/dports/biology/infernal/infernal-1.1.3/easel/ |
H A D | esl_sqio.c | 1763 esl_sq_SetDesc(sqarr[i], buf); in synthesize_testseqs() 1767 esl_sq_GrowTo(sqarr[i], n); in synthesize_testseqs() 1773 *ret_sqarr = sqarr; in synthesize_testseqs() 1946 … if (sq->roff != -1 && sqarr[nseq]->roff != -1 && sq->roff != sqarr[nseq]->roff) esl_fatal(msg); in utest_read_info() 1947 … if (sq->doff != -1 && sqarr[nseq]->doff != -1 && sq->doff != sqarr[nseq]->doff) esl_fatal(msg); in utest_read_info() 1997 esl_sq_Copy(sqarr[nseq], rev); in utest_read_window() 2066 source = sqarr[i]->name; in utest_fetch_subseq() 2216 ESL_SQ **sqarr = NULL; in main() local 2243 sqarr[i]->acc[0] = '\0'; in main() 2245 sqarr[i]->acc[0] = c; in main() [all …]
|
H A D | esl_dsqdata.c | 1546 ESL_SQ **sqarr = NULL; in utest_readwrite() local 1562 if (( sqarr = malloc(sizeof(ESL_SQ *) * nseq)) == NULL) esl_fatal(msg); in utest_readwrite() 1565 sqarr[i] = NULL; in utest_readwrite() 1566 … if (( status = esl_sq_Sample(rng, abc, maxL, &(sqarr[i]))) != eslOK) esl_fatal(msg); in utest_readwrite() 1567 … if (( status = esl_sq_SetAccession(sqarr[i], "")) != eslOK) esl_fatal(msg); in utest_readwrite() 1586 if ( chu->L[i] != sqarr[i+chu->i0]->n ) esl_fatal(msg); in utest_readwrite() 1587 if ( memcmp( chu->dsq[i], sqarr[i+chu->i0]->dsq, chu->L[i]) != 0) esl_fatal(msg); in utest_readwrite() 1588 if ( strcmp( chu->name[i], sqarr[i+chu->i0]->name) != 0) esl_fatal(msg); in utest_readwrite() 1590 if ( strcmp( chu->desc[i], sqarr[i+chu->i0]->desc) != 0) esl_fatal(msg); in utest_readwrite() 1603 for (i = 0; i < nseq; i++) esl_sq_Destroy(sqarr[i]); in utest_readwrite() [all …]
|
/dports/biology/hmmer/hmmer-3.3/easel/ |
H A D | esl_sqio.c | 1763 esl_sq_SetDesc(sqarr[i], buf); in synthesize_testseqs() 1767 esl_sq_GrowTo(sqarr[i], n); in synthesize_testseqs() 1773 *ret_sqarr = sqarr; in synthesize_testseqs() 1946 … if (sq->roff != -1 && sqarr[nseq]->roff != -1 && sq->roff != sqarr[nseq]->roff) esl_fatal(msg); in utest_read_info() 1947 … if (sq->doff != -1 && sqarr[nseq]->doff != -1 && sq->doff != sqarr[nseq]->doff) esl_fatal(msg); in utest_read_info() 1997 esl_sq_Copy(sqarr[nseq], rev); in utest_read_window() 2066 source = sqarr[i]->name; in utest_fetch_subseq() 2216 ESL_SQ **sqarr = NULL; in main() local 2243 sqarr[i]->acc[0] = '\0'; in main() 2245 sqarr[i]->acc[0] = c; in main() [all …]
|
H A D | esl_dsqdata.c | 1546 ESL_SQ **sqarr = NULL; in utest_readwrite() local 1562 if (( sqarr = malloc(sizeof(ESL_SQ *) * nseq)) == NULL) esl_fatal(msg); in utest_readwrite() 1565 sqarr[i] = NULL; in utest_readwrite() 1566 … if (( status = esl_sq_Sample(rng, abc, maxL, &(sqarr[i]))) != eslOK) esl_fatal(msg); in utest_readwrite() 1567 … if (( status = esl_sq_SetAccession(sqarr[i], "")) != eslOK) esl_fatal(msg); in utest_readwrite() 1586 if ( chu->L[i] != sqarr[i+chu->i0]->n ) esl_fatal(msg); in utest_readwrite() 1587 if ( memcmp( chu->dsq[i], sqarr[i+chu->i0]->dsq, chu->L[i]) != 0) esl_fatal(msg); in utest_readwrite() 1588 if ( strcmp( chu->name[i], sqarr[i+chu->i0]->name) != 0) esl_fatal(msg); in utest_readwrite() 1590 if ( strcmp( chu->desc[i], sqarr[i+chu->i0]->desc) != 0) esl_fatal(msg); in utest_readwrite() 1603 for (i = 0; i < nseq; i++) esl_sq_Destroy(sqarr[i]); in utest_readwrite() [all …]
|
/dports/biology/infernal/infernal-1.1.3/easel/miniapps/ |
H A D | cmd_downsample.c | 125 ESL_SQ **sqarr = NULL; // the sample: ptrs to <M> sequences in downsample_seqs() local 137 if (( sqarr = malloc(sizeof(ESL_SQ *) * M)) == NULL) esl_fatal("allocation failed"); in downsample_seqs() 138 for (i = 0; i < M; i++) sqarr[i] = NULL; in downsample_seqs() 146 tmpsq = sqarr[r]; in downsample_seqs() 147 sqarr[r] = sq; in downsample_seqs() 153 sqarr[N-1] = sq; in downsample_seqs() 165 …esl_sqio_Write(stdout, sqarr[i], eslSQFILE_FASTA, /*update=*/FALSE); // FASTA because infile coul… in downsample_seqs() 168 for (i = 0; i < M; i++) esl_sq_Destroy(sqarr[i]); in downsample_seqs() 170 free(sqarr); in downsample_seqs()
