Example usage for java.util List isEmpty

List of usage examples for java.util List isEmpty

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Introduction

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

Prototype

boolean isEmpty();

Source Link

Document

Returns true if this list contains no elements.

Usage

From source file:AmazonKinesisCreate.java

public static void main(String[] args) throws Exception {
    init();//from  w  w  w.  j a  va  2  s  . c o  m

    final String myStreamName = "philsteststream";
    final Integer myStreamSize = 1;

    // Create a stream. The number of shards determines the provisioned throughput.

    CreateStreamRequest createStreamRequest = new CreateStreamRequest();
    createStreamRequest.setStreamName(myStreamName);
    createStreamRequest.setShardCount(myStreamSize);

    // pt
    kinesisClient.createStream(createStreamRequest);

    // The stream is now being created.
    LOG.info("Creating Stream : " + myStreamName);
    waitForStreamToBecomeAvailable(myStreamName);

    // list all of my streams
    ListStreamsRequest listStreamsRequest = new ListStreamsRequest();
    listStreamsRequest.setLimit(10);
    ListStreamsResult listStreamsResult = kinesisClient.listStreams(listStreamsRequest);
    List<String> streamNames = listStreamsResult.getStreamNames();
    while (listStreamsResult.isHasMoreStreams()) {
        if (streamNames.size() > 0) {
            listStreamsRequest.setExclusiveStartStreamName(streamNames.get(streamNames.size() - 1));
        }

        listStreamsResult = kinesisClient.listStreams(listStreamsRequest);
        streamNames.addAll(listStreamsResult.getStreamNames());

    }
    LOG.info("Printing my list of streams : ");

    // print all of my streams.
    if (!streamNames.isEmpty()) {
        System.out.println("List of my streams: ");
    }
    for (int i = 0; i < streamNames.size(); i++) {
        System.out.println(streamNames.get(i));
    }

    LOG.info("Putting records in stream : " + myStreamName);
    // Write 10 records to the stream
    for (int j = 0; j < 10; j++) {

        try {
            PutRecordRequest putRecordRequest = new PutRecordRequest();
            putRecordRequest.setStreamName(myStreamName);
            putRecordRequest.setData(ByteBuffer.wrap(String.format("testData-%d", j).getBytes()));
            putRecordRequest.setPartitionKey(String.format("partitionKey-%d", j));
            PutRecordResult putRecordResult = kinesisClient.putRecord(putRecordRequest);
            System.out.println("Successfully putrecord, partition key : " + putRecordRequest.getPartitionKey()
                    + ", ShardID : " + putRecordResult.getShardId());
            Thread.sleep(1000);

        } catch (Exception e) {
            e.printStackTrace();
        }

    }

    // Delete the stream.

    /*
    LOG.info("Deleting stream : " + myStreamName);
    DeleteStreamRequest deleteStreamRequest = new DeleteStreamRequest();
    deleteStreamRequest.setStreamName(myStreamName);
            
    kinesisClient.deleteStream(deleteStreamRequest);
    // The stream is now being deleted.
    LOG.info("Stream is now being deleted : " + myStreamName);
            
    LOG.info("Streaming completed" + myStreamName);
    */

}

From source file:AmazonKinesisDelete.java

public static void main(String[] args) throws Exception {
    init();//from w  w  w .  j  a va  2 s.co  m

    //final String myStreamName = "anotestBstream";
    //final Integer myStreamSize = 1;

    // Create a stream. The number of shards determines the provisioned throughput.

    //        CreateStreamRequest createStreamRequest = new CreateStreamRequest();
    //        createStreamRequest.setStreamName(myStreamName);
    //        createStreamRequest.setShardCount(myStreamSize);

    // pt
    //       kinesisClient.createStream(createStreamRequest);

    // The stream is now being created.
    //       LOG.info("Creating Stream : " + myStreamName);
    //       waitForStreamToBecomeAvailable(myStreamName);

    // list all of my streams
    ListStreamsRequest listStreamsRequest = new ListStreamsRequest();
    listStreamsRequest.setLimit(10);
    ListStreamsResult listStreamsResult = kinesisClient.listStreams(listStreamsRequest);
    List<String> streamNames = listStreamsResult.getStreamNames();
    while (listStreamsResult.isHasMoreStreams()) {
        if (streamNames.size() > 0) {
            listStreamsRequest.setExclusiveStartStreamName(streamNames.get(streamNames.size() - 1));
        }

        listStreamsResult = kinesisClient.listStreams(listStreamsRequest);
        streamNames.addAll(listStreamsResult.getStreamNames());

    }
    LOG.info("Printing my list of streams : ");

    // print all of my streams.
    if (!streamNames.isEmpty()) {
        System.out.println("List of my streams: ");
    }

    for (int i = 0; i < streamNames.size(); i++) {
        System.out.println(streamNames.get(i));
        String actStreamName = streamNames.get(i);

        DeleteStreamRequest deleteStreamRequest = new DeleteStreamRequest();
        //deleteStreamRequest.setStreamName(myStreamName);
        deleteStreamRequest.setStreamName(actStreamName);

        kinesisClient.deleteStream(deleteStreamRequest);
        // The stream is now being deleted.
        LOG.info("Stream is now being deleted : " + actStreamName);
    }

    /*      
          LOG.info("Putting records in stream : " + myStreamName);
          // Write 10 records to the stream
          for (int j = 0; j < 10; j++) {
    PutRecordRequest putRecordRequest = new PutRecordRequest();
    putRecordRequest.setStreamName(myStreamName);
    putRecordRequest.setData(ByteBuffer.wrap(String.format("testData-%d", j).getBytes()));
    putRecordRequest.setPartitionKey(String.format("partitionKey-%d", j));
    PutRecordResult putRecordResult = kinesisClient.putRecord(putRecordRequest);
    System.out.println("Successfully putrecord, partition key : " + putRecordRequest.getPartitionKey()
            + ", ShardID : " + putRecordResult.getShardId());
          }
    */

    // Delete the stream.

