/dports/biology/seqan/seqan-library-2.4.0/include/seqan/alignment_free/ |
H A D | af_d2.h | 49 void _alignmentFreeComparison(Matrix<TValue, 2> & scoreMatrix, in _alignmentFreeComparison() argument 62 setLength(scoreMatrix, 0, seqNumber); in _alignmentFreeComparison() 63 setLength(scoreMatrix, 1, seqNumber); in _alignmentFreeComparison() 64 resize(scoreMatrix, (TValue) 0); in _alignmentFreeComparison() 92 …_alignmentFreeCompareCounts(value(scoreMatrix, rowIndex, colIndex), kmerCounts[rowIndex], kmerCoun… in _alignmentFreeComparison() 93 …value(scoreMatrix, colIndex, rowIndex) = value(scoreMatrix, rowIndex, colIndex); // Copy symmetri… in _alignmentFreeComparison()
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H A D | af_d2star.h | 51 void _alignmentFreeComparison(Matrix<TValue, 2> & scoreMatrix, in _alignmentFreeComparison() argument 64 setLength(scoreMatrix, 0, seqNumber); in _alignmentFreeComparison() 65 setLength(scoreMatrix, 1, seqNumber); in _alignmentFreeComparison() 66 resize(scoreMatrix, (TValue) 0); in _alignmentFreeComparison() 79 …_d2star(value(scoreMatrix, rowIndex, colIndex), sequenceSet[rowIndex], sequenceSet[colIndex], scor… in _alignmentFreeComparison() 80 …value(scoreMatrix, colIndex, rowIndex) = value(scoreMatrix, rowIndex, colIndex); // Copy symmetri… in _alignmentFreeComparison()
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H A D | alignment_free_comparison.h | 99 void alignmentFreeComparison(Matrix<TValue, 2> & scoreMatrix, TStringSet const & sequenceSet, TComp… in alignmentFreeComparison() argument 101 _alignmentFreeComparison(scoreMatrix, sequenceSet, comparisonMethod); in alignmentFreeComparison()
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/alignment_free/ |
H A D | af_d2.h | 49 void _alignmentFreeComparison(Matrix<TValue, 2> & scoreMatrix, in _alignmentFreeComparison() argument 62 setLength(scoreMatrix, 0, seqNumber); in _alignmentFreeComparison() 63 setLength(scoreMatrix, 1, seqNumber); in _alignmentFreeComparison() 64 resize(scoreMatrix, (TValue) 0); in _alignmentFreeComparison() 92 …_alignmentFreeCompareCounts(value(scoreMatrix, rowIndex, colIndex), kmerCounts[rowIndex], kmerCoun… in _alignmentFreeComparison() 93 …value(scoreMatrix, colIndex, rowIndex) = value(scoreMatrix, rowIndex, colIndex); // Copy symmetri… in _alignmentFreeComparison()
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H A D | af_d2star.h | 51 void _alignmentFreeComparison(Matrix<TValue, 2> & scoreMatrix, in _alignmentFreeComparison() argument 64 setLength(scoreMatrix, 0, seqNumber); in _alignmentFreeComparison() 65 setLength(scoreMatrix, 1, seqNumber); in _alignmentFreeComparison() 66 resize(scoreMatrix, (TValue) 0); in _alignmentFreeComparison() 79 …_d2star(value(scoreMatrix, rowIndex, colIndex), sequenceSet[rowIndex], sequenceSet[colIndex], scor… in _alignmentFreeComparison() 80 …value(scoreMatrix, colIndex, rowIndex) = value(scoreMatrix, rowIndex, colIndex); // Copy symmetri… in _alignmentFreeComparison()
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H A D | alignment_free_comparison.h | 99 void alignmentFreeComparison(Matrix<TValue, 2> & scoreMatrix, TStringSet const & sequenceSet, TComp… in alignmentFreeComparison() argument 101 _alignmentFreeComparison(scoreMatrix, sequenceSet, comparisonMethod); in alignmentFreeComparison()
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/alignment_free/ |
H A D | af_d2.h | 49 void _alignmentFreeComparison(Matrix<TValue, 2> & scoreMatrix, in _alignmentFreeComparison() argument 62 setLength(scoreMatrix, 0, seqNumber); in _alignmentFreeComparison() 63 setLength(scoreMatrix, 1, seqNumber); in _alignmentFreeComparison() 64 resize(scoreMatrix, (TValue) 0); in _alignmentFreeComparison() 92 …_alignmentFreeCompareCounts(value(scoreMatrix, rowIndex, colIndex), kmerCounts[rowIndex], kmerCoun… in _alignmentFreeComparison() 93 …value(scoreMatrix, colIndex, rowIndex) = value(scoreMatrix, rowIndex, colIndex); // Copy symmetri… in _alignmentFreeComparison()
