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Searched refs:gdelval (Results 1 – 25 of 38) sorted by relevance

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/dports/biology/fasta/fasta/
H A Dag_stats.c37 if (!del_set) {*gdelval= -14; *ggapval=-2;} in init_stats()
41 if (!del_set) {*gdelval= -8; *ggapval=-2;} in init_stats()
45 if (!del_set) {*gdelval= -12; *ggapval=-2;} in init_stats()
49 if (!del_set) {*gdelval= -12; *ggapval=-2;} in init_stats()
53 if (!del_set) {*gdelval= -20; *ggapval=-3;} in init_stats()
57 if (!del_set) {*gdelval= -27; *ggapval=-4;} in init_stats()
61 if (!del_set) {*gdelval= -27; *ggapval=-4;} in init_stats()
65 if (!del_set) {*gdelval= -26; *ggapval=-4;} in init_stats()
69 if (!del_set) {*gdelval= -26; *ggapval=-4;} in init_stats()
96 if (del_set) { *gdelval += *ggapval;} in init_stats()
[all …]
H A Dlalign2.c43 int *gdelval, int *ggapval, int del_set, int gap_set);
290 smptr,match,mismh,gdelval,ggapval,e_val); in main()
300 fprintf(outfd,"; pg_gap-pen: %d %d\n",gdelval,ggapval); in main()
302 fprintf(outfd,"; pg_open-ext: %d %d\n",gdelval,ggapval); in main()
319 SIM(aa0-1,aa1-1,n0,n1,m_score,pam2,-(gdelval-ggapval),-ggapval,nseq, in main()
327 SIM(aa0-1,aa1-1,n0,n1,m_score,pam2,-(gdelval-ggapval),-ggapval, in main()
353 gdelval = -14; in initenv()
377 case 'f': sscanf(optarg,"%d",&gdelval); in initenv()
378 if (gdelval > 0) gdelval = -gdelval; in initenv()
431 if (!standard_pam(smstr,&pam,&gdelval,&ggapval,del_set,gap_set) in initenv()
[all …]
H A Dalign.c31 int *gdelval, int *ggapval, int del_set, int gap_set);
159 ,-(gdelval-ggapval) in main()
161 ,-gdelval in main()
177 smptr,gdelval,ggapval); in main()
189 smptr,gdelval,ggapval); in main()
229 case 'f': sscanf(optarg,"%d",&gdelval); del_set = 1; break; in initenv()
250 if (!standard_pam(smstr,&pam,&gdelval,&ggapval,del_set,gap_set) in initenv()
282 if (!del_set) gdelval = -16; in resetp()
284 if (!del_set) gdelval = -12; in resetp()
H A Dscore_al.c218 ,gdelval
220 ,gdelval-ggapval
236 smptr,gdelval,ggapval);
272 case 'f': sscanf(optarg,"%d",&gdelval); del_set = 1; break;
320 if (!gap_set) gdelval = -16;
323 gdelval -= ggapval;
343 int pam2[MAXSQ][MAXSQ], int gdelval, int ggapval) in score_aln() argument
359 else inc = ggapval + gdelval; in score_aln()
H A Dapam.c161 int *gdelval, int *ggapval, int del_set, int gap_set) { in standard_pam() argument
171 if (!del_set) *gdelval = std_pam_p->gdel; in standard_pam()
173 if (!del_set) *gdelval = std_pam_p->gdel - std_pam_p->ggap; in standard_pam()
H A Dupam.gbl6 int gdelval= -12;
8 int gdelval= -10;
308 extern int gdelval, ggapval, gshift;
H A Dpam.c88 gdelval = gdeltmp;
90 gdelval = gdeltmp-ggapval;
H A Dzzlgmata.c98 pam2,-(gdelval-ggapval),-ggapval,optwid);
106 pam2,-(gdelval-ggapval),-ggapval,1,
125 -(gdelval-ggapval), -ggapval,
133 pam2,-(gdelval-ggapval),-ggapval,0,
