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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/ngs_roi/
H A Droi_builder.cpp58 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()
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H A Dproject_interval.cpp68 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()
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/dports/math/R-cran-lpSolve/lpSolve/src/
H A Dcommonlib.c179 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()
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/dports/science/siconos/siconos-4.4.0/externals/SOL/lumod-c/
H A Dcommonlib.c189 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()
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/bs_tools/
H A Dcasbar_realignment.h36 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()
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/store/
H A Dstore_intervaltree.h77 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()
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/dports/biology/seqan1/seqan-1.3.1/seqan/store/
H A Dstore_intervaltree.h78 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()
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/store/
H A Dstore_intervaltree.h77 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()
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/store/
H A Dstore_intervaltree.h77 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()
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/dports/math/lp_solve/lp_solve_5.5/shared/
H A Dcommonlib.c206 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()
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/seq_io/
H A Dgenomic_region.h137 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()
/dports/biology/seqan/seqan-library-2.4.0/include/seqan/seq_io/
H A Dgenomic_region.h137 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()
/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/seq_io/
H A Dgenomic_region.h137 __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()
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/parallel/
H A Dparallel_splitting.h130 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);
/dports/biology/seqan/seqan-library-2.4.0/include/seqan/parallel/
H A Dparallel_splitting.h130 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);
/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/parallel/
H A Dparallel_splitting.h130 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);
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/mason2/
H A Dmason_simulator.cpp369 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
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/tests/store/
H A Dtest_store_io.h58 …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()
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/demos/tutorial/indexed_fasta_io/
H A Dsolution2.cpp41 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()
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/demos/tutorial/sam_and_bam_io/
H A Dexample7.cpp41 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()
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/tests/seq_io/
H A Dtest_genomic_region.h46 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()
/dports/devel/qtcreator/qt-creator-opensource-src-5.0.3/src/plugins/qmakeprojectmanager/
H A Dprofileeditor.cpp148 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()
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/dports/net/kmime/kmime-21.12.3/src/
H A Dkmime_parsers.cpp175 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()
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/tests/bed_io/
H A Dtest_bed_io.cpp226 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()
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/dports/textproc/goldendict/goldendict-73ec1b5/
H A Dfiletype.cc28 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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