bpp-phyl3 3.0.0
bpp::MixtureOfSubstitutionModels Member List

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

AbstractLkTransitionModel()bpp::AbstractLkTransitionModelinline
AbstractMixedTransitionModel(std::shared_ptr< const Alphabet >, std::shared_ptr< const StateMapInterface > stateMap, const std::string &prefix)bpp::AbstractMixedTransitionModel
AbstractMixedTransitionModel(const AbstractMixedTransitionModel &)bpp::AbstractMixedTransitionModel
AbstractParameterAliasable(const std::string &prefix)bpp::AbstractParameterAliasable
AbstractParameterAliasable(const AbstractParameterAliasable &ap)bpp::AbstractParameterAliasable
AbstractParametrizable(const std::string &prefix)bpp::AbstractParametrizable
AbstractTransitionModel(std::shared_ptr< const Alphabet > alpha, std::shared_ptr< const StateMapInterface > stateMap, const std::string &prefix)bpp::AbstractTransitionModel
AbstractTransitionModel(const AbstractTransitionModel &model)=defaultbpp::AbstractTransitionModel
addParameter_(Parameter *parameter)bpp::AbstractParameterAliasableprotectedvirtual
addParameters_(const ParameterList &parameters)bpp::AbstractParameterAliasableprotectedvirtual
bpp::addRateParameter()=0bpp::BranchModelInterfacepure virtual
bpp::AbstractTransitionModel::addRateParameter() overridebpp::AbstractTransitionModelvirtual
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::AbstractTransitionModel::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
bpp::alphabet() const =0bpp::BranchModelInterfacepure virtual
bpp::AbstractTransitionModel::alphabet() const overridebpp::AbstractTransitionModelinlinevirtual
alphabet_bpp::AbstractTransitionModelprotected
BranchModelInterface()bpp::BranchModelInterfaceinline
clone() const overridebpp::MixtureOfSubstitutionModelsinlinevirtual
computeFrequencies() const overridebpp::AbstractMixedTransitionModelinlinevirtual
computeFrequencies(bool yn) overridebpp::AbstractMixedTransitionModelinlinevirtual
bpp::d2Lik_dt2(const Eigen::VectorXd &values, double t) const =0bpp::TransitionModelInterfacepure virtual
bpp::AbstractTransitionModel::d2Lik_dt2(const Eigen::VectorXd &values, double t) const overridebpp::AbstractLkTransitionModelinlinevirtual
bpp::d2Pij_dt2(size_t i, size_t j, double t) const =0bpp::TransitionModelInterfacepure virtual
bpp::AbstractTransitionModel::d2Pij_dt2(size_t i, size_t j, double t) const overridebpp::AbstractTransitionModelinlinevirtual
d2pijt_bpp::AbstractTransitionModelmutableprotected
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::AbstractTransitionModel::dLik_dt(const Eigen::VectorXd &values, double t) const overridebpp::AbstractLkTransitionModelinlinevirtual
bpp::dPij_dt(size_t i, size_t j, double t) const =0bpp::TransitionModelInterfacepure virtual
bpp::AbstractTransitionModel::dPij_dt(size_t i, size_t j, double t) const overridebpp::AbstractTransitionModelinlinevirtual
dpijt_bpp::AbstractTransitionModelmutableprotected
fireParameterChanged(const ParameterList &parameters) overridebpp::AbstractTransitionModelinlinevirtual
bpp::freq(size_t i) const =0bpp::TransitionModelInterfacepure virtual
bpp::AbstractTransitionModel::freq(size_t i) const overridebpp::AbstractTransitionModelinlinevirtual
freq_bpp::AbstractTransitionModelprotected
bpp::frequencySet() const =0bpp::BranchModelInterfacepure virtual
bpp::AbstractTransitionModel::frequencySet() const overridebpp::AbstractTransitionModelinlinevirtual
bpp::getAlias(const std::string &name) const=0bpp::ParameterAliasablepure virtual
bpp::AbstractTransitionModel::bpp::AbstractParameterAliasable::getAlias(const std::string &name) constbpp::AbstractParameterAliasablevirtual
getAliasedParameters(const ParameterList &pl) constbpp::AbstractParameterAliasable
bpp::getAliases() const=0bpp::ParameterAliasablepure virtual
bpp::AbstractTransitionModel::bpp::AbstractParameterAliasable::getAliases() constbpp::AbstractParameterAliasablevirtual
bpp::getAlphabet() const =0bpp::BranchModelInterfacepure virtual
bpp::AbstractTransitionModel::getAlphabet() const overridebpp::AbstractTransitionModelinlinevirtual
bpp::getAlphabetStateAsChar(size_t index) const =0bpp::BranchModelInterfacepure virtual
