Example usage for java.util Vector add

List of usage examples for java.util Vector add

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Introduction

In this page you can find the example usage for java.util Vector add.

Prototype

public synchronized boolean add(E e)

Source Link

Document

Appends the specified element to the end of this Vector.

Usage

From source file:gda.util.PackageMaker.java

/**
 * @param args//from   w ww.  j a va 2  s . c  o m
 */
public static void main(String args[]) {
    String destDir = null;
    if (args.length == 0)
        return;
    String filename = args[0];
    if (args.length > 1)
        destDir = args[1];
    try {
        ClassParser cp = new ClassParser(filename);
        JavaClass classfile = cp.parse();
        String packageName = classfile.getPackageName();
        String apackageName = packageName.replace(".", File.separator);
        if (destDir != null)
            destDir = destDir + File.separator + apackageName;
        else
            destDir = apackageName;
        File destFile = new File(destDir);
        File existFile = new File(filename);
        File parentDir = new File(existFile.getAbsolutePath().substring(0,
                existFile.getAbsolutePath().lastIndexOf(File.separator)));
        String allFiles[] = parentDir.list();
        Vector<String> selectedFiles = new Vector<String>();
        String toMatch = existFile.getName().substring(0, existFile.getName().lastIndexOf("."));
        for (int i = 0; i < allFiles.length; i++) {
            if (allFiles[i].startsWith(toMatch + "$"))
                selectedFiles.add(allFiles[i]);
        }
        FileUtils.copyFileToDirectory(existFile, destFile);
        Object[] filestoCopy = selectedFiles.toArray();
        for (int i = 0; i < filestoCopy.length; i++) {
            FileUtils.copyFileToDirectory(new File((String) filestoCopy[i]), destFile);
        }
    }

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

From source file:com.intel.cosbench.driver.generator.RangeIntGenerator.java

public static void main(String[] args) {
    final String pattern = "r(51,1000)";
    final int all = 5;
    int i = 0;/* w  ww. ja  va2 s  .com*/
    Vector<TestThread> threads = new Vector<TestThread>();
    RangeIntGenerator gen = RangeIntGenerator.parse(pattern);

    for (i = 0; i < all; i++) {
        TestThread thread = new TestThread(gen, i + 1, all);
        threads.add(thread);
        thread.start();
    }

    try {
        for (i = 0; i < all; i++) {
            threads.elementAt(i).join();
        }
    } catch (InterruptedException ie) {
        ie.printStackTrace();
    }
}

From source file:createSod.java

/**
 * @param args/*from  w w  w .j a v  a 2  s.  c  o  m*/
 * @throws CMSException 
 */
public static void main(String[] args) throws Exception {

    try {
        CommandLine options = verifyArgs(args);
        String privateKeyLocation = options.getOptionValue("privatekey");
        String keyPassword = options.getOptionValue("keypass");
        String certificate = options.getOptionValue("certificate");
        String sodContent = options.getOptionValue("content");
        String sod = "";
        if (options.hasOption("out")) {
            sod = options.getOptionValue("out");
        }

        // CHARGEMENT DU FICHIER PKCS#12

        KeyStore ks = null;
        char[] password = null;

        Security.addProvider(new BouncyCastleProvider());
        try {
            ks = KeyStore.getInstance("PKCS12");
            // Password pour le fichier personnal_nyal.p12
            password = keyPassword.toCharArray();
            ks.load(new FileInputStream(privateKeyLocation), password);
        } catch (Exception e) {
            System.out.println("Erreur: fichier " + privateKeyLocation
                    + " n'est pas un fichier pkcs#12 valide ou passphrase incorrect");
            return;
        }

        // RECUPERATION DU COUPLE CLE PRIVEE/PUBLIQUE ET DU CERTIFICAT PUBLIQUE

        X509Certificate cert = null;
        PrivateKey privatekey = null;
        PublicKey publickey = null;

        try {
            Enumeration en = ks.aliases();
            String ALIAS = "";
            Vector vectaliases = new Vector();

            while (en.hasMoreElements())
                vectaliases.add(en.nextElement());
            String[] aliases = (String[]) (vectaliases.toArray(new String[0]));
            for (int i = 0; i < aliases.length; i++)
                if (ks.isKeyEntry(aliases[i])) {
                    ALIAS = aliases[i];
                    break;
                }
            privatekey = (PrivateKey) ks.getKey(ALIAS, password);
            cert = (X509Certificate) ks.getCertificate(ALIAS);
            publickey = ks.getCertificate(ALIAS).getPublicKey();
        } catch (Exception e) {
            e.printStackTrace();
            return;
        }

