import org.itadaki.bzip2.BZip2InputStream; //导入依赖的package包/类
public static File decompress(File inputFile) throws IOException {
    if (!inputFile.exists() || !inputFile.canRead() || !inputFile.getName().endsWith(".bz2")) {
        throw new IOException("Cannot read file " + inputFile.getPath());
    }
    File outputFile = new File(inputFile.toString().substring(0, inputFile.toString().length() - 4));
    if (outputFile.exists()) {
        throw new FileAlreadyExistsException(outputFile.toString());
    }
    try (InputStream fileInputStream = new BufferedInputStream(new FileInputStream(inputFile));
         BZip2InputStream inputStream = new BZip2InputStream(fileInputStream, false);
         OutputStream fileOutputStream = new BufferedOutputStream(new FileOutputStream(outputFile), 524288)) {

        byte[] decoded = new byte[524288];
        int bytesRead;
        while ((bytesRead = inputStream.read(decoded)) != -1) {
            fileOutputStream.write(decoded, 0, bytesRead);
        }
    }
    return outputFile;
}
 

import org.itadaki.bzip2.BZip2InputStream; //导入依赖的package包/类
static void compile(String file, String database){
	DB db = DBMaker.newFileDB(new File(database)).compressionEnable().closeOnJvmShutdown().make();
	NavigableSet<Tuple2<String, Tuple2<String,Double>>> multiset = db.getTreeSet("SW");
	multiset.clear();
	try {
		BufferedReader swFile = new BufferedReader(new InputStreamReader(new BZip2InputStream(new FileInputStream(new File(file)), false), "UTF-8"));
		int entry = 0;
		for(String line=swFile.readLine();line != null;line = swFile.readLine()){
			String key = line.trim();
			String[] values = swFile.readLine().trim().split(" ");
			for(int i = 1;i < values.length;i += 2){
				multiset.add(Fun.t2(key, Fun.t2(values[i-1], Double.parseDouble(values[i]))));
			}
			if(entry++ > 100){
				db.commit();
				entry = 0;
			}
		}
		swFile.close();
	} catch (IOException e) {
		e.printStackTrace();
	}
	db.commit();
	db.close();
}
 

import org.itadaki.bzip2.BZip2InputStream; //导入依赖的package包/类
@Override
public byte[] decompress(byte[] toDecompress) {
	InputStream fileInputStream = new ByteArrayInputStream(toDecompress);
       BZip2InputStream inputStream = new BZip2InputStream(fileInputStream, false);
       ByteArrayOutputStream fileOutputStream = new ByteArrayOutputStream();
       byte[] decoded = new byte [readBufferSize];
       int bytesRead;
       try {
        while ((bytesRead = inputStream.read (decoded)) != -1) {
                fileOutputStream.write(decoded, 0, bytesRead) ;        
        }
        fileOutputStream.close();
        inputStream.close();
	} catch (IOException e) {
		e.printStackTrace();
	}
	return fileOutputStream.toByteArray();
}
 

import org.itadaki.bzip2.BZip2InputStream; //导入依赖的package包/类
/**
 * @throws IOException 
 */
@Test
public void testEmpty() throws IOException {

	byte[] testData = new byte [0];

	// Compress
	ByteArrayOutputStream byteOutput = new ByteArrayOutputStream();
	BZip2OutputStream output = new BZip2OutputStream (byteOutput);
	output.write (testData);
	output.close();

	// Test EOF
	ByteArrayInputStream byteInput = new ByteArrayInputStream (byteOutput.toByteArray());
	BZip2InputStream input = new BZip2InputStream (byteInput, false);
	assertEquals (-1, input.read());

}
 

import org.itadaki.bzip2.BZip2InputStream; //导入依赖的package包/类
/**
 * @throws IOException 
 */
@Test
public void testOneByte() throws IOException {

	byte[] testData = new byte[] { 'A' };

	// Compress
	ByteArrayOutputStream byteOutput = new ByteArrayOutputStream();
	BZip2OutputStream output = new BZip2OutputStream (byteOutput);
	output.write (testData);
	output.close();

