Class YangCodonModel

  • All Implemented Interfaces:
    java.io.Serializable, java.lang.Cloneable, ExternalParameterListener, NamedParameterized, Parameterized, Report, RateMatrix, XMLConstants

    public class YangCodonModel
    extends CodonModel
    implements java.io.Serializable, XMLConstants
    Yang's model of codon evolution More advanced codon Substitution Models (of Neilson and Yang) are now included (the M1, and M2 models). They appear to be correct compare to PAML for the purposes of evaluating the likelihood. More models (eg M3 and others) will be added over time.
    Version:
    $Id: YangCodonModel.java,v 1.25 2004/10/18 01:45:40 matt Exp $
    Author:
    Andrew Rambaut, Alexei Drummond, Matthew Goode
    See Also:
    Serialized Form
    • Constructor Detail

      • YangCodonModel

        public YangCodonModel​(double omega,
                              double kappa,
                              double[] freq,
                              CodonTable codonTable)
        constructor 1
        Parameters:
        omega - N/S rate ratio
        kappa - transition/transversion rate ratio
        freq - codon frequencies
        codonTable - codon table
      • YangCodonModel

        public YangCodonModel​(double omega,
                              double kappa,
                              double[] freq)
        constructor 2 (universal codon table)
        Parameters:
        omega - N/S rate ratio
        kappa - transition/transversion rate ratio
        freq - codon frequencies
      • YangCodonModel

        public YangCodonModel​(double[] params,
                              double[] freq)
        constructor 4 (universal codon table)
        Parameters:
        params - parameter list
        freq - nucleotide frequencies
      • YangCodonModel

        public YangCodonModel​(double[] params,
                              double[] freq,
                              CodonTable codonTable)
        constructor 3
        Parameters:
        params - parameter list
        freq - nucleotide frequencies
        codonTable - codon table
    • 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
      • 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
      • getKappaLowerLimit

        public final double getKappaLowerLimit()
      • getOmegaLowerLimit

        public final double getOmegaLowerLimit()
      • getKappaUpperLimit

        public final double getKappaUpperLimit()
      • getOmegaUpperLimit

        public final double getOmegaUpperLimit()
      • getKappaDefaultValue

        public final double getKappaDefaultValue()
      • getOmegaDefaultValue

        public final double getOmegaDefaultValue()
      • getOmega

        public final double getOmega()
      • getKappa

        public final double getKappa()
      • setKappaSE

        public final void setKappaSE​(double value)
      • setOmegaSE

        public final void setOmegaSE​(double value)
      • setKappa

        public final void setKappa​(double value)
      • setOmega

        public final void setOmega​(double value)
      • 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 java.lang.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 java.lang.String getUniqueName()
        Specified by:
        getUniqueName in interface RateMatrix
        Returns:
        a short unique human-readable identifier for this rate matrix.
      • toString

        public java.lang.String toString()
        Overrides:
        toString in class java.lang.Object
      • createKappaStore

        public static final MutableDouble createKappaStore​(double initialValue)
      • createKappaStore

        public static final MutableDouble createKappaStore​(double initialValue,
                                                           java.lang.String name)
      • createOmegaStore

        public static final MutableDouble createOmegaStore​(double initialValue)
      • createOmegaStore

        public static final MutableDouble createOmegaStore​(double initialValue,
                                                           java.lang.String name)