Package jebl.evolution.substmodel

Interface RateMatrix

All Superinterfaces:
Cloneable, Serializable
All Known Implementing Classes:
AbstractRateMatrix, AminoAcidModel, WAG
public interface RateMatrix extends Cloneable, Serializable
abstract base class for all rate matrices
Version:
$Id: RateMatrix.java 185 2006-01-23 23:03:18Z rambaut $
Author:
Korbinian Strimmer, Alexei Drummond, Matthew Goode

  • Method Details

    • 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.

    • getSequenceType

      SequenceType getSequenceType()
      Get the data type of this rate matrix

    • getRelativeRates

      double[][] getRelativeRates()
      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!