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

Packages that use NSequenceWithQuality

Package	Description
com.milaboratory.core
com.milaboratory.core.io.sequence
com.milaboratory.core.merger
com.milaboratory.core.mutations
com.milaboratory.core.sequence
com.milaboratory.util

Uses of NSequenceWithQuality in com.milaboratory.core

Fields in com.milaboratory.core declared as NSequenceWithQuality

Modifier and Type	Field and Description
NSequenceWithQuality[]	Target.targets

Uses of NSequenceWithQuality in com.milaboratory.core.io.sequence

Methods in com.milaboratory.core.io.sequence that return NSequenceWithQuality

Modifier and Type	Method and Description
NSequenceWithQuality	SingleReadLazy.getData()
NSequenceWithQuality	SingleReadImpl.getData()
NSequenceWithQuality	SingleRead.getData()

Constructors in com.milaboratory.core.io.sequence with parameters of type NSequenceWithQuality

Constructor and Description
SingleReadImpl(long id, NSequenceWithQuality sequenceWithQuality, String description)

Uses of NSequenceWithQuality in com.milaboratory.core.merger

Methods in com.milaboratory.core.merger that return NSequenceWithQuality

Modifier and Type	Method and Description
NSequenceWithQuality	PairedReadMergingResult.getOverlappedSequence()
NSequenceWithQuality	MismatchOnlyPairedReadMerger.overlap(NSequenceWithQuality seq1, NSequenceWithQuality seq2, int offset)

Methods in com.milaboratory.core.merger with parameters of type NSequenceWithQuality

Modifier and Type	Method and Description
static double	MismatchOnlyPairedReadMerger.identity(MergerParameters.IdentityType identityType, NSequenceWithQuality seq1, int offset1, NSequenceWithQuality seq2, int offset2, int length)
PairedReadMergingResult	MismatchOnlyPairedReadMerger.merge(NSequenceWithQuality read1p, NSequenceWithQuality read2p)
PairedReadMergingResult	MismatchOnlyPairedReadMerger.merge(NSequenceWithQuality read1p, NSequenceWithQuality read2p, PairedRead pairedRead)
NSequenceWithQuality	MismatchOnlyPairedReadMerger.overlap(NSequenceWithQuality seq1, NSequenceWithQuality seq2, int offset)

Constructors in com.milaboratory.core.merger with parameters of type NSequenceWithQuality

Constructor and Description
PairedReadMergingResult(PairedRead originalRead, NSequenceWithQuality overlappedSequence, int overlap, int errors, boolean reversed, int offset, MergerParameters.IdentityType identityType, double identity) Constructor for successful merging result.

Uses of NSequenceWithQuality in com.milaboratory.core.mutations

Methods in com.milaboratory.core.mutations that return NSequenceWithQuality

Modifier and Type	Method and Description
static NSequenceWithQuality	MutationsUtil.mutate(NSequenceWithQuality seq, Mutations<NucleotideSequence> mutations)

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

Modifier and Type	Method and Description
static NSequenceWithQuality	MutationsUtil.mutate(NSequenceWithQuality seq, Mutations<NucleotideSequence> mutations)

Uses of NSequenceWithQuality in com.milaboratory.core.sequence

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

Modifier and Type	Field and Description
static NSequenceWithQuality	NSequenceWithQuality.EMPTY

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

Modifier and Type	Method and Description
NSequenceWithQuality	NSequenceWithQuality.concatenate(NSequenceWithQuality other)
NSequenceWithQuality	NSequenceWithQualityBuilder.createAndDestroy()
static NSequenceWithQuality	UnsafeFactory.fastqParse(byte[] buffer, int fromSequence, int fromQuality, int length, byte qualityValueOffset, long id, boolean replaceWildcards)
NSequenceWithQuality	NSequenceWithQuality.get(int id)
NSequenceWithQuality	MultiNSequenceWithQualityImpl.get(int id)
NSequenceWithQuality	MultiNSequenceWithQuality.get(int id)
NSequenceWithQuality	NSequenceWithQuality.getRange(int from, int to)
NSequenceWithQuality	NSequenceWithQuality.getRange(Range range)
NSequenceWithQuality	NSequenceWithQuality.getReverseComplement() Returns reverse complement sequence with reversed quality.

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

Modifier and Type	Method and Description
NSequenceWithQualityBuilder	NSequenceWithQualityBuilder.append(NSequenceWithQuality seq)
NSequenceWithQuality	NSequenceWithQuality.concatenate(NSequenceWithQuality other)

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

Constructor and Description
MultiNSequenceWithQualityImpl(NSequenceWithQuality... seqs)

Uses of NSequenceWithQuality in com.milaboratory.util

Constructors in com.milaboratory.util with parameters of type NSequenceWithQuality

Constructor and Description
NSequenceWithQualityPrintHelper(NSequenceWithQuality seq, int offset, int lineLength)