/dports/biology/seqan-apps/seqan-seqan-v2.4.0/tests/seeds/ |
H A D | test_align_banded_chain_impl.cpp | 63 Score<int,Simple> scoreScheme(5, -3, -5); in testBandedChainAlignmentEmptyChain() local 98 Score<int,Simple> scoreScheme(5, -3, -5); in testBandedChainAlignmentOneSeed() local 123 Score<int,Simple> scoreScheme(5, -3, -5); in testBandedChainAlignmentOneSeed() local 158 Score<int,Simple> scoreScheme(5, -3, -5); in testBandedChainAlignmentOneSeed() local 193 Score<int,Simple> scoreScheme(5, -3, -5); in testBandedChainAlignmentOneSeed() local 228 Score<int,Simple> scoreScheme(5, -3, -5); in testBandedChainAlignmentOneSeed() local 263 Score<int,Simple> scoreScheme(5, -3, -5); in testBandedChainAlignmentOneSeed() local 298 Score<int,Simple> scoreScheme(5, -3, -5); in testBandedChainAlignmentOneSeed() local 333 Score<int,Simple> scoreScheme(5, -3, -5); in testBandedChainAlignmentOneSeed() local 368 Score<int,Simple> scoreScheme(5, -3, -5); in testBandedChainAlignmentOneSeed() local [all …]
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/tests/align/ |
H A D | test_alignment_algorithms_dynamic_gap.h | 73 eScore += scoreGapOpen(scoreScheme); in _validateAlignment() 78 eScore += scoreGapExtend(scoreScheme); in _validateAlignment() 86 eScore += scoreGapOpen(scoreScheme); in _validateAlignment() 91 eScore += scoreGapExtend(scoreScheme); in _validateAlignment() 99 eScore += scoreMatch(scoreScheme); in _validateAlignment() 101 eScore += scoreMismatch(scoreScheme); in _validateAlignment() 118 eScore -= scoreGapOpen(scoreScheme); in _validateAlignment() 134 eScore -= scoreGapOpen(scoreScheme); in _validateAlignment() 150 eScore -= scoreGapOpen(scoreScheme); in _validateAlignment() 166 eScore -= scoreGapOpen(scoreScheme); in _validateAlignment() [all …]
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/align_extend/ |
H A D | align_extend.h | 269 centerScore += scoreGapOpen(scoreScheme); in _extendAlignmentImpl() 273 centerScore += scoreGapExtend(scoreScheme); in _extendAlignmentImpl() 278 centerScore += score(scoreScheme, row0[i], row1[i]); in _extendAlignmentImpl() 417 if (scoreGapOpen(scoreScheme) == scoreGapExtend(scoreScheme)) in _extendAlignmentImpl() 502 Score<TScoreValue, TScoreSpec> const & scoreScheme) in extendAlignment() argument 517 Score<TScoreValue, TScoreSpec> const & scoreScheme) in extendAlignment() argument 534 Score<TScoreValue, TScoreSpec> const & scoreScheme) in extendAlignment() argument 537 0, scoreScheme, True(), False()); in extendAlignment() 554 scoreScheme, True(), False()); in extendAlignment() 570 scoreScheme, False(), True()); in extendAlignment() [all …]
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/align_extend/ |
H A D | align_extend.h | 269 centerScore += scoreGapOpen(scoreScheme); in _extendAlignmentImpl() 273 centerScore += scoreGapExtend(scoreScheme); in _extendAlignmentImpl() 278 centerScore += score(scoreScheme, row0[i], row1[i]); in _extendAlignmentImpl() 417 if (scoreGapOpen(scoreScheme) == scoreGapExtend(scoreScheme)) in _extendAlignmentImpl() 502 Score<TScoreValue, TScoreSpec> const & scoreScheme) in extendAlignment() argument 517 Score<TScoreValue, TScoreSpec> const & scoreScheme) in extendAlignment() argument 534 Score<TScoreValue, TScoreSpec> const & scoreScheme) in extendAlignment() argument 537 0, scoreScheme, True(), False()); in extendAlignment() 554 scoreScheme, True(), False()); in extendAlignment() 570 scoreScheme, False(), True()); in extendAlignment() [all …]
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/align_extend/ |
H A D | align_extend.h | 283 centerScore += scoreGapOpen(scoreScheme); in _extendAlignmentImpl() 287 centerScore += scoreGapExtend(scoreScheme); in _extendAlignmentImpl() 292 centerScore += score(scoreScheme, value(row0, i), in _extendAlignmentImpl() 396 if (scoreGapOpen(scoreScheme) == scoreGapExtend(scoreScheme)) in _extendAlignmentImpl() 477 Score<TScoreValue, TScoreSpec> const & scoreScheme) in extendAlignment() argument 492 Score<TScoreValue, TScoreSpec> const & scoreScheme) in extendAlignment() argument 509 Score<TScoreValue, TScoreSpec> const & scoreScheme) in extendAlignment() argument 512 0, scoreScheme, True(), False()); in extendAlignment() 529 scoreScheme, True(), False()); in extendAlignment() 545 scoreScheme, False(), True()); in extendAlignment() [all …]
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/seeds/ |
