Example usage for java.lang String startsWith

List of usage examples for java.lang String startsWith

Introduction

In this page you can find the example usage for java.lang String startsWith.

Prototype

public boolean startsWith(String prefix) 

Source Link

Document

Tests if this string starts with the specified prefix.

Usage

From source file:com.diversityarrays.dal.server.DalServer.java

public static void main(String[] args) {

    String host = null;//from   w  w  w  . j ava  2s  .c  o m
    int port = DalServerUtil.DEFAULT_DAL_SERVER_PORT;

    int inactiveMins = DalServerUtil.DEFAULT_MAX_INACTIVE_MINUTES;

    File docRoot = null;

    String serviceName = null;

    for (int i = 0; i < args.length; ++i) {
        String argi = args[i];
        if (argi.startsWith("-")) {
            if ("--".equals(argi)) {
                break;
            }

            if ("-version".equals(argi)) {
                System.out.println(DAL_SERVER_VERSION);
                System.exit(0);
            }

            if ("-help".equals(argi)) {
                giveHelpThenExit(0);
            }

            if ("-docroot".equals(argi)) {
                if (++i >= args.length || args[i].startsWith("-")) {
                    fatal("missing value for " + argi);
                }
                docRoot = new File(args[i]);
            } else if ("-sqllog".equals(argi)) {
                SqlUtil.logger = Logger.getLogger(SqlUtil.class.getName());
            } else if ("-expire".equals(argi)) {
                if (++i >= args.length || args[i].startsWith("-")) {
                    fatal("missing value for " + argi);
                }

                try {
                    inactiveMins = Integer.parseInt(args[i], 10);
                    if (inactiveMins <= 0) {
                        fatal("invalid minutes: " + args[i]);
                    }
                } catch (NumberFormatException e) {
                    fatal("invalid minutes: " + args[i]);
                }
            } else if ("-localhost".equals(argi)) {
                host = "localhost";
            } else if ("-port".equals(argi)) {
                if (++i >= args.length || args[i].startsWith("-")) {
                    fatal("missing value for " + argi);
                }
                try {
                    port = Integer.parseInt(args[i], 10);
                    if (port < 0 || port > 65535) {
                        fatal("invalid port number: " + args[i]);
                    }
                } catch (NumberFormatException e) {
                    fatal("invalid port number: " + args[i]);
                }
            } else {
                fatal("invalid option: " + argi);
            }
        } else {
            if (serviceName != null) {
                fatal("multiple serviceNames not supported: " + argi);
            }
            serviceName = argi;
        }
    }

    final DalServerPreferences preferences = new DalServerPreferences(
            Preferences.userNodeForPackage(DalServer.class));

    if (docRoot == null) {
        docRoot = preferences.getWebRoot(new File(System.getProperty("user.dir"), "www"));
    }

    DalServer server = null;

    if (serviceName != null && docRoot.isDirectory()) {
        try {
            DalDatabase db = createDalDatabase(serviceName, preferences);
            if (db.isInitialiseRequired()) {
                Closure<String> progress = new Closure<String>() {
                    @Override
                    public void execute(String msg) {
                        System.out.println("Database Initialisation: " + msg);
                    }
                };
                db.initialise(progress);
            }
            server = create(preferences, host, port, docRoot, db);
        } catch (NoServiceException e) {
            throw new RuntimeException(e);
        } catch (DalDbException e) {
            throw new RuntimeException(e);
        }
    }

    Image serverIconImage = null;
    InputStream imageIs = DalServer.class.getResourceAsStream("dalserver-24.png");
    if (imageIs != null) {
        try {
            serverIconImage = ImageIO.read(imageIs);

            if (Util.isMacOS()) {
                try {
                    MacApplication macapp = new MacApplication(null);
                    macapp.setDockIconImage(serverIconImage);
                } catch (MacApplicationException e) {
                    System.err.println(e.getMessage());
                }
            }

        } catch (IOException ignore) {
        }
    }

    if (server != null) {
        server.setMaxInactiveMinutes(inactiveMins);
    } else {
        AskServerParams asker = new AskServerParams(serverIconImage, null, "DAL Server Start", docRoot,
                preferences);
        GuiUtil.centreOnScreen(asker);
        asker.setVisible(true);

        if (asker.cancelled) {
            System.exit(0);
        }

        host = asker.dalServerHostName;
        port = asker.dalServerPort;
        inactiveMins = asker.maxInactiveMinutes;

        server = create(preferences, host, port, asker.wwwRoot, asker.dalDatabase);
        // server.setUseSimpleDatabase(asker.useSimpleDatabase);
    }

    final DalServer f_server = server;
    final File f_wwwRoot = docRoot;
    final Image f_serverIconImage = serverIconImage;

    SwingUtilities.invokeLater(new Runnable() {
        @Override
        public void run() {
            DalServerFactory factory = new DalServerFactory() {
                @Override
                public DalServer create(String hostName, int port, File wwwRoot, DalDatabase dalDatabase) {
                    return DalServer.create(preferences, hostName, port, wwwRoot, dalDatabase);
                }
            };
            ServerGui gui = new ServerGui(f_serverIconImage, f_server, factory, f_wwwRoot, preferences);
            gui.setVisible(true);
        }
    });

}

From source file:ms1quant.MS1Quant.java

/**
 * @param args the command line arguments MS1Quant parameterfile
 *//*from   ww  w.  ja v a2s . c o  m*/
public static void main(String[] args) throws Exception {

    BufferedReader reader = null;
    try {
        System.out.println(
                "=================================================================================================");
        System.out.println("Umpire MS1 quantification and feature detection analysis (version: "
                + UmpireInfo.GetInstance().Version + ")");
        if (args.length < 3 || !args[1].startsWith("-mode")) {
            System.out
                    .println("command : java -jar -Xmx10G MS1Quant.jar ms1quant.params -mode[1 or 2] [Option]");
            System.out.println("\n-mode");
            System.out.println("\t1:Single file mode--> mzXML_file PepXML_file");
            System.out.println("\t\tEx: -mode1 file1.mzXML file1.pep.xml");
            System.out.println(
                    "\t2:Folder mode--> mzXML_Folder PepXML_Folder, all generated csv tables will be merged into a single csv file");
            System.out.println("\t\tEx: -mode2 /data/mzxml/ /data/pepxml/");
            System.out.println("\nOptions");
            System.out.println(
                    "\t-C\tNo of concurrent files to be processed (only for folder mode), Ex. -C5, default:1");
            System.out.println("\t-p\tMinimum probability, Ex. -p0.9, default:0.9");
            System.out.println("\t-ID\tDetect identified feature only");
            System.out.println("\t-O\toutput folder, Ex. -O/data/");
            return;
        }
        ConsoleLogger consoleLogger = new ConsoleLogger();
        consoleLogger.SetConsoleLogger(Level.DEBUG);
        consoleLogger.SetFileLogger(Level.DEBUG, FilenameUtils.getFullPath(args[0]) + "ms1quant_debug.log");
        Logger logger = Logger.getRootLogger();
        logger.debug("Command: " + Arrays.toString(args));
        logger.info("MS1Quant version: " + UmpireInfo.GetInstance().Version);

        String parameterfile = args[0];
        logger.info("Parameter file: " + parameterfile);
        File paramfile = new File(parameterfile);
        if (!paramfile.exists()) {
            logger.error("Parameter file " + paramfile.getAbsolutePath()
                    + " cannot be found. The program will exit.");
        }

        reader = new BufferedReader(new FileReader(paramfile.getAbsolutePath()));
        String line = "";
        InstrumentParameter param = new InstrumentParameter(InstrumentParameter.InstrumentType.TOF5600);
        int NoCPUs = 2;
        int NoFile = 1;
        param.DetermineBGByID = false;
        param.EstimateBG = true;

        //<editor-fold defaultstate="collapsed" desc="Read parameter file">
        while ((line = reader.readLine()) != null) {
            if (!"".equals(line) && !line.startsWith("#")) {
                logger.info(line);
                //System.out.println(line);
                if (line.split("=").length < 2) {
                    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;
                }
                //<editor-fold defaultstate="collapsed" desc="instrument parameters">

                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);
                }
                case "SE.EndRT": {
                    param.endRT = Float.valueOf(value);
                }

                //</editor-fold>
                }
            }
        }
        //</editor-fold>

        int mode = 1;
        if (args[1].equals("-mode2")) {
            mode = 2;
        } else if (args[1].equals("-mode1")) {
            mode = 1;
        } else {
            logger.error("-mode number not recongized. The program will exit.");
        }

        String mzXML = "";
        String pepXML = "";
        String mzXMLPath = "";
        String pepXMLPath = "";
        File mzXMLfile = null;
        File pepXMLfile = null;
        File mzXMLfolder = null;
        File pepXMLfolder = null;
        int idx = 0;
        if (mode == 1) {
            mzXML = args[2];
            logger.info("Mode1 mzXML file: " + mzXML);
            mzXMLfile = new File(mzXML);
            if (!mzXMLfile.exists()) {
                logger.error("Mode1 mzXML file " + mzXMLfile.getAbsolutePath()
                        + " cannot be found. The program will exit.");
                return;
            }
            pepXML = args[3];
            logger.info("Mode1 pepXML file: " + pepXML);
            pepXMLfile = new File(pepXML);
            if (!pepXMLfile.exists()) {
                logger.error("Mode1 pepXML file " + pepXMLfile.getAbsolutePath()
                        + " cannot be found. The program will exit.");
                return;
            }
            idx = 4;
        } else if (mode == 2) {
            mzXMLPath = args[2];
            logger.info("Mode2 mzXML folder: " + mzXMLPath);
            mzXMLfolder = new File(mzXMLPath);
            if (!mzXMLfolder.exists()) {
                logger.error("Mode2 mzXML folder " + mzXMLfolder.getAbsolutePath()
                        + " does not exist. The program will exit.");
                return;
            }
            pepXMLPath = args[3];
            logger.info("Mode2 pepXML folder: " + pepXMLPath);
            pepXMLfolder = new File(pepXMLPath);
            if (!pepXMLfolder.exists()) {
                logger.error("Mode2 pepXML folder " + pepXMLfolder.getAbsolutePath()
                        + " does not exist. The program will exit.");
                return;
            }
            idx = 4;
        }

