List of usage examples for java.io BufferedReader BufferedReader
public BufferedReader(Reader in)
From source file:com.l2jfree.loginserver.tools.L2GameServerRegistrar.java
/** * Launches the interactive game server registration. * /* ww w . ja v a 2 s .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:de.inpiraten.jdemocrator.TAN.generator.TANGenerator.java
public static void main(String[] args) { //Intro message GPL.printLicenseNotice();/* www . j a v a2s .c o m*/ System.out.println("\njDemocrator Authority TAN Generator"); System.out.println("===================================\n"); System.out.println("This programm will generate voting TANs for a semi-online secrete voting."); try { //Initialize TAN Generator TANGenerator G = new TANGenerator(new BufferedReader(new InputStreamReader(System.in))); //Randomly generate master TANs G.generateMasterTANs(); //Generate TANs from master TANs TAN[][] tans = new TAN[G.event.numberOfElections][]; for (int i = 0; i < tans.length; i++) { try { tans[i] = G.event.TANType.generateFromMasterTAN(G.masterTAN[i], G.event, G.event.numberOfVoters); } catch (NoSuchAlgorithmException e) { System.out.println("The Key Derivation function described as " + G.event.keyDerivationFunction + " is not supported. Exiting."); System.exit(2); } catch (InvalidKeySpecException e) { System.out.println("Invalied Key Spec Exception while generating TANs. Exiting."); System.exit(3); } } //Mix up the TANs for (int i = 0; i < tans.length; i++) { shuffle(tans[i]); } //TODO Write the TANs and master TANs to (printable) files } catch (IOException e) { System.out.println("An I/O Error occured"); System.exit(1); } }
From source file:cc.twittertools.util.ExtractSubcollection.java
@SuppressWarnings("static-access") public static void main(String[] args) throws Exception { Options options = new Options(); options.addOption(OptionBuilder.withArgName("dir").hasArg().withDescription("source collection directory") .create(COLLECTION_OPTION)); options.addOption(//w w w. j a va 2s . co m OptionBuilder.withArgName("file").hasArg().withDescription("list of tweetids").create(ID_OPTION)); 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(COLLECTION_OPTION) || !cmdline.hasOption(ID_OPTION)) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp(ExtractSubcollection.class.getName(), options); System.exit(-1); } String collectionPath = cmdline.getOptionValue(COLLECTION_OPTION); LongOpenHashSet tweetids = new LongOpenHashSet(); File tweetidsFile = new File(cmdline.getOptionValue(ID_OPTION)); if (!tweetidsFile.exists()) { System.err.println("Error: " + tweetidsFile + " does not exist!"); System.exit(-1); } LOG.info("Reading tweetids from " + tweetidsFile); FileInputStream fin = new FileInputStream(tweetidsFile); BufferedReader br = new BufferedReader(new InputStreamReader(fin)); String s; while ((s = br.readLine()) != null) { tweetids.add(Long.parseLong(s)); } br.close(); fin.close(); LOG.info("Read " + tweetids.size() + " tweetids."); File file = new File(collectionPath); if (!file.exists()) { System.err.println("Error: " + file + " does not exist!"); System.exit(-1); } PrintStream out = new PrintStream(System.out, true, "UTF-8"); StatusStream stream = new JsonStatusCorpusReader(file); Status status; while ((status = stream.next()) != null) { if (tweetids.contains(status.getId())) { out.println(status.getJsonObject().toString()); } } stream.close(); out.close(); }
From source file:org.mzd.shap.spring.cli.ConfigSetup.java
public static void main(String[] args) { // check args if (args.length != 1) { exitOnError(1, null);/*w ww .j a v a2 s . c o m*/ } // check file existance File analyzerXML = new File(args[0]); if (!analyzerXML.exists()) { exitOnError(1, "'" + analyzerXML.getPath() + "' did not exist\n"); } // prompt user whether existing data should be purged boolean isPurged = false; String ormContext = null; BufferedReader br = new BufferedReader(new InputStreamReader(System.in)); try { System.out.println("\nDo you wish to purge the database before running setup?"); System.out.println("WARNING: all existing data in SHAP will be lost!"); System.out.println("Really purge? yes/[NO]"); String ans = br.readLine(); if (ans.toLowerCase().equals("yes")) { System.out.println("Purging