	// Decompress
	ByteArrayInputStream byteInput = new ByteArrayInputStream (byteOutput.toByteArray());
	BZip2InputStream input = new BZip2InputStream (byteInput, false);
	byte[] decodedTestData = new byte [testData.length];
	input.read(decodedTestData, 0, decodedTestData.length);

	// Compare
	assertArrayEquals(testData, decodedTestData);
	assertEquals (-1, input.read());

}
 

import org.itadaki.bzip2.BZip2InputStream; //导入依赖的package包/类
/**
 * @throws IOException 
 */
@Test
public void testTwoBytes() throws IOException {

	byte[] testData = new byte[] { 'B', 'A' };

	// Compress
	ByteArrayOutputStream byteOutput = new ByteArrayOutputStream();
	BZip2OutputStream output = new BZip2OutputStream (byteOutput);
	output.write (testData);
	output.close();

	// Decompress
	ByteArrayInputStream byteInput = new ByteArrayInputStream (byteOutput.toByteArray());
	BZip2InputStream input = new BZip2InputStream (byteInput, false);
	byte[] decodedTestData = new byte [testData.length];
	input.read(decodedTestData, 0, decodedTestData.length);

	// Compare
	assertArrayEquals(testData, decodedTestData);
	assertEquals (-1, input.read());

}
 

import org.itadaki.bzip2.BZip2InputStream; //导入依赖的package包/类
/**
 * @throws IOException 
 */
@Test
public void testRegular1() throws IOException {

	byte[] testData = "Mary had a little lamb, its fleece was white as snow".getBytes();

	// Compress
	ByteArrayOutputStream byteOutput = new ByteArrayOutputStream();
	BZip2OutputStream output = new BZip2OutputStream (byteOutput);
	output.write (testData);
	output.close();

	// Decompress
	ByteArrayInputStream byteInput = new ByteArrayInputStream (byteOutput.toByteArray());
	BZip2InputStream input = new BZip2InputStream (byteInput, false);
	byte[] decodedTestData = new byte [testData.length];
	input.read(decodedTestData, 0, decodedTestData.length);

	// Compare
	assertArrayEquals(testData, decodedTestData);
	assertEquals (-1, input.read());

}
 

import org.itadaki.bzip2.BZip2InputStream; //导入依赖的package包/类
/**
 * @throws IOException 
 */
@Test
public void testRegular2() throws IOException {

	byte[] testData = "Mary had a little lamb, its fleece was white as snow".getBytes();

	// Compress
	ByteArrayOutputStream byteOutput = new ByteArrayOutputStream();
	BZip2OutputStream output = new BZip2OutputStream (byteOutput);
	for (int i = 0; i < testData.length; i++) {
		output.write (testData[i]);
	}
	output.close();

	// Decompress
	ByteArrayInputStream byteInput = new ByteArrayInputStream (byteOutput.toByteArray());
	BZip2InputStream input = new BZip2InputStream (byteInput, false);
	byte[] decodedTestData = new byte [testData.length];
	input.read(decodedTestData, 0, decodedTestData.length);

	// Compare
	assertArrayEquals(testData, decodedTestData);
	assertEquals (-1, input.read());

}
 

import org.itadaki.bzip2.BZip2InputStream; //导入依赖的package包/类
/**
 * @throws IOException 
 */
@Test
public void testHeaderless() throws IOException {

	byte[] testData = "Mary had a little lamb, its fleece was white as snow".getBytes();

	// Compress
	ByteArrayOutputStream byteOutput = new ByteArrayOutputStream();
	BZip2OutputStream output = new BZip2OutputStream (byteOutput);
	output.write (testData);
	output.close();

	// Decompress
	byte[] compressedData = byteOutput.toByteArray();
	ByteArrayInputStream byteInput = new ByteArrayInputStream (Arrays.copyOfRange (compressedData, 2, compressedData.length));
	BZip2InputStream input = new BZip2InputStream (byteInput, true);
	byte[] decodedTestData = new byte [testData.length];
	input.read(decodedTestData, 0, decodedTestData.length);

	// Compare
	assertArrayEquals(testData, decodedTestData);
	assertEquals (-1, input.read());