bpp::AbstractTransitionModel::getAlphabetStateAsChar(size_t index) const overridebpp::AbstractTransitionModelinlinevirtual
bpp::getAlphabetStateAsInt(size_t index) const =0bpp::BranchModelInterfacepure virtual
bpp::AbstractTransitionModel::getAlphabetStateAsInt(size_t index) const overridebpp::AbstractTransitionModelinlinevirtual
bpp::getAlphabetStates() const =0bpp::BranchModelInterfacepure virtual
bpp::AbstractTransitionModel::getAlphabetStates() const overridebpp::AbstractTransitionModelinlinevirtual
getd2Pij_dt2(double t) const overridebpp::AbstractMixedTransitionModelvirtual
getdPij_dt(double t) const overridebpp::AbstractMixedTransitionModelvirtual
bpp::getFrequencies() const =0bpp::TransitionModelInterfacepure virtual
bpp::AbstractTransitionModel::getFrequencies() const overridebpp::AbstractTransitionModelinlinevirtual
bpp::getFrequencies_()=0bpp::TransitionModelInterfaceprotectedpure virtual
bpp::AbstractTransitionModel::getFrequencies_() overridebpp::AbstractTransitionModelinlineprotectedvirtual
getFrom(const std::string &name) constbpp::AbstractParameterAliasable
getFromParameters(const ParameterList &pl) constbpp::AbstractParameterAliasable
bpp::getIndependentParameters() const=0bpp::ParameterAliasablepure virtual
bpp::AbstractTransitionModel::bpp::AbstractParameterAliasable::getIndependentParameters() constbpp::AbstractParameterAliasablevirtual
bpp::getInitValue(size_t i, int state) const =0bpp::BranchModelInterfacepure virtual
bpp::AbstractTransitionModel::getInitValue(size_t i, int state) const overridebpp::AbstractTransitionModelvirtual
bpp::getModelStates(int code) const =0bpp::BranchModelInterfacepure virtual
bpp::getModelStates(const std::string &code) const =0bpp::BranchModelInterfacepure virtual
bpp::AbstractTransitionModel::getModelStates(int code) const overridebpp::AbstractTransitionModelinlinevirtual
bpp::AbstractTransitionModel::getModelStates(const std::string &code) const overridebpp::AbstractTransitionModelinlinevirtual
getName() const overridebpp::MixtureOfTransitionModelsinlinevirtual
bpp::getNamespace() const=0bpp::ParameterAliasablepure virtual
bpp::AbstractTransitionModel::bpp::AbstractParameterAliasable::getNamespace() const overridebpp::AbstractParameterAliasablevirtual
getNModel(size_t i) const overridebpp::AbstractMixedTransitionModelinlinevirtual
getNProbability(size_t i) const overridebpp::AbstractMixedTransitionModelinlinevirtual
getNRate(size_t i) const overridebpp::AbstractMixedTransitionModelinlinevirtual
bpp::getNumberOfIndependentParameters() const=0bpp::ParameterAliasablepure virtual
bpp::AbstractTransitionModel::bpp::AbstractParameterAliasable::getNumberOfIndependentParameters() constbpp::AbstractParameterAliasablevirtual
getNumberOfModels() const overridebpp::AbstractMixedTransitionModelinlinevirtual
bpp::getNumberOfParameters() const=0bpp::ParameterAliasablepure virtual
bpp::AbstractTransitionModel::bpp::AbstractParameterAliasable::getNumberOfParameters() const overridebpp::AbstractParameterAliasablevirtual
bpp::getNumberOfStates() const =0bpp::BranchModelInterfacepure virtual
bpp::AbstractTransitionModel::getNumberOfStates() const overridebpp::AbstractTransitionModelinlinevirtual
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::AbstractTransitionModel::bpp::AbstractParameterAliasable::getParameterNameWithoutNamespace(const std::string &name) const overridebpp::AbstractParameterAliasablevirtual
bpp::getParameters() const=0bpp::ParameterAliasablepure virtual
bpp::AbstractTransitionModel::bpp::AbstractParameterAliasable::getParameters() const overridebpp::AbstractParameterAliasablevirtual
bpp::getParameters_()=0bpp::ParameterAliasableprotectedpure virtual
bpp::AbstractTransitionModel::bpp::AbstractParameterAliasable::getParameters_() overridebpp::AbstractParameterAliasableprotectedvirtual
bpp::getParameterValue(const std::string &name) const=0bpp::ParameterAliasablepure virtual
bpp::AbstractTransitionModel::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::AbstractMixedTransitionModelvirtual
getProbabilities() const overridebpp::AbstractMixedTransitionModelinlinevirtual