    /*      LOG.info("Deleting stream : " + myStreamName);
          DeleteStreamRequest deleteStreamRequest = new DeleteStreamRequest();
          deleteStreamRequest.setStreamName(myStreamName);
            
          kinesisClient.deleteStream(deleteStreamRequest);
          // The stream is now being deleted.
          LOG.info("Stream is now being deleted : " + myStreamName);
                  
          LOG.info("Streaming completed" + myStreamName);
    */

}

From source file:edu.osu.ling.pep.Pep.java

/**
 * Invokes Pep from the command line./*from  w ww .  j  a v a 2 s .c  o  m*/
 * <p>
 * The main work this method does, apart from tokenizing the arguments and
 * input tokens, is to load and parse the XML grammar file (as specified by
 * <code>-g</code> or <code>--grammar</code>). If any of the arguments
 * <code>-g</code>, <code>--grammar</code>, <code>-s</code>,
 * <code>--seed</code>, <code>-o</code>, <code>--option</code>, occur with
 * no argument following, this method prints an error notifying the user.
 * 
 * @param args
 *            The expected arguments are as follows, and can occur in any
 *            particular order:
 *            <ul>
 *            <li><code>-g|--grammar &lt;grammar file&gt;</code></li> <li>
 *            <code>-s|--seed &lt;seed category&gt;</code></li> <li><code>
 *            -v|--verbose {verbosity level}</code></li> <li><code>
 *            -o|--option &lt;OPTION_NAME=value&gt;</code></li> <li><code>
 *            -h|--help (prints usage information)</code></li> <li><code>
 *            &lt;token1 ... token<em>n</em>&gt;</code> (or <code>-</code>
 *            for standard input)</li>
 *            </ul>
 *            <code>OPTION_NAME</code> must be the name of one of the
 *            recognized {@link ParserOption options}. If <code>-h</code> or
 *            <code>--help</code> occur anywhere in the arguments, usage
 *            information is printed and no parsing takes place.
 */
@SuppressWarnings("static-access")
public static final void main(final String[] args) {
    try {
        final Options opts = new Options();

        opts.addOption(OptionBuilder.withLongOpt("grammar").withDescription("the grammar to use").hasArg()
                .isRequired().withArgName("grammar file").create('g'));

        opts.addOption(OptionBuilder.withLongOpt("seed").withDescription("the seed category to parse for")
                .hasArg().isRequired().withArgName("seed category").create('s'));

        opts.addOption(OptionBuilder.withLongOpt("verbose").withDescription("0-3").hasOptionalArg()
                .withArgName("verbosity level").create('v'));

        opts.addOption(OptionBuilder.withLongOpt("option").withDescription("sets parser options")
                .withArgName("OPTION=value").hasArgs(2).withValueSeparator()
                .withDescription("use value for given property").create("o"));

        opts.addOption(OptionBuilder.withLongOpt("help").withDescription("prints this message").create('h'));

        final CommandLineParser parser = new GnuParser();
        try {
            final CommandLine line = parser.parse(opts, args);
            if (line.hasOption('h')) {
                Pep.printHelp(opts);
            } else {
                final int v = Integer.parseInt(line.getOptionValue('v', Integer.toString(Pep.V_PARSE)));
                if (v < 0) {
                    throw new PepException("verbosity < 0: " + v);
                }

                Pep.verbosity = v;
                final Map<ParserOption, Boolean> options = new EnumMap<ParserOption, Boolean>(
                        ParserOption.class);

                final Properties props = line.getOptionProperties("o");
                for (final Object key : props.keySet()) {
                    try {
                        options.put(ParserOption.valueOf(key.toString()),
                                Boolean.valueOf(props.get(key).toString()));
                    } catch (final IllegalArgumentException iae) {
                        Pep.printError("no option named " + key.toString());
                        Pep.printHelp(opts);
                        return;
                    }
                }

                final Pep pep = new Pep(options);
                // final Grammar grammar =
                // new GrammarParser(Pep.findGrammar(line
                // .getOptionValue('g'))).t.parse();

                final List<?> ts = line.getArgList();
                List<String> tokens = null;
                if (ts.isEmpty() || ts.get(0).equals("-")) {
                    tokens = Pep.readTokens(new Scanner(System.in));
                } else {
                    tokens = new ArrayList<String>(ts.size());
                    for (final Object t : ts) {
                        tokens.add(t.toString());
                    }
                }

                pep.lastParseStart = System.currentTimeMillis();
                // try {
                // pep.parse(grammar, tokens,
                // new Category(line.getOptionValue('s')));
                // } catch (final PepException ignore) {
                // // ignore here, we're listening
                // }
            }
        } catch (final ParseException pe) {
            Pep.printError("command-line syntax problem: " + pe.getMessage());
            Pep.printHelp(opts);
        }
    } catch (final PepException pe) {
        final Throwable cause = pe.getCause();
        Pep.printError((cause == null) ? pe : cause);
    } catch (final RuntimeException re) {
        Pep.printError(re);
    }
}

From source file:com.acapulcoapp.alloggiatiweb.FileReader.java

public static void main(String[] args) throws UnknownHostException, IOException {
    // TODO code application logic here

    SpringApplication app = new SpringApplication(AcapulcoappApp.class);
    SimpleCommandLinePropertySource source = new SimpleCommandLinePropertySource(args);
    addDefaultProfile(app, source);//from w w w  .j a v a  2 s .  c  o m

    ConfigurableApplicationContext context = app.run(args);

    initBeans(context);

    Map<LocalDate, List<List<String>>> map = new TreeMap<>();

    List<File> files = new ArrayList<>(FileUtils.listFiles(new File("/Users/chiccomask/Downloads/ALLOGGIATI"),
            new String[] { "txt" }, true));

    Collections.reverse(files);

    int count = 0;

    for (File file : files) {

        //            List<String> allLines = FileUtils.readLines(file, "windows-1252");
        List<String> allLines = FileUtils.readLines(file, "UTF-8");

        for (int i = 0; i < allLines.size();) {

            count++;

            List<String> record = new ArrayList<>();

