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Searched refs:ppst (Results 1 – 25 of 62) sorted by relevance

123

/dports/biology/fasta3/fasta-36.3.8/src/
H A Dinitfa.c619 ppst->sq[ppst->nsq] = ppst->sqx[ppst->nsqx] = '\0'; in h_init()
713 if (ppst->pam_l > ppst->pam2[0][p_i][p_j]) ppst->pam_l = ppst->pam2[0][p_i][p_j]; in init_pam2()
714 if (ppst->pam_h < ppst->pam2[0][p_i][p_j]) ppst->pam_h = ppst->pam2[0][p_i][p_j]; in init_pam2()
954 ppst->nsq_e = ppst->nsq; in f_initenv()
1105 if (ppst->gdelval > 0) ppst->gdelval = -ppst->gdelval; in f_getopt()
1116 if (ppst->gshift > 0) ppst->gshift = -ppst->gshift; in f_getopt()
1121 if (ppst->gsubs > 0) ppst->gsubs = -ppst->gsubs; in f_getopt()
1133 if (ppst->gsubs > 0) ppst->gsubs = -ppst->gsubs; in f_getopt()
1138 if (ppst->gsubs > 0) ppst->gsubs = -ppst->gsubs; in f_getopt()
1148 if (ppst->gshift > 0) ppst->gshift = -ppst->gshift; in f_getopt()
[all …]
H A Dprint_pssm.c82 standard_pam(ppst->pamfile,ppst,0,0); in main()
90 ppst->sq[ppst->nsqx+1] = ppst->sqx[ppst->nsqx+1] = '\0'; in main()
149 initpam (ppst->pamfile, ppst); in initenv()
400 ppst->pam_h = -1; ppst->pam_l = 1; in initpam2()
406 ppst->pam2[0][j][i] = ppst->pam2[0][i][j] = pam[k++] - ppst->pamoff; in initpam2()
407 if (ppst->pam_l > ppst->pam2[0][i][j]) ppst->pam_l =ppst->pam2[0][i][j]; in initpam2()
408 if (ppst->pam_h < ppst->pam2[0][i][j]) ppst->pam_h =ppst->pam2[0][i][j]; in initpam2()
412 ppst->nt_align = (ppst->dnaseq== SEQT_DNA || ppst->dnaseq == SEQT_RNA); in initpam2()
423 ppst->pam2[0][sa_x][i] = ppst->pam2[0][i][sa_x]=ppst->pam_xm; in initpam2()
424 ppst->pam2[0][sa_t][i] = ppst->pam2[0][i][sa_t]=ppst->pam_xm; in initpam2()
[all …]
H A Dapam.c52 ppst->pam_ms = 0; in pam_opts()
53 ppst->pamoff = 0; in pam_opts()
98 SAFE_STRNCPY(ppst->pam_name, ppst->pamfile, MAX_FN); in initpam()
107 ppst->nt_align = (ppst->dnaseq == SEQT_DNA || ppst->dnaseq == SEQT_RNA); in initpam()
157 ppst->pam2[0][0][p_j] = ppst->pam2[0][p_j][0] = -BIGNUM; in initpam()
202 ppst->pam2[0][p_i][i] = ppst->pam2[0][p_j][i]; in initpam()
203 ppst->pam2[0][i][p_i] = ppst->pam2[0][i][p_j]; in initpam()
208 if (ppst->ext_sq_set && ppst->pam2[0][p_j][p_j] >= 0) { in initpam()
254 strncat(ppst->pam_name,"-MS",MAX_FN-strlen(ppst->pam_name)-1); in standard_pam()
278 pam_opts(ppst->pamfile, ppst); in min_pam_bits()
[all …]
H A Ddropgsw2.c682 ppst->pam_name, psi_str, ppst->pam_h,ppst->pam_l, in get_param()
683 (ppst->ext_sq_set)?"xS":"\0", ppst->gdelval, ppst->ggapval); in get_param()
691 pg_str,verstr,ppst->pam_name,psi_str,ppst->pam_h,ppst->pam_l, in get_param()
692 (ppst->ext_sq_set)?"xS":"\0",ppst->gdelval,ppst->ggapval); in get_param()
796 -(ppst->gdelval + ppst->ggapval), in do_work()
840 -(ppst->gdelval + ppst->ggapval), in do_work()
854 -(ppst->gdelval - ppst->ggapval), in do_work()
865 (do_karlin(aa1, n1, ppst->pam2[0], ppst,f_str->aa0_f, in do_work()
1021 -ppst->gdelval, -ppst->ggapval, in do_walign()
1026 if (!ppst->show_ident && same_seq(aa0, n0, aa1, n1)) ppst->nseq = 1; in do_walign()
