Example usage for org.apache.commons.cli BasicParser BasicParser

List of usage examples for org.apache.commons.cli BasicParser BasicParser

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

Introduction

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

Prototype

BasicParser

Source Link

Usage

From source file:cdscreator.ParseCLI.java

/**
 * Rutger Ozinga. ParseCLI Parses the commandline input and is able to
 * return the wanted option and value./*from ww w .jav a 2  s  . c om*/
 *
 * @param args are commandline arguments.
 * @throws org.apache.commons.cli.ParseException an exception
 */
public ParseCLI(final String[] args) throws org.apache.commons.cli.ParseException {
    HelpFormatter helpForm = new HelpFormatter();
    Options cliOpt = new Options();
    cliOpt.addOption("h", "help", false, "Displays help");
    cliOpt.addOption("p", true, "Expects a path to a protein fasta file.");
    cliOpt.addOption("t", true, "Expects a path to a transcript fasta file.");
    cliOpt.addOption("nt", true, "Expects a path to place the new tab separated transcript file at.");
    cliOpt.addOption("o", true, "Expects a path to place the new tab separated protein file at");
    if (args.length == 0) {
        helpForm.printHelp("Please enter all the " + "options below. ", cliOpt);
        System.exit(0);
    } else {
        BasicParser parser = new BasicParser();
        CommandLine cliParser = parser.parse(cliOpt, args);
        if (cliParser.getOptions().length < 4) {
            System.out.println(
                    "Error : " + "Please enter all options in" + " order for this program to work" + "!\n");
            helpForm.printHelp("Please enter all of the  " + "option ", cliOpt);
            System.exit(0);
        } else {
            if (cliParser.hasOption("h") && cliParser.hasOption("help")) {
                helpForm.printHelp("Command Line Help:\n", cliOpt);
                System.exit(0);
            } else {
                String snpFileString = cliParser.getOptionValue("p");
                Path snpPath = Paths.get(snpFileString);
                if (Files.exists(snpPath)) {
                    setProtPath(snpPath);
                } else {
                    System.out.println("The entered Path does" + " not exits");
                    helpForm.printHelp("Please enter -p followed by a valid" + " path ", cliOpt);
                    System.exit(0);
                }
                String transcriptFileString = cliParser.getOptionValue("t");
                Path transcriptPath = Paths.get(transcriptFileString);
                if (Files.exists(transcriptPath)) {
                    setTransPath(transcriptPath);
                } else {
                    System.out.println("The entered Path does" + " not exits");
                    helpForm.printHelp("Please enter -t followed by a valid" + " path ", cliOpt);
                    System.exit(0);
                }
                String newFileString = cliParser.getOptionValue("o");
                Matcher match = re.matcher(newFileString);
                String editedFileString = match.replaceAll("");
                Path newPath = Paths.get(editedFileString);
                if (Files.exists(newPath)) {
                    setNewFilePath(newFileString);
                } else {
                    System.out.println("The entered Path does" + " not exits");
                    helpForm.printHelp("Please enter -o followed by a valid" + " path ", cliOpt);
                    System.exit(0);
                }
                String newTranscriptFileString = cliParser.getOptionValue("nt");
                Matcher match2 = re.matcher(newTranscriptFileString);
                String editedTranscriptFileString = match2.replaceAll("");
                Path newTranscriptPath = Paths.get(editedTranscriptFileString);
                if (Files.exists(newTranscriptPath)) {
                    setNewTranscriptFilePath(newTranscriptFileString);
                } else {
                    System.out.println("The entered Path does" + " not exits");
                    helpForm.printHelp("Please enter -nt followed by a valid" + " path ", cliOpt);
                    System.exit(0);
                }
            }
        }
    }
}

From source file:com.shmsoft.dmass.main.SHMcloudMain.java

/**
 * Process the command line arguments/* w  w  w .  j  a  v  a  2 s.  c  om*/
 *
 * @param args command line arguments
 */
private void processOptions(String[] args) {
    String customParameterFile;
    Project project = null;
    try {
        BasicParser parser = new BasicParser();
        commandLine = parser.parse(options, args);