            String line = allLines.get(i);
            String type = TIPO_ALLOGGIO.parse(line);

            switch (type) {
            case "16":
                record.add(line);
                i++;
                break;
            case "17": {
                record.add(line);
                boolean out = false;
                while (!out) {
                    i++;
                    if (i < allLines.size()) {
                        String subline = allLines.get(i);
                        String subtype = TIPO_ALLOGGIO.parse(subline);
                        if (!subtype.equals("19")) {
                            out = true;
                        } else {
                            record.add(subline);
                        }
                    } else {
                        out = true;
                    }
                }
                break;
            }
            case "18": {
                record.add(line);
                boolean out = false;
                while (!out) {
                    i++;
                    if (i < allLines.size()) {
                        String subline = allLines.get(i);
                        String subtype = TIPO_ALLOGGIO.parse(subline);
                        if (!subtype.equals("20")) {
                            out = true;
                        } else {
                            record.add(subline);
                        }
                    } else {
                        out = true;
                    }
                }
                break;
            }
            default:
                break;
            }

            LocalDate arrived = LocalDate.parse(DATA_ARRIVO.parse(line),
                    DateTimeFormatter.ofPattern(DATE_PATTERN));
            if (!map.containsKey(arrived)) {
                map.put(arrived, new ArrayList<>());
            }
            map.get(arrived).add(record);
        }
    }

    for (LocalDate date : map.keySet()) {

        System.out.println();
        System.out.println("process day " + date);

        for (List<String> record : map.get(date)) {

            System.out.println();
            System.out.println("process record ");
            for (String line : record) {
                System.out.println(line);
            }

            CheckinRecord checkinRecord = new CheckinRecord();

            //non lo setto per adesso
            String firstLine = record.get(0);

            String typeStr = TIPO_ALLOGGIO.parse(firstLine);
            CheckinType cht = checkinTypeRepository.find(typeStr);
            checkinRecord.setCheckinType(cht);

            int days = Integer.parseInt(PERMANENZA.parse(firstLine));
            checkinRecord.setDays(days);
            checkinRecord.setArrived(date);

            boolean isMain = true;

            List<Person> others = new ArrayList<>();

            for (String line : record) {
                Person p = extractPerson(line);

                if (p.getDistrictOfBirth() == null) {
                    System.out.println("district of birth not found " + p);
                }

                List<Person> duplicates = personRepository.findDuplicates(p.getSurname(), p.getName(),
                        p.getDateOfBirth());

                if (duplicates.isEmpty()) {
                    System.out.println("add new person " + p.getId() + " " + p);
                    personRepository.saveAndFlush(p);
                } else if (duplicates.size() == 1) {

                    Person found = duplicates.get(0);

                    if (p.getIdentityDocument() != null) {
                        //we sorted by date so we suppose 
                        //the file version is newer so we update the entity
                        p.setId(found.getId());
                        System.out.println("update person " + p.getId() + " " + p);
                        personRepository.saveAndFlush(p);

                    } else if (found.getIdentityDocument() != null) {
                        //on db there are more data so I use them.
                        p = found;
                        System.out.println("use already saved person " + p.getId() + " " + p);
                    } else {
                        p.setId(found.getId());
                        System.out.println("update person " + p.getId() + " " + p);
                        personRepository.saveAndFlush(p);
                    }

                } else {
                    throw new RuntimeException("More duplicated for " + p.getName());
                }

                if (isMain) {
                    checkinRecord.setMainPerson(p);
                    isMain = false;
                } else {
                    others.add(p);
                }
            }

            checkinRecord.setOtherPeople(new HashSet<>(others));

            if (checkinRecordRepository.alreadyExists(checkinRecord.getMainPerson(), date) != null) {
                System.out.println("already exists " + date + " p " + checkinRecord.getMainPerson());
            } else {
                System.out.println("save record ");
                checkinRecordRepository.saveAndFlush(checkinRecord);
            }
        }
    }

    //
    //            if (type.equals("16")) {
    //                List<String> record = new ArrayList<>();
    //                record.add(line);
    //                keepOpen = false;
    //            }
    //
    //            map.get(arrived).add(record);
    //        map.values().forEach((list) -> {
    //
    //            for (String line : list) {
    //
    //                Person p = null;
    //
    //                try {
    //
    //                    p = extractPerson(line);
    //
    //                    List<Person> duplicates = personRepository.findDuplicates(p.getSurname(), p.getName(), p.getDateOfBirth());
    //
    //                    if (duplicates.isEmpty()) {
    //                        personRepository.saveAndFlush(p);
    //
    //                    } else if (duplicates.size() > 1) {
    //                        System.out.println();
    //                        System.out.println("MULIPLE DUPLICATED");
    //
    //                        for (Person dd : duplicates) {
    //                            System.out.println(dd);
    //                        }
    //                        System.out.println("* " + p);
    //                        throw new RuntimeException();
    //                    } else {
    //
    ////                        if (!duplicates.get(0).getDistrictOfBirth().equals(p.getDistrictOfBirth())) {
    ////                        int index = 0;
    ////
    ////                        System.out.println();
    ////                        System.out.println("DUPLICATED");
    ////
    ////                        for (Person dd : duplicates) {
    ////                            System.out.println(dd);
    ////                            index++;
    ////                        }
    ////                        System.out.println("* " + p);
    ////                        System.out.println(file.getAbsolutePath() + " " + p);
    ////
    ////                        System.out.println();
    ////                        System.out.println();
    ////                        }
    ////                        duplicates.remove(0);
    ////                        personRepository.deleteInBatch(duplicates);
    ////                System.out.println();
    ////                System.out.println("Seleziona scelta");
    ////                Scanner s = new Scanner(System.in);
    ////                int selected;
    ////                try {
    ////                    selected = s.nextInt();
    ////                } catch (InputMismatchException e) {
    ////                    selected = 0;
    ////                }
    ////
    ////                if (duplicates.size() <= selected) {
    ////                    personRepository.deleteInBatch(duplicates);
    ////                    personRepository.saveAndFlush(p);
    ////                } else {
    ////                    duplicates.remove(selected);
    ////                    personRepository.deleteInBatch(duplicates);
    ////                }
    //                    }
    //
    //                } catch (Exception e) {
    //
    //                    System.out.println();
    ////                    System.out.println("ERROR READING lineCount=" + allLines.indexOf(line) + " line=" + line);
    ////                    System.out.println(file.getAbsolutePath());
    //                    System.out.println(p);
    //                    e.printStackTrace();
    //                    System.out.println();
    //                }
    //            }
    //        });
    context.registerShutdownHook();

