Package htsjdk.samtools.seekablestream

Class SeekableFileStream

java.lang.Object

java.io.InputStream

htsjdk.samtools.seekablestream.SeekableStream

htsjdk.samtools.seekablestream.SeekableFileStream

All Implemented Interfaces:

Closeable, AutoCloseable

public class SeekableFileStream
extends SeekableStream

Field Summary

Fields inherited from class htsjdk.samtools.seekablestream.SeekableStream

mark

Constructor Summary

Constructors

Constructor	Description
SeekableFileStream(File file)

Method Summary

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

Methods inherited from class htsjdk.samtools.seekablestream.SeekableStream

available, mark, markSupported, readFully, reset

Methods inherited from class java.io.InputStream

nullInputStream, readAllBytes, readNBytes, readNBytes, skipNBytes, transferTo

Methods inherited from class java.lang.Object

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

Constructor Details

SeekableFileStream

public SeekableFileStream(File file)
                   throws FileNotFoundException

Throws:

FileNotFoundException

Method Details

length

public long length()

Specified by:

length in class SeekableStream

Returns:

the length of the stream; 0 if not available or empty.

eof

public boolean eof()
            throws IOException

Specified by:

eof in class SeekableStream

Returns:

true if the stream is already consumed; false otherwise.

Throws:

IOException

seek

public void seek(long position)
          throws IOException

Description copied from class: SeekableStream

Seeks the stream to the provided position.

Specified by:

seek in class SeekableStream

Throws:

IOException

position

public long position()
              throws IOException

Specified by:

position in class SeekableStream

Returns:

the current byte position of the stream.

Throws:

IOException

skip

public long skip(long n)
          throws IOException

Overrides:

skip in class InputStream

Throws:

IOException

read

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

Specified by:

read in class SeekableStream

Throws:

IOException

read

public int read()
         throws IOException

Specified by:

read in class InputStream

Throws:

IOException

read

public int read(byte[] b)
         throws IOException

Overrides:

read in class InputStream

Throws:

IOException

getSource

public 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 IOException

Specified by:

close in interface AutoCloseable

Specified by:

close in interface Closeable

Specified by:

close in class SeekableStream

Throws:

IOException

closeAllInstances

public static void closeAllInstances()