Example usage for java.util.concurrent.atomic AtomicInteger AtomicInteger

Introduction

In this page you can find the example usage for java.util.concurrent.atomic AtomicInteger AtomicInteger.

Prototype

public AtomicInteger() 

Source Link

Document

Creates a new AtomicInteger with initial value 0 .

Usage

From source file:Main.java

public static AtomicInteger newAtomicInteger() {
    AtomicInteger i = new AtomicInteger();
    atomicCounterList.add(i);
    return i;
}

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From source file:Main.java

public static ThreadFactory threadFactory(final String alias) {
    return new ThreadFactory() {

        private final AtomicInteger threadCount = new AtomicInteger();

        @Override//from   w w  w .  j a va  2  s . co m
        public Thread newThread(Runnable r) {
            return new Thread(r, "Ehcache [" + alias + "]-" + threadCount.getAndIncrement());
        }
    };
}

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From source file:Main.java

public static ThreadFactory createThreadFactory(final String prefix) {
    return new ThreadFactory() {
        private AtomicInteger size = new AtomicInteger();

        public Thread newThread(Runnable r) {
            Thread thread = new Thread(r);
            thread.setName(prefix + size.incrementAndGet());
            if (thread.isDaemon()) {
                thread.setDaemon(false);
            }/*from w  ww  . j  ava  2s.co  m*/
            return thread;
        }
    };
}

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From source file:edu.msu.cme.rdp.kmer.KmerFilter.java

public static void main(String[] args) throws Exception {
    final KmerTrie kmerTrie;
    final SeqReader queryReader;
    final SequenceType querySeqType;
    final File queryFile;
    final KmerStartsWriter out;
    final boolean translQuery;
    final int wordSize;
    final int translTable;
    final boolean alignedSeqs;
    final List<String> refLabels = new ArrayList();
    final int maxThreads;

    try {/*  w w w  . jav a 2s .  c o  m*/
        CommandLine cmdLine = new PosixParser().parse(options, args);
        args = cmdLine.getArgs();

        if (args.length < 3) {
            throw new Exception("Unexpected number of arguments");
        }

        if (cmdLine.hasOption("out")) {
            out = new KmerStartsWriter(cmdLine.getOptionValue("out"));
        } else {
            out = new KmerStartsWriter(System.out);
        }

        if (cmdLine.hasOption("aligned")) {
            alignedSeqs = true;
        } else {
            alignedSeqs = false;
        }

        if (cmdLine.hasOption("transl-table")) {
            translTable = Integer.valueOf(cmdLine.getOptionValue("transl-table"));
        } else {
            translTable = 11;
        }

        if (cmdLine.hasOption("threads")) {
            maxThreads = Integer.valueOf(cmdLine.getOptionValue("threads"));
        } else {
            maxThreads = Runtime.getRuntime().availableProcessors();
        }

        queryFile = new File(args[1]);
        wordSize = Integer.valueOf(args[0]);
        SequenceType refSeqType = null;

        querySeqType = SeqUtils.guessSequenceType(queryFile);
        queryReader = new SequenceReader(queryFile);

        if (querySeqType == SequenceType.Protein) {
            throw new Exception("Expected nucl query sequences");
        }

        refSeqType = SeqUtils
                .guessSequenceType(new File(args[2].contains("=") ? args[2].split("=")[1] : args[2]));

        translQuery = refSeqType == SequenceType.Protein;

        if (translQuery && wordSize % 3 != 0) {
            throw new Exception("Word size must be a multiple of 3 for nucl ref seqs");
        }

        int trieWordSize;
        if (translQuery) {
            trieWordSize = wordSize / 3;
        } else {
            trieWordSize = wordSize;
        }
        kmerTrie = new KmerTrie(trieWordSize, translQuery);

        for (int index = 2; index < args.length; index++) {
            String refName;
            String refFileName = args[index];
            if (refFileName.contains("=")) {
                String[] lexemes = refFileName.split("=");
                refName = lexemes[0];
                refFileName = lexemes[1];
            } else {
                String tmpName = new File(refFileName).getName();
                if (tmpName.contains(".")) {
                    refName = tmpName.substring(0, tmpName.lastIndexOf("."));
                } else {
                    refName = tmpName;
                }
            }

