List of usage examples for org.apache.commons.cli Options Options
Options
From source file:diffhunter.DiffHunter.java
/** * @param args the command line arguments * @throws org.apache.commons.cli.ParseException * @throws java.io.IOException/*w w w. j a va 2 s.com*/ */ public static void main(String[] args) throws ParseException, IOException { //String test_ = Paths.get("J:\\VishalData\\additional\\", "Sasan" + "_BDB").toAbsolutePath().toString(); // TODO code application logic here /*args = new String[] { "-i", "-b", "J:\\VishalData\\additional\\Ptbp2_E18_5_cortex_CLIP_mm9_plus_strand_sorted.bed", "-r", "J:\\VishalData\\additional\\mouse_mm9.txt", "-o", "J:\\VishalData" };*/ /*args = new String[] { "-c", "-r", "J:\\VishalData\\additional\\mouse_mm9.txt", "-1", "J:\\VishalData\\Ptbp2_Adult_testis_CLIP_mm9_plus_strand_sorted_BDB", "-2", "J:\\VishalData\\Ptbp2_E18_5_cortex_CLIP_mm9_plus_strand_sorted_BDB", "-w", "200", "-s", "50", "-o", "J:\\VishalData" };*/ Options options = new Options(); // add t option options.addOption("i", "index", false, "Indexing BED files."); options.addOption("b", "bed", true, "bed file to be indexed"); options.addOption("o", "output", true, "Folder that the index/comparison file will be created."); options.addOption("r", "reference", true, "Reference annotation file to be used for indexing"); options.addOption("c", "compare", false, "Finding differences between two conditions"); options.addOption("1", "first", true, "First sample index location"); options.addOption("2", "second", true, "Second sample index location"); options.addOption("w", "window", true, "Length of window for identifying differences"); options.addOption("s", "sliding", true, "Length of sliding"); CommandLineParser parser = new BasicParser(); CommandLine cmd = parser.parse(options, args); boolean indexing = false; boolean comparing = false; //Indexing! if (cmd.hasOption("i")) { //if(cmd.hasOption("1")) //System.err.println("sasan"); //System.out.println("sasa"); indexing = true; } else if (cmd.hasOption("c")) { //System.err.println(""); comparing = true; } else { //System.err.println("Option is not deteced."); HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("diffhunter", options); return; } //Indexing is selected // if (indexing == true) { //Since indexing is true. //User have to provide file for indexing. if (!(cmd.hasOption("o") || cmd.hasOption("r") || cmd.hasOption("b"))) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("diffhunter", options); return; } String bedfile_ = cmd.getOptionValue("b"); String reference_file = cmd.getOptionValue("r"); String folder_loc = cmd.getOptionValue("o"); String sample_name = FilenameUtils.getBaseName(bedfile_); try (Database B2 = BerkeleyDB_Box.Get_BerkeleyDB( Paths.get(folder_loc, sample_name + "_BDB").toAbsolutePath().toString(), true, sample_name)) { Indexer indexing_ = new Indexer(reference_file); indexing_.Make_Index(B2, bedfile_, Paths.get(folder_loc, sample_name + "_BDB").toAbsolutePath().toString()); B2.close(); } } else if (comparing == true) { if (!(cmd.hasOption("o") || cmd.hasOption("w") || cmd.hasOption("s") || cmd.hasOption("1") || cmd.hasOption("2"))) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("diffhunter", options); return; } String folder_loc = cmd.getOptionValue("o"); int window_ = Integer.parseInt(cmd.getOptionValue("w")); //int window_=600; int slide_ = Integer.parseInt(cmd.getOptionValue("s")); String first = cmd.getOptionValue("1").replace("_BDB", ""); String second = cmd.getOptionValue("2").replace("_BDB", ""); String reference_file = cmd.getOptionValue("r"); //String folder_loc=cmd.getOptionValue("o"); String sample_name_first = FilenameUtils.getBaseName(first); String sample_name_second = FilenameUtils.getBaseName(second); Database B1 = BerkeleyDB_Box.Get_BerkeleyDB(first + "_BDB", false, sample_name_first); Database B2 = BerkeleyDB_Box.Get_BerkeleyDB(second + "_BDB", false, sample_name_second); List<String> first_condition_genes = Files .lines(Paths.get(first + "_BDB", sample_name_first + ".txt").toAbsolutePath()) .collect(Collectors.toList()); List<String> second_condition_genes = Files .lines(Paths.get(second + "_BDB", sample_name_second + ".txt").toAbsolutePath()) .collect(Collectors.toList()); System.out.println("First and second condition are loaded!!! "); List<String> intersection_ = new ArrayList<>(first_condition_genes); intersection_.retainAll(second_condition_genes); BufferedWriter output = new