/dports/biology/seqan/seqan-library-2.4.0/include/seqan/align/ |
H A D | dp_scout.h | 169 _scoutBestScore(DPScout_<TDPCell, TSpec> & dpScout, in _scoutBestScore() 185 _scoutBestScore(DPScout_<TDPCell, TSpec> & dpScout, in _scoutBestScore() 196 _scoutBestScore(DPScout_<TDPCell, TSpec> & dpScout, in _scoutBestScore() 210 maxScore(DPScout_<TDPCell, TScoutSpec> const & dpScout) in maxScore() 222 maxHostPosition(DPScout_<TDPCell, TScoutSpec> const & dpScout) in maxHostPosition() 244 terminateScout(DPScout_<TDPCell, Terminator_<TSpec> > & scout) in terminateScout() 278 _preInitScoutVertical(DPScout_<TDPCell, TSpec> const & /*scout*/) in _preInitScoutVertical() 301 _nextHorizontalEndPos(DPScout_<TDPCell, TSpec> const & /*scout*/) in _nextHorizontalEndPos() 312 _nextVerticalEndPos(DPScout_<TDPCell, TSpec> const & /*scout*/) in _nextVerticalEndPos() 323 _incHorizontalPos(DPScout_<TDPCell, TSpec> const & /*scout*/) in _incHorizontalPos() [all …]
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H A D | dp_algorithm_impl.h | 449 using TDPCell = std::decay_t<decltype(value(dpScoreMatrixNavigator))>; in _computeTrack() local 463 _computeAlignmentHelperCheckTerminate(DPScout_<TDPCell, TSpec > const & /**/) in _computeAlignmentHelperCheckTerminate() 470 _computeAlignmentHelperCheckTerminate(DPScout_<TDPCell,Terminator_<TSpec> > const & s) in _computeAlignmentHelperCheckTerminate() 980 typedef typename Value<TDPScoreMatrixNavigator>::Type TDPCell; in _computeHammingDistance() typedef
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H A D | dp_matrix_navigator_score_matrix.h | 387 _preInitCacheDiagonal(TDPCell & /*cacheDiagonal*/, in _preInitCacheDiagonal() argument
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/align/ |
H A D | dp_scout.h | 169 _scoutBestScore(DPScout_<TDPCell, TSpec> & dpScout, in _scoutBestScore() 185 _scoutBestScore(DPScout_<TDPCell, TSpec> & dpScout, in _scoutBestScore() 196 _scoutBestScore(DPScout_<TDPCell, TSpec> & dpScout, in _scoutBestScore() 210 maxScore(DPScout_<TDPCell, TScoutSpec> const & dpScout) in maxScore() 222 maxHostPosition(DPScout_<TDPCell, TScoutSpec> const & dpScout) in maxHostPosition() 244 terminateScout(DPScout_<TDPCell, Terminator_<TSpec> > & scout) in terminateScout() 278 _preInitScoutVertical(DPScout_<TDPCell, TSpec> const & /*scout*/) in _preInitScoutVertical() 301 _nextHorizontalEndPos(DPScout_<TDPCell, TSpec> const & /*scout*/) in _nextHorizontalEndPos() 312 _nextVerticalEndPos(DPScout_<TDPCell, TSpec> const & /*scout*/) in _nextVerticalEndPos() 323 _incHorizontalPos(DPScout_<TDPCell, TSpec> const & /*scout*/) in _incHorizontalPos() [all …]
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H A D | dp_algorithm_impl.h | 449 using TDPCell = std::decay_t<decltype(value(dpScoreMatrixNavigator))>; in _computeTrack() local 463 _computeAlignmentHelperCheckTerminate(DPScout_<TDPCell, TSpec > const & /**/) in _computeAlignmentHelperCheckTerminate() 470 _computeAlignmentHelperCheckTerminate(DPScout_<TDPCell,Terminator_<TSpec> > const & s) in _computeAlignmentHelperCheckTerminate() 980 typedef typename Value<TDPScoreMatrixNavigator>::Type TDPCell; in _computeHammingDistance() typedef
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H A D | dp_matrix_navigator_score_matrix.h | 387 _preInitCacheDiagonal(TDPCell & /*cacheDiagonal*/, in _preInitCacheDiagonal() argument
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/align/ |
H A D | dp_scout.h | 204 _scoutBestScore(DPScout_<TDPCell, TSpec> & dpScout, in _scoutBestScore() 221 _scoutBestScore(DPScout_<TDPCell, TSpec> & dpScout, in _scoutBestScore() 233 _scoutBestScore(DPScout_<TDPCell, TSpec> & dpScout, in _scoutBestScore() 247 maxScore(DPScout_<TDPCell, TScoutSpec> const & dpScout) in maxScore() 259 maxHostPosition(DPScout_<TDPCell, TScoutSpec> const & dpScout) in maxHostPosition() 270 _terminationCriteriumIsMet(DPScout_<TDPCell, Terminator_<TSpec> > const & scout) in _terminationCriteriumIsMet() 281 terminateScout(DPScout_<TDPCell, Terminator_<TSpec> > & scout) in terminateScout()
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H A D | dp_algorithm_impl.h | 429 _computeAlignmentHelperCheckTerminate(DPScout_<TDPCell, TSpec > const & /**/) in _computeAlignmentHelperCheckTerminate() 436 _computeAlignmentHelperCheckTerminate(DPScout_<TDPCell,Terminator_<TSpec> > const & s) in _computeAlignmentHelperCheckTerminate() 1199 typedef typename Value<TDPScoreMatrixNavigator>::Type TDPCell; in _computeHammingDistance() typedef
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/tests/align/ |
