LocARNA::MultipleAlignment Member List

This is the complete list of members for LocARNA::MultipleAlignment, 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]