net.sf.snver.pileup.loader
Class FastaReader

java.lang.Object
  net.sf.snver.pileup.loader.FastaReader

public class FastaReader
extends java.lang.Object

Fasta file reader which is using for reference load

Created by IntelliJ IDEA. User: weicheng hu Date: 10/22/11 Time: 10:46 PM

Constructor Summary

FastaReader(java.lang.String filename)
Constructor

Method Summary

byte[]	getReferenceSeq(int index, java.lang.String name) Return the whole genome reference with validation by genome index and name
boolean	isOpen() Check the reference is loaded or not
static void	main(java.lang.String[] args)

Methods inherited from class java.lang.Object

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

Constructor Detail

FastaReader

public FastaReader(java.lang.String filename)

Constructor

Parameters:

filename - String

Method Detail

getReferenceSeq

public byte[] getReferenceSeq(int index,
                              java.lang.String name)

Return the whole genome reference with validation by genome index and name

Parameters:

index - int

name - String

Returns:

byte[]

isOpen

public boolean isOpen()

Check the reference is loaded or not

Returns:

boolean

main

public static void main(java.lang.String[] args)