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Searched refs:_streamEOF (Results 1 – 25 of 58) sorted by relevance

123

/dports/biology/seqan1/seqan-1.3.1/seqan/misc/
H A Dmisc_parsing.h63 while (!_streamEOF(file)) { in _parseSkipLine()
77 while (!_streamEOF(file)) { in _parseSkipWhitespace()
88 while (!_streamEOF(file)) { in _parseSkipSpace()
109 while (!_streamEOF(file)) { in _parseSkipUntilChar()
151 while (!_streamEOF(file)) { in _parseReadNumber()
167 while (!_streamEOF(file)) { in _parseReadDouble()
183 while (!_streamEOF(file)) { in _parseReadIdentifier()
198 if (!_streamEOF(file)) in _parseReadChar()
211 while (!_streamEOF(file)) { in _parseReadIdentifier()
345 if (!_streamEOF(file)) in _parseSkipLine2()
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/dports/biology/seqan1/seqan-1.3.1/seqan/file/
H A Dfile_format_fasta.h59 if (_streamEOF(host(it))) in goBegin()
74 if (_streamEOF(host(it))) in goBegin()
114 if (_streamEOF(host(it))) in goNext()
125 if (_streamEOF(host(it))) in goNext()
160 SEQAN_ASSERT(!_streamEOF(file)) in _fastaScanLine()
170 while (!_streamEOF(file)) in _fastaScanLine()
181 } while (!_streamEOF(file)); in _fastaScanLine()
216 SEQAN_ASSERT(!_streamEOF(file)) in read()
221 SEQAN_ASSERT(!_streamEOF(file)) in read()
227 if (_streamEOF(file)) in read()
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H A Dfile_format_genbank.h63 if (_streamEOF(host(it))) in goBegin()
91 if (_streamEOF(host(it))) in goBegin()
102 if (_streamEOF(host(it))) in goBegin()
130 it.data_eof = _streamEOF(host(it)); in goBegin()
151 if (_streamEOF(host(it))) in goNext()
163 if (_streamEOF(host(it))) in goNext()
241 if (_streamEOF(file)) in readMeta()
248 while (!_streamEOF(file)) in readMeta()
280 if (_streamEOF(file)) in goNext()
285 while (!_streamEOF(file)) in goNext()
H A Dfile_format_embl.h65 if (_streamEOF(host(it))) in goBegin()
88 if (_streamEOF(host(it))) in goBegin()
113 it.data_eof = _streamEOF(host(it)); in goBegin()
134 if (_streamEOF(host(it))) in goNext()
146 if (_streamEOF(host(it))) in goNext()
220 if (_streamEOF(file)) in readMeta()
227 while (!_streamEOF(file)) in readMeta()
280 if(_streamEOF(file)) in readLineType()
285 while (!_streamEOF(file)) in readLineType()
454 if (_streamEOF(file)) in goNext()
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H A Dfile_format_fasta_align.h77 SEQAN_ASSERT(!_streamEOF(file)) in _fastaAlignScanLine()
82 if (_streamEOF(file)) return; in _fastaAlignScanLine()
97 SEQAN_ASSERT_NOT(_streamEOF(file)); in read()
113 while (!_streamEOF(file)) { in read()
116 SEQAN_ASSERT_NOT(_streamEOF(file)); in read()
140 if (_streamEOF(file)) { in read()
204 SEQAN_ASSERT_NOT(_streamEOF(file)); in readIDs()
214 while ((!_streamEOF(file)) && (c != '>')) c = _streamGet(file); in readIDs()
215 if (!_streamEOF(file)) { in readIDs()
258 SEQAN_ASSERT_NOT(_streamEOF(file)); in goNext()
H A Dfile_format_raw.h74 SEQAN_ASSERT(!_streamEOF(file))
83 for (count = 0; !_streamEOF(file) && count != limit; ++count)
126 if (!_streamEOF(file))
146 if (!_streamEOF(file))
223 SEQAN_ASSERT_TRUE(!_streamEOF(file));
H A Dfile_format.h454 if (_streamEOF(file)) break;
486 if (_streamEOF(file)) break;
518 if (_streamEOF(file)) break;
555 while (!_streamEOF(file)) {
570 while (!_streamEOF(file)) {
H A Dcstream.h119 _streamEOF(::std::FILE * me)
/dports/biology/seqan1/seqan-1.3.1/apps/razers/
H A DparamChooser.h190 if (_streamEOF(file)) return; in qualityDistributionFromPrbFile()
199 while (!_streamEOF(file)) in qualityDistributionFromPrbFile()
264 if (_streamEOF(file)) return; in qualityDistributionFromFastQFile()
269 while (!_streamEOF(file)) in qualityDistributionFromFastQFile()
