/dports/biology/fasta/fasta/ |
H A D | randlib.c | 38 char *aa0, *aa10; /* amino acid sequence data */ variable 90 if ((aa0=calloc(maxn,sizeof(char)))==0) { 181 i,aa0[i],sq[aa0[i]],sq[aa0[i]]); 191 for (i=0; i<n0; i++) aa10[i]=aa0[i]; 198 wshuffle(aa10,aa0,n0,wtmp); 200 else if (wflag==3) shuffle3(aa0,n0,iframe-1); 201 else shuffle(aa0,n0); 204 if (sq[aa0[i]] <= 0) 206 libstr,i,aa0[i],sq[aa0[i]],sq[aa0[i]]); 215 if (sq[aa0[i]] > 0) fputc(sq[aa0[i]],outfd); [all …]
|
H A D | randseq.c | 35 char *aa0, *aa10; /* amino acid sequence data */ variable 99 if ((n0=getseq(tname,aa0,maxn,&dnaseq))==0) { 139 if ((n0=getseq(tname,aa0,maxn,&dnaseq))==0) { 156 for (i=0; i<n0; i++) aa10[i]=aa0[i]; 178 i,aa0[i],sq[aa0[i]],sq[aa0[i]]); 182 if (wflag==1) wshuffle(aa10,aa0,n0,wsiz); 183 else if (wflag==3) shuffle3(aa0,n0,iframe-1); 184 else shuffle(aa0,n0); 188 i,aa0[i],sq[aa0[i]],sq[aa0[i]]); 197 if (sq[aa0[i]] > 0) fputc(sq[aa0[i]],outfd); [all …]
|
H A D | bestscor.c | 17 char *aa0; variable 54 if ((aa0=calloc((size_t)MAXDIAG,sizeof(char)))==0) { 59 if ((n0=getseq(tname,aa0,MAXDIAG,&dnaseq))==0) { 70 smptr,shscore(aa0,n0)); 125 shscore(aa0,n0) /* calculate the 100% identical score */ in shscore() argument 126 char *aa0; int n0; in shscore() 130 sum += pam2[aa0[i]][aa0[i]];
|
H A D | zzlgmata.c | 162 ns = calcons(aa0,n0,aa1,n1,res,&nc); 228 smatch(aa0,n0,aa1,n1,flag) in smatch() argument 229 char *aa0, *aa1; in smatch() 339 nc=calcons(aa0,n0,aa1,n1,res,&lc); 398 calcons(aa0,n0,aa1,n1,res,nc) in calcons() argument 399 char *aa0, *aa1; in calcons() 438 aancpy(seqc0+mins-min0,aa0,min0); 442 aancpy(seqc0,aa0+min0-mins,mins); 451 aancpy(seqc0,aa0+min0-mins,mins); 472 *sp0 = sq[aa0[i0++]]; [all …]
|
H A D | score_al.c | 49 char *aa0, *aa1; /* amino acid sequence data */ variable 200 aa1 = aa0 + n0 + 2; 216 gscore = score_aln(aa0,n0,aa1,n1,pam2 224 nc=calcons(aa0,n0,aa1,n1,&nd); 342 score_aln(char *aa0, int n0, char *aa1, int n1, in score_aln() argument 353 if ((aa0[i]==GCODE) || (aa1[i]==GCODE)) { in score_aln() 354 if (aa0[i]==GCODE) sc0 = '-'; in score_aln() 355 else sc0 = sq[aa0[i]]; in score_aln() 365 score += (inc = pam2[aa0[i]][aa1[i]]); in score_aln() 366 sc0 = sq[aa0[i]]; in score_aln() [all …]
|
H A D | zxlgmata.c | 38 extern unsigned char *aa0, *aa1; /* sequence arrays */ 81 score = lx_align(aa0, n0, aa1y, n1, pam2, -(gdelval-ggapval), 111 ns = calcons(aa0,n0,aa1,n1,res,nres,&nc); 163 pmatch(aa0,n0,aa0t,n0t,aa1,n1,flag) in pmatch() argument 164 unsigned char *aa0, *aa0t, *aa1; in pmatch() 238 calcons(aa0,n0,aa1,n1,res,nres,nc) in calcons() argument 239 char *aa0, *aa1; in calcons() 285 *sp0 = sq[aa0[i0]]; 293 *sp0 = sq[aa0[i0]]; 305 *sp0 = sq[aa0[i0]]; [all …]
|
H A D | align.c | 40 int calcons(unsigned char *aa0, int n0, unsigned char *aa1, int n1, int *res); 54 unsigned char *aa0, *aa1; /* amino acid sequence data */ variable 102 if ((aa0=(unsigned char *)calloc((size_t)MAXTST+MAXLIB,sizeof(char)))==0) { in main() 116 if ((n0=getseq(tname,aa0,maxn,&dnaseq))==0) { in main() 133 if ((n0=getseq(tname,aa0,maxn,&dnaseq))==0) { in main() 146 aa1 = aa0 + n0 + 2; in main() 157 gscore = ALIGN(&aa0[-1],&aa1[-1],n0,n1,pam2 in main() 165 nc=calcons(aa0,n0,aa1,n1,res); in main() 318 calcons(unsigned char *aa0, int n0, in calcons() argument 336 *sp0 = sq[aa0[i0++]]; in calcons() [all …]
