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

Packages that use PipedBatchAligner

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

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

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

Modifier and Type	Interface and Description
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 PipedBatchAligner

Modifier and Type	Class and Description
class	AbstractBatchAligner<S extends Sequence<S>,H extends AlignmentHit<S,?>>
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 PipedBatchAligner in com.milaboratory.core.alignment.blast

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

Modifier and Type	Class and Description
class	AABlastAligner<P>
class	AABlastAlignerExt
class	BlastAligner<S extends Sequence<S>,P>
class	BlastAlignerAbstract<S extends Sequence<S>,P,H extends BlastHit<S,P>>
class	BlastAlignerExt<S extends Sequence<S>>
class	BlastAlignerExtAbstract<S extends Sequence<S>,H extends BlastHitExt<S>> Blast aligner of query sequences with external (non-milib-managed) database of sequences.
class	NBlastAligner<P>
class	NBlastAlignerExt

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

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

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