H A D | banded_chain_alignment.h | 217 Score<TScoreValue, TScoreSpec> const & scoreScheme, 221 … return bandedChainAlignment(align, seedSet, scoreScheme, scoreScheme, alignConfig, bandExtension); 242 Score<TScoreValue, TScoreSpec> const & scoreScheme, 245 …return bandedChainAlignment(align, seedSet, scoreScheme, scoreScheme, AlignConfig<>(), bandExtensi… 288 Score<TScoreValue, TScoreSpec> const & scoreScheme, 292 …return bandedChainAlignment(gapsHorizontal, gapsVertical, seedSet, scoreScheme, scoreScheme, align… 321 …return bandedChainAlignment(gapsHorizontal, gapsVertical, seedSet, scoreScheme, scoreScheme, Align… 369 …return bandedChainAlignment(alignmentGraph, seedSet, scoreScheme, scoreScheme, alignConfig, bandEx… 395 …return bandedChainAlignment(alignmentGraph, seedSet, scoreScheme, scoreScheme, AlignConfig<>(), ba… 440 …return bandedChainAlignment(fragmentString, strings, seedSet, scoreScheme, scoreScheme, alignConfi… [all …]
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H A D | banded_chain_alignment_impl.h | 753 TScoreScheme const & scoreScheme, in _initiaizeBeginningOfBandedChain() argument 772 Nothing(), Nothing(), scoreScheme, in _initiaizeBeginningOfBandedChain() 776 Nothing(), Nothing(), scoreScheme, in _initiaizeBeginningOfBandedChain() 790 Nothing(), Nothing(), scoreScheme, in _initiaizeBeginningOfBandedChain() 794 Nothing(), Nothing(), scoreScheme, in _initiaizeBeginningOfBandedChain() 978 TScoreScheme const & scoreScheme, in _computeGapArea() argument 997 …AN_ASSERT(_checkScoreOverflow(gridEnd.i1 - gridBegin.i1 + gridEnd.i2 - gridBegin.i2, scoreScheme)); in _computeGapArea() 1040 TScoreScheme const & scoreScheme, in _computeAnchorArea() argument 1085 …TScore score = _computeAlignment(localTraceSet, scoutState, infixH, infixV, scoreScheme, band, dpP… in _computeAnchorArea() 1257 TScoreScheme const & scoreScheme, in _computeAlignment() argument [all …]
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/seeds/ |
H A D | banded_chain_alignment.h | 217 Score<TScoreValue, TScoreSpec> const & scoreScheme, 221 … return bandedChainAlignment(align, seedSet, scoreScheme, scoreScheme, alignConfig, bandExtension); 242 Score<TScoreValue, TScoreSpec> const & scoreScheme, 245 …return bandedChainAlignment(align, seedSet, scoreScheme, scoreScheme, AlignConfig<>(), bandExtensi… 288 Score<TScoreValue, TScoreSpec> const & scoreScheme, 292 …return bandedChainAlignment(gapsHorizontal, gapsVertical, seedSet, scoreScheme, scoreScheme, align… 321 …return bandedChainAlignment(gapsHorizontal, gapsVertical, seedSet, scoreScheme, scoreScheme, Align… 369 …return bandedChainAlignment(alignmentGraph, seedSet, scoreScheme, scoreScheme, alignConfig, bandEx… 395 …return bandedChainAlignment(alignmentGraph, seedSet, scoreScheme, scoreScheme, AlignConfig<>(), ba… 440 …return bandedChainAlignment(fragmentString, strings, seedSet, scoreScheme, scoreScheme, alignConfi… [all …]
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H A D | banded_chain_alignment_impl.h | 753 TScoreScheme const & scoreScheme, in _initiaizeBeginningOfBandedChain() argument 772 Nothing(), Nothing(), scoreScheme, in _initiaizeBeginningOfBandedChain() 776 Nothing(), Nothing(), scoreScheme, in _initiaizeBeginningOfBandedChain() 790 Nothing(), Nothing(), scoreScheme, in _initiaizeBeginningOfBandedChain() 794 Nothing(), Nothing(), scoreScheme, in _initiaizeBeginningOfBandedChain() 978 TScoreScheme const & scoreScheme, in _computeGapArea() argument 997 …AN_ASSERT(_checkScoreOverflow(gridEnd.i1 - gridBegin.i1 + gridEnd.i2 - gridBegin.i2, scoreScheme)); in _computeGapArea() 1040 TScoreScheme const & scoreScheme, in _computeAnchorArea() argument 1085 …TScore score = _computeAlignment(localTraceSet, scoutState, infixH, infixV, scoreScheme, band, dpP… in _computeAnchorArea() 1257 TScoreScheme const & scoreScheme, in _computeAlignment() argument [all …]
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/seeds/ |
H A D | banded_chain_alignment.h | 217 Score<TScoreValue, TScoreSpec> const & scoreScheme, 221 … return bandedChainAlignment(align, seedSet, scoreScheme, scoreScheme, alignConfig, bandExtension); 242 Score<TScoreValue, TScoreSpec> const & scoreScheme, 245 …return bandedChainAlignment(align, seedSet, scoreScheme, scoreScheme, AlignConfig<>(), bandExtensi… 288 Score<TScoreValue, TScoreSpec> const & scoreScheme, 292 …return bandedChainAlignment(gapsHorizontal, gapsVertical, seedSet, scoreScheme, scoreScheme, align… 321 …return bandedChainAlignment(gapsHorizontal, gapsVertical, seedSet, scoreScheme, scoreScheme, Align… 369 …return bandedChainAlignment(alignmentGraph, seedSet, scoreScheme, scoreScheme, alignConfig, bandEx… 395 …return bandedChainAlignment(alignmentGraph, seedSet, scoreScheme, scoreScheme, AlignConfig<>(), ba… 440 …return bandedChainAlignment(fragmentString, strings, seedSet, scoreScheme, scoreScheme, alignConfi… [all …]
