Package pal.substmodel

Class HKY

java.lang.Object
pal.substmodel.AbstractRateMatrix
pal.substmodel.NucleotideModel
pal.substmodel.HKY
All Implemented Interfaces:
Serializable, Cloneable, ExternalParameterListener, NamedParameterized, Parameterized, Report, RateMatrix, XMLConstants
public class HKY extends NucleotideModel implements Serializable, XMLConstants
Hasegawa-Kishino-Yano model of nucleotide evolution Hasegawa, M., H. Kishino, and T. Yano. 1985. Dating of the human-ape splitting by a molecular clock of mitchondrial DNA. J. Mol. Evol. 22:160-174.
Version:
$Id: HKY.java,v 1.11 2003/11/30 05:29:22 matt Exp $

Parameters

  1. Kappa

Author:
Korbinian Strimmer, Alexei Drummond
See Also:

  • Field Details

  • Constructor Details

    • HKY

      public HKY(double kappa, double[] freq)
      Constructor 1
      Parameters:
      kappa - transition/transversion rate ratio
      freq - nucleotide frequencies

    • HKY

      public HKY(double[] params, double[] freq)
      Constructor 2
      Parameters:
      params - parameter list
      freq - nucleotide frequencies

  • Method Details

    • clone

      public Object clone()
      Specified by:
      clone in interface RateMatrix
      Overrides:
      clone in class AbstractRateMatrix

    • getModelID

      public int getModelID()
      Description copied from class: AbstractRateMatrix
      get numerical code describing the model type
      Specified by:
      getModelID in interface RateMatrix
      Specified by:
      getModelID in class AbstractRateMatrix
      Returns:
      integer code identifying a substitution model

    • 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

    • 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

    • getParameterName

      public String getParameterName(int i)
      Specified by:
      getParameterName in interface NamedParameterized
      Returns:
      a short identifier for this parameter type. Should be the same for all instances of a given class!

    • getUniqueName

      public String getUniqueName()
      Specified by:
      getUniqueName in interface RateMatrix
      Returns:
      a short unique human-readable identifier for this rate matrix.

    • rebuildRateMatrix

      protected void rebuildRateMatrix(double[][] rate, double[] parameters)
      Specified by:
      rebuildRateMatrix in class AbstractRateMatrix