/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/seeds/ |
H A D | banded_chain_alignment_profile.h | 88 template <typename TFreeEndGaps, typename TDPMatrixLocation, typename TGapCosts, typename TTracebac… 90 struct DPMetaColumn_<DPProfile_<BandedChainAlignment_<TFreeEndGaps, TDPMatrixLocation>, TGapCosts, … 110 template <typename TFreeEndGaps, typename TDPMatrixLocation, typename TGapCosts, typename TTracebac… 132 template <typename TFreeEndGaps, typename TDPMatrixLocation, typename TGapCosts, typename TTracebac… 154 template <typename TFreeEndGaps, typename TDPMatrixLocation, typename TGapCosts, typename TTracebac… 187 template <typename TFreeEndGaps, typename TDPMatrixLocation, typename TDPSide> 188 struct IsFreeEndGap_<BandedChainAlignment_<TFreeEndGaps, TDPMatrixLocation>, TDPSide> : 189 IsFreeEndGap_<TFreeEndGaps, TDPSide> 192 template <typename TFreeEndGaps, typename TDPMatrixLocation, typename TDPSide> 193 struct IsFreeEndGap_<BandedChainAlignment_<TFreeEndGaps, TDPMatrixLocation> const, TDPSide> : [all …]
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H A D | banded_chain_alignment_impl.h | 323 if (IsFreeEndGap_<TFreeEndGaps, DPLastRow>::VALUE) in _determineTrackingOptions() 347 if (IsFreeEndGap_<TFreeEndGaps, DPLastColumn>::VALUE) in _determineTrackingOptions() 369 if (IsFreeEndGap_<TFreeEndGaps, DPLastColumn>::VALUE) in _determineTrackingOptions() 433 typedef DPProfile_<BandedChainAlignment_<TFreeEndGaps, TDPMatrixLocation>, in _computeCell() 747 …pename TScoutState, typename TSizeH, typename TSizeV, typename TScoreScheme, typename TFreeEndGaps, 770 if (IsFreeEndGap_<TFreeEndGaps, DPFirstRow>::VALUE) in _initiaizeBeginningOfBandedChain() 788 if (IsFreeEndGap_<TFreeEndGaps, DPFirstColumn>::VALUE) in _initiaizeBeginningOfBandedChain() 808 typename TScoreScheme, typename TFreeEndGaps, typename TDPMatrixLocation, typename TGaps, 874 … DPProfile_<BandedChainAlignment_<TFreeEndGaps, BandedChainInitialDPMatrix>, TGaps, in _initializeBandedChain() 1275 …typename TScoreSpecAnchor, typename TScoreSpecGap, typename TFreeEndGaps, typename TDPMatrixLocati… [all …]
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H A D | banded_chain_alignment_traceback.h | 62 template <typename TFreeEndGaps, typename TMatrixSpec, typename TTracebackSpec, typename TExecPolic… 63 struct PreferGapsAtEnd_<DPProfile_<BandedChainAlignment_<TFreeEndGaps, TMatrixSpec>, 66 template <typename TFreeEndGaps, typename TTracebackSpec, typename TExecPolicy> 67 struct PreferGapsAtEnd_<DPProfile_<BandedChainAlignment_<TFreeEndGaps, BandedChainFinalDPMatrix>, 237 …typename TSequenceH, typename TSequenceV, typename TBandFlag, typename TFreeEndGaps, typename TDPM… 246 …DPProfile_<BandedChainAlignment_<TFreeEndGaps, TDPMatrixLocation>, TGapCosts, TTracebackSpec, TExe… 363 …typename TFreeEndGaps, typename TDPMatrixLocation, typename TGapCosts, typename TTracebackSpec, ty… 370 …DPProfile_<BandedChainAlignment_<TFreeEndGaps, TDPMatrixLocation>, TGapCosts, TTracebackSpec, TExe…
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/seeds/ |
