com.milaboratory.core.alignment.batch

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

Type Parameters:

S - sequence type

H - hit class

All Known Subinterfaces:

PipedBatchAlignerWithBase<S,P,H>

All Known Implementing Classes:

AABlastAligner, AABlastAlignerExt, AbstractBatchAligner, BlastAligner, BlastAlignerAbstract, BlastAlignerExt, BlastAlignerExtAbstract, KAligner, NBlastAligner, NBlastAlignerExt, SimpleBatchAligner

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

Represents aligner that can align a sequence against a set of other sequences. This type of aligner works only as a pipe processor.

Author:

Dmitry Bolotin, Stanislav Poslavsky

Method Summary

Methods

Modifier and Type	Method and Description
<Q extends HasSequence<S>> cc.redberry.pipe.OutputPort<? extends PipedAlignmentResult<H,Q>>	align(cc.redberry.pipe.OutputPort<Q> input) Starts processing of input sequences and returns pipe of results.
<Q> cc.redberry.pipe.OutputPort<? extends PipedAlignmentResult<H,Q>>	align(cc.redberry.pipe.OutputPort<Q> input, SequenceExtractor<Q,S> extractor) Starts processing of input sequences and returns pipe of results.

Method Detail

align

<Q> cc.redberry.pipe.OutputPort<? extends PipedAlignmentResult<H,Q>> align(cc.redberry.pipe.OutputPort<Q> input,
                                                                         SequenceExtractor<Q,S> extractor)

Starts processing of input sequences and returns pipe of results.

Type Parameters:

Q - type of query object

Parameters:

input - pipe of queries

extractor - extractor of sequences from query object

Returns:

pipe of alignment results

align

<Q extends HasSequence<S>> cc.redberry.pipe.OutputPort<? extends PipedAlignmentResult<H,Q>> align(cc.redberry.pipe.OutputPort<Q> input)

Starts processing of input sequences and returns pipe of results.

Type Parameters:

Q - type of query objects

Parameters:

input - pipe of queries

Returns:

pipe of alignment results