bpp::SENCA Member List

This is the complete list of members for bpp::SENCA, including all inherited members.

AbstractCodonDistanceSubstitutionModel(std::shared_ptr< const AlphabetIndex2 > pdist, std::shared_ptr< const GeneticCode > pgencode, const std::string &prefix, bool paramSynRate=false)	bpp::AbstractCodonDistanceSubstitutionModel
AbstractCodonDistanceSubstitutionModel(const AbstractCodonDistanceSubstitutionModel &model)	bpp::AbstractCodonDistanceSubstitutionModel	inline
AbstractCodonFitnessSubstitutionModel(std::unique_ptr< FrequencySetInterface > pfitset, std::shared_ptr< const GeneticCode > pgencode, const std::string &prefix)	bpp::AbstractCodonFitnessSubstitutionModel
AbstractCodonFitnessSubstitutionModel(const AbstractCodonFitnessSubstitutionModel &model)	bpp::AbstractCodonFitnessSubstitutionModel	inline
AbstractCodonSubstitutionModel(std::shared_ptr< const GeneticCode > gCode, std::unique_ptr< NucleotideSubstitutionModelInterface > pmod, const std::string &st, bool paramRates=false)	bpp::AbstractCodonSubstitutionModel
AbstractCodonSubstitutionModel(std::shared_ptr< const GeneticCode > gCode, std::unique_ptr< NucleotideSubstitutionModelInterface > pmod1, std::unique_ptr< NucleotideSubstitutionModelInterface > pmod2, std::unique_ptr< NucleotideSubstitutionModelInterface > pmod3, const std::string &st, bool paramRates=false)	bpp::AbstractCodonSubstitutionModel
AbstractCodonSubstitutionModel(const AbstractCodonSubstitutionModel &model)	bpp::AbstractCodonSubstitutionModel	inline
AbstractLkTransitionModel()	bpp::AbstractLkTransitionModel	inline
AbstractParameterAliasable(const std::string &prefix)	bpp::AbstractParameterAliasable
AbstractParameterAliasable(const AbstractParameterAliasable &ap)	bpp::AbstractParameterAliasable
AbstractParametrizable(const std::string &prefix)	bpp::AbstractParametrizable
AbstractSubstitutionModel(std::shared_ptr< const Alphabet > alpha, std::shared_ptr< const StateMapInterface > stateMap, const std::string &prefix)	bpp::AbstractSubstitutionModel
AbstractSubstitutionModel(const AbstractSubstitutionModel &model)	bpp::AbstractSubstitutionModel	inline
AbstractTransitionModel(std::shared_ptr< const Alphabet > alpha, std::shared_ptr< const StateMapInterface > stateMap, const std::string &prefix)	bpp::AbstractTransitionModel
AbstractTransitionModel(const AbstractTransitionModel &model)=default	bpp::AbstractTransitionModel
AbstractWordSubstitutionModel(ModelList &modelList, const std::string &prefix)	bpp::AbstractWordSubstitutionModel
AbstractWordSubstitutionModel(std::unique_ptr< SubstitutionModelInterface > model, unsigned int num, const std::string &prefix)	bpp::AbstractWordSubstitutionModel
AbstractWordSubstitutionModel(const AbstractWordSubstitutionModel &)	bpp::AbstractWordSubstitutionModel
AbstractWordSubstitutionModel(std::shared_ptr< const Alphabet > alph, std::shared_ptr< const StateMapInterface > stateMap, const std::string &prefix)	bpp::AbstractWordSubstitutionModel	protected
addParameter_(Parameter *parameter)	bpp::AbstractParameterAliasable	protectedvirtual
addParameters_(const ParameterList &parameters)	bpp::AbstractParameterAliasable	protectedvirtual
bpp::addRateParameter()=0	bpp::BranchModelInterface	pure virtual
bpp::AbstractCodonSubstitutionModel::bpp::AbstractWordSubstitutionModel::addRateParameter() override	bpp::AbstractTransitionModel	virtual
aliasListenersRegister_	bpp::AbstractParameterAliasable	private
bpp::aliasParameters(const std::string &p1, const std::string &p2)=0	bpp::ParameterAliasable	pure virtual
