/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/ngs_roi/ |
H A D | roi_builder.cpp | 58 currentRoi.beginPos = record.beginPos; in createRoi() 85 if ((int)currentRoi.len < record.tLen + (record.beginPos - currentRoi.beginPos)) in extendRoi() 86 currentRoi.len = record.tLen + (record.beginPos - currentRoi.beginPos); in extendRoi() 108 unsigned beginPos = record.beginPos - currentRoi.beginPos; in extendRoi() local 121 connective[beginPos] = true; in extendRoi() 128 connective[beginPos] = true; in extendRoi() 142 beginPos += it->count; in extendRoi() 244 int beginPos = 0; in writeCurrentRecord() local 254 beginPos = i; in writeCurrentRecord() 262 beginPos = i; in writeCurrentRecord() [all …]
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H A D | project_interval.cpp | 68 roiRecord.beginPos = bedRecord.beginPos; in writeEmptyBed() 88 return (rhs.beginPos < lhs.endPos) && (lhs.beginPos < rhs.endPos); in overlap() 145 int beginPos = bedRecord.beginPos; in processFirstBedRecord() local 153 beginPos = std::min(it->beginPos, beginPos); in processFirstBedRecord() 161 resize(connected, endPos - beginPos, false); in processFirstBedRecord() 166 resize(counts, endPos - beginPos, 0); in processFirstBedRecord() 168 for (unsigned j = it->beginPos - beginPos, i = 0; i < length(it->count); ++i, ++j) in processFirstBedRecord() 269 bitmap[pos - beginPos] = true; in updateConnectivity() 311 … appendValue(pairs, TIntPair(bedRecord.beginPos - beginPos, bedRecord.endPos - beginPos)); in writeRois() 369 record.beginPos = beginPos + pairs[i].i1; in writeRois() [all …]
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/dports/math/R-cran-lpSolve/lpSolve/src/ |
H A D | commonlib.c | 179 beginPos = offset; in findIndex() 181 if(endPos < beginPos) in findIndex() 225 beginPos++; in findIndex() 233 beginPos++; in findIndex() 241 return(beginPos); in findIndex() 243 return(-beginPos); in findIndex() 256 beginPos = offset; in findIndexEx() 258 if(endPos < beginPos) in findIndexEx() 309 beginPos++; in findIndexEx() 316 return(beginPos); in findIndexEx() [all …]
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/dports/science/siconos/siconos-4.4.0/externals/SOL/lumod-c/ |
H A D | commonlib.c | 189 beginPos = offset; in findIndex() 191 if(endPos < beginPos) in findIndex() 243 beginPos++; in findIndex() 252 beginPos++; in findIndex() 260 return(beginPos); in findIndex() 262 return(-beginPos); in findIndex() 275 beginPos = offset; in findIndexEx() 277 if(endPos < beginPos) in findIndexEx() 337 beginPos++; in findIndexEx() 344 return(beginPos); in findIndexEx() [all …]
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/bs_tools/ |
H A D | casbar_realignment.h | 36 typename TMatch::TPos ba = _min(a.beginPos, a.endPos); in operator() 37 typename TMatch::TPos bb = _min(b.beginPos, b.endPos); in operator() 111 bool oa = a.beginPos < a.endPos; in operator() 112 bool ob = b.beginPos < b.endPos; in operator() 151 if (std::min(a.beginPos, a.endPos) < std::min(b.beginPos, b.endPos)) in operator() 153 if (std::min(a.beginPos, a.endPos) > std::min(b.beginPos, b.endPos)) in operator() 174 if (std::max(a.endPos,a.beginPos) < std::max(b.endPos,b.beginPos)) return true; in operator() 175 if (std::max(a.endPos,a.beginPos) > std::max(b.endPos,b.beginPos)) return false; in operator() 193 if (_max(a.endPos,a.beginPos) < _max(b.endPos,b.beginPos)) return true; in operator() 194 if (_max(a.endPos,a.beginPos) > _max(b.endPos,b.beginPos)) return false; in operator() [all …]