        // one-time actions
        if (commandLine.hasOption(CommandLineOption.HELP.getName()) || commandLine.getOptions().length == 0) {
            HelpFormatter f = new HelpFormatter();
            f.printHelp("java -jar FreeEed.jar [options]\n\n" + "where options include:", options);
        } else if (commandLine.hasOption(CommandLineOption.VERSION.getName())) {
            System.out.println(Version.getVersionAndBuild());
        } else if (commandLine.hasOption(CommandLineOption.GUI.getName())) {
            openGUI();
        } else if (commandLine.hasOption(CommandLineOption.ENRON.getName())) {
            processEnronDataSet();
        } else {
            if (commandLine.hasOption(CommandLineOption.PARAM_FILE.getName())) {
                // independent actions
                customParameterFile = commandLine.getOptionValue(CommandLineOption.PARAM_FILE.getName());
                project = new Project().loadFromFile(new File(customParameterFile));
                Project.setProject(project);
                SHMcloudLogging.init(false);
            }
            if (commandLine.hasOption(CommandLineOption.DRY.getName())) {
                System.out.println("Dry run - exiting now.");
            } else {
                if (project.isStage()) {
                    stagePackageInput();
                }
                String runWhere = project.getProcessWhere();
                if (runWhere != null) {
                    process(runWhere);
                }
            }
        }
    } catch (Exception e) {
        e.printStackTrace(System.out);
    }
}

From source file:com.predic8.membrane.balancer.client.LBNotificationClient.java

public void run(String[] args) throws Exception {
    CommandLine cl = new BasicParser().parse(getOptions(), args, false);
    if (cl.hasOption('h') || args.length < 2) {
        printUsage();//w w w . j av a2 s.  c  om
        return;
    }
    parseArguments(cl);

    logArguments();

    Response res = notifiyClusterManager();

    if (res.getStatusCode() != 204) {
        throw new Exception("Got StatusCode: " + res.getStatusCode());
    }

    log.info("Sent " + cmd + " message to " + host + ":" + port + (skeySpec != null ? " encrypted" : ""));
}

From source file:com.nilostep.xlsql.ui.XlUi.java

/**
 * Parse and execute.//w w w  .  j  ava2  s. c o  m
 * @throws xlException when parse excepton
 */
public final void doIt() throws xlException {
    try {
        CommandLineParser parser = new BasicParser();
        String[] arguments = getCommand().split(" ");
        commandline = parser.parse(options, arguments);

        XlUiParser cmdlineparser = new XlUiParser();
        IStateCommand cmd = cmdlineparser.parseC(this);

        if (cmd != null) {
            int newstate = cmd.execute();
            state = (newstate > 0) ? newstate : state;
            setState(state);
        } else {
            throw new xlException("?.."); // cannot happen
        }
    } catch (ParseException pe) {
        throw new xlException(pe.getMessage());
    }
}

From source file:main.java.de.tw.ecm.toolkit.ECMToolkit.java

private void parseCmd(Parameters parameters) throws ParseException {
    Options options = new Options();
    options.addOption("u", "user", true, "user login name");
    options.addOption("p", "password", true, "userid password");

    List<String> rawList = parameters.getRaw();

    CommandLineParser parser = new BasicParser();
    CommandLine commandLine = parser.parse(options, (String[]) rawList.toArray(new String[rawList.size()]));
    this.context.put(commandLine);
}

