org.utgenome.util.kmer
Class KmerIntegerFactory

java.lang.Object
  org.utgenome.util.kmer.KmerIntegerFactory

public class KmerIntegerFactory
extends Object

Generator of the bit-integer representation of a k-mer sequence

Author:

leo

Constructor Summary

KmerIntegerFactory(int K)

Method Summary

int	doubleStrandXOR(int kmer) Return the XOR value of the double strand reads of a given k-mer sequence.
int	parseString(String acgt)
int	reverseComplement(int kmerInt)
String	toString(int kmerInt)

Methods inherited from class java.lang.Object

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

Constructor Detail

KmerIntegerFactory

public KmerIntegerFactory(int K)

Method Detail

doubleStrandXOR

public int doubleStrandXOR(int kmer)

Return the XOR value of the double strand reads of a given k-mer sequence. Since XOR is commutative, the result value is the same for both strand reads.

Parameters:

K -

Returns:

reverseComplement

public int reverseComplement(int kmerInt)

parseString

public int parseString(String acgt)
                throws UTGBException

Parameters:

acgt -

Returns:

Throws:

UTGBException - when the input contains a non-ACGT character;

toString

public String toString(int kmerInt)