Example usage for java.util List add

List of usage examples for java.util List add

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Introduction

In this page you can find the example usage for java.util List add.

Prototype

boolean add(E e);

Source Link

Document

Appends the specified element to the end of this list (optional operation).

Usage

From source file:com.actelion.research.spiritcore.util.StatUtils.java

public static void main(String[] args) {
    //      List<Double> list = new ArrayList<Double>();
    ////      list.add(30d); list.add(171d); list.add(184d); list.add(201d); list.add(212d); list.add(250d); list.add(265d); list.add(270d); list.add(272d); list.add(289d); list.add(305d); list.add(306d); list.add(322d); list.add(322d); list.add(336d); list.add(346d); list.add(351d); list.add(370d); list.add(390d); list.add(404d); list.add(409d); list.add(411d); list.add(436d); list.add(437d); list.add(439d); list.add(441d); list.add(444d); list.add(448d); list.add(451d); list.add(453d); list.add(470d); list.add(480d); list.add(482d); list.add(487d); list.add(494d); list.add(495d); list.add(499d); list.add(503d); list.add(514d); list.add(521d); list.add(522d); list.add(527d); list.add(548d); list.add(550d); list.add(559d); list.add(560d); list.add(570d); list.add(572d); list.add(574d); list.add(578d); list.add(585d); list.add(592d); list.add(592d); list.add(607d); list.add(616d); list.add(618d); list.add(621d); list.add(629d); list.add(637d); list.add(638d); list.add(640d); list.add(656d); list.add(668d); list.add(707d); list.add(709d); list.add(719d); list.add(737d); list.add(739d); list.add(752d); list.add(758d); list.add(766d); list.add(792d); list.add(792d); list.add(794d); list.add(802d); list.add(818d); list.add(830d); list.add(832d); list.add(843d); list.add(858d); list.add(860d); list.add(869d); list.add(918d); list.add(925d); list.add(953d); list.add(991d); list.add(1000d); list.add(1005d); list.add(1068d); list.add(1441d); 
    //      list.add(0.0); list.add(156.0); list.add(156.0); list.add(161.0); list.add(176.0); 
    //      /*from w w w .  j  ava  2s. com*/
    //      double[] fences = getFences(list);
    //      System.out.println("median="+getMedian(list));
    //      System.out.println("std="+getStandardDeviationOfMean(list));
    //      System.out.println("fences="+Arrays.toString(fences));

    int count = 0;
    int N = 1000;
    for (int t = 0; t < N; t++) {
        List<double[]> doubles = new ArrayList<double[]>();
        for (int i = 0; i < 3; i++) {
            double[] array = new double[10];
            doubles.add(array);
            for (int j = 0; j < array.length; j++) {
                array[j] = Math.random() * 10;// i<2 || j<10? j: j+100; 
            }
        }
        double r = getKruskalWallis(doubles);
        if (r < 0.05)
            count++;
        System.out.println("[" + t + "] KW=" + r);
    }
    System.out.println("==> percentage of false positive " + (1.0 * count / N) + " ~ 0.05");

}

From source file:org.openbaton.monitoring.interfaces.MonitoringPluginCaller.java

public static void main(String[] args)
        throws IOException, TimeoutException, NotFoundException, ExecutionException, InterruptedException {

    ExecutorService executor = Executors.newFixedThreadPool(3);

    class Exec implements Callable<Object> {

        @Override/*from www .  ja  v  a 2  s . co  m*/
        public Object call() throws Exception {
            List<String> hosts = new ArrayList<>();
            hosts.add("hostname1");
            hosts.add("hostname2");
            return null /* new MonitoringPluginCaller("zabbix").getMeasurementResults(hosts, new ArrayList<String>(), "")*/;
        }
    }

    long time = new Date().getTime();
    System.out.println("Time ---> " + time);
    Future fut1 = executor.submit(new Exec());
    Future fut2 = executor.submit(new Exec());

    System.out.println("2nd call");
    System.out.println(fut2.get());

    System.out.println("1st call");
    System.out.println(fut1.get());
    System.out.println("Time ---> " + (new Date().getTime() - time) / 1000);
}

