com.milaboratory.core.alignment.blast

Class BlastAlignerExt<S extends Sequence<S>>

java.lang.Object

com.milaboratory.core.alignment.blast.BlastAlignerExtAbstract<S,BlastHitExt<S>>

com.milaboratory.core.alignment.blast.BlastAlignerExt<S>

All Implemented Interfaces:

PipedBatchAligner<S,BlastHitExt<S>>

public class BlastAlignerExt<S extends Sequence<S>>
extends BlastAlignerExtAbstract<S,BlastHitExt<S>>

Constructor Summary

Constructors

Constructor and Description
BlastAlignerExt(BlastDB database)
BlastAlignerExt(BlastDB database, BlastAlignerParameters parameters)

Method Summary

Methods

Modifier and Type	Method and Description
protected BlastHitExt<S>	createHit(Alignment alignment, double score, double bitScore, double eValue, Range subjectRange, String subjectId, String subjectTitle)

Methods inherited from class com.milaboratory.core.alignment.blast.BlastAlignerExtAbstract

align, align, setConcurrentBlastProcessCount

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

BlastAlignerExt

public BlastAlignerExt(BlastDB database)

BlastAlignerExt

public BlastAlignerExt(BlastDB database,
               BlastAlignerParameters parameters)

Method Detail

createHit

protected BlastHitExt<S> createHit(Alignment alignment,
                       double score,
                       double bitScore,
                       double eValue,
                       Range subjectRange,
                       String subjectId,
                       String subjectTitle)

Specified by:

createHit in class BlastAlignerExtAbstract<S extends Sequence<S>,BlastHitExt<S extends Sequence<S>>>