| /dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/align/ |
| H A D | dp_matrix_navigator_trace_matrix.h | 67 template <typename TValue, typename TTraceFlag>
101 template <typename TValue, typename TTraceFlag>
107 if (IsSameType<TTraceFlag, TracebackOff>::VALUE) in _init()
118 template <typename TValue, typename TTraceFlag>
127 if (IsSameType<TTraceFlag, TracebackOff>::VALUE) in _init()
161 template <typename TValue, typename TTraceFlag>
193 if (IsSameType<TTraceFlag, TracebackOff>::VALUE) in _goNextCell()
240 template <typename TValue, typename TTraceFlag>
288 template <typename TValue, typename TTraceFlag>
307 template <typename TValue, typename TTraceFlag>
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| H A D | dp_profile.h | 291 template <typename TAlgoSpec, typename TGapCosts, typename TTraceFlag>
292 struct IsGlobalAlignment_<DPProfile_<TAlgoSpec, TGapCosts, TTraceFlag> >:
295 template <typename TAlgoSpec, typename TGapCosts, typename TTraceFlag>
345 template <typename TAlgoSpec, typename TGapCosts, typename TTraceFlag>
346 struct IsLocalAlignment_<DPProfile_<TAlgoSpec, TGapCosts, TTraceFlag> >:
349 template <typename TAlgoSpec, typename TGapCosts, typename TTraceFlag>
370 template <typename TAlgoSpec, typename TGapCosts, typename TTraceFlag>
371 struct IsTracebackEnabled_<DPProfile_<TAlgoSpec, TGapCosts, TTraceFlag> >:
372 IsTracebackEnabled_<TTraceFlag>{};
374 template <typename TAlgoSpec, typename TGapCosts, typename TTraceFlag>
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| H A D | dp_algorithm_impl.h | 456 DPProfile_<TAlignmentAlgo, TGapCosts, TTraceFlag> const & dpProfile) in _computeUnbandedAlignment()
524 typename TTraceFlag>
533 DPProfile_<TAlignmentAlgo, TGapCosts, TTraceFlag> const & dpProfile) in _computeBandedAlignment()
535 typedef DPProfile_<TAlignmentAlgo, TGapCosts, TTraceFlag> TDPProfile; in _computeBandedAlignment()
1184 typename TTraceFlag>
1193 DPProfile_<TAlignmentAlgo, TGapCosts, TTraceFlag> const &) in _computeHammingDistance()
1200 typedef DPProfile_<TAlignmentAlgo, TGapCosts, TTraceFlag> TDPProfile; in _computeHammingDistance()
1387 DPProfile_<TAlignmentAlgorithm, TGapScheme, TTraceFlag> const & dpProfile) in _computeAlignment()
1435 if (IsTracebackEnabled_<TTraceFlag>::VALUE) in _computeAlignment()
1455 if (IsSameType<TTraceFlag, TracebackOff>::VALUE) in _computeAlignment()
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| H A D | dp_formula.h | 206 typename TAlgoTag, typename TTraceFlag>
216 DPProfile_<TAlgoTag, TGapCosts, TTraceFlag> const &) in _doComputeScore()
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| H A D | dp_meta_info.h | 384 template <typename TRecursionDirection, typename TTraceFlag>
385 struct GetRecursionDirection_<DPMetaCell_<TRecursionDirection, TTraceFlag> >
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| H A D | dp_matrix_navigator.h | 74 template <typename TTraceFlag>
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| /dports/biology/seqan/seqan-library-2.4.0/include/seqan/align/ |
| H A D | dp_matrix_navigator_trace_matrix.h | 81 if (IsSameType<TTraceFlag, TracebackOff>::VALUE) in DPMatrixNavigator_()
98 if (std::is_same<TTraceFlag, TracebackOff>::value) in DPMatrixNavigator_()
150 DPTraceMatrix<TTraceFlag>, in _goNextCell() argument
162 DPTraceMatrix<TTraceFlag>, in _goNextCell() argument
177 DPTraceMatrix<TTraceFlag>, in _goNextCell() argument
182 if (IsSameType<TTraceFlag, TracebackOff>::VALUE) in _goNextCell()
195 DPTraceMatrix<TTraceFlag>, in _goNextCell() argument
