bpp-phyl3  3.0.0
bpp::G2001 Member List

This is the complete list of members for bpp::G2001, including all inherited members.

AbstractLkTransitionModel()bpp::AbstractLkTransitionModelinline
AbstractParameterAliasable(const std::string &prefix)bpp::AbstractParameterAliasable
AbstractParameterAliasable(const AbstractParameterAliasable &ap)bpp::AbstractParameterAliasable
AbstractParametrizable(const std::string &prefix)bpp::AbstractParametrizable
addParameter_(Parameter *parameter)bpp::AbstractParameterAliasableprotectedvirtual
addParameters_(const ParameterList &parameters)bpp::AbstractParameterAliasableprotectedvirtual
addRateParameter() overridebpp::G2001inlinevirtual
aliasListenersRegister_bpp::AbstractParameterAliasableprivate
bpp::aliasParameters(const std::string &p1, const std::string &p2)=0bpp::ParameterAliasablepure virtual
bpp::aliasParameters(std::map< std::string, std::string > &unparsedParams, bool verbose)=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::aliasParameters(const std::string &p1, const std::string &p2)bpp::AbstractParameterAliasablevirtual
bpp::AbstractParameterAliasable::aliasParameters(std::map< std::string, std::string > &unparsedParams, bool verbose)bpp::AbstractParameterAliasablevirtual
alphabet() const overridebpp::MarkovModulatedSubstitutionModelinlinevirtual
BranchModelInterface()bpp::BranchModelInterfaceinline
clone() const overridebpp::G2001inlinevirtual
compFreq_bpp::MarkovModulatedSubstitutionModelprotected
computeFrequencies() const overridebpp::MarkovModulatedSubstitutionModelinlinevirtual
computeFrequencies(bool yn) overridebpp::MarkovModulatedSubstitutionModelinlinevirtual
bpp::d2Lik_dt2(const Eigen::VectorXd &values, double t) const =0bpp::TransitionModelInterfacepure virtual
bpp::AbstractLkTransitionModel::d2Lik_dt2(const Eigen::VectorXd &values, double t) const overridebpp::AbstractLkTransitionModelinlinevirtual
d2Pij_dt2(size_t i, size_t j, double t) const overridebpp::MarkovModulatedSubstitutionModelinlinevirtual
d2pijt_bpp::MarkovModulatedSubstitutionModelmutableprotected
deleteParameter_(size_t index)bpp::AbstractParameterAliasableprotectedvirtual
deleteParameter_(std::string &name)bpp::AbstractParameterAliasableprotectedvirtual
deleteParameters_(const std::vector< std::string > &names)bpp::AbstractParameterAliasableprotectedvirtual
bpp::dLik_dt(const Eigen::VectorXd &values, double t) const =0bpp::TransitionModelInterfacepure virtual
bpp::AbstractLkTransitionModel::dLik_dt(const Eigen::VectorXd &values, double t) const overridebpp::AbstractLkTransitionModelinlinevirtual
dPij_dt(size_t i, size_t j, double t) const overridebpp::MarkovModulatedSubstitutionModelinlinevirtual
dpijt_bpp::MarkovModulatedSubstitutionModelmutableprotected
eigenDecompose_bpp::MarkovModulatedSubstitutionModelprotected
eigenValues_bpp::MarkovModulatedSubstitutionModelprotected
enableEigenDecomposition(bool yn) overridebpp::MarkovModulatedSubstitutionModelinlinevirtual
enableEigenDecomposition() overridebpp::MarkovModulatedSubstitutionModelinlinevirtual
exchangeability_bpp::MarkovModulatedSubstitutionModelprotected
exchangeabilityMatrix() const overridebpp::MarkovModulatedSubstitutionModelinlinevirtual
fireParameterChanged(const ParameterList &parameters) overridebpp::G2001inlinevirtual
freq(size_t i) const overridebpp::MarkovModulatedSubstitutionModelinlinevirtual
freq_bpp::MarkovModulatedSubstitutionModelprotected
frequencySet() const overridebpp::MarkovModulatedSubstitutionModelinlinevirtual
G2001(std::unique_ptr< ReversibleSubstitutionModelInterface > model, std::unique_ptr< DiscreteDistributionInterface > rDist, double nu=1., bool normalizeRateChanges=false)bpp::G2001inline
G2001(const G2001 &model)bpp::G2001inline
generator() const overridebpp::MarkovModulatedSubstitutionModelinlinevirtual