        String outputfolder = "";
        float MinProb = 0f;
        for (int i = idx; i < args.length; i++) {
            if (args[i].startsWith("-")) {
                if (args[i].equals("-ID")) {
                    param.TargetIDOnly = true;
                    logger.info("Detect ID feature only: true");
                }
                if (args[i].startsWith("-O")) {
                    outputfolder = args[i].substring(2);
                    logger.info("Output folder: " + outputfolder);

                    File outputfile = new File(outputfolder);
                    if (!outputfolder.endsWith("\\") | outputfolder.endsWith("/")) {
                        outputfolder += "/";
                    }
                    if (!outputfile.exists()) {
                        outputfile.mkdir();
                    }
                }
                if (args[i].startsWith("-C")) {
                    try {
                        NoFile = Integer.parseInt(args[i].substring(2));
                        logger.info("No of concurrent files: " + NoFile);
                    } catch (Exception ex) {
                        logger.error(args[i]
                                + " is not a correct integer format, will process only one file at a time.");
                    }
                }
                if (args[i].startsWith("-p")) {
                    try {
                        MinProb = Float.parseFloat(args[i].substring(2));
                        logger.info("probability threshold: " + MinProb);
                    } catch (Exception ex) {
                        logger.error(args[i] + " is not a correct format, will use 0 as threshold instead.");
                    }
                }
            }
        }

        reader.close();
        TandemParam tandemparam = new TandemParam(DBSearchParam.SearchInstrumentType.TOF5600);
        PTMManager.GetInstance();

        if (param.TargetIDOnly) {
            param.EstimateBG = false;
            param.ApexDelta = 1.5f;
            param.NoMissedScan = 10;
            param.MiniOverlapP = 0.2f;
            param.RemoveGroupedPeaks = false;
            param.CheckMonoIsotopicApex = false;
            param.DetectByCWT = false;
            param.FillGapByBK = false;
            param.IsoCorrThreshold = -1f;
            param.SmoothFactor = 3;
        }

        if (mode == 1) {
            logger.info("Processing " + mzXMLfile.getAbsolutePath() + "....");
            long time = System.currentTimeMillis();
            LCMSPeakMS1 LCMS1 = new LCMSPeakMS1(mzXMLfile.getAbsolutePath(), NoCPUs);
            LCMS1.SetParameter(param);

            LCMS1.Resume = false;
            if (!param.TargetIDOnly) {
                LCMS1.CreatePeakFolder();
            }
            LCMS1.ExportPeakClusterTable = true;

            if (pepXMLfile.exists()) {
                tandemparam.InteractPepXMLPath = pepXMLfile.getAbsolutePath();
                LCMS1.ParsePepXML(tandemparam, MinProb);
                logger.info("No. of PSMs included: " + LCMS1.IDsummary.PSMList.size());
                logger.info("No. of Peptide ions included: " + LCMS1.IDsummary.GetPepIonList().size());
            }

            if (param.TargetIDOnly) {
                LCMS1.SaveSerializationFile = false;
            }

            if (param.TargetIDOnly || !LCMS1.ReadPeakCluster()) {
                LCMS1.PeakClusterDetection();
            }

            if (pepXMLfile.exists()) {
                LCMS1.AssignQuant(false);
                LCMS1.IDsummary.ExportPepID(outputfolder);
            }
            time = System.currentTimeMillis() - time;
            logger.info(LCMS1.ParentmzXMLName + " 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))));
            LCMS1.BaseClearAllPeaks();
            LCMS1.SetSpectrumParser(null);
            LCMS1.IDsummary = null;
            LCMS1 = null;
            System.gc();
        } else if (mode == 2) {

            LCMSID IDsummary = new LCMSID("", "", "");
            logger.info("Parsing all pepXML files in " + pepXMLPath + "....");
            for (File file : pepXMLfolder.listFiles()) {
                if (file.getName().toLowerCase().endsWith("pep.xml")
                        || file.getName().toLowerCase().endsWith("pepxml")) {
                    PepXMLParser pepXMLParser = new PepXMLParser(IDsummary, file.getAbsolutePath(), MinProb);
                }
            }
            HashMap<String, LCMSID> LCMSIDMap = IDsummary.GetLCMSIDFileMap();

            ExecutorService executorPool = null;
            executorPool = Executors.newFixedThreadPool(NoFile);

            logger.info("Processing all mzXML files in " + mzXMLPath + "....");
            for (File file : mzXMLfolder.listFiles()) {
                if (file.getName().toLowerCase().endsWith("mzxml")) {
                    LCMSID id = LCMSIDMap.get(FilenameUtils.getBaseName(file.getName()));
                    if (id == null || id.PSMList == null) {
                        logger.warn("No IDs found in :" + FilenameUtils.getBaseName(file.getName())
                                + ". Quantification for this file is skipped");
                        continue;
                    }
                    if (!id.PSMList.isEmpty()) {
                        MS1TargetQuantThread thread = new MS1TargetQuantThread(file, id, NoCPUs, outputfolder,
                                param);
                        executorPool.execute(thread);
                    }
                }
            }
            LCMSIDMap.clear();
            LCMSIDMap = null;
            IDsummary = null;
            executorPool.shutdown();
            try {
                executorPool.awaitTermination(Long.MAX_VALUE, TimeUnit.NANOSECONDS);
            } catch (InterruptedException e) {
                logger.info("interrupted..");
            }

            if (outputfolder == null | outputfolder.equals("")) {
                outputfolder = mzXMLPath;
            }

            logger.info("Merging PSM files..");
            File output = new File(outputfolder);
            FileWriter writer = new FileWriter(output.getAbsolutePath() + "/PSM_merge.csv");
            boolean header = false;
            for (File csvfile : output.listFiles()) {
                if (csvfile.getName().toLowerCase().endsWith("_psms.csv")) {
                    BufferedReader outreader = new BufferedReader(new FileReader(csvfile));
                    String outline = outreader.readLine();
                    if (!header) {
                        writer.write(outline + "\n");
                        header = true;
                    }
                    while ((outline = outreader.readLine()) != null) {
                        writer.write(outline + "\n");
                    }
                    outreader.close();
                    csvfile.delete();
                }
            }
            writer.close();
        }
        logger.info("MS1 quant module is complete.");
    } catch (Exception e) {
        Logger.getRootLogger().error(ExceptionUtils.getStackTrace(e));
        throw e;
    }
}

From source file:Gen.java

public static void main(String[] args) throws Exception {

    try {//from  ww w.  j  a v  a2  s  . co  m

        File[] files = null;
        if (System.getProperty("dir") != null && !System.getProperty("dir").equals("")) {
            files = new File(System.getProperty("dir")).listFiles(new FilenameFilter() {
                public boolean accept(File dir, String name) {
                    return name.toUpperCase().endsWith(".XML");
                };
            });
        } else {
            String fileName = System.getProperty("file") != null && !System.getProperty("file").equals("")
                    ? System.getProperty("file")
                    : "rjmap.xml";
            files = new File[] { new File(fileName) };
        }

        log.info("files : " + Arrays.toString(files));

        if (files == null || files.length == 0) {
            log.info("no files to parse");
            System.exit(0);
        }

        boolean formatsource = true;
        if (System.getProperty("formatsource") != null && !System.getProperty("formatsource").equals("")
                && System.getProperty("formatsource").equalsIgnoreCase("false")) {
            formatsource = false;
        }

        GEN_ROOT = System.getProperty("outputdir");

        if (GEN_ROOT == null || GEN_ROOT.equals("")) {
            GEN_ROOT = new File(files[0].getAbsolutePath()).getParent() + FILE_SEPARATOR + "distrib";
        }

        GEN_ROOT = new File(GEN_ROOT).getAbsolutePath().replace('\\', '/');
        if (GEN_ROOT.endsWith("/"))
            GEN_ROOT = GEN_ROOT.substring(0, GEN_ROOT.length() - 1);

        System.out.println("GEN ROOT:" + GEN_ROOT);

        MAPPING_JAR_NAME = System.getProperty("mappingjar") != null
                && !System.getProperty("mappingjar").equals("") ? System.getProperty("mappingjar")
                        : "mapping.jar";
        if (!MAPPING_JAR_NAME.endsWith(".jar"))
            MAPPING_JAR_NAME += ".jar";

        GEN_ROOT_SRC = GEN_ROOT + FILE_SEPARATOR + "src";
        GEN_ROOT_LIB = GEN_ROOT + FILE_SEPARATOR + "";

