Uses of Class
com.milaboratory.core.sequence.NucleotideSequence

Packages that use NucleotideSequence

Package	Description
com.milaboratory.core.alignment
com.milaboratory.core.alignment.batch
com.milaboratory.core.alignment.benchmark
com.milaboratory.core.alignment.blast
com.milaboratory.core.alignment.kaligner1
com.milaboratory.core.alignment.kaligner2
com.milaboratory.core.io.sequence.fasta
com.milaboratory.core.mutations
com.milaboratory.core.mutations.generator
com.milaboratory.core.sequence
com.milaboratory.core.sequence.provider

Uses of NucleotideSequence in com.milaboratory.core.alignment

Fields in com.milaboratory.core.alignment with type parameters of type NucleotideSequence

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 types with arguments of type NucleotideSequence

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 Alignment<NucleotideSequence>	BandedLinearAligner.align(LinearGapAlignmentScoring scoring, NucleotideSequence seq1, NucleotideSequence seq2, int width) Classical Banded Alignment
static Alignment<NucleotideSequence>	BandedLinearAligner.align(LinearGapAlignmentScoring scoring, NucleotideSequence seq1, NucleotideSequence seq2, int offset1, int length1, int offset2, int length2, int width) Classical Banded Alignment
static Alignment<NucleotideSequence>	BandedAligner.alignGlobal(AlignmentScoring<NucleotideSequence> scoring, NucleotideSequence seq1, NucleotideSequence seq2, int offset1, int length1, int offset2, int length2, int width) Classical Banded Alignment.
static Alignment<NucleotideSequence>	BandedLinearAligner.alignLeftAdded(LinearGapAlignmentScoring scoring, NucleotideSequence seq1, NucleotideSequence seq2, int offset1, int length1, int addedNucleotides1, int offset2, int length2, int addedNucleotides2, int width) Semi-semi-global alignment with artificially added letters.
static Alignment<NucleotideSequence>	BandedLinearAligner.alignRightAdded(LinearGapAlignmentScoring scoring, NucleotideSequence seq1, NucleotideSequence seq2, int offset1, int length1, int addedNucleotides1, int offset2, int length2, int addedNucleotides2, int width) Semi-semi-global alignment with artificially added letters.
static Alignment<NucleotideSequence>	BandedLinearAligner.alignSemiLocalLeft(LinearGapAlignmentScoring scoring, NucleotideSequence seq1, NucleotideSequence seq2, int width, int stopPenalty) Alignment which identifies what is the highly similar part of the both sequences.
static Alignment<NucleotideSequence>	BandedLinearAligner.alignSemiLocalLeft(LinearGapAlignmentScoring scoring, NucleotideSequence seq1, NucleotideSequence seq2, int offset1, int length1, int offset2, int length2, int width, int stopPenalty) Alignment which identifies what is the highly similar part of the both sequences.
static Alignment<NucleotideSequence>	BandedLinearAligner.alignSemiLocalRight(LinearGapAlignmentScoring scoring, NucleotideSequence seq1, NucleotideSequence seq2, int width, int stopPenalty) Alignment which identifies what is the highly similar part of the both sequences.
static Alignment<NucleotideSequence>	BandedLinearAligner.alignSemiLocalRight(LinearGapAlignmentScoring scoring, NucleotideSequence seq1, NucleotideSequence seq2, int offset1, int length1, int offset2, int length2, int width, int stopPenalty) Alignment which identifies what is the highly similar part of the both sequences.
static LinearGapAlignmentScoring<NucleotideSequence>	LinearGapAlignmentScoring.getNucleotideBLASTScoring() Returns standard Nucleotide BLAST scoring with #gapPenalty=5
static AffineGapAlignmentScoring<NucleotideSequence>	AffineGapAlignmentScoring.getNucleotideBLASTScoring() Returns standard Nucleotide BLAST scoring (#gapOpenPenalty=-10, #gapExtensionPenalty=-1)
static LinearGapAlignmentScoring<NucleotideSequence>	LinearGapAlignmentScoring.getNucleotideBLASTScoring(int gapPenalty) Returns standard Nucleotide BLAST scoring
static AffineGapAlignmentScoring<NucleotideSequence>	AffineGapAlignmentScoring.getNucleotideBLASTScoring(int gapOpenPenalty, int gapExtensionPenalty) Returns Nucleotide BLAST scoring
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 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 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 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)