generator_bpp::MarkovModulatedSubstitutionModelprotected
bpp::getAlias(const std::string &name) const=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::getAlias(const std::string &name) constbpp::AbstractParameterAliasablevirtual
getAliasedParameters(const ParameterList &pl) constbpp::AbstractParameterAliasable
bpp::getAliases() const=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::getAliases() constbpp::AbstractParameterAliasablevirtual
getAlphabet() const overridebpp::MarkovModulatedSubstitutionModelinlinevirtual
getAlphabetStateAsChar(size_t index) const overridebpp::MarkovModulatedSubstitutionModelinlinevirtual
getAlphabetStateAsInt(size_t index) const overridebpp::MarkovModulatedSubstitutionModelinlinevirtual
getAlphabetStates() const overridebpp::MarkovModulatedSubstitutionModelinlinevirtual
getColumnRightEigenVectors() const overridebpp::MarkovModulatedSubstitutionModelinlinevirtual
getd2Pij_dt2(double t) const overridebpp::MarkovModulatedSubstitutionModelvirtual
getdPij_dt(double t) const overridebpp::MarkovModulatedSubstitutionModelvirtual
getEigenValues() const overridebpp::MarkovModulatedSubstitutionModelinlinevirtual
getFrequencies() const overridebpp::MarkovModulatedSubstitutionModelinlinevirtual
getFrequencies_() overridebpp::MarkovModulatedSubstitutionModelinlineprotectedvirtual
getFrom(const std::string &name) constbpp::AbstractParameterAliasable
getFromParameters(const ParameterList &pl) constbpp::AbstractParameterAliasable
getIEigenValues() const overridebpp::MarkovModulatedSubstitutionModelinlinevirtual
bpp::getIndependentParameters() const=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::getIndependentParameters() constbpp::AbstractParameterAliasablevirtual
getInitValue(size_t i, int state) const overridebpp::MarkovModulatedSubstitutionModelvirtual
getModelStates(int code) const overridebpp::MarkovModulatedSubstitutionModelinlinevirtual
getModelStates(const std::string &code) const overridebpp::MarkovModulatedSubstitutionModelinlinevirtual
getName() const overridebpp::G2001inlinevirtual
bpp::getNamespace() const=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::getNamespace() const overridebpp::AbstractParameterAliasablevirtual
bpp::getNumberOfIndependentParameters() const=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::getNumberOfIndependentParameters() constbpp::AbstractParameterAliasablevirtual
bpp::getNumberOfParameters() const=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::getNumberOfParameters() const overridebpp::AbstractParameterAliasablevirtual
getNumberOfStates() const overridebpp::MarkovModulatedSubstitutionModelinlinevirtual
getParameter(const std::string &name) constbpp::AbstractParameterAliasable
getParameter(size_t i) constbpp::AbstractParameterAliasableprotected
getParameter(size_t i)bpp::AbstractParameterAliasableprotected
getParameter_(const std::string &name)bpp::AbstractParameterAliasableprotected
getParameter_(size_t index)bpp::AbstractParameterAliasableprotected
getParameter_(size_t index) constbpp::AbstractParameterAliasableprotected
bpp::getParameterNameWithoutNamespace(const std::string &name) const=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::getParameterNameWithoutNamespace(const std::string &name) const overridebpp::AbstractParameterAliasablevirtual
bpp::getParameters() const=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::getParameters() const overridebpp::AbstractParameterAliasablevirtual
bpp::getParameters_()=0bpp::ParameterAliasableprotectedpure virtual
bpp::AbstractParameterAliasable::getParameters_() overridebpp::AbstractParameterAliasableprotectedvirtual
bpp::getParameterValue(const std::string &name) const=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::getParameterValue(const std::string &name) const overridebpp::AbstractParameterAliasablevirtual