|
/dports/biology/hmmer/hmmer-3.3/easel/miniapps/ |
H A D | cmd_downsample.c | 125 ESL_SQ **sqarr = NULL; // the sample: ptrs to <M> sequences in downsample_seqs() local 137 if (( sqarr = malloc(sizeof(ESL_SQ *) * M)) == NULL) esl_fatal("allocation failed"); in downsample_seqs() 138 for (i = 0; i < M; i++) sqarr[i] = NULL; in downsample_seqs() 146 tmpsq = sqarr[r]; in downsample_seqs() 147 sqarr[r] = sq; in downsample_seqs() 153 sqarr[N-1] = sq; in downsample_seqs() 165 …esl_sqio_Write(stdout, sqarr[i], eslSQFILE_FASTA, /*update=*/FALSE); // FASTA because infile coul… in downsample_seqs() 168 for (i = 0; i < M; i++) esl_sq_Destroy(sqarr[i]); in downsample_seqs() 170 free(sqarr); in downsample_seqs()
|
/dports/biology/infernal/infernal-1.1.3/hmmer/src/ |
H A D | p7_tophits.c | 1454 ESL_SQ **sqarr = NULL; in p7_tophits_Alignment() local 1487 ESL_ALLOC(sqarr, sizeof(ESL_SQ *) * (ndom + inc_n)); in p7_tophits_Alignment() 1490 for (y = 0; y < inc_n; y++) { sqarr[y] = inc_sqarr[y]; trarr[y] = inc_trarr[y]; } in p7_tophits_Alignment() 1491 for (; y < (ndom+inc_n); y++) { sqarr[y] = NULL; trarr[y] = NULL; } in p7_tophits_Alignment() 1501 …if ((status = p7_alidisplay_Backconvert(th->hit[h]->dcl[d].ad, abc, &(sqarr[y]), &(trarr[y]))) != … in p7_tophits_Alignment() 1507 …if ((status = p7_tracealign_Seqs(sqarr, trarr, inc_n+ndom, M, optflags, NULL, &msa)) != eslOK) got… in p7_tophits_Alignment() 1510 for (y = inc_n; y < ndom+inc_n; y++) esl_sq_Destroy(sqarr[y]); in p7_tophits_Alignment() 1512 free(sqarr); in p7_tophits_Alignment() 1518 …if (sqarr != NULL) { for (y = inc_n; y < ndom+inc_n; y++) if (sqarr[y] != NULL) esl_sq_Destroy(sqa… in p7_tophits_Alignment()
|
/dports/biology/hmmer/hmmer-3.3/src/ |
H A D | p7_tophits.c | 1454 ESL_SQ **sqarr = NULL; in p7_tophits_Alignment() local 1487 ESL_ALLOC(sqarr, sizeof(ESL_SQ *) * (ndom + inc_n)); in p7_tophits_Alignment() 1490 for (y = 0; y < inc_n; y++) { sqarr[y] = inc_sqarr[y]; trarr[y] = inc_trarr[y]; } in p7_tophits_Alignment() 1491 for (; y < (ndom+inc_n); y++) { sqarr[y] = NULL; trarr[y] = NULL; } in p7_tophits_Alignment() 1501 …if ((status = p7_alidisplay_Backconvert(th->hit[h]->dcl[d].ad, abc, &(sqarr[y]), &(trarr[y]))) != … in p7_tophits_Alignment() 1507 …if ((status = p7_tracealign_Seqs(sqarr, trarr, inc_n+ndom, M, optflags, NULL, &msa)) != eslOK) got… in p7_tophits_Alignment() 1510 for (y = inc_n; y < ndom+inc_n; y++) esl_sq_Destroy(sqarr[y]); in p7_tophits_Alignment() 1512 free(sqarr); in p7_tophits_Alignment() 1518 …if (sqarr != NULL) { for (y = inc_n; y < ndom+inc_n; y++) if (sqarr[y] != NULL) esl_sq_Destroy(sqa… in p7_tophits_Alignment()
|
/dports/biology/infernal/infernal-1.1.3/src/ |
H A D | cm_tophits.c | 2147 ESL_SQ **sqarr = NULL; /* [0..ninc-1] array of sequences, one for each hit */ in cm_tophits_Alignment() local 2168 ESL_ALLOC(sqarr, sizeof(ESL_SQ *) * (ninc)); in cm_tophits_Alignment() 2171 for (i = 0; i < ninc; i++) sqarr[i] = NULL; in cm_tophits_Alignment() 2179 …if ((status = cm_alidisplay_Backconvert(cm, th->hit[h]->ad, errbuf, &(sqarr[y]), &(trarr[y]), &(pp… in cm_tophits_Alignment() 2185 …if((status = Parsetrees2Alignment(cm, errbuf, cm->abc, sqarr, NULL, trarr, pparr, ninc, NULL, NULL… in cm_tophits_Alignment() 2188 for (y = 0; y < ninc; y++) esl_sq_Destroy(sqarr[y]); in cm_tophits_Alignment() 2191 free(sqarr); in cm_tophits_Alignment() 2199 …if (sqarr != NULL) { for (y = 0; y < ninc; y++) if (sqarr[y] != NULL) esl_sq_Destroy(sqarr[y]); fr… in cm_tophits_Alignment()
|