40 #include "../FrequenciesSet/ProteinFrequenciesSet.h" 42 #include <Bpp/Numeric/Prob/SimpleDiscreteDistribution.h> 56 vector<SubstitutionModel*> vpSM;
64 Vdouble vrate, vproba;
66 for (
unsigned int i=0;i<vpSM.size();i++)
68 vproba.push_back((dynamic_cast<LG10_EX_EHO::EmbeddedModel*> (vpSM[i]))->getProportion());
69 vrate.push_back(vpSM[i]->
getRate());
76 for (
unsigned int i=0;i<pl.size();i++)
80 st=
pmixmodel_->getParameterNameWithoutNamespace(name);
82 addParameter_(
new Parameter(
"LG10_EX_EHO."+st,
84 pmixmodel_->getParameter(st).hasConstraint()?
pmixmodel_->getParameter(st).getConstraint()->clone():0,
true));
109 AbstractParameterAliasable(name),
114 #include "__LG10_EX_EHOExchangeabilityCode" 115 #include "__LG10_EX_EHOFrequenciesCode" 116 #include "__LG10_EX_EHORatesProps"
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()
EmbeddedModel(const ProteicAlphabet *alpha, string name)
virtual void updateMatrices()
Compute and diagonalize the matrix, and fill the eigenValues_, leftEigenVectors_ and rightEigenVecto...
Partial implementation of the ReversibleSubstitutionModel interface.
The Le and Gascuel (2010) EX_EHO substitution model for proteins.
AbstractBiblioMixedSubstitutionModel & operator=(const AbstractBiblioMixedSubstitutionModel &model)
std::auto_ptr< MixtureOfSubstitutionModels > pmixmodel_
LG10_EX_EHO & operator=(const LG10_EX_EHO &)
double getRate() const
Get the rate.
LG10_EX_EHO(const ProteicAlphabet *alpha)
Build a EX_EHO model, with original equilibrium frequencies, probabilities and rates.
Substitution models defined as a mixture of several substitution models.