}
 

import org.itadaki.bzip2.BZip2InputStream; //导入依赖的package包/类
/**
 * @throws IOException 
 */
@Test
public void testReadPastEnd() throws IOException {

	byte[] testData = "Mary had a little lamb, its fleece was white as snow".getBytes();

	// Compress
	ByteArrayOutputStream byteOutput = new ByteArrayOutputStream();
	BZip2OutputStream output = new BZip2OutputStream (byteOutput);
	output.write (testData);
	output.close();

	// Decompress
	ByteArrayInputStream byteInput = new ByteArrayInputStream (byteOutput.toByteArray());
	BZip2InputStream input = new BZip2InputStream (byteInput, false);
	byte[] decodedTestData = new byte [testData.length];
	input.read(decodedTestData, 0, decodedTestData.length);

	// Test
	assertEquals (-1, input.read());
	assertEquals (-1, input.read());

}
 

import org.itadaki.bzip2.BZip2InputStream; //导入依赖的package包/类
/**
 * Test coverage : InputStream throws an exception during BZip2InputStream.close()
 * @throws IOException 
 */
@Test(expected=IOException.class)
public void testExceptionDuringClose() throws IOException {

	byte[] testData = "Mary had a little lamb, its fleece was white as snow".getBytes();

	// Compress
	ByteArrayOutputStream byteOutput = new ByteArrayOutputStream();
	BZip2OutputStream output = new BZip2OutputStream (byteOutput);
	output.write (testData);
	output.close();

	// Decompress
	ByteArrayInputStream byteInput = new ByteArrayInputStream (byteOutput.toByteArray()) {
		@Override
		public void close() throws IOException {
			throw new IOException();
		}
	};
	BZip2InputStream input = new BZip2InputStream (byteInput, false);

	// Test
	input.close();

}
 

import org.itadaki.bzip2.BZip2InputStream; //导入依赖的package包/类
/**
 * @throws IOException 
 */
@Test
public void test4Tables() throws IOException {

	byte[] testData = new byte [1100];

	// Create test block
	Random random = new Random (1234);
	random.nextBytes (testData);

	// Compress
	ByteArrayOutputStream byteOutput = new ByteArrayOutputStream();
	BZip2OutputStream output = new BZip2OutputStream (byteOutput);
	output.write (testData);
	output.close();

	// Decompress
	ByteArrayInputStream byteInput = new ByteArrayInputStream (byteOutput.toByteArray());
	BZip2InputStream input = new BZip2InputStream (byteInput, false);
	byte[] decodedTestData = new byte [testData.length];
	input.read (decodedTestData, 0, decodedTestData.length);

	// Compare
	assertArrayEquals (testData, decodedTestData);
	assertEquals (-1, input.read());
}
 

import org.itadaki.bzip2.BZip2InputStream; //导入依赖的package包/类
/**
 * @throws IOException 
 */
@Test
public void testLongBlank() throws IOException {

	// Blank test block
	byte[] testData = new byte [100000];

	// Compress
	ByteArrayOutputStream byteOutput = new ByteArrayOutputStream();
	BZip2OutputStream output = new BZip2OutputStream (byteOutput);
	output.write (testData);
	output.close();

	// Decompress
	ByteArrayInputStream byteInput = new ByteArrayInputStream (byteOutput.toByteArray());
	BZip2InputStream input = new BZip2InputStream (byteInput, false);
	byte[] decodedTestData = new byte [testData.length];
	input.read (decodedTestData, 0, decodedTestData.length);

	// Compare
	assertArrayEquals (testData, decodedTestData);
	assertEquals (-1, input.read());

}
 

import org.itadaki.bzip2.BZip2InputStream; //导入依赖的package包/类
/**
 * @throws IOException 
 */
@Test
public void testLongSame() throws IOException {

	byte[] testData = new byte [100000];

	// Create test block
	Arrays.fill (testData, (byte)123);

	// Compress
	ByteArrayOutputStream byteOutput = new ByteArrayOutputStream();
	BZip2OutputStream output = new BZip2OutputStream (byteOutput);
	output.write (testData);
	output.close();

	// Decompress
	ByteArrayInputStream byteInput = new ByteArrayInputStream (byteOutput.toByteArray());
	BZip2InputStream input = new BZip2InputStream (byteInput, false);
	byte[] decodedTestData = new byte [testData.length];
	input.read (decodedTestData, 0, decodedTestData.length);

