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Searched refs:scoreScheme (Results 1 – 18 of 18) sorted by relevance

/dports/biology/seqan-apps/seqan-seqan-v2.4.0/tests/seeds/
H A Dtest_align_banded_chain_impl.cpp63 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
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/tests/align/
H A Dtest_alignment_algorithms_dynamic_gap.h73 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()
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/align_extend/
H A Dalign_extend.h269 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()
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/align_extend/
H A Dalign_extend.h269 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()
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/align_extend/
H A Dalign_extend.h283 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()
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/seeds/
H A Dbanded_chain_alignment.h217 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…
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H A Dbanded_chain_alignment_impl.h753 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
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/seeds/
H A Dbanded_chain_alignment.h217 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…
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H A Dbanded_chain_alignment_impl.h753 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
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/seeds/
H A Dbanded_chain_alignment.h217 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…
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H A Dbanded_chain_alignment_impl.h672 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
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/dports/biology/seqan/seqan-library-2.4.0/share/doc/seqan/html/demos/dox/seeds/
H A Dseeds_add_seed.cpp48 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()
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/demos/dox/seeds/
H A Dseeds_add_seed.cpp48 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()
/dports/biology/seqan/seqan-library-2.4.0/share/doc/seqan/html/demos/dox/score/
H A Dscore.cpp17 …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()
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/demos/dox/score/
H A Dscore.cpp17 …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()
/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/align/
H A Ddp_algorithm_impl.h1385 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()
/dports/biology/seqan/seqan-library-2.4.0/include/seqan/align/
H A Ddp_algorithm_impl.h1354 TScoreScheme const & scoreScheme, in _computeAlignment() argument
1417 …ignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, in _computeAlignment()
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/align/
H A Ddp_algorithm_impl.h1354 TScoreScheme const & scoreScheme, in _computeAlignment() argument
1417 …ignmentImpl(dpScout, dpScoreMatrixNavigator, dpTraceMatrixNavigator, seqH, seqV, scoreScheme, band, in _computeAlignment()