Package com.milaboratory.core.alignment.batch

Interface Summary

Interface	Description
AlignmentHit<S extends Sequence<S>,P>
AlignmentResult<H extends AlignmentHit<?,?>>
BatchAligner<S extends Sequence<S>,H extends AlignmentHit<S,?>>	Represents aligner that can align a sequence against a set of other sequences.
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).
BatchAlignerWithBaseParameters
BatchAlignerWithBaseWithFilter<S extends Sequence<S>,P,H extends AlignmentHit<S,P>>
HasSequence<S extends Sequence<S>>	Interface for objects which natively have a sequence as their distinctive property.
PipedAlignmentResult<H extends AlignmentHit<?,?>,Q>
PipedBatchAligner<S extends Sequence<S>,H extends AlignmentHit<? extends S,?>>	Represents aligner that can align a sequence against a set of other sequences.
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).
SequenceExtractor<O,S extends Sequence<S>>	Interface for class to extract sequences from objects
WithBase<S extends Sequence<S>,P>	Interface for aligners with self-managed database (user can directly add subject sequences before running alignment)

Class Summary

Class	Description
AbstractBatchAligner<S extends Sequence<S>,H extends AlignmentHit<S,?>>
AlignmentHitImpl<S extends Sequence<S>,P>
AlignmentResultImpl<H extends AlignmentHit<?,?>>
BatchAlignmentUtil
PipedAlignmentResultImpl<H extends AlignmentHit<?,?>,Q>
SimpleBatchAligner<S extends Sequence<S>,P>	Simplest implementation of BatchAligner, which aligns target sequence with all subjects using classical (low performance) alignment algorithms.
SimpleBatchAlignerParameters<S extends Sequence<S>>	Parameters of SimpleBatchAligner.