| /dports/biology/seqan/seqan-library-2.4.0/include/seqan/align_parallel/ |
| H A D | async_wave_execution_interface.h | 58 template <typename TSeqH, typename TSeqV, typename TSettings>
63 using TAlignmentTask = WavefrontAlignmentTask<TSeqH, TSeqV, TSettings>;
97 typename TSeqV,
102 TSeqV const & seqV, in submit()
135 template <typename TSeqH, typename TSeqV, typename TSettings, typename TWaveSpec>
143 using TAlignmentTask = WavefrontAlignmentTask<TSeqH, TSeqV, TSimdSettings,
183 typename TSeqV,
188 TSeqV const & seqV, in submit()
232 using TSeqV = typename Value<TSetV const>::Type; in alignExecBatch() local
237 AsyncWaveAlignExecutor<TSeqH, TSeqV, TSettings>>; in alignExecBatch()
[all …]
|
| H A D | wavefront_alignment_task.h | 248 typename TSeqV,
258 …using TSeqVBlocks = decltype(TIncubator::createBlocks(std::declval<TSeqV>(), std::declval<size_t…
271 TSeqV const & seqV;
282 TSeqV const & seqV, in WavefrontAlignmentTask()
294 TSeqV const & seqV, in WavefrontAlignmentTask()
|
| H A D | wavefront_task_util.h | 444 using TSeqV = typename TExecTraits::TSeqV;
449 StringSet<TSeqV, Dependent<> > depSetV;
|
| H A D | wavefront_task.h | 134 using TSeqV = typename Value<TSeqVBlocks>::Type;
|
| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/align_parallel/ |
| H A D | async_wave_execution_interface.h | 58 template <typename TSeqH, typename TSeqV, typename TSettings>
63 using TAlignmentTask = WavefrontAlignmentTask<TSeqH, TSeqV, TSettings>;
97 typename TSeqV,
102 TSeqV const & seqV, in submit()
135 template <typename TSeqH, typename TSeqV, typename TSettings, typename TWaveSpec>
143 using TAlignmentTask = WavefrontAlignmentTask<TSeqH, TSeqV, TSimdSettings,
183 typename TSeqV,
188 TSeqV const & seqV, in submit()
232 using TSeqV = typename Value<TSetV const>::Type; in alignExecBatch() local
237 AsyncWaveAlignExecutor<TSeqH, TSeqV, TSettings>>; in alignExecBatch()
[all …]
|
| H A D | wavefront_alignment_task.h | 248 typename TSeqV,
258 …using TSeqVBlocks = decltype(TIncubator::createBlocks(std::declval<TSeqV>(), std::declval<size_t…
271 TSeqV const & seqV;
282 TSeqV const & seqV, in WavefrontAlignmentTask()
294 TSeqV const & seqV, in WavefrontAlignmentTask()
|
| H A D | wavefront_task_util.h | 444 using TSeqV = typename TExecTraits::TSeqV;
449 StringSet<TSeqV, Dependent<> > depSetV;
|
| /dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/seeds/ |
| H A D | banded_chain_alignment_impl.h | 719 template <typename TTraceSet, typename TScoutState, typename TSeed, typename TSeqH, typename TSeqV,
728 TSeqV const & seqV, in _initializeBandedChain()
734 typedef typename Infix<TSeqV const>::Type TInfixV; in _initializeBandedChain()
879 …mplate <typename TTraceSet, typename TDPScoutState, typename TSeed, typename TSeqH, typename TSeqV,
887 TSeqV const & seqV, in _computeGapArea()
892 typedef typename Infix<TSeqV const>::Type TInfixV; in _computeGapArea()
894 typedef typename Position<TSeqV>::Type TPosV; in _computeGapArea()
946 TSeqV const & seqV, in _computeAnchorArea()
951 typedef typename Infix<TSeqV const>::Type TInfixV; in _computeAnchorArea()
1018 TSeqV const & seqV, in _finishBandedChain()
[all …]
|
| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/seeds/ |
| H A D | banded_chain_alignment_impl.h | 807 template <typename TTraceSet, typename TScoutState, typename TSeed, typename TSeqH, typename TSeqV,
816 TSeqV const & seqV, in _initializeBandedChain()
822 typedef typename Infix<TSeqV const>::Type TInfixV; in _initializeBandedChain()
968 …mplate <typename TTraceSet, typename TDPScoutState, typename TSeed, typename TSeqH, typename TSeqV,
977 TSeqV const & seqV, in _computeGapArea()
982 typedef typename Infix<TSeqV const>::Type TInfixV; in _computeGapArea()
984 typedef typename Position<TSeqV>::Type TPosV; in _computeGapArea()
1039 TSeqV const & seqV, in _computeAnchorArea()
1044 typedef typename Infix<TSeqV const>::Type TInfixV; in _computeAnchorArea()
1112 TSeqV const & seqV, in _finishBandedChain()
[all …]
|
| /dports/biology/seqan/seqan-library-2.4.0/include/seqan/seeds/ |
| H A D | banded_chain_alignment_impl.h | 807 template <typename TTraceSet, typename TScoutState, typename TSeed, typename TSeqH, typename TSeqV,
816 TSeqV const & seqV, in _initializeBandedChain()
822 typedef typename Infix<TSeqV const>::Type TInfixV; in _initializeBandedChain()
