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Searched refs:byp_abc (Results 1 – 22 of 22) sorted by relevance

/dports/biology/infernal/infernal-1.1.3/easel/
H A Desl_msafile.h95 extern int esl_msafile_Open (ESL_ALPHABET **byp_abc, const char *msafile, const char *env, i…
96 extern int esl_msafile_OpenMem (ESL_ALPHABET **byp_abc, const char *p, esl_pos_t n, i…
97 extern int esl_msafile_OpenBuffer(ESL_ALPHABET **byp_abc, ESL_BUFFER *bf, i…
H A Desl_msafile.c37 static int msafile_OpenBuffer(ESL_ALPHABET **byp_abc, ESL_BUFFER *bf, int format, ESL_MSAFILE_FMTDA…
197 if ( (status = msafile_OpenBuffer(byp_abc, afp->bf, format, fmtd, afp)) != eslOK) goto ERROR; in esl_msafile_Open()
232 if ( (status = msafile_OpenBuffer(byp_abc, afp->bf, format, fmtd, afp)) != eslOK) goto ERROR; in esl_msafile_OpenMem()
261 if ((status = msafile_OpenBuffer(byp_abc, afp->bf, format, fmtd, afp)) != eslOK) goto ERROR; in esl_msafile_OpenBuffer()
396 msafile_OpenBuffer(ESL_ALPHABET **byp_abc, ESL_BUFFER *bf, int format, ESL_MSAFILE_FMTDATA *fmtd, … in msafile_OpenBuffer() argument
414 if (byp_abc && *byp_abc) /* Digital mode, and caller provided the alphabet */ in msafile_OpenBuffer()
416 abc = *byp_abc; in msafile_OpenBuffer()
419 else if (byp_abc) /* Digital mode, and caller wants us to guess and create an alphabet */ in msafile_OpenBuffer()
456 if (esl_byp_IsReturned(byp_abc)) *byp_abc = abc; in msafile_OpenBuffer()
460 if (abc && ! esl_byp_IsProvided(byp_abc)) { esl_alphabet_Destroy(abc); } in msafile_OpenBuffer()
[all …]
H A Desl_dsqdata.h145 extern int esl_dsqdata_Open (ESL_ALPHABET **byp_abc, char *basename, int nconsumers, ESL_DSQDATA…
H A Desl_dsqdata.c156 esl_dsqdata_Open(ESL_ALPHABET **byp_abc, char *basename, int nconsumers, ESL_DSQDATA **ret_dd) in esl_dsqdata_Open() argument
169 …ESL_DASSERT1(( byp_abc != NULL )); // either *byp_abc == NULL or *byp_abc = the caller's expecte… in esl_dsqdata_Open()
176 dd->abc_r = *byp_abc; // This may be NULL; if so, we create it later. in esl_dsqdata_Open()
327 …*byp_abc = dd->abc_r; // If caller provided <*byp_abc> this is a no-op, because we set abc_r =… in esl_dsqdata_Open()
334 if (*byp_abc == NULL && dd->abc_r) esl_alphabet_Destroy(dd->abc_r); in esl_dsqdata_Open()
341 if (*byp_abc == NULL && dd->abc_r) esl_alphabet_Destroy(dd->abc_r); in esl_dsqdata_Open()
347 if (*byp_abc == NULL && dd->abc_r) esl_alphabet_Destroy(dd->abc_r); in esl_dsqdata_Open()
H A Desl_msafile_stockholm.c2365 utest_good_format(ESL_ALPHABET **byp_abc, int fmt, int expected_nseq, int64_t expected_alen, char *… in utest_good_format() argument
2371 if (esl_msafile_OpenMem(byp_abc, buf, strlen(buf), fmt, NULL, &afp) != eslOK) esl_fatal(msg); in utest_good_format()
2381 utest_identical_io(ESL_ALPHABET **byp_abc, int fmt, char *buf) in utest_identical_io() argument
2395 if (esl_msafile_Open(byp_abc, tmpfile1, NULL, fmt, NULL, &afp) != eslOK) esl_fatal(msg); in utest_identical_io()