            File refFile = new File(refFileName);

            if (refSeqType != SeqUtils.guessSequenceType(refFile)) {
                throw new Exception(
                        "Reference file " + refFile + " contains " + SeqUtils.guessFileFormat(refFile)
                                + " sequences but expected " + refSeqType + " sequences");
            }

            SequenceReader seqReader = new SequenceReader(refFile);
            Sequence seq;

            while ((seq = seqReader.readNextSequence()) != null) {
                if (seq.getSeqName().startsWith("#")) {
                    continue;
                }
                if (alignedSeqs) {
                    kmerTrie.addModelSequence(seq, refLabels.size());
                } else {
                    kmerTrie.addSequence(seq, refLabels.size());
                }
            }
            seqReader.close();

            refLabels.add(refName);
        }

    } catch (Exception e) {
        new HelpFormatter().printHelp("KmerSearch <word_size> <query_file> [name=]<ref_file> ...", options);
        System.err.println(e.getMessage());
        e.printStackTrace();
        System.exit(1);
        throw new RuntimeException("Stupid jvm"); //While this will never get thrown it is required to make sure javac doesn't get confused about uninitialized variables
    }

    long startTime = System.currentTimeMillis();
    long seqCount = 0;
    final int maxTasks = 25000;

    /*
     * if (args.length == 4) { maxThreads = Integer.valueOf(args[3]); } else {
     */

    //}

    System.err.println("Starting kmer mapping at " + new Date());
    System.err.println("*  Number of threads:       " + maxThreads);
    System.err.println("*  References:              " + refLabels);
    System.err.println("*  Reads file:              " + queryFile);
    System.err.println("*  Kmer length:             " + kmerTrie.getWordSize());

    final AtomicInteger processed = new AtomicInteger();
    final AtomicInteger outstandingTasks = new AtomicInteger();

    ExecutorService service = Executors.newFixedThreadPool(maxThreads);

    Sequence querySeq;

    while ((querySeq = queryReader.readNextSequence()) != null) {
        seqCount++;

        String seqString = querySeq.getSeqString();

        if (seqString.length() < 3) {
            System.err.println("Sequence " + querySeq.getSeqName() + "'s length is less than 3");
            continue;
        }

        final Sequence threadSeq = querySeq;

        Runnable r = new Runnable() {

            public void run() {
                try {
                    processSeq(threadSeq, refLabels, kmerTrie, out, wordSize, translQuery, translTable, false);
                    processSeq(threadSeq, refLabels, kmerTrie, out, wordSize, translQuery, translTable, true);
                } catch (IOException e) {
                    throw new RuntimeException(e);
                }

                processed.incrementAndGet();
                outstandingTasks.decrementAndGet();
            }
        };

        outstandingTasks.incrementAndGet();
        service.submit(r);

        while (outstandingTasks.get() >= maxTasks)
            ;

        if ((processed.get() + 1) % 1000000 == 0) {
            System.err.println("Processed " + processed + " sequences in "
                    + (System.currentTimeMillis() - startTime) + " ms");
        }
    }

    service.shutdown();
    service.awaitTermination(1, TimeUnit.DAYS);

    System.err.println("Finished Processed " + processed + " sequences in "
            + (System.currentTimeMillis() - startTime) + " ms");

    out.close();
}

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From source file:org.zenoss.zep.dao.impl.DaoUtilsTest.java

@Test
public void testDeadlockRetry() throws Exception {
    final AtomicInteger i = new AtomicInteger();
    final int returnVal = new Random().nextInt();
    int result = DaoUtils.deadlockRetry(new Callable<Integer>() {
        @Override/* w w  w  .j a va2  s  .c  om*/
        public Integer call() throws Exception {
            if (i.incrementAndGet() < 5) {
                throw new DeadlockLoserDataAccessException("My fake exception", null);
            }
            return returnVal;
        }
    });
    assertEquals(i.get(), 5);
    assertEquals(result, returnVal);
}

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From source file:com.hubrick.raml.mojo.util.JavaNames.java

private static <T> Function<T, Indexed<T>> indexed() {
    final AtomicInteger index = new AtomicInteger();
    return (value) -> new BasicIndexed<>(index.getAndIncrement(), value);
}

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From source file:com.netflix.curator.framework.imps.TestCompression.java

