org.broadinstitute.hellbender.utils.nio

Class ChannelAsSeekableStream

java.lang.Object

java.io.InputStream

htsjdk.samtools.seekablestream.SeekableStream

org.broadinstitute.hellbender.utils.nio.ChannelAsSeekableStream

All Implemented Interfaces:

java.io.Closeable, java.lang.AutoCloseable

public class ChannelAsSeekableStream
extends htsjdk.samtools.seekablestream.SeekableStream

A SeekableByteChannel in SeekableStream clothes. This is key to using NIO Paths with htsjdk (enabling it to work with gcloud-java-nio).

Field Summary

Fields inherited from class htsjdk.samtools.seekablestream.SeekableStream

mark

Constructor Summary

Constructors

Constructor and Description
ChannelAsSeekableStream(java.nio.channels.SeekableByteChannel chan)
ChannelAsSeekableStream(java.nio.channels.SeekableByteChannel chan, java.lang.String source)

Method Summary

Modifier and Type	Method and Description
void	close()
boolean	eof()
java.lang.String	getSource()
long	length()
long	position()
int	read() Reads the next byte of data from the input stream.
int	read(byte[] buffer, int offset, int length)
void	seek(long position)

Methods inherited from class htsjdk.samtools.seekablestream.SeekableStream

available, mark, markSupported, readFully, reset

Methods inherited from class java.io.InputStream

read, skip

Methods inherited from class java.lang.Object

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

Constructor Detail

ChannelAsSeekableStream

public ChannelAsSeekableStream(java.nio.channels.SeekableByteChannel chan)

ChannelAsSeekableStream

public ChannelAsSeekableStream(java.nio.channels.SeekableByteChannel chan,
                               java.lang.String source)

Method Detail

length

public long length()

Specified by:

length in class htsjdk.samtools.seekablestream.SeekableStream

position

public long position()
              throws java.io.IOException

Specified by:

position in class htsjdk.samtools.seekablestream.SeekableStream

Throws:

java.io.IOException

seek

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

Specified by:

seek in class htsjdk.samtools.seekablestream.SeekableStream

Throws:

java.io.IOException

read

public int read()
         throws java.io.IOException

Reads the next byte of data from the input stream. The value byte is returned as an int in the range 0 to 255. If no byte is available because the end of the stream has been reached, the value -1 is returned. This method blocks until input data is available, the end of the stream is detected, or an exception is thrown.

Specified by:

read in class java.io.InputStream

Returns:

the next byte of data, or -1 if the end of the stream is reached.

Throws:

java.io.IOException - if an I/O error occurs.

read

public int read(byte[] buffer,
                int offset,
                int length)
         throws java.io.IOException

Specified by:

read in class htsjdk.samtools.seekablestream.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 htsjdk.samtools.seekablestream.SeekableStream

Throws:

java.io.IOException

eof

public boolean eof()
            throws java.io.IOException

Specified by:

eof in class htsjdk.samtools.seekablestream.SeekableStream

Throws:

java.io.IOException

getSource

public java.lang.String getSource()

Specified by:

getSource in class htsjdk.samtools.seekablestream.SeekableStream

Returns:

String representation of source (e.g. URL, file path, etc.), or null if not available.