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/dports/biology/fasta/fasta/
H A Drandlib.c38 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 Drandseq.c35 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 Dbestscor.c17 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 Dzzlgmata.c162 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 Dscore_al.c49 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 Dzxlgmata.c38 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 Dalign.c40 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 Dlalign2.c141 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 Drelate.c33 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 Drevcomp.c9 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 Daacomp.c9 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 Dpscore.c38 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 Ddropff2.c153 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 Dwork_thr2.c100 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 Ddrop_func.h31 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 Ddropfs2.c225 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 Ddropgsw2.c123 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 Dcomp_lib9.c565 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 Dprint_pssm.c49 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 Ddropnfa.c94 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 Ddropnsw.c100 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 Dcal_cons2.c192 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 Dparser.c67 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 DAFunction_ext.hpp23 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 Dprojector.cl269 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 …]

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