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/dports/biology/seqan1/seqan-1.3.1/seqan/modifier/
H A Dmodifier_shortcuts.h129 unsigned seqCount = length(stringSet); in complement() local
130 for(unsigned seqNo = 0; seqNo < seqCount; ++seqNo) in complement()
138 unsigned seqCount = length(stringSet); in complement() local
139 for(unsigned seqNo = 0; seqNo < seqCount; ++seqNo) in complement()
184 unsigned seqCount = length(stringSet); in reverseComplement() local
185 for(unsigned seqNo = 0; seqNo < seqCount; ++seqNo) in reverseComplement()
194 unsigned seqCount = length(stringSet); in reverseComplement() local
240 unsigned seqCount = length(stringSet); in toLower() local
250 unsigned seqCount = length(stringSet); in toLower() local
294 unsigned seqCount = length(stringSet); in toUpper() local
[all …]
/dports/biology/jalview/jalview/test/jalview/controller/
H A DAlignViewControllerTest.java107 assertEquals(1, seqCount); in testFindColumnsWithFeature()
117 seqCount = avc.findColumnsWithFeature("Metal", sg, bs); in testFindColumnsWithFeature()
118 assertEquals(2, seqCount); in testFindColumnsWithFeature()
131 seqCount = avc.findColumnsWithFeature("Metal", sg, bs); in testFindColumnsWithFeature()
132 assertEquals(1, seqCount); in testFindColumnsWithFeature()
143 assertEquals(0, seqCount); in testFindColumnsWithFeature()
160 assertEquals(1, seqCount); in testFindColumnsWithFeature()
172 assertEquals(0, seqCount); in testFindColumnsWithFeature()
182 assertEquals(1, seqCount); in testFindColumnsWithFeature()
193 seqCount = avc.findColumnsWithFeature("Pfam", sg, bs); in testFindColumnsWithFeature()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/readers/
H A Daln_scanner_clustal.cpp68 int seqCount = 0; member
81 numSeqs = blockInfo.seqCount; in sTerminateBlock()
85 if (numSeqs != blockInfo.seqCount) { in sTerminateBlock()
97 blockInfo.seqCount = 0; in sTerminateBlock()
178 blockInfo.seqCount, in xImportAlignmentData()
184 ++(blockInfo.seqCount); in xImportAlignmentData()
213 int seqCount, in sProcessClustalDataLine() argument
245 if (seqCount >= numSeqs) { in sProcessClustalDataLine()
254 if (seqId != mSeqIds[seqCount].mData) { in sProcessClustalDataLine()
273 if (idPos < seqCount) { in sProcessClustalDataLine()
[all …]
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/readers/
H A Daln_scanner_clustal.cpp68 int seqCount = 0; member
81 numSeqs = blockInfo.seqCount; in sTerminateBlock()
85 if (numSeqs != blockInfo.seqCount) { in sTerminateBlock()
97 blockInfo.seqCount = 0; in sTerminateBlock()
178 blockInfo.seqCount, in xImportAlignmentData()
184 ++(blockInfo.seqCount); in xImportAlignmentData()
213 int seqCount, in sProcessClustalDataLine() argument
245 if (seqCount >= numSeqs) { in sProcessClustalDataLine()
254 if (seqId != mSeqIds[seqCount].mData) { in sProcessClustalDataLine()
273 if (idPos < seqCount) { in sProcessClustalDataLine()
[all …]
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/modifier/
H A Dmodifier_shortcuts.h221 unsigned seqCount = length(stringSet); in complement() local
222 for(unsigned seqNo = 0; seqNo < seqCount; ++seqNo) in complement()
229 unsigned seqCount = length(stringSet); in complement() local
294 int seqCount = length(stringSet); in reverseComplement() local
296 for(int seqNo = 0; seqNo < seqCount; ++seqNo) in reverseComplement()
305 int seqCount = length(stringSet); in reverseComplement() local
307 for(int seqNo = 0; seqNo < seqCount; ++seqNo) in reverseComplement()
376 unsigned seqCount = length(stringSet); in toLower() local
386 unsigned seqCount = length(stringSet); in toLower() local
424 unsigned seqCount = length(stringSet); in toUpper() local