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

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 Alignment<NucleotideSequence>	BandedLinearAligner.align(LinearGapAlignmentScoring scoring, NucleotideSequence seq1, NucleotideSequence seq2, int width) Classical Banded Alignment
static Alignment<NucleotideSequence>	BandedLinearAligner.align(LinearGapAlignmentScoring scoring, NucleotideSequence seq1, NucleotideSequence seq2, int offset1, int length1, int offset2, int length2, int width) Classical Banded Alignment
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 float	BandedLinearAligner.align0(LinearGapAlignmentScoring scoring, NucleotideSequence seq1, NucleotideSequence seq2, int offset1, int length1, int offset2, int length2, int width, MutationsBuilder<NucleotideSequence> mutations, CachedIntArray cachedArray) Classical Banded Alignment
static Alignment<NucleotideSequence>	BandedAligner.alignGlobal(AlignmentScoring<NucleotideSequence> scoring, NucleotideSequence seq1, NucleotideSequence seq2, int offset1, int length1, int offset2, int length2, int width) Classical Banded Alignment.
static Alignment<NucleotideSequence>	BandedLinearAligner.alignLeftAdded(LinearGapAlignmentScoring scoring, NucleotideSequence seq1, NucleotideSequence seq2, int offset1, int length1, int addedNucleotides1, int offset2, int length2, int addedNucleotides2, int width) Semi-semi-global alignment with artificially added letters.
static BandedSemiLocalResult	BandedLinearAligner.alignLeftAdded0(LinearGapAlignmentScoring scoring, NucleotideSequence seq1, NucleotideSequence seq2, int offset1, int length1, int addedNucleotides1, int offset2, int length2, int addedNucleotides2, int width, MutationsBuilder<NucleotideSequence> mutations, CachedIntArray cachedArray) Semi-semi-global alignment with artificially added letters.
static Alignment<NucleotideSequence>	BandedLinearAligner.alignRightAdded(LinearGapAlignmentScoring scoring, NucleotideSequence seq1, NucleotideSequence seq2, int offset1, int length1, int addedNucleotides1, int offset2, int length2, int addedNucleotides2, int width) Semi-semi-global alignment with artificially added letters.
static BandedSemiLocalResult	BandedLinearAligner.alignRightAdded0(LinearGapAlignmentScoring scoring, NucleotideSequence seq1, NucleotideSequence seq2, int offset1, int length1, int addedNucleotides1, int offset2, int length2, int addedNucleotides2, int width, MutationsBuilder<NucleotideSequence> mutations, CachedIntArray cachedArray) Semi-semi-global alignment with artificially added letters.
static Alignment<NucleotideSequence>	BandedLinearAligner.alignSemiLocalLeft(LinearGapAlignmentScoring scoring, NucleotideSequence seq1, NucleotideSequence seq2, int width, int stopPenalty) Alignment which identifies what is the highly similar part of the both sequences.
static Alignment<NucleotideSequence>	BandedLinearAligner.alignSemiLocalLeft(LinearGapAlignmentScoring scoring, NucleotideSequence seq1, NucleotideSequence seq2, int offset1, int length1, int offset2, int length2, int width, int stopPenalty) Alignment which identifies what is the highly similar part of the both sequences.
static BandedSemiLocalResult	BandedLinearAligner.alignSemiLocalLeft0(LinearGapAlignmentScoring scoring, NucleotideSequence seq1, NucleotideSequence seq2, int offset1, int length1, int offset2, int length2, int width, int stopPenalty, MutationsBuilder<NucleotideSequence> mutations, CachedIntArray cachedArray) Alignment which identifies what is the highly similar part of the both sequences.
static Alignment<NucleotideSequence>	BandedLinearAligner.alignSemiLocalRight(LinearGapAlignmentScoring scoring, NucleotideSequence seq1, NucleotideSequence seq2, int width, int stopPenalty) Alignment which identifies what is the highly similar part of the both sequences.
static Alignment<NucleotideSequence>	BandedLinearAligner.alignSemiLocalRight(LinearGapAlignmentScoring scoring, NucleotideSequence seq1, NucleotideSequence seq2, int offset1, int length1, int offset2, int length2, int width, int stopPenalty) Alignment which identifies what is the highly similar part of the both sequences.
static BandedSemiLocalResult	BandedLinearAligner.alignSemiLocalRight0(LinearGapAlignmentScoring scoring, NucleotideSequence seq1, NucleotideSequence seq2, int offset1, int length1, int offset2, int length2, int width, int stopPenalty, MutationsBuilder<NucleotideSequence> mutations, CachedIntArray cachedArray) Alignment which identifies what is the highly similar part of the both sequences.
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)

