oxis.yologp.CommandLineMain.java Source code

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Here is the source code for oxis.yologp.CommandLineMain.java

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/**
 * Copyright (C) 2014 EMBL - European Bioinformatics Institute
 *
 * All rights reserved. This file is part of the YOLogP project.
 *
 * author: oXis (Benjamin Roques)
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License,
 * please visit http://creativecommons.org/licenses/by-nc-sa/4.0/.
 * All we ask is that proper credit is given for my work, which includes
 * - but is not limited to - adding the above copyright notice to the beginning
 * of your source code files, and to any copyright notice that you may distribute
 * with programs based on this work.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
 */
package oxis.yologp;

/**
 *
 * @author John May, edited by oXis
 */
import java.io.File;
import java.util.ArrayList;
import java.util.logging.Level;
import java.util.logging.Logger;
import org.apache.commons.cli.*;

/**
 * Abstract object for when a main is runnable on the command line. The object
 * effectively provides a wrapper for command option processing utilising the
 * Apache Commons CLI library
 *
 * @author John May
 */
public abstract class CommandLineMain extends ArrayList<Option> {

    private final Options options = new Options();
    private final CommandLineParser parser = new PosixParser();
    private CommandLine cmdLine = null;

    public abstract void setupOptions();

    /**
     * Main processing method
     */
    public abstract void process();

    public CommandLineMain(String[] args) {

        setupOptions();

        for (Option opt : this) {
            options.addOption(opt);
        }
        options.addOption(new Option("h", "help", false, "print the help section"));

        try {
            cmdLine = parser.parse(options, args);
        } catch (ParseException ex) {
            Logger.getLogger(CommandLineMain.class.getName()).log(Level.SEVERE, "Could not parse arguments!", ex);
        }

        if (cmdLine.hasOption('h') || cmdLine.hasOption("help")) {
            printHelp();
        }
    }

    public CommandLine getCommandLine() {

        return cmdLine;
    }

    public boolean hasOption(String option) {

        return getCommandLine().hasOption(option);
    }

    /**
     * Convenience method for accessing a file from the parsed options.
     */
    public File getFileOption(String option) throws IllegalArgumentException {

        if (getCommandLine().hasOption(option)) {

            if (new File(getCommandLine().getOptionValue(option)).isFile()) {
                return new File(getCommandLine().getOptionValue(option));
            } else {
                throw new IllegalArgumentException();
            }

        } else {

            throw new IllegalArgumentException();
        }

    }

    public void printHelp() {

        for (Object obj : options.getOptions().toArray(new Option[0])) {
            Option opt = (Option) obj;
            System.out.println(
                    String.format("  -%s|--%-30s ", opt.getOpt(), opt.getLongOpt()) + opt.getDescription());
        }
        System.exit(0);
    }
}