bpp::UniformizationSubstitutionCount Member List

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

AbstractSubstitutionCount(std::shared_ptr< const SubstitutionRegisterInterface > reg)	bpp::AbstractSubstitutionCount	inline
AbstractSubstitutionDistance(std::shared_ptr< const AlphabetIndex2 > distances)	bpp::AbstractSubstitutionDistance	inline
AbstractSubstitutionDistance(const AbstractSubstitutionDistance &index)	bpp::AbstractSubstitutionDistance	inline
AbstractWeightedSubstitutionCount(std::shared_ptr< const AlphabetIndex2 > weights)	bpp::AbstractWeightedSubstitutionCount	inline
AbstractWeightedSubstitutionCount(const AbstractWeightedSubstitutionCount &index)	bpp::AbstractWeightedSubstitutionCount	inline
bMatrices_	bpp::UniformizationSubstitutionCount	private
clone() const override	bpp::UniformizationSubstitutionCount	inlinevirtual
computeCounts_(double length) const	bpp::UniformizationSubstitutionCount	protected
counts_	bpp::UniformizationSubstitutionCount	mutableprivate
currentLength_	bpp::UniformizationSubstitutionCount	mutableprivate
distances_	bpp::AbstractSubstitutionDistance	protected
distancesHaveChanged() override	bpp::UniformizationSubstitutionCount	protectedvirtual
fillBMatrices_()	bpp::UniformizationSubstitutionCount	private
getAllNumbersOfSubstitutions(double length, size_t type=1) const override	bpp::UniformizationSubstitutionCount	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=1) const override	bpp::UniformizationSubstitutionCount	virtual
getNumberOfSubstitutionsPerType(size_t initialState, size_t finalState, double length) const override	bpp::UniformizationSubstitutionCount	virtual
getNumberOfSubstitutionTypes() const	bpp::SubstitutionCountInterface	inlinevirtual
getSubstitutionRegister() const	bpp::AbstractSubstitutionCount	inlinevirtual
getWeights() const	bpp::AbstractWeightedSubstitutionCount	inlinevirtual
hasDistances() const	bpp::AbstractSubstitutionDistance	inlinevirtual
hasSubstitutionRegister() const	bpp::AbstractSubstitutionCount	inlinevirtual
hasWeights() const	bpp::AbstractWeightedSubstitutionCount	inlinevirtual
initBMatrices_()	bpp::UniformizationSubstitutionCount	private
miu_	bpp::UniformizationSubstitutionCount	private
model_	bpp::UniformizationSubstitutionCount	private
nbStates_	bpp::UniformizationSubstitutionCount	private
operator=(const UniformizationSubstitutionCount &usc)	bpp::UniformizationSubstitutionCount	inline
bpp::AbstractWeightedSubstitutionCount::operator=(const AbstractWeightedSubstitutionCount &index)	bpp::AbstractWeightedSubstitutionCount	inline
bpp::AbstractSubstitutionDistance::operator=(const AbstractSubstitutionDistance &index)	bpp::AbstractSubstitutionDistance	inline
power_	bpp::UniformizationSubstitutionCount	mutableprivate
register_	bpp::AbstractSubstitutionCount	protected
resetBMatrices_()	bpp::UniformizationSubstitutionCount	private
s_	bpp::UniformizationSubstitutionCount	mutableprivate
setDistanceBMatrices_()	bpp::UniformizationSubstitutionCount	private
setDistances(std::shared_ptr< const AlphabetIndex2 > distances)	bpp::AbstractSubstitutionDistance	virtual
setSubstitutionModel(std::shared_ptr< const SubstitutionModelInterface > model) override	bpp::UniformizationSubstitutionCount	virtual
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::UniformizationSubstitutionCount	virtual
SubstitutionCountInterface()	bpp::SubstitutionCountInterface	inline
substitutionRegisterHasChanged() override	bpp::UniformizationSubstitutionCount	protectedvirtual
UniformizationSubstitutionCount(std::shared_ptr< const SubstitutionModelInterface > model, std::shared_ptr< const SubstitutionRegisterInterface > reg, std::shared_ptr< const AlphabetIndex2 > weights=nullptr, std::shared_ptr< const AlphabetIndex2 > distances=nullptr)	bpp::UniformizationSubstitutionCount
UniformizationSubstitutionCount(const StateMapInterface &stateMap, std::shared_ptr< const SubstitutionRegisterInterface > reg, std::shared_ptr< const AlphabetIndex2 > weights=nullptr, std::shared_ptr< const AlphabetIndex2 > distances=nullptr)	bpp::UniformizationSubstitutionCount
UniformizationSubstitutionCount(const UniformizationSubstitutionCount &usc)	bpp::UniformizationSubstitutionCount	inline
weights_	bpp::AbstractWeightedSubstitutionCount	protected
weightsHaveChanged() override	bpp::UniformizationSubstitutionCount	protectedvirtual
~AbstractSubstitutionCount()	bpp::AbstractSubstitutionCount	inlinevirtual
~AbstractSubstitutionDistance()	bpp::AbstractSubstitutionDistance	inlinevirtual
~AbstractWeightedSubstitutionCount()	bpp::AbstractWeightedSubstitutionCount	inlinevirtual
~Clonable()=default	bpp::Clonable	virtual
~SubstitutionCountInterface()	bpp::SubstitutionCountInterface	inlinevirtual
~UniformizationSubstitutionCount()	bpp::UniformizationSubstitutionCount	inlinevirtual