List of usage examples for java.lang String length
public int length()
From source file:com.l2jfree.loginserver.tools.L2GameServerRegistrar.java
/** * Launches the interactive game server registration. * /* w ww . j av a 2s. c o m*/ * @param args ignored */ public static void main(String[] args) { // LOW rework this crap Util.printSection("Game Server Registration"); _log.info("Please choose:"); _log.info("list - list registered game servers"); _log.info("reg - register a game server"); _log.info("rem - remove a registered game server"); _log.info("hexid - generate a legacy hexid file"); _log.info("quit - exit this application"); BufferedReader br = new BufferedReader(new InputStreamReader(System.in)); L2GameServerRegistrar reg = new L2GameServerRegistrar(); String line; try { RegistrationState next = RegistrationState.INITIAL_CHOICE; while ((line = br.readLine()) != null) { line = line.trim().toLowerCase(); switch (reg.getState()) { case GAMESERVER_ID: try { int id = Integer.parseInt(line); if (id < 1 || id > 127) throw new IllegalArgumentException("ID must be in [1;127]."); reg.setId(id); reg.setState(next); } catch (RuntimeException e) { _log.info("You must input a number between 1 and 127"); } if (reg.getState() == RegistrationState.ALLOW_BANS) { Connection con = null; try { con = L2Database.getConnection(); PreparedStatement ps = con .prepareStatement("SELECT allowBans FROM gameserver WHERE id = ?"); ps.setInt(1, reg.getId()); ResultSet rs = ps.executeQuery(); if (rs.next()) { _log.info("A game server is already registered on ID " + reg.getId()); reg.setState(RegistrationState.INITIAL_CHOICE); } else _log.info("Allow account bans from this game server? [y/n]:"); ps.close(); } catch (SQLException e) { _log.error("Could not remove a game server!", e); } finally { L2Database.close(con); } } else if (reg.getState() == RegistrationState.REMOVE) { Connection con = null; try { con = L2Database.getConnection(); PreparedStatement ps = con.prepareStatement("DELETE FROM gameserver WHERE id = ?"); ps.setInt(1, reg.getId()); int cnt = ps.executeUpdate(); if (cnt == 0) _log.info("No game server registered on ID " + reg.getId()); else _log.info("Game server removed."); ps.close(); } catch (SQLException e) { _log.error("Could not remove a game server!", e); } finally { L2Database.close(con); } reg.setState(RegistrationState.INITIAL_CHOICE); } else if (reg.getState() == RegistrationState.GENERATE) { Connection con = null; try { con = L2Database.getConnection(); PreparedStatement ps = con .prepareStatement("SELECT authData FROM gameserver WHERE id = ?"); ps.setInt(1, reg.getId()); ResultSet rs = ps.executeQuery(); if (rs.next()) { reg.setAuth(rs.getString("authData")); byte[] b = HexUtil.hexStringToBytes(reg.getAuth()); Properties pro = new Properties(); pro.setProperty("ServerID", String.valueOf(reg.getId())); pro.setProperty("HexID", HexUtil.hexToString(b)); BufferedOutputStream os = new BufferedOutputStream( new FileOutputStream("hexid.txt")); pro.store(os, "the hexID to auth into login"); IOUtils.closeQuietly(os); _log.info("hexid.txt has been generated."); } else _log.info("No game server registered on ID " + reg.getId()); rs.close(); ps.close(); } catch (SQLException e) { _log.error("Could not generate hexid.txt!", e); } finally { L2Database.close(con); } reg.setState(RegistrationState.INITIAL_CHOICE); } break; case ALLOW_BANS: try { if (line.length() != 1) throw new IllegalArgumentException("One char required."); else if (line.charAt(0) == 'y') reg.setTrusted(true); else if (line.charAt(0) == 'n') reg.setTrusted(false); else throw new IllegalArgumentException("Invalid choice."); byte[] auth = Rnd.nextBytes(new byte[BYTES]); reg.setAuth(HexUtil.bytesToHexString(auth)); Connection con = null; try { con = L2Database.getConnection(); PreparedStatement ps = con.prepareStatement( "INSERT INTO gameserver (id, authData, allowBans) VALUES (?, ?, ?)"); ps.setInt(1, reg.getId()); ps.setString(2, reg.getAuth()); ps.setBoolean(3, reg.isTrusted()); ps.executeUpdate(); ps.close(); _log.info("Registered game server on ID " + reg.getId()); _log.info("The authorization string is:"); _log.info(reg.getAuth()); _log.info("Use it when registering this login server."); _log.info("If you need a legacy hexid file, use the 'hexid' command."); } catch (SQLException e) { _log.error("Could not register gameserver!", e); } finally { L2Database.close(con); } reg.setState(RegistrationState.INITIAL_CHOICE); } catch (IllegalArgumentException e) { _log.info("[y/n]?"); } break; default: if (line.equals("list")) { Connection con = null; try { con = L2Database.getConnection(); PreparedStatement ps = con.prepareStatement("SELECT id, allowBans FROM gameserver"); ResultSet rs = ps.executeQuery(); while (rs.next()) _log.info("ID: " + rs.getInt("id") + ", trusted: " + rs.getBoolean("allowBans")); rs.close(); ps.close(); } catch (SQLException e) { _log.error("Could not register gameserver!", e); } finally { L2Database.close(con); } reg.setState(RegistrationState.INITIAL_CHOICE); } else if (line.equals("reg")) { _log.info("Enter the desired ID:"); reg.setState(RegistrationState.GAMESERVER_ID); next = RegistrationState.ALLOW_BANS; } else if (line.equals("rem")) { _log.info("Enter game server ID:"); reg.setState(RegistrationState.GAMESERVER_ID); next = RegistrationState.REMOVE; } else if (line.equals("hexid")) { _log.info("Enter game server ID:"); reg.setState(RegistrationState.GAMESERVER_ID); next = RegistrationState.GENERATE; } else if (line.equals("quit")) Shutdown.exit(TerminationStatus.MANUAL_SHUTDOWN); else _log.info("Incorrect command."); break; } } } catch (IOException e) { _log.fatal("Could not process input!", e); } finally { IOUtils.closeQuietly(br); } }
From source file:au.com.jwatmuff.eventmanager.Main.java
