5 #ifndef BPP_PHYL_MODEL_CODON_ABSTRACTCODONAAFITNESSSUBSTITUTIONMODEL_H
6 #define BPP_PHYL_MODEL_CODON_ABSTRACTCODONAAFITNESSSUBSTITUTIONMODEL_H
9 # ifndef _ABSTRACTCODON_AA_FITNESSSUBSTITUTIONMODEL_H_
10 # define _ABSTRACTCODON_AA_FITNESSSUBSTITUTIONMODEL_H_
14 #include "../FrequencySet/ProteinFrequencySet.h"
43 std::shared_ptr<FrequencySetInterface>
pfitset_;
62 std::shared_ptr<FrequencySetInterface> pfitset,
63 std::shared_ptr<const GeneticCode> pgencode,
64 const std::string& prefix);
99 void setFreq(std::map<int, double>& frequencies)
override;
103 throw NullPointerException(
"AbstractCodonAAFitnessSubstitutionModel::codonFrequencySet. This model does not take codon frequencies. See aaFitness.");
Abstract class for modelling of ratios of substitution rates between codons, whatever they are synony...
bool hasCodonFrequencySet() const override
std::shared_ptr< const GeneticCode > pgencode_
std::shared_ptr< const StateMapInterface > stateMap_
AbstractCodonAAFitnessSubstitutionModel & operator=(const AbstractCodonAAFitnessSubstitutionModel &model)
virtual ~AbstractCodonAAFitnessSubstitutionModel()
std::shared_ptr< FrequencySetInterface > pfitset_
std::shared_ptr< const FrequencySetInterface > getAAFitness() const
void setFreq(std::map< int, double > &frequencies) override
void setNamespace(const std::string &prefix) override
AbstractCodonAAFitnessSubstitutionModel(std::shared_ptr< FrequencySetInterface > pfitset, std::shared_ptr< const GeneticCode > pgencode, const std::string &prefix)
AbstractCodonAAFitnessSubstitutionModel * clone() const override
void fireParameterChanged(const ParameterList ¶meters) override
double getCodonsMulRate(size_t i, size_t j) const override
Returns the multiplicative rate specific to two codons specified by their number. The respective gene...
const FrequencySetInterface & aaFitness() const
std::shared_ptr< const StateMapInterface > protStateMap_
const CodonFrequencySetInterface & codonFrequencySet() const override
AbstractCodonAAFitnessSubstitutionModel(const AbstractCodonAAFitnessSubstitutionModel &model)
double Ns_
The Ns of the model (default: 1), The generator (and all its vectorial components) is independent of ...
void addParameter_(Parameter *parameter)
AbstractParameterAliasable & operator=(const AbstractParameterAliasable &ap)
void setNamespace(const std::string &prefix)
std::string getNamespace() const override
Parametrize a set of state frequencies for codons.
Interface for codon models.
Parametrize a set of state frequencies.
Defines the basic types of data flow nodes.