BufferedWriter( new FileWriter(Paths.get(folder_loc, "differences_" + window_ + "_s" + slide_ + "_c" + ".txt") .toAbsolutePath().toString(), false)); List<Result_Window> final_results = Collections.synchronizedList(new ArrayList<>()); Worker_New worker_class = new Worker_New(); worker_class.Read_Reference(reference_file); while (!intersection_.isEmpty()) { List<String> selected_genes = new ArrayList<>(); //if (intersection_.size()<=10000){selected_genes.addAll(intersection_.subList(0, intersection_.size()));} //else selected_genes.addAll(intersection_.subList(0, 10000)); if (intersection_.size() <= intersection_.size()) { selected_genes.addAll(intersection_.subList(0, intersection_.size())); } else { selected_genes.addAll(intersection_.subList(0, intersection_.size())); } intersection_.removeAll(selected_genes); //System.out.println("Intersection count is:"+intersection_.size()); //final List<Result_Window> resultssss_=new ArrayList<>(); IntStream.range(0, selected_genes.size()).parallel().forEach(i -> { System.out.println(selected_genes.get(i) + "\tprocessing......"); String gene_of_interest = selected_genes.get(i);//"ENSG00000142657|PGD";//intersection_.get(6);////"ENSG00000163395|IGFN1";//"ENSG00000270066|SCARNA2"; int start = worker_class.dic_genes.get(gene_of_interest).start_loc; int end = worker_class.dic_genes.get(gene_of_interest).end_loc; Map<Integer, Integer> first_ = Collections.EMPTY_MAP; try { first_ = BerkeleyDB_Box.Get_Coord_Read(B1, gene_of_interest); } catch (IOException | ClassNotFoundException ex) { Logger.getLogger(DiffHunter.class.getName()).log(Level.SEVERE, null, ex); } Map<Integer, Integer> second_ = Collections.EMPTY_MAP; try { second_ = BerkeleyDB_Box.Get_Coord_Read(B2, gene_of_interest); } catch (IOException | ClassNotFoundException ex) { Logger.getLogger(DiffHunter.class.getName()).log(Level.SEVERE, null, ex); } List<Window> top_windows_first = worker_class.Get_Top_Windows(window_, first_, slide_); List<Window> top_windows_second = worker_class.Get_Top_Windows(window_, second_, slide_); //System.out.println("passed for window peak call for gene \t"+selected_genes.get(i)); // System.out.println("top_window_first_Count\t"+top_windows_first.size()); // System.out.println("top_window_second_Count\t"+top_windows_second.size()); if (top_windows_first.isEmpty() && top_windows_second.isEmpty()) { return; } List<Result_Window> res_temp = new Worker_New().Get_Significant_Windows(gene_of_interest, start, end, top_windows_first, top_windows_second, second_, first_, sample_name_first, sample_name_second, 0.01); if (!res_temp.isEmpty()) { final_results.addAll(res_temp);//final_results.addAll(worker_class.Get_Significant_Windows(gene_of_interest, start, end, top_windows_first, top_windows_second, second_, first_, first_condition, second_condition, 0.01)); } //System.out.println(selected_genes.get(i)+"\tprocessed."); }); /*selected_genes.parallelStream().forEach(i -> { });*/ List<Double> pvals = new ArrayList<>(); for (int i = 0; i < final_results.size(); i++) { pvals.add(final_results.get(i).p_value); } List<Double> qvals = MultipleTestCorrection.benjaminiHochberg(pvals); System.out.println("Writing to file..."); output.append("Gene_Symbol\tContributing_Sample\tStart\tEnd\tOddsRatio\tp_Value\tFDR"); output.newLine(); for (int i = 0; i < final_results.size(); i++) { Result_Window item = final_results.get(i); output.append(item.associated_gene_symbol + "\t" + item.contributing_windows + "\t" + item.start_loc + "\t" + item.end_loc + "\t" + item.oddsratio_ + "\t" + item.p_value + "\t" + qvals.get(i)); //+ "\t" + item.average_other_readcount_cotributing + "\t" + item.average_other_readcount_cotributing + "\t" + item.average_window_readcount_non + "\t" + item.average_other_readcount_non); output.newLine(); } /* for (Result_Window item : final_results) { output.append(item.associated_gene_symbol + "\t" + item.contributing_windows + "\t" + item.start_loc + "\t" + item.end_loc + "\t" + item.oddsratio_ + "\t" + item.p_value); //+ "\t" + item.average_other_readcount_cotributing + "\t" + item.average_other_readcount_cotributing + "\t" + item.average_window_readcount_non + "\t" + item.average_other_readcount_non); output.newLine(); } */ final_results.clear(); } output.close(); } System.out.println("Done."); }
From source file:fr.inria.atlanmod.kyanos.benchmarks.KyanosMapQueryList.java
