com.milaboratory.core.alignment.batch

Interface WithBase<S extends Sequence<S>,P>

Type Parameters:

S - type of sequence

P - type of record payload, used to store additional information along with sequence to simplify it's subsequent identification in result (e.g. Integer to just index sequences.

All Known Subinterfaces:

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

All Known Implementing Classes:

AABlastAligner, BlastAligner, BlastAlignerAbstract, KAligner, KAligner2, NBlastAligner, SimpleBatchAligner

public interface WithBase<S extends Sequence<S>,P>

Interface for aligners with self-managed database (user can directly add subject sequences before running alignment)

Method Summary

Methods

Modifier and Type	Method and Description
void	addReference(S sequence, P payload) Adds a record to the base of this aligner (a set of subject sequences that this instance aligns queries with).

Method Detail

addReference

void addReference(S sequence,
                P payload)

Adds a record to the base of this aligner (a set of subject sequences that this instance aligns queries with).

Parameters:

sequence - sequence

payload - payload to store additional information with this record (can be retrieved from resulting AlignmentHit)