40 #include "../Nucleotide/K80.h" 42 #include "../FrequenciesSet/CodonFrequenciesSet.h" 43 #include <Bpp/Numeric/NumConstants.h> 55 addParameter_(
new Parameter(
"YN98.kappa", 1, &Parameter::R_PLUS_STAR));
56 addParameter_(
new Parameter(
"YN98.omega", 1,
new IntervalConstraint(NumConstants::MILLI(), 999,
true,
true),
true));
59 addParameters_(codonFreqs->getParameters());
63 vector<std::string> v =
pmodel_->getFrequenciesSet()->getParameters().getParameterNames();
65 for (
size_t i = 0; i < v.size(); i++)
std::map< std::string, std::string > mapParNamesFromPmodel_
Tools to make the link between the Parameters of the object and those of pmixmodel_.
ParameterList lParPmodel_
Partial implementation of the SubstitutionModel interface for models that are set for matching the bi...
std::auto_ptr< CodonDistanceFrequenciesSubstitutionModel > pmodel_
virtual void updateMatrices()
The Kimura 2-rates substitution model for nucleotides.
AbstractBiblioSubstitutionModel & operator=(const AbstractBiblioSubstitutionModel &model)
Class for asynonymous substitution models on codons with parameterized equilibrium frequencies and nu...
Parametrize a set of state frequencies.
YN98(const GeneticCode *gc, FrequenciesSet *codonFreqs)
The Yang and Nielsen (1998) substitution model for codons.
YN98 & operator=(const YN98 &)