Example usage for java.lang System getProperty

List of usage examples for java.lang System getProperty

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Introduction

In this page you can find the example usage for java.lang System getProperty.

Prototype

public static String getProperty(String key)

Source Link

Document

Gets the system property indicated by the specified key.

Usage

From source file:com.griddynamics.jagger.JaggerLauncher.java

public static void main(String[] args) throws Exception {
    Thread memoryMonitorThread = new Thread("memory-monitor") {
        @Override/*from ww w .ja  v a  2s  .c om*/
        public void run() {
            for (;;) {
                try {
                    log.info("Memory info: totalMemory={}, freeMemory={}", Runtime.getRuntime().totalMemory(),
                            Runtime.getRuntime().freeMemory());

                    Thread.sleep(60000);
                } catch (InterruptedException e) {
                    throw new RuntimeException(e);
                }
            }
        }
    };
    memoryMonitorThread.setDaemon(true);
    memoryMonitorThread.start();

    String pid = ManagementFactory.getRuntimeMXBean().getName();
    System.out.println(String.format("PID:%s", pid));

    Properties props = System.getProperties();
    for (Map.Entry<Object, Object> prop : props.entrySet()) {
        log.info("{}: '{}'", prop.getKey(), prop.getValue());
    }
    log.info("");

    URL directory = new URL("file:" + System.getProperty("user.dir") + "/");
    loadBootProperties(directory, args[0], environmentProperties);

    log.debug("Bootstrap properties:");
    for (String propName : environmentProperties.stringPropertyNames()) {
        log.debug("   {}={}", propName, environmentProperties.getProperty(propName));
    }

    String[] roles = environmentProperties.getProperty(ROLES).split(",");
    Set<String> rolesSet = Sets.newHashSet(roles);

    if (rolesSet.contains(Role.COORDINATION_SERVER.toString())) {
        launchCoordinationServer(directory);
    }
    if (rolesSet.contains(Role.HTTP_COORDINATION_SERVER.toString())) {
        launchCometdCoordinationServer(directory);
    }
    if (rolesSet.contains(Role.RDB_SERVER.toString())) {
        launchRdbServer(directory);
    }
    if (rolesSet.contains(Role.MASTER.toString())) {
        launchMaster(directory);
    }
    if (rolesSet.contains(Role.KERNEL.toString())) {
        launchKernel(directory);
    }

    if (rolesSet.contains(Role.REPORTER.toString())) {
        launchReporter(directory);
    }

    LaunchManager launchManager = builder.build();

    int result = launchManager.launch();

    System.exit(result);

}

From source file:edu.harvard.hul.ois.fits.clients.FormFileUploaderClientApplication.java

/**
 * Run the program.//from  ww  w.  j a v a2  s  .  co  m
 *
 * @param args First argument is path to the file to analyze; second (optional) is path to server for overriding default value.
 */
public static void main(String[] args) {
    // takes file path from first program's argument
    if (args.length < 1) {
        logger.error("****** Path to input file must be first argument to program! *******");
        logger.error("===== Exiting Program =====");
        System.exit(1);
    }

    String filePath = args[0];
    File uploadFile = new File(filePath);
    if (!uploadFile.exists()) {
        logger.error("****** File does not exist at expected locations! *******");
        logger.error("===== Exiting Program =====");
        System.exit(1);
    }

    if (args.length > 1) {
        serverUrl = args[1];
    }

    logger.info("File to upload: " + filePath);

    CloseableHttpClient httpclient = HttpClients.createDefault();
    try {
        HttpPost httppost = new HttpPost(serverUrl + "false");
        FileBody bin = new FileBody(uploadFile);
        MultipartEntityBuilder builder = MultipartEntityBuilder.create();
        builder.addPart(FITS_FORM_FIELD_DATAFILE, bin);
        HttpEntity reqEntity = builder.build();
        httppost.setEntity(reqEntity);

        logger.info("executing request " + httppost.getRequestLine());
        CloseableHttpResponse response = httpclient.execute(httppost);
        try {
            logger.info("HTTP Response Status Line: " + response.getStatusLine());
            // Expecting a 200 Status Code
            if (response.getStatusLine().getStatusCode() != HttpStatus.SC_OK) {
                String reason = response.getStatusLine().getReasonPhrase();
                logger.warn("Unexpected HTTP response status code:[" + response.getStatusLine().getStatusCode()
                        + "] -- Reason (if available): " + reason);
            } else {
                HttpEntity resEntity = response.getEntity();
                InputStream is = resEntity.getContent();
                BufferedReader in = new BufferedReader(new InputStreamReader(is));