        // Chargement du certificat  partir du fichier

        InputStream inStream = new FileInputStream(certificate);
        CertificateFactory cf = CertificateFactory.getInstance("X.509");
        cert = (X509Certificate) cf.generateCertificate(inStream);
        inStream.close();

        // Chargement du fichier qui va tre sign

        File file_to_sign = new File(sodContent);
        byte[] buffer = new byte[(int) file_to_sign.length()];
        DataInputStream in = new DataInputStream(new FileInputStream(file_to_sign));
        in.readFully(buffer);
        in.close();

        // Chargement des certificats qui seront stocks dans le fichier .p7
        // Ici, seulement le certificat personnal_nyal.cer sera associ.
        // Par contre, la chane des certificats non.

        ArrayList certList = new ArrayList();
        certList.add(cert);
        CertStore certs = CertStore.getInstance("Collection", new CollectionCertStoreParameters(certList),
                "BC");

        CMSSignedDataGenerator signGen = new CMSSignedDataGenerator();

        // privatekey correspond  notre cl prive rcupre du fichier PKCS#12
        // cert correspond au certificat publique personnal_nyal.cer
        // Le dernier argument est l'algorithme de hachage qui sera utilis

        signGen.addSigner(privatekey, cert, CMSSignedDataGenerator.DIGEST_SHA1);
        signGen.addCertificatesAndCRLs(certs);
        CMSProcessable content = new CMSProcessableByteArray(buffer);

        // Generation du fichier CMS/PKCS#7
        // L'argument deux permet de signifier si le document doit tre attach avec la signature
        //     Valeur true:  le fichier est attach (c'est le cas ici)
        //     Valeur false: le fichier est dtach

        CMSSignedData signedData = signGen.generate(content, true, "BC");
        byte[] signeddata = signedData.getEncoded();

        // Ecriture du buffer dans un fichier.   

        if (sod.equals("")) {
            System.out.print(signeddata.toString());
        } else {
            FileOutputStream envfos = new FileOutputStream(sod);
            envfos.write(signeddata);
            envfos.close();
        }

    } catch (OptionException oe) {
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp(NAME, getOptions());
        System.exit(-1);
    } catch (Exception e) {
        e.printStackTrace();
        return;
    }

}

From source file:gov.nih.nci.evs.reportwriter.utils.SimpleSearchUtils.java

public static void main(String[] args) {
    boolean searchExtensionAvaliable = isSearchExtensionAvaliable();
    if (!searchExtensionAvaliable) {
        System.out.println("SearchExtension is not available.");
        System.exit(1);// w  ww  .  j a v a2 s  . c  o  m
    }

    SimpleSearchUtils test = new SimpleSearchUtils();
    try {
        Vector<String> schemes = new Vector();
        Vector<String> versions = new Vector();
        schemes.add("NCI_Thesaurus");
        versions.add(null);

        String matchText = "Tariquidar";

        ResolvedConceptReferencesIteratorWrapper wrapper = test.search(schemes, versions, matchText,
                SimpleSearchUtils.BY_NAME, "contains");
        if (wrapper != null) {
            ResolvedConceptReferencesIterator iterator = wrapper.getIterator();
            if (iterator != null) {
                try {
                    int numRemaining = iterator.numberRemaining();
                    System.out.println("Number of matches: " + numRemaining);
                    dumpIterator(iterator);

                } catch (Exception ex) {
                    ex.printStackTrace();
                }
            }
        } else {
            System.out.println("wrapper is NULL??? " + matchText);
        }

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

From source file:gov.nih.nci.evs.browser.utils.SimpleSearchUtils.java

public static void main(String[] args) {
    boolean searchExtensionAvaliable = isSearchExtensionAvaliable();
    if (!searchExtensionAvaliable) {
        System.out.println("SearchExtension is not available.");
        System.exit(1);/*from ww w.j av a 2s  .com*/
    }

