Example usage for java.io PrintWriter close

List of usage examples for java.io PrintWriter close

Introduction

In this page you can find the example usage for java.io PrintWriter close.

Prototype

public void close() 

Source Link

Document

Closes the stream and releases any system resources associated with it.

Usage

From source file:EchoClient.java

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

        Socket kkSocket = null;/*from   w w  w .  jav  a2  s.  com*/
        PrintWriter out = null;
        BufferedReader in = null;

        try {
            kkSocket = new Socket("taranis", 4444);
            out = new PrintWriter(kkSocket.getOutputStream(), true);
            in = new BufferedReader(new InputStreamReader(kkSocket.getInputStream()));
        } catch (UnknownHostException e) {
            System.err.println("Don't know about host: taranis.");
            System.exit(1);
        } catch (IOException e) {
            System.err.println("Couldn't get I/O for the connection to: taranis.");
            System.exit(1);
        }

        BufferedReader stdIn = new BufferedReader(new InputStreamReader(System.in));
        String fromServer;
        String fromUser;

        while ((fromServer = in.readLine()) != null) {
            System.out.println("Server: " + fromServer);
            if (fromServer.equals("Bye."))
                break;

            fromUser = stdIn.readLine();
            if (fromUser != null) {
                System.out.println("Client: " + fromUser);
                out.println(fromUser);
            }
        }

        out.close();
        in.close();
        stdIn.close();
        kkSocket.close();
    }

From source file:de.tudarmstadt.ukp.experiments.argumentation.convincingness.sampling.Step7aLearningDataProducer.java

@SuppressWarnings("unchecked")
public static void main(String[] args) throws IOException {
    String inputDir = args[0];//w  w  w  . jav a2 s . c  o m
    File outputDir = new File(args[1]);

    if (!outputDir.exists()) {
        outputDir.mkdirs();
    }

    Collection<File> files = IOHelper.listXmlFiles(new File(inputDir));

    // for generating ConvArgStrict use this
    String prefix = "no-eq_DescendingScoreArgumentPairListSorter";

    // for oversampling using graph transitivity properties use this
    //        String prefix = "generated_no-eq_AscendingScoreArgumentPairListSorter";

    Iterator<File> iterator = files.iterator();
    while (iterator.hasNext()) {
        File file = iterator.next();

        if (!file.getName().startsWith(prefix)) {
            iterator.remove();
        }
    }

    int totalGoldPairsCounter = 0;

    Map<String, Integer> goldDataDistribution = new HashMap<>();

    DescriptiveStatistics statsPerTopic = new DescriptiveStatistics();

    int totalPairsWithReasonSameAsGold = 0;

    DescriptiveStatistics ds = new DescriptiveStatistics();

    for (File file : files) {
        List<AnnotatedArgumentPair> argumentPairs = (List<AnnotatedArgumentPair>) XStreamTools.getXStream()
                .fromXML(file);

        int pairsPerTopicCounter = 0;

        String name = file.getName().replaceAll(prefix, "").replaceAll("\\.xml", "");

        PrintWriter pw = new PrintWriter(new File(outputDir, name + ".csv"), "utf-8");

        pw.println("#id\tlabel\ta1\ta2");

        for (AnnotatedArgumentPair argumentPair : argumentPairs) {
            String goldLabel = argumentPair.getGoldLabel();

            if (!goldDataDistribution.containsKey(goldLabel)) {
                goldDataDistribution.put(goldLabel, 0);
            }

            goldDataDistribution.put(goldLabel, goldDataDistribution.get(goldLabel) + 1);

            pw.printf(Locale.ENGLISH, "%s\t%s\t%s\t%s%n", argumentPair.getId(), goldLabel,
                    multipleParagraphsToSingleLine(argumentPair.getArg1().getText()),
                    multipleParagraphsToSingleLine(argumentPair.getArg2().getText()));

            pairsPerTopicCounter++;

            int sameInOnePair = 0;