From source file:io.druid.examples.rabbitmq.RabbitMQProducerMain.java

public static void main(String[] args) throws Exception {
    // We use a List to keep track of option insertion order. See below.
    final List<Option> optionList = new ArrayList<Option>();

    optionList.add(OptionBuilder.withLongOpt("help").withDescription("display this help message").create("h"));
    optionList.add(OptionBuilder.withLongOpt("hostname").hasArg()
            .withDescription("the hostname of the AMQP broker [defaults to AMQP library default]").create("b"));
    optionList.add(OptionBuilder.withLongOpt("port").hasArg()
            .withDescription("the port of the AMQP broker [defaults to AMQP library default]").create("n"));
    optionList.add(OptionBuilder.withLongOpt("username").hasArg()
            .withDescription("username to connect to the AMQP broker [defaults to AMQP library default]")
            .create("u"));
    optionList.add(OptionBuilder.withLongOpt("password").hasArg()
            .withDescription("password to connect to the AMQP broker [defaults to AMQP library default]")
            .create("p"));
    optionList.add(OptionBuilder.withLongOpt("vhost").hasArg()
            .withDescription("name of virtual host on the AMQP broker [defaults to AMQP library default]")
            .create("v"));
    optionList.add(OptionBuilder.withLongOpt("exchange").isRequired().hasArg()
            .withDescription("name of the AMQP exchange [required - no default]").create("e"));
    optionList.add(OptionBuilder.withLongOpt("key").hasArg()
            .withDescription("the routing key to use when sending messages [default: 'default.routing.key']")
            .create("k"));
    optionList.add(OptionBuilder.withLongOpt("type").hasArg()
            .withDescription("the type of exchange to create [default: 'topic']").create("t"));
    optionList.add(OptionBuilder.withLongOpt("durable")
            .withDescription("if set, a durable exchange will be declared [default: not set]").create("d"));
    optionList.add(OptionBuilder.withLongOpt("autodelete")
            .withDescription("if set, an auto-delete exchange will be declared [default: not set]")
            .create("a"));
    optionList.add(OptionBuilder.withLongOpt("single")
            .withDescription("if set, only a single message will be sent [default: not set]").create("s"));
    optionList.add(OptionBuilder.withLongOpt("start").hasArg()
            .withDescription("time to use to start sending messages from [default: 2010-01-01T00:00:00]")
            .create());/*from  w  w w . j  a  v  a  2 s.  c o  m*/
    optionList.add(OptionBuilder.withLongOpt("stop").hasArg().withDescription(
            "time to use to send messages until (format: '2013-07-18T23:45:59') [default: current time]")
            .create());
    optionList.add(OptionBuilder.withLongOpt("interval").hasArg()
            .withDescription("the interval to add to the timestamp between messages in seconds [default: 10]")
            .create());
    optionList.add(OptionBuilder.withLongOpt("delay").hasArg()
            .withDescription("the delay between sending messages in milliseconds [default: 100]").create());

    // An extremely silly hack to maintain the above order in the help formatting.
    HelpFormatter formatter = new HelpFormatter();
    // Add a comparator to the HelpFormatter using the ArrayList above to sort by insertion order.
    formatter.setOptionComparator(new Comparator() {
        @Override
        public int compare(Object o1, Object o2) {
            // I know this isn't fast, but who cares! The list is short.
            return optionList.indexOf(o1) - optionList.indexOf(o2);
        }
    });

    // Now we can add all the options to an Options instance. This is dumb!
    Options options = new Options();
    for (Option option : optionList) {
        options.addOption(option);
    }

    CommandLine cmd = null;

    try {
        cmd = new BasicParser().parse(options, args);

    } catch (ParseException e) {
        formatter.printHelp("RabbitMQProducerMain", e.getMessage(), options, null);
        System.exit(1);
    }

    if (cmd.hasOption("h")) {
        formatter.printHelp("RabbitMQProducerMain", options);
        System.exit(2);
    }

    ConnectionFactory factory = new ConnectionFactory();

    if (cmd.hasOption("b")) {
        factory.setHost(cmd.getOptionValue("b"));
    }
    if (cmd.hasOption("u")) {
        factory.setUsername(cmd.getOptionValue("u"));
    }
    if (cmd.hasOption("p")) {
        factory.setPassword(cmd.getOptionValue("p"));
    }
    if (cmd.hasOption("v")) {
        factory.setVirtualHost(cmd.getOptionValue("v"));
    }
    if (cmd.hasOption("n")) {
        factory.setPort(Integer.parseInt(cmd.getOptionValue("n")));
    }