    SimpleSearchUtils test = new SimpleSearchUtils();
    try {
        Vector<String> schemes = new Vector();
        Vector<String> versions = new Vector();
        schemes.add("NCI_Thesaurus");
        //versions.add("12.05d");
        versions.add("13.03d");

        schemes.add("NCI Metathesaurus");
        versions.add("201105");

        String matchText = "cell aging";

        ResolvedConceptReferencesIteratorWrapper wrapper = test.search(schemes, versions, matchText,
                SimpleSearchUtils.BY_NAME, "contains");
        if (wrapper != null) {
            ResolvedConceptReferencesIterator iterator = wrapper.getIterator();
            if (iterator != null) {
                try {
                    int numRemaining = iterator.numberRemaining();
                    System.out.println("Number of matches: " + numRemaining);
                    dumpIterator(iterator);

                } catch (Exception ex) {
                    ex.printStackTrace();
                }
            }
        } else {
            System.out.println("wrapper is NULL??? " + matchText);
        }

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

From source file:BoxSample.java

public static void main(String args[]) {
    JButton button;//w  w w  .  jav a2s  .  c o  m
    Vector buttons = new Vector();
    Dimension dim;
    JFrame frame = new JFrame("Box Example");
    frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);

    Container contentPane = frame.getContentPane();
    contentPane.setLayout(new BoxLayout(contentPane, BoxLayout.X_AXIS));
    JPanel topLeft = new JPanel();
    topLeft.setLayout(new BoxLayout(topLeft, BoxLayout.X_AXIS));
    topLeft.add(button = new JButton("One"));
    buttons.add(button);
    changeBoth(button);
    topLeft.add(button = new JButton("Two"));
    buttons.add(button);
    changeBoth(button);
    changeWidth(topLeft);
    JPanel bottomLeft = new JPanel();
    bottomLeft.setLayout(new BoxLayout(bottomLeft, BoxLayout.X_AXIS));
    bottomLeft.add(button = new JButton("Six"));
    buttons.add(button);
    changeBoth(button);
    bottomLeft.add(button = new JButton("Seven"));
    buttons.add(button);
    changeBoth(button);
    changeWidth(bottomLeft);
    JPanel left = new JPanel();
    left.setLayout(new BoxLayout(left, BoxLayout.Y_AXIS));
    left.add(topLeft);
    left.add(button = new JButton("Four"));
    buttons.add(button);
    changeBoth(button);
    left.add(bottomLeft);
    changeBoth(left);

    JPanel right = new JPanel();
    right.setLayout(new BoxLayout(right, BoxLayout.Y_AXIS));
    right.add(button = new JButton("Three"));
    buttons.add(button);
    changeWidth(button);
    right.add(button = new JButton("Five"));
    buttons.add(button);
    changeBoth(button);
    changeBoth(right);
    contentPane.add(left);
    contentPane.add(right);
    tweak(buttons);
    frame.pack();
    frame.setVisible(true);
}

From source file:Main.java

public static void main(String[] args) {
    Vector<Double> doubleVector = new Vector<Double>();
    Vector<Integer> integerVector = new Vector<Integer>();
    Vector<Boolean> booleanVector = new Vector<Boolean>();
    Vector<Icon> iconVector = new Vector<Icon>();
    Icon icon1 = ((UIManager.getIcon("OptionPane.errorIcon")));
    Icon icon2 = (UIManager.getIcon("OptionPane.informationIcon"));
    Icon icon3 = (UIManager.getIcon("OptionPane.warningIcon"));
    Icon icon4 = (UIManager.getIcon("OptionPane.questionIcon"));

    doubleVector.addElement(1.001);/*from  ww w .ja v a2s  .  c o  m*/
    doubleVector.addElement(10.00);
    doubleVector.addElement(0.95);
    doubleVector.addElement(4.2);
    JComboBox comboBoxDouble = new JComboBox(doubleVector);
    integerVector.addElement(1);
    integerVector.addElement(2);
    integerVector.addElement(3);
    integerVector.addElement(4);
    JComboBox comboBoxInteger = new JComboBox(integerVector);
    booleanVector.add(Boolean.TRUE);
    booleanVector.add(Boolean.FALSE);
    JComboBox comboBoxBoolean = new JComboBox(booleanVector);
    iconVector.addElement(icon1);
    iconVector.addElement(icon2);
    iconVector.addElement(icon3);
    iconVector.addElement(icon4);
    JComboBox comboBoxIcon = new JComboBox(iconVector);
    JFrame frame = new JFrame();
    frame.setLayout(new GridLayout(2, 2, 5, 5));
    frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
    frame.add(comboBoxDouble);
    frame.add(comboBoxInteger);
    frame.add(comboBoxBoolean);
    frame.add(comboBoxIcon);
    frame.pack();
    frame.setVisible(true);
}