            // get gold reason statistics
            for (AnnotatedArgumentPair.MTurkAssignment assignment : argumentPair.mTurkAssignments) {
                String label = assignment.getValue();

                if (goldLabel.equals(label)) {
                    sameInOnePair++;
                }
            }

            ds.addValue(sameInOnePair);
            totalPairsWithReasonSameAsGold += sameInOnePair;
        }

        totalGoldPairsCounter += pairsPerTopicCounter;
        statsPerTopic.addValue(pairsPerTopicCounter);

        pw.close();
    }

    System.out.println("Total reasons matching gold " + totalPairsWithReasonSameAsGold);
    System.out.println(ds);

    System.out.println("Total gold pairs: " + totalGoldPairsCounter);
    System.out.println(statsPerTopic);

    int totalPairs = 0;
    for (Integer pairs : goldDataDistribution.values()) {
        totalPairs += pairs;
    }
    System.out.println("Total pairs: " + totalPairs);
    System.out.println(goldDataDistribution);

}

From source file:Trace.java

public static void main(String[] args) throws java.io.IOException, TransformerException,
        TransformerConfigurationException, java.util.TooManyListenersException, org.xml.sax.SAXException {
    String fileName = "foo";
    if (args.length > 0)
        fileName = args[0];//from w w  w  .  j  a  v  a  2 s  . com

    // Set up a PrintTraceListener object to print to a file.
    java.io.FileWriter fw = new java.io.FileWriter("events.log");
    java.io.PrintWriter pw = new java.io.PrintWriter(fw, true);
    PrintTraceListener ptl = new PrintTraceListener(pw);

    // Print information as each node is 'executed' in the stylesheet.
    ptl.m_traceElements = true;
    // Print information after each result-tree generation event.
    ptl.m_traceGeneration = true;
    // Print information after each selection event.
    ptl.m_traceSelection = true;
    // Print information whenever a template is invoked.
    ptl.m_traceTemplates = true;
    // Print information whenever an extension call is made.
    ptl.m_traceExtension = true;

    // Set up the transformation    
    TransformerFactory tFactory = TransformerFactory.newInstance();
    Transformer transformer = tFactory.newTransformer(new StreamSource(fileName + ".xsl"));

    // Cast the Transformer object to TransformerImpl.
    if (transformer instanceof TransformerImpl) {
        TransformerImpl transformerImpl = (TransformerImpl) transformer;
        // Register the TraceListener with a TraceManager associated 
        // with the TransformerImpl.
        TraceManager trMgr = transformerImpl.getTraceManager();
        trMgr.addTraceListener(ptl);

        // Perform the transformation --printing information to
        // the events log during the process.
        transformer.transform(new StreamSource(fileName + ".xml"),
                new StreamResult(new java.io.FileWriter(fileName + ".out")));
    }
    // Close the PrintWriter and FileWriter.
    pw.close();
    fw.close();
    System.out.println("**The output is in " + fileName + ".out; the log is in events.log ****");

}

From source file:ArrayFile.java

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

    PrintWriter out = new PrintWriter(new FileWriter("arrayfile.txt"));

    CaBioApplicationService appService = (CaBioApplicationService) ApplicationServiceProvider
            .getApplicationServiceFromUrl("http://cabioapi-qa.nci.nih.gov/cabio42");

    ArrayAnnotationService am = new ArrayAnnotationServiceImpl(appService);

    String arrayName = "HG-U133_Plus_2";

    Collection<ArrayReporter> reps = am.getReportersForPlatform(arrayName);

    out.println("Name\tSymbol\tHUGO Symbol\tUnigene Id\t" + "Sequence Type\tSequence Source\tTarget Id\t"
            + "Target Description\tCytoband\tChromosome\tStart\tEnd");

    int c = 0;// w w  w.ja v  a2 s  .  c  o m
    for (ArrayReporter rep : reps) {

        ExpressionArrayReporter er = (ExpressionArrayReporter) rep;

