Home
last modified time | relevance | path

Searched refs:TGapSpec (Results 1 – 16 of 16) sorted by relevance

/dports/biology/seqan/seqan-library-2.4.0/include/seqan/align/
H A Ddp_cell.h220 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 …]
H A Ddp_setup.h267 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…
H A Ddp_profile.h566 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>:
H A Ddp_meta_info.h457 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>…
H A Ddp_scout_simd.h137 template <typename TValue, typename TGapSpec, typename TSpec,
141 _copySimdCell(DPScout_<DPCell_<TValue, TGapSpec>, SimdAlignmentScout<TSpec> > & dpScout,
142 DPCell_<TValue, TGapSpec> const & activeCell,
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/align/
H A Ddp_cell.h220 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 …]
H A Ddp_setup.h267 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…
H A Ddp_profile.h566 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>:
H A Ddp_meta_info.h457 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>…
H A Ddp_scout_simd.h137 template <typename TValue, typename TGapSpec, typename TSpec,
141 _copySimdCell(DPScout_<DPCell_<TValue, TGapSpec>, SimdAlignmentScout<TSpec> > & dpScout,
142 DPCell_<TValue, TGapSpec> const & activeCell,
/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/align/
H A Ddp_cell.h168 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 …]
H A Ddp_profile.h389 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>:
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/tests/seeds/
H A Dtest_align_banded_chain_impl.cpp952 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()
/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/seeds/
H A Dbanded_chain_alignment_impl.h1181 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()
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/seeds/
H A Dbanded_chain_alignment_impl.h1276 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()
/dports/biology/seqan/seqan-library-2.4.0/include/seqan/seeds/
H A Dbanded_chain_alignment_impl.h1276 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()