bpp::DecompositionReward Member List

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

AbstractReward(std::shared_ptr< const AlphabetIndex1 > alphIndex)	bpp::AbstractReward	inline
AbstractReward(const AbstractReward &ar)	bpp::AbstractReward	inline
alphabetIndex() const	bpp::AbstractReward	inline
alphabetIndexHasChanged() override	bpp::DecompositionReward	protectedvirtual
alphIndex_	bpp::AbstractReward	protected
bMatrices_	bpp::DecompositionMethods	protected
clone() const override	bpp::DecompositionReward	inlinevirtual
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
computeRewards_(double length) const	bpp::DecompositionReward	protected
currentLength_	bpp::DecompositionReward	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
DecompositionReward(std::shared_ptr< const SubstitutionModelInterface > model, std::shared_ptr< const AlphabetIndex1 > alphIndex)	bpp::DecompositionReward
DecompositionReward(const StateMapInterface &stateMap, std::shared_ptr< const AlphabetIndex1 > alphIndex)	bpp::DecompositionReward
DecompositionReward(const DecompositionReward &dr)	bpp::DecompositionReward	inline
fillBMatrice_()	bpp::DecompositionReward	private
getAllRewards(double length) const override	bpp::DecompositionReward	virtual
getAlphabet() const	bpp::Reward	inlinevirtual
getAlphabetIndex() const	bpp::AbstractReward	inlinevirtual
getNumberOfStates() const	bpp::Reward	inlinevirtual
getReward(size_t initialState, size_t finalState, double length) const override	bpp::DecompositionReward	virtual
hasAlphabetIndex() const	bpp::AbstractReward	inlinevirtual
initBMatrices_()	bpp::DecompositionMethods	protected
initRewards_()	bpp::DecompositionReward	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 DecompositionReward &dr)	bpp::DecompositionReward	inline
bpp::AbstractReward::operator=(const AbstractReward &ar)	bpp::AbstractReward	inline
bpp::DecompositionMethods::operator=(const DecompositionMethods &dm)	bpp::DecompositionMethods	inline
Reward()	bpp::Reward	inline
rewards_	bpp::DecompositionReward	mutableprivate
rightEigenVectors_	bpp::DecompositionMethods	protected
rightIEigenVectors_	bpp::DecompositionMethods	protected
setAlphabetIndex(std::shared_ptr< const AlphabetIndex1 > alphIndex)	bpp::AbstractReward	inlinevirtual
setSubstitutionModel(std::shared_ptr< const SubstitutionModelInterface > model) override	bpp::DecompositionReward	virtual
storeAllRewards(double length, Eigen::MatrixXd &mat) const override	bpp::DecompositionReward	virtual
~AbstractReward()	bpp::AbstractReward	inlinevirtual
~Clonable()=default	bpp::Clonable	virtual
~DecompositionMethods()	bpp::DecompositionMethods	inlinevirtual
~DecompositionReward()	bpp::DecompositionReward	inlinevirtual
~Reward()	bpp::Reward	inlinevirtual