        out.println(resolve(er, "name") + "\t" + resolve(er, "gene.symbol") + "\t"
                + resolve(er, "gene.hugoSymbol") + "\t" + resolve(er, "gene.clusterId") + "\t"
                + resolve(er, "sequenceType") + "\t" + resolve(er, "sequenceSource") + "\t"
                + resolve(er, "targetId") + "\t" + resolve(er, "targetDescription") + "\t"
                + resolve(er, "cytogeneticLocationCollection[0].startCytoband.name") + "\t"
                + resolve(er, "physicalLocationCollection[0].chromosome.number") + "\t"
                + resolve(er, "physicalLocationCollection[0].chromosomalStartPosition") + "\t"
                + resolve(er, "physicalLocationCollection[0].chromosomalEndPosition"));

        if (c++ > 500)
            break;
    }

    out.close();
}

From source file:com.ifeng.sorter.NginxApp.java

public static void main(String[] args) {

    String input = "src/test/resources/data/nginx_report.txt";

    PrintWriter pw = null;

    Map<String, List<LogBean>> resultMap = new HashMap<String, List<LogBean>>();
    List<String> ips = new ArrayList<String>();

    try {/*from  w w  w . j  av a2 s  .c  o  m*/
        List<String> lines = FileUtils.readLines(new File(input));
        List<LogBean> items = new ArrayList<LogBean>();

        for (String line : lines) {
            String[] values = line.split("\t");

            if (values != null && values.length == 3) {// ip total seria
                try {
                    String ip = values[0].trim();
                    String total = values[1].trim();
                    String seria = values[2].trim();

                    LogBean bean = new LogBean(ip, Integer.parseInt(total), seria);

                    items.add(bean);

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

        Collections.sort(items);

        for (LogBean bean : items) {
            String key = bean.getIp();

            if (resultMap.containsKey(key)) {
                resultMap.get(key).add(bean);
            } else {
                List<LogBean> keyList = new ArrayList<LogBean>();
                keyList.add(bean);
                resultMap.put(key, keyList);

                ips.add(key);
            }
        }

        pw = new PrintWriter("src/test/resources/output/result.txt", "UTF-8");

        for (String ip : ips) {
            List<LogBean> list = resultMap.get(ip);

            for (LogBean bean : list) {
                pw.append(bean.toString());
                pw.println();
            }
        }

    } catch (IOException e) {
        e.printStackTrace();
    } finally {
        pw.flush();
        pw.close();
    }
}

From source file:eval.dataset.ParseWikiLog.java

public static void main(String[] ss) throws FileNotFoundException, ParserConfigurationException, IOException {
    FileInputStream fin = new FileInputStream("data/enwiki-20151201-pages-logging.xml.gz");
    GzipCompressorInputStream gzIn = new GzipCompressorInputStream(fin);
    InputStreamReader reader = new InputStreamReader(gzIn);
    BufferedReader br = new BufferedReader(reader);
    PrintWriter pw = new PrintWriter(new FileWriter("data/user_page.txt"));
    pw.println(/*www.  j  av a2 s  .  c o  m*/
            "#list of user names and pages that they have edited, deleted or created. These info are mined from logitems of enwiki-20150304-pages-logging.xml.gz");
    TreeMap<String, Set<String>> userPageList = new TreeMap();
    TreeSet<String> pageList = new TreeSet();
    int counterEntry = 0;
    String currentUser = null;
    String currentPage = null;
    try {
        for (String line = br.readLine(); line != null; line = br.readLine()) {

            if (line.trim().equals("</logitem>")) {
                counterEntry++;
                if (currentUser != null && currentPage != null) {
                    updateMap(userPageList, currentUser, currentPage);
                    pw.println(currentUser + "\t" + currentPage);
                    pageList.add(currentPage);
                }
                currentUser = null;
                currentPage = null;
            } else if (line.trim().startsWith("<username>")) {
                currentUser = line.trim().split(">")[1].split("<")[0].replace(" ", "_");

            } else if (line.trim().startsWith("<logtitle>")) {
                String content = line.trim().split(">")[1].split("<")[0];
                if (content.split(":").length == 1) {
                    currentPage = content.replace(" ", "_");
                }
            }
        }
    } catch (IOException ex) {
        Logger.getLogger(ParseWikiLog.class.getName()).log(Level.SEVERE, null, ex);
    }
    pw.println("#analysed " + counterEntry + " entries of wikipesia log file");
    pw.println("#gathered a list of unique user of size " + userPageList.size());
    pw.println("#gathered a list of pages of size " + pageList.size());
    pw.close();
    gzIn.close();