/** * Main method.//from w ww . ja va2s . c om */ public static void main(String args[]) { LogUtils.setupUncaughtExceptionHandler(); /* Set timeout for RMI connections - TODO: move to external file */ System.setProperty("sun.rmi.transport.tcp.handshakeTimeout", "2000"); updateRmiHostName(); /* * Set up menu bar for Mac */ System.setProperty("apple.laf.useScreenMenuBar", "true"); System.setProperty("com.apple.mrj.application.apple.menu.about.name", "Event Manager"); /* * Set look and feel to 'system' style */ try { UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName()); } catch (Exception e) { log.info("Failed to set system look and feel"); } /* * Set workingDir to a writable folder for storing competitions, settings etc. */ String applicationData = System.getenv("APPDATA"); if (applicationData != null) { workingDir = new File(applicationData, "EventManager"); if (workingDir.exists() || workingDir.mkdirs()) { // redirect logging to writable folder LogUtils.reconfigureFileAppenders("log4j.properties", workingDir); } else { workingDir = new File("."); } } // log version for debugging log.info("Running version: " + VISIBLE_VERSION + " (Internal: " + VERSION + ")"); /* * Copy license if necessary */ File license1 = new File("license.lic"); File license2 = new File(workingDir, "license.lic"); if (license1.exists() && !license2.exists()) { try { FileUtils.copyFile(license1, license2); } catch (IOException e) { log.warn("Failed to copy license from " + license1 + " to " + license2, e); } } if (license1.exists() && license2.exists()) { if (license1.lastModified() > license2.lastModified()) { try { FileUtils.copyFile(license1, license2); } catch (IOException e) { log.warn("Failed to copy license from " + license1 + " to " + license2, e); } } } /* * Check if run lock exists, if so ask user if it is ok to continue */ if (!obtainRunLock(false)) { int response = JOptionPane.showConfirmDialog(null, "Unable to obtain run-lock.\nPlease ensure that no other instances of EventManager are running before continuing.\nDo you wish to continue?", "Run-lock detected", JOptionPane.YES_NO_OPTION); if (response == JOptionPane.YES_OPTION) obtainRunLock(true); else System.exit(0); } try { LoadWindow loadWindow = new LoadWindow(); loadWindow.setVisible(true); loadWindow.addMessage("Reading settings.."); /* * Read properties from file */ final Properties props = new Properties(); try { Properties defaultProps = PropertiesLoaderUtils .loadProperties(new ClassPathResource("eventmanager.properties")); props.putAll(defaultProps); } catch (IOException ex) { log.error(ex); } props.putAll(System.getProperties()); File databaseStore = new File(workingDir, "comps"); int rmiPort = Integer.parseInt(props.getProperty("eventmanager.rmi.port")); loadWindow.addMessage("Loading Peer Manager.."); log.info("Loading Peer Manager"); ManualDiscoveryService manualDiscoveryService = new ManualDiscoveryService(); JmDNSRMIPeerManager peerManager = new JmDNSRMIPeerManager(rmiPort, new File(workingDir, "peerid.dat")); peerManager.addDiscoveryService(manualDiscoveryService); monitorNetworkInterfaceChanges(peerManager); loadWindow.addMessage("Loading Database Manager.."); log.info("Loading Database Manager"); DatabaseManager databaseManager = new SQLiteDatabaseManager(databaseStore, peerManager); LicenseManager licenseManager = new LicenseManager(workingDir); loadWindow.addMessage("Loading Load Competition Dialog.."); log.info("Loading Load Competition Dialog"); LoadCompetitionWindow loadCompetitionWindow = new LoadCompetitionWindow(databaseManager, licenseManager, peerManager); loadCompetitionWindow.setTitle(WINDOW_TITLE); loadWindow.dispose(); log.info("Starting Load Competition Dialog"); while (true) { // reset permission checker to use our license licenseManager.updatePermissionChecker(); GUIUtils.runModalJFrame(loadCompetitionWindow); if (loadCompetitionWindow.getSuccess()) { DatabaseInfo info = loadCompetitionWindow.getSelectedDatabaseInfo(); if (!databaseManager.checkLock(info.id)) { String message = "EventManager did not shut down correctly the last time this competition was open. To avoid potential data corruption, you are advised to take the following steps:\n" + "1) Do NOT open this competition\n" + "2) Create a backup of this competition\n" + "3) Delete the competition from this computer\n" + "4) If possible, reload this competition from another computer on the network\n" + "5) Alternatively, you may manually load the backup onto all computers on the network, ensuring the 'Preserve competition ID' option is checked."; String title = "WARNING: Potential Data Corruption Detected"; int status = JOptionPane.showOptionDialog(null, message, title, JOptionPane.YES_NO_OPTION, JOptionPane.ERROR_MESSAGE, null, new Object[] { "Cancel (recommended)", "Open anyway" }, "Cancel (recommended)"); if (status == 0) continue; // return to load competition window } SynchronizingWindow syncWindow = new SynchronizingWindow(); syncWindow.setVisible(true); long t = System.nanoTime(); DistributedDatabase database = databaseManager.activateDatabase(info.id, info.passwordHash); long dt = System.nanoTime() - t; log.debug(String.format("Initial sync in %dms", TimeUnit.MILLISECONDS.convert(dt, TimeUnit.NANOSECONDS))); syncWindow.dispose(); if (loadCompetitionWindow.isNewDatabase()) { GregorianCalendar calendar = new GregorianCalendar(); Date today = calendar.getTime(); calendar.set(Calendar.MONTH, Calendar.DECEMBER); calendar.set(Calendar.DAY_OF_MONTH, 31); Date endOfYear = new java.sql.Date(calendar.getTimeInMillis()); CompetitionInfo ci = new CompetitionInfo(); ci.setName(info.name); ci.setStartDate(today); ci.setEndDate(today); ci.setAgeThresholdDate(endOfYear); //ci.setPasswordHash(info.passwordHash); License license = licenseManager.getLicense(); if (license != null) { ci.setLicenseName(license.getName()); ci.setLicenseType(license.getType().toString()); ci.setLicenseContact(license.getContactPhoneNumber()); } database.add(ci); } // Set PermissionChecker to use database's license type String competitionLicenseType = database.get(CompetitionInfo.class, null).getLicenseType(); PermissionChecker.setLicenseType(LicenseType.valueOf(competitionLicenseType)); TransactionNotifier notifier = new TransactionNotifier(); database.setListener(notifier); MainWindow mainWindow = new MainWindow(); mainWindow.setDatabase(database); mainWindow.setNotifier(notifier); mainWindow.setPeerManager(peerManager); mainWindow.setLicenseManager(licenseManager); mainWindow.setManualDiscoveryService(manualDiscoveryService); mainWindow.setTitle(WINDOW_TITLE); mainWindow.afterPropertiesSet(); TestUtil.setActivatedDatabase(database); // show main window (modally) GUIUtils.runModalJFrame(mainWindow); // shutdown procedures // System.exit(); database.shutdown(); databaseManager.deactivateDatabase(1500); if (mainWindow.getDeleteOnExit()) { for (File file : info.localDirectory.listFiles()) if (!file.isDirectory()) file.delete(); info.localDirectory.deleteOnExit(); } } else { // This can cause an RuntimeException - Peer is disconnected peerManager.stop(); System.exit(0); } } } catch (Throwable e) { log.error("Error in main function", e); String message = e.getMessage(); if (message == null) message = ""; if (message.length() > 100) message = message.substring(0, 97) + "..."; GUIUtils.displayError(null, "An unexpected error has occured.\n\n" + e.getClass().getSimpleName() + "\n" + message); System.exit(0); } }