|
H A D | lalign2.c | 141 if ((aa0=calloc((size_t)MAXTST+MAXLIB,sizeof(char)))==0) { in main() 156 if ((n0=getseq(tname,aa0,maxn,&dnaseq))==0) { in main() 164 if (sqtype[0]=='D') revcomp(aa0,n0); in main() 186 if ((n0=getseq(tname,aa0,maxn,&dnaseq))==0) { in main() 193 if ((sqtype[0]=='D')) revcomp(aa0,n0); in main() 232 aa1 = aa0 + n0 + 2; in main() 252 if (aa0[i]!=aa1[i]) break; in main() 257 aa1 = aa0; in main() 518 calcons(const unsigned char *aa0, int n0, in calcons() argument 546 *sp0 = sq[aa0[i0++]]; in calcons() [all …]
|
H A D | relate.c | 33 char *aa0, *aa1; /* amino acid sequence data */ variable 82 if ((aa0=calloc((size_t)MAXTST+MAXLIB,sizeof(char)))==0) { 98 if ((n0=getseq(tname,aa0,MAXTST,&dnaseq))==0) { 122 if ((n0=getseq(tname,aa0,MAXTST,&dnaseq))==0) { 141 aa1 = aa0 + n0 + 2; 256 addhist(spam(aa0+i0,aa1+i1,ktup)); in dhash() 293 shscore(aa0,n0) /* calculate the 100% identical score */ in shscore() argument 294 char *aa0; int n0; in shscore() 298 sum += pam2[aa0[i]][aa0[i]];
|
H A D | revcomp.c | 9 unsigned char *aa0; variable 31 if ((aa0=(unsigned char *)calloc((size_t)MAXSEQ,sizeof(char)))==NULL) { 47 if ((n0=fgetseq(aa0,MAXSEQ-1,libstr,ntfd))<=0) exit(0); 49 revcomp(aa0,n0); 53 fputc(nt[aa0[i]],stdout);
|
H A D | aacomp.c | 9 char *aa0; variable 46 if ((aa0=calloc((size_t)MAXSEQ,sizeof(char)))==NULL) { 62 if ((n0=fgetseq(aa0,MAXSEQ-1,aafd))<=0) exit(0); 66 for (ia=0; ia<n0; ia++) naac[aa0[ia]]++;
|
H A D | pscore.c | 38 char aa0,aa1,ca0,ca1; local 48 sscanf(rline,"%c %c",&aa0, &aa1); 49 if ((ca0=sascii[aa0])<NA && (ca1=sascii[aa1])<NA) 51 else printf("%c %c - not recognized\n",aa0,aa1);
|
/dports/biology/fasta3/fasta-36.3.8/src/ |
H A D | dropff2.c | 153 for (i=0; i<n0; i++) f_str->aa0[i] = aa0[i]; in init_work() 154 aa0 = f_str->aa0; in init_work() 209 if (aa0[i0] == ESS || aa0[i0] == 0) { in init_work() 223 f_str->pamh2[hv] = ppst->pam2[0][aa0[i0]][aa0[i0]]; in init_work() 384 free(f_str->aa0); in close_work() 556 if (aa0[tpos] >= 32) aa0[tpos] -= 32; in do_fastf() 774 aa0p = &aa0[tpos]; in m1_spam() 914 aa0p = &aa0[tpos]; in m0_spam() 1200 if (f_str->aa0[ib] >= 32) f_str->aa0[ib] -= 32; in do_walign() 1347 if (aa0[i]!=0 && aa0[i]<=nsq) sum += pam2[aa0[i]][aa0[i]]; in shscore() [all …]
|
H A D | work_thr2.c | 100 buf_do_align(unsigned char **aa0, int n0, 145 unsigned char *aa0[6], *aa0s; local 364 *aa0[0]='\0'; 365 aa0[0]++; 368 memcpy(aa0[0],work_info->aa0,n0+1); 372 MPI_Recv(aa0[0],n0+1,MPI_BYTE,0, 387 init_aa0(aa0, n0, nm0, &aa0s, &aa1s, 444 close_work(aa0[0], n0, my_ppst, &f_str[0]); 445 free(aa0[0]-1); 447 close_work(aa0[1], n0, my_ppst, &f_str[1]); [all …]
|
