Class GTR

All Implemented Interfaces:
Serializable, Cloneable, ExternalParameterListener, NamedParameterized, Parameterized, Report, RateMatrix, XMLConstants

public class GTR extends NucleotideModel implements Serializable, XMLConstants
GTR (general time reversible) model of nucleotide evolution Lanave, C., G. Preparata, C. Saccone, and G. Serio. 1984. A new method for calculating evolutionary substitution rates. J Mol Evol 20: 86-93.
Version:
$Id: GTR.java,v 1.13 2003/11/30 05:29:22 matt Exp $

Parameters

  1. A
  2. B
  3. C
  4. D
  5. E

Author:
Korbinian Strimmer
See Also:
  • Constructor Details

    • GTR

      public GTR(double a, double b, double c, double d, double e, double[] freq)
      constructor 1
      Parameters:
      a - entry in rate matrix
      b - entry in rate matrix
      c - entry in rate matrix
      d - entry in rate matrix
      e - entry in rate matrix
      freq - nucleotide frequencies
    • GTR

      public GTR(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
    • getUniqueName

      public String getUniqueName()
      Specified by:
      getUniqueName in interface RateMatrix
      Returns:
      the name of this rate matrix
    • 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!
    • rebuildRateMatrix

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