    PrintWriter pwUser = new PrintWriter(new FileWriter("data/user_list_page_edited.txt"));
    pwUser.println(
            "#list of unique users and pages that they have edited, extracted from logitems of enwiki-20150304-pages-logging.xml.gz");
    for (String user : userPageList.keySet()) {
        pwUser.print(user);
        Set<String> getList = userPageList.get(user);
        for (String page : getList) {
            pwUser.print("\t" + page);
        }
        pwUser.println();
    }
    pwUser.close();

    PrintWriter pwPage = new PrintWriter(new FileWriter("data/all_pages.txt"));
    pwPage.println("#list of the unique pages that are extracted from enwiki-20150304-pages-logging.xml.gz");
    for (String page : pageList) {
        pwPage.println(page);
    }
    pwPage.close();
    System.out.println("#analysed " + counterEntry + " entries of wikipesia log file");
    System.out.println("#gathered a list of unique user of size " + userPageList.size());
    System.out.println("#gathered a list of pages of size " + pageList.size());
}

From source file:com.annuletconsulting.homecommand.server.HomeCommand.java

/**
 * This class will accept commands from a node in each room. For it to react to events on the server
 * computer, it must be also running as a node.  However the server can cause all nodes to react
 * to an event happening on any node, such as an email or text arriving.  A call on a node device
 * could pause all music devices, for example.
 * /*from w ww.j  ava2 s  . com*/
 * @param args
 */
public static void main(String[] args) {
    try {
        socket = Integer.parseInt(HomeComandProperties.getInstance().getServerPort());
        nonJavaUserModulesPath = HomeComandProperties.getInstance().getNonJavaUserDir();
    } catch (Exception exception) {
        System.out.println("Error loading from properties file.");
        exception.printStackTrace();
    }
    try {
        sharedKey = HomeComandProperties.getInstance().getSharedKey();
        if (sharedKey == null)
            System.out.println("shared_key is null, commands without valid signatures will be processed.");
    } catch (Exception exception) {
        System.out.println("shared_key not found in properties file.");
        exception.printStackTrace();
    }
    try {
        if (args.length > 0) {
            String arg0 = args[0];
            if (arg0.equals("help") || arg0.equals("?") || arg0.equals("usage") || arg0.equals("-help")
                    || arg0.equals("-?")) {
                System.out.println(
                        "The defaults can be changed by editing the HomeCommand.properties file, or you can override them temporarily using command line options.");
                System.out.println("\nHome Command Server command line overrride usage:");
                System.out.println(
                        "hcserver [server_port] [java_user_module_directory] [non_java_user_module_directory]"); //TODO make hcserver.sh
                System.out.println("\nDefaults:");
                System.out.println("server_port: " + socket);
                System.out.println("java_user_module_directory: " + userModulesPath);
                System.out.println("non_java_user_module_directory: " + nonJavaUserModulesPath);
                System.out.println("\n2013 | Annulet, LLC");
            }
            socket = Integer.parseInt(arg0);
        }
        if (args.length > 1)
            userModulesPath = args[1];
        if (args.length > 2)
            nonJavaUserModulesPath = args[2];

