bpp::AbstractHmmTransitionMatrix Member List

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

AbstractHmmTransitionMatrix(std::shared_ptr< const HmmStateAlphabet > alph, const std::string &prefix="")	bpp::AbstractHmmTransitionMatrix
AbstractHmmTransitionMatrix(const AbstractHmmTransitionMatrix &hptm)	bpp::AbstractHmmTransitionMatrix
alph_	bpp::AbstractHmmTransitionMatrix	private
clone() const override=0	bpp::HmmTransitionMatrix	pure virtual
eqFreq_	bpp::AbstractHmmTransitionMatrix	mutableprotected
getEquilibriumFrequencies() const =0	bpp::HmmTransitionMatrix	pure virtual
getHmmStateAlphabet() const	bpp::AbstractHmmTransitionMatrix	inlinevirtual
getNamespace() const =0	bpp::Parametrizable	pure virtual
getNumberOfParameters() const =0	bpp::Parametrizable	pure virtual
getNumberOfStates() const	bpp::AbstractHmmTransitionMatrix	inlinevirtual
getParameterNameWithoutNamespace(const std::string &name) const =0	bpp::Parametrizable	pure virtual
getParameters() const =0	bpp::Parametrizable	pure virtual
getParameters_()=0	bpp::Parametrizable	protectedpure virtual
getParameterValue(const std::string &name) const =0	bpp::Parametrizable	pure virtual
getPij() const =0	bpp::HmmTransitionMatrix	pure virtual
hasParameter(const std::string &name) const =0	bpp::Parametrizable	pure virtual
hmmStateAlphabet() const	bpp::AbstractHmmTransitionMatrix	inlinevirtual
matchParametersValues(const ParameterList &parameters)=0	bpp::Parametrizable	pure virtual
operator=(const AbstractHmmTransitionMatrix &hptm)	bpp::AbstractHmmTransitionMatrix
parameter(const std::string &name) const =0	bpp::Parametrizable	pure virtual
Parametrizable()	bpp::Parametrizable	inline
Pij(size_t i, size_t j) const =0	bpp::HmmTransitionMatrix	pure virtual
pij_	bpp::AbstractHmmTransitionMatrix	mutableprotected
removeConstraint(const std::string &name)=0	bpp::Parametrizable	pure virtual
sample(size_t size) const	bpp::AbstractHmmTransitionMatrix
setAllParametersValues(const ParameterList &parameters)=0	bpp::Parametrizable	pure virtual
setConstraint(const std::string &name, std::shared_ptr< ConstraintInterface > constraint)=0	bpp::Parametrizable	pure virtual
setHmmStateAlphabet(std::shared_ptr< const HmmStateAlphabet > stateAlphabet)	bpp::AbstractHmmTransitionMatrix	virtual
setNamespace(const std::string &prefix)=0	bpp::Parametrizable	pure virtual
setParametersValues(const ParameterList &parameters)=0	bpp::Parametrizable	pure virtual
setParameterValue(const std::string &name, double value)=0	bpp::Parametrizable	pure virtual
tmpmat_	bpp::AbstractHmmTransitionMatrix	mutableprotected
upToDate_	bpp::AbstractHmmTransitionMatrix	mutableprotected
~Clonable()=default	bpp::Clonable	virtual
~Parametrizable()	bpp::Parametrizable	inlinevirtual