/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/dbapi/driver/ |
H A D | memory_store.hpp | 94 CMemStore(size_t block_size) { x_Init((TSize) block_size); } in CMemStore() 114 typedef long TSize; typedef in CMemStore 121 TSize free_space; 125 TSize m_BlockSize; 129 TSize m_Pos; 130 TSize m_BlockPos; 131 TSize m_Size; 135 TSize x_SeekHEAD(TSize offset); 136 TSize x_SeekCURR(TSize offset); 137 TSize x_SeekTAIL(TSize offset); [all …]
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/dports/biology/seqan1/seqan-1.3.1/seqan/graph_msa/ |
H A D | graph_align_tcoffee_refinement.h | 170 TSize newGapOpen = n1; in scoreGapOpenHorizontal() 224 TSize newGapOpen = n2; in scoreGapOpenVertical() 282 TSize nseq, in _msaRefinement() 283 TSize splitPos, in _msaRefinement() 293 TSize alignLen = length(mat) / nseq; in _msaRefinement() 304 TSize nseq1 = splitPos; in _msaRefinement() 305 TSize nseq2 = nseq - nseq1; in _msaRefinement() 336 typedef String<TSize> TDelGap; in _msaRefinement() 423 TSize begin1Pos = 0; in _msaRefinement() 424 TSize begin2Pos = 0; in _msaRefinement() [all …]
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H A D | graph_align_tcoffee_base.h | 201 TSize pos1 = 0; TSize pos2 = 0; TSize fragLen = 0; in _scoreMatches() 437 typedef Pair<TSize, TSize> TDistGroup; // Distance, group index in _subTreeSearch() 440 for(TSize i=0; i< (TSize) length(groupRoot); ++i) { in _subTreeSearch() 442 TSize dist = 0; in _subTreeSearch() 456 for(TSize i=0; i< (TSize) length(seqGroups); ++i) { in _subTreeSearch() 466 TSize leftover = 0; in _subTreeSearch() 525 for(TSize i=0; i< (TSize) length(seqGroup); ++i) { in tripletLibraryExtension() 554 for(TSize i=0; i< (TSize) length(seqGroup); ++i) { in tripletLibraryExtension() 877 TSize& gapCount, in alignmentEvaluation() 880 TSize& len) in alignmentEvaluation() [all …]
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/dports/biology/seqan1/seqan-1.3.1/seqan/consensus/ |
H A D | consensus_base.h | 240 TSize pos = 0; in convertAlignment() 344 TSize coverage; in convertAlignment() 434 String<Pair<TSize, TSize> >& begEndPos, in consensusAlignment() argument 493 String<Pair<TSize, TSize> >& begEndPos) in consensusAlignment() argument 513 typedef std::map<TSize, TSize> TComponentLength; in updateContig() 522 TSize len = 0; in updateContig() 537 typedef String<std::pair<TSize, TSize> > TComponentToRank; in updateContig() 543 typedef Pair<TSize, TSize> TRankPair; in updateContig() 567 typedef String<std::pair<TSize, TSize> > TSeqToBegin; in updateContig() 767 TSize pos = 0; in _countLetters() [all …]
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/parallel/ |
H A D | parallel_splitting.h | 128 typedef typename Size<Splitter>::Type TSize; typedef 131 TSize subintervalCount; 132 TSize blockLength; 133 TSize rest; 139 … _resize(*this, endPos - beginPos, _min((TSize)(endPos - beginPos), (TSize)omp_get_max_threads())); in Splitter() 146 … _resize(*this, endPos - beginPos, _min((TSize)(endPos - beginPos), (TSize)omp_get_max_threads())); in Splitter() 153 _resize(*this, endPos - beginPos, _min((TSize)(endPos - beginPos), (TSize)1)); in Splitter() 162 TValue operator[] (TSize i) const 244 template <typename TValue, typename TSpec, typename TSize> 246 resize(Splitter<TValue, TSpec> &splitter, TSize newCount) [all …]
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/parallel/ |
H A D | parallel_splitting.h | 128 typedef typename Size<Splitter>::Type TSize; typedef 131 TSize subintervalCount; 132 TSize blockLength; 133 TSize rest; 139 … _resize(*this, endPos - beginPos, _min((TSize)(endPos - beginPos), (TSize)omp_get_max_threads())); in Splitter() 146 … _resize(*this, endPos - beginPos, _min((TSize)(endPos - beginPos), (TSize)omp_get_max_threads())); in Splitter() 153 _resize(*this, endPos - beginPos, _min((TSize)(endPos - beginPos), (TSize)1)); in Splitter() 162 TValue operator[] (TSize i) const 244 template <typename TValue, typename TSpec, typename TSize> 246 resize(Splitter<TValue, TSpec> &splitter, TSize newCount) [all …]