From source file:edu.ku.brc.specify.dbsupport.cleanuptools.FirstLastVerifier.java

/**
 * @param args/*from  w  w  w  .  j a  v  a  2  s.  c om*/
 */
public static void main(String[] args) {
    if (true) {
        testLastNames();
        return;
    }
    FirstLastVerifier flv = new FirstLastVerifier();
    System.out.println(flv.isFirstName("Bill"));
    System.out.println(flv.isLastName("Bill"));

    System.out.println(flv.isFirstName("Johnson"));
    System.out.println(flv.isLastName("Johnson"));

    try {
        if (false) {
            for (String nm : new String[] { "firstnames", "lastnames" }) {
                File file = new File("/Users/rods/Downloads/" + nm + ".txt");
                try {
                    PrintWriter pw = new PrintWriter("/Users/rods/Downloads/" + nm + ".list");
                    for (String line : (List<String>) FileUtils.readLines(file)) {
                        String[] toks = StringUtils.split(line, '\t');
                        if (toks != null && toks.length > 0)
                            pw.println(toks[0]);
                    }
                    pw.close();

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

        Vector<String> lnames = new Vector<String>();
        File file = XMLHelper.getConfigDir("lastnames.list");
        if (false) {
            for (String name : (List<String>) FileUtils.readLines(file)) {
                if (flv.isFirstName(name)) {
                    System.out.println(name + " is first.");
                } else {
                    lnames.add(name);
                }
            }
            Collections.sort(lnames);
            FileUtils.writeLines(file, lnames);
        }

        lnames.clear();
        file = XMLHelper.getConfigDir("firstnames.list");
        for (String name : (List<String>) FileUtils.readLines(file)) {
            if (flv.isLastName(name)) {
                System.out.println(name + " is first.");
            } else {
                lnames.add(name);
            }
        }
        Collections.sort(lnames);
        //FileUtils.writeLines(file, lnames);

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

From source file:com.seanmadden.fast.ldap.main.Main.java

/**
 * The Main Event./*from  www  . j a va  2s .c o m*/
 * 
 * @param args
 */
@SuppressWarnings("static-access")
public static void main(String[] args) {
    BasicConfigurator.configure();
    log.debug("System initializing");
    try {
        Logger.getRootLogger().addAppender(
                new FileAppender(new PatternLayout(PatternLayout.TTCC_CONVERSION_PATTERN), "log.log"));
    } catch (IOException e1) {
        log.error("Unable to open the log file..?");
    }

    /*
     * Initialize the configuration engine.
     */
    XMLConfiguration config = new XMLConfiguration();
    config.setListDelimiter('|');

    /*
     * Initialize the Command-Line parsing engine.
     */
    CommandLineParser parser = new PosixParser();
    Options opts = new Options();
    opts.addOption(OptionBuilder.withLongOpt("config-file").hasArg()
            .withDescription("The configuration file to load").withArgName("config.xml").create("c"));

    opts.addOption(OptionBuilder.withLongOpt("profile").hasArg().withDescription("The profile to use")
            .withArgName("Default").create("p"));

    opts.addOption(OptionBuilder.withLongOpt("password").hasArg().withDescription("Password to connect with")
            .withArgName("password").create("P"));

    opts.addOption(OptionBuilder.withLongOpt("debug").hasArg(false).create('d'));

    opts.addOption(OptionBuilder.withLongOpt("verbose").hasArg(false).create('v'));

    File configurationFile = new File("config.xml");

    try {
        // Parse the command-line options
        CommandLine cmds = parser.parse(opts, args);

        if (!cmds.hasOption('p')) {
            Logger.getRootLogger().addAppender(new GuiErrorAlerter(Level.ERROR));
        }

