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Searched refs:n_seq (Results 1 – 25 of 136) sorted by relevance

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/dports/biology/viennarna/ViennaRNA-2.4.18/src/ViennaRNA/
H A Dalipfold.c98 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
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H A Dali_plex.c208 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()
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H A Dduplex.c103 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()
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H A Dsequence.c158 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()
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H A Dfold_compound.c304 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()
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H A Deval.c457 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()
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H A Dgquad.c57 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()
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H A Dsnofold.c556 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()
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H A Dgquad.h45 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()
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/dports/biology/viennarna/ViennaRNA-2.4.18/tests/perl5/
H A Dtest-RNA-file-formats.pl16 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…
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/dports/biology/viennarna/ViennaRNA-2.4.18/src/ViennaRNA/utils/
H A Dmsa_utils.c71 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()
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/dports/biology/viennarna/ViennaRNA-2.4.18/tests/python/
H A Dtest-RNA-file-formats.py45 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:
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/dports/biology/viennarna/ViennaRNA-2.4.18/tests/python3/
H A Dtest-RNA-file-formats.py345 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:
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/dports/biology/viennarna/ViennaRNA-2.4.18/src/ViennaRNA/loops/
H A Dmultibranch.c231 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()
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H A Dexternal.c861 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()
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H A Dmultibranch_sc_pf.inc16 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);
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H A Dmultibranch_bt.c566 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()
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H A Dinternal_bt.c101 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()
H A Dhairpin_sc_pf.inc10 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);
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H A Dhairpin_sc.inc10 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);
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H A Dinternal.c158 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()
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H A Dexternal_sc.inc32 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++)
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/dports/biology/viennarna/ViennaRNA-2.4.18/src/bin/
H A DRNAsnoop.c546 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()
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/dports/biology/minimap2/minimap2-2.24/
H A Dindex.c69 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()
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/dports/graphics/graphviz/graphviz-2.44.1/lib/cgraph/
H A Dnode.c41 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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