Example usage for java.util Iterator hasNext

List of usage examples for java.util Iterator hasNext

Introduction

In this page you can find the example usage for java.util Iterator hasNext.

Prototype

boolean hasNext();

Source Link

Document

Returns true if the iteration has more elements.

Usage

From source file:tsp.TSPTestSpring.java

public static void main(String[] args) throws IOException {

    ApplicationContext context = new ClassPathXmlApplicationContext("ApplicationContext.xml");
    ITSPAlgorithm tspBruteForce = (ITSPAlgorithm) context.getBean("tspBruteForce");
    ITSPAlgorithm tspNearestNeighbor = (ITSPAlgorithm) context.getBean("tspNearestNeighbor");
    ITSPAlgorithm tspRandomSelection = (ITSPAlgorithm) context.getBean("tspRandomSelection");
    ITSPAlgorithm tspGeneticAlgorithm = (ITSPAlgorithm) context.getBean("tspGeneticAlgorithm");

    // test// w w  w.  j  ava 2 s .  c o m
    ITSPAlgorithm tspGeneticAlgorithm2 = (ITSPAlgorithm) context.getBean("tspGeneticAlgorithm");
    if (tspGeneticAlgorithm == tspGeneticAlgorithm2)
        System.out.println("[TEST] The Same instance!!!");

    List<TSPPath> bestPathList;
    Iterator it;

    tspBruteForce.getGraph().printGraph();

    // Brute Force
    // if (g.getNumVertex()>100) return;
    System.out.printf("The Best Routes Found By Brute Force:\n");
    bestPathList = tspBruteForce.getBestPathList(3);
    it = bestPathList.iterator();
    while (it.hasNext()) {
        TSPPath path = ((TSPPath) it.next());
        path.printPathStartingFrom(0);
    }
    System.out.println("");

    // Select the best XXX routes from a randomly generated sample pool
    System.out.printf("The Best Routes Found (Approximation By Random Selection and Ranking):\n");
    // System.out.printf("Sample Size: %d\n", tspRandomSelection.getSampleSize());
    bestPathList = tspRandomSelection.getBestPathList(3);
    it = bestPathList.iterator();
    while (it.hasNext()) {
        TSPPath path = ((TSPPath) it.next());
        path.printPathStartingFrom(0);
    }
    System.out.println("");

    // Select the best XXX routes by Nearest Neighbor
    System.out.printf("The Best Routes Found (Approximation By Nearest Neighbor):\n");
    bestPathList = tspNearestNeighbor.getBestPathList(3);
    it = bestPathList.iterator();
    while (it.hasNext()) {
        TSPPath path = ((TSPPath) it.next());
        path.printPathStartingFrom(0);
    }
    System.out.println("");

    // Select the best XXX routes by Genetic Algorithm
    System.out.printf("The Best Routes Found (Approximation By Genetic Algorithm):\n");
    // System.out.printf("Population Size: %d\n", tspGeneticAlgorithm.getPopSize());
    bestPathList = tspGeneticAlgorithm.getBestPathList(3);
    it = bestPathList.iterator();
    while (it.hasNext()) {
        TSPPath path = ((TSPPath) it.next());
        path.printPathStartingFrom(0);
    }
    System.out.println("");

}

From source file:enrichment.Disambiguate.java

/**prerequisites:
 * cd silk_2.5.3/*_links// www.  j  a v  a  2s.  com
 * cat *.nt|sort  -t' ' -k3   > $filename
 * 
 * @param args $filename
 * @throws IOException
 * @throws URISyntaxException
 */
public static void main(String[] args) {
    File file = new File(args[0]);
    if (file.isDirectory()) {
        args = file.list(new OnlyExtFilenameFilter("nt"));
    }

    BufferedReader in;
    for (int q = 0; q < args.length; q++) {
        String filename = null;
        if (file.isDirectory()) {
            filename = file.getPath() + File.separator + args[q];
        } else {
            filename = args[q];
        }
        try {
            FileWriter output = new FileWriter(filename + "_disambiguated.nt");
            String prefix = "@prefix rdrel: <http://rdvocab.info/RDARelationshipsWEMI/> .\n"
                    + "@prefix dbpedia:    <http://de.dbpedia.org/resource/> .\n"
                    + "@prefix frbr:   <http://purl.org/vocab/frbr/core#> .\n"
                    + "@prefix lobid: <http://lobid.org/resource/> .\n"
                    + "@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .\n"
                    + "@prefix foaf: <http://xmlns.com/foaf/0.1/> .\n"
                    + "@prefix mo: <http://purl.org/ontology/mo/> .\n"
                    + "@prefix wikipedia: <https://de.wikipedia.org/wiki/> .";
            output.append(prefix + "\n\n");
            in = new BufferedReader(new InputStreamReader(new FileInputStream(filename)));

