5 #ifndef BPP_PHYL_MODEL_CODON_CODONSUBSTITUTIONMODEL_H
6 #define BPP_PHYL_MODEL_CODON_CODONSUBSTITUTIONMODEL_H
11 #include "../SubstitutionModel.h"
12 #include "../FrequencySet/CodonFrequencySet.h"
44 virtual void setFreq(std::map<int, double>& frequencies) = 0;
Parametrize a set of state frequencies for codons.
Interface for reversible codon models.
virtual CodonReversibleSubstitutionModelInterface * clone() const override=0
CodonReversibleSubstitutionModelInterface()
virtual ~CodonReversibleSubstitutionModelInterface()
virtual ~CodonSubstitutionModelInterface()
virtual std::shared_ptr< const GeneticCode > getGeneticCode() const =0
virtual CodonSubstitutionModelInterface * clone() const override=0
CodonSubstitutionModelInterface()
Interface for codon models.
virtual CoreCodonSubstitutionModelInterface * clone() const override=0
virtual void setFreq(std::map< int, double > &frequencies)=0
CoreCodonSubstitutionModelInterface()
virtual ~CoreCodonSubstitutionModelInterface()
virtual double getCodonsMulRate(size_t, size_t) const =0
Returns the multiplicative rate specific to two codons specified by their number. The respective gene...
virtual const CodonFrequencySetInterface & codonFrequencySet() const =0
virtual bool hasCodonFrequencySet() const =0
Interface for reversible substitution models.
Interface for all substitution models.
Defines the basic types of data flow nodes.