/dports/biology/fasta/fasta/ |
H A D | zzlgmata.c | 171 discons(seqc0,seqc1,ns); 176 discons(seqc0,seqc1,ns); 201 discons(seqc0,seqc1,ns); 210 discons(seqc1,seqc0,ns); 352 discons(seqc0,seqc1,nc); 360 discons(seqc0,seqc1,nc); 389 free(seqc0); free(seqc1); in freeseq() 421 memset(seqc1,' ',mins-min1); 463 sp1 = seqc1+mins; 533 crcknew(seqc0,seqc1,nc,maxcrc) in crcknew() argument [all …]
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H A D | zxlgmata.c | 124 discons(seqc0,seqc1,ns); 128 if (crcknew(seqc0,seqc1,ns)) { 134 discons(seqc0,seqc1,ns); 143 discons(seqc1,seqc0,ns); 200 discons(seqc0,seqc1,nc); 220 seqc1=calloc((size_t)seqsiz,sizeof(char)); 221 if (seqc0==NULL || seqc1==NULL) 229 free(seqc0); free(seqc1); in freeseq() 258 sp1 = seqc1; 263 sp0 = seqc1;
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H A D | ndispn.c | 31 discons(char *seqc0, char *seqc1, int nc) in discons() argument 71 for (i=0; i<nc && seqc1[i]; i++) { in discons() 74 fputc(seqc1[i],outfd); in discons() 108 for (i=0; i<nc && seqc1[i]; i++) { in discons() 109 if (!have_res && seqc1[i]==' ') fputc('-',outfd); in discons() 110 else if (seqc1[i]==' ') break; in discons() 113 fputc(seqc1[i],outfd); in discons() 117 if ((i-1)%50!=49 || seqc1[i-1]==' ') fputc('\n',outfd); in discons() 137 if ((line[2][i]=seqc1[ic])=='-') { in discons() 143 if (seqc1[ic]==' ') {del1++; cl1=rl1=NO;} in discons()
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H A D | align.c | 33 extern void discons(char *seqc0, char *seqc1, int nc); 59 char *seqc0, *seqc1; /* aligned sequences */ variable 182 discons(seqc0,seqc1,nc); in main() 193 discons(seqc0,seqc1,nc); in main() 328 sp1 = seqc1; in calcons() 366 seqc1=calloc((size_t)seqsiz,sizeof(char)); in initseq() 367 if (res==NULL || seqc0==NULL || seqc1==NULL) in initseq() 375 free(seqc0); free(seqc1); in freeseq()
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H A D | fldispn.c | 57 discons(seqc0, seqc1, nc) in discons() argument 58 char *seqc0, *seqc1; in discons() 72 if (seqc0[ii]==' ' || seqc1[ii]==' ') continue; 73 if (seqc0[ii]!='-'&&seqc1[ii]!='-') { 89 else if (seqc1[ii]=='-') { 106 if (seqc0[ii]==' ' || seqc1[ii]==' ') continue; 107 if (seqc0[ii]!='-'&&seqc1[ii]!='-') { 123 else if (seqc1[ii]=='-') {
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H A D | tldispn.c | 50 discons(seqc0, seqc1, nc) in discons() argument 51 char *seqc0, *seqc1; in discons() 71 if (seqc0[ii]==' ' || seqc1[ii]==' ') continue; 72 if (seqc0[ii]!='-'&&seqc1[ii]!='-') { 93 else if (seqc1[ii]=='-') {
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H A D | mtdispn.c | 69 discons(seqc0, seqc1, nc) in discons() argument 70 char *seqc0, *seqc1; in discons() 84 if (seqc0[ii]==' ' || seqc1[ii]==' ') continue; 85 if (seqc0[ii]!='-'&&seqc1[ii]!='-') { 101 else if (seqc1[ii]=='-') {
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H A D | score_al.c | 54 char *seqc0, *seqc1; /* aligned sequences */ variable 380 sp1 = seqc1; in calcons() 404 seqc1=calloc((size_t)seqsiz,sizeof(char)); 405 if (res==NULL || seqc0==NULL || seqc1==NULL) 412 free(seqc0); free(seqc1); in freeseq()
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H A D | ttdispn.c | 54 discons(seqc0, seqc1, nc) in discons() argument 55 char *seqc0, *seqc1; in discons() 69 if (seqc0[ii]==' ' || seqc1[ii]==' ') continue; 70 if (seqc0[ii]!='-'&&seqc1[ii]!='-') { 86 else if (seqc1[ii]=='-') {