public static void main(String[] args) { Options options = new Options(); Option inputOpt = OptionBuilder.create(IN); inputOpt.setArgName("INPUT"); inputOpt.setDescription("Input Kyanos resource directory"); inputOpt.setArgs(1);// w ww . j av a 2 s .c om inputOpt.setRequired(true); Option inClassOpt = OptionBuilder.create(EPACKAGE_CLASS); inClassOpt.setArgName("CLASS"); inClassOpt.setDescription("FQN of EPackage implementation class"); inClassOpt.setArgs(1); inClassOpt.setRequired(true); options.addOption(inputOpt); options.addOption(inClassOpt); CommandLineParser parser = new PosixParser(); try { PersistenceBackendFactoryRegistry.getFactories().put(NeoMapURI.NEO_MAP_SCHEME, new MapPersistenceBackendFactory()); CommandLine commandLine = parser.parse(options, args); URI uri = NeoMapURI.createNeoMapURI(new File(commandLine.getOptionValue(IN))); Class<?> inClazz = KyanosMapQueryList.class.getClassLoader() .loadClass(commandLine.getOptionValue(EPACKAGE_CLASS)); inClazz.getMethod("init").invoke(null); ResourceSet resourceSet = new ResourceSetImpl(); resourceSet.getResourceFactoryRegistry().getProtocolToFactoryMap().put(NeoMapURI.NEO_MAP_SCHEME, PersistentResourceFactory.eINSTANCE); Resource resource = resourceSet.createResource(uri); Map<String, Object> loadOpts = new HashMap<String, Object>(); resource.load(loadOpts); { LOG.log(Level.INFO, "Start query"); long begin = System.currentTimeMillis(); EList<MethodDeclaration> list = JavaQueries.getUnusedMethodsList(resource); long end = System.currentTimeMillis(); LOG.log(Level.INFO, "End query"); LOG.log(Level.INFO, MessageFormat.format("Query result (list) contains {0} elements", list.size())); LOG.log(Level.INFO, MessageFormat.format("Time spent: {0}", MessageUtil.formatMillis(end - begin))); } if (resource instanceof PersistentResourceImpl) { PersistentResourceImpl.shutdownWithoutUnload((PersistentResourceImpl) resource); } else { resource.unload(); } } catch (ParseException e) { MessageUtil.showError(e.toString()); MessageUtil.showError("Current arguments: " + Arrays.toString(args)); HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("java -jar <this-file.jar>", options, true); } catch (Throwable e) { MessageUtil.showError(e.toString()); } }
From source file:gr.forth.ics.isl.preprocessfilter1.controller.Controller.java
public static void main(String[] args) throws XPathExpressionException, ParserConfigurationException, SAXException, IOException, PreprocessFilterException, org.apache.commons.cli.ParseException { PropertyReader prop = new PropertyReader(); //The following block of code is executed if there are arguments from the command line if (args.length > 0) { try {//from w ww . j ava 2s .co m //The values of the arguments are handled as Option instances Options options = new Options(); CommandLineParser PARSER = new PosixParser(); Option inputFile = new Option("inputFile", true, "input xml file"); Option outputFile = new Option("outputFile", true, "output xml file"); Option parentNode = new Option("parentNode", true, "output xml file"); Option delimeter = new Option("delimeter", true, "output xml file"); Option newParentNode = new Option("newParentNode", true, "output xml file"); Option intermediateNodes = new Option("intermediateNodes", true, "output xml file"); Option intermediateNode = new Option("intermediateNode", true, "output xml file"); options.addOption(inputFile).addOption(outputFile).addOption(parentNode).addOption(newParentNode) .addOption(intermediateNode).addOption(intermediateNodes).addOption(delimeter); CommandLine cli = PARSER.parse(options, args); String inputFileArg = cli.getOptionValue("inputFile"); String outputFileArg = cli.getOptionValue("outputFile"); String parentNodeArg = cli.getOptionValue("parentNode"); String newParentNodeArg = cli.getOptionValue("newParentNode"); String intermediateNodeArg = cli.getOptionValue("intermediateNode"); String intermediateNodesArg = cli.getOptionValue("intermediateNodes"); String delimeterArg = cli.getOptionValue("delimeter"); PreprocessFilterUtilities process = new PreprocessFilterUtilities(); //System.out.println("INPUT:"+inputFileArg); //System.out.println("OUTPUT:"+outputFileArg); //System.out.println("PARENT NODE:"+parentNodeArg); //System.out.println("NEW PARENT NODE:"+newParentNodeArg); //System.out.println("INTERMEDIATE NODE:"+intermediateNodeArg); //System.out.println("INTERMEDIATE NODES:"+intermediateNodesArg); //System.out.println("DELIMETER:"+delimeterArg); //The filter's code is executed with the command line arguments as parameters if (process.createOutputFile(inputFileArg, outputFileArg, parentNodeArg, newParentNodeArg, intermediateNodeArg, intermediateNodesArg, delimeterArg)) { System.out.println("Succesfull PreProcessing!!!"); } } catch (PreprocessFilterException ex) { Logger.getLogger(Controller.class.getName()).log(Level.SEVERE, null, ex); throw new PreprocessFilterException("PreProcess Filter Exception:", ex); } } //If there are no command line arguments then the .config file is being used. else { try { String inputFilePathProp = prop.getProperty(inputFilePath); String outputFilePathProp = prop.getProperty(outputFilePath); String parentNodeProp = prop.getProperty(parentNode); String delimeterProp = prop.getProperty(delimeter); String newParentNodeProp = prop.getProperty(newParentNode); String intermediateNodesProp = prop.getProperty(intermediateNodes); String intermediateNodeProp = prop.getProperty(intermediateNode); PreprocessFilterUtilities process = new PreprocessFilterUtilities(); //The filter's code is executed with the .config file's resources as parameters if (process.createOutputFile(inputFilePathProp, outputFilePathProp, parentNodeProp, newParentNodeProp, intermediateNodeProp, intermediateNodesProp, delimeterProp)) { System.out.println("Succesfull PreProcessing!!!"); } } catch (PreprocessFilterException ex) { Logger.getLogger(Controller.class.getName()).log(Level.SEVERE, null, ex); throw new PreprocessFilterException("PreProcess Filter Exception:", ex); } } }
From source file:fr.inria.atlanmod.kyanos.benchmarks.KyanosMapQueryLoop.java
public static void main(String[] args) { Options options = new Options(); Option inputOpt = OptionBuilder.create(IN); inputOpt.setArgName("INPUT"); inputOpt.setDescription("Input Kyanos resource directory"); inputOpt.setArgs(1);/*from ww w . j a va 2 s.com*/ inputOpt.setRequired(true); Option inClassOpt = OptionBuilder.create(EPACKAGE_CLASS); inClassOpt.setArgName("CLASS"); inClassOpt.setDescription("FQN of EPackage implementation class"); inClassOpt.setArgs(1); inClassOpt.setRequired(true); options.addOption(inputOpt); options.addOption(inClassOpt); CommandLineParser parser = new PosixParser(); try { PersistenceBackendFactoryRegistry.getFactories().put(NeoMapURI.NEO_MAP_SCHEME, new MapPersistenceBackendFactory()); CommandLine commandLine = parser.parse(options, args); URI uri = NeoMapURI.createNeoMapURI(new File(commandLine.getOptionValue(IN))); Class<?> inClazz = KyanosMapQueryLoop.class.getClassLoader() .loadClass(commandLine.getOptionValue(EPACKAGE_CLASS)); inClazz.getMethod("init").invoke(null); ResourceSet resourceSet = new ResourceSetImpl(); resourceSet.getResourceFactoryRegistry().getProtocolToFactoryMap().put(NeoMapURI.NEO_MAP_SCHEME, PersistentResourceFactory.eINSTANCE); Resource resource = resourceSet.createResource(uri); Map<String, Object> loadOpts = new HashMap<String, Object>(); resource.load(loadOpts); { LOG.log(Level.INFO, "Start query"); long begin = System.currentTimeMillis(); EList<MethodDeclaration> list = JavaQueries.getUnusedMethodsLoop(resource); long end = System.currentTimeMillis(); LOG.log(Level.INFO, "End query"); LOG.log(Level.INFO, MessageFormat.format("Query result (loops) contains {0} elements", list.size())); LOG.log(Level.INFO, MessageFormat.format("Time spent: {0}", MessageUtil.formatMillis(end - begin))); } if (resource instanceof PersistentResourceImpl) { PersistentResourceImpl.shutdownWithoutUnload((PersistentResourceImpl) resource); } else { resource.unload(); } } catch (ParseException e) { MessageUtil.showError(e.toString()); MessageUtil.showError("Current arguments: " + Arrays.toString(args)); HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("java -jar <this-file.jar>", options, true); } catch (Throwable e) { MessageUtil.showError(e.toString()); } }
From source file:fr.inria.atlanmod.kyanos.benchmarks.KyanosMapQueryGrabats.java
