org.utgenome.format.fasta
Class Kmer

java.lang.Object
  org.utgenome.format.fasta.Kmer

All Implemented Interfaces:

GenomeSequence

public class Kmer
extends Object
implements GenomeSequence

K-mer integer representation of ACGT. The difference with CompactACGT is this K-mer representation is modifiable to facilitate genome sequence editing.

Author:

leo

Constructor Summary

Kmer(CompactACGT acgt)

Kmer(Kmer other)

Kmer(String acgt)

Method Summary

Kmer	append(String acgt)
char	charAt(int index)
Kmer	delete(int deletePos, int deleteLen)
boolean	equals(Object obj)
int	hashCode()
Kmer	insert(int insertPos, String acgt)
int	length()
Kmer	reverseComplement()
void	set(int index, char acgt)
void	set(int index, String acgt)
int	toInt()
int	toInt(int firstKmer)
String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

Kmer

public Kmer(Kmer other)

Kmer

public Kmer(CompactACGT acgt)

Kmer

public Kmer(String acgt)

Method Detail

toInt

public int toInt()

toInt

public int toInt(int firstKmer)

length

public int length()

Specified by:

length in interface GenomeSequence

charAt

public char charAt(int index)

Specified by:

charAt in interface GenomeSequence

Parameters:

index - index on the genome sequence (0-origin)

Returns:

set

public void set(int index,
                char acgt)

set

public void set(int index,
                String acgt)

delete

public Kmer delete(int deletePos,
                   int deleteLen)

append

public Kmer append(String acgt)

insert

public Kmer insert(int insertPos,
                   String acgt)

reverseComplement

public Kmer reverseComplement()

toString

public String toString()

Overrides:

toString in class Object

equals

public boolean equals(Object obj)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object