Example usage for org.apache.commons.cli ParseException printStackTrace

List of usage examples for org.apache.commons.cli ParseException printStackTrace

  1. HOME
  2. Java
  3. org.apache.commons
  4. org.apache.commons.cli.*
  5. ParseException
  6. printStackTrace

Introduction

In this page you can find the example usage for org.apache.commons.cli ParseException printStackTrace.

Prototype

public void printStackTrace()

Source Link

Document

Prints this throwable and its backtrace to the standard error stream.

Usage

From source file:edu.cmu.lti.oaqa.knn4qa.apps.FilterVocabulary.java

public static void main(String[] args) {
    String optKeys[] = { IN_VOC_FILE_PARAM, OUT_VOC_FILE_PARAM, CommonParams.MEM_FWD_INDEX_PARAM,
            CommonParams.MAX_WORD_QTY_PARAM };
    String optDescs[] = { IN_VOC_FILE_DESC, OUT_VOC_FILE_DESC, CommonParams.MEM_FWD_INDEX_DESC,
            CommonParams.MAX_WORD_QTY_DESC };
    boolean hasArg[] = { true, true, true, true };

    ParamHelper mParamHelper = null;/*from  ww w  .j  a v  a2  s . c o  m*/

    try {

        mParamHelper = new ParamHelper(args, optKeys, optDescs, hasArg);

        CommandLine cmd = mParamHelper.getCommandLine();

        String outputFile = cmd.getOptionValue(OUT_VOC_FILE_PARAM);
        if (null == outputFile) {
            UsageSpecify(OUT_VOC_FILE_DESC, mParamHelper.getOptions());
        }

        String inputFile = cmd.getOptionValue(IN_VOC_FILE_PARAM);
        if (null == inputFile) {
            UsageSpecify(IN_VOC_FILE_DESC, mParamHelper.getOptions());
        }

        int maxWordQty = Integer.MAX_VALUE;

        String tmpi = cmd.getOptionValue(CommonParams.MAX_WORD_QTY_PARAM);

        if (null != tmpi) {
            maxWordQty = Integer.parseInt(tmpi);
        }

        String memFwdIndxName = cmd.getOptionValue(CommonParams.MEM_FWD_INDEX_PARAM);
        if (null == memFwdIndxName) {
            UsageSpecify(CommonParams.MEM_FWD_INDEX_DESC, mParamHelper.getOptions());
        }

        VocabularyFilterAndRecoder filter = new FrequentIndexWordFilterAndRecoder(memFwdIndxName, maxWordQty);

        BufferedReader finp = new BufferedReader(
                new InputStreamReader(CompressUtils.createInputStream(inputFile)));
        BufferedWriter fout = new BufferedWriter(
                new OutputStreamWriter(CompressUtils.createOutputStream(outputFile)));
        try {

            String line;

            int wordQty = 0;
            long addedQty = 0;
            long totalQty = 0;

            for (totalQty = 0; (line = finp.readLine()) != null;) {
                ++totalQty;
                // Skip empty lines
                line = line.trim();
                if (line.isEmpty())
                    continue;

                GizaVocRec rec = new GizaVocRec(line);

                if (filter.checkWord(rec.mWord)) {
                    rec.save(fout);
                    addedQty++;
                }

                if (totalQty % REPORT_INTERVAL_QTY == 0)
                    System.out.println(String.format(
                            "Processed %d lines (%d source word entries) from '%s', added %d lines", totalQty,
                            wordQty, inputFile, addedQty));
            }

        } finally {
            finp.close();
            fout.close();
        }
    } catch (ParseException e) {
        Usage("Cannot parse arguments", mParamHelper != null ? mParamHelper.getOptions() : null);
        e.printStackTrace();
    } catch (Exception e) {
        e.printStackTrace();
        System.err.println("Terminating due to an exception: " + e);
        System.exit(1);
    }
}

