/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() 322 SIM(aa0-1,aa1-1,n0,n1,m_score,pam2,-gdelval,-ggapval,nseq,K,z_size); in main() 327 SIM(aa0-1,aa1-1,n0,n1,m_score,pam2,-(gdelval-ggapval),-ggapval, in main() 354 ggapval = -4; in initenv() 381 case 'g': sscanf(optarg,"%d",&ggapval); in initenv() 382 if (ggapval > 0) ggapval = - ggapval; 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() 163 ,-ggapval,res,&nres); in main() 177 smptr,gdelval,ggapval); in main() 189 smptr,gdelval,ggapval); in main() 230 case 'g': sscanf(optarg,"%d",&ggapval); gap_set = 1; break; in initenv() 250 if (!standard_pam(smstr,&pam,&gdelval,&ggapval,del_set,gap_set) in initenv() 286 if (!gap_set) ggapval = -4; in resetp()
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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); 252 r = -ggapval;
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H A D | score_al.c | 220 ,gdelval-ggapval 222 ,ggapval); 236 smptr,gdelval,ggapval); 273 case 'g': sscanf(optarg,"%d",&ggapval); gap_set = 1; break; 321 if (!del_set) ggapval = -4; 323 gdelval -= ggapval; 343 int pam2[MAXSQ][MAXSQ], int gdelval, int ggapval) in score_aln() argument 358 if (gopen_flg) inc = ggapval; in score_aln() 359 else inc = ggapval + gdelval; in score_aln()
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H A D | zxlgmata.c | 81 score = lx_align(aa0, n0, aa1y, n1, pam2, -(gdelval-ggapval), 82 -ggapval,-gshift,hoff,optwid); 84 score = lx_align(aa1, n1, aa0y, n0, pam2, -(gdelval-ggapval), 85 -ggapval,-gshift,hoff,optwid); 178 score = pro_dna(aa1,n1,aa0t,n0,pam2,-(gdelval-ggapval), -ggapval, -gshift,
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H A D | pam.c | 85 if (!gap_set) ggapval = ggaptmp; 90 gdelval = gdeltmp-ggapval;
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H A D | apam.c | 161 int *gdelval, int *ggapval, int del_set, int gap_set) { in standard_pam() argument 175 if (!gap_set) *ggapval = std_pam_p->ggap; in standard_pam()
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H A D | upam.gbl | 12 int ggapval= -2; 308 extern int gdelval, 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); 1075 ggapval = -4; 1079 ggapval = -3; 1084 ggapval = -3; 1142 case 'g': sscanf(optarg,"%d",&ggapval); gap_set=1; 1143 if (ggapval > 0) ggapval = - ggapval; 1253 if (!gap_set) ggapval = -4; 1285 pgap = gdelval+ggapval; in initparm() [all …]
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H A D | prss.c | 377 case 'g': sscanf(optarg,"%d",&ggapval); gap_set = 1; break; 422 if (!gap_set) ggapval = -4; 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() 733 -ppst->ggapval, in do_work() 752 -ppst->ggapval, in do_work() 779 -ppst->ggapval, in do_work() 800 -ppst->ggapval, in do_work() 818 -ppst->ggapval, in do_work() 844 -ppst->ggapval, in do_work() 854 -(ppst->gdelval - ppst->ggapval), in do_work() 858 -ppst->ggapval,0,f_str); in do_work() [all …]
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H A D | ag_stats.c | 17 ag_parm(char *pam_type, int gdelval, int ggapval) in ag_parm() argument 23 t_ggapval = ggapval; in ag_parm() 25 t_gdelval = gdelval+ggapval; in ag_parm() 26 t_ggapval = ggapval; in ag_parm()
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H A D | dropnnw2.c | 104 int gdelval, int ggapval, 302 gap = -2 * ppst->ggapval; in init_work() 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() 564 -(ppst->gdelval - ppst->ggapval), in do_work() 566 -ppst->ggapval, in do_work() 596 -(ppst->gdelval - ppst->ggapval), in do_work() 598 -ppst->ggapval, in do_work() 606 -(ppst->gdelval - ppst->ggapval), in do_work() 610 -ppst->ggapval,f_str->ss); 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() 322 r = -ppst->ggapval; in do_work() 392 -ppst->gdelval, -ppst->ggapval, in do_walign()
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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 | 416 if (cumm_seq_score) *i_spa++ += ppst->ggapval; in calc_cons_a() 417 d1_score += ppst->ggapval; d1_alen++; in calc_cons_a() 418 d0_score += ppst->ggapval; d0_alen++; in calc_cons_a() 436 ppst->ggapval+ppst->gdelval); in calc_cons_a() 475 ppst->ggapval+ppst->gdelval); in calc_cons_a() 989 d1_score += ppst->ggapval; d1_alen++; in calc_code() 990 d0_score += ppst->ggapval; d0_alen++; 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() 1157 -ggapval,window,f_str); 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 | 54 int ggapval; /* value for additional residues in gap (-2) */ member
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H A D | scaleswn.c | 614 t_ggapval = ppst->ggapval; in proc_hist_a() 616 t_gdelval = ppst->gdelval+ppst->ggapval; in proc_hist_a() 617 t_ggapval = 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() [all …]
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H A D | cal_cons2.c | 678 if (cumm_seq_score) *i_spa++ += ppst->ggapval; in calc_cons_u() 679 d1_score += ppst->ggapval; d1_alen++; in calc_cons_u() 680 d0_score += ppst->ggapval; d0_alen++; 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 | apam.c | 262 if (!gap_set) ppst->ggapval = std_pam_p->ggap; in standard_pam() 307 if (!gap_set) ppst->ggapval = std_pam_p->ggap; in min_pam_bits()
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H A D | dropfz3.c | 165 int **pam2, int gdelval, int ggapval, int gshift, 726 ppst->gdelval, ppst->ggapval, in get_param() 1054 ppst->gdelval,ppst->ggapval,ppst->gshift, 1358 int **pam2, int gdelval, int ggapval, int gshift, argument 1368 -(gdelval - ggapval), 1372 -ggapval,-gshift, 1378 -(gdelval - ggapval), 1382 -ggapval,-gshift, 3381 *i_spa++ = ppst->ggapval; 3385 d1_score += ppst->ggapval; [all …]
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/dports/biology/emboss/EMBOSS-6.6.0/emboss/ |
H A D | stretcher.c | 148 ajint ggapval; in main() local 168 ggapval = ajAcdGetInt("gapextend"); 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 | 39 case 'g': ppst->ggapval
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