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

• getNumberOfRateParameters

  public int getNumberOfRateParameters()

  Specified by:

  getNumberOfRateParameters in interface NeoRateMatrix

• getRateParameterLowerBound

  public double getRateParameterLowerBound(int parameter)

  Specified by:

  getRateParameterLowerBound in interface NeoRateMatrix

• getRateParameterUpperBound

  public double getRateParameterUpperBound(int parameter)

  Specified by:

  getRateParameterUpperBound in interface NeoRateMatrix

• getDefaultRateParameters

  public void getDefaultRateParameters(double[] store,
                                       int startIndex)

  Specified by:

  getDefaultRateParameters in interface NeoRateMatrix