        DocumentBuilderFactory domFactory = DocumentBuilderFactory.newInstance();
        domFactory.setNamespaceAware(true);
        domFactory.setValidating(false);
        DocumentBuilder documentBuilder = domFactory.newDocumentBuilder();

        for (int f = 0; f < files.length; ++f) {
            log.info("parsing file : " + files[f]);
            Document document = documentBuilder.parse(files[f]);

            Vector<Node> initNodes = new Vector<Node>();
            Utils.catchNodes(Utils.catchNode(document.getDocumentElement(), "scripts"), "initScript",
                    initNodes);
            for (int i = 0; i < initNodes.size(); ++i) {
                NamedNodeMap attrs = initNodes.elementAt(i).getAttributes();
                boolean embed = attrs.getNamedItem("embed") != null
                        && attrs.getNamedItem("embed").getNodeValue().equalsIgnoreCase("true");
                StringBuffer vbuffer = new StringBuffer();
                if (attrs.getNamedItem("inline") != null) {
                    vbuffer.append(attrs.getNamedItem("inline").getNodeValue());
                    vbuffer.append('\n');
                } else {
                    String fname = attrs.getNamedItem("name").getNodeValue();
                    if (!fname.startsWith("\\") && !fname.startsWith("/") && fname.toCharArray()[1] != ':') {
                        String path = files[f].getAbsolutePath();
                        path = path.substring(0, path.lastIndexOf(FILE_SEPARATOR));
                        fname = new File(path + FILE_SEPARATOR + fname).getCanonicalPath();
                    }
                    vbuffer.append(Utils.getFileAsStringBuffer(fname));
                }
                initScriptBuffer.append(vbuffer);
                if (embed)
                    embedScriptBuffer.append(vbuffer);
            }

            Vector<Node> packageInitNodes = new Vector<Node>();
            Utils.catchNodes(Utils.catchNode(document.getDocumentElement(), "scripts"), "packageScript",
                    packageInitNodes);
            for (int i = 0; i < packageInitNodes.size(); ++i) {
                NamedNodeMap attrs = packageInitNodes.elementAt(i).getAttributes();
                String packageName = attrs.getNamedItem("package").getNodeValue();

                if (packageName.equals(""))
                    packageName = "rGlobalEnv";

                if (!packageName.endsWith("Function"))
                    packageName += "Function";
                if (packageEmbedScriptHashMap.get(packageName) == null) {
                    packageEmbedScriptHashMap.put(packageName, new StringBuffer());
                }
                StringBuffer vbuffer = packageEmbedScriptHashMap.get(packageName);

                // if (!packageName.equals("rGlobalEnvFunction")) {
                // vbuffer.append("library("+packageName.substring(0,packageName.lastIndexOf("Function"))+")\n");
                // }

                if (attrs.getNamedItem("inline") != null) {
                    vbuffer.append(attrs.getNamedItem("inline").getNodeValue() + "\n");
                    initScriptBuffer.append(attrs.getNamedItem("inline").getNodeValue() + "\n");
                } else {
                    String fname = attrs.getNamedItem("name").getNodeValue();
                    if (!fname.startsWith("\\") && !fname.startsWith("/") && fname.toCharArray()[1] != ':') {
                        String path = files[f].getAbsolutePath();
                        path = path.substring(0, path.lastIndexOf(FILE_SEPARATOR));
                        fname = new File(path + FILE_SEPARATOR + fname).getCanonicalPath();
                    }
                    StringBuffer fileBuffer = Utils.getFileAsStringBuffer(fname);
                    vbuffer.append(fileBuffer);
                    initScriptBuffer.append(fileBuffer);
                }
            }

            Vector<Node> functionsNodes = new Vector<Node>();
            Utils.catchNodes(Utils.catchNode(document.getDocumentElement(), "functions"), "function",
                    functionsNodes);
            for (int i = 0; i < functionsNodes.size(); ++i) {
                NamedNodeMap attrs = functionsNodes.elementAt(i).getAttributes();
                String functionName = attrs.getNamedItem("name").getNodeValue();

                boolean forWeb = attrs.getNamedItem("forWeb") != null
                        && attrs.getNamedItem("forWeb").getNodeValue().equalsIgnoreCase("true");

                String signature = (attrs.getNamedItem("signature") == null ? ""
                        : attrs.getNamedItem("signature").getNodeValue() + ",");
                String renameTo = (attrs.getNamedItem("renameTo") == null ? null
                        : attrs.getNamedItem("renameTo").getNodeValue());

                HashMap<String, FAttributes> sigMap = Globals._functionsToPublish.get(functionName);

                if (sigMap == null) {
                    sigMap = new HashMap<String, FAttributes>();
                    Globals._functionsToPublish.put(functionName, sigMap);

                    if (attrs.getNamedItem("returnType") == null) {
                        _functionsVector.add(new String[] { functionName });
                    } else {
                        _functionsVector.add(
                                new String[] { functionName, attrs.getNamedItem("returnType").getNodeValue() });
                    }

                }

                sigMap.put(signature, new FAttributes(renameTo, forWeb));

                if (forWeb)
                    _webPublishingEnabled = true;

            }

            if (System.getProperty("targetjdk") != null && !System.getProperty("targetjdk").equals("")
                    && System.getProperty("targetjdk").compareTo("1.5") < 0) {
                if (_webPublishingEnabled || (System.getProperty("ws.r.api") != null
                        && System.getProperty("ws.r.api").equalsIgnoreCase("true"))) {
                    log.info("be careful, web publishing disabled beacuse target JDK<1.5");
                }
                _webPublishingEnabled = false;
            } else {

                if (System.getProperty("ws.r.api") == null || System.getProperty("ws.r.api").equals("")
                        || !System.getProperty("ws.r.api").equalsIgnoreCase("false")) {
                    _webPublishingEnabled = true;
                }

                if (_webPublishingEnabled && System.getProperty("java.version").compareTo("1.5") < 0) {
                    log.info("be careful, web publishing disabled beacuse a JDK<1.5 is in use");
                    _webPublishingEnabled = false;
                }
            }

            Vector<Node> s4Nodes = new Vector<Node>();
            Utils.catchNodes(Utils.catchNode(document.getDocumentElement(), "s4classes"), "class", s4Nodes);

            if (s4Nodes.size() > 0) {
                String formalArgs = "";
                String signature = "";
                for (int i = 0; i < s4Nodes.size(); ++i) {
                    NamedNodeMap attrs = s4Nodes.elementAt(i).getAttributes();
                    String s4Name = attrs.getNamedItem("name").getNodeValue();
                    formalArgs += "p" + i + (i == s4Nodes.size() - 1 ? "" : ",");
                    signature += "'" + s4Name + "'" + (i == s4Nodes.size() - 1 ? "" : ",");
                }
                String genBeansScriptlet = "setGeneric('" + PUBLISH_S4_HEADER + "', function(" + formalArgs
                        + ") standardGeneric('" + PUBLISH_S4_HEADER + "'));" + "setMethod('" + PUBLISH_S4_HEADER
                        + "', signature(" + signature + ") , function(" + formalArgs + ") {   })";
                initScriptBuffer.append(genBeansScriptlet);
                _functionsVector.add(new String[] { PUBLISH_S4_HEADER, "numeric" });
            }

        }

        if (!new File(GEN_ROOT_LIB).exists())
            regenerateDir(GEN_ROOT_LIB);
        else {
            clean(GEN_ROOT_LIB, true);
        }

        for (int i = 0; i < rwebservicesScripts.length; ++i)
            DirectJNI.getInstance().getRServices().sourceFromResource(rwebservicesScripts[i]);

        String lastStatus = DirectJNI.getInstance().runR(new ExecutionUnit() {
            public void run(Rengine e) {
                DirectJNI.getInstance().toggleMarker();
                DirectJNI.getInstance().sourceFromBuffer(initScriptBuffer.toString());
                log.info(" init  script status : " + DirectJNI.getInstance().cutStatusSinceMarker());

                for (int i = 0; i < _functionsVector.size(); ++i) {

                    String[] functionPair = _functionsVector.elementAt(i);
                    log.info("dealing with : " + functionPair[0]);

                    regenerateDir(GEN_ROOT_SRC);

                    String createMapStr = "createMap(";
                    boolean isGeneric = e.rniGetBoolArrayI(
                            e.rniEval(e.rniParse("isGeneric(\"" + functionPair[0] + "\")", 1), 0))[0] == 1;

                    log.info("is Generic : " + isGeneric);
                    if (isGeneric) {
                        createMapStr += functionPair[0];
                    } else {
                        createMapStr += "\"" + functionPair[0] + "\"";
                    }
                    createMapStr += ", outputDirectory=\"" + GEN_ROOT_SRC
                            .substring(0, GEN_ROOT_SRC.length() - "/src".length()).replace('\\', '/') + "\"";
                    createMapStr += ", typeMode=\"robject\"";
                    createMapStr += (functionPair.length == 1 || functionPair[1] == null
                            || functionPair[1].trim().equals("") ? ""
                                    : ", S4DefaultTypedSig=TypedSignature(returnType=\"" + functionPair[1]
                                            + "\")");
                    createMapStr += ")";

                    log.info("------------------------------------------");
                    log.info("-- createMapStr=" + createMapStr);
                    DirectJNI.getInstance().toggleMarker();
                    e.rniEval(e.rniParse(createMapStr, 1), 0);
                    String createMapStatus = DirectJNI.getInstance().cutStatusSinceMarker();
                    log.info(" createMap status : " + createMapStatus);
                    log.info("------------------------------------------");

                    deleteDir(GEN_ROOT_SRC + "/org/kchine/r/rserviceJms");
                    compile(GEN_ROOT_SRC);
                    jar(GEN_ROOT_SRC, GEN_ROOT_LIB + FILE_SEPARATOR + TEMP_JARS_PREFIX + i + ".jar", null);

