bpp::NaiveSubstitutionCount Member List

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

AbstractSubstitutionCount(std::shared_ptr< const SubstitutionRegisterInterface > reg)	bpp::AbstractSubstitutionCount	inline
AbstractWeightedSubstitutionCount(std::shared_ptr< const AlphabetIndex2 > weights)	bpp::AbstractWeightedSubstitutionCount	inline
AbstractWeightedSubstitutionCount(const AbstractWeightedSubstitutionCount &index)	bpp::AbstractWeightedSubstitutionCount	inline
allowSelf_	bpp::NaiveSubstitutionCount	private
clone() const override	bpp::NaiveSubstitutionCount	inlinevirtual
getAllNumbersOfSubstitutions(double length, size_t type=1) const override	bpp::NaiveSubstitutionCount	virtual
getAlphabet() const	bpp::SubstitutionCountInterface	inlinevirtual
getNumberOfStates() const	bpp::SubstitutionCountInterface	inlinevirtual
getNumberOfSubstitutions(size_t initialState, size_t finalState, double length, size_t type=1) const override	bpp::NaiveSubstitutionCount	inlinevirtual
getNumberOfSubstitutionsPerType(size_t initialState, size_t finalState, double length) const override	bpp::NaiveSubstitutionCount	inlinevirtual
getNumberOfSubstitutionTypes() const	bpp::SubstitutionCountInterface	inlinevirtual
getSubstitutionRegister() const	bpp::AbstractSubstitutionCount	inlinevirtual
getWeights() const	bpp::AbstractWeightedSubstitutionCount	inlinevirtual
hasSubstitutionRegister() const	bpp::AbstractSubstitutionCount	inlinevirtual
hasWeights() const	bpp::AbstractWeightedSubstitutionCount	inlinevirtual
NaiveSubstitutionCount(std::shared_ptr< const SubstitutionModelInterface > model, std::shared_ptr< const SubstitutionRegisterInterface > reg, bool allowSelf=false, std::shared_ptr< const AlphabetIndex2 > weights=nullptr)	bpp::NaiveSubstitutionCount	inline
NaiveSubstitutionCount(std::shared_ptr< const StateMapInterface > stateMap, std::shared_ptr< const SubstitutionRegisterInterface > reg, bool allowSelf=false, std::shared_ptr< const AlphabetIndex2 > weights=nullptr)	bpp::NaiveSubstitutionCount	inline
operator=(const AbstractWeightedSubstitutionCount &index)	bpp::AbstractWeightedSubstitutionCount	inline
register_	bpp::AbstractSubstitutionCount	protected
setSubstitutionModel(std::shared_ptr< const SubstitutionModelInterface > model) override	bpp::NaiveSubstitutionCount	inlinevirtual
setSubstitutionRegister(std::shared_ptr< const SubstitutionRegisterInterface > reg)	bpp::AbstractSubstitutionCount	inlinevirtual
setWeights(std::shared_ptr< const AlphabetIndex2 > weights)	bpp::AbstractWeightedSubstitutionCount	virtual
storeAllNumbersOfSubstitutions(double length, size_t type, Eigen::MatrixXd &mat) const override	bpp::NaiveSubstitutionCount	virtual
SubstitutionCountInterface()	bpp::SubstitutionCountInterface	inline
substitutionRegisterHasChanged() override	bpp::NaiveSubstitutionCount	inlineprivatevirtual
supportedChars_	bpp::NaiveSubstitutionCount	private
weights_	bpp::AbstractWeightedSubstitutionCount	protected
weightsHaveChanged() override	bpp::NaiveSubstitutionCount	inlineprivatevirtual
~AbstractSubstitutionCount()	bpp::AbstractSubstitutionCount	inlinevirtual
~AbstractWeightedSubstitutionCount()	bpp::AbstractWeightedSubstitutionCount	inlinevirtual
~Clonable()=default	bpp::Clonable	virtual
~NaiveSubstitutionCount()	bpp::NaiveSubstitutionCount	inlinevirtual
~SubstitutionCountInterface()	bpp::SubstitutionCountInterface	inlinevirtual