LocARNA::ArcMatchesIndexed Member List

This is the complete list of members for LocARNA::ArcMatchesIndexed, including all inherited members.

am_index(const size_type &arcAIdx, const size_type &arcBIdx) const	LocARNA::ArcMatchesIndexed	[inline]
am_index(const Arc &arcA, const Arc &arcB) const	LocARNA::ArcMatchesIndexed	[inline]
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
ArcMatchesIndexed(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::ArcMatchesIndexed	[inline]
ArcMatchesIndexed(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::ArcMatchesIndexed	[inline]
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]
invalid_am_index() const	LocARNA::ArcMatchesIndexed	[inline]
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