bpp::aliasParameters(std::map< std::string, std::string > &unparsedParams, bool verbose)=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractCodonSubstitutionModel::bpp::AbstractWordSubstitutionModel::bpp::AbstractParameterAliasable::aliasParameters(const std::string &p1, const std::string &p2)	bpp::AbstractParameterAliasable	virtual
bpp::AbstractParameterAliasable::aliasParameters(std::map< std::string, std::string > &unparsedParams, bool verbose)	bpp::AbstractParameterAliasable	virtual
alpha_	bpp::AbstractCodonDistanceSubstitutionModel	private
bpp::alphabet() const =0	bpp::BranchModelInterface	pure virtual
bpp::AbstractCodonSubstitutionModel::bpp::AbstractWordSubstitutionModel::alphabet() const override	bpp::AbstractTransitionModel	inlinevirtual
alphabet_	bpp::AbstractTransitionModel	protected
beta_	bpp::AbstractCodonDistanceSubstitutionModel	private
BranchModelInterface()	bpp::BranchModelInterface	inline
clone() const override	bpp::SENCA	inlinevirtual
codonFrequencySet() const override	bpp::SENCA	inlinevirtual
CodonSubstitutionModelInterface()	bpp::CodonSubstitutionModelInterface	inline
completeMatrices_() override	bpp::AbstractCodonSubstitutionModel	protectedvirtual
computeFreq_	bpp::AbstractSubstitutionModel	protected
bpp::computeFrequencies() const =0	bpp::TransitionModelInterface	pure virtual
bpp::computeFrequencies(bool yn)=0	bpp::TransitionModelInterface	pure virtual
bpp::AbstractCodonSubstitutionModel::bpp::AbstractWordSubstitutionModel::computeFrequencies() const	bpp::AbstractSubstitutionModel	inlinevirtual
bpp::AbstractWordSubstitutionModel::computeFrequencies(bool yn)	bpp::AbstractSubstitutionModel	inlinevirtual
CoreCodonSubstitutionModelInterface()	bpp::CoreCodonSubstitutionModelInterface	inline
bpp::d2Lik_dt2(const Eigen::VectorXd &values, double t) const =0	bpp::TransitionModelInterface	pure virtual
bpp::AbstractCodonSubstitutionModel::bpp::AbstractWordSubstitutionModel::d2Lik_dt2(const Eigen::VectorXd &values, double t) const override	bpp::AbstractLkTransitionModel	inlinevirtual
bpp::d2Pij_dt2(size_t i, size_t j, double t) const =0	bpp::TransitionModelInterface	pure virtual
bpp::AbstractCodonSubstitutionModel::bpp::AbstractWordSubstitutionModel::d2Pij_dt2(size_t i, size_t j, double t) const override	bpp::AbstractTransitionModel	inlinevirtual
d2pijt_	bpp::AbstractTransitionModel	mutableprotected
deleteParameter_(size_t index)	bpp::AbstractParameterAliasable	protectedvirtual
deleteParameter_(std::string &name)	bpp::AbstractParameterAliasable	protectedvirtual
deleteParameters_(const std::vector< std::string > &names)	bpp::AbstractParameterAliasable	protectedvirtual
bpp::dLik_dt(const Eigen::VectorXd &values, double t) const =0	bpp::TransitionModelInterface	pure virtual
bpp::AbstractCodonSubstitutionModel::bpp::AbstractWordSubstitutionModel::dLik_dt(const Eigen::VectorXd &values, double t) const override	bpp::AbstractLkTransitionModel	inlinevirtual
bpp::dPij_dt(size_t i, size_t j, double t) const =0	bpp::TransitionModelInterface	pure virtual
bpp::AbstractCodonSubstitutionModel::bpp::AbstractWordSubstitutionModel::dPij_dt(size_t i, size_t j, double t) const override	bpp::AbstractTransitionModel	inlinevirtual
dpijt_	bpp::AbstractTransitionModel	mutableprotected
eigenDecompose_	bpp::AbstractSubstitutionModel	protected
eigenValues_	bpp::AbstractSubstitutionModel	protected
bpp::enableEigenDecomposition(bool yn)=0	bpp::SubstitutionModelInterface	pure virtual
bpp::enableEigenDecomposition()=0	bpp::SubstitutionModelInterface	pure virtual
