com.milaboratory.core.alignment.kaligner1

Class KAlignmentResult<P>

java.lang.Object

com.milaboratory.core.alignment.kaligner1.KAlignmentResult<P>

All Implemented Interfaces:

AlignmentResult<KAlignmentHit<P>>, Serializable, Iterable<KAlignmentHit<P>>

Direct Known Subclasses:

KAlignmentResultP

public class KAlignmentResult<P>
extends Object
implements AlignmentResult<KAlignmentHit<P>>, Iterable<KAlignmentHit<P>>, Serializable

KAlignmentResult - class which is result of KAligner.align(com.milaboratory.core.sequence.NucleotideSequence), KAligner.align(com.milaboratory.core.sequence.NucleotideSequence, int, int), KAligner#align(com.milaboratory.core.sequence.NucleotideSequence, int, int, boolean) methods.

It contains link to according KMappingResult, list of hits found in target sequence as well as range of target sequence to be aligned.

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
KAlignmentResult(KAligner<P> aligner, KMappingResult mappingResult, NucleotideSequence target, int targetFrom, int targetTo) Creates new KAlignmentResult

Method Summary

Methods

Modifier and Type	Method and Description
void	calculateAllAlignments() Calculates alignments for all hits
KAligner	getAligner() Returns link to aligner
KAlignmentHit	getBestHit() Returns best hit (hit with highest alignment or mapper (if lazy alignment is used) score) or null if there is no hits in this result
List<KAlignmentHit<P>>	getHits() Returns list of hits found in target sequence
KMappingResult	getMappingResult() Returns mapping result
NucleotideSequence	getTarget() Returns target sequence
int	getTargetFrom() Returns position of first nucleotide of target sequence to be aligned
int	getTargetTo() Returns position of last nucleotide of target sequence to be aligned
boolean	hasHits() Checks if there are hits
Iterator<KAlignmentHit<P>>	iterator()
void	refresh() Refresh alignments of all hits
void	sortAccordingToMapperScores() Sorts hits according to KMappingHit alignment score

Methods inherited from class java.lang.Object

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

Constructor Detail

KAlignmentResult

public KAlignmentResult(KAligner<P> aligner,
                KMappingResult mappingResult,
                NucleotideSequence target,
                int targetFrom,
                int targetTo)

Creates new KAlignmentResult

Parameters:

aligner - link to aligner

mappingResult - link to according mapping result (which is result of com.milaboratory.core.sequence.alignment.KMapper#align(com.milaboratory.core.sequence.NucleotideSequence), KMapper.align(com.milaboratory.core.sequence.NucleotideSequence, int, int) methods)

target - target sequence to be aligned

targetFrom - position of first nucleotide of target sequence to be aligned

targetTo - position of last nucleotide of target sequence to be aligned

Method Detail

getAligner

public KAligner getAligner()

Returns link to aligner

Returns:

aligner

getMappingResult

public KMappingResult getMappingResult()

Returns mapping result

Returns:

hasHits

public boolean hasHits()

Checks if there are hits

Specified by:

hasHits in interface AlignmentResult<KAlignmentHit<P>>

Returns:

true if hits array is not empty

getBestHit

public KAlignmentHit getBestHit()

Returns best hit (hit with highest alignment or mapper (if lazy alignment is used) score) or null if there is no hits in this result

Specified by:

getBestHit in interface AlignmentResult<KAlignmentHit<P>>

Returns:

best hit (hit with highest alignment or mapper (if lazy alignment is used) score) or null if there is no hits in this result

getHits

public List<KAlignmentHit<P>> getHits()

Returns list of hits found in target sequence

Specified by:

getHits in interface AlignmentResult<KAlignmentHit<P>>

Returns:

list of hits found in target sequence

getTarget

public NucleotideSequence getTarget()

Returns target sequence

Returns:

target sequence

getTargetFrom

public int getTargetFrom()

Returns position of first nucleotide of target sequence to be aligned

Returns:

position of first nucleotide of target sequence to be aligned

getTargetTo

public int getTargetTo()

Returns position of last nucleotide of target sequence to be aligned

Returns:

position of last nucleotide of target sequence to be aligned

sortAccordingToMapperScores

public void sortAccordingToMapperScores()

Sorts hits according to KMappingHit alignment score

calculateAllAlignments

public void calculateAllAlignments()

Calculates alignments for all hits

refresh

public void refresh()

Refresh alignments of all hits

iterator

public Iterator<KAlignmentHit<P>> iterator()

Specified by:

iterator in interface Iterable<KAlignmentHit<P>>