Package pal.substmodel

Class SimpleRateMatrixGroup

java.lang.Object
pal.substmodel.SimpleRateMatrixGroup
All Implemented Interfaces:
Serializable, RateMatrixGroup
public abstract class SimpleRateMatrixGroup extends Object implements RateMatrixGroup
See Also:

  • Constructor Details

    • SimpleRateMatrixGroup

      public SimpleRateMatrixGroup(NeoRateMatrix[] baseMatrices, double[] equilibriumFrequencies, double[] initialClassProbabilities, DataType dataType)

  • Method Details

    • getNumberOfParameters

      public int getNumberOfParameters()

    • getLowerLimit

      public double getLowerLimit(int n)

    • getUpperLimit

      public double getUpperLimit(int n)

    • getDefaultValue

      public double getDefaultValue(int n)

    • setParameters

      public void setParameters(double[] parameters, double[] categoryProbabilities)

    • getEquilibriumFrequencies

      public double[] getEquilibriumFrequencies()
      Specified by:
      getEquilibriumFrequencies in interface RateMatrixGroup

    • getDataType

      public DataType getDataType()
      Specified by:
      getDataType in interface RateMatrixGroup

    • getNumberOfTransitionCategories

      public int getNumberOfTransitionCategories()
      Specified by:
      getNumberOfTransitionCategories in interface RateMatrixGroup

    • getTransitionProbabilities

      public void getTransitionProbabilities(double branchLength, double[][][] tableStore)
      Specified by:
      getTransitionProbabilities in interface RateMatrixGroup

    • getTransitionProbabilitiesTranspose

      public void getTransitionProbabilitiesTranspose(double branchLength, double[][][] tableStore)
      Specified by:
      getTransitionProbabilitiesTranspose in interface RateMatrixGroup

    • getTransitionProbabilities

      public void getTransitionProbabilities(double branchLength, int category, double[][] tableStore)
      Specified by:
      getTransitionProbabilities in interface RateMatrixGroup

    • getTransitionProbabilitiesTranspose

      public void getTransitionProbabilitiesTranspose(double branchLength, int category, double[][] tableStore)
      Specified by:
      getTransitionProbabilitiesTranspose in interface RateMatrixGroup

    • getSummary

      public String getSummary(double[] parameters, double[] categoryProbabilities)