bpp-seq3
3.0.0
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This is the complete list of members for bpp::Mase, 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::Mase | inlinevirtual |
appendSequencesFromFile(const std::string &path, SequenceContainerInterface &sc) const | bpp::AbstractISequence | inlineprotectedvirtual |
appendSequencesFromStream(std::istream &input, SequenceContainerInterface &sc) const override | bpp::Mase | virtual |
charsByLine_ | bpp::Mase | private |
checkNames() const | bpp::Mase | inline |
checkNames(bool yn) | bpp::Mase | inline |
checkNames_ | bpp::Mase | private |
getDataType() const | bpp::IOSequence | inlinevirtual |
getFormatDescription() const override | bpp::Mase | inlinevirtual |
getFormatName() const override | bpp::Mase | inlinevirtual |
IAlignment() | bpp::IAlignment | inline |
IOFormat() | bpp::IOFormat | |
IOSequence() | bpp::IOSequence | inline |
ISequence() | bpp::ISequence | inline |
Mase(unsigned int charsByLine=100, bool checkSequenceNames=true) | bpp::Mase | inline |
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 |
readHeader_(std::istream &input, MaseHeader &header) const | bpp::Mase | private |
readMeta(std::istream &input, std::shared_ptr< const Alphabet > &alpha, MaseHeader &header) const | bpp::Mase | inline |
readMeta(std::string &path, std::shared_ptr< const Alphabet > &alpha, MaseHeader &header) const | bpp::Mase | inline |
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 |
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 |
writeHeader_(std::ostream &output, const MaseHeader &header) const | bpp::Mase | private |
writeMeta(std::ostream &output, const SequenceContainerInterface &sc, const MaseHeader &header) const | bpp::Mase | inline |
writeMeta(const std::string &path, const SequenceContainerInterface &sc, const MaseHeader &header, bool overwrite=true) const | bpp::Mase | inline |
writeSequences(std::ostream &output, const SequenceContainerInterface &sc) const override | bpp::Mase | virtual |
writeSequences(const std::string &path, const SequenceContainerInterface &sc, bool overwrite=true) const override | bpp::Mase | inlinevirtual |
~AbstractIAlignment() | bpp::AbstractIAlignment | inlinevirtual |
~AbstractISequence() | bpp::AbstractISequence | inlinevirtual |
~AbstractOSequence() | bpp::AbstractOSequence | inlinevirtual |
~AbstractOSequence2() | bpp::AbstractOSequence2 | inlinevirtual |
~IAlignment() | bpp::IAlignment | inlinevirtual |
~IOFormat() | bpp::IOFormat | virtual |
~IOSequence() | bpp::IOSequence | inlinevirtual |
~ISequence() | bpp::ISequence | inlinevirtual |
~Mase() | bpp::Mase | inlinevirtual |
~OAlignment() | bpp::OAlignment | inlinevirtual |
~OSequence() | bpp::OSequence | inlinevirtual |