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package htsjdk.samtools.util.zip;
import htsjdk.samtools.Defaults;
import java.io.File;
import java.net.URL;
import java.util.zip.Deflater;
/**
* This is a copy of java.util.zip.Deflater from OpenJDK 7, with the following changes:
* - package and class name changed
* - static block to load libIntelDeflater library
* - extends java.util.zip.Deflater so that IntelDeflater object can be used as regular Deflater object.
* Note however that all methods of Deflater are overridden.
*
* The shared library is found via one of the following mechanisms:
* 1. if samjdk.intel_deflater_so_path system property is set, this is assumed to be the path of libIntelDeflater.so
* 2. If system property is not set, directory where the jarfile that this class came from lives is tried as location
* of libIntelDeflater.so
* 3. If either of the above fails to find the library, regular LD_LIBRARY_PATH is used to find the library.
* 4. If that doesn't work, class fails to load and code falls back to regular Java Deflater class.
*
*
* The rest of this document is copied verbatim from the original OpenJDK file.
*
* This class provides support for general purpose compression using the
* popular ZLIB compression library. The ZLIB compression library was
* initially developed as part of the PNG graphics standard and is not
* protected by patents. It is fully described in the specifications at
* the <a href="package-summary.html#package_description">java.util.zip
* package description</a>.
*
* <p>The following code fragment demonstrates a trivial compression
* and decompression of a string using <tt>IntelDeflater</tt> and
* <tt>Inflater</tt>.
*
* <blockquote><pre>
* try {
* // Encode a String into bytes
* String inputString = "blahblahblah";
* byte[] input = inputString.getBytes("UTF-8");
*
* // Compress the bytes
* byte[] output = new byte[100];
* IntelDeflater compresser = new IntelDeflater();
* compresser.setInput(input);
* compresser.finish();
* int compressedDataLength = compresser.deflate(output);
* compresser.end();
*
* // Decompress the bytes
* Inflater decompresser = new Inflater();
* decompresser.setInput(output, 0, compressedDataLength);
* byte[] result = new byte[100];
* int resultLength = decompresser.inflate(result);
* decompresser.end();
*
* // Decode the bytes into a String
* String outputString = new String(result, 0, resultLength, "UTF-8");
* } catch(java.io.UnsupportedEncodingException ex) {
* // handle
* } catch (java.util.zip.DataFormatException ex) {
* // handle
* }
* </pre></blockquote>
*
* @see java.util.zip.Inflater
* @author David Connelly
*/
public
class IntelDeflater extends Deflater {
private final ZStreamRef zsRef;
private byte[] buf = new byte[0];
private int off, len;
private int level, strategy;
private boolean setParams;
private boolean finish, finished;
/**
* Compression flush mode used to achieve best compression result.
*
* @see IntelDeflater#deflate(byte[], int, int, int)
* @since 1.7
*/
public static final int NO_FLUSH = 0;
/**
* Compression flush mode used to flush out all pending output; may
* degrade compression for some compression algorithms.
*
* @see IntelDeflater#deflate(byte[], int, int, int)
* @since 1.7
*/
public static final int SYNC_FLUSH = 2;
/**
* Compression flush mode used to flush out all pending output and
* reset the deflater. Using this mode too often can seriously degrade
* compression.
*
* @see IntelDeflater#deflate(byte[], int, int, int)
* @since 1.7
*/
public static final int FULL_FLUSH = 3;
static {
try {
final File sharedLibrary;
if (Defaults.INTEL_DEFLATER_SHARED_LIBRARY_PATH != null) {
// Load via path set by -Dsamjdk.intel_deflater_so_path=<path>
sharedLibrary = new File(Defaults.INTEL_DEFLATER_SHARED_LIBRARY_PATH);
} else {
// Look in directory containing this class for the library
URL jarUrl = IntelDeflater.class.getProtectionDomain().getCodeSource().getLocation();
sharedLibrary = new File(new File(jarUrl.getPath()).getParentFile(), "libIntelDeflater.so");
}
System.load(sharedLibrary.getAbsolutePath());
} catch (Throwable e) {
// Possible exceptions:
// System.load: UnsatisfiedLinkError
// getProtectionDomain: SecurityException
// NullPointerException due to getCodeSource returning null
// Try to find via LD_LIBRARY_PATH
System.loadLibrary("IntelDeflater");
}
initIDs();
}
/**
* Creates a new compressor using the specified compression level.