From source file:dk.statsbiblioteket.netark.dvenabler.Command.java

@SuppressWarnings("CallToPrintStackTrace")
public static void main(String[] args) throws IOException {
    CommandLine cli;//from  w ww. j a v a  2s.c o m
    try {
        cli = new GnuParser().parse(getOptions(), args);
    } catch (ParseException e) {
        System.err.println("Exception parsing arguments");
        e.printStackTrace();
        usage();
        return;
    }

    if (cli.hasOption(HELP)) {
        usage();
        return;
    }

    if (!cli.hasOption(INPUT)) {
        System.err.println("input index must be specified");
        usage();
        return;
    }

    final File in = new File(cli.getOptionValue(INPUT));
    if (!in.exists() || !in.isDirectory()) {
        System.err.println("Unable to access index folder '" + in + "'");
        usage();
        return;
    }

    final boolean verbose = cli.hasOption(VERBOSE);
    if (cli.hasOption(LIST)) {
        list(in, verbose);
        return;
    }

    if (cli.hasOption(CONVERT)) {
        if (!cli.hasOption(OUTPUT)) {
            System.err.println("convert is specified but output is missing");
            usage();
            return;
        }
        final File out = new File(cli.getOptionValue(OUTPUT));
        if (!cli.hasOption(FIELDS)) {
            System.err.println("convert is specified but no fields are defined.\n"
                    + "Use '.' to signal that no fields should be changed");
            usage();
            return;
        }
        final String[] rawFields = cli.getOptionValues(FIELDS);
        List<DVConfig> dvFields = getTweakedFields(in, rawFields);
        if (dvFields == null) {
            System.err.println("Invalid field specification");
            usage();
            return;
        }
        convert(in, out, dvFields, verbose);
        return;
    }

    System.out.println("Nothing to do");
    usage();
}

From source file:bbs.monitor.ListNode.java

public static void main(String[] args) throws Exception {
    boolean printRawForm = false;
    String transport = null;//from w w  w.  j a  v  a  2  s  .c  o m
    String selfAddressAndPort = null;

    // parse command-line arguments
    Options opts = new Options();
    opts.addOption("h", "help", false, "print help");
    opts.addOption("r", "raw", false, "print nodes in the raw form (hostname:port)");
    opts.addOption("t", "transport", true, "transpoft, UDP or TCP");
    opts.addOption("s", "selfipaddress", true, "self IP address (and port)");

    CommandLineParser parser = new PosixParser();
    CommandLine cmd = null;
    try {
        cmd = parser.parse(opts, args);
    } catch (ParseException e) {
        System.out.println("There is an invalid option.");
        e.printStackTrace();
        System.exit(1);
    }

    String optVal;
    if (cmd.hasOption('h')) {
        usage(COMMAND);
        System.exit(1);
    }
    if (cmd.hasOption('r')) {
        printRawForm = true;
    }
    optVal = cmd.getOptionValue('t');
    if (optVal != null) {
        transport = optVal;
    }
    optVal = cmd.getOptionValue('s');
    if (optVal != null) {
        selfAddressAndPort = optVal;
    }

    args = cmd.getArgs();

    // parse initial contact
    String contactHostAndPort = null;
    int contactPort = -1;

    if (args.length < 1) {
        usage(COMMAND);
        System.exit(1);
    }

    contactHostAndPort = args[0];

    if (args.length >= 2)
        contactPort = Integer.parseInt(args[1]);

    //
    // prepare a NodeCollector and invoke it
    //

    // prepare StatConfiguration
    StatConfiguration config = StatFactory.getDefaultConfiguration();
    config.setDoUPnPNATTraversal(false);
    if (transport != null) {
        config.setMessagingTransport(transport);
    }
    if (selfAddressAndPort != null) {
        MessagingUtility.HostAndPort hostAndPort = MessagingUtility.parseHostnameAndPort(selfAddressAndPort,
                config.getSelfPort());

        config.setSelfAddress(hostAndPort.getHostName());
        config.setSelfPort(hostAndPort.getPort());
    }

    // prepare MessageReceiver and initial contact
    MessagingProvider provider = config.deriveMessagingProvider();
    MessageReceiver receiver = config.deriveMessageReceiver(provider);

    MessagingAddress contact;
    try {
        contact = provider.getMessagingAddress(contactHostAndPort, contactPort);
    } catch (IllegalArgumentException e) {
        contact = provider.getMessagingAddress(contactHostAndPort, config.getContactPort());
    }

    // prepare a callback
    NodeCollectorCallback cb;
    if (printRawForm) {
        cb = new NodeCollectorCallback() {
            public void addNode(ID id, MessagingAddress address) {
                System.out.println(new MessagingUtility.HostAndPort(address.getHostname(), address.getPort()));
                // <hostname>:<port>
            }

            public void removeNode(ID id) {
            }
        };
    } else {
        cb = new NodeCollectorCallback() {
            public void addNode(ID id, MessagingAddress address) {
                //System.out.println(HTMLUtil.convertMessagingAddressToURL(address));
                System.out.println("http://" + address.getHostAddress() + ":" + address.getPort() + "/");
                // http://<hostname>:port/
            }

            public void removeNode(ID id) {
            }
        };
    }

    // instantiate and invoke a NodeCollector
    NodeCollector collector = StatFactory.getNodeCollector(config, contact, cb, receiver);

    collector.investigate();