    System.exit(0);
}

From source file:AmazonKinesisGet.java

public static void main(String[] args) throws Exception {
    init();/*from   www  . j  ava 2 s.c  o m*/

    final String myStreamName = "philsteststream";
    final Integer myStreamSize = 1;

    // list all of my streams
    ListStreamsRequest listStreamsRequest = new ListStreamsRequest();
    listStreamsRequest.setLimit(10);
    ListStreamsResult listStreamsResult = kinesisClient.listStreams(listStreamsRequest);
    List<String> streamNames = listStreamsResult.getStreamNames();
    while (listStreamsResult.isHasMoreStreams()) {
        if (streamNames.size() > 0) {
            listStreamsRequest.setExclusiveStartStreamName(streamNames.get(streamNames.size() - 1));
        }

        listStreamsResult = kinesisClient.listStreams(listStreamsRequest);

        streamNames.addAll(listStreamsResult.getStreamNames());

    }
    LOG.info("Printing my list of streams : ");

    // print all of my streams.
    if (!streamNames.isEmpty()) {
        System.out.println("List of my streams: ");
    }
    for (int i = 0; i < streamNames.size(); i++) {
        System.out.println(streamNames.get(i));
    }

    //System.out.println(streamNames.get(0));
    String myownstream = streamNames.get(0);

    // Retrieve the Shards from a Stream
    DescribeStreamRequest describeStreamRequest = new DescribeStreamRequest();
    describeStreamRequest.setStreamName(myownstream);
    DescribeStreamResult describeStreamResult;
    List<Shard> shards = new ArrayList<>();
    String lastShardId = null;

    do {
        describeStreamRequest.setExclusiveStartShardId(lastShardId);
        describeStreamResult = kinesisClient.describeStream(describeStreamRequest);
        shards.addAll(describeStreamResult.getStreamDescription().getShards());
        if (shards.size() > 0) {
            lastShardId = shards.get(shards.size() - 1).getShardId();
        }
    } while (describeStreamResult.getStreamDescription().getHasMoreShards());

    // Get Data from the Shards in a Stream
    // Hard-coded to use only 1 shard
    String shardIterator;
    GetShardIteratorRequest getShardIteratorRequest = new GetShardIteratorRequest();
    getShardIteratorRequest.setStreamName(myownstream);
    //get(0) shows hardcoded to 1 stream
    getShardIteratorRequest.setShardId(shards.get(0).getShardId());
    // using TRIM_HORIZON but could use alternatives
    getShardIteratorRequest.setShardIteratorType("TRIM_HORIZON");

    GetShardIteratorResult getShardIteratorResult = kinesisClient.getShardIterator(getShardIteratorRequest);
    shardIterator = getShardIteratorResult.getShardIterator();

    // Continuously read data records from shard.
    List<Record> records;

    while (true) {
        // Create new GetRecordsRequest with existing shardIterator.
        // Set maximum records to return to 1000.

        GetRecordsRequest getRecordsRequest = new GetRecordsRequest();
        getRecordsRequest.setShardIterator(shardIterator);
        getRecordsRequest.setLimit(1000);

        GetRecordsResult result = kinesisClient.getRecords(getRecordsRequest);

        // Put result into record list. Result may be empty.
        records = result.getRecords();

        // Print records
        for (Record record : records) {
            ByteBuffer byteBuffer = record.getData();
            System.out.println(String.format("Seq No: %s - %s", record.getSequenceNumber(),
                    new String(byteBuffer.array())));
        }

        try {
            Thread.sleep(1000);
        } catch (InterruptedException exception) {
            throw new RuntimeException(exception);
        }

        shardIterator = result.getNextShardIterator();
    }

}

From source file:com.github.xmltopdf.JasperPdfGenerator.java

/**.
 * @param args/*from ww w  .  j  a va  2 s.  c o  m*/
 *            the arguments
 * @throws IOException in case IO error
 */
public static void main(String[] args) throws IOException {
    if (args.length == 0) {
        LOG.info(null, USAGE);
        return;
    }
    List<String> templates = new ArrayList<String>();
    List<String> xmls = new ArrayList<String>();
    List<String> types = new ArrayList<String>();
    for (String arg : args) {
        if (arg.endsWith(".jrxml")) {
            templates.add(arg);
        } else if (arg.endsWith(".xml")) {
            xmls.add(arg);
        } else if (arg.startsWith(DOC_TYPE)) {
            types = Arrays
                    .asList(arg.substring(DOC_TYPE.length()).replaceAll("\\s+", "").toUpperCase().split(","));
        }
    }
    if (templates.isEmpty()) {
        LOG.info(null, USAGE);
        return;
    }
    if (types.isEmpty()) {
        types.add("PDF");
    }
    for (String type : types) {
        ByteArrayOutputStream os = new ByteArrayOutputStream();
        if (DocType.valueOf(type) != null) {
            new JasperPdfGenerator().createDocument(templates, xmls, os, DocType.valueOf(type));
            os.writeTo(
                    new FileOutputStream(templates.get(0).replaceFirst("\\.jrxml$", "." + type.toLowerCase())));
        }
    }
}

From source file:diffhunter.DiffHunter.java

/**
 * @param args the command line arguments
 * @throws org.apache.commons.cli.ParseException
 * @throws java.io.IOException/*  w  ww.  java2  s  .  c om*/
 */
public static void main(String[] args) throws ParseException, IOException {

    //String test_ = Paths.get("J:\\VishalData\\additional\\", "Sasan" + "_BDB").toAbsolutePath().toString();

    // TODO code application logic here
    /*args = new String[]
    {
    "-i", "-b", "J:\\VishalData\\additional\\Ptbp2_E18_5_cortex_CLIP_mm9_plus_strand_sorted.bed", "-r", "J:\\VishalData\\additional\\mouse_mm9.txt", "-o", "J:\\VishalData"
    };*/

