Package htsjdk.samtools.seekablestream

Class SeekableBufferedStream

java.lang.Object

java.io.InputStream

htsjdk.samtools.seekablestream.SeekableStream

htsjdk.samtools.seekablestream.SeekableBufferedStream

All Implemented Interfaces:

Closeable, AutoCloseable

public class SeekableBufferedStream
extends SeekableStream

A wrapper class to provide buffered read access to a SeekableStream. Just wrapping such a stream with a BufferedInputStream will not work as it does not support seeking. In this implementation a seek call is delegated to the wrapped stream, and the buffer reset.

Field Summary

Fields

Modifier and Type	Field	Description
static final int	DEFAULT_BUFFER_SIZE

Fields inherited from class htsjdk.samtools.seekablestream.SeekableStream

mark

Constructor Summary

Constructors

Constructor	Description
SeekableBufferedStream(SeekableStream stream)
SeekableBufferedStream(SeekableStream stream, int bufferSize)

Method Summary

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

Methods inherited from class htsjdk.samtools.seekablestream.SeekableStream

available, mark, markSupported, readFully, reset

Methods inherited from class java.io.InputStream

nullInputStream, read, readAllBytes, readNBytes, readNBytes, skipNBytes, transferTo

Methods inherited from class java.lang.Object

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

Field Details

DEFAULT_BUFFER_SIZE

public static final int DEFAULT_BUFFER_SIZE

See Also:

• Constant Field Values

Constructor Details

SeekableBufferedStream

public SeekableBufferedStream(SeekableStream stream,
 int bufferSize)

SeekableBufferedStream

public SeekableBufferedStream(SeekableStream stream)

Method Details

length

public long length()

Specified by:

length in class SeekableStream

Returns:

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

skip

public long skip(long skipLength)
          throws IOException

Overrides:

skip in class InputStream

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

read

public int read()
         throws IOException

Specified by:

read 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

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

eof

public boolean eof()
            throws IOException

Specified by:

eof in class SeekableStream

Returns:

true if the stream is already consumed; false otherwise.

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.

position

public long position()
              throws IOException

Specified by:

position in class SeekableStream

Returns:

the current byte position of the stream.

Throws:

IOException