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/parallel/ |
H A D | parallel_splitting.h | 128 typedef typename Size<Splitter>::Type TSize; typedef 131 TSize subintervalCount; 132 TSize blockLength; 133 TSize rest; 139 … _resize(*this, endPos - beginPos, _min((TSize)(endPos - beginPos), (TSize)omp_get_max_threads())); in Splitter() 146 … _resize(*this, endPos - beginPos, _min((TSize)(endPos - beginPos), (TSize)omp_get_max_threads())); in Splitter() 153 _resize(*this, endPos - beginPos, _min((TSize)(endPos - beginPos), (TSize)1)); in Splitter() 162 TValue operator[] (TSize i) const 244 template <typename TValue, typename TSpec, typename TSize> 246 resize(Splitter<TValue, TSpec> &splitter, TSize newCount) [all …]
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/index/ |
H A D | radix.h | 54 typedef typename Value<TCountArray>::Type TSize; in radixPass() typedef 56 TSize i, sum = 0, n = length(a); in radixPass() 64 TSize t = getValue(c,i); in radixPass() 104 TSize t = getValue(c,i); in radixPass() 111 TSize j = getValue(a,i); in radixPass() 112 TSize k = j + shift; in radixPass() 135 TSize i, sum = 0, n = length(a); in radixExtend() 143 TSize t = getValue(c,i); in radixExtend() 170 TSize i, sum = 0, n = length(a); in radixExtendClip() 175 TSize j = getValue(a,i); in radixExtendClip() [all …]
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H A D | index_lcp.h | 288 if (sizeof(TSize) > 4) 292 TSize n = length(s); 299 String<TSize, Alloc<> > ISA; 352 if (sizeof(TSize) > 4) 356 TSize n = length(s); 363 TSize mark = ~(~0u>>1); 364 TSize mask = ~0u>>1; 445 if (sizeof(TSize) > 4) 450 TSize n = length(s); 458 TSize mark = ~(~(TSize)0ul >> 1); [all …]
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/dports/biology/seqan1/seqan-1.3.1/seqan/index/ |
H A D | radix.h | 56 TSize i, sum = 0, n = length(a); in radixPass() 64 TSize t = getValue(c,i); in radixPass() 71 TSize j = getValue(a,i); // sort in radixPass() 104 TSize t = getValue(c,i); in radixPass() 111 TSize j = getValue(a,i); in radixPass() 112 TSize k = j + shift; in radixPass() 135 TSize i, sum = 0, n = length(a); in radixExtend() 143 TSize t = getValue(c,i); in radixExtend() 170 TSize i, sum = 0, n = length(a); in radixExtendClip() 175 TSize j = getValue(a,i); in radixExtendClip() [all …]
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H A D | index_wotd.h | 129 …static TSize const LEAF = (TSize)1 << (BitsPerValue<TSize>::VALUE - 1); // this node is a… 130 …static TSize const LAST_CHILD = (TSize)1 << (BitsPerValue<TSize>::VALUE - 2); // this node is t… 918 TSize prefixLen) 949 TSize prefixLen) 978 typename TSize 985 TSize prefixLen) 1182 TSize prefixLen) 1638 TSize dirOfs, 1639 TSize lcp) 1893 TSize size; [all …]
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H A D | index_qgram_openaddressing.h | 189 typedef unsigned long TSize; 196 if (hlen == (TSize)-1) return hash; 197 register TSize h1 = (TSize)(hash % hlen); 200 if (hlen == (TSize)-2) return hash; 201 register TSize h1 = (TSize)(hash & hlen); 222 register TSize step = (TSize)bucketMap.prime; 243 typedef unsigned long TSize; 251 register TSize h1 = (TSize)(hash % hlen); 254 if (hlen == (TSize)-2) return hash; 255 register TSize h1 = (TSize)(hash & hlen); [all …]
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/index/ |
