pal.misc
Interface Parameterized

All Known Subinterfaces:

DeltaModel.Instance, NamedParameterized, ParameterizedTree, RateMatrix, SubstitutionModel

All Known Implementing Classes:

AbstractRateMatrix, AminoAcidModel, BLOSUM62, CachedRateMatrix, ClockTree, CodonModel, ConstantMutationRate, ConstantPopulation, ConstExpConst, ConstExpGrowth, CPREV, Dayhoff, DemographicClockTree, DemographicModel, ExpandingPopulation, ExponentialGrowth, F81, F84, GammaRates, GeneralRateDistributionSubstitutionModel, GTR, HKY, InvariableSites, JTT, LogParameterizedTree, MTREV24, MultiParameterized, MutationRateModel, MutationRateModelTree, NucleotideModel, Parameterized.Null, ParameterizedTree.ParameterizedTreeBase, RateDistribution, RateMatrixHandler, SingleClassSubstitutionModel, SteppedMutationRate, TN, TwoStateModel, UnconstrainedTree, UniformRate, VT, WAG, WindowedMutationRate, YangCodonModel, YangCodonModel.SimpleNeutralSelection, YangCodonModel.SimplePositiveSelection

public interface Parameterized

interface for class with (optimizable) parameters

Version:

$Id: Parameterized.java,v 1.13 2004/08/15 03:00:37 matt Exp $

Author:

Korbinian Strimmer

Nested Class Summary

static class	Parameterized.Null NullParameterized Object Can be used by subclasses to implement parameterized without actually having paramters
static class	Parameterized.ParameterizedBase A Utility class for using as the superclass to subclasses which are based on double arrays
static class	Parameterized.ParameterizedUser A Utility class for using as the superclass to subclasses which work by adding functionality to a general Parameterized object (the base Parameterized object)
static class	Parameterized.Utils

Method Summary

double	getDefaultValue(int n) get default value of parameter
double	getLowerLimit(int n) get lower parameter limit
int	getNumParameters() get number of parameters
double	getParameter(int n) get model parameter
double	getUpperLimit(int n) get upper parameter limit
void	setParameter(double param, int n) set model parameter
void	setParameterSE(double paramSE, int n) set standard errors for model parameter

Method Detail

getNumParameters

int getNumParameters()

get number of parameters

Returns:

number of parameters

setParameter

void setParameter(double param,
                  int n)

set model parameter

Parameters:

param - parameter value

n - parameter number

getParameter

double getParameter(int n)

get model parameter

Parameters:

n - parameter number

Returns:

parameter value

setParameterSE

void setParameterSE(double paramSE,
                    int n)

set standard errors for model parameter

Parameters:

paramSE - standard error of parameter value

n - parameter number

getLowerLimit

double getLowerLimit(int n)

get lower parameter limit

Parameters:

n - parameter number

Returns:

lower bound

getUpperLimit

double getUpperLimit(int n)

get upper parameter limit

Parameters:

n - parameter number

Returns:

upper bound

getDefaultValue

double getDefaultValue(int n)

get default value of parameter

Parameters:

n - parameter number

Returns:

default value