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/dports/biology/infernal/infernal-1.1.3/easel/
H A Desl_sqio.h49 int (*position) (struct esl_sqio_s *sqfp, off_t offset);
50 void (*close) (struct esl_sqio_s *sqfp);
55 int (*read) (struct esl_sqio_s *sqfp, ESL_SQ *sq);
56 int (*read_info) (struct esl_sqio_s *sqfp, ESL_SQ *sq);
57 int (*read_seq) (struct esl_sqio_s *sqfp, ESL_SQ *sq);
65 int (*pos_by_number) (struct esl_sqio_s *sqfp, int which);
71 int (*is_rewindable) (const struct esl_sqio_s *sqfp);
72 const char *(*get_error) (const struct esl_sqio_s *sqfp);
125 extern void esl_sqfile_Close(ESL_SQFILE *sqfp);
141 const char *esl_sqfile_GetErrorBuf(const ESL_SQFILE *sqfp);
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H A Desl_sqio_ascii.c334 sqascii_Close(sqfp); in esl_sqascii_Open()
411 status = loadbuf(sqfp); in sqascii_GuessFileFormat()
789 addbuf(sqfp, sq, n); in sqascii_Read()
989 addbuf(sqfp, sq, n); in sqascii_ReadSequence()
2025 loadmem(ESL_SQFILE *sqfp) in loadmem() argument
2100 loadbuf(ESL_SQFILE *sqfp) in loadbuf() argument
2381 x = sqfp->inmap[c]; in skip_whitespace()
2392 x = sqfp->inmap[c]; in skip_whitespace()
2458 skipbuf(sqfp, nskip); in read_nres()
2736 status = loadbuf(sqfp); in end_embl()
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H A Desl_sqio.c103 if (sqfp->close != NULL) sqfp->close(sqfp); in esl_sqfile_Close()
182 status = esl_sqncbi_Open(sqfp->filename, sqfp->format, sqfp); in sqfile_open()
185 status = esl_sqascii_Open(sqfp->filename, sqfp->format, sqfp); in sqfile_open()
288 sqfp->set_digital(sqfp, abc); in esl_sqfile_SetDigital()
358 return sqfp->read(sqfp, sq); in esl_sqio_Read()
380 return sqfp->read_info(sqfp, sq); in esl_sqio_ReadInfo()
401 return sqfp->read_seq(sqfp, sq); in esl_sqio_ReadSequence()
639 return sqfp->echo(sqfp, sq, ofp); in esl_sqio_Echo()
662 return sqfp->get_error(sqfp); in esl_sqfile_GetErrorBuf()
676 return sqfp->is_rewindable(sqfp); in esl_sqfile_IsRewindable()
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H A Desl_sqio_ncbi.c196 sqncbi_Close(sqfp); in esl_sqncbi_Open()
1708 *ptr = sqfp->inmap[n]; in read_dna()
1712 *ptr = sqfp->inmap[n]; in read_dna()
1716 *ptr = sqfp->inmap[n]; in read_dna()
1720 *ptr = sqfp->inmap[n]; in read_dna()
1729 *ptr = sqfp->inmap[n]; in read_dna()
1751 c = sqfp->inmap[n]; in read_dna()
1917 c = sqfp->inmap[n]; in correct_ambiguity()
2049 *ptr = sqfp->inmap[n]; in read_nres_dna()
2167 sqfp->inmap[x] = y; in inmap_ncbi_dna()
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/dports/biology/hmmer/hmmer-3.3/easel/
H A Desl_sqio.h49 int (*position) (struct esl_sqio_s *sqfp, off_t offset);
50 void (*close) (struct esl_sqio_s *sqfp);
55 int (*read) (struct esl_sqio_s *sqfp, ESL_SQ *sq);
56 int (*read_info) (struct esl_sqio_s *sqfp, ESL_SQ *sq);
57 int (*read_seq) (struct esl_sqio_s *sqfp, ESL_SQ *sq);
65 int (*pos_by_number) (struct esl_sqio_s *sqfp, int which);
71 int (*is_rewindable) (const struct esl_sqio_s *sqfp);
72 const char *(*get_error) (const struct esl_sqio_s *sqfp);
125 extern void esl_sqfile_Close(ESL_SQFILE *sqfp);
