bpp-phyl3 3.0.0
bpp::AbstractWrappedSubstitutionModel Member List

This is the complete list of members for bpp::AbstractWrappedSubstitutionModel, 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
AbstractWrappedModel(const std::string &prefix)bpp::AbstractWrappedModelinline
AbstractWrappedSubstitutionModel(const std::string &prefix)bpp::AbstractWrappedSubstitutionModelinline
AbstractWrappedTransitionModel(const std::string &prefix)bpp::AbstractWrappedTransitionModelinline
addParameter_(Parameter *parameter)bpp::AbstractParameterAliasableprotectedvirtual
addParameters_(const ParameterList &parameters)bpp::AbstractParameterAliasableprotectedvirtual
addRateParameter()=0bpp::BranchModelInterfacepure virtual
aliasListenersRegister_bpp::AbstractParameterAliasableprivate
aliasParameters(const std::string &p1, const std::string &p2)bpp::AbstractParameterAliasablevirtual
aliasParameters(std::map< std::string, std::string > &unparsedParams, bool verbose)bpp::AbstractParameterAliasablevirtual
alphabet() const overridebpp::AbstractWrappedModelinlinevirtual
BranchModelInterface()bpp::BranchModelInterfaceinline
bpp::clone() const=0bpp::AbstractParameterAliasablepure virtual
bpp::WrappedModelInterface::clone() const =0bpp::BranchModelInterfacepure virtual
bpp::AbstractLkTransitionModel::clone() const =0bpp::TransitionModelInterfacepure virtual
bpp::WrappedSubstitutionModelInterface::bpp::SubstitutionModelInterface::clone() const override=0bpp::SubstitutionModelInterfacepure virtual
computeFrequencies() const =0bpp::TransitionModelInterfacepure virtual
computeFrequencies(bool yn)=0bpp::TransitionModelInterfacepure virtual
bpp::d2Lik_dt2(const Eigen::VectorXd &values, double t) const =0bpp::BranchModelInterfacepure 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 =0bpp::TransitionModelInterfacepure virtual
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::BranchModelInterfacepure 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 =0bpp::TransitionModelInterfacepure virtual
enableEigenDecomposition(bool yn)=0bpp::SubstitutionModelInterfacepure virtual
enableEigenDecomposition()=0bpp::SubstitutionModelInterfacepure virtual
exchangeabilityMatrix() const =0bpp::SubstitutionModelInterfacepure virtual
fireParameterChanged(const ParameterList &parameters)bpp::AbstractParameterAliasablevirtual
freq(size_t i) const =0bpp::TransitionModelInterfacepure virtual
frequencySet() const overridebpp::AbstractWrappedTransitionModelinlinevirtual
generator() const =0bpp::SubstitutionModelInterfacepure virtual
getAlias(const std::string &name) constbpp::AbstractParameterAliasablevirtual
getAliasedParameters(const ParameterList &pl) constbpp::AbstractParameterAliasable
getAliases() constbpp::AbstractParameterAliasablevirtual
getAlphabet() const overridebpp::AbstractWrappedModelinlinevirtual
getAlphabetStateAsChar(size_t i) const overridebpp::AbstractWrappedModelinlinevirtual
getAlphabetStateAsInt(size_t i) const overridebpp::AbstractWrappedModelinlinevirtual
getAlphabetStates() const overridebpp::AbstractWrappedModelinlinevirtual
getColumnRightEigenVectors() const =0bpp::SubstitutionModelInterfacepure virtual
getd2Pij_dt2(double t) const =0bpp::TransitionModelInterfacepure virtual
getdPij_dt(double t) const =0bpp::TransitionModelInterfacepure virtual
getEigenValues() const =0bpp::SubstitutionModelInterfacepure virtual
getFrequencies() const =0bpp::TransitionModelInterfacepure virtual
getFrequencies_()=0bpp::TransitionModelInterfaceprotectedpure virtual
getFrom(const std::string &name) constbpp::AbstractParameterAliasable
getFromParameters(const ParameterList &pl) constbpp::AbstractParameterAliasable
getIEigenValues() const =0bpp::SubstitutionModelInterfacepure virtual
getIndependentParameters() constbpp::AbstractParameterAliasablevirtual
getInitValue(size_t i, int state) const =0bpp::BranchModelInterfacepure virtual
getModelStates(int code) const overridebpp::AbstractWrappedModelinlinevirtual
getModelStates(const std::string &code) const overridebpp::AbstractWrappedModelinlinevirtual
getName() const overridebpp::AbstractWrappedModelinlinevirtual
getNamespace() const overridebpp::AbstractParameterAliasablevirtual
getNumberOfIndependentParameters() constbpp::AbstractParameterAliasablevirtual
getNumberOfParameters() const overridebpp::AbstractParameterAliasablevirtual
getNumberOfStates() const overridebpp::AbstractWrappedModelinlinevirtual
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
getParameterNameWithoutNamespace(const std::string &name) const overridebpp::AbstractParameterAliasablevirtual
getParameters() const overridebpp::AbstractParameterAliasablevirtual
getParameters_() overridebpp::AbstractParameterAliasableprotectedvirtual
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 =0bpp::TransitionModelInterfacepure virtual
