/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/seeds/ |
H A D | banded_chain_alignment_scout.h | 75 template <typename TDPCell> 100 template<typename TDPCell> 110 TDPCell _maxScore; 145 template <typename TDPCell> 159 template <typename TDPCell> 303 template <typename TDPCell> 310 template <typename TDPCell> 321 template <typename TDPCell> 328 template <typename TDPCell> 339 template <typename TDPCell> [all …]
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H A D | banded_chain_alignment_impl.h | 256 inline TDPCell & 270 inline TDPCell const & 412 typename TDPCell, 422 TDPCell & current, in _computeCell() 459 typename TDPCell, 469 TDPCell & current, in _computeCell() 525 typename TDPCell, 558 typename TDPCell, 595 typename TDPCell, 628 typename TDPCell, [all …]
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H A D | banded_chain_alignment_traceback.h | 220 typedef DPCell_<TScoreValue, AffineGaps> TDPCell; 223 dpCell._verticalScore = DPCellDefaultInfinity<TDPCell>::VALUE; 224 dpCell._horizontalScore = DPCellDefaultInfinity<TDPCell>::VALUE; 227 dpCell._horizontalScore = DPCellDefaultInfinity<TDPCell>::VALUE; 229 dpCell._verticalScore = DPCellDefaultInfinity<TDPCell>::VALUE; 236 template<typename TTarget, typename TDPTraceMatrixNavigator, typename TDPCell, typename TScoutSpec, 242 DPScout_<TDPCell, TScoutSpec> & dpScout, 248 typedef DPScout_<TDPCell, TScoutSpec> TDPScout_; 360 typename TDPCell, typename TScoutSpec, 366 DPScout_<TDPCell, TScoutSpec> & dpScout, [all …]
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/seeds/ |
H A D | banded_chain_alignment_scout.h | 75 template <typename TDPCell> 100 template<typename TDPCell> 110 TDPCell _maxScore; 145 template <typename TDPCell> 159 template <typename TDPCell> 303 template <typename TDPCell> 310 template <typename TDPCell> 321 template <typename TDPCell> 328 template <typename TDPCell> 339 template <typename TDPCell> [all …]
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H A D | banded_chain_alignment_impl.h | 256 inline TDPCell & 270 inline TDPCell const & 412 typename TDPCell, 422 TDPCell & current, in _computeCell() 459 typename TDPCell, 469 TDPCell & current, in _computeCell() 525 typename TDPCell, 558 typename TDPCell, 595 typename TDPCell, 628 typename TDPCell, [all …]
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/seeds/ |
H A D | banded_chain_alignment_scout.h | 75 template <typename TDPCell> 100 template<typename TDPCell> 110 TDPCell _maxScore; 144 template <typename TDPCell> 158 template <typename TDPCell> 302 template <typename TDPCell> 309 template <typename TDPCell> 320 template <typename TDPCell> 327 template <typename TDPCell> 338 template <typename TDPCell> [all …]
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H A D | banded_chain_alignment_impl.h | 240 inline TDPCell & 254 inline TDPCell const & 679 TDPCell dpInitCellHorizontal; in _initiaizeBeginningOfBandedChain() 680 …_computeScore(dpInitCellHorizontal, TDPCell(), TDPCell(), TDPCell(), Nothing(), Nothing(), Nothing… in _initiaizeBeginningOfBandedChain() 688 …_computeScore(dpInitCellHorizontal, TDPCell(), TDPCell(), TDPCell(), Nothing(), Nothing(), scoreSc… in _initiaizeBeginningOfBandedChain() 691 …_computeScore(dpInitCellHorizontal, TDPCell(), prevCell, TDPCell(), Nothing(), Nothing(), scoreSch… in _initiaizeBeginningOfBandedChain() 696 TDPCell dpInitCellVertical; in _initiaizeBeginningOfBandedChain() 697 …_computeScore(dpInitCellVertical, TDPCell(), TDPCell(), TDPCell(), Nothing(), Nothing(), Nothing(), in _initiaizeBeginningOfBandedChain() 701 TDPCell prevCell = dpInitCellVertical; in _initiaizeBeginningOfBandedChain() 703 …_computeScore(dpInitCellVertical, TDPCell(), TDPCell(), TDPCell(), Nothing(), Nothing(), scoreSche… in _initiaizeBeginningOfBandedChain() [all …]
