/dports/biology/seqan1/seqan-1.3.1/seqan/misc/ |
H A D | misc_parsing.h | 63 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() [all …]
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/dports/biology/seqan1/seqan-1.3.1/seqan/file/ |
H A D | file_format_fasta.h | 59 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() [all …]
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H A D | file_format_genbank.h | 63 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()
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H A D | file_format_embl.h | 65 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() [all …]
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H A D | file_format_fasta_align.h | 77 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()
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H A D | file_format_raw.h | 74 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));
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H A D | file_format.h | 454 if (_streamEOF(file)) break; 486 if (_streamEOF(file)) break; 518 if (_streamEOF(file)) break; 555 while (!_streamEOF(file)) { 570 while (!_streamEOF(file)) {
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H A D | cstream.h | 119 _streamEOF(::std::FILE * me)
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/dports/biology/seqan1/seqan-1.3.1/apps/razers/ |
H A D | paramChooser.h | 190 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() [all …]
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/dports/biology/seqan1/seqan-1.3.1/apps/razers2/ |
H A D | paramChooser.h | 190 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() [all …]
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/dports/biology/seqan1/seqan-1.3.1/apps/splazers/ |
H A D | paramChooser.h | 190 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() [all …]
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/dports/biology/seqan1/seqan-1.3.1/seqan/blast/ |
H A D | blast_parsing.h | 57 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()
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H A D | blast_stream_hit.h | 93 while (!_streamEOF(file) && c != '\n' && c != '\r') in _parseBlastHit()
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H A D | blast_report.h | 440 while (!_streamEOF(file) && c != '\n' && c != '\r') 522 if (_streamEOF(file)) return; 1137 return !blast.next_report || _streamEOF(file);
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/dports/biology/seqan1/seqan-1.3.1/seqan/store/ |
H A D | store_io_gff.h | 66 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() [all …]
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H A D | store_io_sam.h | 346 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()
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H A D | store_io_ucsc.h | 70 while (!_streamEOF(file)) in _parseReadUcscIdentifier() 83 while (!_streamEOF(file)) { in _parseSkipWhiteComma() 395 if (_streamEOF(file)) return; in read() 405 while (!_streamEOF(file)) in read()
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/dports/biology/seqan1/seqan-1.3.1/seqan/graph_msa/ |
H A D | graph_align_tcoffee_io.h | 127 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() [all …]
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/dports/biology/seqan1/seqan-1.3.1/seqan/graph_types/ |
H A D | graph_utility_parsing.h | 65 while (!_streamEOF(file)) { in _loadSequences() 78 for(TSize i = 0; (i < seqCount) && !_streamEOF(file); ++i) { in _loadSequences()
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/dports/biology/seqan1/seqan-1.3.1/apps/insegt/ |
H A D | read_gff.h | 59 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()
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H A D | read_gtf.h | 59 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()
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/dports/biology/seqan1/seqan-1.3.1/seqan/score/ |
H A D | score_matrix.h | 280 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()
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/dports/biology/seqan1/seqan-1.3.1/apps/tree_recon/ |
H A D | tree_recon.cpp | 53 if (_streamEOF(file)) return; in _readPhylipMatrix() 55 while (!_streamEOF(file)) { in _readPhylipMatrix() 56 if (_streamEOF(file)) break; in _readPhylipMatrix()
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/dports/biology/seqan1/seqan-1.3.1/apps/rabema/ |
H A D | intervals.h | 239 while (not _streamEOF(stream) && c == '#') in readWitRecord() 241 if (_streamEOF(stream)) in readWitRecord()
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/dports/biology/seqan1/seqan-1.3.1/seqan/consensus/ |
H A D | consensus_base.h | 1322 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() [all …]
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