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Searched refs:pam2 (Results 1 – 25 of 46) sorted by relevance

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/dports/biology/fasta3/fasta-36.3.8/src/
H A Dprint_pssm.c404 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 …]
H A Dinitfa.c761 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 …]
H A Dapam.c153 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()
H A Dwork_thr2.c274 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]);
H A Dlsim4.h61 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,
H A Dlsim4.c221 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()
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H A Dtatstats.c196 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()
H A Ddropff2.c223 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 …]
H A Ddropgsw2.c77 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()
H A Ddropfs2.c246 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,
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H A Ddropfz2.c176 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],
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H A Dtatstats.h119 int **pam2,
128 int **pam2, int nsq,
H A Ddropnfa.c97 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 …]
H A Ddropnnw2.c85 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()
H A Ddropnsw.c60 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()
/dports/graphics/netpbm/netpbm-10.91.01/analyzer/
H A Dpnmpsnr.c168 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()
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/dports/biology/fasta/fasta/
H A Dlalign2.c319 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()
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H A Dpscore.c50 printf("%c:%c %d\n",sq[ca0],sq[ca1],pam2[ca0][ca1]);
118 pam2[j][i] = pam2[i][j] = pam[k++]; in initpam2()
H A Dbestscor.c130 sum += pam2[aa0[i]][aa0[i]];
141 pam2[j][i] = pam2[i][j] = pam[k++]; in initpam2()
H A Dzzlgmata.c98 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);
H A Dreadme.v21u011 Modify fffasta.c to support the **pam2 global in upam.gbl, rather than
12 pam2[][] - **pam2 was introduced for lalign2.c/lsim3.c.
H A Dalign.c157 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()
H A Dscore_al.c216 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()
H A Drelate.c279 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]];
/dports/science/py-dipy/dipy-1.4.1/dipy/io/tests/
H A Dtest_io_peaks.py32 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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