, including all inherited members.
annotation(const AnnoType::type &annotype) const | LocARNA::MultipleAlignment | |
append(const SeqEntry &seqentry) | LocARNA::MultipleAlignment | |
as_sequence() const | LocARNA::MultipleAlignment | |
avg_deviation_score(const MultipleAlignment &ma) const | LocARNA::MultipleAlignment | |
begin() const | LocARNA::MultipleAlignment | [inline] |
checkAlphabet(const Alphabet< char > &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] |
has_annotation(const AnnoType::type &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 | |
length() const | LocARNA::MultipleAlignment | [inline] |
MultipleAlignment() | LocARNA::MultipleAlignment | |
MultipleAlignment(const std::string &file, FormatType::type format=FormatType::CLUSTAL) | LocARNA::MultipleAlignment | |
MultipleAlignment(std::istream &in, FormatType::type 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 | [inline, static] |
num_of_rows() const | LocARNA::MultipleAlignment | [inline] |
operator+=(const AliColumn &c) | LocARNA::MultipleAlignment | |
operator+=(char c) | 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::type &annotype, const SequenceAnnotation &annotation) | LocARNA::MultipleAlignment | [inline] |
size_type typedef | LocARNA::MultipleAlignment | |
sps(const MultipleAlignment &ma, bool compalign=true) const | LocARNA::MultipleAlignment | |
write(std::ostream &out, FormatType::type format=MultipleAlignment::FormatType::CLUSTAL) const | LocARNA::MultipleAlignment | |
write(std::ostream &out, size_t width, FormatType::type format=MultipleAlignment::FormatType::CLUSTAL) const | LocARNA::MultipleAlignment | |
write(std::ostream &out, size_type start, size_type end, FormatType::type 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] |