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