From source file:CTmousetrack.java
public static void main(String[] args) { String outLoc = new String("." + File.separator + "CTdata"); // Location of the base output data folder; only used when writing out CT data to a local folder String srcName = "CTmousetrack"; // name of the output CT source long blockPts = 10; // points per block flush long sampInterval = 10; // time between sampling updates, msec double trimTime = 0.0; // amount of data to keep (trim time), sec boolean debug = false; // turn on debug? // Specify the CT output connection CTWriteMode writeMode = CTWriteMode.LOCAL; // The selected mode for writing out CT data String serverHost = ""; // Server (FTP or HTTP/S) host:port String serverUser = ""; // Server (FTP or HTTPS) username String serverPassword = ""; // Server (FTP or HTTPS) password // For UDP output mode DatagramSocket udpServerSocket = null; InetAddress udpServerAddress = null; String udpHost = ""; int udpPort = -1; // Concatenate all of the CTWriteMode types String possibleWriteModes = ""; for (CTWriteMode wm : CTWriteMode.values()) { possibleWriteModes = possibleWriteModes + ", " + wm.name(); }//from www. ja va 2 s. c o m // Remove ", " from start of string possibleWriteModes = possibleWriteModes.substring(2); // // Argument processing using Apache Commons CLI // // 1. Setup command line options Options options = new Options(); options.addOption("h", "help", false, "Print this message."); options.addOption(Option.builder("o").argName("base output dir").hasArg().desc( "Base output directory when writing data to local folder (i.e., this is the location of CTdata folder); default = \"" + outLoc + "\".") .build()); options.addOption(Option.builder("s").argName("source name").hasArg() .desc("Name of source to write data to; default = \"" + srcName + "\".").build()); options.addOption(Option.builder("b").argName("points per block").hasArg() .desc("Number of points per block; UDP output mode will use 1 point/block; default = " + Long.toString(blockPts) + ".") .build()); options.addOption(Option.builder("dt").argName("samp interval msec").hasArg() .desc("Sampling period in msec; default = " + Long.toString(sampInterval) + ".").build()); options.addOption(Option.builder("t").argName("trim time sec").hasArg().desc( "Trim (ring-buffer loop) time (sec); this is only used when writing data to local folder; specify 0 for indefinite; default = " + Double.toString(trimTime) + ".") .build()); options.addOption( Option.builder("w").argName("write mode").hasArg() .desc("Type of write connection; one of " + possibleWriteModes + "; all but UDP mode write out to CT; default = " + writeMode.name() + ".") .build()); options.addOption(Option.builder("host").argName("host[:port]").hasArg() .desc("Host:port when writing via FTP, HTTP, HTTPS, UDP.").build()); options.addOption(Option.builder("u").argName("username,password").hasArg() .desc("Comma-delimited username and password when writing to CT via FTP or HTTPS.").build()); options.addOption("x", "debug", false, "Enable CloudTurbine debug output."); // 2. Parse command line options CommandLineParser parser = new DefaultParser(); CommandLine line = null; try { line = parser.parse(options, args); } catch (ParseException exp) { // oops, something went wrong System.err.println("Command line argument parsing failed: " + exp.getMessage()); return; } // 3. Retrieve the command line values if (line.hasOption("help")) { // Display help message and quit HelpFormatter formatter = new HelpFormatter(); formatter.setWidth(120); formatter.printHelp("CTmousetrack", "", options, "NOTE: UDP output is a special non-CT output mode where single x,y points are sent via UDP to the specified host:port."); return; } outLoc = line.getOptionValue("o", outLoc); if (!outLoc.endsWith("\\") && !outLoc.endsWith("/")) { outLoc = outLoc + File.separator; } // Make sure the base output folder location ends in "CTdata" if (!outLoc.endsWith("CTdata\\") && !outLoc.endsWith("CTdata/")) { outLoc = outLoc + "CTdata" + File.separator; } srcName = line.getOptionValue("s", srcName); blockPts = Long.parseLong(line.getOptionValue("b", Long.toString(blockPts))); sampInterval = Long.parseLong(line.getOptionValue("dt", Long.toString(sampInterval))); trimTime = Double.parseDouble(line.getOptionValue("t", Double.toString(trimTime))); // Type of output connection String writeModeStr = line.getOptionValue("w", writeMode.name()); boolean bMatch = false; for (CTWriteMode wm : CTWriteMode.values()) { if (wm.name().toLowerCase().equals(writeModeStr.toLowerCase())) { writeMode = wm; bMatch = true; } } if (!bMatch) { System.err.println("Unrecognized write mode, \"" + writeModeStr + "\"; write mode must be one of " + possibleWriteModes); System.exit(0); } if (writeMode != CTWriteMode.LOCAL) { // User must have specified the host // If FTP or HTTPS, they may also specify username/password serverHost = line.getOptionValue("host", serverHost); if (serverHost.isEmpty()) { System.err.println( "When using write mode \"" + writeModeStr + "\", you must specify the server host."); System.exit(0); } if (writeMode == CTWriteMode.UDP) { // Force blockPts to be 1 blockPts = 1; // User must have specified both host and port int colonIdx = serverHost.indexOf(':'); if ((colonIdx == -1) || (colonIdx >= serverHost.length() - 1)) { System.err.println( "For UDP output mode, both the host and port (<host>:<port>)) must be specified."); System.exit(0); } udpHost = serverHost.substring(0, colonIdx); String udpPortStr = serverHost.substring(colonIdx + 1); try { udpPort = Integer.parseInt(udpPortStr); } catch (NumberFormatException nfe) { System.err.println("The UDP port must be a positive integer."); System.exit(0); } } if ((writeMode == CTWriteMode.FTP) || (writeMode == CTWriteMode.HTTPS)) { String userpassStr = line.getOptionValue("u", ""); if (!userpassStr.isEmpty()) { // This string should be comma-delimited username and password String[] userpassCSV = userpassStr.split(","); if (userpassCSV.length != 2) { System.err.println("When specifying a username and password for write mode \"" + writeModeStr + "\", separate the username and password by a comma."); System.exit(0); } serverUser = userpassCSV[0]; serverPassword = userpassCSV[1]; } } } debug = line.hasOption("debug"); System.err.println("CTmousetrack parameters:"); System.err.println("\toutput mode = " + writeMode.name()); if (writeMode == CTWriteMode.UDP) { System.err.println("\twrite to " + udpHost + ":" + udpPort); } else { System.err.println("\tsource = " + srcName); System.err.println("\ttrim time = " + trimTime + " sec"); } System.err.println("\tpoints per block = " + blockPts); System.err.println("\tsample interval = " + sampInterval + " msec"); try { // // Setup CTwriter or UDP output // CTwriter ctw = null; CTinfo.setDebug(debug); if (writeMode == CTWriteMode.LOCAL) { ctw = new CTwriter(outLoc + srcName, trimTime); System.err.println("\tdata will be written to local folder \"" + outLoc + "\""); } else if (writeMode == CTWriteMode.FTP) { CTftp ctftp = new CTftp(srcName); try { ctftp.login(serverHost, serverUser, serverPassword); } catch (Exception e) { throw new IOException( new String("Error logging into FTP server \"" + serverHost + "\":\n" + e.getMessage())); } ctw = ctftp; // upcast to CTWriter System.err.println("\tdata will be written to FTP server at " + serverHost); } else if (writeMode == CTWriteMode.HTTP) { // Don't send username/pw in HTTP mode since they will be unencrypted CThttp cthttp = new CThttp(srcName, "http://" + serverHost); ctw = cthttp; // upcast to CTWriter System.err.println("\tdata will be written to HTTP server at " + serverHost); } else if (writeMode == CTWriteMode.HTTPS) { CThttp cthttp = new CThttp(srcName, "https://" + serverHost); // Username/pw are optional for HTTPS mode; only use them if username is not empty if (!serverUser.isEmpty()) { try { cthttp.login(serverUser, serverPassword); } catch (Exception e) { throw new IOException(new String( "Error logging into HTTP server \"" + serverHost + "\":\n" + e.getMessage())); } } ctw = cthttp; // upcast to CTWriter System.err.println("\tdata will be written to HTTPS server at " + serverHost); } else if (writeMode == CTWriteMode.UDP) { try { udpServerSocket = new DatagramSocket(); } catch (SocketException se) { System.err.println("Error creating socket for UDP:\n" + se); System.exit(0); } try { udpServerAddress = InetAddress.getByName(udpHost); } catch (UnknownHostException uhe) { System.err.println("Error getting UDP server host address:\n" + uhe); System.exit(0); } } if (writeMode != CTWriteMode.UDP) { ctw.setBlockMode(blockPts > 1, blockPts > 1); ctw.autoFlush(0); // no autoflush ctw.autoSegment(1000); } // screen dims Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize(); double width = screenSize.getWidth(); double height = screenSize.getHeight(); // use Map for consolidated putData Map<String, Object> cmap = new LinkedHashMap<String, Object>(); // loop and write some output for (int i = 0; i < 1000000; i++) { // go until killed long currentTime = System.currentTimeMillis(); Point mousePos = MouseInfo.getPointerInfo().getLocation(); float x_pt = (float) (mousePos.getX() / width); // normalize float y_pt = (float) ((height - mousePos.getY()) / height); // flip Y (so bottom=0) if (writeMode != CTWriteMode.UDP) { // CT output mode ctw.setTime(currentTime); cmap.clear(); cmap.put("x", x_pt); cmap.put("y", y_pt); ctw.putData(cmap); if (((i + 1) % blockPts) == 0) { ctw.flush(); System.err.print("."); } } else { // UDP output mode // We force blockPts to be 1 for UDP output mode, i.e. we "flush" the data every time // Write the following data (21 bytes total): // header = "MOUSE", 5 bytes // current time, long, 8 bytes // 2 floats (x,y) 4 bytes each, 8 bytes int len = 21; ByteBuffer bb = ByteBuffer.allocate(len); String headerStr = "MOUSE"; bb.put(headerStr.getBytes("UTF-8")); bb.putLong(currentTime); bb.putFloat(x_pt); bb.putFloat(y_pt); // Might be able to use the following, but not sure: // byte[] sendData = bb.array(); byte[] sendData = new byte[len]; bb.position(0); bb.get(sendData, 0, len); DatagramPacket sendPacket = new DatagramPacket(sendData, sendData.length, udpServerAddress, udpPort); try { udpServerSocket.send(sendPacket); } catch (IOException e) { System.err.println("Test server caught exception trying to send data to UDP client:\n" + e); } System.err.print("."); } try { Thread.sleep(sampInterval); } catch (Exception e) { } ; } if (writeMode != CTWriteMode.UDP) { ctw.flush(); // wrap up } } catch (Exception e) { System.err.println("CTmousetrack exception: " + e); e.printStackTrace(); } }
From source file:DIA_Umpire_Quant.DIA_Umpire_Quant.java
