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

Introduction

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

Prototype

OptionGroup

Source Link

Usage

From source file:sse.Main.java

@SuppressWarnings("static-access")
private static Options buildOptions() {
    Options options = new Options();

    Option input = OptionBuilder.hasArg().withArgName("file").isRequired().withDescription(
            "The basename of the input files. Can be either a block for search mode or a text for create mode.")
            .create("i");
    OptionGroup mode = new OptionGroup();

    Option output = OptionBuilder.hasArg().withArgName("file")
            .withDescription("The basename of the output files.").create("o");

    Option iv = OptionBuilder.hasArg().withArgName("file")
            .withDescription("The file wich contains the iv and salt.").create("iv");
    Option help = new Option("help", "Prints the help message.");
    Option verbose = new Option("v", "Enables verbose mode.");
    Option backend = OptionBuilder.hasArg().withArgName("backend")
            .withDescription("Sets the backend which is to be used. Either amazon or file-system.")
            .create("backend");

    Option create = new Option("create", "Encrypts the given text");

    Option search = OptionBuilder.hasArg().withArgName("text").withDescription("Searches for the given text.")
            .create("search");

    Option password = OptionBuilder.hasArg().withArgName("password")
            .withDescription("Sets the password used for encryption.").isRequired().create("password");

    mode.addOption(create);//from  w  w w . j a  v  a 2  s.com
    mode.addOption(search);
    options.addOption(output);
    options.addOptionGroup(mode);

    options.addOption(input);
    options.addOption(iv);
    options.addOption(help);
    options.addOption(verbose);
    options.addOption(backend);
    options.addOption(password);

    return options;

}

From source file:treecmp.commandline.CommandLineParser.java

public Command run(String args[]) {
    Command cmd = null;//  ww w. j ava 2 s .c o m
    DefinedMetricsSet DMSet = DefinedMetricsSet.getInstance();

    Option oS = new Option("s", S_DESC);
    Option oW = new Option("w", W_DESC);
    oW.setArgName(W_ARG);
    oW.setArgs(1);
    Option oM = new Option("m", M_DESC);
    Option oR = new Option("r", R_DESC);
    oR.setArgName(R_ARG);
    oR.setArgs(1);

    OptionGroup cmdOpts = new OptionGroup();
    cmdOpts.addOption(oS);
    cmdOpts.addOption(oW);
    cmdOpts.addOption(oM);
    cmdOpts.addOption(oR);

    cmdOpts.setRequired(true);
    //set metric option
    Option oD = new Option("d", D_DESC);
    oD.setArgName(D_ARG);
    oD.setValueSeparator(' ');
    oD.setArgs(DMSet.size());
    oD.setRequired(true);

    Option oI = new Option("i", I_DESC);
    oI.setArgName(I_ARG);
    oI.setArgs(1);
    oI.setRequired(true);

    Option oO = new Option("o", O_DESC);
    oO.setArgs(1);
    oO.setArgName(O_ARG);
    oO.setRequired(true);

    Option oP = new Option("P", P_DESC);
    Option oSS = new Option("N", SS_DESC);
    Option oII = new Option("I", II_DESC);

    Option oOO = new Option("O", OO_DESC);
    Option oA = new Option("A", A_DESC);
    OptionGroup customMOpts = new OptionGroup();
    customMOpts.addOption(oOO);
    customMOpts.addOption(oA);

    Options opts = new Options();

    opts.addOptionGroup(cmdOpts);
    opts.addOption(oD);
    opts.addOption(oI);
    opts.addOption(oO);
    opts.addOption(oP);
    opts.addOption(oSS);
    opts.addOption(oII);
    opts.addOptionGroup(customMOpts);

    //getting version from manifest file
    String version = CommandLineParser.class.getPackage().getImplementationVersion();
    if (version == null) {
        version = "";
    }
    String FOOTER = "";
    String HEADER = " ";
    String APP_NAME = "TreeCmp version " + version + "\n";
    GnuParser parser = new GnuParser();
    HelpFormatter formatter = new HelpFormatter();
    formatter.setOptionComparator(new OptOrder());