        System.out.println("Config loaded, initializing modules.");
        modules.add(new HueLightModule());
        System.out.println("HueLightModule initialized.");
        modules.add(new QuestionModule());
        System.out.println("QuestionModule initialized.");
        modules.add(new MathModule());
        System.out.println("MathModule initialized.");
        modules.add(new MusicModule());
        System.out.println("MusicModule initialized.");
        modules.add(new NonCopyrightInfringingGenericSpaceExplorationTVShowModule());
        System.out.println("NonCopyrightInfringingGenericSpaceExplorationTVShowModule initialized.");
        modules.add(new HelpModule());
        System.out.println("HelpModule initialized.");
        modules.add(new SetUpModule());
        System.out.println("SetUpModule initialized.");
        modules.addAll(NonJavaUserModuleLoader.loadModulesAt(nonJavaUserModulesPath));
        System.out.println("NonJavaUserModuleLoader initialized.");
        ServerSocket serverSocket = new ServerSocket(socket);
        System.out.println("Listening...");
        while (!end) {
            Socket socket = serverSocket.accept();
            InputStreamReader isr = new InputStreamReader(socket.getInputStream());
            PrintWriter output = new PrintWriter(socket.getOutputStream(), true);
            int character;
            StringBuffer inputStrBuffer = new StringBuffer();
            while ((character = isr.read()) != 13) {
                inputStrBuffer.append((char) character);
            }
            System.out.println(inputStrBuffer.toString());
            String[] cmd; // = inputStrBuffer.toString().split(" ");
            String result = "YOUR REQUEST WAS NOT VALID JSON";
            if (inputStrBuffer.substring(0, 1).equals("{")) {
                nodeType = extractElement(inputStrBuffer.toString(), "node_type");
                if (sharedKey != null) {
                    if (validateSignature(extractElement(inputStrBuffer.toString(), "time_stamp"),
                            extractElement(inputStrBuffer.toString(), "signature"))) {
                        if ("Y".equalsIgnoreCase(extractElement(inputStrBuffer.toString(), "cmd_encoded")))
                            cmd = decryptCommand(extractElement(inputStrBuffer.toString(), "command"));
                        else
                            cmd = extractElement(inputStrBuffer.toString(), "command").split(" ");
                        result = getResult(cmd);
                    } else
                        result = "YOUR SIGNATURE DID NOT MATCH, CHECK SHARED KEY";
                } else {
                    cmd = extractElement(inputStrBuffer.toString(), "command").split(" ");
                    result = getResult(cmd);
                }
            }
            System.out.println(result);
            output.print(result);
            output.print((char) 13);
            output.close();
            isr.close();
            socket.close();
        }
        serverSocket.close();
        System.out.println("Shutting down.");
    } catch (Exception exception) {
        exception.printStackTrace();
    }
}

From source file:at.tuwien.ifs.somtoolbox.apps.helper.VectorSimilarityWriter.java

public static void main(String[] args) throws ClassNotFoundException, InstantiationException,
        IllegalAccessException, IOException, SOMToolboxException {
    JSAPResult config = OptionFactory.parseResults(args, OptionFactory.OPTIONS_INPUT_SIMILARITY_COMPUTER);
    String inputVectorDistanceMatrix = config.getString("inputVectorDistanceMatrix");
    String inputVectorFileName = config.getString("inputVectorFile");
    int numNeighbours = config.getInt("numberNeighbours");
    String outputFormat = config.getString("outputFormat");

    InputVectorDistanceMatrix matrix = null;
    InputData data = new SOMLibSparseInputData(inputVectorFileName);

    if (StringUtils.isNotBlank(inputVectorDistanceMatrix)) {
        matrix = InputVectorDistanceMatrix.initFromFile(inputVectorDistanceMatrix);
    } else {//from w ww.java 2 s  . co  m
        String metricName = config.getString("metric");
        DistanceMetric metric = AbstractMetric.instantiate(metricName);
        matrix = new LeightWeightMemoryInputVectorDistanceMatrix(data, metric);
    }

    String outputFileName = config.getString("output");
    PrintWriter w = FileUtils.openFileForWriting("Similarity File", outputFileName);

    if (outputFormat.equals("SAT-DB")) {
        // find feature type
        String type = "";
        if (inputVectorFileName.endsWith(".rh") || inputVectorFileName.endsWith(".rp")
                || inputVectorFileName.endsWith(".ssd")) {
            type = "_" + inputVectorFileName.substring(inputVectorFileName.lastIndexOf(".") + 1);
        }
        w.println("INSERT INTO `sat_track_similarity_ifs" + type
                + "` (`TRACKID`, `SIMILARITYCOUNT`, `SIMILARITYIDS`) VALUES ");
    }

