List of usage examples for java.lang Boolean parseBoolean
public static boolean parseBoolean(String s)
From source file:com.hpe.nv.samples.basic.BasicNVTest.java
public static void main(String[] args) { try {/* ww w. j ava 2s .co m*/ // program arguments Options options = new Options(); options.addOption("i", "server-ip", true, "[mandatory] NV Test Manager IP"); options.addOption("o", "server-port", true, "[mandatory] NV Test Manager port"); options.addOption("u", "username", true, "[mandatory] NV username"); options.addOption("w", "password", true, "[mandatory] NV password"); options.addOption("e", "ssl", true, "[optional] Pass true to use SSL. Default: false"); options.addOption("y", "proxy", true, "[optional] Proxy server host:port"); options.addOption("b", "browser", true, "[optional] The browser for which the Selenium WebDriver is built. Possible values: Chrome and Firefox. Default: Firefox"); options.addOption("d", "debug", true, "[optional] Pass true to view console debug messages during execution. Default: false"); options.addOption("h", "help", false, "[optional] Generates and prints help information"); // parse and validate the command line arguments CommandLineParser parser = new DefaultParser(); CommandLine line = parser.parse(options, args); if (line.hasOption("help")) { // print help if help argument is passed HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("BasicNVTest.java", options); return; } if (line.hasOption("server-ip")) { serverIp = line.getOptionValue("server-ip"); if (serverIp.equals("0.0.0.0")) { throw new Exception( "Please replace the server IP argument value (0.0.0.0) with your NV Test Manager IP"); } } else { throw new Exception("Missing argument -i/--server-ip <serverIp>"); } if (line.hasOption("server-port")) { serverPort = Integer.parseInt(line.getOptionValue("server-port")); } else { throw new Exception("Missing argument -o/--server-port <serverPort>"); } if (line.hasOption("username")) { username = line.getOptionValue("username"); } else { throw new Exception("Missing argument -u/--username <username>"); } if (line.hasOption("password")) { password = line.getOptionValue("password"); } else { throw new Exception("Missing argument -w/--password <password>"); } if (line.hasOption("ssl")) { ssl = Boolean.parseBoolean(line.getOptionValue("ssl")); } if (line.hasOption("proxy")) { proxySetting = line.getOptionValue("proxy"); } if (line.hasOption("browser")) { browser = line.getOptionValue("browser"); } else { browser = "Firefox"; } if (line.hasOption("debug")) { debug = Boolean.parseBoolean(line.getOptionValue("debug")); } String newLine = System.getProperty("line.separator"); String testDescription = "*** This sample demonstrates the use of the most basic NV methods. ***" + newLine + "*** ***" + newLine + "*** First, the sample creates a TestManager object and initializes it. ***" + newLine + "*** The sample starts an NV test over an emulated \"3G Busy\" network. ***" + newLine + "*** (\"3G Busy\" is one of NV's built-in network profiles. A network profile specifies the ***" + newLine + "*** network traffic behavior, including latency, packet loss, and incoming/outgoing bandwidth. ***" + newLine + "*** Network profiles are used to emulate traffic over real-world networks.) ***" + newLine + "*** ***" + newLine + "*** Next, the sample navigates to the home page in the HPE Network Virtualization website ***" + newLine + "*** using the Selenium WebDriver. ***" + newLine + "*** ***" + newLine + "*** Finally, the sample stops the NV test. ***" + newLine + "*** ***" + newLine + "*** You can view the actual steps of this sample in the BasicNVTest.java file. ***" + newLine; // print the sample's description System.out.println(testDescription); // start console spinner if (!debug) { spinner = new Thread(new Spinner()); spinner.start(); } // sample execution steps /***** Part 1 - Create a TestManager object and initialize it *****/ printPartDescription("\b------ Part 1 - Create a TestManager object and initialize it"); initTestManager(); printPartSeparator(); /***** Part 2 - Start the NV test with the "3G Busy" network scenario *****/ printPartDescription("------ Part 2 - Start the NV test with the \"3G Busy\" network scenario"); startTest(); testRunning = true; printPartSeparator(); /***** Part 3 - Navigate to the HPE Network Virtualization website *****/ printPartDescription("------ Part 3 - Navigate to the HPE Network Virtualization website"); buildSeleniumWebDriver(); seleniumNavigateToPage(); driverCloseAndQuit(); printPartSeparator(); /***** Part 4 - Stop the NV test *****/ printPartDescription("------ Part 4 - Stop the NV test"); stopTest(); testRunning = false; printPartSeparator(); doneCallback(); } catch (Exception e) { try { handleError(e.getMessage()); } catch (Exception e2) { System.out.println("Error occurred: " + e2.getMessage()); } } }
From source file:DIA_Umpire_SE.DIA_Umpire_SE.java
/** * @param args the command line arguments DIA_Umpire parameterfile *///from w w w. j a va 2 s . c o m public static void main(String[] args) throws InterruptedException, FileNotFoundException, ExecutionException, IOException, ParserConfigurationException, DataFormatException, SAXException, Exception { System.out.println( "================================================================================================="); System.out.println( "DIA-Umpire singal extraction analysis (version: " + UmpireInfo.GetInstance().Version + ")"); if (args.length < 2 || args.length > 3) { System.out.println( "command format error, the correct format is: java -jar -Xmx8G DIA_Umpire_SE.jar mzMXL_file diaumpire_se.params"); System.out.println( "To fix DIA setting, use : java -jar -Xmx8G DIA_Umpire_SE.jar mzMXL_file diaumpire_se.params -f"); return; } try { //Define logger level for console ConsoleLogger.SetConsoleLogger(Level.INFO); //Define logger level and file path for text log file ConsoleLogger.SetFileLogger(Level.DEBUG, FilenameUtils.getFullPath(args[0]) + "diaumpire_se.log"); } catch (Exception e) { } boolean Fix = false; boolean Resume = false; if (args.length == 3 && args[2].equals("-f")) { Fix = true; } String parameterfile = args[1]; String MSFilePath = args[0]; Logger.getRootLogger().info("Version: " + UmpireInfo.GetInstance().Version); Logger.getRootLogger().info("Parameter file:" + parameterfile); Logger.getRootLogger().info("Spectra file:" + MSFilePath); BufferedReader reader = new BufferedReader(new FileReader(parameterfile)); String line = ""; InstrumentParameter param = new InstrumentParameter(InstrumentParameter.InstrumentType.TOF5600); param.DetermineBGByID = false; param.EstimateBG = true; int NoCPUs = 2; SpectralDataType.DataType dataType = SpectralDataType.DataType.DIA_F_Window; String WindowType = ""; int WindowSize = 25; ArrayList<XYData> WindowList = new ArrayList<>(); boolean ExportPrecursorPeak = false; boolean ExportFragmentPeak = false; //<editor-fold defaultstate="collapsed" desc="Read parameter file"> while ((line = reader.readLine()) != null) { Logger.getRootLogger().info(line); if (!"".equals(line) && !line.startsWith("#")) { //System.out.println(line); if (line.equals("==window setting begin")) { while (!