bpp::AllelicAlphabet Member List

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

AbstractAlphabet()	bpp::AbstractAlphabet	inline
AbstractAlphabet(const AbstractAlphabet &alph)	bpp::AbstractAlphabet	inline
AllelicAlphabet(std::shared_ptr< const Alphabet > alph, unsigned int nbAlleles)	bpp::AllelicAlphabet
AllelicAlphabet(const AllelicAlphabet &bia)	bpp::AllelicAlphabet	inline
alph_	bpp::AllelicAlphabet	protected
Alphabet()	bpp::Alphabet	inline
alphabet_	bpp::AbstractAlphabet	private
charList_	bpp::AbstractAlphabet	mutableprotected
charToInt(const std::string &state) const override	bpp::AllelicAlphabet	inlinevirtual
clone() const override	bpp::AllelicAlphabet	inlinevirtual
computeLikelihoods(const Vdouble &counts, Vdouble &likelihoods) const	bpp::AllelicAlphabet
convertFromStateAlphabet(const CoreSequenceInterface &sequence) const	bpp::AllelicAlphabet
equals(const Alphabet &alphabet) const	bpp::AbstractAlphabet	inlineprotectedvirtual
getAlias(int state) const override	bpp::AllelicAlphabet	virtual
getAlias(const std::string &state) const override	bpp::AllelicAlphabet	virtual
getAlphabetType() const override	bpp::AllelicAlphabet	virtual
getCharCodeAt(size_t stateIndex) const	bpp::AbstractAlphabet	inlinevirtual
getGapCharacterCode() const	bpp::AbstractAlphabet	inlinevirtual
getGeneric(const std::vector< int > &states) const override	bpp::AllelicAlphabet	inlinevirtual
getGeneric(const std::vector< std::string > &states) const override	bpp::AllelicAlphabet	inlinevirtual
getIntCodeAt(size_t stateIndex) const	bpp::AbstractAlphabet	inlinevirtual
getName(const std::string &state) const	bpp::AbstractAlphabet	virtual
getName(int state) const	bpp::AbstractAlphabet	virtual
getNbAlleles() const	bpp::AllelicAlphabet	inline
getNumberOfChars() const	bpp::AbstractAlphabet	inlinevirtual
getNumberOfStates() const	bpp::AbstractAlphabet	inlinevirtual
getNumberOfTypes() const override	bpp::AllelicAlphabet	inlinevirtual
getResolvedChars() const	bpp::AbstractAlphabet	virtual
getSize() const override	bpp::AllelicAlphabet	inlinevirtual
getState(const std::string &letter) const	bpp::AbstractAlphabet	virtual
getState(const std::string &letter)	bpp::AbstractAlphabet
getState(int num) const	bpp::AbstractAlphabet	virtual
getState(int num)	bpp::AbstractAlphabet
getStateAlphabet() const	bpp::AllelicAlphabet	inline
getStateAt(size_t stateIndex)	bpp::AbstractAlphabet	virtual
getStateAt(size_t stateIndex) const	bpp::AbstractAlphabet	virtual
getStateCodingSize() const override	bpp::AllelicAlphabet	inlineprivatevirtual
getStateIndex(int state) const	bpp::AbstractAlphabet	virtual
getStateIndex(const std::string &state) const	bpp::AbstractAlphabet	virtual
getSupportedChars() const	bpp::AbstractAlphabet	virtual
getSupportedInts() const	bpp::AbstractAlphabet	virtual
getUnknownCharacterCode() const override	bpp::AllelicAlphabet	inlinevirtual
intList_	bpp::AbstractAlphabet	mutableprotected
intToChar(int state) const	bpp::AbstractAlphabet	virtual
isCharInAlphabet(const std::string &state) const	bpp::AbstractAlphabet	virtual
isGap(int state) const	bpp::AbstractAlphabet	inlinevirtual
isGap(const std::string &state) const	bpp::AbstractAlphabet	inlinevirtual
isIntInAlphabet(int state) const	bpp::AbstractAlphabet	virtual
isResolvedIn(int state1, int state2) const override	bpp::AllelicAlphabet	virtual
isUnresolved(int state) const override	bpp::AllelicAlphabet	inlinevirtual
isUnresolved(const std::string &state) const override	bpp::AllelicAlphabet	inlinevirtual
letters_	bpp::AbstractAlphabet	private
nbAlleles_	bpp::AllelicAlphabet	protected
nbUnknown_	bpp::AllelicAlphabet	protected
nums_	bpp::AbstractAlphabet	private
operator=(const AbstractAlphabet &alph)	bpp::AbstractAlphabet	inline
registerState(AlphabetState *st)	bpp::AbstractAlphabet	protectedvirtual
remap()	bpp::AbstractAlphabet	inlineprotected
resize(size_t size)	bpp::AbstractAlphabet	inlineprotected
setState(size_t pos, AlphabetState *st)	bpp::AbstractAlphabet	protectedvirtual
stateAlphabet() const	bpp::AllelicAlphabet	inline
updateMaps_(size_t pos, const AlphabetState &st)	bpp::AbstractAlphabet	private
~AbstractAlphabet()	bpp::AbstractAlphabet	inlinevirtual
~AllelicAlphabet()	bpp::AllelicAlphabet	inlinevirtual
~Alphabet()=default	bpp::Alphabet	virtual
~Clonable()=default	bpp::Clonable	virtual