOfSubstitutionClasses

public final int getNumberOfSubstitutionClasses()

getCopy

public final MultiRateMatrixHandler getCopy()

getEquilibriumFrequencies

public final double[] getEquilibriumFrequencies()

getTransitionProbabilities

public void getTransitionProbabilities(double distance,
                                       double[][][] store)

getTransitionProbabilities

public void getTransitionProbabilities(double distance,
                                       int category,
                                       double[][] store)

getTransitionProbabilitiesTranspose

public void getTransitionProbabilitiesTranspose(double distance,
                                                double[][][] store)

getTransitionProbabilitiesTranspose

public void getTransitionProbabilitiesTranspose(double distance,
                                                int category,
                                                double[][] store)

report

public void report(java.io.PrintWriter out)

Reporting stuff

Parameters:

out - where to report too

getSubstitutionClassLowerLimit

public final double getSubstitutionClassLowerLimit()

getSubstitutionClassUpperLimit

public final double getSubstitutionClassUpperLimit()

getSubstitutionClassDefaultValue

public final double getSubstitutionClassDefaultValue()

getLowerLimit

public double getLowerLimit(int n)

Description copied from interface: NeoParameterized

get lower parameter limit

Specified by:

getLowerLimit in interface NeoParameterized

Parameters:

n - parameter number

Returns:

lower bound

getUpperLimit

public double getUpperLimit(int n)

Description copied from interface: NeoParameterized

get upper parameter limit

Specified by:

getUpperLimit in interface NeoParameterized

Parameters:

n - parameter number

Returns:

upper bound

getDefaultValue

public double getDefaultValue(int n)

getNumberOfParameters

public int getNumberOfParameters()

Description copied from interface: NeoParameterized

get number of parameters

Specified by:

getNumberOfParameters in interface NeoParameterized

Returns:

number of parameters

setAllParameters

public void setAllParameters(double[] rateParameters,
                             double[] classProportions)

setParameters

public void setParameters(double[] parameters,
                          int startIndex)

Description copied from interface: NeoParameterized

set model parameter

Specified by:

setParameters in interface NeoParameterized

Parameters:

parameters - the array holding the parameters

startIndex - the index into the array that the related parameters start at

getParameters

public void getParameters(double[] parameterStore,
                          int startIndex)

Description copied from interface: NeoParameterized

get model parameter

Specified by:

getParameters in interface NeoParameterized

startIndex - the index into the array that the related parameters start at

getDefaultValues

public void getDefaultValues(double[] store,
                             int startIndex)

Description copied from interface: NeoParameterized

get default value parameter values

Specified by:

getDefaultValues in interface NeoParameterized