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/align/ |
H A D | dp_scout.h | 85 template <typename TDPCell, typename TSpec> 92 template <typename TDPCell, typename TSpec> 99 TDPCell _maxScore = TDPCell(); 108 template <typename TDPCell, typename TSpec> 109 class DPScout_<TDPCell, Terminator_<TSpec> > 110 : public DPScout_<TDPCell, Default> 170 TDPCell const & activeCell, in _scoutBestScore() 186 TDPCell const & activeCell, in _scoutBestScore() 197 TDPCell const & activeCell, in _scoutBestScore() 209 inline typename Value<TDPCell>::Type const [all …]
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H A D | dp_scout_simd.h | 91 template <typename TDPCell, typename TSpec> 93 public DPScout_<TDPCell, Default> 215 template <typename TDPCell, 221 TDPCell const & activeCell, 240 template <typename TDPCell, typename TTraits, 253 template <typename TDPCell, typename TTraits, 268 template <typename TDPCell, typename TTraits, 291 template <typename TDPCell, typename TTraits, 570 TDPCell const & activeCell, 732 template <typename TDPCell, typename TSeqH> [all …]
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/align/ |
H A D | dp_scout.h | 85 template <typename TDPCell, typename TSpec> 92 template <typename TDPCell, typename TSpec> 99 TDPCell _maxScore = TDPCell(); 108 template <typename TDPCell, typename TSpec> 109 class DPScout_<TDPCell, Terminator_<TSpec> > 110 : public DPScout_<TDPCell, Default> 170 TDPCell const & activeCell, in _scoutBestScore() 186 TDPCell const & activeCell, in _scoutBestScore() 197 TDPCell const & activeCell, in _scoutBestScore() 209 inline typename Value<TDPCell>::Type const [all …]
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H A D | dp_scout_simd.h | 91 template <typename TDPCell, typename TSpec> 93 public DPScout_<TDPCell, Default> 215 template <typename TDPCell, 221 TDPCell const & activeCell, 240 template <typename TDPCell, typename TTraits, 253 template <typename TDPCell, typename TTraits, 268 template <typename TDPCell, typename TTraits, 291 template <typename TDPCell, typename TTraits, 570 TDPCell const & activeCell, 732 template <typename TDPCell, typename TSeqH> [all …]
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/align_parallel/ |
H A D | dp_parallel_scout_simd.h | 174 TDPCell const & activeCell, 179 using TScoutBase = typename DPScout_<TDPCell, 194 using TScoutBase = typename DPScout_<TDPCell, 221 using TScoutBase = typename DPScout_<TDPCell, 235 _preInitScoutVertical(DPScout_<TDPCell, 254 _reachedHorizontalEndPoint(DPScout_<TDPCell, 273 _reachedVerticalEndPoint(DPScout_<TDPCell, 292 _nextHorizontalEndPos(DPScout_<TDPCell, 310 _nextVerticalEndPos(DPScout_<TDPCell, 328 _incHorizontalPos(DPScout_<TDPCell, [all …]
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H A D | dp_parallel_scout.h | 80 using TDPCell = typename Value<typename Value<TBuffer>::Type, 1>::Type; 105 template <typename TDPCell, typename TBuffer, typename TThreadContext> 106 class DPScout_<TDPCell, DPTiled<TBuffer, TThreadContext, void> > : 107 public DPScout_<TDPCell, Default> 110 using TBase = DPScout_<TDPCell, Default>; 155 template <typename TDPCell, typename TBuffer, typename TThreadContext> 165 template <typename TDPCell, typename TBuffer, typename TThreadContext> 174 template <typename TDPCell, typename TBuffer, typename TThreadContext> 187 template <typename TDPCell, typename TBuffer, 193 TDPCell const & activeCell, [all …]