                String output;
                StringBuilder sb = new StringBuilder();
                while ((output = in.readLine()) != null) {
                    sb.append(output);
                    sb.append(System.getProperty("line.separator"));
                }
                logger.info(sb.toString());
                in.close();
                EntityUtils.consume(resEntity);
            }
        } finally {
            response.close();
        }
    } catch (Exception e) {
        logger.error("Caught exception: " + e.getMessage(), e);
    } finally {
        try {
            httpclient.close();
        } catch (IOException e) {
            logger.warn("Exception closing HTTP client: " + e.getMessage(), e);
        }
        logger.info("DONE");
    }
}

From source file:com.opengamma.batch.BatchJobRunner.java

/**
 * Creates an runs a batch job based on a properties file and configuration.
 *///from   www  .ja v  a 2 s. co  m
public static void main(String[] args) throws Exception { // CSIGNORE
    if (args.length == 0) {
        usage();
        System.exit(-1);
    }

    CommandLine line = null;
    Properties configProperties = null;

    final String propertyFile = "batchJob.properties";

    String configPropertyFile = null;

    if (System.getProperty(propertyFile) != null) {
        configPropertyFile = System.getProperty(propertyFile);
        try {
            FileInputStream fis = new FileInputStream(configPropertyFile);
            configProperties = new Properties();
            configProperties.load(fis);
            fis.close();
        } catch (FileNotFoundException e) {
            s_logger.error("The system cannot find " + configPropertyFile);
            System.exit(-1);
        }
    } else {
        try {
            FileInputStream fis = new FileInputStream(propertyFile);
            configProperties = new Properties();
            configProperties.load(fis);
            fis.close();
            configPropertyFile = propertyFile;
        } catch (FileNotFoundException e) {
            // there is no config file so we expect command line arguments
            try {
                CommandLineParser parser = new PosixParser();
                line = parser.parse(getOptions(), args);
            } catch (ParseException e2) {
                usage();
                System.exit(-1);
            }
        }
    }

    RunCreationMode runCreationMode = getRunCreationMode(line, configProperties, configPropertyFile);
    if (runCreationMode == null) {
        // default
        runCreationMode = RunCreationMode.AUTO;
    }

    String engineURI = getProperty("engineURI", line, configProperties, configPropertyFile);

    String brokerURL = getProperty("brokerURL", line, configProperties, configPropertyFile);

    Instant valuationTime = getValuationTime(line, configProperties, configPropertyFile);
    LocalDate observationDate = getObservationDate(line, configProperties, configPropertyFile);

    UniqueId viewDefinitionUniqueId = getViewDefinitionUniqueId(line, configProperties);

    URI vpBase;
    try {
        vpBase = new URI(engineURI);
    } catch (URISyntaxException ex) {
        throw new OpenGammaRuntimeException("Invalid URI", ex);
    }

    ActiveMQConnectionFactory activeMQConnectionFactory = new ActiveMQConnectionFactory(brokerURL);
    activeMQConnectionFactory.setWatchTopicAdvisories(false);

    JmsConnectorFactoryBean jmsConnectorFactoryBean = new JmsConnectorFactoryBean();
    jmsConnectorFactoryBean.setConnectionFactory(activeMQConnectionFactory);
    jmsConnectorFactoryBean.setName("Masters");

    JmsConnector jmsConnector = jmsConnectorFactoryBean.getObjectCreating();
    ScheduledExecutorService heartbeatScheduler = Executors.newSingleThreadScheduledExecutor();
    try {
        ViewProcessor vp = new RemoteViewProcessor(vpBase, jmsConnector, heartbeatScheduler);
        ViewClient vc = vp.createViewClient(UserPrincipal.getLocalUser());

