bpp::Pasta Member List

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

AbstractIProbabilisticAlignment()	bpp::AbstractIProbabilisticAlignment	inline
AbstractOProbabilisticAlignment()	bpp::AbstractOProbabilisticAlignment	inline
AbstractOSequence()	bpp::AbstractOSequence	inline
AbstractOSequence2()	bpp::AbstractOSequence2	inline
appendAlignmentFromFile(const std::string &path, ProbabilisticSequenceContainerInterface &sc) const	bpp::AbstractIProbabilisticAlignment	inlineprotectedvirtual
appendAlignmentFromStream(std::istream &input, ProbabilisticSequenceContainerInterface &psc) const override	bpp::Pasta	virtual
charsByLine_	bpp::Pasta	protected
DataTable typedef	bpp::Pasta
extended_	bpp::Pasta	protected
getDataType() const override	bpp::Pasta	inlinevirtual
getFormatDescription() const override	bpp::Pasta	inlinevirtual
getFormatName() const override	bpp::Pasta	inlinevirtual
IOFormat()	bpp::IOFormat
IOProbabilisticSequence()	bpp::IOProbabilisticSequence	inline
IOSequence()	bpp::IOSequence	inline
IProbabilisticAlignment()	bpp::IProbabilisticAlignment	inline
nextSequence(std::istream &input, ProbabilisticSequence &seq, bool hasLabels, const std::vector< size_t > &permutationMap) const	bpp::Pasta
OAlignment()	bpp::OAlignment	inline
OProbabilisticAlignment()	bpp::OProbabilisticAlignment	inline
OSequence()	bpp::OSequence	inline
Pasta(unsigned int charsByLine=100, bool extended=false, bool strictSequenceNames=false)	bpp::Pasta	inline
readAlignment(std::istream &input, ProbabilisticSequenceContainerInterface &sc) const override	bpp::AbstractIProbabilisticAlignment	inlinevirtual
readAlignment(const std::string &path, ProbabilisticSequenceContainerInterface &sc) const override	bpp::AbstractIProbabilisticAlignment	inlinevirtual
readAlignment(const std::string &path, std::shared_ptr< const Alphabet > alpha) const override	bpp::AbstractIProbabilisticAlignment	inlinevirtual
readAlignment(std::istream &input, std::shared_ptr< const Alphabet > alpha) const override	bpp::AbstractIProbabilisticAlignment	inlinevirtual
readAlignmentFromFile(const std::string &path, std::shared_ptr< const Alphabet > &alpha) const	bpp::AbstractIProbabilisticAlignment	inlineprotectedvirtual
readAlignmentFromStream(std::istream &input, std::shared_ptr< const Alphabet > &alpha) const	bpp::AbstractIProbabilisticAlignment	inlineprotectedvirtual
strictNames_	bpp::Pasta	protected
writeAlignment(std::ostream &output, const ProbabilisticSiteContainerInterface &psc) const override	bpp::Pasta	inlinevirtual
writeAlignment(std::ostream &output, const SiteContainerInterface &sc) const override	bpp::Pasta	inline
writeAlignment(const std::string &path, const SiteContainerInterface &sc, bool overwrite=true) const override	bpp::Pasta	inline
bpp::AbstractOProbabilisticAlignment::writeAlignment(const std::string &path, const ProbabilisticSiteContainerInterface &psc, bool overwrite=true) const override	bpp::AbstractOProbabilisticAlignment	inlinevirtual
bpp::AbstractOSequence2::writeAlignment(std::ostream &output, const SiteContainerInterface &sc) const override	bpp::AbstractOSequence2	inlinevirtual
bpp::AbstractOSequence2::writeAlignment(const std::string &path, const SiteContainerInterface &sc, bool overwrite=true) const override	bpp::AbstractOSequence2	inlinevirtual
writeSequence(std::ostream &output, const ProbabilisticSequence &seq, bool header) const	bpp::Pasta
writeSequence(std::ostream &output, const Sequence &seq, bool header) const	bpp::Pasta
writeSequences(std::ostream &output, const SequenceContainerInterface &sc) const override	bpp::Pasta	inlinevirtual
writeSequences(std::ostream &output, const SequenceContainerInterface &sc) const override=0	bpp::Pasta
writeSequences(const std::string &path, const SequenceContainerInterface &sc, bool overwrite=true) const override	bpp::Pasta	inline
bpp::AbstractOSequence2::writeSequences(const std::string &path, const SequenceContainerInterface &sc, bool overwrite=true) const override	bpp::AbstractOSequence	inlinevirtual
~AbstractIProbabilisticAlignment()	bpp::AbstractIProbabilisticAlignment	inlinevirtual
~AbstractOProbabilisticAlignment()	bpp::AbstractOProbabilisticAlignment	inlinevirtual
~AbstractOSequence()	bpp::AbstractOSequence	inlinevirtual
~AbstractOSequence2()	bpp::AbstractOSequence2	inlinevirtual
~IOFormat()	bpp::IOFormat	virtual
~IOProbabilisticSequence()	bpp::IOProbabilisticSequence	inlinevirtual
~IOSequence()	bpp::IOSequence	inlinevirtual
~IProbabilisticAlignment()	bpp::IProbabilisticAlignment	inlinevirtual
~OAlignment()	bpp::OAlignment	inlinevirtual
~OProbabilisticAlignment()	bpp::OProbabilisticAlignment	inlinevirtual
~OSequence()	bpp::OSequence	inlinevirtual
~Pasta()	bpp::Pasta	inlinevirtual