| Package | Description |
|---|---|
| com.milaboratory.core.alignment.kaligner1 |
| 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
|
| Modifier and Type | Method and Description |
|---|---|
static KMapper |
KMapper.createFromParameters(KAlignerParameters parameters)
Factory method to create KMapper using parametners specified in the
KAlignerParameters
object. |
| Constructor and Description |
|---|
KAligner(KAlignerParameters parameters)
Creates new KAligner.
|
KAligner(KAlignerParameters parameters,
boolean lazyResults)
Creates new KAligner.
|
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