From source file:createconversioncdsfile.ParseCLI.java

/**
 * Rutger Ozinga. ParseCLI Parses the commandline input and is able to
 * return the wanted option and value.//from   w w  w . ja  va  2s  .c  o m
 *
 * @param args are commandline arguments.
 * @throws org.apache.commons.cli.ParseException an exception
 */
public ParseCLI(final String[] args) throws org.apache.commons.cli.ParseException {
    HelpFormatter helpForm = new HelpFormatter();
    Options cliOpt = new Options();
    cliOpt.addOption("h", "help", false, "Displays help");
    cliOpt.addOption("p", true, "Expects a path to a protein fasta file.");
    cliOpt.addOption("t", true, "Expects a path to a transcript fasta file.");
    cliOpt.addOption("c", true, "Expects a path to a conversion file at.");
    cliOpt.addOption("cds", true, "Expects a path to a cds file at.");
    cliOpt.addOption("o", true, "Expects a path to place the new tab separated protein file at");
    if (args.length == 0) {
        helpForm.printHelp("Please enter all the " + "options below. ", cliOpt);
        System.exit(0);
    } else {
        BasicParser parser = new BasicParser();
        CommandLine cliParser = parser.parse(cliOpt, args);
        if (cliParser.getOptions().length < 4) {
            System.out.println(
                    "Error : " + "Please enter all options in" + " order for this program to work" + "!\n");
            helpForm.printHelp("Please enter all of the  " + "option ", cliOpt);
            System.exit(0);
        } else {
            if (cliParser.hasOption("h") && cliParser.hasOption("help")) {
                helpForm.printHelp("Command Line Help:\n", cliOpt);
                System.exit(0);
            } else {
                String snpFileString = cliParser.getOptionValue("p");
                Path snpPath = Paths.get(snpFileString);
                if (Files.exists(snpPath)) {
                    setProtPath(snpPath);
                } else {
                    System.out.println("The entered Path does" + " not exits");
                    helpForm.printHelp("Please enter -p followed by a valid" + " path ", cliOpt);
                    System.exit(0);
                }
                String conversionFileString = cliParser.getOptionValue("c");
                Path conversionPath = Paths.get(conversionFileString);
                if (Files.exists(conversionPath)) {
                    setConversionFilePath(conversionPath);
                } else {
                    System.out.println("The entered Path does" + " not exits");
                    helpForm.printHelp("Please enter -c followed by a valid" + " path ", cliOpt);
                    System.exit(0);
                }
                String cdsFileString = cliParser.getOptionValue("cds");
                Path cdsPath = Paths.get(cdsFileString);
                if (Files.exists(cdsPath)) {
                    setCdsPath(cdsPath);
                } else {
                    System.out.println("The entered Path does" + " not exits");
                    helpForm.printHelp("Please enter -cds followed by a valid" + " path ", cliOpt);
                    System.exit(0);
                }
                String transcriptFileString = cliParser.getOptionValue("t");
                Path transcriptPath = Paths.get(transcriptFileString);
                if (Files.exists(transcriptPath)) {
                    setTransPath(transcriptPath);
                } else {
                    System.out.println("The entered Path does" + " not exits");
                    helpForm.printHelp("Please enter -t followed by a valid" + " path ", cliOpt);
                    System.exit(0);
                }
                String newFileString = cliParser.getOptionValue("o");
                Matcher match = re.matcher(newFileString);
                String editedFileString = match.replaceAll("");
                Path newPath = Paths.get(editedFileString);
                if (Files.exists(newPath)) {
                    setNewFilePath(newFileString);
                } else {
                    System.out.println("The entered Path does" + " not exits");
                    helpForm.printHelp("Please enter -o followed by a valid" + " path ", cliOpt);
                    System.exit(0);
                }
            }
        }
    }
}

From source file:io.github.egonw.base.Cli.java

private static void parse(String[] args) {
    Options options = new Options();
    // Basic Options
    options.addOption("help", false, "Print this message");
    options.addOption("d", "debug", false, "Debug mode");
    options.addOption("v", "verbose", false, "Verbose mode");
    // File Handling
    // options.addOption("i", "input", true, "Input File");
    options.addOption("o", "output", true, "Output file addition");
    options.addOption("l", "log", true, "Log File");
    options.addOption("x", "error", true, "Debug File");
    // Processing Options
    options.addOption("c", "cml", false, "Also write a CML file without annotations: adds -simple to name");
    options.addOption("a", "ann", false, "Include annotations in CML output");
    options.addOption("r", "descr", false, "Include speech descriptions in CML output");
    options.addOption("nonih", "nonih", false, "Do not use the NIH naming service");
    options.addOption("s", "subrings", false, "Do not compute subrings");
    options.addOption("sssr", "sssr", false, "Use SSSR method for sub-ring computation");
    options.addOption("vis", "visualize", false, "Visualize the abstraction graph");
    options.addOption("vr", "vis_recursive", false, "Visualize sub graphs recursively");
    options.addOption("vb", "vis_bw", false, "Visualize graph black and white; default colour");
    options.addOption("vs", "vis_short", false, "Visualize bonds short");
    options.addOption("sf", "structuralformula", false, "Print the structural formula");
    options.addOption("sub", "subscript", false, "Use subscripts with structural formula");
    options.addOption("m", "molcom", true, "Comparison heuristics for molecules given as a comma"
            + "separated list. Currently available heuristics: type, weight, size");