            HashMap<String, HashMap<String, ArrayList<String>>> hm = new HashMap<String, HashMap<String, ArrayList<String>>>();
            String s;
            HashMap<String, ArrayList<String>> hmLobid = new HashMap<String, ArrayList<String>>();
            Stack<String> old_object = new Stack<String>();

            while ((s = in.readLine()) != null) {
                String[] triples = s.split(" ");
                String object = triples[2].substring(1, triples[2].length() - 1);
                if (old_object.size() > 0 && !old_object.firstElement().equals(object)) {
                    hmLobid = new HashMap<String, ArrayList<String>>();
                    old_object = new Stack<String>();
                }
                old_object.push(object);
                String subject = triples[0].substring(1, triples[0].length() - 1);
                System.out.print("\nSubject=" + object);
                System.out.print("\ntriples[2]=" + triples[2]);
                hmLobid.put(subject, getAllCreators(new URI(subject)));
                hm.put(object, hmLobid);

            }
            // get all dbpedia resources
            for (String key_one : hm.keySet()) {
                System.out.print("\n==============\n==== " + key_one + "\n===============");
                int resources_cnt = hm.get(key_one).keySet().size();
                ArrayList<String>[] creators = new ArrayList[resources_cnt];
                HashMap<String, Integer> creators_backed = new HashMap<String, Integer>();
                int x = 0;
                // get all lobid_resources subsumed under the dbpedia resource
                for (String subject_uri : hm.get(key_one).keySet()) {
                    creators[x] = new ArrayList<String>();
                    System.out.print("\n     subject_uri=" + subject_uri);
                    Iterator<String> ite = hm.get(key_one).get(subject_uri).iterator();
                    int y = 0;
                    // get all creators of the lobid resource
                    while (ite.hasNext()) {
                        String creator = ite.next();
                        System.out.print("\n          " + creator);
                        if (creators_backed.containsKey(creator)) {
                            y = creators_backed.get(creator);
                        } else {
                            y = creators_backed.size();
                            creators_backed.put(creator, y);
                        }
                        while (creators[x].size() <= y) {
                            creators[x].add("-");
                        }
                        creators[x].set(y, creator);
                        y++;
                    }
                    x++;
                }
                if (creators_backed.size() == 1) {
                    System.out
                            .println("\n" + "Every resource pointing to " + key_one + " has the same creator!");
                    for (String key_two : hm.get(key_one).keySet()) {
                        output.append("<" + key_two + "> rdrel:workManifested <" + key_one + "> .\n");
                        output.append("<" + key_two + ">  mo:wikipedia <"
                                + key_one.replaceAll("dbpedia\\.org/resource", "wikipedia\\.org/wiki")
                                + "> .\n");
                    }
                } /*else  {
                    for (int a = 0; a < creators.length; a++) {
                       System.out.print(creators[a].toString()+",");
                    }
                  }*/
            }

            output.flush();
            if (output != null) {
                output.close();
            }
        } catch (Exception e) {
            System.out.print("Exception while working on " + filename + ": \n");
            e.printStackTrace(System.out);
        }
    }
}

From source file:ConsumerTool.java

public static void main(String[] args) {
    ArrayList<ConsumerTool> threads = new ArrayList();
    ConsumerTool consumerTool = new ConsumerTool();
    String[] unknown = CommandLineSupport.setOptions(consumerTool, args);
    if (unknown.length > 0) {
        System.out.println("Unknown options: " + Arrays.toString(unknown));
        System.exit(-1);//from w  ww  . j  av a  2 s  .  c o m
    }
    consumerTool.showParameters();
    for (int threadCount = 1; threadCount <= parallelThreads; threadCount++) {
        consumerTool = new ConsumerTool();
        CommandLineSupport.setOptions(consumerTool, args);
        consumerTool.start();
        threads.add(consumerTool);
    }

    while (true) {
        Iterator<ConsumerTool> itr = threads.iterator();
        int running = 0;
        while (itr.hasNext()) {
            ConsumerTool thread = itr.next();
            if (thread.isAlive()) {
                running++;
            }
        }

        if (running <= 0) {
            System.out.println("All threads completed their work");
            break;
        }

        try {
            Thread.sleep(1000);
        } catch (Exception e) {
        }
    }
    Iterator<ConsumerTool> itr = threads.iterator();
    while (itr.hasNext()) {
        ConsumerTool thread = itr.next();
    }
}