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H A D | af_d2star.h | 51 void _alignmentFreeComparison(Matrix<TValue, 2> & scoreMatrix, in _alignmentFreeComparison() argument 64 setLength(scoreMatrix, 0, seqNumber); in _alignmentFreeComparison() 65 setLength(scoreMatrix, 1, seqNumber); in _alignmentFreeComparison() 66 resize(scoreMatrix, (TValue) 0); in _alignmentFreeComparison() 79 …_d2star(value(scoreMatrix, rowIndex, colIndex), sequenceSet[rowIndex], sequenceSet[colIndex], scor… in _alignmentFreeComparison() 80 …value(scoreMatrix, colIndex, rowIndex) = value(scoreMatrix, rowIndex, colIndex); // Copy symmetri… in _alignmentFreeComparison()
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H A D | alignment_free_comparison.h | 99 void alignmentFreeComparison(Matrix<TValue, 2> & scoreMatrix, TStringSet const & sequenceSet, TComp… in alignmentFreeComparison() argument 101 _alignmentFreeComparison(scoreMatrix, sequenceSet, comparisonMethod); in alignmentFreeComparison()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/structure/cd_utils/ |
H A D | cuSeqTreeFactory.cpp | 128 …atrix(const EDistMethod method, AlignmentCollection* alignData, const EScoreMatrixType scoreMatrix, in GetMatrix() argument 142 m_matrix = new DM_Identities(scoreMatrix); in GetMatrix() 150 m_matrix = new DM_Identities(scoreMatrix); in GetMatrix() 158 m_matrix = new DM_AlignedScore(scoreMatrix); in GetMatrix() 165 m_matrix = new DMAlignedOptimalScore(scoreMatrix); in GetMatrix() 172 m_matrix = new FlexiDm(scoreMatrix); in GetMatrix()
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/dports/biology/mothur/mothur-1.46.1/source/commands/ |
H A D | makelookupcommand.cpp | 400 vector<vector<double> > scoreMatrix; scoreMatrix.resize(numQueryFlows+1); in alignFlowGrams() local 405 scoreMatrix[i].resize(numRefFlows+1, 0.00); in alignFlowGrams() 408 scoreMatrix[i][0] = i * gapOpening; in alignFlowGrams() 413 scoreMatrix[0][i] = i * gapOpening; in alignFlowGrams() 425 double up = scoreMatrix[i-1][j] + gapOpening; in alignFlowGrams() 426 double left = scoreMatrix[i][j-1] + gapOpening; in alignFlowGrams() 440 scoreMatrix[i][j] = minScore; in alignFlowGrams() 450 if(scoreMatrix[i][numRefFlows] < minRowScore){ in alignFlowGrams() 451 minRowScore = scoreMatrix[i][numRefFlows]; in alignFlowGrams() 460 if(scoreMatrix[numQueryFlows][i] < minColumnScore){ in alignFlowGrams() [all …]
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/dports/biology/seqan1/seqan-1.3.1/seqan/seeds/ |
H A D | seed_base.h | 636 Score<TPosition2,Simple> const &scoreMatrix, 663 Score<TPosition2, Simple> const &scoreMatrix, 689 Score<TPosition2,Simple> const &scoreMatrix, 788 Score<TScore, Simple> const &scoreMatrix, 807 tmpScore += score(scoreMatrix, xPos, yPos, query, database); 811 tmpScore += score(scoreMatrix, xPos, yPos, query, database); 834 tmpScore += score(scoreMatrix, xPos, yPos, query, database); 838 tmpScore += score(scoreMatrix, xPos, yPos, query, database); 887 Score<TScore, Simple> const & scoreMatrix, 889 TScore gapCost = scoreGap(scoreMatrix); [all …]