enabled"); ormContext = "orm-purge-context.xml"; isPurged = true; } else { System.out.println("Purging disabled"); ormContext = "orm-context.xml"; } } catch (IOException ex) { throw new RuntimeException(ex); } // run tool try { // Using a generic application context since we're referencing // both classpath and filesystem resources. GenericApplicationContext ctx = new GenericApplicationContext(); XmlBeanDefinitionReader xmlReader = new XmlBeanDefinitionReader(ctx); xmlReader.loadBeanDefinitions(new ClassPathResource("datasource-context.xml"), new ClassPathResource(ormContext), new FileSystemResource(analyzerXML)); ctx.refresh(); /* * Create an base admin user. */ if (isPurged) { //only attempted if we've wiped the old database. RoleDao roleDao = (RoleDao) ctx.getBean("roleDao"); Role adminRole = roleDao.saveOrUpdate(new Role("admin", "ROLE_ADMIN")); Role userRole = roleDao.saveOrUpdate(new Role("user", "ROLE_USER")); UserDao userDao = (UserDao) ctx.getBean("userDao"); userDao.saveOrUpdate(new User("admin", "admin", "shap01", adminRole, userRole)); } /* * Create some predefined analyzers. Users should have modified * the configuration file to suit their environment. */ AnnotatorDao annotatorDao = (AnnotatorDao) ctx.getBean("annotatorDao"); DetectorDao detectorDao = (DetectorDao) ctx.getBean("detectorDao"); ConfigSetup config = (ConfigSetup) ctx.getBean("configuration"); for (Annotator an : config.getAnnotators()) { System.out.println("Adding annotator: " + an.getName()); annotatorDao.saveOrUpdate(an); } for (Detector dt : config.getDetectors()) { System.out.println("Adding detector: " + dt.getName()); detectorDao.saveOrUpdate(dt); } System.exit(0); } catch (Throwable t) { System.err.println(t.getMessage()); System.exit(1); } }
From source file:com.genentech.struchk.OEMDLPercieveChecker.java
public static void main(String[] args) throws ParseException, JDOMException, IOException { // create command line Options object Options options = new Options(); Option opt = new Option("i", true, "input file [.ism,.sdf,...]"); opt.setRequired(true);/*from ww w. j a v a2 s .c o m*/ options.addOption(opt); opt = new Option("o", true, "output file"); opt.setRequired(false); options.addOption(opt); opt = new Option("d", false, "debug: wait for user to press key at startup."); opt.setRequired(false); options.addOption(opt); CommandLineParser parser = new PosixParser(); CommandLine cmd = null; try { cmd = parser.parse(options, args); } catch (Exception e) { System.err.println(e.getMessage()); exitWithHelp(options); } args = cmd.getArgs(); if (cmd.hasOption("d")) { System.err.println("Start debugger and press return:"); new BufferedReader(new InputStreamReader(System.in)).readLine(); } if (args.length != 0) { exitWithHelp(options); } String inFile = cmd.getOptionValue("i"); String outFile = cmd.getOptionValue("o"); OEMDLPercieveChecker checker = null; try { checker = new OEMDLPercieveChecker(); oemolostream out = new oemolostream(outFile); oemolistream in = new oemolistream(inFile); OEGraphMol mol = new OEGraphMol(); while (oechem.OEReadMolecule(in, mol)) { if (!checker.checkMol(mol)) oechem.OEWriteMolecule(out, mol); } checker.delete(); in.close(); in.delete(); out.close(); out.delete(); } catch (Exception e) { throw new Error(e); } System.err.println("Done:"); }
From source file:ca.uwaterloo.cpami.mahout.matrix.utils.GramSchmidt.java
public static void main(String[] args) throws IOException { //final Configuration conf = new Configuration(); //final FileSystem fs = FileSystem.get(conf); //final SequenceFile.Reader reader = new SequenceFile.Reader(fs, // new Path("R1.dat"), conf); //IntWritable key = new IntWritable(); //VectorWritable vec = new VectorWritable(); Matrix mat = new SparseMatrix(1500, 100); //SparseRealMatrix mat2 = new OpenMapRealMatrix(12419,1500 ); BufferedReader reader = new BufferedReader(new FileReader("R.3.csv")); String line = null;//from ww w.j av a 2 s. co m while ((line = reader.readLine()) != null) { String[] parts = line.split(","); mat.set(Integer.parseInt(parts[0]), Integer.parseInt(parts[1]), Double.parseDouble(parts[2])); /* Vector v = vec.get(); int i=0; Iterator<Vector.Element> itr = v.iterateNonZero(); while(itr.hasNext()){ double elem = itr.next().get(); if(elem !