List of usage examples for java.lang String toLowerCase
public String toLowerCase()
From source file:com.seanmadden.net.fast.SerialInterface.java
public static void main(String[] args) { SerialInterface inter = new SerialInterface(new JSONObject()); inter.open();/* ww w .j a va 2s . co m*/ System.out.println("Welcome. Commands with 'help'"); String cmd = ""; Scanner scan = new Scanner(System.in); do { System.out.print("> "); cmd = scan.nextLine(); if (cmd.toLowerCase().equals("help")) { System.out.println("Commands:"); System.out.println("help : prints this message"); System.out.println("send <message> : sends <message> to interpretype."); System.out.println("quit : exits this program"); } else if (cmd.toLowerCase().startsWith("send")) { String message = cmd.substring(cmd.toLowerCase().indexOf(' ') + 1); inter.sendDataToPort(message); } } while (!cmd.toLowerCase().equals("quit")); inter.close(); }
From source file:org.apache.flink.benchmark.Runner.java
public static void main(String[] args) throws Exception { final ExecutionEnvironment env = ExecutionEnvironment.getExecutionEnvironment(); env.getConfig().enableObjectReuse(); env.getConfig().disableSysoutLogging(); ParameterTool parameters = ParameterTool.fromArgs(args); if (!(parameters.has("p") && parameters.has("types") && parameters.has("algorithms"))) { printUsage();/* www . j a va 2 s .c o m*/ System.exit(-1); } int parallelism = parameters.getInt("p"); env.setParallelism(parallelism); Set<IdType> types = new HashSet<>(); if (parameters.get("types").equals("all")) { types.add(IdType.INT); types.add(IdType.LONG); types.add(IdType.STRING); } else { for (String type : parameters.get("types").split(",")) { if (type.toLowerCase().equals("int")) { types.add(IdType.INT); } else if (type.toLowerCase().equals("long")) { types.add(IdType.LONG); } else if (type.toLowerCase().equals("string")) { types.add(IdType.STRING); } else { printUsage(); throw new RuntimeException("Unknown type: " + type); } } } Queue<RunnerWithScore> queue = new PriorityQueue<>(); if (parameters.get("algorithms").equals("all")) { for (Map.Entry<String, Class> entry : AVAILABLE_ALGORITHMS.entrySet()) { for (IdType type : types) { AlgorithmRunner runner = (AlgorithmRunner) entry.getValue().newInstance(); runner.initialize(type, SAMPLES, parallelism); runner.warmup(env); queue.add(new RunnerWithScore(runner, 1.0)); } } } else { for (String algorithm : parameters.get("algorithms").split(",")) { double ratio = 1.0; if (algorithm.contains("=")) { String[] split = algorithm.split("="); algorithm = split[0]; ratio = Double.parseDouble(split[1]); } if (AVAILABLE_ALGORITHMS.containsKey(algorithm.toLowerCase())) { Class clazz = AVAILABLE_ALGORITHMS.get(algorithm.toLowerCase()); for (IdType type : types) { AlgorithmRunner runner = (AlgorithmRunner) clazz.newInstance(); runner.initialize(type, SAMPLES, parallelism); runner.warmup(env); queue.add(new RunnerWithScore(runner, ratio)); } } else { printUsage(); throw new RuntimeException("Unknown algorithm: " + algorithm); } } } JsonFactory factory = new JsonFactory(); while (queue.size() > 0) { RunnerWithScore current = queue.poll(); AlgorithmRunner runner = current.getRunner(); StringWriter writer = new StringWriter(); JsonGenerator gen = factory.createGenerator(writer); gen.writeStartObject(); gen.writeStringField("algorithm", runner.getClass().getSimpleName()); boolean running = true; while (running) { try { runner.run(env, gen); running = false; } catch (ProgramInvocationException e) { // only suppress job cancellations if (!(e.getCause() instanceof JobCancellationException)) { throw e; } } } JobExecutionResult result = env.getLastJobExecutionResult(); long runtime_ms = result.getNetRuntime(); gen.writeNumberField("runtime_ms", runtime_ms); current.credit(runtime_ms); if (!runner.finished()) { queue.add(current); } gen.writeObjectFieldStart("accumulators"); for (Map.Entry<String, Object> accumulatorResult : result.getAllAccumulatorResults().entrySet()) { gen.writeStringField(accumulatorResult.getKey(), accumulatorResult.getValue().toString()); } gen.writeEndObject(); gen.writeEndObject(); gen.close(); System.out.println(writer.toString()); } }
From source file:DIA_Umpire_Quant.DIA_Umpire_LCMSIDGen.java
