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Searched refs:ggapval (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()
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 …]
H A Dalign.c31 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()
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);
252 r = -ggapval;
H A Dscore_al.c220 ,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()
H A Dzxlgmata.c81 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,
H A Dpam.c85 if (!gap_set) ggapval = ggaptmp;
90 gdelval = gdeltmp-ggapval;
H A Dapam.c161 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()
H A Dupam.gbl12 int ggapval= -2;
308 extern int gdelval, 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);
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 …]
H A Dprss.c377 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);
/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()
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 …]
H A Dag_stats.c17 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()
H A Ddropnnw2.c104 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 …]
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()
322 r = -ppst->ggapval; in do_work()
392 -ppst->gdelval, -ppst->ggapval, in do_walign()
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.c416 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()
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()
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 …]
H A Dparam.h54 int ggapval; /* value for additional residues in gap (-2) */ member
H A Dscaleswn.c614 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 …]
H A Dcal_cons2.c678 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()
H A Dapam.c262 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()
H A Ddropfz3.c165 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 …]
/dports/biology/emboss/EMBOSS-6.6.0/emboss/
H A Dstretcher.c148 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()
/dports/biology/fasta3/fasta-36.3.8/doc/
H A Dfasta.options39 case 'g': ppst->ggapval

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