Example usage for java.io PrintWriter print

List of usage examples for java.io PrintWriter print

Introduction

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

Prototype

public void print(Object obj) 

Source Link

Document

Prints an object.

Usage

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.
 * /* w w  w  .j a  v a  2 s. c  o m*/
 * @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:GenericClient.java

public static void main(String[] args) throws IOException {
    try {//from  w  ww  .  java2 s. c  o m
        // Check the number of arguments
        if (args.length != 2)
            throw new IllegalArgumentException("Wrong number of args");

        // Parse the host and port specifications
        String host = args[0];
        int port = Integer.parseInt(args[1]);

        // Connect to the specified host and port
        Socket s = new Socket(host, port);

        // Set up streams for reading from and writing to the server.
        // The from_server stream is final for use in the inner class below
        final Reader from_server = new InputStreamReader(s.getInputStream());
        PrintWriter to_server = new PrintWriter(s.getOutputStream());

        // Set up streams for reading from and writing to the console
        // The to_user stream is final for use in the anonymous class below
        BufferedReader from_user = new BufferedReader(new InputStreamReader(System.in));
        // Pass true for auto-flush on println()
        final PrintWriter to_user = new PrintWriter(System.out, true);

        // Tell the user that we've connected
        to_user.println("Connected to " + s.getInetAddress() + ":" + s.getPort());

        // Create a thread that gets output from the server and displays
        // it to the user. We use a separate thread for this so that we
        // can receive asynchronous output
        Thread t = new Thread() {
            public void run() {
                char[] buffer = new char[1024];
                int chars_read;
                try {
                    // Read characters from the server until the
                    // stream closes, and write them to the console
                    while ((chars_read = from_server.read(buffer)) != -1) {
                        to_user.write(buffer, 0, chars_read);
                        to_user.flush();
                    }
                } catch (IOException e) {
                    to_user.println(e);
                }

                // When the server closes the connection, the loop above
                // will end. Tell the user what happened, and call
                // System.exit(), causing the main thread to exit along
                // with this one.
                to_user.println("Connection closed by server.");
                System.exit(0);
            }
        };

        // Now start the server-to-user thread
        t.start();

        // In parallel, read the user's input and pass it on to the server.
        String line;
        while ((line = from_user.readLine()) != null) {
            to_server.print(line + "\r\n");
            to_server.flush();
        }

        // If the user types a Ctrl-D (Unix) or Ctrl-Z (Windows) to end
        // their input, we'll get an EOF, and the loop above will exit.
        // When this happens, we stop the server-to-user thread and close
        // the socket.

        s.close();
        to_user.println("Connection closed by client.");
        System.exit(0);
    }
    // If anything goes wrong, print an error message
    catch (Exception e) {
        System.err.println(e);
        System.err.println("Usage: java GenericClient <hostname> <port>");
    }
}

From source file:eu.fbk.utils.lsa.util.Anvur.java

public static void main(String[] args) throws Exception {
    String logConfig = System.getProperty("log-config");
    if (logConfig == null) {
        logConfig = "log-config.txt";
    }//from  w  w  w .  ja  v  a 2  s  .  com

    PropertyConfigurator.configure(logConfig);
    /*
    if (args.length != 2)
    {
    log.println("Usage: java -mx512M eu.fbk.utils.lsa.util.Anvur in-file out-dir");
    System.exit(1);
    }
            
    File l = new File(args[1]);
    if (!l.exists())
    {
    l.mkdir();
    }
    List<String[]> list = readText(new File(args[0]));
    String oldCategory = "";
    for (int i=0;i<list.size();i++)
    {
    String[] s = list.get(i);
    if (!oldCategory.equals(s[0]))
    {
    File f = new File(args[1] + File.separator + s[0]);
    boolean b = f.mkdir();
    logger.debug(f + " created " + b);
    }
            
    File g = new File(args[1] + File.separator + s[0] + File.separator + s[1] + ".txt");
    logger.debug("writing " + g + "...");
    PrintWriter pw = new PrintWriter(new FileWriter(g));
    //pw.println(tokenize(s[1].substring(0, s[1].indexOf(".")).replace('_', ' ') + " " + s[2]));
    if (s.length == 5)
    {
    pw.println(tokenize(s[1].substring(0, s[1].indexOf(".")).replace('_', ' ') + " " + s[2] + " " + s[4].replace('_', ' ')));
    }
    else
    {
    pw.println(tokenize(s[1].substring(0, s[1].indexOf(".")).replace('_', ' ') + " " + s[2]));
    }
    pw.flush();
    pw.close();
            
