/dports/biology/fasta3/fasta-36.3.8/src/ |
H A D | print_pssm.c | 404 ppst->pam2[0][0][i] = ppst->pam2[0][i][0] = -BIGNUM; in initpam2() 711 ppst->pam2[0][ix_j][0] = ppst->pam2[0][0][ix_j] = -BIGNUM; in init_altpam() 714 max(ppst->pam2[0][ix_i][ix_i],ppst->pam2[0][ix_l][ix_l]); in init_altpam() 719 max(ppst->pam2[0][ix_i][p_i],ppst->pam2[0][ix_l][p_i]); in init_altpam() 721 max(ppst->pam2[0][p_i][ix_i],ppst->pam2[0][p_i][ix_l]); in init_altpam() 730 ppst->pam2[0][ix_j][ix_j] = ppst->pam2[0][ix_i][ix_i]; in init_altpam() 734 ppst->pam2[0][ix_j][p_i] = ppst->pam2[0][ix_i][p_i]; in init_altpam() 735 ppst->pam2[0][p_i][ix_j] = ppst->pam2[0][p_i][ix_i]; in init_altpam() 749 ppst->pam2[0][ix_j][ix_j] = ppst->pam2[0][ix_i][ix_i]; in init_altpam() 753 ppst->pam2[0][ix_j][p_i] = ppst->pam2[0][ix_i][p_i]; in init_altpam() [all …]
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H A D | initfa.c | 761 ppst->pam2[0][ix_j][p_i] = ppst->pam2[0][ix_i][p_i]; in init_altpam() 762 ppst->pam2[0][p_i][ix_j] = ppst->pam2[0][p_i][ix_i]; in init_altpam() 780 ppst->pam2[0][ix_j][p_i] = ppst->pam2[0][ix_i][p_i]; in init_altpam() 781 ppst->pam2[0][p_i][ix_j] = ppst->pam2[0][p_i][ix_i]; in init_altpam() 845 ppst->pam2[0][0][i] = ppst->pam2[0][i][0] = in init_pamx() 850 ppst->pam2[0][i+nsq][j] = ppst->pam2[0][i][j+nsq] = ppst->pam2[0][i+nsq][j+nsq] = in init_pamx() 851 ppst->pam2[1][i][j] = ppst->pam2[0][i][j]; in init_pamx() 856 ppst->pam2[1][i+nsq][j] = ppst->pam2[1][i][j+nsq]= in init_pamx() 866 ppst->pam2[1][nsq][i] = ppst->pam2[1][i][nsq] = in init_pamx() 1902 ppst->pam2[0][i][ix_i] = ppst->pam2[0][i][ix_l] = in last_init() [all …]
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H A D | apam.c | 153 ppst->pam2[0][0][0] = -BIGNUM; in initpam() 157 ppst->pam2[0][0][p_j] = ppst->pam2[0][p_j][0] = -BIGNUM; in initpam() 178 pval=ppst->pam2[0][p_i][p_j]=atoi(lp); /* convert to integer */ 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() 209 ppst->pam2[0][p_j][p_j] = -1; in initpam() 500 fprintf(stderr," %c:%c - %3d\n",sq[i], sq[i], ppst->pam2[ip][i][i]); in print_pam()
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H A D | work_thr2.c | 274 my_pst.pam2[0][i][j] = work_info->ppst->pam2[0][i][j]; 275 my_pst.pam2[1][i][j] = work_info->ppst->pam2[1][i][j]; 284 MPI_Recv(&my_pst.pam2[0][0][0],my_msg.pamd1*my_msg.pamd2,MPI_INT,0, 287 MPI_Recv(&my_pst.pam2[1][0][0],my_msg.pamd1*my_msg.pamd2,MPI_INT,0, 463 free(my_pst.pam2[1][0]); 464 free(my_pst.pam2[0][0]); 465 free(my_pst.pam2[1]); 466 free(my_pst.pam2[0]);
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H A D | lsim4.h | 61 int **pam2, int Q, int R, 69 int **pam2, int Q, int R, 78 int **pam2, int Q, int R, 92 int **pam2, int q, int r,
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H A D | lsim4.c | 221 int **pam2, in big_pass() argument 261 va = pam2[A[i]]; in big_pass() 384 va = pam2[A[i]]; in locate() 431 va = pam2[A[l_ptr->m1]]; in locate() 479 va = pam2[B[l_ptr->n1]]; in locate() 546 int **pam2, int Q, int R, in small_pass() argument 581 va = pam2[A[i]]; in small_pass() 766 int **pam2, int Q, int R, in diff() argument 804 va = pam2[A[1]]; in diff() 845 va = pam2[A[i]]; in diff() [all …]
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H A D | tatstats.c | 196 int **pam2, int nsq, in calc_tatusov() argument 348 generate_tatprobs(query, 0, length - 1, priors, pam2, nsq, &newtat, oldtat); in calc_tatusov() 404 int **pam2, in generate_tatprobs() argument 450 (highrange[i] = highscore + max_score(pam2[query[begin + i]], nsq)); in generate_tatprobs() 453 (lowrange[i] = lowscore + min_score(pam2[query[begin + i]], nsq)); in generate_tatprobs() 484 pamptr = pam2[query[begin]]; in generate_tatprobs() 509 pamptrsave = pam2[query[begin + i]]; in generate_tatprobs()