public static void main(String[] args) { Options options = new Options(); Option inputOpt = OptionBuilder.create(IN); inputOpt.setArgName("INPUT"); inputOpt.setDescription("Input Kyanos resource directory"); inputOpt.setArgs(1);/*w ww. ja v a 2 s . c o m*/ inputOpt.setRequired(true); Option inClassOpt = OptionBuilder.create(EPACKAGE_CLASS); inClassOpt.setArgName("CLASS"); inClassOpt.setDescription("FQN of EPackage implementation class"); inClassOpt.setArgs(1); inClassOpt.setRequired(true); options.addOption(inputOpt); options.addOption(inClassOpt); CommandLineParser parser = new PosixParser(); try { PersistenceBackendFactoryRegistry.getFactories().put(NeoMapURI.NEO_MAP_SCHEME, new MapPersistenceBackendFactory()); CommandLine commandLine = parser.parse(options, args); URI uri = NeoMapURI.createNeoMapURI(new File(commandLine.getOptionValue(IN))); Class<?> inClazz = KyanosMapQueryGrabats.class.getClassLoader() .loadClass(commandLine.getOptionValue(EPACKAGE_CLASS)); inClazz.getMethod("init").invoke(null); ResourceSet resourceSet = new ResourceSetImpl(); resourceSet.getResourceFactoryRegistry().getProtocolToFactoryMap().put(NeoMapURI.NEO_MAP_SCHEME, PersistentResourceFactory.eINSTANCE); Resource resource = resourceSet.createResource(uri); Map<String, Object> loadOpts = new HashMap<String, Object>(); resource.load(loadOpts); { LOG.log(Level.INFO, "Start query"); long begin = System.currentTimeMillis(); EList<ClassDeclaration> list = JavaQueries.grabats09(resource); long end = System.currentTimeMillis(); LOG.log(Level.INFO, "End query"); LOG.log(Level.INFO, MessageFormat.format("Query result contains {0} elements", list.size())); LOG.log(Level.INFO, MessageFormat.format("Time spent: {0}", MessageUtil.formatMillis(end - begin))); } if (resource instanceof PersistentResourceImpl) { PersistentResourceImpl.shutdownWithoutUnload((PersistentResourceImpl) resource); } else { resource.unload(); } } catch (ParseException e) { MessageUtil.showError(e.toString()); MessageUtil.showError("Current arguments: " + Arrays.toString(args)); HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("java -jar <this-file.jar>", options, true); } catch (Throwable e) { MessageUtil.showError(e.toString()); } }
From source file:com.zarkonnen.longan.Main.java
public static void main(String[] args) throws IOException { // Use Apache Commons CLI (packaged into the Jar) to parse command line options. Options options = new Options(); Option helpO = OptionBuilder.withDescription("print help").create("h"); Option versionO = OptionBuilder.withDescription("print version").create("v"); Option outputO = OptionBuilder.withDescription("output file").withLongOpt("out").hasArg() .withArgName("file").create("o"); Option formatO = OptionBuilder .withDescription("output format: one of plaintext (default) and visualize (debug output in png)") .hasArg().withArgName("format").withLongOpt("format").create(); Option serverO = OptionBuilder.withDescription("launches server mode: Server mode reads " + "command line strings one per line exactly as above. If no output file is " + "specified, returns a line containing the number of output lines before the " + "output. If there is an error, returns a single line with the error message. " + "Shut down server by sending \"quit\".").withLongOpt("server").create(); Option openCLO = OptionBuilder .withDescription(/* w ww. j a v a 2 s. co m*/ "enables use of the graphics card to " + "support the OCR system. Defaults to true.") .withLongOpt("enable-opencl").hasArg().withArgName("enabled").create(); options.addOption(helpO); options.addOption(versionO); options.addOption(outputO); options.addOption(formatO); options.addOption(serverO); options.addOption(openCLO); CommandLineParser clp = new GnuParser(); try { CommandLine line = clp.parse(options, args); if (line.hasOption("h")) { new HelpFormatter().printHelp(INVOCATION, options); System.exit(0); } if (line.hasOption("v")) { System.out.println(Longan.VERSION); System.exit(0); } boolean enableOpenCL = true; if (line.hasOption("enable-opencl")) { enableOpenCL = line.getOptionValue("enable-opencl").toLowerCase().equals("true") || line.getOptionValue("enable-opencl").equals("1"); } if (line.hasOption("server")) { Longan longan = Longan.getDefaultImplementation(enableOpenCL); BufferedReader inputR = new BufferedReader(new InputStreamReader(System.in)); while (true) { String input = inputR.readLine(); if (input.trim().equals("quit")) { return; } String[] args2 = splitInput(input); Options o2 = new Options(); o2.addOption(outputO); o2.addOption(formatO); try { line = clp.parse(o2, args2); File outFile = null; if (line.hasOption("o")) { outFile = new File(line.getOptionValue("o")); } ResultConverter format = FORMATS.get(line.getOptionValue("format", "plaintext")); if (format != DEFAULT_FORMAT && outFile == null) { System.out.println("You must specify an output file for non-plaintext output."); continue; } if (line.getArgList().isEmpty()) { System.out.println("Please specify an input image."); continue; } if (line.getArgList().size() > 1) { System.err.println("Please specify one input