    } // end for i
    */

    if (args.length != 7) {
        System.out.println(args.length);
        System.out.println(
                "Usage: java -mx2G eu.fbk.utils.lsa.util.Anvur input threshold size dim idf in-file-csv fields\n\n");
        System.exit(1);
    }

    //
    DecimalFormat dec = new DecimalFormat("#.00");

    File Ut = new File(args[0] + "-Ut");
    File Sk = new File(args[0] + "-S");
    File r = new File(args[0] + "-row");
    File c = new File(args[0] + "-col");
    File df = new File(args[0] + "-df");
    double threshold = Double.parseDouble(args[1]);
    int size = Integer.parseInt(args[2]);
    int dim = Integer.parseInt(args[3]);
    boolean rescaleIdf = Boolean.parseBoolean(args[4]);

    //"author_check"0,   "authors"1,   "title"2,   "year"3,   "pubtype"4,   "publisher"5,   "journal"6,   "volume"7,   "number"8,   "pages"9,   "abstract"10,   "nauthors",   "citedby"
    String[] labels = { "author_check", "authors", "title", "year", "pubtype", "publisher", "journal", "volume",
            "number", "pages", "abstract", "nauthors", "citedby"
            //author_id   authors   title   year   pubtype   publisher   journal   volume   number   pages   abstract   nauthors   citedby

    };
    String name = buildName(labels, args[6]);

    File bwf = new File(args[5] + name + "-bow.txt");
    PrintWriter bw = new PrintWriter(
            new BufferedWriter(new OutputStreamWriter(new FileOutputStream(bwf), "UTF-8")));
    File bdf = new File(args[5] + name + "-bow.csv");
    PrintWriter bd = new PrintWriter(
            new BufferedWriter(new OutputStreamWriter(new FileOutputStream(bdf), "UTF-8")));
    File lwf = new File(args[5] + name + "-ls.txt");
    PrintWriter lw = new PrintWriter(
            new BufferedWriter(new OutputStreamWriter(new FileOutputStream(lwf), "UTF-8")));
    File ldf = new File(args[5] + name + "-ls.csv");
    PrintWriter ld = new PrintWriter(
            new BufferedWriter(new OutputStreamWriter(new FileOutputStream(ldf), "UTF-8")));
    File blwf = new File(args[5] + name + "-bow+ls.txt");
    PrintWriter blw = new PrintWriter(
            new BufferedWriter(new OutputStreamWriter(new FileOutputStream(blwf), "UTF-8")));
    File bldf = new File(args[5] + name + "-bow+ls.csv");
    PrintWriter bld = new PrintWriter(
            new BufferedWriter(new OutputStreamWriter(new FileOutputStream(bldf), "UTF-8")));
    File logf = new File(args[5] + name + ".log");
    PrintWriter log = new PrintWriter(
            new BufferedWriter(new OutputStreamWriter(new FileOutputStream(logf), "UTF-8")));

    //System.exit(0);
    LSM lsm = new LSM(Ut, Sk, r, c, df, dim, rescaleIdf);
    LSSimilarity lss = new LSSimilarity(lsm, size);

    List<String[]> list = readText(new File(args[5]));

    // author_check   authors   title   year   pubtype   publisher   journal   volume   number   pages   abstract   nauthors   citedby

    //header
    for (int i = 0; i < list.size(); i++) {
        String[] s1 = list.get(i);
        String t1 = s1[0].toLowerCase();
        bw.print("\t");
        lw.print("\t");
        blw.print("\t");
        bw.print(i + "(" + s1[0] + ")");
        lw.print(i + "(" + s1[0] + ")");
        blw.print(i + "(" + s1[0] + ")");
    } // end for i

    bw.print("\n");
    lw.print("\n");
    blw.print("\n");
    for (int i = 0; i < list.size(); i++) {
        logger.info(i + "\t");
        String[] s1 = list.get(i);
        String t1 = buildText(s1, args[6]);
        BOW bow1 = new BOW(t1);
        logger.info(bow1);