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H A D | banded_chain_align.h | 60 Score< TScore, Simple> const &scoreMatrix) in bandedChainAlignment() argument 76 if(scoreGapOpen(scoreMatrix)==scoreGapExtend(scoreMatrix)) in bandedChainAlignment() 79 return _chainToAlignmentGotoh(copyChain, k, whole_alignment, scoreMatrix); in bandedChainAlignment() 84 if(scoreGapOpen(scoreMatrix)==scoreGapExtend(scoreMatrix)) in bandedChainAlignment() 87 return _chainToAlignmentGotoh(seedChain, k, whole_alignment, scoreMatrix); in bandedChainAlignment() 95 Score< TScore, Simple> const &scoreMatrix) in _chainToAlignmentNeedlemanWunsch() argument 614 TScoreMatrix const &scoreMatrix) in _calculateBandedSeed() argument 694 TScoreMatrix const &scoreMatrix) in _calculateFirstRectangle() argument 743 TScoreMatrix const &scoreMatrix) in _calculateLastRectangle() argument 761 _needlemanWunsch(matrix_, seg1, seg2, scoreMatrix); in _calculateLastRectangle() [all …]
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H A D | seed_multi.h | 391 Score<TPosition2,Simple> const &scoreMatrix, in _mergeTwoSeedsScore() argument 405 score1 -= firstSeed.seedSet.back().i3*scoreMatch(scoreMatrix); in _mergeTwoSeedsScore() 411 score1 += abs(endDiagonal(firstSeed) - dPos + qPos)*scoreGap(scoreMatrix); in _mergeTwoSeedsScore() 460 Score<TPosition2,Simple> const &scoreMatrix, in _mergeTwoSeedsScore() argument 473 score1 -= firstSeed.seedSet.back().i3*scoreMatch(scoreMatrix); in _mergeTwoSeedsScore() 479 score1 += abs(endDiagonal(firstSeed) - startDiagonal(secondSeed))*scoreGap(scoreMatrix); in _mergeTwoSeedsScore() 587 Score<TPosition2, Simple> &scoreMatrix) in getAlignment() argument 609 seedScore += score(scoreMatrix,(*it1).i1+i, (*it1).i2+i, query, database); in getAlignment() 620 seedScore += gapLength*scoreGap(scoreMatrix); in getAlignment() 629 seedScore += gapLength*scoreGap(scoreMatrix); in getAlignment() [all …]
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H A D | seedSet_score.h | 172 Score<int, Simple> scoreMatrix; 213 Score<int, Simple> scoreMatrix; 297 set.scoreMatrix = matrix; 306 return set.scoreMatrix; 949 Score<TScore, Simple> const &scoreMatrix, 1011 Score<TScore, Simple> const &scoreMatrix, 1255 Score<TScore, Simple> const &scoreMatrix, 1292 tmpScore += it2->i3*scoreMatch(scoreMatrix); 1315 Score<TScore, Simple> const &scoreMatrix, 1966 Score<TValue, Simple> const &scoreMatrix, [all …]
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/dports/biology/seqan1/seqan-1.3.1/demos/ |
H A D | swift_verification.cpp | 31 Score<TScoreValue> scoreMatrix(matchScore, penalty, penalty); in main() local 50 localAlignment(localAlign, scoreMatrix, lowDiag, highDiag, BandedSmithWaterman()); in main() 63 extendSeed(seed, 5*(-penalty), scoreMatrix, seq_0, seq_1, 2, GappedXDrop()); in main() 79 …globalAlignment(leftAlign, leftExtensions, scoreMatrix, lowDiag, highDiag, BandedNeedlemanWunsch()… in main() 98 …globalAlignment(rightAlign, rightExtensions, scoreMatrix, lowDiag, highDiag, BandedNeedlemanWunsch… in main()
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/dports/biology/hyphy/hyphy-2.5.33/src/core/ |
H A D | alignment.cpp | 1280 scoreMatrix.theData[0] = 0.; in CostOnly() 1290 scoreMatrix.theData[k] = cost; in CostOnly() 1296 scoreMatrix.theData[m] = cost; in CostOnly() 1300 scoreMatrix.theData[k] = 0.; in CostOnly() 1400 scoreMatrix.theData[c] = t; in CostOnly() 1457 scoreMatrix.theData[c] = score1; in CostOnly() 1459 scoreMatrix.theData[c] = score2; in CostOnly() 1474 score = scoreMatrix.theData[s2Length]; in CostOnly() 1489 scoreMatrix.theData[0] = 0.0; in CostOnly() 1499 scoreMatrix.theData[k] = score; in CostOnly() [all …]
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/demos/howto/scores/ |
H A D | load_score.cpp | 60 Score<TScoreValue, ScoreMatrix<Dna5, Default> > scoreMatrix; in main() local 61 loadScoreMatrix(scoreMatrix, toCString(getAbsolutePath("demos/howto/scores/dna_example.txt"))); in main() 62 showScoringMatrix(scoreMatrix); in main()
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/dports/biology/seqan1/seqan-1.3.1/demos/tutorial/scores/ |
H A D | load_score.cpp | 63 Score<TScoreValue, ScoreMatrix<Dna, Default> > scoreMatrix; in main() local 64 loadScoreMatrix(scoreMatrix, argv[1]); in main() 65 showScoringMatrix(scoreMatrix); in main()