    CommandLineParser parser = new BasicParser();
    try {/*from   www  .j  a  v  a  2 s . co m*/
        Cli.cl = parser.parse(options, args);
    } catch (ParseException e) {
        usage(options, 1);
    }
    if (Cli.cl.hasOption("help")) {
        usage(options, 0);
    }

    for (int i = 0; i < Cli.cl.getArgList().size(); i++) {
        String fileName = Cli.cl.getArgList().get(i).toString();
        File f = new File(fileName);
        if (f.exists() && !f.isDirectory()) {
            Cli.files.add(fileName);
        } else {
            Cli.warning(fileName);
        }
    }

}

From source file:com.jug.MoMA.java

/**
 * PROJECT MAIN/*from   w  w w  .  j a  va  2s .  c om*/
 *
 * @param args
 */
public static void main(final String[] args) {
    if (showIJ)
        new ImageJ();

    //      // ===== set look and feel ========================================================================
    //      try {
    //         // Set cross-platform Java L&F (also called "Metal")
    //         UIManager.setLookAndFeel(
    //               UIManager.getCrossPlatformLookAndFeelClassName() );
    //      } catch ( final UnsupportedLookAndFeelException e ) {
    //         // handle exception
    //      } catch ( final ClassNotFoundException e ) {
    //         // handle exception
    //      } catch ( final InstantiationException e ) {
    //         // handle exception
    //      } catch ( final IllegalAccessException e ) {
    //         // handle exception
    //      }

    // ===== command line parsing ======================================================================

    // create Options object & the parser
    final Options options = new Options();
    final CommandLineParser parser = new BasicParser();
    // defining command line options
    final Option help = new Option("help", "print this message");

    final Option headless = new Option("h", "headless", false,
            "start without user interface (note: input-folder must be given!)");
    headless.setRequired(false);

    final Option timeFirst = new Option("tmin", "min_time", true, "first time-point to be processed");
    timeFirst.setRequired(false);

    final Option timeLast = new Option("tmax", "max_time", true, "last time-point to be processed");
    timeLast.setRequired(false);

    final Option optRange = new Option("orange", "opt_range", true, "initial optimization range");
    optRange.setRequired(false);

    final Option numChannelsOption = new Option("c", "channels", true,
            "number of channels to be loaded and analyzed.");
    numChannelsOption.setRequired(true);

    final Option minChannelIdxOption = new Option("cmin", "min_channel", true,
            "the smallest channel index (usually 0 or 1, default is 1).");
    minChannelIdxOption.setRequired(false);

    final Option infolder = new Option("i", "infolder", true, "folder to read data from");
    infolder.setRequired(false);

    final Option outfolder = new Option("o", "outfolder", true,
            "folder to write preprocessed data to (equals infolder if not given)");
    outfolder.setRequired(false);

    final Option userProps = new Option("p", "props", true, "properties file to be loaded (mm.properties)");
    userProps.setRequired(false);

    options.addOption(help);
    options.addOption(headless);
    options.addOption(numChannelsOption);
    options.addOption(minChannelIdxOption);
    options.addOption(timeFirst);
    options.addOption(timeLast);
    options.addOption(optRange);
    options.addOption(infolder);
    options.addOption(outfolder);
    options.addOption(userProps);
    // get the commands parsed
    CommandLine cmd = null;
    try {
        cmd = parser.parse(options, args);
    } catch (final ParseException e1) {
        final HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp(
                "... [-p props-file] -i in-folder [-o out-folder] -c <num-channels> [-cmin start-channel-ids] [-tmin idx] [-tmax idx] [-orange num-frames] [-headless]",
                "", options, "Error: " + e1.getMessage());
        System.exit(0);
    }