        Vector d1 = lsm.mapDocument(bow1);
        d1.normalize();
        log.println("d1:" + d1);

        Vector pd1 = lsm.mapPseudoDocument(d1);
        pd1.normalize();
        log.println("pd1:" + pd1);

        Vector m1 = merge(pd1, d1);
        log.println("m1:" + m1);

        // write the orginal line
        for (int j = 0; j < s1.length; j++) {
            bd.print(s1[j]);
            bd.print("\t");
            ld.print(s1[j]);
            ld.print("\t");
            bld.print(s1[j]);
            bld.print("\t");

        }
        // write the bow, ls, and bow+ls vectors
        bd.println(d1);
        ld.println(pd1);
        bld.println(m1);

        bw.print(i + "(" + s1[0] + ")");
        lw.print(i + "(" + s1[0] + ")");
        blw.print(i + "(" + s1[0] + ")");
        for (int j = 0; j < i + 1; j++) {
            bw.print("\t");
            lw.print("\t");
            blw.print("\t");
        } // end for j

        for (int j = i + 1; j < list.size(); j++) {
            logger.info(i + "\t" + j);
            String[] s2 = list.get(j);

            String t2 = buildText(s2, args[6]);
            BOW bow2 = new BOW(t2);

            log.println(i + ":" + j + "(" + s1[0] + ":" + s2[0] + ") t1:" + t1);
            log.println(i + ":" + j + "(" + s1[0] + ":" + s2[0] + ") t2:" + t2);
            log.println(i + ":" + j + "(" + s1[0] + ":" + s2[0] + ") bow1:" + bow1);
            log.println(i + ":" + j + "(" + s1[0] + ":" + s2[0] + ") bow2:" + bow2);

            Vector d2 = lsm.mapDocument(bow2);
            d2.normalize();
            log.println("d2:" + d2);

            Vector pd2 = lsm.mapPseudoDocument(d2);
            pd2.normalize();
            log.println("pd2:" + pd2);

            Vector m2 = merge(pd2, d2);
            log.println("m2:" + m2);

            float cosVSM = d1.dotProduct(d2) / (float) Math.sqrt(d1.dotProduct(d1) * d2.dotProduct(d2));
            float cosLSM = pd1.dotProduct(pd2) / (float) Math.sqrt(pd1.dotProduct(pd1) * pd2.dotProduct(pd2));
            float cosBOWLSM = m1.dotProduct(m2) / (float) Math.sqrt(m1.dotProduct(m1) * m2.dotProduct(m2));
            bw.print("\t");
            bw.print(dec.format(cosVSM));
            lw.print("\t");
            lw.print(dec.format(cosLSM));
            blw.print("\t");
            blw.print(dec.format(cosBOWLSM));

            log.println(i + ":" + j + "(" + s1[0] + ":" + s2[0] + ") bow\t" + cosVSM);
            log.println(i + ":" + j + "(" + s1[0] + ":" + s2[0] + ") ls:\t" + cosLSM);
            log.println(i + ":" + j + "(" + s1[0] + ":" + s2[0] + ") bow+ls:\t" + cosBOWLSM);
        }
        bw.print("\n");
        lw.print("\n");
        blw.print("\n");
    } // end for i

    logger.info("wrote " + bwf);
    logger.info("wrote " + bwf);
    logger.info("wrote " + bdf);
    logger.info("wrote " + lwf);
    logger.info("wrote " + ldf);
    logger.info("wrote " + blwf);
    logger.info("wrote " + bldf);
    logger.info("wrote " + logf);

    ld.close();
    bd.close();
    bld.close();
    bw.close();
    lw.close();
    blw.close();

    log.close();