2403 if (esl_msafile_Open(byp_abc, tmpfile2, NULL, fmt, NULL, &afp) != eslOK) esl_fatal(msg); in utest_identical_io()
2416 utest_bad_open(ESL_ALPHABET **byp_abc, int fmt, int expected_status, char *buf) in utest_bad_open() argument
2421 …if (esl_msafile_OpenMem(byp_abc, buf, strlen(buf), fmt, NULL, &afp) != expected_status) esl_fatal(… in utest_bad_open()
2426 utest_bad_read(ESL_ALPHABET **byp_abc, int fmt, char *expected_errmsg, int expected_line, char *buf) in utest_bad_read() argument
2432 if (esl_msafile_OpenMem(byp_abc, buf, strlen(buf), fmt, NULL, &afp) != eslOK) esl_fatal(msg); in utest_bad_read()
/dports/biology/hmmer/hmmer-3.3/easel/
H A Desl_msafile.h95 extern int esl_msafile_Open (ESL_ALPHABET **byp_abc, const char *msafile, const char *env, i…
96 extern int esl_msafile_OpenMem (ESL_ALPHABET **byp_abc, const char *p, esl_pos_t n, i…
97 extern int esl_msafile_OpenBuffer(ESL_ALPHABET **byp_abc, ESL_BUFFER *bf, i…
H A Desl_msafile.c37 static int msafile_OpenBuffer(ESL_ALPHABET **byp_abc, ESL_BUFFER *bf, int format, ESL_MSAFILE_FMTDA…
197 if ( (status = msafile_OpenBuffer(byp_abc, afp->bf, format, fmtd, afp)) != eslOK) goto ERROR; in esl_msafile_Open()
232 if ( (status = msafile_OpenBuffer(byp_abc, afp->bf, format, fmtd, afp)) != eslOK) goto ERROR; in esl_msafile_OpenMem()
261 if ((status = msafile_OpenBuffer(byp_abc, afp->bf, format, fmtd, afp)) != eslOK) goto ERROR; in esl_msafile_OpenBuffer()
396 msafile_OpenBuffer(ESL_ALPHABET **byp_abc, ESL_BUFFER *bf, int format, ESL_MSAFILE_FMTDATA *fmtd, … in msafile_OpenBuffer() argument
414 if (byp_abc && *byp_abc) /* Digital mode, and caller provided the alphabet */ in msafile_OpenBuffer()
416 abc = *byp_abc; in msafile_OpenBuffer()
419 else if (byp_abc) /* Digital mode, and caller wants us to guess and create an alphabet */ in msafile_OpenBuffer()
456 if (esl_byp_IsReturned(byp_abc)) *byp_abc = abc; in msafile_OpenBuffer()
460 if (abc && ! esl_byp_IsProvided(byp_abc)) { esl_alphabet_Destroy(abc); } in msafile_OpenBuffer()
[all …]
H A Desl_dsqdata.h145 extern int esl_dsqdata_Open (ESL_ALPHABET **byp_abc, char *basename, int nconsumers, ESL_DSQDATA…
H A Desl_dsqdata.c156 esl_dsqdata_Open(ESL_ALPHABET **byp_abc, char *basename, int nconsumers, ESL_DSQDATA **ret_dd) in esl_dsqdata_Open() argument
169 …ESL_DASSERT1(( byp_abc != NULL )); // either *byp_abc == NULL or *byp_abc = the caller's expecte… in esl_dsqdata_Open()
176 dd->abc_r = *byp_abc; // This may be NULL; if so, we create it later. in esl_dsqdata_Open()
327 …*byp_abc = dd->abc_r; // If caller provided <*byp_abc> this is a no-op, because we set abc_r =… in esl_dsqdata_Open()
334 if (*byp_abc == NULL && dd->abc_r) esl_alphabet_Destroy(dd->abc_r); in esl_dsqdata_Open()
341 if (*byp_abc == NULL && dd->abc_r) esl_alphabet_Destroy(dd->abc_r); in esl_dsqdata_Open()
347 if (*byp_abc == NULL && dd->abc_r) esl_alphabet_Destroy(dd->abc_r); in esl_dsqdata_Open()
H A Desl_msafile_stockholm.c2365 utest_good_format(ESL_ALPHABET **byp_abc, int fmt, int expected_nseq, int64_t expected_alen, char *… in utest_good_format() argument
