| /dports/biology/viennarna/ViennaRNA-2.4.18/src/bin/ |
| H A D | RNALfold.c | 38 int dangle_model; member
391 data.dangle_model = md.dangles; in main()
475 int dangle_model = ((hit_data *)data)->dangle_model; in default_callback() local
479 if ((dangle_model == 2) && (start > 1)) { in default_callback()
503 int dangle_model = ((hit_data *)data)->dangle_model; in default_callback_z() local
507 if ((dangle_model == 2) && (start > 1)) { in default_callback_z()
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| H A D | RNALalifold.c | 58 int dangle_model; member
474 data.dangle_model = md.dangles; in main()
584 int columns, dangle_model; in print_hit_cb() local
601 dangle_model = ((hit_data *)data)->dangle_model; in print_hit_cb()
604 if ((dangle_model == 2) && (start > 1)) { in print_hit_cb()
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| /dports/biology/viennarna/ViennaRNA-2.4.18/src/ViennaRNA/ |
| H A D | zscore.c | 162 int info_avg, start, end, dangle_model, length; in get_zscore() local
170 dangle_model = fc->params->model_details.dangles; in get_zscore()
174 start = (dangle_model) ? MAX2(1, i - 1) : i; in get_zscore()
175 end = (dangle_model) ? MIN2(length, j + 1) : j; in get_zscore()
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| H A D | mfe_window.c | 57 int dangle_model; member
621 dangle_model = md->dangles; in fill_arrays()
887 dangle_model = md->dangles; in backtrack()
1218 int dangle_model = ((hit_data *)data)->dangle_model; in default_callback() local
1220 if ((dangle_model == 2) && (start > 1)) in default_callback()
1237 int dangle_model = ((hit_data *)data)->dangle_model; in default_callback_z() local
1239 if ((dangle_model == 2) && (start > 1)) in default_callback_z()
1257 int dangle_model = ((hit_data *)data)->dangle_model; in default_callback_comparative() local
1261 if ((dangle_model == 2) && (start > 1)) in default_callback_comparative()
1266 if ((dangle_model == 2) && (start > 1)) in default_callback_comparative()
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| H A D | subopt.c | 972 if (logML || (dangle_model == 1) || (dangle_model == 3)) /* recalc energy */ in vrna_subopt_cb()
1026 register int dangle_model; in scan_interval() local
1051 dangle_model = md->dangles; in scan_interval()
1141 switch (dangle_model) { in scan_interval()
1390 switch (dangle_model) { in scan_interval()
1437 switch (dangle_model) { in scan_interval()
1734 switch (dangle_model) { in scan_interval()
1839 switch (dangle_model) { in scan_interval()
1990 dangle_model = md->dangles; in repeat()
2133 switch (dangle_model) { in repeat()
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| H A D | eval.c | 1147 int energy, mm5, mm3, bonus, p, q, q_prev, length, dangle_model, n_seq, ss, u, in energy_of_extLoop_pt() local
1166 dangle_model = md->dangles; in energy_of_extLoop_pt()
1182 if (dangle_model % 2 == 1) { in energy_of_extLoop_pt()
1236 switch (dangle_model) { in energy_of_extLoop_pt()
1278 switch (dangle_model) { in energy_of_extLoop_pt()
1338 if (dangle_model % 2 == 1) in energy_of_extLoop_pt()
1387 dangle_model = md->dangles; in energy_of_ml_pt()
1423 if ((dangle_model % 2) || (dangle_model > 2) || (dangle_model < 0)) { in energy_of_ml_pt()
1490 switch (dangle_model) { in energy_of_ml_pt()
1964 int dangle_model = md->dangles; in en_corr_of_loop_gquad_ali() local
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| H A D | cofold.c | 204 int dangle_model, noGUclosure, noLP, hc_decompose, turn; in fill_arrays() local
215 dangle_model = P->model_details.dangles; in fill_arrays()
