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Searched refs:scoutState (Results 1 – 17 of 17) sorted by relevance

/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/seeds/
H A Dbanded_chain_alignment_scout.h119 DPScout_(TScoutState & scoutState) : in DPScout_() argument
121 _dpScoutStatePtr(&scoutState), in DPScout_()
187 scoutState._horizontalNextGridOrigin = originNextMatrixH;
188 scoutState._verticalNextGridOrigin = originNextMatrixV;
191 …arrayFill(begin(scoutState._horizontalInitCurrentMatrix), end(scoutState._horizontalInitCurrentMat…
192 …arrayFill(begin(scoutState._verticalInitCurrentMatrix), end(scoutState._verticalInitCurrentMatrix)…
193 …arrayFill(begin(scoutState._horizontalInitNextMatrix), end(scoutState._horizontalInitNextMatrix), …
194 …arrayFill(begin(scoutState._verticalInitNextMatrix), end(scoutState._verticalInitNextMatrix), TDPC…
209 it != scoutState._nextInitializationCells.end(); ++it)
213 scoutState._verticalInitCurrentMatrix[it->i2] = it->i3;
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H A Dbanded_chain_alignment_impl.h812 TScoutState & scoutState, in _initializeBandedChain() argument
955 scoutState._horizontalNextGridOrigin += gridBegin.i1; in _initializeBandedChain()
956 scoutState._verticalNextGridOrigin += gridBegin.i2; in _initializeBandedChain()
973 TDPScoutState & scoutState, in _computeGapArea() argument
990 TGridPoint gridBegin(scoutState._horizontalNextGridOrigin, scoutState._verticalNextGridOrigin); in _computeGapArea()
1022 scoutState._verticalNextGridOrigin += gridBegin.i2; in _computeGapArea()
1035 TDPScoutState & scoutState, in _computeAnchorArea() argument
1053 TGridPoint gridBegin(scoutState._horizontalNextGridOrigin, scoutState._verticalNextGridOrigin); in _computeAnchorArea()
1093 scoutState._verticalNextGridOrigin += gridBegin.i2; in _computeAnchorArea()
1254 TScoutState & scoutState, in _computeAlignment() argument
[all …]
/dports/biology/seqan/seqan-library-2.4.0/include/seqan/seeds/
H A Dbanded_chain_alignment_scout.h119 DPScout_(TScoutState & scoutState) : in DPScout_() argument
121 _dpScoutStatePtr(&scoutState), in DPScout_()
187 scoutState._horizontalNextGridOrigin = originNextMatrixH;
188 scoutState._verticalNextGridOrigin = originNextMatrixV;
191 …arrayFill(begin(scoutState._horizontalInitCurrentMatrix), end(scoutState._horizontalInitCurrentMat…
192 …arrayFill(begin(scoutState._verticalInitCurrentMatrix), end(scoutState._verticalInitCurrentMatrix)…
193 …arrayFill(begin(scoutState._horizontalInitNextMatrix), end(scoutState._horizontalInitNextMatrix), …
194 …arrayFill(begin(scoutState._verticalInitNextMatrix), end(scoutState._verticalInitNextMatrix), TDPC…
209 it != scoutState._nextInitializationCells.end(); ++it)
213 scoutState._verticalInitCurrentMatrix[it->i2] = it->i3;
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H A Dbanded_chain_alignment_impl.h812 TScoutState & scoutState, in _initializeBandedChain() argument
955 scoutState._horizontalNextGridOrigin += gridBegin.i1; in _initializeBandedChain()
956 scoutState._verticalNextGridOrigin += gridBegin.i2; in _initializeBandedChain()
973 TDPScoutState & scoutState, in _computeGapArea() argument
990 TGridPoint gridBegin(scoutState._horizontalNextGridOrigin, scoutState._verticalNextGridOrigin); in _computeGapArea()
1022 scoutState._verticalNextGridOrigin += gridBegin.i2; in _computeGapArea()
1035 TDPScoutState & scoutState, in _computeAnchorArea() argument
1053 TGridPoint gridBegin(scoutState._horizontalNextGridOrigin, scoutState._verticalNextGridOrigin); in _computeAnchorArea()
1093 scoutState._verticalNextGridOrigin += gridBegin.i2; in _computeAnchorArea()