    int numVectors = matrix.numVectors();
    // numVectors = 10; // for testing
    StdErrProgressWriter progress = new StdErrProgressWriter(numVectors, "Writing similarities for vector ", 1);
    for (int i = 0; i < numVectors; i++) {
        int[] nearest = matrix.getNNearest(i, numNeighbours);
        if (outputFormat.equals("SAT-DB")) {
            w.print("  (" + i + " , NULL, '");
            for (int j = 0; j < nearest.length; j++) {
                String label = data.getLabel(nearest[j]);
                w.print(label.replace(".mp3", "")); // strip ending
                if (j + 1 < nearest.length) {
                    w.print(",");
                } else {
                    w.print("')");
                }
            }
            if (i + 1 < numVectors) {
                w.print(",");
            }
        } else {
            w.print(data.getLabel(i) + ",");
            for (int j = 0; j < nearest.length; j++) {
                w.print(data.getLabel(nearest[j]));
                if (j + 1 < nearest.length) {
                    w.print(",");
                }
            }
        }
        w.println();
        w.flush();
        progress.progress();
    }
    if (outputFormat.equals("SAT-DB")) {
        w.print(";");
    }
    w.flush();
    w.close();
}

From source file:microbiosima.Microbiosima.java

/**
 * @param args//from w  w w .  j av a 2s .co  m
 *            the command line arguments
 * @throws java.io.FileNotFoundException
 * @throws java.io.UnsupportedEncodingException
 */
public static void main(String[] args) throws FileNotFoundException, UnsupportedEncodingException {
    //Init with default values
    int populationSize = 500;
    int microSize = 1000;
    int numberOfSpecies = 150;
    int numberOfGeneration = 10000;
    int numberOfObservation = 100;
    int numberOfReplication = 1;
    double pctEnv = 0;
    double pctPool = 0;

    Options options = new Options();

    Option help = new Option("h", "help", false, "print this message");
    Option version = new Option("v", "version", false, "print the version information and exit");
    options.addOption(help);
    options.addOption(version);

    options.addOption(Option.builder("o").longOpt("obs").hasArg().argName("OBS")
            .desc("Number generation for observation [default: 100]").build());
    options.addOption(Option.builder("r").longOpt("rep").hasArg().argName("REP")
            .desc("Number of replication [default: 1]").build());

    Builder C = Option.builder("c").longOpt("config").numberOfArgs(4).argName("Pop Micro Spec Gen")
            .desc("Four Parameters in the following orders: "
                    + "(1) population size, (2) microbe size, (3) number of species, (4) number of generation"
                    + " [default: 500 1000 150 10000]");
    options.addOption(C.build());

    HelpFormatter formatter = new HelpFormatter();
    String syntax = "microbiosima pctEnv pctPool";
    String header = "\nSimulates the evolutionary and ecological dynamics of microbiomes within a population of hosts.\n\n"
            + "required arguments:\n" + "  pctEnv             Percentage of environmental acquisition\n"
            + "  pctPool            Percentage of pooled environmental component\n" + "\noptional arguments:\n";
    String footer = "\n";

    formatter.setWidth(80);

    CommandLineParser parser = new DefaultParser();
    CommandLine cmd = null;

    try {
        cmd = parser.parse(options, args);
        String[] pct_config = cmd.getArgs();

        if (cmd.hasOption("h") || args.length == 0) {
            formatter.printHelp(syntax, header, options, footer, true);
            System.exit(0);
        }
        if (cmd.hasOption("v")) {
            System.out.println("Microbiosima " + VERSION);
            System.exit(0);
        }
        if (pct_config.length != 2) {
            System.out.println("ERROR! Required exactly two argumennts for pct_env and pct_pool. It got "
                    + pct_config.length + ": " + Arrays.toString(pct_config));
            formatter.printHelp(syntax, header, options, footer, true);
            System.exit(3);
        } else {
            pctEnv = Double.parseDouble(pct_config[0]);
            pctPool = Double.parseDouble(pct_config[1]);
            if (pctEnv < 0 || pctEnv > 1) {
                System.out.println(
                        "ERROR: pctEnv (Percentage of environmental acquisition) must be between 0 and 1 (pctEnv="
                                + pctEnv + ")! EXIT");
                System.exit(3);
            }
            if (pctPool < 0 || pctPool > 1) {
                System.out.println(
                        "ERROR: pctPool (Percentage of pooled environmental component must) must be between 0 and 1 (pctPool="
                                + pctPool + ")! EXIT");
                System.exit(3);
            }