Method parameters in com.milaboratory.core.alignment with type arguments of type NucleotideSequence

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 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 float	BandedLinearAligner.align0(LinearGapAlignmentScoring scoring, NucleotideSequence seq1, NucleotideSequence seq2, int offset1, int length1, int offset2, int length2, int width, MutationsBuilder<NucleotideSequence> mutations, CachedIntArray cachedArray) Classical Banded Alignment
static Alignment<NucleotideSequence>	BandedAligner.alignGlobal(AlignmentScoring<NucleotideSequence> scoring, NucleotideSequence seq1, NucleotideSequence seq2, int offset1, int length1, int offset2, int length2, int width) Classical Banded Alignment.
static BandedSemiLocalResult	BandedLinearAligner.alignLeftAdded0(LinearGapAlignmentScoring scoring, NucleotideSequence seq1, NucleotideSequence seq2, int offset1, int length1, int addedNucleotides1, int offset2, int length2, int addedNucleotides2, int width, MutationsBuilder<NucleotideSequence> mutations, CachedIntArray cachedArray) Semi-semi-global alignment with artificially added letters.
static BandedSemiLocalResult	BandedLinearAligner.alignRightAdded0(LinearGapAlignmentScoring scoring, NucleotideSequence seq1, NucleotideSequence seq2, int offset1, int length1, int addedNucleotides1, int offset2, int length2, int addedNucleotides2, int width, MutationsBuilder<NucleotideSequence> mutations, CachedIntArray cachedArray) Semi-semi-global alignment with artificially added letters.
static BandedSemiLocalResult	BandedLinearAligner.alignSemiLocalLeft0(LinearGapAlignmentScoring scoring, NucleotideSequence seq1, NucleotideSequence seq2, int offset1, int length1, int offset2, int length2, int width, int stopPenalty, MutationsBuilder<NucleotideSequence> mutations, CachedIntArray cachedArray) Alignment which identifies what is the highly similar part of the both sequences.
static BandedSemiLocalResult	BandedLinearAligner.alignSemiLocalRight0(LinearGapAlignmentScoring scoring, NucleotideSequence seq1, NucleotideSequence seq2, int offset1, int length1, int offset2, int length2, int width, int stopPenalty, MutationsBuilder<NucleotideSequence> mutations, CachedIntArray cachedArray) Alignment which identifies what is the highly similar part of the both sequences.
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 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 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 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)
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 NucleotideSequence in com.milaboratory.core.alignment.batch

Methods in com.milaboratory.core.alignment.batch that return types with arguments of type NucleotideSequence