image at a time"); continue; } File inFile = new File((String) line.getArgList().get(0)); if (!inFile.exists()) { System.out.println("The input image does not exist."); continue; } try { Result result = longan.process(ImageIO.read(inFile)); if (outFile == null) { String txt = DEFAULT_FORMAT.convert(result); System.out.println(numNewlines(txt) + 1); System.out.print(txt); } else { if (outFile.getAbsoluteFile().getParentFile() != null && !outFile.getAbsoluteFile().getParentFile().exists()) { outFile.getParentFile().mkdirs(); } FileOutputStream fos = new FileOutputStream(outFile); try { format.write(result, fos); } finally { fos.close(); } } } catch (Exception e) { System.out.println("Processing error: " + exception(e)); } } catch (ParseException e) { System.out.println("Input not recognized: " + exception(e)); } } // End server loop } else { // Single invocation File outFile = null; if (line.hasOption("o")) { outFile = new File(line.getOptionValue("o")); } ResultConverter format = FORMATS.get(line.getOptionValue("format", "plaintext")); if (format != DEFAULT_FORMAT && outFile == null) { System.err.println("You must specify an output file for non-plaintext output."); System.exit(1); } if (line.getArgList().isEmpty()) { System.err.println("Please specify an input image."); new HelpFormatter().printHelp(INVOCATION, options); System.exit(1); } if (line.getArgList().size() > 1) { System.err.println("Please specify one input image only. To process multiple " + "images, use server mode."); System.exit(1); } File inFile = new File((String) line.getArgList().get(0)); if (!inFile.exists()) { System.err.println("The input image does not exist."); System.exit(1); } try { Result result = Longan.getDefaultImplementation(enableOpenCL).process(ImageIO.read(inFile)); if (outFile == null) { String txt = DEFAULT_FORMAT.convert(result); System.out.print(txt); } else { if (outFile.getAbsoluteFile().getParentFile() != null && !outFile.getAbsoluteFile().getParentFile().exists()) { outFile.getParentFile().mkdirs(); } FileOutputStream fos = new FileOutputStream(outFile); try { format.write(format.convert(result), fos); } finally { fos.close(); } } } catch (Exception e) { System.err.println("Processing error: " + exception(e)); System.exit(1); } } } catch (ParseException e) { System.err.println("Parsing command line input failed: " + exception(e)); System.exit(1); } }
From source file:boa.evaluator.BoaEvaluator.java
public static void main(final String[] args) { final Options options = new Options(); options.addOption("i", "input", true, "input Boa source file (*.boa)"); options.addOption("d", "data", true, "path to local data directory"); options.addOption("o", "output", true, "output directory"); options.getOption("i").setRequired(true); options.getOption("d").setRequired(true); try {//from w w w .ja v a2s.co m if (args.length == 0) { printHelp(options, null); return; } else { final CommandLine cl = new PosixParser().parse(options, args); if (cl.hasOption('i') && cl.hasOption('d')) { final BoaEvaluator evaluator; try { if (cl.hasOption('o')) { evaluator = new BoaEvaluator(cl.getOptionValue('i'), cl.getOptionValue('d'), cl.getOptionValue('o')); } else { evaluator = new BoaEvaluator(cl.getOptionValue('i'), cl.getOptionValue('d')); } } catch (final IOException e) { System.err.print(e); return; } if (!evaluator.compile()) { System.err.println("Compilation Failed"); return; } final long start = System.currentTimeMillis(); evaluator.evaluate(); final long end = System.currentTimeMillis(); System.out.println("Total Time Taken: " + (end - start)); System.out.println(evaluator.getResults()); } else { printHelp(options, "missing required options: -i <arg> and -d <arg>"); return; } } } catch (final org.apache.commons.cli.ParseException e) { printHelp(options, e.getMessage()); } }
From source file:com.github.houbin217jz.thumbnail.Thumbnail.java
