Class SubstitutionModel.Utils

java.lang.Object
pal.substmodel.SubstitutionModel.Utils
Enclosing interface:
SubstitutionModel

public static class SubstitutionModel.Utils extends Object
A small Utility class for things relating to Substitution Models in general
  • Constructor Details

    • Utils

      public Utils()
  • Method Details

    • generateTransitionProbabilityTables

      public static final double[][][] generateTransitionProbabilityTables(SubstitutionModel model)
    • createSubstitutionModel

      public static final SubstitutionModel createSubstitutionModel(RateMatrix rm)
      Returns:
      a substitution model base on a rate matrix. There is only one transition category. There is no independent distribution access (as not distribution across one transition category)
    • createSubstitutionModel

      public static final SubstitutionModel createSubstitutionModel(NeoRateMatrix rm, DataType dt, double[] equilibriumFrequencies)
      Returns:
      a substitution model base on a rate matrix. There is only one transition category. There is no independent distribution access (as not distribution across one transition category)
    • createSubstitutionModel

      public static final SubstitutionModel createSubstitutionModel(RateMatrix rm, RateDistribution rd)
      Returns:
      a substitution model base on a rate matrix, and a rate distribution. There are as many transition categories as there are rate categories in the rate distribution. There is no independent distribution access (as rate distributions don't normally allow changing of probabilities for a category without changing the rate of a category - at least none in pal do)
    • createSubstitutionModel

      public static final SubstitutionModel createSubstitutionModel(RateMatrix rm, RateDistribution rd, boolean parameteriseDistribution)
      Parameters:
      parameteriseDistribution - If true will include the distribution parameters as part of the substitution modle parameters, if false then the distribution parameters are set from the point of view of the substitution model.
      Returns:
      a substitution model base on a rate matrix, and a rate distribution. There are as many transition categories as there are rate categories in the rate distribution. There is no independent distribution access (as rate distributions don't normally allow changing of probabilities for a category without changing the rate of a category - at least none in pal do)