307 if (_streamEOF(file)) return; in qualityDistributionFromFastQIntFile()
312 while (!_streamEOF(file)) in qualityDistributionFromFastQIntFile()
453 if (_streamEOF(file)) return 0; in parseShapesFromFile()
458 while (!_streamEOF(file)) in parseShapesFromFile()
828 while (!_streamEOF(file)) { in _parse_readShape()
886 if(_streamEOF(file)) in parseGappedParams()
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/dports/biology/seqan1/seqan-1.3.1/apps/razers2/
H A DparamChooser.h190 if (_streamEOF(file)) return; in qualityDistributionFromPrbFile()
199 while (!_streamEOF(file)) in qualityDistributionFromPrbFile()
264 if (_streamEOF(file)) return; in qualityDistributionFromFastQFile()
269 while (!_streamEOF(file)) in qualityDistributionFromFastQFile()
307 if (_streamEOF(file)) return; in qualityDistributionFromFastQIntFile()
312 while (!_streamEOF(file)) in qualityDistributionFromFastQIntFile()
453 if (_streamEOF(file)) return 0; in parseShapesFromFile()
458 while (!_streamEOF(file)) in parseShapesFromFile()
827 while (!_streamEOF(file)) { in _parse_readShape()
885 if(_streamEOF(file)) in parseGappedParams()
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/dports/biology/seqan1/seqan-1.3.1/apps/splazers/
H A DparamChooser.h190 if (_streamEOF(file)) return; in qualityDistributionFromPrbFile()
199 while (!_streamEOF(file)) in qualityDistributionFromPrbFile()
264 if (_streamEOF(file)) return; in qualityDistributionFromFastQFile()
269 while (!_streamEOF(file)) in qualityDistributionFromFastQFile()
307 if (_streamEOF(file)) return; in qualityDistributionFromFastQIntFile()
312 while (!_streamEOF(file)) in qualityDistributionFromFastQIntFile()
453 if (_streamEOF(file)) return 0; in parseShapesFromFile()
458 while (!_streamEOF(file)) in parseShapesFromFile()
828 while (!_streamEOF(file)) { in _parse_readShape()
886 if(_streamEOF(file)) in parseGappedParams()
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/dports/biology/seqan1/seqan-1.3.1/seqan/blast/
H A Dblast_parsing.h57 while (!_streamEOF(file)) { in _parseReadAlignmentString()
110 while (!_streamEOF(file) && c != '\n' && c != '\r') in _parseReadQueryAndDBName()
118 while (!_streamEOF(file) && c != '\n' && c != '\r') in _parseReadQueryAndDBName()
H A Dblast_stream_hit.h93 while (!_streamEOF(file) && c != '\n' && c != '\r') in _parseBlastHit()
H A Dblast_report.h440 while (!_streamEOF(file) && c != '\n' && c != '\r')
522 if (_streamEOF(file)) return;
1137 return !blast.next_report || _streamEOF(file);
/dports/biology/seqan1/seqan-1.3.1/seqan/store/
H A Dstore_io_gff.h66 while (!_streamEOF(file)) in _parseReadGffIdentifier()
84 while (!_streamEOF(file)) { in _parseSkipEntryUntilWhitespace()
97 while (!_streamEOF(file)) in _parseReadGffKeyValue()
114 while (!_streamEOF(file)) in _parseReadGffKeyValue()
120 if (!_streamEOF(file)) c = _streamGet(file); in _parseReadGffKeyValue()
127 if (!_streamEOF(file)) c = _streamGet(file); in _parseReadGffKeyValue()
136 if (!_streamEOF(file)) c = _streamGet(file); in _parseReadGffKeyValue()
140 if (_streamEOF(file)) break; in _parseReadGffKeyValue()
279 while (!_streamEOF(file) && _parseReadGffKeyValue(file, ctx._key, ctx._value, c)) in _readOneAnnotation()
435 if (_streamEOF(file)) return; in read()
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H A Dstore_io_sam.h346 while (!_streamEOF(file)) in _parseReadCigar()
367 while (!_streamEOF(file)) in _parseReadSamIdentifier()
394 if (!_streamEOF(file)) in _parseReadDnaSeq()
401 for (; !_streamEOF(file) && _parseIsDna(c); c = _streamGet(file)) in _parseReadDnaSeq()
433 if (!_streamEOF(file)) in _parseReadSeqQual()
