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
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public interface Parameterized
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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

Nested Classes
Modifier and Type	Interface and Description
`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

All Methods Instance Methods Abstract Methods
Modifier and Type	Method and Description
`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
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int getNumParameters()
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    get number of parameters
    
    Returns:
    
    number of parameters
  - setParameter
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void setParameter(double param,
                  int n)
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    set model parameter
    
    Parameters:
    
    param - parameter value
    
    n - parameter number
  - getParameter
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double getParameter(int n)
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    get model parameter
    
    Parameters:
    
    n - parameter number
    
    Returns:
    
    parameter value
  - setParameterSE
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void setParameterSE(double paramSE,
                    int n)
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    set standard errors for model parameter
    
    Parameters:
    
    paramSE - standard error of parameter value
    
    n - parameter number
  - getLowerLimit
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double getLowerLimit(int n)
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    get lower parameter limit
    
    Parameters:
    
    n - parameter number
    
    Returns:
    
    lower bound
  - getUpperLimit
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double getUpperLimit(int n)
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    get upper parameter limit
    
    Parameters:
    
    n - parameter number
    
    Returns:
    
    upper bound
  - getDefaultValue
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double getDefaultValue(int n)
```
    get default value of parameter
    
    Parameters:
    
    n - parameter number
    
    Returns:
    
    default value

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