        }
        if (cmd.hasOption("config")) {
            String[] configs = cmd.getOptionValues("config");
            populationSize = Integer.parseInt(configs[0]);
            microSize = Integer.parseInt(configs[1]);
            numberOfSpecies = Integer.parseInt(configs[2]);
            numberOfGeneration = Integer.parseInt(configs[3]);
        }
        if (cmd.hasOption("obs")) {
            numberOfObservation = Integer.parseInt(cmd.getOptionValue("obs"));
        }
        if (cmd.hasOption("rep")) {
            numberOfReplication = Integer.parseInt(cmd.getOptionValue("rep"));
        }

    } catch (ParseException e) {
        e.printStackTrace();
        System.exit(3);
    }

    StringBuilder sb = new StringBuilder();
    sb.append("Configuration Summary:").append("\n\tPopulation size: ").append(populationSize)
            .append("\n\tMicrobe size: ").append(microSize).append("\n\tNumber of species: ")
            .append(numberOfSpecies).append("\n\tNumber of generation: ").append(numberOfGeneration)
            .append("\n\tNumber generation for observation: ").append(numberOfObservation)
            .append("\n\tNumber of replication: ").append(numberOfReplication).append("\n");
    System.out.println(sb.toString());

    //      System.exit(3);
    // LogNormalDistribution lgd=new LogNormalDistribution(0,1);
    // environment=lgd.sample(150);
    // double environment_sum=0;
    // for (int i=0;i<No;i++){
    // environment_sum+=environment[i];
    // }
    // for (int i=0;i<No;i++){
    // environment[i]/=environment_sum;
    // }

    double[] environment = new double[numberOfSpecies];
    for (int i = 0; i < numberOfSpecies; i++) {
        environment[i] = 1 / (double) numberOfSpecies;
    }

    for (int rep = 0; rep < numberOfReplication; rep++) {
        String prefix = "" + (rep + 1) + "_";
        String sufix = "_E" + pctEnv + "_P" + pctPool + ".txt";

        System.out.println("Output 5 result files in the format of: " + prefix + "[****]" + sufix);
        try {

            PrintWriter file1 = new PrintWriter(
                    new BufferedWriter(new FileWriter(prefix + "gamma_diversity" + sufix)));
            PrintWriter file2 = new PrintWriter(
                    new BufferedWriter(new FileWriter(prefix + "alpha_diversity" + sufix)));
            PrintWriter file3 = new PrintWriter(
                    new BufferedWriter(new FileWriter(prefix + "beta_diversity" + sufix)));
            PrintWriter file4 = new PrintWriter(new BufferedWriter(new FileWriter(prefix + "sum" + sufix)));
            PrintWriter file5 = new PrintWriter(
                    new BufferedWriter(new FileWriter(prefix + "inter_generation_distance" + sufix)));
            PrintWriter file6 = new PrintWriter(
                    new BufferedWriter(new FileWriter(prefix + "environment_population_distance" + sufix)));

            Population population = new Population(microSize, environment, populationSize, pctEnv, pctPool, 0,
                    0);

            while (population.getNumberOfGeneration() < numberOfGeneration) {
                population.sumSpecies();
                if (population.getNumberOfGeneration() % numberOfObservation == 0) {
                    file1.println(population.gammaDiversity(true));
                    file2.println(population.alphaDiversity(true));
                    file3.print(population.betaDiversity(true));
                    file3.print("\t");
                    file3.println(population.BrayCurtis(true));
                    file4.println(population.printOut());
                    file5.println(population.interGenerationDistance());
                    file6.println(population.environmentPopulationDistance());
                }
                population.getNextGen();
            }
            file1.close();
            file2.close();
            file3.close();
            file4.close();
            file5.close();
            file6.close();
        } catch (IOException e) {
            e.printStackTrace();
        }
    }
}