H A D | radix.h | 54 typedef typename Value<TCountArray>::Type TSize; in radixPass() typedef 56 TSize i, sum = 0, n = length(a); in radixPass() 64 TSize t = getValue(c,i); in radixPass() 104 TSize t = getValue(c,i); in radixPass() 111 TSize j = getValue(a,i); in radixPass() 112 TSize k = j + shift; in radixPass() 135 TSize i, sum = 0, n = length(a); in radixExtend() 143 TSize t = getValue(c,i); in radixExtend() 170 TSize i, sum = 0, n = length(a); in radixExtendClip() 175 TSize j = getValue(a,i); in radixExtendClip() [all …]
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H A D | index_lcp.h | 288 if (sizeof(TSize) > 4) 292 TSize n = length(s); 299 String<TSize, Alloc<> > ISA; 352 if (sizeof(TSize) > 4) 356 TSize n = length(s); 363 TSize mark = ~(~0u>>1); 364 TSize mask = ~0u>>1; 445 if (sizeof(TSize) > 4) 450 TSize n = length(s); 458 TSize mark = ~(~(TSize)0ul >> 1); [all …]
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/index/ |
H A D | radix.h | 54 typedef typename Value<TCountArray>::Type TSize; in radixPass() typedef 56 TSize i, sum = 0, n = length(a); in radixPass() 64 TSize t = getValue(c,i); in radixPass() 104 TSize t = getValue(c,i); in radixPass() 111 TSize j = getValue(a,i); in radixPass() 112 TSize k = j + shift; in radixPass() 135 TSize i, sum = 0, n = length(a); in radixExtend() 143 TSize t = getValue(c,i); in radixExtend() 170 TSize i, sum = 0, n = length(a); in radixExtendClip() 175 TSize j = getValue(a,i); in radixExtendClip() [all …]
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H A D | index_lcp.h | 288 if (sizeof(TSize) > 4) 292 TSize n = length(s); 299 String<TSize, Alloc<> > ISA; 352 if (sizeof(TSize) > 4) 356 TSize n = length(s); 363 TSize mark = ~(~0u>>1); 364 TSize mask = ~0u>>1; 445 if (sizeof(TSize) > 4) 450 TSize n = length(s); 458 TSize mark = ~(~(TSize)0ul >> 1); [all …]
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/graph_msa/ |
H A D | graph_align_tcoffee_base.h | 228 TSize pos1 = 0; TSize pos2 = 0; TSize fragLen = 0; in _scoreMatches() 407 String<TSize> numLeaves; in _subTreeSearch() 463 typedef Pair<TSize, TSize> TDistGroup; // Distance, group index in _subTreeSearch() 466 for(TSize i=0; i< (TSize) length(groupRoot); ++i) { in _subTreeSearch() 468 TSize dist = 0; in _subTreeSearch() 482 for(TSize i=0; i< (TSize) length(seqGroups); ++i) { in _subTreeSearch() 492 TSize leftover = 0; in _subTreeSearch() 547 String<TSize> seqLabels; in tripletLibraryExtension() 550 for(TSize i=0; i< (TSize) length(seqGroup); ++i) { in tripletLibraryExtension() 579 for(TSize i=0; i< (TSize) length(seqGroup); ++i) { in tripletLibraryExtension() [all …]
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/graph_msa/ |
H A D | graph_align_tcoffee_base.h | 228 TSize pos1 = 0; TSize pos2 = 0; TSize fragLen = 0; in _scoreMatches() 407 String<TSize> numLeaves; in _subTreeSearch() 463 typedef Pair<TSize, TSize> TDistGroup; // Distance, group index in _subTreeSearch() 466 for(TSize i=0; i< (TSize) length(groupRoot); ++i) { in _subTreeSearch() 468 TSize dist = 0; in _subTreeSearch() 482 for(TSize i=0; i< (TSize) length(seqGroups); ++i) { in _subTreeSearch() 492 TSize leftover = 0; in _subTreeSearch() 547 String<TSize> seqLabels; in tripletLibraryExtension() 550 for(TSize i=0; i< (TSize) length(seqGroup); ++i) { in tripletLibraryExtension() 579 for(TSize i=0; i< (TSize) length(seqGroup); ++i) { in tripletLibraryExtension() [all …]
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/graph_msa/ |
H A D | graph_align_tcoffee_base.h | 221 TSize pos1 = 0; TSize pos2 = 0; TSize fragLen = 0; in _scoreMatches() 401 String<TSize> numLeaves; in _subTreeSearch() 457 typedef Pair<TSize, TSize> TDistGroup; // Distance, group index in _subTreeSearch() 460 for(TSize i=0; i< (TSize) length(groupRoot); ++i) { in _subTreeSearch() 462 TSize dist = 0; in _subTreeSearch() 476 for(TSize i=0; i< (TSize) length(seqGroups); ++i) { in _subTreeSearch() 486 TSize leftover = 0; in _subTreeSearch() 542 String<TSize> seqLabels; in tripletLibraryExtension() 545 for(TSize i=0; i< (TSize) length(seqGroup); ++i) { in tripletLibraryExtension() 574 for(TSize i=0; i< (TSize) length(seqGroup); ++i) { in tripletLibraryExtension() [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/util/ |