bpp::getRate() const =0bpp::BranchModelInterfacepure virtual
bpp::AbstractTransitionModel::getRate() const overridebpp::AbstractTransitionModelvirtual
bpp::getStateMap() const =0bpp::BranchModelInterfacepure virtual
bpp::AbstractTransitionModel::getStateMap() const overridebpp::AbstractTransitionModelinlinevirtual
getSubmodelNumbers(const std::string &desc) const overridebpp::MixtureOfTransitionModelsvirtual
getVRates() const overridebpp::AbstractMixedTransitionModelinlinevirtual
hasIndependentParameter(const std::string &name) constbpp::AbstractParameterAliasable
bpp::hasParameter(const std::string &name) const=0bpp::ParameterAliasablepure virtual
bpp::AbstractTransitionModel::bpp::AbstractParameterAliasable::hasParameter(const std::string &name) const overridebpp::AbstractParameterAliasablevirtual
includeParameters_(const ParameterList &parameters)bpp::AbstractParameterAliasableprotectedvirtual
independentParameters_bpp::AbstractParameterAliasableprivate
lik_bpp::AbstractLkTransitionModelmutableprivate
bpp::Lik_t(const Eigen::VectorXd &values, double t) const =0bpp::TransitionModelInterfacepure virtual
bpp::AbstractTransitionModel::Lik_t(const Eigen::VectorXd &values, double t) const overridebpp::AbstractLkTransitionModelinlinevirtual
bpp::matchParametersValues(const ParameterList &parameters)=0bpp::ParameterAliasablepure virtual
bpp::AbstractTransitionModel::bpp::AbstractParameterAliasable::matchParametersValues(const ParameterList &parameters) overridebpp::AbstractParameterAliasablevirtual
MixedTransitionModelInterface()bpp::MixedTransitionModelInterfaceinline
MixtureOfSubstitutionModels(std::shared_ptr< const Alphabet > alpha, std::vector< std::unique_ptr< TransitionModelInterface > > &vpModel)bpp::MixtureOfSubstitutionModelsinline
MixtureOfSubstitutionModels(std::shared_ptr< const Alphabet > alpha, std::vector< std::unique_ptr< TransitionModelInterface > > &vpModel, Vdouble &vproba, Vdouble &vrate)bpp::MixtureOfSubstitutionModelsinline
MixtureOfSubstitutionModels(const MixtureOfSubstitutionModels &model)bpp::MixtureOfSubstitutionModelsinline
MixtureOfTransitionModels(std::shared_ptr< const Alphabet > alpha, std::vector< std::unique_ptr< TransitionModelInterface > > &vpModel)bpp::MixtureOfTransitionModels
MixtureOfTransitionModels(std::shared_ptr< const Alphabet > alpha, std::vector< std::unique_ptr< TransitionModelInterface > > &vpModel, Vdouble &vproba, Vdouble &vrate)bpp::MixtureOfTransitionModels
MixtureOfTransitionModels(const MixtureOfTransitionModels &)bpp::MixtureOfTransitionModels
model(const std::string &name) const overridebpp::MixtureOfTransitionModelsvirtual
model(size_t i) constbpp::MixtureOfTransitionModelsinline
modelsContainer_bpp::AbstractMixedTransitionModelprotected
nModel(size_t i) const overridebpp::AbstractMixedTransitionModelinlinevirtual
nModel_(size_t i) overridebpp::AbstractMixedTransitionModelinlineprotectedvirtual
normalizeVRates() overridebpp::AbstractMixedTransitionModelvirtual
operator=(const MixtureOfSubstitutionModels &model)bpp::MixtureOfSubstitutionModelsinline
bpp::MixtureOfTransitionModels::operator=(const MixtureOfTransitionModels &)bpp::MixtureOfTransitionModels
bpp::AbstractMixedTransitionModel::operator=(const AbstractMixedTransitionModel &)bpp::AbstractMixedTransitionModel
bpp::AbstractTransitionModel::operator=(const AbstractTransitionModel &model)=defaultbpp::AbstractTransitionModel
bpp::AbstractParameterAliasable::operator=(const AbstractParameterAliasable &ap)bpp::AbstractParameterAliasable
bpp::parameter(const std::string &name) const=0bpp::ParameterAliasablepure virtual
bpp::AbstractTransitionModel::bpp::AbstractParameterAliasable::parameter(const std::string &name) const overridebpp::AbstractParameterAliasablevirtual
ParameterAliasable()bpp::ParameterAliasable
parameters_bpp::AbstractParameterAliasableprivate
Parametrizable()bpp::Parametrizable
bpp::Pij_t(size_t i, size_t j, double t) const =0bpp::TransitionModelInterfacepure virtual
bpp::AbstractTransitionModel::Pij_t(size_t i, size_t j, double t) const overridebpp::AbstractTransitionModelinlinevirtual