(line = reader.readLine()).equals("==window setting end")) { if (!"".equals(line)) { WindowList.add(new XYData(Float.parseFloat(line.split("\t")[0]), Float.parseFloat(line.split("\t")[1]))); } } continue; } if (line.split("=").length < 2) { continue; } String type = line.split("=")[0].trim(); if (type.startsWith("para.")) { type = type.replace("para.", "SE."); } String value = line.split("=")[1].trim(); switch (type) { case "Thread": { NoCPUs = Integer.parseInt(value); break; } case "ExportPrecursorPeak": { ExportPrecursorPeak = Boolean.parseBoolean(value); break; } case "ExportFragmentPeak": { ExportFragmentPeak = Boolean.parseBoolean(value); break; } //<editor-fold defaultstate="collapsed" desc="instrument parameters"> case "RPmax": { param.PrecursorRank = Integer.parseInt(value); break; } case "RFmax": { param.FragmentRank = Integer.parseInt(value); break; } case "CorrThreshold": { param.CorrThreshold = Float.parseFloat(value); break; } case "DeltaApex": { param.ApexDelta = Float.parseFloat(value); break; } case "RTOverlap": { param.RTOverlapThreshold = Float.parseFloat(value); break; } case "BoostComplementaryIon": { param.BoostComplementaryIon = Boolean.parseBoolean(value); break; } case "AdjustFragIntensity": { param.AdjustFragIntensity = Boolean.parseBoolean(value); break; } case "SE.MS1PPM": { param.MS1PPM = Float.parseFloat(value); break; } case "SE.MS2PPM": { param.MS2PPM = Float.parseFloat(value); break; } case "SE.SN": { param.SNThreshold = Float.parseFloat(value); break; } case "SE.MS2SN": { param.MS2SNThreshold = Float.parseFloat(value); break; } case "SE.MinMSIntensity": { param.MinMSIntensity = Float.parseFloat(value); break; } case "SE.MinMSMSIntensity": { param.MinMSMSIntensity = Float.parseFloat(value); break; } case "SE.MinRTRange": { param.MinRTRange = Float.parseFloat(value); break; } case "SE.MaxNoPeakCluster": { param.MaxNoPeakCluster = Integer.parseInt(value); param.MaxMS2NoPeakCluster = Integer.parseInt(value); break; } case "SE.MinNoPeakCluster": { param.MinNoPeakCluster = Integer.parseInt(value); param.MinMS2NoPeakCluster = Integer.parseInt(value); break; } case "SE.MinMS2NoPeakCluster": { param.MinMS2NoPeakCluster = Integer.parseInt(value); break; } case "SE.MaxCurveRTRange": { param.MaxCurveRTRange = Float.parseFloat(value); break; } case "SE.Resolution": { param.Resolution = Integer.parseInt(value); break; } case "SE.RTtol": { param.RTtol = Float.parseFloat(value); break; } case "SE.NoPeakPerMin": { param.NoPeakPerMin = Integer.parseInt(value); break; } case "SE.StartCharge": { param.StartCharge = Integer.parseInt(value); break; } case "SE.EndCharge": { param.EndCharge = Integer.parseInt(value); break; } case "SE.MS2StartCharge": { param.MS2StartCharge = Integer.parseInt(value); break; } case "SE.MS2EndCharge": { param.MS2EndCharge = Integer.parseInt(value); break; } case "SE.NoMissedScan": { param.NoMissedScan = Integer.parseInt(value); break; } case "SE.Denoise": { param.Denoise = Boolean.valueOf(value); break; } case "SE.EstimateBG": { param.EstimateBG = Boolean.valueOf(value); break; } case "SE.RemoveGroupedPeaks": { param.RemoveGroupedPeaks = Boolean.valueOf(value); break; } case "SE.MinFrag": { param.MinFrag = Integer.parseInt(value); break; } case "SE.IsoPattern": { param.IsoPattern = Float.valueOf(value); break; } case "SE.StartRT": { param.startRT = Float.valueOf(value); break; } case "SE.EndRT": { param.endRT = Float.valueOf(value); break; } case "SE.RemoveGroupedPeaksRTOverlap": { param.RemoveGroupedPeaksRTOverlap = Float.valueOf(value); break; } case "SE.RemoveGroupedPeaksCorr": { param.RemoveGroupedPeaksCorr = Float.valueOf(value); break; } case "SE.MinMZ": { param.MinMZ = Float.valueOf(value); break; } case "SE.MinPrecursorMass": { param.MinPrecursorMass = Float.valueOf(value); break; } case "SE.MaxPrecursorMass": { param.MaxPrecursorMass = Float.valueOf(value); break; } case "SE.IsoCorrThreshold": { param.IsoCorrThreshold = Float.valueOf(value); break; } case "SE.MassDefectFilter": { param.MassDefectFilter = Boolean.parseBoolean(value); break; } case "SE.MassDefectOffset": { param.MassDefectOffset = Float.valueOf(value); break; } //</editor-fold>//</editor-fold> case "WindowType": { WindowType = value; switch (WindowType) { case "SWATH": { dataType = SpectralDataType.DataType.DIA_F_Window; break; } case "V_SWATH": { dataType = SpectralDataType.DataType.DIA_V_Window; break; } case "MSX": { dataType = SpectralDataType.DataType.MSX; break; } case "MSE": { dataType = SpectralDataType.DataType.MSe; break; } } break; } case "WindowSize": { WindowSize = Integer.parseInt(value); break; } } } } //</editor-fold> try { File MSFile = new File(MSFilePath); if (MSFile.exists()) { long time = System.currentTimeMillis(); Logger.getRootLogger().info( "================================================================================================="); Logger.getRootLogger().info("Processing " + MSFilePath + "...."); //Initialize a DIA file data structure DIAPack DiaFile = new DIAPack(MSFile.getAbsolutePath(), NoCPUs); DiaFile.Resume = Resume; DiaFile.SetDataType(dataType); DiaFile.SetParameter(param); //Set DIA isolation window setting if (dataType == SpectralDataType.DataType.DIA_F_Window) { DiaFile.SetWindowSize(WindowSize); } else if (dataType == SpectralDataType.DataType.DIA_V_Window) { for (XYData window : WindowList) { DiaFile.AddVariableWindow(window); } } DiaFile.SaveDIASetting(); DiaFile.SaveParams(); if (Fix) { DiaFile.FixScanidx(); return; } DiaFile.ExportPrecursorPeak = ExportPrecursorPeak; DiaFile.ExportFragmentPeak = ExportFragmentPeak; Logger.getRootLogger().info("Module A: Signal extraction"); //Start DIA signal extraction process to generate pseudo MS/MS files DiaFile.process(); time = System.currentTimeMillis() - time; Logger.getRootLogger().info(MSFilePath + " 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)))); } else { throw new RuntimeException("file: " + MSFile + "? does not exist!"); } Logger.getRootLogger().info("Job complete"); Logger.getRootLogger().info( "================================================================================================="); } catch (Exception e) { Logger.getRootLogger().error(ExceptionUtils.getStackTrace(e)); throw e; } }
