Package pal.misc
Interface Parameterized
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- 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
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Nested Class Summary
Nested Classes Modifier and Type Interface Description static class
Parameterized.Null
NullParameterized Object Can be used by subclasses to implement parameterized without actually having paramtersstatic class
Parameterized.ParameterizedBase
A Utility class for using as the superclass to subclasses which are based on double arraysstatic 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
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description double
getDefaultValue(int n)
get default value of parameterdouble
getLowerLimit(int n)
get lower parameter limitint
getNumParameters()
get number of parametersdouble
getParameter(int n)
get model parameterdouble
getUpperLimit(int n)
get upper parameter limitvoid
setParameter(double param, int n)
set model parametervoid
setParameterSE(double paramSE, int n)
set standard errors for model parameter
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Method Detail
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getNumParameters
int getNumParameters()
get number of parameters- Returns:
- number of parameters
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setParameter
void setParameter(double param, int n)
set model parameter- Parameters:
param
- parameter valuen
- parameter number
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getParameter
double getParameter(int n)
get model parameter- Parameters:
n
- parameter number- Returns:
- parameter value
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setParameterSE
void setParameterSE(double paramSE, int n)
set standard errors for model parameter- Parameters:
paramSE
- standard error of parameter valuen
- parameter number
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getLowerLimit
double getLowerLimit(int n)
get lower parameter limit- Parameters:
n
- parameter number- Returns:
- lower bound
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getUpperLimit
double getUpperLimit(int n)
get upper parameter limit- Parameters:
n
- parameter number- Returns:
- upper bound
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getDefaultValue
double getDefaultValue(int n)
get default value of parameter- Parameters:
n
- parameter number- Returns:
- default value
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