Modifier and Type	Method and Description
<P> BatchAlignerWithBaseWithFilter<NucleotideSequence,P,? extends AlignmentHit<NucleotideSequence,P>>	BatchAlignerWithBaseParameters.createAligner()
<P> BatchAlignerWithBaseWithFilter<NucleotideSequence,P,? extends AlignmentHit<NucleotideSequence,P>>	BatchAlignerWithBaseParameters.createAligner()
AlignmentScoring<NucleotideSequence>	BatchAlignerWithBaseParameters.getScoring()

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

Fields in com.milaboratory.core.alignment.benchmark declared as NucleotideSequence

Modifier and Type	Field and Description
NucleotideSequence[]	Benchmark.ExceptionData.db
NucleotideSequence	KAlignerQuery.query
NucleotideSequence	Benchmark.ExceptionData.query

Fields in com.milaboratory.core.alignment.benchmark with type parameters of type NucleotideSequence

Modifier and Type	Field and Description
Alignment<NucleotideSequence>	KAlignerQuery.expectedAlignment
List<Mutations<NucleotideSequence>>	KAlignerQuery.mutationsInTarget

Methods in com.milaboratory.core.alignment.benchmark that return NucleotideSequence

Modifier and Type	Method and Description
static NucleotideSequence[]	ChallengeProvider.generateDB(org.apache.commons.math3.random.RandomDataGenerator generator, ChallengeParameters params)
NucleotideSequence[]	Challenge.getDB()

Method parameters in com.milaboratory.core.alignment.benchmark with type arguments of type NucleotideSequence

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 NucleotideSequence

Constructor and Description
Benchmark.ExceptionData(long seed, Throwable exception, NucleotideSequence[] db, NucleotideSequence query, BenchmarkInput input)
Benchmark.ExceptionData(long seed, Throwable exception, NucleotideSequence[] db, NucleotideSequence query, BenchmarkInput input)
Challenge(NucleotideSequence[] db, List<KAlignerQuery> queries, ChallengeParameters parameters, long seed)
KAlignerQuery(int targetId, List<Range> queryClusters, List<Range> targetClusters, List<Mutations<NucleotideSequence>> mutationsInTarget, NucleotideSequence query, Alignment<NucleotideSequence> expectedAlignment)
KAlignerQuery(NucleotideSequence sequence)

Constructor parameters in com.milaboratory.core.alignment.benchmark with type arguments of type NucleotideSequence

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)
KAlignerQuery(int targetId, List<Range> queryClusters, List<Range> targetClusters, List<Mutations<NucleotideSequence>> mutationsInTarget, NucleotideSequence query, Alignment<NucleotideSequence> expectedAlignment)
KAlignerQuery(int targetId, List<Range> queryClusters, List<Range> targetClusters, List<Mutations<NucleotideSequence>> mutationsInTarget, NucleotideSequence query, Alignment<NucleotideSequence> expectedAlignment)

Uses of NucleotideSequence in com.milaboratory.core.alignment.blast

Method parameters in com.milaboratory.core.alignment.blast with type arguments of type NucleotideSequence

Modifier and Type	Method and Description
protected NBlastHitExt	NBlastAlignerExt.createHit(Alignment<NucleotideSequence> alignment, double score, double bitScore, double eValue, Range subjectRange, String subjectId, String subjectTitle)
protected NBlastHit<P>	NBlastAligner.createHit(Alignment<NucleotideSequence> alignment, P recordPayload, BlastHit<NucleotideSequence,?> hit)
protected NBlastHit<P>	NBlastAligner.createHit(Alignment<NucleotideSequence> alignment, P recordPayload, BlastHit<NucleotideSequence,?> hit)

Constructor parameters in com.milaboratory.core.alignment.blast with type arguments of type NucleotideSequence

Constructor and Description
NBlastHit(Alignment<NucleotideSequence> alignment, P recordPayload, BlastHit<NucleotideSequence,?> hit)
NBlastHit(Alignment<NucleotideSequence> alignment, P recordPayload, BlastHit<NucleotideSequence,?> hit)
NBlastHit(Alignment<NucleotideSequence> alignment, P recordPayload, double score, double bitScore, double eValue, Range subjectRange, String subjectId, String subjectTitle)
NBlastHitExt(Alignment<NucleotideSequence> alignment, double score, double bitScore, double eValue, Range subjectRange, String subjectId, String subjectTitle)

