bpp-seq3  3.0.0
bpp::Mase Member List

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

AbstractIAlignment()bpp::AbstractIAlignmentinline
AbstractISequence()bpp::AbstractISequenceinline
AbstractOSequence()bpp::AbstractOSequenceinline
AbstractOSequence2()bpp::AbstractOSequence2inline
appendAlignmentFromFile(const std::string &path, SequenceContainerInterface &sc) constbpp::AbstractIAlignmentinlineprotectedvirtual
appendAlignmentFromStream(std::istream &input, SequenceContainerInterface &sc) const overridebpp::Maseinlinevirtual
appendSequencesFromFile(const std::string &path, SequenceContainerInterface &sc) constbpp::AbstractISequenceinlineprotectedvirtual
appendSequencesFromStream(std::istream &input, SequenceContainerInterface &sc) const overridebpp::Masevirtual
charsByLine_bpp::Maseprivate
checkNames() constbpp::Maseinline
checkNames(bool yn)bpp::Maseinline
checkNames_bpp::Maseprivate
getDataType() constbpp::IOSequenceinlinevirtual
getFormatDescription() const overridebpp::Maseinlinevirtual
getFormatName() const overridebpp::Maseinlinevirtual
IAlignment()bpp::IAlignmentinline
IOFormat()bpp::IOFormat
IOSequence()bpp::IOSequenceinline
ISequence()bpp::ISequenceinline
Mase(unsigned int charsByLine=100, bool checkSequenceNames=true)bpp::Maseinline
OAlignment()bpp::OAlignmentinline
OSequence()bpp::OSequenceinline
readAlignment(std::istream &input, SequenceContainerInterface &sc) const overridebpp::AbstractIAlignmentinlinevirtual
readAlignment(const std::string &path, SequenceContainerInterface &sc) const overridebpp::AbstractIAlignmentinlinevirtual
readAlignment(const std::string &path, std::shared_ptr< const Alphabet > alpha) const overridebpp::AbstractIAlignmentinlinevirtual
readAlignment(std::istream &input, std::shared_ptr< const Alphabet > alpha) const overridebpp::AbstractIAlignmentinlinevirtual
readAlignmentFromFile(const std::string &path, std::shared_ptr< const Alphabet > alpha) constbpp::AbstractIAlignmentinlineprotectedvirtual
readAlignmentFromStream(std::istream &input, std::shared_ptr< const Alphabet > alpha) constbpp::AbstractIAlignmentinlineprotectedvirtual
readHeader_(std::istream &input, MaseHeader &header) constbpp::Maseprivate
readMeta(std::istream &input, std::shared_ptr< const Alphabet > &alpha, MaseHeader &header) constbpp::Maseinline
readMeta(std::string &path, std::shared_ptr< const Alphabet > &alpha, MaseHeader &header) constbpp::Maseinline
readSequences(std::istream &input, SequenceContainerInterface &sc) const overridebpp::AbstractISequenceinlinevirtual
readSequences(const std::string &path, SequenceContainerInterface &sc) const overridebpp::AbstractISequenceinlinevirtual
readSequences(std::istream &input, std::shared_ptr< const Alphabet > alpha) const overridebpp::AbstractISequenceinlinevirtual
readSequences(const std::string &path, std::shared_ptr< const Alphabet > alpha) const overridebpp::AbstractISequenceinlinevirtual
readSequencesFromFile(const std::string &path, std::shared_ptr< const Alphabet > &alpha) constbpp::AbstractISequenceinlineprotected
readSequencesFromStream(std::istream &input, std::shared_ptr< const Alphabet > &alpha) constbpp::AbstractISequenceinlineprotected
writeAlignment(std::ostream &output, const SiteContainerInterface &sc) const overridebpp::AbstractOSequence2inlinevirtual
writeAlignment(const std::string &path, const SiteContainerInterface &sc, bool overwrite=true) const overridebpp::AbstractOSequence2inlinevirtual
writeHeader_(std::ostream &output, const MaseHeader &header) constbpp::Maseprivate
writeMeta(std::ostream &output, const SequenceContainerInterface &sc, const MaseHeader &header) constbpp::Maseinline
writeMeta(const std::string &path, const SequenceContainerInterface &sc, const MaseHeader &header, bool overwrite=true) constbpp::Maseinline
writeSequences(std::ostream &output, const SequenceContainerInterface &sc) const overridebpp::Masevirtual
writeSequences(const std::string &path, const SequenceContainerInterface &sc, bool overwrite=true) const overridebpp::Maseinlinevirtual
~AbstractIAlignment()bpp::AbstractIAlignmentinlinevirtual
~AbstractISequence()bpp::AbstractISequenceinlinevirtual
~AbstractOSequence()bpp::AbstractOSequenceinlinevirtual
~AbstractOSequence2()bpp::AbstractOSequence2inlinevirtual
~IAlignment()bpp::IAlignmentinlinevirtual
~IOFormat()bpp::IOFormatvirtual
~IOSequence()bpp::IOSequenceinlinevirtual
~ISequence()bpp::ISequenceinlinevirtual
~Mase()bpp::Maseinlinevirtual
~OAlignment()bpp::OAlignmentinlinevirtual
~OSequence()bpp::OSequenceinlinevirtual