/** * @param args the command line arguments *//*w w w . j av a 2 s . c om*/ public static void main(String[] args) throws FileNotFoundException, IOException, Exception { System.out.println( "================================================================================================="); System.out.println("DIA-Umpire quantitation with targeted re-extraction analysis (version: " + UmpireInfo.GetInstance().Version + ")"); if (args.length != 1) { System.out.println( "command format error, it should be like: java -jar -Xmx10G DIA_Umpire_Quant.jar diaumpire_quant.params"); return; } try { ConsoleLogger.SetConsoleLogger(Level.INFO); ConsoleLogger.SetFileLogger(Level.DEBUG, FilenameUtils.getFullPath(args[0]) + "diaumpire_quant.log"); } catch (Exception e) { } try { 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; String UserMod = ""; String Combined_Prot = ""; String InternalLibID = ""; String ExternalLibPath = ""; String ExternalLibDecoyTag = "DECOY"; boolean DefaultProtFiltering = true; boolean DataSetLevelPepFDR = false; float ProbThreshold = 0.99f; float ExtProbThreshold = 0.99f; float Freq = 0f; int TopNPep = 6; int TopNFrag = 6; float MinFragMz = 200f; String FilterWeight = "GW"; float MinWeight = 0.9f; float RTWindow_Int = -1f; float RTWindow_Ext = -1f; TandemParam tandemPara = new TandemParam(DBSearchParam.SearchInstrumentType.TOF5600); HashMap<String, File> AssignFiles = new HashMap<>(); boolean InternalLibSearch = false; boolean ExternalLibSearch = false; boolean ExportSaint = false; boolean SAINT_MS1 = false; boolean SAINT_MS2 = true; HashMap<String, String[]> BaitList = new HashMap<>(); HashMap<String, String> BaitName = new HashMap<>(); HashMap<String, String[]> ControlList = new HashMap<>(); HashMap<String, String> ControlName = 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 "TargetedExtraction": { InternalLibSearch = Boolean.parseBoolean(value); break; } case "InternalLibSearch": { InternalLibSearch = Boolean.parseBoolean(value); break; } case "ExternalLibSearch": { ExternalLibSearch = Boolean.parseBoolean(value); break; } case "Path": { WorkFolder = value; break; } case "path": { WorkFolder = value; break; } case "Thread": { NoCPUs = Integer.parseInt(value); break; } case "Fasta": { tandemPara.FastaPath = value; break; } case "Combined_Prot": { Combined_Prot = value; break; } case "DefaultProtFiltering": { DefaultProtFiltering = Boolean.parseBoolean(value); break; } case "DecoyPrefix": { if (!"".equals(value)) { tandemPara.DecoyPrefix = value; } break; } case "UserMod": { UserMod = value; break; } case "ProteinFDR": { tandemPara.ProtFDR = Float.parseFloat(value); break; } case "PeptideFDR": { tandemPara.PepFDR = Float.parseFloat(value); break; } case "DataSetLevelPepFDR": { DataSetLevelPepFDR = Boolean.parseBoolean(value); break; } case "InternalLibID": { InternalLibID = value; break; } case "ExternalLibPath": { ExternalLibPath = value; break; } case "ExtProbThreshold": { ExtProbThreshold = Float.parseFloat(value); break; } case "RTWindow_Int": { RTWindow_Int = Float.parseFloat(value); break; } case "RTWindow_Ext": { RTWindow_Ext = Float.parseFloat(value); break; } case "ExternalLibDecoyTag": { ExternalLibDecoyTag = value; if (ExternalLibDecoyTag.endsWith("_")) { ExternalLibDecoyTag = ExternalLibDecoyTag.substring(0, ExternalLibDecoyTag.length() - 1); } break; } case "ProbThreshold": { ProbThreshold = Float.parseFloat(value); break; } case "ReSearchProb": { //ReSearchProb = Float.parseFloat(value); break; } case "FilterWeight": { FilterWeight = value; break; } case "MinWeight": { MinWeight = Float.parseFloat(value); break; } case "TopNFrag": { TopNFrag = Integer.parseInt(value); break; } case "TopNPep": { TopNPep = Integer.parseInt(value); break; } case "Freq": { Freq = Float.parseFloat(value); break; } case "MinFragMz": { MinFragMz = Float.parseFloat(value); break; } //<editor-fold defaultstate="collapsed" desc="SaintOutput"> case "ExportSaintInput": { ExportSaint = Boolean.parseBoolean(value); break; } case "QuantitationType": { switch (value) { case "MS1": { SAINT_MS1 = true; SAINT_MS2 = false; break; } case "MS2": { SAINT_MS1 = false; SAINT_MS2 = true; break; } case "BOTH": { SAINT_MS1 = true; SAINT_MS2 = true; break; } } break; } // case "BaitInputFile": { // SaintBaitFile = value; // break; // } // case "PreyInputFile": { // SaintPreyFile = value; // break; // } // case "InterationInputFile": { // SaintInteractionFile = value; // break; // } default: { if (type.startsWith("BaitName_")) { BaitName.put(type.substring(9), value); } if (type.startsWith("BaitFile_")) { BaitList.put(type.substring(9), value.split("\t")); } if (type.startsWith("ControlName_")) { ControlName.put(type.substring(12), value); } if (type.startsWith("ControlFile_")) { ControlList.put(type.substring(12), value.split("\t")); } break; } //</editor-fold> } } } //</editor-fold> //Initialize PTM manager using compomics library PTMManager.GetInstance(); if (!UserMod.equals("")) { PTMManager.GetInstance().ImportUserMod(UserMod); } //Check if the fasta file can be found if (!new File(tandemPara.FastaPath).exists()) { Logger.getRootLogger().info("Fasta file :" + tandemPara.FastaPath + " cannot be found, the process will be terminated, please check."); System.exit(1); } //Check if the prot.xml file can be found if (!new File(Combined_Prot).exists()) { Logger.getRootLogger().info("ProtXML file: " + Combined_Prot + " cannot be found, the export protein summary table will be empty."); } LCMSID protID = null; //Parse prot.xml and generate protein master list given an FDR if (Combined_Prot != null && !Combined_Prot.equals("")) { protID = LCMSID.ReadLCMSIDSerialization(Combined_Prot); if (!"".equals(Combined_Prot) && protID == null) { protID = new LCMSID(Combined_Prot, tandemPara.DecoyPrefix, tandemPara.FastaPath); ProtXMLParser protxmlparser = new ProtXMLParser(protID, Combined_Prot, 0f); //Use DIA-Umpire default protein FDR calculation if (DefaultProtFiltering) { protID.RemoveLowLocalPWProtein(0.8f); protID.RemoveLowMaxIniProbProtein(0.9f); protID.FilterByProteinDecoyFDRUsingMaxIniProb(tandemPara.DecoyPrefix, tandemPara.ProtFDR); } //Get protein FDR calculation without other filtering else { protID.FilterByProteinDecoyFDRUsingLocalPW(tandemPara.DecoyPrefix, tandemPara.ProtFDR); } protID.LoadSequence(); protID.WriteLCMSIDSerialization(Combined_Prot); } Logger.getRootLogger().info("Protein No.:" + protID.ProteinList.size()); } HashMap<String, HashMap<String, FragmentPeak>> IDSummaryFragments = new HashMap<>(); //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()); String mzXMLFile = fileEntry.getAbsolutePath(); if (mzXMLFile.toLowerCase().endsWith(".mzxml") | mzXMLFile.toLowerCase().endsWith(".mzml")) { DIAPack DiaFile = new DIAPack(mzXMLFile, NoCPUs); FileList.add(DiaFile); HashMap<String, FragmentPeak> FragMap = new