141 const char *esl_sqfile_GetErrorBuf(const ESL_SQFILE *sqfp);
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H A Desl_sqio_ascii.c334 sqascii_Close(sqfp); in esl_sqascii_Open()
411 status = loadbuf(sqfp); in sqascii_GuessFileFormat()
789 addbuf(sqfp, sq, n); in sqascii_Read()
989 addbuf(sqfp, sq, n); in sqascii_ReadSequence()
2025 loadmem(ESL_SQFILE *sqfp) in loadmem() argument
2100 loadbuf(ESL_SQFILE *sqfp) in loadbuf() argument
2381 x = sqfp->inmap[c]; in skip_whitespace()
2392 x = sqfp->inmap[c]; in skip_whitespace()
2458 skipbuf(sqfp, nskip); in read_nres()
2736 status = loadbuf(sqfp); in end_embl()
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H A Desl_sqio.c103 if (sqfp->close != NULL) sqfp->close(sqfp); in esl_sqfile_Close()
182 status = esl_sqncbi_Open(sqfp->filename, sqfp->format, sqfp); in sqfile_open()
185 status = esl_sqascii_Open(sqfp->filename, sqfp->format, sqfp); in sqfile_open()
288 sqfp->set_digital(sqfp, abc); in esl_sqfile_SetDigital()
358 return sqfp->read(sqfp, sq); in esl_sqio_Read()
380 return sqfp->read_info(sqfp, sq); in esl_sqio_ReadInfo()
401 return sqfp->read_seq(sqfp, sq); in esl_sqio_ReadSequence()
639 return sqfp->echo(sqfp, sq, ofp); in esl_sqio_Echo()
662 return sqfp->get_error(sqfp); in esl_sqfile_GetErrorBuf()
676 return sqfp->is_rewindable(sqfp); in esl_sqfile_IsRewindable()
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H A Desl_sqio_ncbi.c196 sqncbi_Close(sqfp); in esl_sqncbi_Open()
1708 *ptr = sqfp->inmap[n]; in read_dna()
1712 *ptr = sqfp->inmap[n]; in read_dna()
1716 *ptr = sqfp->inmap[n]; in read_dna()
1720 *ptr = sqfp->inmap[n]; in read_dna()
1729 *ptr = sqfp->inmap[n]; in read_dna()
1751 c = sqfp->inmap[n]; in read_dna()
1917 c = sqfp->inmap[n]; in correct_ambiguity()
2049 *ptr = sqfp->inmap[n]; in read_nres_dna()
2167 sqfp->inmap[x] = y; in inmap_ncbi_dna()
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/dports/biology/infernal/infernal-1.1.3/easel/miniapps/
H A Desl-sfetch.c155 …if (! sqfp->data.ascii.do_gzip && ! sqfp->data.ascii.do_stdin && ! esl_sqio_IsAlignment(sqfp->for… in main()
176 …if (! sqfp->data.ascii.do_gzip && ! sqfp->data.ascii.do_stdin && ! esl_sqio_IsAlignment(sqfp->for… in main()
203 esl_sqfile_Close(sqfp); in main()
229 if (esl_newssi_AddFile(ns, sqfp->filename, sqfp->format, &fh) != eslOK) in create_ssi_index()
250 sqfp->filename, esl_sqfile_GetErrorBuf(sqfp)); in create_ssi_index()
255 if (sqfp->data.ascii.bpl > 0 && sqfp->data.ascii.rpl > 0) { in create_ssi_index()
316 if (sqfp->data.ascii.ssi != NULL) { onefetch(go, ofp, key, sqfp); nseq++; } in multifetch()
339 sqfp->filename, esl_sqfile_GetErrorBuf(sqfp)); in multifetch()
381 sqfp->filename, esl_sqfile_GetErrorBuf(sqfp)); in onefetch()
394 sqfp->filename, esl_sqfile_GetErrorBuf(sqfp)); in onefetch()
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H A Desl-translate.c17 do_by_sequences(ESL_GENCODE *gcode, ESL_GENCODE_WORKSTATE *wrk, ESL_SQFILE *sqfp) in do_by_sequences() argument
22 while (( status = esl_sqio_Read(sqfp, sq )) == eslOK) in do_by_sequences()
42 sqfp->filename, sqfp->get_error(sqfp)); in do_by_sequences()