    String exchange = cmd.getOptionValue("e");
    String routingKey = "default.routing.key";
    if (cmd.hasOption("k")) {
        routingKey = cmd.getOptionValue("k");
    }

    boolean durable = cmd.hasOption("d");
    boolean autoDelete = cmd.hasOption("a");
    String type = cmd.getOptionValue("t", "topic");
    boolean single = cmd.hasOption("single");
    int interval = Integer.parseInt(cmd.getOptionValue("interval", "10"));
    int delay = Integer.parseInt(cmd.getOptionValue("delay", "100"));

    SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss");
    Date stop = sdf.parse(cmd.getOptionValue("stop", sdf.format(new Date())));

    Random r = new Random();
    Calendar timer = Calendar.getInstance();
    timer.setTime(sdf.parse(cmd.getOptionValue("start", "2010-01-01T00:00:00")));

    String msg_template = "{\"utcdt\": \"%s\", \"wp\": %d, \"gender\": \"%s\", \"age\": %d}";

    Connection connection = factory.newConnection();
    Channel channel = connection.createChannel();

    channel.exchangeDeclare(exchange, type, durable, autoDelete, null);

    do {
        int wp = (10 + r.nextInt(90)) * 100;
        String gender = r.nextBoolean() ? "male" : "female";
        int age = 20 + r.nextInt(70);

        String line = String.format(msg_template, sdf.format(timer.getTime()), wp, gender, age);

        channel.basicPublish(exchange, routingKey, null, line.getBytes());

        System.out.println("Sent message: " + line);

        timer.add(Calendar.SECOND, interval);

        Thread.sleep(delay);
    } while ((!single && stop.after(timer.getTime())));

    connection.close();
}

From source file:com.act.analysis.surfactant.AnalysisDriver.java

public static void main(String[] args) throws Exception {
    Options opts = new Options();
    for (Option.Builder b : OPTION_BUILDERS) {
        opts.addOption(b.build());/*  ww w .ja va 2s .co m*/
    }

    CommandLine cl = null;
    try {
        CommandLineParser parser = new DefaultParser();
        cl = parser.parse(opts, args);
    } catch (ParseException e) {
        System.err.format("Argument parsing failed: %s\n", e.getMessage());
        HELP_FORMATTER.printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), HELP_MESSAGE, opts, null,
                true);
        System.exit(1);
    }

    if (cl.hasOption("help")) {
        HELP_FORMATTER.printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), HELP_MESSAGE, opts, null,
                true);
        return;
    }

    Set<String> seenOutputIds = new HashSet<>();

    TSVWriter<String, String> tsvWriter = null;
    if (cl.hasOption(OPTION_OUTPUT_FILE)) {
        File outputFile = new File(cl.getOptionValue(OPTION_OUTPUT_FILE));
        List<Map<String, String>> oldResults = null;
        if (outputFile.exists()) {
            System.err.format(
                    "Output file already exists, reading old results and skipping processed molecules.\n");
            TSVParser outputParser = new TSVParser();
            outputParser.parse(outputFile);
            oldResults = outputParser.getResults();
            for (Map<String, String> row : oldResults) {
                // TODO: verify that the last row was written cleanly/completely.
                seenOutputIds.add(row.get("id"));
            }
        }

        List<String> header = new ArrayList<>();
        header.add("name");
        header.add("id");
        header.add("inchi");
        header.add("label");
        for (SurfactantAnalysis.FEATURES f : SurfactantAnalysis.FEATURES.values()) {
            header.add(f.toString());
        }
        // TODO: make this API more auto-closable friendly.
        tsvWriter = new TSVWriter<>(header);
        tsvWriter.open(outputFile);
        if (oldResults != null) {
            System.out.format("Re-writing %d existing result rows\n", oldResults.size());
            tsvWriter.append(oldResults);
        }
    }

    try {
        Map<SurfactantAnalysis.FEATURES, Double> analysisFeatures;