From source file:edu.jhu.hlt.concrete.ingesters.gigaword.GigawordGzProcessor.java

public static void main(String... args) {
    Thread.setDefaultUncaughtExceptionHandler(new LoggedUncaughtExceptionHandler());
    if (args.length != 2) {
        LOGGER.info("This program takes 2 arguments.");
        LOGGER.info("First: the path to a .gz file that is part of the English Gigaword v5 corpus.");
        LOGGER.info("Second: the path to the output file (a .tar.gz with communication files).");
        LOGGER.info("Example usage:");
        LOGGER.info("{} {} {}", GigawordGzProcessor.class.getName(), "/path/to/LDC/sgml/.gz",
                "/path/to/out.tar.gz");
        System.exit(1);//from  w  ww.  j  a va2 s .c  om
    }

    String inPathStr = args[0];
    String outPathStr = args[1];

    Path inPath = Paths.get(inPathStr);
    if (!Files.exists(inPath))
        LOGGER.error("Input path {} does not exist. Try again with the right path.", inPath.toString());

    Path outPath = Paths.get(outPathStr);
    Optional<Path> parent = Optional.ofNullable(outPath.getParent());
    // lambda does not allow caught exceptions.
    if (parent.isPresent()) {
        if (!Files.exists(outPath.getParent())) {
            LOGGER.info("Attempting to create output directory: {}", outPath.toString());
            try {
                Files.createDirectories(outPath);
            } catch (IOException e) {
                LOGGER.error("Caught exception creating output directory.", e);
            }
        }
    }

    GigawordDocumentConverter conv = new GigawordDocumentConverter();
    Iterator<Communication> iter = conv.gzToStringIterator(inPath);
    try (OutputStream os = Files.newOutputStream(outPath);
            BufferedOutputStream bos = new BufferedOutputStream(os, 1024 * 8 * 16);
            GzipCompressorOutputStream gout = new GzipCompressorOutputStream(bos);
            TarArchiver archiver = new TarArchiver(gout);) {
        while (iter.hasNext()) {
            Communication c = iter.next();
            LOGGER.info("Adding Communication {} [UUID: {}] to archive.", c.getId(),
                    c.getUuid().getUuidString());
            archiver.addEntry(new ArchivableCommunication(c));
        }
    } catch (IOException e) {
        LOGGER.error("Caught IOException during output.", e);
    }
}

From source file:com.thesmartweb.vivliocrawlermaven.VivlioCrawlerMavenMain.java

/**
 * @param args the command line arguments
 *///from w w w  .j a v a2 s  .  co  m
public static void main(String[] args) {
    // TODO code application logic here
    try {

        OaiPmhServer server = new OaiPmhServer("http://vivliothmmy.ee.auth.gr/cgi/oai2");
        RecordsList listRecords = server.listRecords("oai_dc");//we capture all the records in oai dc format
        List<VivlioCrawlerMavenMain> listtotal = new ArrayList<VivlioCrawlerMavenMain>();
        //we capture all the names of the professors and former professor of ECE of AUTH from a txt file
        //change the directory to yours
        List<String> profs = Files.readAllLines(Paths.get(
                "/home/themis/NetBeansProjects/VivlioCrawlerMaven/src/main/java/com/thesmartweb/vivliocrawlermaven/profs.txt"));