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H A D | ps_dispn.c | 67 discons(char *seqc0, char *seqc1, int nc) in discons() argument 86 if (seqc0[ii]==' ' || seqc1[ii]==' ') continue; in discons() 87 if (seqc0[ii]!='-'&&seqc1[ii]!='-') { in discons() 108 else if (seqc1[ii]=='-') { in discons()
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H A D | lalign2.c | 65 char *seqc0, *seqc1; /* aligned sequences */ variable 537 sp1 = seqc1+mins; in calcons() 583 seqc1=calloc((size_t)seqsiz,sizeof(char)); 584 if (seqc0==NULL || seqc1==NULL) 592 free(seqc0); free(seqc1); in freeseq()
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H A D | zzgmata.gbl | 12 char *seqc0, *seqc1; /* arrays for the consensus sequence */
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H A D | lsim3.c | 17 extern char *sq, sqnam[], *seqc0, *seqc1; 32 void discons(char *seqc0, char *seqc1, int nc); 321 discons(seqc0,seqc1,ns); in SIM() 331 discons(seqc1,seqc0,ns); in SIM()
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H A D | lsim2.c | 14 extern char *sq, sqnam[], *seqc0, *seqc1; 303 discons(seqc0,seqc1,ns); in SIM() 312 discons(seqc1,seqc0,ns); in SIM()
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/dports/biology/fasta3/fasta-36.3.8/src/ |
H A D | c_dispn.c | 55 char *seqc1, char *seqc1a, in discons() argument 141 for (i=0; i<nc && seqc1[i]; i++) { in discons() 143 fputc(seqc1[i],fd); in discons() 182 for (i=0; i<nc && seqc1[i]; i++) { in discons() 183 if (!have_res && seqc1[i]==' ') fputc('-',fd); in discons() 184 else if (seqc1[i]==' ') break; in discons() 187 fputc(seqc1[i],fd); in discons() 218 if (seqc1[ic] == ' ' || seqc1[ic] == '-' || seqc1[ic] == '/' || seqc1[ic] == '\\') { in discons() 306 if ((line[2][i]=seqc1[ic])=='-' || seqc1[ic]=='\\') { in discons() 309 else if (seqc1[ic]=='/') { in discons() [all …]
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H A D | cal_consf.c | 48 char *seqc0, char *seqc1, char *seqca, int *cumm_seq_score, in calc_cons_a() argument 97 memset(seqc1,' ',mins-a_res->min1); in calc_cons_a() 98 aancpy(seqc1+mins-a_res->min1,(char *)aa1p,a_res->min1,ppst); in calc_cons_a() 102 aancpy(seqc1,(char *)aa1p+a_res->min1-mins,mins,ppst); in calc_cons_a() 110 aancpy(seqc1,(char *)(aa1p+a_res->min1-mins),mins,ppst); in calc_cons_a() 128 aancpy(seqc1,(char *)aa1p+a_res->min1-mins,mins,ppst); in calc_cons_a() 145 sp1 = seqc1+mins; in calc_cons_a() 250 aancpy(seqc1+mins+lenc,(char *)aa1p+a_res->max1,nn1-a_res->max1,ppst); in calc_cons_a() 253 memset(seqc1+mins+lenc+nn1-a_res->max1,' ',nd-(nn1-a_res->max1)); in calc_cons_a() 271 memset(seqc1+mins+lenc+nn1-a_res->max1,' ',nd-(nn1-a_res->max1)); in calc_cons_a() [all …]
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H A D | cal_cons2.c | 136 char *seqc0, char *seqc1, char *seqca, int *smins, in pre_fill_cons() argument 149 memset(seqc1,' ',mins-a_res->min1); in pre_fill_cons() 150 aancpy(seqc1+mins-a_res->min1,(char *)aa1p,a_res->min1,ppst); in pre_fill_cons() 154 aancpy(seqc1,(char *)aa1p+a_res->min1-mins,mins,ppst); in pre_fill_cons() 162 aancpy(seqc1,(char *)(aa1p+a_res->min1-mins),mins,ppst); in pre_fill_cons() 180 aancpy(seqc1,(char *)aa1p+a_res->min1-mins,mins,ppst); in pre_fill_cons() 198 char *seqc0, char *seqc1, in post_fill_cons() argument 238 aancpy(seqc1+mins+lenc,(char *)aa1p+a_res->max1,nd,ppst); in post_fill_cons() 406 sp1_p = seqc1+mins; in calc_cons_u() 840 seqc0, seqc1, seqc0a, seqc1a); in calc_cons_u() [all …]