HashMap<>(); IDSummaryFragments.put(FilenameUtils.getBaseName(mzXMLFile), FragMap); 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); } } } LCMSID combinePepID = null; if (DataSetLevelPepFDR) { combinePepID = LCMSID.ReadLCMSIDSerialization(WorkFolder + "combinePepID.SerFS"); if (combinePepID == null) { FDR_DataSetLevel fdr = new FDR_DataSetLevel(); fdr.GeneratePepIonList(FileList, tandemPara, WorkFolder + "combinePepID.SerFS"); combinePepID = fdr.combineID; combinePepID.WriteLCMSIDSerialization(WorkFolder + "combinePepID.SerFS"); } } //process each DIA file for quantification based on untargeted identifications for (DIAPack DiaFile : FileList) { long time = System.currentTimeMillis(); Logger.getRootLogger().info("Loading identification results " + DiaFile.Filename + "...."); //If the LCMSID serialization is found if (!DiaFile.ReadSerializedLCMSID()) { DiaFile.ParsePepXML(tandemPara, combinePepID); 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(DiaFile.Filename + " 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)))); } //<editor-fold defaultstate="collapsed" desc="Targete re-extraction using internal library"> Logger.getRootLogger().info( "================================================================================================="); if (InternalLibSearch && FileList.size() > 1) { Logger.getRootLogger().info("Module C: Targeted extraction using internal library"); FragmentLibManager libManager = FragmentLibManager.ReadFragmentLibSerialization(WorkFolder, InternalLibID); if (libManager == null) { Logger.getRootLogger().info("Building internal spectral library"); libManager = new FragmentLibManager(InternalLibID); ArrayList<LCMSID> LCMSIDList = new ArrayList<>(); for (DIAPack dia : FileList) { LCMSIDList.add(dia.IDsummary); } libManager.ImportFragLibTopFrag(LCMSIDList, Freq, TopNFrag); libManager.WriteFragmentLibSerialization(WorkFolder); } libManager.ReduceMemoryUsage(); Logger.getRootLogger() .info("Building retention time prediction model and generate candidate peptide list"); for (int i = 0; i < FileList.size(); i++) { FileList.get(i).IDsummary.ClearMappedPep(); } for (int i = 0; i < FileList.size(); i++) { for (int j = i + 1; j < FileList.size(); j++) { RTAlignedPepIonMapping alignment = new RTAlignedPepIonMapping(WorkFolder, FileList.get(i).GetParameter(), FileList.get(i).IDsummary, FileList.get(j).IDsummary); alignment.GenerateModel(); alignment.GenerateMappedPepIon(); } FileList.get(i).ExportID(); FileList.get(i).IDsummary = null; } Logger.getRootLogger().info("Targeted matching........"); for (DIAPack diafile : FileList) { if (diafile.IDsummary == null) { diafile.ReadSerializedLCMSID(); } if (!diafile.IDsummary.GetMappedPepIonList().isEmpty()) { diafile.UseMappedIon = true; diafile.FilterMappedIonByProb = false; diafile.BuildStructure(); diafile.MS1FeatureMap.ReadPeakCluster(); diafile.MS1FeatureMap.ClearMonoisotopicPeakOfCluster(); diafile.GenerateMassCalibrationRTMap(); diafile.TargetedExtractionQuant(false, libManager, 1.1f, RTWindow_Int); diafile.MS1FeatureMap.ClearAllPeaks(); diafile.IDsummary.ReduceMemoryUsage(); diafile.IDsummary.RemoveLowProbMappedIon(ProbThreshold); diafile.ExportID(); Logger.getRootLogger().info("Peptide ions: " + diafile.IDsummary.GetPepIonList().size() + " Mapped ions: " + diafile.IDsummary.GetMappedPepIonList().size()); diafile.ClearStructure(); } diafile.IDsummary = null; System.gc(); } Logger.getRootLogger().info( "================================================================================================="); } //</editor-fold> //<editor-fold defaultstate="collapsed" desc="Targeted re-extraction using external library"> //External library search if (ExternalLibSearch) { Logger.getRootLogger().info("Module C: Targeted extraction using external library"); //Read exteranl library FragmentLibManager ExlibManager = FragmentLibManager.ReadFragmentLibSerialization(WorkFolder, FilenameUtils.getBaseName(ExternalLibPath)); if (ExlibManager == null) { ExlibManager = new FragmentLibManager(FilenameUtils.getBaseName(ExternalLibPath)); //Import traML file ExlibManager.ImportFragLibByTraML(ExternalLibPath, ExternalLibDecoyTag); //Check if there are decoy spectra ExlibManager.CheckDecoys(); //ExlibManager.ImportFragLibBySPTXT(ExternalLibPath); ExlibManager.WriteFragmentLibSerialization(WorkFolder); } Logger.getRootLogger() .info("No. of peptide ions in external lib:" + ExlibManager.PeptideFragmentLib.size()); for (DIAPack diafile : FileList) { if (diafile.IDsummary == null) { diafile.ReadSerializedLCMSID(); } //Generate RT mapping RTMappingExtLib RTmap = new RTMappingExtLib(diafile.IDsummary, ExlibManager, diafile.GetParameter()); RTmap.GenerateModel(); RTmap.GenerateMappedPepIon(); diafile.BuildStructure(); diafile.MS1FeatureMap.ReadPeakCluster(); diafile.GenerateMassCalibrationRTMap(); //Perform targeted re-extraction diafile.TargetedExtractionQuant(false, ExlibManager, ProbThreshold, RTWindow_Ext); diafile.MS1FeatureMap.ClearAllPeaks(); diafile.IDsummary.ReduceMemoryUsage(); //Remove target IDs below the defined probability threshold diafile.IDsummary.RemoveLowProbMappedIon(ExtProbThreshold); diafile.ExportID(); diafile.ClearStructure(); Logger.getRootLogger().info("Peptide ions: " + diafile.IDsummary.GetPepIonList().size() + " Mapped ions: " + diafile.IDsummary.GetMappedPepIonList().size()); } } //</editor-fold> //<editor-fold defaultstate="collapsed" desc="Peptide and fragment selection"> Logger.getRootLogger().info("Peptide and fragment selection across the whole dataset"); ArrayList<LCMSID> SummaryList = new ArrayList<>(); for (DIAPack diafile : FileList) { if (diafile.IDsummary == null) { diafile.ReadSerializedLCMSID(); diafile.IDsummary.ClearAssignPeakCluster(); //diafile.IDsummary.ClearPSMs(); } if (protID != null) { //Generate protein list according to mapping of peptide ions for each DIA file to the master protein list diafile.IDsummary.GenerateProteinByRefIDByPepSeq(protID, true); diafile.IDsummary.ReMapProPep(); } if ("GW".equals(FilterWeight)) { diafile.IDsummary.SetFilterByGroupWeight(); } else if ("PepW".equals(FilterWeight)) { diafile.IDsummary.SetFilterByWeight(); } SummaryList.add(diafile.IDsummary); } FragmentSelection