KAlignerParameters2 (MiLib 1.8.3 API)

java.lang.Object
- com.milaboratory.core.alignment.kaligner2.KAlignerParameters2

All Implemented Interfaces:

BatchAlignerWithBaseParameters, AbstractKAlignerParameters, Serializable, Cloneable
```
public final class KAlignerParameters2
extends Object
implements AbstractKAlignerParameters, Cloneable, Serializable
```
Author:

Dmitry Bolotin, Stanislav Poslavsky

See Also:
Serialized Form

Constructor Summary

Constructors
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)

Method Summary

Methods
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()`

Methods inherited from class java.lang.Object
finalize, getClass, notify, notifyAll, wait, wait, wait

- Constructor Detail
  - KAlignerParameters2
```
public KAlignerParameters2()
```
  - 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)
```
- Method Detail
  - createAligner
```
public <P> KAligner2<P> createAligner()
```
    Specified by:
    
    createAligner in interface BatchAlignerWithBaseParameters
  - getMapperNValue
```
public int getMapperNValue()
```
    Returns kValue (length of kMers or seeds) used by KMapper
    
    Returns:
    kValue (length of kMers or seeds)
  - setMapperNValue
```
public KAlignerParameters2 setMapperNValue(int kValue)
```
    Sets kValue (length of kMers or seeds) used by KMapper
    
    Parameters:
    kValue -
    
    Returns:
    parameters object
  - getMapperKValue
```
public int getMapperKValue()
```
  - setMapperKValue
```
public KAlignerParameters2 setMapperKValue(int mapperKValue)
```
  - getMapperAbsoluteMinClusterScore
```
public int getMapperAbsoluteMinClusterScore()
```
    Returns minimal allowed absolute hit score obtained by KMapper to consider hit as reliable candidate
    
    Returns:
    minimal allowed absolute hit score obtained by KMapper
  - setMapperAbsoluteMinClusterScore
```
public KAlignerParameters2 setMapperAbsoluteMinClusterScore(int mapperAbsoluteMinScore)
```
    Sets minimal allowed absolute hit score obtained by KMapper to consider hit as reliable candidate
    
    Parameters:
    mapperAbsoluteMinScore - minimal allowed absolute hit score value
    
    Returns:
    parameters object
  - getMapperRelativeMinScore
```
public float getMapperRelativeMinScore()
```
    Returns minimal allowed ratio between best hit score and other hits obtained by KMapper to consider hit as reliable candidate
    
    Returns:
    minimal allowed ratio between best hit score and other hits obtained by KMapper
  - setMapperRelativeMinScore
```
public KAlignerParameters2 setMapperRelativeMinScore(float mapperRelativeMinScore)
```
    Sets minimal allowed ratio between best hit score and other hits obtained by KMapper to consider hit as reliable candidate
    
    Parameters:
    mapperRelativeMinScore - minimal allowed ratio between best hit score and other hits
    
    Returns:
    parameters object
  - getMapperMatchScore
```
public int getMapperMatchScore()
```
    Returns reward for successfully mapped seeds (used in KMapper)
    
    Returns:
    reward score for mapped seed
  - setMapperMatchScore
```
public KAlignerParameters2 setMapperMatchScore(int mapperMatchScore)
```
    Sets for successfully mapped seeds (used in KMapper)
    
    Parameters:
    mapperMatchScore - reward for successfully mapped seeds (used in KMapper), must be > 0
    
    Returns:
    parameters object
  - getMapperMismatchScore
```
public int getMapperMismatchScore()
```
    Returns penalty score for not mapped seeds (used in KMapper)
    
    Returns:
    penalty score for not mapped seed
  - setMapperMismatchScore
```
public KAlignerParameters2 setMapperMismatchScore(int mapperMismatchScore)
```
    Sets penalty score for not mapped seed
    
    Parameters:
    mapperMismatchScore - penalty for not mapped seed (used in KMapper), must be < 0
    
    Returns:
    penalty for not mapped seed
  - getMapperOffsetShiftScore
```
public int getMapperOffsetShiftScore()
```
    Returns penalty for different offset between adjacent seeds (used in KMapper)
    
    Returns:
    penalty for different offset between adjacent seeds
  - setMapperOffsetShiftScore
```
public KAlignerParameters2 setMapperOffsetShiftScore(int mapperOffsetShiftScore)
```
    Sets penalty for different offset between adjacent seeds (used in KMapper),
    
    Parameters:
    mapperOffsetShiftScore - penalty for different offset between adjacent seeds, must be < 0
    
    Returns:
    parameters object
  - getMapperExtraClusterScore
```
public int getMapperExtraClusterScore()
```
  - setMapperExtraClusterScore
```
public KAlignerParameters2 setMapperExtraClusterScore(int mapperExtraClusterScore)
```
  - getMapperMinSeedsDistance
```
public int getMapperMinSeedsDistance()
```
    Returns minimal distance between randomly chosen seeds during alignment in KMapper
    
    Returns:
    minimal distance between randomly chosen seeds
  - setMapperMinSeedsDistance
```
public KAlignerParameters2 setMapperMinSeedsDistance(int mapperMinSeedsDistance)
```
    Sets minimal distance between randomly chosen seeds during alignment in KMapper
    
    Parameters:
    mapperMinSeedsDistance - minimal distance between randomly chosen seeds
    
    Returns:
    parameters object
  - getMapperMaxSeedsDistance
```
public int getMapperMaxSeedsDistance()
```
    Returns maximal distance between randomly chosen seeds during alignment in KMapper
    
    Returns:
    maximal distance between randomly chosen seeds
  - setMapperMaxSeedsDistance
```
public KAlignerParameters2 setMapperMaxSeedsDistance(int mapperMaxSeedsDistance)
```
    Sets maximal distance between randomly chosen seeds during alignment in KMapper
    
    Parameters:
    mapperMaxSeedsDistance - maximal distance between randomly chosen seeds
    
    Returns:
    parameters object
  - getMapperSlotCount
```
public int getMapperSlotCount()
```
    Number of simultaneously constructed clusters in one-pass initial cluster detection algorithm
  - setMapperSlotCount
```
public KAlignerParameters2 setMapperSlotCount(int mapperSlotCount)
```
    Number of simultaneously constructed clusters in one-pass initial cluster detection algorithm
  - getMapperMaxClusterIndels
```
public int getMapperMaxClusterIndels()
```
    Max indels inside a cluster (if indel is bigger, alignment will be divided into several clusters)
  - setMapperMaxClusterIndels
```
public KAlignerParameters2 setMapperMaxClusterIndels(int mapperMaxClusterIndels)
```
    Max indels inside a cluster (if indel is bigger, alignment will be divided into several clusters)
  - getMapperKMersPerPosition
```
public int getMapperKMersPerPosition()
```
    If mapperKValue > 0, it is possible to map several seeds with holes in different places to the same position in target sequence. e.g. if mapperKValue = 1 and mapperNValue = 5 there ara 5 different sets of KMers: X = must match; 0 = allow mismatch: 0XXXX X0XXX XX0XX XXX0X XXXX0 and if mapperKMersPerPosition == 5 (which means: try to map all kMer variants listed above to each seed position in target sequence) mapping will be made even if 5-met in the target seed position has 1 substitution compared to database. Constraint: kMersPerPosition <= nValue / kValue
  - setMapperKMersPerPosition
```
public 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. e.g. if mapperKValue = 1 and mapperNValue = 5 there ara 5 different sets of KMers: X = must match; 0 = allow mismatch: 0XXXX X0XXX XX0XX XXX0X XXXX0 and if mapperKMersPerPosition == 5 (which means: try to map all kMer variants listed above to each seed position in target sequence) mapping will be made even if 5-met in the target seed position has 1 substitution compared to database. Constraint: kMersPerPosition <= nValue / kValue
  - getMapperMaxClusters
```
public int getMapperMaxClusters()
```
    Max allowed clusters
  - setMapperMaxClusters
```
public KAlignerParameters2 setMapperMaxClusters(int mapperMaxClusters)
```
    Max allowed clusters
  - getAlignmentStopPenalty
```
public int getAlignmentStopPenalty()
```
    Returns penalty score defining when to stop alignment procedure performed by KAlignmentHit.calculateAlignment()
    