        HistoricalMarketDataSpecification marketDataSpecification = MarketData.historical(observationDate,
                null);

        ViewExecutionOptions executionOptions = ExecutionOptions.batch(valuationTime, marketDataSpecification,
                null);

        vc.attachToViewProcess(viewDefinitionUniqueId, executionOptions);
        vc.waitForCompletion();
    } finally {
        heartbeatScheduler.shutdown();
    }
}

From source file:com.ms.commons.test.tool.GenerateTestCase.java

public static void main(String[] args) {
    if (args.length < 2) {
        System.err.println("Usage:\r\n.frameworktest_maketests antx|maven fileter");
        System.exit(-1);/*from   w w  w  . j a  v  a  2 s. c  o  m*/
    }

    final com.ms.commons.test.runner.filter.expression.internal.Expression filterExpression;
    try {
        System.out.println("Filter: " + args[1]);
        filterExpression = ExpressionParseUtil.parse(args[1], new SimpleExpressionBuiler() {

            public AbstractSimpleExpression build(String value) {
                return new StringExpressionImpl(value);
            }
        });
    } catch (ParseException e) {
        throw ExceptionUtil.wrapToRuntimeException(e);
    }
    final FullClassNameFilter fullClassNameFilter = new FullClassNameFilter() {

        public boolean accept(String fullClassName) {

            return ((Boolean) filterExpression.evaluate(fullClassName)).booleanValue();
        }
    };

    String userDir = System.getProperty("user.dir");

    ProjectPath pp = getProjectPath(args[0]);

    final String mainSource = userDir + File.separator + pp.getMainSource();
    final String testSource = userDir + File.separator + pp.getTestSource();

    FileUtil.listFiles(null, new File(mainSource), new FileFilter() {

        public boolean accept(File pathname) {
            if (pathname.isDirectory()) {
                return !pathname.toString().contains(".svn");
            }
            if (pathname.toString().contains(".svn")) {
                return false;
            }
            if (!pathname.toString().toLowerCase().endsWith(".java")) {
                return false;
            }
            try {
                processJavaFile(pathname, testSource, fullClassNameFilter);
            } catch (Exception e) {
                System.err.println("Parse java file failed:" + pathname);
                e.printStackTrace();
            }
            return false;
        }
    });
}

From source file:org.openspaces.focalserver.FocalServer.java

public static void main(String[] args) throws IOException {
    if (args.length < 1) {
        printUsage();/*w  w  w .  j a v  a2s . co m*/
        System.exit(1);
    }
    LOGGER.info("\n==================================================\n"
            + "GigaSpaces Focal Server starting using " + Arrays.asList(args) + " \n" + "Log created by <"
            + System.getProperty("user.name") + "> on " + new Date().toString() + "\n"
            + "==================================================");
    ApplicationContext applicationContext;
    try {
        applicationContext = new FileSystemXmlApplicationContext(args);
    } catch (Exception e) {
        LOGGER.fine("Failed starting GigaSpaces Focal Server using " + Arrays.asList(args)
                + ", will try to load from classpath. " + e.getMessage());
        applicationContext = new ClassPathXmlApplicationContext(args);
    }

}

From source file:com.hortonworks.streamline.storage.tool.SQLScriptRunner.java

public static void main(String[] args) throws Exception {
    Options options = new Options();

    options.addOption(option(1, "c", OPTION_CONFIG_FILE_PATH, "Config file path"));
    options.addOption(option(Option.UNLIMITED_VALUES, "f", OPTION_SCRIPT_PATH, "Script path to execute"));
    options.addOption(option(Option.UNLIMITED_VALUES, "m", OPTION_MYSQL_JAR_URL_PATH,
            "Mysql client jar url to download"));
    CommandLineParser parser = new BasicParser();
    CommandLine commandLine = parser.parse(options, args);

    if (!commandLine.hasOption(OPTION_CONFIG_FILE_PATH) || !commandLine.hasOption(OPTION_SCRIPT_PATH)
            || commandLine.getOptionValues(OPTION_SCRIPT_PATH).length <= 0) {
        usage(options);/*from   w  w w.  j  a v a 2  s .  co  m*/
        System.exit(1);
    }