/** * @param args the command line arguments *///from w w w .j a v a 2 s.c o m public static void main(String[] args) throws FileNotFoundException, IOException, Exception { System.out.println( "================================================================================================="); System.out.println("DIA-Umpire LCMSID geneartor (version: " + UmpireInfo.GetInstance().Version + ")"); if (args.length != 1) { System.out.println( "command format error, the correct format should be: java -jar -Xmx10G DIA_Umpire_LCMSIDGen.jar diaumpire_module.params"); return; } try { ConsoleLogger.SetConsoleLogger(Level.INFO); ConsoleLogger.SetFileLogger(Level.DEBUG, FilenameUtils.getFullPath(args[0]) + "diaumpire_lcmsidgen.log"); } catch (Exception e) { } Logger.getRootLogger().info("Version: " + UmpireInfo.GetInstance().Version); Logger.getRootLogger().info("Parameter file:" + args[0]); BufferedReader reader = new BufferedReader(new FileReader(args[0])); String line = ""; String WorkFolder = ""; int NoCPUs = 2; TandemParam tandemPara = new TandemParam(DBSearchParam.SearchInstrumentType.TOF5600); HashMap<String, File> AssignFiles = new HashMap<>(); //<editor-fold defaultstate="collapsed" desc="Reading parameter file"> while ((line = reader.readLine()) != null) { line = line.trim(); Logger.getRootLogger().info(line); if (!"".equals(line) && !line.startsWith("#")) { //System.out.println(line); if (line.equals("==File list begin")) { do { line = reader.readLine(); line = line.trim(); if (line.equals("==File list end")) { continue; } else if (!"".equals(line)) { File newfile = new File(line); if (newfile.exists()) { AssignFiles.put(newfile.getAbsolutePath(), newfile); } else { Logger.getRootLogger().info("File: " + newfile + " does not exist."); } } } while (!line.equals("==File list end")); } if (line.split("=").length < 2) { continue; } String type = line.split("=")[0].trim(); String value = line.split("=")[1].trim(); switch (type) { case "Path": { WorkFolder = value; break; } case "path": { WorkFolder = value; break; } case "Thread": { NoCPUs = Integer.parseInt(value); break; } case "DecoyPrefix": { if (!"".equals(value)) { tandemPara.DecoyPrefix = value; } break; } case "PeptideFDR": { tandemPara.PepFDR = Float.parseFloat(value); break; } } } } //</editor-fold> //Initialize PTM manager using compomics library PTMManager.GetInstance(); //Generate DIA file list ArrayList<DIAPack> FileList = new ArrayList<>(); File folder = new File(WorkFolder); if (!folder.exists()) { Logger.getRootLogger().info("The path : " + WorkFolder + " cannot be found."); System.exit(1); } for (final File fileEntry : folder.listFiles()) { if (fileEntry.isFile() && (fileEntry.getAbsolutePath().toLowerCase().endsWith(".mzxml") | fileEntry.getAbsolutePath().toLowerCase().endsWith(".mzml")) && !fileEntry.getAbsolutePath().toLowerCase().endsWith("q1.mzxml") && !fileEntry.getAbsolutePath().toLowerCase().endsWith("q2.mzxml") && !fileEntry.getAbsolutePath().toLowerCase().endsWith("q3.mzxml")) { AssignFiles.put(fileEntry.getAbsolutePath(), fileEntry); } if (fileEntry.isDirectory()) { for (final File fileEntry2 : fileEntry.listFiles()) { if (fileEntry2.isFile() && (fileEntry2.getAbsolutePath().toLowerCase().endsWith(".mzxml") | fileEntry2.getAbsolutePath().toLowerCase().endsWith(".mzml")) && !fileEntry2.getAbsolutePath().toLowerCase().endsWith("q1.mzxml") && !fileEntry2.getAbsolutePath().toLowerCase().endsWith("q2.mzxml") && !fileEntry2.getAbsolutePath().toLowerCase().endsWith("q3.mzxml")) { AssignFiles.put(fileEntry2.getAbsolutePath(), fileEntry2); } } } } Logger.getRootLogger().info("No. of files assigned :" + AssignFiles.size()); for (File fileEntry : AssignFiles.values()) { Logger.getRootLogger().info(fileEntry.getAbsolutePath()); } //process each DIA file to genearate untargeted identifications for (File fileEntry : AssignFiles.values()) { String mzXMLFile = fileEntry.getAbsolutePath(); if (mzXMLFile.toLowerCase().endsWith(".mzxml") | mzXMLFile.toLowerCase().endsWith(".mzml")) { long time = System.currentTimeMillis(); DIAPack DiaFile = new DIAPack(mzXMLFile, NoCPUs); FileList.add(DiaFile); Logger.getRootLogger().info( "================================================================================================="); Logger.getRootLogger().info("Processing " + mzXMLFile); if (!DiaFile.LoadDIASetting()) { Logger.getRootLogger().info("Loading DIA setting failed, job is incomplete"); System.exit(1); } if (!DiaFile.LoadParams()) { Logger.getRootLogger().info("Loading parameters failed, job is incomplete"); System.exit(1); } Logger.getRootLogger().info("Loading identification results " + mzXMLFile + "...."); DiaFile.ParsePepXML(tandemPara, null); DiaFile.BuildStructure(); if (!DiaFile.MS1FeatureMap.ReadPeakCluster()) { Logger.getRootLogger().info("Loading peak and structure failed, job is incomplete"); System.exit(1); } DiaFile.MS1FeatureMap.ClearMonoisotopicPeakOfCluster(); //Generate mapping between index of precursor feature and pseudo MS/MS scan index DiaFile.GenerateClusterScanNomapping(); //Doing quantification DiaFile.AssignQuant(); DiaFile.ClearStructure(); DiaFile.IDsummary.ReduceMemoryUsage(); time = System.currentTimeMillis() - time; Logger.getRootLogger().info(mzXMLFile + " processed time:" + String.format("%d hour, %d min, %d sec", TimeUnit.MILLISECONDS.toHours(time), TimeUnit.MILLISECONDS.toMinutes(time) - TimeUnit.HOURS.toMinutes(TimeUnit.MILLISECONDS.toHours(time)), TimeUnit.MILLISECONDS.toSeconds(time) - TimeUnit.MINUTES.toSeconds(TimeUnit.MILLISECONDS.toMinutes(time)))); } Logger.getRootLogger().info("Job done"); Logger.getRootLogger().info( "================================================================================================="); } }
From source file:me.timothy.ddd.DrunkDuckDispatch.java
License:asdf
public static void main(String[] args) throws LWJGLException { try {/*www. j a v a2s . c om*/ float defaultDisplayWidth = SizeScaleSystem.EXPECTED_WIDTH / 2; float defaultDisplayHeight = SizeScaleSystem.EXPECTED_HEIGHT / 2; boolean fullscreen = false, defaultDisplay = !fullscreen; File resolutionInfo = new File("graphics.json"); if (resolutionInfo.exists()) { try (FileReader fr = new FileReader(resolutionInfo)) { JSONObject obj = (JSONObject) new JSONParser().parse(fr); Set<?> keys = obj.keySet(); for (Object o : keys) { if (o instanceof String) { String key = (String) o; switch (key.toLowerCase()) { case "width": defaultDisplayWidth = JSONCompatible.getFloat(obj, key); break; case "height": defaultDisplayHeight = JSONCompatible.getFloat(obj, key); break; case "fullscreen": fullscreen = JSONCompatible.getBoolean(obj, key); defaultDisplay = !fullscreen; break; } } } } catch (IOException | ParseException e) { e.printStackTrace(); } float expHeight = defaultDisplayWidth * (SizeScaleSystem.EXPECTED_HEIGHT / SizeScaleSystem.EXPECTED_WIDTH); float expWidth = defaultDisplayHeight * (SizeScaleSystem.EXPECTED_WIDTH / SizeScaleSystem.EXPECTED_HEIGHT); if (Math.round(defaultDisplayWidth) != Math.round(expWidth)) { if (defaultDisplayHeight < expHeight) { System.err.printf("%f x %f is an invalid resolution; adjusting to %f x %f\n", defaultDisplayWidth, defaultDisplayHeight, defaultDisplayWidth, expHeight); defaultDisplayHeight = expHeight; } else { System.err.printf("%f x %f is an invalid resolution; adjusting to %f x %f\n", defaultDisplayWidth, defaultDisplayHeight, expWidth, defaultDisplayHeight); defaultDisplayWidth = expWidth; } } } File dir = null; String os = getOS(); if (os.equals("windows")) { dir = new File(System.getenv("APPDATA"), "timgames/"); } else { dir = new File(System.getProperty("user.home"), ".timgames/"); } File lwjglDir = new File(dir, "lwjgl-2.9.1/"); Resources.init(); Resources.downloadIfNotExists(lwjglDir, "lwjgl-2.9.1.zip", "http://umad-barnyard.com/lwjgl-2.9.1.zip", "Necessary LWJGL natives couldn't be found, I can attempt " + "to download it, but I make no promises", "Unfortunately I was unable to download it, so I'll open up the " + "link to the official download. Make sure you get LWJGL version 2.9.1, " + "and you put it at " + dir.getAbsolutePath() + "/lwjgl-2.9.1.zip", new Runnable() { @Override public void run() { if (!Desktop.isDesktopSupported()) { JOptionPane.showMessageDialog(null, "I couldn't " + "even do that! Download it manually and try again"); return; } try { Desktop.getDesktop().browse(new URI("http://www.lwjgl.org/download.php")); } catch (IOException | URISyntaxException e) { JOptionPane.showMessageDialog(null, "Oh cmon.. Address is http://www.lwjgl.org/download.php, good luck"); System.exit(1); } } }, 5843626); Resources.extractIfNotFound(lwjglDir, "lwjgl-2.9.1.zip", "lwjgl-2.9.1"); System.setProperty("org.lwjgl.librarypath", new File(dir, "lwjgl-2.9.1/lwjgl-2.9.1/native/" + os).getAbsolutePath()); // deal w/ it System.setProperty("net.java.games.input.librarypath", System.getProperty("org.lwjgl.librarypath")); Resources.downloadIfNotExists("entities.json", "http://umad-barnyard.com/ddd/entities.json", 16142); Resources.downloadIfNotExists("map.binary", "http://umad-barnyard.com/ddd/map.binary", 