* If 'nowrap' is true then the ZLIB header and checksum fields will
* not be used in order to support the compression format used in
* both GZIP and PKZIP.
* @param level the compression level (0-9)
* @param nowrap if true then use GZIP compatible compression
*/
public IntelDeflater(int level, boolean nowrap) {
this.level = level;
this.strategy = DEFAULT_STRATEGY;
this.zsRef = new ZStreamRef(init(level, DEFAULT_STRATEGY, nowrap));
}
/**
* Creates a new compressor using the specified compression level.
* Compressed data will be generated in ZLIB format.
* @param level the compression level (0-9)
*/
public IntelDeflater(int level) {
this(level, false);
}
/**
* Creates a new compressor with the default compression level.
* Compressed data will be generated in ZLIB format.
*/
public IntelDeflater() {
this(DEFAULT_COMPRESSION, false);
}
/**
* Sets input data for compression. This should be called whenever
* needsInput() returns true indicating that more input data is required.
* @param b the input data bytes
* @param off the start offset of the data
* @param len the length of the data
* @see IntelDeflater#needsInput
*/
@Override
public void setInput(byte[] b, int off, int len) {
if (b== null) {
throw new NullPointerException();
}
if (off < 0 || len < 0 || off > b.length - len) {
throw new ArrayIndexOutOfBoundsException();
}
synchronized (zsRef) {
this.buf = b;
this.off = off;
this.len = len;
}
}
/**
* Sets input data for compression. This should be called whenever
* needsInput() returns true indicating that more input data is required.
* @param b the input data bytes
* @see IntelDeflater#needsInput
*/
@Override
public void setInput(byte[] b) {
setInput(b, 0, b.length);
}
/**
* Sets preset dictionary for compression. A preset dictionary is used
* when the history buffer can be predetermined. When the data is later
* uncompressed with Inflater.inflate(), Inflater.getAdler() can be called
* in order to get the Adler-32 value of the dictionary required for
* decompression.
* @param b the dictionary data bytes
* @param off the start offset of the data
* @param len the length of the data
* @see java.util.zip.Inflater#inflate
* @see java.util.zip.Inflater#getAdler
*/
@Override
public void setDictionary(byte[] b, int off, int len) {
if (b == null) {
throw new NullPointerException();
}
if (off < 0 || len < 0 || off > b.length - len) {
throw new ArrayIndexOutOfBoundsException();
}
synchronized (zsRef) {
ensureOpen();
setDictionary(zsRef.address(), b, off, len);
}
}
/**
* Sets preset dictionary for compression. A preset dictionary is used
* when the history buffer can be predetermined. When the data is later
* uncompressed with Inflater.inflate(), Inflater.getAdler() can be called
* in order to get the Adler-32 value of the dictionary required for
* decompression.
* @param b the dictionary data bytes
* @see java.util.zip.Inflater#inflate
* @see java.util.zip.Inflater#getAdler
*/
@Override
public void setDictionary(byte[] b) {
setDictionary(b, 0, b.length);
}
/**
* Sets the compression strategy to the specified value.
* @param strategy the new compression strategy
* @exception IllegalArgumentException if the compression strategy is
* invalid
*/
@Override
public void setStrategy(int strategy) {
switch (strategy) {
case DEFAULT_STRATEGY:
case FILTERED:
case HUFFMAN_ONLY:
break;
default:
throw new IllegalArgumentException();
}
synchronized (zsRef) {
if (this.strategy != strategy) {
this.strategy = strategy;
setParams = true;
}
}
}
/**
* Sets the current compression level to the specified value.
