Package pal.substmodel

Class AminoAcidModel

java.lang.Object
pal.substmodel.AbstractRateMatrix
pal.substmodel.AminoAcidModel
All Implemented Interfaces:
Serializable, Cloneable, ExternalParameterListener, NamedParameterized, Parameterized, Report, RateMatrix
Direct Known Subclasses:
BLOSUM62, CPREV, Dayhoff, JTT, MTREV24, VT, WAG
public abstract class AminoAcidModel extends AbstractRateMatrix implements RateMatrix
base class of rate matrices for amino acids
Version:
$Id: AminoAcidModel.java,v 1.8 2003/11/13 04:05:39 matt Exp $
Author:
Korbinian Strimmer
See Also:

  • Constructor Details

    • AminoAcidModel

      protected AminoAcidModel(double[] f)

  • Method Details

    • 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(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!

    • printFrequencies

      protected void printFrequencies(PrintWriter out)
      Overrides:
      printFrequencies in class AbstractRateMatrix