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Searched refs:TDPProfile (Results 1 – 25 of 51) sorted by relevance

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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/tests/align/
H A Dtest_alignment_dp_profile.h180 bool result0 = IsGlobalAlignment_<TDPProfile>::VALUE; in testAlignmentDPProfileIsGlobal()
190 bool result0 = IsGlobalAlignment_<TDPProfile>::VALUE; in testAlignmentDPProfileIsGlobal()
200 bool result0 = IsGlobalAlignment_<TDPProfile>::VALUE; in testAlignmentDPProfileIsGlobal()
210 bool result0 = IsGlobalAlignment_<TDPProfile>::VALUE; in testAlignmentDPProfileIsGlobal()
225 bool result0 = IsLocalAlignment_<TDPProfile>::VALUE; in testAlignmentDPProfileIsLocal()
235 bool result0 = IsLocalAlignment_<TDPProfile>::VALUE; in testAlignmentDPProfileIsLocal()
245 bool result0 = IsLocalAlignment_<TDPProfile>::VALUE; in testAlignmentDPProfileIsLocal()
255 bool result0 = IsLocalAlignment_<TDPProfile>::VALUE; in testAlignmentDPProfileIsLocal()
270 bool result0 = IsTracebackEnabled_<TDPProfile>::VALUE; in testAlignmetnDPProfileIsTracebackEnabled()
280 bool result0 = IsTracebackEnabled_<TDPProfile>::VALUE; in testAlignmetnDPProfileIsTracebackEnabled()
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H A Dtest_alignment_algorithms_band_position.h45 typedef DPProfile_<GlobalAlignment_<>, LinearGaps, TracebackOn<> > TDPProfile; in SEQAN_DEFINE_TEST() typedef
110 typedef DPProfile_<GlobalAlignment_<>, LinearGaps, TracebackOn<> > TDPProfile; in SEQAN_DEFINE_TEST() typedef
173 typedef DPProfile_<GlobalAlignment_<>, LinearGaps, TracebackOn<> > TDPProfile; in SEQAN_DEFINE_TEST() typedef
235 typedef DPProfile_<GlobalAlignment_<>, LinearGaps, TracebackOn<> > TDPProfile; in SEQAN_DEFINE_TEST() typedef
296 typedef DPProfile_<GlobalAlignment_<>, LinearGaps, TracebackOn<> > TDPProfile; in SEQAN_DEFINE_TEST() typedef
382 TDPProfile()); in SEQAN_DEFINE_TEST()
446 TDPProfile()); in SEQAN_DEFINE_TEST()
507 TDPProfile()); in SEQAN_DEFINE_TEST()
693 TDPProfile()); in SEQAN_DEFINE_TEST()
880 TDPProfile()); in SEQAN_DEFINE_TEST()
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H A Dtest_alignment_dp_traceback.h45 typedef DPProfile_<GlobalAlignment_<>, AffineGaps, TracebackOn<> > TDPProfile; in SEQAN_DEFINE_TEST() typedef
87 … _computeTraceback(target, navigator, dpScout, str0, str1, DPBandConfig<BandOff>(), TDPProfile()); in SEQAN_DEFINE_TEST()
93 … _computeTraceback(target, navigator, dpScout, str0, str1, DPBandConfig<BandOff>(), TDPProfile()); in SEQAN_DEFINE_TEST()
101 … _computeTraceback(target, navigator, dpScout, str0, str1, DPBandConfig<BandOff>(), TDPProfile()); in SEQAN_DEFINE_TEST()
110 … _computeTraceback(target, navigator, dpScout, str0, str1, DPBandConfig<BandOff>(), TDPProfile()); in SEQAN_DEFINE_TEST()
144 typedef DPProfile_<GlobalAlignment_<>, LinearGaps, TracebackOn<> > TDPProfile; in SEQAN_DEFINE_TEST() typedef
198 typedef DPProfile_<GlobalAlignment_<>, LinearGaps, TracebackOn<> > TDPProfile; in SEQAN_DEFINE_TEST() typedef
254 typedef DPProfile_<GlobalAlignment_<>, LinearGaps, TracebackOn<> > TDPProfile; in SEQAN_DEFINE_TEST() typedef
344 typedef DPProfile_<GlobalAlignment_<>, LinearGaps, TracebackOn<> > TDPProfile; in SEQAN_DEFINE_TEST() typedef
383 typedef DPProfile_<GlobalAlignment_<>, LinearGaps, TracebackOn<> > TDPProfile; in SEQAN_DEFINE_TEST() typedef
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/align/