                    URL url = null;
                    try {
                        url = new URL(
                                "jar:file:" + (GEN_ROOT_LIB + FILE_SEPARATOR + TEMP_JARS_PREFIX + i + ".jar")
                                        .replace('\\', '/') + "!/");
                    } catch (Exception ex) {
                        ex.printStackTrace();
                    }
                    DirectJNI.generateMaps(url, true);
                }

            }
        });

        log.info(lastStatus);

        log.info(DirectJNI._rPackageInterfacesHash);
        regenerateDir(GEN_ROOT_SRC);
        for (int i = 0; i < _functionsVector.size(); ++i) {
            unjar(GEN_ROOT_LIB + FILE_SEPARATOR + TEMP_JARS_PREFIX + i + ".jar", GEN_ROOT_SRC);
        }

        regenerateRPackageClass(true);

        generateS4BeanRef();

        if (formatsource)
            applyJalopy(GEN_ROOT_SRC);

        compile(GEN_ROOT_SRC);

        for (String k : DirectJNI._rPackageInterfacesHash.keySet()) {
            Rmic rmicTask = new Rmic();
            rmicTask.setProject(_project);
            rmicTask.setTaskName("rmic_packages");
            rmicTask.setClasspath(new Path(_project, GEN_ROOT_SRC));
            rmicTask.setBase(new File(GEN_ROOT_SRC));
            rmicTask.setClassname(k + "ImplRemote");
            rmicTask.init();
            rmicTask.execute();
        }

        // DirectJNI._rPackageInterfacesHash=new HashMap<String,
        // Vector<Class<?>>>();
        // DirectJNI._rPackageInterfacesHash.put("org.bioconductor.packages.rGlobalEnv.rGlobalEnvFunction",new
        // Vector<Class<?>>());

        if (_webPublishingEnabled) {

            jar(GEN_ROOT_SRC, GEN_ROOT_LIB + FILE_SEPARATOR + "__temp.jar", null);
            URL url = new URL(
                    "jar:file:" + (GEN_ROOT_LIB + FILE_SEPARATOR + "__temp.jar").replace('\\', '/') + "!/");
            ClassLoader cl = new URLClassLoader(new URL[] { url }, Globals.class.getClassLoader());

            for (String className : DirectJNI._rPackageInterfacesHash.keySet()) {
                if (cl.loadClass(className + "Web").getDeclaredMethods().length == 0)
                    continue;
                log.info("######## " + className);

                WsGen wsgenTask = new WsGen();
                wsgenTask.setProject(_project);
                wsgenTask.setTaskName("wsgen");

                FileSet rjb_fileSet = new FileSet();
                rjb_fileSet.setProject(_project);
                rjb_fileSet.setDir(new File("."));
                rjb_fileSet.setIncludes("RJB.jar");

                DirSet src_dirSet = new DirSet();
                src_dirSet.setDir(new File(GEN_ROOT_LIB + FILE_SEPARATOR + "src/"));
                Path classPath = new Path(_project);
                classPath.addFileset(rjb_fileSet);
                classPath.addDirset(src_dirSet);
                wsgenTask.setClasspath(classPath);
                wsgenTask.setKeep(true);
                wsgenTask.setDestdir(new File(GEN_ROOT_LIB + FILE_SEPARATOR + "src/"));
                wsgenTask.setResourcedestdir(new File(GEN_ROOT_LIB + FILE_SEPARATOR + "src/"));
                wsgenTask.setSei(className + "Web");

                wsgenTask.init();
                wsgenTask.execute();
            }

            new File(GEN_ROOT_LIB + FILE_SEPARATOR + "__temp.jar").delete();

        }

        embedRScripts();

        HashMap<String, String> marker = new HashMap<String, String>();
        marker.put("RJBMAPPINGJAR", "TRUE");

        Properties props = new Properties();
        props.put("PACKAGE_NAMES", PoolUtils.objectToHex(DirectJNI._packageNames));
        props.put("S4BEANS_MAP", PoolUtils.objectToHex(DirectJNI._s4BeansMapping));
        props.put("S4BEANS_REVERT_MAP", PoolUtils.objectToHex(DirectJNI._s4BeansMappingRevert));
        props.put("FACTORIES_MAPPING", PoolUtils.objectToHex(DirectJNI._factoriesMapping));
        props.put("S4BEANS_HASH", PoolUtils.objectToHex(DirectJNI._s4BeansHash));
        props.put("R_PACKAGE_INTERFACES_HASH", PoolUtils.objectToHex(DirectJNI._rPackageInterfacesHash));
        props.put("ABSTRACT_FACTORIES", PoolUtils.objectToHex(DirectJNI._abstractFactories));
        new File(GEN_ROOT_SRC + "/" + "maps").mkdirs();
        FileOutputStream fos = new FileOutputStream(GEN_ROOT_SRC + "/" + "maps/rjbmaps.xml");
        props.storeToXML(fos, null);
        fos.close();

        jar(GEN_ROOT_SRC, GEN_ROOT_LIB + FILE_SEPARATOR + MAPPING_JAR_NAME, marker);

        if (_webPublishingEnabled)
            genWeb();

        DirectJNI._mappingClassLoader = null;

    } finally {

        System.exit(0);

    }
}

From source file:com.genentech.chemistry.tool.align.SDFAlign.java

public static void main(String... args) {
    Options options = new Options();
    Option opt = new Option("in", true, "input sd file");
    opt.setRequired(true);/*from  w ww .j a  v  a  2s .  co  m*/
    options.addOption(opt);

    opt = new Option("out", true, "output file");
    opt.setRequired(true);
    options.addOption(opt);

    opt = new Option("method", true, "fss|sss|MCS|clique (default mcs).");
    options.addOption(opt);

    opt = new Option("ref", true,
            "reference molecule if not given first in file is used. If multiple ref molecules are read the min RMSD is reported");
    options.addOption(opt);

    opt = new Option("mirror", false, "If given and the molecule is not chiral, return best mirror image.");
    options.addOption(opt);

    opt = new Option("rmsdTag", true, "Tagname for output of rmsd, default: no output.");
    options.addOption(opt);

    opt = new Option("atomMatch", true,
            "Sequence of none|default|hcount|noAromatic specifing how atoms are matched cf. oe document.\n"
                    + "noAromatic can be used to make terminal atoms match aliphatic and aromatic atoms.\n"
                    + "Queryfeatures are considered only if default is used.");
    options.addOption(opt);

    opt = new Option("bondMatch", true,
            "Sequence of none|default specifing how bonds are matched cf. oe document.");
    options.addOption(opt);

    opt = new Option("keepCoreHydrogens", false,
            "If not specified the hydrigen atoms are removed from the core.");
    options.addOption(opt);

    opt = new Option("outputMol", true, "aligned|original (def: aligned) use original to just compute rmsd.");
    options.addOption(opt);

    opt = new Option("doNotOptimize", false,
            "If specified the RMSD is computed without moving optimizing the overlay.");
    options.addOption(opt);

    opt = new Option("quiet", false, "Reduced warining messages");
    options.addOption(opt);

    CommandLineParser parser = new BasicParser();
    CommandLine cmd = null;
    try {
        cmd = parser.parse(options, args);
    } catch (Exception e) {
        exitWithHelp(e.getMessage(), options);
    }

    if (cmd.getArgs().length > 0)
        exitWithHelp("To many arguments", options);

    // do not check aromaticity on atoms so that a terminal atom matches aromatic and non aromatic atoms
    int atomExpr = OEExprOpts.DefaultAtoms;
    int bondExpr = OEExprOpts.DefaultBonds;

    String atomMatch = cmd.getOptionValue("atomMatch");
    if (atomMatch == null)
        atomMatch = "";
    atomMatch = '|' + atomMatch.toLowerCase() + '|';

    String bondMatch = cmd.getOptionValue("bondMatch");
    if (bondMatch == null)
        bondMatch = "";
    bondMatch = '|' + bondMatch.toLowerCase() + '|';

    String inFile = cmd.getOptionValue("in");
    String outFile = cmd.getOptionValue("out");
    String refFile = cmd.getOptionValue("ref");
    String method = cmd.getOptionValue("method");
    String rmsdTag = cmd.getOptionValue("rmsdTag");
    String oMol = cmd.getOptionValue("outputMol");
    boolean doMirror = cmd.hasOption("mirror");
    boolean doOptimize = !cmd.hasOption("doNotOptimize");
    boolean quiet = cmd.hasOption("quiet");

    OUTType outputMol = oMol == null ? OUTType.ALIGNED : OUTType.valueOf(oMol.toUpperCase());

    if (atomMatch.startsWith("|none"))
        atomExpr = 0;
    if (atomMatch.contains("|hcount|"))
        atomExpr |= OEExprOpts.HCount;
    if (atomMatch.contains("|noAromatic|"))
        atomExpr &= (~OEExprOpts.Aromaticity);

    if (bondMatch.startsWith("|none"))
        bondExpr = 0;

