40 #ifndef _CODONDISTANCESUBSTITUTIONMODEL_H_ 41 #define _CODONDISTANCESUBSTITUTIONMODEL_H_ 86 const GeneticCode* gCode,
88 const AlphabetIndex2* pdist);
103 const GeneticCode* gCode,
107 const AlphabetIndex2* pdist);
125 #endif //_CODONDISTANCESUBSTITUTIONMODEL_H_ virtual ~CodonDistanceSubstitutionModel()
void fireParameterChanged(const ParameterList ¶meterlist)
Tells the model that a parameter value has changed.
Abstract class for modelling of non-synonymous abd synonymous substitution rates in codon models...
CodonDistanceSubstitutionModel(const GeneticCode *gCode, NucleotideSubstitutionModel *pmod, const AlphabetIndex2 *pdist)
Build a new CodonDistanceSubstitutionModel object from a pointer to NucleotideSubstitutionModel.
std::string getName() const
Get the name of the 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...
CodonDistanceSubstitutionModel * clone() const
Specialisation interface for nucleotide substitution model.
Abstract class for substitution models on codons.
Class for substitution models of codons with non-synonymous/synonymous ratios of substitution rates d...