fr.ens.biologie.genomique.toullig.Main.java Source code

Introduction

Here is the source code for fr.ens.biologie.genomique.toullig.Main.java

Source

package fr.ens.biologie.genomique.toullig;

import java.util.ArrayList;
import java.util.Arrays;

import fr.ens.biologie.genomique.eoulsan.Common;
import fr.ens.biologie.genomique.toullig.actions.GtftogpdAction;
import org.apache.commons.cli.*;

import fr.ens.biologie.genomique.toullig.actions.Fast5tofastqAction;
import fr.ens.biologie.genomique.toullig.actions.TrimAction;

/**
 * Main class of nanoporetools
 * @author Aurelien Birer
 */
public class Main {

    /**
     * Show a message and then exit.
     * @param message the message to show
     */
    public static void showErrorMessageAndExit(final String message) {

        System.err.println(message);
        System.exit(1);
    }

    /**
     * Show a message and then exit.
     * @param message the message to show
     */
    public static void showMessageAndExit(final String message) {

        System.out.println(message);
        System.exit(0);
    }

    /**
     * Create options for command line
     * @return an Options object
     */
    private static Options makeOptions() {

        // create Options object
        final Options options = new Options();

        //
        // General
        //

        // add option for display version
        options.addOption("version", false, "show version of the software");

        // add option for display about
        options.addOption("about", false, "display information about this software");

        // add option for display help
        options.addOption("h", "help", false, "display this help");

        // add option for display license
        options.addOption("license", false, "display information about the license of this software");

        return options;
    }

    /**
     * The main function parse the options of the command line
     */
    public static void main(String[] args) {

        // make options
        final Options options = makeOptions();

        // make parser of the command line
        final CommandLineParser parser = new GnuParser();

        try {

            // parse the command line arguments
            final CommandLine line = parser.parse(options, args, true);

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

                showErrorMessageAndExit(
                        "ERROR: Toullig need in the first argument the tool what you want use!\nSee the help with "
                                + Globals.APP_NAME_LOWER_CASE + ".sh -h, --help\n");

            }

            // display help
            if (line.hasOption("help")) {
                help();
            }

            // About option
            if (line.hasOption("about")) {
                Common.showMessageAndExit(Globals.ABOUT_TXT);
            }

            // Version option
            if (line.hasOption("version")) {
                Common.showMessageAndExit(Globals.WELCOME_MSG);
            }

            // Licence option
            if (line.hasOption("license")) {
                Common.showMessageAndExit(Globals.LICENSE_TXT);
            }

            String mode = args[0];

            switch (mode) {

            // process fast5tofastq module
            case "fast5tofastq":

                new Fast5tofastqAction().action(new ArrayList<>(Arrays.asList(args)).subList(1, args.length));

                break;

            // display help
            default:

                showMessageAndExit("ERROR: The name of the tool is not correct!\nSee the help with "
                        + Globals.APP_NAME_LOWER_CASE + ".sh -h, --help\n");

                break;

            // process trim module
            case "trim":

                new TrimAction().action(new ArrayList<>(Arrays.asList(args)).subList(1, args.length));

                break;

            // process gtftogpd module
            case "gtftogpd":

                new GtftogpdAction().action(new ArrayList<>(Arrays.asList(args)).subList(1, args.length));

                break;

            // // process test module
            // case "test":
            // new SamDiffAnnot();
            // break;

            }
        } catch (ParseException e) {
            e.printStackTrace();
        }
    }

    /**
     * Show command line help.
     */
    private static void help() {

        // Show help message
        System.out.println(Globals.HELP_TXT);

        System.exit(0);
    }
}