org.utgenome.format.fasta
Class FASTADatabase.NSeq

java.lang.Object
  org.utgenome.format.fasta.FASTADatabase.NSeq

Enclosing class:

FASTADatabase

public static class FASTADatabase.NSeq
extends Object

A holder for retrieving compressed genome sequence

Author:

leo

Constructor Summary

FASTADatabase.NSeq()

FASTADatabase.NSeq(int start, int end, byte[] sequence)

Method Summary

int	getEnd()
int	getLength()
byte[]	getSequence()
int	getStart()
String	getSubSequence(int bufStart, int bufEnd) extract sub sequence (0-origin)
void	setEnd(int end)
void	setSequence(byte[] sequence)
void	setStart(int start)
String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

FASTADatabase.NSeq

public FASTADatabase.NSeq()

FASTADatabase.NSeq

public FASTADatabase.NSeq(int start,
                          int end,
                          byte[] sequence)

Method Detail

toString

public String toString()

Overrides:

toString in class Object

setStart

public void setStart(int start)

setEnd

public void setEnd(int end)

getStart

public int getStart()

getEnd

public int getEnd()

getSubSequence

public String getSubSequence(int bufStart,
                             int bufEnd)

extract sub sequence (0-origin)

Parameters:

bufStart -

bufEnd -

Returns:

getLength

public int getLength()

getSequence

public byte[] getSequence()

setSequence

public void setSequence(byte[] sequence)
                 throws IOException

Throws:

IOException