Uses of NucleotideSequence in com.milaboratory.core.alignment.kaligner1

Methods in com.milaboratory.core.alignment.kaligner1 with type parameters of type NucleotideSequence

Modifier and Type	Method and Description
<Q extends HasSequence<NucleotideSequence>> cc.redberry.pipe.OutputPort<KAlignmentResultP<P,Q>>	KAligner.align(cc.redberry.pipe.OutputPort<Q> input)

Methods in com.milaboratory.core.alignment.kaligner1 that return NucleotideSequence

Modifier and Type	Method and Description
NucleotideSequence	KAlignmentHit.getHitSequence()
NucleotideSequence	KAligner.getReference(int id) Returns sequence by its id (order number) in a base.
NucleotideSequence	KAlignmentResult.getTarget() Returns target sequence

Methods in com.milaboratory.core.alignment.kaligner1 that return types with arguments of type NucleotideSequence

Modifier and Type	Method and Description
Alignment<NucleotideSequence>	KAlignmentHit.getAlignment()
LinearGapAlignmentScoring<NucleotideSequence>	KAlignerParameters.getScoring() Returns scoring system used for building alignments

Methods in com.milaboratory.core.alignment.kaligner1 with parameters of type NucleotideSequence

Modifier and Type	Method and Description
int	KMapper.addReference(NucleotideSequence sequence) Adds new reference sequence to the base of this mapper and returns index assigned to it.
int	KAligner.addReference(NucleotideSequence sequence) Adds new reference sequence to the base of this aligner and returns index assigned to it.
int	KMapper.addReference(NucleotideSequence sequence, int offset, int length) Adds new reference sequence to the base of this mapper and returns index assigned to it.
int	KAligner.addReference(NucleotideSequence sequence, int offset, int length) Adds new reference sequence to the base of this mapper and returns index assigned to it.
void	KAligner.addReference(NucleotideSequence sequence, P payload)
KMappingResult	KMapper.align(NucleotideSequence sequence) Performs an alignment.
KAlignmentResult<P>	KAligner.align(NucleotideSequence sequence) Performs a comprehensive alignment of a sequence.
KMappingResult	KMapper.align(NucleotideSequence sequence, int from, int to) Performs an alignment for a part of the target sequence.
KAlignmentResult<P>	KAligner.align(NucleotideSequence sequence, int from, int to) Performs a comprehensive alignment of a sequence.
KMappingResult	KMapper.align(NucleotideSequence sequence, int from, int to, BitArray filter) Performs an alignment for a part of the target sequence.
AlignmentResult<KAlignmentHit<P>>	KAligner.align(NucleotideSequence sequence, int from, int to, BitArray filter)
KAlignmentResult<P>	KAligner.align(NucleotideSequence sequence, int from, int to, boolean restrictToRange, BitArray filter) Performs a comprehensive alignment of a sequence.

Method parameters in com.milaboratory.core.alignment.kaligner1 with type arguments of type NucleotideSequence

Modifier and Type	Method and Description
<Q> cc.redberry.pipe.OutputPort<KAlignmentResultP<P,Q>>	KAligner.align(cc.redberry.pipe.OutputPort<Q> input, SequenceExtractor<Q,NucleotideSequence> extractor)

Constructors in com.milaboratory.core.alignment.kaligner1 with parameters of type NucleotideSequence

Constructor and Description
KAlignmentResult(KAligner<P> aligner, KMappingResult mappingResult, NucleotideSequence target, int targetFrom, int targetTo) Creates new KAlignmentResult
KAlignmentResultP(Q query, KAligner<P> aligner, KMappingResult mappingResult, NucleotideSequence target, int targetFrom, int targetTo)