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/store/ |
H A D | store_intervaltree.h | 77 TId beginPos; in createIntervalTreeStore() local 84 beginPos = getValue(itAnno).beginPos; in createIntervalTreeStore() 86 if (beginPos != INVALID_ID && beginPos <= endPos) in createIntervalTreeStore() 88 interval.i1 = beginPos; in createIntervalTreeStore() 93 else if (beginPos != INVALID_ID && beginPos > endPos) in createIntervalTreeStore() 96 interval.i2 = beginPos; in createIntervalTreeStore() 128 TId beginPos; in createIntervalTreeStore() local 135 beginPos = getValue(itAnno).beginPos; in createIntervalTreeStore() 137 if (beginPos != INVALID_ID) in createIntervalTreeStore() 139 if (beginPos <= endPos) in createIntervalTreeStore() [all …]
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/dports/biology/seqan1/seqan-1.3.1/seqan/store/ |
H A D | store_intervaltree.h | 78 TId beginPos; in createIntervalTreeStore() local 85 beginPos = getValue(itAnno).beginPos; in createIntervalTreeStore() 87 if (beginPos != INVALID_ID && beginPos <= endPos) in createIntervalTreeStore() 89 interval.i1 = beginPos; in createIntervalTreeStore() 94 else if (beginPos != INVALID_ID && beginPos > endPos) in createIntervalTreeStore() 97 interval.i2 = beginPos; in createIntervalTreeStore() 129 TId beginPos; in createIntervalTreeStore() local 136 beginPos = getValue(itAnno).beginPos; in createIntervalTreeStore() 140 if (beginPos <= endPos) in createIntervalTreeStore() 142 interval.i1 = beginPos; in createIntervalTreeStore() [all …]
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/store/ |
H A D | store_intervaltree.h | 77 TId beginPos; in createIntervalTreeStore() local 84 beginPos = getValue(itAnno).beginPos; in createIntervalTreeStore() 86 if (beginPos != INVALID_ID && beginPos <= endPos) in createIntervalTreeStore() 88 interval.i1 = beginPos; in createIntervalTreeStore() 93 else if (beginPos != INVALID_ID && beginPos > endPos) in createIntervalTreeStore() 96 interval.i2 = beginPos; in createIntervalTreeStore() 128 TId beginPos; in createIntervalTreeStore() local 135 beginPos = getValue(itAnno).beginPos; in createIntervalTreeStore() 137 if (beginPos != INVALID_ID) in createIntervalTreeStore() 139 if (beginPos <= endPos) in createIntervalTreeStore() [all …]
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/store/ |
H A D | store_intervaltree.h | 77 TId beginPos; in createIntervalTreeStore() local 84 beginPos = getValue(itAnno).beginPos; in createIntervalTreeStore() 86 if (beginPos != INVALID_ID && beginPos <= endPos) in createIntervalTreeStore() 88 interval.i1 = beginPos; in createIntervalTreeStore() 93 else if (beginPos != INVALID_ID && beginPos > endPos) in createIntervalTreeStore() 96 interval.i2 = beginPos; in createIntervalTreeStore() 128 TId beginPos; in createIntervalTreeStore() local 135 beginPos = getValue(itAnno).beginPos; in createIntervalTreeStore() 137 if (beginPos != INVALID_ID) in createIntervalTreeStore() 139 if (beginPos <= endPos) in createIntervalTreeStore() [all …]
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/dports/math/lp_solve/lp_solve_5.5/shared/ |
H A D | commonlib.c | 206 beginPos = offset; in findIndex() 208 if(endPos < beginPos) in findIndex() 252 beginPos++; in findIndex() 260 beginPos++; in findIndex() 268 return(beginPos); in findIndex() 270 return(-beginPos); in findIndex() 283 beginPos = offset; in findIndexEx() 285 if(endPos < beginPos) in findIndexEx() 336 beginPos++; in findIndexEx() 343 return(beginPos); in findIndexEx() [all …]
