bpp::DecompositionSubstitutionCount Member List

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

AbstractSubstitutionCount(SubstitutionRegister *reg)	bpp::AbstractSubstitutionCount	inline
AbstractSubstitutionCount(const AbstractSubstitutionCount &asc)	bpp::AbstractSubstitutionCount	inline
AbstractWeightedSubstitutionCount(const AlphabetIndex2 *weights, bool ownWeights)	bpp::AbstractWeightedSubstitutionCount	inline
AbstractWeightedSubstitutionCount(const AbstractWeightedSubstitutionCount &index)	bpp::AbstractWeightedSubstitutionCount	inline
bMatrices_	bpp::DecompositionSubstitutionCount	private
clone() const	bpp::DecompositionSubstitutionCount	inlinevirtual
computeCounts_(double length) const	bpp::DecompositionSubstitutionCount	protected
computeEigen_()	bpp::DecompositionSubstitutionCount	private
computeProducts_()	bpp::DecompositionSubstitutionCount	private
counts_	bpp::DecompositionSubstitutionCount	mutableprivate
currentLength_	bpp::DecompositionSubstitutionCount	mutableprivate
DecompositionSubstitutionCount(const ReversibleSubstitutionModel *model, SubstitutionRegister *reg, const AlphabetIndex2 *weights=0)	bpp::DecompositionSubstitutionCount
DecompositionSubstitutionCount(const DecompositionSubstitutionCount &dsc)	bpp::DecompositionSubstitutionCount	inline
fillBMatrices_()	bpp::DecompositionSubstitutionCount	private
getAllNumbersOfSubstitutions(double length, size_t type=1) const	bpp::DecompositionSubstitutionCount	virtual
getAlphabet() const	bpp::SubstitutionCount	inlinevirtual
getNumberOfStates() const	bpp::SubstitutionCount	inlinevirtual
getNumberOfSubstitutions(size_t initialState, size_t finalState, double length, size_t type=1) const	bpp::DecompositionSubstitutionCount	virtual
getNumberOfSubstitutionsForEachType(size_t initialState, size_t finalState, double length) const	bpp::DecompositionSubstitutionCount	virtual
getNumberOfSubstitutionTypes() const	bpp::SubstitutionCount	inlinevirtual
getSubstitutionRegister() const	bpp::AbstractSubstitutionCount	inlinevirtual
getSubstitutionRegister()	bpp::AbstractSubstitutionCount	inlinevirtual
getWeights() const	bpp::AbstractWeightedSubstitutionCount	inlinevirtual
hasSubstitutionRegister() const	bpp::AbstractSubstitutionCount	inlinevirtual
hasWeights() const	bpp::AbstractWeightedSubstitutionCount	inlinevirtual
initBMatrices_()	bpp::DecompositionSubstitutionCount	private
insideProducts_	bpp::DecompositionSubstitutionCount	private
jFunction_(const std::vector< double > &lambda, double t, RowMatrix< double > &result) const	bpp::DecompositionSubstitutionCount	protected
jMat_	bpp::DecompositionSubstitutionCount	mutableprivate
lambda_	bpp::DecompositionSubstitutionCount	mutableprivate
model_	bpp::DecompositionSubstitutionCount	private
nbStates_	bpp::DecompositionSubstitutionCount	private
operator=(const DecompositionSubstitutionCount &dsc)	bpp::DecompositionSubstitutionCount	inline
bpp::AbstractSubstitutionCount::operator=(const AbstractSubstitutionCount &asc)	bpp::AbstractSubstitutionCount	inline
bpp::AbstractWeightedSubstitutionCount::operator=(const AbstractWeightedSubstitutionCount &index)	bpp::AbstractWeightedSubstitutionCount	inline
ownWeights_	bpp::AbstractWeightedSubstitutionCount	protected
register_	bpp::AbstractSubstitutionCount	protected
resetBMatrices_()	bpp::DecompositionSubstitutionCount	private
resetStates_()	bpp::DecompositionSubstitutionCount	private
setSubstitutionModel(const SubstitutionModel *model)	bpp::DecompositionSubstitutionCount	virtual
setSubstitutionRegister(SubstitutionRegister *reg)	bpp::AbstractSubstitutionCount	inlinevirtual
setWeights(const AlphabetIndex2 *weights, bool ownWeights)	bpp::AbstractWeightedSubstitutionCount	virtual
SubstitutionCount()	bpp::SubstitutionCount	inline
substitutionRegisterHasChanged()	bpp::DecompositionSubstitutionCount	protectedvirtual
v_	bpp::DecompositionSubstitutionCount	mutableprivate
vInv_	bpp::DecompositionSubstitutionCount	mutableprivate
weights_	bpp::AbstractWeightedSubstitutionCount	protected
weightsHaveChanged()	bpp::DecompositionSubstitutionCount	protectedvirtual
~AbstractSubstitutionCount()	bpp::AbstractSubstitutionCount	inline
~AbstractWeightedSubstitutionCount()	bpp::AbstractWeightedSubstitutionCount	inlinevirtual
~DecompositionSubstitutionCount()	bpp::DecompositionSubstitutionCount	inlinevirtual
~SubstitutionCount()	bpp::SubstitutionCount	inlinevirtual