getParameterWithNamespace_(const std::string &name)bpp::AbstractParameterAliasableprotected
getParameterWithNamespace_(const std::string &name) constbpp::AbstractParameterAliasableprotected
getPij_t(double t) const overridebpp::MarkovModulatedSubstitutionModelvirtual
getRate() const overridebpp::G2001inlinevirtual
bpp::MarkovModulatedSubstitutionModel::getRate(size_t i) constbpp::MarkovModulatedSubstitutionModelinline
getRowLeftEigenVectors() const overridebpp::MarkovModulatedSubstitutionModelinlinevirtual
getScale() const overridebpp::MarkovModulatedSubstitutionModelinlinevirtual
getStateMap() const overridebpp::MarkovModulatedSubstitutionModelinlinevirtual
hasIndependentParameter(const std::string &name) constbpp::AbstractParameterAliasable
bpp::hasParameter(const std::string &name) const=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::hasParameter(const std::string &name) const overridebpp::AbstractParameterAliasablevirtual
iEigenValues_bpp::MarkovModulatedSubstitutionModelprotected
includeParameters_(const ParameterList &parameters)bpp::AbstractParameterAliasableprotectedvirtual
independentParameters_bpp::AbstractParameterAliasableprivate
isDiagonalizable() const overridebpp::MarkovModulatedSubstitutionModelinlinevirtual
isNonSingular() const overridebpp::MarkovModulatedSubstitutionModelinlinevirtual
isScalable() const overridebpp::MarkovModulatedSubstitutionModelinlinevirtual
leftEigenVectors_bpp::MarkovModulatedSubstitutionModelprotected
lik_bpp::AbstractLkTransitionModelmutableprivate
bpp::Lik_t(const Eigen::VectorXd &values, double t) const =0bpp::TransitionModelInterfacepure virtual
bpp::AbstractLkTransitionModel::Lik_t(const Eigen::VectorXd &values, double t) const overridebpp::AbstractLkTransitionModelinlinevirtual
MarkovModulatedSubstitutionModel(std::unique_ptr< ReversibleSubstitutionModelInterface > model, unsigned int nbRates, bool normalizeRateChanges, const std::string &prefix)bpp::MarkovModulatedSubstitutionModelinline
MarkovModulatedSubstitutionModel(const MarkovModulatedSubstitutionModel &model)bpp::MarkovModulatedSubstitutionModel
bpp::matchParametersValues(const ParameterList &parameters)=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::matchParametersValues(const ParameterList &parameters) overridebpp::AbstractParameterAliasablevirtual
model_bpp::MarkovModulatedSubstitutionModelprotected
nbRates_bpp::MarkovModulatedSubstitutionModelprotected
nbStates_bpp::MarkovModulatedSubstitutionModelprotected
nestedModel() constbpp::MarkovModulatedSubstitutionModelinline
nestedPrefix_bpp::MarkovModulatedSubstitutionModelprotected
nestedRatePrefix_bpp::G2001private
normalize() overridebpp::MarkovModulatedSubstitutionModelinlinevirtual
normalizeRateChanges_bpp::MarkovModulatedSubstitutionModelprotected
operator=(const G2001 &model)bpp::G2001inline
bpp::MarkovModulatedSubstitutionModel::operator=(const MarkovModulatedSubstitutionModel &model)bpp::MarkovModulatedSubstitutionModel
bpp::AbstractParameterAliasable::operator=(const AbstractParameterAliasable &ap)bpp::AbstractParameterAliasable
bpp::parameter(const std::string &name) const=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::parameter(const std::string &name) const overridebpp::AbstractParameterAliasablevirtual
ParameterAliasable()bpp::ParameterAliasable
parameters_bpp::AbstractParameterAliasableprivate
Parametrizable()bpp::Parametrizable
Pij_t(size_t i, size_t j, double t) const overridebpp::MarkovModulatedSubstitutionModelinlinevirtual
pijt_bpp::MarkovModulatedSubstitutionModelmutableprotected
prefix_bpp::AbstractParameterAliasableprivate
Qij(size_t i, size_t j) const overridebpp::MarkovModulatedSubstitutionModelinlinevirtual
rateDistribution() constbpp::G2001inline
rates_bpp::MarkovModulatedSubstitutionModelprotected
