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)