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LocARNA-2.0.0
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This is the complete list of members for LocARNA::AlignerN, including all inherited members.
| align() | LocARNA::AlignerN | |
| align_D() | LocARNA::AlignerN | protected |
| AlignerN(const AlignerN &a) | LocARNA::AlignerN | |
| AlignerN(const AlignerNParams &ap) | LocARNA::AlignerN | |
| alignment | LocARNA::AlignerN | protected |
| Arc typedef | LocARNA::AlignerN | |
| arc_matches | LocARNA::AlignerN | protected |
| ArcIdx typedef | LocARNA::AlignerN | |
| ArcIdxVec typedef | LocARNA::AlignerN | |
| bpsA | LocARNA::AlignerN | protected |
| bpsB | LocARNA::AlignerN | protected |
| compute_E_entry(index_t al, matidx_t i_index, matidx_t j_index, seq_pos_t i_seq_pos, seq_pos_t i_prev_seq_pos, ScoringView sv) | LocARNA::AlignerN | protected |
| compute_F_entry(index_t bl, matidx_t i_index, matidx_t j_index, seq_pos_t i_seq_pos, seq_pos_t i_prev_seq_pos, ScoringView sv) | LocARNA::AlignerN | protected |
| compute_IX(pos_type xl, const Arc &arcY, pos_type i, ScoringView sv) | LocARNA::AlignerN | protected |
| compute_M_entry(index_t al, index_t bl, matidx_t index_i, matidx_t index_j, ScoringView sv) | LocARNA::AlignerN | protected |
| D(const ArcMatch &am) | LocARNA::AlignerN | inlineprotected |
| D(const Arc &arcX, const Arc &arcY) | LocARNA::AlignerN | inlineprotected |
| D(const Arc &arcA, const Arc &arcB) | LocARNA::AlignerN | inlineprotected |
| D_created | LocARNA::AlignerN | protected |
| def_scoring_view | LocARNA::AlignerN | protected |
| Dmat | LocARNA::AlignerN | protected |
| Emat | LocARNA::AlignerN | protected |
| fill_D_entries(pos_type al, pos_type bl) | LocARNA::AlignerN | protected |
| fill_IA_entries(pos_type al, Arc arcB, pos_type max_ar) | LocARNA::AlignerN | protected |
| fill_IB_entries(Arc arcA, pos_type bl, pos_type max_br) | LocARNA::AlignerN | protected |
| fill_M_entries(pos_type al, pos_type ar, pos_type bl, pos_type br) | LocARNA::AlignerN | protected |
| Fmat | LocARNA::AlignerN | protected |
| gapCostMatA | LocARNA::AlignerN | protected |
| gapCostMatB | LocARNA::AlignerN | protected |
| get_alignment() const | LocARNA::AlignerN | inline |
| getGapCostBetween(pos_type leftSide, pos_type rightSide) | LocARNA::AlignerN | inlineprotected |
| IA(const pos_type i, const Arc &b) | LocARNA::AlignerN | inlineprotected |
| IADmat | LocARNA::AlignerN | protected |
| IAmat | LocARNA::AlignerN | protected |
| IB(const Arc &a, const pos_type k) | LocARNA::AlignerN | inlineprotected |
| IBDmat | LocARNA::AlignerN | protected |
| IBmat | LocARNA::AlignerN | protected |
| index_t typedef | LocARNA::AlignerN | |
| init_M_E_F(pos_type al, pos_type ar, pos_type bl, pos_type br, ScoringView sv) | LocARNA::AlignerN | protected |
| initGapCostMat(ScoringView sv) | LocARNA::AlignerN | protected |
| IX(const pos_type i, const Arc &arc) | LocARNA::AlignerN | inlineprotected |
| IXD(const Arc &arc1, const Arc &arc2) | LocARNA::AlignerN | inlineprotected |
| M | LocARNA::AlignerN | protected |
| M_matrix_t typedef | LocARNA::AlignerN | |
| mapperA | LocARNA::AlignerN | protected |
| mapperB | LocARNA::AlignerN | protected |
| matidx_t typedef | LocARNA::AlignerN | |
| max_i | LocARNA::AlignerN | protected |
| max_j | LocARNA::AlignerN | protected |
| min_i | LocARNA::AlignerN | protected |
| min_j | LocARNA::AlignerN | protected |
| mod_scoring | LocARNA::AlignerN | protected |
| mod_scoring_view | LocARNA::AlignerN | protected |
| params | LocARNA::AlignerN | protected |
| r | LocARNA::AlignerN | protected |
| scoring | LocARNA::AlignerN | protected |
| seq_pos_t typedef | LocARNA::AlignerN | |
| seqA | LocARNA::AlignerN | protected |
| seqB | LocARNA::AlignerN | protected |
| trace(ScoringView sv) | LocARNA::AlignerN | protected |
| trace() | LocARNA::AlignerN | |
| trace_D(const Arc &arcA, const Arc &arcB, ScoringView sv) | LocARNA::AlignerN | protected |
| trace_E(pos_type al, matidx_t i_index, pos_type bl, matidx_t j_index, bool top_level, ScoringView sv) | LocARNA::AlignerN | protected |
| trace_F(pos_type al, matidx_t i_index, pos_type bl, matidx_t j_index, bool top_level, ScoringView sv) | LocARNA::AlignerN | protected |
| trace_IX(pos_type xl, pos_type i, const Arc &arcY, ScoringView sv) | LocARNA::AlignerN | protected |
| trace_IXD(const Arc &arcA, const Arc &arcB, ScoringView sv) | LocARNA::AlignerN | protected |
| trace_M(pos_type al, matidx_t i_index, pos_type bl, matidx_t j_index, bool tl, ScoringView sv) | LocARNA::AlignerN | protected |
| trace_M_noex(pos_type al, pos_type i, pos_type bl, pos_type j, bool top_level, ScoringView sv) | LocARNA::AlignerN | protected |
| ~AlignerN() | LocARNA::AlignerN |
1.9.1