151 pam2,-(gdelval-ggapval),-ggapval,res,optwid,n0);
251 q = -(gdelval - ggapval);
H A Dzxlgmata.c81 score = lx_align(aa0, n0, aa1y, n1, pam2, -(gdelval-ggapval),
84 score = lx_align(aa1, n1, aa0y, n0, pam2, -(gdelval-ggapval),
178 score = pro_dna(aa1,n1,aa0t,n0,pam2,-(gdelval-ggapval), -ggapval, -gshift,
H A Dfffasta.c781 bestcut,optcut,ggapval,gdelval,cgap);
986 fprintf(outfd,"; pg_gap-pen: %d %d\n",gdelval,ggapval);
1016 fprintf(outfd,"; pg_gap-pen: %d %d\n",gdelval,ggapval);
1074 gdelval = -16;
1078 gdelval = -15;
1083 gdelval = -15;
1139 case 'f': sscanf(optarg,"%d",&gdelval); del_set=1;
1140 if (gdelval > 0) gdelval = -gdelval;
1252 if (!del_set) gdelval = -16;
1285 pgap = gdelval+ggapval; in initparm()
[all …]
H A Dprss.c376 case 'f': sscanf(optarg,"%d",&gdelval); del_set = 1; break;
421 if (!del_set) gdelval = -16;
521 fprintf(fd,"gap penalties: %d,%d\n",gdelval,ggapval);
/dports/biology/fasta3/fasta-36.3.8/src/
H A Ddropgsw2.c91 int gdelval, int ggapval,
683 (ppst->ext_sq_set)?"xS":"\0", ppst->gdelval, ppst->ggapval); in get_param()
731 -ppst->gdelval, in do_work()
750 -ppst->gdelval, in do_work()
777 -ppst->gdelval, in do_work()
798 -ppst->gdelval, in do_work()
816 -ppst->gdelval, in do_work()
842 -ppst->gdelval, in do_work()
854 -(ppst->gdelval - ppst->ggapval), in do_work()
856 -ppst->gdelval, in do_work()
[all …]
H A Ddropnsw.c73 int gdelval, int ggapval,
275 (ppst->ext_sq_set)?"xS":"\0", ppst->gdelval, ppst->ggapval); in get_param()
285 (ppst->ext_sq_set)?"xS":"\0",ppst->gdelval,ppst->ggapval); in get_param()
318 q = -(ppst->gdelval - ppst->ggapval); in do_work()
320 q = -ppst->gdelval; in do_work()
392 -ppst->gdelval, -ppst->ggapval, in do_walign()
H A Ddropnnw2.c104 int gdelval, int ggapval,
522 (ppst->ext_sq_set)?"xS":"\0", ppst->gdelval, ppst->ggapval); in get_param()
531 (ppst->ext_sq_set)?"xS":"\0",ppst->gdelval,ppst->ggapval); in get_param()
561 -ppst->gdelval, in do_work()
564 -(ppst->gdelval - ppst->ggapval), in do_work()
593 -ppst->gdelval, in do_work()
596 -(ppst->gdelval - ppst->ggapval), in do_work()
606 -(ppst->gdelval - ppst->ggapval), in do_work()
608 -ppst->gdelval, in do_work()
868 -ppst->gdelval, -ppst->ggapval, in do_walign()
H A Dag_stats.c17 ag_parm(char *pam_type, int gdelval, int ggapval) in ag_parm() argument
22 t_gdelval = gdelval; in ag_parm()
25 t_gdelval = gdelval+ggapval; in ag_parm()
H A Dapam.c258 if (!del_set) ppst->gdelval = std_pam_p->gdel+std_pam_p->ggap; in standard_pam()
260 if (!del_set) ppst->gdelval = std_pam_p->gdel; in standard_pam()
303 if (!del_set) ppst->gdelval = std_pam_p->gdel+std_pam_p->ggap; in min_pam_bits()
305 if (!del_set) ppst->gdelval = std_pam_p->gdel; in min_pam_bits()
H A Dwm_align.c152 int gdelval, int ggapval, in nsw_malign() argument
185 gdelval, ggapval, in nsw_malign()
198 pam2p[pam_ix], gdelval, ggapval, in nsw_malign()
