| align_D() | LocARNA::AlignerP< T > | protected |
| align_Dprime() | LocARNA::AlignerP< T > | protected |
| align_inside() | LocARNA::AlignerP< T > | |
| align_inside_arcmatch(size_type al, size_type ar, size_type bl, size_type br) | LocARNA::AlignerP< T > | protected |
| align_outside() | LocARNA::AlignerP< T > | |
| align_outside_arcmatch(size_type al, size_type ar, size_type max_ar, size_type bl, size_type br, size_type max_br) | LocARNA::AlignerP< T > | protected |
| align_reverse(size_type al, size_type ar, size_type bl, size_type br, bool copy=false) | LocARNA::AlignerP< T > | protected |
| AlignerP(const AlignerPParams< T > &ap) | LocARNA::AlignerP< T > | |
| AlignerP(const AlignerP &p) | LocARNA::AlignerP< T > | |
| alloc_inside_matrices() | LocARNA::AlignerP< T > | protected |
| alloc_outside_matrices() | LocARNA::AlignerP< T > | protected |
| am_prob | LocARNA::AlignerP< T > | protected |
| Arc typedef | LocARNA::AlignerP< T > | |
| arc_matches | LocARNA::AlignerP< T > | protected |
| bm_prob | LocARNA::AlignerP< T > | protected |
| bpsA | LocARNA::AlignerP< T > | protected |
| bpsB | LocARNA::AlignerP< T > | protected |
| comp_E_entry(size_type al, size_type bl, size_type i, size_type j) | LocARNA::AlignerP< T > | protected |
| comp_Eprime_entry(size_type al, size_type bl, size_type i, size_type j) | LocARNA::AlignerP< T > | protected |
| comp_Erev_entry(size_type i, size_type j) | LocARNA::AlignerP< T > | protected |
| comp_F_entry(size_type al, size_type bl, size_type i, size_type j) | LocARNA::AlignerP< T > | protected |
| comp_Fprime_entry(size_type al, size_type bl, size_type i, size_type j) | LocARNA::AlignerP< T > | protected |
| comp_Frev_entry(size_type i, size_type j) | LocARNA::AlignerP< T > | protected |
| comp_M_entry(size_type al, size_type bl, size_type i, size_type j) | LocARNA::AlignerP< T > | protected |
| comp_Mprime_entry(size_type al, size_type bl, size_type i, size_type j, size_type max_ar, size_type max_br) | LocARNA::AlignerP< T > | protected |
| comp_Mrev_entry(size_type i, size_type j, size_type ar, size_type br) | LocARNA::AlignerP< T > | protected |
| compute_arcmatch_probabilities() | LocARNA::AlignerP< T > | |
| compute_basematch_probabilities(bool basematch_probs_include_arcmatch) | LocARNA::AlignerP< T > | |
| compute_fragment_match_prob(size_type i, size_type j, size_type k, size_type l) | LocARNA::AlignerP< T > | |
| create() | LocARNA::AlignerP< T > | inlinestatic |
| D(const ArcMatch &am) | LocARNA::AlignerP< T > | protected |
| D(const Arc &arcA, const Arc &arcB) | LocARNA::AlignerP< T > | protected |
| D_created | LocARNA::AlignerP< T > | protected |
| Dmat | LocARNA::AlignerP< T > | protected |
| Dmatprime | LocARNA::AlignerP< T > | protected |
| Dprime(const ArcMatch &am) | LocARNA::AlignerP< T > | protected |
| Dprime(const Arc &arcA, const Arc &arcB) | LocARNA::AlignerP< T > | protected |
| Dprime_created | LocARNA::AlignerP< T > | protected |
| E | LocARNA::AlignerP< T > | protected |
| Eprime | LocARNA::AlignerP< T > | protected |
| Erev | LocARNA::AlignerP< T > | protected |
| Erev_mat | LocARNA::AlignerP< T > | protected |
| F | LocARNA::AlignerP< T > | protected |
| fill_D(size_type al, size_type bl, size_type max_ar, size_type max_br) | LocARNA::AlignerP< T > | protected |
| fill_Dprime(size_type al, size_type bl, size_type min_ar, size_type min_br, size_type max_ar, size_type max_br) | LocARNA::AlignerP< T > | protected |
| Fprime | LocARNA::AlignerP< T > | protected |
| freeD() | LocARNA::AlignerP< T > | inline |
| freeMprime() | LocARNA::AlignerP< T > | inline |
| Frev | LocARNA::AlignerP< T > | protected |
| Frev_mat | LocARNA::AlignerP< T > | protected |
| init_E(size_type al, size_type ar, size_type bl, size_type br) | LocARNA::AlignerP< T > | protected |
| init_Erev(size_type al, size_type ar, size_type bl, size_type br) | LocARNA::AlignerP< T > | protected |
| init_M(size_type al, size_type ar, size_type bl, size_type br) | LocARNA::AlignerP< T > | protected |
| init_Mrev(size_type al, size_type ar, size_type bl, size_type br) | LocARNA::AlignerP< T > | protected |
| leftmost_covering_arc(size_type s, const BasePairs &bps, size_type l, size_type r) const | LocARNA::AlignerP< T > | protected |
| leftmost_covering_arcmatch(size_type al, size_type bl, size_type ar, size_type br) const | LocARNA::AlignerP< T > | protected |
| M | LocARNA::AlignerP< T > | protected |
| Mprime | LocARNA::AlignerP< T > | protected |
| Mrev | LocARNA::AlignerP< T > | protected |
| params | LocARNA::AlignerP< T > | protected |
| partFunc | LocARNA::AlignerP< T > | protected |
| pf_scale | LocARNA::AlignerP< T > | protected |
| pf_score_t typedef (defined in LocARNA::AlignerP< T >) | LocARNA::AlignerP< T > | |
| PFScoreMatrix typedef (defined in LocARNA::AlignerP< T >) | LocARNA::AlignerP< T > | |
| PFScoreVector typedef (defined in LocARNA::AlignerP< T >) | LocARNA::AlignerP< T > | |
| r | LocARNA::AlignerP< T > | protected |
| rightmost_covering_arc(const BasePairs &bps, size_type l, size_type r, size_type s) const | LocARNA::AlignerP< T > | protected |
| rightmost_covering_arcmatch(size_type al, size_type bl, size_type ar, size_type br) const | LocARNA::AlignerP< T > | protected |
| scoring | LocARNA::AlignerP< T > | protected |
| seqA | LocARNA::AlignerP< T > | protected |
| seqB | LocARNA::AlignerP< T > | protected |
| size_pair typedef | LocARNA::AlignerP< T > | |
| size_type typedef | LocARNA::AlignerP< T > | |
| SparsePFScoreMatrix typedef | LocARNA::AlignerP< T > | |
| virtual_Mprime(size_type al, size_type bl, size_type i, size_type j, size_type max_ar, size_type max_br) const | LocARNA::AlignerP< T > | |
| write_arcmatch_probabilities(std::ostream &out) | LocARNA::AlignerP< T > | |
| write_basematch_probabilities(std::ostream &out) | LocARNA::AlignerP< T > | |
| ~AlignerP() | LocARNA::AlignerP< T > | |
