bpp::BppOSubstitutionModelFormat Member List

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

ALL	bpp::BppOSubstitutionModelFormat	static
allowCovarions_	bpp::BppOSubstitutionModelFormat	private
allowGaps_	bpp::BppOSubstitutionModelFormat	private
allowMixed_	bpp::BppOSubstitutionModelFormat	private
alphabetCode_	bpp::BppOSubstitutionModelFormat	private
BINARY	bpp::BppOSubstitutionModelFormat	static
BppOSubstitutionModelFormat(unsigned char alphabetCode, bool allowCovarions, bool allowMixed, bool allowGaps, bool verbose, int warn)	bpp::BppOSubstitutionModelFormat	inline
BppOSubstitutionModelFormat(const BppOSubstitutionModelFormat &format)	bpp::BppOSubstitutionModelFormat	inline
CODON	bpp::BppOSubstitutionModelFormat	static
DNA	bpp::BppOSubstitutionModelFormat	static
geneticCode_	bpp::BppOSubstitutionModelFormat	private
getDataType() const	bpp::IoSubstitutionModel	inlinevirtual
getFormatDescription() const	bpp::BppOSubstitutionModelFormat	inline
getFormatName() const	bpp::BppOSubstitutionModelFormat	inline
getUnparsedArguments() const	bpp::BppOSubstitutionModelFormat	inlinevirtual
initialize_(SubstitutionModel &model, const SiteContainer *data)	bpp::BppOSubstitutionModelFormat	private
IoSubstitutionModel()	bpp::IoSubstitutionModel	inline
ISubstitutionModel()	bpp::ISubstitutionModel	inline
NUCLEOTIDE	bpp::BppOSubstitutionModelFormat	static
operator=(const BppOSubstitutionModelFormat &format)	bpp::BppOSubstitutionModelFormat	inline
OSubstitutionModel()	bpp::OSubstitutionModel	inline
PROTEIN	bpp::BppOSubstitutionModelFormat	static
read(const Alphabet *alphabet, const std::string &modelDescription, const SiteContainer *data=0, bool parseArguments=true)	bpp::BppOSubstitutionModelFormat	virtual
readMixed_(const Alphabet *alphabet, const std::string &modelDescription, const SiteContainer *data)	bpp::BppOSubstitutionModelFormat	private
readWord_(const Alphabet *alphabet, const std::string &modelDescription, const SiteContainer *data)	bpp::BppOSubstitutionModelFormat	private
RNA	bpp::BppOSubstitutionModelFormat	static
setGeneticCode(const GeneticCode *gCode)	bpp::BppOSubstitutionModelFormat	inline
setVerbose(bool verbose)	bpp::BppOSubstitutionModelFormat	inline
unparsedArguments_	bpp::BppOSubstitutionModelFormat	private
verbose_	bpp::BppOSubstitutionModelFormat	private
warningLevel_	bpp::BppOSubstitutionModelFormat	private
WORD	bpp::BppOSubstitutionModelFormat	static
write(const SubstitutionModel &model, OutputStream &out, std::map< std::string, std::string > &globalAliases, std::vector< std::string > &writtenNames) const	bpp::BppOSubstitutionModelFormat	virtual
writeMixed_(const MixedSubstitutionModel &model, OutputStream &out, std::map< std::string, std::string > &globalAliases, std::vector< std::string > &writtenNames) const	bpp::BppOSubstitutionModelFormat	private
~BppOSubstitutionModelFormat()	bpp::BppOSubstitutionModelFormat	inlinevirtual
~IoSubstitutionModel()	bpp::IoSubstitutionModel	inlinevirtual
~ISubstitutionModel()	bpp::ISubstitutionModel	inlinevirtual
~OSubstitutionModel()	bpp::OSubstitutionModel	inlinevirtual