=0) mat2.setEntry(i, key.get(), elem); i++; } */ } //mat = mat.transpose(); System.out.println(mat.viewColumn(0).isDense()); System.out.println(mat.viewRow(0).isDense()); mat = mat.transpose(); GramSchmidt.orthonormalizeColumns(mat); /* System.out.println("started QR"); System.out.println(Runtime.getRuntime().maxMemory()); System.out.println(Runtime.getRuntime().maxMemory()-Runtime.getRuntime().freeMemory()); QRDecomposition qr = new QRDecomposition(mat2); System.out.println(qr.getQ().getColumnDimension()); System.out.println(qr.getQ().getRowDimension()); */ //mat = mat.transpose(); //storeSparseColumns(mat); //for (int i = 0; i < 10; i++) { // System.out.println(mat.viewRow(i).getNumNondefaultElements()); //} }
From source file:cc.twittertools.util.VerifySubcollection.java
@SuppressWarnings("static-access") public static void main(String[] args) throws Exception { Options options = new Options(); options.addOption(OptionBuilder.withArgName("dir").hasArg().withDescription("source collection directory") .create(COLLECTION_OPTION)); options.addOption(//from w w w. j a v a 2s .com OptionBuilder.withArgName("file").hasArg().withDescription("list of tweetids").create(ID_OPTION)); 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(COLLECTION_OPTION) || !cmdline.hasOption(ID_OPTION)) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp(ExtractSubcollection.class.getName(), options); System.exit(-1); } String collectionPath = cmdline.getOptionValue(COLLECTION_OPTION); LongOpenHashSet tweetids = new LongOpenHashSet(); File tweetidsFile = new File(cmdline.getOptionValue(ID_OPTION)); if (!tweetidsFile.exists()) { System.err.println("Error: " + tweetidsFile + " does not exist!"); System.exit(-1); } LOG.info("Reading tweetids from " + tweetidsFile); FileInputStream fin = new FileInputStream(tweetidsFile); BufferedReader br = new BufferedReader(new InputStreamReader(fin)); String s; while ((s = br.readLine()) != null) { tweetids.add(Long.parseLong(s)); } br.close(); fin.close(); LOG.info("Read " + tweetids.size() + " tweetids."); File file = new File(collectionPath); if (!file.exists()) { System.err.println("Error: " + file + " does not exist!"); System.exit(-1); } LongOpenHashSet seen = new LongOpenHashSet(); TreeMap<Long, String> tweets = Maps.newTreeMap(); PrintStream out = new PrintStream(System.out, true, "UTF-8"); StatusStream stream = new JsonStatusCorpusReader(file); Status status; int cnt = 0; while ((status = stream.next()) != null) { if (!tweetids.contains(status.getId())) { LOG.error("tweetid " + status.getId() + " doesn't belong in collection"); continue; } if (seen.contains(status.getId())) { LOG.error("tweetid " + status.getId() + " already seen!"); continue; } tweets.put(status.getId(), status.getJsonObject().toString()); seen.add(status.getId()); cnt++; } LOG.info("total of " + cnt + " tweets in subcollection."); for (Map.Entry<Long, String> entry : tweets.entrySet()) { out.println(entry.getValue()); } stream.close(); out.close(); }
From source file:org.ipinfodb.IpInfoDbClient.java
public static void main(String[] args) throws IOException { if (args.length < 3 || args.length > 4) { System.out.println("Usage: org.ipinfodb.IpInfoDbClient MODE API_KEY [IP_ADDRESS]\n" + "MODE can be either 'ip-country' or 'ip-city'.\n" + "If you don't have an API_KEY yet, you can get one for free by registering at http://www.ipinfodb.com/register.php."); return;//from w ww. j ava 2s . c o m } //Code for Reading the multiple ip addresses from a given txt file. File inputLogFilePath = new File(args[1]); FileReader fr = new FileReader(inputLogFilePath); BufferedReader br = new BufferedReader(fr); String logLine; /*File outputFile=new File("C:/Users/Intelligrape/Desktop/New_Sample_29042014.txt"); // if file doesnt exists, then create it if (!outputFile.exists()) { outputFile.createNewFile(); } FileWriter fw = new FileWriter(outputFile,true); BufferedWriter bw = new BufferedWriter(fw); bw.write("S.no, IPAddress, Country, Region, City, Zipcode"); bw.newLine();*/ try { Class.forName("com.mysql.jdbc.Driver"); System.out.println("Driver found"); } catch (ClassNotFoundException e) { System.out.println("Driver not found: " + e); } String url_db = "jdbc:mysql://mysqldb.c7zitrf2gguq.us-east-1.rds.amazonaws.com/matse?user=shagun&password=shagun001"; Connection