        LicenseManager.setLicenseFile(cl.getOptionValue(OPTION_LICENSE_FILE));
        if (cl.hasOption(OPTION_INCHI)) {
            analysisFeatures = SurfactantAnalysis.performAnalysis(cl.getOptionValue(OPTION_INCHI),
                    cl.hasOption(OPTION_DISPLAY));
            Map<String, String> tsvFeatures = new HashMap<>();
            // Convert features to strings to avoid some weird formatting issues.  It's ugly, but it works.
            for (Map.Entry<SurfactantAnalysis.FEATURES, Double> entry : analysisFeatures.entrySet()) {
                tsvFeatures.put(entry.getKey().toString(), String.format("%.6f", entry.getValue()));
            }
            tsvFeatures.put("name", "direct-inchi-input");
            if (tsvWriter != null) {
                tsvWriter.append(tsvFeatures);
            }
        } else if (cl.hasOption(OPTION_INPUT_FILE)) {
            TSVParser parser = new TSVParser();
            parser.parse(new File(cl.getOptionValue(OPTION_INPUT_FILE)));
            int i = 0;
            List<Map<String, String>> inputRows = parser.getResults();

            for (Map<String, String> row : inputRows) {
                i++; // Just for warning messages.
                if (!row.containsKey("name") || !row.containsKey("id") || !row.containsKey("inchi")) {
                    System.err.format(
                            "WARNING: TSV rows must contain at least name, id, and inchi, skipping row %d\n",
                            i);
                    continue;
                }
                if (seenOutputIds.contains(row.get("id"))) {
                    System.out.format("Skipping input row with id already in output: %s\n", row.get("id"));
                    continue;
                }

                System.out.format("Analysis for chemical %s\n", row.get("name"));
                try {
                    analysisFeatures = SurfactantAnalysis.performAnalysis(row.get("inchi"), false);
                } catch (Exception e) {
                    // Ignore exceptions for now.  Sometimes the regression analysis or Chemaxon processing chokes unexpectedly.
                    System.err.format("ERROR caught exception while processing '%s':\n", row.get("name"));
                    System.err.format("%s\n", e.getMessage());
                    e.printStackTrace(System.err);
                    System.err.println("Skipping...");
                    continue;
                }
                System.out.format("--- Done analysis for chemical %s\n", row.get("name"));

                // This is a duplicate of the OPTION_INCHI block code, but it's inside of a tight loop, so...
                Map<String, String> tsvFeatures = new HashMap<>();
                for (Map.Entry<SurfactantAnalysis.FEATURES, Double> entry : analysisFeatures.entrySet()) {
                    tsvFeatures.put(entry.getKey().toString(), String.format("%.6f", entry.getValue()));
                }
                tsvFeatures.put("name", row.get("name"));
                tsvFeatures.put("id", row.get("id"));
                tsvFeatures.put("inchi", row.get("inchi"));
                tsvFeatures.put("label", row.containsKey("label") ? row.get("label") : "?");
                if (tsvWriter != null) {
                    tsvWriter.append(tsvFeatures);
                    // Flush every time in case we crash or get interrupted.  The features must flow!
                    tsvWriter.flush();
                }
            }
        } else {
            throw new RuntimeException("Must specify inchi or input file");
        }
    } finally {
        if (tsvWriter != null) {
            tsvWriter.close();
        }
    }
}

From source file:com.yahoo.spaclu.data.extract.ExtractFeatureSpark.java

public static void main(String[] args) throws IOException {
    ExtractFeatureOptions optionsFormatRawToDatabase = new ExtractFeatureOptions(args);

    String inputPathString = optionsFormatRawToDatabase.getInputPath();
    String outputPathString = optionsFormatRawToDatabase.getOutputPath();
    // String indexPathString = optionsFormatRawToDatabase.getIndexPath();
    int numberOfPartitions = optionsFormatRawToDatabase.getNumberOfPartitions();
    // int maxCutoffThreshold = optionsFormatRawToDatabase
    // .getMaximumCutoffThreshold();
    // int minCutoffThreshold = optionsFormatRawToDatabase
    // .getMinimumCutoffThreshold();

    /*//from   ww  w  .j  av a2 s . c  o m
     * Set<String> excludingFeatureNames = new HashSet<String>();
     * excludingFeatureNames.add("login");
     * excludingFeatureNames.add("time"); excludingFeatureNames.add("day");
     * excludingFeatureNames.add("hms"); excludingFeatureNames.add("fail");
     */

    sLogger.info("Tool: " + ExtractFeatureSpark.class.getSimpleName());
    sLogger.info(" - input path: " + inputPathString);
    sLogger.info(" - output path: " + outputPathString);
    // sLogger.info(" - index path: " + indexPathString);
    sLogger.info(" - number of partitions: " + numberOfPartitions);
    // sLogger.info(" - maximum cutoff: " + maxCutoffThreshold);
    // sLogger.info(" - minimum cutoff: " + minCutoffThreshold);