H A D | drop_func.h | 31 init_work (unsigned char *aa0, int n0, 42 close_work (const unsigned char *aa0, int n0, 57 do_work (const unsigned char *aa0, int n0, 70 do_opt (const unsigned char *aa0, int n0, 83 do_walign (const unsigned char *aa0, int n0, 110 calc_cons_a(const unsigned char *aa0, int n0, 131 calc_code(const unsigned char *aa0, int n0, 154 calc_id(const unsigned char *aa0, int n0,
|
H A D | dropfs2.c | 225 if (aa0[i0] == ESS || aa0[i0] == 0) nsegs++; in init_work() 246 phv = ppst->pam2[0][aa0[0]][aa0[0]]; in init_work() 250 if (aa0[i0] == ESS || aa0[i0] == 0) { in init_work() 258 hv = ppst->hsq[aa0[i0]]; in init_work() 259 phv = ppst->pam2[0][aa0[i0]][aa0[i0]]; in init_work() 267 f_str->pamh2[hv] = (phv += ppst->pam2[0][aa0[i0]][aa0[i0]]); in init_work() 268 phv -= ppst->pam2[0][aa0[i0 - kt1]][aa0[i0 - kt1]]; in init_work() 306 if (aa0[i0]==EOSEQ) { in init_work() 317 stmp += ppst->pam2[0][aa0[i0]][aa0[i0]]; in init_work() 1322 if (aa0[i] != EOSEQ && aa0[i]<=nsq) sum += pam2[aa0[i]][aa0[i]]; in shscore() [all …]
|
H A D | dropgsw2.c | 123 int same_seq(const unsigned char *aa0, int n0, 132 init_work (unsigned char *aa0, int n0, in init_work() argument 394 data = ppst->pam2[ip][aa0[l]][e] - bias; in init_work() 414 data = ppst->pam2[ip][aa0[l]][e] - bias; in init_work() 708 if (same_seq(aa0,n0,aa1,n1)) { in do_work() 722 score = smith_waterman_altivec_byte(aa0, in do_work() 789 score = smith_waterman_sse2_byte(aa0, in do_work() 834 score = smith_waterman_sse2_word(aa0, in do_work() 851 score = FLOCAL_ALIGN(aa0,aa1,n0,n1,0,0, in do_work() 1001 do_walign (const unsigned char *aa0, int n0, in do_walign() argument [all …]
|
H A D | comp_lib9.c | 565 aa0[0] = NULL; in main() 592 if (aa0[0]==NULL) { in main() 596 *aa0[0]=0; in main() 597 aa0[0]++; in main() 599 aa0[5]=aa0[4]=aa0[3]=aa0[2]=aa0[1]=aa0[0]; in main() 669 if (aa0[0][m_msg.n0-1] == ESS) { m_msg.n0--; aa0[0][m_msg.n0]= '\0';} in main() 684 aa0[0][id++]=aa0[0][is++]; in main() 686 aa0[0][id]=0; in main() 1106 *aa0[1]='\0'; in main() 1107 aa0[1]++; in main() [all …]
|
H A D | print_pssm.c | 49 read_asn_pssm(unsigned char *aa0, int n0, int nsq, 56 double get_lambda(int **pam2p, int n0, int nsq, char *aa0); 67 unsigned char *aa0; in main() local 92 if ((aa0 = calloc(MAXTST,sizeof(char)))==NULL) { in main() 112 read_pssm(aa0, n0, pst.nsq, pst.pamscale, fp, 0, &pst); in main() 436 get_lambda(int **pam2p, int n0, int nsq, char *aa0) { in get_lambda() argument 470 if (aa0[i] < 'A') {aa0i = aa0[i];} in get_lambda() 471 else {aa0i = aascii[aa0[i]];} in get_lambda() 543 read_asn_pssm(unsigned char *aa0, int n0, int nsq, in read_asn_pssm() argument 566 if (!query) { query = (char *)aa0;} in read_asn_pssm() [all …]
|
H A D | dropnfa.c | 94 dmatch (const unsigned char *aa0, int n0, 122 init_work (unsigned char *aa0, int n0, in init_work() argument 255 phv += ppst->pam2[ip][aa0[i0]][aa0[i0]]*ktup; in init_work() 259 if (hsq[aa0[i0]] >= NMAP) { in init_work() 263 if (hsq[aa0[i0]] >= NMAP) { in init_work() 269 phv += ppst->pam2[ip][aa0[i0]][aa0[i0]]*ktup; in init_work() 277 f_str->pamh2[hv] = (phv += ppst->pam2[ip][aa0[i0]][aa0[i0]] * ktup); in init_work() 279 if (hsq[aa0[i0-kt1]]<NMAP) in init_work() 280 phv -= ppst->pam2[ip][aa0[i0 - kt1]][aa0[i0 - kt1]] * ktup; in init_work() 939 if (aa0p < aa0) { return -99; } in spam() [all …]