bpp::AbstractCodonSubstitutionModel::bpp::AbstractWordSubstitutionModel::enableEigenDecomposition(bool yn)	bpp::AbstractSubstitutionModel	inlinevirtual
bpp::AbstractWordSubstitutionModel::enableEigenDecomposition()	bpp::AbstractSubstitutionModel	inlinevirtual
exchangeability_	bpp::AbstractSubstitutionModel	protected
bpp::exchangeabilityMatrix() const =0	bpp::SubstitutionModelInterface	pure virtual
bpp::AbstractCodonSubstitutionModel::bpp::AbstractWordSubstitutionModel::exchangeabilityMatrix() const	bpp::AbstractSubstitutionModel	inlinevirtual
fillBasicGenerator_()	bpp::AbstractWordSubstitutionModel	protectedvirtual
fireParameterChanged(const ParameterList &parameterlist) override	bpp::SENCA	virtual
fitName_	bpp::AbstractCodonFitnessSubstitutionModel	private
fitness() const	bpp::AbstractCodonFitnessSubstitutionModel	inline
bpp::freq(size_t i) const =0	bpp::TransitionModelInterface	pure virtual
bpp::AbstractCodonSubstitutionModel::bpp::AbstractWordSubstitutionModel::freq(size_t i) const override	bpp::AbstractTransitionModel	inlinevirtual
freq_	bpp::AbstractTransitionModel	protected
bpp::frequencySet() const =0	bpp::BranchModelInterface	pure virtual
bpp::AbstractCodonSubstitutionModel::bpp::AbstractWordSubstitutionModel::frequencySet() const override	bpp::AbstractTransitionModel	inlinevirtual
gamma_	bpp::AbstractCodonDistanceSubstitutionModel	private
gCode_	bpp::AbstractCodonSubstitutionModel	private
bpp::generator() const =0	bpp::SubstitutionModelInterface	pure virtual
bpp::AbstractCodonSubstitutionModel::bpp::AbstractWordSubstitutionModel::generator() const	bpp::AbstractSubstitutionModel	inlinevirtual
generator_	bpp::AbstractSubstitutionModel	protected
bpp::getAlias(const std::string &name) const=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractCodonSubstitutionModel::bpp::AbstractWordSubstitutionModel::bpp::AbstractParameterAliasable::getAlias(const std::string &name) const	bpp::AbstractParameterAliasable	virtual
getAliasedParameters(const ParameterList &pl) const	bpp::AbstractParameterAliasable
bpp::getAliases() const=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractCodonSubstitutionModel::bpp::AbstractWordSubstitutionModel::bpp::AbstractParameterAliasable::getAliases() const	bpp::AbstractParameterAliasable	virtual
bpp::getAlphabet() const =0	bpp::BranchModelInterface	pure virtual
bpp::AbstractCodonSubstitutionModel::bpp::AbstractWordSubstitutionModel::getAlphabet() const override	bpp::AbstractTransitionModel	inlinevirtual
bpp::getAlphabetStateAsChar(size_t index) const =0	bpp::BranchModelInterface	pure virtual
bpp::AbstractCodonSubstitutionModel::bpp::AbstractWordSubstitutionModel::getAlphabetStateAsChar(size_t index) const override	bpp::AbstractTransitionModel	inlinevirtual
bpp::getAlphabetStateAsInt(size_t index) const =0	bpp::BranchModelInterface	pure virtual
bpp::AbstractCodonSubstitutionModel::bpp::AbstractWordSubstitutionModel::getAlphabetStateAsInt(size_t index) const override	bpp::AbstractTransitionModel	inlinevirtual
bpp::getAlphabetStates() const =0	bpp::BranchModelInterface	pure virtual
bpp::AbstractCodonSubstitutionModel::bpp::AbstractWordSubstitutionModel::getAlphabetStates() const override	bpp::AbstractTransitionModel	inlinevirtual
getCodonsMulRate(size_t i, size_t j) const override	bpp::SENCA	virtual
bpp::getColumnRightEigenVectors() const =0	bpp::SubstitutionModelInterface	pure virtual
bpp::AbstractCodonSubstitutionModel::bpp::AbstractWordSubstitutionModel::getColumnRightEigenVectors() const	bpp::AbstractSubstitutionModel	inlinevirtual
bpp::getd2Pij_dt2(double t) const =0	bpp::TransitionModelInterface	pure virtual
