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Searched refs:TFreeEndGaps (Results 1 – 25 of 38) sorted by relevance

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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/seeds/
H A Dbanded_chain_alignment_profile.h88 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> :
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H A Dbanded_chain_alignment_impl.h323 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…
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H A Dbanded_chain_alignment_traceback.h62 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…
/dports/biology/seqan/seqan-library-2.4.0/include/seqan/seeds/
H A Dbanded_chain_alignment_profile.h88 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> :
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H A Dbanded_chain_alignment_impl.h323 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…
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H A Dbanded_chain_alignment_traceback.h62 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…
/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/seeds/
H A Dbanded_chain_alignment_profile.h88 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> :
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H A Dbanded_chain_alignment_impl.h307 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…
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H A Dbanded_chain_alignment_traceback.h62 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…
/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/align/
H A Ddp_setup.h215 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>
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H A Ddp_profile.h255 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>
H A Dglobal_alignment_banded.h92 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()
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H A Dglobal_alignment_unbanded.h183 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()
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/align/
H A Ddp_setup.h215 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>
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H A Dglobal_alignment_banded.h92 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
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H A Dglobal_alignment_unbanded.h183 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
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/align/
H A Ddp_setup.h215 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>
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H A Dglobal_alignment_banded.h92 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 …]
H A Dglobal_alignment_unbanded.h183 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
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/align_split/
H A Dalign_split_interface.h246 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…
/dports/biology/seqan/seqan-library-2.4.0/include/seqan/align_split/
H A Dalign_split_interface.h288 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,
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/align_split/
H A Dalign_split_interface.h288 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,
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/align_extend/
H A Dalign_extend.h129 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()
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/align_extend/
H A Dalign_extend.h129 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()
/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/align_extend/
H A Dalign_extend.h144 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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