Uses of Class
com.milaboratory.core.alignment.AffineGapAlignmentScoring

Packages that use AffineGapAlignmentScoring

Package	Description
com.milaboratory.core.alignment
com.milaboratory.core.alignment.benchmark
com.milaboratory.core.alignment.kaligner2

Uses of AffineGapAlignmentScoring in com.milaboratory.core.alignment

Fields in com.milaboratory.core.alignment declared as AffineGapAlignmentScoring

Modifier and Type	Field and Description
static AffineGapAlignmentScoring<NucleotideSequence>	AffineGapAlignmentScoring.IGBLAST_NUCLEOTIDE_SCORING Scoring as used in IgBlast for alignments of V genes

Methods in com.milaboratory.core.alignment that return AffineGapAlignmentScoring

Modifier and Type	Method and Description
static AffineGapAlignmentScoring<AminoAcidSequence>	AffineGapAlignmentScoring.getAminoAcidBLASTScoring(BLASTMatrix matrix) Returns standard AminoAcid BLAST scoring (#gapOpenPenalty=-10, #gapExtensionPenalty=-1)
static AffineGapAlignmentScoring<AminoAcidSequence>	AffineGapAlignmentScoring.getAminoAcidBLASTScoring(BLASTMatrix matrix, int gapOpenPenalty, int gapExtensionPenalty) Returns AminoAcid BLAST scoring
static AffineGapAlignmentScoring<NucleotideSequence>	AffineGapAlignmentScoring.getNucleotideBLASTScoring() Returns standard Nucleotide BLAST scoring (#gapOpenPenalty=-10, #gapExtensionPenalty=-1)
static AffineGapAlignmentScoring<NucleotideSequence>	AffineGapAlignmentScoring.getNucleotideBLASTScoring(int gapOpenPenalty, int gapExtensionPenalty) Returns Nucleotide BLAST scoring
AffineGapAlignmentScoring<S>	AffineGapAlignmentScoring.setGapExtensionScore(int gapExtensionPenalty)
AffineGapAlignmentScoring<S>	AffineGapAlignmentScoring.setGapOpenScore(int gapOpenPenalty)
AffineGapAlignmentScoring<S>	AffineGapAlignmentScoring.setMatchScore(int matchScore)
AffineGapAlignmentScoring<S>	AffineGapAlignmentScoring.setMismatchScore(int mismatchScore)

Methods in com.milaboratory.core.alignment with parameters of type AffineGapAlignmentScoring

Modifier and Type	Method and Description
static Alignment<NucleotideSequence>	BandedAffineAligner.align(AffineGapAlignmentScoring<NucleotideSequence> scoring, NucleotideSequence seq1, NucleotideSequence seq2, int width)
static Alignment<NucleotideSequence>	BandedAffineAligner.align(AffineGapAlignmentScoring<NucleotideSequence> scoring, NucleotideSequence seq1, NucleotideSequence seq2, int offset1, int length1, int offset2, int length2, int width)
static int	BandedAffineAligner.align0(AffineGapAlignmentScoring<NucleotideSequence> scoring, NucleotideSequence seq1, NucleotideSequence seq2, int offset1, int length1, int offset2, int length2, int width, MutationsBuilder<NucleotideSequence> mutations, BandedAffineAligner.MatrixCache cache) Classical Banded Alignment with affine gap scoring.
static <S extends Sequence<S>> Alignment<S>	AlignerCustom.alignAffineSemiLocalLeft0(AffineGapAlignmentScoring<S> scoring, S seq1, S seq2, int offset1, int length1, int offset2, int length2, boolean boundSeq1, boolean boundSeq2, Alphabet<S> alphabet, AlignerCustom.AffineMatrixCache cache)
static <S extends Sequence<S>> Alignment<S>	Aligner.alignGlobalAffine(AffineGapAlignmentScoring<S> scoring, S seq1, S seq2) Performs global alignment using affine gap scoring system (different penalties exist for gap opening and gap extension)
static <S extends Sequence<S>> Alignment<S>	Aligner.alignLocalAffine(AffineGapAlignmentScoring<S> scoring, S seq1, S seq2) Performs local alignment using Affine gap scoring system (different penalties exist for gap opening and gap extension)
static <S extends Sequence<S>> int	AlignmentUtils.calculateScore(S seq1, Range seq1Range, Mutations<S> mutations, AffineGapAlignmentScoring<S> scoring) Calculates score of alignment
static <S extends Sequence<S>> Alignment<S>	AlignmentTrimmer.leftTrimAlignment(Alignment<S> alignment, AffineGapAlignmentScoring<S> scoring) Try increase total alignment score by partially (or fully) trimming it from left side.
static <S extends Sequence<S>> Alignment<S>	AlignmentTrimmer.rightTrimAlignment(Alignment<S> alignment, AffineGapAlignmentScoring<S> scoring) Try increase total alignment score by partially (or fully) trimming it from right side.
static Alignment<NucleotideSequence>	BandedAffineAligner.semiGlobalLeft(AffineGapAlignmentScoring<NucleotideSequence> scoring, NucleotideSequence seq1, NucleotideSequence seq2, int offset1, int length1, int addedNucleotides1, int offset2, int length2, int addedNucleotides2, int width)
static BandedSemiLocalResult	BandedAffineAligner.semiGlobalLeft0(AffineGapAlignmentScoring<NucleotideSequence> scoring, NucleotideSequence seq1, NucleotideSequence seq2, int offset1, int length1, int addedNucleotides1, int offset2, int length2, int addedNucleotides2, int width, MutationsBuilder<NucleotideSequence> mutations, BandedAffineAligner.MatrixCache cache)
static Alignment<NucleotideSequence>	BandedAffineAligner.semiGlobalRight(AffineGapAlignmentScoring<NucleotideSequence> scoring, NucleotideSequence seq1, NucleotideSequence seq2, int offset1, int length1, int addedNucleotides1, int offset2, int length2, int addedNucleotides2, int width)
static BandedSemiLocalResult	BandedAffineAligner.semiGlobalRight0(AffineGapAlignmentScoring<NucleotideSequence> scoring, NucleotideSequence seq1, NucleotideSequence seq2, int offset1, int length1, int addedNucleotides1, int offset2, int length2, int addedNucleotides2, int width, MutationsBuilder<NucleotideSequence> mutations, BandedAffineAligner.MatrixCache cache)
static Alignment<NucleotideSequence>	BandedAffineAligner.semiLocalLeft(AffineGapAlignmentScoring<NucleotideSequence> scoring, NucleotideSequence seq1, NucleotideSequence seq2, int width)
static Alignment<NucleotideSequence>	BandedAffineAligner.semiLocalLeft(AffineGapAlignmentScoring<NucleotideSequence> scoring, NucleotideSequence seq1, NucleotideSequence seq2, int offset1, int length1, int offset2, int length2, int width)
static BandedSemiLocalResult	BandedAffineAligner.semiLocalLeft0(AffineGapAlignmentScoring<NucleotideSequence> scoring, NucleotideSequence seq1, NucleotideSequence seq2, int offset1, int length1, int offset2, int length2, int width, MutationsBuilder<NucleotideSequence> mutations, BandedAffineAligner.MatrixCache cache)
static Alignment<NucleotideSequence>	BandedAffineAligner.semiLocalRight(AffineGapAlignmentScoring<NucleotideSequence> scoring, NucleotideSequence seq1, NucleotideSequence seq2, int width)
static Alignment<NucleotideSequence>	BandedAffineAligner.semiLocalRight(AffineGapAlignmentScoring<NucleotideSequence> scoring, NucleotideSequence seq1, NucleotideSequence seq2, int offset1, int length1, int offset2, int length2, int width)
static BandedSemiLocalResult	BandedAffineAligner.semiLocalRight0(AffineGapAlignmentScoring<NucleotideSequence> scoring, NucleotideSequence seq1, NucleotideSequence seq2, int offset1, int length1, int offset2, int length2, int width, MutationsBuilder<NucleotideSequence> mutations, BandedAffineAligner.MatrixCache cache)