    String confFilePath = commandLine.getOptionValue(OPTION_CONFIG_FILE_PATH);
    String[] scripts = commandLine.getOptionValues(OPTION_SCRIPT_PATH);
    String mysqlJarUrl = commandLine.getOptionValue(OPTION_MYSQL_JAR_URL_PATH);

    try {
        Map<String, Object> conf = Utils.readStreamlineConfig(confFilePath);

        StorageProviderConfigurationReader confReader = new StorageProviderConfigurationReader();
        StorageProviderConfiguration storageProperties = confReader.readStorageConfig(conf);

        String bootstrapDirPath = System.getProperty("bootstrap.dir");

        MySqlDriverHelper.downloadMySQLJarIfNeeded(storageProperties, bootstrapDirPath, mysqlJarUrl);

        SQLScriptRunner sqlScriptRunner = new SQLScriptRunner(storageProperties);
        try {
            sqlScriptRunner.initializeDriver();
        } catch (ClassNotFoundException e) {
            System.err.println(
                    "Driver class is not found in classpath. Please ensure that driver is in classpath.");
            System.exit(1);
        }

        for (String script : scripts) {
            sqlScriptRunner.runScriptWithReplaceDBType(script);
        }
    } catch (IOException e) {
        System.err.println("Error occurred while reading config file: " + confFilePath);
        System.exit(1);
    }
}

From source file:com.hortonworks.registries.storage.tool.TablesInitializer.java

public static void main(String[] args) throws Exception {
    Options options = new Options();

    options.addOption(Option.builder("s").numberOfArgs(1).longOpt(OPTION_SCRIPT_ROOT_PATH)
            .desc("Root directory of script path").build());

    options.addOption(Option.builder("c").numberOfArgs(1).longOpt(OPTION_CONFIG_FILE_PATH)
            .desc("Config file path").build());

    options.addOption(Option.builder("m").numberOfArgs(1).longOpt(OPTION_MYSQL_JAR_URL_PATH)
            .desc("Mysql client jar url to download").build());

    options.addOption(Option.builder().hasArg(false).longOpt(OPTION_EXECUTE_CREATE_TABLE)
            .desc("Execute 'create table' script").build());

    options.addOption(Option.builder().hasArg(false).longOpt(OPTION_EXECUTE_DROP_TABLE)
            .desc("Execute 'drop table' script").build());

    options.addOption(Option.builder().hasArg(false).longOpt(OPTION_EXECUTE_CHECK_CONNECTION)
            .desc("Check the connection for configured data source").build());

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

    if (!commandLine.hasOption(OPTION_CONFIG_FILE_PATH) || !commandLine.hasOption(OPTION_SCRIPT_ROOT_PATH)) {
        usage(options);//from   www . jav a 2s  . c o m
        System.exit(1);
    }

    // either create or drop should be specified, not both
    boolean executeCreate = commandLine.hasOption(OPTION_EXECUTE_CREATE_TABLE);
    boolean executeDrop = commandLine.hasOption(OPTION_EXECUTE_DROP_TABLE);
    boolean checkConnection = commandLine.hasOption(OPTION_EXECUTE_CHECK_CONNECTION);

    boolean moreThanOneOperationIsSpecified = executeCreate == executeDrop ? executeCreate : checkConnection;
    boolean noOperationSpecified = !(executeCreate || executeDrop || checkConnection);

    if (moreThanOneOperationIsSpecified) {
        System.out.println(
                "Only one operation can be execute at once, please select 'create' or 'drop', or 'check-connection'.");
        System.exit(1);
    } else if (noOperationSpecified) {
        System.out.println(
                "One of 'create', 'drop', 'check-connection' operation should be specified to execute.");
        System.exit(1);
    }

    String confFilePath = commandLine.getOptionValue(OPTION_CONFIG_FILE_PATH);
    String scriptRootPath = commandLine.getOptionValue(OPTION_SCRIPT_ROOT_PATH);
    String mysqlJarUrl = commandLine.getOptionValue(OPTION_MYSQL_JAR_URL_PATH);

