bpp::AbstractAlphabet Member List

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

AbstractAlphabet()	bpp::AbstractAlphabet	inline
AbstractAlphabet(const AbstractAlphabet &alph)	bpp::AbstractAlphabet	inline
Alphabet()	bpp::Alphabet	inline
alphabet_	bpp::AbstractAlphabet	private
charList_	bpp::AbstractAlphabet	mutableprotected
charToInt(const std::string &state) const	bpp::AbstractAlphabet	virtual
clone() const =0	bpp::AbstractAlphabet	pure virtual
equals(const Alphabet &alphabet) const	bpp::AbstractAlphabet	inlineprotectedvirtual
getAlias(int state) const	bpp::AbstractAlphabet	virtual
getAlias(const std::string &state) const	bpp::AbstractAlphabet	virtual
getAlphabetType() const =0	bpp::Alphabet	pure virtual
getCharCodeAt(size_t stateIndex) const	bpp::AbstractAlphabet	inlinevirtual
getGapCharacterCode() const	bpp::AbstractAlphabet	inlinevirtual
getGeneric(const std::vector< int > &states) const	bpp::AbstractAlphabet	virtual
getGeneric(const std::vector< std::string > &states) const	bpp::AbstractAlphabet	virtual
getIntCodeAt(size_t stateIndex) const	bpp::AbstractAlphabet	inlinevirtual
getName(const std::string &state) const	bpp::AbstractAlphabet	virtual
getName(int state) const	bpp::AbstractAlphabet	virtual
getNumberOfChars() const	bpp::AbstractAlphabet	inlinevirtual
getNumberOfStates() const	bpp::AbstractAlphabet	inlinevirtual
getNumberOfTypes() const =0	bpp::Alphabet	pure virtual
getResolvedChars() const	bpp::AbstractAlphabet	virtual
getSize() const =0	bpp::Alphabet	pure virtual
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
getStateAt(size_t stateIndex)	bpp::AbstractAlphabet	virtual
getStateAt(size_t stateIndex) const	bpp::AbstractAlphabet	virtual
getStateCodingSize() const	bpp::AbstractAlphabet	inlineprotectedvirtual
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 =0	bpp::Alphabet	pure virtual
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	bpp::AbstractAlphabet	virtual
isUnresolved(int state) const =0	bpp::Alphabet	pure virtual
isUnresolved(const std::string &state) const =0	bpp::Alphabet	pure virtual
letters_	bpp::AbstractAlphabet	private
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
updateMaps_(size_t pos, const AlphabetState &st)	bpp::AbstractAlphabet	private
~AbstractAlphabet()	bpp::AbstractAlphabet	inlinevirtual
~Alphabet()=default	bpp::Alphabet	virtual
~Clonable()=default	bpp::Clonable	virtual