48 const GeneticCode* gCode,
51 const AlphabetIndex2* pdist) :
52 AbstractParameterAliasable(
"CodonDistPhasFreq."),
61 const GeneticCode* gCode,
66 const AlphabetIndex2* pdist) :
67 AbstractParameterAliasable(
"CodonDistPhasFreq."),
77 return (
"CodonDistPhasFreq");
98 AbstractParameterAliasable::setNamespace(st);
100 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...
Abstract Class for substitution models on codons parametrized by a frequency.
std::string getName() const
Get the name of the model.
virtual void fireParameterChanged(const ParameterList ¶meters)
Tells the model that a parameter value has changed.
void fireParameterChanged(const ParameterList ¶meterlist)
Tells the model that a parameter value has changed.
void setFreq(std::map< int, double > &frequencies)
Set equilibrium frequencies.
Parametrize a set of state frequencies.
Abstract class for modelling of non-synonymous abd synonymous substitution rates in codon models...
void updateMatrices()
Diagonalize the matrix, and fill the eigenValues_, iEigenValues_, leftEigenVectors_ and rightEigenVe...
Specialisation interface for nucleotide substitution model.
CodonDistancePhaseFrequenciesSubstitutionModel(const GeneticCode *gCode, NucleotideSubstitutionModel *pmod, FrequenciesSet *pfreq, const AlphabetIndex2 *pdist=0)
Build a new CodonDistancePhaseFrequenciesSubstitutionModel object from three pointers to AbstractSubs...
void setFreq(std::map< int, double > &frequencies)
Set equilibrium frequencies.
void setNamespace(const std::string &prefix)
void fireParameterChanged(const ParameterList ¶meters)
void setNamespace(const std::string &prefix)
void fireParameterChanged(const ParameterList ¶meters)
Abstract class for substitution models on codons.
void setNamespace(const std::string &)
double getCodonsMulRate(size_t i, size_t j) const
Returns the multiplicative rate specific to two codons specified by their number. The respective gene...
virtual double getCodonsMulRate(size_t i, size_t j) const
Method inherited from CodonSubstitutionModel.
double getCodonsMulRate(size_t, size_t) const
Returns the multiplicative rate specific to two codons specified by their number. The respective gene...