460 if (_streamEOF(file)) return; in _parseReadCharsUntilEndOfLine()
465 if (!_streamEOF(file)) in _parseReadCharsUntilEndOfLine()
611 if (_streamEOF(file)) return; in read()
682 while (!_streamEOF(file)) in _readAlignments()
H A Dstore_io_ucsc.h70 while (!_streamEOF(file)) in _parseReadUcscIdentifier()
83 while (!_streamEOF(file)) { in _parseSkipWhiteComma()
395 if (_streamEOF(file)) return; in read()
405 while (!_streamEOF(file)) in read()
/dports/biology/seqan1/seqan-1.3.1/seqan/graph_msa/
H A Dgraph_align_tcoffee_io.h127 if (_streamEOF(file)) return; in read()
145 if (_streamEOF(file)) return; in read()
154 while (!_streamEOF(file)) { in read()
156 if (_streamEOF(file)) break; in read()
242 if (_streamEOF(file)) return; in read()
367 while(!_streamEOF(file)) { in read()
473 while(!_streamEOF(file)) { in read()
575 while (!_streamEOF(file)) { in read()
781 while (!_streamEOF(file)) { in read()
794 if (_streamEOF(file)) { in read()
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/dports/biology/seqan1/seqan-1.3.1/seqan/graph_types/
H A Dgraph_utility_parsing.h65 while (!_streamEOF(file)) { in _loadSequences()
78 for(TSize i = 0; (i < seqCount) && !_streamEOF(file); ++i) { in _loadSequences()
/dports/biology/seqan1/seqan-1.3.1/apps/insegt/
H A Dread_gff.h59 while (!_streamEOF(file)) in readAnnotationsFromGFF()
89 while (!_streamEOF(file)) in readAnnotationsFromGFF()
124 if (!_streamEOF(file) && !(c == '\n' || (c == '\r' && _streamPeek(file) != '\n'))) in readAnnotationsFromGFF()
203 while (!_streamEOF(file)) in readAnnotationsFromGFF()
284 if (!_streamEOF(file) && !(c == '\n' || (c == '\r' && _streamPeek(file) != '\n'))) in readAnnotationsFromGFF()
H A Dread_gtf.h59 while (!_streamEOF(file)) in readAnnotationsFromGTF()
89 while (!_streamEOF(file)) in readAnnotationsFromGTF()
125 if (!_streamEOF(file) && !(c == '\n' || (c == '\r' && _streamPeek(file) != '\n'))) in readAnnotationsFromGTF()
205 while (!_streamEOF(file)) in readAnnotationsFromGTF()
286 if (!_streamEOF(file) && !(c == '\n' || (c == '\r' && _streamPeek(file) != '\n'))) in readAnnotationsFromGTF()
/dports/biology/seqan1/seqan-1.3.1/seqan/score/
H A Dscore_matrix.h280 if (_streamEOF(fl)) return; in readMeta()
285 while (!_streamEOF(fl) && (c == '#')) { in readMeta()
306 if (_streamEOF(fl)) return; in read()
317 } while (!_streamEOF(fl) && (empty(s) || (s[0] == '#'))); in read()
319 if (_streamEOF(fl)) return; in read()
338 while (!_streamEOF(fl)) { in read()
/dports/biology/seqan1/seqan-1.3.1/apps/tree_recon/
H A Dtree_recon.cpp53 if (_streamEOF(file)) return; in _readPhylipMatrix()
55 while (!_streamEOF(file)) { in _readPhylipMatrix()
56 if (_streamEOF(file)) break; in _readPhylipMatrix()
/dports/biology/seqan1/seqan-1.3.1/apps/rabema/
H A Dintervals.h239 while (not _streamEOF(stream) && c == '#') in readWitRecord()
241 if (_streamEOF(stream)) in readWitRecord()
/dports/biology/seqan1/seqan-1.3.1/seqan/consensus/
H A Dconsensus_base.h1322 while (!_streamEOF(file)) { in _convertSimpleReadFile()
1323 if (_streamEOF(file)) break; in _convertSimpleReadFile()
1445 if ((strmRef) && (!_streamEOF(strmRef))) { in _convertSimpleReadFile()
1447 while (!_streamEOF(strmRef)) { in _convertSimpleReadFile()
1448 if (_streamEOF(strmRef)) break; in _convertSimpleReadFile()
1480 if ((strmFrag) && (!_streamEOF(strmFrag))) { in _convertSimpleReadFile()
1482 while (!_streamEOF(strmFrag)) { in _convertSimpleReadFile()
1483 if (_streamEOF(strmFrag)) break; in _convertSimpleReadFile()
1548 if ((strmLib) && (!_streamEOF(strmLib))) { in _convertSimpleReadFile()
1550 while (!_streamEOF(strmLib)) { in _convertSimpleReadFile()
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