40 #ifndef _CODONDISTANCEFITNESSPHASEFREQUENCIESSUBSTITUTIONMODEL_H_ 41 #define _CODONDISTANCEFITNESSPHASEFREQUENCIESSUBSTITUTIONMODEL_H_ 102 const GeneticCode* gCode,
106 const AlphabetIndex2* pdist = 0);
108 const GeneticCode* gCode,
114 const AlphabetIndex2* pdist = 0);
144 void setFreq(std::map<int,double>& frequencies);
Abstract Class for substitution models on codons parametrized by a frequency.
Parametrize a set of state frequencies.
CodonDistanceFitnessPhaseFrequenciesSubstitutionModel(const GeneticCode *gCode, NucleotideSubstitutionModel *pmod, FrequenciesSet *pfit, FrequenciesSet *pfreq, const AlphabetIndex2 *pdist=0)
Abstract class for modelling of non-synonymous abd synonymous substitution rates in codon models...
CodonDistanceFitnessPhaseFrequenciesSubstitutionModel * clone() const
std::string getName() const
Get the name of the model.
void fireParameterChanged(const ParameterList ¶meterlist)
Tells the model that a parameter value has changed.
virtual ~CodonDistanceFitnessPhaseFrequenciesSubstitutionModel()
void setNamespace(const std::string &)
Abstract class for modelling of ratios of substitution rates between codons, whatever they are synony...
Interface for reversible substitution models.
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...
void setFreq(std::map< int, double > &frequencies)
Set equilibrium frequencies.
Abstract class for substitution models on codons.
Class for asynonymous and synonymous substitution models on codons with parameterized equilibrium fre...