uni.bielefeld.cmg.sparkhit.hadoop.decodec.util.HelpParam.java Source code

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Here is the source code for uni.bielefeld.cmg.sparkhit.hadoop.decodec.util.HelpParam.java

Source

package uni.bielefeld.cmg.sparkhit.hadoop.decodec.util;

import org.apache.commons.cli.HelpFormatter;
import org.apache.commons.cli.Option;
import org.apache.commons.cli.Options;

import java.io.PrintWriter;
import java.util.Comparator;
import java.util.Map;

import static java.lang.System.err;

/**
 * Created by Liren Huang on 13/01/16.
 * <p/>
 * SparkHit
 * <p/>
 * Copyright (c) 2015-2015:
 * Liren Huang     <huanglr at cebitec.uni-bielefeld.de>
 * <p/>
 * SparkHit is free software: you can redistribute it and/or modify it
 * under the terms of the GNU General Public License as published by the Free
 * Software Foundation, either version 3 of the License, or (at your option)
 * any later version.
 * <p/>
 * This program is distributed in the hope that it will be useful, but WITHOU
 * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
 * FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
 * more details.
 * <p/>
 * You should have received a copy of the GNU General Public License along
 * with this program. If not, see <http://www.gnu.org/licenses/>.
 */
public class HelpParam {
    private final Options parameter;
    private final Map<String, Integer> parameterMap;

    /**
     *
     * @param parameter
     * @param parameterMap
     */
    public HelpParam(Options parameter, Map<String, Integer> parameterMap) {
        /**
         * utilizes HelpFormatter to dump command line information for using the pipeline
         */
        this.parameter = parameter;
        this.parameterMap = parameterMap;
    }

    /**
     * print out help info with parameters
     */
    public void printHelp() {
        HelpFormatter formatter = new HelpFormatter();
        formatter.setOptionComparator(new Comparator<Option>() {
            public int compare(Option o1, Option o2) {
                return Integer.compare(parameterMap.get(o1.getOpt()), parameterMap.get(o2.getOpt()));
            }
        });

        final String executable = System.getProperty("executable", "Hadoop jar sparkhit-hadoopDecompressor.jar");
        err.println("Name:");
        err.println("\tSparkHit hadoop decompressor");
        err.println();
        err.println("Options:");
        formatter.printOptions(new PrintWriter(err, true), 85, parameter, 2, 3); /* print formatted parameters */
        err.println();
        err.println("Usage:");
        err.println("\tDeompressing BZip2 .bz2 file in parallel using Hadoop Mapper");
        err.println(executable + " [parameters] -bz2 hdfs://master/*/fastq.bz2 -outfile hdfs://master/out_dir");
        err.println(executable + " [parameters] -gz hdfs://master/*/fastq.gz -outfile hdfs://master/out_dir");
        err.println();
    }
}