pijt_bpp::AbstractTransitionModelmutableprotected
prefix_bpp::AbstractParameterAliasableprivate
rate_bpp::AbstractTransitionModelprotected
bpp::removeConstraint(const std::string &name)=0bpp::ParameterAliasablepure virtual
bpp::AbstractTransitionModel::bpp::AbstractParameterAliasable::removeConstraint(const std::string &name) overridebpp::AbstractParameterAliasablevirtual
resetParameters_()bpp::AbstractParameterAliasableprotected
bpp::setAllParametersValues(const ParameterList &parameters)=0bpp::ParameterAliasablepure virtual
bpp::AbstractTransitionModel::bpp::AbstractParameterAliasable::setAllParametersValues(const ParameterList &parameters) overridebpp::AbstractParameterAliasablevirtual
bpp::setConstraint(const std::string &name, std::shared_ptr< ConstraintInterface > constraint)=0bpp::ParameterAliasablepure virtual
bpp::AbstractTransitionModel::bpp::AbstractParameterAliasable::setConstraint(const std::string &name, std::shared_ptr< ConstraintInterface > constraint) overridebpp::AbstractParameterAliasablevirtual
setFreq(std::map< int, double > &) overridebpp::MixtureOfTransitionModelsvirtual
setFreqFromData(const SequenceDataInterface &data, double pseudoCount) overridebpp::AbstractMixedTransitionModelinlinevirtual
bpp::setNamespace(const std::string &prefix)=0bpp::ParameterAliasablepure virtual
bpp::AbstractTransitionModel::bpp::AbstractParameterAliasable::setNamespace(const std::string &prefix)bpp::AbstractParameterAliasablevirtual
setNProbability(size_t i, double prob) overridebpp::AbstractMixedTransitionModelinlinevirtual
bpp::setParametersValues(const ParameterList &parameters)=0bpp::ParameterAliasablepure virtual
bpp::AbstractTransitionModel::bpp::AbstractParameterAliasable::setParametersValues(const ParameterList &parameters) overridebpp::AbstractParameterAliasablevirtual
bpp::setParameterValue(const std::string &name, double value)=0bpp::ParameterAliasablepure virtual
bpp::AbstractTransitionModel::bpp::AbstractParameterAliasable::setParameterValue(const std::string &name, double value) overridebpp::AbstractParameterAliasablevirtual
setRate(double rate) overridebpp::AbstractMixedTransitionModelvirtual
setVerboseLevel(short level)bpp::AbstractTransitionModelinline
setVRates(const Vdouble &vd) overridebpp::MixtureOfTransitionModelsvirtual
shareParameter_(const std::shared_ptr< Parameter > &parameter)bpp::AbstractParameterAliasableprotectedvirtual
shareParameters_(const ParameterList &parameters)bpp::AbstractParameterAliasableprotectedvirtual
size_bpp::AbstractTransitionModelprotected
bpp::stateMap() const =0bpp::BranchModelInterfacepure virtual
bpp::AbstractTransitionModel::stateMap() const overridebpp::AbstractTransitionModelinlinevirtual
stateMap_bpp::AbstractTransitionModelprotected
subModel(const std::string &name) constbpp::MixtureOfSubstitutionModelsinline
TransitionModelInterface()bpp::TransitionModelInterfaceinline
bpp::unaliasParameters(const std::string &p1, const std::string &p2)=0bpp::ParameterAliasablepure virtual
bpp::AbstractTransitionModel::bpp::AbstractParameterAliasable::unaliasParameters(const std::string &p1, const std::string &p2)bpp::AbstractParameterAliasablevirtual
updateMatrices_() overridebpp::MixtureOfTransitionModelsvirtual
verboseLevel() constbpp::AbstractTransitionModelinline
verboseLevel_bpp::AbstractTransitionModelprotected
vProbas_bpp::AbstractMixedTransitionModelprotected
vRates_bpp::AbstractMixedTransitionModelprotected
~AbstractLkTransitionModel()bpp::AbstractLkTransitionModelinlinevirtual
~AbstractParameterAliasable()bpp::AbstractParameterAliasablevirtual
~AbstractParametrizable()bpp::AbstractParametrizablevirtual
~AbstractTransitionModel()bpp::AbstractTransitionModelinlinevirtual
~BranchModelInterface()bpp::BranchModelInterfaceinlinevirtual
~Clonable()=defaultbpp::Clonablevirtual
~MixedTransitionModelInterface()bpp::MixedTransitionModelInterfaceinlinevirtual
~MixtureOfTransitionModels()bpp::MixtureOfTransitionModelsvirtual
~ParameterAliasable()bpp::ParameterAliasablevirtual
~Parametrizable()bpp::Parametrizablevirtual
~TransitionModelInterface()bpp::TransitionModelInterfaceinlinevirtual