htsjdk.samtools.seekablestream

Class SeekableFileStream

java.lang.Object

java.io.InputStream

htsjdk.samtools.seekablestream.SeekableStream

htsjdk.samtools.seekablestream.SeekableFileStream

All Implemented Interfaces:

java.io.Closeable, java.lang.AutoCloseable

public class SeekableFileStream
extends SeekableStream

Constructor Summary

Constructors

Constructor and Description
SeekableFileStream(java.io.File file)

Method Summary

Modifier and Type	Method and Description
void	close()
static void	closeAllInstances()
boolean	eof()
java.lang.String	getSource()
long	length()
long	position()
int	read()
int	read(byte[] b)
int	read(byte[] buffer, int offset, int length)
void	seek(long position)
long	skip(long n)

Methods inherited from class htsjdk.samtools.seekablestream.SeekableStream

readFully

Methods inherited from class java.io.InputStream

available, mark, markSupported, reset

Methods inherited from class java.lang.Object

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

Constructor Detail

SeekableFileStream

public SeekableFileStream(java.io.File file)
                   throws java.io.FileNotFoundException

Throws:

java.io.FileNotFoundException

Method Detail

length

public long length()

Specified by:

length in class SeekableStream

eof

public boolean eof()
            throws java.io.IOException

Specified by:

eof in class SeekableStream

Throws:

java.io.IOException

seek

public void seek(long position)
          throws java.io.IOException

Specified by:

seek in class SeekableStream

Throws:

java.io.IOException

position

public long position()
              throws java.io.IOException

Specified by:

position in class SeekableStream

Throws:

java.io.IOException

skip

public long skip(long n)
          throws java.io.IOException

Overrides:

skip in class java.io.InputStream

Throws:

java.io.IOException

read

public int read(byte[] buffer,
                int offset,
                int length)
         throws java.io.IOException

Specified by:

read in class SeekableStream

Throws:

java.io.IOException

read

public int read()
         throws java.io.IOException

Specified by:

read in class java.io.InputStream

Throws:

java.io.IOException

read

public int read(byte[] b)
         throws java.io.IOException

Overrides:

read in class java.io.InputStream

Throws:

java.io.IOException

getSource

public java.lang.String getSource()

Specified by:

getSource in class SeekableStream

Returns:

String representation of source (e.g. URL, file path, etc.), or null if not available.

close

public void close()
           throws java.io.IOException

Specified by:

close in interface java.io.Closeable

Specified by:

close in interface java.lang.AutoCloseable

Specified by:

close in class SeekableStream

Throws:

java.io.IOException

closeAllInstances

public static void closeAllInstances()