Uses of Class
com.milaboratory.core.alignment.kaligner2.KAlignerParameters2

Packages that use KAlignerParameters2

Package	Description
com.milaboratory.core.alignment.kaligner2

Uses of KAlignerParameters2 in com.milaboratory.core.alignment.kaligner2

Methods in com.milaboratory.core.alignment.kaligner2 that return KAlignerParameters2

Modifier and Type	Method and Description
KAlignerParameters2	KAlignerParameters2.clone()
KAlignerParameters2	KAlignerParameters2.setAbsoluteMinScore(int absoluteMinScore) Sets minimal absolute score of a hit obtained by KAligner
KAlignerParameters2	KAlignerParameters2.setAlignmentStopPenalty(int alignmentStopPenalty) Sets penalty score defining when to stop alignment procedure performed by KAlignmentHit.calculateAlignment()
KAlignerParameters2	KAlignerParameters2.setFloatingLeftBound(boolean floatingLeftBound) Sets left left bound of alignment
KAlignerParameters2	KAlignerParameters2.setFloatingRightBound(boolean floatingRightBound) Sets right left bound of alignment
KAlignerParameters2	KAlignerParameters2.setMapperAbsoluteMinClusterScore(int mapperAbsoluteMinScore) Sets minimal allowed absolute hit score obtained by KMapper to consider hit as reliable candidate
KAlignerParameters2	KAlignerParameters2.setMapperAbsoluteMinScore(int mapperAbsoluteMinScore) Minimal value of total mapping score (sum of cluster scores and mapperExtraClusterScore * (nClusters - 1))
KAlignerParameters2	KAlignerParameters2.setMapperExtraClusterScore(int mapperExtraClusterScore)
KAlignerParameters2	KAlignerParameters2.setMapperKMersPerPosition(int mapperKMersPerPosition) If mapperKValue > 0, it is possible to map several seeds with holes in different places to the same position in target sequence.
KAlignerParameters2	KAlignerParameters2.setMapperKValue(int mapperKValue)
KAlignerParameters2	KAlignerParameters2.setMapperMatchScore(int mapperMatchScore) Sets for successfully mapped seeds (used in KMapper)
KAlignerParameters2	KAlignerParameters2.setMapperMaxClusterIndels(int mapperMaxClusterIndels) Max indels inside a cluster (if indel is bigger, alignment will be divided into several clusters)
KAlignerParameters2	KAlignerParameters2.setMapperMaxClusters(int mapperMaxClusters) Max allowed clusters
KAlignerParameters2	KAlignerParameters2.setMapperMaxSeedsDistance(int mapperMaxSeedsDistance) Sets maximal distance between randomly chosen seeds during alignment in KMapper
KAlignerParameters2	KAlignerParameters2.setMapperMinSeedsDistance(int mapperMinSeedsDistance) Sets minimal distance between randomly chosen seeds during alignment in KMapper
KAlignerParameters2	KAlignerParameters2.setMapperMismatchScore(int mapperMismatchScore) Sets penalty score for not mapped seed
KAlignerParameters2	KAlignerParameters2.setMapperNValue(int kValue) Sets kValue (length of kMers or seeds) used by KMapper
KAlignerParameters2	KAlignerParameters2.setMapperOffsetShiftScore(int mapperOffsetShiftScore) Sets penalty for different offset between adjacent seeds (used in KMapper),
KAlignerParameters2	KAlignerParameters2.setMapperRelativeMinScore(float mapperRelativeMinScore) Sets minimal allowed ratio between best hit score and other hits obtained by KMapper to consider hit as reliable candidate
KAlignerParameters2	KAlignerParameters2.setMapperSlotCount(int mapperSlotCount) Number of simultaneously constructed clusters in one-pass initial cluster detection algorithm
KAlignerParameters2	KAlignerParameters2.setMaxHits(int maxHits) Sets maximal number of hits stored by KAlignmentResult
KAlignerParameters2	KAlignerParameters2.setRelativeMinScore(float relativeMinScore) Sets maximal ratio between best hit score and scores of other hits obtained by KAligner
KAlignerParameters2	KAlignerParameters2.setScoring(AffineGapAlignmentScoring<NucleotideSequence> scoring) Sets scoring system used for building alignments

Methods in com.milaboratory.core.alignment.kaligner2 with parameters of type KAlignerParameters2

Modifier and Type	Method and Description
static KMapper2	KMapper2.createFromParameters(KAlignerParameters2 parameters) Factory method to create KMapper2 using parameters specified in the KAlignerParameters2 object.
static KMapper2	KMapper2.createFromParameters(KAlignerParameters2 parameters, KAligner2Statistics stat) Factory method to create KMapper2 using parameters specified in the KAlignerParameters2 object.

Constructors in com.milaboratory.core.alignment.kaligner2 with parameters of type KAlignerParameters2

Constructor and Description
KAligner2(KAlignerParameters2 parameters)
KAligner2(KAlignerParameters2 parameters, KAligner2Statistics stat)