    ArrayList<OEMol> refmols = new ArrayList<OEMol>();
    if (refFile != null) {
        oemolistream reffs = new oemolistream(refFile);
        if (!is3DFormat(reffs.GetFormat()))
            oechem.OEThrow.Fatal("Invalid input format: need 3D coordinates");
        reffs.SetFormat(OEFormat.MDL);

        int aromodel = OEIFlavor.Generic.OEAroModelOpenEye;
        int qflavor = reffs.GetFlavor(reffs.GetFormat());
        reffs.SetFlavor(reffs.GetFormat(), (qflavor | aromodel));

        OEMol rmol = new OEMol();
        while (oechem.OEReadMDLQueryFile(reffs, rmol)) {
            if (!cmd.hasOption("keepCoreHydrogens"))
                oechem.OESuppressHydrogens(rmol);
            refmols.add(rmol);
            rmol = new OEMol();
        }
        rmol.delete();

        if (refmols.size() == 0)
            throw new Error("reference file had no entries");

        reffs.close();
    }

    oemolistream fitfs = new oemolistream(inFile);
    if (!is3DFormat(fitfs.GetFormat()))
        oechem.OEThrow.Fatal("Invalid input format: need 3D coordinates");

    oemolostream ofs = new oemolostream(outFile);
    if (!is3DFormat(ofs.GetFormat()))
        oechem.OEThrow.Fatal("Invalid output format: need 3D coordinates");

    AlignInterface aligner = null;
    OEGraphMol fitmol = new OEGraphMol();

    if (oechem.OEReadMolecule(fitfs, fitmol)) {
        if (refmols.size() == 0) {
            OEMol rmol = new OEMol(fitmol);
            if (!cmd.hasOption("keepCoreHydrogens"))
                oechem.OESuppressHydrogens(rmol);

            refmols.add(rmol);
        }

        if ("sss".equalsIgnoreCase(method)) {
            aligner = new SSSAlign(refmols, outputMol, rmsdTag, doOptimize, doMirror, atomExpr, bondExpr,
                    quiet);

        } else if ("clique".equalsIgnoreCase(method)) {
            aligner = new CliqueAlign(refmols, outputMol, rmsdTag, doOptimize, doMirror, atomExpr, bondExpr,
                    quiet);

        } else if ("fss".equalsIgnoreCase(method)) {
            if (cmd.hasOption("atomMatch") || cmd.hasOption("bondMatch"))
                exitWithHelp("method fss does not support '-atomMatch' or '-bondMatch'", options);
            aligner = new FSSAlign(refmols, outputMol, rmsdTag, doOptimize, doMirror);

        } else {
            aligner = new McsAlign(refmols, outputMol, rmsdTag, doOptimize, doMirror, atomExpr, bondExpr,
                    quiet);
        }

        do {
            aligner.align(fitmol);
            oechem.OEWriteMolecule(ofs, fitmol);
        } while (oechem.OEReadMolecule(fitfs, fitmol));

    }

    fitmol.delete();
    if (aligner != null)
        aligner.close();
    for (OEMolBase mol : refmols)
        mol.delete();
    fitfs.close();
    ofs.close();
}

From source file:LamportBasicVersion.java

public static void main(String[] args) throws FileNotFoundException, IOException, InterruptedException {
    totalMessageCount = 0;/* w  w w .j a  v a  2  s  . com*/
    //For parsing the file and storing the information
    String line;
    String configurationFile = "configuration.txt";
    int lineCountInFile = 0;
    myProcessId = Integer.parseInt(args[0]);
    FileReader fileReader = new FileReader(configurationFile);
    BufferedReader bufferedReader = new BufferedReader(fileReader);
    while ((line = bufferedReader.readLine()) != null) {
        if ((!(line.startsWith("#"))) && (!(line.isEmpty()))) {
            lineCountInFile = lineCountInFile + 1;
            String[] splitLine = line.split(" ");
            switch (lineCountInFile) {
            case 1:
                numberOfProcesses = Integer.parseInt(splitLine[0]);
                interRequestDelay = Integer.parseInt(splitLine[1]);
                csExecutionTime = Integer.parseInt(splitLine[2]);
                maxNumberOfRequest = Integer.parseInt(splitLine[3]);
                machineNames = new String[Integer.parseInt(splitLine[0])];
                portNumbers = new int[Integer.parseInt(splitLine[0])];
                break;
            default:
                machineNames[lineCountInFile - 2] = splitLine[1];
                portNumbers[lineCountInFile - 2] = Integer.parseInt(splitLine[2]);
                break;
            }
        }
    }
    conditionArray = new int[numberOfProcesses];
    finishFlagArray = new int[numberOfProcesses];
    //Initializing vector class
    VectorClass.initialize(numberOfProcesses);
    //Fill the arrays with zero false value
    for (int o = 0; o < numberOfProcesses; o++) {
        conditionArray[o] = 0;
        finishFlagArray[o] = 0;
    }
    // Write output to file
    filename = filename + Integer.toString(myProcessId) + ".out";
    file = new File(filename);
    file.createNewFile();
    writer = new FileWriter(file);
    // Write clocks to file
    filenameClock = filenameClock + Integer.toString(myProcessId) + ".out";
    fileClock = new File(filenameClock);
    fileClock.createNewFile();
    //writerClock = new FileWriter(fileClock);
    fw = new FileWriter(fileClock);
    bw = new BufferedWriter(fw);
    //
    // Expo mean insert
    csExecutionExpoDelay = new ExponentialDistribution(csExecutionTime);
    interRequestExpoDelay = new ExponentialDistribution(interRequestDelay);
    //
    System.out.println("********************************************************");
    System.out.println("My process id : " + myProcessId);
    System.out.println("Number of processes : " + numberOfProcesses);
    System.out.println("Inter-request delay : " + interRequestDelay);
    System.out.println("Critical section execution time : " + csExecutionTime);
    System.out.println("Maximum number of request : " + maxNumberOfRequest);
    System.out.println(
            "My process name : " + machineNames[myProcessId] + " My port number : " + portNumbers[myProcessId]);
    for (int i = 0; i < numberOfProcesses; i++) {
        System.out.println("Process name : " + machineNames[i] + " Port number : " + portNumbers[i]);
    }
    System.out.println("********************************************************");
    //For hosting server localhost
    SctpServerChannel sctpServerChannel = SctpServerChannel.open();
    InetSocketAddress serverAddr = new InetSocketAddress(portNumbers[myProcessId]);
    sctpServerChannel.bind(serverAddr);
    System.out.println("********************************************************");
    System.out.println("Local server hosted");
    System.out.println("********************************************************");
    //For creating neighbor SCTP channels
    Thread.sleep(30000);
    socketAddress = new SocketAddress[numberOfProcesses];
    sctpChannel = new SctpChannel[numberOfProcesses];
    System.out.println("********************************************************");
    System.out.println("Neighbor channels created");
    System.out.println("********************************************************");
    //Thread spanned for generating critical section request
    new Thread(new LamportBasicVersion()).start();
    //while loop to receive all the requests and other messages
    while (true) {
        try (SctpChannel sctpChannelFromClient = sctpServerChannel.accept()) {
            mutex.acquire();
            byteBufferFromNeighbor.clear();
            String receiveMessage;
            MessageInfo messageInfoFromNeighbor = sctpChannelFromClient.receive(byteBufferFromNeighbor, null,
                    null);
            //System.out.println("Raw Message : " + messageInfoFromNeighbor);
            receiveMessage = byteToString(byteBufferFromNeighbor, messageInfoFromNeighbor);
            //write to file start
            writer.write("Received Message : " + receiveMessage);
            writer.write("\n");
            writer.flush();
            //write to file end
            System.out.println("Received Message : " + receiveMessage);
            if (receiveMessage.contains("Request")) {
                String[] parseMessage = receiveMessage.split("-");
                lamportClock = Math.max(lamportClock, Integer.parseInt(parseMessage[3])) + 1;
                //vector clock update
                String[] stringNumericalTimestamp = parseMessage[4].split(",");
                int[] numericalTimestamp = new int[stringNumericalTimestamp.length];
                for (int d = 0; d < stringNumericalTimestamp.length; d++) {
                    numericalTimestamp[d] = Integer.parseInt(stringNumericalTimestamp[d]);
                }
                VectorClass.update(myProcessId, numericalTimestamp);
                //
                int requestMade = Integer.parseInt(parseMessage[3] + parseMessage[1]);
                queue.add(requestMade);
                //Send reply messages to that process for entering CS
                lamportClock++;
                //vector clock construction
                int[] vector = VectorClass.increment(myProcessId);
                String vectorClockConstruction = "";
                for (int g = 0; g < vector.length; g++) {
                    if (g == 0) {
                        vectorClockConstruction = vectorClockConstruction + Integer.toString(vector[g]);
                    } else {
                        vectorClockConstruction = vectorClockConstruction + "," + Integer.toString(vector[g]);
                    }
                }
                //
                for (int k = 0; k < numberOfProcesses; k++) {
                    if (k == Integer.parseInt(parseMessage[1])) {
                        try {
                            byteBufferToNeighbor.clear();
                            initializeChannels();
                            sctpChannel[k].connect(socketAddress[k]);
                            String sendMessage = "Reply from Process-" + myProcessId + "-"
                                    + Integer.toString(requestMade) + "-" + lamportClock + "-"
                                    + vectorClockConstruction;
                            System.out.println("Message sent is : " + sendMessage);
                            //write to file start
                            writer.write("Message sent is : " + sendMessage);
                            writer.write("\n");
                            writer.flush();
                            //write to file end
                            MessageInfo messageInfoToNeighbor = MessageInfo.createOutgoing(null, 0);
                            byteBufferToNeighbor.put(sendMessage.getBytes());
                            byteBufferToNeighbor.flip();
                            sctpChannel[k].send(byteBufferToNeighbor, messageInfoToNeighbor);
                            totalMessageCount++;
                            sctpChannel[k].close();
                        } catch (IOException ex) {
                            Logger.getLogger(LamportBasicVersion.class.getName()).log(Level.SEVERE, null, ex);
                        }
                    }
                }
            } else if (receiveMessage.contains("Reply")) {
                conditionArray[myProcessId] = 1;
                String[] parseMessage = receiveMessage.split("-");
                lamportClock = Math.max(lamportClock, Integer.parseInt(parseMessage[3])) + 1;
                //vector clock update
                String[] stringNumericalTimestamp = parseMessage[4].split(",");
                int[] numericalTimestamp = new int[stringNumericalTimestamp.length];
                for (int d = 0; d < stringNumericalTimestamp.length; d++) {
                    numericalTimestamp[d] = Integer.parseInt(stringNumericalTimestamp[d]);
                }
                VectorClass.update(myProcessId, numericalTimestamp);
                //
                conditionArray[Integer.parseInt(parseMessage[1])] = 1;
                int count = 0;
                for (int v = 0; v < numberOfProcesses; v++) {
                    if (conditionArray[v] == 1) {
                        count = count + 1;
                    }
                }
                if (count == numberOfProcesses) {
                    L1ConditionFlag = 1;
                    System.out.println("Inside L1");
                    blockingQueue.put("L1");
                    //Clearing condition array after receiving all REPLY
                    for (int z = 0; z < numberOfProcesses; z++) {
                        conditionArray[z] = 0;
                    }
                    if (L2ConditionFlag == 0 && outstandingRequest == 1) {
                        Integer[] queueArray = new Integer[queue.size()];
                        queue.toArray(queueArray);
                        Arrays.sort(queueArray);
                        if (queueArray[0] == currentRequestBeingServed) {
                            System.out.println("Inside L2");
                            L2ConditionFlag = 1;
                            blockingQueue.put("L2");
                        }
                    }
                }
            } else if (receiveMessage.contains("Release")) {
                int present = 0;
                int delete = 0;
                String[] parseMessage = receiveMessage.split("-");
                lamportClock = Math.max(lamportClock, Integer.parseInt(parseMessage[3])) + 1;
                //vector clock update
                String[] stringNumericalTimestamp = parseMessage[4].split(",");
                int[] numericalTimestamp = new int[stringNumericalTimestamp.length];
                for (int d = 0; d < stringNumericalTimestamp.length; d++) {
                    numericalTimestamp[d] = Integer.parseInt(stringNumericalTimestamp[d]);
                }
                VectorClass.update(myProcessId, numericalTimestamp);
                //
                if (queue.size() != 0) {
                    Integer[] queueArray = new Integer[queue.size()];
                    queue.toArray(queueArray);
                    Arrays.sort(queueArray);
                    for (int a = 0; a < queueArray.length; a++) {
                        if (queueArray[a] == Integer.parseInt(parseMessage[2])) {
                            present = 1;
                            delete = a;
                        }
                    }
                    if (present == 1) {
                        for (int s = 0; s <= delete; s++) {
                            queue.remove();
                        }
                    }
                }
                if (L2ConditionFlag == 0 && outstandingRequest == 1) {
                    if (queue.size() != 0) {
                        Integer[] queueArray1 = new Integer[queue.size()];
                        queue.toArray(queueArray1);
                        Arrays.sort(queueArray1);
                        if (currentRequestBeingServed == queueArray1[0]) {
                            L2ConditionFlag = 1;
                            System.out.println("Inside L2");
                            blockingQueue.put("L2");
                        }
                    }
                }
            } else if (receiveMessage.contains("Finish")) {
                String[] parseMessage = receiveMessage.split("-");
                lamportClock = Math.max(lamportClock, Integer.parseInt(parseMessage[3])) + 1;
                //vector clock update
                String[] stringNumericalTimestamp = parseMessage[4].split(",");
                int[] numericalTimestamp = new int[stringNumericalTimestamp.length];
                for (int d = 0; d < stringNumericalTimestamp.length; d++) {
                    numericalTimestamp[d] = Integer.parseInt(stringNumericalTimestamp[d]);
                }
                VectorClass.update(myProcessId, numericalTimestamp);
                //
                finishFlagArray[Integer.parseInt(parseMessage[1])] = 1;
                int count = 0;
                for (int v = 0; v < numberOfProcesses; v++) {
                    if (finishFlagArray[v] == 1) {
                        count = count + 1;
                    }
                }
                if (count == numberOfProcesses) {
                    break;
                }
            }
            //logic for other messages
            //Print the queue to check
            System.out.println("********************************************************");
            for (Object item : queue) {
                System.out.print(item);
                System.out.print("\t");
            }
            System.out.println("********************************************************");
        }
        mutex.release();
    }
}

