51 const std::string& prefix) :
53 AbstractParameterAliasable(prefix),
57 if (dynamic_cast<CodonFrequenciesSet*>(pfreq) == NULL)
58 throw Exception(
"Bad type for equilibrium frequencies " + pfreq->
getName());
62 addParameters_(
pfreqset_->getParameters());
73 pfreqset_->matchParametersValues(parameters);
80 matchParametersValues(
pfreqset_->getParameters());
void setFreq(std::map< int, double > &frequencies)
Set equilibrium frequencies.
AbstractCodonFrequenciesSubstitutionModel(FrequenciesSet *pfreq, const std::string &prefix)
Build a AbstractCodonFrequenciesSubstitutionModel instance.
virtual const std::vector< double > getFrequencies() const =0
Parametrize a set of state frequencies.
virtual ~AbstractCodonFrequenciesSubstitutionModel()
virtual std::string getName() const =0
FrequenciesSet * pfreqset_
double getCodonsMulRate(size_t, size_t) const
Returns the multiplicative rate specific to two codons specified by their number. The respective gene...
void fireParameterChanged(const ParameterList ¶meters)
virtual void setFrequenciesFromAlphabetStatesFrequencies(const std::map< int, double > &frequencies)=0
Set the Frequencies from the one of the map which keys match with a letter of the Alphabet...
Abstract class for codon models.