200 if (IsSameType<TTraceFlag, TracebackOff>::VALUE) in _goNextCell()
324 if (IsSameType<TTraceFlag, TracebackOff>::VALUE) in _goNextCell()
559 if (IsSameType<TTraceFlag, TracebackOff>::VALUE) in coordinate()
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| H A D | dp_profile.h | 445 template <typename TAlgoSpec, typename TGapCosts, typename TTraceFlag, typename TExecPolicy>
446 struct GapTraits<DPProfile_<TAlgoSpec, TGapCosts, TTraceFlag, TExecPolicy> >
468 template <typename TAlgoSpec, typename TGapCosts, typename TTraceFlag, typename TExecPolicy>
469 struct IsGlobalAlignment_<DPProfile_<TAlgoSpec, TGapCosts, TTraceFlag, TExecPolicy> >:
472 template <typename TAlgoSpec, typename TGapCosts, typename TTraceFlag, typename TExecPolicy>
473 struct IsGlobalAlignment_<DPProfile_<TAlgoSpec, TGapCosts, TTraceFlag, TExecPolicy> const>:
523 struct IsLocalAlignment_<DPProfile_<TAlgoSpec, TGapCosts, TTraceFlag, TExecPolicy> >:
527 struct IsLocalAlignment_<DPProfile_<TAlgoSpec, TGapCosts, TTraceFlag, TExecPolicy> const>:
548 struct IsTracebackEnabled_<DPProfile_<TAlgoSpec, TGapCosts, TTraceFlag, TExecPolicy> >:
549 IsTracebackEnabled_<TTraceFlag>{};
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| H A D | dp_algorithm_impl.h | 487 typename TAlignmentAlgo, typename TGapCosts, typename TTraceFlag, typename TExecPolicy>
496 … DPProfile_<TAlignmentAlgo, TGapCosts, TTraceFlag, TExecPolicy> const & dpProfile, in _computeAlignmentImpl() argument
587 typename TAlignmentAlgo, typename TGapCosts, typename TTraceFlag, typename TExecPolicy>
599 typedef DPProfile_<TAlignmentAlgo, TGapCosts, TTraceFlag> TDPProfile; in _computeAlignmentImpl()
965 typename TAlignmentAlgo, typename TGapCosts, typename TTraceFlag, typename TExecPolicy>
974 DPProfile_<TAlignmentAlgo, TGapCosts, TTraceFlag, TExecPolicy> const &) in _computeHammingDistance() argument
981 typedef DPProfile_<TAlignmentAlgo, TGapCosts, TTraceFlag> TDPProfile; in _computeHammingDistance()
1264 inline SEQAN_FUNC_ENABLE_IF(Not<IsTracebackEnabled_<TTraceFlag> >, TScoreValue) in SEQAN_FUNC_ENABLE_IF() argument
1299 if (IsSingleTrace_<TTraceFlag>::VALUE) in SEQAN_FUNC_ENABLE_IF()
1329 if (IsSingleTrace_<TTraceFlag>::VALUE) in SEQAN_FUNC_ENABLE_IF()
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| H A D | dp_formula.h | 273 typename TAlgoTag, typename TTraceFlag, typename TExecPolicy>
283 DPProfile_<TAlgoTag, TGapCosts, TTraceFlag, TExecPolicy> const &) in _computeScore() argument
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| H A D | dp_meta_info.h | 384 template <typename TRecursionDirection, typename TTraceFlag>
385 struct GetRecursionDirection_<DPMetaCell_<TRecursionDirection, TTraceFlag> >
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| H A D | dp_matrix_navigator.h | 74 template <typename TTraceFlag>
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| H A D | dp_formula_dynamic.h | 653 typename TAlgoTag, typename TTraceFlag, typename TExecPolicy>
663 DPProfile_<TAlgoTag, DynamicGaps, TTraceFlag, TExecPolicy> const &) in _computeScore() argument
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/align/ |
| H A D | dp_matrix_navigator_trace_matrix.h | 81 if (IsSameType<TTraceFlag, TracebackOff>::VALUE) in DPMatrixNavigator_()
98 if (std::is_same<TTraceFlag, TracebackOff>::value) in DPMatrixNavigator_()
150 DPTraceMatrix<TTraceFlag>, in _goNextCell() argument
162 DPTraceMatrix<TTraceFlag>, in _goNextCell() argument
177 DPTraceMatrix<TTraceFlag>, in _goNextCell() argument
