bpp::RNY Member List

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

AbstractAlphabet()	bpp::AbstractAlphabet	inline
AbstractAlphabet(const AbstractAlphabet &alph)	bpp::AbstractAlphabet	inline
Alphabet()	bpp::Alphabet	inline
charList_	bpp::AbstractAlphabet	mutableprotected
charToInt(const std::string &state) const	bpp::RNY	virtual
clone() const	bpp::RNY	inlinevirtual
containsGap(const std::string &state) const	bpp::RNY
equals(const Alphabet &alphabet) const	bpp::AbstractAlphabet	inlineprotectedvirtual
getAlias(int state) const	bpp::RNY	virtual
getAlias(const std::string &state) const	bpp::RNY	virtual
getAlphabetType() const	bpp::RNY	inlinevirtual
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
getLetterAlphabet() const	bpp::RNY
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	bpp::RNY	inlinevirtual
getRNY(const std::string &, const std::string &, const std::string &) const	bpp::RNY
getRNY(int, int, int, const Alphabet &) const	bpp::RNY
getSize() const	bpp::RNY	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
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	bpp::RNY	inlinevirtual
intList_	bpp::AbstractAlphabet	mutableprotected
intToChar(int state) const	bpp::RNY	virtual
isCharInAlphabet(const std::string &state) const	bpp::AbstractAlphabet	virtual
isGap(int state) const	bpp::RNY	virtual
bpp::AbstractAlphabet::isGap(const std::string &state) const	bpp::AbstractAlphabet	inlinevirtual
isIntInAlphabet(int state) const	bpp::AbstractAlphabet	virtual
isUnresolved(int state) const	bpp::RNY	virtual
isUnresolved(const std::string &state) const	bpp::RNY	virtual
nuclalph_	bpp::RNY	private
operator=(const RNY &bia)	bpp::RNY	inline
bpp::AbstractAlphabet::operator=(const AbstractAlphabet &alph)	bpp::AbstractAlphabet	inline
registerState(AlphabetState *st)	bpp::AbstractAlphabet	protectedvirtual
remap()	bpp::AbstractAlphabet	inlineprotected
resize(size_t size)	bpp::AbstractAlphabet	inlineprotected
RNY(const NucleicAlphabet &)	bpp::RNY
RNY(const RNY &bia)	bpp::RNY	inline
setState(size_t pos, AlphabetState *st)	bpp::AbstractAlphabet	protectedvirtual
~AbstractAlphabet()	bpp::AbstractAlphabet	inlinevirtual
~Alphabet()	bpp::Alphabet	inlinevirtual
~RNY()	bpp::RNY	inline