H A Ddp_meta_info.h170 template <typename TDPProfile, typename TColumnDescriptor>
178 template <typename TDPProfile, typename TColumnType>
206 typedef typename If<Or<IsLocalAlignment_<TDPProfile>,
210 typedef typename If<Or<IsLocalAlignment_<TDPProfile>,
214 typedef typename If<Or<IsLocalAlignment_<TDPProfile>,
227 template <typename TDPProfile, typename TColumnType>
257 typedef typename If<Or<IsLocalAlignment_<TDPProfile>,
261 typedef typename If<Or<IsLocalAlignment_<TDPProfile>,
265 typedef typename If<Or<IsLocalAlignment_<TDPProfile>,
279 template <typename TDPProfile, typename TColumnType>
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H A Ddp_algorithm_impl.h253 typename TCellDescriptor, typename TDPProfile>
266 TDPProfile const &) in _computeCell()
268 typedef DPMetaColumn_<TDPProfile, TColumnDescriptor> TMetaColumn; in _computeCell()
272 TDPProfile())); in _computeCell()
306 TDPProfile const &) in _computeTrack()
316 TColumnDescriptor(), FirstCell(), TDPProfile()); in _computeTrack()
333 TColumnDescriptor(), InnerCell(), TDPProfile()); in _computeTrack()
345 TColumnDescriptor(), LastCell(), TDPProfile()); in _computeTrack()
535 typedef DPProfile_<TAlignmentAlgo, TGapCosts, TTraceFlag> TDPProfile; in _computeBandedAlignment() typedef
1200 typedef DPProfile_<TAlignmentAlgo, TGapCosts, TTraceFlag> TDPProfile; in _computeHammingDistance() typedef
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H A Ddp_formula.h148 typename TScoringScheme, typename TRecursionDirection, typename TDPProfile>
158 TDPProfile const & dpProfile) in _computeScore()
164 if (IsLocalAlignment_<TDPProfile>::VALUE) in _computeScore()
181 typename TDPProfile>
191 TDPProfile const &) in _doComputeScore()
195 if (!IsTracebackEnabled_<TDPProfile>::VALUE) in _doComputeScore()
H A Ddp_setup.h281 … typename SetupAlignmentProfile_<TDPType, TFreeEndGaps, AffineGaps, TTraceConfig>::Type TDPProfile;
283 TDPProfile());
301 … typename SetupAlignmentProfile_<TDPType, TFreeEndGaps, LinearGaps, TTraceConfig>::Type TDPProfile;
303 TDPProfile());
321 …typename SetupAlignmentProfile_<TDPType, TFreeEndGaps, DynamicGaps, TTraceConfig>::Type TDPProfile;
323 TDPProfile());
/dports/biology/seqan/seqan-library-2.4.0/include/seqan/align/
H A Ddp_meta_info.h170 template <typename TDPProfile, typename TColumnDescriptor>
178 template <typename TDPProfile, typename TColumnType>
206 typedef typename If<Or<IsLocalAlignment_<TDPProfile>,
210 typedef typename If<Or<IsLocalAlignment_<TDPProfile>,
214 typedef typename If<Or<IsLocalAlignment_<TDPProfile>,
227 template <typename TDPProfile, typename TColumnType>
257 typedef typename If<Or<IsLocalAlignment_<TDPProfile>,
261 typedef typename If<Or<IsLocalAlignment_<TDPProfile>,
265 typedef typename If<Or<IsLocalAlignment_<TDPProfile>,
279 template <typename TDPProfile, typename TColumnType>
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H A Ddp_algorithm_impl.h279 typename TCellDescriptor, typename TDPProfile>
292 TDPProfile const &) in _computeCell()
294 typedef DPMetaColumn_<TDPProfile, TColumnDescriptor> TMetaColumn; in _computeCell()
299 TDPProfile())); in _computeCell()
307 if (IsTracebackEnabled_<TDPProfile>::VALUE) in _computeCell()
343 typename TDPProfile>
356 TDPProfile const &) in _computeTrack()
379 TColumnDescriptor(), FirstCell(), TDPProfile()); in _computeTrack()
425 TColumnDescriptor(), LastCell(), TDPProfile()); in _computeTrack()
436 typename TDPProfile>
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/align/
