/dports/biology/seqan-apps/seqan-seqan-v2.4.0/tests/align/ |
H A D | test_alignment_dp_profile.h | 180 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() [all …]
|
H A D | test_alignment_algorithms_band_position.h | 45 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() [all …]
|
H A D | test_alignment_dp_traceback.h | 45 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 [all …]
|
/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/align/ |
H A D | dp_meta_info.h | 170 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> [all …]
|
H A D | dp_algorithm_impl.h | 253 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 [all …]
|
H A D | dp_formula.h | 148 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 D | dp_setup.h | 281 … 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 D | dp_meta_info.h | 170 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> [all …]
|
H A D | dp_algorithm_impl.h | 279 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> [all …]
|
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/align/ |
H A D | dp_meta_info.h | 170 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> [all …]
|
H A D | dp_algorithm_impl.h | 279 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> [all …]
|
/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/align_split/ |
H A D | align_split_interface.h | 148 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; [all …]
|
/dports/biology/seqan/seqan-library-2.4.0/include/seqan/align_parallel/ |
H A D | dp_kernel_adaptor.h | 106 …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; [all …]
|
H A D | wavefront_alignment_task.h | 69 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 D | dp_kernel_adaptor.h | 106 …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; [all …]
|
H A D | wavefront_alignment_task.h | 69 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 D | align_split_interface.h | 184 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; [all …]
|
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/align_split/ |
H A D | align_split_interface.h | 184 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; [all …]
|
/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/seeds/ |
H A D | banded_chain_alignment_impl.h | 371 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() [all …]
|
H A D | banded_chain_alignment_profile.h | 253 …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 D | banded_chain_alignment_impl.h | 394 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 [all …]
|
H A D | banded_chain_alignment_profile.h | 257 …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 D | banded_chain_alignment_impl.h | 394 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 [all …]
|
H A D | banded_chain_alignment_profile.h | 257 …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 D | dp_scout_xdrop.h | 187 typedef DPProfile_<AlignExtend_<XDrop_<TScoreValue> >, TGapCosts, TTraceback> TDPProfile; 188 typedef DPMetaColumn_<TDPProfile, TColumnDescriptor> TMetaColumn; 193 TDPProfile()));
|