        boolean more = true;//it is a flag used if we encounter more entries than the initial capture
        JSONArray array = new JSONArray();//it is going to be our final total json array
        JSONObject jsonObject = new JSONObject();//it is going to be our final total json object
        while (more) {
            for (Record rec : listRecords.asList()) {
                VivlioCrawlerMavenMain vc = new VivlioCrawlerMavenMain();
                Element metadata = rec.getMetadata();
                if (metadata != null) {
                    //System.out.println(rec.getMetadataAsString());
                    List<Element> elements = metadata.elements();
                    //System.out.println(metadata.getStringValue());
                    for (Element element : elements) {
                        String name = element.getName();
                        //we get the title, remove \r, \n and beginning and trailing whitespace
                        if (name.equalsIgnoreCase("title")) {
                            vc.title = element.getStringValue();
                            vc.title = vc.title.trim();
                            vc.title = vc.title.replaceAll("(\\r|\\n)", "");
                            if (!(vc.title.endsWith("."))) {
                                vc.title = vc.title + ".";//we also add dot in the end for the titles to be uniformed
                            }
                        }
                        if (name.equalsIgnoreCase("creator")) {
                            vc.creators.add(element.getStringValue());//we capture the students' names
                        }
                        if (name.equalsIgnoreCase("subject")) {
                            vc.subjects.add(element.getStringValue());//we capture the subjects
                        }
                        if (name.equalsIgnoreCase("description")) {
                            vc.description = element.getStringValue();//we capture the abstract
                        }
                        if (name.equalsIgnoreCase("date")) {
                            vc.datestring = element.getStringValue();
                        }
                        if (name.equalsIgnoreCase("identifier")) {
                            if (element.getStringValue().contains("http://")) {
                                vc.thesisFiles.add(element.getStringValue());//we capture the url of the thesis whole file
                                if (vc.thesisURL == null) {
                                    vc.thesisURL = element.getStringValue().substring(0, 32);
                                }
                            }
                            //if the identifier contains the title then it must be the citation 
                            //out of the citation we need to extract the supevisor's name
                            if (element.getStringValue().contains(vc.title.substring(0, 10))) {
                                vc.citation = element.getStringValue();
                                vc.supervisor = element.getStringValue();
                                Iterator profsIterator = profs.iterator();
                                vc.supervisor = vc.supervisor.replace(vc.title, "");//we remove the title out of the citation
                                //if we have two students we remove the first occurence of "" which stands for "and"
                                if (vc.creators.size() == 2) {
                                    vc.supervisor = vc.supervisor.replaceFirst("", "");
                                }
                                //we remove the students' names
                                Iterator creatorsIterator = vc.creators.iterator();
                                while (creatorsIterator.hasNext()) {
                                    vc.supervisor = vc.supervisor.replace(creatorsIterator.next().toString(),
                                            "");
                                }
                                boolean profFlag = false;//flag used that declares that we found the professor that was supervisor
                                while (profsIterator.hasNext() && !profFlag) {
                                    String prof = profsIterator.next().toString();
                                    //we split the professor's name to surname and name
                                    //because some entries have first the surname and others first the name
                                    String[] profSplitted = prof.split("\\s+");
                                    String supervisorCleared = vc.supervisor;
                                    supervisorCleared = supervisorCleared.replaceAll("\\s+", "");//we clear the white space
                                    supervisorCleared = supervisorCleared.replaceAll("(\\r|\\n)", "");//we remove the \r\n
                                    //now we check if the citation includes any name of the professors from the txt
                                    if (supervisorCleared.contains(profSplitted[0])
                                            && supervisorCleared.contains(profSplitted[1])) {
                                        vc.supervisor = prof;
                                        profFlag = true;
                                    }
                                }
                                //if we don't find the name of the supervisor, we have to perform string manipulation to extract it
                                if (!profFlag) {
                                    vc.supervisor = vc.supervisor.trim();
                                    //we remove the word "" which stands for "Thessaloniki" and "" which stands for Greece
                                    if (vc.supervisor.contains("")) {
                                        vc.supervisor = vc.supervisor.replaceFirst("",
                                                "");
                                    }
                                    if (vc.supervisor.contains("")) {
                                        vc.supervisor = vc.supervisor.replaceFirst("",
                                                "");
                                    }
                                    if (vc.supervisor.contains("")) {
                                        vc.supervisor = vc.supervisor.replaceFirst("", "");
                                    }
                                    if (vc.supervisor.contains("")) {
                                        vc.supervisor = vc.supervisor.replaceFirst("", "");
                                    }
                                    //we remove the year and then we should be left only with the supervisor's name
                                    vc.supervisor = vc.supervisor.replace("(", "");
                                    vc.supervisor = vc.supervisor.trim();
                                    vc.supervisor = vc.supervisor.replace(")", "");
                                    vc.supervisor = vc.supervisor.trim();
                                    vc.supervisor = vc.supervisor.replace(",", "");
                                    vc.supervisor = vc.supervisor.trim();
                                    vc.supervisor = vc.supervisor.replace(".", "");
                                    vc.supervisor = vc.supervisor.trim();
                                    vc.supervisor = vc.supervisor.replace(vc.datestring.substring(0, 4), "");
                                    vc.supervisor = vc.supervisor.trim();
                                }
                                //we put everything in a json object
                                JSONObject obj = new JSONObject();
                                obj.put("title", vc.title);
                                obj.put("description", vc.description);
                                JSONArray creatorsArray = new JSONArray();
                                creatorsArray.add(vc.creators);
                                obj.put("creators", creatorsArray);
                                JSONArray subjectsArray = new JSONArray();
                                List<String> subjectsList = new ArrayList<String>(vc.subjects);
                                subjectsArray.add(subjectsList);
                                obj.put("subjects", subjectsArray);
                                obj.put("datestring", vc.datestring);
                                JSONArray thesisFilesArray = new JSONArray();
                                thesisFilesArray.add(vc.thesisFiles);
                                obj.put("thesisFiles", thesisFilesArray);
                                obj.put("thesisURL", vc.thesisURL);
                                obj.put("supervisor", vc.supervisor);
                                obj.put("citation", vc.citation);
                                //if you are using JSON.simple do this
                                array.add(obj);
                            }
                        }
                    }
                    listtotal.add(vc);//a list containing all the objects
                    //it is not used for now, but created for potential extension of the work
                }
            }
            //the following if clause searches for new records
            if (listRecords.getResumptionToken() != null) {
                listRecords = server.listRecords(listRecords.getResumptionToken());
            } else {
                more = false;
            }
        }
        //we print which records did not have a supervisor
        for (VivlioCrawlerMavenMain vctest : listtotal) {

