com.milaboratory.core.alignment.kaligner1

Class KAlignerParameters

java.lang.Object

com.milaboratory.core.alignment.kaligner1.KAlignerParameters

All Implemented Interfaces:

BatchAlignerWithBaseParameters, AbstractKAlignerParameters, Serializable, Cloneable

public final class KAlignerParameters
extends Object
implements Cloneable, Serializable, AbstractKAlignerParameters

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
KAlignerParameters()
KAlignerParameters(int mapperKValue, boolean floatingLeftBound, boolean floatingRightBound, float mapperAbsoluteMinScore, float mapperRelativeMinScore, float mapperMatchScore, float mapperMismatchPenalty, float mapperOffsetShiftPenalty, int mapperMinSeedsDistance, int mapperMaxSeedsDistance, int minAlignmentLength, int maxAdjacentIndels, int alignmentStopPenalty, float absoluteMinScore, float relativeMinScore, int maxHits, LinearGapAlignmentScoring<NucleotideSequence> scoring) Creates new KAligner

Method Summary

Methods

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

KAlignerParameters

public KAlignerParameters()

KAlignerParameters

public KAlignerParameters(int mapperKValue,
                  boolean floatingLeftBound,
                  boolean floatingRightBound,
                  float mapperAbsoluteMinScore,
                  float mapperRelativeMinScore,
                  float mapperMatchScore,
                  float mapperMismatchPenalty,
                  float mapperOffsetShiftPenalty,
                  int mapperMinSeedsDistance,
                  int mapperMaxSeedsDistance,
                  int minAlignmentLength,
                  int maxAdjacentIndels,
                  int alignmentStopPenalty,
                  float absoluteMinScore,
                  float relativeMinScore,
                  int maxHits,
                  LinearGapAlignmentScoring<NucleotideSequence> scoring)

Creates new KAligner

Parameters:

mapperKValue - length of k-mers (seeds) used by KMapper

floatingLeftBound - true if left bound of alignment could be floating

floatingRightBound - true if right bound of alignment could be floating

mapperAbsoluteMinScore - minimal allowed absolute hit score obtained by KMapper to consider hit as reliable candidate

mapperRelativeMinScore - minimal allowed ratio between best hit score and scores of other hits obtained by KMapper to consider hit as reliable candidate

mapperMatchScore - reward for successfully mapped seeds (used in KMapper), must be > 0

mapperMismatchPenalty - penalty for not mapped seed (used in KMapper), must be < 0

mapperOffsetShiftPenalty - penalty for different offset between adjacent seeds (used in KMapper), must be < 0

mapperMinSeedsDistance - minimal distance between randomly chosen seeds during alignment in KMapper

mapperMaxSeedsDistance - maximal distance between randomly chosen seeds during alignment in KMapper

minAlignmentLength - minimal allowed alignment length

maxAdjacentIndels - maximal allowed number of insertions and deletions between 2 kMers

alignmentStopPenalty - penalty score defining when to stop alignment procedure performed by KAlignmentHit.calculateAlignment()

absoluteMinScore - minimal absolute score of a hit obtained by KAligner

relativeMinScore - maximal ratio between best hit score and scores of other hits obtained by KAligner

maxHits - maximal number of hits stored by KAlignmentResult

scoring - scoring system used for building alignments

Method Detail

getByName

public static KAlignerParameters getByName(String name)

Returns parameters by specified preset name

Parameters:

name - parameters preset name

Returns:

parameters with specified preset name

getAvailableNames

public static Set<String> getAvailableNames()

Returns all available parameters presets

Returns:

all available parameters presets

createAligner

public <P> KAligner<P> createAligner()

Specified by:

createAligner in interface BatchAlignerWithBaseParameters

getMapperKValue

public int getMapperKValue()

Returns kValue (length of kMers or seeds) used by KMapper

Returns:

kValue (length of kMers or seeds)

setMapperKValue

public KAlignerParameters setMapperKValue(int kValue)

Sets kValue (length of kMers or seeds) used by KMapper

Parameters:

kValue -

Returns:

parameters object

getMapperAbsoluteMinScore

public float getMapperAbsoluteMinScore()