From source file:name.wagners.bpp.Bpp.java
public static void main(final String[] args) { // create the command line parser CommandLineParser parser = new PosixParser(); // create the Options Options options = new Options(); options.addOption(OptionBuilder.hasArg().withArgName("int").withLongOpt("generations") .withDescription("Number of generations [default: 50]").create("g")); options.addOption(OptionBuilder.hasArg().withArgName("int").withLongOpt("mutrate") .withDescription("Mutation rate [default: 1]").create()); options.addOption(OptionBuilder.hasArg().withArgName("double").withLongOpt("mutprop") .withDescription("Mutation propability [default: 0.5]").create()); options.addOption(OptionBuilder.hasArg().withArgName("int").withLongOpt("populationsize") .withDescription("Size of population [default: 20]").create()); options.addOption(OptionBuilder.hasArg().withArgName("a|b").withLongOpt("recombalg") .withDescription("Recombination algorithm [default: a]").create()); // options.addOption(OptionBuilder // .hasArg()//from w w w.java 2s . c o m // .withArgName("int") // .withLongOpt("recombrate") // .withDescription("Recombination rate [default: 1]") // .create()); options.addOption(OptionBuilder.hasArg().withArgName("double").withLongOpt("recombprop") .withDescription("Recombination propability [default: 0.8]").create()); options.addOption(OptionBuilder.hasArg().withArgName("a").withLongOpt("selalg") .withDescription("Selection algorithm [default: a]").create()); options.addOption(OptionBuilder.hasArg().withArgName("int").withLongOpt("selectionpressure") .withDescription("Selection pressure [default: 4]").create()); options.addOption(OptionBuilder.hasArg().withArgName("bool").withLongOpt("elitism") .withDescription("Enable Elitism [default: 1]").create("e")); options.addOption(OptionBuilder.hasArg().withArgName("filename") // .isRequired() .withLongOpt("datafile").withDescription("Problem data file [default: \"binpack.txt\"]") .create("f")); options.addOptionGroup(new OptionGroup() .addOption(OptionBuilder.withLongOpt("verbose").withDescription("be extra verbose").create("v")) .addOption(OptionBuilder.withLongOpt("quiet").withDescription("be extra quiet").create("q"))); options.addOption(OptionBuilder.withLongOpt("version") .withDescription("print the version information and exit").create("V")); options.addOption(OptionBuilder.withLongOpt("help").withDescription("print this message").create("h")); try { // parse the command line arguments CommandLine line = parser.parse(options, args); // validate that block-size has been set if (line.hasOption("help")) { // automatically generate the help statement HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("Bpp", options); System.exit(0); } if (line.hasOption("version")) { log.info("Bpp 0.1 (c) 2007 by Daniel Wagner"); } if (line.hasOption("datafile")) { fname = line.getOptionValue("datafile"); } if (line.hasOption("elitism")) { elitism = Boolean.parseBoolean(line.getOptionValue("elitism")); } if (line.hasOption("generations")) { gen = Integer.parseInt(line.getOptionValue("generations")); } if (line.hasOption("mutprop")) { mp = Double.parseDouble(line.getOptionValue("mutprop")); } if (line.hasOption("mutrate")) { mr = Integer.parseInt(line.getOptionValue("mutrate")); } if (line.hasOption("populationsize")) { ps = Integer.parseInt(line.getOptionValue("populationsize")); } if (line.hasOption("recombalg")) { sel = line.getOptionValue("recombalg").charAt(0); } if (line.hasOption("recombprop")) { rp = Double.parseDouble(line.getOptionValue("recombprop")); } if (line.hasOption("selalg")) { selalg = line.getOptionValue("selalg").charAt(0); } if (line.hasOption("selectionpressure")) { sp = Integer.parseInt(line.getOptionValue("selectionpressure")); } } catch (ParseException exp) { log.info("Unexpected exception:" + exp.getMessage(), exp); // automatically generate the help statement HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("Bpp", options); System.exit(1); } // Ausgabe der eingestellten Optionen log.info("Configuration"); log.info(" Datafile: " + fname); log.info(" Generations: " + gen); log.info(" Population size: " + ps); log.info(" Elitism: " + elitism); log.info(" Mutation propapility: " + mp); log.info(" Mutation rate: " + mr); log.info(" Recombination algorithm " + (char) sel); log.info(" Recombination propapility: " + rp); log.info(" Selection pressure: " + sp); // Daten laden instance = new Instance(); instance.load(fname); Evolutionizer e = new Evolutionizer(instance); e.run(); }
From source file:com.hpe.nv.samples.basic.BasicAnalyzeNVTest.java
public static void main(String[] args) { try {/* w w w . j a v a 2s. c o m*/ // program arguments Options options = new Options(); options.addOption("i", "server-ip", true, "[mandatory] NV Test Manager IP"); options.addOption("o", "server-port", true, "[mandatory] NV Test Manager port"); options.addOption("u", "username", true, "[mandatory] NV username"); options.addOption("w", "password", true, "[mandatory] NV password"); options.addOption("e", "ssl", true, "[optional] Pass true to use SSL. Default: false"); options.addOption("y", "proxy", true, "[optional] Proxy server host:port"); options.addOption("z", "zip-result-file-path", true, "[optional] File path to store the analysis results as a .zip file"); options.addOption("k", "analysis-ports", true, "[optional] A comma-separated list of ports for test analysis"); options.addOption("b", "browser", true, "[optional] The browser for which the Selenium WebDriver is built. Possible values: Chrome and Firefox. Default: Firefox"); options.addOption("d", "debug", true, "[optional] Pass true