    StorageProviderConfiguration storageProperties;
    try {
        Map<String, Object> conf = Utils.readConfig(confFilePath);

        StorageProviderConfigurationReader confReader = new StorageProviderConfigurationReader();
        storageProperties = confReader.readStorageConfig(conf);
    } catch (IOException e) {
        System.err.println("Error occurred while reading config file: " + confFilePath);
        System.exit(1);
        throw new IllegalStateException("Shouldn't reach here");
    }

    String bootstrapDirPath = null;
    try {
        bootstrapDirPath = System.getProperty("bootstrap.dir");
        MySqlDriverHelper.downloadMySQLJarIfNeeded(storageProperties, bootstrapDirPath, mysqlJarUrl);
    } catch (Exception e) {
        System.err.println("Error occurred while downloading MySQL jar. bootstrap dir: " + bootstrapDirPath);
        System.exit(1);
        throw new IllegalStateException("Shouldn't reach here");
    }

    try {
        SQLScriptRunner sqlScriptRunner = new SQLScriptRunner(storageProperties);

        try {
            sqlScriptRunner.initializeDriver();
        } catch (ClassNotFoundException e) {
            System.err.println(
                    "Driver class is not found in classpath. Please ensure that driver is in classpath.");
            System.exit(1);
        }

        if (checkConnection) {
            if (!sqlScriptRunner.checkConnection()) {
                System.exit(1);
            }
        } else if (executeDrop) {
            doExecuteDrop(sqlScriptRunner, storageProperties, scriptRootPath);
        } else {
            // executeCreate
            doExecuteCreate(sqlScriptRunner, storageProperties, scriptRootPath);
        }
    } catch (IOException e) {
        System.err.println("Error occurred while reading script file. Script root path: " + scriptRootPath);
        System.exit(1);
    }
}

From source file:edu.duke.igsp.gkde.Main.java

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

    Options opts = new Options();
    opts.addOption("s", true, "wiggle track step (default=1)");
    opts.addOption("l", true, "feature length (default=600)");
    opts.addOption("f", true, "fragment size (default=estimated from data)");
    //    opts.addOption("b", true, "bandwidth (default=200)");
    //    opts.addOption("w", true, "window (default=3800");
    opts.addOption("wg", true, "wg threshold set (defualt = calculated)");
    opts.addOption("c", true, "genomic total read weight (defualt = calculated)");
    opts.addOption("h", false, "print usage");
    opts.addOption(OptionBuilder.withArgName("input dir").hasArg()
            .withDescription("input directory (default=current directory)").isRequired(false).create("d"));
    opts.addOption(OptionBuilder.withArgName("output dir").hasArg()
            .withDescription("output directory (default=current directory)").isRequired(false).create("o"));
    opts.addOption(OptionBuilder.withArgName("background dir").hasArg()
            .withDescription("background directory (default=none)").isRequired(false).create("b"));
    opts.addOption(OptionBuilder.withArgName("ploidy dir").hasArg()
            .withDescription("ploidy/input directory (default=none)").isRequired(false).create("p"));
    opts.addOption(OptionBuilder.withArgName("wig | bed | npf").hasArg()
            .withDescription("output format (default wig)").isRequired(false).create("of"));
    opts.addOption(OptionBuilder.withArgName("dnase | chip | faire | atac").hasArg()
            .withDescription("input data").isRequired(true).create("in"));
    opts.addOption(OptionBuilder.withArgName("weight clip").hasArg()
            .withDescription("weight clip value (default none)").isRequired(false).create("wc"));
    opts.addOption("t", true, "threshold (standard deviations) (default=4.0)");
    //    opts.addOption("r", true, "background ratio (default=2.0)");
    opts.addOption("v", false, "verbose output");

