| align() | LocARNA::AlignerImpl | |
| align_D() | LocARNA::AlignerImpl | |
| align_in_arcmatch(pos_type al, pos_type ar, pos_type bl, pos_type br, bool allow_exclusion) | LocARNA::AlignerImpl | |
| align_noex(int state, pos_type al, pos_type bl, pos_type i, pos_type j, const ScoringView *sv) | LocARNA::AlignerImpl | |
| align_top_level_free_endgaps(const ScoringView *s) | LocARNA::AlignerImpl | |
| align_top_level_locally(const ScoringView *sv) | LocARNA::AlignerImpl | |
| AlignerImpl(const AlignerImpl &a) | LocARNA::AlignerImpl | |
| AlignerImpl(const Sequence &seqA, const Sequence &seqB, const AlignerParams *ap, const Scoring *s) | LocARNA::AlignerImpl | |
| alignment_ | LocARNA::AlignerImpl | |
| Arc typedef | LocARNA::AlignerImpl | |
| arc_matches_ | LocARNA::AlignerImpl | |
| bpsA_ | LocARNA::AlignerImpl | |
| bpsB_ | LocARNA::AlignerImpl | |
| D(const ArcMatch &am) | LocARNA::AlignerImpl | inline |
| D(const Arc &arcA, const Arc &arcB) | LocARNA::AlignerImpl | inline |
| D_created_ | LocARNA::AlignerImpl | |
| def_scoring_view_ | LocARNA::AlignerImpl | |
| Dmat_ | LocARNA::AlignerImpl | |
| E_NO_NO enum value (defined in LocARNA::AlignerImpl) | LocARNA::AlignerImpl | |
| E_NO_OP enum value (defined in LocARNA::AlignerImpl) | LocARNA::AlignerImpl | |
| E_NO_X enum value (defined in LocARNA::AlignerImpl) | LocARNA::AlignerImpl | |
| E_OP_NO enum value (defined in LocARNA::AlignerImpl) | LocARNA::AlignerImpl | |
| E_OP_X enum value (defined in LocARNA::AlignerImpl) | LocARNA::AlignerImpl | |
| E_X_NO enum value (defined in LocARNA::AlignerImpl) | LocARNA::AlignerImpl | |
| E_X_OP enum value (defined in LocARNA::AlignerImpl) | LocARNA::AlignerImpl | |
| E_X_X enum value (defined in LocARNA::AlignerImpl) | LocARNA::AlignerImpl | |
| Es_ | LocARNA::AlignerImpl | |
| fill_D_entries(pos_type al, pos_type bl) | LocARNA::AlignerImpl | |
| fill_D_entries_noLP(pos_type al, pos_type bl) | LocARNA::AlignerImpl | |
| Fs_ | LocARNA::AlignerImpl | |
| init_state(int state, pos_type al, pos_type ar, pos_type bl, pos_type br, bool globalA, bool exclA, bool globalB, bool exclB, const ScoringView *sv) | LocARNA::AlignerImpl | |
| M_matrix_t typedef | LocARNA::AlignerImpl | |
| max_i_ | LocARNA::AlignerImpl | |
| max_j_ | LocARNA::AlignerImpl | |
| min_i_ | LocARNA::AlignerImpl | |
| min_j_ | LocARNA::AlignerImpl | |
| Ms_ | LocARNA::AlignerImpl | |
| normalized_align(score_t L, bool verbose) | LocARNA::AlignerImpl | |
| params_ | LocARNA::AlignerImpl | |
| penalized_align(score_t position_penalty) | LocARNA::AlignerImpl | |
| r_ | LocARNA::AlignerImpl | |
| scoring_ | LocARNA::AlignerImpl | |
| seqA_ | LocARNA::AlignerImpl | |
| seqB_ | LocARNA::AlignerImpl | |
| trace(const ScoringView *sv) | LocARNA::AlignerImpl | |
| trace_arcmatch(const ArcMatch &am) | LocARNA::AlignerImpl | |
| trace_arcmatch_noLP(const ArcMatch &am) | LocARNA::AlignerImpl | |
| trace_in_arcmatch(int state, int al, int i, int bl, int j, bool top_level, const ScoringView *sv) | LocARNA::AlignerImpl | |
| trace_noex(int state, pos_type al, pos_type i, pos_type bl, pos_type j, bool top_level, const ScoringView *sv) | LocARNA::AlignerImpl | |
| ~AlignerImpl() | LocARNA::AlignerImpl | |
