Home
last modified time | relevance | path

Searched refs:seqc1 (Results 1 – 25 of 29) sorted by relevance

12

/dports/biology/fasta/fasta/
H A Dzzlgmata.c171 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 …]
H A Dzxlgmata.c124 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;
H A Dndispn.c31 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()
H A Dalign.c33 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()
H A Dfldispn.c57 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]=='-') {
H A Dtldispn.c50 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]=='-') {
H A Dmtdispn.c69 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]=='-') {
H A Dscore_al.c54 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()
H A Dttdispn.c54 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]=='-') {
H A Dps_dispn.c67 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()
H A Dlalign2.c65 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()
H A Dzzgmata.gbl12 char *seqc0, *seqc1; /* arrays for the consensus sequence */
H A Dlsim3.c17 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()
H A Dlsim2.c14 extern char *sq, sqnam[], *seqc0, *seqc1;
303 discons(seqc0,seqc1,ns); in SIM()
312 discons(seqc1,seqc0,ns); in SIM()
/dports/biology/fasta3/fasta-36.3.8/src/
H A Dc_dispn.c55 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 …]
H A Dcal_consf.c48 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 …]
H A Dcal_cons2.c136 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 …]
H A Dmshowalign2.c106 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 …]
H A Dcal_cons.c130 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 …]
H A Ddrop_func.h116 char *seqc0, char *seqc1, char *seqca, int *seqc_score,
H A Ddropfx2.c2840 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,
/dports/biology/emboss/EMBOSS-6.6.0/emboss/
H A Dstretcher.c130 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()
H A Dmatcher.c269 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()
H A Ddiffseq.c785 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()
/dports/biology/fasta3/fasta-36.3.8/doc/
H A Dfasta_func.doc102 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 */

12