Constructor parameters in com.milaboratory.core.alignment.kaligner1 with type arguments of type NucleotideSequence

Constructor and Description

KAlignerParameters(int mapperKValue, boolean floatingLeftBound, boolean floatingRightBound, float mapperAbsoluteMinScore, float mapperRelativeMinScore, float mapperMatchScore, float mapperMismatchPenalty, float mapperOffsetShiftPenalty, int mapperMinSeedsDistance, int mapperMaxSeedsDistance, int minAlignmentLength, int maxAdjacentIndels, int alignmentStopPenalty, float absoluteMinScore, float relativeMinScore, int maxHits, LinearGapAlignmentScoring<NucleotideSequence> scoring) Creates new KAligner

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

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

Modifier and Type	Method and Description
NucleotideSequence	KAligner2.getReference(int id) Returns sequence by its id (order number) in a base.

Methods in com.milaboratory.core.alignment.kaligner2 that return types with arguments of type NucleotideSequence

Modifier and Type	Method and Description
Alignment<NucleotideSequence>	KAlignmentHit2.getAlignment()
AffineGapAlignmentScoring<NucleotideSequence>	KAlignerParameters2.getScoring() Returns scoring system used for building alignments

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

Modifier and Type	Method and Description
int	KMapper2.addReference(NucleotideSequence sequence) Adds new reference sequence to the base of this mapper and returns index assigned to it.
int	KAligner2.addReference(NucleotideSequence sequence) Adds new reference sequence to the base of this mapper and returns index assigned to it.
void	KAligner2.addReference(NucleotideSequence sequence, P payload)
KMappingResult2	KMapper2.align(NucleotideSequence sequence) Performs an alignment.
KAlignmentResult2<P>	KAligner2.align(NucleotideSequence sequence)
KMappingResult2	KMapper2.align(NucleotideSequence sequence, int from, int to) Performs an alignment for a part of the target sequence.
KAlignmentResult2<P>	KAligner2.align(NucleotideSequence sequence, int from, int to)
KMappingResult2	KMapper2.align(NucleotideSequence sequence, int from, int to, BitArray filter) Performs an alignment for a part of the target sequence.
KAlignmentResult2<P>	KAligner2.align(NucleotideSequence query, int from, int to, BitArray filter)

Method parameters in com.milaboratory.core.alignment.kaligner2 with type arguments of type NucleotideSequence

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 NucleotideSequence

Constructor and Description
KAlignmentResult2(KMappingResult2 mappingResult, List<KAlignmentHit2<P>> hits, NucleotideSequence target, int targetFrom, int targetTo)

Constructor parameters in com.milaboratory.core.alignment.kaligner2 with type arguments of type NucleotideSequence

Constructor and Description
KAlignmentHit2(KAlignmentResult2<P> result, int indexOfMappingHit, Alignment<NucleotideSequence> alignment, P payload)

Uses of NucleotideSequence in com.milaboratory.core.io.sequence.fasta

Constructor parameters in com.milaboratory.core.io.sequence.fasta with type arguments of type NucleotideSequence

Constructor and Description
FastaSequenceReaderWrapper(FastaReader<NucleotideSequence> internalReader)
FastaSequenceReaderWrapper(FastaReader<NucleotideSequence> internalReader, boolean replaceWildcards)

Uses of NucleotideSequence in com.milaboratory.core.mutations

Fields in com.milaboratory.core.mutations with type parameters of type NucleotideSequence

Modifier and Type	Field and Description
static Mutations<NucleotideSequence>	Mutations.EMPTY_NUCLEOTIDE_MUTATIONS Identity mutations object for nucleotide sequences.