[all …]
/dports/biology/seqan/seqan-library-2.4.0/include/seqan/modifier/
H A Dmodifier_shortcuts.h221 unsigned seqCount = length(stringSet); in complement() local
222 for(unsigned seqNo = 0; seqNo < seqCount; ++seqNo) in complement()
229 unsigned seqCount = length(stringSet); in complement() local
294 int seqCount = length(stringSet); in reverseComplement() local
296 for(int seqNo = 0; seqNo < seqCount; ++seqNo) in reverseComplement()
305 int seqCount = length(stringSet); in reverseComplement() local
307 for(int seqNo = 0; seqNo < seqCount; ++seqNo) in reverseComplement()
376 unsigned seqCount = length(stringSet); in toLower() local
386 unsigned seqCount = length(stringSet); in toLower() local
424 unsigned seqCount = length(stringSet); in toUpper() local
[all …]
/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/modifier/
H A Dmodifier_shortcuts.h221 unsigned seqCount = length(stringSet); in complement() local
222 for(unsigned seqNo = 0; seqNo < seqCount; ++seqNo) in complement()
229 unsigned seqCount = length(stringSet); in complement() local
294 int seqCount = length(stringSet); in reverseComplement() local
296 for(int seqNo = 0; seqNo < seqCount; ++seqNo) in reverseComplement()
305 int seqCount = length(stringSet); in reverseComplement() local
307 for(int seqNo = 0; seqNo < seqCount; ++seqNo) in reverseComplement()
376 unsigned seqCount = length(stringSet); in toLower() local
386 unsigned seqCount = length(stringSet); in toLower() local
424 unsigned seqCount = length(stringSet); in toUpper() local
[all …]
/dports/science/dakota/dakota-6.13.0-release-public.src-UI/src/
H A DSeqHybridMetaIterator.cpp289 for (seqCount=0; seqCount<num_iterators; seqCount++) { in run_sequential()
292 Iterator& curr_iterator = selectedIterators[seqCount]; in run_sequential()
298 << methodStrings[seqCount] << ".\n"; in run_sequential()
316 if (seqCount == 0) // initialize numIteratorJobs in run_sequential()
400 seqCount+1 < num_iterators) { in run_sequential()
458 for (seqCount=0; seqCount<num_iterators; seqCount++) { in run_sequential_adaptive()
463 Iterator& curr_iterator = selectedIterators[seqCount]; in run_sequential_adaptive()
473 << methodStrings[seqCount] << '\n'; in run_sequential_adaptive()
496 selectedModels[seqCount].stop_servers(); in run_sequential_adaptive()
504 Iterator& curr_iterator = selectedIterators[seqCount]; in update_local_results()
[all …]
H A DSeqHybridMetaIterator.hpp136 size_t seqCount; member in Dakota::SeqHybridMetaIterator
241 selectedModels[seqCount].active_variables(param_sets[0]); in initialize_iterator()
242 else if (selectedIterators[seqCount].accepts_multiple_points()) in initialize_iterator()
243 selectedIterators[seqCount].initial_points(param_sets); in initialize_iterator()
254 if (seqCount) { // else default initialization is used in initialize_iterator()
265 if (seqCount) { // else default initialization is used in pack_parameters_buffer()
276 if (seqCount) { // else default initialization is used in unpack_parameters_initialize()
/dports/biology/seqan1/seqan-1.3.1/demos/howto/
H A Defficiently_import_sequences.cpp23 unsigned seqCount = length(multiSeqFile); in main() local
27 reserve(seqs, seqCount, Exact()); in main()
28 reserve(seqIDs, seqCount, Exact()); in main()
35 for (unsigned i = 0; i < seqCount; ++i) in main()
53 std::cout << "Loading " << seqCount << " sequences took " << SEQAN_PROTIMEDIFF(loadTime); in main()
55 for (unsigned i = 0; i < seqCount && i < 10; ++i) in main()
/dports/biology/seqan1/seqan-1.3.1/demos/
H A Dindex_mummy.cpp37 int runMummy(int argc, const char *argv[], unsigned seqCount, unsigned minLen) in runMummy() argument