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H A D | dp_kernel_adaptor.h | 86 typename TDPCell, 95 TDPCell & current, 125 typename TDPCell, 133 TDPCell & current, 157 typename TDPCell, 165 TDPCell & current, 207 typename TDPCell, 215 TDPCell & current, 253 typename TDPCell, 261 TDPCell & current, [all …]
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/align_parallel/ |
H A D | dp_parallel_scout_simd.h | 174 TDPCell const & activeCell, 179 using TScoutBase = typename DPScout_<TDPCell, 194 using TScoutBase = typename DPScout_<TDPCell, 221 using TScoutBase = typename DPScout_<TDPCell, 235 _preInitScoutVertical(DPScout_<TDPCell, 254 _reachedHorizontalEndPoint(DPScout_<TDPCell, 273 _reachedVerticalEndPoint(DPScout_<TDPCell, 292 _nextHorizontalEndPos(DPScout_<TDPCell, 310 _nextVerticalEndPos(DPScout_<TDPCell, 328 _incHorizontalPos(DPScout_<TDPCell, [all …]
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H A D | dp_parallel_scout.h | 80 using TDPCell = typename Value<typename Value<TBuffer>::Type, 1>::Type; 105 template <typename TDPCell, typename TBuffer, typename TThreadContext> 106 class DPScout_<TDPCell, DPTiled<TBuffer, TThreadContext, void> > : 107 public DPScout_<TDPCell, Default> 110 using TBase = DPScout_<TDPCell, Default>; 155 template <typename TDPCell, typename TBuffer, typename TThreadContext> 165 template <typename TDPCell, typename TBuffer, typename TThreadContext> 174 template <typename TDPCell, typename TBuffer, typename TThreadContext> 187 template <typename TDPCell, typename TBuffer, 193 TDPCell const & activeCell, [all …]
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H A D | dp_kernel_adaptor.h | 86 typename TDPCell, 95 TDPCell & current, 125 typename TDPCell, 133 TDPCell & current, 157 typename TDPCell, 165 TDPCell & current, 207 typename TDPCell, 215 TDPCell & current, 253 typename TDPCell, 261 TDPCell & current, [all …]
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/align/ |
H A D | dp_scout.h | 85 template <typename TDPCell, typename TSpec> 92 template <typename TDPCell, typename TSpec> 98 TDPCell _maxScore; 122 template <typename TDPCell, typename TSpec> 123 class DPScout_<TDPCell, Terminator_<TSpec> > 124 : public DPScout_<TDPCell, Default> 205 TDPCell const & activeCell, in _scoutBestScore() 222 TDPCell const & activeCell, in _scoutBestScore() 234 TDPCell const & activeCell, in _scoutBestScore() 246 inline typename Value<TDPCell>::Type const [all …]
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/align_extend/ |
H A D | dp_scout_xdrop.h | 104 template <typename TDPCell> 107 TDPCell, Terminator_<XDrop_< typename Value<TDPCell>::Type> > > > 126 TDPCell const & activeCell, 131 typedef typename Value<TDPCell>::Type TScoreValue; 146 TDPCell const & activeCell, 151 typedef typename Value<TDPCell>::Type TScoreValue; 168 typename TDPCell, 175 TDPCell & current, 176 TDPCell & diagonal, 177 TDPCell const & horizontal, [all …]
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/align_extend/ |
H A D | dp_scout_xdrop.h | 104 template <typename TDPCell> 107 TDPCell, Terminator_<XDrop_< typename Value<TDPCell>::Type> > > > 126 TDPCell const & activeCell, 131 typedef typename Value<TDPCell>::Type TScoreValue; 146 TDPCell const & activeCell, 151 typedef typename Value<TDPCell>::Type TScoreValue; 168 typename TDPCell, 175 TDPCell & current, 176 TDPCell & diagonal, 177 TDPCell const & horizontal, [all …]