H A D | banded_chain_alignment_profile.h | 88 template <typename TFreeEndGaps, typename TDPMatrixLocation, typename TGapCosts, typename TTracebac… 90 struct DPMetaColumn_<DPProfile_<BandedChainAlignment_<TFreeEndGaps, TDPMatrixLocation>, TGapCosts, … 110 template <typename TFreeEndGaps, typename TDPMatrixLocation, typename TGapCosts, typename TTracebac… 132 template <typename TFreeEndGaps, typename TDPMatrixLocation, typename TGapCosts, typename TTracebac… 154 template <typename TFreeEndGaps, typename TDPMatrixLocation, typename TGapCosts, typename TTracebac… 187 template <typename TFreeEndGaps, typename TDPMatrixLocation, typename TDPSide> 188 struct IsFreeEndGap_<BandedChainAlignment_<TFreeEndGaps, TDPMatrixLocation>, TDPSide> : 189 IsFreeEndGap_<TFreeEndGaps, TDPSide> 192 template <typename TFreeEndGaps, typename TDPMatrixLocation, typename TDPSide> 193 struct IsFreeEndGap_<BandedChainAlignment_<TFreeEndGaps, TDPMatrixLocation> const, TDPSide> : [all …]
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H A D | banded_chain_alignment_impl.h | 323 if (IsFreeEndGap_<TFreeEndGaps, DPLastRow>::VALUE) in _determineTrackingOptions() 347 if (IsFreeEndGap_<TFreeEndGaps, DPLastColumn>::VALUE) in _determineTrackingOptions() 369 if (IsFreeEndGap_<TFreeEndGaps, DPLastColumn>::VALUE) in _determineTrackingOptions() 433 typedef DPProfile_<BandedChainAlignment_<TFreeEndGaps, TDPMatrixLocation>, in _computeCell() 747 …pename TScoutState, typename TSizeH, typename TSizeV, typename TScoreScheme, typename TFreeEndGaps, 770 if (IsFreeEndGap_<TFreeEndGaps, DPFirstRow>::VALUE) in _initiaizeBeginningOfBandedChain() 788 if (IsFreeEndGap_<TFreeEndGaps, DPFirstColumn>::VALUE) in _initiaizeBeginningOfBandedChain() 808 typename TScoreScheme, typename TFreeEndGaps, typename TDPMatrixLocation, typename TGaps, 874 … DPProfile_<BandedChainAlignment_<TFreeEndGaps, BandedChainInitialDPMatrix>, TGaps, in _initializeBandedChain() 1275 …typename TScoreSpecAnchor, typename TScoreSpecGap, typename TFreeEndGaps, typename TDPMatrixLocati… [all …]
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H A D | banded_chain_alignment_traceback.h | 62 template <typename TFreeEndGaps, typename TMatrixSpec, typename TTracebackSpec, typename TExecPolic… 63 struct PreferGapsAtEnd_<DPProfile_<BandedChainAlignment_<TFreeEndGaps, TMatrixSpec>, 66 template <typename TFreeEndGaps, typename TTracebackSpec, typename TExecPolicy> 67 struct PreferGapsAtEnd_<DPProfile_<BandedChainAlignment_<TFreeEndGaps, BandedChainFinalDPMatrix>, 237 …typename TSequenceH, typename TSequenceV, typename TBandFlag, typename TFreeEndGaps, typename TDPM… 246 …DPProfile_<BandedChainAlignment_<TFreeEndGaps, TDPMatrixLocation>, TGapCosts, TTracebackSpec, TExe… 363 …typename TFreeEndGaps, typename TDPMatrixLocation, typename TGapCosts, typename TTracebackSpec, ty… 370 …DPProfile_<BandedChainAlignment_<TFreeEndGaps, TDPMatrixLocation>, TGapCosts, TTracebackSpec, TExe…
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/seeds/ |
H A D | banded_chain_alignment_profile.h | 88 template <typename TFreeEndGaps, typename TDPMatrixLocation, typename TGapCosts, typename TTracebac… 89 struct DPMetaColumn_<DPProfile_<BandedChainAlignment_<TFreeEndGaps, TDPMatrixLocation>, TGapCosts, … 110 struct DPMetaColumn_<DPProfile_<BandedChainAlignment_<TFreeEndGaps, TDPMatrixLocation>, TGapCosts, … 131 struct DPMetaColumn_<DPProfile_<BandedChainAlignment_<TFreeEndGaps, TDPMatrixLocation>, TGapCosts, … 152 struct DPMetaColumn_<DPProfile_<BandedChainAlignment_<TFreeEndGaps, TDPMatrixLocation>, TGapCosts, … 183 template <typename TFreeEndGaps, typename TDPMatrixLocation, typename TDPSide> 184 struct IsFreeEndGap_<BandedChainAlignment_<TFreeEndGaps, TDPMatrixLocation>, TDPSide> : 185 IsFreeEndGap_<TFreeEndGaps, TDPSide> 188 template <typename TFreeEndGaps, typename TDPMatrixLocation, typename TDPSide> 189 struct IsFreeEndGap_<BandedChainAlignment_<TFreeEndGaps, TDPMatrixLocation> const, TDPSide> : [all …]