    Returns:
    penalty score
  - setAlignmentStopPenalty
```
public KAlignerParameters2 setAlignmentStopPenalty(int alignmentStopPenalty)
```
    Sets penalty score defining when to stop alignment procedure performed by KAlignmentHit.calculateAlignment()
    
    Parameters:
    alignmentStopPenalty - penalty score
    
    Returns:
    parameters object
  - getScoring
```
public AffineGapAlignmentScoring<NucleotideSequence> getScoring()
```
    Returns scoring system used for building alignments
    
    Specified by:
    
    getScoring in interface BatchAlignerWithBaseParameters
    
    Returns:
    scoring system
  - setScoring
```
public KAlignerParameters2 setScoring(AffineGapAlignmentScoring<NucleotideSequence> scoring)
```
    Sets scoring system used for building alignments
    
    Parameters:
    scoring - scoring system
    
    Returns:
    parameters object
  - isFloatingLeftBound
```
public boolean isFloatingLeftBound()
```
    Checks if left bound of alignment is floating
    
    Specified by:
    
    isFloatingLeftBound in interface AbstractKAlignerParameters
    
    Returns:
    true if left bound of alignment is floating
  - setFloatingLeftBound
```
public KAlignerParameters2 setFloatingLeftBound(boolean floatingLeftBound)
```
    Sets left left bound of alignment
    
