LocARNA-1.9.2
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add(seqpos_t posA, seqpos_t posB, char c) | LocARNA::EPM | [inline] |
add_am(const Arc &a, const Arc &b) | LocARNA::EPM | [inline] |
am_begin() const | LocARNA::EPM | [inline] |
am_end() const | LocARNA::EPM | [inline] |
Arc typedef | LocARNA::EPM | |
ArcIdx typedef | LocARNA::EPM | |
begin() const | LocARNA::EPM | [inline] |
clear_am_to_do() | LocARNA::EPM | [inline] |
el_pat_vec typedef | LocARNA::EPM | |
end() const | LocARNA::EPM | [inline] |
EPM() | LocARNA::EPM | [inline] |
get_am(PairArcIdxVec::size_type idx) const | LocARNA::EPM | [inline] |
get_cur_pos() const | LocARNA::EPM | [inline] |
get_first_insertion() const | LocARNA::EPM | [inline] |
get_max_tol_left() const | LocARNA::EPM | [inline] |
get_score() const | LocARNA::EPM | [inline] |
get_state() const | LocARNA::EPM | [inline] |
includes(const EPM &epm_to_test) const | LocARNA::EPM | [inline] |
includes_am(const EPM &epm_to_test) const | LocARNA::EPM | [inline] |
insert_epm(const EPM &epm_to_insert) | LocARNA::EPM | [inline] |
is_invalid() const | LocARNA::EPM | [inline] |
last_matched_pos() | LocARNA::EPM | [inline] |
matpos_t typedef | LocARNA::EPM | |
next_arcmatch() | LocARNA::EPM | [inline] |
number_of_am() | LocARNA::EPM | [inline] |
overwrite(seqpos_t posA, seqpos_t posB, char c, pat_vec_t::size_type pos) | LocARNA::EPM | [inline] |
pair_seqpos_t typedef | LocARNA::EPM | |
PairArcIdx typedef | LocARNA::EPM | |
PairArcIdxVec typedef | LocARNA::EPM | |
pat_vec_at(pat_vec_t::size_type idx) const | LocARNA::EPM | [inline] |
pat_vec_size() const | LocARNA::EPM | [inline] |
pat_vec_t typedef | LocARNA::EPM | |
print_epm(std::ostream &out, bool verbose) const | LocARNA::EPM | [inline] |
seqpos_t typedef | LocARNA::EPM | |
set_cur_pos(const matpos_t &cur_pos_) | LocARNA::EPM | [inline] |
set_first_insertion(bool first_insertion_) | LocARNA::EPM | [inline] |
set_invalid() | LocARNA::EPM | [inline] |
set_max_tol_left(score_t tol) | LocARNA::EPM | [inline] |
set_score(score_t score_) | LocARNA::EPM | [inline] |
set_state(int state_) | LocARNA::EPM | [inline] |
sort_am_to_do() | LocARNA::EPM | [inline] |
sort_patVec() | LocARNA::EPM | [inline] |
store_am(const Arc &a, const Arc &b) | LocARNA::EPM | [inline] |
~EPM() | LocARNA::EPM | [inline, virtual] |