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

List of usage examples for java.util.concurrent.atomic AtomicInteger AtomicInteger

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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:edu.msu.cme.rdp.kmer.cli.FastKmerFilter.java

public static void main(String[] args) throws Exception {
    final KmerSet<Set<RefKmer>> kmerSet;
    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;
    final int trieWordSize;

    try {/*  w  w w . j  a v a  2 s . 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");
        }

        if (translQuery) {
            trieWordSize = wordSize / 3;
        } else {
            trieWordSize = wordSize;
        }
        kmerSet = new KmerSet<Set<RefKmer>>();//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;
                }

                KmerGenerator kmers;
                try {
                    if (translQuery) { //protein ref
                        kmers = new ProtKmerGenerator(seq.getSeqString(), trieWordSize, alignedSeqs);
                    } else {
                        kmers = new NuclKmerGenerator(seq.getSeqString(), trieWordSize, alignedSeqs);
                    }
                    while (kmers.hasNext()) {
                        Kmer temp = kmers.next();
                        long[] next = temp.getLongKmers();
                        Set<RefKmer> refKmers = kmerSet.get(next);
                        if (refKmers == null) {
                            refKmers = new HashSet();
                            kmerSet.add(next, refKmers);
                        }

                        RefKmer kmerRef = new RefKmer();
                        kmerRef.modelPos = kmers.getPosition();
                        kmerRef.refFileIndex = refLabels.size();
                        kmerRef.refSeqid = seq.getSeqName();
                        refKmers.add(kmerRef);
                    }
                } catch (IllegalArgumentException ex) {
                    //System.err.println(seq.getSeqName()+ " " + ex.getMessage());
                }
            }
            seqReader.close();

            refLabels.add(refName);
        }

    } catch (Exception e) {
        new HelpFormatter().printHelp(
                "KmerSearch <kmerSize> <query_file> [name=]<ref_file> ...\nkmerSize should be multiple of 3, (recommend 45, minimum 30, maximum 63) ",
                options);
        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;

    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:             " + trieWordSize);
    System.err.println("*  Kmer Refset Size:        " + kmerSet.size());

    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 ((!translQuery && seqString.length() < wordSize)
                || (translQuery && seqString.length() < wordSize + 2)) {
            //System.err.println(querySeq.getSeqName() + "\t" + seqString.length());
            continue;
        }

        final Sequence threadSeq = querySeq;

        Runnable r = new Runnable() {

            public void run() {
                try {
                    processSeq(threadSeq, refLabels, kmerSet, out, wordSize, translQuery, translTable, false);
                    processSeq(threadSeq, refLabels, kmerSet, out, wordSize, translQuery, translTable, true);

                    processed.incrementAndGet();
                    outstandingTasks.decrementAndGet();
                } catch (Exception e) {
                    e.printStackTrace();
                }
            }
        };

        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();
}

From source file:io.watchcat.node.metrics.MemoryUsage.java

public MemoryUsage() {
    command = new ShellCommand(
            "/usr/bin/free -tmo | /usr/bin/awk '{print $1\",\"$2\",\"$3-$6-$7\",\"$4+$6+$7}'");

    totalMemory = new AtomicInteger();
    totalSwap = new AtomicInteger();
    usedMemory = new AtomicInteger();
    usedSwap = new AtomicInteger();
}

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

@Test
public void testDeadlockRetryNestedException() throws Exception {
    final AtomicInteger i = new AtomicInteger();
    final int returnVal = new Random().nextInt();
    int result = DaoUtils.deadlockRetry(new Callable<Integer>() {
        @Override//from w ww  .j a v a 2s.  co m
        public Integer call() throws Exception {
            if (i.incrementAndGet() < 5) {
                throw new RuntimeException(new DeadlockLoserDataAccessException("My fake exception", null));
            }
            return returnVal;
        }
    });
    assertEquals(i.get(), 5);
    assertEquals(result, returnVal);
}

From source file:com.weibo.datasys.crawler.impl.strategy.rule.save.StatisticSaveRule.java

@Override
public Null apply(ParseInfo in) {
    String url = in.getThisCrawlInfo().getSeedData().getUrl();
    String host = URLUtil.getHost(url);
    AtomicInteger count = hostCountMap.get(host);
    if (count == null) {
        synchronized (StatisticSaveRule.class) {
            if (count == null) {
                count = new AtomicInteger();
                hostCountMap.put(host, count);
            } else {
                count = hostCountMap.get(host);
            }//from w  ww. j av  a2  s .co m
        }
    }
    count.incrementAndGet();
    saveResult();
    return null;
}

From source file:com.predic8.membrane.core.interceptor.apimanagement.AMRateLimitInterceptorTest.java

@Test
public void testHandleRequestRateLimit5SecondConcurrency() throws Exception {

    final Exchange exc = new Exchange(null);
    exc.setResponse(Response.ResponseBuilder.newInstance().build());
    exc.setProperty(Exchange.API_KEY, "junit");
    exc.setRule(new ServiceProxy());
    exc.getRule().setName("junit API");

    final AMRateLimiter rli = new AMRateLimiter();
    ApiManagementConfiguration amc = new ApiManagementConfiguration(System.getProperty("user.dir"),
            "src\\test\\resources\\apimanagement\\api.yaml");
    rli.setAmc(amc);//from w ww .  jav a2s.c o m

