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

Packages that use WithBase

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

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

Subinterfaces of WithBase in com.milaboratory.core.alignment.batch

Modifier and Type	Interface and Description
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	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 WithBase

Modifier and Type	Class and Description
class	SimpleBatchAligner<S extends Sequence<S>,P> Simplest implementation of BatchAligner, which aligns target sequence with all subjects using classical (low performance) alignment algorithms.

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

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

Modifier and Type	Class and Description
class	AABlastAligner<P>
class	BlastAligner<S extends Sequence<S>,P>
class	BlastAlignerAbstract<S extends Sequence<S>,P,H extends BlastHit<S,P>>
class	NBlastAligner<P>

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

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

Modifier and Type	Class and Description
class	KAligner<P> KAligner is a comprehensive aligner for nucleotide sequences.

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

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

Modifier and Type	Class and Description
class	KAligner2<P>