com.hfg.bio.seq.alignment

Class KMerBitSet

java.lang.Object

java.util.BitSet

com.hfg.bio.seq.alignment.KMerBitSet

All Implemented Interfaces:

Serializable, Cloneable

public class KMerBitSet
extends BitSet

BitSet container for holding detected k-mer instances from a sequence.

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
KMerBitSet(BioSequenceType inSeqType, int inKMerSize)

Method Summary

Modifier and Type	Method and Description
void	fill(BioSequence inSequence)
BioSequenceType	getBioSequenceType()
int	getCommonKMerCount(KMerBitSet inComparisonKMerBitSet)

Methods inherited from class java.util.BitSet

and, andNot, cardinality, clear, clear, clear, clone, equals, flip, flip, get, get, hashCode, intersects, isEmpty, length, nextClearBit, nextSetBit, or, previousClearBit, previousSetBit, set, set, set, set, size, stream, toByteArray, toLongArray, toString, valueOf, valueOf, valueOf, valueOf, xor

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

KMerBitSet

public KMerBitSet(BioSequenceType inSeqType,
                  int inKMerSize)

Method Detail

getBioSequenceType

public BioSequenceType getBioSequenceType()

fill

public void fill(BioSequence inSequence)

getCommonKMerCount

public int getCommonKMerCount(KMerBitSet inComparisonKMerBitSet)