2371 if (esl_msafile_OpenMem(byp_abc, buf, strlen(buf), fmt, NULL, &afp) != eslOK) esl_fatal(msg); in utest_good_format()
2381 utest_identical_io(ESL_ALPHABET **byp_abc, int fmt, char *buf) in utest_identical_io() argument
2395 if (esl_msafile_Open(byp_abc, tmpfile1, NULL, fmt, NULL, &afp) != eslOK) esl_fatal(msg); in utest_identical_io()
2403 if (esl_msafile_Open(byp_abc, tmpfile2, NULL, fmt, NULL, &afp) != eslOK) esl_fatal(msg); in utest_identical_io()
2416 utest_bad_open(ESL_ALPHABET **byp_abc, int fmt, int expected_status, char *buf) in utest_bad_open() argument
2421 …if (esl_msafile_OpenMem(byp_abc, buf, strlen(buf), fmt, NULL, &afp) != expected_status) esl_fatal(… in utest_bad_open()
2426 utest_bad_read(ESL_ALPHABET **byp_abc, int fmt, char *expected_errmsg, int expected_line, char *buf) in utest_bad_read() argument
2432 if (esl_msafile_OpenMem(byp_abc, buf, strlen(buf), fmt, NULL, &afp) != eslOK) esl_fatal(msg); in utest_bad_read()
/dports/biology/infernal/infernal-1.1.3/hmmer/src/impl_sse/
H A Dio.c231 p7_oprofile_ReadMSV(P7_HMMFILE *hfp, ESL_ALPHABET **byp_abc, P7_OPROFILE **ret_om) in p7_oprofile_ReadMSV() argument
263 …if (byp_abc == NULL || *byp_abc == NULL) { /* alphabet unknown: whether wanted or unwanted, make a… in p7_oprofile_ReadMSV()
266 abc = *byp_abc; in p7_oprofile_ReadMSV()
302 …if (byp_abc != NULL) *byp_abc = abc; /* pass alphabet (whether new or not) back to caller, if cal… in p7_oprofile_ReadMSV()
307 …if (abc != NULL && (byp_abc == NULL || *byp_abc == NULL)) esl_alphabet_Destroy(abc); /* destroy al… in p7_oprofile_ReadMSV()
352 p7_oprofile_ReadInfoMSV(P7_HMMFILE *hfp, ESL_ALPHABET **byp_abc, P7_OPROFILE **ret_om) in p7_oprofile_ReadInfoMSV() argument
384 …if (byp_abc == NULL || *byp_abc == NULL) { /* alphabet unknown: whether wanted or unwanted, make a… in p7_oprofile_ReadInfoMSV()
387 abc = *byp_abc; in p7_oprofile_ReadInfoMSV()
414 …if (byp_abc != NULL) *byp_abc = abc; /* pass alphabet (whether new or not) back to caller, if cal… in p7_oprofile_ReadInfoMSV()
419 …if (abc != NULL && (byp_abc == NULL || *byp_abc == NULL)) esl_alphabet_Destroy(abc); /* destroy al… in p7_oprofile_ReadInfoMSV()
[all …]
H A Dimpl_sse.h314 extern int p7_oprofile_ReadMSV (P7_HMMFILE *hfp, ESL_ALPHABET **byp_abc, P7_OPROFILE **ret_om);
315 extern int p7_oprofile_ReadInfoMSV(P7_HMMFILE *hfp, ESL_ALPHABET **byp_abc, P7_OPROFILE **ret_om);
316 extern int p7_oprofile_ReadBlockMSV(P7_HMMFILE *hfp, ESL_ALPHABET **byp_abc, P7_OM_BLOCK *hmmBlock);
/dports/biology/infernal/infernal-1.1.3/hmmer/src/impl_vmx/
H A Dio.c233 p7_oprofile_ReadMSV(P7_HMMFILE *hfp, ESL_ALPHABET **byp_abc, P7_OPROFILE **ret_om) in p7_oprofile_ReadMSV() argument
264 …if (byp_abc == NULL || *byp_abc == NULL) { /* alphabet unknown: whether wanted or unwanted, make a… in p7_oprofile_ReadMSV()
267 abc = *byp_abc; in p7_oprofile_ReadMSV()
300 …if (byp_abc != NULL) *byp_abc = abc; /* pass alphabet (whether new or not) back to caller, if cal… in p7_oprofile_ReadMSV()