    // stop MessageReceiver to prevent
    // handling incoming messages and submissions to a thread pool
    receiver.stop();
}

From source file:edu.internet2.middleware.psp.PspCLI.java

/**
 * Run this application./*  w ww .ja v a2 s .c o  m*/
 * 
 * @param args the command line arguments
 */
public static void main(String[] args) {

    PspOptions options = new PspOptions(args);

    try {
        if (args.length == 0) {
            options.printUsage();
            return;
        }

        options.parseCommandLineOptions();

        PspCLI pspCLI = new PspCLI(options);

        if (options.getInterval() == 0) {
            pspCLI.run();
        } else {
            pspCLI.schedule();
        }

    } catch (ParseException e) {
        options.printUsage();
        System.err.println(e.getMessage());
        e.printStackTrace();
    } catch (ResourceException e) {
        System.err.println(e.getMessage());
        e.printStackTrace();
    } catch (IOException e) {
        System.err.println(e.getMessage());
        e.printStackTrace();
    }
}

From source file:alluxio.cli.LogLevel.java

/**
 * Sets or gets log level of master and worker through their REST API.
 *
 * @param args same arguments as {@link LogLevel}
 *//*  w  w w .  j  av  a2  s .c o m*/
public static void main(String[] args) {
    int exitCode = 1;
    try {
        logLevel(args);
        exitCode = 0;
    } catch (ParseException e) {
        printHelp("Unable to parse input args: " + e.getMessage());
    } catch (IOException e) {
        e.printStackTrace();
        System.err.println(String.format("Failed to set log level: %s", e.getMessage()));
    }
    System.exit(exitCode);
}

From source file:dhtaccess.benchmark.ThroughputMeasure.java

public static void main(String[] args) {
    boolean details = false;
    int repeats = DEFAULT_REPEATS;
    int queryFreq = DEFAULT_QUERIES_PER_SEC;
    boolean doPut = true;

    // parse options
    Options options = new Options();
    options.addOption("h", "help", false, "print help");
    options.addOption("d", "details", false, "requests secret hash and TTL");
    options.addOption("r", "repeats", true, "number of requests");
    options.addOption("f", "freq", true, "number of queries per second");
    options.addOption("n", "no-put", false, "does not put");

    CommandLineParser parser = new PosixParser();
    CommandLine cmd = null;//  ww  w.  ja v  a 2 s.  c o m
    try {
        cmd = parser.parse(options, args);
    } catch (ParseException e) {
        System.out.println("There is an invalid option.");
        e.printStackTrace();
        System.exit(1);
    }

    String optVal;
    if (cmd.hasOption('h')) {
        usage(COMMAND);
        System.exit(1);
    }
    if (cmd.hasOption('d')) {
        details = true;
    }
    optVal = cmd.getOptionValue('r');
    if (optVal != null) {
        repeats = Integer.parseInt(optVal);
    }
    optVal = cmd.getOptionValue('f');
    if (optVal != null) {
        queryFreq = Integer.parseInt(optVal);
    }
    if (cmd.hasOption('n')) {
        doPut = false;
    }

    args = cmd.getArgs();

    // parse arguments
    if (args.length < 1) {
        usage(COMMAND);
        System.exit(1);
    }

    (new ThroughputMeasure()).start(details, repeats, queryFreq, doPut, args);
}

From source file:de.moritzrupp.stockreader.Main.java

/**
 * main/*w  w w. j  a v a 2 s .c  o m*/
 * @param args
 */
public static void main(String[] args) {

    initOptions();
    clParser = new GnuParser();

    if (args.length == 0) { // if no arguments

        formatter.printHelp("stockreader", header, options, footer);
        System.exit(1);
    }

    try {

        CommandLine line = clParser.parse(options, args);

        if (line.hasOption("h")) {

            printHelp();
        }

        if (line.hasOption("v")) {

            System.out.println("stockreader version " + VERSION
                    + ". Copyright 2013 by Moritz Rupp. All rights reserved.\n"
                    + "This application is licensed under The MIT License (MIT). See https://github.com/moritzrupp/stockreader/blob/master/LICENSE.md");
            System.exit(0);
        }

