htsjdk.tribble.readers

Class PositionalBufferedStream

java.lang.Object

java.io.InputStream

htsjdk.tribble.readers.PositionalBufferedStream

All Implemented Interfaces:

LocationAware, Positional, java.io.Closeable, java.lang.AutoCloseable

public final class PositionalBufferedStream
extends java.io.InputStream
implements Positional

A wrapper around an InputStream which performs it's own buffering, and keeps track of the position.

Constructor Summary

Constructors

Constructor and Description
PositionalBufferedStream(java.io.InputStream is)
PositionalBufferedStream(java.io.InputStream is, int bufferSize)

Method Summary

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

Methods inherited from class java.io.InputStream

available, mark, markSupported, reset

Methods inherited from class java.lang.Object

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

Constructor Detail

PositionalBufferedStream

public PositionalBufferedStream(java.io.InputStream is)

PositionalBufferedStream

public PositionalBufferedStream(java.io.InputStream is,
                                int bufferSize)

Method Detail

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 java.io.IOException

Specified by:

read in class java.io.InputStream

Throws:

java.io.IOException

read

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

Overrides:

read in class java.io.InputStream

Throws:

java.io.IOException

read

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

Overrides:

read in class java.io.InputStream

Throws:

java.io.IOException

isDone

public final boolean isDone()
                     throws java.io.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:

java.io.IOException

peek

public final int peek()
               throws java.io.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:

java.io.IOException

skip

public final long skip(long nBytes)
                throws java.io.IOException

Description copied from interface: Positional

Skip the next nBytes in the stream.

Specified by:

skip in interface Positional

Overrides:

skip in class java.io.InputStream

Parameters:

nBytes - to skip, must be >= 0

Returns:

the number of bytes actually skippped.

Throws:

java.io.IOException

close

public final void close()

Specified by:

close in interface java.io.Closeable

Specified by:

close in interface java.lang.AutoCloseable

Overrides:

close in class java.io.InputStream

main

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

Throws:

java.lang.Exception