/dports/biology/seqan/seqan-library-2.4.0/include/seqan/align/ |
H A D | dp_cell.h | 220 template <typename TScoreValue, typename TGapSpec> 221 inline typename Reference<DPCell_<TScoreValue, TGapSpec> >::Type 222 _verticalScoreOfCell(DPCell_<TScoreValue, TGapSpec> & dpCell) 227 template <typename TScoreValue, typename TGapSpec> 239 template <typename TScoreValue, typename TGapSpec> 258 template <typename TScoreValue, typename TGapSpec> 260 _horizontalScoreOfCell(DPCell_<TScoreValue, TGapSpec> & dpCell) 265 template <typename TScoreValue, typename TGapSpec> 277 template <typename TScoreValue, typename TGapSpec> 320 template <typename TScoreValue, typename TGapSpec, [all …]
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H A D | dp_setup.h | 267 template <typename TScoreValue, typename TGapSpec, typename TTraceValue, typename TScoreMat, typena… 275 _setUpAndRunAlignment(DPContext<DPCell_<TScoreValue, TGapSpec>, TTraceValue, TScoreMat, TTraceMat> … 286 …typedef typename SetupAlignmentProfile_<TDPType, TFreeEndGaps, TGapSpec, TTraceConfig>::Type TDPPr… 329 template <typename TScoreValue, typename TGapSpec, typename TTraceValue, typename TScoreMat, typena… 337 _setUpAndRunAlignment(DPContext<DPCell_<TScoreValue, TGapSpec>, TTraceValue, TScoreMat, TTraceMat> … 348 …typedef typename SetupAlignmentProfile_<TDPType, TFreeEndGaps, TGapSpec, TTraceConfig>::Type TDPPr…
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H A D | dp_profile.h | 566 template <typename TAlgorithm, typename TGapSpec, typename TTraceConfig, typename TExecPolicy> 567 struct IsGapsLeft_<DPProfile_<TAlgorithm, TGapSpec, TTraceConfig, TExecPolicy> > 582 template <typename TAlgorithm, typename TGapSpec, typename TTraceConfig, typename TExecPolicy> 583 struct IsSingleTrace_<DPProfile_<TAlgorithm, TGapSpec, TTraceConfig, TExecPolicy> > : IsSingleTrace… 595 template <typename TAlignmentSpec, typename TGapSpec, typename TTracebackSpec, typename TExecPolicy… 596 struct IsFreeEndGap_<DPProfile_<TAlignmentSpec, TGapSpec, TTracebackSpec, TExecPolicy> const, TDPSi… 599 template <typename TAlignmentSpec, typename TGapSpec, typename TTracebackSpec, typename TExecPolicy… 600 struct IsFreeEndGap_<DPProfile_<TAlignmentSpec, TGapSpec, TTracebackSpec, TExecPolicy>, TDPSide>:
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H A D | dp_meta_info.h | 457 template <typename TAlgo, typename TGapSpec, typename TTraceSpec, typename TColumnDescriptor> 458 struct LastColumnEnabled_<DPProfile_<TAlgo, TGapSpec, TTraceSpec>, TColumnDescriptor> : 474 template <typename TAlgo, typename TGapSpec, typename TTraceSpec, typename TCellDescriptor, typenam… 475 struct LastRowEnabled_<DPProfile_<TAlgo, TGapSpec, TTraceSpec>, TCellDescriptor, TColumnDescriptor>…
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H A D | dp_scout_simd.h | 137 template <typename TValue, typename TGapSpec, typename TSpec, 141 _copySimdCell(DPScout_<DPCell_<TValue, TGapSpec>, SimdAlignmentScout<TSpec> > & dpScout, 142 DPCell_<TValue, TGapSpec> const & activeCell,
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/align/ |
H A D | dp_cell.h | 220 template <typename TScoreValue, typename TGapSpec> 221 inline typename Reference<DPCell_<TScoreValue, TGapSpec> >::Type 222 _verticalScoreOfCell(DPCell_<TScoreValue, TGapSpec> & dpCell) 227 template <typename TScoreValue, typename TGapSpec> 239 template <typename TScoreValue, typename TGapSpec> 258 template <typename TScoreValue, typename TGapSpec> 260 _horizontalScoreOfCell(DPCell_<TScoreValue, TGapSpec> & dpCell) 265 template <typename TScoreValue, typename TGapSpec> 277 template <typename TScoreValue, typename TGapSpec> 320 template <typename TScoreValue, typename TGapSpec, [all …]
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H A D | dp_setup.h | 267 template <typename TScoreValue, typename TGapSpec, typename TTraceValue, typename TScoreMat, typena… 275 _setUpAndRunAlignment(DPContext<DPCell_<TScoreValue, TGapSpec>, TTraceValue, TScoreMat, TTraceMat> … 286 …typedef typename SetupAlignmentProfile_<TDPType, TFreeEndGaps, TGapSpec, TTraceConfig>::Type TDPPr… 329 template <typename TScoreValue, typename TGapSpec, typename TTraceValue, typename TScoreMat, typena… 337 _setUpAndRunAlignment(DPContext<DPCell_<TScoreValue, TGapSpec>, TTraceValue, TScoreMat, TTraceMat> … 348 …typedef typename SetupAlignmentProfile_<TDPType, TFreeEndGaps, TGapSpec, TTraceConfig>::Type TDPPr…
