public final class KAlignerParameters2 extends Object implements AbstractKAlignerParameters, Cloneable, Serializable
| Constructor and Description |
|---|
KAlignerParameters2() |
KAlignerParameters2(int mapperNValue,
int mapperKValue,
boolean floatingLeftBound,
boolean floatingRightBound,
int mapperAbsoluteMinClusterScore,
int mapperExtraClusterScore,
int mapperAbsoluteMinScore,
float mapperRelativeMinScore,
int mapperMatchScore,
int mapperMismatchScore,
int mapperOffsetShiftScore,
int mapperMinSeedsDistance,
int mapperMaxSeedsDistance,
int mapperSlotCount,
int mapperMaxClusters,
int mapperMaxClusterIndels,
int mapperKMersPerPosition,
int alignmentStopPenalty,
int absoluteMinScore,
float relativeMinScore,
int maxHits,
AffineGapAlignmentScoring scoring) |
| Modifier and Type | Method and Description |
|---|---|
KAlignerParameters2 |
clone() |
<P> KAligner2<P> |
createAligner() |
boolean |
equals(Object o) |
int |
getAbsoluteMinScore()
Returns minimal absolute score of a hit obtained by
KAligner |
int |
getAlignmentStopPenalty()
Returns penalty score defining when to stop alignment procedure performed by
KAlignmentHit.calculateAlignment() |
int |
getMapperAbsoluteMinClusterScore()
Returns minimal allowed absolute hit score obtained by
KMapper
to consider hit as reliable candidate |
int |
getMapperAbsoluteMinScore()
Minimal value of total mapping score (sum of cluster scores and mapperExtraClusterScore * (nClusters - 1))
|
int |
getMapperExtraClusterScore() |
int |
getMapperKMersPerPosition()
If mapperKValue > 0, it is possible to map several seeds with holes in different places to the same position in
target sequence.
|
int |
getMapperKValue() |
int |
getMapperMatchScore()
Returns reward for successfully mapped seeds (used in
KMapper) |
int |
getMapperMaxClusterIndels()
Max indels inside a cluster (if indel is bigger, alignment will be divided into several clusters)
|
int |
getMapperMaxClusters()
Max allowed clusters
|
int |
getMapperMaxSeedsDistance()
Returns maximal distance between randomly chosen seeds during alignment in
KMapper |
int |
getMapperMinSeedsDistance()
Returns minimal distance between randomly chosen seeds during alignment in
KMapper |
int |
getMapperMismatchScore()
Returns penalty score for not mapped seeds (used in
KMapper) |
int |
getMapperNValue()
Returns kValue (length of kMers or seeds) used by
KMapper |
int |
getMapperOffsetShiftScore()
Returns penalty for different offset between adjacent seeds (used in
KMapper) |
float |
getMapperRelativeMinScore()
Returns minimal allowed ratio between best hit score and other hits obtained by
KMapper to consider hit as reliable candidate |
int |
getMapperSlotCount()
Number of simultaneously constructed clusters in one-pass initial cluster detection algorithm
|
int |
getMaxHits()
Returns maximal number of hits stored by
KAlignmentResult |
float |
getRelativeMinScore()
Returns maximal ratio between best hit score and scores of other hits obtained by
KAligner |
AffineGapAlignmentScoring<NucleotideSequence> |
getScoring()
Returns scoring system used for building alignments
|
int |
hashCode() |
boolean |
isFloatingLeftBound()
Checks if left bound of alignment is floating
|
boolean |
isFloatingRightBound()
Checks if right bound of alignment is floating
|
KAlignerParameters2 |
setAbsoluteMinScore(int absoluteMinScore)
Sets minimal absolute score of a hit obtained by
KAligner |
KAlignerParameters2 |
setAlignmentStopPenalty(int alignmentStopPenalty)
Sets penalty score defining when to stop alignment procedure performed by
KAlignmentHit.calculateAlignment() |
KAlignerParameters2 |
setFloatingLeftBound(boolean floatingLeftBound)
Sets left left bound of alignment
|
KAlignerParameters2 |