}

From source file:microbiosima.SelectiveMicrobiosima.java

/**
 * @param args// w  w w .ja va  2  s . co  m
 *            the command line arguments
 * @throws java.io.FileNotFoundException
 * @throws java.io.UnsupportedEncodingException
 */

public static void main(String[] args) throws FileNotFoundException, UnsupportedEncodingException {
    int populationSize = 500;//Integer.parseInt(parameters[1]);
    int microSize = 1000;//Integer.parseInt(parameters[2]);
    int numberOfSpecies = 150;//Integer.parseInt(parameters[3]);
    int numberOfGeneration = 10000;
    int Ngene = 10;
    int numberOfObservation = 100;
    int numberOfReplication = 10;
    double Ngenepm = 5;
    double pctEnv = 0;
    double pctPool = 0;
    double msCoeff = 1;
    double hsCoeff = 1;
    boolean HMS_or_TMS = true;

    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(6).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, (5) number of total traits, (6)number of traits per microbe"
                    + " [default: 500 1000 150 10000 10 5]");
    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"
            + "  msCoeff            Parameter related to microbe selection strength\n"
            + "  hsCoeff            Parameter related to host selection strength\n"
            + "  HMS_or_TMS         String HMS or TMS to specify host-mediated or trait-mediated microbe selection\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 != 5) {
            System.out.println(
                    "ERROR! Required exactly five argumennts for pct_env, pct_pool, msCoeff, hsCoeff and HMS_or_TMS. 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]);
            msCoeff = Double.parseDouble(pct_config[2]);
            hsCoeff = Double.parseDouble(pct_config[3]);
            if (pct_config[4].equals("HMS"))
                HMS_or_TMS = true;
            if (pct_config[4].equals("TMS"))
                HMS_or_TMS = false;
            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 (msCoeff < 1) {
                System.out.println(
                        "ERROR: msCoeff (parameter related to microbe selection strength) must be not less than 1 (msCoeff="
                                + msCoeff + ")! EXIT");
                System.exit(3);
            }
            if (hsCoeff < 1) {
                System.out.println(
                        "ERROR: hsCoeff (parameter related to host selection strength) must be not less than 1 (hsCoeff="
                                + hsCoeff + ")! EXIT");
                System.exit(3);
            }
            if (!(pct_config[4].equals("HMS") || pct_config[4].equals("TMS"))) {
                System.out.println(
                        "ERROR: HMS_or_TMS (parameter specifying host-mediated or trait-mediated selection) must be either 'HMS' or 'TMS' (HMS_or_TMS="
                                + pct_config[4] + ")! 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]);
            Ngene = Integer.parseInt(configs[4]);
            Ngenepm = Double.parseDouble(configs[5]);
            if (Ngenepm > Ngene) {
                System.out.println(
                        "ERROR: number of traits per microbe must not be greater than number of total traits! EXIT");
                System.exit(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\tNumber of total traits: ").append(Ngene).append("\n\tNumber of traits per microbe: ")
            .append(Ngenepm).append("\n");
    System.out.println(sb.toString());

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

    for (int rep = 0; rep < numberOfReplication; rep++) {
        String prefix = "" + (rep + 1) + "_";
        String sufix;
        if (HMS_or_TMS)
            sufix = "_E" + pctEnv + "_P" + pctPool + "_HS" + hsCoeff + "_HMS" + msCoeff + ".txt";
        else
            sufix = "_E" + pctEnv + "_P" + pctPool + "_HS" + hsCoeff + "_TMS" + msCoeff + ".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)));
            PrintWriter file7 = new PrintWriter(
                    new BufferedWriter(new FileWriter(prefix + "host_fitness" + sufix)));
            PrintWriter file8 = new PrintWriter(
                    new BufferedWriter(new FileWriter(prefix + "cos_theta" + sufix)));
            PrintWriter file9 = new PrintWriter(
                    new BufferedWriter(new FileWriter(prefix + "host_fitness_distribution" + sufix)));
            PrintWriter file10 = new PrintWriter(
                    new BufferedWriter(new FileWriter(prefix + "microbiome_fitness_distribution" + sufix)));
            PrintWriter file11 = new PrintWriter(
                    new BufferedWriter(new FileWriter(prefix + "bacteria_contents" + sufix)));
            PrintWriter file12 = new PrintWriter(
                    new BufferedWriter(new FileWriter(prefix + "individual_bacteria_contents" + sufix)));
            for (int i = 0; i < Ngene; i++) {
                fitnessToMicrobe[i] = MathUtil.getNextInt(2) - 1;
                fitnessToHost[i] = MathUtil.getNextInt(2) - 1;
            }
            MathUtil.setSeed(rep % numberOfReplication);
            SelectiveSpeciesRegistry ssr = new SelectiveSpeciesRegistry(numberOfSpecies, Ngene, Ngenepm,
                    msCoeff, fitnessToHost, fitnessToMicrobe);
            MathUtil.setSeed();
            SelectivePopulation population = new SelectivePopulation(microSize, environment, populationSize,
                    pctEnv, pctPool, 0, 0, ssr, hsCoeff, HMS_or_TMS);

