| annotation(const AnnoType &annotype) const | LocARNA::MultipleAlignment | |
| AnnoType enum name | LocARNA::MultipleAlignment | |
| AnnoTypes | LocARNA::MultipleAlignment | static |
| append(const SeqEntry &seqentry) | LocARNA::MultipleAlignment | |
| avg_deviation_score(const MultipleAlignment &ma) const | LocARNA::MultipleAlignment | |
| begin() const | LocARNA::MultipleAlignment | inline |
| checkAlphabet(const Alphabet< char, N > &alphabet) const | LocARNA::MultipleAlignment | |
| cmfinder_realignment_score(const MultipleAlignment &ma) const | LocARNA::MultipleAlignment | |
| column(size_type col_index) const | LocARNA::MultipleAlignment | inline |
| consensus_sequence() const | LocARNA::MultipleAlignment | |
| const_iterator typedef | LocARNA::MultipleAlignment | |
| contains(const std::string &name) const | LocARNA::MultipleAlignment | |
| deviation(const MultipleAlignment &ma) const | LocARNA::MultipleAlignment | |
| empty() const | LocARNA::MultipleAlignment | inline |
| end() const | LocARNA::MultipleAlignment | inline |
| FormatType enum name | LocARNA::MultipleAlignment | |
| FormatTypes | LocARNA::MultipleAlignment | static |
| has_annotation(const AnnoType &annotype) const | LocARNA::MultipleAlignment | inline |
| index(const std::string &name) const | LocARNA::MultipleAlignment | inline |
| init(const AlignmentEdges &edges, const Sequence &seqA, const Sequence &seqB, bool special_gap_symbols) | LocARNA::MultipleAlignment | protected |
| is_proper() const | LocARNA::MultipleAlignment | |
| iterator typedef | LocARNA::MultipleAlignment | |
| length() const | LocARNA::MultipleAlignment | inline |
| MultipleAlignment() | LocARNA::MultipleAlignment | |
| MultipleAlignment(const MultipleAlignment &ma)=default | LocARNA::MultipleAlignment | |
| MultipleAlignment(MultipleAlignment &&ma)=default | LocARNA::MultipleAlignment | |
| MultipleAlignment(const std::string &file, FormatType format=FormatType::CLUSTAL) | LocARNA::MultipleAlignment | |
| MultipleAlignment(std::istream &in, FormatType format=FormatType::CLUSTAL) | LocARNA::MultipleAlignment | |
| MultipleAlignment(const std::string &name, const std::string &sequence) | LocARNA::MultipleAlignment | |
| MultipleAlignment(const std::string &nameA, const std::string &nameB, const std::string &alistringA, const std::string &alistringB) | LocARNA::MultipleAlignment | |
| MultipleAlignment(const Alignment &alignment, bool only_local=false, bool special_gap_symbols=false) | LocARNA::MultipleAlignment | |
| MultipleAlignment(const AlignmentEdges &edges, const Sequence &seqA, const Sequence &seqB) | LocARNA::MultipleAlignment | |
| normalize_rna_symbols() | LocARNA::MultipleAlignment | |
| num_of_annotypes() | LocARNA::MultipleAlignment | inlinestatic |
| num_of_rows() const | LocARNA::MultipleAlignment | inline |
| operator+=(const AliColumn &c) | LocARNA::MultipleAlignment | |
| operator+=(char c) | LocARNA::MultipleAlignment | |
| operator=(const MultipleAlignment &ma)=default | LocARNA::MultipleAlignment | |
| operator=(MultipleAlignment &&ma)=default | LocARNA::MultipleAlignment | |
| prepend(const SeqEntry &seqentry) | LocARNA::MultipleAlignment | |
| reverse() | LocARNA::MultipleAlignment | |
| seqentry(size_type index) const | LocARNA::MultipleAlignment | inline |
| seqentry(const std::string &name) const | LocARNA::MultipleAlignment | inline |
| set_annotation(const AnnoType &annotype, const SequenceAnnotation &annotation) | LocARNA::MultipleAlignment | inline |
| sps(const MultipleAlignment &ma, bool compalign=true) const | LocARNA::MultipleAlignment | |
| value_type typedef (defined in LocARNA::MultipleAlignment) | LocARNA::MultipleAlignment | |
| write(std::ostream &out, FormatType format=MultipleAlignment::FormatType::CLUSTAL) const | LocARNA::MultipleAlignment | |
| write(std::ostream &out, size_t width, FormatType format=MultipleAlignment::FormatType::CLUSTAL) const | LocARNA::MultipleAlignment | |
| write(std::ostream &out, size_type start, size_type end, FormatType format=MultipleAlignment::FormatType::CLUSTAL) const | LocARNA::MultipleAlignment | |
| write_debug(std::ostream &out=std::cout) const | LocARNA::MultipleAlignment | |
| write_name_sequence_line(std::ostream &out, const std::string &name, const std::string &sequence, size_t namewidth) const | LocARNA::MultipleAlignment | |
| ~MultipleAlignment() | LocARNA::MultipleAlignment | virtual |