H A D | ncbi_cache.hpp | 61 template <class TKey, class TSize> 65 typedef TSize TSizeType; 151 class TSize = Uint4> 157 typedef TSize TSizeType; 338 CCache<TKey, TValue, THandler, TLock, TSize>::~CCache(void) in ~CCache() 350 void CCache<TKey, TValue, THandler, TLock, TSize>::x_EraseElement( in x_EraseElement() 377 CCache<TKey, TValue, THandler, TLock, TSize>::x_InsertElement( in x_InsertElement() 419 typename CCache<TKey, TValue, THandler, TLock, TSize>::TOrder 506 typename CCache<TKey, TValue, THandler, TLock, TSize>::TOrder 572 typename CCache<TKey, TValue, THandler, TLock, TSize>::TValueType [all …]
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/util/ |
H A D | ncbi_cache.hpp | 61 template <class TKey, class TSize> 65 typedef TSize TSizeType; 151 class TSize = Uint4> 157 typedef TSize TSizeType; 338 CCache<TKey, TValue, THandler, TLock, TSize>::~CCache(void) in ~CCache() 350 void CCache<TKey, TValue, THandler, TLock, TSize>::x_EraseElement( in x_EraseElement() 377 CCache<TKey, TValue, THandler, TLock, TSize>::x_InsertElement( in x_InsertElement() 419 typename CCache<TKey, TValue, THandler, TLock, TSize>::TOrder 506 typename CCache<TKey, TValue, THandler, TLock, TSize>::TOrder 572 typename CCache<TKey, TValue, THandler, TLock, TSize>::TValueType [all …]
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/seeds/ |
H A D | seeds_extension.h | 493 inline TSize 495 TSize offset, in _initAntiDiag3() 496 TSize maxCol, in _initAntiDiag3() 497 TSize antiDiagNo, in _initAntiDiag3() 520 TSize minCol, in _calcExtendedLowerDiag() 531 TSize maxCol, in _calcExtendedUpperDiag() 543 TSize cols, in _updateExtendedSeed() 544 TSize rows, in _updateExtendedSeed() 648 TSize minCol = 1; in _extendSeedGappedXDropOneDirection() 649 TSize maxCol = 2; in _extendSeedGappedXDropOneDirection() [all …]
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/seeds/ |
H A D | seeds_extension.h | 493 inline TSize 495 TSize offset, in _initAntiDiag3() 496 TSize maxCol, in _initAntiDiag3() 497 TSize antiDiagNo, in _initAntiDiag3() 520 TSize minCol, in _calcExtendedLowerDiag() 531 TSize maxCol, in _calcExtendedUpperDiag() 543 TSize cols, in _updateExtendedSeed() 544 TSize rows, in _updateExtendedSeed() 648 TSize minCol = 1; in _extendSeedGappedXDropOneDirection() 649 TSize maxCol = 2; in _extendSeedGappedXDropOneDirection() [all …]
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/seeds/ |
H A D | seeds_extension.h | 493 inline TSize 495 TSize offset, in _initAntiDiag3() 496 TSize maxCol, in _initAntiDiag3() 497 TSize antiDiagNo, in _initAntiDiag3() 520 TSize minCol, in _calcExtendedLowerDiag() 531 TSize maxCol, in _calcExtendedUpperDiag() 543 TSize cols, in _updateExtendedSeed() 544 TSize rows, in _updateExtendedSeed() 648 TSize minCol = 1; in _extendSeedGappedXDropOneDirection() 649 TSize maxCol = 2; in _extendSeedGappedXDropOneDirection() [all …]
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/dports/biology/seqan1/seqan-1.3.1/seqan/refinement/ |
H A D | graph_impl_align.h | 157 TSize data_begin; 167 FragmentInfo(TId id, TSize beg, TSize len) : 516 if ( (TSize) begin + len == (TSize) interval->first.second) { 1628 TSize len = 0; 1635 TSize row = 0; 1636 TSize col = 0; 1740 typedef std::pair<TSize, TSize> TResiduePair; 1852 TSize i = m; 1853 TSize j = n; 1971 TSize pos = 0; [all …]
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