Uses of AffineGapAlignmentScoring in com.milaboratory.core.alignment.benchmark

Methods in com.milaboratory.core.alignment.benchmark with parameters of type AffineGapAlignmentScoring

Modifier and Type	Method and Description
static ChallengeParameters	ChallengeProvider.getParams1NoGap(AffineGapAlignmentScoring<NucleotideSequence> scoring, int minAlignmentScoring, int maxAlignmentScoring, double multiplier)
static ChallengeParameters	ChallengeProvider.getParamsOneCluster(AffineGapAlignmentScoring<NucleotideSequence> scoring, int minAlignmentScoring, int maxAlignmentScoring, double multiplier)
static ChallengeParameters	ChallengeProvider.getParamsTwoClusters(AffineGapAlignmentScoring<NucleotideSequence> scoring, int minAlignmentScoring, int maxAlignmentScoring, double multiplier)

Constructors in com.milaboratory.core.alignment.benchmark with parameters of type AffineGapAlignmentScoring

Constructor and Description

ChallengeParameters(int dbSize, int dbMinSeqLength, int dbMaxSeqLength, int queryCount, int falseCount, int minClusters, int maxClusters, int minClusterLength, int maxClusterLength, int minIndelLength, int maxIndelLength, double insertionProbability, double deletionProbability, double boundaryInsertProbability, NucleotideMutationModel mutationModel, int minAlignmentScoring, int maxAlignmentScoring, AffineGapAlignmentScoring<NucleotideSequence> scoring)

Uses of AffineGapAlignmentScoring in com.milaboratory.core.alignment.kaligner2

Methods in com.milaboratory.core.alignment.kaligner2 that return AffineGapAlignmentScoring

Modifier and Type	Method and Description
AffineGapAlignmentScoring<NucleotideSequence>	KAlignerParameters2.getScoring() Returns scoring system used for building alignments

Methods in com.milaboratory.core.alignment.kaligner2 with parameters of type AffineGapAlignmentScoring

Modifier and Type	Method and Description
KAlignerParameters2	KAlignerParameters2.setScoring(AffineGapAlignmentScoring<NucleotideSequence> scoring) Sets scoring system used for building alignments

Constructors in com.milaboratory.core.alignment.kaligner2 with parameters of type AffineGapAlignmentScoring

Constructor and Description

KAlignerParameters2(int mapperNValue, int mapperKValue, boolean floatingLeftBound, boolean floatingRightBound, int mapperAbsoluteMinClusterScore, int mapperExtraClusterScore, int mapperAbsoluteMinScore, float mapperRelativeMinScore, int mapperMatchScore, int mapperMismatchScore, int mapperOffsetShiftScore, int mapperMinSeedsDistance, int mapperMaxSeedsDistance, int mapperSlotCount, int mapperMaxClusters, int mapperMaxClusterIndels, int mapperKMersPerPosition, int alignmentStopPenalty, int absoluteMinScore, float relativeMinScore, int maxHits, AffineGapAlignmentScoring scoring)