bpp::ProteinReversibleSubstitutionModelInterface Member List

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

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::ProteinReversibleSubstitutionModelInterface	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
enableEigenDecomposition(bool yn)=0	bpp::SubstitutionModelInterface	pure virtual
enableEigenDecomposition()=0	bpp::SubstitutionModelInterface	pure virtual
exchangeabilityMatrix() const =0	bpp::SubstitutionModelInterface	pure virtual
freq(size_t i) const =0	bpp::TransitionModelInterface	pure virtual
frequencySet() const =0	bpp::BranchModelInterface	pure virtual
generator() const =0	bpp::SubstitutionModelInterface	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
getColumnRightEigenVectors() const =0	bpp::SubstitutionModelInterface	pure virtual
getd2Pij_dt2(double t) const =0	bpp::TransitionModelInterface	pure virtual
getdPij_dt(double t) const =0	bpp::TransitionModelInterface	pure virtual
getEigenValues() const =0	bpp::SubstitutionModelInterface	pure virtual
getFrequencies() const =0	bpp::TransitionModelInterface	pure virtual
getFrequencies_()=0	bpp::TransitionModelInterface	protectedpure virtual
getIEigenValues() const =0	bpp::SubstitutionModelInterface	pure 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
getNumberOfIndependentParameters() const=0	bpp::ParameterAliasable	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
getProteicAlphabet() const =0	bpp::ProteinSubstitutionModelInterface	pure virtual
getRate() const =0	bpp::BranchModelInterface	pure virtual
getRowLeftEigenVectors() const =0	bpp::SubstitutionModelInterface	pure virtual
getScale() const =0	bpp::SubstitutionModelInterface	pure virtual
getStateMap() const =0	bpp::BranchModelInterface	pure virtual
hasParameter(const std::string &name) const=0	bpp::ParameterAliasable	pure virtual
isDiagonalizable() const =0	bpp::SubstitutionModelInterface	pure virtual
isNonSingular() const =0	bpp::SubstitutionModelInterface	pure virtual
isScalable() const =0	bpp::SubstitutionModelInterface	pure virtual
Lik_t(const Eigen::VectorXd &values, double t) const =0	bpp::TransitionModelInterface	pure virtual
matchParametersValues(const ParameterList &parameters)=0	bpp::ParameterAliasable	pure virtual
normalize()=0	bpp::SubstitutionModelInterface	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
Qij(size_t i, size_t j) const =0	bpp::SubstitutionModelInterface	pure virtual
removeConstraint(const std::string &name)=0	bpp::ParameterAliasable	pure virtual
ReversibleSubstitutionModelInterface()	bpp::ReversibleSubstitutionModelInterface	inline
setAllParametersValues(const ParameterList &parameters)=0	bpp::ParameterAliasable	pure virtual
setConstraint(const std::string &name, std::shared_ptr< ConstraintInterface > constraint)=0	bpp::ParameterAliasable	pure virtual
setDiagonal()=0	bpp::SubstitutionModelInterface	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
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
setScalable(bool scalable)=0	bpp::SubstitutionModelInterface	pure virtual
setScale(double scale)=0	bpp::SubstitutionModelInterface	pure virtual
Sij(size_t i, size_t j) const =0	bpp::SubstitutionModelInterface	pure virtual
stateMap() const =0	bpp::BranchModelInterface	pure virtual
SubstitutionModelInterface()	bpp::SubstitutionModelInterface	inline
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
~ParameterAliasable()	bpp::ParameterAliasable	virtual
~Parametrizable()	bpp::Parametrizable	virtual
~ProteinReversibleSubstitutionModelInterface()	bpp::ProteinReversibleSubstitutionModelInterface	inlinevirtual
~ProteinSubstitutionModelInterface()	bpp::ProteinSubstitutionModelInterface	inlinevirtual
~ReversibleSubstitutionModelInterface()	bpp::ReversibleSubstitutionModelInterface	inlinevirtual
~SubstitutionModelInterface()	bpp::SubstitutionModelInterface	inlinevirtual
~TransitionModelInterface()	bpp::TransitionModelInterface	inlinevirtual