16142); Resources.downloadIfNotExists("victory.txt", "http://umad-barnyard.com/ddd/victory.txt", 168); Resources.downloadIfNotExists("failure.txt", "http://umad-barnyard.com/ddd/failure.txt", 321); File resFolder = new File("resources/"); if (!resFolder.exists() && !new File("player-still.png").exists()) { Resources.downloadIfNotExists("resources.zip", "http://umad-barnyard.com/ddd/resources.zip", 54484); Resources.extractIfNotFound(new File("."), "resources.zip", "player-still.png"); new File("resources.zip").delete(); } File soundFolder = new File("sounds/"); if (!soundFolder.exists()) { soundFolder.mkdirs(); Resources.downloadIfNotExists("sounds/sounds.zip", "http://umad-barnyard.com/ddd/sounds.zip", 1984977); Resources.extractIfNotFound(soundFolder, "sounds.zip", "asdfasdffadasdf"); new File(soundFolder, "sounds.zip").delete(); } AppGameContainer appgc; ddd = new DrunkDuckDispatch(); appgc = new AppGameContainer(ddd); appgc.setTargetFrameRate(60); appgc.setShowFPS(false); appgc.setAlwaysRender(true); if (fullscreen) { DisplayMode[] modes = Display.getAvailableDisplayModes(); DisplayMode current, best = null; float ratio = 0f; for (int i = 0; i < modes.length; i++) { current = modes[i]; float rX = (float) current.getWidth() / SizeScaleSystem.EXPECTED_WIDTH; float rY = (float) current.getHeight() / SizeScaleSystem.EXPECTED_HEIGHT; System.out.println(current.getWidth() + "x" + current.getHeight() + " -> " + rX + "x" + rY); if (rX == rY && rX > ratio) { best = current; ratio = rX; } } if (best == null) { System.out.println("Failed to find an appropriately scaled resolution, using default display"); defaultDisplay = true; } else { appgc.setDisplayMode(best.getWidth(), best.getHeight(), true); SizeScaleSystem.setRealHeight(best.getHeight()); SizeScaleSystem.setRealWidth(best.getWidth()); System.out.println("I choose " + best.getWidth() + "x" + best.getHeight()); } } if (defaultDisplay) { SizeScaleSystem.setRealWidth(Math.round(defaultDisplayWidth)); SizeScaleSystem.setRealHeight(Math.round(defaultDisplayHeight)); appgc.setDisplayMode(Math.round(defaultDisplayWidth), Math.round(defaultDisplayHeight), false); } ddd.logger.info( "SizeScaleSystem: " + SizeScaleSystem.getRealWidth() + "x" + SizeScaleSystem.getRealHeight()); appgc.start(); } catch (SlickException ex) { LogManager.getLogger(DrunkDuckDispatch.class.getSimpleName()).catching(Level.ERROR, ex); } }
From source file:com.betfair.cougar.test.socket.app.SocketCompatibilityTestingApp.java
public static void main(String[] args) throws Exception { Parser parser = new PosixParser(); Options options = new Options(); options.addOption("r", "repo", true, "Repository type to search: local|central"); options.addOption("c", "client-concurrency", true, "Max threads to allow each client tester to run tests, defaults to 10"); options.addOption("t", "test-concurrency", true, "Max client testers to run concurrently, defaults to 5"); options.addOption("m", "max-time", true, "Max time (in minutes) to allow tests to complete, defaults to 10"); options.addOption("v", "version", false, "Print version and exit"); options.addOption("h", "help", false, "This help text"); CommandLine commandLine = parser.parse(options, args); if (commandLine.hasOption("h")) { System.out.println(options); System.exit(0);/*from w w w . ja va 2 s.c o m*/ } if (commandLine.hasOption("v")) { System.out.println("How the hell should I know?"); System.exit(0); } // 1. Find all testers in given repos List<RepoSearcher> repoSearchers = new ArrayList<>(); for (String repo : commandLine.getOptionValues("r")) { if ("local".equals(repo.toLowerCase())) { repoSearchers.add(new LocalRepoSearcher()); } else if ("central".equals(repo.toLowerCase())) { repoSearchers.add(new CentralRepoSearcher()); } else { System.err.println("Unrecognized repo: " + repo); System.err.println(options); System.exit(1); } } int clientConcurrency = 10; if (commandLine.hasOption("c")) { try { clientConcurrency = Integer.parseInt(commandLine.getOptionValue("c")); } catch (NumberFormatException nfe) { System.err.println( "client-concurrency is not a valid integer: '" + commandLine.getOptionValue("c") + "'"); System.exit(1); } } int testConcurrency = 5; if (commandLine.hasOption("t")) { try { testConcurrency = Integer.parseInt(commandLine.getOptionValue("t")); } catch (NumberFormatException nfe) { System.err.println( "test-concurrency is not a valid integer: '" + commandLine.getOptionValue("t") + "'"); System.exit(1); } } int