| AbstractParameterAliasable(const std::string &prefix) | bpp::AbstractParameterAliasable | |
| AbstractParameterAliasable(const AbstractParameterAliasable &ap) | bpp::AbstractParameterAliasable | |
| AbstractParametrizable(const std::string &prefix) | bpp::AbstractParametrizable | |
| AbstractWrappedModel(const std::string &prefix) | bpp::AbstractWrappedModel | inline |
| addParameter_(Parameter *parameter) | bpp::AbstractParameterAliasable | protectedvirtual |
| addParameters_(const ParameterList ¶meters) | bpp::AbstractParameterAliasable | protectedvirtual |
| addRateParameter()=0 | bpp::BranchModelInterface | pure virtual |
| aliasListenersRegister_ | bpp::AbstractParameterAliasable | private |
| aliasParameters(const std::string &p1, const std::string &p2) | bpp::AbstractParameterAliasable | virtual |
| aliasParameters(std::map< std::string, std::string > &unparsedParams, bool verbose) | bpp::AbstractParameterAliasable | virtual |
| alphabet() const override | bpp::AbstractWrappedModel | inlinevirtual |
| BranchModelInterface() | bpp::BranchModelInterface | inline |
| bpp::clone() const=0 | bpp::AbstractParameterAliasable | pure virtual |
| bpp::WrappedModelInterface::clone() const =0 | bpp::BranchModelInterface | pure virtual |
| d2Lik_dt2(const Eigen::VectorXd &values, double t) const =0 | bpp::BranchModelInterface | pure virtual |
| deleteParameter_(size_t index) | bpp::AbstractParameterAliasable | protectedvirtual |
| deleteParameter_(std::string &name) | bpp::AbstractParameterAliasable | protectedvirtual |
| deleteParameters_(const std::vector< std::string > &names) | bpp::AbstractParameterAliasable | protectedvirtual |
| dLik_dt(const Eigen::VectorXd &values, double t) const =0 | bpp::BranchModelInterface | pure virtual |
| fireParameterChanged(const ParameterList ¶meters) | bpp::AbstractParameterAliasable | virtual |
| frequencySet() const override | bpp::AbstractWrappedModel | inlinevirtual |
| getAlias(const std::string &name) const | bpp::AbstractParameterAliasable | virtual |
| getAliasedParameters(const ParameterList &pl) const | bpp::AbstractParameterAliasable | |
| getAliases() const | bpp::AbstractParameterAliasable | virtual |
| getAlphabet() const override | bpp::AbstractWrappedModel | inlinevirtual |
| getAlphabetStateAsChar(size_t i) const override | bpp::AbstractWrappedModel | inlinevirtual |
| getAlphabetStateAsInt(size_t i) const override | bpp::AbstractWrappedModel | inlinevirtual |
| getAlphabetStates() const override | bpp::AbstractWrappedModel | inlinevirtual |
| getFrom(const std::string &name) const | bpp::AbstractParameterAliasable | |
| getFromParameters(const ParameterList &pl) const | bpp::AbstractParameterAliasable | |
| getIndependentParameters() const | bpp::AbstractParameterAliasable | virtual |
| getInitValue(size_t i, int state) const =0 | bpp::BranchModelInterface | pure virtual |
| getModelStates(int code) const override | bpp::AbstractWrappedModel | inlinevirtual |
| getModelStates(const std::string &code) const override | bpp::AbstractWrappedModel | inlinevirtual |
| getName() const override | bpp::AbstractWrappedModel | inlinevirtual |
| getNamespace() const override | bpp::AbstractParameterAliasable | virtual |
| getNumberOfIndependentParameters() const | bpp::AbstractParameterAliasable | virtual |
| getNumberOfParameters() const override | bpp::AbstractParameterAliasable | virtual |
| getNumberOfStates() const override | bpp::AbstractWrappedModel | 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 |
| getParameterNameWithoutNamespace(const std::string &name) const override | bpp::AbstractParameterAliasable | virtual |
| getParameters() const override | bpp::AbstractParameterAliasable | virtual |
| getParameters_() override | bpp::AbstractParameterAliasable | protectedvirtual |
| 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 |
| getRate() const =0 | bpp::BranchModelInterface | pure virtual |
| getStateMap() const override | bpp::AbstractWrappedModel | inlinevirtual |
| hasIndependentParameter(const std::string &name) const | bpp::AbstractParameterAliasable | |
| hasParameter(const std::string &name) const override | bpp::AbstractParameterAliasable | virtual |
| includeParameters_(const ParameterList ¶meters) | bpp::AbstractParameterAliasable | protectedvirtual |
| independentParameters_ | bpp::AbstractParameterAliasable | private |
| Lik_t(const Eigen::VectorXd &values, double t) const =0 | bpp::BranchModelInterface | pure virtual |
| matchParametersValues(const ParameterList ¶meters) override | bpp::AbstractParameterAliasable | virtual |
| model() const =0 | bpp::WrappedModelInterface | pure virtual |
| operator=(const AbstractParameterAliasable &ap) | bpp::AbstractParameterAliasable | |
| parameter(const std::string &name) const override | bpp::AbstractParameterAliasable | virtual |
| ParameterAliasable() | bpp::ParameterAliasable | |
| parameters_ | bpp::AbstractParameterAliasable | private |
| Parametrizable() | bpp::Parametrizable | |
| prefix_ | bpp::AbstractParameterAliasable | private |
| removeConstraint(const std::string &name) override | bpp::AbstractParameterAliasable | virtual |
| resetParameters_() | bpp::AbstractParameterAliasable | protected |
| setAllParametersValues(const ParameterList ¶meters) override | bpp::AbstractParameterAliasable | virtual |
| setConstraint(const std::string &name, std::shared_ptr< ConstraintInterface > constraint) override | bpp::AbstractParameterAliasable | virtual |
| setNamespace(const std::string &prefix) | bpp::AbstractParameterAliasable | virtual |
| setParametersValues(const ParameterList ¶meters) override | bpp::AbstractParameterAliasable | virtual |
| setParameterValue(const std::string &name, double value) override | bpp::AbstractParameterAliasable | virtual |
| setRate(double rate)=0 | bpp::BranchModelInterface | pure virtual |
| shareParameter_(const std::shared_ptr< Parameter > ¶meter) | bpp::AbstractParameterAliasable | protectedvirtual |
| shareParameters_(const ParameterList ¶meters) | bpp::AbstractParameterAliasable | protectedvirtual |
| stateMap() const override | bpp::AbstractWrappedModel | inlinevirtual |
| unaliasParameters(const std::string &p1, const std::string &p2) | bpp::AbstractParameterAliasable | virtual |
| WrappedModelInterface() | bpp::WrappedModelInterface | inline |
| ~AbstractParameterAliasable() | bpp::AbstractParameterAliasable | virtual |
| ~AbstractParametrizable() | bpp::AbstractParametrizable | virtual |
| ~AbstractWrappedModel() | bpp::AbstractWrappedModel | inlinevirtual |
| ~BranchModelInterface() | bpp::BranchModelInterface | inlinevirtual |
| ~Clonable()=default | bpp::Clonable | virtual |
| ~ParameterAliasable() | bpp::ParameterAliasable | virtual |
| ~Parametrizable() | bpp::Parametrizable | virtual |
| ~WrappedModelInterface() | bpp::WrappedModelInterface | inlinevirtual |
1.9.4