/dports/biology/viennarna/ViennaRNA-2.4.18/src/ViennaRNA/ |
H A D | alipfold.c | 98 int i, n_seq; in wrap_alipf_fold() local 106 for (n_seq = 0; sequences[n_seq]; n_seq++) ; /* count the sequences */ in wrap_alipf_fold() 136 vc->exp_params = vrna_exp_params_comparative(n_seq, &(vc->params->model_details)); in wrap_alipf_fold() 155 for (n_seq = 0; n_seq < backward_compat_compound->n_seq; n_seq++) in wrap_alipf_fold() 156 free(backward_compat_a2s[n_seq]); in wrap_alipf_fold() 165 backward_compat_a2s = (unsigned short **)vrna_alloc(sizeof(unsigned short *) * (vc->n_seq + 1)); in wrap_alipf_fold() 166 for (n_seq = 0; n_seq < vc->n_seq; n_seq++) { in wrap_alipf_fold() 167 backward_compat_a2s[n_seq] = in wrap_alipf_fold() 170 backward_compat_a2s[n_seq][i] = (unsigned short)vc->a2s[n_seq][i]; in wrap_alipf_fold() 258 int n_seq = backward_compat_compound->n_seq; in alipbacktrack() local [all …]
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H A D | ali_plex.c | 208 n_seq = s; in aliduplexfold() 340 n_seq = s; in alibacktrack() 471 n_seq = s; in aliLduplexfold() 838 for (n_seq = 0; s1[n_seq] != NULL; n_seq++); in alifind_max() 930 int n_seq; in aliplot_max() local 932 for (n_seq = 0; !(s1[n_seq] == NULL); n_seq++); in aliplot_max() 956 s3[n_seq] = s4[n_seq] = NULL; in aliplot_max() 1000 n_seq = s; in aliduplexfold_XS() 1179 n_seq = s; in alibacktrack_XS() 1684 for (n_seq = 0; s1[n_seq] != NULL; n_seq++); in alifind_max_XS() [all …]
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H A D | duplex.c | 103 int n_seq); 414 n_seq = s; in aliduplexfold_cu() 416 if (n_seq != s) in aliduplexfold_cu() 434 for (s = 0; s < n_seq; s++) { in aliduplexfold_cu() 519 for (s = 0; s < n_seq; s++) { in aliduplexfold_cu() 548 n_seq = s; in aliduplex_subopt() 652 n_seq = s; in alibacktrack() 654 if (n_seq != s) in alibacktrack() 744 int n_seq) in covscore() argument 764 for (s = 0; s < n_seq; s++) in covscore() [all …]
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H A D | sequence.c | 158 msa->n_seq = s; in vrna_msa_add() 168 for (s = 0; s < msa->n_seq; s++) { in vrna_msa_add() 175 if (num_names != msa->n_seq) { in vrna_msa_add() 179 msa->n_seq, in vrna_msa_add() 194 for (s = 0; s < msa->n_seq; s++) { in vrna_msa_add() 201 if (s != msa->n_seq) { in vrna_msa_add() 205 msa->n_seq, in vrna_msa_add() 216 for (s = 0; s < msa->n_seq; s++) { in vrna_msa_add() 223 if (s != msa->n_seq) { in vrna_msa_add() 245 if (s != msa->n_seq) { in vrna_msa_add() [all …]
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H A D | fold_compound.c | 304 n_seq = s; in vrna_fold_compound_comparative2() 317 for (s = 0; s < n_seq; s++) in vrna_fold_compound_comparative2() 327 fc->n_seq = n_seq; in vrna_fold_compound_comparative2() 695 fc->S5[fc->n_seq] = NULL; in set_fold_compound() 696 fc->S3[fc->n_seq] = NULL; in set_fold_compound() 697 fc->a2s[fc->n_seq] = NULL; in set_fold_compound() 698 fc->Ss[fc->n_seq] = NULL; in set_fold_compound() 699 fc->S[fc->n_seq] = NULL; in set_fold_compound() 739 int n_seq = fc->n_seq; in make_pscores() local 776 for (s = 0; s < n_seq; s++) { in make_pscores() [all …]
