48 const GeneticCode* gCode,
50 const AlphabetIndex2* pdist) :
51 AbstractParameterAliasable(
"CodonDist."),
59 const GeneticCode* gCode,
63 const AlphabetIndex2* pdist) :
64 AbstractParameterAliasable(
"CodonDist."),
double getCodonsMulRate(size_t i, size_t j) const
Returns the multiplicative rate specific to two codons specified by their number. The respective gene...
void fireParameterChanged(const ParameterList ¶meterlist)
Tells the model that a parameter value has changed.
virtual void fireParameterChanged(const ParameterList ¶meters)
Tells the model that a parameter value has changed.
Abstract class for modelling of non-synonymous abd synonymous substitution rates in codon models...
CodonDistanceSubstitutionModel(const GeneticCode *gCode, NucleotideSubstitutionModel *pmod, const AlphabetIndex2 *pdist)
Build a new CodonDistanceSubstitutionModel object from a pointer to NucleotideSubstitutionModel.
std::string getName() const
Get the name of the model.
double getCodonsMulRate(size_t i, size_t j) const
Returns the multiplicative rate specific to two codons specified by their number. The respective gene...
void updateMatrices()
Diagonalize the matrix, and fill the eigenValues_, iEigenValues_, leftEigenVectors_ and rightEigenVe...
Specialisation interface for nucleotide substitution model.
void fireParameterChanged(const ParameterList ¶meters)
Abstract class for substitution models on codons.
virtual double getCodonsMulRate(size_t i, size_t j) const
Method inherited from CodonSubstitutionModel.