bpp::AbstractCodonSubstitutionModel::bpp::AbstractWordSubstitutionModel::getd2Pij_dt2(double t) const	bpp::AbstractSubstitutionModel	virtual
bpp::getdPij_dt(double t) const =0	bpp::TransitionModelInterface	pure virtual
bpp::AbstractCodonSubstitutionModel::bpp::AbstractWordSubstitutionModel::getdPij_dt(double t) const	bpp::AbstractSubstitutionModel	virtual
bpp::getEigenValues() const =0	bpp::SubstitutionModelInterface	pure virtual
bpp::AbstractCodonSubstitutionModel::bpp::AbstractWordSubstitutionModel::getEigenValues() const	bpp::AbstractSubstitutionModel	inlinevirtual
bpp::getFrequencies() const =0	bpp::TransitionModelInterface	pure virtual
bpp::AbstractCodonSubstitutionModel::bpp::AbstractWordSubstitutionModel::getFrequencies() const override	bpp::AbstractTransitionModel	inlinevirtual
bpp::getFrequencies_()=0	bpp::TransitionModelInterface	protectedpure virtual
bpp::AbstractCodonSubstitutionModel::bpp::AbstractWordSubstitutionModel::getFrequencies_() override	bpp::AbstractTransitionModel	inlineprotectedvirtual
getFrom(const std::string &name) const	bpp::AbstractParameterAliasable
getFromParameters(const ParameterList &pl) const	bpp::AbstractParameterAliasable
getGeneticCode() const override	bpp::AbstractCodonSubstitutionModel	inlinevirtual
bpp::getIEigenValues() const =0	bpp::SubstitutionModelInterface	pure virtual
bpp::AbstractCodonSubstitutionModel::bpp::AbstractWordSubstitutionModel::getIEigenValues() const	bpp::AbstractSubstitutionModel	inlinevirtual
bpp::getIndependentParameters() const=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractCodonSubstitutionModel::bpp::AbstractWordSubstitutionModel::bpp::AbstractParameterAliasable::getIndependentParameters() const	bpp::AbstractParameterAliasable	virtual
bpp::getInitValue(size_t i, int state) const =0	bpp::BranchModelInterface	pure virtual
bpp::AbstractCodonSubstitutionModel::bpp::AbstractWordSubstitutionModel::getInitValue(size_t i, int state) const override	bpp::AbstractTransitionModel	virtual
bpp::getModelStates(int code) const =0	bpp::BranchModelInterface	pure virtual
bpp::getModelStates(const std::string &code) const =0	bpp::BranchModelInterface	pure virtual
bpp::AbstractCodonSubstitutionModel::bpp::AbstractWordSubstitutionModel::getModelStates(int code) const override	bpp::AbstractTransitionModel	inlinevirtual
bpp::AbstractWordSubstitutionModel::getModelStates(const std::string &code) const override	bpp::AbstractTransitionModel	inlinevirtual
getName() const override	bpp::SENCA	inlinevirtual
bpp::getNamespace() const=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractCodonSubstitutionModel::bpp::AbstractWordSubstitutionModel::bpp::AbstractParameterAliasable::getNamespace() const override	bpp::AbstractParameterAliasable	virtual
bpp::getNumberOfIndependentParameters() const=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractCodonSubstitutionModel::bpp::AbstractWordSubstitutionModel::bpp::AbstractParameterAliasable::getNumberOfIndependentParameters() const	bpp::AbstractParameterAliasable	virtual
getNumberOfModels() const	bpp::AbstractWordSubstitutionModel	inline
bpp::getNumberOfParameters() const=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractCodonSubstitutionModel::bpp::AbstractWordSubstitutionModel::bpp::AbstractParameterAliasable::getNumberOfParameters() const override	bpp::AbstractParameterAliasable	virtual
bpp::getNumberOfStates() const =0	bpp::BranchModelInterface	pure virtual
bpp::AbstractCodonSubstitutionModel::bpp::AbstractWordSubstitutionModel::getNumberOfStates() const override	bpp::AbstractTransitionModel	inlinevirtual