305 …if (abc != NULL && (byp_abc == NULL || *byp_abc == NULL)) esl_alphabet_Destroy(abc); /* destroy al… in p7_oprofile_ReadMSV()
350 p7_oprofile_ReadInfoMSV(P7_HMMFILE *hfp, ESL_ALPHABET **byp_abc, P7_OPROFILE **ret_om) in p7_oprofile_ReadInfoMSV() argument
381 …if (byp_abc == NULL || *byp_abc == NULL) { /* alphabet unknown: whether wanted or unwanted, make a… in p7_oprofile_ReadInfoMSV()
384 abc = *byp_abc; in p7_oprofile_ReadInfoMSV()
410 …if (byp_abc != NULL) *byp_abc = abc; /* pass alphabet (whether new or not) back to caller, if cal… in p7_oprofile_ReadInfoMSV()
415 …if (abc != NULL && (byp_abc == NULL || *byp_abc == NULL)) esl_alphabet_Destroy(abc); /* destroy al… in p7_oprofile_ReadInfoMSV()
[all …]
H A Dimpl_vmx.h306 extern int p7_oprofile_ReadMSV (P7_HMMFILE *hfp, ESL_ALPHABET **byp_abc, P7_OPROFILE **ret_om);
307 extern int p7_oprofile_ReadInfoMSV(P7_HMMFILE *hfp, ESL_ALPHABET **byp_abc, P7_OPROFILE **ret_om);
308 extern int p7_oprofile_ReadBlockMSV(P7_HMMFILE *hfp, ESL_ALPHABET **byp_abc, P7_OM_BLOCK *hmmBlock);
/dports/biology/hmmer/hmmer-3.3/src/impl_sse/
H A Dio.c231 p7_oprofile_ReadMSV(P7_HMMFILE *hfp, ESL_ALPHABET **byp_abc, P7_OPROFILE **ret_om) in p7_oprofile_ReadMSV() argument
263 …if (byp_abc == NULL || *byp_abc == NULL) { /* alphabet unknown: whether wanted or unwanted, make a… in p7_oprofile_ReadMSV()
266 abc = *byp_abc; in p7_oprofile_ReadMSV()
302 …if (byp_abc != NULL) *byp_abc = abc; /* pass alphabet (whether new or not) back to caller, if cal… in p7_oprofile_ReadMSV()
307 …if (abc != NULL && (byp_abc == NULL || *byp_abc == NULL)) esl_alphabet_Destroy(abc); /* destroy al… in p7_oprofile_ReadMSV()
352 p7_oprofile_ReadInfoMSV(P7_HMMFILE *hfp, ESL_ALPHABET **byp_abc, P7_OPROFILE **ret_om) in p7_oprofile_ReadInfoMSV() argument
384 …if (byp_abc == NULL || *byp_abc == NULL) { /* alphabet unknown: whether wanted or unwanted, make a… in p7_oprofile_ReadInfoMSV()
387 abc = *byp_abc; in p7_oprofile_ReadInfoMSV()
414 …if (byp_abc != NULL) *byp_abc = abc; /* pass alphabet (whether new or not) back to caller, if cal… in p7_oprofile_ReadInfoMSV()
419 …if (abc != NULL && (byp_abc == NULL || *byp_abc == NULL)) esl_alphabet_Destroy(abc); /* destroy al… in p7_oprofile_ReadInfoMSV()
[all …]
H A Dimpl_sse.h314 extern int p7_oprofile_ReadMSV (P7_HMMFILE *hfp, ESL_ALPHABET **byp_abc, P7_OPROFILE **ret_om);
315 extern int p7_oprofile_ReadInfoMSV(P7_HMMFILE *hfp, ESL_ALPHABET **byp_abc, P7_OPROFILE **ret_om);
316 extern int p7_oprofile_ReadBlockMSV(P7_HMMFILE *hfp, ESL_ALPHABET **byp_abc, P7_OM_BLOCK *hmmBlock);
/dports/biology/hmmer/hmmer-3.3/src/impl_vmx/
H A Dio.c233 p7_oprofile_ReadMSV(P7_HMMFILE *hfp, ESL_ALPHABET **byp_abc, P7_OPROFILE **ret_om) in p7_oprofile_ReadMSV() argument
264 …if (byp_abc == NULL || *byp_abc == NULL) { /* alphabet unknown: whether wanted or unwanted, make a… in p7_oprofile_ReadMSV()
267 abc = *byp_abc; in p7_oprofile_ReadMSV()
