bpp::Fasta Member List

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

AbstractIAlignment()	bpp::AbstractIAlignment	inline
AbstractISequence()	bpp::AbstractISequence	inline
AbstractOSequence()	bpp::AbstractOSequence	inline
AbstractOSequence2()	bpp::AbstractOSequence2	inline
appendAlignmentFromFile(const std::string &path, SequenceContainerInterface &sc) const	bpp::AbstractIAlignment	inlineprotectedvirtual
appendAlignmentFromStream(std::istream &input, SequenceContainerInterface &sc) const override	bpp::Fasta	inlinevirtual
appendSequencesFromFile(const std::string &path, SequenceContainerInterface &sc) const	bpp::AbstractISequence	inlineprotectedvirtual
appendSequencesFromStream(std::istream &input, SequenceContainerInterface &sc) const override	bpp::Fasta	virtual
charsByLine_	bpp::Fasta	protected
checkNames() const	bpp::Fasta	inline
checkNames(bool yn)	bpp::Fasta	inline
checkNames_	bpp::Fasta	protected
extended_	bpp::Fasta	protected
Fasta(unsigned int charsByLine=100, bool checkSequenceNames=true, bool extended=false, bool strictSequenceNames=false)	bpp::Fasta	inline
getDataType() const	bpp::IOSequence	inlinevirtual
getFormatDescription() const override	bpp::Fasta	inlinevirtual
getFormatName() const override	bpp::Fasta	inlinevirtual
IAlignment()	bpp::IAlignment	inline
IOFormat()	bpp::IOFormat
IOSequence()	bpp::IOSequence	inline
IOSequenceStream()	bpp::IOSequenceStream	inline
ISequence()	bpp::ISequence	inline
nextSequence(std::istream &input, Sequence &seq) const override	bpp::Fasta
bpp::TemplateISequenceStream::nextSequence(std::istream &input, SequenceType &seq) const =0	bpp::TemplateISequenceStream< SequenceType >	pure virtual
OAlignment()	bpp::OAlignment	inline
OSequence()	bpp::OSequence	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, SequenceContainerInterface &sc) const override	bpp::AbstractISequence	inlinevirtual
readSequences(const std::string &path, SequenceContainerInterface &sc) const override	bpp::AbstractISequence	inlinevirtual
readSequences(std::istream &input, std::shared_ptr< const Alphabet > alpha) const override	bpp::AbstractISequence	inlinevirtual
readSequences(const std::string &path, std::shared_ptr< const Alphabet > alpha) const override	bpp::AbstractISequence	inlinevirtual
readSequencesFromFile(const std::string &path, std::shared_ptr< const Alphabet > &alpha) const	bpp::AbstractISequence	inlineprotected
readSequencesFromStream(std::istream &input, std::shared_ptr< const Alphabet > &alpha) const	bpp::AbstractISequence	inlineprotected
strictNames() const	bpp::Fasta	inline
strictNames(bool yn)	bpp::Fasta	inline
strictNames_	bpp::Fasta	protected
TemplateISequenceStream()	bpp::TemplateISequenceStream< SequenceType >	inline
TemplateOSequenceStream()	bpp::TemplateOSequenceStream< SequenceType >	inline
writeAlignment(std::ostream &output, const SiteContainerInterface &sc) const override	bpp::AbstractOSequence2	inlinevirtual
writeAlignment(const std::string &path, const SiteContainerInterface &sc, bool overwrite=true) const override	bpp::AbstractOSequence2	inlinevirtual
writeSequence(std::ostream &output, const Sequence &seq) const override	bpp::Fasta
bpp::TemplateOSequenceStream::writeSequence(std::ostream &output, const SequenceType &seq) const =0	bpp::TemplateOSequenceStream< SequenceType >	pure virtual
writeSequences(std::ostream &output, const SequenceContainerInterface &sc) const override	bpp::Fasta	virtual
writeSequences(const std::string &path, const SequenceContainerInterface &sc, bool overwrite=true) const override	bpp::Fasta	inlinevirtual
~AbstractIAlignment()	bpp::AbstractIAlignment	inlinevirtual
~AbstractISequence()	bpp::AbstractISequence	inlinevirtual
~AbstractOSequence()	bpp::AbstractOSequence	inlinevirtual
~AbstractOSequence2()	bpp::AbstractOSequence2	inlinevirtual
~Fasta()	bpp::Fasta	inlinevirtual
~IAlignment()	bpp::IAlignment	inlinevirtual
~IOFormat()	bpp::IOFormat	virtual
~IOSequence()	bpp::IOSequence	inlinevirtual
~IOSequenceStream()	bpp::IOSequenceStream	inlinevirtual
~ISequence()	bpp::ISequence	inlinevirtual
~OAlignment()	bpp::OAlignment	inlinevirtual
~OSequence()	bpp::OSequence	inlinevirtual
~TemplateISequenceStream()	bpp::TemplateISequenceStream< SequenceType >	inlinevirtual
~TemplateOSequenceStream()	bpp::TemplateOSequenceStream< SequenceType >	inlinevirtual