            if (vctest.supervisor == null) {
                System.out.println(vctest.title);
                System.out.println(vctest.citation);
            }
        }
        //we create a pretty json with GSON and we write it into a file
        jsonObject.put("VivliothmmyOldArray", array);
        JsonParser parser = new JsonParser();
        JsonObject json = parser.parse(jsonObject.toJSONString()).getAsJsonObject();
        Gson gson = new GsonBuilder().setPrettyPrinting().create();
        String prettyJson = gson.toJson(json);
        try {

            FileWriter file = new FileWriter(
                    "/home/themis/NetBeansProjects/VivlioCrawlerMaven/src/main/java/com/thesmartweb/vivliocrawlermaven/VivliothmmyOldRecords.json");
            file.write(prettyJson);
            file.flush();
            file.close();

        } catch (IOException e) {
            System.out.println("Exception: " + e);
        }

        //System.out.print(prettyJson);

        //int j=0;

    } catch (OAIException | IOException e) {
        System.out.println("Exception: " + e);
    }
}

From source file:TwitterClustering.java

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

    File outFile = new File(args[3]);
    Scanner s = new Scanner(new File(args[1])).useDelimiter(",");
    JSONParser parser = new JSONParser();
    Set<Cluster> clusterSet = new HashSet<Cluster>();
    HashMap<String, Tweet> tweets = new HashMap();
    FileWriter fw = new FileWriter(outFile.getAbsoluteFile());
    BufferedWriter bw = new BufferedWriter(fw);

    // init/*  w  ww . j  a  v  a 2  s  . c o  m*/
    try {

        Object obj = parser.parse(new FileReader(args[2]));

        JSONArray jsonArray = (JSONArray) obj;

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

            Tweet twt = new Tweet();
            JSONObject jObj = (JSONObject) jsonArray.get(i);
            String text = jObj.get("text").toString();

            long sum = 0;
            for (int y = 0; y < text.toCharArray().length; y++) {

                sum += (int) text.toCharArray()[y];
            }

            String[] token = text.split(" ");
            String tID = jObj.get("id").toString();

            Set<String> mySet = new HashSet<String>(Arrays.asList(token));
            twt.setAttributeValue(sum);
            twt.setText(mySet);
            twt.setTweetID(tID);
            tweets.put(tID, twt);

        }

        // preparing initial clusters
        int i = 0;
        while (s.hasNext()) {
            String id = s.next();// id
            Tweet t = tweets.get(id.trim());
            clusterSet.add(new Cluster(i + 1, t, new LinkedList()));
            i++;
        }

        Iterator it = tweets.entrySet().iterator();

        for (int l = 0; l < 2; l++) { // limit to 25 iterations

            while (it.hasNext()) {
                Map.Entry me = (Map.Entry) it.next();

                // calculate distance to each centroid
                Tweet p = (Tweet) me.getValue();
                HashMap<Cluster, Float> distMap = new HashMap();

                for (Cluster clust : clusterSet) {

                    distMap.put(clust, jaccardDistance(p.getText(), clust.getCentroid().getText()));
                }

                HashMap<Cluster, Float> sorted = (HashMap<Cluster, Float>) sortByValue(distMap);

                sorted.keySet().iterator().next().getMembers().add(p);

