/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/misc/ |
H A D | edit_environment.h | 171 typedef typename MakeSigned_<TSize>::Type TSignedSize; typedef 172 typedef StringEnumeratorHammingModifier_<TSignedSize> TModifier; 235 typedef typename MakeSigned_<TSize>::Type TSignedSize; typedef 236 typedef StringEnumeratorLevenshteinModifier_<TSignedSize> TModifier; 360 if (_mod.errorPos >= (TSignedSize)(pos - 1)) in _reinit() 367 if (_mod.errorPos >= (TSignedSize)pos) in _reinit() 377 if (_mod.errorPos > (TSignedSize)pos) in _reinit() 677 typedef StringEnumeratorHammingModifier_<TSignedSize> TModifier; 748 typedef StringEnumeratorHammingModifier_<TSignedSize> TModifier; 768 typedef StringEnumeratorHammingModifier_<TSignedSize> TModifier; [all …]
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/misc/ |
H A D | edit_environment.h | 171 typedef typename MakeSigned_<TSize>::Type TSignedSize; typedef 172 typedef StringEnumeratorHammingModifier_<TSignedSize> TModifier; 235 typedef typename MakeSigned_<TSize>::Type TSignedSize; typedef 236 typedef StringEnumeratorLevenshteinModifier_<TSignedSize> TModifier; 360 if (_mod.errorPos >= (TSignedSize)(pos - 1)) in _reinit() 367 if (_mod.errorPos >= (TSignedSize)pos) in _reinit() 377 if (_mod.errorPos > (TSignedSize)pos) in _reinit() 677 typedef StringEnumeratorHammingModifier_<TSignedSize> TModifier; 748 typedef StringEnumeratorHammingModifier_<TSignedSize> TModifier; 768 typedef StringEnumeratorHammingModifier_<TSignedSize> TModifier; [all …]
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/misc/ |
H A D | edit_environment.h | 171 typedef typename MakeSigned_<TSize>::Type TSignedSize; typedef 172 typedef StringEnumeratorHammingModifier_<TSignedSize> TModifier; 235 typedef typename MakeSigned_<TSize>::Type TSignedSize; typedef 236 typedef StringEnumeratorLevenshteinModifier_<TSignedSize> TModifier; 360 if (_mod.errorPos >= (TSignedSize)(pos - 1)) in _reinit() 367 if (_mod.errorPos >= (TSignedSize)pos) in _reinit() 377 if (_mod.errorPos > (TSignedSize)pos) in _reinit() 677 typedef StringEnumeratorHammingModifier_<TSignedSize> TModifier; 748 typedef StringEnumeratorHammingModifier_<TSignedSize> TModifier; 768 typedef StringEnumeratorHammingModifier_<TSignedSize> TModifier; [all …]
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/dports/biology/seqan1/seqan-1.3.1/seqan/misc/ |
H A D | edit_environment.h | 151 typedef typename MakeSigned_<TSize>::Type TSignedSize; 212 typedef typename MakeSigned_<TSize>::Type TSignedSize; 270 typedef typename MakeSigned_<TSize>::Type TSignedSize; 285 typedef typename MakeSigned_<TSize>::Type TSignedSize; 309 typedef typename MakeSigned_<TSize>::Type TSignedSize; 418 typedef typename MakeSigned_<TSize>::Type TSignedSize; 531 if (_mod.errorPos >= (TSignedSize)(pos - 1)) 535 if (_mod.errorPos >= (TSignedSize)pos) 542 if (_mod.errorPos > (TSignedSize)pos) 793 typedef typename MakeSigned_<TSize>::Type TSignedSize; [all …]
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/seeds/ |
H A D | banded_chain_alignment_impl.h | 120 typedef typename MakeSigned<TSize>::Type TSignedSize; in _isCrossingBeginHorizontal() typedef 121 if ((TSignedSize) horizontalSeedBeginPos - (TSignedSize) bandExtension <= 0) in _isCrossingBeginHorizontal() 134 typedef typename MakeSigned<TSize>::Type TSignedSize; in _isCrossingBeginVertical() typedef 136 if ((TSignedSize) verticalSeedBeginPos - (TSignedSize) bandExtension <= 0) in _isCrossingBeginVertical() 152 typedef typename MakeSigned<TSize>::Type TSignedSize; in _isCrossingEndHorizontal() typedef 154 if ((TSignedSize) horizontalSeedEndPos + (TSignedSize) bandSize >= (TSignedSize) length(seqH)) in _isCrossingEndHorizontal() 170 typedef typename MakeSigned<TSize>::Type TSignedSize; in _isCrossingEndVertical() typedef 172 if ((TSignedSize) verticalSeedEndPos + (TSignedSize) bandSize >= (TSignedSize) length(seqV)) in _isCrossingEndVertical() 738 typedef typename MakeSigned<TSeedSize>::Type TSignedSize; in _initializeBandedChain() typedef 953 typedef typename MakeSigned<TSize>::Type TSignedSize; in _computeAnchorArea() typedef [all …]
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/seeds/ |