fragselection = new FragmentSelection(SummaryList); fragselection.freqPercent = Freq; fragselection.MinFragMZ = MinFragMz; fragselection.GeneratePepFragScoreMap(); fragselection.GenerateTopFragMap(TopNFrag); fragselection.GenerateProtPepScoreMap(MinWeight); fragselection.GenerateTopPepMap(TopNPep); //</editor-fold> //<editor-fold defaultstate="collapsed" desc="Writing general reports"> ExportTable export = new ExportTable(WorkFolder, SummaryList, IDSummaryFragments, protID, fragselection); export.Export(TopNPep, TopNFrag, Freq); //</editor-fold> //<editor-fold defaultstate="collapsed" desc="//<editor-fold defaultstate="collapsed" desc="Generate SAINT input files"> if (ExportSaint && protID != null) { HashMap<String, DIAPack> Filemap = new HashMap<>(); for (DIAPack DIAfile : FileList) { Filemap.put(DIAfile.GetBaseName(), DIAfile); } FileWriter baitfile = new FileWriter(WorkFolder + "SAINT_Bait_" + DateTimeTag.GetTag() + ".txt"); FileWriter preyfile = new FileWriter(WorkFolder + "SAINT_Prey_" + DateTimeTag.GetTag() + ".txt"); FileWriter interactionfileMS1 = null; FileWriter interactionfileMS2 = null; if (SAINT_MS1) { interactionfileMS1 = new FileWriter( WorkFolder + "SAINT_Interaction_MS1_" + DateTimeTag.GetTag() + ".txt"); } if (SAINT_MS2) { interactionfileMS2 = new FileWriter( WorkFolder + "SAINT_Interaction_MS2_" + DateTimeTag.GetTag() + ".txt"); } HashMap<String, String> PreyID = new HashMap<>(); for (String samplekey : ControlName.keySet()) { String name = ControlName.get(samplekey); for (String file : ControlList.get(samplekey)) { baitfile.write(FilenameUtils.getBaseName(file) + "\t" + name + "\t" + "C\n"); LCMSID IDsummary = Filemap.get(FilenameUtils.getBaseName(file)).IDsummary; if (SAINT_MS1) { SaintOutput(protID, IDsummary, fragselection, interactionfileMS1, file, name, PreyID, 1); } if (SAINT_MS2) { SaintOutput(protID, IDsummary, fragselection, interactionfileMS2, file, name, PreyID, 2); } } } for (String samplekey : BaitName.keySet()) { String name = BaitName.get(samplekey); for (String file : BaitList.get(samplekey)) { baitfile.write(FilenameUtils.getBaseName(file) + "\t" + name + "\t" + "T\n"); LCMSID IDsummary = Filemap.get(FilenameUtils.getBaseName(file)).IDsummary; if (SAINT_MS1) { SaintOutput(protID, IDsummary, fragselection, interactionfileMS1, file, name, PreyID, 1); } if (SAINT_MS2) { SaintOutput(protID, IDsummary, fragselection, interactionfileMS2, file, name, PreyID, 2); } } } baitfile.close(); if (SAINT_MS1) { interactionfileMS1.close(); } if (SAINT_MS2) { interactionfileMS2.close(); } for (String AccNo : PreyID.keySet()) { preyfile.write(AccNo + "\t" + PreyID.get(AccNo) + "\n"); } preyfile.close(); } //</editor-fold> Logger.getRootLogger().info("Job done"); Logger.getRootLogger().info( "================================================================================================="); } catch (Exception e) { Logger.getRootLogger().error(ExceptionUtils.getStackTrace(e)); throw e; } }
From source file:org.aksw.facete2.web.main.DebuggingTest.java
public static void main(String[] args) throws Exception { String qs; //http://localhost:7532/cache/sparql //String qs = "Select ?p_1 ?_c_ {{{ Select ?p_1 (Count(*) As ?_c_) {{ Select ?p_1 ?o_1 {{ Select ?p_1 ?o_1 {?s ?p_1 ?o_1 . Filter((?p_1 In (<http://dcat.cc/ontology/hasEndpoints>)))} Limit 1000 }} }} Group By ?p_1 }} Union {{ Select ?p_1 (Count(*) As ?_c_) {{ Select ?p_1 ?o_1 {{ Select ?p_1 ?o_1 {?s ?p_1 ?o_1 . Filter((?p_1 In (<http://dcat.cc/ontology/url>)))} Limit 1000 }} }} Group By ?p_1 }} Union {{ Select ?p_1 (Count(*) As ?_c_) {{ Select ?p_1 ?o_1 {{ Select ?p_1 ?o_1 {?s ?p_1 ?o_1 . Filter((?p_1 In (<http://www.w3.org/2000/01/rdf-schema#label>)))} Limit 1000 }} }} Group By ?p_1 }} Union {{ Select ?p_1 (Count(*) As ?_c_) {{ Select ?p_1 ?o_1 {{ Select ?p_1 ?o_1 {?s ?p_1 ?o_1 . Filter((?p_1 In (<http://dcat.cc/ontology/owner>)))} Limit 1000 }} }} Group By ?p_1 }} Union {{ Select ?p_1 (Count(*) As ?_c_) {{ Select ?p_1 ?o_1 {{ Select ?p_1 ?o_1 {?s ?p_1 ?o_1 . Filter((?p_1 In (<http://dcat.cc/ontology/hasDownloads>)))} Limit 1000 }} }} Group By ?p_1 }} Union {{ Select ?p_1 (Count(*) As ?_c_) {{ Select ?p_1 ?o_1 {{ Select ?p_1 ?o_1 {?s ?p_1 ?o_1 . Filter((?p_1 In (<http://dcat.cc/ontology/version>)))} Limit 1000 }} }} Group By ?p_1 }} Union {{ Select ?p_1 (Count(*) As ?_c_) {{ Select ?p_1 ?o_1 {{ Select ?p_1 ?o_1 {?s ?p_1 ?o_1 . Filter((?p_1 In (<http://www.w3.org/1999/02/22-rdf-syntax-ns#type>)))} Limit 1000 }} }} Group By ?p_1 }} Union {{ Select ?p_1 (Count(*) As ?_c_) {{ Select ?p_1 ?o_1 {{ Select ?p_1 ?o_1 {?s ?p_1 ?o_1 . Filter((?p_1 In (<http://dcat.cc/ontology/hasDefaultGraphs>)))} Limit 1000 }} }} Group By ?p_1 }} Union {{ Select ?p_1 (Count(*) As ?_c_) {{ Select ?p_1 ?o_1 {{ Select ?p_1 ?o_1 {?s ?p_1 ?o_1 . Filter((?p_1 In (<http://dcat.cc/ontology/groupId>)))} Limit 1000 }} }} Group By ?p_1 }} Union {{ Select ?p_1 (Count(*) As ?_c_) {{ Select ?p_1 ?o_1 {{ Select ?p_1 ?o_1 {?s ?p_1 ?o_1 . Filter((?p_1 In (<http://dcat.cc/ontology/artifactId>)))} Limit 1000 }} }} Group By ?p_1 }}} Limit 1000"; //String qs = "Select ?p_1 ?_c_ {{{ Select ?p_1 (Count(*) As ?_c_) {{ Select ?p_1 ?o_1 {{ Select ?p_1 ?o_1 {?s ?p_1 ?o_1 . Filter((?p_1 In (<http://dcat.cc/ontology/hasEndpoints>)))} Limit 1000 }} }} Group By ?p_1 }}} Limit 1000"; //qs = "Select ?p_1 ?_c_ {{{ Select ?p_1 (Count(*) As ?_c_) {{ Select ?p_1 ?o_1 {{ Select ?p_1 ?o_1 {?s ?p_1 ?o_1 . Filter((?p_1 In (<http://dcat.cc/ontology/hasEndpoints>)))} Limit 1000 }} }} Group By ?p_1 }} Union {{ Select ?p_1 (Count(*) As ?_c_) {{ Select ?p_1 ?o_1 {{ Select ?p_1 ?o_1 {?s ?p_1 ?o_1 . Filter((?p_1 In (<http://dcat.cc/ontology/url>)))} Limit 1000 }} }} Group By ?p_1 }} Union {{ Select ?p_1 (Count(*) As ?_c_) {{ Select ?p_1 ?o_1 {{ Select ?p_1 ?o_1 {?s ?p_1 ?o_1 . Filter((?p_1 In (<http://www.w3.org/2000/01/rdf-schema#label>)))} Limit 1000 }} }} Group By ?p_1 }} Union {{ Select ?p_1 (Count(*) As ?_c_) {{ Select ?p_1 ?o_1 {{ Select ?p_1 ?o_1 {?s ?p_1 ?o_1 . Filter((?p_1 In (<http://dcat.cc/ontology/owner>)))} Limit 1000 }} }} Group By ?p_1 }} Union {{ Select ?p_1 (Count(*) As ?