Uses of Class
com.milaboratory.core.alignment.kaligner1.KAlignerParameters

Packages that use KAlignerParameters

Package	Description
com.milaboratory.core.alignment.kaligner1

Uses of KAlignerParameters in com.milaboratory.core.alignment.kaligner1

Methods in com.milaboratory.core.alignment.kaligner1 that return KAlignerParameters

Modifier and Type	Method and Description
KAlignerParameters	KAlignerParameters.clone()
static KAlignerParameters	KAlignerParameters.getByName(String name) Returns parameters by specified preset name
KAlignerParameters	KAlignerParameters.setAbsoluteMinScore(float absoluteMinScore) Sets minimal absolute score of a hit obtained by KAligner
KAlignerParameters	KAlignerParameters.setAlignmentStopPenalty(int alignmentStopPenalty) Sets penalty score defining when to stop alignment procedure performed by KAlignmentHit.calculateAlignment()
KAlignerParameters	KAlignerParameters.setFloatingLeftBound(boolean floatingLeftBound) Sets left left bound of alignment
KAlignerParameters	KAlignerParameters.setFloatingRightBound(boolean floatingRightBound) Sets right left bound of alignment
KAlignerParameters	KAlignerParameters.setMapperAbsoluteMinScore(float mapperAbsoluteMinScore) Sets minimal allowed absolute hit score obtained by KMapper to consider hit as reliable candidate
KAlignerParameters	KAlignerParameters.setMapperKValue(int kValue) Sets kValue (length of kMers or seeds) used by KMapper
KAlignerParameters	KAlignerParameters.setMapperMatchScore(float mapperMatchScore) Sets for successfully mapped seeds (used in KMapper)
KAlignerParameters	KAlignerParameters.setMapperMaxSeedsDistance(int mapperMaxSeedsDistance) Sets maximal distance between randomly chosen seeds during alignment in KMapper
KAlignerParameters	KAlignerParameters.setMapperMinSeedsDistance(int mapperMinSeedsDistance) Sets minimal distance between randomly chosen seeds during alignment in KMapper
KAlignerParameters	KAlignerParameters.setMapperMismatchPenalty(float mapperMismatchPenalty) Sets penalty score for not mapped seed
KAlignerParameters	KAlignerParameters.setMapperOffsetShiftPenalty(float mapperOffsetShiftPenalty) Sets penalty for different offset between adjacent seeds (used in KMapper),
KAlignerParameters	KAlignerParameters.setMapperRelativeMinScore(float mapperRelativeMinScore) Sets minimal allowed ratio between best hit score and other hits obtained by KMapper to consider hit as reliable candidate
KAlignerParameters	KAlignerParameters.setMaxAdjacentIndels(int maxAdjacentIndels) Sets maximal allowed number of insertions and deletions between 2 kMers
KAlignerParameters	KAlignerParameters.setMaxHits(int maxHits) Sets maximal number of hits stored by KAlignmentResult
KAlignerParameters	KAlignerParameters.setMinAlignmentLength(int minAlignmentLength) Sets minimal allowed alignment length
KAlignerParameters	KAlignerParameters.setRelativeMinScore(float relativeMinScore) Sets maximal ratio between best hit score and scores of other hits obtained by KAligner
KAlignerParameters	KAlignerParameters.setScoring(LinearGapAlignmentScoring scoring) Sets scoring system used for building alignments

Methods in com.milaboratory.core.alignment.kaligner1 with parameters of type KAlignerParameters

Modifier and Type	Method and Description
static KMapper	KMapper.createFromParameters(KAlignerParameters parameters) Factory method to create KMapper using parametners specified in the KAlignerParameters object.

Constructors in com.milaboratory.core.alignment.kaligner1 with parameters of type KAlignerParameters

Constructor and Description
KAligner(KAlignerParameters parameters) Creates new KAligner.
KAligner(KAlignerParameters parameters, boolean lazyResults) Creates new KAligner.