Class InvariableSites

All Implemented Interfaces:
Serializable, Cloneable, Parameterized, Report

public class InvariableSites extends RateDistribution implements 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:
  • Constructor Details

    • InvariableSites

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

    • report

      public void report(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()