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Searched refs:TDPCell (Results 1 – 25 of 46) sorted by relevance

12

/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/seeds/
H A Dbanded_chain_alignment_scout.h75 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>
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H A Dbanded_chain_alignment_impl.h256 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,
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H A Dbanded_chain_alignment_traceback.h220 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,
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/seeds/
H A Dbanded_chain_alignment_scout.h75 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>
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H A Dbanded_chain_alignment_impl.h256 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,
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/seeds/
H A Dbanded_chain_alignment_scout.h75 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>
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H A Dbanded_chain_alignment_impl.h240 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()
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/align/
H A Ddp_scout.h85 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
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H A Ddp_scout_simd.h91 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>
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/align/
H A Ddp_scout.h85 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
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H A Ddp_scout_simd.h91 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>
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/align_parallel/
H A Ddp_parallel_scout_simd.h174 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,
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H A Ddp_parallel_scout.h80 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,
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H A Ddp_kernel_adaptor.h86 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,
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/align_parallel/
H A Ddp_parallel_scout_simd.h174 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,
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H A Ddp_parallel_scout.h80 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,
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H A Ddp_kernel_adaptor.h86 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,
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/align/
H A Ddp_scout.h85 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
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/align_extend/
H A Ddp_scout_xdrop.h104 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,
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/align_extend/
H A Ddp_scout_xdrop.h104 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,
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/align_extend/
H A Ddp_scout_xdrop.h104 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,
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/align_split/
H A Ddp_scout_split.h76 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()
/dports/biology/seqan/seqan-library-2.4.0/include/seqan/align_split/
H A Ddp_scout_split.h77 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()
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/align_split/
H A Ddp_scout_split.h77 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()
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/tests/align/
H A Dtest_alignment_dp_matrix_navigator.h78 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()
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