maxMinutes = 10; if (commandLine.hasOption("m")) { try { maxMinutes = Integer.parseInt(commandLine.getOptionValue("m")); } catch (NumberFormatException nfe) { System.err.println("max-time is not a valid integer: '" + commandLine.getOptionValue("m") + "'"); System.exit(1); } } Properties clientProps = new Properties(); clientProps.setProperty("client.concurrency", String.valueOf(clientConcurrency)); File baseRunDir = new File(System.getProperty("user.dir") + "/run"); baseRunDir.mkdirs(); File tmpDir = new File(baseRunDir, "jars"); tmpDir.mkdirs(); List<ServerRunner> serverRunners = new ArrayList<>(); List<ClientRunner> clientRunners = new ArrayList<>(); for (RepoSearcher searcher : repoSearchers) { List<File> jars = searcher.findAndCache(tmpDir); for (File f : jars) { ServerRunner serverRunner = new ServerRunner(f, baseRunDir); System.out.println("Found tester: " + serverRunner.getVersion()); serverRunners.add(serverRunner); clientRunners.add(new ClientRunner(f, baseRunDir, clientProps)); } } // 2. Start servers and collect ports System.out.println(); System.out.println("Starting " + serverRunners.size() + " servers..."); for (ServerRunner server : serverRunners) { server.startServer(); } System.out.println(); List<TestCombo> tests = new ArrayList<>(serverRunners.size() * clientRunners.size()); for (ServerRunner server : serverRunners) { for (ClientRunner client : clientRunners) { tests.add(new TestCombo(server, client)); } } System.out.println("Enqueued " + tests.size() + " test combos to run..."); long startTime = System.currentTimeMillis(); // 3. Run every client against every server, collecting results BlockingQueue<Runnable> workQueue = new ArrayBlockingQueue(serverRunners.size() * clientRunners.size()); ThreadPoolExecutor service = new ThreadPoolExecutor(testConcurrency, testConcurrency, 5000, TimeUnit.MILLISECONDS, workQueue); service.prestartAllCoreThreads(); workQueue.addAll(tests); while (!workQueue.isEmpty()) { Thread.sleep(1000); } service.shutdown(); service.awaitTermination(maxMinutes, TimeUnit.MINUTES); long endTime = System.currentTimeMillis(); long totalTimeSecs = Math.round((endTime - startTime) / 1000.0); for (ServerRunner server : serverRunners) { server.shutdownServer(); } System.out.println(); System.out.println("======="); System.out.println("Results"); System.out.println("-------"); // print a summary int totalTests = 0; int totalSuccess = 0; for (TestCombo combo : tests) { String clientVer = combo.getClientVersion(); String serverVer = combo.getServerVersion(); String results = combo.getClientResults(); ObjectMapper mapper = new ObjectMapper(new JsonFactory()); JsonNode node = mapper.reader().readTree(results); JsonNode resultsArray = node.get("results"); int numTests = resultsArray.size(); int numSuccess = 0; for (int i = 0; i < numTests; i++) { if ("success".equals(resultsArray.get(i).get("result").asText())) { numSuccess++; } } totalSuccess += numSuccess; totalTests += numTests; System.out.println(clientVer + "/" + serverVer + ": " + numSuccess + "/" + numTests + " succeeded - took " + String.format("%2f", combo.getRunningTime()) + " seconds"); } System.out.println("-------"); System.out.println( "Overall: " + totalSuccess + "/" + totalTests + " succeeded - took " + totalTimeSecs + " seconds"); FileWriter out = new FileWriter("results.json"); PrintWriter pw = new PrintWriter(out); // 4. Output full results pw.println("{\n \"results\": ["); for (TestCombo combo : tests) { combo.emitResults(pw, " "); } pw.println(" ],"); pw.println(" \"servers\": ["); for (ServerRunner server : serverRunners) { server.emitInfo(pw, " "); } pw.println(" ],"); pw.close(); }
From source file:POP3Demo.java
public static void main(String[] args) throws Exception { int POP3Port = 110; Socket client = new Socket("127.0.0.1", POP3Port); InputStream is = client.getInputStream(); BufferedReader sockin = new BufferedReader(new InputStreamReader(is)); OutputStream os = client.getOutputStream(); PrintWriter sockout = new PrintWriter(os, true); String cmd = "user Smith"; sockout.println(cmd);/*from w w w . ja va2 s. co m*/ String reply = sockin.readLine(); cmd = "pass "; sockout.println(cmd + "popPassword"); reply = sockin.readLine(); cmd = "stat"; sockout.println(cmd); reply = sockin.readLine(); if (reply == null) return; cmd = "retr 1"; sockout.println(cmd); if (cmd.toLowerCase().startsWith("retr") && reply.charAt(0) == '+') do { reply = sockin.readLine(); System.out.println("S:" + reply); if (reply != null && reply.length() > 0) if (reply.charAt(0) == '.') break; } while (true); cmd = "quit"; sockout.println(cmd); client.close(); }