            while (population.getNumberOfGeneration() < numberOfGeneration) {
                population.sumSpecies();
                if (population.getNumberOfGeneration() % numberOfObservation == 0) {
                    //file1.print(population.gammaDiversity(false));
                    //file2.print(population.alphaDiversity(false));
                    //file1.print("\t");
                    //file2.print("\t");
                    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());
                    file7.print(population.averageHostFitness());
                    file7.print("\t");
                    file7.println(population.varianceHostFitness());
                    file8.println(population.cosOfMH());
                    file9.println(population.printOutHFitness());
                    file10.println(population.printOutMFitness());
                    file11.println(population.printBacteriaContents());
                }
                population.getNextGen();
            }
            for (SelectiveIndividual host : population.getIndividuals()) {
                file12.println(host.printBacteriaContents());
            }
            file1.close();
            file2.close();
            file3.close();
            file4.close();
            file5.close();
            file6.close();
            file7.close();
            file8.close();
            file9.close();
            file10.close();
            file11.close();
            file12.close();
        } catch (IOException e) {
            e.printStackTrace();
        }
    }
}

From source file:com.bluemarsh.jswat.console.Main.java

/**
 * Kicks off the application./*from  w w w. ja va  2  s.c o m*/
 *
 * @param  args  the command line arguments.
 */
public static void main(String[] args) {
    //
    // An attempt was made early on to use the Console class in java.io,
    // but that is not designed to handle asynchronous output from
    // multiple threads, so we just use the usual System.out for output
    // and System.in for input. Note that automatic flushing is used to
    // ensure output is shown in a timely fashion.
    //

    //
    // Where console mode seems to work:
    // - bash
    // - emacs
    //
    // Where console mode does not seem to work:
    // - NetBeans: output from event listeners is never shown and the
    //   cursor sometimes lags behind the output
    //

    // Turn on flushing so printing the prompt will flush
    // all buffered output generated from other threads.
    PrintWriter output = new PrintWriter(System.out, true);

    // Make sure we have the JPDA classes.
    try {
        Bootstrap.virtualMachineManager();
    } catch (NoClassDefFoundError ncdfe) {
        output.println(NbBundle.getMessage(Main.class, "MSG_Main_NoJPDA"));
        System.exit(1);
    }

    // Ensure we can create the user directory by requesting the
    // platform service. Simply asking for it has the desired effect.
    PlatformProvider.getPlatformService();

    // Define the logging configuration.
    LogManager manager = LogManager.getLogManager();
    InputStream is = Main.class.getResourceAsStream("logging.properties");
    try {
        manager.readConfiguration(is);
    } catch (IOException ioe) {
        ioe.printStackTrace();
        System.exit(1);
    }

    // Print out some useful debugging information.
    logSystemDetails();

    // Add a shutdown hook to make sure we exit cleanly.
    Runtime.getRuntime().addShutdownHook(new Thread(new Runnable() {

        @Override
        public void run() {
            // Save the command aliases.
            CommandParser parser = CommandProvider.getCommandParser();
            parser.saveSettings();
            // Save the runtimes to persistent storage.
            RuntimeManager rm = RuntimeProvider.getRuntimeManager();
            rm.saveRuntimes();
            // Save the sessions to persistent storage and have them
            // close down in preparation to exit.
            SessionManager sm = SessionProvider.getSessionManager();
            sm.saveSessions(true);
        }
    }));

    // Initialize the command parser and load the aliases.
    CommandParser parser = CommandProvider.getCommandParser();
    parser.loadSettings();
    parser.setOutput(output);