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H A D | banded_chain_alignment_impl.h | 307 if (IsFreeEndGap_<TFreeEndGaps, DPLastRow>::VALUE) in _determineTrackingOptions() 331 if (IsFreeEndGap_<TFreeEndGaps, DPLastColumn>::VALUE) in _determineTrackingOptions() 353 if (IsFreeEndGap_<TFreeEndGaps, DPLastColumn>::VALUE) in _determineTrackingOptions() 396 …typename TCellDescriptor, typename TFreeEndGaps, typename TDPMatrixLocation, typename TTracebackCo… 666 …pename TScoutState, typename TSizeH, typename TSizeV, typename TScoreScheme, typename TFreeEndGaps, 687 if (IsFreeEndGap_<TFreeEndGaps, DPFirstRow>::VALUE) in _initiaizeBeginningOfBandedChain() 702 if (IsFreeEndGap_<TFreeEndGaps, DPFirstColumn>::VALUE) in _initiaizeBeginningOfBandedChain() 720 typename TScoreScheme, typename TFreeEndGaps, typename TDPMatrixLocation, typename TGaps, 842 … DPProfile_<GlobalAlignment_<TFreeEndGaps>, TGaps, TracebackOn<TTracebackConfig> >()); in _initializeBandedChain() 1180 …typename TScoreSpecAnchor, typename TScoreSpecGap, typename TFreeEndGaps, typename TDPMatrixLocati… [all …]
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H A D | banded_chain_alignment_traceback.h | 62 template <typename TFreeEndGaps, typename TMatrixSpec, typename TTracebackSpec> 63 struct PreferGapsAtEnd_<DPProfile_<BandedChainAlignment_<TFreeEndGaps, TMatrixSpec>, 66 template <typename TFreeEndGaps, typename TTracebackSpec> 67 struct PreferGapsAtEnd_<DPProfile_<BandedChainAlignment_<TFreeEndGaps, BandedChainFinalDPMatrix>, 237 …typename TSequenceH, typename TSequenceV, typename TBandFlag, typename TFreeEndGaps, typename TDPM… 246 …DPProfile_<BandedChainAlignment_<TFreeEndGaps, TDPMatrixLocation>, TGapCosts, TTracebackSpec> cons… 359 typename TBandFlag, typename TFreeEndGaps, typename TDPMatrixLocation, typename TGapCosts, typename… 366 …DPProfile_<BandedChainAlignment_<TFreeEndGaps, TDPMatrixLocation>, TGapCosts, TTracebackSpec> cons…
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/align/ |
H A D | dp_setup.h | 215 template <typename TFreeEndGaps, typename TGapCosts, typename TTraceSwitch> 216 struct SetupAlignmentProfile_<DPGlobal, TFreeEndGaps, TGapCosts, TTraceSwitch> 218 typedef DPProfile_<GlobalAlignment_<TFreeEndGaps>, TGapCosts, TTraceSwitch> Type; 222 template <typename TFreeEndGaps, typename TGapCosts, typename TTraceSwitch> 223 struct SetupAlignmentProfile_<DPLocal, TFreeEndGaps, TGapCosts, TTraceSwitch> 229 template <typename TFreeEndGaps, typename TGapCosts, typename TTraceSwitch> 230 struct SetupAlignmentProfile_<DPLocalEnumerate, TFreeEndGaps, TGapCosts, TTraceSwitch> 268 typename TBand, typename TFreeEndGaps, typename TTraceConfig> 288 typename TBand, typename TFreeEndGaps, typename TTraceConfig> 308 typename TBand, typename TFreeEndGaps, typename TTraceConfig> [all …]
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H A D | dp_profile.h | 255 template <typename TDPType, typename TBand, typename TFreeEndGaps = FreeEndGaps_<False, False, Fals… 435 template <typename TFreeEndGaps, typename TDPSide> 436 struct IsFreeEndGap_<GlobalAlignment_<TFreeEndGaps> const, TDPSide>: 437 IsFreeEndGap_<TFreeEndGaps, TDPSide> 440 template <typename TFreeEndGaps, typename TDPSide> 441 struct IsFreeEndGap_<GlobalAlignment_<TFreeEndGaps>, TDPSide>: 442 IsFreeEndGap_<TFreeEndGaps const, TDPSide>