182 if (IsSameType<TTraceFlag, TracebackOff>::VALUE) in _goNextCell()
195 DPTraceMatrix<TTraceFlag>, in _goNextCell() argument
200 if (IsSameType<TTraceFlag, TracebackOff>::VALUE) in _goNextCell()
324 if (IsSameType<TTraceFlag, TracebackOff>::VALUE) in _goNextCell()
559 if (IsSameType<TTraceFlag, TracebackOff>::VALUE) in coordinate()
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| H A D | dp_profile.h | 445 template <typename TAlgoSpec, typename TGapCosts, typename TTraceFlag, typename TExecPolicy>
446 struct GapTraits<DPProfile_<TAlgoSpec, TGapCosts, TTraceFlag, TExecPolicy> >
468 template <typename TAlgoSpec, typename TGapCosts, typename TTraceFlag, typename TExecPolicy>
469 struct IsGlobalAlignment_<DPProfile_<TAlgoSpec, TGapCosts, TTraceFlag, TExecPolicy> >:
472 template <typename TAlgoSpec, typename TGapCosts, typename TTraceFlag, typename TExecPolicy>
473 struct IsGlobalAlignment_<DPProfile_<TAlgoSpec, TGapCosts, TTraceFlag, TExecPolicy> const>:
523 struct IsLocalAlignment_<DPProfile_<TAlgoSpec, TGapCosts, TTraceFlag, TExecPolicy> >:
527 struct IsLocalAlignment_<DPProfile_<TAlgoSpec, TGapCosts, TTraceFlag, TExecPolicy> const>:
548 struct IsTracebackEnabled_<DPProfile_<TAlgoSpec, TGapCosts, TTraceFlag, TExecPolicy> >:
549 IsTracebackEnabled_<TTraceFlag>{};
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| H A D | dp_algorithm_impl.h | 487 typename TAlignmentAlgo, typename TGapCosts, typename TTraceFlag, typename TExecPolicy>
496 … DPProfile_<TAlignmentAlgo, TGapCosts, TTraceFlag, TExecPolicy> const & dpProfile, in _computeAlignmentImpl() argument
587 typename TAlignmentAlgo, typename TGapCosts, typename TTraceFlag, typename TExecPolicy>
599 typedef DPProfile_<TAlignmentAlgo, TGapCosts, TTraceFlag> TDPProfile; in _computeAlignmentImpl()
965 typename TAlignmentAlgo, typename TGapCosts, typename TTraceFlag, typename TExecPolicy>
974 DPProfile_<TAlignmentAlgo, TGapCosts, TTraceFlag, TExecPolicy> const &) in _computeHammingDistance() argument
981 typedef DPProfile_<TAlignmentAlgo, TGapCosts, TTraceFlag> TDPProfile; in _computeHammingDistance()
1264 inline SEQAN_FUNC_ENABLE_IF(Not<IsTracebackEnabled_<TTraceFlag> >, TScoreValue) in SEQAN_FUNC_ENABLE_IF() argument
1299 if (IsSingleTrace_<TTraceFlag>::VALUE) in SEQAN_FUNC_ENABLE_IF()
1329 if (IsSingleTrace_<TTraceFlag>::VALUE) in SEQAN_FUNC_ENABLE_IF()
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| H A D | dp_formula.h | 273 typename TAlgoTag, typename TTraceFlag, typename TExecPolicy>
283 DPProfile_<TAlgoTag, TGapCosts, TTraceFlag, TExecPolicy> const &) in _computeScore() argument
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| H A D | dp_meta_info.h | 384 template <typename TRecursionDirection, typename TTraceFlag>
385 struct GetRecursionDirection_<DPMetaCell_<TRecursionDirection, TTraceFlag> >
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| H A D | dp_matrix_navigator.h | 74 template <typename TTraceFlag>
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| H A D | dp_formula_dynamic.h | 653 typename TAlgoTag, typename TTraceFlag, typename TExecPolicy>
663 DPProfile_<TAlgoTag, DynamicGaps, TTraceFlag, TExecPolicy> const &) in _computeScore() argument
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| /dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/align_split/ |
| H A D | align_split_interface.h | 101 template <typename TAlgoSpec, typename TGapCosts, typename TTraceFlag>
102 struct IsSplitAlignment_<DPProfile_<TAlgoSpec, TGapCosts, TTraceFlag> >:
105 template <typename TAlgoSpec, typename TGapCosts, typename TTraceFlag>