285 if (dangle_model == 3) { in fill_arrays()
593 int inc, type, energy, en, length, j, left, right, dangle_model, with_gquad, *indx, in free_end() local
604 dangle_model = P->model_details.dangles; in free_end()
670 switch (dangle_model) { in free_end()
728 if (dangle_model % 2 == 1) { in free_end()
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| H A D | mfe.c | 377 dangle_model, turn, s, n_seq; in postprocess_circular() local
397 dangle_model = md->dangles; in postprocess_circular()
642 if ((dangle_model == 1) || (dangle_model == 3)) { in postprocess_circular()
1737 int e, new_c, energy, stackEnergy, ij, dangle_model, noLP, in decompose_pair() local
1742 dangle_model = fc->params->model_details.dangles; in decompose_pair()
1763 if (dangle_model == 3) { in decompose_pair()
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| H A D | gquad.h | 787 int mm, dangle_model, k, l, maxl, minl, c0, l1, ss, tt, eee, u1, u2; in backtrack_GQuad_IntLoop_L_comparative() local
789 dangle_model = P->model_details.dangles; in backtrack_GQuad_IntLoop_L_comparative()
795 if (dangle_model == 2) in backtrack_GQuad_IntLoop_L_comparative()
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| /dports/biology/viennarna/ViennaRNA-2.4.18/src/ViennaRNA/loops/ |
| H A D | external_bt.c | 199 dangle_model = md->dangles; in BT_ext_loop_f5()
306 switch (dangle_model) { in BT_ext_loop_f5()
585 dangle_model = md->dangles; in BT_ext_loop_f5_comparative()
625 switch (dangle_model) { in BT_ext_loop_f5_comparative()
736 dangle_model = md->dangles; in BT_ext_loop_f3()
775 switch (dangle_model) { in BT_ext_loop_f3()
1047 dangle_model = md->dangles; in BT_ext_loop_f3_comparative()
1089 switch (dangle_model) { in BT_ext_loop_f3_comparative()
1193 dangle_model = md->dangles; in BT_ext_loop_f3_pp()
1225 switch (dangle_model) { in BT_ext_loop_f3_pp()
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| H A D | multibranch.c | 570 dangle_model = md->dangles; in E_mb_loop_fake()
596 switch (dangle_model) { in E_mb_loop_fake()
612 if (dangle_model % 2) { in E_mb_loop_fake()
666 dangle_model = md->dangles; in E_mb_loop_fast()
683 switch (dangle_model) { in E_mb_loop_fast()
935 dangle_model = md->dangles; in extend_fm_3p()
956 if (dangle_model == 2) in extend_fm_3p()
964 if (dangle_model == 2) { in extend_fm_3p()
1086 dangle_model = md->dangles; in E_ml_stems_fast()
1150 if (dangle_model % 2) { in E_ml_stems_fast()
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| H A D | multibranch_bt.c | 114 *idx, with_gquad, dangle_model, turn, type; in vrna_BT_mb_loop_fake() local
135 dangle_model = md->dangles; in vrna_BT_mb_loop_fake()
171 switch (dangle_model) { in vrna_BT_mb_loop_fake()
333 switch (dangle_model) { in vrna_BT_mb_loop_fake()
549 dangle_model = md->dangles; in BT_mb_loop_split()
732 switch (dangle_model) { in BT_mb_loop_split()
955 if (dangle_model == 3) { in BT_mb_loop_split()
1061 dangle_model = md->dangles; in BT_mb_loop()
1085 switch (dangle_model) { in BT_mb_loop()
1364 if (dangle_model == 3) { in BT_mb_loop()
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| H A D | external.c | 229 int en, j, length, *f5, dangle_model, with_gquad, turn; in vrna_E_ext_loop_5() local
239 dangle_model = P->model_details.dangles; in vrna_E_ext_loop_5()
262 switch (dangle_model) { in vrna_E_ext_loop_5()
340 int e, en, dangle_model, with_gquad; in vrna_E_ext_loop_3() local
351 dangle_model = md->dangles; in vrna_E_ext_loop_3()
361 switch (dangle_model) { in vrna_E_ext_loop_3()
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