SeekableBufferedStream (htsjdk 2.14.3 API)

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 int DEFAULT_BUFFER_SIZE
- Fields inherited from class htsjdk.samtools.seekablestream.SeekableStream
  mark

Fields
Modifier and Type	Field	Description
`static int`	`DEFAULT_BUFFER_SIZE`

Constructor Summary

Constructors
Constructor Description

SeekableBufferedStream(SeekableStream stream)

SeekableBufferedStream(SeekableStream stream, int bufferSize)

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

Method Summary

All Methods Instance Methods Concrete Methods
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 java.io.InputStream
read, readAllBytes, readNBytes, transferTo

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from class htsjdk.samtools.seekablestream.SeekableStream
available, mark, markSupported, readFully, reset

- 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
    
    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 java.io.InputStream

Methods inherited from class java.lang.Object

Methods inherited from class htsjdk.samtools.seekablestream.SeekableStream

Field Detail

DEFAULT_BUFFER_SIZE

Constructor Detail

SeekableBufferedStream

SeekableBufferedStream

Method Detail

length

skip

seek

read

read

close

eof

getSource

position