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

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

All Implemented Interfaces:

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

public class SCLFileReader
extends IlluminaFileReader

This class is a reader of a scl file

Field Summary

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

fileName, inputStream

Constructor Summary

SCLFileReader(java.lang.String sclFileName)
constructor to generate scl file input stream, and read the number of clusters and read all bases to an array

Method Summary

int	getCurrentCluster()
int	getTotalClusters()
boolean	hasNext() check any more clusters in the file stream
static void	main(java.lang.String[] args)
java.lang.Character	next()

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

SCLFileReader

public SCLFileReader(java.lang.String sclFileName)
              throws java.lang.Exception

constructor to generate scl file input stream, and read the number of clusters and read all bases to an array

Parameters:

sclFileName - scl 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

next

public java.lang.Character next()

Specified by:

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

Overrides:

next in class IlluminaFileReader

Returns:

next second base call

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