1254 TScoutState & scoutState, in _computeAlignment() argument
[all …]
/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/seeds/
H A Dbanded_chain_alignment_scout.h119 DPScout_(TScoutState & scoutState) : in DPScout_() argument
121 _dpScoutStatePtr(&scoutState), in DPScout_()
186 scoutState._horizontalNextGridOrigin = originNextMatrixH;
187 scoutState._verticalNextGridOrigin = originNextMatrixV;
190 …arrayFill(begin(scoutState._horizontalInitCurrentMatrix), end(scoutState._horizontalInitCurrentMat…
191 …arrayFill(begin(scoutState._verticalInitCurrentMatrix), end(scoutState._verticalInitCurrentMatrix)…
192 …arrayFill(begin(scoutState._horizontalInitNextMatrix), end(scoutState._horizontalInitNextMatrix), …
193 …arrayFill(begin(scoutState._verticalInitNextMatrix), end(scoutState._verticalInitNextMatrix), TDPC…
208 it != scoutState._nextInitializationCells.end(); ++it)
212 scoutState._verticalInitCurrentMatrix[it->i2] = it->i3;
[all …]
H A Dbanded_chain_alignment_impl.h724 TScoutState & scoutState, in _initializeBandedChain() argument
866 scoutState._horizontalNextGridOrigin += gridBegin.i1; in _initializeBandedChain()
867 scoutState._verticalNextGridOrigin += gridBegin.i2; in _initializeBandedChain()
883 TDPScoutState & scoutState, in _computeGapArea() argument
900 TGridPoint gridBegin(scoutState._horizontalNextGridOrigin, scoutState._verticalNextGridOrigin); in _computeGapArea()
930 scoutState._verticalNextGridOrigin += gridBegin.i2; in _computeGapArea()
942 TDPScoutState & scoutState, in _computeAnchorArea() argument
960 TGridPoint gridBegin(scoutState._horizontalNextGridOrigin, scoutState._verticalNextGridOrigin); in _computeAnchorArea()
1000 scoutState._verticalNextGridOrigin += gridBegin.i2; in _computeAnchorArea()
1159 TScoutState & scoutState, in _computeAlignment() argument
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/tests/align/
H A Dtest_alignment_algorithms_band_position.h49 DPScoutState_<Default> scoutState; in SEQAN_DEFINE_TEST() local
114 DPScoutState_<Default> scoutState; in SEQAN_DEFINE_TEST() local
177 DPScoutState_<Default> scoutState; in SEQAN_DEFINE_TEST() local
239 DPScoutState_<Default> scoutState; in SEQAN_DEFINE_TEST() local
300 DPScoutState_<Default> scoutState; in SEQAN_DEFINE_TEST() local
364 DPScoutState_<Default> scoutState; in SEQAN_DEFINE_TEST() local
427 DPScoutState_<Default> scoutState; in SEQAN_DEFINE_TEST() local
490 DPScoutState_<Default> scoutState; in SEQAN_DEFINE_TEST() local
552 DPScoutState_<Default> scoutState; in SEQAN_DEFINE_TEST() local
614 DPScoutState_<Default> scoutState; in SEQAN_DEFINE_TEST() local
[all …]
/dports/biology/seqan/seqan-library-2.4.0/include/seqan/align_extend/
H A Dalign_extend.h133 DPScoutState_<Default> scoutState; in _setUpAndRunAlignImpl() local
134 …return _setUpAndRunAlignment(alignContext.dpContext, alignContext.traceSegment, scoutState, str0, … in _setUpAndRunAlignImpl()
156 DPScoutState_<Default> scoutState; in _setUpAndRunAlignImpl() local
157 …return _setUpAndRunAlignment(alignContext.dpContext, alignContext.traceSegment, scoutState, str0, … in _setUpAndRunAlignImpl()
179 DPScoutState_<Terminator_<XDrop_<TScoreValue> > > scoutState(xDrop); in _setUpAndRunAlignImpl()
180 …return _setUpAndRunAlignment(alignContext.dpContext, alignContext.traceSegment, scoutState, str0, … in _setUpAndRunAlignImpl()
202 DPScoutState_<Terminator_<XDrop_<TScoreValue> > > scoutState(xDrop); in _setUpAndRunAlignImpl()
203 …return _setUpAndRunAlignment(alignContext.dpContext, alignContext.traceSegment, scoutState, str0, … in _setUpAndRunAlignImpl()
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/align_extend/