to view console debug messages during execution. Default: false"); options.addOption("h", "help", false, "[optional] Generates and prints help information"); // parse and validate the command line arguments CommandLineParser parser = new DefaultParser(); CommandLine line = parser.parse(options, args); if (line.hasOption("help")) { // print help if help argument is passed HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("BasicAnalyzeNVTest.java", options); return; } if (line.hasOption("server-ip")) { serverIp = line.getOptionValue("server-ip"); if (serverIp.equals("0.0.0.0")) { throw new Exception( "Please replace the server IP argument value (0.0.0.0) with your NV Test Manager IP"); } } else { throw new Exception("Missing argument -i/--server-ip <serverIp>"); } if (line.hasOption("server-port")) { serverPort = Integer.parseInt(line.getOptionValue("server-port")); } else { throw new Exception("Missing argument -o/--server-port <serverPort>"); } if (line.hasOption("username")) { username = line.getOptionValue("username"); } else { throw new Exception("Missing argument -u/--username <username>"); } if (line.hasOption("password")) { password = line.getOptionValue("password"); } else { throw new Exception("Missing argument -w/--password <password>"); } if (line.hasOption("ssl")) { ssl = Boolean.parseBoolean(line.getOptionValue("ssl")); } if (line.hasOption("zip-result-file-path")) { zipResultFilePath = line.getOptionValue("zip-result-file-path"); } if (line.hasOption("proxy")) { proxySetting = line.getOptionValue("proxy"); } if (line.hasOption("analysis-ports")) { String analysisPortsStr = line.getOptionValue("analysis-ports"); analysisPorts = analysisPortsStr.split(","); } else { analysisPorts = new String[] { "80", "8080" }; } if (line.hasOption("browser")) { browser = line.getOptionValue("browser"); } else { browser = "Firefox"; } if (line.hasOption("debug")) { debug = Boolean.parseBoolean(line.getOptionValue("debug")); } String newLine = System.getProperty("line.separator"); String testDescription = "*** This sample demonstrates the use of the most basic NV methods. ***" + newLine + "*** ***" + newLine + "*** First, the sample creates a TestManager object and initializes it. ***" + newLine + "*** The sample starts an NV test over an emulated \"3G Busy\" network. ***" + newLine + "*** ***" + newLine + "*** Next, the sample navigates to the home page in the HPE Network Virtualization website ***" + newLine + "*** using the Selenium WebDriver. ***" + newLine + "*** ***" + newLine + "*** Finally, the sample stops the NV test, analyzes it, and prints the path of the analysis .zip file to the console. ***" + newLine + "*** ***" + newLine + "*** You can view the actual steps of this sample in the BasicAnalyzeNVTest.java file. ***" + newLine; // print the sample's description System.out.println(testDescription); // start console spinner if (!debug) { spinner = new Thread(new Spinner()); spinner.start(); } // sample execution steps /***** Part 1 - Create a TestManager object and initialize it *****/ printPartDescription("\b------ Part 1 - Create a TestManager object and initialize it"); initTestManager(); printPartSeparator(); /***** Part 2 - Start the NV test with the "3G Busy" network scenario *****/ printPartDescription("------ Part 2 - Start the NV test with the \"3G Busy\" network scenario"); startTest(); testRunning = true; printPartSeparator(); /***** Part 3 - Navigate to the HPE Network Virtualization website *****/ printPartDescription("------ Part 3 - Navigate to the HPE Network Virtualization website"); buildSeleniumWebDriver(); seleniumNavigateToPage(); driverCloseAndQuit(); printPartSeparator(); /***** Part 4 - Stop the NV test, analyze it and print the results to the console *****/ printPartDescription( "------ Part 4 - Stop the NV test, analyze it and print the results to the console"); stopTestAndAnalyze(); testRunning = false; printPartSeparator(); doneCallback(); } catch (Exception e) { try { handleError(e.getMessage()); } catch (Exception e2) { System.out.println("Error occurred: " + e2.getMessage()); } } }
From source file:com.hzih.sslvpn.servlet.TelnetClientExample.java
/** * Main for the TelnetClientExample.//from w ww .j a v a 2 s . com * * */ public static void main(String[] args) throws Exception { FileOutputStream fout = null; if (args.length < 1) { System.err.println("Usage: TelnetClientExample1 <remote-ip> [<remote-port>]"); System.exit(1); } String remoteip = args[0]; int remoteport; if (args.length > 1) { remoteport = (new Integer(args[1])).intValue(); } else { remoteport = 23; } try { fout = new FileOutputStream("spy.log", true); } catch (IOException e) { System.err.println("Exception while opening the spy file: " + e.getMessage()); } tc = new TelnetClient(); TerminalTypeOptionHandler ttopt = new TerminalTypeOptionHandler("VT100", false, false, true, false); EchoOptionHandler echoopt = new EchoOptionHandler(true, false, true, false); SuppressGAOptionHandler gaopt = new SuppressGAOptionHandler(true, true, true, true); try { tc.addOptionHandler(ttopt); tc.addOptionHandler(echoopt); tc.addOptionHandler(gaopt); } catch (InvalidTelnetOptionException e) { System.err.println("Error registering option handlers: " + e.getMessage()); } while (true) { boolean end_loop = false; try { tc.connect(remoteip, remoteport); Thread reader = new Thread(new TelnetClientExample()); tc.registerNotifHandler(new TelnetClientExample()); System.out.println("TelnetClientExample"); System.out.println("Type AYT to send an AYT telnet command"); System.out.println("Type OPT to print a report of status of options (0-24)"); System.out.println("Type REGISTER to register a new SimpleOptionHandler"); System.out.println("Type UNREGISTER to unregister an OptionHandler"); System.out.println("Type SPY to register the spy (connect to port 3333 to spy)"); System.out.println("Type UNSPY to stop spying the connection"); reader.start(); OutputStream outstr = tc.getOutputStream(); byte[] buff = new byte[1024]; int ret_read = 0; do { try { ret_read = System.in.read(buff); if (ret_read > 0) { if ((new String(buff, 0, ret_read)).startsWith("AYT")) { try { System.out.println("Sending AYT"); System.out.println("AYT response:" + tc.sendAYT(5000)); } catch (IOException e) { System.err.println("Exception waiting AYT response: " + e.getMessage()); } } else if ((new String(buff, 0, ret_read)).startsWith("OPT")) { System.out.println("Status of options:"); for (int ii = 0; ii < 25; ii++) { System.out.println("Local Option " + ii + ":" + tc.getLocalOptionState(ii) + " Remote Option " + ii + ":" + tc.getRemoteOptionState(ii)); } } else if ((new String(buff, 0, ret_read)).startsWith("REGISTER")) { StringTokenizer st = new StringTokenizer(new String(buff)); try { st.nextToken(); int opcode = Integer.parseInt(st.nextToken()); boolean initlocal = Boolean.parseBoolean(st.nextToken()); boolean initremote = Boolean.parseBoolean(st.nextToken()); boolean acceptlocal = Boolean.parseBoolean(st.nextToken()); boolean acceptremote = Boolean.parseBoolean(st.nextToken()); SimpleOptionHandler opthand = new SimpleOptionHandler(opcode, initlocal, initremote, acceptlocal, acceptremote); tc.addOptionHandler(opthand); } catch (Exception e) { if (e instanceof InvalidTelnetOptionException) { System.err.println("Error registering option: " + e.getMessage()); } else { System.err.println("Invalid REGISTER command."); System.err.println( "Use REGISTER optcode initlocal initremote acceptlocal acceptremote"); System.err.println("(optcode is an integer.)"); System.err.println( "(initlocal, initremote, acceptlocal, acceptremote are boolean)"); } } } else if ((new String(buff, 0, ret_read)).startsWith("UNREGISTER")) { StringTokenizer st = new StringTokenizer(new String(buff)); try { st.nextToken(); int opcode = (new Integer(st.nextToken())).intValue(); tc.deleteOptionHandler(opcode); } catch (Exception e) { if (e instanceof InvalidTelnetOptionException) { System.err.println("Error unregistering option: " + e.getMessage()); } else { System.err.println("Invalid UNREGISTER command."); System.err.println("Use UNREGISTER optcode"); System.err.println("(optcode is an integer)"); } } } else if ((new String(buff, 0, ret_read)).startsWith("SPY")) { tc.registerSpyStream(fout); } else if ((new String(buff, 0, ret_read)).startsWith("UNSPY")) { tc.stopSpyStream(); } else { try { outstr.write(buff, 0, ret_read); outstr.flush(); } catch (IOException e) { end_loop = true; } } } } catch (IOException e) { System.err.println("Exception while reading keyboard:" + e.getMessage()); end_loop = true; } } while ((ret_read > 0) && (end_loop == false)); try { tc.disconnect(); } catch (IOException e) { System.err.println("Exception while connecting:" + e.getMessage()); } } catch (IOException e) { System.err.println("Exception while connecting:" + e.getMessage()); System.exit(1); } } }
From source file:com.groupC1.control.network.TelnetClientExample.java
/*** * Main for the TelnetClient./* w w w.j av a 2 s . c om*/ ***/ public static void main(String[] args) throws Exception { args = new String[] { "169.254.0.10", "10001" }; FileOutputStream fout = null; if (args.length < 1) { System.err.println("Usage: TelnetClientExample1 <remote-ip> [<remote-port>]"); System.exit(1); } String remoteip = args[0]; int remoteport; if (args.length > 1) { remoteport = (new Integer(args[1])).intValue(); } else { remoteport = 23; } try { fout = new FileOutputStream("spy.log", true); } catch (IOException e) { System.err.println("Exception while opening the spy file: " + e.getMessage()); } tc = new org.apache.commons.net.telnet.TelnetClient(); TerminalTypeOptionHandler ttopt = new TerminalTypeOptionHandler("VT100", false, false, true, false); EchoOptionHandler echoopt = new EchoOptionHandler(true, false, true, false); SuppressGAOptionHandler gaopt = new SuppressGAOptionHandler(true, true, true, true); try { tc.addOptionHandler(ttopt); tc.addOptionHandler(echoopt); tc.addOptionHandler(gaopt); } catch (InvalidTelnetOptionException e) { System.err.println("Error registering option handlers: " + e.getMessage()); } while (true) { boolean end_loop = false; try { tc.connect(remoteip, remoteport); Thread reader = new Thread(new TelnetClientExample()); tc.registerNotifHandler(new TelnetClientExample()); System.out.println("TelnetClient"); System.out.println("Type AYT to send an AYT telnet command"); System.out.println("Type OPT to print a report of status of options (0-24)"); System.out.println("Type REGISTER to register a new SimpleOptionHandler"); System.out.println("Type UNREGISTER to unregister an OptionHandler"); System.out.println("Type SPY to register the spy (connect to port 3333 to spy)"); System.out.println("Type UNSPY to stop spying the connection"); reader.start(); OutputStream outstr = tc.getOutputStream(); byte[] buff = new byte[1024]; int ret_read = 0; do { try { ret_read = System.in.read(buff); if (ret_read > 0) { if ((new String(buff, 0, ret_read)).startsWith("AYT")) { try { System.out.println("Sending AYT"); System.out.println("AYT response:" + tc.sendAYT(5000)); } catch (IOException e) { System.err.println("Exception waiting AYT response: " + e.getMessage()); } } else if ((new String(buff, 0, ret_read)).startsWith("OPT")) { System.out.println("Status of options:"); for (int ii = 0; ii < 25; ii++) { System.out.println("Local Option " + ii + ":" + tc.getLocalOptionState(ii) + " Remote Option " + ii + ":" + tc.getRemoteOptionState(ii)); } } else if ((new String(buff, 0, ret_read)).startsWith("REGISTER")) { StringTokenizer st = new StringTokenizer(new String(buff)); try { st.nextToken(); int opcode = Integer.parseInt(st.nextToken()); boolean initlocal = Boolean.parseBoolean(st.nextToken()); boolean initremote = Boolean.parseBoolean(st.nextToken()); boolean acceptlocal = Boolean.parseBoolean(st.nextToken()); boolean acceptremote = Boolean.parseBoolean(st.nextToken()); SimpleOptionHandler opthand = new SimpleOptionHandler(opcode, initlocal, initremote, acceptlocal, acceptremote); tc.addOptionHandler(opthand); } catch (Exception e) { if (e instanceof InvalidTelnetOptionException) { System.err.println("Error registering option: " + e.getMessage()); } else { System.err.println("Invalid REGISTER command."); System.err.println( "Use REGISTER optcode initlocal initremote acceptlocal acceptremote"); System.err.println("(optcode is an integer.)"); System.err.println( "(initlocal, initremote, acceptlocal, acceptremote are boolean)"); } } } else if ((new String(buff, 0, ret_read)).startsWith("UNREGISTER")) { StringTokenizer st = new StringTokenizer(new String(buff)); try { st.nextToken(); int opcode = (new Integer(st.nextToken())).intValue(); tc.deleteOptionHandler(opcode); } catch (Exception e) { if (e instanceof InvalidTelnetOptionException) { System.err.println("Error unregistering option: " + e.getMessage()); } else { System.err.println("Invalid UNREGISTER command."); System.err.println("Use UNREGISTER optcode"); System.err.println("(optcode is an integer)"); } } } else if ((new String(buff, 0, ret_read)).startsWith("SPY")) { tc.registerSpyStream(fout); } else if ((new String(buff, 0, ret_read)).startsWith("UNSPY")) { tc.stopSpyStream(); } else { try { outstr.write(buff, 0, ret_read); outstr.flush(); } catch (IOException e) { end_loop = true; } } } } catch (IOException e) { System.err.println("Exception while reading keyboard:" + e.getMessage()); end_loop = true; } } while ((ret_read > 0) && (end_loop == false)); try { tc.disconnect(); } catch (IOException e) { System.err.println("Exception while connecting:" + e.getMessage()); } } catch (IOException e) { System.err.println("Exception while connecting:" + e.getMessage()); System.exit(1); } } }
From source file:com.cloud.test.stress.StressTestDirectAttach.java
public static void main(String[] args) { String host = "http://localhost"; String port = "8092"; String devPort = "8080"; String apiUrl = "/client/api"; try {/*from ww w. ja v a 2 s.co m*/ // Parameters List<String> argsList = Arrays.asList(args); Iterator<String> iter = argsList.iterator(); while (iter.hasNext()) { String arg = iter.next(); // host if (arg.equals("-h")) { host = "http://" + iter.next(); } if (arg.equals("-p")) { port = iter.next(); } if (arg.equals("-dp")) { devPort = iter.next(); } if (arg.equals("-t")) { numThreads = Integer.parseInt(iter.next()); } if (arg.equals("-s")) { sleepTime = Long.parseLong(iter.next()); } if (arg.equals("-a")) { accountName = iter.next(); } if (arg.equals("-c")) { cleanUp = Boolean.parseBoolean(iter.next()); if (!cleanUp) sleepTime = 0L; // no need to wait if we don't ever // cleanup } if (arg.equals("-r")) { repeat = Boolean.parseBoolean(iter.next()); } if (arg.equals("-i")) { internet = Boolean.parseBoolean(iter.next()); } if (arg.equals("-w")) { wait = Integer.parseInt(iter.next()); } if (arg.equals("-z")) { zoneId = iter.next(); } if (arg.equals("-so")) { serviceOfferingId = iter.next(); } } final String server = host + ":" + port + "/"; final String developerServer = host + ":" + devPort + apiUrl; s_logger.info("Starting test against server: " + server + " with " + numThreads + " thread(s)"); if (cleanUp) s_logger.info("Clean up is enabled, each test will wait " + sleepTime + " ms before cleaning up"); for (int i = 0; i < numThreads; i++) { new Thread(new Runnable() { @Override public void run() { do { String username = null; try { long now = System.currentTimeMillis(); Random ran = new Random(); username = Math.abs(ran.nextInt()) + "-user"; NDC.push(username); s_logger.info("Starting test for the user " + username); int response = executeDeployment(server, developerServer, username); boolean success = false; String reason = null; if (response == 200) { success = true; if (internet) { s_logger.info("Deploy successful...waiting 5 minute before SSH tests"); Thread.sleep(300000L); // Wait 60 // seconds so // the windows VM // can boot up and do a sys prep. s_logger.info("Begin Linux SSH test for account " + _account.get()); reason = sshTest(_linuxIP.get(), _linuxPassword.get()); if (reason == null) { s_logger.info( "Linux SSH test successful for account " + _account.get()); } } if (reason == null) { if (internet) { s_logger.info( "Windows SSH test successful for account " + _account.get()); } else { s_logger.info("deploy test successful....now cleaning up"); if (cleanUp) { s_logger.info( "Waiting " + sleepTime + " ms before cleaning up vms"); Thread.sleep(sleepTime); } else { success = true; } } if (usageIterator >= numThreads) { int eventsAndBillingResponseCode = executeEventsAndBilling(server, developerServer); s_logger.info( "events and usage records command finished with response code: " + eventsAndBillingResponseCode); usageIterator = 1; } else { s_logger.info( "Skipping events and usage records for this user: usageIterator " + usageIterator + " and number of Threads " + numThreads); usageIterator++; } if ((users == null) && (accountName == null)) { s_logger.info("Sending cleanup command"); int cleanupResponseCode = executeCleanup(server, developerServer, username); s_logger.info("cleanup command finished with response code: " + cleanupResponseCode); success = (cleanupResponseCode == 200); } else { s_logger.info("Sending stop DomR / destroy VM command"); int stopResponseCode = executeStop(server, developerServer, username); s_logger.info("stop(destroy) command finished with response code: " + stopResponseCode); success = (stopResponseCode == 200); } } else { // Just stop but don't destroy the // VMs/Routers s_logger.info("SSH test failed for account " + _account.get() + "with reason '" + reason + "', stopping VMs"); int stopResponseCode = executeStop(server, developerServer, username); s_logger.info( "stop command finished with response code: " + stopResponseCode); success = false; // since the SSH test // failed, mark the // whole test as // failure } } else { // Just stop but don't destroy the // VMs/Routers s_logger.info("Deploy test failed with reason '" + reason + "', stopping VMs"); int stopResponseCode = executeStop(server, developerServer, username); s_logger.info("stop command finished with response code: " + stopResponseCode); success = false; // since the deploy test // failed, mark the // whole test as failure } if (success) { s_logger.info("***** Completed test for user : " + username + " in " + ((System.currentTimeMillis() - now) / 1000L) + " seconds"); } else { s_logger.info("##### FAILED test for user : " + username + " in " + ((System.currentTimeMillis() - now) / 1000L) + " seconds with reason : " + reason); } s_logger.info("Sleeping for " + wait + " seconds before starting next iteration"); Thread.sleep(wait); } catch (Exception e) { s_logger.warn("Error in thread", e); try { int stopResponseCode = executeStop(server, developerServer, username); s_logger.info("stop response code: " + stopResponseCode); } catch (Exception e1) { } } finally { NDC.clear(); } } while (repeat); } }).start(); } } catch (Exception e) { s_logger.error(e); } }
From source file:DIA_Umpire_Quant.DIA_Umpire_ProtQuant.java
