Uses of Interface
com.milaboratory.core.alignment.batch.AlignmentHit

Packages that use AlignmentHit

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

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

Classes in com.milaboratory.core.alignment.batch with type parameters of type AlignmentHit

Modifier and Type	Class and Description
class	AbstractBatchAligner<S extends Sequence<S>,H extends AlignmentHit<S,?>>
interface	AlignmentResult<H extends AlignmentHit<?,?>>
class	AlignmentResultImpl<H extends AlignmentHit<?,?>>
interface	BatchAligner<S extends Sequence<S>,H extends AlignmentHit<S,?>> Represents aligner that can align a sequence against a set of other sequences.
interface	BatchAlignerWithBase<S extends Sequence<S>,P,H extends AlignmentHit<S,P>> BatchAligner with self-managed database (user can directly add subject sequences before running alignment).
interface	BatchAlignerWithBaseWithFilter<S extends Sequence<S>,P,H extends AlignmentHit<S,P>>
interface	PipedAlignmentResult<H extends AlignmentHit<?,?>,Q>
class	PipedAlignmentResultImpl<H extends AlignmentHit<?,?>,Q>
interface	PipedBatchAligner<S extends Sequence<S>,H extends AlignmentHit<? extends S,?>> Represents aligner that can align a sequence against a set of other sequences.
interface	PipedBatchAlignerWithBase<S extends Sequence<S>,P,H extends AlignmentHit<? extends S,? extends P>> PipedBatchAligner with self-managed database (user can directly add subject sequences before running alignment).

Classes in com.milaboratory.core.alignment.batch that implement AlignmentHit

Modifier and Type	Class and Description
class	AlignmentHitImpl<S extends Sequence<S>,P>

Fields in com.milaboratory.core.alignment.batch with type parameters of type AlignmentHit

Modifier and Type	Field and Description
static Comparator<AlignmentHit<?,?>>	BatchAlignmentUtil.ALIGNMENT_SCORE_HIT_COMPARATOR

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

Modifier and Type	Method and Description
AlignmentResult<AlignmentHit<S,P>>	SimpleBatchAligner.align(S sequence)
AlignmentResult<AlignmentHit<S,P>>	SimpleBatchAligner.align(S sequence, int from, int to)
<P> BatchAlignerWithBaseWithFilter<NucleotideSequence,P,? extends AlignmentHit<NucleotideSequence,P>>	BatchAlignerWithBaseParameters.createAligner()

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

Classes in com.milaboratory.core.alignment.blast that implement AlignmentHit

Modifier and Type	Class and Description
class	AABlastHit<P>
class	AABlastHitExt
class	BlastHit<S extends Sequence<S>,P>
class	BlastHitExt<S extends Sequence<S>>
class	NBlastHit<P>
class	NBlastHitExt

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

Classes in com.milaboratory.core.alignment.kaligner1 that implement AlignmentHit

Modifier and Type	Class and Description
class	KAlignmentHit<P> KAlignmentHit - class which represents single hit for KAlignmentResult

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

Classes in com.milaboratory.core.alignment.kaligner2 that implement AlignmentHit

Modifier and Type	Class and Description
class	KAlignmentHit2<P>