From source file:POP3Mail.java

public static void main(String[] args) {
    try {/* w ww  . j a  va 2s .c  om*/
        LogManager.getLogManager().readConfiguration(new FileInputStream("logging.properties"));
    } catch (Exception e1) {
        // TODO Auto-generated catch block
        e1.printStackTrace();
    }
    String server = null;
    String username = null;
    String password = null;
    if (new File("mail.properties").exists()) {
        Properties properties = new Properties();
        try {
            properties.load(new FileInputStream(new File("mail.properties")));
            server = properties.getProperty("server");
            username = properties.getProperty("username");
            password = properties.getProperty("password");
            ArrayList<String> list = new ArrayList<String>(
                    Arrays.asList(new String[] { server, username, password }));
            list.addAll(Arrays.asList(args));
            args = list.toArray(new String[list.size()]);
        } catch (FileNotFoundException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        } catch (IOException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        }
    }
    if (args.length < 3) {
        System.err
                .println("Usage: POP3Mail <pop3 server hostname> <username> <password> [TLS [true=implicit]]");
        System.exit(1);
    }

    server = args[0];
    username = args[1];
    password = args[2];
    String proto = null;
    int messageid = -1;
    boolean implicit = false;
    for (int i = 3; i < args.length; ++i) {
        if (args[i].equals("-m")) {
            i += 1;
            messageid = Integer.parseInt(args[i]);
        }
    }

    // String proto = args.length > 3 ? args[3] : null;
    // boolean implicit = args.length > 4 ? Boolean.parseBoolean(args[4])
    // : false;

    POP3Client pop3;

    if (proto != null) {
        System.out.println("Using secure protocol: " + proto);
        pop3 = new POP3SClient(proto, implicit);
    } else {
        pop3 = new POP3Client();
    }
    pop3.setDefaultPort(110);
    System.out.println("Connecting to server " + server + " on " + pop3.getDefaultPort());

    // We want to timeout if a response takes longer than 60 seconds
    pop3.setDefaultTimeout(60000);
    // suppress login details
    pop3.addProtocolCommandListener(new PrintCommandListener(new PrintWriter(System.out), true));

    try {
        pop3.connect(server);
    } catch (IOException e) {
        System.err.println("Could not connect to server.");
        e.printStackTrace();
        System.exit(1);
    }

    try {
        if (!pop3.login(username, password)) {
            System.err.println("Could not login to server.  Check password.");
            pop3.disconnect();
            System.exit(1);
        }
        PrintWriter printWriter = new PrintWriter(new FileWriter("messages.csv"), true);
        POP3MessageInfo[] messages = null;
        POP3MessageInfo[] identifiers = null;
        if (messageid == -1) {
            messages = pop3.listMessages();
            identifiers = pop3.listUniqueIdentifiers();
        } else {
            messages = new POP3MessageInfo[] { pop3.listMessage(messageid) };
        }
        if (messages == null) {
            System.err.println("Could not retrieve message list.");
            pop3.disconnect();
            return;
        } else if (messages.length == 0) {
            System.out.println("No messages");
            pop3.logout();
            pop3.disconnect();
            return;
        }
        new File("../json").mkdirs();
        int count = 0;
        for (POP3MessageInfo msginfo : messages) {
            if (msginfo.number != identifiers[count].number) {
                throw new RuntimeException();
            }
            msginfo.identifier = identifiers[count].identifier;
            BufferedReader reader = (BufferedReader) pop3.retrieveMessageTop(msginfo.number, 0);
            ++count;
            if (count % 100 == 0) {
                logger.finest(String.format("%d %s", msginfo.number, msginfo.identifier));
            }
            System.out.println(String.format("%d %s", msginfo.number, msginfo.identifier));
            if (reader == null) {
                System.err.println("Could not retrieve message header.");
                pop3.disconnect();
                System.exit(1);
            }
            if (printMessageInfo(reader, msginfo.number, printWriter)) {
            }
        }
        printWriter.close();
        pop3.logout();
        pop3.disconnect();
    } catch (IOException e) {
        e.printStackTrace();
        return;
    }
}