Class AminoAcidModel

    • Constructor Detail

      • AminoAcidModel

        protected AminoAcidModel​(double[] f)
    • Method Detail

      • getInstance

        public static AminoAcidModel getInstance​(int modelID,
                                                 double[] freq)
        Create amino acid model according to model type
        Parameters:
        modelID - model code
        freq - model frequencies
        Returns:
        amino acid rate matrix
      • getSuitableModelID

        public static int getSuitableModelID​(double[] freq)
        get numerical code of amino acid model that would probably be suitable for a given sequence data set
        Parameters:
        freq - amino acid frequencies of the data set
        Returns:
        numerical code of suitable AminoAcidModel
      • report

        public abstract 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
      • 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!