    // Create a default hadoop configuration
    Configuration conf = new Configuration();

    // Parse created config to the HDFS
    FileSystem fs = FileSystem.get(conf);

    Path outputPath = new Path(outputPathString);
    if (fs.exists(outputPath)) {
        fs.delete(outputPath, true);
    }

    SparkConf sparkConf = new SparkConf().setAppName(optionsFormatRawToDatabase.toString());

    JavaSparkContext sc = new JavaSparkContext(sparkConf);

    List<Integer> listOfFeatureIndices = new LinkedList<Integer>();
    listOfFeatureIndices.add(CBBingCombinedFields.CBBingCombined_exactCanonicalQuery.ordinal());
    listOfFeatureIndices.add(CBBingCombinedFields.CBBingCombined_title.ordinal());
    listOfFeatureIndices.add(CBBingCombinedFields.CBBingCombined_description.ordinal());
    listOfFeatureIndices.add(CBBingCombinedFields.CBBingCombined_displayUrl.ordinal());
    listOfFeatureIndices.add(CBBingCombinedFields.CBBingCombined_targetUrl.ordinal());

    JavaRDD<String> rawLines = sc.textFile(inputPathString).repartition(numberOfPartitions);

    JavaRDD<String> tokenizedLines = rawLines.map(new LineFilter(listOfFeatureIndices));
    tokenizedLines.saveAsTextFile(outputPathString);

    /*
     * Iterator<String[]> strArrIter = tokenizedLines.collect().iterator();
     * while(strArrIter.hasNext()){
     * sLogger.info(Arrays.toString(strArrIter.next())); }
     */

    sc.stop();
}

From source file:com.l2jfree.tools.ProjectSettingsSynchronizer.java

public static void main(String[] args) throws IOException {
    final File src = new File(".").getCanonicalFile();
    System.out.println("Copying from: " + src);
    System.out.println();/* ww w .j  ava2  s.c o m*/

    final List<File> destinations = new ArrayList<File>();
    for (File dest : src.getParentFile().listFiles()) {
        if (dest.isHidden() || !dest.isDirectory())
            continue;

        destinations.add(dest);
        System.out.println("Copying to: " + dest);
    }
    System.out.println();

    // .project
    System.out.println(".project");
    System.out.println("================================================================================");
    {
        final List<String> lines = FileUtils.readLines(new File(src, ".project"));

        for (File dest : destinations) {
            lines.set(2, lines.get(2).replaceAll(src.getName(), dest.getName()));
            writeLines(dest, ".project", lines);
            lines.set(2, lines.get(2).replaceAll(dest.getName(), src.getName()));
        }
    }
    System.out.println();

    // .classpath
    System.out.println(".classpath");
    System.out.println("================================================================================");
    {
        final List<String> lines = FileUtils.readLines(new File(src, ".classpath"));

        for (File dest : destinations) {
            if (dest.getName().endsWith("-main") || dest.getName().endsWith("-datapack")) {
                final ArrayList<String> tmp = new ArrayList<String>();

                for (String line : lines)
                    if (!line.contains("classpathentry"))
                        tmp.add(line);

                writeLines(dest, ".classpath", tmp);
                continue;
            }

            writeLines(dest, ".classpath", lines);
        }
    }
    System.out.println();

    // .settings
    System.out.println(".settings");
    System.out.println("================================================================================");
    for (File settingsFile : new File(src, ".settings").listFiles()) {
        if (settingsFile.getName().endsWith(".prefs")) {
            System.out.println(".settings/" + settingsFile.getName());
            System.out.println(
                    "--------------------------------------------------------------------------------");

            final List<String> lines = FileUtils.readLines(settingsFile);

            if (lines.get(0).startsWith("#"))
                lines.remove(0);

            for (File dest : destinations) {
                writeLines(new File(dest, ".settings"), settingsFile.getName(), lines);
            }
            System.out.println();
        }
    }
    System.out.println();
}

From source file:com.boonya.http.async.examples.nio.client.AsyncClientPipelinedStreaming.java

public static void main(final String[] args) throws Exception {
    CloseableHttpPipeliningClient httpclient = HttpAsyncClients.createPipelining();
    try {/*from w w w .  j av  a 2 s  .co m*/
        httpclient.start();