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H A D | eval.c | 457 unsigned int s, n_seq, **a2s; in eval_ext_int_loop() local 488 n_seq = vc->n_seq; in eval_ext_int_loop() 493 n_seq = vc->n_seq; in eval_ext_int_loop() 639 unsigned int s, n_seq; in eval_circ_pt() local 686 n_seq = vc->n_seq; in eval_circ_pt() 1174 n_seq = (vc->type == VRNA_FC_TYPE_SINGLE) ? 1 : vc->n_seq; in energy_of_extLoop_pt() 1397 n_seq = (vc->type == VRNA_FC_TYPE_SINGLE) ? 1 : vc->n_seq; in energy_of_ml_pt() 1881 energy += P->MLclosing * n_seq; in energy_of_ml_pt() 1963 int n_seq = vc->n_seq; in en_corr_of_loop_gquad_ali() local 2166 e_plus += n_seq * e_temp; in en_corr_of_loop_gquad_ali() [all …]
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H A D | gquad.c | 57 int n_seq; member 451 gq_help.n_seq = n_seq; in exp_E_gquad_ali() 600 gq_help.n_seq = n_seq; in get_gquad_pf_matrix_comparative() 638 gq_help.n_seq = n_seq; in get_gquad_ali_matrix() 685 vc->n_seq, in vrna_gquad_mx_local_update() 788 gq_help.n_seq = n_seq; in create_aliL_matrix() 937 gq_help.n_seq = n_seq; in get_gquad_pattern_mfe_ali() 1021 gq_help.n_seq = fc->n_seq; in vrna_get_gquad_pattern_pf() 1172 gq_help.n_seq = fc->n_seq; in vrna_get_plist_gquad_from_pr_max() 1576 n_seq = gq_help->n_seq; in gquad_pf_ali() [all …]
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H A D | snofold.c | 556 n_seq = s; in alisnofold() 558 for (s = 0; s < n_seq; s++) { in alisnofold() 567 for (s = 0; s < n_seq; s++) in alisnofold() 589 int bonus, n_seq, s; in alifill_arrays() local 592 for (n_seq = 0; strings[n_seq] != NULL; n_seq++) ; in alifill_arrays() 736 int bonus, n_seq, *type; in alibacktrack() local 740 for (n_seq = 0; strings[n_seq] != NULL; n_seq++) ; in alibacktrack() 1241 int n_seq, s, length; in alisnobacktrack_fold_from_pair() local 1245 n_seq = s; in alisnobacktrack_fold_from_pair() 1252 for (s = 0; s < n_seq; s++) { in alisnobacktrack_fold_from_pair() [all …]
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H A D | gquad.h | 45 unsigned int n_seq, 265 int l[3], L, a, n_seq; in vrna_BT_gquad_mfe() local 279 n_seq = vc->n_seq; in vrna_BT_gquad_mfe() 544 for (ss = 0; ss < n_seq; ss++) { in backtrack_GQuad_IntLoop_comparative() 792 for (ss = 0; ss < n_seq; ss++) { in backtrack_GQuad_IntLoop_L_comparative() 1078 for (s = 0; s < n_seq; s++) { in E_GQuad_IntLoop_comparative() 1139 for (s = 0; s < n_seq; s++) { in E_GQuad_IntLoop_comparative() 1166 for (s = 0; s < n_seq; s++) { in E_GQuad_IntLoop_comparative() 1201 for (s = 0; s < n_seq; s++) { in E_GQuad_IntLoop_L_comparative() 1262 for (s = 0; s < n_seq; s++) { in E_GQuad_IntLoop_L_comparative() [all …]
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/dports/biology/viennarna/ViennaRNA-2.4.18/tests/perl5/ |