            }

            // calculate new centroid and update Clusterset
            for (Cluster clust : clusterSet) {

                TreeMap<String, Long> tDistMap = new TreeMap();

                Tweet newCentroid = null;
                Long avgSumDist = new Long(0);
                for (int j = 0; j < clust.getMembers().size(); j++) {

                    avgSumDist += clust.getMembers().get(j).getAttributeValue();
                    tDistMap.put(clust.getMembers().get(j).getTweetID(),
                            clust.getMembers().get(j).getAttributeValue());
                }
                if (clust.getMembers().size() != 0) {
                    avgSumDist /= (clust.getMembers().size());
                }

                ArrayList<Long> listValues = new ArrayList<Long>(tDistMap.values());

                if (tDistMap.containsValue(findClosestNumber(listValues, avgSumDist))) {
                    // found closest
                    newCentroid = tweets
                            .get(getKeyByValue(tDistMap, findClosestNumber(listValues, avgSumDist)));
                    clust.setCentroid(newCentroid);
                }

            }

        }
        // create an iterator
        Iterator iterator = clusterSet.iterator();

        // check values
        while (iterator.hasNext()) {

            Cluster c = (Cluster) iterator.next();
            bw.write(c.getId() + "\t");
            System.out.print(c.getId() + "\t");

            for (Tweet t : c.getMembers()) {
                bw.write(t.getTweetID() + ", ");
                System.out.print(t.getTweetID() + ",");

            }
            bw.write("\n");
            System.out.println("");
        }

        System.out.println("");

        System.out.println("SSE " + sumSquaredErrror(clusterSet));

    } catch (Exception e) {
        e.printStackTrace();
    } finally {
        bw.close();
        fw.close();
    }
}

From source file:edu.cornell.med.icb.goby.reads.ColorSpaceConverter.java

public static void main(final String[] args) throws JSAPException, IOException {
    final JSAP jsap = new JSAP();

    final FlaggedOption sequenceOption = new FlaggedOption("input");
    sequenceOption.setRequired(true);// w  w w  . jav a 2s  .  com
    sequenceOption.setLongFlag("input");
    sequenceOption.setShortFlag('i');
    sequenceOption.setStringParser(FileStringParser.getParser().setMustBeFile(true).setMustExist(true));
    sequenceOption.setHelp("The input file (in Fasta format) to convert");
    jsap.registerParameter(sequenceOption);

    final FlaggedOption outputOption = new FlaggedOption("output");
    outputOption.setRequired(false);
    outputOption.setLongFlag("output");
    outputOption.setShortFlag('o');
    outputOption.setStringParser(FileStringParser.getParser().setMustBeFile(true));
    outputOption.setHelp("The output file to write to (default = stdout)");
    jsap.registerParameter(outputOption);

    final FlaggedOption titleOption = new FlaggedOption("title");
    titleOption.setRequired(false);
    titleOption.setLongFlag("title");
    titleOption.setShortFlag('t');
    titleOption.setHelp("Title for this conversion");
    jsap.registerParameter(titleOption);

    final Switch verboseOption = new Switch("verbose");
    verboseOption.setLongFlag("verbose");
    verboseOption.setShortFlag('v');
    verboseOption.setHelp("Verbose output");
    jsap.registerParameter(verboseOption);

    final Switch helpOption = new Switch("help");
    helpOption.setLongFlag("help");
    helpOption.setShortFlag('h');
    helpOption.setHelp("Print this message");
    jsap.registerParameter(helpOption);

    jsap.setUsage("Usage: " + ColorSpaceConverter.class.getName() + " " + jsap.getUsage());

    final JSAPResult result = jsap.parse(args);

    if (result.getBoolean("help")) {
        System.out.println(jsap.getHelp());
        System.exit(0);
    }

    if (!result.success()) {
        final Iterator<String> errors = result.getErrorMessageIterator();
        while (errors.hasNext()) {
            System.err.println(errors.next());
        }
        System.err.println(jsap.getUsage());
        System.exit(1);
    }

    final boolean verbose = result.getBoolean("verbose");

    final File sequenceFile = result.getFile("input");
    if (verbose) {
        System.out.println("Reading sequence from: " + sequenceFile);
    }

    // extract the title to use for the output header
    final String title;
    if (result.contains("title")) {
        title = result.getString("title");
    } else {
        title = sequenceFile.getName();
    }