[all …]
H A Ddropnsw.c101 struct pstruct *ppst, in init_work() argument
113 ppst->stats_mod = 1; in init_work()
274 ppst->pam_name, psi_str, ppst->pam_h,ppst->pam_l, in get_param()
275 (ppst->ext_sq_set)?"xS":"\0", ppst->gdelval, ppst->ggapval); in get_param()
284 pg_str,verstr,psi_str,ppst->pam_h,ppst->pam_l, 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()
355 (do_karlin(aa1, n1, ppst->pam2[0], ppst,f_str->aa0_f, in do_work()
392 -ppst->gdelval, -ppst->ggapval, in do_walign()
397 if (!ppst->show_ident && same_seq(aa0, n0, aa1, n1)) ppst->nseq = 1; in do_walign()
[all …]
H A Ddropnnw2.c249 if (ppst->pam_pssm) { in init_work()
304 if (ppst->pam_pssm) { in init_work()
521 ppst->pam_name, psi_str, ppst->pam_h,ppst->pam_l, in get_param()
522 (ppst->ext_sq_set)?"xS":"\0", ppst->gdelval, ppst->ggapval); in get_param()
530 pg_str,verstr,psi_str,ppst->pam_h,ppst->pam_l, 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()
596 -(ppst->gdelval - ppst->ggapval), in do_work()
606 -(ppst->gdelval - ppst->ggapval), in do_work()
616 (do_karlin(aa1, n1, ppst->pam2[0], ppst,f_str->aa0_f, in do_work()
[all …]
H A Dlast_thresh.c46 const struct mngmsg *m_msg, struct pstruct *ppst in last_calc() argument
55 if (ppst->zdb_size < 0 ) ppst->zdb_size = m_msg->db.entries; in last_calc()
56 …ppst->repeat_thresh = E1_to_s(ppst->e_cut, m_msg->n0, bptr[0]->seq->n1, ppst->zdb_size, pstat_str); in last_calc()
58 ppst->other_info = thresh_str; in last_calc()
59 sprintf(thresh_str,"Threshold: E() < %.2g score: %d\n",ppst->e_cut, ppst->repeat_thresh); in last_calc()
H A Ddropfz2.c447 ppst->param_u.fa.pgap = ppst->gdelval + ppst->ggapval; in init_work()
449 ppst->param_u.fa.pgap = ppst->gdelval + 2*ppst->ggapval; in init_work()
511 ppst->pam2[ip],-ppst->gshift,-ppst->gsubs,naat); in init_work()
513 ppst->pam2[0],-ppst->gshift,-ppst->gsubs,naat); in init_work()
724 ppst->pam_name, ppst->pam_h,ppst->pam_l, in get_param()
726 ppst->gdelval, ppst->ggapval, in get_param()
727 ppst->gshift,ppst->gsubs, in get_param()
740 pg_str,verstr,ppst->pam_name, ppst->pam_h,ppst->pam_l, in get_param()
856 … c_gap = ELK_to_s(ppst->param_u.fa.E_join*ktup_sq*2.5, n0, n1, ppst->pLambda, ppst->pK, ppst->pH);
1054 ppst->gdelval,ppst->ggapval,ppst->gshift,
[all …]
H A Ddropfx.c260 ppst->param_u.fa.pgap = ppst->gdelval + ppst->ggapval; in init_work()
262 ppst->param_u.fa.pgap = ppst->gdelval + 2*ppst->ggapval; in init_work()
265 ppst->param_u.fa.cgap = max(ppst->param_u.fa.cgap, -ppst->param_u.fa.pgap); in init_work()
541 ppst->pam_name, ppst->pam_h,ppst->pam_l, in get_param()
543 ppst->gdelval, ppst->ggapval, ppst->gshift, in get_param()
556 pg_str,verstr,ppst->pam_name, ppst->pam_h,ppst->pam_l, in get_param()
698 … c_gap = ELK_to_s(ppst->param_u.fa.E_join*ktup_sq, n0_eff, n1, ppst->pLambda, ppst->pK, ppst->pH);
699 …opt_cut = ELK_to_s(ppst->param_u.fa.E_band_opt*ktup_sq, n0_eff, n1, ppst->pLambda, ppst->pK, ppst-…
952 -ppst->ggapval,-ppst->gshift,
2286 -(ppst->gdelval - ppst->ggapval),
[all …]