H A D | test-RNA-file-formats.pl | 16 my $n_seq; 52 ($n_seq, $sequence_identifiers, $alignment, $alignment_id, $consensus_structure) = RNA::file_msa_re… 56 ok($n_seq == 712); 70 while ( (($n_seq, $sequence_identifiers, $alignment, $alignment_id, $consensus_structure) = RNA::fi… 73 next if $n_seq == 0; 88 ok($n_seq == 2); 101 ok($n_seq == 2); 110 ($n_seq, $sequence_identifiers, $alignment, $alignment_id, $consensus_structure) = RNA::file_msa_re… 114 ok($n_seq == 5); 126 …($n_seq, $sequence_identifiers, $alignment, $alignment_id, $consensus_structure) = RNA::file_msa_r… [all …]
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/dports/biology/viennarna/ViennaRNA-2.4.18/src/ViennaRNA/utils/ |
H A D | msa_utils.c | 71 n_seq = s; in vrna_aln_mpi() 129 int n_seq = vc->n_seq; in vrna_aln_pinfo() local 228 n_seq = s; in vrna_aln_pscore() 355 for (n_seq = 0; alignment[n_seq] != NULL; n_seq++); in vrna_aln_slice() 377 int n_seq; in vrna_aln_free() local 380 for (n_seq = 0; alignment[n_seq] != NULL; n_seq++) in vrna_aln_free() 444 n_seq = s; in vrna_aln_conservation_struct() 503 n_seq = s; in vrna_aln_conservation_col() 573 n_seq = s; in vrna_aln_consensus_sequence() 644 n_seq = s; in vrna_aln_consensus_mis() [all …]
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/dports/biology/viennarna/ViennaRNA-2.4.18/tests/python/ |
H A D | test-RNA-file-formats.py | 45 n_seq, sequence_identifiers, alignment, alignment_id, consensus_structure = \ 51 self.assertTrue(n_seq == 712) 64 n_seq, sequence_identifiers, alignment, alignment_id, consensus_structure = \ 70 self.assertTrue(n_seq == 2) 80 n_seq, sequence_identifiers, alignment, alignment_id, consensus_structure = \ 86 self.assertTrue(n_seq == 2) 102 self.assertTrue(n_seq == 5) 119 if n_seq == -1: 123 if n_seq == 0: 143 if n_seq == -1: [all …]
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/dports/biology/viennarna/ViennaRNA-2.4.18/tests/python3/ |
H A D | test-RNA-file-formats.py3 | 45 n_seq, sequence_identifiers, alignment, alignment_id, consensus_structure = \ 51 self.assertTrue(n_seq == 712) 64 n_seq, sequence_identifiers, alignment, alignment_id, consensus_structure = \ 70 self.assertTrue(n_seq == 2) 80 n_seq, sequence_identifiers, alignment, alignment_id, consensus_structure = \ 86 self.assertTrue(n_seq == 2) 102 self.assertTrue(n_seq == 5) 119 if n_seq == -1: 123 if n_seq == 0: 143 if n_seq == -1: [all …]
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/dports/biology/viennarna/ViennaRNA-2.4.18/src/ViennaRNA/loops/ |
H A D | multibranch.c | 231 n_seq = fc->n_seq; in ml_pair_d0() 325 n_seq = fc->n_seq; in ml_pair_d2() 391 n_seq = fc->n_seq; in ml_pair5() 401 n_seq; in ml_pair5() 457 n_seq = fc->n_seq; in ml_pair3() 525 n_seq = fc->n_seq; in ml_pair53() 732 n_seq = (fc->type == VRNA_FC_TYPE_SINGLE) ? 1 : fc->n_seq; in E_mb_loop_stack() 990 n_seq; in extend_fm_3p() 1000 n_seq; in extend_fm_3p() 1074 n_seq = (fc->type == VRNA_FC_TYPE_SINGLE) ? 1 : fc->n_seq; in E_ml_stems_fast() [all …]