    CommandLineParser parser = new GnuParser();
    int fragment_size = -1;
    int fragment_offset = 0;
    long featureLength = 600l;
    //    float thresh = 2;
    float threshold = KDEChromosome.Settings.DEFAULT_THRESHOLD;
    int step = 1;
    boolean showHelp = false;
    boolean verbose = false;
    String inputDirectory = null;
    String backgroundDirectory = null;
    String ploidyDirectory = null;
    String[] files = null;/*  w w w . ja v a2  s .  co  m*/
    String[] bgfiles = {};
    String[] ipfiles = {};
    String outputFormat = "wig";
    String inputDataType = "dnase";
    File outputDirectory = new File(System.getProperty("user.dir"));

    long bandwidth = 0l;
    long window = 0l;
    double ncuts = 0.0d;
    float temp_threshold = 0f;
    int weight_clip = 0;

    System.out.println("F-Seq Version 1.85");

    try {
        CommandLine cmd = parser.parse(opts, argv);
        showHelp = (cmd.hasOption("h"));
        verbose = (cmd.hasOption("v"));
        if (cmd.hasOption("s"))
            step = Integer.parseInt(cmd.getOptionValue("s"));
        if (cmd.hasOption("f"))
            fragment_size = Integer.parseInt(cmd.getOptionValue("f"));
        if (cmd.hasOption("d")) //input directory
            inputDirectory = cmd.getOptionValue("d");
        if (cmd.hasOption("b")) //background directory
            backgroundDirectory = cmd.getOptionValue("b");
        if (cmd.hasOption("p")) //ploidy|input directory
            ploidyDirectory = cmd.getOptionValue("p");
        if (cmd.hasOption("l")) // bandwidth
            featureLength = Long.parseLong(cmd.getOptionValue("l"));
        if (cmd.hasOption("of")) { // output format
            outputFormat = cmd.getOptionValue("of");
            if (!outputFormat.equals("wig") && !outputFormat.equals("bed") && !outputFormat.equals("npf")) {
                System.out.println("Parameter error: output format must be 'wig' or 'bed'.");
                showHelp = true;
            }
        }
        if (cmd.hasOption("in")) { // input data type
            inputDataType = cmd.getOptionValue("in");
            if (!inputDataType.equals("dnase") && !inputDataType.equals("chip")
                    && !inputDataType.equals("faire") && !inputDataType.equals("atac")) {
                System.out.println(
                        "Parameter error: input data type must be 'dnase', 'chip', 'faire', or 'atac'.");
                showHelp = true;
            }
        }
        if (cmd.hasOption("wc")) { // weight clip
            weight_clip = Integer.parseInt(cmd.getOptionValue("wc"));
        }
        if (cmd.hasOption("t")) { // threshold (standard deviations)
            threshold = Float.parseFloat(cmd.getOptionValue("t"));
        }
        if (cmd.hasOption("o")) { // output directory
            String out = cmd.getOptionValue("o");
            outputDirectory = new File(out);
            if (!outputDirectory.exists() && !outputDirectory.isDirectory()) {
                System.out.println("Output directory '" + out + "' is not a valid directory.");
                showHelp = true;
            }
        }

        if (cmd.hasOption("wg"))
            temp_threshold = Float.parseFloat(cmd.getOptionValue("wg"));
        if (cmd.hasOption("c"))
            ncuts = Double.parseDouble(cmd.getOptionValue("c"));

        // TESTING ONLY
        //   if(cmd.hasOption("w")) // window
        //     window = Long.parseLong(cmd.getOptionValue("w"));
        //if(cmd.hasOption("b")) // window
        //  bandwidth = Long.parseLong(cmd.getOptionValue("b"));

        files = cmd.getArgs(); // input files
        //bgfiles = cmd.getArgs(); // background files
    } catch (Exception e) {
        System.out.println("Error parsing arguments: " + e.getMessage());
        e.printStackTrace();
        showHelp = true;
    }

    if (showHelp || (inputDirectory == null && files.length == 0)) {
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp("fseq [options]... [file(s)]...", opts);
        System.exit(1);
    }

    File[] pfiles = getFiles(inputDirectory, files);
    File[] background_files = getFiles(backgroundDirectory, bgfiles);
    File[] ploidy_files = getFiles(ploidyDirectory, ipfiles);