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H A D | dp_profile.h | 566 template <typename TAlgorithm, typename TGapSpec, typename TTraceConfig, typename TExecPolicy> 567 struct IsGapsLeft_<DPProfile_<TAlgorithm, TGapSpec, TTraceConfig, TExecPolicy> > 582 template <typename TAlgorithm, typename TGapSpec, typename TTraceConfig, typename TExecPolicy> 583 struct IsSingleTrace_<DPProfile_<TAlgorithm, TGapSpec, TTraceConfig, TExecPolicy> > : IsSingleTrace… 595 template <typename TAlignmentSpec, typename TGapSpec, typename TTracebackSpec, typename TExecPolicy… 596 struct IsFreeEndGap_<DPProfile_<TAlignmentSpec, TGapSpec, TTracebackSpec, TExecPolicy> const, TDPSi… 599 template <typename TAlignmentSpec, typename TGapSpec, typename TTracebackSpec, typename TExecPolicy… 600 struct IsFreeEndGap_<DPProfile_<TAlignmentSpec, TGapSpec, TTracebackSpec, TExecPolicy>, TDPSide>:
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H A D | dp_meta_info.h | 457 template <typename TAlgo, typename TGapSpec, typename TTraceSpec, typename TColumnDescriptor> 458 struct LastColumnEnabled_<DPProfile_<TAlgo, TGapSpec, TTraceSpec>, TColumnDescriptor> : 474 template <typename TAlgo, typename TGapSpec, typename TTraceSpec, typename TCellDescriptor, typenam… 475 struct LastRowEnabled_<DPProfile_<TAlgo, TGapSpec, TTraceSpec>, TCellDescriptor, TColumnDescriptor>…
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H A D | dp_scout_simd.h | 137 template <typename TValue, typename TGapSpec, typename TSpec, 141 _copySimdCell(DPScout_<DPCell_<TValue, TGapSpec>, SimdAlignmentScout<TSpec> > & dpScout, 142 DPCell_<TValue, TGapSpec> const & activeCell,
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/align/ |
H A D | dp_cell.h | 168 template <typename TScoreValue, typename TGapSpec> 169 inline typename Reference<DPCell_<TScoreValue, TGapSpec> >::Type 170 _verticalScoreOfCell(DPCell_<TScoreValue, TGapSpec> & dpCell) 175 template <typename TScoreValue, typename TGapSpec> 177 _verticalScoreOfCell(DPCell_<TScoreValue, TGapSpec> const & dpCell) 187 template <typename TScoreValue, typename TGapSpec> 199 template <typename TScoreValue, typename TGapSpec> 200 inline typename Reference<DPCell_<TScoreValue, TGapSpec> >::Type 201 _horizontalScoreOfCell(DPCell_<TScoreValue, TGapSpec> & dpCell) 206 template <typename TScoreValue, typename TGapSpec> [all …]
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H A D | dp_profile.h | 389 template <typename TAlgorithm, typename TGapSpec, typename TTraceConfig> 390 struct IsGapsLeft_<DPProfile_<TAlgorithm, TGapSpec, TTraceConfig> > 404 template <typename TAlgorithm, typename TGapSpec, typename TTraceConfig> 405 struct IsSingleTrace_<DPProfile_<TAlgorithm, TGapSpec, TTraceConfig> > 417 template <typename TAlignmentSpec, typename TGapSpec, typename TTracebackSpec, typename TDPSide> 418 struct IsFreeEndGap_<DPProfile_<TAlignmentSpec, TGapSpec, TTracebackSpec> const, TDPSide>: 421 template <typename TAlignmentSpec, typename TGapSpec, typename TTracebackSpec, typename TDPSide> 422 struct IsFreeEndGap_<DPProfile_<TAlignmentSpec, TGapSpec, TTracebackSpec>, TDPSide>:
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/tests/seeds/ |
H A D | test_align_banded_chain_impl.cpp | 952 template <typename TGapSpec> 953 void testBandedChainAlignmentBandExtension(TGapSpec) in testBandedChainAlignmentBandExtension() argument 966 if (IsSameType<TGapSpec, AffineGaps>::VALUE) in testBandedChainAlignmentBandExtension() 978 if (IsSameType<TGapSpec, LinearGaps>::VALUE) in testBandedChainAlignmentBandExtension()
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/seeds/ |
H A D | banded_chain_alignment_impl.h | 1181 typename TGapSpec, typename TTracebackConfig> 1190 DPProfile_<BandedChainAlignment_<TFreeEndGaps, TDPMatrixLocation>, TGapSpec, in _computeAlignment() argument 1199 typedef DPCell_<TScoreValue, TGapSpec> TDPCell; in _computeAlignment() 1245 … BandedChainFinalDPMatrix>, TGapSpec, TracebackOn<TTracebackConfig> >()); in _computeAlignment()
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/seeds/ |
H A D | banded_chain_alignment_impl.h | 1276 typename TGapSpec, typename TTracebackConfig, typename TExecPolicy> 1285 DPProfile_<BandedChainAlignment_<TFreeEndGaps, TDPMatrixLocation>, TGapSpec, in _computeAlignment() argument 1292 typedef DPCell_<TScoreValue, TGapSpec> TDPCell; in _computeAlignment() 1338 … BandedChainFinalDPMatrix>, TGapSpec, TracebackOn<TTracebackConfig>, TExecPolicy>()); in _computeAlignment()
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/seeds/ |
H A D | banded_chain_alignment_impl.h | 1276 typename TGapSpec, typename TTracebackConfig, typename TExecPolicy> 1285 DPProfile_<BandedChainAlignment_<TFreeEndGaps, TDPMatrixLocation>, TGapSpec, in _computeAlignment() argument 1292 typedef DPCell_<TScoreValue, TGapSpec> TDPCell; in _computeAlignment() 1338 … BandedChainFinalDPMatrix>, TGapSpec, TracebackOn<TTracebackConfig>, TExecPolicy>()); in _computeAlignment()
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