	// Compare
	assertArrayEquals (testData, decodedTestData);
	assertEquals (-1, input.read());

}
 

import org.itadaki.bzip2.BZip2InputStream; //导入依赖的package包/类
/**
 * @throws IOException 
 */
@Test
public void testDecompressionBug2() throws IOException {

	byte[] testData = new byte [0];

	// Compress
	ByteArrayOutputStream byteOutput = new ByteArrayOutputStream();
	BZip2OutputStream output = new BZip2OutputStream (byteOutput);
	output.write (testData);
	output.close();

	// Decompress
	ByteArrayInputStream byteInput = new ByteArrayInputStream (byteOutput.toByteArray());
	BZip2InputStream input = new BZip2InputStream (byteInput, false);

	// Compare
	assertEquals (-1, input.read());
	assertEquals (-1, input.read());

}
 

import org.itadaki.bzip2.BZip2InputStream; //导入依赖的package包/类
/**
 * @throws IOException 
 */
@Test
public void testCompressionBug1() throws IOException {

	byte[] testData = new byte [4];

	// Compress
	ByteArrayOutputStream byteOutput = new ByteArrayOutputStream();
	BZip2OutputStream output = new BZip2OutputStream (byteOutput);
	output.write (testData);
	output.close();

	// Decompress
	ByteArrayInputStream byteInput = new ByteArrayInputStream (byteOutput.toByteArray());
	BZip2InputStream input = new BZip2InputStream (byteInput, false);
	byte[] decodedTestData = new byte [testData.length];
	input.read (decodedTestData, 0, decodedTestData.length);

	// Compare
	assertArrayEquals (testData, decodedTestData);
	assertEquals (-1, input.read());

}
 

import org.itadaki.bzip2.BZip2InputStream; //导入依赖的package包/类
protected FastQFile(FastQCConfig config,File file) throws SequenceFormatException, IOException {
	this.file = file;
	if (file.getName().equals("stdin")) {
		fileSize = Long.MAX_VALUE;
	}
	else {
		fileSize = file.length();
	}
	name = file.getName();

	if (config.casava) {
		casavaMode = true;
		if (config.nofilter) {
			nofilter = true;
		}
	}

	if (!file.getName().equals("stdin")) {
		fis = new FileInputStream(file);
	}
	
	if (file.getName().equals("stdin")) {
		br = new BufferedReader(new InputStreamReader(System.in));
	}
	else if (file.getName().toLowerCase().endsWith(".gz")) {
		br = new BufferedReader(new InputStreamReader(new MultiMemberGZIPInputStream(fis)));
	} 
	else if (file.getName().toLowerCase().endsWith(".bz2")) {
		br = new BufferedReader(new InputStreamReader(new BZip2InputStream(fis,false)));
	} 

	else {
		br = new BufferedReader(new InputStreamReader(fis));
	}
	readNext();
}
 

import org.itadaki.bzip2.BZip2InputStream; //导入依赖的package包/类
/**
 * Creates a full-fledged installation by downloading a map of the
 * governmental district of Karlsruhe from {@code geofabrik.de} and
 * executing a precalculation for {@link Profile#defaultCar}.
 * <p>
 * {@link MapManager} and {@link ProfileMapManager} are expected to have
 * been initialized already.
 * 
 * @param rootDir
 *            The root directory of the routeKIT installation.
 * @param pr
 *            The {@link ProgressReporter} to report progress to.
 */
public static void createInstall(File rootDir, ProgressReporter pr)
		throws IOException, SAXException {
	pr.setSubTasks(new float[] { .05f, .05f, .9f });
	pr.pushTask("Lade Standardkarte herunter");
	URL url = new URL(
			"http://download.geofabrik.de/europe/germany/baden-wuerttemberg/karlsruhe-regbez-latest.osm.bz2");
	File file = File.createTempFile("routeKIT_map_", ".osm");
	try (InputStream is = new BZip2InputStream(url.openStream(), false);
			FileOutputStream fos = new FileOutputStream(file)) {
		byte[] data = new byte[65536];
		while (true) {
			int read = is.read(data);
			if (read == -1) {
				break;
			}
			fos.write(data, 0, read);
		}

