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 | |