/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/seeds/ |
H A D | banded_chain_alignment_scout.h | 119 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; [all …]
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H A D | banded_chain_alignment_impl.h | 812 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 …]
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/seeds/ |
H A D | banded_chain_alignment_scout.h | 119 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; [all …]
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H A D | banded_chain_alignment_impl.h | 812 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 …]
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/seeds/ |
H A D | banded_chain_alignment_scout.h | 119 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 …]
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H A D | banded_chain_alignment_impl.h | 724 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 [all …]
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/tests/align/ |
H A D | test_alignment_algorithms_band_position.h | 49 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 …]
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/align_extend/ |
H A D | align_extend.h | 133 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()
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/align_extend/ |
H A D | align_extend.h | 133 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()
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/align_extend/ |
H A D | align_extend.h | 148 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()
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/align_parallel/ |
H A D | wavefront_task_util.h | 479 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);
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H A D | wavefront_task.h | 275 typename TExecTraits::TDPScoutState scoutState(buffer.horizontalBuffer[column(task)], 278 typename TExecTraits::TDPScout scout(scoutState);
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/align_parallel/ |
H A D | wavefront_task_util.h | 479 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);
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H A D | wavefront_task.h | 275 typename TExecTraits::TDPScoutState scoutState(buffer.horizontalBuffer[column(task)], 278 typename TExecTraits::TDPScout scout(scoutState);
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/align/ |
H A D | dp_algorithm_impl.h | 1382 TScoutState & scoutState, in _computeAlignment() argument 1444 TDPScout dpScout(scoutState); in _computeAlignment()
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/align/ |
H A D | dp_algorithm_impl.h | 1351 TScoutState & scoutState, in _computeAlignment() argument 1411 TDPScout dpScout(scoutState); in _computeAlignment()
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/align/ |
H A D | dp_algorithm_impl.h | 1351 TScoutState & scoutState, in _computeAlignment() argument 1411 TDPScout dpScout(scoutState); in _computeAlignment()
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