		pr.nextTask("Importiere und speichere Standardkarte");
		StreetMap karlsruhe_big = new OSMMapImporter().importMap(file,
				"Karlsruhe", pr);
		MapManager.getInstance().saveMap(karlsruhe_big);
		Properties p = new Properties();
		p.setProperty("default", "true");
		try (FileWriter writer = new FileWriter(new File(new File(rootDir,
				"Karlsruhe"), "Karlsruhe.properties"))) {
			p.store(writer, null);
		}
		pr.nextTask("Erstelle Standard-Vorberechnung");
		ProfileMapCombination karlsruheCar = new ProfileMapCombination(
				karlsruhe_big, Profile.defaultCar);
		new PreCalculator().doPrecalculation(karlsruheCar, pr);
		ProfileMapManager.getInstance().setCurrentCombination(karlsruheCar);
		ProfileMapManager.getInstance().savePrecalculation(karlsruheCar);
		pr.popTask();
	}
}
 

import org.itadaki.bzip2.BZip2InputStream; //导入依赖的package包/类
/**
 * Compresses and decompresses each of a list of files, using a temporary file to hold the compressed data
 * @param files The files to compress
 * @throws IOException On any error compressing or decompressing the files
 */
private static void roundTrip (List<File> files) throws IOException {

	File tempFile = File.createTempFile ("rtr", ".tmp");

	for (File inputFile : files) {

		long inputLength = inputFile.length();
		System.out.print (inputLength + " " + inputFile);

		// Compress file
		InputStream fileInputStream = new BufferedInputStream (new FileInputStream (inputFile));
		OutputStream compressedOutputStream = new BufferedOutputStream (new FileOutputStream (tempFile));
		BZip2OutputStream bzip2OutputStream = new BZip2OutputStream (compressedOutputStream);

		byte[] buffer = new byte [524288];
		int bytesRead;
		while ((bytesRead = fileInputStream.read (buffer, 0, buffer.length)) != -1) {
			bzip2OutputStream.write (buffer, 0, bytesRead);
		}
		bzip2OutputStream.close();
		compressedOutputStream.close();
		fileInputStream.close();

		long compressedLength = tempFile.length();
		System.out.printf(" (%.1f%%)\n", ((float)(inputLength - compressedLength) / inputLength) * 100);

		// Decompress file
		InputStream compressedInputStream = new BufferedInputStream (new FileInputStream (tempFile));
		BZip2InputStream bzip2InputStream = new BZip2InputStream (compressedInputStream, false);
		byte[] decoded = new byte [524288];
		while ((bytesRead = bzip2InputStream.read (decoded)) != -1);

		compressedInputStream.close();
		bzip2InputStream.close();

	}

}
 

import org.itadaki.bzip2.BZip2InputStream; //导入依赖的package包/类
/**
 * @param args
 * @throws IOException 
 */
public static void main (String[] args) throws IOException {

	if (args.length == 0) {
		System.err.println ("Demonstration BZip2 decompressor\n\nUsage:\n  java demo.Decompress <filename>\n");
		System.exit (1);
	}

	File inputFile = new File (args[0]);
	if (!inputFile.exists() || !inputFile.canRead() || !args[0].endsWith(".bz2")) {
		System.err.println ("Cannot read file " + inputFile.getPath());
		System.exit (1);
	}

	File outputFile = new File (args[0].substring (0, args[0].length() - 4));
	if (outputFile.exists()) {
		System.err.println ("File " + outputFile.getPath() + " already exists");
		System.exit (1);
	}

	InputStream fileInputStream = new BufferedInputStream (new FileInputStream (inputFile));
	BZip2InputStream inputStream = new BZip2InputStream (fileInputStream, false);
	OutputStream fileOutputStream = new BufferedOutputStream (new FileOutputStream (outputFile), 524288);

	byte[] decoded = new byte [524288];
	int bytesRead;
	while ((bytesRead = inputStream.read (decoded)) != -1) {
		fileOutputStream.write (decoded, 0, bytesRead) ;	
	}
	fileOutputStream.close();

}