46 resize(indexText(index), seqCount); in runMummy()
106 unsigned seqCount = 0; in main() local
133 ++seqCount; in main()
138 return runMummy<External<> >(argc, argv, seqCount, optMinLen); in main()
140 return runMummy<Alloc<> >(argc, argv, seqCount, optMinLen); in main()
/dports/biology/seqan1/seqan-1.3.1/docs/
H A Dindex_mummy.cpp37 int runMummy(int argc, const char *argv[], unsigned seqCount, unsigned minLen) in runMummy() argument
46 resize(indexText(index), seqCount); in runMummy()
106 unsigned seqCount = 0; in main() local
133 ++seqCount; in main()
138 return runMummy<External<> >(argc, argv, seqCount, optMinLen); in main()
140 return runMummy<Alloc<> >(argc, argv, seqCount, optMinLen); in main()
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/demos/howto/
H A Defficiently_import_sequences.cpp26 size_t seqCount = 0; in main() local
27 for (; !atEnd(seqFile); ++seqCount) in main()
43 std::cout << "Loading " << seqCount << " sequences took " << SEQAN_PROTIMEDIFF(loadTime); in main()
45 for (unsigned i = 0; i < seqCount && i < 10; ++i) in main()
/dports/biology/seqan1/seqan-1.3.1/seqan/graph_types/
H A Dgraph_utility_parsing.h59 TSize seqCount = 0; in _loadSequences() local
70 ++seqCount; in _loadSequences()
76 resize(origStrSet, seqCount); in _loadSequences()
78 for(TSize i = 0; (i < seqCount) && !_streamEOF(file); ++i) { in _loadSequences()
/dports/biology/seqan/seqan-library-2.4.0/include/seqan/index/
H A Dindex_esa_algs_multi.h95 TSize seqCount;
102 seqCount(0)
108 seqCount(countSequences(_tree)),
121 seqCount(countSequences(_tree)),
131 seqCount(countSequences(container(_origin))),
506 unsigned seqCount;
626 seqCount(0)
631 seqCount(countSequences(container(_maxIt)))
637 return !subState[seqCount - 1].charsEqual;
642 for(unsigned seq = 0; seq < seqCount; ++seq)
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/index/
H A Dindex_esa_algs_multi.h95 TSize seqCount;
102 seqCount(0)
108 seqCount(countSequences(_tree)),
121 seqCount(countSequences(_tree)),
131 seqCount(countSequences(container(_origin))),
506 unsigned seqCount;
626 seqCount(0)
631 seqCount(countSequences(container(_maxIt)))
637 return !subState[seqCount - 1].charsEqual;
642 for(unsigned seq = 0; seq < seqCount; ++seq)
[all …]
/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/index/
H A Dindex_esa_algs_multi.h95 TSize seqCount;
102 seqCount(0)
108 seqCount(countSequences(_tree)),
121 seqCount(countSequences(_tree)),
131 seqCount(countSequences(container(_origin))),
506 unsigned seqCount;
626 seqCount(0)
631 seqCount(countSequences(container(_maxIt)))
637 return !subState[seqCount - 1].charsEqual;
642 for(unsigned seq = 0; seq < seqCount; ++seq)
[all …]
/dports/biology/seqan/seqan-library-2.4.0/share/doc/seqan/html/demos/dox/index/
H A Dmummy.cpp36 int runMummy(int argc, const char * argv[], unsigned seqCount, unsigned minLen) in runMummy() argument
109 unsigned seqCount = 0; in main() local
144 ++seqCount; in main()
149 return runMummy<External<> >(argc, argv, seqCount, optMinLen); in main()
151 return runMummy<Alloc<> >(argc, argv, seqCount, optMinLen); in main()
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/demos/dox/index/
H A Dmummy.cpp36 int runMummy(int argc, const char * argv[], unsigned seqCount, unsigned minLen) in runMummy() argument
109 unsigned seqCount = 0; in main() local
144 ++seqCount; in main()
149 return runMummy<External<> >(argc, argv, seqCount, optMinLen); in main()
151 return runMummy<Alloc<> >(argc, argv, seqCount, optMinLen); in main()
/dports/biology/hyphy/hyphy-2.5.33/res/TemplateBatchFiles/
H A DSeqAlignmentNucShared.ibf55 seqCount = Rows(UnalignedSeqs) * Columns(UnalignedSeqs);