H A Ddp_meta_info.h170 template <typename TDPProfile, typename TColumnDescriptor>
178 template <typename TDPProfile, typename TColumnType>
206 typedef typename If<Or<IsLocalAlignment_<TDPProfile>,
210 typedef typename If<Or<IsLocalAlignment_<TDPProfile>,
214 typedef typename If<Or<IsLocalAlignment_<TDPProfile>,
227 template <typename TDPProfile, typename TColumnType>
257 typedef typename If<Or<IsLocalAlignment_<TDPProfile>,
261 typedef typename If<Or<IsLocalAlignment_<TDPProfile>,
265 typedef typename If<Or<IsLocalAlignment_<TDPProfile>,
279 template <typename TDPProfile, typename TColumnType>
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H A Ddp_algorithm_impl.h279 typename TCellDescriptor, typename TDPProfile>
292 TDPProfile const &) in _computeCell()
294 typedef DPMetaColumn_<TDPProfile, TColumnDescriptor> TMetaColumn; in _computeCell()
299 TDPProfile())); in _computeCell()
307 if (IsTracebackEnabled_<TDPProfile>::VALUE) in _computeCell()
343 typename TDPProfile>
356 TDPProfile const &) in _computeTrack()
379 TColumnDescriptor(), FirstCell(), TDPProfile()); in _computeTrack()
425 TColumnDescriptor(), LastCell(), TDPProfile()); in _computeTrack()
436 typename TDPProfile>
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/align_split/
H A Dalign_split_interface.h148 typedef DPProfile_<SplitAlignment_<TSpec>, TGapCosts, TTraceFlag> TDPProfile;
149 typedef typename IsLocalAlignment_<TDPProfile>::Type TIsLocal;
158 …typename If<IsFreeEndGap_<TDPProfile, DPFirstColumn>, RecursionDirectionZero, RecursionDirectionVe…
161 …typename If<IsFreeEndGap_<TDPProfile, DPFirstColumn>, RecursionDirectionZero, RecursionDirectionVe…
173 typedef DPProfile_<SplitAlignment_<TSpec>, TGapCosts, TTraceFlag> TDPProfile;
174 typedef typename IsLocalAlignment_<TDPProfile>::Type TIsLocal;
185 …typename If<IsFreeEndGap_<TDPProfile, DPFirstColumn>, RecursionDirectionZero, RecursionDirectionVe…
199 typedef DPProfile_<SplitAlignment_<TSpec>, TGapCosts, TTraceFlag> TDPProfile;
200 typedef typename IsLocalAlignment_<TDPProfile>::Type TIsLocal;
222 typedef DPProfile_<SplitAlignment_<TSpec>, TGapCosts, TTraceFlag> TDPProfile;
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/align_parallel/
H A Ddp_kernel_adaptor.h106 …typedef DPProfile_<TAlgo, TGapCosts, TTraceConfig, Parallel> TDPProfile;
107 …typedef DPMetaColumn_<TDPProfile, MetaColumnDescriptor<DPInitialColumn, FullColumn> > TMetaColum…
176 …typedef DPProfile_<TAlgo, TGapCosts, TTraceConfig, Parallel> TDPProfile;
177 …typedef DPMetaColumn_<TDPProfile, MetaColumnDescriptor<DPInnerColumn, FullColumn> > TMetaColum…
182 TDPProfile()));
226 …typedef DPProfile_<TAlgo, TGapCosts, TTraceConfig, Parallel> TDPProfile;
227 …typedef DPMetaColumn_<TDPProfile, MetaColumnDescriptor<DPFinalColumn, FullColumn> > TMetaColum…
272 …typedef DPProfile_<TAlgo, TGapCosts, TTraceConfig, Parallel> TDPProfile;
278 TDPProfile()));
320 …typedef DPProfile_<TAlgo, TGapCosts, TTraceConfig, Parallel> TDPProfile;
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H A Dwavefront_alignment_task.h69 using TDPProfile = DPProfile_<TAlgorithmType, TGapType, TTracebackType, Parallel>; member
165 …using TDPMetaColH = DPMetaColumn_<typename TWatc::TDPProfile, MetaColumnDescriptor<DPInnerColumn, … in createBlockBuffer()
166 …using TDPMetaColV = DPMetaColumn_<typename TWatc::TDPProfile, MetaColumnDescriptor<DPInitialColumn… in createBlockBuffer()
172 RecursionDirectionZero(), typename TWatc::TDPProfile()); in createBlockBuffer()