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H A D | dropff2.c | 223 f_str->pamh2[hv] = ppst->pam2[0][aa0[i0]][aa0[i0]]; in init_work() 274 f_str->pamh1[i0] = ppst->pam2[0][i0][i0]; in init_work() 551 ppst->pam2[0], ppst->pam_l, f_str); in do_fastf() 738 struct savestr *dmax, int **pam2, int pam_l, in m1_spam() argument 805 int **pam2; in ma_spam() local 815 pam2 = ppst->pam2[0]; in ma_spam() 883 struct savestr *dmax, int **pam2, in m0_spam() argument 922 if ((pv = pam2[aa0p[ii]][*aa1p]) > ctot) { in m0_spam() 974 ppst->pam2[0],ppst->nsq, f_str, in sconn() 995 ppst->pam2[0], ppst->nsq, f_str, in sconn() [all …]
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H A D | dropgsw2.c | 77 int **pam2, const struct pstruct *ppst, 253 *pwaa_s++ = f_str->pam2p[ip][f][e]= ppst->pam2[ip][aa0[f]][e]; in init_work() 254 *pwaa_a++ = f_str->pam2p[0][f][e] = ppst->pam2[0][aa0[f]][e]; in init_work() 373 data = ppst->pam2[ip][i][j]; in init_work() 394 data = ppst->pam2[ip][aa0[l]][e] - bias; in init_work() 414 data = ppst->pam2[ip][aa0[l]][e] - bias; in init_work() 545 data = ppst->pam2[ip][i][j]; in init_work() 569 data = ppst->pam2[ip][aa0[i]][f]; in init_work() 588 data = ppst->pam2[ip][aa0[i]][f] - bias; in init_work() 865 (do_karlin(aa1, n1, ppst->pam2[0], ppst,f_str->aa0_f, in do_work()
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H A D | dropfs2.c | 246 phv = ppst->pam2[0][aa0[0]][aa0[0]]; in init_work() 259 phv = ppst->pam2[0][aa0[i0]][aa0[i0]]; in init_work() 317 stmp += ppst->pam2[0][aa0[i0]][aa0[i0]]; in init_work() 457 f_str->pamh1[i0] = ppst->pam2[0][i0][i0]; in init_work() 1024 struct savestr *dmax, int **pam2, in spam() argument 1041 tot += pam2[*aa0p++][*aa1p++]; in spam() 1088 tot += pam2[*aa0p++][*aa1p++]; in spam() 1153 ppst->pam2[0], ppst->nsq, f_str, in sconn() 1190 ppst->pam2[0], ppst->nsq, f_str, in sconn() 1494 ppst->pam2[0], ppst->nsq, f_str, [all …]
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H A D | dropfz2.c | 176 struct savestr *dmax, int **pam2, 584 phv += ppst->pam2[ip][aa0[i0]][aa0[i0]]*ktup; in init_work() 660 *pwaa = ppst->pam2[ip][i][aa0[j]]; in init_work() 1053 ppst->pam2[ip], 1191 struct savestr *dmax, int **pam2, argument 1207 tot += pam2[*aa0p++][*aa1p++]; 1366 pam2, 1376 pam2, 1563 sum += pam2[aa0[i]][aa0[i]]; 2406 ppst->pam2[0], [all …]
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H A D | tatstats.h | 119 int **pam2, 128 int **pam2, int nsq,
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H A D | dropnfa.c | 97 int **pam2, int gdelval, int ggapval, 255 phv += ppst->pam2[ip][aa0[i0]][aa0[i0]]*ktup; in init_work() 269 phv += ppst->pam2[ip][aa0[i0]][aa0[i0]]*ktup; in init_work() 809 ppst->param_u.fa.optwid, ppst->pam2[ip], in do_fasta() 923 struct savestr *dmax, int **pam2, int xdrop, in spam() argument 946 tot += pam2[*aa0p++][*aa1p++]; in spam() 981 tot += pam2[*(++aa0p)][*(++aa1p)]; in spam() 999 tot += pam2[*(--aa0p)][*(--aa1p)]; in spam() 1130 int **pam2, int gdelval, int ggapval, in dmatch() argument 1151 pam2, in dmatch() [all …]
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H A D | dropnnw2.c | 85 int **pam2, const struct pstruct *ppst, 260 *pwaa_s++ = f_str->pam2p[ip][f][e]= ppst->pam2[ip][aa0[f]][e]; in init_work() 261 *pwaa_a++ = f_str->pam2p[0][f][e] = ppst->pam2[0][aa0[f]][e]; in init_work() 372 data = ppst->pam2[ip][i][j]; in init_work() 399 data = ppst->pam2[ip][aa0[i]][f] + gap; in init_work() 418 data = ppst->pam2[ip][aa0[i]][f] + gap; in init_work() 616 (do_karlin(aa1, n1, ppst->pam2[0], ppst,f_str->aa0_f, in do_work()