Methods in com.milaboratory.core.mutations that return types with arguments of type NucleotideSequence

Modifier and Type	Method and Description
static Mutations<NucleotideSequence>	Mutations.decodeNuc(String string)

Methods in com.milaboratory.core.mutations with parameters of type NucleotideSequence

Modifier and Type	Method and Description
static Mutations<AminoAcidSequence>	MutationsUtil.nt2aa(NucleotideSequence seq1, Mutations<NucleotideSequence> mutations, TranslationParameters translationParameters)
static Mutations<AminoAcidSequence>	MutationsUtil.nt2aa(NucleotideSequence seq1, Mutations<NucleotideSequence> mutations, TranslationParameters translationParameters, int maxShiftedTriplets)
static MutationsUtil.MutationNt2AADescriptor[]	MutationsUtil.nt2aaDetailed(NucleotideSequence seq1, Mutations<NucleotideSequence> mutations, TranslationParameters translationParameters, int maxShiftedTriplets) Performs a comprehensive translation of mutations present in a nucleotide sequence to effective mutations in corresponding amino acid sequence.
static MutationsUtil.MutationsWitMapping	MutationsUtil.nt2aaWithMapping(NucleotideSequence seq1, Mutations<NucleotideSequence> mutations, TranslationParameters translationParameters, int maxShiftedTriplets)
static int[]	MutationsUtil.nt2IndividualAA(NucleotideSequence seq1, Mutations<NucleotideSequence> mutations, TranslationParameters translationParameters)

Method parameters in com.milaboratory.core.mutations with type arguments of type NucleotideSequence

Modifier and Type	Method and Description
static NSequenceWithQuality	MutationsUtil.mutate(NSequenceWithQuality seq, Mutations<NucleotideSequence> mutations)
static Mutations<AminoAcidSequence>	MutationsUtil.nt2aa(NucleotideSequence seq1, Mutations<NucleotideSequence> mutations, TranslationParameters translationParameters)
static Mutations<AminoAcidSequence>	MutationsUtil.nt2aa(NucleotideSequence seq1, Mutations<NucleotideSequence> mutations, TranslationParameters translationParameters, int maxShiftedTriplets)
static MutationsUtil.MutationNt2AADescriptor[]	MutationsUtil.nt2aaDetailed(NucleotideSequence seq1, Mutations<NucleotideSequence> mutations, TranslationParameters translationParameters, int maxShiftedTriplets) Performs a comprehensive translation of mutations present in a nucleotide sequence to effective mutations in corresponding amino acid sequence.
static MutationsUtil.MutationsWitMapping	MutationsUtil.nt2aaWithMapping(NucleotideSequence seq1, Mutations<NucleotideSequence> mutations, TranslationParameters translationParameters, int maxShiftedTriplets)
static int[]	MutationsUtil.nt2IndividualAA(NucleotideSequence seq1, Mutations<NucleotideSequence> mutations, TranslationParameters translationParameters)

Uses of NucleotideSequence in com.milaboratory.core.mutations.generator

Methods in com.milaboratory.core.mutations.generator that return types with arguments of type NucleotideSequence

Modifier and Type	Method and Description
static Mutations<NucleotideSequence>	MutationsGenerator.generateMutations(NucleotideSequence sequence, NucleotideMutationModel model)
static Mutations<NucleotideSequence>	MutationsGenerator.generateMutations(NucleotideSequence sequence, NucleotideMutationModel model, int from, int to)
static Mutations<NucleotideSequence>	MutationsGenerator.generateMutations(NucleotideSequence sequence, NucleotideMutationModel model, Range range)

Methods in com.milaboratory.core.mutations.generator with parameters of type NucleotideSequence

Modifier and Type	Method and Description
static Mutations<NucleotideSequence>	MutationsGenerator.generateMutations(NucleotideSequence sequence, NucleotideMutationModel model)
static Mutations<NucleotideSequence>	MutationsGenerator.generateMutations(NucleotideSequence sequence, NucleotideMutationModel model, int from, int to)
static Mutations<NucleotideSequence>	MutationsGenerator.generateMutations(NucleotideSequence sequence, NucleotideMutationModel model, Range range)