H A Ddropnfa.c170 (ppst->param_u.fa.bktup - ppst->param_u.fa.ktup); in init_work()
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()
626 c_gap = ELK_to_s(ppst->param_u.fa.E_join*ktup_sq, n0, n1, ppst->pLambda, ppst->pK, ppst->pH); in do_fasta()
627 …opt_cut = ELK_to_s(ppst->param_u.fa.E_band_opt*ktup_sq, n0, n1, ppst->pLambda, ppst->pK, ppst->pH); in do_fasta()
809 ppst->param_u.fa.optwid, ppst->pam2[ip], in do_fasta()
810 ppst->gdelval,ppst->ggapval,f_str); in do_fasta()
856 (do_karlin(aa1, n1, ppst->pam2[0], ppst,f_str->aa0_f, in do_work()
1410 -ppst->gdelval, -ppst->ggapval, in bd_malign()
1577 ppst->pam2[0], -ppst->gdelval, -ppst->ggapval, in bd_walign()
[all …]
H A Dcal_cons.c129 struct pstruct *ppst, in calc_cons_a() argument
178 if (ppst->ext_sq_set) { in calc_cons_a()
179 sq = ppst->sqx; in calc_cons_a()
182 sq = ppst->sq; in calc_cons_a()
325 if (ppst->pam_pssm) {aa0_pam2_p = ppst->pam2p[0][i0];} in calc_cons_a()
436 ppst->ggapval+ppst->gdelval); in calc_cons_a()
475 ppst->ggapval+ppst->gdelval); in calc_cons_a()
802 if (ppst->ext_sq_set) { sq = ppst->sqx;} in calc_code()
803 else {sq = ppst->sq;} in calc_code()
878 if (ppst->pam_pssm) {aa0_pam2_p = ppst->pam2p[0][i0];} in calc_code()
[all …]
H A Dmshowbest.c203 if (ppst->show_ident) { in showbest()
261 if (ppst->zsflag >= 0) { in showbest()
265 if (ppst->zsflag > 20) { in showbest()
272 if (ppst->zsflag > 20) { in showbest()
328 if (ppst->do_rep) { in showbest()
330 min(E1_to_s(ppst->e_cut_r, m_msp->n0, bbp->seq->n1,ppst->zdb_size, m_msp->pstat_void), in showbest()
497 if (ppst->zsflag>=0) { in showbest()
500 zs_to_E(lzscore, n1, ppst->dnaseq, ppst->zdb_size, m_msp->db), in showbest()
508 zs_to_E(lzscore, n1, ppst->dnaseq, ppst->zdb_size, m_msp->db), in showbest()
524 zs_to_E(lzscore,n1,ppst->dnaseq,ppst->zdb_size,m_msp->db)); in showbest()
[all …]
H A Ddropfx2.c262 ppst->param_u.fa.pgap = ppst->gdelval + ppst->ggapval; in init_work()
264 ppst->param_u.fa.pgap = ppst->gdelval + 2*ppst->ggapval; in init_work()
267 ppst->param_u.fa.cgap = max(ppst->param_u.fa.cgap, -ppst->param_u.fa.pgap); in init_work()
543 ppst->pam_name, ppst->pam_h,ppst->pam_l, in get_param()
545 ppst->gdelval, ppst->ggapval, ppst->gshift, in get_param()
558 pg_str,verstr,ppst->pam_name, ppst->pam_h,ppst->pam_l, in get_param()
700 … c_gap = ELK_to_s(ppst->param_u.fa.E_join*ktup_sq, n0_eff, n1, ppst->pLambda, ppst->pK, ppst->pH);
701 …opt_cut = ELK_to_s(ppst->param_u.fa.E_band_opt*ktup_sq, n0_eff, n1, ppst->pLambda, ppst->pK, ppst-…
954 -ppst->ggapval,-ppst->gshift,
2288 -(ppst->gdelval - ppst->ggapval),
[all …]
H A Dkarlin.c99 kar_range = ppst->pam_h - ppst->pam_l + 1; in init_karlin()
164 kar_range = ppst->pam_h - ppst->pam_l + 1; in init_karlin_a()
173 if (ppst->nt_align) { in init_karlin_a()
177 else if (ppst->dnaseq==SEQT_PROT || ppst->dnaseq == SEQT_UNK) { in init_karlin_a()
182 kar_nsq = ppst->nsq; in init_karlin_a()
204 kar_nsq = ppst->nsq; in do_karlin()
205 kar_min = ppst->pam_l; in do_karlin()
206 kar_max = ppst->pam_h; in do_karlin()