From source file:DocumentTracer.java

/** Main. */
public static void main(String[] argv) throws Exception {

    // is there anything to do?
    if (argv.length == 0) {
        printUsage();/*  w w  w .j a  v  a2s.co  m*/
        System.exit(1);
    }

    // variables
    DocumentTracer tracer = new DocumentTracer();
    PrintWriter out = new PrintWriter(System.out);
    XMLReader parser = null;
    boolean namespaces = DEFAULT_NAMESPACES;
    boolean namespacePrefixes = DEFAULT_NAMESPACE_PREFIXES;
    boolean validation = DEFAULT_VALIDATION;
    boolean externalDTD = DEFAULT_LOAD_EXTERNAL_DTD;
    boolean schemaValidation = DEFAULT_SCHEMA_VALIDATION;
    boolean schemaFullChecking = DEFAULT_SCHEMA_FULL_CHECKING;
    boolean honourAllSchemaLocations = DEFAULT_HONOUR_ALL_SCHEMA_LOCATIONS;
    boolean validateAnnotations = DEFAULT_VALIDATE_ANNOTATIONS;
    boolean dynamicValidation = DEFAULT_DYNAMIC_VALIDATION;
    boolean xincludeProcessing = DEFAULT_XINCLUDE;
    boolean xincludeFixupBaseURIs = DEFAULT_XINCLUDE_FIXUP_BASE_URIS;
    boolean xincludeFixupLanguage = DEFAULT_XINCLUDE_FIXUP_LANGUAGE;

    // process arguments
    for (int i = 0; i < argv.length; i++) {
        String arg = argv[i];
        if (arg.startsWith("-")) {
            String option = arg.substring(1);
            if (option.equals("p")) {
                // get parser name
                if (++i == argv.length) {
                    System.err.println("error: Missing argument to -p option.");
                }
                String parserName = argv[i];

                // create parser
                try {
                    parser = XMLReaderFactory.createXMLReader(parserName);
                } catch (Exception e) {
                    try {
                        Parser sax1Parser = ParserFactory.makeParser(parserName);
                        parser = new ParserAdapter(sax1Parser);
                        System.err.println("warning: Features and properties not supported on SAX1 parsers.");
                    } catch (Exception ex) {
                        parser = null;
                        System.err.println("error: Unable to instantiate parser (" + parserName + ")");
                    }
                }
                continue;
            }
            if (option.equalsIgnoreCase("n")) {
                namespaces = option.equals("n");
                continue;
            }
            if (option.equalsIgnoreCase("np")) {
                namespacePrefixes = option.equals("np");
                continue;
            }
            if (option.equalsIgnoreCase("v")) {
                validation = option.equals("v");
                continue;
            }
            if (option.equalsIgnoreCase("xd")) {
                externalDTD = option.equals("xd");
                continue;
            }
            if (option.equalsIgnoreCase("s")) {
                schemaValidation = option.equals("s");
                continue;
            }
            if (option.equalsIgnoreCase("f")) {
                schemaFullChecking = option.equals("f");
                continue;
            }
            if (option.equalsIgnoreCase("hs")) {
                honourAllSchemaLocations = option.equals("hs");
                continue;
            }
            if (option.equalsIgnoreCase("va")) {
                validateAnnotations = option.equals("va");
                continue;
            }
            if (option.equalsIgnoreCase("dv")) {
                dynamicValidation = option.equals("dv");
                continue;
            }
            if (option.equalsIgnoreCase("xi")) {
                xincludeProcessing = option.equals("xi");
                continue;
            }
            if (option.equalsIgnoreCase("xb")) {
                xincludeFixupBaseURIs = option.equals("xb");
                continue;
            }
            if (option.equalsIgnoreCase("xl")) {
                xincludeFixupLanguage = option.equals("xl");
                continue;
            }
            if (option.equals("h")) {
                printUsage();
                continue;
            }
        }

        // use default parser?
        if (parser == null) {

            // create parser
            try {
                parser = XMLReaderFactory.createXMLReader(DEFAULT_PARSER_NAME);
            } catch (Exception e) {
                System.err.println("error: Unable to instantiate parser (" + DEFAULT_PARSER_NAME + ")");
                continue;
            }
        }