182 typename TWatc::TDPProfile()); in createBlockBuffer()
188 RecursionDirectionZero(), typename TWatc::TDPProfile()); in createBlockBuffer()
201 typename TWatc::TDPProfile()); in createBlockBuffer()
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/align_parallel/
H A Ddp_kernel_adaptor.h106 …typedef DPProfile_<TAlgo, TGapCosts, TTraceConfig, Parallel> TDPProfile;
107 …typedef DPMetaColumn_<TDPProfile, MetaColumnDescriptor<DPInitialColumn, FullColumn> > TMetaColum…
176 …typedef DPProfile_<TAlgo, TGapCosts, TTraceConfig, Parallel> TDPProfile;
177 …typedef DPMetaColumn_<TDPProfile, MetaColumnDescriptor<DPInnerColumn, FullColumn> > TMetaColum…
182 TDPProfile()));
226 …typedef DPProfile_<TAlgo, TGapCosts, TTraceConfig, Parallel> TDPProfile;
227 …typedef DPMetaColumn_<TDPProfile, MetaColumnDescriptor<DPFinalColumn, FullColumn> > TMetaColum…
272 …typedef DPProfile_<TAlgo, TGapCosts, TTraceConfig, Parallel> TDPProfile;
278 TDPProfile()));
320 …typedef DPProfile_<TAlgo, TGapCosts, TTraceConfig, Parallel> TDPProfile;
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H A Dwavefront_alignment_task.h69 using TDPProfile = DPProfile_<TAlgorithmType, TGapType, TTracebackType, Parallel>; member
165 …using TDPMetaColH = DPMetaColumn_<typename TWatc::TDPProfile, MetaColumnDescriptor<DPInnerColumn, … in createBlockBuffer()
166 …using TDPMetaColV = DPMetaColumn_<typename TWatc::TDPProfile, MetaColumnDescriptor<DPInitialColumn… in createBlockBuffer()
172 RecursionDirectionZero(), typename TWatc::TDPProfile()); in createBlockBuffer()
182 typename TWatc::TDPProfile()); in createBlockBuffer()
188 RecursionDirectionZero(), typename TWatc::TDPProfile()); in createBlockBuffer()
201 typename TWatc::TDPProfile()); in createBlockBuffer()
/dports/biology/seqan/seqan-library-2.4.0/include/seqan/align_split/
H A Dalign_split_interface.h184 typedef DPProfile_<SplitAlignment_<TSpec>, TGapCosts, TTraceFlag, TExecPolicy> TDPProfile;
185 typedef typename IsLocalAlignment_<TDPProfile>::Type TIsLocal;
194 …typename If<IsFreeEndGap_<TDPProfile, DPFirstColumn>, RecursionDirectionZero, RecursionDirectionVe…
211 typedef DPProfile_<SplitAlignment_<TSpec>, TGapCosts, TTraceFlag> TDPProfile;
212 typedef typename IsLocalAlignment_<TDPProfile>::Type TIsLocal;
239 typedef DPProfile_<SplitAlignment_<TSpec>, TGapCosts, TTraceFlag, TExecPolicy> TDPProfile;
240 typedef typename IsLocalAlignment_<TDPProfile>::Type TIsLocal;
264 typedef DPProfile_<SplitAlignment_<TSpec>, TGapCosts, TTraceFlag, TExecPolicy> TDPProfile;
265 typedef typename IsLocalAlignment_<TDPProfile>::Type TIsLocal;
339 … typename SetupAlignmentProfile_<TDPType, TFreeEndGaps, LinearGaps, TTraceConfig>::Type TDPProfile;
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/align_split/
H A Dalign_split_interface.h184 typedef DPProfile_<SplitAlignment_<TSpec>, TGapCosts, TTraceFlag, TExecPolicy> TDPProfile;
185 typedef typename IsLocalAlignment_<TDPProfile>::Type TIsLocal;
194 …typename If<IsFreeEndGap_<TDPProfile, DPFirstColumn>, RecursionDirectionZero, RecursionDirectionVe…
211 typedef DPProfile_<SplitAlignment_<TSpec>, TGapCosts, TTraceFlag> TDPProfile;
212 typedef typename IsLocalAlignment_<TDPProfile>::Type TIsLocal;
239 typedef DPProfile_<SplitAlignment_<TSpec>, TGapCosts, TTraceFlag, TExecPolicy> TDPProfile;
240 typedef typename IsLocalAlignment_<TDPProfile>::Type TIsLocal;
264 typedef DPProfile_<SplitAlignment_<TSpec>, TGapCosts, TTraceFlag, TExecPolicy> TDPProfile;
265 typedef typename IsLocalAlignment_<TDPProfile>::Type TIsLocal;