    ArrayList<Thread> threads = new ArrayList<Thread>();
    final AtomicInteger continues = new AtomicInteger();
    final AtomicInteger returns = new AtomicInteger();
    for (int i = 0; i < 1000; i++) {
        Thread t = new Thread(new Runnable() {

            @Override
            public void run() {
                try {
                    Outcome out = rli.handleRequest(exc);
                    if (out == Outcome.CONTINUE) {
                        continues.incrementAndGet();
                    } else if (out == Outcome.RETURN) {
                        returns.incrementAndGet();
                    }
                } catch (Exception e) {
                    e.printStackTrace();
                }
            }
        });
        threads.add(t);
        t.start();
    }
    for (Thread t : threads) {
        t.join();
    }
    assertEquals(5, continues.get());
    assertEquals(995, returns.get());
    Thread.sleep(2000);
    assertEquals(Outcome.CONTINUE, rli.handleRequest(exc));
}

From source file:io.pravega.test.integration.selftest.Producer.java

/**
 * Creates a new instance of the Producer class.
 *
 * @param id         The Id of the producer.
 * @param config     Test Configuration.
 * @param dataSource DataSource for the Producer.
 * @param store      A StoreAdapter to execute operations on.
 * @param executor   An Executor to use for async operations.
 *//*w ww .  jav a2  s  .c o  m*/
Producer(int id, TestConfig config, ProducerDataSource dataSource, StoreAdapter store,
        ScheduledExecutorService executor) {
    super(config, dataSource, store, executor);

    this.id = id;
    this.logId = String.format("Producer[%s]", id);
    this.iterationCount = new AtomicInteger();
    this.canContinue = new AtomicBoolean(true);
}

From source file:dk.netarkivet.common.utils.warc.WARCUtils.java

/**
 * Create new WARCWriter, writing to warcfile newFile.
 * @param newFile the WARCfile, that the WARCWriter writes to.
 * @return new WARCWriter, writing to warcfile newFile.
 *///from   w  w w .  j  a va2  s. c o m
public static WARCWriter createWARCWriter(File newFile) {
    WARCWriter writer;
    PrintStream ps = null;
    try {
        ps = new PrintStream(new FileOutputStream(newFile));
        writer = new WARCWriterNAS(new AtomicInteger(), ps,
                //This name is used for the first (file metadata) record
                newFile, false, //Don't compress
                //Use current time
                ArchiveDateConverter.getWarcDateFormat().format(new Date()), null //No particular file metadata to add
        );
    } catch (IOException e) {
        if (ps != null) {
            ps.close();
        }
        String message = "Could not create WARCWriter to file '" + newFile + "'.\n";
        log.warn(message);
        throw new IOFailure(message, e);
    }
    return writer;
}

From source file:com.astamuse.asta4d.web.util.timeout.DefaultSessionAwareExpirableDataManager.java

public DefaultSessionAwareExpirableDataManager() {
    dataMap = createThreadSafeDataMap();
    dataCounter = new AtomicInteger();
}

From source file:org.apache.servicemix.jbi.cluster.engine.ClusterEndpointLoadTest.java

public void testLoadInOnly() throws Exception {
    createRoute(Transacted.Jms, true, false, true);

    final int nbThreads = 10;
    final int nbExchanges = 10;
    final ReadWriteLock lock = new ReentrantReadWriteLock();
    final CountDownLatch latch = new CountDownLatch(nbThreads);
    final AtomicInteger id = new AtomicInteger();
    lock.writeLock().lock();/*from w w w.jav  a2  s.  com*/
    for (int i = 0; i < nbThreads; i++) {
        new Thread() {
            public void run() {
                Channel client = null;
                try {
                    client = nmr1.createChannel();
                    lock.readLock().lock();
                    for (int i = 0; i < nbExchanges; i++) {
                        Exchange exchange = client.createExchange(Pattern.InOnly);
                        exchange.getIn()
                                .setBody(new StringSource("<hello id='" + id.getAndIncrement() + "'/>"));
                        exchange.setTarget(nmr1.getEndpointRegistry()
                                .lookup(ServiceHelper.createMap(Endpoint.NAME, PROXY_ENDPOINT_NAME)));
                        client.sendSync(exchange);
                        assertEquals(Status.Done, exchange.getStatus());
                    }
                } catch (Exception e) {
                    e.printStackTrace();
                } finally {
                    lock.readLock().unlock();
                    latch.countDown();
                    if (client != null) {
                        client.close();
                    }
                }
            }
        }.start();
    }

    long t0, t1;

    t0 = System.currentTimeMillis();
    lock.writeLock().unlock();

    latch.await();

    receiver.assertExchangesReceived(nbThreads * nbExchanges, TIMEOUT);

    t1 = System.currentTimeMillis();

    System.err.println("Elapsed time: " + (t1 - t0) + " ms");
    System.err.println("Throuput: " + (nbThreads * nbExchanges * 1000 / (t1 - t0)) + " messages/sec");
}

From source file:org.apache.asterix.experiment.client.StatisticsQueryGenerator.java

public StatisticsQueryGenerator(StatisticsQueryGeneratorConfig config) {
    threadPool = Executors.newCachedThreadPool(new ThreadFactory() {

        private final AtomicInteger count = new AtomicInteger();

        @Override/*from www  .j a  v  a2 s .c o m*/
        public Thread newThread(Runnable r) {
            int tid = count.getAndIncrement();
            Thread t = new Thread(r, "DataGeneratorThread: " + tid);
            t.setDaemon(true);
            return t;
        }
    });
    this.config = config;
}