        // set parser features
        try {
            parser.setFeature(NAMESPACES_FEATURE_ID, namespaces);
        } catch (SAXException e) {
            System.err.println("warning: Parser does not support feature (" + NAMESPACES_FEATURE_ID + ")");
        }
        try {
            parser.setFeature(NAMESPACE_PREFIXES_FEATURE_ID, namespacePrefixes);
        } catch (SAXException e) {
            System.err.println(
                    "warning: Parser does not support feature (" + NAMESPACE_PREFIXES_FEATURE_ID + ")");
        }
        try {
            parser.setFeature(VALIDATION_FEATURE_ID, validation);
        } catch (SAXException e) {
            System.err.println("warning: Parser does not support feature (" + VALIDATION_FEATURE_ID + ")");
        }
        try {
            parser.setFeature(LOAD_EXTERNAL_DTD_FEATURE_ID, externalDTD);
        } catch (SAXNotRecognizedException e) {
            System.err.println(
                    "warning: Parser does not recognize feature (" + LOAD_EXTERNAL_DTD_FEATURE_ID + ")");
        } catch (SAXNotSupportedException e) {
            System.err
                    .println("warning: Parser does not support feature (" + LOAD_EXTERNAL_DTD_FEATURE_ID + ")");
        }
        try {
            parser.setFeature(SCHEMA_VALIDATION_FEATURE_ID, schemaValidation);
        } catch (SAXNotRecognizedException e) {
            System.err.println(
                    "warning: Parser does not recognize feature (" + SCHEMA_VALIDATION_FEATURE_ID + ")");
        } catch (SAXNotSupportedException e) {
            System.err
                    .println("warning: Parser does not support feature (" + SCHEMA_VALIDATION_FEATURE_ID + ")");
        }
        try {
            parser.setFeature(SCHEMA_FULL_CHECKING_FEATURE_ID, schemaFullChecking);
        } catch (SAXNotRecognizedException e) {
            System.err.println(
                    "warning: Parser does not recognize feature (" + SCHEMA_FULL_CHECKING_FEATURE_ID + ")");
        } catch (SAXNotSupportedException e) {
            System.err.println(
                    "warning: Parser does not support feature (" + SCHEMA_FULL_CHECKING_FEATURE_ID + ")");
        }
        try {
            parser.setFeature(HONOUR_ALL_SCHEMA_LOCATIONS_ID, honourAllSchemaLocations);
        } catch (SAXNotRecognizedException e) {
            System.err.println(
                    "warning: Parser does not recognize feature (" + HONOUR_ALL_SCHEMA_LOCATIONS_ID + ")");
        } catch (SAXNotSupportedException e) {
            System.err.println(
                    "warning: Parser does not support feature (" + HONOUR_ALL_SCHEMA_LOCATIONS_ID + ")");
        }
        try {
            parser.setFeature(VALIDATE_ANNOTATIONS_ID, validateAnnotations);
        } catch (SAXNotRecognizedException e) {
            System.err.println("warning: Parser does not recognize feature (" + VALIDATE_ANNOTATIONS_ID + ")");
        } catch (SAXNotSupportedException e) {
            System.err.println("warning: Parser does not support feature (" + VALIDATE_ANNOTATIONS_ID + ")");
        }
        try {
            parser.setFeature(DYNAMIC_VALIDATION_FEATURE_ID, dynamicValidation);
        } catch (SAXNotRecognizedException e) {
            System.err.println(
                    "warning: Parser does not recognize feature (" + DYNAMIC_VALIDATION_FEATURE_ID + ")");
        } catch (SAXNotSupportedException e) {
            System.err.println(
                    "warning: Parser does not support feature (" + DYNAMIC_VALIDATION_FEATURE_ID + ")");
        }
        try {
            parser.setFeature(XINCLUDE_FEATURE_ID, xincludeProcessing);
        } catch (SAXNotRecognizedException e) {
            System.err.println("warning: Parser does not recognize feature (" + XINCLUDE_FEATURE_ID + ")");
        } catch (SAXNotSupportedException e) {
            System.err.println("warning: Parser does not support feature (" + XINCLUDE_FEATURE_ID + ")");
        }
        try {
            parser.setFeature(XINCLUDE_FIXUP_BASE_URIS_FEATURE_ID, xincludeFixupBaseURIs);
        } catch (SAXNotRecognizedException e) {
            System.err.println(
                    "warning: Parser does not recognize feature (" + XINCLUDE_FIXUP_BASE_URIS_FEATURE_ID + ")");
        } catch (SAXNotSupportedException e) {
            System.err.println(
                    "warning: Parser does not support feature (" + XINCLUDE_FIXUP_BASE_URIS_FEATURE_ID + ")");
        }
        try {
            parser.setFeature(XINCLUDE_FIXUP_LANGUAGE_FEATURE_ID, xincludeFixupLanguage);
        } catch (SAXNotRecognizedException e) {
            System.err.println(
                    "warning: Parser does not recognize feature (" + XINCLUDE_FIXUP_LANGUAGE_FEATURE_ID + ")");
        } catch (SAXNotSupportedException e) {
            System.err.println(
                    "warning: Parser does not support feature (" + XINCLUDE_FIXUP_LANGUAGE_FEATURE_ID + ")");
        }

        // set handlers
        parser.setDTDHandler(tracer);
        parser.setErrorHandler(tracer);
        if (parser instanceof XMLReader) {
            parser.setContentHandler(tracer);
            try {
                parser.setProperty("http://xml.org/sax/properties/declaration-handler", tracer);
            } catch (SAXException e) {
                e.printStackTrace(System.err);
            }
            try {
                parser.setProperty("http://xml.org/sax/properties/lexical-handler", tracer);
            } catch (SAXException e) {
                e.printStackTrace(System.err);
            }
        } else {
            ((Parser) parser).setDocumentHandler(tracer);
        }

        // parse file
        try {
            parser.parse(arg);
        } catch (SAXParseException e) {
            // ignore
        } catch (Exception e) {
            System.err.println("error: Parse error occurred - " + e.getMessage());
            if (e instanceof SAXException) {
                Exception nested = ((SAXException) e).getException();
                if (nested != null) {
                    e = nested;
                }
            }
            e.printStackTrace(System.err);
        }
    }

}

From source file:com.spinn3r.api.Main.java

public static void main(String[] args) throws Exception {

    // NOTE this could be cleaned up to pass the values into the config
    // object directly.

    // parse out propeties.

    String api = null;//from www  .  j a  v  a 2s.co m

    for (int i = 0; i < args.length; ++i) {
        String v = args[i];

        if (v.startsWith("--api")) {
            api = getOpt(v);
        }

    }

    if (api == null)
        api = "permalink";

    // First. Determine which API you'd like to use.

    long after = -1;
    Format format = Format.PROTOSTREAM;
    String vendor = null;
    String remoteFilter = null;
    Long sleep_duration = null;
    boolean skip_description = false;
    String host = "api.spinn3r.com";

    for (int i = 0; i < args.length; ++i) {

        String v = args[i];

        if (v.startsWith("--vendor")) {
            vendor = getOpt(v);
            continue;
        }

        if (v.startsWith("--filter")) {
            filter = getOpt(v);
            continue;
        }

        if (v.startsWith("--remote-filter")) {
            remoteFilter = getOpt(v);
            continue;
        }

        if (v.startsWith("--show_results")) {
            show_results = Integer.parseInt(getOpt(v));
            continue;
        }

        /*
         * The code for the --afterTimestamp must come
         * before the code for --after because --afterTimestamp
         * also matches startsWith("after");
         */
        if (v.startsWith("--afterTimestamp")) {
            after = Long.parseLong(getOpt(v));
            continue;
        }

        if (v.startsWith("--after")) {
            after = getOptAsTimeInMillis(v);
            continue;
        }

        /*
         * The code for the --beforeTimestamp must come
         * before the code for --before because --beforeTimestamp
         * also matches startsWith("before");
         */
        if (v.startsWith("--beforeTimestamp")) {
            before = Long.parseLong(getOpt(v));
            continue;
        }

        if (v.startsWith("--before")) {
            before = getOptAsTimeInMillis(v);
            continue;
        }

        if (v.startsWith("--range")) {
            range = Long.parseLong(getOpt(v));
            continue;
        }

        if (v.startsWith("--recover")) {
            restore = true;
            continue;
        }

        if (v.startsWith("--sleep_duration")) {
            sleep_duration = Long.parseLong(getOpt(v));
            continue;
        }

        if (v.startsWith("--save=")) {
            save = getOpt(v);
            continue;
        }

        if (v.startsWith("--save_method=")) {
            save_method = getOpt(v);
            continue;
        }

        if (v.startsWith("--skip_description=")) {
            skip_description = Boolean.parseBoolean(getOpt(v));
            continue;
        }

        if (v.startsWith("--save_compressed=")) {
            saveCompressed = Boolean.parseBoolean(getOpt(v));
            continue;
        }

        if (v.startsWith("--timing")) {
            timing = "true".equals(getOpt(v));
            continue;
        }

        if (v.startsWith("--debug")) {
            logLevel = Level.FINE;
            debugLogFilePath = getOpt(v);
            continue;
        }

