/dports/biology/fasta/fasta/ |
H A D | ag_stats.c | 37 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 …]
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H A D | lalign2.c | 43 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 …]
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H A D | align.c | 31 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()
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H A D | score_al.c | 218 ,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()
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H A D | apam.c | 161 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()
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H A D | upam.gbl | 6 int gdelval= -12; 8 int gdelval= -10; 308 extern int gdelval, ggapval, gshift;
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H A D | pam.c | 88 gdelval = gdeltmp; 90 gdelval = gdeltmp-ggapval;
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H A D | zzlgmata.c | 98 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);
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H A D | zxlgmata.c | 81 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,
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H A D | fffasta.c | 781 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 …]
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H A D | prss.c | 376 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);
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/dports/biology/fasta3/fasta-36.3.8/src/ |
H A D | dropgsw2.c | 91 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 …]
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H A D | dropnsw.c | 73 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()
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H A D | dropnnw2.c | 104 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()
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H A D | ag_stats.c | 17 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()
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H A D | apam.c | 258 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()
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H A D | wm_align.c | 152 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()
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H A D | cal_cons.c | 412 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()
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H A D | dropnfa.c | 97 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 …]
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H A D | param.h | 53 int gdelval; /* value gap open (-10) */ member
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H A D | cal_cons2.c | 674 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()
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H A D | dropfz3.c | 726 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 …]
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H A D | scaleswn.c | 613 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 …]
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/dports/biology/emboss/EMBOSS-6.6.0/emboss/ |
H A D | stretcher.c | 147 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()
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/dports/biology/fasta3/fasta-36.3.8/doc/ |
H A D | fasta.options | 38 case 'f': ppst->gdelval
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