htsjdk.samtools.seekablestream

Class SeekableBufferedStream

java.lang.Object

java.io.InputStream

htsjdk.samtools.seekablestream.SeekableStream

htsjdk.samtools.seekablestream.SeekableBufferedStream

All Implemented Interfaces:

java.io.Closeable, java.lang.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 and Description
static int	DEFAULT_BUFFER_SIZE

Constructor Summary

Constructors

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

Method Summary

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

Methods inherited from class htsjdk.samtools.seekablestream.SeekableStream

readFully

Methods inherited from class java.io.InputStream

available, mark, markSupported, read, reset

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_BUFFER_SIZE

public static final int DEFAULT_BUFFER_SIZE

See Also:

Constant Field Values

Constructor Detail

SeekableBufferedStream

public SeekableBufferedStream(SeekableStream stream,
                              int bufferSize)

SeekableBufferedStream

public SeekableBufferedStream(SeekableStream stream)

Method Detail

length

public long length()

Specified by:

length in class SeekableStream

skip

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

Overrides:

skip in class java.io.InputStream

Throws:

java.io.IOException

seek

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

Specified by:

seek 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[] buffer,
                int offset,
                int length)
         throws java.io.IOException

Specified by:

read in class SeekableStream

Throws:

java.io.IOException

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

eof

public boolean eof()
            throws java.io.IOException

Specified by:

eof in class SeekableStream

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.

position

public long position()
              throws java.io.IOException

Specified by:

position in class SeekableStream

Throws:

java.io.IOException