com.milaboratory.core.alignment.blast

Class NBlastAlignerExt

java.lang.Object

com.milaboratory.core.alignment.blast.BlastAlignerExtAbstract<NucleotideSequence,NBlastHitExt>

com.milaboratory.core.alignment.blast.NBlastAlignerExt

All Implemented Interfaces:

PipedBatchAligner<NucleotideSequence,NBlastHitExt>

public class NBlastAlignerExt
extends BlastAlignerExtAbstract<NucleotideSequence,NBlastHitExt>

Constructor Summary

Constructors

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

Method Summary

Methods

Modifier and Type	Method and Description
protected NBlastHitExt	createHit(Alignment<NucleotideSequence> 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

NBlastAlignerExt

public NBlastAlignerExt(BlastDB database)

NBlastAlignerExt

public NBlastAlignerExt(BlastDB database,
                BlastAlignerParameters parameters)

Method Detail

createHit

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

Specified by:

createHit in class BlastAlignerExtAbstract<NucleotideSequence,NBlastHitExt>