This is the complete list of members for core::sequence::SequenceAlignment, including all inherited members.

add_sequence(SequenceOP myseq)	core::sequence::SequenceAlignment
alignment_id() const	core::sequence::SequenceAlignment
calculate_per_position_scores(ScoringSchemeOP ss) const	core::sequence::SequenceAlignment
calculate_score_sum_of_pairs(ScoringSchemeOP ss) const	core::sequence::SequenceAlignment
clear()	core::sequence::SequenceAlignment	inline
clone() const	core::sequence::SequenceAlignment	inline
comment(std::string const &comment)	core::sequence::SequenceAlignment
comments() const	core::sequence::SequenceAlignment
comments_	core::sequence::SequenceAlignment	private
data_integrity_check() const	core::sequence::SequenceAlignment
gapped_positions() const	core::sequence::SequenceAlignment
identities() const	core::sequence::SequenceAlignment
is_gapped(Size const col_idx) const	core::sequence::SequenceAlignment
length() const	core::sequence::SequenceAlignment
max_gap_percentage() const	core::sequence::SequenceAlignment
operator<(SequenceAlignment const &lhs, SequenceAlignment const &rhs)	core::sequence::SequenceAlignment	friend
operator<<(std::ostream &out, const SequenceAlignment &sa)	core::sequence::SequenceAlignment	friend
operator=(SequenceAlignment const &src)	core::sequence::SequenceAlignment
operator==(const SequenceAlignment &other) const	core::sequence::SequenceAlignment	inline
operator>>(std::istream &in, SequenceAlignment &aln)	core::sequence::SequenceAlignment	friend
printGrishinFormat(std::ostream &out) const	core::sequence::SequenceAlignment
read_data(std::istream &in)	core::sequence::SequenceAlignment
read_from_file(std::string const &filename)	core::sequence::SequenceAlignment
remove_gapped_positions()	core::sequence::SequenceAlignment
score(Real const &sc)	core::sequence::SequenceAlignment
score() const	core::sequence::SequenceAlignment
score(std::string const &name) const	core::sequence::SequenceAlignment
score(std::string const &name, Real const value)	core::sequence::SequenceAlignment
scores() const	core::sequence::SequenceAlignment
scores(std::map< std::string, core::Real > new_scores)	core::sequence::SequenceAlignment
scores_	core::sequence::SequenceAlignment	private
sequence(Size idx) const	core::sequence::SequenceAlignment
sequence_indices(core::Size const column) const	core::sequence::SequenceAlignment
sequence_mapping(core::Size const idx1, core::Size const idx2) const	core::sequence::SequenceAlignment
SequenceAlignment()	core::sequence::SequenceAlignment	inline
SequenceAlignment(SequenceAlignment const &src)	core::sequence::SequenceAlignment
sequences_	core::sequence::SequenceAlignment	private
sequences_are_in_frame() const	core::sequence::SequenceAlignment
size() const	core::sequence::SequenceAlignment
to_string() const	core::sequence::SequenceAlignment
~SequenceAlignment() override	core::sequence::SequenceAlignment