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

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

All Implemented Interfaces:

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

Direct Known Subclasses:

BCLFileReader, FilterFileReader, PositionFileReader, SCLFileReader

public class IlluminaFileReader
extends java.lang.Object
implements java.util.Iterator<java.lang.Object>, java.io.Closeable

This class tries to open a Illumina file into a data input stream. It is a base class for all file reader classes.

Field Summary

protected java.lang.String	fileName
protected java.io.DataInputStream	inputStream

Constructor Summary

IlluminaFileReader(java.lang.String fileName)

Method Summary

void	close() close file input stream
java.lang.String	getFileName()
boolean	hasNext()
java.lang.Object	next()
int	readFourBytes() read four bytes from its input stream and convert to unsigned integer
int	readFourBytes(java.io.DataInputStream inputStream) read four bytes from an input stream and convert to unsigned integer
void	remove()

Methods inherited from class java.lang.Object

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

Field Detail

fileName

protected final java.lang.String fileName

inputStream

protected java.io.DataInputStream inputStream

Constructor Detail

IlluminaFileReader

public IlluminaFileReader(java.lang.String fileName)
                   throws java.io.FileNotFoundException

Parameters:

fileName - bcl, scl, clocs, locs, pos and filter etc Illumina file name

Throws:

java.io.FileNotFoundException

Method Detail

hasNext

public boolean hasNext()

Specified by:

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

next

public java.lang.Object next()

Specified by:

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

remove

public void remove()

Specified by:

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

close

public void close()

close file input stream

Specified by:

close in interface java.io.Closeable

readFourBytes

public int readFourBytes()
                  throws java.io.IOException

read four bytes from its input stream and convert to unsigned integer

Returns:

an unsigned integer

Throws:

java.io.IOException

readFourBytes

public int readFourBytes(java.io.DataInputStream inputStream)
                  throws java.io.IOException

read four bytes from an input stream and convert to unsigned integer

Parameters:

inputStream -

Returns:

an unsigned integer

Throws:

java.io.IOException

getFileName

public java.lang.String getFileName()

Returns:

the fileName