    Reader inputReader = null;
    PrintWriter outputWriter = null;

    try {
        if ("gz".equals(FilenameUtils.getExtension(sequenceFile.getName()))) {
            inputReader = new InputStreamReader(new GZIPInputStream(FileUtils.openInputStream(sequenceFile)));
        } else {
            inputReader = new FileReader(sequenceFile);
        }
        final FastaParser fastaParser = new FastaParser(inputReader);

        final File outputFile = result.getFile("output");
        final OutputStream outputStream;
        if (outputFile != null) {
            outputStream = FileUtils.openOutputStream(outputFile);
            if (verbose) {
                System.out.println("Writing sequence : " + outputFile);
            }
        } else {
            outputStream = System.out;
        }
        outputWriter = new PrintWriter(outputStream);

        // write the header portion of the output
        outputWriter.print("# ");
        outputWriter.print(new Date());
        outputWriter.print(' ');
        outputWriter.print(ColorSpaceConverter.class.getName());
        for (final String arg : args) {
            outputWriter.print(' ');
            outputWriter.print(arg);
        }
        outputWriter.println();
        outputWriter.print("# Cwd: ");
        outputWriter.println(new File(".").getCanonicalPath());
        outputWriter.print("# Title: ");
        outputWriter.println(title);

        // now parse the input sequence
        long sequenceCount = 0;
        final MutableString descriptionLine = new MutableString();
        final MutableString sequence = new MutableString();
        final MutableString colorSpaceSequence = new MutableString();

        while (fastaParser.hasNext()) {
            fastaParser.next(descriptionLine, sequence);
            outputWriter.print('>');
            outputWriter.println(descriptionLine);

            convert(sequence, colorSpaceSequence);
            CompactToFastaMode.writeSequence(outputWriter, colorSpaceSequence);

            sequenceCount++;
            if (verbose && sequenceCount % 10000 == 0) {
                System.out.println("Converted " + sequenceCount + " entries");
            }
        }

        if (verbose) {
            System.out.println("Conversion complete!");
        }
    } finally {
        IOUtils.closeQuietly(inputReader);
        IOUtils.closeQuietly(outputWriter);
    }
}

From source file:com.github.aliteralmind.codelet.examples.non_xbn.PrintJDBlocksStartStopLineNumsXmpl.java

/**
   <p>The main function.</p>
 *//*from w w  w.  j  av a 2s  .  co m*/
public static final void main(String[] as_1RqdJavaSourcePath) {

    //Read command-line parameter
    String sJPath = null;
    try {
        sJPath = as_1RqdJavaSourcePath[0];
    } catch (ArrayIndexOutOfBoundsException aibx) {
        throw new NullPointerException(
                "Missing one-and-only required parameter: Path to java source-code file.");
    }
    System.out.println("Java source: " + sJPath);

    //Establish line-iterator
    Iterator<String> lineItr = null;
    try {
        lineItr = FileUtils.lineIterator(new File(sJPath)); //Throws npx if null
    } catch (IOException iox) {
        throw new RTIOException("PrintJDBlocksStartStopLinesXmpl", iox);
    }
    Pattern pTrmdJDBlockStart = Pattern.compile("^[\\t ]*/\\*\\*");

    String sDD = "..";
    int lineNum = 1;
    boolean bInJDBlock = false;
    while (lineItr.hasNext()) {
        String sLn = lineItr.next();
        if (!bInJDBlock) {
            if (pTrmdJDBlockStart.matcher(sLn).matches()) {
                bInJDBlock = true;
                System.out.print(lineNum + sDD);
            }
        } else if (sLn.indexOf("*/") != -1) {
            bInJDBlock = false;
            System.out.println(lineNum);
        }
        lineNum++;
    }
    if (bInJDBlock) {
        throw new IllegalStateException("Reach end of file. JavaDoc not closed.");
    }
}

From source file:com.github.liyp.test.TestMain.java

@SuppressWarnings("unchecked")
public static void main(String[] args) {
    // add a shutdown hook to stop the server
    Runtime.getRuntime().addShutdownHook(new Thread(new Runnable() {
        @Override// w w w . ja v  a2s.c om
        public void run() {
            System.out.println("########### shoutdown begin....");
            try {
                Thread.sleep(10000);
            } catch (InterruptedException e) {
                e.printStackTrace();
            }
            System.out.println("########### shoutdown end....");
        }
    }));