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/dports/biology/seqan1/seqan-1.3.1/apps/stellar/ |
H A D | stellar.h | 62 Score<TScoreValue> const & scoreMatrix, in _appendNegativeSegment() argument 71 score += scoreGap(scoreMatrix); in _appendNegativeSegment() 73 score += scoreMismatch(scoreMatrix); in _appendNegativeSegment() 89 Score<TScoreValue> const & scoreMatrix, in _appendPositiveSegment() argument 101 score += scoreMatch(scoreMatrix); in _appendPositiveSegment() 165 Score<TScoreValue> & scoreMatrix, in _splitAtXDrops() argument 186 _appendPositiveSegment(align, pos, aliLength, scoreMatrix, queue); in _splitAtXDrops() 187 _appendNegativeSegment(align, pos, aliLength, scoreMatrix, queue); in _splitAtXDrops() 401 Score<TScore> scoreMatrix(match, mismatchIndel, mismatchIndel); in verifySwiftHit() 468 Score<TScore> scoreMatrix(match, mismatchIndel, mismatchIndel); in verifySwiftHit() [all …]
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/stellar/ |
H A D | stellar.h | 65 Score<TScoreValue> const & scoreMatrix, in _appendNegativeSegment() argument 73 score += scoreGap(scoreMatrix); in _appendNegativeSegment() 75 score += scoreMismatch(scoreMatrix); in _appendNegativeSegment() 91 Score<TScoreValue> const & scoreMatrix, in _appendPositiveSegment() argument 102 score += scoreMatch(scoreMatrix); in _appendPositiveSegment() 164 Score<TScoreValue> & scoreMatrix, in _splitAtXDrops() argument 184 _appendPositiveSegment(align, pos, aliLength, scoreMatrix, queue); in _splitAtXDrops() 185 _appendNegativeSegment(align, pos, aliLength, scoreMatrix, queue); in _splitAtXDrops() 445 Score<TScore> scoreMatrix(match, mismatchIndel, mismatchIndel); in verifySwiftHit() 512 Score<TScore> scoreMatrix(match, mismatchIndel, mismatchIndel); in verifySwiftHit() [all …]
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/dports/biology/seqan1/seqan-1.3.1/demos/tutorial/seeds/ |
H A D | seeds_extend_bandedAlign.cpp | 30 Score<TScore, Simple> scoreMatrix(1, -1, -1); in main() local 32 extendSeed(seed, scoreDropOff, scoreMatrix, seq0, seq1, 2, GappedXDrop()); in main() 44 std::cout << "Score: " << bandedAlignment(align, seed, 2, scoreMatrix) << std::endl; in main()
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H A D | seeds_chain.cpp | 18 Score<TScore, Simple> scoreMatrix(1, -1, -1); in main() local 22 TSeedSet seedSet(limit, scoreMin, scoreMatrix); in main() 56 bandedChainAlignment(chain, band, align, scoreMatrix); in main()
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/dports/biology/star/STAR-2.7.9a/source/opal/ |
H A D | opal.cpp | 190 int score = scoreMatrix[r * alphabetLength + c]; in searchDatabaseSW_() 261 int* scoreMatrixRow = scoreMatrix + letter*alphabetLength; in searchDatabaseSW_() 514 gapOpen, gapExt, scoreMatrix, alphabetLength, results_, in searchDatabaseSW() 622 int score = scoreMatrix[r * alphabetLength + c]; in searchDatabase_() 703 int* scoreMatrixRow = scoreMatrix + letter*alphabetLength; in searchDatabase_() 1002 gapOpen, gapExt, scoreMatrix, alphabetLength, results_, in searchDatabase() 1257 arrayMax(scoreMatrix, alphabetLength * alphabetLength)); in findAlignment() 1438 int gapOpen, int gapExt, int* scoreMatrix, int alphabetLength, in opalSearchDatabase() argument 1469 gapOpen, gapExt, scoreMatrix, alphabetLength, in opalSearchDatabase() 1496 gapOpen, gapExt, scoreMatrix, alphabetLength, in opalSearchDatabase() [all …]
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H A D | opal.h | 152 int dbSeqLengths[], int gapOpen, int gapExt, int* scoreMatrix, 164 int dbSeqLengths[], int gapOpen, int gapExt, int* scoreMatrix,
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