/*
* The MIT License (MIT)
*
* Copyright (c) 2007-2015 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package org.broad.igv.util;
import org.apache.log4j.Logger;
import org.broad.igv.Globals;
import java.io.*;
import java.util.zip.Deflater;
import java.util.zip.Inflater;
/**
* Created by IntelliJ IDEA.
* User: jrobinso, mdecautis
* Date: Dec 13, 2009
* Time: 4:16:42 PM
* To change this template use File | Settings | File Templates.
*/
public class CompressionUtils {
private static Logger log = Logger.getLogger(CompressionUtils.class);
private Deflater deflater;
private Inflater decompressor;
public CompressionUtils() {
decompressor = new Inflater();
deflater = new Deflater();
deflater.setLevel(Deflater.DEFAULT_COMPRESSION);
}
public byte[] decompress(byte[] data) {
return decompress(data, data.length * 4);
}
/**
* @param data -- the data to decompress
* @param uncompressedChunkSize -- an estimate of the uncompressed chunk size. This need not be exact.
* @return
*/
public synchronized byte[] decompress(byte[] data, int uncompressedChunkSize) {
// mpd: new code
int rem = data.length;
// Create an expandable byte array to hold the decompressed data
ByteArrayOutputStream bos = new ByteArrayOutputStream(uncompressedChunkSize);
// Decompress the data
byte[] outbuf = new byte[uncompressedChunkSize];
decompressor.reset();
decompressor.setInput(data);
while (rem > 0) {
// If we are finished with the current chunk start a new one
if (decompressor.finished()) {
decompressor = new Inflater();
int offset = data.length - rem;
decompressor.setInput(data, offset, rem);
}
try {
int count = decompressor.inflate(outbuf, 0, outbuf.length);
rem = decompressor.getRemaining();
bos.write(outbuf, 0, count);
} catch (Exception e) {
e.printStackTrace();
}
}
try {
bos.close();
} catch (IOException e) {
// Ignore -- no resources open
}
// Return the decompressed data
return bos.toByteArray();
}
public synchronized byte[] compress(byte[] data) {
// Give the compressor the data to compress
deflater.reset();
deflater.setInput(data);
deflater.finish();
// Create an expandable byte array to hold the compressed data.
// You cannot use an array that's the same size as the orginal because
// there is no guarantee that the compressed data will be smaller than
// the uncompressed data.
ByteArrayOutputStream bos = new ByteArrayOutputStream(data.length);
// Compress the data
byte[] buf = new byte[1024];
while (!deflater.finished()) {
int count = deflater.deflate(buf);
bos.write(buf, 0, count);
}
try {
bos.close();
} catch (IOException e) {
System.err.println("Error clossing ByteArrayOutputStream");
e.printStackTrace();
}
byte[] compressedData = bos.toByteArray();
return compressedData;
}
public synchronized byte[] compress(byte[] data, int chunkSize) {
ByteArrayOutputStream bos = new ByteArrayOutputStream(data.length);
int bytesRemaining = data.length;
while (bytesRemaining > 0) {
int sz = Math.min(bytesRemaining, chunkSize);
int position = data.length - bytesRemaining;
byte[] chunk = new byte[sz];
System.arraycopy(data, position, chunk, 0, sz);
byte[] compressedChunk = compress(chunk);
bos.write(compressedChunk, 0, compressedChunk.length);
bytesRemaining -= sz;
}
byte[] compressedData = bos.toByteArray();
return compressedData;
}
/**
* Copy data from srcPath to destPath, ungzipping if necessary.
* destPath is overwritten if it exists
*
* @param srcPath
* @param destPath If null, strip gz from inputFile
* @return Where the ungipped file was written to. If destPath != null,
* this will be destPath.
*/
public static String ungzipFile(String srcPath, String destPath) throws IOException {
InputStream inputStream = null;
OutputStream outputStream = null;
if (destPath == null) {
if (srcPath.endsWith(Globals.GZIP_FILE_EXTENSION)) {
destPath = srcPath.substring(0, srcPath.length() - Globals.GZIP_FILE_EXTENSION.length());
} else {
throw new IllegalArgumentException(srcPath + " does not have a gzip extension and destPath is null. Don't know where to write out");
}
}
try {
inputStream = ParsingUtils.openInputStream(srcPath);
outputStream = new FileOutputStream(destPath, false);
int buffersize = 4096;
byte[] buffer = new byte[buffersize];
int len = inputStream.read(buffer);
while (len > 0) {
outputStream.write(buffer, 0, len);
len = inputStream.read(buffer);
}
outputStream.flush();
} catch (IOException e) {
e.printStackTrace();
log.error(e.getMessage());
} finally {
if (inputStream != null) inputStream.close();
if (outputStream != null) outputStream.close();
}
return destPath;
}
}