public static void main(String[] args) { Options options = new Options(); options.addOption("s", "src", true, "????????????"); options.addOption("d", "dst", true, ""); options.addOption("r", "ratio", true, "/??, 30%???0.3????????"); options.addOption("w", "width", true, "(px)"); options.addOption("h", "height", true, "?(px)"); options.addOption("R", "recursive", false, "???????"); HelpFormatter formatter = new HelpFormatter(); String formatstr = "java -jar thumbnail.jar " + "[-s/--src <path>] " + "[-d/--dst <path>] " + "[-r/--ratio double] " + "[-w/--width integer] " + "[-h/--height integer] " + "[-R/--recursive] "; CommandLineParser parser = new PosixParser(); CommandLine cmd = null;/* ww w. j a v a 2s . c o m*/ try { cmd = parser.parse(options, args); } catch (ParseException e1) { formatter.printHelp(formatstr, options); return; } final Path srcDir, dstDir; final Integer width, height; final Double ratio; // if (cmd.hasOption("s")) { srcDir = Paths.get(cmd.getOptionValue("s")).toAbsolutePath(); } else { srcDir = Paths.get("").toAbsolutePath(); //?? } // if (cmd.hasOption("d")) { dstDir = Paths.get(cmd.getOptionValue("d")).toAbsolutePath(); } else { formatter.printHelp(formatstr, options); return; } if (!Files.exists(srcDir, LinkOption.NOFOLLOW_LINKS) || !Files.isDirectory(srcDir, LinkOption.NOFOLLOW_LINKS)) { System.out.println("[" + srcDir.toAbsolutePath() + "]??????"); return; } if (Files.exists(dstDir, LinkOption.NOFOLLOW_LINKS)) { if (!Files.isDirectory(dstDir, LinkOption.NOFOLLOW_LINKS)) { //???????? System.out.println("????????"); return; } } else { //???????? try { Files.createDirectories(dstDir); } catch (IOException e) { e.printStackTrace(); return; } } //?? if (cmd.hasOption("w") && cmd.hasOption("h")) { try { width = Integer.valueOf(cmd.getOptionValue("width")); height = Integer.valueOf(cmd.getOptionValue("height")); } catch (NumberFormatException e) { System.out.println("??????"); return; } } else { width = null; height = null; } //? if (cmd.hasOption("r")) { try { ratio = Double.valueOf(cmd.getOptionValue("r")); } catch (NumberFormatException e) { System.out.println("?????"); return; } } else { ratio = null; } if (width != null && ratio != null) { System.out.println("??????????????"); return; } if (width == null && ratio == null) { System.out.println("????????????"); return; } // int maxDepth = 1; if (cmd.hasOption("R")) { maxDepth = Integer.MAX_VALUE; } try { //Java 7 ??@see http://docs.oracle.com/javase/jp/7/api/java/nio/file/Files.html Files.walkFileTree(srcDir, EnumSet.of(FileVisitOption.FOLLOW_LINKS), maxDepth, new SimpleFileVisitor<Path>() { @Override public FileVisitResult visitFile(Path path, BasicFileAttributes basicFileAttributes) throws IOException { //???&??? String filename = path.getFileName().toString().toLowerCase(); if (filename.endsWith(".jpg") || filename.endsWith(".jpeg")) { //Jpeg?? /* * relative??: * rootPath: /a/b/c/d * filePath: /a/b/c/d/e/f.jpg * rootPath.relativize(filePath) = e/f.jpg */ /* * resolve?? * rootPath: /a/b/c/output * relativePath: e/f.jpg * rootPath.resolve(relativePath) = /a/b/c/output/e/f.jpg */ Path dst = dstDir.resolve(srcDir.relativize(path)); if (!Files.exists(dst.getParent(), LinkOption.NOFOLLOW_LINKS)) { Files.createDirectories(dst.getParent()); } doResize(path.toFile(), dst.toFile(), width, height, ratio); } return FileVisitResult.CONTINUE; } }); } catch (IOException e) { e.printStackTrace(); } }
From source file:fr.inria.atlanmod.kyanos.benchmarks.KyanosMapQuery.java
public static void main(String[] args) { Options options = new Options(); Option inputOpt = OptionBuilder.create(IN); inputOpt.setArgName("INPUT"); inputOpt.setDescription("Input Kyanos resource directory"); inputOpt.setArgs(1);//from w ww.j a v a2 s . c om inputOpt.setRequired(true); Option inClassOpt = OptionBuilder.create(EPACKAGE_CLASS); inClassOpt.setArgName("CLASS"); inClassOpt.setDescription("FQN of EPackage implementation class"); inClassOpt.setArgs(1); inClassOpt.setRequired(true); options.addOption(inputOpt); options.addOption(inClassOpt); CommandLineParser parser = new PosixParser(); try { PersistenceBackendFactoryRegistry.getFactories().put(NeoMapURI.NEO_MAP_SCHEME, new MapPersistenceBackendFactory()); CommandLine commandLine = parser.parse(options, args); URI uri = NeoMapURI.createNeoMapURI(new File(commandLine.getOptionValue(IN))); Class<?> inClazz = KyanosMapQuery.class.getClassLoader() .loadClass(commandLine.getOptionValue(EPACKAGE_CLASS)); inClazz.getMethod("init").invoke(null); ResourceSet resourceSet = new ResourceSetImpl(); resourceSet.getResourceFactoryRegistry().getProtocolToFactoryMap().put(NeoMapURI.NEO_MAP_SCHEME, PersistentResourceFactory.eINSTANCE); Resource resource = resourceSet.createResource(uri); Map<String, Object> loadOpts = new HashMap<String, Object>(); resource.load(loadOpts); { LOG.log(Level.INFO, "Start query"); long begin = System.currentTimeMillis(); EList<MethodDeclaration> list = JavaQueries.getUnusedMethodsList(resource); long end = System.currentTimeMillis(); LOG.log(Level.INFO, "End