Uses of Class
com.milaboratory.util.BitArray

Packages that use BitArray

Package	Description
com.milaboratory.core.alignment
com.milaboratory.core.alignment.batch
com.milaboratory.core.alignment.kaligner1
com.milaboratory.core.alignment.kaligner2
com.milaboratory.util

Uses of BitArray in com.milaboratory.core.alignment

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

Modifier and Type	Field and Description
protected BitArray	AlignmentHelper.match

Constructors in com.milaboratory.core.alignment with parameters of type BitArray

Constructor and Description
AlignmentHelper(String seq1String, String seq2String, int[] seq1Position, int[] seq2Position, BitArray match)
AlignmentHelper(String seq1String, String seq2String, int[] seq1Position, int[] seq2Position, BitArray match, int offset)

Uses of BitArray in com.milaboratory.core.alignment.batch

Methods in com.milaboratory.core.alignment.batch that return BitArray

Modifier and Type	Method and Description
BitArray	BatchAlignerWithBaseWithFilter.createFilter(cc.redberry.primitives.Filter<P> filter)

Methods in com.milaboratory.core.alignment.batch with parameters of type BitArray

Modifier and Type	Method and Description
AlignmentResult<H>	BatchAlignerWithBaseWithFilter.align(S sequence, int from, int to, BitArray filter)

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

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

Modifier and Type	Method and Description
BitArray	KAligner.createFilter(cc.redberry.primitives.Filter<P> filter)

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

Modifier and Type	Method and Description
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.

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

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

Modifier and Type	Method and Description
BitArray	KAligner2.createFilter(cc.redberry.primitives.Filter<P> filter)

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

Modifier and Type	Method and Description
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)

Uses of BitArray in com.milaboratory.util

Methods in com.milaboratory.util that return BitArray

Modifier and Type	Method and Description
BitArray	BitArray.clone()
static BitArray	BitArray.construct(byte[] data, int size)
BitArray	BitArray.getRange(int from, int to)

Methods in com.milaboratory.util with parameters of type BitArray

Modifier and Type	Method and Description
void	BitArray.and(BitArray bitArray)
static byte[]	BitArray.extractRawDataArray(BitArray array)
boolean	BitArray.intersects(BitArray bitArray)
void	BitArray.loadValueFrom(BitArray bitArray)
void	BitArray.or(BitArray bitArray)
void	BitArray.set(BitArray ba)
void	BitArray.xor(BitArray bitArray)