_c_) {{ Select ?p_1 ?o_1 {{ Select ?p_1 ?o_1 {?s ?p_1 ?o_1 . Filter((?p_1 In (<http://dcat.cc/ontology/hasDownloads>)))} Limit 1000 }} }} Group By ?p_1 }} Union {{ Select ?p_1 (Count(*) As ?_c_) {{ Select ?p_1 ?o_1 {{ Select ?p_1 ?o_1 {?s ?p_1 ?o_1 . Filter((?p_1 In (<http://dcat.cc/ontology/version>)))} Limit 1000 }} }} Group By ?p_1 }} Union {{ Select ?p_1 (Count(*) As ?_c_) {{ Select ?p_1 ?o_1 {{ Select ?p_1 ?o_1 {?s ?p_1 ?o_1 . Filter((?p_1 In (<http://www.w3.org/1999/02/22-rdf-syntax-ns#type>)))} Limit 1000 }} }} Group By ?p_1 }} Union {{ Select ?p_1 (Count(*) As ?_c_) {{ Select ?p_1 ?o_1 {{ Select ?p_1 ?o_1 {?s ?p_1 ?o_1 . Filter((?p_1 In (<http://dcat.cc/ontology/hasDefaultGraphs>)))} Limit 1000 }} }} Group By ?p_1 }}}"; String lastWorking = "Select ?p_1 ?_c_ {{{ Select ?p_1 (Count(*) As ?_c_) {{ Select ?p_1 ?o_1 {{ Select ?p_1 ?o_1 {?s ?p_1 ?o_1 . Filter((?p_1 In (<http://dcat.cc/ontology/hasEndpoints>)))} Limit 1000 }} }} Group By ?p_1 }} Union {{ Select ?p_1 (Count(*) As ?_c_) {{ Select ?p_1 ?o_1 {{ Select ?p_1 ?o_1 {?s ?p_1 ?o_1 . Filter((?p_1 In (<http://dcat.cc/ontology/url>)))} Limit 1000 }} }} Group By ?p_1 }} Union {{ Select ?p_1 (Count(*) As ?_c_) {{ Select ?p_1 ?o_1 {{ Select ?p_1 ?o_1 {?s ?p_1 ?o_1 . Filter((?p_1 In (<http://www.w3.org/2000/01/rdf-schema#label>)))} Limit 1000 }} }} Group By ?p_1 }} Union {{ Select ?p_1 (Count(*) As ?_c_) {{ Select ?p_1 ?o_1 {{ Select ?p_1 ?o_1 {?s ?p_1 ?o_1 . Filter((?p_1 In (<http://dcat.cc/ontology/owner>)))} Limit 1000 }} }} Group By ?p_1 }} Union {{ Select ?p_1 (Count(*) As ?_c_) {{ Select ?p_1 ?o_1 {{ Select ?p_1 ?o_1 {?s ?p_1 ?o_1 . Filter((?p_1 In (<http://dcat.cc/ontology/hasDownloads>)))} Limit 1000 }} }} Group By ?p_1 }} Union {{ Select ?p_1 (Count(*) As ?_c_) {{ Select ?p_1 ?o_1 {{ Select ?p_1 ?o_1 {?s ?p_1 ?o_1 . Filter((?p_1 In (<http://dcat.cc/ontology/version>)))} Limit 1000 }} }} Group By ?p_1 }} Union {{ Select ?p_1 (Count(*) As ?_c_) {{ Select ?p_1 ?o_1 {{ Select ?p_1 ?o_1 {?s ?p_1 ?o_1 . Filter((?p_1 In (<http://www.w3.org/1999/02/22-rdf-syntax-ns#type>)))} Limit 1000 }} }} Group By ?p_1 }}}"; String firstNotWorking = "Select ?p_1 ?_c_ {{{ Select ?p_1 (Count(*) As ?_c_) {{ Select ?p_1 ?o_1 {{ Select ?p_1 ?o_1 {?s ?p_1 ?o_1 . Filter((?p_1 In (<http://dcat.cc/ontology/hasEndpoints>)))} Limit 1000 }} }} Group By ?p_1 }} Union {{ Select ?p_1 (Count(*) As ?_c_) {{ Select ?p_1 ?o_1 {{ Select ?p_1 ?o_1 {?s ?p_1 ?o_1 . Filter((?p_1 In (<http://dcat.cc/ontology/url>)))} Limit 1000 }} }} Group By ?p_1 }} Union {{ Select ?p_1 (Count(*) As ?_c_) {{ Select ?p_1 ?o_1 {{ Select ?p_1 ?o_1 {?s ?p_1 ?o_1 . Filter((?p_1 In (<http://www.w3.org/2000/01/rdf-schema#label>)))} Limit 1000 }} }} Group By ?p_1 }} Union {{ Select ?p_1 (Count(*) As ?_c_) {{ Select ?p_1 ?o_1 {{ Select ?p_1 ?o_1 {?s ?p_1 ?o_1 . Filter((?p_1 In (<http://dcat.cc/ontology/owner>)))} Limit 1000 }} }} Group By ?p_1 }} Union {{ Select ?p_1 (Count(*) As ?_c_) {{ Select ?p_1 ?o_1 {{ Select ?p_1 ?o_1 {?s ?p_1 ?o_1 . Filter((?p_1 In (<http://dcat.cc/ontology/hasDownloads>)))} Limit 1000 }} }} Group By ?p_1 }} Union {{ Select ?p_1 (Count(*) As ?_c_) {{ Select ?p_1 ?o_1 {{ Select ?p_1 ?o_1 {?s ?p_1 ?o_1 . Filter((?p_1 In (<http://dcat.cc/ontology/version>)))} Limit 1000 }} }} Group By ?p_1 }} Union {{ Select ?p_1 (Count(*) As ?_c_) {{ Select ?p_1 ?o_1 {{ Select ?p_1 ?o_1 {?s ?p_1 ?o_1 . Filter((?p_1 In (<http://www.w3.org/1999/02/22-rdf-syntax-ns#type>)))} Limit 1000 }} }} Group By ?p_1 }}}"; //qs = lastWorking; qs = firstNotWorking;// ww w . ja v a 2 s . co m System.out.println(qs.length()); //qs = "Select ?p_1 ?_c_ {{{ Select ?p_1 (Count(*) As ?_c_) {{ Select ?p_1 ?o_1 {{ Select ?p_1 ?o_1 {?s ?p_1 ?o_1 . Filter((?p_1 In (<http://dcat.cc/ontology/hasEndpoints>)))} Limit 1000 }} }} Group By ?p_1 }} Union {{ Select ?p_1 (Count(*) As ?_c_) {{ Select ?p_1 ?o_1 {{ Select ?p_1 ?o_1 {?s ?p_1 ?o_1 . Filter((?p_1 In (<http://dcat.cc/ontology/url>)))} Limit 1000 }} }} Group By ?p_1 }} Union {{ Select ?p_1 (Count(*) As ?_c_) {{ Select ?p_1 ?o_1 {{ Select ?p_1 ?o_1 {?s ?p_1 ?o_1 . Filter((?p_1 In (<http://www.w3.org/2000/01/rdf-schema#label>)))} Limit 1000 }} }} Group By ?p_1 }} Union {{ Select ?p_1 (Count(*) As ?_c_) {{ Select ?p_1 ?o_1 {{ Select ?p_1 ?o_1 {?s ?p_1 ?o_1 . Filter((?p_1 In (<http://dcat.cc/ontology/owner>)))} Limit 1000 }} }} Group By ?p_1 }} Union {{ Select ?p_1 (Count(*) As ?_c_) {{ Select ?p_1 ?o_1 {{ Select ?p_1 ?o_1 {?s ?p_1 ?o_1 . Filter((?p_1 In (<http://dcat.cc/ontology/hasDownloads>)))} Limit 1000 }} }} Group By ?p_1 }} Union {{ Select ?p_1 (Count(*) As ?_c_) {{ Select ?p_1 ?o_1 {{ Select ?p_1 ?o_1 {?s ?p_1 ?o_1 . Filter((?p_1 In (<http://dcat.cc/ontology/version>)))} Limit 1000 }} }} Group By ?p_1 }} Union {{ Select ?p_1 (Count(*) As ?_c_) {{ Select ?p_1 ?o_1 {{ Select ?p_1 ?o_1 {?s ?p_1 ?o_1 . Filter((?p_1 In (<http://www.w3.org/1999/02/22-rdf-syntax-ns#type>)))} Limit 1000 }} }} Group By ?p_1 }}}"; //String qs = "Select * { ?s ?p ?o }"; QueryEngineHTTP qe = new QueryEngineHTTP("http://localhost:7533/api/sparql", qs); ResultSet rs = qe.execSelect(); String str = ResultSetFormatter.asText(rs); System.out.println(str); }
From source file:Main.java
public static String capitalize(String s) { if (s.length() == 0) { return s; }/*ww w.j a v a 2 s .co m*/ return s.substring(0, 1).toUpperCase() + s.substring(1).toLowerCase(); }
From source file:Main.java
public static boolean isJavaIdentifier(String s) { if (s.length() == 0 || !Character.isJavaIdentifierStart(s.charAt(0))) { return false; }// ww w.ja va 2 s .c o m for (int i = 1; i < s.length(); i++) { if (!Character.isJavaIdentifierPart(s.charAt(i))) { return false; } } return true; }
From source file:Main.java
private static String removeLastChar(String str) { return str.substring(0, str.length() - 1); }
From source file:Main.java
public static boolean containsOnlyNumbers(String str) { for (int i = 0; i < str.length(); i++) { if (!Character.isDigit(str.charAt(i))) return false; }//from www.ja v a 2s . c om return true; }
From source file:Main.java
public static String compare(String st1, String st2) { if (st1.length() > st2.length()) { return st1; } else {/*from ww w .j a v a 2 s.c o m*/ return st2; } }