From source file:com.github.braully.graph.UtilResult.java
public static void main(String... args) throws Exception { Options options = new Options(); Option input = new Option("i", "input", true, "input file path"); input.setRequired(false);//w w w . ja v a 2s . co m options.addOption(input); Option verb = new Option("v", "verbose", false, "verbose process"); input.setRequired(false); options.addOption(verb); Option output = new Option("o", "output", true, "output file"); output.setRequired(false); options.addOption(output); CommandLineParser parser = new DefaultParser(); HelpFormatter formatter = new HelpFormatter(); CommandLine cmd; try { cmd = parser.parse(options, args); } catch (ParseException e) { System.out.println(e.getMessage()); formatter.printHelp("UtilResult", options); System.exit(1); return; } String inputFilePath = cmd.getOptionValue("input"); if (inputFilePath == null) { inputFilePath = "/home/strike/grafos-para-processar/mft2/resultado.txt"; } if (inputFilePath != null) { if (inputFilePath.toLowerCase().endsWith(".txt")) { processFileTxt(inputFilePath); } else if (inputFilePath.toLowerCase().endsWith(".json")) { processFileJson(inputFilePath); } } }
From source file:kindleclippings.word.QuizletSync.java
public static void main(String[] args) throws IOException, JSONException, URISyntaxException, InterruptedException, BackingStoreException, BadLocationException { JFileChooser fc = new JFileChooser(); fc.setFileFilter(new FileNameExtensionFilter("Word documents", "doc", "rtf", "txt")); fc.setMultiSelectionEnabled(true);//from ww w . j ava2 s .c o m int result = fc.showOpenDialog(null); if (result != JFileChooser.APPROVE_OPTION) { return; } File[] clf = fc.getSelectedFiles(); if (clf == null || clf.length == 0) return; ProgressMonitor progress = new ProgressMonitor(null, "QuizletSync", "loading notes files", 0, 100); progress.setMillisToPopup(0); progress.setMillisToDecideToPopup(0); progress.setProgress(0); try { progress.setNote("checking Quizlet account"); progress.setProgress(5); Preferences prefs = kindleclippings.quizlet.QuizletSync.getPrefs(); QuizletAPI api = new QuizletAPI(prefs.get("access_token", null)); Collection<TermSet> sets = null; try { progress.setNote("checking Quizlet library"); progress.setProgress(10); sets = api.getSets(prefs.get("user_id", null)); } catch (IOException e) { if (e.toString().contains("401")) { // Not Authorized => Token has been revoked kindleclippings.quizlet.QuizletSync.clearPrefs(); prefs = kindleclippings.quizlet.QuizletSync.getPrefs(); api = new QuizletAPI(prefs.get("access_token", null)); sets = api.getSets(prefs.get("user_id", null)); } else { throw e; } } progress.setProgress(15); progress.setMaximum(15 + clf.length * 10); progress.setNote("uploading new notes"); int pro = 15; int addedSets = 0; int updatedTerms = 0; int updatedSets = 0; for (File f : clf) { progress.setProgress(pro); List<Clipping> clippings = readClippingsFile(f); if (clippings == null) { pro += 10; continue; } if (clippings.isEmpty()) { pro += 10; continue; } if (clippings.size() < 2) { pro += 10; continue; } String book = clippings.get(0).getBook(); progress.setNote(book); TermSet termSet = null; String x = book.toLowerCase().replaceAll("\\W", ""); for (TermSet t : sets) { if (t.getTitle().toLowerCase().replaceAll("\\W", "").equals(x)) { termSet = t; break; } } if (termSet == null) { addSet(api, book, clippings); addedSets++; pro += 10; continue; } // compare against existing terms boolean hasUpdated = false; for (Clipping cl : clippings) { if (!kindleclippings.quizlet.QuizletSync.checkExistingTerm(cl, termSet)) { kindleclippings.quizlet.QuizletSync.addTerm(api, termSet, cl); updatedTerms++; hasUpdated = true; } } pro += 10; if (hasUpdated) updatedSets++; } if (updatedTerms == 0 && addedSets == 0) { JOptionPane.showMessageDialog(null, "Done.\nNo new data was uploaded", "QuizletSync", JOptionPane.OK_OPTION); } else { if (addedSets > 0) { JOptionPane.showMessageDialog(null, String.format("Done.\nCreated %d new sets and added %d cards to %d existing sets", addedSets, updatedSets, updatedTerms), "QuizletSync", JOptionPane.OK_OPTION); } else { JOptionPane.showMessageDialog(null, String.format("Done.\nAdded %d cards to %d existing sets", updatedTerms, updatedSets), "QuizletSync", JOptionPane.OK_OPTION); } } } finally { progress.close(); } System.exit(0); }