300 …if (byp_abc != NULL) *byp_abc = abc; /* pass alphabet (whether new or not) back to caller, if cal… in p7_oprofile_ReadMSV()
305 …if (abc != NULL && (byp_abc == NULL || *byp_abc == NULL)) esl_alphabet_Destroy(abc); /* destroy al… in p7_oprofile_ReadMSV()
350 p7_oprofile_ReadInfoMSV(P7_HMMFILE *hfp, ESL_ALPHABET **byp_abc, P7_OPROFILE **ret_om) in p7_oprofile_ReadInfoMSV() argument
381 …if (byp_abc == NULL || *byp_abc == NULL) { /* alphabet unknown: whether wanted or unwanted, make a… in p7_oprofile_ReadInfoMSV()
384 abc = *byp_abc; in p7_oprofile_ReadInfoMSV()
410 …if (byp_abc != NULL) *byp_abc = abc; /* pass alphabet (whether new or not) back to caller, if cal… in p7_oprofile_ReadInfoMSV()
415 …if (abc != NULL && (byp_abc == NULL || *byp_abc == NULL)) esl_alphabet_Destroy(abc); /* destroy al… in p7_oprofile_ReadInfoMSV()
[all …]
H A Dimpl_vmx.h306 extern int p7_oprofile_ReadMSV (P7_HMMFILE *hfp, ESL_ALPHABET **byp_abc, P7_OPROFILE **ret_om);
307 extern int p7_oprofile_ReadInfoMSV(P7_HMMFILE *hfp, ESL_ALPHABET **byp_abc, P7_OPROFILE **ret_om);
308 extern int p7_oprofile_ReadBlockMSV(P7_HMMFILE *hfp, ESL_ALPHABET **byp_abc, P7_OM_BLOCK *hmmBlock);
/dports/biology/hmmer/hmmer-3.3/easel/documentation/
H A Dcodestyle.md350 esl_module_Function(ESL_FOOOBJ **byp_abc)
352 …ESL_ALPHABET *abc = (byp_abc == NULL || *byp_abc == NULL) ? esl_alphabet_Create(eslAMINO) : *byp_a…
354 if (byp_abc != NULL) *byp_abc = abc;
362 esl_module_Function(ESL_FOOOBJ **byp_abc)
364 …LPHABET *abc = (esl_byp_IsInternal(byp_abc) || esl_byp_IsReturned(byp_abc)) ? esl_alphabet_Create(…
366 if (esl_byp_IsReturned(byp_abc)) *byp_abc = abc;
/dports/biology/infernal/infernal-1.1.3/easel/documentation/
H A Dcodestyle.md350 esl_module_Function(ESL_FOOOBJ **byp_abc)
352 …ESL_ALPHABET *abc = (byp_abc == NULL || *byp_abc == NULL) ? esl_alphabet_Create(eslAMINO) : *byp_a…
354 if (byp_abc != NULL) *byp_abc = abc;
362 esl_module_Function(ESL_FOOOBJ **byp_abc)
364 …LPHABET *abc = (esl_byp_IsInternal(byp_abc) || esl_byp_IsReturned(byp_abc)) ? esl_alphabet_Create(…
366 if (esl_byp_IsReturned(byp_abc)) *byp_abc = abc;
/dports/biology/infernal/infernal-1.1.3/src/
H A Dcm_file.c1367 cm_p7_oprofile_ReadMSV(CM_FILE *cmfp, int read_scores, ESL_ALPHABET **byp_abc, off_t *ret_cm_offset… in cm_p7_oprofile_ReadMSV() argument
1396 …if ((status = p7_oprofile_ReadMSV(cmfp->hfp, byp_abc, &om)) != eslOK) ESL_XFAIL(status, … in cm_p7_oprofile_ReadMSV()
1399 …if ((status = p7_oprofile_ReadInfoMSV(cmfp->hfp, byp_abc, &om)) != eslOK) ESL_XFAIL(status, … in cm_p7_oprofile_ReadMSV()
1451 cm_p7_oprofile_ReadBlockMSV(CM_FILE *cmfp, int64_t idx0, ESL_ALPHABET **byp_abc, CM_P7_OM_BLOCK *hm… in cm_p7_oprofile_ReadBlockMSV() argument
1460 status = cm_p7_oprofile_ReadMSV(cmfp, TRUE, byp_abc, in cm_p7_oprofile_ReadBlockMSV()
H A Dinfernal.h2788 extern int cm_p7_oprofile_ReadMSV(CM_FILE *cmfp, int read_scores, ESL_ALPHABET **byp_abc, off_t…
2789 extern int cm_p7_oprofile_ReadBlockMSV(CM_FILE *cmfp, int64_t cm_idx, ESL_ALPHABET **byp_abc, C…