339 … typename SetupAlignmentProfile_<TDPType, TFreeEndGaps, LinearGaps, TTraceConfig>::Type TDPProfile;
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/seeds/
H A Dbanded_chain_alignment_impl.h371 typename TCellDescriptor, typename TDPProfile>
378 TDPProfile const &) in _applyBandedChainTracking()
412 typedef DPMetaColumn_<TDPProfile, TColumnDescriptor> TMetaColumnProfile; in _computeCell()
418 TDPProfile())); in _computeCell()
466 TDPProfile const &) in _computeHorizontalInitCell()
681 RecursionDirectionZero(), TDPProfile()); in _initiaizeBeginningOfBandedChain()
689 RecursionDirectionZero(), TDPProfile()); in _initiaizeBeginningOfBandedChain()
692 RecursionDirectionHorizontal(), TDPProfile()); in _initiaizeBeginningOfBandedChain()
698 RecursionDirectionZero(), TDPProfile()); in _initiaizeBeginningOfBandedChain()
704 RecursionDirectionZero(), TDPProfile()); in _initiaizeBeginningOfBandedChain()
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H A Dbanded_chain_alignment_profile.h253 …ename SetupBandedChainAlignmentProfile_<TAlignConfig, AffineGaps, TGapsPlacement>::Type TDPProfile;
255 TDPProfile());
259 …ename SetupBandedChainAlignmentProfile_<TAlignConfig, LinearGaps, TGapsPlacement>::Type TDPProfile;
261 TDPProfile());
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/seeds/
H A Dbanded_chain_alignment_impl.h394 TDPProfile const &) in _applyBandedChainTracking()
436 TExecPolicy> TDPProfile; in _computeCell() typedef
443 TDPProfile())); in _computeCell()
449 TDPProfile()); in _computeCell()
483 TExecPolicy> TDPProfile; in _computeCell() typedef
494 TDPProfile()); in _computeCell()
509 TDPProfile const &) in _computeHorizontalInitCell()
547 TExecPolicy> TDPProfile; in _computeCell() typedef
580 TExecPolicy> TDPProfile; in _computeCell() typedef
617 TExecPolicy> TDPProfile; in _computeCell() typedef
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H A Dbanded_chain_alignment_profile.h257 …ename SetupBandedChainAlignmentProfile_<TAlignConfig, AffineGaps, TGapsPlacement>::Type TDPProfile;
259 TDPProfile());
263 …ename SetupBandedChainAlignmentProfile_<TAlignConfig, LinearGaps, TGapsPlacement>::Type TDPProfile;
265 TDPProfile());
/dports/biology/seqan/seqan-library-2.4.0/include/seqan/seeds/
H A Dbanded_chain_alignment_impl.h394 TDPProfile const &) in _applyBandedChainTracking()
436 TExecPolicy> TDPProfile; in _computeCell() typedef
443 TDPProfile())); in _computeCell()
449 TDPProfile()); in _computeCell()
483 TExecPolicy> TDPProfile; in _computeCell() typedef
494 TDPProfile()); in _computeCell()
509 TDPProfile const &) in _computeHorizontalInitCell()
547 TExecPolicy> TDPProfile; in _computeCell() typedef
580 TExecPolicy> TDPProfile; in _computeCell() typedef
617 TExecPolicy> TDPProfile; in _computeCell() typedef
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H A Dbanded_chain_alignment_profile.h257 …ename SetupBandedChainAlignmentProfile_<TAlignConfig, AffineGaps, TGapsPlacement>::Type TDPProfile;
259 TDPProfile());
263 …ename SetupBandedChainAlignmentProfile_<TAlignConfig, LinearGaps, TGapsPlacement>::Type TDPProfile;
265 TDPProfile());
/dports/biology/seqan/seqan-library-2.4.0/include/seqan/align_extend/
H A Ddp_scout_xdrop.h187 typedef DPProfile_<AlignExtend_<XDrop_<TScoreValue> >, TGapCosts, TTraceback> TDPProfile;
188 typedef DPMetaColumn_<TDPProfile, TColumnDescriptor> TMetaColumn;
193 TDPProfile()));

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