|
H A D | dropnsw.c | 100 void init_work (unsigned char *aa0, int n0, in init_work() argument 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() 231 void close_work (const unsigned char *aa0, int n0, in close_work() argument 290 void do_work (const unsigned char *aa0, int n0, in do_work() argument 338 for (ssj = ss, aa0p = aa0; ssj < ss+n0; ssj++) { in do_work() 363 void do_opt (const unsigned char *aa0, int n0, in do_opt() argument 372 do_walign (const unsigned char *aa0, int n0, in do_walign() argument 397 if (!ppst->show_ident && same_seq(aa0, n0, aa1, n1)) ppst->nseq = 1; in do_walign() 400 SIM(aa0-1, aa1-1, n0, n1, ppst, ppst->nseq, repeat_thresh, ppst->max_repeat, a_res); in do_walign()
|
H A D | cal_cons2.c | 192 post_fill_cons(const unsigned char *aa0, int n0, in post_fill_cons() argument 300 const unsigned char *aa0, int n0, in calc_cons_u() argument 550 *sp0_p = sq[aa0[i0]]; in calc_cons_u() 601 if (sq[aa0[i0]] != *sp0_p) { in calc_cons_u() 607 sq[aa0[i0]], sim_sym[t_spa], ann_comment, in calc_cons_u() 745 *sp0_p = sq[aa0[i0]]; in calc_cons_u() 838 nd = post_fill_cons(aa0, n0, aa1p, nn1, in calc_cons_u() 872 aa0, n0, aa1, n1, in calc_cons_a() 1043 aa0, n0, aa1, n1, in calc_code() 1055 int calc_id(const unsigned char *aa0, int n0, in calc_id() argument [all …]
|
/dports/www/phalcon/cphalcon-3.4.5/ext/phalcon/annotations/ |
H A D | parser.c | 67 phannot_TOKENTYPE aa0; member 372 if ((aapminor->aa0)) { in aa_destructor() 374 efree((aapminor->aa0)->token); in aa_destructor() 376 efree((aapminor->aa0)); in aa_destructor() 829 #define ATOKEN (aaminor.aa0) in aa_syntax_error() 937 aaminorunion.aa0 = aaminor; in phannot_() 1111 phannot_TOKENTYPE aa0; member 1416 if ((aapminor->aa0)) { in aa_destructor() 1420 efree((aapminor->aa0)); in aa_destructor() 1873 #define ATOKEN (aaminor.aa0) in aa_syntax_error() [all …]
|
/dports/math/freefem++/FreeFem-sources-4.6/src/fflib/ |
H A D | AFunction_ext.hpp | 23 Expression aa0, in E_F_F0F0s_() argument 25 : f(ff), a0(aa0), a1(aa1) {} // extend (2th arg.) in E_F_F0F0s_() 74 Expression aa0, in E_F_F0F0F0s_() argument 77 : f(ff), a0(aa0), a1(aa1), a2(aa2) {} // extend (2th arg.) in E_F_F0F0F0s_() 132 Expression aa0, in E_F_F0F0F0F0_() argument 136 : f(ff), a0(aa0), a1(aa1), a2(aa2), a3(aa3) {} // extend (4th arg.) in E_F_F0F0F0F0_() 181 Expression aa0, in E_F_F0F0F0F0s_() argument 238 Expression aa0, in E_F_F0F0F0F0F0_() argument 298 Expression aa0, in E_F_F0F0F0F0F0F0_() argument 363 Expression aa0, in E_F_F0F0F0F0F0F0F0_() argument [all …]
|
/dports/science/octopus/octopus-10.5/share/opencl/ |
H A D | projector.cl | 269 double aa0 = 0.0; 275 aa0 += matrix[matrix_offset + ip + nppj]*psi[((map[map_offset + ip] - 1)<<ldpsi) + ist]; 314 double2 aa0 = 0.0; 321 aa0 += matrix[matrix_offset + ip + nppj]*phasepsi; 361 double2 aa0 = 0.0; 370 aa0 += matrix[matrix_offset + ip + nppj]*phasepsi; 505 double aa0 = 0.0; 550 double2 aa0 = 0.0; 563 aa0 = complex_mul(phase, aa0); 601 double2 aa0 = 0.0; [all …]
|