58 for (seqCounter = 0; seqCounter < seqCount; seqCounter = seqCounter+1)
66 if (doLongestSequence > 0 && seqCounter < seqCount - (refSeq2 > 0))
121 startingPosition = {seqCount,2};
126 //pairwiseDistances = {seqCount,1};
132 for (seqCounter = 0; seqCounter < seqCount; seqCounter += 1) {
199 …NG, "Performing pairwise alignment with reference sequences ("+seqCounter+"/"+seqCount+" done)",0);
234 for (seqCounter = 0; seqCounter < seqCount; seqCounter += 1)
280 if (refSeq2 && seqCounter == seqCount-1) {
/dports/biology/seqan1/seqan-1.3.1/seqan/index/
H A Dindex_esa_algs_multi.h88 TSize seqCount;
95 seqCount(countSequences(_tree)),
108 seqCount(countSequences(_tree)),
118 seqCount(countSequences(container(_origin))),
479 unsigned seqCount;
599 seqCount(countSequences(container(_maxIt)))
605 return !subState[seqCount - 1].charsEqual;
610 for(unsigned seq = 0; seq < seqCount; ++seq)
616 for(unsigned seq = 0; seq < seqCount; ++seq)
634 resize(subState, seqCount);
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/dports/biology/seqan1/seqan-1.3.1/demos/tutorial/
H A Dfind_motif.cpp19 TSize seqCount = length(dataset); in main() local
28 TSize numPos = seqCount * (seqLength - motifLength + 1); in main()
30 TMotifFinder finder_proj(seqCount, motifLength, numPos, mm, is_exact); in main()
/dports/emulators/ppsspp/ppsspp-1.12.3/ext/zstd/lib/compress/
H A Dzstd_compress_superblock.c449 size_t litSize, seqCount; in ZSTD_compressSubBlock_multi() local
458 seqCount = 0; in ZSTD_compressSubBlock_multi()
464 const seqDef* const sequence = sp + seqCount; in ZSTD_compressSubBlock_multi()
467 seqCount++; in ZSTD_compressSubBlock_multi()
479 …ockSizeEstimate = ZSTD_estimateSubBlockSize(lp, litSize, ofCodePtr, llCodePtr, mlCodePtr, seqCount, in ZSTD_compressSubBlock_multi()
487 sp, seqCount, in ZSTD_compressSubBlock_multi()
500 sp += seqCount; in ZSTD_compressSubBlock_multi()
503 llCodePtr += seqCount; in ZSTD_compressSubBlock_multi()
504 mlCodePtr += seqCount; in ZSTD_compressSubBlock_multi()
505 ofCodePtr += seqCount; in ZSTD_compressSubBlock_multi()
[all …]
/dports/archivers/zstd/zstd-1.5.0/lib/compress/
H A Dzstd_compress_superblock.c449 size_t litSize, seqCount; in ZSTD_compressSubBlock_multi() local
458 seqCount = 0; in ZSTD_compressSubBlock_multi()
464 const seqDef* const sequence = sp + seqCount; in ZSTD_compressSubBlock_multi()
467 seqCount++; in ZSTD_compressSubBlock_multi()
479 …ockSizeEstimate = ZSTD_estimateSubBlockSize(lp, litSize, ofCodePtr, llCodePtr, mlCodePtr, seqCount, in ZSTD_compressSubBlock_multi()
487 sp, seqCount, in ZSTD_compressSubBlock_multi()
500 sp += seqCount; in ZSTD_compressSubBlock_multi()
503 llCodePtr += seqCount; in ZSTD_compressSubBlock_multi()
504 mlCodePtr += seqCount; in ZSTD_compressSubBlock_multi()
505 ofCodePtr += seqCount; in ZSTD_compressSubBlock_multi()
[all …]
/dports/archivers/py-zstd/zstd-1.5.0.4/zstd/lib/compress/
H A Dzstd_compress_superblock.c449 size_t litSize, seqCount; in ZSTD_compressSubBlock_multi() local
458 seqCount = 0; in ZSTD_compressSubBlock_multi()
464 const seqDef* const sequence = sp + seqCount; in ZSTD_compressSubBlock_multi()
467 seqCount++; in ZSTD_compressSubBlock_multi()
479 …ockSizeEstimate = ZSTD_estimateSubBlockSize(lp, litSize, ofCodePtr, llCodePtr, mlCodePtr, seqCount, in ZSTD_compressSubBlock_multi()
487 sp, seqCount, in ZSTD_compressSubBlock_multi()
500 sp += seqCount; in ZSTD_compressSubBlock_multi()
503 llCodePtr += seqCount; in ZSTD_compressSubBlock_multi()
504 mlCodePtr += seqCount; in ZSTD_compressSubBlock_multi()
505 ofCodePtr += seqCount; in ZSTD_compressSubBlock_multi()
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