Package pal.substmodel

Class MultiRateMatrixHandler

java.lang.Object
pal.substmodel.MultiRateMatrixHandler
All Implemented Interfaces:
Serializable, NeoParameterized
public class MultiRateMatrixHandler extends Object implements NeoParameterized, Serializable
See Also:

  • Constructor Details

    • MultiRateMatrixHandler

      public MultiRateMatrixHandler(NeoRateMatrix[] rateMatrices, double[] equilibriumFrequencies, double[] initialClassProportions)

  • Method Details

    • setSubstitutionClassProbabilities

      public void setSubstitutionClassProbabilities(double[] classProportions)

    • setSubstitutionClassProbabilities

      public void setSubstitutionClassProbabilities(double[] classProportions, int startIndex)

    • getNumberOfSubstitutionClasses

      public final int getNumberOfSubstitutionClasses()

    • getCopy

      public final MultiRateMatrixHandler getCopy()

    • getEquilibriumFrequencies

      public final double[] getEquilibriumFrequencies()

    • getTransitionProbabilities

      public void getTransitionProbabilities(double distance, double[][][] store)

    • getTransitionProbabilities

      public void getTransitionProbabilities(double distance, int category, double[][] store)

    • getTransitionProbabilitiesTranspose

      public void getTransitionProbabilitiesTranspose(double distance, double[][][] store)

    • getTransitionProbabilitiesTranspose

      public void getTransitionProbabilitiesTranspose(double distance, int category, double[][] store)

    • report

      public void report(PrintWriter out)
      Reporting stuff
      Parameters:
      out - where to report too

    • getSubstitutionClassLowerLimit

      public final double getSubstitutionClassLowerLimit()

    • getSubstitutionClassUpperLimit

      public final double getSubstitutionClassUpperLimit()

    • getSubstitutionClassDefaultValue

      public final double getSubstitutionClassDefaultValue()

    • getLowerLimit

      public double getLowerLimit(int n)
      Description copied from interface: NeoParameterized
      get lower parameter limit
      Specified by:
      getLowerLimit in interface NeoParameterized
      Parameters:
      n - parameter number
      Returns:
      lower bound

    • getUpperLimit

      public double getUpperLimit(int n)
      Description copied from interface: NeoParameterized
      get upper parameter limit
      Specified by:
      getUpperLimit in interface NeoParameterized
      Parameters:
      n - parameter number
      Returns:
      upper bound

    • getDefaultValue

      public double getDefaultValue(int n)

    • getNumberOfParameters

      public int getNumberOfParameters()
      Description copied from interface: NeoParameterized
      get number of parameters
      Specified by:
      getNumberOfParameters in interface NeoParameterized
      Returns:
      number of parameters

    • setAllParameters

      public void setAllParameters(double[] rateParameters, double[] classProportions)

    • setParameters

      public void setParameters(double[] parameters, int startIndex)
      Description copied from interface: NeoParameterized
      set model parameter
      Specified by:
      setParameters in interface NeoParameterized
      Parameters:
      parameters - the array holding the parameters
      startIndex - the index into the array that the related parameters start at

    • getParameters

      public void getParameters(double[] parameterStore, int startIndex)
      Description copied from interface: NeoParameterized
      get model parameter
      Specified by:
      getParameters in interface NeoParameterized
      startIndex - the index into the array that the related parameters start at

    • getDefaultValues

      public void getDefaultValues(double[] store, int startIndex)
      Description copied from interface: NeoParameterized
      get default value parameter values
      Specified by:
      getDefaultValues in interface NeoParameterized