H A D | test_alignment_dp_matrix_navigator.h | 73 typedef Value<TDPMatrix>::Type TDPCell; in testAlignmentDPMatrixNavigatorScoreMarixInitUnbanded() typedef 93 typedef Value<TDPMatrix>::Type TDPCell; in testAlignmentDPMatrixNavigatorScoreMarixSparseInitUnbanded() typedef 116 typedef Value<TDPMatrix>::Type TDPCell; in testAlignmentDPMatrixNavigatorScoreMarixInitBanded() typedef 170 typedef Value<TDPMatrix>::Type TDPCell; in testAlignmentDPMatrixNavigatorScoreMarixSparseInitBanded() typedef 221 typedef Value<TDPMatrix>::Type TDPCell; in testAlignmentDPMatrixNavigatorScoreMarixGoNextCell() typedef 291 typedef Value<TDPMatrix>::Type TDPCell; in testAlignmentDPMatrixNavigatorScoreMarixSparseGoNextCell() typedef 362 typedef typename Value<TDPMatrix>::Type TDPCell; in testAlignmentDPScoreMatrixNavigatorAssignValue() typedef 384 typedef typename Value<TDPMatrix>::Type TDPCell; in testAlignmentDPScoreMatrixNavigatorValue() typedef 411 typedef typename Value<TDPMatrix>::Type TDPCell; in testAlignmentDPScoreMatrixNavigatorPreviousCellHorizontal() typedef 437 typedef typename Value<TDPMatrix>::Type TDPCell; in testAlignmentDPScoreMatrixNavigatorCoordinate() typedef [all …]
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H A D | test_alignment_dp_cell.h | 47 typedef DPCell_<int, TGapCosts> TDPCell; in testDPCellValue() typedef 63 typedef DPCell_<int, TGapCosts> TDPCell; in testDPCellReference() typedef 80 typedef DPCell_<int, TGapCosts> TDPCell; in testDPCellDefaultInfinity() typedef
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H A D | test_alignment_dp_formula.h | 1585 typedef DPCell_<int, DynamicGaps> TDPCell; in SEQAN_DEFINE_TEST() typedef 1674 typedef DPCell_<int, DynamicGaps> TDPCell; in SEQAN_DEFINE_TEST() typedef 1795 typedef DPCell_<int, DynamicGaps> TDPCell; in SEQAN_DEFINE_TEST() typedef 1893 typedef DPCell_<int, DynamicGaps> TDPCell; in SEQAN_DEFINE_TEST() typedef
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/align_split/ |
H A D | dp_scout_split.h | 105 _scoutBestScore(DPScout_<TDPCell, SplitAlignmentScout> & dpScout, 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 | 106 _scoutBestScore(DPScout_<TDPCell, SplitAlignmentScout> & dpScout, 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 | 106 _scoutBestScore(DPScout_<TDPCell, SplitAlignmentScout> & dpScout, in _scoutBestScore()
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/align_parallel/ |
H A D | wavefront_alignment_task.h | 63 using TDPCell = DPCell_<TScoreValue, TGapType>; member 158 using TDPCell = typename TWatc::TDPCell; in createBlockBuffer() local
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/align_parallel/ |
H A D | wavefront_alignment_task.h | 63 using TDPCell = DPCell_<TScoreValue, TGapType>; member 158 using TDPCell = typename TWatc::TDPCell; in createBlockBuffer() local
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/seeds/ |
H A D | banded_chain_alignment_impl.h | 257 _verticalCellInitialization(DPScout_<TDPCell, BandedChainAlignmentScout> const & dpScout, in _verticalCellInitialization() 271 _horizontalCellInitialization(DPScout_<TDPCell, BandedChainAlignmentScout> const & dpScout, in _horizontalCellInitialization() 757 typedef typename Value<TInitCell, 3>::Type TDPCell; in _initiaizeBeginningOfBandedChain() typedef 1292 typedef DPCell_<TScoreValue, TGapSpec> TDPCell; in _computeAlignment() typedef
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/seeds/ |
H A D | banded_chain_alignment_impl.h | 257 _verticalCellInitialization(DPScout_<TDPCell, BandedChainAlignmentScout> const & dpScout, in _verticalCellInitialization() 271 _horizontalCellInitialization(DPScout_<TDPCell, BandedChainAlignmentScout> const & dpScout, in _horizontalCellInitialization() 757 typedef typename Value<TInitCell, 3>::Type TDPCell; in _initiaizeBeginningOfBandedChain() typedef 1292 typedef DPCell_<TScoreValue, TGapSpec> TDPCell; in _computeAlignment() typedef
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/seeds/ |
H A D | banded_chain_alignment_impl.h | 241 _verticalCellInitialization(DPScout_<TDPCell, BandedChainAlignmentScout> const & dpScout, in _verticalCellInitialization() 255 _horizontalCellInitialization(DPScout_<TDPCell, BandedChainAlignmentScout> const & dpScout, in _horizontalCellInitialization() 676 typedef typename Value<TInitCell, 3>::Type TDPCell; in _initiaizeBeginningOfBandedChain() typedef 1199 typedef DPCell_<TScoreValue, TGapSpec> TDPCell; in _computeAlignment() typedef
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