216 gdelval, ggapval, ss, tmpl_ares, in nsw_malign()
250 gdelval, ggapval, ss, tmpr_ares, in nsw_malign()
H A Dcal_cons.c412 if (cumm_seq_score) *i_spa = ppst->gdelval; in calc_cons_a()
413 d1_score += ppst->gdelval; in calc_cons_a()
414 d0_score += ppst->gdelval; in calc_cons_a()
436 ppst->ggapval+ppst->gdelval); in calc_cons_a()
475 ppst->ggapval+ppst->gdelval); in calc_cons_a()
985 d1_score += ppst->gdelval; in calc_code()
986 d0_score += ppst->gdelval; in calc_code()
H A Ddropnfa.c97 int **pam2, int gdelval, int ggapval,
196 ppst->param_u.fa.pgap = ppst->gdelval + 2*ppst->ggapval; in init_work()
198 ppst->param_u.fa.pgap = ppst->gdelval + ppst->ggapval; in init_work()
472 ppstr->gdelval, ppstr->ggapval, in get_param()
810 ppst->gdelval,ppst->ggapval,f_str); in do_fasta()
1130 int **pam2, int gdelval, int ggapval, in dmatch() argument
1153 -(gdelval-ggapval), in dmatch()
1155 -gdelval, in dmatch()
1410 -ppst->gdelval, -ppst->ggapval, in bd_malign()
1577 ppst->pam2[0], -ppst->gdelval, -ppst->ggapval, in bd_walign()
[all …]
H A Dparam.h53 int gdelval; /* value gap open (-10) */ member
H A Dcal_cons2.c674 if (cumm_seq_score) *i_spa = ppst->gdelval; in calc_cons_u()
675 d1_score += ppst->gdelval; in calc_cons_u()
676 d0_score += ppst->gdelval; in calc_cons_u()
704 ppst->ggapval+ppst->gdelval); in calc_cons_u()
759 ppst->ggapval+ppst->gdelval); in calc_cons_u()
H A Ddropfz3.c726 ppst->gdelval, ppst->ggapval, in get_param()
1358 int **pam2, int gdelval, int ggapval, int gshift, argument
1368 -(gdelval - ggapval),
1370 -gdelval,
1378 -(gdelval - ggapval),
1380 -gdelval,
3380 if (prev_match) *i_spa = ppst->gdelval;
3384 if (prev_match) d1_score += ppst->gdelval;
3409 if (prev_match) *i_spa = ppst->gdelval;
3410 *i_spa++ += ppst->gdelval;
[all …]
H A Dscaleswn.c613 t_gdelval = ppst->gdelval; in proc_hist_a()
616 t_gdelval = ppst->gdelval+ppst->ggapval; in proc_hist_a()
687 r_v = look_p(bl50_p,gdelval,ggapval,&K,&Lambda,&H); in ag_parm()
689 r_v = look_p(bl62_p,gdelval,ggapval,&K,&Lambda,&H); in ag_parm()
691 r_v = look_p(p250_p,gdelval,ggapval,&K,&Lambda,&H); in ag_parm()
693 r_v = look_p(p120_p,gdelval,ggapval,&K,&Lambda,&H); in ag_parm()
695 r_v = look_p(md10_p,gdelval,ggapval,&K,&Lambda,&H); in ag_parm()
697 r_v = look_p(md20_p,gdelval,ggapval,&K,&Lambda,&H); in ag_parm()
699 r_v = look_p(md40_p,gdelval,ggapval,&K,&Lambda,&H); in ag_parm()
701 r_v = look_p(nt54_p,gdelval,ggapval, &K,&Lambda,&H); in ag_parm()
[all …]
/dports/biology/emboss/EMBOSS-6.6.0/emboss/
H A Dstretcher.c147 ajint gdelval; in main() local
167 gdelval = ajAcdGetInt("gapopen"); in main()
217 (gdelval-ggapval),ggapval,glres,&nres); in main()
253 ajAlignSetGapI(align, gdelval, ggapval); in main()
/dports/biology/fasta3/fasta-36.3.8/doc/
H A Dfasta.options38 case 'f': ppst->gdelval

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