Package pal.substmodel

Class RateMatrixHandler

java.lang.Object
pal.substmodel.RateMatrixHandler
All Implemented Interfaces:
Serializable, Parameterized
public class RateMatrixHandler extends Object implements Parameterized, Serializable
See Also:

  • Constructor Details

    • RateMatrixHandler

      public RateMatrixHandler(NeoRateMatrix rateMatrix, double[] equilibriumFrequencies)

  • Method Details

    • getCopy

      public final RateMatrixHandler getCopy()

    • getEquilibriumFrequencies

      public final double[] getEquilibriumFrequencies()

    • getTransitionProbabilities

      public void getTransitionProbabilities(double distance, double[][] store)

    • getTransitionProbabilitiesTranspose

      public void getTransitionProbabilitiesTranspose(double distance, double[][] store)

    • report

      public void report(PrintWriter out)
      Reporting stuff
      Parameters:
      out - where to report too

    • 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