40 #include "../FrequenciesSet/ProteinFrequenciesSet.h" 42 #include <Bpp/Numeric/Prob/SimpleDiscreteDistribution.h> 56 vector<SubstitutionModel*> vpSM;
60 Vdouble vrate, vproba;
62 for (
unsigned int i = 0; i < vpSM.size(); i++)
64 vproba.push_back((dynamic_cast<LLG08_EX2::EmbeddedModel*>(vpSM[i]))->getProportion());
65 vrate.push_back(vpSM[i]->
getRate());
71 ParameterList pl =
pmixmodel_->getParameters();
72 for (
size_t i = 0; i < pl.size(); i++)
74 name = pl[i].getName();
76 st =
pmixmodel_->getParameterNameWithoutNamespace(name);
78 addParameter_(
new Parameter(
"LLG08_EX2." + st,
80 pmixmodel_->getParameter(st).hasConstraint() ?
pmixmodel_->getParameter(st).getConstraint()->clone() : 0,
true));
104 AbstractParameterAliasable(name),
109 #include "__LLG08_EX2ExchangeabilityCode" 110 #include "__LLG08_EX2FrequenciesCode" 111 #include "__LLG08_EX2RatesProps"
std::map< std::string, std::string > mapParNamesFromPmodel_
Tools to make the link between the Parameters of the object and those of pmixmodel_.
ParameterList lParPmodel_
Abstract class for mixture models based on the bibliography.
This class implements a state map where all resolved states are modeled.
virtual void updateMatrices()
The Le et al (2008) EX2 substitution model for proteins.
virtual void updateMatrices()
Compute and diagonalize the matrix, and fill the eigenValues_, leftEigenVectors_ and rightEigenVecto...
LLG08_EX2(const ProteicAlphabet *alpha)
Build a EX2 model, with original equilibrium frequencies, probabilities and rates.
Partial implementation of the ReversibleSubstitutionModel interface.
LLG08_EX2 & operator=(const LLG08_EX2 &)
AbstractBiblioMixedSubstitutionModel & operator=(const AbstractBiblioMixedSubstitutionModel &model)
double getRate() const
Get the rate.
EmbeddedModel(const ProteicAlphabet *alpha, string name)
std::auto_ptr< MixtureOfSubstitutionModels > pmixmodel_
Substitution models defined as a mixture of several substitution models.