Interface NeoRateMatrix

All Superinterfaces:
Serializable
All Known Implementing Classes:
GeneralPoissonRateMatrix, GeneralREVRateMatrix

public interface NeoRateMatrix extends Serializable
The new RateMatrix class. Replaces the old RateMatrix, and will in turn be renamed to RateMatrix at a later point. A NeoRateMatix object should be stateless (with regard to parameters used in likelihood searching). State is given by the parameter values which are administered externally.
Version:
$Id: NeoRateMatrix.java,v 1.3 2004/08/15 03:00:37 matt Exp $
Author:
Matthew Goode
  • 3 May 2004 - Created file
  • Method Details

    • getUniqueName

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

      boolean isReversible()
      Is the relative rate matrix described by this rate matrix meant to represent a reversible process? If true only the upper part of the rate matrix needs to be filled in (eg in matrix[i][j], for all where j > i );
      Returns:
      true if reversible
    • getDimension

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

      boolean isDataTypeCompatible(DataType dt)
      Check the compatibility of a data type to be used with the rate matrix
      Parameters:
      dt - the data type to test
      Returns:
      true if data type compatible (false otherwise)
    • createRelativeRates

      void createRelativeRates(double[][] rateStore, double[] rateParameters, int startIndex)
      Create the relative rates array
      Parameters:
      rateStore - The place where the relative rates are stored (should be assumed to be large enough - based on dimension)
      rateParameters - The parameters to be used to construct the rate store
      startIndex - The index into the rateParameters to start reading parameters
    • getNumberOfRateParameters

      int getNumberOfRateParameters()
    • getRateParameterLowerBound

      double getRateParameterLowerBound(int parameter)
    • getRateParameterUpperBound

      double getRateParameterUpperBound(int parameter)
    • getDefaultRateParameters

      void getDefaultRateParameters(double[] parameterStore, int startIndex)