40 #ifndef _CODONRATEFREQUENCIESSUBSTITUTIONMODEL_H_ 41 #define _CODONRATEFREQUENCIESSUBSTITUTIONMODEL_H_ 81 const GeneticCode* gCode,
99 const GeneticCode* gCode,
107 #ifndef NO_VIRTUAL_COV 123 void setFreq(std::map<int,double>& frequencies);
CodonRateFrequenciesSubstitutionModel * clone() const
Parametrize a set of state frequencies.
void setNamespace(const std::string &st)
Specialisation interface for nucleotide substitution 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...
Abstract Class for substitution models on codons parametrized by frequencies.
virtual ~CodonRateFrequenciesSubstitutionModel()
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.
Abstract class for substitution models on codons.
void fireParameterChanged(const ParameterList ¶meterlist)
Tells the model that a parameter value has changed.
Class for substitution models on non stop codons, with different parametrized rates on the models...