    Parameters:
    floatingLeftBound - true if left bound of alignment could be floating
    
    Returns:
    parameters object
  - isFloatingRightBound
```
public boolean isFloatingRightBound()
```
    Checks if right bound of alignment is floating
    
    Specified by:
    
    isFloatingRightBound in interface AbstractKAlignerParameters
    
    Returns:
    true if right bound of alignment is floating
  - setFloatingRightBound
```
public KAlignerParameters2 setFloatingRightBound(boolean floatingRightBound)
```
    Sets right left bound of alignment
    
    Parameters:
    floatingRightBound - true if right bound of alignment could be floating
    
    Returns:
    parameters object
  - getMapperAbsoluteMinScore
```
public int getMapperAbsoluteMinScore()
```
    Minimal value of total mapping score (sum of cluster scores and mapperExtraClusterScore * (nClusters - 1))
  - setMapperAbsoluteMinScore
```
public KAlignerParameters2 setMapperAbsoluteMinScore(int mapperAbsoluteMinScore)
```
    Minimal value of total mapping score (sum of cluster scores and mapperExtraClusterScore * (nClusters - 1))
  - getAbsoluteMinScore
```
public int getAbsoluteMinScore()
```
    Returns minimal absolute score of a hit obtained by KAligner
    
    Returns:
    minimal absolute score
  - setAbsoluteMinScore
```
public KAlignerParameters2 setAbsoluteMinScore(int absoluteMinScore)
```
    Sets minimal absolute score of a hit obtained by KAligner
    
    Parameters:
    absoluteMinScore - minimal absolute score of a hit
    
    Returns:
    parameters object
  - getRelativeMinScore
```
public float getRelativeMinScore()
```
    Returns maximal ratio between best hit score and scores of other hits obtained by KAligner
    
    Specified by:
    
    getRelativeMinScore in interface AbstractKAlignerParameters
    
    Returns:
    maximal ratio between best hit score and scores of other hits
  - setRelativeMinScore
```
public KAlignerParameters2 setRelativeMinScore(float relativeMinScore)
```
    Sets maximal ratio between best hit score and scores of other hits obtained by KAligner
    
    Parameters:
    relativeMinScore - maximal ratio between best hit score and scores of other hits
    
    Returns:
    parameters object
  - getMaxHits
```
public int getMaxHits()
```
    Returns maximal number of hits stored by KAlignmentResult
    
    Specified by:
    
    getMaxHits in interface AbstractKAlignerParameters
    
    Returns:
    maximal number of stored hits
  - setMaxHits
```
public KAlignerParameters2 setMaxHits(int maxHits)
```
    Sets maximal number of hits stored by KAlignmentResult
    
    Parameters:
    maxHits - maximal number of stored hits
    
    Returns:
    parameters object
  - clone
```
public KAlignerParameters2 clone()
```
    Specified by:
    
    clone in interface BatchAlignerWithBaseParameters
    
    Specified by:
    
    clone in interface AbstractKAlignerParameters
    
    Overrides:
    
    clone in class Object
  - equals
```
public boolean equals(Object o)
```
    Overrides:
    
    equals in class Object
  - hashCode
```
public int hashCode()
```
    Overrides:
    
    hashCode in class Object
  - toString
```
public String toString()
```
    Overrides:
    
    toString in class Object

Class KAlignerParameters2

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

KAlignerParameters2

KAlignerParameters2

Method Detail

createAligner

getMapperNValue

setMapperNValue

getMapperKValue

setMapperKValue

getMapperAbsoluteMinClusterScore

setMapperAbsoluteMinClusterScore

getMapperRelativeMinScore

setMapperRelativeMinScore

getMapperMatchScore

setMapperMatchScore

getMapperMismatchScore

setMapperMismatchScore

getMapperOffsetShiftScore

setMapperOffsetShiftScore

getMapperExtraClusterScore

setMapperExtraClusterScore

getMapperMinSeedsDistance

setMapperMinSeedsDistance

getMapperMaxSeedsDistance

setMapperMaxSeedsDistance

getMapperSlotCount

setMapperSlotCount

getMapperMaxClusterIndels

setMapperMaxClusterIndels

getMapperKMersPerPosition

setMapperKMersPerPosition

getMapperMaxClusters

setMapperMaxClusters

getAlignmentStopPenalty

setAlignmentStopPenalty

getScoring

setScoring

isFloatingLeftBound

setFloatingLeftBound

isFloatingRightBound

setFloatingRightBound

getMapperAbsoluteMinScore

setMapperAbsoluteMinScore

getAbsoluteMinScore

setAbsoluteMinScore

getRelativeMinScore

setRelativeMinScore

getMaxHits

setMaxHits

clone

equals

hashCode

toString