query"); LOG.log(Level.INFO, MessageFormat.format("Query result (list) contains {0} elements", list.size())); LOG.log(Level.INFO, MessageFormat.format("Time spent: {0}", MessageUtil.formatMillis(end - begin))); } { LOG.log(Level.INFO, "Start query"); long begin = System.currentTimeMillis(); EList<MethodDeclaration> list = JavaQueries.getUnusedMethodsLoop(resource); long end = System.currentTimeMillis(); LOG.log(Level.INFO, "End query"); LOG.log(Level.INFO, MessageFormat.format("Query result (loops) contains {0} elements", list.size())); LOG.log(Level.INFO, MessageFormat.format("Time spent: {0}", MessageUtil.formatMillis(end - begin))); } if (resource instanceof PersistentResourceImpl) { PersistentResourceImpl.shutdownWithoutUnload((PersistentResourceImpl) resource); } else { resource.unload(); } } catch (ParseException e) { MessageUtil.showError(e.toString()); MessageUtil.showError("Current arguments: " + Arrays.toString(args)); HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("java -jar <this-file.jar>", options, true); } catch (Throwable e) { MessageUtil.showError(e.toString()); } }
From source file:cc.twittertools.search.api.SearchStatusesThrift.java
@SuppressWarnings("static-access") public static void main(String[] args) throws Exception { Options options = new Options(); options.addOption(new Option(HELP_OPTION, "show help")); options.addOption(OptionBuilder.withArgName("string").hasArg().withDescription("host").create(HOST_OPTION)); options.addOption(OptionBuilder.withArgName("port").hasArg().withDescription("port").create(PORT_OPTION)); options.addOption(/*from www .j ava 2 s.c o m*/ OptionBuilder.withArgName("string").hasArg().withDescription("query id").create(QID_OPTION)); options.addOption( OptionBuilder.withArgName("string").hasArg().withDescription("query text").create(QUERY_OPTION)); options.addOption( OptionBuilder.withArgName("string").hasArg().withDescription("runtag").create(RUNTAG_OPTION)); options.addOption(OptionBuilder.withArgName("num").hasArg().withDescription("maxid").create(MAX_ID_OPTION)); options.addOption(OptionBuilder.withArgName("num").hasArg().withDescription("number of results to return") .create(NUM_RESULTS_OPTION)); options.addOption( OptionBuilder.withArgName("string").hasArg().withDescription("group id").create(GROUP_OPTION)); options.addOption( OptionBuilder.withArgName("string").hasArg().withDescription("access token").create(TOKEN_OPTION)); options.addOption(new Option(VERBOSE_OPTION, "print out complete document")); CommandLine cmdline = null; CommandLineParser parser = new GnuParser(); try { cmdline = parser.parse(options, args); } catch (ParseException exp) { System.err.println("Error parsing command line: " + exp.getMessage()); System.exit(-1); } if (cmdline.hasOption(HELP_OPTION) || !cmdline.hasOption(HOST_OPTION) || !cmdline.hasOption(PORT_OPTION)) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp(SearchStatusesThrift.class.getName(), options); System.exit(-1); } String qid = cmdline.hasOption(QID_OPTION) ? cmdline.getOptionValue(QID_OPTION) : DEFAULT_QID; String query = cmdline.hasOption(QUERY_OPTION) ? cmdline.getOptionValue(QUERY_OPTION) : DEFAULT_Q; String runtag = cmdline.hasOption(RUNTAG_OPTION) ? cmdline.getOptionValue(RUNTAG_OPTION) : DEFAULT_RUNTAG; long maxId = cmdline.hasOption(MAX_ID_OPTION) ? Long.parseLong(cmdline.getOptionValue(MAX_ID_OPTION)) : DEFAULT_MAX_ID; int numResults = cmdline.hasOption(NUM_RESULTS_OPTION) ? Integer.parseInt(cmdline.getOptionValue(NUM_RESULTS_OPTION)) : DEFAULT_NUM_RESULTS; boolean verbose = cmdline.hasOption(VERBOSE_OPTION); String group = cmdline.hasOption(GROUP_OPTION) ? cmdline.getOptionValue(GROUP_OPTION) : null; String token = cmdline.hasOption(TOKEN_OPTION) ? cmdline.getOptionValue(TOKEN_OPTION) : null; TrecSearchThriftClient client = new TrecSearchThriftClient(cmdline.getOptionValue(HOST_OPTION), Integer.parseInt(cmdline.getOptionValue(PORT_OPTION)), group, token); System.err.println("qid: " + qid); System.err.println("q: " + query); System.err.println("max_id: " + maxId); System.err.println("num_results: " + numResults); PrintStream out = new PrintStream(System.out, true, "UTF-8"); List<TResult> results = client.search(query, maxId, numResults); int i = 1; for (TResult result : results) { out.println(String.format("%s Q0 %d %d %f %s", qid, result.id, i, result.rsv, runtag)); if (verbose) { System.out.println("# " + result.toString().replaceAll("[\\n\\r]+", " ")); } i++; } out.close(); }