40 #ifndef _CODONDISTANCEFREQUENCIESSUBSTITUTIONMODEL_H_ 41 #define _CODONDISTANCEFREQUENCIESSUBSTITUTIONMODEL_H_ 106 const GeneticCode* gCode,
109 const AlphabetIndex2* pdist = 0,
110 bool paramSynRate =
false);
129 const GeneticCode* gCode,
134 const AlphabetIndex2* pdist = 0,
135 bool paramSynRate =
false);
153 void setFreq(std::map<int,double>& frequencies);
virtual ~CodonDistanceFrequenciesSubstitutionModel()
void setNamespace(const std::string &)
Class for asynonymous substitution models on codons with parameterized equilibrium frequencies and nu...
Parametrize a set of state frequencies.
Abstract class for modelling of non-synonymous abd synonymous substitution rates in codon models...
std::string getName() const
Get the name of the model.
CodonDistanceFrequenciesSubstitutionModel(const GeneticCode *gCode, NucleotideSubstitutionModel *pmod, FrequenciesSet *pfreq, const AlphabetIndex2 *pdist=0, bool paramSynRate=false)
Build a new CodonDistanceFrequenciesSubstitutionModel object from three pointers to AbstractSubstitut...
void fireParameterChanged(const ParameterList ¶meterlist)
Tells the model that a parameter value has changed.
Specialisation interface for nucleotide substitution model.
Abstract Class for substitution models on codons parametrized by frequencies.
double getCodonsMulRate(size_t i, size_t j) const
Returns the multiplicative rate specific to two codons specified by their number. The respective gene...
CodonDistanceFrequenciesSubstitutionModel * clone() const
Abstract class for substitution models on codons.
void setFreq(std::map< int, double > &frequencies)
Set equilibrium frequencies.