org.utgenome.format.fasta
Class CompactACGT

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

All Implemented Interfaces:

GenomeSequence

public class CompactACGT
extends Object
implements GenomeSequence

Compact array for ACGT (and N) sequences

Author:

leo

Method Summary

char	charAt(int index)
static CompactACGT	createFromString(String seq)
OverlappingKmerIterator	getKmerIterator(int K)
int	length()
CompactACGT	reverseComplement()
CompactACGT	subSequence(int start, int length) return a subsequence of this ACGT string.
String	toString()

Methods inherited from class java.lang.Object

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

Method Detail

subSequence

public CompactACGT subSequence(int start,
                               int length)
                        throws UTGBException

return a subsequence of this ACGT string. The returned CompactACGT holds the references to the sequence byte arrays, and no buffer copy will be performed.

Parameters:

start -

length -

Returns:

Throws:

UTGBException

reverseComplement

public CompactACGT reverseComplement()
                              throws UTGBException

Throws:

UTGBException

getKmerIterator

public OverlappingKmerIterator getKmerIterator(int K)

createFromString

public static CompactACGT createFromString(String seq)
                                    throws IOException,
                                           UTGBException

Throws:

IOException

UTGBException

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:

toString

public String toString()

Overrides:

toString in class Object