    /*args = new String[]
    {
    "-c", "-r", "J:\\VishalData\\additional\\mouse_mm9.txt", "-1", "J:\\VishalData\\Ptbp2_Adult_testis_CLIP_mm9_plus_strand_sorted_BDB", "-2", "J:\\VishalData\\Ptbp2_E18_5_cortex_CLIP_mm9_plus_strand_sorted_BDB", "-w", "200", "-s", "50", "-o", "J:\\VishalData"
    };*/
    Options options = new Options();

    // add t option
    options.addOption("i", "index", false, "Indexing BED files.");
    options.addOption("b", "bed", true, "bed file to be indexed");
    options.addOption("o", "output", true, "Folder that the index/comparison file will be created.");
    options.addOption("r", "reference", true, "Reference annotation file to be used for indexing");
    options.addOption("c", "compare", false, "Finding differences between two conditions");
    options.addOption("1", "first", true, "First sample index location");
    options.addOption("2", "second", true, "Second sample index location");
    options.addOption("w", "window", true, "Length of window for identifying differences");
    options.addOption("s", "sliding", true, "Length of sliding");

    CommandLineParser parser = new BasicParser();
    CommandLine cmd = parser.parse(options, args);

    boolean indexing = false;
    boolean comparing = false;

    //Indexing!
    if (cmd.hasOption("i")) {
        //if(cmd.hasOption("1"))
        //System.err.println("sasan");

        //System.out.println("sasa");
        indexing = true;

    } else if (cmd.hasOption("c")) {
        //System.err.println("");
        comparing = true;

    } else {
        //System.err.println("Option is not deteced.");
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp("diffhunter", options);
        return;
    }

    //Indexing is selected
    //
    if (indexing == true) {
        //Since indexing is true.
        //User have to provide file for indexing.
        if (!(cmd.hasOption("o") || cmd.hasOption("r") || cmd.hasOption("b"))) {
            HelpFormatter formatter = new HelpFormatter();
            formatter.printHelp("diffhunter", options);
            return;
        }
        String bedfile_ = cmd.getOptionValue("b");
        String reference_file = cmd.getOptionValue("r");
        String folder_loc = cmd.getOptionValue("o");

        String sample_name = FilenameUtils.getBaseName(bedfile_);

        try (Database B2 = BerkeleyDB_Box.Get_BerkeleyDB(
                Paths.get(folder_loc, sample_name + "_BDB").toAbsolutePath().toString(), true, sample_name)) {
            Indexer indexing_ = new Indexer(reference_file);
            indexing_.Make_Index(B2, bedfile_,
                    Paths.get(folder_loc, sample_name + "_BDB").toAbsolutePath().toString());
            B2.close();

        }
    } else if (comparing == true) {
        if (!(cmd.hasOption("o") || cmd.hasOption("w") || cmd.hasOption("s") || cmd.hasOption("1")
                || cmd.hasOption("2"))) {
            HelpFormatter formatter = new HelpFormatter();
            formatter.printHelp("diffhunter", options);
            return;
        }
        String folder_loc = cmd.getOptionValue("o");
        int window_ = Integer.parseInt(cmd.getOptionValue("w"));
        //int window_=600;

        int slide_ = Integer.parseInt(cmd.getOptionValue("s"));

        String first = cmd.getOptionValue("1").replace("_BDB", "");
        String second = cmd.getOptionValue("2").replace("_BDB", "");
        String reference_file = cmd.getOptionValue("r");
        //String folder_loc=cmd.getOptionValue("o");

        String sample_name_first = FilenameUtils.getBaseName(first);
        String sample_name_second = FilenameUtils.getBaseName(second);

        Database B1 = BerkeleyDB_Box.Get_BerkeleyDB(first + "_BDB", false, sample_name_first);
        Database B2 = BerkeleyDB_Box.Get_BerkeleyDB(second + "_BDB", false, sample_name_second);

        List<String> first_condition_genes = Files
                .lines(Paths.get(first + "_BDB", sample_name_first + ".txt").toAbsolutePath())
                .collect(Collectors.toList());
        List<String> second_condition_genes = Files
                .lines(Paths.get(second + "_BDB", sample_name_second + ".txt").toAbsolutePath())
                .collect(Collectors.toList());
        System.out.println("First and second condition are loaded!!! ");
        List<String> intersection_ = new ArrayList<>(first_condition_genes);
        intersection_.retainAll(second_condition_genes);

        BufferedWriter output = new BufferedWriter(
                new FileWriter(Paths.get(folder_loc, "differences_" + window_ + "_s" + slide_ + "_c" + ".txt")
                        .toAbsolutePath().toString(), false));
        List<Result_Window> final_results = Collections.synchronizedList(new ArrayList<>());
        Worker_New worker_class = new Worker_New();
        worker_class.Read_Reference(reference_file);

        while (!intersection_.isEmpty()) {
            List<String> selected_genes = new ArrayList<>();
            //if (intersection_.size()<=10000){selected_genes.addAll(intersection_.subList(0, intersection_.size()));}
            //else selected_genes.addAll(intersection_.subList(0, 10000));
            if (intersection_.size() <= intersection_.size()) {
                selected_genes.addAll(intersection_.subList(0, intersection_.size()));
            } else {
                selected_genes.addAll(intersection_.subList(0, intersection_.size()));
            }
            intersection_.removeAll(selected_genes);
            //System.out.println("Intersection count is:"+intersection_.size());
            //final List<Result_Window> resultssss_=new ArrayList<>();
            IntStream.range(0, selected_genes.size()).parallel().forEach(i -> {
                System.out.println(selected_genes.get(i) + "\tprocessing......");
                String gene_of_interest = selected_genes.get(i);//"ENSG00000142657|PGD";//intersection_.get(6);////"ENSG00000163395|IGFN1";//"ENSG00000270066|SCARNA2";
                int start = worker_class.dic_genes.get(gene_of_interest).start_loc;
                int end = worker_class.dic_genes.get(gene_of_interest).end_loc;

