bpp::CodonAlphabet Member List

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

AbstractAlphabet()	bpp::AbstractAlphabet	inline
AbstractAlphabet(const AbstractAlphabet &alph)	bpp::AbstractAlphabet	inline
Alphabet()	bpp::Alphabet	inline
alphabet_	bpp::AbstractAlphabet	private
build_()	bpp::CodonAlphabet	private
charList_	bpp::AbstractAlphabet	mutableprotected
charToInt(const std::string &state) const override	bpp::CodonAlphabet	inlinevirtual
clone() const override	bpp::CodonAlphabet	inlinevirtual
CodonAlphabet(std::shared_ptr< const NucleicAlphabet > alpha)	bpp::CodonAlphabet	inline
CodonAlphabet(const CodonAlphabet &bia)	bpp::CodonAlphabet	inline
containsGap(const std::string &state) const override	bpp::CodonAlphabet	privatevirtual
containsUnresolved(const std::string &state) const override	bpp::CodonAlphabet	privatevirtual
CoreWordAlphabet()	bpp::CoreWordAlphabet	inline
equals(const Alphabet &alphabet) const	bpp::AbstractAlphabet	inlineprotectedvirtual
getAlias(int state) const override	bpp::CodonAlphabet	virtual
getAlias(const std::string &state) const override	bpp::CodonAlphabet	virtual
getAlphabetType() const override	bpp::CodonAlphabet	inlinevirtual
getCharCodeAt(size_t stateIndex) const	bpp::AbstractAlphabet	inlinevirtual
getCodon(int pos1, int pos2, int pos3) const	bpp::CodonAlphabet	inline
getCodon(const std::string &pos1, const std::string &pos2, const std::string &pos3) const	bpp::CodonAlphabet	inline
getFirstPosition(int codon) const	bpp::CodonAlphabet	inline
getFirstPosition(const std::string &codon) const	bpp::CodonAlphabet	inline
getGapCharacterCode() const	bpp::AbstractAlphabet	inlinevirtual
getGCinCodon(int codon) const	bpp::CodonAlphabet
getGeneric(const std::vector< int > &states) const override	bpp::CodonAlphabet	inlinevirtual
getGeneric(const std::vector< std::string > &states) const override	bpp::CodonAlphabet	inlinevirtual
getIntCodeAt(size_t stateIndex) const	bpp::AbstractAlphabet	inlinevirtual
getLength() const override	bpp::CodonAlphabet	inlinevirtual
getNAlphabet(size_t n) const override	bpp::CodonAlphabet	inlinevirtual
getName(const std::string &state) const	bpp::AbstractAlphabet	virtual
getName(int state) const	bpp::AbstractAlphabet	virtual
getNPosition(int codon, size_t pos) const override	bpp::CodonAlphabet	inlinevirtual
getNPosition(const std::string &codon, size_t pos) const override	bpp::CodonAlphabet	inlinevirtual
getNucleicAlphabet() const	bpp::CodonAlphabet	inline
getNumberOfChars() const	bpp::AbstractAlphabet	inlinevirtual
getNumberOfStates() const	bpp::AbstractAlphabet	inlinevirtual
getNumberOfTypes() const override	bpp::CodonAlphabet	inlinevirtual
getPositions(int word) const override	bpp::CodonAlphabet	inlinevirtual
getPositions(const std::string &word) const override	bpp::CodonAlphabet	inlinevirtual
getResolvedChars() const	bpp::AbstractAlphabet	virtual
getSecondPosition(int codon) const	bpp::CodonAlphabet	inline
getSecondPosition(const std::string &codon) const	bpp::CodonAlphabet	inline
getSize() const override	bpp::CodonAlphabet	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 override	bpp::CodonAlphabet	inlinevirtual
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
getThirdPosition(int codon) const	bpp::CodonAlphabet	inline
getThirdPosition(const std::string &codon) const	bpp::CodonAlphabet	inline
getUnknownCharacterCode() const override	bpp::CodonAlphabet	inlinevirtual
getWord(const Sequence &seq, size_t pos=0) const override	bpp::CodonAlphabet	inlinevirtual
getWord(const std::vector< std::string > &vpos, size_t pos=0) const override	bpp::CodonAlphabet	inlinevirtual
getWord(const std::vector< int > &vpos, size_t pos=0) const override	bpp::CodonAlphabet	inlinevirtual
hasUniqueAlphabet() const override	bpp::CodonAlphabet	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::CodonAlphabet	virtual
isUnresolved(int state) const override	bpp::CodonAlphabet	inlinevirtual
isUnresolved(const std::string &state) const override	bpp::CodonAlphabet	inlinevirtual
letters_	bpp::AbstractAlphabet	private
nAlph_	bpp::CodonAlphabet	protected
nums_	bpp::AbstractAlphabet	private
operator=(const CodonAlphabet &bia)	bpp::CodonAlphabet	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
reverse(const SequenceInterface &sequence) const override	bpp::CodonAlphabet	virtual
setState(size_t pos, AlphabetState *st)	bpp::AbstractAlphabet	protectedvirtual
translate(const SequenceInterface &sequence, size_t=0) const override	bpp::CodonAlphabet	virtual
updateMaps_(size_t pos, const AlphabetState &st)	bpp::AbstractAlphabet	private
~AbstractAlphabet()	bpp::AbstractAlphabet	inlinevirtual
~Alphabet()=default	bpp::Alphabet	virtual
~Clonable()=default	bpp::Clonable	virtual
~CodonAlphabet()	bpp::CodonAlphabet	inlinevirtual
~CoreWordAlphabet()	bpp::CoreWordAlphabet	inlinevirtual