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

Class SeekableBufferedStream

Field Summary

Fields inherited from class htsjdk.samtools.seekablestream.SeekableStream

Constructor Summary

Method Summary

Methods inherited from class htsjdk.samtools.seekablestream.SeekableStream

Methods inherited from class java.io.InputStream

Methods inherited from class java.lang.Object

Field Details

DEFAULT_BUFFER_SIZE

Constructor Details

SeekableBufferedStream

SeekableBufferedStream

Method Details

length

skip

seek

read

read

close

eof

getSource

position