Class InvariableSites

  • All Implemented Interfaces:
    java.io.Serializable, java.lang.Cloneable, Parameterized, Report

    public class InvariableSites
    extends RateDistribution
    implements java.io.Serializable
    invariable sites model (two-rate model with mean rate = 1.0)
    Version:
    $Id: InvariableSites.java,v 1.4 2003/06/11 05:26:46 matt Exp $
    Author:
    Korbinian Strimmer
    See Also:
    Serialized Form
    • Constructor Detail

      • InvariableSites

        public InvariableSites​(double f)
        construct discrete rate distribution with two rates (one invariable and one variable)
        Parameters:
        f - fraction of invariable sites
    • Method Detail

      • report

        public void report​(java.io.PrintWriter out)
        Description copied from interface: Report
        print human readable report (e.g., on parameters and associated model)
        Specified by:
        report in interface Report
        Parameters:
        out - output stream
      • getNumParameters

        public int getNumParameters()
        Description copied from interface: Parameterized
        get number of parameters
        Specified by:
        getNumParameters in interface Parameterized
        Returns:
        number of parameters
      • setParameter

        public void setParameter​(double param,
                                 int n)
        Description copied from interface: Parameterized
        set model parameter
        Specified by:
        setParameter in interface Parameterized
        Parameters:
        param - parameter value
        n - parameter number
      • getParameter

        public double getParameter​(int n)
        Description copied from interface: Parameterized
        get model parameter
        Specified by:
        getParameter in interface Parameterized
        Parameters:
        n - parameter number
        Returns:
        parameter value
      • setParameterSE

        public void setParameterSE​(double paramSE,
                                   int n)
        Description copied from interface: Parameterized
        set standard errors for model parameter
        Specified by:
        setParameterSE in interface Parameterized
        Parameters:
        paramSE - standard error of parameter value
        n - parameter number
      • getLowerLimit

        public double getLowerLimit​(int n)
        Description copied from interface: Parameterized
        get lower parameter limit
        Specified by:
        getLowerLimit in interface Parameterized
        Parameters:
        n - parameter number
        Returns:
        lower bound
      • getUpperLimit

        public double getUpperLimit​(int n)
        Description copied from interface: Parameterized
        get upper parameter limit
        Specified by:
        getUpperLimit in interface Parameterized
        Parameters:
        n - parameter number
        Returns:
        upper bound
      • getDefaultValue

        public double getDefaultValue​(int n)
        Description copied from interface: Parameterized
        get default value of parameter
        Specified by:
        getDefaultValue in interface Parameterized
        Parameters:
        n - parameter number
        Returns:
        default value
      • isDistributionIndependentlyMutable

        public boolean isDistributionIndependentlyMutable()