        Logger.getRootLogger().setLevel(Level.ERROR);
        if (cmds.hasOption('v')) {
            Logger.getRootLogger().setLevel(Level.INFO);
        }
        if (cmds.hasOption('d')) {
            Logger.getRootLogger().setLevel(Level.DEBUG);
        }

        log.debug("Enabling configuration file parsing");
        // The user has given us a file to parse.
        if (cmds.hasOption("c")) {
            configurationFile = new File(cmds.getOptionValue("c"));
        }
        log.debug("Config file: " + configurationFile);

        // Load the configuration file
        if (configurationFile.exists()) {
            config.load(configurationFile);
        } else {
            log.error("Cannot find config file");
        }

        /*
         * Convert the profiles into memory
         */
        Vector<ConnectionProfile> profs = new Vector<ConnectionProfile>();
        List<?> profList = config.configurationAt("Profiles").configurationsAt("Profile");
        for (Object p : profList) {
            SubnodeConfiguration profile = (SubnodeConfiguration) p;
            String name = profile.getString("[@name]");
            String auth = profile.getString("LdapAuthString");
            String server = profile.getString("LdapServerString");
            String group = profile.getString("LdapGroupsLocation");
            ConnectionProfile prof = new ConnectionProfile(name, server, auth, group);
            profs.add(prof);
        }
        ConnectionProfile prof = null;
        if (!cmds.hasOption('p')) {
            /*
             * Deploy the profile selector, to select a profile
             */
            ProfileSelector profSel = new ProfileSelector(profs);
            prof = profSel.getSelection();
            if (prof == null) {
                return;
            }
            /*
             * Empty the profiles and load a clean copy - then save it back
             * to the file
             */
            config.clearTree("Profiles");
            for (ConnectionProfile p : profSel.getProfiles()) {
                config.addProperty("Profiles.Profile(-1)[@name]", p.getName());
                config.addProperty("Profiles.Profile.LdapAuthString", p.getLdapAuthString());
                config.addProperty("Profiles.Profile.LdapServerString", p.getLdapServerString());
                config.addProperty("Profiles.Profile.LdapGroupsLocation", p.getLdapGroupsString());
            }
            config.save(configurationFile);
        } else {
            for (ConnectionProfile p : profs) {
                if (p.getName().equals(cmds.getOptionValue('p'))) {
                    prof = p;
                    break;
                }
            }
        }

        log.info("User selected " + prof);

        String password = "";
        if (cmds.hasOption('P')) {
            password = cmds.getOptionValue('P');
        } else {
            password = PasswordPrompter.promptForPassword("Password?");
        }

        if (password.equals("")) {
            return;
        }

        LdapInterface ldap = new LdapInterface(prof.getLdapServerString(), prof.getLdapAuthString(),
                prof.getLdapGroupsString(), password);

        /*
         * Gather options information from the configuration engine for the
         * specified report.
         */
        Hashtable<String, Hashtable<String, ReportOption>> reportDataStructure = new Hashtable<String, Hashtable<String, ReportOption>>();
        List<?> repConfig = config.configurationAt("Reports").configurationsAt("Report");
        for (Object p : repConfig) {
            SubnodeConfiguration repNode = (SubnodeConfiguration) p;

            // TODO Do something with the report profile.
            // Allowing the user to deploy "profiles" is a nice feature
            // String profile = repNode.getString("[@profile]");

            String reportName = repNode.getString("[@report]");
            Hashtable<String, ReportOption> reportOptions = new Hashtable<String, ReportOption>();
            reportDataStructure.put(reportName, reportOptions);
            // Loop through the options and add each to the table.
            for (Object o : repNode.configurationsAt("option")) {
                SubnodeConfiguration option = (SubnodeConfiguration) o;
                String name = option.getString("[@name]");
                String type = option.getString("[@type]");
                String value = option.getString("[@value]");

                ReportOption ro = new ReportOption();
                ro.setName(name);

                if (type.toLowerCase().equals("boolean")) {
                    ro.setBoolValue(Boolean.parseBoolean(value));
                } else if (type.toLowerCase().equals("integer")) {
                    ro.setIntValue(Integer.valueOf(value));
                } else {
                    // Assume a string type here then.
                    ro.setStrValue(value);
                }
                reportOptions.put(name, ro);
                log.debug(ro);
            }
        }
        System.out.println(reportDataStructure);