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H A D | external.c | 861 unsigned int s, n_seq, type; in get_stem_contributions_d0() local 878 n_seq = (fc->type == VRNA_FC_TYPE_SINGLE) ? 1 : fc->n_seq; in get_stem_contributions_d0() 979 n_seq = (fc->type == VRNA_FC_TYPE_SINGLE) ? 1 : fc->n_seq; in f3_get_stem_contributions_d0() 1186 n_seq = fc->n_seq; in get_stem_contributions_d2() 1364 n_seq = fc->n_seq; in f3_get_stem_contributions_d2() 1490 n_seq = fc->n_seq; in f5_get_stem_contributions_d5() 1659 n_seq = fc->n_seq; in f3_get_stem_contributions_d3() 1782 n_seq = fc->n_seq; in f5_get_stem_contributions_d3() 1958 n_seq = fc->n_seq; in f3_get_stem_contributions_d5() 2086 n_seq = fc->n_seq; in f5_get_stem_contributions_d53() [all …]
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H A D | multibranch_sc_pf.inc | 16 unsigned int n_seq; 60 for (s = 0; s < data->n_seq; s++) 87 for (s = 0; s < data->n_seq; s++) 116 for (s = 0; s < data->n_seq; s++) 378 sc_wrapper->n_seq = 1; 472 sc_wrapper->n_seq = fc->n_seq; 484 fc->n_seq); 488 fc->n_seq); 492 fc->n_seq); 496 fc->n_seq); [all …]
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H A D | multibranch_bt.c | 566 n_seq; in BT_mb_loop_split() 620 n_seq; in BT_mb_loop_split() 674 n_seq; in BT_mb_loop_split() 693 n_seq; in BT_mb_loop_split() 717 n_seq; in BT_mb_loop_split() 962 n_seq; in BT_mb_loop_split() 1191 n_seq; in BT_mb_loop() 1243 n_seq; in BT_mb_loop() 1282 n_seq; in BT_mb_loop() 1323 n_seq; in BT_mb_loop() [all …]
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H A D | internal_bt.c | 101 unsigned int n, n_seq, s, *sn, *ss, type, type_2; in BT_stack() local 112 n_seq = (fc->type == VRNA_FC_TYPE_SINGLE) ? 1 : fc->n_seq; in BT_stack() 176 for (s = 0; s < n_seq; s++) { in BT_stack() 214 unsigned int n, n_seq, s, *sn, type, *tt; in BT_int_loop() local 226 n_seq = (fc->type == VRNA_FC_TYPE_SINGLE) ? 1 : fc->n_seq; in BT_int_loop() 334 tt = (unsigned int *)vrna_alloc(sizeof(unsigned int) * n_seq); in BT_int_loop() 336 for (s = 0; s < n_seq; s++) in BT_int_loop() 342 fc->matrices->ggg_local, &p, &q, n_seq, in BT_int_loop() 353 n_seq, in BT_int_loop()
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H A D | hairpin_sc_pf.inc | 10 unsigned int n_seq; 51 for (s = 0; s < data->n_seq; s++) 80 for (s = 0; s < data->n_seq; s++) 107 for (s = 0; s < data->n_seq; s++) 409 sc_wrapper->n_seq = 1; 496 sc_wrapper->n_seq = fc->n_seq; 510 fc->n_seq); 514 fc->n_seq); 518 fc->n_seq); 522 fc->n_seq); [all …]
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H A D | hairpin_sc.inc | 10 unsigned int n_seq; 51 for (s = 0; s < data->n_seq; s++) 80 for (s = 0; s < data->n_seq; s++) 107 for (s = 0; s < data->n_seq; s++) 407 sc_wrapper->n_seq = 1; 494 sc_wrapper->n_seq = fc->n_seq; 508 fc->n_seq); 512 fc->n_seq); 516 fc->n_seq); 520 fc->n_seq); [all …]