@Test
public void testCompressionProvider() throws Exception {
    final byte[] data = "here's a string".getBytes();

    final AtomicInteger compressCounter = new AtomicInteger();
    final AtomicInteger decompressCounter = new AtomicInteger();
    CompressionProvider compressionProvider = new CompressionProvider() {
        @Override/*from ww w  .java 2 s.co m*/
        public byte[] compress(String path, byte[] data) throws Exception {
            compressCounter.incrementAndGet();

            byte[] bytes = new byte[data.length * 2];
            System.arraycopy(data, 0, bytes, 0, data.length);
            System.arraycopy(data, 0, bytes, data.length, data.length);
            return bytes;
        }

        @Override
        public byte[] decompress(String path, byte[] compressedData) throws Exception {
            decompressCounter.incrementAndGet();

            byte[] bytes = new byte[compressedData.length / 2];
            System.arraycopy(compressedData, 0, bytes, 0, bytes.length);
            return bytes;
        }
    };

    CuratorFramework client = CuratorFrameworkFactory.builder().compressionProvider(compressionProvider)
            .connectString(server.getConnectString()).retryPolicy(new RetryOneTime(1)).build();
    try {
        client.start();

        client.create().compressed().creatingParentsIfNeeded().forPath("/a/b/c", data);

        Assert.assertNotEquals(data, client.getData().forPath("/a/b/c"));
        Assert.assertEquals(data.length, client.getData().decompressed().forPath("/a/b/c").length);
    } finally {
        IOUtils.closeQuietly(client);
    }

    Assert.assertEquals(compressCounter.get(), 1);
    Assert.assertEquals(decompressCounter.get(), 1);
}

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From source file:com.raphfrk.craftproxyclient.gui.GUIManager.java

public static JSONObject getPreviousLoginDetails() {
    JSONObject loginInfo = AuthManager.refreshAccessToken();
    if (loginInfo == null) {
        return null;
    }/*from  w w  w.j  a  v a  2s.com*/
    final AtomicInteger option = new AtomicInteger();
    Runnable r = new Runnable() {
        public void run() {
            option.set(JOptionPane.showConfirmDialog(CraftProxyClient.getGUI(),
                    "Login as " + AuthManager.getUsername() + "?", "Login", JOptionPane.YES_NO_OPTION));
        }
    };

    if (SwingUtilities.isEventDispatchThread()) {
        r.run();
    } else {
        try {
            SwingUtilities.invokeAndWait(r);
        } catch (InvocationTargetException | InterruptedException e) {
            return null;
        }
    }
    if (option.get() == 0) {
        return loginInfo;
    } else {
        return null;
    }
}

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From source file:org.zenoss.zep.dao.impl.DaoUtilsTest.java

@Test
public void testDeadlockRetryAllFailed() throws Exception {
    final AtomicInteger i = new AtomicInteger();
    try {//from   w  w w .j a  v  a2  s. c om
        DaoUtils.deadlockRetry(new Callable<Integer>() {
            @Override
            public Integer call() throws Exception {
                throw new DeadlockLoserDataAccessException(String.valueOf(i.incrementAndGet()), null);
            }
        });
        fail("Should have thrown an exception after 5 retries");
    } catch (DeadlockLoserDataAccessException e) {
        assertEquals("5", e.getMessage());
    }
}

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From source file:jcuda.jcublas.kernel.TestMultipleThreads.java

@Test
public void testMultipleThreads() throws InterruptedException {
    int numThreads = 10;
    final INDArray array = Nd4j.rand(3000, 3000);
    final INDArray expected = array.dup().mmul(array).mmul(array).div(array).div(array);
    final AtomicInteger correct = new AtomicInteger();
    final CountDownLatch latch = new CountDownLatch(numThreads);

    ExecutorService executors = Executors.newCachedThreadPool();

    for (int x = 0; x < numThreads; x++) {
        executors.execute(new Runnable() {
            @Override//w w  w.  j av  a 2 s . co m
            public void run() {
                try {
                    int total = 10;
                    int right = 0;
                    for (int x = 0; x < total; x++) {
                        StopWatch watch = new StopWatch();
                        watch.start();
                        INDArray actual = array.dup().mmul(array).mmul(array).div(array).div(array);
                        watch.stop();
                        System.out.println("MMUL took " + watch.getTime());
                        if (expected.equals(actual))
                            right++;
                    }

                    if (total == right)
                        correct.incrementAndGet();
                } finally {
                    latch.countDown();
                }

            }
        });
    }

    latch.await();

    assertEquals(numThreads, correct.get());

}

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