Package pal.substmodel

Interface SubstitutionModel

All Superinterfaces:
Parameterized, Report, Serializable
All Known Implementing Classes:
GeneralRateDistributionSubstitutionModel, SingleClassSubstitutionModel, YangCodonModel.SimpleNeutralSelection, YangCodonModel.SimplePositiveSelection
public interface SubstitutionModel extends Parameterized, Report, Serializable
model of sequence substitution (rate matrix + rate variation). provides a convenient interface for the computation of transition probabilities
Version:
$Id: SubstitutionModel.java,v 1.33 2004/05/19 04:05:21 matt Exp $
Author:
Alexei Drummond, Matthew Goode

  • Method Details

    • getDataType

      DataType getDataType()

    • getNumberOfTransitionCategories

      int getNumberOfTransitionCategories()

    • getTransitionCategoryProbability

      double getTransitionCategoryProbability(int category)

    • getTransitionCategoryProbabilities

      double[] getTransitionCategoryProbabilities()
      Returns:
      all the category probabilites for each category respectively.

    • getTransitionProbabilities

      void getTransitionProbabilities(double branchLength, double[][][] tableStore)
      Table is organized as [transition_group][from][to]

    • getTransitionProbabilitiesTranspose

      void getTransitionProbabilitiesTranspose(double branchLength, double[][][] tableStore)
      Table is organized as [transition_group][to][from]

    • getTransitionProbabilities

      void getTransitionProbabilities(double branchLength, int category, double[][] tableStore)
      Table is organized as [transition_group][from][to]

    • getTransitionProbabilitiesTranspose

      void getTransitionProbabilitiesTranspose(double branchLength, int category, double[][] tableStore)
      Table is organized as [transition_group][to][from]

    • getEquilibriumFrequencies

      double[] getEquilibriumFrequencies()
      Should return a double[] array of the related equilibrium frequencies. As a rule, callers should not alter the returned array (it may be used internally)

    • addPalObjectListener

      void addPalObjectListener(PalObjectListener l)

    • removePalObjectListener

      void removePalObjectListener(PalObjectListener l)

    • getOrthogonalHints

      OrthogonalHints getOrthogonalHints()
      May return null

    • clone

      Object clone()