    if (cmd.hasOption("help")) {
        final HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp("... -i <in-folder> -o [out-folder] [-headless]", options);
        System.exit(0);
    }

    if (cmd.hasOption("h")) {
        System.out.println(">>> Starting MM in headless mode.");
        HEADLESS = true;
        if (!cmd.hasOption("i")) {
            final HelpFormatter formatter = new HelpFormatter();
            formatter.printHelp("Headless-mode requires option '-i <in-folder>'...", options);
            System.exit(0);
        }
    }

    File inputFolder = null;
    if (cmd.hasOption("i")) {
        inputFolder = new File(cmd.getOptionValue("i"));

        if (!inputFolder.isDirectory()) {
            System.out.println("Error: Input folder is not a directory!");
            System.exit(2);
        }
        if (!inputFolder.canRead()) {
            System.out.println("Error: Input folder cannot be read!");
            System.exit(2);
        }
    }

    File outputFolder = null;
    if (!cmd.hasOption("o")) {
        if (inputFolder == null) {
            System.out.println(
                    "Error: Output folder would be set to a 'null' input folder! Please check your command line arguments...");
            System.exit(3);
        }
        outputFolder = inputFolder;
        STATS_OUTPUT_PATH = outputFolder.getAbsolutePath();
    } else {
        outputFolder = new File(cmd.getOptionValue("o"));

        if (!outputFolder.isDirectory()) {
            System.out.println("Error: Output folder is not a directory!");
            System.exit(3);
        }
        if (!inputFolder.canWrite()) {
            System.out.println("Error: Output folder cannot be written to!");
            System.exit(3);
        }

        STATS_OUTPUT_PATH = outputFolder.getAbsolutePath();
    }

    fileUserProps = null;
    if (cmd.hasOption("p")) {
        fileUserProps = new File(cmd.getOptionValue("p"));
    }

    if (cmd.hasOption("cmin")) {
        minChannelIdx = Integer.parseInt(cmd.getOptionValue("cmin"));
    }
    if (cmd.hasOption("c")) {
        numChannels = Integer.parseInt(cmd.getOptionValue("c"));
    }

    if (cmd.hasOption("tmin")) {
        minTime = Integer.parseInt(cmd.getOptionValue("tmin"));
    }
    if (cmd.hasOption("tmax")) {
        maxTime = Integer.parseInt(cmd.getOptionValue("tmax"));
    }

    if (cmd.hasOption("orange")) {
        initOptRange = Integer.parseInt(cmd.getOptionValue("orange"));
    }

    // ******** CHECK GUROBI ********* CHECK GUROBI ********* CHECK GUROBI *********
    final String jlp = System.getProperty("java.library.path");
    //      System.out.println( jlp );
    try {
        new GRBEnv("MoMA_gurobi.log");
    } catch (final GRBException e) {
        final String msgs = "Initial Gurobi test threw exception... check your Gruobi setup!\n\nJava library path: "
                + jlp;
        if (HEADLESS) {
            System.out.println(msgs);
        } else {
            JOptionPane.showMessageDialog(MoMA.guiFrame, msgs, "Gurobi Error?", JOptionPane.ERROR_MESSAGE);
        }
        e.printStackTrace();
        System.exit(98);
    } catch (final UnsatisfiedLinkError ulr) {
        final String msgs = "Could initialize Gurobi.\n"
                + "You might not have installed Gurobi properly or you miss a valid license.\n"
                + "Please visit 'www.gurobi.com' for further information.\n\n" + ulr.getMessage()
                + "\nJava library path: " + jlp;
        if (HEADLESS) {
            System.out.println(msgs);
        } else {
            JOptionPane.showMessageDialog(MoMA.guiFrame, msgs, "Gurobi Error?", JOptionPane.ERROR_MESSAGE);
            ulr.printStackTrace();
        }
        System.out.println("\n>>>>> Java library path: " + jlp + "\n");
        System.exit(99);
    }
    // ******* END CHECK GUROBI **** END CHECK GUROBI **** END CHECK GUROBI ********

    final MoMA main = new MoMA();
    if (!HEADLESS) {
        guiFrame = new JFrame();
        main.initMainWindow(guiFrame);
    }

