bpp::Phylip Member List

This is the complete list of members for bpp::Phylip, 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::Phylip	virtual
charsByLine_	bpp::Phylip	private
extended_	bpp::Phylip	private
getDataType() const	bpp::IOSequence	inlinevirtual
getFormatDescription() const override	bpp::Phylip	virtual
getFormatName() const override	bpp::Phylip	virtual
getNumberOfSequences(const std::string &path) const	bpp::Phylip
getSizedNames(const std::vector< std::string > &names) const	bpp::Phylip	protected
getSplit() const	bpp::Phylip	inline
IAlignment()	bpp::IAlignment	inline
IOFormat()	bpp::IOFormat
IOSequence()	bpp::IOSequence	inline
ISequence()	bpp::ISequence	inline
namesSplit_	bpp::Phylip	private
OAlignment()	bpp::OAlignment	inline
Phylip(bool extended=true, bool sequential=true, unsigned int charsByLine=100, const std::string &split=" ")	bpp::Phylip	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
readInterleaved(std::istream &in, SequenceContainerInterface &asc) const	bpp::Phylip	protected
readSequences(std::istream &input, std::shared_ptr< const Alphabet > alpha) const override	bpp::Phylip	inlinevirtual
readSequences(const std::string &path, std::shared_ptr< const Alphabet > alpha) const override	bpp::Phylip	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
readSequential(std::istream &in, SequenceContainerInterface &asc) const	bpp::Phylip	protected
sequential_	bpp::Phylip	private
setSplit(const std::string &split)	bpp::Phylip	inline
splitNameAndSequence(const std::string &s) const	bpp::Phylip	protected
writeAlignment(std::ostream &output, const SiteContainerInterface &sc) const override	bpp::Phylip	virtual
writeAlignment(const std::string &path, const SiteContainerInterface &sc, bool overwrite) const override	bpp::Phylip	inlinevirtual
writeInterleaved(std::ostream &out, const SiteContainerInterface &sc) const	bpp::Phylip	protected
writeSequential(std::ostream &out, const SiteContainerInterface &sc) const	bpp::Phylip	protected
~AbstractIAlignment()	bpp::AbstractIAlignment	inlinevirtual
~AbstractIAlignment2()	bpp::AbstractIAlignment2	inlinevirtual
~AbstractOAlignment()	bpp::AbstractOAlignment	inlinevirtual
~IAlignment()	bpp::IAlignment	inlinevirtual
~IOFormat()	bpp::IOFormat	virtual
~IOSequence()	bpp::IOSequence	inlinevirtual
~ISequence()	bpp::ISequence	inlinevirtual
~OAlignment()	bpp::OAlignment	inlinevirtual
~Phylip()	bpp::Phylip	inlinevirtual