        /*
         * At this point, we now need to deploy the reports window to have
         * the user pick a report and select some happy options to allow
         * that report to work. Let's go.
         */
        /*
         * Deploy the Reports selector, to select a report
         */
        Reports.getInstance().setLdapConnection(ldap);
        ReportsWindow reports = new ReportsWindow(Reports.getInstance().getAllReports(), reportDataStructure);
        Report report = reports.getSelection();
        if (report == null) {
            return;
        }
        /*
         * Empty the profiles and load a clean copy - then save it back to
         * the file
         */
        config.clearTree("Reports");
        for (Report r : Reports.getInstance().getAllReports()) {
            config.addProperty("Reports.Report(-1)[@report]", r.getClass().getCanonicalName());
            config.addProperty("Reports.Report[@name]", "Standard");
            for (ReportOption ro : r.getOptions().values()) {
                config.addProperty("Reports.Report.option(-1)[@name]", ro.getName());
                config.addProperty("Reports.Report.option[@type]", ro.getType());
                config.addProperty("Reports.Report.option[@value]", ro.getStrValue());
            }
        }
        config.save(configurationFile);
        ProgressBar bar = new ProgressBar();
        bar.start();
        report.execute();
        ASCIIFormatter format = new ASCIIFormatter();
        ReportResult res = report.getResult();
        format.format(res, new File(res.getForName() + "_" + res.getReportName() + ".txt"));
        bar.stop();

        JOptionPane.showMessageDialog(null,
                "The report is at " + res.getForName() + "_" + res.getReportName() + ".txt", "Success",
                JOptionPane.INFORMATION_MESSAGE);

    } catch (ParseException e) {
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp("FAST Ldap Searcher", opts);
    } catch (ConfigurationException e) {
        e.printStackTrace();
        log.fatal("OH EM GEES!  Configuration errors.");
    } catch (Exception e) {
        e.printStackTrace();
    }

}

From source file:mzmatch.ipeak.align.CowCoda.java

@SuppressWarnings("unchecked")
public static void main(String args[]) {
    final String lbl_mcq = "mcq";

    try {// w  ww  .ja  v  a  2 s .  c o m
        Tool.init();

        // parse the commandline options
        final Options options = new Options();
        CmdLineParser cmdline = new CmdLineParser(options);

        // check whether we need to show the help
        cmdline.parse(args);
        if (options.help) {
            Tool.printHeader(System.out, application, version);
            cmdline.printUsage(System.out, "");
            return;
        }

        if (options.verbose) {
            Tool.printHeader(System.out, application, version);
            cmdline.printOptions();
        }

        // check the command-line parameters
        int filetype = JFreeChartTools.PDF;
        {
            if (options.ppm == -1) {
                System.err.println("[ERROR]: the ppm-value needs to be set.");
                System.exit(0);
            }
            if (options.order == -1) {
                System.err.println("[ERROR]: the order for the polynomial fit needs to be set.");
                System.exit(0);
            }
            if (options.maxrt == -1) {
                System.err.println("[ERROR]: the maximum retention time shift is not set.");
                System.exit(0);
            }

            if (options.image != null) {
                String extension = options.image.substring(options.image.lastIndexOf('.') + 1);
                if (extension.toLowerCase().equals("png"))
                    filetype = JFreeChartTools.PNG;
                else if (extension.toLowerCase().equals("pdf"))
                    filetype = JFreeChartTools.PDF;
                else {
                    System.err.println(
                            "[ERROR]: file extension of the image file needs to be either PDF or PNG.");
                    System.exit(0);
                }
            }

            // if the output directories do not exist, create them
            if (options.output != null)
                Tool.createFilePath(options.output, true);
            if (options.image != null)
                Tool.createFilePath(options.image, true);
            if (options.selection != null)
                Tool.createFilePath(options.selection, true);
        }

        // load the data
        if (options.verbose)
            System.out.println("Loading the data");
        double maxrt = 0;
        Vector<ParseResult> data = new Vector<ParseResult>();
        Vector<IPeakSet<IPeak>> matchdata = new Vector<IPeakSet<IPeak>>();
        for (String file : options.input) {
            System.out.println("- " + new File(file).getName());

            // load the mass chromatogram data
            ParseResult result = PeakMLParser.parse(new FileInputStream(file), true);
            data.add(result);

            // select the best mass chromatograms
            Vector<IPeak> selection = new Vector<IPeak>();
            for (IPeak peak : (IPeakSet<IPeak>) result.measurement) {
                maxrt = Math.max(maxrt, maxRT(peak));

                double mcq = codaDW(peak);
                peak.addAnnotation(lbl_mcq, Double.toString(mcq), Annotation.ValueType.DOUBLE);
                if (mcq >= options.codadw)
                    selection.add(peak);
            }