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/seq_io/ |
H A D | genomic_region.h | 137 int32_t beginPos; member 157 GenomicRegion() : rID(INVALID_ID), beginPos(INVALID_POS), endPos(INVALID_POS) in GenomicRegion() 160 …GenomicRegion(CharString const & str) : rID(INVALID_ID), beginPos(INVALID_POS), endPos(INVALID_POS) in GenomicRegion() 179 if (beginPos + 1 == endPos) in toString() 181 appendNumber(out, beginPos + 1); in toString() 185 appendNumber(out, beginPos + 1); in toString() 218 region.beginPos = region.INVALID_POS; in clear() 258 lexicalCastWithException(region.beginPos, buffer); in parse() 260 if (region.beginPos < 1) in parse() 263 region.beginPos--; // Adjust to 0-based. in parse()
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/seq_io/ |
H A D | genomic_region.h | 137 int32_t beginPos; member 157 GenomicRegion() : rID(INVALID_ID), beginPos(INVALID_POS), endPos(INVALID_POS) in GenomicRegion() 160 …GenomicRegion(CharString const & str) : rID(INVALID_ID), beginPos(INVALID_POS), endPos(INVALID_POS) in GenomicRegion() 179 if (beginPos + 1 == endPos) in toString() 181 appendNumber(out, beginPos + 1); in toString() 185 appendNumber(out, beginPos + 1); in toString() 218 region.beginPos = region.INVALID_POS; in clear() 258 lexicalCastWithException(region.beginPos, buffer); in parse() 260 if (region.beginPos < 1) in parse() 263 region.beginPos--; // Adjust to 0-based. in parse()
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/seq_io/ |
H A D | genomic_region.h | 137 __int32 beginPos; member 157 GenomicRegion() : rID(INVALID_ID), beginPos(INVALID_POS), endPos(INVALID_POS) in GenomicRegion() 160 …GenomicRegion(CharString const & str) : rID(INVALID_ID), beginPos(INVALID_POS), endPos(INVALID_POS) in GenomicRegion() 179 if (beginPos + 1 == endPos) in toString() 181 appendNumber(out, beginPos + 1); in toString() 185 appendNumber(out, beginPos + 1); in toString() 218 region.beginPos = region.INVALID_POS; in clear() 258 lexicalCastWithException(region.beginPos, buffer); in parse() 260 if (region.beginPos < 1) in parse() 263 region.beginPos--; // Adjust to 0-based. in parse()
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/parallel/ |
H A D | parallel_splitting.h | 130 TValue beginPos; variable 136 beginPos(beginPos_) in Splitter() 139 … _resize(*this, endPos - beginPos, _min((TSize)(endPos - beginPos), (TSize)omp_get_max_threads())); in Splitter() 143 beginPos(beginPos_) in Splitter() 146 … _resize(*this, endPos - beginPos, _min((TSize)(endPos - beginPos), (TSize)omp_get_max_threads())); in Splitter() 150 beginPos(beginPos_) in Splitter() 153 _resize(*this, endPos - beginPos, _min((TSize)(endPos - beginPos), (TSize)1)); in Splitter() 157 beginPos(beginPos_) in Splitter() 159 _resize(*this, endPos - beginPos, subintervalCount); in Splitter() 165 return beginPos + blockLength * i + std::min(i, rest);
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/parallel/ |
H A D | parallel_splitting.h | 130 TValue beginPos; variable 136 beginPos(beginPos_) in Splitter() 139 … _resize(*this, endPos - beginPos, _min((TSize)(endPos - beginPos), (TSize)omp_get_max_threads())); in Splitter() 143 beginPos(beginPos_) in Splitter() 146 … _resize(*this, endPos - beginPos, _min((TSize)(endPos - beginPos), (TSize)omp_get_max_threads())); in Splitter() 150 beginPos(beginPos_) in Splitter() 153 _resize(*this, endPos - beginPos, _min((TSize)(endPos - beginPos), (TSize)1)); in Splitter() 157 beginPos(beginPos_) in Splitter() 159 _resize(*this, endPos - beginPos, subintervalCount); in Splitter() 165 return beginPos + blockLength * i + std::min(i, rest);
