htsjdk.samtools.util

Class AsyncBlockCompressedInputStream

java.lang.Object

java.io.InputStream

htsjdk.samtools.util.BlockCompressedInputStream

htsjdk.samtools.util.AsyncBlockCompressedInputStream

All Implemented Interfaces:

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

public class AsyncBlockCompressedInputStream
extends BlockCompressedInputStream

Asynchronous read-ahead implementation of BlockCompressedInputStream. Note that this implementation is not synchronized. If multiple threads access an instance concurrently, it must be synchronized externally.

Nested Class Summary

Nested classes/interfaces inherited from class htsjdk.samtools.util.BlockCompressedInputStream

BlockCompressedInputStream.DecompressedBlock, BlockCompressedInputStream.FileTermination

Field Summary

Fields inherited from class htsjdk.samtools.util.BlockCompressedInputStream

CANNOT_SEEK_CLOSED_STREAM_MSG, CANNOT_SEEK_STREAM_MSG, INCORRECT_HEADER_SIZE_MSG, INVALID_FILE_PTR_MSG, PREMATURE_END_MSG, UNEXPECTED_BLOCK_LENGTH_MSG

Constructor Summary

Constructors

Constructor and Description
AsyncBlockCompressedInputStream(java.io.File file)
AsyncBlockCompressedInputStream(java.io.File file, InflaterFactory inflaterFactory)
AsyncBlockCompressedInputStream(java.io.InputStream stream)
AsyncBlockCompressedInputStream(java.io.InputStream stream, InflaterFactory inflaterFactory)
AsyncBlockCompressedInputStream(SeekableStream strm)
AsyncBlockCompressedInputStream(SeekableStream strm, InflaterFactory inflaterFactory)
AsyncBlockCompressedInputStream(java.net.URL url)
AsyncBlockCompressedInputStream(java.net.URL url, InflaterFactory inflaterFactory)

Method Summary

Modifier and Type	Method and Description
void	close() Closes the underlying InputStream or RandomAccessFile
protected BlockCompressedInputStream.DecompressedBlock	nextBlock(byte[] bufferAvailableForReuse) Reads and decompresses the next block
protected void	prepareForSeek() Performs cleanup required before seek is called on the underlying stream

Methods inherited from class htsjdk.samtools.util.BlockCompressedInputStream

assertNonDefectiveFile, available, checkTermination, checkTermination, checkTermination, endOfBlock, getFileBlock, getFilePointer, getPosition, isValidFile, processNextBlock, read, read, read, readLine, seek, setCheckCrcs

Methods inherited from class java.io.InputStream

mark, markSupported, reset, skip

Methods inherited from class java.lang.Object

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

Constructor Detail

AsyncBlockCompressedInputStream

public AsyncBlockCompressedInputStream(java.io.InputStream stream)

AsyncBlockCompressedInputStream

public AsyncBlockCompressedInputStream(java.io.InputStream stream,
                                       InflaterFactory inflaterFactory)

AsyncBlockCompressedInputStream

public AsyncBlockCompressedInputStream(java.io.File file)
                                throws java.io.IOException

Throws:

java.io.IOException

AsyncBlockCompressedInputStream

public AsyncBlockCompressedInputStream(java.io.File file,
                                       InflaterFactory inflaterFactory)
                                throws java.io.IOException

Throws:

java.io.IOException

AsyncBlockCompressedInputStream

public AsyncBlockCompressedInputStream(java.net.URL url)

AsyncBlockCompressedInputStream

public AsyncBlockCompressedInputStream(java.net.URL url,
                                       InflaterFactory inflaterFactory)

AsyncBlockCompressedInputStream

public AsyncBlockCompressedInputStream(SeekableStream strm)

AsyncBlockCompressedInputStream

public AsyncBlockCompressedInputStream(SeekableStream strm,
                                       InflaterFactory inflaterFactory)

Method Detail

nextBlock

protected BlockCompressedInputStream.DecompressedBlock nextBlock(byte[] bufferAvailableForReuse)

Description copied from class: BlockCompressedInputStream

Reads and decompresses the next block

Overrides:

nextBlock in class BlockCompressedInputStream

Parameters:

bufferAvailableForReuse - decompression buffer available for reuse

Returns:

next block in the decompressed stream

prepareForSeek

protected void prepareForSeek()

Description copied from class: BlockCompressedInputStream

Performs cleanup required before seek is called on the underlying stream

Overrides:

prepareForSeek in class BlockCompressedInputStream

close

public void close()
           throws java.io.IOException

Description copied from class: BlockCompressedInputStream

Closes the underlying InputStream or RandomAccessFile

Specified by:

close in interface java.io.Closeable

Specified by:

close in interface java.lang.AutoCloseable

Overrides:

close in class BlockCompressedInputStream

Throws:

java.io.IOException