com.milaboratory.core.alignment.batch

Interface BatchAligner<S extends Sequence<S>,H extends AlignmentHit<S,?>>

Type Parameters:

S - sequence type

P - type of record payload, used to store additional information sequence in base to simplify it's subsequent identification in result (e.g. Integer to just index sequences, or com.milaboratory.core.alignment.blast.BlastDBRecord etc...)

All Known Subinterfaces:

BatchAlignerWithBase<S,P,H>, BatchAlignerWithBaseWithFilter<S,P,H>

All Known Implementing Classes:

AbstractBatchAligner, KAligner, KAligner2, SimpleBatchAligner

public interface BatchAligner<S extends Sequence<S>,H extends AlignmentHit<S,?>>

Represents aligner that can align a sequence against a set of other sequences.

Author:

Dmitry Bolotin, Stanislav Poslavsky

Method Summary

Methods

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

Method Detail

align

AlignmentResult<H> align(S sequence)

align

AlignmentResult<H> align(S sequence,
                       int from,
                       int to)