* @param level the new compression level (0-9)
* @exception IllegalArgumentException if the compression level is invalid
*/
@Override
public void setLevel(int level) {
if ((level < 0 || level > 9) && level != DEFAULT_COMPRESSION) {
throw new IllegalArgumentException("invalid compression level");
}
synchronized (zsRef) {
if (this.level != level) {
this.level = level;
setParams = true;
}
}
}
/**
* Returns true if the input data buffer is empty and setInput()
* should be called in order to provide more input.
* @return true if the input data buffer is empty and setInput()
* should be called in order to provide more input
*/
@Override
public boolean needsInput() {
return len <= 0;
}
/**
* When called, indicates that compression should end with the current
* contents of the input buffer.
*/
@Override
public void finish() {
synchronized (zsRef) {
finish = true;
}
}
/**
* Returns true if the end of the compressed data output stream has
* been reached.
* @return true if the end of the compressed data output stream has
* been reached
*/
@Override
public boolean finished() {
synchronized (zsRef) {
return finished;
}
}
/**
* Compresses the input data and fills specified buffer with compressed
* data. Returns actual number of bytes of compressed data. A return value
* of 0 indicates that {@link #needsInput() needsInput} should be called
* in order to determine if more input data is required.
*
* <p>This method uses {@link #NO_FLUSH} as its compression flush mode.
* An invocation of this method of the form {@code deflater.deflate(b, off, len)}
* yields the same result as the invocation of
* {@code deflater.deflate(b, off, len, IntelDeflater.NO_FLUSH)}.
*
* @param b the buffer for the compressed data
* @param off the start offset of the data
* @param len the maximum number of bytes of compressed data
* @return the actual number of bytes of compressed data written to the
* output buffer
*/
@Override
public int deflate(byte[] b, int off, int len) {
return deflate(b, off, len, NO_FLUSH);
}
/**
* Compresses the input data and fills specified buffer with compressed
* data. Returns actual number of bytes of compressed data. A return value
* of 0 indicates that {@link #needsInput() needsInput} should be called
* in order to determine if more input data is required.
*
* <p>This method uses {@link #NO_FLUSH} as its compression flush mode.
* An invocation of this method of the form {@code deflater.deflate(b)}
* yields the same result as the invocation of
* {@code deflater.deflate(b, 0, b.length, IntelDeflater.NO_FLUSH)}.
*
* @param b the buffer for the compressed data
* @return the actual number of bytes of compressed data written to the
* output buffer
*/
@Override
public int deflate(byte[] b) {
return deflate(b, 0, b.length, NO_FLUSH);
}
/**
* Compresses the input data and fills the specified buffer with compressed
* data. Returns actual number of bytes of data compressed.
*
* <p>Compression flush mode is one of the following three modes:
*
* <ul>
* <li>{@link #NO_FLUSH}: allows the deflater to decide how much data
* to accumulate, before producing output, in order to achieve the best
* compression (should be used in normal use scenario). A return value
* of 0 in this flush mode indicates that {@link #needsInput()} should
* be called in order to determine if more input data is required.
*
* <li>{@link #SYNC_FLUSH}: all pending output in the deflater is flushed,
* to the specified output buffer, so that an inflater that works on
* compressed data can get all input data available so far (In particular
* the {@link #needsInput()} returns {@code true} after this invocation
* if enough output space is provided). Flushing with {@link #SYNC_FLUSH}
* may degrade compression for some compression algorithms and so it
* should be used only when necessary.
*
* <li>{@link #FULL_FLUSH}: all pending output is flushed out as with
* {@link #SYNC_FLUSH}. The compression state is reset so that the inflater
* that works on the compressed output data can restart from this point
* if previous compressed data has been damaged or if random access is
* desired. Using {@link #FULL_FLUSH} too often can seriously degrade
* compression.