getParameter(const std::string &name) const	bpp::AbstractParameterAliasable
getParameter(size_t i) const	bpp::AbstractParameterAliasable	protected
getParameter(size_t i)	bpp::AbstractParameterAliasable	protected
getParameter_(const std::string &name)	bpp::AbstractParameterAliasable	protected
getParameter_(size_t index)	bpp::AbstractParameterAliasable	protected
getParameter_(size_t index) const	bpp::AbstractParameterAliasable	protected
bpp::getParameterNameWithoutNamespace(const std::string &name) const=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractCodonSubstitutionModel::bpp::AbstractWordSubstitutionModel::bpp::AbstractParameterAliasable::getParameterNameWithoutNamespace(const std::string &name) const override	bpp::AbstractParameterAliasable	virtual
bpp::getParameters() const=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractCodonSubstitutionModel::bpp::AbstractWordSubstitutionModel::bpp::AbstractParameterAliasable::getParameters() const override	bpp::AbstractParameterAliasable	virtual
bpp::getParameters_()=0	bpp::ParameterAliasable	protectedpure virtual
bpp::AbstractCodonSubstitutionModel::bpp::AbstractWordSubstitutionModel::bpp::AbstractParameterAliasable::getParameters_() override	bpp::AbstractParameterAliasable	protectedvirtual
bpp::getParameterValue(const std::string &name) const=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractCodonSubstitutionModel::bpp::AbstractWordSubstitutionModel::bpp::AbstractParameterAliasable::getParameterValue(const std::string &name) const override	bpp::AbstractParameterAliasable	virtual
getParameterWithNamespace_(const std::string &name)	bpp::AbstractParameterAliasable	protected
getParameterWithNamespace_(const std::string &name) const	bpp::AbstractParameterAliasable	protected
bpp::getPij_t(double t) const =0	bpp::TransitionModelInterface	pure virtual
bpp::AbstractCodonSubstitutionModel::bpp::AbstractWordSubstitutionModel::getPij_t(double t) const	bpp::AbstractSubstitutionModel	virtual
bpp::getRate() const =0	bpp::BranchModelInterface	pure virtual
bpp::AbstractCodonSubstitutionModel::bpp::AbstractWordSubstitutionModel::getRate() const override	bpp::AbstractTransitionModel	virtual
bpp::getRowLeftEigenVectors() const =0	bpp::SubstitutionModelInterface	pure virtual
bpp::AbstractCodonSubstitutionModel::bpp::AbstractWordSubstitutionModel::getRowLeftEigenVectors() const	bpp::AbstractSubstitutionModel	inlinevirtual
bpp::getScale() const =0	bpp::SubstitutionModelInterface	pure virtual
bpp::AbstractCodonSubstitutionModel::bpp::AbstractWordSubstitutionModel::getScale() const	bpp::AbstractSubstitutionModel	virtual
bpp::getStateMap() const =0	bpp::BranchModelInterface	pure virtual
bpp::AbstractCodonSubstitutionModel::bpp::AbstractWordSubstitutionModel::getStateMap() const override	bpp::AbstractTransitionModel	inlinevirtual
hasCodonFrequencySet() const override	bpp::SENCA	inlinevirtual
hasIndependentParameter(const std::string &name) const	bpp::AbstractParameterAliasable
bpp::hasParameter(const std::string &name) const=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractCodonSubstitutionModel::bpp::AbstractWordSubstitutionModel::bpp::AbstractParameterAliasable::hasParameter(const std::string &name) const override	bpp::AbstractParameterAliasable	virtual
hasParametrizedRates_	bpp::AbstractCodonSubstitutionModel	private
iEigenValues_	bpp::AbstractSubstitutionModel	protected
includeParameters_(const ParameterList &parameters)	bpp::AbstractParameterAliasable	protectedvirtual