From source file:com.genentech.chemistry.tool.align.SDFAlign.java
public static void main(String... args) { Options options = new Options(); Option opt = new Option("in", true, "input sd file"); opt.setRequired(true);/*from w ww . ja va 2 s . c om*/ options.addOption(opt); opt = new Option("out", true, "output file"); opt.setRequired(true); options.addOption(opt); opt = new Option("method", true, "fss|sss|MCS|clique (default mcs)."); options.addOption(opt); opt = new Option("ref", true, "reference molecule if not given first in file is used. If multiple ref molecules are read the min RMSD is reported"); options.addOption(opt); opt = new Option("mirror", false, "If given and the molecule is not chiral, return best mirror image."); options.addOption(opt); opt = new Option("rmsdTag", true, "Tagname for output of rmsd, default: no output."); options.addOption(opt); opt = new Option("atomMatch", true, "Sequence of none|default|hcount|noAromatic specifing how atoms are matched cf. oe document.\n" + "noAromatic can be used to make terminal atoms match aliphatic and aromatic atoms.\n" + "Queryfeatures are considered only if default is used."); options.addOption(opt); opt = new Option("bondMatch", true, "Sequence of none|default specifing how bonds are matched cf. oe document."); options.addOption(opt); opt = new Option("keepCoreHydrogens", false, "If not specified the hydrigen atoms are removed from the core."); options.addOption(opt); opt = new Option("outputMol", true, "aligned|original (def: aligned) use original to just compute rmsd."); options.addOption(opt); opt = new Option("doNotOptimize", false, "If specified the RMSD is computed without moving optimizing the overlay."); options.addOption(opt); opt = new Option("quiet", false, "Reduced warining messages"); options.addOption(opt); CommandLineParser parser = new BasicParser(); CommandLine cmd = null; try { cmd = parser.parse(options, args); } catch (Exception e) { exitWithHelp(e.getMessage(), options); } if (cmd.getArgs().length > 0) exitWithHelp("To many arguments", options); // do not check aromaticity on atoms so that a terminal atom matches aromatic and non aromatic atoms int atomExpr = OEExprOpts.DefaultAtoms; int bondExpr = OEExprOpts.DefaultBonds; String atomMatch = cmd.getOptionValue("atomMatch"); if (atomMatch == null) atomMatch = ""; atomMatch = '|' + atomMatch.toLowerCase() + '|'; String bondMatch = cmd.getOptionValue("bondMatch"); if (bondMatch == null) bondMatch = ""; bondMatch = '|' + bondMatch.toLowerCase() + '|'; String inFile = cmd.getOptionValue("in"); String outFile = cmd.getOptionValue("out"); String refFile = cmd.getOptionValue("ref"); String method = cmd.getOptionValue("method"); String rmsdTag = cmd.getOptionValue("rmsdTag"); String oMol = cmd.getOptionValue("outputMol"); boolean doMirror = cmd.hasOption("mirror"); boolean doOptimize = !cmd.hasOption("doNotOptimize"); boolean quiet = cmd.hasOption("quiet"); OUTType outputMol = oMol == null ? OUTType.ALIGNED : OUTType.valueOf(oMol.toUpperCase()); if (atomMatch.startsWith("|none")) atomExpr = 0; if (atomMatch.contains("|hcount|")) atomExpr |= OEExprOpts.HCount; if (atomMatch.contains("|noAromatic|")) atomExpr &= (~OEExprOpts.Aromaticity); if (bondMatch.startsWith("|none")) bondExpr = 0; ArrayList<OEMol> refmols = new ArrayList<OEMol>(); if (refFile != null) { oemolistream reffs = new oemolistream(refFile); if (!is3DFormat(reffs.GetFormat())) oechem.OEThrow.Fatal("Invalid input format: need 3D coordinates"); reffs.SetFormat(OEFormat.MDL); int aromodel = OEIFlavor.Generic.OEAroModelOpenEye; int qflavor = reffs.GetFlavor(reffs.GetFormat()); reffs.SetFlavor(reffs.GetFormat(), (qflavor | aromodel)); OEMol rmol = new OEMol(); while (oechem.OEReadMDLQueryFile(reffs, rmol)) { if (!cmd.hasOption("keepCoreHydrogens")) oechem.OESuppressHydrogens(rmol); refmols.add(rmol); rmol = new OEMol(); } rmol.delete(); if (refmols.size() == 0) throw new Error("reference file had no entries"); reffs.close(); } oemolistream fitfs = new oemolistream(inFile); if (!is3DFormat(fitfs.GetFormat())) oechem.OEThrow.Fatal("Invalid input format: need 3D coordinates"); oemolostream ofs = new oemolostream(outFile); if (!is3DFormat(ofs.GetFormat())) oechem.OEThrow.Fatal("Invalid output format: need 3D coordinates"); AlignInterface aligner = null; OEGraphMol fitmol = new