H A D | banded_chain_alignment_impl.h | 136 typedef typename MakeSigned<TSize>::Type TSignedSize; in _isCrossingBeginHorizontal() typedef 137 if ((TSignedSize) horizontalSeedBeginPos - (TSignedSize) bandExtension <= 0) in _isCrossingBeginHorizontal() 150 typedef typename MakeSigned<TSize>::Type TSignedSize; in _isCrossingBeginVertical() typedef 152 if ((TSignedSize) verticalSeedBeginPos - (TSignedSize) bandExtension <= 0) in _isCrossingBeginVertical() 168 typedef typename MakeSigned<TSize>::Type TSignedSize; in _isCrossingEndHorizontal() typedef 170 if ((TSignedSize) horizontalSeedEndPos + (TSignedSize) bandSize >= (TSignedSize) length(seqH)) in _isCrossingEndHorizontal() 186 typedef typename MakeSigned<TSize>::Type TSignedSize; in _isCrossingEndVertical() typedef 188 if ((TSignedSize) verticalSeedEndPos + (TSignedSize) bandSize >= (TSignedSize) length(seqV)) in _isCrossingEndVertical() 826 typedef typename MakeSigned<TSeedSize>::Type TSignedSize; in _initializeBandedChain() typedef 1046 typedef typename MakeSigned<TSize>::Type TSignedSize; in _computeAnchorArea() typedef [all …]
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/seeds/ |
H A D | banded_chain_alignment_impl.h | 136 typedef typename MakeSigned<TSize>::Type TSignedSize; in _isCrossingBeginHorizontal() typedef 137 if ((TSignedSize) horizontalSeedBeginPos - (TSignedSize) bandExtension <= 0) in _isCrossingBeginHorizontal() 150 typedef typename MakeSigned<TSize>::Type TSignedSize; in _isCrossingBeginVertical() typedef 152 if ((TSignedSize) verticalSeedBeginPos - (TSignedSize) bandExtension <= 0) in _isCrossingBeginVertical() 168 typedef typename MakeSigned<TSize>::Type TSignedSize; in _isCrossingEndHorizontal() typedef 170 if ((TSignedSize) horizontalSeedEndPos + (TSignedSize) bandSize >= (TSignedSize) length(seqH)) in _isCrossingEndHorizontal() 186 typedef typename MakeSigned<TSize>::Type TSignedSize; in _isCrossingEndVertical() typedef 188 if ((TSignedSize) verticalSeedEndPos + (TSignedSize) bandSize >= (TSignedSize) length(seqV)) in _isCrossingEndVertical() 826 typedef typename MakeSigned<TSeedSize>::Type TSignedSize; in _initializeBandedChain() typedef 1046 typedef typename MakeSigned<TSize>::Type TSignedSize; in _computeAnchorArea() typedef [all …]
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/align/ |
H A D | dp_matrix_navigator_score_matrix_sparse.h | 84 typedef std::make_signed_t<TSize> TSignedSize; in DPMatrixNavigator_() typedef 100 …_laneLeap = _max(lowerDiagonal(band), 1 - static_cast<TSignedSize>(length(matrix, DPMatrixDimensio… in DPMatrixNavigator_()
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H A D | dp_algorithm_impl.h | 198 typedef typename MakeSigned<typename Size<TSequenceH>::Type>::Type TSignedSize; in _checkBandProperties() typedef 201 if (upperDiagonal(band) < (0 - static_cast<TSignedSize>(length(seqV))) || in _checkBandProperties() 202 lowerDiagonal(band) > static_cast<TSignedSize>(length(seqH))) in _checkBandProperties() 219 …if (upperDiagonal(band) + static_cast<TSignedSize>(length(seqV)) < static_cast<TSignedSize>(length… in _checkBandProperties() 227 …if (lowerDiagonal(band) + static_cast<TSignedSize>(length(seqV)) > static_cast<TSignedSize>(length… in _checkBandProperties()
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H A D | dp_matrix_navigator_score_matrix.h | 87 using TSignedSize = std::make_signed_t<TMatrixSize>; in DPMatrixNavigator_() local 105 int lastPos = _max(-static_cast<TSignedSize>(lengthVertical - 1), lowerDiagonal(band)); in DPMatrixNavigator_()
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H A D | dp_matrix_navigator_trace_matrix.h | 96 using TSignedSize = std::make_signed_t<TMatrixSize>; in DPMatrixNavigator_() local 120 int lastPos = _max(-static_cast<TSignedSize>(lengthVertical - 1), lowerDiagonal(band)); in DPMatrixNavigator_()
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/align/ |
H A D | dp_matrix_navigator_score_matrix_sparse.h | 84 typedef std::make_signed_t<TSize> TSignedSize; in DPMatrixNavigator_() typedef 100 …_laneLeap = _max(lowerDiagonal(band), 1 - static_cast<TSignedSize>(length(matrix, DPMatrixDimensio… in DPMatrixNavigator_()
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H A D | dp_algorithm_impl.h | 198 typedef typename MakeSigned<typename Size<TSequenceH>::Type>::Type TSignedSize; in _checkBandProperties() typedef 201 if (upperDiagonal(band) < (0 - static_cast<TSignedSize>(length(seqV))) || in _checkBandProperties() 202 lowerDiagonal(band) > static_cast<TSignedSize>(length(seqH))) in _checkBandProperties() 219 …if (upperDiagonal(band) + static_cast<TSignedSize>(length(seqV)) < static_cast<TSignedSize>(length… in _checkBandProperties() 227 …if (lowerDiagonal(band) + static_cast<TSignedSize>(length(seqV)) > static_cast<TSignedSize>(length… in _checkBandProperties()