ratesExchangeability_bpp::MarkovModulatedSubstitutionModelprotected
ratesFreq_bpp::MarkovModulatedSubstitutionModelprotected
ratesGenerator_bpp::MarkovModulatedSubstitutionModelprotected
rDist_bpp::G2001private
bpp::removeConstraint(const std::string &name)=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::removeConstraint(const std::string &name) overridebpp::AbstractParameterAliasablevirtual
resetParameters_()bpp::AbstractParameterAliasableprotected
ReversibleSubstitutionModelInterface()bpp::ReversibleSubstitutionModelInterfaceinline
rightEigenVectors_bpp::MarkovModulatedSubstitutionModelprotected
bpp::setAllParametersValues(const ParameterList &parameters)=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::setAllParametersValues(const ParameterList &parameters) overridebpp::AbstractParameterAliasablevirtual
bpp::setConstraint(const std::string &name, std::shared_ptr< ConstraintInterface > constraint)=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::setConstraint(const std::string &name, std::shared_ptr< ConstraintInterface > constraint) overridebpp::AbstractParameterAliasablevirtual
setDiagonal() overridebpp::MarkovModulatedSubstitutionModelvirtual
setFreq(std::map< int, double > &frequencies) overridebpp::MarkovModulatedSubstitutionModelinlinevirtual
setFreqFromData(const SequenceDataInterface &data, double pseudoCount=0) overridebpp::MarkovModulatedSubstitutionModelinlinevirtual
setNamespace(const std::string &prefix) overridebpp::G2001inlinevirtual
bpp::setParametersValues(const ParameterList &parameters)=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::setParametersValues(const ParameterList &parameters) overridebpp::AbstractParameterAliasablevirtual
bpp::setParameterValue(const std::string &name, double value)=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::setParameterValue(const std::string &name, double value) overridebpp::AbstractParameterAliasablevirtual
setRate(double rate) overridebpp::G2001inlinevirtual
setScalable(bool scalable) overridebpp::MarkovModulatedSubstitutionModelinlinevirtual
setScale(double scale) overridebpp::MarkovModulatedSubstitutionModelinlinevirtual
shareParameter_(const std::shared_ptr< Parameter > &parameter)bpp::AbstractParameterAliasableprotectedvirtual
shareParameters_(const ParameterList &parameters)bpp::AbstractParameterAliasableprotectedvirtual
Sij(size_t i, size_t j) const overridebpp::MarkovModulatedSubstitutionModelinlinevirtual
stateMap() const overridebpp::MarkovModulatedSubstitutionModelinlinevirtual
stateMap_bpp::MarkovModulatedSubstitutionModelprotected
SubstitutionModelInterface()bpp::SubstitutionModelInterfaceinline
TransitionModelInterface()bpp::TransitionModelInterfaceinline
bpp::unaliasParameters(const std::string &p1, const std::string &p2)=0bpp::ParameterAliasablepure virtual
bpp::AbstractParameterAliasable::unaliasParameters(const std::string &p1, const std::string &p2)bpp::AbstractParameterAliasablevirtual
updateMatrices_()bpp::MarkovModulatedSubstitutionModelprotectedvirtual
updateRatesModel_() overridebpp::G2001inlineprotectedvirtual
~AbstractLkTransitionModel()bpp::AbstractLkTransitionModelinlinevirtual
~AbstractParameterAliasable()bpp::AbstractParameterAliasablevirtual
~AbstractParametrizable()bpp::AbstractParametrizablevirtual
~BranchModelInterface()bpp::BranchModelInterfaceinlinevirtual
~Clonable()=defaultbpp::Clonablevirtual
~G2001()bpp::G2001inlinevirtual
~MarkovModulatedSubstitutionModel()bpp::MarkovModulatedSubstitutionModelinlinevirtual
~ParameterAliasable()bpp::ParameterAliasablevirtual
~Parametrizable()bpp::Parametrizablevirtual
~ReversibleSubstitutionModelInterface()bpp::ReversibleSubstitutionModelInterfaceinlinevirtual
~SubstitutionModelInterface()bpp::SubstitutionModelInterfaceinlinevirtual
~TransitionModelInterface()bpp::TransitionModelInterfaceinlinevirtual