        /*
         * if ( v.startsWith( "--spam_probability" ) ) {
         * config.setSpamProbability( Double.parseDouble( getOpt( v ) ) );
         * continue; }
         */

        if (v.startsWith("--dump_fields=")) {
            dumpFields = Boolean.parseBoolean(getOpt(v));
            continue;
        }

        if (v.startsWith("--dump=")) {
            dump = Boolean.parseBoolean(getOpt(v));
            continue;
        }

        if (v.startsWith("--csv=")) {
            csv = Boolean.parseBoolean(getOpt(v));
            continue;
        }

        if (v.startsWith("--memory")) {

            System.out.printf("max memory: %s\n", Runtime.getRuntime().maxMemory());
            System.exit(0);
        }

        if (v.startsWith("--host")) {
            host = getOpt(v);
            continue;
        }

        if (v.startsWith("--enable3")) {
            // is now default
            continue;
        }

        if (v.startsWith("com.spinn3r"))
            continue;

        if (v.startsWith("--api"))
            continue;

        // That's an unknown command line option. Exit.
        System.err.printf("Unknown command line option: %s\n", v);
        syntax();
        System.exit(1);

    }

    /*
     * Set the log level
     */
    Logger anonymousLogger = Logger.getAnonymousLogger();
    anonymousLogger.setLevel(logLevel);
    if (debugLogFilePath != null) {
        anonymousLogger.addHandler(new FileHandler(debugLogFilePath));
    }

    Factory factory = new Factory();
    String restoreURL = null;

    if (save != null && restore) {
        File savedir = new File(save);
        Collection<File> logFiles = getLogFiles(savedir);
        PermalinkLogReaderAdapter adapter = getRestoreURLS(logFiles);

        restoreURL = adapter.getLastUrl();
        long ctr = adapter.getLastCtr();

        for (File file : logFiles) {
            if (!file.delete())
                throw new IOException("Failed to delete " + file.toString());
        }

        factory.enableLogging(savedir, 1000000);
        if (restoreURL != null) {
            factory.enableRestart(ctr, restoreURL);
        }
        logManager = factory.getInjector().getInstance(TransactionHistoryManager.class);
    } else {
        logManager = factory.getInjector().getInstance(TransactionHistoryManager.class);
    }

    Config<? extends BaseResult> config = null;
    BaseClient<? extends BaseResult> client = null;

    if (api.startsWith("feed")) {
        config = new FeedConfig();
        client = new FeedClient();
    } else if (api.startsWith("comment")) {
        config = new CommentConfig();
        client = new CommentClient();
    } else {
        config = new PermalinkConfig();
        client = new PermalinkClient(
                restoreURL != null ? ImmutableList.of(restoreURL) : Collections.<String>emptyList());
    }

    config.setCommandLine(StringUtils.join(args, " "));

    config.setApi(api);
    config.setFormat(format);
    config.setVendor(vendor);
    config.setHost(host);
    config.setFilter(remoteFilter);
    config.setSkipDescription(skip_description);
    if (sleep_duration != null)
        client.setSleepDuration(sleep_duration);

    // assert that we have all required options.

    if (config.getVendor() == null) {
        syntax();
        System.exit(1);
    }

    long maxMemory = Runtime.getRuntime().maxMemory();
    long requiredMemory = (save == null) ? PARSE_REQUIRED_MEMORY : SAVE_REQUIRED_MEMORY;

    if (maxMemory < requiredMemory) {

        System.out.printf("ERROR: Reference client requires at least 2GB of memory.\n");
        System.out.printf("\n");
        System.out.printf("Now running with: %s vs %s required\n", maxMemory, requiredMemory);
        System.out.printf("\n");
        System.out.printf("Add -Xmx%dM to your command line and run again.\n", requiredMemory / (1024 * 1024));

        System.exit(1);

    }

    // use defaults

    System.out.println("Using vendor: " + config.getVendor());
    System.out.println("Using api:    " + api);

    if (after > -1)
        System.out.printf("After: %s (%s)\n", ISO8601DateParser.toString(Config.timestampToDate(after)), after);

    if (before > -1)
        System.out.printf("Before: %s (%s)\n", ISO8601DateParser.toString(Config.timestampToDate(before)),
                before);

    System.out.println("Saving results to disk: " + save);

    // Fetch for the last 5 minutes and then try to get up to date. In
    // production you'd want to call setFirstRequestURL from the
    // getLastRequestURL returned from fetch() below

    if (after == -1) {
        after = Config.millisecondsToTimestamp(System.currentTimeMillis());
        after = after - INTERVAL;
    }

    config.setAfterTimestamp(after);

    new Main().exec(client, config);

}

From source file:ImageInfo.java

/**
 * To use this class as a command line application, give it either
 * some file names as parameters (information on them will be
 * printed to standard output, one line per file) or call
 * it with no parameters. It will then check data given to it
 * via standard input.//from  w  w w . ja va2  s  . c o  m
 *
 * @param args the program arguments which must be file names
 */
public static void main(String[] args) {
    ImageInfo imageInfo = new ImageInfo();
    imageInfo.setDetermineImageNumber(true);
    boolean verbose = determineVerbosity(args);
    if (args.length == 0) {
        run(null, System.in, imageInfo, verbose);
    } else {
        int index = 0;
        while (index < args.length) {
            InputStream in = null;
            try {
                String name = args[index++];
                System.out.print(name + ";");
                if (name.startsWith("http://")) {
                    in = new URL(name).openConnection().getInputStream();
                } else {
                    in = new FileInputStream(name);
                }
                run(name, in, imageInfo, verbose);
                in.close();
            } catch (Exception e) {
                System.out.println(e);
                try {
                    in.close();
                } catch (Exception ee) {
                }
            }
        }
    }
}

From source file:luisjosediez.Ejercicio2.java

/**
 * @param args the command line arguments
 *///w ww .  j  a  v a2 s. c o  m
public static void main(String[] args) {
    // TODO code application logic here
    System.out.println("Introduce la direccin de un servidor ftp: ");
    FTPClient cliente = new FTPClient();
    String servFTP = cadena();
    String clave = "";
    System.out.println("Introduce usuario (vaco para conexin annima): ");
    String usuario = cadena();
    String opcion;
    if (usuario.equals("")) {
        clave = "";
    } else {
        System.out.println("Introduce contrasea: ");
        clave = cadena();
    }
    try {
        cliente.setPassiveNatWorkaround(false);
        cliente.connect(servFTP, 21);
        boolean login = cliente.login(usuario, clave);
        if (login) {
            System.out.println("Conexin ok");
        } else {
            System.out.println("Login incorrecto");
            cliente.disconnect();
            System.exit(1);
        }
        do {

            System.out.println("Orden [exit para salir]: ");
            opcion = cadena();
            if (opcion.equals("ls")) {
                FTPFile[] files = cliente.listFiles();
                String tipos[] = { "Fichero", "Directorio", "Enlace" };
                for (int i = 0; i < files.length; i++) {
                    System.out.println("\t" + files[i].getName() + "\t=> " + tipos[files[i].getType()]);
                }
            } else if (opcion.startsWith("cd ")) {
                try {
                    cliente.changeWorkingDirectory(opcion.substring(3));
                } catch (IOException e) {
                }
            } else if (opcion.equals("help")) {
                System.out.println(
                        "Puede ejecutar los comandos 'exit', 'ls', 'cd', 'get' y 'upload'. Para ms detalles utilice 'help <comando>'.");
            } else if (opcion.startsWith("help ")) {
                if (opcion.endsWith(" get")) {
                    System.out.println(
                            "Permite descargar un archivo concreto. Uso: 'get <rutaArchivoADescargar>'.");
                } else if (opcion.endsWith(" ls")) {
                    System.out.println("Lista los ficheros y directorios en la ubicacin actual. Uso: 'ls'.");
                } else if (opcion.endsWith(" cd")) {
                    System.out.println("Permite cambiar la ubicacin actual. Uso: 'cd <rutaDestino>'.");
                } else if (opcion.endsWith(" put")) {
                    System.out.println(
                            "Permite subir un archivo al directorio actual. Uso: 'put <rutaArchivoASubir>'.");
                }
            } else if (opcion.startsWith("get ")) {
                try {
                    System.out.println("Indique la carpeta de descarga: ");
                    try (FileOutputStream fos = new FileOutputStream(cadena() + opcion.substring(4))) {
                        cliente.retrieveFile(opcion.substring(4), fos);
                    } catch (IOException e) {
                        e.printStackTrace();
                    }
                } catch (Exception e) {
                }
            } else if (opcion.startsWith("put ")) {
                try {
                    try {

                        System.out.println(opcion.substring(4));

                        File local = new File(opcion.substring(4));

                        System.out.println(local.getName());

                        InputStream is = new FileInputStream(opcion.substring(4));

                        OutputStream os = cliente.storeFileStream(local.getName());

                        byte[] bytesIn = new byte[4096];

                        int read = 0;

                        while ((read = is.read(bytesIn)) != -1) {

                            os.write(bytesIn, 0, read);

                        }

                        is.close();
                        os.close();

                        boolean completed = cliente.completePendingCommand();

                        if (completed) {
                            System.out.println("The file is uploaded successfully.");
                        }

                    } catch (IOException e) {
                        e.printStackTrace();
                    }
                } catch (Exception e) {
                }
            }

        } while (!(opcion.equals("exit")));

        boolean logout = cliente.logout();
        if (logout)
            System.out.println("Logout...");
        else
            System.out.println("Logout incorrecto");

        cliente.disconnect();

    } catch (Exception e) {
        e.printStackTrace();
    }
}

From source file:DIA_Umpire_SE.DIA_Umpire_SE.java

/**
 * @param args the command line arguments DIA_Umpire parameterfile
 *///from  www  .  j  a v  a2s  . co  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;
    }
}