OEGraphMol(); if (oechem.OEReadMolecule(fitfs, fitmol)) { if (refmols.size() == 0) { OEMol rmol = new OEMol(fitmol); if (!cmd.hasOption("keepCoreHydrogens")) oechem.OESuppressHydrogens(rmol); refmols.add(rmol); } if ("sss".equalsIgnoreCase(method)) { aligner = new SSSAlign(refmols, outputMol, rmsdTag, doOptimize, doMirror, atomExpr, bondExpr, quiet); } else if ("clique".equalsIgnoreCase(method)) { aligner = new CliqueAlign(refmols, outputMol, rmsdTag, doOptimize, doMirror, atomExpr, bondExpr, quiet); } else if ("fss".equalsIgnoreCase(method)) { if (cmd.hasOption("atomMatch") || cmd.hasOption("bondMatch")) exitWithHelp("method fss does not support '-atomMatch' or '-bondMatch'", options); aligner = new FSSAlign(refmols, outputMol, rmsdTag, doOptimize, doMirror); } else { aligner = new McsAlign(refmols, outputMol, rmsdTag, doOptimize, doMirror, atomExpr, bondExpr, quiet); } do { aligner.align(fitmol); oechem.OEWriteMolecule(ofs, fitmol); } while (oechem.OEReadMolecule(fitfs, fitmol)); } fitmol.delete(); if (aligner != null) aligner.close(); for (OEMolBase mol : refmols) mol.delete(); fitfs.close(); ofs.close(); }
From source file:com.nextdoor.bender.Bender.java
/** * Main entrypoint for the Bender CLI tool - handles the argument parsing and triggers the * appropriate methods for ultimately invoking a Bender Handler. * * @param args/*from www . j ava 2 s.co m*/ * @throws ParseException */ public static void main(String[] args) throws ParseException { /* * Create the various types of options that we support */ Option help = Option.builder("H").longOpt("help").desc("Print this message").build(); Option handler = Option.builder("h").longOpt("handler").hasArg() .desc("Which Event Handler do you want to simulate? \n" + "Your options are: KinesisHandler, S3Handler. \n" + "Default: KinesisHandler") .build(); Option source_file = Option.builder("s").longOpt("source_file").required().hasArg() .desc("Reference to the file that you want to process. Usage depends " + "on the Handler you chose. If you chose KinesisHandler " + "then this is a local file (file://path/to/file). If you chose " + "S3Handler, then this is the path to the file in S3 that you want to process " + "(s3://bucket/file...)") .build(); Option kinesis_stream_name = Option.builder().longOpt("kinesis_stream_name").hasArg() .desc("What stream name should we mimic? " + "Default: " + KINESIS_STREAM_NAME + " (Kinesis Handler Only)") .build(); /* * Build out the option handler and parse the options */ Options options = new Options(); options.addOption(help); options.addOption(handler); options.addOption(kinesis_stream_name); options.addOption(source_file); /* * Prepare our help formatter */ HelpFormatter formatter = new HelpFormatter(); formatter.setWidth(100); formatter.setSyntaxPrefix("usage: BENDER_CONFIG=file://config.yaml java -jar"); /* * Parse the options themselves. Throw an error and help if necessary. */ CommandLineParser parser = new DefaultParser(); CommandLine cmd = null; try { cmd = parser.parse(options, args); } catch (UnrecognizedOptionException | MissingOptionException | MissingArgumentException e) { logger.error(e.getMessage()); formatter.printHelp(name, options); System.exit(1); } /* * The CLI tool doesn't have any configuration files built into it. We require that the user set * BENDER_CONFIG to something reasonable. */ if (System.getenv("BENDER_CONFIG") == null) { logger.error("You must set the BENDER_CONFIG environment variable. \n" + "Valid options include: file://<file>"); formatter.printHelp(name, options); System.exit(1); } if (cmd.hasOption("help")) { formatter.printHelp(name, options); System.exit(0); } /* * Depending on the desired Handler, we invoke a specific method and pass in the options (or * defaults) required for that handler. */ String handler_value = cmd.getOptionValue(handler.getLongOpt(), KINESIS); try { switch (handler_value.toLowerCase()) { case KINESIS: invokeKinesisHandler(cmd.getOptionValue(kinesis_stream_name.getLongOpt(), KINESIS_STREAM_NAME), cmd.getOptionValue(source_file.getLongOpt())); break; case S3: invokeS3Handler(cmd.getOptionValue(source_file.getLongOpt())); break; /* * Error out if an invalid handler was supplied. */ default: logger.error("Invalid Handler Option (" + handler_value + "), valid options are: " + KINESIS); formatter.printHelp(name, options); System.exit(1); } } catch (HandlerException e) { logger.error("Error executing handler: " + e); System.exit(1); } }