48 const GeneticCode* gCode,
51 const AlphabetIndex2* pdist,
53 AbstractParameterAliasable(
"CodonDistFreq."),
62 const GeneticCode* gCode,
67 const AlphabetIndex2* pdist,
69 AbstractParameterAliasable(
"CodonDistFreq."),
79 return "CodonDistFreq";
100 AbstractParameterAliasable::setNamespace(st);
102 AbstractCodonDistanceSubstitutionModel::setNamespace(st);
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 setFreq(std::map< int, double > &frequencies)
Set equilibrium frequencies.
virtual void fireParameterChanged(const ParameterList ¶meters)
Tells the model that a parameter value has changed.
void setNamespace(const std::string &)
Parametrize a set of state frequencies.
Abstract class for modelling of non-synonymous abd synonymous substitution rates in codon models...
std::string getName() const
Get the name of the model.
void setNamespace(const std::string &prefix)
CodonDistanceFrequenciesSubstitutionModel(const GeneticCode *gCode, NucleotideSubstitutionModel *pmod, FrequenciesSet *pfreq, const AlphabetIndex2 *pdist=0, bool paramSynRate=false)
Build a new CodonDistanceFrequenciesSubstitutionModel object from three pointers to AbstractSubstitut...
void updateMatrices()
Diagonalize the matrix, and fill the eigenValues_, iEigenValues_, leftEigenVectors_ and rightEigenVe...
void fireParameterChanged(const ParameterList ¶meterlist)
Tells the model that a parameter value has changed.
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)
Abstract Class for substitution models on codons parametrized by frequencies.
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 ¶meters)
void setNamespace(const std::string &prefix)
Abstract class for substitution models on codons.
void setFreq(std::map< int, double > &frequencies)
Set equilibrium frequencies.
virtual double getCodonsMulRate(size_t i, size_t j) const
Method inherited from CodonSubstitutionModel.