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H A D | mshowalign2.c | 106 char *seqc1, char *seqc1a, 161 char *seqc0, *seqc0a, *seqc1, *seqc1a, *seqca; in showalign() local 449 initseq(&seqc0, &seqc1, &seqca, maxc); in showalign() 521 seqc0, seqc1, seqca, cumm_seq_score, in showalign() 590 if (max(strlen(seqc0),strlen(seqc1)) > nc) { in showalign() 592 nc,maxc,strlen(seqc0),strlen(seqc1)); in showalign() 764 freeseq(&seqc0,&seqc1, &seqca); in showalign() 930 *seqc1=*seqc0 + seqsiz; in initseq() 931 *seqca=*seqc1 + seqsiz; in initseq() 934 void freeseq(char **seqc0, char **seqc1, char **seqca) in freeseq() argument [all …]
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H A D | cal_cons.c | 130 char *seqc0, char *seqc1, char *seqca, int *cumm_seq_score, in calc_cons_a() argument 212 memset(seqc1,' ',mins-a_res->min1); in calc_cons_a() 213 aancpy(seqc1+mins-a_res->min1,(char *)aa1p,a_res->min1,ppst); in calc_cons_a() 217 aancpy(seqc1,(char *)aa1p+a_res->min1-mins,mins,ppst); in calc_cons_a() 225 aancpy(seqc1,(char *)(aa1p+a_res->min1-mins),mins,ppst); in calc_cons_a() 243 aancpy(seqc1,(char *)aa1p+a_res->min1-mins,mins,ppst); in calc_cons_a() 262 sp1 = seqc1+mins; in calc_cons_a() 548 aancpy(seqc1+mins+lenc,(char *)aa1p+a_res->max1,nn1-a_res->max1,ppst); in calc_cons_a() 551 memset(seqc1+mins+lenc+nn1-a_res->max1,' ',nd-(nn1-a_res->max1)); in calc_cons_a() 564 memset(seqc1+mins+lenc+nn1-a_res->max1,' ',nd-(nn1-a_res->max1)); in calc_cons_a() [all …]
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H A D | drop_func.h | 116 char *seqc0, char *seqc1, char *seqca, int *seqc_score,
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H A D | dropfx2.c | 2840 char *seqc0, char *seqc1, char *seqca, int *cumm_seq_score, argument 2911 sp1_p = seqc1; /* protein */ 2968 sp0_p = seqc1; /* sp0 points to DNA */ 3563 char *seqc0, char *seqc1, char *seqca, int *cumm_seq_score, argument 3576 nc, seqc0, seqc1, seqca, cumm_seq_score,
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/dports/biology/emboss/EMBOSS-6.6.0/emboss/ |
H A D | stretcher.c | 130 static char *seqc1; /* aligned sequences */ variable 213 AJCNEW(seqc1, ajSeqGetLen(glseq0)+ajSeqGetLen(glseq1)); in main() 246 res1 = ajSeqNewRangeC(seqc1, ajSeqGetOffset(glseq1), ajSeqGetOffend(glseq1), in main() 267 AJFREE(seqc1); in main() 602 sp1 = seqc1; in stretcher_Calcons()
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H A D | matcher.c | 269 static ajint matcher_Calcons(char *seqc0, char *seqc1, 401 char *seqc0, *seqc1; /* aligned sequences */ in matcher_Sim() local 416 AJCNEW(seqc1,i); in matcher_Sim() 483 matcher_Calcons(seqc0,seqc1, in matcher_Sim() 493 strlen(seqc0), strlen(seqc1)); in matcher_Sim() 495 ajDebug("Matcher seqc1: %s\n", seqc1); in matcher_Sim() 502 res1 = ajSeqNewRangeC(seqc1, min1+beg1, ajSeqGetOffend(seq1) + ajSeqGetLen(seq1) - max1, in matcher_Sim() 574 AJFREE(seqc1); in matcher_Sim() 1507 static ajint matcher_Calcons(char *seqc0,char *seqc1, in matcher_Calcons() argument 1529 sp1 = seqc1 /*+mins*/; in matcher_Calcons()
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H A D | diffseq.c | 785 const char *seqc1; in diffseq_DiffList() local 790 seqc1 = ajSeqGetSeqC(seq1); in diffseq_DiffList() 844 tolower((ajint)seqc1[i]) == tolower((ajint)seqc2[i]); i++) in diffseq_DiffList() 908 tolower((ajint)seqc1[i-1]) == tolower((ajint)seqc2[j-1]); in diffseq_DiffList()
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/dports/biology/fasta3/fasta-36.3.8/doc/ |
H A D | fasta_func.doc | 102 void initseq() /* setup seqc0/seqc1 which contain alignment characters */ 220 calcons() /* calculate ascii alignment seqc0,seqc1 from res[]*/ 259 discons() /* display alignment from seqc0, seqc1 */
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