bpp::AbstractSubstitutionDistance Member List

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

AbstractSubstitutionDistance(std::shared_ptr< const AlphabetIndex2 > distances)	bpp::AbstractSubstitutionDistance	inline
AbstractSubstitutionDistance(const AbstractSubstitutionDistance &index)	bpp::AbstractSubstitutionDistance	inline
clone() const =0	bpp::SubstitutionCountInterface	pure virtual
distances_	bpp::AbstractSubstitutionDistance	protected
distancesHaveChanged()=0	bpp::AbstractSubstitutionDistance	protectedpure virtual
getAllNumbersOfSubstitutions(double length, size_t type) const =0	bpp::SubstitutionCountInterface	pure virtual
getAlphabet() const	bpp::SubstitutionCountInterface	inlinevirtual
getDistances() const	bpp::AbstractSubstitutionDistance	inlinevirtual
getNumberOfStates() const	bpp::SubstitutionCountInterface	inlinevirtual
getNumberOfSubstitutions(size_t initialState, size_t finalState, double length, size_t type) const =0	bpp::SubstitutionCountInterface	pure virtual
getNumberOfSubstitutionsPerType(size_t initialState, size_t finalState, double length) const =0	bpp::SubstitutionCountInterface	pure virtual
getNumberOfSubstitutionTypes() const	bpp::SubstitutionCountInterface	inlinevirtual
getSubstitutionRegister() const =0	bpp::SubstitutionCountInterface	pure virtual
hasDistances() const	bpp::AbstractSubstitutionDistance	inlinevirtual
hasSubstitutionRegister() const =0	bpp::SubstitutionCountInterface	pure virtual
operator=(const AbstractSubstitutionDistance &index)	bpp::AbstractSubstitutionDistance	inline
setDistances(std::shared_ptr< const AlphabetIndex2 > distances)	bpp::AbstractSubstitutionDistance	virtual
setSubstitutionModel(std::shared_ptr< const SubstitutionModelInterface > model)=0	bpp::SubstitutionCountInterface	pure virtual
setSubstitutionRegister(std::shared_ptr< const SubstitutionRegisterInterface > reg)=0	bpp::SubstitutionCountInterface	pure virtual
storeAllNumbersOfSubstitutions(double length, size_t type, Eigen::MatrixXd &mat) const =0	bpp::SubstitutionCountInterface	pure virtual
SubstitutionCountInterface()	bpp::SubstitutionCountInterface	inline
~AbstractSubstitutionDistance()	bpp::AbstractSubstitutionDistance	inlinevirtual
~Clonable()=default	bpp::Clonable	virtual
~SubstitutionCountInterface()	bpp::SubstitutionCountInterface	inlinevirtual