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H A D | global_alignment_banded.h | 92 typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps; in globalAlignment() typedef 93 typedef AlignConfig2<DPGlobal, DPBandConfig<BandOn>, TFreeEndGaps> TAlignConfig2; in globalAlignment() 169 typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps; in globalAlignment() typedef 170 typedef AlignConfig2<DPGlobal, DPBandConfig<BandOn>, TFreeEndGaps> TAlignConfig2; in globalAlignment() 251 typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps; in globalAlignment() typedef 252 typedef AlignConfig2<DPGlobal, DPBandConfig<BandOn>, TFreeEndGaps> TAlignConfig2; in globalAlignment() 331 typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps; in globalAlignment() typedef 332 typedef AlignConfig2<DPGlobal, DPBandConfig<BandOn>, TFreeEndGaps> TAlignConfig2; in globalAlignment() 411 typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps; in globalAlignmentScore() typedef 412 typedef AlignConfig2<DPGlobal, DPBandConfig<BandOn>, TFreeEndGaps, TracebackOff> TAlignConfig2; in globalAlignmentScore() [all …]
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H A D | global_alignment_unbanded.h | 183 typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps; in globalAlignment() typedef 184 typedef AlignConfig2<DPGlobal, DPBandConfig<BandOff>, TFreeEndGaps> TAlignConfig2; in globalAlignment() 252 typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps; in globalAlignment() typedef 253 typedef AlignConfig2<DPGlobal, DPBandConfig<BandOff>, TFreeEndGaps> TAlignConfig2; in globalAlignment() 325 typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps; in globalAlignment() typedef 326 typedef AlignConfig2<DPGlobal, DPBandConfig<BandOff>, TFreeEndGaps> TAlignConfig2; in globalAlignment() 396 typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps; in globalAlignment() typedef 397 typedef AlignConfig2<DPGlobal, DPBandConfig<BandOff>, TFreeEndGaps> TAlignConfig2; in globalAlignment() 506 typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps; in globalAlignmentScore() typedef 507 typedef AlignConfig2<DPGlobal, DPBandConfig<BandOff>, TFreeEndGaps, TracebackOff> TAlignConfig2; in globalAlignmentScore() [all …]
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/align/ |
H A D | dp_setup.h | 215 template <typename TFreeEndGaps, typename TGapCosts, typename TTraceSwitch> 216 struct SetupAlignmentProfile_<DPGlobal, TFreeEndGaps, TGapCosts, TTraceSwitch> 222 template <typename TFreeEndGaps, typename TGapCosts, typename TTraceSwitch> 223 struct SetupAlignmentProfile_<DPLocal, TFreeEndGaps, TGapCosts, TTraceSwitch> 229 template <typename TFreeEndGaps, typename TGapCosts, typename TTraceSwitch> 230 struct SetupAlignmentProfile_<DPLocalEnumerate, TFreeEndGaps, TGapCosts, TTraceSwitch> 273 typename TDPType, typename TBand, typename TFreeEndGaps, typename TTraceConfig> 296 typename TDPType, typename TBand, typename TFreeEndGaps, typename TTraceConfig, 313 typename TBand, typename TFreeEndGaps, typename TTraceConfig> 335 typename TDPType, typename TBand, typename TFreeEndGaps, typename TTraceConfig> [all …]
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H A D | global_alignment_banded.h | 92 typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps; in globalAlignment() typedef 93 typedef AlignConfig2<DPGlobal, DPBandConfig<BandOn>, TFreeEndGaps> TAlignConfig2; in globalAlignment() 169 typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps; in globalAlignment() typedef 170 typedef AlignConfig2<DPGlobal, DPBandConfig<BandOn>, TFreeEndGaps> TAlignConfig2; in globalAlignment() 251 typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps; in