bpp::AbstractHmmTransitionMatrix Member List

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

AbstractHmmTransitionMatrix(const HmmStateAlphabet *alph, const std::string &prefix="")	bpp::AbstractHmmTransitionMatrix
AbstractHmmTransitionMatrix(const AbstractHmmTransitionMatrix &hptm)	bpp::AbstractHmmTransitionMatrix
alph_	bpp::AbstractHmmTransitionMatrix	private
Clonable()	bpp::Clonable	inline
clone() const =0	bpp::Clonable	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
getParameter(const std::string &name) const =0	bpp::Parametrizable	pure virtual
getParameterNameWithoutNamespace(const std::string &name) const =0	bpp::Parametrizable	pure virtual
getParameters() const =0	bpp::Parametrizable	pure 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
matchParametersValues(const ParameterList &parameters)=0	bpp::Parametrizable	pure virtual
operator=(const AbstractHmmTransitionMatrix &hptm)	bpp::AbstractHmmTransitionMatrix
Parametrizable()	bpp::Parametrizable	inline
Pij(size_t i, size_t j) const =0	bpp::HmmTransitionMatrix	pure virtual
pij_	bpp::AbstractHmmTransitionMatrix	mutableprotected
setAllParametersValues(const ParameterList &parameters)=0	bpp::Parametrizable	pure virtual
setHmmStateAlphabet(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()	bpp::Clonable	inlinevirtual
~Parametrizable()	bpp::Parametrizable	inlinevirtual