    KDEChromosome[] chrs = null;
    // assume all files are of the same type, if not we'll get parsing errors
    String path = pfiles[0].getPath();
    String extension = path.substring(path.lastIndexOf('.')).toLowerCase();
    System.out.println("Path: " + path + ", extension: " + extension);
    if (extension.equals(".bed")) {
        System.out.println("Parsing BED file.");
        chrs = BedReader.read(pfiles);
    } else if (extension.equals(".sam") || extension.equals(".bam")) {
        System.out.println("Parsing SAM/BAM file.");
        chrs = SamReader.read(pfiles, weight_clip);
    }
    //KDEChromosome[] input = BedReader.read(ifiles);

    //compute fragment offset
    if (fragment_size == -1) {
        fragment_size = wgShiftCalc(chrs);
    }
    fragment_offset = (int) (fragment_size / 2);

    if (ncuts == 0.0d) {
        for (int i = 0; i < chrs.length; ++i) {
            // computes the total read weight of all cuts on a chromosome
            ncuts += chrs[i].getTotalWeight();
        }
    }

    KDEChromosome.Settings settings = null;
    if (bandwidth > 0 || window > 0) {
        settings = new KDEChromosome.Settings(bandwidth, window, threshold, fragment_offset, ncuts,
                inputDataType);
    } else {
        settings = new KDEChromosome.Settings(featureLength, threshold, fragment_offset, ncuts, inputDataType);
    }

    float wg_threshold = wgThreshold(settings, chrs);
    if (temp_threshold != 0f) {
        wg_threshold = temp_threshold;
    }
    //KDEChromosome.Settings bg_settings = null;
    //bg_settings = new KDEChromosome.Settings(featureLength*2, threshold, fragment_offset);

    //int background_size = 0;
    //int input_size = 0;
    //float bg_ratio = 0;
    //float sd = 0;

    if (verbose) {
        System.out.println("Settings: ");
        System.out.println("\twindow=" + (settings.window * 2));
        System.out.println("\tbandwidth=" + (settings.bandwidth));
        //System.out.println("\tfragment offset=" + (settings.offset));
        System.out.println("\tthreshold = " + wg_threshold);
        System.out.println("\test. fragment size = " + fragment_size);
        System.out.println("\tsequence length = " + chrs[0].getSequenceLength());
    }

    //    if(backgroundDirectory != null) {
    //       for(int i = 0; i < input.length; ++i) {
    //          background_size += input[i].getLength();
    //       }
    //       for(int i = 0; i < chrs.length; ++i) {
    //          input_size += chrs[i].getLength();
    //       }
    //       bg_ratio = (float)input_size/(float)background_size;
    //       sd = computeSD(bg_settings, input);
    //       //System.out.println("Sample Ratio: " + bg_ratio);
    //       //System.out.println("Input Size: " + input_size);
    //       //System.out.println("Background Size: " + background_size);
    //       //System.out.println("Input standard deviation: " + (settings.threshold * (float)Math.sqrt((double)bg_ratio * (double)sd * (double)sd)));
    //       //System.out.println("Data standard deviation: " + settings.threshold * computeSD(settings, chrs));
    //    }

    for (int i = 0; i < chrs.length; ++i) {
        if (chrs[i].getFirstPos() == chrs[i].getLastPos()) {
            System.out.println("Warning: " + chrs[i].getChromosome() + " has size zero.  Skipping.");
            continue;
        }
        File ofile = Util.makeUniqueFileWithExtension(outputDirectory, chrs[i].getChromosome(), outputFormat);

        DensityWriter dw = null;
        if (outputFormat.equals("wig")) {
            dw = new WiggleDensityWriter(ofile, chrs[i].getChromosome(), chrs[i].getFirstPos(), step);
        } else {
            if (outputFormat.equals("npf")) {
                dw = new NpfDensityWriter(ofile, chrs[i].getChromosome(), chrs[i].getFirstPos(), step);
            } else {
                dw = new BedDensityWriter(ofile, chrs[i].getChromosome(), chrs[i].getFirstPos(), step);
            }
        }

