/dports/biology/seqan1/seqan-1.3.1/seqan/modifier/ |
H A D | modifier_shortcuts.h | 129 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 …]
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/dports/biology/jalview/jalview/test/jalview/controller/ |
H A D | AlignViewControllerTest.java | 107 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() [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/readers/ |
H A D | aln_scanner_clustal.cpp | 68 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 …]
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/readers/ |
H A D | aln_scanner_clustal.cpp | 68 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 …]
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/modifier/ |
H A D | modifier_shortcuts.h | 221 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 …]
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/modifier/ |
H A D | modifier_shortcuts.h | 221 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 …]
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/modifier/ |
H A D | modifier_shortcuts.h | 221 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 …]
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/dports/science/dakota/dakota-6.13.0-release-public.src-UI/src/ |
H A D | SeqHybridMetaIterator.cpp | 289 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 …]
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H A D | SeqHybridMetaIterator.hpp | 136 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()
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/dports/biology/seqan1/seqan-1.3.1/demos/howto/ |
H A D | efficiently_import_sequences.cpp | 23 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()
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/dports/biology/seqan1/seqan-1.3.1/demos/ |
H A D | index_mummy.cpp | 37 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()
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/dports/biology/seqan1/seqan-1.3.1/docs/ |
H A D | index_mummy.cpp | 37 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()
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/demos/howto/ |
H A D | efficiently_import_sequences.cpp | 26 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()
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/dports/biology/seqan1/seqan-1.3.1/seqan/graph_types/ |
H A D | graph_utility_parsing.h | 59 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()
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/index/ |
H A D | index_esa_algs_multi.h | 95 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 …]
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/index/ |
H A D | index_esa_algs_multi.h | 95 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 …]
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/index/ |
H A D | index_esa_algs_multi.h | 95 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 …]
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/dports/biology/seqan/seqan-library-2.4.0/share/doc/seqan/html/demos/dox/index/ |
H A D | mummy.cpp | 36 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()
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/demos/dox/index/ |
H A D | mummy.cpp | 36 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()
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/dports/biology/hyphy/hyphy-2.5.33/res/TemplateBatchFiles/ |
H A D | SeqAlignmentNucShared.ibf | 55 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) {
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/dports/biology/seqan1/seqan-1.3.1/seqan/index/ |
H A D | index_esa_algs_multi.h | 88 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); [all …]
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/dports/biology/seqan1/seqan-1.3.1/demos/tutorial/ |
H A D | find_motif.cpp | 19 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()
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/dports/emulators/ppsspp/ppsspp-1.12.3/ext/zstd/lib/compress/ |
H A D | zstd_compress_superblock.c | 449 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 …]
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/dports/archivers/zstd/zstd-1.5.0/lib/compress/ |
H A D | zstd_compress_superblock.c | 449 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 …]
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/dports/archivers/py-zstd/zstd-1.5.0.4/zstd/lib/compress/ |
H A D | zstd_compress_superblock.c | 449 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 …]
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