getRate() const =0bpp::BranchModelInterfacepure virtual
getRowLeftEigenVectors() const =0bpp::SubstitutionModelInterfacepure virtual
getScale() const =0bpp::SubstitutionModelInterfacepure virtual
getStateMap() const overridebpp::AbstractWrappedModelinlinevirtual
hasIndependentParameter(const std::string &name) constbpp::AbstractParameterAliasable
hasParameter(const std::string &name) const overridebpp::AbstractParameterAliasablevirtual
includeParameters_(const ParameterList &parameters)bpp::AbstractParameterAliasableprotectedvirtual
independentParameters_bpp::AbstractParameterAliasableprivate
isDiagonalizable() const =0bpp::SubstitutionModelInterfacepure virtual
isNonSingular() const =0bpp::SubstitutionModelInterfacepure virtual
isScalable() const =0bpp::SubstitutionModelInterfacepure virtual
lik_bpp::AbstractLkTransitionModelmutableprivate
bpp::Lik_t(const Eigen::VectorXd &values, double t) const =0bpp::BranchModelInterfacepure virtual
bpp::AbstractLkTransitionModel::Lik_t(const Eigen::VectorXd &values, double t) const overridebpp::AbstractLkTransitionModelinlinevirtual
matchParametersValues(const ParameterList &parameters) overridebpp::AbstractParameterAliasablevirtual
model() const overridebpp::AbstractWrappedTransitionModelinlinevirtual
model_()bpp::AbstractWrappedTransitionModelinlineprotected
normalize()=0bpp::SubstitutionModelInterfacepure virtual
operator=(const AbstractParameterAliasable &ap)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 =0bpp::TransitionModelInterfacepure virtual
prefix_bpp::AbstractParameterAliasableprivate
Qij(size_t i, size_t j) const =0bpp::SubstitutionModelInterfacepure virtual
removeConstraint(const std::string &name) overridebpp::AbstractParameterAliasablevirtual
resetParameters_()bpp::AbstractParameterAliasableprotected
setAllParametersValues(const ParameterList &parameters) overridebpp::AbstractParameterAliasablevirtual
setConstraint(const std::string &name, std::shared_ptr< ConstraintInterface > constraint) overridebpp::AbstractParameterAliasablevirtual
setDiagonal()=0bpp::SubstitutionModelInterfacepure virtual
setFreq(std::map< int, double > &frequencies)=0bpp::TransitionModelInterfacepure virtual
setFreqFromData(const SequenceDataInterface &data, double pseudoCount=0)=0bpp::TransitionModelInterfacepure virtual
setNamespace(const std::string &prefix)bpp::AbstractParameterAliasablevirtual
setParametersValues(const ParameterList &parameters) overridebpp::AbstractParameterAliasablevirtual
setParameterValue(const std::string &name, double value) overridebpp::AbstractParameterAliasablevirtual
setRate(double rate)=0bpp::BranchModelInterfacepure virtual
setScalable(bool scalable)=0bpp::SubstitutionModelInterfacepure virtual
setScale(double scale)=0bpp::SubstitutionModelInterfacepure virtual
shareParameter_(const std::shared_ptr< Parameter > &parameter)bpp::AbstractParameterAliasableprotectedvirtual
shareParameters_(const ParameterList &parameters)bpp::AbstractParameterAliasableprotectedvirtual
Sij(size_t i, size_t j) const =0bpp::SubstitutionModelInterfacepure virtual
stateMap() const overridebpp::AbstractWrappedModelinlinevirtual
substitutionModel() const =0bpp::WrappedSubstitutionModelInterfacepure virtual
substitutionModel_()=0bpp::AbstractWrappedSubstitutionModelprotectedpure virtual
SubstitutionModelInterface()bpp::SubstitutionModelInterfaceinline
transitionModel() constbpp::AbstractWrappedSubstitutionModelinlinevirtual
transitionModel_()bpp::AbstractWrappedSubstitutionModelinlineprotectedvirtual
TransitionModelInterface()bpp::TransitionModelInterfaceinline
unaliasParameters(const std::string &p1, const std::string &p2)bpp::AbstractParameterAliasablevirtual
WrappedModelInterface()bpp::WrappedModelInterfaceinline
WrappedSubstitutionModelInterface()bpp::WrappedSubstitutionModelInterfaceinline
WrappedTransitionModelInterface()bpp::WrappedTransitionModelInterfaceinline
~AbstractLkTransitionModel()bpp::AbstractLkTransitionModelinlinevirtual
~AbstractParameterAliasable()bpp::AbstractParameterAliasablevirtual
~AbstractParametrizable()bpp::AbstractParametrizablevirtual
~AbstractWrappedModel()bpp::AbstractWrappedModelinlinevirtual
~AbstractWrappedSubstitutionModel()bpp::AbstractWrappedSubstitutionModelinlinevirtual
~BranchModelInterface()bpp::BranchModelInterfaceinlinevirtual
~Clonable()=defaultbpp::Clonablevirtual
~ParameterAliasable()bpp::ParameterAliasablevirtual
~Parametrizable()bpp::Parametrizablevirtual
~SubstitutionModelInterface()bpp::SubstitutionModelInterfaceinlinevirtual
~TransitionModelInterface()bpp::TransitionModelInterfaceinlinevirtual
~WrappedModelInterface()bpp::WrappedModelInterfaceinlinevirtual
~WrappedSubstitutionModelInterface()bpp::WrappedSubstitutionModelInterfaceinlinevirtual
~WrappedTransitionModelInterface()bpp::WrappedTransitionModelInterfaceinlinevirtual