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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/dbapi/driver/
H A Dmemory_store.hpp94 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);
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/dports/biology/seqan1/seqan-1.3.1/seqan/graph_msa/
H A Dgraph_align_tcoffee_refinement.h170 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()
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H A Dgraph_align_tcoffee_base.h201 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()
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/dports/biology/seqan1/seqan-1.3.1/seqan/consensus/
H A Dconsensus_base.h240 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()
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/parallel/
H A Dparallel_splitting.h128 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)
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/parallel/
H A Dparallel_splitting.h128 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)
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/parallel/
H A Dparallel_splitting.h128 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)
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/index/
H A Dradix.h54 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()
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H A Dindex_lcp.h288 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);
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/dports/biology/seqan1/seqan-1.3.1/seqan/index/
H A Dradix.h56 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()
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H A Dindex_wotd.h129 …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;
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H A Dindex_qgram_openaddressing.h189 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);
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/index/
H A Dradix.h54 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()
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H A Dindex_lcp.h288 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);
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/index/
H A Dradix.h54 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()
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H A Dindex_lcp.h288 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);
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/graph_msa/
H A Dgraph_align_tcoffee_base.h228 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()
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/graph_msa/
H A Dgraph_align_tcoffee_base.h228 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()
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/graph_msa/
H A Dgraph_align_tcoffee_base.h221 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()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/util/
H A Dncbi_cache.hpp61 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
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/util/
H A Dncbi_cache.hpp61 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
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/seeds/
H A Dseeds_extension.h493 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()
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/seeds/
H A Dseeds_extension.h493 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()
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/seeds/
H A Dseeds_extension.h493 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()
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/dports/biology/seqan1/seqan-1.3.1/seqan/refinement/
H A Dgraph_impl_align.h157 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;
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