H A Dalign_extend.h133 DPScoutState_<Default> scoutState; in _setUpAndRunAlignImpl() local
134 …return _setUpAndRunAlignment(alignContext.dpContext, alignContext.traceSegment, scoutState, str0, … in _setUpAndRunAlignImpl()
156 DPScoutState_<Default> scoutState; in _setUpAndRunAlignImpl() local
157 …return _setUpAndRunAlignment(alignContext.dpContext, alignContext.traceSegment, scoutState, str0, … in _setUpAndRunAlignImpl()
179 DPScoutState_<Terminator_<XDrop_<TScoreValue> > > scoutState(xDrop); in _setUpAndRunAlignImpl()
180 …return _setUpAndRunAlignment(alignContext.dpContext, alignContext.traceSegment, scoutState, str0, … in _setUpAndRunAlignImpl()
202 DPScoutState_<Terminator_<XDrop_<TScoreValue> > > scoutState(xDrop); in _setUpAndRunAlignImpl()
203 …return _setUpAndRunAlignment(alignContext.dpContext, alignContext.traceSegment, scoutState, str0, … in _setUpAndRunAlignImpl()
/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/align_extend/
H A Dalign_extend.h148 DPScoutState_<Default> scoutState; in _setUpAndRunAlignImpl() local
149 …return _setUpAndRunAlignment(alignContext.dpContext, alignContext.traceSegment, scoutState, str0, … in _setUpAndRunAlignImpl()
171 DPScoutState_<Default> scoutState; in _setUpAndRunAlignImpl() local
172 …return _setUpAndRunAlignment(alignContext.dpContext, alignContext.traceSegment, scoutState, str0, … in _setUpAndRunAlignImpl()
194 DPScoutState_<Terminator_<XDrop_<TScoreValue> > > scoutState(xDrop); in _setUpAndRunAlignImpl()
195 …return _setUpAndRunAlignment(alignContext.dpContext, alignContext.traceSegment, scoutState, str0, … in _setUpAndRunAlignImpl()
217 DPScoutState_<Terminator_<XDrop_<TScoreValue> > > scoutState(xDrop); in _setUpAndRunAlignImpl()
218 …return _setUpAndRunAlignment(alignContext.dpContext, alignContext.traceSegment, scoutState, str0, … in _setUpAndRunAlignImpl()
/dports/biology/seqan/seqan-library-2.4.0/include/seqan/align_parallel/
H A Dwavefront_task_util.h479 TScoutState scoutState(bufferH, bufferV);
480 _prepareSimdAlignment(stringSimdH, stringSimdV, depSetH, depSetV, scoutState);
485 TDPScout dpScout(scoutState);
527 TScoutState scoutState(bufferH, bufferV);
528 … _prepareSimdAlignment(stringSimdH, stringSimdV, depSetH, depSetV, lengthsH, lengthsV, scoutState);
533 TDPScout dpScout(scoutState);
H A Dwavefront_task.h275 typename TExecTraits::TDPScoutState scoutState(buffer.horizontalBuffer[column(task)],
278 typename TExecTraits::TDPScout scout(scoutState);
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/align_parallel/
H A Dwavefront_task_util.h479 TScoutState scoutState(bufferH, bufferV);
480 _prepareSimdAlignment(stringSimdH, stringSimdV, depSetH, depSetV, scoutState);
485 TDPScout dpScout(scoutState);
527 TScoutState scoutState(bufferH, bufferV);
528 … _prepareSimdAlignment(stringSimdH, stringSimdV, depSetH, depSetV, lengthsH, lengthsV, scoutState);
533 TDPScout dpScout(scoutState);
H A Dwavefront_task.h275 typename TExecTraits::TDPScoutState scoutState(buffer.horizontalBuffer[column(task)],
278 typename TExecTraits::TDPScout scout(scoutState);
/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/align/
H A Ddp_algorithm_impl.h1382 TScoutState & scoutState, in _computeAlignment() argument
1444 TDPScout dpScout(scoutState); in _computeAlignment()
/dports/biology/seqan/seqan-library-2.4.0/include/seqan/align/
H A Ddp_algorithm_impl.h1351 TScoutState & scoutState, in _computeAlignment() argument
1411 TDPScout dpScout(scoutState); in _computeAlignment()
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/align/
H A Ddp_algorithm_impl.h1351 TScoutState & scoutState, in _computeAlignment() argument
1411 TDPScout dpScout(scoutState); in _computeAlignment()