                Map<Integer, Integer> first_ = Collections.EMPTY_MAP;
                try {
                    first_ = BerkeleyDB_Box.Get_Coord_Read(B1, gene_of_interest);
                } catch (IOException | ClassNotFoundException ex) {
                    Logger.getLogger(DiffHunter.class.getName()).log(Level.SEVERE, null, ex);
                }

                Map<Integer, Integer> second_ = Collections.EMPTY_MAP;
                try {
                    second_ = BerkeleyDB_Box.Get_Coord_Read(B2, gene_of_interest);
                } catch (IOException | ClassNotFoundException ex) {
                    Logger.getLogger(DiffHunter.class.getName()).log(Level.SEVERE, null, ex);
                }
                List<Window> top_windows_first = worker_class.Get_Top_Windows(window_, first_, slide_);
                List<Window> top_windows_second = worker_class.Get_Top_Windows(window_, second_, slide_);
                //System.out.println("passed for window peak call for gene \t"+selected_genes.get(i));
                // System.out.println("top_window_first_Count\t"+top_windows_first.size());
                // System.out.println("top_window_second_Count\t"+top_windows_second.size());
                if (top_windows_first.isEmpty() && top_windows_second.isEmpty()) {
                    return;
                }

                List<Result_Window> res_temp = new Worker_New().Get_Significant_Windows(gene_of_interest, start,
                        end, top_windows_first, top_windows_second, second_, first_, sample_name_first,
                        sample_name_second, 0.01);
                if (!res_temp.isEmpty()) {
                    final_results.addAll(res_temp);//final_results.addAll(worker_class.Get_Significant_Windows(gene_of_interest, start, end, top_windows_first, top_windows_second, second_, first_, first_condition, second_condition, 0.01));

                } //System.out.println(selected_genes.get(i)+"\tprocessed.");

            });

            /*selected_genes.parallelStream().forEach(i ->
             {
                    
                    
             });*/
            List<Double> pvals = new ArrayList<>();

            for (int i = 0; i < final_results.size(); i++) {
                pvals.add(final_results.get(i).p_value);
            }
            List<Double> qvals = MultipleTestCorrection.benjaminiHochberg(pvals);

            System.out.println("Writing to file...");
            output.append("Gene_Symbol\tContributing_Sample\tStart\tEnd\tOddsRatio\tp_Value\tFDR");
            output.newLine();

            for (int i = 0; i < final_results.size(); i++) {
                Result_Window item = final_results.get(i);
                output.append(item.associated_gene_symbol + "\t" + item.contributing_windows + "\t"
                        + item.start_loc + "\t" + item.end_loc + "\t" + item.oddsratio_ + "\t" + item.p_value
                        + "\t" + qvals.get(i)); //+ "\t" + item.average_other_readcount_cotributing + "\t" + item.average_other_readcount_cotributing + "\t" + item.average_window_readcount_non + "\t" + item.average_other_readcount_non);
                output.newLine();
            }

            /* for (Result_Window item : final_results)
             {
            output.append(item.associated_gene_symbol + "\t" + item.contributing_windows + "\t" + item.start_loc + "\t" + item.end_loc + "\t" + item.oddsratio_ + "\t" + item.p_value); //+ "\t" + item.average_other_readcount_cotributing + "\t" + item.average_other_readcount_cotributing + "\t" + item.average_window_readcount_non + "\t" + item.average_other_readcount_non);
            output.newLine();
             }
               */
            final_results.clear();

        }
        output.close();

    }
    System.out.println("Done.");

}

From source file:bear.core.BearMain.java

/**
 * -VbearMain.appConfigDir=src/main/groovy/examples -VbearMain.buildDir=.bear/classes -VbearMain.script=dumpSampleGrid -VbearMain.projectClass=SecureSocialDemoProject -VbearMain.propertiesFile=.bear/test.properties
 */// ww w  .  j a v  a 2  s .co m
public static void main(String[] args) throws Exception {
    int i = ArrayUtils.indexOf(args, "--log-level");

    if (i != -1) {
        LoggingBooter.changeLogLevel(LogManager.ROOT_LOGGER_NAME, Level.toLevel(args[i + 1]));
    }

    i = ArrayUtils.indexOf(args, "-q");

    if (i != -1) {
        LoggingBooter.changeLogLevel(LogManager.ROOT_LOGGER_NAME, Level.WARN);
    }

    GlobalContext global = GlobalContext.getInstance();

    BearMain bearMain = null;

    try {
        bearMain = new BearMain(global, getCompilerManager(), args);
    } catch (Exception e) {
        if (e.getClass().getSimpleName().equals("MissingRequiredOptionException")) {
            System.out.println(e.getMessage());
        } else {
            Throwables.getRootCause(e).printStackTrace();
        }

        System.exit(-1);
    }

    if (bearMain.checkHelpAndVersion()) {
        return;
    }

    AppOptions2 options2 = bearMain.options;

    if (options2.has(AppOptions2.UNPACK_DEMOS)) {
        String filesAsText = ProjectGenerator.readResource("/demoFiles.txt");

        int count = 0;

        for (String resource : filesAsText.split("::")) {
            File dest = new File(BEAR_DIR + resource);
            System.out.printf("copying %s to %s...%n", resource, dest);

            writeStringToFile(dest, ProjectGenerator.readResource(resource));

            count++;
        }

        System.out.printf("extracted %d files%n", count);

        return;
    }

    if (options2.has(AppOptions2.CREATE_NEW)) {
        String dashedTitle = options2.get(AppOptions2.CREATE_NEW);

        String user = options2.get(AppOptions2.USER);
        String pass = options2.get(AppOptions2.PASSWORD);

        List<String> hosts = options2.getList(AppOptions2.HOSTS);

        List<String> template;

        if (options2.has(AppOptions2.TEMPLATE)) {
            template = options2.getList(AppOptions2.TEMPLATE);
        } else {
            template = emptyList();
        }

        ProjectGenerator g = new ProjectGenerator(dashedTitle, user, pass, hosts, template);

        if (options2.has(AppOptions2.ORACLE_USER)) {
            g.oracleUser = options2.get(AppOptions2.ORACLE_USER);
        }

        if (options2.has(AppOptions2.ORACLE_PASSWORD)) {
            g.oraclePassword = options2.get(AppOptions2.ORACLE_PASSWORD);
        }