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/parallel/ |
H A D | parallel_splitting.h | 130 TValue beginPos; variable 136 beginPos(beginPos_) in Splitter() 139 … _resize(*this, endPos - beginPos, _min((TSize)(endPos - beginPos), (TSize)omp_get_max_threads())); in Splitter() 143 beginPos(beginPos_) in Splitter() 146 … _resize(*this, endPos - beginPos, _min((TSize)(endPos - beginPos), (TSize)omp_get_max_threads())); in Splitter() 150 beginPos(beginPos_) in Splitter() 153 _resize(*this, endPos - beginPos, _min((TSize)(endPos - beginPos), (TSize)1)); in Splitter() 157 beginPos(beginPos_) in Splitter() 159 _resize(*this, endPos - beginPos, subintervalCount); in Splitter() 165 return beginPos + blockLength * i + std::min(i, rest);
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/mason2/ |
H A D | mason_simulator.cpp | 369 if (recordL.beginPos < recordR.beginPos) in build() 370 recordL.tLen = recordR.beginPos + lenR - recordL.beginPos; in build() 372 recordL.tLen = recordL.beginPos + lenL - recordR.beginPos; in build() 394 recordR.beginPos = recordL.beginPos; in build() 404 recordL.beginPos = recordR.beginPos; in build() 698 int beginPos = infos[i].beginPos, endPos = infos[i].beginPos + infos[i].lengthInRef(); in _simulatePairedEnd() local 703 beginPos = infos[i + 1].beginPos; in _simulatePairedEnd() 731 query.pos = beginPos; in countSmallVars() 758 int beginPos = infos[i].beginPos, endPos = infos[i].beginPos + infos[i].lengthInRef(); in _simulateSingleEnd() local 918 unsigned beginPos = 0; in buildGapIntervals() local [all …]
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/tests/store/ |
H A D | test_store_io.h | 58 …SEQAN_ASSERT_EQ(getAnnotation(it).beginPos, std::numeric_limits<decltype(getAnnotation(it).beginPo… in SEQAN_DEFINE_TEST() 66 SEQAN_ASSERT_EQ(getAnnotation(it).beginPos, 33031813); in SEQAN_DEFINE_TEST() 74 SEQAN_ASSERT_EQ(getAnnotation(it).beginPos, 33026870); in SEQAN_DEFINE_TEST() 181 …SEQAN_ASSERT_EQ(getAnnotation(it).beginPos, std::numeric_limits<decltype(getAnnotation(it).beginPo… in SEQAN_DEFINE_TEST() 357 …SEQAN_ASSERT_EQ(getAnnotation(it).beginPos, std::numeric_limits<decltype(getAnnotation(it).beginPo… in SEQAN_DEFINE_TEST() 365 SEQAN_ASSERT_EQ(getAnnotation(it).beginPos, 1299); in SEQAN_DEFINE_TEST() 373 SEQAN_ASSERT_EQ(getAnnotation(it).beginPos, 1299); in SEQAN_DEFINE_TEST() 381 SEQAN_ASSERT_EQ(getAnnotation(it).beginPos, 1049); in SEQAN_DEFINE_TEST() 419 …SEQAN_ASSERT_EQ(getAnnotation(it).beginPos, std::numeric_limits<decltype(getAnnotation(it).beginPo… in SEQAN_DEFINE_TEST() 443 SEQAN_ASSERT_EQ(getAnnotation(it).beginPos, 8522); in SEQAN_DEFINE_TEST() [all …]
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/demos/tutorial/indexed_fasta_io/ |
H A D | solution2.cpp | 41 unsigned beginPos = 0, endPos = 0; in main() local 42 if (!lexicalCast(beginPos, argv[3])) in main() 54 if (beginPos > sequenceLength(faiIndex, idx)) in main() 55 beginPos = sequenceLength(faiIndex, idx); in main() 58 if (beginPos > endPos) in main() 59 endPos = beginPos; in main() 63 readRegion(sequenceInfix, faiIndex, idx, beginPos, endPos); in main()
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/demos/tutorial/sam_and_bam_io/ |
H A D | example7.cpp | 41 int beginPos = 9, endPos = 30; in main() local 44 beginPos -= 1; in main() 52 if (!jumpToRegion(inFile, hasAlignments, rID, beginPos, endPos, baiIndex)) in main() 54 std::cerr << "ERROR: Could not jump to " << beginPos << ":" << endPos << "\n"; in main() 70 if (record.rID == -1 || record.rID > rID || record.beginPos >= endPos) in main() 73 if (record.beginPos < beginPos) in main()
