org.utgenome.format.fasta
Class Kmer

java.lang.Object
  extended by 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


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