/** * @param args the command line arguments *///from w w w. j a v a2s. c om public static void main(String[] args) throws FileNotFoundException, IOException, Exception { System.out.println( "================================================================================================="); System.out.println( "DIA-Umpire protein quantitation module (version: " + UmpireInfo.GetInstance().Version + ")"); if (args.length != 1) { System.out.println( "command format error, the correct format should be: java -jar -Xmx10G DIA_Umpire_PortQuant.jar diaumpire_module.params"); return; } try { ConsoleLogger.SetConsoleLogger(Level.INFO); ConsoleLogger.SetFileLogger(Level.DEBUG, FilenameUtils.getFullPath(args[0]) + "diaumpire_orotquant.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 Combined_Prot = ""; boolean DefaultProtFiltering = true; float Freq = 0f; int TopNPep = 6; int TopNFrag = 6; String FilterWeight = "GW"; float MinWeight = 0.9f; TandemParam tandemPara = new TandemParam(DBSearchParam.SearchInstrumentType.TOF5600); HashMap<String, File> AssignFiles = new HashMap<>(); 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 "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 "ProteinFDR": { tandemPara.ProtFDR = 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; } //<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(); //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<>(); try { 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.ClearAssignPeakCluster(); FileList.add(DiaFile); HashMap<String, FragmentPeak> FragMap = new HashMap<>(); IDSummaryFragments.put(FilenameUtils.getBaseName(mzXMLFile), FragMap); } } } //<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 (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.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:eu.fbk.utils.lsa.util.Anvur.java
public static void main(String[] args) throws Exception { String logConfig = System.getProperty("log-config"); if (logConfig == null) { logConfig = "log-config.txt"; }//from w w w .jav a 2 s .co m PropertyConfigurator.configure(logConfig); /* if (args.length != 2) { log.println("Usage: java -mx512M eu.fbk.utils.lsa.util.Anvur in-file out-dir"); System.exit(1); } File l = new File(args[1]); if (!l.exists()) { l.mkdir(); } List<String[]> list = readText(new File(args[0])); String oldCategory = ""; for (int i=0;i<list.size();i++) { String[] s = list.get(i); if (!oldCategory.equals(s[0])) { File f = new File(args[1] + File.separator + s[0]); boolean b = f.mkdir(); logger.debug(f + " created " + b); } File g = new File(args[1] + File.separator + s[0] + File.separator + s[1] + ".txt"); logger.debug("writing " + g + "..."); PrintWriter pw = new PrintWriter(new FileWriter(g)); //pw.println(tokenize(s[1].substring(0, s[1].indexOf(".")).replace('_', ' ') + " " + s[2])); if (s.length == 5) { pw.println(tokenize(s[1].substring(0, s[1].indexOf(".")).replace('_', ' ') + " " + s[2] + " " + s[4].replace('_', ' '))); } else { pw.println(tokenize(s[1].substring(0, s[1].indexOf(".")).replace('_', ' ') + " " + s[2])); } pw.flush(); pw.close(); } // end for i */ if (args.length != 7) { System.out.println(args.length); System.out.println( "Usage: java -mx2G eu.fbk.utils.lsa.util.Anvur input threshold size dim idf in-file-csv fields\n\n"); System.exit(1); } // DecimalFormat dec = new DecimalFormat("#.00"); File Ut = new File(args[0] + "-Ut"); File Sk = new File(args[0] + "-S"); File r = new File(args[0] + "-row"); File c = new File(args[0] + "-col"); File df = new File(args[0] + "-df"); double threshold = Double.parseDouble(args[1]); int size = Integer.parseInt(args[2]); int dim = Integer.parseInt(args[3]); boolean rescaleIdf = Boolean.parseBoolean(args[4]); //"author_check"0, "authors"1, "title"2, "year"3, "pubtype"4, "publisher"5, "journal"6, "volume"7, "number"8, "pages"9, "abstract"10, "nauthors", "citedby" String[] labels = { "author_check", "authors", "title", "year", "pubtype", "publisher", "journal", "volume", "number", "pages", "abstract", "nauthors", "citedby" //author_id authors title year pubtype publisher journal volume number pages abstract nauthors citedby }; String name = buildName(labels, args[6]); File bwf = new File(args[5] + name + "-bow.txt"); PrintWriter bw = new PrintWriter( new BufferedWriter(new OutputStreamWriter(new FileOutputStream(bwf), "UTF-8"))); File bdf = new File(args[5] + name + "-bow.csv"); PrintWriter bd = new PrintWriter( new BufferedWriter(new OutputStreamWriter(new FileOutputStream(bdf), "UTF-8"))); File lwf = new File(args[5] + name + "-ls.txt"); PrintWriter lw = new PrintWriter( new BufferedWriter(new OutputStreamWriter(new FileOutputStream(lwf), "UTF-8"))); File ldf = new File(args[5] + name + "-ls.csv"); PrintWriter ld = new PrintWriter( new BufferedWriter(new OutputStreamWriter(new FileOutputStream(ldf), "UTF-8"))); File blwf = new File(args[5] + name + "-bow+ls.txt"); PrintWriter blw = new PrintWriter( new BufferedWriter(new OutputStreamWriter(new FileOutputStream(blwf), "UTF-8"))); File bldf = new File(args[5] + name + "-bow+ls.csv"); PrintWriter bld = new PrintWriter( new BufferedWriter(new OutputStreamWriter(new FileOutputStream(bldf), "UTF-8"))); File logf = new File(args[5] + name + ".log"); PrintWriter log = new PrintWriter( new BufferedWriter(new OutputStreamWriter(new FileOutputStream(logf), "UTF-8"))); //System.exit(0); LSM lsm = new LSM(Ut, Sk, r, c, df, dim, rescaleIdf); LSSimilarity lss = new LSSimilarity(lsm, size); List<String[]> list = readText(new File(args[5])); // author_check authors title year pubtype publisher journal volume number pages abstract nauthors citedby //header for (int i = 0; i < list.size(); i++) { String[] s1 = list.get(i); String t1 = s1[0].toLowerCase(); bw.print("\t"); lw.print("\t"); blw.print("\t"); bw.print(i + "(" + s1[0] + ")"); lw.print(i + "(" + s1[0] + ")"); blw.print(i + "(" + s1[0] + ")"); } // end for i bw.print("\n"); lw.print("\n"); blw.print("\n"); for (int i = 0; i < list.size(); i++) { logger.info(i + "\t"); String[] s1 = list.get(i); String t1 = buildText(s1, args[6]); BOW bow1 = new BOW(t1); logger.info(bow1); Vector d1 = lsm.mapDocument(bow1); d1.normalize(); log.println("d1:" + d1); Vector pd1 = lsm.mapPseudoDocument(d1); pd1.normalize(); log.println("pd1:" + pd1); Vector m1 = merge(pd1, d1); log.println("m1:" + m1); // write the orginal line for (int j = 0; j < s1.length; j++) { bd.print(s1[j]); bd.print("\t"); ld.print(s1[j]); ld.print("\t"); bld.print(s1[j]); bld.print("\t"); } // write the bow, ls, and bow+ls vectors bd.println(d1); ld.println(pd1); bld.println(m1); bw.print(i + "(" + s1[0] + ")"); lw.print(i + "(" + s1[0] + ")"); blw.print(i + "(" + s1[0] + ")"); for (int j = 0; j < i + 1; j++) { bw.print("\t"); lw.print("\t"); blw.print("\t"); } // end for j for (int j = i + 1; j < list.size(); j++) { logger.info(i + "\t" + j); String[] s2 = list.get(j); String t2 = buildText(s2, args[6]); BOW bow2 = new BOW(t2); log.println(i + ":" + j + "(" + s1[0] + ":" + s2[0] + ") t1:" + t1); log.println(i + ":" + j + "(" + s1[0] + ":" + s2[0] + ") t2:" + t2); log.println(i + ":" + j + "(" + s1[0] + ":" + s2[0] + ") bow1:" + bow1); log.println(i + ":" + j + "(" + s1[0] + ":" + s2[0] + ") bow2:" + bow2); Vector d2 = lsm.mapDocument(bow2); d2.normalize(); log.println("d2:" + d2); Vector pd2 = lsm.mapPseudoDocument(d2); pd2.normalize(); log.println("pd2:" + pd2); Vector m2 = merge(pd2, d2); log.println("m2:" + m2); float cosVSM = d1.dotProduct(d2) / (float) Math.sqrt(d1.dotProduct(d1) * d2.dotProduct(d2)); float cosLSM = pd1.dotProduct(pd2) / (float) Math.sqrt(pd1.dotProduct(pd1) * pd2.dotProduct(pd2)); float cosBOWLSM = m1.dotProduct(m2) / (float) Math.sqrt(m1.dotProduct(m1) * m2.dotProduct(m2)); bw.print("\t"); bw.print(dec.format(cosVSM)); lw.print("\t"); lw.print(dec.format(cosLSM)); blw.print("\t"); blw.print(dec.format(cosBOWLSM)); log.println(i + ":" + j + "(" + s1[0] + ":" + s2[0] + ") bow\t" + cosVSM); log.println(i + ":" + j + "(" + s1[0] + ":" + s2[0] + ") ls:\t" + cosLSM); log.println(i + ":" + j + "(" + s1[0] + ":" + s2[0] + ") bow+ls:\t" + cosBOWLSM); } bw.print("\n"); lw.print("\n"); blw.print("\n"); } // end for i logger.info("wrote " + bwf); logger.info("wrote " + bwf); logger.info("wrote " + bdf); logger.info("wrote " + lwf); logger.info("wrote " + ldf); logger.info("wrote " + blwf); logger.info("wrote " + bldf); logger.info("wrote " + logf); ld.close(); bd.close(); bld.close(); bw.close(); lw.close(); blw.close(); log.close(); }
From source file:puma.central.pdp.CentralPUMAPDP.java
public static void main(String[] args) { // initialize log4j BasicConfigurator.configure();/*from w w w .ja va2 s. c om*/ CommandLineParser parser = new BasicParser(); Options options = new Options(); options.addOption("ph", "policy-home", true, "The folder where to find the policy file given with the given policy id. " + "For default operation, this folder should contain the central PUMA policy (called " + CENTRAL_PUMA_POLICY_FILENAME + ")"); options.addOption("pid", "policy-id", true, "The id of the policy to be evaluated on decision requests. Default value: " + GLOBAL_PUMA_POLICY_ID + ")"); options.addOption("s", "log-disabled", true, "Verbose mode (true/false)"); String policyHome = ""; String policyId = ""; // read command line try { CommandLine line = parser.parse(options, args); if (line.hasOption("help")) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp("Simple PDP Test", options); return; } if (line.hasOption("policy-home")) { policyHome = line.getOptionValue("policy-home"); } else { logger.log(Level.WARNING, "Incorrect arguments given."); return; } if (line.hasOption("log-disabled") && Boolean.parseBoolean(line.getOptionValue("log-disabled"))) { logger.log(Level.INFO, "Now switching to silent mode"); LogManager.getLogManager().getLogger("").setLevel(Level.WARNING); //LogManager.getLogManager().reset(); } if (line.hasOption("policy-id")) { policyId = line.getOptionValue("policy-id"); } else { logger.log(Level.INFO, "Using default policy id: " + GLOBAL_PUMA_POLICY_ID); policyId = GLOBAL_PUMA_POLICY_ID; } } catch (ParseException e) { logger.log(Level.WARNING, "Incorrect arguments given.", e); return; } // // STARTUP THE RMI SERVER // // if (System.getSecurityManager() == null) { // System.setSecurityManager(new SecurityManager()); // } final CentralPUMAPDP pdp; try { pdp = new CentralPUMAPDP(policyHome, policyId); } catch (IOException e) { logger.log(Level.SEVERE, "FAILED to set up the CentralPUMAPDP. Quitting.", e); return; } try { Registry registry; try { registry = LocateRegistry.createRegistry(RMI_REGISITRY_PORT); logger.info("Created new RMI registry"); } catch (RemoteException e) { // MDC: I hope this means the registry already existed. registry = LocateRegistry.getRegistry(RMI_REGISITRY_PORT); logger.info("Reusing existing RMI registry"); } CentralPUMAPDPRemote stub = (CentralPUMAPDPRemote) UnicastRemoteObject.exportObject(pdp, 0); registry.bind(CENTRAL_PUMA_PDP_RMI_NAME, stub); logger.info( "Central PUMA PDP up and running (available using RMI with name \"central-puma-pdp\" on RMI registry port " + RMI_REGISITRY_PORT + ")"); Thread.sleep(100); // MDC: vroeger eindigde de Thread om n of andere reden, dit lijkt te werken... } catch (Exception e) { logger.log(Level.SEVERE, "FAILED to set up PDP as RMI server", e); } // // STARTUP THE THRIFT PEP SERVER // //logger.log(Level.INFO, "Not setting up the Thrift server"); // set up server // PEPServer handler = new PEPServer(new CentralPUMAPEP(pdp)); // RemotePEPService.Processor<PEPServer> processor = new RemotePEPService.Processor<PEPServer>(handler); // TServerTransport serverTransport; // try { // serverTransport = new TServerSocket(THRIFT_PEP_PORT); // } catch (TTransportException e) { // e.printStackTrace(); // return; // } // TServer server = new TSimpleServer(new TServer.Args(serverTransport).processor(processor)); // System.out.println("Setting up the Thrift PEP server on port " + THRIFT_PEP_PORT); // server.serve(); // // STARTUP THE THRIFT PEP SERVER // //logger.log(Level.INFO, "Not setting up the Thrift server"); // set up server // do this in another thread not to block the main thread new Thread(new Runnable() { @Override public void run() { RemotePDPService.Processor<CentralPUMAPDP> pdpProcessor = new RemotePDPService.Processor<CentralPUMAPDP>( pdp); TServerTransport pdpServerTransport; try { pdpServerTransport = new TServerSocket(THRIFT_PDP_PORT); } catch (TTransportException e) { e.printStackTrace(); return; } TServer pdpServer = new TThreadPoolServer( new TThreadPoolServer.Args(pdpServerTransport).processor(pdpProcessor)); logger.info("Setting up the Thrift PDP server on port " + THRIFT_PDP_PORT); pdpServer.serve(); } }).start(); }