        File projectFile = new File(BEAR_DIR, g.getProjectTitle() + ".groovy");
        File pomFile = new File(BEAR_DIR, "pom.xml");

        writeStringToFile(projectFile, g.processTemplate("TemplateProject.template"));

        writeStringToFile(new File(BEAR_DIR, dashedTitle + ".properties"),
                g.processTemplate("project-properties.template"));
        writeStringToFile(new File(BEAR_DIR, "demos.properties"),
                g.processTemplate("project-properties.template"));
        writeStringToFile(new File(BEAR_DIR, "bear-fx.properties"),
                g.processTemplate("bear-fx.properties.template"));

        writeStringToFile(pomFile, g.generatePom(dashedTitle));

        System.out.printf("Created project file: %s%n", projectFile.getPath());
        System.out.printf("Created maven pom: %s%n", pomFile.getPath());

        System.out.println("\nProject files have been created. You may now: " + "\n a) Run `bear "
                + g.getShortName() + ".ls` to quick-test your minimal setup"
                + "\n b) Import the project to IDE or run smoke tests, find more details at the project wiki: https://github.com/chaschev/bear/wiki/.");

        return;
    }

    Bear bear = global.bear;

    if (options2.has(AppOptions2.QUIET)) {
        global.put(bear.quiet, true);
        LoggingBooter.changeLogLevel(LogManager.ROOT_LOGGER_NAME, Level.WARN);
    }

    if (options2.has(AppOptions2.USE_UI)) {
        global.put(bear.useUI, true);
    }

    if (options2.has(AppOptions2.NO_UI)) {
        global.put(bear.useUI, false);
    }

    List<?> list = options2.getOptionSet().nonOptionArguments();

    if (list.size() > 1) {
        throw new IllegalArgumentException("too many arguments: " + list + ", "
                + "please specify an invoke line, project.method(arg1, arg2)");
    }

    if (list.isEmpty()) {
        throw new UnsupportedOperationException("todo implement running a single project");
    }

    String invokeLine = (String) list.get(0);

    String projectName;
    String method;

    if (invokeLine.contains(".")) {
        projectName = StringUtils.substringBefore(invokeLine, ".");
        method = StringUtils.substringAfter(invokeLine, ".");
    } else {
        projectName = invokeLine;
        method = null;
    }

    if (method == null || method.isEmpty())
        method = "deploy()";
    if (!method.contains("("))
        method += "()";

    Optional<CompiledEntry<? extends BearProject>> optional = bearMain.compileManager.findProject(projectName);

    if (!optional.isPresent()) {
        throw new IllegalArgumentException("project was not found: " + projectName + ", loaded classes: \n"
                + Joiner.on("\n").join(bearMain.compileManager.findProjects()) + ", searched in: "
                + bearMain.compileManager.getSourceDirs() + ", ");
    }

    BearProject project = OpenBean.newInstance(optional.get().aClass).injectMain(bearMain);

    GroovyShell shell = new GroovyShell();

    shell.setVariable("project", project);
    shell.evaluate("project." + method);
}

From source file:com.bericotech.clavin.index.IndexDirectoryBuilder.java

/**
 * Turns a GeoNames gazetteer file into a Lucene index, and adds
 * some supplementary gazetteer records at the end.
 *
 * @param args              not used//from  w w w.j av  a 2  s.  c om
 * @throws IOException
 */
public static void main(String[] args) throws IOException {
    Options options = getOptions();
    CommandLine cmd = null;
    CommandLineParser parser = new GnuParser();
    try {
        cmd = parser.parse(options, args);
    } catch (ParseException pe) {
        LOG.error(pe.getMessage());
        printHelp(options);
        System.exit(-1);
    }

    if (cmd.hasOption(HELP_OPTION)) {
        printHelp(options);
        System.exit(0);
    }

    String indexPath = cmd.getOptionValue(INDEX_PATH_OPTION, DEFAULT_INDEX_DIRECTORY);
    String[] gazetteerPaths = cmd.getOptionValues(GAZETTEER_FILES_OPTION);
    if (gazetteerPaths == null || gazetteerPaths.length == 0) {
        gazetteerPaths = DEFAULT_GAZETTEER_FILES;
    }
    boolean replaceIndex = cmd.hasOption(REPLACE_INDEX_OPTION);
    boolean fullAncestry = cmd.hasOption(FULL_ANCESTRY_OPTION);

    File idir = new File(indexPath);
    // if the index directory exists, delete it if we are replacing, otherwise
    // exit gracefully
    if (idir.exists()) {
        if (replaceIndex) {
            LOG.info("Replacing index: {}", idir.getAbsolutePath());
            FileUtils.deleteDirectory(idir);
        } else {
            LOG.info("{} exists. Remove the directory and try again.", idir.getAbsolutePath());
            System.exit(-1);
        }
    }

    List<File> gazetteerFiles = new ArrayList<File>();
    for (String gp : gazetteerPaths) {
        File gf = new File(gp);
        if (gf.isFile() && gf.canRead()) {
            gazetteerFiles.add(gf);
        } else {
            LOG.info("Unable to read Gazetteer file: {}", gf.getAbsolutePath());
        }
    }
    if (gazetteerFiles.isEmpty()) {
        LOG.error("No Gazetteer files found.");
        System.exit(-1);
    }

    String altNamesPath = cmd.getOptionValue(ALTERNATE_NAMES_OPTION);
    File altNamesFile = altNamesPath != null ? new File(altNamesPath) : null;
    if (altNamesFile != null && !(altNamesFile.isFile() && altNamesFile.canRead())) {
        LOG.error("Unable to read alternate names file: {}", altNamesPath);
        System.exit(-1);
    }

    new IndexDirectoryBuilder(fullAncestry).buildIndex(idir, gazetteerFiles, altNamesFile);
}

From source file:de.huxhorn.lilith.Lilith.java

public static void main(String[] args) {
    {//from  w w w. j a va  2  s .  co m
        // initialize java.util.logging to use slf4j...
        Handler handler = new Slf4JHandler();
        java.util.logging.Logger rootLogger = java.util.logging.Logger.getLogger("");
        rootLogger.addHandler(handler);
        rootLogger.setLevel(java.util.logging.Level.WARNING);
    }

