bpp::DecompositionSubstitutionCount Member List

This is the complete list of members for bpp::DecompositionSubstitutionCount, 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::DecompositionMethods	protected
clone() const override	bpp::DecompositionSubstitutionCount	inlinevirtual
computeCounts_(double length) const	bpp::DecompositionSubstitutionCount	protected
computeExpectations(RowMatrix< double > &mapping, double length) const	bpp::DecompositionMethods	protected
computeExpectations(std::vector< RowMatrix< double >> &mappings, double length) const	bpp::DecompositionMethods	protected
computeProducts_()	bpp::DecompositionMethods	protected
counts_	bpp::DecompositionSubstitutionCount	mutableprivate
currentLength_	bpp::DecompositionSubstitutionCount	mutableprivate
DecompositionMethods(std::shared_ptr< const SubstitutionModelInterface > model, std::shared_ptr< const SubstitutionRegisterInterface > reg)	bpp::DecompositionMethods
DecompositionMethods(std::shared_ptr< const SubstitutionRegisterInterface > reg)	bpp::DecompositionMethods
DecompositionMethods(std::shared_ptr< const SubstitutionModelInterface > model)	bpp::DecompositionMethods
DecompositionMethods(const StateMapInterface &stateMap)	bpp::DecompositionMethods
DecompositionMethods(const DecompositionMethods &dm)	bpp::DecompositionMethods	inline
DecompositionSubstitutionCount(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::DecompositionSubstitutionCount
DecompositionSubstitutionCount(std::shared_ptr< const SubstitutionRegisterInterface > reg, std::shared_ptr< const AlphabetIndex2 > weights=nullptr, std::shared_ptr< const AlphabetIndex2 > distances=nullptr)	bpp::DecompositionSubstitutionCount
DecompositionSubstitutionCount(const DecompositionSubstitutionCount &dsc)	bpp::DecompositionSubstitutionCount	inline
distances_	bpp::AbstractSubstitutionDistance	protected
distancesHaveChanged() override	bpp::DecompositionSubstitutionCount	protectedvirtual
fillBMatrices_()	bpp::DecompositionSubstitutionCount	private
getAllNumbersOfSubstitutions(double length, size_t type=1) const override	bpp::DecompositionSubstitutionCount	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::DecompositionSubstitutionCount	virtual
getNumberOfSubstitutionsPerType(size_t initialState, size_t finalState, double length) const override	bpp::DecompositionSubstitutionCount	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::DecompositionMethods	protected
initCounts_()	bpp::DecompositionSubstitutionCount	protected
initStates_()	bpp::DecompositionMethods	protected
insideIProducts_	bpp::DecompositionMethods	protected
insideProducts_	bpp::DecompositionMethods	protected
jFunction_(const std::vector< double > &lambda, double t, RowMatrix< double > &result) const	bpp::DecompositionMethods	protected
jFunction_(const std::vector< double > &lambda, const std::vector< double > &ilambda, double t, RowMatrix< double > &result, RowMatrix< double > &iresult) const	bpp::DecompositionMethods	protected
jIMat_	bpp::DecompositionMethods	protected
jMat_	bpp::DecompositionMethods	mutableprotected
leftEigenVectors_	bpp::DecompositionMethods	protected
leftIEigenVectors_	bpp::DecompositionMethods	protected
model_	bpp::DecompositionMethods	protected
nbStates_	bpp::DecompositionMethods	protected
nbTypes_	bpp::DecompositionMethods	protected
operator=(const DecompositionSubstitutionCount &dsc)	bpp::DecompositionSubstitutionCount	inline
bpp::AbstractWeightedSubstitutionCount::operator=(const AbstractWeightedSubstitutionCount &index)	bpp::AbstractWeightedSubstitutionCount	inline
bpp::AbstractSubstitutionDistance::operator=(const AbstractSubstitutionDistance &index)	bpp::AbstractSubstitutionDistance	inline
bpp::DecompositionMethods::operator=(const DecompositionMethods &dm)	bpp::DecompositionMethods	inline
register_	bpp::AbstractSubstitutionCount	protected
rightEigenVectors_	bpp::DecompositionMethods	protected
rightIEigenVectors_	bpp::DecompositionMethods	protected
setDistanceBMatrices_()	bpp::DecompositionSubstitutionCount	private
setDistances(std::shared_ptr< const AlphabetIndex2 > distances)	bpp::AbstractSubstitutionDistance	virtual
setSubstitutionModel(std::shared_ptr< const SubstitutionModelInterface > model) override	bpp::DecompositionSubstitutionCount	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::DecompositionSubstitutionCount	virtual
SubstitutionCountInterface()	bpp::SubstitutionCountInterface	inline
substitutionRegisterHasChanged() override	bpp::DecompositionSubstitutionCount	protectedvirtual
weights_	bpp::AbstractWeightedSubstitutionCount	protected
weightsHaveChanged() override	bpp::DecompositionSubstitutionCount	protectedvirtual
~AbstractSubstitutionCount()	bpp::AbstractSubstitutionCount	inlinevirtual
~AbstractSubstitutionDistance()	bpp::AbstractSubstitutionDistance	inlinevirtual
~AbstractWeightedSubstitutionCount()	bpp::AbstractWeightedSubstitutionCount	inlinevirtual
~Clonable()=default	bpp::Clonable	virtual
~DecompositionMethods()	bpp::DecompositionMethods	inlinevirtual
~DecompositionSubstitutionCount()	bpp::DecompositionSubstitutionCount	inlinevirtual
~SubstitutionCountInterface()	bpp::SubstitutionCountInterface	inlinevirtual