249 kar_min = ppst->pam_l; in do_karlin_a()
250 kar_max = ppst->pam_h; in do_karlin_a()
[all …]
H A Ddropfz3.c447 ppst->param_u.fa.pgap = ppst->gdelval + ppst->ggapval; in init_work()
449 ppst->param_u.fa.pgap = ppst->gdelval + 2*ppst->ggapval; in init_work()
511 ppst->pam2[ip],-ppst->gshift,-ppst->gsubs,naat); in init_work()
513 ppst->pam2[0],-ppst->gshift,-ppst->gsubs,naat); in init_work()
724 ppst->pam_name, ppst->pam_h,ppst->pam_l, in get_param()
726 ppst->gdelval, ppst->ggapval, in get_param()
727 ppst->gshift,ppst->gsubs, in get_param()
740 pg_str,verstr,ppst->pam_name, ppst->pam_h,ppst->pam_l, in get_param()
856 … c_gap = ELK_to_s(ppst->param_u.fa.E_join*ktup_sq*2.5, n0, n1, ppst->pLambda, ppst->pK, ppst->pH);
1054 ppst->gdelval,ppst->ggapval,ppst->gshift,
[all …]
H A Ddropfs2.c125 ppst->param_u.fa.pgap = ppst->gdelval + ppst->ggapval; in init_work()
134 if (ppst->hsq[NMAP_X] == NMAP ) {ppst->hsq[NMAP_X]=1;} in init_work()
140 if (ppst->hsq[i0] < NMAP && ppst->hsq[i0] > mhv) mhv = ppst->hsq[i0]; in init_work()
1153 ppst->pam2[0], ppst->nsq, f_str, in sconn()
1154 ppst->pseudocts, opt_prob, ppst->zsflag); in sconn()
1190 ppst->pam2[0], ppst->nsq, f_str, in sconn()
1191 ppst->pseudocts, opt_prob, ppst->zsflag); in sconn()
1494 ppst->pam2[0], ppst->nsq, f_str,
1495 ppst->pseudocts, 1, ppst->zsflag);
1519 ppst->pam2[0], ppst->nsq, f_str,
[all …]
H A Ddropff2.c128 if (ppst->hsq[NMAP_X] == NMAP ) {ppst->hsq[NMAP_X]=1;} in init_work()
129 if (ppst->hsq[NMAP_Z] == NMAP ) {ppst->hsq[NMAP_Z]=1;} in init_work()
135 if (ppst->hsq[i0] < NMAP && ppst->hsq[i0] > mhv) mhv = ppst->hsq[i0]; in init_work()
276 ppst->param_u.fa.cgap = shscore(aa0,f_str->nmoff-1,ppst->pam2[0],ppst->nsq)/3; in init_work()
277 if (ppst->param_u.fa.cgap > ppst->param_u.fa.bestmax/4) in init_work()
278 ppst->param_u.fa.cgap = ppst->param_u.fa.bestmax/4; in init_work()
551 ppst->pam2[0], ppst->pam_l, f_str); in do_fastf()
974 ppst->pam2[0],ppst->nsq, f_str, in sconn()
975 ppst->pseudocts, opt_prob,ppst->zsflag); in sconn()
995 ppst->pam2[0], ppst->nsq, f_str, in sconn()
[all …]
H A Dcal_consf.c47 struct pstruct *ppst, in calc_cons_a() argument
199 *sp1 = ppst->sq[aa1p[i1++]]; in calc_cons_a()
222 *sp1++ = ppst->sq[aa1p[i1++]]; in calc_cons_a()
259 n0t-a_res->max0,ppst); in calc_cons_a()
315 struct pstruct *ppst, in calc_code() argument
359 if (ppst->ext_sq_set) {sq = ppst->sqx;} in calc_code()
360 else {sq = ppst->sq;} in calc_code()
422 sp0 = ppst->sq[f_str->aa0t[i0]]; in calc_code()
423 sp1 = ppst->sq[aa1p[i1]]; in calc_code()
509 struct pstruct *ppst, in calc_id() argument
[all …]
H A Dcal_cons2.c134 struct pstruct *ppst, in pre_fill_cons() argument
195 struct pstruct *ppst, in post_fill_cons() argument
303 struct pstruct *ppst, in calc_cons_u() argument
365 if (ppst->ext_sq_set) { sq = ppst->sqx;} in calc_cons_u()
366 else {sq = ppst->sq;} in calc_cons_u()
545 if (ppst->pam_pssm) {aa0_pam2_p = ppst->pam2p[0][i0];} in calc_cons_u()
704 ppst->ggapval+ppst->gdelval); in calc_cons_u()
