This is the complete list of members for LocARNA::ArcMatches, including all inherited members.
| Arc typedef | LocARNA::ArcMatches | |
| arc_matches_vec | LocARNA::ArcMatches | protected |
| arcmatch(size_type idx) const | LocARNA::ArcMatches | inline |
| ArcMatches(const Sequence &seqA_, const Sequence &seqB_, const std::string &arcmatch_scores_file, int probability_scale, size_type max_length_diff, size_type max_diff_at_am, const MatchController &trace_controller, const AnchorConstraints &constraints) | LocARNA::ArcMatches | |
| ArcMatches(const RnaData &rnadataA, const RnaData &rnadataB, double min_prob, size_type max_length_diff, size_type max_diff_at_am, const MatchController &trace_controller, const AnchorConstraints &constraints) | LocARNA::ArcMatches | |
| begin() const | LocARNA::ArcMatches | inline |
| bpsA | LocARNA::ArcMatches | protected |
| bpsB | LocARNA::ArcMatches | protected |
| common_left_end_list(size_type i, size_type j) const | LocARNA::ArcMatches | inline |
| common_left_end_lists | LocARNA::ArcMatches | protected |
| common_right_end_list(size_type i, size_type j) const | LocARNA::ArcMatches | inline |
| common_right_end_lists | LocARNA::ArcMatches | protected |
| const_iterator typedef | LocARNA::ArcMatches | |
| constraints | LocARNA::ArcMatches | protected |
| end() const | LocARNA::ArcMatches | inline |
| exists_inner_arc_match(const ArcMatch &am) const | LocARNA::ArcMatches | inline |
| explicit_scores() const | LocARNA::ArcMatches | inline |
| get_base_pairsA() const | LocARNA::ArcMatches | inline |
| get_base_pairsB() const | LocARNA::ArcMatches | inline |
| get_max_right_ends(size_type al, size_type bl, size_type *max_ar, size_type *max_br, bool no_lonely_pairs) const | LocARNA::ArcMatches | |
| get_min_right_ends(size_type al, size_type bl, size_type *min_ar, size_type *min_br) const | LocARNA::ArcMatches | |
| get_score(const ArcMatch &am) const | LocARNA::ArcMatches | inline |
| init_inner_arc_matchs() | LocARNA::ArcMatches | protected |
| inner_arc_match(const ArcMatch &am) const | LocARNA::ArcMatches | inline |
| inner_arcmatch_idxs | LocARNA::ArcMatches | protected |
| is_valid_arcmatch(const Arc &arcA, const Arc &arcB) const | LocARNA::ArcMatches | protected |
| lenA | LocARNA::ArcMatches | protected |
| lenB | LocARNA::ArcMatches | protected |
| maintain_explicit_scores | LocARNA::ArcMatches | protected |
| make_scores_explicit(const Scoring &scoring) | LocARNA::ArcMatches | |
| match_controller | LocARNA::ArcMatches | protected |
| max_diff_at_am | LocARNA::ArcMatches | protected |
| max_length_diff | LocARNA::ArcMatches | protected |
| num_arc_matches() const | LocARNA::ArcMatches | inline |
| number_of_arcmatches | LocARNA::ArcMatches | protected |
| read_arcmatch_scores(const std::string &arcmatch_scores_file, int probability_scale) | LocARNA::ArcMatches | |
| scores | LocARNA::ArcMatches | protected |
| size_type typedef | LocARNA::ArcMatches | |
| sort_right_adjacency_lists() | LocARNA::ArcMatches | |
| write_arcmatch_scores(const std::string &arcmatch_scores_file, const Scoring &scoring) const | LocARNA::ArcMatches | |
| ~ArcMatches() | LocARNA::ArcMatches | |