        if (line.hasOption("p")) {

            priceArg = true;
        }

        if (line.hasOption("f")) {

            fileArg = true;
            theFile = new File(line.getOptionValue("f"));
        }

        host = line.getOptionValue("host");
        username = line.getOptionValue("user");
        passwd = line.getOptionValue("password");
        from = line.getOptionValue("from");
        to = line.getOptionValue("to");
    } catch (ParseException exp) {
        // TODO Auto-generated catch block
        exp.printStackTrace();
    }

    try {

        reader = new StockReader(';', new StockQuote(), "UTF-8",
                (fileArg) ? theFile.toString()
                        : new File(".").getCanonicalPath()
                                + ((System.getProperty("os.name").toLowerCase().startsWith("win")) ? "\\" : "/")
                                + "stocks.csv");

        for (int i = 0; i < args.length; i++) {

            switch (args[i].charAt(0)) {

            case '-':
                if (args[i].length() < 2) {

                    System.err.println("Not a valid argument: " + args[i]);
                    printHelp();
                    System.exit(1);
                }

                if (args[i].charAt(1) == 'f' || (args[i].charAt(1) == '-' && args[i].charAt(2) == 'f')) {

                    // get the path and set it to "nosymbol"
                    args[i + 1] = "nosymbol";
                }

                break;
            default:
                if (!args[i].equals("nosymbol")) {
                    reader.addSymbol(args[i]);
                }
                break;
            }
        }

        reader.getQuotes();
        reader.writeToCSV(priceArg);
        reader.sendmail(from, to, "Aktienkurse", host, username, passwd);
    } catch (IOException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    } catch (JAXBException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    } catch (java.text.ParseException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }
}

From source file:net.mmberg.nadia.processor.NadiaProcessor.java

/**
 * @param args/*from  w w  w.  java  2s  .  c o  m*/
 */
@SuppressWarnings("static-access")
public static void main(String[] args) {

    Class<? extends UserInterface> ui_class = ConsoleInterface.class; //default UI
    String dialog_file = default_dialog; //default dialogue

    //process command line args
    Options cli_options = new Options();
    cli_options.addOption("h", "help", false, "print this message");
    cli_options.addOption(OptionBuilder.withLongOpt("interface").withDescription("select user interface")
            .hasArg(true).withArgName("console, rest").create("i"));
    cli_options.addOption("f", "file", true, "specify dialogue path and file, e.g. -f /res/dialogue1.xml");
    cli_options.addOption("r", "resource", true, "load dialogue (by name) from resources, e.g. -r dialogue1");
    cli_options.addOption("s", "store", true, "load dialogue (by name) from internal store, e.g. -s dialogue1");

    CommandLineParser parser = new org.apache.commons.cli.BasicParser();
    try {
        CommandLine cmd = parser.parse(cli_options, args);

        //Help
        if (cmd.hasOption("h")) {
            HelpFormatter formatter = new HelpFormatter();
            formatter.printHelp("nadia", cli_options, true);
            return;
        }

        //UI
        if (cmd.hasOption("i")) {
            String interf = cmd.getOptionValue("i");
            if (interf.equals("console"))
                ui_class = ConsoleInterface.class;
            else if (interf.equals("rest"))
                ui_class = RESTInterface.class;
        }

        //load dialogue from path file
        if (cmd.hasOption("f")) {
            dialog_file = "file:///" + cmd.getOptionValue("f");
        }
        //load dialogue from resources
        if (cmd.hasOption("r")) {
            dialog_file = config.getProperty(NadiaProcessorConfig.DIALOGUEDIR) + "/" + cmd.getOptionValue("r")
                    + ".xml";
        }
        //load dialogue from internal store
        if (cmd.hasOption("s")) {
            Dialog store_dialog = DialogStore.getInstance().getDialogFromStore((cmd.getOptionValue("s")));
            store_dialog.save();
            dialog_file = config.getProperty(NadiaProcessorConfig.DIALOGUEDIR) + "/" + cmd.getOptionValue("s")
                    + ".xml";
        }

    } catch (ParseException e1) {
        logger.severe("NADIA: loading by main-method failed. " + e1.getMessage());
        e1.printStackTrace();
    }