    System.out.println(APP_NAME);
    if (args.length == 0) {
        formatter.printHelp(CMD_LINE_SYNTAX, HEADER, opts, FOOTER, false);
        return null;
    }

    try {
        CommandLine commandLine = parser.parse(opts, args);
        if (commandLine != null) {
            // process these values
            //set IO settings
            String inputFileName = (String) commandLine.getOptionValue(oI.getOpt());
            String outputFileName = (String) commandLine.getOptionValue(oO.getOpt());

            if (inputFileName == null) {
                System.out.println("Error: input file not specified!");
                formatter.printHelp(CMD_LINE_SYNTAX, HEADER, opts, FOOTER, false);

                return null;
            }
            if (outputFileName == null) {
                System.out.println("Error: output file not specified!");
                formatter.printHelp(CMD_LINE_SYNTAX, HEADER, opts, FOOTER, false);
                return null;
            }

            //commandLine.
            IOSettings IOset = IOSettings.getIOSettings();
            IOset.setInputFile(inputFileName);
            IOset.setOutputFile(outputFileName);

            //custom additinal options
            ArrayList<Option> custOpts = new ArrayList<Option>();

            if (commandLine.hasOption(oP.getOpt())) {
                IOset.setPruneTrees(true);
                custOpts.add(oP);
            }
            if (commandLine.hasOption(oSS.getOpt())) {
                IOset.setRandomComparison(true);
                custOpts.add(oSS);
            }
            if (commandLine.hasOption(oA.getOpt())) {
                IOset.setGenAlignments(true);
                custOpts.add(oA);
            }
            if (commandLine.hasOption(oOO.getOpt())) {
                IOset.setOptMsMcByRf(true);
                custOpts.add(oOO);
            }
            if (commandLine.hasOption(oII.getOpt())) {
                IOset.setGenSummary(true);
                custOpts.add(oII);
            }
            Collections.sort(custOpts, new OptOrder());

            //set active metrics
            ActiveMetricsSet AMSet = ActiveMetricsSet.getInstance();

            final String[] metrics = commandLine.getOptionValues(oD.getOpt());
            for (int i = 0; i < metrics.length; i++) {

                final DefinedMetric definedMetric = DMSet.getDefinedMetric(metrics[i]);
                if (definedMetric != null) {
                    AMSet.addMetric(definedMetric);
                } else {
                    System.out.print("Error: ");
                    System.out.println("Metric: " + metrics[i] + " is unknown\n.");
                    formatter.printHelp(CMD_LINE_SYNTAX, HEADER, opts, FOOTER, false);
                    return null;
                }

            }

            //set active command
            String analysisType = "";

            if (commandLine.hasOption(oW.getOpt())) {
                String sWindowSize = (String) commandLine.getOptionValue(oW.getOpt());
                int iWindowSize = Integer.parseInt(sWindowSize);
                cmd = new RunWCommand(1, "-w", iWindowSize);
                analysisType = "window comparison mode (-w) with window size: " + iWindowSize;
            } else if (commandLine.hasOption(oM.getOpt())) {
                cmd = new RunMCommand(0, "-m");
                analysisType = "matrix comparison mode (-m)";
            } else if (commandLine.hasOption(oS.getOpt())) {
                cmd = new RunSCommand(0, "-s");
                analysisType = "overlapping pair comparison mode (-s)";
            } else if (commandLine.hasOption(oR.getOpt())) {
                String sRefTreeFile = (String) commandLine.getOptionValue(oR.getOpt());
                cmd = new RunRCommand(0, "-r", sRefTreeFile);
                analysisType = " ref-to-all comparison mode (-r)";
            } else {
                System.out.println("Error: type of the analysis not specified correctly!");
                formatter.printHelp(CMD_LINE_SYNTAX, HEADER, opts, FOOTER, false);
                return null;
            }

            printOptionsInEffect(analysisType, AMSet, inputFileName, outputFileName, custOpts);

            return cmd;
        } else {
            //Error during parsing command line
            return null;
        }
    } catch (ParseException ex) {
        log.log(Level.WARNING, "Could not parse command line arguments.", ex);
        System.out.println(CMD_ERROR);

        formatter.printHelp(CMD_LINE_SYNTAX, HEADER, opts, FOOTER, false);

    } catch (NumberFormatException ex) {
        System.out.print("Error: ");
        System.out.println("window size should be an integer.\n");
        formatter.printHelp(CMD_LINE_SYNTAX, HEADER, opts, FOOTER, false);

    }
    return cmd;
}

From source file:uk.ac.imperial.presage2.core.cli.Presage2CLI.java

private OptionGroup getCommands() {
    OptionGroup cmdGroup = new OptionGroup();
    for (String cmd : commands.keySet()) {
        cmdGroup.addOption(new Option(cmd, commands.get(cmd).getAnnotation(Command.class).description()));
    }//w ww . j  a v  a 2 s .  c  o  m
    return cmdGroup;
}