    System.out.println("VERSION: " + VERSION_STRING);

    props = main.loadParams();
    BGREM_TEMPLATE_XMIN = Integer
            .parseInt(props.getProperty("BGREM_TEMPLATE_XMIN", Integer.toString(BGREM_TEMPLATE_XMIN)));
    BGREM_TEMPLATE_XMAX = Integer
            .parseInt(props.getProperty("BGREM_TEMPLATE_XMAX", Integer.toString(BGREM_TEMPLATE_XMAX)));
    BGREM_X_OFFSET = Integer.parseInt(props.getProperty("BGREM_X_OFFSET", Integer.toString(BGREM_X_OFFSET)));
    GL_WIDTH_IN_PIXELS = Integer
            .parseInt(props.getProperty("GL_WIDTH_IN_PIXELS", Integer.toString(GL_WIDTH_IN_PIXELS)));
    MOTHER_CELL_BOTTOM_TRICK_MAX_PIXELS = Integer.parseInt(props.getProperty(
            "MOTHER_CELL_BOTTOM_TRICK_MAX_PIXELS", Integer.toString(MOTHER_CELL_BOTTOM_TRICK_MAX_PIXELS)));
    GL_FLUORESCENCE_COLLECTION_WIDTH_IN_PIXELS = Integer
            .parseInt(props.getProperty("GL_FLUORESCENCE_COLLECTION_WIDTH_IN_PIXELS",
                    Integer.toString(GL_FLUORESCENCE_COLLECTION_WIDTH_IN_PIXELS)));
    GL_OFFSET_BOTTOM = Integer
            .parseInt(props.getProperty("GL_OFFSET_BOTTOM", Integer.toString(GL_OFFSET_BOTTOM)));
    if (GL_OFFSET_BOTTOM == -1) {
        GL_OFFSET_BOTTOM_AUTODETECT = true;
    } else {
        GL_OFFSET_BOTTOM_AUTODETECT = false;
    }
    GL_OFFSET_TOP = Integer.parseInt(props.getProperty("GL_OFFSET_TOP", Integer.toString(GL_OFFSET_TOP)));
    GL_OFFSET_LATERAL = Integer
            .parseInt(props.getProperty("GL_OFFSET_LATERAL", Integer.toString(GL_OFFSET_LATERAL)));
    MIN_CELL_LENGTH = Integer.parseInt(props.getProperty("MIN_CELL_LENGTH", Integer.toString(MIN_CELL_LENGTH)));
    MIN_GAP_CONTRAST = Float
            .parseFloat(props.getProperty("MIN_GAP_CONTRAST", Float.toString(MIN_GAP_CONTRAST)));
    SIGMA_PRE_SEGMENTATION_X = Float.parseFloat(
            props.getProperty("SIGMA_PRE_SEGMENTATION_X", Float.toString(SIGMA_PRE_SEGMENTATION_X)));
    SIGMA_PRE_SEGMENTATION_Y = Float.parseFloat(
            props.getProperty("SIGMA_PRE_SEGMENTATION_Y", Float.toString(SIGMA_PRE_SEGMENTATION_Y)));
    SIGMA_GL_DETECTION_X = Float
            .parseFloat(props.getProperty("SIGMA_GL_DETECTION_X", Float.toString(SIGMA_GL_DETECTION_X)));
    SIGMA_GL_DETECTION_Y = Float
            .parseFloat(props.getProperty("SIGMA_GL_DETECTION_Y", Float.toString(SIGMA_GL_DETECTION_Y)));
    SEGMENTATION_MIX_CT_INTO_PMFRF = Float.parseFloat(props.getProperty("SEGMENTATION_MIX_CT_INTO_PMFRF",
            Float.toString(SEGMENTATION_MIX_CT_INTO_PMFRF)));
    SEGMENTATION_CLASSIFIER_MODEL_FILE = props.getProperty("SEGMENTATION_CLASSIFIER_MODEL_FILE",
            SEGMENTATION_CLASSIFIER_MODEL_FILE);
    CELLSIZE_CLASSIFIER_MODEL_FILE = props.getProperty("CELLSIZE_CLASSIFIER_MODEL_FILE",
            CELLSIZE_CLASSIFIER_MODEL_FILE);
    DEFAULT_PATH = props.getProperty("DEFAULT_PATH", DEFAULT_PATH);