globalAlignment() typedef 252 typedef AlignConfig2<DPGlobal, DPBandConfig<BandOn>, TFreeEndGaps> TAlignConfig2; in globalAlignment() 331 typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps; in globalAlignment() typedef 415 typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps; in SEQAN_FUNC_DISABLE_IF() typedef 489 typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps; in globalAlignmentScore() typedef 576 typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps; in SEQAN_FUNC_ENABLE_IF() typedef [all …]
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H A D | global_alignment_unbanded.h | 183 typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps; in globalAlignment() typedef 184 typedef AlignConfig2<DPGlobal, DPBandConfig<BandOff>, TFreeEndGaps> TAlignConfig2; in globalAlignment() 252 typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps; in globalAlignment() typedef 253 typedef AlignConfig2<DPGlobal, DPBandConfig<BandOff>, TFreeEndGaps> TAlignConfig2; in globalAlignment() 325 typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps; in globalAlignment() typedef 326 typedef AlignConfig2<DPGlobal, DPBandConfig<BandOff>, TFreeEndGaps> TAlignConfig2; in globalAlignment() 396 typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps; in globalAlignment() typedef 530 typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps; in SEQAN_FUNC_DISABLE_IF() typedef 595 typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps; in globalAlignmentScore() typedef 670 typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps; in SEQAN_FUNC_ENABLE_IF() typedef [all …]
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/align/ |
H A D | dp_setup.h | 215 template <typename TFreeEndGaps, typename TGapCosts, typename TTraceSwitch> 216 struct SetupAlignmentProfile_<DPGlobal, TFreeEndGaps, TGapCosts, TTraceSwitch> 222 template <typename TFreeEndGaps, typename TGapCosts, typename TTraceSwitch> 223 struct SetupAlignmentProfile_<DPLocal, TFreeEndGaps, TGapCosts, TTraceSwitch> 229 template <typename TFreeEndGaps, typename TGapCosts, typename TTraceSwitch> 230 struct SetupAlignmentProfile_<DPLocalEnumerate, TFreeEndGaps, TGapCosts, TTraceSwitch> 273 typename TDPType, typename TBand, typename TFreeEndGaps, typename TTraceConfig> 296 typename TDPType, typename TBand, typename TFreeEndGaps, typename TTraceConfig, 313 typename TBand, typename TFreeEndGaps, typename TTraceConfig> 335 typename TDPType, typename TBand, typename TFreeEndGaps, typename TTraceConfig> [all …]
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H A D | global_alignment_banded.h | 92 typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps; in globalAlignment() typedef 93 typedef AlignConfig2<DPGlobal, DPBandConfig<BandOn>, TFreeEndGaps> TAlignConfig2; in globalAlignment() 169 typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps; in globalAlignment() typedef 170 typedef AlignConfig2<DPGlobal, DPBandConfig<BandOn>, TFreeEndGaps> TAlignConfig2; in globalAlignment() 251 typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps; in globalAlignment() typedef 252 typedef AlignConfig2<DPGlobal, DPBandConfig<BandOn>, TFreeEndGaps> TAlignConfig2; in globalAlignment() 331 typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps; in globalAlignment() typedef 415 typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps; in SEQAN_FUNC_DISABLE_IF() typedef 489 typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps; in globalAlignmentScore() typedef 576 typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps; in SEQAN_FUNC_ENABLE_IF() typedef [all …]