    // Create an OutputAdapter to display debuggee output.
    OutputAdapter adapter = new OutputAdapter(output);
    SessionManager sessionMgr = SessionProvider.getSessionManager();
    sessionMgr.addSessionManagerListener(adapter);
    // Create a SessionWatcher to monitor the session status.
    SessionWatcher swatcher = new SessionWatcher();
    sessionMgr.addSessionManagerListener(swatcher);
    // Create a BreakpointWatcher to monitor the breakpoints.
    BreakpointWatcher bwatcher = new BreakpointWatcher();
    sessionMgr.addSessionManagerListener(bwatcher);

    // Add the watchers and adapters to the open sessions.
    Iterator<Session> iter = sessionMgr.iterateSessions();
    while (iter.hasNext()) {
        Session s = iter.next();
        s.addSessionListener(adapter);
        s.addSessionListener(swatcher);
    }

    // Find and run the RC file.
    try {
        runStartupFile(parser, output);
    } catch (IOException ioe) {
        logger.log(Level.SEVERE, null, ioe);
    }

    // Process command line arguments.
    try {
        processArguments(args);
    } catch (ParseException pe) {
        // Report the problem and keep going.
        System.err.println("Option parsing failed: " + pe.getMessage());
        logger.log(Level.SEVERE, null, pe);
    }

    // Display a helpful greeting.
    output.println(NbBundle.getMessage(Main.class, "MSG_Main_Welcome"));
    if (jdbEmulationMode) {
        output.println(NbBundle.getMessage(Main.class, "MSG_Main_Jdb_Emulation"));
    }

    // Enter the main loop of processing user input.
    BufferedReader input = new BufferedReader(new InputStreamReader(System.in));
    while (true) {
        // Keep the prompt format identical to jdb for compatibility
        // with emacs and other possible wrappers.
        output.print("> ");
        output.flush();
        try {
            String command = input.readLine();
            // A null value indicates end of stream.
            if (command != null) {
                performCommand(output, parser, command);
            }
            // Sleep briefly to give the event processing threads,
            // and the automatic output flushing, a chance to catch
            // up before printing the input prompt again.
            Thread.sleep(250);
        } catch (InterruptedException ie) {
            logger.log(Level.WARNING, null, ie);
        } catch (IOException ioe) {
            logger.log(Level.SEVERE, null, ioe);
            output.println(NbBundle.getMessage(Main.class, "ERR_Main_IOError", ioe));
        } catch (Exception x) {
            // Don't ever let an internal bug (e.g. in the command parser)
            // hork the console, as it really irritates people.
            logger.log(Level.SEVERE, null, x);
            output.println(NbBundle.getMessage(Main.class, "ERR_Main_Exception", x));
        }
    }
}

From source file:Main.java

/**
 * Write XML header (UTF-8).//from w  w  w.ja  va  2s . co m
 * 
 * @param out
 *            The writer.
 */
public static void writeXmlHeader(PrintWriter out) {
    out.print("<?xml version=\"1.0\" encoding=\"UTF-8\"?>");
}

From source file:Main.java

/**
 * Generates the end of an XML tag &lt;/fieldName&gt;
 *
 * @param fieldName/*from  w  w  w  .  j a  v a  2 s. c  om*/
 * @param pw
 */
static public void writeXMLEnd(String fieldName, PrintWriter pw) {
    pw.print("</");
    pw.print(fieldName);
    pw.println('>');
}

From source file:Main.java

/**
 * Write close element.// w  w w.jav a  2s.  c om
 * 
 * @param out
 *            The writer.
 * @param element
 *            The element name.
 */
public static void writeCloseElement(PrintWriter out, String element) {
    out.print("</");
    out.print(element);
    out.print('>');
}

From source file:Main.java

/**
 * Writes a DOM node (and all its ancestors) to the given output stream
 * //w w w.  ja v  a 2  s  .c  o  m
 * @param n
 *            the node to write
 * @param o
 *            the output stream to write the node to
 */
public static void writeNode(Node n, FileOutputStream o) {
    PrintWriter w = new PrintWriter(o);
    w.print(n.toString());
    w.close();
}

From source file:com.jjtree.utilities.JResponse.java

public static void sendJson(HttpServletResponse response, JSONObject json) throws IOException {
    PrintWriter writer = response.getWriter();
    writer.print(json);
    writer.flush();//w w  w  . j  a v a 2  s  . co m
}