    GUROBI_TIME_LIMIT = Double
            .parseDouble(props.getProperty("GUROBI_TIME_LIMIT", Double.toString(GUROBI_TIME_LIMIT)));
    GUROBI_MAX_OPTIMALITY_GAP = Double.parseDouble(
            props.getProperty("GUROBI_MAX_OPTIMALITY_GAP", Double.toString(GUROBI_MAX_OPTIMALITY_GAP)));

    GUI_POS_X = Integer.parseInt(props.getProperty("GUI_POS_X", Integer.toString(DEFAULT_GUI_POS_X)));
    GUI_POS_Y = Integer.parseInt(props.getProperty("GUI_POS_Y", Integer.toString(DEFAULT_GUI_POS_X)));
    GUI_WIDTH = Integer.parseInt(props.getProperty("GUI_WIDTH", Integer.toString(GUI_WIDTH)));
    GUI_HEIGHT = Integer.parseInt(props.getProperty("GUI_HEIGHT", Integer.toString(GUI_HEIGHT)));
    GUI_CONSOLE_WIDTH = Integer
            .parseInt(props.getProperty("GUI_CONSOLE_WIDTH", Integer.toString(GUI_CONSOLE_WIDTH)));

    if (!HEADLESS) {
        // Iterate over all currently attached monitors and check if sceen
        // position is actually possible,
        // otherwise fall back to the DEFAULT values and ignore the ones
        // coming from the properties-file.
        boolean pos_ok = false;
        final GraphicsEnvironment ge = GraphicsEnvironment.getLocalGraphicsEnvironment();
        final GraphicsDevice[] gs = ge.getScreenDevices();
        for (int i = 0; i < gs.length; i++) {
            if (gs[i].getDefaultConfiguration().getBounds()
                    .contains(new java.awt.Point(GUI_POS_X, GUI_POS_Y))) {
                pos_ok = true;
            }
        }
        // None of the screens contained the top-left window coordinates -->
        // fall back onto default values...
        if (!pos_ok) {
            GUI_POS_X = DEFAULT_GUI_POS_X;
            GUI_POS_Y = DEFAULT_GUI_POS_Y;
        }
    }

    String path = props.getProperty("import_path", System.getProperty("user.home"));
    if (inputFolder == null || inputFolder.equals("")) {
        inputFolder = main.showStartupDialog(guiFrame, path);
    }
    System.out.println("Default filename decoration = " + inputFolder.getName());
    defaultFilenameDecoration = inputFolder.getName();
    path = inputFolder.getAbsolutePath();
    props.setProperty("import_path", path);

    GrowthLineSegmentationMagic.setClassifier(SEGMENTATION_CLASSIFIER_MODEL_FILE, "");

    if (!HEADLESS) {
        // Setting up console window...
        main.initConsoleWindow();
        main.showConsoleWindow(true);
    }

    // ------------------------------------------------------------------------------------------------------
    // ------------------------------------------------------------------------------------------------------
    final MoMAModel mmm = new MoMAModel(main);
    instance = main;
    try {
        main.processDataFromFolder(path, minTime, maxTime, minChannelIdx, numChannels);
    } catch (final Exception e) {
        e.printStackTrace();
        System.exit(11);
    }
    // ------------------------------------------------------------------------------------------------------
    // ------------------------------------------------------------------------------------------------------