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/tests/seq_io/ |
H A D | test_genomic_region.h | 46 SEQAN_ASSERT(region.beginPos == region.INVALID_POS); in SEQAN_DEFINE_TEST() 56 SEQAN_ASSERT_EQ(region.beginPos, 999); in SEQAN_DEFINE_TEST() 65 region.beginPos = 100; in SEQAN_DEFINE_TEST() 71 SEQAN_ASSERT(region.beginPos == region.INVALID_POS); in SEQAN_DEFINE_TEST() 82 SEQAN_ASSERT(region.beginPos == region.INVALID_POS); in SEQAN_DEFINE_TEST() 93 SEQAN_ASSERT_EQ(region.beginPos, 999); in SEQAN_DEFINE_TEST() 104 SEQAN_ASSERT_EQ(region.beginPos, 999); in SEQAN_DEFINE_TEST() 112 region.beginPos = 1000; in SEQAN_DEFINE_TEST() 124 region.beginPos = 1000; in SEQAN_DEFINE_TEST()
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/dports/devel/qtcreator/qt-creator-opensource-src-5.0.3/src/plugins/qmakeprojectmanager/ |
H A D | profileeditor.cpp | 148 int beginPos = positionInBlock - 1; in findLinkAt() local 167 beginPos = chunkStart + posCurlyPwd - 1; in findLinkAt() 176 beginPos = start - 1; in findLinkAt() 182 while (doBackwardScan && beginPos >= 0) { in findLinkAt() 183 QChar c = block.at(beginPos); in findLinkAt() 186 beginPos--; in findLinkAt() 193 && beginPos > 0 in findLinkAt() 195 …&& (block.at(beginPos + pwd.count() - 1) == '/' || block.at(beginPos + pwd.count() - 1) == '\\')) { in findLinkAt() 197 beginPos -= 2; in findLinkAt() 199 && beginPos >= curlyPwd.count() - 1 in findLinkAt() [all …]
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/dports/net/kmime/kmime-21.12.3/src/ |
H A D | kmime_parsers.cpp | 175 int beginPos = currentPos; in parse() local 188 (beginPos == 0 || m_src.at(beginPos - 1) == '\n')) { in parse() 190 uuStart = m_src.indexOf('\n', beginPos); in parse() 198 beginPos = currentPos; in parse() 246 if (beginPos > 0) { in parse() 252 fileName = m_src.mid(beginPos + 10, uuStart - beginPos - 11); in parse() 326 int beginPos = currentPos; in parse() local 332 (beginPos == 0 || m_src.at(beginPos - 1) == '\n')) { in parse() 333 yencStart = m_src.indexOf('\n', beginPos); in parse() 352 QByteArray meta = m_src.mid(beginPos, yencStart - beginPos); in parse() [all …]
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/tests/bed_io/ |
H A D | test_bed_io.cpp | 226 record1.beginPos = 123; in SEQAN_DEFINE_TEST() 232 record2.beginPos = 999; in SEQAN_DEFINE_TEST() 251 record1.beginPos = 123; in SEQAN_DEFINE_TEST() 258 record2.beginPos = 999; in SEQAN_DEFINE_TEST() 278 record1.beginPos = 123; in SEQAN_DEFINE_TEST() 286 record2.beginPos = 999; in SEQAN_DEFINE_TEST() 307 record1.beginPos = 123; in SEQAN_DEFINE_TEST() 316 record2.beginPos = 999; in SEQAN_DEFINE_TEST() 338 record1.beginPos = 123; in SEQAN_DEFINE_TEST() 357 record2.beginPos = 999; in SEQAN_DEFINE_TEST() [all …]
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/dports/textproc/goldendict/goldendict-73ec1b5/ |
H A D | filetype.cc | 28 size_t beginPos = 0; in simplifyString() local 30 while( beginPos < str.size() && Utf8::isspace( str[ beginPos ] ) ) in simplifyString() 31 ++beginPos; in simplifyString() 38 if( endPos <= beginPos ) in simplifyString() 41 result.reserve( endPos - beginPos ); in simplifyString() 43 while( beginPos < endPos ) in simplifyString() 44 result.push_back( lowercase ? tolower( str[ beginPos++ ] ) : str[ beginPos++ ] ); in simplifyString()
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