            // keep track of the selected mass chromatograms
            int id = options.input.indexOf(file);
            IPeakSet<IPeak> peakset = new IPeakSet<IPeak>(selection);
            peakset.setMeasurementID(id);
            for (IPeak mc : peakset)
                mc.setMeasurementID(id);
            matchdata.add(peakset);
        }

        // match the selection together
        if (options.verbose)
            System.out.println("Matching the data");
        Vector<IPeakSet<IPeak>> matches = IPeak.match((Vector) matchdata, options.ppm,
                new IPeak.MatchCompare<IPeak>() {
                    public double distance(IPeak peak1, IPeak peak2) {
                        double diff = Math.abs(peak1.getRetentionTime() - peak2.getRetentionTime());
                        if (diff > options.maxrt)
                            return -1;

                        Signal signal1 = new Signal(peak1.getSignal());
                        signal1.normalize();
                        Signal signal2 = new Signal(peak2.getSignal());
                        signal2.normalize();

                        double offset = bestOffSet(peak1, peak2, options.maxrt);
                        for (int i = 0; i < signal2.getSize(); ++i)
                            signal2.getX()[i] += offset;

                        double correlation = signal2
                                .pearsonsCorrelation(signal1)[Statistical.PEARSON_CORRELATION];
                        if (correlation < 0.5)
                            return -1;

                        // the match-function optimizes toward 0 (it's a distance)
                        return 1 - correlation;
                    }
                });

        // filter out all incomplete sets
        Vector<IPeakSet<IPeak>> valids = new Vector<IPeakSet<IPeak>>();
        for (IPeakSet<IPeak> set : matches) {
            if (set.size() < options.input.size())
                continue;
            valids.add((IPeakSet) set);
        }

        // calculate the alignment factors
        if (options.verbose)
            System.out.println("Calculating the alignment factors");
        double medians[] = new double[valids.size() + 2];
        DataFrame.Double dataframe = new DataFrame.Double(valids.size() + 2, options.input.size());

        medians[0] = 0;
        medians[medians.length - 1] = maxrt;
        for (int i = 0; i < options.input.size(); ++i) {
            dataframe.set(0, i, 0.1);
            dataframe.set(dataframe.getNrRows() - 1, i, 0);
        }

        for (int matchid = 0; matchid < valids.size(); ++matchid) {
            IPeakSet<IPeak> match = valids.get(matchid);

            // find the most central
            double offsets[][] = new double[match.size()][match.size()];
            for (int i = 0; i < match.size(); ++i)
                for (int j = i + 1; j < match.size(); ++j) {
                    offsets[i][j] = bestOffSet(match.get(i), match.get(j), options.maxrt);
                    offsets[j][i] = -offsets[i][j];
                }

            int besti = 0;
            double bestabssum = Double.MAX_VALUE;
            for (int i = 0; i < match.size(); ++i) {
                double abssum = 0;
                for (int j = 0; j < match.size(); ++j)
                    abssum += Math.abs(offsets[i][j]);
                if (abssum < bestabssum) {
                    besti = i;
                    bestabssum = abssum;
                }
            }

            for (int i = 0; i < match.size(); ++i)
                dataframe.set(matchid + 1, match.get(i).getMeasurementID(),
                        (i == besti ? 0 : offsets[i][besti]));

            medians[matchid + 1] = match.get(besti).getRetentionTime();
            dataframe.setRowName(matchid, Double.toString(match.get(besti).getRetentionTime()));
        }
        double minmedian = Statistical.min(medians);
        double maxmedian = Statistical.max(medians);

        // calculate for each profile the correction function
        PolynomialFunction functions[] = new PolynomialFunction[valids.size()];
        for (int i = 0; i < options.input.size(); ++i)
            functions[i] = PolynomialFunction.fit(options.order, medians, dataframe.getCol(i));

        // make a nice plot out of the whole thing
        if (options.verbose)
            System.out.println("Writing results");
        if (options.image != null) {
            org.jfree.data.xy.XYSeriesCollection dataset = new org.jfree.data.xy.XYSeriesCollection();
            JFreeChart linechart = ChartFactory.createXYLineChart(null, "Retention Time (seconds)", "offset",
                    dataset, PlotOrientation.VERTICAL, true, // legend
                    false, // tooltips
                    false // urls
            );