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H A D | internal.c | 158 n_seq = (fc->type == VRNA_FC_TYPE_SINGLE) ? 1 : fc->n_seq; in eval_int_loop() 209 for (s = 0; s < n_seq; s++) { in eval_int_loop() 265 unsigned int n, n_seq, s, **a2s; in eval_ext_int_loop() local 274 n_seq = (fc->type == VRNA_FC_TYPE_SINGLE) ? 1 : fc->n_seq; in eval_ext_int_loop() 309 for (s = 0; s < n_seq; s++) { in eval_ext_int_loop() 387 n_seq = (fc->type == VRNA_FC_TYPE_SINGLE) ? 1 : fc->n_seq; in E_internal_loop() 433 for (s = 0; s < n_seq; s++) in E_internal_loop() 837 n_seq = (fc->type == VRNA_FC_TYPE_SINGLE) ? 1 : fc->n_seq; in E_ext_internal_loop() 858 for (s = 0; s < n_seq; s++) in E_ext_internal_loop() 932 n_seq = (fc->type == VRNA_FC_TYPE_SINGLE) ? 1 : fc->n_seq; in E_stack() [all …]
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H A D | external_sc.inc | 32 int n_seq; 55 int n_seq; 451 sc_wrapper->n_seq = fc->n_seq; 519 sc_wrapper->n_seq = 1; 564 sc_wrapper->n_seq = fc->n_seq; 772 for (s = 0; s < data->n_seq; s++) 793 for (s = 0; s < data->n_seq; s++) 878 for (s = 0; s < data->n_seq; s++) 899 for (s = 0; s < data->n_seq; s++) 1086 for (s = 0; s < data->n_seq; s++) [all …]
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/dports/biology/viennarna/ViennaRNA-2.4.18/src/bin/ |
H A D | RNAsnoop.c | 546 int n_seq, n_seq2; in main() local 549 if (n_seq != n_seq2) { in main() 571 AS1[n_seq] = NULL; in main() 572 AS2[n_seq] = NULL; in main() 724 int n_seq, s; in aliprint_struc() local 726 n_seq = s; in aliprint_struc() 747 …dup->Duplex_El / n_seq, dup->Duplex_Er / n_seq, dup->Loop_E / n_seq, dup->Loop_D / n_seq, dup->psc… in aliprint_struc() 1148 int n_seq, n_seq2; in redraw_output() local 1151 if (n_seq != n_seq2) { in redraw_output() 1173 AS1[n_seq] = NULL; in redraw_output() [all …]
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/dports/biology/minimap2/minimap2-2.24/ |
H A D | index.c | 69 for (i = 0; i < mi->n_seq; ++i) in mm_idx_destroy() 74 for (i = 0; i < mi->n_seq; ++i) in mm_idx_destroy() 106 for (i = 0; i < mi->n_seq; ++i) in mm_idx_stat() 131 for (i = 0; i < mi->n_seq; ++i) { in mm_idx_index_name() 288 int n_seq; member 313 assert((uint64_t)p->mi->n_seq + s->n_seq <= UINT32_MAX); // to prevent integer overflow in worker_pipeline() 315 old_m = p->mi->n_seq, m = p->mi->n_seq + s->n_seq; in worker_pipeline() 358 for (i = 0; i < s->n_seq; ++i) { in worker_pipeline() 423 mi->n_seq = n; in mm_idx_str() 470 for (i = 0; i < mi->n_seq; ++i) { in mm_idx_dump() [all …]
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/dports/graphics/graphviz/graphviz-2.44.1/lib/cgraph/ |
H A D | node.c | 41 sn = (Agsubnode_t *) dtfirst(g->n_seq); in agfstnode() 49 if (sn) sn = ((Agsubnode_t *) dtnext(g->n_seq, sn)); in agnxtnode() 56 sn = (Agsubnode_t *) dtlast(g->n_seq); in aglstnode() 64 if (sn) sn = ((Agsubnode_t *) dtprev(g->n_seq, sn)); in agprvnode() 92 assert(dtsize(g->n_id) == dtsize(g->n_seq)); in installnode() 98 dtinsert(g->n_seq, sn); in installnode() 99 assert(dtsize(g->n_id) == dtsize(g->n_seq)); in installnode() 189 dtdelete(g->n_seq, &template); in agdelnodeimage() 342 dtsearch(g->n_seq,&template); in agnodesetfinger() 348 dtrenew(g->n_seq, dtfinger(g->n_seq)); in agnoderenew()
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