LocARNA-1.9.2
LocARNA::ArcMatches Member List
This is the complete list of members for LocARNA::ArcMatches, including all inherited members.
Arc typedefLocARNA::ArcMatches
arc_matches_vecLocARNA::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]
bpsALocARNA::ArcMatches [protected]
bpsBLocARNA::ArcMatches [protected]
common_left_end_list(size_type i, size_type j) const LocARNA::ArcMatches [inline]
common_left_end_listsLocARNA::ArcMatches [protected]
common_right_end_list(size_type i, size_type j) const LocARNA::ArcMatches [inline]
common_right_end_listsLocARNA::ArcMatches [protected]
const_iterator typedefLocARNA::ArcMatches
constraintsLocARNA::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_idxsLocARNA::ArcMatches [protected]
is_valid_arcmatch(const Arc &arcA, const Arc &arcB) const LocARNA::ArcMatches [protected]
lenALocARNA::ArcMatches [protected]
lenBLocARNA::ArcMatches [protected]
maintain_explicit_scoresLocARNA::ArcMatches [protected]
make_scores_explicit(const Scoring &scoring)LocARNA::ArcMatches
match_controllerLocARNA::ArcMatches [protected]
max_diff_at_amLocARNA::ArcMatches [protected]
max_length_diffLocARNA::ArcMatches [protected]
num_arc_matches() const LocARNA::ArcMatches [inline]
number_of_arcmatchesLocARNA::ArcMatches [protected]
read_arcmatch_scores(const std::string &arcmatch_scores_file, int probability_scale)LocARNA::ArcMatches
scoresLocARNA::ArcMatches [protected]
size_type typedefLocARNA::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
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