Java tutorial
package uni.bielefeld.cmg.sparkhit.util; /** * Created by Liren Huang on 13/01/16. * * SparkHit * Copyright (c) 2015-2015: * Liren Huang <huanglr at cebitec.uni-bielefeld.de> * * 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. * * 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. * * You should have received a copy of the GNU General Public License along * with this program. If not, see <http://www.gnu.org/licenses/>. */ import org.apache.commons.cli.*; import java.io.File; import java.io.IOException; import java.util.HashMap; import java.util.Map; public class ParameterForCorrelationer { private String[] arguments; private InfoDumper info = new InfoDumper(); public ParameterForCorrelationer(String[] arguments) throws IOException, ParseException { this.arguments = arguments; } private static final Options parameter = new Options(); DefaultParam param = new DefaultParam(); /* parameter IDs */ private static final String INPUT_VCF = "vcf", INPUT_TAB = "tab", OUTPUT_LINE = "outfile", COLUMN = "column", CACHE = "cache", PARTITIONS = "partition", VERSION = "version", HELP2 = "h", HELP = "help"; private static final Map<String, Integer> parameterMap = new HashMap<String, Integer>(); public void putParameterID() { int o = 0; parameterMap.put(INPUT_VCF, o++); parameterMap.put(INPUT_TAB, o++); parameterMap.put(OUTPUT_LINE, o++); parameterMap.put(COLUMN, o++); parameterMap.put(CACHE, o++); parameterMap.put(PARTITIONS, o++); parameterMap.put(VERSION, o++); parameterMap.put(HELP, o++); parameterMap.put(HELP2, o++); } public void addParameterInfo() { /* use Object parameter of Options class to store parameter information */ parameter.addOption(OptionBuilder.withArgName("input VCF file").hasArg() .withDescription("Input vcf file containing variation info").create(INPUT_VCF)); parameter.addOption(OptionBuilder.withArgName("input tabular file").hasArg() .withDescription("Input tabular file containing variation info").create(INPUT_TAB)); parameter.addOption(OptionBuilder.withArgName("output file").hasArg() .withDescription("Output alleles p value").create(OUTPUT_LINE)); parameter.addOption(OptionBuilder.withArgName("Columns for Alleles").hasArg() .withDescription("columns where allele info is set").create(COLUMN)); parameter.addOption(OptionBuilder.withArgName("Cache data").hasArg(false) .withDescription("weather to cache data in memory or not, default no").create(CACHE)); parameter.addOption(OptionBuilder.withArgName("re-partition num").hasArg().withDescription( "even the load of each task, 1 partition for a task or 4 partitions for a task is recommended. Default, not re-partition") .create(PARTITIONS)); parameter .addOption(OptionBuilder.hasArg(false).withDescription("show version information").create(VERSION)); parameter.addOption( OptionBuilder.hasArg(false).withDescription("print and show this information").create(HELP)); parameter.addOption(OptionBuilder.hasArg(false).withDescription("").create(HELP2)); } /* main method */ public DefaultParam importCommandLine() { /* Assigning Parameter ID to an ascending number */ putParameterID(); /* Assigning parameter descriptions to each parameter ID */ addParameterInfo(); /* need a Object parser of PosixParser class for the function parse of CommandLine class */ PosixParser parser = new PosixParser(); /* print out help information */ HelpParam help = new HelpParam(parameter, parameterMap); /* check each parameter for assignment */ try { long input_limit = -1; int threads = Runtime.getRuntime().availableProcessors(); /* Set Object cl of CommandLine class for Parameter storage */ CommandLine cl = parser.parse(parameter, arguments, true); if (cl.hasOption(HELP)) { help.printStatisticerHelp(); System.exit(0); } if (cl.hasOption(HELP2)) { help.printStatisticerHelp(); System.exit(0); } if (cl.hasOption(VERSION)) { System.exit(0); } /* Checking all parameters */ String value; if ((value = cl.getOptionValue(PARTITIONS)) != null) { param.partitions = Integer.decode(value); } if ((value = cl.getOptionValue(COLUMN)) != null) { param.columns = value; param.columnStart = Integer.decode(value.split("-")[0]); param.columnEnd = Integer.decode(value.split("-")[1]); } else { param.columnStart = Integer.decode(param.columns.split("-")[0]); param.columnEnd = Integer.decode(param.columns.split("-")[1]); } if (cl.hasOption(CACHE)) { param.cache = true; } if ((value = cl.getOptionValue(INPUT_VCF)) != null) { param.inputFqPath = value; } else if ((value = cl.getOptionValue(INPUT_TAB)) != null) { param.inputFqPath = value; } else { help.printStatisticerHelp(); System.exit(0); // throw new IOException("Input file not specified.\nUse -help for list of options"); } /* not applicable for HDFS and S3 */ /* using TextFileBufferInput for such purpose */ // File inputFastq = new File(param.inputFqPath).getAbsoluteFile(); // if (!inputFastq.exists()){ // err.println("Input query file not found."); // return; //i } if ((value = cl.getOptionValue(OUTPUT_LINE)) != null) { param.outputPath = value; } else { help.printStatisticerHelp(); info.readMessage("Output file not set with -outfile options"); info.screenDump(); System.exit(0); } File outfile = new File(param.outputPath).getAbsoluteFile(); if (outfile.exists()) { info.readParagraphedMessages( "Output file : \n\t" + param.outputPath + "\nalready exists, will be overwrite."); info.screenDump(); Runtime.getRuntime().exec("rm -rf " + param.outputPath); } } catch (IOException e) { // Don`t catch this, NaNaNaNa, U can`t touch this. info.readMessage("Parameter settings incorrect."); info.screenDump(); e.printStackTrace(); System.exit(0); } catch (RuntimeException e) { info.readMessage("Parameter settings incorrect."); info.screenDump(); e.printStackTrace(); System.exit(0); } catch (ParseException e) { info.readMessage("Parameter settings incorrect."); info.screenDump(); e.printStackTrace(); System.exit(0); } return param; } }