        HttpHost targetHost = new HttpHost("localhost", 8080);
        HttpGet[] resquests = { new HttpGet("/docs/index.html"), new HttpGet("/docs/introduction.html"),
                new HttpGet("/docs/setup.html"), new HttpGet("/docs/config/index.html") };

        List<MyRequestProducer> requestProducers = new ArrayList<MyRequestProducer>();
        List<MyResponseConsumer> responseConsumers = new ArrayList<MyResponseConsumer>();
        for (HttpGet request : resquests) {
            requestProducers.add(new MyRequestProducer(targetHost, request));
            responseConsumers.add(new MyResponseConsumer(request));
        }

        Future<List<Boolean>> future = httpclient.execute(targetHost, requestProducers, responseConsumers,
                null);
        future.get();
        System.out.println("Shutting down");
    } finally {
        httpclient.close();
    }
    System.out.println("Done");
}

From source file:net.padaf.xmpbox.parser.XMLValueTypeDescriptionManager.java

/**
 * Sample of using to write/read information
 * //from  w w w .java2  s .c  o m
 * @param args
 *            not used
 * @throws BuildPDFAExtensionSchemaDescriptionException
 *             When errors during building/reading xml file
 */
public static void main(String[] args) throws BuildPDFAExtensionSchemaDescriptionException {
    XMLValueTypeDescriptionManager vtMaker = new XMLValueTypeDescriptionManager();

    // add Descriptions
    for (int i = 0; i < 3; i++) {
        vtMaker.addValueTypeDescription("testType" + i, "nsURI" + i, "prefix" + i, "description" + i);

    }
    List<FieldDescription> fieldSample = new ArrayList<FieldDescription>();
    for (int i = 0; i < 2; i++) {
        fieldSample.add(new FieldDescription("fieldName" + i, "valueType" + i, "description" + i));
    }
    vtMaker.addValueTypeDescription("testTypeField", "http://test.withfield.com/vt/", "prefTest",
            " value type description", fieldSample);

    // Display XML conversion
    System.out.println("Display XML Result:");
    vtMaker.toXML(System.out);

    // Sample to show how to build object from XML file
    ByteArrayOutputStream bos = new ByteArrayOutputStream();
    vtMaker.toXML(bos);
    IOUtils.closeQuietly(bos);

    // emulate a new reading
    InputStream is = new ByteArrayInputStream(bos.toByteArray());
    vtMaker = new XMLValueTypeDescriptionManager();
    vtMaker.loadListFromXML(is);
    List<ValueTypeDescription> result = vtMaker.getValueTypesDescriptionList();
    System.out.println();
    System.out.println();
    System.out.println("Result of XML Loading :");
    for (ValueTypeDescription propertyDescription : result) {
        System.out.println(propertyDescription.getType() + " :" + propertyDescription.getDescription());
        if (propertyDescription.getFields() != null) {
            Iterator<FieldDescription> fit = propertyDescription.getFields().iterator();
            FieldDescription field;
            while (fit.hasNext()) {
                field = fit.next();
                System.out.println("Field " + field.getName() + " :" + field.getValueType());
            }
        }
    }

}

From source file:com.twentyn.chemicalClassifier.Runner.java

public static void main(String[] args) throws Exception {
    BufferedReader reader = new BufferedReader(new FileReader(args[0]));
    BufferedWriter writer = new BufferedWriter(new FileWriter(args[1]));

    try {/*from w  ww  .  j ava  2 s .c om*/
        Oscar oscar = new Oscar();

        String line = null;
        /* NOTE: this is exactly the wrong way to write a TSV reader.  Caveat emptor.
         * See http://tburette.github.io/blog/2014/05/25/so-you-want-to-write-your-own-CSV-code/
         * and then use org.apache.commons.csv.CSVParser instead.
         */
        while ((line = reader.readLine()) != null) {
            // TSV means split on tabs!  Nothing else will do.
            List<String> fields = Arrays.asList(line.split("\t"));
            // Choke if our invariants aren't satisfied.  We expect ever line to have a name and an InChI.
            if (fields.size() != 2) {
                throw new RuntimeException(
                        String.format("Found malformed line (all lines must have two fields: %s", line));
            }
            String name = fields.get(1);
            List<ResolvedNamedEntity> entities = oscar.findAndResolveNamedEntities(name);