setFloatingRightBound(boolean floatingRightBound)
Sets right left bound of alignment
|
KAlignerParameters2 |
setMapperAbsoluteMinClusterScore(int mapperAbsoluteMinScore)
Sets minimal allowed absolute hit score obtained by
KMapper to
consider hit as reliable candidate |
KAlignerParameters2 |
setMapperAbsoluteMinScore(int mapperAbsoluteMinScore)
Minimal value of total mapping score (sum of cluster scores and mapperExtraClusterScore * (nClusters - 1))
|
KAlignerParameters2 |
setMapperExtraClusterScore(int mapperExtraClusterScore) |
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 |
setMapperKValue(int mapperKValue) |
KAlignerParameters2 |
setMapperMatchScore(int mapperMatchScore)
Sets for successfully mapped seeds (used in
KMapper) |
KAlignerParameters2 |
setMapperMaxClusterIndels(int mapperMaxClusterIndels)
Max indels inside a cluster (if indel is bigger, alignment will be divided into several clusters)
|
KAlignerParameters2 |
setMapperMaxClusters(int mapperMaxClusters)
Max allowed clusters
|
KAlignerParameters2 |
setMapperMaxSeedsDistance(int mapperMaxSeedsDistance)
Sets maximal distance between randomly chosen seeds during alignment in
KMapper |
KAlignerParameters2 |
setMapperMinSeedsDistance(int mapperMinSeedsDistance)
Sets minimal distance between randomly chosen seeds during alignment in
KMapper |
KAlignerParameters2 |
setMapperMismatchScore(int mapperMismatchScore)
Sets penalty score for not mapped seed
|
KAlignerParameters2 |
setMapperNValue(int kValue)
Sets kValue (length of kMers or seeds) used by
KMapper |
KAlignerParameters2 |
setMapperOffsetShiftScore(int mapperOffsetShiftScore)
Sets penalty for different offset between adjacent seeds (used in
KMapper), |
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 |
setMapperSlotCount(int mapperSlotCount)
Number of simultaneously constructed clusters in one-pass initial cluster detection algorithm
|
KAlignerParameters2 |
setMaxHits(int maxHits)
Sets maximal number of hits stored by
KAlignmentResult |
KAlignerParameters2 |
setRelativeMinScore(float relativeMinScore)
Sets maximal ratio between best hit score and scores of other hits obtained by
KAligner |
KAlignerParameters2 |
setScoring(AffineGapAlignmentScoring<NucleotideSequence> scoring)
Sets scoring system used for building alignments
|
String |
toString() |
public KAlignerParameters2()
public KAlignerParameters2(int mapperNValue,
int mapperKValue,
boolean floatingLeftBound,
boolean floatingRightBound,
int mapperAbsoluteMinClusterScore,
int mapperExtraClusterScore,
int mapperAbsoluteMinScore,
float mapperRelativeMinScore,
int mapperMatchScore,
int mapperMismatchScore,
int mapperOffsetShiftScore,
int mapperMinSeedsDistance,
int mapperMaxSeedsDistance,
int mapperSlotCount,
int mapperMaxClusters,
int mapperMaxClusterIndels,
int mapperKMersPerPosition,
int alignmentStopPenalty,
int absoluteMinScore,
float relativeMinScore,
int maxHits,
AffineGapAlignmentScoring scoring)
public <P> KAligner2<P> createAligner()
createAligner in interface BatchAlignerWithBaseParameterspublic int getMapperNValue()
KMapperpublic KAlignerParameters2 setMapperNValue(int kValue)
KMapperkValue - public int getMapperKValue()
public KAlignerParameters2 setMapperKValue(int mapperKValue)
public int getMapperAbsoluteMinClusterScore()
KMapper
to consider hit as reliable candidateKMapperpublic KAlignerParameters2 setMapperAbsoluteMinClusterScore(int mapperAbsoluteMinScore)
KMapper to
consider hit as reliable candidatemapperAbsoluteMinScore - minimal allowed absolute hit score valuepublic float getMapperRelativeMinScore()
KMapper to consider hit as reliable candidateKMapperpublic KAlignerParameters2 setMapperRelativeMinScore(float mapperRelativeMinScore)
