Package htsjdk.tribble.readers

Class PositionalBufferedStream

java.lang.Object

java.io.InputStream

htsjdk.tribble.readers.PositionalBufferedStream

All Implemented Interfaces:

LocationAware, Positional, Closeable, AutoCloseable

public final class PositionalBufferedStream
extends InputStream
implements Positional

A wrapper around an InputStream which performs it's own buffering, and keeps track of the position. TODO: This class implements Positional, which in turn extends LocationAware, which requires preservation of virtual file pointers on BGZF inputs. However, if the inputStream wrapped by this class is a BlockCompressedInputStream, it violates that contract by wrapping the stream and returning positional file offsets instead.

Constructor Summary

Constructors

Constructor	Description
PositionalBufferedStream(InputStream is)
PositionalBufferedStream(InputStream is, int bufferSize)

Method Summary

Modifier and Type	Method	Description
final void	close()
final long	getPosition()	The current offset, in bytes, of this stream/writer/file.
final boolean	isDone()	Is the stream done? Equivalent to ! hasNext() for an iterator?
static void	main(String[] args)
final int	peek()	Return the next byte in the first, without actually reading it from the stream.
final int	read()
final int	read(byte[] bytes)
final int	read(byte[] bytes, int start, int len)
final long	skip(long nBytes)	Skip the next nBytes in the stream.

Methods inherited from class java.io.InputStream

available, mark, markSupported, nullInputStream, readAllBytes, readNBytes, readNBytes, reset, skipNBytes, transferTo

Methods inherited from class java.lang.Object

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

Constructor Details

PositionalBufferedStream

public PositionalBufferedStream(InputStream is)

PositionalBufferedStream

public PositionalBufferedStream(InputStream is,
 int bufferSize)

Method Details

getPosition

public final long getPosition()

Description copied from interface: LocationAware

The current offset, in bytes, of this stream/writer/file. Or, if this is an iterator/producer, the offset (in bytes) of the END of the most recently returned record (since a produced record corresponds to something that has been read already). See class javadoc for more. Note that for BGZF files, this does not represent an actually file position, but a virtual file pointer.

Specified by:

getPosition in interface LocationAware

read

public final int read()
               throws IOException

Specified by:

read in class InputStream

Throws:

IOException

read

public final int read(byte[] bytes,
 int start,
 int len)
               throws IOException

Overrides:

read in class InputStream

Throws:

IOException

read

public final int read(byte[] bytes)
               throws IOException

Overrides:

read in class InputStream

Throws:

IOException

isDone

public final boolean isDone()
                     throws IOException

Description copied from interface: Positional

Is the stream done? Equivalent to ! hasNext() for an iterator?

Specified by:

isDone in interface Positional

Returns:

true if the stream has reached EOF, false otherwise

Throws:

IOException

peek

public final int peek()
               throws IOException

Description copied from interface: Positional

Return the next byte in the first, without actually reading it from the stream. Has the same output as read()

Specified by:

peek in interface Positional

Returns:

the next byte, or -1 if EOF encountered

Throws:

IOException

skip

public final long skip(long nBytes)
                throws IOException

Description copied from interface: Positional

Skip the next nBytes in the stream.

Specified by:

skip in interface Positional

Overrides:

skip in class InputStream

Parameters:

nBytes - to skip, must be >= 0

Returns:

the number of bytes actually skippped.

Throws:

IOException

close

public final void close()

Specified by:

close in interface AutoCloseable

Specified by:

close in interface Closeable

Overrides:

close in class InputStream

main

public static void main(String[] args)
                 throws Exception

Throws:

Exception