39 # ifndef _ABSTRACTCODONFITNESSSUBSTITUTIONMODEL_H_ 40 # define _ABSTRACTCODONFITNESSSUBSTITUTIONMODEL_H_ 43 #include "../FrequenciesSet/CodonFrequenciesSet.h" 67 public virtual AbstractParameterAliasable
75 AbstractParameterAliasable(model),
81 AbstractParameterAliasable::operator=(model);
92 void setFreq(std::map<int, double>& frequencies);
AbstractCodonFitnessSubstitutionModel & operator=(const AbstractCodonFitnessSubstitutionModel &model)
virtual ~AbstractCodonFitnessSubstitutionModel()
FrequenciesSet * clone() const =0
Parametrize a set of state frequencies.
AbstractCodonFitnessSubstitutionModel(FrequenciesSet *pfitset, const std::string &prefix)
Abstract class for modelling of ratios of substitution rates between codons, whatever they are synony...
void setNamespace(const std::string &prefix)
void setFreq(std::map< int, double > &frequencies)
Set equilibrium frequencies.
FrequenciesSet * pfitset_
const FrequenciesSet & getFreq() const
const FrequenciesSet * getFitness() const
Abstract class for codon models.
virtual CodonSubstitutionModel * clone() const =0
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)
AbstractCodonFitnessSubstitutionModel(const AbstractCodonFitnessSubstitutionModel &model)