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/align_extend/ |
H A D | dp_scout_xdrop.h | 104 template <typename TDPCell> 107 TDPCell, Terminator_<XDrop_< typename Value<TDPCell>::Type> > > > 109 typedef Terminator_<XDrop_<typename Value<TDPCell>::Type> > Type; 123 template <typename TDPCell, typename TTraceMatrixNavigator, typename TDPCellValue, typename TIsLast… 125 _scoutBestScore(DPScout_<TDPCell, Terminator_<XDrop_<TDPCellValue> > > & dpScout, 126 TDPCell const & activeCell, 131 typedef typename Value<TDPCell>::Type TScoreValue; 133 typedef DPScout_<TDPCell, Terminator_<TXDrop> > TDPScout; 145 _scoutBestScore(DPScout_<TDPCell, Terminator_<XDrop_<TDPCellValue> > > & dpScout, 146 TDPCell const & activeCell, [all …]
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/align_split/ |
H A D | dp_scout_split.h | 76 template <typename TDPCell> 77 class DPScout_<TDPCell, SplitAlignmentScout> : public DPScout_<TDPCell, Default> 80 typedef DPScout_<TDPCell, Default> TParent; 103 template <typename TDPCell, typename TTraceMatrixNavigator, typename TIsLastColumn, typename TIsLas… 105 _scoutBestScore(DPScout_<TDPCell, SplitAlignmentScout> & dpScout, in _scoutBestScore() argument 106 TDPCell const & activeCell, in _scoutBestScore() 123 typedef DPScout_<TDPCell, SplitAlignmentScout> TDPScout; in _scoutBestScore()
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/align_split/ |
H A D | dp_scout_split.h | 77 template <typename TDPCell> 78 class DPScout_<TDPCell, SplitAlignmentScout> : public DPScout_<TDPCell, Default> 81 typedef DPScout_<TDPCell, Default> TParent; 104 template <typename TDPCell, typename TTraceMatrixNavigator, typename TIsLastColumn, typename TIsLas… 106 _scoutBestScore(DPScout_<TDPCell, SplitAlignmentScout> & dpScout, in _scoutBestScore() argument 107 TDPCell const & activeCell, in _scoutBestScore() 129 typedef DPScout_<TDPCell, SplitAlignmentScout> TDPScout; in _scoutBestScore()
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/align_split/ |
H A D | dp_scout_split.h | 77 template <typename TDPCell> 78 class DPScout_<TDPCell, SplitAlignmentScout> : public DPScout_<TDPCell, Default> 81 typedef DPScout_<TDPCell, Default> TParent; 104 template <typename TDPCell, typename TTraceMatrixNavigator, typename TIsLastColumn, typename TIsLas… 106 _scoutBestScore(DPScout_<TDPCell, SplitAlignmentScout> & dpScout, in _scoutBestScore() argument 107 TDPCell const & activeCell, in _scoutBestScore() 129 typedef DPScout_<TDPCell, SplitAlignmentScout> TDPScout; in _scoutBestScore()
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/tests/align/ |
H A D | test_alignment_dp_matrix_navigator.h | 78 resize(dpMatrix, TDPCell{}); in testAlignmentDPMatrixNavigatorScoreMarixInitUnbanded() 99 resize(dpMatrix, TDPCell{}); in testAlignmentDPMatrixNavigatorScoreMarixSparseInitUnbanded() 226 resize(dpMatrix, TDPCell{}); in testAlignmentDPMatrixNavigatorScoreMarixGoNextCell() 231 TDPCell cell; in testAlignmentDPMatrixNavigatorScoreMarixGoNextCell() 296 resize(dpMatrix, TDPCell{}); in testAlignmentDPMatrixNavigatorScoreMarixSparseGoNextCell() 301 TDPCell cell; in testAlignmentDPMatrixNavigatorScoreMarixSparseGoNextCell() 367 resize(dpMatrix, TDPCell{}); in testAlignmentDPScoreMatrixNavigatorAssignValue() 371 TDPCell tmp; in testAlignmentDPScoreMatrixNavigatorAssignValue() 389 resize(dpMatrix, TDPCell{}); in testAlignmentDPScoreMatrixNavigatorValue() 394 TDPCell tmp; in testAlignmentDPScoreMatrixNavigatorValue() [all …]
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