    // show loaded and annotated data
    if (showIJ) {
        new ImageJ();
        ImageJFunctions.show(main.imgRaw, "Rotated & cropped raw data");
        // ImageJFunctions.show( main.imgTemp, "Temporary" );
        // ImageJFunctions.show( main.imgAnnotated, "Annotated ARGB data" );

        // main.getCellSegmentedChannelImgs()
        // ImageJFunctions.show( main.imgClassified, "Classification" );
        // ImageJFunctions.show( main.getCellSegmentedChannelImgs(), "Segmentation" );
    }

    gui = new MoMAGui(mmm);

    if (!HEADLESS) {
        System.out.print("Build GUI...");
        main.showConsoleWindow(false);

        //         final JFrameSnapper snapper = new JFrameSnapper();
        //         snapper.addFrame( main.frameConsoleWindow );
        //         snapper.addFrame( guiFrame );

        gui.setVisible(true);
        guiFrame.add(gui);
        guiFrame.setSize(GUI_WIDTH, GUI_HEIGHT);
        guiFrame.setLocation(GUI_POS_X, GUI_POS_Y);
        guiFrame.setVisible(true);

        //         SwingUtilities.invokeLater( new Runnable() {
        //
        //            @Override
        //            public void run() {
        //               snapper.snapFrames( main.frameConsoleWindow, guiFrame, JFrameSnapper.EAST );
        //            }
        //         } );
        System.out.println(" done!");
    } else {
        //         final String name = inputFolder.getName();

        gui.exportHtmlOverview();
        gui.exportDataFiles();

        instance.saveParams();

        System.exit(0);
    }
}

From source file:com.continuuity.loom.runtime.MockProvisionerMain.java

@Override
public void init(String[] args) {
    Options options = new Options();
    options.addOption("i", "id", true, "Id for the provisioner. Defaults to 'dummy'");
    options.addOption("h", "host", true, "Loom server to connect to. Defaults to 'localhost'");
    options.addOption("p", "port", true, "Loom server port to connect to. Defaults to 55054");
    options.addOption("c", "capacity", true, "total worker capacity for the provisioner. Defaults to 10");
    options.addOption("f", "frequency", true,
            "milliseconds for workers to wait between taking tasks. Defaults to 1000");
    options.addOption("d", "duration", true, "milliseconds a task should take to complete. Defaults to 1000");

    try {//  ww w.j  a v a 2s.  c o  m
        CommandLineParser parser = new BasicParser();
        CommandLine cmd = parser.parse(options, args);
        String id = cmd.hasOption('i') ? cmd.getOptionValue('i') : "dummy";
        String host = cmd.hasOption('h') ? cmd.getOptionValue('h') : "localhost";
        int port = cmd.hasOption('p') ? Integer.valueOf(cmd.getOptionValue('p')) : 55054;
        int capacity = cmd.hasOption('c') ? Integer.valueOf(cmd.getOptionValue('c')) : 10;
        long msBetweenTasks = cmd.hasOption('f') ? Long.valueOf(cmd.getOptionValue('f')) : 1000;
        long taskMs = cmd.hasOption('d') ? Long.valueOf(cmd.getOptionValue('d')) : 1000;
        String serverUrl = "http://" + host + ":" + port;
        LOG.info("id = {}, capacity = {}, server url = {}, task frequency = {}, task duration = {}", id,
                capacity, serverUrl, msBetweenTasks, taskMs);

        mockProvisionerService = new MockProvisionerService(id, serverUrl, capacity, taskMs, msBetweenTasks);
    } catch (ParseException e) {
        Throwables.propagate(e);
    }
}

From source file:ca.nines.ise.cmd.Command.java

/**
 * Parse the command line args[] array and return the result.
 *
 * @param opts//from ww w.ja v a  2s. c  o  m
 * @param args
 * @return CommandLine
 * @throws ParseException
 */
public CommandLine getCommandLine(Options opts, String[] args) throws ParseException {
    CommandLine cmd;
    CommandLineParser parser = new BasicParser();
    cmd = parser.parse(opts, args);
    return cmd;
}