44 status, sqfp->filename); in do_by_sequences()
52 do_by_windows(ESL_GENCODE *gcode, ESL_GENCODE_WORKSTATE *wrk, ESL_SQFILE *sqfp) in do_by_windows() argument
73 …al("Parsing failed in sequence file %s:\n%s", sqfp->filename, esl_sqfile_GetErrorBuf(sqfp… in do_by_windows()
74 …al("Invalid residue(s) found in sequence file %s\n%s", sqfp->filename, esl_sqfile_GetErrorBuf(sqfp… in do_by_windows()
127 ESL_SQFILE *sqfp = NULL; in main() local
200 if (esl_opt_GetBoolean(go, "-W")) do_by_windows(gcode, wrk, sqfp); in main()
201 else do_by_sequences(gcode, wrk, sqfp); in main()
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H A Desl-seqrange.c53 static void range_by_seqnum(ESL_SQFILE *sqfp, int nproc, int64_t **ret_final_sqidx);
61 ESL_SQFILE *sqfp = NULL; /* open sequence file */ in main() local
92 status = esl_sqfile_Open(seqfile, infmt, NULL, &sqfp); in main()
99 …if (sqfp->data.ascii.do_gzip) cmdline_failure(argv[0], "Can't determine seq range for a … in main()
100 …if (sqfp->data.ascii.do_stdin) cmdline_failure(argv[0], "Can't determine seq range for a … in main()
104 status = esl_sqfile_OpenSSI(sqfp, NULL); in main()
110 ESL_SQASCII_DATA *ascii = &sqfp->data.ascii; in main()
114 range_by_seqnum(sqfp, nproc, &(final_sqidx)); in main()
120 esl_sqfile_Close(sqfp); in main()
131 range_by_seqnum(ESL_SQFILE *sqfp, int nproc, int64_t **ret_final_sqidx) in range_by_seqnum() argument
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H A Dcmd_downsample.c122 ESL_SQFILE *sqfp = NULL; in downsample_seqs() local
132 status = esl_sqfile_Open(infile, infmt, NULL, &sqfp); in downsample_seqs()
140 while ( (status = esl_sqio_Read(sqfp, sq)) == eslOK) in downsample_seqs()
159 … == eslEFORMAT) esl_fatal("Sequence input parse failed:\n %s", esl_sqfile_GetErrorBuf(sqfp)); in downsample_seqs()
167 esl_sqfile_Close(sqfp); in downsample_seqs()
206 ESL_SQFILE *sqfp = NULL; in downsample_seqs_big() local
218 status = esl_sqfile_Open(infile, infmt, NULL, &sqfp); in downsample_seqs_big()
224 …if ( esl_sqio_IsAlignment(sqfp->format) ) esl_fatal("To use -S, <infile> must be an unaligned seq… in downsample_seqs_big()
228 while ((status = esl_sqio_ReadInfo(sqfp, sq)) == eslOK) in downsample_seqs_big()
237 … == eslEFORMAT) esl_fatal("Sequence input parse failed:\n %s", esl_sqfile_GetErrorBuf(sqfp)); in downsample_seqs_big()
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H A Desl-mask.c77 ESL_SQFILE *sqfp = NULL; /* open sequence file */ in main() local
115 status = esl_sqfile_Open(seqfile, infmt, NULL, &sqfp); in main()
121 if (do_fetching && sqfp->data.ascii.ssi == NULL) in main()
154 status = esl_sqio_Fetch(sqfp, source, sq); in main()
156 …else if (status == eslEINVAL) esl_fatal("No SSI index or can't reposition in file %s\n", sqfp->… in main()
157 …else if (status == eslEFORMAT) esl_fatal("Parse failed:\n%s\n", esl_sqfile_GetErrorBuf(sqfp)); … in main()
162 status = esl_sqio_Read(sqfp, sq); in main()
163 …if (status == eslEOF) esl_fatal("File %s ended prematurely; didn't find %s\n", sqfp->fil… in main()