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H A D | dp_matrix_navigator_score_matrix.h | 87 using TSignedSize = std::make_signed_t<TMatrixSize>; in DPMatrixNavigator_() local 105 int lastPos = _max(-static_cast<TSignedSize>(lengthVertical - 1), lowerDiagonal(band)); in DPMatrixNavigator_()
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H A D | dp_matrix_navigator_trace_matrix.h | 96 using TSignedSize = std::make_signed_t<TMatrixSize>; in DPMatrixNavigator_() local 120 int lastPos = _max(-static_cast<TSignedSize>(lengthVertical - 1), lowerDiagonal(band)); in DPMatrixNavigator_()
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/align/ |
H A D | dp_algorithm_impl.h | 174 typedef typename MakeSigned<typename Size<TSequenceH>::Type>::Type TSignedSize; in _checkBandProperties() typedef 177 if (upperDiagonal(band) < (0 - static_cast<TSignedSize>(length(seqV))) || in _checkBandProperties() 178 lowerDiagonal(band) > static_cast<TSignedSize>(length(seqH))) in _checkBandProperties() 195 …if (upperDiagonal(band) + static_cast<TSignedSize>(length(seqV)) < static_cast<TSignedSize>(length… in _checkBandProperties() 203 …if (lowerDiagonal(band) + static_cast<TSignedSize>(length(seqV)) > static_cast<TSignedSize>(length… in _checkBandProperties()
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H A D | dp_matrix_navigator_score_matrix_sparse.h | 122 typedef typename MakeSigned<TSize>::Type TSignedSize; in _init() typedef 138 …navigator._laneLeap = _max(lowerDiagonal(band), 1 - static_cast<TSignedSize>(length(dpMatrix, DPMa… in _init()
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H A D | dp_matrix_navigator_score_matrix.h | 122 typedef typename MakeSigned<TMatrixSize>::Type TSignedSize; in _init() typedef 140 int lastPos = _max(-static_cast<TSignedSize>(lengthVertical - 1), lowerDiagonal(band)); in _init()
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H A D | dp_matrix_navigator_trace_matrix.h | 125 typedef typename MakeSigned<TMatrixSize>::Type TSignedSize; in _init() typedef 149 int lastPos = _max(-static_cast<TSignedSize>(lengthVertical - 1), lowerDiagonal(band)); in _init()
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/journaled_string_tree/ |
H A D | delta_store.h | 563 typedef typename MakeSigned<typename Size<TStore>::Type>::Type TSignedSize; 564 return static_cast<TSignedSize>(insertionSize(store, pos, TTag())) - 565 static_cast<TSignedSize>(deletionSize(store, pos, TTag()));
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/journaled_string_tree/ |
H A D | delta_store.h | 563 typedef typename MakeSigned<typename Size<TStore>::Type>::Type TSignedSize; 564 return static_cast<TSignedSize>(insertionSize(store, pos, TTag())) - 565 static_cast<TSignedSize>(deletionSize(store, pos, TTag()));
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/graph_msa/ |
H A D | graph_align_tcoffee_library.h | 807 typedef typename MakeSigned<TSize>::Type TSignedSize; in assureBandedRestriction_() typedef 809 TSignedSize lenH = length(pairSet[0]); in assureBandedRestriction_() 810 TSignedSize lenV = length(pairSet[1]); in assureBandedRestriction_() 811 TSignedSize halfWidth = bandWidth / 2; in assureBandedRestriction_()
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/graph_msa/ |
H A D | graph_align_tcoffee_library.h | 807 typedef typename MakeSigned<TSize>::Type TSignedSize; in assureBandedRestriction_() typedef 809 TSignedSize lenH = length(pairSet[0]); in assureBandedRestriction_() 810 TSignedSize lenV = length(pairSet[1]); in assureBandedRestriction_() 811 TSignedSize halfWidth = bandWidth / 2; in assureBandedRestriction_()
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/index/ |
H A D | index_shims.h | 227 typedef typename MakeSigned<TSize>::Type TSignedSize; in createInvSuffixArray() typedef 235 for (TSignedSize job = 0; job < static_cast<TSignedSize>(length(splitter)); ++job) in createInvSuffixArray()
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/index/ |
H A D | index_shims.h | 227 typedef typename MakeSigned<TSize>::Type TSignedSize; in createInvSuffixArray() typedef 235 for (TSignedSize job = 0; job < static_cast<TSignedSize>(length(splitter)); ++job) in createInvSuffixArray()
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