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H A D | dropnsw.c | 60 int **pam2, const struct pstruct *ppst, 220 *pwaa_s++ = f_str->pam2p[ip][f][e]= ppst->pam2[ip][e][aa0[f]]; in init_work() 221 *pwaa_a++ = f_str->pam2p[0][f][e] = ppst->pam2[0][e][aa0[f]]; in init_work() 355 (do_karlin(aa1, n1, ppst->pam2[0], ppst,f_str->aa0_f, in do_work()
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/dports/graphics/netpbm/netpbm-10.91.01/analyzer/ |
H A D | pnmpsnr.c | 168 struct pam const pam2) { in validateInput() argument 170 if (pam1.width != pam2.width) in validateInput() 174 pam1.width, pam2.width); in validateInput() 175 if (pam1.height != pam2.height) in validateInput() 179 pam1.height, pam2.height); in validateInput() 181 if (pam1.maxval != pam2.maxval) in validateInput() 189 if (!streq(pam1.tuple_type, pam2.tuple_type)) in validateInput() 192 pam1.tuple_type, pam2.tuple_type); in validateInput() 579 struct pam pam1, pam2; in main() local 594 validateInput(pam1, pam2); in main() [all …]
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/dports/biology/fasta/fasta/ |
H A D | lalign2.c | 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() 330 SIM(aa0-1,aa1-1,n0,n1,m_score,pam2,-gdelval,-ggapval,nseq,K,z_size); in main() 487 if ((pam2 = (int **)calloc(MAXSQ, sizeof(int *)))==NULL) { in initpam2() 492 if ((pam2[i] = (int *)calloc(MAXSQ, sizeof(int *)))==NULL) { in initpam2() 501 tmp=pam2[j][i] = pam2[i][j] = pam[k++]; in initpam2() 508 tmp = pam2[nascii['G']][nascii['G']] - 1; in initpam2() 509 pam2[nascii['A']][nascii['G']] = in initpam2() 510 pam2[nascii['C']][nascii['T']] = in initpam2() [all …]
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H A D | pscore.c | 50 printf("%c:%c %d\n",sq[ca0],sq[ca1],pam2[ca0][ca1]); 118 pam2[j][i] = pam2[i][j] = pam[k++]; in initpam2()
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H A D | bestscor.c | 130 sum += pam2[aa0[i]][aa0[i]]; 141 pam2[j][i] = pam2[i][j] = pam[k++]; in initpam2()
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H A D | zzlgmata.c | 98 pam2,-(gdelval-ggapval),-ggapval,optwid); 106 pam2,-(gdelval-ggapval),-ggapval,1, 124 RLOCAL_ALIGN(aa0-1,aa1-1,s0+1,s1+1, low, up, pam2, 133 pam2,-(gdelval-ggapval),-ggapval,0, 151 pam2,-(gdelval-ggapval),-ggapval,res,optwid,n0); 266 waa1=pam2[aa1[i]]; 299 h = max(max(ss[j].E,f),p+pam2[aa0[j]][aa1[i]]); 321 ALIGN(&aa0[min0-2],&aa1[min1-2],max0-min0+1,max1-min1+1,pam2,q,r,res,&nres);
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H A D | readme.v21u0 | 11 Modify fffasta.c to support the **pam2 global in upam.gbl, rather than 12 pam2[][] - **pam2 was introduced for lalign2.c/lsim3.c.
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H A D | align.c | 157 gscore = ALIGN(&aa0[-1],&aa1[-1],n0,n1,pam2 in main() 299 if ((pam2 = (int **)calloc(MAXSQ, sizeof(int *)))==NULL) { in initpam2() 304 if ((pam2[i] = (int *)calloc(MAXSQ, sizeof(int *)))==NULL) { in initpam2() 312 pam2[j][i] = pam2[i][j] = pam[k++]; in initpam2()
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H A D | score_al.c | 216 gscore = score_aln(aa0,n0,aa1,n1,pam2 339 pam2[j][i] = pam2[i][j] = pam[k++]; in initpam2() 343 int pam2[MAXSQ][MAXSQ], int gdelval, int ggapval) in score_aln() 365 score += (inc = pam2[aa0[i]][aa1[i]]); in score_aln()
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H A D | relate.c | 279 while (n-->0) tot += pam2[*sq0++][*sq1++]; 290 pam2[j][i] = pam2[i][j] = pam[k++]; in initpam2() 298 sum += pam2[aa0[i]][aa0[i]];
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/dports/science/py-dipy/dipy-1.4.1/dipy/io/tests/ |
H A D | test_io_peaks.py | 32 pam2 = load_peaks(fname, verbose=True) 33 npt.assert_array_equal(pam.peak_dirs, pam2.peak_dirs) 35 pam2.affine = None 38 save_peaks(fname2, pam2, np.eye(4))
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