48 const GeneticCode* gCode,
51 AbstractParameterAliasable(
"CodonRateFreq."),
59 const GeneticCode* gCode,
64 AbstractParameterAliasable(
"CodonRateFreq."),
73 return "CodonRateFreq";
92 AbstractParameterAliasable::setNamespace(st);
void setFreq(std::map< int, double > &frequencies)
Set equilibrium frequencies.
virtual void fireParameterChanged(const ParameterList ¶meters)
Tells the model that a parameter value has changed.
Parametrize a set of state frequencies.
void setNamespace(const std::string &prefix)
void setNamespace(const std::string &st)
void updateMatrices()
Diagonalize the matrix, and fill the eigenValues_, iEigenValues_, leftEigenVectors_ and rightEigenVe...
Specialisation interface for nucleotide substitution model.
double getCodonsMulRate(size_t, size_t) const
Returns the multiplicative rate specific to two codons specified by their number. The respective gene...
void fireParameterChanged(const ParameterList ¶meters)
double getCodonsMulRate(size_t i, size_t j) const
Returns the multiplicative rate specific to two codons specified by their number. The respective gene...
Abstract Class for substitution models on codons parametrized by frequencies.
void setFreq(std::map< int, double > &frequencies)
Set equilibrium frequencies.
CodonRateFrequenciesSubstitutionModel(const GeneticCode *gCode, NucleotideSubstitutionModel *pmod, FrequenciesSet *pfreq)
Build a new CodonRateSubstitutionModel object from a pointer to NucleotideSubstitutionModels.
std::string getName() const
Get the name of the model.
void setNamespace(const std::string &prefix)
Abstract class for substitution models on codons.
void fireParameterChanged(const ParameterList ¶meterlist)
Tells the model that a parameter value has changed.
virtual double getCodonsMulRate(size_t i, size_t j) const
Method inherited from CodonSubstitutionModel.