bpp::GCSynonymousSubstitutionRegister Member List

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

AbstractSubstitutionRegister(std::shared_ptr< const StateMapInterface > stateMap, const std::string &name)	bpp::AbstractSubstitutionRegister	inline
AbstractSubstitutionRegister(const AbstractSubstitutionRegister &asr)	bpp::AbstractSubstitutionRegister	inline
allowWithin() const	bpp::CategorySubstitutionRegister	inlinevirtual
alphabet() const override	bpp::AbstractSubstitutionRegister	inlinevirtual
categories_	bpp::CategorySubstitutionRegister	mutableprotected
categoryNames_	bpp::CategorySubstitutionRegister	protected
CategorySubstitutionRegister(std::shared_ptr< const StateMapInterface > stateMap, bool within=false)	bpp::CategorySubstitutionRegister	inline
clone() const	bpp::GCSynonymousSubstitutionRegister	inlinevirtual
GCSynonymousSubstitutionRegister(std::shared_ptr< const StateMapInterface > stateMap, std::shared_ptr< const GeneticCode > genCode, bool within=false)	bpp::GCSynonymousSubstitutionRegister	inline
GCSynonymousSubstitutionRegister(const GCSynonymousSubstitutionRegister &reg)	bpp::GCSynonymousSubstitutionRegister	inline
genCode_	bpp::GCSynonymousSubstitutionRegister	private
getAlphabet() const override	bpp::AbstractSubstitutionRegister	inlinevirtual
getCategory(size_t state) const	bpp::CategorySubstitutionRegister	inlinevirtual
getCategoryFrom(size_t type) const	bpp::CategorySubstitutionRegister	inlinevirtual
getCategoryName(size_t category) const	bpp::CategorySubstitutionRegister	inlinevirtual
getCategoryTo(size_t type) const	bpp::CategorySubstitutionRegister	inlinevirtual
getName() const override	bpp::AbstractSubstitutionRegister	inlinevirtual
getNumberOfCategories() const	bpp::CategorySubstitutionRegister	inline
getNumberOfSubstitutionTypes() const	bpp::CategorySubstitutionRegister	inlinevirtual
getStateMap() const override	bpp::AbstractSubstitutionRegister	inlinevirtual
getType(size_t fromState, size_t toState) const	bpp::GCSynonymousSubstitutionRegister	inlinevirtual
getTypeName(size_t type) const	bpp::GCSynonymousSubstitutionRegister	inlinevirtual
index_	bpp::CategorySubstitutionRegister	protected
isStationary() const	bpp::CategorySubstitutionRegister	inline
name_	bpp::AbstractSubstitutionRegister	protected
nbCategories_	bpp::CategorySubstitutionRegister	protected
operator=(const GCSynonymousSubstitutionRegister &reg)	bpp::GCSynonymousSubstitutionRegister	inline
bpp::CategorySubstitutionRegister::operator=(const AbstractSubstitutionRegister &asr)	bpp::AbstractSubstitutionRegister	inline
revIndex_	bpp::CategorySubstitutionRegister	protected
setAlphabetCategories(const std::map< int, T > &categories)	bpp::CategorySubstitutionRegister	inlineprotected
setModelCategories(const std::map< size_t, T > &categories)	bpp::CategorySubstitutionRegister	inlineprotected
setStationarity(bool stat)	bpp::CategorySubstitutionRegister	inline
stateMap() const override	bpp::AbstractSubstitutionRegister	inlinevirtual
stateMap_	bpp::AbstractSubstitutionRegister	protected
stationarity_	bpp::CategorySubstitutionRegister	protected
SubstitutionRegisterInterface()	bpp::SubstitutionRegisterInterface	inline
within_	bpp::CategorySubstitutionRegister	protected
~AbstractSubstitutionRegister()	bpp::AbstractSubstitutionRegister	inlinevirtual
~Clonable()=default	bpp::Clonable	virtual
~SubstitutionRegisterInterface()	bpp::SubstitutionRegisterInterface	inlinevirtual