106 struct IsSplitAlignment_<DPProfile_<TAlgoSpec, TGapCosts, TTraceFlag> const>:
145 template <typename TSpec, typename TGapCosts, typename TTraceFlag, typename TColumnType>
148 typedef DPProfile_<SplitAlignment_<TSpec>, TGapCosts, TTraceFlag> TDPProfile;
170 template <typename TSpec, typename TGapCosts, typename TTraceFlag, typename TColumnType>
173 typedef DPProfile_<SplitAlignment_<TSpec>, TGapCosts, TTraceFlag> TDPProfile;
196 template <typename TSpec, typename TGapCosts, typename TTraceFlag, typename TColumnType>
199 typedef DPProfile_<SplitAlignment_<TSpec>, TGapCosts, TTraceFlag> TDPProfile;
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| /dports/biology/seqan/seqan-library-2.4.0/include/seqan/align_split/ |
| H A D | align_split_interface.h | 101 template <typename TAlgoSpec, typename TGapCosts, typename TTraceFlag, typename TExecPolicy>
102 struct IsSplitAlignment_<DPProfile_<TAlgoSpec, TGapCosts, TTraceFlag, TExecPolicy> >:
105 template <typename TAlgoSpec, typename TGapCosts, typename TTraceFlag, typename TExecPolicy>
106 struct IsSplitAlignment_<DPProfile_<TAlgoSpec, TGapCosts, TTraceFlag, TExecPolicy> const>:
179 template <typename TSpec, typename TGapCosts, typename TTraceFlag, typename TExecPolicy,
181 struct DPMetaColumn_<DPProfile_<SplitAlignment_<TSpec>, TGapCosts, TTraceFlag, TExecPolicy>,
206 template <typename TSpec, typename TGapCosts, typename TTraceFlag, typename TExecPolicy,
208 struct DPMetaColumn_<DPProfile_<SplitAlignment_<TSpec>, TGapCosts, TTraceFlag, TExecPolicy>,
211 typedef DPProfile_<SplitAlignment_<TSpec>, TGapCosts, TTraceFlag> TDPProfile;
234 template <typename TSpec, typename TGapCosts, typename TTraceFlag, typename TExecPolicy,
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/align_split/ |
| H A D | align_split_interface.h | 101 template <typename TAlgoSpec, typename TGapCosts, typename TTraceFlag, typename TExecPolicy>
102 struct IsSplitAlignment_<DPProfile_<TAlgoSpec, TGapCosts, TTraceFlag, TExecPolicy> >:
105 template <typename TAlgoSpec, typename TGapCosts, typename TTraceFlag, typename TExecPolicy>
106 struct IsSplitAlignment_<DPProfile_<TAlgoSpec, TGapCosts, TTraceFlag, TExecPolicy> const>:
179 template <typename TSpec, typename TGapCosts, typename TTraceFlag, typename TExecPolicy,
181 struct DPMetaColumn_<DPProfile_<SplitAlignment_<TSpec>, TGapCosts, TTraceFlag, TExecPolicy>,
206 template <typename TSpec, typename TGapCosts, typename TTraceFlag, typename TExecPolicy,
208 struct DPMetaColumn_<DPProfile_<SplitAlignment_<TSpec>, TGapCosts, TTraceFlag, TExecPolicy>,
211 typedef DPProfile_<SplitAlignment_<TSpec>, TGapCosts, TTraceFlag> TDPProfile;
234 template <typename TSpec, typename TGapCosts, typename TTraceFlag, typename TExecPolicy,
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| /dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/seeds/ |
| H A D | banded_chain_alignment_impl.h | 1156 … typename TScoreScheme, typename TBandSwitch, typename TAlignmentAlgorithm, typename TTraceFlag>
1164 DPProfile_<TAlignmentAlgorithm, TGapScheme, TTraceFlag> const & dpProfile) in _computeAlignment()
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/seeds/ |
| H A D | banded_chain_alignment_impl.h | 1250 … typename TScoreScheme, typename TBandSwitch, typename TAlignmentAlgorithm, typename TTraceFlag,
1259 … DPProfile_<TAlignmentAlgorithm, TGapScheme, TTraceFlag, TExecPolicy> const & dpProfile) in _computeAlignment() argument
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