bpp::MixedTransitionModelInterface Member List

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

AbstractBiblioMixedTransitionModel class	bpp::MixedTransitionModelInterface	friend
addRateParameter()=0	bpp::BranchModelInterface	pure virtual
aliasParameters(const std::string &p1, const std::string &p2)=0	bpp::ParameterAliasable	pure virtual
aliasParameters(std::map< std::string, std::string > &unparsedParams, bool verbose)=0	bpp::ParameterAliasable	pure virtual
alphabet() const =0	bpp::BranchModelInterface	pure virtual
BranchModelInterface()	bpp::BranchModelInterface	inline
clone() const override=0	bpp::MixedTransitionModelInterface	pure virtual
computeFrequencies() const =0	bpp::TransitionModelInterface	pure virtual
computeFrequencies(bool yn)=0	bpp::TransitionModelInterface	pure virtual
d2Lik_dt2(const Eigen::VectorXd &values, double t) const =0	bpp::TransitionModelInterface	pure virtual
d2Pij_dt2(size_t i, size_t j, double t) const =0	bpp::TransitionModelInterface	pure virtual
dLik_dt(const Eigen::VectorXd &values, double t) const =0	bpp::TransitionModelInterface	pure virtual
dPij_dt(size_t i, size_t j, double t) const =0	bpp::TransitionModelInterface	pure virtual
freq(size_t i) const =0	bpp::TransitionModelInterface	pure virtual
frequencySet() const =0	bpp::BranchModelInterface	pure virtual
getAlias(const std::string &name) const=0	bpp::ParameterAliasable	pure virtual
getAliases() const=0	bpp::ParameterAliasable	pure virtual
getAlphabet() const =0	bpp::BranchModelInterface	pure virtual
getAlphabetStateAsChar(size_t index) const =0	bpp::BranchModelInterface	pure virtual
getAlphabetStateAsInt(size_t index) const =0	bpp::BranchModelInterface	pure virtual
getAlphabetStates() const =0	bpp::BranchModelInterface	pure virtual
getd2Pij_dt2(double t) const =0	bpp::TransitionModelInterface	pure virtual
getdPij_dt(double t) const =0	bpp::TransitionModelInterface	pure virtual
getFrequencies() const =0	bpp::TransitionModelInterface	pure virtual
getFrequencies_()=0	bpp::TransitionModelInterface	protectedpure virtual
getIndependentParameters() const=0	bpp::ParameterAliasable	pure virtual
getInitValue(size_t i, int state) const =0	bpp::BranchModelInterface	pure virtual
getModelStates(int code) const =0	bpp::BranchModelInterface	pure virtual
getModelStates(const std::string &code) const =0	bpp::BranchModelInterface	pure virtual
getName() const =0	bpp::BranchModelInterface	pure virtual
getNamespace() const=0	bpp::ParameterAliasable	pure virtual
getNModel(size_t i) const =0	bpp::MixedTransitionModelInterface	pure virtual
getNProbability(size_t i) const =0	bpp::MixedTransitionModelInterface	pure virtual
getNRate(size_t i) const =0	bpp::MixedTransitionModelInterface	pure virtual
getNumberOfIndependentParameters() const=0	bpp::ParameterAliasable	pure virtual
getNumberOfModels() const =0	bpp::MixedTransitionModelInterface	pure virtual
getNumberOfParameters() const=0	bpp::ParameterAliasable	pure virtual
getNumberOfStates() const =0	bpp::BranchModelInterface	pure virtual
getParameterNameWithoutNamespace(const std::string &name) const=0	bpp::ParameterAliasable	pure virtual
getParameters() const=0	bpp::ParameterAliasable	pure virtual
getParameters_()=0	bpp::ParameterAliasable	protectedpure virtual
getParameterValue(const std::string &name) const=0	bpp::ParameterAliasable	pure virtual
getPij_t(double t) const =0	bpp::TransitionModelInterface	pure virtual
getProbabilities() const =0	bpp::MixedTransitionModelInterface	pure virtual
getRate() const =0	bpp::BranchModelInterface	pure virtual
getStateMap() const =0	bpp::BranchModelInterface	pure virtual
getSubmodelNumbers(const std::string &desc) const =0	bpp::MixedTransitionModelInterface	pure virtual
getVRates() const =0	bpp::MixedTransitionModelInterface	pure virtual
hasParameter(const std::string &name) const=0	bpp::ParameterAliasable	pure virtual
InMixedSubstitutionModel class	bpp::MixedTransitionModelInterface	friend
Lik_t(const Eigen::VectorXd &values, double t) const =0	bpp::TransitionModelInterface	pure virtual
matchParametersValues(const ParameterList &parameters)=0	bpp::ParameterAliasable	pure virtual
MixedTransitionModelInterface()	bpp::MixedTransitionModelInterface	inline
model(const std::string &name) const =0	bpp::MixedTransitionModelInterface	pure virtual
nModel(size_t i) const =0	bpp::MixedTransitionModelInterface	pure virtual
nModel_(size_t i)=0	bpp::MixedTransitionModelInterface	protectedpure virtual
normalizeVRates()=0	bpp::MixedTransitionModelInterface	pure virtual
parameter(const std::string &name) const=0	bpp::ParameterAliasable	pure virtual
ParameterAliasable()	bpp::ParameterAliasable
Parametrizable()	bpp::Parametrizable
Pij_t(size_t i, size_t j, double t) const =0	bpp::TransitionModelInterface	pure virtual
removeConstraint(const std::string &name)=0	bpp::ParameterAliasable	pure virtual
setAllParametersValues(const ParameterList &parameters)=0	bpp::ParameterAliasable	pure virtual
setConstraint(const std::string &name, std::shared_ptr< ConstraintInterface > constraint)=0	bpp::ParameterAliasable	pure virtual
setFreq(std::map< int, double > &frequencies)=0	bpp::TransitionModelInterface	pure virtual
setFreqFromData(const SequenceDataInterface &data, double pseudoCount=0)=0	bpp::TransitionModelInterface	pure virtual
setNamespace(const std::string &prefix)=0	bpp::ParameterAliasable	pure virtual
setNProbability(size_t i, double prob)=0	bpp::MixedTransitionModelInterface	pure virtual
setParametersValues(const ParameterList &parameters)=0	bpp::ParameterAliasable	pure virtual
setParameterValue(const std::string &name, double value)=0	bpp::ParameterAliasable	pure virtual
setRate(double rate)=0	bpp::BranchModelInterface	pure virtual
setVRates(const Vdouble &vd)=0	bpp::MixedTransitionModelInterface	pure virtual
stateMap() const =0	bpp::BranchModelInterface	pure virtual
TransitionModelInterface()	bpp::TransitionModelInterface	inline
unaliasParameters(const std::string &p1, const std::string &p2)=0	bpp::ParameterAliasable	pure virtual
~BranchModelInterface()	bpp::BranchModelInterface	inlinevirtual
~Clonable()=default	bpp::Clonable	virtual
~MixedTransitionModelInterface()	bpp::MixedTransitionModelInterface	inlinevirtual
~ParameterAliasable()	bpp::ParameterAliasable	virtual
~Parametrizable()	bpp::Parametrizable	virtual
~TransitionModelInterface()	bpp::TransitionModelInterface	inlinevirtual