164 else if (status == eslEFORMAT) esl_fatal("Parse failed:\n%s\n", esl_sqfile_GetErrorBuf(sqfp)); in main()
165 …else if (status != eslOK) esl_fatal("Unexpected error reading sequence file %s\n", sqfp->fil… in main()
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H A Desl-seqstat.c76 ESL_SQFILE *sqfp = NULL; in main() local
115 status = esl_sqfile_Open(seqfile, infmt, NULL, &sqfp); in main()
124 status = esl_sqfile_GuessAlphabet(sqfp, &alphatype); in main()
127 sqfp->filename, esl_sqfile_GetErrorBuf(sqfp)); in main()
133 esl_sqfile_SetDigital(sqfp, abc); in main()
152 while ((wstatus = esl_sqio_ReadWindow(sqfp, 0, 4096, sq)) != eslEOF) in main()
187 sqfp->filename, esl_sqfile_GetErrorBuf(sqfp)); in main()
189 wstatus, sqfp->filename); in main()
194 printf("Format: %s\n", esl_sqio_DecodeFormat(sqfp->format)); in main()
209 esl_sqfile_Close(sqfp); in main()
/dports/biology/hmmer/hmmer-3.3/easel/miniapps/
H A Desl-sfetch.c155 …if (! sqfp->data.ascii.do_gzip && ! sqfp->data.ascii.do_stdin && ! esl_sqio_IsAlignment(sqfp->for… in main()
176 …if (! sqfp->data.ascii.do_gzip && ! sqfp->data.ascii.do_stdin && ! esl_sqio_IsAlignment(sqfp->for… in main()
203 esl_sqfile_Close(sqfp); in main()
229 if (esl_newssi_AddFile(ns, sqfp->filename, sqfp->format, &fh) != eslOK) in create_ssi_index()
250 sqfp->filename, esl_sqfile_GetErrorBuf(sqfp)); in create_ssi_index()
255 if (sqfp->data.ascii.bpl > 0 && sqfp->data.ascii.rpl > 0) { in create_ssi_index()
316 if (sqfp->data.ascii.ssi != NULL) { onefetch(go, ofp, key, sqfp); nseq++; } in multifetch()
339 sqfp->filename, esl_sqfile_GetErrorBuf(sqfp)); in multifetch()
381 sqfp->filename, esl_sqfile_GetErrorBuf(sqfp)); in onefetch()
394 sqfp->filename, esl_sqfile_GetErrorBuf(sqfp)); in onefetch()
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H A Desl-translate.c17 do_by_sequences(ESL_GENCODE *gcode, ESL_GENCODE_WORKSTATE *wrk, ESL_SQFILE *sqfp) in do_by_sequences() argument
22 while (( status = esl_sqio_Read(sqfp, sq )) == eslOK) in do_by_sequences()
42 sqfp->filename, sqfp->get_error(sqfp)); in do_by_sequences()
44 status, sqfp->filename); in do_by_sequences()
52 do_by_windows(ESL_GENCODE *gcode, ESL_GENCODE_WORKSTATE *wrk, ESL_SQFILE *sqfp) in do_by_windows() argument
73 …al("Parsing failed in sequence file %s:\n%s", sqfp->filename, esl_sqfile_GetErrorBuf(sqfp… in do_by_windows()
74 …al("Invalid residue(s) found in sequence file %s\n%s", sqfp->filename, esl_sqfile_GetErrorBuf(sqfp… in do_by_windows()
127 ESL_SQFILE *sqfp = NULL; in main() local
200 if (esl_opt_GetBoolean(go, "-W")) do_by_windows(gcode, wrk, sqfp); in main()
201 else do_by_sequences(gcode, wrk, sqfp); in main()
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H A Desl-seqrange.c53 static void range_by_seqnum(ESL_SQFILE *sqfp, int nproc, int64_t **ret_final_sqidx);
61 ESL_SQFILE *sqfp = NULL; /* open sequence file */ in main() local
92 status = esl_sqfile_Open(seqfile, infmt, NULL, &sqfp); in main()
99 …if (sqfp->data.ascii.do_gzip) cmdline_failure(argv[0], "Can't determine seq range for a … in main()
100 …if (sqfp->data.ascii.do_stdin) cmdline_failure(argv[0], "Can't determine seq range for a … in main()
