Java tutorial
package uni.bielefeld.cmg.sparkhit.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", "spark-submit [spark parameter] --class uni.bielefeld.cmg.sparkhit.main.Main"); err.println("Name:"); err.println("\tSparkHit Main"); 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("\tBuild reference : "); err.println(executable + " [parameters] -build reference.fa"); err.println("\trun fragment recruitment : "); err.println(executable + " [parameters] -fastq query.fq -reference reference.fa -outfile output_file.txt"); err.println(executable + " [parameters] -line query.txt -reference reference.fa -outfile output_file.txt"); err.println(); } public void printConverterHelp() { 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", "spark-submit [spark parameter] --class uni.bielefeld.cmg.sparkhit.main.MainOfConverter Sparkhit.jar"); err.println("Name:"); err.println("\tSparkHit Converter"); 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("\tConvert different file format :"); err.println(executable + " [parameters] -fastq query.fq.tar.bz2 -outfile ./outdir"); err.println(); } public void printReporterHelp() { 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", "spark-submit [spark parameter] --class uni.bielefeld.cmg.sparkhit.main.MainOfReporter Sparkhit.jar"); err.println("Name:"); err.println("\tSparkHit Reporter"); 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("\tReport mappint summary"); err.println(executable + " [parameters] -input ./sparkhit.out -outfile ./sparkhit.report"); err.println(); } public void printScriptPiperHelp() { 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", "spark-submit [spark parameter] --class uni.bielefeld.cmg.sparkhit.main.MainOfPiper Sparkhit.jar"); err.println("Name:"); err.println("\tSparkHit ScriptPiper (bwa, bowtie2 or other aligner)"); 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("\tParallelize your own tool like bwa mem:"); err.println(executable + " [parameters] -fastq query.fq.tar.bz2 -outfile ./outbams_dir -tool \"/mypath/bwa mem\" -toolparam \"/mypath/reference.fa -t 32\""); err.println(); } public void printStatisticerHelp() { 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", "spark-submit [spark parameter] --class uni.bielefeld.cmg.sparkhit.main.MainOfPiper Sparkhit.jar"); err.println("Name:"); err.println("\tSparkHit Machine Learning library"); 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("\tMachine learning library for vcf or tabular file:"); err.println(executable + " [parameters] -vcf genotype.vcf -outfile ./result -column 2-10 -cache"); err.println(); } public void printDecompresserHelp() { 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", "spark-submit [spark parameter] --class uni.bielefeld.cmg.sparkhit.main.MainOfPiper Sparkhit.jar"); err.println("Name:"); err.println("\tSparkHit Decompresser"); 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("\tDecomress zipball and tarball using spark codec:"); err.println(executable + " [parameters] -fastq genotype.vcf -outfile ./decompressed"); err.println(); } }