com.milaboratory.core.alignment.kaligner2

Class KAligner2Statistics

java.lang.Object

com.milaboratory.core.alignment.kaligner2.KAligner2Statistics

public final class KAligner2Statistics
extends Object

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	KAligner2Statistics.ClusterTrimmingType
static class	KAligner2Statistics.State

Field Summary

Fields

Modifier and Type	Field and Description
AtomicHistogram	alignerTime
AtomicHistogram	allInitialClusters
AtomicHistogram	allInitialRecordsCount
AtomicHistogram	allRemovedByTrimming
AtomicHistogram	allRemovedByUntangling
AtomicEnumHistogram<KAligner2Statistics.ClusterTrimmingType>	allTrimming
AtomicHistogram	allUntangledClusters
AtomicLong	changeOfTop1
AtomicLong	changeOfTop2
AtomicHistogram	filteredHitsByAlignments
AtomicHistogram	hitCalculationTime
AtomicLong	inputQueries
AtomicHistogram	mapperTotalTime
AtomicHistogram	numberOfAlignmentsHits
AtomicHistogram	numberOfMappingHits
AtomicLong	rerun
AtomicHistogram	seedExtractionTime
AtomicHistogram	topInitialClusters
AtomicHistogram	topInitialRecordsCount
AtomicHistogram	topRemovedByTrimming
AtomicHistogram	topRemovedByUntangling
AtomicEnumHistogram<KAligner2Statistics.ClusterTrimmingType>	topTrimming
AtomicHistogram	topUntangledClusters
AtomicHistogram	totalTime

Constructor Summary

Constructors

Constructor and Description
KAligner2Statistics()

Method Summary

Methods

Modifier and Type	Method and Description
void	afterCandidatesArrayDone(IntArrayList[] candidates)
void	afterTrimming(int id, IntArrayList results)
void	afterUntangling(IntArrayList untangled)
static int	countClusters(IntArrayList results)
void	initialClusters(int id, IntArrayList results)
void	kAlignerResult(KAlignmentResult2 result)
void	kMappingResults(KMappingResult2 result)
void	nextQuery()
void	reRunBecauseOfMicroTangling()
String	toString()
void	trimmingEvent(KAligner2Statistics.ClusterTrimmingType type)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

inputQueries

public final AtomicLong inputQueries

allInitialRecordsCount

public final AtomicHistogram allInitialRecordsCount

topInitialRecordsCount

public final AtomicHistogram topInitialRecordsCount

allInitialClusters

public final AtomicHistogram allInitialClusters

topInitialClusters

public final AtomicHistogram topInitialClusters

allRemovedByTrimming

public final AtomicHistogram allRemovedByTrimming

topRemovedByTrimming

public final AtomicHistogram topRemovedByTrimming

allRemovedByUntangling

public final AtomicHistogram allRemovedByUntangling

topRemovedByUntangling

public final AtomicHistogram topRemovedByUntangling

allUntangledClusters

public final AtomicHistogram allUntangledClusters

topUntangledClusters

public final AtomicHistogram topUntangledClusters

allTrimming

public final AtomicEnumHistogram<KAligner2Statistics.ClusterTrimmingType> allTrimming

topTrimming

public final AtomicEnumHistogram<KAligner2Statistics.ClusterTrimmingType> topTrimming

rerun

public final AtomicLong rerun

changeOfTop1

public final AtomicLong changeOfTop1

changeOfTop2

public final AtomicLong changeOfTop2

numberOfMappingHits

public final AtomicHistogram numberOfMappingHits

numberOfAlignmentsHits

public final AtomicHistogram numberOfAlignmentsHits

filteredHitsByAlignments

public final AtomicHistogram filteredHitsByAlignments

seedExtractionTime

public final AtomicHistogram seedExtractionTime

hitCalculationTime

public final AtomicHistogram hitCalculationTime

mapperTotalTime

public final AtomicHistogram mapperTotalTime

alignerTime

public final AtomicHistogram alignerTime

totalTime

public final AtomicHistogram totalTime

Constructor Detail

KAligner2Statistics

public KAligner2Statistics()

Method Detail

nextQuery

public void nextQuery()

afterCandidatesArrayDone

public void afterCandidatesArrayDone(IntArrayList[] candidates)

initialClusters

public void initialClusters(int id,
                   IntArrayList results)

trimmingEvent

public void trimmingEvent(KAligner2Statistics.ClusterTrimmingType type)

afterTrimming

public void afterTrimming(int id,
                 IntArrayList results)

afterUntangling

public void afterUntangling(IntArrayList untangled)

reRunBecauseOfMicroTangling

public void reRunBecauseOfMicroTangling()

kMappingResults

public void kMappingResults(KMappingResult2 result)

kAlignerResult

public void kAlignerResult(KAlignmentResult2 result)

toString

public String toString()

Overrides:

toString in class Object

countClusters

public static int countClusters(IntArrayList results)