bpp::BppOBranchModelFormat Member List

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

ALL	bpp::BppOSubstitutionModelFormat	static
allowCovarions_	bpp::BppOSubstitutionModelFormat	protected
allowGaps_	bpp::BppOSubstitutionModelFormat	protected
allowMixed_	bpp::BppOSubstitutionModelFormat	protected
alphabetCode_	bpp::BppOSubstitutionModelFormat	protected
BINARY	bpp::BppOSubstitutionModelFormat	static
BppOBranchModelFormat(unsigned char alphabetCode, bool allowCovarions, bool allowMixed, bool allowGaps, bool verbose, int warn)	bpp::BppOBranchModelFormat	inline
BppOBranchModelFormat(const BppOTransitionModelFormat &format)	bpp::BppOBranchModelFormat	inline
BppOSubstitutionModelFormat(unsigned char alphabetCode, bool allowCovarions, bool allowMixed, bool allowGaps, bool verbose, int warn)	bpp::BppOSubstitutionModelFormat	inline
BppOSubstitutionModelFormat(const BppOSubstitutionModelFormat &format)	bpp::BppOSubstitutionModelFormat	inline
BppOTransitionModelFormat(unsigned char alphabetCode, bool allowCovarions, bool allowMixed, bool allowGaps, bool verbose, int warn)	bpp::BppOTransitionModelFormat	inline
BppOTransitionModelFormat(const BppOTransitionModelFormat &format)	bpp::BppOTransitionModelFormat	inline
CODON	bpp::BppOSubstitutionModelFormat	static
DNA	bpp::BppOSubstitutionModelFormat	static
geneticCode_	bpp::BppOSubstitutionModelFormat	protected
getDataType() const	bpp::IoSubstitutionModel	inlinevirtual
getFormatDescription() const override	bpp::BppOSubstitutionModelFormat	inlinevirtual
getFormatName() const override	bpp::BppOSubstitutionModelFormat	inlinevirtual
getUnparsedArguments() const override	bpp::BppOSubstitutionModelFormat	inlinevirtual
initialize_(BranchModelInterface &model, std::shared_ptr< const AlignmentDataInterface > data)	bpp::BppOSubstitutionModelFormat	protected
INTEGER	bpp::BppOSubstitutionModelFormat	static
IOFormat()	bpp::IOFormat
IoSubstitutionModel()	bpp::IoSubstitutionModel	inline
ISubstitutionModel()	bpp::ISubstitutionModel	inline
NUCLEOTIDE	bpp::BppOSubstitutionModelFormat	static
operator=(const BppOBranchModelFormat &format)	bpp::BppOBranchModelFormat	inline
bpp::BppOTransitionModelFormat::operator=(const BppOTransitionModelFormat &format)	bpp::BppOTransitionModelFormat	inline
bpp::BppOSubstitutionModelFormat::operator=(const BppOSubstitutionModelFormat &format)	bpp::BppOSubstitutionModelFormat	inline
OSubstitutionModel()	bpp::OSubstitutionModel	inline
PROTEIN	bpp::BppOSubstitutionModelFormat	static
readBranchModel(std::shared_ptr< const Alphabet > alphabet, const std::string &modelDescription, const std::map< size_t, std::shared_ptr< const AlignmentDataInterface >> &mData, size_t nData, bool parseArguments=true)	bpp::BppOBranchModelFormat
readMixed_(std::shared_ptr< const Alphabet > alphabet, const std::string &modelDescription, const std::map< size_t, std::shared_ptr< const AlignmentDataInterface >> &mData, size_t nData)	bpp::BppOTransitionModelFormat	private
readSubstitutionModel(std::shared_ptr< const Alphabet > alphabet, const std::string &modelDescription, const std::map< size_t, std::shared_ptr< const AlignmentDataInterface >> &mData, size_t nData, bool parseArguments=true) override	bpp::BppOSubstitutionModelFormat	virtual
readTransitionModel(std::shared_ptr< const Alphabet > alphabet, const std::string &modelDescription, const std::map< size_t, std::shared_ptr< const AlignmentDataInterface >> &mData, size_t nData, bool parseArguments=true)	bpp::BppOTransitionModelFormat
readWord_(std::shared_ptr< const Alphabet > alphabet, const std::string &modelDescription, const std::map< size_t, std::shared_ptr< const AlignmentDataInterface >> &mData, size_t nData)	bpp::BppOSubstitutionModelFormat	private
RNA	bpp::BppOSubstitutionModelFormat	static
setGeneticCode(std::shared_ptr< const GeneticCode > gCode)	bpp::BppOSubstitutionModelFormat	inline
setVerbose(bool verbose)	bpp::BppOSubstitutionModelFormat	inline
unparsedArguments_	bpp::BppOSubstitutionModelFormat	protected
updateParameters_(BranchModelInterface &model, std::map< std::string, std::string > &args)	bpp::BppOSubstitutionModelFormat	protected
verbose_	bpp::BppOSubstitutionModelFormat	protected
warningLevel_	bpp::BppOSubstitutionModelFormat	protected
WORD	bpp::BppOSubstitutionModelFormat	static
write(const BranchModelInterface &model, OutputStream &out, std::map< std::string, std::string > &globalAliases, std::vector< std::string > &writtenNames) const override	bpp::BppOSubstitutionModelFormat	virtual
writeMixed_(const MixedTransitionModelInterface &model, OutputStream &out, std::map< std::string, std::string > &globalAliases, std::vector< std::string > &writtenNames) const	bpp::BppOSubstitutionModelFormat	private
~BppOSubstitutionModelFormat()	bpp::BppOSubstitutionModelFormat	inlinevirtual
~BppOTransitionModelFormat()	bpp::BppOTransitionModelFormat	inlinevirtual
~IOFormat()	bpp::IOFormat	virtual
~IoSubstitutionModel()	bpp::IoSubstitutionModel	inlinevirtual
~ISubstitutionModel()	bpp::ISubstitutionModel	inlinevirtual
~OSubstitutionModel()	bpp::OSubstitutionModel	inlinevirtual