40 #include <Bpp/Numeric/NumConstants.h> 49 const AlphabetIndex2* pdist,
50 const std::string& prefix,
53 AbstractParameterAliasable(prefix),
60 addParameter_(
new Parameter(prefix +
"alpha", 10000, &Parameter::R_PLUS_STAR));
63 addParameter_(
new Parameter(prefix +
"gamma", 1,
new IntervalConstraint(NumConstants::SMALL(), 999,
true,
true),
true));
65 addParameter_(
new Parameter(prefix +
"beta", 1,
new IntervalConstraint(NumConstants::SMALL(), 999,
true,
true),
true));
71 alpha_ = getParameterValue(
"alpha");
73 if (hasParameter(
"gamma"))
74 gamma_ = getParameterValue(
"gamma");
75 beta_ = getParameterValue(
"beta");
double getCodonsMulRate(size_t i, size_t j) const
Returns the multiplicative rate specific to two codons specified by their number. The respective gene...
AbstractCodonDistanceSubstitutionModel(const AlphabetIndex2 *pdist, const std::string &prefix, bool paramSynRate=false)
Build a new AbstractCodonDistanceSubstitutionModel object from a pointer to NucleotideSubstitutionMod...
const AlphabetIndex2 * pdistance_
void fireParameterChanged(const ParameterList ¶meters)
Abstract class for codon models.
virtual const GeneticCode * getGeneticCode() const =0