            // setup the colorkey
            Colormap colormap = new Colormap(Colormap.EXCEL);

            // get the structure behind the graph
            XYPlot plot = (XYPlot) linechart.getPlot();
            XYLineAndShapeRenderer renderer = (XYLineAndShapeRenderer) plot.getRenderer();

            // setup the plot area
            linechart.setBackgroundPaint(java.awt.Color.WHITE);
            linechart.setBorderVisible(false);
            linechart.setAntiAlias(true);

            plot.setBackgroundPaint(java.awt.Color.WHITE);
            plot.setDomainGridlinesVisible(true);
            plot.setRangeGridlinesVisible(true);

            // create the datasets
            for (int i = 0; i < options.input.size(); ++i) {
                org.jfree.data.xy.XYSeries series = new org.jfree.data.xy.XYSeries(dataframe.getColName(i));
                org.jfree.data.xy.XYSeries function = new org.jfree.data.xy.XYSeries(
                        dataframe.getColName(i) + "-function");
                dataset.addSeries(series);
                dataset.addSeries(function);

                renderer.setSeriesPaint(dataset.getSeriesCount() - 1, new java.awt.Color(colormap.getColor(i)));
                renderer.setSeriesPaint(dataset.getSeriesCount() - 2, new java.awt.Color(colormap.getColor(i)));

                renderer.setSeriesLinesVisible(dataset.getSeriesCount() - 2, false);
                renderer.setSeriesShapesVisible(dataset.getSeriesCount() - 2, true);

                // add the data-points
                for (int j = 0; j < valids.size(); ++j)
                    series.add(medians[j], dataframe.get(j, i));
                for (double x = minmedian; x < maxmedian; ++x)
                    function.add(x, functions[i].getY(x));
            }

            dataset.removeAllSeries();
            for (int i = 0; i < options.input.size(); ++i) {
                Function function = functions[i];

                org.jfree.data.xy.XYSeries series = new org.jfree.data.xy.XYSeries(dataframe.getColName(i));
                dataset.addSeries(series);

                renderer.setSeriesPaint(i, new java.awt.Color(colormap.getColor(i)));
                renderer.setSeriesLinesVisible(i, false);
                renderer.setSeriesShapesVisible(i, true);

                // add the data-points
                for (int j = 0; j < valids.size(); ++j)
                    series.add(medians[j], dataframe.get(j, i) - function.getY(medians[j]));
            }

            JFreeChartTools.writeAs(filetype, new FileOutputStream(options.image), linechart, 800, 500);
        }

        // save the selected
        if (options.selection != null) {
            Header header = new Header();

            // set the number of peaks to be stored
            header.setNrPeaks(valids.size());

            // create a set for the measurements
            SetInfo set = new SetInfo("", SetInfo.SET);
            header.addSetInfo(set);

            // create the measurement infos
            for (int i = 0; i < options.input.size(); ++i) {
                String file = options.input.get(i);

                // create the measurement info
                MeasurementInfo measurement = new MeasurementInfo(i, data.get(i).header.getMeasurementInfo(0));
                measurement.addFileInfo(new FileInfo(file, file));

                header.addMeasurementInfo(measurement);

                // add the file to the set
                set.addChild(new SetInfo(file, SetInfo.SET, i));
            }

            // write the data
            PeakMLWriter.write(header, (Vector) valids, null,
                    new GZIPOutputStream(new FileOutputStream(options.selection)), null);
        }

        // correct the values with the found function and save them
        for (int i = 0; i < options.input.size(); ++i) {
            Function function = functions[i];
            ParseResult result = data.get(i);

            IPeakSet<MassChromatogram<Peak>> peakset = (IPeakSet<MassChromatogram<Peak>>) result.measurement;
            for (IPeak peak : peakset)
                align(peak, function);

            File filename = new File(options.input.get(i));
            String name = filename.getName();

            PeakMLWriter.write(result.header, (Vector) peakset.getPeaks(), null,
                    new GZIPOutputStream(new FileOutputStream(options.output + "/" + name)), null);
        }
    } catch (Exception e) {
        Tool.unexpectedError(e, application);
    }
}