968 …mplate <typename TTraceSet, typename TDPScoutState, typename TSeed, typename TSeqH, typename TSeqV,
977 TSeqV const & seqV, in _computeGapArea()
982 typedef typename Infix<TSeqV const>::Type TInfixV; in _computeGapArea()
984 typedef typename Position<TSeqV>::Type TPosV; in _computeGapArea()
1039 TSeqV const & seqV, in _computeAnchorArea()
1044 typedef typename Infix<TSeqV const>::Type TInfixV; in _computeAnchorArea()
1112 TSeqV const & seqV, in _finishBandedChain()
[all …]
|
| /dports/biology/seqan/seqan-library-2.4.0/include/seqan/align/ |
| H A D | local_alignment_unbanded.h | 451 typename TSeqV,
456 … And<Is<ContainerConcept<TSeqV>>, Is<ContainerConcept<typename Value<TSeqV>::Type>>> in SEQAN_FUNC_ENABLE_IF() argument
459 TSeqV const & stringsV, in SEQAN_FUNC_ENABLE_IF()
|
| H A D | local_alignment_banded.h | 328 typename TSeqV,
333 … And<Is<ContainerConcept<TSeqV>>, Is<ContainerConcept<typename Value<TSeqV>::Type>>> in SEQAN_FUNC_ENABLE_IF() argument
336 TSeqV const & stringsV, in SEQAN_FUNC_ENABLE_IF()
|
| H A D | dp_setup.h | 244 template <typename TScoringScheme, typename TSeqH, typename TSeqV>
248 TSeqV const & seqV)
251 typedef typename SequenceEntryForScore<TScoringScheme, TSeqV>::Type TSequenceVEntry;
|
| H A D | dp_scout_simd.h | 73 using TSizeV = typename Size<typename TTraits::TSeqV>::Type;
753 template <typename TDPCell, typename TSeqV>
756 TSeqV const & seqV)
761 template <typename TDPCell, typename TTraits, typename TSeqV>
764 TSeqV const & /*seqV*/)
|
| H A D | dp_algorithm_impl.h | 1261 typename TSeqV,
1269 TSeqV const & /*seqV*/, in SEQAN_FUNC_ENABLE_IF()
1280 typename TSeqV,
1288 TSeqV const & seqV, in SEQAN_FUNC_ENABLE_IF()
1317 typename TSeqV,
1325 TSeqV const & seqV, in SEQAN_FUNC_ENABLE_IF()
|
| H A D | global_alignment_banded.h | 559 typename TSeqV,
564 … And<Is<ContainerConcept<TSeqV>>, Is<ContainerConcept<typename Value<TSeqV>::Type>>> in SEQAN_FUNC_ENABLE_IF() argument
568 TSeqV const & stringsV, in SEQAN_FUNC_ENABLE_IF()
|
| H A D | global_alignment_unbanded.h | 654 typename TSeqV,
659 … And<Is<ContainerConcept<TSeqV>>, Is<ContainerConcept<typename Value<TSeqV>::Type>>> in SEQAN_FUNC_ENABLE_IF() argument
663 TSeqV const & stringsV, in SEQAN_FUNC_ENABLE_IF()
|
| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/align/ |
| H A D | local_alignment_unbanded.h | 451 typename TSeqV,
456 … And<Is<ContainerConcept<TSeqV>>, Is<ContainerConcept<typename Value<TSeqV>::Type>>> in SEQAN_FUNC_ENABLE_IF() argument
459 TSeqV const & stringsV, in SEQAN_FUNC_ENABLE_IF()
|
| H A D | local_alignment_banded.h | 328 typename TSeqV,
333 … And<Is<ContainerConcept<TSeqV>>, Is<ContainerConcept<typename Value<TSeqV>::Type>>> in SEQAN_FUNC_ENABLE_IF() argument
336 TSeqV const & stringsV, in SEQAN_FUNC_ENABLE_IF()
|
| H A D | dp_setup.h | 244 template <typename TScoringScheme, typename TSeqH, typename TSeqV>
248 TSeqV const & seqV)
251 typedef typename SequenceEntryForScore<TScoringScheme, TSeqV>::Type TSequenceVEntry;
|
| H A D | dp_scout_simd.h | 73 using TSizeV = typename Size<typename TTraits::TSeqV>::Type;
753 template <typename TDPCell, typename TSeqV>
756 TSeqV const & seqV)
761 template <typename TDPCell, typename TTraits, typename TSeqV>
764 TSeqV const & /*seqV*/)
|
| H A D | dp_algorithm_impl.h | 1261 typename TSeqV,
1269 TSeqV const & /*seqV*/, in SEQAN_FUNC_ENABLE_IF()
1280 typename TSeqV,
1288 TSeqV const & seqV, in SEQAN_FUNC_ENABLE_IF()
1317 typename TSeqV,
1325 TSeqV const & seqV, in SEQAN_FUNC_ENABLE_IF()
|
| H A D | global_alignment_banded.h | 559 typename TSeqV,
564 … And<Is<ContainerConcept<TSeqV>>, Is<ContainerConcept<typename Value<TSeqV>::Type>>> in SEQAN_FUNC_ENABLE_IF() argument
568 TSeqV const & stringsV, in SEQAN_FUNC_ENABLE_IF()
|
| H A D | global_alignment_unbanded.h | 654 typename TSeqV,
659 … And<Is<ContainerConcept<TSeqV>>, Is<ContainerConcept<typename Value<TSeqV>::Type>>> in SEQAN_FUNC_ENABLE_IF() argument
663 TSeqV const & stringsV, in SEQAN_FUNC_ENABLE_IF()
|
| /dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/align/ |
| H A D | dp_setup.h | 244 template <typename TScoringScheme, typename TSeqH, typename TSeqV>
248 TSeqV const & seqV)
251 typedef typename SequenceEntryForScore<TScoringScheme, TSeqV>::Type TSequenceVEntry;
|