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H A D | global_alignment_unbanded.h | 183 typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps; in globalAlignment() typedef 184 typedef AlignConfig2<DPGlobal, DPBandConfig<BandOff>, TFreeEndGaps> TAlignConfig2; in globalAlignment() 252 typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps; in globalAlignment() typedef 253 typedef AlignConfig2<DPGlobal, DPBandConfig<BandOff>, TFreeEndGaps> TAlignConfig2; in globalAlignment() 325 typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps; in globalAlignment() typedef 326 typedef AlignConfig2<DPGlobal, DPBandConfig<BandOff>, TFreeEndGaps> TAlignConfig2; in globalAlignment() 396 typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps; in globalAlignment() typedef 530 typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps; in SEQAN_FUNC_DISABLE_IF() typedef 595 typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps; in globalAlignmentScore() typedef 670 typedef typename SubstituteAlignConfig_<TAlignConfig>::Type TFreeEndGaps; in SEQAN_FUNC_ENABLE_IF() typedef [all …]
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/align_split/ |
H A D | align_split_interface.h | 246 template <typename TFreeEndGaps, typename TGapCosts, typename TTraceSwitch> 247 struct SetupAlignmentProfile_<SplitAlignmentAlgo, TFreeEndGaps, TGapCosts, TTraceSwitch> 249 typedef DPProfile_<SplitAlignment_<TFreeEndGaps>, TGapCosts, TTraceSwitch> Type; 300 typedef FreeEndGaps_<False, False, True, True> TFreeEndGaps; 314 …typedef AlignConfig2<SplitAlignmentAlgo, DPBandConfig<BandOff>, TFreeEndGaps, TracebackOn<Tracebac… 319 …typedef AlignConfig2<SplitAlignmentAlgo, DPBandConfig<BandOn>, TFreeEndGaps, TracebackOn<Traceback… 337 …typedef AlignConfig2<SplitAlignmentAlgo, DPBandConfig<BandOff>, TFreeEndGaps, TracebackOn<Tracebac… 342 …typedef AlignConfig2<SplitAlignmentAlgo, DPBandConfig<BandOn>, TFreeEndGaps, TracebackOn<Traceback…
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/align_split/ |
H A D | align_split_interface.h | 288 template <typename TFreeEndGaps, typename TGapCosts, typename TTraceSwitch> 289 struct SetupAlignmentProfile_<SplitAlignmentAlgo, TFreeEndGaps, TGapCosts, TTraceSwitch> 291 typedef DPProfile_<SplitAlignment_<TFreeEndGaps>, TGapCosts, TTraceSwitch, Serial> Type; 331 typename TDPType, typename TBandSwitch, typename TFreeEndGaps, typename TTraceConfig> 337 … AlignConfig2<TDPType, DPBandConfig<TBandSwitch>, TFreeEndGaps, TTraceConfig> const & config) 339 …typedef typename SetupAlignmentProfile_<TDPType, TFreeEndGaps, LinearGaps, TTraceConfig>::Type TDP… 490 …def typename SubstituteAlignConfig_<AlignConfig<TTop, TRight, TLeft, TBottom> >::Type TFreeEndGaps; 494 typedef AlignConfig2<SplitAlignmentAlgo, DPBandConfig<BandOn>, TFreeEndGaps, 496 typedef AlignConfig2<SplitAlignmentAlgo, DPBandConfig<BandOn>, TFreeEndGaps, 505 typedef AlignConfig2<SplitAlignmentAlgo, DPBandConfig<BandOff>, TFreeEndGaps, [all …]
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/align_split/ |