independentParameters_	bpp::AbstractParameterAliasable	private
bpp::isDiagonalizable() const =0	bpp::SubstitutionModelInterface	pure virtual
bpp::AbstractCodonSubstitutionModel::bpp::AbstractWordSubstitutionModel::isDiagonalizable() const	bpp::AbstractSubstitutionModel	inlinevirtual
isDiagonalizable_	bpp::AbstractSubstitutionModel	protected
bpp::isNonSingular() const =0	bpp::SubstitutionModelInterface	pure virtual
bpp::AbstractCodonSubstitutionModel::bpp::AbstractWordSubstitutionModel::isNonSingular() const	bpp::AbstractSubstitutionModel	inlinevirtual
isNonSingular_	bpp::AbstractSubstitutionModel	protected
bpp::isScalable() const =0	bpp::SubstitutionModelInterface	pure virtual
bpp::AbstractCodonSubstitutionModel::bpp::AbstractWordSubstitutionModel::isScalable() const	bpp::AbstractSubstitutionModel	inlinevirtual
isScalable_	bpp::AbstractSubstitutionModel	protected
leftEigenVectors_	bpp::AbstractSubstitutionModel	protected
lik_	bpp::AbstractLkTransitionModel	mutableprivate
bpp::Lik_t(const Eigen::VectorXd &values, double t) const =0	bpp::TransitionModelInterface	pure virtual
bpp::AbstractCodonSubstitutionModel::bpp::AbstractWordSubstitutionModel::Lik_t(const Eigen::VectorXd &values, double t) const override	bpp::AbstractLkTransitionModel	inlinevirtual
bpp::matchParametersValues(const ParameterList &parameters)=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractCodonSubstitutionModel::bpp::AbstractWordSubstitutionModel::bpp::AbstractParameterAliasable::matchParametersValues(const ParameterList &parameters) override	bpp::AbstractParameterAliasable	virtual
newAlphabet_	bpp::AbstractWordSubstitutionModel	private
nModel(size_t i) const	bpp::AbstractWordSubstitutionModel	inline
bpp::normalize()=0	bpp::SubstitutionModelInterface	pure virtual
bpp::AbstractCodonSubstitutionModel::bpp::AbstractWordSubstitutionModel::normalize()	bpp::AbstractSubstitutionModel	virtual
bpp::operator=(const AbstractCodonSubstitutionModel &model)	bpp::AbstractCodonSubstitutionModel	inline
bpp::AbstractWordSubstitutionModel::operator=(const AbstractWordSubstitutionModel &)	bpp::AbstractWordSubstitutionModel
bpp::AbstractSubstitutionModel::operator=(const AbstractSubstitutionModel &model)	bpp::AbstractSubstitutionModel	inline
bpp::AbstractTransitionModel::operator=(const AbstractTransitionModel &model)=default	bpp::AbstractTransitionModel
bpp::AbstractParameterAliasable::operator=(const AbstractParameterAliasable &ap)	bpp::AbstractParameterAliasable
bpp::AbstractCodonDistanceSubstitutionModel::operator=(const AbstractCodonDistanceSubstitutionModel &model)	bpp::AbstractCodonDistanceSubstitutionModel	inline
bpp::AbstractCodonFitnessSubstitutionModel::operator=(const AbstractCodonFitnessSubstitutionModel &model)	bpp::AbstractCodonFitnessSubstitutionModel	inline
bpp::parameter(const std::string &name) const=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractCodonSubstitutionModel::bpp::AbstractWordSubstitutionModel::bpp::AbstractParameterAliasable::parameter(const std::string &name) const override	bpp::AbstractParameterAliasable	virtual
ParameterAliasable()	bpp::ParameterAliasable
parameters_	bpp::AbstractParameterAliasable	private
Parametrizable()	bpp::Parametrizable
pdistance_	bpp::AbstractCodonDistanceSubstitutionModel	private
pfitset_	bpp::AbstractCodonFitnessSubstitutionModel	private
bpp::pgencode_	bpp::AbstractCodonDistanceSubstitutionModel	private
bpp::Pij_t(size_t i, size_t j, double t) const =0	bpp::TransitionModelInterface	pure virtual