con = null; int insertCounter = 0; int count = 1; while ((logLine = br.readLine()) != null) { String mode = args[2]; String apiKey = args[3]; String url = "http://api.ipinfodb.com/v3/" + mode + "/?format=json&key=" + apiKey; String[] split = logLine.split(","); String ip = split[3]; url += "&ip=" + ip; try { HttpGet request = new HttpGet(url); HttpResponse response = HTTP_CLIENT.execute(request, new BasicHttpContext()); if (response.getStatusLine().getStatusCode() != HttpStatus.SC_OK) { throw new RuntimeException("IpInfoDb response is " + response.getStatusLine()); } String responseBody = EntityUtils.toString(response.getEntity()); IpCityResponse ipCityResponse = MAPPER.readValue(responseBody, IpCityResponse.class); if ("OK".equals(ipCityResponse.getStatusCode())) { //System.out.print(count+", "+ip+", "+ipCityResponse.getCountryCode() + ", " + ipCityResponse.getRegionName() + ", " + ipCityResponse.getCityName() + ", " + ipCityResponse.zipCode+ ", " + ipCityResponse.countryName + ", " + ipCityResponse.latitude + ", " + ipCityResponse.longitude + ", " + ipCityResponse.timeZone); //bw.write(count+", "+ip+", "+ipCityResponse.getCountryCode() + ", " + ipCityResponse.getRegionName() + ", " + ipCityResponse.getCityName() + ", " + ipCityResponse.zipCode + ", " + ipCityResponse.countryName + ", " + ipCityResponse.latitude + ", " + ipCityResponse.longitude + ", " + ipCityResponse.timeZone); try { con = DriverManager.getConnection(url_db); //System.out.println("Connected successfully"); Statement stmt = con.createStatement(); //System.out.println(logLine); //System.out.println(split.length); int result = stmt.executeUpdate("INSERT INTO LOGDATA1 VALUES('" + split[0] + "','" + split[1].trim() + "','" + split[2] + "','" + split[3] + "','" + split[4] + "','" + ipCityResponse.statusCode + "','" + ipCityResponse.countryCode + "','" + ipCityResponse.countryName + "','" + ipCityResponse.regionName + "','" + ipCityResponse.cityName + "','" + ipCityResponse.zipCode + "','" + ipCityResponse.latitude + "','" + ipCityResponse.longitude + "','" + ipCityResponse.timeZone + "')"); ++insertCounter; con.close(); System.out.println(insertCounter); } catch (SQLException e) { System.out.println("something wrong in the connection string: " + e); } } else { System.out.print("API status message is '" + ipCityResponse.getStatusMessage() + "'"); } } finally { //HTTP_CLIENT.getConnectionManager().shutdown(); } ++count; } HTTP_CLIENT.getConnectionManager().shutdown(); }
From source file:DIA_Umpire_Quant.DIA_Umpire_ExtLibSearch.java
/** * @param args the command line arguments *///from w ww . 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 targeted re-extraction analysis using external library (version: " + UmpireInfo.GetInstance().Version + ")"); if (args.length != 1) { System.out.println( "command format error, the correct format should be: java -jar -Xmx10G DIA_Umpire_ExtLibSearch.jar diaumpire_module.params"); return; } try { ConsoleLogger.SetConsoleLogger(Level.INFO); ConsoleLogger.SetFileLogger(Level.DEBUG, FilenameUtils.getFullPath(args[0]) + "diaumpire_extlibsearch.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; String ExternalLibPath = ""; String ExternalLibDecoyTag = "DECOY"; float ExtProbThreshold = 0.99f; float RTWindow_Ext = -1f; 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 "Fasta": { tandemPara.FastaPath = value; break; } case "DecoyPrefix": { if (!"".equals(value)) { tandemPara.DecoyPrefix = value; } break; } case "ExternalLibPath": { ExternalLibPath = value; break; } case "ExtProbThreshold": { ExtProbThreshold = 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; } } } } //</editor-fold> //Initialize PTM manager using compomics library PTMManager.GetInstance(); //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); } //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()); } for (File fileEntry : AssignFiles.values()) { String mzXMLFile = fileEntry.getAbsolutePath(); if (mzXMLFile.toLowerCase().endsWith(".mzxml") | mzXMLFile.toLowerCase().endsWith(".mzml")) { DIAPack DiaFile = new DIAPack(mzXMLFile, NoCPUs); 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 + "...."); //If the serialization file for ID file existed if (DiaFile.ReadSerializedLCMSID()) { DiaFile.IDsummary.ReduceMemoryUsage(); DiaFile.IDsummary.FastaPath = tandemPara.FastaPath; FileList.add(DiaFile); } } } //<editor-fold defaultstate="collapsed" desc="Targeted re-extraction using external library"> //External library search Logger.getRootLogger().info("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, ExtProbThreshold, 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> Logger.getRootLogger().info("Job done"); Logger.getRootLogger().info( "================================================================================================="); }
