pal.substmodel

Class RateMatrixHandler

java.lang.Object

pal.substmodel.RateMatrixHandler

All Implemented Interfaces:

java.io.Serializable, Parameterized

public class RateMatrixHandler
extends java.lang.Object
implements Parameterized, java.io.Serializable

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from interface pal.misc.Parameterized

Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser, Parameterized.Utils

Constructor Summary

Constructors

Constructor and Description
RateMatrixHandler(NeoRateMatrix rateMatrix, double[] equilibriumFrequencies)

Method Summary

Methods

Modifier and Type	Method and Description
RateMatrixHandler	getCopy()
double	getDefaultValue(int n) get default value of parameter
double[]	getEquilibriumFrequencies()
double	getLowerLimit(int n) get lower parameter limit
int	getNumParameters() get number of parameters
double	getParameter(int n) get model parameter
void	getTransitionProbabilities(double distance, double[][] store)
void	getTransitionProbabilitiesTranspose(double distance, double[][] store)
double	getUpperLimit(int n) get upper parameter limit
void	report(java.io.PrintWriter out) Reporting stuff
void	setParameter(double param, int n) set model parameter
void	setParameterSE(double paramSE, int n) set standard errors for model parameter

Methods inherited from class java.lang.Object

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

Constructor Detail

RateMatrixHandler

public RateMatrixHandler(NeoRateMatrix rateMatrix,
                 double[] equilibriumFrequencies)

Method Detail

getCopy

public final RateMatrixHandler getCopy()

getEquilibriumFrequencies

public final double[] getEquilibriumFrequencies()

getTransitionProbabilities

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

getTransitionProbabilitiesTranspose

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

report

public void report(java.io.PrintWriter out)

Reporting stuff

Parameters:

out - where to report too

getNumParameters

public int getNumParameters()

Description copied from interface: Parameterized

get number of parameters

Specified by:

getNumParameters in interface Parameterized

Returns:

number of parameters

setParameter

public void setParameter(double param,
                int n)

Description copied from interface: Parameterized

set model parameter

Specified by:

setParameter in interface Parameterized

Parameters:

param - parameter value

n - parameter number

getParameter

public double getParameter(int n)

Description copied from interface: Parameterized

get model parameter

Specified by:

getParameter in interface Parameterized

Parameters:

n - parameter number

Returns:

parameter value

setParameterSE

public void setParameterSE(double paramSE,
                  int n)

Description copied from interface: Parameterized

set standard errors for model parameter

Specified by:

setParameterSE in interface Parameterized

Parameters:

paramSE - standard error of parameter value

n - parameter number

getLowerLimit

public double getLowerLimit(int n)

Description copied from interface: Parameterized

get lower parameter limit

Specified by:

getLowerLimit in interface Parameterized

Parameters:

n - parameter number

Returns:

lower bound

getUpperLimit

public double getUpperLimit(int n)

Description copied from interface: Parameterized

get upper parameter limit

Specified by:

getUpperLimit in interface Parameterized

Parameters:

n - parameter number

Returns:

upper bound

getDefaultValue

public double getDefaultValue(int n)

Description copied from interface: Parameterized

get default value of parameter

Specified by:

getDefaultValue in interface Parameterized

Parameters:

n - parameter number

Returns:

default value