bpp::AbstractCodonSubstitutionModel::bpp::AbstractWordSubstitutionModel::Pij_t(size_t i, size_t j, double t) const override	bpp::AbstractTransitionModel	inlinevirtual
pijt_	bpp::AbstractTransitionModel	mutableprotected
prefix_	bpp::AbstractParameterAliasable	private
bpp::Qij(size_t i, size_t j) const =0	bpp::SubstitutionModelInterface	pure virtual
bpp::AbstractCodonSubstitutionModel::bpp::AbstractWordSubstitutionModel::Qij(size_t i, size_t j) const	bpp::AbstractSubstitutionModel	inlinevirtual
rate_	bpp::AbstractTransitionModel	protected
bpp::removeConstraint(const std::string &name)=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractCodonSubstitutionModel::bpp::AbstractWordSubstitutionModel::bpp::AbstractParameterAliasable::removeConstraint(const std::string &name) override	bpp::AbstractParameterAliasable	virtual
resetParameters_()	bpp::AbstractParameterAliasable	protected
rightEigenVectors_	bpp::AbstractSubstitutionModel	protected
SENCA(std::shared_ptr< const GeneticCode > gCode, std::unique_ptr< NucleotideSubstitutionModelInterface > pmod, std::unique_ptr< FrequencySetInterface > pfit, std::shared_ptr< const AlphabetIndex2 > pdist=nullptr)	bpp::SENCA
SENCA(std::shared_ptr< const GeneticCode > gCode, std::unique_ptr< NucleotideSubstitutionModelInterface > pmod1, std::unique_ptr< NucleotideSubstitutionModelInterface > pmod2, std::unique_ptr< NucleotideSubstitutionModelInterface > pmod3, std::unique_ptr< FrequencySetInterface > pfit, std::shared_ptr< const AlphabetIndex2 > pdist=nullptr)	bpp::SENCA
bpp::setAllParametersValues(const ParameterList &parameters)=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractCodonSubstitutionModel::bpp::AbstractWordSubstitutionModel::bpp::AbstractParameterAliasable::setAllParametersValues(const ParameterList &parameters) override	bpp::AbstractParameterAliasable	virtual
bpp::setConstraint(const std::string &name, std::shared_ptr< ConstraintInterface > constraint)=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractCodonSubstitutionModel::bpp::AbstractWordSubstitutionModel::bpp::AbstractParameterAliasable::setConstraint(const std::string &name, std::shared_ptr< ConstraintInterface > constraint) override	bpp::AbstractParameterAliasable	virtual
bpp::setDiagonal()=0	bpp::SubstitutionModelInterface	pure virtual
bpp::AbstractCodonSubstitutionModel::bpp::AbstractWordSubstitutionModel::setDiagonal()	bpp::AbstractSubstitutionModel	virtual
setFreq(std::map< int, double > &frequencies) override	bpp::SENCA	virtual
bpp::setFreqFromData(const SequenceDataInterface &data, double pseudoCount=0)=0	bpp::TransitionModelInterface	pure virtual
bpp::AbstractCodonSubstitutionModel::bpp::AbstractWordSubstitutionModel::setFreqFromData(const SequenceDataInterface &data, double pseudoCount=0) override	bpp::AbstractTransitionModel	virtual
setNamespace(const std::string &) override	bpp::SENCA	virtual
bpp::setParametersValues(const ParameterList &parameters)=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractCodonSubstitutionModel::bpp::AbstractWordSubstitutionModel::bpp::AbstractParameterAliasable::setParametersValues(const ParameterList &parameters) override	bpp::AbstractParameterAliasable	virtual
bpp::setParameterValue(const std::string &name, double value)=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractCodonSubstitutionModel::bpp::AbstractWordSubstitutionModel::bpp::AbstractParameterAliasable::setParameterValue(const std::string &name, double value) override	bpp::AbstractParameterAliasable	virtual
bpp::setRate(double rate)=0	bpp::BranchModelInterface	pure virtual