Uses of NucleotideSequence in com.milaboratory.core.sequence

Fields in com.milaboratory.core.sequence declared as NucleotideSequence

Modifier and Type	Field and Description
static NucleotideSequence	NucleotideSequence.EMPTY Empty instance

Methods in com.milaboratory.core.sequence that return NucleotideSequence

Modifier and Type	Method and Description
static NucleotideSequence	SequencesUtils.convertBit2ArrayToNSequence(Bit2Array bar) Used to read legacy file formats.
static NucleotideSequence	NucleotideSequence.fromSequence(byte[] sequence, int offset, int length) Creates nucleotide sequence from specified byte array.
NucleotideSequence	NucleotideSequence.getRange(Range range)
NucleotideSequence	NucleotideSequence.getReverseComplement() Returns reverse complement of this sequence.

Methods in com.milaboratory.core.sequence with parameters of type NucleotideSequence

Modifier and Type	Method and Description
static Bit2Array	SequencesUtils.convertNSequenceToBit2Array(NucleotideSequence seq) Used to write legacy file formats.
static byte	AminoAcidSequence.getAminoAcid(NucleotideSequence nSequence, int tripletStart) Returns amino acid encoded by triplet starting from specified position (in terms of standard genetic code)
static int	AminoAcidSequence.getTriplet(NucleotideSequence nSequence, int tripletStart) Extracts int representation of triplet starting from specified position (see implementation for details).
static void	GeneticCode.translate(byte[] dest, int offsetInDest, NucleotideSequence sequence, int offsetInSeq, int seqLength)
static AminoAcidSequence	AminoAcidSequence.translate(NucleotideSequence sequence) Translates sequence having length divisible by 3, starting from first nucleotide.
static AminoAcidSequence	AminoAcidSequence.translate(NucleotideSequence sequence, int frame) Translate sequence in one of frames (-1, -2, -3 frames are not implemented, use getReverseComplement()) discarding all incomplete codons on both boundaries.
static AminoAcidSequence	AminoAcidSequence.translate(NucleotideSequence ns, TranslationParameters translationParameters) Use one of specialized method instead: AminoAcidSequence.translateFromLeft(NucleotideSequence) AminoAcidSequence.translateFromRight(NucleotideSequence) AminoAcidSequence.translateFromCenter(NucleotideSequence)
static AminoAcidSequence	AminoAcidSequence.translateFromCenter(NucleotideSequence ns) Translates sequence from both sides, so the first nucleotide of the first triplet matches first nucleotide of the sequence, and last (3rd) nucleotide of last triplet matches last nucleotide of the sequence.
static AminoAcidSequence	AminoAcidSequence.translateFromLeft(NucleotideSequence ns) Translates sequence from the left side, so the first nucleotide of the first triplet matches first nucleotide of the sequence.
static AminoAcidSequence	AminoAcidSequence.translateFromRight(NucleotideSequence ns) Translates sequence from the right side, so the last (3rd) nucleotide of last triplet matches last nucleotide of the sequence.

Constructors in com.milaboratory.core.sequence with parameters of type NucleotideSequence

Constructor and Description
NSequenceWithQuality(NucleotideSequence sequence)
NSequenceWithQuality(NucleotideSequence sequence, byte quality)
NSequenceWithQuality(NucleotideSequence sequence, SequenceQuality quality) Creates nucleotide sequence with its quality

Uses of NucleotideSequence in com.milaboratory.core.sequence.provider

Methods in com.milaboratory.core.sequence.provider that return types with arguments of type NucleotideSequence

Modifier and Type	Method and Description
static SequenceProvider<NucleotideSequence>	SequenceProviderUtils.reversedProvider(SequenceProvider<NucleotideSequence> provider)

Method parameters in com.milaboratory.core.sequence.provider with type arguments of type NucleotideSequence

Modifier and Type	Method and Description
static SequenceProvider<NucleotideSequence>	SequenceProviderUtils.reversedProvider(SequenceProvider<NucleotideSequence> provider)