    StringBuilder appTitle = new StringBuilder();
    appTitle.append(APP_NAME).append(" V").append(APP_VERSION);
    if (APP_SNAPSHOT) {
        // always append timestamp for SNAPSHOT
        appTitle.append(" (").append(APP_TIMESTAMP_DATE).append(")");
    }

    CommandLineArgs cl = new CommandLineArgs();
    JCommander commander = new JCommander(cl);
    Cat cat = new Cat();
    commander.addCommand(Cat.NAME, cat);
    Tail tail = new Tail();
    commander.addCommand(Tail.NAME, tail);
    Filter filter = new Filter();
    commander.addCommand(Filter.NAME, filter);
    Index index = new Index();
    commander.addCommand(Index.NAME, index);
    Md5 md5 = new Md5();
    commander.addCommand(Md5.NAME, md5);
    Help help = new Help();
    commander.addCommand(Help.NAME, help);

    try {
        commander.parse(args);
    } catch (ParameterException ex) {
        printAppInfo(appTitle.toString(), false);
        System.out.println(ex.getMessage() + "\n");
        printHelp(commander);
        System.exit(-1);
    }
    if (cl.verbose) {
        if (!APP_SNAPSHOT) {
            // timestamp is always appended for SNAPSHOT
            // don't append it twice
            appTitle.append(" (").append(APP_TIMESTAMP_DATE).append(")");
        }
        appTitle.append(" - ").append(APP_REVISION);
    }

    String appTitleString = appTitle.toString();
    if (cl.showHelp) {
        printAppInfo(appTitleString, false);
        printHelp(commander);
        System.exit(0);
    }

    String command = commander.getParsedCommand();
    if (!Tail.NAME.equals(command) && !Cat.NAME.equals(command) && !Filter.NAME.equals(command)) // don't print info in case of cat, tail or filter
    {
        printAppInfo(appTitleString, true);
    }

    if (cl.logbackConfig != null) {
        File logbackFile = new File(cl.logbackConfig);
        if (!logbackFile.isFile()) {
            System.out.println(logbackFile.getAbsolutePath() + " is not a valid file.");
            System.exit(-1);
        }
        try {
            initLogbackConfig(logbackFile.toURI().toURL());
        } catch (MalformedURLException e) {
            System.out.println("Failed to convert " + logbackFile.getAbsolutePath() + " to URL. " + e);
            System.exit(-1);
        }
    } else if (cl.verbose) {
        initVerboseLogging();
    }

    if (cl.printBuildTimestamp) {
        System.out.println("Build-Date     : " + APP_TIMESTAMP_DATE);
        System.out.println("Build-Revision : " + APP_REVISION);
        System.out.println("Build-Timestamp: " + APP_TIMESTAMP);
        System.exit(0);
    }

    if (Help.NAME.equals(command)) {
        commander.usage();
        if (help.commands == null || help.commands.size() == 0) {
            commander.usage(Help.NAME);
        } else {
            Map<String, JCommander> commands = commander.getCommands();
            for (String current : help.commands) {
                if (commands.containsKey(current)) {
                    commander.usage(current);
                } else {
                    System.out.println("Unknown command '" + current + "'!");
                }
            }
        }
        System.exit(0);
    }

    if (Md5.NAME.equals(command)) {
        List<String> files = md5.files;
        if (files == null || files.isEmpty()) {
            printHelp(commander);
            System.out.println("Missing files!");
            System.exit(-1);
        }
        boolean error = false;
        for (String current : files) {
            if (!CreateMd5Command.createMd5(new File(current))) {
                error = true;
            }
        }
        if (error) {
            System.exit(-1);
        }
        System.exit(0);
    }

    if (Index.NAME.equals(command)) {
        if (!cl.verbose && cl.logbackConfig == null) {
            initCLILogging();
        }
        List<String> files = index.files;
        if (files == null || files.size() == 0) {
            printHelp(commander);
            System.exit(-1);
        }
        boolean error = false;
        for (String current : files) {
            if (!IndexCommand.indexLogFile(new File(current))) {
                error = true;
            }
        }
        if (error) {
            System.exit(-1);
        }
        System.exit(0);
    }

    if (Cat.NAME.equals(command)) {
        if (!cl.verbose && cl.logbackConfig == null) {
            initCLILogging();
        }
        List<String> files = cat.files;
        if (files == null || files.size() != 1) {
            printHelp(commander);
            System.exit(-1);
        }
        if (CatCommand.catFile(new File(files.get(0)), cat.pattern, cat.numberOfLines)) {
            System.exit(0);
        }
        System.exit(-1);
    }

    if (Tail.NAME.equals(command)) {
        if (!cl.verbose && cl.logbackConfig == null) {
            initCLILogging();
        }
        List<String> files = tail.files;
        if (files == null || files.size() != 1) {
            printHelp(commander);
            System.exit(-1);
        }
        if (TailCommand.tailFile(new File(files.get(0)), tail.pattern, tail.numberOfLines, tail.keepRunning)) {
            System.exit(0);
        }
        System.exit(-1);
    }

    if (Filter.NAME.equals(command)) {
        if (!cl.verbose && cl.logbackConfig == null) {
            initCLILogging();
        }
        if (FilterCommand.filterFile(new File(filter.input), new File(filter.output),
                new File(filter.condition), filter.searchString, filter.pattern, filter.overwrite,
                filter.keepRunning, filter.exclusive)) {
            System.exit(0);
        }
        System.exit(-1);
    }

    if (cl.flushPreferences) {
        flushPreferences();
    }

    if (cl.exportPreferencesFile != null) {
        exportPreferences(cl.exportPreferencesFile);
    }

    if (cl.importPreferencesFile != null) {
        importPreferences(cl.importPreferencesFile);
    }

    if (cl.exportPreferencesFile != null || cl.importPreferencesFile != null) {
        System.exit(0);
    }

    if (cl.flushLicensed) {
        flushLicensed();
    }

    startLilith(appTitleString);
}