759 ppst->ggapval+ppst->gdelval); in calc_cons_u()
861 struct pstruct *ppst, in calc_cons_a() argument
1027 struct pstruct *ppst, in calc_code() argument
[all …]
H A Ddrop_func.h32 struct pstruct *ppst,
43 struct pstruct *ppst,
60 const struct pstruct *ppst,
73 struct pstruct *ppst,
86 struct pstruct *ppst,
115 struct pstruct *ppst,
135 struct pstruct *ppst,
158 struct pstruct *ppst,
H A Ddoinit.c270 ppst->tr_type = 0; in initenv()
271 ppst->debug_lib = 0; in initenv()
273 ppst->max_repeat = 50; in initenv()
325 ppst->LK_set = 0; in initenv()
327 ppst->e_cut_r = ppst->e_cut / 10.0; in initenv()
328 ppst->do_rep = 1; in initenv()
329 ppst->zs_win = 0; in initenv()
330 ppst->show_ident = 0; in initenv()
332 ppst->zdb_size = -1; in initenv()
333 ppst->zdb_size_set = 0; in initenv()
[all …]
H A Dscaleswn.c239 return ppst->zsflag; in process_hist()
298 if (ppst->zsflag2 == AG_STATS) ppst->zsflag2 = MLE_STATS; in process_hist()
308 if (!ppst->zdb_size_set) ppst->zdb_size = m_msp->db.entries; in process_hist()
372 if (ppst->dnaseq == SEQT_DNA || ppst->dnaseq == SEQT_RNA) { in calc_thresh()
504 if (ppst->zsflag == REG2_STATS || ppst->zsflag == 10+REG2_STATS || in proc_hist_r()
616 t_gdelval = ppst->gdelval+ppst->ggapval; in proc_hist_a()
644 if (strcmp(ppst->pam_name,"DNA")==0 || (ppst->pam_h==5 && ppst->pam_l == -4)) in proc_hist_a()
646 else if (strcmp(ppst->pam_name,"+3/-2")==0 || (ppst->pam_h==3 && ppst->pam_l == -2)) in proc_hist_a()
648 else if (strcmp(ppst->pam_name,"+1/-3")==0 || (ppst->pam_h==1 && ppst->pam_l == -3)) in proc_hist_a()
2857 if (ppst->zsflag < 0 || ppst->zsflag_f < 0) { in scale_scores()
[all …]
H A Dmshowalign2.c250 if (ppst->can_pre_align) { in showalign()
255 min(E1_to_s(ppst->e_cut_r, m_msp->n0, bbp->seq->n1,ppst->zdb_size, m_msp->pstat_void), in showalign()
275 min(E1_to_s(ppst->e_cut_r, m_msp->n0, bbp->seq->n1,ppst->zdb_size, m_msp->pstat_void), in showalign()
506 if (ppst->nseq == 1) { in showalign()
617 zs_to_E(lzscore, bbp->seq->n1, ppst->dnaseq, ppst->zdb_size, m_msp->db)); in showalign()
683 if (ppst->zsflag>=0) { in showalign()
687 zs_to_E(lzscore, bbp->seq->n1, ppst->dnaseq, ppst->zdb_size, m_msp->db), in showalign()
689 if (ppst->zsflag > 20) { in showalign()
699 zs_to_E(lzscore, bbp->seq->n1, ppst->dnaseq, ppst->zdb_size, m_msp->db)); in showalign()
719 if (ppst->zsflag>=0) in showalign()
[all …]
/dports/biology/fasta3/fasta-36.3.8/doc/
H A Dfasta.options4 case 'D': ppst->debug_lib = 1;
18 case 'v': ppst->zs_win
22 case 'z': ppst->zsflag
23 case 'v': ppst->zs_win
25 case 'Z': ppst->zdb_size
38 case 'f': ppst->gdelval
39 case 'g': ppst->ggapval
42 case 'j': ppst->gshift, ppst->gsubs
49 case 'r': ppst->p_d_mat,&ppst->p_d_mis
53 case 'x': ppst->pam_x
[all …]
/dports/devel/erlang-katana/erlang-katana-0.4.0/src/
H A Dktn_debug.erl7 [ ppst/0
8 , ppst/1
11 -spec ppst() ->
13 ppst() -> function
14 ppst(erlang:get_stacktrace()).
16 -spec ppst([any()]) ->
18 ppst(StackTrace) -> function

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