KMapper to consider hit as reliable candidatemapperRelativeMinScore - minimal allowed ratio between best hit score and other hitspublic int getMapperMatchScore()
KMapper)public KAlignerParameters2 setMapperMatchScore(int mapperMatchScore)
KMapper)mapperMatchScore - reward for successfully mapped seeds (used in KMapper),
must be > 0public int getMapperMismatchScore()
KMapper)public KAlignerParameters2 setMapperMismatchScore(int mapperMismatchScore)
mapperMismatchScore - penalty for not mapped seed (used in KMapper),
must be < 0public int getMapperOffsetShiftScore()
KMapper)public KAlignerParameters2 setMapperOffsetShiftScore(int mapperOffsetShiftScore)
KMapper),mapperOffsetShiftScore - penalty for different offset between adjacent seeds, must be < 0public int getMapperExtraClusterScore()
public KAlignerParameters2 setMapperExtraClusterScore(int mapperExtraClusterScore)
public int getMapperMinSeedsDistance()
KMapperpublic KAlignerParameters2 setMapperMinSeedsDistance(int mapperMinSeedsDistance)
KMappermapperMinSeedsDistance - minimal distance between randomly chosen seedspublic int getMapperMaxSeedsDistance()
KMapperpublic KAlignerParameters2 setMapperMaxSeedsDistance(int mapperMaxSeedsDistance)
KMappermapperMaxSeedsDistance - maximal distance between randomly chosen seedspublic int getMapperSlotCount()
public KAlignerParameters2 setMapperSlotCount(int mapperSlotCount)
public int getMapperMaxClusterIndels()
public KAlignerParameters2 setMapperMaxClusterIndels(int mapperMaxClusterIndels)
public int getMapperKMersPerPosition()
public KAlignerParameters2 setMapperKMersPerPosition(int mapperKMersPerPosition)
public int getMapperMaxClusters()
public KAlignerParameters2 setMapperMaxClusters(int mapperMaxClusters)
public int getAlignmentStopPenalty()
KAlignmentHit.calculateAlignment()public KAlignerParameters2 setAlignmentStopPenalty(int alignmentStopPenalty)
KAlignmentHit.calculateAlignment()alignmentStopPenalty - penalty scorepublic AffineGapAlignmentScoring<NucleotideSequence> getScoring()
getScoring in interface BatchAlignerWithBaseParameterspublic KAlignerParameters2 setScoring(AffineGapAlignmentScoring<NucleotideSequence> scoring)
scoring - scoring systempublic boolean isFloatingLeftBound()
isFloatingLeftBound in interface AbstractKAlignerParameterstrue if left bound of alignment is floatingpublic KAlignerParameters2 setFloatingLeftBound(boolean floatingLeftBound)
floatingLeftBound - true if left bound of alignment could be floatingpublic boolean isFloatingRightBound()
isFloatingRightBound in interface AbstractKAlignerParameterstrue if right bound of alignment is floatingpublic KAlignerParameters2 setFloatingRightBound(boolean floatingRightBound)
floatingRightBound - true if right bound of alignment could be floatingpublic int getMapperAbsoluteMinScore()
public KAlignerParameters2 setMapperAbsoluteMinScore(int mapperAbsoluteMinScore)
public int getAbsoluteMinScore()
KAlignerpublic KAlignerParameters2 setAbsoluteMinScore(int absoluteMinScore)
KAlignerabsoluteMinScore - minimal absolute score of a hitpublic float getRelativeMinScore()
KAlignergetRelativeMinScore in interface AbstractKAlignerParameterspublic KAlignerParameters2 setRelativeMinScore(float relativeMinScore)
KAlignerrelativeMinScore - maximal ratio between best hit score and scores of other hitspublic int getMaxHits()
KAlignmentResultgetMaxHits in interface AbstractKAlignerParameterspublic KAlignerParameters2 setMaxHits(int maxHits)
KAlignmentResultmaxHits - maximal number of stored hitspublic KAlignerParameters2 clone()
clone in interface BatchAlignerWithBaseParametersclone in interface AbstractKAlignerParametersclone in class ObjectCopyright © 2018. All rights reserved.