104 status = esl_sqfile_OpenSSI(sqfp, NULL); in main()
110 ESL_SQASCII_DATA *ascii = &sqfp->data.ascii; in main()
114 range_by_seqnum(sqfp, nproc, &(final_sqidx)); in main()
120 esl_sqfile_Close(sqfp); in main()
131 range_by_seqnum(ESL_SQFILE *sqfp, int nproc, int64_t **ret_final_sqidx) in range_by_seqnum() argument
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H A Dcmd_downsample.c122 ESL_SQFILE *sqfp = NULL; in downsample_seqs() local
132 status = esl_sqfile_Open(infile, infmt, NULL, &sqfp); in downsample_seqs()
140 while ( (status = esl_sqio_Read(sqfp, sq)) == eslOK) in downsample_seqs()
159 … == eslEFORMAT) esl_fatal("Sequence input parse failed:\n %s", esl_sqfile_GetErrorBuf(sqfp)); in downsample_seqs()
167 esl_sqfile_Close(sqfp); in downsample_seqs()
206 ESL_SQFILE *sqfp = NULL; in downsample_seqs_big() local
218 status = esl_sqfile_Open(infile, infmt, NULL, &sqfp); in downsample_seqs_big()
224 …if ( esl_sqio_IsAlignment(sqfp->format) ) esl_fatal("To use -S, <infile> must be an unaligned seq… in downsample_seqs_big()
228 while ((status = esl_sqio_ReadInfo(sqfp, sq)) == eslOK) in downsample_seqs_big()
237 … == eslEFORMAT) esl_fatal("Sequence input parse failed:\n %s", esl_sqfile_GetErrorBuf(sqfp)); in downsample_seqs_big()
[all …]
H A Desl-mask.c77 ESL_SQFILE *sqfp = NULL; /* open sequence file */ in main() local
115 status = esl_sqfile_Open(seqfile, infmt, NULL, &sqfp); in main()
121 if (do_fetching && sqfp->data.ascii.ssi == NULL) in main()
154 status = esl_sqio_Fetch(sqfp, source, sq); in main()
156 …else if (status == eslEINVAL) esl_fatal("No SSI index or can't reposition in file %s\n", sqfp->… in main()
157 …else if (status == eslEFORMAT) esl_fatal("Parse failed:\n%s\n", esl_sqfile_GetErrorBuf(sqfp)); … in main()
162 status = esl_sqio_Read(sqfp, sq); in main()
163 …if (status == eslEOF) esl_fatal("File %s ended prematurely; didn't find %s\n", sqfp->fil… in main()
164 else if (status == eslEFORMAT) esl_fatal("Parse failed:\n%s\n", esl_sqfile_GetErrorBuf(sqfp)); in main()
165 …else if (status != eslOK) esl_fatal("Unexpected error reading sequence file %s\n", sqfp->fil… in main()
[all …]
H A Desl-seqstat.c76 ESL_SQFILE *sqfp = NULL; in main() local
115 status = esl_sqfile_Open(seqfile, infmt, NULL, &sqfp); in main()
124 status = esl_sqfile_GuessAlphabet(sqfp, &alphatype); in main()
127 sqfp->filename, esl_sqfile_GetErrorBuf(sqfp)); in main()
133 esl_sqfile_SetDigital(sqfp, abc); in main()
152 while ((wstatus = esl_sqio_ReadWindow(sqfp, 0, 4096, sq)) != eslEOF) in main()
187 sqfp->filename, esl_sqfile_GetErrorBuf(sqfp)); in main()
189 wstatus, sqfp->filename); in main()
194 printf("Format: %s\n", esl_sqio_DecodeFormat(sqfp->format)); in main()
209 esl_sqfile_Close(sqfp); in main()
/dports/biology/ncbi-toolkit/ncbi/sequin/
H A Dsequin2.c10778 switch (sqfp->tagFromPage [sqfp->currentPage]) { in ExportSequencesForm()
10838 switch (sqfp->tagFromPage [sqfp->currentPage]) { in ImportSequencesForm()
10900 switch (sqfp->tagFromPage [sqfp->currentPage]) { in SetOrgNucProtImportExportItems()
