bpp::Clustal Member List

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

AbstractIAlignment()	bpp::AbstractIAlignment	inline
AbstractIAlignment2()	bpp::AbstractIAlignment2	inline
AbstractOAlignment()	bpp::AbstractOAlignment	inline
appendAlignmentFromFile(const std::string &path, SequenceContainerInterface &sc) const	bpp::AbstractIAlignment	inlineprotectedvirtual
appendAlignmentFromStream(std::istream &input, SequenceContainerInterface &sc) const override	bpp::Clustal	virtual
charsByLine_	bpp::Clustal	private
checkNames() const	bpp::Clustal	inline
checkNames(bool yn)	bpp::Clustal	inline
checkNames_	bpp::Clustal	private
Clustal(bool checkSequenceNames=true, unsigned int nbExtraSpacesBeforeSeq=5, unsigned int charsByLine=100)	bpp::Clustal	inline
getDataType() const	bpp::IOSequence	inlinevirtual
getFormatDescription() const override	bpp::Clustal	inlinevirtual
getFormatName() const override	bpp::Clustal	inlinevirtual
IAlignment()	bpp::IAlignment	inline
IOFormat()	bpp::IOFormat
IOSequence()	bpp::IOSequence	inline
ISequence()	bpp::ISequence	inline
nbSpacesBeforeSeq_	bpp::Clustal	private
OAlignment()	bpp::OAlignment	inline
readAlignment(std::istream &input, SequenceContainerInterface &sc) const override	bpp::AbstractIAlignment	inlinevirtual
readAlignment(const std::string &path, SequenceContainerInterface &sc) const override	bpp::AbstractIAlignment	inlinevirtual
readAlignment(const std::string &path, std::shared_ptr< const Alphabet > alpha) const override	bpp::AbstractIAlignment	inlinevirtual
readAlignment(std::istream &input, std::shared_ptr< const Alphabet > alpha) const override	bpp::AbstractIAlignment	inlinevirtual
readAlignmentFromFile(const std::string &path, std::shared_ptr< const Alphabet > alpha) const	bpp::AbstractIAlignment	inlineprotectedvirtual
readAlignmentFromStream(std::istream &input, std::shared_ptr< const Alphabet > alpha) const	bpp::AbstractIAlignment	inlineprotectedvirtual
readSequences(std::istream &input, std::shared_ptr< const Alphabet > alpha) const override	bpp::Clustal	inlinevirtual
readSequences(const std::string &path, std::shared_ptr< const Alphabet > alpha) const override	bpp::Clustal	inlinevirtual
bpp::AbstractIAlignment2::readSequences(std::istream &input, SequenceContainerInterface &sc) const override	bpp::AbstractIAlignment2	inlinevirtual
bpp::AbstractIAlignment2::readSequences(const std::string &path, SequenceContainerInterface &sc) const override	bpp::AbstractIAlignment2	inlinevirtual
writeAlignment(std::ostream &output, const SiteContainerInterface &sc) const override	bpp::Clustal	virtual
writeAlignment(const std::string &path, const SiteContainerInterface &sc, bool overwrite=true) const override	bpp::Clustal	inlinevirtual
~AbstractIAlignment()	bpp::AbstractIAlignment	inlinevirtual
~AbstractIAlignment2()	bpp::AbstractIAlignment2	inlinevirtual
~AbstractOAlignment()	bpp::AbstractOAlignment	inlinevirtual
~Clustal()	bpp::Clustal	inlinevirtual
~IAlignment()	bpp::IAlignment	inlinevirtual
~IOFormat()	bpp::IOFormat	virtual
~IOSequence()	bpp::IOSequence	inlinevirtual
~ISequence()	bpp::ISequence	inlinevirtual
~OAlignment()	bpp::OAlignment	inlinevirtual