Returns minimal allowed absolute hit score obtained by KMapper to consider hit as reliable candidate

Returns:

minimal allowed absolute hit score obtained by KMapper

setMapperAbsoluteMinScore

public KAlignerParameters setMapperAbsoluteMinScore(float 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 KAlignerParameters 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 float getMapperMatchScore()

Returns reward for successfully mapped seeds (used in KMapper)

Returns:

reward score for mapped seed

setMapperMatchScore

public KAlignerParameters setMapperMatchScore(float 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

getMapperMismatchPenalty

public float getMapperMismatchPenalty()

Returns penalty score for not mapped seeds (used in KMapper)

Returns:

penalty score for not mapped seed

setMapperMismatchPenalty

public KAlignerParameters setMapperMismatchPenalty(float mapperMismatchPenalty)

Sets penalty score for not mapped seed

Parameters:

mapperMismatchPenalty - penalty for not mapped seed (used in KMapper), must be < 0

Returns:

penalty for not mapped seed

getMinAlignmentLength

public int getMinAlignmentLength()

Returns minimal allowed alignment length

Returns:

minimal allowed alignment length

setMinAlignmentLength

public KAlignerParameters setMinAlignmentLength(int minAlignmentLength)

Sets minimal allowed alignment length

Parameters:

minAlignmentLength - minimal allowed alignment length

Returns:

parameters object

getMaxAdjacentIndels

public int getMaxAdjacentIndels()

Returns maximal allowed number of insertions and deletions between 2 kMers

Returns:

maximal allowed number of insertions and deletions between 2 kMers

setMaxAdjacentIndels

public KAlignerParameters setMaxAdjacentIndels(int maxAdjacentIndels)

Sets maximal allowed number of insertions and deletions between 2 kMers

Parameters:

maxAdjacentIndels - maximal allowed number of insertions and deletions between 2 kMers

Returns:

parameters object

getMapperMinSeedsDistance

public int getMapperMinSeedsDistance()

Returns minimal distance between randomly chosen seeds during alignment in KMapper

Returns:

minimal distance between randomly chosen seeds

setMapperMinSeedsDistance

public KAlignerParameters 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 KAlignerParameters 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

getAlignmentStopPenalty

public int getAlignmentStopPenalty()

Returns penalty score defining when to stop alignment procedure performed by KAlignmentHit.calculateAlignment()

Returns:

penalty score

setAlignmentStopPenalty

public KAlignerParameters 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 LinearGapAlignmentScoring<NucleotideSequence> getScoring()

Returns scoring system used for building alignments

Specified by:

getScoring in interface BatchAlignerWithBaseParameters

Returns:

scoring system

setScoring

public KAlignerParameters setScoring(LinearGapAlignmentScoring 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 KAlignerParameters 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 KAlignerParameters setFloatingRightBound(boolean floatingRightBound)

Sets right left bound of alignment

Parameters:

floatingRightBound - true if right bound of alignment could be floating

Returns:

parameters object

getMapperOffsetShiftPenalty

public float getMapperOffsetShiftPenalty()

Returns penalty for different offset between adjacent seeds (used in KMapper)

Returns:

penalty for different offset between adjacent seeds

setMapperOffsetShiftPenalty

public KAlignerParameters setMapperOffsetShiftPenalty(float mapperOffsetShiftPenalty)

Sets penalty for different offset between adjacent seeds (used in KMapper),

Parameters:

mapperOffsetShiftPenalty - penalty for different offset between adjacent seeds, must be < 0

Returns:

parameters object

getAbsoluteMinScore

public float getAbsoluteMinScore()

Returns minimal absolute score of a hit obtained by KAligner

Returns:

minimal absolute score

setAbsoluteMinScore

public KAlignerParameters setAbsoluteMinScore(float 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 KAlignerParameters 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 KAlignerParameters setMaxHits(int maxHits)

Sets maximal number of hits stored by KAlignmentResult

Parameters:

maxHits - maximal number of stored hits

Returns:

parameters object

clone

public KAlignerParameters 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