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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/alignment_free/
H A Daf_d2.h49 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()
H A Daf_d2star.h51 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()
H A Dalignment_free_comparison.h99 void alignmentFreeComparison(Matrix<TValue, 2> & scoreMatrix, TStringSet const & sequenceSet, TComp… in alignmentFreeComparison() argument
101 _alignmentFreeComparison(scoreMatrix, sequenceSet, comparisonMethod); in alignmentFreeComparison()
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/alignment_free/
H A Daf_d2.h49 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()
H A Daf_d2star.h51 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()
H A Dalignment_free_comparison.h99 void alignmentFreeComparison(Matrix<TValue, 2> & scoreMatrix, TStringSet const & sequenceSet, TComp… in alignmentFreeComparison() argument
101 _alignmentFreeComparison(scoreMatrix, sequenceSet, comparisonMethod); in alignmentFreeComparison()
/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/alignment_free/
H A Daf_d2.h49 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()
H A Daf_d2star.h51 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()
H A Dalignment_free_comparison.h99 void alignmentFreeComparison(Matrix<TValue, 2> & scoreMatrix, TStringSet const & sequenceSet, TComp… in alignmentFreeComparison() argument
101 _alignmentFreeComparison(scoreMatrix, sequenceSet, comparisonMethod); in alignmentFreeComparison()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/structure/cd_utils/
H A DcuSeqTreeFactory.cpp128 …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()
/dports/biology/mothur/mothur-1.46.1/source/commands/
H A Dmakelookupcommand.cpp400 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()
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/dports/biology/seqan1/seqan-1.3.1/seqan/seeds/
H A Dseed_base.h636 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);
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H A Dbanded_chain_align.h60 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()
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H A Dseed_multi.h391 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()
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H A DseedSet_score.h172 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,
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/dports/biology/seqan1/seqan-1.3.1/demos/
H A Dswift_verification.cpp31 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()
/dports/biology/hyphy/hyphy-2.5.33/src/core/
H A Dalignment.cpp1280 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()
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/demos/howto/scores/
H A Dload_score.cpp60 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()
/dports/biology/seqan1/seqan-1.3.1/demos/tutorial/scores/
H A Dload_score.cpp63 Score<TScoreValue, ScoreMatrix<Dna, Default> > scoreMatrix; in main() local
64 loadScoreMatrix(scoreMatrix, argv[1]); in main()
65 showScoringMatrix(scoreMatrix); in main()
/dports/biology/seqan1/seqan-1.3.1/apps/stellar/
H A Dstellar.h62 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()
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/stellar/
H A Dstellar.h65 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()
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/dports/biology/seqan1/seqan-1.3.1/demos/tutorial/seeds/
H A Dseeds_extend_bandedAlign.cpp30 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()
H A Dseeds_chain.cpp18 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()
/dports/biology/star/STAR-2.7.9a/source/opal/
H A Dopal.cpp190 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()
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H A Dopal.h152 int dbSeqLengths[], int gapOpen, int gapExt, int* scoreMatrix,
164 int dbSeqLengths[], int gapOpen, int gapExt, int* scoreMatrix,

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