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H A D | banded_chain_alignment_impl.h | 672 TScoreScheme const & scoreScheme, in _initiaizeBeginningOfBandedChain() argument 688 …puteScore(dpInitCellHorizontal, TDPCell(), TDPCell(), TDPCell(), Nothing(), Nothing(), scoreScheme, in _initiaizeBeginningOfBandedChain() 691 …mputeScore(dpInitCellHorizontal, TDPCell(), prevCell, TDPCell(), Nothing(), Nothing(), scoreScheme, in _initiaizeBeginningOfBandedChain() 703 …omputeScore(dpInitCellVertical, TDPCell(), TDPCell(), TDPCell(), Nothing(), Nothing(), scoreScheme, in _initiaizeBeginningOfBandedChain() 706 …computeScore(dpInitCellVertical, TDPCell(), TDPCell(), prevCell, Nothing(), Nothing(), scoreScheme, in _initiaizeBeginningOfBandedChain() 888 TScoreScheme const & scoreScheme, in _computeGapArea() argument 922 …TScoreValue score = _computeAlignment(localTraceSet, scoutState, infixH, infixV, scoreScheme, TBan… in _computeGapArea() 947 TScoreScheme const & scoreScheme, in _computeAnchorArea() argument 992 …TScore score = _computeAlignment(localTraceSet, scoutState, infixH, infixV, scoreScheme, band, dpP… in _computeAnchorArea() 1162 TScoreScheme const & scoreScheme, in _computeAlignment() argument [all …]
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/dports/biology/seqan/seqan-library-2.4.0/share/doc/seqan/html/demos/dox/seeds/ |
H A D | seeds_add_seed.cpp | 48 Score<int, Simple> scoreScheme(2, -1, -2); in main() local 49 if (!addSeed(seedSet, seed0, 2, 1, scoreScheme, seqH, seqV, Chaos())) in main() 51 if (!addSeed(seedSet, seed1, 2, 1, scoreScheme, seqH, seqV, Chaos())) in main() 53 if (!addSeed(seedSet, seed2, 2, 1, scoreScheme, seqH, seqV, Chaos())) in main() 55 if (!addSeed(seedSet, seed3, 2, 1, scoreScheme, seqH, seqV, Chaos())) in main()
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/demos/dox/seeds/ |
H A D | seeds_add_seed.cpp | 48 Score<int, Simple> scoreScheme(2, -1, -2); in main() local 49 if (!addSeed(seedSet, seed0, 2, 1, scoreScheme, seqH, seqV, Chaos())) in main() 51 if (!addSeed(seedSet, seed1, 2, 1, scoreScheme, seqH, seqV, Chaos())) in main() 53 if (!addSeed(seedSet, seed2, 2, 1, scoreScheme, seqH, seqV, Chaos())) in main() 55 if (!addSeed(seedSet, seed3, 2, 1, scoreScheme, seqH, seqV, Chaos())) in main()
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/dports/biology/seqan/seqan-library-2.4.0/share/doc/seqan/html/demos/dox/score/ |
H A D | score.cpp | 17 …Score<int> scoreScheme(5, -6, -2, -11); // Initialize Score object with affine gap costs. in main() local 18 …int score = globalAlignment(align, scoreScheme); // Computes a global alignment usign the defined… in main()
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/demos/dox/score/ |
H A D | score.cpp | 17 …Score<int> scoreScheme(5, -6, -2, -11); // Initialize Score object with affine gap costs. in main() local 18 …int score = globalAlignment(align, scoreScheme); // Computes a global alignment usign the defined… in main()
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/align/ |
H A D | dp_algorithm_impl.h | 1385 TScoreScheme const & scoreScheme, in _computeAlignment() argument 1448 …nment(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, dpProfile); in _computeAlignment() 1450 …e(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, dpProfil… in _computeAlignment() 1452 …teBandedAlignment(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, in _computeAlignment()
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/align/ |
H A D | dp_algorithm_impl.h | 1354 TScoreScheme const & scoreScheme, in _computeAlignment() argument 1417 …ignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, in _computeAlignment()
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/align/ |
H A D | dp_algorithm_impl.h | 1354 TScoreScheme const & scoreScheme, in _computeAlignment() argument 1417 …ignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, in _computeAlignment()
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