Uses of Class
com.milaboratory.util.IntArrayList

Packages that use IntArrayList

Package	Description
com.milaboratory.core.alignment.kaligner1
com.milaboratory.core.alignment.kaligner2
com.milaboratory.core.mutations
com.milaboratory.util

Uses of IntArrayList in com.milaboratory.core.alignment.kaligner1

Constructors in com.milaboratory.core.alignment.kaligner1 with parameters of type IntArrayList

Constructor and Description
KMappingResult(IntArrayList seeds, List<KMappingHit> hits) Creates new KMappingResult

Uses of IntArrayList in com.milaboratory.core.alignment.kaligner2

Methods in com.milaboratory.core.alignment.kaligner2 with parameters of type IntArrayList

Modifier and Type	Method and Description
void	KAligner2Statistics.afterCandidatesArrayDone(IntArrayList[] candidates)
void	KAligner2Statistics.afterTrimming(int id, IntArrayList results)
void	KAligner2Statistics.afterUntangling(IntArrayList untangled)
KMappingHit2	KMapper2.calculateHit(int id, IntArrayList data, IntArrayList seedPositions) Array list wrapper for KMapper2.calculateHit(int, int[], int, int, IntArrayList).
void	OffsetPacksAccumulator.calculateInitialPartitioning(IntArrayList list)
static int	KAligner2Statistics.countClusters(IntArrayList results)
void	KAligner2Statistics.initialClusters(int id, IntArrayList results)
static int	KMapper2.positionInTarget(IntArrayList seedPositions, int record)
static String	OffsetPacksAccumulator.toString(IntArrayList results, IntArrayList seedPositions, int[] data)

Constructors in com.milaboratory.core.alignment.kaligner2 with parameters of type IntArrayList

Constructor and Description
KMappingResult2(IntArrayList seeds, List<KMappingHit2> hits) Creates new KMappingResult

Uses of IntArrayList in com.milaboratory.core.mutations

Constructors in com.milaboratory.core.mutations with parameters of type IntArrayList

Constructor and Description
Mutations(Alphabet<S> alphabet, IntArrayList mutations)

Uses of IntArrayList in com.milaboratory.util

Methods in com.milaboratory.util that return IntArrayList

Modifier and Type	Method and Description
IntArrayList	IntArrayList.clone()

Methods in com.milaboratory.util with parameters of type IntArrayList

Modifier and Type	Method and Description
void	IntArrayList.addAll(IntArrayList intArrayList)
void	IntArrayList.copyFrom(IntArrayList other)
static int[]	IntArrayList.getArrayReference(IntArrayList list)