    //start Nadia with selected UI
    default_dialog = dialog_file;
    NadiaProcessor nadia = new NadiaProcessor();
    try {
        ui = ui_class.newInstance();
        ui.register(nadia);
        ui.start();
    } catch (Exception e) {
        e.printStackTrace();
    }
}

From source file:dhtaccess.benchmark.LatencyMeasure.java

public static void main(String[] args) {
    boolean details = false;
    int repeats = DEFAULT_REPEATS;
    boolean doPut = true;

    // parse options
    Options options = new Options();
    options.addOption("h", "help", false, "print help");
    options.addOption("d", "details", false, "requests secret hash and TTL");
    options.addOption("r", "repeats", true, "number of requests");
    options.addOption("n", "no-put", false, "does not put");

    CommandLineParser parser = new PosixParser();
    CommandLine cmd = null;//from  w  ww .  ja  va 2 s .  co m
    try {
        cmd = parser.parse(options, args);
    } catch (ParseException e) {
        System.out.println("There is an invalid option.");
        e.printStackTrace();
        System.exit(1);
    }

    String optVal;
    if (cmd.hasOption('h')) {
        usage(COMMAND);
        System.exit(1);
    }
    if (cmd.hasOption('d')) {
        details = true;
    }
    optVal = cmd.getOptionValue('r');
    if (optVal != null) {
        repeats = Integer.parseInt(optVal);
    }
    if (cmd.hasOption('n')) {
        doPut = false;
    }

    args = cmd.getArgs();

    // parse arguments
    if (args.length < 1) {
        usage(COMMAND);
        System.exit(1);
    }

    // prepare for RPC
    int numAccessor = args.length;
    DHTAccessor[] accessorArray = new DHTAccessor[numAccessor];
    try {
        for (int i = 0; i < numAccessor; i++) {
            accessorArray[i] = new DHTAccessor(args[i]);
        }
    } catch (MalformedURLException e) {
        e.printStackTrace();
        System.exit(1);
    }

    // generate key prefix
    Random rnd = new Random(System.currentTimeMillis());

    StringBuilder sb = new StringBuilder();
    for (int i = 0; i < KEY_PREFIX_LENGTH; i++) {
        sb.append((char) ('a' + rnd.nextInt(26)));
    }
    String keyPrefix = sb.toString();
    String valuePrefix = VALUE_PREFIX;

    // benchmarking
    System.out.println("Repeats " + repeats + " times.");

    if (doPut) {
        System.out.println("Putting: " + keyPrefix + "<number>");

        for (int i = 0; i < repeats; i++) {
            byte[] key = null, value = null;
            try {
                key = (keyPrefix + i).getBytes(ENCODE);
                value = (valuePrefix + i).getBytes(ENCODE);
            } catch (UnsupportedEncodingException e) {
                e.printStackTrace();
                System.exit(1);
            }

            int accIndex = rnd.nextInt(numAccessor);
            DHTAccessor acc = accessorArray[accIndex];
            acc.put(key, value, TTL);
        }
    }

    System.out.println("Benchmarking by getting.");

    int count = 0;
    long startTime = System.currentTimeMillis();

    if (details) {
        for (int i = 0; i < repeats; i++) {
            byte[] key = null;
            try {
                key = (keyPrefix + i).getBytes(ENCODE);
            } catch (UnsupportedEncodingException e) {
                e.printStackTrace();
                System.exit(1);
            }

            int accIndex = rnd.nextInt(numAccessor);
            DHTAccessor acc = accessorArray[accIndex];
            Set<DetailedGetResult> valueSet = acc.getDetails(key);
            if (valueSet != null && !valueSet.isEmpty()) {
                count++;
            }
        }
    } else {
        for (int i = 0; i < repeats; i++) {
            byte[] key = null;
            try {
                key = (keyPrefix + i).getBytes(ENCODE);
            } catch (UnsupportedEncodingException e) {
                e.printStackTrace();
                System.exit(1);
            }

            int accIndex = rnd.nextInt(numAccessor);
            DHTAccessor acc = accessorArray[accIndex];
            Set<byte[]> valueSet = acc.get(key);
            if (valueSet != null && !valueSet.isEmpty()) {
                count++;
            }
        }
    }

    System.out.println(System.currentTimeMillis() - startTime + " msec.");
    System.out.println("Rate of successful gets: " + count + " / " + repeats);
}

From source file:microbiosima.Microbiosima.java

/**
 * @param args/*w  w w. ja v  a 2 s .c  o 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();
        }
    }
}