H A D | align_split_interface.h | 288 template <typename TFreeEndGaps, typename TGapCosts, typename TTraceSwitch> 289 struct SetupAlignmentProfile_<SplitAlignmentAlgo, TFreeEndGaps, TGapCosts, TTraceSwitch> 291 typedef DPProfile_<SplitAlignment_<TFreeEndGaps>, TGapCosts, TTraceSwitch, Serial> Type; 331 typename TDPType, typename TBandSwitch, typename TFreeEndGaps, typename TTraceConfig> 337 … AlignConfig2<TDPType, DPBandConfig<TBandSwitch>, TFreeEndGaps, TTraceConfig> const & config) 339 …typedef typename SetupAlignmentProfile_<TDPType, TFreeEndGaps, LinearGaps, TTraceConfig>::Type TDP… 490 …def typename SubstituteAlignConfig_<AlignConfig<TTop, TRight, TLeft, TBottom> >::Type TFreeEndGaps; 494 typedef AlignConfig2<SplitAlignmentAlgo, DPBandConfig<BandOn>, TFreeEndGaps, 496 typedef AlignConfig2<SplitAlignmentAlgo, DPBandConfig<BandOn>, TFreeEndGaps, 505 typedef AlignConfig2<SplitAlignmentAlgo, DPBandConfig<BandOff>, TFreeEndGaps, [all …]
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/align_extend/ |
H A D | align_extend.h | 129 typedef FreeEndGaps_<False, False, True, True> TFreeEndGaps; in _setUpAndRunAlignImpl() typedef 130 typedef AlignConfig2<AlignExtend_<>, DPBandConfig<BandOff>, TFreeEndGaps, in _setUpAndRunAlignImpl() 152 typedef FreeEndGaps_<False, False, True, True> TFreeEndGaps; in _setUpAndRunAlignImpl() typedef 153 typedef AlignConfig2<AlignExtend_<>, DPBandConfig<BandOn>, TFreeEndGaps, in _setUpAndRunAlignImpl() 175 typedef FreeEndGaps_<False, False, True, True> TFreeEndGaps; in _setUpAndRunAlignImpl() typedef 176 typedef AlignConfig2<AlignExtend_<XDrop_<TScoreValue> >, DPBandConfig<BandOff>, TFreeEndGaps, in _setUpAndRunAlignImpl() 198 typedef FreeEndGaps_<False, False, True, True> TFreeEndGaps; in _setUpAndRunAlignImpl() typedef 199 typedef AlignConfig2<AlignExtend_<XDrop_<TScoreValue> >, DPBandConfig<BandOn>, TFreeEndGaps, in _setUpAndRunAlignImpl()
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/align_extend/ |
H A D | align_extend.h | 129 typedef FreeEndGaps_<False, False, True, True> TFreeEndGaps; in _setUpAndRunAlignImpl() typedef 130 typedef AlignConfig2<AlignExtend_<>, DPBandConfig<BandOff>, TFreeEndGaps, in _setUpAndRunAlignImpl() 152 typedef FreeEndGaps_<False, False, True, True> TFreeEndGaps; in _setUpAndRunAlignImpl() typedef 153 typedef AlignConfig2<AlignExtend_<>, DPBandConfig<BandOn>, TFreeEndGaps, in _setUpAndRunAlignImpl() 175 typedef FreeEndGaps_<False, False, True, True> TFreeEndGaps; in _setUpAndRunAlignImpl() typedef 176 typedef AlignConfig2<AlignExtend_<XDrop_<TScoreValue> >, DPBandConfig<BandOff>, TFreeEndGaps, in _setUpAndRunAlignImpl() 198 typedef FreeEndGaps_<False, False, True, True> TFreeEndGaps; in _setUpAndRunAlignImpl() typedef 199 typedef AlignConfig2<AlignExtend_<XDrop_<TScoreValue> >, DPBandConfig<BandOn>, TFreeEndGaps, in _setUpAndRunAlignImpl()
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/align_extend/ |
H A D | align_extend.h | 144 typedef FreeEndGaps_<False, False, True, True> TFreeEndGaps; in _setUpAndRunAlignImpl() typedef 145 typedef AlignConfig2<AlignExtend_<>, DPBandConfig<BandOff>, TFreeEndGaps, in _setUpAndRunAlignImpl() 167 typedef FreeEndGaps_<False, False, True, True> TFreeEndGaps; in _setUpAndRunAlignImpl() typedef 168 typedef AlignConfig2<AlignExtend_<>, DPBandConfig<BandOn>, TFreeEndGaps, in _setUpAndRunAlignImpl() 190 typedef FreeEndGaps_<False, False, True, True> TFreeEndGaps; in _setUpAndRunAlignImpl() typedef 191 typedef AlignConfig2<AlignExtend_<XDrop_<TScoreValue> >, DPBandConfig<BandOff>, TFreeEndGaps, in _setUpAndRunAlignImpl() 213 typedef FreeEndGaps_<False, False, True, True> TFreeEndGaps; in _setUpAndRunAlignImpl() typedef 214 typedef AlignConfig2<AlignExtend_<XDrop_<TScoreValue> >, DPBandConfig<BandOn>, TFreeEndGaps, in _setUpAndRunAlignImpl()
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