Package 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

    Nested Classes
    Modifier and Type
    Interface
    Description
    static class 
    NullParameterized Object Can be used by subclasses to implement parameterized without actually having paramters
    static class 
    A Utility class for using as the superclass to subclasses which are based on double arrays
    static class 
    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 final class 
     
  • Method Summary

    Modifier and Type
    Method
    Description
    double
    get default value of parameter
    double
    get lower parameter limit
    int
    get number of parameters
    double
    getParameter(int n)
    get model parameter
    double
    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 Details

    • 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