Package jebl.evolution.substmodel

Class AbstractRateMatrix

java.lang.Object
jebl.evolution.substmodel.AbstractRateMatrix
All Implemented Interfaces:
Serializable, Cloneable, RateMatrix
Direct Known Subclasses:
AminoAcidModel
public abstract class AbstractRateMatrix extends Object implements RateMatrix
abstract base class for all rate matrices
Version:
$Id: AbstractRateMatrix.java 185 2006-01-23 23:03:18Z rambaut $
Author:
Korbinian Strimmer, Alexei Drummond
See Also:

  • Method Details

    • getDimension

      public int getDimension()
      Specified by:
      getDimension in interface RateMatrix
      Returns:
      the dimension of this rate matrix.

    • getEquilibriumFrequencies

      public double[] getEquilibriumFrequencies()
      Specified by:
      getEquilibriumFrequencies in interface RateMatrix
      Returns:
      stationary frequencies (sum = 1.0)

    • getEquilibriumFrequency

      public double getEquilibriumFrequency(int i)
      Specified by:
      getEquilibriumFrequency in interface RateMatrix
      Returns:
      stationary frequencie (sum = 1.0) for ith state

    • getSequenceType

      public SequenceType getSequenceType()
      Description copied from interface: RateMatrix
      Get the data type of this rate matrix
      Specified by:
      getSequenceType in interface RateMatrix

    • getRelativeRates

      public double[][] getRelativeRates()
      Specified by:
      getRelativeRates in interface RateMatrix
      Returns:
      rate matrix (transition: from 1st index to 2nd index)

    • getTransitionProbability

      public double getTransitionProbability(int fromState, int toState)
      Specified by:
      getTransitionProbability in interface RateMatrix
      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

    • rebuild

      public final void rebuild()

    • setDistance

      public final void setDistance(double distance)
      Sets the distance (such as time/branch length) used when calculating the probabilities.
      Specified by:
      setDistance in interface RateMatrix

    • setDistanceTranspose

      public final void setDistanceTranspose(double distance)
      Sets the distance (such as time/branch length) used when calculating the probabilities. The resulting transition probabilities will be in reverse (that is in the matrix instead of [from][to] it's [to][from])

    • getTransitionProbabilities

      public final void getTransitionProbabilities(double[][] probabilityStore)
      A utility method for speed, transfers trans prob information quickly into store
      Specified by:
      getTransitionProbabilities in interface RateMatrix

    • scale

      public void scale(double scale)

    • setParametersNoScale

      public double setParametersNoScale(double[] parameters)