    System.out.println(args.length);
    Iterator<String> iterator1 = IteratorUtils
            .arrayIterator(new String[] { "one", "two", "three", "11", "22", "AB" });
    Iterator<String> iterator2 = IteratorUtils.arrayIterator(new String[] { "a", "b", "c", "33", "ab", "aB" });

    Iterator<String> chainedIter = IteratorUtils.chainedIterator(iterator1, iterator2);

    System.out.println("==================");

    Iterator<String> iter = IteratorUtils.filteredIterator(chainedIter, new Predicate() {
        @Override
        public boolean evaluate(Object arg0) {
            System.out.println("xx:" + arg0.toString());
            String str = (String) arg0;
            return str.matches("([a-z]|[A-Z]){2}");
        }
    });
    while (iter.hasNext()) {
        System.out.println(iter.next());
    }

    System.out.println("===================");

    System.out.println("asas".matches("[a-z]{4}"));

    System.out.println("Y".equals(null));

    System.out.println(String.format("%02d", 1000L));

    System.out.println(ArrayUtils.toString(splitAndTrim(" 11, 21,12 ,", ",")));

    System.out.println(new ArrayList<String>().toString());

    JSONObject json = new JSONObject("{\"keynull\":null}");
    json.put("bool", false);
    json.put("keya", "as");
    json.put("key2", 2212222222222222222L);
    System.out.println(json);
    System.out.println(json.get("keynull").equals(null));

    String a = String.format("{\"id\":%d,\"method\":\"testCrossSync\"," + "\"circle\":%d},\"isEnd\":true", 1,
            1);
    System.out.println(a.getBytes().length);

    System.out.println(new String[] { "a", "b" });

    System.out.println(new JSONArray("[\"aa\",\"\"]"));

    String data = String.format("%9d %s", 1, RandomStringUtils.randomAlphanumeric(10));
    System.out.println(data.getBytes().length);

    System.out.println(ArrayUtils.toString("1|2| 3|  333||| 3".split("\\|")));

    JSONObject j1 = new JSONObject("{\"a\":\"11111\"}");
    JSONObject j2 = new JSONObject(j1.toString());
    j2.put("b", "22222");
    System.out.println(j1 + " | " + j2);

    System.out.println("======================");

    String regex = "\\d+(\\-\\d+){2} \\d+(:\\d+){2}";
    Pattern pattern = Pattern.compile(regex);
    Matcher matcher = pattern.matcher("2015-12-28 15:46:14  _NC250_MD:motion de\n");
    String eventDate = matcher.find() ? matcher.group() : "";

    System.out.println(eventDate);
}

From source file:org.openiot.gsn.utils.VSMonitor.java

public static void main(String[] args) {

    PropertyConfigurator.configure(DEFAULT_GSN_LOG4J_PROPERTIES);
    String configFileName;//w w w. j  ava  2 s .c o  m

    if (args.length >= 2) {
        configFileName = args[0];
        System.out.println("Using config file: " + configFileName);
        for (int i = 1; i < args.length; i++) {
            System.out.println("Adding e-mail: " + args[i]);
            listOfMails.add(args[i]);
        }
    } else {
        System.out.println("Usage java -jar VSMonitor.jar <config_file> <list_of_mails>");
        System.out.println("e.g.  java -jar VSMonitor.jar conf/monitoring.cfg user@gmail.com admin@gmail.com");
        return;
    }

    initFromFile(configFileName);

    // for each monitored GSN server
    Iterator iter = listOfGSNSessions.iterator();
    while (iter.hasNext()) {

        try {
            readStatus((GSNSessionAddress) iter.next());
        } catch (Exception e) {
            logger.error("Exception: " + e.getMessage());
            logger.error("StackTrace:\n" + getStackTrace(e));
        }
    }

    checkUpdateTimes();

    // Generate Report
    report.append("\n[ERROR]\n" + errorsBuffer).append("\n[WARNING]\n" + warningsBuffer)
            .append("\n[INFO]\n" + infosBuffer);

    if ((nSensorsLate > 0) || (nHostsDown > 0)) {
        summary.append("WARNING: ");
        if (nHostsDown > 0)
            summary.append(nHostsDown + " host(s) down. ");
        if (nSensorsLate > 0)
            summary.append(nSensorsLate + " sensor(s) not updated. ");

        // Send e-mail only if there are errors
        try {
            sendMail();
        } catch (EmailException e) {
            logger.error("Cannot send e-mail. " + e.getMessage());
            logger.error("StackTrace:\n" + getStackTrace(e));
        }
    }

    // Showing report
    System.out.println(summary);
    System.out.println(report);
}