Package pal.substmodel

Interface RateMatrix

All Superinterfaces:
Cloneable, NamedParameterized, Parameterized, Report, Serializable
All Known Implementing Classes:
AbstractRateMatrix, AminoAcidModel, BLOSUM62, CachedRateMatrix, CodonModel, CPREV, Dayhoff, F81, F84, GTR, HKY, JTT, MTREV24, NucleotideModel, TN, TwoStateModel, VT, WAG, YangCodonModel
public interface RateMatrix extends NamedParameterized, Report, Cloneable, Serializable
abstract base class for all rate matrices
Version:
$Id: RateMatrix.java,v 1.34 2003/11/13 04:05:39 matt Exp $
Author:
Korbinian Strimmer, Alexei Drummond, Matthew Goode

  • Method Details

    • getTypeID

      int getTypeID()
      get numerical code describing the data type
      Returns:
      integer code identifying a data type

    • getModelID

      int getModelID()
      get numerical code describing the model type
      Returns:
      integer code identifying a substitution model

    • getUniqueName

      String getUniqueName()
      Returns:
      a short unique human-readable identifier for this rate matrix.

    • getDimension

      int getDimension()
      Returns:
      the dimension of this rate matrix.

    • getEquilibriumFrequencies

      double[] getEquilibriumFrequencies()
      Returns:
      stationary frequencies (sum = 1.0)

    • getEquilibriumFrequency

      double getEquilibriumFrequency(int i)
      Returns:
      stationary frequency (sum = 1.0) for ith state Preferred method for infrequent use.

    • getDataType

      DataType getDataType()
      Get the data type of this rate matrix

    • getRelativeRates

      double[][] getRelativeRates()
      Deprecated.
      try not to use.
      Returns:
      rate matrix (transition: from 1st index to 2nd index)

    • getTransitionProbability

      double getTransitionProbability(int fromState, int toState)
      Parameters:
      fromState - The state from which we are starting
      toState - The resulting state
      Returns:
      the probability of going from one state to another given the current distance

    • getTransitionProbabilities

      void getTransitionProbabilities(double[][] probabilityStore)
      A utility method for speed, transfers trans prob information quickly into store

    • setDistance

      void setDistance(double distance)
      Sets the distance (such as time/branch length) used when calculating the probabilities. This method may well take the most time!

    • setDistanceTranspose

      void setDistanceTranspose(double distance)
      Sets the distance (such as time/branch length) used when calculating the probabilities.

    • addPalObjectListener

      void addPalObjectListener(PalObjectListener pol)
      Add a PalObjectListener to be notified of changes to the model. Only the parametersChanged method will generally be called

    • removePalObjectListener

      void removePalObjectListener(PalObjectListener pol)

    • getOrthogonalHints

      OrthogonalHints getOrthogonalHints()
      Returns:
      an orthogonal hints object for orthogonal optimisation (may return null for no hints)

    • clone

      Object clone()

    • setParametersNoScale

      double setParametersNoScale(double[] parameters)

    • scale

      void scale(double scaleValue)