            System.out.println("**********");
            System.out.println("Name: " + name);
            List<String> outputFields = new ArrayList<>(fields.size() + 1);
            outputFields.addAll(fields);
            if (entities.size() == 0) {
                System.out.println("No match");
                outputFields.add("noMatch");
            } else if (entities.size() == 1) {
                ResolvedNamedEntity entity = entities.get(0);
                NamedEntity ne = entity.getNamedEntity();
                if (ne.getStart() != 0 || ne.getEnd() != name.length()) {
                    System.out.println("Partial match");
                    printEntity(entity);
                    outputFields.add("partialMatch");
                } else {
                    System.out.println("Exact match");
                    printEntity(entity);
                    outputFields.add("exactMatch");
                    List<ChemicalStructure> structures = entity.getChemicalStructures(FormatType.STD_INCHI);
                    for (ChemicalStructure s : structures) {
                        outputFields.add(s.getValue());
                    }
                }
            } else { // Multiple matches found!
                System.out.println("Multiple matches");
                for (ResolvedNamedEntity e : entities) {
                    printEntity(e);
                }
                outputFields.add("multipleMatches");
            }

            writer.write(String.join("\t", outputFields));
            writer.newLine();
        }
    } finally {
        writer.flush();
        writer.close();
    }
}

From source file:gr.demokritos.iit.demos.Demo.java

public static void main(String[] args) {
    try {/*from   w  ww  .jav a2 s .c om*/
        Options options = new Options();
        options.addOption("h", HELP, false, "show help.");
        options.addOption("i", INPUT, true,
                "The file containing JSON " + " representations of tweets or SAG posts - 1 per line"
                        + " default file looked for is " + DEFAULT_INFILE);
        options.addOption("o", OUTPUT, true,
                "Where to write the output " + " default file looked for is " + DEFAULT_OUTFILE);
        options.addOption("p", PROCESS, true, "Type of processing to do "
                + " ner for Named Entity Recognition re for Relation Extraction" + " default is NER");
        options.addOption("s", SAG, false,
                "Whether to process as SAG posts" + " default is off - if passed means process as SAG posts");

        CommandLineParser parser = new BasicParser();
        CommandLine cmd = parser.parse(options, args);
        // DEFAULTS
        String filename = DEFAULT_INFILE;
        String outfilename = DEFAULT_OUTFILE;
        String process = NER;
        boolean isSAG = false;

        if (cmd.hasOption(HELP)) {
            HelpFormatter formatter = new HelpFormatter();
            formatter.printHelp("NER + RE extraction module", options);
            System.exit(0);
        }
        if (cmd.hasOption(INPUT)) {
            filename = cmd.getOptionValue(INPUT);
        }
        if (cmd.hasOption(OUTPUT)) {
            outfilename = cmd.getOptionValue(OUTPUT);
        }
        if (cmd.hasOption(SAG)) {
            isSAG = true;
        }
        if (cmd.hasOption(PROCESS)) {
            process = cmd.getOptionValue(PROCESS);
        }
        System.out.println();
        System.out.println("Reading from file: " + filename);
        System.out.println("Process type: " + process);
        System.out.println("Processing SAG: " + isSAG);
        System.out.println("Writing to file: " + outfilename);
        System.out.println();

        List<String> jsoni = new ArrayList();
        Scanner in = new Scanner(new FileReader(filename));
        while (in.hasNextLine()) {
            String json = in.nextLine();
            jsoni.add(json);
        }
        PrintWriter writer = new PrintWriter(outfilename, "UTF-8");
        System.out.println("Read " + jsoni.size() + " lines from " + filename);
        if (process.equalsIgnoreCase(RE)) {
            System.out.println("Running Relation Extraction");
            System.out.println();
            String json = API.RE(jsoni, isSAG);
            System.out.println(json);
            writer.print(json);
        } else {
            System.out.println("Running Named Entity Recognition");
            System.out.println();
            jsoni = API.NER(jsoni, isSAG);
            /*
            for(String json: jsoni){
               NamedEntityList nel = NamedEntityList.fromJSON(json);
               nel.prettyPrint();
            }
            */
            for (String json : jsoni) {
                System.out.println(json);
                writer.print(json);
            }
        }
        writer.close();
    } catch (ParseException | UnsupportedEncodingException | FileNotFoundException ex) {
        Logger.getLogger(Demo.class.getName()).log(Level.SEVERE, null, ex);
    }
}