        //Function takes all? or new function for each?
        //      if(backgroundDirectory != null) {
        //         boolean hit = false;
        //         for(int j = 0; j < background_files.length; ++j) {
        //            if(background_files[j].getName().equals(chrs[i].getChromosome() + ".bff")) {
        //               System.out.println("Running background on Chromosome " + chrs[i].getChromosome());
        //               chrs[i].runBG(settings, dw, verbose, wg_threshold, background_files[j]);
        //               hit = true;
        //            }
        //         }
        //         if(!hit)
        //            System.out.println("No background for Chromosome " + chrs[i].getChromosome());
        //      } else {
        //         if(ploidyDirectory !=)
        //         chrs[i].run(settings, dw, verbose, wg_threshold);
        //      }
        chrs[i].run(settings, dw, verbose, wg_threshold, background_files, ploidy_files);
        dw.close();
    }

    //kde.showGraph();
}

From source file:com.sshtools.j2ssh.agent.SshAgentSocketListener.java

/**
 * The main entry point for the application. This method currently accepts
 * the -start parameter which will look for the sshtools.agent system
 * property. To configure the agent and to get a valid location call with
 * -configure, set the system sshtools.home system property and start.
 *
 * @param args the programs arguments/*from  w  w  w . j a v  a 2s. c  o  m*/
 */
public static void main(String[] args) {
    if (args.length > 0) {
        if (args[0].equals("-start")) {
            Thread thread = new Thread(new Runnable() {
                public void run() {
                    try {
                        SshAgentSocketListener agent = new SshAgentSocketListener(
                                System.getProperty("sshtools.agent"), new KeyStore());
                        agent.start();
                    } catch (Exception ex) {
                        ex.printStackTrace();
                    }
                }
            });

            thread.start();
        }

        if (args[0].equals("-configure")) {
            System.out.println("SET SSHTOOLS_AGENT=localhost:" + String.valueOf(configureNewLocation()));
        }
    }
}

From source file:com.jsystem.j2autoit.AutoItAgent.java

/**
 * Launch the server side//from   ww w  .  ja v a  2s. c  om
 * 
 * @param args
 */
public static void main(String[] args) {
    try {
        Log.initLog();
        isDebug = AutoItProperties.DEBUG_MODE_KEY.getValue(isDebug);
        isAutoDeleteFiles = AutoItProperties.AUTO_DELETE_TEMPORARY_SCRIPT_FILE_KEY.getValue(isAutoDeleteFiles);
        if (isAutoDeleteFiles) {
            Integer tempHistory = AutoItProperties.AUTO_IT_SCRIPT_HISTORY_SIZE_KEY
                    .getValue(DEFAULT_HistorySize);

            HistoryFile.init();
            HistoryFile.setHistory_Size(tempHistory);
        }
        isForceAutoItShutDown = AutoItProperties.FORCE_AUTO_IT_PROCESS_SHUTDOWN_KEY
                .getValue(isForceAutoItShutDown);
        webServicePort = AutoItProperties.AGENT_PORT_KEY.getValue(webServicePort);
        serverState = AutoItProperties.SERVER_UP_ON_INIT_KEY.getValue(serverState);

        Log.setLogMode(false, isDebug);
        Runtime.getRuntime().addShutdownHook(new ExitThread());
        Log.info(System.getProperty("user.dir") + NEW_LINE);
        Log.info("AutoIt Location: " + getAutoExecuterItLocation("Unable to find") + NEW_LINE);
        startAutoItWebServer(webServicePort);
        if (serverState) {
            serverState = false;
            runWebServer();
        }

        UIManager.setLookAndFeel("com.sun.java.swing.plaf.windows.WindowsLookAndFeel");

    } catch (Exception exception) {
        Log.throwable(exception.getMessage() + NEW_LINE, exception);
    }

    /* Turn off metal's use of bold fonts */
    UIManager.put("swing.boldMetal", Boolean.FALSE);
    //Schedule a job for the event-dispatching thread:
    //adding TrayIcon.
    SwingUtilities.invokeLater(new Runnable() {
        @Override
        public void run() {
            createAndShowGUI();
        }
    });
}