From source file:edu.cmu.lti.oaqa.apps.Client.java
public static void main(String args[]) { BufferedReader inp = new BufferedReader(new InputStreamReader(System.in)); Options opt = new Options(); Option o = new Option(PORT_SHORT_PARAM, PORT_LONG_PARAM, true, PORT_DESC); o.setRequired(true);/*w ww. j a v a 2 s . c om*/ opt.addOption(o); o = new Option(HOST_SHORT_PARAM, HOST_LONG_PARAM, true, HOST_DESC); o.setRequired(true); opt.addOption(o); opt.addOption(K_SHORT_PARAM, K_LONG_PARAM, true, K_DESC); opt.addOption(R_SHORT_PARAM, R_LONG_PARAM, true, R_DESC); opt.addOption(QUERY_TIME_SHORT_PARAM, QUERY_TIME_LONG_PARAM, true, QUERY_TIME_DESC); opt.addOption(RET_OBJ_SHORT_PARAM, RET_OBJ_LONG_PARAM, false, RET_OBJ_DESC); opt.addOption(RET_EXTERN_ID_SHORT_PARAM, RET_EXTERN_ID_LONG_PARAM, false, RET_EXTERN_ID_DESC); CommandLineParser parser = new org.apache.commons.cli.GnuParser(); try { CommandLine cmd = parser.parse(opt, args); String host = cmd.getOptionValue(HOST_SHORT_PARAM); String tmp = null; tmp = cmd.getOptionValue(PORT_SHORT_PARAM); int port = -1; try { port = Integer.parseInt(tmp); } catch (NumberFormatException e) { Usage("Port should be integer!"); } boolean retObj = cmd.hasOption(RET_OBJ_SHORT_PARAM); boolean retExternId = cmd.hasOption(RET_EXTERN_ID_SHORT_PARAM); String queryTimeParams = cmd.getOptionValue(QUERY_TIME_SHORT_PARAM); if (null == queryTimeParams) queryTimeParams = ""; SearchType searchType = SearchType.kKNNSearch; int k = 0; double r = 0; if (cmd.hasOption(K_SHORT_PARAM)) { if (cmd.hasOption(R_SHORT_PARAM)) { Usage("Range search is not allowed if the KNN search is specified!"); } tmp = cmd.getOptionValue(K_SHORT_PARAM); try { k = Integer.parseInt(tmp); } catch (NumberFormatException e) { Usage("K should be integer!"); } searchType = SearchType.kKNNSearch; } else if (cmd.hasOption(R_SHORT_PARAM)) { if (cmd.hasOption(K_SHORT_PARAM)) { Usage("KNN search is not allowed if the range search is specified!"); } searchType = SearchType.kRangeSearch; tmp = cmd.getOptionValue(R_SHORT_PARAM); try { r = Double.parseDouble(tmp); } catch (NumberFormatException e) { Usage("The range value should be numeric!"); } } else { Usage("One has to specify either range or KNN-search parameter"); } String separator = System.getProperty("line.separator"); StringBuffer sb = new StringBuffer(); String s; while ((s = inp.readLine()) != null) { sb.append(s); sb.append(separator); } String queryObj = sb.toString(); try { TTransport transport = new TSocket(host, port); transport.open(); TProtocol protocol = new TBinaryProtocol(transport); QueryService.Client client = new QueryService.Client(protocol); if (!queryTimeParams.isEmpty()) client.setQueryTimeParams(queryTimeParams); List<ReplyEntry> res = null; long t1 = System.nanoTime(); if (searchType == SearchType.kKNNSearch) { System.out.println(String.format("Running a %d-NN search", k)); res = client.knnQuery(k, queryObj, retExternId, retObj); } else { System.out.println(String.format("Running a range search (r=%g)", r)); res = client.rangeQuery(r, queryObj, retExternId, retObj); } long t2 = System.nanoTime(); System.out.println(String.format("Finished in %g ms", (t2 - t1) / 1e6)); for (ReplyEntry e : res) { System.out.println(String.format("id=%d dist=%g %s", e.getId(), e.getDist(), retExternId ? "externId=" + e.getExternId() : "")); if (retObj) System.out.println(e.getObj()); } transport.close(); // Close transport/socket ! } catch (TException te) { System.err.println("Apache Thrift exception: " + te); te.printStackTrace(); } } catch (ParseException e) { Usage("Cannot parse arguments"); } catch (Exception e) { e.printStackTrace(); System.exit(1); } }