uk.ac.sanger.npg.illumina.file.reader
Class BCLFileReader

java.lang.Object
  uk.ac.sanger.npg.illumina.file.reader.IlluminaFileReader
      uk.ac.sanger.npg.illumina.file.reader.BCLFileReader

All Implemented Interfaces:

java.io.Closeable, java.util.Iterator<java.lang.Object>

public class BCLFileReader
extends IlluminaFileReader

This class is a reader of a bcl file

Field Summary

Fields inherited from class uk.ac.sanger.npg.illumina.file.reader.IlluminaFileReader

fileName, inputStream

Constructor Summary

BCLFileReader(java.lang.String bclFileName)
constructor to generate bcl file input stream and read the number of clusters

Method Summary

int	getCurrentCluster()
int	getTotalClusters()
boolean	hasNext() check any more clusters in the file stream
static void	main(java.lang.String[] args)
byte[]	next() get base and quality for next cluster

Methods inherited from class uk.ac.sanger.npg.illumina.file.reader.IlluminaFileReader

close, getFileName, readFourBytes, readFourBytes, remove

Methods inherited from class java.lang.Object

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

Constructor Detail

BCLFileReader

public BCLFileReader(java.lang.String bclFileName)
              throws java.lang.Exception

constructor to generate bcl file input stream and read the number of clusters

Parameters:

bclFileName - bcl file name

Throws:

java.lang.Exception

Method Detail

hasNext

public boolean hasNext()

check any more clusters in the file stream

Specified by:

hasNext in interface java.util.Iterator<java.lang.Object>

Overrides:

hasNext in class IlluminaFileReader

Returns:

true if there is next cluster available

next

public byte[] next()

get base and quality for next cluster

Specified by:

next in interface java.util.Iterator<java.lang.Object>

Overrides:

next in class IlluminaFileReader

Returns:

byte [] base byte for the first element and quality byte as the second element

getCurrentCluster

public int getCurrentCluster()

Returns:

the currentCluster

getTotalClusters

public int getTotalClusters()

Returns:

the totalClusters

main

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

Parameters:

args -

Throws:

java.lang.Exception