/dports/biology/fasta3/fasta-36.3.8/src/ |
H A D | wm_align.c | 182 cur_ares->next = NULL; in nsw_malign() 186 ss, cur_ares); in nsw_malign() 195 CHECK_SCORE(cur_ares->min0, &aa1[cur_ares->min1-1], in nsw_malign() 196 cur_ares->max0 - cur_ares->min0, cur_ares->max1-cur_ares->min1, in nsw_malign() 197 cur_ares->res, in nsw_malign() 201 if (!do_rep || cur_ares->rst.score[score_ix] <= score_thresh) { return cur_ares;} in nsw_malign() 242 memcpy(local_aa1,aa1+cur_ares->max1,n1-cur_ares->max1); in nsw_malign() 289 return cur_ares; in nsw_malign() 292 cur_ares = merge_ares_chains(cur_ares, tmpl_ares, score_ix, "left"); in nsw_malign() 293 cur_ares = merge_ares_chains(cur_ares, tmpr_ares, score_ix, "right"); in nsw_malign() [all …]
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H A D | dropnfa.c | 1354 cur_ares->next = NULL; in bd_malign() 1355 cur_ares->n1 = n1; in bd_malign() 1415 cur_ares->n1 += l_min; in bd_malign() 1423 cur_ares->sw_score = bd_walign(aa0, n0, aa1, n1, ppst, f_str, hoff, cur_ares); in bd_malign() 1427 cur_ares->nres = 0; in bd_malign() 1428 cur_ares->sw_score=0; in bd_malign() 1429 cur_ares->rst.score[0] = cur_ares->rst.score[1] = cur_ares->rst.score[2] = 0; in bd_malign() 1434 if (!ppst->do_rep || cur_ares->rst.score[score_ix] <= score_thresh) {return cur_ares;} in bd_malign() 1529 cur_ares = merge_ares_chains(cur_ares, tmpl_ares, score_ix, "left"); in bd_malign() 1530 cur_ares = merge_ares_chains(cur_ares, tmpr_ares, score_ix, "right"); in bd_malign() [all …]
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H A D | lsim4.c | 50 struct a_res_str *cur_ares, *tmp_ares; in SIM() local 113 cur_ares = a_res; in SIM() 117 cur_ares->next = tmp_ares; in SIM() 118 cur_ares = tmp_ares; in SIM() 146 cur_ares->n1 = N; in SIM() 147 cur_ares->sw_score = cur_ares->rst.score[ppst->score_ix] = score; in SIM() 148 cur_ares->min0 = stari-1; in SIM() 149 cur_ares->min1 = starj-1; in SIM() 152 cur_ares->next = NULL; in SIM() 159 cur_ares->res,ppst->pam2[0],q,r,&cur_ares->nres); in SIM() [all …]
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H A D | dropfz3.c | 2455 struct a_res_str *cur_ares, argument 2484 cur_ares->next = NULL; 2493 return cur_ares; 2505 cur_ares->v_start = sq_start = 0; 2508 else {sq_end = n1 - cur_ares->max1;} 2511 sq_save = sq_end = cur_ares->min0; 2562 sq_start = cur_ares->max0+1; 2581 local_aa1, cur_ares->v_len, 2618 cur_ares = merge_ares_chains(cur_ares, tmpl_ares, score_ix, "left"); 2619 cur_ares = merge_ares_chains(cur_ares, tmpr_ares, score_ix, "right"); [all …]
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H A D | dropfz2.c | 2455 struct a_res_str *cur_ares, argument 2484 cur_ares->next = NULL; 2493 return cur_ares; 2505 cur_ares->v_start = sq_start = 0; 2508 else {sq_end = n1 - cur_ares->max1;} 2511 sq_save = sq_end = cur_ares->min0; 2562 sq_start = cur_ares->max0+1; 2581 local_aa1, cur_ares->v_len, 2618 cur_ares = merge_ares_chains(cur_ares, tmpl_ares, score_ix, "left"); 2619 cur_ares = merge_ares_chains(cur_ares, tmpr_ares, score_ix, "right"); [all …]
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H A D | dropfx2.c | 2359 struct a_res_str *cur_ares, argument 2383 cur_ares->next = NULL; 2415 return cur_ares; 2422 nxyaa = cur_ares->min1; 2424 nxyaa = cur_ares->min0; 2474 nxyaa = n1 - cur_ares->max1 - 1; 2478 nxyaa = n1 - cur_ares->max0 - 1; 2554 return cur_ares; 2557 cur_ares = merge_ares_chains(cur_ares, tmpl_ares, score_ix, "left"); 2558 cur_ares = merge_ares_chains(cur_ares, tmpr_ares, score_ix, "right"); [all …]
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H A D | dropfx.c | 2357 struct a_res_str *cur_ares, argument 2381 cur_ares->next = NULL; 2413 return cur_ares; 2420 nxyaa = cur_ares->min1; 2422 nxyaa = cur_ares->min0; 2472 nxyaa = n1 - cur_ares->max1 - 1; 2476 nxyaa = n1 - cur_ares->max0 - 1; 2552 return cur_ares; 2555 cur_ares = merge_ares_chains(cur_ares, tmpl_ares, score_ix, "left"); 2556 cur_ares = merge_ares_chains(cur_ares, tmpr_ares, score_ix, "right"); [all …]
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H A D | dropnsw.c | 75 struct a_res_str *cur_ares,
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H A D | compacc2.c | 1116 merge_ares_chains(struct a_res_str *cur_ares, in merge_ares_chains() argument 1123 if (!tmp_ares) return cur_ares; in merge_ares_chains() 1127 for (max_next = cur_ares; max_next; max_next = max_next->next) { in merge_ares_chains() 1141 if (cur_ares->rst.score[score_ix] >= tmp_ares->rst.score[score_ix]) { in merge_ares_chains() 1142 max_ares = max_next = prev_next = cur_ares; in merge_ares_chains() 1147 alt_ares = cur_ares; in merge_ares_chains()
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H A D | compacc2e.c | 1117 merge_ares_chains(struct a_res_str *cur_ares, in merge_ares_chains() argument 1124 if (!tmp_ares) return cur_ares; in merge_ares_chains() 1128 for (max_next = cur_ares; max_next; max_next = max_next->next) { in merge_ares_chains() 1142 if (cur_ares->rst.score[score_ix] >= tmp_ares->rst.score[score_ix]) { in merge_ares_chains() 1143 max_ares = max_next = prev_next = cur_ares; in merge_ares_chains() 1148 alt_ares = cur_ares; in merge_ares_chains()
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H A D | dropnnw2.c | 106 struct a_res_str *cur_ares,
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H A D | dropgsw2.c | 93 struct a_res_str *cur_ares,
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