Example usage for org.apache.commons.cli HelpFormatter printOptions

Introduction

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

Prototype

public void printOptions(PrintWriter pw, int width, Options options, int leftPad, int descPad) 

Source Link

Document

Print the help for the specified Options to the specified writer, using the specified width, left padding and description padding.

Usage

From source file:uni.bielefeld.cmg.sparkhit.util.HelpParam.java

/**
 * print out help info with parameters//from  w  w  w.j av a 2  s  .c om
 */
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();
}

---

From source file:uni.bielefeld.cmg.sparkhit.util.HelpParam.java

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()));
        }/*from w w w  .  ja  v a  2  s  .c  o  m*/
    });

    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();
}

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From source file:uni.bielefeld.cmg.sparkhit.util.HelpParam.java

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()));
        }// w  w  w .ja v a  2 s. co m
    });

    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();
}

---

From source file:uni.bielefeld.cmg.sparkhit.util.HelpParam.java

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()));
        }/*from  w  ww .  j a  va  2 s.  co m*/
    });

    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();
}

---

From source file:uni.bielefeld.cmg.sparkhit.util.HelpParam.java

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()));
        }//from  w w w  .  j  ava 2  s . co m
    });

    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();
}

---

From source file:uni.bielefeld.cmg.sparkhit.util.HelpParam.java

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()));
        }/*from  ww  w. j av  a2  s . co m*/
    });

    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();
}

---

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