bpp::AbstractCodonSubstitutionModel::bpp::AbstractWordSubstitutionModel::setRate(double rate) override	bpp::AbstractTransitionModel	virtual
bpp::setScalable(bool scalable)=0	bpp::SubstitutionModelInterface	pure virtual
bpp::AbstractCodonSubstitutionModel::bpp::AbstractWordSubstitutionModel::setScalable(bool scalable)	bpp::AbstractSubstitutionModel	inlinevirtual
bpp::setScale(double scale)=0	bpp::SubstitutionModelInterface	pure virtual
bpp::AbstractCodonSubstitutionModel::bpp::AbstractWordSubstitutionModel::setScale(double scale)	bpp::AbstractSubstitutionModel	virtual
setVerboseLevel(short level)	bpp::AbstractTransitionModel	inline
shareParameter_(const std::shared_ptr< Parameter > &parameter)	bpp::AbstractParameterAliasable	protectedvirtual
shareParameters_(const ParameterList &parameters)	bpp::AbstractParameterAliasable	protectedvirtual
bpp::Sij(size_t i, size_t j) const =0	bpp::SubstitutionModelInterface	pure virtual
bpp::AbstractCodonSubstitutionModel::bpp::AbstractWordSubstitutionModel::Sij(size_t i, size_t j) const	bpp::AbstractSubstitutionModel	inlinevirtual
size_	bpp::AbstractTransitionModel	protected
bpp::stateMap() const =0	bpp::BranchModelInterface	pure virtual
bpp::AbstractCodonSubstitutionModel::bpp::AbstractWordSubstitutionModel::stateMap() const override	bpp::AbstractTransitionModel	inlinevirtual
bpp::stateMap_	bpp::AbstractTransitionModel	protected
SubstitutionModelInterface()	bpp::SubstitutionModelInterface	inline
tmpMat_	bpp::AbstractSubstitutionModel	mutableprotected
TransitionModelInterface()	bpp::TransitionModelInterface	inline
bpp::unaliasParameters(const std::string &p1, const std::string &p2)=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractCodonSubstitutionModel::bpp::AbstractWordSubstitutionModel::bpp::AbstractParameterAliasable::unaliasParameters(const std::string &p1, const std::string &p2)	bpp::AbstractParameterAliasable	virtual
updateMatrices_() override	bpp::AbstractCodonSubstitutionModel	protectedvirtual
verboseLevel() const	bpp::AbstractTransitionModel	inline
verboseLevel_	bpp::AbstractTransitionModel	protected
VnestedPrefix_	bpp::AbstractWordSubstitutionModel	protected
vPowGen_	bpp::AbstractSubstitutionModel	protected
Vrate_	bpp::AbstractWordSubstitutionModel	protected
VSubMod_	bpp::AbstractWordSubstitutionModel	protected
~AbstractCodonDistanceSubstitutionModel()	bpp::AbstractCodonDistanceSubstitutionModel	inlinevirtual
~AbstractCodonFitnessSubstitutionModel()	bpp::AbstractCodonFitnessSubstitutionModel	virtual
~AbstractCodonSubstitutionModel()	bpp::AbstractCodonSubstitutionModel	inlinevirtual
~AbstractLkTransitionModel()	bpp::AbstractLkTransitionModel	inlinevirtual
~AbstractParameterAliasable()	bpp::AbstractParameterAliasable	virtual
~AbstractParametrizable()	bpp::AbstractParametrizable	virtual
~AbstractSubstitutionModel()	bpp::AbstractSubstitutionModel	inlinevirtual
~AbstractTransitionModel()	bpp::AbstractTransitionModel	inlinevirtual
~AbstractWordSubstitutionModel()	bpp::AbstractWordSubstitutionModel	inlinevirtual
~BranchModelInterface()	bpp::BranchModelInterface	inlinevirtual
~Clonable()=default	bpp::Clonable	virtual
~CodonSubstitutionModelInterface()	bpp::CodonSubstitutionModelInterface	inlinevirtual
~CoreCodonSubstitutionModelInterface()	bpp::CoreCodonSubstitutionModelInterface	inlinevirtual
~ParameterAliasable()	bpp::ParameterAliasable	virtual
~Parametrizable()	bpp::Parametrizable	virtual
~SENCA()	bpp::SENCA	inlinevirtual
~SubstitutionModelInterface()	bpp::SubstitutionModelInterface	inlinevirtual
~TransitionModelInterface()	bpp::TransitionModelInterface	inlinevirtual