11201 switch (sqfp->tagFromPage [sqfp->currentPage]) { in SequencesFormDeleteProc()
17512 if (sqfp == NULL || sqfp->annot_tbs == NULL) in GetStandardTableDisplayDialogWidth()
25650 SetObjectExtra (sqfp->molecule_btn, sqfp, NULL); in CreateNucleotideTab()
25653 SetObjectExtra (sqfp->topology_btn, sqfp, NULL); in CreateNucleotideTab()
25981 SetObjectExtra (sqfp->prevBtn, sqfp, NULL); in CreateInitOrgNucProtForm()
25984 SetObjectExtra (sqfp->nextBtn, sqfp, NULL); in CreateInitOrgNucProtForm()
26003 Show (sqfp->pages [sqfp->currentPage]); in CreateInitOrgNucProtForm()
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/dports/biology/infernal/infernal-1.1.3/src/
H A Dtrcyk.c21 ESL_SQFILE *sqfp; in main() local
43 sqfp = NULL; in main()
68 if ( esl_sqfile_Open(seqfile, format, NULL, &sqfp) != eslOK ) in main()
77 while ( esl_sqio_Read(sqfp, seq) == eslOK ) in main()
125 esl_sqfile_Close(sqfp); in main()
H A Dstats.c171 int GetDBSize (ESL_SQFILE *sqfp, char *errbuf, long *ret_N, int *ret_nseq, int *ret_namewidth) in GetDBSize() argument
181 while ((status = esl_sqio_ReadInfo(sqfp, sq)) == eslOK) { in GetDBSize()
189 sqfp->filename, esl_sqfile_GetErrorBuf(sqfp)); in GetDBSize()
192 esl_sqfile_Position(sqfp, (off_t) 0); /* rewind sequence file to beginning */ in GetDBSize()
218 int GetDBInfo (const ESL_ALPHABET *abc, ESL_SQFILE *sqfp, char *errbuf, long *ret_N, int *ret_nseq,… in GetDBInfo() argument
236 esl_sqfile_SetDigital(sqfp, abc); in GetDBInfo()
238 while ((status = esl_sqio_Read(sqfp, sq)) == eslOK) { in GetDBInfo()
267 sqfp->filename, esl_sqfile_GetErrorBuf(sqfp)); in GetDBInfo()
269 esl_sqfile_Position(sqfp, (off_t) 0); in GetDBInfo()
/dports/biology/infernal/infernal-1.1.3/hmmer/src/
H A Dcachedb_shard.c71 ESL_SQFILE *sqfp = NULL; in p7_seqcache_Open_master() local
92 ascii = &sqfp->data.ascii; in p7_seqcache_Open_master()
164 while ((status = esl_sqio_Read(sqfp, sq)) == eslOK) { in p7_seqcache_Open_master()
265 esl_sqfile_Close(sqfp); in p7_seqcache_Open_master()
343 ESL_SQFILE *sqfp = NULL; in p7_seqcache_Open_shard() local
364 ascii = &sqfp->data.ascii; in p7_seqcache_Open_shard()
442 while ((status = esl_sqio_Read(sqfp, sq)) == eslOK) { in p7_seqcache_Open_shard()
596 esl_sqfile_Close(sqfp); in p7_seqcache_Open_shard()
719 ESL_SQFILE *sqfp = NULL; in main() local
782 while ((status = esl_sqio_Read(sqfp, sq)) == eslOK) { in main()
[all …]
/dports/biology/hmmer/hmmer-3.3/src/
H A Dcachedb_shard.c71 ESL_SQFILE *sqfp = NULL; in p7_seqcache_Open_master() local
92 ascii = &sqfp->data.ascii; in p7_seqcache_Open_master()
164 while ((status = esl_sqio_Read(sqfp, sq)) == eslOK) { in p7_seqcache_Open_master()
265 esl_sqfile_Close(sqfp); in p7_seqcache_Open_master()
343 ESL_SQFILE *sqfp = NULL; in p7_seqcache_Open_shard() local
364 ascii = &sqfp->data.ascii; in p7_seqcache_Open_shard()
442 while ((status = esl_sqio_Read(sqfp, sq)) == eslOK) { in p7_seqcache_Open_shard()
596 esl_sqfile_Close(sqfp); in p7_seqcache_Open_shard()
719 ESL_SQFILE *sqfp = NULL; in main() local
782 while ((status = esl_sqio_Read(sqfp, sq)) == eslOK) { in main()
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