Class GeneralPoissonRateMatrix

  • All Implemented Interfaces:
    java.io.Serializable, NeoRateMatrix

    public class GeneralPoissonRateMatrix
    extends java.lang.Object
    implements NeoRateMatrix
    A general rate matrix class for JC69/F81 style rate matrices (but for all data types)
    Version:
    $Id: GeneralPoissonRateMatrix.java,v 1.3 2004/08/15 03:00:37 matt Exp $
    Author:
    Matthew Goode
    • 11 May 2004 - Created file
    See Also:
    Serialized Form
    • Constructor Detail

      • GeneralPoissonRateMatrix

        public GeneralPoissonRateMatrix​(int dimension)
    • Method Detail

      • getUniqueName

        public java.lang.String getUniqueName()
        Specified by:
        getUniqueName in interface NeoRateMatrix
        Returns:
        a short unique human-readable identifier for this rate matrix.
      • isReversible

        public boolean isReversible()
        Description copied from interface: NeoRateMatrix
        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 );
        Specified by:
        isReversible in interface NeoRateMatrix
        Returns:
        true (doesn't really matter)
      • getDimension

        public int getDimension()
        Specified by:
        getDimension in interface NeoRateMatrix
        Returns:
        the dimension of this rate matrix. (as for construction)
      • isDataTypeCompatible

        public boolean isDataTypeCompatible​(DataType dt)
        Check the compatibility of a data type to be used with the rate matrix
        Specified by:
        isDataTypeCompatible in interface NeoRateMatrix
        Parameters:
        dt - the data type to test
        Returns:
        true if data type state count is equal to dimension
      • createRelativeRates

        public void createRelativeRates​(double[][] rateStore,
                                        double[] rateParameters,
                                        int startIndex)
        Description copied from interface: NeoRateMatrix
        Create the relative rates array
        Specified by:
        createRelativeRates in interface NeoRateMatrix
        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