* </ul>
*
* <p>In the case of {@link #FULL_FLUSH} or {@link #SYNC_FLUSH}, if
* the return value is {@code len}, the space available in output
* buffer {@code b}, this method should be invoked again with the same
* {@code flush} parameter and more output space.
*
* @param b the buffer for the compressed data
* @param off the start offset of the data
* @param len the maximum number of bytes of compressed data
* @param flush the compression flush mode
* @return the actual number of bytes of compressed data written to
* the output buffer
*
* @throws IllegalArgumentException if the flush mode is invalid
* @since 1.7
*/
public int deflate(byte[] b, int off, int len, int flush) {
//System.out.println("Inside IntelDeflater\n");
if (b == null) {
throw new NullPointerException();
}
if (off < 0 || len < 0 || off > b.length - len) {
throw new ArrayIndexOutOfBoundsException();
}
synchronized (zsRef) {
ensureOpen();
if (flush == NO_FLUSH || flush == SYNC_FLUSH ||
flush == FULL_FLUSH)
return deflateBytes(zsRef.address(), b, off, len, flush);
throw new IllegalArgumentException();
}
}
/**
* Returns the ADLER-32 value of the uncompressed data.
* @return the ADLER-32 value of the uncompressed data
*/
@Override
public int getAdler() {
synchronized (zsRef) {
ensureOpen();
return getAdler(zsRef.address());
}
}
/**
* Returns the total number of uncompressed bytes input so far.
*
* <p>Since the number of bytes may be greater than
* Integer.MAX_VALUE, the {@link #getBytesRead()} method is now
* the preferred means of obtaining this information.</p>
*
* @return the total number of uncompressed bytes input so far
*/
@Override
public int getTotalIn() {
return (int) getBytesRead();
}
/**
* Returns the total number of uncompressed bytes input so far.</p>
*
* @return the total (non-negative) number of uncompressed bytes input so far
* @since 1.5
*/
@Override
public long getBytesRead() {
synchronized (zsRef) {
ensureOpen();
return getBytesRead(zsRef.address());
}
}
/**
* Returns the total number of compressed bytes output so far.
*
* <p>Since the number of bytes may be greater than
* Integer.MAX_VALUE, the {@link #getBytesWritten()} method is now
* the preferred means of obtaining this information.</p>
*
* @return the total number of compressed bytes output so far
*/
@Override
public int getTotalOut() {
return (int) getBytesWritten();
}
/**
* Returns the total number of compressed bytes output so far.</p>
*
* @return the total (non-negative) number of compressed bytes output so far
* @since 1.5
*/
@Override
public long getBytesWritten() {
synchronized (zsRef) {
ensureOpen();
return getBytesWritten(zsRef.address());
}
}
/**
* Resets deflater so that a new set of input data can be processed.
* Keeps current compression level and strategy settings.
*/
@Override
public void reset() {
synchronized (zsRef) {
ensureOpen();
reset(zsRef.address());
finish = false;
finished = false;
off = len = 0;
}
}
/**
* Closes the compressor and discards any unprocessed input.
* This method should be called when the compressor is no longer
* being used, but will also be called automatically by the
* finalize() method. Once this method is called, the behavior
* of the IntelDeflater object is undefined.
*/
@Override
public void end() {
synchronized (zsRef) {
long addr = zsRef.address();
zsRef.clear();
if (addr != 0) {
end(addr);
buf = null;
}
}
}
/**
* Closes the compressor when garbage is collected.
*/
protected void finalize() {
end();
}
private void ensureOpen() {
assert Thread.holdsLock(zsRef);
if (zsRef.address() == 0)
throw new NullPointerException("IntelDeflater has been closed");
}
private static native void initIDs();
private native static long init(int level, int strategy, boolean nowrap);
private native static void setDictionary(long addr, byte[] b, int off, int len);
private native int deflateBytes(long addr, byte[] b, int off, int len,
int flush);
private native static int getAdler(long addr);
private native static long getBytesRead(long addr);
private native static long getBytesWritten(long addr);
private native static void reset(long addr);
private native static void end(long addr);
}